c2pfam

AT4G12740.1 :

Domain Description Evalue Bits GA Start End
Cid2 Caffeine-induced death protein 2 5.2E-06 18 25.00 6 108
Paf1 Paf1 0.002 8 20.40 15 112
Pox_Ag35 Pox virus Ag35 surface protein 0.0095 7 24.10 16 108
dsRBD2 Double-stranded RNA binding domain 2 0.0012 10 25.00 24 89
NOA36 NOA36 protein 0.00059 10 25.00 25 113
MRNIP MRN-interacting protein 0.0043 9 27.00 26 109
PPP4R2 PPP4R2 0.0011 10 25.00 30 113
DUF3987 Protein of unknown function (DUF3987) 0.0053 7 27.00 35 110
BUD22 BUD22 0.00011 13 37.00 42 129
tRNA_bind_2 Possible tRNA binding domain 0.019 6 27.00 43 149
TFIIA Transcription factor IIA, alpha/beta subunit 0.0084 7 29.20 44 122
RR_TM4-6 Ryanodine Receptor TM 4-6 0.0037 8 25.10 44 113
DDHD DDHD domain 0.01 7 20.70 46 123
RNA_pol_3_Rpc31 DNA-directed RNA polymerase III subunit Rpc31 0.0017 10 22.80 48 118
BORG_CEP Cdc42 effector 0.038 6 25.00 48 148
Presenilin Presenilin 0.0029 8 23.60 50 137
SpoIIP Stage II sporulation protein P (SpoIIP) 0.0082 7 20.10 51 109
Sec62 Translocation protein Sec62 0.025 5 22.40 51 126
DUF2151 Cell cycle and development regulator 0.0052 7 17.50 52 160
Borrelia_P83 Borrelia P83/100 protein 0.001 9 21.90 52 130
Vfa1 AAA-ATPase Vps4-associated protein 1 0.012 7 24.20 55 111
FYDLN_acid Protein of unknown function (FYDLN_acid) 0.014 7 22.70 56 125
RPN2_C 26S proteasome regulatory subunit RPN2 C-terminal domain 0.0038 8 26.80 58 112
Spore_coat_CotO Spore coat protein CotO 0.0032 9 35.00 58 114
Nop53 Nop53 (60S ribosomal biogenesis) 1.7E-05 16 23.20 58 114
Adaptin_binding Alpha and gamma adaptin binding protein p34 0.0014 11 32.00 59 132
Merozoite_SPAM Merozoite surface protein (SPAM) 0.00018 13 24.30 59 159
DUF2457 Protein of unknown function (DUF2457) 1.4E-05 16 30.00 61 112
RNA_pol_Rpc4 RNA polymerase III RPC4 0.0039 9 20.60 61 109
Nop14 Nop14-like family 0.0034 7 34.90 62 128
HhH-GPD HhH-GPD superfamily base excision DNA repair protein 8.7E-20 63 21.90 166 318
HHH Helix-hairpin-helix motif 2.6E-07 22 23.80 253 277
EndIII_4Fe-2S Iron-sulfur binding domain of endonuclease III 0.00031 12 20.50 341 357
DUF3678 Protein of unknown function (DUF3678) 0.00086 10 20.40 342 361
Whib Transcription factor WhiB 0.00017 14 21.70 345 366
NUDIX_4 NUDIX domain 9.6E-16 49 35.00 403 529

630

Cid2
Paf1
Pox_Ag35
dsRBD2
NOA36
MRNIP
PPP4R2
DUF3987
BUD22
tRNA_bind_2
TFIIA
RR_TM4-6
DDHD
RNA_pol_3_Rpc31
BORG_CEP
Presenilin
SpoIIP
Sec62
DUF2151
Borrelia_P83
Vfa1
FYDLN_acid
RPN2_C
Spore_coat_CotO
Nop53
Adaptin_binding
Merozoite_SPAM
DUF2457
RNA_pol_Rpc4
Nop14
HhH-GPD
HHH
EndIII_4Fe-2S
DUF3678
Whib
NUDIX_4

References:

RR_TM4-6

Adaptin_binding
10477754 Gamma-synergin: an EH domain-containing protein that interacts with gamma-adaptin. J Cell Biol. 1999;146:993-1004.

Spore_coat_CotO

HhH-GPD
10499592 The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 1999;401:301-304.
10706276 Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 2000;403:859-866.

HHH
8692686 The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res 1996;24:2488-2497.
8832889 Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Science 1996;274:415-421.
12832627 An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Mol Biol Evol 2003;20:1603-1611.
10908318 Common fold in helix-hairpin-helix proteins. Nucleic Acids Res 2000;28:2643-2650.
18439896 Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol Cell. 2008;30:167-178.

EndIII_4Fe-2S
7664751 Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J. 1995;14:4108-4120.
9045706 Cloning and expression of the cDNA encoding the human homologue of the DNA repair enzyme, Escherichia coli endonuclease III. J Biol Chem. 1997;272:6733-6740.
16096281 Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analyses. J Biol Chem. 2005;280:34378-34384.
16967954 Direct electrochemistry of endonuclease III in the presence and absence of DNA. J Am Chem Soc. 2006;128:12082-12083.

Nop53
10708517 A transcript map of the chromosome 19q-arm glioma tumor suppressor region. Genomics 2000;64:44-50.
10196275 A novel cellular protein, p60, interacting with both herpes simplex virus 1 regulatory proteins ICP22 and ICP0 is modified in a cell-type-specific manner and Is recruited to the nucleus after infection. J Virol 1999;73:3810-3817.
15686447 Nop53p is a novel nucleolar 60S ribosomal biogenesis protein. Biochem J 2005; [Epub ahead of print]

Nop14
11694595 Novel stress-responsive genes EMG1 and NOP14 encode conserved, interacting proteins required for 40S ribosome biogenesis. Mol Biol Cell 2001;12:3644-3657.

RNA_pol_3_Rpc31
16877568 Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III. Nucleic Acids Res. 2006;34:3615-3624.

Vfa1

DUF3678

DDHD
10022914 Identification of a novel family of targets of PYK2 related to Drosophila retinal degeneration B (rdgB) protein. Mol Cell Biol 1999;19:2278-2288.

DUF2151
15737938 Drosophila genome-scale screen for PAN GU kinase substrates identifies Mat89Bb as a cell cycle regulator. Dev Cell. 2005;8:435-442.

MRNIP

Whib
8506145 Streptomyces aureofaciens whiB gene encoding putative transcription factor essential for differentiation. Nucleic Acid Res 1993;21:2512-2512.

BUD22
11452010 A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell. 2001;12:2147-2170.

RPN2_C

tRNA_bind_2

Presenilin
9384549 Presenilins and Alzheimer's disease. Curr Opin Neurobiol 1997;7:683-688.
9384549 Presenilins and Alzheimer's disease. Curr Opin Neurobiol 1997;7:683-688.
9437013 Interaction of presenilins with the filamin family of actin-binding proteins. J Neurosci 1998;18:914-922.
9790190 Destabilisation of beta-catenin by mutations in presenilin-1 potentiates neuronal apoptosis. Nature 1998;395:698-702.

FYDLN_acid

BORG_CEP

NUDIX_4

DUF2457

Borrelia_P83

Pox_Ag35
8128622 Vaccinia virion surface polypeptide Ag35 expressed from a baculovirus vector is targeted to analogous poxvirus and insect virus components. Virology 1994;200:207-219.
1707568 A prominent antigenic surface polypeptide involved in the biogenesis and function of the vaccinia virus envelope. Virology 1991;181:671-686.

NOA36

Paf1
11927560 The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 2002;21:1764-1774.
11884586 Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol 2002;22:1971-1980.

Merozoite_SPAM
7891748 Molecular variation in a novel polymorphic antigen associated with Plasmodium falciparum merozoites. Mol Biochem Parasitol 1994;68:53-67.
7893643 Solution structure of a polypeptide containing four heptad repeat units from a merozoite surface antigen of Plasmodium falciparum. Biochemistry 1995;34:3479-3491.

TFIIA
11089979 A transcription reinitiation intermediate that is stabilized by activator. Nature 2000;408:225-229.
8224848 A single cDNA, hTFIIA/alpha, encodes both the p35 and p19 subunits of human TFIIA. Genes Dev 1993;7:2220-2234.
8610010 Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 1996;381:127-151.

DUF3987

SpoIIP
10096082 A vital stain for studying membrane dynamics in bacteria: a novel mechanism controlling septation during Bacillus subtilis sporulation. Mol Microbiol. 1999;31:1149-1159.
17376078 Engulfment during sporulation in Bacillus subtilis is governed by a multi-protein complex containing tandemly acting autolysins. Mol Microbiol. 2007;64:139-152.
17824930 Dual localization pathways for the engulfment proteins during Bacillus subtilis sporulation. Mol Microbiol. 2007;65:1534-1546.

Sec62

PPP4R2
16857015 The Saccharomyces cerevisiae orthologue of the human protein phosphatase 4 core regulatory subunit R2 confers resistance to the anticancer drug cisplatin. FEBS J. 2006;273:3322-3334.

RNA_pol_Rpc4
1429657 Biochemical and genetic dissection of the Saccharomyces cerevisiae RNA polymerase C53 subunit through the analysis of a mitochondrially mis-sorted mutant construct. J Biol Chem 1992;267:23099-23107.

Cid2
10036242 Caffeine can override the S-M checkpoint in fission yeast. J Cell Sci. 1999;112:927-937.

dsRBD2

Domain	Description	Evalue	Bits	GA	Start	End
Cid2	Caffeine-induced death protein 2	5.2E-06	18	25.00	6	108
Paf1	Paf1	0.002	8	20.40	15	112
Pox_Ag35	Pox virus Ag35 surface protein	0.0095	7	24.10	16	108
dsRBD2	Double-stranded RNA binding domain 2	0.0012	10	25.00	24	89
NOA36	NOA36 protein	0.00059	10	25.00	25	113
MRNIP	MRN-interacting protein	0.0043	9	27.00	26	109
PPP4R2	PPP4R2	0.0011	10	25.00	30	113
DUF3987	Protein of unknown function (DUF3987)	0.0053	7	27.00	35	110
BUD22	BUD22	0.00011	13	37.00	42	129
tRNA_bind_2	Possible tRNA binding domain	0.019	6	27.00	43	149
TFIIA	Transcription factor IIA, alpha/beta subunit	0.0084	7	29.20	44	122
RR_TM4-6	Ryanodine Receptor TM 4-6	0.0037	8	25.10	44	113
DDHD	DDHD domain	0.01	7	20.70	46	123
RNA_pol_3_Rpc31	DNA-directed RNA polymerase III subunit Rpc31	0.0017	10	22.80	48	118
BORG_CEP	Cdc42 effector	0.038	6	25.00	48	148
Presenilin	Presenilin	0.0029	8	23.60	50	137
SpoIIP	Stage II sporulation protein P (SpoIIP)	0.0082	7	20.10	51	109
Sec62	Translocation protein Sec62	0.025	5	22.40	51	126
DUF2151	Cell cycle and development regulator	0.0052	7	17.50	52	160
Borrelia_P83	Borrelia P83/100 protein	0.001	9	21.90	52	130
Vfa1	AAA-ATPase Vps4-associated protein 1	0.012	7	24.20	55	111
FYDLN_acid	Protein of unknown function (FYDLN_acid)	0.014	7	22.70	56	125
RPN2_C	26S proteasome regulatory subunit RPN2 C-terminal domain	0.0038	8	26.80	58	112
Spore_coat_CotO	Spore coat protein CotO	0.0032	9	35.00	58	114
Nop53	Nop53 (60S ribosomal biogenesis)	1.7E-05	16	23.20	58	114
Adaptin_binding	Alpha and gamma adaptin binding protein p34	0.0014	11	32.00	59	132
Merozoite_SPAM	Merozoite surface protein (SPAM)	0.00018	13	24.30	59	159
DUF2457	Protein of unknown function (DUF2457)	1.4E-05	16	30.00	61	112
RNA_pol_Rpc4	RNA polymerase III RPC4	0.0039	9	20.60	61	109
Nop14	Nop14-like family	0.0034	7	34.90	62	128
HhH-GPD	HhH-GPD superfamily base excision DNA repair protein	8.7E-20	63	21.90	166	318
HHH	Helix-hairpin-helix motif	2.6E-07	22	23.80	253	277
EndIII_4Fe-2S	Iron-sulfur binding domain of endonuclease III	0.00031	12	20.50	341	357
DUF3678	Protein of unknown function (DUF3678)	0.00086	10	20.40	342	361
Whib	Transcription factor WhiB	0.00017	14	21.70	345	366
NUDIX_4	NUDIX domain	9.6E-16	49	35.00	403	529