c2pfam

AT5G04810.1 :

Domain Description Evalue Bits GA Start End
RRM_7 RNA recognition motif 2E-05 15 27.00 166 223
RRM_1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 3.2E-15 46 20.70 167 236
Nup35_RRM_2 Nup53/35/40-type RNA recognition motif 0.00026 12 27.00 183 224
PPR PPR repeat 1.2E-05 16 25.00 314 340
PPR_2 PPR repeat family 4E-07 21 30.00 315 355
PPR_1 PPR repeat 0.016 6 23.80 315 336
PPR_3 Pentatricopeptide repeat domain 5.4E-05 14 25.00 317 344
PPR_long Pentacotripeptide-repeat region of PRORP 3.1E-11 33 27.00 325 398
ATP13 Mitochondrial ATPase expression 0.0015 9 26.70 338 370
PPR_1 PPR repeat 1.2E-05 16 23.80 338 371
Wzy_C_2 Virulence factor membrane-bound polymerase, C-terminal 0.19 2 28.50 341 371
PPR_2 PPR repeat family 3.5E-11 34 30.00 343 391
TPR_1 Tetratricopeptide repeat 0.57 1 20.40 345 366
PPR PPR repeat 2.7E-09 28 25.00 346 375
PPR_3 Pentatricopeptide repeat domain 1E-10 32 25.00 347 389
Polysacc_deac_1 Polysaccharide deacetylase 0.19 2 22.10 347 383
Radical_SAM Radical SAM superfamily 0.69 1 29.30 347 387
MA3 MA3 domain 0.00047 11 20.70 348 383
Alba Alba 0.018 6 20.90 355 385
PPR_1 PPR repeat 0.00092 10 23.80 374 398
PPR PPR repeat 7.6E-05 14 25.00 380 407
PPR_long Pentacotripeptide-repeat region of PRORP 1.3E-08 25 27.00 391 522
PPR_2 PPR repeat family 0.00016 12 30.00 413 458
PPR_1 PPR repeat 0.0027 8 23.80 413 441
PPR PPR repeat 1.6E-05 16 25.00 416 445
FtsK_gamma Ftsk gamma domain 0.27 2 25.10 431 445
PPR_3 Pentatricopeptide repeat domain 1.5E-11 35 25.00 436 494
PPR_2 PPR repeat family 5.3E-06 17 30.00 450 492
PPR PPR repeat 0.0011 10 25.00 451 480
MRP-S27 Mitochondrial 28S ribosomal protein S27 0.0063 6 25.90 469 547
PPR_1 PPR repeat 2.6E-08 24 23.80 479 511
PPR_2 PPR repeat family 5E-15 46 30.00 482 531
PPR PPR repeat 8.5E-07 20 25.00 485 515
TPR_1 Tetratricopeptide repeat 0.048 4 20.40 486 505
PPR_3 Pentatricopeptide repeat domain 1.8E-07 22 25.00 487 530
Alba Alba 0.12 3 20.90 500 517
PPR_long Pentacotripeptide-repeat region of PRORP 5.2E-15 46 27.00 501 623
PPR_1 PPR repeat 2.7E-06 18 23.80 514 546
RPM2 Mitochondrial ribonuclease P subunit (RPM2) 0.029 5 26.10 516 566
PPR PPR repeat 4.2E-08 24 25.00 521 549
PPR_2 PPR repeat family 3.1E-08 24 30.00 525 554
SPOB_a Sensor_kinase_SpoOB-type, alpha-helical domain 0.21 2 28.10 526 548
PPR_3 Pentatricopeptide repeat domain 1.3E-12 38 25.00 541 596
ATP13 Mitochondrial ATPase expression 0.0007 10 26.70 548 582
PPR_1 PPR repeat 1.9E-11 34 23.80 549 581
Wzy_C_2 Virulence factor membrane-bound polymerase, C-terminal 0.12 3 28.50 550 582
PPR_2 PPR repeat family 1.2E-10 32 30.00 552 592
PPR PPR repeat 4.8E-07 20 25.00 556 583
TPR_1 Tetratricopeptide repeat 0.072 4 20.40 556 575
SPOB_a Sensor_kinase_SpoOB-type, alpha-helical domain 0.48 1 28.10 560 580
Radical_SAM Radical SAM superfamily 0.12 3 29.30 561 599
MRP-S27 Mitochondrial 28S ribosomal protein S27 0.031 4 25.90 574 656
ATP13 Mitochondrial ATPase expression 0.014 6 26.70 585 614
PPR_1 PPR repeat 2E-06 18 23.80 586 616
PPR_2 PPR repeat family 1.2E-12 38 30.00 587 635
PPR_3 Pentatricopeptide repeat domain 9.5E-10 29 25.00 591 633
PPR PPR repeat 2.1E-08 25 25.00 594 620
PPR_long Pentacotripeptide-repeat region of PRORP 1.4E-15 48 27.00 600 729
RPM2 Mitochondrial ribonuclease P subunit (RPM2) 0.17 3 26.10 603 642
PPR_1 PPR repeat 6.5E-10 29 23.80 619 651
ATP13 Mitochondrial ATPase expression 0.19 2 26.70 621 650
PPR_2 PPR repeat family 9.7E-15 45 30.00 622 670
PPR PPR repeat 8.4E-08 23 25.00 626 654
SPOB_a Sensor_kinase_SpoOB-type, alpha-helical domain 0.037 4 28.10 630 651
Polysacc_deac_1 Polysaccharide deacetylase 0.077 4 22.10 638 701
Mtf2 Mtf2 family 0.02 5 27.00 641 662
PPR_3 Pentatricopeptide repeat domain 4.4E-10 30 25.00 646 705
Wzy_C_2 Virulence factor membrane-bound polymerase, C-terminal 0.084 3 28.50 651 756
PPR_1 PPR repeat 0.004 8 23.80 654 682
BTAD Bacterial transcriptional activator domain 0.014 6 21.00 656 686
PPR_2 PPR repeat family 4.2E-11 34 30.00 660 706
PPR PPR repeat 3.2E-05 15 25.00 661 690
ATP13 Mitochondrial ATPase expression 0.77 0 26.70 661 705
MA3 MA3 domain 1 0 20.70 663 690
MRP-S27 Mitochondrial 28S ribosomal protein S27 0.00031 10 25.90 684 755
PPR_3 Pentatricopeptide repeat domain 1.4E-08 25 25.00 685 737
PPR_1 PPR repeat 1.9E-08 25 23.80 689 721
Radical_SAM Radical SAM superfamily 0.68 1 29.30 690 735
PPR_2 PPR repeat family 2.7E-13 41 30.00 693 740
PPR PPR repeat 4E-07 21 25.00 695 725
BTAD Bacterial transcriptional activator domain 0.63 1 21.00 697 718
PPR_3 Pentatricopeptide repeat domain 7.1E-11 33 25.00 716 775
PPR_1 PPR repeat 4.2E-09 27 23.80 724 756
PPR_2 PPR repeat family 1.7E-16 51 30.00 728 775
PPR PPR repeat 5.5E-09 27 25.00 731 760
Mtf2 Mtf2 family 0.00074 10 27.00 731 767
Polysacc_deac_1 Polysaccharide deacetylase 0.039 5 22.10 738 789
ATP13 Mitochondrial ATPase expression 0.025 5 26.70 745 789
Radical_SAM Radical SAM superfamily 0.26 2 29.30 746 812
FtsK_gamma Ftsk gamma domain 0.33 1 25.10 748 760
PPR_long Pentacotripeptide-repeat region of PRORP 4.5E-16 49 27.00 750 842
PPR_3 Pentatricopeptide repeat domain 2.8E-16 50 25.00 751 807
PPR_1 PPR repeat 2.1E-09 28 23.80 759 791
Wzy_C_2 Virulence factor membrane-bound polymerase, C-terminal 0.33 1 28.50 761 793
RPM2 Mitochondrial ribonuclease P subunit (RPM2) 0.00017 13 26.10 765 848
PPR PPR repeat 9.4E-08 23 25.00 766 795
PPR_2 PPR repeat family 2.3E-13 41 30.00 766 810
Mtf2 Mtf2 family 0.0046 7 27.00 778 803
FtsK_gamma Ftsk gamma domain 0.041 4 25.10 781 795
PPR_3 Pentatricopeptide repeat domain 2.5E-10 31 25.00 788 841
PPR_1 PPR repeat 1.3E-07 22 23.80 794 826
PPR PPR repeat 2.2E-09 28 25.00 801 830
PPR_2 PPR repeat family 1.6E-08 25 30.00 804 844
Mtf2 Mtf2 family 0.34 1 27.00 819 835
PPR_1 PPR repeat 0.77 0 23.80 828 843

952

RRM_7
RRM_1
Nup35_RRM_2
PPR
PPR_2
PPR_1
PPR_3
PPR_long
ATP13
PPR_1
Wzy_C_2
PPR_2
TPR_1
PPR
PPR_3
Polysacc_deac_1
Radical_SAM
MA3
Alba
PPR_1
PPR
PPR_long
PPR_2
PPR_1
PPR
FtsK_gamma
PPR_3
PPR_2
PPR
MRP-S27
PPR_1
PPR_2
PPR
TPR_1
PPR_3
Alba
PPR_long
PPR_1
RPM2
PPR
PPR_2
SPOB_a
PPR_3
ATP13
PPR_1
Wzy_C_2
PPR_2
PPR
TPR_1
SPOB_a
Radical_SAM
MRP-S27
ATP13
PPR_1
PPR_2
PPR_3
PPR
PPR_long
RPM2
PPR_1
ATP13
PPR_2
PPR
SPOB_a
Polysacc_deac_1
Mtf2
PPR_3
Wzy_C_2
PPR_1
BTAD
PPR_2
PPR
ATP13
MA3
MRP-S27
PPR_3
PPR_1
Radical_SAM
PPR_2
PPR
BTAD
PPR_3
PPR_1
PPR_2
PPR
Mtf2
Polysacc_deac_1
ATP13
Radical_SAM
FtsK_gamma
PPR_long
PPR_3
PPR_1
Wzy_C_2
RPM2
PPR
PPR_2
Mtf2
FtsK_gamma
PPR_3
PPR_1
PPR
PPR_2
Mtf2
PPR_1

References:

RRM_1
8290338 Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acid Res 1993;21:5803-5816.

Radical_SAM
11222759 Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res 2001;29:1097-1106.
17335281 Anaerobic sulfatase-maturating enzymes: radical SAM enzymes able to catalyze in vitro sulfatase post-translational modification. J Am Chem Soc. 2007;129:3462-3463.
16766528 A new type of bacterial sulfatase reveals a novel maturation pathway in prokaryotes. J Biol Chem. 2006;281:22464-22470.

Polysacc_deac_1
9163424 Molecular basis of symbiosis between Rhizobium and legumes. Nature 1997;387:394-401.
9133736 Cloning and expression of two chitin deacetylase genes of Saccharomyces cerevisiae. Yeast 1996;13:327-336.
8170399 Evidence for a general role for high-affinity non-catalytic cellulose binding domains in microbial plant cell wall hydrolases. Mol Microbiol 1994;11:375-382.

TPR_1
7667876 Tetratrico peptide repeat interactions: to TPR or not to TPR? Trends Biochem Sci 1995;20:257-259.
9482716 The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. EMBO J 1998;17:1192-1199.

Wzy_C_2

MRP-S27
11344316 Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach. Protein Sci. 2001;10:471-481.

PPR_long

PPR_3

PPR_2

PPR_1

RPM2
1409716 A 105-kDa protein is required for yeast mitochondrial RNase P activity. Proc Natl Acad Sci U S A. 1992;89:9875-9879.
16024791 Rpm2p, a component of yeast mitochondrial RNase P, acts as a transcriptional activator in the nucleus. Mol Cell Biol. 2005;25:6546-6558.

MA3
10973054 Novel eIF4G domain homologues linking mRNA translation with nonsense-mediated mRNA decay. Trends Biochem Sci 2000;25:423-426.

Alba
14519199 The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism. Genome Biol 2003;4:R64.
11935028 The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 2002;296:148-151.
10869069 An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion. J Bacteriol 2000;182:3929-3933.
10320587 Identification of the gene encoding archeal-specific DNA-binding proteins of the Sac10b family. Mol Microbiol 1999;32:669-670.

Nup35_RRM_2

FtsK_gamma
17057717 The FtsK gamma domain directs oriented DNA translocation by interacting with KOPS. Nat Struct Mol Biol. 2006;13:965-972.

ATP13

Mtf2

RRM_7

BTAD
12625841 New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol 2003;3:3-3.

PPR
7664742 The product of the nuclear gene PET309 is required for translation of mature mRNA and stability or production of intron-containing RNAs derived from the mitochondrial COX1 locus of Saccharomyces cerevisiae. EMBO J 1995;14:4031-4043.
8039510 A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO J 1994;13:3170-3181.
10664580 The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 2000;25:45-47.

SPOB_a

Domain	Description	Evalue	Bits	GA	Start	End
RRM_7	RNA recognition motif	2E-05	15	27.00	166	223
RRM_1	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	3.2E-15	46	20.70	167	236
Nup35_RRM_2	Nup53/35/40-type RNA recognition motif	0.00026	12	27.00	183	224
PPR	PPR repeat	1.2E-05	16	25.00	314	340
PPR_2	PPR repeat family	4E-07	21	30.00	315	355
PPR_1	PPR repeat	0.016	6	23.80	315	336
PPR_3	Pentatricopeptide repeat domain	5.4E-05	14	25.00	317	344
PPR_long	Pentacotripeptide-repeat region of PRORP	3.1E-11	33	27.00	325	398
ATP13	Mitochondrial ATPase expression	0.0015	9	26.70	338	370
PPR_1	PPR repeat	1.2E-05	16	23.80	338	371
Wzy_C_2	Virulence factor membrane-bound polymerase, C-terminal	0.19	2	28.50	341	371
PPR_2	PPR repeat family	3.5E-11	34	30.00	343	391
TPR_1	Tetratricopeptide repeat	0.57	1	20.40	345	366
PPR	PPR repeat	2.7E-09	28	25.00	346	375
PPR_3	Pentatricopeptide repeat domain	1E-10	32	25.00	347	389
Polysacc_deac_1	Polysaccharide deacetylase	0.19	2	22.10	347	383
Radical_SAM	Radical SAM superfamily	0.69	1	29.30	347	387
MA3	MA3 domain	0.00047	11	20.70	348	383
Alba	Alba	0.018	6	20.90	355	385
PPR_1	PPR repeat	0.00092	10	23.80	374	398
PPR	PPR repeat	7.6E-05	14	25.00	380	407
PPR_long	Pentacotripeptide-repeat region of PRORP	1.3E-08	25	27.00	391	522
PPR_2	PPR repeat family	0.00016	12	30.00	413	458
PPR_1	PPR repeat	0.0027	8	23.80	413	441
PPR	PPR repeat	1.6E-05	16	25.00	416	445
FtsK_gamma	Ftsk gamma domain	0.27	2	25.10	431	445
PPR_3	Pentatricopeptide repeat domain	1.5E-11	35	25.00	436	494
PPR_2	PPR repeat family	5.3E-06	17	30.00	450	492
PPR	PPR repeat	0.0011	10	25.00	451	480
MRP-S27	Mitochondrial 28S ribosomal protein S27	0.0063	6	25.90	469	547
PPR_1	PPR repeat	2.6E-08	24	23.80	479	511
PPR_2	PPR repeat family	5E-15	46	30.00	482	531
PPR	PPR repeat	8.5E-07	20	25.00	485	515
TPR_1	Tetratricopeptide repeat	0.048	4	20.40	486	505
PPR_3	Pentatricopeptide repeat domain	1.8E-07	22	25.00	487	530
Alba	Alba	0.12	3	20.90	500	517
PPR_long	Pentacotripeptide-repeat region of PRORP	5.2E-15	46	27.00	501	623
PPR_1	PPR repeat	2.7E-06	18	23.80	514	546
RPM2	Mitochondrial ribonuclease P subunit (RPM2)	0.029	5	26.10	516	566
PPR	PPR repeat	4.2E-08	24	25.00	521	549
PPR_2	PPR repeat family	3.1E-08	24	30.00	525	554
SPOB_a	Sensor_kinase_SpoOB-type, alpha-helical domain	0.21	2	28.10	526	548
PPR_3	Pentatricopeptide repeat domain	1.3E-12	38	25.00	541	596
ATP13	Mitochondrial ATPase expression	0.0007	10	26.70	548	582
PPR_1	PPR repeat	1.9E-11	34	23.80	549	581
Wzy_C_2	Virulence factor membrane-bound polymerase, C-terminal	0.12	3	28.50	550	582
PPR_2	PPR repeat family	1.2E-10	32	30.00	552	592
PPR	PPR repeat	4.8E-07	20	25.00	556	583
TPR_1	Tetratricopeptide repeat	0.072	4	20.40	556	575
SPOB_a	Sensor_kinase_SpoOB-type, alpha-helical domain	0.48	1	28.10	560	580
Radical_SAM	Radical SAM superfamily	0.12	3	29.30	561	599
MRP-S27	Mitochondrial 28S ribosomal protein S27	0.031	4	25.90	574	656
ATP13	Mitochondrial ATPase expression	0.014	6	26.70	585	614
PPR_1	PPR repeat	2E-06	18	23.80	586	616
PPR_2	PPR repeat family	1.2E-12	38	30.00	587	635
PPR_3	Pentatricopeptide repeat domain	9.5E-10	29	25.00	591	633
PPR	PPR repeat	2.1E-08	25	25.00	594	620
PPR_long	Pentacotripeptide-repeat region of PRORP	1.4E-15	48	27.00	600	729
RPM2	Mitochondrial ribonuclease P subunit (RPM2)	0.17	3	26.10	603	642
PPR_1	PPR repeat	6.5E-10	29	23.80	619	651
ATP13	Mitochondrial ATPase expression	0.19	2	26.70	621	650
PPR_2	PPR repeat family	9.7E-15	45	30.00	622	670
PPR	PPR repeat	8.4E-08	23	25.00	626	654
SPOB_a	Sensor_kinase_SpoOB-type, alpha-helical domain	0.037	4	28.10	630	651
Polysacc_deac_1	Polysaccharide deacetylase	0.077	4	22.10	638	701
Mtf2	Mtf2 family	0.02	5	27.00	641	662
PPR_3	Pentatricopeptide repeat domain	4.4E-10	30	25.00	646	705
Wzy_C_2	Virulence factor membrane-bound polymerase, C-terminal	0.084	3	28.50	651	756
PPR_1	PPR repeat	0.004	8	23.80	654	682
BTAD	Bacterial transcriptional activator domain	0.014	6	21.00	656	686
PPR_2	PPR repeat family	4.2E-11	34	30.00	660	706
PPR	PPR repeat	3.2E-05	15	25.00	661	690
ATP13	Mitochondrial ATPase expression	0.77	0	26.70	661	705
MA3	MA3 domain	1	0	20.70	663	690
MRP-S27	Mitochondrial 28S ribosomal protein S27	0.00031	10	25.90	684	755
PPR_3	Pentatricopeptide repeat domain	1.4E-08	25	25.00	685	737
PPR_1	PPR repeat	1.9E-08	25	23.80	689	721
Radical_SAM	Radical SAM superfamily	0.68	1	29.30	690	735
PPR_2	PPR repeat family	2.7E-13	41	30.00	693	740
PPR	PPR repeat	4E-07	21	25.00	695	725
BTAD	Bacterial transcriptional activator domain	0.63	1	21.00	697	718
PPR_3	Pentatricopeptide repeat domain	7.1E-11	33	25.00	716	775
PPR_1	PPR repeat	4.2E-09	27	23.80	724	756
PPR_2	PPR repeat family	1.7E-16	51	30.00	728	775
PPR	PPR repeat	5.5E-09	27	25.00	731	760
Mtf2	Mtf2 family	0.00074	10	27.00	731	767
Polysacc_deac_1	Polysaccharide deacetylase	0.039	5	22.10	738	789
ATP13	Mitochondrial ATPase expression	0.025	5	26.70	745	789
Radical_SAM	Radical SAM superfamily	0.26	2	29.30	746	812
FtsK_gamma	Ftsk gamma domain	0.33	1	25.10	748	760
PPR_long	Pentacotripeptide-repeat region of PRORP	4.5E-16	49	27.00	750	842
PPR_3	Pentatricopeptide repeat domain	2.8E-16	50	25.00	751	807
PPR_1	PPR repeat	2.1E-09	28	23.80	759	791
Wzy_C_2	Virulence factor membrane-bound polymerase, C-terminal	0.33	1	28.50	761	793
RPM2	Mitochondrial ribonuclease P subunit (RPM2)	0.00017	13	26.10	765	848
PPR	PPR repeat	9.4E-08	23	25.00	766	795
PPR_2	PPR repeat family	2.3E-13	41	30.00	766	810
Mtf2	Mtf2 family	0.0046	7	27.00	778	803
FtsK_gamma	Ftsk gamma domain	0.041	4	25.10	781	795
PPR_3	Pentatricopeptide repeat domain	2.5E-10	31	25.00	788	841
PPR_1	PPR repeat	1.3E-07	22	23.80	794	826
PPR	PPR repeat	2.2E-09	28	25.00	801	830
PPR_2	PPR repeat family	1.6E-08	25	30.00	804	844
Mtf2	Mtf2 family	0.34	1	27.00	819	835
PPR_1	PPR repeat	0.77	0	23.80	828	843