Query 030575
Match_columns 175
No_of_seqs 176 out of 531
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 15:48:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030575.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030575hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 2.1E-32 4.6E-37 257.3 13.9 104 1-104 78-193 (846)
2 PF03101 FAR1: FAR1 DNA-bindin 100.0 7.5E-30 1.6E-34 180.7 9.2 91 11-101 1-91 (91)
3 PF08731 AFT: Transcription fa 99.2 4.9E-10 1.1E-14 82.3 10.3 90 3-99 1-111 (111)
4 PF03108 DBD_Tnp_Mut: MuDR fam 97.7 0.00021 4.5E-09 47.6 7.3 59 1-88 8-67 (67)
5 PF04500 FLYWCH: FLYWCH zinc f 90.4 0.18 3.8E-06 32.0 1.6 25 70-97 38-62 (62)
6 PF03106 WRKY: WRKY DNA -bindi 89.4 0.5 1.1E-05 31.0 3.2 28 71-98 31-59 (60)
7 COG5470 Uncharacterized conser 75.6 1.4 2.9E-05 31.8 0.9 26 1-26 58-83 (96)
8 PF07576 BRAP2: BRCA1-associat 72.3 2.4 5.2E-05 31.2 1.6 18 1-18 59-76 (110)
9 smart00774 WRKY DNA binding do 71.6 5.1 0.00011 26.3 2.8 28 70-97 31-59 (59)
10 PF04800 ETC_C1_NDUFA4: ETC co 65.9 5 0.00011 29.1 2.1 24 1-28 53-76 (101)
11 PF07045 DUF1330: Protein of u 61.0 3.6 7.8E-05 26.9 0.6 15 1-15 44-58 (65)
12 PF12441 DUF3680: Protein of u 50.4 14 0.00031 22.5 1.9 14 2-15 7-20 (42)
13 PF15299 ALS2CR8: Amyotrophic 47.6 14 0.00031 30.2 2.2 19 61-79 69-87 (225)
14 PF08222 HTH_CodY: CodY helix- 41.8 17 0.00037 23.9 1.4 19 150-168 13-31 (61)
15 PF04684 BAF1_ABF1: BAF1 / ABF 38.9 74 0.0016 29.3 5.4 41 2-48 27-67 (496)
16 PF04684 BAF1_ABF1: BAF1 / ABF 37.8 21 0.00046 32.7 1.8 22 83-104 164-185 (496)
17 cd08815 Death_TNFRSF25_DR3 Dea 37.3 1.2E+02 0.0025 21.0 5.1 46 122-170 27-72 (77)
18 PF12883 DUF3828: Protein of u 30.9 60 0.0013 23.7 3.1 21 73-93 97-118 (120)
19 PF07526 POX: Associated with 30.3 1E+02 0.0022 23.5 4.3 44 111-154 74-120 (140)
20 PRK04158 transcriptional repre 28.6 1.8E+02 0.0038 24.7 5.8 34 135-168 186-228 (256)
21 PF14389 Lzipper-MIP1: Leucine 27.8 1.3E+02 0.0028 21.0 4.2 23 147-169 48-70 (88)
22 PF12998 ING: Inhibitor of gro 27.7 91 0.002 21.6 3.5 33 140-172 2-34 (105)
23 PRK08179 prfH peptide chain re 26.0 2.1E+02 0.0044 23.3 5.6 43 7-49 20-62 (200)
24 smart00574 POX domain associat 24.9 1.5E+02 0.0033 22.8 4.3 43 112-154 75-120 (140)
25 PRK10884 SH3 domain-containing 24.8 2.7E+02 0.0058 22.6 6.1 75 95-169 81-162 (206)
26 PF00847 AP2: AP2 domain; Int 24.6 86 0.0019 19.2 2.6 19 2-20 35-53 (56)
27 PF05377 FlaC_arch: Flagella a 24.4 67 0.0015 20.8 2.0 29 137-165 12-40 (55)
28 cd08875 START_ArGLABRA2_like C 24.3 1.1E+02 0.0024 25.4 3.8 33 64-97 126-158 (229)
29 COG4465 CodY Pleiotropic trans 22.8 3.6E+02 0.0078 22.6 6.4 34 135-168 189-231 (261)
30 PRK11370 YciI-like protein; Re 22.4 46 0.00099 23.4 1.0 14 2-15 64-77 (99)
31 PF09954 DUF2188: Uncharacteri 22.3 2.2E+02 0.0047 18.0 5.0 34 2-40 24-58 (62)
32 PHA02047 phage lambda Rz1-like 22.2 1.6E+02 0.0035 21.3 3.7 29 112-140 32-60 (101)
33 TIGR03072 release_prfH putativ 22.1 2.7E+02 0.0059 22.6 5.6 44 7-50 19-62 (200)
34 PF03462 PCRF: PCRF domain; I 20.7 3.4E+02 0.0073 19.6 6.3 36 7-43 66-101 (115)
35 PF08672 APC2: Anaphase promot 20.6 1.9E+02 0.004 18.8 3.6 39 132-170 12-50 (60)
36 CHL00165 ftrB ferredoxin thior 20.4 86 0.0019 23.4 2.1 24 4-27 11-34 (116)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=99.98 E-value=2.1e-32 Score=257.34 Aligned_cols=104 Identities=36% Similarity=0.630 Sum_probs=90.2
Q ss_pred CccCCHHHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCC-C-----------CCCCCCCCCcc
Q 030575 1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKG-T-----------NGPEKKPRPSA 68 (175)
Q Consensus 1 M~F~s~eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~-~-----------~~~~~~~r~~t 68 (175)
|+|+|+||||+|||.||+++||+||+++++|++.+|+|++++|||||||+++.... . ....+++|+.+
T Consensus 78 MeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~~rR~~t 157 (846)
T PLN03097 78 MEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGTGRRSCA 157 (846)
T ss_pred CeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccccccccccc
Confidence 89999999999999999999999999999999999999999999999998754211 0 00112457789
Q ss_pred cccCcceeEEEeeeCCeEEEEEecccCCCCCCCCCC
Q 030575 69 REGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTAN 104 (175)
Q Consensus 69 RtgC~A~~~v~~~~~g~W~V~~~~~eHNH~L~~~~~ 104 (175)
||||+|+|+|++..+|+|+|++|++||||||.|+..
T Consensus 158 RtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~ 193 (846)
T PLN03097 158 KTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQA 193 (846)
T ss_pred CCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccc
Confidence 999999999999878999999999999999998654
No 2
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=99.96 E-value=7.5e-30 Score=180.74 Aligned_cols=91 Identities=42% Similarity=0.734 Sum_probs=82.7
Q ss_pred HHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCCCCCCCCCCCCcccccCcceeEEEeeeCCeEEEEE
Q 030575 11 KFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKMEKSGKWVVTR 90 (175)
Q Consensus 11 ~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~~~~~~~~~r~~tRtgC~A~~~v~~~~~g~W~V~~ 90 (175)
+||+.||..+||+||+..+++++.+|.+++..|+|+++|++..........+++++++||||||+|.|++..+|.|.|+.
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~ 80 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTS 80 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEE
Confidence 59999999999999999999988899999999999999999765443345678899999999999999987789999999
Q ss_pred ecccCCCCCCC
Q 030575 91 FIKDHNHPLVV 101 (175)
Q Consensus 91 ~~~eHNH~L~~ 101 (175)
|++||||||.|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999987
No 3
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=99.15 E-value=4.9e-10 Score=82.26 Aligned_cols=90 Identities=22% Similarity=0.366 Sum_probs=69.8
Q ss_pred cCCHHHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCCC--------------------CCCCC
Q 030575 3 FDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGT--------------------NGPEK 62 (175)
Q Consensus 3 F~s~eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~~--------------------~~~~~ 62 (175)
|++.+|...|....++..||+|++-+|..+ ...|.|--.|........ .....
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~-------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 73 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK-------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK 73 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCc-------eEEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence 899999999999999999999999876532 235889888776443221 11122
Q ss_pred CCCCcccccCcceeEEEee-eCCeEEEEEecccCCCCC
Q 030575 63 KPRPSAREGCKATILVKME-KSGKWVVTRFIKDHNHPL 99 (175)
Q Consensus 63 ~~r~~tRtgC~A~~~v~~~-~~g~W~V~~~~~eHNH~L 99 (175)
+.-.+..++||++|+.... ...+|-|..+..+|||||
T Consensus 74 k~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 74 KRTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred CcccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 2335678899999998875 589999999999999998
No 4
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=97.73 E-value=0.00021 Score=47.63 Aligned_cols=59 Identities=19% Similarity=0.401 Sum_probs=48.7
Q ss_pred CccCCHHHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCCCCCCCCCCCCcccccCcceeEEEe
Q 030575 1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKM 80 (175)
Q Consensus 1 M~F~s~eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~~~~~~~~~r~~tRtgC~A~~~v~~ 80 (175)
|.|+|.+|++.-...||-..||.+++..+.+ .+...+|. + .|||++|..+.
T Consensus 8 ~~F~~~~e~k~av~~yai~~~~~~~v~ksd~-------~r~~~~C~--~--------------------~~C~Wrv~as~ 58 (67)
T PF03108_consen 8 QTFPSKEEFKEAVREYAIKNGFEFKVKKSDK-------KRYRAKCK--D--------------------KGCPWRVRASK 58 (67)
T ss_pred CEECCHHHHHHHHHHHHHhcCcEEEEeccCC-------EEEEEEEc--C--------------------CCCCEEEEEEE
Confidence 7899999999999999999999999876542 46678886 1 25999999987
Q ss_pred e-eCCeEEE
Q 030575 81 E-KSGKWVV 88 (175)
Q Consensus 81 ~-~~g~W~V 88 (175)
. .++.|.|
T Consensus 59 ~~~~~~~~I 67 (67)
T PF03108_consen 59 RKRSDTFQI 67 (67)
T ss_pred cCCCCEEEC
Confidence 6 4578876
No 5
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=90.36 E-value=0.18 Score=31.99 Aligned_cols=25 Identities=36% Similarity=0.720 Sum_probs=10.5
Q ss_pred ccCcceeEEEeeeCCeEEEEEecccCCC
Q 030575 70 EGCKATILVKMEKSGKWVVTRFIKDHNH 97 (175)
Q Consensus 70 tgC~A~~~v~~~~~g~W~V~~~~~eHNH 97 (175)
.+|+|++.+. .+++ .|.....+|||
T Consensus 38 ~~C~a~~~~~-~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD-AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE---TT--EEEE-S---SS
T ss_pred CCCeEEEEEE-CCCC--EEEECCCccCC
Confidence 6899999988 2233 45666689999
No 6
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=89.39 E-value=0.5 Score=31.04 Aligned_cols=28 Identities=32% Similarity=0.617 Sum_probs=21.5
Q ss_pred cCcceeEEEee-eCCeEEEEEecccCCCC
Q 030575 71 GCKATILVKME-KSGKWVVTRFIKDHNHP 98 (175)
Q Consensus 71 gC~A~~~v~~~-~~g~W~V~~~~~eHNH~ 98 (175)
||+|.=.|... +++.-+++-...+||||
T Consensus 31 ~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 31 GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 89999888875 47788889999999997
No 7
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=75.60 E-value=1.4 Score=31.79 Aligned_cols=26 Identities=31% Similarity=0.383 Sum_probs=20.2
Q ss_pred CccCCHHHHHHHHHHHhhhcCeEEEE
Q 030575 1 MEFDSEDAARKFYMGYARRMGFVVRI 26 (175)
Q Consensus 1 M~F~s~eeA~~FY~~YA~~~GF~ir~ 26 (175)
|+|+|++.|++|||.=+...=-++|.
T Consensus 58 iEFps~~~ar~~y~SpeYq~a~~~Rq 83 (96)
T COG5470 58 IEFPSLEAARDCYNSPEYQAAAAIRQ 83 (96)
T ss_pred EEcCCHHHHHHHhcCHHHHHHHHHHh
Confidence 68999999999999766655555544
No 8
>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []. These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.
Probab=72.26 E-value=2.4 Score=31.21 Aligned_cols=18 Identities=22% Similarity=0.658 Sum_probs=16.2
Q ss_pred CccCCHHHHHHHHHHHhh
Q 030575 1 MEFDSEDAARKFYMGYAR 18 (175)
Q Consensus 1 M~F~s~eeA~~FY~~YA~ 18 (175)
|.|++.+.|.+||..|-.
T Consensus 59 ikF~~~~~Ad~Fy~~fNG 76 (110)
T PF07576_consen 59 IKFRDQESADEFYEEFNG 76 (110)
T ss_pred EEECCHHHHHHHHHHhCC
Confidence 589999999999999954
No 9
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=71.61 E-value=5.1 Score=26.30 Aligned_cols=28 Identities=25% Similarity=0.431 Sum_probs=22.6
Q ss_pred ccCcceeEEEee-eCCeEEEEEecccCCC
Q 030575 70 EGCKATILVKME-KSGKWVVTRFIKDHNH 97 (175)
Q Consensus 70 tgC~A~~~v~~~-~~g~W~V~~~~~eHNH 97 (175)
.||+|+=.|... +++.-.++-...+|||
T Consensus 31 ~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 31 QGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 689998777665 4678888888999998
No 10
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=65.85 E-value=5 Score=29.15 Aligned_cols=24 Identities=33% Similarity=0.606 Sum_probs=18.6
Q ss_pred CccCCHHHHHHHHHHHhhhcCeEEEEee
Q 030575 1 MEFDSEDAARKFYMGYARRMGFVVRIMQ 28 (175)
Q Consensus 1 M~F~s~eeA~~FY~~YA~~~GF~ir~~~ 28 (175)
|.|+|.|+|.. ||.+.|..-.+..
T Consensus 53 l~F~skE~Ai~----yaer~G~~Y~V~~ 76 (101)
T PF04800_consen 53 LKFDSKEDAIA----YAERNGWDYEVEE 76 (101)
T ss_dssp EEESSHHHHHH----HHHHCT-EEEEE-
T ss_pred eeeCCHHHHHH----HHHHcCCeEEEeC
Confidence 57999999985 6889998887764
No 11
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=60.99 E-value=3.6 Score=26.90 Aligned_cols=15 Identities=40% Similarity=0.711 Sum_probs=13.3
Q ss_pred CccCCHHHHHHHHHH
Q 030575 1 MEFDSEDAARKFYMG 15 (175)
Q Consensus 1 M~F~s~eeA~~FY~~ 15 (175)
++|+|.++|..||+.
T Consensus 44 ieFPs~~aa~~~~~s 58 (65)
T PF07045_consen 44 IEFPSMEAAKAWYNS 58 (65)
T ss_dssp EEESSHHHHHHHHCS
T ss_pred EECCCHHHHHHHHCC
Confidence 479999999999975
No 12
>PF12441 DUF3680: Protein of unknown function (DUF3680) ; InterPro: IPR022148 This domain family is found in bacteria and archaea, and is approximately 40 amino acids in length.
Probab=50.38 E-value=14 Score=22.49 Aligned_cols=14 Identities=43% Similarity=0.774 Sum_probs=12.9
Q ss_pred ccCCHHHHHHHHHH
Q 030575 2 EFDSEDAARKFYMG 15 (175)
Q Consensus 2 ~F~s~eeA~~FY~~ 15 (175)
+|.|++||.+|+..
T Consensus 7 ~f~se~Ee~eFW~~ 20 (42)
T PF12441_consen 7 EFKSEEEEREFWDT 20 (42)
T ss_pred CCCCHHHHHHHHHh
Confidence 69999999999987
No 13
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=47.65 E-value=14 Score=30.22 Aligned_cols=19 Identities=32% Similarity=0.788 Sum_probs=15.9
Q ss_pred CCCCCCcccccCcceeEEE
Q 030575 61 EKKPRPSAREGCKATILVK 79 (175)
Q Consensus 61 ~~~~r~~tRtgC~A~~~v~ 79 (175)
..+..++.+.+|||+|.|+
T Consensus 69 ~~~~~~skK~~CPA~I~Ik 87 (225)
T PF15299_consen 69 RRRSKPSKKRDCPARIYIK 87 (225)
T ss_pred ccccccccCCCCCeEEEEE
Confidence 4456688999999999987
No 14
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=41.83 E-value=17 Score=23.86 Aligned_cols=19 Identities=37% Similarity=0.522 Sum_probs=13.7
Q ss_pred ccchhHHHHHHHHHHHHhH
Q 030575 150 ELSSKIQVIVDNIRKVESE 168 (175)
Q Consensus 150 ~Ls~k~qdi~~~~r~~e~~ 168 (175)
.+.++-..|+|.||||||-
T Consensus 13 ~~GiTRSvIVNALRKleSa 31 (61)
T PF08222_consen 13 RVGITRSVIVNALRKLESA 31 (61)
T ss_dssp HHT--HHHHHHHHHHHHHT
T ss_pred HhCccHHHHHHHHHHHHhc
Confidence 3456677899999999984
No 15
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=38.87 E-value=74 Score=29.27 Aligned_cols=41 Identities=12% Similarity=0.182 Sum_probs=33.6
Q ss_pred ccCCHHHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccC
Q 030575 2 EFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQ 48 (175)
Q Consensus 2 ~F~s~eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~Csre 48 (175)
.|+|+++=|.-.|.|-...---|....+.|. .-.+|.|..-
T Consensus 27 ~f~tl~~wy~v~ndyefq~rcpiilknsh~n------khftfachlk 67 (496)
T PF04684_consen 27 KFPTLEAWYNVINDYEFQSRCPIILKNSHRN------KHFTFACHLK 67 (496)
T ss_pred CCCcHHHHHHHHhhhhhhhcCceeecccccc------cceEEEeecc
Confidence 5999999999999999988888877776664 3568999654
No 16
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=37.82 E-value=21 Score=32.67 Aligned_cols=22 Identities=41% Similarity=0.626 Sum_probs=18.5
Q ss_pred CCeEEEEEecccCCCCCCCCCC
Q 030575 83 SGKWVVTRFIKDHNHPLVVTAN 104 (175)
Q Consensus 83 ~g~W~V~~~~~eHNH~L~~~~~ 104 (175)
.|-++|++++.-|||||...-+
T Consensus 164 ~g~f~v~k~~~~h~h~l~~nl~ 185 (496)
T PF04684_consen 164 KGPFVVTKIEPYHNHPLESNLS 185 (496)
T ss_pred cCceEEEeeccccCCccccccc
Confidence 5779999999999999976443
No 17
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=37.31 E-value=1.2e+02 Score=21.01 Aligned_cols=46 Identities=11% Similarity=0.271 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHhHhh
Q 030575 122 ELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEML 170 (175)
Q Consensus 122 el~~~~~~~~~~~~~l~~il~~~~g~~~~Ls~k~qdi~~~~r~~e~~~~ 170 (175)
+|+.....-+.++++.+..|+-...++ |..+.++...|.+|+....
T Consensus 27 ~Ie~~E~~~~~~rda~y~ML~~W~~q~---~a~~n~Ll~aL~~m~l~g~ 72 (77)
T cd08815 27 EIEAVELEIGRFRDQQYEMLKRWRQQQ---PAGLDAVYAALERMGLAGC 72 (77)
T ss_pred HHHHHHhcccchHHHHHHHHHHHHHcC---CCcHHHHHHHHHHHHHHHH
Confidence 344433333557899999999999988 5789999999999987543
No 18
>PF12883 DUF3828: Protein of unknown function (DUF3828); InterPro: IPR024289 This domain currently has no known function.; PDB: 3KZT_A.
Probab=30.95 E-value=60 Score=23.68 Aligned_cols=21 Identities=24% Similarity=0.601 Sum_probs=14.5
Q ss_pred cceeEEEee-eCCeEEEEEecc
Q 030575 73 KATILVKME-KSGKWVVTRFIK 93 (175)
Q Consensus 73 ~A~~~v~~~-~~g~W~V~~~~~ 93 (175)
+-.+.+.+. .+|+|.|.++..
T Consensus 97 ~~~~~~~l~ke~g~WkI~~V~~ 118 (120)
T PF12883_consen 97 KQTVIVCLVKENGRWKIDDVRD 118 (120)
T ss_dssp EEEEEEEEEEETTEEEEEEES-
T ss_pred CEEEEEEEEEECCEEEEEEeec
Confidence 344666654 589999999853
No 19
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=30.32 E-value=1e+02 Score=23.52 Aligned_cols=44 Identities=11% Similarity=0.173 Sum_probs=34.1
Q ss_pred CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---ccccccchh
Q 030575 111 DKDKKIEELTLELERQEQLCAAYREKLFNFMNNVE---EQTEELSSK 154 (175)
Q Consensus 111 ~~~kkI~el~~el~~~~~~~~~~~~~l~~il~~~~---g~~~~Ls~k 154 (175)
+-+++...|...|+.-++++..|.+||..|.+-++ |....-||+
T Consensus 74 e~q~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~Yt 120 (140)
T PF07526_consen 74 ELQRKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYT 120 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhH
Confidence 35788889999999999999999999988887554 443444544
No 20
>PRK04158 transcriptional repressor CodY; Validated
Probab=28.59 E-value=1.8e+02 Score=24.67 Aligned_cols=34 Identities=24% Similarity=0.427 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhccc---------cccchhHHHHHHHHHHHHhH
Q 030575 135 EKLFNFMNNVEEQT---------EELSSKIQVIVDNIRKVESE 168 (175)
Q Consensus 135 ~~l~~il~~~~g~~---------~~Ls~k~qdi~~~~r~~e~~ 168 (175)
+.+..|++.+.|.- +.+..|=--|||-|||+||-
T Consensus 186 eAv~hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESA 228 (256)
T PRK04158 186 EAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA 228 (256)
T ss_pred HHHHHHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcc
Confidence 45677788776642 25566667899999999984
No 21
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=27.82 E-value=1.3e+02 Score=20.98 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=19.4
Q ss_pred cccccchhHHHHHHHHHHHHhHh
Q 030575 147 QTEELSSKIQVIVDNIRKVESEM 169 (175)
Q Consensus 147 ~~~~Ls~k~qdi~~~~r~~e~~~ 169 (175)
.+..||.+++..+..+--+|.+.
T Consensus 48 ~~~~lp~~~keLL~EIA~lE~eV 70 (88)
T PF14389_consen 48 SPSSLPKKAKELLEEIALLEAEV 70 (88)
T ss_pred ccccCChHHHHHHHHHHHHHHHH
Confidence 34689999999999999888875
No 22
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=27.69 E-value=91 Score=21.58 Aligned_cols=33 Identities=15% Similarity=0.332 Sum_probs=27.0
Q ss_pred HHHHhhccccccchhHHHHHHHHHHHHhHhhhh
Q 030575 140 FMNNVEEQTEELSSKIQVIVDNIRKVESEMLKS 172 (175)
Q Consensus 140 il~~~~g~~~~Ls~k~qdi~~~~r~~e~~~~~~ 172 (175)
+|.+.-+..++||..++....-+|+|..+.++.
T Consensus 2 ~le~f~d~~~~LP~el~r~l~~irelD~~~~~~ 34 (105)
T PF12998_consen 2 YLEDFLDSLENLPAELQRNLTLIRELDAKSQDL 34 (105)
T ss_dssp HHHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHChHHHHHHHHHHHHhhhhHHHH
Confidence 567777888899999999999999998876543
No 23
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=25.99 E-value=2.1e+02 Score=23.28 Aligned_cols=43 Identities=16% Similarity=0.161 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCC
Q 030575 7 DAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQG 49 (175)
Q Consensus 7 eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG 49 (175)
++....|..||...||.+.+-....+...|.+.+..|...-+|
T Consensus 20 ~~L~~my~~~a~~~g~~~~ii~~~~~~~~gg~ksa~~~i~G~~ 62 (200)
T PRK08179 20 AKALERLLKEAARQGVRVTVLETETGRYPDTLRSALVSLDGDN 62 (200)
T ss_pred HHHHHHHHHHHHHcCCeEEEEeCCCCCCCCceEEEEEEEEccC
Confidence 4567889999999999999876544333355777777776555
No 24
>smart00574 POX domain associated with HOX domains.
Probab=24.85 E-value=1.5e+02 Score=22.77 Aligned_cols=43 Identities=14% Similarity=0.159 Sum_probs=33.4
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---ccccccchh
Q 030575 112 KDKKIEELTLELERQEQLCAAYREKLFNFMNNVE---EQTEELSSK 154 (175)
Q Consensus 112 ~~kkI~el~~el~~~~~~~~~~~~~l~~il~~~~---g~~~~Ls~k 154 (175)
.+.+...|...|+.-+++...|.+||.++.+-++ |.....||+
T Consensus 75 ~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt 120 (140)
T smart00574 75 LQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYT 120 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHH
Confidence 5778888888999999999999999999888655 443445544
No 25
>PRK10884 SH3 domain-containing protein; Provisional
Probab=24.84 E-value=2.7e+02 Score=22.59 Aligned_cols=75 Identities=15% Similarity=0.212 Sum_probs=45.0
Q ss_pred CCCCCCCCCCcccccCCcccchHHHHHHHHHHHHHHHHHHH-------HHHHHHHHhhccccccchhHHHHHHHHHHHHh
Q 030575 95 HNHPLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYRE-------KLFNFMNNVEEQTEELSSKIQVIVDNIRKVES 167 (175)
Q Consensus 95 HNH~L~~~~~~~~~~~~~~kkI~el~~el~~~~~~~~~~~~-------~l~~il~~~~g~~~~Ls~k~qdi~~~~r~~e~ 167 (175)
|.--|...|..+..+|.-.+.+.+++.+|...++....-.. +.-..++++.+....|....+.+.+.+..+|.
T Consensus 81 ~~~~Ls~~p~~~~rlp~le~el~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~ 160 (206)
T PRK10884 81 PLKQLSTTPSLRTRVPDLENQVKTLTDKLNNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANL 160 (206)
T ss_pred EHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555544444454566677777666665554332222 23445566777788888888888887777766
Q ss_pred Hh
Q 030575 168 EM 169 (175)
Q Consensus 168 ~~ 169 (175)
+-
T Consensus 161 ~~ 162 (206)
T PRK10884 161 QL 162 (206)
T ss_pred HH
Confidence 53
No 26
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=24.62 E-value=86 Score=19.20 Aligned_cols=19 Identities=16% Similarity=0.350 Sum_probs=15.7
Q ss_pred ccCCHHHHHHHHHHHhhhc
Q 030575 2 EFDSEDAARKFYMGYARRM 20 (175)
Q Consensus 2 ~F~s~eeA~~FY~~YA~~~ 20 (175)
.|+++++|..-|..++...
T Consensus 35 ~fg~~~eA~~~a~~~r~~~ 53 (56)
T PF00847_consen 35 KFGFEEEAKRAAIEARKEL 53 (56)
T ss_dssp CCCCHHHHHHHHHHHHHHC
T ss_pred cCCCHHHHHHHHHHHHHHh
Confidence 5899999999999887653
No 27
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=24.36 E-value=67 Score=20.77 Aligned_cols=29 Identities=24% Similarity=0.508 Sum_probs=21.0
Q ss_pred HHHHHHHhhccccccchhHHHHHHHHHHH
Q 030575 137 LFNFMNNVEEQTEELSSKIQVIVDNIRKV 165 (175)
Q Consensus 137 l~~il~~~~g~~~~Ls~k~qdi~~~~r~~ 165 (175)
+-+-++.++...+.|+..++.|-+++++|
T Consensus 12 ~~~~i~tvk~en~~i~~~ve~i~envk~l 40 (55)
T PF05377_consen 12 IESSINTVKKENEEISESVEKIEENVKDL 40 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33446677777778888888888888775
No 28
>cd08875 START_ArGLABRA2_like C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of the Arabidopsis homeobox protein GLABRA 2 and related proteins. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Most proteins in this subgroup contain an N-terminal homeobox DNA-binding domain, some contain a leucine zipper. ArGLABRA2 plays a role in the differentiation of hairless epidermal cells of the Arabidopsis root. It acts in a cell-position-dependent manner to suppress root hair formation in those cells.
Probab=24.28 E-value=1.1e+02 Score=25.36 Aligned_cols=33 Identities=21% Similarity=0.254 Sum_probs=24.9
Q ss_pred CCCcccccCcceeEEEeeeCCeEEEEEecccCCC
Q 030575 64 PRPSAREGCKATILVKMEKSGKWVVTRFIKDHNH 97 (175)
Q Consensus 64 ~r~~tRtgC~A~~~v~~~~~g~W~V~~~~~eHNH 97 (175)
|-..+|.=|-.+..-.+ .+|.|.|..+..+|.|
T Consensus 126 pLVp~Re~~fLRyc~~l-~dG~w~VvdvSld~~~ 158 (229)
T cd08875 126 PLVPTREFYFLRYCKQL-EDGLWAVVDVSIDGVQ 158 (229)
T ss_pred ccccCCeEEEEEEEEEe-CCCeEEEEEEeecccc
Confidence 44567777766666445 4899999999999976
No 29
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=22.82 E-value=3.6e+02 Score=22.60 Aligned_cols=34 Identities=24% Similarity=0.392 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhcccc---------ccchhHHHHHHHHHHHHhH
Q 030575 135 EKLFNFMNNVEEQTE---------ELSSKIQVIVDNIRKVESE 168 (175)
Q Consensus 135 ~~l~~il~~~~g~~~---------~Ls~k~qdi~~~~r~~e~~ 168 (175)
+.+..|+..+.|..- .+..+-..|||.||||||-
T Consensus 189 eAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESA 231 (261)
T COG4465 189 EAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA 231 (261)
T ss_pred HHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhc
Confidence 456677777766433 3455666799999999984
No 30
>PRK11370 YciI-like protein; Reviewed
Probab=22.36 E-value=46 Score=23.42 Aligned_cols=14 Identities=36% Similarity=0.482 Sum_probs=12.8
Q ss_pred ccCCHHHHHHHHHH
Q 030575 2 EFDSEDAARKFYMG 15 (175)
Q Consensus 2 ~F~s~eeA~~FY~~ 15 (175)
+|+|.++|.+|++.
T Consensus 64 ea~s~~~a~~~~~~ 77 (99)
T PRK11370 64 EFESLEAAQAWADA 77 (99)
T ss_pred EECCHHHHHHHHHC
Confidence 78999999999986
No 31
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=22.31 E-value=2.2e+02 Score=18.03 Aligned_cols=34 Identities=24% Similarity=0.214 Sum_probs=28.0
Q ss_pred ccCCHHHHHHHHHHHhhhc-CeEEEEeeeeeccCCCceEE
Q 030575 2 EFDSEDAARKFYMGYARRM-GFVVRIMQRRRSRTDGTTLA 40 (175)
Q Consensus 2 ~F~s~eeA~~FY~~YA~~~-GF~ir~~~~~rs~~dg~i~~ 40 (175)
.|+|.++|.+.=...|+.. |=.+.+. +.||.|..
T Consensus 24 ~~~Tk~eAi~~Ar~~a~~~~~~el~Ih-----~~dG~i~~ 58 (62)
T PF09954_consen 24 TFDTKAEAIEAARELAKNQGGGELIIH-----GRDGKIRE 58 (62)
T ss_pred ccCcHHHHHHHHHHHHHhCCCcEEEEE-----CCCCeEEE
Confidence 6999999999999999997 7777765 35887754
No 32
>PHA02047 phage lambda Rz1-like protein
Probab=22.22 E-value=1.6e+02 Score=21.32 Aligned_cols=29 Identities=17% Similarity=0.147 Sum_probs=25.8
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHH
Q 030575 112 KDKKIEELTLELERQEQLCAAYREKLFNF 140 (175)
Q Consensus 112 ~~kkI~el~~el~~~~~~~~~~~~~l~~i 140 (175)
-|+.+..+..+|+.....-+.|+.++..+
T Consensus 32 ~h~~a~~la~qLE~a~~r~~~~Q~~V~~l 60 (101)
T PHA02047 32 AHEEAKRQTARLEALEVRYATLQRHVQAV 60 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48889999999999999999999998764
No 33
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=22.11 E-value=2.7e+02 Score=22.58 Aligned_cols=44 Identities=14% Similarity=0.120 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCC
Q 030575 7 DAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGF 50 (175)
Q Consensus 7 eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~ 50 (175)
++....|..||...|+.+.+-....+...|.+.+..|...-++-
T Consensus 19 ~~L~~my~~~a~~~g~~~eii~~~~~~~~gg~ksa~~~i~G~~a 62 (200)
T TIGR03072 19 AKALERLTREAAARGVRVEVLEQEPGEVPGTLRSALVSLDGEAA 62 (200)
T ss_pred HHHHHHHHHHHHHcCCeEEEEeCCCCCCCCceEEEEEEEEccCH
Confidence 45678899999999999998765443333556777777766653
No 34
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=20.71 E-value=3.4e+02 Score=19.62 Aligned_cols=36 Identities=22% Similarity=0.453 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEE
Q 030575 7 DAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRL 43 (175)
Q Consensus 7 eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~ 43 (175)
.+-...|..||.+.||.+.+-....+. -|-+....|
T Consensus 66 ~~L~~MY~~~a~~~gw~~~~l~~~~~~-~~G~k~a~~ 101 (115)
T PF03462_consen 66 EELFRMYQRYAERRGWKVEVLDYSPGE-EGGIKSATL 101 (115)
T ss_dssp HHHHHHHHHHHHHTT-EEEEEEEEE-S-SSSEEEEEE
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCCC-ccceeEEEE
Confidence 355789999999999999887654432 234444443
No 35
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=20.60 E-value=1.9e+02 Score=18.76 Aligned_cols=39 Identities=3% Similarity=0.099 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHhHhh
Q 030575 132 AYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEML 170 (175)
Q Consensus 132 ~~~~~l~~il~~~~g~~~~Ls~k~qdi~~~~r~~e~~~~ 170 (175)
.|.+.|.++|+-+-.++...+.+.+++..+|-++..+.+
T Consensus 12 l~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~ 50 (60)
T PF08672_consen 12 LPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGK 50 (60)
T ss_dssp EEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCc
Confidence 677889999998877778899999999999998887765
No 36
>CHL00165 ftrB ferredoxin thioreductase subunit beta; Validated
Probab=20.36 E-value=86 Score=23.38 Aligned_cols=24 Identities=33% Similarity=0.342 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHHHhhhcCeEEEEe
Q 030575 4 DSEDAARKFYMGYARRMGFVVRIM 27 (175)
Q Consensus 4 ~s~eeA~~FY~~YA~~~GF~ir~~ 27 (175)
+|.++.++|-..||...|+-.-..
T Consensus 11 ~~~e~m~~f~ekya~~~G~~fnpD 34 (116)
T CHL00165 11 ESLEAMRKFAETYAKRTNTFFCSD 34 (116)
T ss_pred hhHHHHHHHHHHHHHHhCCeeCCC
Confidence 478999999999999999987544
Done!