Query 028717
Match_columns 205
No_of_seqs 184 out of 581
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 15:54:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028717.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028717hhsearch_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 3.2E-35 6.9E-40 286.4 16.2 123 4-126 57-192 (846)
2 PF03101 FAR1: FAR1 DNA-bindin 100.0 1.3E-28 2.8E-33 180.2 8.6 90 35-124 1-91 (91)
3 PF08731 AFT: Transcription fa 99.1 8E-10 1.7E-14 84.0 9.6 89 27-122 1-111 (111)
4 PF03108 DBD_Tnp_Mut: MuDR fam 98.2 1.1E-05 2.5E-10 55.7 7.9 62 22-111 5-67 (67)
5 PF04500 FLYWCH: FLYWCH zinc f 91.2 0.49 1.1E-05 30.9 4.4 25 93-120 38-62 (62)
6 PF03106 WRKY: WRKY DNA -bindi 90.6 1.8 3.9E-05 29.4 6.8 28 94-121 31-59 (60)
7 COG5470 Uncharacterized conser 85.8 0.46 1E-05 35.4 1.5 45 7-51 40-84 (96)
8 PF04800 ETC_C1_NDUFA4: ETC co 64.7 6.1 0.00013 29.7 2.5 28 22-53 50-77 (101)
9 smart00774 WRKY DNA binding do 63.8 10 0.00022 25.8 3.2 28 93-120 31-59 (59)
10 smart00461 WH1 WASP homology r 63.2 4.8 0.0001 30.2 1.7 20 22-41 84-103 (106)
11 cd00837 EVH1 EVH1 (Enabled, Va 61.7 5.4 0.00012 29.7 1.7 20 22-41 82-101 (104)
12 PF07576 BRAP2: BRCA1-associat 59.3 7.5 0.00016 29.6 2.1 19 24-42 58-76 (110)
13 cd01205 WASP WASP-type EVH1 do 58.2 7 0.00015 29.6 1.8 28 11-41 75-102 (105)
14 PF00568 WH1: WH1 domain; Int 58.0 7.2 0.00016 29.3 1.8 20 22-41 89-108 (111)
15 PF07045 DUF1330: Protein of u 52.9 6.8 0.00015 26.5 0.9 31 9-39 28-58 (65)
16 PF04684 BAF1_ABF1: BAF1 / ABF 52.6 31 0.00068 32.7 5.4 44 24-73 25-68 (496)
17 PF15299 ALS2CR8: Amyotrophic 51.5 12 0.00026 31.8 2.3 19 84-102 69-87 (225)
18 PF08222 HTH_CodY: CodY helix- 43.8 11 0.00024 25.7 0.8 19 180-198 13-31 (61)
19 KOG3671 Actin regulatory prote 42.9 20 0.00044 34.3 2.6 42 8-52 106-147 (569)
20 cd01207 Ena-Vasp Enabled-VASP- 39.8 19 0.00042 27.5 1.7 19 22-40 85-103 (111)
21 PF12441 DUF3680: Protein of u 38.9 24 0.00052 22.3 1.7 14 26-39 7-20 (42)
22 PF08672 APC2: Anaphase promot 37.6 73 0.0016 21.5 4.1 40 161-200 11-50 (60)
23 PF01693 Cauli_VI: Caulimoviru 36.7 26 0.00057 21.9 1.7 13 24-36 32-44 (44)
24 PF08471 Ribonuc_red_2_N: Clas 32.3 38 0.00083 25.1 2.2 17 26-42 72-88 (93)
25 PF04684 BAF1_ABF1: BAF1 / ABF 30.8 31 0.00067 32.7 1.8 22 106-127 164-185 (496)
26 PF08414 NADPH_Ox: Respiratory 23.8 63 0.0014 24.3 2.0 25 22-47 53-77 (100)
27 PF11132 SplA: Transcriptional 23.2 62 0.0013 23.0 1.8 16 25-40 58-73 (75)
28 PF03462 PCRF: PCRF domain; I 21.0 3E+02 0.0066 20.6 5.4 25 31-55 66-90 (115)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=3.2e-35 Score=286.40 Aligned_cols=123 Identities=34% Similarity=0.582 Sum_probs=106.2
Q ss_pred cccccccccccCCCCCCCccCCeeCCHHHHHHHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCC--
Q 028717 4 NVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRR-- 81 (205)
Q Consensus 4 ~~~~~~~~~~e~~~~~~P~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~-- 81 (205)
++.+.+.++.+.++..+|++||+|+|+||||+||+.||+++||+||+.+++|++.+|.|++++|+|+|+|+++.+.+.
T Consensus 57 ~~~~~~~~~~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~ 136 (846)
T PLN03097 57 NSPTGELVEFKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFN 136 (846)
T ss_pred cccccccccccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccc
Confidence 344566677888999999999999999999999999999999999999999999999999999999999996432110
Q ss_pred -----------CCCCCCCcccccCCccEEEEEEecCCcEEEEEEeecCCcccccCC
Q 028717 82 -----------SENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIP 126 (205)
Q Consensus 82 -----------~~~~r~r~~tRtgC~A~m~vk~~~~gkW~V~~~~~eHNH~L~~~~ 126 (205)
...+++|+.+||||+|+|+|++.++|+|+|++|++||||||.|+.
T Consensus 137 ~~~~~~~k~~~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~ 192 (846)
T PLN03097 137 RPRARQTKQDPENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQ 192 (846)
T ss_pred cccccccccCcccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCcc
Confidence 011235778999999999999988899999999999999999764
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=99.95 E-value=1.3e-28 Score=180.23 Aligned_cols=90 Identities=41% Similarity=0.757 Sum_probs=82.0
Q ss_pred HHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCC-CCCCCCCcccccCCccEEEEEEecCCcEEEEE
Q 028717 35 VFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRR-SENRKPRAVTREGCKAMIVVKKEKTGKWVVTR 113 (205)
Q Consensus 35 ~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~-~~~~r~r~~tRtgC~A~m~vk~~~~gkW~V~~ 113 (205)
+||+.||..+||+||+.++++++.+|.+++..|+|+++|+++.+... ...+++++++||||||+|.|++..+|.|.|+.
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 59999999999999999999988899999999999999997665443 45678899999999999999998789999999
Q ss_pred EeecCCccccc
Q 028717 114 FVKEHNHPLVA 124 (205)
Q Consensus 114 ~~~eHNH~L~~ 124 (205)
|+++|||||+|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999986
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=99.10 E-value=8e-10 Score=84.00 Aligned_cols=89 Identities=19% Similarity=0.367 Sum_probs=69.2
Q ss_pred eCCHHHHHHHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCC--------------------CCCCC
Q 028717 27 FESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRR--------------------SENRK 86 (205)
Q Consensus 27 F~S~eeA~~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~--------------------~~~~r 86 (205)
|++.+|...|....++..||+|++.+|..+ ...|.|--.|..+..... ...+.
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 889999999999999999999999988653 347999887774332110 11122
Q ss_pred CC-cccccCCccEEEEEEe-cCCcEEEEEEeecCCccc
Q 028717 87 PR-AVTREGCKAMIVVKKE-KTGKWVVTRFVKEHNHPL 122 (205)
Q Consensus 87 ~r-~~tRtgC~A~m~vk~~-~~gkW~V~~~~~eHNH~L 122 (205)
++ .+..++||++|+-... ...+|.|..+..+|||||
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 33 4556999999998876 579999999999999997
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=98.19 E-value=1.1e-05 Score=55.66 Aligned_cols=62 Identities=26% Similarity=0.416 Sum_probs=52.2
Q ss_pred ccCCeeCCHHHHHHHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCCCCCCCCCcccccCCccEEEE
Q 028717 22 YLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVV 101 (205)
Q Consensus 22 ~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~~~~~r~r~~tRtgC~A~m~v 101 (205)
.+||.|+|.+|+......||-..||.++..++.+ .+..++|. + .|||++|..
T Consensus 5 ~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~-------~r~~~~C~--~-------------------~~C~Wrv~a 56 (67)
T PF03108_consen 5 EVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK-------KRYRAKCK--D-------------------KGCPWRVRA 56 (67)
T ss_pred ccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC-------EEEEEEEc--C-------------------CCCCEEEEE
Confidence 5799999999999999999999999999987643 36778886 1 369999999
Q ss_pred EEec-CCcEEE
Q 028717 102 KKEK-TGKWVV 111 (205)
Q Consensus 102 k~~~-~gkW~V 111 (205)
...+ ++.|.|
T Consensus 57 s~~~~~~~~~I 67 (67)
T PF03108_consen 57 SKRKRSDTFQI 67 (67)
T ss_pred EEcCCCCEEEC
Confidence 8874 578876
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=91.17 E-value=0.49 Score=30.94 Aligned_cols=25 Identities=40% Similarity=0.694 Sum_probs=10.7
Q ss_pred cCCccEEEEEEecCCcEEEEEEeecCCc
Q 028717 93 EGCKAMIVVKKEKTGKWVVTRFVKEHNH 120 (205)
Q Consensus 93 tgC~A~m~vk~~~~gkW~V~~~~~eHNH 120 (205)
.+|+|++.+. ++.-.|.....+|||
T Consensus 38 ~~C~a~~~~~---~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD---AGDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE-----TTEEEE-S---SS
T ss_pred CCCeEEEEEE---CCCCEEEECCCccCC
Confidence 6899999987 233345556689999
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=90.57 E-value=1.8 Score=29.41 Aligned_cols=28 Identities=36% Similarity=0.656 Sum_probs=21.6
Q ss_pred CCccEEEEEEec-CCcEEEEEEeecCCcc
Q 028717 94 GCKAMIVVKKEK-TGKWVVTRFVKEHNHP 121 (205)
Q Consensus 94 gC~A~m~vk~~~-~gkW~V~~~~~eHNH~ 121 (205)
||+|.=.|.+.. ++.-+++...-+||||
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 899998888763 7788899999999997
No 7
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=85.80 E-value=0.46 Score=35.41 Aligned_cols=45 Identities=22% Similarity=0.229 Sum_probs=34.5
Q ss_pred ccccccccCCCCCCCccCCeeCCHHHHHHHHHHHhhhcCcEEEEc
Q 028717 7 DQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVD 51 (205)
Q Consensus 7 ~~~~~~~e~~~~~~P~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~ 51 (205)
|++..+.|++-.-.+.+=++|+|.+.|++|||+=+...=-++|..
T Consensus 40 GG~v~~lEG~w~ptr~vviEFps~~~ar~~y~SpeYq~a~~~Rq~ 84 (96)
T COG5470 40 GGEVETLEGEWRPTRNVVIEFPSLEAARDCYNSPEYQAAAAIRQA 84 (96)
T ss_pred CCCeeeccCCCCcccEEEEEcCCHHHHHHHhcCHHHHHHHHHHhh
Confidence 455677788877678888999999999999998666655555443
No 8
>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=64.69 E-value=6.1 Score=29.73 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=21.1
Q ss_pred ccCCeeCCHHHHHHHHHHHhhhcCcEEEEcce
Q 028717 22 YLGMEFESEEAAKVFYDAYATHMGFIMRVDAF 53 (205)
Q Consensus 22 ~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~~s 53 (205)
.+.|.|+|.|+|.. ||.+.|....+..-
T Consensus 50 ~v~l~F~skE~Ai~----yaer~G~~Y~V~~p 77 (101)
T PF04800_consen 50 SVRLKFDSKEDAIA----YAERNGWDYEVEEP 77 (101)
T ss_dssp -CEEEESSHHHHHH----HHHHCT-EEEEE-S
T ss_pred eeEeeeCCHHHHHH----HHHHcCCeEEEeCC
Confidence 36789999999987 68888888877643
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=63.79 E-value=10 Score=25.79 Aligned_cols=28 Identities=29% Similarity=0.481 Sum_probs=22.6
Q ss_pred cCCccEEEEEEe-cCCcEEEEEEeecCCc
Q 028717 93 EGCKAMIVVKKE-KTGKWVVTRFVKEHNH 120 (205)
Q Consensus 93 tgC~A~m~vk~~-~~gkW~V~~~~~eHNH 120 (205)
.||+|+=.|... +++.-.++-..-+|||
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 589998777666 4677888888999998
No 10
>smart00461 WH1 WASP homology region 1. Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain.
Probab=63.18 E-value=4.8 Score=30.17 Aligned_cols=20 Identities=40% Similarity=0.542 Sum_probs=17.5
Q ss_pred ccCCeeCCHHHHHHHHHHHh
Q 028717 22 YLGMEFESEEAAKVFYDAYA 41 (205)
Q Consensus 22 ~~Gm~F~S~eeA~~FY~~YA 41 (205)
.+|..|.|++||..|++.-.
T Consensus 84 ~~GLnF~se~EA~~F~~~v~ 103 (106)
T smart00461 84 VYGLNFASEEEAKKFRKKVL 103 (106)
T ss_pred EEEeecCCHHHHHHHHHHHH
Confidence 47999999999999998654
No 11
>cd00837 EVH1 EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. The EVH1 domain binds to other proteins at proline rich sequences in either FPPPP or PPXXF motifs. It is found in the cytoskeletal reorganization proteins Enabled VASP, and WASP, and in the synaptic scaffolding protein Homer. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=61.69 E-value=5.4 Score=29.72 Aligned_cols=20 Identities=35% Similarity=0.486 Sum_probs=17.6
Q ss_pred ccCCeeCCHHHHHHHHHHHh
Q 028717 22 YLGMEFESEEAAKVFYDAYA 41 (205)
Q Consensus 22 ~~Gm~F~S~eeA~~FY~~YA 41 (205)
.+|..|.|++||.+|++.-.
T Consensus 82 ~~GL~F~se~eA~~F~~~v~ 101 (104)
T cd00837 82 VYGLNFASEEEAAQFRKKVL 101 (104)
T ss_pred EEEEeeCCHHHHHHHHHHHH
Confidence 68999999999999998643
No 12
>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=59.31 E-value=7.5 Score=29.61 Aligned_cols=19 Identities=26% Similarity=0.628 Sum_probs=16.9
Q ss_pred CCeeCCHHHHHHHHHHHhh
Q 028717 24 GMEFESEEAAKVFYDAYAT 42 (205)
Q Consensus 24 Gm~F~S~eeA~~FY~~YA~ 42 (205)
=|.|.+.+.|.+||..|-.
T Consensus 58 LikF~~~~~Ad~Fy~~fNG 76 (110)
T PF07576_consen 58 LIKFRDQESADEFYEEFNG 76 (110)
T ss_pred EEEECCHHHHHHHHHHhCC
Confidence 3699999999999999964
No 13
>cd01205 WASP WASP-type EVH1 domain. WASP-type EVH1 domain. Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disease, characterized by eczema, immunodeficiency, and thrombocytopenia. The majority of patients with WAS, or a milder version of the disorder, X-linked thrombocytopenia (XLT), have point mutations in the EVH1 domain of WASP (Wiskott-Aldrich syndrome protein). WASP is an actin regulatory protein consisting of an N-terminal EVH1 domain, a basic region, a GTP binding domain, a proline rich region and a WH2 acidic region. Yeast members lack the GTP binding domain. WASP binds a 25 residue proline rich motif from the WASP Interacting Protein (WIP) via its N-terminal EVH1 domain.
Probab=58.16 E-value=7 Score=29.62 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=21.4
Q ss_pred ccccCCCCCCCccCCeeCCHHHHHHHHHHHh
Q 028717 11 AVTKGSSDGEPYLGMEFESEEAAKVFYDAYA 41 (205)
Q Consensus 11 ~~~e~~~~~~P~~Gm~F~S~eeA~~FY~~YA 41 (205)
.+++.| .=.+|..|.+++||..||+.-.
T Consensus 75 htFe~d---~c~~GL~Fade~EA~~F~k~v~ 102 (105)
T cd01205 75 HTFEGD---DCVVGLNFADETEAAEFRKKVL 102 (105)
T ss_pred EEEecc---CcEEEEEECCHHHHHHHHHHHH
Confidence 445555 3457999999999999998643
No 14
>PF00568 WH1: WH1 domain; InterPro: IPR000697 The EVH1 (WH1, RanBP1-WASP) domain is found in multi-domain proteins implicated in a diverse range of signalling, nuclear transport and cytoskeletal events. This domain of around 115 amino acids is present in species ranging from yeast to mammals. Many EVH1-containing proteins associate with actin-based structures and play a role in cytoskeletal organisation. EVH1 domains recognise and bind the proline-rich motif FPPPP with low-affinity, further interactions then form between flanking residues [][]. WASP family proteins contain a EVH1 (WH1) in their N-terminals which bind proline-rich sequences in the WASP interacting protein. Proteins of the RanBP1 family contain a WH1 domain in their N-terminal region, which seems to bind a different sequence motif present in the C-terminal part of RanGTP protein [,]. Tertiary structure of the WH1 domain of the Mena protein revealed structure similarities with the pleckstrin homology (PH) domain. The overall fold consists of a compact parallel beta-sandwich, closed along one edge by a long alpha-helix. A highly conserved cluster of three surface-exposed aromatic side-chains forms the recognition site for the molecules target ligands. [].; GO: 0005515 protein binding; PDB: 1I2H_A 1DDV_A 1DDW_A 1EGX_A 3SYX_A 1TJ6_B 1XOD_B 1EVH_A 1I7A_B 2JP2_A ....
Probab=58.02 E-value=7.2 Score=29.27 Aligned_cols=20 Identities=40% Similarity=0.677 Sum_probs=17.9
Q ss_pred ccCCeeCCHHHHHHHHHHHh
Q 028717 22 YLGMEFESEEAAKVFYDAYA 41 (205)
Q Consensus 22 ~~Gm~F~S~eeA~~FY~~YA 41 (205)
..|..|.|++||..|++.--
T Consensus 89 ~~GLnF~se~eA~~F~~~v~ 108 (111)
T PF00568_consen 89 VYGLNFASEEEADQFYKKVQ 108 (111)
T ss_dssp EEEEEESSHHHHHHHHHHHH
T ss_pred EEEEecCCHHHHHHHHHHHh
Confidence 78999999999999998653
No 15
>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=52.94 E-value=6.8 Score=26.50 Aligned_cols=31 Identities=39% Similarity=0.523 Sum_probs=20.8
Q ss_pred ccccccCCCCCCCccCCeeCCHHHHHHHHHH
Q 028717 9 EMAVTKGSSDGEPYLGMEFESEEAAKVFYDA 39 (205)
Q Consensus 9 ~~~~~e~~~~~~P~~Gm~F~S~eeA~~FY~~ 39 (205)
.....|++....-.+=.+|+|.++|..||+.
T Consensus 28 ~~~~leG~~~~~~~viieFPs~~aa~~~~~s 58 (65)
T PF07045_consen 28 EPEVLEGDWDPDRVVIIEFPSMEAAKAWYNS 58 (65)
T ss_dssp EEEEEEST-SSSEEEEEEESSHHHHHHHHCS
T ss_pred ceeEEecCCCCCeEEEEECCCHHHHHHHHCC
Confidence 3345555333333445799999999999985
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=52.61 E-value=31 Score=32.71 Aligned_cols=44 Identities=14% Similarity=0.152 Sum_probs=37.1
Q ss_pred CCeeCCHHHHHHHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccC
Q 028717 24 GMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEG 73 (205)
Q Consensus 24 Gm~F~S~eeA~~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG 73 (205)
+..|+|.++=|.-.|.|-...---|....|.|++ -.+|.|..-.
T Consensus 25 ~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk------hftfachlk~ 68 (496)
T PF04684_consen 25 ARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK------HFTFACHLKN 68 (496)
T ss_pred ccCCCcHHHHHHHHhhhhhhhcCceeeccccccc------ceEEEeeccC
Confidence 6789999999999999999998889888887752 6789996543
No 17
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=51.52 E-value=12 Score=31.80 Aligned_cols=19 Identities=26% Similarity=0.600 Sum_probs=15.5
Q ss_pred CCCCCcccccCCccEEEEE
Q 028717 84 NRKPRAVTREGCKAMIVVK 102 (205)
Q Consensus 84 ~~r~r~~tRtgC~A~m~vk 102 (205)
.++...+.+.+|||.|.|+
T Consensus 69 ~~~~~~skK~~CPA~I~Ik 87 (225)
T PF15299_consen 69 RRRSKPSKKRDCPARIYIK 87 (225)
T ss_pred ccccccccCCCCCeEEEEE
Confidence 3456788999999999876
No 18
>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=43.84 E-value=11 Score=25.66 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=14.6
Q ss_pred CCccchhHHHHHHHHHHHh
Q 028717 180 HLSRNIDDIVQSVKQIEAK 198 (205)
Q Consensus 180 ~l~~~~~di~N~~k~~e~~ 198 (205)
.+++|..-|+|.+|+||+-
T Consensus 13 ~~GiTRSvIVNALRKleSa 31 (61)
T PF08222_consen 13 RVGITRSVIVNALRKLESA 31 (61)
T ss_dssp HHT--HHHHHHHHHHHHHT
T ss_pred HhCccHHHHHHHHHHHHhc
Confidence 4678889999999999984
No 19
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=42.86 E-value=20 Score=34.30 Aligned_cols=42 Identities=21% Similarity=0.267 Sum_probs=34.2
Q ss_pred cccccccCCCCCCCccCCeeCCHHHHHHHHHHHhhhcCcEEEEcc
Q 028717 8 QEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDA 52 (205)
Q Consensus 8 ~~~~~~e~~~~~~P~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~~ 52 (205)
.-..++|.|+- .+|..|-|++||.+||...-.+.+..=|+..
T Consensus 106 ~ffhtFegddc---~aGLnF~~E~EA~~F~k~V~~r~~~~nrk~~ 147 (569)
T KOG3671|consen 106 TFFHTFEGDDC---QAGLNFASEEEAQKFRKKVQDRICHRNRKES 147 (569)
T ss_pred cceeeeccccc---eeeecccCHHHHHHHHHHHHHHhhhhhhhcc
Confidence 34477887776 7899999999999999999888877755554
No 20
>cd01207 Ena-Vasp Enabled-VASP-type homology (EVH1) domain. Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=39.81 E-value=19 Score=27.51 Aligned_cols=19 Identities=37% Similarity=0.592 Sum_probs=16.8
Q ss_pred ccCCeeCCHHHHHHHHHHH
Q 028717 22 YLGMEFESEEAAKVFYDAY 40 (205)
Q Consensus 22 ~~Gm~F~S~eeA~~FY~~Y 40 (205)
..|..|.|++||..|...-
T Consensus 85 v~GLnF~Se~eA~~F~~~v 103 (111)
T cd01207 85 VYGLNFGSKEDATMFASAM 103 (111)
T ss_pred EEeeccCCHHHHHHHHHHH
Confidence 6799999999999998764
No 21
>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=38.89 E-value=24 Score=22.31 Aligned_cols=14 Identities=50% Similarity=0.914 Sum_probs=13.0
Q ss_pred eeCCHHHHHHHHHH
Q 028717 26 EFESEEAAKVFYDA 39 (205)
Q Consensus 26 ~F~S~eeA~~FY~~ 39 (205)
+|.|++||.+|+..
T Consensus 7 ~f~se~Ee~eFW~~ 20 (42)
T PF12441_consen 7 EFKSEEEEREFWDT 20 (42)
T ss_pred CCCCHHHHHHHHHh
Confidence 79999999999987
No 22
>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=37.56 E-value=73 Score=21.48 Aligned_cols=40 Identities=3% Similarity=0.140 Sum_probs=31.0
Q ss_pred hhcHHHHHHHHHHhcCCCCCCccchhHHHHHHHHHHHhhh
Q 028717 161 AAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRI 200 (205)
Q Consensus 161 ~i~~~~i~~il~~~~g~~~~l~~~~~di~N~~k~~e~~~~ 200 (205)
+.|..+|.++|+-+-.+....+++.+++..+|-++-.+++
T Consensus 11 sl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~ 50 (60)
T PF08672_consen 11 SLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGK 50 (60)
T ss_dssp SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTS
T ss_pred CCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCc
Confidence 4999999999999977789999999999999999887654
No 23
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=36.71 E-value=26 Score=21.86 Aligned_cols=13 Identities=31% Similarity=0.442 Sum_probs=11.1
Q ss_pred CCeeCCHHHHHHH
Q 028717 24 GMEFESEEAAKVF 36 (205)
Q Consensus 24 Gm~F~S~eeA~~F 36 (205)
=+.|+|.+||.+|
T Consensus 32 ~k~F~t~~eA~~~ 44 (44)
T PF01693_consen 32 YKSFKTREEAEEF 44 (44)
T ss_dssp EEEESSHHHHHHH
T ss_pred ECCcCCHHHHhhC
Confidence 3789999999987
No 24
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=32.33 E-value=38 Score=25.14 Aligned_cols=17 Identities=41% Similarity=0.679 Sum_probs=14.6
Q ss_pred eeCCHHHHHHHHHHHhh
Q 028717 26 EFESEEAAKVFYDAYAT 42 (205)
Q Consensus 26 ~F~S~eeA~~FY~~YA~ 42 (205)
-|+|+++|..||..-+.
T Consensus 72 YF~t~eDA~~FydEl~~ 88 (93)
T PF08471_consen 72 YFATEEDAEAFYDELTY 88 (93)
T ss_pred CcCCHHHHHHHHHHHHH
Confidence 59999999999987654
No 25
>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=30.85 E-value=31 Score=32.74 Aligned_cols=22 Identities=41% Similarity=0.608 Sum_probs=18.8
Q ss_pred CCcEEEEEEeecCCcccccCCC
Q 028717 106 TGKWVVTRFVKEHNHPLVAIPA 127 (205)
Q Consensus 106 ~gkW~V~~~~~eHNH~L~~~~~ 127 (205)
.|-++|+++++-|||||....+
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 4779999999999999986544
No 26
>PF08414 NADPH_Ox: Respiratory burst NADPH oxidase; InterPro: IPR013623 This domain is found in plant proteins such as respiratory burst NADPH oxidase proteins which produce reactive oxygen species as a defence mechanism. It tends to occur to the N terminus of an EF-hand (IPR002048 from INTERPRO), which suggests a direct regulatory effect of Ca2+ on the activity of the NADPH oxidase in plants []. ; GO: 0004601 peroxidase activity, 0050664 oxidoreductase activity, acting on NADH or NADPH, oxygen as acceptor, 0055114 oxidation-reduction process; PDB: 3A8R_A.
Probab=23.76 E-value=63 Score=24.32 Aligned_cols=25 Identities=36% Similarity=0.561 Sum_probs=18.3
Q ss_pred ccCCeeCCHHHHHHHHHHHhhhcCcE
Q 028717 22 YLGMEFESEEAAKVFYDAYATHMGFI 47 (205)
Q Consensus 22 ~~Gm~F~S~eeA~~FY~~YA~~~GF~ 47 (205)
+|||. +|.|=|-+-|.+-|++-|-.
T Consensus 53 CIGM~-dSkeFA~eLFdALaRrr~i~ 77 (100)
T PF08414_consen 53 CIGMK-DSKEFAGELFDALARRRGIK 77 (100)
T ss_dssp HHT---S-HHHHHHHHHHHHHHTT--
T ss_pred hcCCc-ccHHHHHHHHHHHHHhcCCc
Confidence 68999 99999999999999987654
No 27
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=23.23 E-value=62 Score=23.03 Aligned_cols=16 Identities=38% Similarity=0.490 Sum_probs=14.4
Q ss_pred CeeCCHHHHHHHHHHH
Q 028717 25 MEFESEEAAKVFYDAY 40 (205)
Q Consensus 25 m~F~S~eeA~~FY~~Y 40 (205)
-.|.|++||.+-|+.|
T Consensus 58 Avfss~~eAe~ay~~~ 73 (75)
T PF11132_consen 58 AVFSSYEEAEQAYHEY 73 (75)
T ss_pred hhhcCHHHHHHHHHHh
Confidence 4799999999999877
No 28
>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=20.97 E-value=3e+02 Score=20.59 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhhhcCcEEEEcceee
Q 028717 31 EAAKVFYDAYATHMGFIMRVDAFRR 55 (205)
Q Consensus 31 eeA~~FY~~YA~~~GF~ir~~~s~r 55 (205)
.+....|..||.+.||.+.+-....
T Consensus 66 ~~L~~MY~~~a~~~gw~~~~l~~~~ 90 (115)
T PF03462_consen 66 EELFRMYQRYAERRGWKVEVLDYSP 90 (115)
T ss_dssp HHHHHHHHHHHHHTT-EEEEEEEEE
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCC
Confidence 3557889999999999999887554
Done!