Query 031272
Match_columns 162
No_of_seqs 167 out of 455
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 11:45:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031272.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031272hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03101 FAR1: FAR1 DNA-bindin 99.9 1.4E-27 3.1E-32 167.2 9.2 87 2-88 5-91 (91)
2 PLN03097 FHY3 Protein FAR-RED 99.9 1.5E-27 3.3E-32 222.2 11.6 154 2-161 92-258 (846)
3 PF08731 AFT: Transcription fa 98.1 2.1E-05 4.5E-10 57.5 8.2 77 3-86 14-111 (111)
4 PF03106 WRKY: WRKY DNA -bindi 91.3 0.33 7.3E-06 31.6 3.6 28 58-85 31-59 (60)
5 PF04500 FLYWCH: FLYWCH zinc f 90.3 0.2 4.2E-06 31.4 1.8 25 57-84 38-62 (62)
6 PF03108 DBD_Tnp_Mut: MuDR fam 80.3 4.3 9.4E-05 26.2 4.4 45 2-75 22-67 (67)
7 smart00774 WRKY DNA binding do 76.1 3.6 7.7E-05 26.8 2.9 29 56-84 30-59 (59)
8 PF05377 FlaC_arch: Flagella a 74.0 14 0.0003 23.8 5.2 30 123-152 11-40 (55)
9 PF06156 DUF972: Protein of un 67.7 11 0.00024 27.3 4.3 37 123-159 5-41 (107)
10 PF06295 DUF1043: Protein of u 61.5 51 0.0011 24.3 7.0 51 101-151 25-75 (128)
11 PRK13169 DNA replication intia 54.0 27 0.00058 25.5 4.2 30 127-156 9-38 (110)
12 PRK11677 hypothetical protein; 51.6 92 0.002 23.5 6.9 51 100-150 28-78 (134)
13 PF15299 ALS2CR8: Amyotrophic 51.3 17 0.00038 29.4 3.2 19 48-66 69-87 (225)
14 PF02185 HR1: Hr1 repeat; Int 49.0 72 0.0016 20.7 7.0 57 102-158 2-65 (70)
15 PF03670 UPF0184: Uncharacteri 46.9 97 0.0021 21.6 6.6 42 117-158 31-72 (83)
16 PRK10884 SH3 domain-containing 44.7 66 0.0014 25.9 5.5 34 125-158 131-164 (206)
17 PF14723 SSFA2_C: Sperm-specif 41.3 76 0.0017 25.1 5.2 73 72-150 71-158 (179)
18 PF05778 Apo-CIII: Apolipoprot 40.8 20 0.00044 24.0 1.7 29 126-154 6-34 (70)
19 PF03791 KNOX2: KNOX2 domain ; 40.5 91 0.002 19.7 4.6 39 114-159 12-50 (52)
20 PRK10920 putative uroporphyrin 38.2 81 0.0018 28.0 5.5 84 73-158 257-340 (390)
21 PF08946 Osmo_CC: Osmosensory 38.1 43 0.00093 20.7 2.7 28 132-159 11-38 (46)
22 PRK00846 hypothetical protein; 37.9 1.3E+02 0.0029 20.5 6.2 37 119-155 23-63 (77)
23 PF04684 BAF1_ABF1: BAF1 / ABF 36.5 23 0.0005 32.2 1.8 21 70-90 164-184 (496)
24 PF05739 SNARE: SNARE domain; 34.6 1.1E+02 0.0025 18.8 7.0 53 101-153 4-59 (63)
25 PRK14154 heat shock protein Gr 33.6 2E+02 0.0043 23.3 6.7 38 101-138 52-89 (208)
26 PF07106 TBPIP: Tat binding pr 32.6 1.5E+02 0.0033 22.4 5.7 55 100-154 78-137 (169)
27 PHA02047 phage lambda Rz1-like 31.4 1.8E+02 0.0039 20.9 5.3 29 100-128 33-61 (101)
28 PF08656 DASH_Dad3: DASH compl 31.2 1.8E+02 0.0038 20.0 5.9 14 143-156 37-50 (78)
29 PF04642 DUF601: Protein of un 30.4 94 0.002 26.3 4.3 36 125-160 195-230 (311)
30 PF10046 BLOC1_2: Biogenesis o 29.7 2E+02 0.0043 20.1 7.0 52 106-158 47-98 (99)
31 PRK14162 heat shock protein Gr 28.6 2.8E+02 0.0061 22.2 6.7 47 100-146 38-84 (194)
32 PRK14143 heat shock protein Gr 28.2 2.8E+02 0.0062 22.8 6.8 46 100-145 66-111 (238)
33 PRK14140 heat shock protein Gr 28.0 2.6E+02 0.0057 22.3 6.4 44 100-143 36-79 (191)
34 PF05596 Taeniidae_ag: Taeniid 27.6 1.3E+02 0.0029 19.8 3.9 35 121-155 29-64 (64)
35 PF12495 Vip3A_N: Vegetative i 27.5 2.8E+02 0.006 21.0 6.8 40 113-152 99-138 (177)
36 PF07889 DUF1664: Protein of u 27.5 2.4E+02 0.0052 21.0 5.7 23 134-156 97-119 (126)
37 PF02024 Leptin: Leptin; Inte 27.1 91 0.002 24.0 3.5 67 79-153 21-91 (146)
38 PF12883 DUF3828: Protein of u 26.3 93 0.002 22.4 3.3 20 61-80 98-118 (120)
39 PRK02793 phi X174 lysis protei 25.5 2.1E+02 0.0045 19.0 6.1 37 119-155 18-58 (72)
40 PRK09974 putative regulator Pr 25.0 2.5E+02 0.0055 20.5 5.4 27 61-87 36-62 (111)
41 PF04740 LXG: LXG domain of WX 24.8 2.4E+02 0.0052 21.7 5.7 31 129-159 141-171 (204)
42 PRK14147 heat shock protein Gr 24.3 3.3E+02 0.0071 21.2 6.3 16 120-135 37-52 (172)
43 PRK14139 heat shock protein Gr 24.0 3.6E+02 0.0078 21.4 6.5 44 101-144 32-75 (185)
44 PF08222 HTH_CodY: CodY helix- 23.8 63 0.0014 21.1 1.7 12 144-155 20-31 (61)
45 cd08875 START_ArGLABRA2_like C 22.4 1.3E+02 0.0028 24.7 3.8 33 51-84 126-158 (229)
46 PF05761 5_nucleotid: 5' nucle 22.1 2.6E+02 0.0057 25.2 6.0 59 101-159 322-388 (448)
47 PF04375 HemX: HemX; InterPro 20.7 1.6E+02 0.0035 25.6 4.3 72 85-158 263-334 (372)
48 KOG4603 TBP-1 interacting prot 20.2 1.7E+02 0.0037 23.3 3.9 30 102-131 117-146 (201)
49 PRK06975 bifunctional uroporph 20.2 2.1E+02 0.0045 27.0 5.1 73 84-158 565-637 (656)
50 PRK00736 hypothetical protein; 20.2 2.7E+02 0.0058 18.3 6.1 36 120-155 16-55 (68)
No 1
>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=1.4e-27 Score=167.18 Aligned_cols=87 Identities=41% Similarity=0.718 Sum_probs=78.9
Q ss_pred ccccccCeEEEEeceeecCCCCceEEEEEEecCCCCCCCCCCCCCCCCCCCCccccCCceEEEEEEeeCCcEEEEEEeec
Q 031272 2 GYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKMEKSGKWVVTRFIKD 81 (162)
Q Consensus 2 ~YA~~~GF~iR~~~~~rs~~~g~i~~~~~vCsreG~~~~~~~~~~~~~~~r~~tR~gC~A~i~v~~~~~gkW~V~~f~~e 81 (162)
+||+.+||+||+.++++++.+|.+++..|+|+++|+...+.......+++++++||||+|+|.|++..+|+|.|+.|+.|
T Consensus 5 ~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~~~~~ 84 (91)
T PF03101_consen 5 SYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTSFVLE 84 (91)
T ss_pred HhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEECcCC
Confidence 59999999999999999889999999999999999997654333456778999999999999999987899999999999
Q ss_pred CCcCccc
Q 031272 82 HNHPLVV 88 (162)
Q Consensus 82 HNH~L~~ 88 (162)
|||||+|
T Consensus 85 HNH~L~P 91 (91)
T PF03101_consen 85 HNHPLCP 91 (91)
T ss_pred cCCCCCC
Confidence 9999987
No 2
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=99.95 E-value=1.5e-27 Score=222.17 Aligned_cols=154 Identities=21% Similarity=0.394 Sum_probs=103.5
Q ss_pred ccccccCeEEEEeceeecCCCCceEEEEEEecCCCCCCCCCCCC------------CCCCCCCCccccCCceEEEEEEee
Q 031272 2 GYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTN------------GPEKKPRPSAREGCKATILVKMEK 69 (162)
Q Consensus 2 ~YA~~~GF~iR~~~~~rs~~~g~i~~~~~vCsreG~~~~~~~~~------------~~~~~~r~~tR~gC~A~i~v~~~~ 69 (162)
+||+++||+||++++++++.+|.|++++|||||||+++.+.... ....++|+.+||||+|+|+|++.+
T Consensus 92 ~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~~rR~~tRtGC~A~m~Vk~~~ 171 (846)
T PLN03097 92 EYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGTGRRSCAKTDCKASMHVKRRP 171 (846)
T ss_pred HHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCcccccccccccCCCCceEEEEEEcC
Confidence 59999999999999999999999999999999999975321100 011235778999999999999988
Q ss_pred CCcEEEEEEeecCCcCcccCCCcCcccCccccchhHHH-HHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHH
Q 031272 70 SGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT-LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDN 148 (162)
Q Consensus 70 ~gkW~V~~f~~eHNH~L~~~~~~~~~~~s~~rkI~el~-~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~ 148 (162)
+|+|+|++|++||||||.|+... ....++|-... .++.....+. .......+.+... ....--..+++.++++
T Consensus 172 ~gkW~V~~fv~eHNH~L~p~~~~----~~~~r~~~~~~~~~~~~~~~v~-~~~~d~~~~~~~~-r~~~~~~gD~~~ll~y 245 (846)
T PLN03097 172 DGKWVIHSFVKEHNHELLPAQAV----SEQTRKMYAAMARQFAEYKNVV-GLKNDSKSSFDKG-RNLGLEAGDTKILLDF 245 (846)
T ss_pred CCeEEEEEEecCCCCCCCCcccc----chhhhhhHHHHHhhhhcccccc-ccchhhcchhhHH-HhhhcccchHHHHHHH
Confidence 89999999999999999986531 11123332211 1111100000 0000111112111 0111124689999999
Q ss_pred HHHHHhhhhhccc
Q 031272 149 IRKVESEMLKSFL 161 (162)
Q Consensus 149 ~k~~e~~~~~~~~ 161 (162)
|+++..+++.||.
T Consensus 246 f~~~q~~nP~Ffy 258 (846)
T PLN03097 246 FTQMQNMNSNFFY 258 (846)
T ss_pred HHHHHhhCCCceE
Confidence 9999999999973
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=98.11 E-value=2.1e-05 Score=57.54 Aligned_cols=77 Identities=22% Similarity=0.348 Sum_probs=53.5
Q ss_pred cccccCeEEEEeceeecCCCCceEEEEEEecCCCCCCCCCCC--------------------CCCCCCCCCccccCCceE
Q 031272 3 YARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGT--------------------NGPEKKPRPSAREGCKAT 62 (162)
Q Consensus 3 YA~~~GF~iR~~~~~rs~~~g~i~~~~~vCsreG~~~~~~~~--------------------~~~~~~~r~~tR~gC~A~ 62 (162)
.++..||+|.+.+|..+ .| .|-|--.|........ .....+.-.+..++||-+
T Consensus 14 ~~~~~Gi~iVIerSd~~----ki---~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~t~srk~~CPFr 86 (111)
T PF08731_consen 14 IFYPQGIGIVIERSDKK----KI---VFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKKRTKSRKNTCPFR 86 (111)
T ss_pred HhhhcCceEEEEecCCc----eE---EEEEecCCCcccccccccccccccccccccccccccccccCCcccccccCCCeE
Confidence 35678999999976432 23 5778666655322210 111122235678999999
Q ss_pred EEEEEe-eCCcEEEEEEeecCCcCc
Q 031272 63 ILVKME-KSGKWVVTRFIKDHNHPL 86 (162)
Q Consensus 63 i~v~~~-~~gkW~V~~f~~eHNH~L 86 (162)
|+.... ...+|-|.-+..+|||||
T Consensus 87 iRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 87 IRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred EEEEEEecCCeEEEEEecCCcCCCC
Confidence 999876 578999999999999998
No 4
>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=91.32 E-value=0.33 Score=31.64 Aligned_cols=28 Identities=32% Similarity=0.617 Sum_probs=22.3
Q ss_pred CCceEEEEEEe-eCCcEEEEEEeecCCcC
Q 031272 58 GCKATILVKME-KSGKWVVTRFIKDHNHP 85 (162)
Q Consensus 58 gC~A~i~v~~~-~~gkW~V~~f~~eHNH~ 85 (162)
||+|.=.|.+. +++.-+++...-+||||
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 99999999886 47888899999999997
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=90.32 E-value=0.2 Score=31.44 Aligned_cols=25 Identities=36% Similarity=0.682 Sum_probs=10.7
Q ss_pred cCCceEEEEEEeeCCcEEEEEEeecCCc
Q 031272 57 EGCKATILVKMEKSGKWVVTRFIKDHNH 84 (162)
Q Consensus 57 ~gC~A~i~v~~~~~gkW~V~~f~~eHNH 84 (162)
.+|+|.+.+. . +.-.|.....+|||
T Consensus 38 ~~C~a~~~~~-~--~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD-A--GDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE-----TTEEEE-S---SS
T ss_pred CCCeEEEEEE-C--CCCEEEECCCccCC
Confidence 6899999998 2 33445555589999
No 6
>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=80.26 E-value=4.3 Score=26.21 Aligned_cols=45 Identities=22% Similarity=0.468 Sum_probs=33.6
Q ss_pred ccccccCeEEEEeceeecCCCCceEEEEEEecCCCCCCCCCCCCCCCCCCCCccccCCceEEEEEEee-CCcEEE
Q 031272 2 GYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKMEK-SGKWVV 75 (162)
Q Consensus 2 ~YA~~~GF~iR~~~~~rs~~~g~i~~~~~vCsreG~~~~~~~~~~~~~~~r~~tR~gC~A~i~v~~~~-~gkW~V 75 (162)
.||-..||.+++..+.+ .+....|. -.|||-+|.....+ ++.|.|
T Consensus 22 ~yai~~~~~~~v~ksd~-------~r~~~~C~----------------------~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 22 EYAIKNGFEFKVKKSDK-------KRYRAKCK----------------------DKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred HHHHhcCcEEEEeccCC-------EEEEEEEc----------------------CCCCCEEEEEEEcCCCCEEEC
Confidence 58899999999886532 25678884 23599999999874 577865
No 7
>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=76.11 E-value=3.6 Score=26.82 Aligned_cols=29 Identities=24% Similarity=0.414 Sum_probs=24.0
Q ss_pred ccCCceEEEEEEe-eCCcEEEEEEeecCCc
Q 031272 56 REGCKATILVKME-KSGKWVVTRFIKDHNH 84 (162)
Q Consensus 56 R~gC~A~i~v~~~-~~gkW~V~~f~~eHNH 84 (162)
..||+|.=.|... +|+.-+++-..-+|||
T Consensus 30 ~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 30 SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 3689998888776 4678888889999998
No 8
>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=74.02 E-value=14 Score=23.77 Aligned_cols=30 Identities=23% Similarity=0.521 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhchhhhhhhHHHHHHHHHHH
Q 031272 123 KLFNFMNNVEEQTEELSSKIQVIVDNIRKV 152 (162)
Q Consensus 123 ~L~~~l~~meeh~~~ls~kvq~iv~~~k~~ 152 (162)
.+-+.++.++..++.++..|+.+=+++|+|
T Consensus 11 ~~~~~i~tvk~en~~i~~~ve~i~envk~l 40 (55)
T PF05377_consen 11 RIESSINTVKKENEEISESVEKIEENVKDL 40 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455668888999999999999999998876
No 9
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=67.73 E-value=11 Score=27.27 Aligned_cols=37 Identities=16% Similarity=0.362 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhhc
Q 031272 123 KLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKS 159 (162)
Q Consensus 123 ~L~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~~ 159 (162)
.|..-|..|+++...|..+|+.+...+.+|..|+..+
T Consensus 5 ~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L 41 (107)
T PF06156_consen 5 ELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARL 41 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555566666666666666666666666666665544
No 10
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=61.52 E-value=51 Score=24.33 Aligned_cols=51 Identities=22% Similarity=0.357 Sum_probs=40.6
Q ss_pred cchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHH
Q 031272 101 KKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRK 151 (162)
Q Consensus 101 rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~ 151 (162)
+....+..||+...+-.+.|++.+..=|..-.+-...|..+-+++.++|-+
T Consensus 25 ~~q~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y~~l~~Hla~ 75 (128)
T PF06295_consen 25 QKQAKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDYQKLYQHLAK 75 (128)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556788889998888888999999888877777777777777777777654
No 11
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=53.98 E-value=27 Score=25.51 Aligned_cols=30 Identities=10% Similarity=0.225 Sum_probs=12.8
Q ss_pred HHHHHHhchhhhhhhHHHHHHHHHHHHhhh
Q 031272 127 FMNNVEEQTEELSSKIQVIVDNIRKVESEM 156 (162)
Q Consensus 127 ~l~~meeh~~~ls~kvq~iv~~~k~~e~~~ 156 (162)
-|..|+++...+...+..+...|.+|..|+
T Consensus 9 ~l~~le~~l~~l~~el~~LK~~~~el~EEN 38 (110)
T PRK13169 9 ALDDLEQNLGVLLKELGALKKQLAELLEEN 38 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444444444333
No 12
>PRK11677 hypothetical protein; Provisional
Probab=51.64 E-value=92 Score=23.49 Aligned_cols=51 Identities=16% Similarity=0.322 Sum_probs=38.6
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHH
Q 031272 100 DKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIR 150 (162)
Q Consensus 100 ~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k 150 (162)
.++..++..||+......+-|++.+..=|..-.+=...|..+-+++.+||-
T Consensus 28 ~~~q~~le~eLe~~k~ele~YkqeV~~HFa~TA~Ll~~L~~~Y~~Ly~HlA 78 (134)
T PRK11677 28 LRQQQALQYELEKNKAELEEYRQELVSHFARSAELLDTMAKDYRQLYQHMA 78 (134)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467788999999999988889999977776666666666666666666663
No 13
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=51.32 E-value=17 Score=29.39 Aligned_cols=19 Identities=32% Similarity=0.788 Sum_probs=15.9
Q ss_pred CCCCCCccccCCceEEEEE
Q 031272 48 EKKPRPSAREGCKATILVK 66 (162)
Q Consensus 48 ~~~~r~~tR~gC~A~i~v~ 66 (162)
..+..++.+.+|||.|.|+
T Consensus 69 ~~~~~~skK~~CPA~I~Ik 87 (225)
T PF15299_consen 69 RRRSKPSKKRDCPARIYIK 87 (225)
T ss_pred ccccccccCCCCCeEEEEE
Confidence 3445688999999999998
No 14
>PF02185 HR1: Hr1 repeat; InterPro: IPR000861 The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ] known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography []. It forms an antiparallel coiled-coil fold termed an ACC finger. This entry includes domains found within rho-associated protein kinases.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1CXZ_B 3O0Z_C 2RMK_B 1URF_A.
Probab=49.00 E-value=72 Score=20.72 Aligned_cols=57 Identities=19% Similarity=0.359 Sum_probs=43.1
Q ss_pred chhHHHHHHHHHHHHhHHHHHHHHH-------HHHHHHhchhhhhhhHHHHHHHHHHHHhhhhh
Q 031272 102 KIEELTLELERQEQLCAAYREKLFN-------FMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 158 (162)
Q Consensus 102 kI~el~~el~~~~q~~~~y~~~L~~-------~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~ 158 (162)
+|.++..+|+.+.+.-++....+-. +...++.....-+.+|+.+-..|.++....+.
T Consensus 2 ~i~~L~~~i~~E~ki~~Gae~m~~~~~t~~~~~~~~~~~~l~~s~~kI~~L~~~L~~l~~~~~~ 65 (70)
T PF02185_consen 2 RIEELQKKIDKELKIKEGAENMLQAYSTDKKKVLSEAESQLRESNQKIELLREQLEKLQQRSQN 65 (70)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC
Confidence 4788999999999988887655442 35667777888888999999988888776543
No 15
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=46.88 E-value=97 Score=21.57 Aligned_cols=42 Identities=14% Similarity=0.388 Sum_probs=35.2
Q ss_pred hHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhh
Q 031272 117 CAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 158 (162)
Q Consensus 117 ~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~ 158 (162)
-+...++|.+.|..||+-+..|..+++.++++=|+.-.+-++
T Consensus 31 ins~LD~Lns~LD~LE~rnD~l~~~L~~LLesnrq~R~e~~~ 72 (83)
T PF03670_consen 31 INSMLDQLNSCLDHLEQRNDHLHAQLQELLESNRQIRLEFQE 72 (83)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 344567899999999999999999999999999987665543
No 16
>PRK10884 SH3 domain-containing protein; Provisional
Probab=44.65 E-value=66 Score=25.90 Aligned_cols=34 Identities=12% Similarity=0.266 Sum_probs=25.9
Q ss_pred HHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhh
Q 031272 125 FNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 158 (162)
Q Consensus 125 ~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~ 158 (162)
....+.+++.+..|...++.+-..+..+|.+...
T Consensus 131 ~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~ 164 (206)
T PRK10884 131 DSVINGLKEENQKLKNQLIVAQKKVDAANLQLDD 164 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455668888888888888888888887777543
No 17
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=41.27 E-value=76 Score=25.13 Aligned_cols=73 Identities=15% Similarity=0.270 Sum_probs=41.3
Q ss_pred cEEEEEEeecCCcCcccCCCcCcccCccccchhHHHH----HHHHHHHHhHHHHHHHH-----------HHHHHHHhchh
Q 031272 72 KWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELTL----ELERQEQLCAAYREKLF-----------NFMNNVEEQTE 136 (162)
Q Consensus 72 kW~V~~f~~eHNH~L~~~~~~~~~~~s~~rkI~el~~----el~~~~q~~~~y~~~L~-----------~~l~~meeh~~ 136 (162)
-|-......-+.+.+...+- +..+-+.+|-. |++..++.|+.|+++|. .|+++|-+--.
T Consensus 71 ~q~l~q~~~~~g~~~~~~~~------~~~~sv~~L~~~T~~Elq~mr~~ln~FR~qm~dlE~~l~~QQalvy~hMSeeER 144 (179)
T PF14723_consen 71 LQNLSQYPVMRGSDLNADPY------STQRSVRELYSCTVQELQQMRRSLNSFREQMMDLELHLMRQQALVYRHMSEEER 144 (179)
T ss_pred HHHhcccccccccccccccc------ccchhHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCHHHH
Confidence 45444444445555543221 11235666555 88889999999999994 56677743333
Q ss_pred hhhhhHHHHHHHHH
Q 031272 137 ELSSKIQVIVDNIR 150 (162)
Q Consensus 137 ~ls~kvq~iv~~~k 150 (162)
.--..+|.+-..||
T Consensus 145 ~EaeQLQsLR~avR 158 (179)
T PF14723_consen 145 EEAEQLQSLRSAVR 158 (179)
T ss_pred HHHHHHHHHHHHHH
Confidence 33344455544444
No 18
>PF05778 Apo-CIII: Apolipoprotein CIII (Apo-CIII); InterPro: IPR008403 This family consists of several mammalian apolipoprotein CIII (Apo-CIII) sequences. Apolipoprotein C-III is a 79-residue glycoprotein. It is synthesised in the intestine and liver as part of the very low density lipoprotein (VLDL) and the high density lipoprotein (HDL) particles. Owing to its positive correlation with plasma triglyceride (Tg) levels, Apo-CIII is suggested to play a role in Tg metabolism and is therefore of interest regarding atherosclerosis. However, unlike other apolipoproteins such as Apo-AI, Apo E or CII for which many naturally occurring mutations are known, the structure-function relationships of apo C-III remains a subject of debate. One possibility is that apo C-III inhibits lipoprotein lipase (LPL) activity, as shown by in vitro experiments. Another suggestion, is that elevated levels of Apo-CIII displace other apolipoproteins at the lipoprotein surface, modifying their clearance from plasma [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region; PDB: 2JQ3_A.
Probab=40.84 E-value=20 Score=24.04 Aligned_cols=29 Identities=3% Similarity=0.229 Sum_probs=24.3
Q ss_pred HHHHHHHhchhhhhhhHHHHHHHHHHHHh
Q 031272 126 NFMNNVEEQTEELSSKIQVIVDNIRKVES 154 (162)
Q Consensus 126 ~~l~~meeh~~~ls~kvq~iv~~~k~~e~ 154 (162)
++|+.|+++.++-++..|+++.+|+|.+-
T Consensus 6 sll~~mqdYmqqAtktAqdaLtsVqES~v 34 (70)
T PF05778_consen 6 SLLGAMQDYMQQATKTAQDALTSVQESQV 34 (70)
T ss_dssp -THHHHHHHHHHHGGGHHHHHHGGGGGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788888999999999999999987653
No 19
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=40.54 E-value=91 Score=19.75 Aligned_cols=39 Identities=26% Similarity=0.364 Sum_probs=27.1
Q ss_pred HHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhhc
Q 031272 114 EQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKS 159 (162)
Q Consensus 114 ~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~~ 159 (162)
++-+++|-..| .+..++|+.-++.++..++++|++-..+
T Consensus 12 DqFMeaYc~~L-------~kykeeL~~p~~EA~~f~~~ie~qL~~L 50 (52)
T PF03791_consen 12 DQFMEAYCDML-------VKYKEELQRPFQEAMEFCREIEQQLSSL 50 (52)
T ss_pred HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566665444 4456667777779999999999886654
No 20
>PRK10920 putative uroporphyrinogen III C-methyltransferase; Provisional
Probab=38.18 E-value=81 Score=27.95 Aligned_cols=84 Identities=12% Similarity=0.190 Sum_probs=63.6
Q ss_pred EEEEEEeecCCcCcccCCCcCcccCccccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHH
Q 031272 73 WVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKV 152 (162)
Q Consensus 73 W~V~~f~~eHNH~L~~~~~~~~~~~s~~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~ 152 (162)
+++++-..+---||.+|.. ..++++ --+++=+++++...++..++|+..|...-.-+..|-..=+..++.+++.|.+|
T Consensus 257 ~I~Irrrd~~~~pLLsP~Q-~~yLRE-NLrLrLl~AqlAll~~q~~~Y~~sL~~A~~wl~~YFD~~~~~t~~~l~~L~~L 334 (390)
T PRK10920 257 FITIRRRDDTAEPLLAPNQ-DVYLRE-NIRSRLLVAAQAVPRHQEETYKQSLENVSTWVRAYFDTDDATTKAFLDEVDQL 334 (390)
T ss_pred eEEEEeCCCCccCCcChhH-HHHHHH-HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 3333333344556665444 355565 36666788899999999999999999999999999998899999999999999
Q ss_pred Hhhhhh
Q 031272 153 ESEMLK 158 (162)
Q Consensus 153 e~~~~~ 158 (162)
......
T Consensus 335 ~~~~I~ 340 (390)
T PRK10920 335 SQQNIS 340 (390)
T ss_pred HhCCCC
Confidence 877654
No 21
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=38.09 E-value=43 Score=20.73 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=16.8
Q ss_pred HhchhhhhhhHHHHHHHHHHHHhhhhhc
Q 031272 132 EEQTEELSSKIQVIVDNIRKVESEMLKS 159 (162)
Q Consensus 132 eeh~~~ls~kvq~iv~~~k~~e~~~~~~ 159 (162)
++|...+-.||++|=.-+.+||.+.+.+
T Consensus 11 qe~~d~IEqkiedid~qIaeLe~KR~~L 38 (46)
T PF08946_consen 11 QEHYDNIEQKIEDIDEQIAELEAKRQRL 38 (46)
T ss_dssp ----THHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHhHHHHHHHHHHHHHHHHHH
Confidence 5566666677777777777777766554
No 22
>PRK00846 hypothetical protein; Provisional
Probab=37.86 E-value=1.3e+02 Score=20.52 Aligned_cols=37 Identities=14% Similarity=0.301 Sum_probs=25.2
Q ss_pred HHHHHHHHHHH----HHHhchhhhhhhHHHHHHHHHHHHhh
Q 031272 119 AYREKLFNFMN----NVEEQTEELSSKIQVIVDNIRKVESE 155 (162)
Q Consensus 119 ~y~~~L~~~l~----~meeh~~~ls~kvq~iv~~~k~~e~~ 155 (162)
+|++.+.--|+ .-......|...++.+++.|++++..
T Consensus 23 AfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~~s 63 (77)
T PRK00846 23 SFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVRST 63 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34444444443 34556777888899999999999854
No 23
>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=36.50 E-value=23 Score=32.18 Aligned_cols=21 Identities=43% Similarity=0.642 Sum_probs=17.9
Q ss_pred CCcEEEEEEeecCCcCcccCC
Q 031272 70 SGKWVVTRFIKDHNHPLVVTA 90 (162)
Q Consensus 70 ~gkW~V~~f~~eHNH~L~~~~ 90 (162)
.|-|+|++++.-|||||-..-
T Consensus 164 ~g~f~v~k~~~~h~h~l~~nl 184 (496)
T PF04684_consen 164 KGPFVVTKIEPYHNHPLESNL 184 (496)
T ss_pred cCceEEEeeccccCCcccccc
Confidence 478999999999999997543
No 24
>PF05739 SNARE: SNARE domain; InterPro: IPR000727 The process of vesicular fusion with target membranes depends on a set of SNAREs (SNAP-Receptors), which are associated with the fusing membranes [, ]. Target SNAREs (t-SNAREs) are localised on the target membrane and belong to two different families, the syntaxin-like family and the SNAP-25 like family. One member of each family, together with a v-SNARE localised on the vesicular membrane, are required for fusion. The Syntaxins are type-I transmembrane proteins that contain several regions with coiled-coil propensity in their cytosolic part, the SNARE motif. SNAP-25 (IPR000928 from INTERPRO) is a protein consisting of two coiled-coil regions, which is associated with the membrane by lipid anchors. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in alpha-helical secondary structure []. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Recently, it was shown that the two coiled-coil regions of SNAP-25 and one of the coiled-coil regions of the syntaxins are related []. This domain is found in both Syntaxin and SNAP-25 families as well as in other proteins.; GO: 0005515 protein binding; PDB: 1URQ_B 3RL0_R 1HVV_B 1SFC_B 1N7S_B 3IPD_B 3C98_B 3HD7_F 3RK2_B 1KIL_B ....
Probab=34.63 E-value=1.1e+02 Score=18.84 Aligned_cols=53 Identities=11% Similarity=0.312 Sum_probs=34.5
Q ss_pred cchhHHHHHHHHHHHHhHHHHHHH---HHHHHHHHhchhhhhhhHHHHHHHHHHHH
Q 031272 101 KKIEELTLELERQEQLCAAYREKL---FNFMNNVEEQTEELSSKIQVIVDNIRKVE 153 (162)
Q Consensus 101 rkI~el~~el~~~~q~~~~y~~~L---~~~l~~meeh~~~ls~kvq~iv~~~k~~e 153 (162)
..|.++...+...++....-...+ ..++.+|+.+.......|+.....|+++-
T Consensus 4 ~~l~~l~~~i~~l~~~~~~i~~ev~~Q~~~ld~i~~~vd~~~~~l~~~~~~l~ka~ 59 (63)
T PF05739_consen 4 EELDELEQSIQELKQMFQDIGEEVEEQNEMLDRIEDNVDRANENLKKGNKKLKKAL 59 (63)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666666655555433332222 55678888888888888888888887654
No 25
>PRK14154 heat shock protein GrpE; Provisional
Probab=33.61 E-value=2e+02 Score=23.30 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=19.6
Q ss_pred cchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhh
Q 031272 101 KKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEEL 138 (162)
Q Consensus 101 rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~l 138 (162)
-.|.++..+|....+..+.+++.++-...++++.....
T Consensus 52 ~~~~~l~~el~~le~e~~elkd~~lRl~ADfeNyRKR~ 89 (208)
T PRK14154 52 PSREKLEGQLTRMERKVDEYKTQYLRAQAEMDNLRKRI 89 (208)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445555555555555555555555555555544333
No 26
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=32.63 E-value=1.5e+02 Score=22.45 Aligned_cols=55 Identities=25% Similarity=0.411 Sum_probs=36.5
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHHHHHHH-----HHHhchhhhhhhHHHHHHHHHHHHh
Q 031272 100 DKKIEELTLELERQEQLCAAYREKLFNFMN-----NVEEQTEELSSKIQVIVDNIRKVES 154 (162)
Q Consensus 100 ~rkI~el~~el~~~~q~~~~y~~~L~~~l~-----~meeh~~~ls~kvq~iv~~~k~~e~ 154 (162)
+..|.+|+.++....+-+......|..+.+ +|......|...++.+-+.|..|..
T Consensus 78 d~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 78 DAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 556889999888888877777666665553 4455666666666655555555554
No 27
>PHA02047 phage lambda Rz1-like protein
Probab=31.40 E-value=1.8e+02 Score=20.90 Aligned_cols=29 Identities=17% Similarity=0.129 Sum_probs=23.8
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHHHHHH
Q 031272 100 DKKIEELTLELERQEQLCAAYREKLFNFM 128 (162)
Q Consensus 100 ~rkI~el~~el~~~~q~~~~y~~~L~~~l 128 (162)
|+.+..+.++|+....+-..|+++...+=
T Consensus 33 h~~a~~la~qLE~a~~r~~~~Q~~V~~l~ 61 (101)
T PHA02047 33 HEEAKRQTARLEALEVRYATLQRHVQAVE 61 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 68888899999999999898988875443
No 28
>PF08656 DASH_Dad3: DASH complex subunit Dad3; InterPro: IPR013965 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=31.24 E-value=1.8e+02 Score=19.98 Aligned_cols=14 Identities=21% Similarity=0.646 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHhhh
Q 031272 143 QVIVDNIRKVESEM 156 (162)
Q Consensus 143 q~iv~~~k~~e~~~ 156 (162)
+.+++.||+||-+.
T Consensus 37 ~~lL~~LR~LE~K~ 50 (78)
T PF08656_consen 37 EELLDGLRELERKI 50 (78)
T ss_pred HHHHHHHHHHHHHH
Confidence 38999999999775
No 29
>PF04642 DUF601: Protein of unknown function, DUF601; InterPro: IPR006736 This family consists of several uncharacterised plant proteins which share a conserved region.
Probab=30.41 E-value=94 Score=26.26 Aligned_cols=36 Identities=14% Similarity=0.264 Sum_probs=29.8
Q ss_pred HHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhhcc
Q 031272 125 FNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSF 160 (162)
Q Consensus 125 ~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~~~ 160 (162)
+.-|+..|+-+.....+-..|++-|+++|++.+++-
T Consensus 195 l~sfK~sEeeNar~V~kAnsVldRmk~aEaqvneLE 230 (311)
T PF04642_consen 195 LESFKRSEEENARAVEKANSVLDRMKEAEAQVNELE 230 (311)
T ss_pred HHHHhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhee
Confidence 344567788888888999999999999999988764
No 30
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=29.66 E-value=2e+02 Score=20.11 Aligned_cols=52 Identities=23% Similarity=0.329 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhh
Q 031272 106 LTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 158 (162)
Q Consensus 106 l~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~ 158 (162)
+...+...++..+... ..+.-+..|++++..|-.-|+.+=.+.++||++-..
T Consensus 47 l~~~~~~l~~k~~~l~-~~l~~Id~Ie~~V~~LE~~v~~LD~ysk~LE~k~k~ 98 (99)
T PF10046_consen 47 LEKNLEDLNQKYEELQ-PYLQQIDQIEEQVTELEQTVYELDEYSKELESKFKK 98 (99)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3333344444444442 334445778888888888888888889999987654
No 31
>PRK14162 heat shock protein GrpE; Provisional
Probab=28.62 E-value=2.8e+02 Score=22.16 Aligned_cols=47 Identities=9% Similarity=0.206 Sum_probs=30.2
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHH
Q 031272 100 DKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIV 146 (162)
Q Consensus 100 ~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv 146 (162)
+..+.++..++....+..+.+.+.++-...++++........++++.
T Consensus 38 ~~e~~~l~~~l~~l~~e~~elkd~~lR~~AEfeN~rkR~~kE~e~~~ 84 (194)
T PRK14162 38 QNPVEDLEKEIADLKAKNKDLEDKYLRSQAEIQNMQNRYAKERAQLI 84 (194)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666777777776666666777777777777665555555544433
No 32
>PRK14143 heat shock protein GrpE; Provisional
Probab=28.16 E-value=2.8e+02 Score=22.83 Aligned_cols=46 Identities=13% Similarity=0.205 Sum_probs=32.2
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHH
Q 031272 100 DKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVI 145 (162)
Q Consensus 100 ~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~i 145 (162)
...+.++..+|....+..+.++++++-...++++......+.++++
T Consensus 66 ~~~~~~l~~el~~l~~e~~elkd~~lR~~AdfeN~RKR~~kE~e~~ 111 (238)
T PRK14143 66 AARLAQLEQELESLKQELEELNSQYMRIAADFDNFRKRTSREQEDL 111 (238)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788888887777777777788777777777666655554443
No 33
>PRK14140 heat shock protein GrpE; Provisional
Probab=27.97 E-value=2.6e+02 Score=22.27 Aligned_cols=44 Identities=9% Similarity=0.192 Sum_probs=25.7
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHH
Q 031272 100 DKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQ 143 (162)
Q Consensus 100 ~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq 143 (162)
+-.|.++..++....+..+.+.+.++-...++++.....-..++
T Consensus 36 ~~~~~~l~~~i~~l~~ei~elkd~~lR~~Ae~eN~rkR~~rE~~ 79 (191)
T PRK14140 36 AELLDEEQAKIAELEAKLDELEERYLRLQADFENYKRRIQKENE 79 (191)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666666666666665566666666666666554444433333
No 34
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=27.56 E-value=1.3e+02 Score=19.79 Aligned_cols=35 Identities=17% Similarity=0.353 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhchhhhhhhHH-HHHHHHHHHHhh
Q 031272 121 REKLFNFMNNVEEQTEELSSKIQ-VIVDNIRKVESE 155 (162)
Q Consensus 121 ~~~L~~~l~~meeh~~~ls~kvq-~iv~~~k~~e~~ 155 (162)
.++|..+++++.+-...+..||. .+.+|+|.|+.|
T Consensus 29 GqkIa~l~kdw~~~~~~~r~KiR~~L~ey~k~L~~e 64 (64)
T PF05596_consen 29 GQKIAQLAKDWNEICQEVRKKIRAALAEYCKGLKNE 64 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence 45677777888887788888887 566788888754
No 35
>PF12495 Vip3A_N: Vegetative insecticide protein 3A N terminal ; InterPro: IPR022180 This family of proteins is found in bacteria. Proteins in this family are typically between 170 and 789 amino acids in length. The family is found in association with PF02018 from PFAM. Vip3A represents a novel class of proteins insecticidal to lepidopteran insect larvae.
Probab=27.49 E-value=2.8e+02 Score=21.05 Aligned_cols=40 Identities=18% Similarity=0.354 Sum_probs=26.6
Q ss_pred HHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHH
Q 031272 113 QEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKV 152 (162)
Q Consensus 113 ~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~ 152 (162)
.+--..+|.-.+.+.++++-.++-.||..|+-+-+.+.|+
T Consensus 99 in~~l~~ylpkitsmls~vmkqny~lslqie~ls~qlqei 138 (177)
T PF12495_consen 99 INSMLNTYLPKITSMLSDVMKQNYVLSLQIEFLSKQLQEI 138 (177)
T ss_pred HHHHHHHHhHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHH
Confidence 3334557888888889888777666666666555555444
No 36
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=27.45 E-value=2.4e+02 Score=21.03 Aligned_cols=23 Identities=4% Similarity=0.323 Sum_probs=10.6
Q ss_pred chhhhhhhHHHHHHHHHHHHhhh
Q 031272 134 QTEELSSKIQVIVDNIRKVESEM 156 (162)
Q Consensus 134 h~~~ls~kvq~iv~~~k~~e~~~ 156 (162)
-...+..+|+.+=.-|..||.+.
T Consensus 97 dv~~i~~dv~~v~~~V~~Le~ki 119 (126)
T PF07889_consen 97 DVSQIGDDVDSVQQMVEGLEGKI 119 (126)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444455555443
No 37
>PF02024 Leptin: Leptin; InterPro: IPR000065 Leptin, a metabolic monitor of food intake and energy need, is expressed by the ob obesity gene. The protein may function as part of a signalling pathway from adipose tissue that acts to regulate the size of the body fat depot [], the hormone effectively turning the brain's appetite message off when it senses that the body is satiated. Obese humans have high levels of the protein, suggesting a similarity to type II (adult onset) diabetes, in which sufferers over-produce insulin, but can't respond to it metabolically - they have become insulin resistant. Similarly, it is thought that obese individuals may be leptin resistant.; GO: 0005179 hormone activity, 0007165 signal transduction, 0005576 extracellular region; PDB: 1AX8_A.
Probab=27.06 E-value=91 Score=23.95 Aligned_cols=67 Identities=21% Similarity=0.344 Sum_probs=30.8
Q ss_pred eecCCcCcccCCC----cCcccCccccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHHH
Q 031272 79 IKDHNHPLVVTAN----GYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVE 153 (162)
Q Consensus 79 ~~eHNH~L~~~~~----~~~~~~s~~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~e 153 (162)
+.+|+|.+..++. .-.++|. +.-|. .|....+-.++|++-|.+ |-. .|..+++.|+++..+.|..+=
T Consensus 21 I~~~~~~~~vssk~~I~gldfiPg-~~pi~----sLs~mdqTL~~yQ~IL~s-Lps--~nv~QIsnDlenLr~lL~~la 91 (146)
T PF02024_consen 21 INDHSHQQSVSSKQRITGLDFIPG-LQPIL----SLSSMDQTLAIYQQILTS-LPS--GNVSQISNDLENLRDLLHLLA 91 (146)
T ss_dssp HHH-----------------S----SS--S----SHHHHHHHHHHHHHHHHT-S----HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhcchhccCCccccccCcccCCC-cchhc----cHHHHHHHHHHHHHHHHh-CCh--hhHHHHHHHHHHHHHHHHHHH
Confidence 4689999854443 1123343 23332 344566678888754433 322 477888899998888887553
No 38
>PF12883 DUF3828: Protein of unknown function (DUF3828); InterPro: IPR024289 This domain currently has no known function.; PDB: 3KZT_A.
Probab=26.26 E-value=93 Score=22.44 Aligned_cols=20 Identities=20% Similarity=0.577 Sum_probs=13.8
Q ss_pred eEEEEEEe-eCCcEEEEEEee
Q 031272 61 ATILVKME-KSGKWVVTRFIK 80 (162)
Q Consensus 61 A~i~v~~~-~~gkW~V~~f~~ 80 (162)
-.+.+.+. .+|+|.|.++..
T Consensus 98 ~~~~~~l~ke~g~WkI~~V~~ 118 (120)
T PF12883_consen 98 QTVIVCLVKENGRWKIDDVRD 118 (120)
T ss_dssp EEEEEEEEEETTEEEEEEES-
T ss_pred EEEEEEEEEECCEEEEEEeec
Confidence 34566654 589999998853
No 39
>PRK02793 phi X174 lysis protein; Provisional
Probab=25.49 E-value=2.1e+02 Score=18.99 Aligned_cols=37 Identities=14% Similarity=0.355 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHH----HhchhhhhhhHHHHHHHHHHHHhh
Q 031272 119 AYREKLFNFMNNV----EEQTEELSSKIQVIVDNIRKVESE 155 (162)
Q Consensus 119 ~y~~~L~~~l~~m----eeh~~~ls~kvq~iv~~~k~~e~~ 155 (162)
+|++.+..-|+++ +.....|...++.+++.+++++..
T Consensus 18 afQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~~~ 58 (72)
T PRK02793 18 AFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLKASQPS 58 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3555555555433 445688888999999999988754
No 40
>PRK09974 putative regulator PrlF; Provisional
Probab=25.04 E-value=2.5e+02 Score=20.52 Aligned_cols=27 Identities=15% Similarity=0.364 Sum_probs=19.0
Q ss_pred eEEEEEEeeCCcEEEEEEeecCCcCcc
Q 031272 61 ATILVKMEKSGKWVVTRFIKDHNHPLV 87 (162)
Q Consensus 61 A~i~v~~~~~gkW~V~~f~~eHNH~L~ 87 (162)
-.|.+.+.++|.-+|.....+|+-|..
T Consensus 36 dkI~f~i~~dG~V~i~~~~~~~~Dp~i 62 (111)
T PRK09974 36 DSIHYEILPGGQVFICRLGDEEEDPVL 62 (111)
T ss_pred CEEEEEEeCCCEEEEEECCCCCCCchH
Confidence 346666666788888888777777653
No 41
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=24.79 E-value=2.4e+02 Score=21.73 Aligned_cols=31 Identities=13% Similarity=0.246 Sum_probs=22.5
Q ss_pred HHHHhchhhhhhhHHHHHHHHHHHHhhhhhc
Q 031272 129 NNVEEQTEELSSKIQVIVDNIRKVESEMLKS 159 (162)
Q Consensus 129 ~~meeh~~~ls~kvq~iv~~~k~~e~~~~~~ 159 (162)
..+.+.......+++++++.|..++.+....
T Consensus 141 ~~~~~~~~~~~~~l~~~lekL~~fd~~~~~~ 171 (204)
T PF04740_consen 141 SSFIDSLEKAKKKLQETLEKLRAFDQQSSSI 171 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 3445555666778899999999998876644
No 42
>PRK14147 heat shock protein GrpE; Provisional
Probab=24.33 E-value=3.3e+02 Score=21.22 Aligned_cols=16 Identities=13% Similarity=0.175 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHhch
Q 031272 120 YREKLFNFMNNVEEQT 135 (162)
Q Consensus 120 y~~~L~~~l~~meeh~ 135 (162)
+++.++-...+++++.
T Consensus 37 lkd~~lR~~Ad~eN~r 52 (172)
T PRK14147 37 VKADALRERADLENQR 52 (172)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333333334443333
No 43
>PRK14139 heat shock protein GrpE; Provisional
Probab=23.95 E-value=3.6e+02 Score=21.35 Aligned_cols=44 Identities=14% Similarity=0.180 Sum_probs=22.9
Q ss_pred cchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHH
Q 031272 101 KKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQV 144 (162)
Q Consensus 101 rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~ 144 (162)
..+..+..+|....+..+-+++.++-...++++....+...+++
T Consensus 32 ~e~~~l~~~l~~le~e~~elkd~~lR~~AefeN~rKR~~kE~e~ 75 (185)
T PRK14139 32 DAAPALEAELAEAEAKAAELQDSFLRAKAETENVRRRAQEDVAK 75 (185)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555544455555555555655554444444443
No 44
>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=23.76 E-value=63 Score=21.12 Aligned_cols=12 Identities=58% Similarity=0.861 Sum_probs=10.2
Q ss_pred HHHHHHHHHHhh
Q 031272 144 VIVDNIRKVESE 155 (162)
Q Consensus 144 ~iv~~~k~~e~~ 155 (162)
.||+.||+||+-
T Consensus 20 vIVNALRKleSa 31 (61)
T PF08222_consen 20 VIVNALRKLESA 31 (61)
T ss_dssp HHHHHHHHHHHT
T ss_pred HHHHHHHHHHhc
Confidence 589999999974
No 45
>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=22.44 E-value=1.3e+02 Score=24.71 Aligned_cols=33 Identities=24% Similarity=0.278 Sum_probs=26.6
Q ss_pred CCCccccCCceEEEEEEeeCCcEEEEEEeecCCc
Q 031272 51 PRPSAREGCKATILVKMEKSGKWVVTRFIKDHNH 84 (162)
Q Consensus 51 ~r~~tR~gC~A~i~v~~~~~gkW~V~~f~~eHNH 84 (162)
|-..+|.-|-.+..-.+. +|.|.|.++-.+|.|
T Consensus 126 pLVp~Re~~fLRyc~~l~-dG~w~VvdvSld~~~ 158 (229)
T cd08875 126 PLVPTREFYFLRYCKQLE-DGLWAVVDVSIDGVQ 158 (229)
T ss_pred ccccCCeEEEEEEEEEeC-CCeEEEEEEeecccc
Confidence 566788888777775555 799999999999976
No 46
>PF05761 5_nucleotid: 5' nucleotidase family; InterPro: IPR008380 This family includes a 5'-nucleotidase, 3.1.3.5 from EC, specific for purines (IMP and GMP) []. These enzymes are members of the Haloacid Dehalogenase (HAD) superfamily. HAD members are recognised by three short motifs {hhhhDxDx(T/V)}, {hhhh(T/S)}, and either {hhhh(D/E)(D/E)x(3-4)(G/N)} or {hhhh(G/N)(D/E)x(3-4)(D/E)} (where "h" stands for a hydrophobic residue). Crystal structures of many HAD enzymes has verified PSI-PRED predictions of secondary structural elements which show each of the "hhhh" sequences of the motifs as part of beta sheets. This subfamily of enzymes is part of "Subfamily I" of the HAD superfamily by virtue of a "cap" domain in between motifs 1 and 2. This subfamily's cap domain has a different predicted secondary structure than all other known HAD enzymes and thus has been designated "subfamily IG", the domain appears to consist of a mixed alpha/beta fold.; PDB: 2BDE_A 2XCW_A 2XCX_A 2XCV_A 2XJB_A 2JCM_A 2XJE_A 2J2C_A 2XJF_A 2XJD_A ....
Probab=22.14 E-value=2.6e+02 Score=25.19 Aligned_cols=59 Identities=20% Similarity=0.287 Sum_probs=36.0
Q ss_pred cchhHHHHHHHHHHHHhHHH--HHHHHHHHHHHHhchh------hhhhhHHHHHHHHHHHHhhhhhc
Q 031272 101 KKIEELTLELERQEQLCAAY--REKLFNFMNNVEEQTE------ELSSKIQVIVDNIRKVESEMLKS 159 (162)
Q Consensus 101 rkI~el~~el~~~~q~~~~y--~~~L~~~l~~meeh~~------~ls~kvq~iv~~~k~~e~~~~~~ 159 (162)
--|.||..|+...++..... .+.|...+..++++.. .+...++.+.+..+++..+....
T Consensus 322 ~Ii~ELe~Ei~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 388 (448)
T PF05761_consen 322 AIIPELEQEIEIWNSKKYRFEELQELEELLEELQDHLDQLRSSSELRPDISELRKERRELRREMKEL 388 (448)
T ss_dssp EE-TTHHHHHHHHHHTHHHHHHHHHHHHHCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred EEehhhhhhhhhhhhcchhhhHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHhhh
Confidence 45889999999888755444 3345555566766633 44555566666666666655444
No 47
>PF04375 HemX: HemX; InterPro: IPR007470 The majority of proteins in this family are annotated as uroporphyrin-III C-methyltransferase (2.1.1.107 from EC) []; however, there is no direct evidence to support this annotation for these proteins, which come from mainly pathogenic Gram-negative organisms. There is some evidence to suggest that the proteins are membrane anchored as they have a predicted N-terminal signal peptide and transmembrane domain and may be involved in haem transport [].
Probab=20.75 E-value=1.6e+02 Score=25.56 Aligned_cols=72 Identities=10% Similarity=0.147 Sum_probs=56.5
Q ss_pred CcccCCCcCcccCccccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhh
Q 031272 85 PLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 158 (162)
Q Consensus 85 ~L~~~~~~~~~~~s~~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~ 158 (162)
||.+|.. ..++++ --++.=+++++.-.++-.++|+..|...-.-+.+|-..=+..++.+++.|++|......
T Consensus 263 ~LLsP~q-~~~lre-nLrL~L~~AqlAlL~~~~~~y~~sL~~A~~wl~~yFd~~~~~~~~~l~~L~~L~~~~i~ 334 (372)
T PF04375_consen 263 PLLSPEQ-QFFLRE-NLRLRLEQAQLALLRRDQELYQQSLQRAQQWLNRYFDTDSPAVQAFLAELQQLAQQPIT 334 (372)
T ss_pred CCCCHHH-HHHHHH-HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhCCcc
Confidence 4444333 344555 35666677788888899999999999999999999888899999999999999877544
No 48
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=20.16 E-value=1.7e+02 Score=23.33 Aligned_cols=30 Identities=30% Similarity=0.439 Sum_probs=21.3
Q ss_pred chhHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 031272 102 KIEELTLELERQEQLCAAYREKLFNFMNNV 131 (162)
Q Consensus 102 kI~el~~el~~~~q~~~~y~~~L~~~l~~m 131 (162)
-+.|++.++...++.|+.|++.|-+|=...
T Consensus 117 t~eemQe~i~~L~kev~~~~erl~~~k~g~ 146 (201)
T KOG4603|consen 117 TTEEMQEEIQELKKEVAGYRERLKNIKAGT 146 (201)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344566666777788899998887776544
No 49
>PRK06975 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed
Probab=20.16 E-value=2.1e+02 Score=27.01 Aligned_cols=73 Identities=16% Similarity=0.178 Sum_probs=59.1
Q ss_pred cCcccCCCcCcccCccccchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHhchhhhhhhHHHHHHHHHHHHhhhhh
Q 031272 84 HPLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 158 (162)
Q Consensus 84 H~L~~~~~~~~~~~s~~rkI~el~~el~~~~q~~~~y~~~L~~~l~~meeh~~~ls~kvq~iv~~~k~~e~~~~~ 158 (162)
-||.+|.+ ..++++ --+++=+++++...++..++|+..|...-.-+..|-..=+..++.+++.|++|......
T Consensus 565 ~~LLsp~Q-~~~lre-Nlrl~L~~A~lAll~~~~~~y~~~L~~a~~wl~~yFd~~~~~~~~~~~~L~~L~~~~i~ 637 (656)
T PRK06975 565 AMLLSPDQ-GYFLRE-NLKLRLLNARLSLLSRNDAAFKSDLHAAQAALARYFDTASKDTQTVQDLLKQVDAASLT 637 (656)
T ss_pred ccCCChhH-HHHHHH-HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCc
Confidence 45555444 355565 36677788899999999999999999999999999999999999999999999876543
No 50
>PRK00736 hypothetical protein; Provisional
Probab=20.16 E-value=2.7e+02 Score=18.25 Aligned_cols=36 Identities=14% Similarity=0.285 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHH----HhchhhhhhhHHHHHHHHHHHHhh
Q 031272 120 YREKLFNFMNNV----EEQTEELSSKIQVIVDNIRKVESE 155 (162)
Q Consensus 120 y~~~L~~~l~~m----eeh~~~ls~kvq~iv~~~k~~e~~ 155 (162)
|++.+.--|+++ ......|...++.+++-+++++..
T Consensus 16 fqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~~~~ 55 (68)
T PRK00736 16 EQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSLEEQ 55 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 444444444433 445688888999999999888753
Done!