Query 024535
Match_columns 266
No_of_seqs 178 out of 504
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 05:19:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024535.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024535hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03018 Dirigent: Dirigent-li 100.0 1.3E-46 2.9E-51 316.5 18.0 143 59-266 1-144 (144)
2 PF06351 Allene_ox_cyc: Allene 97.4 0.0027 5.8E-08 55.8 11.5 89 150-244 34-126 (176)
3 PLN02343 allene oxide cyclase 96.5 0.025 5.5E-07 51.5 10.0 89 150-244 85-177 (229)
4 PF11528 DUF3224: Protein of u 73.3 53 0.0012 27.9 10.1 74 169-244 39-120 (134)
5 PF07172 GRP: Glycine rich pro 60.4 6 0.00013 31.8 1.8 27 27-53 1-28 (95)
6 PF02981 FokI_N: Restriction e 25.5 34 0.00074 29.9 1.0 15 14-28 108-122 (145)
7 PF06344 Parecho_VpG: Parechov 22.8 54 0.0012 19.7 1.2 16 89-104 3-18 (20)
8 COG3040 Blc Bacterial lipocali 18.8 1.7E+02 0.0037 26.4 4.0 65 152-228 66-130 (174)
9 COG0806 RimM RimM protein, req 12.0 1.1E+02 0.0024 27.1 1.0 9 64-72 100-108 (174)
10 PF08239 SH3_3: Bacterial SH3 10.2 2.2E+02 0.0048 19.1 1.9 16 161-176 4-19 (55)
No 1
>PF03018 Dirigent: Dirigent-like protein; InterPro: IPR004265 This family contains a number of proteins which are induced during disease response in plants.
Probab=100.00 E-value=1.3e-46 Score=316.50 Aligned_cols=143 Identities=41% Similarity=0.716 Sum_probs=130.1
Q ss_pred CCCeEEEEEeeccCCCCCcceeeeccccccccCCcccccCCCCCCCCCCcccCCCCCCccccccCccccccCCCCCCCCC
Q 024535 59 EHPILEFYMHDILGGSNPTARPITGLLGNIYSGQVPFARPIGFLPPQDGVAIPNANGAIPIVNAGTTFAGEGNQQNLNGN 138 (266)
Q Consensus 59 ~~~~l~FymHDil~GsnpTa~~Vtg~~~~~~~gq~pfakp~g~~p~~~g~~~~~~n~~~p~~n~g~~~~~~~~~~~~~~n 138 (266)
|++||+|||||+++|+|||+.+|+. |.+
T Consensus 1 ~~t~l~fY~H~~~~g~n~t~~~v~~--------------~~~-------------------------------------- 28 (144)
T PF03018_consen 1 KETHLHFYMHDIVSGPNPTAVVVAE--------------PPG-------------------------------------- 28 (144)
T ss_pred CceEEEEEeeecCCCCCCCEEEecc--------------CCC--------------------------------------
Confidence 6789999999999999999999964 100
Q ss_pred cccccCCCCCCCCceeEEEEccccccCCCCCCcceeeeEEEEEEeCCCCceeeeEEEEEEecCccCC-eEEEeeeccCCC
Q 024535 139 TQTQLGPDGLGLGFGTITVIDDILTASPELRSQALGKAQGVYVASSADGSTQMMAFTAMIEEGEYGD-SLNFYGVYKIGS 217 (266)
Q Consensus 139 ~~~~~~p~~~~~~FGtv~ViDD~LTeGpe~~SklVGRAQG~yv~ss~dg~s~~ma~t~vF~~g~y~G-SLs~~G~~~~~~ 217 (266)
+ ...+||+++||||+||+||+++||+||||||+|+.+++++.+++++++++|++++||| ||+++|+++..+
T Consensus 29 ------~--~~~~FG~~~V~D~~lt~gp~~~S~~VGraqG~~~~~s~~~~~~~~~~~~vF~~g~~~GStl~v~G~~~~~~ 100 (144)
T PF03018_consen 29 ------P--SSSGFGTVVVFDDPLTEGPDPDSKLVGRAQGFYVSASLDGSSWFMSFTLVFEDGEYNGSTLSVMGRDPFFE 100 (144)
T ss_pred ------C--CCCCCcEEEEEeeceEcCCCCCCccceEEEEEEEeecccCccEEEEEEEEEEecccCCCeEEEeCCCcccC
Confidence 0 0137999999999999999999999999999999999999999999999999999998 699999999999
Q ss_pred cceeeEEEeccCcccceeeEEEEeeecCCCccccCCCceEEEEEEEEEC
Q 024535 218 TMSHLSVTGGTGKFKHACGLAEVRPLIPAGQHVTDGAESLLRITANLKY 266 (266)
Q Consensus 218 ~~rElaVVGGTG~Fr~ArGyA~~kt~~~~gq~~t~g~~~vle~~V~L~y 266 (266)
++||||||||||+||||||||+++++. +.++.+.|+||+|||+|
T Consensus 101 ~~~e~~VVGGTG~Fr~ArG~~~~~~~~-----~~~~~~~v~e~~v~~~h 144 (144)
T PF03018_consen 101 PVRELAVVGGTGEFRMARGYAKLRTVF-----DSSGGNAVLELNVHLFH 144 (144)
T ss_pred cccEEeEecCCCeEcceEEEEEEEEEe-----ecCCCCEEEEEEEEEEC
Confidence 999999999999999999999999982 35678999999999987
No 2
>PF06351 Allene_ox_cyc: Allene oxide cyclase; InterPro: IPR009410 This family consists of several plant specific allene oxide cyclase proteins (5.3.99.6 from EC). The allene oxide cyclase (AOC)-catalysed step in jasmonate (JA) biosynthesis is important in the wound response of tomato [].; GO: 0016853 isomerase activity, 0009507 chloroplast; PDB: 2GIN_A 2DIO_B 2BRJ_B 2Q4I_B 1Z8K_A 1ZVC_A.
Probab=97.39 E-value=0.0027 Score=55.82 Aligned_cols=89 Identities=20% Similarity=0.329 Sum_probs=67.8
Q ss_pred CCceeEEEEccccccCCCCCCcceeeeEEEEEEeCC----CCceeeeEEEEEEecCccCCeEEEeeeccCCCcceeeEEE
Q 024535 150 LGFGTITVIDDILTASPELRSQALGKAQGVYVASSA----DGSTQMMAFTAMIEEGEYGDSLNFYGVYKIGSTMSHLSVT 225 (266)
Q Consensus 150 ~~FGtv~ViDD~LTeGpe~~SklVGRAQG~yv~ss~----dg~s~~ma~t~vF~~g~y~GSLs~~G~~~~~~~~rElaVV 225 (266)
...|.++=+.|+|.+|.- -+.+|--+|+++.-.. .|-.+--.+++.|-+ -|.|+++|..-.. ...-++|.
T Consensus 34 nslGDlvpFsNklY~g~l--~~rlGitaG~Cvliq~~p~k~GdryEaiySfyfGd---yGhISvqGpy~t~-eDtyLAVT 107 (176)
T PF06351_consen 34 NSLGDLVPFSNKLYDGDL--QKRLGITAGICVLIQHVPEKKGDRYEAIYSFYFGD---YGHISVQGPYLTY-EDTYLAVT 107 (176)
T ss_dssp S-TT-EEEEEEEEEETTS--S-EEEEEEEEEEEEEEECCCTEEEEEEEEEEE-GG---GEEEEEEEEEETT-S-EEEEEE
T ss_pred hhcccccccccccccchh--hhhhcccceEEEEEEeccccCCceEEEEEEEEecc---cceEEEecccccc-cceeEEEe
Confidence 458999999999999865 5889999999998664 344455666777754 3789999998765 34579999
Q ss_pred eccCcccceeeEEEEeeec
Q 024535 226 GGTGKFKHACGLAEVRPLI 244 (266)
Q Consensus 226 GGTG~Fr~ArGyA~~kt~~ 244 (266)
||||-|+.|+|-++++.+.
T Consensus 108 GGtGiF~g~~GqVkL~qiv 126 (176)
T PF06351_consen 108 GGTGIFEGVYGQVKLHQIV 126 (176)
T ss_dssp EEEETTTT-EEEEEEEEEE
T ss_pred ccCceeecceEEEEEEEee
Confidence 9999999999999999874
No 3
>PLN02343 allene oxide cyclase
Probab=96.49 E-value=0.025 Score=51.52 Aligned_cols=89 Identities=19% Similarity=0.342 Sum_probs=72.8
Q ss_pred CCceeEEEEccccccCCCCCCcceeeeEEEEEEeCC----CCceeeeEEEEEEecCccCCeEEEeeeccCCCcceeeEEE
Q 024535 150 LGFGTITVIDDILTASPELRSQALGKAQGVYVASSA----DGSTQMMAFTAMIEEGEYGDSLNFYGVYKIGSTMSHLSVT 225 (266)
Q Consensus 150 ~~FGtv~ViDD~LTeGpe~~SklVGRAQG~yv~ss~----dg~s~~ma~t~vF~~g~y~GSLs~~G~~~~~~~~rElaVV 225 (266)
...|.++=|.+.|..|.- -|.+|--.|+++.... .+-.+--.+++.|-| -|-|++||..-..+. .-++|.
T Consensus 85 ~sLGDlVPFsNKlY~g~L--~kRlGiTaG~Cvliq~~pek~gDryEa~ySfyfGD---yGHisvqGpyltyeD-t~LaiT 158 (229)
T PLN02343 85 NALGDLVPFTNKLYTGDL--KKRLGITAGLCVLIQHVPEKKGDRYEAIYSFYFGD---YGHISVQGPYLTYED-TYLAIT 158 (229)
T ss_pred ccccceeccccccccchh--hhhhcccceeEEEEEeccccCCceeEEEEEEEecC---cceeEEecccccccc-ceEEee
Confidence 468999999999998853 4789999999998765 344567778888865 278999999876544 479999
Q ss_pred eccCcccceeeEEEEeeec
Q 024535 226 GGTGKFKHACGLAEVRPLI 244 (266)
Q Consensus 226 GGTG~Fr~ArGyA~~kt~~ 244 (266)
||+|-|+.|+|-++++.+.
T Consensus 159 GGsGiFega~GqvkL~qiv 177 (229)
T PLN02343 159 GGSGIFEGAYGQVKLHQIV 177 (229)
T ss_pred cCcceeecceeEEEEeeee
Confidence 9999999999999998865
No 4
>PF11528 DUF3224: Protein of unknown function (DUF3224); InterPro: IPR021607 This bacterial family of proteins has no known function. ; PDB: 2OOJ_B 2Q03_B.
Probab=73.30 E-value=53 Score=27.90 Aligned_cols=74 Identities=26% Similarity=0.436 Sum_probs=48.7
Q ss_pred CCcceeeeEEEEEEeCC-CCceeeeEEEEEEecCcc---CCe--EEEeeeccCCCcceeeEEE--eccCcccceeeEEEE
Q 024535 169 RSQALGKAQGVYVASSA-DGSTQMMAFTAMIEEGEY---GDS--LNFYGVYKIGSTMSHLSVT--GGTGKFKHACGLAEV 240 (266)
Q Consensus 169 ~SklVGRAQG~yv~ss~-dg~s~~ma~t~vF~~g~y---~GS--Ls~~G~~~~~~~~rElaVV--GGTG~Fr~ArGyA~~ 240 (266)
.-.+.|++++-|+..-. ++...+.++.-+ .|.. +|| |+-.|.........+|-|| -|||++...+|-..+
T Consensus 39 ~G~l~Gts~~~~L~~y~~~g~a~yva~E~~--~Gtl~Gr~GsFvl~h~G~~~~g~~~~~~~VVPgSGTGeL~Gl~Gsg~~ 116 (134)
T PF11528_consen 39 SGDLEGTSTGEYLMAYDPDGSAGYVAFERF--TGTLDGRSGSFVLQHSGTFDAGTASSSFTVVPGSGTGELAGLSGSGTI 116 (134)
T ss_dssp -TTEEEEEEEEEEEEEECTTEEEEEEEEEE--EEEETTEEEEEEEEEEEEEETTEEEEEEEE-TT--EETTTTEEEEEEE
T ss_pred EeEEEEEEEEEEEEEEcCCCcEEEEEEEEE--EEEECCceEEEEEEEEEEEcCCcceEEEEEeCCCCchhhcCCEEEEEE
Confidence 34578888888887765 455455544432 2233 467 6666776655566789999 999999999999998
Q ss_pred eeec
Q 024535 241 RPLI 244 (266)
Q Consensus 241 kt~~ 244 (266)
+...
T Consensus 117 ~~~~ 120 (134)
T PF11528_consen 117 TIDE 120 (134)
T ss_dssp EEET
T ss_pred EECC
Confidence 8753
No 5
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=60.35 E-value=6 Score=31.83 Aligned_cols=27 Identities=26% Similarity=0.203 Sum_probs=17.2
Q ss_pred ccchhHHHHHHHHHHHh-hhhhecccCC
Q 024535 27 FNSKRSSLFTMLILTSQ-MTIFVAAVDP 53 (266)
Q Consensus 27 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 53 (266)
|+|++.++|+||||+++ +++-+++.|.
T Consensus 1 MaSK~~llL~l~LA~lLlisSevaa~~~ 28 (95)
T PF07172_consen 1 MASKAFLLLGLLLAALLLISSEVAAREL 28 (95)
T ss_pred CchhHHHHHHHHHHHHHHHHhhhhhHHh
Confidence 56899888888876644 4434554443
No 6
>PF02981 FokI_N: Restriction endonuclease FokI, recognition domain; InterPro: IPR004234 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions (IPR004233 from INTERPRO), respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=25.54 E-value=34 Score=29.92 Aligned_cols=15 Identities=33% Similarity=0.516 Sum_probs=12.2
Q ss_pred hhhhhhhHhhhhhcc
Q 024535 14 SRLGYLRYAHYMMFN 28 (266)
Q Consensus 14 ~~~~~~~~~~~~~~~ 28 (266)
..-||||+||+|+|=
T Consensus 108 ~Ad~flrwAvslgfl 122 (145)
T PF02981_consen 108 TADGFLRWAVSLGFL 122 (145)
T ss_dssp HHHHHHHHHHHTTSE
T ss_pred CccceeeeeeeeCce
Confidence 345999999999874
No 7
>PF06344 Parecho_VpG: Parechovirus Genome-linked protein; InterPro: IPR009407 The viral polyprotein of parechoviruses contains: coat protein VP0 (P1AB); coat protein VP3 (P1C); coat protein VP1 (P1D); picornain 2A (3.4.22.29 from EC, core protein P2A); core protein P2B; core protein P2C; core protein P3A; genome-linked protein VPg (P3B); picornain 3C (3.4.22.28 from EC, MEROPS peptidase subfamily 3CF: parechovirus picornain 3C (P3C)) []. This entry consists of the genome-linked protein Vpg type P3B.; GO: 0019015 viral genome
Probab=22.84 E-value=54 Score=19.71 Aligned_cols=16 Identities=38% Similarity=0.820 Sum_probs=12.6
Q ss_pred ccCCcccccCCCCCCC
Q 024535 89 YSGQVPFARPIGFLPP 104 (266)
Q Consensus 89 ~~gq~pfakp~g~~p~ 104 (266)
|+--+|-+||-|.+|.
T Consensus 3 ynptlp~~kpkgtfpv 18 (20)
T PF06344_consen 3 YNPTLPVAKPKGTFPV 18 (20)
T ss_pred cCccccccccCCcccc
Confidence 5666888999888776
No 8
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=18.79 E-value=1.7e+02 Score=26.41 Aligned_cols=65 Identities=18% Similarity=0.171 Sum_probs=38.1
Q ss_pred ceeEEEEccccccCCCCCCcceeeeEEEEEEeCCCCceeeeEEEEEEecCccCCeEEEeeeccCCCcceeeEEEecc
Q 024535 152 FGTITVIDDILTASPELRSQALGKAQGVYVASSADGSTQMMAFTAMIEEGEYGDSLNFYGVYKIGSTMSHLSVTGGT 228 (266)
Q Consensus 152 FGtv~ViDD~LTeGpe~~SklVGRAQG~yv~ss~dg~s~~ma~t~vF~~g~y~GSLs~~G~~~~~~~~rElaVVGGT 228 (266)
=|+|.|+|.-.+...+.-|+.-|+|. +.+...... +.+.|-. .|.|.-.|+-.+ ++.-|+|||+-
T Consensus 66 ~~~I~V~n~c~~~~~~~~~~ieGkA~---i~~~~~~a~----LkVsF~~-pF~g~Y~Vl~~d----~eYs~aiVgsP 130 (174)
T COG3040 66 DGGISVINRCRTGDGGKWSQIEGKAK---IVDNATRAK----LKVSFFG-PFYGDYWVLALD----PEYSWAIVGSP 130 (174)
T ss_pred CCceEEEeccccCCCCCceeecceEE---EecCccccE----EEEEecC-CccccEEEEEEC----CCccEEEEeCC
Confidence 47899999999999886688888873 333322222 3333322 333443344333 24568888764
No 9
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=11.96 E-value=1.1e+02 Score=27.14 Aligned_cols=9 Identities=67% Similarity=1.519 Sum_probs=8.2
Q ss_pred EEEEeeccC
Q 024535 64 EFYMHDILG 72 (266)
Q Consensus 64 ~FymHDil~ 72 (266)
+|||||+++
T Consensus 100 EfY~~DLiG 108 (174)
T COG0806 100 EFYYHDLIG 108 (174)
T ss_pred cEEeEeecC
Confidence 599999997
No 10
>PF08239 SH3_3: Bacterial SH3 domain; InterPro: IPR013247 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.; PDB: 3PVQ_B 3NPF_B 3H41_A 2KQ8_A 2KRS_A 2KYB_A 2KT8_A.
Probab=10.16 E-value=2.2e+02 Score=19.13 Aligned_cols=16 Identities=19% Similarity=0.395 Sum_probs=12.2
Q ss_pred ccccCCCCCCcceeee
Q 024535 161 ILTASPELRSQALGKA 176 (266)
Q Consensus 161 ~LTeGpe~~SklVGRA 176 (266)
.|+.+|+.+|++|+.+
T Consensus 4 nvR~~p~~~s~~i~~l 19 (55)
T PF08239_consen 4 NVRSGPSTNSPVIGQL 19 (55)
T ss_dssp EEESSSSTTSTEEEEE
T ss_pred EEEeCCCCCChhhEEE
Confidence 3677888888888764
Done!