Query psy8890
Match_columns 150
No_of_seqs 162 out of 714
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 22:02:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8890.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8890hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03098 An_peroxidase: Animal 100.0 4.9E-31 1.1E-35 235.1 3.5 89 61-149 1-92 (530)
2 KOG2408|consensus 100.0 8E-29 1.7E-33 227.9 8.4 92 58-149 148-240 (719)
3 PLN02283 alpha-dioxygenase 99.8 9.5E-22 2.1E-26 179.2 6.9 79 57-145 81-162 (633)
4 PF13940 Ldr_toxin: Toxin Ldr, 51.2 12 0.00025 22.2 1.5 14 132-145 3-16 (35)
5 PTZ00304 NADH dehydrogenase [u 35.6 17 0.00036 33.0 0.9 16 72-87 444-459 (461)
6 PF02425 GBP_PSP: Paralytic/GB 28.4 21 0.00045 19.1 0.1 15 55-69 6-20 (23)
7 PF08219 TOM13: Outer membrane 18.7 65 0.0014 22.4 1.1 21 125-145 42-62 (77)
8 PF12073 DUF3553: Protein of u 17.3 69 0.0015 20.6 0.9 9 70-78 9-17 (52)
9 PF06971 Put_DNA-bind_N: Putat 17.0 87 0.0019 19.7 1.3 21 13-33 29-49 (50)
10 PF01190 Pollen_Ole_e_I: Polle 12.0 1.5E+02 0.0032 20.4 1.5 30 54-83 68-97 (97)
No 1
>PF03098 An_peroxidase: Animal haem peroxidase; InterPro: IPR002007 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, a number of animal haem peroxidases can be categorised as members of a superfamily: myeloperoxidase (MPO); eosinophil peroxidase (EPO); lactoperoxidase (LPO); thyroid peroxidase (TPO); prostaglandin H synthase (PGHS); and peroxidasin [, , ]. MPO plays a major role in the oxygen-dependent microbicidal system of neutrophils. EPO from eosinophilic granulocytes participates in immunological reactions, and potentiates tumor necrosis factor (TNF) production and hydrogen peroxide release by human monocyte-derived macrophages [, ]. In the main, MPO (and possibly EPO) utilises Cl-ions and H2O2 to form hypochlorous acid (HOCl), which can effectively kill bacteria or parasites. In secreted fluids, LPO catalyses the oxidation of thiocyanate ions (SCN-) by H2O2, producing the weak oxidising agent hypothiocyanite (OSCN-), which has bacteriostatic activity []. TPO uses I- ions and H2O2 to generate iodine, and plays a central role in the biosynthesis of thyroid hormones T(3) and T(4). To date, the 3D structures of MPO and PGHS have been reported. MPO is a homodimer: each monomer consists of a light (A or B) and a heavy (C or D) chain resulting from post-translational excision of 6 residues from the common precursor. Monomers are linked by a single inter-chain disulphide. Each monomer includes a bound calcium ion []. PGHS exists as a symmetric dimer, each monomer of which consists of 3 domains: an N-terminal epidermal growth factor (EGF) like module; a membrane-binding domain; and a large C-terminal catalytic domain containing the cyclooxygenase and the peroxidase active sites. The catalytic domain shows striking structural similarity to MPO. The cyclooxygenase active site, which catalyses the formation of prostaglandin G2 (PGG2) from arachidonic acid, resides at the apex of a long hydrophobic channel, extending from the membrane-binding domain to the centre of the molecule. The peroxidase active site, which catalyses the reduction of PGG2 to PGH2, is located on the other side of the molecule, at the haem binding site []. Both MPO and the catalytic domain of PGHS are mainly alpha-helical, 19 helices being identified as topologically and spatially equivalent; PGHS contains 5 additional N-terminal helices that have no equivalent in MPO. In both proteins, three Asn residues in each monomer are glycosylated.; GO: 0004601 peroxidase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 1FE2_A 1PGG_B 1PGF_A 3N8W_B 1IGZ_A 3KK6_B 3N8Z_A 1Q4G_A 1PTH_A 1EQH_A ....
Probab=99.96 E-value=4.9e-31 Score=235.10 Aligned_cols=89 Identities=44% Similarity=0.922 Sum_probs=70.0
Q ss_pred cccccccCcCCCCCCCCCCCCCcccccCCCCCCCCCCCcccCCCCCCCchhhhhhhhcCCCC---CCCCchHHHHHHHHH
Q psy8890 61 YRRYDGLCTNLKHPTWGAVNTPFQRLIGPLFSDGLTSPRISNKGGNLPLARVVSSTMHPDEN---KHEHAATVMLVAWGQ 137 (150)
Q Consensus 61 yRt~DGsCNNl~~P~wG~a~tpf~Rllp~~Y~DG~~~Pr~s~~g~~LP~~R~VS~~l~~~~~---~~~~~~t~~~~~wgQ 137 (150)
|||+||+|||+.||.||++++||.|++||.|+||+++||.+.+|.+||+||+||+.|+.... ..++.+|+|+|+|||
T Consensus 1 yRt~dG~cNN~~~p~~G~~~~~~~Rllp~~Y~dg~~~pr~~~~g~~lP~pR~is~~l~~~~~~~~~~~~~~t~l~~~~gQ 80 (530)
T PF03098_consen 1 YRTYDGSCNNLANPSWGAAGTPFRRLLPPAYADGVSEPRGSSNGSPLPNPREISNALFRRKDGFDPSHSGLTALFMQWGQ 80 (530)
T ss_dssp S--SSSTTSSSSSTTTT-SSEE-BESS-B--TTSSSBTTTSBTTBS---HHHHHHHHTB-SSGTTBEEEEEEHHHHHHHH
T ss_pred CCCCCCCccCCCcccccCCCCcccccCCccccccccccccccCCccCCCHHHHHHHHhhcccccCCCCCcchHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999997643 344678999999999
Q ss_pred HHHhhccCCCCC
Q psy8890 138 FMDHDFTLTATP 149 (150)
Q Consensus 138 fi~HDi~~t~~~ 149 (150)
||+|||++++..
T Consensus 81 fi~HDi~~~~~~ 92 (530)
T PF03098_consen 81 FIDHDITLTPDS 92 (530)
T ss_dssp HHHHHH--BEBT
T ss_pred HHhhhhcccccc
Confidence 999999998754
No 2
>KOG2408|consensus
Probab=99.95 E-value=8e-29 Score=227.92 Aligned_cols=92 Identities=41% Similarity=0.778 Sum_probs=87.6
Q ss_pred CCccccccccCcCCCCCCCCCCCCCcccccCCCCCCCCCCCcccCCCCCCCchhhhhhhhcCCC-CCCCCchHHHHHHHH
Q psy8890 58 PGKYRRYDGLCTNLKHPTWGAVNTPFQRLIGPLFSDGLTSPRISNKGGNLPLARVVSSTMHPDE-NKHEHAATVMLVAWG 136 (150)
Q Consensus 58 ~~~yRt~DGsCNNl~~P~wG~a~tpf~Rllp~~Y~DG~~~Pr~s~~g~~LP~~R~VS~~l~~~~-~~~~~~~t~~~~~wg 136 (150)
..+|||+||+|||+.+|.||+++++|.|++||.|+||++.||.+..+.+||+||+||+.|+.+. ..++.++|+|+||||
T Consensus 148 ~~~yRt~dG~CNN~~~P~~Gas~~~~~Rllpp~Yedg~~~p~~~~~~~~lP~~R~vS~~l~~~~~~~~~~~~~~~~mqwg 227 (719)
T KOG2408|consen 148 HSKYRTIDGTCNNLRNPTLGASNSPFRRLLPPKYEDGFSTPRGWSDGTPLPSARLVSNKLLSRSFSPPDSKFNHMAMQWG 227 (719)
T ss_pred ccCccccccccCCCCCCCcccccChhhccCCccccccccCccccccCCCCCchHHhhHhhhccccCCCCcchhHHHHHHH
Confidence 4799999999999999999999999999999999999999999887899999999999999887 778899999999999
Q ss_pred HHHHhhccCCCCC
Q psy8890 137 QFMDHDFTLTATP 149 (150)
Q Consensus 137 Qfi~HDi~~t~~~ 149 (150)
|||+|||++++.+
T Consensus 228 QFi~HDl~~~~~~ 240 (719)
T KOG2408|consen 228 QFIDHDLYFTPLS 240 (719)
T ss_pred HHhcccccccCCc
Confidence 9999999999864
No 3
>PLN02283 alpha-dioxygenase
Probab=99.85 E-value=9.5e-22 Score=179.23 Aligned_cols=79 Identities=27% Similarity=0.356 Sum_probs=67.3
Q ss_pred CCCccccccccCcCCCCCCCCCCCCCcccccCCC-CCCCCCCCcccCCCCCCCchhhhhhhhcCCCCCC--CCchHHHHH
Q psy8890 57 KPGKYRRYDGLCTNLKHPTWGAVNTPFQRLIGPL-FSDGLTSPRISNKGGNLPLARVVSSTMHPDENKH--EHAATVMLV 133 (150)
Q Consensus 57 ~~~~yRt~DGsCNNl~~P~wG~a~tpf~Rllp~~-Y~DG~~~Pr~s~~g~~LP~~R~VS~~l~~~~~~~--~~~~t~~~~ 133 (150)
+..+|||+||+|||+.||.||++||+|.|++||. |.||+ .+|+||.||+.++.+.... ....|+|++
T Consensus 81 ~~~~yRt~DGscNNl~~P~~G~agt~f~R~v~p~~~~~~~----------~~P~pr~vs~~ll~r~~f~~~~~~~n~~~~ 150 (633)
T PLN02283 81 AEYPYRTADGKCNDPFNEGAGSQGTFFGRNMPPVDQKDKL----------LDPHPSVVATKLLARKKFIDTGKQFNMIAA 150 (633)
T ss_pred ccccccCCCCCCcCCCCcccccCCCccccCCCccccCCCC----------CCCCHHHHHHHHHhhccccCCCCcchHHHH
Confidence 3469999999999999999999999999999996 55554 4699999999999765443 346899999
Q ss_pred HHHHHHHhhccC
Q psy8890 134 AWGQFMDHDFTL 145 (150)
Q Consensus 134 ~wgQfi~HDi~~ 145 (150)
+|||||+|||..
T Consensus 151 ~w~Qf~~HD~~~ 162 (633)
T PLN02283 151 SWIQFMIHDWID 162 (633)
T ss_pred HHHHHHHhhhhh
Confidence 999999999843
No 4
>PF13940 Ldr_toxin: Toxin Ldr, type I toxin-antitoxin system
Probab=51.21 E-value=12 Score=22.16 Aligned_cols=14 Identities=29% Similarity=0.337 Sum_probs=12.1
Q ss_pred HHHHHHHHHhhccC
Q psy8890 132 LVAWGQFMDHDFTL 145 (150)
Q Consensus 132 ~~~wgQfi~HDi~~ 145 (150)
+.|||-.++||+.-
T Consensus 3 Laqlg~~~WhDLAA 16 (35)
T PF13940_consen 3 LAQLGIAFWHDLAA 16 (35)
T ss_pred HHHHHHHHHHHhHh
Confidence 68999999999863
No 5
>PTZ00304 NADH dehydrogenase [ubiquinone] flavoprotein 1; Provisional
Probab=35.58 E-value=17 Score=32.97 Aligned_cols=16 Identities=31% Similarity=0.916 Sum_probs=14.4
Q ss_pred CCCCCCCCCCCccccc
Q psy8890 72 KHPTWGAVNTPFQRLI 87 (150)
Q Consensus 72 ~~P~wG~a~tpf~Rll 87 (150)
++|.||.+++|.+|+-
T Consensus 444 ~~~~~~~~~~~~~~~~ 459 (461)
T PTZ00304 444 ANPHWGKSGSPWRRWK 459 (461)
T ss_pred cCchhcccCCCCcccc
Confidence 6899999999999973
No 6
>PF02425 GBP_PSP: Paralytic/GBP/PSP peptide; InterPro: IPR003463 This family includes insect peptides that are short (23 amino acids) and contain 1 disulphide bridge. The family includes growth-blocking peptide (GBP) of Pseudaletia separata (Oriental armyworm) and the paralytic peptides from Manduca sexta (Tobacco hawkmoth), Heliothis virescens (Noctuid moth), and Spodoptera exigua (Beet armyworm) [] as well as plasmatocyte-spreading peptide (PSP1) []. These peptides function to halt metamorphosis from larvae to pupae.; PDB: 1V28_A 2DJC_A 2EQQ_A 2EQH_A 2EQT_A 1BQF_A 2DJ9_A 1HRL_A 1IRR_A 1B5N_A ....
Probab=28.40 E-value=21 Score=19.12 Aligned_cols=15 Identities=40% Similarity=0.837 Sum_probs=11.5
Q ss_pred CCCCCccccccccCc
Q psy8890 55 ECKPGKYRRYDGLCT 69 (150)
Q Consensus 55 ~C~~~~yRt~DGsCN 69 (150)
-|.+.--|+.||.|-
T Consensus 6 gc~~gy~rtadgrck 20 (23)
T PF02425_consen 6 GCATGYMRTADGRCK 20 (23)
T ss_dssp SSSTTEEEETTTEEE
T ss_pred cccccceEcCCcccc
Confidence 466666799999994
No 7
>PF08219 TOM13: Outer membrane protein TOM13; InterPro: IPR013262 The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins [].; GO: 0005741 mitochondrial outer membrane
Probab=18.73 E-value=65 Score=22.36 Aligned_cols=21 Identities=14% Similarity=0.431 Sum_probs=16.4
Q ss_pred CCchHHHHHHHHHHHHhhccC
Q psy8890 125 EHAATVMLVAWGQFMDHDFTL 145 (150)
Q Consensus 125 ~~~~t~~~~~wgQfi~HDi~~ 145 (150)
-+..+-|+.-||..++|++.+
T Consensus 42 LPFiNG~MLGFGEl~AhE~~f 62 (77)
T PF08219_consen 42 LPFINGMMLGFGELFAHEIAF 62 (77)
T ss_pred hhhhhhhhHhHHHHHHHHHHH
Confidence 345577778899999999853
No 8
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=17.35 E-value=69 Score=20.62 Aligned_cols=9 Identities=44% Similarity=1.221 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q psy8890 70 NLKHPTWGA 78 (150)
Q Consensus 70 Nl~~P~wG~ 78 (150)
+..+|.||.
T Consensus 9 HP~~pdWG~ 17 (52)
T PF12073_consen 9 HPDHPDWGI 17 (52)
T ss_pred CCCCCCCcc
Confidence 567899983
No 9
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=17.03 E-value=87 Score=19.70 Aligned_cols=21 Identities=19% Similarity=0.298 Sum_probs=16.1
Q ss_pred hhhHHHHHHcCCCHHHHHhcC
Q psy8890 13 QGTKTLKAIYDLSYEEVEKGL 33 (150)
Q Consensus 13 ~~s~~~~~~~~l~~~~~~~gl 33 (150)
..|..|++..|+++.|+...|
T Consensus 29 vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 29 VSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp E-HHHHHHHHTS-HHHHHHHH
T ss_pred ECHHHHHHHHCCCHHHhcccC
Confidence 348999999999999997654
No 10
>PF01190 Pollen_Ole_e_I: Pollen proteins Ole e I like; InterPro: IPR006041 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ole e 1. A number of plant pollen proteins, whose biological function is not yet known, are structurally related []. These proteins are most probably secreted and consist of about 145 residues. There are six cysteines which are conserved in the sequence of these proteins. They seem to be involved in disulphide bonds.
Probab=11.98 E-value=1.5e+02 Score=20.35 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=23.6
Q ss_pred CCCCCCccccccccCcCCCCCCCCCCCCCc
Q psy8890 54 VECKPGKYRRYDGLCTNLKHPTWGAVNTPF 83 (150)
Q Consensus 54 ~~C~~~~yRt~DGsCNNl~~P~wG~a~tpf 83 (150)
..|...--++.+..||......+|..|.++
T Consensus 68 ~~C~v~l~~sp~~~C~~~~~~~~G~~ga~l 97 (97)
T PF01190_consen 68 SSCRVKLVSSPDPSCNVPTNSNGGRTGAKL 97 (97)
T ss_pred CCcEEEEeCCCcCcCCCCcCCCCCccCCcC
Confidence 456655567788899999999999988764
Done!