Query psy11155
Match_columns 101
No_of_seqs 102 out of 594
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 19:23:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11155.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11155hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2408|consensus 99.5 1.2E-14 2.7E-19 125.1 3.1 64 31-94 447-511 (719)
2 PF03098 An_peroxidase: Animal 99.4 5.8E-14 1.3E-18 116.4 4.0 66 28-94 284-350 (530)
3 PLN02283 alpha-dioxygenase 98.0 8.6E-06 1.9E-10 70.1 4.4 38 34-73 361-398 (633)
4 PF15502 MPLKIP: M-phase-speci 78.1 0.92 2E-05 32.6 0.7 17 84-100 117-133 (151)
5 COG2978 AbgT Putative p-aminob 20.3 57 0.0012 28.2 1.3 18 45-62 432-449 (516)
6 COG1036 Archaeal flavoproteins 16.8 77 0.0017 23.9 1.2 28 40-67 93-120 (187)
7 PF02044 Bombesin: Bombesin-li 16.3 51 0.0011 14.9 0.1 8 7-14 6-13 (14)
8 PF08998 Epsilon_antitox: Bact 15.6 1.1E+02 0.0023 20.6 1.5 29 42-70 9-38 (89)
9 PF14698 ASL_C2: Argininosucci 15.5 45 0.00098 20.7 -0.3 23 52-74 16-38 (70)
10 PF02772 S-AdoMet_synt_M: S-ad 12.4 95 0.0021 21.7 0.6 19 1-19 23-41 (120)
No 1
>KOG2408|consensus
Probab=99.49 E-value=1.2e-14 Score=125.13 Aligned_cols=64 Identities=42% Similarity=0.673 Sum_probs=57.8
Q ss_pred cCCCCCCCCCCCCchhHHHHHHHHHHHhhhhcccccccCCCCCcccCC-ccchhhcccChhhhhh
Q psy11155 31 KVFFDGYNPNIAADISNVFATVALRFGHTLINPILTRLNENYTTIPEV-NISWLKWIQPVQMFLS 94 (101)
Q Consensus 31 ~g~~~gYd~~vdPsIsneFatAAfRfgHSlI~~~i~~~~~~~~~~~~~-~i~L~d~ff~P~~l~~ 94 (101)
.|+|.|||++|||+|+||||+||||||||||++.+.++++++++.... .+.+.+.||+|..+..
T Consensus 447 ~g~~~gY~~~~dp~IsneFataAfRfgHsli~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~i~~ 511 (719)
T KOG2408|consen 447 LGGYRGYDPNVDPTISNEFATAAFRFGHSLIPPFFQRLDENFQPIGEVVNLPLHDAFFNPWLILN 511 (719)
T ss_pred CccccCcCCCCChhhhhhhhHHHHhhhcccCchhhhhhcccCcccccccCchhhhhhcchhhhhh
Confidence 589999999999999999999999999999999999999999986432 7889999998887765
No 2
>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=99.44 E-value=5.8e-14 Score=116.42 Aligned_cols=66 Identities=30% Similarity=0.567 Sum_probs=47.7
Q ss_pred ccccCCCCCCCCCCCCchhHHHHHHHHHHHhhhhcccccccCCCCCcccCCccchhhcccChh-hhhh
Q psy11155 28 EHQKVFFDGYNPNIAADISNVFATVALRFGHTLINPILTRLNENYTTIPEVNISWLKWIQPVQ-MFLS 94 (101)
Q Consensus 28 ~~~~g~~~gYd~~vdPsIsneFatAAfRfgHSlI~~~i~~~~~~~~~~~~~~i~L~d~ff~P~-~l~~ 94 (101)
....+++.+|+++++|+|+||||+||||||||||++.+.+.++++.. ..+.++|.|.|++|. .+..
T Consensus 284 ~~~~g~~~~y~~~~~~~i~~EFa~aA~RfgHs~i~~~~~~~~~~~~~-~~~~~~L~d~f~~~~~~~~~ 350 (530)
T PF03098_consen 284 PLNNGYYKGYDPSVDPSISNEFAAAAYRFGHSMIPDTYDRWDENFEI-PEPSLPLSDAFFNPSNRLLE 350 (530)
T ss_dssp ----GCGTTS-TTS--S-BTTH-HHHGGGGGGGS-SEEEEBTTTSBE-TTSEEEGGGGBT-HH-HHHT
T ss_pred ccccccccCCCCCCCCchhHHHHHHHHHhhheeehhhhhhccccCCc-ccccccccccccCcchhhhh
Confidence 44556899999999999999999999999999999999999988832 236899999999999 4443
No 3
>PLN02283 alpha-dioxygenase
Probab=97.96 E-value=8.6e-06 Score=70.08 Aligned_cols=38 Identities=18% Similarity=0.222 Sum_probs=30.4
Q ss_pred CCCCCCCCCCchhHHHHHHHHHHHhhhhcccccccCCCCC
Q psy11155 34 FDGYNPNIAADISNVFATVALRFGHTLINPILTRLNENYT 73 (101)
Q Consensus 34 ~~gYd~~vdPsIsneFatAAfRfgHSlI~~~i~~~~~~~~ 73 (101)
...+++.|+++|+||| +||||| ||+|++.+.+.+...+
T Consensus 361 ~~~~~~~v~~~is~EF-~aaYR~-Hslip~~~~~~~~~~~ 398 (633)
T PLN02283 361 KKPNNHGVPYSLTEEF-TSVYRM-HSLLPDHLILRDITAA 398 (633)
T ss_pred CccccCCCCcchhHHH-HHHHhh-hhcCCCceeccccccc
Confidence 3345567889999999 579998 9999999888776543
No 4
>PF15502 MPLKIP: M-phase-specific PLK1-interacting protein
Probab=78.14 E-value=0.92 Score=32.62 Aligned_cols=17 Identities=12% Similarity=0.178 Sum_probs=15.1
Q ss_pred hcccChhhhhhhhhhhc
Q psy11155 84 KWIQPVQMFLSSWVECM 100 (101)
Q Consensus 84 d~ff~P~~l~~~w~~~~ 100 (101)
+.|++|..|++||+.|+
T Consensus 117 e~Yy~pSMLEDPW~~L~ 133 (151)
T PF15502_consen 117 EQYYHPSMLEDPWAHLE 133 (151)
T ss_pred HHhcCHHhhhChHHHhh
Confidence 56899999999999876
No 5
>COG2978 AbgT Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]
Probab=20.27 E-value=57 Score=28.20 Aligned_cols=18 Identities=33% Similarity=0.519 Sum_probs=14.9
Q ss_pred hhHHHHHHHHHHHhhhhc
Q psy11155 45 ISNVFATVALRFGHTLIN 62 (101)
Q Consensus 45 IsneFatAAfRfgHSlI~ 62 (101)
.+.||+.||||.|.|...
T Consensus 432 ysPe~tQaayRigDS~tn 449 (516)
T COG2978 432 YSPEFTQAAYRIGDSVTN 449 (516)
T ss_pred CCHHHHHHHHHhcccccc
Confidence 456999999999998653
No 6
>COG1036 Archaeal flavoproteins [Energy production and conversion]
Probab=16.81 E-value=77 Score=23.89 Aligned_cols=28 Identities=25% Similarity=0.349 Sum_probs=24.3
Q ss_pred CCCCchhHHHHHHHHHHHhhhhcccccc
Q psy11155 40 NIAADISNVFATVALRFGHTLINPILTR 67 (101)
Q Consensus 40 ~vdPsIsneFatAAfRfgHSlI~~~i~~ 67 (101)
-|.|+++|..|-.|++++.|++...+-.
T Consensus 93 lvaPaTsNTvAKIa~GIADtLVTNAVaq 120 (187)
T COG1036 93 LVAPATSNTVAKIAYGIADTLVTNAVAQ 120 (187)
T ss_pred EEcccccchHHHHHhhhHHHHHHHHHHH
Confidence 3899999999999999999999865544
No 7
>PF02044 Bombesin: Bombesin-like peptide; InterPro: IPR000874 Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies [, ]; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known [, ], gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide whose function is not yet clear. Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.; GO: 0007218 neuropeptide signaling pathway; PDB: 1C9A_A 1C98_A.
Probab=16.29 E-value=51 Score=14.95 Aligned_cols=8 Identities=63% Similarity=0.875 Sum_probs=3.0
Q ss_pred HHhhhhhh
Q psy11155 7 VTHQMGEK 14 (101)
Q Consensus 7 ~~~~~~~~ 14 (101)
++|-||.|
T Consensus 6 vGh~Mgkk 13 (14)
T PF02044_consen 6 VGHFMGKK 13 (14)
T ss_dssp HHCT----
T ss_pred eeeeeccC
Confidence 67888865
No 8
>PF08998 Epsilon_antitox: Bacterial epsilon antitoxin; InterPro: IPR015090 The epsilon antitoxin, produced by various prokaryotes, forms part of a post-segregational killing system, which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly interacts with the zeta toxin, inactivating it []. ; GO: 0015643 toxin binding, 0009636 response to toxin, 0031342 negative regulation of cell killing; PDB: 1GVN_C 3Q8X_C.
Probab=15.56 E-value=1.1e+02 Score=20.58 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=16.7
Q ss_pred CCchhHHHHHHHH-HHHhhhhcccccccCC
Q psy11155 42 AADISNVFATVAL-RFGHTLINPILTRLNE 70 (101)
Q Consensus 42 dPsIsneFatAAf-RfgHSlI~~~i~~~~~ 70 (101)
.-.|.|||+++.| |...-.+...+..-|+
T Consensus 9 kiEilnEfs~~vy~rvlnyVlnheldk~ds 38 (89)
T PF08998_consen 9 KIEILNEFSSSVYNRVLNYVLNHELDKNDS 38 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTT--TT-T
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence 3458999998887 5544455555554443
No 9
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=15.50 E-value=45 Score=20.72 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=15.6
Q ss_pred HHHHHHhhhhcccccccCCCCCc
Q psy11155 52 VALRFGHTLINPILTRLNENYTT 74 (101)
Q Consensus 52 AAfRfgHSlI~~~i~~~~~~~~~ 74 (101)
.-||=.|-.+...+....+.+..
T Consensus 16 ipFR~AH~iVg~~V~~a~~~~~~ 38 (70)
T PF14698_consen 16 IPFREAHHIVGRLVRLAEEEGKP 38 (70)
T ss_dssp S-HHHHHHHHHHHHHHHHHTTS-
T ss_pred CCHHHHHHHHHHHHHHHHHcCCC
Confidence 35899999998888765555444
No 10
>PF02772 S-AdoMet_synt_M: S-adenosylmethionine synthetase, central domain; InterPro: IPR022629 The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. This entry represents the central domain and is found in association with PF00438 from PFAM and PF02773 from PFAM. S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP []. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis. In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family. The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance []; GO: 0004478 methionine adenosyltransferase activity; PDB: 3S82_B 2OBV_A 3RV2_A 1FUG_A 1RG9_D 1XRA_A 1P7L_C 1XRB_A 1MXA_A 1MXB_A ....
Probab=12.43 E-value=95 Score=21.67 Aligned_cols=19 Identities=21% Similarity=0.567 Sum_probs=14.9
Q ss_pred CCcchhHHhhhhhhhccCC
Q psy11155 1 MPIPQYVTHQMGEKRHNSS 19 (101)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~ 19 (101)
||+|-+|.|.+..++...+
T Consensus 23 MPl~i~lAh~L~~~l~~~R 41 (120)
T PF02772_consen 23 MPLPIVLAHRLARRLAEVR 41 (120)
T ss_dssp S-HHHHHHHHHHHHHHHHH
T ss_pred CChHHHHHHHHHHHHHHHH
Confidence 8999999999999884333
Done!