Query 030454
Match_columns 177
No_of_seqs 162 out of 744
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 13:58:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030454hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05922 Inhibitor_I9: Peptida 99.5 3.5E-14 7.7E-19 99.2 5.7 78 83-164 1-82 (82)
2 KOG0723 Molecular chaperone (D 28.1 21 0.00045 28.0 0.1 41 132-174 47-94 (112)
3 PF03927 NapD: NapD protein; 22.7 76 0.0016 22.7 2.2 17 141-157 55-71 (79)
4 PRK10553 assembly protein for 19.4 88 0.0019 23.1 2.0 16 141-156 58-73 (87)
5 PF03352 Adenine_glyco: Methyl 17.3 27 0.00059 29.1 -1.2 29 125-153 49-81 (179)
6 PF11080 DUF2622: Protein of u 17.3 3.6E+02 0.0079 20.5 5.0 68 78-148 3-70 (96)
7 PF01037 AsnC_trans_reg: AsnC 16.8 1.5E+02 0.0033 19.3 2.6 17 140-156 13-29 (74)
8 cd04901 ACT_3PGDH C-terminal A 16.7 1.4E+02 0.0031 19.1 2.4 19 138-156 49-67 (69)
9 cd00408 DHDPS-like Dihydrodipi 16.5 6E+02 0.013 21.3 6.8 51 97-156 107-157 (281)
10 TIGR00624 tag DNA-3-methyladen 16.4 43 0.00094 27.9 -0.2 29 125-153 53-85 (179)
No 1
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=99.50 E-value=3.5e-14 Score=99.21 Aligned_cols=78 Identities=21% Similarity=0.336 Sum_probs=54.9
Q ss_pred EEEEEecCCCCCCCchHHHHHHHHHHHHHhhCC----hhhhhcceeEEecCcceeeeeecCHHHHHHhhCCCCeEEEeCC
Q 030454 83 HWLIVMEFPNPSELSEEEMINAYVKTLAAVVGS----EEEAKKKIYSVCTTTYTGFGALIDEELSYKVKGQPGVLWVLPD 158 (177)
Q Consensus 83 tYIV~M~~~~~~~~~~~~~~~~h~s~LaSVlgS----~e~Ak~~IlYSYt~af~GFAA~LTeeEA~~Lk~~PGVlSVfPD 158 (177)
+|||.|+.+... ....++|.+++.+++.+ .......++|+|+.+|+||+|+|+++++++|+++|+|.+|.||
T Consensus 1 ~YIV~~k~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~Gfs~~l~~~~i~~L~~~p~V~~Ve~D 76 (82)
T PF05922_consen 1 RYIVVFKDDASA----ASSFSSHKSWQASILKSALKSASSINAKVLYSYDNAFNGFSAKLSEEEIEKLRKDPGVKSVEPD 76 (82)
T ss_dssp EEEEEE-TTSTH----HCHHHHHHHHHH----HHHHTH-TTT-EEEEEESSTSSEEEEEE-HHHHHHHHTSTTEEEEEEE
T ss_pred CEEEEECCCCCc----chhHHHHHHHHHHHHhhhhhhhcccCCceEEEEeeeEEEEEEEeCHHHHHHHHcCCCeEEEEeC
Confidence 699999866432 22345555555544332 1234567999999999999999999999999999999999999
Q ss_pred CCccCC
Q 030454 159 SYIDVP 164 (177)
Q Consensus 159 ~~~~L~ 164 (177)
+.+++|
T Consensus 77 ~~v~l~ 82 (82)
T PF05922_consen 77 QVVSLH 82 (82)
T ss_dssp CEEEE-
T ss_pred ceEecC
Confidence 988775
No 2
>KOG0723 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=28.09 E-value=21 Score=28.02 Aligned_cols=41 Identities=20% Similarity=0.261 Sum_probs=28.8
Q ss_pred eeeeeecCHHHHHHhhCCCCeEEEeCCCCcc-------CCCCCCCCcccc
Q 030454 132 TGFGALIDEELSYKVKGQPGVLWVLPDSYID-------VPNKDYGGRYFL 174 (177)
Q Consensus 132 ~GFAA~LTeeEA~~Lk~~PGVlSVfPD~~~~-------L~~k~yg~~~~~ 174 (177)
-||..++|..||..+-+.- -++-+++..+ ...+|-||-+|+
T Consensus 47 GGF~~kMsr~EA~lIL~v~--~s~~k~KikeaHrriM~~NHPD~GGSPYl 94 (112)
T KOG0723|consen 47 GGFEPKMSRREAALILGVT--PSLDKDKIKEAHRRIMLANHPDRGGSPYL 94 (112)
T ss_pred cccccccchHHHHHHhCCC--ccccHHHHHHHHHHHHHcCCCcCCCCHHH
Confidence 4999999999999965544 2333343332 456899998886
No 3
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=22.69 E-value=76 Score=22.68 Aligned_cols=17 Identities=29% Similarity=0.364 Sum_probs=13.3
Q ss_pred HHHHHhhCCCCeEEEeC
Q 030454 141 ELSYKVKGQPGVLWVLP 157 (177)
Q Consensus 141 eEA~~Lk~~PGVlSVfP 157 (177)
+..++|+.+|||+++-.
T Consensus 55 ~~~~~i~~l~GVlsa~l 71 (79)
T PF03927_consen 55 DLIDAINALPGVLSASL 71 (79)
T ss_dssp HHHHHHCCSTTEEEEEE
T ss_pred HHHHHHHcCCCceEEEE
Confidence 44577889999999853
No 4
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=19.45 E-value=88 Score=23.08 Aligned_cols=16 Identities=31% Similarity=0.256 Sum_probs=13.3
Q ss_pred HHHHHhhCCCCeEEEe
Q 030454 141 ELSYKVKGQPGVLWVL 156 (177)
Q Consensus 141 eEA~~Lk~~PGVlSVf 156 (177)
+..+.|+.+|||+++-
T Consensus 58 ~~i~~I~~l~GVlsa~ 73 (87)
T PRK10553 58 QTIESVRNVEGVLAVS 73 (87)
T ss_pred HHHHHHHcCCCceEEE
Confidence 5567889999999984
No 5
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=17.34 E-value=27 Score=29.08 Aligned_cols=29 Identities=28% Similarity=0.558 Sum_probs=23.5
Q ss_pred EEecCcceeee----eecCHHHHHHhhCCCCeE
Q 030454 125 SVCTTTYTGFG----ALIDEELSYKVKGQPGVL 153 (177)
Q Consensus 125 YSYt~af~GFA----A~LTeeEA~~Lk~~PGVl 153 (177)
-.|..+|.||- |+++|++.++|..-|+++
T Consensus 49 ~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~~iI 81 (179)
T PF03352_consen 49 EAFREAFAGFDPEKVAKMDEEDIERLMQDPGII 81 (179)
T ss_dssp HHHHHHTGGGHHHHHHT--HHHHHHHTTSTTSS
T ss_pred HHHHHHHHCCCHHHHHcCCHHHHHHHhcCcchh
Confidence 35778999995 899999999999999976
No 6
>PF11080 DUF2622: Protein of unknown function (DUF2622); InterPro: IPR022597 This family is conserved in the Enterobacteriaceae family. The function is not known.
Probab=17.33 E-value=3.6e+02 Score=20.48 Aligned_cols=68 Identities=9% Similarity=0.063 Sum_probs=39.4
Q ss_pred CCCceEEEEEecCCCCCCCchHHHHHHHHHHHHHhhCChhhhhcceeEEecCcceeeeeecCHHHHHHhhC
Q 030454 78 GCDYQHWLIVMEFPNPSELSEEEMINAYVKTLAAVVGSEEEAKKKIYSVCTTTYTGFGALIDEELSYKVKG 148 (177)
Q Consensus 78 g~d~ktYIV~M~~~~~~~~~~~~~~~~h~s~LaSVlgS~e~Ak~~IlYSYt~af~GFAA~LTeeEA~~Lk~ 148 (177)
..+...|||.+.-....- .+.-.-+..+-..-+...-....-+.|--.+.=+|+--.|+++|++.|.+
T Consensus 3 ~~~~~~YVVt~~~~e~~l---~d~~~L~~~lt~~GF~~tl~D~~G~~HeLgtntfgl~S~l~~~eV~~la~ 70 (96)
T PF11080_consen 3 SSDITRYVVTFEYQEAGL---TDINELNNHLTRAGFSTTLTDEDGNPHELGTNTFGLISALSAEEVAQLAR 70 (96)
T ss_pred CCcceEEEEEEEeccCCh---HHHHHHHHHHHhcCceeEEecCCCCEeecCCCeEEEEecCCHHHHHHHHH
Confidence 456789999998665421 12222222222211111101122367888888889999999999988764
No 7
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=16.84 E-value=1.5e+02 Score=19.27 Aligned_cols=17 Identities=18% Similarity=0.251 Sum_probs=13.3
Q ss_pred HHHHHHhhCCCCeEEEe
Q 030454 140 EELSYKVKGQPGVLWVL 156 (177)
Q Consensus 140 eeEA~~Lk~~PGVlSVf 156 (177)
++-+++|+++|+|..++
T Consensus 13 ~~~~~~l~~~p~V~~~~ 29 (74)
T PF01037_consen 13 DEFAEALAEIPEVVECY 29 (74)
T ss_dssp HHHHHHHHTSTTEEEEE
T ss_pred HHHHHHHHcCCCEEEEE
Confidence 34568888999998876
No 8
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=16.73 E-value=1.4e+02 Score=19.11 Aligned_cols=19 Identities=32% Similarity=0.515 Sum_probs=16.3
Q ss_pred cCHHHHHHhhCCCCeEEEe
Q 030454 138 IDEELSYKVKGQPGVLWVL 156 (177)
Q Consensus 138 LTeeEA~~Lk~~PGVlSVf 156 (177)
..++-.++|+++|||..|.
T Consensus 49 ~l~~li~~l~~~~~V~~v~ 67 (69)
T cd04901 49 VSEELLEALRAIPGTIRVR 67 (69)
T ss_pred CCHHHHHHHHcCCCeEEEE
Confidence 5667789999999999885
No 9
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=16.53 E-value=6e+02 Score=21.31 Aligned_cols=51 Identities=16% Similarity=0.173 Sum_probs=31.9
Q ss_pred chHHHHHHHHHHHHHhhCChhhhhcceeEEecCcceeeeeecCHHHHHHhhCCCCeEEEe
Q 030454 97 SEEEMINAYVKTLAAVVGSEEEAKKKIYSVCTTTYTGFGALIDEELSYKVKGQPGVLWVL 156 (177)
Q Consensus 97 ~~~~~~~~h~s~LaSVlgS~e~Ak~~IlYSYt~af~GFAA~LTeeEA~~Lk~~PGVlSVf 156 (177)
+.+++.+++......+ ..+-++|.+-. .+ ...|+.+...+|.+.|+|+.+-
T Consensus 107 ~~~~~~~~~~~ia~~~------~~pi~iYn~P~-~t--g~~l~~~~~~~L~~~~~v~giK 157 (281)
T cd00408 107 SQEGIVAHFKAVADAS------DLPVILYNIPG-RT--GVDLSPETIARLAEHPNIVGIK 157 (281)
T ss_pred CHHHHHHHHHHHHhcC------CCCEEEEECcc-cc--CCCCCHHHHHHHhcCCCEEEEE
Confidence 4455555554443321 13345665532 23 3589999999999999999875
No 10
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=16.42 E-value=43 Score=27.93 Aligned_cols=29 Identities=14% Similarity=0.305 Sum_probs=25.2
Q ss_pred EEecCcceee----eeecCHHHHHHhhCCCCeE
Q 030454 125 SVCTTTYTGF----GALIDEELSYKVKGQPGVL 153 (177)
Q Consensus 125 YSYt~af~GF----AA~LTeeEA~~Lk~~PGVl 153 (177)
-.|..+|.|| .|.++|++.++|..-||++
T Consensus 53 ~~fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~II 85 (179)
T TIGR00624 53 ENYRRAFSGFDIVKVARMTDADVERLLQDDGII 85 (179)
T ss_pred HHHHHHHcCCCHHHHhCCCHHHHHHHhcCccch
Confidence 3577889999 4899999999999999976
Done!