Query 025802
Match_columns 248
No_of_seqs 169 out of 755
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:42:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025802hhsearch_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 8.5E-14 1.9E-18 101.8 5.3 78 83-164 1-82 (82)
2 smart00754 CHRD A domain in th 34.9 30 0.00065 27.3 2.1 42 129-179 76-117 (118)
3 PF01479 S4: S4 domain; Inter 28.2 40 0.00087 22.3 1.6 18 170-187 26-43 (48)
4 PF07452 CHRD: CHRD domain; I 24.4 78 0.0017 24.7 2.8 48 122-178 63-118 (119)
5 cd00408 DHDPS-like Dihydrodipi 23.4 3.1E+02 0.0068 24.4 6.8 55 95-158 105-159 (281)
6 PF07816 DUF1645: Protein of u 23.0 36 0.00079 29.7 0.7 11 171-181 3-14 (193)
7 cd00952 CHBPH_aldolase Trans-o 22.8 3.1E+02 0.0068 25.4 6.9 54 96-157 117-170 (309)
8 PRK04147 N-acetylneuraminate l 20.7 3.5E+02 0.0076 24.6 6.7 53 96-157 113-165 (293)
9 PRK03170 dihydrodipicolinate s 20.6 3.6E+02 0.0079 24.3 6.7 52 96-156 110-161 (292)
10 COG1097 RRP4 RNA-binding prote 19.7 61 0.0013 30.2 1.5 35 152-186 123-157 (239)
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=99.46 E-value=8.5e-14 Score=101.78 Aligned_cols=78 Identities=21% Similarity=0.331 Sum_probs=55.3
Q ss_pred eEEEEecCCCCCCCChHHHHHHHHHHHHHhhCC----hhhhhcceeEEecCcceeeeeecCHHHHHHhhCCCCeEEEeCC
Q 025802 83 HWLIVMEFPNPSELSEEEMINAYVKTLAAVVGS----EEEAKKKIYSVCTTTYTGFGALIDEELSYKVKGQPGVLWVLPD 158 (248)
Q Consensus 83 tYIV~M~~p~~p~~s~~~~~~sh~s~LaSVLgS----ee~Ak~~ILYSYt~afnGFAArLTeEEAekLk~lPGVVSVfPD 158 (248)
+|||.|..+.. .....++|.+|+.+++.+ .......++|+|+.+|+||+|+||++++++|+++|+|.+|.||
T Consensus 1 ~YIV~~k~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~Gfs~~l~~~~i~~L~~~p~V~~Ve~D 76 (82)
T PF05922_consen 1 RYIVVFKDDAS----AASSFSSHKSWQASILKSALKSASSINAKVLYSYDNAFNGFSAKLSEEEIEKLRKDPGVKSVEPD 76 (82)
T ss_dssp EEEEEE-TTST----HHCHHHHHHHHHH----HHHHTH-TTT-EEEEEESSTSSEEEEEE-HHHHHHHHTSTTEEEEEEE
T ss_pred CEEEEECCCCC----cchhHHHHHHHHHHHHhhhhhhhcccCCceEEEEeeeEEEEEEEeCHHHHHHHHcCCCeEEEEeC
Confidence 59999997642 122345555555544332 1234567999999999999999999999999999999999999
Q ss_pred CCcCCC
Q 025802 159 SYIDVP 164 (248)
Q Consensus 159 s~~qLH 164 (248)
..++||
T Consensus 77 ~~v~l~ 82 (82)
T PF05922_consen 77 QVVSLH 82 (82)
T ss_dssp CEEEE-
T ss_pred ceEecC
Confidence 999886
No 2
>smart00754 CHRD A domain in the BMP inhibitor chordin and in microbial proteins.
Probab=34.86 E-value=30 Score=27.31 Aligned_cols=42 Identities=21% Similarity=0.334 Sum_probs=32.2
Q ss_pred CcceeeeeecCHHHHHHhhCCCCeEEEeCCCCcCCCCCCCCCcccccceee
Q 025802 129 TTYTGFGALIDEELSYKVKGQPGVLWVLPDSYIDVPNKDYGGDLFVDGKVI 179 (248)
Q Consensus 129 ~afnGFAArLTeEEAekLk~lPGVVSVfPDs~~qLHTkdygg~~~~~g~~~ 179 (248)
..+.|....|++++++.|.. | +-++.+||++|=+ ..|-|||+
T Consensus 76 ~~~~g~~~~l~~~~l~~l~~--g------~~yvnvhT~~~p~-GeIRGqi~ 117 (118)
T smart00754 76 GPFAGSVKTLTDEELRQLLA--G------NLYVNVHTKANPG-GEIRGQVA 117 (118)
T ss_pred ceeccccccCCHHHHHHHhc--C------CeEEEeecccCCC-ceEeeEEc
Confidence 44677777999999999998 3 4477899999974 33778775
No 3
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=28.17 E-value=40 Score=22.30 Aligned_cols=18 Identities=39% Similarity=0.748 Sum_probs=15.5
Q ss_pred CcccccceeecCCccccc
Q 025802 170 GDLFVDGKVIHRPQYRFT 187 (248)
Q Consensus 170 g~~~~~g~~~~~~~~~~~ 187 (248)
|..+|||+++.+|.+...
T Consensus 26 g~V~VNg~~v~~~~~~v~ 43 (48)
T PF01479_consen 26 GRVKVNGKVVKDPSYIVK 43 (48)
T ss_dssp TTEEETTEEESSTTSBES
T ss_pred CEEEECCEEEcCCCCCCC
Confidence 679999999999987655
No 4
>PF07452 CHRD: CHRD domain; InterPro: IPR010895 CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made [].
Probab=24.38 E-value=78 Score=24.65 Aligned_cols=48 Identities=13% Similarity=0.207 Sum_probs=35.2
Q ss_pred ceeEEe-----cCcceeeee---ecCHHHHHHhhCCCCeEEEeCCCCcCCCCCCCCCccccccee
Q 025802 122 KIYSVC-----TTTYTGFGA---LIDEELSYKVKGQPGVLWVLPDSYIDVPNKDYGGDLFVDGKV 178 (248)
Q Consensus 122 ~ILYSY-----t~afnGFAA---rLTeEEAekLk~lPGVVSVfPDs~~qLHTkdygg~~~~~g~~ 178 (248)
.+++.+ ...+.|+.. .|+++++..|..= +-++.+||++|-+ ..|-|||
T Consensus 63 ~v~~~l~~~~~~~~~~g~~~~~~~l~~~~~~~l~~g--------~lyvnvhT~~~p~-GeIRGql 118 (119)
T PF07452_consen 63 PVLVELSFSFNTGMISGVWSGSFRLTPAQLRALLAG--------QLYVNVHTENFPG-GEIRGQL 118 (119)
T ss_pred CeEEEeeeccCCCccccceeccccCCHHHHHhhhcC--------CEEEEEEeCCCCC-CEEEEEE
Confidence 455555 556788888 9999999986543 3367899999985 4477776
No 5
>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=23.40 E-value=3.1e+02 Score=24.41 Aligned_cols=55 Identities=15% Similarity=0.152 Sum_probs=35.1
Q ss_pred CCChHHHHHHHHHHHHHhhCChhhhhcceeEEecCcceeeeeecCHHHHHHhhCCCCeEEEeCC
Q 025802 95 ELSEEEMINAYVKTLAAVVGSEEEAKKKIYSVCTTTYTGFGALIDEELSYKVKGQPGVLWVLPD 158 (248)
Q Consensus 95 ~~s~~~~~~sh~s~LaSVLgSee~Ak~~ILYSYt~afnGFAArLTeEEAekLk~lPGVVSVfPD 158 (248)
.++.+.+.++|..+...+ ..+-+||.+.. .+ ...|+.+...+|.+.|.|+.+--.
T Consensus 105 ~~~~~~~~~~~~~ia~~~------~~pi~iYn~P~-~t--g~~l~~~~~~~L~~~~~v~giK~s 159 (281)
T cd00408 105 KPSQEGIVAHFKAVADAS------DLPVILYNIPG-RT--GVDLSPETIARLAEHPNIVGIKDS 159 (281)
T ss_pred CCCHHHHHHHHHHHHhcC------CCCEEEEECcc-cc--CCCCCHHHHHHHhcCCCEEEEEeC
Confidence 344566666665544321 13446666542 23 358999999999999999987543
No 6
>PF07816 DUF1645: Protein of unknown function (DUF1645); InterPro: IPR012442 These sequences are derived from a number of hypothetical plant proteins. The region in question is approximately 270 amino acids long. Some members of this family are annotated as yeast pheromone receptor proteins AR781 but no literature was found to support this.
Probab=23.02 E-value=36 Score=29.73 Aligned_cols=11 Identities=36% Similarity=0.761 Sum_probs=10.3
Q ss_pred cccccceeec-C
Q 025802 171 DLFVDGKVIH-R 181 (248)
Q Consensus 171 ~~~~~g~~~~-~ 181 (248)
|||.||+|.| .
T Consensus 3 ELF~~GkIrPl~ 14 (193)
T PF07816_consen 3 ELFDNGKIRPLK 14 (193)
T ss_pred ccccCCEEeecC
Confidence 7999999999 6
No 7
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=22.76 E-value=3.1e+02 Score=25.42 Aligned_cols=54 Identities=11% Similarity=-0.051 Sum_probs=33.4
Q ss_pred CChHHHHHHHHHHHHHhhCChhhhhcceeEEecCcceeeeeecCHHHHHHhhCCCCeEEEeC
Q 025802 96 LSEEEMINAYVKTLAAVVGSEEEAKKKIYSVCTTTYTGFGALIDEELSYKVKGQPGVLWVLP 157 (248)
Q Consensus 96 ~s~~~~~~sh~s~LaSVLgSee~Ak~~ILYSYt~afnGFAArLTeEEAekLk~lPGVVSVfP 157 (248)
++.+.+.++|..+...+ + .-+-+||.+-. .+| ..|+++..++|.++|+|+.|--
T Consensus 117 ~~~~~l~~yf~~va~a~-~----~lPv~iYn~P~-~tg--~~l~~~~l~~L~~~pnivgiKd 170 (309)
T cd00952 117 LDVDTAVQFYRDVAEAV-P----EMAIAIYANPE-AFK--FDFPRAAWAELAQIPQVVAAKY 170 (309)
T ss_pred CCHHHHHHHHHHHHHhC-C----CCcEEEEcCch-hcC--CCCCHHHHHHHhcCCCEEEEEe
Confidence 34455666664443321 0 02335555542 344 5899999999999999998754
No 8
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=20.71 E-value=3.5e+02 Score=24.64 Aligned_cols=53 Identities=19% Similarity=0.167 Sum_probs=33.6
Q ss_pred CChHHHHHHHHHHHHHhhCChhhhhcceeEEecCcceeeeeecCHHHHHHhhCCCCeEEEeC
Q 025802 96 LSEEEMINAYVKTLAAVVGSEEEAKKKIYSVCTTTYTGFGALIDEELSYKVKGQPGVLWVLP 157 (248)
Q Consensus 96 ~s~~~~~~sh~s~LaSVLgSee~Ak~~ILYSYt~afnGFAArLTeEEAekLk~lPGVVSVfP 157 (248)
++.+.+.++|......+ ..+-++|... ..+|+ .|+.+...+|.++|+|+.+--
T Consensus 113 ~~~~~l~~~f~~va~a~------~lPv~iYn~P-~~tg~--~l~~~~l~~L~~~pnvvgiK~ 165 (293)
T PRK04147 113 FSFEEICDYYREIIDSA------DNPMIVYNIP-ALTGV--NLSLDQFNELFTLPKVIGVKQ 165 (293)
T ss_pred CCHHHHHHHHHHHHHhC------CCCEEEEeCc-hhhcc--CCCHHHHHHHhcCCCEEEEEe
Confidence 34456666665543321 1234555533 34565 899999999999999988754
No 9
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=20.63 E-value=3.6e+02 Score=24.35 Aligned_cols=52 Identities=15% Similarity=0.127 Sum_probs=33.7
Q ss_pred CChHHHHHHHHHHHHHhhCChhhhhcceeEEecCcceeeeeecCHHHHHHhhCCCCeEEEe
Q 025802 96 LSEEEMINAYVKTLAAVVGSEEEAKKKIYSVCTTTYTGFGALIDEELSYKVKGQPGVLWVL 156 (248)
Q Consensus 96 ~s~~~~~~sh~s~LaSVLgSee~Ak~~ILYSYt~afnGFAArLTeEEAekLk~lPGVVSVf 156 (248)
++.+.+.++|..+...+ ..+-++|.+-. ..|+ .|+.+..++|.+.|.|+.+-
T Consensus 110 ~~~~~i~~~~~~ia~~~------~~pv~lYn~P~-~~g~--~l~~~~~~~L~~~p~v~giK 161 (292)
T PRK03170 110 PTQEGLYQHFKAIAEAT------DLPIILYNVPG-RTGV--DILPETVARLAEHPNIVGIK 161 (292)
T ss_pred CCHHHHHHHHHHHHhcC------CCCEEEEECcc-ccCC--CCCHHHHHHHHcCCCEEEEE
Confidence 34466666665554321 13445665532 3444 69999999999999998876
No 10
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=19.72 E-value=61 Score=30.16 Aligned_cols=35 Identities=23% Similarity=0.328 Sum_probs=30.8
Q ss_pred eEEEeCCCCcCCCCCCCCCcccccceeecCCcccc
Q 025802 152 VLWVLPDSYIDVPNKDYGGDLFVDGKVIHRPQYRF 186 (248)
Q Consensus 152 VVSVfPDs~~qLHTkdygg~~~~~g~~~~~~~~~~ 186 (248)
|..|.++....||+|+-|-....||++|.=++++.
T Consensus 123 V~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kV 157 (239)
T COG1097 123 VVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKV 157 (239)
T ss_pred EEEccCCCceEEEeecCCCccccCCEEEEEchhhc
Confidence 88999999999999998888999999999777543
Done!