Query 030335
Match_columns 179
No_of_seqs 132 out of 574
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 12:10:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030335.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030335hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05922 Inhibitor_I9: Peptida 99.4 4.9E-13 1.1E-17 93.4 4.2 77 79-160 1-82 (82)
2 PF03927 NapD: NapD protein; 26.2 60 0.0013 23.3 2.3 17 137-153 55-71 (79)
3 PRK10553 assembly protein for 23.7 64 0.0014 24.0 2.1 16 137-152 58-73 (87)
4 COG3062 NapD Uncharacterized p 18.5 1E+02 0.0022 23.7 2.2 16 137-152 58-73 (94)
5 cd04888 ACT_PheB-BS C-terminal 18.1 1.2E+02 0.0026 20.0 2.3 14 139-152 60-73 (76)
6 cd04901 ACT_3PGDH C-terminal A 17.9 1.3E+02 0.0029 19.4 2.5 21 132-152 47-67 (69)
7 PF13291 ACT_4: ACT domain; PD 16.6 1.2E+02 0.0026 20.7 2.1 14 139-152 66-79 (80)
8 smart00754 CHRD A domain in th 16.0 1.1E+02 0.0024 22.7 2.0 37 125-169 76-112 (118)
9 PF00403 HMA: Heavy-metal-asso 14.3 1.4E+02 0.0029 19.3 1.8 14 140-153 18-31 (62)
10 PF01037 AsnC_trans_reg: AsnC 14.3 2E+02 0.0043 18.8 2.6 16 137-152 14-29 (74)
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=99.37 E-value=4.9e-13 Score=93.42 Aligned_cols=77 Identities=23% Similarity=0.431 Sum_probs=55.5
Q ss_pred eEEEEecCCCCCCCChhhhHHHHHHHHHHhhCCh----Hhhhcce-eeEeecceeeeeccCCHHHHHHhhCCCCeEEEeC
Q 030335 79 HWLIVMEFPKDPAPTREQMIETYLNTLATVLGSM----EEAKKNM-YAFSTTTYTGFQCTVSEETSEKFKGLPGVLWVLP 153 (179)
Q Consensus 79 tYIVyM~~~~~~~~s~~~~~~~h~~~LaSVLgS~----eeAk~~I-YSYs~~af~GFAArLTeeEA~~Ls~~PGVVSVfP 153 (179)
+|||.|+.... .....+.|.+|+.+++.+. ......+ |+|. ..++||+++|+++++++|+++|+|.+|.|
T Consensus 1 ~YIV~~k~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~-~~~~Gfs~~l~~~~i~~L~~~p~V~~Ve~ 75 (82)
T PF05922_consen 1 RYIVVFKDDAS----AASSFSSHKSWQASILKSALKSASSINAKVLYSYD-NAFNGFSAKLSEEEIEKLRKDPGVKSVEP 75 (82)
T ss_dssp EEEEEE-TTST----HHCHHHHHHHHHH----HHHHTH-TTT-EEEEEES-STSSEEEEEE-HHHHHHHHTSTTEEEEEE
T ss_pred CEEEEECCCCC----cchhHHHHHHHHHHHHhhhhhhhcccCCceEEEEe-eeEEEEEEEeCHHHHHHHHcCCCeEEEEe
Confidence 59999987632 2234677888888765532 1234455 9999 89999999999999999999999999999
Q ss_pred CCCcccC
Q 030335 154 DSYIDVK 160 (179)
Q Consensus 154 D~~~kLH 160 (179)
|..+++|
T Consensus 76 D~~v~l~ 82 (82)
T PF05922_consen 76 DQVVSLH 82 (82)
T ss_dssp ECEEEE-
T ss_pred CceEecC
Confidence 9998876
No 2
>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=26.22 E-value=60 Score=23.33 Aligned_cols=17 Identities=29% Similarity=0.436 Sum_probs=13.0
Q ss_pred HHHHHhhCCCCeEEEeC
Q 030335 137 ETSEKFKGLPGVLWVLP 153 (179)
Q Consensus 137 eEA~~Ls~~PGVVSVfP 153 (179)
+..++|+.+|||+++-.
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 34467889999999853
No 3
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=23.71 E-value=64 Score=23.95 Aligned_cols=16 Identities=38% Similarity=0.466 Sum_probs=13.0
Q ss_pred HHHHHhhCCCCeEEEe
Q 030335 137 ETSEKFKGLPGVLWVL 152 (179)
Q Consensus 137 eEA~~Ls~~PGVVSVf 152 (179)
+..+.|+.+|||+++-
T Consensus 58 ~~i~~I~~l~GVlsa~ 73 (87)
T PRK10553 58 QTIESVRNVEGVLAVS 73 (87)
T ss_pred HHHHHHHcCCCceEEE
Confidence 4567888999999985
No 4
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=18.50 E-value=1e+02 Score=23.66 Aligned_cols=16 Identities=56% Similarity=0.738 Sum_probs=12.7
Q ss_pred HHHHHhhCCCCeEEEe
Q 030335 137 ETSEKFKGLPGVLWVL 152 (179)
Q Consensus 137 eEA~~Ls~~PGVVSVf 152 (179)
+..+.++.+|||++|.
T Consensus 58 ~tie~i~nl~gVlav~ 73 (94)
T COG3062 58 ETIESIRNLPGVLAVS 73 (94)
T ss_pred HHHHHHhcCCceeEEE
Confidence 4456788999999885
No 5
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=18.08 E-value=1.2e+02 Score=19.96 Aligned_cols=14 Identities=29% Similarity=0.311 Sum_probs=11.8
Q ss_pred HHHhhCCCCeEEEe
Q 030335 139 SEKFKGLPGVLWVL 152 (179)
Q Consensus 139 A~~Ls~~PGVVSVf 152 (179)
.++|+++|||.+|.
T Consensus 60 ~~~L~~i~~V~~v~ 73 (76)
T cd04888 60 LEELREIDGVEKVE 73 (76)
T ss_pred HHHHhcCCCeEEEE
Confidence 47899999999874
No 6
>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=17.86 E-value=1.3e+02 Score=19.36 Aligned_cols=21 Identities=38% Similarity=0.591 Sum_probs=16.9
Q ss_pred ccCCHHHHHHhhCCCCeEEEe
Q 030335 132 CTVSEETSEKFKGLPGVLWVL 152 (179)
Q Consensus 132 ArLTeeEA~~Ls~~PGVVSVf 152 (179)
....++-.++|+++|||..|.
T Consensus 47 ~~~l~~li~~l~~~~~V~~v~ 67 (69)
T cd04901 47 SEVSEELLEALRAIPGTIRVR 67 (69)
T ss_pred CCCCHHHHHHHHcCCCeEEEE
Confidence 335667779999999999885
No 7
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=16.61 E-value=1.2e+02 Score=20.66 Aligned_cols=14 Identities=36% Similarity=0.619 Sum_probs=11.8
Q ss_pred HHHhhCCCCeEEEe
Q 030335 139 SEKFKGLPGVLWVL 152 (179)
Q Consensus 139 A~~Ls~~PGVVSVf 152 (179)
.++|+++|||..|.
T Consensus 66 i~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 66 IRKLRQIPGVISVE 79 (80)
T ss_dssp HHHHCTSTTEEEEE
T ss_pred HHHHHCCCCeeEEE
Confidence 36889999999985
No 8
>smart00754 CHRD A domain in the BMP inhibitor chordin and in microbial proteins.
Probab=15.98 E-value=1.1e+02 Score=22.73 Aligned_cols=37 Identities=22% Similarity=0.388 Sum_probs=28.3
Q ss_pred cceeeeeccCCHHHHHHhhCCCCeEEEeCCCCcccCcccCCcccc
Q 030335 125 TTYTGFQCTVSEETSEKFKGLPGVLWVLPDSYIDVKNKDYGGLYL 169 (179)
Q Consensus 125 ~af~GFAArLTeeEA~~Ls~~PGVVSVfPD~~~kLHT~Df~G~~~ 169 (179)
..+.|....|++++++.|.. | +-++.+||++|-+--+
T Consensus 76 ~~~~g~~~~l~~~~l~~l~~--g------~~yvnvhT~~~p~GeI 112 (118)
T smart00754 76 GPFAGSVKTLTDEELRQLLA--G------NLYVNVHTKANPGGEI 112 (118)
T ss_pred ceeccccccCCHHHHHHHhc--C------CeEEEeecccCCCceE
Confidence 45677777999999999988 4 4478899998875433
No 9
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=14.34 E-value=1.4e+02 Score=19.30 Aligned_cols=14 Identities=36% Similarity=0.418 Sum_probs=11.1
Q ss_pred HHhhCCCCeEEEeC
Q 030335 140 EKFKGLPGVLWVLP 153 (179)
Q Consensus 140 ~~Ls~~PGVVSVfP 153 (179)
+.|+++|||.+|-=
T Consensus 18 ~~l~~~~GV~~v~v 31 (62)
T PF00403_consen 18 KALSKLPGVKSVKV 31 (62)
T ss_dssp HHHHTSTTEEEEEE
T ss_pred HHHhcCCCCcEEEE
Confidence 47899999987743
No 10
>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=14.33 E-value=2e+02 Score=18.79 Aligned_cols=16 Identities=25% Similarity=0.356 Sum_probs=12.8
Q ss_pred HHHHHhhCCCCeEEEe
Q 030335 137 ETSEKFKGLPGVLWVL 152 (179)
Q Consensus 137 eEA~~Ls~~PGVVSVf 152 (179)
+-+++|+++|+|+.++
T Consensus 14 ~~~~~l~~~p~V~~~~ 29 (74)
T PF01037_consen 14 EFAEALAEIPEVVECY 29 (74)
T ss_dssp HHHHHHHTSTTEEEEE
T ss_pred HHHHHHHcCCCEEEEE
Confidence 4467889999999876
Done!