Query 027488
Match_columns 222
No_of_seqs 160 out of 539
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 10:40:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027488.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027488hhsearch_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 5.3E-13 1.1E-17 95.7 5.7 77 79-160 1-82 (82)
2 KOG0723 Molecular chaperone (D 29.4 11 0.00024 30.9 -1.2 45 128-174 47-98 (112)
3 COG1097 RRP4 RNA-binding prote 25.0 43 0.00092 30.7 1.6 31 148-178 123-153 (239)
4 smart00754 CHRD A domain in th 19.0 1.1E+02 0.0023 23.7 2.6 41 125-175 76-117 (118)
5 PF03927 NapD: NapD protein; 18.8 1E+02 0.0022 23.0 2.3 16 137-152 55-70 (79)
6 PRK10553 assembly protein for 16.4 1.1E+02 0.0024 23.6 2.1 16 137-152 58-73 (87)
7 COG3062 NapD Uncharacterized p 14.0 1.5E+02 0.0033 23.8 2.2 16 137-152 58-73 (94)
8 cd04888 ACT_PheB-BS C-terminal 12.6 2E+02 0.0043 19.6 2.3 14 139-152 60-73 (76)
9 PRK09929 hypothetical protein; 12.5 83 0.0018 24.8 0.4 26 126-152 16-46 (91)
10 PF01037 AsnC_trans_reg: AsnC 12.3 2.4E+02 0.0051 19.1 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=99.39 E-value=5.3e-13 Score=95.75 Aligned_cols=77 Identities=23% Similarity=0.436 Sum_probs=56.7
Q ss_pred eEEEEecCCCCCCCChhhhHHHHHHHHHHHhCCh----Hhhhcce-eeeeccceeeeecccCHHHHHHhhCCCCeEEEeC
Q 027488 79 HWLIVMEFPKDPAPTREQMIETYLNTLATVLGSM----EEAKKNM-YAFSTTTYTGFQCTVSEETSEKFKGLPGVLWVLP 153 (222)
Q Consensus 79 tYIVyMd~p~~p~~s~~~v~ssh~~~LASVLGS~----eeAk~~I-YSYs~hsfnGFAArLTeEEAekLs~~PGVVSVfP 153 (222)
.|||.|+... ......+.|.+|+++++.+. ......+ |+|. .+|+||+|+|+++++++|+++|+|.+|.|
T Consensus 1 ~YIV~~k~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~-~~~~Gfs~~l~~~~i~~L~~~p~V~~Ve~ 75 (82)
T PF05922_consen 1 RYIVVFKDDA----SAASSFSSHKSWQASILKSALKSASSINAKVLYSYD-NAFNGFSAKLSEEEIEKLRKDPGVKSVEP 75 (82)
T ss_dssp EEEEEE-TTS----THHCHHHHHHHHHH----HHHHTH-TTT-EEEEEES-STSSEEEEEE-HHHHHHHHTSTTEEEEEE
T ss_pred CEEEEECCCC----CcchhHHHHHHHHHHHHhhhhhhhcccCCceEEEEe-eeEEEEEEEeCHHHHHHHHcCCCeEEEEe
Confidence 5999998653 22335788999999876542 2234456 9999 79999999999999999999999999999
Q ss_pred CCCcccC
Q 027488 154 DSYIDVK 160 (222)
Q Consensus 154 Ds~~kLh 160 (222)
|..++||
T Consensus 76 D~~v~l~ 82 (82)
T PF05922_consen 76 DQVVSLH 82 (82)
T ss_dssp ECEEEE-
T ss_pred CceEecC
Confidence 9999886
No 2
>KOG0723 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=29.43 E-value=11 Score=30.94 Aligned_cols=45 Identities=22% Similarity=0.377 Sum_probs=32.2
Q ss_pred eeeecccCHHHHHHhhCCCCeEEEeCCCCccc-------CCCCCCCccccccee
Q 027488 128 TGFQCTVSEETSEKFKGLPGVLWVLPDSYIDV-------KNKDYGGDKYVNGEI 174 (222)
Q Consensus 128 nGFAArLTeEEAekLs~~PGVVSVfPDs~~kL-------hTk~ygG~~~~ng~~ 174 (222)
-||..+++.-||..|=++- -++-+++..+- -.+|-||.+|+-.+|
T Consensus 47 GGF~~kMsr~EA~lIL~v~--~s~~k~KikeaHrriM~~NHPD~GGSPYlAsKI 98 (112)
T KOG0723|consen 47 GGFEPKMSRREAALILGVT--PSLDKDKIKEAHRRIMLANHPDRGGSPYLASKI 98 (112)
T ss_pred cccccccchHHHHHHhCCC--ccccHHHHHHHHHHHHHcCCCcCCCCHHHHHHH
Confidence 5899999999999976655 23334444332 357999999987665
No 3
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=24.98 E-value=43 Score=30.69 Aligned_cols=31 Identities=32% Similarity=0.348 Sum_probs=29.6
Q ss_pred eEEEeCCCCcccCCCCCCCcccccceeccCC
Q 027488 148 VLWVLPDSYIDVKNKDYGGDKYVNGEIIPCT 178 (222)
Q Consensus 148 VVSVfPDs~~kLhTk~ygG~~~~ng~~~p~~ 178 (222)
|+.|.++....||+|+-|-.++.||.+|.-+
T Consensus 123 V~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~ 153 (239)
T COG1097 123 VVDVDRDGEVELTLKDEGLGKLKNGQIVKIP 153 (239)
T ss_pred EEEccCCCceEEEeecCCCccccCCEEEEEc
Confidence 8999999999999999999999999999876
No 4
>smart00754 CHRD A domain in the BMP inhibitor chordin and in microbial proteins.
Probab=19.00 E-value=1.1e+02 Score=23.70 Aligned_cols=41 Identities=22% Similarity=0.520 Sum_probs=30.2
Q ss_pred cceeeeecccCHHHHHHhhCCCCeEEEeCCCCcccCCCCCC-Ccccccceec
Q 027488 125 TTYTGFQCTVSEETSEKFKGLPGVLWVLPDSYIDVKNKDYG-GDKYVNGEII 175 (222)
Q Consensus 125 hsfnGFAArLTeEEAekLs~~PGVVSVfPDs~~kLhTk~yg-G~~~~ng~~~ 175 (222)
..+.|....|++++++.|.. | +-++.+||++|= |+ |-|.|+
T Consensus 76 ~~~~g~~~~l~~~~l~~l~~--g------~~yvnvhT~~~p~Ge--IRGqi~ 117 (118)
T smart00754 76 GPFAGSVKTLTDEELRQLLA--G------NLYVNVHTKANPGGE--IRGQVA 117 (118)
T ss_pred ceeccccccCCHHHHHHHhc--C------CeEEEeecccCCCce--EeeEEc
Confidence 45677777999999999988 3 556789999874 44 555553
No 5
>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=18.79 E-value=1e+02 Score=23.03 Aligned_cols=16 Identities=31% Similarity=0.511 Sum_probs=12.6
Q ss_pred HHHHHhhCCCCeEEEe
Q 027488 137 ETSEKFKGLPGVLWVL 152 (222)
Q Consensus 137 EEAekLs~~PGVVSVf 152 (222)
+..++|+.+|||+++-
T Consensus 55 ~~~~~i~~l~GVlsa~ 70 (79)
T PF03927_consen 55 DLIDAINALPGVLSAS 70 (79)
T ss_dssp HHHHHHCCSTTEEEEE
T ss_pred HHHHHHHcCCCceEEE
Confidence 3456788999999985
No 6
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=16.37 E-value=1.1e+02 Score=23.59 Aligned_cols=16 Identities=38% Similarity=0.466 Sum_probs=13.0
Q ss_pred HHHHHhhCCCCeEEEe
Q 027488 137 ETSEKFKGLPGVLWVL 152 (222)
Q Consensus 137 EEAekLs~~PGVVSVf 152 (222)
+..+.|..+|||++|-
T Consensus 58 ~~i~~I~~l~GVlsa~ 73 (87)
T PRK10553 58 QTIESVRNVEGVLAVS 73 (87)
T ss_pred HHHHHHHcCCCceEEE
Confidence 4567888999999985
No 7
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=14.00 E-value=1.5e+02 Score=23.76 Aligned_cols=16 Identities=56% Similarity=0.738 Sum_probs=12.5
Q ss_pred HHHHHhhCCCCeEEEe
Q 027488 137 ETSEKFKGLPGVLWVL 152 (222)
Q Consensus 137 EEAekLs~~PGVVSVf 152 (222)
+..+.++.+|||++|.
T Consensus 58 ~tie~i~nl~gVlav~ 73 (94)
T COG3062 58 ETIESIRNLPGVLAVS 73 (94)
T ss_pred HHHHHHhcCCceeEEE
Confidence 4456688999999986
No 8
>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=12.57 E-value=2e+02 Score=19.57 Aligned_cols=14 Identities=29% Similarity=0.311 Sum_probs=11.9
Q ss_pred HHHhhCCCCeEEEe
Q 027488 139 SEKFKGLPGVLWVL 152 (222)
Q Consensus 139 AekLs~~PGVVSVf 152 (222)
.++|+++|||.+|.
T Consensus 60 ~~~L~~i~~V~~v~ 73 (76)
T cd04888 60 LEELREIDGVEKVE 73 (76)
T ss_pred HHHHhcCCCeEEEE
Confidence 57899999999884
No 9
>PRK09929 hypothetical protein; Provisional
Probab=12.48 E-value=83 Score=24.81 Aligned_cols=26 Identities=8% Similarity=0.247 Sum_probs=17.7
Q ss_pred ceeeeecc-cCHHHHH----HhhCCCCeEEEe
Q 027488 126 TYTGFQCT-VSEETSE----KFKGLPGVLWVL 152 (222)
Q Consensus 126 sfnGFAAr-LTeEEAe----kLs~~PGVVSVf 152 (222)
+|.-|||. ++.+|++ .|.++ |+|+|-
T Consensus 16 S~~A~AA~~i~~~qa~~~~~~l~ki-GtVSvs 46 (91)
T PRK09929 16 VTNVYAAELMTKAEFEKVESQYEKI-GTISTS 46 (91)
T ss_pred chhhhhhhhhCHHHhhhhhccccee-EEEEEc
Confidence 35568875 7777764 35566 888885
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=12.33 E-value=2.4e+02 Score=19.10 Aligned_cols=16 Identities=25% Similarity=0.356 Sum_probs=13.1
Q ss_pred HHHHHhhCCCCeEEEe
Q 027488 137 ETSEKFKGLPGVLWVL 152 (222)
Q Consensus 137 EEAekLs~~PGVVSVf 152 (222)
+-+++|+++|+|+.++
T Consensus 14 ~~~~~l~~~p~V~~~~ 29 (74)
T PF01037_consen 14 EFAEALAEIPEVVECY 29 (74)
T ss_dssp HHHHHHHTSTTEEEEE
T ss_pred HHHHHHHcCCCEEEEE
Confidence 4567899999999886
Done!