Query 029233
Match_columns 197
No_of_seqs 152 out of 339
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 09:38:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029233hhsearch_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 3.9E-13 8.5E-18 95.3 5.3 77 76-156 1-81 (82)
2 PF05922 Inhibitor_I9: Peptida 95.9 0.0085 1.8E-07 42.1 3.1 30 11-40 49-78 (82)
3 cd04888 ACT_PheB-BS C-terminal 39.7 25 0.00055 23.7 2.1 16 21-36 58-73 (76)
4 cd04901 ACT_3PGDH C-terminal A 37.7 29 0.00062 23.0 2.1 17 20-36 51-67 (69)
5 cd04879 ACT_3PGDH-like ACT_3PG 35.5 33 0.00071 22.0 2.1 18 19-36 52-69 (71)
6 cd04877 ACT_TyrR N-terminal AC 31.4 39 0.00085 23.4 2.0 18 20-37 52-69 (74)
7 PF13291 ACT_4: ACT domain; PD 28.4 51 0.0011 22.9 2.2 26 11-36 49-79 (80)
8 PF03927 NapD: NapD protein; 26.1 57 0.0012 23.8 2.1 18 21-38 55-72 (79)
9 cd04902 ACT_3PGDH-xct C-termin 25.9 52 0.0011 21.8 1.8 19 18-36 51-69 (73)
10 PF00633 HHH: Helix-hairpin-he 24.1 40 0.00088 20.6 0.9 11 22-32 9-19 (30)
11 PRK10553 assembly protein for 23.7 61 0.0013 24.5 2.0 18 133-150 57-74 (87)
12 KOG2648 Diphthamide biosynthes 22.5 63 0.0014 31.5 2.3 35 8-43 84-134 (453)
13 KOG0723 Molecular chaperone (D 21.9 15 0.00032 29.4 -1.7 44 126-171 48-98 (112)
14 cd04903 ACT_LSD C-terminal ACT 21.2 77 0.0017 20.3 1.9 20 18-37 51-70 (71)
15 cd04878 ACT_AHAS N-terminal AC 20.8 87 0.0019 20.1 2.1 16 20-35 56-71 (72)
16 KOG4205 RNA-binding protein mu 20.7 1.1E+02 0.0023 28.2 3.3 51 140-195 56-107 (311)
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=99.40 E-value=3.9e-13 Score=95.32 Aligned_cols=77 Identities=18% Similarity=0.242 Sum_probs=57.8
Q ss_pred eEEEEecCCCCCCcchhhHHHHHHHHHHHHhCCc----hhcccceEEEeecceeeEEeEeCHHHHHHhcCCCCeEEEcCC
Q 029233 76 HWLVRMDKPGVGVVTKAQMVDRYAQILTKVLGNE----KDAQMCIYHVSWQSNFGFCCELDDECAQELTGVPGVLSVQPD 151 (197)
Q Consensus 76 ~YIV~M~~p~~~~~~~~~~~~sH~q~LasVLgS~----e~Ak~sI~ysYt~~f~GFAA~LTeeeA~kLs~lPGVVSVfPD 151 (197)
.|||.|+.+.... ...+.|.+|+++++.+. ......++|.|...++||+|+|+++++++|+++|+|.+|.||
T Consensus 1 ~YIV~~k~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~Gfs~~l~~~~i~~L~~~p~V~~Ve~D 76 (82)
T PF05922_consen 1 RYIVVFKDDASAA----SSFSSHKSWQASILKSALKSASSINAKVLYSYDNAFNGFSAKLSEEEIEKLRKDPGVKSVEPD 76 (82)
T ss_dssp EEEEEE-TTSTHH----CHHHHHHHHHH----HHHHTH-TTT-EEEEEESSTSSEEEEEE-HHHHHHHHTSTTEEEEEEE
T ss_pred CEEEEECCCCCcc----hhHHHHHHHHHHHHhhhhhhhcccCCceEEEEeeeEEEEEEEeCHHHHHHHHcCCCeEEEEeC
Confidence 5999999875433 25778888888776542 234567999999999999999999999999999999999999
Q ss_pred CCcCC
Q 029233 152 ENFGS 156 (197)
Q Consensus 152 ~~~~~ 156 (197)
..+++
T Consensus 77 ~~v~l 81 (82)
T PF05922_consen 77 QVVSL 81 (82)
T ss_dssp CEEEE
T ss_pred ceEec
Confidence 88754
No 2
>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=95.89 E-value=0.0085 Score=42.07 Aligned_cols=30 Identities=37% Similarity=0.591 Sum_probs=26.8
Q ss_pred eeeeEeeeChHhHHHhhcCCCeEEEccCCC
Q 029233 11 HFGFCCNVDEETSRELARLPGVLTVRPDPD 40 (197)
Q Consensus 11 ~~~f~c~i~ee~s~~l~~lpgv~~v~pd~~ 40 (197)
--||-.+++++..++|+++|+|..|.||.-
T Consensus 49 ~~Gfs~~l~~~~i~~L~~~p~V~~Ve~D~~ 78 (82)
T PF05922_consen 49 FNGFSAKLSEEEIEKLRKDPGVKSVEPDQV 78 (82)
T ss_dssp SSEEEEEE-HHHHHHHHTSTTEEEEEEECE
T ss_pred EEEEEEEeCHHHHHHHHcCCCeEEEEeCce
Confidence 569999999999999999999999999963
No 3
>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=39.69 E-value=25 Score=23.73 Aligned_cols=16 Identities=38% Similarity=0.443 Sum_probs=13.4
Q ss_pred HhHHHhhcCCCeEEEc
Q 029233 21 ETSRELARLPGVLTVR 36 (197)
Q Consensus 21 e~s~~l~~lpgv~~v~ 36 (197)
++-++|+++|||..|.
T Consensus 58 ~l~~~L~~i~~V~~v~ 73 (76)
T cd04888 58 ELLEELREIDGVEKVE 73 (76)
T ss_pred HHHHHHhcCCCeEEEE
Confidence 4567999999999885
No 4
>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=37.66 E-value=29 Score=22.99 Aligned_cols=17 Identities=41% Similarity=0.681 Sum_probs=15.4
Q ss_pred hHhHHHhhcCCCeEEEc
Q 029233 20 EETSRELARLPGVLTVR 36 (197)
Q Consensus 20 ee~s~~l~~lpgv~~v~ 36 (197)
+++-++|+++|||..|+
T Consensus 51 ~~li~~l~~~~~V~~v~ 67 (69)
T cd04901 51 EELLEALRAIPGTIRVR 67 (69)
T ss_pred HHHHHHHHcCCCeEEEE
Confidence 68889999999999986
No 5
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 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 bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli 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
Probab=35.49 E-value=33 Score=22.00 Aligned_cols=18 Identities=50% Similarity=0.804 Sum_probs=15.8
Q ss_pred ChHhHHHhhcCCCeEEEc
Q 029233 19 DEETSRELARLPGVLTVR 36 (197)
Q Consensus 19 ~ee~s~~l~~lpgv~~v~ 36 (197)
.+++-++|+++|||..|+
T Consensus 52 ~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 52 PEEVLEELKALPGIIRVR 69 (71)
T ss_pred CHHHHHHHHcCCCeEEEE
Confidence 458899999999999886
No 6
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=31.36 E-value=39 Score=23.40 Aligned_cols=18 Identities=28% Similarity=0.446 Sum_probs=15.4
Q ss_pred hHhHHHhhcCCCeEEEcc
Q 029233 20 EETSRELARLPGVLTVRP 37 (197)
Q Consensus 20 ee~s~~l~~lpgv~~v~p 37 (197)
+.+-++|+++|||..|.-
T Consensus 52 ~~li~~L~~i~gV~~V~R 69 (74)
T cd04877 52 QTLMPEIRRIDGVEDVKT 69 (74)
T ss_pred HHHHHHHhCCCCceEEEE
Confidence 567789999999999864
No 7
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=28.38 E-value=51 Score=22.92 Aligned_cols=26 Identities=27% Similarity=0.617 Sum_probs=19.4
Q ss_pred eeeeEeeeCh-----HhHHHhhcCCCeEEEc
Q 029233 11 HFGFCCNVDE-----ETSRELARLPGVLTVR 36 (197)
Q Consensus 11 ~~~f~c~i~e-----e~s~~l~~lpgv~~v~ 36 (197)
..-|.+++.. .+-.+|+++|||..|.
T Consensus 49 ~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 49 RITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 3445666654 6778999999999885
No 8
>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=26.12 E-value=57 Score=23.84 Aligned_cols=18 Identities=28% Similarity=0.427 Sum_probs=14.3
Q ss_pred HhHHHhhcCCCeEEEccC
Q 029233 21 ETSRELARLPGVLTVRPD 38 (197)
Q Consensus 21 e~s~~l~~lpgv~~v~pd 38 (197)
+.-.+|+.||||+.+-+-
T Consensus 55 ~~~~~i~~l~GVlsa~lv 72 (79)
T PF03927_consen 55 DLIDAINALPGVLSASLV 72 (79)
T ss_dssp HHHHHHCCSTTEEEEEES
T ss_pred HHHHHHHcCCCceEEEEE
Confidence 456788999999998764
No 9
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 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 bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=25.86 E-value=52 Score=21.83 Aligned_cols=19 Identities=42% Similarity=0.760 Sum_probs=16.3
Q ss_pred eChHhHHHhhcCCCeEEEc
Q 029233 18 VDEETSRELARLPGVLTVR 36 (197)
Q Consensus 18 i~ee~s~~l~~lpgv~~v~ 36 (197)
+.+++-++|++++||..|+
T Consensus 51 ~~~~~~~~l~~~~~v~~v~ 69 (73)
T cd04902 51 VPDEVLEELRALPGILSAK 69 (73)
T ss_pred CCHHHHHHHHcCCCccEEE
Confidence 4578999999999998875
No 10
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=24.05 E-value=40 Score=20.56 Aligned_cols=11 Identities=45% Similarity=0.939 Sum_probs=8.1
Q ss_pred hHHHhhcCCCe
Q 029233 22 TSRELARLPGV 32 (197)
Q Consensus 22 ~s~~l~~lpgv 32 (197)
.-++|.+||||
T Consensus 9 s~eeL~~lpGI 19 (30)
T PF00633_consen 9 SIEELMKLPGI 19 (30)
T ss_dssp SHHHHHTSTT-
T ss_pred CHHHHHhCCCc
Confidence 34689999998
No 11
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=23.66 E-value=61 Score=24.48 Aligned_cols=18 Identities=28% Similarity=0.364 Sum_probs=14.5
Q ss_pred HHHHHHhcCCCCeEEEcC
Q 029233 133 DECAQELTGVPGVLSVQP 150 (197)
Q Consensus 133 eeeA~kLs~lPGVVSVfP 150 (197)
-+...+|..+|||+|+-.
T Consensus 57 ~~~i~~I~~l~GVlsa~l 74 (87)
T PRK10553 57 LQTIESVRNVEGVLAVSL 74 (87)
T ss_pred HHHHHHHHcCCCceEEEE
Confidence 355788999999999854
No 12
>KOG2648 consensus Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]
Probab=22.53 E-value=63 Score=31.47 Aligned_cols=35 Identities=46% Similarity=0.672 Sum_probs=27.0
Q ss_pred cCceeeeEeeeChHhHHHh----------------hcCCCeEEEccCCCCCC
Q 029233 8 CDTHFGFCCNVDEETSREL----------------ARLPGVLTVRPDPDYNS 43 (197)
Q Consensus 8 ~~~~~~f~c~i~ee~s~~l----------------~~lpgv~~v~pd~~~~~ 43 (197)
-||.||=|| |||=+++-+ ..+|.|+.|..+.-+|.
T Consensus 84 aDttYGsCC-VDevaA~h~~ad~lVHyG~aCLsp~~~~~~~lYVf~~i~Idl 134 (453)
T KOG2648|consen 84 GDTTYGSCC-VDEVAAEHLDADALVHYGHACLSPIDRLPVVLYVFVDIPIDL 134 (453)
T ss_pred ecCcccccc-cchHHHhhcCCCEEEEecccccCccccCCceEEEeecccccH
Confidence 478889888 677666654 67999999999877764
No 13
>KOG0723 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=21.92 E-value=15 Score=29.43 Aligned_cols=44 Identities=25% Similarity=0.328 Sum_probs=31.1
Q ss_pred eEEeEeCHHHHHHhcCCCCeEEEcCCCC-------cCCCCcCCCCCcccCCCC
Q 029233 126 GFCCELDDECAQELTGVPGVLSVQPDEN-------FGSENKDYGGNNLQNSMV 171 (197)
Q Consensus 126 GFAA~LTeeeA~kLs~lPGVVSVfPD~~-------~~~~~k~ygg~~~~~~~~ 171 (197)
||..++|..||..|-++- -++-+++. +-....|=||.+|+-.+|
T Consensus 48 GF~~kMsr~EA~lIL~v~--~s~~k~KikeaHrriM~~NHPD~GGSPYlAsKI 98 (112)
T KOG0723|consen 48 GFEPKMSRREAALILGVT--PSLDKDKIKEAHRRIMLANHPDRGGSPYLASKI 98 (112)
T ss_pred ccccccchHHHHHHhCCC--ccccHHHHHHHHHHHHHcCCCcCCCCHHHHHHH
Confidence 999999999999987665 33333322 223678889999886654
No 14
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.19 E-value=77 Score=20.34 Aligned_cols=20 Identities=30% Similarity=0.551 Sum_probs=16.3
Q ss_pred eChHhHHHhhcCCCeEEEcc
Q 029233 18 VDEETSRELARLPGVLTVRP 37 (197)
Q Consensus 18 i~ee~s~~l~~lpgv~~v~p 37 (197)
.-+++-++|+++|||.-|+.
T Consensus 51 ~~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 51 IDEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred CCHHHHHHHHcCCCceEEEE
Confidence 34578899999999998863
No 15
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=20.85 E-value=87 Score=20.05 Aligned_cols=16 Identities=38% Similarity=0.578 Sum_probs=13.0
Q ss_pred hHhHHHhhcCCCeEEE
Q 029233 20 EETSRELARLPGVLTV 35 (197)
Q Consensus 20 ee~s~~l~~lpgv~~v 35 (197)
+++-.+|+++|||..|
T Consensus 56 ~~l~~~l~~~~~v~~v 71 (72)
T cd04878 56 EQIVKQLNKLVDVLKV 71 (72)
T ss_pred HHHHHHHhCCccEEEe
Confidence 3456899999999887
No 16
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=20.73 E-value=1.1e+02 Score=28.25 Aligned_cols=51 Identities=20% Similarity=0.255 Sum_probs=30.0
Q ss_pred cCCCCeEEEcCCCCcCCCCcCCCCCcccCCCCCCCCCCC-Cccccccceeeeccccc
Q 029233 140 TGVPGVLSVQPDENFGSENKDYGGNNLQNSMVPSDSSEA-SPTQIKTKKLFVTGIQW 195 (197)
Q Consensus 140 s~lPGVVSVfPD~~~~~~~k~ygg~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 195 (197)
+.-++|..|.-.+.++++.+.-.-.. .++|-... ....-+|||+||.||++
T Consensus 56 ~~~~~v~~vl~~~~h~~dgr~ve~k~-----av~r~~~~~~~~~~~tkkiFvGG~~~ 107 (311)
T KOG4205|consen 56 ATPEGVDAVLNARTHKLDGRSVEPKR-----AVSREDQTKVGRHLRTKKIFVGGLPP 107 (311)
T ss_pred CCCcchheeecccccccCCcccccee-----ccCcccccccccccceeEEEecCcCC
Confidence 34457777777777777666555322 22222111 11233699999999986
Done!