Query psy7121
Match_columns 79
No_of_seqs 105 out of 159
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 18:40:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7121hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3169|consensus 100.0 3.4E-34 7.5E-39 210.6 5.6 69 10-78 56-124 (208)
2 PF04934 Med6: MED6 mediator s 100.0 4.1E-34 8.9E-39 198.0 -1.7 71 8-78 52-122 (140)
3 COG5097 MED6 RNA polymerase II 99.9 3.8E-24 8.2E-29 157.0 5.2 69 10-78 59-127 (210)
4 PF13162 DUF3997: Protein of u 73.7 4.8 0.0001 27.5 3.2 26 32-57 45-79 (115)
5 PF01144 CoA_trans: Coenzyme A 63.5 11 0.00023 26.6 3.3 35 13-47 131-165 (217)
6 PF00278 Orn_DAP_Arg_deC: Pyri 62.0 5.7 0.00012 25.0 1.6 32 35-66 6-37 (116)
7 PRK13813 orotidine 5'-phosphat 35.4 29 0.00063 24.3 1.9 20 51-70 186-205 (215)
8 cd06911 VirB9_CagX_TrbG VirB9/ 33.2 27 0.0006 21.6 1.3 31 29-59 37-67 (86)
9 PRK00230 orotidine 5'-phosphat 32.7 36 0.00078 24.7 2.0 21 50-70 200-220 (230)
10 PF12924 APP_Cu_bd: Copper-bin 30.5 24 0.00051 21.7 0.7 11 15-25 45-55 (58)
11 smart00344 HTH_ASNC helix_turn 30.1 75 0.0016 19.6 3.0 29 8-36 77-105 (108)
12 PF05922 Inhibitor_I9: Peptida 29.5 27 0.0006 20.3 0.8 16 10-25 59-74 (82)
13 PF06962 rRNA_methylase: Putat 28.2 62 0.0013 22.6 2.5 29 10-38 105-140 (140)
14 PF00403 HMA: Heavy-metal-asso 25.3 1.2E+02 0.0026 16.8 3.0 30 9-38 14-43 (62)
15 PF07660 STN: Secretin and Ton 22.5 1.4E+02 0.0031 16.1 2.9 26 10-39 27-52 (52)
16 PF03524 CagX: Conjugal transf 21.5 48 0.001 23.5 1.0 31 30-60 167-197 (214)
17 KOG2239|consensus 21.4 88 0.0019 23.7 2.4 27 14-40 77-103 (209)
18 PF00173 Cyt-b5: Cytochrome b5 20.2 1E+02 0.0023 17.7 2.1 17 48-64 12-28 (76)
19 PF01037 AsnC_trans_reg: AsnC 20.1 1.8E+02 0.0039 16.3 3.1 31 8-38 12-42 (74)
No 1
>KOG3169|consensus
Probab=100.00 E-value=3.4e-34 Score=210.64 Aligned_cols=69 Identities=52% Similarity=0.961 Sum_probs=66.9
Q ss_pred hhhhhcccCcceeEEEeecCCCceEEEEEeeecCCCCceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121 10 HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTG 78 (79)
Q Consensus 10 ~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~ 78 (79)
.++++|.+|+||||+|.|++||.|||||||+|+++++++|||+||||||+||||||+|+|++|||++|+
T Consensus 56 ~~~e~L~~m~GieYvl~~~~~P~LfVIrKQ~R~n~tev~PLa~YYII~g~VYqAPd~ysiv~sRml~a~ 124 (208)
T KOG3169|consen 56 DLEEHLFSMVGIEYVLLHSREPILFVIRKQRRHNPTEVIPLADYYIINGNVYQAPDLYSIVQSRMLNAV 124 (208)
T ss_pred chHHHHhhCcCeEEEEEecCCCeEEEEehhhcCCCccceeeeeEEEECceeeeCccHHHHHHHHHHHHH
Confidence 368999999999999999999999999999999999999999999999999999999999999999874
No 2
>PF04934 Med6: MED6 mediator sub complex component; InterPro: IPR007018 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Regulation of mRNA synthesis requires intermediary proteins that transduce regulatory signals from upstream transcriptional activator proteins to basal transcription machinery at the core promoter. Three types of intermediary factors that enable the basal transcription machinery to respond to transcriptional activator proteins bound to regulatory DNA sequences have been identified: (i) TAFIIs, which associate with TATA-binding protein (TBP) to form TFIID; (ii) mediator, which associates with RNA polymerase II to form a holo-polymerase; and (iii) coactivators such as human upstream stimulatory activity (USA), mammalian CBP/P300, yeast ADA complex, and HMG proteins. The interaction of these multiprotein complexes with activators and general transcription factors is essential for transcriptional regulation. This family of proteins represent the transcriptional mediator protein subunit 6 that is required for activation of many RNA polymerase II promoters and which are conserved from yeast to humans []..; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3RJ1_N.
Probab=99.97 E-value=4.1e-34 Score=197.97 Aligned_cols=71 Identities=52% Similarity=0.820 Sum_probs=18.0
Q ss_pred hhhhhhhcccCcceeEEEeecCCCceEEEEEeeecCCCCceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121 8 VLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTG 78 (79)
Q Consensus 8 ~~~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~ 78 (79)
...++++|++|+|+||+|+|++||+|||||||+|++|++++|+|+|||+||+||||||+++|++|||++++
T Consensus 52 ~~~~~~~L~~m~GiEY~l~~~~eP~l~vI~Kq~r~~~~~~~~la~YYIi~g~IYqAPsl~~vl~sRl~~~~ 122 (140)
T PF04934_consen 52 REAFEQQLRNMKGIEYVLAHVQEPGLFVIRKQRRQSPDEVTPLAYYYIINGNIYQAPSLYSVLSSRLLSAV 122 (140)
T ss_dssp SHHHHHTTTS--------------------------------------------------SSSSSTTTHHH
T ss_pred hHHHHHHHhhcCCeEEEEeccCCCCEEEEEEeeccCCCcceEeEEEEEECCEEEeCCCHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999999864
No 3
>COG5097 MED6 RNA polymerase II transcriptional regulation mediator [Transcription]
Probab=99.90 E-value=3.8e-24 Score=157.01 Aligned_cols=69 Identities=29% Similarity=0.416 Sum_probs=66.6
Q ss_pred hhhhhcccCcceeEEEeecCCCceEEEEEeeecCCCCceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121 10 HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTG 78 (79)
Q Consensus 10 ~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~ 78 (79)
+++++|+...|++||+.|.+||.|||||||+|+..++++|+.+|||+|.||||||+.|+++.+||++++
T Consensus 59 ql~~~l~~l~g~~~V~ss~rep~lwVIrKq~r~n~~e~~pl~~Y~i~g~NIY~aPt~y~i~~~Rm~~s~ 127 (210)
T COG5097 59 QLSKLLSMLGGFYEVESSNREPTLWVIRKQYRHNDTEETPLMYYIIHGHNIYAAPTNYSIYRCRMGDSM 127 (210)
T ss_pred HHHHHHHhccCEEEEEecCCCCcEEEEehhhhcCCcccccceEEEEecCceeeCcchhhhhhhhhhhhH
Confidence 578899999999999999999999999999999999999999999999999999999999999999874
No 4
>PF13162 DUF3997: Protein of unknown function (DUF3997)
Probab=73.72 E-value=4.8 Score=27.50 Aligned_cols=26 Identities=27% Similarity=0.441 Sum_probs=17.0
Q ss_pred ceEEEEEee-ecCCCCce--------eeeEEEEec
Q psy7121 32 ILYVIRKQH-RHSMEQTT--------PIADYYIIA 57 (79)
Q Consensus 32 ~lfVIrKq~-R~sp~~~~--------~la~YYIi~ 57 (79)
+.|||+||. ..+.+... .+..||||+
T Consensus 45 d~yIiaKq~p~~~~d~~~~~~~~~~~~~e~Y~IId 79 (115)
T PF13162_consen 45 DDYIIAKQKPEIKSDPNNPKSYIYNKSSEEYWIID 79 (115)
T ss_pred CeeEEEEccccccCCCCCccceeccCCCceEEEEE
Confidence 599999999 54433222 233699994
No 5
>PF01144 CoA_trans: Coenzyme A transferase; InterPro: IPR004165 Coenzyme A (CoA) transferases belong to an evolutionary conserved [, ] family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. They have been identified in many prokaryotes and in mammalian tissues. The bacterial enzymes are heterodimer of two subunits (A and B) of about 25 Kd each while eukaryotic SCOT consist of a single chain which is colinear with the two bacterial subunits.; GO: 0008410 CoA-transferase activity, 0008152 metabolic process; PDB: 3DLX_C 1K6D_A 3OXO_H 1M3E_D 3K6M_C 2NRC_A 1OOY_B 1O9L_C 1OOZ_A 1OPE_B ....
Probab=63.47 E-value=11 Score=26.64 Aligned_cols=35 Identities=17% Similarity=0.298 Sum_probs=29.7
Q ss_pred hhcccCcceeEEEeecCCCceEEEEEeeecCCCCc
Q psy7121 13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQT 47 (79)
Q Consensus 13 ~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~ 47 (79)
.++..+.|-++++..+..|++|+||-+.+....++
T Consensus 131 ~~~~~~~G~~~l~~~a~~~dva~i~~~~ad~~gnv 165 (217)
T PF01144_consen 131 VRLPGFGGAEYLAVPAIRPDVAIIHHQKADFVGNV 165 (217)
T ss_dssp SEEEEETTEEEEEEESTSEEEEEEECEEEETTSSE
T ss_pred eeeeccCCcEEEEecCCccEEEEEEEcccCCcCeE
Confidence 47788899999999999999999999998765443
No 6
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=62.03 E-value=5.7 Score=24.96 Aligned_cols=32 Identities=22% Similarity=0.314 Sum_probs=18.0
Q ss_pred EEEEeeecCCCCceeeeEEEEecCeEeeCCCh
Q psy7121 35 VIRKQHRHSMEQTTPIADYYIIAGVVYQAPDL 66 (79)
Q Consensus 35 VIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l 66 (79)
||.|+.+...+....-..++++|+.+|++++.
T Consensus 6 Vi~~k~~~~~~~~~~~~~~~~vd~G~~~~~~~ 37 (116)
T PF00278_consen 6 VIGVKRRRDSDLKNKKRRWYYVDDGVYGSFDP 37 (116)
T ss_dssp EEEEEEETT---HCTTEEEEEESS-TTTCCHH
T ss_pred EEEEEEcCCCccccceeeEEEEeCChhhChHH
Confidence 66676666533222233456699999999654
No 7
>PRK13813 orotidine 5'-phosphate decarboxylase; Provisional
Probab=35.45 E-value=29 Score=24.30 Aligned_cols=20 Identities=35% Similarity=0.584 Sum_probs=17.0
Q ss_pred eEEEEecCeEeeCCChHHHH
Q psy7121 51 ADYYIIAGVVYQAPDLASVI 70 (79)
Q Consensus 51 a~YYIi~g~VYQAP~l~~vl 70 (79)
++++|+|.+|+|+||....+
T Consensus 186 ad~iV~Gr~I~~~~d~~~~~ 205 (215)
T PRK13813 186 ADYVIVGRSIYNAADPREAA 205 (215)
T ss_pred CCEEEECcccCCCCCHHHHH
Confidence 78999999999999965544
No 8
>cd06911 VirB9_CagX_TrbG VirB9/CagX/TrbG, a component of the type IV secretion system. VirB9 is a component of the type IV secretion system, which is employed by pathogenic bacteria to export virulence proteins directly from the bacterial cytoplasm into the host cell. Unlike the more common type III secretion system, type IV systems evolved from the conjugative apparatus, which is used to transfer DNA between cells. VirB9 was initially identified as an essential virulence gene on the Agrobacterium tumefaciens Ti plasmid. In the pilin-like conjugative structure, VirB9 appears to form a stabilizing complex in the outer membrane, by interacting with the lipoprotein VirB7. The heterodimer has been shown to stabilize other components of the type IV system. This alignment model spans the C-terminal domain of VirB9. CagX is a component of the Helicobacter pylori cag PAI-encoded type IV secretion system. Some other members of this family are involved in conjugal transfer to T-DNA of plant cells
Probab=33.21 E-value=27 Score=21.61 Aligned_cols=31 Identities=19% Similarity=0.481 Sum_probs=20.1
Q ss_pred CCCceEEEEEeeecCCCCceeeeEEEEecCe
Q psy7121 29 QEPILYVIRKQHRHSMEQTTPIADYYIIAGV 59 (79)
Q Consensus 29 ~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~ 59 (79)
.-|.+|++......+.-+......|||+++.
T Consensus 37 ~~Pavf~~~~~g~~~lvn~~~~~~~~vV~~v 67 (86)
T cd06911 37 ELPAIFVVDPDGKESLVNYRVEGNYIVVDGV 67 (86)
T ss_pred CCCcEEEECCCCCEEeceeEEECCEEEEecc
Confidence 3578998876534444455556678888765
No 9
>PRK00230 orotidine 5'-phosphate decarboxylase; Reviewed
Probab=32.66 E-value=36 Score=24.73 Aligned_cols=21 Identities=29% Similarity=0.385 Sum_probs=17.9
Q ss_pred eeEEEEecCeEeeCCChHHHH
Q psy7121 50 IADYYIIAGVVYQAPDLASVI 70 (79)
Q Consensus 50 la~YYIi~g~VYQAP~l~~vl 70 (79)
-++|-|+|.+||||++-....
T Consensus 200 Gad~iVvGR~I~~a~dP~~~a 220 (230)
T PRK00230 200 GSDYIVVGRPITQAADPAAAY 220 (230)
T ss_pred CCCEEEECCcccCCCCHHHHH
Confidence 479999999999999976654
No 10
>PF12924 APP_Cu_bd: Copper-binding of amyloid precursor, CuBD; InterPro: IPR011178 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. This entry represents a copper-binding domain found within the extracellular domain, which is at the N-terminal of amyloidogenic glycoproteins such as amyloid-beta precursor protein (APP, or A4). The copper-binding domain has a dodecin-like fold consisting of a 2-layer alpha/beta topology []. More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein [].; GO: 0005488 binding, 0016021 integral to membrane; PDB: 3KTM_E 2FK3_D 2FK1_A 2FMA_A 2FJZ_A 2FKL_A 1OWT_A 2FK2_A.
Probab=30.48 E-value=24 Score=21.74 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=8.8
Q ss_pred cccCcceeEEE
Q psy7121 15 ILNMTGLEYIV 25 (79)
Q Consensus 15 L~~m~GiEy~l 25 (79)
+..+.|+|||=
T Consensus 45 ~D~F~GvEfVC 55 (58)
T PF12924_consen 45 IDRFRGVEFVC 55 (58)
T ss_dssp TTEEEEEEEEE
T ss_pred cccccceeEec
Confidence 56789999984
No 11
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=30.12 E-value=75 Score=19.59 Aligned_cols=29 Identities=7% Similarity=-0.003 Sum_probs=24.2
Q ss_pred hhhhhhhcccCcceeEEEeecCCCceEEE
Q psy7121 8 VLHVQEPILNMTGLEYIVLHVQEPILYVI 36 (79)
Q Consensus 8 ~~~~~~~L~~m~GiEy~l~~~~eP~lfVI 36 (79)
.+.+.+.|++++++.++-.-.-++++|+.
T Consensus 77 ~~~v~~~l~~~p~v~~~~~~~G~~d~~~~ 105 (108)
T smart00344 77 LEEFLEKLEKLPEVVEVYLVTGDYDYLLK 105 (108)
T ss_pred HHHHHHHHhCCcceEEeeEecCCCCEEEE
Confidence 35788899999999999887888888765
No 12
>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=29.49 E-value=27 Score=20.26 Aligned_cols=16 Identities=13% Similarity=0.148 Sum_probs=13.4
Q ss_pred hhhhhcccCcceeEEE
Q psy7121 10 HVQEPILNMTGLEYIV 25 (79)
Q Consensus 10 ~~~~~L~~m~GiEy~l 25 (79)
..-++|++++||+|+.
T Consensus 59 ~~i~~L~~~p~V~~Ve 74 (82)
T PF05922_consen 59 EEIEKLRKDPGVKSVE 74 (82)
T ss_dssp HHHHHHHTSTTEEEEE
T ss_pred HHHHHHHcCCCeEEEE
Confidence 4458899999999986
No 13
>PF06962 rRNA_methylase: Putative rRNA methylase; InterPro: IPR010719 This family contains a number of putative rRNA methylases.; PDB: 3EEY_H 3LBY_A 3MTI_A.
Probab=28.19 E-value=62 Score=22.64 Aligned_cols=29 Identities=31% Similarity=0.498 Sum_probs=19.5
Q ss_pred hhhhhcccCcceeEEEeec-------CCCceEEEEE
Q psy7121 10 HVQEPILNMTGLEYIVLHV-------QEPILYVIRK 38 (79)
Q Consensus 10 ~~~~~L~~m~GiEy~l~~~-------~eP~lfVIrK 38 (79)
.+++-+++..--+|.|.+. .||.+++|+|
T Consensus 105 av~~~~~~L~~~~~~V~~~~~~N~~~~pp~l~~ieK 140 (140)
T PF06962_consen 105 AVEEFLASLDQKEFNVLKYQFINQKNNPPLLVIIEK 140 (140)
T ss_dssp HHHHHHHTS-TTTEEEEEEEESS-SS---EEEEEEE
T ss_pred HHHHHHHhCCcceEEEEEEEccCCCCCCCEEEEEEC
Confidence 6677788888888888773 4677888877
No 14
>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=25.28 E-value=1.2e+02 Score=16.82 Aligned_cols=30 Identities=10% Similarity=0.273 Sum_probs=23.0
Q ss_pred hhhhhhcccCcceeEEEeecCCCceEEEEE
Q psy7121 9 LHVQEPILNMTGLEYIVLHVQEPILYVIRK 38 (79)
Q Consensus 9 ~~~~~~L~~m~GiEy~l~~~~eP~lfVIrK 38 (79)
..++..|++++|++-+-+....-.+-|.-.
T Consensus 14 ~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~ 43 (62)
T PF00403_consen 14 KKVEKALSKLPGVKSVKVDLETKTVTVTYD 43 (62)
T ss_dssp HHHHHHHHTSTTEEEEEEETTTTEEEEEES
T ss_pred HHHHHHHhcCCCCcEEEEECCCCEEEEEEe
Confidence 467899999999998888776666666543
No 15
>PF07660 STN: Secretin and TonB N terminus short domain; InterPro: IPR011662 This is a conserved region found at the N-terminal region of bacterial proteins involved in either protein secretion or the uptake of selective substrates, including: Bundle-forming pilus protein B, an outer-membrane protein absolutely required for pilus biogenesis, and for enteropathogenic Escherichia coli localized adherence and autoaggregation []. PilQ, which is required for type IV pilus biogenesis and competence and is thought to function both as a pore for exit of the pilus and as a channel for entry of haem and antimicrobial agents and uptake of transforming DNA []. PupB, a specific receptor for the siderophores ferric pseudobactin BN8 and ferric pseudobactin BN7, iron chelating molecules that allow the organism to extract iron from the environment, especially under iron-restricted conditions []. TonB, which couples the electrochemical potential of the cytoplasmic membrane to the active transport of iron-siderophores and vitamin B12 across the outer membrane []. ; GO: 0019867 outer membrane; PDB: 2D1U_A 1ZZV_A 2W75_B 2O5P_A 2W77_A 2W16_A 2W6U_B 2W6T_A 2W76_B 2W78_B ....
Probab=22.53 E-value=1.4e+02 Score=16.14 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=17.3
Q ss_pred hhhhhcccCcceeEEEeecCCCceEEEEEe
Q psy7121 10 HVQEPILNMTGLEYIVLHVQEPILYVIRKQ 39 (79)
Q Consensus 10 ~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq 39 (79)
..-++|-+-+|+.|.+ ....++|+++
T Consensus 27 ~~L~~ll~~t~l~y~~----~~~~i~I~~k 52 (52)
T PF07660_consen 27 EALDQLLKGTGLTYKI----SGNTIVISPK 52 (52)
T ss_dssp HHHHHHTTTSTEEEEE----ETTEEEEEE-
T ss_pred HHHHHHHccCCcEEEE----ECCEEEEEEC
Confidence 3445666779999998 3456777664
No 16
>PF03524 CagX: Conjugal transfer protein; InterPro: IPR010258 Several bacterial pathogens utilise conjugation machines to export effector molecules during infection. Such systems are members of the type IV or 'adapted conjugation' secretion family. The prototypical type IV system is the Agrobacterium tumefaciens T-DNA transfer machine, which delivers oncogenic nucleoprotein particles to plant cells. Other pathogens, including Bordetella pertussis, Legionella pneumophila, Brucella spp. and Helicobacter pylori (Campylobacter pylori), use type IV machines to export effector proteins to the extracellular milieu or the mammalian cell cytosol. Conjugation machines of Gram-negative bacteria consist of two surface structures, the mating channel through which the DNA transfer intermediate and proteins are translocated and the conjugal pilus for contacting recipient cells. Various conjugative pili have been visualised, but to date there is no ultrastructural information about the mating channel. Recent work on the A. tumefaciens T-DNA transfer system has focused on identifying interactions among the VirB protein subunits and defining steps in the transporter assembly pathway. There are three functional groups of VirB proteins: proteins localised exocellularly forming the T-pilus or other adhesive structures; mating-channel components; and cytoplasmic membrane ATPases. Although all of these proteins probably assemble as a supramolecular complex, as yet there is no direct evidence for a physical association between the conjugative pilus and the mating channel. Several lines of evidence suggest that VirB6-VirB10 are probable channel subunits. VirB6, a highly hydrophobic protein, is thought to span the cytoplasmic membrane several times and presently is the best candidate for a channel-forming protein. VirB7, an outer membrane lipoprotein, interacts with itself and with VirB9 via disulphide bonds between unique reactive cysteines present in each protein. The VirB7-VirB9 heterodimer localises at the outer membrane and plays a critical role in stabilising other VirB proteins during assembly of the transfer machine. VirB9 is also required for formation of chemically crosslinked VirB10 oligomers probably corresponding to homotrimers [].; PDB: 3JQO_i 2OFQ_A.
Probab=21.54 E-value=48 Score=23.50 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=16.7
Q ss_pred CCceEEEEEeeecCCCCceeeeEEEEecCeE
Q psy7121 30 EPILYVIRKQHRHSMEQTTPIADYYIIAGVV 60 (79)
Q Consensus 30 eP~lfVIrKq~R~sp~~~~~la~YYIi~g~V 60 (79)
-|.+|++......+.-+...-..|||+++..
T Consensus 167 ~Pavf~~~~dg~~~lvn~~~~~~~~vV~~v~ 197 (214)
T PF03524_consen 167 LPAVFVVDPDGKESLVNYRVKGNYYVVDRVA 197 (214)
T ss_dssp --EEEEE-TTSSEE---EEEES-EEEESS--
T ss_pred CCeEEEECCCCCEEeeeeEEECCEEEEeecC
Confidence 4789998876656666666677888888753
No 17
>KOG2239|consensus
Probab=21.45 E-value=88 Score=23.73 Aligned_cols=27 Identities=26% Similarity=0.487 Sum_probs=22.4
Q ss_pred hcccCcceeEEEeecCCCceEEEEEee
Q psy7121 14 PILNMTGLEYIVLHVQEPILYVIRKQH 40 (79)
Q Consensus 14 ~L~~m~GiEy~l~~~~eP~lfVIrKq~ 40 (79)
-|+.++||.=|.+..--..||||-|-.
T Consensus 77 Glk~v~gV~RVti~ksKNilfvI~kPd 103 (209)
T KOG2239|consen 77 GLKQVTGVTRVTIRKSKNILFVITKPD 103 (209)
T ss_pred CCccccceeEEEEEecccEEEEecCCc
Confidence 488999999988777778899998743
No 18
>PF00173 Cyt-b5: Cytochrome b5-like Heme/Steroid binding domain This prints entry is a subset of the Pfam entry; InterPro: IPR001199 Cytochromes b5 are ubiquitous electron transport proteins found in animals, plants and yeasts []. The microsomal and mitochondrial variants are membrane-bound, while those from erythrocytes and other animal tissues are water-soluble [, ]. The 3D structure of bovine cyt b5 is known, the fold belonging to the alpha+beta class, with 5 strands and 5 short helices forming a framework for supporting a central haem group []. The cytochrome b5 domain is similar to that of a number of oxidoreductases, such as plant and fungal nitrate reductases, sulphite oxidase, yeast flavocytochrome b2 (L-lactate dehydrogenase) and plant cyt b5/acyl lipid desaturase fusion protein.; GO: 0020037 heme binding; PDB: 2I96_A 3KS0_A 1KBI_B 1KBJ_B 1LTD_A 1SZG_B 1SZF_A 1LDC_B 2OZ0_B 1LCO_A ....
Probab=20.15 E-value=1e+02 Score=17.67 Aligned_cols=17 Identities=29% Similarity=0.382 Sum_probs=12.3
Q ss_pred eeeeEEEEecCeEeeCC
Q psy7121 48 TPIADYYIIAGVVYQAP 64 (79)
Q Consensus 48 ~~la~YYIi~g~VYQAP 64 (79)
..-..|.+++|+||=..
T Consensus 12 ~~~~~~v~i~g~VYDvt 28 (76)
T PF00173_consen 12 KKGDCWVIIDGKVYDVT 28 (76)
T ss_dssp ETTEEEEEETTEEEECT
T ss_pred CCCCEEEEECCEEcccc
Confidence 44567889999999443
No 19
>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=20.12 E-value=1.8e+02 Score=16.25 Aligned_cols=31 Identities=10% Similarity=-0.065 Sum_probs=24.0
Q ss_pred hhhhhhhcccCcceeEEEeecCCCceEEEEE
Q psy7121 8 VLHVQEPILNMTGLEYIVLHVQEPILYVIRK 38 (79)
Q Consensus 8 ~~~~~~~L~~m~GiEy~l~~~~eP~lfVIrK 38 (79)
...|.+.|++++++..+-.-+-+.++++.-.
T Consensus 12 ~~~~~~~l~~~p~V~~~~~vtG~~d~~~~v~ 42 (74)
T PF01037_consen 12 YDEFAEALAEIPEVVECYSVTGEYDLILKVR 42 (74)
T ss_dssp HHHHHHHHHTSTTEEEEEEESSSSSEEEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEeCCCCEEEEEE
Confidence 4578999999999998877777777666543
Done!