Query 028452
Match_columns 208
No_of_seqs 108 out of 516
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 11:43:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028452.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028452hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01222 ERG4_ERG24: Ergostero 100.0 1.2E-55 2.6E-60 408.7 17.8 175 29-204 65-245 (432)
2 KOG1435 Sterol reductase/lamin 100.0 1.1E-50 2.4E-55 369.1 13.7 184 20-204 55-242 (428)
3 PF03967 PRCH: Photosynthetic 28.2 83 0.0018 25.3 3.6 44 31-74 11-54 (136)
4 PF07330 DUF1467: Protein of u 20.9 3.5E+02 0.0076 19.9 5.8 7 47-53 17-23 (85)
5 PF05499 DMAP1: DNA methyltran 15.6 1.2E+02 0.0025 25.6 2.1 41 146-187 117-157 (176)
6 PF02655 ATP-grasp_3: ATP-gras 15.0 59 0.0013 25.9 0.2 21 135-155 133-159 (161)
7 PF08935 VP4_2: Viral protein 13.8 73 0.0016 23.4 0.4 19 132-150 13-31 (80)
8 PF13535 ATP-grasp_4: ATP-gras 13.7 66 0.0014 25.0 0.2 11 146-156 171-181 (184)
9 PF12412 DUF3667: Protein of u 13.7 84 0.0018 20.3 0.7 33 50-85 12-44 (46)
10 TIGR01150 puhA photosynthetic 13.6 2.9E+02 0.0064 24.5 4.1 33 32-64 12-44 (252)
No 1
>PF01222 ERG4_ERG24: Ergosterol biosynthesis ERG4/ERG24 family; InterPro: IPR001171 The two fungal enzymes, C-14 sterol reductase (gene ERG24 in budding yeast and erg3 in Neurospora crassa) and C-24(28) sterol reductase (gene ERG4 in budding yeast and sts1 in fission yeast), are involved in ergosterol biosynthesis. They act by reducing double bonds in precursors of ergosterol []. These proteins are highly hydrophobic and seem to contain seven or eight transmembrane regions. Chicken lamin B receptor that is thought to anchor the lamina to the inner nuclear membrane belongs to this family.; GO: 0016020 membrane
Probab=100.00 E-value=1.2e-55 Score=408.67 Aligned_cols=175 Identities=41% Similarity=0.733 Sum_probs=168.7
Q ss_pred CCcHHHHHHHHHHHHHHHHHHhhCCcceeeCcCCCCCCCcccccchhHHHHHHHHHHHHHHHhcccccceehhhHHHHHH
Q 028452 29 IPTAVAWKLIACFGAFEAALQLLLPGKRVEGPISPTGHRPVYKANGVASYAVTLITYLSLWWFGIFNPTIVYDHLGEIYS 108 (208)
Q Consensus 29 ~~t~~a~~~y~~~~~~q~lL~~~lPG~~v~G~~~~~G~rl~Yk~NGl~~~~~t~~~~~~~~~~~~~~~~~i~d~~~~ll~ 108 (208)
.||+++|++|++|+++|++++.++|||+++|+++|+|+|++|||||++++++|+++++++++.+++++++|+|||+++++
T Consensus 65 ~~~~~a~~~~~~~~~~qa~l~~~lPG~~v~G~~l~~G~rL~Yk~NGl~~~~~tl~~~~~l~~~~~~~~~~i~d~~~~L~~ 144 (432)
T PF01222_consen 65 LWDWEAWKVYLAWFAFQALLYLVLPGKRVEGPPLPDGKRLKYKCNGLQSFLVTLALFAVLHYYGIFPLTFIYDHFGQLLT 144 (432)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCceEEECcCcCCCCcccEEeCCHHHHHHHHHHHHHHHHcCCCChHhHHHHHHHHHH
Confidence 37899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcccCCCC------CCCCCCCChhhhhhcCcccCCccccceecccccccchhHHHHHHHHHHHHH
Q 028452 109 ALIFGSFIFCIFLYIKGHLAPSS------TDSGSCGNIIIDFYWGMELYPRIGKNFDIKVFTNCRFGMMSWAVLAVTYCI 182 (208)
Q Consensus 109 a~~i~s~~~s~~lyvk~~~~p~~------~~~g~sGn~iyDff~G~ELNPRig~~~DlK~f~e~R~g~i~w~li~ls~a~ 182 (208)
+++++|+++|+++|+||+..|+. +++++|||++|||||||||||||| ++|+|+|+|+|||||+|.++|+|+|+
T Consensus 145 ~~~i~s~~~s~~lyik~~~~~~~~~d~~l~~~~~sGn~iyDff~G~ELNPRig-~~DlK~F~e~R~gli~w~li~ls~a~ 223 (432)
T PF01222_consen 145 AANIFSFILSIFLYIKSFRAPSHPKDRQLAPGGNSGNFIYDFFMGRELNPRIG-GFDLKMFCELRPGLIGWLLINLSFAA 223 (432)
T ss_pred HHHHHHHHHHHHHHHhhhccCCccccccccccCCCCceeeeeeeccccCCCee-eEeeeeeeccChHHHHHHHHHHHHHH
Confidence 99999999999999999999872 368999999999999999999999 89999999999999999999999999
Q ss_pred HHHHhcCCCCHHHHHHHHHhcc
Q 028452 183 KQFCSHCFLTCELKAWCVQVGM 204 (208)
Q Consensus 183 kQye~~G~vt~~~~~~~~~~~~ 204 (208)
||||++|++|+||++++++|.+
T Consensus 224 ~qye~~G~vs~sm~~~~~~~~~ 245 (432)
T PF01222_consen 224 KQYEQYGYVSPSMILVVLLQFL 245 (432)
T ss_pred HHHHHhCCCChHHHHHHHHHHH
Confidence 9999999999999999998865
No 2
>KOG1435 consensus Sterol reductase/lamin B receptor [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-50 Score=369.09 Aligned_cols=184 Identities=40% Similarity=0.680 Sum_probs=169.8
Q ss_pred cccccccCCC-CcHHHH--HHHHHHHHHHHHHHhhCCcceeeCcCCCCCCCcccccchhHHHHHHHHHHHHHHHhccccc
Q 028452 20 LQGFIDIWPI-PTAVAW--KLIACFGAFEAALQLLLPGKRVEGPISPTGHRPVYKANGVASYAVTLITYLSLWWFGIFNP 96 (208)
Q Consensus 20 ~~~~~~~~~~-~t~~a~--~~y~~~~~~q~lL~~~lPG~~v~G~~~~~G~rl~Yk~NGl~~~~~t~~~~~~~~~~~~~~~ 96 (208)
...+.++|+. ++-... .++..|..+|+++|.++||++++|++++||+|++|||||++++++|+++.+.+++.+.+++
T Consensus 55 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~q~i~y~~lpg~~~~G~~l~~g~rl~Y~~Ngl~a~~lt~~l~~~~~~~~~~~~ 134 (428)
T KOG1435|consen 55 IAGLYELWPCTPTLAVYFAHLFALWFAIQAILYLVLPGKVVEGLPLSDGSRLKYKINGLAALILTLLLLGVLASLGVFRP 134 (428)
T ss_pred cchheeccccccceEEEehhhhhhHHHHhhhhhcccCceeeeeeecCCCCcceeeechHHHHHHHHHHHHHHHHhCCCCc
Confidence 3445566773 322222 2788999999999999999999999999999999999999999999999999999999999
Q ss_pred ceehhhHHHHHHHHHHHHHHHHHHHHhhcccCCCC-CCCCCCCChhhhhhcCcccCCccccceecccccccchhHHHHHH
Q 028452 97 TIVYDHLGEIYSALIFGSFIFCIFLYIKGHLAPSS-TDSGSCGNIIIDFYWGMELYPRIGKNFDIKVFTNCRFGMMSWAV 175 (208)
Q Consensus 97 ~~i~d~~~~ll~a~~i~s~~~s~~lyvk~~~~p~~-~~~g~sGn~iyDff~G~ELNPRig~~~DlK~f~e~R~g~i~w~l 175 (208)
++|+||+++++++++++|+++|+++|+|++..|+. +++|+|||++|||||||||||||| .+|+|+|+|+||||++|.+
T Consensus 135 ~~v~d~~l~l~~~a~i~afv~s~~lY~~~~~~~~~~~~~g~sGN~iyDff~G~eLNPRig-~~D~K~F~e~R~g~~~w~l 213 (428)
T KOG1435|consen 135 TFVYDHFLPLMSAAIIFAFVFSAFLYVKGLFAPRSLADGGSSGNFIYDFFMGRELNPRIG-RFDLKMFFELRPGMIGWVL 213 (428)
T ss_pred eehHHhhhHHHHHHHHHHHHHHHHHHHHHhhccccccCCCcCCCcHHhhhhccccCCcee-echHHHHhhccchHHHHHH
Confidence 99999999999999999999999999999999885 889999999999999999999999 8999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhcc
Q 028452 176 LAVTYCIKQFCSHCFLTCELKAWCVQVGM 204 (208)
Q Consensus 176 i~ls~a~kQye~~G~vt~~~~~~~~~~~~ 204 (208)
||+++++||||++|++||+|.+++..|.+
T Consensus 214 I~ls~~~~q~e~~G~vs~amvlv~~~qll 242 (428)
T KOG1435|consen 214 INLSALLKQYETYGKVSPAMVLVNSFQLL 242 (428)
T ss_pred HHHHHHHHHHHHhCcCChHHHHHHHHHHH
Confidence 99999999999999999999999988865
No 3
>PF03967 PRCH: Photosynthetic reaction centre, H-chain N-terminal region; InterPro: IPR015810 The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors []. LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) []. Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP [, , ]. The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits []. RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain []. In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface. This entry represents the N-terminal domain of the photosynthetic reaction centre H subunit, which includes the transmembrane domain and part of the cytoplasmic domain [].; GO: 0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity, 0019684 photosynthesis, light reaction, 0030077 plasma membrane light-harvesting complex; PDB: 1RZZ_H 1PST_H 2J8D_H 3DUQ_H 1FNP_H 1KBY_H 1E14_H 2HG3_H 1UMX_H 1YST_H ....
Probab=28.22 E-value=83 Score=25.33 Aligned_cols=44 Identities=18% Similarity=0.118 Sum_probs=33.9
Q ss_pred cHHHHHHHHHHHHHHHHHHhhCCcceeeCcCCCCCCCcccccch
Q 028452 31 TAVAWKLIACFGAFEAALQLLLPGKRVEGPISPTGHRPVYKANG 74 (208)
Q Consensus 31 t~~a~~~y~~~~~~q~lL~~~lPG~~v~G~~~~~G~rl~Yk~NG 74 (208)
+-....+|+.|++|-.+++.+--=.+-||.|+.+...-+.+..|
T Consensus 11 DvAql~lyaFwiFFagLi~YLrrEdkREGYPLe~d~~~~~~~~g 54 (136)
T PF03967_consen 11 DVAQLVLYAFWIFFAGLIYYLRREDKREGYPLESDDGGRAKNQG 54 (136)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHTTSSSTSSB-TTSSCSSSSH
T ss_pred cHHHHHHHHHHHHHHHHHHHHhccccccCCCcccCCCCccccCC
Confidence 46677889999999999998888888899998765545555555
No 4
>PF07330 DUF1467: Protein of unknown function (DUF1467); InterPro: IPR009935 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=20.85 E-value=3.5e+02 Score=19.89 Aligned_cols=7 Identities=43% Similarity=0.653 Sum_probs=4.5
Q ss_pred HHHhhCC
Q 028452 47 ALQLLLP 53 (208)
Q Consensus 47 lL~~~lP 53 (208)
.|..+||
T Consensus 17 ~lF~vLP 23 (85)
T PF07330_consen 17 VLFAVLP 23 (85)
T ss_pred HHHHHcc
Confidence 4566677
No 5
>PF05499 DMAP1: DNA methyltransferase 1-associated protein 1 (DMAP1); InterPro: IPR008468 DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic N terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=15.55 E-value=1.2e+02 Score=25.57 Aligned_cols=41 Identities=15% Similarity=0.129 Sum_probs=32.9
Q ss_pred cCcccCCccccceecccccccchhHHHHHHHHHHHHHHHHHh
Q 028452 146 WGMELYPRIGKNFDIKVFTNCRFGMMSWAVLAVTYCIKQFCS 187 (208)
Q Consensus 146 ~G~ELNPRig~~~DlK~f~e~R~g~i~w~li~ls~a~kQye~ 187 (208)
+|.++|| +.-.==.++|.|+|--+++..=+--++...+||.
T Consensus 117 lgv~~~P-mPTe~Ic~~fneLRsdivlL~eLk~a~~~~E~El 157 (176)
T PF05499_consen 117 LGVDLNP-MPTEEICQEFNELRSDIVLLYELKQALQNCEYEL 157 (176)
T ss_pred cCCCCCC-CChHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 7999999 6423346889999999998888888888888875
No 6
>PF02655 ATP-grasp_3: ATP-grasp domain; InterPro: IPR003806 The ATP-grasp fold is one of several distinct ATP-binding folds, and is found in enzymes that catalyze the formation of amide bonds, catalyzing the ATP-dependent ligation of a carboxylate-containing molecule to an amino or thiol group-containing molecule []. This fold is found in many different enzyme families, including various peptide synthetases, biotin carboxylase, synapsin, succinyl-CoA synthetase, pyruvate phosphate dikinase, and glutathione synthetase, amongst others []. These enzymes contribute predominantly to macromolecular synthesis, using ATP-hydrolysis to activate their substrates. The ATP-grasp fold shares functional and structural similarities with the PIPK (phosphatidylinositol phosphate kinase) and protein kinase superfamilies. The ATP-grasp domain consists of two subdomains with different alpha+beta folds, which grasp the ATP molecule between them. Each subdomain provides a variable loop that forms part of the active site, with regions from other domains also contributing to the active site, even though these other domains are not conserved between the various ATP-grasp enzymes []. This entry describes a type of ATP-grasp fold that is found in a set of proteins of unknown function.; GO: 0005524 ATP binding, 0046872 metal ion binding; PDB: 3DF7_A.
Probab=15.02 E-value=59 Score=25.86 Aligned_cols=21 Identities=38% Similarity=0.638 Sum_probs=11.5
Q ss_pred CCCCChhhhhhcC------cccCCccc
Q 028452 135 GSCGNIIIDFYWG------MELYPRIG 155 (208)
Q Consensus 135 g~sGn~iyDff~G------~ELNPRig 155 (208)
+-.|..--||.+. .|+|||+.
T Consensus 133 gl~G~~giD~I~~~~~~~viEINPR~t 159 (161)
T PF02655_consen 133 GLRGYVGIDFILDDGGPYVIEINPRFT 159 (161)
T ss_dssp T--EEEEEEEEESS-SEEEEEEESS--
T ss_pred CCeeeEeEEEEEeCCcEEEEEEcCCCC
Confidence 4445555566654 59999986
No 7
>PF08935 VP4_2: Viral protein VP4 subunit; InterPro: IPR015031 This entry represents the VP4 coat protein found in Picornaviruses, small RNA-containing mammalian viruses such as Foot-and-mouth disease virus (FMDV) [], Mengo encephalomyocarditis virus [] and Theiler's murine encephalomyelitis virus (strain DA) (TMEV) []. The viral capsid of Picornaviruses is composed of 60 icosahedral copies of four capsid proteins, VP1, VP2, VP3 and VP4, enclosing the viral positive-strand RNA genome. VP4 lies on the inner surface of the protein shell formed by the major capsid proteins, VP1, VP2 and VP3. The three major capsid proteins have a conserved beta-barrel fold, while VP4 has little regular secondary structure. The organisation of the three major capsid proteins leads to surface depressions, or pits, thought to be involved in receptor binding, while the variable outer rim is involved in antibody recognition. The small VP4 is thought to be involved in the initial disassembly and final assembly stages [].; GO: 0019030 icosahedral viral capsid; PDB: 2WZR_4 1QQP_4 1ZBA_4 1ZBE_4 2MEV_4 1MEC_4 3CJI_D 1FOD_4 1FMD_4 2XBO_4 ....
Probab=13.81 E-value=73 Score=23.40 Aligned_cols=19 Identities=26% Similarity=0.552 Sum_probs=12.4
Q ss_pred CCCCCCCChhhhhhcCccc
Q 028452 132 TDSGSCGNIIIDFYWGMEL 150 (208)
Q Consensus 132 ~~~g~sGn~iyDff~G~EL 150 (208)
...|++|.+++.|||=.=-
T Consensus 13 n~SGN~G~IvnNyY~nqYq 31 (80)
T PF08935_consen 13 NSSGNSGTIVNNYYMNQYQ 31 (80)
T ss_dssp SSSSS--SSSGGSS-HHHH
T ss_pred cCCCCcceeehHHHHHHHh
Confidence 5689999999999984433
No 8
>PF13535 ATP-grasp_4: ATP-grasp domain; PDB: 3VMM_A 3LN6_A 3LN7_B 2PN1_A 4DIM_A.
Probab=13.72 E-value=66 Score=25.01 Aligned_cols=11 Identities=36% Similarity=0.764 Sum_probs=6.9
Q ss_pred cCcccCCcccc
Q 028452 146 WGMELYPRIGK 156 (208)
Q Consensus 146 ~G~ELNPRig~ 156 (208)
.=.|+|||++|
T Consensus 171 ~~iEiN~R~~G 181 (184)
T PF13535_consen 171 YFIEINPRFGG 181 (184)
T ss_dssp EEEEEESS--S
T ss_pred EEEEECccCCC
Confidence 34799999974
No 9
>PF12412 DUF3667: Protein of unknown function (DUF3667); InterPro: IPR022134 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Probab=13.72 E-value=84 Score=20.28 Aligned_cols=33 Identities=27% Similarity=0.431 Sum_probs=23.1
Q ss_pred hhCCcceeeCcCCCCCCCcccccchhHHHHHHHHHH
Q 028452 50 LLLPGKRVEGPISPTGHRPVYKANGVASYAVTLITY 85 (208)
Q Consensus 50 ~~lPG~~v~G~~~~~G~rl~Yk~NGl~~~~~t~~~~ 85 (208)
.+-||+..++.. +|+|.+|- |-+..++++..++
T Consensus 12 ~~rPG~~~~~Yi--~G~R~~Y~-~P~r~~~~~~~i~ 44 (46)
T PF12412_consen 12 LLRPGEVTREYI--EGKRKRYV-NPFRLFLFASFIF 44 (46)
T ss_pred HhCHHHHHHHHH--cCcccccC-CHHHHHHHHHHHH
Confidence 345888776554 68888885 8887776665544
No 10
>TIGR01150 puhA photosynthetic reaction center, subunit H, bacterial. This model describes the photosynthetic reaction center H subunit in non-oxygenic photosynthetic bacteria. The reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reaction center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in the form of NADH. Ultimately, the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is an organic acid rather than water. Much of our current functional understanding of photosynthesis comes from the structural determination
Probab=13.58 E-value=2.9e+02 Score=24.45 Aligned_cols=33 Identities=15% Similarity=0.052 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCcceeeCcCCCC
Q 028452 32 AVAWKLIACFGAFEAALQLLLPGKRVEGPISPT 64 (208)
Q Consensus 32 ~~a~~~y~~~~~~q~lL~~~lPG~~v~G~~~~~ 64 (208)
-....+|+.|++|-.+++.+--=.+-||.|+.+
T Consensus 12 vAq~~ly~FwiFFA~Li~YLrrEd~REGYPLe~ 44 (252)
T TIGR01150 12 LAQLVIYAFWIFLAGLIYYLRREDRREGYPLEN 44 (252)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccccCCCccc
Confidence 566788999999999888888888889988753
Done!