Query psy3869
Match_columns 203
No_of_seqs 141 out of 209
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 19:29:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3869hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5602 SIN3 Histone deacetyla 99.9 4.9E-27 1.1E-31 229.2 8.5 153 1-183 906-1059(1163)
2 PF09060 L27_N: L27_N; InterP 63.1 9.8 0.00021 25.8 2.9 28 33-61 2-29 (49)
3 KOG4479|consensus 27.3 57 0.0012 24.6 2.4 43 16-58 38-80 (92)
4 smart00035 CLa CLUSTERIN alpha 20.4 5.9E+02 0.013 22.4 7.7 47 96-159 153-209 (216)
5 KOG0417|consensus 18.1 2E+02 0.0042 23.9 4.0 49 18-66 84-133 (148)
6 cd08767 Cdt1_c The C-terminal 17.5 1.6E+02 0.0035 23.1 3.3 46 16-61 47-92 (126)
7 PF00440 TetR_N: Bacterial reg 16.2 62 0.0013 20.5 0.5 24 17-40 3-26 (47)
8 PF06702 DUF1193: Protein of u 14.9 1E+02 0.0022 27.1 1.6 28 2-31 97-124 (221)
9 KOG0817|consensus 14.2 3.3E+02 0.0072 22.2 4.4 58 31-90 3-61 (142)
10 PF01093 Clusterin: Clusterin; 12.6 8.8E+02 0.019 23.4 7.3 48 95-159 365-423 (436)
No 1
>COG5602 SIN3 Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=99.94 E-value=4.9e-27 Score=229.18 Aligned_cols=153 Identities=18% Similarity=0.233 Sum_probs=136.8
Q ss_pred ChhccccCCCCchhhHHHHHHhhccceeeeeeHHHHHHHHHHhhhHhhcccchHHHHHHHHHHhhcCCCCCCcchhhhhh
Q psy3869 1 MVKNVLDGNMESNSYEDTLRELFGIHAYIAFTLDKIVSNAVRQLQHLVSDETCIECYETFLKESKKGATGGLCETAHQRV 80 (203)
Q Consensus 1 m~~~LldG~iD~~~FED~lR~~fg~~AY~LfTiDKLI~~lvKqlq~ivsD~~s~ell~Lf~~eR~~~~tg~~~st~~~r~ 80 (203)
||++|+.|.+++.+||+.||.+|++++|++||||||.++|+||+|+|+.|.|...++.||..++..+.+ +.
T Consensus 906 ~s~rli~g~l~~~efekylr~fynntcykiytidrl~qsl~kq~h~i~~d~Ky~~~~~lfe~nsaaS~k---------~~ 976 (1163)
T COG5602 906 DSYRLIFGALTPCEFEKYLRPFYNNTCYKIYTIDRLRQSLKKQLHPITYDIKYIAKSELFEMNSAASSK---------RK 976 (1163)
T ss_pred HHHHHHhccccHHHHHHHHHHhccCcccccccHHHHHHHHHHHhcccccchHHHHHHHHHHhccccCcC---------cc
Confidence 588999999999999999999999999999999999999999999999999999999999999886433 23
Q ss_pred hhHHHHHHHHHHhc-CCCCeEEEEEecCCCEEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcChhhhhhHhhhc
Q psy3869 81 HLEQGYQKKSEVAM-TDENCFKIIIFKKDCKLTIELLDTESSDNEGEDNDNDNDEDKDDNEHDPDQSTQDSEKWSPYEEE 159 (203)
Q Consensus 81 ~~ei~Yr~~ae~ll-~Den~fRI~~~~~~~~ltIqLl~~dd~t~~~~~~~~~~de~~d~~~~~~~~~~~~~ekW~~Yv~s 159 (203)
+.++.||.+||++| ++++||||.|.+..++++||.|.++|.|++ +.+.....|.|||+|
T Consensus 977 ~dq~~yrl~ves~l~p~e~~Fr~~w~~~~k~~~Iq~~~~adLt~~--------------------~~~~~~~~wkyYV~s 1036 (1163)
T COG5602 977 QDQTKYRLEVESLLNPDEILFRFCWINKFKSFGIQIMKRADLTVD--------------------QSLDTQRVWKYYVQS 1036 (1163)
T ss_pred chhhHHHHHHHHhcCchhheeeeeecchhheeeeeEeeccccccc--------------------cccChHHHHHHHHHh
Confidence 68999999999999 999999999999999999999999999991 123555589999999
Q ss_pred cCCCCCCChhcccccccCCcCCCC
Q psy3869 160 PFPERNTAPANEETLVEPKVESEP 183 (203)
Q Consensus 160 y~~~~~t~~~~~~~l~~k~~~~~~ 183 (203)
|...++|+|....++ .-|++.|+
T Consensus 1037 Yai~h~TEgi~~~~~-k~PFL~R~ 1059 (1163)
T COG5602 1037 YAIQHLTEGISYKNY-KCPFLCRN 1059 (1163)
T ss_pred hccccccccCchhhc-cchHHHHH
Confidence 999999998888887 44555444
No 2
>PF09060 L27_N: L27_N; InterPro: IPR015145 The L27_N domain plays a role in the biogenesis of tight junctions and in the establishment of cell polarity in epithelial cells. Each L27_N domain consists of three alpha-helices, the first two of which form an antiparallel coiled-coil. Two L27 domains come together to form a four-helical bundle with the antiparallel coiled-coils formed by the first two helices. The third helix of each domain forms another coiled-coil packing at one end of the four-helix bundle, creating a large hydrophobic interface: the hydrophobic interactions are the major force that drives heterodimer formation []. ; PDB: 1Y76_B 3UIT_B 1VF6_C.
Probab=63.09 E-value=9.8 Score=25.82 Aligned_cols=28 Identities=25% Similarity=0.510 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhhhHhhcccchHHHHHHHH
Q psy3869 33 LDKIVSNAVRQLQHLVSDETCIECYETFL 61 (203)
Q Consensus 33 iDKLI~~lvKqlq~ivsD~~s~ell~Lf~ 61 (203)
+|.|+++ .|++||+++|..|++=+.|..
T Consensus 2 leell~s-Lk~iqh~L~D~qSQ~Dv~lll 29 (49)
T PF09060_consen 2 LEELLSS-LKHIQHCLNDSQSQQDVELLL 29 (49)
T ss_dssp HHHHHHH-HHHHHCCH-SHHHHHHHHHHH
T ss_pred HHHHHHH-HHHHHHhhccHhhHHhHHHHH
Confidence 4566665 599999999988887544433
No 3
>KOG4479|consensus
Probab=27.32 E-value=57 Score=24.64 Aligned_cols=43 Identities=16% Similarity=0.169 Sum_probs=37.7
Q ss_pred HHHHHHhhccceeeeeeHHHHHHHHHHhhhHhhcccchHHHHH
Q psy3869 16 EDTLRELFGIHAYIAFTLDKIVSNAVRQLQHLVSDETCIECYE 58 (203)
Q Consensus 16 ED~lR~~fg~~AY~LfTiDKLI~~lvKqlq~ivsD~~s~ell~ 58 (203)
-+-||++.--+|--=||+|.|+..|+-+..++|.|..-.+|+.
T Consensus 38 k~mcrniimEkG~~n~tvdqL~AeitPkaRaLVPd~VKkEll~ 80 (92)
T KOG4479|consen 38 KEMCRNIIMEKGVDNITVDQLAAEITPKARALVPDVVKKELLL 80 (92)
T ss_pred HHHHHHHHHHhccccccHHHHHHHhCchhhhhchHHHHHHHHH
Confidence 4568888888888889999999999999999999988888774
No 4
>smart00035 CLa CLUSTERIN alpha chain.
Probab=20.44 E-value=5.9e+02 Score=22.35 Aligned_cols=47 Identities=17% Similarity=0.333 Sum_probs=34.8
Q ss_pred CCCeEEEEEecC----------CCEEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcChhhhhhHhhhc
Q psy3869 96 DENCFKIIIFKK----------DCKLTIELLDTESSDNEGEDNDNDNDEDKDDNEHDPDQSTQDSEKWSPYEEE 159 (203)
Q Consensus 96 Den~fRI~~~~~----------~~~ltIqLl~~dd~t~~~~~~~~~~de~~d~~~~~~~~~~~~~ekW~~Yv~s 159 (203)
+++.|+|+-+.. ..+++|+|++....|+ -.|++.....-++..||..
T Consensus 153 ~~~~f~v~tv~~~~~e~~~~~~~t~v~V~lf~S~~~T~-----------------~vP~e~s~~dp~F~e~Va~ 209 (216)
T smart00035 153 DQYYLQVTTVPSHTSDSSVPSGTTKVVVKLFDSDPITL-----------------TIPEEVSADNPKFMETVAE 209 (216)
T ss_pred CCceEEEEEeecCCCCCCCCCCCCeEEEEecCCCCeEE-----------------eCCcccCCCCccHHHHHHH
Confidence 667889887632 1469999999999998 4555555556688889863
No 5
>KOG0417|consensus
Probab=18.11 E-value=2e+02 Score=23.86 Aligned_cols=49 Identities=14% Similarity=0.116 Sum_probs=39.4
Q ss_pred HHHHhhccceeeeeeHHHHHHHHHHhhhHhhc-ccchHHHHHHHHHHhhc
Q psy3869 18 TLRELFGIHAYIAFTLDKIVSNAVRQLQHLVS-DETCIECYETFLKESKK 66 (203)
Q Consensus 18 ~lR~~fg~~AY~LfTiDKLI~~lvKqlq~ivs-D~~s~ell~Lf~~eR~~ 66 (203)
-|-.+++.+=-..-||.||+.+|+.-|..-.. |+...++-.+|..+|.+
T Consensus 84 IclDILk~~WsPAl~i~~VllsI~sLL~~PnpddPL~~~ia~~~k~d~~~ 133 (148)
T KOG0417|consen 84 ICLDILKDQWSPALTISKVLLSICSLLSDPNPDDPLVPDIAELYKTDRAK 133 (148)
T ss_pred chHHhhhccCChhhHHHHHHHHHHHHhcCCCCCccccHHHHHHHHhhHHH
Confidence 46667777766778999999999988888877 47888999999987763
No 6
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=17.52 E-value=1.6e+02 Score=23.08 Aligned_cols=46 Identities=15% Similarity=0.201 Sum_probs=36.2
Q ss_pred HHHHHHhhccceeeeeeHHHHHHHHHHhhhHhhcccchHHHHHHHH
Q psy3869 16 EDTLRELFGIHAYIAFTLDKIVSNAVRQLQHLVSDETCIECYETFL 61 (203)
Q Consensus 16 ED~lR~~fg~~AY~LfTiDKLI~~lvKqlq~ivsD~~s~ell~Lf~ 61 (203)
=+.+|.+|-..-=.+||++.|+..|+.-.-.+++-....+.+.|..
T Consensus 47 a~~v~~if~s~~k~~l~~e~l~~kl~~S~~~~~s~~E~E~~l~LL~ 92 (126)
T cd08767 47 ARILRNIFVSEKKTVLPLEELVYKLQASYPSILSRGEVEEHLRLLA 92 (126)
T ss_pred HHHHHHHHHhcccccccHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 4678888888888899999999999887777777666666666665
No 7
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=16.24 E-value=62 Score=20.51 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=19.9
Q ss_pred HHHHHhhccceeeeeeHHHHHHHH
Q psy3869 17 DTLRELFGIHAYIAFTLDKIVSNA 40 (203)
Q Consensus 17 D~lR~~fg~~AY~LfTiDKLI~~l 40 (203)
++..++|..+||--.||++|...+
T Consensus 3 ~aa~~l~~~~G~~~~s~~~Ia~~~ 26 (47)
T PF00440_consen 3 EAALELFAEKGYEAVSIRDIARRA 26 (47)
T ss_dssp HHHHHHHHHHHTTTSSHHHHHHHH
T ss_pred HHHHHHHHHhCHHhCCHHHHHHHH
Confidence 567888999999999999987654
No 8
>PF06702 DUF1193: Protein of unknown function (DUF1193); InterPro: IPR009581 This family is baesd on the C terminus of several hypothetical eukaryotic proteins of unknown function. Proteins in this entry contain two conserved motifs: DRHHYE and QCC, as well as a number of conserved cysteine residues.
Probab=14.88 E-value=1e+02 Score=27.11 Aligned_cols=28 Identities=29% Similarity=0.530 Sum_probs=23.6
Q ss_pred hhccccCCCCchhhHHHHHHhhccceeeee
Q psy3869 2 VKNVLDGNMESNSYEDTLRELFGIHAYIAF 31 (203)
Q Consensus 2 ~~~LldG~iD~~~FED~lR~~fg~~AY~Lf 31 (203)
|..+|.||+|=.+|| +-++||+.++++|
T Consensus 97 IFDFLigN~DRhhye--~f~~fgn~~~l~~ 124 (221)
T PF06702_consen 97 IFDFLIGNMDRHHYE--TFNKFGNEGFLLH 124 (221)
T ss_pred HHHHHhcCCcchhhh--hhhccCCCceEEE
Confidence 568899999999999 6688888887765
No 9
>KOG0817|consensus
Probab=14.24 E-value=3.3e+02 Score=22.19 Aligned_cols=58 Identities=19% Similarity=0.130 Sum_probs=39.6
Q ss_pred eeHHHHHHHHHHhhhHhhcccchHHHHHHHHHHhhcCCCCCCcchh-hhhhhhHHHHHHHH
Q psy3869 31 FTLDKIVSNAVRQLQHLVSDETCIECYETFLKESKKGATGGLCETA-HQRVHLEQGYQKKS 90 (203)
Q Consensus 31 fTiDKLI~~lvKqlq~ivsD~~s~ell~Lf~~eR~~~~tg~~~st~-~~r~~~ei~Yr~~a 90 (203)
.|+...+.+.+..++++.+....-++|.||-.+.. .|-|.|++. +.-...+.-+..+|
T Consensus 3 ~~~~~~Fe~a~~~~~~l~~~p~~ee~L~lYglyKQ--At~G~~~~~kPg~~d~~~k~Kw~A 61 (142)
T KOG0817|consen 3 ATLEAKFEAAAEAVKNLKKKPSNEELLKLYGLYKQ--ATVGDCNTPKPGFFDEEGKAKWQA 61 (142)
T ss_pred chHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHh--hccCCCCCCCCchhhHHHHHHHHH
Confidence 46777888999999999999999999999988876 344455332 11123344455555
No 10
>PF01093 Clusterin: Clusterin; InterPro: IPR000753 Clusterin is a vertebrate glycoprotein [], the exact function of which is not yet clear. Clusterin expression is complex, appearing as different forms in different cell compartments. One set of proteins is directed for secretion, and other clusterin species are expressed in the cytoplasm and nucleus. The secretory form of the clusterin protein (sCLU) is targeted to the ER by an initial leader peptide. This ~60kDa pre-sCLU protein is further glycosylated and proteolytically cleaved into alpha- and beta-subunits, held together by disulphide bonds. External sCLU is an 80kDa protein and may act as a molecular chaperone, scavenging denatured proteins outside cells following specific stress-induced injury such as heat shock. sCLU possesses nonspecific binding activity to hydrophobic domains of various proteins in vitro []. A specific nuclear form of CLU (nCLU) acts as a pro-death signal, inhibiting cell growth and survival. The nCLU protein has two coiled-coil domains, one at its N terminus that is unable to bind Ku70, and a C-terminal coiled-coil domain that is uniquely able to associate with Ku70 and is minimally required for cell death. Clusterin is synthesized as a precursor polypeptide of about 400 amino acids which is post-translationally cleaved to form two subunits of about 200 amino acids each. The two subunits are linked by five disulphide bonds to form an antiparallel ladder-like structure []. In each of the mature subunits the five cysteines that are involved in disulphide bonds are clustered in domains of about 30 amino acids located in the central part of the subunits. This entry represents the clusterin precursor and related proteins.; GO: 0008219 cell death
Probab=12.56 E-value=8.8e+02 Score=23.42 Aligned_cols=48 Identities=19% Similarity=0.340 Sum_probs=35.4
Q ss_pred CCCCeEEEEEec----------C-CCEEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcChhhhhhHhhhc
Q psy3869 95 TDENCFKIIIFK----------K-DCKLTIELLDTESSDNEGEDNDNDNDEDKDDNEHDPDQSTQDSEKWSPYEEE 159 (203)
Q Consensus 95 ~Den~fRI~~~~----------~-~~~ltIqLl~~dd~t~~~~~~~~~~de~~d~~~~~~~~~~~~~ekW~~Yv~s 159 (203)
.++++|+|.-+- . ...|.++|++....|+ ..|++.....-++..||+.
T Consensus 365 ~~~~iF~v~tV~s~~~e~~~~p~~~T~V~v~i~~S~p~T~-----------------~vP~e~~~~dp~Fie~Va~ 423 (436)
T PF01093_consen 365 GPENIFNVTTVVSRSSEDSSSPSDDTEVEVSIFDSPPFTV-----------------TVPGELSWDDPKFIEYVAQ 423 (436)
T ss_pred CCCCeEEEEEEecCCCCCCCCCCCCceEEEEecCCCCeEE-----------------eccCCCCCCCCcHHHHHHH
Confidence 478999987652 1 2678999999999998 3455555566688888863
Done!