Query 023996
Match_columns 274
No_of_seqs 162 out of 958
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 08:10:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023996.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023996hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 3.7E-44 8E-49 294.4 6.2 129 4-136 1-129 (129)
2 PHA00692 hypothetical protein 40.8 11 0.00024 27.2 0.4 9 3-11 36-44 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 27.7 53 0.0012 19.9 1.8 19 13-31 4-22 (27)
4 PF07960 CBP4: CBP4; InterPro 20.8 51 0.0011 27.4 1.1 12 10-21 29-40 (128)
5 PF02180 BH4: Bcl-2 homology r 17.5 1.2E+02 0.0027 18.4 2.0 17 14-30 5-21 (27)
6 PF13822 ACC_epsilon: Acyl-CoA 15.7 77 0.0017 22.7 0.9 9 11-19 10-18 (62)
7 cd00490 Met_repressor_MetJ Met 15.2 1.7E+02 0.0037 22.8 2.8 38 11-53 50-87 (103)
8 PLN02417 dihydrodipicolinate s 14.7 1E+02 0.0023 28.2 1.8 18 4-22 103-120 (280)
9 smart00707 RPEL Repeat in Dros 14.3 1.2E+02 0.0025 18.3 1.3 13 7-19 6-18 (26)
10 KOG1334 WD40 repeat protein [G 14.2 3.7E+02 0.008 27.4 5.5 89 15-112 303-425 (559)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=3.7e-44 Score=294.38 Aligned_cols=129 Identities=47% Similarity=0.976 Sum_probs=96.2
Q ss_pred CCCCceEcCChHHHHHHHHHHHhcCCCCCCCCceeeccCCCCCCCCCccccccccCCCCceEEEeccCcccccCCCCCcc
Q 023996 4 LPPGYRFFPTEEELVSFYLINKLEGKRQELHRVIPVIRLYEIEPWHLPKLCGEKCQGDTEQWFFFTPRQEREERGGRPSR 83 (274)
Q Consensus 4 LPpGfRF~PTDeELV~~YL~~Ki~g~~~~~~~~I~~~Dvy~~~PwdLp~~~~~~~~g~~~~wyFFt~r~~k~~~G~R~~R 83 (274)
|||||||+|||+|||.+||++|+.|.+++...+|+++|||++|||+|+... .+.+++||||+++++++.+|.|++|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~----~~~~~~~yFF~~~~~~~~~~~r~~R 76 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKF----KGGDEEWYFFSPRKKKYPNGGRPNR 76 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHS----SS-SSEEEEEEE----------S-E
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhc----cCCCceEEEEEecccccCCcccccc
Confidence 899999999999999999999999999877789999999999999999521 1244479999999999999999999
Q ss_pred ccccceEEecCCCeeeecCCCcEEEEEEEEEEecCcCCCCCccCcEEEEEEeC
Q 023996 84 TTASGYWKATGSPSYVYSSDNRVIGVKKTMVFYKGKAPTGRKTKWKMHEYRAI 136 (274)
Q Consensus 84 ~t~~G~Wk~~G~~k~V~~~~g~viG~Kktl~Fy~g~~~~g~kT~W~M~EY~l~ 136 (274)
++++|+||++|+.+.|.+.++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 77 ~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 77 VTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999999999977999999999999998888899999999999983
No 2
>PHA00692 hypothetical protein
Probab=40.81 E-value=11 Score=27.16 Aligned_cols=9 Identities=67% Similarity=1.368 Sum_probs=7.4
Q ss_pred CCCCCceEc
Q 023996 3 ELPPGYRFF 11 (274)
Q Consensus 3 ~LPpGfRF~ 11 (274)
+.||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999995
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=27.72 E-value=53 Score=19.94 Aligned_cols=19 Identities=32% Similarity=0.333 Sum_probs=15.1
Q ss_pred ChHHHHHHHHHHHhcCCCC
Q 023996 13 TEEELVSFYLINKLEGKRQ 31 (274)
Q Consensus 13 TDeELV~~YL~~Ki~g~~~ 31 (274)
+-.|||.+|+.-||.-+-.
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999975443
No 4
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=20.83 E-value=51 Score=27.36 Aligned_cols=12 Identities=58% Similarity=0.703 Sum_probs=9.8
Q ss_pred EcCChHHHHHHH
Q 023996 10 FFPTEEELVSFY 21 (274)
Q Consensus 10 F~PTDeELV~~Y 21 (274)
=.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 369999999764
No 5
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=17.45 E-value=1.2e+02 Score=18.38 Aligned_cols=17 Identities=35% Similarity=0.462 Sum_probs=13.7
Q ss_pred hHHHHHHHHHHHhcCCC
Q 023996 14 EEELVSFYLINKLEGKR 30 (274)
Q Consensus 14 DeELV~~YL~~Ki~g~~ 30 (274)
-.|||.+|+.-||.-+-
T Consensus 5 nR~lV~~yi~yKLsQrg 21 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRG 21 (27)
T ss_dssp HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhhhcC
Confidence 47999999999996543
No 6
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=15.72 E-value=77 Score=22.67 Aligned_cols=9 Identities=56% Similarity=0.818 Sum_probs=7.6
Q ss_pred cCChHHHHH
Q 023996 11 FPTEEELVS 19 (274)
Q Consensus 11 ~PTDeELV~ 19 (274)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999864
No 7
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=15.24 E-value=1.7e+02 Score=22.83 Aligned_cols=38 Identities=16% Similarity=0.168 Sum_probs=31.1
Q ss_pred cCChHHHHHHHHHHHhcCCCCCCCCceeeccCCCCCCCCCccc
Q 023996 11 FPTEEELVSFYLINKLEGKRQELHRVIPVIRLYEIEPWHLPKL 53 (274)
Q Consensus 11 ~PTDeELV~~YL~~Ki~g~~~~~~~~I~~~Dvy~~~PwdLp~~ 53 (274)
|-|..||++.-...-..|+|++. +.|+-...|..+|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~-----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD-----DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC-----hhhhhhcCcccccHH
Confidence 56888999988888889999854 578888889999874
No 8
>PLN02417 dihydrodipicolinate synthase
Probab=14.69 E-value=1e+02 Score=28.21 Aligned_cols=18 Identities=22% Similarity=0.418 Sum_probs=14.4
Q ss_pred CCCCceEcCChHHHHHHHH
Q 023996 4 LPPGYRFFPTEEELVSFYL 22 (274)
Q Consensus 4 LPpGfRF~PTDeELV~~YL 22 (274)
+|| |.|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 455 568999999999874
No 9
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=14.29 E-value=1.2e+02 Score=18.28 Aligned_cols=13 Identities=38% Similarity=0.332 Sum_probs=11.0
Q ss_pred CceEcCChHHHHH
Q 023996 7 GYRFFPTEEELVS 19 (274)
Q Consensus 7 GfRF~PTDeELV~ 19 (274)
...++||-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
No 10
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=14.17 E-value=3.7e+02 Score=27.41 Aligned_cols=89 Identities=22% Similarity=0.375 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHhcCCCC--CCCCceeecc-----------CCCCCCCCCccccccccCCCCceEEEeccCccccc-----
Q 023996 15 EELVSFYLINKLEGKRQ--ELHRVIPVIR-----------LYEIEPWHLPKLCGEKCQGDTEQWFFFTPRQEREE----- 76 (274)
Q Consensus 15 eELV~~YL~~Ki~g~~~--~~~~~I~~~D-----------vy~~~PwdLp~~~~~~~~g~~~~wyFFt~r~~k~~----- 76 (274)
.|.+..|=.+++..... .+..+.+..+ +|.+++-+|-.. ..++..|||.+ ..+..
T Consensus 303 dqf~RvYD~R~~~~e~~n~~~~~f~p~hl~~d~~v~ITgl~Ysh~~sElLaS------YnDe~IYLF~~-~~~~G~~p~~ 375 (559)
T KOG1334|consen 303 DQFARVYDQRRIDKEENNGVLDKFCPHHLVEDDPVNITGLVYSHDGSELLAS------YNDEDIYLFNK-SMGDGSEPDP 375 (559)
T ss_pred hhhhhhhcccchhhccccchhhhcCCccccccCcccceeEEecCCccceeee------ecccceEEecc-ccccCCCCCC
Confidence 35566677777776533 2233333333 455555555431 23445799944 32222
Q ss_pred ------------CCCCCcccccc-ceEEecCCCeeeecC-C-CcE-EEEEEE
Q 023996 77 ------------RGGRPSRTTAS-GYWKATGSPSYVYSS-D-NRV-IGVKKT 112 (274)
Q Consensus 77 ------------~G~R~~R~t~~-G~Wk~~G~~k~V~~~-~-g~v-iG~Kkt 112 (274)
+|.|-+||+++ -+|-+.. ..|+++ | |.| |..|++
T Consensus 376 ~s~~~~~~k~vYKGHrN~~TVKgVNFfGPrs--EyVvSGSDCGhIFiW~K~t 425 (559)
T KOG1334|consen 376 SSPREQYVKRVYKGHRNSRTVKGVNFFGPRS--EYVVSGSDCGHIFIWDKKT 425 (559)
T ss_pred CcchhhccchhhcccccccccceeeeccCcc--ceEEecCccceEEEEecch
Confidence 35566677653 4564332 234443 3 554 566554
Done!