Query 037309
Match_columns 287
No_of_seqs 180 out of 939
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 10:55:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037309.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037309hhsearch_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 1.2E-41 2.6E-46 282.4 6.8 123 1-125 5-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 30.3 60 0.0013 20.4 2.4 20 6-25 4-23 (27)
3 PF15102 TMEM154: TMEM154 prot 20.4 1.2E+02 0.0026 26.4 3.3 17 203-219 125-141 (146)
4 cd00490 Met_repressor_MetJ Met 20.3 93 0.002 25.0 2.4 39 4-46 50-88 (103)
5 KOG1334 WD40 repeat protein [G 18.8 1.3E+02 0.0028 31.2 3.6 69 9-81 304-403 (559)
6 PRK05264 transcriptional repre 18.4 1E+02 0.0022 25.0 2.3 39 4-46 51-89 (105)
7 COG3060 MetJ Transcriptional r 18.3 77 0.0017 25.3 1.6 39 4-46 51-89 (105)
8 cd00933 barnase Barnase, a mem 16.3 4.2E+02 0.009 21.9 5.5 24 6-32 2-25 (107)
9 PF02180 BH4: Bcl-2 homology r 15.7 1.5E+02 0.0032 18.7 2.1 20 6-25 4-23 (27)
10 PF07960 CBP4: CBP4; InterPro 14.8 80 0.0017 26.9 1.0 11 4-14 30-40 (128)
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=1.2e-41 Score=282.44 Aligned_cols=123 Identities=44% Similarity=0.874 Sum_probs=95.8
Q ss_pred CcccCChHHHHHHHHHHhHhCCCCCC-CceeeccCCCCCCcccccccccCCCceEEEEeecCCCCCCCCCCccccCCCCe
Q 037309 1 YRFVPTCKELVTYYLRNKILERPLPP-SKIREANIYKHSPTELSEKYDKEGSGVMYFFTPRDRKYPEGERPKRSVDGNGF 79 (287)
Q Consensus 1 FRF~PTDEELV~~YL~~Ki~g~pl~~-~~I~evDVY~~ePwdLp~~~~~~ge~ewYFFs~r~~k~~~G~R~nRaVt~~G~ 79 (287)
|||+|||||||.+||++|+.|.+++. .+|+++|||++|||+|+... ..++++||||+++++++++|.|++|+ +++|+
T Consensus 5 ~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~-~~~~~~~yFF~~~~~~~~~~~r~~R~-~~~G~ 82 (129)
T PF02365_consen 5 FRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKF-KGGDEEWYFFSPRKKKYPNGGRPNRV-TGGGY 82 (129)
T ss_dssp EEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHS-SS-SSEEEEEEE----------S-EE-ETTEE
T ss_pred eEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhc-cCCCceEEEEEecccccCCccccccc-ccceE
Confidence 79999999999999999999999886 89999999999999999544 45678999999999999999999998 99999
Q ss_pred EEecccCeeEee-CCeEEEEEEEEEEeeCcCCCCCCcCeEEEEEeeC
Q 037309 80 WKASGKAEEVEN-FDILIAKKRSLVYYQGSYKKPKKTDWLMQEFFMT 125 (287)
Q Consensus 80 WK~tG~~k~I~~-~g~~VG~KKtLvFy~gr~p~g~kT~WvMhEYrL~ 125 (287)
||++|++++|.. +|++||+||+|+||.++.+++.+|+|+||||+|.
T Consensus 83 Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 83 WKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred EeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999995 9999999999999999889999999999999984
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=30.26 E-value=60 Score=20.41 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=16.2
Q ss_pred ChHHHHHHHHHHhHhCCCCC
Q 037309 6 TCKELVTYYLRNKILERPLP 25 (287)
Q Consensus 6 TDEELV~~YL~~Ki~g~pl~ 25 (287)
+-.|||.+|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 46899999999999866544
No 3
>PF15102 TMEM154: TMEM154 protein family
Probab=20.42 E-value=1.2e+02 Score=26.41 Aligned_cols=17 Identities=18% Similarity=0.282 Sum_probs=13.2
Q ss_pred hHHHHhhhccccCCCCC
Q 037309 203 QAMHAISSQMSTYNNGQ 219 (287)
Q Consensus 203 ~~~~~~~~~~~~~~~~~ 219 (287)
..|+.++.||.+-|++.
T Consensus 125 iEmeeldkwm~s~n~n~ 141 (146)
T PF15102_consen 125 IEMEELDKWMNSMNRNA 141 (146)
T ss_pred hhHHHHHhHHHhhccCc
Confidence 46889999998876554
No 4
>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=20.27 E-value=93 Score=25.03 Aligned_cols=39 Identities=26% Similarity=0.365 Sum_probs=33.0
Q ss_pred cCChHHHHHHHHHHhHhCCCCCCCceeeccCCCCCCccccccc
Q 037309 4 VPTCKELVTYYLRNKILERPLPPSKIREANIYKHSPTELSEKY 46 (287)
Q Consensus 4 ~PTDEELV~~YL~~Ki~g~pl~~~~I~evDVY~~ePwdLp~~~ 46 (287)
|-|..||++.-...-..|+|+|. +.|+-+..|.++|...
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHHH
Confidence 45788999888888889999986 4789999999999876
No 5
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=18.77 E-value=1.3e+02 Score=31.23 Aligned_cols=69 Identities=22% Similarity=0.379 Sum_probs=39.4
Q ss_pred HHHHHHHHHhHhCCCCCC---Cceeecc-----------CCCCCCcccccccccCCCceEEEEeecCCCCC---------
Q 037309 9 ELVTYYLRNKILERPLPP---SKIREAN-----------IYKHSPTELSEKYDKEGSGVMYFFTPRDRKYP--------- 65 (287)
Q Consensus 9 ELV~~YL~~Ki~g~pl~~---~~I~evD-----------VY~~ePwdLp~~~~~~ge~ewYFFs~r~~k~~--------- 65 (287)
|.+.-|=.|++...+... .+.+..+ +|.++|-+|...+ .+...|||. +.+++.
T Consensus 304 qf~RvYD~R~~~~e~~n~~~~~f~p~hl~~d~~v~ITgl~Ysh~~sElLaSY---nDe~IYLF~-~~~~~G~~p~~~s~~ 379 (559)
T KOG1334|consen 304 QFARVYDQRRIDKEENNGVLDKFCPHHLVEDDPVNITGLVYSHDGSELLASY---NDEDIYLFN-KSMGDGSEPDPSSPR 379 (559)
T ss_pred hhhhhhcccchhhccccchhhhcCCccccccCcccceeEEecCCccceeeee---cccceEEec-cccccCCCCCCCcch
Confidence 455557777777654321 1222222 4556666665544 467789994 333322
Q ss_pred --------CCCCCccccCCCCeEE
Q 037309 66 --------EGERPKRSVDGNGFWK 81 (287)
Q Consensus 66 --------~G~R~nRaVt~~G~WK 81 (287)
.|.|-+|+|.+.-+|=
T Consensus 380 ~~~~k~vYKGHrN~~TVKgVNFfG 403 (559)
T KOG1334|consen 380 EQYVKRVYKGHRNSRTVKGVNFFG 403 (559)
T ss_pred hhccchhhcccccccccceeeecc
Confidence 3567778777777884
No 6
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=18.44 E-value=1e+02 Score=24.97 Aligned_cols=39 Identities=23% Similarity=0.344 Sum_probs=32.9
Q ss_pred cCChHHHHHHHHHHhHhCCCCCCCceeeccCCCCCCccccccc
Q 037309 4 VPTCKELVTYYLRNKILERPLPPSKIREANIYKHSPTELSEKY 46 (287)
Q Consensus 4 ~PTDEELV~~YL~~Ki~g~pl~~~~I~evDVY~~ePwdLp~~~ 46 (287)
|-|..||++.-...-..|+|||. +.|+-+..|.++|..+
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHHH
Confidence 45788999888888889999986 4789999999999776
No 7
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=18.28 E-value=77 Score=25.33 Aligned_cols=39 Identities=26% Similarity=0.371 Sum_probs=32.8
Q ss_pred cCChHHHHHHHHHHhHhCCCCCCCceeeccCCCCCCccccccc
Q 037309 4 VPTCKELVTYYLRNKILERPLPPSKIREANIYKHSPTELSEKY 46 (287)
Q Consensus 4 ~PTDEELV~~YL~~Ki~g~pl~~~~I~evDVY~~ePwdLp~~~ 46 (287)
|-|..||++.-...-..|+|+|. +.|+.+.-|.++|+.+
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 45778999888888889999875 5799999999999876
No 8
>cd00933 barnase Barnase, a member of the family of homologous microbial ribonucleases, catalyses the cleavage of single-stranded RNA via a two-step mechanism thought to be similar to that of pancreatic ribonuclease. The mechanism involves a transesterification to give a 2', 3'-cyclic phosphate intermediate, followed by hydrolysis to yield a 3' nucleotide. The active site residues His and Glu act as general acid-base groups during catalysis, while the Arg and Lys residues are important in binding the reactive phosphate, the latter probably binding the phosphate in the transition state. Barstar, a small 89 residue intracellular protein is a natural inhibitor of Barnase.
Probab=16.31 E-value=4.2e+02 Score=21.90 Aligned_cols=24 Identities=25% Similarity=0.304 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHHhHhCCCCCCCceeec
Q 037309 6 TCKELVTYYLRNKILERPLPPSKIREA 32 (287)
Q Consensus 6 TDEELV~~YL~~Ki~g~pl~~~~I~ev 32 (287)
|+.|-|..||.. ...||..+|.-.
T Consensus 2 ~~~~~V~~y~~~---~~~LP~~yiTK~ 25 (107)
T cd00933 2 NTFQGVADYLQT---YHRLPDNYITKS 25 (107)
T ss_pred chHHHHHHHHHH---hCcCCcceEeHH
Confidence 445556679988 334888888644
No 9
>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=15.72 E-value=1.5e+02 Score=18.70 Aligned_cols=20 Identities=30% Similarity=0.416 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHHhHhCCCCC
Q 037309 6 TCKELVTYYLRNKILERPLP 25 (287)
Q Consensus 6 TDEELV~~YL~~Ki~g~pl~ 25 (287)
.-.|||.+|+.-|+.-+..+
T Consensus 4 ~nR~lV~~yi~yKLsQrgy~ 23 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQRGYV 23 (27)
T ss_dssp HHHHHHHHHHHHHHHHTTST
T ss_pred cHHHHHHHHHHHHhhhcCCC
Confidence 35799999999999865544
No 10
>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=14.85 E-value=80 Score=26.86 Aligned_cols=11 Identities=45% Similarity=0.670 Sum_probs=9.2
Q ss_pred cCChHHHHHHH
Q 037309 4 VPTCKELVTYY 14 (287)
Q Consensus 4 ~PTDEELV~~Y 14 (287)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999865
Done!