Query 021877
Match_columns 306
No_of_seqs 174 out of 957
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:20:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021877hhsearch_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 5.3E-42 1.1E-46 287.3 5.7 127 25-153 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 26.4 79 0.0017 19.9 2.5 20 34-53 4-23 (27)
3 KOG3238 Chloride ion current i 19.5 1.5E+02 0.0033 27.3 4.0 48 24-71 108-155 (216)
4 PHA00692 hypothetical protein 16.9 54 0.0012 24.5 0.4 9 24-32 36-44 (74)
5 PF02180 BH4: Bcl-2 homology r 16.6 1.5E+02 0.0033 18.7 2.3 19 35-53 5-23 (27)
6 PF07960 CBP4: CBP4; InterPro 16.3 73 0.0016 27.3 1.1 11 32-42 30-40 (128)
7 cd00490 Met_repressor_MetJ Met 16.2 1.6E+02 0.0034 23.9 2.9 36 32-71 50-85 (103)
8 PF01340 MetJ: Met Apo-repress 15.7 1.6E+02 0.0035 23.8 2.9 36 32-71 50-85 (104)
9 smart00707 RPEL Repeat in Dros 14.5 1.1E+02 0.0024 19.1 1.3 14 28-41 6-19 (26)
10 PRK05264 transcriptional repre 14.5 1.7E+02 0.0036 23.8 2.6 36 32-71 51-86 (105)
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=5.3e-42 Score=287.29 Aligned_cols=127 Identities=52% Similarity=1.046 Sum_probs=96.3
Q ss_pred CCCCceecCChHHHHHHHHHHHHhCCCCCc-CceeeccCCCCCCCCCC-CCCCCCceEEEEeeecccccCCCCCcccccC
Q 021877 25 MLPGFRFHPTDEELVGFYLRRKVEKKPISI-EIIKQADIYKYDPWDLP-MSTVGDKEWYFFCIRGRKYRNSIRPNRVTGS 102 (306)
Q Consensus 25 lpPGfRF~PTDeELV~~YL~~Ki~g~plp~-~~I~evDVY~~~PwdLp-~~~~~e~ewYFFt~r~~k~~~g~R~~R~tgg 102 (306)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+|+ ....++++||||+++.+++.++.|.+|++++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~ 80 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG 80 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc
Confidence 789999999999999999999999999887 79999999999999999 3335677999999999999999999999999
Q ss_pred ceeeccCCCccEecCCCCceeEEEEEEEeeeeCCCCCCCccCceeeeeecC
Q 021877 103 GFWKATGIDKPIHSAKEPHECIGLKKSLVYYRGSAGKGTKTDWMMHEFRLP 153 (306)
Q Consensus 103 G~Wk~~G~~k~I~~~~~~g~~IG~Kk~L~Fy~g~~~~g~kT~W~MhEY~L~ 153 (306)
|+||.+|+.++|... ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~--~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDP--GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE---TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccc--cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999985 5899999999999998888899999999999983
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=26.38 E-value=79 Score=19.94 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHHHHhCCCCC
Q 021877 34 TDEELVGFYLRRKVEKKPIS 53 (306)
Q Consensus 34 TDeELV~~YL~~Ki~g~plp 53 (306)
+-.|||.+|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999765544
No 3
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=19.54 E-value=1.5e+02 Score=27.31 Aligned_cols=48 Identities=19% Similarity=0.326 Sum_probs=27.9
Q ss_pred CCCCCceecCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCC
Q 021877 24 VMLPGFRFHPTDEELVGFYLRRKVEKKPISIEIIKQADIYKYDPWDLP 71 (306)
Q Consensus 24 ~lpPGfRF~PTDeELV~~YL~~Ki~g~plp~~~I~evDVY~~~PwdLp 71 (306)
-..-+|||+|+|.--+.-----...++.+-+....+.+-|.-+=|+.-
T Consensus 108 e~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~me 155 (216)
T KOG3238|consen 108 EPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDME 155 (216)
T ss_pred cccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhh
Confidence 344599999999877765333344444443333455555655555554
No 4
>PHA00692 hypothetical protein
Probab=16.89 E-value=54 Score=24.49 Aligned_cols=9 Identities=56% Similarity=1.003 Sum_probs=7.1
Q ss_pred CCCCCceec
Q 021877 24 VMLPGFRFH 32 (306)
Q Consensus 24 ~lpPGfRF~ 32 (306)
.-||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 368999995
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=16.60 E-value=1.5e+02 Score=18.71 Aligned_cols=19 Identities=26% Similarity=0.405 Sum_probs=15.1
Q ss_pred hHHHHHHHHHHHHhCCCCC
Q 021877 35 DEELVGFYLRRKVEKKPIS 53 (306)
Q Consensus 35 DeELV~~YL~~Ki~g~plp 53 (306)
-.|||.+|+.-|+..+..+
T Consensus 5 nR~lV~~yi~yKLsQrgy~ 23 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRGYV 23 (27)
T ss_dssp HHHHHHHHHHHHHHHTTST
T ss_pred HHHHHHHHHHHHhhhcCCC
Confidence 4799999999999765544
No 6
>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=16.28 E-value=73 Score=27.25 Aligned_cols=11 Identities=55% Similarity=0.827 Sum_probs=9.6
Q ss_pred cCChHHHHHHH
Q 021877 32 HPTDEELVGFY 42 (306)
Q Consensus 32 ~PTDeELV~~Y 42 (306)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
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=16.22 E-value=1.6e+02 Score=23.88 Aligned_cols=36 Identities=25% Similarity=0.348 Sum_probs=30.1
Q ss_pred cCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCC
Q 021877 32 HPTDEELVGFYLRRKVEKKPISIEIIKQADIYKYDPWDLP 71 (306)
Q Consensus 32 ~PTDeELV~~YL~~Ki~g~plp~~~I~evDVY~~~PwdLp 71 (306)
|-|..||++.-...-..|+|||. +.|+-+..|..+|
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP 85 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIP 85 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCccccc
Confidence 56788999888888889999995 5688888888888
No 8
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=15.74 E-value=1.6e+02 Score=23.82 Aligned_cols=36 Identities=25% Similarity=0.418 Sum_probs=23.5
Q ss_pred cCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCC
Q 021877 32 HPTDEELVGFYLRRKVEKKPISIEIIKQADIYKYDPWDLP 71 (306)
Q Consensus 32 ~PTDeELV~~YL~~Ki~g~plp~~~I~evDVY~~~PwdLp 71 (306)
|-|..||++.-...-..|+|||. +.|+-+..|..+|
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~----D~dl~kd~~d~ip 85 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT----DDDLRKDRPDEIP 85 (104)
T ss_dssp S-SHHHHHHHHHHHHHH----------TTGGGSTSGSSS-
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCCccch
Confidence 56888999888888899999995 5688888888888
No 9
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=14.51 E-value=1.1e+02 Score=19.09 Aligned_cols=14 Identities=36% Similarity=0.330 Sum_probs=11.2
Q ss_pred CceecCChHHHHHH
Q 021877 28 GFRFHPTDEELVGF 41 (306)
Q Consensus 28 GfRF~PTDeELV~~ 41 (306)
...++|+.||||..
T Consensus 6 kl~~RP~~eeLv~r 19 (26)
T smart00707 6 KLSQRPTREELEER 19 (26)
T ss_pred HHHcCCCHHHHHHc
Confidence 45689999999973
No 10
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=14.47 E-value=1.7e+02 Score=23.83 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=29.9
Q ss_pred cCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCC
Q 021877 32 HPTDEELVGFYLRRKVEKKPISIEIIKQADIYKYDPWDLP 71 (306)
Q Consensus 32 ~PTDeELV~~YL~~Ki~g~plp~~~I~evDVY~~~PwdLp 71 (306)
|-|-.||++.-...-..|+|||. +-|+-+..|..+|
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip 86 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIP 86 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccch
Confidence 56788999888888889999995 5678888888888
Done!