Query 036898
Match_columns 396
No_of_seqs 152 out of 947
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:30:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036898hhsearch_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 7.4E-37 1.6E-41 264.6 7.3 121 1-140 7-129 (129)
2 PTZ00444 hypothetical protein; 20.7 27 0.00059 33.1 -0.5 31 306-346 47-77 (184)
3 smart00265 BH4 BH4 Bcl-2 homol 14.2 1.9E+02 0.0041 19.5 2.4 19 4-22 4-22 (27)
4 PF05865 Cypo_polyhedrin: Cypo 8.9 3.2E+02 0.007 26.0 3.0 27 85-111 141-168 (248)
5 smart00707 RPEL Repeat in Dros 8.5 2.3E+02 0.005 18.9 1.4 10 1-10 9-18 (26)
6 KOG4286 Dystrophin-like protei 8.5 78 0.0017 36.3 -1.4 54 101-168 613-678 (966)
7 PF12590 Acyl-thio_N: Acyl-ATP 8.5 1.2E+02 0.0027 27.3 0.1 11 325-335 93-103 (129)
8 PF04700 Baculo_gp41: Structur 8.2 3.3E+02 0.0072 26.1 2.8 20 4-23 6-27 (186)
9 PF02180 BH4: Bcl-2 homology r 7.6 3.6E+02 0.0078 18.2 2.0 17 5-21 5-21 (27)
10 PF07960 CBP4: CBP4; InterPro 7.3 2.2E+02 0.0048 25.7 1.1 11 2-12 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=7.4e-37 Score=264.56 Aligned_cols=121 Identities=45% Similarity=0.831 Sum_probs=92.1
Q ss_pred CCCChHHHHHHHHHHHHcCCCCCC-CceeecCCCCCCchhhhHhhhhhhhcCCCceEEEeccccccCCCCCccceeccCC
Q 036898 1 FCPLDWELLVCYLKKKVKNEPLPP-NRIMEIKLYNFTPEQLKQELKVKYKDLREKEMFFFTPRERKHQNGTRLNRVTGSG 79 (396)
Q Consensus 1 F~PTDEELV~~YL~~Ki~G~plp~-~~I~evDVY~~ePweLp~~~~~~~~~~~e~eWYFFspr~rK~~nG~R~nRttG~g 79 (396)
|+|||+|||.+||++|+.|.+++. ++|+++|||+++||+|+.. ...++++||||+++++++.+|.|.+|++
T Consensus 7 F~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~-----~~~~~~~~yFF~~~~~~~~~~~r~~R~~--- 78 (129)
T PF02365_consen 7 FRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAK-----FKGGDEEWYFFSPRKKKYPNGGRPNRVT--- 78 (129)
T ss_dssp E---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHH-----SSS-SSEEEEEEE----------S-EEE---
T ss_pred ecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhh-----ccCCCceEEEEEecccccCCcccccccc---
Confidence 899999999999999999999887 8999999999999999953 3346779999999999999999999988
Q ss_pred CCCCCceEeecCCCceEee-CCeeEEEEEEeeeecCCCCCCCCCCCCCccccCeeEEeeecC
Q 036898 80 PDSGSGYWKSTGADKSIKF-KGALVGFKKQLVYYRKNPEAGGEGEKNDWIKTDWIMHEFRVP 140 (396)
Q Consensus 80 ~~~ggG~WK~tG~~k~I~~-~G~vVG~KKtLvFy~gr~p~G~~G~~~~~~KT~WvMhEYrL~ 140 (396)
++|+||.+|+.+.|.+ .|.+||+|++|+||.++.+++ .+|+|+||||+|.
T Consensus 79 ---~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~--------~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 ---GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNG--------KKTGWVMHEYSLE 129 (129)
T ss_dssp ---TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS---------EEEEEEEEEEEE-
T ss_pred ---cceEEeecccccccccccceeeeeEEEEEEEeccCCCC--------CcCCeEEEEEEeC
Confidence 8999999999999998 689999999999998877777 8999999999984
No 2
>PTZ00444 hypothetical protein; Provisional
Probab=20.73 E-value=27 Score=33.15 Aligned_cols=31 Identities=39% Similarity=0.459 Sum_probs=21.9
Q ss_pred cccccCCcchhhhhccCCCCCcccchhhhccChhhhccccc
Q 036898 306 SIAFESMPTQAQVFADNVNLPEWSSLITAVVDPEIQKLDSY 346 (396)
Q Consensus 306 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 346 (396)
-.++|+|||++||.+. |-++-+-+|.|||.-
T Consensus 47 k~~~e~lPt~~~v~~~----------~~~id~e~~~kl~~~ 77 (184)
T PTZ00444 47 KLASETLPTPEQVSAK----------IHRIDKEVIKKLDKD 77 (184)
T ss_pred HHHHhcCCCHHHHHHH----------HHhcCHHHHHHHHHH
Confidence 3689999999997654 555555566677653
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=14.21 E-value=1.9e+02 Score=19.47 Aligned_cols=19 Identities=26% Similarity=0.333 Sum_probs=15.0
Q ss_pred ChHHHHHHHHHHHHcCCCC
Q 036898 4 LDWELLVCYLKKKVKNEPL 22 (396)
Q Consensus 4 TDEELV~~YL~~Ki~G~pl 22 (396)
+-.|||.+|+.-|+.-...
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999965443
No 4
>PF05865 Cypo_polyhedrin: Cypovirus polyhedrin protein; InterPro: IPR008464 This family consists of several Cypovirus polyhedrin proteins. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells [].; PDB: 2OH7_A 2OH5_A 2OH6_A.
Probab=8.89 E-value=3.2e+02 Score=26.04 Aligned_cols=27 Identities=26% Similarity=0.571 Sum_probs=17.9
Q ss_pred ceEeecC-CCceEeeCCeeEEEEEEeee
Q 036898 85 GYWKSTG-ADKSIKFKGALVGFKKQLVY 111 (396)
Q Consensus 85 G~WK~tG-~~k~I~~~G~vVG~KKtLvF 111 (396)
--|.++| +-+.|...|++||+...|..
T Consensus 141 hpweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 141 HPWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp -S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred CCccccCceEEEeeccceEeeeeeeeec
Confidence 4599998 56778888999999988865
No 5
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=8.54 E-value=2.3e+02 Score=18.88 Aligned_cols=10 Identities=30% Similarity=-0.004 Sum_probs=8.2
Q ss_pred CCCChHHHHH
Q 036898 1 FCPLDWELLV 10 (396)
Q Consensus 1 F~PTDEELV~ 10 (396)
++|+-+|||.
T Consensus 9 ~RP~~eeLv~ 18 (26)
T smart00707 9 QRPTREELEE 18 (26)
T ss_pred cCCCHHHHHH
Confidence 4799999985
No 6
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=8.48 E-value=78 Score=36.28 Aligned_cols=54 Identities=17% Similarity=0.375 Sum_probs=37.6
Q ss_pred eeEEEE-EEee----------eecCCCCCCCCCCCCCccccCeeEEeeecCCCCCCCCCCCCCCcc-ceEEEEEEEcCCC
Q 036898 101 ALVGFK-KQLV----------YYRKNPEAGGEGEKNDWIKTDWIMHEFRVPNNPTPRKKDGTNMEL-DWALCKIYKKVYK 168 (396)
Q Consensus 101 ~vVG~K-KtLv----------Fy~gr~p~G~~G~~~~~~KT~WvMhEYrL~~~~~~~~~~~~~~~~-d~VLCRIykK~~~ 168 (396)
.+||+| |+|+ |..|++.+| .|++.-|.||.....+.. .++. --|||--|+.++.
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgraak~--------hk~~~pM~Ey~~~tts~~------d~rdfak~L~nkfr~~~~ 678 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGRAAKG--------HKMHYPMVEYCTPTTSGE------DVRDFAKVLKNKFRTKRY 678 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhcccccC--------CCCCCCceeeeCCCCChh------hHHHHHHHHHhhhccchh
Confidence 678888 4443 557788777 999999999998875531 1222 4478887776553
No 7
>PF12590 Acyl-thio_N: Acyl-ATP thioesterase; InterPro: IPR021113 This entry represents the N-terminal domain of acyl-ATP thioesterases from bacteria and eukaryotes. These proteins are typically between 120 and 131 amino acids in length. The plant acyl-acyl carrier protein (ACP) thioesterases (TEs) play an essential role in chain termination during de novo fatty acid synthesis [].; GO: 0016790 thiolester hydrolase activity
Probab=8.47 E-value=1.2e+02 Score=27.33 Aligned_cols=11 Identities=55% Similarity=1.277 Sum_probs=9.7
Q ss_pred CCcccchhhhc
Q 036898 325 LPEWSSLITAV 335 (396)
Q Consensus 325 ~~~~~~~~~~~ 335 (396)
|||||-|+.|+
T Consensus 93 LPDWSMLLAAI 103 (129)
T PF12590_consen 93 LPDWSMLLAAI 103 (129)
T ss_pred CccHHHHHHHH
Confidence 99999998775
No 8
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=8.16 E-value=3.3e+02 Score=26.09 Aligned_cols=20 Identities=40% Similarity=0.547 Sum_probs=14.4
Q ss_pred ChHHHHHHH--HHHHHcCCCCC
Q 036898 4 LDWELLVCY--LKKKVKNEPLP 23 (396)
Q Consensus 4 TDEELV~~Y--L~~Ki~G~plp 23 (396)
+|+|||.|| |.+|..|...+
T Consensus 6 sDe~Li~yY~~L~K~~g~~~~~ 27 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGSDVP 27 (186)
T ss_pred cHHHHHHHHHHHHHHhCCCCCC
Confidence 799999998 44666665544
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=7.63 E-value=3.6e+02 Score=18.22 Aligned_cols=17 Identities=24% Similarity=0.356 Sum_probs=13.5
Q ss_pred hHHHHHHHHHHHHcCCC
Q 036898 5 DWELLVCYLKKKVKNEP 21 (396)
Q Consensus 5 DEELV~~YL~~Ki~G~p 21 (396)
-.|||.+|+.-|+.-+.
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 47999999999986443
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=7.28 E-value=2.2e+02 Score=25.70 Aligned_cols=11 Identities=36% Similarity=0.537 Sum_probs=9.3
Q ss_pred CCChHHHHHHH
Q 036898 2 CPLDWELLVCY 12 (396)
Q Consensus 2 ~PTDEELV~~Y 12 (396)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 59999999765
Done!