Query 021785
Match_columns 307
No_of_seqs 180 out of 959
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 05:40:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021785hhsearch_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 9E-43 1.9E-47 292.0 5.2 128 25-154 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 30.2 63 0.0014 20.3 2.5 20 34-53 4-23 (27)
3 KOG3238 Chloride ion current i 20.9 1.2E+02 0.0026 28.0 3.6 47 25-71 109-155 (216)
4 PF02180 BH4: Bcl-2 homology r 19.9 1.2E+02 0.0025 19.2 2.3 20 35-54 5-24 (27)
5 PHA00692 hypothetical protein 16.1 59 0.0013 24.2 0.4 8 25-32 37-44 (74)
6 smart00707 RPEL Repeat in Dros 14.4 1.1E+02 0.0024 19.0 1.3 14 28-41 6-19 (26)
7 PF07960 CBP4: CBP4; InterPro 14.2 89 0.0019 26.7 1.1 11 32-42 30-40 (128)
8 PF01473 CW_binding_1: Putativ 12.4 1.4E+02 0.003 16.5 1.2 8 78-85 7-14 (19)
9 PLN02417 dihydrodipicolinate s 11.5 1.3E+02 0.0029 28.2 1.5 20 24-43 101-120 (280)
10 cd00490 Met_repressor_MetJ Met 10.8 2.7E+02 0.0058 22.5 2.7 38 32-73 50-87 (103)
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=9e-43 Score=292.04 Aligned_cols=128 Identities=52% Similarity=1.037 Sum_probs=96.8
Q ss_pred CCCCceecCChHHHHHHHHHHHHhCCCCCc-CceeeccCCCCCCCCCCCccCCCCceEEEEeeeccccCCCCCCcccccC
Q 021785 25 MLPGFRFHPTDEELVGFYLRRKVEKKPISI-EIIKQADIYKYDPWDLPKVSTVGDKEWYFFCIRGRKYRNSIRPNRVTGS 103 (307)
Q Consensus 25 lpPGfRF~PTDeELV~~YL~~Ki~g~pl~~-~~I~~~DVY~~~PwdLp~~~~~gd~ewYFFs~r~~k~~~g~R~~R~tg~ 103 (307)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+|++....++++||||+++++++.++.|.+|++++
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 799999999999999999999999999887 6999999999999999953333677999999999999999999999999
Q ss_pred ceeeecCCCcceecCCCCceeeEEEEEEeeecCCCCCCCccCceeeeEEcC
Q 021785 104 GFWKATGIDKPIHSAKEPHECIGLKKSLVYYRGSAGKGTKTDWMMHEFRLP 154 (307)
Q Consensus 104 G~Wk~~G~~k~I~~~~~~g~~IG~Kk~L~Fy~g~~~~~~kT~W~MhEYrL~ 154 (307)
|+||++|+.++|... ++.+||+|++|+||.++.+++.+|+|+||||+|.
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 6899999999999998888899999999999983
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=30.18 E-value=63 Score=20.33 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=15.9
Q ss_pred ChHHHHHHHHHHHHhCCCCC
Q 021785 34 TDEELVGFYLRRKVEKKPIS 53 (307)
Q Consensus 34 TDeELV~~YL~~Ki~g~pl~ 53 (307)
+-.|||.+|+.-||.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999766544
No 3
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=20.95 E-value=1.2e+02 Score=27.97 Aligned_cols=47 Identities=19% Similarity=0.347 Sum_probs=27.2
Q ss_pred CCCCceecCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCC
Q 021785 25 MLPGFRFHPTDEELVGFYLRRKVEKKPISIEIIKQADIYKYDPWDLP 71 (307)
Q Consensus 25 lpPGfRF~PTDeELV~~YL~~Ki~g~pl~~~~I~~~DVY~~~PwdLp 71 (307)
..-+|||+|+|.--+..---....+..+-+....+.+-|.-+=|+.-
T Consensus 109 ~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~me 155 (216)
T KOG3238|consen 109 PITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDME 155 (216)
T ss_pred ccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhh
Confidence 33599999999887765333333444443333445555655555554
No 4
>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=19.91 E-value=1.2e+02 Score=19.16 Aligned_cols=20 Identities=25% Similarity=0.355 Sum_probs=15.7
Q ss_pred hHHHHHHHHHHHHhCCCCCc
Q 021785 35 DEELVGFYLRRKVEKKPISI 54 (307)
Q Consensus 35 DeELV~~YL~~Ki~g~pl~~ 54 (307)
-.|||.+|+.-|+.-+..++
T Consensus 5 nR~lV~~yi~yKLsQrgy~w 24 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRGYVW 24 (27)
T ss_dssp HHHHHHHHHHHHHHHTTSTS
T ss_pred HHHHHHHHHHHHhhhcCCCC
Confidence 47999999999997665543
No 5
>PHA00692 hypothetical protein
Probab=16.08 E-value=59 Score=24.22 Aligned_cols=8 Identities=63% Similarity=1.206 Sum_probs=6.7
Q ss_pred CCCCceec
Q 021785 25 MLPGFRFH 32 (307)
Q Consensus 25 lpPGfRF~ 32 (307)
-||||||-
T Consensus 37 yppgfrfg 44 (74)
T PHA00692 37 YPPGFRFG 44 (74)
T ss_pred cCCCcccc
Confidence 58999995
No 6
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=14.36 E-value=1.1e+02 Score=19.03 Aligned_cols=14 Identities=36% Similarity=0.330 Sum_probs=11.3
Q ss_pred CceecCChHHHHHH
Q 021785 28 GFRFHPTDEELVGF 41 (307)
Q Consensus 28 GfRF~PTDeELV~~ 41 (307)
...++|+.+|||..
T Consensus 6 kl~~RP~~eeLv~r 19 (26)
T smart00707 6 KLSQRPTREELEER 19 (26)
T ss_pred HHHcCCCHHHHHHc
Confidence 45689999999973
No 7
>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=14.18 E-value=89 Score=26.69 Aligned_cols=11 Identities=55% Similarity=0.827 Sum_probs=9.5
Q ss_pred cCChHHHHHHH
Q 021785 32 HPTDEELVGFY 42 (307)
Q Consensus 32 ~PTDeELV~~Y 42 (307)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 8
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=12.39 E-value=1.4e+02 Score=16.47 Aligned_cols=8 Identities=38% Similarity=1.369 Sum_probs=5.9
Q ss_pred CceEEEEe
Q 021785 78 DKEWYFFC 85 (307)
Q Consensus 78 d~ewYFFs 85 (307)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 46799993
No 9
>PLN02417 dihydrodipicolinate synthase
Probab=11.51 E-value=1.3e+02 Score=28.23 Aligned_cols=20 Identities=10% Similarity=0.218 Sum_probs=15.6
Q ss_pred CCCCCceecCChHHHHHHHH
Q 021785 24 VMLPGFRFHPTDEELVGFYL 43 (307)
Q Consensus 24 ~lpPGfRF~PTDeELV~~YL 43 (307)
++.|.|.|.||++||+.||-
T Consensus 101 ~~~~P~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 101 LHINPYYGKTSQEGLIKHFE 120 (280)
T ss_pred EEcCCccCCCCHHHHHHHHH
Confidence 34456779999999999863
No 10
>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=10.82 E-value=2.7e+02 Score=22.51 Aligned_cols=38 Identities=24% Similarity=0.341 Sum_probs=30.3
Q ss_pred cCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCCCc
Q 021785 32 HPTDEELVGFYLRRKVEKKPISIEIIKQADIYKYDPWDLPKV 73 (307)
Q Consensus 32 ~PTDeELV~~YL~~Ki~g~pl~~~~I~~~DVY~~~PwdLp~~ 73 (307)
|-|-.||++.-...-..|+|||. +.|+-+..|..+|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHH
Confidence 46778888887778889999994 467888888888864
Done!