Query 036036
Match_columns 98
No_of_seqs 104 out of 680
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 08:48:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036036hhsearch_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 99.9 2.3E-26 5E-31 154.8 8.9 77 5-82 53-129 (129)
2 PF01473 CW_binding_1: Putativ 54.9 10 0.00022 16.9 1.4 9 6-14 6-14 (19)
3 COG3323 Uncharacterized protei 11.4 4.6E+02 0.01 17.4 3.6 19 29-47 42-60 (109)
4 KOG3761 Choline transporter [L 11.4 87 0.0019 25.5 0.2 19 68-86 298-316 (591)
5 cd08540 SAM_PNT-ERG Sterile al 11.2 24 0.00053 21.7 -2.4 13 73-85 18-30 (75)
6 PF10983 DUF2793: Protein of u 10.8 1.3E+02 0.0028 19.0 0.8 15 3-17 52-66 (87)
7 cd08543 SAM_PNT-ETS-2 Sterile 9.9 33 0.00071 22.0 -2.2 14 72-85 31-44 (89)
8 PF14888 PBP-Tp47_c: Penicilli 9.7 1.9E+02 0.0042 20.4 1.4 16 23-38 118-133 (161)
9 cd08533 SAM_PNT-ETS-1,2 Steril 9.0 35 0.00077 20.8 -2.2 12 73-84 17-28 (71)
10 smart00456 WW Domain with 2 co 8.8 2.8E+02 0.0061 13.2 1.5 13 5-17 10-22 (32)
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=99.94 E-value=2.3e-26 Score=154.82 Aligned_cols=77 Identities=52% Similarity=0.957 Sum_probs=58.6
Q ss_pred cCCCeEEEEEeccCCCcCCCcceeeecceEEEEeCCCeeEEcCCCCeEEEEEEEEEEeeccCCCCcccCeEEEEEEeC
Q 036036 5 RDDDEWYFFSEHNKKYANSARTERTTRAGHWKVTGKDRQIWDKNRKEVIGVKKNLVFYEGRGSNAVKTSWVIHEYHSN 82 (98)
Q Consensus 5 ~~~~~wYFFs~~~~k~~~g~R~~R~t~~G~Wk~~g~~k~I~~~~~~~~iG~kk~l~Fy~g~~~~~~kT~WvM~EY~l~ 82 (98)
.++++||||+++.+++.++.|.+|++++|+||++|+.++|.+. ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 53 ~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 53 GGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp S-SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred CCCceEEEEEecccccCCcccccccccceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 4567999999999999999999999999999999999999985 7779999999999999888999999999999984
No 2
>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=54.86 E-value=10 Score=16.93 Aligned_cols=9 Identities=44% Similarity=1.571 Sum_probs=6.9
Q ss_pred CCCeEEEEE
Q 036036 6 DDDEWYFFS 14 (98)
Q Consensus 6 ~~~~wYFFs 14 (98)
.++.||||.
T Consensus 6 ~~~~wYy~~ 14 (19)
T PF01473_consen 6 DNGNWYYFD 14 (19)
T ss_dssp ETTEEEEET
T ss_pred ECCEEEEeC
Confidence 358999993
No 3
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=11.43 E-value=4.6e+02 Score=17.41 Aligned_cols=19 Identities=5% Similarity=0.185 Sum_probs=14.6
Q ss_pred eecceEEEEeCCCeeEEcC
Q 036036 29 TTRAGHWKVTGKDRQIWDK 47 (98)
Q Consensus 29 ~t~~G~Wk~~g~~k~I~~~ 47 (98)
..+.|+|++.....|....
T Consensus 42 ~~g~G~frP~egAnP~iGe 60 (109)
T COG3323 42 SEGTGQFRPLEGANPFIGE 60 (109)
T ss_pred eeeeEEEeecCCCCCcccc
Confidence 3578999998888887753
No 4
>KOG3761 consensus Choline transporter [Lipid transport and metabolism]
Probab=11.36 E-value=87 Score=25.47 Aligned_cols=19 Identities=21% Similarity=0.422 Sum_probs=15.6
Q ss_pred CCcccCeEEEEEEeCCCCC
Q 036036 68 NAVKTSWVIHEYHSNNASA 86 (98)
Q Consensus 68 ~~~kT~WvM~EY~l~~~~~ 86 (98)
-+..|+|-|..|.++++..
T Consensus 298 i~~ntdw~~t~y~~~d~~t 316 (591)
T KOG3761|consen 298 IAANTDWNMTAYGLPDNGT 316 (591)
T ss_pred hhccCcccccccCCCCCCc
Confidence 4568999999999988754
No 5
>cd08540 SAM_PNT-ERG Sterile alpha motif (SAM)/Pointed domain of ERG transcription factor. SAM Pointed domain of ERG subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It may participate in formation of homodimers or heterodimers with ETS-2, Fli-1, ER81, and Pu-1. However, dimeric forms are inactive and SAM Pointed domain is not essential for dimerization, since ER81 and Pu-1 do not have it. In mouse, a regulator of this type binds the ESET histone H3-specific methyltransferase (human homolog is SETDB1), followed by modification of local chromatin structure through histone methylation. ERG regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. The Erg gene is a proto-oncogene. It is a target of chromosomal translocations resulting in fusions with new neighboring genes. Chimeric proteins were found in solid tumors such as myeloid leukemia or Ewing's sarcoma. Members of this subfamily are po
Probab=11.20 E-value=24 Score=21.73 Aligned_cols=13 Identities=23% Similarity=0.718 Sum_probs=10.6
Q ss_pred CeEEEEEEeCCCC
Q 036036 73 SWVIHEYHSNNAS 85 (98)
Q Consensus 73 ~WvM~EY~l~~~~ 85 (98)
.|+|.||.|....
T Consensus 18 ~Wa~~ef~L~~~~ 30 (75)
T cd08540 18 EWAVKEYGLPDVD 30 (75)
T ss_pred HHHHHHhCCCCCC
Confidence 5999999997744
No 6
>PF10983 DUF2793: Protein of unknown function (DUF2793); InterPro: IPR021251 This entry is represented by Bacteriophage D3112, Orf54. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=10.82 E-value=1.3e+02 Score=19.02 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=12.1
Q ss_pred cccCCCeEEEEEecc
Q 036036 3 AIRDDDEWYFFSEHN 17 (98)
Q Consensus 3 a~~~~~~wYFFs~~~ 17 (98)
|...++.|.|++|+.
T Consensus 52 A~~~~g~W~f~~P~~ 66 (87)
T PF10983_consen 52 AAWQDGAWRFLTPRP 66 (87)
T ss_pred EEEECCeEEEeCCCC
Confidence 456678899999886
No 7
>cd08543 SAM_PNT-ETS-2 Sterile alpha motif (SAM)/Pointed domain of ETS-2. SAM Pointed domain of ETS-2 subfamily of ETS transcriptional regulators is a protein-protein interaction domain. It contains a docking site for Cdk10 (cyclin-dependent kinase 10), a member of the Cdc2 kinase family. The interaction between ETS-2 and Cdk10 kinase inhibits ETS-2 transactivation activity in mammals. ETS-2 is also regulated by ERK2 MAP kinase. ETS-2, which is phosphorylated by ERK2, can interact with coactivators and enhance transactivation. ETS-2 transcriptional activators are involved in embryonic development and cell cycle control. The Ets-2 gene is a proto-oncogene. It is overexpressed in breast and prostate cancer cells and its overexpression is necessary for transformation of such cells. Members of ETS-2 subfamily are potential molecular targets for selective cancer therapy.
Probab=9.93 E-value=33 Score=21.96 Aligned_cols=14 Identities=21% Similarity=0.489 Sum_probs=10.8
Q ss_pred cCeEEEEEEeCCCC
Q 036036 72 TSWVIHEYHSNNAS 85 (98)
Q Consensus 72 T~WvM~EY~l~~~~ 85 (98)
-.|.|+||.|..-+
T Consensus 31 L~Wa~~ef~L~~i~ 44 (89)
T cd08543 31 LLWATNEFSLVNVN 44 (89)
T ss_pred HHHHHHHcCCCCCC
Confidence 35899999998643
No 8
>PF14888 PBP-Tp47_c: Penicillin-binding protein Tp47 domain C; PDB: 1O75_B.
Probab=9.70 E-value=1.9e+02 Score=20.38 Aligned_cols=16 Identities=25% Similarity=0.482 Sum_probs=9.4
Q ss_pred CCcceeeecceEEEEe
Q 036036 23 SARTERTTRAGHWKVT 38 (98)
Q Consensus 23 g~R~~R~t~~G~Wk~~ 38 (98)
.+++.-+.+.|||+.+
T Consensus 118 c~lp~GtdGtGYw~lT 133 (161)
T PF14888_consen 118 CQLPKGTDGTGYWSLT 133 (161)
T ss_dssp SGGGTT---SEEEEEE
T ss_pred ecccCCCCCCceEEEE
Confidence 4455667789999975
No 9
>cd08533 SAM_PNT-ETS-1,2 Sterile alpha motif (SAM)/Pointed domain of ETS-1,2 family. SAM Pointed domain of ETS-1,2 family of transcriptional activators is a protein-protein interaction domain. It carries a kinase docking site and mediates interaction between ETS transcriptional activators and protein kinases. This group of transcriptional factors is involved in the Ras/MAP kinase signaling pathway. MAP kinases phosphorylate the transcription factors. Phosphorylated factors then recruit coactivators and enhance transactivation. Members of this group play a role in regulation of different embryonic developmental processes. ETS-1,2 transcriptional activators are proto-oncogenes involved in malignant transformation and tumor progression. They are potential molecular targets for selective cancer therapy.
Probab=9.00 E-value=35 Score=20.78 Aligned_cols=12 Identities=17% Similarity=0.675 Sum_probs=9.6
Q ss_pred CeEEEEEEeCCC
Q 036036 73 SWVIHEYHSNNA 84 (98)
Q Consensus 73 ~WvM~EY~l~~~ 84 (98)
.|.++||.|..-
T Consensus 17 ~Wa~~ef~L~~v 28 (71)
T cd08533 17 LWAVNEFSLEGV 28 (71)
T ss_pred HHHHHHcCCCCC
Confidence 489999999753
No 10
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=8.76 E-value=2.8e+02 Score=13.15 Aligned_cols=13 Identities=15% Similarity=0.498 Sum_probs=8.5
Q ss_pred cCCCeEEEEEecc
Q 036036 5 RDDDEWYFFSEHN 17 (98)
Q Consensus 5 ~~~~~wYFFs~~~ 17 (98)
+.++..||+....
T Consensus 10 ~~~g~~yy~n~~t 22 (32)
T smart00456 10 DPDGRPYYYNHET 22 (32)
T ss_pred CCCCCEEEEECCC
Confidence 4457888886543
Done!