Query 031935
Match_columns 150
No_of_seqs 105 out of 834
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 07:23:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031935.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031935hhsearch_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 2.4E-47 5.2E-52 273.4 6.9 126 1-132 1-129 (129)
2 PHA00692 hypothetical protein 45.7 8.7 0.00019 23.8 0.5 8 1-8 37-44 (74)
3 KOG3238 Chloride ion current i 37.2 34 0.00074 26.4 2.6 59 3-63 111-170 (216)
4 smart00265 BH4 BH4 Bcl-2 homol 31.8 48 0.001 17.2 1.9 18 10-27 4-22 (27)
5 PF09174 Maf1: Maf1 regulator; 29.3 19 0.0004 27.1 0.1 12 33-45 137-148 (179)
6 PF01473 CW_binding_1: Putativ 29.2 42 0.00092 15.3 1.3 9 57-65 7-15 (19)
7 PF05865 Cypo_polyhedrin: Cypo 22.6 1.2E+02 0.0027 22.8 3.4 28 82-109 140-168 (248)
8 cd00490 Met_repressor_MetJ Met 21.3 85 0.0018 21.1 2.0 39 8-52 50-89 (103)
9 PF08847 DUF1817: Domain of un 21.0 53 0.0011 24.1 1.1 11 3-13 96-107 (150)
10 PRK05264 transcriptional repre 19.8 86 0.0019 21.2 1.8 38 8-51 51-89 (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=2.4e-47 Score=273.43 Aligned_cols=126 Identities=39% Similarity=0.751 Sum_probs=92.8
Q ss_pred CCCCceecCCH-HHHHHHhHHhhcCCCCCCCCCeeecCcccCCCCCCCCCcccCCCCCceEEEEecccccccCCCccccc
Q 031935 1 MESGYKFQPSD-ELILRLLKEKRLNPHFSQHHPIKDIDHICSLEPWDLPTESKTESEDQVFYFFYEPRYKYRNSNRVDRR 79 (150)
Q Consensus 1 lp~G~rF~PtD-ELi~~yL~~k~~g~~~~~~~~I~~~D~vy~~~P~~L~~~~~~~~~~~~~yFF~~~~~~~~~g~r~~R~ 79 (150)
|||||||+||| |||.+||++|+.|+++...++|+++| ||++|||+|++.. .+++++||||+++++++.+++|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~D-iy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVD-IYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE---GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecc-cCccChHHhhhhc--cCCCceEEEEEecccccCCccccccc
Confidence 89999999999 99999999999999985558999999 9999999999422 23567999999999999999999999
Q ss_pred ccCceeEeccCceEEee-CCeEEeeeEEEEEEecC-CCCCCCCcCCeEEEEEEeC
Q 031935 80 TEAGQWKITSEDSHIEA-GNGLTGTKKFLTFYCRG-PDSKVPVKTDWLMHEYHVK 132 (150)
Q Consensus 80 ~~~G~W~~~g~~~~i~~-~g~~iG~kk~l~f~~~~-~~~~~~~kt~W~M~EY~l~ 132 (150)
+++|+||.+|+.+.|.+ +|.++|+|++|+||.++ ++ +.+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~---~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPN---GKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS----EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCC---CCcCCeEEEEEEeC
Confidence 99999999999999998 78999999999999876 44 78999999999984
No 2
>PHA00692 hypothetical protein
Probab=45.71 E-value=8.7 Score=23.77 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=6.1
Q ss_pred CCCCceec
Q 031935 1 MESGYKFQ 8 (150)
Q Consensus 1 lp~G~rF~ 8 (150)
.||||||-
T Consensus 37 yppgfrfg 44 (74)
T PHA00692 37 YPPGFRFG 44 (74)
T ss_pred cCCCcccc
Confidence 38888885
No 3
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=37.19 E-value=34 Score=26.39 Aligned_cols=59 Identities=15% Similarity=0.264 Sum_probs=31.1
Q ss_pred CCceecCCH-HHHHHHhHHhhcCCCCCCCCCeeecCcccCCCCCCCCCcccCCCCCceEEEE
Q 031935 3 SGYKFQPSD-ELILRLLKEKRLNPHFSQHHPIKDIDHICSLEPWDLPTESKTESEDQVFYFF 63 (150)
Q Consensus 3 ~G~rF~PtD-ELi~~yL~~k~~g~~~~~~~~I~~~D~vy~~~P~~L~~~~~~~~~~~~~yFF 63 (150)
-+|||.|+| --+...-.-..-.+.+.+.+ ..+.| -|+-+=|+.-+.....++...||=.
T Consensus 111 ~e~rfvpsDk~~l~a~f~qfcecqel~p~P-~ED~~-~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 111 TEFRFVPSDKSALEAMFTQFCECQELNPDP-DEDED-DYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred ccceecCCchhHHHHHHHHHHhhhhcCCCc-ccccc-ccccchhhhhhhhccCCCCcccccc
Confidence 379999999 44443333233333332222 44555 6666767765554434444445443
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=31.79 E-value=48 Score=17.18 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=14.6
Q ss_pred CH-HHHHHHhHHhhcCCCC
Q 031935 10 SD-ELILRLLKEKRLNPHF 27 (150)
Q Consensus 10 tD-ELi~~yL~~k~~g~~~ 27 (150)
+. |||..|+.-|+.-...
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 45 9999999999976544
No 5
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=29.34 E-value=19 Score=27.07 Aligned_cols=12 Identities=50% Similarity=0.648 Sum_probs=6.8
Q ss_pred eeecCcccCCCCC
Q 031935 33 IKDIDHICSLEPW 45 (150)
Q Consensus 33 I~~~D~vy~~~P~ 45 (150)
+.+|| ||++.|.
T Consensus 137 l~~C~-iYsy~pd 148 (179)
T PF09174_consen 137 LKDCD-IYSYNPD 148 (179)
T ss_dssp GGG-E-EEEE---
T ss_pred ccCce-EEEEccC
Confidence 56799 9999994
No 6
>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=29.15 E-value=42 Score=15.30 Aligned_cols=9 Identities=22% Similarity=0.737 Sum_probs=6.6
Q ss_pred CceEEEEec
Q 031935 57 DQVFYFFYE 65 (150)
Q Consensus 57 ~~~~yFF~~ 65 (150)
++.||||..
T Consensus 7 ~~~wYy~~~ 15 (19)
T PF01473_consen 7 NGNWYYFDS 15 (19)
T ss_dssp TTEEEEETT
T ss_pred CCEEEEeCC
Confidence 468999953
No 7
>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=22.56 E-value=1.2e+02 Score=22.81 Aligned_cols=28 Identities=14% Similarity=0.389 Sum_probs=17.8
Q ss_pred CceeEeccC-ceEEeeCCeEEeeeEEEEE
Q 031935 82 AGQWKITSE-DSHIEAGNGLTGTKKFLTF 109 (150)
Q Consensus 82 ~G~W~~~g~-~~~i~~~g~~iG~kk~l~f 109 (150)
+--|.++|. -+.|..+|+++|+...|..
T Consensus 140 shpweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 140 SHPWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp --S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred cCCccccCceEEEeeccceEeeeeeeeec
Confidence 346999984 5678889999999988765
No 8
>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=21.29 E-value=85 Score=21.08 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=28.7
Q ss_pred cCCH-HHHHHHhHHhhcCCCCCCCCCeeecCcccCCCCCCCCCccc
Q 031935 8 QPSD-ELILRLLKEKRLNPHFSQHHPIKDIDHICSLEPWDLPTESK 52 (150)
Q Consensus 8 ~PtD-ELi~~yL~~k~~g~~~~~~~~I~~~D~vy~~~P~~L~~~~~ 52 (150)
|-|. ||++.-...-..|+|+ |. +.| +-...|.+||....
T Consensus 50 HATNSELLCEAFLHAfTGQPL-P~----D~D-l~K~~~d~iP~~ak 89 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPL-PD----DAD-LRKERSDEIPEAAK 89 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCC-CC----hhh-hhhcCcccccHHHH
Confidence 4578 8887766667889998 32 455 88889999987653
No 9
>PF08847 DUF1817: Domain of unknown function (DUF1817); InterPro: IPR014946 Members of this entry are functionally uncharacterised.
Probab=20.99 E-value=53 Score=24.13 Aligned_cols=11 Identities=36% Similarity=0.884 Sum_probs=9.7
Q ss_pred CCceecCCH-HH
Q 031935 3 SGYKFQPSD-EL 13 (150)
Q Consensus 3 ~G~rF~PtD-EL 13 (150)
.|.+|+|-. ||
T Consensus 96 eGi~fnPEALEi 107 (150)
T PF08847_consen 96 EGIQFNPEALEI 107 (150)
T ss_pred cCceeCHHHHHH
Confidence 489999999 88
No 10
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=19.75 E-value=86 Score=21.19 Aligned_cols=38 Identities=13% Similarity=0.215 Sum_probs=28.2
Q ss_pred cCCH-HHHHHHhHHhhcCCCCCCCCCeeecCcccCCCCCCCCCcc
Q 031935 8 QPSD-ELILRLLKEKRLNPHFSQHHPIKDIDHICSLEPWDLPTES 51 (150)
Q Consensus 8 ~PtD-ELi~~yL~~k~~g~~~~~~~~I~~~D~vy~~~P~~L~~~~ 51 (150)
|-|. ||++.-...-..|+|+ |. +.| +-...|.++|...
T Consensus 51 HATNSELLCEAFLHA~TGQPL-P~----D~D-l~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPL-PD----DED-LRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCC-CC----hhh-hhhcCcccchHHH
Confidence 4578 8887766667889998 32 455 8888999998655
Done!