Query 032371
Match_columns 142
No_of_seqs 118 out of 833
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 13:13:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032371.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032371hhsearch_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 5E-47 1.1E-51 269.3 7.0 126 5-135 1-129 (129)
2 PHA00692 hypothetical protein 59.0 3.6 7.8E-05 25.3 0.3 11 3-13 35-45 (74)
3 KOG3238 Chloride ion current i 36.7 37 0.00079 26.0 2.7 61 5-66 109-170 (216)
4 PF01473 CW_binding_1: Putativ 30.1 39 0.00085 15.3 1.3 8 60-67 7-14 (19)
5 smart00265 BH4 BH4 Bcl-2 homol 27.8 78 0.0017 16.3 2.2 20 14-33 4-24 (27)
6 PF09174 Maf1: Maf1 regulator; 26.8 18 0.00039 26.9 -0.4 34 36-70 137-172 (179)
7 COG4741 Predicted secreted end 23.0 33 0.00072 25.3 0.4 15 4-18 97-112 (175)
8 PF10107 Endonuc_Holl: Endonuc 22.0 33 0.00071 25.2 0.2 13 4-16 84-96 (156)
9 PF06214 SLAM: Signaling lymph 19.0 33 0.00072 23.9 -0.3 47 23-69 75-123 (126)
10 PF07677 A2M_recep: A-macroglo 15.6 38 0.00082 22.1 -0.7 16 1-16 6-21 (91)
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=5e-47 Score=269.31 Aligned_cols=126 Identities=35% Similarity=0.613 Sum_probs=95.0
Q ss_pred CCCCceEcCCHH-HHHHHHhhhhcCCCCCC-CCeeeccCCCCCCccCccccccccCCCceEEEeecCcccccCCCccccc
Q 032371 5 MGQGYKFQPSDE-LSVSLLKEKRLDPHFSY-GPIKDIGHICSLEPEDLATESETESEDQACYFFYEPHYKYRNSNRVHRR 82 (142)
Q Consensus 5 lp~G~rF~PtD~-Li~~YL~~ki~g~~l~~-~~I~~~~Dvy~~~P~~L~~~~~~~~~~~~wyFF~~~~~~~~~g~r~~r~ 82 (142)
|||||||+|||+ ||.+||.+|+.|.+++. .+|+++ |||++|||+|+.... .++.+||||+++++++.+++|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~-Diy~~~P~~L~~~~~--~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDV-DIYSAHPWELPAKFK--GGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE---GGGS-GGGCHHHSS--S-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeec-ccCccChHHhhhhcc--CCCceEEEEEecccccCCccccccc
Confidence 899999999999 99999999999999887 789999 999999999994322 3567999999999999999999999
Q ss_pred ccCCeeEeecCcceEee-CCeEEeeEEEEEEEecCCCCCCCcCCCeEEEEEEeC
Q 032371 83 TEAGQWKITSEDSQIEA-SNRLSGTKKFLTFYRRSPGSKVPVKTDWVMHEYHVK 135 (142)
Q Consensus 83 ~~~G~Wk~~g~~~~i~~-~g~~iG~k~~l~fy~~~~~~~~~~~t~W~M~Ey~l~ 135 (142)
+++|+||++|+.++|.+ ++.+||+|++|+||.++.+++ .+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~--~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNG--KKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS---EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCCC--CcCCeEEEEEEeC
Confidence 99999999999999999 699999999999998877666 8999999999984
No 2
>PHA00692 hypothetical protein
Probab=58.97 E-value=3.6 Score=25.30 Aligned_cols=11 Identities=18% Similarity=0.492 Sum_probs=8.3
Q ss_pred CCCCCCceEcC
Q 032371 3 SHMGQGYKFQP 13 (142)
Q Consensus 3 ~~lp~G~rF~P 13 (142)
+..||||||--
T Consensus 35 veyppgfrfgg 45 (74)
T PHA00692 35 VEYPPGFRFGG 45 (74)
T ss_pred EecCCCccccc
Confidence 35799999953
No 3
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=36.68 E-value=37 Score=26.04 Aligned_cols=61 Identities=15% Similarity=0.196 Sum_probs=32.1
Q ss_pred CCCCceEcCCHH-HHHHHHhhhhcCCCCCCCCeeeccCCCCCCccCccccccccCCCceEEEe
Q 032371 5 MGQGYKFQPSDE-LSVSLLKEKRLDPHFSYGPIKDIGHICSLEPEDLATESETESEDQACYFF 66 (142)
Q Consensus 5 lp~G~rF~PtD~-Li~~YL~~ki~g~~l~~~~I~~~~Dvy~~~P~~L~~~~~~~~~~~~wyFF 66 (142)
.--++||.|+|. -+...-......+.+-.....+. +-|+-+=|+........++...||=.
T Consensus 109 ~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~-~~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 109 PITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDE-DDYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred ccccceecCCchhHHHHHHHHHHhhhhcCCCccccc-cccccchhhhhhhhccCCCCcccccc
Confidence 345899999999 65552233333333322234555 56666666665543333334444433
No 4
>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=30.15 E-value=39 Score=15.30 Aligned_cols=8 Identities=25% Similarity=0.708 Sum_probs=6.4
Q ss_pred CceEEEee
Q 032371 60 DQACYFFY 67 (142)
Q Consensus 60 ~~~wyFF~ 67 (142)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899994
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=27.83 E-value=78 Score=16.27 Aligned_cols=20 Identities=15% Similarity=0.270 Sum_probs=15.0
Q ss_pred CHH-HHHHHHhhhhcCCCCCC
Q 032371 14 SDE-LSVSLLKEKRLDPHFSY 33 (142)
Q Consensus 14 tD~-Li~~YL~~ki~g~~l~~ 33 (142)
+.. ||.+|+.-|+.....++
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 445 99999999998665443
No 6
>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=26.75 E-value=18 Score=26.89 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=14.2
Q ss_pred eeeccCCCCCCccCcccccc--ccCCCceEEEeecCc
Q 032371 36 IKDIGHICSLEPEDLATESE--TESEDQACYFFYEPH 70 (142)
Q Consensus 36 I~~~~Dvy~~~P~~L~~~~~--~~~~~~~wyFF~~~~ 70 (142)
+.++ |||++.|..-...+. ...=...+|||.++.
T Consensus 137 l~~C-~iYsy~pd~~~dPf~e~g~lws~~yff~nkk~ 172 (179)
T PF09174_consen 137 LKDC-DIYSYNPDSDSDPFAEDGCLWSFNYFFYNKKL 172 (179)
T ss_dssp GGG--EEEEE---GGG-TT-S---SEEEEEEEEETTT
T ss_pred ccCc-eEEEEccCCCCCccccccchheeeeeEEecCc
Confidence 5678 999999843332221 111123456665554
No 7
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=23.00 E-value=33 Score=25.28 Aligned_cols=15 Identities=20% Similarity=0.468 Sum_probs=11.6
Q ss_pred CCCCCceEcCCHH-HH
Q 032371 4 HMGQGYKFQPSDE-LS 18 (142)
Q Consensus 4 ~lp~G~rF~PtD~-Li 18 (142)
++-|+|+|+|.|. .|
T Consensus 97 Pffp~f~ynPkD~RfI 112 (175)
T COG4741 97 PFFPEFKYNPKDARFI 112 (175)
T ss_pred ccccCCCcCCccceee
Confidence 4567999999997 44
No 8
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=21.98 E-value=33 Score=25.19 Aligned_cols=13 Identities=15% Similarity=0.457 Sum_probs=11.1
Q ss_pred CCCCCceEcCCHH
Q 032371 4 HMGQGYKFQPSDE 16 (142)
Q Consensus 4 ~lp~G~rF~PtD~ 16 (142)
++.|+|.++|+|.
T Consensus 84 P~lp~F~ynP~D~ 96 (156)
T PF10107_consen 84 PFLPEFPYNPKDA 96 (156)
T ss_pred hccCCCCCChhhh
Confidence 4569999999997
No 9
>PF06214 SLAM: Signaling lymphocytic activation molecule (SLAM) protein; InterPro: IPR010407 This entry is found in several mammalian signalling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70 kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones []. SLAM has also been recognised as a receptor for Measles virus [].; GO: 0004872 receptor activity, 0046649 lymphocyte activation, 0009986 cell surface, 0016021 integral to membrane; PDB: 3ALX_D 3ALZ_B 3ALW_A.
Probab=18.96 E-value=33 Score=23.95 Aligned_cols=47 Identities=23% Similarity=0.273 Sum_probs=22.3
Q ss_pred hhhhcCCCCCCCC-eeeccCCCCCCccCcccccc-ccCCCceEEEeecC
Q 032371 23 KEKRLDPHFSYGP-IKDIGHICSLEPEDLATESE-TESEDQACYFFYEP 69 (142)
Q Consensus 23 ~~ki~g~~l~~~~-I~~~~Dvy~~~P~~L~~~~~-~~~~~~~wyFF~~~ 69 (142)
++||..-+++..- -.-+.|=|.+++.+|--.-- -+-+++.|||-+-.
T Consensus 75 kkKIvSldl~eg~sp~yledgY~FhlEnLsL~Il~SrkE~EGWYfmtlE 123 (126)
T PF06214_consen 75 KKKIVSLDLSEGGSPRYLEDGYKFHLENLSLEILESRKEDEGWYFMTLE 123 (126)
T ss_dssp -EEEEEE-TTS-SS-EESSSSEEEETTTTEEEETT--GGG-EEEEEEEE
T ss_pred hheEEEeccccCCCccccccccEEecccceeehhccccccCceEEEEee
Confidence 4455554444321 12233777788887743221 12245779998743
No 10
>PF07677 A2M_recep: A-macroglobulin receptor; InterPro: IPR009048 This entry represents the receptor-binding domain (RBD) of alpha-2-macroglobulin proteins. The RBD is located at the C terminus, its structure having an immunoglobulin-like fold consists of a sandwich of nine strands in two sheets with a Greek-key topology [, ]. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0005576 extracellular region; PDB: 1AYO_A 2B39_B 3HS0_C 3PRX_B 3PVM_D 3HRZ_C 3FRP_B 1EDY_A 3KLS_B 3KM9_B ....
Probab=15.56 E-value=38 Score=22.08 Aligned_cols=16 Identities=19% Similarity=0.252 Sum_probs=10.9
Q ss_pred CCCCCCCCceEcCCHH
Q 032371 1 MESHMGQGYKFQPSDE 16 (142)
Q Consensus 1 ~~~~lp~G~rF~PtD~ 16 (142)
|+++||.||.-...+.
T Consensus 6 ~eV~lpSGf~~~~~~l 21 (91)
T PF07677_consen 6 MEVGLPSGFVPDQDSL 21 (91)
T ss_dssp EEEE-STTEEEEHHHH
T ss_pred EEEcCCCceeEChhHh
Confidence 5778888887766555
Done!