Query 040419
Match_columns 198
No_of_seqs 120 out of 900
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 08:14:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040419.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040419hhsearch_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 5.8E-45 1.3E-49 279.2 6.7 127 3-133 1-129 (129)
2 PHA00692 hypothetical protein 43.4 8.9 0.00019 25.4 0.3 9 2-10 36-44 (74)
3 KOG3238 Chloride ion current i 33.6 36 0.00077 28.1 2.4 60 5-64 111-171 (216)
4 PF07960 CBP4: CBP4; InterPro 29.6 27 0.0006 26.7 1.0 9 10-18 30-38 (128)
5 smart00707 RPEL Repeat in Dros 27.1 40 0.00086 18.6 1.1 13 6-18 6-18 (26)
6 PF01473 CW_binding_1: Putativ 25.1 51 0.0011 16.2 1.2 9 57-65 7-15 (19)
7 PF07131 DUF1382: Protein of u 23.5 80 0.0017 20.9 2.2 20 5-24 22-48 (61)
8 cd00950 DHDPS Dihydrodipicolin 23.4 72 0.0016 27.0 2.6 27 3-30 102-128 (284)
9 PF13822 ACC_epsilon: Acyl-CoA 23.1 44 0.00095 22.1 1.0 9 10-18 10-18 (62)
10 PRK03170 dihydrodipicolinate s 19.9 97 0.0021 26.3 2.7 27 3-30 103-129 (292)
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=5.8e-45 Score=279.21 Aligned_cols=127 Identities=43% Similarity=0.739 Sum_probs=95.0
Q ss_pred CCCCceeCCCHHHHHH-HHHHhhcCCCCCc-cceEeccCCCCCCCCCCCCCcccCCcceEEEeecccccccCCCcceecc
Q 040419 3 SLVGFRFYPTDEEIIR-LLKKKRLDPAFFV-HTIKEIDFYSFEPWELPCHSEIQSEEEVWYFFCEPDYKYAKSRRVNRGT 80 (198)
Q Consensus 3 lp~G~rF~PtDeELi~-yL~~ki~g~~l~~-~~I~~~Dvy~~~P~~Lp~~~~~~~~~~~wyFF~~~~~~~~~g~R~~R~~ 80 (198)
|||||||+|||+|||. ||++|+.|.+++. ++|+++|||++|||+|++.. .+++.+||||+++.+++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhc--cCCCceEEEEEecccccCCcccccccc
Confidence 8999999999999999 9999999999988 89999999999999999422 234779999999999999999999999
Q ss_pred CCceEEecCCCceEEeCCCCeEEEEEEEEEeeeecCCCCCCccCeEEEEEEeC
Q 040419 81 NEGTWKKTGNGSKIKRKYSTEVIGTKRILSFSCHDSASKKAKTEWVMHEIAVE 133 (198)
Q Consensus 81 ~~G~W~~~g~~~~I~~~~~g~viG~k~~l~F~~~g~~~~~~kT~W~M~EY~l~ 133 (198)
++|+|+.+++.+.|.+. ++.+||+|++|+|| .++.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~-~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFY-SGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE--TTCEEEEEEEEEEE-ESSTTS-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccc-cceeeeeEEEEEEE-eccCCCCCcCCeEEEEEEeC
Confidence 99999999999999997 37899999999999 88778889999999999984
No 2
>PHA00692 hypothetical protein
Probab=43.35 E-value=8.9 Score=25.41 Aligned_cols=9 Identities=44% Similarity=0.600 Sum_probs=7.2
Q ss_pred CCCCCceeC
Q 040419 2 NSLVGFRFY 10 (198)
Q Consensus 2 ~lp~G~rF~ 10 (198)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 469999994
No 3
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=33.57 E-value=36 Score=28.13 Aligned_cols=60 Identities=18% Similarity=0.277 Sum_probs=38.2
Q ss_pred CCceeCCCHHHHHH-HHHHhhcCCCCCccceEeccCCCCCCCCCCCCCcccCCcceEEEee
Q 040419 5 VGFRFYPTDEEIIR-LLKKKRLDPAFFVHTIKEIDFYSFEPWELPCHSEIQSEEEVWYFFC 64 (198)
Q Consensus 5 ~G~rF~PtDeELi~-yL~~ki~g~~l~~~~I~~~Dvy~~~P~~Lp~~~~~~~~~~~wyFF~ 64 (198)
-+|||.|+|.--+. .---......+-+....+.+-|.-+=|+.-+....+++...||=+.
T Consensus 111 ~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 111 TEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTYD 171 (216)
T ss_pred ccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCccccccc
Confidence 47999999998888 4444445544444336667777777777755444445555666554
No 4
>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=29.62 E-value=27 Score=26.74 Aligned_cols=9 Identities=44% Similarity=0.911 Sum_probs=8.5
Q ss_pred CCCHHHHHH
Q 040419 10 YPTDEEIIR 18 (198)
Q Consensus 10 ~PtDeELi~ 18 (198)
.||||||+.
T Consensus 30 tPTeEeL~~ 38 (128)
T PF07960_consen 30 TPTEEELFK 38 (128)
T ss_pred CCCHHHHHH
Confidence 799999998
No 5
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=27.09 E-value=40 Score=18.59 Aligned_cols=13 Identities=31% Similarity=0.355 Sum_probs=11.0
Q ss_pred CceeCCCHHHHHH
Q 040419 6 GFRFYPTDEEIIR 18 (198)
Q Consensus 6 G~rF~PtDeELi~ 18 (198)
...++|+-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
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=25.06 E-value=51 Score=16.17 Aligned_cols=9 Identities=33% Similarity=1.073 Sum_probs=7.0
Q ss_pred cceEEEeec
Q 040419 57 EEVWYFFCE 65 (198)
Q Consensus 57 ~~~wyFF~~ 65 (198)
++.||||..
T Consensus 7 ~~~wYy~~~ 15 (19)
T PF01473_consen 7 NGNWYYFDS 15 (19)
T ss_dssp TTEEEEETT
T ss_pred CCEEEEeCC
Confidence 688999953
No 7
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=23.51 E-value=80 Score=20.94 Aligned_cols=20 Identities=50% Similarity=0.782 Sum_probs=14.0
Q ss_pred CCceeCC----CHHHHHH---HHHHhh
Q 040419 5 VGFRFYP----TDEEIIR---LLKKKR 24 (198)
Q Consensus 5 ~G~rF~P----tDeELi~---yL~~ki 24 (198)
.|+||.| ||+|... -|..|+
T Consensus 22 ~GIRFVpiPv~~dee~~~L~s~~~~kL 48 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHTLSSQLSQKL 48 (61)
T ss_pred cCceeeccccccHHHHHHHHHHHHHHH
Confidence 5899988 6777654 555655
No 8
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=23.40 E-value=72 Score=26.97 Aligned_cols=27 Identities=11% Similarity=0.017 Sum_probs=20.3
Q ss_pred CCCCceeCCCHHHHHHHHHHhhcCCCCC
Q 040419 3 SLVGFRFYPTDEEIIRLLKKKRLDPAFF 30 (198)
Q Consensus 3 lp~G~rF~PtDeELi~yL~~ki~g~~l~ 30 (198)
+||.| |.|+++||+.|.+.-+...++|
T Consensus 102 ~~P~~-~~~~~~~l~~~~~~ia~~~~~p 128 (284)
T cd00950 102 VTPYY-NKPSQEGLYAHFKAIAEATDLP 128 (284)
T ss_pred ccccc-CCCCHHHHHHHHHHHHhcCCCC
Confidence 56754 8899999999887777655555
No 9
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=23.09 E-value=44 Score=22.07 Aligned_cols=9 Identities=56% Similarity=0.815 Sum_probs=7.7
Q ss_pred CCCHHHHHH
Q 040419 10 YPTDEEIIR 18 (198)
Q Consensus 10 ~PtDeELi~ 18 (198)
+||||||--
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999865
No 10
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=19.88 E-value=97 Score=26.34 Aligned_cols=27 Identities=15% Similarity=0.055 Sum_probs=20.1
Q ss_pred CCCCceeCCCHHHHHHHHHHhhcCCCCC
Q 040419 3 SLVGFRFYPTDEEIIRLLKKKRLDPAFF 30 (198)
Q Consensus 3 lp~G~rF~PtDeELi~yL~~ki~g~~l~ 30 (198)
+||-| |.|++++|+.|...-+...++|
T Consensus 103 ~pP~~-~~~~~~~i~~~~~~ia~~~~~p 129 (292)
T PRK03170 103 VTPYY-NKPTQEGLYQHFKAIAEATDLP 129 (292)
T ss_pred CCCcC-CCCCHHHHHHHHHHHHhcCCCC
Confidence 56655 8899999999777766655555
Done!