Query 045647
Match_columns 218
No_of_seqs 178 out of 992
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 04:02:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045647.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045647hhsearch_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-45 1.9E-49 285.2 7.0 127 8-141 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 36.3 37 0.00081 19.5 2.1 20 17-36 4-23 (27)
3 PHA00692 hypothetical protein 35.9 15 0.00033 25.1 0.5 9 7-15 36-44 (74)
4 PF11285 DUF3086: Protein of u 35.5 9.8 0.00021 33.5 -0.6 26 46-73 128-153 (283)
5 PF07960 CBP4: CBP4; InterPro 29.5 29 0.00063 27.4 1.2 12 14-25 29-40 (128)
6 PRK02079 pyrroloquinoline quin 28.2 34 0.00075 25.0 1.3 15 1-15 1-15 (88)
7 PF01473 CW_binding_1: Putativ 26.2 48 0.001 16.8 1.3 8 68-75 7-14 (19)
8 COG4472 Uncharacterized protei 24.3 48 0.001 24.1 1.4 11 19-29 74-84 (88)
9 PF06214 SLAM: Signaling lymph 23.3 21 0.00045 27.7 -0.6 48 27-76 75-122 (126)
10 PF13822 ACC_epsilon: Acyl-CoA 23.0 44 0.00095 22.7 1.0 9 15-23 10-18 (62)
11 PLN02417 dihydrodipicolinate s 22.3 63 0.0014 28.3 2.1 19 7-26 102-120 (280)
12 smart00707 RPEL Repeat in Dros 22.0 64 0.0014 18.4 1.4 13 11-23 6-18 (26)
13 cd00490 Met_repressor_MetJ Met 21.8 97 0.0021 23.0 2.6 39 15-60 50-88 (103)
14 PF04700 Baculo_gp41: Structur 21.1 99 0.0021 25.9 2.8 20 17-36 6-27 (186)
15 cd00954 NAL N-Acetylneuraminic 20.1 74 0.0016 27.8 2.1 18 8-26 103-120 (288)
16 PRK05264 transcriptional repre 20.0 1.1E+02 0.0023 22.9 2.6 39 15-60 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=9e-45 Score=285.20 Aligned_cols=127 Identities=38% Similarity=0.727 Sum_probs=92.5
Q ss_pred CCCCCccCCCHHHHHHHHHhhhhcCCCCCCCCCcccccCCCCCCCCCchhhhcccccCCCCceEEEEEecccccCCCCcc
Q 045647 8 LPLGCKFQPSDEQLVLFYLFNKISGTPAPFLDDFVRTENLYGNKEPWQIWRQFGVRDLEDGEDLYFFTRLKKKSVNGSRI 87 (218)
Q Consensus 8 LppGfRF~PTDeELV~~YL~~Ki~g~~~p~~~~ii~~~DvY~~~~Pw~L~~~~~~~~~~~~~~wyFFs~~~kk~~~g~R~ 87 (218)
|||||||+|||+|||.+||++|+.|.+++.. .+|+++|||+ +|||+|+... ..++++||||+++++++.++.|.
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~-~~i~~~Diy~-~~P~~L~~~~----~~~~~~~yFF~~~~~~~~~~~r~ 74 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCE-DVIHDVDIYS-AHPWELPAKF----KGGDEEWYFFSPRKKKYPNGGRP 74 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS--CHSEE--GGG-S-GGGCHHHS----SS-SSEEEEEEE----------S
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcc-cceeecccCc-cChHHhhhhc----cCCCceEEEEEecccccCCcccc
Confidence 8999999999999999999999999998875 4677779999 8999999532 23567999999999999999999
Q ss_pred cccccCceeeecCCCceEEeCCCCeEEeeEEeEeeecCCCC--CCcCeEEEEEEeC
Q 045647 88 DRRVGTGTWQGEDAGKAVVSRNSRKKIGSKKRFRYEKDQSP--HNCCWILHEYSLN 141 (218)
Q Consensus 88 ~R~~~~G~Wk~~g~~k~I~~~~~g~~vG~kktl~f~~g~~~--~~T~WvM~EY~l~ 141 (218)
+|++++|+||++|+.+.|.+. ++++||+|++|+||.++.+ .+|+|+||||+|.
T Consensus 75 ~R~~~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 75 NRVTGGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp -EEETTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cccccceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999999999875 8899999999999976554 4899999999984
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=36.27 E-value=37 Score=19.53 Aligned_cols=20 Identities=25% Similarity=0.316 Sum_probs=16.0
Q ss_pred CHHHHHHHHHhhhhcCCCCC
Q 045647 17 SDEQLVLFYLFNKISGTPAP 36 (218)
Q Consensus 17 TDeELV~~YL~~Ki~g~~~p 36 (218)
+-.|||.+|+.-|+.-+-.+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999876443
No 3
>PHA00692 hypothetical protein
Probab=35.90 E-value=15 Score=25.11 Aligned_cols=9 Identities=33% Similarity=0.715 Sum_probs=7.3
Q ss_pred CCCCCCccC
Q 045647 7 PLPLGCKFQ 15 (218)
Q Consensus 7 ~LppGfRF~ 15 (218)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999995
No 4
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=35.47 E-value=9.8 Score=33.55 Aligned_cols=26 Identities=42% Similarity=0.864 Sum_probs=18.6
Q ss_pred CCCCCCCCCchhhhcccccCCCCceEEE
Q 045647 46 NLYGNKEPWQIWRQFGVRDLEDGEDLYF 73 (218)
Q Consensus 46 DvY~~~~Pw~L~~~~~~~~~~~~~~wyF 73 (218)
|.|+ +||.|-..+.+.+...=+.|||
T Consensus 128 DyYg--~PWqLRRtfe~~hae~v~~WFF 153 (283)
T PF11285_consen 128 DYYG--PPWQLRRTFEPIHAERVEDWFF 153 (283)
T ss_pred CccC--ChHHHHhcccHHHHHHHHHHHh
Confidence 7887 8999987776654433456876
No 5
>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=29.51 E-value=29 Score=27.40 Aligned_cols=12 Identities=33% Similarity=0.598 Sum_probs=10.1
Q ss_pred cCCCHHHHHHHH
Q 045647 14 FQPSDEQLVLFY 25 (218)
Q Consensus 14 F~PTDeELV~~Y 25 (218)
-.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 379999999875
No 6
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=28.18 E-value=34 Score=25.00 Aligned_cols=15 Identities=33% Similarity=0.532 Sum_probs=12.2
Q ss_pred CCCCCCCCCCCCccC
Q 045647 1 MQGTRPPLPLGCKFQ 15 (218)
Q Consensus 1 m~~~~~~LppGfRF~ 15 (218)
|-+..+.|++||||+
T Consensus 1 ~~~~~p~l~~~~rl~ 15 (88)
T PRK02079 1 DRNQVPTLRPGYRFQ 15 (88)
T ss_pred CCCCCcccCCCcccc
Confidence 446678999999987
No 7
>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=26.18 E-value=48 Score=16.83 Aligned_cols=8 Identities=25% Similarity=0.875 Sum_probs=6.3
Q ss_pred CceEEEEE
Q 045647 68 GEDLYFFT 75 (218)
Q Consensus 68 ~~~wyFFs 75 (218)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899994
No 8
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.33 E-value=48 Score=24.14 Aligned_cols=11 Identities=45% Similarity=0.769 Sum_probs=9.3
Q ss_pred HHHHHHHHhhh
Q 045647 19 EQLVLFYLFNK 29 (218)
Q Consensus 19 eELV~~YL~~K 29 (218)
||||.+||+.+
T Consensus 74 EElvk~YLk~~ 84 (88)
T COG4472 74 EELVKYYLKGN 84 (88)
T ss_pred HHHHHHHHhhc
Confidence 79999999754
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=23.26 E-value=21 Score=27.68 Aligned_cols=48 Identities=17% Similarity=0.000 Sum_probs=24.5
Q ss_pred hhhhcCCCCCCCCCcccccCCCCCCCCCchhhhcccccCCCCceEEEEEe
Q 045647 27 FNKISGTPAPFLDDFVRTENLYGNKEPWQIWRQFGVRDLEDGEDLYFFTR 76 (218)
Q Consensus 27 ~~Ki~g~~~p~~~~ii~~~DvY~~~~Pw~L~~~~~~~~~~~~~~wyFFs~ 76 (218)
++||..-+++.....-..-|=|. +++.+|--.--. .+..++.|||.+-
T Consensus 75 kkKIvSldl~eg~sp~yledgY~-FhlEnLsL~Il~-SrkE~EGWYfmtl 122 (126)
T PF06214_consen 75 KKKIVSLDLSEGGSPRYLEDGYK-FHLENLSLEILE-SRKEDEGWYFMTL 122 (126)
T ss_dssp -EEEEEE-TTS-SS-EESSSSEE-EETTTTEEEETT---GGG-EEEEEEE
T ss_pred hheEEEeccccCCCccccccccE-Eecccceeehhc-cccccCceEEEEe
Confidence 46666655554332222337888 899988432111 1234567999875
No 10
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=23.03 E-value=44 Score=22.74 Aligned_cols=9 Identities=44% Similarity=0.840 Sum_probs=7.5
Q ss_pred CCCHHHHHH
Q 045647 15 QPSDEQLVL 23 (218)
Q Consensus 15 ~PTDeELV~ 23 (218)
+||||||--
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999854
No 11
>PLN02417 dihydrodipicolinate synthase
Probab=22.31 E-value=63 Score=28.27 Aligned_cols=19 Identities=16% Similarity=0.093 Sum_probs=14.9
Q ss_pred CCCCCCccCCCHHHHHHHHH
Q 045647 7 PLPLGCKFQPSDEQLVLFYL 26 (218)
Q Consensus 7 ~LppGfRF~PTDeELV~~YL 26 (218)
-+|| |.|.||++||+.||-
T Consensus 102 ~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 102 HINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EcCC-ccCCCCHHHHHHHHH
Confidence 3566 568999999999873
No 12
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=21.99 E-value=64 Score=18.36 Aligned_cols=13 Identities=23% Similarity=0.253 Sum_probs=10.9
Q ss_pred CCccCCCHHHHHH
Q 045647 11 GCKFQPSDEQLVL 23 (218)
Q Consensus 11 GfRF~PTDeELV~ 23 (218)
...++||-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
No 13
>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=21.81 E-value=97 Score=22.98 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHhhhhcCCCCCCCCCcccccCCCCCCCCCchhhhc
Q 045647 15 QPSDEQLVLFYLFNKISGTPAPFLDDFVRTENLYGNKEPWQIWRQF 60 (218)
Q Consensus 15 ~PTDeELV~~YL~~Ki~g~~~p~~~~ii~~~DvY~~~~Pw~L~~~~ 60 (218)
|-|..||+..-...-..|+|||... |+-+ ..|.++|+..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D~------Dl~K-~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDDA------DLRK-ERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCChh------hhhh-cCcccccHHH
Confidence 4566777776566778999999742 7766 6788888753
No 14
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=21.05 E-value=99 Score=25.91 Aligned_cols=20 Identities=45% Similarity=0.805 Sum_probs=14.3
Q ss_pred CHHHHHHHH--HhhhhcCCCCC
Q 045647 17 SDEQLVLFY--LFNKISGTPAP 36 (218)
Q Consensus 17 TDeELV~~Y--L~~Ki~g~~~p 36 (218)
+|||||.|| |.++..|...+
T Consensus 6 sDe~Li~yY~~L~K~~g~~~~~ 27 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGSDVP 27 (186)
T ss_pred cHHHHHHHHHHHHHHhCCCCCC
Confidence 799999999 55555555443
No 15
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=20.07 E-value=74 Score=27.85 Aligned_cols=18 Identities=17% Similarity=0.130 Sum_probs=13.7
Q ss_pred CCCCCccCCCHHHHHHHHH
Q 045647 8 LPLGCKFQPSDEQLVLFYL 26 (218)
Q Consensus 8 LppGfRF~PTDeELV~~YL 26 (218)
+||- .|.||++||+.||.
T Consensus 103 ~~P~-y~~~~~~~i~~~~~ 120 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYR 120 (288)
T ss_pred eCCC-CCCCCHHHHHHHHH
Confidence 4554 48899999999863
No 16
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=20.01 E-value=1.1e+02 Score=22.87 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHhhhhcCCCCCCCCCcccccCCCCCCCCCchhhhc
Q 045647 15 QPSDEQLVLFYLFNKISGTPAPFLDDFVRTENLYGNKEPWQIWRQF 60 (218)
Q Consensus 15 ~PTDeELV~~YL~~Ki~g~~~p~~~~ii~~~DvY~~~~Pw~L~~~~ 60 (218)
|-|..||+..-...-..|+|||... |+-+ ..|.++|+..
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~D~------Dl~K-d~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPDDE------DLRK-ERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCChh------hhhh-cCcccchHHH
Confidence 4566777776566778999999742 7766 6788888653
Done!