Query 025990
Match_columns 245
No_of_seqs 170 out of 950
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 11:54:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025990.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025990hhsearch_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 1.1E-44 2.3E-49 291.3 7.7 126 15-143 1-129 (129)
2 PHA00692 hypothetical protein 37.1 14 0.0003 25.9 0.4 10 13-22 35-44 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 27.0 75 0.0016 18.7 2.3 20 24-43 4-23 (27)
4 PF07960 CBP4: CBP4; InterPro 24.1 40 0.00087 27.2 1.1 11 22-32 30-40 (128)
5 PLN02417 dihydrodipicolinate s 22.0 51 0.0011 29.5 1.5 21 12-33 100-120 (280)
6 cd00490 Met_repressor_MetJ Met 22.0 1.1E+02 0.0023 23.3 3.0 38 22-63 50-87 (103)
7 PF06214 SLAM: Signaling lymph 21.1 19 0.00041 28.6 -1.2 42 33-74 74-122 (126)
8 PF01340 MetJ: Met Apo-repress 20.3 1.1E+02 0.0023 23.4 2.7 38 22-63 50-87 (104)
9 KOG1334 WD40 repeat protein [G 20.2 1.7E+02 0.0038 29.0 4.7 48 27-74 304-365 (559)
10 cd00952 CHBPH_aldolase Trans-o 19.6 62 0.0013 29.5 1.6 21 11-32 106-126 (309)
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=1.1e-44 Score=291.29 Aligned_cols=126 Identities=44% Similarity=0.896 Sum_probs=96.3
Q ss_pred CCCCceecCChHHHHHHHHHHHHcCCCCCC-cceeccCCCCCCCCCCCCc--CCCCeEEEEeccccccccCCCCcccccc
Q 025990 15 LPIGYRFRPTDEELVVHYLKRKVFGLPLPA-SIIPELDVFQSHPLGLPGD--MKEKKRYFFSNIRNESAIDNDGKCKIAA 91 (245)
Q Consensus 15 LPpGfRF~PTDeELV~~YL~~K~~g~plp~-~~I~~~Dvy~~~PwdLp~~--~~~~~wYFFs~~~k~~k~~~g~R~~R~t 91 (245)
|||||||+|||+|||.+||++|+.|.++|. .+|+++|||++|||+|+.. .++++||||++ +..++.+++|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~--~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSP--RKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE------------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEe--cccccCCcccccccc
Confidence 899999999999999999999999999988 8999999999999999942 45679999999 777788899999999
Q ss_pred cceeeecCCCcceEEeCCCceEEEEEEEEEeecCcCCCCcccCeEEEEEEeC
Q 025990 92 GSGYWKPVGKNRQILASGTKQVVGIRKTLIFCEGKRGHETKTQWVMHQYHLV 143 (245)
Q Consensus 92 g~G~Wk~~g~~k~I~~~~~g~~vG~kktl~Fy~g~~~~g~rT~W~MhEY~l~ 143 (245)
++|+||++|+.++|... ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999999843 8999999999999998888899999999999983
No 2
>PHA00692 hypothetical protein
Probab=37.09 E-value=14 Score=25.92 Aligned_cols=10 Identities=40% Similarity=1.012 Sum_probs=8.3
Q ss_pred cCCCCCceec
Q 025990 13 LKLPIGYRFR 22 (245)
Q Consensus 13 ~~LPpGfRF~ 22 (245)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4689999995
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=27.01 E-value=75 Score=18.74 Aligned_cols=20 Identities=30% Similarity=0.358 Sum_probs=15.4
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 025990 24 TDEELVVHYLKRKVFGLPLP 43 (245)
Q Consensus 24 TDeELV~~YL~~K~~g~plp 43 (245)
+-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999998755443
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=24.08 E-value=40 Score=27.25 Aligned_cols=11 Identities=55% Similarity=0.927 Sum_probs=9.5
Q ss_pred cCChHHHHHHH
Q 025990 22 RPTDEELVVHY 32 (245)
Q Consensus 22 ~PTDeELV~~Y 32 (245)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 5
>PLN02417 dihydrodipicolinate synthase
Probab=22.04 E-value=51 Score=29.55 Aligned_cols=21 Identities=24% Similarity=0.428 Sum_probs=16.0
Q ss_pred ccCCCCCceecCChHHHHHHHH
Q 025990 12 GLKLPIGYRFRPTDEELVVHYL 33 (245)
Q Consensus 12 ~~~LPpGfRF~PTDeELV~~YL 33 (245)
.+-+|| |.|.||+++|+.||-
T Consensus 100 v~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 100 ALHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EEEcCC-ccCCCCHHHHHHHHH
Confidence 345666 568999999998773
No 6
>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=22.02 E-value=1.1e+02 Score=23.30 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=30.9
Q ss_pred cCChHHHHHHHHHHHHcCCCCCCcceeccCCCCCCCCCCCCc
Q 025990 22 RPTDEELVVHYLKRKVFGLPLPASIIPELDVFQSHPLGLPGD 63 (245)
Q Consensus 22 ~PTDeELV~~YL~~K~~g~plp~~~I~~~Dvy~~~PwdLp~~ 63 (245)
|-|-.||++.-...-..|+|||.+ .|+-+..|-++|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D----~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD----ADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCcccccHH
Confidence 567788888777778899999985 58888889888865
No 7
>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=21.11 E-value=19 Score=28.57 Aligned_cols=42 Identities=24% Similarity=0.371 Sum_probs=25.7
Q ss_pred HHHHHcCCCCCCcceec--cCCCCCCCCCCCCc-----CCCCeEEEEec
Q 025990 33 LKRKVFGLPLPASIIPE--LDVFQSHPLGLPGD-----MKEKKRYFFSN 74 (245)
Q Consensus 33 L~~K~~g~plp~~~I~~--~Dvy~~~PwdLp~~-----~~~~~wYFFs~ 74 (245)
.++||.+.+++..--++ -|=|.+|+..|--. .+++.|||.+-
T Consensus 74 vkkKIvSldl~eg~sp~yledgY~FhlEnLsL~Il~SrkE~EGWYfmtl 122 (126)
T PF06214_consen 74 VKKKIVSLDLSEGGSPRYLEDGYKFHLENLSLEILESRKEDEGWYFMTL 122 (126)
T ss_dssp --EEEEEE-TTS-SS-EESSSSEEEETTTTEEEETT--GGG-EEEEEEE
T ss_pred hhheEEEeccccCCCccccccccEEecccceeehhccccccCceEEEEe
Confidence 36777777776533333 48899999998433 45678999876
No 8
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=20.29 E-value=1.1e+02 Score=23.35 Aligned_cols=38 Identities=26% Similarity=0.483 Sum_probs=24.0
Q ss_pred cCChHHHHHHHHHHHHcCCCCCCcceeccCCCCCCCCCCCCc
Q 025990 22 RPTDEELVVHYLKRKVFGLPLPASIIPELDVFQSHPLGLPGD 63 (245)
Q Consensus 22 ~PTDeELV~~YL~~K~~g~plp~~~I~~~Dvy~~~PwdLp~~ 63 (245)
|-|-.||++.-...-..|+|||.+ .|+-+..|-.+|..
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~D----~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPTD----DDLRKDRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------T----TGGGSTSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCCccchHH
Confidence 568888888777778899999985 58888899998865
No 9
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=20.17 E-value=1.7e+02 Score=28.96 Aligned_cols=48 Identities=15% Similarity=0.277 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHcCCC--------CCCcceec------cCCCCCCCCCCCCcCCCCeEEEEec
Q 025990 27 ELVVHYLKRKVFGLP--------LPASIIPE------LDVFQSHPLGLPGDMKEKKRYFFSN 74 (245)
Q Consensus 27 ELV~~YL~~K~~g~p--------lp~~~I~~------~Dvy~~~PwdLp~~~~~~~wYFFs~ 74 (245)
|.+.-|=.|++...+ +|...+.+ .=+|.++|-+|...+.+...|||.+
T Consensus 304 qf~RvYD~R~~~~e~~n~~~~~f~p~hl~~d~~v~ITgl~Ysh~~sElLaSYnDe~IYLF~~ 365 (559)
T KOG1334|consen 304 QFARVYDQRRIDKEENNGVLDKFCPHHLVEDDPVNITGLVYSHDGSELLASYNDEDIYLFNK 365 (559)
T ss_pred hhhhhhcccchhhccccchhhhcCCccccccCcccceeEEecCCccceeeeecccceEEecc
Confidence 445557777776653 23332221 1267888888888877788999944
No 10
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=19.64 E-value=62 Score=29.54 Aligned_cols=21 Identities=14% Similarity=0.056 Sum_probs=16.4
Q ss_pred CccCCCCCceecCChHHHHHHH
Q 025990 11 GGLKLPIGYRFRPTDEELVVHY 32 (245)
Q Consensus 11 ~~~~LPpGfRF~PTDeELV~~Y 32 (245)
+.+-+|| |.|.||+++|+.||
T Consensus 106 ~vlv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 106 GTMLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EEEECCC-cCCCCCHHHHHHHH
Confidence 3456777 66999999999866
Done!