Query 043513
Match_columns 406
No_of_seqs 150 out of 984
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:48:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043513hhsearch_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 2E-40 4.4E-45 288.5 7.4 127 8-141 1-129 (129)
2 PHA00692 hypothetical protein 19.7 45 0.00097 26.4 0.5 9 7-15 36-44 (74)
3 PRK14390 hypothetical protein; 11.2 1.3E+02 0.0028 23.9 1.1 20 4-23 9-28 (63)
4 KOG1334 WD40 repeat protein [G 10.9 3.9E+02 0.0085 29.4 4.8 98 20-126 304-435 (559)
5 PF07960 CBP4: CBP4; InterPro 10.3 1.4E+02 0.003 27.0 1.1 14 12-25 26-40 (128)
6 PRK14373 hypothetical protein; 10.0 1.5E+02 0.0032 24.3 1.1 20 4-23 20-39 (73)
7 smart00265 BH4 BH4 Bcl-2 homol 10.0 2.3E+02 0.0051 19.0 1.8 18 17-34 4-21 (27)
8 PF11285 DUF3086: Protein of u 8.8 40 0.00087 33.8 -3.1 27 46-74 128-154 (283)
9 PF08338 DUF1731: Domain of un 8.8 2.2E+02 0.0048 21.0 1.6 16 10-25 31-47 (48)
10 PRK14382 hypothetical protein; 8.7 1.8E+02 0.0039 23.4 1.1 21 4-24 16-36 (68)
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=2e-40 Score=288.45 Aligned_cols=127 Identities=38% Similarity=0.727 Sum_probs=92.6
Q ss_pred CCCCCeEcCChHHHHHHHHHHhHcCCCCCCcceeeEeccCCCCCCCcchhhhcCCCCCCCCceEEEEecccccCCCCCcc
Q 043513 8 LPVGCKFLPSEEQLVHYYLFNKISGIPTPFVEYFVKDVDLYDYEEPWDIWKQFGGPNLEDGEDLYFFTNLKKKSINGSRI 87 (406)
Q Consensus 8 LPpGfRF~PTDEELV~~YL~rKi~G~plp~~~~vI~evDVY~~~ePWdLp~~~~~~~~~d~eeWYFFspr~rk~~nG~R~ 87 (406)
|||||||+|||+|||.+||++|+.|.+++. ..+|.++|||++ +||+|++.+. .++++||||+++++++.+|+|.
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~-~~~i~~~Diy~~-~P~~L~~~~~----~~~~~~yFF~~~~~~~~~~~r~ 74 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPC-EDVIHDVDIYSA-HPWELPAKFK----GGDEEWYFFSPRKKKYPNGGRP 74 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS--CHSEE--GGGS--GGGCHHHSS----S-SSEEEEEEE----------S
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCc-ccceeecccCcc-ChHHhhhhcc----CCCceEEEEEecccccCCcccc
Confidence 899999999999999999999999999887 367999999996 9999995432 2455899999999999999999
Q ss_pred ceecccceeecccCCeEEEeCCCCcceeeEEeEeeeCCCCC--CCcCeEEEEEEeC
Q 043513 88 NRKVGSGAWQGEDAGELVLSRNSNRPIGSKKIFRYENDNFP--HNRCWIMHEYTLN 141 (406)
Q Consensus 88 ~R~tggG~WKatG~~k~I~~~~~g~vIG~KKtL~Fy~g~sp--~kT~WiMhEY~L~ 141 (406)
+|++++|+||++|+.+.|.+. +|++||+||+|+||.++.+ .+|+|+||||+|.
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 999999999999999999985 8899999999999965444 4899999999984
No 2
>PHA00692 hypothetical protein
Probab=19.72 E-value=45 Score=26.40 Aligned_cols=9 Identities=33% Similarity=0.526 Sum_probs=7.4
Q ss_pred CCCCCCeEc
Q 043513 7 ILPVGCKFL 15 (406)
Q Consensus 7 ~LPpGfRF~ 15 (406)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 469999994
No 3
>PRK14390 hypothetical protein; Provisional
Probab=11.16 E-value=1.3e+02 Score=23.94 Aligned_cols=20 Identities=25% Similarity=0.374 Sum_probs=15.3
Q ss_pred ccCCCCCCCeEcCChHHHHH
Q 043513 4 RSRILPVGCKFLPSEEQLVH 23 (406)
Q Consensus 4 ~~~~LPpGfRF~PTDEELV~ 23 (406)
++.-+|+-+||.||=-|=..
T Consensus 9 iSp~~~~~CRf~PTCS~Ya~ 28 (63)
T PRK14390 9 FSPFFGPRCRFIPSCSSYGY 28 (63)
T ss_pred hCCCCCCCCCcCccHHHHHH
Confidence 46678999999999665433
No 4
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=10.91 E-value=3.9e+02 Score=29.40 Aligned_cols=98 Identities=20% Similarity=0.310 Sum_probs=53.5
Q ss_pred HHHHHHHHHhHcCCCC--------CC----cceeeEeccCCCCCCCcchhhhcCCCCCCCCceEEEEecccccC------
Q 043513 20 QLVHYYLFNKISGIPT--------PF----VEYFVKDVDLYDYEEPWDIWKQFGGPNLEDGEDLYFFTNLKKKS------ 81 (406)
Q Consensus 20 ELV~~YL~rKi~G~pl--------p~----~~~vI~evDVY~~~ePWdLp~~~~~~~~~d~eeWYFFspr~rk~------ 81 (406)
|.+.-|=.|++..... |. +..+-..+=+|+. .+-+|...+ .++..|||.+-....
T Consensus 304 qf~RvYD~R~~~~e~~n~~~~~f~p~hl~~d~~v~ITgl~Ysh-~~sElLaSY------nDe~IYLF~~~~~~G~~p~~~ 376 (559)
T KOG1334|consen 304 QFARVYDQRRIDKEENNGVLDKFCPHHLVEDDPVNITGLVYSH-DGSELLASY------NDEDIYLFNKSMGDGSEPDPS 376 (559)
T ss_pred hhhhhhcccchhhccccchhhhcCCccccccCcccceeEEecC-Cccceeeee------cccceEEeccccccCCCCCCC
Confidence 4555577777766521 10 1111222336774 788886543 345589995432221
Q ss_pred ----------CCCCccceeccc-ceeecccCCeEEEe-CCCCcc-eeeEEe---EeeeCCC
Q 043513 82 ----------INGSRINRKVGS-GAWQGEDAGELVLS-RNSNRP-IGSKKI---FRYENDN 126 (406)
Q Consensus 82 ----------~nG~R~~R~tgg-G~WKatG~~k~I~~-~~~g~v-IG~KKt---L~Fy~g~ 126 (406)
=+|.|-+|++++ .+|-. +..-|.+ .++|.| |+.|++ +.|.+|.
T Consensus 377 s~~~~~~k~vYKGHrN~~TVKgVNFfGP--rsEyVvSGSDCGhIFiW~K~t~eii~~MegD 435 (559)
T KOG1334|consen 377 SPREQYVKRVYKGHRNSRTVKGVNFFGP--RSEYVVSGSDCGHIFIWDKKTGEIIRFMEGD 435 (559)
T ss_pred cchhhccchhhcccccccccceeeeccC--ccceEEecCccceEEEEecchhHHHHHhhcc
Confidence 137787888865 78875 2334554 356775 555554 5565553
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=10.32 E-value=1.4e+02 Score=26.99 Aligned_cols=14 Identities=43% Similarity=0.850 Sum_probs=10.7
Q ss_pred CeE-cCChHHHHHHH
Q 043513 12 CKF-LPSEEQLVHYY 25 (406)
Q Consensus 12 fRF-~PTDEELV~~Y 25 (406)
|++ .||||||+..|
T Consensus 26 ~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 26 VKYTTPTEEELFKRY 40 (128)
T ss_pred heecCCCHHHHHHhc
Confidence 444 59999999765
No 6
>PRK14373 hypothetical protein; Provisional
Probab=10.02 E-value=1.5e+02 Score=24.25 Aligned_cols=20 Identities=25% Similarity=0.574 Sum_probs=15.5
Q ss_pred ccCCCCCCCeEcCChHHHHH
Q 043513 4 RSRILPVGCKFLPSEEQLVH 23 (406)
Q Consensus 4 ~~~~LPpGfRF~PTDEELV~ 23 (406)
++.-+|+-+||.||=-|=..
T Consensus 20 iSp~~~~~CRf~PTCS~Ya~ 39 (73)
T PRK14373 20 ISPLIPPRCRYTPTCSQYAV 39 (73)
T ss_pred hCCCCCCCCCcCcCHHHHHH
Confidence 56778999999999665443
No 7
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=10.00 E-value=2.3e+02 Score=18.98 Aligned_cols=18 Identities=28% Similarity=0.277 Sum_probs=14.5
Q ss_pred ChHHHHHHHHHHhHcCCC
Q 043513 17 SEEQLVHYYLFNKISGIP 34 (406)
Q Consensus 17 TDEELV~~YL~rKi~G~p 34 (406)
.-.|||.+|+.-|+.-.-
T Consensus 4 ~nRelV~~yv~yKLsQrg 21 (27)
T smart00265 4 DNRELVVDYVTYKLSQNG 21 (27)
T ss_pred chHHHHHHHHHHHHhhcC
Confidence 457999999999996543
No 8
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=8.83 E-value=40 Score=33.82 Aligned_cols=27 Identities=33% Similarity=0.708 Sum_probs=16.9
Q ss_pred cCCCCCCCcchhhhcCCCCCCCCceEEEE
Q 043513 46 DLYDYEEPWDIWKQFGGPNLEDGEDLYFF 74 (406)
Q Consensus 46 DVY~~~ePWdLp~~~~~~~~~d~eeWYFF 74 (406)
|.|+ +||.|-..|.+.....-+.|||=
T Consensus 128 DyYg--~PWqLRRtfe~~hae~v~~WFF~ 154 (283)
T PF11285_consen 128 DYYG--PPWQLRRTFEPIHAERVEDWFFN 154 (283)
T ss_pred CccC--ChHHHHhcccHHHHHHHHHHHhc
Confidence 5786 89999877765433223348553
No 9
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=8.79 E-value=2.2e+02 Score=21.04 Aligned_cols=16 Identities=25% Similarity=0.463 Sum_probs=9.0
Q ss_pred CCCeEc-CChHHHHHHH
Q 043513 10 VGCKFL-PSEEQLVHYY 25 (406)
Q Consensus 10 pGfRF~-PTDEELV~~Y 25 (406)
-||+|+ |+=++.+.+.
T Consensus 31 ~GF~F~~p~l~~AL~~l 47 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDL 47 (48)
T ss_dssp TT---S-SSHHHHHHH-
T ss_pred CCCcccCCCHHHHHhcc
Confidence 599995 8888877654
No 10
>PRK14382 hypothetical protein; Provisional
Probab=8.67 E-value=1.8e+02 Score=23.41 Aligned_cols=21 Identities=24% Similarity=0.542 Sum_probs=16.2
Q ss_pred ccCCCCCCCeEcCChHHHHHH
Q 043513 4 RSRILPVGCKFLPSEEQLVHY 24 (406)
Q Consensus 4 ~~~~LPpGfRF~PTDEELV~~ 24 (406)
++.-+++-+||.||=-|-...
T Consensus 16 iSp~~~~~CRf~PTCS~Ya~~ 36 (68)
T PRK14382 16 ISPLYPSSCRFYPTCSTYAIL 36 (68)
T ss_pred cCCCCCCCCCCccCHHHHHHH
Confidence 467789999999997665443
Done!