Query 042765
Match_columns 296
No_of_seqs 149 out of 960
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:13:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042765.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042765hhsearch_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 7.6E-42 1.6E-46 284.8 6.3 127 30-164 1-129 (129)
2 COG0832 UreB Urea amidohydrola 27.7 25 0.00055 28.7 0.6 40 2-45 39-80 (106)
3 PRK13202 ureB urease subunit b 27.3 26 0.00056 28.7 0.5 37 2-42 40-78 (104)
4 PHA00692 hypothetical protein 26.3 25 0.00054 26.0 0.3 10 28-37 35-44 (74)
5 smart00265 BH4 BH4 Bcl-2 homol 26.1 70 0.0015 20.0 2.2 21 39-59 4-24 (27)
6 KOG1334 WD40 repeat protein [G 24.8 1.2E+02 0.0026 31.4 4.8 103 38-150 301-436 (559)
7 PRK13203 ureB urease subunit b 21.3 43 0.00093 27.3 0.8 37 2-42 39-77 (102)
8 KOG0703 Predicted GTPase-activ 20.6 70 0.0015 30.7 2.2 47 9-58 78-124 (287)
9 PRK13201 ureB urease subunit b 17.3 59 0.0013 27.8 0.8 37 2-42 39-77 (136)
10 cd00490 Met_repressor_MetJ Met 17.1 1.3E+02 0.0028 24.1 2.6 38 37-80 50-87 (103)
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=7.6e-42 Score=284.79 Aligned_cols=127 Identities=37% Similarity=0.616 Sum_probs=92.9
Q ss_pred CCCcceECCChHHHHHHHHHHhhcCCCCCccccccccccCCCCCCccccccCCCCcccCCceEEEEecccccCCCCCccc
Q 042765 30 LPHGFQFRPSDEELIEHYLKKKVSGILIPLAEYFIRDCNLYETKPSEIWDSHGGPFFNIDEDLYFFTQLKKKSSKGSRID 109 (296)
Q Consensus 30 LPpGfRF~PTDeELI~~YL~~Ki~g~~lp~~~~~I~~vDVY~~~PwdLp~~~~~~~~~~~~ewYFFs~r~~k~~~g~R~~ 109 (296)
|||||||+|||+|||.+||++|+.|.+++.. .+|+++|||++|||+|+... ..++++||||+++++++.++.|.+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~-~~i~~~Diy~~~P~~L~~~~----~~~~~~~yFF~~~~~~~~~~~r~~ 75 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCE-DVIHDVDIYSAHPWELPAKF----KGGDEEWYFFSPRKKKYPNGGRPN 75 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS--CHSEE--GGGS-GGGCHHHS----SS-SSEEEEEEE----------S-
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcc-cceeecccCccChHHhhhhc----cCCCceEEEEEecccccCCccccc
Confidence 8999999999999999999999999998874 48999999999999999532 236779999999999999999999
Q ss_pred eeecCCCceeeecCCCceEEeCCCCeEEeeEEeEEeecC--CCCCCCCeEEEEEEeC
Q 042765 110 RKVSSSSGAWQWEDAGKDIVSGQSKVKIGSKKRFRYEKK--GCEDYGPWIMHECTLH 164 (296)
Q Consensus 110 R~t~~~~G~Wk~tG~~k~I~~~~~g~~iG~KktL~F~~g--~~~~kT~WvMhEY~l~ 164 (296)
|++ ++|+||++|+.++|... ++.+||+|++|+||.+ +++.+|+|+||||+|.
T Consensus 76 R~~--~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 76 RVT--GGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEE--TTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccc--cceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 988 99999999999999986 6899999999999964 3567999999999984
No 2
>COG0832 UreB Urea amidohydrolase (urease) beta subunit [Amino acid transport and metabolism]
Probab=27.71 E-value=25 Score=28.65 Aligned_cols=40 Identities=38% Similarity=0.607 Sum_probs=32.3
Q ss_pred cceeeeeeehhhhhhhcccccccCCCCCCCCc--ceECCChHHHHH
Q 042765 2 HQHIFSVNQHTIELTIFFSNKCKNTDLFLPHG--FQFRPSDEELIE 45 (296)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LPpG--fRF~PTDeELI~ 45 (296)
|-|.|-||-+- .|-+...-++-+..|.| +||-|-|+-.|.
T Consensus 39 HfHF~EvN~aL----~FDR~~a~G~RLdIpagTAVRFEPG~~k~V~ 80 (106)
T COG0832 39 HFHFFEVNRAL----SFDREKAYGMRLDIPAGTAVRFEPGDEKEVE 80 (106)
T ss_pred ceeehhhCcce----eechhhhcceEecccCCceEeeCCCCccEEE
Confidence 88999999764 46677777888899998 899999886665
No 3
>PRK13202 ureB urease subunit beta; Reviewed
Probab=27.27 E-value=26 Score=28.69 Aligned_cols=37 Identities=22% Similarity=0.386 Sum_probs=28.5
Q ss_pred cceeeeeeehhhhhhhcccccccCCCCCCCCc--ceECCChHH
Q 042765 2 HQHIFSVNQHTIELTIFFSNKCKNTDLFLPHG--FQFRPSDEE 42 (296)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LPpG--fRF~PTDeE 42 (296)
|-|.|-||-+ ++ |=+...-++-+..|.| .||-|-++-
T Consensus 40 HyHF~E~N~a-L~---FDR~~A~G~RLdIpaGTavRFEPG~~k 78 (104)
T PRK13202 40 HVHLPQANRA-LS---FDRATAHGYRLDIPAATAVRFEPGIPQ 78 (104)
T ss_pred ccchhhcCcc-ee---ecHhHhcCcccccCCCCeEEECCCCeE
Confidence 8899999987 34 3355555677899998 899998765
No 4
>PHA00692 hypothetical protein
Probab=26.25 E-value=25 Score=26.03 Aligned_cols=10 Identities=40% Similarity=0.849 Sum_probs=8.3
Q ss_pred CCCCCcceEC
Q 042765 28 LFLPHGFQFR 37 (296)
Q Consensus 28 ~~LPpGfRF~ 37 (296)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4679999995
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=26.14 E-value=70 Score=19.98 Aligned_cols=21 Identities=24% Similarity=0.271 Sum_probs=16.9
Q ss_pred ChHHHHHHHHHHhhcCCCCCc
Q 042765 39 SDEELIEHYLKKKVSGILIPL 59 (296)
Q Consensus 39 TDeELI~~YL~~Ki~g~~lp~ 59 (296)
+-.|||.+|+.-|+..+..+.
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 457999999999998765543
No 6
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=24.76 E-value=1.2e+02 Score=31.39 Aligned_cols=103 Identities=22% Similarity=0.265 Sum_probs=57.9
Q ss_pred CChHHHHHHHHHHhhcCCCCCc------cccccc------cccCCCCCCccccccCCCCcccCCceEEEEecccccC---
Q 042765 38 PSDEELIEHYLKKKVSGILIPL------AEYFIR------DCNLYETKPSEIWDSHGGPFFNIDEDLYFFTQLKKKS--- 102 (296)
Q Consensus 38 PTDeELI~~YL~~Ki~g~~lp~------~~~~I~------~vDVY~~~PwdLp~~~~~~~~~~~~ewYFFs~r~~k~--- 102 (296)
|.| |.+.-|=.|++..+..-. .+..+. ..=+|.++|.+|.. .+.+...|||.+-....
T Consensus 301 G~d-qf~RvYD~R~~~~e~~n~~~~~f~p~hl~~d~~v~ITgl~Ysh~~sElLa------SYnDe~IYLF~~~~~~G~~p 373 (559)
T KOG1334|consen 301 GSD-QFARVYDQRRIDKEENNGVLDKFCPHHLVEDDPVNITGLVYSHDGSELLA------SYNDEDIYLFNKSMGDGSEP 373 (559)
T ss_pred Chh-hhhhhhcccchhhccccchhhhcCCccccccCcccceeEEecCCccceee------eecccceEEeccccccCCCC
Confidence 444 455667888887653211 001111 22357778888763 35677889995432211
Q ss_pred -------------CCCCccceeecCCCceeeecCCCceEEeC-CCCeE-EeeEEe---EEeecCCC
Q 042765 103 -------------SKGSRIDRKVSSSSGAWQWEDAGKDIVSG-QSKVK-IGSKKR---FRYEKKGC 150 (296)
Q Consensus 103 -------------~~g~R~~R~t~~~~G~Wk~tG~~k~I~~~-~~g~~-iG~Kkt---L~F~~g~~ 150 (296)
=.|.|.+|++ .+-.+|-+ +..-|+++ +.|.+ |+.|++ +.|.++.+
T Consensus 374 ~~~s~~~~~~k~vYKGHrN~~TV-KgVNFfGP--rsEyVvSGSDCGhIFiW~K~t~eii~~MegDr 436 (559)
T KOG1334|consen 374 DPSSPREQYVKRVYKGHRNSRTV-KGVNFFGP--RSEYVVSGSDCGHIFIWDKKTGEIIRFMEGDR 436 (559)
T ss_pred CCCcchhhccchhhccccccccc-ceeeeccC--ccceEEecCccceEEEEecchhHHHHHhhccc
Confidence 1266777776 35567865 35556665 55654 777766 55555543
No 7
>PRK13203 ureB urease subunit beta; Reviewed
Probab=21.31 E-value=43 Score=27.32 Aligned_cols=37 Identities=27% Similarity=0.573 Sum_probs=28.8
Q ss_pred cceeeeeeehhhhhhhcccccccCCCCCCCCc--ceECCChHH
Q 042765 2 HQHIFSVNQHTIELTIFFSNKCKNTDLFLPHG--FQFRPSDEE 42 (296)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LPpG--fRF~PTDeE 42 (296)
|-|.|-||.+ .+| =+...-++-+..|.| .||-|-++-
T Consensus 39 H~HF~E~N~a-L~F---DR~~A~G~RLdIpaGTavRFEPG~~k 77 (102)
T PRK13203 39 HYHFFEVNPA-LSF---DREAARGMRLNIPAGTAVRFEPGQTR 77 (102)
T ss_pred ccchhhcCcc-hhc---cHhhhcCcccccCCCCeEeECCCCeE
Confidence 8899999988 443 355555678899998 899998765
No 8
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=20.61 E-value=70 Score=30.71 Aligned_cols=47 Identities=21% Similarity=0.364 Sum_probs=37.0
Q ss_pred eehhhhhhhcccccccCCCCCCCCcceECCChHHHHHHHHHHhhcCCCCC
Q 042765 9 NQHTIELTIFFSNKCKNTDLFLPHGFQFRPSDEELIEHYLKKKVSGILIP 58 (296)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~LPpGfRF~PTDeELI~~YL~~Ki~g~~lp 58 (296)
++-||++-|-..|..= +..||.+|+ .|+++.++.+|.|.|..-+..-
T Consensus 78 v~~m~~~GN~~an~~~--ea~~p~~~~-~p~~d~~~e~FIR~KYE~kkf~ 124 (287)
T KOG0703|consen 78 VDFMISMGNAKANSYY--EAKLPDPFR-RPGPDDLVEQFIRDKYERKKFL 124 (287)
T ss_pred HHHHHHHcchhhhhhc--cccCCcccc-CCChHHHHHHHHHHHHhhhhhc
Confidence 4778888888888774 455887765 7888889999999999876643
No 9
>PRK13201 ureB urease subunit beta; Reviewed
Probab=17.27 E-value=59 Score=27.80 Aligned_cols=37 Identities=27% Similarity=0.591 Sum_probs=29.0
Q ss_pred cceeeeeeehhhhhhhcccccccCCCCCCCCc--ceECCChHH
Q 042765 2 HQHIFSVNQHTIELTIFFSNKCKNTDLFLPHG--FQFRPSDEE 42 (296)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LPpG--fRF~PTDeE 42 (296)
|-|.|-||.+ ++ |=+...-++-+..|.| +||-|-++-
T Consensus 39 HyHF~EvN~a-L~---FDR~~A~G~RLdIPAGTAVRFEPG~~k 77 (136)
T PRK13201 39 HFHFYEANAA-LD---FEREMAYGKHLDIPAGAAVRFEPGDKK 77 (136)
T ss_pred ccchhhcCcc-cc---ccHhhhcCcccccCCCCeEeECCCCeE
Confidence 8899999977 33 3455566678899998 999998876
No 10
>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=17.13 E-value=1.3e+02 Score=24.08 Aligned_cols=38 Identities=18% Similarity=0.322 Sum_probs=29.6
Q ss_pred CCChHHHHHHHHHHhhcCCCCCccccccccccCCCCCCcccccc
Q 042765 37 RPSDEELIEHYLKKKVSGILIPLAEYFIRDCNLYETKPSEIWDS 80 (296)
Q Consensus 37 ~PTDeELI~~YL~~Ki~g~~lp~~~~~I~~vDVY~~~PwdLp~~ 80 (296)
|-|..||++.-...-..|+|+|.+ .|+-+..|.++|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D------~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD------ADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh------hhhhhcCcccccHH
Confidence 567778887766677889999975 57788888888764
Done!