Query 023427
Match_columns 282
No_of_seqs 166 out of 938
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 03:56:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023427.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023427hhsearch_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 5.1E-43 1.1E-47 289.8 6.8 127 7-135 2-129 (129)
2 KOG1334 WD40 repeat protein [G 24.0 1.1E+02 0.0025 31.4 4.5 70 43-117 343-434 (559)
3 PF10107 Endonuc_Holl: Endonuc 23.0 20 0.00043 31.2 -0.9 46 2-69 79-126 (156)
4 cd00490 Met_repressor_MetJ Met 20.5 77 0.0017 25.3 2.0 39 13-55 50-88 (103)
5 PF07960 CBP4: CBP4; InterPro 18.2 61 0.0013 27.4 1.1 12 12-23 29-40 (128)
6 PRK05264 transcriptional repre 18.1 84 0.0018 25.2 1.8 39 13-55 51-89 (105)
7 TIGR03874 4cys_cytochr c-type 17.4 1.2E+02 0.0025 26.0 2.6 28 5-32 90-120 (143)
8 COG3060 MetJ Transcriptional r 17.3 67 0.0014 25.4 1.0 39 13-55 51-89 (105)
9 smart00265 BH4 BH4 Bcl-2 homol 16.1 1.6E+02 0.0035 18.3 2.3 19 15-33 4-22 (27)
10 KOG0256 1-aminocyclopropane-1- 15.8 73 0.0016 32.2 1.1 20 2-21 302-324 (471)
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=5.1e-43 Score=289.79 Aligned_cols=127 Identities=52% Similarity=1.034 Sum_probs=96.8
Q ss_pred CCcceEcCChHHHHHHHHHHHHcCCCCCc-ceeeeccCCCCCCCCCCCccccCceeEEEEeecCCcCCCCCCCceecccc
Q 023427 7 LPGFRFHPTEDELLNFYLRNIVFGKKSHF-DIIGFLNIYHHDPWELPGLSKIGEREWYFFVPRDRKHGSGGRPNRTTEHG 85 (282)
Q Consensus 7 lPGfRF~PTDeELV~~YL~~ki~G~pl~~-~~I~evDvY~~~PwdLp~~~~~ge~ewYFFt~r~rk~~~g~R~~R~tg~G 85 (282)
+|||||+|||+|||.+||++|+.|.+++. ++|+++|||++|||+|++....++++||||+++.+++.+++|.+|++++|
T Consensus 2 P~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G 81 (129)
T PF02365_consen 2 PPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGG 81 (129)
T ss_dssp -TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETTE
T ss_pred CCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccce
Confidence 57999999999999999999999999888 69999999999999999543446779999999999999999999999999
Q ss_pred eeeeeCCCceEEecCCCCeEEEEEEEEEeeecCCCCCCccCEEEEEEEcC
Q 023427 86 FWKATGSDRKIVSLSDPKRVIGLRKTLVFYEGRAPKGHKTDWVMNEYRLP 135 (282)
Q Consensus 86 ~Wk~tG~~k~I~~~~d~g~viG~KktL~Fy~g~~~~g~kT~WvMhEY~L~ 135 (282)
+||.+|+.+.|... ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 82 ~Wk~~g~~~~i~~~--~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 82 YWKSTGKEKPIKDP--GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEECEEEEEEE---TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred EEeecccccccccc--cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999974 6789999999999998888899999999999983
No 2
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=23.99 E-value=1.1e+02 Score=31.35 Aligned_cols=70 Identities=33% Similarity=0.493 Sum_probs=41.4
Q ss_pred CCCCCCCCCCCccccCceeEEEEeecCCcCC-----------------CCCCCceeccc-ceeeeeCCCceEEecCCCCe
Q 023427 43 IYHHDPWELPGLSKIGEREWYFFVPRDRKHG-----------------SGGRPNRTTEH-GFWKATGSDRKIVSLSDPKR 104 (282)
Q Consensus 43 vY~~~PwdLp~~~~~ge~ewYFFt~r~rk~~-----------------~g~R~~R~tg~-G~Wk~tG~~k~I~~~~d~g~ 104 (282)
+|++++-+|.... .+...|||. +.++.+ .|.|.+|++++ .||-. +..-|++++|.|.
T Consensus 343 ~Ysh~~sElLaSY--nDe~IYLF~-~~~~~G~~p~~~s~~~~~~k~vYKGHrN~~TVKgVNFfGP--rsEyVvSGSDCGh 417 (559)
T KOG1334|consen 343 VYSHDGSELLASY--NDEDIYLFN-KSMGDGSEPDPSSPREQYVKRVYKGHRNSRTVKGVNFFGP--RSEYVVSGSDCGH 417 (559)
T ss_pred EecCCccceeeee--cccceEEec-cccccCCCCCCCcchhhccchhhcccccccccceeeeccC--ccceEEecCccce
Confidence 4667777775443 355678884 444433 46676777654 67732 2234677778887
Q ss_pred E-EEEEEE---EEeeec
Q 023427 105 V-IGLRKT---LVFYEG 117 (282)
Q Consensus 105 v-iG~Kkt---L~Fy~g 117 (282)
| |.-|++ +.|.+|
T Consensus 418 IFiW~K~t~eii~~Meg 434 (559)
T KOG1334|consen 418 IFIWDKKTGEIIRFMEG 434 (559)
T ss_pred EEEEecchhHHHHHhhc
Confidence 7 555544 556554
No 3
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=22.97 E-value=20 Score=31.19 Aligned_cols=46 Identities=24% Similarity=0.406 Sum_probs=27.1
Q ss_pred CCCCCC--CcceEcCChHHHHHHHHHHHHcCCCCCcceeeeccCCCCCCCCCCCccccCceeEEEEeecC
Q 023427 2 TPELEL--PGFRFHPTEDELLNFYLRNIVFGKKSHFDIIGFLNIYHHDPWELPGLSKIGEREWYFFVPRD 69 (282)
Q Consensus 2 a~~~~l--PGfRF~PTDeELV~~YL~~ki~G~pl~~~~I~evDvY~~~PwdLp~~~~~ge~ewYFFt~r~ 69 (282)
++.+-| |+|.|+|+|.--| |.| +++|..-.+-. ....+..|.-.+.
T Consensus 79 ~EqlaP~lp~F~ynP~D~RFl---------G~P--VD~IvF~Gls~-----------~~~~eIvfiEVKt 126 (156)
T PF10107_consen 79 SEQLAPFLPEFPYNPKDARFL---------GSP--VDFIVFDGLSD-----------GNIIEIVFIEVKT 126 (156)
T ss_pred HHHhhhccCCCCCChhhheec---------CCC--ceEEEEcCCCC-----------CCcceEEEEEecc
Confidence 444543 9999999996443 454 46665433322 2345667776553
No 4
>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=20.48 E-value=77 Score=25.27 Aligned_cols=39 Identities=21% Similarity=0.158 Sum_probs=31.9
Q ss_pred cCChHHHHHHHHHHHHcCCCCCcceeeeccCCCCCCCCCCCcc
Q 023427 13 HPTEDELLNFYLRNIVFGKKSHFDIIGFLNIYHHDPWELPGLS 55 (282)
Q Consensus 13 ~PTDeELV~~YL~~ki~G~pl~~~~I~evDvY~~~PwdLp~~~ 55 (282)
|-|..||++.-...-..|+|||. +.|+-...|-++|...
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHHH
Confidence 56788998877777889999986 6788888999998754
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=18.17 E-value=61 Score=27.35 Aligned_cols=12 Identities=50% Similarity=0.802 Sum_probs=9.5
Q ss_pred EcCChHHHHHHH
Q 023427 12 FHPTEDELLNFY 23 (282)
Q Consensus 12 F~PTDeELV~~Y 23 (282)
=.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 369999998765
No 6
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=18.14 E-value=84 Score=25.18 Aligned_cols=39 Identities=21% Similarity=0.145 Sum_probs=31.7
Q ss_pred cCChHHHHHHHHHHHHcCCCCCcceeeeccCCCCCCCCCCCcc
Q 023427 13 HPTEDELLNFYLRNIVFGKKSHFDIIGFLNIYHHDPWELPGLS 55 (282)
Q Consensus 13 ~PTDeELV~~YL~~ki~G~pl~~~~I~evDvY~~~PwdLp~~~ 55 (282)
|-|..||++.-...-..|+|||. +-|+-...|-++|...
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHHH
Confidence 56788998877777889999986 6788888899998654
No 7
>TIGR03874 4cys_cytochr c-type cytochrome, methanol metabolism-related. This family represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others.
Probab=17.38 E-value=1.2e+02 Score=26.03 Aligned_cols=28 Identities=29% Similarity=0.261 Sum_probs=21.8
Q ss_pred CCCCcceEcCChH-HH--HHHHHHHHHcCCC
Q 023427 5 LELPGFRFHPTED-EL--LNFYLRNIVFGKK 32 (282)
Q Consensus 5 ~~lPGfRF~PTDe-EL--V~~YL~~ki~G~p 32 (282)
..+|+|.-..+|+ || |..||+.+..|.-
T Consensus 90 ~~MPaF~~~LsD~~eIa~L~~YLR~~~~g~~ 120 (143)
T TIGR03874 90 NVMPAFGDNPNVMCYLDDLYVYLRARGTDAL 120 (143)
T ss_pred CCCCCccccCCcHHHHHHHHHHHHhccCCCc
Confidence 3579999999997 66 5668988887753
No 8
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=17.31 E-value=67 Score=25.44 Aligned_cols=39 Identities=21% Similarity=0.178 Sum_probs=31.4
Q ss_pred cCChHHHHHHHHHHHHcCCCCCcceeeeccCCCCCCCCCCCcc
Q 023427 13 HPTEDELLNFYLRNIVFGKKSHFDIIGFLNIYHHDPWELPGLS 55 (282)
Q Consensus 13 ~PTDeELV~~YL~~ki~G~pl~~~~I~evDvY~~~PwdLp~~~ 55 (282)
|-|..||++.-...-..|+|+|. +.|+...-|.++|..+
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 56778888877777889999986 6788888888898764
No 9
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=16.06 E-value=1.6e+02 Score=18.27 Aligned_cols=19 Identities=16% Similarity=0.090 Sum_probs=15.2
Q ss_pred ChHHHHHHHHHHHHcCCCC
Q 023427 15 TEDELLNFYLRNIVFGKKS 33 (282)
Q Consensus 15 TDeELV~~YL~~ki~G~pl 33 (282)
+-.|||.+|+.-|+.-+..
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999876544
No 10
>KOG0256 consensus 1-aminocyclopropane-1-carboxylate synthase, and related proteins [Signal transduction mechanisms]
Probab=15.79 E-value=73 Score=32.16 Aligned_cols=20 Identities=25% Similarity=0.738 Sum_probs=13.7
Q ss_pred CCCCCCCcceE---cCChHHHHH
Q 023427 2 TPELELPGFRF---HPTEDELLN 21 (282)
Q Consensus 2 a~~~~lPGfRF---~PTDeELV~ 21 (282)
..++||||||| +-+++++|.
T Consensus 302 SKD~GlpGfRvGviYS~ne~Vvs 324 (471)
T KOG0256|consen 302 SKDFGLPGFRVGVIYSNNEDVVS 324 (471)
T ss_pred ccccCCCceEEEEEEecChHHHH
Confidence 56899999998 344444443
Done!