Query 024547
Match_columns 266
No_of_seqs 147 out of 319
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 05:24:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024547hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03634 TCP: TCP family trans 100.0 5.3E-35 1.1E-39 234.6 7.0 66 35-100 2-71 (138)
2 PLN03105 TCP24 transcription f 99.9 1.5E-27 3.2E-32 217.5 6.6 82 13-96 27-113 (324)
3 PLN03106 TCP2 Protein TCP2; Pr 99.9 5E-27 1.1E-31 221.6 7.9 72 24-95 60-136 (447)
4 PF10200 Ndufs5: NADH:ubiquino 40.9 13 0.00028 30.3 0.9 20 61-84 3-22 (96)
5 PHA02570 dexA exonuclease; Pro 39.2 27 0.00057 32.2 2.7 31 62-92 49-80 (220)
6 PF13986 DUF4224: Domain of un 35.8 27 0.00058 24.7 1.7 22 63-84 7-28 (47)
7 PRK02967 nickel responsive reg 32.4 58 0.0013 27.5 3.5 34 51-84 6-39 (139)
8 cd07977 TFIIE_beta_winged_heli 29.2 26 0.00056 26.7 0.8 27 60-86 27-54 (75)
9 PF01402 RHH_1: Ribbon-helix-h 22.1 96 0.0021 19.7 2.4 31 51-82 4-34 (39)
10 TIGR02793 nikR nickel-responsi 20.1 1.3E+02 0.0029 25.1 3.4 34 51-84 5-38 (129)
No 1
>PF03634 TCP: TCP family transcription factor; InterPro: IPR005333 The TCP transcription factor family was named after: teosinte branched 1 (tb1, Zea mays (Maize)) [], cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) [] and PCF in rice (Oryza sativa) [, ]. The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits []. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event []. This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators [].
Probab=100.00 E-value=5.3e-35 Score=234.56 Aligned_cols=66 Identities=35% Similarity=0.617 Sum_probs=62.2
Q ss_pred CCCCCCccccc----CCCceeecCHHHHHHhhhhhhhhCCCCCchHHHHHHHhchHHHHHhhCCCCCCCc
Q 024547 35 PPSKDRHSKVD----GRGRRIRMPIICAARVFQLTRELGHKSDGQTIEWLLRQAEPSIIAATGTGTTPAS 100 (266)
Q Consensus 35 ~~~KDRHSKV~----~RDRRvRLs~~~A~rfF~LQDeLGfdkaSkTIEWLL~qak~AI~~atgtgt~Pas 100 (266)
+.+|||||||| +||||||||++||++||+||||||||||||||||||++||+||++|+.+.+.|.+
T Consensus 2 ~~~kdrhski~Ta~g~RdRRvRLs~~~Ar~FFdLQDmLGfDKaSKTveWLL~kSk~AIkeL~~~~~~~~s 71 (138)
T PF03634_consen 2 AGKKDRHSKIHTAQGPRDRRVRLSLEIARKFFDLQDMLGFDKASKTVEWLLTKSKKAIKELTQSSSSSSS 71 (138)
T ss_pred CCCCCCCCccccccCCCCCceecCHHHHHHHHHHHHHhcCCCCCchHHHHHHhCHHHHHHHHHhhccccc
Confidence 46899999999 9999999999999999999999999999999999999999999999999766654
No 2
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=99.94 E-value=1.5e-27 Score=217.50 Aligned_cols=82 Identities=32% Similarity=0.502 Sum_probs=73.2
Q ss_pred CccccCCCCCCCCCCCccccCC-CCCCCCccccc----CCCceeecCHHHHHHhhhhhhhhCCCCCchHHHHHHHhchHH
Q 024547 13 NGAIIDPQRQQPPGNGALTVKK-PPSKDRHSKVD----GRGRRIRMPIICAARVFQLTRELGHKSDGQTIEWLLRQAEPS 87 (266)
Q Consensus 13 ng~ivd~~~q~~~~~~~~~~kk-~~~KDRHSKV~----~RDRRvRLs~~~A~rfF~LQDeLGfdkaSkTIEWLL~qak~A 87 (266)
|.+|...|. .|++++++++| .++|||||||+ +||||||||++||++||+|||||||||+||||||||++||+|
T Consensus 27 ~~gl~r~w~--~pssrivrvsRa~g~KDRHSKI~TAqGpRDRRvRLSv~iArkFFdLQDmLGFDKaSKTVEWLL~kSk~A 104 (324)
T PLN03105 27 NTGLMRNWN--NPSSRIIRVSRASGGKDRHSKVLTSKGLRDRRIRLSVATAIQFYDLQDRLGFDQPSKAVEWLINAASDS 104 (324)
T ss_pred cccccccCC--CCcceEEEeeccCCCCCcccceecccCCcccceecCHHHHHHHhhHHHHhCCCCcchHHHHHHHHhHHH
Confidence 556666554 47888888865 66999999999 999999999999999999999999999999999999999999
Q ss_pred HHHhhCCCC
Q 024547 88 IIAATGTGT 96 (266)
Q Consensus 88 I~~atgtgt 96 (266)
|++|+...+
T Consensus 105 I~ELp~l~~ 113 (324)
T PLN03105 105 ITDLPLLNT 113 (324)
T ss_pred HHhcccCcc
Confidence 999988764
No 3
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=99.94 E-value=5e-27 Score=221.64 Aligned_cols=72 Identities=32% Similarity=0.523 Sum_probs=66.4
Q ss_pred CCCCCccccCC-CCCCCCccccc----CCCceeecCHHHHHHhhhhhhhhCCCCCchHHHHHHHhchHHHHHhhCCC
Q 024547 24 PPGNGALTVKK-PPSKDRHSKVD----GRGRRIRMPIICAARVFQLTRELGHKSDGQTIEWLLRQAEPSIIAATGTG 95 (266)
Q Consensus 24 ~~~~~~~~~kk-~~~KDRHSKV~----~RDRRvRLs~~~A~rfF~LQDeLGfdkaSkTIEWLL~qak~AI~~atgtg 95 (266)
+.++++++++| .++|||||||+ +||||||||++||++||+|||||||||+||||||||++||+||+||+...
T Consensus 60 ~~~~ri~rvsRasg~KDRHSKI~Ta~G~RDRRvRLS~~~ArkFFdLQD~LGfDkaSKTvEWLL~~Sk~AI~EL~~l~ 136 (447)
T PLN03106 60 HHSSRIIRVSRASGGKDRHSKVLTSKGLRDRRVRLSVSTAIQFYDLQDRLGYDQPSKAVEWLIKAAEDSISELPSLN 136 (447)
T ss_pred ccCCceeeeecccCCCCcccceecccCCcccceeccHHHHHHHHhHHHHhCCCCcchHHHHHHHHhHHHHHHhhccc
Confidence 34678888854 66999999999 99999999999999999999999999999999999999999999998755
No 4
>PF10200 Ndufs5: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa; InterPro: IPR019342 Proteins in this entry form part of the NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The mammalian complex I is composed of 45 different subunits. The proteins in this entry represent a component of the iron-sulphur (IP) fragment of the enzyme, that is not involved in catalysis. These proteins carry four highly conserved cysteine residues, but these do not appear to be in a configuration which would favour metal binding, so the exact function of the protein is uncertain [].
Probab=40.86 E-value=13 Score=30.27 Aligned_cols=20 Identities=35% Similarity=0.745 Sum_probs=17.3
Q ss_pred hhhhhhhhCCCCCchHHHHHHHhc
Q 024547 61 VFQLTRELGHKSDGQTIEWLLRQA 84 (266)
Q Consensus 61 fF~LQDeLGfdkaSkTIEWLL~qa 84 (266)
||+||..||++-| .||+.+|
T Consensus 3 ~~~~~~~~~~~~d----~~~~~~s 22 (96)
T PF10200_consen 3 FLDLQKRLGINLD----RWMLIQS 22 (96)
T ss_pred hhhHHHHhCcCHH----HHHHHhc
Confidence 8999999999754 7998887
No 5
>PHA02570 dexA exonuclease; Provisional
Probab=39.20 E-value=27 Score=32.17 Aligned_cols=31 Identities=29% Similarity=0.402 Sum_probs=24.2
Q ss_pred hhhhhhhC-CCCCchHHHHHHHhchHHHHHhh
Q 024547 62 FQLTRELG-HKSDGQTIEWLLRQAEPSIIAAT 92 (266)
Q Consensus 62 F~LQDeLG-fdkaSkTIEWLL~qak~AI~~at 92 (266)
|++....| ...+..||+|-++|+..|=.++.
T Consensus 49 ~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~ 80 (220)
T PHA02570 49 FDLKSQKGKRLFDKSTIEWWKNQSPEARKNLK 80 (220)
T ss_pred cchhhccCCCccCchHHHHHHhCCHHHHHhcc
Confidence 34445567 78899999999999998866664
No 6
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=35.80 E-value=27 Score=24.66 Aligned_cols=22 Identities=32% Similarity=0.560 Sum_probs=19.1
Q ss_pred hhhhhhCCCCCchHHHHHHHhc
Q 024547 63 QLTRELGHKSDGQTIEWLLRQA 84 (266)
Q Consensus 63 ~LQDeLGfdkaSkTIEWLL~qa 84 (266)
+|+++-|+++.++-++||-.+-
T Consensus 7 El~elTG~k~~~~Q~~~L~~~G 28 (47)
T PF13986_consen 7 ELQELTGYKRPSKQIRWLRRNG 28 (47)
T ss_pred HHHHHHCCCCHHHHHHHHHHCC
Confidence 5788899999999999997653
No 7
>PRK02967 nickel responsive regulator; Provisional
Probab=32.44 E-value=58 Score=27.54 Aligned_cols=34 Identities=24% Similarity=0.171 Sum_probs=31.8
Q ss_pred eecCHHHHHHhhhhhhhhCCCCCchHHHHHHHhc
Q 024547 51 IRMPIICAARVFQLTRELGHKSDGQTIEWLLRQA 84 (266)
Q Consensus 51 vRLs~~~A~rfF~LQDeLGfdkaSkTIEWLL~qa 84 (266)
|+||-+...+|=.+..+.||.+-|+.|..|++..
T Consensus 6 vslp~~ll~~lD~~~~~~gy~sRSeaIrd~iR~~ 39 (139)
T PRK02967 6 ITLDDDLLETLDSLIARRGYQNRSEAIRDLLRAA 39 (139)
T ss_pred EEcCHHHHHHHHHHHHHcCCCCHhHHHHHHHHHH
Confidence 7899999999999999999999999999998764
No 8
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=29.24 E-value=26 Score=26.73 Aligned_cols=27 Identities=19% Similarity=0.176 Sum_probs=23.3
Q ss_pred HhhhhhhhhC-CCCCchHHHHHHHhchH
Q 024547 60 RVFQLTRELG-HKSDGQTIEWLLRQAEP 86 (266)
Q Consensus 60 rfF~LQDeLG-fdkaSkTIEWLL~qak~ 86 (266)
.|=++.++|. +|...+.++||.+.++.
T Consensus 27 t~~EIl~~ls~~d~~~~~~~~L~~~~~~ 54 (75)
T cd07977 27 TLDEILDYLSLLDIGPKLKEWLKSEALV 54 (75)
T ss_pred cHHHHHHHHhccCccHHHHHHHHhhhhc
Confidence 4668999999 99999999999887765
No 9
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=22.11 E-value=96 Score=19.66 Aligned_cols=31 Identities=35% Similarity=0.494 Sum_probs=24.6
Q ss_pred eecCHHHHHHhhhhhhhhCCCCCchHHHHHHH
Q 024547 51 IRMPIICAARVFQLTRELGHKSDGQTIEWLLR 82 (266)
Q Consensus 51 vRLs~~~A~rfF~LQDeLGfdkaSkTIEWLL~ 82 (266)
||||.+...+|=.+..++| .+-|+-|.-+++
T Consensus 4 i~l~~~~~~~l~~~a~~~g-~s~s~~ir~ai~ 34 (39)
T PF01402_consen 4 IRLPDELYERLDELAKELG-RSRSELIREAIR 34 (39)
T ss_dssp EEEEHHHHHHHHHHHHHHT-SSHHHHHHHHHH
T ss_pred EEeCHHHHHHHHHHHHHHC-cCHHHHHHHHHH
Confidence 7999999999999999999 455555555443
No 10
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=20.10 E-value=1.3e+02 Score=25.06 Aligned_cols=34 Identities=21% Similarity=0.169 Sum_probs=31.2
Q ss_pred eecCHHHHHHhhhhhhhhCCCCCchHHHHHHHhc
Q 024547 51 IRMPIICAARVFQLTRELGHKSDGQTIEWLLRQA 84 (266)
Q Consensus 51 vRLs~~~A~rfF~LQDeLGfdkaSkTIEWLL~qa 84 (266)
|+||-+...+|=++..+.||..-|+.|.=+++..
T Consensus 5 vslp~~ll~~lD~~~~~~g~~~RSe~ir~~ir~~ 38 (129)
T TIGR02793 5 ITLDDDLLETLDRLIARRGYQNRSEAIRDLLRSG 38 (129)
T ss_pred EEcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 7899999999999999999999999999887654
Done!