Query 021111
Match_columns 317
No_of_seqs 152 out of 301
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 07:41:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021111.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021111hhsearch_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 6.5E-35 1.4E-39 239.9 7.1 68 68-135 2-73 (138)
2 PLN03106 TCP2 Protein TCP2; Pr 99.9 2.8E-27 6E-32 227.7 7.6 63 66-128 70-136 (447)
3 PLN03105 TCP24 transcription f 99.9 5.6E-27 1.2E-31 217.8 6.7 64 66-129 46-113 (324)
4 PRK02967 nickel responsive reg 39.8 39 0.00085 29.3 3.7 34 84-117 6-39 (139)
5 PF10200 Ndufs5: NADH:ubiquino 36.6 17 0.00037 30.4 1.0 21 94-118 3-23 (96)
6 PHA02570 dexA exonuclease; Pro 27.3 50 0.0011 31.2 2.5 30 96-125 50-80 (220)
7 PF13986 DUF4224: Domain of un 26.2 50 0.0011 23.9 1.8 22 96-117 7-28 (47)
8 PF01402 RHH_1: Ribbon-helix-h 25.4 83 0.0018 20.5 2.6 31 84-115 4-34 (39)
9 cd07977 TFIIE_beta_winged_heli 24.6 35 0.00075 26.7 0.8 27 93-119 27-54 (75)
10 TIGR02793 nikR nickel-responsi 24.5 1E+02 0.0022 26.5 3.6 34 84-117 5-38 (129)
11 PF10723 RepB-RCR_reg: Replica 22.9 81 0.0018 25.4 2.6 37 83-120 45-81 (84)
12 PRK04460 nickel responsive reg 22.8 1.1E+02 0.0023 26.6 3.5 34 84-117 7-40 (137)
13 PF12045 DUF3528: Protein of u 21.1 33 0.0007 30.8 0.0 20 264-284 101-120 (143)
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=6.5e-35 Score=239.88 Aligned_cols=68 Identities=31% Similarity=0.564 Sum_probs=62.9
Q ss_pred CCCCCcccccc----CCCceeecCHHHHHHHHhhhhhhCCCCCchHHHHHHHhchHHHHHHhcCCCCCCccc
Q 021111 68 SSNKDRHTKVE----GRGRRIRMPALCAARIFQLTRELGHKSDGETIQWLLQQAEPSIIAATGTGTIPASAL 135 (317)
Q Consensus 68 s~~KDRHSKV~----~RDRRvRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~qak~AI~~lt~tgtiP~~~~ 135 (317)
+++|||||||| +||||||||++||++||+||||||||||||||||||++||+||++|+.....|.+.|
T Consensus 2 ~~~kdrhski~Ta~g~RdRRvRLs~~~Ar~FFdLQDmLGfDKaSKTveWLL~kSk~AIkeL~~~~~~~~s~~ 73 (138)
T PF03634_consen 2 AGKKDRHSKIHTAQGPRDRRVRLSLEIARKFFDLQDMLGFDKASKTVEWLLTKSKKAIKELTQSSSSSSSEC 73 (138)
T ss_pred CCCCCCCCccccccCCCCCceecCHHHHHHHHHHHHHhcCCCCCchHHHHHHhCHHHHHHHHHhhccccccc
Confidence 57899999999 999999999999999999999999999999999999999999999998866666444
No 2
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=99.94 E-value=2.8e-27 Score=227.71 Aligned_cols=63 Identities=33% Similarity=0.568 Sum_probs=60.0
Q ss_pred CCCCCCCcccccc----CCCceeecCHHHHHHHHhhhhhhCCCCCchHHHHHHHhchHHHHHHhcCC
Q 021111 66 KRSSNKDRHTKVE----GRGRRIRMPALCAARIFQLTRELGHKSDGETIQWLLQQAEPSIIAATGTG 128 (317)
Q Consensus 66 krs~~KDRHSKV~----~RDRRvRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~qak~AI~~lt~tg 128 (317)
+++++|||||||+ +||||||||++||++||+||||||||||||||||||++||+||+||+...
T Consensus 70 Rasg~KDRHSKI~Ta~G~RDRRvRLS~~~ArkFFdLQD~LGfDkaSKTvEWLL~~Sk~AI~EL~~l~ 136 (447)
T PLN03106 70 RASGGKDRHSKVLTSKGLRDRRVRLSVSTAIQFYDLQDRLGYDQPSKAVEWLIKAAEDSISELPSLN 136 (447)
T ss_pred cccCCCCcccceecccCCcccceeccHHHHHHHHhHHHHhCCCCcchHHHHHHHHhHHHHHHhhccc
Confidence 4667999999999 99999999999999999999999999999999999999999999998754
No 3
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=99.93 E-value=5.6e-27 Score=217.78 Aligned_cols=64 Identities=34% Similarity=0.551 Sum_probs=60.2
Q ss_pred CCCCCCCcccccc----CCCceeecCHHHHHHHHhhhhhhCCCCCchHHHHHHHhchHHHHHHhcCCC
Q 021111 66 KRSSNKDRHTKVE----GRGRRIRMPALCAARIFQLTRELGHKSDGETIQWLLQQAEPSIIAATGTGT 129 (317)
Q Consensus 66 krs~~KDRHSKV~----~RDRRvRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~qak~AI~~lt~tgt 129 (317)
+..++|||||||+ +||||||||++||++||+||||||||||||||||||++||+||++|+...+
T Consensus 46 Ra~g~KDRHSKI~TAqGpRDRRvRLSv~iArkFFdLQDmLGFDKaSKTVEWLL~kSk~AI~ELp~l~~ 113 (324)
T PLN03105 46 RASGGKDRHSKVLTSKGLRDRRIRLSVATAIQFYDLQDRLGFDQPSKAVEWLINAASDSITDLPLLNT 113 (324)
T ss_pred ccCCCCCcccceecccCCcccceecCHHHHHHHhhHHHHhCCCCcchHHHHHHHHhHHHHHhcccCcc
Confidence 4567999999999 999999999999999999999999999999999999999999999987653
No 4
>PRK02967 nickel responsive regulator; Provisional
Probab=39.77 E-value=39 Score=29.32 Aligned_cols=34 Identities=24% Similarity=0.211 Sum_probs=32.1
Q ss_pred eecCHHHHHHHHhhhhhhCCCCCchHHHHHHHhc
Q 021111 84 IRMPALCAARIFQLTRELGHKSDGETIQWLLQQA 117 (317)
Q Consensus 84 vRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~qa 117 (317)
|+||-+.+.+|=.+-.+.||.+-||.|..|++..
T Consensus 6 vslp~~ll~~lD~~~~~~gy~sRSeaIrd~iR~~ 39 (139)
T PRK02967 6 ITLDDDLLETLDSLIARRGYQNRSEAIRDLLRAA 39 (139)
T ss_pred EEcCHHHHHHHHHHHHHcCCCCHhHHHHHHHHHH
Confidence 7899999999999999999999999999999865
No 5
>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=36.60 E-value=17 Score=30.37 Aligned_cols=21 Identities=33% Similarity=0.749 Sum_probs=17.7
Q ss_pred HHhhhhhhCCCCCchHHHHHHHhch
Q 021111 94 IFQLTRELGHKSDGETIQWLLQQAE 118 (317)
Q Consensus 94 fF~Lqd~LGfdk~skTIeWLL~qak 118 (317)
|||||.+||++-| .||+-+|-
T Consensus 3 ~~~~~~~~~~~~d----~~~~~~s~ 23 (96)
T PF10200_consen 3 FLDLQKRLGINLD----RWMLIQSA 23 (96)
T ss_pred hhhHHHHhCcCHH----HHHHHhcc
Confidence 8999999999755 69988773
No 6
>PHA02570 dexA exonuclease; Provisional
Probab=27.27 E-value=50 Score=31.21 Aligned_cols=30 Identities=23% Similarity=0.322 Sum_probs=23.3
Q ss_pred hhhhhhC-CCCCchHHHHHHHhchHHHHHHh
Q 021111 96 QLTRELG-HKSDGETIQWLLQQAEPSIIAAT 125 (317)
Q Consensus 96 ~Lqd~LG-fdk~skTIeWLL~qak~AI~~lt 125 (317)
++....| ...+..||+|-++|+..|=.++.
T Consensus 50 d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~ 80 (220)
T PHA02570 50 DLKSQKGKRLFDKSTIEWWKNQSPEARKNLK 80 (220)
T ss_pred chhhccCCCccCchHHHHHHhCCHHHHHhcc
Confidence 3444457 78899999999999998866653
No 7
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=26.16 E-value=50 Score=23.91 Aligned_cols=22 Identities=27% Similarity=0.524 Sum_probs=19.2
Q ss_pred hhhhhhCCCCCchHHHHHHHhc
Q 021111 96 QLTRELGHKSDGETIQWLLQQA 117 (317)
Q Consensus 96 ~Lqd~LGfdk~skTIeWLL~qa 117 (317)
+|++.-|++.+++=++||-.+-
T Consensus 7 El~elTG~k~~~~Q~~~L~~~G 28 (47)
T PF13986_consen 7 ELQELTGYKRPSKQIRWLRRNG 28 (47)
T ss_pred HHHHHHCCCCHHHHHHHHHHCC
Confidence 5788889999999999998764
No 8
>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=25.37 E-value=83 Score=20.54 Aligned_cols=31 Identities=35% Similarity=0.539 Sum_probs=24.7
Q ss_pred eecCHHHHHHHHhhhhhhCCCCCchHHHHHHH
Q 021111 84 IRMPALCAARIFQLTRELGHKSDGETIQWLLQ 115 (317)
Q Consensus 84 vRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~ 115 (317)
||||.+...+|=.+..++| .+-|+-|.-++.
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 555555554443
No 9
>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=24.58 E-value=35 Score=26.73 Aligned_cols=27 Identities=15% Similarity=0.166 Sum_probs=23.5
Q ss_pred HHHhhhhhhC-CCCCchHHHHHHHhchH
Q 021111 93 RIFQLTRELG-HKSDGETIQWLLQQAEP 119 (317)
Q Consensus 93 rfF~Lqd~LG-fdk~skTIeWLL~qak~ 119 (317)
.|=++.++|. +|...+.++||...++.
T Consensus 27 t~~EIl~~ls~~d~~~~~~~~L~~~~~~ 54 (75)
T cd07977 27 TLDEILDYLSLLDIGPKLKEWLKSEALV 54 (75)
T ss_pred cHHHHHHHHhccCccHHHHHHHHhhhhc
Confidence 4568899999 99999999999988876
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=24.52 E-value=1e+02 Score=26.49 Aligned_cols=34 Identities=21% Similarity=0.209 Sum_probs=31.5
Q ss_pred eecCHHHHHHHHhhhhhhCCCCCchHHHHHHHhc
Q 021111 84 IRMPALCAARIFQLTRELGHKSDGETIQWLLQQA 117 (317)
Q Consensus 84 vRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~qa 117 (317)
|+||.+.+.+|=.+-.+.||..-|+.|.=+++..
T Consensus 5 vslp~~ll~~lD~~~~~~g~~~RSe~ir~~ir~~ 38 (129)
T TIGR02793 5 ITLDDDLLETLDRLIARRGYQNRSEAIRDLLRSG 38 (129)
T ss_pred EEcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 7899999999999999999999999999888754
No 11
>PF10723 RepB-RCR_reg: Replication regulatory protein RepB; InterPro: IPR019661 This family of proteins regulates the replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of the replication of the RCR plasmids occurs mainly at the initiation of leading strand synthesis at the dso, such that concentration of Rep protein controls plasmid replication []. ; PDB: 2KEL_B.
Probab=22.87 E-value=81 Score=25.36 Aligned_cols=37 Identities=22% Similarity=0.353 Sum_probs=29.2
Q ss_pred eeecCHHHHHHHHhhhhhhCCCCCchHHHHHHHhchHH
Q 021111 83 RIRMPALCAARIFQLTRELGHKSDGETIQWLLQQAEPS 120 (317)
Q Consensus 83 RvRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~qak~A 120 (317)
.|+++.++..+|-.|-.+.| -+-++-||.||.....+
T Consensus 45 ~v~I~~~~K~~L~~lc~~~G-lTQae~IE~LI~~~~~~ 81 (84)
T PF10723_consen 45 NVFIPNELKERLEELCKEQG-LTQAEMIERLIKSELQQ 81 (84)
T ss_dssp EEEEEHHHHHHHHHHHHHS----HHHHHHHHHHHHHHH
T ss_pred EEEECHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHH
Confidence 47799999999999999999 56789999999876443
No 12
>PRK04460 nickel responsive regulator; Provisional
Probab=22.75 E-value=1.1e+02 Score=26.64 Aligned_cols=34 Identities=18% Similarity=0.236 Sum_probs=31.5
Q ss_pred eecCHHHHHHHHhhhhhhCCCCCchHHHHHHHhc
Q 021111 84 IRMPALCAARIFQLTRELGHKSDGETIQWLLQQA 117 (317)
Q Consensus 84 vRLs~~~A~rfF~Lqd~LGfdk~skTIeWLL~qa 117 (317)
|+||-+.+.+|=.+-.+.||.+-||.|.-+++..
T Consensus 7 vslp~~ll~~lD~~~~~~gy~sRSe~ird~ir~~ 40 (137)
T PRK04460 7 VSLDSDLLEKFDELIEEKGYQNRSEAIRDLIRDF 40 (137)
T ss_pred EEeCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 7899999999999999999999999999888754
No 13
>PF12045 DUF3528: Protein of unknown function (DUF3528); InterPro: IPR021918 This domain of unknown function is found at the N terminus of some Homeobox proteins belonging to the ABD-B family. It is found in association with PF00046 from PFAM.
Probab=21.11 E-value=33 Score=30.83 Aligned_cols=20 Identities=35% Similarity=0.554 Sum_probs=16.0
Q ss_pred cCCccceecchhhHHHHHHhh
Q 021111 264 QDGHIGVLNPQTLTQIYQQMG 284 (317)
Q Consensus 264 qdgh~gvln~q~~~q~yqqmg 284 (317)
--|+-||| ||+|-|||.-.-
T Consensus 101 ~VGRNgVL-PQ~FDQFfetay 120 (143)
T PF12045_consen 101 NVGRNGVL-PQGFDQFFETAY 120 (143)
T ss_pred ccccCCcC-ccccchhccccc
Confidence 34678998 899999998743
Done!