Query T0559 BvR153, , 69 residues
Match_columns 69
No_of_seqs 48 out of 50
Neff 3.6
Searched_HMMs 11830
Date Tue May 25 15:38:04 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0559.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0559.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10771 DUF2582: Protein of u 100.0 8.6E-30 7.2E-34 172.9 7.3 65 3-68 1-65 (65)
2 PF08221 HTH_9: RNA polymerase 88.6 0.22 1.8E-05 25.7 4.1 54 5-59 8-61 (62)
3 PF08784 RPA_C: Replication pr 88.3 0.23 1.9E-05 25.6 4.1 50 8-58 45-98 (102)
4 PF01978 TrmB: Sugar-specific 85.4 0.56 4.7E-05 23.6 4.8 58 9-67 7-64 (68)
5 PF02616 ScpA_ScpB: ScpA/B pro 62.5 4.6 0.00039 18.8 4.4 54 15-69 186-242 (242)
6 PF01325 Fe_dep_repress: Iron 56.3 6 0.00051 18.2 4.5 58 4-62 2-59 (60)
7 PF05584 Sulfolobus_pRN: Sulfo 56.1 6.1 0.00051 18.2 4.6 45 12-58 7-51 (72)
8 PF08220 HTH_DeoR: DeoR-like h 54.0 5.6 0.00047 18.4 3.6 43 13-56 3-45 (57)
9 PF10357 Kin17_mid: Domain of 44.7 4.1 0.00035 19.1 1.8 52 11-69 39-91 (127)
10 PF08280 HTH_Mga: M protein tr 43.2 8.8 0.00075 17.4 3.3 32 14-46 9-40 (59)
11 PF04703 FaeA: FaeA-like prote 42.1 7.8 0.00066 17.6 2.9 45 14-59 4-49 (62)
12 PF09012 FeoC: FeoC like trans 38.9 9 0.00076 17.3 2.7 47 14-61 4-50 (69)
13 PF07638 Sigma70_ECF: ECF sigm 31.7 12 0.001 16.7 2.4 30 23-52 150-182 (185)
14 PF01035 DNA_binding_1: 6-O-me 29.0 18 0.0015 15.8 2.9 42 12-56 4-48 (85)
15 PF11994 DUF3489: Protein of u 27.0 6.6 0.00055 18.0 0.4 24 14-37 14-37 (72)
16 PF08279 HTH_11: HTH domain; 25.1 21 0.0018 15.4 3.9 45 14-60 4-49 (55)
17 PF07022 Phage_CI_repr: Bacter 24.2 12 0.001 16.6 1.4 20 28-47 4-23 (66)
18 PF02002 TFIIE_alpha: TFIIE al 23.9 22 0.0019 15.3 2.9 54 5-59 8-61 (105)
19 PF11601 Shal-type: Shal-type 21.7 9.3 0.00078 17.2 0.4 10 42-51 11-20 (28)
20 PF02186 TFIIE_beta: TFIIE bet 20.9 26 0.0022 15.0 3.6 45 20-66 21-69 (74)
No 1
>PF10771 DUF2582: Protein of unknown function (DUF2582)
Probab=99.96 E-value=8.6e-30 Score=172.90 Aligned_cols=65 Identities=46% Similarity=0.761 Sum_probs=63.7
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEEECCEEEEEE
Q ss_conf 416777678999999761788447888988848980046886431441268135764077388875
Q T0559 3 MLKEKAGALAGQIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSEVEGEIFVKL 68 (69)
Q Consensus 3 M~k~~IG~nAG~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e~~gel~v~L 68 (69)
|+|+.||+|||+||++||++++||+++|+|+++| +|+|+++|||||||||||+|+++++++||+|
T Consensus 1 M~k~~IG~nAG~Iw~~L~e~~~~s~~~Lkk~~~l-~~~~~~~AiGWLarE~KI~~~~~~~~~~v~L 65 (65)
T PF10771_consen 1 MDKESIGENAGKIWHLLNENGEWSYKELKKATGL-SDKELALAIGWLARENKIEFEEKNGELYVSL 65 (65)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHCCCEEEEEECCCEEEEEC
T ss_conf 9477888989999999733887889999988498-9899999888885167167873088788869
No 2
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa . This region is probably a DNA-binding helix-turn-helix.
Probab=88.59 E-value=0.22 Score=25.69 Aligned_cols=54 Identities=26% Similarity=0.347 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEE
Q ss_conf 6777678999999761788447888988848980046886431441268135764
Q T0559 5 KEKAGALAGQIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSE 59 (69)
Q Consensus 5 k~~IG~nAG~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e 59 (69)
++.-|+.|.+|-..|...|..+.++|.+.|+++ .+.+-.|+==|.+-|=+.|.+
T Consensus 8 ~~~FGe~~~~V~~~L~~~g~ltl~~i~~~t~l~-~~~Vk~~L~~Liqh~~V~y~~ 61 (62)
T PF08221_consen 8 EDHFGEIAAKVFECLLSRGRLTLREIVRRTKLS-PSQVKKALAVLIQHNCVQYFE 61 (62)
T ss_pred HHHHCHHHHHHHHHHHHCCCCCHHHHHHHCCCC-HHHHHHHHHHHHHCCCCHHCC
T ss_conf 988074899999999975894999999783999-999999999999808612215
No 3
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1quq_A 2pqa_C 2pi2_C 1l1o_B 1z1d_A 2z6k_B 1dpu_A.
Probab=88.34 E-value=0.23 Score=25.59 Aligned_cols=50 Identities=12% Similarity=0.219 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHCC----CCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEE
Q ss_conf 76789999997617----8844788898884898004688643144126813576
Q T0559 8 AGALAGQIWEALNG----TEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTS 58 (69)
Q Consensus 8 IG~nAG~IW~~L~e----~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~ 58 (69)
....+-+|.++|.+ +...++.+|.+.++++ ..++..|+-+|..|+.|+..
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~eGv~v~~i~~~l~~~-~~~v~~a~~~L~~eG~IYsT 98 (102)
T PF08784_consen 45 LSPLQQRVLNFIKQSPQSEEGVHVDEIAQKLGMP-ENEVRKAIDELSDEGLIYST 98 (102)
T ss_dssp --HHHHHHHHHHHC--------BHHHHHHHSTS--HHHHHHHHHHHHH---EEES
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCEEECC
T ss_conf 8889999999998446887871899999996939-99999999999859847266
No 4
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively . Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2d1h_A 1sfx_A.
Probab=85.42 E-value=0.56 Score=23.58 Aligned_cols=58 Identities=14% Similarity=0.144 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEEECCEEEEE
Q ss_conf 67899999976178844788898884898004688643144126813576407738887
Q T0559 9 GALAGQIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSEVEGEIFVK 67 (69)
Q Consensus 9 G~nAG~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e~~gel~v~ 67 (69)
-.+--+|..+|-++++.+..+|.+.++++ ...+..++-.|.+.+-|.-.+.....|..
T Consensus 7 s~~e~~v~~~L~~~~~~t~~eia~~~~i~-~~~v~~~l~~L~~~GlV~~~~~~~~~Y~a 64 (68)
T PF01978_consen 7 SEYEAKVYLALLENGGATASEIAEKLGIS-RSTVYRILKRLEEKGLVEREKGKPKKYRA 64 (68)
T ss_dssp -HHHHHHHHHHHHTS-EEHHHHHHHHT---HHHHHHHHHHHHH---EEEEE----EEEE
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEEECCCEEEEEE
T ss_conf 99999999999957995999999998909-99999999999988998997685069998
No 5
>PF02616 ScpA_ScpB: ScpA/B protein; InterPro: IPR003768 This family represents ScpA, which along with ScpB (IPR005234 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation , . The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli , where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes .
Probab=62.52 E-value=4.6 Score=18.81 Aligned_cols=54 Identities=28% Similarity=0.393 Sum_probs=39.7
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHHCCCEEEEEEEC--CEEEEEEC
Q ss_conf 9997617884478889888489800-4688643144126813576407--73888758
Q T0559 15 IWEALNGTEGLTQKQIKKATKLKAD-KDFFLGLGWLLREDKVVTSEVE--GEIFVKLV 69 (69)
Q Consensus 15 IW~~L~e~~~~s~~~Lkk~t~l~~d-~el~~AiGWLaRE~KI~~~e~~--gel~v~Lv 69 (69)
|+..|+..+.+++.+|-....- .+ --.++|+==|+|+++|.+.+.+ |++|++++
T Consensus 186 il~~l~~~~~~~f~~l~~~~~~-~~~V~~FLAlLeL~k~~~I~l~Q~~~f~~I~I~~~ 242 (242)
T PF02616_consen 186 ILEKLSKKGWVSFSELFKDPSR-SEVVVTFLALLELVKEGKIELEQEEPFGEIYIRLI 242 (242)
T ss_pred HHHHCCCCCEEEHHHHHCCCCC-CEEHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEC
T ss_conf 2331166876748997276887-74599999999998389659997489871798859
No 6
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group . In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N-terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation .; GO: 0003700 transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2h09_A 1ddn_A 1bi3_B 1g3t_A 1f5t_C 2qqb_A 2qq9_A 1bi0_A 1bi2_B 1c0w_C ....
Probab=56.25 E-value=6 Score=18.21 Aligned_cols=58 Identities=17% Similarity=0.090 Sum_probs=47.0
Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEEECC
Q ss_conf 16777678999999761788447888988848980046886431441268135764077
Q T0559 4 LKEKAGALAGQIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSEVEG 62 (69)
Q Consensus 4 ~k~~IG~nAG~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e~~g 62 (69)
..+..-..--.||.+..+++..+.++|++..+.+ -..+.-++.=|.+++=|..+.-.|
T Consensus 2 ls~~~e~YL~~I~~l~~~~~~v~~~~IA~~L~vs-~~TVs~ml~kL~~~Glv~~~~y~g 59 (60)
T PF01325_consen 2 LSESEEDYLKAIYELSEEGGPVSTSDIAERLGVS-PPTVSEMLKKLEEEGLVEYEKYGG 59 (60)
T ss_dssp CSSHHHHHHHHHHHHHHH-S--BHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEETTSB
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC-CHHHHHHHHHHHHCCCEEECCCCC
T ss_conf 8806999999999998069972199999997899-078999999999889988514698
No 7
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=56.06 E-value=6.1 Score=18.20 Aligned_cols=45 Identities=18% Similarity=0.247 Sum_probs=37.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEE
Q ss_conf 99999976178844788898884898004688643144126813576
Q T0559 12 AGQIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTS 58 (69)
Q Consensus 12 AG~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~ 58 (69)
-.+|=-.|+.+ -.|+.+|.+.||++ ..++--.+-+|+.|++|.=.
T Consensus 7 ~~~Il~~ls~~-c~tLeeL~e~Tgi~-k~~llV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 7 TQLILIVLSKN-CCTLEELEEKTGIK-KNELLVYLSRLAKEGIIYRK 51 (72)
T ss_pred HHHHHHHHHHC-CCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEEE
T ss_conf 99999999754-35699999996898-77999999999878926643
No 8
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after Escherichia coli deoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerization domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping , . ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=54.03 E-value=5.6 Score=18.40 Aligned_cols=43 Identities=16% Similarity=0.137 Sum_probs=37.5
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEE
Q ss_conf 99999761788447888988848980046886431441268135
Q T0559 13 GQIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVV 56 (69)
Q Consensus 13 G~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~ 56 (69)
.+|-++|.+++..|.++|.+..+.+ +..+-.-+-=|..+++|.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 3 QQILELLKQHGKVSVKELAEEFGVS-EMTIRRDLNELEEQGLIR 45 (57)
T ss_pred HHHHHHHHHCCCEEHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
T ss_conf 9999999996989799999998949-889999899999889889
No 9
>PF10357 Kin17_mid: Domain of Kin17 curved DNA-binding protein; PDB: 2v1n_A.
Probab=44.72 E-value=4.1 Score=19.07 Aligned_cols=52 Identities=19% Similarity=0.297 Sum_probs=33.6
Q ss_pred HHHHHHHH-HCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEEECCEEEEEEC
Q ss_conf 89999997-617884478889888489800468864314412681357640773888758
Q T0559 11 LAGQIWEA-LNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSEVEGEIFVKLV 69 (69)
Q Consensus 11 nAG~IW~~-L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e~~gel~v~Lv 69 (69)
+|-+|++- .++..+.-+- +|.-. .|.-=+-||.|++|+..++.+.-+|++.|
T Consensus 39 ~AN~vYqEyI~Dk~HvHMN----aTrW~---sLT~FvkyLgr~G~c~Veetekg~~I~yI 91 (127)
T PF10357_consen 39 NANKVYQEYIADKDHVHMN----ATRWT---SLTEFVKYLGREGKCKVEETEKGWFITYI 91 (127)
T ss_dssp EHHHHHHHHTTSS----GG----GSS-S---SHHHHHHH------EEEE------EEEE-
T ss_pred ECHHHHHHHHCCCCCCEEC----CCCCH---HHHHHHHHHHHCCEEEEECCCCCEEEEEE
T ss_conf 2219899986255651204----53003---09999999704684787517876478740
No 10
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions .
Probab=43.21 E-value=8.8 Score=17.36 Aligned_cols=32 Identities=19% Similarity=0.212 Sum_probs=24.9
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHH
Q ss_conf 999976178844788898884898004688643
Q T0559 14 QIWEALNGTEGLTQKQIKKATKLKADKDFFLGL 46 (69)
Q Consensus 14 ~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~Ai 46 (69)
++-++|.+++..|+++|++.++++ ++.+-.-|
T Consensus 9 ~Ll~~L~~~~~~t~~ela~~l~~S-~~ti~~~I 40 (59)
T PF08280_consen 9 KLLELLLKNGWITLKELAKKLGLS-ERTIRNDI 40 (59)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHH
T ss_conf 999999977979799999997988-99999999
No 11
>PF04703 FaeA: FaeA-like protein; InterPro: IPR006793 This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase , .; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription, 0009289 fimbrium; PDB: 2htj_A 2jt1_A.
Probab=42.09 E-value=7.8 Score=17.63 Aligned_cols=45 Identities=24% Similarity=0.144 Sum_probs=36.5
Q ss_pred HHHHHHCC-CCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEE
Q ss_conf 99997617-88447888988848980046886431441268135764
Q T0559 14 QIWEALNG-TEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSE 59 (69)
Q Consensus 14 ~IW~~L~e-~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e 59 (69)
+|-.++.. +++.+..++...++++ ...+..-+=-|++|++|.-..
T Consensus 4 ~Il~~i~~~~~p~~t~eiA~~~gls-~~qaR~~L~~L~~eG~Vk~~~ 49 (62)
T PF04703_consen 4 KILEYIKRQNGPCSTREIAEALGLS-IYQARYYLQKLEKEGKVKRSP 49 (62)
T ss_dssp CHHHHHHHH---B-HHHHHHHHTS--HHHHHHHHHHHHH---EEEE-
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEEEC
T ss_conf 8999999627998899999996988-999999999998879778520
No 12
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This set of hypothetical proteins is found in prokaryotes. ; PDB: 2k02_A 1xn7_A.
Probab=38.85 E-value=9 Score=17.32 Aligned_cols=47 Identities=19% Similarity=0.174 Sum_probs=38.4
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEEEC
Q ss_conf 999976178844788898884898004688643144126813576407
Q T0559 14 QIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSEVE 61 (69)
Q Consensus 14 ~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e~~ 61 (69)
.|=.+|..++..|.++|.+..+++.+ .+-.-+.=|-|-+||.-....
T Consensus 4 ~i~~~l~~~g~~s~~eLa~~f~~s~~-~v~aMLe~l~~kG~i~k~~~~ 50 (69)
T PF09012_consen 4 QIRDYLALRGRVSLSELARHFGISPD-AVEAMLEQLIRKGKIEKVEDS 50 (69)
T ss_dssp HHHHHHHH---EEHHHHHHHTT--HH-HHHHHHHHHHC---EEEEEEE
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHH-HHHHHHHHHHHCCCEEEECCC
T ss_conf 99999999398189999999790999-999999999988916873169
No 13
>PF07638 Sigma70_ECF: ECF sigma factor; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent
Probab=31.68 E-value=12 Score=16.69 Aligned_cols=30 Identities=33% Similarity=0.635 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHCCC---CCHHHHHHHHHHHCC
Q ss_conf 844788898884898---004688643144126
Q T0559 23 EGLTQKQIKKATKLK---ADKDFFLGLGWLLRE 52 (69)
Q Consensus 23 ~~~s~~~Lkk~t~l~---~d~el~~AiGWLaRE 52 (69)
++.|+.|+....|.+ +++++..|-.||.+|
T Consensus 150 ~Glt~~EiA~~LgiS~~Tv~R~~~~aR~wl~~~ 182 (185)
T PF07638_consen 150 GGLTVEEIAEALGISERTVERDWRFARAWLRRE 182 (185)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 799999999896969999999999999999998
No 14
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme . This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources .; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1eh6_A 1qnt_A 1eh8_A 1t39_B 1yfh_C 1t38_A 1eh7_A 3gyh_X 3gva_A 3gx4_X ....
Probab=28.99 E-value=18 Score=15.82 Aligned_cols=42 Identities=21% Similarity=0.253 Sum_probs=33.0
Q ss_pred HHHHHHHHCCC---CCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEE
Q ss_conf 99999976178---8447888988848980046886431441268135
Q T0559 12 AGQIWEALNGT---EGLTQKQIKKATKLKADKDFFLGLGWLLREDKVV 56 (69)
Q Consensus 12 AG~IW~~L~e~---~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~ 56 (69)
.-.||+.+..- ...||.+|.+..+.+ .-+.++|+-.+.|.+.
T Consensus 4 ~~~V~~~l~~IP~G~v~TYg~iA~~~g~p---~~aRaVg~al~~np~~ 48 (85)
T PF01035_consen 4 QQRVWEALRQIPYGKVTTYGEIAEAAGRP---KAARAVGSALARNPLP 48 (85)
T ss_dssp HHHHHHHHTTS----BEEHHHHHHHTT-T---TTTTTHHHTTTTSSBT
T ss_pred HHHHHHHHHCCCCCCCEEHHHHHHHHCCC---CCHHHHHHHHHHCCCC
T ss_conf 99999999748999747199999995899---8379999999858998
No 15
>PF11994 DUF3489: Protein of unknown function (DUF3489)
Probab=26.95 E-value=6.6 Score=18.03 Aligned_cols=24 Identities=33% Similarity=0.383 Sum_probs=10.0
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf 999976178844788898884898
Q T0559 14 QIWEALNGTEGLTQKQIKKATKLK 37 (69)
Q Consensus 14 ~IW~~L~e~~~~s~~~Lkk~t~l~ 37 (69)
++=.+|.--...++.+|.++||-.
T Consensus 14 ~~i~mL~~p~Gati~~i~~atGWq 37 (72)
T PF11994_consen 14 QVIAMLRRPEGATIAEISEATGWQ 37 (72)
T ss_pred HHHHHHCCCCCCCHHHHHHHHCCC
T ss_conf 999997087899899999853860
No 16
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 . The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon . It is also found in other proteins including regulators of amino acid biosynthsis such as LysM , and regulators of carbohydrate metabolisms such as LicR and FrvR , .; PDB: 1j5y_A 2ewn_B 1hxd_B 1bia_A 1bib_A 2dbb_B 1i1g_B 2cg4_B.
Probab=25.14 E-value=21 Score=15.44 Aligned_cols=45 Identities=18% Similarity=0.184 Sum_probs=31.6
Q ss_pred HHHHHH-CCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEEE
Q ss_conf 999976-17884478889888489800468864314412681357640
Q T0559 14 QIWEAL-NGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSEV 60 (69)
Q Consensus 14 ~IW~~L-~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e~ 60 (69)
+|-.+| ...+.+|.++|++..+.+ ...+.-.|-=|-..+ +.++..
T Consensus 4 ~Il~~L~~~~~~it~~eLA~~l~vS-~~Ti~~~i~~L~~~g-~~I~s~ 49 (55)
T PF08279_consen 4 QILELLLKNDGPITAKELAEELGVS-RRTIRRDIKELEEEG-IPIESK 49 (55)
T ss_dssp HHHHHHHHCCTTS-HHHHHHHCTS--HHHHHHHHHHHHH---EB-BB-
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCC-CEEEEE
T ss_conf 9999999859998899999996979-999999999999869-969860
No 17
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic .; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription; PDB: 2fjr_A 3bd1_B.
Probab=24.24 E-value=12 Score=16.62 Aligned_cols=20 Identities=35% Similarity=0.549 Sum_probs=11.1
Q ss_pred HHHHHHHCCCCCHHHHHHHH
Q ss_conf 88988848980046886431
Q T0559 28 KQIKKATKLKADKDFFLGLG 47 (69)
Q Consensus 28 ~~Lkk~t~l~~d~el~~AiG 47 (69)
.+|++++++++++|++-.+|
T Consensus 4 ~Rl~~~~g~~~~~elA~~Lg 23 (66)
T PF07022_consen 4 ERLKEAYGIKTDKELAEKLG 23 (66)
T ss_dssp HHHHHH----SCHHHHCCTT
T ss_pred HHHHHHHCCCCHHHHHHHHC
T ss_conf 99999968996999999919
No 18
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR002853 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha P29083 from SWISSPROT and TFIIE-beta P29084 from SWISSPROT and joins the preinitiation complex after RNA polymerase II and TFIIF . This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also .; GO: 0003702 RNA polymerase II transcription factor activity, 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1q1h_A 1vd4_A.
Probab=23.94 E-value=22 Score=15.31 Aligned_cols=54 Identities=20% Similarity=0.149 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEE
Q ss_conf 6777678999999761788447888988848980046886431441268135764
Q T0559 5 KEKAGALAGQIWEALNGTEGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSE 59 (69)
Q Consensus 5 k~~IG~nAG~IW~~L~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLaRE~KI~~~e 59 (69)
+...|..+-.|-.+|..++..+..+|++.++++ .+++-..+.=|....=|...+
T Consensus 8 r~~yg~~~~~Vl~~L~~~~~l~ee~La~~l~i~-~k~lR~~L~~L~e~~lv~~~~ 61 (105)
T PF02002_consen 8 RAFYGDEAVRVLDALLRHGELTEEDLAELLGIK-SKELRKILYKLYEDKLVKYRR 61 (105)
T ss_dssp HTT---TTHHHHHHHHH---B-HHHHHHTT-S--HHHHHHHHHHHHH----EEEE
T ss_pred HHHCCHHHHHHHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEEEE
T ss_conf 998396699999999986990899999890999-899999999999889837898
No 19
>PF11601 Shal-type: Shal-type voltage-gated potassium channels ; PDB: 1s6c_B 2nz0_D 2i2r_J.
Probab=21.67 E-value=9.3 Score=17.25 Aligned_cols=10 Identities=20% Similarity=0.497 Sum_probs=7.3
Q ss_pred HHHHHHHHHC
Q ss_conf 8864314412
Q T0559 42 FFLGLGWLLR 51 (69)
Q Consensus 42 l~~AiGWLaR 51 (69)
-++||||+--
T Consensus 11 raaAIGW~pv 20 (28)
T PF11601_consen 11 RAAAIGWVPV 20 (28)
T ss_dssp HHHH----ST
T ss_pred HHHHHCCEEE
T ss_conf 8765152450
No 20
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 General transcription factor TFIIE consists of two subunits, TFIIE alpha IPR002853 from INTERPRO and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.; GO: 0003702 RNA polymerase II transcription factor activity, 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1d8k_A 1d8j_A.
Probab=20.85 E-value=26 Score=14.97 Aligned_cols=45 Identities=20% Similarity=0.113 Sum_probs=31.7
Q ss_pred CCCCCCCHHHHHHHHCCCCCHHHHHHHHHHH----CCCEEEEEEECCEEEE
Q ss_conf 1788447888988848980046886431441----2681357640773888
Q T0559 20 NGTEGLTQKQIKKATKLKADKDFFLGLGWLL----REDKVVTSEVEGEIFV 66 (69)
Q Consensus 20 ~e~~~~s~~~Lkk~t~l~~d~el~~AiGWLa----RE~KI~~~e~~gel~v 66 (69)
.++.+.++.+|-..+.+ .|.+ ..-+-||. .-+||.+.....-.|.
T Consensus 21 ~~~~PltleeIldyls~-~di~-~~~~~~L~~~L~~n~kI~~dp~~~f~fk 69 (74)
T PF02186_consen 21 GDDHPLTLEEILDYLSL-LDIG-PKQKPWLKEELKNNPKIEYDPDGTFSFK 69 (74)
T ss_dssp ---S-B-HHHHHHHHT--S-----HHHHHHHCTHHH-TTEEE-----EEE-
T ss_pred CCCCCEEHHHHHHHHHC-CCCC-HHHHHHHHHHHHCCCCEEEECCCCEEEC
T ss_conf 79982419999999833-6876-4799999988620994898458867846
Done!