Query T0560 BtR375, , 74 residues
Match_columns 74
No_of_seqs 57 out of 59
Neff 3.8
Searched_HMMs 11830
Date Tue May 25 15:38:37 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0560.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0560.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10771 DUF2582: Protein of u 100.0 4.2E-29 3.6E-33 171.6 7.5 65 1-65 1-65 (65)
2 PF08784 RPA_C: Replication pr 93.8 0.033 2.8E-06 30.3 4.5 50 6-55 45-98 (102)
3 PF01978 TrmB: Sugar-specific 93.2 0.067 5.7E-06 28.7 5.2 59 7-65 7-65 (68)
4 PF08221 HTH_9: RNA polymerase 92.6 0.066 5.6E-06 28.8 4.5 53 3-55 8-60 (62)
5 PF05584 Sulfolobus_pRN: Sulfo 83.8 0.77 6.5E-05 23.2 4.9 45 10-55 7-51 (72)
6 PF01325 Fe_dep_repress: Iron 71.0 3.2 0.00027 19.9 5.3 58 2-59 2-59 (60)
7 PF08220 HTH_DeoR: DeoR-like h 69.0 2.5 0.00022 20.4 4.1 43 11-53 3-45 (57)
8 PF04703 FaeA: FaeA-like prote 68.3 1.6 0.00014 21.5 3.0 44 12-55 4-48 (62)
9 PF09012 FeoC: FeoC like trans 61.3 3.3 0.00028 19.9 3.5 46 12-57 4-49 (69)
10 PF00888 Cullin: Cullin family 54.1 2.7 0.00023 20.3 2.0 54 13-66 526-579 (589)
11 PF08280 HTH_Mga: M protein tr 52.1 6.8 0.00058 18.2 3.8 32 12-43 9-40 (59)
12 PF02002 TFIIE_alpha: TFIIE al 45.8 9.4 0.00079 17.5 4.1 54 4-57 9-62 (105)
13 PF09275 Pertus-S4-tox: Pertus 45.5 1.9 0.00016 21.2 0.1 16 59-74 38-53 (110)
14 PF08279 HTH_11: HTH domain; 45.4 9.5 0.00081 17.4 4.5 48 11-59 3-51 (55)
15 PF12324 HTH_15: Helix-turn-he 45.2 6.1 0.00051 18.5 2.7 35 13-47 29-63 (77)
16 PF00392 GntR: Bacterial regul 43.2 9 0.00076 17.6 3.3 42 19-60 20-62 (64)
17 PF09339 HTH_IclR: IclR helix- 38.3 12 0.0011 16.8 4.4 46 8-53 3-49 (52)
18 PF01022 HTH_5: Bacterial regu 35.0 14 0.0012 16.5 3.8 40 12-52 6-45 (47)
19 PF07638 Sigma70_ECF: ECF sigm 33.2 13 0.0011 16.7 2.8 29 21-49 150-182 (185)
20 PF11994 DUF3489: Protein of u 31.1 6.2 0.00053 18.4 0.9 22 27-48 18-39 (72)
21 PF02796 HTH_7: Helix-turn-hel 30.2 17 0.0014 16.1 3.0 30 11-42 12-41 (45)
22 PF04361 DUF494: Protein of un 29.0 14 0.0012 16.6 2.4 30 23-52 24-53 (155)
23 PF10264 Stork_head: Winged he 29.0 11 0.00093 17.1 1.9 45 12-56 19-71 (80)
24 PF01035 DNA_binding_1: 6-O-me 28.7 13 0.0011 16.8 2.1 43 10-54 4-49 (85)
25 PF00325 Crp: Bacterial regula 28.1 17 0.0014 16.1 2.7 31 22-52 2-32 (32)
26 PF02295 z-alpha: Adenosine de 27.3 20 0.0016 15.8 3.0 48 8-55 4-53 (66)
27 PF02186 TFIIE_beta: TFIIE bet 26.7 20 0.0017 15.7 3.0 40 19-59 22-65 (74)
28 PF02616 ScpA_ScpB: ScpA/B pro 25.2 21 0.0018 15.6 3.7 51 15-65 188-241 (242)
29 PF09107 SelB-wing_3: Elongati 25.0 22 0.0018 15.6 3.4 37 14-50 2-38 (50)
30 PF01853 MOZ_SAS: MOZ/SAS fami 22.2 25 0.0021 15.3 4.0 35 12-46 137-174 (188)
31 PF10357 Kin17_mid: Domain of 21.6 16 0.0014 16.2 1.6 52 8-65 38-90 (127)
No 1
>PF10771 DUF2582: Protein of unknown function (DUF2582)
Probab=99.95 E-value=4.2e-29 Score=171.64 Aligned_cols=65 Identities=51% Similarity=0.779 Sum_probs=64.2
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEECCEEEEEE
Q ss_conf 96134556788999987078951778899884899889886521441168134664077378853
Q T0560 1 MDKKIVGANAGKVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIERKNGLIEIYN 65 (74)
Q Consensus 1 M~k~~IG~nAG~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~~g~l~v~~ 65 (74)
|+|++||+|||+||++|+++++||+++|+|+++|+|+|+++|||||||||||.|+++++++|||+
T Consensus 1 M~k~~IG~nAG~Iw~~L~e~~~~s~~~Lkk~~~l~~~~~~~AiGWLarE~KI~~~~~~~~~~v~L 65 (65)
T PF10771_consen 1 MDKESIGENAGKIWHLLNENGEWSYKELKKATGLSDKELALAIGWLARENKIEFEEKNGELYVSL 65 (65)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEECCCEEEEEC
T ss_conf 94778889899999997338878899999884989899999888885167167873088788869
No 2
>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=93.85 E-value=0.033 Score=30.34 Aligned_cols=50 Identities=16% Similarity=0.308 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 55678899998707----895177889988489988988652144116813466
Q T0560 6 VGANAGKVWHALNE----ADGISIPELARKVNLSVESTALAVGWLARENKVVIE 55 (74)
Q Consensus 6 IG~nAG~VW~~L~e----~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~ 55 (74)
....+-+|.++|.+ ....++.+|++..+++..++..|+-+|.-|+.|+-.
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~eGv~v~~i~~~l~~~~~~v~~a~~~L~~eG~IYsT 98 (102)
T PF08784_consen 45 LSPLQQRVLNFIKQSPQSEEGVHVDEIAQKLGMPENEVRKAIDELSDEGLIYST 98 (102)
T ss_dssp --HHHHHHHHHHHC--------BHHHHHHHSTS-HHHHHHHHHHHHH---EEES
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEECC
T ss_conf 888999999999844688787189999999693999999999999859847266
No 3
>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=93.21 E-value=0.067 Score=28.73 Aligned_cols=59 Identities=22% Similarity=0.165 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEECCEEEEEE
Q ss_conf 56788999987078951778899884899889886521441168134664077378853
Q T0560 7 GANAGKVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIERKNGLIEIYN 65 (74)
Q Consensus 7 G~nAG~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~~g~l~v~~ 65 (74)
-.+--+|+.+|-+++..+..+|++.++++...+.-++-.|.+.|-|.-.+.....|...
T Consensus 7 s~~e~~v~~~L~~~~~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 7 SEYEAKVYLALLENGGATASEIAEKLGISRSTVYRILKRLEEKGLVEREKGKPKKYRAV 65 (68)
T ss_dssp -HHHHHHHHHHHHTS-EEHHHHHHHHT--HHHHHHHHHHHHH---EEEEE----EEEEE
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEEEE
T ss_conf 99999999999957995999999998909999999999999889989976850699984
No 4
>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=92.58 E-value=0.066 Score=28.78 Aligned_cols=53 Identities=25% Similarity=0.290 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 13455678899998707895177889988489988988652144116813466
Q T0560 3 KKIVGANAGKVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIE 55 (74)
Q Consensus 3 k~~IG~nAG~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~ 55 (74)
++.-|+.|.+|...|...+..++.+|.+.|+++.+.+..|+==|.+-|=+.+.
T Consensus 8 ~~~FGe~~~~V~~~L~~~g~ltl~~i~~~t~l~~~~Vk~~L~~Liqh~~V~y~ 60 (62)
T PF08221_consen 8 EDHFGEIAAKVFECLLSRGRLTLREIVRRTKLSPSQVKKALAVLIQHNCVQYF 60 (62)
T ss_pred HHHHCHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCCHHC
T ss_conf 98807489999999997589499999978399999999999999980861221
No 5
>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=83.82 E-value=0.77 Score=23.18 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=38.2
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 8899998707895177889988489988988652144116813466
Q T0560 10 AGKVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIE 55 (74)
Q Consensus 10 AG~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~ 55 (74)
-..|--.|+.+ -.|+.||.+.|+++..++---+-+|++||+|.=.
T Consensus 7 ~~~Il~~ls~~-c~tLeeL~e~Tgi~k~~llV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 7 TQLILIVLSKN-CCTLEELEEKTGIKKNELLVYLSRLAKEGIIYRK 51 (72)
T ss_pred HHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf 99999999754-3569999999689877999999999878926643
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=71.00 E-value=3.2 Score=19.92 Aligned_cols=58 Identities=16% Similarity=0.179 Sum_probs=47.5
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEECC
Q ss_conf 6134556788999987078951778899884899889886521441168134664077
Q T0560 2 DKKIVGANAGKVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIERKNG 59 (74)
Q Consensus 2 ~k~~IG~nAG~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~~g 59 (74)
.-+..-..--.||++..+++..+.++|++..+.+..-+.-++-=|.++|=|..+.--|
T Consensus 2 ls~~~e~YL~~I~~l~~~~~~v~~~~IA~~L~vs~~TVs~ml~kL~~~Glv~~~~y~g 59 (60)
T PF01325_consen 2 LSESEEDYLKAIYELSEEGGPVSTSDIAERLGVSPPTVSEMLKKLEEEGLVEYEKYGG 59 (60)
T ss_dssp CSSHHHHHHHHHHHHHHH-S--BHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTSB
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCC
T ss_conf 8806999999999998069972199999997899078999999999889988514698
No 7
>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=68.99 E-value=2.5 Score=20.44 Aligned_cols=43 Identities=16% Similarity=0.219 Sum_probs=39.0
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEE
Q ss_conf 8999987078951778899884899889886521441168134
Q T0560 11 GKVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVV 53 (74)
Q Consensus 11 G~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~ 53 (74)
.+|-++|.+++..|+++|++..+.|.+-+-.-+-=|..+++|.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 3 QQILELLKQHGKVSVKELAEEFGVSEMTIRRDLNELEEQGLIR 45 (57)
T ss_pred HHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf 9999999996989799999998949889999899999889889
No 8
>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=68.27 E-value=1.6 Score=21.48 Aligned_cols=44 Identities=23% Similarity=0.243 Sum_probs=38.3
Q ss_pred HHHHHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 99998707-895177889988489988988652144116813466
Q T0560 12 KVWHALNE-ADGISIPELARKVNLSVESTALAVGWLARENKVVIE 55 (74)
Q Consensus 12 ~VW~~L~e-~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~ 55 (74)
+|-..|.. +++.+..+|+.+++++..-+-.=+==|++||+|.-.
T Consensus 4 ~Il~~i~~~~~p~~t~eiA~~~gls~~qaR~~L~~L~~eG~Vk~~ 48 (62)
T PF04703_consen 4 KILEYIKRQNGPCSTREIAEALGLSIYQARYYLQKLEKEGKVKRS 48 (62)
T ss_dssp CHHHHHHHH---B-HHHHHHHHTS-HHHHHHHHHHHHH---EEEE
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf 899999962799889999999698899999999999887977852
No 9
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This set of hypothetical proteins is found in prokaryotes. ; PDB: 2k02_A 1xn7_A.
Probab=61.30 E-value=3.3 Score=19.86 Aligned_cols=46 Identities=22% Similarity=0.285 Sum_probs=40.2
Q ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEE
Q ss_conf 9999870789517788998848998898865214411681346640
Q T0560 12 KVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIERK 57 (74)
Q Consensus 12 ~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~ 57 (74)
.|=.+|..++..|.++|++..+++...+-.-+.=|-|-|||.-...
T Consensus 4 ~i~~~l~~~g~~s~~eLa~~f~~s~~~v~aMLe~l~~kG~i~k~~~ 49 (69)
T PF09012_consen 4 QIRDYLALRGRVSLSELARHFGISPDAVEAMLEQLIRKGKIEKVED 49 (69)
T ss_dssp HHHHHHHH---EEHHHHHHHTT--HHHHHHHHHHHHC---EEEEEE
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf 9999999939818999999979099999999999998891687316
No 10
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) , play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins , , . This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2hye_C 3dpl_C 3dqv_C 1ldk_B 1u6g_A 1ldj_A.
Probab=54.07 E-value=2.7 Score=20.32 Aligned_cols=54 Identities=9% Similarity=0.205 Sum_probs=40.2
Q ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEECCEEEEEEC
Q ss_conf 999870789517788998848998898865214411681346640773788536
Q T0560 13 VWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIERKNGLIEIYNE 66 (74)
Q Consensus 13 VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~~g~l~v~~~ 66 (74)
|=-+.|+...+|+.+|...||+++.++-.++--|.....+.....+..--++.+
T Consensus 526 iLllFn~~~~~t~~~i~~~t~~~~~~l~~~L~~l~~~~~~~~~~~~~~~~~~~~ 579 (589)
T PF00888_consen 526 ILLLFNDQEELTVEEISERTGISEDELKRQLQSLIKAKLLILLKSPKGKSISPN 579 (589)
T ss_dssp HHHCCCTTSEEEHHHHHHHC---HHHHHHHHHHHHCTTTESCCETTTCGG----
T ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCC
T ss_conf 999956778857999998879199999999999983883133158766779999
No 11
>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=52.15 E-value=6.8 Score=18.20 Aligned_cols=32 Identities=28% Similarity=0.336 Sum_probs=26.0
Q ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99998707895177889988489988988652
Q T0560 12 KVWHALNEADGISIPELARKVNLSVESTALAV 43 (74)
Q Consensus 12 ~VW~~L~e~~~~s~~el~k~t~lsd~el~lAi 43 (74)
++-++|.+++.+++++|++.+++|..-+---|
T Consensus 9 ~Ll~~L~~~~~~t~~ela~~l~~S~~ti~~~I 40 (59)
T PF08280_consen 9 KLLELLLKNGWITLKELAKKLGLSERTIRNDI 40 (59)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999997797979999999798899999999
No 12
>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=45.83 E-value=9.4 Score=17.47 Aligned_cols=54 Identities=19% Similarity=0.159 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEE
Q ss_conf 345567889999870789517788998848998898865214411681346640
Q T0560 4 KIVGANAGKVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKVVIERK 57 (74)
Q Consensus 4 ~~IG~nAG~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~ 57 (74)
.-.|..+-.|-.+|..++..+-.+|++.++++..++-..+.=|...+=|...+.
T Consensus 9 ~~yg~~~~~Vl~~L~~~~~l~ee~La~~l~i~~k~lR~~L~~L~e~~lv~~~~~ 62 (105)
T PF02002_consen 9 AFYGDEAVRVLDALLRHGELTEEDLAELLGIKSKELRKILYKLYEDKLVKYRRV 62 (105)
T ss_dssp TT---TTHHHHHHHHH---B-HHHHHHTT-S-HHHHHHHHHHHHH----EEEEE
T ss_pred HHCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 983966999999999869908999998909998999999999998898378988
No 13
>PF09275 Pertus-S4-tox: Pertussis toxin S4 subunit; InterPro: IPR015355 Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology . ; PDB: 1bcp_D 1pto_K 1prt_K.
Probab=45.50 E-value=1.9 Score=21.17 Aligned_cols=16 Identities=31% Similarity=0.611 Sum_probs=11.0
Q ss_pred CEEEEEECCEEEEECC
Q ss_conf 7378853682655419
Q T0560 59 GLIEIYNEGHFDFSFG 74 (74)
Q Consensus 59 g~l~v~~~~n~~F~fg 74 (74)
|-.--|.+.+|+||||
T Consensus 38 gaaasspdahvpfcfg 53 (110)
T PF09275_consen 38 GAAASSPDAHVPFCFG 53 (110)
T ss_dssp ---TTSGGGSB-EEE-
T ss_pred CCCCCCCCCCCCCEEC
T ss_conf 4244798874651105
No 14
>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=45.44 E-value=9.5 Score=17.43 Aligned_cols=48 Identities=25% Similarity=0.333 Sum_probs=35.8
Q ss_pred HHHHHHH-HCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEECC
Q ss_conf 8999987-078951778899884899889886521441168134664077
Q T0560 11 GKVWHAL-NEADGISIPELARKVNLSVESTALAVGWLARENKVVIERKNG 59 (74)
Q Consensus 11 G~VW~~L-~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~~g 59 (74)
-+|-++| ...+.+|.++|++..+.|..-+.-.|-=|-..+ +.++.+.|
T Consensus 3 ~~Il~~L~~~~~~it~~eLA~~l~vS~~Ti~~~i~~L~~~g-~~I~s~~~ 51 (55)
T PF08279_consen 3 QQILELLLKNDGPITAKELAEELGVSRRTIRRDIKELEEEG-IPIESKPG 51 (55)
T ss_dssp HHHHHHHHHCCTTS-HHHHHHHCTS-HHHHHHHHHHHHH---EB-BB-TT
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC-CEEEEECC
T ss_conf 99999999859998899999996979999999999999869-96986078
No 15
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; PDB: 3f2f_A 3f0p_B 3f0o_B 3f2g_A 3fn8_A 3f2h_B 1s6l_A.
Probab=45.17 E-value=6.1 Score=18.46 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=28.6
Q ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 99987078951778899884899889886521441
Q T0560 13 VWHALNEADGISIPELARKVNLSVESTALAVGWLA 47 (74)
Q Consensus 13 VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLa 47 (74)
+.+.|...++.|..+|+.++|.+.+++..++.=+.
T Consensus 29 llr~LA~G~PVt~~~LA~atG~~ve~V~~~L~~~p 63 (77)
T PF12324_consen 29 LLRLLADGRPVTVETLAAATGWPVEEVRAALAQMP 63 (77)
T ss_dssp HHHHHT----B-HHHH-------HHHHHHHHHH-T
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 99999768982699999997989999999998576
No 16
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon . Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined . In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies . This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2ra5_A 3by6_D 2ek5_C 2du9_A 1v4r_A 3bwg_A 3eet_B 1h9t_B 1hw2_B 1hw1_B ....
Probab=43.20 E-value=9 Score=17.56 Aligned_cols=42 Identities=24% Similarity=0.234 Sum_probs=36.2
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEECCE
Q ss_conf 78951-7788998848998898865214411681346640773
Q T0560 19 EADGI-SIPELARKVNLSVESTALAVGWLARENKVVIERKNGL 60 (74)
Q Consensus 19 e~~~~-s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~~g~ 60 (74)
.+..+ |..+|++..+.|..-+--|+..|..|+=|......|-
T Consensus 20 ~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~~~G~ 62 (64)
T PF00392_consen 20 PGDRLPSERELAERFGVSRTTVREALKRLEEEGLIERRPGRGT 62 (64)
T ss_dssp TTSB---HHHHHHHHT--HHHHHHHHHHHHHTTSEEEETT---
T ss_pred CCCEECCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEE
T ss_conf 9999368999998868798999999999998895899769636
No 17
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N-terminus that is similar to that of other DNA-binding proteins .; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2ia2_C 2g7u_D 2o0y_D 1mkm_B.
Probab=38.27 E-value=12 Score=16.81 Aligned_cols=46 Identities=22% Similarity=0.242 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHCCCEEE
Q ss_conf 678899998707895-1778899884899889886521441168134
Q T0560 8 ANAGKVWHALNEADG-ISIPELARKVNLSVESTALAVGWLARENKVV 53 (74)
Q Consensus 8 ~nAG~VW~~L~e~~~-~s~~el~k~t~lsd~el~lAiGWLarE~KI~ 53 (74)
.+|-.|-.+|.+.+. +++++|++.++++..-++.-+-=|.+.|=|.
T Consensus 3 ~ral~iL~~l~~~~~~~t~~eia~~~gl~~st~~r~l~~L~~~g~v~ 49 (52)
T PF09339_consen 3 ERALQILEALARAPRPLTLSEIARALGLPKSTVHRLLQTLEEAGFVE 49 (52)
T ss_dssp HHHHHHHHTHCTTBSSEEHHHHHHHTT--HHHHHHHHHHHHHT--EE
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf 99999999998789998999999998919999999999999991942
No 18
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins . The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C-terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) . It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA . The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers . The dimer interface is formed by helix 5 and an N-terminal part . Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N-terminus, called the alpha3(N) site . The second metal-binding site is located in helix 5 (and C-terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites , . Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognized by multimeric arsR-type metalloregulators. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1uly_A 2cwe_A 1ku9_A 3gw2_A 2p4w_B 3f6v_A 3f6o_B 2oqg_D 2ia0_B 2zny_C ....
Probab=35.02 E-value=14 Score=16.53 Aligned_cols=40 Identities=23% Similarity=0.332 Sum_probs=33.1
Q ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEE
Q ss_conf 99998707895177889988489988988652144116813
Q T0560 12 KVWHALNEADGISIPELARKVNLSVESTALAVGWLARENKV 52 (74)
Q Consensus 12 ~VW~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI 52 (74)
+|-.+|.+ ++.++.+|++.++++..-+..-+..|-.-|=|
T Consensus 6 ~Il~~L~~-~~~~~~eia~~l~~s~~tvs~HL~~L~~~glV 45 (47)
T PF01022_consen 6 KILKLLSE-GPLSVSEIAEELGISQSTVSRHLKKLEEAGLV 45 (47)
T ss_dssp HHHHHHHH-SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCC
T ss_conf 99999986-89679998836123565899999999998084
No 19
>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=33.23 E-value=13 Score=16.72 Aligned_cols=29 Identities=31% Similarity=0.613 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHCCCH----HHHHHHHHHHHCC
Q ss_conf 9517788998848998----8988652144116
Q T0560 21 DGISIPELARKVNLSV----ESTALAVGWLARE 49 (74)
Q Consensus 21 ~~~s~~el~k~t~lsd----~el~lAiGWLarE 49 (74)
+++|++|++...|+|. .++..|-.||.+|
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 20
>PF11994 DUF3489: Protein of unknown function (DUF3489)
Probab=31.10 E-value=6.2 Score=18.41 Aligned_cols=22 Identities=27% Similarity=0.454 Sum_probs=13.0
Q ss_pred HHHHHHCCCHHHHHHHHHHHHC
Q ss_conf 8998848998898865214411
Q T0560 27 ELARKVNLSVESTALAVGWLAR 48 (74)
Q Consensus 27 el~k~t~lsd~el~lAiGWLar 48 (74)
-|.+..|-+..++..|.||.++
T Consensus 18 mL~~p~Gati~~i~~atGWq~H 39 (72)
T PF11994_consen 18 MLRRPEGATIAEISEATGWQAH 39 (72)
T ss_pred HHCCCCCCCHHHHHHHHCCCHH
T ss_conf 9708789989999985386043
No 21
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known . The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second , called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1jko_C 1jkp_C 1jj8_C 1hcr_A 1jkq_C 1jj6_C 1ijw_C 1jkr_C 1zr4_B 2gm4_A ....
Probab=30.17 E-value=17 Score=16.13 Aligned_cols=30 Identities=17% Similarity=0.267 Sum_probs=23.3
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 89999870789517788998848998898865
Q T0560 11 GKVWHALNEADGISIPELARKVNLSVESTALA 42 (74)
Q Consensus 11 G~VW~~L~e~~~~s~~el~k~t~lsd~el~lA 42 (74)
-.|..++.+. +|+++|++.+++|..-++--
T Consensus 12 ~~i~~l~~~G--~s~~~IAk~~gvsr~TvyR~ 41 (45)
T PF02796_consen 12 EEIRELYAQG--MSISEIAKRFGVSRSTVYRY 41 (45)
T ss_dssp HHHHHHHH------HHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHCC--CCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999979--99999999989199999999
No 22
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=28.98 E-value=14 Score=16.60 Aligned_cols=30 Identities=13% Similarity=0.219 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCCEE
Q ss_conf 177889988489988988652144116813
Q T0560 23 ISIPELARKVNLSVESTALAVGWLARENKV 52 (74)
Q Consensus 23 ~s~~el~k~t~lsd~el~lAiGWLarE~KI 52 (74)
-++.+--.+.|++++|+..|+.||-.=..+
T Consensus 24 d~L~~~L~~aGF~~~eI~~AL~WLe~La~~ 53 (155)
T PF04361_consen 24 DELTDELSAAGFEQEEIYKALDWLENLADL 53 (155)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHC
T ss_conf 999999998599999999999999998851
No 23
>PF10264 Stork_head: Winged helix Storkhead-box1 domain
Probab=28.97 E-value=11 Score=17.10 Aligned_cols=45 Identities=16% Similarity=0.127 Sum_probs=30.8
Q ss_pred HHHHHHHCCCCCCHHHHHHHH-----C---CCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf 999987078951778899884-----8---99889886521441168134664
Q T0560 12 KVWHALNEADGISIPELARKV-----N---LSVESTALAVGWLARENKVVIER 56 (74)
Q Consensus 12 ~VW~~L~e~~~~s~~el~k~t-----~---lsd~el~lAiGWLarE~KI~~~~ 56 (74)
.||.+=+.....+...|.... + =|.+.++-+||=|.||+||...-
T Consensus 19 aI~dln~~~~~at~e~l~~~L~~~~p~i~~Ps~e~~~~tL~~L~~e~kIY~t~ 71 (80)
T PF10264_consen 19 AIADLNSQGQPATQEALRQHLTKHFPGIQIPSTEVLYNTLGTLIKERKIYHTG 71 (80)
T ss_pred HHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCEEECC
T ss_conf 99998627985049999999998698999986899999999999716325479
No 24
>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=28.66 E-value=13 Score=16.79 Aligned_cols=43 Identities=26% Similarity=0.334 Sum_probs=31.9
Q ss_pred HHHHHHHHHCC---CCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEE
Q ss_conf 88999987078---9517788998848998898865214411681346
Q T0560 10 AGKVWHALNEA---DGISIPELARKVNLSVESTALAVGWLARENKVVI 54 (74)
Q Consensus 10 AG~VW~~L~e~---~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~ 54 (74)
.-.||++|..- ...||.+|++..+. ..-..++|+-.+.|.+.+
T Consensus 4 ~~~V~~~l~~IP~G~v~TYg~iA~~~g~--p~~aRaVg~al~~np~~~ 49 (85)
T PF01035_consen 4 QQRVWEALRQIPYGKVTTYGEIAEAAGR--PKAARAVGSALARNPLPL 49 (85)
T ss_dssp HHHHHHHHTTS----BEEHHHHHHHTT---TTTTTTHHHTTTTSSBTT
T ss_pred HHHHHHHHHCCCCCCCEEHHHHHHHHCC--CCCHHHHHHHHHHCCCCC
T ss_conf 9999999974899974719999999589--983799999998589988
No 25
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA , . Within this family, the HTH motif is situated towards the C-terminus. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2gzw_A 1o3q_A 1lb2_A 1i6x_A 1ruo_B 1hw5_B 1zrf_A 1i5z_B 1j59_B 1o3s_A ....
Probab=28.08 E-value=17 Score=16.11 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCCCEE
Q ss_conf 5177889988489988988652144116813
Q T0560 22 GISIPELARKVNLSVESTALAVGWLARENKV 52 (74)
Q Consensus 22 ~~s~~el~k~t~lsd~el~lAiGWLarE~KI 52 (74)
++|-++|+...|.+.+-+...+.-|.+++=|
T Consensus 2 ~lt~~elA~~~G~tretvsR~l~~l~~~GlI 32 (32)
T PF00325_consen 2 PLTHQELADLLGTTRETVSRILSRLRKEGLI 32 (32)
T ss_dssp E--HHHHHHHCTC-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCC
T ss_conf 9799999988698699999999999996799
No 26
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase () converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1sfu_A 1xmk_A 3eyi_A 1qbj_A 3f23_B 3f21_B 3f22_B 2acj_D 2gxb_B 1qgp_A ....
Probab=27.25 E-value=20 Score=15.80 Aligned_cols=48 Identities=17% Similarity=0.181 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCC--HHHHHHHHHHHHCCCEEEEE
Q ss_conf 6788999987078951778899884899--88988652144116813466
Q T0560 8 ANAGKVWHALNEADGISIPELARKVNLS--VESTALAVGWLARENKVVIE 55 (74)
Q Consensus 8 ~nAG~VW~~L~e~~~~s~~el~k~t~ls--d~el~lAiGWLarE~KI~~~ 55 (74)
..+-+|-.+|.+.++.....+.++-+|+ -+++...+==|-++|++.-.
T Consensus 4 ~~e~kIl~~L~~~g~~~a~~i~~~~~l~~~k~~vNr~LY~L~k~g~v~~~ 53 (66)
T PF02295_consen 4 ELEEKILDFLKNSGKSTATAIAKALGLSVPKKEVNRQLYRLEKSGKVCKS 53 (66)
T ss_dssp HHHHHHHHHHHHT--EECCHHHHHHHCTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEECC
T ss_conf 38999999999779718999999836125288999999999977966527
No 27
>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=26.73 E-value=20 Score=15.74 Aligned_cols=40 Identities=13% Similarity=0.248 Sum_probs=29.5
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHH----CCCEEEEEEECC
Q ss_conf 78951778899884899889886521441----168134664077
Q T0560 19 EADGISIPELARKVNLSVESTALAVGWLA----RENKVVIERKNG 59 (74)
Q Consensus 19 e~~~~s~~el~k~t~lsd~el~lAiGWLa----rE~KI~~~~~~g 59 (74)
++.+.++.||...+.+.|-+-. -+-||. .-+||.++....
T Consensus 22 ~~~PltleeIldyls~~di~~~-~~~~L~~~L~~n~kI~~dp~~~ 65 (74)
T PF02186_consen 22 DDHPLTLEEILDYLSLLDIGPK-QKPWLKEELKNNPKIEYDPDGT 65 (74)
T ss_dssp --S-B-HHHHHHHHT-S----H-HHHHHHCTHHH-TTEEE-----
T ss_pred CCCCEEHHHHHHHHHCCCCCHH-HHHHHHHHHHCCCCEEEECCCC
T ss_conf 9982419999999833687647-9999998862099489845886
No 28
>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=25.16 E-value=21 Score=15.58 Aligned_cols=51 Identities=31% Similarity=0.275 Sum_probs=37.5
Q ss_pred HHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHCCCEEEEEEE--CCEEEEEE
Q ss_conf 987078951778899884899-8898865214411681346640--77378853
Q T0560 15 HALNEADGISIPELARKVNLS-VESTALAVGWLARENKVVIERK--NGLIEIYN 65 (74)
Q Consensus 15 ~~L~e~~~~s~~el~k~t~ls-d~el~lAiGWLarE~KI~~~~~--~g~l~v~~ 65 (74)
..|+..+.+++.+|-+....+ .--+++|+==|+|+++|.+.+. .|.++|++
T Consensus 188 ~~l~~~~~~~f~~l~~~~~~~~~V~~FLAlLeL~k~~~I~l~Q~~~f~~I~I~~ 241 (242)
T PF02616_consen 188 EKLSKKGWVSFSELFKDPSRSEVVVTFLALLELVKEGKIELEQEEPFGEIYIRL 241 (242)
T ss_pred HHCCCCCEEEHHHHHCCCCCCEEHHHHHHHHHHHHCCCEEEEECCCCCCEEEEE
T ss_conf 311668767489972768877459999999999838965999748987179885
No 29
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing . Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity . ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2pjp_A 2uwm_B 2ply_A 1wsu_D 1lva_A.
Probab=25.00 E-value=22 Score=15.57 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=28.1
Q ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
Q ss_conf 9987078951778899884899889886521441168
Q T0560 14 WHALNEADGISIPELARKVNLSVESTALAVGWLAREN 50 (74)
Q Consensus 14 W~~L~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~ 50 (74)
=+++.+++..++++.+.++|+|.+-.-.=+-+|-+++
T Consensus 2 ~~~~~~~~~i~va~~rd~~g~sRK~ai~lLE~~D~~~ 38 (50)
T PF09107_consen 2 RELLKKNGEITVAEFRDALGLSRKYAIPLLEYFDREG 38 (50)
T ss_dssp HHHHHT---BEHHHHHHH----HHHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf 5788248957299999997853999999999875029
No 30
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases but this similarity is not supported by standard sequence analysis.; PDB: 2pq8_A 2giv_A 1mjb_A 1fy7_A 1mj9_A 1mja_A 2ou2_A 2rc4_A 2ozu_A.
Probab=22.24 E-value=25 Score=15.27 Aligned_cols=35 Identities=20% Similarity=0.265 Sum_probs=26.2
Q ss_pred HHHHHHHCCC---CCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9999870789---5177889988489988988652144
Q T0560 12 KVWHALNEAD---GISIPELARKVNLSVESTALAVGWL 46 (74)
Q Consensus 12 ~VW~~L~e~~---~~s~~el~k~t~lsd~el~lAiGWL 46 (74)
.|-+.|.+.. ..|+.+|.++|++..+|+..++--|
T Consensus 137 ~il~~L~~~~~~~~isi~dis~~T~i~~~DIi~tL~~l 174 (188)
T PF01853_consen 137 VILEYLLEHKGEDSISIEDISKETGIRPEDIISTLQSL 174 (188)
T ss_dssp HHHHHHHCTSSE--EEHHHHHHHH--THHHHHHHHHHT
T ss_pred HHHHHHHHCCCCCCEEHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 99999986388760079999888689888999999986
No 31
>PF10357 Kin17_mid: Domain of Kin17 curved DNA-binding protein; PDB: 2v1n_A.
Probab=21.60 E-value=16 Score=16.21 Aligned_cols=52 Identities=25% Similarity=0.285 Sum_probs=30.1
Q ss_pred HHHHHHHHHH-HCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEECCEEEEEE
Q ss_conf 6788999987-078951778899884899889886521441168134664077378853
Q T0560 8 ANAGKVWHAL-NEADGISIPELARKVNLSVESTALAVGWLARENKVVIERKNGLIEIYN 65 (74)
Q Consensus 8 ~nAG~VW~~L-~e~~~~s~~el~k~t~lsd~el~lAiGWLarE~KI~~~~~~g~l~v~~ 65 (74)
.+|-+||+-. ++..+.-+- +|.-+ .|--=+-||.|+||+.+++.+.-+||+.
T Consensus 38 V~AN~vYqEyI~Dk~HvHMN----aTrW~--sLT~FvkyLgr~G~c~Veetekg~~I~y 90 (127)
T PF10357_consen 38 VNANKVYQEYIADKDHVHMN----ATRWT--SLTEFVKYLGREGKCKVEETEKGWFITY 90 (127)
T ss_dssp EEHHHHHHHHTTSS----GG----GSS-S--SHHHHHHH------EEEE------EEEE
T ss_pred EECHHHHHHHHCCCCCCEEC----CCCCH--HHHHHHHHHHHCCEEEEECCCCCEEEEE
T ss_conf 62219899986255651204----53003--0999999970468478751787647874
Done!