Query T0611 YP_960827.1, Marinobacter aquaeolei vt8, 227 residues
Match_columns 227
No_of_seqs 159 out of 8127
Neff 9.5
Searched_HMMs 11830
Date Mon Jul 5 09:14:57 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0611.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0611.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00440 TetR_N: Bacterial reg 99.1 2.6E-11 2.2E-15 100.8 6.4 47 9-55 1-47 (47)
2 PF08362 TetR_C_3: YcdC-like p 98.2 2.5E-05 2.1E-09 56.0 13.5 139 57-198 2-141 (143)
3 PF08359 TetR_C_4: YsiA-like p 97.4 0.0011 9.4E-08 43.5 10.4 104 57-163 6-112 (133)
4 PF02796 HTH_7: Helix-turn-hel 94.1 0.021 1.8E-06 33.9 4.0 34 10-47 11-44 (45)
5 PF08361 TetR_C_2: MAATS-type 93.3 0.23 1.9E-05 26.2 11.0 89 76-164 2-98 (121)
6 PF08360 TetR_C_5: QacR-like p 93.2 0.11 9.6E-06 28.4 6.4 78 76-154 19-98 (131)
7 PF00356 LacI: Bacterial regul 92.8 0.031 2.6E-06 32.7 3.0 34 26-59 1-34 (46)
8 PF01726 LexA_DNA_bind: LexA D 92.2 0.097 8.2E-06 29.0 4.9 42 6-48 8-50 (65)
9 PF06056 Terminase_5: Putative 90.8 0.13 1.1E-05 28.1 4.4 33 10-46 3-35 (58)
10 PF01022 HTH_5: Bacterial regu 90.6 0.14 1.1E-05 27.9 4.3 38 4-48 2-39 (47)
11 PF03811 Ins_element1: Inserti 90.5 0.14 1.1E-05 27.9 4.2 35 5-47 52-86 (88)
12 PF08279 HTH_11: HTH domain; 90.0 0.14 1.2E-05 27.7 4.1 33 16-50 9-41 (55)
13 PF04967 HTH_10: HTH DNA bindi 90.0 0.15 1.3E-05 27.5 4.1 37 8-48 7-47 (53)
14 PF01710 Transposase_14: Trans 88.0 0.3 2.5E-05 25.3 4.5 40 3-51 5-44 (119)
15 PF05225 HTH_psq: helix-turn-h 86.5 0.32 2.7E-05 25.1 4.0 41 7-50 2-42 (45)
16 PF10654 DUF2481: Protein of u 86.4 0.58 4.9E-05 23.1 5.2 42 11-52 67-109 (126)
17 PF11740 KfrA_N: Plasmid repli 84.0 0.71 6E-05 22.5 4.8 40 5-46 2-42 (120)
18 PF09339 HTH_IclR: IclR helix- 83.9 0.23 2E-05 26.1 2.3 34 14-48 9-42 (52)
19 PF10668 Phage_terminase: Phag 83.6 0.5 4.2E-05 23.6 3.9 37 11-49 10-46 (60)
20 PF00292 PAX: 'Paired box' dom 83.3 0.53 4.5E-05 23.4 3.9 35 1-43 18-52 (125)
21 PF04218 CENP-B_N: CENP-B N-te 81.3 0.86 7.3E-05 21.9 4.3 28 26-53 24-51 (53)
22 PF01325 Fe_dep_repress: Iron 81.2 0.9 7.6E-05 21.7 4.4 43 2-46 2-44 (60)
23 PF00165 HTH_AraC: Bacterial r 80.7 0.51 4.3E-05 23.6 3.0 30 19-48 3-32 (42)
24 PF08220 HTH_DeoR: DeoR-like h 79.5 1.1 9.2E-05 21.1 4.4 34 14-49 6-39 (57)
25 PF08281 Sigma70_r4_2: Sigma-7 79.3 0.45 3.8E-05 24.0 2.4 34 13-46 15-48 (54)
26 PF12116 SpoIIID: Stage III sp 78.7 1.2 9.9E-05 20.8 4.4 37 6-46 5-41 (82)
27 PF00196 GerE: Bacterial regul 78.5 0.49 4.2E-05 23.7 2.4 26 22-47 16-41 (58)
28 PF01418 HTH_6: Helix-turn-hel 76.1 1.8 0.00015 19.4 4.8 39 6-46 18-56 (107)
29 PF01381 HTH_3: Helix-turn-hel 76.1 0.54 4.6E-05 23.4 2.0 32 23-54 8-39 (55)
30 PF04297 UPF0122: Putative hel 75.8 1.5 0.00013 20.1 4.2 41 14-54 23-63 (101)
31 PF04703 FaeA: FaeA-like prote 75.1 1.3 0.00011 20.4 3.8 35 6-45 2-36 (62)
32 PF04182 B-block_TFIIIC: B-blo 73.1 1.3 0.00011 20.6 3.3 39 12-50 6-44 (75)
33 PF05043 Mga: Mga helix-turn-h 71.3 1.8 0.00015 19.5 3.7 33 21-53 27-59 (87)
34 PF00046 Homeobox: Homeobox do 70.1 1.6 0.00014 19.8 3.3 41 10-50 12-53 (57)
35 PF02082 Rrf2: Transcriptional 69.4 2.5 0.00022 18.3 5.1 44 3-46 3-47 (83)
36 PF01978 TrmB: Sugar-specific 69.1 1.2 0.0001 20.8 2.4 27 23-49 21-47 (68)
37 PF05930 Phage_AlpA: Prophage 68.0 1 8.5E-05 21.4 1.9 24 25-48 4-27 (51)
38 PF00376 MerR: MerR family reg 67.7 1.1 9.7E-05 20.9 2.1 20 26-45 1-20 (38)
39 PF05732 RepL: Firmicute plasm 65.8 2.7 0.00023 18.1 3.7 40 7-46 58-97 (165)
40 PF03444 DUF293: Domain of unk 63.3 3.3 0.00028 17.5 5.4 46 5-51 5-50 (78)
41 PF02001 DUF134: Protein of un 58.9 2.3 0.00019 18.7 2.3 27 21-47 54-80 (106)
42 PF07022 Phage_CI_repr: Bacter 58.7 1.9 0.00016 19.3 1.9 34 18-53 8-41 (66)
43 PF01527 Transposase_8: Transp 55.1 0.86 7.2E-05 21.9 -0.4 24 23-46 22-45 (76)
44 PF02954 HTH_8: Bacterial regu 54.5 3 0.00025 17.8 2.3 22 24-45 18-39 (42)
45 PF06163 DUF977: Bacterial pro 53.8 4.6 0.00039 16.4 5.0 40 5-46 9-48 (127)
46 PF08280 HTH_Mga: M protein tr 50.1 5.2 0.00044 16.0 4.3 37 15-53 12-48 (59)
47 PF07750 GcrA: GcrA cell cycle 49.8 3.5 0.0003 17.3 2.1 28 11-42 9-37 (162)
48 PF00382 TFIIB: Transcription 48.6 5.5 0.00047 15.8 3.2 21 123-143 15-35 (71)
49 PF04036 DUF372: Domain of unk 47.4 2.4 0.0002 18.5 0.9 17 31-47 4-20 (38)
50 PF10078 DUF2316: Uncharacteri 46.1 6 0.00051 15.5 5.6 44 5-48 4-47 (89)
51 PF06971 Put_DNA-bind_N: Putat 45.8 4.1 0.00035 16.7 1.9 37 9-45 13-49 (50)
52 PF04545 Sigma70_r4: Sigma-70, 44.9 1.2 0.0001 20.7 -0.9 25 21-45 17-41 (50)
53 PF04552 Sigma54_DBD: Sigma-54 44.5 1.9 0.00016 19.3 0.0 41 9-49 32-74 (160)
54 PF01047 MarR: MarR family; I 44.2 6.4 0.00054 15.3 4.1 30 15-46 10-39 (59)
55 PF06322 Phage_NinH: Phage Nin 40.2 5 0.00042 16.1 1.6 29 26-54 18-46 (64)
56 PF08667 BetR: BetR domain; I 39.3 7.5 0.00063 14.8 4.7 46 6-51 3-49 (147)
57 PF03690 UPF0160: Uncharacteri 39.2 7.5 0.00064 14.8 3.8 40 36-75 81-131 (318)
58 PF00392 GntR: Bacterial regul 39.1 7.6 0.00064 14.8 5.2 39 7-45 3-45 (64)
59 PF08784 RPA_C: Replication pr 35.3 8.6 0.00073 14.4 3.4 16 125-140 81-96 (102)
60 PF04539 Sigma70_r3: Sigma-70 35.2 8.6 0.00073 14.4 4.2 38 7-45 4-41 (78)
61 PF01498 Transposase_5: Transp 34.5 8.5 0.00072 14.4 2.1 21 25-45 14-39 (72)
62 PF08535 KorB: KorB domain; I 33.3 8 0.00068 14.6 1.8 24 23-46 2-25 (93)
63 PF06230 DUF1009: Protein of u 31.3 9.9 0.00084 13.9 4.2 49 7-55 52-100 (214)
64 PF07453 NUMOD1: NUMOD1 domain 30.9 10 0.00085 13.9 2.5 20 25-44 17-36 (37)
65 PF07498 Rho_N: Rho terminatio 30.0 8.9 0.00075 14.2 1.5 30 26-59 9-38 (43)
66 PF08006 DUF1700: Protein of u 28.8 11 0.00091 13.6 4.1 37 1-37 17-53 (181)
67 PF09862 DUF2089: Protein of u 27.6 11 0.00096 13.5 3.4 18 26-43 51-68 (113)
68 PF04963 Sigma54_CBD: Sigma-54 24.5 8.5 0.00072 14.4 0.6 32 8-39 36-67 (195)
69 PF08822 DUF1804: Protein of u 24.4 13 0.0011 13.1 14.0 24 22-45 17-40 (165)
70 PF03374 ANT: Phage antirepres 24.3 13 0.0011 13.1 3.5 17 195-211 91-107 (111)
71 PF07471 Phage_Nu1: Phage DNA 23.7 13 0.0011 13.0 2.0 23 24-46 2-24 (164)
72 PF04760 IF2_N: Translation in 23.3 13 0.0011 12.9 2.0 23 23-45 2-24 (54)
73 PF11849 DUF3369: Domain of un 22.7 11 0.00089 13.7 0.8 37 7-43 22-61 (174)
74 PF00126 HTH_1: Bacterial regu 20.4 15 0.0013 12.5 4.3 34 15-52 8-41 (60)
75 PF04269 DUF440: Protein of un 20.3 15 0.0013 12.5 3.2 31 1-31 1-31 (103)
No 1
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD , , . Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution . TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1zk8_A 2oi8_A 2g7l_A 2opt_B 3b6a_F 3b6c_B 2hxo_A 2hxi_B 1z0x_B 1bjy_A ....
Probab=99.15 E-value=2.6e-11 Score=100.81 Aligned_cols=47 Identities=34% Similarity=0.656 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHHH
Q ss_conf 99999999987281036579999985778778999834489999999
Q T0611 9 ILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEI 55 (227)
Q Consensus 9 Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av 55 (227)
||++|.++|.++||.++||++||+++|||++++|+||+||++|+.++
T Consensus 1 Il~aa~~l~~~~G~~~~t~~~ia~~agvs~~~iy~~F~~k~~L~~av 47 (47)
T PF00440_consen 1 ILDAAIELFAERGYEAVTIRDIAERAGVSRGSIYRHFPSKEDLLEAV 47 (47)
T ss_dssp HHHHHHHHHHHS-GTTSSHHHHHHHHTSBHHHHHHHSSSHHHHHHHH
T ss_pred CHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHCCCHHHHHHHC
T ss_conf 99999999998592218799999876479350256569999999669
No 2
>PF08362 TetR_C_3: YcdC-like protein, C-terminal region; InterPro: IPR013573 This entry represents the C-terminal domain found in the hypothetical transcriptional regulators RutR and YcdC (P75899 from SWISSPROT) from Escherichia coli. Both of these proteins are member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. RutR negatively controls the transcription of the rut operon involved in pyrimidine utilization. The C-terminal domains of RutR, YsiA and TetR share a multi-helical, interlocking structure. These proteins also contain helix-turn-helix (HTH) DNA-binding domains.; GO: 0016564 transcription repressor activity, 0016481 negative regulation of transcription; PDB: 1pb6_C.
Probab=98.23 E-value=2.5e-05 Score=55.96 Aligned_cols=139 Identities=14% Similarity=0.119 Sum_probs=106.7
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998752217998778999999999999998778865444-441268899999999999999999999999986
Q T0611 57 QEYEKLVDYYLDIPEDRPITLEDMTFYLESVFDGLWSYRFFHRDLE-YLLDSDPRLRQDYREFTNRCLAAINRIFAKLAD 135 (227)
Q Consensus 57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~ 135 (227)
++..+.....+.......+|.+.+..|++..++...++|...+.+. ++....|.+............+....+|+.+++
T Consensus 2 ~~il~~Wl~~~~~~~~~~dP~~aL~~YIr~Kl~~sr~~P~~Srlfa~Eii~Gap~l~~~l~~~l~~~~~~~~~vI~~Wi~ 81 (143)
T PF08362_consen 2 EDILEDWLAPLDDIDAEDDPAEALRAYIRAKLEMSRDHPEASRLFANEIIQGAPRLKDYLSEELKPWVDEKVAVIERWIA 81 (143)
T ss_dssp HHHHHHHTHHHHT--TTS-HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH---TTTHHHH---HHHHHHHHHHHH-----
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 77899999888756867999999999999999999889416399999998484666999999999999989999999998
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf 598889938899999999999999988776553100220001089999999999998712189
Q T0611 136 AGIIQPQPEDLRSAMSLNVWLVITNWMAFLKTAHAAEEPASLSLTELKQGIYQVLTLEVPYLT 198 (227)
Q Consensus 136 ~G~l~~~~~~~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~p~lt 198 (227)
+|.+++.++. .+..+||.++..+..|.............+..++.++...+..++...+.
T Consensus 82 ~G~i~~vdP~---hLlf~IWa~TQhYADf~~Qi~~~~g~~~~~~~~~~~a~~~v~~lvL~g~g 141 (143)
T PF08362_consen 82 QGKIAPVDPH---HLLFSIWATTQHYADFDAQIRALLGKDELDEDDFEQAAEFVTRLVLRGCG 141 (143)
T ss_dssp -----S--HH---HHHHHHHHHHHHHHHTHHHHHHH----TTSHHHHHHHHHHHHHHHH----
T ss_pred CCCCCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 6998998999---99999999852063379999998598858888999999999999996168
No 3
>PF08359 TetR_C_4: YsiA-like protein, C-terminal region; InterPro: IPR013570 This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YsiA (P94548 from SWISSPROT) from Bacillus subtilis, which is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YsiA and TetR share a multi-helical, interlocking structure.; PDB: 1vi0_B.
Probab=97.37 E-value=0.0011 Score=43.53 Aligned_cols=104 Identities=15% Similarity=0.183 Sum_probs=73.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998752217998778999999999999998778865444-441268899999999999999999999999986
Q T0611 57 QEYEKLVDYYLDIPEDRPITLEDMTFYLESVFDGLWSYRFFHRDLE-YLLDSDPRLRQDYREFTNRCLAAINRIFAKLAD 135 (227)
Q Consensus 57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~ 135 (227)
.+..+.+...+ .+..++.+.+...+..++.....++.+...+. +....++++.....+...++...+..+|.+|++
T Consensus 6 ~~~~~~~~~~~---~~~~~~~ekL~~~i~~hl~~~~~~~~~~~v~~~E~~~~~~~~~~~i~~~~~~y~~~i~~iI~eGq~ 82 (133)
T PF08359_consen 6 NELLEELEEAL---ASEDSPREKLRALIRAHLRFLEENPDLAIVFQLELRQSNPELREEINELRREYFRLIEEIIEEGQE 82 (133)
T ss_dssp --HHHHHHHHH---CC--SHHHHHHHHHHHHHHHH---HHHHHHHHCTTS-SSHHHHHHHHHHH---HHHH---------
T ss_pred HHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999987---168999999999999999999809974874899887578999999999999999999999999998
Q ss_pred CCCCCCCHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf 598889938--8999999999999999887
Q T0611 136 AGIIQPQPE--DLRSAMSLNVWLVITNWMA 163 (227)
Q Consensus 136 ~G~l~~~~~--~~~~~l~~~~~~~~~~w~~ 163 (227)
.|.++++.+ .+...+..++..++..|+-
T Consensus 83 ~G~fr~dld~~~~~~~i~G~i~~~v~~w~~ 112 (133)
T PF08359_consen 83 QGEFRPDLDPELAARMIFGTINGTVTQWVL 112 (133)
T ss_dssp ---B-----HHHHHHHH---HHHHHHHHHH
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 598889899999999999999999999986
No 4
>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=94.14 E-value=0.021 Score=33.91 Aligned_cols=34 Identities=21% Similarity=0.437 Sum_probs=26.9
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 99999999872810365799999857787789998344
Q T0611 10 LLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRN 47 (227)
Q Consensus 10 l~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~s 47 (227)
++.+.+|.. .| .|+.+||+..|||+.|||+|+..
T Consensus 11 ~~~i~~l~~-~G---~s~~~IAk~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 11 IEEIRELYA-QG---MSISEIAKRFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHHH--------HHHHHHHCTS-HHHHHHHHCC
T ss_pred HHHHHHHHH-CC---CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 999999999-79---99999999989199999999741
No 5
>PF08361 TetR_C_2: MAATS-type transcriptional repressor, C-terminal region; InterPro: IPR013572 This entry is named after the various transcriptional regulatory proteins that it contains, including MtrR (Q6RV06 from SWISSPROT), AcrR (P34000 from SWISSPROT), ArpR (Q9KJC4 from SWISSPROT), TtgR (Q9AIU0 from SWISSPROT) and SmeT (Q8KLP4 from SWISSPROT). These are members of the TetR (tetracycline resistance) family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins , , . ; GO: 0003677 DNA binding; PDB: 2w53_B 2uxu_A 2uxp_A 2uxi_B 2uxo_B 2uxh_A 2qop_A 3bcg_A.
Probab=93.35 E-value=0.23 Score=26.21 Aligned_cols=89 Identities=16% Similarity=0.141 Sum_probs=54.8
Q ss_pred CHHHHHHHHHHHHHHHHHH---HHHHHHH---HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHH--HHH
Q ss_conf 7789999999999999987---7886544---4441268899999999999999999999999986598889938--899
Q T0611 76 TLEDMTFYLESVFDGLWSY---RFFHRDL---EYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQPE--DLR 147 (227)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~---~~~~~~l---~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~G~l~~~~~--~~~ 147 (227)
|+..++..+...+...... +.++..+ ++.......+.++...........+...++.++++|.+.++.+ ...
T Consensus 2 PL~~Lr~~~~~~l~~l~~d~~~Rrv~~Il~~KcE~~~E~~~~~~r~~~~~~~~~~~i~~~l~~a~~~g~L~~~ld~~~AA 81 (121)
T PF08361_consen 2 PLERLRELLIYALRQLAEDERTRRVFEILFHKCEFVEEMAPVLERRREAQQEFYARIERLLRRAIARGQLPADLDPRLAA 81 (121)
T ss_dssp HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHS---BTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSC-TTB-HHHHH
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf 68999999999999996079898999999997101024299999999999999999999999999869999998999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999998877
Q T0611 148 SAMSLNVWLVITNWMAF 164 (227)
Q Consensus 148 ~~l~~~~~~~~~~w~~~ 164 (227)
..+...+..+...|+..
T Consensus 82 ~~l~a~~~GL~~~WL~~ 98 (121)
T PF08361_consen 82 IMLHALLSGLLHNWLLD 98 (121)
T ss_dssp HHHHHHH---HHHHHHS
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 99999999999998569
No 6
>PF08360 TetR_C_5: QacR-like protein, C-terminal region; InterPro: IPR013571 This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (P23217 from SWISSPROT) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (P23215 from SWISSPROT), a multidrug efflux pump . The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites . The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.; GO: 0003700 transcription factor activity, 0016481 negative regulation of transcription; PDB: 2hq5_E 1rkw_B 1qvt_B 1jum_B 2gby_B 2dtz_D 1rpw_D 1jtx_A 1jup_A 1jus_E ....
Probab=93.17 E-value=0.11 Score=28.45 Aligned_cols=78 Identities=10% Similarity=0.090 Sum_probs=53.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 778999999999999998778--865444441268899999999999999999999999986598889938899999999
Q T0611 76 TLEDMTFYLESVFDGLWSYRF--FHRDLEYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQPEDLRSAMSLN 153 (227)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~G~l~~~~~~~~~~l~~~ 153 (227)
..+.+..+...++..+ ++|. ...++..-...+|++..+...+..+....+..+|++|+++|.+++++......+..+
T Consensus 19 a~eKLyg~a~~~l~~~-~~pl~~a~~EF~~~~~~~~ev~e~l~~l~~~~~~~~~~Ii~eGI~~GeF~~~n~~~~~~il~s 97 (131)
T PF08360_consen 19 ATEKLYGMAEFVLYDI-QTPLLRAIEEFYSSQYKSPEVLERLNELRRKYLDFYRDIIEEGIQSGEFRIENVEELALILIS 97 (131)
T ss_dssp HHHHHHHHHHHHHHSS-SGGGHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHHHHHHHH----------STHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHC-CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf 8999999999999870-350689999998753499899999999999999999999999988698217889999999999
Q ss_pred H
Q ss_conf 9
Q T0611 154 V 154 (227)
Q Consensus 154 ~ 154 (227)
+
T Consensus 98 l 98 (131)
T PF08360_consen 98 L 98 (131)
T ss_dssp H
T ss_pred H
T ss_conf 9
No 7
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR , . Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1l1m_B 2bjc_A 1lcc_A 1osl_A 2pe5_A 1lcd_A 1efa_A 1cjg_B 1lqc_A 1jwl_A ....
Probab=92.77 E-value=0.031 Score=32.71 Aligned_cols=34 Identities=15% Similarity=0.102 Sum_probs=26.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 5799999857787789998344899999999999
Q T0611 26 TTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEY 59 (227)
Q Consensus 26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av~~~~ 59 (227)
||.|||+.+|||++|+-+++.++..+-.+.-+++
T Consensus 1 Ti~diA~~agvS~~TVSr~Ln~~~~vs~~tr~rI 34 (46)
T PF00356_consen 1 TIKDIAKAAGVSVATVSRVLNGPPRVSEETRERI 34 (46)
T ss_dssp SHHHHHHHTTSSHHHHHHHHHTCTTSTHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 9999998989499999999758999989999999
No 8
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif . This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0008992 repressor LexA activity, 0006508 proteolysis; PDB: 1lea_A 1jhh_A 1jhf_A 1leb_A.
Probab=92.17 E-value=0.097 Score=28.98 Aligned_cols=42 Identities=19% Similarity=0.305 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC-HHHHHHHHCCH
Q ss_conf 99999999999987281036579999985778-77899983448
Q T0611 6 RDKILLSSLELFNDKGERNITTNHIAAHLAIS-PGNLYYHFRNK 48 (227)
Q Consensus 6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs-~gtlY~~F~sK 48 (227)
-++||+.-.+-+.++||. -|+++|+++.|++ ++++++|-+.=
T Consensus 8 Q~~vL~~I~~~~~~~G~~-Pt~rEI~~~~gl~S~~tV~~~L~~L 50 (65)
T PF01726_consen 8 QQEVLDFIKDYIREHGYP-PTVREIAEALGLKSPSTVHKHLKAL 50 (65)
T ss_dssp HHHHHHHHHHHHHH-------HHHHHHH----SHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCC-CCHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 999999999999983889-8899999881999809999999999
No 9
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after . Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=90.84 E-value=0.13 Score=28.10 Aligned_cols=33 Identities=24% Similarity=0.314 Sum_probs=28.3
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9999999987281036579999985778778999834
Q T0611 10 LLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 10 l~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
-..|..||. .|.|..+||+.+|||..|||++..
T Consensus 3 r~~A~~Ly~----~G~~~~eIA~~Lgv~~~TV~~W~~ 35 (58)
T PF06056_consen 3 RRQARELYL----QGYTPKEIAEELGVSRRTVYSWKK 35 (58)
T ss_pred HHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 899999999----689999999998868889999999
No 10
>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=90.62 E-value=0.14 Score=27.89 Aligned_cols=38 Identities=32% Similarity=0.338 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf 779999999999998728103657999998577877899983448
Q T0611 4 KTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNK 48 (227)
Q Consensus 4 ~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK 48 (227)
.||-+||..-.+ ...++.+|++..|+|++++++|.+.=
T Consensus 2 ~~R~~Il~~L~~-------~~~~~~eia~~l~~s~~tvs~HL~~L 39 (47)
T PF01022_consen 2 PTRLKILKLLSE-------GPLSVSEIAEELGISQSTVSRHLKKL 39 (47)
T ss_dssp HHHHHHHHHHHH-------SCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHH-------CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 889999999986-------89679998836123565899999999
No 11
>PF03811 Ins_element1: Insertion element protein; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. This protein is absolutely required for transposition of insertion element 1.; GO: 0006313 transposition, DNA-mediated
Probab=90.47 E-value=0.14 Score=27.90 Aligned_cols=35 Identities=26% Similarity=0.306 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 7999999999999872810365799999857787789998344
Q T0611 5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRN 47 (227)
Q Consensus 5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~s 47 (227)
++++|++.. ..+.++++||+..|||..|++++.++
T Consensus 52 ~k~~i~~l~--------~~G~siR~iArvl~Is~~Tv~r~lK~ 86 (88)
T PF03811_consen 52 VKQKILELM--------VEGMSIRDIARVLGISINTVLRWLKN 86 (88)
T ss_pred HHHHHHHHH--------HCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 999999998--------76851999999868789999999862
No 12
>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=90.05 E-value=0.14 Score=27.67 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=26.7
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf 99872810365799999857787789998344899
Q T0611 16 LFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSD 50 (227)
Q Consensus 16 lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~ 50 (227)
|+..+|+ +|.++||+.+|||+.|++++...=++
T Consensus 9 L~~~~~~--it~~eLA~~l~vS~~Ti~~~i~~L~~ 41 (55)
T PF08279_consen 9 LLKNDGP--ITAKELAEELGVSRRTIRRDIKELEE 41 (55)
T ss_dssp HHHCCTT--S-HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHCCCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 9985999--88999999969799999999999998
No 13
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium halobium and described as a putative bacterio-opsin activator.
Probab=89.96 E-value=0.15 Score=27.52 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHCCC----CCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf 999999999987281----03657999998577877899983448
Q T0611 8 KILLSSLELFNDKGE----RNITTNHIAAHLAISPGNLYYHFRNK 48 (227)
Q Consensus 8 ~Il~aA~~lf~e~G~----~~~t~~~IA~~aGvs~gtlY~~F~sK 48 (227)
.+|.+|. +.|| .++|+.+||+++|||++|+.+|-..=
T Consensus 7 e~L~~A~----~~GYfd~PR~~tl~elA~~lgis~~T~~~~LRra 47 (53)
T PF04967_consen 7 EVLRTAY----EMGYFDWPRRITLEELAEELGISKSTFSEHLRRA 47 (53)
T ss_pred HHHHHHH----HCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999999----8688779875889999989499999999999999
No 14
>PF01710 Transposase_14: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily . More information about these proteins can be found at Protein of the Month: Transposase .
Probab=88.03 E-value=0.3 Score=25.31 Aligned_cols=40 Identities=13% Similarity=0.382 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHH
Q ss_conf 3779999999999998728103657999998577877899983448999
Q T0611 3 MKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDI 51 (227)
Q Consensus 3 ~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~L 51 (227)
..=|++||++ .+. |-|.+++|+.-|||+.|+|+... +.+.
T Consensus 5 ~DlR~kvi~~-----~~~---G~S~~eaA~~F~VS~~Tv~rW~k-~~~~ 44 (119)
T PF01710_consen 5 IDLRQKVIAY-----VEQ---GMSIREAAKRFGVSRSTVYRWLK-RRET 44 (119)
T ss_pred HHHHHHHHHH-----HHC---CCCHHHHHHHHCCCHHHHHHHHH-HHHC
T ss_conf 9999999999-----995---99999999996955999999998-6411
No 15
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster . In pipsqueak this domain binds to GAGA sequence . The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex .; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2cob_A.
Probab=86.53 E-value=0.32 Score=25.08 Aligned_cols=41 Identities=12% Similarity=0.259 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf 99999999999872810365799999857787789998344899
Q T0611 7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSD 50 (227)
Q Consensus 7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~ 50 (227)
+.-|+.|++.+...+ .|++..|+.-||++.||+++..++..
T Consensus 2 ee~l~~Ai~~v~~g~---~Si~~aA~~ygVp~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 2 EERLQEAIEAVKNGK---LSIRKAARKYGVPRSTLRRRLKGKPS 42 (45)
T ss_dssp HHHHHHHHHHHH--------HHHHHHH----HHHHHHHHHH---
T ss_pred HHHHHHHHHHHHCCC---CCHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf 699999999999099---57999999989398999999927877
No 16
>PF10654 DUF2481: Protein of unknown function (DUF2481)
Probab=86.37 E-value=0.58 Score=23.13 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=29.5
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC-CHHHHH
Q ss_conf 999999987281036579999985778778999834-489999
Q T0611 11 LSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR-NKSDII 52 (227)
Q Consensus 11 ~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~-sKe~Ll 52 (227)
++.+.-|...-+.|+|-.+||+--|||++++|.|.. +|++-.
T Consensus 67 ei~i~Ef~~lR~AGvt~~~IAd~F~Isks~v~Nf~qrNk~ey~ 109 (126)
T PF10654_consen 67 EITIREFAELRHAGVTWYAIADHFNISKSTVFNFTQRNKEEYR 109 (126)
T ss_pred CCCHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 1219999999964887899999828739999999998099999
No 17
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term
Probab=84.01 E-value=0.71 Score=22.50 Aligned_cols=40 Identities=15% Similarity=0.176 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHHHHHHC
Q ss_conf 7999999999999872810365799999857-78778999834
Q T0611 5 TRDKILLSSLELFNDKGERNITTNHIAAHLA-ISPGNLYYHFR 46 (227)
Q Consensus 5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aG-vs~gtlY~~F~ 46 (227)
|+++|.+||-.|+.+.. ..|++.|=+++| .|+.+|-.|.+
T Consensus 2 t~e~V~~Aa~~L~~~G~--~PTv~~VR~~lG~GS~~ti~~~lk 42 (120)
T PF11740_consen 2 TYEDVAAAADALLAAGK--RPTVDAVRERLGTGSMSTISKHLK 42 (120)
T ss_pred CHHHHHHHHHHHHHCCC--CCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf 69999999999987489--998999999987958899999999
No 18
>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=83.89 E-value=0.23 Score=26.12 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=26.5
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf 99998728103657999998577877899983448
Q T0611 14 LELFNDKGERNITTNHIAAHLAISPGNLYYHFRNK 48 (227)
Q Consensus 14 ~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK 48 (227)
++.|.+++-. .|+.+||++.|++++|+|++..+=
T Consensus 9 L~~l~~~~~~-~t~~eia~~~gl~~st~~r~l~~L 42 (52)
T PF09339_consen 9 LEALARAPRP-LTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HHTHCTTBSS-EEHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHCCCC-CCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999878999-899999999891999999999999
No 19
>PF10668 Phage_terminase: Phage terminase small subunit
Probab=83.62 E-value=0.5 Score=23.63 Aligned_cols=37 Identities=16% Similarity=0.431 Sum_probs=30.4
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf 999999987281036579999985778778999834489
Q T0611 11 LSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKS 49 (227)
Q Consensus 11 ~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe 49 (227)
+-|++++.++| ...+..+||+++|||..+|- .+++++
T Consensus 10 dkA~e~y~~~~-g~~~~k~IAe~lgvs~~tIr-~WKs~d 46 (60)
T PF10668_consen 10 DKAFEIYKESN-GKIKLKDIAEKLGVSESTIR-KWKSRD 46 (60)
T ss_pred HHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHH-HHHHHC
T ss_conf 99999999818-98419999999797999987-341022
No 20
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see ) , . Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0007275 multicellular organismal development, 0005634 nucleus; PDB: 6pax_A 1pdn_C 1k78_E 1mdm_A 2k27_A.
Probab=83.26 E-value=0.53 Score=23.44 Aligned_cols=35 Identities=17% Similarity=0.262 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9737799999999999987281036579999985778778999
Q T0611 1 MTMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYY 43 (227)
Q Consensus 1 ~~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~ 43 (227)
++..+|++|++.+. .+++..+||+..+||+|.+..
T Consensus 18 lp~~~R~rIv~l~~--------~G~r~~~Isr~l~VS~gcVsK 52 (125)
T PF00292_consen 18 LPNELRQRIVELAH--------EGVRPCDISRQLRVSHGCVSK 52 (125)
T ss_dssp S-HHHHHHHHHHHH------------HHHHHHHHT-----HHH
T ss_pred CCHHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHH
T ss_conf 88999999999976--------258774899876514769999
No 21
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure .; GO: 0003677 DNA binding, 0000775 chromosome, pericentric region; PDB: 2elh_A 1hlv_A 1bw6_A.
Probab=81.27 E-value=0.86 Score=21.86 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=26.4
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf 5799999857787789998344899999
Q T0611 26 TTNHIAAHLAISPGNLYYHFRNKSDIIY 53 (227)
Q Consensus 26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~ 53 (227)
|..+||+..||++.|++.--++|+.++.
T Consensus 24 s~~~iAr~fgi~~sTi~~i~k~k~~i~~ 51 (53)
T PF04218_consen 24 SQREIAREFGISRSTISRILKNKEKILE 51 (53)
T ss_dssp -HHHHHHHHT--CCHHHHHCCTHHHHCC
T ss_pred CHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 8999998919988899999983999985
No 22
>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=81.20 E-value=0.9 Score=21.73 Aligned_cols=43 Identities=21% Similarity=0.301 Sum_probs=33.3
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 737799999999999987281036579999985778778999834
Q T0611 2 TMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 2 ~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
--.+.|.-|.+=..+-. .-..++..+||+++|||++|+..-.+
T Consensus 2 ls~~~e~YL~~I~~l~~--~~~~v~~~~IA~~L~vs~~TVs~ml~ 44 (60)
T PF01325_consen 2 LSESEEDYLKAIYELSE--EGGPVSTSDIAERLGVSPPTVSEMLK 44 (60)
T ss_dssp CSSHHHHHHHHHHHHHH--H-S--BHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 88069999999999980--69972199999997899078999999
No 23
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; InterPro: IPR000005 Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' (HTH) motif. One major subfamily of these proteins , is related to the arabinose operon regulatory protein AraC , . Except for celD , all of these proteins seem to be positive transcriptional factors. Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C-terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The N-terminal and central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerization . The known structure of MarA (P27246 from SWISSPROT) shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27 angstroms, which causes the cognate DNA to bend.; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1xs9_A 1bl0_A 1d5y_A 1wpk_A 2k9s_A 1zgw_A 1u8b_A.
Probab=80.70 E-value=0.51 Score=23.55 Aligned_cols=30 Identities=23% Similarity=0.360 Sum_probs=25.1
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf 728103657999998577877899983448
Q T0611 19 DKGERNITTNHIAAHLAISPGNLYYHFRNK 48 (227)
Q Consensus 19 e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK 48 (227)
++=-...|+.+||.++|+|+..+++.|+..
T Consensus 3 ~~~~~~~~i~~iA~~~g~s~~~~~r~Fk~~ 32 (42)
T PF00165_consen 3 EHLSEPISIEDIAEELGYSPSYFSRLFKKE 32 (42)
T ss_dssp TTTCSS--HHHHHHHTTSSHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 756898979999999798999999999999
No 24
>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=79.50 E-value=1.1 Score=21.11 Aligned_cols=34 Identities=18% Similarity=0.396 Sum_probs=27.7
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf 999987281036579999985778778999834489
Q T0611 14 LELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKS 49 (227)
Q Consensus 14 ~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe 49 (227)
++++.++|+ +|+.++|+..|||..|+.+++..-+
T Consensus 6 l~~l~~~~~--~s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 6 LELLKQHGK--VSVKELAEEFGVSEMTIRRDLNELE 39 (57)
T ss_pred HHHHHHCCC--EEHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999698--9799999998949889999899999
No 25
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 , . Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2h27_D 1or7_A 2o8x_B.
Probab=79.29 E-value=0.45 Score=23.98 Aligned_cols=34 Identities=21% Similarity=0.189 Sum_probs=28.8
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9999987281036579999985778778999834
Q T0611 13 SLELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 13 A~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
-..+|.-+=+++.|..+||+..|+|.++++.+..
T Consensus 15 ~r~i~~l~~~~g~s~~eIA~~l~is~~tv~~~l~ 48 (54)
T PF08281_consen 15 QREIFLLRYFEGLSYKEIAEILGISESTVKSRLS 48 (54)
T ss_dssp HHHHHHHHHT----HHHHHHHCTS----HHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999999695899999998919999999999
No 26
>PF12116 SpoIIID: Stage III sporulation protein D
Probab=78.71 E-value=1.2 Score=20.85 Aligned_cols=37 Identities=11% Similarity=0.181 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99999999999987281036579999985778778999834
Q T0611 6 RDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
.+|.++.|-=.... ..|++..|+.-||||+|++.-+.
T Consensus 5 eeR~~~ia~yIi~~----~aTVR~tAk~FGVSKSTVHkDvT 41 (82)
T PF12116_consen 5 EERVLEIANYIIEN----KATVRQTAKVFGVSKSTVHKDVT 41 (82)
T ss_pred HHHHHHHHHHHHHC----CHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999999974----51699999997852999989999
No 27
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers , , . LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase , . Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria : V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE . B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT . E. coli malT (activates maltose operon; MalT binds ATP and maltotriose) ; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1fse_B 2jpc_A 1x3u_A 1yio_A 1zn2_A 1p4w_A 3clo_B 1l3l_C 1h0m_B 2q0o_A ....
Probab=78.46 E-value=0.49 Score=23.69 Aligned_cols=26 Identities=27% Similarity=0.387 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 10365799999857787789998344
Q T0611 22 ERNITTNHIAAHLAISPGNLYYHFRN 47 (227)
Q Consensus 22 ~~~~t~~~IA~~aGvs~gtlY~~F~s 47 (227)
..|.|..+||+.+|+|..|+.+|-.+
T Consensus 16 ~~G~~~~eIA~~l~is~~TV~~~~~~ 41 (58)
T PF00196_consen 16 AQGLSNKEIAERLGISEKTVKSHRRR 41 (58)
T ss_dssp CTT--HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHCCCCHHHHHHHCCCHHHHHHHHHH
T ss_conf 97398378998835452479999999
No 28
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif . Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2o3f_C.
Probab=76.11 E-value=1.8 Score=19.43 Aligned_cols=39 Identities=18% Similarity=0.199 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99999999999987281036579999985778778999834
Q T0611 6 RDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
-.+|.+.=++-..+ +...|+.+||+.+|||+.|+.+.-+
T Consensus 18 e~~Ia~yil~~~~~--~~~~si~~lA~~~~vS~atv~Rf~k 56 (107)
T PF01418_consen 18 EKKIADYILNNPDK--IANMSISELAKAAGVSPATVVRFCK 56 (107)
T ss_dssp HHHHHHHHHH-HHH--HTT--HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHCHHH--HHHCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999929999--9775499999997989889999999
No 29
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2ef8_B 3f6w_A 3eus_A 1x57_A 1utx_A 2gzu_A 1rio_A 1lli_A 1lmb_3 3bdn_B ....
Probab=76.11 E-value=0.54 Score=23.37 Aligned_cols=32 Identities=22% Similarity=0.252 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHH
Q ss_conf 03657999998577877899983448999999
Q T0611 23 RNITTNHIAAHLAISPGNLYYHFRNKSDIIYE 54 (227)
Q Consensus 23 ~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~a 54 (227)
.+.|..++|+.+|+|+++++.+..++...=..
T Consensus 8 ~gls~~~la~~~gis~~~i~~~e~g~~~~~~~ 39 (55)
T PF01381_consen 8 RGLSQEELARRLGISRSTISRIENGKRNPSIE 39 (55)
T ss_dssp TT--HHHHHHHHTS-HHHHHHHHTTSSGSBHH
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHH
T ss_conf 69999999886498787888997699899999
No 30
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway .; PDB: 1s7o_B 1xsv_A.
Probab=75.81 E-value=1.5 Score=20.06 Aligned_cols=41 Identities=20% Similarity=0.256 Sum_probs=32.8
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHH
Q ss_conf 99998728103657999998577877899983448999999
Q T0611 14 LELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYE 54 (227)
Q Consensus 14 ~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~a 54 (227)
.+.|...=....|+.+||+..|||+.++|-..+.=+..+..
T Consensus 23 ~~~l~lyy~eDlSlsEIAe~~~iSRqaVyD~ikr~~~~L~~ 63 (101)
T PF04297_consen 23 KEYLELYYNEDLSLSEIAEELGISRQAVYDNIKRAEKKLEE 63 (101)
T ss_dssp HHHHHHHCTS---HHHHHHHCT--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 99999998879989999989698899999999999999999
No 31
>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=75.07 E-value=1.3 Score=20.43 Aligned_cols=35 Identities=26% Similarity=0.223 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999999998728103657999998577877899983
Q T0611 6 RDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F 45 (227)
+++||+.=.++ ....|+++||+.+|+|.-+..+|-
T Consensus 2 ke~Il~~i~~~-----~~p~~t~eiA~~~gls~~qaR~~L 36 (62)
T PF04703_consen 2 KEKILEYIKRQ-----NGPCSTREIAEALGLSIYQARYYL 36 (62)
T ss_dssp HHCHHHHHHHH--------B-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHC-----CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 28899999962-----799889999999698899999999
No 32
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding .
Probab=73.10 E-value=1.3 Score=20.57 Aligned_cols=39 Identities=18% Similarity=0.308 Sum_probs=34.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf 999999872810365799999857787789998344899
Q T0611 12 SSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSD 50 (227)
Q Consensus 12 aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~ 50 (227)
..++..+..++.|.+-.++++..|+.+.+++|+.+.=++
T Consensus 6 ~lLe~Ia~~r~~Gi~q~dL~k~~~~D~r~~~~~~k~L~~ 44 (75)
T PF04182_consen 6 CLLERIARSRYNGITQSDLWKLFGQDPRSVFYRVKKLED 44 (75)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 999999967768820537799858992256899999977
No 33
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 . The family also contains VirR like proteins which match only at the C terminus of the alignment.
Probab=71.28 E-value=1.8 Score=19.47 Aligned_cols=33 Identities=15% Similarity=0.379 Sum_probs=27.0
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf 810365799999857787789998344899999
Q T0611 21 GERNITTNHIAAHLAISPGNLYYHFRNKSDIIY 53 (227)
Q Consensus 21 G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~ 53 (227)
--+.+|+.++|+...||++|+++..+.=...+.
T Consensus 27 ~~~~~~~~~la~~l~vS~sTi~~~lk~i~~~L~ 59 (87)
T PF05043_consen 27 NNEYVSIEDLAEELYVSRSTIYRDLKKINQILK 59 (87)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 489968999999979899999999999999999
No 34
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates , , . Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies . The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA . The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1ftz_A 1jgg_B 1hdd_D 1p7i_D 3hdd_B 2hot_A 1du0_B 2hdd_A 1enh_A 1ztr_A ....
Probab=70.10 E-value=1.6 Score=19.77 Aligned_cols=41 Identities=20% Similarity=0.225 Sum_probs=29.9
Q ss_pred HHHHHHHHHHCCC-CCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf 9999999987281-0365799999857787789998344899
Q T0611 10 LLSSLELFNDKGE-RNITTNHIAAHLAISPGNLYYHFRNKSD 50 (227)
Q Consensus 10 l~aA~~lf~e~G~-~~~t~~~IA~~aGvs~gtlY~~F~sKe~ 50 (227)
+..--+.|....| ..-.+..||...|++...|..+|.++..
T Consensus 12 ~~~Le~~f~~~~~P~~~~~~~La~~~~l~~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 12 LEILEEYFEKNPYPSEEEIEELAKELGLSEKQVKNWFQNRRA 53 (57)
T ss_dssp HHHHHHHHHHSSSCCHHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999998757565005565423343200455124998788
No 35
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 1xd7_A 1ylf_A.
Probab=69.39 E-value=2.5 Score=18.33 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 3779999999999998728103-6579999985778778999834
Q T0611 3 MKTRDKILLSSLELFNDKGERN-ITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 3 ~~TR~~Il~aA~~lf~e~G~~~-~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
.+++-..---++-.+..+.-.. +|+++||++.|+|+..+...+.
T Consensus 3 ls~~~~~ai~~L~~La~~~~~~~~t~~~IA~~~~i~~~~v~kil~ 47 (83)
T PF02082_consen 3 LSKRFDYAIRILIYLARQPDGKPVTSKEIAERLGISPSYVRKILQ 47 (83)
T ss_dssp --HHHHHHHHHHHHHHCSTTCC---HHHHHHHHTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 882788999999999809999849899999888909999999999
No 36
>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=69.10 E-value=1.2 Score=20.80 Aligned_cols=27 Identities=26% Similarity=0.364 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf 036579999985778778999834489
Q T0611 23 RNITTNHIAAHLAISPGNLYYHFRNKS 49 (227)
Q Consensus 23 ~~~t~~~IA~~aGvs~gtlY~~F~sKe 49 (227)
.+.|.++||+..|+|+.++|++..+=+
T Consensus 21 ~~~t~~eia~~~~i~~~~v~~~l~~L~ 47 (68)
T PF01978_consen 21 GGATASEIAEKLGISRSTVYRILKRLE 47 (68)
T ss_dssp S-EEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 995999999998909999999999999
No 37
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This family consists of several short bacterial and phage proteins, which are related to the Escherichia coli protein AlpA. AlpA suppresses two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light . Several of the sequences in this family are thought to be DNA-binding proteins.; PDB: 1z4h_A.
Probab=68.05 E-value=1 Score=21.37 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=20.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf 657999998577877899983448
Q T0611 25 ITTNHIAAHLAISPGNLYYHFRNK 48 (227)
Q Consensus 25 ~t~~~IA~~aGvs~gtlY~~F~sK 48 (227)
+++.++++..|+|+.|+|.+-+..
T Consensus 4 l~~~ev~~~lgvs~~t~y~~~~~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTLYRLIKDG 27 (51)
T ss_dssp E-HHHHHHH-----HHHHHHHH--
T ss_pred ECHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 249999999894999999997758
No 38
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA , , , , , . Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1r8d_B 1jbg_A 3hh0_C 3d6z_A 3d71_A 3d6y_A 1r8e_A 1exi_A 1exj_A 1q06_A ....
Probab=67.71 E-value=1.1 Score=20.93 Aligned_cols=20 Identities=30% Similarity=0.290 Sum_probs=17.5
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q ss_conf 57999998577877899983
Q T0611 26 TTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 26 t~~~IA~~aGvs~gtlY~~F 45 (227)
||.++|+.+|||..+|-+|=
T Consensus 1 ti~e~a~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 1 TIGEVAKLLGVSVRTLRYYE 20 (38)
T ss_dssp EHHHHHHHCT--HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 98999999896999999999
No 39
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This family consists of Firmicute RepL proteins which are involved in plasmid replication.; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=65.77 E-value=2.7 Score=18.08 Aligned_cols=40 Identities=23% Similarity=0.243 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9999999999987281036579999985778778999834
Q T0611 7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
-+||-.-++-....+.--.|-++||++.|+|++|++.-|+
T Consensus 58 ~~Vl~~ll~~~d~~N~v~~t~~~Ia~~lgiS~~Tv~r~iK 97 (165)
T PF05732_consen 58 FRVLMFLLENMDSDNAVVATQKEIAEELGISKPTVSRTIK 97 (165)
T ss_pred HHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999984377983987899999997988889999999
No 40
>PF03444 DUF293: Domain of unknown function; InterPro: IPR005104 This domain is always found N-terminal to a pair of cystathionine-beta-synthase (CBS) domains IPR000644 from INTERPRO. This region may be distantly related to the HrcA proteins of prokaryotes.
Probab=63.25 E-value=3.3 Score=17.50 Aligned_cols=46 Identities=22% Similarity=0.417 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHH
Q ss_conf 79999999999998728103657999998577877899983448999
Q T0611 5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDI 51 (227)
Q Consensus 5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~L 51 (227)
...+||.+-.+++.+.| .-+.-+.||+.+++|.+|+.+--.+=++|
T Consensus 5 rq~~IL~~lv~~Y~~~~-~PVgSk~ia~~l~~s~aTIRN~M~~Le~l 50 (78)
T PF03444_consen 5 RQREILKALVELYIETG-EPVGSKTIAEELDRSPATIRNEMADLEEL 50 (78)
T ss_pred HHHHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 99999999999999739-97766999998688908899999999987
No 41
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=58.95 E-value=2.3 Score=18.70 Aligned_cols=27 Identities=11% Similarity=0.208 Sum_probs=17.0
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 810365799999857787789998344
Q T0611 21 GERNITTNHIAAHLAISPGNLYYHFRN 47 (227)
Q Consensus 21 G~~~~t~~~IA~~aGvs~gtlY~~F~s 47 (227)
-|.+.|-.+=|..+|||++|+.+-..+
T Consensus 54 D~egl~QeeAA~~MgVSR~Tf~ril~~ 80 (106)
T PF02001_consen 54 DYEGLTQEEAAEQMGVSRQTFQRILKS 80 (106)
T ss_pred HHHCCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 881798999999849779999999999
No 42
>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=58.75 E-value=1.9 Score=19.29 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=24.8
Q ss_pred HHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf 872810365799999857787789998344899999
Q T0611 18 NDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIY 53 (227)
Q Consensus 18 ~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~ 53 (227)
...|+. |-.++|+.+|||++++.+.+..+..+=.
T Consensus 8 ~~~g~~--~~~elA~~LgIs~stvs~~~~~r~~~P~ 41 (66)
T PF07022_consen 8 EAYGIK--TDKELAEKLGISQSTVSHTWKKRNSIPF 41 (66)
T ss_dssp HH------SCHHHHCCTT--HHHHH-HHHH-----H
T ss_pred HHHCCC--CHHHHHHHHCCCHHHHHHHHHHCCCCCH
T ss_conf 996899--6999999919988885567641688989
No 43
>PF01527 Transposase_8: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 . More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2rn7_A 2jn6_A.
Probab=55.08 E-value=0.86 Score=21.88 Aligned_cols=24 Identities=29% Similarity=0.497 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 036579999985778778999834
Q T0611 23 RNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 23 ~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
.+.|+.+||.+.|||.++||+.-.
T Consensus 22 ~g~s~~~va~~~gI~~~tl~~W~~ 45 (76)
T PF01527_consen 22 EGRSVSEVAREYGISPSTLYRWVR 45 (76)
T ss_dssp H-HHHHHHCCC----HHHHHHHHH
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 799799999970533026669999
No 44
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences ,. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli . Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor . The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution ,. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as 'feelers' suitable for DNA or protein (invertase) recognition . Other proteins belonging to this subfamily include: Escherichia coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ojl_E 1fip_A 1etw_B 4fis_B 1fia_A 1etq_D 3fis_A 1f36_A 1ety_B 1etx_A ....
Probab=54.48 E-value=3 Score=17.83 Aligned_cols=22 Identities=27% Similarity=0.300 Sum_probs=18.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 3657999998577877899983
Q T0611 24 NITTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 24 ~~t~~~IA~~aGvs~gtlY~~F 45 (227)
+-++...|+.+|||+.+||+--
T Consensus 18 ~gn~~~aA~~Lgi~r~tL~~kl 39 (42)
T PF02954_consen 18 GGNISKAARLLGISRSTLYRKL 39 (42)
T ss_dssp TT-HHHHHHH----HHHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9989999999798999999999
No 45
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=53.77 E-value=4.6 Score=16.38 Aligned_cols=40 Identities=23% Similarity=0.298 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 799999999999987281036579999985778778999834
Q T0611 5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
-|+.|..-=+++..++|. .|++++.+.-|+|+-|+-.||.
T Consensus 9 eR~ei~~rIVElVR~~GR--iTi~ql~~~TG~sR~T~k~~lr 48 (127)
T PF06163_consen 9 EREEIKARIVELVREHGR--ITIRQLVKMTGASRNTAKKYLR 48 (127)
T ss_pred HHHHHHHHHHHHHHHHCH--HHHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999999999998163--0299999997867999999999
No 46
>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=50.14 E-value=5.2 Score=15.98 Aligned_cols=37 Identities=19% Similarity=0.205 Sum_probs=27.9
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf 999872810365799999857787789998344899999
Q T0611 15 ELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIY 53 (227)
Q Consensus 15 ~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~ 53 (227)
.++.+ -...|+.+||+..|+|..++-++...=.+.+.
T Consensus 12 ~~L~~--~~~~t~~ela~~l~~S~~ti~~~I~~l~~~f~ 48 (59)
T PF08280_consen 12 ELLLK--NGWITLKELAKKLGLSERTIRNDINELNEEFP 48 (59)
T ss_pred HHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 99997--79797999999979889999999999999863
No 47
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis . During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes . More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery .
Probab=49.80 E-value=3.5 Score=17.26 Aligned_cols=28 Identities=18% Similarity=0.316 Sum_probs=20.5
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHHH
Q ss_conf 9999999872810365799999857-7877899
Q T0611 11 LSSLELFNDKGERNITTNHIAAHLA-ISPGNLY 42 (227)
Q Consensus 11 ~aA~~lf~e~G~~~~t~~~IA~~aG-vs~gtlY 42 (227)
+...+|+. +|.|-.+||+++| ||+.++-
T Consensus 9 e~Lk~lw~----eGlSasqIA~~LGgvsRNAVi 37 (162)
T PF07750_consen 9 ERLKKLWA----EGLSASQIAKQLGGVSRNAVI 37 (162)
T ss_pred HHHHHHHH----CCCCHHHHHHHHCCCCHHHHH
T ss_conf 99999998----588899999997552066677
No 48
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles , and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including herpesvirus saimiri and Kaposi's sarcoma-associated herpesvirus. These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus . In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognized by RNA polymerase II , . TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB . This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex , .; GO: 0003700 transcription factor activity, 0005515 protein binding, 0006350 transcription, 0005634 nucleus; PDB: 1c9b_M 2phg_A 1vol_A 1tfb_A 1ais_B 1d3u_B.
Probab=48.61 E-value=5.5 Score=15.81 Aligned_cols=21 Identities=14% Similarity=0.491 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHCCCCCCCH
Q ss_conf 999999999998659888993
Q T0611 123 LAAINRIFAKLADAGIIQPQP 143 (227)
Q Consensus 123 ~~~~~~~l~~~i~~G~l~~~~ 143 (227)
.+....+++.+.+.|.+++-.
T Consensus 15 ~~~A~~i~~~~~~~~~~~Gr~ 35 (71)
T PF00382_consen 15 IETAKEIYKKAVEKGLLKGRS 35 (71)
T ss_dssp HHHHHHHHHHHHHCTT-----
T ss_pred HHHHHHHHHHHHHCCCCCCCC
T ss_conf 999999999998768757998
No 49
>PF04036 DUF372: Domain of unknown function (DUF372); InterPro: IPR007179 This is a group of proteins of unknown function. It is found N-terminal to another domain of unknown function, DUF381 (IPR007181 from INTERPRO).; PDB: 2i52_B 2ogf_B 2iec_D.
Probab=47.36 E-value=2.4 Score=18.53 Aligned_cols=17 Identities=29% Similarity=0.428 Sum_probs=13.8
Q ss_pred HHHHCCCHHHHHHHHCC
Q ss_conf 99857787789998344
Q T0611 31 AAHLAISPGNLYYHFRN 47 (227)
Q Consensus 31 A~~aGvs~gtlY~~F~s 47 (227)
.=++||+-|+|||-|-+
T Consensus 4 ~FEaGIklGalyHQf~G 20 (38)
T PF04036_consen 4 VFEAGIKLGALYHQFVG 20 (38)
T ss_dssp HHH-------HHHHH--
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 76500257578886517
No 50
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316)
Probab=46.12 E-value=6 Score=15.54 Aligned_cols=44 Identities=18% Similarity=0.188 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf 79999999999998728103657999998577877899983448
Q T0611 5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNK 48 (227)
Q Consensus 5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK 48 (227)
|++++-.++.+|=+..-..+.|..+||+.+|+|..-+=+-+.=|
T Consensus 4 n~~e~~~T~~ELqanf~l~~Ls~~~ia~dL~~s~~~ve~vL~l~ 47 (89)
T PF10078_consen 4 NKEERKATRKELQANFELSGLSIEQIAKDLGTSPEKVEQVLNLK 47 (89)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 89999976999999999849999999999689999999898604
No 51
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria . They modulate transcription in response to changes in cellular NADH/NAD^(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0016564 transcription repressor activity, 0006980 redox signal response, 0016481 negative regulation of transcription, 0005737 cytoplasm; PDB: 1xcb_F 2dt5_A 2vt3_A 2vt2_B.
Probab=45.81 E-value=4.1 Score=16.75 Aligned_cols=37 Identities=22% Similarity=0.468 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999998728103657999998577877899983
Q T0611 9 ILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 9 Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F 45 (227)
+---.++.+.+.|...+|-.+||+.+||+...+-.=|
T Consensus 13 ~Y~r~L~~l~~~g~~~iSS~eLa~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 13 LYLRYLKQLQEEGVERISSKELAEALGITPSQVRKDL 49 (50)
T ss_dssp HHHHHHHHHHH----B--TTTHHHCCSS-HHHHHHHH
T ss_pred HHHHHHHHHHHCCCEEECHHHHHHHHCCCHHHHHCCC
T ss_conf 9999999999859945879999999797999961225
No 52
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 , . Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif . Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2p7v_B 1tlh_B 1tty_A 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F 2a69_F ....
Probab=44.85 E-value=1.2 Score=20.73 Aligned_cols=25 Identities=24% Similarity=0.231 Sum_probs=21.3
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 8103657999998577877899983
Q T0611 21 GERNITTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 21 G~~~~t~~~IA~~aGvs~gtlY~~F 45 (227)
=|++.|..+||+..|+|.+++....
T Consensus 17 ~~~~~t~~eIa~~lg~s~~~V~~~~ 41 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISESTVRQRL 41 (50)
T ss_dssp HTST-CTCCCHHHHHHHHHHHHHHH
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 8499999999989797999998999
No 53
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins .; PDB: 2o9l_A 2ahq_A 2o8k_A.
Probab=44.47 E-value=1.9 Score=19.30 Aligned_cols=41 Identities=20% Similarity=0.260 Sum_probs=30.4
Q ss_pred HHHHHHHHHH--HCCCCCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf 9999999998--7281036579999985778778999834489
Q T0611 9 ILLSSLELFN--DKGERNITTNHIAAHLAISPGNLYYHFRNKS 49 (227)
Q Consensus 9 Il~aA~~lf~--e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe 49 (227)
|++-=.+-|. .....-.||.+||+++|++.+|+-+--.+|.
T Consensus 32 Iv~~Q~~Ff~~g~~~l~Pltl~~vA~~lglheSTVSRav~~Ky 74 (160)
T PF04552_consen 32 IVERQEDFFLEGPKALKPLTLKDVAEELGLHESTVSRAVSNKY 74 (160)
T ss_dssp -------------------------------------------
T ss_pred HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCCE
T ss_conf 9999999985585357685499999983988305779874853
No 54
>PF01047 MarR: MarR family; InterPro: IPR000835 The marR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the marR/slyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli marR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds , , . The crystal structures of marR, mexR and slyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerization. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerization, as most marR-like transcription regulators form dimers , . ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3bj6_A 2fbi_A 3e6m_E 3cjn_A 3cdh_A 2fxa_B 2fa5_B 1lnw_B 3ech_A 1jgs_A ....
Probab=44.21 E-value=6.4 Score=15.34 Aligned_cols=30 Identities=17% Similarity=0.321 Sum_probs=22.1
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99987281036579999985778778999834
Q T0611 15 ELFNDKGERNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 15 ~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
..+.+.| +.|+.+||+.+|++++++.....
T Consensus 10 ~~l~~~~--~~t~~~la~~l~~~~~~vs~~i~ 39 (59)
T PF01047_consen 10 RILYENP--GMTQSELAERLGISKSTVSRIIK 39 (59)
T ss_dssp HHHHHSS--SEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHCC--CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999879--98999999998868738999999
No 55
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=40.20 E-value=5 Score=16.14 Aligned_cols=29 Identities=14% Similarity=0.039 Sum_probs=22.9
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCHHHHHHH
Q ss_conf 57999998577877899983448999999
Q T0611 26 TTNHIAAHLAISPGNLYYHFRNKSDIIYE 54 (227)
Q Consensus 26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~a 54 (227)
.|.++|..++++++|+-.|-.+|++=-.+
T Consensus 18 N~teVaR~L~c~R~TVrkY~~D~~g~~Ha 46 (64)
T PF06322_consen 18 NQTEVARMLNCYRATVRKYARDKEGKKHA 46 (64)
T ss_pred CHHHHHHHHCCHHHHHHHHHCCCCCCEEE
T ss_conf 68988788510188799772255662478
No 56
>PF08667 BetR: BetR domain; InterPro: IPR013975 This entry includes an N-terminal helix-turn-helix domain.
Probab=39.34 E-value=7.5 Score=14.82 Aligned_cols=46 Identities=22% Similarity=0.211 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHCCCCC-CCHHHHHHHHCCCHHHHHHHHCCHHHH
Q ss_conf 9999999999998728103-657999998577877899983448999
Q T0611 6 RDKILLSSLELFNDKGERN-ITTNHIAAHLAISPGNLYYHFRNKSDI 51 (227)
Q Consensus 6 R~~Il~aA~~lf~e~G~~~-~t~~~IA~~aGvs~gtlY~~F~sKe~L 51 (227)
.+.|.+--.+++..+|+.. =...+|++-+|+|+++.|+-..+|-..
T Consensus 3 ~~~~~~rvr~ll~~~GI~kr~~~~~La~iL~Is~saa~RKL~G~~~f 49 (147)
T PF08667_consen 3 DQAIAERVRELLDRHGIPKRQHNTELADILGISKSAASRKLNGKSPF 49 (147)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCC
T ss_conf 48999999999997499820138999998788999985873799997
No 57
>PF03690 UPF0160: Uncharacterised protein family (UPF0160); InterPro: IPR003226 The function of this domain is not known, but it is found in several uncharacterised proteins and a probable metal dependent protein hydrolase.
Probab=39.18 E-value=7.5 Score=14.80 Aligned_cols=40 Identities=18% Similarity=0.203 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCH-----------HHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 7877899983448-----------999999999999999998752217998
Q T0611 36 ISPGNLYYHFRNK-----------SDIIYEIFQEYEKLVDYYLDIPEDRPI 75 (227)
Q Consensus 36 vs~gtlY~~F~sK-----------e~Ll~av~~~~~~~~~~~~~~~~~~~~ 75 (227)
-|-|.||.||+.+ ++.+..+...+...+.+.++..+++..
T Consensus 81 SSAGLVykhfG~~ii~~~~~~~~~~~~~~~l~~k~y~~fi~~iDaiDNGv~ 131 (318)
T PF03690_consen 81 SSAGLVYKHFGREIIANILGLPVDEEDVDLLYDKVYKSFIEPIDAIDNGVS 131 (318)
T ss_pred ECHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 013369999879999987434798799999999999887432152017965
No 58
>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=39.07 E-value=7.6 Score=14.79 Aligned_cols=39 Identities=5% Similarity=0.039 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHCCC---CCC-CHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999999987281---036-57999998577877899983
Q T0611 7 DKILLSSLELFNDKGE---RNI-TTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 7 ~~Il~aA~~lf~e~G~---~~~-t~~~IA~~aGvs~gtlY~~F 45 (227)
++|.+.=.+.+....+ +.. |.+++|++.|||+.++..-+
T Consensus 3 ~~v~~~i~~~I~~g~l~~G~~lPs~~~La~~~~vSr~tvr~Al 45 (64)
T PF00392_consen 3 EQVYEYIRRDILSGELKPGDRLPSERELAERFGVSRTTVREAL 45 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999999984999999993689999988687989999999
No 59
>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=35.31 E-value=8.6 Score=14.37 Aligned_cols=16 Identities=25% Similarity=0.598 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHCCCCC
Q ss_conf 9999999998659888
Q T0611 125 AINRIFAKLADAGIIQ 140 (227)
Q Consensus 125 ~~~~~l~~~i~~G~l~ 140 (227)
.+...++.+.+.|.|-
T Consensus 81 ~v~~a~~~L~~eG~IY 96 (102)
T PF08784_consen 81 EVRKAIDELSDEGLIY 96 (102)
T ss_dssp HHHHHHHHHHH---EE
T ss_pred HHHHHHHHHHHCCEEE
T ss_conf 9999999998598472
No 60
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 1tty_A 1rp3_G 1sc5_A 1l0o_C 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F ....
Probab=35.23 E-value=8.6 Score=14.36 Aligned_cols=38 Identities=29% Similarity=0.284 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999999998728103657999998577877899983
Q T0611 7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F 45 (227)
.+|-.|..+|..+.|-. -|..+||+.+|+|..-++...
T Consensus 4 ~ki~~a~~~L~~~lgR~-Pt~eEIA~~lgis~~~v~~~~ 41 (78)
T PF04539_consen 4 NKIKKAKRELEQELGRE-PTEEEIAEELGISEEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHC------BHHHHHHH----HHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999999995889-899999999788899999999
No 61
>PF01498 Transposase_5: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in . Tc3 is a member of the Tc1/mariner family of transposable elements. More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration, 0005634 nucleus; PDB: 3f2k_B 1u78_A.
Probab=34.47 E-value=8.5 Score=14.40 Aligned_cols=21 Identities=24% Similarity=0.357 Sum_probs=13.4
Q ss_pred CCHHHHHHHH-----CCCHHHHHHHH
Q ss_conf 6579999985-----77877899983
Q T0611 25 ITTNHIAAHL-----AISPGNLYYHF 45 (227)
Q Consensus 25 ~t~~~IA~~a-----Gvs~gtlY~~F 45 (227)
.|..+|+.++ +||+.|+.+.+
T Consensus 14 ~T~~~l~~~l~~~~~~vS~~Tv~R~L 39 (72)
T PF01498_consen 14 ITLRELARELQEEGISVSKSTVRRRL 39 (72)
T ss_dssp --HHHHHHHT---T--S-HHHHHHHH
T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 24999999998658997999999999
No 62
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon . This domain includes the DNA-binding HTH motif . ; PDB: 1r71_B.
Probab=33.34 E-value=8 Score=14.59 Aligned_cols=24 Identities=29% Similarity=0.308 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 036579999985778778999834
Q T0611 23 RNITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 23 ~~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
.|.|-.+||+++|-|+..+-+|-.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~L~ 25 (93)
T PF08535_consen 2 FGLTQEEIAKRLGKSRSWVSNHLR 25 (93)
T ss_dssp -------HHHH----HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 899999999998879999999999
No 63
>PF06230 DUF1009: Protein of unknown function (DUF1009); InterPro: IPR010415 This is a family of uncharacterised bacterial proteins.
Probab=31.27 E-value=9.9 Score=13.91 Aligned_cols=49 Identities=18% Similarity=0.203 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHHH
Q ss_conf 9999999999987281036579999985778778999834489999999
Q T0611 7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEI 55 (227)
Q Consensus 7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av 55 (227)
+.||.+-.+.|.++||.=++-.+++...=...|.+...=+|+++.-...
T Consensus 52 d~lL~ai~~~~E~~G~~vv~a~~~~p~ll~~~G~lt~~~P~~~~~~Di~ 100 (214)
T PF06230_consen 52 DALLRAIIDEFEEEGFEVVGAHEILPELLAPEGVLTGRKPSKEERADIA 100 (214)
T ss_pred HHHHHHHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCCCHHHHHHHH
T ss_conf 9999999999997799997178953874689876679996988999999
No 64
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases .
Probab=30.87 E-value=10 Score=13.87 Aligned_cols=20 Identities=20% Similarity=0.107 Sum_probs=16.4
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 65799999857787789998
Q T0611 25 ITTNHIAAHLAISPGNLYYH 44 (227)
Q Consensus 25 ~t~~~IA~~aGvs~gtlY~~ 44 (227)
-|+++-|+.+|+|+++|-+|
T Consensus 17 ~Si~eAa~~l~~~~~tI~~~ 36 (37)
T PF07453_consen 17 SSIREAARALNISHSTISKY 36 (37)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 48999999809987789875
No 65
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers . This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0003715 transcription termination factor activity, 0006353 transcription termination; PDB: 1pvo_F 1xpo_C 2a8v_B 1pv4_D 1a62_A 1a8v_A 1xpr_C 1xpu_D 1a63_A 2ht1_B ....
Probab=29.95 E-value=8.9 Score=14.25 Aligned_cols=30 Identities=27% Similarity=0.442 Sum_probs=20.9
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 5799999857787789998344899999999999
Q T0611 26 TTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEY 59 (227)
Q Consensus 26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av~~~~ 59 (227)
-+++||++.||+ .+.=-.|++|+.++++..
T Consensus 9 eL~~iA~elgI~----~~s~mrK~eLI~~Il~~q 38 (43)
T PF07498_consen 9 ELREIAKELGIE----NYSKMRKQELIFAILKAQ 38 (43)
T ss_dssp HHHH------------SGTTS-HHHHHHHHHHHT
T ss_pred HHHHHHHHCCCC----CCCCCCHHHHHHHHHHHH
T ss_conf 999999995998----856478999999999999
No 66
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=28.85 E-value=11 Score=13.63 Aligned_cols=37 Identities=27% Similarity=0.394 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf 9737799999999999987281036579999985778
Q T0611 1 MTMKTRDKILLSSLELFNDKGERNITTNHIAAHLAIS 37 (227)
Q Consensus 1 ~~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs 37 (227)
|+-+.|+.|++--.+-|.+.|-+|-|=++|.+++|=.
T Consensus 17 Lp~~e~~dil~~Y~eyf~e~~~~G~sEeeii~~LG~P 53 (181)
T PF08006_consen 17 LPEEEREDILEYYEEYFDEGGEEGKSEEEIIAELGSP 53 (181)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCH
T ss_conf 9999999999999999998756899999999782999
No 67
>PF09862 DUF2089: Protein of unknown function(DUF2089)
Probab=27.62 E-value=11 Score=13.48 Aligned_cols=18 Identities=22% Similarity=0.205 Sum_probs=7.2
Q ss_pred CHHHHHHHHCCCHHHHHH
Q ss_conf 579999985778778999
Q T0611 26 TTNHIAAHLAISPGNLYY 43 (227)
Q Consensus 26 t~~~IA~~aGvs~gtlY~ 43 (227)
++.++|+..|||-.|+-+
T Consensus 51 nlKe~ak~lgiSYpTvR~ 68 (113)
T PF09862_consen 51 NLKEVAKELGISYPTVRN 68 (113)
T ss_pred CHHHHHHHHCCCHHHHHH
T ss_conf 899999997888289999
No 68
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme . The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation; PDB: 2k9l_A 2k9m_A.
Probab=24.54 E-value=8.5 Score=14.41 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 99999999998728103657999998577877
Q T0611 8 KILLSSLELFNDKGERNITTNHIAAHLAISPG 39 (227)
Q Consensus 8 ~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~g 39 (227)
.|...=+....++||=..++.+||+..|++..
T Consensus 36 ~ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~ 67 (195)
T PF04963_consen 36 EIAEYIIDNLDDDGYLRESLEEIAEELGVSEE 67 (195)
T ss_dssp HHHHHHCCCBTT---BSS-HHHHHHHCTS-HH
T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHH
T ss_conf 99999998279999889999999978198999
No 69
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry consists of a bacterial protein which is uncharacterised.
Probab=24.37 E-value=13 Score=13.06 Aligned_cols=24 Identities=13% Similarity=0.029 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 103657999998577877899983
Q T0611 22 ERNITTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 22 ~~~~t~~~IA~~aGvs~gtlY~~F 45 (227)
|++.|+..+|..+|||-+|.-++=
T Consensus 17 ~~~~~Le~aA~~~gVs~~TArrWK 40 (165)
T PF08822_consen 17 FDRLSLEEAAKKAGVSYGTARRWK 40 (165)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 768989999989299888899999
No 70
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=24.32 E-value=13 Score=13.05 Aligned_cols=17 Identities=24% Similarity=0.255 Sum_probs=11.0
Q ss_pred HCCCHHHHHHHHHHHHH
Q ss_conf 21898899999999998
Q T0611 195 PYLTPEYRERVLALREK 211 (227)
Q Consensus 195 p~lt~~~~~~l~~l~~~ 211 (227)
+..|++|+..+..+...
T Consensus 91 ~~vT~kG~~~i~~~l~~ 107 (111)
T PF03374_consen 91 TRVTPKGQEWIAEKLKK 107 (111)
T ss_pred EEEEHHHHHHHHHHHHH
T ss_conf 89901579999999985
No 71
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA .; PDB: 1j9i_B.
Probab=23.75 E-value=13 Score=12.98 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 36579999985778778999834
Q T0611 24 NITTNHIAAHLAISPGNLYYHFR 46 (227)
Q Consensus 24 ~~t~~~IA~~aGvs~gtlY~~F~ 46 (227)
.++-.++|+..|||+.||..+-.
T Consensus 2 ~vnk~~lA~~~gVS~~ti~~W~~ 24 (164)
T PF07471_consen 2 EVNKKQLAEILGVSERTITKWQR 24 (164)
T ss_dssp EEEHHHHHHH----HHHHHHHTT
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 66899999997989999999998
No 72
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms . Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1nd9_A.
Probab=23.35 E-value=13 Score=12.92 Aligned_cols=23 Identities=17% Similarity=0.317 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 03657999998577877899983
Q T0611 23 RNITTNHIAAHLAISPGNLYYHF 45 (227)
Q Consensus 23 ~~~t~~~IA~~aGvs~gtlY~~F 45 (227)
..+|+.++|+++|++...|-...
T Consensus 2 ~~~rV~elAk~l~~~~~~ii~~L 24 (54)
T PF04760_consen 2 EKIRVYELAKELGVSSKEIIKKL 24 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH
T ss_pred CCEEHHHHHHHHCCCHHHHHHHH
T ss_conf 95369999999892999999999
No 73
>PF11849 DUF3369: Domain of unknown function (DUF3369)
Probab=22.70 E-value=11 Score=13.69 Aligned_cols=37 Identities=24% Similarity=0.416 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHCCCCCC---CHHHHHHHHCCCHHHHHH
Q ss_conf 9999999999987281036---579999985778778999
Q T0611 7 DKILLSSLELFNDKGERNI---TTNHIAAHLAISPGNLYY 43 (227)
Q Consensus 7 ~~Il~aA~~lf~e~G~~~~---t~~~IA~~aGvs~gtlY~ 43 (227)
++||+++..+|..+..+.. -+..|+.-.|++...+|-
T Consensus 22 e~Ii~as~~l~~~~sl~~fa~gVL~Ql~~Ll~~~~~~l~~ 61 (174)
T PF11849_consen 22 EKIIDASANLFQLQSLQEFASGVLTQLASLLNLPSSGLYC 61 (174)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 9999988988633789999999999999995899870898
No 74
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI , , , , . The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ixc_B 1iz1_Q 2esn_D 1o7l_B 1b9n_A 1b9m_B 3fzv_B.
Probab=20.37 E-value=15 Score=12.50 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=22.5
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHH
Q ss_conf 99987281036579999985778778999834489999
Q T0611 15 ELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDII 52 (227)
Q Consensus 15 ~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll 52 (227)
..+.+.| |+..-|+.+|+|.+++.++-+.-|+-+
T Consensus 8 ~~l~~~g----s~~~AA~~l~~s~~~vs~~i~~LE~~l 41 (60)
T PF00126_consen 8 VALAETG----SFSRAAEQLGISQSAVSRRIKRLEEEL 41 (60)
T ss_dssp HHHHHHS-----HHHHHHHHTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHC----CHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 9999979----999999870899538999999999982
No 75
>PF04269 DUF440: Protein of unknown function, DUF440; InterPro: IPR007376 This entry represents hypothetical proteins such as HI1450 (DUF440), which is believed to act as a putative dsDNA mimic. HI1450 is an acidic protein with a core structure consisting of alpha(2)-beta(4), where the alpha-helices are packed against the side of an anti-parallel 4-stranded beta meander. As such, it has some similarity to the dsDNA mimics uracil-DNA glycosylase inhibitor and nuclease A inhibitor (NuiA), including the distribution of surface charges and the position of the hydrophobic cavity . DNA mimics act to inhibit or regulate dsDNA-binding proteins. ; PDB: 1nnv_A.
Probab=20.27 E-value=15 Score=12.49 Aligned_cols=31 Identities=19% Similarity=0.359 Sum_probs=21.9
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf 9737799999999999987281036579999
Q T0611 1 MTMKTRDKILLSSLELFNDKGERNITTNHIA 31 (227)
Q Consensus 1 ~~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA 31 (227)
|-+.|-+.+++.|-++|.|.--++..-.+|.
T Consensus 1 ~~~~t~de~id~AYDiFLE~A~dNL~paDi~ 31 (103)
T PF04269_consen 1 MNLITEDEAIDQAYDIFLELAPDNLEPADII 31 (103)
T ss_dssp -----HHHHHHHHHHHHHHH----S-HHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf 9858888999999999998625319999999
Done!