Query T0575 YP_001636308.1, CHLOROFLEXUS AURANTIACUS, 216 residues
Match_columns 216
No_of_seqs 285 out of 18403
Neff 11.4
Searched_HMMs 11830
Date Fri Jun 4 14:57:58 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0575.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0575.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00440 TetR_N: Bacterial reg 99.0 2.3E-10 1.9E-14 96.2 5.8 47 17-63 1-47 (47)
2 PF08359 TetR_C_4: YsiA-like p 98.3 7.5E-06 6.4E-10 61.2 11.6 114 66-180 3-116 (133)
3 PF08362 TetR_C_3: YcdC-like p 98.1 6E-05 5.1E-09 54.2 12.9 141 66-216 3-143 (143)
4 PF08361 TetR_C_2: MAATS-type 97.5 0.0044 3.7E-07 39.8 14.6 97 85-181 1-102 (121)
5 PF08360 TetR_C_5: QacR-like p 97.3 0.003 2.6E-07 41.0 12.0 116 81-215 14-131 (131)
6 PF09209 DUF1956: Domain of un 94.8 0.12 9.8E-06 28.8 9.0 118 86-213 1-125 (125)
7 PF02796 HTH_7: Helix-turn-hel 93.7 0.018 1.5E-06 35.0 2.9 34 18-55 11-44 (45)
8 PF01726 LexA_DNA_bind: LexA D 93.0 0.045 3.8E-06 31.9 4.1 43 12-55 6-49 (65)
9 PF04967 HTH_10: HTH DNA bindi 91.7 0.057 4.8E-06 31.2 3.2 41 12-56 3-47 (53)
10 PF00356 LacI: Bacterial regul 90.9 0.039 3.3E-06 32.5 1.8 30 34-63 1-30 (46)
11 PF08279 HTH_11: HTH domain; 89.6 0.12 1E-05 28.6 3.5 39 14-57 2-40 (55)
12 PF06056 Terminase_5: Putative 86.9 0.26 2.2E-05 26.1 3.7 32 18-53 3-34 (58)
13 PF03811 Ins_element1: Inserti 86.2 0.32 2.7E-05 25.3 3.9 38 10-55 49-86 (88)
14 PF06163 DUF977: Bacterial pro 85.2 0.65 5.5E-05 23.0 5.0 49 1-55 1-49 (127)
15 PF10668 Phage_terminase: Phag 83.9 0.44 3.7E-05 24.3 3.7 46 1-57 1-46 (60)
16 PF03444 DUF293: Domain of unk 83.5 0.49 4.2E-05 23.9 3.8 46 12-58 4-49 (78)
17 PF01022 HTH_5: Bacterial regu 83.4 0.43 3.6E-05 24.4 3.4 38 12-56 2-39 (47)
18 PF10654 DUF2481: Protein of u 82.3 0.54 4.6E-05 23.6 3.6 42 19-60 67-109 (126)
19 PF01710 Transposase_14: Trans 81.9 0.69 5.8E-05 22.8 4.0 42 9-59 3-44 (119)
20 PF09339 HTH_IclR: IclR helix- 81.3 0.21 1.8E-05 26.8 1.2 33 23-56 10-42 (52)
21 PF12116 SpoIIID: Stage III sp 78.5 0.96 8.1E-05 21.7 3.9 37 13-53 4-40 (82)
22 PF05225 HTH_psq: helix-turn-h 77.8 0.51 4.3E-05 23.8 2.3 39 16-57 3-41 (45)
23 PF00292 PAX: 'Paired box' dom 77.2 0.99 8.4E-05 21.6 3.6 36 8-51 17-52 (125)
24 PF07638 Sigma70_ECF: ECF sigm 76.4 0.71 6E-05 22.7 2.7 11 63-73 22-32 (185)
25 PF01325 Fe_dep_repress: Iron 76.2 1.5 0.00013 20.2 4.3 39 12-52 4-42 (60)
26 PF04218 CENP-B_N: CENP-B N-te 76.2 1.7 0.00015 19.7 4.6 32 27-61 20-51 (53)
27 PF00165 HTH_AraC: Bacterial r 75.0 0.51 4.3E-05 23.8 1.7 29 28-56 4-32 (42)
28 PF08220 HTH_DeoR: DeoR-like h 73.7 1.1 9E-05 21.3 3.0 34 22-57 6-39 (57)
29 PF08281 Sigma70_r4_2: Sigma-7 69.6 0.74 6.3E-05 22.5 1.5 31 23-53 17-47 (54)
30 PF01381 HTH_3: Helix-turn-hel 69.4 0.65 5.5E-05 23.0 1.2 34 31-64 8-41 (55)
31 PF04297 UPF0122: Putative hel 69.4 1.2 0.0001 20.9 2.5 39 23-61 24-62 (101)
32 PF04703 FaeA: FaeA-like prote 69.1 1.5 0.00013 20.1 3.0 35 14-53 2-36 (62)
33 PF01978 TrmB: Sugar-specific 68.6 1.6 0.00013 20.0 3.0 30 26-57 18-47 (68)
34 PF01418 HTH_6: Helix-turn-hel 67.7 0.88 7.5E-05 22.0 1.5 37 15-53 19-55 (107)
35 PF11740 KfrA_N: Plasmid repli 66.3 2.3 0.0002 18.7 3.4 39 13-53 2-41 (120)
36 PF00196 GerE: Bacterial regul 66.1 1.1 9.7E-05 21.1 1.9 25 31-55 17-41 (58)
37 PF01527 Transposase_8: Transp 65.6 0.79 6.7E-05 22.3 1.0 36 10-52 8-43 (76)
38 PF05930 Phage_AlpA: Prophage 65.1 0.94 7.9E-05 21.8 1.2 22 33-54 4-25 (51)
39 PF00376 MerR: MerR family reg 63.8 1.1 9.1E-05 21.3 1.4 19 34-52 1-19 (38)
40 PF04182 B-block_TFIIIC: B-blo 61.7 2.4 0.0002 18.7 2.8 39 20-58 6-44 (75)
41 PF02954 HTH_8: Bacterial regu 60.6 3.6 0.00031 17.2 4.1 33 14-52 6-38 (42)
42 PF05043 Mga: Mga helix-turn-h 60.1 2 0.00017 19.2 2.2 31 31-61 29-59 (87)
43 PF05732 RepL: Firmicute plasm 59.1 2.4 0.0002 18.6 2.5 46 12-57 55-100 (165)
44 PF00392 GntR: Bacterial regul 56.4 4.2 0.00036 16.7 4.1 38 15-52 3-44 (64)
45 PF00046 Homeobox: Homeobox do 55.4 2.1 0.00018 19.0 1.6 43 13-57 10-52 (57)
46 PF08280 HTH_Mga: M protein tr 54.3 4 0.00034 16.9 2.9 43 12-60 5-47 (59)
47 PF02042 RWP-RK: RWP-RK domain 53.6 3.4 0.00028 17.5 2.5 26 17-46 18-43 (52)
48 PF08822 DUF1804: Protein of u 53.3 4.7 0.0004 16.3 14.8 37 10-53 4-40 (165)
49 PF04539 Sigma70_r3: Sigma-70 51.1 5.1 0.00043 16.1 4.0 40 12-52 1-40 (78)
50 PF04552 Sigma54_DBD: Sigma-54 50.7 1.3 0.00011 20.6 0.0 48 11-58 19-75 (160)
51 PF04545 Sigma70_r4: Sigma-70, 48.5 1.7 0.00014 19.8 0.3 23 30-52 18-40 (50)
52 PF07022 Phage_CI_repr: Bacter 48.5 3.7 0.00031 17.1 2.0 36 23-60 5-40 (66)
53 PF01257 Complex1_24kDa: Respi 47.4 3.5 0.0003 17.3 1.8 44 13-56 11-61 (145)
54 PF01371 Trp_repressor: Trp re 46.2 3.4 0.00029 17.4 1.5 20 32-51 49-68 (87)
55 PF02001 DUF134: Protein of un 45.6 3.3 0.00028 17.5 1.4 30 26-55 51-80 (106)
56 PF08006 DUF1700: Protein of u 45.5 6.1 0.00051 15.5 4.0 39 8-46 16-54 (181)
57 PF06322 Phage_NinH: Phage Nin 44.1 3.2 0.00027 17.6 1.1 26 34-59 18-43 (64)
58 PF06971 Put_DNA-bind_N: Putat 40.0 6.4 0.00054 15.3 2.1 40 13-52 9-48 (50)
59 PF00382 TFIIB: Transcription 38.4 7.7 0.00065 14.7 3.6 32 17-49 39-71 (71)
60 PF07750 GcrA: GcrA cell cycle 38.3 6.4 0.00054 15.3 1.9 20 31-50 17-37 (162)
61 PF04036 DUF372: Domain of unk 36.4 2.8 0.00024 18.0 -0.1 17 38-54 3-19 (38)
62 PF01047 MarR: MarR family; I 35.2 8.5 0.00072 14.3 3.3 30 22-53 9-38 (59)
63 PF10975 DUF2802: Protein of u 33.8 8.1 0.00069 14.5 1.9 15 33-47 45-59 (70)
64 PF10078 DUF2316: Uncharacteri 32.1 9.5 0.0008 14.0 3.5 39 18-56 9-47 (89)
65 PF02082 Rrf2: Transcriptional 31.1 9.8 0.00083 13.8 3.9 28 26-53 18-46 (83)
66 PF04963 Sigma54_CBD: Sigma-54 26.9 7.2 0.00061 14.9 0.6 35 13-47 33-67 (195)
67 PF08535 KorB: KorB domain; I 25.9 8.9 0.00075 14.2 1.0 23 32-54 3-25 (93)
68 PF07453 NUMOD1: NUMOD1 domain 25.0 12 0.001 13.1 1.9 20 33-52 17-36 (37)
69 PF07900 DUF1670: Protein of u 24.4 13 0.0011 13.0 4.1 27 26-53 100-126 (220)
70 PF01498 Transposase_5: Transp 24.0 12 0.001 13.2 1.3 21 33-53 14-39 (72)
71 PF02909 TetR_C: Tetracyclin r 23.5 13 0.0011 12.9 12.4 118 82-216 4-138 (139)
72 PF04760 IF2_N: Translation in 22.2 13 0.0011 12.9 1.2 21 31-51 2-22 (54)
73 PF00325 Crp: Bacterial regula 22.1 14 0.0012 12.7 1.6 22 32-53 2-23 (32)
74 PF08784 RPA_C: Replication pr 22.0 14 0.0012 12.7 3.1 13 32-44 65-77 (102)
75 PF06230 DUF1009: Protein of u 21.9 14 0.0012 12.7 5.6 51 15-65 52-102 (214)
76 PF01475 FUR: Ferric uptake re 21.9 14 0.0012 12.7 3.1 35 13-52 9-48 (120)
77 PF09012 FeoC: FeoC like trans 21.6 14 0.0012 12.6 2.4 17 32-48 14-30 (69)
78 PF03374 ANT: Phage antirepres 20.9 15 0.0012 12.5 2.9 36 19-56 13-48 (111)
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=98.99 E-value=2.3e-10 Score=96.21 Aligned_cols=47 Identities=36% Similarity=0.722 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHHHHHHH
Q ss_conf 99999999987491035479999984778545540268888999999
Q T0575 17 LIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKDCYLYL 63 (216)
Q Consensus 17 Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~L~~~~ 63 (216)
|+++|.++|.++||+++|+++||+++|+|+++||+||+||++|+.++
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
>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=98.27 E-value=7.5e-06 Score=61.19 Aligned_cols=114 Identities=21% Similarity=0.247 Sum_probs=88.7
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999998752155664689999999999999870808999999998616404899999999999999999999998
Q T0575 66 LGIEQKTAFLRQTPPASTTDMFAYLRWLLDVGIQFQFHNPRLAQIAYKALYDDVPLPAETMQVIRHGSFAYFKQLVEQGI 145 (216)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 145 (216)
..++.+.+.+..... ...++.++++.++...+.....+|.+..+...+.....+............+...+.+++.+|+
T Consensus 3 ~~~~~~~~~~~~~~~-~~~~~~ekL~~~i~~hl~~~~~~~~~~~v~~~E~~~~~~~~~~~i~~~~~~y~~~i~~iI~eGq 81 (133)
T PF08359_consen 3 ERMNELLEELEEALA-SEDSPREKLRALIRAHLRFLEENPDLAIVFQLELRQSNPELREEINELRREYFRLIEEIIEEGQ 81 (133)
T ss_dssp HH---HHHHHHHHHC-C--SHHHHHHHHHHHHHHHH---HHHHHHHHCTTS-SSHHHHHHHHHHH---HHHH--------
T ss_pred HHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 889999999999871-6899999999999999999980997487489988757899999999999999999999999999
Q ss_pred HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 64889999998899999999999999999963389
Q T0575 146 ADGSLVPDLDADTAAFVLNVVFTELGNHLIERFAV 180 (216)
Q Consensus 146 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (216)
+.|++++++|+..++.++.+++.+....|......
T Consensus 82 ~~G~fr~dld~~~~~~~i~G~i~~~v~~w~~~~~~ 116 (133)
T PF08359_consen 82 EQGEFRPDLDPELAARMIFGTINGTVTQWVLSDGK 116 (133)
T ss_dssp ----B-----HHHHHHHH---HHHHHHHHHHTTT-
T ss_pred HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 85988898999999999999999999999864898
No 3
>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=98.08 E-value=6e-05 Score=54.20 Aligned_cols=141 Identities=15% Similarity=0.107 Sum_probs=105.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999998752155664689999999999999870808999999998616404899999999999999999999998
Q T0575 66 LGIEQKTAFLRQTPPASTTDMFAYLRWLLDVGIQFQFHNPRLAQIAYKALYDDVPLPAETMQVIRHGSFAYFKQLVEQGI 145 (216)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 145 (216)
..++.+.+.+... ....+|.+.+..++...+++..+||...+++..+.....+.....+....+...+.-..+++.++
T Consensus 3 ~il~~Wl~~~~~~--~~~~dP~~aL~~YIr~Kl~~sr~~P~~Srlfa~Eii~Gap~l~~~l~~~l~~~~~~~~~vI~~Wi 80 (143)
T PF08362_consen 3 DILEDWLAPLDDI--DAEDDPAEALRAYIRAKLEMSRDHPEASRLFANEIIQGAPRLKDYLSEELKPWVDEKVAVIERWI 80 (143)
T ss_dssp HHHHHHTHHHHT----TTS-HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH---TTTHHHH---HHHHHHHHHHHH----
T ss_pred HHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7899999888756--86799999999999999999988941639999999848466699999999999998999999999
Q ss_pred HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 64889999998899999999999999999963389907789999999889999999999999999700169
Q T0575 146 ADGSLVPDLDADTAAFVLNVVFTELGNHLIERFAVNPAELLREGGIVLLQPAMRRVIEQVIDILERGMRRR 216 (216)
Q Consensus 146 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~Gl~~r 216 (216)
+.|.+. .+||..+...++++.+.+..+-..-..... ........+....+.+.+++.+|+..|
T Consensus 81 ~~G~i~-~vdP~hLlf~IWa~TQhYADf~~Qi~~~~g-------~~~~~~~~~~~a~~~v~~lvL~g~g~~ 143 (143)
T PF08362_consen 81 AQGKIA-PVDPHHLLFSIWATTQHYADFDAQIRALLG-------KDELDEDDFEQAAEFVTRLVLRGCGPR 143 (143)
T ss_dssp -------S--HHHHHHHHHHHHHHHHHTHHHHHHH-----------TTSHHHHHHHHHHHHHHHH------
T ss_pred HCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 869989-989999999999985206337999999859-------885888899999999999999616889
No 4
>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=97.49 E-value=0.0044 Score=39.78 Aligned_cols=97 Identities=21% Similarity=0.230 Sum_probs=71.5
Q ss_pred CHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH-----HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHH
Q ss_conf 46899999999999998708089999999986-----1640489999999999999999999999864889999998899
Q T0575 85 DMFAYLRWLLDVGIQFQFHNPRLAQIAYKALY-----DDVPLPAETMQVIRHGSFAYFKQLVEQGIADGSLVPDLDADTA 159 (216)
Q Consensus 85 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~g~~~~~~~~~~~ 159 (216)
+|...++..+...+.....+|..-+++..... +......+............+...+..+++.|.+++++|+...
T Consensus 1 dPL~~Lr~~~~~~l~~l~~d~~~Rrv~~Il~~KcE~~~E~~~~~~r~~~~~~~~~~~i~~~l~~a~~~g~L~~~ld~~~A 80 (121)
T PF08361_consen 1 DPLERLRELLIYALRQLAEDERTRRVFEILFHKCEFVEEMAPVLERRREAQQEFYARIERLLRRAIARGQLPADLDPRLA 80 (121)
T ss_dssp -HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHS---BTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSC-TTB-HHHH
T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHH
T ss_conf 96899999999999999607989899999999710102429999999999999999999999999986999999899999
Q ss_pred HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999999999999633899
Q T0575 160 AFVLNVVFTELGNHLIERFAVN 181 (216)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~ 181 (216)
+..+++.+.|+...|+......
T Consensus 81 A~~l~a~~~GL~~~WL~~p~~f 102 (121)
T PF08361_consen 81 AIMLHALLSGLLHNWLLDPESF 102 (121)
T ss_dssp HHHHHHHH---HHHHHHSTTTS
T ss_pred HHHHHHHHHHHHHHHHCCCCCC
T ss_conf 9999999999999985698458
No 5
>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=97.30 E-value=0.003 Score=41.01 Aligned_cols=116 Identities=16% Similarity=0.326 Sum_probs=82.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf 556646899999999999998708089999999986--164048999999999999999999999986488999999889
Q T0575 81 ASTTDMFAYLRWLLDVGIQFQFHNPRLAQIAYKALY--DDVPLPAETMQVIRHGSFAYFKQLVEQGIADGSLVPDLDADT 158 (216)
Q Consensus 81 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~g~~~~~~~~~~ 158 (216)
....+..+++..+....+ ....+|... ....... ...+...+.+..+.......+.+++++|++.|+++++ |++.
T Consensus 14 ~~~~ta~eKLyg~a~~~l-~~~~~pl~~-a~~EF~~~~~~~~ev~e~l~~l~~~~~~~~~~Ii~eGI~~GeF~~~-n~~~ 90 (131)
T PF08360_consen 14 KTYTTATEKLYGMAEFVL-YDIQTPLLR-AIEEFYSSQYKSPEVLERLNELRRKYLDFYRDIIEEGIQSGEFRIE-NVEE 90 (131)
T ss_dssp GG-SSHHHHHHHHHHHHH-HSSSGGGHH-HHHHHHHHCSSSHHHHHHHHHHHHHHHHHHHHHHH----------S-THHH
T ss_pred HHCCCHHHHHHHHHHHHH-HHCCCCHHH-HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CHHH
T ss_conf 843778999999999999-870350689-9999987534998999999999999999999999999886982178-8999
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999999999999999996338990778999999988999999999999999970016
Q T0575 159 AAFVLNVVFTELGNHLIERFAVNPAELLREGGIVLLQPAMRRVIEQVIDILERGMRR 215 (216)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~Gl~~ 215 (216)
++..+.+++.|+..++.. .+ ...++...++.++++++||.+
T Consensus 91 ~~~il~sll~GL~~~~~~------~~----------~~~l~~l~k~ai~ifL~Gi~~ 131 (131)
T PF08360_consen 91 LALILISLLNGLCQWYHE------KD----------IEELEALYKKAIDIFLKGISK 131 (131)
T ss_dssp HHHHHHHHH---TTTGTS------S-----------HHHHHHHHHHHHHHHHT----
T ss_pred HHHHHHHHHHHHHHHHHC------CC----------HHHHHHHHHHHHHHHHHHCCC
T ss_conf 999999999889998532------68----------999999999999999976019
No 6
>PF09209 DUF1956: Domain of unknown function (DUF1956); InterPro: IPR015292 This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YbiH from bacteria such as Salmonella typhimurium and Escherichia coli. YbiH is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YbiH and TetR share a multi-helical, interlocking structure.; PDB: 1t33_B.
Probab=94.80 E-value=0.12 Score=28.77 Aligned_cols=118 Identities=9% Similarity=0.042 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHHHHHHC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf 6899999999999998708---0899999999861640489999999999999999999999864889999998899999
Q T0575 86 MFAYLRWLLDVGIQFQFHN---PRLAQIAYKALYDDVPLPAETMQVIRHGSFAYFKQLVEQGIADGSLVPDLDADTAAFV 162 (216)
Q Consensus 86 ~~~~l~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~g~~~~~~~~~~~~~~ 162 (216)
|.++++.++..++...... .+..+++..+..+..+.....+..........+..++.+....+ .+...+...
T Consensus 1 p~~~L~~~i~~~l~~l~~~~~~~~~~rl~~RE~~~Pt~~~~~i~~~~~~P~~~~l~~ll~~~~g~~-----~~~~~~~~~ 75 (125)
T PF09209_consen 1 PEERLRAFIRAMLSRLLSDPEPEWHSRLMAREMLEPTPALEIIVEEAIRPLHEALVRLLAEILGEP-----ADDPEVRLC 75 (125)
T ss_dssp -HHHHHHHHHHHHHHTTSG-GGHHHHHHHHHHHHS--HHHHHHHHHTHHHHHHHHHHHHHHH---------TTSHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-----CCCHHHHHH
T ss_conf 989999999999999872655167999999980085199999999986169999999999986819-----983699999
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999996338990778999----9999889999999999999999700
Q T0575 163 LNVVFTELGNHLIERFAVNPAELLRE----GGIVLLQPAMRRVIEQVIDILERGM 213 (216)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~l~~l~~Gl 213 (216)
..+++..+..+.... ...... .........+...++.+.+++..||
T Consensus 76 ~~sivgq~l~~~~~r-----~~~~~~~~~~~~~~~~~~~i~~~~~~~~~f~L~gl 125 (125)
T PF09209_consen 76 ALSIVGQCLFFRIAR-----PVVLRLLPWESIDPEEAEDIEALAEHITRFSLAGL 125 (125)
T ss_dssp HHHH----GGGT--------HHHHHH----S--HHHHHHHHHHHHHHHHHHH---
T ss_pred HHHHHHHHHHHHHHH-----HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 999999999999958-----99996688554898998679999999999977539
No 7
>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=93.67 E-value=0.018 Score=35.03 Aligned_cols=34 Identities=26% Similarity=0.644 Sum_probs=26.4
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 99999999874910354799999847785455402688
Q T0575 18 IDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFAD 55 (216)
Q Consensus 18 l~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~s 55 (216)
++.+.++.. .| .|+.+||+..|||++|||+|++.
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 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=93.00 E-value=0.045 Score=31.92 Aligned_cols=43 Identities=14% Similarity=0.355 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC-HHHHHCCCCC
Q ss_conf 8899999999999987491035479999984778-5455402688
Q T0575 12 EKRSRLIDVLLDEFAQNDYDSVSINRITERAGIA-KGSFYQYFAD 55 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs-~~tiY~~F~s 55 (216)
+|+++|++.-.+-+.++||. -|+++||+..|++ ++++++|-..
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~-Pt~rEI~~~~gl~S~~tV~~~L~~ 49 (65)
T PF01726_consen 6 PRQQEVLDFIKDYIREHGYP-PTVREIAEALGLKSPSTVHKHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHHH-------HHHHHHH----SHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCC-CCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 99999999999999983889-889999988199980999999999
No 9
>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=91.66 E-value=0.057 Score=31.19 Aligned_cols=41 Identities=15% Similarity=0.451 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHCCC----CCCCHHHHHHHHCCCHHHHHCCCCCH
Q ss_conf 8899999999999987491----03547999998477854554026888
Q T0575 12 EKRSRLIDVLLDEFAQNDY----DSVSINRITERAGIAKGSFYQYFADK 56 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~----~~~t~~~IA~~agvs~~tiY~~F~sK 56 (216)
++...++.+|.+. || .++|+.+||++.|||++|+.+|-..-
T Consensus 3 ~~q~e~L~~A~~~----GYfd~PR~~tl~elA~~lgis~~T~~~~LRra 47 (53)
T PF04967_consen 3 DRQREVLRTAYEM----GYFDWPRRITLEELAEELGISKSTFSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHHHC----CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 8999999999986----88779875889999989499999999999999
No 10
>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=90.91 E-value=0.039 Score=32.46 Aligned_cols=30 Identities=13% Similarity=0.167 Sum_probs=24.8
Q ss_pred CHHHHHHHHCCCHHHHHCCCCCHHHHHHHH
Q ss_conf 479999984778545540268888999999
Q T0575 34 SINRITERAGIAKGSFYQYFADKKDCYLYL 63 (216)
Q Consensus 34 t~~~IA~~agvs~~tiY~~F~sKe~L~~~~ 63 (216)
||++||+.+|||++|+-+++.++..+=.+.
T Consensus 1 Ti~diA~~agvS~~TVSr~Ln~~~~vs~~t 30 (46)
T PF00356_consen 1 TIKDIAKAAGVSVATVSRVLNGPPRVSEET 30 (46)
T ss_dssp SHHHHHHHTTSSHHHHHHHHHTCTTSTHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
T ss_conf 999999898949999999975899998999
No 11
>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=89.64 E-value=0.12 Score=28.56 Aligned_cols=39 Identities=5% Similarity=0.322 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHH
Q ss_conf 99999999999987491035479999984778545540268888
Q T0575 14 RSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKK 57 (216)
Q Consensus 14 r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe 57 (216)
+.+|+.. |+..+|+ +|..+||+..|||+.|++++-..-+
T Consensus 2 ~~~Il~~---L~~~~~~--it~~eLA~~l~vS~~Ti~~~i~~L~ 40 (55)
T PF08279_consen 2 QQQILEL---LLKNDGP--ITAKELAEELGVSRRTIRRDIKELE 40 (55)
T ss_dssp HHHHHHH---HHHCCTT--S-HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHH---HHHCCCC--CCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 8999999---9985999--8899999996979999999999999
No 12
>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=86.90 E-value=0.26 Score=26.10 Aligned_cols=32 Identities=13% Similarity=0.276 Sum_probs=26.6
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 999999998749103547999998477854554026
Q T0575 18 IDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 18 l~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
-..|..|+. +| .|..+||+..|+|+.|||++.
T Consensus 3 r~~A~~Ly~-~G---~~~~eIA~~Lgv~~~TV~~W~ 34 (58)
T PF06056_consen 3 RRQARELYL-QG---YTPKEIAEELGVSRRTVYSWK 34 (58)
T ss_pred HHHHHHHHH-CC---CCHHHHHHHHCCCHHHHHHHH
T ss_conf 899999999-68---999999999886888999999
No 13
>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=86.24 E-value=0.32 Score=25.35 Aligned_cols=38 Identities=16% Similarity=0.456 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 7888999999999999874910354799999847785455402688
Q T0575 10 PEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFAD 55 (216)
Q Consensus 10 ~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~s 55 (216)
+.+.+++|++-. +++.++++||+..|||..|+++..++
T Consensus 49 ~~~~k~~i~~l~--------~~G~siR~iArvl~Is~~Tv~r~lK~ 86 (88)
T PF03811_consen 49 KPEVKQKILELM--------VEGMSIRDIARVLGISINTVLRWLKN 86 (88)
T ss_pred CHHHHHHHHHHH--------HCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 886999999998--------76851999999868789999999862
No 14
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=85.16 E-value=0.65 Score=23.00 Aligned_cols=49 Identities=14% Similarity=0.380 Sum_probs=38.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 9888667887888999999999999874910354799999847785455402688
Q T0575 1 MPTETFFNLPEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFAD 55 (216)
Q Consensus 1 Mp~~~~~~~~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~s 55 (216)
|++.. .|+ -|+.|..--.++..++| .+|+.++++..|+|+.|+-.||..
T Consensus 1 Mar~~---T~~-eR~ei~~rIVElVR~~G--RiTi~ql~~~TG~sR~T~k~~lr~ 49 (127)
T PF06163_consen 1 MARVF---TPE-EREEIKARIVELVREHG--RITIRQLVKMTGASRNTAKKYLRE 49 (127)
T ss_pred CCCCC---CHH-HHHHHHHHHHHHHHHHC--HHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99878---889-99999999999999816--302999999978679999999999
No 15
>PF10668 Phage_terminase: Phage terminase small subunit
Probab=83.91 E-value=0.44 Score=24.30 Aligned_cols=46 Identities=15% Similarity=0.463 Sum_probs=34.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHH
Q ss_conf 988866788788899999999999987491035479999984778545540268888
Q T0575 1 MPTETFFNLPEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKK 57 (216)
Q Consensus 1 Mp~~~~~~~~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe 57 (216)
||++.. | .| +-|.+++.++| ..++..+||++.|||..||- .+++++
T Consensus 1 Mar~Rs---p--~R----dkA~e~y~~~~-g~~~~k~IAe~lgvs~~tIr-~WKs~d 46 (60)
T PF10668_consen 1 MARQRS---P--NR----DKAFEIYKESN-GKIKLKDIAEKLGVSESTIR-KWKSRD 46 (60)
T ss_pred CCCCCC---C--CH----HHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHH-HHHHHC
T ss_conf 998889---5--88----99999999818-98419999999797999987-341022
No 16
>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=83.47 E-value=0.49 Score=23.92 Aligned_cols=46 Identities=15% Similarity=0.346 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHH
Q ss_conf 88999999999999874910354799999847785455402688889
Q T0575 12 EKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKD 58 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~ 58 (216)
+|+++||.+-.+++.+.| .-+.=+.||+..++|.+|+.+--.+-++
T Consensus 4 ~rq~~IL~~lv~~Y~~~~-~PVgSk~ia~~l~~s~aTIRN~M~~Le~ 49 (78)
T PF03444_consen 4 ERQREILKALVELYIETG-EPVGSKTIAEELDRSPATIRNEMADLEE 49 (78)
T ss_pred HHHHHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 899999999999999739-9776699999868890889999999998
No 17
>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=83.35 E-value=0.43 Score=24.40 Aligned_cols=38 Identities=18% Similarity=0.399 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCH
Q ss_conf 889999999999998749103547999998477854554026888
Q T0575 12 EKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADK 56 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sK 56 (216)
.+|-+|+..-. + | ..++.+|++..|+|++|+++|...-
T Consensus 2 ~~R~~Il~~L~----~-~--~~~~~eia~~l~~s~~tvs~HL~~L 39 (47)
T PF01022_consen 2 PTRLKILKLLS----E-G--PLSVSEIAEELGISQSTVSRHLKKL 39 (47)
T ss_dssp HHHHHHHHHHH----H-S--CEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHH----H-C--CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 88999999998----6-8--9679998836123565899999999
No 18
>PF10654 DUF2481: Protein of unknown function (DUF2481)
Probab=82.30 E-value=0.54 Score=23.60 Aligned_cols=42 Identities=19% Similarity=0.389 Sum_probs=28.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC-CCHHHHH
Q ss_conf 99999998749103547999998477854554026-8888999
Q T0575 19 DVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF-ADKKDCY 60 (216)
Q Consensus 19 ~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F-~sKe~L~ 60 (216)
++.+.-|...-++++|-.+||+--|||++++|+|. .+|++-.
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 19
>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=81.92 E-value=0.69 Score=22.79 Aligned_cols=42 Identities=17% Similarity=0.513 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHHH
Q ss_conf 878889999999999998749103547999998477854554026888899
Q T0575 9 LPEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKDC 59 (216)
Q Consensus 9 ~~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~L 59 (216)
.|-+-|++|+++. ++| .|++++|+.-|||++|+|+... +.+.
T Consensus 3 yS~DlR~kvi~~~-----~~G---~S~~eaA~~F~VS~~Tv~rW~k-~~~~ 44 (119)
T PF01710_consen 3 YSIDLRQKVIAYV-----EQG---MSIREAAKRFGVSRSTVYRWLK-RRET 44 (119)
T ss_pred CCHHHHHHHHHHH-----HCC---CCHHHHHHHHCCCHHHHHHHHH-HHHC
T ss_conf 7899999999999-----959---9999999996955999999998-6411
No 20
>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=81.27 E-value=0.21 Score=26.83 Aligned_cols=33 Identities=12% Similarity=0.327 Sum_probs=25.4
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCH
Q ss_conf 9998749103547999998477854554026888
Q T0575 23 DEFAQNDYDSVSINRITERAGIAKGSFYQYFADK 56 (216)
Q Consensus 23 ~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sK 56 (216)
+.|.+.+ ...|+.+||++.|++++|+|++-.+-
T Consensus 10 ~~l~~~~-~~~t~~eia~~~gl~~st~~r~l~~L 42 (52)
T PF09339_consen 10 EALARAP-RPLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HTHCTTB-SSEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9998789-99899999999891999999999999
No 21
>PF12116 SpoIIID: Stage III sporulation protein D
Probab=78.55 E-value=0.96 Score=21.68 Aligned_cols=37 Identities=8% Similarity=0.197 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 89999999999998749103547999998477854554026
Q T0575 13 KRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 13 ~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
-.++.++.|.-++.. +.|+++.|+.-|||++|++.-.
T Consensus 4 IeeR~~~ia~yIi~~----~aTVR~tAk~FGVSKSTVHkDv 40 (82)
T PF12116_consen 4 IEERVLEIANYIIEN----KATVRQTAKVFGVSKSTVHKDV 40 (82)
T ss_pred HHHHHHHHHHHHHHC----CHHHHHHHHHHCCCHHHHHHHH
T ss_conf 999999999999974----5169999999785299998999
No 22
>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=77.83 E-value=0.51 Score=23.82 Aligned_cols=39 Identities=10% Similarity=0.310 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHH
Q ss_conf 999999999987491035479999984778545540268888
Q T0575 16 RLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKK 57 (216)
Q Consensus 16 ~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe 57 (216)
.-|+.|++-+...+ .|++..|+.-||++.|++++...+.
T Consensus 3 e~l~~Ai~~v~~g~---~Si~~aA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 3 ERLQEAIEAVKNGK---LSIRKAARKYGVPRSTLRRRLKGKP 41 (45)
T ss_dssp HHHHHHHHHHH--------HHHHHHH----HHHHHHHHHH--
T ss_pred HHHHHHHHHHHCCC---CCHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf 99999999999099---5799999998939899999992787
No 23
>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=77.23 E-value=0.99 Score=21.56 Aligned_cols=36 Identities=22% Similarity=0.445 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHC
Q ss_conf 88788899999999999987491035479999984778545540
Q T0575 8 NLPEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQ 51 (216)
Q Consensus 8 ~~~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~ 51 (216)
.+|.+.|++|++.+. .+++..+||++.+||.|++..
T Consensus 17 Plp~~~R~rIv~l~~--------~G~r~~~Isr~l~VS~gcVsK 52 (125)
T PF00292_consen 17 PLPNELRQRIVELAH--------EGVRPCDISRQLRVSHGCVSK 52 (125)
T ss_dssp -S-HHHHHHHHHHHH------------HHHHHHHHT-----HHH
T ss_pred CCCHHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHH
T ss_conf 288999999999976--------258774899876514769999
No 24
>PF07638 Sigma70_ECF: ECF sigma factor; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent
Probab=76.41 E-value=0.71 Score=22.69 Aligned_cols=11 Identities=18% Similarity=0.087 Sum_probs=3.7
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999999
Q T0575 63 LIQLGIEQKTA 73 (216)
Q Consensus 63 ~~~~~~~~~~~ 73 (216)
++..+...+..
T Consensus 22 L~~~~y~~Lr~ 32 (185)
T PF07638_consen 22 LLPRVYEELRR 32 (185)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999999
No 25
>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=76.22 E-value=1.5 Score=20.18 Aligned_cols=39 Identities=18% Similarity=0.318 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCC
Q ss_conf 88999999999999874910354799999847785455402
Q T0575 12 EKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQY 52 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~ 52 (216)
++.+.-|.+-..+-.+. ..++..+||+..|||++|+..-
T Consensus 4 ~~~e~YL~~I~~l~~~~--~~v~~~~IA~~L~vs~~TVs~m 42 (60)
T PF01325_consen 4 ESEEDYLKAIYELSEEG--GPVSTSDIAERLGVSPPTVSEM 42 (60)
T ss_dssp SHHHHHHHHHHHHHHH---S--BHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCCHHHHHH
T ss_conf 06999999999998069--9721999999978990789999
No 26
>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=76.21 E-value=1.7 Score=19.72 Aligned_cols=32 Identities=16% Similarity=0.269 Sum_probs=27.9
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHHHHH
Q ss_conf 74910354799999847785455402688889999
Q T0575 27 QNDYDSVSINRITERAGIAKGSFYQYFADKKDCYL 61 (216)
Q Consensus 27 ~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~L~~ 61 (216)
+.|- |..+||+.-||+++|++.--++|+.+..
T Consensus 20 e~g~---s~~~iAr~fgi~~sTi~~i~k~k~~i~~ 51 (53)
T PF04218_consen 20 EEGK---SQREIAREFGISRSTISRILKNKEKILE 51 (53)
T ss_dssp HC-T----HHHHHHHHT--CCHHHHHCCTHHHHCC
T ss_pred HCCC---CHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 8499---8999998919988899999983999985
No 27
>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=74.96 E-value=0.51 Score=23.80 Aligned_cols=29 Identities=24% Similarity=0.409 Sum_probs=24.3
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHCCCCCH
Q ss_conf 49103547999998477854554026888
Q T0575 28 NDYDSVSINRITERAGIAKGSFYQYFADK 56 (216)
Q Consensus 28 ~G~~~~t~~~IA~~agvs~~tiY~~F~sK 56 (216)
+--+..|+.+||.++|+|+..+++.|+..
T Consensus 4 ~~~~~~~i~~iA~~~g~s~~~~~r~Fk~~ 32 (42)
T PF00165_consen 4 HLSEPISIEDIAEELGYSPSYFSRLFKKE 32 (42)
T ss_dssp TTCSS--HHHHHHHTTSSHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 56898979999999798999999999999
No 28
>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=73.69 E-value=1.1 Score=21.32 Aligned_cols=34 Identities=18% Similarity=0.333 Sum_probs=27.2
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHH
Q ss_conf 999987491035479999984778545540268888
Q T0575 22 LDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKK 57 (216)
Q Consensus 22 ~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe 57 (216)
.+++.++|+ +|+.++|+..|||..|+.+++..-+
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 29
>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=69.61 E-value=0.74 Score=22.53 Aligned_cols=31 Identities=19% Similarity=0.348 Sum_probs=25.1
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 9998749103547999998477854554026
Q T0575 23 DEFAQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 23 ~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
.+|.-+=+++.|..+||+..|+|.+|++.+.
T Consensus 17 ~i~~l~~~~g~s~~eIA~~l~is~~tv~~~l 47 (54)
T PF08281_consen 17 EIFLLRYFEGLSYKEIAEILGISESTVKSRL 47 (54)
T ss_dssp HHHHHHHT----HHHHHHHCTS----HHHHH
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999969589999999891999999999
No 30
>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=69.45 E-value=0.65 Score=22.96 Aligned_cols=34 Identities=15% Similarity=0.272 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHCCCCCHHHHHHHHH
Q ss_conf 0354799999847785455402688889999999
Q T0575 31 DSVSINRITERAGIAKGSFYQYFADKKDCYLYLI 64 (216)
Q Consensus 31 ~~~t~~~IA~~agvs~~tiY~~F~sKe~L~~~~~ 64 (216)
.+.|..++|+.+|+|+++++++..++...=...+
T Consensus 8 ~gls~~~la~~~gis~~~i~~~e~g~~~~~~~~l 41 (55)
T PF01381_consen 8 RGLSQEELARRLGISRSTISRIENGKRNPSIETL 41 (55)
T ss_dssp TT--HHHHHHHHTS-HHHHHHHHTTSSGSBHHHH
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHH
T ss_conf 6999999988649878788899769989999999
No 31
>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=69.35 E-value=1.2 Score=20.88 Aligned_cols=39 Identities=15% Similarity=0.270 Sum_probs=29.7
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHHHHH
Q ss_conf 999874910354799999847785455402688889999
Q T0575 23 DEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKDCYL 61 (216)
Q Consensus 23 ~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~L~~ 61 (216)
+.+.-.=.+..|+.+||+.-|||+.++|...+--+..+.
T Consensus 24 ~~l~lyy~eDlSlsEIAe~~~iSRqaVyD~ikr~~~~L~ 62 (101)
T PF04297_consen 24 EYLELYYNEDLSLSEIAEELGISRQAVYDNIKRAEKKLE 62 (101)
T ss_dssp HHHHHHCTS---HHHHHHHCT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 999999887998999998969889999999999999999
No 32
>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=69.11 E-value=1.5 Score=20.11 Aligned_cols=35 Identities=14% Similarity=0.300 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 9999999999998749103547999998477854554026
Q T0575 14 RSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 14 r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
+++|++.-.++ ....|.++||+.+|+|..+..+|-
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 33
>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=68.60 E-value=1.6 Score=19.98 Aligned_cols=30 Identities=20% Similarity=0.468 Sum_probs=23.6
Q ss_pred HHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHH
Q ss_conf 87491035479999984778545540268888
Q T0575 26 AQNDYDSVSINRITERAGIAKGSFYQYFADKK 57 (216)
Q Consensus 26 ~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe 57 (216)
.++| ..|+++||+..|+|++++|++..+-+
T Consensus 18 ~~~~--~~t~~eia~~~~i~~~~v~~~l~~L~ 47 (68)
T PF01978_consen 18 LENG--GATASEIAEKLGISRSTVYRILKRLE 47 (68)
T ss_dssp HHTS---EEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred HHCC--CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9579--95999999998909999999999999
No 34
>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=67.71 E-value=0.88 Score=21.95 Aligned_cols=37 Identities=16% Similarity=0.425 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 999999999998749103547999998477854554026
Q T0575 15 SRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 15 ~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
.+|.+.-..-.. .+...|+.+||+.+|||++|+-+.-
T Consensus 19 ~~Ia~yil~~~~--~~~~~si~~lA~~~~vS~atv~Rf~ 55 (107)
T PF01418_consen 19 KKIADYILNNPD--KIANMSISELAKAAGVSPATVVRFC 55 (107)
T ss_dssp HHHHHHHHH-HH--HHTT--HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHHCHH--HHHHCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999992999--9977549999999798988999999
No 35
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term
Probab=66.26 E-value=2.3 Score=18.70 Aligned_cols=39 Identities=8% Similarity=0.075 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHHHCCC
Q ss_conf 8999999999999874910354799999847-7854554026
Q T0575 13 KRSRLIDVLLDEFAQNDYDSVSINRITERAG-IAKGSFYQYF 53 (216)
Q Consensus 13 ~r~~Il~aA~~lf~~~G~~~~t~~~IA~~ag-vs~~tiY~~F 53 (216)
+++.|..||..|+ ..|- ..|+..|-+..| .|+.||-.|.
T Consensus 2 t~e~V~~Aa~~L~-~~G~-~PTv~~VR~~lG~GS~~ti~~~l 41 (120)
T PF11740_consen 2 TYEDVAAAADALL-AAGK-RPTVDAVRERLGTGSMSTISKHL 41 (120)
T ss_pred CHHHHHHHHHHHH-HCCC-CCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 6999999999998-7489-99899999998795889999999
No 36
>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=66.11 E-value=1.1 Score=21.08 Aligned_cols=25 Identities=24% Similarity=0.276 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 0354799999847785455402688
Q T0575 31 DSVSINRITERAGIAKGSFYQYFAD 55 (216)
Q Consensus 31 ~~~t~~~IA~~agvs~~tiY~~F~s 55 (216)
.+.|..+||+..|+|..|+.+|-.+
T Consensus 17 ~G~~~~eIA~~l~is~~TV~~~~~~ 41 (58)
T PF00196_consen 17 QGLSNKEIAERLGISEKTVKSHRRR 41 (58)
T ss_dssp TT--HHHHHHHHTS-HHHHHHHHHH
T ss_pred HCCCCHHHHHHHCCCHHHHHHHHHH
T ss_conf 7398378998835452479999999
No 37
>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=65.65 E-value=0.79 Score=22.32 Aligned_cols=36 Identities=14% Similarity=0.433 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCC
Q ss_conf 7888999999999999874910354799999847785455402
Q T0575 10 PEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQY 52 (216)
Q Consensus 10 ~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~ 52 (216)
|.+-|.+|+.-+ .+ .+.|+.+||++.|||.++||+.
T Consensus 8 s~efK~~~V~~~----~~---~g~s~~~va~~~gI~~~tl~~W 43 (76)
T PF01527_consen 8 SPEFKLQIVEEA----LE---EGRSVSEVAREYGISPSTLYRW 43 (76)
T ss_dssp -HHHHHHHHHHH----CH---H-HHHHHHCCC----HHHHHHH
T ss_pred CHHHHHHHHHHH----HH---CCCCHHHHHHHCCCCHHHHHHH
T ss_conf 999999999999----98---7997999999705330266699
No 38
>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=65.09 E-value=0.94 Score=21.76 Aligned_cols=22 Identities=18% Similarity=0.576 Sum_probs=19.7
Q ss_pred CCHHHHHHHHCCCHHHHHCCCC
Q ss_conf 5479999984778545540268
Q T0575 33 VSINRITERAGIAKGSFYQYFA 54 (216)
Q Consensus 33 ~t~~~IA~~agvs~~tiY~~F~ 54 (216)
+++.++|+..|+|+.|+|.+-.
T Consensus 4 l~~~ev~~~lgvs~~t~y~~~~ 25 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTLYRLIK 25 (51)
T ss_dssp E-HHHHHHH-----HHHHHHHH
T ss_pred ECHHHHHHHHCCCHHHHHHHHH
T ss_conf 2499999998949999999977
No 39
>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=63.81 E-value=1.1 Score=21.29 Aligned_cols=19 Identities=16% Similarity=0.417 Sum_probs=17.0
Q ss_pred CHHHHHHHHCCCHHHHHCC
Q ss_conf 4799999847785455402
Q T0575 34 SINRITERAGIAKGSFYQY 52 (216)
Q Consensus 34 t~~~IA~~agvs~~tiY~~ 52 (216)
||.++|+.+|||..||-+|
T Consensus 1 ti~e~a~~~gvs~~tlR~y 19 (38)
T PF00376_consen 1 TIGEVAKLLGVSVRTLRYY 19 (38)
T ss_dssp EHHHHHHHCT--HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 9899999989699999999
No 40
>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=61.73 E-value=2.4 Score=18.66 Aligned_cols=39 Identities=18% Similarity=0.318 Sum_probs=33.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHH
Q ss_conf 999999874910354799999847785455402688889
Q T0575 20 VLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKD 58 (216)
Q Consensus 20 aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~ 58 (216)
..++.++..++++++-.++++..|+...+++++.+.-++
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 41
>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=60.59 E-value=3.6 Score=17.18 Aligned_cols=33 Identities=21% Similarity=0.446 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCC
Q ss_conf 999999999999874910354799999847785455402
Q T0575 14 RSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQY 52 (216)
Q Consensus 14 r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~ 52 (216)
-..+|..|++- .| =++...|+..|+|+.|+|+.
T Consensus 6 E~~~i~~aL~~---~~---gn~~~aA~~Lgi~r~tL~~k 38 (42)
T PF02954_consen 6 ERELIEEALER---HG---GNISKAARLLGISRSTLYRK 38 (42)
T ss_dssp HHHHHHHHHHH---TT---T-HHHHHHH----HHHHHHH
T ss_pred HHHHHHHHHHH---HC---CCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999998---29---98999999979899999999
No 42
>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=60.12 E-value=2 Score=19.16 Aligned_cols=31 Identities=16% Similarity=0.303 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHCCCCCHHHHHH
Q ss_conf 0354799999847785455402688889999
Q T0575 31 DSVSINRITERAGIAKGSFYQYFADKKDCYL 61 (216)
Q Consensus 31 ~~~t~~~IA~~agvs~~tiY~~F~sKe~L~~ 61 (216)
+.+|+.++|+...||++|+++..+.-...+.
T Consensus 29 ~~~~~~~la~~l~vS~sTi~~~lk~i~~~L~ 59 (87)
T PF05043_consen 29 EYVSIEDLAEELYVSRSTIYRDLKKINQILK 59 (87)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 9968999999979899999999999999999
No 43
>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=59.08 E-value=2.4 Score=18.56 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHH
Q ss_conf 8899999999999987491035479999984778545540268888
Q T0575 12 EKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKK 57 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe 57 (216)
.++-+|+--.++-....+.--.|.++||++.|+|++|+++-|+.-+
T Consensus 55 ~k~~~Vl~~ll~~~d~~N~v~~t~~~Ia~~lgiS~~Tv~r~iK~L~ 100 (165)
T PF05732_consen 55 NKKFRVLMFLLENMDSDNAVVATQKEIAEELGISKPTVSRTIKELE 100 (165)
T ss_pred CCHHHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 1479999999984377983987899999997988889999999998
No 44
>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=56.36 E-value=4.2 Score=16.68 Aligned_cols=38 Identities=13% Similarity=0.336 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHCCC---CCC-CHHHHHHHHCCCHHHHHCC
Q ss_conf 9999999999987491---035-4799999847785455402
Q T0575 15 SRLIDVLLDEFAQNDY---DSV-SINRITERAGIAKGSFYQY 52 (216)
Q Consensus 15 ~~Il~aA~~lf~~~G~---~~~-t~~~IA~~agvs~~tiY~~ 52 (216)
++|.+.-.+.+....+ +.+ |.+++|++.|||+.++..-
T Consensus 3 ~~v~~~i~~~I~~g~l~~G~~lPs~~~La~~~~vSr~tvr~A 44 (64)
T PF00392_consen 3 EQVYEYIRRDILSGELKPGDRLPSERELAERFGVSRTTVREA 44 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHT--HHHHHHH
T ss_pred HHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999998499999999368999998868798999999
No 45
>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=55.42 E-value=2.1 Score=19.04 Aligned_cols=43 Identities=7% Similarity=0.337 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHH
Q ss_conf 899999999999987491035479999984778545540268888
Q T0575 13 KRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKK 57 (216)
Q Consensus 13 ~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe 57 (216)
..-.+|++.... ..=.+.-.+..||+..|++...|...|.++-
T Consensus 10 ~q~~~Le~~f~~--~~~P~~~~~~~La~~~~l~~~~V~~WF~nrR 52 (57)
T PF00046_consen 10 EQLEILEEYFEK--NPYPSEEEIEELAKELGLSEKQVKNWFQNRR 52 (57)
T ss_dssp HHHHHHHHHHHH--SSSCCHHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999987--5756500556542334320045512499878
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=54.33 E-value=4 Score=16.88 Aligned_cols=43 Identities=7% Similarity=0.362 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHHHH
Q ss_conf 8899999999999987491035479999984778545540268888999
Q T0575 12 EKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKDCY 60 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~L~ 60 (216)
.|+-+|++ ++.++| .+|+.+||+..|+|..|+.++...-.+.+
T Consensus 5 ~r~~~Ll~----~L~~~~--~~t~~ela~~l~~S~~ti~~~I~~l~~~f 47 (59)
T PF08280_consen 5 KRQLKLLE----LLLKNG--WITLKELAKKLGLSERTIRNDINELNEEF 47 (59)
T ss_pred HHHHHHHH----HHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 99999999----999779--79799999997988999999999999986
No 47
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development .
Probab=53.59 E-value=3.4 Score=17.45 Aligned_cols=26 Identities=8% Similarity=0.215 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCH
Q ss_conf 999999999874910354799999847785
Q T0575 17 LIDVLLDEFAQNDYDSVSINRITERAGIAK 46 (216)
Q Consensus 17 Il~aA~~lf~~~G~~~~t~~~IA~~agvs~ 46 (216)
|-+||.+| |+..+++..+|.+.||++
T Consensus 18 i~~AAk~L----gv~~T~lKk~CR~~GI~R 43 (52)
T PF02042_consen 18 IKEAAKEL----GVCTTTLKKRCRQLGIPR 43 (52)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHCCCCC
T ss_conf 99999995----887569999999869988
No 48
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry consists of a bacterial protein which is uncharacterised.
Probab=53.34 E-value=4.7 Score=16.33 Aligned_cols=37 Identities=22% Similarity=0.522 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 78889999999999998749103547999998477854554026
Q T0575 10 PEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 10 ~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
|+++|+++-. .+. +++.|+..+|+.+|||.+|.-++=
T Consensus 4 ~~etR~~vR~----~YV---~~~~~Le~aA~~~gVs~~TArrWK 40 (165)
T PF08822_consen 4 PQETRDAVRR----LYV---FDRLSLEEAAKKAGVSYGTARRWK 40 (165)
T ss_pred CHHHHHHHHH----HHH---HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 6899999999----999---768989999989299888899999
No 49
>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=51.11 E-value=5.1 Score=16.08 Aligned_cols=40 Identities=15% Similarity=0.150 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCC
Q ss_conf 88999999999999874910354799999847785455402
Q T0575 12 EKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQY 52 (216)
Q Consensus 12 e~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~ 52 (216)
|+-.+|-.|..+|..+.| ..-|..+||+..|+|..-++..
T Consensus 1 E~~~ki~~a~~~L~~~lg-R~Pt~eEIA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 1 EKLNKIKKAKRELEQELG-REPTEEEIAEELGISEEEVREL 40 (78)
T ss_dssp HHHHHHHHHHHHHHHC------BHHHHHHH----HHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHCCCHHHHHHH
T ss_conf 978999999999999958-8989999999978889999999
No 50
>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=50.66 E-value=1.3 Score=20.59 Aligned_cols=48 Identities=13% Similarity=0.239 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHH------H---CCCCCCCHHHHHHHHCCCHHHHHCCCCCHHH
Q ss_conf 8889999999999998------7---4910354799999847785455402688889
Q T0575 11 EEKRSRLIDVLLDEFA------Q---NDYDSVSINRITERAGIAKGSFYQYFADKKD 58 (216)
Q Consensus 11 ee~r~~Il~aA~~lf~------~---~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~ 58 (216)
++|++-|+..+..++. . ....-+||.+||++.|++.+||-+--.+|.-
T Consensus 19 ~~R~~Tll~v~~~Iv~~Q~~Ff~~g~~~l~Pltl~~vA~~lglheSTVSRav~~Ky~ 75 (160)
T PF04552_consen 19 EQRNQTLLRVAEAIVERQEDFFLEGPKALKPLTLKDVAEELGLHESTVSRAVSNKYI 75 (160)
T ss_dssp ---------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCCEE
T ss_conf 999999999999999999999855853576854999999839883057798748536
No 51
>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=48.54 E-value=1.7 Score=19.78 Aligned_cols=23 Identities=26% Similarity=0.599 Sum_probs=20.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHCC
Q ss_conf 10354799999847785455402
Q T0575 30 YDSVSINRITERAGIAKGSFYQY 52 (216)
Q Consensus 30 ~~~~t~~~IA~~agvs~~tiY~~ 52 (216)
+++.|..+||+..|+|.+++...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISESTVRQR 40 (50)
T ss_dssp TST-CTCCCHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 49999999998979799999899
No 52
>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=48.50 E-value=3.7 Score=17.14 Aligned_cols=36 Identities=8% Similarity=0.145 Sum_probs=26.1
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHHHH
Q ss_conf 99987491035479999984778545540268888999
Q T0575 23 DEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKDCY 60 (216)
Q Consensus 23 ~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~L~ 60 (216)
++....|+. |-.++|+..|||++++.+.+..+..+=
T Consensus 5 Rl~~~~g~~--~~~elA~~LgIs~stvs~~~~~r~~~P 40 (66)
T PF07022_consen 5 RLKEAYGIK--TDKELAEKLGISQSTVSHTWKKRNSIP 40 (66)
T ss_dssp HHHHH------SCHHHHCCTT--HHHHH-HHHH-----
T ss_pred HHHHHHCCC--CHHHHHHHHCCCHHHHHHHHHHCCCCC
T ss_conf 999996899--699999991998888556764168898
No 53
>PF01257 Complex1_24kDa: Respiratory-chain NADH dehydrogenase 24 Kd subunit; InterPro: IPR002023 Respiratory-chain NADH dehydrogenase (ubiquinone) (1.6.5.3 from EC) , (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase). Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to , : Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0006118 electron transport; PDB: 2auv_A 1m2b_A 1m2d_A 1f37_B 1m2a_A 2fug_T.
Probab=47.43 E-value=3.5 Score=17.29 Aligned_cols=44 Identities=34% Similarity=0.571 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHCCCHH------HHHCCCCCH
Q ss_conf 899999999999987491-03547999998477854------554026888
Q T0575 13 KRSRLIDVLLDEFAQNDY-DSVSINRITERAGIAKG------SFYQYFADK 56 (216)
Q Consensus 13 ~r~~Il~aA~~lf~~~G~-~~~t~~~IA~~agvs~~------tiY~~F~sK 56 (216)
++..+|..-..+=.+.|| ..-.++.||+..|++.+ |||.+|..+
T Consensus 11 ~~~~ll~~L~~iQ~~~g~i~~~~~~~iA~~l~i~~~~v~~v~tFY~~f~~~ 61 (145)
T PF01257_consen 11 KRSALLPILHEIQEEFGYIPPEAIEEIAERLGIPPAEVYGVATFYSMFRRQ 61 (145)
T ss_dssp -GGGHHHHHHHHHHH-----HHHHHHHHHH----HHHH---TTTSSSS-SS
T ss_pred CHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCC
T ss_conf 777899999999998099999999999999798899999999987561217
No 54
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1trr_K 1tro_E 1p6z_R 1jhg_A 1co0_A 1rcs_B 3wrp_A 1zt9_B 1wrp_R 1wrt_S ....
Probab=46.23 E-value=3.4 Score=17.44 Aligned_cols=20 Identities=20% Similarity=0.293 Sum_probs=12.4
Q ss_pred CCCHHHHHHHHCCCHHHHHC
Q ss_conf 35479999984778545540
Q T0575 32 SVSINRITERAGIAKGSFYQ 51 (216)
Q Consensus 32 ~~t~~~IA~~agvs~~tiY~ 51 (216)
+.|-++|+++.|+|.+||-+
T Consensus 49 ~~syreI~~~tG~S~aTIsR 68 (87)
T PF01371_consen 49 GKSYREIAEETGASIATISR 68 (87)
T ss_dssp THSHHHHHHH----HHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHH
T ss_conf 99899999997877889999
No 55
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=45.65 E-value=3.3 Score=17.48 Aligned_cols=30 Identities=17% Similarity=0.449 Sum_probs=22.8
Q ss_pred HHCCCCCCCHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 874910354799999847785455402688
Q T0575 26 AQNDYDSVSINRITERAGIAKGSFYQYFAD 55 (216)
Q Consensus 26 ~~~G~~~~t~~~IA~~agvs~~tiY~~F~s 55 (216)
.=..|++.|-.+-|...|||++||.+-..+
T Consensus 51 RL~D~egl~QeeAA~~MgVSR~Tf~ril~~ 80 (106)
T PF02001_consen 51 RLVDYEGLTQEEAAEQMGVSRQTFQRILKS 80 (106)
T ss_pred HHHHHHCCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 998881798999999849779999999999
No 56
>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=45.55 E-value=6.1 Score=15.47 Aligned_cols=39 Identities=26% Similarity=0.421 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH
Q ss_conf 887888999999999999874910354799999847785
Q T0575 8 NLPEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAK 46 (216)
Q Consensus 8 ~~~ee~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~ 46 (216)
++|++-|+.+++--.+-|.+.+-++-|=++|+++.|-.+
T Consensus 16 ~Lp~~e~~dil~~Y~eyf~e~~~~G~sEeeii~~LG~P~ 54 (181)
T PF08006_consen 16 KLPEEEREDILEYYEEYFDEGGEEGKSEEEIIAELGSPK 54 (181)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCHH
T ss_conf 299999999999999999987568999999997829999
No 57
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=44.07 E-value=3.2 Score=17.64 Aligned_cols=26 Identities=12% Similarity=0.181 Sum_probs=22.9
Q ss_pred CHHHHHHHHCCCHHHHHCCCCCHHHH
Q ss_conf 47999998477854554026888899
Q T0575 34 SINRITERAGIAKGSFYQYFADKKDC 59 (216)
Q Consensus 34 t~~~IA~~agvs~~tiY~~F~sKe~L 59 (216)
.+.++|...+++++|+-.|-.+|++=
T Consensus 18 N~teVaR~L~c~R~TVrkY~~D~~g~ 43 (64)
T PF06322_consen 18 NQTEVARMLNCYRATVRKYARDKEGK 43 (64)
T ss_pred CHHHHHHHHCCHHHHHHHHHCCCCCC
T ss_conf 68988788510188799772255662
No 58
>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=39.98 E-value=6.4 Score=15.29 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCC
Q ss_conf 8999999999999874910354799999847785455402
Q T0575 13 KRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQY 52 (216)
Q Consensus 13 ~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~ 52 (216)
+|--+---.++.+.+.|.+.+|-.++|+.+|++...+-+-
T Consensus 9 ~RLp~Y~r~L~~l~~~g~~~iSS~eLa~~~gi~~~qVRKD 48 (50)
T PF06971_consen 9 RRLPLYLRYLKQLQEEGVERISSKELAEALGITPSQVRKD 48 (50)
T ss_dssp HHHHHHHHHHHHHHH----B--TTTHHHCCSS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCEEECHHHHHHHHCCCHHHHHCC
T ss_conf 9999999999999985994587999999979799996122
No 59
>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=38.45 E-value=7.7 Score=14.69 Aligned_cols=32 Identities=13% Similarity=0.198 Sum_probs=14.6
Q ss_pred HHHHHHHHH-HHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 999999999-874910354799999847785455
Q T0575 17 LIDVLLDEF-AQNDYDSVSINRITERAGIAKGSF 49 (216)
Q Consensus 17 Il~aA~~lf-~~~G~~~~t~~~IA~~agvs~~ti 49 (216)
|..|++-+- ...|. ..|+++|++.+|||..||
T Consensus 39 iaAA~iY~acr~~~~-~~t~~eia~~~~Vs~~tI 71 (71)
T PF00382_consen 39 IAAACIYLACRLEGV-PRTLKEIAEVAGVSEKTI 71 (71)
T ss_dssp HHHHHHHHHHHHCTS--SSHHHHHHHCTSSCCCH
T ss_pred HHHHHHHHHHHHCCC-CCCHHHHHHHHCCCCCCC
T ss_conf 999999999998399-828999999968896869
No 60
>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=38.26 E-value=6.4 Score=15.30 Aligned_cols=20 Identities=15% Similarity=0.488 Sum_probs=16.5
Q ss_pred CCCCHHHHHHHHC-CCHHHHH
Q ss_conf 0354799999847-7854554
Q T0575 31 DSVSINRITERAG-IAKGSFY 50 (216)
Q Consensus 31 ~~~t~~~IA~~ag-vs~~tiY 50 (216)
++.|-.+||++.| ||+.++-
T Consensus 17 eGlSasqIA~~LGgvsRNAVi 37 (162)
T PF07750_consen 17 EGLSASQIAKQLGGVSRNAVI 37 (162)
T ss_pred CCCCHHHHHHHHCCCCHHHHH
T ss_conf 588899999997552066677
No 61
>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=36.35 E-value=2.8 Score=18.04 Aligned_cols=17 Identities=35% Similarity=0.594 Sum_probs=13.9
Q ss_pred HHHHHCCCHHHHHCCCC
Q ss_conf 99984778545540268
Q T0575 38 ITERAGIAKGSFYQYFA 54 (216)
Q Consensus 38 IA~~agvs~~tiY~~F~ 54 (216)
-+=++||+-|++||.|-
T Consensus 3 A~FEaGIklGalyHQf~ 19 (38)
T PF04036_consen 3 AVFEAGIKLGALYHQFV 19 (38)
T ss_dssp HHHH-------HHHHH-
T ss_pred HHHHHHHHHHHHHHHHC
T ss_conf 17650025757888651
No 62
>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=35.19 E-value=8.5 Score=14.32 Aligned_cols=30 Identities=23% Similarity=0.399 Sum_probs=22.3
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 99998749103547999998477854554026
Q T0575 22 LDEFAQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 22 ~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
+..+.+.| +.|+.+||+..|++++++.+..
T Consensus 9 L~~l~~~~--~~t~~~la~~l~~~~~~vs~~i 38 (59)
T PF01047_consen 9 LRILYENP--GMTQSELAERLGISKSTVSRII 38 (59)
T ss_dssp HHHHHHSS--SEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHCC--CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999879--9899999999886873899999
No 63
>PF10975 DUF2802: Protein of unknown function (DUF2802)
Probab=33.77 E-value=8.1 Score=14.49 Aligned_cols=15 Identities=13% Similarity=0.554 Sum_probs=6.4
Q ss_pred CCHHHHHHHHCCCHH
Q ss_conf 547999998477854
Q T0575 33 VSINRITERAGIAKG 47 (216)
Q Consensus 33 ~t~~~IA~~agvs~~ 47 (216)
.++++|++++|+|++
T Consensus 45 a~~~el~~~CgL~~A 59 (70)
T PF10975_consen 45 ADIDELMQECGLPRA 59 (70)
T ss_pred CCHHHHHHHHCCCHH
T ss_conf 999999988099899
No 64
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316)
Probab=32.13 E-value=9.5 Score=13.97 Aligned_cols=39 Identities=18% Similarity=0.127 Sum_probs=26.2
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCH
Q ss_conf 999999998749103547999998477854554026888
Q T0575 18 IDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADK 56 (216)
Q Consensus 18 l~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sK 56 (216)
...+.+|=...-..++|..+||+..|+|..-+-+-+.=|
T Consensus 9 ~~T~~ELqanf~l~~Ls~~~ia~dL~~s~~~ve~vL~l~ 47 (89)
T PF10078_consen 9 KATRKELQANFELSGLSIEQIAKDLGTSPEKVEQVLNLK 47 (89)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 976999999999849999999999689999999898604
No 65
>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=31.11 E-value=9.8 Score=13.85 Aligned_cols=28 Identities=25% Similarity=0.335 Sum_probs=19.9
Q ss_pred HHCCCCC-CCHHHHHHHHCCCHHHHHCCC
Q ss_conf 8749103-547999998477854554026
Q T0575 26 AQNDYDS-VSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 26 ~~~G~~~-~t~~~IA~~agvs~~tiY~~F 53 (216)
..+.-.. +|+++||++.|+|+..+.+..
T Consensus 18 a~~~~~~~~t~~~IA~~~~i~~~~v~kil 46 (83)
T PF02082_consen 18 ARQPDGKPVTSKEIAERLGISPSYVRKIL 46 (83)
T ss_dssp HCSTTCC---HHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 80999984989999988890999999999
No 66
>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=26.91 E-value=7.2 Score=14.89 Aligned_cols=35 Identities=17% Similarity=0.459 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 89999999999998749103547999998477854
Q T0575 13 KRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKG 47 (216)
Q Consensus 13 ~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~ 47 (216)
+...|...-+.-+.++||=..++.+||...|++..
T Consensus 33 ~~~~ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~ 67 (195)
T PF04963_consen 33 EEREIAEYIIDNLDDDGYLRESLEEIAEELGVSEE 67 (195)
T ss_dssp -HHHHHHHHCCCBTT---BSS-HHHHHHHCTS-HH
T ss_pred HHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHH
T ss_conf 99999999998279999889999999978198999
No 67
>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=25.94 E-value=8.9 Score=14.20 Aligned_cols=23 Identities=13% Similarity=0.232 Sum_probs=18.8
Q ss_pred CCCHHHHHHHHCCCHHHHHCCCC
Q ss_conf 35479999984778545540268
Q T0575 32 SVSINRITERAGIAKGSFYQYFA 54 (216)
Q Consensus 32 ~~t~~~IA~~agvs~~tiY~~F~ 54 (216)
+.|-.+||++.|-|++.|-+|-.
T Consensus 3 G~tq~eIA~~lGks~s~Vs~~L~ 25 (93)
T PF08535_consen 3 GLTQEEIAKRLGKSRSWVSNHLR 25 (93)
T ss_dssp ------HHHH----HHHHHHHHG
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999998879999999999
No 68
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases .
Probab=25.02 E-value=12 Score=13.09 Aligned_cols=20 Identities=20% Similarity=0.346 Sum_probs=15.4
Q ss_pred CCHHHHHHHHCCCHHHHHCC
Q ss_conf 54799999847785455402
Q T0575 33 VSINRITERAGIAKGSFYQY 52 (216)
Q Consensus 33 ~t~~~IA~~agvs~~tiY~~ 52 (216)
-|+++.|+..|+|+++|-+|
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 69
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=24.38 E-value=13 Score=13.00 Aligned_cols=27 Identities=4% Similarity=0.063 Sum_probs=21.1
Q ss_pred HHCCCCCCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 8749103547999998477854554026
Q T0575 26 AQNDYDSVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 26 ~~~G~~~~t~~~IA~~agvs~~tiY~~F 53 (216)
.++| .-.|-.|+|.-.|+|.+|+-+|-
T Consensus 100 ~dQg-alLT~~Dla~LL~~S~~TI~~~v 126 (220)
T PF07900_consen 100 YDQG-ALLTQEDLAILLGVSPKTISRDV 126 (220)
T ss_pred HHCC-CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 8647-85759999999888988899999
No 70
>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=24.02 E-value=12 Score=13.21 Aligned_cols=21 Identities=5% Similarity=0.332 Sum_probs=15.0
Q ss_pred CCHHHHHHHH-----CCCHHHHHCCC
Q ss_conf 5479999984-----77854554026
Q T0575 33 VSINRITERA-----GIAKGSFYQYF 53 (216)
Q Consensus 33 ~t~~~IA~~a-----gvs~~tiY~~F 53 (216)
.|..+|+.+. +||+.|+.+.+
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 71
>PF02909 TetR_C: Tetracyclin repressor, C-terminal all-alpha domain; InterPro: IPR004111 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification , : Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria . There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity . The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline . Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein involves 10 alpha-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.; GO: 0016566 specific transcriptional repressor activity, 0016481 negative regulation of transcription; PDB: 2hxi_B 2hxo_A 1z0x_B 2opt_B 3b6a_F 3b6c_B 2g7l_A 3bqy_A 2vpr_A 1bjy_A ....
Probab=23.51 E-value=13 Score=12.88 Aligned_cols=118 Identities=14% Similarity=0.113 Sum_probs=57.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf 56646899999999999998708089999999986164048999999999999999999999986488999999889999
Q T0575 82 STTDMFAYLRWLLDVGIQFQFHNPRLAQIAYKALYDDVPLPAETMQVIRHGSFAYFKQLVEQGIADGSLVPDLDADTAAF 161 (216)
Q Consensus 82 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~g~~~~~~~~~~~~~ 161 (216)
...++.+.++.+...+.+....||....+..... +.....+ ..+..++......| .+++....
T Consensus 4 ~~~~Wr~~l~~~a~~~r~~l~~hP~~a~l~~~~~----~~~p~~l--------~~~e~~l~~L~~aG-----~~~~~a~~ 66 (139)
T PF02909_consen 4 PGDDWRERLRALARALRAALLRHPWLAELLLSRP----PTGPNAL--------RLIEALLAALRDAG-----FSPEQAVR 66 (139)
T ss_dssp TT--HHHHHHHHHHHHHHHHHCSTTHHHHHHTS-------SHHHH--------HHHHHHHHHHHH---------HHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC----CCCHHHH--------HHHHHHHHHHHHCC-----CCHHHHHH
T ss_conf 9999999999999999999998928999987527----8870389--------99999999999869-----79999999
Q ss_pred HHHHHHHHHHHHHH--------HHCCCCHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999999999999--------6338990778999999---------9889999999999999999700169
Q T0575 162 VLNVVFTELGNHLI--------ERFAVNPAELLREGGI---------VLLQPAMRRVIEQVIDILERGMRRR 216 (216)
Q Consensus 162 ~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~l~~l~~Gl~~r 216 (216)
.+..+...+..... ................ ......-...++..++++..||.+|
T Consensus 67 ~~~~l~~~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~l~~~~~~~~~~~~~~~F~~gL~~iL~Glea~ 138 (139)
T PF02909_consen 67 AISALSSYVLGFALAEAAGLPRPSQRASQAADLDAALDPPHLAAAVQAAASADSDERFEFGLELILDGLEAR 138 (139)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCCS-HHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 999999999999848840366621000000038765158379999986156987789999999999999863
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=22.23 E-value=13 Score=12.92 Aligned_cols=21 Identities=5% Similarity=0.373 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHC
Q ss_conf 035479999984778545540
Q T0575 31 DSVSINRITERAGIAKGSFYQ 51 (216)
Q Consensus 31 ~~~t~~~IA~~agvs~~tiY~ 51 (216)
+.+|+.++|++.|++...+-.
T Consensus 2 ~~~rV~elAk~l~~~~~~ii~ 22 (54)
T PF04760_consen 2 EKIRVYELAKELGVSSKEIIK 22 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHH
T ss_pred CCEEHHHHHHHHCCCHHHHHH
T ss_conf 953699999998929999999
No 73
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA , . Within this family, the HTH motif is situated towards the C-terminus. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2gzw_A 1o3q_A 1lb2_A 1i6x_A 1ruo_B 1hw5_B 1zrf_A 1i5z_B 1j59_B 1o3s_A ....
Probab=22.11 E-value=14 Score=12.69 Aligned_cols=22 Identities=5% Similarity=0.249 Sum_probs=16.8
Q ss_pred CCCHHHHHHHHCCCHHHHHCCC
Q ss_conf 3547999998477854554026
Q T0575 32 SVSINRITERAGIAKGSFYQYF 53 (216)
Q Consensus 32 ~~t~~~IA~~agvs~~tiY~~F 53 (216)
.+|-++||+.+|+++-|+-+.+
T Consensus 2 ~lt~~elA~~~G~tretvsR~l 23 (32)
T PF00325_consen 2 PLTHQELADLLGTTRETVSRIL 23 (32)
T ss_dssp E--HHHHHHHCTC-HHHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9799999988698699999999
No 74
>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=22.02 E-value=14 Score=12.67 Aligned_cols=13 Identities=23% Similarity=0.672 Sum_probs=4.6
Q ss_pred CCCHHHHHHHHCC
Q ss_conf 3547999998477
Q T0575 32 SVSINRITERAGI 44 (216)
Q Consensus 32 ~~t~~~IA~~agv 44 (216)
++++++|+++.++
T Consensus 65 Gv~v~~i~~~l~~ 77 (102)
T PF08784_consen 65 GVHVDEIAQKLGM 77 (102)
T ss_dssp --BHHHHHHHSTS
T ss_pred CCCHHHHHHHHCC
T ss_conf 7189999999693
No 75
>PF06230 DUF1009: Protein of unknown function (DUF1009); InterPro: IPR010415 This is a family of uncharacterised bacterial proteins.
Probab=21.92 E-value=14 Score=12.66 Aligned_cols=51 Identities=16% Similarity=0.240 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf 999999999998749103547999998477854554026888899999999
Q T0575 15 SRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADKKDCYLYLIQ 65 (216)
Q Consensus 15 ~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sKe~L~~~~~~ 65 (216)
+.|+.+....|.++||+=++-.+++...=...|.+-..=||+++.-....-
T Consensus 52 d~lL~ai~~~~E~~G~~vv~a~~~~p~ll~~~G~lt~~~P~~~~~~Di~~g 102 (214)
T PF06230_consen 52 DALLRAIIDEFEEEGFEVVGAHEILPELLAPEGVLTGRKPSKEERADIAFG 102 (214)
T ss_pred HHHHHHHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 999999999999779999717895387468987667999698899999999
No 76
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator or FUR family includes metal ion uptake regulator proteins, which bind to the operator DNA and control the transcription of metal ion-responsive genes. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2w57_A 2fu4_A 1mzb_A 2o03_A 3f8n_A 2rgv_A 2fe3_A 3eyy_A.
Probab=21.90 E-value=14 Score=12.66 Aligned_cols=35 Identities=17% Similarity=0.379 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHH-----CCCHHHHHCC
Q ss_conf 899999999999987491035479999984-----7785455402
Q T0575 13 KRSRLIDVLLDEFAQNDYDSVSINRITERA-----GIAKGSFYQY 52 (216)
Q Consensus 13 ~r~~Il~aA~~lf~~~G~~~~t~~~IA~~a-----gvs~~tiY~~ 52 (216)
.|..|++ ++.+.+- ..|.++|.+.+ .+|.+|+|+-
T Consensus 9 qR~~Il~----~l~~~~~-~~sa~ei~~~l~~~~~~is~aTVYR~ 48 (120)
T PF01475_consen 9 QRRAILE----VLEESKE-HLSAEEIYDRLREKGPSISLATVYRT 48 (120)
T ss_dssp HHHHHHH----HHHHGGS-SEEHHHHHHHHHHT-TT--HHHHHHH
T ss_pred HHHHHHH----HHHHCCC-CCCHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 9999999----9982799-99999999998861899986249999
No 77
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This set of hypothetical proteins is found in prokaryotes. ; PDB: 2k02_A 1xn7_A.
Probab=21.63 E-value=14 Score=12.62 Aligned_cols=17 Identities=24% Similarity=0.470 Sum_probs=8.0
Q ss_pred CCCHHHHHHHHCCCHHH
Q ss_conf 35479999984778545
Q T0575 32 SVSINRITERAGIAKGS 48 (216)
Q Consensus 32 ~~t~~~IA~~agvs~~t 48 (216)
.+|..+||++.++|..+
T Consensus 14 ~~s~~eLa~~f~~s~~~ 30 (69)
T PF09012_consen 14 RVSLSELARHFGISPDA 30 (69)
T ss_dssp -EEHHHHHHHTT--HHH
T ss_pred CCCHHHHHHHHCCCHHH
T ss_conf 81899999997909999
No 78
>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=20.86 E-value=15 Score=12.50 Aligned_cols=36 Identities=14% Similarity=0.346 Sum_probs=24.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHCCCCCH
Q ss_conf 99999998749103547999998477854554026888
Q T0575 19 DVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYFADK 56 (216)
Q Consensus 19 ~aA~~lf~~~G~~~~t~~~IA~~agvs~~tiY~~F~sK 56 (216)
++.-.++... ...|++++|+..|++...|+..-..+
T Consensus 13 ~~~d~~~~~~--~~~~i~~~AK~lgi~~~~l~~~Lr~~ 48 (111)
T PF03374_consen 13 EFYDRFLNSD--GSMTIREAAKILGIGPNKLFKWLREK 48 (111)
T ss_pred HHHHHHHCCC--CCEEHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 9999995689--95779999999399999999999986
Done!