Query T0596 3NI7, Nitrosomonas europaea ATCC 19718, 213 residues
Match_columns 213
No_of_seqs 102 out of 12091
Neff 10.0
Searched_HMMs 11830
Date Mon Jul 5 09:16:09 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0596.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0596.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00440 TetR_N: Bacterial reg 99.0 2.4E-10 2E-14 96.5 6.0 47 12-58 1-47 (47)
2 PF08511 COQ9: COQ9; InterPro 97.3 0.0014 1.2E-07 43.5 10.6 75 114-191 3-77 (79)
3 PF01726 LexA_DNA_bind: LexA D 94.2 0.028 2.3E-06 33.4 4.7 45 6-51 5-50 (65)
4 PF02796 HTH_7: Helix-turn-hel 94.1 0.019 1.6E-06 34.6 3.7 34 13-50 11-44 (45)
5 PF00356 LacI: Bacterial regul 91.5 0.038 3.2E-06 32.3 2.2 35 29-63 1-35 (46)
6 PF04967 HTH_10: HTH DNA bindi 91.5 0.065 5.5E-06 30.5 3.4 45 7-51 3-47 (53)
7 PF06056 Terminase_5: Putative 89.5 0.15 1.3E-05 27.5 3.9 34 13-50 3-36 (58)
8 PF08279 HTH_11: HTH domain; 89.2 0.18 1.5E-05 27.1 4.0 41 8-53 1-41 (55)
9 PF01022 HTH_5: Bacterial regu 88.2 0.16 1.4E-05 27.3 3.3 40 6-52 1-40 (47)
10 PF08359 TetR_C_4: YsiA-like p 88.0 0.66 5.6E-05 22.6 8.5 110 63-173 5-121 (133)
11 PF03811 Ins_element1: Inserti 86.2 0.34 2.9E-05 24.9 3.9 36 7-50 51-86 (88)
12 PF01710 Transposase_14: Trans 83.2 0.55 4.6E-05 23.2 3.9 39 7-54 6-44 (119)
13 PF09339 HTH_IclR: IclR helix- 82.7 0.23 1.9E-05 26.2 1.8 35 17-52 9-43 (52)
14 PF00165 HTH_AraC: Bacterial r 78.2 0.49 4.1E-05 23.7 2.3 30 22-51 3-32 (42)
15 PF05225 HTH_psq: helix-turn-h 76.8 0.7 5.9E-05 22.4 2.8 40 10-52 2-41 (45)
16 PF07638 Sigma70_ECF: ECF sigm 76.4 0.6 5E-05 23.0 2.3 14 55-68 19-32 (185)
17 PF04703 FaeA: FaeA-like prote 75.6 1.1 9.1E-05 20.9 3.4 35 9-48 2-36 (62)
18 PF03444 DUF293: Domain of unk 75.0 1.4 0.00012 20.1 3.9 48 6-54 3-50 (78)
19 PF08220 HTH_DeoR: DeoR-like h 74.6 1.1 9.6E-05 20.8 3.4 34 17-52 6-39 (57)
20 PF01325 Fe_dep_repress: Iron 74.3 1.5 0.00013 19.9 3.9 40 7-48 4-43 (60)
21 PF00292 PAX: 'Paired box' dom 73.5 1.5 0.00013 19.8 3.7 34 5-46 19-52 (125)
22 PF04218 CENP-B_N: CENP-B N-te 73.2 0.87 7.4E-05 21.7 2.5 28 29-56 24-51 (53)
23 PF10654 DUF2481: Protein of u 72.2 0.82 6.9E-05 21.9 2.2 36 14-49 67-102 (126)
24 PF12116 SpoIIID: Stage III sp 70.9 2.3 0.00019 18.4 4.6 40 6-49 2-41 (82)
25 PF06163 DUF977: Bacterial pro 70.4 2.3 0.0002 18.3 5.1 42 7-50 8-49 (127)
26 PF01381 HTH_3: Helix-turn-hel 69.8 0.83 7E-05 21.9 1.7 38 19-59 4-41 (55)
27 PF01418 HTH_6: Helix-turn-hel 69.4 2.4 0.00021 18.2 4.5 52 7-60 16-72 (107)
28 PF08281 Sigma70_r4_2: Sigma-7 69.4 0.99 8.4E-05 21.2 2.1 32 17-48 16-47 (54)
29 PF00196 GerE: Bacterial regul 68.4 1.2 0.00011 20.4 2.4 25 26-50 17-41 (58)
30 PF00376 MerR: MerR family reg 68.0 0.97 8.2E-05 21.3 1.8 19 29-47 1-19 (38)
31 PF04297 UPF0122: Putative hel 66.0 2 0.00017 18.9 3.0 39 18-56 24-62 (101)
32 PF04182 B-block_TFIIIC: B-blo 65.4 2 0.00017 18.8 3.0 39 15-53 6-44 (75)
33 PF10668 Phage_terminase: Phag 64.1 3 0.00025 17.5 3.6 46 1-52 1-46 (60)
34 PF01527 Transposase_8: Transp 63.9 0.57 4.8E-05 23.1 -0.1 36 7-49 10-45 (76)
35 PF10078 DUF2316: Uncharacteri 63.2 3.1 0.00027 17.3 3.9 47 1-51 1-47 (89)
36 PF00046 Homeobox: Homeobox do 63.0 2.5 0.00021 18.1 3.1 40 11-52 13-52 (57)
37 PF05930 Phage_AlpA: Prophage 61.8 1.1 9E-05 21.0 1.0 23 28-50 4-26 (51)
38 PF01978 TrmB: Sugar-specific 60.1 1.2 0.00011 20.5 1.1 29 22-52 19-47 (68)
39 PF05043 Mga: Mga helix-turn-h 57.0 2.8 0.00023 17.8 2.5 32 25-56 28-59 (87)
40 PF01257 Complex1_24kDa: Respi 56.6 2.5 0.00021 18.1 2.2 46 7-52 10-62 (145)
41 PF06322 Phage_NinH: Phage Nin 55.7 1.9 0.00016 19.1 1.4 26 29-54 18-43 (64)
42 PF07374 DUF1492: Protein of u 54.9 2.7 0.00023 17.8 2.2 23 25-47 69-91 (100)
43 PF08280 HTH_Mga: M protein tr 54.4 4.2 0.00036 16.3 3.1 45 7-57 5-49 (59)
44 PF11740 KfrA_N: Plasmid repli 53.3 4.5 0.00038 16.1 8.4 42 8-51 2-44 (120)
45 PF00392 GntR: Bacterial regul 52.8 4.6 0.00038 16.0 4.3 39 10-48 3-45 (64)
46 PF05732 RepL: Firmicute plasm 52.3 4.3 0.00037 16.2 2.8 45 9-53 57-101 (165)
47 PF07022 Phage_CI_repr: Bacter 50.6 1.6 0.00014 19.5 0.4 39 19-59 6-44 (66)
48 PF02954 HTH_8: Bacterial regu 50.3 5 0.00042 15.8 4.4 32 10-47 7-38 (42)
49 PF02001 DUF134: Protein of un 49.2 3.5 0.00029 17.0 2.0 33 16-51 49-81 (106)
50 PF07750 GcrA: GcrA cell cycle 46.2 5.4 0.00045 15.5 2.5 26 17-45 11-37 (162)
51 PF01371 Trp_repressor: Trp re 45.1 4.4 0.00037 16.1 2.0 21 26-46 48-68 (87)
52 PF04223 CitF: Citrate lyase, 44.8 4.9 0.00042 15.8 2.2 48 28-75 6-56 (466)
53 PF01047 MarR: MarR family; I 42.1 6.5 0.00055 14.9 3.6 31 16-48 8-38 (59)
54 PF04545 Sigma70_r4: Sigma-70, 40.7 2.2 0.00018 18.6 -0.2 23 25-47 18-40 (50)
55 PF04539 Sigma70_r3: Sigma-70 38.7 7.2 0.00061 14.5 4.0 41 7-48 1-41 (78)
56 PF04552 Sigma54_DBD: Sigma-54 36.9 2.9 0.00025 17.6 0.0 49 6-54 19-76 (160)
57 PF06971 Put_DNA-bind_N: Putat 36.1 4.7 0.00039 16.0 0.9 34 15-48 16-49 (50)
58 PF02082 Rrf2: Transcriptional 34.6 8.3 0.0007 14.0 4.5 31 19-49 16-47 (83)
59 PF06892 Phage_CP76: Phage reg 33.8 8.5 0.00072 13.9 4.0 39 7-49 4-42 (162)
60 PF04036 DUF372: Domain of unk 33.3 4.1 0.00035 16.4 0.3 18 33-50 3-20 (38)
61 PF02042 RWP-RK: RWP-RK domain 33.1 8.7 0.00073 13.9 2.9 21 21-41 23-43 (52)
62 PF08535 KorB: KorB domain; I 32.4 7.4 0.00063 14.4 1.5 23 27-49 3-25 (93)
63 PF00126 HTH_1: Bacterial regu 32.1 9 0.00076 13.7 1.9 27 29-55 15-41 (60)
64 PF10975 DUF2802: Protein of u 31.3 8.7 0.00073 13.9 1.7 16 28-43 45-60 (70)
65 PF08006 DUF1700: Protein of u 31.3 9.3 0.00078 13.6 3.6 46 5-61 18-63 (181)
66 PF03374 ANT: Phage antirepres 29.2 10 0.00084 13.4 3.1 35 16-52 15-49 (111)
67 PF04963 Sigma54_CBD: Sigma-54 27.9 6.9 0.00058 14.6 0.7 38 6-43 31-68 (195)
68 PF11268 DUF3071: Protein of u 27.5 11 0.0009 13.2 2.2 21 27-47 69-89 (170)
69 PF08362 TetR_C_3: YcdC-like p 27.4 11 0.0009 13.1 11.0 40 75-114 16-55 (143)
70 PF04558 tRNA_synt_1c_R1: Glut 25.9 11 0.00095 13.0 3.2 28 14-41 4-31 (164)
71 PF08784 RPA_C: Replication pr 25.6 11 0.00096 12.9 3.4 36 8-45 48-83 (102)
72 PF01070 FMN_dh: FMN-dependent 24.8 12 0.001 12.8 2.0 45 20-65 91-135 (354)
73 PF04760 IF2_N: Translation in 24.2 10 0.00086 13.3 1.0 23 26-48 2-24 (54)
74 PF00325 Crp: Bacterial regula 24.0 12 0.001 12.8 1.3 23 28-50 3-25 (32)
75 PF01498 Transposase_5: Transp 23.8 12 0.001 12.7 2.5 28 20-49 8-40 (72)
76 PF08667 BetR: BetR domain; I 22.9 13 0.0011 12.6 4.6 45 10-54 4-49 (147)
77 PF07453 NUMOD1: NUMOD1 domain 21.5 14 0.0011 12.4 2.2 20 28-47 17-36 (37)
78 PF00382 TFIIB: Transcription 20.7 14 0.0012 12.2 2.9 13 29-41 56-68 (71)
79 PF01475 FUR: Ferric uptake re 20.1 14 0.0012 12.1 3.7 40 4-48 5-49 (120)
80 PF06230 DUF1009: Protein of u 20.1 14 0.0012 12.1 5.2 50 10-59 52-101 (214)
No 1
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD , , . Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution . TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1zk8_A 2oi8_A 2g7l_A 2opt_B 3b6a_F 3b6c_B 2hxo_A 2hxi_B 1z0x_B 1bjy_A ....
Probab=99.00 E-value=2.4e-10 Score=96.52 Aligned_cols=47 Identities=43% Similarity=0.568 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999986484121499999984887778763158988999999
Q T0596 12 IVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELIDAW 58 (213)
Q Consensus 12 Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~a~ 58 (213)
|+++|.++|.++||.++|+++||+++||++++||+||+||++|+.++
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
>PF08511 COQ9: COQ9; InterPro: IPR013718 COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q . It may either catalyse a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role.
Probab=97.34 E-value=0.0014 Score=43.50 Aligned_cols=75 Identities=24% Similarity=0.298 Sum_probs=61.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 858899999999999999999706787787778999999999999999873599977589999999999999988776
Q T0596 114 HIHIQIPAVMRVSRTVQWVREAAQRDATFMRRALEESTLTTIYLMTFFFWMRDESENSRHTRQFLKRHLTMAAWLGQK 191 (213)
Q Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~l~~~ 191 (213)
+.....+......+.|+ ...|+...++.++.....+..+|..+..+|+.|.++++..+..|+++.+.....++..
T Consensus 3 n~~~sl~~l~~l~D~Iw---~~aGD~S~D~~wYTKRa~La~iY~stel~~l~D~S~~~~~T~~Fl~rRi~~v~~~~~~ 77 (79)
T PF08511_consen 3 NAPTSLRELWRLADDIW---YAAGDRSTDFNWYTKRATLAAIYASTELFMLQDKSPDFADTWAFLDRRIEDVMKLGKM 77 (79)
T ss_pred CHHHHHHHHHHHHHHHH---HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 57579999999999999---9808964560289999999999999999997189977899999999999999999864
No 3
>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=94.19 E-value=0.028 Score=33.40 Aligned_cols=45 Identities=11% Similarity=0.236 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCC-HHHHHHHCCCH
Q ss_conf 78999999999999986484121499999984887-77876315898
Q T0596 6 DPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVS-LDEIRLYFREK 51 (213)
Q Consensus 6 ~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs-~~t~y~yF~sK 51 (213)
.++.++|++.-.+.+.++||. -|+++||+..|++ ++++++|-..-
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~-Pt~rEI~~~~gl~S~~tV~~~L~~L 50 (65)
T PF01726_consen 5 TPRQQEVLDFIKDYIREHGYP-PTVREIAEALGLKSPSTVHKHLKAL 50 (65)
T ss_dssp -HHHHHHHHHHHHHHHH-------HHHHHHH----SHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHCCCC-CCHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 999999999999999983889-8899999881999809999999999
No 4
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known . The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second , called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1jko_C 1jkp_C 1jj8_C 1hcr_A 1jkq_C 1jj6_C 1ijw_C 1jkr_C 1zr4_B 2gm4_A ....
Probab=94.07 E-value=0.019 Score=34.60 Aligned_cols=34 Identities=26% Similarity=0.428 Sum_probs=26.4
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCC
Q ss_conf 99999999864841214999999848877787631589
Q T0596 13 VDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 13 l~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~s 50 (213)
++.+.+|.. .| .|+.+||+..|||+.|||+|++.
T Consensus 11 ~~~i~~l~~-~G---~s~~~IAk~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 11 IEEIRELYA-QG---MSISEIAKRFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHHH--------HHHHHHHCTS-HHHHHHHHCC
T ss_pred HHHHHHHHH-CC---CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 999999999-79---99999999989199999999741
No 5
>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=91.52 E-value=0.038 Score=32.35 Aligned_cols=35 Identities=17% Similarity=0.152 Sum_probs=27.6
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 49999998488777876315898899999999999
Q T0596 29 RLYDIAARLAVSLDEIRLYFREKDELIDAWFDRAD 63 (213)
Q Consensus 29 tv~~IA~~aGvs~~t~y~yF~sKe~L~~a~~~~~~ 63 (213)
||.+||+.+|||++|+-++|.++..+-.+.-+++.
T Consensus 1 Ti~diA~~agvS~~TVSr~Ln~~~~vs~~tr~rI~ 35 (46)
T PF00356_consen 1 TIKDIAKAAGVSVATVSRVLNGPPRVSEETRERIL 35 (46)
T ss_dssp SHHHHHHHTTSSHHHHHHHHHTCTTSTHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 99999989894999999997589999899999999
No 6
>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=91.51 E-value=0.065 Score=30.48 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCH
Q ss_conf 899999999999998648412149999998488777876315898
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREK 51 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sK 51 (213)
++...++..|.++=-=.-...+|+.+||+..|||++|+.+|-..-
T Consensus 3 ~~q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~~T~~~~LRra 47 (53)
T PF04967_consen 3 DRQREVLRTAYEMGYFDWPRRITLEELAEELGISKSTFSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 899999999998688779875889999989499999999999999
No 7
>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=89.55 E-value=0.15 Score=27.55 Aligned_cols=34 Identities=24% Similarity=0.220 Sum_probs=27.4
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCC
Q ss_conf 99999999864841214999999848877787631589
Q T0596 13 VDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 13 l~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~s 50 (213)
-..|..|+. +|| |+.+||+..||+..|+|++..-
T Consensus 3 r~~A~~Ly~-~G~---~~~eIA~~Lgv~~~TV~~W~~r 36 (58)
T PF06056_consen 3 RRQARELYL-QGY---TPKEIAEELGVSRRTVYSWKKR 36 (58)
T ss_pred HHHHHHHHH-CCC---CHHHHHHHHCCCHHHHHHHHHH
T ss_conf 899999999-689---9999999988688899999997
No 8
>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=89.24 E-value=0.18 Score=27.06 Aligned_cols=41 Identities=24% Similarity=0.305 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHH
Q ss_conf 9999999999999864841214999999848877787631589889
Q T0596 8 MRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDE 53 (213)
Q Consensus 8 ~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~ 53 (213)
|+.+|+.. |+..+|+ +|..+||+..|||+.|+++|...-++
T Consensus 1 R~~~Il~~---L~~~~~~--it~~eLA~~l~vS~~Ti~~~i~~L~~ 41 (55)
T PF08279_consen 1 RQQQILEL---LLKNDGP--ITAKELAEELGVSRRTIRRDIKELEE 41 (55)
T ss_dssp HHHHHHHH---HHHCCTT--S-HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHH---HHHCCCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 98999999---9985999--88999999969799999999999998
No 9
>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=88.20 E-value=0.16 Score=27.34 Aligned_cols=40 Identities=23% Similarity=0.365 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 78999999999999986484121499999984887778763158988
Q T0596 6 DPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 6 ~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
+++|-+|+..-.+ | ..++.+|++..|++++++++|...-+
T Consensus 1 d~~R~~Il~~L~~-----~--~~~~~eia~~l~~s~~tvs~HL~~L~ 40 (47)
T PF01022_consen 1 DPTRLKILKLLSE-----G--PLSVSEIAEELGISQSTVSRHLKKLE 40 (47)
T ss_dssp SHHHHHHHHHHHH-----S--CEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHH-----C--CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9889999999986-----8--96799988361235658999999999
No 10
>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=88.01 E-value=0.66 Score=22.59 Aligned_cols=110 Identities=15% Similarity=0.089 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH---HHHHHHHHHHHHHHHHCCC
Q ss_conf 9999988754320134578899999999999987518999999998744678588999---9999999999999970678
Q T0596 63 DSRMLKEAESAGFLDLVASERIHHLIMIWLDALAVQRKVTRQMIMSKLEFGHIHIQIP---AVMRVSRTVQWVREAAQRD 139 (213)
Q Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 139 (213)
+.++...+........++.+++..++...+.....++............ ........ ....+...+..++..+...
T Consensus 5 ~~~~~~~~~~~~~~~~~~~ekL~~~i~~hl~~~~~~~~~~~v~~~E~~~-~~~~~~~~i~~~~~~y~~~i~~iI~eGq~~ 83 (133)
T PF08359_consen 5 MNELLEELEEALASEDSPREKLRALIRAHLRFLEENPDLAIVFQLELRQ-SNPELREEINELRREYFRLIEEIIEEGQEQ 83 (133)
T ss_dssp ---HHHHHHHHHCC--SHHHHHHHHHHHHHHHH---HHHHHHHHCTTS--SSHHHHHHHHHHH---HHHH----------
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999871689999999999999999998099748748998875-789999999999999999999999999985
Q ss_pred ---CCCCCHHHHHHHHHHHHHHHHHHHHC-CCCCCHHH
Q ss_conf ---77877789999999999999998735-99977589
Q T0596 140 ---ATFMRRALEESTLTTIYLMTFFFWMR-DESENSRH 173 (213)
Q Consensus 140 ---~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 173 (213)
..+........++.++...++..|.. +...+...
T Consensus 84 G~fr~dld~~~~~~~i~G~i~~~v~~w~~~~~~~~l~~ 121 (133)
T PF08359_consen 84 GEFRPDLDPELAARMIFGTINGTVTQWVLSDGKFDLEE 121 (133)
T ss_dssp --B-----HHHHHHHH---HHHHHHHHHHTTT-S-CGG
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf 98889899999999999999999999986489879999
No 11
>PF03811 Ins_element1: Insertion element protein; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. This protein is absolutely required for transposition of insertion element 1.; GO: 0006313 transposition, DNA-mediated
Probab=86.17 E-value=0.34 Score=24.89 Aligned_cols=36 Identities=19% Similarity=0.430 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCC
Q ss_conf 89999999999999864841214999999848877787631589
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~s 50 (213)
..+++|++-. .++.++++||+..||+..|++++.++
T Consensus 51 ~~k~~i~~l~--------~~G~siR~iArvl~Is~~Tv~r~lK~ 86 (88)
T PF03811_consen 51 EVKQKILELM--------VEGMSIRDIARVLGISINTVLRWLKN 86 (88)
T ss_pred HHHHHHHHHH--------HCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 6999999998--------76851999999868789999999862
No 12
>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=83.18 E-value=0.55 Score=23.24 Aligned_cols=39 Identities=15% Similarity=0.339 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHH
Q ss_conf 899999999999998648412149999998488777876315898899
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDEL 54 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L 54 (213)
+-|++||++ .+.|. |++++|++-|||++|+|+++. +.+.
T Consensus 6 DlR~kvi~~-----~~~G~---S~~eaA~~F~VS~~Tv~rW~k-~~~~ 44 (119)
T PF01710_consen 6 DLRQKVIAY-----VEQGM---SIREAAKRFGVSRSTVYRWLK-RRET 44 (119)
T ss_pred HHHHHHHHH-----HHCCC---CHHHHHHHHCCCHHHHHHHHH-HHHC
T ss_conf 999999999-----99599---999999996955999999998-6411
No 13
>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=82.71 E-value=0.23 Score=26.23 Aligned_cols=35 Identities=17% Similarity=0.259 Sum_probs=26.7
Q ss_pred HHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 999986484121499999984887778763158988
Q T0596 17 VELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 17 ~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
++.|.+.+-. .|+.+||++.|++++|+|+|..+-.
T Consensus 9 L~~l~~~~~~-~t~~eia~~~gl~~st~~r~l~~L~ 43 (52)
T PF09339_consen 9 LEALARAPRP-LTLSEIARALGLPKSTVHRLLQTLE 43 (52)
T ss_dssp HHTHCTTBSS-EEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHCCCC-CCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999878999-8999999998919999999999999
No 14
>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=78.17 E-value=0.49 Score=23.66 Aligned_cols=30 Identities=23% Similarity=0.278 Sum_probs=24.7
Q ss_pred HCCCCHHHHHHHHHHHCCCHHHHHHHCCCH
Q ss_conf 648412149999998488777876315898
Q T0596 22 HTSWEAVRLYDIAARLAVSLDEIRLYFREK 51 (213)
Q Consensus 22 e~G~~~~tv~~IA~~aGvs~~t~y~yF~sK 51 (213)
++--...||.+||.++|+|+..|++.|+..
T Consensus 3 ~~~~~~~~i~~iA~~~g~s~~~~~r~Fk~~ 32 (42)
T PF00165_consen 3 EHLSEPISIEDIAEELGYSPSYFSRLFKKE 32 (42)
T ss_dssp TTTCSS--HHHHHHHTTSSHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 756898979999999798999999999999
No 15
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster . In pipsqueak this domain binds to GAGA sequence . The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex .; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2cob_A.
Probab=76.84 E-value=0.7 Score=22.41 Aligned_cols=40 Identities=15% Similarity=0.251 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 9999999999986484121499999984887778763158988
Q T0596 10 DAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 10 ~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
+.-++.|++-+...+ .|++.+|+.-||+++|++++...+.
T Consensus 2 ee~l~~Ai~~v~~g~---~Si~~aA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 2 EERLQEAIEAVKNGK---LSIRKAARKYGVPRSTLRRRLKGKP 41 (45)
T ss_dssp HHHHHHHHHHHH--------HHHHHHH----HHHHHHHHHH--
T ss_pred HHHHHHHHHHHHCCC---CCHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf 699999999999099---5799999998939899999992787
No 16
>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=76.44 E-value=0.6 Score=22.96 Aligned_cols=14 Identities=14% Similarity=0.245 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999998
Q T0596 55 IDAWFDRADSRMLK 68 (213)
Q Consensus 55 ~~a~~~~~~~~~~~ 68 (213)
++.++..+..++..
T Consensus 19 ~~~L~~~~y~~Lr~ 32 (185)
T PF07638_consen 19 ADQLLPRVYEELRR 32 (185)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999999999
No 17
>PF04703 FaeA: FaeA-like protein; InterPro: IPR006793 This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase , .; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription, 0009289 fimbrium; PDB: 2htj_A 2jt1_A.
Probab=75.56 E-value=1.1 Score=20.94 Aligned_cols=35 Identities=20% Similarity=0.315 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHC
Q ss_conf 9999999999998648412149999998488777876315
Q T0596 9 RDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 9 R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF 48 (213)
++.|++--... ...+|+++||+.+|++.....+|-
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 18
>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=75.03 E-value=1.4 Score=20.14 Aligned_cols=48 Identities=29% Similarity=0.232 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHH
Q ss_conf 7899999999999998648412149999998488777876315898899
Q T0596 6 DPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDEL 54 (213)
Q Consensus 6 ~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L 54 (213)
+++...||.+-+++..+.|- .+.=..||+..++|.+|+.+--.+-++|
T Consensus 3 t~rq~~IL~~lv~~Y~~~~~-PVgSk~ia~~l~~s~aTIRN~M~~Le~l 50 (78)
T PF03444_consen 3 TERQREILKALVELYIETGE-PVGSKTIAEELDRSPATIRNEMADLEEL 50 (78)
T ss_pred CHHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 88999999999999997399-7766999998688908899999999987
No 19
>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=74.59 E-value=1.1 Score=20.77 Aligned_cols=34 Identities=26% Similarity=0.288 Sum_probs=27.8
Q ss_pred HHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 999986484121499999984887778763158988
Q T0596 17 VELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 17 ~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
++++.++|+ +|+.++|+..|||..|+.+++...+
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 20
>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=74.26 E-value=1.5 Score=19.85 Aligned_cols=40 Identities=25% Similarity=0.280 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHC
Q ss_conf 899999999999998648412149999998488777876315
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF 48 (213)
++.+.-|.+-..+..++ ..++..+||++.||+++|+..-.
T Consensus 4 ~~~e~YL~~I~~l~~~~--~~v~~~~IA~~L~vs~~TVs~ml 43 (60)
T PF01325_consen 4 ESEEDYLKAIYELSEEG--GPVSTSDIAERLGVSPPTVSEML 43 (60)
T ss_dssp SHHHHHHHHHHHHHHH---S--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 06999999999998069--97219999999789907899999
No 21
>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=73.54 E-value=1.5 Score=19.84 Aligned_cols=34 Identities=35% Similarity=0.422 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHH
Q ss_conf 178999999999999986484121499999984887778763
Q T0596 5 NDPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRL 46 (213)
Q Consensus 5 ~~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~ 46 (213)
+++.|++|++.+. .+++..+|+++.+||.+.+..
T Consensus 19 p~~~R~rIv~l~~--------~G~r~~~Isr~l~VS~gcVsK 52 (125)
T PF00292_consen 19 PNELRQRIVELAH--------EGVRPCDISRQLRVSHGCVSK 52 (125)
T ss_dssp -HHHHHHHHHHHH------------HHHHHHHHT-----HHH
T ss_pred CHHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHH
T ss_conf 8999999999976--------258774899876514769999
No 22
>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=73.19 E-value=0.87 Score=21.67 Aligned_cols=28 Identities=18% Similarity=0.396 Sum_probs=26.3
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCHHHHHH
Q ss_conf 4999999848877787631589889999
Q T0596 29 RLYDIAARLAVSLDEIRLYFREKDELID 56 (213)
Q Consensus 29 tv~~IA~~aGvs~~t~y~yF~sKe~L~~ 56 (213)
|..+||+.-||+.+|+|..-.+|+.++.
T Consensus 24 s~~~iAr~fgi~~sTi~~i~k~k~~i~~ 51 (53)
T PF04218_consen 24 SQREIAREFGISRSTISRILKNKEKILE 51 (53)
T ss_dssp -HHHHHHHHT--CCHHHHHCCTHHHHCC
T ss_pred CHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 8999998919988899999983999985
No 23
>PF10654 DUF2481: Protein of unknown function (DUF2481)
Probab=72.16 E-value=0.82 Score=21.86 Aligned_cols=36 Identities=17% Similarity=0.237 Sum_probs=28.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCC
Q ss_conf 999999986484121499999984887778763158
Q T0596 14 DTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFR 49 (213)
Q Consensus 14 ~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~ 49 (213)
+..+.-|.+.-++|+|..+||+.-|||++++|.|..
T Consensus 67 ei~i~Ef~~lR~AGvt~~~IAd~F~Isks~v~Nf~q 102 (126)
T PF10654_consen 67 EITIREFAELRHAGVTWYAIADHFNISKSTVFNFTQ 102 (126)
T ss_pred CCCHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 121999999996488789999982873999999999
No 24
>PF12116 SpoIIID: Stage III sporulation protein D
Probab=70.86 E-value=2.3 Score=18.38 Aligned_cols=40 Identities=13% Similarity=0.162 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCC
Q ss_conf 78999999999999986484121499999984887778763158
Q T0596 6 DPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFR 49 (213)
Q Consensus 6 ~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~ 49 (213)
+...++.++.+-=++.. ..||+..|+.-|||++|++.-+.
T Consensus 2 ~yIeeR~~~ia~yIi~~----~aTVR~tAk~FGVSKSTVHkDvT 41 (82)
T PF12116_consen 2 DYIEERVLEIANYIIEN----KATVRQTAKVFGVSKSTVHKDVT 41 (82)
T ss_pred CHHHHHHHHHHHHHHHC----CHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 28999999999999974----51699999997852999989999
No 25
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=70.45 E-value=2.3 Score=18.32 Aligned_cols=42 Identities=21% Similarity=0.321 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCC
Q ss_conf 89999999999999864841214999999848877787631589
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~s 50 (213)
+-|+.|...-+++..++|. .|+.++.+.-|+++.|+-+||..
T Consensus 8 ~eR~ei~~rIVElVR~~GR--iTi~ql~~~TG~sR~T~k~~lr~ 49 (127)
T PF06163_consen 8 EEREEIKARIVELVREHGR--ITIRQLVKMTGASRNTAKKYLRE 49 (127)
T ss_pred HHHHHHHHHHHHHHHHHCH--HHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999999999998163--02999999978679999999999
No 26
>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=69.84 E-value=0.83 Score=21.85 Aligned_cols=38 Identities=18% Similarity=0.087 Sum_probs=28.3
Q ss_pred HHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHH
Q ss_conf 99864841214999999848877787631589889999999
Q T0596 19 LAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELIDAWF 59 (213)
Q Consensus 19 l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~a~~ 59 (213)
+..++|+ |..++|+.+|+++++++++..++...=...+
T Consensus 4 ~r~~~gl---s~~~la~~~gis~~~i~~~e~g~~~~~~~~l 41 (55)
T PF01381_consen 4 LREERGL---SQEELARRLGISRSTISRIENGKRNPSIETL 41 (55)
T ss_dssp HHHHTT-----HHHHHHHHTS-HHHHHHHHTTSSGSBHHHH
T ss_pred HHHHCCC---CHHHHHHHCCCCHHHHHHHHCCCCCCCHHHH
T ss_conf 8978699---9999988649878788899769989999999
No 27
>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=69.41 E-value=2.4 Score=18.16 Aligned_cols=52 Identities=15% Similarity=0.178 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHH-----CCCHHHHHHHHHH
Q ss_conf 89999999999999864841214999999848877787631-----5898899999999
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLY-----FREKDELIDAWFD 60 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~y-----F~sKe~L~~a~~~ 60 (213)
+.-.+|.+--..-..+ +...|+.+||+.+|||++|+.+. |.+-.++-..+..
T Consensus 16 ~~e~~Ia~yil~~~~~--~~~~si~~lA~~~~vS~atv~Rf~kkLGf~gf~efk~~l~~ 72 (107)
T PF01418_consen 16 PSEKKIADYILNNPDK--IANMSISELAKAAGVSPATVVRFCKKLGFSGFSEFKVDLAK 72 (107)
T ss_dssp HHHHHHHHHHHH-HHH--HTT--HHHHHHHTT--HHHHHHHHHH------HHHHHHH--
T ss_pred HHHHHHHHHHHHCHHH--HHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9999999999929999--97754999999979898899999999289999999999999
No 28
>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=69.37 E-value=0.99 Score=21.23 Aligned_cols=32 Identities=19% Similarity=0.232 Sum_probs=26.2
Q ss_pred HHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHC
Q ss_conf 99998648412149999998488777876315
Q T0596 17 VELAAHTSWEAVRLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 17 ~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF 48 (213)
..+|.-+=+++.|..+||+..|+|.++++.+.
T Consensus 16 r~i~~l~~~~g~s~~eIA~~l~is~~tv~~~l 47 (54)
T PF08281_consen 16 REIFLLRYFEGLSYKEIAEILGISESTVKSRL 47 (54)
T ss_dssp HHHHHHHHT----HHHHHHHCTS----HHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999969589999999891999999999
No 29
>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=68.42 E-value=1.2 Score=20.44 Aligned_cols=25 Identities=24% Similarity=0.312 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHHCCCHHHHHHHCCC
Q ss_conf 1214999999848877787631589
Q T0596 26 EAVRLYDIAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 26 ~~~tv~~IA~~aGvs~~t~y~yF~s 50 (213)
.|.|..+||+..|+|..|+++|..+
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 30
>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=68.01 E-value=0.97 Score=21.30 Aligned_cols=19 Identities=32% Similarity=0.544 Sum_probs=17.4
Q ss_pred HHHHHHHHHCCCHHHHHHH
Q ss_conf 4999999848877787631
Q T0596 29 RLYDIAARLAVSLDEIRLY 47 (213)
Q Consensus 29 tv~~IA~~aGvs~~t~y~y 47 (213)
||.++|+.+||+..++.+|
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 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=66.05 E-value=2 Score=18.90 Aligned_cols=39 Identities=18% Similarity=0.216 Sum_probs=30.6
Q ss_pred HHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHH
Q ss_conf 999864841214999999848877787631589889999
Q T0596 18 ELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELID 56 (213)
Q Consensus 18 ~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~ 56 (213)
+.+.-.=.+..|+.+||..-|||+.++|....--+..+.
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
>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=65.44 E-value=2 Score=18.77 Aligned_cols=39 Identities=8% Similarity=0.136 Sum_probs=34.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHH
Q ss_conf 999999864841214999999848877787631589889
Q T0596 15 TAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDE 53 (213)
Q Consensus 15 AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~ 53 (213)
..++.++..++.|.+..++++..|+.+.+++++...-++
T Consensus 6 ~lLe~Ia~~r~~Gi~q~dL~k~~~~D~r~~~~~~k~L~~ 44 (75)
T PF04182_consen 6 CLLERIARSRYNGITQSDLWKLFGQDPRSVFYRVKKLED 44 (75)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 999999967768820537799858992256899999977
No 33
>PF10668 Phage_terminase: Phage terminase small subunit
Probab=64.10 E-value=3 Score=17.52 Aligned_cols=46 Identities=35% Similarity=0.551 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 9997178999999999999986484121499999984887778763158988
Q T0596 1 MTINNDPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 1 ~t~~~~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
|-..+++.|+. |.+++.++| +..+..+||+..||+..+|- .+.+++
T Consensus 1 Mar~Rsp~Rdk----A~e~y~~~~-g~~~~k~IAe~lgvs~~tIr-~WKs~d 46 (60)
T PF10668_consen 1 MARQRSPNRDK----AFEIYKESN-GKIKLKDIAEKLGVSESTIR-KWKSRD 46 (60)
T ss_pred CCCCCCCCHHH----HHHHHHHCC-CCCCHHHHHHHHCCCHHHHH-HHHHHC
T ss_conf 99888958899----999999818-98419999999797999987-341022
No 34
>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=63.85 E-value=0.57 Score=23.14 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCC
Q ss_conf 8999999999999986484121499999984887778763158
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFR 49 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~ 49 (213)
+-+.+||..+ .+. +.|+.+||++.||++++||++-.
T Consensus 10 efK~~~V~~~----~~~---g~s~~~va~~~gI~~~tl~~W~~ 45 (76)
T PF01527_consen 10 EFKLQIVEEA----LEE---GRSVSEVAREYGISPSTLYRWVR 45 (76)
T ss_dssp HHHHHHHHHH----CHH----HHHHHHCCC----HHHHHHHHH
T ss_pred HHHHHHHHHH----HHC---CCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 9999999999----987---99799999970533026669999
No 35
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316)
Probab=63.22 E-value=3.1 Score=17.30 Aligned_cols=47 Identities=21% Similarity=0.310 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCH
Q ss_conf 999717899999999999998648412149999998488777876315898
Q T0596 1 MTINNDPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREK 51 (213)
Q Consensus 1 ~t~~~~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sK 51 (213)
|+.|.+|++.- ..+|=...-..++|+.+||+..|+|..-+-+-+.=|
T Consensus 1 MSLn~~e~~~T----~~ELqanf~l~~Ls~~~ia~dL~~s~~~ve~vL~l~ 47 (89)
T PF10078_consen 1 MSLNKEERKAT----RKELQANFELSGLSIEQIAKDLGTSPEKVEQVLNLK 47 (89)
T ss_pred CCCCHHHHHHH----HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 99889999976----999999999849999999999689999999898604
No 36
>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=62.98 E-value=2.5 Score=18.08 Aligned_cols=40 Identities=15% Similarity=0.297 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 999999999986484121499999984887778763158988
Q T0596 11 AIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 11 ~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
.+|+..... ..=.+.-.+..||+..|++...|..+|.++-
T Consensus 13 ~~Le~~f~~--~~~P~~~~~~~La~~~~l~~~~V~~WF~nrR 52 (57)
T PF00046_consen 13 EILEEYFEK--NPYPSEEEIEELAKELGLSEKQVKNWFQNRR 52 (57)
T ss_dssp HHHHHHHHH--SSSCCHHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHH--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999987--5756500556542334320045512499878
No 37
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This family consists of several short bacterial and phage proteins, which are related to the Escherichia coli protein AlpA. AlpA suppresses two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light . Several of the sequences in this family are thought to be DNA-binding proteins.; PDB: 1z4h_A.
Probab=61.78 E-value=1.1 Score=20.97 Aligned_cols=23 Identities=22% Similarity=0.388 Sum_probs=20.2
Q ss_pred HHHHHHHHHHCCCHHHHHHHCCC
Q ss_conf 14999999848877787631589
Q T0596 28 VRLYDIAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 28 ~tv~~IA~~aGvs~~t~y~yF~s 50 (213)
+++.++|+..|+|++|+|++-.+
T Consensus 4 l~~~ev~~~lgvs~~t~y~~~~~ 26 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTLYRLIKD 26 (51)
T ss_dssp E-HHHHHHH-----HHHHHHHH-
T ss_pred ECHHHHHHHHCCCHHHHHHHHHC
T ss_conf 24999999989499999999775
No 38
>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=60.11 E-value=1.2 Score=20.46 Aligned_cols=29 Identities=14% Similarity=0.260 Sum_probs=23.2
Q ss_pred HCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 6484121499999984887778763158988
Q T0596 22 HTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 22 e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
++| ..|+.+|++..|++++++|++..+-+
T Consensus 19 ~~~--~~t~~eia~~~~i~~~~v~~~l~~L~ 47 (68)
T PF01978_consen 19 ENG--GATASEIAEKLGISRSTVYRILKRLE 47 (68)
T ss_dssp HTS---EEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred HCC--CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 579--95999999998909999999999999
No 39
>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=56.99 E-value=2.8 Score=17.75 Aligned_cols=32 Identities=25% Similarity=0.293 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHH
Q ss_conf 41214999999848877787631589889999
Q T0596 25 WEAVRLYDIAARLAVSLDEIRLYFREKDELID 56 (213)
Q Consensus 25 ~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~ 56 (213)
-+.+|+.++|+..+||++|+++....-+..+.
T Consensus 28 ~~~~~~~~la~~l~vS~sTi~~~lk~i~~~L~ 59 (87)
T PF05043_consen 28 NEYVSIEDLAEELYVSRSTIYRDLKKINQILK 59 (87)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 89968999999979899999999999999999
No 40
>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=56.63 E-value=2.5 Score=18.10 Aligned_cols=46 Identities=20% Similarity=0.296 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHCCCHH------HHHHHCCCHH
Q ss_conf 8999999999999986484-12149999998488777------8763158988
Q T0596 7 PMRDAIVDTAVELAAHTSW-EAVRLYDIAARLAVSLD------EIRLYFREKD 52 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~-~~~tv~~IA~~aGvs~~------t~y~yF~sKe 52 (213)
..++.+|..-..+=.+.|| ..-.+..||+..|++.+ |||.+|..+.
T Consensus 10 ~~~~~ll~~L~~iQ~~~g~i~~~~~~~iA~~l~i~~~~v~~v~tFY~~f~~~p 62 (145)
T PF01257_consen 10 RKRSALLPILHEIQEEFGYIPPEAIEEIAERLGIPPAEVYGVATFYSMFRRQP 62 (145)
T ss_dssp --GGGHHHHHHHHHHH-----HHHHHHHHHH----HHHH---TTTSSSS-SS-
T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCC
T ss_conf 97778999999999980999999999999997988999999999875612179
No 41
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=55.72 E-value=1.9 Score=19.10 Aligned_cols=26 Identities=23% Similarity=0.303 Sum_probs=23.5
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCHHHH
Q ss_conf 49999998488777876315898899
Q T0596 29 RLYDIAARLAVSLDEIRLYFREKDEL 54 (213)
Q Consensus 29 tv~~IA~~aGvs~~t~y~yF~sKe~L 54 (213)
++.++|+..|++++|+-.|-.+|++=
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 42
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown.
Probab=54.89 E-value=2.7 Score=17.79 Aligned_cols=23 Identities=13% Similarity=0.098 Sum_probs=14.7
Q ss_pred CCHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 41214999999848877787631
Q T0596 25 WEAVRLYDIAARLAVSLDEIRLY 47 (213)
Q Consensus 25 ~~~~tv~~IA~~aGvs~~t~y~y 47 (213)
++..+..+||...|+|++++|+.
T Consensus 69 i~~~~~~~I~~~L~iS~~tyYr~ 91 (100)
T PF07374_consen 69 IDKLSWDEICEELNISRSTYYRK 91 (100)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 83598999999987889999999
No 43
>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=54.37 E-value=4.2 Score=16.30 Aligned_cols=45 Identities=22% Similarity=0.237 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHH
Q ss_conf 899999999999998648412149999998488777876315898899999
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELIDA 57 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~a 57 (213)
.++-.|+ .++.++| ..|+.+||+..|+|..++.+|...-.+.|..
T Consensus 5 ~r~~~Ll----~~L~~~~--~~t~~ela~~l~~S~~ti~~~I~~l~~~f~~ 49 (59)
T PF08280_consen 5 KRQLKLL----ELLLKNG--WITLKELAKKLGLSERTIRNDINELNEEFPE 49 (59)
T ss_pred HHHHHHH----HHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 9999999----9999779--7979999999798899999999999998635
No 44
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term
Probab=53.25 E-value=4.5 Score=16.10 Aligned_cols=42 Identities=19% Similarity=0.166 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC-CCHHHHHHHCCCH
Q ss_conf 9999999999999864841214999999848-8777876315898
Q T0596 8 MRDAIVDTAVELAAHTSWEAVRLYDIAARLA-VSLDEIRLYFREK 51 (213)
Q Consensus 8 ~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aG-vs~~t~y~yF~sK 51 (213)
+++.|.+|+-.|+.+.. ..|+..|=++.| .|.+++-.|.+..
T Consensus 2 t~e~V~~Aa~~L~~~G~--~PTv~~VR~~lG~GS~~ti~~~lk~w 44 (120)
T PF11740_consen 2 TYEDVAAAADALLAAGK--RPTVDAVRERLGTGSMSTISKHLKEW 44 (120)
T ss_pred CHHHHHHHHHHHHHCCC--CCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 69999999999987489--99899999998795889999999999
No 45
>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=52.83 E-value=4.6 Score=16.05 Aligned_cols=39 Identities=13% Similarity=0.151 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHCCC---CHH-HHHHHHHHHCCCHHHHHHHC
Q ss_conf 9999999999986484---121-49999998488777876315
Q T0596 10 DAIVDTAVELAAHTSW---EAV-RLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 10 ~~Il~AA~~l~~e~G~---~~~-tv~~IA~~aGvs~~t~y~yF 48 (213)
++|.+.-.+.+....| +.+ |.+++|++.|||+.++..-+
T Consensus 3 ~~v~~~i~~~I~~g~l~~G~~lPs~~~La~~~~vSr~tvr~Al 45 (64)
T PF00392_consen 3 EQVYEYIRRDILSGELKPGDRLPSERELAERFGVSRTTVREAL 45 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999999984999999993689999988687989999999
No 46
>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=52.31 E-value=4.3 Score=16.22 Aligned_cols=45 Identities=16% Similarity=0.118 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHH
Q ss_conf 999999999999864841214999999848877787631589889
Q T0596 9 RDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDE 53 (213)
Q Consensus 9 R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~ 53 (213)
+-+|+--.+.-+...+.=-.|.++||+..|+|++|+++-|..-++
T Consensus 57 ~~~Vl~~ll~~~d~~N~v~~t~~~Ia~~lgiS~~Tv~r~iK~L~e 101 (165)
T PF05732_consen 57 KFRVLMFLLENMDSDNAVVATQKEIAEELGISKPTVSRTIKELEE 101 (165)
T ss_pred HHHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 799999999843779839878999999979888899999999987
No 47
>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=50.59 E-value=1.6 Score=19.54 Aligned_cols=39 Identities=13% Similarity=0.319 Sum_probs=26.4
Q ss_pred HHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHH
Q ss_conf 99864841214999999848877787631589889999999
Q T0596 19 LAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELIDAWF 59 (213)
Q Consensus 19 l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~a~~ 59 (213)
+....|+. |..++|+..||++++|.+.+..++.+=...+
T Consensus 6 l~~~~g~~--~~~elA~~LgIs~stvs~~~~~r~~~P~~~~ 44 (66)
T PF07022_consen 6 LKEAYGIK--TDKELAEKLGISQSTVSHTWKKRNSIPFEWL 44 (66)
T ss_dssp HHHH------SCHHHHCCTT--HHHHH-HHHH-----HHHH
T ss_pred HHHHHCCC--CHHHHHHHHCCCHHHHHHHHHHCCCCCHHHH
T ss_conf 99996899--6999999919988885567641688989999
No 48
>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=50.29 E-value=5 Score=15.76 Aligned_cols=32 Identities=16% Similarity=0.188 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999999864841214999999848877787631
Q T0596 10 DAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLY 47 (213)
Q Consensus 10 ~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~y 47 (213)
..+|..+++ ..|+ ++...|+..|+++.+||+.
T Consensus 7 ~~~i~~aL~---~~~g---n~~~aA~~Lgi~r~tL~~k 38 (42)
T PF02954_consen 7 RELIEEALE---RHGG---NISKAARLLGISRSTLYRK 38 (42)
T ss_dssp HHHHHHHHH---HTTT----HHHHHHH----HHHHHHH
T ss_pred HHHHHHHHH---HHCC---CHHHHHHHHCCCHHHHHHH
T ss_conf 999999999---8299---8999999979899999999
No 49
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=49.21 E-value=3.5 Score=16.97 Aligned_cols=33 Identities=18% Similarity=0.339 Sum_probs=24.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCH
Q ss_conf 999998648412149999998488777876315898
Q T0596 16 AVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREK 51 (213)
Q Consensus 16 A~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sK 51 (213)
|++|. -|.+.|-.+-|.+.|||++||.+-..+-
T Consensus 49 AiRL~---D~egl~QeeAA~~MgVSR~Tf~ril~~A 81 (106)
T PF02001_consen 49 AIRLV---DYEGLTQEEAAEQMGVSRQTFQRILKSA 81 (106)
T ss_pred HHHHH---HHHCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 99998---8817989999998497799999999999
No 50
>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=46.20 E-value=5.4 Score=15.50 Aligned_cols=26 Identities=19% Similarity=0.172 Sum_probs=18.7
Q ss_pred HHHHHHCCCCHHHHHHHHHHHC-CCHHHHH
Q ss_conf 9999864841214999999848-8777876
Q T0596 17 VELAAHTSWEAVRLYDIAARLA-VSLDEIR 45 (213)
Q Consensus 17 ~~l~~e~G~~~~tv~~IA~~aG-vs~~t~y 45 (213)
+.-++..| .|-++||++.| ||++++-
T Consensus 11 Lk~lw~eG---lSasqIA~~LGgvsRNAVi 37 (162)
T PF07750_consen 11 LKKLWAEG---LSASQIAKQLGGVSRNAVI 37 (162)
T ss_pred HHHHHHCC---CCHHHHHHHHCCCCHHHHH
T ss_conf 99999858---8899999997552066677
No 51
>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=45.08 E-value=4.4 Score=16.14 Aligned_cols=21 Identities=19% Similarity=0.177 Sum_probs=16.5
Q ss_pred CHHHHHHHHHHHCCCHHHHHH
Q ss_conf 121499999984887778763
Q T0596 26 EAVRLYDIAARLAVSLDEIRL 46 (213)
Q Consensus 26 ~~~tv~~IA~~aGvs~~t~y~ 46 (213)
.+.|-++|++..|+|..|+-+
T Consensus 48 ~~~syreI~~~tG~S~aTIsR 68 (87)
T PF01371_consen 48 GGKSYREIAEETGASIATISR 68 (87)
T ss_dssp TTHSHHHHHHH----HHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHH
T ss_conf 799899999997877889999
No 52
>PF04223 CitF: Citrate lyase, alpha subunit (CitF); InterPro: IPR006472 These sequences, from both Gram-positive and Gram-negative bacteria, represent the alpha subunit of the holoenzyme citrate lyase composed of alpha (2.8.3.10 from EC), beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The alpha subunit catalyzes the reaction Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The protein from Lactococcus lactis subsp. lactis has been experimentally characterised . ; GO: 0008814 citrate CoA-transferase activity, 0006084 acetyl-CoA metabolic process, 0005737 cytoplasm, 0009346 citrate lyase complex; PDB: 2hj0_B 2nvv_D 2g39_B 1xr4_B.
Probab=44.82 E-value=4.9 Score=15.79 Aligned_cols=48 Identities=10% Similarity=0.131 Sum_probs=35.9
Q ss_pred HHHHHHHHHHCCCHH---HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 149999998488777---876315898899999999999999988754320
Q T0596 28 VRLYDIAARLAVSLD---EIRLYFREKDELIDAWFDRADSRMLKEAESAGF 75 (213)
Q Consensus 28 ~tv~~IA~~aGvs~~---t~y~yF~sKe~L~~a~~~~~~~~~~~~~~~~~~ 75 (213)
.|+++.-+++|+..| +|.|||.+-|-++.-+++...+.-...+.-+..
T Consensus 6 ~si~eai~~~glkDGMTiSFHHh~R~GD~v~n~Vm~~i~~mGikdltia~S 56 (466)
T PF04223_consen 6 SSIEEAIEKCGLKDGMTISFHHHFRNGDYVLNMVMEEIAKMGIKDLTIAAS 56 (466)
T ss_dssp SSHHHHHHHTT-----EEEE--TT-----HHHHHHHHHHH----SEEEEES
T ss_pred HHHHHHHHHCCCCCCCEEEEEHHHCCCCHHHHHHHHHHHHCCCCCCEEECC
T ss_conf 639999997088678589853210371489999999999748677277033
No 53
>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=42.10 E-value=6.5 Score=14.86 Aligned_cols=31 Identities=13% Similarity=0.192 Sum_probs=23.9
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHC
Q ss_conf 999998648412149999998488777876315
Q T0596 16 AVELAAHTSWEAVRLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 16 A~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF 48 (213)
.+..+.+.|- .|+.+||+..|++++++.+..
T Consensus 8 iL~~l~~~~~--~t~~~la~~l~~~~~~vs~~i 38 (59)
T PF01047_consen 8 ILRILYENPG--MTQSELAERLGISKSTVSRII 38 (59)
T ss_dssp HHHHHHHSSS--EEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCC--CCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999998799--899999999886873899999
No 54
>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=40.69 E-value=2.2 Score=18.56 Aligned_cols=23 Identities=35% Similarity=0.525 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 41214999999848877787631
Q T0596 25 WEAVRLYDIAARLAVSLDEIRLY 47 (213)
Q Consensus 25 ~~~~tv~~IA~~aGvs~~t~y~y 47 (213)
|++.|..+||+..|+|.+++...
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 55
>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=38.73 E-value=7.2 Score=14.49 Aligned_cols=41 Identities=24% Similarity=0.245 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHC
Q ss_conf 899999999999998648412149999998488777876315
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF 48 (213)
+.-.+|-.+..+|..+.|-. -|..+||+..|++...++...
T Consensus 1 E~~~ki~~a~~~L~~~lgR~-Pt~eEIA~~lgis~~~v~~~~ 41 (78)
T PF04539_consen 1 EKLNKIKKAKRELEQELGRE-PTEEEIAEELGISEEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHHC------BHHHHHHH----HHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHH
T ss_conf 97899999999999995889-899999999788899999999
No 56
>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=36.94 E-value=2.9 Score=17.56 Aligned_cols=49 Identities=12% Similarity=0.160 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHH-------H--HCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHH
Q ss_conf 789999999999999-------8--648412149999998488777876315898899
Q T0596 6 DPMRDAIVDTAVELA-------A--HTSWEAVRLYDIAARLAVSLDEIRLYFREKDEL 54 (213)
Q Consensus 6 ~~~R~~Il~AA~~l~-------~--e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L 54 (213)
++|++-|+.-+..++ . .....-+|+.+||+..|++.+|+-+--.+|.--
T Consensus 19 ~~R~~Tll~v~~~Iv~~Q~~Ff~~g~~~l~Pltl~~vA~~lglheSTVSRav~~Ky~~ 76 (160)
T PF04552_consen 19 EQRNQTLLRVAEAIVERQEDFFLEGPKALKPLTLKDVAEELGLHESTVSRAVSNKYIQ 76 (160)
T ss_dssp ----------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCCEEE
T ss_conf 9999999999999999999998558535768549999998398830577987485363
No 57
>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=36.12 E-value=4.7 Score=15.96 Aligned_cols=34 Identities=12% Similarity=0.184 Sum_probs=28.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHC
Q ss_conf 9999998648412149999998488777876315
Q T0596 15 TAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 15 AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF 48 (213)
-.++.+.+.|...+|=.+||+.+|++...+-+=|
T Consensus 16 r~L~~l~~~g~~~iSS~eLa~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 16 RYLKQLQEEGVERISSKELAEALGITPSQVRKDL 49 (50)
T ss_dssp HHHHHHHH----B--TTTHHHCCSS-HHHHHHHH
T ss_pred HHHHHHHHCCCEEECHHHHHHHHCCCHHHHHCCC
T ss_conf 9999999859945879999999797999961225
No 58
>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=34.57 E-value=8.3 Score=14.02 Aligned_cols=31 Identities=26% Similarity=0.250 Sum_probs=22.6
Q ss_pred HHHHCCCC-HHHHHHHHHHHCCCHHHHHHHCC
Q ss_conf 99864841-21499999984887778763158
Q T0596 19 LAAHTSWE-AVRLYDIAARLAVSLDEIRLYFR 49 (213)
Q Consensus 19 l~~e~G~~-~~tv~~IA~~aGvs~~t~y~yF~ 49 (213)
.+..+.-. .+|+.+||++.|+++..+...+.
T Consensus 16 ~La~~~~~~~~t~~~IA~~~~i~~~~v~kil~ 47 (83)
T PF02082_consen 16 YLARQPDGKPVTSKEIAERLGISPSYVRKILQ 47 (83)
T ss_dssp HHHCSTTCC---HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99809999849899999888909999999999
No 59
>PF06892 Phage_CP76: Phage regulatory protein CII (CP76); InterPro: IPR009679 This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny .
Probab=33.81 E-value=8.5 Score=13.93 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCC
Q ss_conf 8999999999999986484121499999984887778763158
Q T0596 7 PMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFR 49 (213)
Q Consensus 7 ~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~ 49 (213)
..++.=++.|..-|....= +..||+++|++++++++...
T Consensus 4 ~~k~~~~~~Ac~~Fa~~~~----~~~LA~~lGm~~~~LrNKLN 42 (162)
T PF06892_consen 4 ESKQPHFDEACRAFALSHN----MEELAERLGMSPQVLRNKLN 42 (162)
T ss_pred CCCCHHHHHHHHHHHHHCC----HHHHHHHHCCCHHHHHHHCC
T ss_conf 0003669999999987346----99999994999999986439
No 60
>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=33.25 E-value=4.1 Score=16.38 Aligned_cols=18 Identities=11% Similarity=0.106 Sum_probs=14.1
Q ss_pred HHHHHCCCHHHHHHHCCC
Q ss_conf 999848877787631589
Q T0596 33 IAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 33 IA~~aGvs~~t~y~yF~s 50 (213)
-+=++|++-|++||-|-+
T Consensus 3 A~FEaGIklGalyHQf~G 20 (38)
T PF04036_consen 3 AVFEAGIKLGALYHQFVG 20 (38)
T ss_dssp HHHH-------HHHHH--
T ss_pred HHHHHHHHHHHHHHHHCC
T ss_conf 176500257578886517
No 61
>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=33.15 E-value=8.7 Score=13.85 Aligned_cols=21 Identities=10% Similarity=0.020 Sum_probs=14.6
Q ss_pred HHCCCCHHHHHHHHHHHCCCH
Q ss_conf 864841214999999848877
Q T0596 21 AHTSWEAVRLYDIAARLAVSL 41 (213)
Q Consensus 21 ~e~G~~~~tv~~IA~~aGvs~ 41 (213)
.+-|...+++..+|++.||.+
T Consensus 23 k~Lgv~~T~lKk~CR~~GI~R 43 (52)
T PF02042_consen 23 KELGVCTTTLKKRCRQLGIPR 43 (52)
T ss_pred HHHCCCHHHHHHHHHHCCCCC
T ss_conf 995887569999999869988
No 62
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon . This domain includes the DNA-binding HTH motif . ; PDB: 1r71_B.
Probab=32.41 E-value=7.4 Score=14.39 Aligned_cols=23 Identities=26% Similarity=0.213 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHCCCHHHHHHHCC
Q ss_conf 21499999984887778763158
Q T0596 27 AVRLYDIAARLAVSLDEIRLYFR 49 (213)
Q Consensus 27 ~~tv~~IA~~aGvs~~t~y~yF~ 49 (213)
+.|-.+||++.|-|++.+-+|-.
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 63
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI , , , , . The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ixc_B 1iz1_Q 2esn_D 1o7l_B 1b9n_A 1b9m_B 3fzv_B.
Probab=32.11 E-value=9 Score=13.73 Aligned_cols=27 Identities=15% Similarity=0.231 Sum_probs=23.1
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCHHHHH
Q ss_conf 499999984887778763158988999
Q T0596 29 RLYDIAARLAVSLDEIRLYFREKDELI 55 (213)
Q Consensus 29 tv~~IA~~aGvs~~t~y~yF~sKe~L~ 55 (213)
|+...|+..|++.+++.++-..-|+-+
T Consensus 15 s~~~AA~~l~~s~~~vs~~i~~LE~~l 41 (60)
T PF00126_consen 15 SFSRAAEQLGISQSAVSRRIKRLEEEL 41 (60)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 999999870899538999999999982
No 64
>PF10975 DUF2802: Protein of unknown function (DUF2802)
Probab=31.29 E-value=8.7 Score=13.86 Aligned_cols=16 Identities=6% Similarity=0.150 Sum_probs=9.7
Q ss_pred HHHHHHHHHHCCCHHH
Q ss_conf 1499999984887778
Q T0596 28 VRLYDIAARLAVSLDE 43 (213)
Q Consensus 28 ~tv~~IA~~aGvs~~t 43 (213)
.++.+|++++|++++-
T Consensus 45 a~~~el~~~CgL~~AE 60 (70)
T PF10975_consen 45 ADIDELMQECGLPRAE 60 (70)
T ss_pred CCHHHHHHHHCCCHHH
T ss_conf 9999999880998999
No 65
>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=31.26 E-value=9.3 Score=13.63 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 178999999999999986484121499999984887778763158988999999999
Q T0596 5 NDPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELIDAWFDR 61 (213)
Q Consensus 5 ~~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~a~~~~ 61 (213)
+++-|+.|++=--+.|.+.+-++-|-++|.++.|- =+++..++...
T Consensus 18 p~~e~~dil~~Y~eyf~e~~~~G~sEeeii~~LG~-----------P~~iA~ei~a~ 63 (181)
T PF08006_consen 18 PEEEREDILEYYEEYFDEGGEEGKSEEEIIAELGS-----------PKEIAKEILAD 63 (181)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCC-----------HHHHHHHHHHH
T ss_conf 99999999999999999875689999999978299-----------99999999886
No 66
>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=29.16 E-value=10 Score=13.37 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=25.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHH
Q ss_conf 9999986484121499999984887778763158988
Q T0596 16 AVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKD 52 (213)
Q Consensus 16 A~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe 52 (213)
.-.++... +..|++++|+..|+++..|+.+-..+.
T Consensus 15 ~d~~~~~~--~~~~i~~~AK~lgi~~~~l~~~Lr~~~ 49 (111)
T PF03374_consen 15 YDRFLNSD--GSMTIREAAKILGIGPNKLFKWLREKG 49 (111)
T ss_pred HHHHHCCC--CCEEHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 99995689--957799999993999999999999869
No 67
>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=27.91 E-value=6.9 Score=14.65 Aligned_cols=38 Identities=21% Similarity=0.241 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHH
Q ss_conf 78999999999999986484121499999984887778
Q T0596 6 DPMRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDE 43 (213)
Q Consensus 6 ~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t 43 (213)
++....|...-+..+.++||=..++.+||+..|++...
T Consensus 31 ~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~~ 68 (195)
T PF04963_consen 31 SEEEREIAEYIIDNLDDDGYLRESLEEIAEELGVSEEE 68 (195)
T ss_dssp ---HHHHHHHHCCCBTT---BSS-HHHHHHHCTS-HHH
T ss_pred CHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHHH
T ss_conf 99999999999982799998899999999781989999
No 68
>PF11268 DUF3071: Protein of unknown function (DUF3071)
Probab=27.53 E-value=11 Score=13.17 Aligned_cols=21 Identities=10% Similarity=0.311 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHCCCHHHHHHH
Q ss_conf 214999999848877787631
Q T0596 27 AVRLYDIAARLAVSLDEIRLY 47 (213)
Q Consensus 27 ~~tv~~IA~~aGvs~~t~y~y 47 (213)
+.|..+||+.+|++..-+-+|
T Consensus 69 Gas~eeVA~~~G~~~~rV~rf 89 (170)
T PF11268_consen 69 GASAEEVAEEAGVPVERVERF 89 (170)
T ss_pred CCCHHHHHHHHCCCHHHHHHC
T ss_conf 999999999959999996752
No 69
>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=27.37 E-value=11 Score=13.15 Aligned_cols=40 Identities=10% Similarity=-0.021 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 0134578899999999999987518999999998744678
Q T0596 75 FLDLVASERIHHLIMIWLDALAVQRKVTRQMIMSKLEFGH 114 (213)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (213)
....+|.+.+..+++..++....+|..-..+..+...+..
T Consensus 16 ~~~~dP~~aL~~YIr~Kl~~sr~~P~~Srlfa~Eii~Gap 55 (143)
T PF08362_consen 16 DAEDDPAEALRAYIRAKLEMSRDHPEASRLFANEIIQGAP 55 (143)
T ss_dssp -TTS-HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH---T
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCH
T ss_conf 8679999999999999999998894163999999984846
No 70
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . This is a region found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function .; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm
Probab=25.89 E-value=11 Score=12.96 Aligned_cols=28 Identities=14% Similarity=0.126 Sum_probs=20.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHCCCH
Q ss_conf 9999999864841214999999848877
Q T0596 14 DTAVELAAHTSWEAVRLYDIAARLAVSL 41 (213)
Q Consensus 14 ~AA~~l~~e~G~~~~tv~~IA~~aGvs~ 41 (213)
+...++|..-|++..+..++.+-.-++.
T Consensus 4 eel~~lF~~iGL~e~kaketlKN~kvs~ 31 (164)
T PF04558_consen 4 EELIELFSSIGLSEKKAKETLKNKKVSA 31 (164)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHCHHHHH
T ss_conf 8999999983987266999884799999
No 71
>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=25.64 E-value=11 Score=12.93 Aligned_cols=36 Identities=22% Similarity=0.396 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 99999999999998648412149999998488777876
Q T0596 8 MRDAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIR 45 (213)
Q Consensus 8 ~R~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y 45 (213)
..++|++.-.. .-.+-+++++.+|+++.+++...|.
T Consensus 48 ~~~~Vl~~i~~--~~~~~eGv~v~~i~~~l~~~~~~v~ 83 (102)
T PF08784_consen 48 LQQRVLNFIKQ--SPQSEEGVHVDEIAQKLGMPENEVR 83 (102)
T ss_dssp HHHHHHHHHHC----------BHHHHHHHSTS-HHHHH
T ss_pred HHHHHHHHHHH--CCCCCCCCCHHHHHHHHCCCHHHHH
T ss_conf 99999999984--4688787189999999693999999
No 72
>PF01070 FMN_dh: FMN-dependent dehydrogenase; InterPro: IPR000262 A number of oxidoreductases that act on alpha-hydroxy acids and which are FMN-containing flavoproteins have been shown , , to be structurally related. The first step in the reaction mechanism of these enzymes is the abstraction of the proton from the alpha-carbon of the substrate producing a carbanion which can subsequently attach to the N5 atom of FMN. A conserved histidine has been shown to be involved in the removal of the proton. The region around this active site residue is highly conserved and contains an arginine residue which is involved in substrate binding.; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2a7n_A 2a7p_A 2a85_A 1p0k_A 1p0n_A 2zry_C 2zrz_B 2zrw_D 2zrx_A 2zru_D ....
Probab=24.76 E-value=12 Score=12.81 Aligned_cols=45 Identities=18% Similarity=0.277 Sum_probs=35.4
Q ss_pred HHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 9864841214999999848877787631589889999999999999
Q T0596 20 AAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELIDAWFDRADSR 65 (213)
Q Consensus 20 ~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~a~~~~~~~~ 65 (213)
+.=..++..|+.+|++.++ +..-|.-|+..-.++...++++....
T Consensus 91 ~~lSt~ss~slEeVa~a~~-~~~wfQLY~~~Dr~~~~~ll~RA~~a 135 (354)
T PF01070_consen 91 MVLSTQSSTSLEEVAAAAP-GPRWFQLYVPKDREITEDLLRRAEAA 135 (354)
T ss_dssp EEEETTSSS-HHHHHHHSS-S-EEEEEE-BSSHHHHHHHHHHHHH-
T ss_pred EEECCCCCCCHHHHHHHCC-CCEEEEEEEECCHHHHHHHHHHHHHC
T ss_conf 8607987789999998505-98399997507889999999999975
No 73
>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=24.18 E-value=10 Score=13.33 Aligned_cols=23 Identities=39% Similarity=0.580 Sum_probs=18.1
Q ss_pred CHHHHHHHHHHHCCCHHHHHHHC
Q ss_conf 12149999998488777876315
Q T0596 26 EAVRLYDIAARLAVSLDEIRLYF 48 (213)
Q Consensus 26 ~~~tv~~IA~~aGvs~~t~y~yF 48 (213)
+.++|.++|+..|++...+...+
T Consensus 2 ~~~rV~elAk~l~~~~~~ii~~L 24 (54)
T PF04760_consen 2 EKIRVYELAKELGVSSKEIIKKL 24 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH
T ss_pred CCEEHHHHHHHHCCCHHHHHHHH
T ss_conf 95369999999892999999999
No 74
>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=23.97 E-value=12 Score=12.78 Aligned_cols=23 Identities=9% Similarity=0.176 Sum_probs=18.5
Q ss_pred HHHHHHHHHHCCCHHHHHHHCCC
Q ss_conf 14999999848877787631589
Q T0596 28 VRLYDIAARLAVSLDEIRLYFRE 50 (213)
Q Consensus 28 ~tv~~IA~~aGvs~~t~y~yF~s 50 (213)
+|-.+||.-.|+++-++-+.++.
T Consensus 3 lt~~elA~~~G~tretvsR~l~~ 25 (32)
T PF00325_consen 3 LTHQELADLLGTTRETVSRILSR 25 (32)
T ss_dssp --HHHHHHHCTC-HHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 79999998869869999999999
No 75
>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=23.80 E-value=12 Score=12.68 Aligned_cols=28 Identities=21% Similarity=0.344 Sum_probs=19.8
Q ss_pred HHHCCCCHHHHHHHHHHH-----CCCHHHHHHHCC
Q ss_conf 986484121499999984-----887778763158
Q T0596 20 AAHTSWEAVRLYDIAARL-----AVSLDEIRLYFR 49 (213)
Q Consensus 20 ~~e~G~~~~tv~~IA~~a-----Gvs~~t~y~yF~ 49 (213)
+.+... .|..+|+.+. +||+.|+++++.
T Consensus 8 i~~~p~--~T~~~l~~~l~~~~~~vS~~Tv~R~L~ 40 (72)
T PF01498_consen 8 IRRNPR--ITLRELARELQEEGISVSKSTVRRRLK 40 (72)
T ss_dssp HHHH------HHHHHHHT---T--S-HHHHHHHHH
T ss_pred HHHCCC--CCHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 987886--249999999986589979999999999
No 76
>PF08667 BetR: BetR domain; InterPro: IPR013975 This entry includes an N-terminal helix-turn-helix domain.
Probab=22.93 E-value=13 Score=12.56 Aligned_cols=45 Identities=18% Similarity=0.158 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHCCCCH-HHHHHHHHHHCCCHHHHHHHCCCHHHH
Q ss_conf 999999999998648412-149999998488777876315898899
Q T0596 10 DAIVDTAVELAAHTSWEA-VRLYDIAARLAVSLDEIRLYFREKDEL 54 (213)
Q Consensus 10 ~~Il~AA~~l~~e~G~~~-~tv~~IA~~aGvs~~t~y~yF~sKe~L 54 (213)
+.+..--.+++..+|+.. -...+||+-.|++++++|+-..+|-.-
T Consensus 4 ~~~~~rvr~ll~~~GI~kr~~~~~La~iL~Is~saa~RKL~G~~~f 49 (147)
T PF08667_consen 4 QAIAERVRELLDRHGIPKRQHNTELADILGISKSAASRKLNGKSPF 49 (147)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCC
T ss_conf 8999999999997499820138999998788999985873799997
No 77
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases .
Probab=21.49 E-value=14 Score=12.35 Aligned_cols=20 Identities=25% Similarity=0.333 Sum_probs=15.9
Q ss_pred HHHHHHHHHHCCCHHHHHHH
Q ss_conf 14999999848877787631
Q T0596 28 VRLYDIAARLAVSLDEIRLY 47 (213)
Q Consensus 28 ~tv~~IA~~aGvs~~t~y~y 47 (213)
-|+++.|+..|++++++-+|
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 78
>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=20.71 E-value=14 Score=12.23 Aligned_cols=13 Identities=38% Similarity=0.281 Sum_probs=4.7
Q ss_pred HHHHHHHHHCCCH
Q ss_conf 4999999848877
Q T0596 29 RLYDIAARLAVSL 41 (213)
Q Consensus 29 tv~~IA~~aGvs~ 41 (213)
|+.+|++.+||+.
T Consensus 56 t~~eia~~~~Vs~ 68 (71)
T PF00382_consen 56 TLKEIAEVAGVSE 68 (71)
T ss_dssp SHHHHHHHCTSSC
T ss_pred CHHHHHHHHCCCC
T ss_conf 8999999968896
No 79
>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=20.11 E-value=14 Score=12.14 Aligned_cols=40 Identities=23% Similarity=0.291 Sum_probs=22.9
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-----CCCHHHHHHHC
Q ss_conf 7178999999999999986484121499999984-----88777876315
Q T0596 4 NNDPMRDAIVDTAVELAAHTSWEAVRLYDIAARL-----AVSLDEIRLYF 48 (213)
Q Consensus 4 ~~~~~R~~Il~AA~~l~~e~G~~~~tv~~IA~~a-----Gvs~~t~y~yF 48 (213)
+.+..|..|++. +.+.+- ..|..+|-+.+ .|+.+|+|+--
T Consensus 5 r~T~qR~~Il~~----l~~~~~-~~sa~ei~~~l~~~~~~is~aTVYR~L 49 (120)
T PF01475_consen 5 RLTPQRRAILEV----LEESKE-HLSAEEIYDRLREKGPSISLATVYRTL 49 (120)
T ss_dssp HHHHHHHHHHHH----HHHGGS-SEEHHHHHHHHHHT-TT--HHHHHHHH
T ss_pred CCCHHHHHHHHH----HHHCCC-CCCHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf 779999999999----982799-999999999988618999862499999
No 80
>PF06230 DUF1009: Protein of unknown function (DUF1009); InterPro: IPR010415 This is a family of uncharacterised bacterial proteins.
Probab=20.08 E-value=14 Score=12.14 Aligned_cols=50 Identities=20% Similarity=0.202 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHH
Q ss_conf 99999999999864841214999999848877787631589889999999
Q T0596 10 DAIVDTAVELAAHTSWEAVRLYDIAARLAVSLDEIRLYFREKDELIDAWF 59 (213)
Q Consensus 10 ~~Il~AA~~l~~e~G~~~~tv~~IA~~aGvs~~t~y~yF~sKe~L~~a~~ 59 (213)
+.|+.+-++.|.+.||.=++-.+++...=...|.+-..=||+++.-+..+
T Consensus 52 d~lL~ai~~~~E~~G~~vv~a~~~~p~ll~~~G~lt~~~P~~~~~~Di~~ 101 (214)
T PF06230_consen 52 DALLRAIIDEFEEEGFEVVGAHEILPELLAPEGVLTGRKPSKEERADIAF 101 (214)
T ss_pred HHHHHHHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 99999999999977999971789538746898766799969889999999
Done!