Query psy11140
Match_columns 89
No_of_seqs 109 out of 302
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 19:01:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11140hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08016 PKD_channel: Polycyst 100.0 2.9E-30 6.2E-35 199.8 11.2 84 2-85 115-198 (425)
2 KOG3599|consensus 99.9 2.2E-27 4.7E-32 197.4 9.3 83 3-85 371-453 (798)
3 PLN03223 Polycystin cation cha 99.9 3.6E-24 7.8E-29 183.9 10.8 76 10-85 1086-1163(1634)
4 smart00419 HTH_CRP helix_turn_ 87.0 1.2 2.5E-05 23.7 3.2 29 19-47 18-46 (48)
5 PF05848 CtsR: Firmicute trans 81.3 2.2 4.7E-05 30.0 3.3 22 22-43 94-115 (152)
6 PF13545 HTH_Crp_2: Crp-like h 78.9 2.8 6.1E-05 24.5 2.9 29 20-48 39-67 (76)
7 PF13463 HTH_27: Winged helix 70.7 9.7 0.00021 21.6 3.7 33 19-51 28-65 (68)
8 cd00092 HTH_CRP helix_turn_hel 67.5 10 0.00022 21.3 3.3 26 18-43 34-59 (67)
9 PF12793 SgrR_N: Sugar transpo 64.5 6.8 0.00015 25.9 2.4 22 20-41 30-51 (115)
10 TIGR02337 HpaR homoprotocatech 63.8 12 0.00025 23.9 3.4 33 19-51 52-89 (118)
11 smart00420 HTH_DEOR helix_turn 63.6 8 0.00017 20.4 2.2 24 19-42 24-47 (53)
12 PRK13918 CRP/FNR family transc 63.0 12 0.00027 25.4 3.6 30 19-48 159-188 (202)
13 PF13730 HTH_36: Helix-turn-he 60.7 9.6 0.00021 21.0 2.3 22 18-39 34-55 (55)
14 smart00345 HTH_GNTR helix_turn 56.1 13 0.00028 20.1 2.3 26 18-43 29-54 (60)
15 COG2873 MET17 O-acetylhomoseri 56.0 7.9 0.00017 31.3 1.8 21 39-60 144-164 (426)
16 PF09339 HTH_IclR: IclR helix- 55.6 11 0.00025 20.8 2.0 24 18-41 27-50 (52)
17 cd07377 WHTH_GntR Winged helix 55.4 15 0.00032 20.3 2.5 25 19-43 35-59 (66)
18 smart00529 HTH_DTXR Helix-turn 54.9 18 0.0004 21.9 3.0 26 19-44 9-34 (96)
19 PF08544 GHMP_kinases_C: GHMP 53.5 21 0.00046 20.9 3.1 25 12-36 58-82 (85)
20 TIGR03697 NtcA_cyano global ni 53.3 21 0.00046 23.9 3.4 30 19-48 153-182 (193)
21 PF07848 PaaX: PaaX-like prote 53.1 11 0.00025 22.8 1.8 26 17-42 31-56 (70)
22 PRK10402 DNA-binding transcrip 52.1 20 0.00044 25.2 3.3 31 18-48 178-208 (226)
23 PF09648 YycI: YycH protein; 50.5 89 0.0019 22.2 6.7 54 24-87 164-218 (228)
24 PF12802 MarR_2: MarR family; 50.0 16 0.00034 20.3 2.0 25 18-42 30-54 (62)
25 PF01047 MarR: MarR family; I 49.8 16 0.00034 20.2 2.0 24 19-42 27-50 (59)
26 PF02631 RecX: RecX family; I 46.5 17 0.00036 23.5 2.0 22 20-41 5-26 (121)
27 PRK11512 DNA-binding transcrip 46.2 36 0.00078 22.4 3.6 33 19-51 64-101 (144)
28 PF05670 DUF814: Domain of unk 44.8 34 0.00075 21.2 3.1 29 10-38 3-32 (90)
29 PF05036 SPOR: Sporulation rel 44.6 18 0.0004 20.5 1.8 25 12-36 2-28 (76)
30 smart00418 HTH_ARSR helix_turn 43.3 28 0.00061 18.5 2.3 23 19-41 20-42 (66)
31 PRK11161 fumarate/nitrate redu 43.3 37 0.00079 23.7 3.4 31 18-48 193-223 (235)
32 PRK13626 transcriptional regul 43.0 20 0.00042 29.1 2.2 22 20-41 34-55 (552)
33 PF01325 Fe_dep_repress: Iron 42.3 24 0.00052 20.5 2.0 25 18-42 31-55 (60)
34 smart00344 HTH_ASNC helix_turn 41.5 33 0.00072 21.2 2.7 24 18-41 26-49 (108)
35 PRK03573 transcriptional regul 40.5 45 0.00097 21.8 3.3 33 19-51 56-93 (144)
36 PF13412 HTH_24: Winged helix- 39.2 33 0.00071 18.3 2.2 22 19-40 27-48 (48)
37 TIGR01605 PYST-D Plasmodium yo 39.1 6.3 0.00014 23.2 -0.9 20 48-67 20-39 (55)
38 PF01978 TrmB: Sugar-specific 38.4 31 0.00067 19.8 2.1 23 19-41 32-54 (68)
39 TIGR00315 cdhB CO dehydrogenas 37.3 61 0.0013 22.8 3.7 39 16-59 104-142 (162)
40 PRK14165 winged helix-turn-hel 37.2 42 0.0009 24.6 3.0 25 18-42 30-54 (217)
41 PRK09391 fixK transcriptional 37.1 50 0.0011 23.3 3.4 25 19-43 189-213 (230)
42 smart00347 HTH_MARR helix_turn 36.9 68 0.0015 18.8 3.5 23 19-41 34-56 (101)
43 PF10340 DUF2424: Protein of u 36.0 43 0.00093 26.7 3.1 37 10-52 128-164 (374)
44 PF00325 Crp: Bacterial regula 35.0 46 0.00099 17.4 2.2 21 19-39 12-32 (32)
45 COG4738 Predicted transcriptio 34.8 24 0.00053 24.0 1.3 19 24-42 56-74 (124)
46 smart00550 Zalpha Z-DNA-bindin 33.6 50 0.0011 19.4 2.5 25 18-42 31-55 (68)
47 PF08704 GCD14: tRNA methyltra 33.5 40 0.00086 25.1 2.4 37 11-47 137-173 (247)
48 PRK11633 cell division protein 32.6 70 0.0015 23.7 3.6 30 9-38 144-175 (226)
49 PRK00215 LexA repressor; Valid 32.0 1.8E+02 0.0038 20.2 5.8 51 19-69 33-90 (205)
50 PF00392 GntR: Bacterial regul 31.6 40 0.00086 19.2 1.8 25 18-42 33-57 (64)
51 PRK13412 fkp bifunctional fuco 31.4 1E+02 0.0022 27.7 4.8 45 5-52 920-964 (974)
52 COG4533 ABC-type uncharacteriz 30.0 43 0.00093 28.2 2.3 23 20-42 34-56 (564)
53 TIGR01889 Staph_reg_Sar staphy 29.5 1.1E+02 0.0025 19.2 3.8 33 19-51 53-90 (109)
54 cd00090 HTH_ARSR Arsenical Res 29.4 60 0.0013 17.6 2.3 24 19-42 30-53 (78)
55 PRK14137 recX recombination re 28.6 51 0.0011 23.7 2.2 23 20-42 68-90 (195)
56 PF03374 ANT: Phage antirepres 27.7 1.6E+02 0.0035 18.4 4.4 56 26-85 38-95 (111)
57 smart00346 HTH_ICLR helix_turn 26.4 70 0.0015 18.9 2.3 25 18-42 29-53 (91)
58 PF12142 PPO1_DWL: Polyphenol 26.4 75 0.0016 18.6 2.3 21 35-62 4-24 (54)
59 TIGR01884 cas_HTH CRISPR locus 26.2 75 0.0016 22.3 2.7 25 19-43 167-191 (203)
60 PF04937 DUF659: Protein of un 25.8 85 0.0018 21.5 2.9 25 36-61 39-63 (153)
61 PRK14136 recX recombination re 25.4 60 0.0013 25.4 2.2 22 20-41 190-211 (309)
62 PF12101 DUF3577: Protein of u 25.4 2.1E+02 0.0045 19.8 4.7 50 12-64 48-98 (137)
63 PRK00117 recX recombination re 25.3 66 0.0014 21.5 2.2 23 20-42 39-61 (157)
64 TIGR01610 phage_O_Nterm phage 25.1 72 0.0016 19.9 2.3 23 19-41 57-79 (95)
65 KOG1818|consensus 25.1 52 0.0011 28.1 2.0 41 12-55 139-180 (634)
66 PF15480 DUF4640: Domain of un 24.9 40 0.00088 26.1 1.2 27 17-43 81-107 (292)
67 COG2137 OraA Uncharacterized p 24.9 65 0.0014 22.9 2.2 23 20-42 48-70 (174)
68 COG4463 CtsR Transcriptional r 24.5 59 0.0013 22.9 1.9 8 10-17 62-69 (153)
69 cd04449 DEP_DEPDC5-like DEP (D 24.5 81 0.0018 19.3 2.3 23 21-43 47-69 (83)
70 COG0320 LipA Lipoate synthase 24.1 96 0.0021 24.2 3.1 30 8-37 212-241 (306)
71 PF05649 Peptidase_M13_N: Pept 24.0 24 0.00053 26.0 -0.1 16 30-45 359-374 (390)
72 PLN02150 terpene synthase/cycl 23.4 38 0.00082 21.6 0.7 26 15-40 13-38 (96)
73 PF07864 DUF1651: Protein of u 22.8 72 0.0016 19.2 1.8 18 22-39 51-68 (75)
74 PF01726 LexA_DNA_bind: LexA D 22.3 92 0.002 18.4 2.2 21 22-42 39-59 (65)
75 TIGR03698 clan_AA_DTGF clan AA 22.2 1.3E+02 0.0027 19.2 3.0 32 47-78 1-33 (107)
76 PF01022 HTH_5: Bacterial regu 22.1 98 0.0021 16.6 2.2 23 18-40 24-46 (47)
77 PRK14134 recX recombination re 22.1 78 0.0017 23.9 2.3 22 20-41 89-110 (283)
78 PF07574 SMC_Nse1: Nse1 non-SM 22.0 68 0.0015 22.7 1.9 22 20-41 163-184 (200)
79 PF12894 Apc4_WD40: Anaphase-p 21.8 1.6E+02 0.0034 16.3 3.0 17 48-64 14-30 (47)
80 PRK00286 xseA exodeoxyribonucl 21.7 94 0.002 24.4 2.7 41 2-42 77-126 (438)
81 COG3147 DedD Uncharacterized p 21.5 90 0.002 23.4 2.4 28 11-38 148-177 (226)
82 PF06970 RepA_N: Replication i 21.1 1.2E+02 0.0026 18.5 2.6 35 16-51 16-54 (76)
83 TIGR02431 pcaR_pcaU beta-ketoa 21.0 98 0.0021 22.2 2.5 27 18-44 33-59 (248)
84 PF04703 FaeA: FaeA-like prote 21.0 93 0.002 18.4 2.0 23 19-41 25-47 (62)
85 PRK13777 transcriptional regul 20.9 1.6E+02 0.0034 21.0 3.5 32 20-51 70-106 (185)
86 PRK06450 threonine synthase; V 20.2 96 0.0021 23.8 2.4 28 24-51 210-237 (338)
No 1
>PF08016 PKD_channel: Polycystin cation channel; InterPro: IPR013122 Polycystic kidney diseases (PKD) are disorders characterised by large numbers of cysts distributed throughout grossly-enlarged kidneys. Cyst development is associated with impairment of kidney function, and ultimately kidney failure and death []. Most cases of autosomal dominant PKD result from mutations in the PKD1 gene that cause premature protein termination. A second gene for autosomal dominant polycystic kidney disease has been identified by positional cloning []. The predicted 968-amino acid sequence of the PKD2 gene product (polycystin-2) contains 6 transmembrane domains, with intracellular N- and C-termini. Polycystin-2 shares some similarity with the family of voltage-activated calcium (and sodium) channels, and contains a potential calcium-binding domain. Polycystin-2 is strongly expressed in ovary, foetal and adult kidney, testis, and small intestine. Polycystin-1 requires the presence of this protein for stable expression and is believed to interact with it via its C terminus. All mutations between exons 1 and 11 result in a truncated polycystin-2 that lacks a calcium-binding EF-hand domain and the cytoplasmic domains required for the interaction of polycystin-2 with polycystin-1 []. PKD2, although clinically milder than PKD1, has a deleterious impact on life expectancy. This entry contains proteins belonging to the polycystin family including Mucolipin and Polycystin-1 and -2 (PKD1 and PKD2). The domain contains the cation channel region of PKD1 and PKD2 proteins. PKD1 and PKD2 may function through a common signalling pathway that is necessary for normal tubulogenesis. The PKD2 gene product has six transmembrane spans with intracellular amino- and carboxyl-termini []. Mucolipin is a cationic channel which probably plays a role in the endocytic pathway and in the control of membrane trafficking of proteins and lipids. It could play a major role in the calcium ion transport regulating lysosomal exocytosis [, , ].
Probab=99.97 E-value=2.9e-30 Score=199.80 Aligned_cols=84 Identities=29% Similarity=0.483 Sum_probs=82.0
Q ss_pred cccceeeeeCCCCeEEEcCCCHHHHHHHHHhhhhCCcccCCccEEEEEEeeeeCCCCeEEEEEEEEEEcCccceeeeeEE
Q psy11140 2 SVGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAIIAVSLMIERLGSHNYLTDSEV 81 (89)
Q Consensus 2 ~~~G~~~~Y~ggGY~~~L~~~~~~a~~~l~~L~~~~WiD~~TRav~vEftlYN~n~nLF~~vtll~E~~~tG~~~~s~~v 81 (89)
++.|++++|+||||+++|++++++|.++|++||+++|||++||||++||++||||+||||++++++|+||+|++.|+.+|
T Consensus 115 ~~~G~~~~Y~~gGY~~~L~~~~~~a~~~l~~L~~~~WiD~~Trav~vef~~YN~~~nlf~~v~l~~E~~~~G~~~~s~~i 194 (425)
T PF08016_consen 115 PYWGQFGTYGGGGYVVDLGRNKDEARSILQYLQQNNWIDRSTRAVFVEFTLYNPNTNLFSVVTLLFEFPPTGGVIPSASI 194 (425)
T ss_pred ceeeeeeeeCCCcEEEECCCCHHHHHHHHHHHHhCcCcccCCceEEEEEEEEcCCCCeeEEEEEEEEEcCCCceeeecce
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEee
Q psy11140 82 GIRG 85 (89)
Q Consensus 82 ~~~~ 85 (89)
+++.
T Consensus 195 ~~~~ 198 (425)
T PF08016_consen 195 QTFR 198 (425)
T ss_pred eEEE
Confidence 9874
No 2
>KOG3599|consensus
Probab=99.94 E-value=2.2e-27 Score=197.44 Aligned_cols=83 Identities=29% Similarity=0.403 Sum_probs=80.6
Q ss_pred ccceeeeeCCCCeEEEcCCCHHHHHHHHHhhhhCCcccCCccEEEEEEeeeeCCCCeEEEEEEEEEEcCccceeeeeEEE
Q psy11140 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAIIAVSLMIERLGSHNYLTDSEVG 82 (89)
Q Consensus 3 ~~G~~~~Y~ggGY~~~L~~~~~~a~~~l~~L~~~~WiD~~TRav~vEftlYN~n~nLF~~vtll~E~~~tG~~~~s~~v~ 82 (89)
..|.+++|+||||+++|+.+++++...+++|++++|||++||||||||++||||+||||+|+|++|+||+|+++|+.+++
T Consensus 371 ~~g~l~~Y~~gGY~~~l~~sr~es~~~i~~L~~~~WlD~~TrAvfidftlYNa~inlF~~v~L~vE~p~~G~~~ps~~l~ 450 (798)
T KOG3599|consen 371 HWGLLASYGGGGYVVLLSLSRTESLKAISYLRENNWLDRGTRAVFIDFTLYNADINLFCVVTLRVEFPPTGGVLPSLQLE 450 (798)
T ss_pred cccceeEecCCCEEEEecCchHhHHHHHHHHHHhccccCCCcEEEEeccccCCCCCeeEEEEEEEEecCcccccccceEE
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Eee
Q psy11140 83 IRG 85 (89)
Q Consensus 83 ~~~ 85 (89)
.+-
T Consensus 451 S~~ 453 (798)
T KOG3599|consen 451 SFK 453 (798)
T ss_pred EEe
Confidence 873
No 3
>PLN03223 Polycystin cation channel protein; Provisional
Probab=99.91 E-value=3.6e-24 Score=183.88 Aligned_cols=76 Identities=20% Similarity=0.267 Sum_probs=73.0
Q ss_pred eCCC-CeEEEcCCCHHHHHHHHHhhhhCCcccC-CccEEEEEEeeeeCCCCeEEEEEEEEEEcCccceeeeeEEEEee
Q psy11140 10 YNGG-GYVKDLGSSESNMAQGLSQMIIHKWLDE-RTRVILIECSLYNPNINAIIAVSLMIERLGSHNYLTDSEVGIRG 85 (89)
Q Consensus 10 Y~gg-GY~~~L~~~~~~a~~~l~~L~~~~WiD~-~TRav~vEftlYN~n~nLF~~vtll~E~~~tG~~~~s~~v~~~~ 85 (89)
|++| ||+++|+.++++|.++|++|+++.|||+ +|||||+||++||||+||||+|++++|||++|++.|+++|+++-
T Consensus 1086 y~DGfgyv~DL~lSa~eA~~~L~~LKdnlWIDr~~TRAVFVEFTVYNANVNLFSvVtLLfEF~~TGGV~~s~~IqTfR 1163 (1634)
T PLN03223 1086 YADGFPYFFDINLSAAEAQTWLDYMIYGLMIDDVKTRKVTAQVVVYNAELGYFGNVMVFFEFTDGGKIEVTHRLNTIR 1163 (1634)
T ss_pred CCCCceEEEECCCCHHHHHHHHHHHHhCCCcccccceeEEEEEEEEcCCCCeEEEEEEEEEEcCCCceeeeeeEEEEE
Confidence 5544 9999999999999999999999999999 99999999999999999999999999999999999999999874
No 4
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=87.01 E-value=1.2 Score=23.70 Aligned_cols=29 Identities=14% Similarity=0.257 Sum_probs=23.9
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCccEEE
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERTRVIL 47 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~TRav~ 47 (89)
++.++..+...|+.|.+.+||+...+.+.
T Consensus 18 l~~s~~tv~~~l~~L~~~g~l~~~~~~~~ 46 (48)
T smart00419 18 LGLTRETVSRTLKRLEKEGLISREGGRIV 46 (48)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEeCCEEE
Confidence 46678899999999999999987766543
No 5
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=81.30 E-value=2.2 Score=30.05 Aligned_cols=22 Identities=14% Similarity=0.290 Sum_probs=17.4
Q ss_pred CHHHHHHHHHhhhhCCcccCCc
Q psy11140 22 SESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 22 ~~~~a~~~l~~L~~~~WiD~~T 43 (89)
+..+|...++.|.++++|++.-
T Consensus 94 s~~~a~~ii~~L~e~~~it~RE 115 (152)
T PF05848_consen 94 SQQDAEDIIQRLLEEGLITERE 115 (152)
T ss_dssp -HHHHHHHHHHHHHTTSS-HHH
T ss_pred CHHHHHHHHHHHHHCCCCCHHH
Confidence 4688999999999999998643
No 6
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=78.86 E-value=2.8 Score=24.51 Aligned_cols=29 Identities=17% Similarity=0.264 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHHhhhhCCcccCCccEEEE
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDERTRVILI 48 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~~TRav~v 48 (89)
|.++...-..|+.|++.+||+..-+-+.|
T Consensus 39 g~sr~tv~r~l~~l~~~g~I~~~~~~i~I 67 (76)
T PF13545_consen 39 GVSRETVSRILKRLKDEGIIEVKRGKIII 67 (76)
T ss_dssp TSCHHHHHHHHHHHHHTTSEEEETTEEEE
T ss_pred CCCHHHHHHHHHHHHHCCCEEEcCCEEEE
Confidence 45667888999999999999876555443
No 7
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=70.71 E-value=9.7 Score=21.57 Aligned_cols=33 Identities=15% Similarity=0.202 Sum_probs=22.9
Q ss_pred cCCCHHHHHHHHHhhhhCCcccC-----CccEEEEEEe
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDE-----RTRVILIECS 51 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~-----~TRav~vEft 51 (89)
++.++......|+.|.+.+||.+ .-|...+.+|
T Consensus 28 ~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT 65 (68)
T PF13463_consen 28 LGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLT 65 (68)
T ss_dssp TT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-
T ss_pred HCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeC
Confidence 56778889999999999999933 3454666554
No 8
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=67.46 E-value=10 Score=21.31 Aligned_cols=26 Identities=15% Similarity=0.265 Sum_probs=21.9
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCCc
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~T 43 (89)
.++.++..+...|+.|++.+||....
T Consensus 34 ~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 34 YLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 35677889999999999999998754
No 9
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=64.47 E-value=6.8 Score=25.90 Aligned_cols=22 Identities=23% Similarity=0.194 Sum_probs=19.5
Q ss_pred CCCHHHHHHHHHhhhhCCcccC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
.-+..+++..|+.|++.+||+=
T Consensus 30 ~cS~Rn~r~lLkkm~~~gWi~W 51 (115)
T PF12793_consen 30 FCSRRNARTLLKKMQEEGWITW 51 (115)
T ss_pred CCCHHHHHHHHHHHHHCCCeee
Confidence 4677899999999999999974
No 10
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=63.84 E-value=12 Score=23.91 Aligned_cols=33 Identities=9% Similarity=0.058 Sum_probs=26.1
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCc-----cEEEEEEe
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERT-----RVILIECS 51 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~T-----Rav~vEft 51 (89)
++.++......++.|.+.+||.+.. |...+..|
T Consensus 52 ~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT 89 (118)
T TIGR02337 52 ACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLT 89 (118)
T ss_pred hCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEEC
Confidence 4566778899999999999999855 76666543
No 11
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=63.55 E-value=8 Score=20.43 Aligned_cols=24 Identities=25% Similarity=0.329 Sum_probs=20.9
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
|+.+...+...|+.|.+.+||.+.
T Consensus 24 l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 24 LGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEe
Confidence 567788999999999999999764
No 12
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=63.01 E-value=12 Score=25.39 Aligned_cols=30 Identities=10% Similarity=0.227 Sum_probs=24.5
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCccEEEE
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERTRVILI 48 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~TRav~v 48 (89)
||.+++..-..|++|++.++|+..-+.+.|
T Consensus 159 lG~tretvsR~l~~l~~~g~I~~~~~~i~I 188 (202)
T PRK13918 159 VGSVRETVTKVIGELSREGYIRSGYGKIQL 188 (202)
T ss_pred hCccHHHHHHHHHHHHHCCCEEcCCCEEEE
Confidence 467778888999999999999987666544
No 13
>PF13730 HTH_36: Helix-turn-helix domain
Probab=60.67 E-value=9.6 Score=21.03 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=19.3
Q ss_pred EcCCCHHHHHHHHHhhhhCCcc
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWL 39 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~Wi 39 (89)
.+|.++....+.|+.|++.+||
T Consensus 34 ~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 34 DLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHCcCHHHHHHHHHHHHHCcCC
Confidence 4577788999999999999997
No 14
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=56.08 E-value=13 Score=20.11 Aligned_cols=26 Identities=23% Similarity=0.409 Sum_probs=21.8
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCCc
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~T 43 (89)
.++-++......++.|.+.+||++..
T Consensus 29 ~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 29 QLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 45677889999999999999997644
No 15
>COG2873 MET17 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]
Probab=56.02 E-value=7.9 Score=31.33 Aligned_cols=21 Identities=29% Similarity=0.708 Sum_probs=18.2
Q ss_pred ccCCccEEEEEEeeeeCCCCeE
Q psy11140 39 LDERTRVILIECSLYNPNINAI 60 (89)
Q Consensus 39 iD~~TRav~vEftlYN~n~nLF 60 (89)
||.+|||||+| |+=||..|+.
T Consensus 144 I~~nTkavf~E-tigNP~~~v~ 164 (426)
T COG2873 144 IDENTKAVFAE-TIGNPGLDVL 164 (426)
T ss_pred hCcccceEEEE-eccCCCcccc
Confidence 78999999999 8889888753
No 16
>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: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=55.58 E-value=11 Score=20.81 Aligned_cols=24 Identities=17% Similarity=0.364 Sum_probs=20.2
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
.++.++..+...|+.|.+.+|+.+
T Consensus 27 ~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHCcCHHHHHHHHHHHHHCcCeec
Confidence 357788999999999999999975
No 17
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=55.40 E-value=15 Score=20.27 Aligned_cols=25 Identities=20% Similarity=0.408 Sum_probs=21.2
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCc
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~T 43 (89)
++-++......|+.|.+.+||++..
T Consensus 35 ~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 35 LGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecC
Confidence 5667888999999999999998653
No 18
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=54.92 E-value=18 Score=21.89 Aligned_cols=26 Identities=15% Similarity=0.132 Sum_probs=22.7
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCcc
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERTR 44 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~TR 44 (89)
|+-++......++.|.+.+||.+...
T Consensus 9 l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 9 LNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred hCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 56778889999999999999999763
No 19
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=53.45 E-value=21 Score=20.87 Aligned_cols=25 Identities=24% Similarity=0.247 Sum_probs=21.2
Q ss_pred CCCeEEEcCCCHHHHHHHHHhhhhC
Q psy11140 12 GGGYVKDLGSSESNMAQGLSQMIIH 36 (89)
Q Consensus 12 ggGY~~~L~~~~~~a~~~l~~L~~~ 36 (89)
+|+.++-|..+.+.+.++.+.|++.
T Consensus 58 ~G~~v~~l~~~~~~~~~v~~~l~~~ 82 (85)
T PF08544_consen 58 GGPTVFALCKDEDDAERVAEALREH 82 (85)
T ss_dssp SSSEEEEEESSHHHHHHHHHHHHHH
T ss_pred CCCeEEEEECCHHHHHHHHHHHHHh
Confidence 4899999998999999998888653
No 20
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=53.28 E-value=21 Score=23.87 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=23.8
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCccEEEE
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERTRVILI 48 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~TRav~v 48 (89)
||.+++..-+.|++|++.++|+..-+-+.|
T Consensus 153 lG~tretvsR~l~~l~~~g~I~~~~~~i~I 182 (193)
T TIGR03697 153 IGSTRVTITRLLGDLRKKKLISIHKKKITV 182 (193)
T ss_pred hCCcHHHHHHHHHHHHHCCCEEecCCEEEE
Confidence 356667788889999999999877766554
No 21
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=53.07 E-value=11 Score=22.83 Aligned_cols=26 Identities=31% Similarity=0.620 Sum_probs=20.9
Q ss_pred EEcCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 17 KDLGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 17 ~~L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
..+|.+...++..|..|++.+||+..
T Consensus 31 ~~~Gv~e~avR~alsRl~~~G~L~~~ 56 (70)
T PF07848_consen 31 AAFGVSESAVRTALSRLVRRGWLESE 56 (70)
T ss_dssp CCTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHcCCChHHHHHHHHHHHHcCceeee
Confidence 35788889999999999999999764
No 22
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=52.12 E-value=20 Score=25.20 Aligned_cols=31 Identities=32% Similarity=0.357 Sum_probs=25.8
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCCccEEEE
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDERTRVILI 48 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~TRav~v 48 (89)
.||.+++..-..|+.|++.++|+...+-+.|
T Consensus 178 ~lG~sretvsR~L~~L~~~G~I~~~~~~i~I 208 (226)
T PRK10402 178 YLGVSYRHLLYVLAQFIQDGYLKKSKRGYLI 208 (226)
T ss_pred HHCCcHHHHHHHHHHHHHCCCEEeeCCEEEE
Confidence 4677888888999999999999988776544
No 23
>PF09648 YycI: YycH protein; InterPro: IPR018604 The YycFG two-component system is the only signal transduction system in Bacillus subtilis known to be essential for cell viability. This system is highly conserved in low-G+C Gram-positive bacteria, regulating important processes such as cell wall homeostasis, cell membrane integrity, and cell division. Four other genes, yycHIJK, are organised within the same operon with yycF and yycG in B. subtilis. YycI and YycH proteins interact to control the activity of the YycG kinase. Both YycI and YycH proteins are localized outside the cytoplasm and attached to the membrane by an N-terminal transmembrane sequence. Bacterial two-hybrid data showed that the YycH, YycI, and the kinase YycG form a ternary complex. The data suggest that YycH and YycI control the activity of YycG in the periplasm and that this control is crucial in regulating important cellular processes [, ]. ; PDB: 2O3O_G.
Probab=50.48 E-value=89 Score=22.19 Aligned_cols=54 Identities=15% Similarity=0.268 Sum_probs=40.9
Q ss_pred HHHHHHHHhhhhCCcccCCccEEEEEEeeeeCCCCeEEEEEEE-EEEcCccceeeeeEEEEeecc
Q psy11140 24 SNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAIIAVSLM-IERLGSHNYLTDSEVGIRGKS 87 (89)
Q Consensus 24 ~~a~~~l~~L~~~~WiD~~TRav~vEftlYN~n~nLF~~vtll-~E~~~tG~~~~s~~v~~~~~~ 87 (89)
=.+.+.|..|.+++=|.+.++..=+++.-| +++ ..-...+-++|.++|.+.++.
T Consensus 164 Isa~~Al~~Ly~~~~i~~~s~I~~i~LGYy----------~~~~~~~~~~~v~~P~W~I~v~~~~ 218 (228)
T PF09648_consen 164 ISAQEALETLYQNNEIPNNSKITWIELGYY----------SLLQWTVADSQVYVPVWRIEVKNGD 218 (228)
T ss_dssp --HHHHHHHHHHTT-S-TTEEEEEEEEEEE------------EEEEETTEEEEEEEEEEEEEEEE
T ss_pred cCHHHHHHHHHHcCcCCCCCEEEEEEEeEe----------EeeccccCceEEEEEEEEEEEEcCC
Confidence 457788899999999999999999999988 222 356777889999999998764
No 24
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=50.02 E-value=16 Score=20.33 Aligned_cols=25 Identities=16% Similarity=0.266 Sum_probs=20.3
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
.++.++......++.|.+.+||.+.
T Consensus 30 ~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 30 RLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 3567888999999999999999763
No 25
>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 dimerisation. 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 dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=49.78 E-value=16 Score=20.25 Aligned_cols=24 Identities=17% Similarity=0.290 Sum_probs=19.8
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
++.++......++.|.+.+||.+.
T Consensus 27 ~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 27 LGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HCCChhHHHHHHHHHHHCCCEEec
Confidence 466788899999999999999764
No 26
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=46.49 E-value=17 Score=23.46 Aligned_cols=22 Identities=18% Similarity=0.373 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHHhhhhCCcccC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
+.+.+....+|..|++.+|||.
T Consensus 5 g~~~e~I~~vi~~l~~~gyidD 26 (121)
T PF02631_consen 5 GFSEEAIEEVIDRLKELGYIDD 26 (121)
T ss_dssp T--HHHHHHHHHHHHHTTSS-H
T ss_pred CCCHHHHHHHHHHHHHcCCCCH
Confidence 3467788999999999999986
No 27
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=46.18 E-value=36 Score=22.42 Aligned_cols=33 Identities=15% Similarity=0.432 Sum_probs=26.3
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCc-----cEEEEEEe
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERT-----RVILIECS 51 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~T-----Rav~vEft 51 (89)
++.++......++.|.+.+||.+.. |...+..|
T Consensus 64 l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT 101 (144)
T PRK11512 64 LSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLT 101 (144)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEC
Confidence 4677888999999999999998754 66666543
No 28
>PF05670 DUF814: Domain of unknown function (DUF814); InterPro: IPR008532 This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from O34693 from SWISSPROT where the N-terminal region is involved in this activity []. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Probab=44.76 E-value=34 Score=21.18 Aligned_cols=29 Identities=7% Similarity=-0.010 Sum_probs=23.7
Q ss_pred eCCCCeEEEcCCCHHHHHHH-HHhhhhCCc
Q psy11140 10 YNGGGYVKDLGSSESNMAQG-LSQMIIHKW 38 (89)
Q Consensus 10 Y~ggGY~~~L~~~~~~a~~~-l~~L~~~~W 38 (89)
....||.+..|+|..+.... ++.++.+++
T Consensus 3 ~s~~g~~i~vGrn~~eNe~L~~k~~~~~D~ 32 (90)
T PF05670_consen 3 ISSDGFKIIVGRNAKENEMLTKKYARPNDL 32 (90)
T ss_pred EecCCeEEEEeCCHHHHHHHHHHhhhhcce
Confidence 35789999999999999888 777777754
No 29
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=44.62 E-value=18 Score=20.49 Aligned_cols=25 Identities=32% Similarity=0.480 Sum_probs=18.2
Q ss_pred CCCeEEEcC--CCHHHHHHHHHhhhhC
Q psy11140 12 GGGYVKDLG--SSESNMAQGLSQMIIH 36 (89)
Q Consensus 12 ggGY~~~L~--~~~~~a~~~l~~L~~~ 36 (89)
+++|.+.++ .+.++|...++.|+..
T Consensus 2 ~~~y~vQv~s~~~~~~A~~~~~~l~~~ 28 (76)
T PF05036_consen 2 SSGYYVQVGSFSSEENAERLLAKLKKK 28 (76)
T ss_dssp --EEEEEEEEES-HHHHHHHHHHHHHH
T ss_pred CCcEEEEEEEcCCHHHHHHHHHHHHhc
Confidence 467888776 6778888888888877
No 30
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=43.33 E-value=28 Score=18.53 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=20.2
Q ss_pred cCCCHHHHHHHHHhhhhCCcccC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
|+.++..+...|+.|.+.+|+..
T Consensus 20 l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 20 LGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCeee
Confidence 56778899999999999999974
No 31
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=43.26 E-value=37 Score=23.69 Aligned_cols=31 Identities=19% Similarity=0.213 Sum_probs=25.3
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCCccEEEE
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDERTRVILI 48 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~TRav~v 48 (89)
.||.+++..-..|+.|++.+||+..-+.+.|
T Consensus 193 ~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i 223 (235)
T PRK11161 193 YLGLTVETISRLLGRFQKSGMLAVKGKYITI 223 (235)
T ss_pred HhCCcHHHHHHHHHHHHHCCCEEecCCEEEE
Confidence 3567778888889999999999987776654
No 32
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=42.97 E-value=20 Score=29.06 Aligned_cols=22 Identities=27% Similarity=0.338 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHhhhhCCcccC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
.-++.+++..|+.|++.+||+=
T Consensus 34 ~cs~R~~~~~l~~~~~~gwl~w 55 (552)
T PRK13626 34 NCSRRHMRTLLNTMQQRGWLTW 55 (552)
T ss_pred cCChhHHHHHHHHHHHCCCeee
Confidence 5678899999999999999984
No 33
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=42.29 E-value=24 Score=20.52 Aligned_cols=25 Identities=16% Similarity=0.244 Sum_probs=20.9
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
.|+.++..+..+++.|.+.++++..
T Consensus 31 ~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 31 RLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHCCChHHHHHHHHHHHHCCCEEec
Confidence 4678889999999999999999763
No 34
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.45 E-value=33 Score=21.23 Aligned_cols=24 Identities=13% Similarity=0.165 Sum_probs=21.2
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
.++.+.......++.|.+++||.+
T Consensus 26 ~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 26 KVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHCcCHHHHHHHHHHHHHCCCeec
Confidence 357788999999999999999985
No 35
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=40.50 E-value=45 Score=21.80 Aligned_cols=33 Identities=15% Similarity=0.286 Sum_probs=26.0
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCC-----ccEEEEEEe
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDER-----TRVILIECS 51 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~-----TRav~vEft 51 (89)
++.++......+..|.+.+||.+. -|+..|..|
T Consensus 56 l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT 93 (144)
T PRK03573 56 IGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLT 93 (144)
T ss_pred hCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEC
Confidence 466778889999999999999764 377776654
No 36
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=39.25 E-value=33 Score=18.34 Aligned_cols=22 Identities=23% Similarity=0.308 Sum_probs=17.8
Q ss_pred cCCCHHHHHHHHHhhhhCCccc
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLD 40 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD 40 (89)
++-+.......|+.|.+.+||.
T Consensus 27 ~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 27 LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEE
T ss_pred hCCCHHHHHHHHHHHHHCcCcC
Confidence 5667788999999999999873
No 37
>TIGR01605 PYST-D Plasmodium yoelii subtelomeric family PYST-D. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. These genes are generally very short (ca. 50 residues). There are no obvious homologs to these genes in any other organism.
Probab=39.05 E-value=6.3 Score=23.21 Aligned_cols=20 Identities=35% Similarity=0.482 Sum_probs=15.3
Q ss_pred EEEeeeeCCCCeEEEEEEEE
Q psy11140 48 IECSLYNPNINAIIAVSLMI 67 (89)
Q Consensus 48 vEftlYN~n~nLF~~vtll~ 67 (89)
+++-.||.|+||.++..-++
T Consensus 20 lhlifyn~ntnlIyV~~rmf 39 (55)
T TIGR01605 20 LHLIFYNSNTNIIYVFSRMF 39 (55)
T ss_pred hHhhhhhcccceEeeehHHh
Confidence 46678999999988865443
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 3QPH_A 1SFX_A.
Probab=38.40 E-value=31 Score=19.84 Aligned_cols=23 Identities=22% Similarity=0.304 Sum_probs=20.4
Q ss_pred cCCCHHHHHHHHHhhhhCCcccC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
++.++.++...|+.|.+.+|+.+
T Consensus 32 l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 32 LGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HTSSHHHHHHHHHHHHHTTSEEE
T ss_pred HCcCHHHHHHHHHHHHHCCCEEE
Confidence 56778999999999999999965
No 39
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=37.34 E-value=61 Score=22.75 Aligned_cols=39 Identities=28% Similarity=0.278 Sum_probs=33.4
Q ss_pred EEEcCCCHHHHHHHHHhhhhCCcccCCccEEEEEEeeeeCCCCe
Q psy11140 16 VKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINA 59 (89)
Q Consensus 16 ~~~L~~~~~~a~~~l~~L~~~~WiD~~TRav~vEftlYN~n~nL 59 (89)
++-+|.+..-+-+.|+.||... | +|.|-++ -.|+||.++
T Consensus 104 vlfvG~~~y~~~~~ls~lk~f~--~--~~~i~l~-~~y~pnA~~ 142 (162)
T TIGR00315 104 VLFLGIIYYYLSQMLSSLKHFS--H--IVTIAID-KYYQPNADY 142 (162)
T ss_pred EEEeCCcchHHHHHHHHHHhhc--C--cEEEEec-CCCCCCCce
Confidence 6778888888899999999887 3 8888888 999999876
No 40
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=37.24 E-value=42 Score=24.65 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=21.7
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
.|+.++..+...|+.|.+.+||.+.
T Consensus 30 ~L~iS~~Tvsr~Lk~LEe~GlI~R~ 54 (217)
T PRK14165 30 HTGTSSKTAARILKQLEDEGYITRT 54 (217)
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3567889999999999999999774
No 41
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=37.09 E-value=50 Score=23.33 Aligned_cols=25 Identities=20% Similarity=0.219 Sum_probs=21.0
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCc
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~T 43 (89)
||-+++..-+.|+.|++.++|+...
T Consensus 189 lGisretlsR~L~~L~~~GlI~~~~ 213 (230)
T PRK09391 189 LGLTIETVSRALSQLQDRGLIGLSG 213 (230)
T ss_pred HCCCHHHHHHHHHHHHHCCcEEecC
Confidence 4667788888999999999998654
No 42
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=36.94 E-value=68 Score=18.78 Aligned_cols=23 Identities=22% Similarity=0.293 Sum_probs=19.3
Q ss_pred cCCCHHHHHHHHHhhhhCCcccC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
++.++......|+.|.+.+||.+
T Consensus 34 ~~~s~~~i~~~l~~L~~~g~v~~ 56 (101)
T smart00347 34 LGVSPSTVTRVLDRLEKKGLIRR 56 (101)
T ss_pred HCCCchhHHHHHHHHHHCCCeEe
Confidence 45667788899999999999964
No 43
>PF10340 DUF2424: Protein of unknown function (DUF2424); InterPro: IPR019436 Sterol homeostasis in eukaryotic cells relies on the reciprocal interconversion of free sterols and steryl esters. In Saccharomyces cerevisiae (Baker's yeast) sterol acetylation requires the acetyltransferase Atf2, whereas deacetylation requires Say1, a membrane-anchored deacetylase with a putative active site in the ER lumen. Lack of Say1 results in the secretion of acetylated sterols into the culture medium, indicating that the substrate specificity of Say1 determines whether acetylated sterols are secreted from the cells or whether they are deacetylated and retained. In S. cerevisiae cells lacking Say1 or Atf2 are sensitive against the plant-derived allylbenzene eugenol and both Say1 and Atf2 affect pregnenolone toxicity, indicating that lipid acetylation acts as a detoxification pathway []. Homologues of Say1 are present in the mammalian genome and can functionally substitute for Say1 in yeast demonstrating that part of this pathway has been evolutionarily conserved [].
Probab=36.00 E-value=43 Score=26.67 Aligned_cols=37 Identities=19% Similarity=0.466 Sum_probs=25.4
Q ss_pred eCCCCeEEEcCCCHHHHHHHHHhhhhCCcccCCccEEEEEEee
Q psy11140 10 YNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSL 52 (89)
Q Consensus 10 Y~ggGY~~~L~~~~~~a~~~l~~L~~~~WiD~~TRav~vEftl 52 (89)
+.||||...+...+-+....+.++.+ ....+++|.++
T Consensus 128 lHGGGY~l~~~p~qi~~L~~i~~~l~------~~SILvLDYsL 164 (374)
T PF10340_consen 128 LHGGGYFLGTTPSQIEFLLNIYKLLP------EVSILVLDYSL 164 (374)
T ss_pred EcCCeeEecCCHHHHHHHHHHHHHcC------CCeEEEEeccc
Confidence 45999999988776666666666643 23677777554
No 44
>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 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=34.99 E-value=46 Score=17.36 Aligned_cols=21 Identities=14% Similarity=0.260 Sum_probs=17.3
Q ss_pred cCCCHHHHHHHHHhhhhCCcc
Q psy11140 19 LGSSESNMAQGLSQMIIHKWL 39 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~Wi 39 (89)
||.+.+..-..+..|++.+.|
T Consensus 12 lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 12 LGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HTS-HHHHHHHHHHHHHTTSE
T ss_pred hCCcHHHHHHHHHHHHHcCCC
Confidence 677888999999999998875
No 45
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=34.79 E-value=24 Score=24.03 Aligned_cols=19 Identities=21% Similarity=0.532 Sum_probs=14.8
Q ss_pred HHHHHHHHhhhhCCcccCC
Q psy11140 24 SNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 24 ~~a~~~l~~L~~~~WiD~~ 42 (89)
.+.--..+.|++++|+|..
T Consensus 56 PEVSiAMr~Lre~gWV~~R 74 (124)
T COG4738 56 PEVSIAMRYLRENGWVDER 74 (124)
T ss_pred chhHHHHHHHHHccccchH
Confidence 4445667999999999964
No 46
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=33.62 E-value=50 Score=19.41 Aligned_cols=25 Identities=12% Similarity=0.141 Sum_probs=21.7
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
.||-++......|..|++.+++.+.
T Consensus 31 ~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 31 NLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEec
Confidence 4678888999999999999999763
No 47
>PF08704 GCD14: tRNA methyltransferase complex GCD14 subunit; InterPro: IPR014816 GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA []. ; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity, 0030488 tRNA methylation; PDB: 2YVL_C 1YB2_A 2B25_B 1O54_A 2PWY_B 1I9G_A 3LGA_B 3LHD_C 3MB5_A.
Probab=33.47 E-value=40 Score=25.12 Aligned_cols=37 Identities=16% Similarity=0.231 Sum_probs=30.9
Q ss_pred CCCCeEEEcCCCHHHHHHHHHhhhhCCcccCCccEEE
Q psy11140 11 NGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVIL 47 (89)
Q Consensus 11 ~ggGY~~~L~~~~~~a~~~l~~L~~~~WiD~~TRav~ 47 (89)
..||.+.-+..+-+|....++.|++++|.|-.|--++
T Consensus 137 ~~gG~i~~fsP~ieQv~~~~~~L~~~gf~~i~~~Evl 173 (247)
T PF08704_consen 137 KPGGRICCFSPCIEQVQKTVEALREHGFTDIETVEVL 173 (247)
T ss_dssp EEEEEEEEEESSHHHHHHHHHHHHHTTEEEEEEEEEE
T ss_pred cCCceEEEECCCHHHHHHHHHHHHHCCCeeeEEEEEE
Confidence 3578888888899999999999999999987654443
No 48
>PRK11633 cell division protein DedD; Provisional
Probab=32.60 E-value=70 Score=23.70 Aligned_cols=30 Identities=17% Similarity=0.388 Sum_probs=25.4
Q ss_pred eeCCCCeEEEcC--CCHHHHHHHHHhhhhCCc
Q psy11140 9 IYNGGGYVKDLG--SSESNMAQGLSQMIIHKW 38 (89)
Q Consensus 9 ~Y~ggGY~~~L~--~~~~~a~~~l~~L~~~~W 38 (89)
...+++|++.|| ++.+++......|+..+.
T Consensus 144 ~~~~~~~vVQlgaf~n~~~A~~l~~kL~~~G~ 175 (226)
T PRK11633 144 APTGKAYVVQLGALKNADKVNEIVAKLRLSGY 175 (226)
T ss_pred CCCCCcEEEEecccCCHHHHHHHHHHHHHCCC
Confidence 356889999998 678999999999998875
No 49
>PRK00215 LexA repressor; Validated
Probab=32.00 E-value=1.8e+02 Score=20.21 Aligned_cols=51 Identities=18% Similarity=0.193 Sum_probs=32.9
Q ss_pred cCC-CHHHHHHHHHhhhhCCcccC---CccEEEE---EEeeeeCCCCeEEEEEEEEEE
Q psy11140 19 LGS-SESNMAQGLSQMIIHKWLDE---RTRVILI---ECSLYNPNINAIIAVSLMIER 69 (89)
Q Consensus 19 L~~-~~~~a~~~l~~L~~~~WiD~---~TRav~v---EftlYN~n~nLF~~vtll~E~ 69 (89)
++. ++..+...|+.|.+.+||.+ ..|++.+ .+..-+...+-+..+-++-+.
T Consensus 33 ~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~~~~~~~~~~~~~~~~iPv~~~v 90 (205)
T PRK00215 33 LGLRSPSAVHEHLKALERKGFIRRDPGRSRAIEVAAPAQLELPEEEPEAVGLPLVGRV 90 (205)
T ss_pred hCCCChHHHHHHHHHHHHCCCEEeCCCCcceEEeccccccccccccCCceeeeeEEEE
Confidence 565 88999999999999999944 5677777 333322222234445555444
No 50
>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 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=31.62 E-value=40 Score=19.22 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=20.5
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
.++-++..+++.+..|.+.+||...
T Consensus 33 ~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 33 RYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HhccCCcHHHHHHHHHHHCCcEEEE
Confidence 3567789999999999999999764
No 51
>PRK13412 fkp bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional
Probab=31.39 E-value=1e+02 Score=27.70 Aligned_cols=45 Identities=18% Similarity=0.172 Sum_probs=30.0
Q ss_pred ceeeeeCCCCeEEEcCCCHHHHHHHHHhhhhCCcccCCccEEEEEEee
Q psy11140 5 PKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSL 52 (89)
Q Consensus 5 G~~~~Y~ggGY~~~L~~~~~~a~~~l~~L~~~~WiD~~TRav~vEftl 52 (89)
+++.==||||++.-|..+.+.+.++.+.|++.. ..-++.+++|.+
T Consensus 920 aKLTGAGGGGcvI~Lak~~~~a~~I~~~L~~~~---~~~~~~~~~~~l 964 (974)
T PRK13412 920 YKLPGAGGGGYLYMVAKDPGAAERIRKILTENA---PNPRARFVDMSL 964 (974)
T ss_pred EEecccCcccEEEEEECChhhHHHHHHHHHhcc---cCCceeEEEEEE
Confidence 344444789999999888877777777776632 234456666665
No 52
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=29.99 E-value=43 Score=28.20 Aligned_cols=23 Identities=26% Similarity=0.183 Sum_probs=20.1
Q ss_pred CCCHHHHHHHHHhhhhCCcccCC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
.-+..+++..|+.|++.+|||-.
T Consensus 34 fCS~Rh~R~lL~q~q~~gWL~W~ 56 (564)
T COG4533 34 FCSRRHARTLLRQMQEAGWLTWQ 56 (564)
T ss_pred ccCHHHHHHHHHHHHHcCCEEec
Confidence 45678999999999999999854
No 53
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=29.55 E-value=1.1e+02 Score=19.17 Aligned_cols=33 Identities=12% Similarity=0.264 Sum_probs=25.4
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCC-----ccEEEEEEe
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDER-----TRVILIECS 51 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~-----TRav~vEft 51 (89)
++.++......++.|.+.+||-+. -|++.+.+|
T Consensus 53 l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT 90 (109)
T TIGR01889 53 ILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISIN 90 (109)
T ss_pred HCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEEC
Confidence 466788899999999999999753 366666543
No 54
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=29.45 E-value=60 Score=17.58 Aligned_cols=24 Identities=25% Similarity=0.386 Sum_probs=20.2
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
++.+...+...++.|.+.+||-..
T Consensus 30 ~~i~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 30 LGLSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred HCcCHhHHHHHHHHHHHCCCeEEE
Confidence 566778889999999999999753
No 55
>PRK14137 recX recombination regulator RecX; Provisional
Probab=28.58 E-value=51 Score=23.69 Aligned_cols=23 Identities=13% Similarity=0.182 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHhhhhCCcccCC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
+.+.+....+|..|++.+|||..
T Consensus 68 g~~~e~Ie~vI~rL~e~gyLDD~ 90 (195)
T PRK14137 68 SEDEALVTEVLERVQELGYQDDA 90 (195)
T ss_pred CCCHHHHHHHHHHHHHcCCCCHH
Confidence 55678888999999999999874
No 56
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. 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=27.71 E-value=1.6e+02 Score=18.37 Aligned_cols=56 Identities=13% Similarity=-0.006 Sum_probs=32.0
Q ss_pred HHHHHHhhhhCCcccCC--ccEEEEEEeeeeCCCCeEEEEEEEEEEcCccceeeeeEEEEee
Q psy11140 26 MAQGLSQMIIHKWLDER--TRVILIECSLYNPNINAIIAVSLMIERLGSHNYLTDSEVGIRG 85 (89)
Q Consensus 26 a~~~l~~L~~~~WiD~~--TRav~vEftlYN~n~nLF~~vtll~E~~~tG~~~~s~~v~~~~ 85 (89)
.....+.|++++||.+. .+-.- .-.-.+..+|.+-.-..+.+. |...++.+.-+-.
T Consensus 38 ~~~l~~~Lr~~g~l~~~~~~~~~p---~q~~~~~G~~~~k~~~~~~~~-g~~~~~~~~~iT~ 95 (111)
T PF03374_consen 38 RNKLFQWLREKGWLYRRGKGRNLP---YQKYIDAGYFEVKETTYTHSD-GEGKTSSQTRITP 95 (111)
T ss_pred HHHHHHHHHhCCceEECCCCCccc---ChhhhccceEEEeeeEeecCC-CCcEEEEEEEEeh
Confidence 34667889999999883 12111 112244557777666666555 5555555544433
No 57
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=26.40 E-value=70 Score=18.89 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=21.3
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCC
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
.++.++......|+.|.+.+||.+.
T Consensus 29 ~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 29 RLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HhCCCHHHHHHHHHHHHHCCCeeec
Confidence 3567789999999999999999764
No 58
>PF12142 PPO1_DWL: Polyphenol oxidase middle domain; InterPro: IPR022739 This domain is found in bacteria and eukaryotes and is approximately 50 amino acids in length. It is found in association with PF00264 from PFAM and PF12143 from PFAM. Most members are annotated as being polyphenol oxidases, and many are from plants or plastids. There is a conserved DWL sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process; PDB: 1BT3_A 1BUG_B 1BT1_B 1BT2_B 2P3X_A.
Probab=26.39 E-value=75 Score=18.60 Aligned_cols=21 Identities=19% Similarity=0.392 Sum_probs=13.4
Q ss_pred hCCcccCCccEEEEEEeeeeCCCCeEEE
Q psy11140 35 IHKWLDERTRVILIECSLYNPNINAIIA 62 (89)
Q Consensus 35 ~~~WiD~~TRav~vEftlYN~n~nLF~~ 62 (89)
+..|||. +|.+|+.|.++..+
T Consensus 4 D~dWLns-------~F~FYDen~~lVrv 24 (54)
T PF12142_consen 4 DPDWLNS-------SFLFYDENGQLVRV 24 (54)
T ss_dssp -HHHHT--------EEEEE-TTS-EEEE
T ss_pred ccccccC-------eeEEECCCCCEEEE
Confidence 3457763 78999999998765
No 59
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=26.19 E-value=75 Score=22.29 Aligned_cols=25 Identities=20% Similarity=0.356 Sum_probs=21.2
Q ss_pred cCCCHHHHHHHHHhhhhCCcccCCc
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~~T 43 (89)
++.++......|+.|.+.+||.+..
T Consensus 167 l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 167 LGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 4667788999999999999998764
No 60
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=25.82 E-value=85 Score=21.55 Aligned_cols=25 Identities=24% Similarity=0.591 Sum_probs=20.6
Q ss_pred CCcccCCccEEEEEEeeeeCCCCeEE
Q psy11140 36 HKWLDERTRVILIECSLYNPNINAII 61 (89)
Q Consensus 36 ~~WiD~~TRav~vEftlYN~n~nLF~ 61 (89)
.+|-|+.-|.+ +-|.+|.|.--.|-
T Consensus 39 DgWtd~~~~~l-Inf~v~~~~g~~Fl 63 (153)
T PF04937_consen 39 DGWTDRKGRSL-INFMVYCPEGTVFL 63 (153)
T ss_pred ecCcCCCCCeE-EEEEEEcccccEEE
Confidence 48999999988 57999999876663
No 61
>PRK14136 recX recombination regulator RecX; Provisional
Probab=25.44 E-value=60 Score=25.36 Aligned_cols=22 Identities=14% Similarity=0.342 Sum_probs=19.0
Q ss_pred CCCHHHHHHHHHhhhhCCcccC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
+...+....+|.+|++.+|||.
T Consensus 190 G~~ee~IE~VIerLke~gYLDD 211 (309)
T PRK14136 190 ADESDSVEPLLDALEREGWLSD 211 (309)
T ss_pred CCCHHHHHHHHHHHHHcCCcCH
Confidence 4566788899999999999986
No 62
>PF12101 DUF3577: Protein of unknown function (DUF3577); InterPro: IPR021960 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.
Probab=25.42 E-value=2.1e+02 Score=19.84 Aligned_cols=50 Identities=10% Similarity=0.009 Sum_probs=40.0
Q ss_pred CCCe-EEEcCCCHHHHHHHHHhhhhCCcccCCccEEEEEEeeeeCCCCeEEEEE
Q psy11140 12 GGGY-VKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAIIAVS 64 (89)
Q Consensus 12 ggGY-~~~L~~~~~~a~~~l~~L~~~~WiD~~TRav~vEftlYN~n~nLF~~vt 64 (89)
...| .+|+--.-++|...++.+++. .+.-|-|++-|.+=++.++.|+--+
T Consensus 48 ~~ey~~fD~~V~G~eA~~Lv~r~~~a---v~~~~KVli~FrlgDl~~d~f~~~~ 98 (137)
T PF12101_consen 48 NPEYRYFDCRVVGEEAKELVRRCQKA---VDEDKKVLIGFRLGDLWADTFTYKK 98 (137)
T ss_pred CccEEEEEEEEecHHHHHHHHHHHhh---cccCCcEEEEEEecCCceeeEEecc
Confidence 4456 367777779999999999988 2467889999999999999887533
No 63
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=25.26 E-value=66 Score=21.53 Aligned_cols=23 Identities=26% Similarity=0.306 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHhhhhCCcccCC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
|.+.+.....|..|.+.+|||..
T Consensus 39 g~~~~~i~~vl~~l~~~~~ldD~ 61 (157)
T PRK00117 39 GFSEEVIEAVLDRLKEEGLLDDE 61 (157)
T ss_pred CCCHHHHHHHHHHHHHcCCCCHH
Confidence 56778889999999999999874
No 64
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=25.13 E-value=72 Score=19.89 Aligned_cols=23 Identities=9% Similarity=0.226 Sum_probs=19.6
Q ss_pred cCCCHHHHHHHHHhhhhCCcccC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
++.+++.....|+.|.+.+||-+
T Consensus 57 ~g~sr~tVsr~L~~Le~~GlI~r 79 (95)
T TIGR01610 57 TGLSRTHVSDAIKSLARRRIIFR 79 (95)
T ss_pred HCcCHHHHHHHHHHHHHCCCeee
Confidence 46677888899999999999974
No 65
>KOG1818|consensus
Probab=25.11 E-value=52 Score=28.12 Aligned_cols=41 Identities=22% Similarity=0.264 Sum_probs=30.1
Q ss_pred CCCeEEEcCCCHHHHHHHHHhhhhCCccc-CCccEEEEEEeeeeC
Q psy11140 12 GGGYVKDLGSSESNMAQGLSQMIIHKWLD-ERTRVILIECSLYNP 55 (89)
Q Consensus 12 ggGY~~~L~~~~~~a~~~l~~L~~~~WiD-~~TRav~vEftlYN~ 55 (89)
+||+++...... ...+.....-+|+| .----+-+.|++.|-
T Consensus 139 ~~g~~Fpe~~e~---d~mf~~~~~pdW~D~~~C~rCr~~F~~~~r 180 (634)
T KOG1818|consen 139 GGGHVFPELDEN---DAMFDAETAPDWIDSEECLRCRVKFGLTNR 180 (634)
T ss_pred cCCccccccccc---hhhhcccCCcccccccccceeeeeeeeccc
Confidence 789986554433 33899999999999 455566778888873
No 66
>PF15480 DUF4640: Domain of unknown function (DUF4640)
Probab=24.94 E-value=40 Score=26.05 Aligned_cols=27 Identities=22% Similarity=0.304 Sum_probs=22.6
Q ss_pred EEcCCCHHHHHHHHHhhhhCCcccCCc
Q psy11140 17 KDLGSSESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 17 ~~L~~~~~~a~~~l~~L~~~~WiD~~T 43 (89)
+++|.+..++.+.+..=.++.|+|.+.
T Consensus 81 iDv~sd~sDS~~nwdln~~nqW~Dk~p 107 (292)
T PF15480_consen 81 IDVGSDNSDSIANWDLNGDNQWTDKYP 107 (292)
T ss_pred eccCCCchhhhhhhhccccccccccCh
Confidence 788888888888877777999999864
No 67
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=24.86 E-value=65 Score=22.90 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHhhhhCCcccCC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
+.+...-..+|..|++.+|||..
T Consensus 48 ~~~~~~Ie~Vi~~l~~~~~ldD~ 70 (174)
T COG2137 48 EFSEEIIEEVIDRLAEEGYLDDT 70 (174)
T ss_pred cCCHHHHHHHHHHHHHcCcccHH
Confidence 34556678899999999999963
No 68
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=24.46 E-value=59 Score=22.90 Aligned_cols=8 Identities=50% Similarity=1.331 Sum_probs=6.0
Q ss_pred eCCCCeEE
Q psy11140 10 YNGGGYVK 17 (89)
Q Consensus 10 Y~ggGY~~ 17 (89)
=|||||+.
T Consensus 62 RGGGGYIR 69 (153)
T COG4463 62 RGGGGYIR 69 (153)
T ss_pred cCCCceEE
Confidence 36899984
No 69
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=24.45 E-value=81 Score=19.31 Aligned_cols=23 Identities=0% Similarity=0.063 Sum_probs=20.6
Q ss_pred CCHHHHHHHHHhhhhCCcccCCc
Q psy11140 21 SSESNMAQGLSQMIIHKWLDERT 43 (89)
Q Consensus 21 ~~~~~a~~~l~~L~~~~WiD~~T 43 (89)
.++++|....+.|.++++|.+-+
T Consensus 47 ~~r~eAv~lgq~Ll~~g~I~hv~ 69 (83)
T cd04449 47 DTREEAVELGQELMNEGLIEHVS 69 (83)
T ss_pred CCHHHHHHHHHHHHHCCCEEecC
Confidence 57899999999999999998755
No 70
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=24.11 E-value=96 Score=24.24 Aligned_cols=30 Identities=13% Similarity=0.221 Sum_probs=26.8
Q ss_pred eeeCCCCeEEEcCCCHHHHHHHHHhhhhCC
Q psy11140 8 IIYNGGGYVKDLGSSESNMAQGLSQMIIHK 37 (89)
Q Consensus 8 ~~Y~ggGY~~~L~~~~~~a~~~l~~L~~~~ 37 (89)
..+...|-++.||.+.++-.+.+++|++++
T Consensus 212 ~i~TKSgiMlGLGEt~~Ev~e~m~DLr~~g 241 (306)
T COG0320 212 DIPTKSGLMVGLGETDEEVIEVMDDLRSAG 241 (306)
T ss_pred CcccccceeeecCCcHHHHHHHHHHHHHcC
Confidence 356788999999999999999999999875
No 71
>PF05649 Peptidase_M13_N: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR008753 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M13 (neprilysin family, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0008237 metallopeptidase activity, 0006508 proteolysis; PDB: 3DWB_A 3ZUK_A 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A.
Probab=23.99 E-value=24 Score=25.98 Aligned_cols=16 Identities=31% Similarity=0.569 Sum_probs=10.7
Q ss_pred HHhhhhCCcccCCccE
Q psy11140 30 LSQMIIHKWLDERTRV 45 (89)
Q Consensus 30 l~~L~~~~WiD~~TRa 45 (89)
...|+++.|||+.||.
T Consensus 359 ~~~i~~~~Wld~~tk~ 374 (390)
T PF05649_consen 359 RERIEESDWLDEETKK 374 (390)
T ss_dssp HHHHCT-TTS-HHHHH
T ss_pred HHHHhhCCCCCHHHHH
Confidence 3456788999999985
No 72
>PLN02150 terpene synthase/cyclase family protein
Probab=23.39 E-value=38 Score=21.59 Aligned_cols=26 Identities=23% Similarity=0.395 Sum_probs=22.3
Q ss_pred eEEEcCCCHHHHHHHHHhhhhCCccc
Q psy11140 15 YVKDLGSSESNMAQGLSQMIIHKWLD 40 (89)
Q Consensus 15 Y~~~L~~~~~~a~~~l~~L~~~~WiD 40 (89)
|..+-|.+.++|.+.|+.|.++.|=|
T Consensus 13 YMke~g~seeeA~~~i~~li~~~WK~ 38 (96)
T PLN02150 13 YMKQHGVTKEEAVSELKKMIRDNYKI 38 (96)
T ss_pred HhccCCCCHHHHHHHHHHHHHHHHHH
Confidence 45566888999999999999999976
No 73
>PF07864 DUF1651: Protein of unknown function (DUF1651); InterPro: IPR012447 The proteins in this entry have not been characterised.
Probab=22.76 E-value=72 Score=19.16 Aligned_cols=18 Identities=6% Similarity=0.178 Sum_probs=16.0
Q ss_pred CHHHHHHHHHhhhhCCcc
Q psy11140 22 SESNMAQGLSQMIIHKWL 39 (89)
Q Consensus 22 ~~~~a~~~l~~L~~~~Wi 39 (89)
..++|.+.-+.|++.+|=
T Consensus 51 ~~~~A~e~W~~L~~~GW~ 68 (75)
T PF07864_consen 51 TREEARELWKELQKTGWR 68 (75)
T ss_pred EHHHHHHHHHHHHHcCCE
Confidence 359999999999999993
No 74
>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: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=22.29 E-value=92 Score=18.38 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=18.3
Q ss_pred CHHHHHHHHHhhhhCCcccCC
Q psy11140 22 SESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 22 ~~~~a~~~l~~L~~~~WiD~~ 42 (89)
+...+...|+.|.+.+||.+.
T Consensus 39 S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 39 STSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp SHHHHHHHHHHHHHTTSEEEG
T ss_pred ChHHHHHHHHHHHHCcCccCC
Confidence 478899999999999999763
No 75
>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family. Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria.
Probab=22.23 E-value=1.3e+02 Score=19.18 Aligned_cols=32 Identities=16% Similarity=0.191 Sum_probs=25.7
Q ss_pred EEEEeeeeCCCCeEEEEEEEEEEcCccce-eee
Q psy11140 47 LIECSLYNPNINAIIAVSLMIERLGSHNY-LTD 78 (89)
Q Consensus 47 ~vEftlYN~n~nLF~~vtll~E~~~tG~~-~~s 78 (89)
++++.+.||+-.-+..|.+++..-++|-+ +|.
T Consensus 1 ~~~v~~~~p~~~~~~~v~~LVDTGat~~~~l~~ 33 (107)
T TIGR03698 1 TLDVELSNPKNPEFMEVRALVDTGFSGFLLVPP 33 (107)
T ss_pred CEEEEEeCCCCCCceEEEEEEECCCCeEEecCH
Confidence 47889999954448899999999999886 664
No 76
>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 recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=22.10 E-value=98 Score=16.56 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=18.4
Q ss_pred EcCCCHHHHHHHHHhhhhCCccc
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLD 40 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD 40 (89)
.++.++.....-|+.|++.++|.
T Consensus 24 ~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 24 ELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEE
T ss_pred hccccchHHHHHHHHHHHCcCee
Confidence 35677888899999999999875
No 77
>PRK14134 recX recombination regulator RecX; Provisional
Probab=22.09 E-value=78 Score=23.88 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHhhhhCCcccC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
+.+.+....+|+.|++.+|||.
T Consensus 89 ~~~~~~Ie~vI~~L~e~~yldD 110 (283)
T PRK14134 89 EYDEDAVNRVIRFLKEYNFIDD 110 (283)
T ss_pred CCCHHHHHHHHHHHHHCCCCCH
Confidence 5667888899999999999986
No 78
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=22.01 E-value=68 Score=22.70 Aligned_cols=22 Identities=27% Similarity=0.462 Sum_probs=16.2
Q ss_pred CCCHHHHHHHHHhhhhCCcccC
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
+-++.++...|..|-+.+|+.+
T Consensus 163 ~L~~~eae~lL~~lv~~gWl~~ 184 (200)
T PF07574_consen 163 GLSKSEAESLLDRLVEDGWLYR 184 (200)
T ss_dssp ----HHHHHHHHHHHHTTSE-E
T ss_pred cchHHHHHHHHHHHHHCCCcee
Confidence 4457899999999999999965
No 79
>PF12894 Apc4_WD40: Anaphase-promoting complex subunit 4 WD40 domain
Probab=21.82 E-value=1.6e+02 Score=16.28 Aligned_cols=17 Identities=18% Similarity=0.499 Sum_probs=15.1
Q ss_pred EEEeeeeCCCCeEEEEE
Q psy11140 48 IECSLYNPNINAIIAVS 64 (89)
Q Consensus 48 vEftlYN~n~nLF~~vt 64 (89)
|++..|+|..+|..+.+
T Consensus 14 v~~~~w~P~mdLiA~~t 30 (47)
T PF12894_consen 14 VSCMSWCPTMDLIALGT 30 (47)
T ss_pred EEEEEECCCCCEEEEEE
Confidence 77899999999998876
No 80
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=21.66 E-value=94 Score=24.45 Aligned_cols=41 Identities=20% Similarity=0.237 Sum_probs=28.6
Q ss_pred cccceeeeeCCCC-eEEE---c-----CCCHHHHHHHHHhhhhCCcccCC
Q psy11140 2 SVGPKNIIYNGGG-YVKD---L-----GSSESNMAQGLSQMIIHKWLDER 42 (89)
Q Consensus 2 ~~~G~~~~Y~ggG-Y~~~---L-----~~~~~~a~~~l~~L~~~~WiD~~ 42 (89)
-|.|.+.+|...| |.+. + |.-..+-.+..+.|.+.+|+|..
T Consensus 77 ~v~g~~~~y~~~g~~ql~v~~i~~~g~G~l~~~~~~lk~~L~~eGlfd~~ 126 (438)
T PRK00286 77 LVRGKVSLYEPRGDYQLIVEEIEPAGIGALAAAFEQLKEKLAAEGLFDPE 126 (438)
T ss_pred EEEEEEEEECCCCCEEEEEEEeeeCCccHHHHHHHHHHHHHHHCCCCChh
Confidence 4789999999666 6532 2 22235556677889999999965
No 81
>COG3147 DedD Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.46 E-value=90 Score=23.39 Aligned_cols=28 Identities=14% Similarity=0.305 Sum_probs=23.2
Q ss_pred CCCCeEEEcC--CCHHHHHHHHHhhhhCCc
Q psy11140 11 NGGGYVKDLG--SSESNMAQGLSQMIIHKW 38 (89)
Q Consensus 11 ~ggGY~~~L~--~~~~~a~~~l~~L~~~~W 38 (89)
.+++|++.|| .+.+.+.+.+..||..++
T Consensus 148 ~~~a~~VQLgAl~n~dranel~~~Lr~~G~ 177 (226)
T COG3147 148 TGQAFVVQLGALKNADRANELVAKLRGAGY 177 (226)
T ss_pred CCcceeehhhhhhhHHHHHHHHHHHHhCCC
Confidence 3689999998 567889999999998764
No 82
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=21.12 E-value=1.2e+02 Score=18.52 Aligned_cols=35 Identities=23% Similarity=0.331 Sum_probs=19.2
Q ss_pred EEEcCCCHHHHHHHHHhh----hhCCcccCCccEEEEEEe
Q psy11140 16 VKDLGSSESNMAQGLSQM----IIHKWLDERTRVILIECS 51 (89)
Q Consensus 16 ~~~L~~~~~~a~~~l~~L----~~~~WiD~~TRav~vEft 51 (89)
..+|+.+..-....|.+- ++++|+|..-+ |++.|+
T Consensus 16 y~~Ls~~Ak~lY~ll~dR~~lS~kn~wiDe~G~-vYi~~s 54 (76)
T PF06970_consen 16 YKKLSNDAKILYSLLLDRLRLSLKNGWIDENGN-VYIIFS 54 (76)
T ss_pred cccCCHHHHHHHHHHHHHHHhhhhcCcCCCCCC-EEEEee
Confidence 355665544333333322 37899999865 444443
No 83
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=21.02 E-value=98 Score=22.18 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=22.8
Q ss_pred EcCCCHHHHHHHHHhhhhCCcccCCcc
Q psy11140 18 DLGSSESNMAQGLSQMIIHKWLDERTR 44 (89)
Q Consensus 18 ~L~~~~~~a~~~l~~L~~~~WiD~~TR 44 (89)
.++.++..+...|+.|.+.+|+.+..+
T Consensus 33 ~lglpksT~~RlL~tL~~~G~l~~~~~ 59 (248)
T TIGR02431 33 ATGLTRAAARRFLLTLVELGYVTSDGR 59 (248)
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEeCCC
Confidence 357788999999999999999987554
No 84
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=20.96 E-value=93 Score=18.44 Aligned_cols=23 Identities=17% Similarity=0.063 Sum_probs=19.4
Q ss_pred cCCCHHHHHHHHHhhhhCCcccC
Q psy11140 19 LGSSESNMAQGLSQMIIHKWLDE 41 (89)
Q Consensus 19 L~~~~~~a~~~l~~L~~~~WiD~ 41 (89)
++-+..+++..|+.|.+.+.|.+
T Consensus 25 ~gls~~~aR~yL~~Le~eG~V~~ 47 (62)
T PF04703_consen 25 LGLSIYQARYYLEKLEKEGKVER 47 (62)
T ss_dssp HTS-HHHHHHHHHHHHHCTSEEE
T ss_pred hCCCHHHHHHHHHHHHHCCCEEE
Confidence 56778999999999999999964
No 85
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=20.91 E-value=1.6e+02 Score=20.96 Aligned_cols=32 Identities=16% Similarity=-0.014 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHhhhhCCcccCC-----ccEEEEEEe
Q psy11140 20 GSSESNMAQGLSQMIIHKWLDER-----TRVILIECS 51 (89)
Q Consensus 20 ~~~~~~a~~~l~~L~~~~WiD~~-----TRav~vEft 51 (89)
..++......++.|.+.+||-+. -|...|..|
T Consensus 70 ~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LT 106 (185)
T PRK13777 70 VMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELT 106 (185)
T ss_pred CCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEEC
Confidence 34567788899999999999875 466666543
No 86
>PRK06450 threonine synthase; Validated
Probab=20.19 E-value=96 Score=23.82 Aligned_cols=28 Identities=7% Similarity=0.278 Sum_probs=23.6
Q ss_pred HHHHHHHHhhhhCCcccCCccEEEEEEe
Q psy11140 24 SNMAQGLSQMIIHKWLDERTRVILIECS 51 (89)
Q Consensus 24 ~~a~~~l~~L~~~~WiD~~TRav~vEft 51 (89)
.-...-+++|...+|||+.+|.+.+|-.
T Consensus 210 ~Gi~~g~~el~~~G~i~~~prii~Vq~~ 237 (338)
T PRK06450 210 LGVYSGFKHLLDSGVISEMPKIVAVQTE 237 (338)
T ss_pred HHHHHHHHHHHhcCCccCCCeEEEEeeC
Confidence 4556778889999999999999999963
Done!