Query psy14514
Match_columns 91
No_of_seqs 104 out of 300
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 21:51:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14514.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14514hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08016 PKD_channel: Polycyst 99.9 4.8E-24 1.1E-28 167.6 8.1 64 28-91 114-177 (425)
2 KOG3599|consensus 99.9 1.9E-22 4E-27 171.6 7.1 78 8-91 345-432 (798)
3 PLN03223 Polycystin cation cha 99.7 3.7E-17 8.1E-22 144.6 7.2 55 37-91 1086-1142(1634)
4 smart00419 HTH_CRP helix_turn_ 80.8 3.1 6.6E-05 22.4 3.3 29 46-74 18-46 (48)
5 PF05848 CtsR: Firmicute trans 75.0 3.1 6.8E-05 29.9 2.7 21 50-70 95-115 (152)
6 PF13463 HTH_27: Winged helix 69.6 11 0.00025 21.6 3.9 34 45-78 27-65 (68)
7 PF13545 HTH_Crp_2: Crp-like h 65.8 8.6 0.00019 22.8 2.9 29 46-74 38-66 (76)
8 PF12793 SgrR_N: Sugar transpo 64.3 7 0.00015 26.4 2.5 24 45-68 28-51 (115)
9 TIGR02337 HpaR homoprotocatech 60.0 15 0.00032 23.9 3.4 34 45-78 51-89 (118)
10 cd00092 HTH_CRP helix_turn_hel 55.3 22 0.00048 20.2 3.3 26 45-70 34-59 (67)
11 PRK13918 CRP/FNR family transc 52.8 23 0.0005 24.3 3.6 31 45-75 158-188 (202)
12 PF13730 HTH_36: Helix-turn-he 52.6 16 0.00034 20.5 2.3 22 45-66 34-55 (55)
13 PF08544 GHMP_kinases_C: GHMP 49.6 26 0.00056 20.8 3.1 23 40-62 59-81 (85)
14 smart00420 HTH_DEOR helix_turn 49.2 19 0.00042 19.2 2.2 24 46-69 24-47 (53)
15 COG2873 MET17 O-acetylhomoseri 48.7 12 0.00025 31.1 1.7 21 66-87 144-164 (426)
16 PF12802 MarR_2: MarR family; 44.5 21 0.00046 20.1 2.0 25 45-69 30-54 (62)
17 smart00529 HTH_DTXR Helix-turn 44.3 34 0.00073 21.0 3.1 26 46-71 9-34 (96)
18 PF05036 SPOR: Sporulation rel 44.0 19 0.00042 20.7 1.8 25 39-63 2-28 (76)
19 smart00345 HTH_GNTR helix_turn 43.9 27 0.00058 19.1 2.3 26 45-70 29-54 (60)
20 PRK13626 transcriptional regul 43.7 19 0.00041 29.6 2.2 24 45-68 32-55 (552)
21 KOG2915|consensus 43.6 17 0.00037 29.1 1.9 53 20-73 184-236 (314)
22 PRK11512 DNA-binding transcrip 43.3 42 0.00091 22.5 3.6 34 45-78 63-101 (144)
23 TIGR03697 NtcA_cyano global ni 43.1 38 0.00083 22.9 3.4 31 45-75 152-182 (193)
24 PF09339 HTH_IclR: IclR helix- 42.0 25 0.00054 19.8 2.0 24 45-68 27-50 (52)
25 PF05670 DUF814: Domain of unk 41.9 35 0.00075 21.6 2.9 30 36-65 2-32 (90)
26 PF01047 MarR: MarR family; I 41.4 25 0.00055 19.8 2.0 24 46-69 27-50 (59)
27 PRK10402 DNA-binding transcrip 39.2 42 0.00091 23.9 3.3 31 45-75 178-208 (226)
28 PRK03573 transcriptional regul 39.2 48 0.001 22.0 3.4 34 45-78 55-93 (144)
29 cd07377 WHTH_GntR Winged helix 38.4 40 0.00087 18.7 2.5 25 46-70 35-59 (66)
30 PF06970 RepA_N: Replication i 38.2 41 0.00089 21.1 2.7 35 44-79 17-55 (76)
31 PF07848 PaaX: PaaX-like prote 37.5 30 0.00065 21.4 2.0 26 44-69 31-56 (70)
32 TIGR00315 cdhB CO dehydrogenas 37.5 60 0.0013 23.3 3.8 39 43-86 104-142 (162)
33 KOG1515|consensus 34.7 33 0.00072 27.2 2.3 31 7-45 74-104 (336)
34 smart00347 HTH_MARR helix_turn 34.0 80 0.0017 18.8 3.5 32 46-77 34-70 (101)
35 PRK11161 fumarate/nitrate redu 33.4 65 0.0014 22.8 3.5 31 45-75 193-223 (235)
36 PF00392 GntR: Bacterial regul 33.3 74 0.0016 18.4 3.2 24 45-68 33-56 (64)
37 COG4533 ABC-type uncharacteriz 33.2 34 0.00074 29.4 2.3 23 46-68 33-55 (564)
38 smart00418 HTH_ARSR helix_turn 32.3 54 0.0012 17.6 2.4 24 45-68 19-42 (66)
39 PF02631 RecX: RecX family; I 31.6 50 0.0011 21.6 2.4 22 47-68 5-26 (121)
40 PRK13412 fkp bifunctional fuco 30.9 97 0.0021 28.4 4.8 48 33-83 921-968 (974)
41 PRK14165 winged helix-turn-hel 30.5 73 0.0016 23.9 3.4 34 45-78 30-65 (217)
42 PF10340 DUF2424: Protein of u 29.5 64 0.0014 26.2 3.2 40 34-79 125-164 (374)
43 smart00344 HTH_ASNC helix_turn 29.3 68 0.0015 20.1 2.7 25 45-69 26-50 (108)
44 PF05608 DUF778: Protein of un 28.1 49 0.0011 23.3 2.0 23 28-50 8-30 (136)
45 PF00325 Crp: Bacterial regula 27.0 75 0.0016 17.0 2.2 21 46-66 12-32 (32)
46 PF11729 Capsid-VNN: nodavirus 26.9 36 0.00079 27.3 1.3 33 30-62 111-143 (340)
47 PF12101 DUF3577: Protein of u 26.9 2.2E+02 0.0047 20.2 5.1 47 40-89 49-96 (137)
48 COG4738 Predicted transcriptio 26.5 39 0.00085 23.7 1.3 19 51-69 56-74 (124)
49 PRK09391 fixK transcriptional 26.2 98 0.0021 22.2 3.4 26 45-70 188-213 (230)
50 PF01978 TrmB: Sugar-specific 25.9 66 0.0014 18.8 2.1 25 45-69 31-55 (68)
51 PF13412 HTH_24: Winged helix- 24.8 81 0.0018 17.1 2.2 21 46-66 27-47 (48)
52 smart00550 Zalpha Z-DNA-bindin 24.2 93 0.002 18.6 2.5 25 45-69 31-55 (68)
53 COG1846 MarR Transcriptional r 23.9 1.5E+02 0.0033 18.0 3.6 34 45-78 45-83 (126)
54 TIGR01889 Staph_reg_Sar staphy 23.9 1.7E+02 0.0036 18.8 3.9 34 45-78 52-90 (109)
55 PF09383 NIL: NIL domain; Int 22.2 1.4E+02 0.0031 17.7 3.1 35 30-64 33-70 (76)
56 PF08704 GCD14: tRNA methyltra 22.2 80 0.0017 24.0 2.4 49 22-71 122-170 (247)
57 TIGR01610 phage_O_Nterm phage 21.6 90 0.002 19.9 2.2 25 45-69 56-80 (95)
58 PF04937 DUF659: Protein of un 21.5 1.1E+02 0.0025 21.4 2.9 24 63-87 39-62 (153)
59 PRK00215 LexA repressor; Valid 21.3 1.5E+02 0.0033 20.9 3.6 31 45-75 32-66 (205)
60 cd00090 HTH_ARSR Arsenical Res 21.3 1.1E+02 0.0024 16.7 2.3 26 45-70 29-54 (78)
61 PF01325 Fe_dep_repress: Iron 21.2 89 0.0019 18.5 2.0 24 45-68 31-54 (60)
62 COG0320 LipA Lipoate synthase 21.2 1.2E+02 0.0026 24.3 3.2 29 36-64 213-241 (306)
63 PF14305 ATPgrasp_TupA: TupA-l 20.9 46 0.001 24.8 0.8 19 29-47 209-227 (239)
64 COG4463 CtsR Transcriptional r 20.7 70 0.0015 23.2 1.7 8 38-45 63-70 (153)
65 PRK13777 transcriptional regul 20.5 1.6E+02 0.0034 21.4 3.5 32 47-78 70-106 (185)
66 cd00642 GTP_cyclohydro1 GTP cy 20.2 1.9E+02 0.0041 21.2 3.9 48 29-78 82-144 (185)
67 PRK09347 folE GTP cyclohydrola 20.0 1.6E+02 0.0034 21.7 3.4 48 28-77 84-146 (188)
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=99.90 E-value=4.8e-24 Score=167.58 Aligned_cols=64 Identities=41% Similarity=0.758 Sum_probs=61.1
Q ss_pred CCccceeeecCCCCeEEECCCCHHHHHHHHHHhhhCCcccCCCcEEEEEeeeeecCCceEEEeC
Q psy14514 28 DYYTGQVGSYPYSGFYQDLSANHNDFLAQLDMLRKGGWITRATRVVFIDFSMYNANVNLFCFVK 91 (91)
Q Consensus 28 ~~~~G~~~~Y~gGGYv~~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfvEFtlYN~n~nLF~vVk 91 (91)
.|+.|++++|+||||+++|++++++|.++|++||+++|||++||||+|||++||||+||||+|+
T Consensus 114 ~~~~G~~~~Y~~gGY~~~L~~~~~~a~~~l~~L~~~~WiD~~Trav~vef~~YN~~~nlf~~v~ 177 (425)
T PF08016_consen 114 YPYWGQFGTYGGGGYVVDLGRNKDEARSILQYLQQNNWIDRSTRAVFVEFTLYNPNTNLFSVVT 177 (425)
T ss_pred CceeeeeeeeCCCcEEEECCCCHHHHHHHHHHHHhCcCcccCCceEEEEEEEEcCCCCeeEEEE
Confidence 3455999999999999999999999999999999999999999999999999999999999985
No 2
>KOG3599|consensus
Probab=99.87 E-value=1.9e-22 Score=171.64 Aligned_cols=78 Identities=37% Similarity=0.666 Sum_probs=71.0
Q ss_pred hhhcCccCCCC----------CCCCCccccCCccceeeecCCCCeEEECCCCHHHHHHHHHHhhhCCcccCCCcEEEEEe
Q psy14514 8 LKGIYEENLPV----------FEGSSVWDSDYYTGQVGSYPYSGFYQDLSANHNDFLAQLDMLRKGGWITRATRVVFIDF 77 (91)
Q Consensus 8 ~~~i~~~~~~~----------~~~~~~w~~~~~~G~~~~Y~gGGYv~~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfvEF 77 (91)
.|++|.++.++ +.+.+.| |.+++|+||||+++|+.+++++.+++++|++++|||++||||||||
T Consensus 345 ~~~~~~~~~~~e~~~~~~~~~L~~~~~~------g~l~~Y~~gGY~~~l~~sr~es~~~i~~L~~~~WlD~~TrAvfidf 418 (798)
T KOG3599|consen 345 PWSPYGPWAGDEFTYSTSKELLLGLEHW------GLLASYGGGGYVVLLSLSRTESLKAISYLRENNWLDRGTRAVFIDF 418 (798)
T ss_pred CccccCCCcccccccccccccccccccc------cceeEecCCCEEEEecCchHhHHHHHHHHHHhccccCCCcEEEEec
Confidence 47777777766 5555566 9999999999999999999999999999999999999999999999
Q ss_pred eeeecCCceEEEeC
Q psy14514 78 SMYNANVNLFCFVK 91 (91)
Q Consensus 78 tlYN~n~nLF~vVk 91 (91)
|+||||+||||+|+
T Consensus 419 tlYNa~inlF~~v~ 432 (798)
T KOG3599|consen 419 TLYNADINLFCVVT 432 (798)
T ss_pred cccCCCCCeeEEEE
Confidence 99999999999985
No 3
>PLN03223 Polycystin cation channel protein; Provisional
Probab=99.69 E-value=3.7e-17 Score=144.62 Aligned_cols=55 Identities=25% Similarity=0.336 Sum_probs=52.4
Q ss_pred cCCC-CeEEECCCCHHHHHHHHHHhhhCCcccC-CCcEEEEEeeeeecCCceEEEeC
Q psy14514 37 YPYS-GFYQDLSANHNDFLAQLDMLRKGGWITR-ATRVVFIDFSMYNANVNLFCFVK 91 (91)
Q Consensus 37 Y~gG-GYv~~L~~~~~~a~~~L~~L~~~~WiD~-~TRAvfvEFtlYN~n~nLF~vVk 91 (91)
|++| ||+++|+.++++|.++|++|+++.|||+ +||||||||++||||+||||+|+
T Consensus 1086 y~DGfgyv~DL~lSa~eA~~~L~~LKdnlWIDr~~TRAVFVEFTVYNANVNLFSvVt 1142 (1634)
T PLN03223 1086 YADGFPYFFDINLSAAEAQTWLDYMIYGLMIDDVKTRKVTAQVVVYNAELGYFGNVM 1142 (1634)
T ss_pred CCCCceEEEECCCCHHHHHHHHHHHHhCCCcccccceeEEEEEEEEcCCCCeEEEEE
Confidence 5555 9999999999999999999999999999 99999999999999999999985
No 4
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=80.82 E-value=3.1 Score=22.40 Aligned_cols=29 Identities=24% Similarity=0.316 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHHHHhhhCCcccCCCcEEE
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITRATRVVF 74 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~~TRAvf 74 (91)
++-++..+.+.|+.|++.+||++..+.+.
T Consensus 18 l~~s~~tv~~~l~~L~~~g~l~~~~~~~~ 46 (48)
T smart00419 18 LGLTRETVSRTLKRLEKEGLISREGGRIV 46 (48)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEeCCEEE
Confidence 56677889999999999999998765443
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=74.98 E-value=3.1 Score=29.90 Aligned_cols=21 Identities=24% Similarity=0.249 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhhhCCcccCCC
Q psy14514 50 HNDFLAQLDMLRKGGWITRAT 70 (91)
Q Consensus 50 ~~~a~~~L~~L~~~~WiD~~T 70 (91)
..+|..+++.|.+.+.|+++-
T Consensus 95 ~~~a~~ii~~L~e~~~it~RE 115 (152)
T PF05848_consen 95 QQDAEDIIQRLLEEGLITERE 115 (152)
T ss_dssp HHHHHHHHHHHHHTTSS-HHH
T ss_pred HHHHHHHHHHHHHCCCCCHHH
Confidence 578999999999999998754
No 6
>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=69.59 E-value=11 Score=21.63 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=23.9
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccC-----CCcEEEEEee
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITR-----ATRVVFIDFS 78 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~-----~TRAvfvEFt 78 (91)
.++.++......|+.|.+.+||.+ ..|...+++|
T Consensus 27 ~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT 65 (68)
T PF13463_consen 27 RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLT 65 (68)
T ss_dssp HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeC
Confidence 367778888999999999999943 3455666654
No 7
>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=65.80 E-value=8.6 Score=22.75 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHHHHhhhCCcccCCCcEEE
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITRATRVVF 74 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~~TRAvf 74 (91)
+|-+++...+.|+.|++.+||+..-+-+.
T Consensus 38 ~g~sr~tv~r~l~~l~~~g~I~~~~~~i~ 66 (76)
T PF13545_consen 38 LGVSRETVSRILKRLKDEGIIEVKRGKII 66 (76)
T ss_dssp HTSCHHHHHHHHHHHHHTTSEEEETTEEE
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEcCCEEE
Confidence 34555778889999999999997555443
No 8
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=64.28 E-value=7 Score=26.41 Aligned_cols=24 Identities=25% Similarity=0.414 Sum_probs=21.0
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
.|..+..+++.+|+.|++.+||+=
T Consensus 28 ~l~cS~Rn~r~lLkkm~~~gWi~W 51 (115)
T PF12793_consen 28 LLFCSRRNARTLLKKMQEEGWITW 51 (115)
T ss_pred HhCCCHHHHHHHHHHHHHCCCeee
Confidence 356788999999999999999973
No 9
>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=59.99 E-value=15 Score=23.86 Aligned_cols=34 Identities=24% Similarity=0.384 Sum_probs=26.9
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCC-----cEEEEEee
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRAT-----RVVFIDFS 78 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~T-----RAvfvEFt 78 (91)
.++-++......++.|.+.+||.+.. |.+.+..|
T Consensus 51 ~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT 89 (118)
T TIGR02337 51 QACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLT 89 (118)
T ss_pred HhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEEC
Confidence 35666778899999999999999854 77766654
No 10
>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=55.30 E-value=22 Score=20.18 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=22.2
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRAT 70 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~T 70 (91)
.+|.++....+.|+.|++.++|.+.-
T Consensus 34 ~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 34 YLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 46677889999999999999998754
No 11
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=52.77 E-value=23 Score=24.34 Aligned_cols=31 Identities=10% Similarity=0.209 Sum_probs=24.9
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCCcEEEE
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRATRVVFI 75 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfv 75 (91)
.||-+++...+.|+.|++.++|+..-+.+.|
T Consensus 158 ~lG~tretvsR~l~~l~~~g~I~~~~~~i~I 188 (202)
T PRK13918 158 AVGSVRETVTKVIGELSREGYIRSGYGKIQL 188 (202)
T ss_pred HhCccHHHHHHHHHHHHHCCCEEcCCCEEEE
Confidence 3677778888999999999999987665543
No 12
>PF13730 HTH_36: Helix-turn-helix domain
Probab=52.64 E-value=16 Score=20.51 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=19.2
Q ss_pred ECCCCHHHHHHHHHHhhhCCcc
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWI 66 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~Wi 66 (91)
.+|-++....+.|+.|++.+||
T Consensus 34 ~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 34 DLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHCcCHHHHHHHHHHHHHCcCC
Confidence 4677788999999999999997
No 13
>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=49.60 E-value=26 Score=20.82 Aligned_cols=23 Identities=17% Similarity=0.137 Sum_probs=20.5
Q ss_pred CCeEEECCCCHHHHHHHHHHhhh
Q psy14514 40 SGFYQDLSANHNDFLAQLDMLRK 62 (91)
Q Consensus 40 GGYv~~L~~~~~~a~~~L~~L~~ 62 (91)
||.++-|..+++++.++.+.|++
T Consensus 59 G~~v~~l~~~~~~~~~v~~~l~~ 81 (85)
T PF08544_consen 59 GPTVFALCKDEDDAERVAEALRE 81 (85)
T ss_dssp SSEEEEEESSHHHHHHHHHHHHH
T ss_pred CCeEEEEECCHHHHHHHHHHHHH
Confidence 89999999899999999998875
No 14
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=49.16 E-value=19 Score=19.19 Aligned_cols=24 Identities=25% Similarity=0.392 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
++-++..+...|+.|++.+||.+.
T Consensus 24 l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 24 LGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEe
Confidence 566788999999999999999864
No 15
>COG2873 MET17 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]
Probab=48.72 E-value=12 Score=31.12 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=17.5
Q ss_pred ccCCCcEEEEEeeeeecCCceE
Q psy14514 66 ITRATRVVFIDFSMYNANVNLF 87 (91)
Q Consensus 66 iD~~TRAvfvEFtlYN~n~nLF 87 (91)
||.+|||||+| |+=||..|+-
T Consensus 144 I~~nTkavf~E-tigNP~~~v~ 164 (426)
T COG2873 144 IDENTKAVFAE-TIGNPGLDVL 164 (426)
T ss_pred hCcccceEEEE-eccCCCcccc
Confidence 78999999999 6778877653
No 16
>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=44.45 E-value=21 Score=20.12 Aligned_cols=25 Identities=20% Similarity=0.294 Sum_probs=20.7
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
.++.++......++.|++.+||.+.
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 4677888999999999999999764
No 17
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=44.32 E-value=34 Score=21.04 Aligned_cols=26 Identities=19% Similarity=0.229 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHHHHhhhCCcccCCCc
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITRATR 71 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~~TR 71 (91)
++-++......|+.|++.+||.+...
T Consensus 9 l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 9 LNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred hCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 56677888999999999999999763
No 18
>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=43.96 E-value=19 Score=20.72 Aligned_cols=25 Identities=24% Similarity=0.410 Sum_probs=17.3
Q ss_pred CCCeEEECC--CCHHHHHHHHHHhhhC
Q psy14514 39 YSGFYQDLS--ANHNDFLAQLDMLRKG 63 (91)
Q Consensus 39 gGGYv~~L~--~~~~~a~~~L~~L~~~ 63 (91)
+++|.+.++ .++++|.+.++.|+..
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 467777776 5678888888888876
No 19
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=43.86 E-value=27 Score=19.13 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=21.6
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRAT 70 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~T 70 (91)
.++-++....+.++.|++.++|.+..
T Consensus 29 ~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 29 QLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 45677889999999999999998643
No 20
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=43.68 E-value=19 Score=29.64 Aligned_cols=24 Identities=21% Similarity=0.513 Sum_probs=21.2
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
.|..++.+++.+|+.|++.+||+=
T Consensus 32 ~l~cs~R~~~~~l~~~~~~gwl~w 55 (552)
T PRK13626 32 LLNCSRRHMRTLLNTMQQRGWLTW 55 (552)
T ss_pred HhcCChhHHHHHHHHHHHCCCeee
Confidence 357788999999999999999973
No 21
>KOG2915|consensus
Probab=43.59 E-value=17 Score=29.05 Aligned_cols=53 Identities=17% Similarity=0.116 Sum_probs=42.9
Q ss_pred CCCCccccCCccceeeecCCCCeEEECCCCHHHHHHHHHHhhhCCcccCCCcEE
Q psy14514 20 EGSSVWDSDYYTGQVGSYPYSGFYQDLSANHNDFLAQLDMLRKGGWITRATRVV 73 (91)
Q Consensus 20 ~~~~~w~~~~~~G~~~~Y~gGGYv~~L~~~~~~a~~~L~~L~~~~WiD~~TRAv 73 (91)
+-+-.|+.+|+.-. ..=.+||+++.++.=-++..+..+.|++-+|+|-.|--|
T Consensus 184 DlPaPw~AiPha~~-~lk~~g~r~csFSPCIEQvqrtce~l~~~gf~~i~~vEv 236 (314)
T KOG2915|consen 184 DLPAPWEAIPHAAK-ILKDEGGRLCSFSPCIEQVQRTCEALRSLGFIEIETVEV 236 (314)
T ss_pred cCCChhhhhhhhHH-HhhhcCceEEeccHHHHHHHHHHHHHHhCCCceEEEEEe
Confidence 33446788888877 666778899999999999999999999999999755433
No 22
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=43.27 E-value=42 Score=22.48 Aligned_cols=34 Identities=29% Similarity=0.484 Sum_probs=27.6
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCC-----cEEEEEee
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRAT-----RVVFIDFS 78 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~T-----RAvfvEFt 78 (91)
.++-++......++.|.+.+||.+.. |++.|..|
T Consensus 63 ~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT 101 (144)
T PRK11512 63 VLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLT 101 (144)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEC
Confidence 46778889999999999999998854 77766654
No 23
>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=43.14 E-value=38 Score=22.93 Aligned_cols=31 Identities=16% Similarity=0.194 Sum_probs=24.3
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCCcEEEE
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRATRVVFI 75 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfv 75 (91)
.||-+++...+.|+.|++.++|...-+-|.|
T Consensus 152 ~lG~tretvsR~l~~l~~~g~I~~~~~~i~I 182 (193)
T TIGR03697 152 AIGSTRVTITRLLGDLRKKKLISIHKKKITV 182 (193)
T ss_pred HhCCcHHHHHHHHHHHHHCCCEEecCCEEEE
Confidence 3566677788889999999999987665554
No 24
>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=42.02 E-value=25 Score=19.82 Aligned_cols=24 Identities=21% Similarity=0.343 Sum_probs=20.2
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
.+|-++..+...|+.|.+.+|+.+
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 467788999999999999999875
No 25
>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=41.91 E-value=35 Score=21.62 Aligned_cols=30 Identities=13% Similarity=0.026 Sum_probs=23.7
Q ss_pred ecCCCCeEEECCCCHHHHHHH-HHHhhhCCc
Q psy14514 36 SYPYSGFYQDLSANHNDFLAQ-LDMLRKGGW 65 (91)
Q Consensus 36 ~Y~gGGYv~~L~~~~~~a~~~-L~~L~~~~W 65 (91)
+...+|+.+..|++..++..+ +++++.+.+
T Consensus 2 F~s~~g~~i~vGrn~~eNe~L~~k~~~~~D~ 32 (90)
T PF05670_consen 2 FISSDGFKIIVGRNAKENEMLTKKYARPNDL 32 (90)
T ss_pred EEecCCeEEEEeCCHHHHHHHHHHhhhhcce
Confidence 345789999999999999888 676776553
No 26
>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=41.36 E-value=25 Score=19.75 Aligned_cols=24 Identities=25% Similarity=0.347 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
++.++......++.|.+.+||.+.
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 566788899999999999999874
No 27
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=39.19 E-value=42 Score=23.94 Aligned_cols=31 Identities=19% Similarity=0.336 Sum_probs=25.6
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCCcEEEE
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRATRVVFI 75 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfv 75 (91)
.||-+++.-.+.|+.|++.++|....+-+.|
T Consensus 178 ~lG~sretvsR~L~~L~~~G~I~~~~~~i~I 208 (226)
T PRK10402 178 YLGVSYRHLLYVLAQFIQDGYLKKSKRGYLI 208 (226)
T ss_pred HHCCcHHHHHHHHHHHHHCCCEEeeCCEEEE
Confidence 4778888888999999999999987765543
No 28
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=39.17 E-value=48 Score=22.04 Aligned_cols=34 Identities=24% Similarity=0.421 Sum_probs=27.2
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC-----CcEEEEEee
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA-----TRVVFIDFS 78 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~-----TRAvfvEFt 78 (91)
.++-++......++.|.+.+||.+. -|++.|..|
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT 93 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLT 93 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEC
Confidence 4567778888999999999999874 377777655
No 29
>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=38.38 E-value=40 Score=18.74 Aligned_cols=25 Identities=20% Similarity=0.298 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHHHhhhCCcccCCC
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITRAT 70 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~~T 70 (91)
++-+.......|+.|++.+||++..
T Consensus 35 ~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 35 LGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4566788899999999999998643
No 30
>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=38.22 E-value=41 Score=21.13 Aligned_cols=35 Identities=31% Similarity=0.463 Sum_probs=22.3
Q ss_pred EECCCCHHHHHHHHHHh----hhCCcccCCCcEEEEEeee
Q psy14514 44 QDLSANHNDFLAQLDML----RKGGWITRATRVVFIDFSM 79 (91)
Q Consensus 44 ~~L~~~~~~a~~~L~~L----~~~~WiD~~TRAvfvEFtl 79 (91)
..|+.+..-....|.+- .+++|+|..-+ |++.|+.
T Consensus 17 ~~Ls~~Ak~lY~ll~dR~~lS~kn~wiDe~G~-vYi~~s~ 55 (76)
T PF06970_consen 17 KKLSNDAKILYSLLLDRLRLSLKNGWIDENGN-VYIIFSI 55 (76)
T ss_pred ccCCHHHHHHHHHHHHHHHhhhhcCcCCCCCC-EEEEeeH
Confidence 55666654444443322 27899999977 7777763
No 31
>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=37.50 E-value=30 Score=21.44 Aligned_cols=26 Identities=15% Similarity=0.411 Sum_probs=21.4
Q ss_pred EECCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 44 QDLSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 44 ~~L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
..+|-+...++..|..|++.+||++.
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 46788889999999999999999874
No 32
>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=37.46 E-value=60 Score=23.30 Aligned_cols=39 Identities=18% Similarity=0.112 Sum_probs=33.2
Q ss_pred EEECCCCHHHHHHHHHHhhhCCcccCCCcEEEEEeeeeecCCce
Q psy14514 43 YQDLSANHNDFLAQLDMLRKGGWITRATRVVFIDFSMYNANVNL 86 (91)
Q Consensus 43 v~~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfvEFtlYN~n~nL 86 (91)
+.-+|.+..-+-..|+.||+.. | ++.|-++ ..|+||+++
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 6788999888999999999877 3 7888888 999999864
No 33
>KOG1515|consensus
Probab=34.74 E-value=33 Score=27.25 Aligned_cols=31 Identities=13% Similarity=0.115 Sum_probs=21.5
Q ss_pred hhhhcCccCCCCCCCCCccccCCccceeeecCCCCeEEE
Q psy14514 7 VLKGIYEENLPVFEGSSVWDSDYYTGQVGSYPYSGFYQD 45 (91)
Q Consensus 7 ~~~~i~~~~~~~~~~~~~w~~~~~~G~~~~Y~gGGYv~~ 45 (91)
+..|||.|...... .-+ +-+=.|.|||++..
T Consensus 74 l~vRly~P~~~~~~--~~~------p~lvyfHGGGf~~~ 104 (336)
T KOG1515|consen 74 LPVRLYRPTSSSSE--TKL------PVLVYFHGGGFCLG 104 (336)
T ss_pred eEEEEEcCCCCCcc--cCc------eEEEEEeCCccEeC
Confidence 45788888765553 223 55778999999854
No 34
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=33.99 E-value=80 Score=18.78 Aligned_cols=32 Identities=31% Similarity=0.450 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHHHhhhCCcccCC-----CcEEEEEe
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITRA-----TRVVFIDF 77 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~~-----TRAvfvEF 77 (91)
++.++......|+.|.+.+||.+. .|...+..
T Consensus 34 ~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~l 70 (101)
T smart00347 34 LGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSL 70 (101)
T ss_pred HCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEE
Confidence 566677888999999999999743 35555443
No 35
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=33.44 E-value=65 Score=22.75 Aligned_cols=31 Identities=16% Similarity=0.195 Sum_probs=25.5
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCCcEEEE
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRATRVVFI 75 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfv 75 (91)
.||-+++...++|+.|++.++|...-+.+.|
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 4677788888899999999999987776554
No 36
>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=33.29 E-value=74 Score=18.41 Aligned_cols=24 Identities=21% Similarity=0.274 Sum_probs=19.9
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
.++-++..+++.+..|.+.++|.+
T Consensus 33 ~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 33 RYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HhccCCcHHHHHHHHHHHCCcEEE
Confidence 356677899999999999999987
No 37
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=33.24 E-value=34 Score=29.39 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHHhhhCCcccC
Q psy14514 46 LSANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
|..++..++..|+.|++.+|||-
T Consensus 33 lfCS~Rh~R~lL~q~q~~gWL~W 55 (564)
T COG4533 33 LFCSRRHARTLLRQMQEAGWLTW 55 (564)
T ss_pred hccCHHHHHHHHHHHHHcCCEEe
Confidence 56788999999999999999985
No 38
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=32.34 E-value=54 Score=17.60 Aligned_cols=24 Identities=21% Similarity=0.321 Sum_probs=20.6
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
.|+-++......|+.|.+.+|+..
T Consensus 19 ~l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 19 ILGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeee
Confidence 356677899999999999999985
No 39
>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=31.55 E-value=50 Score=21.60 Aligned_cols=22 Identities=18% Similarity=0.311 Sum_probs=16.6
Q ss_pred CCCHHHHHHHHHHhhhCCcccC
Q psy14514 47 SANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 47 ~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
|.+.+....+|+.|++.+|||.
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 4466788899999999999985
No 40
>PRK13412 fkp bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional
Probab=30.90 E-value=97 Score=28.38 Aligned_cols=48 Identities=13% Similarity=0.196 Sum_probs=32.2
Q ss_pred eeeecCCCCeEEECCCCHHHHHHHHHHhhhCCcccCCCcEEEEEeeeeecC
Q psy14514 33 QVGSYPYSGFYQDLSANHNDFLAQLDMLRKGGWITRATRVVFIDFSMYNAN 83 (91)
Q Consensus 33 ~~~~Y~gGGYv~~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfvEFtlYN~n 83 (91)
++.==+|||++..|..+.+.+.++-+.|++.. ..-.++|+||.+=...
T Consensus 921 KLTGAGGGGcvI~Lak~~~~a~~I~~~L~~~~---~~~~~~~~~~~l~~~G 968 (974)
T PRK13412 921 KLPGAGGGGYLYMVAKDPGAAERIRKILTENA---PNPRARFVDMSLSDKG 968 (974)
T ss_pred EecccCcccEEEEEECChhhHHHHHHHHHhcc---cCCceeEEEEEECCCC
Confidence 34444568999999888888877777776632 2345677787764433
No 41
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=30.50 E-value=73 Score=23.87 Aligned_cols=34 Identities=24% Similarity=0.337 Sum_probs=26.1
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC--CcEEEEEee
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA--TRVVFIDFS 78 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~--TRAvfvEFt 78 (91)
.|+-++..+.+.|+.|++.+||.|. .|...+..|
T Consensus 30 ~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LT 65 (217)
T PRK14165 30 HTGTSSKTAARILKQLEDEGYITRTIVPRGQLITIT 65 (217)
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEEC
Confidence 4677889999999999999999874 355554443
No 42
>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=29.49 E-value=64 Score=26.24 Aligned_cols=40 Identities=15% Similarity=0.350 Sum_probs=28.2
Q ss_pred eeecCCCCeEEECCCCHHHHHHHHHHhhhCCcccCCCcEEEEEeee
Q psy14514 34 VGSYPYSGFYQDLSANHNDFLAQLDMLRKGGWITRATRVVFIDFSM 79 (91)
Q Consensus 34 ~~~Y~gGGYv~~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfvEFtl 79 (91)
+-.+.||||...+....-+....+.++- | ....+++|.++
T Consensus 125 lIYlHGGGY~l~~~p~qi~~L~~i~~~l-----~-~~SILvLDYsL 164 (374)
T PF10340_consen 125 LIYLHGGGYFLGTTPSQIEFLLNIYKLL-----P-EVSILVLDYSL 164 (374)
T ss_pred EEEEcCCeeEecCCHHHHHHHHHHHHHc-----C-CCeEEEEeccc
Confidence 4467789999999887766666666653 3 33777777765
No 43
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=29.26 E-value=68 Score=20.14 Aligned_cols=25 Identities=12% Similarity=0.161 Sum_probs=21.5
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
.+|-+.....+.++.|++.+||.+.
T Consensus 26 ~l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 26 KVGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHCcCHHHHHHHHHHHHHCCCeece
Confidence 3677888999999999999999853
No 44
>PF05608 DUF778: Protein of unknown function (DUF778); InterPro: IPR008496 This family consists of several eukaryotic proteins of unknown function.
Probab=28.06 E-value=49 Score=23.33 Aligned_cols=23 Identities=17% Similarity=0.309 Sum_probs=19.4
Q ss_pred CCccceeeecCCCCeEEECCCCH
Q psy14514 28 DYYTGQVGSYPYSGFYQDLSANH 50 (91)
Q Consensus 28 ~~~~G~~~~Y~gGGYv~~L~~~~ 50 (91)
+|..|.++++.+.|-+.|.....
T Consensus 8 ~PfIGH~GIc~s~GvI~DFaG~y 30 (136)
T PF05608_consen 8 FPFIGHMGICDSDGVIRDFAGPY 30 (136)
T ss_pred hhhccceEeecCCceEEecCCCc
Confidence 58899999999999998876553
No 45
>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=26.97 E-value=75 Score=17.01 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHHHhhhCCcc
Q psy14514 46 LSANHNDFLAQLDMLRKGGWI 66 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~Wi 66 (91)
||-+.+...+.+..|++.+-|
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 677888889999999998764
No 46
>PF11729 Capsid-VNN: nodavirus capsid protein ; InterPro: IPR024292 The capsid or coat protein of this family is expressed in Nodaviridae, that are ssRNA positive-strand viruses, with no DNA stage. These viruses are the causative agents of viral nervous necrosis in marine fish [].
Probab=26.90 E-value=36 Score=27.34 Aligned_cols=33 Identities=12% Similarity=0.097 Sum_probs=20.8
Q ss_pred ccceeeecCCCCeEEECCCCHHHHHHHHHHhhh
Q psy14514 30 YTGQVGSYPYSGFYQDLSANHNDFLAQLDMLRK 62 (91)
Q Consensus 30 ~~G~~~~Y~gGGYv~~L~~~~~~a~~~L~~L~~ 62 (91)
+.-++.+=.|||||+.+-.+..+....++.|+.
T Consensus 111 IQ~~cPanTGGGYVagFl~DPtd~d~t~~Alqa 143 (340)
T PF11729_consen 111 IQPMCPANTGGGYVAGFLPDPTDGDHTFDALQA 143 (340)
T ss_pred EeccCccccCCceEEEEcCCCCcccHHHHHHHH
Confidence 445566677899998776665444444555543
No 47
>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=26.85 E-value=2.2e+02 Score=20.20 Aligned_cols=47 Identities=13% Similarity=0.215 Sum_probs=38.3
Q ss_pred CCeE-EECCCCHHHHHHHHHHhhhCCcccCCCcEEEEEeeeeecCCceEEE
Q psy14514 40 SGFY-QDLSANHNDFLAQLDMLRKGGWITRATRVVFIDFSMYNANVNLFCF 89 (91)
Q Consensus 40 GGYv-~~L~~~~~~a~~~L~~L~~~~WiD~~TRAvfvEFtlYN~n~nLF~v 89 (91)
.-|. +|+.-..++|...++.+++. .| .-|-|+|.|.+=+..++.|+-
T Consensus 49 ~ey~~fD~~V~G~eA~~Lv~r~~~a--v~-~~~KVli~FrlgDl~~d~f~~ 96 (137)
T PF12101_consen 49 PEYRYFDCRVVGEEAKELVRRCQKA--VD-EDKKVLIGFRLGDLWADTFTY 96 (137)
T ss_pred ccEEEEEEEEecHHHHHHHHHHHhh--cc-cCCcEEEEEEecCCceeeEEe
Confidence 4675 68877789999999999998 34 466799999998888888863
No 48
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=26.55 E-value=39 Score=23.66 Aligned_cols=19 Identities=21% Similarity=0.616 Sum_probs=14.8
Q ss_pred HHHHHHHHHhhhCCcccCC
Q psy14514 51 NDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 51 ~~a~~~L~~L~~~~WiD~~ 69 (91)
.+-.-..+.||+++|+|.+
T Consensus 56 PEVSiAMr~Lre~gWV~~R 74 (124)
T COG4738 56 PEVSIAMRYLRENGWVDER 74 (124)
T ss_pred chhHHHHHHHHHccccchH
Confidence 3444568999999999975
No 49
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=26.21 E-value=98 Score=22.19 Aligned_cols=26 Identities=19% Similarity=0.155 Sum_probs=21.5
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRAT 70 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~T 70 (91)
.||-+++...++|+.|++.+.|+...
T Consensus 188 ~lGisretlsR~L~~L~~~GlI~~~~ 213 (230)
T PRK09391 188 YLGLTIETVSRALSQLQDRGLIGLSG 213 (230)
T ss_pred HHCCCHHHHHHHHHHHHHCCcEEecC
Confidence 35677788888899999999999754
No 50
>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=25.94 E-value=66 Score=18.77 Aligned_cols=25 Identities=20% Similarity=0.391 Sum_probs=21.2
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
.++-++......|+.|.+.+|+-+.
T Consensus 31 ~l~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 31 ELGISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3567788999999999999999763
No 51
>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=24.80 E-value=81 Score=17.09 Aligned_cols=21 Identities=24% Similarity=0.292 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHhhhCCcc
Q psy14514 46 LSANHNDFLAQLDMLRKGGWI 66 (91)
Q Consensus 46 L~~~~~~a~~~L~~L~~~~Wi 66 (91)
+|-+.......|+.|.+.++|
T Consensus 27 ~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 27 LGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HTS-HHHHHHHHHHHHHTTSE
T ss_pred hCCCHHHHHHHHHHHHHCcCc
Confidence 566778888999999999887
No 52
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=24.16 E-value=93 Score=18.63 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=22.0
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
.||-++....+.|..|++.+++.+.
T Consensus 31 ~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 31 NLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEec
Confidence 5778888999999999999999874
No 53
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=23.89 E-value=1.5e+02 Score=17.99 Aligned_cols=34 Identities=24% Similarity=0.388 Sum_probs=26.8
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCC-----cEEEEEee
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRAT-----RVVFIDFS 78 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~T-----RAvfvEFt 78 (91)
.++-++......++.|.+.++|.+.. |.++++.|
T Consensus 45 ~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT 83 (126)
T COG1846 45 RLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLT 83 (126)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEEC
Confidence 45667888999999999999998843 57776654
No 54
>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=23.89 E-value=1.7e+02 Score=18.75 Aligned_cols=34 Identities=18% Similarity=0.451 Sum_probs=26.8
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC-----CcEEEEEee
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA-----TRVVFIDFS 78 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~-----TRAvfvEFt 78 (91)
.++.++......++.|.+.+||-+. -|++.|..|
T Consensus 52 ~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT 90 (109)
T TIGR01889 52 EILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISIN 90 (109)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEEC
Confidence 4667788899999999999999863 367776654
No 55
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=22.18 E-value=1.4e+02 Score=17.72 Aligned_cols=35 Identities=17% Similarity=0.388 Sum_probs=26.2
Q ss_pred ccceeeecCCC--Ce-EEECCCCHHHHHHHHHHhhhCC
Q psy14514 30 YTGQVGSYPYS--GF-YQDLSANHNDFLAQLDMLRKGG 64 (91)
Q Consensus 30 ~~G~~~~Y~gG--GY-v~~L~~~~~~a~~~L~~L~~~~ 64 (91)
.+|.+....+. |. ++.|..+.++..+.+++|++.+
T Consensus 33 l~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~~~ 70 (76)
T PF09383_consen 33 LHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLREQG 70 (76)
T ss_dssp EEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHTT
T ss_pred EEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHHCC
Confidence 45778877773 44 5788888888899999999864
No 56
>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=22.16 E-value=80 Score=23.97 Aligned_cols=49 Identities=14% Similarity=0.116 Sum_probs=37.1
Q ss_pred CCccccCCccceeeecCCCCeEEECCCCHHHHHHHHHHhhhCCcccCCCc
Q psy14514 22 SSVWDSDYYTGQVGSYPYSGFYQDLSANHNDFLAQLDMLRKGGWITRATR 71 (91)
Q Consensus 22 ~~~w~~~~~~G~~~~Y~gGGYv~~L~~~~~~a~~~L~~L~~~~WiD~~TR 71 (91)
+..|+.+|+.-..- =..||.++-...+-++..+.++.|++++|.|-.|-
T Consensus 122 p~Pw~~i~~~~~~L-~~~gG~i~~fsP~ieQv~~~~~~L~~~gf~~i~~~ 170 (247)
T PF08704_consen 122 PDPWEAIPHAKRAL-KKPGGRICCFSPCIEQVQKTVEALREHGFTDIETV 170 (247)
T ss_dssp SSGGGGHHHHHHHE--EEEEEEEEEESSHHHHHHHHHHHHHTTEEEEEEE
T ss_pred CCHHHHHHHHHHHH-hcCCceEEEECCCHHHHHHHHHHHHHCCCeeeEEE
Confidence 34566666544332 25689999999999999999999999999887553
No 57
>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=21.61 E-value=90 Score=19.85 Aligned_cols=25 Identities=12% Similarity=0.060 Sum_probs=20.6
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRA 69 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~ 69 (91)
.+|-+++...+.|+.|++.+||-+.
T Consensus 56 ~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 56 LTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred HHCcCHHHHHHHHHHHHHCCCeeee
Confidence 3566778888999999999999853
No 58
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=21.48 E-value=1.1e+02 Score=21.35 Aligned_cols=24 Identities=33% Similarity=0.772 Sum_probs=20.1
Q ss_pred CCcccCCCcEEEEEeeeeecCCceE
Q psy14514 63 GGWITRATRVVFIDFSMYNANVNLF 87 (91)
Q Consensus 63 ~~WiD~~TRAvfvEFtlYN~n~nLF 87 (91)
++|-|+.-|.+ |-|.++.|.--.|
T Consensus 39 DgWtd~~~~~l-Inf~v~~~~g~~F 62 (153)
T PF04937_consen 39 DGWTDRKGRSL-INFMVYCPEGTVF 62 (153)
T ss_pred ecCcCCCCCeE-EEEEEEcccccEE
Confidence 58999999987 6799999976666
No 59
>PRK00215 LexA repressor; Validated
Probab=21.29 E-value=1.5e+02 Score=20.88 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=25.4
Q ss_pred ECCC-CHHHHHHHHHHhhhCCcccC---CCcEEEE
Q psy14514 45 DLSA-NHNDFLAQLDMLRKGGWITR---ATRVVFI 75 (91)
Q Consensus 45 ~L~~-~~~~a~~~L~~L~~~~WiD~---~TRAvfv 75 (91)
.+|- ++..+...|+.|++.+||.+ ..|++.+
T Consensus 32 ~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~~~l 66 (205)
T PRK00215 32 ALGLRSPSAVHEHLKALERKGFIRRDPGRSRAIEV 66 (205)
T ss_pred HhCCCChHHHHHHHHHHHHCCCEEeCCCCcceEEe
Confidence 3566 78899999999999999966 4677777
No 60
>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=21.26 E-value=1.1e+02 Score=16.75 Aligned_cols=26 Identities=15% Similarity=0.279 Sum_probs=21.3
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccCCC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITRAT 70 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~~T 70 (91)
.++.+.......++.|++.+||.+..
T Consensus 29 ~~~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 29 RLGLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHCcCHhHHHHHHHHHHHCCCeEEEE
Confidence 45667788899999999999998643
No 61
>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=21.25 E-value=89 Score=18.46 Aligned_cols=24 Identities=17% Similarity=0.201 Sum_probs=20.4
Q ss_pred ECCCCHHHHHHHHHHhhhCCcccC
Q psy14514 45 DLSANHNDFLAQLDMLRKGGWITR 68 (91)
Q Consensus 45 ~L~~~~~~a~~~L~~L~~~~WiD~ 68 (91)
.|+-++..+...++.|++.+.+++
T Consensus 31 ~L~vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 31 RLGVSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHCCChHHHHHHHHHHHHCCCEEe
Confidence 578888999999999999999886
No 62
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=21.21 E-value=1.2e+02 Score=24.29 Aligned_cols=29 Identities=24% Similarity=0.381 Sum_probs=26.3
Q ss_pred ecCCCCeEEECCCCHHHHHHHHHHhhhCC
Q psy14514 36 SYPYSGFYQDLSANHNDFLAQLDMLRKGG 64 (91)
Q Consensus 36 ~Y~gGGYv~~L~~~~~~a~~~L~~L~~~~ 64 (91)
.+.-+|-++.||.+.++-.+.+++|++.+
T Consensus 213 i~TKSgiMlGLGEt~~Ev~e~m~DLr~~g 241 (306)
T COG0320 213 IPTKSGLMVGLGETDEEVIEVMDDLRSAG 241 (306)
T ss_pred cccccceeeecCCcHHHHHHHHHHHHHcC
Confidence 66678999999999999999999999875
No 63
>PF14305 ATPgrasp_TupA: TupA-like ATPgrasp
Probab=20.93 E-value=46 Score=24.82 Aligned_cols=19 Identities=26% Similarity=0.396 Sum_probs=15.1
Q ss_pred CccceeeecCCCCeEEECC
Q psy14514 29 YYTGQVGSYPYSGFYQDLS 47 (91)
Q Consensus 29 ~~~G~~~~Y~gGGYv~~L~ 47 (91)
++.|+++.|+|+|+....+
T Consensus 209 iyFGElTf~p~~G~~~~~p 227 (239)
T PF14305_consen 209 IYFGELTFTPGAGFEPFFP 227 (239)
T ss_pred EEEEeeecCCCCcCCCCCC
Confidence 4779999999999874443
No 64
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=20.71 E-value=70 Score=23.16 Aligned_cols=8 Identities=13% Similarity=0.148 Sum_probs=5.6
Q ss_pred CCCCeEEE
Q psy14514 38 PYSGFYQD 45 (91)
Q Consensus 38 ~gGGYv~~ 45 (91)
+||||+.-
T Consensus 63 GGGGYIRI 70 (153)
T COG4463 63 GGGGYIRI 70 (153)
T ss_pred CCCceEEE
Confidence 56899843
No 65
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=20.48 E-value=1.6e+02 Score=21.37 Aligned_cols=32 Identities=16% Similarity=0.299 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHhhhCCcccCC-----CcEEEEEee
Q psy14514 47 SANHNDFLAQLDMLRKGGWITRA-----TRVVFIDFS 78 (91)
Q Consensus 47 ~~~~~~a~~~L~~L~~~~WiD~~-----TRAvfvEFt 78 (91)
.-++......++.|++.+||-|. -|+..|..|
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 34456788899999999999976 466666654
No 66
>cd00642 GTP_cyclohydro1 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4. This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively.
Probab=20.17 E-value=1.9e+02 Score=21.23 Aligned_cols=48 Identities=15% Similarity=0.020 Sum_probs=29.4
Q ss_pred Cccceee-ecCCCCeEEECCCCH--------------HHHHHHHHHhhhCCcccCCCcEEEEEee
Q psy14514 29 YYTGQVG-SYPYSGFYQDLSANH--------------NDFLAQLDMLRKGGWITRATRVVFIDFS 78 (91)
Q Consensus 29 ~~~G~~~-~Y~gGGYv~~L~~~~--------------~~a~~~L~~L~~~~WiD~~TRAvfvEFt 78 (91)
|++|..+ .|-.+|.|+.|++-. .-+.++.+.|.+. ++..--||+||-.
T Consensus 82 Pf~G~~~VaYiP~~~ViGLSKl~RiV~~~arRlQiQERLt~qIa~al~~~--l~~~gVaV~i~A~ 144 (185)
T cd00642 82 PFYGKVHIAYIPKDKVIGLSKLARIVEFFSRRLQVQERLTKQIAVAIQEI--LGPQGVAVVIEAT 144 (185)
T ss_pred ceEEEEEEEEecCCeeeeHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHh--hCCCcEEEEEEEE
Confidence 5669876 676689998888654 2334444444443 4455556666643
No 67
>PRK09347 folE GTP cyclohydrolase I; Provisional
Probab=20.04 E-value=1.6e+02 Score=21.71 Aligned_cols=48 Identities=19% Similarity=0.079 Sum_probs=30.5
Q ss_pred CCccceee-ecCCCCeEEECCCCH--------------HHHHHHHHHhhhCCcccCCCcEEEEEe
Q psy14514 28 DYYTGQVG-SYPYSGFYQDLSANH--------------NDFLAQLDMLRKGGWITRATRVVFIDF 77 (91)
Q Consensus 28 ~~~~G~~~-~Y~gGGYv~~L~~~~--------------~~a~~~L~~L~~~~WiD~~TRAvfvEF 77 (91)
+|++|..+ .|-.+|.|+.|++-. .-+.++.+.|++. |+..--||.||-
T Consensus 84 lPf~G~~hIaYiP~~~ViGLSKl~Riv~~~arRlQiQERlT~qIa~al~~~--l~p~gV~V~ieA 146 (188)
T PRK09347 84 LPFIGKAHVAYIPKGKVIGLSKIARIVDFFARRPQVQERLTAQIADALQEI--LGPRGVAVVIEA 146 (188)
T ss_pred CceeeEEEEEEeCCCccccHHHHHHHHHHHHcCchhHHHHHHHHHHHHHHh--hCCCceEEEEEE
Confidence 36669876 676689998887654 3344555555554 555666666664
Done!