Query 023360
Match_columns 283
No_of_seqs 141 out of 972
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:25:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023360.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023360hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03063 TRX_Fd_FDH_beta TRX-li 99.7 2.3E-18 5E-23 137.6 7.4 76 191-274 2-81 (92)
2 cd03064 TRX_Fd_NuoE TRX-like [ 99.7 6.1E-18 1.3E-22 128.7 7.1 70 189-269 1-79 (80)
3 cd02980 TRX_Fd_family Thioredo 99.7 1.5E-17 3.2E-22 123.8 7.4 72 190-270 1-77 (77)
4 cd03081 TRX_Fd_NuoE_FDH_gamma 99.7 1.7E-17 3.7E-22 127.5 6.7 70 189-269 1-79 (80)
5 cd03083 TRX_Fd_NuoE_hoxF TRX-l 99.7 2.4E-17 5.1E-22 126.8 6.7 70 189-269 1-79 (80)
6 PRK07539 NADH dehydrogenase su 99.7 1.1E-16 2.3E-21 136.9 7.8 75 185-270 70-153 (154)
7 TIGR01958 nuoE_fam NADH-quinon 99.7 1.3E-16 2.8E-21 135.4 7.6 75 185-270 64-147 (148)
8 PF01257 2Fe-2S_thioredx: Thio 99.7 1.1E-16 2.4E-21 135.5 7.2 75 185-270 61-144 (145)
9 COG1905 NuoE NADH:ubiquinone o 99.6 1E-15 2.3E-20 133.3 8.2 77 185-272 73-158 (160)
10 cd03082 TRX_Fd_NuoE_W_FDH_beta 99.6 8.2E-16 1.8E-20 117.0 6.5 69 190-269 2-71 (72)
11 PRK07571 bidirectional hydroge 99.6 2E-15 4.4E-20 132.1 7.9 76 185-271 84-168 (169)
12 PRK05988 formate dehydrogenase 99.6 2.9E-15 6.2E-20 129.2 8.4 76 185-271 71-155 (156)
13 cd03062 TRX_Fd_Sucrase TRX-lik 99.5 6E-14 1.3E-18 111.9 7.7 80 190-277 2-89 (97)
14 PRK12373 NADH dehydrogenase su 99.4 3.5E-13 7.7E-18 131.5 8.5 79 185-274 85-173 (400)
15 KOG3196 NADH:ubiquinone oxidor 99.2 2.5E-11 5.5E-16 109.6 7.2 83 186-279 110-201 (233)
16 COG3411 Ferredoxin [Energy pro 99.1 5.3E-11 1.1E-15 90.2 4.0 46 221-275 4-49 (64)
17 PF06999 Suc_Fer-like: Sucrase 97.8 9.1E-05 2E-09 66.1 7.6 83 187-275 130-220 (230)
18 PF07845 DUF1636: Protein of u 97.5 0.00022 4.7E-09 59.7 5.4 70 192-269 1-85 (116)
19 COG5469 Predicted metal-bindin 96.5 0.0064 1.4E-07 52.8 5.9 74 185-268 13-104 (143)
20 PF07293 DUF1450: Protein of u 95.1 0.076 1.6E-06 41.9 6.2 69 190-274 3-75 (78)
21 PRK13669 hypothetical protein; 92.6 0.35 7.6E-06 38.3 5.6 69 190-274 3-75 (78)
22 KOG3116 Predicted C3H1-type Zn 83.6 0.72 1.6E-05 41.1 2.0 13 35-47 35-47 (177)
23 PRK13752 putative transcriptio 81.4 2.8 6.1E-05 35.9 4.8 85 21-120 25-109 (144)
24 PF04889 Cwf_Cwc_15: Cwf15/Cwc 77.9 4.4 9.5E-05 38.0 5.2 37 94-130 145-181 (244)
25 cd04783 HTH_MerR1 Helix-Turn-H 77.5 5 0.00011 33.0 4.9 93 11-119 9-101 (126)
26 cd04785 HTH_CadR-PbrR-like Hel 74.2 9.1 0.0002 31.6 5.6 85 21-120 18-104 (126)
27 cd04790 HTH_Cfa-like_unk Helix 73.7 6.4 0.00014 34.5 4.9 89 12-120 11-99 (172)
28 cd04768 HTH_BmrR-like Helix-Tu 73.4 4.4 9.6E-05 32.0 3.5 77 21-116 18-94 (96)
29 cd04770 HTH_HMRTR Helix-Turn-H 72.2 12 0.00026 30.4 5.8 85 21-120 18-104 (123)
30 cd04784 HTH_CadR-PbrR Helix-Tu 71.1 12 0.00025 30.8 5.6 85 21-120 18-104 (127)
31 cd04782 HTH_BltR Helix-Turn-He 69.7 11 0.00024 29.8 5.0 73 26-116 23-95 (97)
32 KOG4055 Uncharacterized conser 69.7 23 0.00049 32.8 7.5 76 31-107 26-115 (213)
33 KOG4848 Extracellular matrix-a 67.8 12 0.00026 34.7 5.4 28 98-125 192-220 (225)
34 cd04776 HTH_GnyR Helix-Turn-He 67.5 17 0.00036 30.0 5.8 50 71-120 51-105 (118)
35 TIGR02051 MerR Hg(II)-responsi 66.8 12 0.00025 30.9 4.8 94 11-120 8-101 (124)
36 cd01111 HTH_MerD Helix-Turn-He 65.0 20 0.00044 29.0 5.8 75 21-110 18-95 (107)
37 PF10147 CR6_interact: Growth 64.9 23 0.0005 33.0 6.7 8 21-28 68-75 (217)
38 TIGR02054 MerD mercuric resist 63.6 18 0.00039 30.3 5.3 85 21-120 21-105 (120)
39 cd04786 HTH_MerR-like_sg7 Heli 62.6 16 0.00035 30.8 4.9 73 34-121 31-104 (131)
40 TIGR02047 CadR-PbrR Cd(II)/Pb( 62.5 18 0.0004 30.0 5.2 82 25-121 22-105 (127)
41 PRK15002 redox-sensitivie tran 61.6 20 0.00044 31.2 5.5 84 21-120 29-115 (154)
42 PRK10227 DNA-binding transcrip 57.2 29 0.00063 29.3 5.6 86 21-121 18-105 (135)
43 cd01109 HTH_YyaN Helix-Turn-He 56.0 36 0.00079 27.3 5.7 49 71-119 53-103 (113)
44 PF05501 DUF755: Domain of unk 55.4 13 0.00028 31.6 3.1 48 54-107 12-61 (123)
45 cd04766 HTH_HspR Helix-Turn-He 54.3 15 0.00034 28.4 3.2 67 25-119 23-89 (91)
46 KOG3228 Uncharacterized conser 54.2 26 0.00057 32.7 5.1 38 94-131 125-162 (226)
47 cd01108 HTH_CueR Helix-Turn-He 53.0 42 0.00091 27.7 5.8 80 26-120 23-104 (127)
48 cd01282 HTH_MerR-like_sg3 Heli 52.8 38 0.00081 27.4 5.3 91 12-119 10-105 (112)
49 PF05812 Herpes_BLRF2: Herpesv 51.8 25 0.00055 30.0 4.3 26 96-121 4-29 (118)
50 PRK09514 zntR zinc-responsive 51.4 36 0.00079 28.8 5.2 85 21-120 19-106 (140)
51 cd04787 HTH_HMRTR_unk Helix-Tu 50.7 39 0.00085 28.1 5.3 93 12-120 10-104 (133)
52 cd04777 HTH_MerR-like_sg1 Heli 49.0 42 0.00091 26.7 5.0 55 57-118 44-104 (107)
53 cd04772 HTH_TioE_rpt1 First He 48.7 46 0.00099 26.5 5.2 87 12-115 10-96 (99)
54 TIGR02043 ZntR Zn(II)-responsi 48.1 37 0.0008 28.3 4.7 79 27-120 25-106 (131)
55 PF05781 MRVI1: MRVI1 protein; 47.7 31 0.00067 36.2 5.0 51 59-109 255-306 (538)
56 PHA03155 hypothetical protein; 45.8 28 0.00061 29.7 3.6 26 96-121 9-34 (115)
57 PF09403 FadA: Adhesion protei 44.1 85 0.0018 26.9 6.3 47 69-124 10-56 (126)
58 PHA03162 hypothetical protein; 44.0 32 0.0007 30.0 3.8 25 97-121 15-39 (135)
59 TIGR02044 CueR Cu(I)-responsiv 43.3 68 0.0015 26.4 5.6 72 34-120 31-104 (127)
60 cd04788 HTH_NolA-AlbR Helix-Tu 42.9 30 0.00066 27.2 3.3 42 71-116 53-94 (96)
61 cd04769 HTH_MerR2 Helix-Turn-H 40.0 66 0.0014 26.1 4.9 52 71-122 52-106 (116)
62 PF09278 MerR-DNA-bind: MerR, 37.8 1.3E+02 0.0028 21.4 5.7 48 71-119 10-60 (65)
63 PF08496 Peptidase_S49_N: Pept 37.8 36 0.00078 29.9 3.2 38 93-130 47-91 (155)
64 PF13815 Dzip-like_N: Iguana/D 37.6 1.2E+02 0.0026 24.9 6.2 40 91-131 76-115 (118)
65 TIGR01950 SoxR redox-sensitive 36.5 80 0.0017 27.0 5.1 79 26-120 24-105 (142)
66 KOG1830 Wiskott Aldrich syndro 36.3 38 0.00082 34.9 3.5 14 93-106 452-465 (518)
67 KOG4727 U1-like Zn-finger prot 35.4 93 0.002 28.6 5.5 29 92-123 133-161 (193)
68 PF11208 DUF2992: Protein of u 34.7 1.1E+02 0.0024 26.4 5.6 35 92-126 83-117 (132)
69 KOG0416 Ubiquitin-protein liga 34.6 37 0.0008 31.1 2.8 24 132-155 162-185 (189)
70 PF08701 GN3L_Grn1: GNL3L/Grn1 34.4 1.1E+02 0.0024 24.3 5.2 29 86-122 41-69 (79)
71 PF06658 DUF1168: Protein of u 33.1 3E+02 0.0064 24.2 8.1 16 108-123 82-97 (142)
72 cd01107 HTH_BmrR Helix-Turn-He 32.9 1.1E+02 0.0023 24.6 5.0 46 71-119 54-99 (108)
73 cd04781 HTH_MerR-like_sg6 Heli 32.8 87 0.0019 25.5 4.6 48 71-120 52-99 (120)
74 PRK13749 transcriptional regul 32.6 93 0.002 26.2 4.8 52 21-87 21-72 (121)
75 cd01106 HTH_TipAL-Mta Helix-Tu 32.5 1.1E+02 0.0025 24.0 5.1 44 71-118 53-96 (103)
76 PF03879 Cgr1: Cgr1 family; I 31.5 92 0.002 26.2 4.5 20 95-114 44-63 (108)
77 PF14038 YqzE: YqzE-like prote 31.2 44 0.00096 25.0 2.3 28 96-123 9-36 (54)
78 PF06936 Selenoprotein_S: Sele 30.9 2.1E+02 0.0046 26.0 7.1 38 84-123 77-114 (190)
79 PF08496 Peptidase_S49_N: Pept 30.4 98 0.0021 27.2 4.7 23 107-129 72-94 (155)
80 cd04773 HTH_TioE_rpt2 Second H 30.0 1.6E+02 0.0035 23.6 5.7 87 12-114 10-97 (108)
81 smart00165 UBA Ubiquitin assoc 29.9 19 0.0004 23.3 0.1 33 68-101 5-37 (37)
82 PF15509 DUF4650: Domain of un 29.6 57 0.0012 34.1 3.5 44 50-107 323-373 (520)
83 KOG1156 N-terminal acetyltrans 28.4 47 0.001 35.8 2.8 29 103-131 578-607 (700)
84 KOG2985 Uncharacterized conser 27.7 43 0.00094 32.4 2.2 22 102-123 132-153 (306)
85 PF05890 Ebp2: Eukaryotic rRNA 27.1 2.6E+02 0.0056 26.7 7.3 49 60-108 85-143 (271)
86 KOG2138 Predicted RNA binding 26.8 53 0.0012 35.8 2.9 8 64-71 767-774 (883)
87 COG0789 SoxR Predicted transcr 26.6 1.4E+02 0.003 23.6 4.7 46 71-116 53-101 (124)
88 KOG3088 Secretory carrier memb 26.3 1.1E+02 0.0023 30.2 4.6 32 90-121 59-90 (313)
89 PF10870 DUF2729: Protein of u 26.2 23 0.00049 26.3 0.0 15 57-71 7-21 (53)
90 PRK11778 putative inner membra 25.8 1.1E+02 0.0024 30.1 4.7 46 189-237 154-199 (330)
91 KOG0286 G-protein beta subunit 25.8 70 0.0015 31.7 3.3 26 101-126 1-26 (343)
92 KOG2070 Guanine nucleotide exc 25.8 1.2E+02 0.0026 32.2 5.1 36 91-126 612-647 (661)
93 COG0394 Wzb Protein-tyrosine-p 25.7 60 0.0013 27.6 2.5 27 188-214 2-28 (139)
94 PF01451 LMWPc: Low molecular 24.4 86 0.0019 25.4 3.2 38 191-228 1-39 (138)
95 COG5665 NOT5 CCR4-NOT transcri 23.7 3.6E+02 0.0078 27.9 7.8 28 92-119 116-143 (548)
96 cd04775 HTH_Cfa-like Helix-Tur 23.3 1.4E+02 0.003 23.8 4.0 72 27-120 25-96 (102)
97 cd04779 HTH_MerR-like_sg4 Heli 23.2 4.2E+02 0.0091 22.5 7.2 58 12-86 10-67 (134)
98 PF10147 CR6_interact: Growth 22.9 5E+02 0.011 24.3 8.1 15 59-73 121-135 (217)
99 TIGR02435 CobG precorrin-3B sy 22.2 1.5E+02 0.0033 29.0 4.9 47 188-234 325-376 (390)
100 KOG3083 Prohibitin [Posttransl 21.9 1.6E+02 0.0036 28.2 4.8 52 72-126 159-211 (271)
101 PF14473 RD3: RD3 protein 21.4 1.9E+02 0.0041 25.2 4.7 27 97-123 24-51 (133)
102 KOG3535 Adaptor protein Disabl 21.4 55 0.0012 33.9 1.7 62 63-126 124-185 (557)
103 PHA00727 hypothetical protein 21.2 1.2E+02 0.0027 28.5 3.8 27 96-122 51-77 (278)
104 PHA00451 protein kinase 20.8 2.8E+02 0.0061 27.6 6.3 15 73-88 223-237 (362)
105 TIGR02573 LcrG_PcrG type III s 20.4 75 0.0016 26.1 2.0 40 70-109 28-67 (90)
106 PF07795 DUF1635: Protein of u 20.3 3.1E+02 0.0067 25.7 6.2 34 85-123 3-36 (214)
107 PF11853 DUF3373: Protein of u 20.3 1.4E+02 0.0029 31.2 4.2 22 97-118 33-54 (489)
108 cd01110 HTH_SoxR Helix-Turn-He 20.3 2.7E+02 0.0057 23.6 5.4 82 21-118 19-103 (139)
109 PTZ00399 cysteinyl-tRNA-synthe 20.3 1.7E+02 0.0038 31.1 5.2 12 98-109 551-562 (651)
110 PF15086 UPF0542: Uncharacteri 20.2 1.5E+02 0.0033 23.6 3.6 16 107-122 48-63 (74)
111 KOG4118 Uncharacterized conser 20.2 1.6E+02 0.0035 23.2 3.7 27 104-130 9-38 (74)
112 COG4759 Uncharacterized protei 20.1 1.8E+02 0.004 28.7 4.9 71 189-269 131-209 (316)
No 1
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=99.75 E-value=2.3e-18 Score=137.62 Aligned_cols=76 Identities=20% Similarity=0.174 Sum_probs=69.5
Q ss_pred EEEEecCCcccccchHHHHHHHHHHhcCCC---cEEeecCCCCCCCCCeEEEeCCcccCCCCCCC-CcccCCChhhHHHH
Q 023360 191 RVEVCMGNKCKKSGGGALFEEFQRAMGAEG---DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPN-PLCIGVALEDVGAI 266 (283)
Q Consensus 191 ~I~VC~GtsC~~~GA~~VLeaLeeeLg~~G---tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~g-vlY~~VtpEDV~eI 266 (283)
+|+||+||+|.+.||.+|+++|+++++..| +++.+||+|+|..||+|.|.. |++ ++|.+|+|+||++|
T Consensus 2 ~I~Vc~gT~ciAaGA~~V~~al~~ei~~~gl~v~v~~tGC~G~C~~ePlV~V~~--------p~g~v~Y~~V~~edv~~I 73 (92)
T cd03063 2 RIYVPRDAAALALGADEVAEAIEAEAAARGLAATIVRNGSRGMYWLEPLVEVET--------PGGRVAYGPVTPADVASL 73 (92)
T ss_pred EEEEeCChhhhhhCHHHHHHHHHHHHHHcCCeEEEEEecCceecCCCCEEEEEe--------CCCcEEEEeCCHHHHHHH
Confidence 599999999999999999999999999877 789999999999999999961 445 89999999999999
Q ss_pred HHHHHhcC
Q 023360 267 VGNLFTQG 274 (283)
Q Consensus 267 Vee~l~~~ 274 (283)
|++|+.+.
T Consensus 74 v~~~~~~~ 81 (92)
T cd03063 74 LDAGALEG 81 (92)
T ss_pred HHHHhhcC
Confidence 99998854
No 2
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=99.73 E-value=6.1e-18 Score=128.65 Aligned_cols=70 Identities=26% Similarity=0.573 Sum_probs=63.8
Q ss_pred CcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCC
Q 023360 189 TKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVA 259 (283)
Q Consensus 189 k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~Vt 259 (283)
+++|.||+|++|..+||++++++|+++++.. + ++..++|||.|..||+|.|+ ++||.+||
T Consensus 1 ~~~v~vC~~~~C~~~Ga~~~~~~l~~~l~~~~~~~~~~~~v~v~~t~ClG~C~~gP~v~v~-----------g~~y~~vt 69 (80)
T cd03064 1 KHVIRVCTGTACHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECLGACDLAPVMMIN-----------DDVYGRLT 69 (80)
T ss_pred CEEEEECCCcHHHhCCHHHHHHHHHHHhCCCCCCcCCCCEEEEEEecCcCcCCCCCEEEEC-----------CEEECCCC
Confidence 5899999999999999999999999999743 2 78999999999999999996 36999999
Q ss_pred hhhHHHHHHH
Q 023360 260 LEDVGAIVGN 269 (283)
Q Consensus 260 pEDV~eIVee 269 (283)
|++|++||++
T Consensus 70 ~~~i~~i~~~ 79 (80)
T cd03064 70 PEKVDAILEA 79 (80)
T ss_pred HHHHHHHHHh
Confidence 9999999975
No 3
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=99.72 E-value=1.5e-17 Score=123.84 Aligned_cols=72 Identities=31% Similarity=0.573 Sum_probs=66.1
Q ss_pred cEEEEecCCcccccchHHHHHHHHHHhcCCC-----cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCChhhHH
Q 023360 190 KRVEVCMGNKCKKSGGGALFEEFQRAMGAEG-----DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVALEDVG 264 (283)
Q Consensus 190 ~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~G-----tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~VtpEDV~ 264 (283)
++|+||+++.|..+|+.+|+++|+++++..+ ++..++|+|.|..||+|.|+| ++.||.+|++++++
T Consensus 1 ~~I~VC~~~~C~~~G~~~l~~~l~~~~~~~~~~~~v~v~~~~Clg~C~~~P~v~i~~---------~~~~y~~v~~~~~~ 71 (77)
T cd02980 1 HHILVCTGTACGLRGAEELLEALEKELGIRGGDGRVTVERVGCLGACGLAPVVVVYP---------DGVWYGRVTPEDVE 71 (77)
T ss_pred CEEEEccCCCcccCCHHHHHHHHHHHHhhhcCCCeEEEEEcCCcCcccCCCEEEEeC---------CCeEEccCCHHHHH
Confidence 5799999999999999999999999998753 889999999999999999985 46799999999999
Q ss_pred HHHHHH
Q 023360 265 AIVGNL 270 (283)
Q Consensus 265 eIVee~ 270 (283)
+||++|
T Consensus 72 ~il~~~ 77 (77)
T cd02980 72 EIVEEL 77 (77)
T ss_pred HHHHhC
Confidence 999864
No 4
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=99.71 E-value=1.7e-17 Score=127.53 Aligned_cols=70 Identities=20% Similarity=0.433 Sum_probs=63.7
Q ss_pred CcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCC
Q 023360 189 TKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVA 259 (283)
Q Consensus 189 k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~Vt 259 (283)
+|+|.||+|++|+.+||++|+++|++.|+.. | +|..++|+|.|..||+|+|++ .||.+++
T Consensus 1 ~~~i~vC~~~~C~~~G~~~ll~~l~~~l~~~~g~~~~dg~~~l~~~~ClG~C~~gP~~~v~~-----------~~~~~~~ 69 (80)
T cd03081 1 RHVLKLCRAEACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMIDG-----------EVHGRVD 69 (80)
T ss_pred CeEEEEcCChHHHhCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEeeecCccCCCCEEEECC-----------EEECCCC
Confidence 5899999999999999999999999999742 3 899999999999999999964 5788999
Q ss_pred hhhHHHHHHH
Q 023360 260 LEDVGAIVGN 269 (283)
Q Consensus 260 pEDV~eIVee 269 (283)
|++|++||++
T Consensus 70 ~e~i~~il~~ 79 (80)
T cd03081 70 PEKFDALLAE 79 (80)
T ss_pred HHHHHHHHHc
Confidence 9999999975
No 5
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=99.70 E-value=2.4e-17 Score=126.78 Aligned_cols=70 Identities=17% Similarity=0.339 Sum_probs=63.4
Q ss_pred CcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCC
Q 023360 189 TKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVA 259 (283)
Q Consensus 189 k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~Vt 259 (283)
+|+|.||.+++|+++||.+|+++|+++++.. | ++..++|||.|..||+|+|++ +||.+|+
T Consensus 1 ~~~i~vC~~~~C~~~Ga~~v~~~l~~~l~~~~~~~t~d~~v~l~~~gClG~C~~~P~v~V~~-----------~~y~~v~ 69 (80)
T cd03083 1 KYRIYLSDSITDRMNGYKAVLDALCRELGIRFGEVDEDGMVGLFFTSCTGLCDQGPALLINN-----------RVFTRLT 69 (80)
T ss_pred CEEEEEcCChHHHhCCHHHHHHHHHHHHCCCCCCcCCCCeEEEEEeceecCcCCCCeEEECC-----------EEECCCC
Confidence 5899999999999999999999999999743 2 789999999999999999963 5889999
Q ss_pred hhhHHHHHHH
Q 023360 260 LEDVGAIVGN 269 (283)
Q Consensus 260 pEDV~eIVee 269 (283)
|+|+++||+.
T Consensus 70 ~~~v~~iv~~ 79 (80)
T cd03083 70 PGRIDQIAEL 79 (80)
T ss_pred HHHHHHHHhc
Confidence 9999999974
No 6
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=99.67 E-value=1.1e-16 Score=136.90 Aligned_cols=75 Identities=20% Similarity=0.513 Sum_probs=67.5
Q ss_pred CCCCCcEEEEecCCcccccchHHHHHHHHHHhcC-C------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcc
Q 023360 185 DDGMTKRVEVCMGNKCKKSGGGALFEEFQRAMGA-E------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLC 255 (283)
Q Consensus 185 ~~~~k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~-~------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY 255 (283)
.++++++|.||+|++|+.+||.+|+++|+++++. . | ++..++|+|.|+.||+|+|++ .||
T Consensus 70 ~p~gk~~I~VC~g~~C~~~Ga~~l~~~l~~~L~i~~g~tt~dg~~~l~~~~ClG~C~~gPvv~V~~-----------~~y 138 (154)
T PRK07539 70 QPVGRHVIQVCTSTPCWLRGGEAILAALKKKLGIKPGETTADGRFTLLEVECLGACDNAPVVMIND-----------DTY 138 (154)
T ss_pred CCCCCEEEEEcCCchHHHCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEccccCccCCCCEEEECC-----------EEe
Confidence 4678999999999999999999999999999983 2 2 789999999999999999984 478
Q ss_pred cCCChhhHHHHHHHH
Q 023360 256 IGVALEDVGAIVGNL 270 (283)
Q Consensus 256 ~~VtpEDV~eIVee~ 270 (283)
.+|||++|++||+++
T Consensus 139 ~~vt~e~v~~il~~~ 153 (154)
T PRK07539 139 EDLTPEKIDELLDEL 153 (154)
T ss_pred CCCCHHHHHHHHHhc
Confidence 899999999999864
No 7
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=99.67 E-value=1.3e-16 Score=135.44 Aligned_cols=75 Identities=19% Similarity=0.434 Sum_probs=67.7
Q ss_pred CCCCCcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcc
Q 023360 185 DDGMTKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLC 255 (283)
Q Consensus 185 ~~~~k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY 255 (283)
.++++++|.||+|++|+.+||.+|+++|++.|+.+ | ++..++|+|.|+.||+|+|++ .+|
T Consensus 64 ~p~gk~~I~VC~g~~C~~~Ga~~v~~~l~~~L~i~~g~~t~dg~~~l~~~~ClG~C~~aP~v~V~~-----------~~y 132 (148)
T TIGR01958 64 EPVGRYHLQVCTNVPCALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGACGNAPVMMIND-----------DYY 132 (148)
T ss_pred CCCCCEEEEEcCCchhhhcCHHHHHHHHHHHhCCCCCCCCCCCeEEEEEcCccCccCCCCEEEECC-----------EEe
Confidence 46789999999999999999999999999999853 2 889999999999999999985 378
Q ss_pred cCCChhhHHHHHHHH
Q 023360 256 IGVALEDVGAIVGNL 270 (283)
Q Consensus 256 ~~VtpEDV~eIVee~ 270 (283)
.+|||+++++||+++
T Consensus 133 ~~vt~e~v~~il~~~ 147 (148)
T TIGR01958 133 EFLTPEKLDELLERY 147 (148)
T ss_pred CCCCHHHHHHHHHhc
Confidence 889999999999864
No 8
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=99.67 E-value=1.1e-16 Score=135.46 Aligned_cols=75 Identities=25% Similarity=0.524 Sum_probs=65.3
Q ss_pred CCCCCcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcc
Q 023360 185 DDGMTKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLC 255 (283)
Q Consensus 185 ~~~~k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY 255 (283)
.+.++++|.||+|++|+.+||.+|+++|++.++.+ | ++..++|+|.|..||+|+||+ .||
T Consensus 61 ~p~gk~~I~VC~g~~C~~~Ga~~l~~~l~~~l~i~~g~~~~dg~~~l~~~~ClG~C~~aP~v~V~~-----------~~y 129 (145)
T PF01257_consen 61 EPKGKHHIRVCTGTSCHLRGAEELLEALEEELGIKPGETTEDGKFTLEETGCLGACDQAPVVMVDG-----------EWY 129 (145)
T ss_dssp SS--SEEEEEE-SHHHHTTTHHHHHHHHHHHHCTSCCCCSTTTTEEEEEESSSSSGGGSSEEEECC-----------CEE
T ss_pred CCCCCcEEEeCCCchHHhCCCHHHHHHHHHHhCCcccccCCCceEEEEECCCccccCCCCEEEECC-----------EEE
Confidence 46689999999999999999999999999999632 3 899999999999999999974 478
Q ss_pred cCCChhhHHHHHHHH
Q 023360 256 IGVALEDVGAIVGNL 270 (283)
Q Consensus 256 ~~VtpEDV~eIVee~ 270 (283)
.+|||++|++||+++
T Consensus 130 ~~vt~e~v~~il~~l 144 (145)
T PF01257_consen 130 GNVTPEKVDEILEEL 144 (145)
T ss_dssp ESSSCCHHHHHHHHH
T ss_pred CCCCHHHHHHHHHhc
Confidence 899999999999875
No 9
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=99.62 E-value=1e-15 Score=133.33 Aligned_cols=77 Identities=22% Similarity=0.479 Sum_probs=69.4
Q ss_pred CCCCCcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcc
Q 023360 185 DDGMTKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLC 255 (283)
Q Consensus 185 ~~~~k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY 255 (283)
.+.++|+|.||++++|+.+|+++|+++|++.++.+ | ++.+++|+|+|+.||+|+||++.|+
T Consensus 73 ~P~Gr~~i~VC~~t~C~l~Gs~~l~~~l~~~lgi~~gett~DG~ftl~~v~ClGaC~~AP~vmind~~~~---------- 142 (160)
T COG1905 73 KPVGRHHIRVCTGTACHLKGSEALLKALEKKLGIKPGETTADGKFTLEPVECLGACGQAPVVMINDDVYG---------- 142 (160)
T ss_pred CcCCCeEEEEeCCcHHhhcChHHHHHHHHHHhCCCCCCcCCCCeEEEeeeeeecccccCCEEEECCchhc----------
Confidence 36789999999999999999999999999999852 3 8999999999999999999988664
Q ss_pred cCCChhhHHHHHHHHHh
Q 023360 256 IGVALEDVGAIVGNLFT 272 (283)
Q Consensus 256 ~~VtpEDV~eIVee~l~ 272 (283)
++|||.+.+||+.+..
T Consensus 143 -~lt~e~l~eil~~~~~ 158 (160)
T COG1905 143 -RLTPEKLEEILEKLKA 158 (160)
T ss_pred -cCCHHHHHHHHHHHhc
Confidence 5799999999998754
No 10
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=99.62 E-value=8.2e-16 Score=116.98 Aligned_cols=69 Identities=28% Similarity=0.525 Sum_probs=63.0
Q ss_pred cEEEEecCCcccccchHHHHHHHHHHhcCCC-cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCChhhHHHHHH
Q 023360 190 KRVEVCMGNKCKKSGGGALFEEFQRAMGAEG-DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVALEDVGAIVG 268 (283)
Q Consensus 190 ~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~G-tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~VtpEDV~eIVe 268 (283)
++|.||+|++|+.+||.+|+++|++.|+.+. ++..++|||.|+.||+|+||++. |.++||++|+++++
T Consensus 2 ~~I~vC~~~~C~~~Ga~~l~~~l~~~L~~~~v~l~~~~ClG~C~~gP~v~V~~~~-----------~~~~t~~~i~~~~~ 70 (72)
T cd03082 2 LTVRVCDSLSCAMAGAEELLAALEAGLGPEGVRVVRAPCVGRCERAPAALVGQRP-----------VDGATPAAVAAAVE 70 (72)
T ss_pred eEEEEcCChHHHHCCHHHHHHHHHHHhCCCeEEEEecCcCCccCCCCeEEECCEE-----------eCCcCHHHHHHHHh
Confidence 6899999999999999999999999998766 89999999999999999999764 55779999999986
Q ss_pred H
Q 023360 269 N 269 (283)
Q Consensus 269 e 269 (283)
.
T Consensus 71 ~ 71 (72)
T cd03082 71 A 71 (72)
T ss_pred c
Confidence 3
No 11
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=99.60 E-value=2e-15 Score=132.08 Aligned_cols=76 Identities=22% Similarity=0.438 Sum_probs=68.4
Q ss_pred CCCCCcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcc
Q 023360 185 DDGMTKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLC 255 (283)
Q Consensus 185 ~~~~k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY 255 (283)
.++++|+|.||+|++|+.+||.+|+++|++.|+.+ | ++..+.|+|.|+.||+|+||++. |
T Consensus 84 ~P~Gk~~I~VC~g~aC~~~G~~~ll~~l~~~Lgi~~gett~DG~ftL~~~~ClG~C~~AP~~~Vn~~~-----------~ 152 (169)
T PRK07571 84 KPSGEHTCVVCTGTACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDGKV-----------A 152 (169)
T ss_pred CCCCCEEEEEcCChHHHHCCcHHHHHHHHHHhCCCCCCcCCCCeEEEEEecccCccCCCCeEEECCEE-----------e
Confidence 35699999999999999999999999999999853 3 89999999999999999999764 5
Q ss_pred cCCChhhHHHHHHHHH
Q 023360 256 IGVALEDVGAIVGNLF 271 (283)
Q Consensus 256 ~~VtpEDV~eIVee~l 271 (283)
.++|++++++||++|.
T Consensus 153 ~~lt~e~v~~il~~~~ 168 (169)
T PRK07571 153 GKQTPESVLEKVQGWL 168 (169)
T ss_pred CCCCHHHHHHHHHHHh
Confidence 6789999999999873
No 12
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=99.59 E-value=2.9e-15 Score=129.25 Aligned_cols=76 Identities=18% Similarity=0.349 Sum_probs=68.3
Q ss_pred CCCCCcEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcc
Q 023360 185 DDGMTKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLC 255 (283)
Q Consensus 185 ~~~~k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY 255 (283)
.++++|+|.||+|++|+.+||.+|+++|+++|+.+ | ++..+.|+|.|+.||+|+||++. |
T Consensus 71 ~p~Gk~~I~VC~~~~C~~~G~~~ll~~l~~~Lgi~~gett~Dg~ftL~~~~ClG~C~~aP~~~in~~~-----------~ 139 (156)
T PRK05988 71 HPPGRHVLKLCRAEACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDGEV-----------H 139 (156)
T ss_pred CCCCCEEEEEeCCchhhcCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECCEE-----------e
Confidence 46799999999999999999999999999999853 3 89999999999999999998754 5
Q ss_pred cCCChhhHHHHHHHHH
Q 023360 256 IGVALEDVGAIVGNLF 271 (283)
Q Consensus 256 ~~VtpEDV~eIVee~l 271 (283)
.++|++++++||+++.
T Consensus 140 ~~lt~~~~~~il~~~~ 155 (156)
T PRK05988 140 GRLDPQRLDALLAEAR 155 (156)
T ss_pred CCCCHHHHHHHHHHhh
Confidence 6789999999998763
No 13
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
Probab=99.50 E-value=6e-14 Score=111.86 Aligned_cols=80 Identities=24% Similarity=0.292 Sum_probs=68.4
Q ss_pred cEEEEecC----CcccccchHHHHHHHHHHhcCCC----cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCChh
Q 023360 190 KRVEVCMG----NKCKKSGGGALFEEFQRAMGAEG----DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVALE 261 (283)
Q Consensus 190 ~~I~VC~G----tsC~~~GA~~VLeaLeeeLg~~G----tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~VtpE 261 (283)
.+|+||++ ..|...| ..++++|++++...| .+..++|+|.|..||||.|+|.. +++||..|+|+
T Consensus 2 ~~ilVCth~rrd~~C~~~g-~~l~~~l~~~l~~~~~~~v~v~~~~clG~c~~gp~vvvyP~~-------~g~wy~~v~p~ 73 (97)
T cd03062 2 PLVLVCTHGKRDKRCGICG-PPLAAELRAELPEHGPGGVRVWEVSHVGGHKFAGNVIIYPKG-------DGIWYGRVTPE 73 (97)
T ss_pred CEEEEeCCCCCCcChhhcC-HHHHHHHHHHHHHhCCCceEEEeCCcCCccCcCCEEEEEeCC-------CeeEEeecCHH
Confidence 57999995 6798888 689999999997543 78999999999999999998420 68999999999
Q ss_pred hHHHHHHHHHhcCCcc
Q 023360 262 DVGAIVGNLFTQGSKS 277 (283)
Q Consensus 262 DV~eIVee~l~~~~~~ 277 (283)
||++||++|+..+..-
T Consensus 74 ~v~~Iv~~hl~~g~~v 89 (97)
T cd03062 74 HVPPIVDRLILGGKII 89 (97)
T ss_pred HHHHHHHHHhcCCcCC
Confidence 9999999999875543
No 14
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=99.42 E-value=3.5e-13 Score=131.50 Aligned_cols=79 Identities=20% Similarity=0.369 Sum_probs=69.7
Q ss_pred CCCCC-cEEEEecCCcccccchHHHHHHHHHHhcCC-------C--cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCc
Q 023360 185 DDGMT-KRVEVCMGNKCKKSGGGALFEEFQRAMGAE-------G--DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPL 254 (283)
Q Consensus 185 ~~~~k-~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-------G--tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvl 254 (283)
.+.++ ++|.||++++|+.+|+.+|+++|++.|++. | ++..+.|||.|.+||+|+||++ +
T Consensus 85 ~P~Gk~~~I~VC~~t~C~l~Ga~~ll~~le~~Lgik~GeTT~DG~FTLe~veCLGaC~~APv~~Ind~-----------~ 153 (400)
T PRK12373 85 QPVGTRAHIQVCGTTPCMLRGSEALMAVCKSKIHAHPHELNADGTLSWEEVECLGACVNAPMVQIGKD-----------Y 153 (400)
T ss_pred cCCCCceEEEEcCChHHHhCChHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECCE-----------E
Confidence 35676 899999999999999999999999999864 3 8999999999999999999875 4
Q ss_pred ccCCChhhHHHHHHHHHhcC
Q 023360 255 CIGVALEDVGAIVGNLFTQG 274 (283)
Q Consensus 255 Y~~VtpEDV~eIVee~l~~~ 274 (283)
|.++|++++.+||+++....
T Consensus 154 y~~LTpe~v~~IL~~l~ag~ 173 (400)
T PRK12373 154 YEDLTPERLEEIIDAFAAGK 173 (400)
T ss_pred eCCCCHHHHHHHHHHHhCCC
Confidence 56789999999999886544
No 15
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=99.21 E-value=2.5e-11 Score=109.59 Aligned_cols=83 Identities=17% Similarity=0.374 Sum_probs=72.8
Q ss_pred CCCCcEEEEecCCcccccchHHHHHHHHHHhcCC-C--------cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCccc
Q 023360 186 DGMTKRVEVCMGNKCKKSGGGALFEEFQRAMGAE-G--------DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCI 256 (283)
Q Consensus 186 ~~~k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~-G--------tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~ 256 (283)
.+++++|.||+.+.|..+|++++++++.+.++.. | +|..++|||+|-+||.|.|+++. |.
T Consensus 110 p~gKy~v~VC~ttpC~lrg~d~i~ea~~k~lgi~~Gett~d~~Ftl~e~eClGaCvnaPmi~IND~y-----------ye 178 (233)
T KOG3196|consen 110 PVGKYHVQVCTTTPCMLRGSDDILEACKKQLGIKVGETTKDGLFTLEEVECLGACVNAPMIAINDDY-----------YE 178 (233)
T ss_pred CCCCceEEEecCcHHhhhccHHHHHHHHHHhCccccccccccceeeecchhhhhhccCceeeecchh-----------hc
Confidence 6899999999999999999999999999999873 2 99999999999999999999864 56
Q ss_pred CCChhhHHHHHHHHHhcCCcccc
Q 023360 257 GVALEDVGAIVGNLFTQGSKSLE 279 (283)
Q Consensus 257 ~VtpEDV~eIVee~l~~~~~~~~ 279 (283)
.+|++|+.+|++.+.....+--|
T Consensus 179 dlt~k~l~eIle~L~~~k~pp~G 201 (233)
T KOG3196|consen 179 DLTPKKLVEILEDLKAGKKPPAG 201 (233)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCC
Confidence 78999999999988766544433
No 16
>COG3411 Ferredoxin [Energy production and conversion]
Probab=99.12 E-value=5.3e-11 Score=90.16 Aligned_cols=46 Identities=30% Similarity=0.569 Sum_probs=41.3
Q ss_pred cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCChhhHHHHHHHHHhcCC
Q 023360 221 DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVALEDVGAIVGNLFTQGS 275 (283)
Q Consensus 221 tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~VtpEDV~eIVee~l~~~~ 275 (283)
.+..++|||.|..||+|.|+ |+++||.+|+|+|+++||++|+.++-
T Consensus 4 ~~t~tgCl~~C~~gPvl~vY---------pegvWY~~V~p~~a~rIv~~hl~~Gr 49 (64)
T COG3411 4 RVTRTGCLGVCQDGPVLVVY---------PEGVWYTRVDPEDARRIVQSHLLGGR 49 (64)
T ss_pred EEeecchhhhhccCCEEEEe---------cCCeeEeccCHHHHHHHHHHHHhCCC
Confidence 46789999999999999998 46799999999999999999987654
No 17
>PF06999 Suc_Fer-like: Sucrase/ferredoxin-like; InterPro: IPR009737 This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity [].
Probab=97.75 E-value=9.1e-05 Score=66.08 Aligned_cols=83 Identities=23% Similarity=0.317 Sum_probs=68.5
Q ss_pred CCCcEEEEecC----CcccccchHHHHHHHHHHhcCCC----cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCC
Q 023360 187 GMTKRVEVCMG----NKCKKSGGGALFEEFQRAMGAEG----DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGV 258 (283)
Q Consensus 187 ~~k~~I~VC~G----tsC~~~GA~~VLeaLeeeLg~~G----tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~V 258 (283)
..+..|+||+. ..|... +..|+++|++.+...+ .|-.+..+|-+.-+|||+|+.. ..|.++||..|
T Consensus 130 ~~~~~iLVCtHg~RD~rCg~~-Gp~l~~~l~~~~~~~~l~~~~V~~iSHiGGHkfAgNvIiy~~-----~~p~g~wyGrv 203 (230)
T PF06999_consen 130 PDKPLILVCTHGKRDKRCGIL-GPPLARELEKELRERGLSRDRVWEISHIGGHKFAGNVIIYSK-----PKPDGIWYGRV 203 (230)
T ss_pred CCCCEEEEcCCCCcCCchhcc-cHHHHHHHHHHhhhcCCccceEEEecccccceecCeEEEEec-----CCCcEEEEEee
Confidence 46788999995 578877 5678899999998765 3889999999999999999921 12678999999
Q ss_pred ChhhHHHHHHHHHhcCC
Q 023360 259 ALEDVGAIVGNLFTQGS 275 (283)
Q Consensus 259 tpEDV~eIVee~l~~~~ 275 (283)
+|++|+.||++.+.++.
T Consensus 204 ~p~~v~~iv~~t~~~g~ 220 (230)
T PF06999_consen 204 TPEDVEGIVDATILDGK 220 (230)
T ss_pred CHHHHHHHHHHHHhCCc
Confidence 99999999998555543
No 18
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=97.47 E-value=0.00022 Score=59.66 Aligned_cols=70 Identities=26% Similarity=0.453 Sum_probs=55.4
Q ss_pred EEEecCCccccc---------chHHHHHHHHHHhcCC----C-cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccC
Q 023360 192 VEVCMGNKCKKS---------GGGALFEEFQRAMGAE----G-DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIG 257 (283)
Q Consensus 192 I~VC~GtsC~~~---------GA~~VLeaLeeeLg~~----G-tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~ 257 (283)
|.|| ++|... +++.++++|++.+... + +|.++.||..|..+-+|-+....- -.-+|.+
T Consensus 1 l~VC--~tCr~~~~~~~~~~~~G~~L~~aL~~~~~~~~~~~~v~v~~v~CL~~C~r~CtVA~~~~gK------~tYlfGd 72 (116)
T PF07845_consen 1 LFVC--TTCRRSGEDPEDGPRPGAALLDALRAALADAPLPDGVEVRPVECLSACDRPCTVALQAPGK------WTYLFGD 72 (116)
T ss_pred CEEe--CCCCCCCCCCCCCCChHHHHHHHHHHHHhcCCCCCceEEEeccHHhcCCCceEEEEEcCCC------cEEEEec
Confidence 4677 466654 8999999999998654 2 899999999999999999874321 1247889
Q ss_pred CCh-hhHHHHHHH
Q 023360 258 VAL-EDVGAIVGN 269 (283)
Q Consensus 258 Vtp-EDV~eIVee 269 (283)
++| ++++.|++-
T Consensus 73 l~p~~~a~~il~~ 85 (116)
T PF07845_consen 73 LDPDEDAEDILAF 85 (116)
T ss_pred CCcccCHHHHHHH
Confidence 999 899999983
No 19
>COG5469 Predicted metal-binding protein [Function unknown]
Probab=96.49 E-value=0.0064 Score=52.77 Aligned_cols=74 Identities=19% Similarity=0.407 Sum_probs=58.2
Q ss_pred CCCCCcEEEEecCCcccc----------cchHHHHHHHHHHhcCCC-----cEEeecCCCCCCCCCeEEEeCCcccCCCC
Q 023360 185 DDGMTKRVEVCMGNKCKK----------SGGGALFEEFQRAMGAEG-----DVVACKCMGKCRDGPNVRLFHSDAYHHLT 249 (283)
Q Consensus 185 ~~~~k~~I~VC~GtsC~~----------~GA~~VLeaLeeeLg~~G-----tV~~tgCLG~C~~GPnV~V~~e~~~~V~~ 249 (283)
....+|++.||. +|+. .++..+++.|++...... +|.+++||..|..|-+|.+.+.
T Consensus 13 ~~~~~htlfVCk--sC~~~~~~~~~~~p~~G~~Ll~kl~~l~qe~~~~~e~~I~~VeCl~~C~r~c~vA~~~~------- 83 (143)
T COG5469 13 NGMPKHTLFVCK--SCRDVSQEGKENGPSDGSILLDKLQELAQEWEIAHEFEIQTVECLAACNRGCVVAFSGP------- 83 (143)
T ss_pred cccCceEEEEec--cccccccCCccCCCCcHHHHHHHHHHHHhhhhhhccceeeeeHhhhhcCCCeEEEEecC-------
Confidence 456789999995 5543 467889999987664432 8999999999999998887643
Q ss_pred CCCC--cccCCChhh-HHHHHH
Q 023360 250 PPNP--LCIGVALED-VGAIVG 268 (283)
Q Consensus 250 P~gv--lY~~VtpED-V~eIVe 268 (283)
+++ +|.+++|+| ..+||+
T Consensus 84 -~k~sYLFgdL~p~d~a~dLl~ 104 (143)
T COG5469 84 -GKPSYLFGDLTPDDSASDLLE 104 (143)
T ss_pred -CCceEEEccCCccccHHHHHH
Confidence 443 677999999 888987
No 20
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=95.10 E-value=0.076 Score=41.90 Aligned_cols=69 Identities=17% Similarity=0.338 Sum_probs=52.1
Q ss_pred cEEEEecCCcccccchHHHHHHHHHHhcCCC-cEEeecCCCCC---CCCCeEEEeCCcccCCCCCCCCcccCCChhhHHH
Q 023360 190 KRVEVCMGNKCKKSGGGALFEEFQRAMGAEG-DVVACKCMGKC---RDGPNVRLFHSDAYHHLTPPNPLCIGVALEDVGA 265 (283)
Q Consensus 190 ~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~G-tV~~tgCLG~C---~~GPnV~V~~e~~~~V~~P~gvlY~~VtpEDV~e 265 (283)
-.|.+|.+ ....|++.+++.|++. .+ .+...||++.| ...|=..||++.. ..-|+|++-+
T Consensus 3 piVefC~~--Nl~~g~~~~~~~Le~~---p~~~Vie~gCl~~Cg~C~~~pFAlVnG~~V-----------~A~t~eeL~~ 66 (78)
T PF07293_consen 3 PIVEFCVS--NLASGTDQVYEKLEKD---PDIDVIEYGCLSYCGPCAKKPFALVNGEIV-----------AAETAEELLE 66 (78)
T ss_pred ceEEEccc--CchhhhHHHHHHHhcC---CCccEEEcChhhhCcCCCCCccEEECCEEE-----------ecCCHHHHHH
Confidence 45889965 4567999999999864 33 78899999877 4678888988754 3458888777
Q ss_pred HHHHHHhcC
Q 023360 266 IVGNLFTQG 274 (283)
Q Consensus 266 IVee~l~~~ 274 (283)
-|.+++.++
T Consensus 67 kI~~~i~e~ 75 (78)
T PF07293_consen 67 KIKEKIEEN 75 (78)
T ss_pred HHHHHHhcc
Confidence 777777664
No 21
>PRK13669 hypothetical protein; Provisional
Probab=92.57 E-value=0.35 Score=38.35 Aligned_cols=69 Identities=25% Similarity=0.408 Sum_probs=50.1
Q ss_pred cEEEEecCCcccccchHHHHHHHHHHhcCCC-cEEeecCCCCC---CCCCeEEEeCCcccCCCCCCCCcccCCChhhHHH
Q 023360 190 KRVEVCMGNKCKKSGGGALFEEFQRAMGAEG-DVVACKCMGKC---RDGPNVRLFHSDAYHHLTPPNPLCIGVALEDVGA 265 (283)
Q Consensus 190 ~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~G-tV~~tgCLG~C---~~GPnV~V~~e~~~~V~~P~gvlY~~VtpEDV~e 265 (283)
-.|.+|.+.- ..|++.+++.|++ ..+ .|...||++.| ..+|=..|+++... .-|||++-+
T Consensus 3 piVEfC~sNl--~~G~~~~~~~Le~---dP~~dVie~gCls~CG~C~~~~FAlVng~~V~-----------a~t~eeL~~ 66 (78)
T PRK13669 3 PIVEFCVSNL--ASGSQAAFEKLEK---DPNLDVLEYGCLGYCGICSEGLFALVNGEVVE-----------GETPEELVE 66 (78)
T ss_pred ceeeehhcch--hhhHHHHHHHHHh---CCCceEEEcchhhhCcCcccCceEEECCeEee-----------cCCHHHHHH
Confidence 3588898663 5788888887754 222 78899999776 56788899987643 457887777
Q ss_pred HHHHHHhcC
Q 023360 266 IVGNLFTQG 274 (283)
Q Consensus 266 IVee~l~~~ 274 (283)
-|..++.++
T Consensus 67 kI~~~i~e~ 75 (78)
T PRK13669 67 NIYAHLEEN 75 (78)
T ss_pred HHHHHHhhc
Confidence 777777663
No 22
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=83.63 E-value=0.72 Score=41.11 Aligned_cols=13 Identities=15% Similarity=0.028 Sum_probs=10.4
Q ss_pred CCCcccccccccc
Q 023360 35 EHQHHGGFVEMKK 47 (283)
Q Consensus 35 d~ghl~yy~~~~~ 47 (283)
.-||..|-+-.|+
T Consensus 35 q~GHWtYECk~kR 47 (177)
T KOG3116|consen 35 QAGHWTYECKNKR 47 (177)
T ss_pred hhccceeeecCce
Confidence 3499999887777
No 23
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=81.38 E-value=2.8 Score=35.89 Aligned_cols=85 Identities=18% Similarity=0.314 Sum_probs=48.1
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhhhHHHHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVL 100 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l 100 (283)
||----|.+...-.+++..|||...-= .++++++. |..+||..+.=..+++........++.++|
T Consensus 25 RyYE~~GLl~p~~r~~~gyR~Y~~~~l--------~rl~~I~~-------lr~~G~sL~eI~~ll~~~~~~~~~~~~~ll 89 (144)
T PRK13752 25 RFYQRKGLLPEPDKPYGSIRRYGEADV--------TRVRFVKS-------AQRLGFSLDEIAELLRLEDGTHCEEASSLA 89 (144)
T ss_pred HHHHHCCCCCCCccCCCCCeecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhccCCCCHHHHHHHH
Confidence 444344665443456677799987422 23566665 778888877433444322121124455666
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 023360 101 MKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 101 ~~~l~~~~~~~k~~k~~~k~ 120 (283)
-+++++++.+..++.+.+..
T Consensus 90 ~~k~~~l~~~i~~L~~~~~~ 109 (144)
T PRK13752 90 EHKLKDVREKMADLARMEAV 109 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 67777777777666555443
No 24
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=77.94 E-value=4.4 Score=37.96 Aligned_cols=37 Identities=24% Similarity=0.458 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023360 94 SEAAEVLMKQLEQLKTEEKKLKRKRKQEKANKLKAKI 130 (283)
Q Consensus 94 sea~e~l~~~l~~~~~~~k~~k~~~k~ek~a~~ka~k 130 (283)
.|=++.||+||+..|.|+.+.+.++.+++++.....+
T Consensus 145 eDd~~~Ll~ELekIKkER~ee~~~~e~~~~~~~~~~~ 181 (244)
T PF04889_consen 145 EDDTAALLRELEKIKKERAEEKARKEEEKAEEEEKER 181 (244)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999988888877777654443333
No 25
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=77.47 E-value=5 Score=33.03 Aligned_cols=93 Identities=23% Similarity=0.357 Sum_probs=49.9
Q ss_pred cCCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh
Q 023360 11 TSSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG 90 (283)
Q Consensus 11 ~~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~ 90 (283)
.+|.+++|= |+----|.+...-.+++-.+||...-= .++++++. |..+||....=..+++....
T Consensus 9 ~~gvs~~tl-R~Ye~~GLl~~~~r~~~gyR~Y~~~~l--------~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~ 72 (126)
T cd04783 9 AAGVNVETI-RYYQRRGLLPEPPRPEGGYRRYPEETV--------TRLRFIKR-------AQELGFTLDEIAELLELDDG 72 (126)
T ss_pred HHCcCHHHH-HHHHHCCCCCCCCcCCCCCeecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhcccC
Confidence 334444443 333344554422345556688876421 22455554 67788887633344433222
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 91 KMISEAAEVLMKQLEQLKTEEKKLKRKRK 119 (283)
Q Consensus 91 ~~~sea~e~l~~~l~~~~~~~k~~k~~~k 119 (283)
.-..+..+.|..+++++..+..++.+.+.
T Consensus 73 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~ 101 (126)
T cd04783 73 TDCSEARELAEQKLAEVDEKIADLQRMRA 101 (126)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22345566677788888777777765543
No 26
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=74.19 E-value=9.1 Score=31.62 Aligned_cols=85 Identities=16% Similarity=0.335 Sum_probs=49.7
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh--hhHHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG--KMISEAAE 98 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~--~~~sea~e 98 (283)
|+---.|.+.....+++-.+||...-= ..+++++. |..+||..+.=..+++.... .-..+..+
T Consensus 18 R~Ye~~Gll~~~~r~~~g~R~Y~~~~l--------~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~ 82 (126)
T cd04785 18 RYYESIGLLPEPARTAGGYRLYGAAHV--------ERLRFIRR-------ARDLGFSLEEIRALLALSDRPDRSCAEADA 82 (126)
T ss_pred HHHHHCCCCCCCCcCCCCccccCHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHhhhhcCCCCHHHHHH
Confidence 443334554443455656688876422 23566665 67888887744455543321 12345566
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 023360 99 VLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 99 ~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
+|.++++++..+-.++...++.
T Consensus 83 ~l~~~~~~l~~~i~~L~~~~~~ 104 (126)
T cd04785 83 IARAHLADVRARIADLRRLEAE 104 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 7778888887777777666544
No 27
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=73.71 E-value=6.4 Score=34.51 Aligned_cols=89 Identities=18% Similarity=0.342 Sum_probs=51.1
Q ss_pred CCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhh
Q 023360 12 SSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGK 91 (283)
Q Consensus 12 ~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~ 91 (283)
+|.++.|=+ |----|++.....+++..|||...-= .++.+++. |.++||+.+.=..+++...
T Consensus 11 ~gvs~~tLR-yYe~~GLl~p~~r~~~gyR~Y~~~dl--------~rL~~I~~-------lr~~G~sL~eI~~ll~~~~-- 72 (172)
T cd04790 11 FGLSRSTLL-YYERIGLLSPSARSESNYRLYGERDL--------ERLEQICA-------YRSAGVSLEDIRSLLQQPG-- 72 (172)
T ss_pred HCcCHHHHH-HHHHCCCCCCCccCCCCCccCCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhcCC--
Confidence 333333433 33334665554466777788876411 12445554 6778888774334443221
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 92 MISEAAEVLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 92 ~~sea~e~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
.++.++|.++++++..+-.+++..++.
T Consensus 73 --~~~~~~L~~~~~~l~~ei~~L~~~~~~ 99 (172)
T cd04790 73 --DDATDVLRRRLAELNREIQRLRQQQRA 99 (172)
T ss_pred --hhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 255667788888887777777666554
No 28
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=73.37 E-value=4.4 Score=32.00 Aligned_cols=77 Identities=13% Similarity=0.273 Sum_probs=45.1
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhhhHHHHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVL 100 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l 100 (283)
|+---.|.+...-.+++..+||...-= ..+++++. |..+||..+.=..+++.. ..+..+.|
T Consensus 18 Ryye~~Gll~p~~~~~~gyR~Y~~~~l--------~~l~~I~~-------lr~~G~~l~~I~~~l~~~----~~~~~~~l 78 (96)
T cd04768 18 RHYDDIGLFKPAKIAENGYRYYSYAQL--------YQLQFILF-------LRELGFSLAEIKELLDTE----MEELTAML 78 (96)
T ss_pred HHHHHCCCCCCCccCCCCeeeCCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhcC----cHHHHHHH
Confidence 333334665555456777888876421 22555554 677888877333333321 12566677
Q ss_pred HHHHHHHHHHHHHHHH
Q 023360 101 MKQLEQLKTEEKKLKR 116 (283)
Q Consensus 101 ~~~l~~~~~~~k~~k~ 116 (283)
-+++++++++..+++.
T Consensus 79 ~~~~~~l~~~i~~l~~ 94 (96)
T cd04768 79 LEKKQAIQQKIDRLQQ 94 (96)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7777777777777654
No 29
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=72.18 E-value=12 Score=30.42 Aligned_cols=85 Identities=16% Similarity=0.312 Sum_probs=48.4
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh--hhHHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG--KMISEAAE 98 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~--~~~sea~e 98 (283)
|+----|.+.....+++..|||...-= ..+.+++. |..+||....=..+++.... ....+..+
T Consensus 18 RyYe~~GLl~p~~r~~~gyR~Y~~~~i--------~~l~~I~~-------lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~ 82 (123)
T cd04770 18 RYYERIGLLPPPQRSENGYRLYGEADL--------ARLRFIRR-------AQALGFSLAEIRELLSLRDDGAAPCAEVRA 82 (123)
T ss_pred HHHHHCCCCCCCCCCCCCCccCCHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHHhhhcCCCCHHHHHH
Confidence 444334554444455666788865311 12444443 67788887744455544332 12345567
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 023360 99 VLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 99 ~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
.|-++++++.++.+++.+.+..
T Consensus 83 ~l~~~~~~l~~~i~~l~~~~~~ 104 (123)
T cd04770 83 LLEEKLAEVEAKIAELQALRAE 104 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 7888888887777777665543
No 30
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=71.14 E-value=12 Score=30.82 Aligned_cols=85 Identities=15% Similarity=0.256 Sum_probs=47.9
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh--hhHHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG--KMISEAAE 98 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~--~~~sea~e 98 (283)
||----|.+.....+++-.|||...-= .++++++. |..+||....=..+++.... ....+..+
T Consensus 18 RyYe~~GLl~p~~r~~~gyR~Y~~~~l--------~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~ 82 (127)
T cd04784 18 RYYEKEGLLPAPARSANNYRLYDEEHL--------ERLLFIRR-------CRSLDMSLDEIRTLLQLQDDPEASCAEVNA 82 (127)
T ss_pred HHHHHCCCCCCCCcCCCCCeecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHhhhcCCCcHHHHHH
Confidence 433334444333345555688876421 22455554 67788887744445543221 12355667
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 023360 99 VLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 99 ~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
+|.++++++..+..++.+.++.
T Consensus 83 ~l~~~~~~l~~~i~~L~~~~~~ 104 (127)
T cd04784 83 LIDEHLAHVRARIAELQALEKQ 104 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 7888888888777777665543
No 31
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=69.72 E-value=11 Score=29.81 Aligned_cols=73 Identities=16% Similarity=0.290 Sum_probs=43.7
Q ss_pred cCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhhhHHHHHHHHHHHHH
Q 023360 26 LGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLE 105 (283)
Q Consensus 26 ~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~ 105 (283)
.|.+...-.+++..+||...-= ..+.+++. |..+||..+.=..+++. .-+.+..+.|-++++
T Consensus 23 ~Gll~p~~~~~~gyR~Y~~~~~--------~~l~~I~~-------lr~~G~~l~eI~~~l~~---~~~~~~~~~l~~~~~ 84 (97)
T cd04782 23 IGLFKPEIVKENGYRYYTLEQF--------EQLDIILL-------LKELGISLKEIKDYLDN---RNPDELIELLKKQEK 84 (97)
T ss_pred CCCCCCCccCCCCCccCCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhc---CCHHHHHHHHHHHHH
Confidence 4554443355667788865321 12444444 67788888633333322 234566778888888
Q ss_pred HHHHHHHHHHH
Q 023360 106 QLKTEEKKLKR 116 (283)
Q Consensus 106 ~~~~~~k~~k~ 116 (283)
++.++.+++.+
T Consensus 85 ~l~~~i~~l~~ 95 (97)
T cd04782 85 EIKEEIEELQK 95 (97)
T ss_pred HHHHHHHHHHh
Confidence 88888777764
No 32
>KOG4055 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.66 E-value=23 Score=32.77 Aligned_cols=76 Identities=20% Similarity=0.161 Sum_probs=33.6
Q ss_pred cccCCCCcccccccccccc-cccchHHHHHHHHhhhcccccc--cccccccccchhHHHHHHhhh-----------HHHH
Q 023360 31 KQSHEHQHHGGFVEMKKKE-KVGSIKKKLKLLKGLSKDLSTF--SQMGFAVDQDQNLLAQVRGKM-----------ISEA 96 (283)
Q Consensus 31 ~~~~d~ghl~yy~~~~~~~-~~~~~kkk~kll~~ls~dl~~~--~~~g~~~d~~~~l~~~~~~~~-----------~sea 96 (283)
+.-.|.+-++.-.-+|+-. .+--+-.|.+|-.-+. +...| --||-.+++.-+=|+.-+... +.-+
T Consensus 26 k~aaDl~rlkl~rl~knpdkp~~ip~~k~~lr~~~e-~vp~fVrnv~GSSAgaGSgeFHvYR~lRRrEq~Rl~~md~~a~ 104 (213)
T KOG4055|consen 26 KKAADLQRLKLERLMKNPDKPVPIPDEKVKLRAPLE-NVPEFVRNVMGSSAGAGSGEFHVYRHLRRREQDRLDYMDADAN 104 (213)
T ss_pred hhhhhHhhhHHHHHhcCCCcCCCCchHHHHHhcccc-cccHHHHhcccccccCCCchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446666666655555531 1111113333322111 11222 135555555555666554332 2234
Q ss_pred HHHHHHHHHHH
Q 023360 97 AEVLMKQLEQL 107 (283)
Q Consensus 97 ~e~l~~~l~~~ 107 (283)
-+.|+.++++.
T Consensus 105 Ke~~daefq~r 115 (213)
T KOG4055|consen 105 KELLDAEFQIR 115 (213)
T ss_pred HHHHHHHHHHH
Confidence 45666666544
No 33
>KOG4848 consensus Extracellular matrix-associated peroxidase [Extracellular structures; Defense mechanisms]
Probab=67.79 E-value=12 Score=34.74 Aligned_cols=28 Identities=43% Similarity=0.434 Sum_probs=14.2
Q ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 023360 98 EVLMKQLEQL-KTEEKKLKRKRKQEKANK 125 (283)
Q Consensus 98 e~l~~~l~~~-~~~~k~~k~~~k~ek~a~ 125 (283)
+++|+|+|.- |..-||-|+|+|+||-++
T Consensus 192 ~emLqqkEkeekK~~KeaKrk~k~ekr~A 220 (225)
T KOG4848|consen 192 EEMLQQKEKEEKKAVKEAKRKEKQEKRFA 220 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555432 334455566666666533
No 34
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=67.46 E-value=17 Score=29.96 Aligned_cols=50 Identities=16% Similarity=0.302 Sum_probs=30.5
Q ss_pred ccccccccccchhHHHHHHh-----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRG-----KMISEAAEVLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~-----~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
+..+||..+.=..+++.... ..+.+..+.|-++++++..+..+++...+.
T Consensus 51 lr~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~ 105 (118)
T cd04776 51 GKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAE 105 (118)
T ss_pred HHHCCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56678887644455554322 123455667777777777777777665544
No 35
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=66.79 E-value=12 Score=30.93 Aligned_cols=94 Identities=20% Similarity=0.349 Sum_probs=52.0
Q ss_pred cCCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh
Q 023360 11 TSSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG 90 (283)
Q Consensus 11 ~~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~ 90 (283)
.+|..++|=| +---.|.+.....+++-.+||...-= ..+.+++. +..+||..+.=..+++-...
T Consensus 8 ~~gvs~~tlR-~Ye~~GLl~~~~r~~~g~R~Y~~~~l--------~~l~~I~~-------l~~~G~sl~eI~~~l~~~~~ 71 (124)
T TIGR02051 8 AAGVNVETIR-YYERKGLLPEPDRPEGGYRRYPEETV--------KRLRFIKR-------AQELGFSLEEIGGLLGLVDG 71 (124)
T ss_pred HHCcCHHHHH-HHHHCCCCCCCccCCCCCEeECHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHhcccC
Confidence 3444455543 32333443322244444577754311 22455554 67788887744455543332
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 91 KMISEAAEVLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 91 ~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
.-..+..+.|-++++.++++..++.+.+..
T Consensus 72 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~ 101 (124)
T TIGR02051 72 THCREMYELASRKLKSVQAKMADLLRIERL 101 (124)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 224566777888888888888887766543
No 36
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=65.02 E-value=20 Score=29.05 Aligned_cols=75 Identities=13% Similarity=0.176 Sum_probs=36.5
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhh---hHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGK---MISEAA 97 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~---~~sea~ 97 (283)
|+---.|++.....+++=.+||.+.-= .++.+++. |..+||+...=..+++.+... ...+..
T Consensus 18 R~ye~~GLl~p~~r~~~g~R~Y~~~~l--------~~l~~I~~-------lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~ 82 (107)
T cd01111 18 RDYLLRGLLHPVARTEGGYGLFDDCAL--------QRLRFVRA-------AFEAGIGLDELARLCRALDAGDGKQPEACL 82 (107)
T ss_pred HHHHHCCCCCCCCcCCCCCeecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHHHhCCChhhHHHHH
Confidence 333334665554445555677766422 23555554 667788766434444443222 133334
Q ss_pred HHHHHHHHHHHHH
Q 023360 98 EVLMKQLEQLKTE 110 (283)
Q Consensus 98 e~l~~~l~~~~~~ 110 (283)
+.+..+|++..++
T Consensus 83 ~~~~~~l~~~~~~ 95 (107)
T cd01111 83 AQLRQKIEVRRAA 95 (107)
T ss_pred HHHHHHHHHHHHH
Confidence 4444444444333
No 37
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=64.93 E-value=23 Score=32.98 Aligned_cols=8 Identities=38% Similarity=0.700 Sum_probs=5.0
Q ss_pred ccccccCc
Q 023360 21 RYSAGLGF 28 (283)
Q Consensus 21 r~~~~~gf 28 (283)
||+.-||.
T Consensus 68 RYG~aSgV 75 (217)
T PF10147_consen 68 RYGLASGV 75 (217)
T ss_pred hhhhhcCC
Confidence 66666665
No 38
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=63.63 E-value=18 Score=30.28 Aligned_cols=85 Identities=13% Similarity=0.137 Sum_probs=48.3
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhhhHHHHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVL 100 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l 100 (283)
|+---.|++.....+.+-.+||...-- ..+++++. +..+||+.+.=..+++.+...-..+....+
T Consensus 21 R~Ye~~GLL~p~~r~~~gyR~Y~~~~l--------~rL~~I~~-------lr~~G~~L~eI~~ll~~~~~~~~~~~~~~~ 85 (120)
T TIGR02054 21 RDYLLRGLLHPVRRTTSGYGIFDDASL--------QRLRFVRA-------AFEAGIGLGELARLCRALDAANGDDTAACL 85 (120)
T ss_pred HHHHHCCCCCCCccCCCCCeeCCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHhhccCCHHHHHHHH
Confidence 333334666655566677788876422 33677776 788899888555565544433223333344
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 023360 101 MKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 101 ~~~l~~~~~~~k~~k~~~k~ 120 (283)
-..++++.++..+|..-+++
T Consensus 86 ~~~~~~i~~ki~~L~~l~~~ 105 (120)
T TIGR02054 86 AVLRQLVEARREALAALEVQ 105 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44445555555555554444
No 39
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=62.60 E-value=16 Score=30.75 Aligned_cols=73 Identities=16% Similarity=0.219 Sum_probs=42.8
Q ss_pred CCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh-hhHHHHHHHHHHHHHHHHHHHH
Q 023360 34 HEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG-KMISEAAEVLMKQLEQLKTEEK 112 (283)
Q Consensus 34 ~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~-~~~sea~e~l~~~l~~~~~~~k 112 (283)
.+++-.+||...-= ..+++++. |..+||..+.=..+++.... .-..+..+.|-++++++.++.+
T Consensus 31 r~~~gyR~Y~~~~v--------~~l~~I~~-------lr~~GfsL~eI~~ll~~~~~~~~~~~~~~~l~~k~~~i~~~i~ 95 (131)
T cd04786 31 RSANGYRDYPPETV--------WVLEIISS-------AQQAGFSLDEIRQLLPADASNWQHDELLAALERKVADIEALEA 95 (131)
T ss_pred cCCCCCeecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 44555688876421 22566665 67788877644444443211 1124555677778888888877
Q ss_pred HHHHHHHHH
Q 023360 113 KLKRKRKQE 121 (283)
Q Consensus 113 ~~k~~~k~e 121 (283)
++.+.+..=
T Consensus 96 ~L~~~~~~L 104 (131)
T cd04786 96 RLAQNKAQL 104 (131)
T ss_pred HHHHHHHHH
Confidence 777666443
No 40
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=62.54 E-value=18 Score=29.97 Aligned_cols=82 Identities=12% Similarity=0.189 Sum_probs=47.9
Q ss_pred ccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHH-h-hhHHHHHHHHHH
Q 023360 25 GLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVR-G-KMISEAAEVLMK 102 (283)
Q Consensus 25 ~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~-~-~~~sea~e~l~~ 102 (283)
-.|.+.....+.+-.+||...-= ..+++++. |..+||....=..+++... + .-..+..++|-+
T Consensus 22 ~~GLl~~~~r~~~gyR~Y~~~~l--------~~l~~I~~-------lr~lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~ 86 (127)
T TIGR02047 22 KQGLLPPPARTDNNYRVYTVGHV--------ERLAFIRN-------CRTLDMSLAEIRQLLRYQDKPEKSCSDVNALLDE 86 (127)
T ss_pred HCCCCCCCCcCCCCCCcCCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHhhhCCCCCHHHHHHHHHH
Confidence 34554433455566788876421 22566665 6778888874444544211 1 113455667777
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 023360 103 QLEQLKTEEKKLKRKRKQE 121 (283)
Q Consensus 103 ~l~~~~~~~k~~k~~~k~e 121 (283)
+++++.++..++...+..=
T Consensus 87 ~~~~l~~~i~~L~~~~~~L 105 (127)
T TIGR02047 87 HISHVRARIIKLQALIEQL 105 (127)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8888888887777665543
No 41
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=61.57 E-value=20 Score=31.19 Aligned_cols=84 Identities=11% Similarity=0.158 Sum_probs=45.1
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHH-hh--hHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVR-GK--MISEAA 97 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~-~~--~~sea~ 97 (283)
|+---.|.+...-.+.|| +||...- =..+++++. |..+||..+.=..+++... +. ...+-.
T Consensus 29 RyYE~~GLi~~~r~~~g~-R~Y~~~~--------i~~L~~I~~-------lr~lG~sL~eIk~ll~~~~~~~~~~~~~~~ 92 (154)
T PRK15002 29 HFYESKGLITSIRNSGNQ-RRYKRDV--------LRYVAIIKI-------AQRIGIPLATIGEAFGVLPEGHTLSAKEWK 92 (154)
T ss_pred HHHHHCCCCCCccCCCCC-EEECHHH--------HHHHHHHHH-------HHHcCCCHHHHHHHHHHhhcCCCCCHHHHH
Confidence 333334443333345566 7775521 123566655 7889999885545555432 11 122344
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 023360 98 EVLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 98 e~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
+.|-++++++..+-.+++..++.
T Consensus 93 ~ll~~k~~~l~~~I~~L~~~~~~ 115 (154)
T PRK15002 93 QLSSQWREELDRRIHTLVALRDE 115 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666667777666666655543
No 42
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=57.20 E-value=29 Score=29.33 Aligned_cols=86 Identities=15% Similarity=0.311 Sum_probs=47.5
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh--hhHHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG--KMISEAAE 98 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~--~~~sea~e 98 (283)
||---.|++...-.+++-.|||...-= ..+.+++. +..+||..+.=..+++.... .-..+..+
T Consensus 18 RyYE~~GLl~p~~r~~~gyR~Y~~~~l--------~~l~~I~~-------lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~ 82 (135)
T PRK10227 18 RFYEEKGLVTPPMRSENGYRTYTQQHL--------NELTLLRQ-------ARQVGFNLEESGELVNLFNDPQRHSADVKR 82 (135)
T ss_pred HHHHHCCCCCCcccCCCCcccCCHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHHhhccCCCCHHHHHH
Confidence 333334444333344455588876421 22555554 67788887743344443221 11345566
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 023360 99 VLMKQLEQLKTEEKKLKRKRKQE 121 (283)
Q Consensus 99 ~l~~~l~~~~~~~k~~k~~~k~e 121 (283)
.|.++++++.++..+|...+..=
T Consensus 83 ~l~~~~~~l~~~i~~L~~~~~~L 105 (135)
T PRK10227 83 RTLEKVAEIERHIEELQSMRDQL 105 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 77788888888877777766653
No 43
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=55.99 E-value=36 Score=27.33 Aligned_cols=49 Identities=18% Similarity=0.276 Sum_probs=30.3
Q ss_pred ccccccccccchhHHHHHHh--hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRG--KMISEAAEVLMKQLEQLKTEEKKLKRKRK 119 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~--~~~sea~e~l~~~l~~~~~~~k~~k~~~k 119 (283)
|..+||..+.=..+++.... ..+.+..+.|.++++++..+..+++....
T Consensus 53 lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~ 103 (113)
T cd01109 53 LRNTGMSIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQETLA 103 (113)
T ss_pred HHHcCCCHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66788887743344443221 12356667777888888777777766554
No 44
>PF05501 DUF755: Domain of unknown function (DUF755) ; InterPro: IPR008474 This family is predominated by ORFs from Anelloviridae. The function of this family remains to be determined.
Probab=55.37 E-value=13 Score=31.59 Aligned_cols=48 Identities=25% Similarity=0.221 Sum_probs=38.7
Q ss_pred hHHHHHHHHhhhcccccccccccccccchhHHHHHHhhhHHHHHH--HHHHHHHHH
Q 023360 54 IKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAE--VLMKQLEQL 107 (283)
Q Consensus 54 ~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e--~l~~~l~~~ 107 (283)
-.+..|++=+-..|...++.-|...+ +-++.+++-|-.. -||.=|+||
T Consensus 12 S~~~YK~~tr~~~~~~~~St~GTsd~------~~L~~qLlKEC~kt~~L~~l~~ql 61 (123)
T PF05501_consen 12 SLKQYKSRTRNSSDPNQSSTPGTSDV------DSLQKQLLKECQKTSQLMQLLQQL 61 (123)
T ss_pred CHHHHHHHHhCCCCCCCCCcCCcchH------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667888888888888999998888 7788888888765 677777777
No 45
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=54.35 E-value=15 Score=28.43 Aligned_cols=67 Identities=19% Similarity=0.414 Sum_probs=38.0
Q ss_pred ccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhhhHHHHHHHHHHHH
Q 023360 25 GLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQL 104 (283)
Q Consensus 25 ~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l 104 (283)
-.|++.. ..+++..+||...-= ..+..++.|-+| +||....=..+++ |++|+
T Consensus 23 ~~Gli~p-~r~~~g~R~y~~~dv--------~~l~~i~~L~~d------~g~~l~~i~~~l~-------------l~~~~ 74 (91)
T cd04766 23 RLGLLSP-SRTDGGTRRYSERDI--------ERLRRIQRLTQE------LGVNLAGVKRILE-------------LEEEL 74 (91)
T ss_pred HCCCcCC-CcCCCCCeeECHHHH--------HHHHHHHHHHHH------cCCCHHHHHHHHH-------------HHHHH
Confidence 3577544 345555567765311 225666654333 5666552222222 88888
Q ss_pred HHHHHHHHHHHHHHH
Q 023360 105 EQLKTEEKKLKRKRK 119 (283)
Q Consensus 105 ~~~~~~~k~~k~~~k 119 (283)
++++++-.+++++..
T Consensus 75 ~~l~~~l~~l~~~~~ 89 (91)
T cd04766 75 AELRAELDELRARLR 89 (91)
T ss_pred HHHHHHHHHHHHHhc
Confidence 888888888876543
No 46
>KOG3228 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.19 E-value=26 Score=32.65 Aligned_cols=38 Identities=16% Similarity=0.323 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023360 94 SEAAEVLMKQLEQLKTEEKKLKRKRKQEKANKLKAKIQ 131 (283)
Q Consensus 94 sea~e~l~~~l~~~~~~~k~~k~~~k~ek~a~~ka~k~ 131 (283)
.|-|+.||.||++.+.|+.|.+-.+.+|.++.-.-.+|
T Consensus 125 eDdt~aLlaele~ikkERaee~~~~e~e~k~~e~r~r~ 162 (226)
T KOG3228|consen 125 EDDTQALLAELENIKKERAEEQARKEEEQKAEEERIRM 162 (226)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 56789999999999988888766655555544433344
No 47
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=53.02 E-value=42 Score=27.70 Aligned_cols=80 Identities=15% Similarity=0.363 Sum_probs=44.1
Q ss_pred cCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh--hhHHHHHHHHHHH
Q 023360 26 LGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG--KMISEAAEVLMKQ 103 (283)
Q Consensus 26 ~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~--~~~sea~e~l~~~ 103 (283)
-|.+.....+++-.+||...-= .++++++. |..+||....=..+++.... ....+..+.|-++
T Consensus 23 ~GLl~~~~r~~~g~R~Y~~~~~--------~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~ 87 (127)
T cd01108 23 IGLIPPPSRSDNGYRVYNQRDI--------EELRFIRR-------ARDLGFSLEEIRELLALWRDPSRASADVKALALEH 87 (127)
T ss_pred CCCCCCCCcCCCCceecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 3554333344455677765311 23555554 66788877643344443221 1234556677778
Q ss_pred HHHHHHHHHHHHHHHHH
Q 023360 104 LEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 104 l~~~~~~~k~~k~~~k~ 120 (283)
++++..+..++.+.+..
T Consensus 88 ~~~l~~~i~~L~~~~~~ 104 (127)
T cd01108 88 IAELERKIAELQAMRRT 104 (127)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 88887777777655543
No 48
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=52.79 E-value=38 Score=27.45 Aligned_cols=91 Identities=15% Similarity=0.342 Sum_probs=51.6
Q ss_pred CCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh-
Q 023360 12 SSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG- 90 (283)
Q Consensus 12 ~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~- 90 (283)
+|.++.|=+-|- -.|++... .+++-.+||...-= ..+++++. |..+||..+.=..+++....
T Consensus 10 ~gvs~~tlR~Ye-~~GLl~p~-r~~~g~R~Y~~~~~--------~~l~~I~~-------lr~~G~sl~eI~~~l~~~~~~ 72 (112)
T cd01282 10 TGVSVRSLRYYE-EQGLLVPE-RSANGYRDYDEAAV--------DRVRQIRR-------LLAAGLTLEEIREFLPCLRGG 72 (112)
T ss_pred HCCCHHHHHHHH-HCCCCCCC-cCCCCCeecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHHhhCC
Confidence 344444444332 24665543 44455577765311 22566665 67788888744455554332
Q ss_pred ----hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 91 ----KMISEAAEVLMKQLEQLKTEEKKLKRKRK 119 (283)
Q Consensus 91 ----~~~sea~e~l~~~l~~~~~~~k~~k~~~k 119 (283)
....+..+.|-.+++++.++-.++...+.
T Consensus 73 ~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~ 105 (112)
T cd01282 73 EPTFRPCPDLLAVLRRELARIDRQIADLTRSRD 105 (112)
T ss_pred CccCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 23445567777788888777777766554
No 49
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=51.81 E-value=25 Score=30.01 Aligned_cols=26 Identities=38% Similarity=0.540 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 96 AAEVLMKQLEQLKTEEKKLKRKRKQE 121 (283)
Q Consensus 96 a~e~l~~~l~~~~~~~k~~k~~~k~e 121 (283)
..|.|..||++|+-|-|.||+|.++-
T Consensus 4 t~EeLaaeL~kLqmENk~LKkkl~~~ 29 (118)
T PF05812_consen 4 TMEELAAELQKLQMENKALKKKLRQS 29 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 46889999999999999999987753
No 50
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=51.36 E-value=36 Score=28.78 Aligned_cols=85 Identities=15% Similarity=0.327 Sum_probs=46.1
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHH---hhhHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVR---GKMISEAA 97 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~---~~~~sea~ 97 (283)
|+---.|++.....+++-.|||...-= .++..++. |..+||....=..+++... .....+..
T Consensus 19 R~Ye~~GLl~p~~r~~~gyR~Y~~~~l--------~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~ 83 (140)
T PRK09514 19 RFYEKQGLMDPEVRTEGGYRLYTEQDL--------QRLRFIRR-------AKQLGFTLEEIRELLSIRLDPEHHTCQEVK 83 (140)
T ss_pred HHHHHCCCCCCcccCCCCCeeeCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHhcccCCcCCHHHHH
Confidence 333333554443344555577765311 12444444 6677887764444443221 11245566
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 023360 98 EVLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 98 e~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
++|-++++++..+..++.+.+..
T Consensus 84 ~~l~~~~~~l~~~i~~L~~~~~~ 106 (140)
T PRK09514 84 GIVDEKLAEVEAKIAELQHMRRS 106 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 77788888887777777665433
No 51
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=50.70 E-value=39 Score=28.10 Aligned_cols=93 Identities=15% Similarity=0.272 Sum_probs=50.1
Q ss_pred CCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh-
Q 023360 12 SSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG- 90 (283)
Q Consensus 12 ~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~- 90 (283)
+|.++.|= |+----|.+...-.+++-.|||...-- ..+++++. |..+||..+.=..+++....
T Consensus 10 ~gvs~~TL-RyYE~~GLl~p~r~~~~gyR~Y~~~~~--------~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~ 73 (133)
T cd04787 10 AGVTPDTV-RFYTRIGLLRPTRDPVNGYRLYSEKDL--------SRLRFILS-------ARQLGFSLKDIKEILSHADQG 73 (133)
T ss_pred HCcCHHHH-HHHHHCCCCCCCcCCCCCeeeCCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhhhccC
Confidence 33333333 443344554433233244588876422 23566655 77889988744455543321
Q ss_pred -hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 91 -KMISEAAEVLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 91 -~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
....+..+.|-++++++.++..++.+.+..
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~ 104 (133)
T cd04787 74 ESPCPMVRRLIEQRLAETERRIKELLKLRDR 104 (133)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 112345567777888887777777655443
No 52
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=49.02 E-value=42 Score=26.71 Aligned_cols=55 Identities=18% Similarity=0.260 Sum_probs=34.5
Q ss_pred HHHHHHhhhcccccccccccccccchhHHHHHHh--hh----HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 57 KLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG--KM----ISEAAEVLMKQLEQLKTEEKKLKRKR 118 (283)
Q Consensus 57 k~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~--~~----~sea~e~l~~~l~~~~~~~k~~k~~~ 118 (283)
.+++++. |.++||..+.=..+++.... .. ..+..+.|.++++++..+..++.+.+
T Consensus 44 ~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~ 104 (107)
T cd04777 44 DLEFILE-------LKGLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKKAI 104 (107)
T ss_pred HHHHHHH-------HHHCCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566665 77889998854455543221 10 23346778888888888777776654
No 53
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=48.69 E-value=46 Score=26.48 Aligned_cols=87 Identities=15% Similarity=0.249 Sum_probs=44.8
Q ss_pred CCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhh
Q 023360 12 SSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGK 91 (283)
Q Consensus 12 ~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~ 91 (283)
+|.+++|=|.|.. -|.+-..-.+++..+||...-= ..+++++.|- .||+.+--..+++.+...
T Consensus 10 ~gvs~~tlR~Ye~-~Gll~~~~r~~~g~R~Y~~~~v--------~~l~~I~~l~--------~g~~l~~i~~~~~~~~~~ 72 (99)
T cd04772 10 IGLSPQTVRNYES-LGLIPPAERTANGYRIYTDKHI--------AALRAYRALL--------PGYGYRVAQRIMRAVHAG 72 (99)
T ss_pred HCcCHHHHHHHHH-cCCCCCCCcCCCCCeecCHHHH--------HHHHHHHHHh--------hCCCHHHHHHHHHHHhcC
Confidence 3444444443332 3333222245556677765321 2356666532 234433223355555444
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 92 MISEAAEVLMKQLEQLKTEEKKLK 115 (283)
Q Consensus 92 ~~sea~e~l~~~l~~~~~~~k~~k 115 (283)
-..++.+.|-++++.+..+.+++.
T Consensus 73 ~~~~~~~ll~~~~~~l~~~i~~L~ 96 (99)
T cd04772 73 IVASALALVDAAHALLQRYRQQLD 96 (99)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455777777777777777776664
No 54
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=48.08 E-value=37 Score=28.32 Aligned_cols=79 Identities=16% Similarity=0.333 Sum_probs=44.9
Q ss_pred CccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHH---hhhHHHHHHHHHHH
Q 023360 27 GFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVR---GKMISEAAEVLMKQ 103 (283)
Q Consensus 27 gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~---~~~~sea~e~l~~~ 103 (283)
|.+.....+++=.+||...-= .++++++. +..+||....=..+++... .....+..+.|-++
T Consensus 25 GLl~p~~r~~~gyR~Y~~~~l--------~~l~~I~~-------lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~ 89 (131)
T TIGR02043 25 GLIKPAGRTDSGYRLYTDEDQ--------KRLRFILK-------AKELGFTLDEIKELLSIKLDATEHSCAEVKAIVDAK 89 (131)
T ss_pred CCCCCCCcCCCCceecCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHH
Confidence 554333344444577765311 22555554 6677888774445554321 11235566778888
Q ss_pred HHHHHHHHHHHHHHHHH
Q 023360 104 LEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 104 l~~~~~~~k~~k~~~k~ 120 (283)
++++..+..++.+.+..
T Consensus 90 ~~~l~~~i~~L~~~~~~ 106 (131)
T TIGR02043 90 LELVDEKINELTKIRRS 106 (131)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 88888887777666543
No 55
>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].
Probab=47.72 E-value=31 Score=36.16 Aligned_cols=51 Identities=27% Similarity=0.472 Sum_probs=34.1
Q ss_pred HHHHhhhcccccccccccccccchhHHHHHHhh-hHHHHHHHHHHHHHHHHH
Q 023360 59 KLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGK-MISEAAEVLMKQLEQLKT 109 (283)
Q Consensus 59 kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~-~~sea~e~l~~~l~~~~~ 109 (283)
.+++.|-++|+++.+.--..-.-..++++|++. .+|.|+||.|+-+|.+|-
T Consensus 255 e~~~kl~~~l~~l~~~~~rvss~AE~lGAv~QE~R~SkAvevM~qhvenLkr 306 (538)
T PF05781_consen 255 EIIQKLQKSLDVLHQCATRVSSRAEMLGAVHQESRVSKAVEVMIQHVENLKR 306 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555666655444433334577777654 599999999999999854
No 56
>PHA03155 hypothetical protein; Provisional
Probab=45.76 E-value=28 Score=29.67 Aligned_cols=26 Identities=46% Similarity=0.532 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 96 AAEVLMKQLEQLKTEEKKLKRKRKQE 121 (283)
Q Consensus 96 a~e~l~~~l~~~~~~~k~~k~~~k~e 121 (283)
..|.|-.||++|+-|-|.||+|.++.
T Consensus 9 tvEeLaaeL~kL~~ENK~LKkkl~~~ 34 (115)
T PHA03155 9 DVEELEKELQKLKIENKALKKKLLQH 34 (115)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 36889999999999999999998763
No 57
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=44.06 E-value=85 Score=26.89 Aligned_cols=47 Identities=26% Similarity=0.297 Sum_probs=21.3
Q ss_pred ccccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 69 STFSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKRKQEKAN 124 (283)
Q Consensus 69 ~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~a 124 (283)
=.+++++|+++.- ..+.|+ .+-|=.|++++-.+|.+++.++++++.+
T Consensus 10 lllss~sfaA~~~--------~~v~~~-l~~LEae~q~L~~kE~~r~~~~k~~ae~ 56 (126)
T PF09403_consen 10 LLLSSISFAATAT--------ASVESE-LNQLEAEYQQLEQKEEARYNEEKQEAEA 56 (126)
T ss_dssp ---------------------HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcccc--------hHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578889998841 122222 4556777777877777777777766653
No 58
>PHA03162 hypothetical protein; Provisional
Probab=43.99 E-value=32 Score=30.01 Aligned_cols=25 Identities=36% Similarity=0.470 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 97 AEVLMKQLEQLKTEEKKLKRKRKQE 121 (283)
Q Consensus 97 ~e~l~~~l~~~~~~~k~~k~~~k~e 121 (283)
.|.|-.||++|+-|-|.||+|.++.
T Consensus 15 mEeLaaeL~kLqmENK~LKkkl~~~ 39 (135)
T PHA03162 15 MEDLAAEIAKLQLENKALKKKIKEG 39 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 6889999999999999999988654
No 59
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=43.27 E-value=68 Score=26.39 Aligned_cols=72 Identities=14% Similarity=0.297 Sum_probs=40.8
Q ss_pred CCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh--hhHHHHHHHHHHHHHHHHHHH
Q 023360 34 HEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG--KMISEAAEVLMKQLEQLKTEE 111 (283)
Q Consensus 34 ~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~--~~~sea~e~l~~~l~~~~~~~ 111 (283)
.+++=.|||...-= ..+++++. +..+||..+.=..+++.... ....+..+.|.++++++..+.
T Consensus 31 r~~~gyR~Y~~~~l--------~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i 95 (127)
T TIGR02044 31 RSEGGYRTYTQQHL--------DELRLISR-------ARQVGFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKI 95 (127)
T ss_pred cCCCCCeecCHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHH
Confidence 33444567765311 23555554 66788887633344442211 123455667788888887777
Q ss_pred HHHHHHHHH
Q 023360 112 KKLKRKRKQ 120 (283)
Q Consensus 112 k~~k~~~k~ 120 (283)
.++...+..
T Consensus 96 ~~L~~~~~~ 104 (127)
T TIGR02044 96 SELQSMRDQ 104 (127)
T ss_pred HHHHHHHHH
Confidence 777666544
No 60
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=42.86 E-value=30 Score=27.23 Aligned_cols=42 Identities=21% Similarity=0.344 Sum_probs=26.5
Q ss_pred ccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKTEEKKLKR 116 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~ 116 (283)
|..+||....=..+++... .+..+.|.++++++..+..++..
T Consensus 53 lr~~G~~l~eI~~~l~~~~----~~~~~~l~~~~~~l~~~i~~l~~ 94 (96)
T cd04788 53 LRRLGFSLREIGRALDGPD----FDPLELLRRQLARLEEQLELATR 94 (96)
T ss_pred HHHcCCCHHHHHHHHhCCC----hhHHHHHHHHHHHHHHHHHHHHh
Confidence 6667887763334444321 25567788888888777777654
No 61
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.98 E-value=66 Score=26.06 Aligned_cols=52 Identities=13% Similarity=0.238 Sum_probs=33.2
Q ss_pred ccccccccccchhHHHHHHh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRG---KMISEAAEVLMKQLEQLKTEEKKLKRKRKQEK 122 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~---~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek 122 (283)
|+.+||+...=..+++.... ....+..++|.++++++..+.+++.+.+..=.
T Consensus 52 lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~ 106 (116)
T cd04769 52 ARQLGFTLAELKAIFAGHEGRAVLPWPHLQQALEDKKQEIRAQITELQQLLARLD 106 (116)
T ss_pred HHHcCCCHHHHHHHHhccccCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77788887744444443332 12344567788888888888888777666543
No 62
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=37.84 E-value=1.3e+02 Score=21.39 Aligned_cols=48 Identities=19% Similarity=0.428 Sum_probs=27.6
Q ss_pred ccccccccccchhHHHHH---HhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQV---RGKMISEAAEVLMKQLEQLKTEEKKLKRKRK 119 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~---~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k 119 (283)
+..+||..+-=..++ ++ .+.-..+..+.|-++++++.....++.+-++
T Consensus 10 ~r~lGfsL~eI~~~l-~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~~~~ 60 (65)
T PF09278_consen 10 LRELGFSLEEIRELL-ELYDQGDPPCADRRALLEEKLEEIEEQIAELQALRA 60 (65)
T ss_dssp HHHTT--HHHHHHHH-HHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHH-hccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677888887444444 22 2334555666777777777777666665443
No 63
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=37.77 E-value=36 Score=29.93 Aligned_cols=38 Identities=32% Similarity=0.292 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHhhh
Q 023360 93 ISEAAEVLMKQLEQL-------KTEEKKLKRKRKQEKANKLKAKI 130 (283)
Q Consensus 93 ~sea~e~l~~~l~~~-------~~~~k~~k~~~k~ek~a~~ka~k 130 (283)
|+|-.+-+-++|++. |...|+.|+++|+++|+.+++.|
T Consensus 47 Lne~Y~~~k~~L~~all~k~e~K~~~K~~KK~~K~~~K~~k~~~k 91 (155)
T PF08496_consen 47 LNERYEDMKEQLKQALLDKKELKAWEKAEKKEEKAKAKAEKKAAK 91 (155)
T ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence 455555555555444 44444555554444444444433
No 64
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=37.62 E-value=1.2e+02 Score=24.92 Aligned_cols=40 Identities=33% Similarity=0.452 Sum_probs=29.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023360 91 KMISEAAEVLMKQLEQLKTEEKKLKRKRKQEKANKLKAKIQ 131 (283)
Q Consensus 91 ~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~a~~ka~k~ 131 (283)
+.|++-.+.|.++++.+..+-++++++.++.+ ++++.+|.
T Consensus 76 ~~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~-~~~k~lk~ 115 (118)
T PF13815_consen 76 EYLSSQLEQLEERLQELQQEIEKLKQKLKKQK-EEIKKLKK 115 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH
Confidence 34556678888888888888888888888776 46666654
No 65
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=36.51 E-value=80 Score=26.96 Aligned_cols=79 Identities=14% Similarity=0.194 Sum_probs=41.4
Q ss_pred cCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhh---hHHHHHHHHHH
Q 023360 26 LGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGK---MISEAAEVLMK 102 (283)
Q Consensus 26 ~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~---~~sea~e~l~~ 102 (283)
-|.+... .+++-.+||...- =.++.+++. +..+||..+.=..++..+... ...+..+.|.+
T Consensus 24 ~GLl~~~-r~~~g~R~Y~~~d--------i~~l~~I~~-------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~ 87 (142)
T TIGR01950 24 KGLITSI-RNSGNQRRYKRDV--------LRRVAVIKA-------AQRVGIPLATIGEALAVLPEGRTPTADDWARLSSQ 87 (142)
T ss_pred CCCCCCc-cCCCCCEEECHHH--------HHHHHHHHH-------HHHcCCCHHHHHHHHHhcccCCCCCHHHHHHHHHH
Confidence 3554332 3444347776421 122555555 667888877444455433211 13344556666
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 023360 103 QLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 103 ~l~~~~~~~k~~k~~~k~ 120 (283)
+++.+..+-++|...+..
T Consensus 88 ~~~~l~~ki~~L~~~~~~ 105 (142)
T TIGR01950 88 WREELDERIDQLNALRDQ 105 (142)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 677777766666655543
No 66
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=36.33 E-value=38 Score=34.93 Aligned_cols=14 Identities=29% Similarity=0.420 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHH
Q 023360 93 ISEAAEVLMKQLEQ 106 (283)
Q Consensus 93 ~sea~e~l~~~l~~ 106 (283)
+|||...||.++.+
T Consensus 452 ~sDaRsdLL~aIr~ 465 (518)
T KOG1830|consen 452 ISDARSDLLAAIRS 465 (518)
T ss_pred CCchHHHHHHHHHh
Confidence 78888888877654
No 67
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=35.44 E-value=93 Score=28.58 Aligned_cols=29 Identities=28% Similarity=0.400 Sum_probs=17.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 92 MISEAAEVLMKQLEQLKTEEKKLKRKRKQEKA 123 (283)
Q Consensus 92 ~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~ 123 (283)
.+..-+|+.|+|.+. ||+.++..+++.++
T Consensus 133 ~ke~~vE~r~~e~qe---ee~rlkd~~kEK~k 161 (193)
T KOG4727|consen 133 QKEYDVEERLRETQE---EEERLKDTRKEKKK 161 (193)
T ss_pred hHHHHHHHHHHHHHH---HHHHHHHHHHHHHH
Confidence 355666777766654 55566655555443
No 68
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=34.66 E-value=1.1e+02 Score=26.40 Aligned_cols=35 Identities=26% Similarity=0.346 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 92 MISEAAEVLMKQLEQLKTEEKKLKRKRKQEKANKL 126 (283)
Q Consensus 92 ~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~a~~ 126 (283)
+-+.|-+.|=.|.|+.+.+.|...+.++++.++..
T Consensus 83 ~~TkAQ~ALk~q~E~~K~~rk~~~k~~re~~k~~k 117 (132)
T PF11208_consen 83 ISTKAQQALKLQREQRKKERKKRSKEQREAEKERK 117 (132)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34677788888999998888888777777665444
No 69
>KOG0416 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.62 E-value=37 Score=31.05 Aligned_cols=24 Identities=33% Similarity=0.321 Sum_probs=15.0
Q ss_pred ccccCCCCCCcccccccceEEccc
Q 023360 132 SSACESSDSSDSECEEEEVVQMID 155 (283)
Q Consensus 132 ~~~~~ssess~sec~~~~v~~m~~ 155 (283)
++++.|++|+.||-+++++.+|+.
T Consensus 162 ~d~d~s~~~~~sd~ddd~~~~~~~ 185 (189)
T KOG0416|consen 162 SDDDSSSESSGSDSDDDEAGDMEL 185 (189)
T ss_pred cccccccccccccccchhhhhhhh
Confidence 334455666667766667777754
No 70
>PF08701 GN3L_Grn1: GNL3L/Grn1 putative GTPase; InterPro: IPR014813 Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA []. This family contains a potential nuclear localisation signal.
Probab=34.41 E-value=1.1e+02 Score=24.26 Aligned_cols=29 Identities=21% Similarity=0.400 Sum_probs=14.2
Q ss_pred HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 86 AQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKRKQEK 122 (283)
Q Consensus 86 ~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek 122 (283)
-.+++.||.+ +++.+....+.+..++++.
T Consensus 41 ~PfKe~iL~e--------ie~~k~~~ee~k~~~ke~r 69 (79)
T PF08701_consen 41 FPFKEEILKE--------IEEKKERAEEEKEKQKEAR 69 (79)
T ss_pred CcCHHHHHHH--------HHHHHHHHHHHHHHHHHHH
Confidence 4566665544 4455444444444444443
No 71
>PF06658 DUF1168: Protein of unknown function (DUF1168); InterPro: IPR009548 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=33.10 E-value=3e+02 Score=24.17 Aligned_cols=16 Identities=44% Similarity=0.686 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHH
Q 023360 108 KTEEKKLKRKRKQEKA 123 (283)
Q Consensus 108 ~~~~k~~k~~~k~ek~ 123 (283)
|++.+-.||+++.+++
T Consensus 82 kTaKkR~KR~KkK~kk 97 (142)
T PF06658_consen 82 KTAKKRAKRQKKKQKK 97 (142)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4444445555555544
No 72
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.85 E-value=1.1e+02 Score=24.61 Aligned_cols=46 Identities=22% Similarity=0.448 Sum_probs=30.3
Q ss_pred ccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKRK 119 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k 119 (283)
|..+||+...=..+++.... .+..+.|-.+++++.++..++....+
T Consensus 54 lr~~G~sl~~i~~l~~~~~~---~~~~~~l~~~~~~l~~~i~~l~~~~~ 99 (108)
T cd01107 54 LRDLGFPLEEIKEILDADND---DELRKLLREKLAELEAEIEELQRILR 99 (108)
T ss_pred HHHcCCCHHHHHHHHhcCCH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66788887644455554332 67777788888888777777755543
No 73
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=32.82 E-value=87 Score=25.51 Aligned_cols=48 Identities=19% Similarity=0.254 Sum_probs=27.5
Q ss_pred ccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKRKQ 120 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ 120 (283)
|.++||+.+.=..+++.-. -..+..+.|.+++++++++.+++.+.++.
T Consensus 52 lr~~G~~L~eI~~~l~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~~~~~ 99 (120)
T cd04781 52 GRAAGFSLDEIQAMLSHDG--KPPIDRQLLKAKAAELDQQIQRLQAMREL 99 (120)
T ss_pred HHHcCCCHHHHHHHHhccC--CcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7778888773334443211 01223456777777777777776655543
No 74
>PRK13749 transcriptional regulator MerD; Provisional
Probab=32.63 E-value=93 Score=26.22 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=32.2
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQ 87 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~ 87 (283)
|+----|.+.....|+|-.|||.+.-- ..+++++. ++.+||+.+.=..|++-
T Consensus 21 R~YE~~GLl~p~~r~~~gyR~Y~~~~l--------~rL~~I~~-------~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 21 RDYLLRGLLRPVACTTGGYGLFDDAAL--------QRLCFVRA-------AFEAGIGLDALARLCRA 72 (121)
T ss_pred HHHHHCCCCCCCCcCCCCCccCCHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHhh
Confidence 444445666666677788899987533 23566665 67788877644444443
No 75
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=32.51 E-value=1.1e+02 Score=24.03 Aligned_cols=44 Identities=23% Similarity=0.416 Sum_probs=26.7
Q ss_pred ccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKR 118 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~ 118 (283)
|..+||+.+.=..+++... .+..+.|-.++..+.++..+++...
T Consensus 53 lr~~g~~l~~i~~~~~~~~----~~~~~~l~~~~~~l~~~i~~l~~~~ 96 (103)
T cd01106 53 LKELGFSLKEIKELLKDPS----EDLLEALREQKELLEEKKERLDKLI 96 (103)
T ss_pred HHHcCCCHHHHHHHHHcCc----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5567887774444444322 5566677777777777766665443
No 76
>PF03879 Cgr1: Cgr1 family; InterPro: IPR005579 Cgr1 is involved in nucleolar integrity and is required for processing pre-rRNA for the 60S ribosome subunit. In Saccharomyces cerevisiae, this protein is conserved and contributes to compartmentalisation of nucleolar constituents []. Cgr1 is a small hydrophilic protein and members of this family are coiled-coil proteins []. Its primary role appears to be in ribosome biogenesis [, ]. Expression of CGR1 is also associated with a cessation of yeast cell growth, which is a prerequisite for germination in this organism [].
Probab=31.50 E-value=92 Score=26.18 Aligned_cols=20 Identities=25% Similarity=0.263 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 023360 95 EAAEVLMKQLEQLKTEEKKL 114 (283)
Q Consensus 95 ea~e~l~~~l~~~~~~~k~~ 114 (283)
+++-.+.+||.+-+.++++.
T Consensus 44 ~~~K~~ekElKeEKe~er~~ 63 (108)
T PF03879_consen 44 KAIKEKEKELKEEKEAERQR 63 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444333333
No 77
>PF14038 YqzE: YqzE-like protein
Probab=31.16 E-value=44 Score=24.97 Aligned_cols=28 Identities=32% Similarity=0.464 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 96 AAEVLMKQLEQLKTEEKKLKRKRKQEKA 123 (283)
Q Consensus 96 a~e~l~~~l~~~~~~~k~~k~~~k~ek~ 123 (283)
.|+.+++=+++=|+|+|+.|..+|++|.
T Consensus 9 ~Tqq~V~YmdtPkeERk~~k~~rK~~k~ 36 (54)
T PF14038_consen 9 MTQQFVKYMDTPKEERKERKEERKEEKE 36 (54)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHHhcCC
Confidence 4566677777778998888887777763
No 78
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=30.91 E-value=2.1e+02 Score=26.05 Aligned_cols=38 Identities=29% Similarity=0.297 Sum_probs=20.5
Q ss_pred HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 84 LLAQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKRKQEKA 123 (283)
Q Consensus 84 l~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~ 123 (283)
.+.+.|+.|- |+..=|+|....++++...|+++++|.|
T Consensus 77 ~v~~rqEa~e--aAR~RmQEE~dakA~~~kEKq~q~EEEK 114 (190)
T PF06936_consen 77 VVVRRQEAME--AARRRMQEELDAKAEEYKEKQKQEEEEK 114 (190)
T ss_dssp HHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444442 3333366666667776666666555554
No 79
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=30.40 E-value=98 Score=27.23 Aligned_cols=23 Identities=48% Similarity=0.407 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 023360 107 LKTEEKKLKRKRKQEKANKLKAK 129 (283)
Q Consensus 107 ~~~~~k~~k~~~k~ek~a~~ka~ 129 (283)
.|++.|+.|++.|.+|++.+++.
T Consensus 72 ~K~~KK~~K~~~K~~k~~~k~~~ 94 (155)
T PF08496_consen 72 EKAEKKEEKAKAKAEKKAAKKAK 94 (155)
T ss_pred HHHHHHHHHHHhhhhhhhhhccC
Confidence 35666666666666666555555
No 80
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=30.02 E-value=1.6e+02 Score=23.62 Aligned_cols=87 Identities=13% Similarity=0.171 Sum_probs=40.6
Q ss_pred CCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHh-
Q 023360 12 SSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRG- 90 (283)
Q Consensus 12 ~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~- 90 (283)
.|.+..|=+.|.. .|++...-.+++-.+||...-= ..+.+++. |..+||+.+.=..+++.+..
T Consensus 10 ~gvs~~tlR~ye~-~Gll~p~~~~~~g~R~Y~~~dl--------~~l~~I~~-------lr~~G~~l~~I~~~l~~~~~~ 73 (108)
T cd04773 10 LGVPPSTLRHWEK-EGLLSPDREPETGYRVYDPSDV--------RDARLIHL-------LRRGGYLLEQIATVVEQLRHA 73 (108)
T ss_pred HCcCHHHHHHHHH-CCCCCCCcCCCCCceeeCHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHHHhhcC
Confidence 3444444443333 3554443344455677765311 12444444 66778877644455554421
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHH
Q 023360 91 KMISEAAEVLMKQLEQLKTEEKKL 114 (283)
Q Consensus 91 ~~~sea~e~l~~~l~~~~~~~k~~ 114 (283)
.-..+..+.|-++++++..+-.++
T Consensus 74 ~~~~~~~~~l~~~~~~l~~~~~~~ 97 (108)
T cd04773 74 GGTEALAAALEQRRVALTQRGRAM 97 (108)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 112344445555555554443333
No 81
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=29.91 E-value=19 Score=23.29 Aligned_cols=33 Identities=27% Similarity=0.534 Sum_probs=21.4
Q ss_pred cccccccccccccchhHHHHHHhhhHHHHHHHHH
Q 023360 68 LSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVLM 101 (283)
Q Consensus 68 l~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~ 101 (283)
+..|..|||..+....-+..-.++ +..|++.|+
T Consensus 5 v~~L~~mGf~~~~a~~aL~~~~~d-~~~A~~~L~ 37 (37)
T smart00165 5 IDQLLEMGFSREEALKALRAANGN-VERAAEYLL 37 (37)
T ss_pred HHHHHHcCCCHHHHHHHHHHhCCC-HHHHHHHHC
Confidence 456788999888444444454554 777777663
No 82
>PF15509 DUF4650: Domain of unknown function (DUF4650)
Probab=29.61 E-value=57 Score=34.09 Aligned_cols=44 Identities=32% Similarity=0.360 Sum_probs=30.6
Q ss_pred cccchHHHHHHHHhhh-------cccccccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHH
Q 023360 50 KVGSIKKKLKLLKGLS-------KDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQL 107 (283)
Q Consensus 50 ~~~~~kkk~kll~~ls-------~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~ 107 (283)
|-+++||||-.|.++. +|+...++-|=.-| +|+.|-||+|||.-
T Consensus 323 KLKAKKkKLAsL~s~~~~g~~~se~~e~~sq~gS~nd--------------~eslqdlL~ELQ~q 373 (520)
T PF15509_consen 323 KLKAKKKKLASLMSSPQNGKPPSENLEHVSQCGSPND--------------CESLQDLLNELQYQ 373 (520)
T ss_pred HHHHhHHHHHHHHhhhhcCCCCccccccCCCCCCCCc--------------hHHHHHHHHHHHHh
Confidence 4578888998888764 45555566333333 77888899999864
No 83
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=28.44 E-value=47 Score=35.75 Aligned_cols=29 Identities=41% Similarity=0.633 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHhhhh
Q 023360 103 QLEQLKTEEKKLK-RKRKQEKANKLKAKIQ 131 (283)
Q Consensus 103 ~l~~~~~~~k~~k-~~~k~ek~a~~ka~k~ 131 (283)
+++.|-+|+|+++ +++|++|||++.|.++
T Consensus 578 ~~~~ms~e~kk~~~k~rk~~kk~~~e~~~~ 607 (700)
T KOG1156|consen 578 EIEKMSDEEKKIKKKQRKAKKKAKKEAKKK 607 (700)
T ss_pred hhhhccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444556666665 4445555555555554
No 84
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.68 E-value=43 Score=32.41 Aligned_cols=22 Identities=27% Similarity=0.501 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 023360 102 KQLEQLKTEEKKLKRKRKQEKA 123 (283)
Q Consensus 102 ~~l~~~~~~~k~~k~~~k~ek~ 123 (283)
-+++...-+||+.|++-+.+||
T Consensus 132 ~~~ek~~~~ek~~kk~s~k~kk 153 (306)
T KOG2985|consen 132 GEVEKVSSEEKEEKKSSDKDKK 153 (306)
T ss_pred hhhHHHHHHHHhhhhhhhhhhh
Confidence 4667777788888888777776
No 85
>PF05890 Ebp2: Eukaryotic rRNA processing protein EBP2; InterPro: IPR008610 This family consists of several eukaryotic rRNA processing protein EBP2 sequences. Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis [].
Probab=27.10 E-value=2.6e+02 Score=26.75 Aligned_cols=49 Identities=12% Similarity=0.318 Sum_probs=30.3
Q ss_pred HHHhhhcccccccccccccccchhHH----------HHHHhhhHHHHHHHHHHHHHHHH
Q 023360 60 LLKGLSKDLSTFSQMGFAVDQDQNLL----------AQVRGKMISEAAEVLMKQLEQLK 108 (283)
Q Consensus 60 ll~~ls~dl~~~~~~g~~~d~~~~l~----------~~~~~~~~sea~e~l~~~l~~~~ 108 (283)
.|.++-.-+..|..||+++---...| .-|+++||.++..+-..|.....
T Consensus 85 Al~av~~a~~~L~~~gip~~RP~DYfAEMvKSD~HM~KVr~kLl~~~~~ie~~E~~rk~ 143 (271)
T PF05890_consen 85 ALEAVKEARPRLKKLGIPFKRPDDYFAEMVKSDEHMEKVRQKLLKEQKRIEASEEARKQ 143 (271)
T ss_pred HHHHHHHHHHHHHHcCCCccCCCcchHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555666777777654333343 34889999988876655554443
No 86
>KOG2138 consensus Predicted RNA binding protein, contains G-patch domain [RNA processing and modification]
Probab=26.82 E-value=53 Score=35.84 Aligned_cols=8 Identities=25% Similarity=0.252 Sum_probs=3.9
Q ss_pred hhcccccc
Q 023360 64 LSKDLSTF 71 (283)
Q Consensus 64 ls~dl~~~ 71 (283)
+|.||++.
T Consensus 767 ~~~diq~~ 774 (883)
T KOG2138|consen 767 PSFDIQKM 774 (883)
T ss_pred Cccchhhh
Confidence 35555543
No 87
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=26.61 E-value=1.4e+02 Score=23.63 Aligned_cols=46 Identities=22% Similarity=0.440 Sum_probs=27.7
Q ss_pred ccccccccccchhHHHHHHh---hhHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 71 FSQMGFAVDQDQNLLAQVRG---KMISEAAEVLMKQLEQLKTEEKKLKR 116 (283)
Q Consensus 71 ~~~~g~~~d~~~~l~~~~~~---~~~sea~e~l~~~l~~~~~~~k~~k~ 116 (283)
|+.+||....=..+++.... ..+......+.+++.++..+..++.+
T Consensus 53 ~r~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~ 101 (124)
T COG0789 53 LRELGFSLAEIKELLDLLSAGESIALELRERLLAERLEELEAKIAELQR 101 (124)
T ss_pred HHHcCCCHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55678887755455554443 23455556666777777666666654
No 88
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.32 E-value=1.1e+02 Score=30.19 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=23.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 90 GKMISEAAEVLMKQLEQLKTEEKKLKRKRKQE 121 (283)
Q Consensus 90 ~~~~sea~e~l~~~l~~~~~~~k~~k~~~k~e 121 (283)
.+-+..+...|++.-|+|+-+|.||||++.+-
T Consensus 59 a~~~~~kq~eL~~rqeEL~Rke~ELdRREr~~ 90 (313)
T KOG3088|consen 59 AKDLAKKQAELLKKQEELRRKEQELDRRERAL 90 (313)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 34455566788888888888888888876654
No 89
>PF10870 DUF2729: Protein of unknown function (DUF2729); InterPro: IPR022621 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf72; it is a family of uncharacterised viral proteins. This Alphabaculovirus family of proteins has no known function.
Probab=26.17 E-value=23 Score=26.34 Aligned_cols=15 Identities=53% Similarity=0.747 Sum_probs=12.0
Q ss_pred HHHHHHhhhcccccc
Q 023360 57 KLKLLKGLSKDLSTF 71 (283)
Q Consensus 57 k~kll~~ls~dl~~~ 71 (283)
|+||+|++||.++.|
T Consensus 7 KlKlvK~~sKt~~~L 21 (53)
T PF10870_consen 7 KLKLVKSVSKTVSAL 21 (53)
T ss_pred ehHHHHHHHHHHHHH
Confidence 689999999985543
No 90
>PRK11778 putative inner membrane peptidase; Provisional
Probab=25.85 E-value=1.1e+02 Score=30.08 Aligned_cols=46 Identities=17% Similarity=0.186 Sum_probs=23.9
Q ss_pred CcEEEEecCCcccccchHHHHHHHHHHhcCCCcEEeecCCCCCCCCCeE
Q 023360 189 TKRVEVCMGNKCKKSGGGALFEEFQRAMGAEGDVVACKCMGKCRDGPNV 237 (283)
Q Consensus 189 k~~I~VC~GtsC~~~GA~~VLeaLeeeLg~~GtV~~tgCLG~C~~GPnV 237 (283)
...|.+|++.-|. +|++-+.-+-.+.+....++ +|..|.=..-|++
T Consensus 154 ~kpVva~v~~~AA-SggY~iAsaAD~I~A~P~a~--vGSIGVi~~~~~~ 199 (330)
T PRK11778 154 GIPLTVAVDKVAA-SGGYMMACVADKIIAAPFAI--VGSIGVVAQIPNF 199 (330)
T ss_pred CCCEEEEECCchh-hHHHHHHHhCCEEEECCCCe--EEeeeeeeeccCH
Confidence 3467888877774 66665544433333222222 4555555445543
No 91
>KOG0286 consensus G-protein beta subunit [General function prediction only]
Probab=25.85 E-value=70 Score=31.70 Aligned_cols=26 Identities=31% Similarity=0.497 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 101 MKQLEQLKTEEKKLKRKRKQEKANKL 126 (283)
Q Consensus 101 ~~~l~~~~~~~k~~k~~~k~ek~a~~ 126 (283)
+.||+|++.|-+.||.|-+++++++.
T Consensus 1 ~~~~~~l~~Eae~L~~qi~~~r~~~~ 26 (343)
T KOG0286|consen 1 MEELEQLRQEAEQLKNQIRDARKKLN 26 (343)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 36889999999999999888887544
No 92
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=25.80 E-value=1.2e+02 Score=32.16 Aligned_cols=36 Identities=19% Similarity=0.381 Sum_probs=31.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 91 KMISEAAEVLMKQLEQLKTEEKKLKRKRKQEKANKL 126 (283)
Q Consensus 91 ~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~a~~ 126 (283)
|-|-+++-.|-.|+.+|+.+.+.+|+.-.+|.||..
T Consensus 612 kslvdtvyalkd~v~~lqqd~~kmkk~leeEqkaRr 647 (661)
T KOG2070|consen 612 KSLVDTVYALKDEVSELQQDNKKMKKVLEEEQKARR 647 (661)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 557789999999999999999999999999987543
No 93
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=25.69 E-value=60 Score=27.64 Aligned_cols=27 Identities=33% Similarity=0.573 Sum_probs=22.6
Q ss_pred CCcEEEEecCCcccccchHHHHHHHHH
Q 023360 188 MTKRVEVCMGNKCKKSGGGALFEEFQR 214 (283)
Q Consensus 188 ~k~~I~VC~GtsC~~~GA~~VLeaLee 214 (283)
....+.||+|+.|.+-=|+.+++.+-.
T Consensus 2 ~~kVLFVC~gN~cRSpmAE~l~~~~~~ 28 (139)
T COG0394 2 MMKVLFVCTGNICRSPMAEALLRHLAP 28 (139)
T ss_pred CceEEEEcCCCcccCHHHHHHHHHhcc
Confidence 356789999999999989888887754
No 94
>PF01451 LMWPc: Low molecular weight phosphotyrosine protein phosphatase; InterPro: IPR023485 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [, ]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 alpha-helices and 4 beta-strands forming a 3-layer alpha-beta-alpha sandwich architecture.; PDB: 3RH0_B 1JL3_B 2IPA_B 1Z2D_A 1Z2E_A 2CWD_D 2L18_A 2L17_A 2L19_A 1BVH_A ....
Probab=24.37 E-value=86 Score=25.41 Aligned_cols=38 Identities=21% Similarity=0.369 Sum_probs=27.3
Q ss_pred EEEEecCCcccccchHHHHHHHHHHh-cCCCcEEeecCC
Q 023360 191 RVEVCMGNKCKKSGGGALFEEFQRAM-GAEGDVVACKCM 228 (283)
Q Consensus 191 ~I~VC~GtsC~~~GA~~VLeaLeeeL-g~~GtV~~tgCL 228 (283)
.+.||+|..|.+.=|+.+++.+-+.. +..-.+...|=.
T Consensus 1 ILFvC~~N~cRS~mAEai~~~~~~~~~~~~~~v~SAG~~ 39 (138)
T PF01451_consen 1 ILFVCTGNICRSPMAEAILRHLLKQRLGDRFEVESAGTE 39 (138)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHTHTTTEEEEEEESS
T ss_pred CEEEeCCCcchHHHHHHHHHHhccccccCCcEEEEEeec
Confidence 36899999999999999999887663 221155555444
No 95
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=23.67 E-value=3.6e+02 Score=27.94 Aligned_cols=28 Identities=32% Similarity=0.495 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 92 MISEAAEVLMKQLEQLKTEEKKLKRKRK 119 (283)
Q Consensus 92 ~~sea~e~l~~~l~~~~~~~k~~k~~~k 119 (283)
.|++|++.|-+|||+..|+|-|-.-.|-
T Consensus 116 ~i~~~~~el~~q~e~~ea~e~e~~~erh 143 (548)
T COG5665 116 FIHDCLDELQKQLEQYEAQENEEQTERH 143 (548)
T ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 4999999999999999999877654443
No 96
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=23.28 E-value=1.4e+02 Score=23.77 Aligned_cols=72 Identities=17% Similarity=0.310 Sum_probs=37.7
Q ss_pred CccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhhhHHHHHHHHHHHHHH
Q 023360 27 GFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQ 106 (283)
Q Consensus 27 gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~ 106 (283)
|.... -.+++-.+||...-= ..++.++. |..+||..+.=..++.. .+..+.|.+++++
T Consensus 25 Gll~~-~r~~~g~R~Y~~~dl--------~~l~~I~~-------l~~~G~~l~ei~~~~~~------~~~~~~l~~~~~~ 82 (102)
T cd04775 25 GLIPS-ARSEANYRLYSEADL--------SRLEKIVF-------LQAGGLPLEEIAGCLAQ------PHVQAILEERLQS 82 (102)
T ss_pred CCCCC-CCCCCCCeeeCHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHcC------CcHHHHHHHHHHH
Confidence 55422 244444577765311 12444544 45667776522222221 1245677777777
Q ss_pred HHHHHHHHHHHHHH
Q 023360 107 LKTEEKKLKRKRKQ 120 (283)
Q Consensus 107 ~~~~~k~~k~~~k~ 120 (283)
+.++..+++..++.
T Consensus 83 l~~~i~~l~~~~~~ 96 (102)
T cd04775 83 LNREIQRLRQQQQV 96 (102)
T ss_pred HHHHHHHHHHHHHH
Confidence 77777777665543
No 97
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.22 E-value=4.2e+02 Score=22.46 Aligned_cols=58 Identities=14% Similarity=0.264 Sum_probs=26.7
Q ss_pred CCCccccccccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHH
Q 023360 12 SSAGMDTQRRYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLA 86 (283)
Q Consensus 12 ~~~~~~~~~r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~ 86 (283)
+|.+..|=+.|. --|.+... .+++-.+||...-= .+++.++. |..+||..+.=..+++
T Consensus 10 ~gvs~~TLR~Ye-~~GLl~p~-r~~~g~R~Y~~~~l--------~~l~~I~~-------lr~~G~sL~eI~~~l~ 67 (134)
T cd04779 10 AGVSKRTIDYYT-NLGLLTPE-RSDSNYRYYDETAL--------DRLQLIEH-------LKGQRLSLAEIKDQLE 67 (134)
T ss_pred HCcCHHHHHHHH-HCCCCCCc-cCCCCCeeECHHHH--------HHHHHHHH-------HHHCCCCHHHHHHHHH
Confidence 333334433333 33554432 33334577765321 22455554 4567777663334443
No 98
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=22.90 E-value=5e+02 Score=24.31 Aligned_cols=15 Identities=13% Similarity=0.308 Sum_probs=9.5
Q ss_pred HHHHhhhcccccccc
Q 023360 59 KLLKGLSKDLSTFSQ 73 (283)
Q Consensus 59 kll~~ls~dl~~~~~ 73 (283)
--.+.++++|..++.
T Consensus 121 ~Rek~Ia~nM~Kmpk 135 (217)
T PF10147_consen 121 AREKEIAKNMAKMPK 135 (217)
T ss_pred HHHHHHHHHHHhHHH
Confidence 345556677777776
No 99
>TIGR02435 CobG precorrin-3B synthase. An iron-sulfur protein. An oxygen atom from dioxygen is incorporated into the macrocycle at C-20. In the aerobic cobalamin biosythesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. The first of the four steps is carried out by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively.
Probab=22.21 E-value=1.5e+02 Score=28.96 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=33.6
Q ss_pred CCcEEEEecC-Cccc--ccchHHHHHHHHHHhcCCC--cEEeecCCCCCCCC
Q 023360 188 MTKRVEVCMG-NKCK--KSGGGALFEEFQRAMGAEG--DVVACKCMGKCRDG 234 (283)
Q Consensus 188 ~k~~I~VC~G-tsC~--~~GA~~VLeaLeeeLg~~G--tV~~tgCLG~C~~G 234 (283)
...+|..|.| +.|. ..-+..+..+|.+.++... .+.-+||...|+.-
T Consensus 325 ~~~~v~aC~G~~~C~~~~~~t~~~a~~l~~~~~~~~~~~i~vSGC~n~C~~~ 376 (390)
T TIGR02435 325 PRARIIACTGAPGCASALADTRADAEALAAYCEPTAPITVHLSGCAKGCAHP 376 (390)
T ss_pred CeeeEEECCCccccccchhhHHHHHHHHHHHhcccCCcEEEEeCCcccccCC
Confidence 3556999999 5885 4455566666666665432 78889999999873
No 100
>KOG3083 consensus Prohibitin [Posttranslational modification, protein turnover, chaperones]
Probab=21.87 E-value=1.6e+02 Score=28.21 Aligned_cols=52 Identities=29% Similarity=0.423 Sum_probs=36.9
Q ss_pred cccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q 023360 72 SQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKTEEKK-LKRKRKQEKANKL 126 (283)
Q Consensus 72 ~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~~~k~-~k~~~k~ek~a~~ 126 (283)
...|+-.| |.++++---++-.++|+| ++|.-|-.||+-. ...|-.|||+|+.
T Consensus 159 ~~Fgl~Ld-dvsiThltfGkEFt~AvE--~KQVAQQEAErarFvVeKAeQqk~aav 211 (271)
T KOG3083|consen 159 ATFGLILD-DVSITHLTFGKEFTEAVE--AKQVAQQEAERARFVVEKAEQQKKAAV 211 (271)
T ss_pred HhhCeeec-hhhhhhhhhhHHHHHHHH--HHHHHHHHHHHHHHHHHHHhhhhhhhe
Confidence 34566666 667778778888888888 5788777777765 5666677776543
No 101
>PF14473 RD3: RD3 protein
Probab=21.41 E-value=1.9e+02 Score=25.22 Aligned_cols=27 Identities=37% Similarity=0.685 Sum_probs=17.8
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 023360 97 AEVLMKQLE-QLKTEEKKLKRKRKQEKA 123 (283)
Q Consensus 97 ~e~l~~~l~-~~~~~~k~~k~~~k~ek~ 123 (283)
++.||.||+ |+|..|.....+..++++
T Consensus 24 ~~tLm~EL~~~lke~Er~~~Ere~E~r~ 51 (133)
T PF14473_consen 24 TETLMRELEWQLKERERQQRERENEERK 51 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578999997 456666555555555554
No 102
>KOG3535 consensus Adaptor protein Disabled [Signal transduction mechanisms]
Probab=21.38 E-value=55 Score=33.88 Aligned_cols=62 Identities=16% Similarity=0.245 Sum_probs=40.8
Q ss_pred hhhcccccccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 63 GLSKDLSTFSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKRKQEKANKL 126 (283)
Q Consensus 63 ~ls~dl~~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~a~~ 126 (283)
-++||.+--++.|++-+.+.. +++-..-+-.|+|-++=-|..|=.--.|+|||+.+|||+..
T Consensus 124 fIArD~tD~RAFGyVcG~eG~--hkF~aIKTaQaAep~VldlrDlFQvIye~Kkkeee~kK~q~ 185 (557)
T KOG3535|consen 124 FIARDSTDARAFGYVCGEEGK--HKFYAIKTAQAAEPAVLDLRDLFQVIYEMKKKEEEQKKQQQ 185 (557)
T ss_pred eeecccccccceeeeecCCCc--eeEEEEecccccchhhHhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 367899999999988775531 22222224566675555565565567888888888887544
No 103
>PHA00727 hypothetical protein
Probab=21.20 E-value=1.2e+02 Score=28.55 Aligned_cols=27 Identities=48% Similarity=0.486 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 96 AAEVLMKQLEQLKTEEKKLKRKRKQEK 122 (283)
Q Consensus 96 a~e~l~~~l~~~~~~~k~~k~~~k~ek 122 (283)
-.|+-.+|.+|+|+|--..|++.|.||
T Consensus 51 efelk~~qf~qlkael~kkkkk~kkek 77 (278)
T PHA00727 51 EFELKKQQFEQLKAELSKKKKKFKKEK 77 (278)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 356788999999999887777777776
No 104
>PHA00451 protein kinase
Probab=20.83 E-value=2.8e+02 Score=27.55 Aligned_cols=15 Identities=47% Similarity=0.875 Sum_probs=9.0
Q ss_pred ccccccccchhHHHHH
Q 023360 73 QMGFAVDQDQNLLAQV 88 (283)
Q Consensus 73 ~~g~~~d~~~~l~~~~ 88 (283)
.-||..||+ .|+.+|
T Consensus 223 e~GF~ldPd-~LiaEv 237 (362)
T PHA00451 223 EPGFPLDPD-ELIAEV 237 (362)
T ss_pred CCCCCCCHH-HHHHHH
Confidence 346888876 444444
No 105
>TIGR02573 LcrG_PcrG type III secretion protein LcrG. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium.
Probab=20.44 E-value=75 Score=26.08 Aligned_cols=40 Identities=10% Similarity=0.359 Sum_probs=27.5
Q ss_pred cccccccccccchhHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 023360 70 TFSQMGFAVDQDQNLLAQVRGKMISEAAEVLMKQLEQLKT 109 (283)
Q Consensus 70 ~~~~~g~~~d~~~~l~~~~~~~~~sea~e~l~~~l~~~~~ 109 (283)
++-.||++.....-||+..-.....-|-+.||.|++.+|.
T Consensus 28 m~~gLgl~p~ag~~Lf~~~~~e~~~~AEqELL~EiqRrr~ 67 (90)
T TIGR02573 28 MWQGLGLGPVAGEVLFGGLNAELMQHAEQELLEEVQRRRS 67 (90)
T ss_pred HHHHcCCChHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666666777766666677777778877777664
No 106
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=20.33 E-value=3.1e+02 Score=25.72 Aligned_cols=34 Identities=29% Similarity=0.432 Sum_probs=23.5
Q ss_pred HHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023360 85 LAQVRGKMISEAAEVLMKQLEQLKTEEKKLKRKRKQEKA 123 (283)
Q Consensus 85 ~~~~~~~~~sea~e~l~~~l~~~~~~~k~~k~~~k~ek~ 123 (283)
+|++|.+++--. -|||++|++-+|--||++++-+
T Consensus 3 ~EELRq~Ll~TT-----lELE~~k~~A~EElRk~eeqi~ 36 (214)
T PF07795_consen 3 MEELRQKLLYTT-----LELEATKMEANEELRKREEQIA 36 (214)
T ss_pred HHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH
Confidence 477887776433 3688888887777777766654
No 107
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=20.32 E-value=1.4e+02 Score=31.19 Aligned_cols=22 Identities=41% Similarity=0.578 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 023360 97 AEVLMKQLEQLKTEEKKLKRKR 118 (283)
Q Consensus 97 ~e~l~~~l~~~~~~~k~~k~~~ 118 (283)
.|.|-+||++||++.++++++-
T Consensus 33 ie~L~kql~~Lk~q~~~l~~~v 54 (489)
T PF11853_consen 33 IEALKKQLEELKAQQDDLNDRV 54 (489)
T ss_pred HHHHHHHHHHHHHhhccccccc
Confidence 4667777777777777766653
No 108
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=20.25 E-value=2.7e+02 Score=23.56 Aligned_cols=82 Identities=10% Similarity=0.181 Sum_probs=39.0
Q ss_pred ccccccCccccccCCCCcccccccccccccccchHHHHHHHHhhhcccccccccccccccchhHHHHHHhh---hHHHHH
Q 023360 21 RYSAGLGFVNKQSHEHQHHGGFVEMKKKEKVGSIKKKLKLLKGLSKDLSTFSQMGFAVDQDQNLLAQVRGK---MISEAA 97 (283)
Q Consensus 21 r~~~~~gf~~~~~~d~ghl~yy~~~~~~~~~~~~kkk~kll~~ls~dl~~~~~~g~~~d~~~~l~~~~~~~---~~sea~ 97 (283)
|+---.|++... .+++=.+||...-= .++.+++. |..+||..+.=..++...... ...+-.
T Consensus 19 RyYE~~GLl~p~-r~~~g~R~Y~~~dl--------~~l~~I~~-------lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~ 82 (139)
T cd01110 19 HFYEQKGLIASW-RNAGNQRRYPRDVL--------RRIAFIKV-------AQRLGLSLAEIAEALATLPEDRTPTKADWE 82 (139)
T ss_pred HHHHHCCCCCCC-cCCCCCeEECHHHH--------HHHHHHHH-------HHHcCCCHHHHHHHHHHhccCCCCCHHHHH
Confidence 443333554432 44444577765311 22555554 567788776433444332211 123333
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 023360 98 EVLMKQLEQLKTEEKKLKRKR 118 (283)
Q Consensus 98 e~l~~~l~~~~~~~k~~k~~~ 118 (283)
++|.++++++..+..++.+.+
T Consensus 83 ~~l~~~~~~l~~~i~~L~~~~ 103 (139)
T cd01110 83 RLSRAWRDRLDERIAELQQLR 103 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 444455555555555555444
No 109
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=20.25 E-value=1.7e+02 Score=31.07 Aligned_cols=12 Identities=25% Similarity=0.335 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHH
Q 023360 98 EVLMKQLEQLKT 109 (283)
Q Consensus 98 e~l~~~l~~~~~ 109 (283)
+.|++|.++-++
T Consensus 551 ~~~~~~~~~~~~ 562 (651)
T PTZ00399 551 EELQREKEEKEA 562 (651)
T ss_pred HHHHHHHHHHHH
Confidence 557777665543
No 110
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=20.24 E-value=1.5e+02 Score=23.56 Aligned_cols=16 Identities=31% Similarity=0.576 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHH
Q 023360 107 LKTEEKKLKRKRKQEK 122 (283)
Q Consensus 107 ~~~~~k~~k~~~k~ek 122 (283)
++++|++.|+|.|.+.
T Consensus 48 ie~~ere~K~k~Kr~~ 63 (74)
T PF15086_consen 48 IEKEEREKKKKAKRQA 63 (74)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3566777766655543
No 111
>KOG4118 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.17 E-value=1.6e+02 Score=23.19 Aligned_cols=27 Identities=37% Similarity=0.374 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHhhh
Q 023360 104 LEQLKTEEKKLKRKRK---QEKANKLKAKI 130 (283)
Q Consensus 104 l~~~~~~~k~~k~~~k---~ek~a~~ka~k 130 (283)
+.|.|..||.-|-|++ ++|+|+++|+-
T Consensus 9 qSQqknaeKqAkakk~~G~DQK~AA~~aL~ 38 (74)
T KOG4118|consen 9 QSQQKNAEKQAKAKKKQGHDQKAAAMAALH 38 (74)
T ss_pred HHHHHHHHHHHHHHHHcCccHHHHHHHHHH
Confidence 3456667776655555 57778888874
No 112
>COG4759 Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones]
Probab=20.15 E-value=1.8e+02 Score=28.69 Aligned_cols=71 Identities=15% Similarity=0.257 Sum_probs=53.9
Q ss_pred CcEEEEecCC----cccccchHHHHHHHHHHhcCCC----cEEeecCCCCCCCCCeEEEeCCcccCCCCCCCCcccCCCh
Q 023360 189 TKRVEVCMGN----KCKKSGGGALFEEFQRAMGAEG----DVVACKCMGKCRDGPNVRLFHSDAYHHLTPPNPLCIGVAL 260 (283)
Q Consensus 189 k~~I~VC~Gt----sC~~~GA~~VLeaLeeeLg~~G----tV~~tgCLG~C~~GPnV~V~~e~~~~V~~P~gvlY~~Vtp 260 (283)
...|+||+.+ +| ++=+.-++..++..++... .|=.+.=+|-=..+|.+.- +|.|..|+++.+
T Consensus 131 ~RdiLVCTHgn~D~cC-arfG~P~Y~~~r~~~a~l~~~~lRvWq~SHfgGHrFAPTlid---------lP~GqyyG~Ld~ 200 (316)
T COG4759 131 TRDILVCTHGNVDVCC-ARFGYPFYQQLRAQYADLNLENLRVWQSSHFGGHRFAPTLID---------LPQGQYYGHLDP 200 (316)
T ss_pred hceEEEecCCChhhhh-hhcCcHHHHHHHHhhhhccccceEEEEecccCccccCchhhc---------CCCCceeeecCH
Confidence 3469999964 55 5566789999999887643 4555666777788997743 478899999999
Q ss_pred hhHHHHHHH
Q 023360 261 EDVGAIVGN 269 (283)
Q Consensus 261 EDV~eIVee 269 (283)
+-.+.||..
T Consensus 201 ~~~~~l~~r 209 (316)
T COG4759 201 ESLDSLLTR 209 (316)
T ss_pred HHHHHHHhc
Confidence 999988863
Done!