Query psy2182
Match_columns 67
No_of_seqs 104 out of 219
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 18:21:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2182.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2182hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00292 PAX: 'Paired box' dom 100.0 4.8E-35 1E-39 192.4 3.8 66 2-67 52-117 (125)
2 KOG3517|consensus 100.0 3.6E-33 7.8E-38 203.3 3.4 66 2-67 55-120 (334)
3 KOG3862|consensus 99.9 1.9E-27 4.2E-32 174.0 4.1 66 2-67 60-125 (327)
4 KOG0849|consensus 99.8 4.6E-22 1E-26 147.0 3.5 66 2-67 50-116 (354)
5 cd00131 PAX Paired Box domain 99.7 3.2E-17 6.9E-22 106.6 6.0 66 2-67 52-117 (128)
6 smart00351 PAX Paired Box doma 99.7 1.1E-16 2.3E-21 103.3 6.3 66 2-67 52-117 (125)
7 PF13565 HTH_32: Homeodomain-l 97.8 4.9E-05 1.1E-09 44.0 4.9 53 2-56 4-61 (77)
8 PF13551 HTH_29: Winged helix- 97.2 0.00045 9.8E-09 41.5 3.4 56 2-57 31-94 (112)
9 COG3415 Transposase and inacti 96.9 0.0023 4.9E-08 42.8 4.6 54 4-58 42-96 (138)
10 PF01710 HTH_Tnp_IS630: Transp 95.6 0.017 3.8E-07 36.6 3.5 41 7-53 41-81 (119)
11 PF13072 DUF3936: Protein of u 89.7 0.25 5.5E-06 26.8 1.6 11 46-56 16-26 (38)
12 cd04059 Peptidases_S8_Protein_ 80.5 2.2 4.8E-05 29.6 3.1 34 22-55 261-294 (297)
13 cd07498 Peptidases_S8_15 Pepti 79.8 2.4 5.2E-05 28.5 3.0 33 23-55 209-241 (242)
14 PF00600 Flu_NS1: Influenza no 77.5 1.1 2.4E-05 31.9 0.9 19 43-61 12-30 (217)
15 cd07493 Peptidases_S8_9 Peptid 75.4 3.6 7.7E-05 28.3 3.0 33 23-55 226-258 (261)
16 cd07483 Peptidases_S8_Subtilis 75.2 3.9 8.4E-05 29.0 3.2 35 23-57 256-290 (291)
17 cd07492 Peptidases_S8_8 Peptid 72.2 5.7 0.00012 26.5 3.3 33 23-55 187-219 (222)
18 cd05562 Peptidases_S53_like Pe 70.5 6.7 0.00014 27.9 3.5 33 23-55 216-248 (275)
19 cd04848 Peptidases_S8_Autotran 69.9 8.3 0.00018 25.7 3.7 33 23-55 232-264 (267)
20 PF13089 PP_kinase_N: Polyphos 68.4 0.76 1.7E-05 29.0 -1.5 51 8-59 56-106 (109)
21 PF13411 MerR_1: MerR HTH fami 68.3 8.1 0.00018 21.3 2.9 49 4-55 17-68 (69)
22 cd04852 Peptidases_S8_3 Peptid 67.1 6.9 0.00015 27.6 3.0 33 23-55 272-304 (307)
23 cd07474 Peptidases_S8_subtilis 67.0 7.6 0.00016 26.8 3.1 36 23-58 235-270 (295)
24 cd07494 Peptidases_S8_10 Pepti 65.2 10 0.00022 27.2 3.6 36 22-57 247-282 (298)
25 cd07473 Peptidases_S8_Subtilis 62.9 12 0.00025 25.4 3.4 33 23-55 224-256 (259)
26 cd01111 HTH_MerD Helix-Turn-He 62.9 23 0.0005 22.0 4.5 52 4-55 17-69 (107)
27 cd07487 Peptidases_S8_1 Peptid 62.2 14 0.0003 24.8 3.6 33 23-55 229-261 (264)
28 cd07496 Peptidases_S8_13 Pepti 62.1 9.9 0.00021 26.5 3.0 33 23-55 252-284 (285)
29 cd07482 Peptidases_S8_Lantibio 62.1 12 0.00025 25.7 3.3 34 22-55 259-293 (294)
30 cd07477 Peptidases_S8_Subtilis 62.0 12 0.00025 24.8 3.2 33 23-55 196-228 (229)
31 cd04077 Peptidases_S8_PCSK9_Pr 60.3 12 0.00026 25.5 3.1 34 23-56 219-252 (255)
32 cd04782 HTH_BltR Helix-Turn-He 60.0 28 0.00061 21.0 4.4 50 4-55 17-69 (97)
33 cd07481 Peptidases_S8_Bacillop 59.4 12 0.00025 25.8 2.9 33 23-55 227-261 (264)
34 cd04780 HTH_MerR-like_sg5 Heli 59.1 19 0.00041 21.9 3.5 52 4-55 17-70 (95)
35 cd01105 HTH_GlnR-like Helix-Tu 58.6 29 0.00063 20.6 4.2 52 4-57 18-72 (88)
36 TIGR01529 argR_whole arginine 58.5 18 0.00039 23.9 3.5 28 32-59 5-32 (146)
37 cd07490 Peptidases_S8_6 Peptid 58.4 15 0.00032 24.8 3.2 32 24-55 220-251 (254)
38 PF13034 DUF3895: Protein of u 57.2 24 0.00052 21.7 3.7 33 28-60 3-35 (78)
39 PF15311 HYLS1_C: Hydrolethalu 56.9 11 0.00024 23.7 2.2 13 45-57 43-55 (89)
40 cd07484 Peptidases_S8_Thermita 56.8 13 0.00029 25.2 2.8 33 23-56 223-255 (260)
41 cd04773 HTH_TioE_rpt2 Second H 56.7 25 0.00055 21.7 3.9 52 4-55 17-69 (108)
42 cd01104 HTH_MlrA-CarA Helix-Tu 54.6 32 0.0007 18.7 3.8 49 4-53 17-67 (68)
43 cd05561 Peptidases_S8_4 Peptid 54.4 14 0.0003 25.4 2.6 33 23-56 191-223 (239)
44 COG4367 Uncharacterized protei 52.5 27 0.00058 22.4 3.4 28 26-55 35-62 (97)
45 PRK07122 RNA polymerase sigma 51.7 28 0.00062 24.5 3.9 43 16-58 4-50 (264)
46 COG0789 SoxR Predicted transcr 51.7 50 0.0011 20.0 4.6 53 4-56 17-70 (124)
47 PF11554 DUF3232: Protein of u 51.2 6.4 0.00014 27.0 0.5 39 2-40 99-141 (152)
48 cd04765 HTH_MlrA-like_sg2 Heli 50.8 56 0.0012 20.0 4.7 51 6-57 19-72 (99)
49 PF10061 DUF2299: Uncharacteri 50.7 6.2 0.00013 26.1 0.4 33 27-59 57-89 (138)
50 cd07485 Peptidases_S8_Fervidol 50.5 24 0.00051 24.4 3.3 33 23-55 239-272 (273)
51 PRK08558 adenine phosphoribosy 50.1 12 0.00026 26.5 1.8 45 3-60 39-85 (238)
52 PF11116 DUF2624: Protein of u 49.6 31 0.00067 21.5 3.4 31 26-56 31-62 (85)
53 PRK13749 transcriptional regul 49.1 64 0.0014 20.8 4.9 51 6-56 22-73 (121)
54 cd04772 HTH_TioE_rpt1 First He 48.4 61 0.0013 19.7 4.8 51 4-54 17-67 (99)
55 cd01106 HTH_TipAL-Mta Helix-Tu 48.4 44 0.00096 20.1 4.0 50 4-55 17-69 (103)
56 cd04847 Peptidases_S8_Subtilis 47.5 27 0.00058 24.4 3.2 32 24-55 257-288 (291)
57 cd00306 Peptidases_S8_S53 Pept 46.9 30 0.00066 22.0 3.2 34 22-55 207-240 (241)
58 PF00082 Peptidase_S8: Subtila 45.0 25 0.00055 23.7 2.7 33 24-56 222-254 (282)
59 PF09106 SelB-wing_2: Elongati 44.9 25 0.00053 19.4 2.2 24 32-55 3-29 (59)
60 PF10078 DUF2316: Uncharacteri 43.8 22 0.00047 22.2 2.1 30 25-55 34-63 (89)
61 PF03584 Herpes_ICP4_N: Herpes 43.7 27 0.00058 24.5 2.7 40 10-49 14-56 (173)
62 PF01799 Fer2_2: [2Fe-2S] bind 43.4 36 0.00079 20.3 2.9 34 25-59 28-61 (75)
63 PF01316 Arg_repressor: Argini 43.2 48 0.001 19.5 3.4 30 30-59 6-35 (70)
64 PF08218 Citrate_ly_lig: Citra 43.1 16 0.00035 25.7 1.5 36 29-64 14-60 (182)
65 PF13011 LZ_Tnp_IS481: leucine 42.6 27 0.00058 21.6 2.3 34 2-39 44-84 (85)
66 smart00550 Zalpha Z-DNA-bindin 42.4 65 0.0014 18.3 3.9 27 27-53 4-32 (68)
67 PRK03341 arginine repressor; P 41.6 49 0.0011 22.5 3.7 32 28-59 14-45 (168)
68 cd00756 MoaE MoaE family. Memb 41.3 15 0.00033 23.7 1.1 36 7-42 69-110 (124)
69 KOG1436|consensus 39.9 14 0.0003 28.7 0.9 20 7-26 120-140 (398)
70 PRK11566 hdeB acid-resistance 39.6 42 0.00091 21.6 2.9 26 31-56 74-99 (102)
71 cd07489 Peptidases_S8_5 Peptid 39.5 39 0.00085 23.8 3.1 36 23-58 230-266 (312)
72 PF10273 WGG: Pre-rRNA-process 38.9 44 0.00095 20.0 2.8 38 18-55 24-61 (82)
73 cd04843 Peptidases_S8_11 Pepti 38.7 55 0.0012 23.3 3.7 36 22-57 236-276 (277)
74 PRK10227 DNA-binding transcrip 38.6 1.1E+02 0.0023 19.8 4.9 51 4-54 17-68 (135)
75 cd04779 HTH_MerR-like_sg4 Heli 38.6 71 0.0015 20.7 4.0 51 4-57 17-70 (134)
76 TIGR02054 MerD mercuric resist 38.5 1E+02 0.0023 19.7 4.7 50 5-54 21-71 (120)
77 cd04762 HTH_MerR-trunc Helix-T 37.7 30 0.00065 16.9 1.7 29 4-32 17-45 (49)
78 PF01498 HTH_Tnp_Tc3_2: Transp 37.5 19 0.0004 20.2 1.0 25 34-58 4-28 (72)
79 PTZ00262 subtilisin-like prote 37.4 60 0.0013 26.8 4.1 37 22-58 555-591 (639)
80 cd04766 HTH_HspR Helix-Turn-He 37.2 75 0.0016 18.7 3.7 49 4-53 18-68 (91)
81 PHA02754 hypothetical protein; 36.8 24 0.00053 21.0 1.4 15 45-59 19-33 (67)
82 cd01279 HTH_HspR-like Helix-Tu 36.8 79 0.0017 19.1 3.8 50 4-54 18-69 (98)
83 PRK04280 arginine repressor; P 35.5 71 0.0015 21.2 3.7 29 31-59 6-34 (148)
84 PF12614 RRF_GI: Ribosome recy 35.5 52 0.0011 22.0 3.0 26 24-49 83-108 (128)
85 TIGR02043 ZntR Zn(II)-responsi 35.2 1.2E+02 0.0026 19.2 4.7 49 4-54 18-69 (131)
86 TIGR03193 4hydroxCoAred 4-hydr 34.9 57 0.0012 22.0 3.1 32 27-59 101-132 (148)
87 COG1438 ArgR Arginine represso 34.6 69 0.0015 21.7 3.5 30 30-59 7-36 (150)
88 cd01107 HTH_BmrR Helix-Turn-He 34.0 1.1E+02 0.0024 18.6 4.2 52 4-55 17-70 (108)
89 PRK05066 arginine repressor; P 33.9 1.1E+02 0.0023 20.6 4.3 31 29-59 9-39 (156)
90 cd01109 HTH_YyaN Helix-Turn-He 33.7 1.1E+02 0.0025 18.6 4.8 50 4-55 17-69 (113)
91 TIGR02044 CueR Cu(I)-responsiv 33.5 1.2E+02 0.0026 19.0 4.3 51 4-54 17-68 (127)
92 cd04788 HTH_NolA-AlbR Helix-Tu 33.2 1E+02 0.0022 18.4 3.9 50 4-55 17-69 (96)
93 cd04767 HTH_HspR-like_MBC Heli 32.7 79 0.0017 20.5 3.4 50 4-55 18-69 (120)
94 TIGR00722 ttdA_fumA_fumB hydro 32.5 24 0.00051 26.0 1.0 41 16-56 182-223 (273)
95 cd04778 HTH_MerR-like_sg2 Heli 32.3 1.3E+02 0.0029 21.0 4.8 49 5-55 19-69 (219)
96 PRK00441 argR arginine repress 32.0 84 0.0018 20.8 3.6 31 29-59 4-34 (149)
97 PRK05927 hypothetical protein; 32.0 93 0.002 23.2 4.1 51 8-58 89-158 (350)
98 COG5530 Predicted integral mem 31.8 42 0.00091 24.5 2.2 24 29-54 35-58 (247)
99 PF12949 HeH: HeH/LEM domain; 31.4 40 0.00086 17.6 1.5 22 43-64 3-24 (35)
100 cd07963 Anticodon_Ia_Cys Antic 31.2 33 0.00071 22.1 1.5 16 46-61 131-146 (156)
101 COG1582 FlgEa Uncharacterized 31.0 36 0.00078 20.5 1.5 22 24-48 41-62 (67)
102 PF09107 SelB-wing_3: Elongati 30.5 77 0.0017 17.5 2.7 20 34-53 1-20 (50)
103 PF05902 4_1_CTD: 4.1 protein 30.4 51 0.0011 21.6 2.2 18 28-45 85-102 (114)
104 PF04255 DUF433: Protein of un 30.3 1E+02 0.0022 16.9 4.1 42 13-54 3-54 (56)
105 COG3695 Predicted methylated D 30.3 54 0.0012 21.2 2.3 21 42-62 70-90 (103)
106 PF02037 SAP: SAP domain; Int 29.7 72 0.0016 16.0 2.4 21 43-63 3-23 (35)
107 cd04763 HTH_MlrA-like Helix-Tu 29.7 1E+02 0.0023 16.9 4.2 46 5-53 18-67 (68)
108 PRK09514 zntR zinc-responsive 28.9 1.3E+02 0.0029 19.3 4.1 51 4-54 18-69 (140)
109 cd01110 HTH_SoxR Helix-Turn-He 28.5 1.6E+02 0.0035 18.9 4.4 50 4-54 18-68 (139)
110 cd04764 HTH_MlrA-like_sg1 Heli 28.4 1.1E+02 0.0024 16.7 3.9 48 5-53 18-66 (67)
111 TIGR03198 pucE xanthine dehydr 28.0 86 0.0019 21.1 3.1 32 27-59 102-133 (151)
112 PF13412 HTH_24: Winged helix- 27.9 95 0.0021 15.9 3.8 25 29-53 3-27 (48)
113 cd04776 HTH_GnyR Helix-Turn-He 27.7 1.4E+02 0.0031 18.6 3.9 48 4-55 17-67 (118)
114 PF09748 Med10: Transcription 27.7 49 0.0011 21.3 1.8 27 28-56 66-92 (128)
115 cd03412 CbiK_N Anaerobic cobal 27.6 1.3E+02 0.0029 18.9 3.8 34 25-58 14-53 (127)
116 PLN02826 dihydroorotate dehydr 27.2 12 0.00025 28.8 -1.4 41 7-47 110-152 (409)
117 PF01979 Amidohydro_1: Amidohy 27.1 25 0.00054 24.0 0.4 17 2-18 310-326 (333)
118 cd04774 HTH_YfmP Helix-Turn-He 26.8 1.5E+02 0.0033 17.8 3.9 49 4-54 17-68 (96)
119 cd04786 HTH_MerR-like_sg7 Heli 26.7 1.6E+02 0.0035 18.9 4.1 52 4-55 17-69 (131)
120 PRK14137 recX recombination re 26.7 1.8E+02 0.004 20.1 4.6 34 26-59 34-70 (195)
121 KOG3185|consensus 26.6 88 0.0019 22.8 3.1 37 20-56 207-243 (245)
122 PF12752 SUZ: SUZ domain; Int 26.5 41 0.00088 18.9 1.2 45 1-45 5-55 (59)
123 KOG4146|consensus 26.4 22 0.00048 22.9 0.0 12 7-18 57-68 (101)
124 cd04789 HTH_Cfa Helix-Turn-Hel 26.3 1.6E+02 0.0034 17.8 4.1 47 4-53 18-67 (102)
125 PF11943 DUF3460: Protein of u 26.2 66 0.0014 18.8 2.0 20 27-46 4-23 (60)
126 TIGR02625 YiiL_rotase L-rhamno 26.2 58 0.0013 20.4 1.9 27 32-60 11-38 (102)
127 PF14441 OTT_1508_deam: OTT_15 25.8 16 0.00035 23.5 -0.7 23 2-24 73-95 (142)
128 COG0314 MoaE Molybdopterin con 25.0 38 0.00081 22.8 0.9 37 6-42 81-123 (149)
129 cd04790 HTH_Cfa-like_unk Helix 24.9 1.8E+02 0.0039 19.4 4.2 50 4-55 18-70 (172)
130 PLN02390 molybdopterin synthas 24.3 40 0.00087 21.5 0.9 36 7-42 58-99 (111)
131 PRK15002 redox-sensitivie tran 24.1 1.5E+02 0.0034 19.6 3.8 49 4-54 28-78 (154)
132 PF14077 WD40_alt: Alternative 24.0 56 0.0012 18.4 1.4 28 20-47 13-40 (48)
133 cd04768 HTH_BmrR-like Helix-Tu 23.9 1.7E+02 0.0037 17.4 4.1 50 4-55 17-69 (96)
134 COG0855 Ppk Polyphosphate kina 23.2 54 0.0012 27.4 1.7 47 13-59 69-115 (696)
135 PF14090 HTH_39: Helix-turn-he 23.1 1.3E+02 0.0029 17.0 2.9 22 31-52 3-24 (70)
136 cd07479 Peptidases_S8_SKI-1_li 23.0 1.1E+02 0.0024 21.2 3.0 33 24-56 213-249 (255)
137 cd04787 HTH_HMRTR_unk Helix-Tu 22.8 1.9E+02 0.0042 18.2 3.9 49 4-54 17-68 (133)
138 PF02618 YceG: YceG-like famil 22.6 84 0.0018 22.8 2.4 57 4-63 33-98 (297)
139 smart00581 PSP proline-rich do 22.2 32 0.00069 19.8 0.1 15 39-53 3-17 (54)
140 cd07480 Peptidases_S8_12 Pepti 21.8 99 0.0021 21.7 2.6 33 23-55 237-269 (297)
141 PHA00687 hypothetical protein 21.6 45 0.00097 19.0 0.7 24 22-45 31-54 (56)
142 PRK10963 hypothetical protein; 21.3 65 0.0014 22.4 1.6 23 31-55 5-27 (223)
143 PF04046 PSP: PSP; InterPro: 21.3 56 0.0012 18.3 1.0 13 41-53 1-13 (48)
144 TIGR02051 MerR Hg(II)-responsi 21.1 2.1E+02 0.0045 17.9 3.8 51 4-54 16-67 (124)
145 PRK10678 moaE molybdopterin gu 20.9 47 0.001 22.3 0.8 36 7-42 82-123 (150)
146 smart00513 SAP Putative DNA-bi 20.7 1.3E+02 0.0028 14.8 2.7 20 43-62 3-22 (35)
147 TIGR01950 SoxR redox-sensitive 20.7 1.9E+02 0.0041 18.8 3.6 48 4-54 18-68 (142)
148 PRK15043 transcriptional regul 20.5 2.2E+02 0.0047 20.6 4.2 48 6-56 21-73 (243)
149 PF14909 SPATA6: Spermatogenes 20.3 31 0.00068 23.2 -0.2 16 1-16 26-41 (140)
150 PRK00117 recX recombination re 20.2 2E+02 0.0043 18.3 3.6 34 25-59 8-41 (157)
151 cd04784 HTH_CadR-PbrR Helix-Tu 20.1 2.3E+02 0.005 17.6 4.3 49 4-54 17-68 (127)
152 PF02650 HTH_WhiA: WhiA C-term 20.0 1.3E+02 0.0029 18.3 2.6 27 27-53 38-64 (85)
No 1
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=100.00 E-value=4.8e-35 Score=192.44 Aligned_cols=66 Identities=65% Similarity=1.080 Sum_probs=50.4
Q ss_pred cccchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcCCCCCCCCC
Q psy2182 2 YSEEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPSL 67 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc~~~~~psv 67 (67)
|||+||+|||||+||+|||||||++||+++.+|++|+++||+||+|||||+|+++|||+++|+|||
T Consensus 52 KIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~Psv 117 (125)
T PF00292_consen 52 KILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSV 117 (125)
T ss_dssp HHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--H
T ss_pred HHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCH
Confidence 899999999999999999999999999999999999999999999999999999999999999996
No 2
>KOG3517|consensus
Probab=99.97 E-value=3.6e-33 Score=203.27 Aligned_cols=66 Identities=58% Similarity=0.926 Sum_probs=65.5
Q ss_pred cccchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcCCCCCCCCC
Q psy2182 2 YSEEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPSL 67 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc~~~~~psv 67 (67)
|||.||.|||||-||+||||||+|+||.|++.|.+||+..|+||||||||||+.+||||+.|||||
T Consensus 55 KILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvPSV 120 (334)
T KOG3517|consen 55 KILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLSDGICDKYNVPSV 120 (334)
T ss_pred HHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhhcccccccCCcch
Confidence 899999999999999999999999999999999999999999999999999999999999999997
No 3
>KOG3862|consensus
Probab=99.94 E-value=1.9e-27 Score=173.95 Aligned_cols=66 Identities=65% Similarity=1.072 Sum_probs=65.3
Q ss_pred cccchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcCCCCCCCCC
Q psy2182 2 YSEEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPSL 67 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc~~~~~psv 67 (67)
|||.||+|||||+||.|||||||++||.|+++|..||++||.||+||||++|+.++||+.++||||
T Consensus 60 kil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsV 125 (327)
T KOG3862|consen 60 KILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSV 125 (327)
T ss_pred hHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchH
Confidence 899999999999999999999999999999999999999999999999999999999999999997
No 4
>KOG0849|consensus
Probab=99.85 E-value=4.6e-22 Score=147.00 Aligned_cols=66 Identities=59% Similarity=1.026 Sum_probs=64.5
Q ss_pred cccchhhhcccccccccCCCCCC-cCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcCCCCCCCCC
Q psy2182 2 YSEEGYYETGSIKPRAIGGSKPR-VATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPSL 67 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~iGGskpk-~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc~~~~~psv 67 (67)
||||||++||+|+||.|||++|+ +++++++.+|++|++++|++|+||||++|+.+++|+..++|||
T Consensus 50 ~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~~~~~~~~~t~Ps~ 116 (354)
T KOG0849|consen 50 KILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLLHEGLCTQATLPSV 116 (354)
T ss_pred hhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhcccCcccccCCCCCCh
Confidence 79999999999999999999998 9999999999999999999999999999999999999999985
No 5
>cd00131 PAX Paired Box domain
Probab=99.70 E-value=3.2e-17 Score=106.57 Aligned_cols=66 Identities=67% Similarity=1.091 Sum_probs=62.7
Q ss_pred cccchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcCCCCCCCCC
Q psy2182 2 YSEEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPSL 67 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc~~~~~psv 67 (67)
+++.||.|||++.|++.||.+|+..+++++..|..+.++||++|+|||+++|.++|+|.+++.||+
T Consensus 52 r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~ 117 (128)
T cd00131 52 KILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSV 117 (128)
T ss_pred HHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCH
Confidence 578999999999999999999999999999999999999999999999999999999999999985
No 6
>smart00351 PAX Paired Box domain.
Probab=99.68 E-value=1.1e-16 Score=103.33 Aligned_cols=66 Identities=71% Similarity=1.161 Sum_probs=63.6
Q ss_pred cccchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcCCCCCCCCC
Q psy2182 2 YSEEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPSL 67 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc~~~~~psv 67 (67)
|++.||.+||++.|++.||.+|+..+++++..|.++.+++|++++|||++.|.++|||...++||+
T Consensus 52 kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~ 117 (125)
T smart00351 52 KILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSV 117 (125)
T ss_pred HHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCCh
Confidence 578999999999999999999999999999999999999999999999999999999999999985
No 7
>PF13565 HTH_32: Homeodomain-like domain
Probab=97.84 E-value=4.9e-05 Score=43.95 Aligned_cols=53 Identities=25% Similarity=0.210 Sum_probs=44.5
Q ss_pred cccchhhhcc-----cccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 2 YSEEGYYETG-----SIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 2 ~~L~Ry~eTG-----si~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
+.+.||+++| +..+++-+|-.++ ++++++.|.++..++|.....+|.+.|.++
T Consensus 4 rw~~ry~~~G~~gL~~~~~~~~~Grp~~--~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~ 61 (77)
T PF13565_consen 4 RWLKRYREEGLEGLKDRKRRPRPGRPRK--DPEQRERIIALIEEHPRWTPREIAEYLEEE 61 (77)
T ss_pred HHHHHHHhhCchhhhcccccCCCCCCCC--cHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 4678999999 7655565555444 889999999999999999999999999987
No 8
>PF13551 HTH_29: Winged helix-turn helix
Probab=97.21 E-value=0.00045 Score=41.50 Aligned_cols=56 Identities=21% Similarity=0.308 Sum_probs=44.2
Q ss_pred cccchhhhcc--cccc-cccCCCCCCcCCHHHHHHHHHHHhhCC-----CccHHHHHHHHHhcC
Q psy2182 2 YSEEGYYETG--SIKP-RAIGGSKPRVATNGVVTKIADYKRECP-----SIFAWEIRDRLLAEG 57 (67)
Q Consensus 2 ~~L~Ry~eTG--si~P-g~iGGskpk~~t~~v~~~I~~~k~~~p-----~ifawEiR~~L~~~G 57 (67)
+.+.+|.++| .+.+ +.-||..++..++++.+.|.++..++| ..+.-+|++.|+++.
T Consensus 31 r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~ 94 (112)
T PF13551_consen 31 RWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEE 94 (112)
T ss_pred HHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhc
Confidence 4678999999 7888 555555554589999999999999998 467788898886554
No 9
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=96.88 E-value=0.0023 Score=42.79 Aligned_cols=54 Identities=24% Similarity=0.198 Sum_probs=42.5
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHH-hcCc
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLL-AEGV 58 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~-~~Gv 58 (67)
++||.|||+..|...||.+|+..+++..+.++...++.. .++-|+++.|. +.||
T Consensus 42 v~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~~e~gv 96 (138)
T COG3415 42 VRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEELGLEFGV 96 (138)
T ss_pred HHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHHHhhhcCe
Confidence 689999999999999999999888887777777655543 77777777765 5555
No 10
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=95.63 E-value=0.017 Score=36.60 Aligned_cols=41 Identities=24% Similarity=0.460 Sum_probs=33.2
Q ss_pred hhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHH
Q psy2182 7 YYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRL 53 (67)
Q Consensus 7 y~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L 53 (67)
..+||++.|++-|+. +. + .+.+.++..++|+++++||.++|
T Consensus 41 ~~~~G~~~~k~r~~~--Ki--d--~~~L~~~v~~~pd~tl~Ela~~l 81 (119)
T PF01710_consen 41 RKETGDLEPKPRGRK--KI--D--RDELKALVEENPDATLRELAERL 81 (119)
T ss_pred hcccccccccccccc--cc--c--HHHHHHHHHHCCCcCHHHHHHHc
Confidence 578999999997766 33 2 45688888999999999998876
No 11
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=89.66 E-value=0.25 Score=26.80 Aligned_cols=11 Identities=55% Similarity=0.924 Sum_probs=9.4
Q ss_pred HHHHHHHHHhc
Q psy2182 46 AWEIRDRLLAE 56 (67)
Q Consensus 46 awEiR~~L~~~ 56 (67)
|||||+.|.+=
T Consensus 16 AWeIr~~Lkey 26 (38)
T PF13072_consen 16 AWEIRAKLKEY 26 (38)
T ss_pred HHHHHHHHHHH
Confidence 89999999763
No 12
>cd04059 Peptidases_S8_Protein_convertases_Kexins_Furin-like Peptidase S8 family domain in Protein convertases. Protein convertases, whose members include furins and kexins, are members of the peptidase S8 or Subtilase clan of proteases. They have an Asp/His/Ser catalytic triad that is not homologous to trypsin. Kexins are involved in the activation of peptide hormones, growth factors, and viral proteins. Furin cleaves cell surface vasoactive peptides and proteins involved in cardiovascular tissue remodeling in the TGN, at cell surface, or in endosomes but rarely in the ER. Furin also plays a key role in blood pressure regulation though the activation of transforming growth factor (TGF)-beta. High specificity is seen for cleavage after dibasic (Lys-Arg or Arg-Arg) or multiple basic residues in protein convertases. There is also strong sequence conservation.
Probab=80.52 E-value=2.2 Score=29.59 Aligned_cols=34 Identities=15% Similarity=0.037 Sum_probs=30.5
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 22 KPRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 22 kpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
-.+.++|-|+-.+.-+++++|++..-|||+.|++
T Consensus 261 GTS~AaP~VAG~aAll~~~~p~lt~~~v~~~L~~ 294 (297)
T cd04059 261 GTSAAAPLAAGVIALMLEANPNLTWRDVQHILAL 294 (297)
T ss_pred CcchhhhhhHhHHHHhhccCCCCCHHHHHHHHHH
Confidence 3578899999999999999999999999999975
No 13
>cd07498 Peptidases_S8_15 Peptidase S8 family domain, uncharacterized subfamily 15. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=79.77 E-value=2.4 Score=28.54 Aligned_cols=33 Identities=18% Similarity=0.092 Sum_probs=29.0
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+.-+++.+|++...|||+.|..
T Consensus 209 TS~Aap~vaG~~All~~~~p~l~~~~i~~~L~~ 241 (242)
T cd07498 209 TSFASPVAAGVAALILSANPNLTPAEVEDILTS 241 (242)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence 356888899988899999999999999999874
No 14
>PF00600 Flu_NS1: Influenza non-structural protein (NS1); InterPro: IPR000256 NS1 is a homodimeric RNA-binding protein found in influenza virus that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA [].; GO: 0003723 RNA binding; PDB: 2Z0A_C 3P39_E 3P38_C 3P31_C 3M8A_H 3M5R_D 3EE9_B 3KWI_A 3KWG_B 2RHK_A ....
Probab=77.54 E-value=1.1 Score=31.91 Aligned_cols=19 Identities=21% Similarity=0.630 Sum_probs=14.7
Q ss_pred CccHHHHHHHHHhcCcCCC
Q psy2182 43 SIFAWEIRDRLLAEGVCNN 61 (67)
Q Consensus 43 ~ifawEiR~~L~~~Gvc~~ 61 (67)
+||+|-+|.+++.+++||.
T Consensus 12 dCfLWHvrKr~ad~~lgDA 30 (217)
T PF00600_consen 12 DCFLWHVRKRFADQELGDA 30 (217)
T ss_dssp HHHHHHHHHHHHHTT---H
T ss_pred eehhhHHHHHhhhcccccc
Confidence 5899999999999999874
No 15
>cd07493 Peptidases_S8_9 Peptidase S8 family domain, uncharacterized subfamily 9. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=75.44 E-value=3.6 Score=28.28 Aligned_cols=33 Identities=15% Similarity=0.160 Sum_probs=29.4
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
-+.++|-|.-.+..+++++|++...|||+.|+.
T Consensus 226 TS~AaP~vaG~aAll~~~~p~lt~~~i~~~l~~ 258 (261)
T cd07493 226 TSFSCPLIAGLIACLWQAHPNWTNLQIKEAILK 258 (261)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 356788999999999999999999999999975
No 16
>cd07483 Peptidases_S8_Subtilisin_Novo-like Peptidase S8 family domain in Subtilisin_Novo-like proteins. Subtilisins are a group of alkaline proteinases originating from different strains of Bacillus subtilis. Novo is one of the strains that produced enzymes belonging to this group. The enzymes obtained from the Novo and BPN' strains are identical. The Carlsburg and Novo subtilisins are thought to have arisen from a common ancestral protein. They have similar peptidase and esterase activities, pH profiles, catalyze transesterification reactions, and are both inhibited by diispropyl fluorophosphate, though they differ in 85 positions in the amino acid sequence. Members of the peptidases S8 and S35 clan include endopeptidases, exopeptidases and also a tripeptidyl-peptidase. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The S53 family contains a cat
Probab=75.15 E-value=3.9 Score=28.98 Aligned_cols=35 Identities=23% Similarity=0.187 Sum_probs=30.9
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcC
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEG 57 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~G 57 (67)
.+.++|-|.-.+.-+++.+|.+..-|||+.|++-+
T Consensus 256 TS~AaP~vaG~aAl~~s~~p~lt~~~v~~~L~~ta 290 (291)
T cd07483 256 TSMAAPVVSGVAALIWSYYPNLTAKEVKQIILESG 290 (291)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence 36778889999999999999999999999998755
No 17
>cd07492 Peptidases_S8_8 Peptidase S8 family domain, uncharacterized subfamily 8. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=72.20 E-value=5.7 Score=26.46 Aligned_cols=33 Identities=24% Similarity=0.148 Sum_probs=29.5
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+.-+.+.+|++..-|||+.|.+
T Consensus 187 TS~Aap~vaG~~All~~~~p~l~~~~v~~~L~~ 219 (222)
T cd07492 187 NSFAAPHVTGMVALLLSEKPDIDANDLKRLLQR 219 (222)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 467788999999999999999999999999975
No 18
>cd05562 Peptidases_S53_like Peptidase domain in the S53 family. Members of the peptidase S53 (sedolisin) family include endopeptidases and exopeptidases. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of Asn in subtilisin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. Characterized sedolisins include Kumamolisin, an extracellular calcium-dependent thermostable endopeptidase from Bacillus. The enzyme is synthesized with a 188 amino acid N-terminal preprotein region which is cleaved after the extraction into the extracellular space with low pH. One kumamolysin paralog, kumamolisin-As, is believed to be a collagenase. TPP1 is a serine protease that functi
Probab=70.46 E-value=6.7 Score=27.90 Aligned_cols=33 Identities=21% Similarity=0.145 Sum_probs=28.3
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
-+.++|-|.-.+.-+++.+|++...+||+.|..
T Consensus 216 TS~AaP~VaG~aALl~~~~p~lt~~~v~~~L~~ 248 (275)
T cd05562 216 TSAAAPHAAGVAALVLSANPGLTPADIRDALRS 248 (275)
T ss_pred chHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 356778888888888899999999999999976
No 19
>cd04848 Peptidases_S8_Autotransporter_serine_protease_like Peptidase S8 family domain in Autotransporter serine proteases. Autotransporter serine proteases belong to Peptidase S8 or Subtilase family. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). Autotransporters are a superfamily of outer membrane/secreted proteins of gram-negative bacteria. The presence of these subtilisin-like domains in these autotransporters are may enable them to be auto-catalytic and may also serve to allow them to act as a maturation protease cleaving other outer membrane proteins at the cell surface.
Probab=69.87 E-value=8.3 Score=25.65 Aligned_cols=33 Identities=24% Similarity=0.220 Sum_probs=29.5
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
-+.++|-|.-.+..+++.+|++..-+||+.|+.
T Consensus 232 TS~Aap~vaG~~Al~~~~~p~l~~~~v~~~l~~ 264 (267)
T cd04848 232 TSFAAPHVSGAAALLAQKFPWLTADQVRQTLLT 264 (267)
T ss_pred eEchHHHHHHHHHHHHHHCCCCCHHHHHHHHHh
Confidence 467899999999999999999999999999874
No 20
>PF13089 PP_kinase_N: Polyphosphate kinase N-terminal domain; PDB: 2O8R_A 1XDP_A 1XDO_B.
Probab=68.38 E-value=0.76 Score=29.03 Aligned_cols=51 Identities=22% Similarity=0.319 Sum_probs=34.4
Q ss_pred hhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 8 YETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 8 ~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
.+.|.-.+. ..|-.|+....++.+.+..+.+++=.+|--+|...|.++||+
T Consensus 56 ~~~g~~~~~-~~g~tP~eqL~~I~~~v~~l~~~q~~~~~~~Llp~L~~~GI~ 106 (109)
T PF13089_consen 56 IEAGVKKRD-PDGLTPQEQLDAIRKRVHELVEEQYEIYNEELLPELAEEGIH 106 (109)
T ss_dssp CCHHHCC----S---HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHCTTEE
T ss_pred HHhccCCCC-cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE
Confidence 334433333 445566666777888888888888788888899999999986
No 21
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=68.31 E-value=8.1 Score=21.25 Aligned_cols=49 Identities=16% Similarity=0.199 Sum_probs=33.4
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHH---HHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIAD---YKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~---~k~~~p~ifawEiR~~L~~ 55 (67)
|..|.+.|-+.|.. .....+.-+++.+..+.. ++. -++..-||++.|.+
T Consensus 17 lr~y~~~gll~~~~-~~~g~r~y~~~dv~~l~~i~~l~~--~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 17 LRYYEREGLLPPPR-DENGYRYYSEEDVERLREIKELRK--QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHTTSSTTBE-STTSSEEE-HHHHHHHHHHHHHHH--TTTHHHHHHHHH--
T ss_pred HHHHHHhcCccccc-ccCceeeccHHHHHHHHHHHHHHH--CcCCHHHHHHHHcc
Confidence 67889999999988 333446667766665554 444 58999999988754
No 22
>cd04852 Peptidases_S8_3 Peptidase S8 family domain, uncharacterized subfamily 3. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=67.09 E-value=6.9 Score=27.62 Aligned_cols=33 Identities=21% Similarity=0.177 Sum_probs=28.5
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+.-+++.+|++..-|||+.|+.
T Consensus 272 TS~AaP~vaG~aALl~~~~p~~t~~~v~~~L~~ 304 (307)
T cd04852 272 TSMASPHVAGVAALLKSAHPDWSPAAIKSALMT 304 (307)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 356688888888888999999999999999975
No 23
>cd07474 Peptidases_S8_subtilisin_Vpr-like Peptidase S8 family domain in Vpr-like proteins. The maturation of the peptide antibiotic (lantibiotic) subtilin in Bacillus subtilis ATCC 6633 includes posttranslational modifications of the propeptide and proteolytic cleavage of the leader peptide. Vpr was identified as one of the proteases, along with WprA, that are capable of processing subtilin. Asp, Ser, His triadPeptidases S8 or Subtilases are a serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=67.01 E-value=7.6 Score=26.81 Aligned_cols=36 Identities=19% Similarity=0.170 Sum_probs=31.1
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCc
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGV 58 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gv 58 (67)
.+.++|-|.-.+.-+++.+|.+...++|+.|+.-..
T Consensus 235 TS~AaP~vaG~aAll~~~~p~l~~~~v~~~L~~tA~ 270 (295)
T cd07474 235 TSMAAPHVAGAAALLKQAHPDWSPAQIKAALMNTAK 270 (295)
T ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhCc
Confidence 457788899999999999999999999999987654
No 24
>cd07494 Peptidases_S8_10 Peptidase S8 family domain, uncharacterized subfamily 10. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=65.21 E-value=10 Score=27.22 Aligned_cols=36 Identities=17% Similarity=0.030 Sum_probs=30.2
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcC
Q psy2182 22 KPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEG 57 (67)
Q Consensus 22 kpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~G 57 (67)
--+.++|-|.-.+.-+++.+|++...+||+.|.+--
T Consensus 247 GTS~Aap~vaG~aAll~~~~p~~~~~~v~~~l~~ta 282 (298)
T cd07494 247 GTSAAAPQVAGVCALMLQANPGLSPERARSLLNKTA 282 (298)
T ss_pred cchHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence 345778888888888899999999999999997644
No 25
>cd07473 Peptidases_S8_Subtilisin_like Peptidase S8 family domain in Subtilisin-like proteins. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=62.94 E-value=12 Score=25.37 Aligned_cols=33 Identities=27% Similarity=0.255 Sum_probs=29.7
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+.-+.+.+|.+...|+|+.|+.
T Consensus 224 TS~AaP~vaG~~All~~~~~~~t~~~v~~~L~~ 256 (259)
T cd07473 224 TSMATPHVAGAAALLLSLNPNLTAAQIKDAILS 256 (259)
T ss_pred HhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 467888899999999999999999999999975
No 26
>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=62.93 E-value=23 Score=21.98 Aligned_cols=52 Identities=13% Similarity=0.011 Sum_probs=37.6
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L~~ 55 (67)
|.-|-+.|-+.|.....+.-+.-+++++..+...+. ..-++..-||++-|..
T Consensus 17 lR~ye~~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (107)
T cd01111 17 VRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA 69 (107)
T ss_pred HHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 455778899999654444566778888777777655 4468999999987743
No 27
>cd07487 Peptidases_S8_1 Peptidase S8 family domain, uncharacterized subfamily 1. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=62.18 E-value=14 Score=24.85 Aligned_cols=33 Identities=24% Similarity=0.121 Sum_probs=29.4
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+..+.+.+|.+..-|||+.|+.
T Consensus 229 TS~Aap~vaG~~All~~~~p~~~~~~ik~~L~~ 261 (264)
T cd07487 229 TSMATPHVSGAIALLLQANPILTPDEVKCILRD 261 (264)
T ss_pred cchHHHHHHHHHHHHHHHCcCCCHHHHHHHHHh
Confidence 467788999999999999999999999999975
No 28
>cd07496 Peptidases_S8_13 Peptidase S8 family domain, uncharacterized subfamily 13. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=62.14 E-value=9.9 Score=26.48 Aligned_cols=33 Identities=24% Similarity=0.149 Sum_probs=28.6
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
-+.++|-|.-.+.-+.+.+|++...|||+.|..
T Consensus 252 TS~AaP~vaG~aAlv~~~~p~lt~~~v~~~L~~ 284 (285)
T cd07496 252 TSMAAPHVAGVAALMKSVNPSLTPAQIESLLQS 284 (285)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence 356788888888888999999999999999864
No 29
>cd07482 Peptidases_S8_Lantibiotic_specific_protease Peptidase S8 family domain in Lantiobiotic (lanthionine-containing antibiotics) specific proteases. Lantiobiotic (lanthionine-containing antibiotics) specific proteases are very similar in structure to serine proteases. Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides with antimicrobial activities against Gram-positive bacteria. The proteases that cleave the N-terminal leader peptides from lantiobiotics include: epiP, nsuP, mutP, and nisP. EpiP, from Staphylococcus, is thought to cleave matured epidermin. NsuP, a dehydratase from Streptococcus and NisP, a membrane-anchored subtilisin-like serine protease from Lactococcus cleave nisin. MutP is highly similar to epiP and nisP and is thought to process the prepeptide mutacin III of S. mutans. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and exopeptidases. The S8 family h
Probab=62.12 E-value=12 Score=25.74 Aligned_cols=34 Identities=18% Similarity=-0.031 Sum_probs=29.8
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCccH-HHHHHHHHh
Q psy2182 22 KPRVATNGVVTKIADYKRECPSIFA-WEIRDRLLA 55 (67)
Q Consensus 22 kpk~~t~~v~~~I~~~k~~~p~ifa-wEiR~~L~~ 55 (67)
-.+.++|-|.-.+.-+.+++|.+.. -|||+.|.+
T Consensus 259 GTS~AaP~VaG~aAll~~~~p~~~~~~~v~~~L~~ 293 (294)
T cd07482 259 GTSLAAPKVSGALALIIDKNPLKKPPDEAIRILYN 293 (294)
T ss_pred chhhhhHHHHHHHHHHHHHCCCCCcHHHHHHHHhh
Confidence 3567899999999999999999999 999999874
No 30
>cd07477 Peptidases_S8_Subtilisin_subset Peptidase S8 family domain in Subtilisin proteins. This group is composed of many different subtilisins: Pro-TK-subtilisin, subtilisin Carlsberg, serine protease Pb92 subtilisin, and BPN subtilisins just to name a few. Pro-TK-subtilisin is a serine protease from the hyperthermophilic archaeon Thermococcus kodakaraensis and consists of a signal peptide, a propeptide, and a mature domain. TK-subtilisin is matured from pro-TK-subtilisin upon autoprocessing and degradation of the propeptide. Unlike other subtilisins though, the folding of the unprocessed form of pro-TK-subtilisin is induced by Ca2+ binding which is almost completed prior to autoprocessing. Ca2+ is required for activity unlike the bacterial subtilisins. The propeptide is not required for folding of the mature domain unlike the bacterial subtilases because of the stability produced from Ca2+ binding. Subtilisin Carlsberg is extremely similar in structure to subtilisin BPN'/Novo thoug
Probab=61.96 E-value=12 Score=24.76 Aligned_cols=33 Identities=21% Similarity=0.118 Sum_probs=29.7
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.+.++|-+...+..+++.+|.+..-+||+.|..
T Consensus 196 TS~Aap~vag~~All~~~~~~~~~~~i~~~l~~ 228 (229)
T cd07477 196 TSMATPHVAGVAALVWSKRPELTNAQVRQALNK 228 (229)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence 567889999999999999999999999999874
No 31
>cd04077 Peptidases_S8_PCSK9_ProteinaseK_like Peptidase S8 family domain in ProteinaseK-like proteins. The peptidase S8 or Subtilase clan of proteases have a Asp/His/Ser catalytic triad that is not homologous to trypsin. This CD contains several members of this clan including: PCSK9 (Proprotein convertase subtilisin/kexin type 9), Proteinase_K, Proteinase_T, and other subtilisin-like serine proteases. PCSK9 posttranslationally regulates hepatic low-density lipoprotein receptors (LDLRs) by binding to LDLRs on the cell surface, leading to their degradation. The binding site of PCSK9 has been localized to the epidermal growth factor-like repeat A (EGF-A) domain of the LDLR. Characterized Proteinases K are secreted endopeptidases with a high degree of sequence conservation. Proteinases K are not substrate-specific and function in a wide variety of species in different pathways. It can hydrolyze keratin and other proteins with subtilisin-like specificity. The number of calcium-binding moti
Probab=60.33 E-value=12 Score=25.45 Aligned_cols=34 Identities=24% Similarity=0.175 Sum_probs=30.3
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
-+.++|-|.-.+.-+.+.+|.+..-|||+.|+.-
T Consensus 219 TS~Aap~vaG~~All~~~~p~~~~~~v~~~L~~t 252 (255)
T cd04077 219 TSMAAPHVAGLAAYLLSLGPDLSPAEVKARLLNL 252 (255)
T ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Confidence 4678899999999999999999999999999853
No 32
>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=59.99 E-value=28 Score=20.98 Aligned_cols=50 Identities=26% Similarity=0.141 Sum_probs=32.6
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHH---HHHHHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTK---IADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~---I~~~k~~~p~ifawEiR~~L~~ 55 (67)
|.-|.+.|-+.|-..+.+.-+.-+++.+.. |..++.. ++..-||++-|..
T Consensus 17 lR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~--G~~l~eI~~~l~~ 69 (97)
T cd04782 17 LFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKEL--GISLKEIKDYLDN 69 (97)
T ss_pred HHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHhc
Confidence 456778899999654444455556655444 4444444 7999999987653
No 33
>cd07481 Peptidases_S8_BacillopeptidaseF-like Peptidase S8 family domain in BacillopeptidaseF-like proteins. Bacillus subtilis produces and secretes proteases and other types of exoenzymes at the end of the exponential phase of growth. The ones that make up this group is known as bacillopeptidase F, encoded by bpr, a serine protease with high esterolytic activity which is inhibited by PMSF. Like other members of the peptidases S8 family these have a Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity.
Probab=59.38 E-value=12 Score=25.82 Aligned_cols=33 Identities=18% Similarity=-0.093 Sum_probs=28.6
Q ss_pred CCcCCHHHHHHHHHHHhhCCC--ccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPS--IFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~--ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+.-+++++|+ +..-|||+.|..
T Consensus 227 TS~AaP~vaG~aAll~~~~p~~~l~~~~v~~~L~~ 261 (264)
T cd07481 227 TSMAAPHVAGVAALLWSANPSLIGDVDATEAILTE 261 (264)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHH
Confidence 456778898888889999999 999999999875
No 34
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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=59.13 E-value=19 Score=21.94 Aligned_cols=52 Identities=12% Similarity=0.026 Sum_probs=35.8
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhC--CCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKREC--PSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~--p~ifawEiR~~L~~ 55 (67)
|.-|.+.|-|.|-.-.++--+.-+++.+..+...+.-. =++..-||++.|-.
T Consensus 17 lR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 17 IKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 44577889998843322222467888888887766543 48999999987765
No 35
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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 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 dissimilar C-terminal domains bind specific coactivator molecules.
Probab=58.63 E-value=29 Score=20.61 Aligned_cols=52 Identities=15% Similarity=0.091 Sum_probs=34.8
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHH---HHHhhCCCccHHHHHHHHHhcC
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIA---DYKRECPSIFAWEIRDRLLAEG 57 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~---~~k~~~p~ifawEiR~~L~~~G 57 (67)
|..|.+.|-+.|....+...+.-+++.+..+. .++. -++..-||++.|..+.
T Consensus 18 LR~ye~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~--~G~sl~~i~~~l~~~~ 72 (88)
T cd01105 18 LRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLD--EGFTLAAAVEKLRRRR 72 (88)
T ss_pred HHHHHHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHcc
Confidence 55677899998866543334445565554444 4444 5899999999888765
No 36
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=58.49 E-value=18 Score=23.86 Aligned_cols=28 Identities=25% Similarity=0.146 Sum_probs=24.8
Q ss_pred HHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 32 TKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 32 ~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
+.|.++.++++-..+.||.++|.+.|+.
T Consensus 5 ~~i~~Li~~~~i~tqeeL~~~L~~~G~~ 32 (146)
T TIGR01529 5 ERIKEIITEEKISTQEELVALLKAEGIE 32 (146)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHhCCC
Confidence 4677888899999999999999999985
No 37
>cd07490 Peptidases_S8_6 Peptidase S8 family domain, uncharacterized subfamily 6. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=58.39 E-value=15 Score=24.77 Aligned_cols=32 Identities=22% Similarity=0.183 Sum_probs=28.2
Q ss_pred CcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 24 RVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 24 k~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
+.++|-|.-.+..+++.+|++..-+||+.|+.
T Consensus 220 S~AaP~vaG~aAl~~~~~p~~~~~~i~~~L~~ 251 (254)
T cd07490 220 SMAAPHVAGVAALLAAAHPDLSPEQIKDALTE 251 (254)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 45688888888889999999999999999975
No 38
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=57.16 E-value=24 Score=21.70 Aligned_cols=33 Identities=21% Similarity=0.104 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhhCCCccHHHHHHHHHhcCcCC
Q psy2182 28 NGVVTKIADYKRECPSIFAWEIRDRLLAEGVCN 60 (67)
Q Consensus 28 ~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc~ 60 (67)
+-..+.|.+|-...-.|.|-|+++.|++.|=..
T Consensus 3 ~~e~~~i~~yi~n~~~Isa~elcE~LI~~~~~~ 35 (78)
T PF13034_consen 3 ELEKEFINWYIQNEEEISARELCEYLIENGGSP 35 (78)
T ss_pred HHHHHHHHHHHhccccccHHHHHHHHHHcCCCc
Confidence 345567888888878999999999999988653
No 39
>PF15311 HYLS1_C: Hydrolethalus syndrome protein 1 C-terminus
Probab=56.94 E-value=11 Score=23.69 Aligned_cols=13 Identities=31% Similarity=0.917 Sum_probs=11.6
Q ss_pred cHHHHHHHHHhcC
Q psy2182 45 FAWEIRDRLLAEG 57 (67)
Q Consensus 45 fawEiR~~L~~~G 57 (67)
.=|+||++|+.+.
T Consensus 43 lRw~IRe~ml~~~ 55 (89)
T PF15311_consen 43 LRWNIREQMLYQD 55 (89)
T ss_pred HHHHHHHHHHhCC
Confidence 4599999999988
No 40
>cd07484 Peptidases_S8_Thermitase_like Peptidase S8 family domain in Thermitase-like proteins. Thermitase is a non-specific, trypsin-related serine protease with a very high specific activity. It contains a subtilisin like domain. The tertiary structure of thermitase is similar to that of subtilisin BPN'. It contains a Asp/His/Ser catalytic triad. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid
Probab=56.78 E-value=13 Score=25.23 Aligned_cols=33 Identities=30% Similarity=0.238 Sum_probs=28.6
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
.+.++|-|...+.-+++.+| +...+||+.|+.-
T Consensus 223 TS~Aap~vag~~Al~~~~~p-~t~~~i~~~L~~t 255 (260)
T cd07484 223 TSMATPHVAGVAALLYSQGP-LSASEVRDALKKT 255 (260)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CCHHHHHHHHHHh
Confidence 35778889999999999999 9999999999863
No 41
>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=56.70 E-value=25 Score=21.65 Aligned_cols=52 Identities=12% Similarity=-0.029 Sum_probs=34.8
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhC-CCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKREC-PSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~-p~ifawEiR~~L~~ 55 (67)
|..|.+.|-+.|..-.++.-+.-++..+..+...+.-. -++..-||++-|..
T Consensus 17 lR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 17 LRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred HHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 56788899999876544455556666555555543333 37889999988764
No 42
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=54.56 E-value=32 Score=18.68 Aligned_cols=49 Identities=12% Similarity=0.138 Sum_probs=28.1
Q ss_pred cchhhhc-ccccccccCCCCCCcCCHHHHHHHHHHHhhC-CCccHHHHHHHH
Q psy2182 4 EEGYYET-GSIKPRAIGGSKPRVATNGVVTKIADYKREC-PSIFAWEIRDRL 53 (67)
Q Consensus 4 L~Ry~eT-Gsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~-p~ifawEiR~~L 53 (67)
|.+|.+. |-+.|..-.+. .+.-+++.+..+..++.-. -++..-||++-|
T Consensus 17 lr~w~~~~g~~~~~r~~~~-~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 17 LRAWERRYGLPAPQRTDGG-HRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHhCCCCCCCcCCCC-CeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 4556653 76666543332 2445555555555443322 589999998866
No 43
>cd05561 Peptidases_S8_4 Peptidase S8 family domain, uncharacterized subfamily 4. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=54.41 E-value=14 Score=25.40 Aligned_cols=33 Identities=24% Similarity=0.209 Sum_probs=28.6
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
-+.++|-|.-.+..+++.+| +...+|++.|++-
T Consensus 191 TS~AaP~vaG~aAll~~~~p-~~~~~i~~~L~~t 223 (239)
T cd05561 191 TSFAAPFVTAALALLLQASP-LAPDDARARLAAT 223 (239)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CCHHHHHHHHHHH
Confidence 45778888888888999999 9999999999864
No 44
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.46 E-value=27 Score=22.36 Aligned_cols=28 Identities=29% Similarity=0.428 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 26 ATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 26 ~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.|+...++|+++.+. | --.|.+||-|..
T Consensus 35 ~t~~~lekil~~tqr-~-~dvW~lRd~l~~ 62 (97)
T COG4367 35 WTEVKLEKILQVTQR-P-ADVWRLRDFLVQ 62 (97)
T ss_pred CCHHHHHHHHHHhhc-c-chhHHHHHHHHH
Confidence 578889999999865 4 667999998875
No 45
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=51.72 E-value=28 Score=24.54 Aligned_cols=43 Identities=30% Similarity=0.376 Sum_probs=27.3
Q ss_pred cccCCCCCCcCCHH---HHHHHHHHHhh-CCCccHHHHHHHHHhcCc
Q psy2182 16 RAIGGSKPRVATNG---VVTKIADYKRE-CPSIFAWEIRDRLLAEGV 58 (67)
Q Consensus 16 g~iGGskpk~~t~~---v~~~I~~~k~~-~p~ifawEiR~~L~~~Gv 58 (67)
.+.|||+|+..+.+ +...+..|... -.+--.++.|++|+...+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~Lv~~~l 50 (264)
T PRK07122 4 RAAGGSRPRASTDEYADVPEMFRELAGLPAGSPEFQRQRDRIVTRCL 50 (264)
T ss_pred ccCCCCCCCCchhhhhhHHHHHHHHHhccCCCHHHHHHHHHHHHHhH
Confidence 46799999977654 44556666421 124445667888887543
No 46
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=51.67 E-value=50 Score=19.98 Aligned_cols=53 Identities=17% Similarity=-0.008 Sum_probs=37.9
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhh-CCCccHHHHHHHHHhc
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRE-CPSIFAWEIRDRLLAE 56 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~-~p~ifawEiR~~L~~~ 56 (67)
|.-|.+-|-|.|-.-..+.-|.-+++....+...+.- .=++..-||++-|-..
T Consensus 17 LRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~~ 70 (124)
T COG0789 17 LRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDLL 70 (124)
T ss_pred HHHHHHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 4567888999998766556666777766666654433 3589999999988654
No 47
>PF11554 DUF3232: Protein of unknown function (DUF3232); InterPro: IPR021618 This bacterial family of proteins has no known function. ; PDB: 2RDC_A.
Probab=51.22 E-value=6.4 Score=27.03 Aligned_cols=39 Identities=18% Similarity=0.149 Sum_probs=28.6
Q ss_pred cccchhhhcccccc----cccCCCCCCcCCHHHHHHHHHHHhh
Q psy2182 2 YSEEGYYETGSIKP----RAIGGSKPRVATNGVVTKIADYKRE 40 (67)
Q Consensus 2 ~~L~Ry~eTGsi~P----g~iGGskpk~~t~~v~~~I~~~k~~ 40 (67)
|||||+.+--...| |-.||++++.-.-+-...|.++.-+
T Consensus 99 kIlNR~aek~~~~~l~~a~f~Gn~e~r~evaef~~aIvdf~ge 141 (152)
T PF11554_consen 99 KILNRMAEKENQEPLSEAGFQGNIEDRPEVAEFCQAIVDFCGE 141 (152)
T ss_dssp HHHHHHHHHHHHHHHHHTT-TTTTSS-STTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCcccccccccCCCCCChhHHHHHHHHHHHhhh
Confidence 79999999888876 6789999998877777777774433
No 48
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=50.76 E-value=56 Score=19.95 Aligned_cols=51 Identities=16% Similarity=0.046 Sum_probs=34.5
Q ss_pred hhhhc-ccccccccCCCCCCcCCHHHHHHHHHHHh--hCCCccHHHHHHHHHhcC
Q psy2182 6 GYYET-GSIKPRAIGGSKPRVATNGVVTKIADYKR--ECPSIFAWEIRDRLLAEG 57 (67)
Q Consensus 6 Ry~eT-Gsi~Pg~iGGskpk~~t~~v~~~I~~~k~--~~p~ifawEiR~~L~~~G 57 (67)
.|.+. |-+.|-.-.| ..+.-+++.+..+...+. ..-++..-||++.|...+
T Consensus 19 ~ye~~~gli~p~r~~~-g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~ 72 (99)
T cd04765 19 YWETEFPQLKPVKRAG-GRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDG 72 (99)
T ss_pred HHHHHcCCCCCcCCCC-CCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcc
Confidence 34334 7777744332 355677887777777765 457899999999887643
No 49
>PF10061 DUF2299: Uncharacterized conserved protein (DUF2299); InterPro: IPR018747 Members of this family of hypothetical bacterial proteins have no known function. ; PDB: 3CXJ_D.
Probab=50.68 E-value=6.2 Score=26.13 Aligned_cols=33 Identities=27% Similarity=0.328 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 27 TNGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 27 t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
.+.|.+.+..++.+...=|.|+|+..|+.-++|
T Consensus 57 ~~~H~~~l~~l~~~eR~~fl~~i~~~ll~~~vd 89 (138)
T PF10061_consen 57 SPEHQRALRSLKPEEREEFLWEIKRELLRMPVD 89 (138)
T ss_dssp -HHHHHHHHHS-HHHHHHHHHHHHHHHTTTT-E
T ss_pred CHHHHHHHHhCCHHHHHHHHHHHHHHHHhCCCc
Confidence 578888898887777777999999999999887
No 50
>cd07485 Peptidases_S8_Fervidolysin_like Peptidase S8 family domain in Fervidolysin. Fervidolysin found in Fervidobacterium pennivorans is an extracellular subtilisin-like keratinase. It is contains a signal peptide, a propeptide, and a catalytic region. The tertiary structure of fervidolysin is similar to that of subtilisin. It contains a Asp/His/Ser catalytic triad and is a member of the peptidase S8 (subtilisin and kexin) family. The catalytic triad is similar to that found in trypsin-like proteases, but it does not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. Howev
Probab=50.51 E-value=24 Score=24.41 Aligned_cols=33 Identities=21% Similarity=0.095 Sum_probs=29.3
Q ss_pred CCcCCHHHHHHHHHHHhhCCC-ccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPS-IFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~-ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+.-+++.+|. +..-|||+.|..
T Consensus 239 TS~AaP~VaG~aAll~~~~~~~~~~~~i~~~L~~ 272 (273)
T cd07485 239 TSMAAPHVSGVAALVLSKFPDVFTPEQIRKLLEE 272 (273)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHh
Confidence 468899999999999999999 999999998864
No 51
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=50.15 E-value=12 Score=26.51 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=25.8
Q ss_pred ccchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHH--HhcCcCC
Q psy2182 3 SEEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRL--LAEGVCN 60 (67)
Q Consensus 3 ~L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L--~~~Gvc~ 60 (67)
+||||.. |++-|+. +...+.+..+....+. +.|+++++ ...|..+
T Consensus 39 ~l~RYv~-g~~~P~~----------~~a~~~~~~l~~~~~~--~~~l~~ri~~~~~gy~d 85 (238)
T PRK08558 39 VLNRYVN-GHVLPSV----------ERAREIVEKLGPYYNL--EEEVKARIKVDDEGYVD 85 (238)
T ss_pred HHHHHHc-CCcCCCH----------HHHHHHHHHHHHhhhh--HHHHHhhcccCCCCEEE
Confidence 5899987 8888873 3444444444444222 35566666 5555544
No 52
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=49.56 E-value=31 Score=21.45 Aligned_cols=31 Identities=32% Similarity=0.336 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHhhC-CCccHHHHHHHHHhc
Q psy2182 26 ATNGVVTKIADYKREC-PSIFAWEIRDRLLAE 56 (67)
Q Consensus 26 ~t~~v~~~I~~~k~~~-p~ifawEiR~~L~~~ 56 (67)
.|++-++.|..+-+.+ .++|--+-|.+|+++
T Consensus 31 it~~QA~~I~~~lr~k~inIfn~~~r~~llke 62 (85)
T PF11116_consen 31 ITKKQAEQIANILRGKNINIFNEQERKKLLKE 62 (85)
T ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 4677778888875555 499999999999875
No 53
>PRK13749 transcriptional regulator MerD; Provisional
Probab=49.06 E-value=64 Score=20.81 Aligned_cols=51 Identities=12% Similarity=0.023 Sum_probs=37.3
Q ss_pred hhhhcccccccccCCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHHHhc
Q psy2182 6 GYYETGSIKPRAIGGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 6 Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L~~~ 56 (67)
=|.+.|=+.|-.-.-+.-+.-+++++..+..++. ..-++.+-||++-|.-.
T Consensus 22 ~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~ 73 (121)
T PRK13749 22 DYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRAL 73 (121)
T ss_pred HHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhh
Confidence 3566788888655445556778888888877765 44699999999887654
No 54
>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=48.45 E-value=61 Score=19.67 Aligned_cols=51 Identities=16% Similarity=0.162 Sum_probs=35.7
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~ 54 (67)
|..|.+.|-+.|-.-+..--+.-+++.+..+...+.-..++-.-++++-+.
T Consensus 17 lR~Ye~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i~~~~~ 67 (99)
T cd04772 17 VRNYESLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQRIMR 67 (99)
T ss_pred HHHHHHcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence 456888899988544444456678888888777766545777888876443
No 55
>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=48.44 E-value=44 Score=20.13 Aligned_cols=50 Identities=22% Similarity=0.165 Sum_probs=33.8
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHH---HHHHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKI---ADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I---~~~k~~~p~ifawEiR~~L~~ 55 (67)
|..|.+.|-+.|..-++...+.-+++.+..+ ..++. -++..-||+.-+-.
T Consensus 17 lR~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~--~g~~l~~i~~~~~~ 69 (103)
T cd01106 17 LHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKE--LGFSLKEIKELLKD 69 (103)
T ss_pred HHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHH--cCCCHHHHHHHHHc
Confidence 4568889999886554444466677666554 44444 48999999887643
No 56
>cd04847 Peptidases_S8_Subtilisin_like_2 Peptidase S8 family domain in Subtilisin-like proteins. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=47.47 E-value=27 Score=24.38 Aligned_cols=32 Identities=22% Similarity=0.120 Sum_probs=28.2
Q ss_pred CcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 24 RVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 24 k~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
+.++|-|......+.+++|++..-+||+.|+.
T Consensus 257 S~AaP~Vag~aAll~~~~p~~t~~~ikalL~~ 288 (291)
T cd04847 257 SFAAPLAARLAAGLFAELPELSPETIRALLIH 288 (291)
T ss_pred hHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHh
Confidence 56788888888889999999999999999974
No 57
>cd00306 Peptidases_S8_S53 Peptidase domain in the S8 and S53 families. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. However, the aspartic acid residue that acts as an electrophile is quite different. In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members hav
Probab=46.92 E-value=30 Score=21.99 Aligned_cols=34 Identities=18% Similarity=0.132 Sum_probs=29.9
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 22 KPRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 22 kpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
-.+.++|-+.-.+.-+++.+|++..-|+|+.|+.
T Consensus 207 GTS~Aap~vaG~~Al~~~~~~~~~~~~~~~~l~~ 240 (241)
T cd00306 207 GTSMAAPIVAGVAALLLSANPDLTPAQVKAALLS 240 (241)
T ss_pred cHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhh
Confidence 4567889999999999999999999999998864
No 58
>PF00082 Peptidase_S8: Subtilase family This is family S8 in the peptidase classification. ; InterPro: IPR000209 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 group of serine peptidases belong to the MEROPS peptidase families S8 (subfamilies S8A (subtilisin) and S8B (kexin)) and S53 (sedolisin) both of which are members of clan SB. The subtilisin family is the second largest serine protease family characterised to date. Over 200 subtilises are presently known, more than 170 of which with their complete amino acid sequence []. It is widespread, being found in eubacteria, archaebacteria, eukaryotes and viruses []. The vast majority of the family are endopeptidases, although there is an exopeptidase, tripeptidyl peptidase [, ]. Structures have been determined for several members of the subtilisin family: they exploit the same catalytic triad as the chymotrypsins, although the residues occur in a different order (HDS in chymotrypsin and DHS in subtilisin), but the structures show no other similarity [, ]. Some subtilisins are mosaic proteins, while others contain N- and C-terminal extensions that show no sequence similarity to any other known protein []. Based on sequence homology, a subdivision into six families has been proposed []. The proprotein-processing endopeptidases kexin, furin and related enzymes form a distinct subfamily known as the kexin subfamily (S8B). These preferentially cleave C-terminally to paired basic amino acids. Members of this subfamily can be identified by subtly different motifs around the active site [, ]. Members of the kexin family, along with endopeptidases R, T and K from the yeast Tritirachium and cuticle-degrading peptidase from Metarhizium, require thiol activation. This can be attributed to the presence of Cys-173 near to the active histidine [].Only 1 viral member of the subtilisin family is known, a 56kDa protease from herpes virus 1, which infects the channel catfish []. Sedolisins (serine-carboxyl peptidases) are proteolytic enzymes whose fold resembles that of subtilisin; however, they are considerably larger, with the mature catalytic domains containing approximately 375 amino acids. The defining features of these enzymes are a unique catalytic triad, Ser-Glu-Asp, as well as the presence of an aspartic acid residue in the oxyanion hole. High-resolution crystal structures have now been solved for sedolisin from Pseudomonas sp. 101, as well as for kumamolisin from a thermophilic bacterium, Bacillus sp. MN-32. Mutations in the human gene leads to a fatal neurodegenerative disease []. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3EIF_A 1XF1_B 3F7M_A 3F7O_B 2QTW_B 2W2O_A 3GCX_A 3P5B_A 3M0C_B 2XTJ_A ....
Probab=45.02 E-value=25 Score=23.70 Aligned_cols=33 Identities=21% Similarity=0.171 Sum_probs=28.5
Q ss_pred CcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 24 RVATNGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 24 k~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
+.++|-+...+..+.+.+|.+..-|||+.|+.-
T Consensus 222 S~Aap~vag~~All~~~~p~~~~~~i~~~l~~t 254 (282)
T PF00082_consen 222 SFAAPVVAGAAALLLSKYPNLTPAEIKALLINT 254 (282)
T ss_dssp HHHHHHHHHHHHHHHHHSTTSHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHCCCCCHHHHHHHHHHh
Confidence 467888999999999999999999999977654
No 59
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=44.88 E-value=25 Score=19.42 Aligned_cols=24 Identities=38% Similarity=0.619 Sum_probs=13.3
Q ss_pred HHHHHHHhhCC---CccHHHHHHHHHh
Q psy2182 32 TKIADYKRECP---SIFAWEIRDRLLA 55 (67)
Q Consensus 32 ~~I~~~k~~~p---~ifawEiR~~L~~ 55 (67)
+.+.+|.++|| +|---|+|.++..
T Consensus 3 ~~L~~yH~~~Plr~G~~keeLrsrl~~ 29 (59)
T PF09106_consen 3 EILAEYHRENPLRPGMPKEELRSRLFK 29 (59)
T ss_dssp HHHHHHHHH-TTSS-EEHHHHHHHCST
T ss_pred HHHHHHHHHCcCccCcCHHHHHHHHhh
Confidence 45566666665 6666666665543
No 60
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=43.77 E-value=22 Score=22.24 Aligned_cols=30 Identities=20% Similarity=0.362 Sum_probs=23.9
Q ss_pred cCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 25 VATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 25 ~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
..++++++.|++++...|.- .|-+||-|.+
T Consensus 34 ~~s~~~le~vL~l~~~~~~~-vW~lRdyL~~ 63 (89)
T PF10078_consen 34 GTSPEHLEQVLNLKQPFPED-VWILRDYLND 63 (89)
T ss_pred CCCHHHHHHHHcCCCCCccc-chHHHHHHHH
Confidence 35788999999999777643 6999998765
No 61
>PF03584 Herpes_ICP4_N: Herpesvirus ICP4-like protein N-terminal region; InterPro: IPR005206 The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0042025 host cell nucleus
Probab=43.67 E-value=27 Score=24.48 Aligned_cols=40 Identities=18% Similarity=0.292 Sum_probs=30.0
Q ss_pred cccccccccCCCCCCcC-CHHHHHHHHHHHhhCC--CccHHHH
Q psy2182 10 TGSIKPRAIGGSKPRVA-TNGVVTKIADYKRECP--SIFAWEI 49 (67)
Q Consensus 10 TGsi~Pg~iGGskpk~~-t~~v~~~I~~~k~~~p--~ifawEi 49 (67)
.|.++-|.+|++++... .|+|++.+..|-...- -.|.-|+
T Consensus 14 ~grv~~Gg~Gd~R~gLwd~peV~~A~~rf~as~~p~pVyv~Em 56 (173)
T PF03584_consen 14 PGRVRYGGSGDSRPGLWDDPEVREAAARFEASPGPVPVYVPEM 56 (173)
T ss_pred CCceeeCCCCCCCccccCCHHHHHHHHHHHhccCCcceehHhh
Confidence 37788899999999755 8999999999866543 3444443
No 62
>PF01799 Fer2_2: [2Fe-2S] binding domain; InterPro: IPR002888 The [2Fe-2S] binding domain is found in a range of enzymes including dehydrogenases, oxidases and oxidoreductases. The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands [].; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 2E3T_A 1WYG_A 3AN1_B 2E1Q_C 2CKJ_A 3B9J_I 3NVY_J 1FO4_B 3NRZ_J 3AM9_A ....
Probab=43.44 E-value=36 Score=20.26 Aligned_cols=34 Identities=26% Similarity=0.392 Sum_probs=24.9
Q ss_pred cCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 25 VATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 25 ~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
-=||..+-.+..+.+++|.-.-.|||+.|.. .+|
T Consensus 28 fCtpG~im~~~~ll~~~~~p~~~ei~~al~g-nlC 61 (75)
T PF01799_consen 28 FCTPGMIMAAYALLRRNPDPTEEEIREALSG-NLC 61 (75)
T ss_dssp SSHHHHHHHHHHHHHHSSS-CHHHHHHHTTT-S--
T ss_pred cchHHHHHHHHHHhhcccchhhHHHHHHHHc-Ccc
Confidence 3467777778888899999999999998864 444
No 63
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=43.17 E-value=48 Score=19.55 Aligned_cols=30 Identities=20% Similarity=0.065 Sum_probs=21.9
Q ss_pred HHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 30 VVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 30 v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
-.+.|.++-++++=-...||.+.|.+.|+.
T Consensus 6 R~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~ 35 (70)
T PF01316_consen 6 RQELIKELISEHEISSQEELVELLEEEGIE 35 (70)
T ss_dssp HHHHHHHHHHHS---SHHHHHHHHHHTT-T
T ss_pred HHHHHHHHHHHCCcCCHHHHHHHHHHcCCC
Confidence 346788888888888889999999999985
No 64
>PF08218 Citrate_ly_lig: Citrate lyase ligase C-terminal domain; InterPro: IPR013166 [Citrate (pro-3S)-lyase] ligase (6.2.1.22 from EC), also known as citrate lyase ligase, is responsible for acetylation of the prosthetic group (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase. It converts the inactive thiol form of the enzyme to the active form. In Clostridium sphenoides, citrate lyase ligase actively degrades citrate. In Clostridium sporosphaeroides and Lactococcus lactis, however, the enzyme is under stringent regulatory control. The enzyme's activity in anaerobic bacteria is modulated by phosphorylation and dephosphorylation []. The proteins in this entry represent the C-terminal domain of citrate lyase ligase.; GO: 0008771 [citrate (pro-3S)-lyase] ligase activity
Probab=43.07 E-value=16 Score=25.67 Aligned_cols=36 Identities=28% Similarity=0.362 Sum_probs=27.9
Q ss_pred HHHHHHHHHHh-----------hCCCccHHHHHHHHHhcCcCCCCCC
Q psy2182 29 GVVTKIADYKR-----------ECPSIFAWEIRDRLLAEGVCNNDNI 64 (67)
Q Consensus 29 ~v~~~I~~~k~-----------~~p~ifawEiR~~L~~~Gvc~~~~~ 64 (67)
-|.-+|++--+ |+.+.|..+.|-.|+++|+.+-.||
T Consensus 14 GH~yLiE~Aa~~~d~l~vFVV~eD~S~Fpf~~R~~LVk~G~~~L~NV 60 (182)
T PF08218_consen 14 GHRYLIEQAAKECDWLHVFVVSEDRSLFPFADRYELVKEGTADLPNV 60 (182)
T ss_pred HHHHHHHHHHHhCCEEEEEEEccccCcCCHHHHHHHHHHHhCcCCCE
Confidence 45555655544 4478999999999999999988776
No 65
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=42.63 E-value=27 Score=21.64 Aligned_cols=34 Identities=24% Similarity=0.385 Sum_probs=23.2
Q ss_pred cccchhhhccc-------ccccccCCCCCCcCCHHHHHHHHHHHh
Q psy2182 2 YSEEGYYETGS-------IKPRAIGGSKPRVATNGVVTKIADYKR 39 (67)
Q Consensus 2 ~~L~Ry~eTGs-------i~Pg~iGGskpk~~t~~v~~~I~~~k~ 39 (67)
|-+.||.+.|. =+|. ..|..+.++++..|.++++
T Consensus 44 kW~~Ryra~G~~GL~DRSSRP~----~sP~~t~~~~~~~I~~lRr 84 (85)
T PF13011_consen 44 KWLARYRAEGEAGLQDRSSRPH----RSPRRTPPEVERRIIELRR 84 (85)
T ss_pred HHHHHHHHcCcccccccCCCCC----CCCccCCHHHHHHHHHHhc
Confidence 55788888773 2332 2455667889999988775
No 66
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=42.40 E-value=65 Score=18.28 Aligned_cols=27 Identities=15% Similarity=0.258 Sum_probs=20.4
Q ss_pred CHHHHHHHHHHHhhCCC--ccHHHHHHHH
Q psy2182 27 TNGVVTKIADYKRECPS--IFAWEIRDRL 53 (67)
Q Consensus 27 t~~v~~~I~~~k~~~p~--ifawEiR~~L 53 (67)
-...++.|+++-.++++ +.+-||-+.|
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~l 32 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNL 32 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHH
Confidence 35678889998888876 9999885543
No 67
>PRK03341 arginine repressor; Provisional
Probab=41.59 E-value=49 Score=22.53 Aligned_cols=32 Identities=16% Similarity=0.058 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 28 NGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 28 ~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
.+--+.|.++-++++-...-||.+.|.++|+.
T Consensus 14 ~~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~ 45 (168)
T PRK03341 14 AARQARIVAILSRQSVRSQAELAALLADEGIE 45 (168)
T ss_pred HHHHHHHHHHHHHCCCccHHHHHHHHHHcCCc
Confidence 35667888999999999999999999999995
No 68
>cd00756 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits.
Probab=41.30 E-value=15 Score=23.68 Aligned_cols=36 Identities=17% Similarity=0.266 Sum_probs=31.3
Q ss_pred hhhcccccccc------cCCCCCCcCCHHHHHHHHHHHhhCC
Q psy2182 7 YYETGSIKPRA------IGGSKPRVATNGVVTKIADYKRECP 42 (67)
Q Consensus 7 y~eTGsi~Pg~------iGGskpk~~t~~v~~~I~~~k~~~p 42 (67)
++..|.+.||- +.+..++.+-.+....|+.+|.+-|
T Consensus 69 ~HR~G~l~vGe~~v~i~v~a~hR~~af~A~~~~id~lK~~~P 110 (124)
T cd00756 69 IHRVGRLPPGEAIVLVAVSSPHRKEAFEACEFLIDRLKHRAP 110 (124)
T ss_pred EEEEcccCCCCEEEEEEEecCCHHHHHHHHHHHHHHHHhhCC
Confidence 57889999995 5788888999999999999999876
No 69
>KOG1436|consensus
Probab=39.91 E-value=14 Score=28.70 Aligned_cols=20 Identities=45% Similarity=0.856 Sum_probs=16.1
Q ss_pred hhhcccccccccCCC-CCCcC
Q psy2182 7 YYETGSIKPRAIGGS-KPRVA 26 (67)
Q Consensus 7 y~eTGsi~Pg~iGGs-kpk~~ 26 (67)
|.|+||+.|.+.-|. |||+-
T Consensus 120 ~ieigSvTp~pqeGNPkPRvf 140 (398)
T KOG1436|consen 120 FIEIGSVTPKPQEGNPKPRVF 140 (398)
T ss_pred eEEecccccCCCCCCCCCceE
Confidence 789999999996555 99853
No 70
>PRK11566 hdeB acid-resistance protein; Provisional
Probab=39.58 E-value=42 Score=21.63 Aligned_cols=26 Identities=19% Similarity=0.387 Sum_probs=22.7
Q ss_pred HHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 31 VTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 31 ~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
+.++.+|-+.+|+-.+|++++++...
T Consensus 74 tPkvie~Ckk~P~~~L~~~~~~i~~~ 99 (102)
T PRK11566 74 VPKVIEYCKKNPQKKLSTIKNQIKND 99 (102)
T ss_pred chHHHHHHHhCCcchHHHHHHHHHHH
Confidence 67788899999999999999998653
No 71
>cd07489 Peptidases_S8_5 Peptidase S8 family domain, uncharacterized subfamily 5. gap in seq This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=39.51 E-value=39 Score=23.79 Aligned_cols=36 Identities=22% Similarity=0.092 Sum_probs=30.2
Q ss_pred CCcCCHHHHHHHHHHHhhC-CCccHHHHHHHHHhcCc
Q psy2182 23 PRVATNGVVTKIADYKREC-PSIFAWEIRDRLLAEGV 58 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~-p~ifawEiR~~L~~~Gv 58 (67)
-+.++|-+...+..+.+.+ |.++.-|||+.|+.-..
T Consensus 230 TS~Aap~vaG~~Al~~~~~~~~~~~~~v~~~l~~ta~ 266 (312)
T cd07489 230 TSMATPYVAGAAALLIQARHGKLSPAELRDLLASTAK 266 (312)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCc
Confidence 4677888888888888888 99999999999987643
No 72
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=38.86 E-value=44 Score=20.03 Aligned_cols=38 Identities=21% Similarity=0.180 Sum_probs=31.2
Q ss_pred cCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 18 IGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 18 iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.||...+......+..|.++...++...+.||-+-|..
T Consensus 24 wGG~~s~~K~~~l~~~i~~~f~~~~~~~~~~le~~L~~ 61 (82)
T PF10273_consen 24 WGGPDSQEKADWLAEVIVDWFTENKDPDADDLEDFLED 61 (82)
T ss_pred cCCccHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 57777767777788889999999988889999887754
No 73
>cd04843 Peptidases_S8_11 Peptidase S8 family domain, uncharacterized subfamily 11. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=38.70 E-value=55 Score=23.25 Aligned_cols=36 Identities=25% Similarity=0.280 Sum_probs=24.2
Q ss_pred CCCcCCHHHH---HHHHHH-Hhh-CCCccHHHHHHHHHhcC
Q psy2182 22 KPRVATNGVV---TKIADY-KRE-CPSIFAWEIRDRLLAEG 57 (67)
Q Consensus 22 kpk~~t~~v~---~~I~~~-k~~-~p~ifawEiR~~L~~~G 57 (67)
-.+.++|-|. .+|..+ ++. +|++...|+|+.|.+-|
T Consensus 236 GTS~AaP~VaG~aALl~s~~~~~~~p~lt~~~v~~~L~~t~ 276 (277)
T cd04843 236 GTSSASPIVAGAAASIQGIAKQKGGTPLTPIEMRELLTATG 276 (277)
T ss_pred ccchhhHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhcC
Confidence 3456677544 444443 334 49999999999998754
No 74
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=38.60 E-value=1.1e+02 Score=19.75 Aligned_cols=51 Identities=14% Similarity=0.053 Sum_probs=34.3
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L~ 54 (67)
|.=|.+.|=+.|..-..+--+.-+++.+..+...+. ..-++.+-||++-|-
T Consensus 17 lRyYE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~ 68 (135)
T PRK10227 17 IRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN 68 (135)
T ss_pred HHHHHHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 334777888988644334446667777776666544 345899999998764
No 75
>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=38.60 E-value=71 Score=20.75 Aligned_cols=51 Identities=20% Similarity=0.197 Sum_probs=34.2
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHH---HHHHHHHhhCCCccHHHHHHHHHhcC
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVV---TKIADYKRECPSIFAWEIRDRLLAEG 57 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~---~~I~~~k~~~p~ifawEiR~~L~~~G 57 (67)
|..|.+.|-+.|....+ .-+.-++..+ ..|..++. =++..-||++-+....
T Consensus 17 LR~Ye~~GLl~p~r~~~-g~R~Y~~~~l~~l~~I~~lr~--~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 17 IDYYTNLGLLTPERSDS-NYRYYDETALDRLQLIEHLKG--QRLSLAEIKDQLEEVQ 70 (134)
T ss_pred HHHHHHCCCCCCccCCC-CCeeECHHHHHHHHHHHHHHH--CCCCHHHHHHHHHhhc
Confidence 56788999999977543 3344455544 44555554 4799999999876544
No 76
>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=38.52 E-value=1e+02 Score=19.68 Aligned_cols=50 Identities=12% Similarity=0.024 Sum_probs=34.5
Q ss_pred chhhhcccccccccCCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHHH
Q psy2182 5 EGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRLL 54 (67)
Q Consensus 5 ~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L~ 54 (67)
.=|.+.|=+.|..-..+--+.-+++++..+...+. ..-++..-||++-|.
T Consensus 21 R~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~ 71 (120)
T TIGR02054 21 RDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCR 71 (120)
T ss_pred HHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 34667899988765444456667777777666655 345899999998654
No 77
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=37.68 E-value=30 Score=16.94 Aligned_cols=29 Identities=14% Similarity=0.242 Sum_probs=17.4
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVT 32 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~ 32 (67)
|.+|.+.|.+.+...+|...+-...++..
T Consensus 17 l~~~~~~g~~~~~~~~~~~~~~~~~ei~~ 45 (49)
T cd04762 17 LRRWVKEGKLKAIRTPGGHRRFPEEDLER 45 (49)
T ss_pred HHHHHHcCCCCceeCCCCceecCHHHHHH
Confidence 56788889887765555444444444443
No 78
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=37.50 E-value=19 Score=20.20 Aligned_cols=25 Identities=36% Similarity=0.468 Sum_probs=7.2
Q ss_pred HHHHHhhCCCccHHHHHHHHHhcCc
Q psy2182 34 IADYKRECPSIFAWEIRDRLLAEGV 58 (67)
Q Consensus 34 I~~~k~~~p~ifawEiR~~L~~~Gv 58 (67)
|..+.+++|.+.+-||...|.+.|+
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~~~ 28 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEAGI 28 (72)
T ss_dssp ------------HHHHHHHT---T-
T ss_pred HHHHHHHCCCCCHHHHHHHHHHccC
Confidence 5566677888888888888766654
No 79
>PTZ00262 subtilisin-like protease; Provisional
Probab=37.42 E-value=60 Score=26.75 Aligned_cols=37 Identities=19% Similarity=-0.017 Sum_probs=31.2
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCc
Q psy2182 22 KPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGV 58 (67)
Q Consensus 22 kpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gv 58 (67)
-.+.++|-|...+.-++..+|++...||++.|..--.
T Consensus 555 GTSmAAP~VAGvAALLlS~~P~LT~~qV~~iL~~TA~ 591 (639)
T PTZ00262 555 GTSMAAPHVAAIASLILSINPSLSYEEVIRILKESIV 591 (639)
T ss_pred CCchhHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCc
Confidence 4567888888888888999999999999999977643
No 80
>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=37.25 E-value=75 Score=18.72 Aligned_cols=49 Identities=14% Similarity=0.156 Sum_probs=31.9
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhh--CCCccHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRE--CPSIFAWEIRDRL 53 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~--~p~ifawEiR~~L 53 (67)
|..|.+.|-|.|....| ..+.-++..+..+...+.- .-++..-+|+.-|
T Consensus 18 Lr~ye~~Gli~p~r~~~-g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 18 LRLYERLGLLSPSRTDG-GTRRYSERDIERLRRIQRLTQELGVNLAGVKRIL 68 (91)
T ss_pred HHHHHHCCCcCCCcCCC-CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 56788999999965433 3355677666666665432 2478888876544
No 81
>PHA02754 hypothetical protein; Provisional
Probab=36.84 E-value=24 Score=21.03 Aligned_cols=15 Identities=27% Similarity=0.399 Sum_probs=12.9
Q ss_pred cHHHHHHHHHhcCcC
Q psy2182 45 FAWEIRDRLLAEGVC 59 (67)
Q Consensus 45 fawEiR~~L~~~Gvc 59 (67)
|-.|+||.|-+.||-
T Consensus 19 ~MRelkD~LSe~GiY 33 (67)
T PHA02754 19 AMRELKDILSEAGIY 33 (67)
T ss_pred HHHHHHHHHhhCceE
Confidence 558999999999983
No 82
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 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 dissimilar C-terminal domains bind specific coactivator molecules.
Probab=36.83 E-value=79 Score=19.09 Aligned_cols=50 Identities=16% Similarity=0.141 Sum_probs=31.1
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhhC--CCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKREC--PSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~--p~ifawEiR~~L~ 54 (67)
|..|.+.|-+.|..-.| ..+.-++..+..+...+.-. -++..-||+.-|.
T Consensus 18 LR~ye~~Gli~p~r~~~-g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~ 69 (98)
T cd01279 18 LRVYDRLGLVSPARTNG-GGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIE 69 (98)
T ss_pred HHHHHHCCCCCCCcCCC-CCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 56788999999843222 33445666665555544322 4888888876654
No 83
>PRK04280 arginine repressor; Provisional
Probab=35.51 E-value=71 Score=21.17 Aligned_cols=29 Identities=28% Similarity=0.166 Sum_probs=25.8
Q ss_pred HHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 31 VTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 31 ~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
-++|.++-++++=-..-||.+.|.++|+.
T Consensus 6 ~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~ 34 (148)
T PRK04280 6 HIKIREIITNNEIETQDELVDRLREEGFN 34 (148)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCC
Confidence 35788888999999999999999999985
No 84
>PF12614 RRF_GI: Ribosome recycling factor ; InterPro: IPR022253 This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Probab=35.48 E-value=52 Score=21.95 Aligned_cols=26 Identities=19% Similarity=0.147 Sum_probs=21.4
Q ss_pred CcCCHHHHHHHHHHHhhCCCccHHHH
Q psy2182 24 RVATNGVVTKIADYKRECPSIFAWEI 49 (67)
Q Consensus 24 k~~t~~v~~~I~~~k~~~p~ifawEi 49 (67)
....+..+.++.++-.+||.|++.||
T Consensus 83 ~dkle~l~~~L~~Li~~nP~iTlaEL 108 (128)
T PF12614_consen 83 SDKLEPLEDKLARLIPQNPNITLAEL 108 (128)
T ss_pred ccccchHHHHHHHHHHhCCcccHHHH
Confidence 34456677888999999999999997
No 85
>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=35.15 E-value=1.2e+02 Score=19.23 Aligned_cols=49 Identities=24% Similarity=0.181 Sum_probs=32.2
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHH---HHHHhhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKI---ADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I---~~~k~~~p~ifawEiR~~L~ 54 (67)
|.-|.+.|-|.|..-..+.-+.-+++.+..+ ..++. -++..-||++-|.
T Consensus 18 lR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~--~G~sl~eI~~~l~ 69 (131)
T TIGR02043 18 LRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKE--LGFTLDEIKELLS 69 (131)
T ss_pred HHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHH--cCCCHHHHHHHHH
Confidence 4567888999996543344455556555444 44443 4899999998775
No 86
>TIGR03193 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme.
Probab=34.93 E-value=57 Score=22.00 Aligned_cols=32 Identities=31% Similarity=0.394 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 27 TNGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 27 t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
||..+-...++.++||+-..+|||+.|. -.+|
T Consensus 101 tPG~vms~~~ll~~~p~ps~~ei~~al~-GnLC 132 (148)
T TIGR03193 101 TPGMIMAAEALLRRNPSPSRDEIRAALA-GNLC 132 (148)
T ss_pred CccHHHHHHHHHHcCCCCCHHHHHHHHc-CCcc
Confidence 4555555667778899999999999875 3444
No 87
>COG1438 ArgR Arginine repressor [Transcription]
Probab=34.55 E-value=69 Score=21.71 Aligned_cols=30 Identities=20% Similarity=0.093 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 30 VVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 30 v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
--++|.++-.++.=-+.-||.+.|.++|++
T Consensus 7 R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~ 36 (150)
T COG1438 7 RLELIKEIITEEKISTQEELVELLQEEGIE 36 (150)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCe
Confidence 446778888888888899999999999997
No 88
>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=34.03 E-value=1.1e+02 Score=18.61 Aligned_cols=52 Identities=19% Similarity=0.144 Sum_probs=34.8
Q ss_pred cchhhhcccccccccC-CCCCCcCCHHHHHHHHHHHhhCC-CccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIG-GSKPRVATNGVVTKIADYKRECP-SIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iG-Gskpk~~t~~v~~~I~~~k~~~p-~ifawEiR~~L~~ 55 (67)
|.-|.+.|=|.|-... .+.-+.-++.++..|...+.-.. ++..-||++-+-.
T Consensus 17 lR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~ 70 (108)
T cd01107 17 LRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDA 70 (108)
T ss_pred HHHHHHcCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3447778999886544 35667777877766665544333 7888999875543
No 89
>PRK05066 arginine repressor; Provisional
Probab=33.86 E-value=1.1e+02 Score=20.56 Aligned_cols=31 Identities=19% Similarity=0.038 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 29 GVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 29 ~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
..-+.|.++-++++=-+..||++.|.+.|+.
T Consensus 9 ~r~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~ 39 (156)
T PRK05066 9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFD 39 (156)
T ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHCCCC
Confidence 3457788888999999999999999999997
No 90
>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=33.68 E-value=1.1e+02 Score=18.58 Aligned_cols=50 Identities=12% Similarity=0.045 Sum_probs=32.2
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHH---HHHHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKI---ADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I---~~~k~~~p~ifawEiR~~L~~ 55 (67)
|.-|.+.|-+.|-.-..+.-+.-+++.+..+ ..++. -++.+-||++-|..
T Consensus 17 lr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~--~G~sL~eI~~~l~~ 69 (113)
T cd01109 17 LRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRN--TGMSIKDIKEYAEL 69 (113)
T ss_pred HHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHH--cCCCHHHHHHHHHH
Confidence 5567788988664433334455666655554 55554 48999999987753
No 91
>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=33.51 E-value=1.2e+02 Score=19.00 Aligned_cols=51 Identities=18% Similarity=0.055 Sum_probs=31.0
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHH-hhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYK-RECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k-~~~p~ifawEiR~~L~ 54 (67)
|.-|.+.|-+.|-.-..+.-+.-+++.+..+...+ -..-++.+-||++-|.
T Consensus 17 lRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 17 IRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 44577789898854333334555565554444432 2234899999998764
No 92
>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=33.22 E-value=1e+02 Score=18.41 Aligned_cols=50 Identities=18% Similarity=0.172 Sum_probs=31.9
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHH---HHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVV---TKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~---~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
|.-|.+.|-+.|..-..+.-+.-+++.+ ..|..++.. ++..-||++-|..
T Consensus 17 lR~ye~~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~--G~~l~eI~~~l~~ 69 (96)
T cd04788 17 LHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRL--GFSLREIGRALDG 69 (96)
T ss_pred HHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHc--CCCHHHHHHHHhC
Confidence 5567888999985432222344456554 455555554 7999999987753
No 93
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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 spe
Probab=32.70 E-value=79 Score=20.45 Aligned_cols=50 Identities=18% Similarity=0.173 Sum_probs=33.6
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHhh--CCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKRE--CPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~--~p~ifawEiR~~L~~ 55 (67)
|..|.+.|-+.|..-|| .+.-+++.+..+...+.- +.++..-||+.-|..
T Consensus 18 LR~wE~~GLl~p~r~~G--~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~l 69 (120)
T cd04767 18 LRIWERHGLIKPARRNG--QRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILSM 69 (120)
T ss_pred HHHHHHCCCCCCcCCCC--cEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 56677889999976533 355566655555544332 269999999998643
No 94
>TIGR00722 ttdA_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=32.51 E-value=24 Score=26.04 Aligned_cols=41 Identities=22% Similarity=0.161 Sum_probs=28.9
Q ss_pred cc-cCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 16 RA-IGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 16 g~-iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
|. |||+--+.+.=+=......+-+.||+-...++.++|++.
T Consensus 182 GVGIGGt~d~aa~LaK~Allr~ig~~n~d~~~a~lE~elle~ 223 (273)
T TIGR00722 182 GVGIGGSFETAAKLAKKALLRPIGERHPNPKIAKLELELLEE 223 (273)
T ss_pred EEEeCCCHHHHHHHHHHHhhhhhccCCCChhHHHHHHHHHHH
Confidence 55 888765555444444566667789998888888888764
No 95
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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=32.29 E-value=1.3e+02 Score=21.05 Aligned_cols=49 Identities=14% Similarity=0.191 Sum_probs=36.9
Q ss_pred chhhhccccccccc-CCCCCCcCCHHHHHHHHHHHhhC-CCccHHHHHHHHHh
Q psy2182 5 EGYYETGSIKPRAI-GGSKPRVATNGVVTKIADYKREC-PSIFAWEIRDRLLA 55 (67)
Q Consensus 5 ~Ry~eTGsi~Pg~i-GGskpk~~t~~v~~~I~~~k~~~-p~ifawEiR~~L~~ 55 (67)
.-|.+.|=+.|-.. ||. +.-++++++.+..++.-+ .++.+-||++.|-.
T Consensus 19 R~Ye~~GLL~p~r~~~~~--r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~ 69 (219)
T cd04778 19 RAYQDRGLLPPPRRRGRV--AIYNDSHLARLRLINQLLERGYTLAHIAELLAA 69 (219)
T ss_pred HHHHHCCCCCCcccCCCC--cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 34777888877544 444 378999999988887754 68999999987754
No 96
>PRK00441 argR arginine repressor; Provisional
Probab=32.01 E-value=84 Score=20.80 Aligned_cols=31 Identities=16% Similarity=0.011 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 29 GVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 29 ~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
+-.+.|+++-+++.-...-||.+.|.++|+.
T Consensus 4 ~R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~ 34 (149)
T PRK00441 4 SRHAKILEIINSKEIETQEELAEELKKMGFD 34 (149)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHHhcCCC
Confidence 3456788888999999999999999999984
No 97
>PRK05927 hypothetical protein; Provisional
Probab=31.97 E-value=93 Score=23.20 Aligned_cols=51 Identities=20% Similarity=0.259 Sum_probs=37.6
Q ss_pred hhcccccccccCCCCCCcCCHHHHHHHHHHHhhCCCcc-------------------HHHHHHHHHhcCc
Q psy2182 8 YETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIF-------------------AWEIRDRLLAEGV 58 (67)
Q Consensus 8 ~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~if-------------------awEiR~~L~~~Gv 58 (67)
.+.|--+---.||-.|....+-+++.|...|++.|++. ..|.=++|.+.|+
T Consensus 89 ~~~G~~~i~i~gG~~p~~~~e~~~~~i~~ik~~~p~l~~~~~s~~ei~~~~~~~G~~~~e~l~~Lk~aGl 158 (350)
T PRK05927 89 VSAGVKTVLLQGGVHPQLGIDYLEELVRITVKEFPSLHPHFFSAVEIAHAAQVSGISTEQALERLWDAGQ 158 (350)
T ss_pred HHCCCCEEEEeCCCCCCCCHHHHHHHHHHHHHHCCCCcccCCCHHHHHHHHHhcCCCHHHHHHHHHHcCc
Confidence 34454444557899999888889999999999988663 4455567777777
No 98
>COG5530 Predicted integral membrane protein [Function unknown]
Probab=31.76 E-value=42 Score=24.45 Aligned_cols=24 Identities=33% Similarity=0.476 Sum_probs=18.9
Q ss_pred HHHHHHHHHHhhCCCccHHHHHHHHH
Q psy2182 29 GVVTKIADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 29 ~v~~~I~~~k~~~p~ifawEiR~~L~ 54 (67)
.+...|--|+.|-..|..| ||+|-
T Consensus 35 ~~NaliH~yRaEigrMagw--RdRlD 58 (247)
T COG5530 35 QANALIHLYRAEIGRMAGW--RDRLD 58 (247)
T ss_pred HHHHHHHHHHHHHHHHhHH--HHhhh
Confidence 4566666788888899999 88874
No 99
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=31.37 E-value=40 Score=17.59 Aligned_cols=22 Identities=18% Similarity=0.160 Sum_probs=13.5
Q ss_pred CccHHHHHHHHHhcCcCCCCCC
Q psy2182 43 SIFAWEIRDRLLAEGVCNNDNI 64 (67)
Q Consensus 43 ~ifawEiR~~L~~~Gvc~~~~~ 64 (67)
++..-|||..|.+.||--++++
T Consensus 3 sltV~~Lk~iL~~~~I~~ps~A 24 (35)
T PF12949_consen 3 SLTVAQLKRILDEHGIEFPSNA 24 (35)
T ss_dssp T--SHHHHHHHHHHT---SSS-
T ss_pred cCcHHHHHHHHHHcCCCCCCCC
Confidence 4667899999999999766554
No 100
>cd07963 Anticodon_Ia_Cys Anticodon-binding domain of cysteinyl tRNA synthetases. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA.
Probab=31.15 E-value=33 Score=22.05 Aligned_cols=16 Identities=44% Similarity=0.518 Sum_probs=12.6
Q ss_pred HHHHHHHHHhcCcCCC
Q psy2182 46 AWEIRDRLLAEGVCNN 61 (67)
Q Consensus 46 awEiR~~L~~~Gvc~~ 61 (67)
|=+||++|.+.||--.
T Consensus 131 AD~IRd~L~~~Gi~i~ 146 (156)
T cd07963 131 ADRIRDELAAQGIILE 146 (156)
T ss_pred HHHHHHHHHHCCcEEE
Confidence 3459999999999643
No 101
>COG1582 FlgEa Uncharacterized protein, possibly involved in motility [Cell motility and secretion]
Probab=30.97 E-value=36 Score=20.47 Aligned_cols=22 Identities=27% Similarity=0.511 Sum_probs=16.9
Q ss_pred CcCCHHHHHHHHHHHhhCCCccHHH
Q psy2182 24 RVATNGVVTKIADYKRECPSIFAWE 48 (67)
Q Consensus 24 k~~t~~v~~~I~~~k~~~p~ifawE 48 (67)
+-..++|.++|..|++. |++|+
T Consensus 41 kEsveEVi~kI~~y~rk---I~~~~ 62 (67)
T COG1582 41 KESVEEVINKIIEYRRK---IGSLA 62 (67)
T ss_pred cccHHHHHHHHHHHHHH---hheeh
Confidence 34578999999999987 66654
No 102
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=30.49 E-value=77 Score=17.46 Aligned_cols=20 Identities=30% Similarity=0.295 Sum_probs=15.9
Q ss_pred HHHHHhhCCCccHHHHHHHH
Q psy2182 34 IADYKRECPSIFAWEIRDRL 53 (67)
Q Consensus 34 I~~~k~~~p~ifawEiR~~L 53 (67)
|.++-+++..+...|.||.|
T Consensus 1 i~~~~~~~~~itv~~~rd~l 20 (50)
T PF09107_consen 1 IRELLQKNGEITVAEFRDLL 20 (50)
T ss_dssp HHHHHHTTSSBEHHHHHHHH
T ss_pred ChHHHhcCCcCcHHHHHHHH
Confidence 34566678899999999987
No 103
>PF05902 4_1_CTD: 4.1 protein C-terminal domain (CTD); InterPro: IPR008379 There is a unique sequence domain at the C terminus of all known 4.1 proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24 kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates [].; GO: 0003779 actin binding, 0005198 structural molecule activity, 0005856 cytoskeleton
Probab=30.38 E-value=51 Score=21.62 Aligned_cols=18 Identities=17% Similarity=0.346 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHhhCCCcc
Q psy2182 28 NGVVTKIADYKRECPSIF 45 (67)
Q Consensus 28 ~~v~~~I~~~k~~~p~if 45 (67)
.+.++.|.+-++.||+|.
T Consensus 85 qaLa~aI~eAk~q~Pdm~ 102 (114)
T PF05902_consen 85 QALAQAIKEAKEQHPDMS 102 (114)
T ss_pred HHHHHHHHHHHHhCCCce
Confidence 467899999999999985
No 104
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=30.27 E-value=1e+02 Score=16.90 Aligned_cols=42 Identities=24% Similarity=0.456 Sum_probs=23.5
Q ss_pred ccccccCCC----CCCcCCHHHHHH------HHHHHhhCCCccHHHHHHHHH
Q psy2182 13 IKPRAIGGS----KPRVATNGVVTK------IADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 13 i~Pg~iGGs----kpk~~t~~v~~~------I~~~k~~~p~ifawEiR~~L~ 54 (67)
+.|+..||- ..+.....+... .++..++.|++..-+|++.|.
T Consensus 3 ~dp~~~~G~P~i~GTRI~v~~i~~~~~~G~s~eeI~~~yp~Lt~~~i~aAl~ 54 (56)
T PF04255_consen 3 IDPDILGGQPVIRGTRIPVRDILDLLAAGESPEEIAEDYPSLTLEDIRAALA 54 (56)
T ss_dssp --TTSGGG--EETTSS-BHHHHHHHHHTT--HHHHHHHSTT--HHHHHHHHH
T ss_pred eCccccCCcceEcCceecHHHHHHHHHcCCCHHHHHHHCCCCCHHHHHHHHH
Confidence 346666664 124555555555 345667889999999988874
No 105
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=30.26 E-value=54 Score=21.21 Aligned_cols=21 Identities=43% Similarity=0.398 Sum_probs=16.9
Q ss_pred CCccHHHHHHHHHhcCcCCCC
Q psy2182 42 PSIFAWEIRDRLLAEGVCNND 62 (67)
Q Consensus 42 p~ifawEiR~~L~~~Gvc~~~ 62 (67)
|+.-.||-|+.|.++||+..+
T Consensus 70 ~~~~~~~Q~~lL~aEGv~~~~ 90 (103)
T COG3695 70 PGPDKQRQRELLLAEGVEFSD 90 (103)
T ss_pred CCccHHHHHHHHHHcCceecc
Confidence 444678999999999998654
No 106
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=29.72 E-value=72 Score=16.02 Aligned_cols=21 Identities=14% Similarity=0.358 Sum_probs=15.7
Q ss_pred CccHHHHHHHHHhcCcCCCCC
Q psy2182 43 SIFAWEIRDRLLAEGVCNNDN 63 (67)
Q Consensus 43 ~ifawEiR~~L~~~Gvc~~~~ 63 (67)
.+..-|||+.|.+.|+-...+
T Consensus 3 ~l~v~eLk~~l~~~gL~~~G~ 23 (35)
T PF02037_consen 3 KLTVAELKEELKERGLSTSGK 23 (35)
T ss_dssp TSHHHHHHHHHHHTTS-STSS
T ss_pred cCcHHHHHHHHHHCCCCCCCC
Confidence 467789999999999876543
No 107
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=29.71 E-value=1e+02 Score=16.87 Aligned_cols=46 Identities=13% Similarity=0.315 Sum_probs=25.7
Q ss_pred chhhhc-ccccccccCCCCCCcCCHHHHHH---HHHHHhhCCCccHHHHHHHH
Q psy2182 5 EGYYET-GSIKPRAIGGSKPRVATNGVVTK---IADYKRECPSIFAWEIRDRL 53 (67)
Q Consensus 5 ~Ry~eT-Gsi~Pg~iGGskpk~~t~~v~~~---I~~~k~~~p~ifawEiR~~L 53 (67)
..|.+. |-+.|..-.|..+ .-+.+.+.. |..+++ -++..-||+.-|
T Consensus 18 r~ye~~~gl~~~~r~~~g~R-~yt~~di~~l~~i~~l~~--~g~~l~~i~~~l 67 (68)
T cd04763 18 RAWEREFGLLKPQRSDGGHR-LFNDADIDRILEIKRWID--NGVQVSKVKKLL 67 (68)
T ss_pred HHHHHhcCCCCCCcCCCCCc-ccCHHHHHHHHHHHHHHH--cCCCHHHHHHHh
Confidence 344444 7777755444333 444444333 344443 688888888654
No 108
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=28.93 E-value=1.3e+02 Score=19.29 Aligned_cols=51 Identities=18% Similarity=0.123 Sum_probs=32.7
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHH-hhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYK-RECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k-~~~p~ifawEiR~~L~ 54 (67)
|.-|.+.|-|.|..-..+.-+.-+++.+..+...+ -..-++.+-||++-|.
T Consensus 18 lR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 69 (140)
T PRK09514 18 LRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS 69 (140)
T ss_pred HHHHHHCCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45677889999865444444566666555544432 2234899999998764
No 109
>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=28.52 E-value=1.6e+02 Score=18.94 Aligned_cols=50 Identities=24% Similarity=0.177 Sum_probs=32.8
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L~ 54 (67)
|.-|.+.|-+.|..-.| .-+.-+++.+..|...+. .+-++..-||++-|.
T Consensus 18 LRyYE~~GLl~p~r~~~-g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~ 68 (139)
T cd01110 18 LHFYEQKGLIASWRNAG-NQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA 68 (139)
T ss_pred HHHHHHCCCCCCCcCCC-CCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 44566789998854433 345567776666655433 335899999998774
No 110
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=28.42 E-value=1.1e+02 Score=16.69 Aligned_cols=48 Identities=15% Similarity=0.039 Sum_probs=24.3
Q ss_pred chhhhcccccccccCCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHH
Q psy2182 5 EGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRL 53 (67)
Q Consensus 5 ~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L 53 (67)
..|.+.|-+.+..-. +..+.-+++.+..+...+. .+-++..-||+.-|
T Consensus 18 R~~~~~g~l~~~~~~-~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 18 RYYEKEFNLYIPRTE-NGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred HHHHHhcCCCCCCCC-CCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 344445666543222 2334455554444444322 22578888888754
No 111
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=27.97 E-value=86 Score=21.07 Aligned_cols=32 Identities=25% Similarity=0.411 Sum_probs=23.0
Q ss_pred CHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 27 TNGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 27 t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
||-.+-....+.+++|+-...|||+.|. -.+|
T Consensus 102 tpG~im~~~~ll~~~p~p~~~ei~~al~-gnlC 133 (151)
T TIGR03198 102 TPGMVVALKALFRETPQPSDEDMEEGLS-GNLC 133 (151)
T ss_pred CccHHHHHHHHHHcCCCCCHHHHHHHHc-CCCc
Confidence 4545555567777889989999999875 3455
No 112
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=27.93 E-value=95 Score=15.86 Aligned_cols=25 Identities=36% Similarity=0.516 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhhCCCccHHHHHHHH
Q psy2182 29 GVVTKIADYKRECPSIFAWEIRDRL 53 (67)
Q Consensus 29 ~v~~~I~~~k~~~p~ifawEiR~~L 53 (67)
+....|..+-.++|.+..-||-+++
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~ 27 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKL 27 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHh
Confidence 4556788888899999998886654
No 113
>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=27.70 E-value=1.4e+02 Score=18.63 Aligned_cols=48 Identities=25% Similarity=0.223 Sum_probs=33.3
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHH---HHHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIA---DYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~---~~k~~~p~ifawEiR~~L~~ 55 (67)
|.-|.+.|-|.|...+| -+.-++.++..+. .++. -++.+-||++-|..
T Consensus 17 lRyYe~~GLl~p~r~~g--yR~Y~~~~l~~l~~I~~lr~--~G~~L~~I~~~l~~ 67 (118)
T cd04776 17 LRFYEDKGLLSPERRGQ--TRVYSRRDRARLKLILRGKR--LGFSLEEIRELLDL 67 (118)
T ss_pred HHHHHHCCCCCCcCCCC--ccccCHHHHHHHHHHHHHHH--CCCCHHHHHHHHHh
Confidence 34467889999976653 4566777666655 4443 58999999987754
No 114
>PF09748 Med10: Transcription factor subunit Med10 of Mediator complex; InterPro: IPR019145 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med10 is one of the protein subunits of the Mediator complex, tethered to Med14 (Rgr1) protein. Med10 specifically mediates basal-level HIS4 transcription via Gcn4. In addition, there is a putative requirement for Med10 in Bas2-mediated transcription []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=27.65 E-value=49 Score=21.35 Aligned_cols=27 Identities=26% Similarity=0.336 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 28 NGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 28 ~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
.+|.+.|++ ..||++|..|.=++..+.
T Consensus 66 ~evl~yID~--GrNPDiyTre~vE~~~~~ 92 (128)
T PF09748_consen 66 LEVLEYIDD--GRNPDIYTREFVELVRRE 92 (128)
T ss_pred HHHHHHHhC--CCCchHHHHHHHHHHHHH
Confidence 378899998 789999999987766554
No 115
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=27.56 E-value=1.3e+02 Score=18.88 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=21.9
Q ss_pred cCCHHHHHHHHHHHhhCCC------ccHHHHHHHHHhcCc
Q psy2182 25 VATNGVVTKIADYKRECPS------IFAWEIRDRLLAEGV 58 (67)
Q Consensus 25 ~~t~~v~~~I~~~k~~~p~------ifawEiR~~L~~~Gv 58 (67)
..-.........++++.|+ ..+-=+|.+|.++|+
T Consensus 14 ~~~~~~~~i~~~l~~~~p~~~V~~afts~~i~~~l~~~~~ 53 (127)
T cd03412 14 TAEKTIDAIEDKVRAAFPDYEVRWAFTSRMIRKKLKKRGI 53 (127)
T ss_pred HHHHHHHHHHHHHHHHCCCCeEEEEecHHHHHHHHHhcCC
Confidence 3344555556666777774 334457999998874
No 116
>PLN02826 dihydroorotate dehydrogenase
Probab=27.19 E-value=12 Score=28.80 Aligned_cols=41 Identities=29% Similarity=0.389 Sum_probs=29.2
Q ss_pred hhhcccccccc-cCCCCCC-cCCHHHHHHHHHHHhhCCCccHH
Q psy2182 7 YYETGSIKPRA-IGGSKPR-VATNGVVTKIADYKRECPSIFAW 47 (67)
Q Consensus 7 y~eTGsi~Pg~-iGGskpk-~~t~~v~~~I~~~k~~~p~ifaw 47 (67)
|.|+|+|.|.+ -|..+|+ .++++....|..+--.|+++..|
T Consensus 110 ~vevgTVT~~pq~GNp~PR~frl~~~~aiiN~~Gfnn~G~~~~ 152 (409)
T PLN02826 110 FVEIGSVTPLPQPGNPKPRVFRLREEGAIINRYGFNSEGIVAV 152 (409)
T ss_pred eEEeCCccCCCCCCCCCCcEEecCCCceeEecCCCCCcCHHHH
Confidence 67899999988 5555888 44665556666666667777666
No 117
>PF01979 Amidohydro_1: Amidohydrolase family; InterPro: IPR006680 This group of enzymes represents a large metal dependent hydrolase superfamily []. The family includes adenine deaminase (3.5.4.2 from EC) that hydrolyses adenine to form hypoxanthine and ammonia. The adenine deaminase reaction is important for adenine utilization as a purine and also as a nitrogen source []. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases (3.5.1.25 from EC). These enzymes catalyse the reaction: N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetateThis family includes dihydroorotase and urease which belong to MEROPS peptidase family M38 (beta-aspartyl dipeptidase, clan MJ), where they are classified as non-peptidase homologs. ; GO: 0016787 hydrolase activity; PDB: 1O12_A 2KAU_C 1FWD_C 1A5M_C 1FWC_C 1FWI_C 1EJV_C 1FWH_C 1A5L_C 1KRA_C ....
Probab=27.14 E-value=25 Score=24.02 Aligned_cols=17 Identities=24% Similarity=0.036 Sum_probs=14.5
Q ss_pred cccchhhhccccccccc
Q psy2182 2 YSEEGYYETGSIKPRAI 18 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~i 18 (67)
|+|+.+.+.|||+||..
T Consensus 310 k~lg~~~~~G~i~~G~~ 326 (333)
T PF01979_consen 310 KILGLDDDKGSIEPGKD 326 (333)
T ss_dssp HHTTSTTTSSSSSTTSB
T ss_pred HHcCCCCCEEEeCcCCC
Confidence 67888999999999953
No 118
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. 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=26.75 E-value=1.5e+02 Score=17.83 Aligned_cols=49 Identities=16% Similarity=0.196 Sum_probs=30.9
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHH---HHHHhhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKI---ADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I---~~~k~~~p~ifawEiR~~L~ 54 (67)
|..|.+.|-+.|....| ..+.-++..+..+ ..++.+ -++..-||+.-|.
T Consensus 17 LR~ye~~Gll~p~r~~~-g~R~Y~~~dv~~l~~I~~L~~~-~G~~l~ei~~~l~ 68 (96)
T cd04774 17 LKYYEEIGLVSPERSEG-RYRLYSEEDLKRLERILRLREV-LGFSLQEVTHFLE 68 (96)
T ss_pred HHHHHHCCCCCCCcCCC-CCEEECHHHHHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 55677889998866443 3444555544444 444442 4899999987664
No 119
>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=26.65 E-value=1.6e+02 Score=18.85 Aligned_cols=52 Identities=17% Similarity=0.001 Sum_probs=31.4
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L~~ 55 (67)
|.-|.+.|=+.|-.-.++.-+.-++..+..+...+. ..=++.+-||++-|..
T Consensus 17 LRyYE~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 17 IRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred HHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 345667898988543333445555655554444322 2237999999987754
No 120
>PRK14137 recX recombination regulator RecX; Provisional
Probab=26.65 E-value=1.8e+02 Score=20.07 Aligned_cols=34 Identities=15% Similarity=0.157 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHH---HhhCCCccHHHHHHHHHhcCcC
Q psy2182 26 ATNGVVTKIADY---KRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 26 ~t~~v~~~I~~~---k~~~p~ifawEiR~~L~~~Gvc 59 (67)
+.++..+.+..+ .-..-+-+.-|||++|.+.|+-
T Consensus 34 ~~~e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~kg~~ 70 (195)
T PRK14137 34 TPDEAREALLAYAFRALAARAMTAAELRAKLERRSED 70 (195)
T ss_pred CHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHhcCCC
Confidence 445555555554 1222456778999999998863
No 121
>KOG3185|consensus
Probab=26.62 E-value=88 Score=22.84 Aligned_cols=37 Identities=24% Similarity=0.357 Sum_probs=28.8
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhc
Q psy2182 20 GSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 20 Gskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~ 56 (67)
|.+.-.+--.|++-|-.+.+++|+...-++|+.|++.
T Consensus 207 G~dTTa~ElsViesiFkL~~aqp~~i~~~~R~~lid~ 243 (245)
T KOG3185|consen 207 GLDTTATELSVIESIFKLNEAQPSSISSELRDTLIDS 243 (245)
T ss_pred ccCCcchhHHHHHHHHhhcccCchhHHHHHHHHHHHh
Confidence 3333333446888899999999999999999999874
No 122
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=26.49 E-value=41 Score=18.91 Aligned_cols=45 Identities=13% Similarity=0.120 Sum_probs=24.7
Q ss_pred Ccccchhhhccccc------ccccCCCCCCcCCHHHHHHHHHHHhhCCCcc
Q psy2182 1 MYSEEGYYETGSIK------PRAIGGSKPRVATNGVVTKIADYKRECPSIF 45 (67)
Q Consensus 1 ~~~L~Ry~eTGsi~------Pg~iGGskpk~~t~~v~~~I~~~k~~~p~if 45 (67)
|+||.|=..+++-. ....+.+.+......+++.-.+|.++.--||
T Consensus 5 ~~IlkRp~~~~~~~~~~~~~~~~~~~~~~~~~~kSlEERE~eY~~AR~RIF 55 (59)
T PF12752_consen 5 RKILKRPSKGSSSSDSGSSGSSPNSSSRKKRPSKSLEEREAEYAEARARIF 55 (59)
T ss_pred CeEecCCCCCCCcccccccccCCCcccccccccCCHHHHHHHHHHHHHHHh
Confidence 68898832222211 1122223344555567888888887755555
No 123
>KOG4146|consensus
Probab=26.43 E-value=22 Score=22.88 Aligned_cols=12 Identities=33% Similarity=0.802 Sum_probs=9.9
Q ss_pred hhhccccccccc
Q psy2182 7 YYETGSIKPRAI 18 (67)
Q Consensus 7 y~eTGsi~Pg~i 18 (67)
|-+.||++||.|
T Consensus 57 Fi~~gsvrpGii 68 (101)
T KOG4146|consen 57 FIHHGSVRPGII 68 (101)
T ss_pred EeeCCcCcCcEE
Confidence 567799999986
No 124
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. 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=26.28 E-value=1.6e+02 Score=17.84 Aligned_cols=47 Identities=13% Similarity=0.037 Sum_probs=29.1
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHH---HHHHhhCCCccHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKI---ADYKRECPSIFAWEIRDRL 53 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I---~~~k~~~p~ifawEiR~~L 53 (67)
|.-|.+.|-+.|..-. +--+.-++..+..+ ..++. -++..-||++-+
T Consensus 18 lR~ye~~Gll~~~r~~-~g~R~Y~~~~l~~l~~I~~l~~--~G~~l~ei~~~l 67 (102)
T cd04789 18 LLYYEKLGLITGTRNA-NGYRLYPDSDLQRLLLIQQLQA--GGLSLKECLACL 67 (102)
T ss_pred HHHHHHCCCCCCCcCC-CCCeeCCHHHHHHHHHHHHHHH--CCCCHHHHHHHH
Confidence 4567788999885433 33344455544444 44433 479999998865
No 125
>PF11943 DUF3460: Protein of unknown function (DUF3460); InterPro: IPR021853 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.
Probab=26.21 E-value=66 Score=18.84 Aligned_cols=20 Identities=10% Similarity=0.210 Sum_probs=16.6
Q ss_pred CHHHHHHHHHHHhhCCCccH
Q psy2182 27 TNGVVTKIADYKRECPSIFA 46 (67)
Q Consensus 27 t~~v~~~I~~~k~~~p~ifa 46 (67)
.+++-+.|.+++..+|++-+
T Consensus 4 ~Se~TqFl~~lk~~~Pele~ 23 (60)
T PF11943_consen 4 QSEITQFLNQLKAKHPELEE 23 (60)
T ss_pred cCHHHHHHHHHHHhCCchHH
Confidence 35788999999999998744
No 126
>TIGR02625 YiiL_rotase L-rhamnose 1-epimerase. Members of this protein family are rhamnose mutarotase from Escherichia coli, previously designated YiiL as an uncharacterized protein, and close homologs also associated with rhamnose dissimilation operons in other bacterial genomes. Mutarotase is a term for an epimerase that changes optical activity. This enzyme was shown experimentally to interconvert alpha and beta stereoisomers of the pyranose form of L-rhamnose. The crystal structure of this small (104 amino acid) protein shows a locally asymmetric dimer with active site residues of His, Tyr, and Trp.
Probab=26.21 E-value=58 Score=20.44 Aligned_cols=27 Identities=26% Similarity=0.631 Sum_probs=22.4
Q ss_pred HHHHHHHhhCCCccHH-HHHHHHHhcCcCC
Q psy2182 32 TKIADYKRECPSIFAW-EIRDRLLAEGVCN 60 (67)
Q Consensus 32 ~~I~~~k~~~p~ifaw-EiR~~L~~~Gvc~ 60 (67)
..|.+|++.+..+ | ||.+.|.+-||.+
T Consensus 11 ~~~~eY~~~H~~v--WPEv~~~L~~~Gi~~ 38 (102)
T TIGR02625 11 DAHEEYQKRHNEI--WPELKEVLKSHGAHN 38 (102)
T ss_pred HHHHHHHHHHHcc--CHHHHHHHHHCCCeE
Confidence 4688999998866 6 6999999999864
No 127
>PF14441 OTT_1508_deam: OTT_1508-like deaminase
Probab=25.83 E-value=16 Score=23.45 Aligned_cols=23 Identities=30% Similarity=0.229 Sum_probs=14.3
Q ss_pred cccchhhhcccccccccCCCCCC
Q psy2182 2 YSEEGYYETGSIKPRAIGGSKPR 24 (67)
Q Consensus 2 ~~L~Ry~eTGsi~Pg~iGGskpk 24 (67)
.+|..|...+.-.+..||+||+.
T Consensus 73 ~ll~~~~~~~~~~~~yIG~SK~~ 95 (142)
T PF14441_consen 73 QLLDHLERHFDPPPRYIGCSKPS 95 (142)
T ss_pred HHHHHHHHhcCCCCCEEEEeCch
Confidence 34555555534556669999885
No 128
>COG0314 MoaE Molybdopterin converting factor, large subunit [Coenzyme metabolism]
Probab=24.96 E-value=38 Score=22.82 Aligned_cols=37 Identities=16% Similarity=0.170 Sum_probs=30.6
Q ss_pred hhhhcccccccc------cCCCCCCcCCHHHHHHHHHHHhhCC
Q psy2182 6 GYYETGSIKPRA------IGGSKPRVATNGVVTKIADYKRECP 42 (67)
Q Consensus 6 Ry~eTGsi~Pg~------iGGskpk~~t~~v~~~I~~~k~~~p 42 (67)
=++.+|.+.||- .-+..++.+-++....|+.+|.+-|
T Consensus 81 i~HriG~l~~Ge~~v~v~v~s~HR~~Af~a~~~~id~lK~~aP 123 (149)
T COG0314 81 IIHRIGELKIGEAIVLVGVASAHRKEAFEACEYIIDRLKHRAP 123 (149)
T ss_pred EEEeeccccCCCcEEEEEEecccHHHHHHHHHHHHHHHHhhCC
Confidence 367899999995 4566778889999999999999877
No 129
>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=24.93 E-value=1.8e+02 Score=19.41 Aligned_cols=50 Identities=22% Similarity=0.234 Sum_probs=31.2
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHH---HHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVV---TKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~---~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
|.-|-+.|-+.|..-..+.-+.-+++.+ ..|..++. =++.+-||+.-|-.
T Consensus 18 LRyYe~~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~--~G~sL~eI~~ll~~ 70 (172)
T cd04790 18 LLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRS--AGVSLEDIRSLLQQ 70 (172)
T ss_pred HHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHH--cCCCHHHHHHHHhc
Confidence 4567888999996533333444555544 44455544 47888999987653
No 130
>PLN02390 molybdopterin synthase catalytic subunit
Probab=24.35 E-value=40 Score=21.51 Aligned_cols=36 Identities=14% Similarity=0.142 Sum_probs=30.1
Q ss_pred hhhcccccccc------cCCCCCCcCCHHHHHHHHHHHhhCC
Q psy2182 7 YYETGSIKPRA------IGGSKPRVATNGVVTKIADYKRECP 42 (67)
Q Consensus 7 y~eTGsi~Pg~------iGGskpk~~t~~v~~~I~~~k~~~p 42 (67)
++.+|.+.||- ..+..++.+-.+....|+.+|.+-|
T Consensus 58 ~HR~G~l~vge~~v~v~v~s~HR~~Af~A~~~~id~lK~~vP 99 (111)
T PLN02390 58 AHRLGPVPVGETSVFVAVSSVHRADALDACKFLIDELKASVP 99 (111)
T ss_pred EEeeecccCCCEEEEEEEECCCHHHHHHHHHHHHHHHhhcCC
Confidence 57889999995 4677888889999999999999876
No 131
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=24.14 E-value=1.5e+02 Score=19.64 Aligned_cols=49 Identities=20% Similarity=0.065 Sum_probs=31.3
Q ss_pred cchhhhccccccccc-CCCCCCcCCHHHHHHHHHHHh-hCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAI-GGSKPRVATNGVVTKIADYKR-ECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~i-GGskpk~~t~~v~~~I~~~k~-~~p~ifawEiR~~L~ 54 (67)
|.-|.+.|-|.|... ||. +.-.+.++.++.-.+. ..=++.+-||++-|.
T Consensus 28 lRyYE~~GLi~~~r~~~g~--R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~ 78 (154)
T PRK15002 28 LHFYESKGLITSIRNSGNQ--RRYKRDVLRYVAIIKIAQRIGIPLATIGEAFG 78 (154)
T ss_pred HHHHHHCCCCCCccCCCCC--EEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 456788899998543 443 4556665555544322 223799999999775
No 132
>PF14077 WD40_alt: Alternative WD40 repeat motif
Probab=23.96 E-value=56 Score=18.44 Aligned_cols=28 Identities=11% Similarity=0.277 Sum_probs=23.8
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCccHH
Q psy2182 20 GSKPRVATNGVVTKIADYKRECPSIFAW 47 (67)
Q Consensus 20 Gskpk~~t~~v~~~I~~~k~~~p~ifaw 47 (67)
|..-++++.+.++-+..+++-|.++|-.
T Consensus 13 ~e~l~vrv~eLEeEV~~LrKINrdLfdF 40 (48)
T PF14077_consen 13 QEQLRVRVSELEEEVRTLRKINRDLFDF 40 (48)
T ss_pred cchheeeHHHHHHHHHHHHHHhHHHHhh
Confidence 3477899999999999999999998754
No 133
>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=23.91 E-value=1.7e+02 Score=17.43 Aligned_cols=50 Identities=18% Similarity=0.159 Sum_probs=31.9
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHH---HHHHhhCCCccHHHHHHHHHh
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKI---ADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I---~~~k~~~p~ifawEiR~~L~~ 55 (67)
|.-|.+.|-+.|..-..+.-+.-+.+.+..+ ..++.. ++..-||++-|..
T Consensus 17 LRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~--G~~l~~I~~~l~~ 69 (96)
T cd04768 17 LRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLREL--GFSLAEIKELLDT 69 (96)
T ss_pred HHHHHHCCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHhc
Confidence 4457778999997543334455555555444 444443 7999999987754
No 134
>COG0855 Ppk Polyphosphate kinase [Inorganic ion transport and metabolism]
Probab=23.22 E-value=54 Score=27.39 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=39.4
Q ss_pred ccccccCCCCCCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 13 IKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 13 i~Pg~iGGskpk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
+..+...|.-|+.....+-+.+.++..++=.+|.-.|+..|.++||+
T Consensus 69 ~~~~~~dg~tp~~qL~~I~~~~~~l~~~q~~~~~~~l~~~l~~~gI~ 115 (696)
T COG0855 69 IEQRSPDGLTPREQLGRIQERVLKLVQEQDRLFNELLLPLLAKEGIF 115 (696)
T ss_pred cCcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeE
Confidence 44446678888888888888888888888889988899999999997
No 135
>PF14090 HTH_39: Helix-turn-helix domain
Probab=23.08 E-value=1.3e+02 Score=17.04 Aligned_cols=22 Identities=27% Similarity=0.214 Sum_probs=15.7
Q ss_pred HHHHHHHHhhCCCccHHHHHHH
Q psy2182 31 VTKIADYKRECPSIFAWEIRDR 52 (67)
Q Consensus 31 ~~~I~~~k~~~p~ifawEiR~~ 52 (67)
.+.|+++-+.++.++.+|.++.
T Consensus 3 ~~rIL~~L~~~~~it~~ea~~~ 24 (70)
T PF14090_consen 3 CKRILAALRRGGSITTLEARRE 24 (70)
T ss_pred HHHHHHHHHcCCCcCHHHHHHH
Confidence 4567777777788888885543
No 136
>cd07479 Peptidases_S8_SKI-1_like Peptidase S8 family domain in SKI-1-like proteins. SKI-1 (type I membrane-bound subtilisin-kexin-isoenzyme) proteins are secretory Ca2+-dependent serine proteinases cleave at nonbasic residues: Thr, Leu, and Lys. SKI-1s play a critical role in the regulation of the synthesis and metabolism of cholesterol and fatty acid metabolism. Members of the peptidases S8 and S35 clan include endopeptidases, exopeptidases and also a tripeptidyl-peptidase. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The S53 family contains a catalytic triad Glu/Asp/Ser. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme tem
Probab=23.01 E-value=1.1e+02 Score=21.17 Aligned_cols=33 Identities=21% Similarity=0.202 Sum_probs=25.1
Q ss_pred CcCCHHHHHHHHHHHhhCC----CccHHHHHHHHHhc
Q psy2182 24 RVATNGVVTKIADYKRECP----SIFAWEIRDRLLAE 56 (67)
Q Consensus 24 k~~t~~v~~~I~~~k~~~p----~ifawEiR~~L~~~ 56 (67)
+.++|-|.-.+.-+.+.+| .+..-+||+.|.+-
T Consensus 213 S~AaP~VaG~aAll~s~~p~~~~~~~p~~vk~~L~~s 249 (255)
T cd07479 213 SVASPVVAGAVALLLSTVPEKRDLINPASMKQALIES 249 (255)
T ss_pred HHHHHHHHHHHHHHHHhCccccCCCCHHHHHHHHHhh
Confidence 4567777776666677777 78999999999864
No 137
>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=22.81 E-value=1.9e+02 Score=18.21 Aligned_cols=49 Identities=14% Similarity=0.093 Sum_probs=30.8
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHH---HHHHHHHhhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVV---TKIADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~---~~I~~~k~~~p~ifawEiR~~L~ 54 (67)
|.-|-+.|=|.|..-.++--|.-+++.+ ..|..++. -++.+-||++-|-
T Consensus 17 LRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~--~G~sL~eI~~~l~ 68 (133)
T cd04787 17 VRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQ--LGFSLKDIKEILS 68 (133)
T ss_pred HHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHH--cCCCHHHHHHHHh
Confidence 4456778999996543233344555444 44555554 4799999998664
No 138
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=22.60 E-value=84 Score=22.75 Aligned_cols=57 Identities=12% Similarity=0.184 Sum_probs=25.0
Q ss_pred cchhhh-cccccccc--cCCCCCCcCCHHHHHHHHHHHhhC------CCccHHHHHHHHHhcCcCCCCC
Q psy2182 4 EEGYYE-TGSIKPRA--IGGSKPRVATNGVVTKIADYKREC------PSIFAWEIRDRLLAEGVCNNDN 63 (67)
Q Consensus 4 L~Ry~e-TGsi~Pg~--iGGskpk~~t~~v~~~I~~~k~~~------p~ifawEiR~~L~~~Gvc~~~~ 63 (67)
+.++.. .+.|+||. + ++..+..++.+.+..=+... ++.++++|-++|.+.+.|+...
T Consensus 33 ~~~~~~~~~~lkaG~Y~l---~~~mS~~eil~~L~~g~~~~~~vTIpEG~t~~~i~~~l~~~~~~~~~~ 98 (297)
T PF02618_consen 33 YAKLNGYDSKLKAGTYEL---NPGMSYKEILSILTSGKVAQVRVTIPEGFTLEQIAQRLAEKGGISKED 98 (297)
T ss_dssp -------------EEEEE----TT--HHHHHHHHHH-----EEEEE-TT--HHHHHHHHHCSTTEE---
T ss_pred HHHhCCCCCceeeeEEEe---CCCCCHHHHHHHHHhcccceeEEEecCCCcHHHHHHHHHhccCCCHHH
Confidence 334443 46788887 4 44556666777665544433 5889999999999999986543
No 139
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=22.16 E-value=32 Score=19.79 Aligned_cols=15 Identities=27% Similarity=0.304 Sum_probs=11.8
Q ss_pred hhCCCccHHHHHHHH
Q psy2182 39 RECPSIFAWEIRDRL 53 (67)
Q Consensus 39 ~~~p~ifawEiR~~L 53 (67)
+-.|+..+-|+|+.|
T Consensus 3 ~~kPG~lS~~LR~AL 17 (54)
T smart00581 3 HFKPGRISDELREAL 17 (54)
T ss_pred CccCCcCCHHHHHHc
Confidence 446888888999887
No 140
>cd07480 Peptidases_S8_12 Peptidase S8 family domain, uncharacterized subfamily 12. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=21.80 E-value=99 Score=21.68 Aligned_cols=33 Identities=21% Similarity=0.104 Sum_probs=27.4
Q ss_pred CCcCCHHHHHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 23 PRVATNGVVTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 23 pk~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
.+.++|-|.-.+.-+++.+|.+..-++++.|.+
T Consensus 237 TS~AaP~VaG~aAll~~~~p~~~~~~~~~~l~~ 269 (297)
T cd07480 237 TSMATPHVAGVAALWAEALPKAGGRALAALLQA 269 (297)
T ss_pred HHHHHHHHHHHHHHHHHhCcccCHHHHHHHHHH
Confidence 457788899999999999999998888777774
No 141
>PHA00687 hypothetical protein
Probab=21.58 E-value=45 Score=19.05 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=16.9
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCcc
Q psy2182 22 KPRVATNGVVTKIADYKRECPSIF 45 (67)
Q Consensus 22 kpk~~t~~v~~~I~~~k~~~p~if 45 (67)
.|-.+..+++..-+..|++.|.+|
T Consensus 31 dplarvkaiekatervkrqyphff 54 (56)
T PHA00687 31 DPLARVKAIEKATERVKRQYPHFF 54 (56)
T ss_pred ChHHHHHHHHHHHHHHHHhcchhh
Confidence 444556667777777888888776
No 142
>PRK10963 hypothetical protein; Provisional
Probab=21.35 E-value=65 Score=22.36 Aligned_cols=23 Identities=26% Similarity=0.465 Sum_probs=16.9
Q ss_pred HHHHHHHHhhCCCccHHHHHHHHHh
Q psy2182 31 VTKIADYKRECPSIFAWEIRDRLLA 55 (67)
Q Consensus 31 ~~~I~~~k~~~p~ifawEiR~~L~~ 55 (67)
++.|.+|-++||++|.. ...|++
T Consensus 5 ~~~V~~yL~~~PdFf~~--h~~Ll~ 27 (223)
T PRK10963 5 DRAVVDYLLQNPDFFIR--NARLVE 27 (223)
T ss_pred HHHHHHHHHHCchHHhh--CHHHHH
Confidence 46688999999999976 444443
No 143
>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins.
Probab=21.33 E-value=56 Score=18.31 Aligned_cols=13 Identities=31% Similarity=0.468 Sum_probs=10.6
Q ss_pred CCCccHHHHHHHH
Q psy2182 41 CPSIFAWEIRDRL 53 (67)
Q Consensus 41 ~p~ifawEiR~~L 53 (67)
.|+..+-|+|+.|
T Consensus 1 kPG~lS~~LR~AL 13 (48)
T PF04046_consen 1 KPGKLSDELREAL 13 (48)
T ss_pred CCcccCHHHHHHc
Confidence 3778888999887
No 144
>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=21.13 E-value=2.1e+02 Score=17.87 Aligned_cols=51 Identities=16% Similarity=-0.025 Sum_probs=28.6
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHHHHHHH-hhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTKIADYK-RECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~I~~~k-~~~p~ifawEiR~~L~ 54 (67)
|.-|-+.|=+.|-.-..+.-+.-+++.+..+...+ -..-++..-||++-|-
T Consensus 16 lR~Ye~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~ 67 (124)
T TIGR02051 16 IRYYERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLG 67 (124)
T ss_pred HHHHHHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence 44566778887543222223334555544444432 2234799999998774
No 145
>PRK10678 moaE molybdopterin guanine dinucleotide biosynthesis protein MoaE; Provisional
Probab=20.91 E-value=47 Score=22.33 Aligned_cols=36 Identities=14% Similarity=0.144 Sum_probs=30.0
Q ss_pred hhhcccccccc------cCCCCCCcCCHHHHHHHHHHHhhCC
Q psy2182 7 YYETGSIKPRA------IGGSKPRVATNGVVTKIADYKRECP 42 (67)
Q Consensus 7 y~eTGsi~Pg~------iGGskpk~~t~~v~~~I~~~k~~~p 42 (67)
++.+|.+.||- ..+..++.+-.+....|+.+|.+-|
T Consensus 82 ~HR~G~l~~Ge~~v~Vav~s~HR~~Af~A~~~~id~lK~~vP 123 (150)
T PRK10678 82 IHRVGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAP 123 (150)
T ss_pred EEeEecccCCCEEEEEEEECCCHHHHHHHHHHHHHHHhhcCC
Confidence 57889999995 4677888888999999999998876
No 146
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=20.66 E-value=1.3e+02 Score=14.83 Aligned_cols=20 Identities=20% Similarity=0.376 Sum_probs=15.5
Q ss_pred CccHHHHHHHHHhcCcCCCC
Q psy2182 43 SIFAWEIRDRLLAEGVCNND 62 (67)
Q Consensus 43 ~ifawEiR~~L~~~Gvc~~~ 62 (67)
.+..-|||+.|.+.|+-...
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G 22 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSG 22 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCC
Confidence 46678899999998886544
No 147
>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=20.65 E-value=1.9e+02 Score=18.79 Aligned_cols=48 Identities=23% Similarity=0.197 Sum_probs=30.9
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHHH---HHHHHhhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVTK---IADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~~---I~~~k~~~p~ifawEiR~~L~ 54 (67)
|.-|.+.|-|.|..-.|.. +.-+++.+.. |..++.. ++.+-||++-|.
T Consensus 18 LRyYE~~GLl~~~r~~~g~-R~Y~~~di~~l~~I~~lr~~--G~sL~eI~~~l~ 68 (142)
T TIGR01950 18 LHFYESKGLITSIRNSGNQ-RRYKRDVLRRVAVIKAAQRV--GIPLATIGEALA 68 (142)
T ss_pred HHHHHHCCCCCCccCCCCC-EEECHHHHHHHHHHHHHHHc--CCCHHHHHHHHH
Confidence 4457778999885543433 4455655544 4555443 799999999875
No 148
>PRK15043 transcriptional regulator MirA; Provisional
Probab=20.50 E-value=2.2e+02 Score=20.62 Aligned_cols=48 Identities=17% Similarity=0.320 Sum_probs=30.0
Q ss_pred hhhh--cccccccccCCCCCCcCCHHHHHHH---HHHHhhCCCccHHHHHHHHHhc
Q psy2182 6 GYYE--TGSIKPRAIGGSKPRVATNGVVTKI---ADYKRECPSIFAWEIRDRLLAE 56 (67)
Q Consensus 6 Ry~e--TGsi~Pg~iGGskpk~~t~~v~~~I---~~~k~~~p~ifawEiR~~L~~~ 56 (67)
||+| .|-+.|....|.. |.-+++.++.| ..++. -++..-||+.-|..+
T Consensus 21 R~wErr~GLL~P~Rt~~G~-R~Ys~~dv~rL~~I~~l~~--~G~~i~eIk~ll~~~ 73 (243)
T PRK15043 21 RAWQRRYGLLKPQRTDGGH-RLFNDADIDRIREIKRWID--NGVQVSKVKMLLSNE 73 (243)
T ss_pred HHHHHhcCCCCCccCCCCC-EEECHHHHHHHHHHHHHHH--cCCCHHHHHHHHhcc
Confidence 5554 5999997654332 44455544444 44443 378889998877654
No 149
>PF14909 SPATA6: Spermatogenesis-assoc protein 6
Probab=20.31 E-value=31 Score=23.22 Aligned_cols=16 Identities=19% Similarity=0.214 Sum_probs=12.6
Q ss_pred Ccccchhhhccccccc
Q psy2182 1 MYSEEGYYETGSIKPR 16 (67)
Q Consensus 1 ~~~L~Ry~eTGsi~Pg 16 (67)
+++|++|.+|+.+.|=
T Consensus 26 v~~lg~~~~T~~~ppv 41 (140)
T PF14909_consen 26 VCILGQYKRTRCLPPV 41 (140)
T ss_pred EEEcccEeecccCCCc
Confidence 3688999999988763
No 150
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=20.17 E-value=2e+02 Score=18.34 Aligned_cols=34 Identities=15% Similarity=0.092 Sum_probs=22.6
Q ss_pred cCCHHHHHHHHHHHhhCCCccHHHHHHHHHhcCcC
Q psy2182 25 VATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVC 59 (67)
Q Consensus 25 ~~t~~v~~~I~~~k~~~p~ifawEiR~~L~~~Gvc 59 (67)
.......+....|-.. -+-+.-|||++|.+.|+-
T Consensus 8 ~~~~~a~~~al~~L~~-r~~s~~el~~kL~~kg~~ 41 (157)
T PRK00117 8 RMYASARARALRLLAR-REHSRAELRRKLAAKGFS 41 (157)
T ss_pred cHHHHHHHHHHHHHcc-chhHHHHHHHHHHhcCCC
Confidence 3444455555555444 367889999999999874
No 151
>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=20.15 E-value=2.3e+02 Score=17.55 Aligned_cols=49 Identities=18% Similarity=0.104 Sum_probs=32.4
Q ss_pred cchhhhcccccccccCCCCCCcCCHHHHH---HHHHHHhhCCCccHHHHHHHHH
Q psy2182 4 EEGYYETGSIKPRAIGGSKPRVATNGVVT---KIADYKRECPSIFAWEIRDRLL 54 (67)
Q Consensus 4 L~Ry~eTGsi~Pg~iGGskpk~~t~~v~~---~I~~~k~~~p~ifawEiR~~L~ 54 (67)
|.-|.+.|-+.|-.-..+.-+.-+++.+. .|..+++- ++.+-||++-|.
T Consensus 17 LRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~--G~sL~eI~~~l~ 68 (127)
T cd04784 17 IRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSL--DMSLDEIRTLLQ 68 (127)
T ss_pred HHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHc--CCCHHHHHHHHH
Confidence 44577789888644333444566666654 55555555 799999998764
No 152
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=20.01 E-value=1.3e+02 Score=18.28 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=19.9
Q ss_pred CHHHHHHHHHHHhhCCCccHHHHHHHH
Q psy2182 27 TNGVVTKIADYKRECPSIFAWEIRDRL 53 (67)
Q Consensus 27 t~~v~~~I~~~k~~~p~ifawEiR~~L 53 (67)
.|+-...+.+++.++|+..+-||=+.|
T Consensus 38 l~~~l~~~a~lRl~~Pd~SL~EL~~~~ 64 (85)
T PF02650_consen 38 LPEKLREFAELRLENPDASLKELGELL 64 (85)
T ss_dssp S-HHHHHHHHHHHH-TTS-HHHHHHTT
T ss_pred CCHHHHHHHHHHHHCccccHHHHHHHH
Confidence 456677788999999999999997755
Done!