Query 002388
Match_columns 929
No_of_seqs 364 out of 1505
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 22:54:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002388hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0954 PHD finger protein [Ge 100.0 5.1E-44 1.1E-48 408.3 7.1 517 3-596 328-892 (893)
2 COG5141 PHD zinc finger-contai 100.0 2.2E-34 4.8E-39 317.9 5.1 206 702-923 190-409 (669)
3 KOG0954 PHD finger protein [Ge 100.0 2.3E-33 5.1E-38 321.4 5.5 166 703-886 269-440 (893)
4 KOG0956 PHD finger protein AF1 100.0 4.1E-33 8.8E-38 316.9 6.2 170 702-887 2-185 (900)
5 KOG0955 PHD finger protein BR1 100.0 6.3E-32 1.4E-36 327.2 8.1 168 702-885 216-396 (1051)
6 KOG0957 PHD finger protein [Ge 99.9 1.5E-28 3.2E-33 272.3 4.2 185 707-908 121-324 (707)
7 PF13832 zf-HC5HC2H_2: PHD-zin 99.9 5.7E-25 1.2E-29 206.8 5.9 107 2-113 4-110 (110)
8 KOG0956 PHD finger protein AF1 99.9 5E-24 1.1E-28 243.4 2.6 114 3-120 67-187 (900)
9 PF13832 zf-HC5HC2H_2: PHD-zin 99.9 3.5E-23 7.5E-28 194.7 7.5 106 776-882 2-110 (110)
10 COG5141 PHD zinc finger-contai 99.9 2.9E-23 6.2E-28 230.4 2.7 116 3-120 252-369 (669)
11 KOG0955 PHD finger protein BR1 99.8 7.1E-22 1.5E-26 240.4 3.8 114 2-117 277-397 (1051)
12 PF13771 zf-HC5HC2H: PHD-like 99.7 2.1E-18 4.7E-23 156.4 4.4 88 23-114 1-90 (90)
13 KOG0957 PHD finger protein [Ge 99.7 6.2E-18 1.3E-22 188.6 1.3 112 3-118 187-303 (707)
14 PF13771 zf-HC5HC2H: PHD-like 99.5 8.9E-15 1.9E-19 132.8 3.5 85 797-883 1-90 (90)
15 PF13831 PHD_2: PHD-finger; PD 98.9 3.8E-10 8.3E-15 87.1 0.1 34 719-752 2-36 (36)
16 KOG1080 Histone H3 (Lys4) meth 98.8 4.6E-09 9.9E-14 129.8 5.9 143 700-865 568-715 (1005)
17 KOG1080 Histone H3 (Lys4) meth 97.7 1.4E-05 3.1E-10 99.6 2.1 86 2-95 631-716 (1005)
18 PF00628 PHD: PHD-finger; Int 97.5 5.1E-05 1.1E-09 62.1 1.8 46 707-753 1-50 (51)
19 smart00249 PHD PHD zinc finger 97.5 0.00012 2.6E-09 57.5 3.6 44 707-751 1-47 (47)
20 KOG1244 Predicted transcriptio 97.0 0.00029 6.4E-09 75.9 1.8 51 704-755 280-332 (336)
21 KOG1512 PHD Zn-finger protein 96.7 0.00076 1.7E-08 73.1 1.7 49 700-749 309-357 (381)
22 KOG1084 Transcription factor T 96.6 0.0012 2.6E-08 75.6 2.7 86 17-114 236-321 (375)
23 KOG4323 Polycomb-like PHD Zn-f 96.4 0.0033 7.1E-08 73.1 4.6 134 706-883 84-222 (464)
24 COG5034 TNG2 Chromatin remodel 96.2 0.014 3.1E-07 62.9 8.1 52 699-753 215-269 (271)
25 KOG4323 Polycomb-like PHD Zn-f 96.2 0.0026 5.7E-08 73.9 2.4 53 703-755 166-225 (464)
26 KOG1084 Transcription factor T 96.1 0.0025 5.5E-08 73.0 2.0 97 775-883 222-321 (375)
27 PF15446 zf-PHD-like: PHD/FYVE 95.2 0.022 4.9E-07 58.2 4.6 72 707-787 1-84 (175)
28 KOG4299 PHD Zn-finger protein 93.9 0.025 5.4E-07 67.5 1.4 48 706-754 254-305 (613)
29 KOG0825 PHD Zn-finger protein 93.8 0.031 6.8E-07 67.7 2.1 53 701-754 211-266 (1134)
30 smart00249 PHD PHD zinc finger 93.2 0.078 1.7E-06 41.4 2.8 32 829-862 1-34 (47)
31 KOG1973 Chromatin remodeling p 92.0 0.089 1.9E-06 58.1 2.3 50 702-754 216-268 (274)
32 PF14446 Prok-RING_1: Prokaryo 91.4 0.13 2.9E-06 43.7 2.2 32 705-736 5-36 (54)
33 TIGR02844 spore_III_D sporulat 91.2 0.22 4.9E-06 45.5 3.6 50 222-272 9-60 (80)
34 PF09012 FeoC: FeoC like trans 88.8 0.21 4.6E-06 43.7 1.4 32 223-254 4-35 (69)
35 KOG0383 Predicted helicase [Ge 87.3 0.27 5.8E-06 60.5 1.5 49 700-752 42-92 (696)
36 PF08220 HTH_DeoR: DeoR-like h 87.3 0.39 8.5E-06 40.7 2.1 34 222-255 3-36 (57)
37 PF10198 Ada3: Histone acetylt 87.1 4.2 9.1E-05 40.6 9.4 82 531-612 14-104 (131)
38 PF00628 PHD: PHD-finger; Int 84.4 0.51 1.1E-05 38.5 1.3 30 829-860 1-32 (51)
39 PF00356 LacI: Bacterial regul 83.7 0.8 1.7E-05 37.7 2.2 44 235-278 1-45 (46)
40 PF02796 HTH_7: Helix-turn-hel 81.5 0.9 2E-05 36.7 1.7 32 222-254 11-42 (45)
41 TIGR02607 antidote_HigA addict 76.7 3.2 7E-05 36.4 3.8 55 218-272 2-58 (78)
42 KOG4443 Putative transcription 76.0 1.4 3E-05 53.5 1.7 49 706-755 69-119 (694)
43 smart00530 HTH_XRE Helix-turn- 73.7 3.6 7.9E-05 31.5 3.1 48 225-272 2-50 (56)
44 PF13412 HTH_24: Winged helix- 73.2 2.2 4.8E-05 34.4 1.8 33 222-254 6-38 (48)
45 PF13404 HTH_AsnC-type: AsnC-t 71.6 2.6 5.7E-05 33.9 1.8 32 223-254 7-38 (42)
46 PF01381 HTH_3: Helix-turn-hel 71.1 4.3 9.4E-05 33.2 3.1 48 225-272 1-49 (55)
47 PF02318 FYVE_2: FYVE-type zin 71.0 3.1 6.7E-05 40.4 2.5 48 706-754 55-103 (118)
48 PF00130 C1_1: Phorbol esters/ 69.4 4.1 8.8E-05 33.6 2.5 34 705-738 11-45 (53)
49 PF07649 C1_3: C1-like domain; 69.3 2.1 4.7E-05 31.7 0.8 28 707-735 2-29 (30)
50 PF13443 HTH_26: Cro/C1-type H 69.3 4.1 9E-05 34.3 2.6 48 225-272 2-51 (63)
51 KOG1973 Chromatin remodeling p 69.3 2.3 4.9E-05 47.2 1.3 49 827-885 219-268 (274)
52 PF01978 TrmB: Sugar-specific 68.1 3.2 6.9E-05 35.9 1.7 34 221-254 10-43 (68)
53 cd00569 HTH_Hin_like Helix-tur 67.8 7 0.00015 27.4 3.3 32 220-252 9-40 (42)
54 KOG1512 PHD Zn-finger protein 67.7 2.9 6.2E-05 46.4 1.7 48 705-752 258-315 (381)
55 KOG1245 Chromatin remodeling c 67.4 1.5 3.4E-05 58.1 -0.5 51 704-755 1107-1159(1404)
56 PF13542 HTH_Tnp_ISL3: Helix-t 66.8 4 8.7E-05 33.3 2.0 31 222-254 18-48 (52)
57 cd00029 C1 Protein kinase C co 66.1 3.4 7.4E-05 33.1 1.4 34 705-738 11-45 (50)
58 KOG1473 Nucleosome remodeling 65.8 6 0.00013 50.8 4.1 116 700-858 339-458 (1414)
59 PF10668 Phage_terminase: Phag 65.3 2.9 6.3E-05 36.5 0.9 22 231-252 20-41 (60)
60 smart00109 C1 Protein kinase C 64.4 3.1 6.8E-05 33.0 0.9 33 705-737 11-43 (49)
61 cd00093 HTH_XRE Helix-turn-hel 64.1 8.1 0.00018 29.7 3.2 48 224-271 3-51 (58)
62 PF13936 HTH_38: Helix-turn-he 63.3 3.7 8E-05 33.2 1.1 30 224-254 12-41 (44)
63 PF04967 HTH_10: HTH DNA bindi 63.2 5.1 0.00011 34.1 2.0 31 224-254 8-44 (53)
64 KOG1044 Actin-binding LIM Zn-f 62.1 3.3 7.1E-05 49.8 0.8 35 828-866 193-228 (670)
65 smart00420 HTH_DEOR helix_turn 62.0 5.9 0.00013 31.4 2.1 32 223-254 4-35 (53)
66 smart00550 Zalpha Z-DNA-bindin 60.4 5.8 0.00013 34.9 1.9 33 222-254 9-43 (68)
67 TIGR03070 couple_hipB transcri 60.2 12 0.00026 30.3 3.7 36 220-255 2-37 (58)
68 PF13518 HTH_28: Helix-turn-he 59.9 5.9 0.00013 31.9 1.8 28 224-253 5-32 (52)
69 cd04718 BAH_plant_2 BAH, or Br 59.6 5.7 0.00012 40.5 1.9 28 730-757 1-30 (148)
70 PF03107 C1_2: C1 domain; Int 58.6 7.8 0.00017 28.9 2.1 27 707-735 2-29 (30)
71 PRK10681 DNA-binding transcrip 55.9 7.5 0.00016 42.4 2.3 35 221-255 9-43 (252)
72 PF13901 DUF4206: Domain of un 55.2 9.7 0.00021 40.5 2.9 44 704-754 151-198 (202)
73 PF08279 HTH_11: HTH domain; 54.8 8 0.00017 31.9 1.8 33 222-254 3-36 (55)
74 PF01022 HTH_5: Bacterial regu 54.8 6.7 0.00015 31.8 1.3 31 223-254 6-36 (47)
75 KOG1701 Focal adhesion adaptor 54.7 4.9 0.00011 46.9 0.7 153 707-883 276-459 (468)
76 PF14197 Cep57_CLD_2: Centroso 51.5 50 0.0011 29.6 6.3 60 545-611 2-63 (69)
77 PF01325 Fe_dep_repress: Iron 50.1 12 0.00026 32.3 2.2 25 230-254 19-43 (60)
78 PF12844 HTH_19: Helix-turn-he 50.1 16 0.00034 30.9 2.9 49 224-272 3-52 (64)
79 PF04760 IF2_N: Translation in 50.0 6.6 0.00014 32.8 0.5 23 232-254 2-24 (54)
80 COG5034 TNG2 Chromatin remodel 49.7 10 0.00022 41.8 1.9 33 825-857 218-252 (271)
81 PF00165 HTH_AraC: Bacterial r 48.6 7.1 0.00015 30.7 0.5 25 231-255 6-30 (42)
82 PRK09492 treR trehalose repres 48.4 13 0.00028 40.5 2.6 52 231-282 2-54 (315)
83 smart00354 HTH_LACI helix_turn 47.7 15 0.00032 32.3 2.4 47 234-280 1-48 (70)
84 PRK10014 DNA-binding transcrip 47.5 13 0.00029 40.9 2.6 51 232-282 5-56 (342)
85 PF05043 Mga: Mga helix-turn-h 47.4 16 0.00034 33.0 2.6 43 222-274 19-61 (87)
86 KOG1244 Predicted transcriptio 46.7 13 0.00028 41.3 2.2 49 706-754 225-284 (336)
87 PRK09726 antitoxin HipB; Provi 45.5 26 0.00056 32.1 3.7 59 218-276 10-69 (88)
88 KOG0825 PHD Zn-finger protein 45.4 22 0.00048 44.4 4.1 51 827-887 215-268 (1134)
89 PRK05472 redox-sensing transcr 44.3 12 0.00026 39.6 1.6 35 221-255 18-54 (213)
90 PHA01976 helix-turn-helix prot 44.2 31 0.00068 29.3 3.8 52 220-271 2-54 (67)
91 COG1349 GlpR Transcriptional r 43.9 14 0.00029 40.5 1.9 35 221-255 7-41 (253)
92 KOG3799 Rab3 effector RIM1 and 43.6 11 0.00024 37.8 1.1 49 705-753 65-115 (169)
93 PRK14987 gluconate operon tran 43.5 15 0.00033 40.4 2.3 52 231-282 3-55 (331)
94 PF11793 FANCL_C: FANCL C-term 42.6 17 0.00037 32.3 2.0 32 706-737 3-38 (70)
95 smart00418 HTH_ARSR helix_turn 42.4 16 0.00034 29.7 1.7 31 224-255 2-32 (66)
96 PF08280 HTH_Mga: M protein tr 42.3 17 0.00037 31.0 1.9 34 222-255 8-41 (59)
97 smart00344 HTH_ASNC helix_turn 41.9 17 0.00036 33.9 2.0 32 223-254 7-38 (108)
98 PHA02591 hypothetical protein; 41.3 22 0.00048 32.8 2.5 34 220-254 47-80 (83)
99 TIGR02405 trehalos_R_Ecol treh 40.3 20 0.00042 39.3 2.5 50 233-282 1-51 (311)
100 TIGR00373 conserved hypothetic 39.7 18 0.00039 37.1 1.9 34 222-255 17-50 (158)
101 smart00345 HTH_GNTR helix_turn 39.4 22 0.00047 28.9 2.1 21 235-255 22-42 (60)
102 PF14446 Prok-RING_1: Prokaryo 38.9 30 0.00065 29.8 2.8 38 827-866 5-45 (54)
103 PRK10141 DNA-binding transcrip 38.4 20 0.00043 35.2 1.9 34 222-255 19-52 (117)
104 PF12840 HTH_20: Helix-turn-he 38.2 21 0.00045 30.4 1.8 33 222-254 13-45 (61)
105 PRK11169 leucine-responsive tr 38.2 17 0.00037 37.1 1.5 33 222-254 17-49 (164)
106 KOG4443 Putative transcription 37.9 12 0.00027 45.8 0.5 49 706-754 19-71 (694)
107 TIGR02531 yecD_yerC TrpR-relat 37.9 20 0.00042 33.6 1.7 29 223-252 41-69 (88)
108 PF03107 C1_2: C1 domain; Int 37.7 21 0.00046 26.6 1.6 27 829-857 2-30 (30)
109 PRK10434 srlR DNA-bindng trans 37.6 20 0.00044 39.2 2.1 34 222-255 8-41 (256)
110 PRK04424 fatty acid biosynthes 37.4 21 0.00046 37.3 2.1 37 219-255 7-43 (185)
111 PRK06266 transcription initiat 37.4 22 0.00047 37.3 2.1 34 222-255 25-58 (178)
112 COG5194 APC11 Component of SCF 37.3 12 0.00026 34.6 0.2 32 828-859 21-65 (88)
113 PF12324 HTH_15: Helix-turn-he 37.1 21 0.00045 32.8 1.7 35 221-255 26-60 (77)
114 smart00342 HTH_ARAC helix_turn 37.0 19 0.00042 30.7 1.5 29 226-254 43-72 (84)
115 COG1321 TroR Mn-dependent tran 36.9 22 0.00047 36.4 2.0 36 220-255 10-46 (154)
116 PRK11179 DNA-binding transcrip 36.6 22 0.00047 35.8 2.0 33 222-254 12-44 (153)
117 PF07227 DUF1423: Protein of u 36.4 27 0.00058 41.4 2.9 30 707-736 130-161 (446)
118 smart00347 HTH_MARR helix_turn 36.3 28 0.0006 31.1 2.4 35 220-254 11-45 (101)
119 PRK13509 transcriptional repre 36.2 24 0.00053 38.5 2.4 35 221-255 7-41 (251)
120 smart00744 RINGv The RING-vari 35.9 12 0.00026 31.1 0.0 31 707-737 1-34 (49)
121 PRK15431 ferrous iron transpor 35.2 30 0.00065 31.9 2.4 29 226-254 9-37 (78)
122 PF08221 HTH_9: RNA polymerase 35.1 24 0.00053 30.6 1.7 35 221-255 15-49 (62)
123 PF07649 C1_3: C1-like domain; 34.9 20 0.00043 26.6 1.0 27 829-857 2-30 (30)
124 PF01047 MarR: MarR family; I 34.7 30 0.00065 28.7 2.2 35 220-254 4-38 (59)
125 smart00342 HTH_ARAC helix_turn 34.5 24 0.00051 30.2 1.6 23 233-255 1-23 (84)
126 TIGR03830 CxxCG_CxxCG_HTH puta 34.5 45 0.00098 31.9 3.7 52 223-274 68-119 (127)
127 PRK10339 DNA-binding transcrip 34.4 27 0.00059 38.3 2.5 49 233-281 1-52 (327)
128 PF13551 HTH_29: Winged helix- 34.3 37 0.0008 31.3 3.0 50 228-277 7-76 (112)
129 COG5194 APC11 Component of SCF 34.2 15 0.00032 34.0 0.2 32 57-88 21-65 (88)
130 cd00090 HTH_ARSR Arsenical Res 34.0 33 0.00072 28.4 2.4 35 219-254 7-41 (78)
131 PF12802 MarR_2: MarR family; 34.0 28 0.00061 28.9 1.9 33 222-254 8-42 (62)
132 smart00421 HTH_LUXR helix_turn 33.9 24 0.00051 28.1 1.4 30 224-255 11-40 (58)
133 PF04218 CENP-B_N: CENP-B N-te 33.4 18 0.00039 30.5 0.6 26 227-253 17-42 (53)
134 PF06971 Put_DNA-bind_N: Putat 33.2 28 0.0006 29.4 1.7 31 222-252 15-47 (50)
135 smart00346 HTH_ICLR helix_turn 33.0 28 0.00061 31.2 1.9 32 223-254 9-41 (91)
136 cd00092 HTH_CRP helix_turn_hel 32.5 37 0.00081 28.5 2.5 25 230-254 22-46 (67)
137 KOG4362 Transcriptional regula 32.2 14 0.00031 45.7 -0.2 67 16-88 328-394 (684)
138 TIGR00180 parB_part ParB-like 31.9 33 0.00071 35.7 2.4 52 217-268 104-155 (187)
139 PF13639 zf-RING_2: Ring finge 31.8 18 0.00039 28.7 0.4 30 707-737 2-31 (44)
140 cd01392 HTH_LacI Helix-turn-he 31.7 42 0.00091 27.0 2.6 42 237-278 1-43 (52)
141 PRK10727 DNA-binding transcrip 31.6 32 0.0007 38.1 2.5 51 233-283 1-52 (343)
142 PRK10401 DNA-binding transcrip 31.5 33 0.0007 38.1 2.5 50 233-282 1-51 (346)
143 PF14569 zf-UDP: Zinc-binding 30.9 11 0.00023 34.7 -1.2 49 704-753 8-59 (80)
144 PRK10703 DNA-binding transcrip 30.8 34 0.00075 37.7 2.5 51 233-283 1-52 (341)
145 PF01527 HTH_Tnp_1: Transposas 30.6 26 0.00057 30.5 1.3 33 219-251 9-41 (76)
146 KOG4299 PHD Zn-finger protein 30.5 20 0.00043 43.8 0.6 30 56-88 253-285 (613)
147 PRK10411 DNA-binding transcrip 30.5 30 0.00065 37.6 1.9 35 221-255 6-40 (240)
148 PRK10072 putative transcriptio 30.4 52 0.0011 31.3 3.2 51 225-275 38-88 (96)
149 PF08746 zf-RING-like: RING-li 29.9 23 0.00051 28.7 0.7 30 830-859 1-30 (43)
150 COG1522 Lrp Transcriptional re 29.6 34 0.00073 33.7 2.0 33 222-254 11-43 (154)
151 PRK09526 lacI lac repressor; R 29.3 38 0.00083 37.2 2.6 52 232-283 4-56 (342)
152 PF10367 Vps39_2: Vacuolar sor 28.9 46 0.001 30.7 2.6 29 706-736 79-107 (109)
153 PF13743 Thioredoxin_5: Thiore 28.7 1.2E+02 0.0025 31.4 5.8 60 550-612 86-146 (176)
154 cd07377 WHTH_GntR Winged helix 28.6 43 0.00094 27.7 2.2 35 221-255 6-47 (66)
155 TIGR02702 SufR_cyano iron-sulf 28.6 35 0.00075 35.9 1.9 32 223-254 5-36 (203)
156 PF08746 zf-RING-like: RING-li 28.5 35 0.00076 27.7 1.5 30 59-88 1-30 (43)
157 KOG2752 Uncharacterized conser 27.9 50 0.0011 37.6 3.0 112 711-863 58-170 (345)
158 PF12833 HTH_18: Helix-turn-he 27.9 41 0.0009 29.5 2.0 28 221-248 33-60 (81)
159 PRK10906 DNA-binding transcrip 27.3 40 0.00088 36.9 2.2 34 221-254 7-40 (252)
160 PRK09802 DNA-binding transcrip 27.0 41 0.00089 37.2 2.3 36 219-254 17-52 (269)
161 PF10367 Vps39_2: Vacuolar sor 26.9 27 0.00058 32.3 0.7 30 828-858 79-108 (109)
162 PF00440 TetR_N: Bacterial reg 26.9 48 0.001 26.7 2.1 21 232-252 15-35 (47)
163 KOG1844 PHD Zn-finger proteins 26.8 37 0.0008 40.5 2.0 46 709-754 89-135 (508)
164 TIGR01481 ccpA catabolite cont 26.6 43 0.00094 36.6 2.4 49 234-282 2-51 (329)
165 PRK12522 RNA polymerase sigma 26.0 46 0.001 33.4 2.2 40 231-276 133-172 (173)
166 PF13384 HTH_23: Homeodomain-l 25.5 44 0.00095 26.9 1.6 27 224-252 10-36 (50)
167 KOG0695 Serine/threonine prote 25.3 27 0.00059 40.2 0.5 35 705-739 141-176 (593)
168 PLN02638 cellulose synthase A 25.2 44 0.00095 43.7 2.3 50 704-754 16-68 (1079)
169 PF13413 HTH_25: Helix-turn-he 25.0 42 0.0009 29.2 1.5 32 224-255 1-32 (62)
170 PLN02400 cellulose synthase 24.5 54 0.0012 42.9 2.9 50 704-754 35-87 (1085)
171 PF10497 zf-4CXXC_R1: Zinc-fin 24.3 65 0.0014 31.1 2.8 64 701-786 3-82 (105)
172 PRK10046 dpiA two-component re 24.2 43 0.00092 35.1 1.7 31 223-254 166-198 (225)
173 PLN02436 cellulose synthase A 24.0 51 0.0011 43.1 2.5 49 705-754 36-87 (1094)
174 PF11793 FANCL_C: FANCL C-term 24.0 36 0.00078 30.3 0.9 32 828-859 3-39 (70)
175 PF13309 HTH_22: HTH domain 23.6 50 0.0011 28.9 1.7 35 218-252 23-61 (64)
176 PF09824 ArsR: ArsR transcript 23.5 62 0.0013 33.5 2.6 35 220-254 108-142 (160)
177 PF04405 ScdA_N: Domain of Unk 23.4 34 0.00073 29.4 0.6 37 220-256 14-54 (56)
178 PLN02195 cellulose synthase A 22.6 56 0.0012 42.4 2.5 49 705-754 6-57 (977)
179 smart00109 C1 Protein kinase C 22.3 44 0.00096 26.3 1.1 32 828-861 12-46 (49)
180 cd04767 HTH_HspR-like_MBC Heli 22.1 62 0.0013 32.0 2.2 62 234-295 2-76 (120)
181 PRK04217 hypothetical protein; 22.1 90 0.002 30.5 3.3 33 222-255 48-80 (110)
182 PRK09413 IS2 repressor TnpA; R 21.7 70 0.0015 31.1 2.5 34 217-251 13-47 (121)
183 PHA00542 putative Cro-like pro 21.5 98 0.0021 28.2 3.2 46 227-272 25-72 (82)
184 PRK12547 RNA polymerase sigma 21.5 68 0.0015 32.1 2.4 23 232-254 127-149 (164)
185 KOG4628 Predicted E3 ubiquitin 21.4 53 0.0011 38.0 1.8 47 706-754 230-276 (348)
186 PF12906 RINGv: RING-variant d 21.4 13 0.00029 30.6 -2.2 30 708-737 1-33 (47)
187 cd06170 LuxR_C_like C-terminal 21.4 67 0.0015 25.6 2.0 27 228-255 11-37 (57)
188 PRK09647 RNA polymerase sigma 21.4 61 0.0013 34.0 2.2 34 231-274 152-185 (203)
189 PF01418 HTH_6: Helix-turn-hel 21.2 70 0.0015 28.6 2.2 51 223-273 24-76 (77)
190 PF10078 DUF2316: Uncharacteri 21.1 72 0.0016 30.2 2.3 27 229-255 19-45 (89)
191 PRK11050 manganese transport r 21.1 72 0.0016 32.3 2.5 36 220-255 37-73 (152)
192 PRK04172 pheS phenylalanyl-tRN 20.8 66 0.0014 38.7 2.5 35 220-254 7-41 (489)
193 TIGR03826 YvyF flagellar opero 20.8 75 0.0016 32.2 2.5 35 220-254 31-67 (137)
194 COG3413 Predicted DNA binding 20.7 59 0.0013 34.5 1.9 34 222-255 161-200 (215)
195 PRK13890 conjugal transfer pro 20.4 1.2E+02 0.0026 29.7 3.8 35 221-255 6-40 (120)
196 PF07638 Sigma70_ECF: ECF sigm 20.4 57 0.0012 33.7 1.6 33 232-274 150-182 (185)
197 PHA02862 5L protein; Provision 20.3 35 0.00076 34.9 0.1 49 705-753 2-50 (156)
198 PRK09641 RNA polymerase sigma 20.3 81 0.0018 31.8 2.7 33 232-274 151-183 (187)
199 PF02954 HTH_8: Bacterial regu 20.1 72 0.0015 25.4 1.8 31 224-254 9-39 (42)
No 1
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=100.00 E-value=5.1e-44 Score=408.33 Aligned_cols=517 Identities=30% Similarity=0.393 Sum_probs=319.8
Q ss_pred CCCCCCCCcccccCCCCCcHhhHhhcccCceeeccCccccccccccCchhhcccccccccccccCceeeCCCCCCCcccc
Q 002388 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFH 82 (929)
Q Consensus 3 lCP~~gGALK~T~~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~~FH 82 (929)
|||++||+||+|.+| ..|||+.||||+|||+|++++.|+||++|+.|+..||.|.|++|+.+.||||||+.+.|.++||
T Consensus 328 LCPkkGGamK~~~sg-T~wAHvsCALwIPEVsie~~ekmePItkfs~IpesRwslvC~LCk~k~GACIqCs~k~C~t~fH 406 (893)
T KOG0954|consen 328 LCPKKGGAMKPTKSG-TKWAHVSCALWIPEVSIECPEKMEPITKFSHIPESRWSLVCNLCKVKSGACIQCSNKTCRTAFH 406 (893)
T ss_pred eccccCCcccccCCC-CeeeEeeeeeccceeeccCHhhcCcccccCCCcHHHHHHHHHHhcccCcceEEecccchhhhcc
Confidence 799999999999988 4999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCceEEeccccCCccceeeecCCCCCCCCCCCCCCCCCCCCCCCCC--ccccccccccccccCccceeeeeccC
Q 002388 83 PICAREARHRLEVWGKYGCNNVELRAFCAKHSDIQDNSSTPRTGDPCSAIGS--ESCVSNNLHETLSMSKLHKLKFSCKN 160 (929)
Q Consensus 83 vtCA~~aG~~~e~~~~~g~~~v~~~~fC~~Hr~~~~~~~~~~~~~~~~~d~~--~~~~~~~~~~~l~~~~l~Qlq~~~~~ 160 (929)
++||+++|..|.++.+. .+.+.|++||.+|+.-+...+..+.++....... .......+....+.+.++++.-.
T Consensus 407 v~CA~~aG~~~~~~~~~-~D~v~~~s~c~khs~~~~~~s~g~~~e~p~p~~~~p~~~~~e~~~~s~r~q~l~~~e~e--- 482 (893)
T KOG0954|consen 407 VTCAFEAGLEMKTILKE-NDEVKFKSYCSKHSDHREGKSLGNEAESPHPRCHLPEQSVGEGHRSSDRAQKLQELEGE--- 482 (893)
T ss_pred chhhhhcCCeeeeeecc-CCchhheeecccccccccccccccccCCCCccccChhhhhhhhhhhhHHHHHHhhcchh---
Confidence 99999999999999754 7788999999999988853322211211111000 00123344445555555555422
Q ss_pred CCeeeeeeecCCCCCCCCCCCcccccCCCccccccccccccCCCCCCCCCCCCCCCCcchHHHHHHHHHhhCccccccch
Q 002388 161 GDKIGVHTETSDANSDRSTDSEVTGFSDSRLISVPTSECTNAGKPDRSEFEDVNPSDALNFTLILKKLIDRGKVNVKDIA 240 (929)
Q Consensus 161 gd~~~~~~~t~~~~~n~~~~~ev~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~l~kli~~gkv~v~d~~ 240 (929)
.|.-.|.....+...+|.-..+ ++-.-+- ++..+-+..+..+..|.+|.+|+||++|+|||+++++|
T Consensus 483 ----------f~~~v~~~diae~l~~~e~~vs--~iynywk-lkrks~~n~~lippk~d~~~~i~kk~~~~~kv~~kl~a 549 (893)
T KOG0954|consen 483 ----------FYDIVRNEDIAELLSMPEFAVS--AIYNYWK-LKRKSRFNKELIPPKSDEVGLIAKKLEDLGKVRVKLVA 549 (893)
T ss_pred ----------HhhhhhHHHHHHHhcCchHHHH--HHHHHHH-HhhhccCCCcCCCCcchhccchhhHHHHhhhhhhHHHH
Confidence 2222222222222223322222 1111111 44455555688899999999999999999999999999
Q ss_pred hhhccChhhhhhhccccccccch-----------hHHHHHHhhhcccccccccceeeccccccccccc-------ccccC
Q 002388 241 SDIGISPDLLKTTLADGTFASDL-----------QCKLVKWLSNHAYLGGLLKNVKLKIKSSISSKAD-------IKNSD 302 (929)
Q Consensus 241 ~~~gis~~~l~~~~~~~~~~~~~-----------~~k~~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~ 302 (929)
-++ +|.+.+-+...|.+--. |.--..+|-.|.||++.++...++.+.++.+..- +.-.+
T Consensus 550 hlr---qdlerv~~~~~~~trrekas~s~~ki~eq~f~~ql~l~~q~~~~~~~~~n~~~n~~f~~~~r~tl~~k~~~s~~ 626 (893)
T KOG0954|consen 550 HLR---QDLERVRNLCYTKTRREKASNSYAKIDEQLFPDQLLLQHQHMGSSDKGKNLKRNTTFYSERRATLCTKGIVSLD 626 (893)
T ss_pred HHH---HHHHHhhcccchhcccchhhhhHHHHHhHHHHHHHHHHHHhhcccccchhhhhhccccCCcchhHhhhccccCC
Confidence 988 77776665522222211 1111233678999999999998887666544332 22233
Q ss_pred CCCcccc---ccCCCCccccccc--------------------CCCccccccceeccCCcccccccceec-CCCcccccc
Q 002388 303 SDGLMVS---ESDVADPVAVKSV--------------------PPRRRTKSSIRILRDDKMVSSSEEIFS-GNGIAADKD 358 (929)
Q Consensus 303 ~~~~~~~---~~~~~~~~~~~~v--------------------p~~~r~k~~~~il~dn~~~cs~e~~~~-~ng~~~~~~ 358 (929)
+++...+ .--+..+.+++.+ +.----++|.|+|+.-..+=+-+---+ -|-+..+
T Consensus 627 ~d~~~~a~q~lq~il~p~~~~~~~~i~n~~r~~~t~n~rkns~~~v~ak~~nnrl~~s~Shsp~~~h~~sp~~~t~s~-- 704 (893)
T KOG0954|consen 627 SDILDPAVQKLQSILRPHEINICNNITNNTRCTLTENCRKNSIVVVPAKANNNRLLKSGSHSPAPDHSPSPKNSTVSD-- 704 (893)
T ss_pred ccccCHHHHHhhcccCcchhhhhhccccCcccccChhhccCcceeeecccccCccccCCCcCCccccCCCcCCCccch--
Confidence 4443221 1112222222111 000001222233322222111100000 0000000
Q ss_pred hhhhcccCCCCcccCccccCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCcccccccccccchhhccc---cC
Q 002388 359 EVKVEQLDGEEPAIHNKVSTPDCTEKSPTDPTGSEDSLARGSPMSEGSAAKPSDCGFFESCQSEEAALPDQINLL---NV 435 (929)
Q Consensus 359 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~ 435 (929)
++. .-.+-|..|+ +...++. ++.+ .+.+-+.++- |+
T Consensus 705 -------~~~--h~gk~g~~pr-------~d~~s~s----asss---------------------~n~ksq~~skirsn~ 743 (893)
T KOG0954|consen 705 -------QKV--HHGKSGVIPR-------DDHGSQS----ASSS---------------------SNVKSQNASKIRSNS 743 (893)
T ss_pred -------hhc--CCccCCCCcc-------ccccccc----cccc---------------------cCcccccccccccCc
Confidence 000 0001111111 1111100 0000 0111111111 33
Q ss_pred CCCCCCCCCCCCccccccCCCCCCccccchhhhhh-hccccCccCCCcccccCCcccccccccccCCCcccCccCccCcc
Q 002388 436 DQENPICSSVDTLVPYFINAKPSSGFFWHPYIHKS-LQMQSGLLSGNKVHKSDGDTEISRLEASSTASVCCNHQGRHSKC 514 (929)
Q Consensus 436 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~hp~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 (929)
.++--.-+...+.++.++|.+.+.+|..|-||++. ..+-...+++ ...+..+.+|..+..-+.=.-..++++..
T Consensus 744 s~~s~n~ni~~~~sss~~~~~~~p~fsph~~~~~s~s~s~~e~~sk-----s~~~s~~~~~kq~y~~~~~~~~~~~q~~g 818 (893)
T KOG0954|consen 744 SQNSGNGNIPNPISSSLFNQEAYPGFSPHRYIHKSLSESGKEQTSK-----SSTDSDVARMKQTYTHLAGSEEGNKQLQG 818 (893)
T ss_pred ccccCCCcCCCCcchhhhccccCCCCCcchhhhhhhhhhccccccc-----ccccCCcchhhheecccccccchhhHHHH
Confidence 33322223346777799999999999999999999 5554444332 34445555554222111111222222222
Q ss_pred CCCcccCCccchHHHHHhhhccccccCCCcchhhHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHhhhhcchhHH
Q 002388 515 NDMSCKSDGVNLEQVFKARTRGVLELSPTDEVEGEIIYFQHRLLGNAFSRKRLADNLVCKAVKTLNQEIDVARGRRWDAV 594 (929)
Q Consensus 515 ~~~~~~~~~~~~~q~~~~~~~~~~~~~p~de~e~E~~~~q~~ll~~~~~~~~~~~~lv~~v~k~~~~e~~~~~~r~~d~~ 594 (929)
...+-|+++|+-+|+++.+|.|+.|+|.+|.|..+++.+..+++..+++..+++++++.|++....|+||..
T Consensus 819 --------~e~~~~~s~~~p~~~~d~s~~D~e~~~~~~~q~~~~g~~r~rkqssd~~n~~~asr~~~~~~~~~g~~~~~s 890 (893)
T KOG0954|consen 819 --------AETFLQLSKARPLGILDLSPEDEEEGELLYYQLQLLGTARSRKQSSDNLNYEVASRLPLEIDEQHGRRWDDS 890 (893)
T ss_pred --------HHHHHHhhccCCcccccCCCCchhhhhHHhhhhccccceecccccccCcChhhhccCCCccccccCcCcchh
Confidence 367889999999999999999999999999999999999999999999999999999999999999999965
Q ss_pred HH
Q 002388 595 LV 596 (929)
Q Consensus 595 ~~ 596 (929)
++
T Consensus 891 ~~ 892 (893)
T KOG0954|consen 891 LV 892 (893)
T ss_pred hc
Confidence 43
No 2
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=100.00 E-value=2.2e-34 Score=317.86 Aligned_cols=206 Identities=30% Similarity=0.615 Sum_probs=170.6
Q ss_pred CCCCCcCcccCCCCC-CCCCEEEecccCcccccccccCccCCCCceecccccccccCCCCCCCCCCccCCCccccccccC
Q 002388 702 KEHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLC 780 (929)
Q Consensus 702 ke~d~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C~LC 780 (929)
.+-+..|.+|...+. ..|.||+|++|.++|||.||||..+|+|.|+|++|.+.. +...-|.+|
T Consensus 190 d~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~peG~WlCrkCi~~~----------------~~i~~C~fC 253 (669)
T COG5141 190 DEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGE----------------YQIRCCSFC 253 (669)
T ss_pred hhhhhhhHhccccccCCcceEEEecCcchhhhhhcccceecCcchhhhhhhcccc----------------cceeEEEec
Confidence 356788999999875 478999999999999999999999999999999999862 224559999
Q ss_pred CCCCCceeeccCcchhhhccccccccceeecC-ccccccccccccCC--CCcceeCCCCCCceeecCCcCcccccchhhh
Q 002388 781 GGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTFHPTCA 857 (929)
Q Consensus 781 p~~gGaLK~T~~g~WVHv~CAlw~pev~f~~~-~~~~Vegie~I~k~--k~~C~iC~~~~GacIqC~~~~C~~~FH~~CA 857 (929)
|..+||||.|.+|.|+|++||+|+|++.|.+- .+++|+||.++++. ++.|+||+..+|+||||++.+|.++||++||
T Consensus 254 ps~dGaFkqT~dgrW~H~iCA~~~pelsF~~l~~~dpI~~i~sVs~srwkl~C~iCk~~~GtcIqCs~~nC~~aYHVtCA 333 (669)
T COG5141 254 PSSDGAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCA 333 (669)
T ss_pred cCCCCceeeccCCchHhHhHHHhcchhccccccccchhhhhcccchhhHhheeeEEcccCcceeeecccchhhhhhhhhh
Confidence 99999999999999999999999999999987 78999999998876 6999999999999999999999999999999
Q ss_pred hhcCceEEE----eeCCCcceeeeccccccchhh-hhHhhhchhhhhhh--hhh-hhe--eeeccccccCCccCce
Q 002388 858 RSAGFYLNV----KSTGGNFQHKAYCEKHSLEQK-MKAETQKHGVEELK--GIK-QIR--VRVLCPFANFLGRACS 923 (929)
Q Consensus 858 ~~aGl~~~~----k~~~g~~~~~ayC~kHs~~qr-~k~~~q~~~~eE~k--smk-~~R--vRllc~r~n~~~~~c~ 923 (929)
+++|+++.- .+....+...-||.+|.|..- .....++++.+++. .|. .++ +|.--.+..++++.|-
T Consensus 334 rrag~f~~~~~s~n~~s~~id~e~~c~kh~p~gy~~~~~~r~f~~~kl~~~~~~T~ip~~~~a~~~~~~~f~k~~w 409 (669)
T COG5141 334 RRAGYFDLNIYSHNGISYCIDHEPLCRKHYPLGYGRMNGLRYFGYEKLRYKNPPTAIPRKVRAARPRATLFMKLCW 409 (669)
T ss_pred hhcchhhhhhhcccccceeecchhhhcCCCCcchhccchhccccHHHHhccCCccccchhhhccCCchhhhhcccc
Confidence 999999863 122223445669999998754 25567788877766 444 222 4666666666666663
No 3
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=99.97 E-value=2.3e-33 Score=321.37 Aligned_cols=166 Identities=32% Similarity=0.785 Sum_probs=149.6
Q ss_pred CCCCcCcccCCCCC-CCCCEEEecccCcccccccccCccCCCCceecccccccccCCCCCCCCCCccCCCccccccccCC
Q 002388 703 EHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLCG 781 (929)
Q Consensus 703 e~d~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C~LCp 781 (929)
+++..|+||..++. +.|+||||+.|++.||+.||||..+|+++|+|..|... ..+.|+|||
T Consensus 269 dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg------------------~~ppCvLCP 330 (893)
T KOG0954|consen 269 DEDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALG------------------IEPPCVLCP 330 (893)
T ss_pred cccceeceecCCCccccceeEEeccchhHHHHhhhceeecCCCCeeehhcccc------------------CCCCeeecc
Confidence 37789999999886 58999999999999999999999999999999999875 156899999
Q ss_pred CCCCceeeccCc-chhhhccccccccceeecC-ccccccccccccCC--CCcceeCCCCCCceeecCCcCcccccchhhh
Q 002388 782 GTTGAFRKSANG-QWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTFHPTCA 857 (929)
Q Consensus 782 ~~gGaLK~T~~g-~WVHv~CAlw~pev~f~~~-~~~~Vegie~I~k~--k~~C~iC~~~~GacIqC~~~~C~~~FH~~CA 857 (929)
..||+||.+..+ +|+|++||||+||++|.+. .|+||..|+.|+.. .+.|.+|+.+.|+||+|+..+|.++||++||
T Consensus 331 kkGGamK~~~sgT~wAHvsCALwIPEVsie~~ekmePItkfs~IpesRwslvC~LCk~k~GACIqCs~k~C~t~fHv~CA 410 (893)
T KOG0954|consen 331 KKGGAMKPTKSGTKWAHVSCALWIPEVSIECPEKMEPITKFSHIPESRWSLVCNLCKVKSGACIQCSNKTCRTAFHVTCA 410 (893)
T ss_pred ccCCcccccCCCCeeeEeeeeeccceeeccCHhhcCcccccCCCcHHHHHHHHHHhcccCcceEEecccchhhhccchhh
Confidence 999999998776 5999999999999999887 79999999999877 4999999999999999999999999999999
Q ss_pred hhcCceEEEeeC-CCcceeeeccccccchh
Q 002388 858 RSAGFYLNVKST-GGNFQHKAYCEKHSLEQ 886 (929)
Q Consensus 858 ~~aGl~~~~k~~-~g~~~~~ayC~kHs~~q 886 (929)
+.+|..|.+-.. +....+..||.+|+..+
T Consensus 411 ~~aG~~~~~~~~~~D~v~~~s~c~khs~~~ 440 (893)
T KOG0954|consen 411 FEAGLEMKTILKENDEVKFKSYCSKHSDHR 440 (893)
T ss_pred hhcCCeeeeeeccCCchhheeecccccccc
Confidence 999999987432 44567889999998766
No 4
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=99.97 E-value=4.1e-33 Score=316.92 Aligned_cols=170 Identities=34% Similarity=0.790 Sum_probs=145.6
Q ss_pred CCCCCcCcccCCCCC-CCCCEEEecc--cCcccccccccCccCCCCceecccccccccCCCCCCCCCCccCCCccccccc
Q 002388 702 KEHPRSCDICRRSET-ILNPILICSG--CKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECS 778 (929)
Q Consensus 702 ke~d~~CsVC~~~E~-~~N~Ll~Cd~--C~vaVHq~CYGi~~~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C~ 778 (929)
||.-.-|+||-+--. ..|+|||||+ |-++|||.||||.++|.|+|||++|+.... . ..+.|.
T Consensus 2 KEMVGGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqer--a-------------arvrCe 66 (900)
T KOG0956|consen 2 KEMVGGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQER--A-------------ARVRCE 66 (900)
T ss_pred cccccceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhhh--h-------------ccceee
Confidence 455567999998544 4799999996 999999999999999999999999987521 1 268999
Q ss_pred cCCCCCCceeeccCcchhhhccccccccceeecC-ccccccccccccCC--CCcceeCCCC-------CCceeecCCcCc
Q 002388 779 LCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHK-------HGICIKCNYGNC 848 (929)
Q Consensus 779 LCp~~gGaLK~T~~g~WVHv~CAlw~pev~f~~~-~~~~Vegie~I~k~--k~~C~iC~~~-------~GacIqC~~~~C 848 (929)
|||.++||||+|+++-|+||+||||+||+.|.+- .|+||- +..++.. +..|+||+.. .|+||+|...+|
T Consensus 67 LCP~kdGALKkTDn~GWAHVVCALYIPEVrFgNV~TMEPIi-Lq~VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~C 145 (900)
T KOG0956|consen 67 LCPHKDGALKKTDNGGWAHVVCALYIPEVRFGNVHTMEPII-LQDVPHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGC 145 (900)
T ss_pred cccCcccceecccCCCceEEEEEeeccceeeccccccccee-eccCchhhhcceeeeecccCCccccccccceecccccc
Confidence 9999999999999999999999999999999987 688866 4556654 6899999973 899999999999
Q ss_pred ccccchhhhhhcCceEEEee-CCCcceeeeccccccchhh
Q 002388 849 QTTFHPTCARSAGFYLNVKS-TGGNFQHKAYCEKHSLEQK 887 (929)
Q Consensus 849 ~~~FH~~CA~~aGl~~~~k~-~~g~~~~~ayC~kHs~~qr 887 (929)
.+.|||+||+++|+..+..+ .-+++.|-=||+.|-.+.+
T Consensus 146 kqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~HfsKlk 185 (900)
T KOG0956|consen 146 KQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFSKLK 185 (900)
T ss_pred hhhhhhhHhhhhccceeccccccccceechhHHHHHHHhh
Confidence 99999999999999998763 3456788999999965433
No 5
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=99.97 E-value=6.3e-32 Score=327.21 Aligned_cols=168 Identities=36% Similarity=0.832 Sum_probs=150.1
Q ss_pred CCCCCcCcccCCCCC-CCCCEEEecccCcccccccccCccCCCCceecccccccccCCCCCCCCCCccCCCccccccccC
Q 002388 702 KEHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLC 780 (929)
Q Consensus 702 ke~d~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C~LC 780 (929)
-+.|..|+||.+.+. ..|.||+||+|+++|||.|||++.+|+|.|+|..|..... ..+.|.+|
T Consensus 216 ~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipeg~WlCr~Cl~s~~----------------~~v~c~~c 279 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPEGQWLCRRCLQSPQ----------------RPVRCLLC 279 (1051)
T ss_pred cCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCCCcEeehhhccCcC----------------cccceEec
Confidence 356789999999985 4689999999999999999999999999999999987522 25799999
Q ss_pred CCCCCceeeccCcchhhhccccccccceeecC-ccccccccccccCC--CCcceeCCCCC-CceeecCCcCcccccchhh
Q 002388 781 GGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKH-GICIKCNYGNCQTTFHPTC 856 (929)
Q Consensus 781 p~~gGaLK~T~~g~WVHv~CAlw~pev~f~~~-~~~~Vegie~I~k~--k~~C~iC~~~~-GacIqC~~~~C~~~FH~~C 856 (929)
|..+||||+|.+|+|+|++||+|+|++.|.+. .+++|++|+.|+.. ++.|++|+.++ |+||||+..+|..+||++|
T Consensus 280 p~~~gAFkqt~dgrw~Hv~caiwipev~F~nt~~~E~I~~i~~i~~aRwkL~cy~cK~~~~gaciqcs~~~c~~a~hvtc 359 (1051)
T KOG0955|consen 280 PSKGGAFKQTDDGRWAHVVCAIWIPEVSFANTVFLEPIDSIENIPPARWKLTCYICKQKGLGACIQCSKANCYTAFHVTC 359 (1051)
T ss_pred cCCCCcceeccCCceeeeehhhcccccccccchhhccccchhcCcHhhhhceeeeeccCCCCcceecchhhhhhhhhhhh
Confidence 99999999999999999999999999999987 78999999999865 79999999998 9999999999999999999
Q ss_pred hhhcCceEEEeeCC-----C---cceeeeccccccch
Q 002388 857 ARSAGFYLNVKSTG-----G---NFQHKAYCEKHSLE 885 (929)
Q Consensus 857 A~~aGl~~~~k~~~-----g---~~~~~ayC~kHs~~ 885 (929)
|+++|++|...... + ......||+.|.|.
T Consensus 360 a~~agl~m~~~~~~~~s~~~~s~~v~~~syC~~H~pp 396 (1051)
T KOG0955|consen 360 ARRAGLYMKSNTVKELSKNGTSQSVNKISYCDKHTPP 396 (1051)
T ss_pred HhhcCceEeecccccccccccccccceeeeccCCCCc
Confidence 99999999853211 1 14678999999998
No 6
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=99.94 E-value=1.5e-28 Score=272.32 Aligned_cols=185 Identities=31% Similarity=0.653 Sum_probs=149.0
Q ss_pred cCcccCCCCC-CCCCEEEecccCcccccccccCcc---CC-------CCceecccccccccCCCCCCCCCCccCCCcccc
Q 002388 707 SCDICRRSET-ILNPILICSGCKVAVHLDCYRNAK---ES-------TGPWYCELCEELLSSRSSGAPSVNFWEKPYFVA 775 (929)
Q Consensus 707 ~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~~---~p-------~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~ 775 (929)
.|+||...-. +.|.||+|++|++.||..|||+.. ++ ..+|||+.|.+..+ .+
T Consensus 121 iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs-----------------~P 183 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVS-----------------LP 183 (707)
T ss_pred EEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCCC-----------------CC
Confidence 6999998654 478999999999999999999862 22 36899999999732 47
Q ss_pred ccccCCCCCCceeeccCcchhhhccccccccceeecC-ccccccc--cccccCCCCcceeCCCC----CCceeecCCcCc
Q 002388 776 ECSLCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAG--MEAFPKGIDVCCICRHK----HGICIKCNYGNC 848 (929)
Q Consensus 776 ~C~LCp~~gGaLK~T~~g~WVHv~CAlw~pev~f~~~-~~~~Veg--ie~I~k~k~~C~iC~~~----~GacIqC~~~~C 848 (929)
.|-|||.++|+||.|.-|+|||++||||+|++.|... .+.+|.. |.....+...|++|..+ .|+||.|..+.|
T Consensus 184 ~CElCPn~~GifKetDigrWvH~iCALYvpGVafg~~~~l~~Vtl~em~ysk~Gak~Cs~Ced~~fARtGvci~CdaGMC 263 (707)
T KOG0957|consen 184 HCELCPNRFGIFKETDIGRWVHAICALYVPGVAFGQTHTLCGVTLEEMDYSKFGAKTCSACEDKIFARTGVCIRCDAGMC 263 (707)
T ss_pred ccccCCCcCCcccccchhhHHHHHHHhhcCccccccccccccccHHHhhhhhhccchhccccchhhhhcceeeeccchhh
Confidence 8999999999999999999999999999999999765 4445442 22223346899999974 899999999999
Q ss_pred ccccchhhhhhcCceEEEeeCCCc-ceeeeccccccchhhhhHhhhchhhhhhhhhhhhee
Q 002388 849 QTTFHPTCARSAGFYLNVKSTGGN-FQHKAYCEKHSLEQKMKAETQKHGVEELKGIKQIRV 908 (929)
Q Consensus 849 ~~~FH~~CA~~aGl~~~~k~~~g~-~~~~ayC~kHs~~qr~k~~~q~~~~eE~ksmk~~Rv 908 (929)
..+|||+||+..|+.++....+.. ..+.+||++|+.....+-..+.|--.+...|+|+++
T Consensus 264 k~YfHVTCAQk~GlLvea~~e~DiAdpfya~CK~Ht~r~~~K~~rrny~~l~~~~~~r~~~ 324 (707)
T KOG0957|consen 264 KEYFHVTCAQKLGLLVEATDENDIADPFYAFCKKHTNRDNLKPYRRNYDDLEKSEARRITV 324 (707)
T ss_pred hhhhhhhHHhhhcceeeccccccchhhHHHHHHhhcchhhhhhhhhhhHHHHHHHHHHHHH
Confidence 999999999999999987544432 468899999997655454555565566666777766
No 7
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=99.91 E-value=5.7e-25 Score=206.78 Aligned_cols=107 Identities=42% Similarity=0.859 Sum_probs=99.0
Q ss_pred CCCCCCCCCcccccCCCCCcHhhHhhcccCceeeccCccccccccccCchhhcccccccccccccCceeeCCCCCCCccc
Q 002388 2 CSLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSF 81 (929)
Q Consensus 2 ClCP~~gGALK~T~~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~~F 81 (929)
.+||.+|||||+|.++ .|||++||+|+|+++|.+...++||. +..|+++|++++|.||+++.|+||+|++++|.++|
T Consensus 4 ~lC~~~~Galk~t~~~--~WvHv~Cal~~~~~~~~~~~~~~~v~-~~~i~~~~~~~~C~iC~~~~G~~i~C~~~~C~~~f 80 (110)
T PF13832_consen 4 VLCPKRGGALKRTSDG--QWVHVLCALWIPEVIFNNGESMEPVD-ISNIPPSRFKLKCSICGKSGGACIKCSHPGCSTAF 80 (110)
T ss_pred EeCCCCCCcccCccCC--cEEEeEccceeCccEEeechhcCccc-ceeecchhcCCcCcCCCCCCceeEEcCCCCCCcCC
Confidence 4799999999999966 89999999999999999999999995 99999999999999999999999999999999999
Q ss_pred chhhhhhcCceEEeccccCCccceeeecCCCC
Q 002388 82 HPICAREARHRLEVWGKYGCNNVELRAFCAKH 113 (929)
Q Consensus 82 HvtCA~~aG~~~e~~~~~g~~~v~~~~fC~~H 113 (929)
|++||+.+|+.+++...+. ...+.+||++|
T Consensus 81 H~~CA~~~g~~~~~~~~~~--~~~~~~~C~~H 110 (110)
T PF13832_consen 81 HPTCARKAGLYFEIENEED--NVQFIAYCPKH 110 (110)
T ss_pred CHHHHHHCCCeEEeeecCC--CceEEEECCCC
Confidence 9999999999998864322 67899999999
No 8
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=99.88 E-value=5e-24 Score=243.39 Aligned_cols=114 Identities=32% Similarity=0.647 Sum_probs=105.0
Q ss_pred CCCCCCCCcccccCCCCCcHhhHhhcccCceeeccCccccccccccCchhhcccccccccccc-------cCceeeCCCC
Q 002388 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVK-------CGACVRCSHG 75 (929)
Q Consensus 3 lCP~~gGALK~T~~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k-------~GAcIqCs~~ 75 (929)
|||.+.||||+|+.| .|+||+||||||||.|.|+..||||+ +..||..|++..|+||.+. .|||++|...
T Consensus 67 LCP~kdGALKkTDn~--GWAHVVCALYIPEVrFgNV~TMEPIi-Lq~VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs 143 (900)
T KOG0956|consen 67 LCPHKDGALKKTDNG--GWAHVVCALYIPEVRFGNVHTMEPII-LQDVPHDRFNKTCYICNEEGRPNKAAKGACMTCNKS 143 (900)
T ss_pred cccCcccceecccCC--CceEEEEEeeccceeeccccccccee-eccCchhhhcceeeeecccCCccccccccceecccc
Confidence 799999999999966 79999999999999999999999996 9999999999999999863 7999999999
Q ss_pred CCCcccchhhhhhcCceEEeccccCCccceeeecCCCCCCCCCCC
Q 002388 76 TCRTSFHPICAREARHRLEVWGKYGCNNVELRAFCAKHSDIQDNS 120 (929)
Q Consensus 76 ~C~~~FHvtCA~~aG~~~e~~~~~g~~~v~~~~fC~~Hr~~~~~~ 120 (929)
.|.++||||||+.+|+++|..+ +.-++|+|-.||++|-.+-.+.
T Consensus 144 ~CkqaFHVTCAQ~~GLLCEE~g-n~~dNVKYCGYCk~HfsKlkk~ 187 (900)
T KOG0956|consen 144 GCKQAFHVTCAQRAGLLCEEEG-NISDNVKYCGYCKYHFSKLKKS 187 (900)
T ss_pred cchhhhhhhHhhhhccceeccc-cccccceechhHHHHHHHhhcC
Confidence 9999999999999999999865 5678999999999998766543
No 9
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=99.88 E-value=3.5e-23 Score=194.69 Aligned_cols=106 Identities=43% Similarity=0.980 Sum_probs=97.4
Q ss_pred ccccCCCCCCceeeccCcchhhhccccccccceeecC-ccccccccccccCC--CCcceeCCCCCCceeecCCcCccccc
Q 002388 776 ECSLCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTF 852 (929)
Q Consensus 776 ~C~LCp~~gGaLK~T~~g~WVHv~CAlw~pev~f~~~-~~~~Vegie~I~k~--k~~C~iC~~~~GacIqC~~~~C~~~F 852 (929)
.|.||+..+||||+|.++.|||++||+|+|++.|.+. .+++++ ++.+++. +..|.+|+++.|++|+|.+++|.++|
T Consensus 2 ~C~lC~~~~Galk~t~~~~WvHv~Cal~~~~~~~~~~~~~~~v~-~~~i~~~~~~~~C~iC~~~~G~~i~C~~~~C~~~f 80 (110)
T PF13832_consen 2 SCVLCPKRGGALKRTSDGQWVHVLCALWIPEVIFNNGESMEPVD-ISNIPPSRFKLKCSICGKSGGACIKCSHPGCSTAF 80 (110)
T ss_pred ccEeCCCCCCcccCccCCcEEEeEccceeCccEEeechhcCccc-ceeecchhcCCcCcCCCCCCceeEEcCCCCCCcCC
Confidence 6999999999999999999999999999999999987 577777 7777765 79999999999999999999999999
Q ss_pred chhhhhhcCceEEEeeCCCcceeeeccccc
Q 002388 853 HPTCARSAGFYLNVKSTGGNFQHKAYCEKH 882 (929)
Q Consensus 853 H~~CA~~aGl~~~~k~~~g~~~~~ayC~kH 882 (929)
||+||+.+|+++++...+...++.+||++|
T Consensus 81 H~~CA~~~g~~~~~~~~~~~~~~~~~C~~H 110 (110)
T PF13832_consen 81 HPTCARKAGLYFEIENEEDNVQFIAYCPKH 110 (110)
T ss_pred CHHHHHHCCCeEEeeecCCCceEEEECCCC
Confidence 999999999999987665567899999999
No 10
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=99.87 E-value=2.9e-23 Score=230.40 Aligned_cols=116 Identities=27% Similarity=0.598 Sum_probs=104.2
Q ss_pred CCCCCCCCcccccCCCCCcHhhHhhcccCceeeccCccccccccccCchhhcccccccccccccCceeeCCCCCCCcccc
Q 002388 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFH 82 (929)
Q Consensus 3 lCP~~gGALK~T~~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~~FH 82 (929)
+||.+.||||.|.+| +|+|++||+|+||.+|.+...++||.||..++..||++.|.||+.+.|+||||++..|.++||
T Consensus 252 fCps~dGaFkqT~dg--rW~H~iCA~~~pelsF~~l~~~dpI~~i~sVs~srwkl~C~iCk~~~GtcIqCs~~nC~~aYH 329 (669)
T COG5141 252 FCPSSDGAFKQTSDG--RWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYH 329 (669)
T ss_pred eccCCCCceeeccCC--chHhHhHHHhcchhccccccccchhhhhcccchhhHhheeeEEcccCcceeeecccchhhhhh
Confidence 699999999999988 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCceEE-eccccCC-ccceeeecCCCCCCCCCCC
Q 002388 83 PICAREARHRLE-VWGKYGC-NNVELRAFCAKHSDIQDNS 120 (929)
Q Consensus 83 vtCA~~aG~~~e-~~~~~g~-~~v~~~~fC~~Hr~~~~~~ 120 (929)
+|||++||+++- +...++- +.+....||++|.|.....
T Consensus 330 VtCArrag~f~~~~~s~n~~s~~id~e~~c~kh~p~gy~~ 369 (669)
T COG5141 330 VTCARRAGYFDLNIYSHNGISYCIDHEPLCRKHYPLGYGR 369 (669)
T ss_pred hhhhhhcchhhhhhhcccccceeecchhhhcCCCCcchhc
Confidence 999999999875 3333332 2245677999999999864
No 11
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=99.84 E-value=7.1e-22 Score=240.45 Aligned_cols=114 Identities=36% Similarity=0.692 Sum_probs=104.1
Q ss_pred CCCCCCCCCcccccCCCCCcHhhHhhcccCceeeccCccccccccccCchhhccccccccccccc-CceeeCCCCCCCcc
Q 002388 2 CSLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKC-GACVRCSHGTCRTS 80 (929)
Q Consensus 2 ClCP~~gGALK~T~~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k~-GAcIqCs~~~C~~~ 80 (929)
.+||+++||||+|.+| +|+|++||+|+||++|.+...++||.+|++|+..||+|.|.+|+++. ||||||+.-+|.++
T Consensus 277 ~~cp~~~gAFkqt~dg--rw~Hv~caiwipev~F~nt~~~E~I~~i~~i~~aRwkL~cy~cK~~~~gaciqcs~~~c~~a 354 (1051)
T KOG0955|consen 277 LLCPSKGGAFKQTDDG--RWAHVVCAIWIPEVSFANTVFLEPIDSIENIPPARWKLTCYICKQKGLGACIQCSKANCYTA 354 (1051)
T ss_pred EeccCCCCcceeccCC--ceeeeehhhcccccccccchhhccccchhcCcHhhhhceeeeeccCCCCcceecchhhhhhh
Confidence 5899999999999988 89999999999999999999999999999999999999999999998 99999999999999
Q ss_pred cchhhhhhcCceEEec-cccC----C-ccceeeecCCCCCCCC
Q 002388 81 FHPICAREARHRLEVW-GKYG----C-NNVELRAFCAKHSDIQ 117 (929)
Q Consensus 81 FHvtCA~~aG~~~e~~-~~~g----~-~~v~~~~fC~~Hr~~~ 117 (929)
||+|||+++|++|... ..++ . ..+.+.+||.+|.|..
T Consensus 355 ~hvtca~~agl~m~~~~~~~~s~~~~s~~v~~~syC~~H~pp~ 397 (1051)
T KOG0955|consen 355 FHVTCARRAGLYMKSNTVKELSKNGTSQSVNKISYCDKHTPPG 397 (1051)
T ss_pred hhhhhHhhcCceEeecccccccccccccccceeeeccCCCCch
Confidence 9999999999999843 1111 1 3368899999999996
No 12
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=99.73 E-value=2.1e-18 Score=156.44 Aligned_cols=88 Identities=42% Similarity=0.737 Sum_probs=80.6
Q ss_pred hhHhhcccCceeeccCcc--ccccccccCchhhcccccccccccccCceeeCCCCCCCcccchhhhhhcCceEEeccccC
Q 002388 23 HLFCSLLMPEVYIEDTMK--VEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFHPICAREARHRLEVWGKYG 100 (929)
Q Consensus 23 Hv~CALw~PEv~f~~~~~--~epV~~V~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~~FHvtCA~~aG~~~e~~~~~g 100 (929)
|++||||+||+++.+... +.++.+|..++.++++++|++|+++.||+|+|.+++|.+.||++||+.+|+.+++..
T Consensus 1 H~~Calwsp~v~~~~~~~~~~~~i~~v~~~~~~~~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~~~~~~~~~--- 77 (90)
T PF13771_consen 1 HENCALWSPEVYFDESEDIGGFSIEDVEKEIKRRRKLKCSICKKKGGACIGCSHPGCSRSFHVPCARKAGCFIEFDE--- 77 (90)
T ss_pred ChHHheecCceEEeCCCccccccHHhHHHHHHHHhCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccCCeEEEEcc---
Confidence 899999999999988764 678889999999999999999998889999999999999999999999999998874
Q ss_pred CccceeeecCCCCC
Q 002388 101 CNNVELRAFCAKHS 114 (929)
Q Consensus 101 ~~~v~~~~fC~~Hr 114 (929)
++..+.+||++|+
T Consensus 78 -~~~~~~~~C~~H~ 90 (90)
T PF13771_consen 78 -DNGKFRIFCPKHS 90 (90)
T ss_pred -CCCceEEEChhcC
Confidence 3347899999996
No 13
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=99.68 E-value=6.2e-18 Score=188.59 Aligned_cols=112 Identities=26% Similarity=0.539 Sum_probs=97.4
Q ss_pred CCCCCCCCcccccCCCCCcHhhHhhcccCceeeccCccccccccccCchhhcccc-cccccccc----cCceeeCCCCCC
Q 002388 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKL-VCNICRVK----CGACVRCSHGTC 77 (929)
Q Consensus 3 lCP~~gGALK~T~~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~L-kC~iC~~k----~GAcIqCs~~~C 77 (929)
|||+++|+||.|+.| +|||++||||+|+|-|++...+-+|. +.......|.. .|++|-.+ .|.||.|..|.|
T Consensus 187 lCPn~~GifKetDig--rWvH~iCALYvpGVafg~~~~l~~Vt-l~em~ysk~Gak~Cs~Ced~~fARtGvci~CdaGMC 263 (707)
T KOG0957|consen 187 LCPNRFGIFKETDIG--RWVHAICALYVPGVAFGQTHTLCGVT-LEEMDYSKFGAKTCSACEDKIFARTGVCIRCDAGMC 263 (707)
T ss_pred cCCCcCCcccccchh--hHHHHHHHhhcCcccccccccccccc-HHHhhhhhhccchhccccchhhhhcceeeeccchhh
Confidence 799999999999987 89999999999999999999998884 55565555554 89999864 899999999999
Q ss_pred CcccchhhhhhcCceEEeccccCCccceeeecCCCCCCCCC
Q 002388 78 RTSFHPICAREARHRLEVWGKYGCNNVELRAFCAKHSDIQD 118 (929)
Q Consensus 78 ~~~FHvtCA~~aG~~~e~~~~~g~~~v~~~~fC~~Hr~~~~ 118 (929)
.++||||||+.+|++++...++ +-.++|++||++|..+..
T Consensus 264 k~YfHVTCAQk~GlLvea~~e~-DiAdpfya~CK~Ht~r~~ 303 (707)
T KOG0957|consen 264 KEYFHVTCAQKLGLLVEATDEN-DIADPFYAFCKKHTNRDN 303 (707)
T ss_pred hhhhhhhHHhhhcceeeccccc-cchhhHHHHHHhhcchhh
Confidence 9999999999999999887533 234689999999988765
No 14
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=99.50 E-value=8.9e-15 Score=132.80 Aligned_cols=85 Identities=34% Similarity=0.686 Sum_probs=73.0
Q ss_pred hhccccccccceeecCc---cccccccccccCC--CCcceeCCCCCCceeecCCcCcccccchhhhhhcCceEEEeeCCC
Q 002388 797 HAFCAEWVFESTFRRGQ---VNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTFHPTCARSAGFYLNVKSTGG 871 (929)
Q Consensus 797 Hv~CAlw~pev~f~~~~---~~~Vegie~I~k~--k~~C~iC~~~~GacIqC~~~~C~~~FH~~CA~~aGl~~~~k~~~g 871 (929)
|+.||+|+|++.+.+.. +..+.+++.+.+. ++.|++|+++.|++|+|..++|.+.||+.||+.+|+.+++.. .
T Consensus 1 H~~Calwsp~v~~~~~~~~~~~~i~~v~~~~~~~~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~~~~~~~~~--~ 78 (90)
T PF13771_consen 1 HENCALWSPEVYFDESEDIGGFSIEDVEKEIKRRRKLKCSICKKKGGACIGCSHPGCSRSFHVPCARKAGCFIEFDE--D 78 (90)
T ss_pred ChHHheecCceEEeCCCccccccHHhHHHHHHHHhCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccCCeEEEEcc--C
Confidence 89999999999998764 4566677665544 699999999989999999999999999999999999998864 2
Q ss_pred cceeeecccccc
Q 002388 872 NFQHKAYCEKHS 883 (929)
Q Consensus 872 ~~~~~ayC~kHs 883 (929)
...+.+||++|+
T Consensus 79 ~~~~~~~C~~H~ 90 (90)
T PF13771_consen 79 NGKFRIFCPKHS 90 (90)
T ss_pred CCceEEEChhcC
Confidence 337899999996
No 15
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=98.87 E-value=3.8e-10 Score=87.14 Aligned_cols=34 Identities=47% Similarity=1.195 Sum_probs=21.5
Q ss_pred CCEEEecccCcccccccccCccCCCC-ceeccccc
Q 002388 719 NPILICSGCKVAVHLDCYRNAKESTG-PWYCELCE 752 (929)
Q Consensus 719 N~Ll~Cd~C~vaVHq~CYGi~~~p~g-~WlCd~C~ 752 (929)
|+||+|++|++.||+.|||+...+.+ +|+|++|+
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 78999999999999999999988865 89999995
No 16
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=98.79 E-value=4.6e-09 Score=129.79 Aligned_cols=143 Identities=34% Similarity=0.752 Sum_probs=120.1
Q ss_pred CCCCCCCcCcccCCCCC-CCCCEEEecccCcccccccccCccCC-CCceecccccccccCCCCCCCCCCccCCCcccccc
Q 002388 700 FSKEHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKES-TGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAEC 777 (929)
Q Consensus 700 ~ske~d~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p-~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C 777 (929)
........|.+|...+. ..|.++.|+.|...+|..|||....+ ...|+|+.|.... ....|
T Consensus 568 l~~~~t~~c~~~~~~~~~~~n~~~~~~~~~~~~~s~~~g~~~~~~~~~~~~~~~~~~~-----------------~~r~~ 630 (1005)
T KOG1080|consen 568 LSKWTTERCAVCRDDEDWEKNVSIICDRCTRSVHSECYGNLKSYDGTSWVCDSCETLD-----------------IKRSC 630 (1005)
T ss_pred hcCCCcccccccccccccccceeeeeccccccCCCcccccCCCCCCCcchhhcccccc-----------------CCchh
Confidence 45556688999999875 57899999999999999999988766 5579999998641 14689
Q ss_pred ccCCCCCCceeeccCcchhhhccccccccceeecC-ccccccccccccCC--CCcceeCCCCCCceeecCCcCcccccch
Q 002388 778 SLCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTFHP 854 (929)
Q Consensus 778 ~LCp~~gGaLK~T~~g~WVHv~CAlw~pev~f~~~-~~~~Vegie~I~k~--k~~C~iC~~~~GacIqC~~~~C~~~FH~ 854 (929)
++|+..+|+++++..+.|+|+-|+.|.++..+... .+.+..++..++.. ...|.+ .|.|.+|. .|...||.
T Consensus 631 ~l~~~~g~al~p~d~gr~~~~e~a~~~~e~~~~~~~~~~p~~~~~~~p~~~~~~~~~~----~~~~~~~~--~~~~~~~~ 704 (1005)
T KOG1080|consen 631 CLCPVKGGALKPTDEGRWVHVECAWFRPEVCLASPERMEPAVGTFKIPALSFLKICFI----HGSCRQCC--KCETGSHA 704 (1005)
T ss_pred hhccccCcccCCCCccchhhhhchhccccccCCCccCCCCcccccccCccchhhhccc----cccccccc--hhhhccee
Confidence 99999999999999999999999999999998776 67777777666654 255555 57788898 89999999
Q ss_pred hhhhhcCceEE
Q 002388 855 TCARSAGFYLN 865 (929)
Q Consensus 855 ~CA~~aGl~~~ 865 (929)
.||+.+|+.+.
T Consensus 705 ~~a~~~~~~~~ 715 (1005)
T KOG1080|consen 705 MCASRAGYIME 715 (1005)
T ss_pred hhhcCccChhh
Confidence 99999998874
No 17
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=97.70 E-value=1.4e-05 Score=99.57 Aligned_cols=86 Identities=34% Similarity=0.696 Sum_probs=79.1
Q ss_pred CCCCCCCCCcccccCCCCCcHhhHhhcccCceeeccCccccccccccCchhhcccccccccccccCceeeCCCCCCCccc
Q 002388 2 CSLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSF 81 (929)
Q Consensus 2 ClCP~~gGALK~T~~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~~F 81 (929)
|+||.+||||+|++.| .|+|+-||.|.||+.+.++..|+|+.++..++...+...|.+ .|-|.||. .|.+.|
T Consensus 631 ~l~~~~g~al~p~d~g--r~~~~e~a~~~~e~~~~~~~~~~p~~~~~~~p~~~~~~~~~~----~~~~~~~~--~~~~~~ 702 (1005)
T KOG1080|consen 631 CLCPVKGGALKPTDEG--RWVHVECAWFRPEVCLASPERMEPAVGTFKIPALSFLKICFI----HGSCRQCC--KCETGS 702 (1005)
T ss_pred hhccccCcccCCCCcc--chhhhhchhccccccCCCccCCCCcccccccCccchhhhccc----cccccccc--hhhhcc
Confidence 8999999999999965 899999999999999999999999999999999999998888 58888888 899999
Q ss_pred chhhhhhcCceEEe
Q 002388 82 HPICAREARHRLEV 95 (929)
Q Consensus 82 HvtCA~~aG~~~e~ 95 (929)
|..||..+|+.++.
T Consensus 703 ~~~~a~~~~~~~~~ 716 (1005)
T KOG1080|consen 703 HAMCASRAGYIMEA 716 (1005)
T ss_pred eehhhcCccChhhh
Confidence 99999999887654
No 18
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.48 E-value=5.1e-05 Score=62.12 Aligned_cols=46 Identities=26% Similarity=0.795 Sum_probs=38.0
Q ss_pred cCcccCCCCCCCCCEEEecccCcccccccccCccC----CCCceecccccc
Q 002388 707 SCDICRRSETILNPILICSGCKVAVHLDCYRNAKE----STGPWYCELCEE 753 (929)
Q Consensus 707 ~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~~~----p~g~WlCd~C~~ 753 (929)
+|.||...+ ..+.+|+|+.|+..+|..|+++... +.+.|+|..|+.
T Consensus 1 ~C~vC~~~~-~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSD-DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSC-TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcC-CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 488999933 4789999999999999999998743 355899999963
No 19
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.00 E-value=0.00029 Score=75.87 Aligned_cols=51 Identities=33% Similarity=0.813 Sum_probs=43.6
Q ss_pred CCCcCcccCCCCCCCCCEEEecccCcccccccccCc--cCCCCceecccccccc
Q 002388 704 HPRSCDICRRSETILNPILICSGCKVAVHLDCYRNA--KESTGPWYCELCEELL 755 (929)
Q Consensus 704 ~d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~--~~p~g~WlCd~C~~~~ 755 (929)
+--.|+||+-+|. +++||||+.|...+|.+|...+ ..|+|.|-|.+|....
T Consensus 280 eck~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~~~ 332 (336)
T KOG1244|consen 280 ECKYCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEEL 332 (336)
T ss_pred ecceeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHHH
Confidence 4567999998875 6899999999999999999865 4569999999998763
No 21
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.66 E-value=0.00076 Score=73.13 Aligned_cols=49 Identities=22% Similarity=0.504 Sum_probs=42.3
Q ss_pred CCCCCCCcCcccCCCCCCCCCEEEecccCcccccccccCccCCCCceecc
Q 002388 700 FSKEHPRSCDICRRSETILNPILICSGCKVAVHLDCYRNAKESTGPWYCE 749 (929)
Q Consensus 700 ~ske~d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd 749 (929)
+.--.-..|.||..++- ..+++|||.|+..+|..|.|...+|.|.|.||
T Consensus 309 W~C~~C~lC~IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~G~WICD 357 (381)
T KOG1512|consen 309 WKCSSCELCRICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPRGEWICD 357 (381)
T ss_pred hhhcccHhhhccCCccc-chheeccccccCCCCccccccccccCccchhh
Confidence 33345577999998763 57899999999999999999999999999999
No 22
>KOG1084 consensus Transcription factor TCF20 [Transcription]
Probab=96.58 E-value=0.0012 Score=75.55 Aligned_cols=86 Identities=21% Similarity=0.380 Sum_probs=67.1
Q ss_pred CCCCcHhhHhhcccCceeeccCccccccccccCchhhcccccccccccccCceeeCCCCCCCcccchhhhhhcCceEEec
Q 002388 17 GSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFHPICAREARHRLEVW 96 (929)
Q Consensus 17 G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~~FHvtCA~~aG~~~e~~ 96 (929)
|...|.|+.|++|.|++.+.+...+..+ .....+-+.+.|..|.++ |+.+.|...+|...+|.+|+..+-... ..
T Consensus 236 ~~~~~~h~~c~~~~~~~~~~q~~~l~~~---~~~v~r~~~~~c~~c~k~-ga~~~c~~~~~~~~~h~~c~~~~~~~~-~~ 310 (375)
T KOG1084|consen 236 GFELWYHRYCALWAPNVHESQGGQLTNV---DNAVIRFPSLQCILCQKP-GATLKCVQASLLSNAHFPCARAKNGIP-LD 310 (375)
T ss_pred chhHHHHHHHHhcCCcceeccCccccCc---hhhhhcccchhcccccCC-CCchhhhhhhhhcccCcccccCccccc-ch
Confidence 5567999999999999999988777544 433334444899999975 999999999999999999998766532 11
Q ss_pred cccCCccceeeecCCCCC
Q 002388 97 GKYGCNNVELRAFCAKHS 114 (929)
Q Consensus 97 ~~~g~~~v~~~~fC~~Hr 114 (929)
..-..+|..|+
T Consensus 311 -------~~r~v~~~~h~ 321 (375)
T KOG1084|consen 311 -------YDRKVSCPRHR 321 (375)
T ss_pred -------hhhhccCCCCC
Confidence 01267999999
No 23
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=96.37 E-value=0.0033 Score=73.10 Aligned_cols=134 Identities=16% Similarity=0.238 Sum_probs=85.7
Q ss_pred CcCcccCCCCC-CCCCEEEecccCcccccccccCccCCCCceecccccccccCCCCCCCCCCccCCCccccccccCCCCC
Q 002388 706 RSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLCGGTT 784 (929)
Q Consensus 706 ~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C~LCp~~g 784 (929)
..|.||...-. ..|.++.|.+|+...||.|--......+.|.+..|..... .+.|
T Consensus 84 ~~~nv~~s~~~~p~~e~~~~~r~~~~~~q~~~i~~~~~~~~~~~~~c~~~~~------------------------~~~g 139 (464)
T KOG4323|consen 84 LNPNVLTSETVLPENEKVICGRCKSGYHQGCNIPRFPSLDIGESTECVFPIF------------------------SQEG 139 (464)
T ss_pred cCCcccccccccCchhhhhhhhhccCcccccCccCcCcCCcccccccccccc------------------------cccc
Confidence 66999987543 4789999999999999999654444477899988876521 1346
Q ss_pred CceeeccCcchhhhccccccccceeecCccccccccccccCCCCcceeCCCC----CCceeecCCcCcccccchhhhhhc
Q 002388 785 GAFRKSANGQWVHAFCAEWVFESTFRRGQVNPVAGMEAFPKGIDVCCICRHK----HGICIKCNYGNCQTTFHPTCARSA 860 (929)
Q Consensus 785 GaLK~T~~g~WVHv~CAlw~pev~f~~~~~~~Vegie~I~k~k~~C~iC~~~----~GacIqC~~~~C~~~FH~~CA~~a 860 (929)
|++|.. .-+| +-+.|..... ++ ....+..+.|+||..- .--+|+|. +|.++||-.|-+.-
T Consensus 140 ~a~K~g---~~a~-------~~l~y~~~~l---~w-D~~~~~n~qc~vC~~g~~~~~NrmlqC~--~C~~~fHq~Chqp~ 203 (464)
T KOG4323|consen 140 GALKKG---RLAR-------PSLPYPEASL---DW-DSGHKVNLQCSVCYCGGPGAGNRMLQCD--KCRQWYHQACHQPL 203 (464)
T ss_pred cccccc---cccc-------ccccCccccc---cc-CccccccceeeeeecCCcCccceeeeec--ccccHHHHHhccCC
Confidence 666653 3344 2222221110 00 1122334669999852 22789999 99999999998654
Q ss_pred CceEEEeeCCCcceeeecccccc
Q 002388 861 GFYLNVKSTGGNFQHKAYCEKHS 883 (929)
Q Consensus 861 Gl~~~~k~~~g~~~~~ayC~kHs 883 (929)
--.+.+ +...+..||..-.
T Consensus 204 i~~~l~----~D~~~~w~C~~C~ 222 (464)
T KOG4323|consen 204 IKDELA----GDPFYEWFCDVCN 222 (464)
T ss_pred CCHhhc----cCccceEeehhhc
Confidence 333333 3356677887654
No 24
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.22 E-value=0.014 Score=62.92 Aligned_cols=52 Identities=29% Similarity=0.779 Sum_probs=41.5
Q ss_pred CCCCCCCCcCcccCCCCCCCCCEEEecc--cCc-ccccccccCccCCCCceecccccc
Q 002388 699 DFSKEHPRSCDICRRSETILNPILICSG--CKV-AVHLDCYRNAKESTGPWYCELCEE 753 (929)
Q Consensus 699 ~~ske~d~~CsVC~~~E~~~N~Ll~Cd~--C~v-aVHq~CYGi~~~p~g~WlCd~C~~ 753 (929)
+.+.++.++| .|.+.- -++||-||+ |.. =||..|.|....|.|.|+|+-|+.
T Consensus 215 d~se~e~lYC-fCqqvS--yGqMVaCDn~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 215 DNSEGEELYC-FCQQVS--YGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKK 269 (271)
T ss_pred ccccCceeEE-Eecccc--cccceecCCCCCchhheeccccccCCCCCCcEeCHHhHh
Confidence 4455566666 466643 489999996 876 499999999999999999999975
No 25
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=96.17 E-value=0.0026 Score=73.89 Aligned_cols=53 Identities=21% Similarity=0.556 Sum_probs=42.9
Q ss_pred CCCCcCcccCCCCC-CCCCEEEecccCcccccccccCcc------CCCCceecccccccc
Q 002388 703 EHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAK------ESTGPWYCELCEELL 755 (929)
Q Consensus 703 e~d~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~~------~p~g~WlCd~C~~~~ 755 (929)
..++.|+||....+ ..|+||+|++|+--+|+.|.-... ++...|+|..|.+..
T Consensus 166 ~~n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 166 KVNLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred cccceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 34577999997764 689999999999999999985432 346789999998763
No 26
>KOG1084 consensus Transcription factor TCF20 [Transcription]
Probab=96.12 E-value=0.0025 Score=72.97 Aligned_cols=97 Identities=25% Similarity=0.418 Sum_probs=71.5
Q ss_pred cccccCCCCCCceeec-cCcchhhhccccccccceeecC-ccccccccccccCC-CCcceeCCCCCCceeecCCcCcccc
Q 002388 775 AECSLCGGTTGAFRKS-ANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG-IDVCCICRHKHGICIKCNYGNCQTT 851 (929)
Q Consensus 775 ~~C~LCp~~gGaLK~T-~~g~WVHv~CAlw~pev~f~~~-~~~~Vegie~I~k~-k~~C~iC~~~~GacIqC~~~~C~~~ 851 (929)
..|++++... ... ....|+|+.|++|.+.+.+..+ ++..+.. .+.+. .+.|..|.++ |+.+.|....|...
T Consensus 222 ~~~~l~~~~~---~~d~~~~~~~h~~c~~~~~~~~~~q~~~l~~~~~--~v~r~~~~~c~~c~k~-ga~~~c~~~~~~~~ 295 (375)
T KOG1084|consen 222 FFCALSPKAT---IPDIGFELWYHRYCALWAPNVHESQGGQLTNVDN--AVIRFPSLQCILCQKP-GATLKCVQASLLSN 295 (375)
T ss_pred hhhhhcCCCc---CCccchhHHHHHHHHhcCCcceeccCccccCchh--hhhcccchhcccccCC-CCchhhhhhhhhcc
Confidence 3677776432 233 4467999999999999998776 6666553 23232 3799999996 99999999999999
Q ss_pred cchhhhhhcCceEEEeeCCCcceeeecccccc
Q 002388 852 FHPTCARSAGFYLNVKSTGGNFQHKAYCEKHS 883 (929)
Q Consensus 852 FH~~CA~~aGl~~~~k~~~g~~~~~ayC~kHs 883 (929)
+|..|+.....+.... ...++|..|.
T Consensus 296 ~h~~c~~~~~~~~~~~------~r~v~~~~h~ 321 (375)
T KOG1084|consen 296 AHFPCARAKNGIPLDY------DRKVSCPRHR 321 (375)
T ss_pred cCcccccCcccccchh------hhhccCCCCC
Confidence 9999997765543221 2467999998
No 27
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=95.25 E-value=0.022 Score=58.24 Aligned_cols=72 Identities=21% Similarity=0.554 Sum_probs=50.3
Q ss_pred cCcccCCC-C-CCCCCEEEecccCcccccccccCc--------cCCCCc--eecccccccccCCCCCCCCCCccCCCccc
Q 002388 707 SCDICRRS-E-TILNPILICSGCKVAVHLDCYRNA--------KESTGP--WYCELCEELLSSRSSGAPSVNFWEKPYFV 774 (929)
Q Consensus 707 ~CsVC~~~-E-~~~N~Ll~Cd~C~vaVHq~CYGi~--------~~p~g~--WlCd~C~~~~~~~~s~~~~~~~~~~p~~~ 774 (929)
.|++|... . ...++||+|.+|-.++|+.|.|.. ++.++. --|.+|......+.. ..| ..
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~--------~aP-~~ 71 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDP--------RAP-HH 71 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccC--------CCC-CC
Confidence 49999753 2 357899999999999999999964 344444 569999876433221 123 36
Q ss_pred cccccCCCCCCce
Q 002388 775 AECSLCGGTTGAF 787 (929)
Q Consensus 775 ~~C~LCp~~gGaL 787 (929)
-.|.-|...|-+-
T Consensus 72 ~~C~~C~~~G~~c 84 (175)
T PF15446_consen 72 GMCQQCKKPGPSC 84 (175)
T ss_pred CcccccCCCCCCC
Confidence 7899998876543
No 28
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.86 E-value=0.025 Score=67.50 Aligned_cols=48 Identities=29% Similarity=0.793 Sum_probs=41.8
Q ss_pred CcCcccCCCCCCCCCEEEecccCcccccccccCc----cCCCCceeccccccc
Q 002388 706 RSCDICRRSETILNPILICSGCKVAVHLDCYRNA----KESTGPWYCELCEEL 754 (929)
Q Consensus 706 ~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~----~~p~g~WlCd~C~~~ 754 (929)
.+|+-|...+.- |.++.|++|...||+.|.-.+ .+|.|.|+|.-|..-
T Consensus 254 ~fCsaCn~~~~F-~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 254 DFCSACNGSGLF-NDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHhCCcccc-ccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 589999998754 899999999999999999765 467899999999763
No 29
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.82 E-value=0.031 Score=67.69 Aligned_cols=53 Identities=26% Similarity=0.748 Sum_probs=43.8
Q ss_pred CCCCCCcCcccCCCCCCCCCEEEecccCcc-cccccccCc--cCCCCceeccccccc
Q 002388 701 SKEHPRSCDICRRSETILNPILICSGCKVA-VHLDCYRNA--KESTGPWYCELCEEL 754 (929)
Q Consensus 701 ske~d~~CsVC~~~E~~~N~Ll~Cd~C~va-VHq~CYGi~--~~p~g~WlCd~C~~~ 754 (929)
+......|.||...+. .+-||.|+.|+.. +|.+|.... .+|-+.|+|+-|...
T Consensus 211 ~~~E~~~C~IC~~~Dp-EdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 211 LSQEEVKCDICTVHDP-EDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLL 266 (1134)
T ss_pred cccccccceeeccCCh-HHhheeecccccceeeccccCcccccccccceecCcchhh
Confidence 3345577999998775 5678999999999 999999754 578999999999765
No 30
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=92.02 E-value=0.089 Score=58.12 Aligned_cols=50 Identities=22% Similarity=0.625 Sum_probs=40.6
Q ss_pred CCCCCcCcccCCCCCCCCCEEEecc--cC-cccccccccCccCCCCceeccccccc
Q 002388 702 KEHPRSCDICRRSETILNPILICSG--CK-VAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 702 ke~d~~CsVC~~~E~~~N~Ll~Cd~--C~-vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
.++..+|-.. ....+.||-||+ |. -=||..|.|+..-|.|.|||..|...
T Consensus 216 ~~e~~yC~Cn---qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 216 PDEPTYCICN---QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGKWYCPRCKAE 268 (274)
T ss_pred CCCCEEEEec---ccccccccccCCCCCCcceEEEeccccccCCCCcccchhhhhh
Confidence 3455666544 223689999998 99 78999999999999999999999875
No 32
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=91.45 E-value=0.13 Score=43.69 Aligned_cols=32 Identities=25% Similarity=0.696 Sum_probs=28.7
Q ss_pred CCcCcccCCCCCCCCCEEEecccCcccccccc
Q 002388 705 PRSCDICRRSETILNPILICSGCKVAVHLDCY 736 (929)
Q Consensus 705 d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CY 736 (929)
...|.+|.+.-..++.+|+|..|+..+|+.||
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 46799999876568899999999999999999
No 33
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=91.22 E-value=0.22 Score=45.52 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=45.4
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhccc--cccccchhHHHHHHhh
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLAD--GTFASDLQCKLVKWLS 272 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~--~~~~~~~~~k~~~wl~ 272 (929)
..|+.-|.+ |+|+++|||.+.|+|..++--.|.. ..++|..+.+|..-.+
T Consensus 9 ~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 9 LEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence 578888888 9999999999999999999999985 4789999999998877
No 34
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=88.78 E-value=0.21 Score=43.71 Aligned_cols=32 Identities=34% Similarity=0.643 Sum_probs=25.2
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
-|+.=|.++|.|++.|||.++|+||+.|++.|
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL 35 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAML 35 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 34455779999999999999999999999988
No 35
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=87.35 E-value=0.27 Score=60.53 Aligned_cols=49 Identities=22% Similarity=0.669 Sum_probs=40.1
Q ss_pred CCCCCCCcCcccCCCCCCCCCEEEecccCcccccccccCc--cCCCCceeccccc
Q 002388 700 FSKEHPRSCDICRRSETILNPILICSGCKVAVHLDCYRNA--KESTGPWYCELCE 752 (929)
Q Consensus 700 ~ske~d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~--~~p~g~WlCd~C~ 752 (929)
.+..+...|.||.+ .+.++.|+.|...||.+|-+.+ .++.+.|+|.+|.
T Consensus 42 ~~~~~~e~c~ic~~----~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 42 WDDAEQEACRICAD----GGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCF 92 (696)
T ss_pred cchhhhhhhhhhcC----CCcEEEeccccHHHHHHccCCCCCcCCccceeeeeec
Confidence 34456688999999 5788999999999999999865 4555669999993
No 36
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=87.27 E-value=0.39 Score=40.74 Aligned_cols=34 Identities=35% Similarity=0.602 Sum_probs=31.0
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
..||+-|-+.|+|+++|+|.++|||+.|+..-|+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 4688899999999999999999999999998773
No 37
>PF10198 Ada3: Histone acetyltransferases subunit 3; InterPro: IPR019340 This entry is found in Ada3 and homologous proteins which function as part of histone acetyltransferase complexes []. Ada3 is an essential component of the Ada transcriptional coactivator (alteration/deficiency in activation) complex. It plays a key role in linking histone acetyltransferase-containing complexes to p53 (tumour suppressor protein) thereby regulating p53 acetylation, stability and transcriptional activation following DNA damage [].
Probab=87.11 E-value=4.2 Score=40.59 Aligned_cols=82 Identities=20% Similarity=0.197 Sum_probs=54.4
Q ss_pred Hhhhcccc---------ccCCCcchhhHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHhhhhcchhHHHHHHHHH
Q 002388 531 KARTRGVL---------ELSPTDEVEGEIIYFQHRLLGNAFSRKRLADNLVCKAVKTLNQEIDVARGRRWDAVLVNQYLC 601 (929)
Q Consensus 531 ~~~~~~~~---------~~~p~de~e~E~~~~q~~ll~~~~~~~~~~~~lv~~v~k~~~~e~~~~~~r~~d~~~~nq~L~ 601 (929)
-.+..||+ .-..+|||-.||..+|.+|-.....|+.+...|+.-+..++...=-+.-..-.|.....-|++
T Consensus 14 EL~~~Gll~~~d~~d~~~~~eDDEI~aeLR~lQ~eLr~~~~~N~~rk~rL~~~~~e~ma~QE~~~~l~~lD~~V~~aY~K 93 (131)
T PF10198_consen 14 ELRYIGLLSEDDDPDWQDNREDDEISAELRRLQAELREQSAHNNARKKRLLKIAKEEMARQEYKRILDDLDKQVEQAYKK 93 (131)
T ss_pred HHHHcCCcCCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888 336689999999999999999988888888877755555553322222233445444555777
Q ss_pred HHHHHHHccCc
Q 002388 602 ELREAKKQGRK 612 (929)
Q Consensus 602 ~~rea~k~~~~ 612 (929)
-.+..++..++
T Consensus 94 r~~~~~kkkk~ 104 (131)
T PF10198_consen 94 RMRARKKKKKK 104 (131)
T ss_pred HHHHhhcccCc
Confidence 77665554443
No 38
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=84.42 E-value=0.51 Score=38.53 Aligned_cols=30 Identities=27% Similarity=0.835 Sum_probs=25.1
Q ss_pred cceeCCCC--CCceeecCCcCcccccchhhhhhc
Q 002388 829 VCCICRHK--HGICIKCNYGNCQTTFHPTCARSA 860 (929)
Q Consensus 829 ~C~iC~~~--~GacIqC~~~~C~~~FH~~CA~~a 860 (929)
.|.+|++. .+.+|+|. .|.++||..|....
T Consensus 1 ~C~vC~~~~~~~~~i~C~--~C~~~~H~~C~~~~ 32 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD--SCNRWYHQECVGPP 32 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS--TTSCEEETTTSTSS
T ss_pred eCcCCCCcCCCCCeEEcC--CCChhhCcccCCCC
Confidence 47788873 78999999 89999999998554
No 39
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=83.70 E-value=0.8 Score=37.66 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=39.1
Q ss_pred ccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhccccc
Q 002388 235 NVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLG 278 (929)
Q Consensus 235 ~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~ 278 (929)
+++|||.+.|+|+.++--+|+ ....++..+-||.+..+..-|.+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB-S
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCCC
Confidence 468999999999999999999 57899999999999999887765
No 40
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=81.48 E-value=0.9 Score=36.71 Aligned_cols=32 Identities=25% Similarity=0.409 Sum_probs=23.6
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.--+++|.++| .++.+||.++|||..||---|
T Consensus 11 ~~~i~~l~~~G-~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELYAEG-MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHHTT---HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHH
Confidence 34456699999 999999999999999886554
No 41
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=76.67 E-value=3.2 Score=36.39 Aligned_cols=55 Identities=18% Similarity=0.326 Sum_probs=42.5
Q ss_pred cchHHHHHH-HHHhhCccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhh
Q 002388 218 ALNFTLILK-KLIDRGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLS 272 (929)
Q Consensus 218 s~~~~~~l~-kli~~gkv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~ 272 (929)
+....-.|+ .|++.-.++..|+|..+|||..++..-+. ...+.++.-.+|.+.|.
T Consensus 2 ~~~~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~ 58 (78)
T TIGR02607 2 PAHPGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALG 58 (78)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcC
Confidence 344566677 89999999999999999999999998887 33455666666666554
No 42
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=75.98 E-value=1.4 Score=53.52 Aligned_cols=49 Identities=31% Similarity=0.813 Sum_probs=36.4
Q ss_pred CcCcccCCCCCCCCCEEEecccCcccccccccCc--cCCCCceecccccccc
Q 002388 706 RSCDICRRSETILNPILICSGCKVAVHLDCYRNA--KESTGPWYCELCEELL 755 (929)
Q Consensus 706 ~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~--~~p~g~WlCd~C~~~~ 755 (929)
..|-.|... .+.+.+++|++|.+++|-+|--.. .++.++|+|.+|....
T Consensus 69 rvCe~c~~~-gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c~ 119 (694)
T KOG4443|consen 69 RVCEACGTT-GDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRCR 119 (694)
T ss_pred eeeeecccc-CCcccccccccccccccccccCCccccccCcccccHHHHhhh
Confidence 445555521 246789999999999998886533 5789999999997653
No 43
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=73.72 E-value=3.6 Score=31.49 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=36.3
Q ss_pred HHHHHhhCccccccchhhhccChhhhhhhcccc-ccccchhHHHHHHhh
Q 002388 225 LKKLIDRGKVNVKDIASDIGISPDLLKTTLADG-TFASDLQCKLVKWLS 272 (929)
Q Consensus 225 l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~-~~~~~~~~k~~~wl~ 272 (929)
|++++++-+++..|+|..+||++.++..-+... ...++...+|..+|.
T Consensus 2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~ 50 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALG 50 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhC
Confidence 456777788999999999999999998877633 335556666776663
No 44
>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=73.16 E-value=2.2 Score=34.37 Aligned_cols=33 Identities=27% Similarity=0.429 Sum_probs=27.5
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.-||.-|.+.|.++++|||..+|||..++...|
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence 458899999999999999999999999887665
No 45
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=71.60 E-value=2.6 Score=33.92 Aligned_cols=32 Identities=22% Similarity=0.506 Sum_probs=25.3
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
-||+-|.+-|..+..+||.++|+|+.++..-+
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri 38 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRI 38 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHH
Confidence 47888999999999999999999999887654
No 46
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=71.09 E-value=4.3 Score=33.18 Aligned_cols=48 Identities=23% Similarity=0.264 Sum_probs=37.0
Q ss_pred HHHHHhhCccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhh
Q 002388 225 LKKLIDRGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLS 272 (929)
Q Consensus 225 l~kli~~gkv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~ 272 (929)
||++.++-..+.+|+|..+|||+.+|..-+. .....++.-.+|-+-|.
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~ 49 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALG 49 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHT
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHC
Confidence 6788888889999999999999999999887 34566666667766554
No 47
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=71.00 E-value=3.1 Score=40.43 Aligned_cols=48 Identities=25% Similarity=0.645 Sum_probs=36.0
Q ss_pred CcCcccCCCC-CCCCCEEEecccCcccccccccCccCCCCceeccccccc
Q 002388 706 RSCDICRRSE-TILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 706 ~~CsVC~~~E-~~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
..|..|...- ...|.-..|..|...|=..| |+.......|+|..|...
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C-~~~~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVDCKHRVCKKC-GVYSKKEPIWLCKVCQKQ 103 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETTTTEEEETTS-EEETSSSCCEEEHHHHHH
T ss_pred cchhhhCCcccccCCCCCcCCcCCccccCcc-CCcCCCCCCEEChhhHHH
Confidence 4599998753 34677799999999999999 444445789999999764
No 48
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=69.37 E-value=4.1 Score=33.56 Aligned_cols=34 Identities=26% Similarity=0.608 Sum_probs=25.9
Q ss_pred CCcCcccCCCC-CCCCCEEEecccCcccccccccC
Q 002388 705 PRSCDICRRSE-TILNPILICSGCKVAVHLDCYRN 738 (929)
Q Consensus 705 d~~CsVC~~~E-~~~N~Ll~Cd~C~vaVHq~CYGi 738 (929)
...|++|...= ....+-+.|..|++.+|..|...
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 46799999854 23578999999999999999853
No 49
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=69.34 E-value=2.1 Score=31.74 Aligned_cols=28 Identities=29% Similarity=0.710 Sum_probs=12.2
Q ss_pred cCcccCCCCCCCCCEEEecccCccccccc
Q 002388 707 SCDICRRSETILNPILICSGCKVAVHLDC 735 (929)
Q Consensus 707 ~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~C 735 (929)
.|++|...-. ++....|..|+..+|..|
T Consensus 2 ~C~~C~~~~~-~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPID-GGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS-----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCC-CCceEECccCCCccChhc
Confidence 5999998543 247889999999999988
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=69.32 E-value=4.1 Score=34.35 Aligned_cols=48 Identities=31% Similarity=0.349 Sum_probs=31.5
Q ss_pred HHHHHhhCccccccchhhhccChhhhhhhcccc--ccccchhHHHHHHhh
Q 002388 225 LKKLIDRGKVNVKDIASDIGISPDLLKTTLADG--TFASDLQCKLVKWLS 272 (929)
Q Consensus 225 l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~--~~~~~~~~k~~~wl~ 272 (929)
|++|+++-.++..|+|.++|||..+|..-+... .+.-+.-.+|-+.|.
T Consensus 2 L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 2 LKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp HHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcC
Confidence 677777777899999999999999999888743 455555556665553
No 51
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=69.32 E-value=2.3 Score=47.21 Aligned_cols=49 Identities=31% Similarity=0.619 Sum_probs=35.8
Q ss_pred CCcceeCCCCCCceeecCCcCcc-cccchhhhhhcCceEEEeeCCCcceeeeccccccch
Q 002388 827 IDVCCICRHKHGICIKCNYGNCQ-TTFHPTCARSAGFYLNVKSTGGNFQHKAYCEKHSLE 885 (929)
Q Consensus 827 k~~C~iC~~~~GacIqC~~~~C~-~~FH~~CA~~aGl~~~~k~~~g~~~~~ayC~kHs~~ 885 (929)
..+|......+|.+|.|...+|. .|||..|. |+....+ |.| ||++-...
T Consensus 219 ~~yC~Cnqvsyg~Mi~CDn~~C~~eWFH~~CV---GL~~~Pk---gkW----yC~~C~~~ 268 (274)
T KOG1973|consen 219 PTYCICNQVSYGKMIGCDNPGCPIEWFHFTCV---GLKTKPK---GKW----YCPRCKAE 268 (274)
T ss_pred CEEEEecccccccccccCCCCCCcceEEEecc---ccccCCC---Ccc----cchhhhhh
Confidence 35555554569999999999999 99999997 6665332 334 88866544
No 52
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=68.06 E-value=3.2 Score=35.93 Aligned_cols=34 Identities=24% Similarity=0.400 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
=+-|+.-|++.|.+++.|||.++|||..++...|
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L 43 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEELGISRSTVYRAL 43 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3668889999999999999999999999988776
No 53
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=67.80 E-value=7 Score=27.40 Aligned_cols=32 Identities=25% Similarity=0.390 Sum_probs=24.5
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhh
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKT 252 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~ 252 (929)
+.-..+.++++.|. ++.+||.++|||..++-.
T Consensus 9 ~~~~~i~~~~~~~~-s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 9 EQIEEARRLLAAGE-SVAEIARRLGVSRSTLYR 40 (42)
T ss_pred HHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHH
Confidence 33445566788876 999999999999887653
No 54
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=67.70 E-value=2.9 Score=46.37 Aligned_cols=48 Identities=23% Similarity=0.375 Sum_probs=37.2
Q ss_pred CCcCcccCCCCC-----CCCCEEEecccCcccccccccCcc-----CCCCceeccccc
Q 002388 705 PRSCDICRRSET-----ILNPILICSGCKVAVHLDCYRNAK-----ESTGPWYCELCE 752 (929)
Q Consensus 705 d~~CsVC~~~E~-----~~N~Ll~Cd~C~vaVHq~CYGi~~-----~p~g~WlCd~C~ 752 (929)
...|.+|++..+ .-|-++.|.-|..+.|..|..... +-.-.|.|--|+
T Consensus 258 ~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 258 RNERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred hhhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 467999998763 237799999999999999987553 235578888884
No 55
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=67.43 E-value=1.5 Score=58.11 Aligned_cols=51 Identities=31% Similarity=0.762 Sum_probs=42.6
Q ss_pred CCCcCcccCCCCCCCCCEEEecccCcccccccccCc--cCCCCceecccccccc
Q 002388 704 HPRSCDICRRSETILNPILICSGCKVAVHLDCYRNA--KESTGPWYCELCEELL 755 (929)
Q Consensus 704 ~d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~--~~p~g~WlCd~C~~~~ 755 (929)
....|-||..... ...++.|+.|.-.+|..|.... ..+.++|+|..|....
T Consensus 1107 ~~~~c~~cr~k~~-~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQ-DEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred chhhhhhhhhccc-chhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 4688999998542 4689999999999999999754 5779999999998764
No 56
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=66.79 E-value=4 Score=33.26 Aligned_cols=31 Identities=29% Similarity=0.460 Sum_probs=25.7
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
+.|++.|.+. .++++||.+.|||++++..-+
T Consensus 18 ~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 18 QYILKLLRES--RSFKDVARELGVSWSTVRRIF 48 (52)
T ss_pred HHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHH
Confidence 4577777755 899999999999999987655
No 57
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=66.13 E-value=3.4 Score=33.11 Aligned_cols=34 Identities=41% Similarity=0.812 Sum_probs=26.8
Q ss_pred CCcCcccCCCCC-CCCCEEEecccCcccccccccC
Q 002388 705 PRSCDICRRSET-ILNPILICSGCKVAVHLDCYRN 738 (929)
Q Consensus 705 d~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi 738 (929)
...|++|...-. ...+-+.|+.|++.||..|...
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 467999987542 1257889999999999999853
No 58
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=65.83 E-value=6 Score=50.83 Aligned_cols=116 Identities=22% Similarity=0.370 Sum_probs=74.2
Q ss_pred CCCCCCCcCcccCCCCCCCCCEEEecccCcccccccccCc--cCCCCceecccccccccCCCCCCCCCCccCCCcccccc
Q 002388 700 FSKEHPRSCDICRRSETILNPILICSGCKVAVHLDCYRNA--KESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAEC 777 (929)
Q Consensus 700 ~ske~d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~--~~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C 777 (929)
....-+..|-+|.+ .+.++.|..|...||..|.--+ ..+...|-|..|..-+.+. .+.|
T Consensus 339 ~~~~~ddhcrf~~d----~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hkvng---------------vvd~ 399 (1414)
T KOG1473|consen 339 GEIEYDDHCRFCHD----LGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHKVNG---------------VVDC 399 (1414)
T ss_pred cceeecccccccCc----ccceeecccCCceEEeeecCCccccCCCccchhhhhhhhccCc---------------cccc
Confidence 44455678999988 7899999999999999998654 3568899999997653321 4557
Q ss_pred ccCCCCCCceee-ccCcchhhhccccccccceeecCccccccccccccCCCCcceeCCCCCCceeecCCcCcccccch-h
Q 002388 778 SLCGGTTGAFRK-SANGQWVHAFCAEWVFESTFRRGQVNPVAGMEAFPKGIDVCCICRHKHGICIKCNYGNCQTTFHP-T 855 (929)
Q Consensus 778 ~LCp~~gGaLK~-T~~g~WVHv~CAlw~pev~f~~~~~~~Vegie~I~k~k~~C~iC~~~~GacIqC~~~~C~~~FH~-~ 855 (929)
+|=+...+...+ +..|. .+ .-...+. ....|.||+.. |. .-|.|+.|.+.||. .
T Consensus 400 vl~~~K~~~~iR~~~iG~---------------dr-~gr~ywf------i~rrl~Ie~~d-et-~l~yysT~pqly~ll~ 455 (1414)
T KOG1473|consen 400 VLPPSKNVDSIRHTPIGR---------------DR-YGRKYWF------ISRRLRIEGMD-ET-LLWYYSTCPQLYHLLR 455 (1414)
T ss_pred ccChhhcccceeccCCCc---------------Cc-cccchhc------eeeeeEEecCC-Cc-EEEEecCcHHHHHHHH
Confidence 776655444422 22111 00 0000011 12578888853 44 44566779999999 7
Q ss_pred hhh
Q 002388 856 CAR 858 (929)
Q Consensus 856 CA~ 858 (929)
|.-
T Consensus 456 cLd 458 (1414)
T KOG1473|consen 456 CLD 458 (1414)
T ss_pred Hhc
Confidence 753
No 59
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=65.26 E-value=2.9 Score=36.47 Aligned_cols=22 Identities=36% Similarity=0.755 Sum_probs=19.7
Q ss_pred hCccccccchhhhccChhhhhh
Q 002388 231 RGKVNVKDIASDIGISPDLLKT 252 (929)
Q Consensus 231 ~gkv~v~d~~~~~gis~~~l~~ 252 (929)
.|++.++|||.+||||+.++..
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHH
Confidence 6899999999999999988753
No 60
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=64.35 E-value=3.1 Score=32.99 Aligned_cols=33 Identities=39% Similarity=0.632 Sum_probs=25.5
Q ss_pred CCcCcccCCCCCCCCCEEEecccCccccccccc
Q 002388 705 PRSCDICRRSETILNPILICSGCKVAVHLDCYR 737 (929)
Q Consensus 705 d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYG 737 (929)
...|.+|...-....+-+.|..|++.+|..|..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~ 43 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAE 43 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHh
Confidence 467999998542111578999999999999975
No 61
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=64.12 E-value=8.1 Score=29.72 Aligned_cols=48 Identities=21% Similarity=0.219 Sum_probs=36.0
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhhcccc-ccccchhHHHHHHh
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLADG-TFASDLQCKLVKWL 271 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~-~~~~~~~~k~~~wl 271 (929)
.|+..+++-+++..++|..+|||+.++..-+... .+.++...+|...|
T Consensus 3 ~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~ 51 (58)
T cd00093 3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 4666677778999999999999999998777633 45556666666555
No 62
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=63.29 E-value=3.7 Score=33.16 Aligned_cols=30 Identities=23% Similarity=0.552 Sum_probs=21.1
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.+..|.++| .++.+||..+|.|+.|+-..|
T Consensus 12 ~I~~l~~~G-~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 12 QIEALLEQG-MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp HHHHHHCS----HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcC-CCHHHHHHHHCcCcHHHHHHH
Confidence 467888899 899999999999999987654
No 63
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=63.20 E-value=5.1 Score=34.08 Aligned_cols=31 Identities=29% Similarity=0.600 Sum_probs=24.9
Q ss_pred HHHHHHhhC------ccccccchhhhccChhhhhhhc
Q 002388 224 ILKKLIDRG------KVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 224 ~l~kli~~g------kv~v~d~~~~~gis~~~l~~~~ 254 (929)
+|+.-++.| +++++|||.++|||+-++.--|
T Consensus 8 ~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 8 ILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred HHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 556666666 6899999999999999887665
No 64
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=62.13 E-value=3.3 Score=49.85 Aligned_cols=35 Identities=29% Similarity=0.527 Sum_probs=24.4
Q ss_pred CcceeCCCC-CCceeecCCcCcccccchhhhhhcCceEEE
Q 002388 828 DVCCICRHK-HGICIKCNYGNCQTTFHPTCARSAGFYLNV 866 (929)
Q Consensus 828 ~~C~iC~~~-~GacIqC~~~~C~~~FH~~CA~~aGl~~~~ 866 (929)
.+|..|.+- .|..++=. + ..|||+||+-..+.-.|
T Consensus 193 vkc~~c~~fisgkvLqag--~--kh~HPtCARCsRCgqmF 228 (670)
T KOG1044|consen 193 VKCEECEKFISGKVLQAG--D--KHFHPTCARCSRCGQMF 228 (670)
T ss_pred eehHHhhhhhhhhhhhcc--C--cccCcchhhhhhhcccc
Confidence 577777763 55555544 4 88999999887666544
No 65
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=61.97 E-value=5.9 Score=31.44 Aligned_cols=32 Identities=34% Similarity=0.554 Sum_probs=28.8
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.||+.|.+.|.+++.+||..+|+|+.++...|
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l 35 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDL 35 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 57888888899999999999999999987766
No 66
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=60.40 E-value=5.8 Score=34.88 Aligned_cols=33 Identities=21% Similarity=0.366 Sum_probs=29.9
Q ss_pred HHHHHHHHhhCc--cccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGK--VNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gk--v~v~d~~~~~gis~~~l~~~~ 254 (929)
.-||.-|-++|. ++++|||.++||+.-++...|
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L 43 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVL 43 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 578999999998 999999999999999887776
No 67
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=60.15 E-value=12 Score=30.31 Aligned_cols=36 Identities=8% Similarity=0.169 Sum_probs=32.1
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
.|+..|+++.++=..+..|+|..+|||+.++..-..
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 367789999999999999999999999999888775
No 68
>PF13518 HTH_28: Helix-turn-helix domain
Probab=59.92 E-value=5.9 Score=31.95 Aligned_cols=28 Identities=29% Similarity=0.508 Sum_probs=21.3
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhh
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTT 253 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~ 253 (929)
|++... +|+ ++.+||.++|||+.+|..-
T Consensus 5 iv~~~~-~g~-s~~~~a~~~gis~~tv~~w 32 (52)
T PF13518_consen 5 IVELYL-EGE-SVREIAREFGISRSTVYRW 32 (52)
T ss_pred HHHHHH-cCC-CHHHHHHHHCCCHhHHHHH
Confidence 334444 788 9999999999999887543
No 69
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=59.59 E-value=5.7 Score=40.52 Aligned_cols=28 Identities=36% Similarity=0.784 Sum_probs=22.3
Q ss_pred ccccccccCc--cCCCCceecccccccccC
Q 002388 730 AVHLDCYRNA--KESTGPWYCELCEELLSS 757 (929)
Q Consensus 730 aVHq~CYGi~--~~p~g~WlCd~C~~~~~~ 757 (929)
.+|..|...+ .+|+|+|+|..|......
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~ 30 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSG 30 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCC
Confidence 3799999754 678999999999876443
No 70
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=58.60 E-value=7.8 Score=28.92 Aligned_cols=27 Identities=37% Similarity=0.898 Sum_probs=21.7
Q ss_pred cCcccCCCCCCCCC-EEEecccCccccccc
Q 002388 707 SCDICRRSETILNP-ILICSGCKVAVHLDC 735 (929)
Q Consensus 707 ~CsVC~~~E~~~N~-Ll~Cd~C~vaVHq~C 735 (929)
.|+||.+.-+ +. ...|..|...+|..|
T Consensus 2 ~C~~C~~~~~--~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKID--GFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcC--CCEeEEeCCCCCeEcCcc
Confidence 4999977432 33 889999999999988
No 71
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=55.88 E-value=7.5 Score=42.39 Aligned_cols=35 Identities=26% Similarity=0.394 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
...|+..|-..|+|+|+|+|.++|+|++|+..-|.
T Consensus 9 ~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~ 43 (252)
T PRK10681 9 IGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLN 43 (252)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHH
Confidence 46799999999999999999999999999998884
No 72
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=55.18 E-value=9.7 Score=40.47 Aligned_cols=44 Identities=25% Similarity=0.703 Sum_probs=34.6
Q ss_pred CCCcCcccCCCCC----CCCCEEEecccCcccccccccCccCCCCceeccccccc
Q 002388 704 HPRSCDICRRSET----ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 704 ~d~~CsVC~~~E~----~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
.+..|.+|.+.+. ..+..+.|..|+..+|+.|+.- =-|.+|...
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~-------~~CpkC~R~ 198 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK-------KSCPKCARR 198 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC-------CCCCCcHhH
Confidence 4577999998773 2457899999999999999962 129999764
No 73
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=54.80 E-value=8 Score=31.87 Aligned_cols=33 Identities=24% Similarity=0.556 Sum_probs=26.5
Q ss_pred HHHHHHHHhhCc-cccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGK-VNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gk-v~v~d~~~~~gis~~~l~~~~ 254 (929)
.-||+-|...+. |++++||.++|||.-++...|
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 357777865554 999999999999999998877
No 74
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=54.78 E-value=6.7 Score=31.76 Aligned_cols=31 Identities=32% Similarity=0.572 Sum_probs=25.4
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
-||+.|.+ |..+|.|||.++|+|..++---|
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHh-CCCchhhHHHhccccchHHHHHH
Confidence 47777777 99999999999999998876554
No 75
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=54.71 E-value=4.9 Score=46.87 Aligned_cols=153 Identities=21% Similarity=0.388 Sum_probs=83.6
Q ss_pred cCcccCCCCCCCCCEEEecccCcccccccccC----------cc-CCCCceecccccccccCCCCCCCCCCccCCCcccc
Q 002388 707 SCDICRRSETILNPILICSGCKVAVHLDCYRN----------AK-ESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVA 775 (929)
Q Consensus 707 ~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi----------~~-~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~ 775 (929)
.|.-|...-. ++-.-|.-=+..+|..|.-. .. .-++.-+|+.|-.. -.-
T Consensus 276 iC~~C~K~V~--g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~------------------tle 335 (468)
T KOG1701|consen 276 ICAFCHKTVS--GQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQD------------------TLE 335 (468)
T ss_pred hhhhcCCccc--CcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHH------------------HHH
Confidence 6888876432 22223333344455555421 11 22566778887543 145
Q ss_pred ccccCCCCCCceeeccCcchhh------hccccccccceeecCcccccccccccc-CCCCcceeCCCC--------CCce
Q 002388 776 ECSLCGGTTGAFRKSANGQWVH------AFCAEWVFESTFRRGQVNPVAGMEAFP-KGIDVCCICRHK--------HGIC 840 (929)
Q Consensus 776 ~C~LCp~~gGaLK~T~~g~WVH------v~CAlw~pev~f~~~~~~~Vegie~I~-k~k~~C~iC~~~--------~Gac 840 (929)
+|..|+..---.....-|+-+| |+|+--+-++.|.-+.-+.|-=+.+.. +..-+|.+|++. .-+-
T Consensus 336 kC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvR 415 (468)
T KOG1701|consen 336 KCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVR 415 (468)
T ss_pred HHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEE
Confidence 7888885311111112234444 455555566666544334444344433 346899999984 2344
Q ss_pred eecCCcCcccccchhhhhhcCceEEEee-CC--Cc--ceeeecccccc
Q 002388 841 IKCNYGNCQTTFHPTCARSAGFYLNVKS-TG--GN--FQHKAYCEKHS 883 (929)
Q Consensus 841 IqC~~~~C~~~FH~~CA~~aGl~~~~k~-~~--g~--~~~~ayC~kHs 883 (929)
|-|. .+.||+.|-+-..+-|.... .. |. +.-+++|+.-.
T Consensus 416 vvam----dr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch 459 (468)
T KOG1701|consen 416 VVAM----DRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCH 459 (468)
T ss_pred EEEc----cccccccceehhhcCccccccCCCCcceeccCceeechhh
Confidence 5555 57899999988877776642 12 21 34578897654
No 76
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=51.50 E-value=50 Score=29.60 Aligned_cols=60 Identities=32% Similarity=0.272 Sum_probs=47.2
Q ss_pred chhhHHHHHHHHH--hhhhhhhhhhhHHHHHHHHHHHHHHHHhhhhcchhHHHHHHHHHHHHHHHHccC
Q 002388 545 EVEGEIIYFQHRL--LGNAFSRKRLADNLVCKAVKTLNQEIDVARGRRWDAVLVNQYLCELREAKKQGR 611 (929)
Q Consensus 545 e~e~E~~~~q~~l--l~~~~~~~~~~~~lv~~v~k~~~~e~~~~~~r~~d~~~~nq~L~~~rea~k~~~ 611 (929)
.+|.|+..||.+| +.+-.+ .++ ...+.|..|-+.|-.+--+...-++-|++..++.++.-
T Consensus 2 ~Lea~~~~Lr~rLd~~~rk~~---~~~----~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el 63 (69)
T PF14197_consen 2 KLEAEIATLRNRLDSLTRKNS---VHE----IENKRLRRERDSAERQLGDAYEENNKLKEENEALRKEL 63 (69)
T ss_pred hHHHHHHHHHHHHHHHHHHHH---HHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999998 433332 122 55688999999999999998888999999999987763
No 77
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=50.15 E-value=12 Score=32.27 Aligned_cols=25 Identities=40% Similarity=0.682 Sum_probs=22.1
Q ss_pred hhCccccccchhhhccChhhhhhhc
Q 002388 230 DRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 230 ~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
+.|.|+.+|||..+|+||-|....|
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCccHHHHHHHHCCChHHHHHHH
Confidence 7889999999999999999988776
No 78
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=50.07 E-value=16 Score=30.90 Aligned_cols=49 Identities=22% Similarity=0.241 Sum_probs=32.9
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhh
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLS 272 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~ 272 (929)
-||+|.++-..+..|+|..+||++.+|..-.. ...++++.-.+|.+-|.
T Consensus 3 ~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~ 52 (64)
T PF12844_consen 3 RLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALG 52 (64)
T ss_dssp HHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 47899999999999999999999888877776 33445555555554443
No 79
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=50.04 E-value=6.6 Score=32.76 Aligned_cols=23 Identities=22% Similarity=0.521 Sum_probs=19.8
Q ss_pred CccccccchhhhccChhhhhhhc
Q 002388 232 GKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 232 gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.+++|.|+|.++||++..|...|
T Consensus 2 ~~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 2 EKIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH
T ss_pred CceEHHHHHHHHCcCHHHHHHHH
Confidence 47899999999999999998888
No 80
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=49.69 E-value=10 Score=41.81 Aligned_cols=33 Identities=30% Similarity=0.891 Sum_probs=27.4
Q ss_pred CCCCcceeCCC-CCCceeecCCcCccc-ccchhhh
Q 002388 825 KGIDVCCICRH-KHGICIKCNYGNCQT-TFHPTCA 857 (929)
Q Consensus 825 k~k~~C~iC~~-~~GacIqC~~~~C~~-~FH~~CA 857 (929)
.++..-+||++ ..|-||.|...+|.. |||..|.
T Consensus 218 e~e~lYCfCqqvSyGqMVaCDn~nCkrEWFH~~CV 252 (271)
T COG5034 218 EGEELYCFCQQVSYGQMVACDNANCKREWFHLECV 252 (271)
T ss_pred cCceeEEEecccccccceecCCCCCchhheecccc
Confidence 34455668887 599999999999987 8999996
No 81
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=48.60 E-value=7.1 Score=30.71 Aligned_cols=25 Identities=28% Similarity=0.541 Sum_probs=17.8
Q ss_pred hCccccccchhhhccChhhhhhhcc
Q 002388 231 RGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 231 ~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
+-+.+|+|||..+|+|+..|.....
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3468999999999999988877664
No 82
>PRK09492 treR trehalose repressor; Provisional
Probab=48.37 E-value=13 Score=40.47 Aligned_cols=52 Identities=15% Similarity=0.283 Sum_probs=45.3
Q ss_pred hCccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhccccccccc
Q 002388 231 RGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLK 282 (929)
Q Consensus 231 ~gkv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (929)
++|++++|||.+.|+|.-|+--+|+ ....++..+.||.+-.+.--|.+....
T Consensus 2 ~~~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a 54 (315)
T PRK09492 2 QNKLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSPSKSA 54 (315)
T ss_pred CCCCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCcCHHH
Confidence 3589999999999999999999998 567899999999999988888775543
No 83
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=47.70 E-value=15 Score=32.31 Aligned_cols=47 Identities=19% Similarity=0.338 Sum_probs=40.2
Q ss_pred cccccchhhhccChhhhhhhccc-cccccchhHHHHHHhhhccccccc
Q 002388 234 VNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWLSNHAYLGGL 280 (929)
Q Consensus 234 v~v~d~~~~~gis~~~l~~~~~~-~~~~~~~~~k~~~wl~~~~~~~~~ 280 (929)
++..|||..+|+|..++--.|++ ...+|....+|.+-++..-|.+..
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCCH
Confidence 45789999999999999999984 456789999999999999886553
No 84
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=47.54 E-value=13 Score=40.88 Aligned_cols=51 Identities=14% Similarity=0.270 Sum_probs=45.2
Q ss_pred CccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhccccccccc
Q 002388 232 GKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLK 282 (929)
Q Consensus 232 gkv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (929)
+||+++|||.+.|+|.-|+-.+|+ ....++..+.||.+-.+..-|.+....
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~~~a 56 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQA 56 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcCHHH
Confidence 479999999999999999999999 567899999999999999988775544
No 85
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=47.44 E-value=16 Score=33.04 Aligned_cols=43 Identities=28% Similarity=0.387 Sum_probs=33.8
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhccccccccchhHHHHHHhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNH 274 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~~wl~~~ 274 (929)
-.+++-|+.++.+++.|+|.+++||.-++...+ .+|-+||+..
T Consensus 19 ~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i----------~~l~~~l~~~ 61 (87)
T PF05043_consen 19 YQLLKLLLNNEYVSIEDLAEELFISRSTIYRDI----------KKLNKYLKKY 61 (87)
T ss_dssp HHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHH----------HHHHHHHHCC
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHH----------HHHHHHHHHc
Confidence 457788899999999999999999999999887 5667788743
No 86
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=46.68 E-value=13 Score=41.34 Aligned_cols=49 Identities=27% Similarity=0.588 Sum_probs=37.7
Q ss_pred CcCcccCCCC-----C-CCCCEEEecccCcccccccccCcc-----CCCCceeccccccc
Q 002388 706 RSCDICRRSE-----T-ILNPILICSGCKVAVHLDCYRNAK-----ESTGPWYCELCEEL 754 (929)
Q Consensus 706 ~~CsVC~~~E-----~-~~N~Ll~Cd~C~vaVHq~CYGi~~-----~p~g~WlCd~C~~~ 754 (929)
-+|+.|+... + -..+||.|+.|+..-|.+|.-... +-.-.|.|.-|++-
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~c 284 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYC 284 (336)
T ss_pred cccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeeccee
Confidence 6799999754 1 245799999999999999986432 23567999999874
No 87
>PRK09726 antitoxin HipB; Provisional
Probab=45.50 E-value=26 Score=32.08 Aligned_cols=59 Identities=12% Similarity=0.096 Sum_probs=44.8
Q ss_pred cchHHHHHHHHHhhCccccccchhhhccChhhhhhhcccc-ccccchhHHHHHHhhhccc
Q 002388 218 ALNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLADG-TFASDLQCKLVKWLSNHAY 276 (929)
Q Consensus 218 s~~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~-~~~~~~~~k~~~wl~~~~~ 276 (929)
...|+--||++..+-.++..++|..+|||+.+|..-.... ....+.-.+|.+.|.=.+.
T Consensus 10 ~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~ 69 (88)
T PRK09726 10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69 (88)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcc
Confidence 4467888999999999999999999999999998777632 3444555666666654433
No 88
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=45.42 E-value=22 Score=44.45 Aligned_cols=51 Identities=24% Similarity=0.479 Sum_probs=36.7
Q ss_pred CCcceeCCCC--CCceeecCCcCcccc-cchhhhhhcCceEEEeeCCCcceeeeccccccchhh
Q 002388 827 IDVCCICRHK--HGICIKCNYGNCQTT-FHPTCARSAGFYLNVKSTGGNFQHKAYCEKHSLEQK 887 (929)
Q Consensus 827 k~~C~iC~~~--~GacIqC~~~~C~~~-FH~~CA~~aGl~~~~k~~~g~~~~~ayC~kHs~~qr 887 (929)
.-.|.||... .-.+|-|. .|... ||..|.-..-+-+-+ -..||......+.
T Consensus 215 ~~~C~IC~~~DpEdVLLLCD--sCN~~~YH~YCLDPdl~eiP~--------~eWYC~NC~dL~~ 268 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCD--SCNKVYYHVYCLDPDLSESPV--------NEWYCTNCSLLEI 268 (1134)
T ss_pred cccceeeccCChHHhheeec--ccccceeeccccCcccccccc--------cceecCcchhhhh
Confidence 5789999986 56889999 99998 999998554322222 1248887766544
No 89
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=44.28 E-value=12 Score=39.56 Aligned_cols=35 Identities=26% Similarity=0.567 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhC--ccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRG--KVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~g--kv~v~d~~~~~gis~~~l~~~~~ 255 (929)
...||+.|..+| .|+++++|..+||||.++..=|.
T Consensus 18 ~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~ 54 (213)
T PRK05472 18 YYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLS 54 (213)
T ss_pred HHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHH
Confidence 367899999999 99999999999999998887664
No 90
>PHA01976 helix-turn-helix protein
Probab=44.15 E-value=31 Score=29.33 Aligned_cols=52 Identities=17% Similarity=0.163 Sum_probs=37.5
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhhhcccc-ccccchhHHHHHHh
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLADG-TFASDLQCKLVKWL 271 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~-~~~~~~~~k~~~wl 271 (929)
+|+--||+|-++=..+..++|..+|||+.++-.-.... ....+.-.||-+.|
T Consensus 2 ~~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l 54 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADAL 54 (67)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 46778899999989999999999999998887766422 22333334555444
No 91
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=43.90 E-value=14 Score=40.54 Aligned_cols=35 Identities=31% Similarity=0.497 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
...||+-|..+|+|+|+|+|..+|+|++|+..=|.
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~ 41 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLN 41 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHH
Confidence 36799999999999999999999999999998763
No 92
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.59 E-value=11 Score=37.79 Aligned_cols=49 Identities=22% Similarity=0.510 Sum_probs=36.0
Q ss_pred CCcCcccCCCCCCCCCEEEecccCcccccccccCccCC--CCceecccccc
Q 002388 705 PRSCDICRRSETILNPILICSGCKVAVHLDCYRNAKES--TGPWYCELCEE 753 (929)
Q Consensus 705 d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~~~p--~g~WlCd~C~~ 753 (929)
+..|-||......++---.|.-|.+.+-..|-|-.... .--|.|.+|.-
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k 115 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRK 115 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcH
Confidence 46799999876555555578888888888887755444 34599999954
No 93
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=43.54 E-value=15 Score=40.36 Aligned_cols=52 Identities=15% Similarity=0.275 Sum_probs=45.8
Q ss_pred hCccccccchhhhccChhhhhhhccc-cccccchhHHHHHHhhhccccccccc
Q 002388 231 RGKVNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWLSNHAYLGGLLK 282 (929)
Q Consensus 231 ~gkv~v~d~~~~~gis~~~l~~~~~~-~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (929)
+++|+++|||.+.|+|.-|+--.|+. ...++..+.||.+-.+..=|.+....
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a 55 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNRAP 55 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCccHHH
Confidence 67899999999999999999999984 46899999999999999888775544
No 94
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=42.62 E-value=17 Score=32.33 Aligned_cols=32 Identities=28% Similarity=0.600 Sum_probs=12.9
Q ss_pred CcCcccCCCCCC--CCCEEEec--ccCccccccccc
Q 002388 706 RSCDICRRSETI--LNPILICS--GCKVAVHLDCYR 737 (929)
Q Consensus 706 ~~CsVC~~~E~~--~N~Ll~Cd--~C~vaVHq~CYG 737 (929)
..|.||...... .-+.+.|. .|+..+|..|..
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~ 38 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLS 38 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGH
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHH
Confidence 569999986532 23578998 899999999984
No 95
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=42.40 E-value=16 Score=29.66 Aligned_cols=31 Identities=32% Similarity=0.471 Sum_probs=25.8
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
||+-|. .+.+++.||+.++|||+-++...|.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~ 32 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLK 32 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHH
Confidence 455555 8889999999999999999888773
No 96
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=42.33 E-value=17 Score=31.00 Aligned_cols=34 Identities=21% Similarity=0.383 Sum_probs=29.7
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
..+|.-|++.+.++++++|..+|+|.-+|..-+.
T Consensus 8 ~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 8 LKLLELLLKNKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 4578889999999999999999999999988775
No 97
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.91 E-value=17 Score=33.92 Aligned_cols=32 Identities=22% Similarity=0.560 Sum_probs=29.4
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
-||+.|-+.|.++..+||.++|||+.++...+
T Consensus 7 ~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l 38 (108)
T smart00344 7 KILEELQKDARISLAELAKKVGLSPSTVHNRV 38 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHH
Confidence 57888989999999999999999999998777
No 98
>PHA02591 hypothetical protein; Provisional
Probab=41.32 E-value=22 Score=32.75 Aligned_cols=34 Identities=26% Similarity=0.437 Sum_probs=29.0
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
|+--+-++|.++| .++.+||..+|||-+++..-|
T Consensus 47 d~~~vA~eL~eqG-lSqeqIA~~LGVsqetVrKYL 80 (83)
T PHA02591 47 DLISVTHELARKG-FTVEKIASLLGVSVRKVRRYL 80 (83)
T ss_pred hHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Confidence 6677889999999 599999999999988876554
No 99
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=40.29 E-value=20 Score=39.26 Aligned_cols=50 Identities=14% Similarity=0.262 Sum_probs=43.5
Q ss_pred ccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhccccccccc
Q 002388 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLK 282 (929)
Q Consensus 233 kv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (929)
||+++|||.+.|+|.-|+--+|+ ....++..+.||.+-.+..-|.+....
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~~a 51 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPSKSA 51 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcCHHH
Confidence 78999999999999999999998 446789999999999998888775543
No 100
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=39.75 E-value=18 Score=37.09 Aligned_cols=34 Identities=24% Similarity=0.373 Sum_probs=31.4
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
-.||.-|+..|.++..|||.++||+.-++...|.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~ 50 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALY 50 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999999999999988874
No 101
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=39.36 E-value=22 Score=28.93 Aligned_cols=21 Identities=19% Similarity=0.544 Sum_probs=19.2
Q ss_pred ccccchhhhccChhhhhhhcc
Q 002388 235 NVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 235 ~v~d~~~~~gis~~~l~~~~~ 255 (929)
++.+||..+|||..++..+|.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~ 42 (60)
T smart00345 22 SERELAAQLGVSRTTVREALS 42 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 899999999999999998883
No 102
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.93 E-value=30 Score=29.81 Aligned_cols=38 Identities=26% Similarity=0.542 Sum_probs=32.7
Q ss_pred CCcceeCCCC---CCceeecCCcCcccccchhhhhhcCceEEE
Q 002388 827 IDVCCICRHK---HGICIKCNYGNCQTTFHPTCARSAGFYLNV 866 (929)
Q Consensus 827 k~~C~iC~~~---~GacIqC~~~~C~~~FH~~CA~~aGl~~~~ 866 (929)
..+|.+|+.+ .+..|.|- .|.+.||-.|.-..|--+..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp--~CgapyHR~C~~~~g~C~~~ 45 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCP--ECGAPYHRDCWEKAGGCINY 45 (54)
T ss_pred CccChhhCCcccCCCCEEECC--CCCCcccHHHHhhCCceEec
Confidence 4689999985 67899999 99999999999888877654
No 103
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=38.36 E-value=20 Score=35.21 Aligned_cols=34 Identities=24% Similarity=0.262 Sum_probs=29.0
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
.-||+.|.+.|.++|.|||..+||++-++..-|.
T Consensus 19 l~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 19 LGIVLLLRESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4578888888999999999999999998865553
No 104
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=38.21 E-value=21 Score=30.36 Aligned_cols=33 Identities=30% Similarity=0.504 Sum_probs=27.3
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.-||+-|-..|..++.+||.++||++-++.-.|
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 457777779999999999999999999876655
No 105
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=38.20 E-value=17 Score=37.05 Aligned_cols=33 Identities=21% Similarity=0.433 Sum_probs=29.4
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.-||+.|.+-|.++..+||.++|+|+-++..-+
T Consensus 17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri 49 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLSPTPCLERV 49 (164)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 357889999999999999999999999887665
No 106
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=37.93 E-value=12 Score=45.79 Aligned_cols=49 Identities=27% Similarity=0.580 Sum_probs=35.7
Q ss_pred CcCcccCCCCC-CCCCEEEecccCcccccccccCc---cCCCCceeccccccc
Q 002388 706 RSCDICRRSET-ILNPILICSGCKVAVHLDCYRNA---KESTGPWYCELCEEL 754 (929)
Q Consensus 706 ~~CsVC~~~E~-~~N~Ll~Cd~C~vaVHq~CYGi~---~~p~g~WlCd~C~~~ 754 (929)
+.|-+|..... ..+.++.|..|+...|.+|..+. -+..+.|.|..|.--
T Consensus 19 ~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvC 71 (694)
T KOG4443|consen 19 LMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVC 71 (694)
T ss_pred hhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceee
Confidence 45677765543 36889999999999999998643 122455999998653
No 107
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=37.93 E-value=20 Score=33.58 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=24.8
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhh
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKT 252 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~ 252 (929)
.-+.+|+++|+ ++++||..+|||.-++..
T Consensus 41 ~~I~~ll~~G~-S~~eIA~~LgISrsTIyR 69 (88)
T TIGR02531 41 LQVAKMLKQGK-TYSDIEAETGASTATISR 69 (88)
T ss_pred HHHHHHHHCCC-CHHHHHHHHCcCHHHHHH
Confidence 45567889996 999999999999998875
No 108
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=37.73 E-value=21 Score=26.61 Aligned_cols=27 Identities=41% Similarity=0.968 Sum_probs=22.0
Q ss_pred cceeCCCC-CCc-eeecCCcCcccccchhhh
Q 002388 829 VCCICRHK-HGI-CIKCNYGNCQTTFHPTCA 857 (929)
Q Consensus 829 ~C~iC~~~-~Ga-cIqC~~~~C~~~FH~~CA 857 (929)
.|.+|++. .|. .-.|. .|.-.+|+.||
T Consensus 2 ~C~~C~~~~~~~~~Y~C~--~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCS--ECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeC--CCCCeEcCccC
Confidence 58899886 556 67896 78899999997
No 109
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=37.57 E-value=20 Score=39.18 Aligned_cols=34 Identities=24% Similarity=0.393 Sum_probs=31.0
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
..||..|-.+|+|+|+|+|..+|+|.+++..-|.
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~ 41 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLV 41 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHH
Confidence 5788889999999999999999999999988773
No 110
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=37.40 E-value=21 Score=37.32 Aligned_cols=37 Identities=8% Similarity=0.128 Sum_probs=33.4
Q ss_pred chHHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 219 LNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 219 ~~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
--...||..|-.+|.|+++|+|..+|+|..|+.--|.
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 3457899999999999999999999999999998774
No 111
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.37 E-value=22 Score=37.29 Aligned_cols=34 Identities=32% Similarity=0.499 Sum_probs=31.2
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
-.||.-|+.+|.++..|||.++||+...+...|.
T Consensus 25 ~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~ 58 (178)
T PRK06266 25 FEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILY 58 (178)
T ss_pred hHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999999999999988873
No 112
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=37.30 E-value=12 Score=34.56 Aligned_cols=32 Identities=44% Similarity=1.163 Sum_probs=27.1
Q ss_pred CcceeCCCC-CCceeecCC------------cCcccccchhhhhh
Q 002388 828 DVCCICRHK-HGICIKCNY------------GNCQTTFHPTCARS 859 (929)
Q Consensus 828 ~~C~iC~~~-~GacIqC~~------------~~C~~~FH~~CA~~ 859 (929)
..|.||+.. .|.|++|.. +-|..+||..|-.+
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~r 65 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYR 65 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHH
Confidence 589999986 899999976 46999999999754
No 113
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=37.14 E-value=21 Score=32.82 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=26.7
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
|-.+||-|.+=.-|++.++|..+|.+-|.++++|+
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~ 60 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALA 60 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 44577777776779999999999999999999996
No 114
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=37.02 E-value=19 Score=30.72 Aligned_cols=29 Identities=21% Similarity=0.479 Sum_probs=24.0
Q ss_pred HHHHhhCccccccchhhhcc-Chhhhhhhc
Q 002388 226 KKLIDRGKVNVKDIASDIGI-SPDLLKTTL 254 (929)
Q Consensus 226 ~kli~~gkv~v~d~~~~~gi-s~~~l~~~~ 254 (929)
.++|..+..++.|||.++|+ |+..|....
T Consensus 43 ~~~l~~~~~~~~~ia~~~g~~s~~~f~r~F 72 (84)
T smart00342 43 RRLLRDTDLSVTEIALRVGFSSQSYFSRAF 72 (84)
T ss_pred HHHHHcCCCCHHHHHHHhCCCChHHHHHHH
Confidence 45666779999999999999 888877665
No 115
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=36.88 E-value=22 Score=36.40 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=28.0
Q ss_pred hHHHHHHHHH-hhCccccccchhhhccChhhhhhhcc
Q 002388 220 NFTLILKKLI-DRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 220 ~~~~~l~kli-~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
|-..++..|+ +.|.|.++|||..+||||-|....|.
T Consensus 10 dYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 10 DYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred HHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHH
Confidence 4444444444 79999999999999999999977663
No 116
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=36.57 E-value=22 Score=35.79 Aligned_cols=33 Identities=21% Similarity=0.483 Sum_probs=29.4
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
--||+.|-.-|..+..+||.++|+|+.++..-+
T Consensus 12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri 44 (153)
T PRK11179 12 RGILEALMENARTPYAELAKQFGVSPGTIHVRV 44 (153)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 357888989999999999999999999987766
No 117
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=36.44 E-value=27 Score=41.38 Aligned_cols=30 Identities=33% Similarity=0.646 Sum_probs=23.9
Q ss_pred cCcccCCCCCCCC--CEEEecccCcccccccc
Q 002388 707 SCDICRRSETILN--PILICSGCKVAVHLDCY 736 (929)
Q Consensus 707 ~CsVC~~~E~~~N--~Ll~Cd~C~vaVHq~CY 736 (929)
.|.||...+...| .-|.|+.|+...|..|-
T Consensus 130 ~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCA 161 (446)
T PF07227_consen 130 MCCICSKFDDNKNTCSWIGCDVCGHWCHLDCA 161 (446)
T ss_pred CccccCCcccCCCCeeEEeccCCCceehhhhh
Confidence 4778877765445 47899999999999995
No 118
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=36.28 E-value=28 Score=31.13 Aligned_cols=35 Identities=29% Similarity=0.581 Sum_probs=29.3
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
+-..||.-|-..|.+++++||.+++||+.++...|
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l 45 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVL 45 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHH
Confidence 44677888888899999999999999988876555
No 119
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=36.16 E-value=24 Score=38.46 Aligned_cols=35 Identities=26% Similarity=0.481 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
...||+.|-.+|.++++|+|..+|+|..++..-|.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~ 41 (251)
T PRK13509 7 HQILLELLAQLGFVTVEKVIERLGISPATARRDIN 41 (251)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999999999999999987773
No 120
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=35.93 E-value=12 Score=31.08 Aligned_cols=31 Identities=29% Similarity=0.688 Sum_probs=20.3
Q ss_pred cCcccCCCCCCCCCEE-Ee--cccCccccccccc
Q 002388 707 SCDICRRSETILNPIL-IC--SGCKVAVHLDCYR 737 (929)
Q Consensus 707 ~CsVC~~~E~~~N~Ll-~C--d~C~vaVHq~CYG 737 (929)
.|-||++.++..++++ -| .+-...||+.|.-
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~ 34 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLE 34 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHH
Confidence 4899998444455555 33 3334679999974
No 121
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=35.23 E-value=30 Score=31.86 Aligned_cols=29 Identities=17% Similarity=0.375 Sum_probs=26.4
Q ss_pred HHHHhhCccccccchhhhccChhhhhhhc
Q 002388 226 KKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 226 ~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.-|-++|.+++.+||..+++|++.++|-|
T Consensus 9 d~l~~~gr~s~~~Ls~~~~~p~~~VeaML 37 (78)
T PRK15431 9 DLLALRGRMEAAQISQTLNTPQPMINAML 37 (78)
T ss_pred HHHHHcCcccHHHHHHHHCcCHHHHHHHH
Confidence 34567999999999999999999999998
No 122
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=35.09 E-value=24 Score=30.63 Aligned_cols=35 Identities=26% Similarity=0.558 Sum_probs=29.0
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
.+-|..-|+.+|..++.+|...+|+++..+..+|.
T Consensus 15 ~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~ 49 (62)
T PF08221_consen 15 VAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALV 49 (62)
T ss_dssp HHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 46788889999999999999999999999999884
No 123
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=34.92 E-value=20 Score=26.59 Aligned_cols=27 Identities=26% Similarity=0.717 Sum_probs=12.4
Q ss_pred cceeCCCCCC--ceeecCCcCcccccchhhh
Q 002388 829 VCCICRHKHG--ICIKCNYGNCQTTFHPTCA 857 (929)
Q Consensus 829 ~C~iC~~~~G--acIqC~~~~C~~~FH~~CA 857 (929)
.|.+|+.+.+ ..-.|. .|.-.+|..||
T Consensus 2 ~C~~C~~~~~~~~~Y~C~--~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCS--ECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-T--TT-----HHHH
T ss_pred cCCcCCCcCCCCceEECc--cCCCccChhcC
Confidence 5888998744 577898 99999999997
No 124
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=34.74 E-value=30 Score=28.67 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=29.1
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.-..+|..|-+.|.+++.|||..+|+++-++...+
T Consensus 4 ~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 4 SQFRILRILYENGGITQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp HHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHH
Confidence 34578899999999999999999999998876554
No 125
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=34.54 E-value=24 Score=30.18 Aligned_cols=23 Identities=26% Similarity=0.574 Sum_probs=20.9
Q ss_pred ccccccchhhhccChhhhhhhcc
Q 002388 233 KVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 233 kv~v~d~~~~~gis~~~l~~~~~ 255 (929)
+++|++||.++|+|+..|...+.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 46899999999999999998887
No 126
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=34.47 E-value=45 Score=31.90 Aligned_cols=52 Identities=13% Similarity=0.144 Sum_probs=38.9
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhccccccccchhHHHHHHhhhc
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNH 274 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~~wl~~~ 274 (929)
.-||.+..+=.++..++|..+|||+.++..-.......+.-..+|+++|..+
T Consensus 68 ~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~~~~l~~~l~~~ 119 (127)
T TIGR03830 68 PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKH 119 (127)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHC
Confidence 3467777777899999999999999999887764443344456677776655
No 127
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=34.37 E-value=27 Score=38.34 Aligned_cols=49 Identities=18% Similarity=0.287 Sum_probs=43.6
Q ss_pred ccccccchhhhccChhhhhhhcccc---ccccchhHHHHHHhhhcccccccc
Q 002388 233 KVNVKDIASDIGISPDLLKTTLADG---TFASDLQCKLVKWLSNHAYLGGLL 281 (929)
Q Consensus 233 kv~v~d~~~~~gis~~~l~~~~~~~---~~~~~~~~k~~~wl~~~~~~~~~~ 281 (929)
+++++|||...|+|.-|.--+|+.- ..++..+.||.+-.+..-|.+...
T Consensus 1 ~~ti~dIA~~agVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~lgY~pn~~ 52 (327)
T PRK10339 1 MATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTSSA 52 (327)
T ss_pred CCCHHHHHHHhCCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHhCCCCchh
Confidence 4789999999999999999999954 389999999999999999987753
No 128
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.31 E-value=37 Score=31.28 Aligned_cols=50 Identities=20% Similarity=0.331 Sum_probs=37.5
Q ss_pred HHhhCccccccchhhhccChhhhhhhcc-----------c--------cc-cccchhHHHHHHhhhcccc
Q 002388 228 LIDRGKVNVKDIASDIGISPDLLKTTLA-----------D--------GT-FASDLQCKLVKWLSNHAYL 277 (929)
Q Consensus 228 li~~gkv~v~d~~~~~gis~~~l~~~~~-----------~--------~~-~~~~~~~k~~~wl~~~~~~ 277 (929)
|+.+|.-++.+||..+|||+.++...+. + .+ +.+.....|+.|+..+...
T Consensus 7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~ 76 (112)
T PF13551_consen 7 LLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPE 76 (112)
T ss_pred HHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCC
Confidence 4566766899999999999999876554 1 12 6667777888888877654
No 129
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=34.18 E-value=15 Score=34.02 Aligned_cols=32 Identities=41% Similarity=0.997 Sum_probs=26.7
Q ss_pred ccccccccc-cCceeeCCC------------CCCCcccchhhhhh
Q 002388 57 LVCNICRVK-CGACVRCSH------------GTCRTSFHPICARE 88 (929)
Q Consensus 57 LkC~iC~~k-~GAcIqCs~------------~~C~~~FHvtCA~~ 88 (929)
-.|.||+.. .|.|++|.. |.|.-+||.-|-.+
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~r 65 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYR 65 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHH
Confidence 479999976 799999987 56888999999754
No 130
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=34.00 E-value=33 Score=28.43 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=28.4
Q ss_pred chHHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 219 LNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 219 ~~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.+-..||.-|.+.+ +++.|||..+||+.-++...|
T Consensus 7 ~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l 41 (78)
T cd00090 7 PTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHL 41 (78)
T ss_pred hHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHH
Confidence 34567788888877 999999999999988876555
No 131
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=33.98 E-value=28 Score=28.95 Aligned_cols=33 Identities=18% Similarity=0.279 Sum_probs=28.6
Q ss_pred HHHHHHHHhhCc--cccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGK--VNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gk--v~v~d~~~~~gis~~~l~~~~ 254 (929)
..||.-|-..|. +++.|||..+||++-++...+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v 42 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIV 42 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 568888889998 999999999999999988776
No 132
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=33.91 E-value=24 Score=28.11 Aligned_cols=30 Identities=40% Similarity=0.691 Sum_probs=24.3
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
|+ .++.+| .+.++||.++|||..++...+.
T Consensus 11 i~-~~~~~g-~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 11 VL-RLLAEG-LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HH-HHHHcC-CCHHHHHHHHCCCHHHHHHHHH
Confidence 44 346677 4999999999999999988763
No 133
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=33.42 E-value=18 Score=30.47 Aligned_cols=26 Identities=31% Similarity=0.580 Sum_probs=19.0
Q ss_pred HHHhhCccccccchhhhccChhhhhhh
Q 002388 227 KLIDRGKVNVKDIASDIGISPDLLKTT 253 (929)
Q Consensus 227 kli~~gkv~v~d~~~~~gis~~~l~~~ 253 (929)
++.|.|. ++.+||.+.||+.-+|..-
T Consensus 17 ~~~e~g~-s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 17 KRLEEGE-SKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp HHHHCTT--HHHHHHHHT--CCHHHHH
T ss_pred HHHHcCC-CHHHHHHHhCCCHHHHHHH
Confidence 4579999 9999999999998776543
No 134
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=33.21 E-value=28 Score=29.41 Aligned_cols=31 Identities=26% Similarity=0.540 Sum_probs=23.5
Q ss_pred HHHHHHHHhhCc--cccccchhhhccChhhhhh
Q 002388 222 TLILKKLIDRGK--VNVKDIASDIGISPDLLKT 252 (929)
Q Consensus 222 ~~~l~kli~~gk--v~v~d~~~~~gis~~~l~~ 252 (929)
.-+|++|.++|. |+=.++|..+||+|..+.-
T Consensus 15 ~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 15 LRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 347899999997 6668999999999988754
No 135
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=33.02 E-value=28 Score=31.16 Aligned_cols=32 Identities=22% Similarity=0.484 Sum_probs=26.4
Q ss_pred HHHHHHHhh-CccccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDR-GKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~-gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.||+-|-+. |.+++.|||.++||+.-++...|
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l 41 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLL 41 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 366666666 78999999999999999987766
No 136
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=32.50 E-value=37 Score=28.46 Aligned_cols=25 Identities=20% Similarity=0.329 Sum_probs=21.6
Q ss_pred hhCccccccchhhhccChhhhhhhc
Q 002388 230 DRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 230 ~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
..+.++..|||.++|+|+.++...|
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l 46 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTL 46 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHH
Confidence 3467999999999999999997766
No 137
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=32.24 E-value=14 Score=45.73 Aligned_cols=67 Identities=24% Similarity=0.350 Sum_probs=55.1
Q ss_pred CCCCCcHhhHhhcccCceeeccCccccccccccCchhhcccccccccccccCceeeCCCCCCCcccchhhhhh
Q 002388 16 GGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFHPICARE 88 (929)
Q Consensus 16 ~G~~~WvHv~CALw~PEv~f~~~~~~epV~~V~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~~FHvtCA~~ 88 (929)
+++...+|+.|.+|.+.++...... +...++.+.+...|.+|+.+ |+=.+|-.+.|...||++||+.
T Consensus 328 ~~~~~~~~v~~~~d~~~v~d~cs~~-----~~~~~l~r~~~~~~~~c~l~-~~h~~~~~~s~~~~~~~~~a~~ 394 (684)
T KOG4362|consen 328 NGNVRKPSVAVSDDDEQVLDECSTS-----GKECELGRSFPITCEDCKLK-GAHLGCLEKSCGSSEHVKCARG 394 (684)
T ss_pred CccccccccccccchHHHHHhcccc-----ccccccccCCcceeeecccc-chhhhhhhcccccceeeeeccc
Confidence 4456789999999999888765433 33456778888999999976 9999999999999999999954
No 138
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=31.94 E-value=33 Score=35.72 Aligned_cols=52 Identities=19% Similarity=0.273 Sum_probs=42.7
Q ss_pred CcchHHHHHHHHHhhCccccccchhhhccChhhhhhhccccccccchhHHHH
Q 002388 217 DALNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLV 268 (929)
Q Consensus 217 ~s~~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~ 268 (929)
...+.+...++|++.+..+.++||..+|+|...+...|.-..+.+.++-.+-
T Consensus 104 t~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~lp~~v~~~~~ 155 (187)
T TIGR00180 104 SPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIP 155 (187)
T ss_pred CHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHcCCHHHHHHHH
Confidence 5577899999999887789999999999999999998875556666665443
No 139
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=31.79 E-value=18 Score=28.70 Aligned_cols=30 Identities=20% Similarity=0.458 Sum_probs=23.3
Q ss_pred cCcccCCCCCCCCCEEEecccCccccccccc
Q 002388 707 SCDICRRSETILNPILICSGCKVAVHLDCYR 737 (929)
Q Consensus 707 ~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYG 737 (929)
.|.||++.-...+.++... |+-.||..|..
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~ 31 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIK 31 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHH
Confidence 5999998654356666666 99999999974
No 140
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=31.73 E-value=42 Score=27.03 Aligned_cols=42 Identities=19% Similarity=0.254 Sum_probs=34.7
Q ss_pred ccchhhhccChhhhhhhcccc-ccccchhHHHHHHhhhccccc
Q 002388 237 KDIASDIGISPDLLKTTLADG-TFASDLQCKLVKWLSNHAYLG 278 (929)
Q Consensus 237 ~d~~~~~gis~~~l~~~~~~~-~~~~~~~~k~~~wl~~~~~~~ 278 (929)
+|||..+|||+.++--.|... ..+++...+|.+.++..-|.+
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~ 43 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRP 43 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCC
Confidence 479999999999999999844 568889999988888876643
No 141
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=31.64 E-value=32 Score=38.05 Aligned_cols=51 Identities=12% Similarity=0.122 Sum_probs=45.0
Q ss_pred ccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhcccccccccc
Q 002388 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLKN 283 (929)
Q Consensus 233 kv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~~ 283 (929)
+++++|||.+.|+|.-|+--.|+ ....++....||.+-.+..=|.+.....
T Consensus 1 ~~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~~ar 52 (343)
T PRK10727 1 MATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANAR 52 (343)
T ss_pred CCCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCHHHH
Confidence 47899999999999999999998 5569999999999999999998766543
No 142
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=31.46 E-value=33 Score=38.09 Aligned_cols=50 Identities=18% Similarity=0.280 Sum_probs=43.5
Q ss_pred ccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhccccccccc
Q 002388 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLK 282 (929)
Q Consensus 233 kv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (929)
+|+++|||.+.|+|.-|+--+|+ ....++..+-||.+=.+..=|.+....
T Consensus 1 ~~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn~~a 51 (346)
T PRK10401 1 MITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANA 51 (346)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHHH
Confidence 47899999999999999999998 456899999999999999888765543
No 143
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=30.86 E-value=11 Score=34.67 Aligned_cols=49 Identities=24% Similarity=0.577 Sum_probs=23.1
Q ss_pred CCCcCcccCCCC--C-CCCCEEEecccCcccccccccCccCCCCceecccccc
Q 002388 704 HPRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEE 753 (929)
Q Consensus 704 ~d~~CsVC~~~E--~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~ 753 (929)
+...|.||++.- + .++..+-|..|.+.|-+.||--. ..+|.-.|..|..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE-rkeg~q~CpqCkt 59 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE-RKEGNQVCPQCKT 59 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH-HHTS-SB-TTT--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH-hhcCcccccccCC
Confidence 457799999853 2 46788999999999999999532 3467777888864
No 144
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=30.80 E-value=34 Score=37.67 Aligned_cols=51 Identities=14% Similarity=0.204 Sum_probs=44.7
Q ss_pred ccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhcccccccccc
Q 002388 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLKN 283 (929)
Q Consensus 233 kv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~~ 283 (929)
+++++|||.+.|+|.-|+--+|+ ....++..+.||.+-.+..=|.+.....
T Consensus 1 ~~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn~~a~ 52 (341)
T PRK10703 1 MATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVAR 52 (341)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCHHHH
Confidence 46899999999999999999998 4568999999999999999998865543
No 145
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=30.61 E-value=26 Score=30.45 Aligned_cols=33 Identities=27% Similarity=0.343 Sum_probs=21.6
Q ss_pred chHHHHHHHHHhhCccccccchhhhccChhhhh
Q 002388 219 LNFTLILKKLIDRGKVNVKDIASDIGISPDLLK 251 (929)
Q Consensus 219 ~~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~ 251 (929)
.+|-.=+=++.-++..+|.+||.+.||+|.+|-
T Consensus 9 ~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~ 41 (76)
T PF01527_consen 9 PEFKLQAVREYLESGESVSEVAREYGISPSTLY 41 (76)
T ss_dssp HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHHHCCCceEeeeccccccccccc
Confidence 344333333334566999999999999997753
No 146
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=30.50 E-value=20 Score=43.84 Aligned_cols=30 Identities=30% Similarity=0.765 Sum_probs=25.7
Q ss_pred cccccccccccCce---eeCCCCCCCcccchhhhhh
Q 002388 56 KLVCNICRVKCGAC---VRCSHGTCRTSFHPICARE 88 (929)
Q Consensus 56 ~LkC~iC~~k~GAc---IqCs~~~C~~~FHvtCA~~ 88 (929)
...|+.|+++ |.. |+|. .|.++||.+|--.
T Consensus 253 ~~fCsaCn~~-~~F~~~i~CD--~Cp~sFH~~CLeP 285 (613)
T KOG4299|consen 253 EDFCSACNGS-GLFNDIICCD--GCPRSFHQTCLEP 285 (613)
T ss_pred HHHHHHhCCc-cccccceeec--CCchHHHHhhcCC
Confidence 4589999976 888 9999 5999999999754
No 147
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=30.46 E-value=30 Score=37.60 Aligned_cols=35 Identities=14% Similarity=0.352 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
...||+.|...|++++.|||..+|+|..++..-|.
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~ 40 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLN 40 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 35688899999999999999999999999988773
No 148
>PRK10072 putative transcriptional regulator; Provisional
Probab=30.43 E-value=52 Score=31.30 Aligned_cols=51 Identities=18% Similarity=0.278 Sum_probs=40.9
Q ss_pred HHHHHhhCccccccchhhhccChhhhhhhccccccccchhHHHHHHhhhcc
Q 002388 225 LKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNHA 275 (929)
Q Consensus 225 l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~~wl~~~~ 275 (929)
+|+|..+-+.+-.++|..+|||.-++..-.........-.+.++++|+.+.
T Consensus 38 ik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~Ll~~L~~~P 88 (96)
T PRK10072 38 FEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANP 88 (96)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhhCH
Confidence 788888889999999999999999988887755544444577888887764
No 149
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=29.91 E-value=23 Score=28.70 Aligned_cols=30 Identities=20% Similarity=0.639 Sum_probs=15.9
Q ss_pred ceeCCCCCCceeecCCcCcccccchhhhhh
Q 002388 830 CCICRHKHGICIKCNYGNCQTTFHPTCARS 859 (929)
Q Consensus 830 C~iC~~~~GacIqC~~~~C~~~FH~~CA~~ 859 (929)
|.+|+.-.-.-+.|...+|...+|..|+..
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~ 30 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKK 30 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHH
Confidence 566776544557899999999999999843
No 150
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.60 E-value=34 Score=33.73 Aligned_cols=33 Identities=21% Similarity=0.473 Sum_probs=29.1
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.-||+-|-+-|..+..+||.++|||+.++..-+
T Consensus 11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri 43 (154)
T COG1522 11 RRILRLLQEDARISNAELAERVGLSPSTVLRRI 43 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHH
Confidence 358999999999999999999999998876544
No 151
>PRK09526 lacI lac repressor; Reviewed
Probab=29.34 E-value=38 Score=37.25 Aligned_cols=52 Identities=15% Similarity=0.206 Sum_probs=45.2
Q ss_pred CccccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhcccccccccc
Q 002388 232 GKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLKN 283 (929)
Q Consensus 232 gkv~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~~ 283 (929)
++|+++|||.+.|+|.-|+--+|+ ....++..+.||.+=.+..=|.+.....
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a~ 56 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVAQ 56 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcCHHHH
Confidence 579999999999999999999999 4558899999999999998887765543
No 152
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=28.89 E-value=46 Score=30.70 Aligned_cols=29 Identities=24% Similarity=0.674 Sum_probs=20.7
Q ss_pred CcCcccCCCCCCCCCEEEecccCcccccccc
Q 002388 706 RSCDICRRSETILNPILICSGCKVAVHLDCY 736 (929)
Q Consensus 706 ~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CY 736 (929)
..|.||...= ++..+.---|+..||..|+
T Consensus 79 ~~C~vC~k~l--~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPL--GNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcC--CCceEEEeCCCeEEecccc
Confidence 5699999853 3444444456799999997
No 153
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=28.69 E-value=1.2e+02 Score=31.44 Aligned_cols=60 Identities=12% Similarity=0.170 Sum_probs=44.5
Q ss_pred HHHHHHHHhhhhhhhhhhhH-HHHHHHHHHHHHHHHhhhhcchhHHHHHHHHHHHHHHHHccCc
Q 002388 550 IIYFQHRLLGNAFSRKRLAD-NLVCKAVKTLNQEIDVARGRRWDAVLVNQYLCELREAKKQGRK 612 (929)
Q Consensus 550 ~~~~q~~ll~~~~~~~~~~~-~lv~~v~k~~~~e~~~~~~r~~d~~~~nq~L~~~rea~k~~~~ 612 (929)
+..+|..+..++. ...+ .++.++|+++.-+++.|.+.+-....+..+..|.+.|++.+-+
T Consensus 86 L~~lQ~a~~~~~~---~~s~~~~l~~iA~~~gLD~~~F~~d~~S~~~~~~~~~D~~la~~m~I~ 146 (176)
T PF13743_consen 86 LRALQEALFLEGK---NYSDEELLLEIAEELGLDVEMFKEDLHSDEAKQAFQEDQQLAREMGIT 146 (176)
T ss_dssp HHHHHHHHHTS------TTSHHHHHHHHHHTT--HHHHHHHHTSHHHHHHHHHHHHHHHHTT-S
T ss_pred HHHHHHHHHhcCC---CCCHHHHHHHHHHHhCCCHHHHHHHHhChHHHHHHHHHHHHHHHcCCC
Confidence 4667777765544 4566 7888999999999999998888778889999999999888755
No 154
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=28.60 E-value=43 Score=27.70 Aligned_cols=35 Identities=20% Similarity=0.397 Sum_probs=24.7
Q ss_pred HHHHHHHHHhhCc-------cccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGK-------VNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gk-------v~v~d~~~~~gis~~~l~~~~~ 255 (929)
+.--++++|..+. .++.|||..+|||..++..+|.
T Consensus 6 ~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~ 47 (66)
T cd07377 6 IADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALR 47 (66)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3444455544443 3489999999999999987773
No 155
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=28.58 E-value=35 Score=35.94 Aligned_cols=32 Identities=28% Similarity=0.509 Sum_probs=27.9
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.||.-|...|.+++.+||..+||++-++...|
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L 36 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHL 36 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 57888888899999999999999998887766
No 156
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=28.55 E-value=35 Score=27.72 Aligned_cols=30 Identities=27% Similarity=0.709 Sum_probs=16.8
Q ss_pred ccccccccCceeeCCCCCCCcccchhhhhh
Q 002388 59 CNICRVKCGACVRCSHGTCRTSFHPICARE 88 (929)
Q Consensus 59 C~iC~~k~GAcIqCs~~~C~~~FHvtCA~~ 88 (929)
|.+|+.-.-.-+.|....|...+|..|+..
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~ 30 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKK 30 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHH
Confidence 667876555567899999999999999954
No 157
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=27.94 E-value=50 Score=37.63 Aligned_cols=112 Identities=17% Similarity=0.317 Sum_probs=66.8
Q ss_pred cCCCCCCCCCEEEecccCcccccccccCccCCCCceecccccccccCCCCCCCCCCccCCCccccccccCCCCCCceeec
Q 002388 711 CRRSETILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLCGGTTGAFRKS 790 (929)
Q Consensus 711 C~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~~~~~~s~~~~~~~~~~p~~~~~C~LCp~~gGaLK~T 790 (929)
|..-.+++....+|-.|.+..|-.=-++.......|.|+-|..--. ...|.| ...+-.+ .
T Consensus 58 ClTC~P~~~~agvC~~C~~~CH~~H~lveL~tKR~FrCDCg~sk~g-----------------~~sc~l--~~~~~~~-n 117 (345)
T KOG2752|consen 58 CLTCTPAPEMAGVCYACSLSCHDGHELVELYTKRNFRCDCGNSKFG-----------------RCSCNL--LEDKDAE-N 117 (345)
T ss_pred eecccCChhhceeEEEeeeeecCCceeeeccccCCccccccccccc-----------------cccccc--ccccccc-c
Confidence 4433333446679999999888776555544578899998865311 222222 2233333 5
Q ss_pred cCcchhhhccccccccceeecCccccccccccccCCCCcceeCCCCCCceeecCCcCcccccc-hhhhhhcCce
Q 002388 791 ANGQWVHAFCAEWVFESTFRRGQVNPVAGMEAFPKGIDVCCICRHKHGICIKCNYGNCQTTFH-PTCARSAGFY 863 (929)
Q Consensus 791 ~~g~WVHv~CAlw~pev~f~~~~~~~Vegie~I~k~k~~C~iC~~~~GacIqC~~~~C~~~FH-~~CA~~aGl~ 863 (929)
..+.|.|-+=.++.---.+.+ .|+..+ .|.++||. -|.-||| -.|.....+.
T Consensus 118 ~~N~YNhNfqG~~C~Cd~~Yp---dp~~~~----------------e~~m~QC~--iCEDWFHce~c~~~~~~~ 170 (345)
T KOG2752|consen 118 SENLYNHNFQGLFCKCDTPYP---DPVRTE----------------EGEMLQCV--ICEDWFHCEGCMQAKTFL 170 (345)
T ss_pred chhhhhhhhcceeEEecCCCC---Cccccc----------------cceeeeEE--eccchhcccccCcccchh
Confidence 667899987666552222211 122211 47889998 7999999 7776554443
No 158
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=27.92 E-value=41 Score=29.52 Aligned_cols=28 Identities=18% Similarity=0.306 Sum_probs=19.5
Q ss_pred HHHHHHHHHhhCccccccchhhhccChh
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPD 248 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~ 248 (929)
+..+.+-|++.+..+++|||.++|.+.-
T Consensus 33 ~~~a~~~L~~~~~~~i~~ia~~~Gf~~~ 60 (81)
T PF12833_consen 33 LQRAKELLRQNTDLSIAEIAEECGFSSQ 60 (81)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHTT-SSH
T ss_pred HHHHHHHHHHhhcccHHHHHHHcCCCCH
Confidence 3455566778899999999999999853
No 159
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=27.28 E-value=40 Score=36.88 Aligned_cols=34 Identities=18% Similarity=0.453 Sum_probs=31.0
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
...||+.|=..|+|+|+|+|..+|+|.+|+..-|
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL 40 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDL 40 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHH
Confidence 4678889999999999999999999999998876
No 160
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=27.03 E-value=41 Score=37.18 Aligned_cols=36 Identities=25% Similarity=0.421 Sum_probs=32.4
Q ss_pred chHHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 219 LNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 219 ~~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.-...||+.|-..|.|+|.|+|..+|+|..|+.--|
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL 52 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDL 52 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHH
Confidence 446788999999999999999999999999998877
No 161
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=26.87 E-value=27 Score=32.26 Aligned_cols=30 Identities=20% Similarity=0.616 Sum_probs=17.6
Q ss_pred CcceeCCCCCCceeecCCcCcccccchhhhh
Q 002388 828 DVCCICRHKHGICIKCNYGNCQTTFHPTCAR 858 (929)
Q Consensus 828 ~~C~iC~~~~GacIqC~~~~C~~~FH~~CA~ 858 (929)
..|.+|+++-|...--.+ -|...||..|+.
T Consensus 79 ~~C~vC~k~l~~~~f~~~-p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVF-PCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEe-CCCeEEeccccc
Confidence 568888877553222222 244777888764
No 162
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=26.86 E-value=48 Score=26.67 Aligned_cols=21 Identities=29% Similarity=0.441 Sum_probs=18.2
Q ss_pred CccccccchhhhccChhhhhh
Q 002388 232 GKVNVKDIASDIGISPDLLKT 252 (929)
Q Consensus 232 gkv~v~d~~~~~gis~~~l~~ 252 (929)
.++++.|||.+.|||.-+|-.
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~ 35 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYR 35 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHH
T ss_pred HhCCHHHHHHHHccchhhHHH
Confidence 379999999999999988754
No 163
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=26.82 E-value=37 Score=40.48 Aligned_cols=46 Identities=20% Similarity=0.432 Sum_probs=36.9
Q ss_pred cccCCCCCCCCCEEEecccCcccccccccCccCCC-Cceeccccccc
Q 002388 709 DICRRSETILNPILICSGCKVAVHLDCYRNAKEST-GPWYCELCEEL 754 (929)
Q Consensus 709 sVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~~~p~-g~WlCd~C~~~ 754 (929)
++|...++..+.++.|+.|..--|..|+|+..... ..+.|..|...
T Consensus 89 c~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~p~~y~c~~c~~~ 135 (508)
T KOG1844|consen 89 CDCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTKPDKYVCEICTPR 135 (508)
T ss_pred cccccccCCCceeeCCcccCcccCceeeeecCCCCchhceeeeeccc
Confidence 35666554368899999999999999999876554 78999999654
No 164
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=26.60 E-value=43 Score=36.60 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=43.3
Q ss_pred cccccchhhhccChhhhhhhcc-ccccccchhHHHHHHhhhccccccccc
Q 002388 234 VNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLK 282 (929)
Q Consensus 234 v~v~d~~~~~gis~~~l~~~~~-~~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (929)
|+++|||.+.|+|+-|+--+|+ ....++..+.||.+=.+..-|.+....
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~~a 51 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNAVA 51 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCHHH
Confidence 6789999999999999999999 456899999999999999999776543
No 165
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=25.97 E-value=46 Score=33.44 Aligned_cols=40 Identities=13% Similarity=0.116 Sum_probs=31.9
Q ss_pred hCccccccchhhhccChhhhhhhccccccccchhHHHHHHhhhccc
Q 002388 231 RGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNHAY 276 (929)
Q Consensus 231 ~gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~~wl~~~~~ 276 (929)
-.-.+.++||..+|||+.++...|.- -..+|-++|++-+|
T Consensus 133 ~~~~s~~EIA~~lgis~~tV~~~l~R------a~~~Lr~~l~~~~~ 172 (173)
T PRK12522 133 YEQYSYKEMSEILNIPIGTVKYRLNY------AKKQMREHLEGFVH 172 (173)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH------HHHHHHHHHHHHhc
Confidence 35679999999999999999999832 35677777777665
No 166
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.48 E-value=44 Score=26.88 Aligned_cols=27 Identities=22% Similarity=0.447 Sum_probs=17.8
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhh
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKT 252 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~ 252 (929)
|++-+.+ -.++.+||..+|||+.|+.-
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~ 36 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYR 36 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHH
Confidence 4444444 57999999999999987653
No 167
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=25.30 E-value=27 Score=40.16 Aligned_cols=35 Identities=26% Similarity=0.471 Sum_probs=28.5
Q ss_pred CCcCcccCCCC-CCCCCEEEecccCcccccccccCc
Q 002388 705 PRSCDICRRSE-TILNPILICSGCKVAVHLDCYRNA 739 (929)
Q Consensus 705 d~~CsVC~~~E-~~~N~Ll~Cd~C~vaVHq~CYGi~ 739 (929)
-..|.||.+.- ..+.+-..|-.|++.||+.|.+..
T Consensus 141 r~~c~ic~d~iwglgrqgyrcinckl~vhkkch~~v 176 (593)
T KOG0695|consen 141 RAYCGICSDRIWGLGRQGYRCINCKLLVHKKCHGLV 176 (593)
T ss_pred ceeeeechhhhhhcccccceeecceeehhhhhcccc
Confidence 46799998754 246678999999999999999753
No 168
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.21 E-value=44 Score=43.66 Aligned_cols=50 Identities=26% Similarity=0.584 Sum_probs=39.9
Q ss_pred CCCcCcccCCCC--C-CCCCEEEecccCcccccccccCccCCCCceeccccccc
Q 002388 704 HPRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 704 ~d~~CsVC~~~E--~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
+...|.||++.- + .++..|-|.-|...|-+.||- .+..+|.=.|..|+..
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE-YEr~eG~q~CPqCktr 68 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE-YERKDGNQSCPQCKTK 68 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhh-hhhhcCCccCCccCCc
Confidence 346899999853 3 456789999999999999993 4456888899999764
No 169
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=24.99 E-value=42 Score=29.22 Aligned_cols=32 Identities=19% Similarity=0.271 Sum_probs=23.2
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
+||+.=.+=..++.|||.+++|++..|+|-=.
T Consensus 1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~ 32 (62)
T PF13413_consen 1 RLREAREAKGLSLEDVAEETKISVSYLEAIEN 32 (62)
T ss_dssp -HHHHHHCTT--HHHHHHHCS--HHHHHHHHC
T ss_pred ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 47777888889999999999999999987554
No 170
>PLN02400 cellulose synthase
Probab=24.51 E-value=54 Score=42.91 Aligned_cols=50 Identities=24% Similarity=0.595 Sum_probs=39.8
Q ss_pred CCCcCcccCCCC--C-CCCCEEEecccCcccccccccCccCCCCceeccccccc
Q 002388 704 HPRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 704 ~d~~CsVC~~~E--~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
+...|.||++.- + .++..|-|..|...|-..||- .+..+|.=.|..|+..
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE-YERkeGnq~CPQCkTr 87 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE-YERKDGTQCCPQCKTR 87 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhh-eecccCCccCcccCCc
Confidence 346899999853 3 466789999999999999994 4455888899999764
No 171
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=24.34 E-value=65 Score=31.08 Aligned_cols=64 Identities=23% Similarity=0.560 Sum_probs=41.7
Q ss_pred CCCCCCcCcccCCCCCCCCCEEEe------cccCcccccccccCc---------c-CCCCceecccccccccCCCCCCCC
Q 002388 701 SKEHPRSCDICRRSETILNPILIC------SGCKVAVHLDCYRNA---------K-ESTGPWYCELCEELLSSRSSGAPS 764 (929)
Q Consensus 701 ske~d~~CsVC~~~E~~~N~Ll~C------d~C~vaVHq~CYGi~---------~-~p~g~WlCd~C~~~~~~~~s~~~~ 764 (929)
+..+...|-.|..... +..+.| ..|...-=+.||+.. + ..+..|.|..|...
T Consensus 3 d~~~g~~CHqCrqKt~--~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi---------- 70 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTL--DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI---------- 70 (105)
T ss_pred cCCCCCCchhhcCCCC--CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCe----------
Confidence 3456678999988543 555677 778333334666431 1 23678999999864
Q ss_pred CCccCCCccccccccCCCCCCc
Q 002388 765 VNFWEKPYFVAECSLCGGTTGA 786 (929)
Q Consensus 765 ~~~~~~p~~~~~C~LCp~~gGa 786 (929)
-.|..|.+..|.
T Consensus 71 ----------CnCs~Crrk~g~ 82 (105)
T PF10497_consen 71 ----------CNCSFCRRKRGW 82 (105)
T ss_pred ----------eCCHhhhccCCC
Confidence 678888876554
No 172
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=24.15 E-value=43 Score=35.13 Aligned_cols=31 Identities=19% Similarity=0.221 Sum_probs=25.7
Q ss_pred HHHHHHHhhCc--cccccchhhhccChhhhhhhc
Q 002388 223 LILKKLIDRGK--VNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 223 ~~l~kli~~gk--v~v~d~~~~~gis~~~l~~~~ 254 (929)
-|| +||..|. .+.++||.++|||+.|++.-+
T Consensus 166 ~Vl-~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~ 198 (225)
T PRK10046 166 AVR-KLFKEPGVQHTAETVAQALTISRTTARRYL 198 (225)
T ss_pred HHH-HHHHcCCCCcCHHHHHHHhCccHHHHHHHH
Confidence 344 5788885 799999999999999998765
No 173
>PLN02436 cellulose synthase A
Probab=24.03 E-value=51 Score=43.10 Aligned_cols=49 Identities=27% Similarity=0.626 Sum_probs=39.0
Q ss_pred CCcCcccCCCC--C-CCCCEEEecccCcccccccccCccCCCCceeccccccc
Q 002388 705 PRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 705 d~~CsVC~~~E--~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
...|.||++.- + +++..|-|.-|+..|-..||- .+..+|.=.|..|+..
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye-yer~eg~~~Cpqckt~ 87 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE-YERREGNQACPQCKTR 87 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhh-hhhhcCCccCcccCCc
Confidence 45799999853 3 456788999999999999993 4455788899999764
No 174
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=23.96 E-value=36 Score=30.28 Aligned_cols=32 Identities=28% Similarity=0.589 Sum_probs=13.1
Q ss_pred CcceeCCCC---CC--ceeecCCcCcccccchhhhhh
Q 002388 828 DVCCICRHK---HG--ICIKCNYGNCQTTFHPTCARS 859 (929)
Q Consensus 828 ~~C~iC~~~---~G--acIqC~~~~C~~~FH~~CA~~ 859 (929)
..|.||... .+ ..+.|....|...||..|...
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~ 39 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSE 39 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHH
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHH
Confidence 468888863 22 357899999999999999744
No 175
>PF13309 HTH_22: HTH domain
Probab=23.62 E-value=50 Score=28.90 Aligned_cols=35 Identities=23% Similarity=0.305 Sum_probs=27.4
Q ss_pred cchHHHHHHHHHhhCc----cccccchhhhccChhhhhh
Q 002388 218 ALNFTLILKKLIDRGK----VNVKDIASDIGISPDLLKT 252 (929)
Q Consensus 218 s~~~~~~l~kli~~gk----v~v~d~~~~~gis~~~l~~ 252 (929)
..+=--|++.|-++|= =.|..||..+|||..|+=.
T Consensus 23 ~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 23 KEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred HHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHH
Confidence 3455678999999995 4566799999999988744
No 176
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=23.54 E-value=62 Score=33.55 Aligned_cols=35 Identities=20% Similarity=0.527 Sum_probs=30.4
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
++.--+.++|..|-+++.||+..+|+||=-|.+..
T Consensus 108 ~~~e~i~~~v~~Gn~Sl~~lsr~l~~sp~firglA 142 (160)
T PF09824_consen 108 DYVEKIEKEVEAGNTSLSDLSRKLGISPVFIRGLA 142 (160)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHH
Confidence 56667889999999999999999999998887654
No 177
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=23.38 E-value=34 Score=29.45 Aligned_cols=37 Identities=19% Similarity=0.433 Sum_probs=31.2
Q ss_pred hHHHHHHHH-Hh---hCccccccchhhhccChhhhhhhccc
Q 002388 220 NFTLILKKL-ID---RGKVNVKDIASDIGISPDLLKTTLAD 256 (929)
Q Consensus 220 ~~~~~l~kl-i~---~gkv~v~d~~~~~gis~~~l~~~~~~ 256 (929)
..+-|++|+ || -|+.++.+.+.+-||+++.|.+.|.+
T Consensus 14 ~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L~~ 54 (56)
T PF04405_consen 14 RAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEELNA 54 (56)
T ss_pred HHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHH
Confidence 346677776 66 59999999999999999999999854
No 178
>PLN02195 cellulose synthase A
Probab=22.61 E-value=56 Score=42.35 Aligned_cols=49 Identities=16% Similarity=0.384 Sum_probs=39.0
Q ss_pred CCcCcccCCCC--C-CCCCEEEecccCcccccccccCccCCCCceeccccccc
Q 002388 705 PRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 705 d~~CsVC~~~E--~-~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
...|.||++.- + .++..|-|.-|...|-+.||- .+..+|.=-|..|+..
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCye-yer~eg~q~CpqCkt~ 57 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLE-YEIKEGRKVCLRCGGP 57 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhh-hhhhcCCccCCccCCc
Confidence 45799999853 2 466789999999999999993 4456888889999654
No 179
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=22.31 E-value=44 Score=26.28 Aligned_cols=32 Identities=28% Similarity=0.794 Sum_probs=25.8
Q ss_pred CcceeCCCCCC---ceeecCCcCcccccchhhhhhcC
Q 002388 828 DVCCICRHKHG---ICIKCNYGNCQTTFHPTCARSAG 861 (929)
Q Consensus 828 ~~C~iC~~~~G---acIqC~~~~C~~~FH~~CA~~aG 861 (929)
..|.+|++... .-++|. .|....|..|+....
T Consensus 12 ~~C~~C~~~i~~~~~~~~C~--~C~~~~H~~C~~~v~ 46 (49)
T smart00109 12 TKCCVCRKSIWGSFQGLRCS--WCKVKCHKKCAEKVP 46 (49)
T ss_pred CCccccccccCcCCCCcCCC--CCCchHHHHHHhhcC
Confidence 57999998633 368898 999999999997654
No 180
>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=22.14 E-value=62 Score=32.01 Aligned_cols=62 Identities=18% Similarity=0.131 Sum_probs=41.2
Q ss_pred cccccchhhhccChhhhhhhccccccccc-------------hhHHHHHHhhhcccccccccceeeccccccccc
Q 002388 234 VNVKDIASDIGISPDLLKTTLADGTFASD-------------LQCKLVKWLSNHAYLGGLLKNVKLKIKSSISSK 295 (929)
Q Consensus 234 v~v~d~~~~~gis~~~l~~~~~~~~~~~~-------------~~~k~~~wl~~~~~~~~~~~~~~~~~~~~~~~~ 295 (929)
.++++||..+|||+.+|.---....+.|. .++++|+.|.+...|+-.....-+++.+..++|
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~GLl~p~r~~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~~~ 76 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILSMYPCWSIR 76 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCcCCCCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcccccc
Confidence 37899999999999999854333333332 467888888876666655555545555444444
No 181
>PRK04217 hypothetical protein; Provisional
Probab=22.08 E-value=90 Score=30.48 Aligned_cols=33 Identities=18% Similarity=0.293 Sum_probs=25.5
Q ss_pred HHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
..++. |......++++||..+|||..++...|.
T Consensus 48 reai~-l~~~eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 48 FEALR-LVDYEGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred HHHHH-HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34443 4444556999999999999999999884
No 182
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=21.67 E-value=70 Score=31.05 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=24.4
Q ss_pred CcchHHH-HHHHHHhhCccccccchhhhccChhhhh
Q 002388 217 DALNFTL-ILKKLIDRGKVNVKDIASDIGISPDLLK 251 (929)
Q Consensus 217 ~s~~~~~-~l~kli~~gkv~v~d~~~~~gis~~~l~ 251 (929)
=|.+|-. ++..+++.| .+|.+||.++|||+.+|-
T Consensus 13 ys~EfK~~aV~~~~~~g-~sv~evA~e~gIs~~tl~ 47 (121)
T PRK09413 13 RTTQEKIAIVQQSFEPG-MTVSLVARQHGVAASQLF 47 (121)
T ss_pred CCHHHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHH
Confidence 3556644 555566655 599999999999987654
No 183
>PHA00542 putative Cro-like protein
Probab=21.51 E-value=98 Score=28.20 Aligned_cols=46 Identities=13% Similarity=0.021 Sum_probs=32.5
Q ss_pred HHHhhCccccccchhhhccChhhhhhhccccc--cccchhHHHHHHhh
Q 002388 227 KLIDRGKVNVKDIASDIGISPDLLKTTLADGT--FASDLQCKLVKWLS 272 (929)
Q Consensus 227 kli~~gkv~v~d~~~~~gis~~~l~~~~~~~~--~~~~~~~k~~~wl~ 272 (929)
++.+....+..++|..+|||+.+|-.-+.... ..++.-.+|.+.+.
T Consensus 25 ~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~ 72 (82)
T PHA00542 25 CALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVL 72 (82)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence 34455568999999999999999988886442 44445556655544
No 184
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=21.48 E-value=68 Score=32.06 Aligned_cols=23 Identities=17% Similarity=0.228 Sum_probs=21.4
Q ss_pred CccccccchhhhccChhhhhhhc
Q 002388 232 GKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 232 gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
...++++||.++|||+.++...|
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l 149 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRV 149 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 66899999999999999999988
No 185
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.43 E-value=53 Score=38.02 Aligned_cols=47 Identities=19% Similarity=0.464 Sum_probs=30.7
Q ss_pred CcCcccCCCCCCCCCEEEecccCcccccccccCccCCCCceeccccccc
Q 002388 706 RSCDICRRSETILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 754 (929)
Q Consensus 706 ~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~~ 754 (929)
..|+||.+....++.+.. --|+-.+|..|--.= .....=+|..|+..
T Consensus 230 ~~CaIClEdY~~GdklRi-LPC~H~FH~~CIDpW-L~~~r~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRI-LPCSHKFHVNCIDPW-LTQTRTFCPVCKRD 276 (348)
T ss_pred ceEEEeecccccCCeeeE-ecCCCchhhccchhh-HhhcCccCCCCCCc
Confidence 589999986543444444 789999999995211 00112359999875
No 186
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=21.39 E-value=13 Score=30.57 Aligned_cols=30 Identities=33% Similarity=0.736 Sum_probs=19.0
Q ss_pred CcccCCCCCCCCCEE-Ee--cccCccccccccc
Q 002388 708 CDICRRSETILNPIL-IC--SGCKVAVHLDCYR 737 (929)
Q Consensus 708 CsVC~~~E~~~N~Ll-~C--d~C~vaVHq~CYG 737 (929)
|-||++.++..++++ -| .+=-..||+.|.-
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~ 33 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLE 33 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHH
Confidence 678998776555565 33 3333499999984
No 187
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=21.37 E-value=67 Score=25.62 Aligned_cols=27 Identities=41% Similarity=0.544 Sum_probs=22.3
Q ss_pred HHhhCccccccchhhhccChhhhhhhcc
Q 002388 228 LIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 228 li~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
|+..| .+.++||..+|+|+.++...+.
T Consensus 11 ~~~~~-~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 11 LLAEG-KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HHHcC-CCHHHHHHHHCCCHHHHHHHHH
Confidence 34455 6999999999999999988773
No 188
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.37 E-value=61 Score=34.04 Aligned_cols=34 Identities=12% Similarity=0.226 Sum_probs=27.3
Q ss_pred hCccccccchhhhccChhhhhhhccccccccchhHHHHHHhhhc
Q 002388 231 RGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNH 274 (929)
Q Consensus 231 ~gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~~wl~~~ 274 (929)
-.-.++++||..+|||+.++...| .+..++|+.+
T Consensus 152 ~~g~s~~EIA~~Lgis~~tV~~~l----------~RArk~Lr~~ 185 (203)
T PRK09647 152 IEGLSYEEIAATLGVKLGTVRSRI----------HRGRQQLRAA 185 (203)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH----------HHHHHHHHHH
Confidence 355899999999999999999998 4455666654
No 189
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.25 E-value=70 Score=28.62 Aligned_cols=51 Identities=20% Similarity=0.283 Sum_probs=33.1
Q ss_pred HHHHHHHhhCccccccchhhhccChhhhhhhcccccc--ccchhHHHHHHhhh
Q 002388 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTF--ASDLQCKLVKWLSN 273 (929)
Q Consensus 223 ~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~~~~~--~~~~~~k~~~wl~~ 273 (929)
.||+..-+-...++.|||.++|+|+-++..-...--| -++||..+.+.|++
T Consensus 24 yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~efk~~l~~~~~~ 76 (77)
T PF01418_consen 24 YILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKEFKIALAQELSQ 76 (77)
T ss_dssp HHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHHHHHHHHCHHHS
T ss_pred HHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHhc
Confidence 4566666778899999999999999998766553222 25666666665554
No 190
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=21.12 E-value=72 Score=30.15 Aligned_cols=27 Identities=30% Similarity=0.592 Sum_probs=23.5
Q ss_pred HhhCccccccchhhhccChhhhhhhcc
Q 002388 229 IDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 229 i~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
.++--+++.+||.++|||++-|+..|.
T Consensus 19 f~~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 19 FELSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 344458999999999999999999997
No 191
>PRK11050 manganese transport regulator MntR; Provisional
Probab=21.09 E-value=72 Score=32.28 Aligned_cols=36 Identities=25% Similarity=0.462 Sum_probs=28.6
Q ss_pred hHHHHHHHHHh-hCccccccchhhhccChhhhhhhcc
Q 002388 220 NFTLILKKLID-RGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 220 ~~~~~l~kli~-~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
++..+|..+|. .|.+++.|||.++|||+-++...|.
T Consensus 37 ~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~ 73 (152)
T PRK11050 37 DYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLK 73 (152)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44445555664 5889999999999999999988874
No 192
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=20.82 E-value=66 Score=38.67 Aligned_cols=35 Identities=20% Similarity=0.418 Sum_probs=30.9
Q ss_pred hHHHHHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 220 ~~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
.=..||+.|-+.|.++..+||..+|+++.++..++
T Consensus 7 ~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i 41 (489)
T PRK04172 7 NEKKVLKALKELKEATLEELAEKLGLPPEAVMRAA 41 (489)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 33678999999999999999999999999988765
No 193
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.76 E-value=75 Score=32.20 Aligned_cols=35 Identities=23% Similarity=0.400 Sum_probs=29.1
Q ss_pred hHHHHHHHHHhhCc--cccccchhhhccChhhhhhhc
Q 002388 220 NFTLILKKLIDRGK--VNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 220 ~~~~~l~kli~~gk--v~v~d~~~~~gis~~~l~~~~ 254 (929)
+|..|-+=|-|... ++|.+|+.++|||.+.|..-+
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~I 67 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFI 67 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 67788888888888 999999999999998665433
No 194
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.69 E-value=59 Score=34.50 Aligned_cols=34 Identities=32% Similarity=0.521 Sum_probs=27.7
Q ss_pred HHHHHHHHhhC------ccccccchhhhccChhhhhhhcc
Q 002388 222 TLILKKLIDRG------KVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 222 ~~~l~kli~~g------kv~v~d~~~~~gis~~~l~~~~~ 255 (929)
.-||+.=.++| .|+++|||.++|||+-++.--|-
T Consensus 161 ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 161 LEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred HHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence 34677777777 69999999999999998877663
No 195
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.44 E-value=1.2e+02 Score=29.73 Aligned_cols=35 Identities=20% Similarity=0.352 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhCccccccchhhhccChhhhhhhcc
Q 002388 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (929)
Q Consensus 221 ~~~~l~kli~~gkv~v~d~~~~~gis~~~l~~~~~ 255 (929)
|.--|++|+++-.++.+|+|..+|||..++..-..
T Consensus 6 ~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 6 FFTNVLRLLDERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 44456777777778999999999999988876665
No 196
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.39 E-value=57 Score=33.74 Aligned_cols=33 Identities=27% Similarity=0.522 Sum_probs=27.3
Q ss_pred CccccccchhhhccChhhhhhhccccccccchhHHHHHHhhhc
Q 002388 232 GKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNH 274 (929)
Q Consensus 232 gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~~wl~~~ 274 (929)
+-.++++||..+|||+.++.-.| ..+-.||+.+
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l----------~~aR~~l~~~ 182 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRL----------RRARAWLRRE 182 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHH----------HHHHHHHHHH
Confidence 34699999999999999999988 3456888765
No 197
>PHA02862 5L protein; Provisional
Probab=20.31 E-value=35 Score=34.91 Aligned_cols=49 Identities=22% Similarity=0.358 Sum_probs=32.8
Q ss_pred CCcCcccCCCCCCCCCEEEecccCcccccccccCccCCCCceecccccc
Q 002388 705 PRSCDICRRSETILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEE 753 (929)
Q Consensus 705 d~~CsVC~~~E~~~N~Ll~Cd~C~vaVHq~CYGi~~~p~g~WlCd~C~~ 753 (929)
+..|=||++.+.+...-=.|.|-.--||+.|..-=......=.|+.|+.
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkt 50 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKT 50 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCC
Confidence 3579999997654444557888899999999752222344445666644
No 198
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=20.29 E-value=81 Score=31.77 Aligned_cols=33 Identities=15% Similarity=0.236 Sum_probs=26.8
Q ss_pred CccccccchhhhccChhhhhhhccccccccchhHHHHHHhhhc
Q 002388 232 GKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNH 274 (929)
Q Consensus 232 gkv~v~d~~~~~gis~~~l~~~~~~~~~~~~~~~k~~~wl~~~ 274 (929)
...+.++||.++|||+.++...| ....++|+..
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l----------~Rar~~Lr~~ 183 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRI----------HRGREALRKQ 183 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHH----------HHHHHHHHHH
Confidence 67899999999999999998877 4556666553
No 199
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=20.08 E-value=72 Score=25.39 Aligned_cols=31 Identities=29% Similarity=0.394 Sum_probs=23.0
Q ss_pred HHHHHHhhCccccccchhhhccChhhhhhhc
Q 002388 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (929)
Q Consensus 224 ~l~kli~~gkv~v~d~~~~~gis~~~l~~~~ 254 (929)
+++..+++-.=|+...|..+|||+.+|-..|
T Consensus 9 ~i~~aL~~~~gn~~~aA~~Lgisr~tL~~kl 39 (42)
T PF02954_consen 9 LIRQALERCGGNVSKAARLLGISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHTTT-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 5566667777889999999999999986544
Done!