Query 001260
Match_columns 1113
No_of_seqs 424 out of 1537
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 20:07:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001260.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001260hhsearch_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 7.3E-43 1.6E-47 404.9 8.3 516 3-593 328-892 (893)
2 KOG0954 PHD finger protein [Ge 100.0 2.9E-36 6.2E-41 350.3 7.8 167 699-883 268-440 (893)
3 KOG0956 PHD finger protein AF1 100.0 1.6E-35 3.4E-40 341.4 5.9 170 699-884 2-185 (900)
4 COG5141 PHD zinc finger-contai 100.0 2.4E-35 5.1E-40 330.4 4.1 168 700-883 191-366 (669)
5 KOG0955 PHD finger protein BR1 100.0 9.5E-35 2.1E-39 357.1 9.6 169 699-883 216-397 (1051)
6 KOG0957 PHD finger protein [Ge 100.0 5.6E-33 1.2E-37 311.8 4.1 285 704-1026 121-430 (707)
7 PF13832 zf-HC5HC2H_2: PHD-zin 99.9 1.8E-24 3.8E-29 207.3 5.9 107 2-113 4-110 (110)
8 KOG0956 PHD finger protein AF1 99.9 6.5E-24 1.4E-28 246.1 2.6 113 3-119 67-186 (900)
9 PF13832 zf-HC5HC2H_2: PHD-zin 99.9 5.7E-23 1.2E-27 196.9 7.9 106 773-879 2-110 (110)
10 COG5141 PHD zinc finger-contai 99.9 4.4E-23 9.6E-28 232.4 2.7 117 3-121 252-370 (669)
11 KOG0955 PHD finger protein BR1 99.8 1.1E-21 2.4E-26 242.6 3.5 114 2-117 277-397 (1051)
12 PF13771 zf-HC5HC2H: PHD-like 99.7 5.9E-18 1.3E-22 156.5 4.6 88 23-114 1-90 (90)
13 KOG0957 PHD finger protein [Ge 99.7 1.8E-18 4E-23 195.7 1.3 113 3-119 187-304 (707)
14 PF13771 zf-HC5HC2H: PHD-like 99.5 8.1E-15 1.8E-19 135.7 2.9 85 794-880 1-90 (90)
15 KOG1080 Histone H3 (Lys4) meth 99.0 2.4E-10 5.3E-15 143.2 6.2 143 697-862 568-715 (1005)
16 PF13831 PHD_2: PHD-finger; PD 98.9 2.1E-10 4.5E-15 90.5 0.2 35 715-749 1-36 (36)
17 PF00628 PHD: PHD-finger; Int 97.7 2.4E-05 5.3E-10 65.4 2.3 46 704-750 1-50 (51)
18 KOG1080 Histone H3 (Lys4) meth 97.6 2E-05 4.3E-10 100.1 2.0 86 2-95 631-716 (1005)
19 smart00249 PHD PHD zinc finger 97.6 5.9E-05 1.3E-09 60.5 3.4 44 704-748 1-47 (47)
20 KOG1244 Predicted transcriptio 97.2 0.00017 3.7E-09 79.0 1.9 53 700-753 279-333 (336)
21 KOG1512 PHD Zn-finger protein 97.0 0.00029 6.3E-09 77.6 1.7 46 700-746 312-357 (381)
22 KOG1084 Transcription factor T 96.9 0.00042 9.1E-09 80.8 1.8 98 771-880 221-321 (375)
23 KOG4323 Polycomb-like PHD Zn-f 96.8 0.0013 2.8E-08 77.8 4.7 135 703-881 84-223 (464)
24 KOG4323 Polycomb-like PHD Zn-f 96.6 0.00087 1.9E-08 79.1 2.1 51 701-751 167-224 (464)
25 KOG1084 Transcription factor T 96.5 0.0014 3E-08 76.5 2.7 86 17-114 236-321 (375)
26 PF15446 zf-PHD-like: PHD/FYVE 96.4 0.004 8.6E-08 64.8 4.6 128 704-856 1-141 (175)
27 KOG0825 PHD Zn-finger protein 95.7 0.0055 1.2E-07 75.0 2.3 53 698-751 211-266 (1134)
28 KOG4299 PHD Zn-finger protein 95.2 0.0082 1.8E-07 72.8 1.6 48 703-751 254-305 (613)
29 COG5034 TNG2 Chromatin remodel 95.1 0.17 3.6E-06 56.1 10.9 52 696-750 215-269 (271)
30 KOG1973 Chromatin remodeling p 94.0 0.026 5.5E-07 63.6 1.8 50 699-751 216-268 (274)
31 PF14446 Prok-RING_1: Prokaryo 92.3 0.099 2.1E-06 45.4 2.4 33 701-733 4-36 (54)
32 smart00249 PHD PHD zinc finger 91.5 0.15 3.3E-06 40.6 2.6 32 826-859 1-34 (47)
33 KOG0383 Predicted helicase [Ge 91.0 0.17 3.7E-06 63.3 3.5 50 697-750 42-93 (696)
34 KOG4443 Putative transcription 90.6 0.13 2.9E-06 62.9 2.1 49 702-751 68-118 (694)
35 TIGR02844 spore_III_D sporulat 87.6 0.76 1.6E-05 43.1 4.3 50 222-272 9-60 (80)
36 KOG1512 PHD Zn-finger protein 84.9 0.47 1E-05 53.3 1.7 49 701-749 257-315 (381)
37 PF09012 FeoC: FeoC like trans 83.1 0.78 1.7E-05 41.1 2.1 31 224-254 5-35 (69)
38 PF10198 Ada3: Histone acetylt 83.0 7.3 0.00016 39.8 9.2 82 528-609 14-104 (131)
39 PF00628 PHD: PHD-finger; Int 82.2 0.85 1.9E-05 38.1 1.9 30 826-857 1-32 (51)
40 KOG1044 Actin-binding LIM Zn-f 80.8 0.81 1.8E-05 55.7 1.7 87 771-863 133-228 (670)
41 PF00356 LacI: Bacterial regul 79.3 1.9 4.1E-05 36.3 2.9 44 235-278 1-45 (46)
42 KOG1245 Chromatin remodeling c 78.2 0.63 1.4E-05 62.7 -0.3 51 701-752 1107-1159(1404)
43 KOG1473 Nucleosome remodeling 77.5 2.2 4.8E-05 55.4 4.1 117 696-855 338-458 (1414)
44 PF08220 HTH_DeoR: DeoR-like h 76.0 1.9 4.1E-05 37.5 2.1 33 222-254 3-35 (57)
45 PF00130 C1_1: Phorbol esters/ 73.0 3.1 6.7E-05 35.1 2.6 35 702-736 11-46 (53)
46 KOG4443 Putative transcription 71.7 1.5 3.3E-05 54.1 0.7 47 703-749 19-69 (694)
47 PF02318 FYVE_2: FYVE-type zin 71.6 2.6 5.6E-05 41.9 2.2 48 703-751 55-103 (118)
48 KOG1973 Chromatin remodeling p 69.7 2.1 4.6E-05 48.4 1.3 47 825-881 220-267 (274)
49 cd00029 C1 Protein kinase C co 69.1 2.8 6E-05 34.5 1.5 34 702-735 11-45 (50)
50 cd04718 BAH_plant_2 BAH, or Br 68.1 3.1 6.8E-05 43.2 1.9 27 727-753 1-29 (148)
51 smart00530 HTH_XRE Helix-turn- 66.2 8.5 0.00018 30.1 3.8 48 225-272 2-50 (56)
52 smart00109 C1 Protein kinase C 65.8 2.9 6.3E-05 34.0 1.0 33 702-734 11-43 (49)
53 TIGR02607 antidote_HigA addict 65.5 10 0.00023 34.0 4.6 54 219-272 3-58 (78)
54 PF02796 HTH_7: Helix-turn-hel 64.7 7.3 0.00016 32.3 3.1 31 223-254 12-42 (45)
55 PF13443 HTH_26: Cro/C1-type H 62.7 8.4 0.00018 33.2 3.3 48 225-272 2-51 (63)
56 PF07649 C1_3: C1-like domain; 62.0 3.6 7.9E-05 31.3 0.8 28 704-732 2-29 (30)
57 PF01381 HTH_3: Helix-turn-hel 59.1 13 0.00029 31.0 3.8 48 225-272 1-49 (55)
58 PF13404 HTH_AsnC-type: AsnC-t 57.3 9.5 0.00021 31.5 2.5 32 223-254 7-38 (42)
59 KOG1701 Focal adhesion adaptor 55.8 5.3 0.00011 47.6 1.1 154 704-881 276-460 (468)
60 PF13901 DUF4206: Domain of un 53.8 11 0.00024 40.9 3.2 43 702-751 152-198 (202)
61 PF13412 HTH_24: Winged helix- 53.2 11 0.00024 31.1 2.3 33 222-254 6-38 (48)
62 cd00093 HTH_XRE Helix-turn-hel 51.1 23 0.00051 27.8 3.9 48 224-271 3-51 (58)
63 PF01978 TrmB: Sugar-specific 50.0 12 0.00026 33.2 2.2 33 222-254 11-43 (68)
64 PF10668 Phage_terminase: Phag 49.0 10 0.00022 34.0 1.5 22 231-252 20-41 (60)
65 PF03107 C1_2: C1 domain; Int 48.9 13 0.00029 28.4 2.0 27 704-732 2-29 (30)
66 PF07227 DUF1423: Protein of u 48.0 13 0.00029 44.7 2.8 47 704-750 130-191 (446)
67 PF13542 HTH_Tnp_ISL3: Helix-t 47.4 17 0.00037 30.3 2.6 31 222-254 18-48 (52)
68 TIGR03070 couple_hipB transcri 46.8 33 0.00072 28.4 4.3 36 220-255 2-37 (58)
69 KOG0825 PHD Zn-finger protein 46.6 32 0.00068 44.0 5.7 49 824-882 215-266 (1134)
70 PF14197 Cep57_CLD_2: Centroso 46.1 64 0.0014 29.7 6.2 60 542-608 2-63 (69)
71 PF07649 C1_3: C1-like domain; 44.4 13 0.00029 28.2 1.4 27 826-854 2-30 (30)
72 COG5034 TNG2 Chromatin remodel 43.9 13 0.00028 41.8 1.7 46 823-878 219-266 (271)
73 PHA02591 hypothetical protein; 43.1 25 0.00054 33.2 3.1 37 217-254 44-80 (83)
74 PRK09492 treR trehalose repres 43.0 21 0.00046 39.6 3.3 51 231-281 2-53 (315)
75 cd00569 HTH_Hin_like Helix-tur 42.9 34 0.00075 24.3 3.4 30 222-252 11-40 (42)
76 smart00550 Zalpha Z-DNA-bindin 42.8 19 0.00042 32.4 2.4 33 222-254 9-43 (68)
77 PRK10014 DNA-binding transcrip 42.2 22 0.00047 40.0 3.3 51 231-281 4-55 (342)
78 PF13936 HTH_38: Helix-turn-he 42.0 16 0.00035 30.2 1.6 30 224-254 12-41 (44)
79 KOG4236 Serine/threonine prote 41.3 16 0.00034 45.1 2.0 35 700-734 154-189 (888)
80 PRK14987 gluconate operon tran 40.7 23 0.00049 39.9 3.1 51 231-281 3-54 (331)
81 smart00420 HTH_DEOR helix_turn 40.4 24 0.00052 28.6 2.4 32 223-254 4-35 (53)
82 PF14446 Prok-RING_1: Prokaryo 38.5 24 0.00053 31.1 2.2 36 825-862 6-44 (54)
83 PF13518 HTH_28: Helix-turn-he 38.1 22 0.00049 29.2 2.0 28 224-253 5-32 (52)
84 KOG3799 Rab3 effector RIM1 and 37.8 14 0.00031 37.8 0.9 49 702-750 65-115 (169)
85 smart00354 HTH_LACI helix_turn 37.6 33 0.00071 30.8 3.1 47 234-280 1-48 (70)
86 PF12324 HTH_15: Helix-turn-he 37.0 25 0.00054 33.1 2.2 34 222-255 27-60 (77)
87 COG5194 APC11 Component of SCF 36.1 13 0.00028 35.2 0.2 32 57-88 21-65 (88)
88 PF04967 HTH_10: HTH DNA bindi 35.8 21 0.00045 31.2 1.4 22 233-254 23-44 (53)
89 KOG1244 Predicted transcriptio 35.3 20 0.00042 40.8 1.5 48 703-750 225-283 (336)
90 PF10367 Vps39_2: Vacuolar sor 35.2 30 0.00064 32.7 2.5 30 702-733 78-107 (109)
91 PF14569 zf-UDP: Zinc-binding 35.0 8.8 0.00019 36.0 -1.0 50 701-751 8-60 (80)
92 PHA01976 helix-turn-helix prot 34.9 66 0.0014 28.0 4.5 52 220-271 2-54 (67)
93 PRK10339 DNA-binding transcrip 34.9 33 0.00071 38.6 3.2 49 233-281 1-52 (327)
94 PF13764 E3_UbLigase_R4: E3 ub 34.7 92 0.002 40.7 7.4 30 697-726 463-497 (802)
95 PF12844 HTH_19: Helix-turn-he 34.7 49 0.0011 28.6 3.6 48 224-271 3-51 (64)
96 PRK10681 DNA-binding transcrip 34.5 30 0.00064 38.6 2.8 34 222-255 10-43 (252)
97 PF08279 HTH_11: HTH domain; 34.4 30 0.00065 29.2 2.2 32 223-254 4-36 (55)
98 PF11793 FANCL_C: FANCL C-term 33.7 21 0.00045 32.6 1.1 32 703-734 3-38 (70)
99 TIGR02405 trehalos_R_Ecol treh 33.3 36 0.00077 38.1 3.2 49 233-281 1-50 (311)
100 PRK15431 ferrous iron transpor 33.2 26 0.00057 33.0 1.7 27 228-254 11-37 (78)
101 PF01022 HTH_5: Bacterial regu 33.1 32 0.00069 28.5 2.1 31 223-254 6-36 (47)
102 PF03107 C1_2: C1 domain; Int 32.9 29 0.00062 26.6 1.6 27 826-854 2-30 (30)
103 PF00165 HTH_AraC: Bacterial r 32.5 23 0.0005 28.5 1.1 25 231-255 6-30 (42)
104 PRK09726 antitoxin HipB; Provi 32.1 69 0.0015 30.0 4.4 58 219-276 11-69 (88)
105 KOG4362 Transcriptional regula 30.6 15 0.00033 46.4 -0.3 67 16-88 328-394 (684)
106 COG1349 GlpR Transcriptional r 30.6 37 0.0008 38.0 2.7 33 222-254 8-40 (253)
107 PF08746 zf-RING-like: RING-li 30.0 31 0.00068 28.7 1.5 30 827-856 1-30 (43)
108 KOG4299 PHD Zn-finger protein 29.7 21 0.00046 44.5 0.6 30 56-88 253-285 (613)
109 smart00744 RINGv The RING-vari 29.6 18 0.00039 30.8 0.0 31 704-734 1-34 (49)
110 PF01325 Fe_dep_repress: Iron 29.5 50 0.0011 29.2 2.8 25 230-254 19-43 (60)
111 KOG0383 Predicted helicase [Ge 29.1 34 0.00075 43.7 2.3 31 825-858 48-78 (696)
112 PRK06266 transcription initiat 28.4 43 0.00093 35.9 2.6 35 221-255 24-58 (178)
113 smart00345 HTH_GNTR helix_turn 28.2 53 0.0011 27.3 2.6 20 235-254 22-41 (60)
114 PRK10703 DNA-binding transcrip 27.5 52 0.0011 37.1 3.2 50 233-282 1-51 (341)
115 COG2522 Predicted transcriptio 27.4 51 0.0011 33.4 2.8 33 222-255 12-44 (119)
116 PF08746 zf-RING-like: RING-li 27.2 38 0.00081 28.2 1.5 30 59-88 1-30 (43)
117 KOG1844 PHD Zn-finger proteins 27.0 35 0.00076 41.5 1.9 46 706-751 89-135 (508)
118 PF08221 HTH_9: RNA polymerase 26.5 49 0.0011 29.5 2.2 35 221-255 15-49 (62)
119 TIGR00180 parB_part ParB-like 26.4 55 0.0012 34.9 3.0 52 217-268 104-155 (187)
120 TIGR00373 conserved hypothetic 26.4 47 0.001 34.8 2.4 34 222-255 17-50 (158)
121 KOG0696 Serine/threonine prote 26.4 21 0.00046 42.9 -0.1 33 702-734 56-89 (683)
122 PLN02638 cellulose synthase A 26.3 40 0.00086 44.9 2.2 50 701-751 16-68 (1079)
123 PRK05472 redox-sensing transcr 26.3 43 0.00093 36.3 2.2 34 222-255 19-54 (213)
124 TIGR03830 CxxCG_CxxCG_HTH puta 26.2 1.1E+02 0.0024 29.9 4.9 53 222-274 67-119 (127)
125 PRK10401 DNA-binding transcrip 26.2 55 0.0012 37.1 3.2 49 233-281 1-50 (346)
126 PRK09526 lacI lac repressor; R 26.0 59 0.0013 36.6 3.3 52 231-282 3-55 (342)
127 PF10367 Vps39_2: Vacuolar sor 25.9 30 0.00065 32.7 0.8 30 825-855 79-108 (109)
128 PLN02400 cellulose synthase 25.5 49 0.0011 44.1 2.8 49 702-751 36-87 (1085)
129 PRK10727 DNA-binding transcrip 25.4 59 0.0013 36.8 3.2 50 233-282 1-51 (343)
130 KOG0695 Serine/threonine prote 25.2 27 0.00059 41.0 0.4 35 702-736 141-176 (593)
131 PF10497 zf-4CXXC_R1: Zinc-fin 24.8 58 0.0013 32.1 2.6 62 699-782 4-81 (105)
132 COG5194 APC11 Component of SCF 24.4 29 0.00062 32.9 0.4 33 825-857 21-66 (88)
133 PF13639 zf-RING_2: Ring finge 24.4 28 0.0006 28.3 0.3 30 704-734 2-31 (44)
134 PF04760 IF2_N: Translation in 23.9 34 0.00075 29.2 0.7 23 232-254 2-24 (54)
135 TIGR02531 yecD_yerC TrpR-relat 23.6 58 0.0013 31.2 2.3 29 223-252 41-69 (88)
136 PRK11169 leucine-responsive tr 23.4 53 0.0011 34.3 2.1 33 222-254 17-49 (164)
137 PLN02195 cellulose synthase A 22.8 54 0.0012 43.4 2.4 49 702-751 6-57 (977)
138 PLN02436 cellulose synthase A 22.2 56 0.0012 43.6 2.4 49 702-751 36-87 (1094)
139 PF08280 HTH_Mga: M protein tr 22.1 78 0.0017 27.7 2.6 33 223-255 9-41 (59)
140 smart00342 HTH_ARAC helix_turn 22.1 70 0.0015 27.9 2.4 42 233-274 1-49 (84)
141 PRK10072 putative transcriptio 21.8 1.1E+02 0.0024 29.8 3.8 52 224-275 37-88 (96)
142 PRK10434 srlR DNA-bindng trans 21.8 65 0.0014 36.1 2.6 33 222-254 8-40 (256)
143 PF05043 Mga: Mga helix-turn-h 21.8 86 0.0019 29.0 3.0 42 222-273 19-60 (87)
144 smart00344 HTH_ASNC helix_turn 21.6 70 0.0015 30.5 2.4 32 223-254 7-38 (108)
145 PF13551 HTH_29: Winged helix- 21.6 1.1E+02 0.0023 28.9 3.6 50 228-277 7-76 (112)
146 PRK04424 fatty acid biosynthes 21.0 74 0.0016 34.1 2.7 35 221-255 9-43 (185)
147 PHA02862 5L protein; Provision 20.8 35 0.00075 35.7 0.2 33 702-734 2-34 (156)
148 PF11793 FANCL_C: FANCL C-term 20.7 52 0.0011 30.0 1.3 33 825-857 3-40 (70)
149 smart00342 HTH_ARAC helix_turn 20.7 67 0.0014 28.0 2.0 29 226-254 43-72 (84)
150 TIGR01481 ccpA catabolite cont 20.4 82 0.0018 35.2 3.1 48 234-281 2-50 (329)
151 PF10078 DUF2316: Uncharacteri 20.3 62 0.0014 31.3 1.7 42 231-272 21-62 (89)
152 PF04405 ScdA_N: Domain of Unk 20.2 52 0.0011 29.0 1.1 37 220-256 14-54 (56)
153 PLN02915 cellulose synthase A 20.1 64 0.0014 43.0 2.3 49 702-751 15-66 (1044)
154 PRK10141 DNA-binding transcrip 20.1 78 0.0017 31.8 2.5 33 222-254 19-51 (117)
155 PRK11179 DNA-binding transcrip 20.0 75 0.0016 32.7 2.4 33 222-254 12-44 (153)
No 1
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=100.00 E-value=7.3e-43 Score=404.86 Aligned_cols=516 Identities=30% Similarity=0.400 Sum_probs=320.3
Q ss_pred CCCCCCCCcceecCCCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccccccccccccCceeeCCCCCCCcccc
Q 001260 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFH 82 (1113)
Q Consensus 3 lCP~kgGALK~T~~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~sFH 82 (1113)
|||++|||||+|..| .+|||+.||||||||+|+++..|+||++|+.|+..||.|.|.+|+.+.||||||+.+.|.++||
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 799999999999987 5999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCceEEEccccCCcceeeeeccCCCCCCCCCCCCCCCCC---CCCCCCCccccccccccccccCccceeeeecc
Q 001260 83 PICAREARHRLEVWGKYGCNNVELRAFCAKHSDIQDNSSTPRTGD---PCSAIGSESCVSNNLHETLSMSKLHKLKFSCK 159 (1113)
Q Consensus 83 vtCA~~aG~~~e~~~~~g~~~~~~~~fC~~Hr~~~~~~~~~~~~~---~~~~d~s~~~~~~~~~~~L~~~~l~Q~q~~~~ 159 (1113)
++||+.+|..|.++... .+.+.|.+||.+|+.-+...+.-+.++ +.-..+ ++..........+.+.++++...
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-NDEVKFKSYCSKHSDHREGKSLGNEAESPHPRCHLP-EQSVGEGHRSSDRAQKLQELEGE-- 482 (893)
T ss_pred chhhhhcCCeeeeeecc-CCchhheeecccccccccccccccccCCCCccccCh-hhhhhhhhhhhHHHHHHhhcchh--
Confidence 99999999999999754 677899999999998875322211111 000000 00123344444555555554422
Q ss_pred CCCeeeeeeecCCCCCCCCCCccccccCCCccccccccccccCCCCCCCCCCCCCCCCCcchHHHHHHHhhhCCcchhhh
Q 001260 160 NGDKIGVHTETSDANSDRSTDSEVTGFSDSRLISVPTSECTNAGKPDRSEFEDVNPSDALNFTLILKKLIDRGKVNVKDI 239 (1113)
Q Consensus 160 ~Gd~~~~~~~t~~~~s~~~~~~e~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lkkli~~gkv~~~~~ 239 (1113)
.|.-.++.-.-|..++|.-.+++. -.=+. .+..+-....-.+..+.+|.+++||++|.|||+++++
T Consensus 483 -----------f~~~v~~~diae~l~~~e~~vs~i--ynywk-lkrks~~n~~lippk~d~~~~i~kk~~~~~kv~~kl~ 548 (893)
T KOG0954|consen 483 -----------FYDIVRNEDIAELLSMPEFAVSAI--YNYWK-LKRKSRFNKELIPPKSDEVGLIAKKLEDLGKVRVKLV 548 (893)
T ss_pred -----------HhhhhhHHHHHHHhcCchHHHHHH--HHHHH-HhhhccCCCcCCCCcchhccchhhHHHHhhhhhhHHH
Confidence 112222211233344555444441 00011 4445555568899999999999999999999999999
Q ss_pred hhhhcCChhhhhhccccccccc-----------hhhHHHHHHhhhcccccccccceeeccccccccccc-------cccC
Q 001260 240 ASDIGISPDLLKTTLADGTFAS-----------DLQCKLVKWLSNHAYLGGLLKNVKLKIKSSISSKAD-------IKNS 301 (1113)
Q Consensus 240 a~~~g~s~~~~~a~l~~~~~~~-----------~~~~k~~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~ 301 (1113)
|..+ +|.+.+.+-..+.+- +-|.--..+|-.|.||++.++...++.+.++.+..- +.-.
T Consensus 549 ahlr---qdlerv~~~~~~~trrekas~s~~ki~eq~f~~ql~l~~q~~~~~~~~~n~~~n~~f~~~~r~tl~~k~~~s~ 625 (893)
T KOG0954|consen 549 AHLR---QDLERVRNLCYTKTRREKASNSYAKIDEQLFPDQLLLQHQHMGSSDKGKNLKRNTTFYSERRATLCTKGIVSL 625 (893)
T ss_pred HHHH---HHHHHhhcccchhcccchhhhhHHHHHhHHHHHHHHHHHHhhcccccchhhhhhccccCCcchhHhhhccccC
Confidence 9988 777776644222221 112222234778999999999988887665544322 2223
Q ss_pred CCCCcccc---ccCCCCccccccc--------------------CCCCcccccceecccCcccccccceec-CCCccccc
Q 001260 302 DSDGLMVS---ESDVADPVAVKSV--------------------PPRRRTKSSIRILRDDKMVSSSEEIFS-GNGIAADK 357 (1113)
Q Consensus 302 ~~~~~~~~---~~~~~~~~~~~~v--------------------p~~~rt~~~~~il~dn~~~cs~e~~~~-~~g~~~~~ 357 (1113)
|+++...+ .--+..|.+++.+ +.----++|.|||+....+=+-+---+ -|-+..+
T Consensus 626 ~~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 626 DSDILDPAVQKLQSILRPHEINICNNITNNTRCTLTENCRKNSIVVVPAKANNNRLLKSGSHSPAPDHSPSPKNSTVSD- 704 (893)
T ss_pred CccccCHHHHHhhcccCcchhhhhhccccCcccccChhhccCcceeeecccccCccccCCCcCCccccCCCcCCCccch-
Confidence 34443221 1112222222111 000011222222222221111100000 0000000
Q ss_pred chhhhcccCCCCCccCccccCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCcccccccccccchhhccc---c
Q 001260 358 DEVKVEQLDGEEPAIHNKVSTPDCTEKSPTDPTGSEDSLARGSPMSEGSAAKPSDCGFFESCQSEEAALPDQINLL---N 434 (1113)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~ 434 (1113)
++. .-++-|..|+. -... ..++.++. .+-+.+|- |
T Consensus 705 --------~~~--h~gk~g~~pr~-------d~~s----~sasss~n---------------------~ksq~~skirsn 742 (893)
T KOG0954|consen 705 --------QKV--HHGKSGVIPRD-------DHGS----QSASSSSN---------------------VKSQNASKIRSN 742 (893)
T ss_pred --------hhc--CCccCCCCccc-------cccc----cccccccC---------------------cccccccccccC
Confidence 000 00111111111 1111 11111111 11111111 3
Q ss_pred CCCCCCCCCCCCCcccccccCCCCCccccchhhhhh-hccccCcccCCcccCcccchhhccccCCCccccccCccCccCC
Q 001260 435 VDQENPICSSVDTLVPYFINAKPSSGFFWHPYIHKS-LQMQSGLLSGNKVHKSDEISRLEASSTASVCCNHQGRHSKCND 513 (1113)
Q Consensus 435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~y~hp~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 (1113)
+.++--.-+...+.++.+++.+.+.+|..|-||++. ..+.-..++ ....+..+.+|..+..-+.=.-..++++..
T Consensus 743 ~s~~s~n~ni~~~~sss~~~~~~~p~fsph~~~~~s~s~s~~e~~s--ks~~~s~~~~~kq~y~~~~~~~~~~~q~~g-- 818 (893)
T KOG0954|consen 743 SSQNSGNGNIPNPISSSLFNQEAYPGFSPHRYIHKSLSESGKEQTS--KSSTDSDVARMKQTYTHLAGSEEGNKQLQG-- 818 (893)
T ss_pred cccccCCCcCCCCcchhhhccccCCCCCcchhhhhhhhhhcccccc--cccccCCcchhhheecccccccchhhHHHH--
Confidence 333333333334677799999999999999999999 554443333 233444444444111111111122222222
Q ss_pred CcccCCcccHHHHHHhhhccccccCCCcchhhHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhhHHHHhhhhcchhHHHH
Q 001260 514 MSCKSDGVNLEQVFKARTRGVLELSPTDEVEGEIIYFQHRLLGNAFSRKRLADNLVCKAVKTLNQEIDVARGRRWDAVLV 593 (1113)
Q Consensus 514 ~~~~~~~~~~~q~~~~~~~~~~~~~p~de~e~E~~~~q~~ll~~~~~~~~~~~~lv~eV~k~l~~e~~~~~~r~~d~~~~ 593 (1113)
...+-|+++++.+|+++.+|.|+.++|.+|.|..+++.+..+++..+++..+++++++.|++....|+||..++
T Consensus 819 ------~e~~~~~s~~~p~~~~d~s~~D~e~~~~~~~q~~~~g~~r~rkqssd~~n~~~asr~~~~~~~~~g~~~~~s~~ 892 (893)
T KOG0954|consen 819 ------AETFLQLSKARPLGILDLSPEDEEEGELLYYQLQLLGTARSRKQSSDNLNYEVASRLPLEIDEQHGRRWDDSLV 892 (893)
T ss_pred ------HHHHHHhhccCCcccccCCCCchhhhhHHhhhhccccceecccccccCcChhhhccCCCccccccCcCcchhhc
Confidence 36789999999999999999999999999999999999999999999999999999999999999999998765
No 2
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=100.00 E-value=2.9e-36 Score=350.30 Aligned_cols=167 Identities=32% Similarity=0.767 Sum_probs=151.1
Q ss_pred CCCCCcCcccCCCCC-CCCCeEEccccCcccccccccCcccCCCccccccccccccCCCCCCCCCCccCCCccccccccC
Q 001260 699 KEHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLC 777 (1113)
Q Consensus 699 ke~~~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~~C~LC 777 (1113)
.+++..|+||..+++ ..|+|||||+|++.|||.||||..+|+++|||+.|... + .+.|+||
T Consensus 268 ~dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg----------------~--~ppCvLC 329 (893)
T KOG0954|consen 268 YDEDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALG----------------I--EPPCVLC 329 (893)
T ss_pred ccccceeceecCCCccccceeEEeccchhHHHHhhhceeecCCCCeeehhcccc----------------C--CCCeeec
Confidence 347889999999887 58999999999999999999999999999999999875 1 6789999
Q ss_pred CCCCCcceecCCC-cceecccccccccceecCC-ccccccCccccCCCC--cccccccCcCCceeecCCCCcccccchhh
Q 001260 778 GGTTGAFRKSANG-QWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKGI--DVCCICRHKHGICIKCNYGNCQTTFHPTC 853 (1113)
Q Consensus 778 p~~gGALKrT~~g-~WVHV~CALW~PEv~f~n~-~lepVegie~I~k~r--~~C~iC~~~~GA~IqCs~~~C~~~FHvtC 853 (1113)
|.+||+||.+..| .|+|++||||+|||+|.+. .|+||..++.|+..+ +.|.+|+.+.||||+|+.+.|.++||++|
T Consensus 330 PkkGGamK~~~sgT~wAHvsCALwIPEVsie~~ekmePItkfs~IpesRwslvC~LCk~k~GACIqCs~k~C~t~fHv~C 409 (893)
T KOG0954|consen 330 PKKGGAMKPTKSGTKWAHVSCALWIPEVSIECPEKMEPITKFSHIPESRWSLVCNLCKVKSGACIQCSNKTCRTAFHVTC 409 (893)
T ss_pred cccCCcccccCCCCeeeEeeeeeccceeeccCHhhcCcccccCCCcHHHHHHHHHHhcccCcceEEecccchhhhccchh
Confidence 9999999999877 6999999999999999987 799999999999875 89999999999999999999999999999
Q ss_pred hhhcCceEEEee-CCCceeeeecCCCCChhh
Q 001260 854 ARSAGFYLNVKS-TGGNFQHKAYCEKHSLEQ 883 (1113)
Q Consensus 854 A~~aG~~~~~k~-~~g~~~~~iyC~kHs~~~ 883 (1113)
|+.+|..|.+.. .++...++.||.+|+.-+
T Consensus 410 A~~aG~~~~~~~~~~D~v~~~s~c~khs~~~ 440 (893)
T KOG0954|consen 410 AFEAGLEMKTILKENDEVKFKSYCSKHSDHR 440 (893)
T ss_pred hhhcCCeeeeeeccCCchhheeecccccccc
Confidence 999999998643 456677889999887644
No 3
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=100.00 E-value=1.6e-35 Score=341.45 Aligned_cols=170 Identities=35% Similarity=0.800 Sum_probs=147.1
Q ss_pred CCCCCcCcccCCCCC-CCCCeEEccc--cCcccccccccCcccCCCccccccccccccCCCCCCCCCCccCCCccccccc
Q 001260 699 KEHPRSCDICRRSET-ILNPILICSG--CKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECS 775 (1113)
Q Consensus 699 ke~~~~CsVC~~~E~-~~N~IV~Cd~--C~laVHq~CYGi~~ipeg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~~C~ 775 (1113)
||+-.-|+||-|.-. .+|+|||||+ |-++|||.||||.++|+|+|||++|+... +. ..+.|.
T Consensus 2 KEMVGGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqe--ra-------------arvrCe 66 (900)
T KOG0956|consen 2 KEMVGGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQE--RA-------------ARVRCE 66 (900)
T ss_pred cccccceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhh--hh-------------ccceee
Confidence 566677999998545 4899999996 99999999999999999999999998741 11 268999
Q ss_pred cCCCCCCcceecCCCcceecccccccccceecCC-ccccccCccccCCC--CcccccccCc-------CCceeecCCCCc
Q 001260 776 LCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHK-------HGICIKCNYGNC 845 (1113)
Q Consensus 776 LCp~~gGALKrT~~g~WVHV~CALW~PEv~f~n~-~lepVegie~I~k~--r~~C~iC~~~-------~GA~IqCs~~~C 845 (1113)
|||.++||||+|++|.|+||+||||+|||.|.|- .|+||- +..|+.. ..+|+||+.. .|||++|+..+|
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 9999999999999999999999999999999997 788876 4566655 5899999973 799999999999
Q ss_pred ccccchhhhhhcCceEEEee-CCCceeeeecCCCCChhhH
Q 001260 846 QTTFHPTCARSAGFYLNVKS-TGGNFQHKAYCEKHSLEQK 884 (1113)
Q Consensus 846 ~~~FHvtCA~~aG~~~~~k~-~~g~~~~~iyC~kHs~~~k 884 (1113)
.+.|||+||+.+|+..+..+ .-++++|--||+.|-.+.+
T Consensus 146 kqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~HfsKlk 185 (900)
T KOG0956|consen 146 KQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFSKLK 185 (900)
T ss_pred hhhhhhhHhhhhccceeccccccccceechhHHHHHHHhh
Confidence 99999999999999997653 3457888899999986543
No 4
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=100.00 E-value=2.4e-35 Score=330.44 Aligned_cols=168 Identities=32% Similarity=0.721 Sum_probs=148.0
Q ss_pred CCCCcCcccCCCCC-CCCCeEEccccCcccccccccCcccCCCccccccccccccCCCCCCCCCCccCCCccccccccCC
Q 001260 700 EHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLCG 778 (1113)
Q Consensus 700 e~~~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~~C~LCp 778 (1113)
+.+..|.+|...+. +.|.|||||+|+++|||.||||..+|+|.|||++|.+.. +...-|.+||
T Consensus 191 ~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~peG~WlCrkCi~~~----------------~~i~~C~fCp 254 (669)
T COG5141 191 EFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGE----------------YQIRCCSFCP 254 (669)
T ss_pred hhhhhhHhccccccCCcceEEEecCcchhhhhhcccceecCcchhhhhhhcccc----------------cceeEEEecc
Confidence 45778999998876 579999999999999999999999999999999999862 2245699999
Q ss_pred CCCCcceecCCCcceecccccccccceecCC-ccccccCccccCCC--CcccccccCcCCceeecCCCCcccccchhhhh
Q 001260 779 GTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTFHPTCAR 855 (1113)
Q Consensus 779 ~~gGALKrT~~g~WVHV~CALW~PEv~f~n~-~lepVegie~I~k~--r~~C~iC~~~~GA~IqCs~~~C~~~FHvtCA~ 855 (1113)
..+||||+|.+|.|+|++||+|+||++|.+- .++||+||.+++.. ++.|++|+..+|+||||++.+|.++||++||+
T Consensus 255 s~dGaFkqT~dgrW~H~iCA~~~pelsF~~l~~~dpI~~i~sVs~srwkl~C~iCk~~~GtcIqCs~~nC~~aYHVtCAr 334 (669)
T COG5141 255 SSDGAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCAR 334 (669)
T ss_pred CCCCceeeccCCchHhHhHHHhcchhccccccccchhhhhcccchhhHhheeeEEcccCcceeeecccchhhhhhhhhhh
Confidence 9999999999999999999999999999987 79999999999987 58899999999999999999999999999999
Q ss_pred hcCceEE-EeeCCC---ceeeeecCCCCChhh
Q 001260 856 SAGFYLN-VKSTGG---NFQHKAYCEKHSLEQ 883 (1113)
Q Consensus 856 ~aG~~~~-~k~~~g---~~~~~iyC~kHs~~~ 883 (1113)
++|+++. ....++ .+....||++|.+..
T Consensus 335 rag~f~~~~~s~n~~s~~id~e~~c~kh~p~g 366 (669)
T COG5141 335 RAGYFDLNIYSHNGISYCIDHEPLCRKHYPLG 366 (669)
T ss_pred hcchhhhhhhcccccceeecchhhhcCCCCcc
Confidence 9999885 222222 234566999998853
No 5
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=100.00 E-value=9.5e-35 Score=357.13 Aligned_cols=169 Identities=36% Similarity=0.815 Sum_probs=151.1
Q ss_pred CCCCCcCcccCCCCC-CCCCeEEccccCcccccccccCcccCCCccccccccccccCCCCCCCCCCccCCCccccccccC
Q 001260 699 KEHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLC 777 (1113)
Q Consensus 699 ke~~~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~~C~LC 777 (1113)
-+.+.+|+||.+.+. +.|.|||||+|+++|||+|||++.+|+|.|+|+.|.... ...+.|.||
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 LEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPEGQWLCRRCLQSP----------------QRPVRCLLC 279 (1051)
T ss_pred cCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCCCcEeehhhccCc----------------CcccceEec
Confidence 356789999999886 579999999999999999999999999999999998762 236799999
Q ss_pred CCCCCcceecCCCcceecccccccccceecCC-ccccccCccccCCC--CcccccccCcC-CceeecCCCCcccccchhh
Q 001260 778 GGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKH-GICIKCNYGNCQTTFHPTC 853 (1113)
Q Consensus 778 p~~gGALKrT~~g~WVHV~CALW~PEv~f~n~-~lepVegie~I~k~--r~~C~iC~~~~-GA~IqCs~~~C~~~FHvtC 853 (1113)
|..+||||+|++|+|+|++||+|+||+.|.+. .+++|.++++|+.. ++.|++|+.++ |+||||+..+|..+||++|
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 99999999999999999999999999999997 89999999999965 68999999998 9999999999999999999
Q ss_pred hhhcCceEEEeeC--C---C---ceeeeecCCCCChhh
Q 001260 854 ARSAGFYLNVKST--G---G---NFQHKAYCEKHSLEQ 883 (1113)
Q Consensus 854 A~~aG~~~~~k~~--~---g---~~~~~iyC~kHs~~~ 883 (1113)
|+++|++|..... . + .+....||++|.+..
T Consensus 360 a~~agl~m~~~~~~~~s~~~~s~~v~~~syC~~H~pp~ 397 (1051)
T KOG0955|consen 360 ARRAGLYMKSNTVKELSKNGTSQSVNKISYCDKHTPPG 397 (1051)
T ss_pred HhhcCceEeecccccccccccccccceeeeccCCCCch
Confidence 9999999984311 1 1 246788999999863
No 6
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=99.97 E-value=5.6e-33 Score=311.76 Aligned_cols=285 Identities=25% Similarity=0.466 Sum_probs=198.2
Q ss_pred cCcccCCCCC-CCCCeEEccccCcccccccccCcc---cC-------CCccccccccccccCCCCCCCCCCccCCCcccc
Q 001260 704 SCDICRRSET-ILNPILICSGCKVAVHLDCYRNAK---ES-------TGPWYCELCEELLSSRSSGAPSVNFWEKPYFVA 772 (1113)
Q Consensus 704 ~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~---ip-------eg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~ 772 (1113)
.|+||...-. +-|.||.||+|++.||..|||+.. ++ ..+|||+.|.+..+ .+
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 7999997544 479999999999999999999862 22 36899999999743 46
Q ss_pred ccccCCCCCCcceecCCCcceecccccccccceecCC-ccccccC--ccccCCCCcccccccCc----CCceeecCCCCc
Q 001260 773 ECSLCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAG--MEAFPKGIDVCCICRHK----HGICIKCNYGNC 845 (1113)
Q Consensus 773 ~C~LCp~~gGALKrT~~g~WVHV~CALW~PEv~f~n~-~lepVeg--ie~I~k~r~~C~iC~~~----~GA~IqCs~~~C 845 (1113)
.|.|||.++|+||.|+-|+|||++||||+|+|.|+.. .+.+|.- |.....+...|++|..+ .|.||.|..+.|
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 9999999999999999999999999999999999875 5666553 33233446899999974 899999999999
Q ss_pred ccccchhhhhhcCceEEEeeCCCc-eeeeecCCCCChhhHhhhhhcccchhhhhhhHHHHHHHHHH----HHHHHHHHHH
Q 001260 846 QTTFHPTCARSAGFYLNVKSTGGN-FQHKAYCEKHSLEQKMKAETQKHGVEELKGIKQIRVELERL----RLLCERIIKR 920 (1113)
Q Consensus 846 ~~~FHvtCA~~aG~~~~~k~~~g~-~~~~iyC~kHs~~~k~k~~~q~~~~ee~kslrr~rv~lE~l----rll~~ri~kR 920 (1113)
..+|||+||+..|+.++...+++. ..+.+||++|+.....|.-...|..++...++|+|+..... ..-...--.|
T Consensus 264 k~YfHVTCAQk~GlLvea~~e~DiAdpfya~CK~Ht~r~~~K~~rrny~~l~~~~~~r~~~k~~L~~~e~~~~p~~~eaq 343 (707)
T KOG0957|consen 264 KEYFHVTCAQKLGLLVEATDENDIADPFYAFCKKHTNRDNLKPYRRNYDDLEKSEARRITVKRRLRSGELEKNPQKKEAQ 343 (707)
T ss_pred hhhhhhhHHhhhcceeeccccccchhhHHHHHHhhcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHhcccccCCCccHHH
Confidence 999999999999999987655543 45788999999866544445566666666777776431110 0000000111
Q ss_pred HHHHHHHhhchHHHHHhhccccccccccccCccCCCCCCccccccccccCCCCCCChhHhhccCCCeeeecccccccccc
Q 001260 921 EKIKRELILCSHEILAFKRDHHAARLVHGRIPFFPPDVSSESATTSLKGHTDSFKSCSEAFQRSDDVTVDSAASVKNRIK 1000 (1113)
Q Consensus 921 EklKrel~~~~~dila~k~d~~~a~s~~v~sp~~~~~~s~~~a~t~~~g~~~~~~s~~~~~~r~d~~~~ds~~s~k~~~~ 1000 (1113)
-++++++....+ +. ..+... -..+|+|.... .+.++|+-.|+.|...++..-+++.++ ++
T Consensus 344 ari~~~l~kv~~----k~---~~~k~~-~p~~wvp~~K~-----------~RlLtsSAsa~rrl~~KAE~mg~s~~~-f~ 403 (707)
T KOG0957|consen 344 ARIREELDKVIE----KE---CKNKPK-GPISWVPKPKQ-----------ARLLTSSASAFRRLETKAEEMGLSRKE-FR 403 (707)
T ss_pred HHHHHHHHHHHH----HH---HhccCC-CCCCCCccccc-----------cccccchHHHHHHHHHHHHHhcccHhh-hc
Confidence 122222221111 11 112221 23467777633 355778888999999999999999888 55
Q ss_pred cccccccccccC--CcCCCCCCCCCCCc
Q 001260 1001 VYVPMDADQRTD--DSSMSQNLYPRKPS 1026 (1113)
Q Consensus 1001 ~~~~~d~~~~~~--~~s~s~~~~~~~~~ 1026 (1113)
+.- -|.--+++ .=|+.++.|+..+.
T Consensus 404 ~~e-ad~~~~id~r~k~Hv~pafs~efi 430 (707)
T KOG0957|consen 404 QRE-ADPFFNIDLRSKSHVPPAFSKEFI 430 (707)
T ss_pred ccc-cCccccccccccccCCccccHHHH
Confidence 311 12222211 23577888776654
No 7
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=99.90 E-value=1.8e-24 Score=207.28 Aligned_cols=107 Identities=42% Similarity=0.859 Sum_probs=98.9
Q ss_pred CCCCCCCCCcceecCCCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccccccccccccCceeeCCCCCCCccc
Q 001260 2 CSLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSF 81 (1113)
Q Consensus 2 ClCP~kgGALK~T~~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~sF 81 (1113)
.|||.+|||||+|.++ .|||++||+|+|+++|.+...+++|. +..|+.+|++++|.||+++.|+||+|++++|.++|
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 4899999999999965 89999999999999999999999995 99999999999999999999999999999999999
Q ss_pred chhhhhhcCceEEEccccCCcceeeeeccCCC
Q 001260 82 HPICAREARHRLEVWGKYGCNNVELRAFCAKH 113 (1113)
Q Consensus 82 HvtCA~~aG~~~e~~~~~g~~~~~~~~fC~~H 113 (1113)
||+||+.+|+.+++...+. ...+.+||.+|
T Consensus 81 H~~CA~~~g~~~~~~~~~~--~~~~~~~C~~H 110 (110)
T PF13832_consen 81 HPTCARKAGLYFEIENEED--NVQFIAYCPKH 110 (110)
T ss_pred CHHHHHHCCCeEEeeecCC--CceEEEECCCC
Confidence 9999999999999875322 56799999999
No 8
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=99.88 E-value=6.5e-24 Score=246.09 Aligned_cols=113 Identities=31% Similarity=0.646 Sum_probs=104.5
Q ss_pred CCCCCCCCcceecCCCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccccccccccc-------cCceeeCCCC
Q 001260 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVK-------CGACVRCSHG 75 (1113)
Q Consensus 3 lCP~kgGALK~T~~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k-------~GAcIqCs~~ 75 (1113)
|||.+.||||+|+.| .|+||+||||||||.|.++..||||+ +..||.+|++..|+||... .|||++|...
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 9999999999999999853 7999999999
Q ss_pred CCCcccchhhhhhcCceEEEccccCCcceeeeeccCCCCCCCCC
Q 001260 76 TCRTSFHPICAREARHRLEVWGKYGCNNVELRAFCAKHSDIQDN 119 (1113)
Q Consensus 76 ~C~~sFHvtCA~~aG~~~e~~~~~g~~~~~~~~fC~~Hr~~~~~ 119 (1113)
.|..+||||||+.+|+++|..+ .+-++|.|-.||++|-.+-.+
T Consensus 144 ~CkqaFHVTCAQ~~GLLCEE~g-n~~dNVKYCGYCk~HfsKlkk 186 (900)
T KOG0956|consen 144 GCKQAFHVTCAQRAGLLCEEEG-NISDNVKYCGYCKYHFSKLKK 186 (900)
T ss_pred cchhhhhhhHhhhhccceeccc-cccccceechhHHHHHHHhhc
Confidence 9999999999999999999775 466899999999999876554
No 9
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=99.88 E-value=5.7e-23 Score=196.89 Aligned_cols=106 Identities=43% Similarity=0.980 Sum_probs=97.3
Q ss_pred ccccCCCCCCcceecCCCcceecccccccccceecCC-ccccccCccccCCC--CcccccccCcCCceeecCCCCccccc
Q 001260 773 ECSLCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTF 849 (1113)
Q Consensus 773 ~C~LCp~~gGALKrT~~g~WVHV~CALW~PEv~f~n~-~lepVegie~I~k~--r~~C~iC~~~~GA~IqCs~~~C~~~F 849 (1113)
.|.|||..|||||+|.++.|||++||+|+|++.|.+. .+++++ ++.|+.. +.+|.+|++..|++|+|..++|.++|
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 577877 7788765 68999999999999999999999999
Q ss_pred chhhhhhcCceEEEeeCCCceeeeecCCCC
Q 001260 850 HPTCARSAGFYLNVKSTGGNFQHKAYCEKH 879 (1113)
Q Consensus 850 HvtCA~~aG~~~~~k~~~g~~~~~iyC~kH 879 (1113)
||+||+.+|+++++...+....+.+||++|
T Consensus 81 H~~CA~~~g~~~~~~~~~~~~~~~~~C~~H 110 (110)
T PF13832_consen 81 HPTCARKAGLYFEIENEEDNVQFIAYCPKH 110 (110)
T ss_pred CHHHHHHCCCeEEeeecCCCceEEEECCCC
Confidence 999999999999987655566789999999
No 10
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=99.86 E-value=4.4e-23 Score=232.41 Aligned_cols=117 Identities=26% Similarity=0.589 Sum_probs=105.5
Q ss_pred CCCCCCCCcceecCCCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccccccccccccCceeeCCCCCCCcccc
Q 001260 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFH 82 (1113)
Q Consensus 3 lCP~kgGALK~T~~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~sFH 82 (1113)
+||.+.||||.|.+| +|+|++||+|+||.+|.+...++||.||..++..||++.|.||+.+.|+||||++..|.++||
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 689999999999987 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCceEE-EccccCC-cceeeeeccCCCCCCCCCCC
Q 001260 83 PICAREARHRLE-VWGKYGC-NNVELRAFCAKHSDIQDNSS 121 (1113)
Q Consensus 83 vtCA~~aG~~~e-~~~~~g~-~~~~~~~fC~~Hr~~~~~~~ 121 (1113)
||||++||+++- +...+|- ..+....||++|.|......
T Consensus 330 VtCArrag~f~~~~~s~n~~s~~id~e~~c~kh~p~gy~~~ 370 (669)
T COG5141 330 VTCARRAGYFDLNIYSHNGISYCIDHEPLCRKHYPLGYGRM 370 (669)
T ss_pred hhhhhhcchhhhhhhcccccceeecchhhhcCCCCcchhcc
Confidence 999999999876 4433442 23456789999999998653
No 11
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=99.83 E-value=1.1e-21 Score=242.57 Aligned_cols=114 Identities=37% Similarity=0.728 Sum_probs=103.9
Q ss_pred CCCCCCCCCcceecCCCCCcHhhHhhcccCceeeccCCcccccccccCchhhccccccccccccc-CceeeCCCCCCCcc
Q 001260 2 CSLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKC-GACVRCSHGTCRTS 80 (1113)
Q Consensus 2 ClCP~kgGALK~T~~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k~-GAcIqCs~~~C~~s 80 (1113)
++||+++||||+|.+| +|+|++||+|+|||+|.+...++||.+|+.|+.+||+|.|.+|+++. ||||||+..+|.++
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 5899999999999987 89999999999999999999999999999999999999999999998 99999999999999
Q ss_pred cchhhhhhcCceEEEc-cc----cCC-cceeeeeccCCCCCCC
Q 001260 81 FHPICAREARHRLEVW-GK----YGC-NNVELRAFCAKHSDIQ 117 (1113)
Q Consensus 81 FHvtCA~~aG~~~e~~-~~----~g~-~~~~~~~fC~~Hr~~~ 117 (1113)
||||||+++|++|... .. .|. ..+.+.+||.+|.|..
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 11 121 3367899999999985
No 12
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=99.71 E-value=5.9e-18 Score=156.54 Aligned_cols=88 Identities=42% Similarity=0.737 Sum_probs=80.5
Q ss_pred hhHhhcccCceeeccCCc--ccccccccCchhhcccccccccccccCceeeCCCCCCCcccchhhhhhcCceEEEccccC
Q 001260 23 HLFCSLLMPEVYIEDTMK--VEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFHPICAREARHRLEVWGKYG 100 (1113)
Q Consensus 23 Hv~CALwiPEv~f~~~~~--~epV~~I~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~sFHvtCA~~aG~~~e~~~~~g 100 (1113)
|++||||+||+++.+... +.++.+|..++.++++++|++|+++.||+|+|.+++|.++||++||+.+|+.+++..
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 899999999999988864 677889999999999999999998889999999999999999999999999998874
Q ss_pred CcceeeeeccCCCC
Q 001260 101 CNNVELRAFCAKHS 114 (1113)
Q Consensus 101 ~~~~~~~~fC~~Hr 114 (1113)
++..+.+||++|+
T Consensus 78 -~~~~~~~~C~~H~ 90 (90)
T PF13771_consen 78 -DNGKFRIFCPKHS 90 (90)
T ss_pred -CCCceEEEChhcC
Confidence 2346899999996
No 13
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=99.70 E-value=1.8e-18 Score=195.74 Aligned_cols=113 Identities=26% Similarity=0.525 Sum_probs=98.5
Q ss_pred CCCCCCCCcceecCCCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccc-cccccccc----cCceeeCCCCCC
Q 001260 3 SLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKL-VCNICRVK----CGACVRCSHGTC 77 (1113)
Q Consensus 3 lCP~kgGALK~T~~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~L-kC~iC~~k----~GAcIqCs~~~C 77 (1113)
|||+++|+||.|+.| +|||++||||+|+|.|+++..+-+|. +..+....|.. .|++|..+ .|.||.|..|.|
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 66666666655 79999864 899999999999
Q ss_pred CcccchhhhhhcCceEEEccccCCcceeeeeccCCCCCCCCC
Q 001260 78 RTSFHPICAREARHRLEVWGKYGCNNVELRAFCAKHSDIQDN 119 (1113)
Q Consensus 78 ~~sFHvtCA~~aG~~~e~~~~~g~~~~~~~~fC~~Hr~~~~~ 119 (1113)
.++||||||+.+|++++...++ +-.++|++||++|..+...
T Consensus 264 k~YfHVTCAQk~GlLvea~~e~-DiAdpfya~CK~Ht~r~~~ 304 (707)
T KOG0957|consen 264 KEYFHVTCAQKLGLLVEATDEN-DIADPFYAFCKKHTNRDNL 304 (707)
T ss_pred hhhhhhhHHhhhcceeeccccc-cchhhHHHHHHhhcchhhh
Confidence 9999999999999999987532 2347899999999987643
No 14
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=99.49 E-value=8.1e-15 Score=135.66 Aligned_cols=85 Identities=34% Similarity=0.686 Sum_probs=72.9
Q ss_pred ecccccccccceecCCc---cccccCccccCCC--CcccccccCcCCceeecCCCCcccccchhhhhhcCceEEEeeCCC
Q 001260 794 HAFCAEWVFESTFRRGQ---VNPVAGMEAFPKG--IDVCCICRHKHGICIKCNYGNCQTTFHPTCARSAGFYLNVKSTGG 868 (1113)
Q Consensus 794 HV~CALW~PEv~f~n~~---lepVegie~I~k~--r~~C~iC~~~~GA~IqCs~~~C~~~FHvtCA~~aG~~~~~k~~~g 868 (1113)
|++||+|+|++++.+.. +.++.+++.+.+. +++|++|+++.||+|+|..++|...||++||+.+|+.+.+.. .
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 89999999999998763 4567777666544 689999999989999999999999999999999999998864 2
Q ss_pred ceeeeecCCCCC
Q 001260 869 NFQHKAYCEKHS 880 (1113)
Q Consensus 869 ~~~~~iyC~kHs 880 (1113)
...+.+||++|+
T Consensus 79 ~~~~~~~C~~H~ 90 (90)
T PF13771_consen 79 NGKFRIFCPKHS 90 (90)
T ss_pred CCceEEEChhcC
Confidence 336899999996
No 15
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=99.02 E-value=2.4e-10 Score=143.16 Aligned_cols=143 Identities=34% Similarity=0.747 Sum_probs=122.5
Q ss_pred CCCCCCCcCcccCCCCC-CCCCeEEccccCcccccccccCcccCC-CccccccccccccCCCCCCCCCCccCCCcccccc
Q 001260 697 FSKEHPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKEST-GPWYCELCEELLSSRSSGAPSVNFWEKPYFVAEC 774 (1113)
Q Consensus 697 ~~ke~~~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~ipe-g~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~~C 774 (1113)
+.......|.+|++.+. ..|.++.|+.|...||+.|||....+. ..|+|+.|... .....|
T Consensus 568 l~~~~t~~c~~~~~~~~~~~n~~~~~~~~~~~~~s~~~g~~~~~~~~~~~~~~~~~~-----------------~~~r~~ 630 (1005)
T KOG1080|consen 568 LSKWTTERCAVCRDDEDWEKNVSIICDRCTRSVHSECYGNLKSYDGTSWVCDSCETL-----------------DIKRSC 630 (1005)
T ss_pred hcCCCcccccccccccccccceeeeeccccccCCCcccccCCCCCCCcchhhccccc-----------------cCCchh
Confidence 45556678999998764 689999999999999999999887764 56999999864 125789
Q ss_pred ccCCCCCCcceecCCCcceecccccccccceecCC-ccccccCccccCCCC--cccccccCcCCceeecCCCCcccccch
Q 001260 775 SLCGGTTGAFRKSANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKGI--DVCCICRHKHGICIKCNYGNCQTTFHP 851 (1113)
Q Consensus 775 ~LCp~~gGALKrT~~g~WVHV~CALW~PEv~f~n~-~lepVegie~I~k~r--~~C~iC~~~~GA~IqCs~~~C~~~FHv 851 (1113)
++|+..|||++.++.|.|+|+-||.|.|++.+.+. .+.|..++..++... ..|.+ .|-|.+|. .|...||.
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 99999999999999999999999999999999887 788888887777653 55666 57788888 89999999
Q ss_pred hhhhhcCceEE
Q 001260 852 TCARSAGFYLN 862 (1113)
Q Consensus 852 tCA~~aG~~~~ 862 (1113)
.||..+|+.+.
T Consensus 705 ~~a~~~~~~~~ 715 (1005)
T KOG1080|consen 705 MCASRAGYIME 715 (1005)
T ss_pred hhhcCccChhh
Confidence 99999999884
No 16
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=98.92 E-value=2.1e-10 Score=90.47 Aligned_cols=35 Identities=46% Similarity=1.149 Sum_probs=21.7
Q ss_pred CCCeEEccccCcccccccccCcccCCC-cccccccc
Q 001260 715 LNPILICSGCKVAVHLDCYRNAKESTG-PWYCELCE 749 (1113)
Q Consensus 715 ~N~IV~Cd~C~laVHq~CYGi~~ipeg-~WlCd~C~ 749 (1113)
.|+||+|++|++.||+.|||+...+++ .|+|++|+
T Consensus 1 ~n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 1 TNPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp -CEEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred CCceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 389999999999999999999988866 89999995
No 17
>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=97.66 E-value=2.4e-05 Score=65.39 Aligned_cols=46 Identities=26% Similarity=0.775 Sum_probs=38.4
Q ss_pred cCcccCCCCCCCCCeEEccccCcccccccccCccc----CCCccccccccc
Q 001260 704 SCDICRRSETILNPILICSGCKVAVHLDCYRNAKE----STGPWYCELCEE 750 (1113)
Q Consensus 704 ~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~~i----peg~WlCd~C~~ 750 (1113)
+|.||... ...+.+|+|+.|+..||..|+|++.. +.+.|+|..|..
T Consensus 1 ~C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 48899983 34789999999999999999998743 356899999964
No 18
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=97.63 E-value=2e-05 Score=100.12 Aligned_cols=86 Identities=34% Similarity=0.696 Sum_probs=78.7
Q ss_pred CCCCCCCCCcceecCCCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccccccccccccCceeeCCCCCCCccc
Q 001260 2 CSLPKAGGALKPVNGGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSF 81 (1113)
Q Consensus 2 ClCP~kgGALK~T~~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~sF 81 (1113)
|+||.+||||++++.| .|+|+-||.|.||+.+.....|+|..++..++...+..+|.+ .|-|.||. .|.+.|
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 8999999999999955 899999999999999999999999999999999999998888 58888888 888999
Q ss_pred chhhhhhcCceEEE
Q 001260 82 HPICAREARHRLEV 95 (1113)
Q Consensus 82 HvtCA~~aG~~~e~ 95 (1113)
|..||..+|+.++.
T Consensus 703 ~~~~a~~~~~~~~~ 716 (1005)
T KOG1080|consen 703 HAMCASRAGYIMEA 716 (1005)
T ss_pred eehhhcCccChhhh
Confidence 99999998887654
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=97.16 E-value=0.00017 Score=79.02 Aligned_cols=53 Identities=32% Similarity=0.750 Sum_probs=44.9
Q ss_pred CCCCcCcccCCCCCCCCCeEEccccCcccccccccCcc--cCCCcccccccccccc
Q 001260 700 EHPRSCDICRRSETILNPILICSGCKVAVHLDCYRNAK--ESTGPWYCELCEELLS 753 (1113)
Q Consensus 700 e~~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~~--ipeg~WlCd~C~~~~~ 753 (1113)
.+--.|+||+-+|. +++|||||.|...+|-+|...+. .|+|.|-|..|.....
T Consensus 279 ieck~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~~~~ 333 (336)
T KOG1244|consen 279 IECKYCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEELK 333 (336)
T ss_pred eecceeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHHHh
Confidence 35567999998765 68999999999999999998764 5799999999987643
No 21
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.99 E-value=0.00029 Score=77.60 Aligned_cols=46 Identities=24% Similarity=0.530 Sum_probs=41.2
Q ss_pred CCCCcCcccCCCCCCCCCeEEccccCcccccccccCcccCCCccccc
Q 001260 700 EHPRSCDICRRSETILNPILICSGCKVAVHLDCYRNAKESTGPWYCE 746 (1113)
Q Consensus 700 e~~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd 746 (1113)
-+-..|.||+.++- ..+++|||.|+..+|..|.|...+|.|.|.||
T Consensus 312 ~~C~lC~IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~G~WICD 357 (381)
T KOG1512|consen 312 SSCELCRICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPRGEWICD 357 (381)
T ss_pred cccHhhhccCCccc-chheeccccccCCCCccccccccccCccchhh
Confidence 34567999998654 68999999999999999999999999999999
No 22
>KOG1084 consensus Transcription factor TCF20 [Transcription]
Probab=96.87 E-value=0.00042 Score=80.76 Aligned_cols=98 Identities=23% Similarity=0.421 Sum_probs=73.5
Q ss_pred ccccccCCCCCCcceec-CCCcceecccccccccceecCC-ccccccCccccCCC-CcccccccCcCCceeecCCCCccc
Q 001260 771 VAECSLCGGTTGAFRKS-ANGQWVHAFCAEWVFESTFRRG-QVNPVAGMEAFPKG-IDVCCICRHKHGICIKCNYGNCQT 847 (1113)
Q Consensus 771 ~~~C~LCp~~gGALKrT-~~g~WVHV~CALW~PEv~f~n~-~lepVegie~I~k~-r~~C~iC~~~~GA~IqCs~~~C~~ 847 (1113)
...|++++..+ ... ....|+|+.|++|.|.+.+..+ .+..+... +-+. .+.|..|+++ |+.+.|....|..
T Consensus 221 e~~~~l~~~~~---~~d~~~~~~~h~~c~~~~~~~~~~q~~~l~~~~~~--v~r~~~~~c~~c~k~-ga~~~c~~~~~~~ 294 (375)
T KOG1084|consen 221 EFFCALSPKAT---IPDIGFELWYHRYCALWAPNVHESQGGQLTNVDNA--VIRFPSLQCILCQKP-GATLKCVQASLLS 294 (375)
T ss_pred hhhhhhcCCCc---CCccchhHHHHHHHHhcCCcceeccCccccCchhh--hhcccchhcccccCC-CCchhhhhhhhhc
Confidence 34777776533 333 4457999999999999999876 66665542 2222 3799999996 9999999999999
Q ss_pred ccchhhhhhcCceEEEeeCCCceeeeecCCCCC
Q 001260 848 TFHPTCARSAGFYLNVKSTGGNFQHKAYCEKHS 880 (1113)
Q Consensus 848 ~FHvtCA~~aG~~~~~k~~~g~~~~~iyC~kHs 880 (1113)
.+|.+|+......... ...+++|+.|+
T Consensus 295 ~~h~~c~~~~~~~~~~------~~r~v~~~~h~ 321 (375)
T KOG1084|consen 295 NAHFPCARAKNGIPLD------YDRKVSCPRHR 321 (375)
T ss_pred ccCcccccCcccccch------hhhhccCCCCC
Confidence 9999999888655521 13567999999
No 23
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=96.76 E-value=0.0013 Score=77.76 Aligned_cols=135 Identities=16% Similarity=0.229 Sum_probs=86.8
Q ss_pred CcCcccCCCCC-CCCCeEEccccCcccccccccCcccCCCccccccccccccCCCCCCCCCCccCCCccccccccCCCCC
Q 001260 703 RSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAECSLCGGTT 781 (1113)
Q Consensus 703 ~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~~C~LCp~~g 781 (1113)
..|.||..... ..|.++.|++|+..+||.|.-......+.|.|..|..... ...|
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 56999997433 4799999999999999999655444467899988876421 1347
Q ss_pred CcceecCCCcceecccccccccceecCCccccccCccccCCCCcccccccCc----CCceeecCCCCcccccchhhhhhc
Q 001260 782 GAFRKSANGQWVHAFCAEWVFESTFRRGQVNPVAGMEAFPKGIDVCCICRHK----HGICIKCNYGNCQTTFHPTCARSA 857 (1113)
Q Consensus 782 GALKrT~~g~WVHV~CALW~PEv~f~n~~lepVegie~I~k~r~~C~iC~~~----~GA~IqCs~~~C~~~FHvtCA~~a 857 (1113)
|++|... -+| |-+.|....+.. ....+..+.|+||..- .--+|+|. .|.++||-.|-+--
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 GALKKGR---LAR-------PSLPYPEASLDW----DSGHKVNLQCSVCYCGGPGAGNRMLQCD--KCRQWYHQACHQPL 203 (464)
T ss_pred ccccccc---ccc-------ccccCccccccc----CccccccceeeeeecCCcCccceeeeec--ccccHHHHHhccCC
Confidence 7777643 344 333332111110 1122334569999952 23789999 99999999998765
Q ss_pred CceEEEeeCCCceeeeecCCCCCh
Q 001260 858 GFYLNVKSTGGNFQHKAYCEKHSL 881 (1113)
Q Consensus 858 G~~~~~k~~~g~~~~~iyC~kHs~ 881 (1113)
--.+.+ +...+..||..-..
T Consensus 204 i~~~l~----~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 204 IKDELA----GDPFYEWFCDVCNR 223 (464)
T ss_pred CCHhhc----cCccceEeehhhcc
Confidence 333322 22445667876554
No 24
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=96.63 E-value=0.00087 Score=79.14 Aligned_cols=51 Identities=22% Similarity=0.585 Sum_probs=42.0
Q ss_pred CCCcCcccCCCCC-CCCCeEEccccCcccccccccCcc------cCCCcccccccccc
Q 001260 701 HPRSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAK------ESTGPWYCELCEEL 751 (1113)
Q Consensus 701 ~~~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~------ipeg~WlCd~C~~~ 751 (1113)
.++.|+||..+.+ ..|+||+|++|+--||+.|.-... .+...|+|..|.+.
T Consensus 167 ~n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 167 VNLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred ccceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 3566999997654 689999999999999999986432 35678999999885
No 25
>KOG1084 consensus Transcription factor TCF20 [Transcription]
Probab=96.51 E-value=0.0014 Score=76.52 Aligned_cols=86 Identities=21% Similarity=0.380 Sum_probs=66.8
Q ss_pred CCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccccccccccccCceeeCCCCCCCcccchhhhhhcCceEEEc
Q 001260 17 GSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFHPICAREARHRLEVW 96 (1113)
Q Consensus 17 G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~sFHvtCA~~aG~~~e~~ 96 (1113)
+...|.|+.|++|-|++.+.+...+..+ .....+-+.+.|..|.++ |+.+.|....|...+|.+|+..+-... .+
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 5568999999999999999988777544 333333333899999975 999999999999999999997765431 11
Q ss_pred cccCCcceeeeeccCCCC
Q 001260 97 GKYGCNNVELRAFCAKHS 114 (1113)
Q Consensus 97 ~~~g~~~~~~~~fC~~Hr 114 (1113)
..-.++|..|+
T Consensus 311 -------~~r~v~~~~h~ 321 (375)
T KOG1084|consen 311 -------YDRKVSCPRHR 321 (375)
T ss_pred -------hhhhccCCCCC
Confidence 11367999999
No 26
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=96.35 E-value=0.004 Score=64.83 Aligned_cols=128 Identities=16% Similarity=0.402 Sum_probs=72.9
Q ss_pred cCcccCCC-C-CCCCCeEEccccCcccccccccCc--------ccCCCc--cccccccccccCCCCCCCCCCccCCCccc
Q 001260 704 SCDICRRS-E-TILNPILICSGCKVAVHLDCYRNA--------KESTGP--WYCELCEELLSSRSSGAPSVNFWEKPYFV 771 (1113)
Q Consensus 704 ~CsVC~~~-E-~~~N~IV~Cd~C~laVHq~CYGi~--------~ipeg~--WlCd~C~~~~~~~~s~~~~vn~~~kp~~~ 771 (1113)
.|++|... + ...++||+|.||-.++|+.|.|.. ++.++. .-|+.|......... ..| ..
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 49999752 3 357899999999999999999964 333443 569999875333221 113 25
Q ss_pred cccccCCCCCCcceecCCCcceeccccccc-ccceecCCccccccCccccCCCCcccccccCcCCceeecCCCCcccccc
Q 001260 772 AECSLCGGTTGAFRKSANGQWVHAFCAEWV-FESTFRRGQVNPVAGMEAFPKGIDVCCICRHKHGICIKCNYGNCQTTFH 850 (1113)
Q Consensus 772 ~~C~LCp~~gGALKrT~~g~WVHV~CALW~-PEv~f~n~~lepVegie~I~k~r~~C~iC~~~~GA~IqCs~~~C~~~FH 850 (1113)
-.|.-|...|-+-++.....- .+. -.....|+-..||..+..-.-+ ...-.++.|. .|...||
T Consensus 72 ~~C~~C~~~G~~c~pfr~r~T------~kQEe~~ReeNgG~DPit~Vd~~lvn--------N~~nVLFRC~--~C~RawH 135 (175)
T PF15446_consen 72 GMCQQCKKPGPSCKPFRPRKT------PKQEEKLREENGGVDPITPVDPELVN--------NPDNVLFRCT--SCHRAWH 135 (175)
T ss_pred CcccccCCCCCCCcccCCCCC------cHHHHHHHHHcCCCCCCccCCHHHcc--------ChhheEEecC--Cccceee
Confidence 689999887654332211100 000 0112223334454443321111 1134567788 8999999
Q ss_pred hhhhhh
Q 001260 851 PTCARS 856 (1113)
Q Consensus 851 vtCA~~ 856 (1113)
..-.-.
T Consensus 136 ~~HLP~ 141 (175)
T PF15446_consen 136 FEHLPP 141 (175)
T ss_pred hhhCCC
Confidence 765433
No 27
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.68 E-value=0.0055 Score=75.05 Aligned_cols=53 Identities=26% Similarity=0.748 Sum_probs=44.5
Q ss_pred CCCCCCcCcccCCCCCCCCCeEEccccCcc-cccccccCc--ccCCCcccccccccc
Q 001260 698 SKEHPRSCDICRRSETILNPILICSGCKVA-VHLDCYRNA--KESTGPWYCELCEEL 751 (1113)
Q Consensus 698 ~ke~~~~CsVC~~~E~~~N~IV~Cd~C~la-VHq~CYGi~--~ipeg~WlCd~C~~~ 751 (1113)
+..+...|.||...|. .+.||.||.|+.. +|-+|...+ .+|-+.|+|+-|...
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 3445577999998766 6889999999999 999999865 478899999999764
No 28
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.20 E-value=0.0082 Score=72.76 Aligned_cols=48 Identities=29% Similarity=0.800 Sum_probs=42.0
Q ss_pred CcCcccCCCCCCCCCeEEccccCcccccccccCc----ccCCCcccccccccc
Q 001260 703 RSCDICRRSETILNPILICSGCKVAVHLDCYRNA----KESTGPWYCELCEEL 751 (1113)
Q Consensus 703 ~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~----~ipeg~WlCd~C~~~ 751 (1113)
.+|+-|...+. .|.|+.||+|..+|||.|.-.+ .+|.|.|+|.-|..-
T Consensus 254 ~fCsaCn~~~~-F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 254 DFCSACNGSGL-FNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHhCCccc-cccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 58999999765 4999999999999999999876 367899999999764
No 29
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=95.05 E-value=0.17 Score=56.07 Aligned_cols=52 Identities=29% Similarity=0.789 Sum_probs=41.5
Q ss_pred cCCCCCCCcCcccCCCCCCCCCeEEccc--cCcc-cccccccCcccCCCccccccccc
Q 001260 696 DFSKEHPRSCDICRRSETILNPILICSG--CKVA-VHLDCYRNAKESTGPWYCELCEE 750 (1113)
Q Consensus 696 e~~ke~~~~CsVC~~~E~~~N~IV~Cd~--C~la-VHq~CYGi~~ipeg~WlCd~C~~ 750 (1113)
+.+.++.++| -|.+. ..++||-||+ |..- ||..|.|+...|.|.|+|+-|+.
T Consensus 215 d~se~e~lYC-fCqqv--SyGqMVaCDn~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 215 DNSEGEELYC-FCQQV--SYGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKK 269 (271)
T ss_pred ccccCceeEE-Eeccc--ccccceecCCCCCchhheeccccccCCCCCCcEeCHHhHh
Confidence 3444555655 57664 3699999997 8774 89999999999999999999975
No 30
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=93.99 E-value=0.026 Score=63.58 Aligned_cols=50 Identities=24% Similarity=0.721 Sum_probs=40.6
Q ss_pred CCCCCcCcccCCCCCCCCCeEEccc--cC-cccccccccCcccCCCcccccccccc
Q 001260 699 KEHPRSCDICRRSETILNPILICSG--CK-VAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 699 ke~~~~CsVC~~~E~~~N~IV~Cd~--C~-laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
.++...|- |.. ...+.||-||+ |. -=||..|.|+...|.|.|||..|...
T Consensus 216 ~~e~~yC~-Cnq--vsyg~Mi~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 216 PDEPTYCI-CNQ--VSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGKWYCPRCKAE 268 (274)
T ss_pred CCCCEEEE-ecc--cccccccccCCCCCCcceEEEeccccccCCCCcccchhhhhh
Confidence 34455564 442 33689999999 99 78999999999999999999999875
No 31
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=92.27 E-value=0.099 Score=45.43 Aligned_cols=33 Identities=24% Similarity=0.679 Sum_probs=28.5
Q ss_pred CCCcCcccCCCCCCCCCeEEccccCcccccccc
Q 001260 701 HPRSCDICRRSETILNPILICSGCKVAVHLDCY 733 (1113)
Q Consensus 701 ~~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CY 733 (1113)
....|.+|.+.-..++++|+|..|+..+|+.||
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 346799999854457999999999999999999
No 32
>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 KOG0383 consensus Predicted helicase [General function prediction only]
Probab=90.99 E-value=0.17 Score=63.29 Aligned_cols=50 Identities=22% Similarity=0.626 Sum_probs=40.6
Q ss_pred CCCCCCCcCcccCCCCCCCCCeEEccccCcccccccccCcc--cCCCccccccccc
Q 001260 697 FSKEHPRSCDICRRSETILNPILICSGCKVAVHLDCYRNAK--ESTGPWYCELCEE 750 (1113)
Q Consensus 697 ~~ke~~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~~--ipeg~WlCd~C~~ 750 (1113)
++..+...|.||.+ +..++.|+.|..+||.+|.+.+. +|.+.|+|.+|..
T Consensus 42 ~~~~~~e~c~ic~~----~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~ 93 (696)
T KOG0383|consen 42 WDDAEQEACRICAD----GGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFC 93 (696)
T ss_pred cchhhhhhhhhhcC----CCcEEEeccccHHHHHHccCCCCCcCCccceeeeeecc
Confidence 44556678999988 57788999999999999998764 5556699999943
No 34
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=90.63 E-value=0.13 Score=62.95 Aligned_cols=49 Identities=31% Similarity=0.796 Sum_probs=36.8
Q ss_pred CCcCcccCCCCCCCCCeEEccccCcccccccccCc--ccCCCcccccccccc
Q 001260 702 PRSCDICRRSETILNPILICSGCKVAVHLDCYRNA--KESTGPWYCELCEEL 751 (1113)
Q Consensus 702 ~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~--~ipeg~WlCd~C~~~ 751 (1113)
...|-.|+. -.+.+.+++|++|.+++|-+|--.+ .++.|+|+|.+|...
T Consensus 68 crvCe~c~~-~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 68 CRVCEACGT-TGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred ceeeeeccc-cCCcccccccccccccccccccCCccccccCcccccHHHHhh
Confidence 345555552 2246789999999999999886543 578999999999754
No 35
>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=87.56 E-value=0.76 Score=43.07 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=45.3
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcccc--ccccchhhHHHHHHhh
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLAD--GTFASDLQCKLVKWLS 272 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~--~~~~~~~~~k~~~wl~ 272 (1113)
..|+.-|.+ |+++++|||.+.|+|..++--.|.. ..++|....+|..-.+
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 567888888 9999999999999999999999985 4799999999998877
No 36
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=84.85 E-value=0.47 Score=53.26 Aligned_cols=49 Identities=22% Similarity=0.371 Sum_probs=38.4
Q ss_pred CCCcCcccCCCCC-----CCCCeEEccccCcccccccccCcc-----cCCCcccccccc
Q 001260 701 HPRSCDICRRSET-----ILNPILICSGCKVAVHLDCYRNAK-----ESTGPWYCELCE 749 (1113)
Q Consensus 701 ~~~~CsVC~~~E~-----~~N~IV~Cd~C~laVHq~CYGi~~-----ipeg~WlCd~C~ 749 (1113)
-...|-+|++... .-|.++.|.-|..+.|.+|...+. +..-.|-|--|+
T Consensus 257 ~~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 257 RRNERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred chhhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 3457999998642 258899999999999999997543 346789988885
No 37
>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=83.09 E-value=0.78 Score=41.10 Aligned_cols=31 Identities=35% Similarity=0.694 Sum_probs=24.2
Q ss_pred HHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 224 ~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
|+.-|.++|.||+.+||.++|+||+.|++-|
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL 35 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAML 35 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 4444668999999999999999999999986
No 38
>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=83.02 E-value=7.3 Score=39.78 Aligned_cols=82 Identities=20% Similarity=0.197 Sum_probs=55.0
Q ss_pred Hhhhcccc---------ccCCCcchhhHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhhHHHHhhhhcchhHHHHHHHHH
Q 001260 528 KARTRGVL---------ELSPTDEVEGEIIYFQHRLLGNAFSRKRLADNLVCKAVKTLNQEIDVARGRRWDAVLVNQYLC 598 (1113)
Q Consensus 528 ~~~~~~~~---------~~~p~de~e~E~~~~q~~ll~~~~~~~~~~~~lv~eV~k~l~~e~~~~~~r~~d~~~~nq~L~ 598 (1113)
-.+..||+ .-..+|||-.||..+|.+|-.-...|+.+...|..-|..++...=-+.-..--|..+..-|++
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 57888998 336678999999999999998777777766666655555553222222223345556677888
Q ss_pred HHHHHHHccCc
Q 001260 599 ELREAKKQGRK 609 (1113)
Q Consensus 599 ~~reakkq~~k 609 (1113)
.++..++..++
T Consensus 94 r~~~~~kkkk~ 104 (131)
T PF10198_consen 94 RMRARKKKKKK 104 (131)
T ss_pred HHHHhhcccCc
Confidence 88776555443
No 39
>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=82.23 E-value=0.85 Score=38.09 Aligned_cols=30 Identities=27% Similarity=0.835 Sum_probs=25.5
Q ss_pred ccccccCc--CCceeecCCCCcccccchhhhhhc
Q 001260 826 VCCICRHK--HGICIKCNYGNCQTTFHPTCARSA 857 (1113)
Q Consensus 826 ~C~iC~~~--~GA~IqCs~~~C~~~FHvtCA~~a 857 (1113)
.|.+|++. .+.+|+|. .|..+||..|....
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 47888873 68999999 99999999998655
No 40
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=80.76 E-value=0.81 Score=55.70 Aligned_cols=87 Identities=25% Similarity=0.395 Sum_probs=46.8
Q ss_pred ccccccCCC---CCCcceecCCCcceecccccccccceecCCccccccCccccCC-----CCcccccccCc-CCceeecC
Q 001260 771 VAECSLCGG---TTGAFRKSANGQWVHAFCAEWVFESTFRRGQVNPVAGMEAFPK-----GIDVCCICRHK-HGICIKCN 841 (1113)
Q Consensus 771 ~~~C~LCp~---~gGALKrT~~g~WVHV~CALW~PEv~f~n~~lepVegie~I~k-----~r~~C~iC~~~-~GA~IqCs 841 (1113)
...|+-|.. .|++|.-.+. +| ||.|..-.....+.++.+..-+++.--.+ ...+|..|.+- .|..++=-
T Consensus 133 ps~cagc~~~lk~gq~llald~-qw-hv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag 210 (670)
T KOG1044|consen 133 PSTCAGCGEELKNGQALLALDK-QW-HVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAG 210 (670)
T ss_pred Cccccchhhhhhccceeeeecc-ce-eeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhcc
Confidence 457888865 3455544433 66 66665443333333332222222211111 13577777763 45555533
Q ss_pred CCCcccccchhhhhhcCceEEE
Q 001260 842 YGNCQTTFHPTCARSAGFYLNV 863 (1113)
Q Consensus 842 ~~~C~~~FHvtCA~~aG~~~~~ 863 (1113)
+ ..|||+||+-..|--.|
T Consensus 211 --~--kh~HPtCARCsRCgqmF 228 (670)
T KOG1044|consen 211 --D--KHFHPTCARCSRCGQMF 228 (670)
T ss_pred --C--cccCcchhhhhhhcccc
Confidence 4 79999999988775544
No 41
>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=79.30 E-value=1.9 Score=36.34 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=39.2
Q ss_pred chhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhhhccccc
Q 001260 235 NVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLG 278 (1113)
Q Consensus 235 ~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~~~~~~~ 278 (1113)
+++|||.+.|+|.-++--+|+ ....++..+.+|....+..-|.+
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 478999999999999999999 57799999999999999888865
No 42
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=78.17 E-value=0.63 Score=62.73 Aligned_cols=51 Identities=31% Similarity=0.762 Sum_probs=43.0
Q ss_pred CCCcCcccCCCCCCCCCeEEccccCcccccccccCc--ccCCCccccccccccc
Q 001260 701 HPRSCDICRRSETILNPILICSGCKVAVHLDCYRNA--KESTGPWYCELCEELL 752 (1113)
Q Consensus 701 ~~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~--~ipeg~WlCd~C~~~~ 752 (1113)
....|-||+.... .+.|+.|+.|.-.+|..|..+. ..|.++|+|..|....
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 5678999998533 4789999999999999999754 5788999999998764
No 43
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=77.50 E-value=2.2 Score=55.42 Aligned_cols=117 Identities=21% Similarity=0.370 Sum_probs=75.4
Q ss_pred cCCCCCCCcCcccCCCCCCCCCeEEccccCcccccccccCcc--cCCCccccccccccccCCCCCCCCCCccCCCccccc
Q 001260 696 DFSKEHPRSCDICRRSETILNPILICSGCKVAVHLDCYRNAK--ESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVAE 773 (1113)
Q Consensus 696 e~~ke~~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~~--ipeg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~~ 773 (1113)
+++..-+..|-+|.+ .+.++.|..|...||..|.--+. .|...|-|..|..-+-+ + .+.
T Consensus 338 e~~~~~ddhcrf~~d----~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hkvn---------g------vvd 398 (1414)
T KOG1473|consen 338 EGEIEYDDHCRFCHD----LGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHKVN---------G------VVD 398 (1414)
T ss_pred ccceeecccccccCc----ccceeecccCCceEEeeecCCccccCCCccchhhhhhhhccC---------c------ccc
Confidence 345556778999987 68999999999999999986553 56788999999764221 1 445
Q ss_pred cccCCCCCCccee-cCCCcceecccccccccceecCCccccccCccccCCCCcccccccCcCCceeecCCCCcccccch-
Q 001260 774 CSLCGGTTGAFRK-SANGQWVHAFCAEWVFESTFRRGQVNPVAGMEAFPKGIDVCCICRHKHGICIKCNYGNCQTTFHP- 851 (1113)
Q Consensus 774 C~LCp~~gGALKr-T~~g~WVHV~CALW~PEv~f~n~~lepVegie~I~k~r~~C~iC~~~~GA~IqCs~~~C~~~FHv- 851 (1113)
|+|=+.+.+...+ +..|.==|- + .+..+ ...|.||+.. |. .-|++..|...||.
T Consensus 399 ~vl~~~K~~~~iR~~~iG~dr~g------r-------~ywfi---------~rrl~Ie~~d-et-~l~yysT~pqly~ll 454 (1414)
T KOG1473|consen 399 CVLPPSKNVDSIRHTPIGRDRYG------R-------KYWFI---------SRRLRIEGMD-ET-LLWYYSTCPQLYHLL 454 (1414)
T ss_pred cccChhhcccceeccCCCcCccc------c-------chhce---------eeeeEEecCC-Cc-EEEEecCcHHHHHHH
Confidence 7776665544432 221110000 0 00001 2478899864 43 44666789999999
Q ss_pred hhhh
Q 001260 852 TCAR 855 (1113)
Q Consensus 852 tCA~ 855 (1113)
.|.-
T Consensus 455 ~cLd 458 (1414)
T KOG1473|consen 455 RCLD 458 (1414)
T ss_pred HHhc
Confidence 7864
No 44
>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=75.98 E-value=1.9 Score=37.49 Aligned_cols=33 Identities=36% Similarity=0.624 Sum_probs=29.7
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
..||+-|-+.|+++++++|..+|+|+.++.--|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl 35 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDL 35 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHH
Confidence 457888888999999999999999999998876
No 45
>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=73.01 E-value=3.1 Score=35.10 Aligned_cols=35 Identities=26% Similarity=0.592 Sum_probs=26.3
Q ss_pred CCcCcccCCCC-CCCCCeEEccccCcccccccccCc
Q 001260 702 PRSCDICRRSE-TILNPILICSGCKVAVHLDCYRNA 736 (1113)
Q Consensus 702 ~~~CsVC~~~E-~~~N~IV~Cd~C~laVHq~CYGi~ 736 (1113)
...|++|...= +...+-+.|..|++.+|..|....
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 45799999753 246789999999999999998643
No 46
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=71.70 E-value=1.5 Score=54.14 Aligned_cols=47 Identities=28% Similarity=0.629 Sum_probs=34.4
Q ss_pred CcCcccCCCCC-CCCCeEEccccCcccccccccCcc---cCCCcccccccc
Q 001260 703 RSCDICRRSET-ILNPILICSGCKVAVHLDCYRNAK---ESTGPWYCELCE 749 (1113)
Q Consensus 703 ~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi~~---ipeg~WlCd~C~ 749 (1113)
+.|-+|..... ..+.|+.|..|+..+|.+|..+.. +..+-|.|..|.
T Consensus 19 ~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~cr 69 (694)
T KOG4443|consen 19 LMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCR 69 (694)
T ss_pred hhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCce
Confidence 45677765432 468899999999999999987431 223449999996
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=71.61 E-value=2.6 Score=41.86 Aligned_cols=48 Identities=25% Similarity=0.645 Sum_probs=36.2
Q ss_pred CcCcccCCCC-CCCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 703 RSCDICRRSE-TILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 703 ~~CsVC~~~E-~~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
..|..|...- ...|.-..|..|...|=+.| |+....+..|+|..|...
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 4699998743 34677799999999999999 444445788999999864
No 48
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=69.69 E-value=2.1 Score=48.42 Aligned_cols=47 Identities=28% Similarity=0.616 Sum_probs=34.5
Q ss_pred cccccccCcCCceeecCCCCcc-cccchhhhhhcCceEEEeeCCCceeeeecCCCCCh
Q 001260 825 DVCCICRHKHGICIKCNYGNCQ-TTFHPTCARSAGFYLNVKSTGGNFQHKAYCEKHSL 881 (1113)
Q Consensus 825 ~~C~iC~~~~GA~IqCs~~~C~-~~FHvtCA~~aG~~~~~k~~~g~~~~~iyC~kHs~ 881 (1113)
..|..+...+|.+|.|...+|. .|||..|. |+.. .+.|.| ||+.-..
T Consensus 220 ~yC~Cnqvsyg~Mi~CDn~~C~~eWFH~~CV---GL~~---~PkgkW----yC~~C~~ 267 (274)
T KOG1973|consen 220 TYCICNQVSYGKMIGCDNPGCPIEWFHFTCV---GLKT---KPKGKW----YCPRCKA 267 (274)
T ss_pred EEEEecccccccccccCCCCCCcceEEEecc---cccc---CCCCcc----cchhhhh
Confidence 4555555569999999999999 99999996 4433 334567 9986554
No 49
>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=69.08 E-value=2.8 Score=34.46 Aligned_cols=34 Identities=41% Similarity=0.812 Sum_probs=26.8
Q ss_pred CCcCcccCCCCC-CCCCeEEccccCcccccccccC
Q 001260 702 PRSCDICRRSET-ILNPILICSGCKVAVHLDCYRN 735 (1113)
Q Consensus 702 ~~~CsVC~~~E~-~~N~IV~Cd~C~laVHq~CYGi 735 (1113)
..+|++|...=. ...+-+.|+.|++.||..|...
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 467999987432 2357889999999999999853
No 50
>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=68.07 E-value=3.1 Score=43.25 Aligned_cols=27 Identities=37% Similarity=0.808 Sum_probs=22.3
Q ss_pred ccccccccCc--ccCCCcccccccccccc
Q 001260 727 AVHLDCYRNA--KESTGPWYCELCEELLS 753 (1113)
Q Consensus 727 aVHq~CYGi~--~ipeg~WlCd~C~~~~~ 753 (1113)
.+|..|...+ .+|+|+|+|..|.....
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~ 29 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKS 29 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCC
Confidence 4799999865 58899999999997643
No 51
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=66.19 E-value=8.5 Score=30.10 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=36.2
Q ss_pred HHHHhhhCCcchhhhhhhhcCChhhhhhccccc-cccchhhHHHHHHhh
Q 001260 225 LKKLIDRGKVNVKDIASDIGISPDLLKTTLADG-TFASDLQCKLVKWLS 272 (1113)
Q Consensus 225 lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~~-~~~~~~~~k~~~wl~ 272 (1113)
++++++..+++..++|..+|+++.+|..-+... ....+...+|..+|.
T Consensus 2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~ 50 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALG 50 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhC
Confidence 456677888999999999999999998776533 335566667776663
No 52
>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=65.79 E-value=2.9 Score=33.97 Aligned_cols=33 Identities=39% Similarity=0.632 Sum_probs=25.3
Q ss_pred CCcCcccCCCCCCCCCeEEccccCccccccccc
Q 001260 702 PRSCDICRRSETILNPILICSGCKVAVHLDCYR 734 (1113)
Q Consensus 702 ~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYG 734 (1113)
..+|.+|...-....+-+.|..|++.||..|..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~ 43 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAE 43 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHh
Confidence 467999997532111578999999999999975
No 53
>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=65.53 E-value=10 Score=33.95 Aligned_cols=54 Identities=19% Similarity=0.330 Sum_probs=41.4
Q ss_pred cchHHHHH-HHhhhCCcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhh
Q 001260 219 LNFTLILK-KLIDRGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLS 272 (1113)
Q Consensus 219 ~~~~~~lk-kli~~gkv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~ 272 (1113)
......++ .|++...++..++|..+|||..+|-.-+. ...+.++.-.+|.+.|.
T Consensus 3 ~~~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~ 58 (78)
T TIGR02607 3 AHPGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALG 58 (78)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcC
Confidence 34455677 89999999999999999999999988776 33455666666666554
No 54
>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=64.74 E-value=7.3 Score=32.25 Aligned_cols=31 Identities=26% Similarity=0.429 Sum_probs=22.8
Q ss_pred HHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 223 ~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
--+++|.+.| .++.+||.++|||..+|---|
T Consensus 12 ~~i~~l~~~G-~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 12 EEIKELYAEG-MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHTT---HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHH
Confidence 4455688899 999999999999998886554
No 55
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=62.71 E-value=8.4 Score=33.24 Aligned_cols=48 Identities=31% Similarity=0.349 Sum_probs=31.8
Q ss_pred HHHHhhhCCcchhhhhhhhcCChhhhhhccccc--cccchhhHHHHHHhh
Q 001260 225 LKKLIDRGKVNVKDIASDIGISPDLLKTTLADG--TFASDLQCKLVKWLS 272 (1113)
Q Consensus 225 lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~~--~~~~~~~~k~~~wl~ 272 (1113)
|++|+++..++..++|..+|||..+|..-+... .+.-+.-.+|-+.|.
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 678888888899999999999999998887743 455555556665553
No 56
>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=62.05 E-value=3.6 Score=31.30 Aligned_cols=28 Identities=29% Similarity=0.710 Sum_probs=12.2
Q ss_pred cCcccCCCCCCCCCeEEccccCccccccc
Q 001260 704 SCDICRRSETILNPILICSGCKVAVHLDC 732 (1113)
Q Consensus 704 ~CsVC~~~E~~~N~IV~Cd~C~laVHq~C 732 (1113)
.|++|...-. ++....|..|+..+|..|
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 5999987533 247889999999999988
No 57
>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=59.13 E-value=13 Score=31.04 Aligned_cols=48 Identities=23% Similarity=0.264 Sum_probs=36.9
Q ss_pred HHHHhhhCCcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhh
Q 001260 225 LKKLIDRGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLS 272 (1113)
Q Consensus 225 lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~ 272 (1113)
||++.++-..|.+|+|..+|+|+.+|..-+. ......+.-.+|-+-|.
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 5778888999999999999999999998876 45566666677766654
No 58
>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=57.30 E-value=9.5 Score=31.49 Aligned_cols=32 Identities=22% Similarity=0.506 Sum_probs=25.2
Q ss_pred HHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 223 ~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
-||+-|.+-|..+..+||.++|+|+.++..-+
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 47788888999999999999999999987653
No 59
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=55.78 E-value=5.3 Score=47.56 Aligned_cols=154 Identities=19% Similarity=0.415 Sum_probs=86.3
Q ss_pred cCcccCCCCCCCCCeEEccccCcccccccccC----------c-ccCCCccccccccccccCCCCCCCCCCccCCCcccc
Q 001260 704 SCDICRRSETILNPILICSGCKVAVHLDCYRN----------A-KESTGPWYCELCEELLSSRSSGAPSVNFWEKPYFVA 772 (1113)
Q Consensus 704 ~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi----------~-~ipeg~WlCd~C~~~~~~~~s~~~~vn~~~kp~~~~ 772 (1113)
.|.-|...- ..+-.-|.-=+..+|..|+-- . ..-++.-+|+.|-... .-
T Consensus 276 iC~~C~K~V--~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t------------------le 335 (468)
T KOG1701|consen 276 ICAFCHKTV--SGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT------------------LE 335 (468)
T ss_pred hhhhcCCcc--cCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH------------------HH
Confidence 688887632 122233444455667766621 1 1236677788775431 44
Q ss_pred ccccCCCCC-Cccee-c----CCCcceecccccccccceecCCccccccCccccCCC-CcccccccCc----C----Cce
Q 001260 773 ECSLCGGTT-GAFRK-S----ANGQWVHAFCAEWVFESTFRRGQVNPVAGMEAFPKG-IDVCCICRHK----H----GIC 837 (1113)
Q Consensus 773 ~C~LCp~~g-GALKr-T----~~g~WVHV~CALW~PEv~f~n~~lepVegie~I~k~-r~~C~iC~~~----~----GA~ 837 (1113)
+|..|...- ..+.+ + --+-|+=|+|+--+..+-|.-+.-+.|.=+...-+. .-+|++|+.. . -.-
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 788887521 11111 1 123455566776777777764444444444444333 5789999984 1 233
Q ss_pred eecCCCCcccccchhhhhhcCceEEEe-eCCCc----eeeeecCCCCCh
Q 001260 838 IKCNYGNCQTTFHPTCARSAGFYLNVK-STGGN----FQHKAYCEKHSL 881 (1113)
Q Consensus 838 IqCs~~~C~~~FHvtCA~~aG~~~~~k-~~~g~----~~~~iyC~kHs~ 881 (1113)
|-|. .+.||+.|-+-..|.|.+. ..+++ +.-.++|+.-..
T Consensus 416 vvam----dr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~ 460 (468)
T KOG1701|consen 416 VVAM----DRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHL 460 (468)
T ss_pred EEEc----cccccccceehhhcCccccccCCCCcceeccCceeechhhh
Confidence 3454 4789999998887777654 22221 344678876443
No 60
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=53.80 E-value=11 Score=40.88 Aligned_cols=43 Identities=26% Similarity=0.715 Sum_probs=33.8
Q ss_pred CCcCcccCCCCC----CCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 702 PRSCDICRRSET----ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 702 ~~~CsVC~~~E~----~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
...|-+|.+.+. ..+..+.|..|+..+|+.|+.- --|.+|.-.
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~-------~~CpkC~R~ 198 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK-------KSCPKCARR 198 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC-------CCCCCcHhH
Confidence 467999998763 2457889999999999999972 129999754
No 61
>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=53.17 E-value=11 Score=31.10 Aligned_cols=33 Identities=27% Similarity=0.429 Sum_probs=27.1
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
--||.-|.+.|.++.++||..+|+|..++...|
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 457888999999999999999999999887664
No 62
>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=51.10 E-value=23 Score=27.76 Aligned_cols=48 Identities=21% Similarity=0.219 Sum_probs=36.3
Q ss_pred HHHHHhhhCCcchhhhhhhhcCChhhhhhccccc-cccchhhHHHHHHh
Q 001260 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLADG-TFASDLQCKLVKWL 271 (1113)
Q Consensus 224 ~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~~-~~~~~~~~k~~~wl 271 (1113)
.++..+++.+++..++|..+|+++.+|..-+... .+.++...+|...|
T Consensus 3 ~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~ 51 (58)
T cd00093 3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 4566677788999999999999999998776533 55566666666655
No 63
>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=49.95 E-value=12 Score=33.16 Aligned_cols=33 Identities=24% Similarity=0.452 Sum_probs=29.9
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
+-|+.-|+..|.+++.|||.++||+..++...|
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L 43 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGISRSTVYRAL 43 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 567888999999999999999999999988775
No 64
>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=48.99 E-value=10 Score=34.00 Aligned_cols=22 Identities=36% Similarity=0.755 Sum_probs=19.8
Q ss_pred hCCcchhhhhhhhcCChhhhhh
Q 001260 231 RGKVNVKDIASDIGISPDLLKT 252 (1113)
Q Consensus 231 ~gkv~~~~~a~~~g~s~~~~~a 252 (1113)
.|++..+|||.++|+|+.+|..
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHH
Confidence 6899999999999999988764
No 65
>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=48.90 E-value=13 Score=28.40 Aligned_cols=27 Identities=37% Similarity=0.898 Sum_probs=21.3
Q ss_pred cCcccCCCCCCCCC-eEEccccCccccccc
Q 001260 704 SCDICRRSETILNP-ILICSGCKVAVHLDC 732 (1113)
Q Consensus 704 ~CsVC~~~E~~~N~-IV~Cd~C~laVHq~C 732 (1113)
.|+||++.-. +. .-.|..|...+|..|
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 4999976322 33 789999999999988
No 66
>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=48.02 E-value=13 Score=44.70 Aligned_cols=47 Identities=26% Similarity=0.523 Sum_probs=33.1
Q ss_pred cCcccCCCCCCCC--CeEEccccCcccccccc--------cCcc-----cCCCccccccccc
Q 001260 704 SCDICRRSETILN--PILICSGCKVAVHLDCY--------RNAK-----ESTGPWYCELCEE 750 (1113)
Q Consensus 704 ~CsVC~~~E~~~N--~IV~Cd~C~laVHq~CY--------Gi~~-----ipeg~WlCd~C~~ 750 (1113)
.|.||...+.+.| .-|.||-|+...|..|- |+.. ..++.++|..|-.
T Consensus 130 ~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~ 191 (446)
T PF07227_consen 130 MCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGK 191 (446)
T ss_pred CccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCC
Confidence 4778887765444 57899999999999995 1111 1255688888854
No 67
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=47.37 E-value=17 Score=30.29 Aligned_cols=31 Identities=29% Similarity=0.460 Sum_probs=25.8
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
..|++.|.+. .++++||.+.|+|.++|..-+
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 5677777755 899999999999999997654
No 68
>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=46.79 E-value=33 Score=28.40 Aligned_cols=36 Identities=8% Similarity=0.169 Sum_probs=31.7
Q ss_pred chHHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 220 ~~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
.|+..|+++.++-..+..++|..+|+|+.+|..-..
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 367789999999999999999999999998887764
No 69
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=46.61 E-value=32 Score=44.02 Aligned_cols=49 Identities=24% Similarity=0.542 Sum_probs=34.5
Q ss_pred CcccccccCc--CCceeecCCCCcccc-cchhhhhhcCceEEEeeCCCceeeeecCCCCChh
Q 001260 824 IDVCCICRHK--HGICIKCNYGNCQTT-FHPTCARSAGFYLNVKSTGGNFQHKAYCEKHSLE 882 (1113)
Q Consensus 824 r~~C~iC~~~--~GA~IqCs~~~C~~~-FHvtCA~~aG~~~~~k~~~g~~~~~iyC~kHs~~ 882 (1113)
...|.||... .-.+|.|. .|... ||..|.-..-+.+-+ +.| ||..-...
T Consensus 215 ~~~C~IC~~~DpEdVLLLCD--sCN~~~YH~YCLDPdl~eiP~----~eW----YC~NC~dL 266 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCD--SCNKVYYHVYCLDPDLSESPV----NEW----YCTNCSLL 266 (1134)
T ss_pred cccceeeccCChHHhheeec--ccccceeeccccCcccccccc----cce----ecCcchhh
Confidence 4789999985 56788999 99987 999997554322211 223 88877654
No 70
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=46.08 E-value=64 Score=29.66 Aligned_cols=60 Identities=32% Similarity=0.233 Sum_probs=47.2
Q ss_pred chhhHHHHHHHHH--hhhhhhhhhhhHHHHHHHHHHhhHHHHhhhhcchhHHHHHHHHHHHHHHHHccC
Q 001260 542 EVEGEIIYFQHRL--LGNAFSRKRLADNLVCKAVKTLNQEIDVARGRRWDAVLVNQYLCELREAKKQGR 608 (1113)
Q Consensus 542 e~e~E~~~~q~~l--l~~~~~~~~~~~~lv~eV~k~l~~e~~~~~~r~~d~~~~nq~L~~~reakkq~~ 608 (1113)
.+|.|+..||.+| +.+-.+ .-....+.|..|-+.+-.+--+...-+.-|++..++.++.-
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-------VHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKEL 63 (69)
T ss_pred hHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999998 443332 23355688999999999888788889999999999987763
No 71
>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=44.44 E-value=13 Score=28.25 Aligned_cols=27 Identities=26% Similarity=0.717 Sum_probs=12.3
Q ss_pred ccccccCcCC--ceeecCCCCcccccchhhh
Q 001260 826 VCCICRHKHG--ICIKCNYGNCQTTFHPTCA 854 (1113)
Q Consensus 826 ~C~iC~~~~G--A~IqCs~~~C~~~FHvtCA 854 (1113)
.|..|+.+.+ ..-.|. .|...+|..||
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 6899998754 466798 99999999997
No 72
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=43.92 E-value=13 Score=41.83 Aligned_cols=46 Identities=28% Similarity=0.821 Sum_probs=33.2
Q ss_pred CCcccccccC-cCCceeecCCCCcc-cccchhhhhhcCceEEEeeCCCceeeeecCCC
Q 001260 823 GIDVCCICRH-KHGICIKCNYGNCQ-TTFHPTCARSAGFYLNVKSTGGNFQHKAYCEK 878 (1113)
Q Consensus 823 ~r~~C~iC~~-~~GA~IqCs~~~C~-~~FHvtCA~~aG~~~~~k~~~g~~~~~iyC~k 878 (1113)
+...-++|++ ..|-+|.|...+|. .|||..|.=..+ .+.|.| ||+.
T Consensus 219 ~e~lYCfCqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~------pPKG~W----YC~e 266 (271)
T COG5034 219 GEELYCFCQQVSYGQMVACDNANCKREWFHLECVGLKE------PPKGKW----YCPE 266 (271)
T ss_pred CceeEEEecccccccceecCCCCCchhheeccccccCC------CCCCcE----eCHH
Confidence 3445557776 58999999999998 799999963222 334566 8864
No 73
>PHA02591 hypothetical protein; Provisional
Probab=43.07 E-value=25 Score=33.20 Aligned_cols=37 Identities=24% Similarity=0.371 Sum_probs=31.3
Q ss_pred CCcchHHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 217 DALNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 217 ~~~~~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
+-.|+--+-++|.++| .++.+||..+|++-+++..-|
T Consensus 44 ~~dd~~~vA~eL~eqG-lSqeqIA~~LGVsqetVrKYL 80 (83)
T PHA02591 44 SEDDLISVTHELARKG-FTVEKIASLLGVSVRKVRRYL 80 (83)
T ss_pred ccchHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Confidence 3457788889999999 699999999999999887654
No 74
>PRK09492 treR trehalose repressor; Provisional
Probab=42.97 E-value=21 Score=39.65 Aligned_cols=51 Identities=16% Similarity=0.291 Sum_probs=44.7
Q ss_pred hCCcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhhhcccccccc
Q 001260 231 RGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLL 281 (1113)
Q Consensus 231 ~gkv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~~~~~~~~~~ 281 (1113)
+.|++++|||.+.|+|.-+|--+|+ ....++..+.||.+-.+.--|.+...
T Consensus 2 ~~~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~ 53 (315)
T PRK09492 2 QNKLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSPSKS 53 (315)
T ss_pred CCCCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCcCHH
Confidence 3589999999999999999999998 46789999999999998888877543
No 75
>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=42.89 E-value=34 Score=24.29 Aligned_cols=30 Identities=27% Similarity=0.434 Sum_probs=23.1
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhh
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKT 252 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a 252 (1113)
-..+.++++.|. ++++||.++|+|.-++-.
T Consensus 11 ~~~i~~~~~~~~-s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 11 IEEARRLLAAGE-SVAEIARRLGVSRSTLYR 40 (42)
T ss_pred HHHHHHHHHcCC-CHHHHHHHHCCCHHHHHH
Confidence 345556677776 999999999999887643
No 76
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=42.81 E-value=19 Score=32.38 Aligned_cols=33 Identities=21% Similarity=0.366 Sum_probs=29.4
Q ss_pred HHHHHHHhhhCC--cchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGK--VNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gk--v~~~~~a~~~g~s~~~~~a~l 254 (1113)
.-||.-|-++|. +++++||.++||+..++...|
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 568888888988 999999999999999888776
No 77
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=42.20 E-value=22 Score=40.03 Aligned_cols=51 Identities=14% Similarity=0.269 Sum_probs=44.9
Q ss_pred hCCcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhhhcccccccc
Q 001260 231 RGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLL 281 (1113)
Q Consensus 231 ~gkv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~~~~~~~~~~ 281 (1113)
..||+++|||.+.|+|.-+|-.+|+ ....++..+.||.+-.+..=|.+...
T Consensus 4 ~~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~~~ 55 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQ 55 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcCHH
Confidence 3579999999999999999999999 56689999999999999988877544
No 78
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=42.01 E-value=16 Score=30.20 Aligned_cols=30 Identities=23% Similarity=0.552 Sum_probs=20.6
Q ss_pred HHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 224 ~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
.+..|.++| .|+.+||..+|.|+.+|-..|
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 466788888 899999999999999986553
No 79
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=41.34 E-value=16 Score=45.14 Aligned_cols=35 Identities=29% Similarity=0.655 Sum_probs=26.5
Q ss_pred CCCCcCcccCCCC-CCCCCeEEccccCccccccccc
Q 001260 700 EHPRSCDICRRSE-TILNPILICSGCKVAVHLDCYR 734 (1113)
Q Consensus 700 e~~~~CsVC~~~E-~~~N~IV~Cd~C~laVHq~CYG 734 (1113)
.-..+|+-|+..= ..--+-|.|.+|++.+|+.|--
T Consensus 154 ~~PtFCD~CGEmL~GLvrQGlKC~gCglNyHKRCa~ 189 (888)
T KOG4236|consen 154 KAPTFCDFCGEMLFGLVRQGLKCEGCGLNYHKRCAF 189 (888)
T ss_pred cCchHHHHHHHHHHHHHHccccccCCCCcHhhhhhh
Confidence 3357899998642 1235668999999999999963
No 80
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=40.72 E-value=23 Score=39.87 Aligned_cols=51 Identities=16% Similarity=0.284 Sum_probs=45.4
Q ss_pred hCCcchhhhhhhhcCChhhhhhcccc-ccccchhhHHHHHHhhhcccccccc
Q 001260 231 RGKVNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWLSNHAYLGGLL 281 (1113)
Q Consensus 231 ~gkv~~~~~a~~~g~s~~~~~a~l~~-~~~~~~~~~k~~~wl~~~~~~~~~~ 281 (1113)
+++|+.+|||...|+|.-+|--+|+. ...++..+.||.+-.+..=|.+...
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~ 54 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNRA 54 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCccHH
Confidence 68899999999999999999999984 4589999999999999988876544
No 81
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=40.44 E-value=24 Score=28.62 Aligned_cols=32 Identities=34% Similarity=0.554 Sum_probs=28.0
Q ss_pred HHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 223 ~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
.+++.|.+.|.+++.++|..+|+|+.++...|
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l 35 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDL 35 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 47778888889999999999999999987765
No 82
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.53 E-value=24 Score=31.07 Aligned_cols=36 Identities=28% Similarity=0.623 Sum_probs=31.5
Q ss_pred cccccccCc---CCceeecCCCCcccccchhhhhhcCceEE
Q 001260 825 DVCCICRHK---HGICIKCNYGNCQTTFHPTCARSAGFYLN 862 (1113)
Q Consensus 825 ~~C~iC~~~---~GA~IqCs~~~C~~~FHvtCA~~aG~~~~ 862 (1113)
.+|.+|+.+ .+..|.|- .|.+.||-.|....|-.+.
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp--~CgapyHR~C~~~~g~C~~ 44 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCP--ECGAPYHRDCWEKAGGCIN 44 (54)
T ss_pred ccChhhCCcccCCCCEEECC--CCCCcccHHHHhhCCceEe
Confidence 589999985 68899999 9999999999988887664
No 83
>PF13518 HTH_28: Helix-turn-helix domain
Probab=38.15 E-value=22 Score=29.23 Aligned_cols=28 Identities=29% Similarity=0.508 Sum_probs=21.2
Q ss_pred HHHHHhhhCCcchhhhhhhhcCChhhhhhc
Q 001260 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTT 253 (1113)
Q Consensus 224 ~lkkli~~gkv~~~~~a~~~g~s~~~~~a~ 253 (1113)
+++... +|+ ++.++|.++|||+.+|..-
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 344444 787 9999999999999877543
No 84
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.76 E-value=14 Score=37.81 Aligned_cols=49 Identities=22% Similarity=0.510 Sum_probs=35.0
Q ss_pred CCcCcccCCCCCCCCCeEEccccCcccccccccCcccC--CCccccccccc
Q 001260 702 PRSCDICRRSETILNPILICSGCKVAVHLDCYRNAKES--TGPWYCELCEE 750 (1113)
Q Consensus 702 ~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~~ip--eg~WlCd~C~~ 750 (1113)
+..|-||......++---.|.-|++.+-..|-|-.... ..-|.|.+|.-
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 56799999865444444578888888888887755443 34599999965
No 85
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=37.62 E-value=33 Score=30.83 Aligned_cols=47 Identities=19% Similarity=0.338 Sum_probs=40.4
Q ss_pred cchhhhhhhhcCChhhhhhcccc-ccccchhhHHHHHHhhhccccccc
Q 001260 234 VNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWLSNHAYLGGL 280 (1113)
Q Consensus 234 v~~~~~a~~~g~s~~~~~a~l~~-~~~~~~~~~k~~~wl~~~~~~~~~ 280 (1113)
++..|||...|+|..+|--.|+. ...+|....+|.+-++..-|.+..
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 46789999999999999999985 456789999999999999996553
No 86
>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=37.04 E-value=25 Score=33.06 Aligned_cols=34 Identities=24% Similarity=0.389 Sum_probs=26.6
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
-++|+-|.+=+-|++.++|.++|.+-|.|+++|+
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~ 60 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALA 60 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 5677888877779999999999999999999986
No 87
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=36.07 E-value=13 Score=35.15 Aligned_cols=32 Identities=41% Similarity=0.997 Sum_probs=26.6
Q ss_pred ccccccccc-cCceeeCCC------------CCCCcccchhhhhh
Q 001260 57 LVCNICRVK-CGACVRCSH------------GTCRTSFHPICARE 88 (1113)
Q Consensus 57 LkC~iC~~k-~GAcIqCs~------------~~C~~sFHvtCA~~ 88 (1113)
-.|.||+.. .|.|++|.. |.|.-+||.-|-.+
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 379999976 799999987 56889999999744
No 88
>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=35.80 E-value=21 Score=31.22 Aligned_cols=22 Identities=23% Similarity=0.604 Sum_probs=19.4
Q ss_pred CcchhhhhhhhcCChhhhhhcc
Q 001260 233 KVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 233 kv~~~~~a~~~g~s~~~~~a~l 254 (1113)
+++++|||.++|||+-++.--|
T Consensus 23 ~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHH
Confidence 7999999999999998887655
No 89
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=35.28 E-value=20 Score=40.76 Aligned_cols=48 Identities=25% Similarity=0.597 Sum_probs=37.4
Q ss_pred CcCcccCCCC--C----CCCCeEEccccCcccccccccCcc-----cCCCccccccccc
Q 001260 703 RSCDICRRSE--T----ILNPILICSGCKVAVHLDCYRNAK-----ESTGPWYCELCEE 750 (1113)
Q Consensus 703 ~~CsVC~~~E--~----~~N~IV~Cd~C~laVHq~CYGi~~-----ipeg~WlCd~C~~ 750 (1113)
..|+.|.... . ....||.|..|+.+-|.+|.-... +....|-|.-|++
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~ 283 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKY 283 (336)
T ss_pred cccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecce
Confidence 5799999642 1 245799999999999999996432 3467899999986
No 90
>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=35.23 E-value=30 Score=32.74 Aligned_cols=30 Identities=23% Similarity=0.656 Sum_probs=20.5
Q ss_pred CCcCcccCCCCCCCCCeEEccccCcccccccc
Q 001260 702 PRSCDICRRSETILNPILICSGCKVAVHLDCY 733 (1113)
Q Consensus 702 ~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CY 733 (1113)
...|.||...= +|..+.---|+..||..|+
T Consensus 78 ~~~C~vC~k~l--~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPL--GNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcC--CCceEEEeCCCeEEecccc
Confidence 35699999743 3343333356699999996
No 91
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=35.03 E-value=8.8 Score=36.01 Aligned_cols=50 Identities=24% Similarity=0.551 Sum_probs=24.1
Q ss_pred CCCcCcccCCCC--C-CCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 701 HPRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 701 ~~~~CsVC~~~E--~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
+...|.||++.- + .++..|-|..|+..|-+.||--. ..+|.-.|..|...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE-rkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE-RKEGNQVCPQCKTR 60 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH-HHTS-SB-TTT--B
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH-hhcCcccccccCCC
Confidence 346799999853 2 47788999999999999999522 34777889999753
No 92
>PHA01976 helix-turn-helix protein
Probab=34.93 E-value=66 Score=28.01 Aligned_cols=52 Identities=17% Similarity=0.164 Sum_probs=37.0
Q ss_pred chHHHHHHHhhhCCcchhhhhhhhcCChhhhhhcccc-ccccchhhHHHHHHh
Q 001260 220 NFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWL 271 (1113)
Q Consensus 220 ~~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~-~~~~~~~~~k~~~wl 271 (1113)
+|+.-||+|-++...+.+++|..+|+|+.+|-.-... .....+.-.||.+.|
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 4677789999999999999999999999888775432 222333334555444
No 93
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=34.89 E-value=33 Score=38.58 Aligned_cols=49 Identities=18% Similarity=0.284 Sum_probs=43.9
Q ss_pred CcchhhhhhhhcCChhhhhhcccccc---ccchhhHHHHHHhhhcccccccc
Q 001260 233 KVNVKDIASDIGISPDLLKTTLADGT---FASDLQCKLVKWLSNHAYLGGLL 281 (1113)
Q Consensus 233 kv~~~~~a~~~g~s~~~~~a~l~~~~---~~~~~~~k~~~wl~~~~~~~~~~ 281 (1113)
+++++|||...|+|.-++--+|+... .++..+.||.+-.+..-|.+...
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 47999999999999999999999553 88999999999999999987753
No 94
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=34.73 E-value=92 Score=40.72 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=21.4
Q ss_pred CCCCCCCcCcccCCCCC-C----CCCeEEccccCc
Q 001260 697 FSKEHPRSCDICRRSET-I----LNPILICSGCKV 726 (1113)
Q Consensus 697 ~~ke~~~~CsVC~~~E~-~----~N~IV~Cd~C~l 726 (1113)
...+....|+||+++-. . .+.-.|+.+|++
T Consensus 463 l~ee~gl~C~ICrEGy~~~p~~~lGiY~f~kr~~l 497 (802)
T PF13764_consen 463 LEEEDGLTCCICREGYKFRPDEVLGIYAFSKRVNL 497 (802)
T ss_pred ccccCCCeEEEcCCccccCCccceeeEEEeecccc
Confidence 34577899999998652 2 344568888988
No 95
>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=34.70 E-value=49 Score=28.58 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=31.4
Q ss_pred HHHHHhhhCCcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHh
Q 001260 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWL 271 (1113)
Q Consensus 224 ~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl 271 (1113)
-||+|.+.-..+.+++|..+|+++-.|..-.. ...+.++.-.+|.+-|
T Consensus 3 ~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~ 51 (64)
T PF12844_consen 3 RLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEAL 51 (64)
T ss_dssp HHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHh
Confidence 47889999999999999999999887776655 3344445545554444
No 96
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=34.46 E-value=30 Score=38.64 Aligned_cols=34 Identities=26% Similarity=0.395 Sum_probs=31.0
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
..|+..|-..|+|+|+|+|..+|+|++++..=|.
T Consensus 10 ~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~ 43 (252)
T PRK10681 10 GQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLN 43 (252)
T ss_pred HHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHH
Confidence 5688888899999999999999999999998874
No 97
>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=34.45 E-value=30 Score=29.16 Aligned_cols=32 Identities=25% Similarity=0.554 Sum_probs=25.3
Q ss_pred HHHHHHhhhC-CcchhhhhhhhcCChhhhhhcc
Q 001260 223 LILKKLIDRG-KVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 223 ~~lkkli~~g-kv~~~~~a~~~g~s~~~~~a~l 254 (1113)
.||+-|...+ .|+.+++|.++|+|.-++.-.|
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 4677775554 4999999999999999998876
No 98
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=33.68 E-value=21 Score=32.59 Aligned_cols=32 Identities=28% Similarity=0.593 Sum_probs=12.4
Q ss_pred CcCcccCCCCC--CCCCeEEcc--ccCccccccccc
Q 001260 703 RSCDICRRSET--ILNPILICS--GCKVAVHLDCYR 734 (1113)
Q Consensus 703 ~~CsVC~~~E~--~~N~IV~Cd--~C~laVHq~CYG 734 (1113)
..|.||..... ..-+.+.|+ .|+..+|..|.-
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 56999997543 223568998 899999999984
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=33.31 E-value=36 Score=38.06 Aligned_cols=49 Identities=14% Similarity=0.270 Sum_probs=42.9
Q ss_pred CcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhhhcccccccc
Q 001260 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLL 281 (1113)
Q Consensus 233 kv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~~~~~~~~~~ 281 (1113)
||+++|||.+.|+|.-+|--+|+ ....++..+.||.+-.+..-|.+...
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~~ 50 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPSKS 50 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcCHH
Confidence 78999999999999999999998 44578899999999999888876544
No 100
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=33.19 E-value=26 Score=33.00 Aligned_cols=27 Identities=19% Similarity=0.422 Sum_probs=25.1
Q ss_pred HhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 228 LIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 228 li~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
|-++|.++.+++|..++++++.|+|-|
T Consensus 11 l~~~gr~s~~~Ls~~~~~p~~~VeaML 37 (78)
T PRK15431 11 LALRGRMEAAQISQTLNTPQPMINAML 37 (78)
T ss_pred HHHcCcccHHHHHHHHCcCHHHHHHHH
Confidence 456999999999999999999999997
No 101
>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=33.09 E-value=32 Score=28.54 Aligned_cols=31 Identities=32% Similarity=0.572 Sum_probs=25.1
Q ss_pred HHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 223 ~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
-||+.|.+ |..++.|||.++|+|.-++---|
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 46777776 99999999999999998876543
No 102
>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=32.86 E-value=29 Score=26.62 Aligned_cols=27 Identities=41% Similarity=0.968 Sum_probs=21.7
Q ss_pred ccccccCc-CCc-eeecCCCCcccccchhhh
Q 001260 826 VCCICRHK-HGI-CIKCNYGNCQTTFHPTCA 854 (1113)
Q Consensus 826 ~C~iC~~~-~GA-~IqCs~~~C~~~FHvtCA 854 (1113)
.|.+|++. .|- .-.|. .|...+|+.||
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 58999986 455 66796 88899999997
No 103
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=32.48 E-value=23 Score=28.51 Aligned_cols=25 Identities=28% Similarity=0.541 Sum_probs=17.5
Q ss_pred hCCcchhhhhhhhcCChhhhhhccc
Q 001260 231 RGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 231 ~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
.-+.+|+|||...|+|+..+.....
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 4468999999999999988876643
No 104
>PRK09726 antitoxin HipB; Provisional
Probab=32.08 E-value=69 Score=30.03 Aligned_cols=58 Identities=12% Similarity=0.106 Sum_probs=43.6
Q ss_pred cchHHHHHHHhhhCCcchhhhhhhhcCChhhhhhcccc-ccccchhhHHHHHHhhhccc
Q 001260 219 LNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWLSNHAY 276 (1113)
Q Consensus 219 ~~~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~-~~~~~~~~~k~~~wl~~~~~ 276 (1113)
..++--||+|..+..++.+++|..+|||+.+|..-... .....+.-.+|.+.|.=.+.
T Consensus 11 ~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~ 69 (88)
T PRK09726 11 TQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69 (88)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcc
Confidence 35677899999999999999999999999999876653 23444555666666654444
No 105
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=30.56 E-value=15 Score=46.37 Aligned_cols=67 Identities=24% Similarity=0.350 Sum_probs=54.9
Q ss_pred CCCCCcHhhHhhcccCceeeccCCcccccccccCchhhcccccccccccccCceeeCCCCCCCcccchhhhhh
Q 001260 16 GGSMEFAHLFCSLLMPEVYIEDTMKVEPLMNVGGIKETRMKLVCNICRVKCGACVRCSHGTCRTSFHPICARE 88 (1113)
Q Consensus 16 ~G~~~WvHv~CALwiPEv~f~~~~~~epV~~I~~I~~~R~~LkC~iC~~k~GAcIqCs~~~C~~sFHvtCA~~ 88 (1113)
+++..-+|+.|.+|.+.++-..... +...++.+.+...|.+|+.+ |+=.+|-.+.|...||++||+.
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 4566889999999999887655332 34456778888999999986 9999999999999999999954
No 106
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=30.55 E-value=37 Score=38.03 Aligned_cols=33 Identities=33% Similarity=0.531 Sum_probs=30.1
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
..||+-|.++|+|+|+|+|..+|+|++++.-=|
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL 40 (253)
T COG1349 8 QKILELLKEKGKVSVEELAELFGVSEMTIRRDL 40 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhH
Confidence 568888889999999999999999999999865
No 107
>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=29.95 E-value=31 Score=28.70 Aligned_cols=30 Identities=20% Similarity=0.639 Sum_probs=16.4
Q ss_pred cccccCcCCceeecCCCCcccccchhhhhh
Q 001260 827 CCICRHKHGICIKCNYGNCQTTFHPTCARS 856 (1113)
Q Consensus 827 C~iC~~~~GA~IqCs~~~C~~~FHvtCA~~ 856 (1113)
|.+|+.-.-.-+.|...+|...+|..|+..
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 677887644456799999999999999864
No 108
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=29.68 E-value=21 Score=44.50 Aligned_cols=30 Identities=30% Similarity=0.765 Sum_probs=25.4
Q ss_pred cccccccccccCce---eeCCCCCCCcccchhhhhh
Q 001260 56 KLVCNICRVKCGAC---VRCSHGTCRTSFHPICARE 88 (1113)
Q Consensus 56 ~LkC~iC~~k~GAc---IqCs~~~C~~sFHvtCA~~ 88 (1113)
...|+.|+++ |.- |+|. .|.++||.+|--.
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 3489999986 888 8998 4999999999754
No 109
>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=29.58 E-value=18 Score=30.85 Aligned_cols=31 Identities=29% Similarity=0.685 Sum_probs=19.9
Q ss_pred cCcccCCCCCCCCCeE-Ecc--ccCccccccccc
Q 001260 704 SCDICRRSETILNPIL-ICS--GCKVAVHLDCYR 734 (1113)
Q Consensus 704 ~CsVC~~~E~~~N~IV-~Cd--~C~laVHq~CYG 734 (1113)
+|-||++.+..++.++ -|. |--..||+.|.-
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~ 34 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLE 34 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHH
Confidence 4899998444455554 333 233679999974
No 110
>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=29.51 E-value=50 Score=29.24 Aligned_cols=25 Identities=40% Similarity=0.682 Sum_probs=22.0
Q ss_pred hhCCcchhhhhhhhcCChhhhhhcc
Q 001260 230 DRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 230 ~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
+.+.|+.+|||..+|+||-|+...|
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 6889999999999999999998775
No 111
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=29.14 E-value=34 Score=43.69 Aligned_cols=31 Identities=29% Similarity=0.817 Sum_probs=24.2
Q ss_pred cccccccCcCCceeecCCCCcccccchhhhhhcC
Q 001260 825 DVCCICRHKHGICIKCNYGNCQTTFHPTCARSAG 858 (1113)
Q Consensus 825 ~~C~iC~~~~GA~IqCs~~~C~~~FHvtCA~~aG 858 (1113)
..|.+|... |..+-|. .|..+||..|....+
T Consensus 48 e~c~ic~~~-g~~l~c~--tC~~s~h~~cl~~pl 78 (696)
T KOG0383|consen 48 EACRICADG-GELLWCD--TCPASFHASCLGPPL 78 (696)
T ss_pred hhhhhhcCC-CcEEEec--cccHHHHHHccCCCC
Confidence 478889884 7777788 899999999974443
No 112
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.44 E-value=43 Score=35.91 Aligned_cols=35 Identities=31% Similarity=0.435 Sum_probs=31.4
Q ss_pred hHHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 221 ~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
--.||.-|+.+|-++..|+|.++||+..+|.-.|.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~ 58 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILY 58 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 36788899999999999999999999999988763
No 113
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=28.21 E-value=53 Score=27.30 Aligned_cols=20 Identities=20% Similarity=0.552 Sum_probs=18.8
Q ss_pred chhhhhhhhcCChhhhhhcc
Q 001260 235 NVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 235 ~~~~~a~~~g~s~~~~~a~l 254 (1113)
++.++|..+|+|..++..+|
T Consensus 22 s~~~la~~~~vs~~tv~~~l 41 (60)
T smart00345 22 SERELAAQLGVSRTTVREAL 41 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 89999999999999999886
No 114
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=27.45 E-value=52 Score=37.12 Aligned_cols=50 Identities=14% Similarity=0.207 Sum_probs=44.2
Q ss_pred CcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhhhccccccccc
Q 001260 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLK 282 (1113)
Q Consensus 233 kv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (1113)
+++.+|||.+.|+|.-++--+|+ ....++..+.||.+-.+..=|.+....
T Consensus 1 ~~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn~~a 51 (341)
T PRK10703 1 MATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVA 51 (341)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCHHH
Confidence 47899999999999999999998 456899999999999999999886543
No 115
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=27.41 E-value=51 Score=33.41 Aligned_cols=33 Identities=24% Similarity=0.395 Sum_probs=29.2
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
+++-+.||++ ..|..+||..+|||+-+|-.-|-
T Consensus 12 a~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 12 ALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred HHHHHHHHHc-CCcHHHHHHHhCCCHHHHHHHHc
Confidence 6788899999 79999999999999999877663
No 116
>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=27.25 E-value=38 Score=28.24 Aligned_cols=30 Identities=27% Similarity=0.709 Sum_probs=16.8
Q ss_pred ccccccccCceeeCCCCCCCcccchhhhhh
Q 001260 59 CNICRVKCGACVRCSHGTCRTSFHPICARE 88 (1113)
Q Consensus 59 C~iC~~k~GAcIqCs~~~C~~sFHvtCA~~ 88 (1113)
|.+|+.-.-.-+.|....|...+|..|+..
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 677886555568999899999999999954
No 117
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=27.05 E-value=35 Score=41.52 Aligned_cols=46 Identities=20% Similarity=0.432 Sum_probs=36.7
Q ss_pred cccCCCCCCCCCeEEccccCcccccccccCcccCC-Ccccccccccc
Q 001260 706 DICRRSETILNPILICSGCKVAVHLDCYRNAKEST-GPWYCELCEEL 751 (1113)
Q Consensus 706 sVC~~~E~~~N~IV~Cd~C~laVHq~CYGi~~ipe-g~WlCd~C~~~ 751 (1113)
++|...+...+.++.|+.|..--|..|+|+..... ....|..|...
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 46766544478899999999999999999876544 67889999764
No 118
>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=26.51 E-value=49 Score=29.47 Aligned_cols=35 Identities=26% Similarity=0.558 Sum_probs=29.1
Q ss_pred hHHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 221 ~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
++-|..-|+.+|..++.+|....++++..+..+|+
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 47788889999999999999999999999999974
No 119
>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=26.41 E-value=55 Score=34.86 Aligned_cols=52 Identities=19% Similarity=0.273 Sum_probs=42.9
Q ss_pred CCcchHHHHHHHhhhCCcchhhhhhhhcCChhhhhhccccccccchhhHHHH
Q 001260 217 DALNFTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLV 268 (1113)
Q Consensus 217 ~~~~~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~~~~~~~~~~k~~ 268 (1113)
...+-+...++|++.+..+.++||..+|+|...|...|.-..+.++++-.+-
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 4456688899999887889999999999999999999886667777766554
No 120
>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=26.36 E-value=47 Score=34.84 Aligned_cols=34 Identities=24% Similarity=0.373 Sum_probs=31.3
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
-.|+..|+..|.++..|||.++||+.-.|...|.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~ 50 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALY 50 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 6789999999999999999999999999998863
No 121
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=26.36 E-value=21 Score=42.91 Aligned_cols=33 Identities=24% Similarity=0.491 Sum_probs=27.5
Q ss_pred CCcCcccCCCC-CCCCCeEEccccCccccccccc
Q 001260 702 PRSCDICRRSE-TILNPILICSGCKVAVHLDCYR 734 (1113)
Q Consensus 702 ~~~CsVC~~~E-~~~N~IV~Cd~C~laVHq~CYG 734 (1113)
..+|+-|.+.- .-+-+-++|.-|...||+.|.-
T Consensus 56 PTfCsHCkDFiwGfgKQGfQCqvC~fvvHkrChe 89 (683)
T KOG0696|consen 56 PTFCSHCKDFIWGFGKQGFQCQVCCFVVHKRCHE 89 (683)
T ss_pred CchhhhhhhheeccccCceeeeEEeehhhhhhcc
Confidence 46899999854 2467889999999999999983
No 122
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=26.33 E-value=40 Score=44.91 Aligned_cols=50 Identities=26% Similarity=0.584 Sum_probs=39.5
Q ss_pred CCCcCcccCCCC--C-CCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 701 HPRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 701 ~~~~CsVC~~~E--~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
+...|.||++.- + +++..|-|.-|+..|-..||- .+..+|.=-|..|+.-
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 346899999852 2 467889999999999999993 3455888899999653
No 123
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=26.29 E-value=43 Score=36.29 Aligned_cols=34 Identities=26% Similarity=0.534 Sum_probs=30.5
Q ss_pred HHHHHHHhhhC--CcchhhhhhhhcCChhhhhhccc
Q 001260 222 TLILKKLIDRG--KVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 222 ~~~lkkli~~g--kv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
..+|+.|..+| .|+++++|...|+||.++..=|.
T Consensus 19 ~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~ 54 (213)
T PRK05472 19 YRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLS 54 (213)
T ss_pred HHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHH
Confidence 56899999999 99999999999999998887654
No 124
>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=26.21 E-value=1.1e+02 Score=29.93 Aligned_cols=53 Identities=13% Similarity=0.142 Sum_probs=39.4
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhccccccccchhhHHHHHHhhhc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNH 274 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~~~~~~~~~~k~~~wl~~~ 274 (1113)
..-||.+..+-.++-+++|..+|+|+.+|..-.......+.-..+|+++|..+
T Consensus 67 ~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~~~~l~~~l~~~ 119 (127)
T TIGR03830 67 PPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKH 119 (127)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHC
Confidence 44578888888999999999999999999877654443334456677776655
No 125
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=26.19 E-value=55 Score=37.10 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=43.0
Q ss_pred CcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhhhcccccccc
Q 001260 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLL 281 (1113)
Q Consensus 233 kv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~~~~~~~~~~ 281 (1113)
+++++|||.+.|+|.-+|--+|+ ....++..+-||++=.+..=|.+...
T Consensus 1 ~~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn~~ 50 (346)
T PRK10401 1 MITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNAN 50 (346)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
Confidence 47899999999999999999998 45688999999999999988876544
No 126
>PRK09526 lacI lac repressor; Reviewed
Probab=26.01 E-value=59 Score=36.62 Aligned_cols=52 Identities=15% Similarity=0.208 Sum_probs=45.0
Q ss_pred hCCcchhhhhhhhcCChhhhhhcccc-ccccchhhHHHHHHhhhccccccccc
Q 001260 231 RGKVNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWLSNHAYLGGLLK 282 (1113)
Q Consensus 231 ~gkv~~~~~a~~~g~s~~~~~a~l~~-~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (1113)
.++|+++|||.+.|+|.-+|--+|+. ...++..+.||.+-.+..=|.+....
T Consensus 3 ~~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a 55 (342)
T PRK09526 3 SKPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVA 55 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcCHHH
Confidence 36799999999999999999999984 45889999999999999888776544
No 127
>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=25.89 E-value=30 Score=32.72 Aligned_cols=30 Identities=20% Similarity=0.616 Sum_probs=17.5
Q ss_pred cccccccCcCCceeecCCCCcccccchhhhh
Q 001260 825 DVCCICRHKHGICIKCNYGNCQTTFHPTCAR 855 (1113)
Q Consensus 825 ~~C~iC~~~~GA~IqCs~~~C~~~FHvtCA~ 855 (1113)
..|.+|+++-|...---+ -|...||..|+.
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 568888877543222222 344777888764
No 128
>PLN02400 cellulose synthase
Probab=25.50 E-value=49 Score=44.15 Aligned_cols=49 Identities=24% Similarity=0.599 Sum_probs=39.1
Q ss_pred CCcCcccCCCC--C-CCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 702 PRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 702 ~~~CsVC~~~E--~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
...|.||++.- + +++..|-|.-|...|-.-||- .+..+|.=.|..|+-.
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE-YERkeGnq~CPQCkTr 87 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE-YERKDGTQCCPQCKTR 87 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhh-eecccCCccCcccCCc
Confidence 45899999852 2 467889999999999999993 3345888899999654
No 129
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=25.39 E-value=59 Score=36.82 Aligned_cols=50 Identities=12% Similarity=0.123 Sum_probs=44.4
Q ss_pred CcchhhhhhhhcCChhhhhhccc-cccccchhhHHHHHHhhhccccccccc
Q 001260 233 KVNVKDIASDIGISPDLLKTTLA-DGTFASDLQCKLVKWLSNHAYLGGLLK 282 (1113)
Q Consensus 233 kv~~~~~a~~~g~s~~~~~a~l~-~~~~~~~~~~k~~~wl~~~~~~~~~~~ 282 (1113)
+++++|||.+.|+|.-+|--.|+ ....++....||.+-.+..=|.+....
T Consensus 1 ~~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~~a 51 (343)
T PRK10727 1 MATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANA 51 (343)
T ss_pred CCCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCHHH
Confidence 47899999999999999999998 456999999999999999999876543
No 130
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=25.16 E-value=27 Score=40.97 Aligned_cols=35 Identities=26% Similarity=0.471 Sum_probs=28.3
Q ss_pred CCcCcccCCCC-CCCCCeEEccccCcccccccccCc
Q 001260 702 PRSCDICRRSE-TILNPILICSGCKVAVHLDCYRNA 736 (1113)
Q Consensus 702 ~~~CsVC~~~E-~~~N~IV~Cd~C~laVHq~CYGi~ 736 (1113)
...|.||.+.- ..+-+-..|-+|.+.||+.|.+..
T Consensus 141 r~~c~ic~d~iwglgrqgyrcinckl~vhkkch~~v 176 (593)
T KOG0695|consen 141 RAYCGICSDRIWGLGRQGYRCINCKLLVHKKCHGLV 176 (593)
T ss_pred ceeeeechhhhhhcccccceeecceeehhhhhcccc
Confidence 46799998753 246678899999999999999754
No 131
>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=24.76 E-value=58 Score=32.14 Aligned_cols=62 Identities=24% Similarity=0.599 Sum_probs=40.1
Q ss_pred CCCCCcCcccCCCCCCCCCeEEc------cccCcccccccccC-------c--c-cCCCccccccccccccCCCCCCCCC
Q 001260 699 KEHPRSCDICRRSETILNPILIC------SGCKVAVHLDCYRN-------A--K-ESTGPWYCELCEELLSSRSSGAPSV 762 (1113)
Q Consensus 699 ke~~~~CsVC~~~E~~~N~IV~C------d~C~laVHq~CYGi-------~--~-ipeg~WlCd~C~~~~~~~~s~~~~v 762 (1113)
......|-.|+.... +..+.| ..|...-=+.||+- . . ..+..|.|..|...
T Consensus 4 ~~~g~~CHqCrqKt~--~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi----------- 70 (105)
T PF10497_consen 4 SVNGKTCHQCRQKTL--DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI----------- 70 (105)
T ss_pred CCCCCCchhhcCCCC--CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCe-----------
Confidence 345678999988543 555678 77833333466642 1 1 23678999999873
Q ss_pred CccCCCccccccccCCCCCC
Q 001260 763 NFWEKPYFVAECSLCGGTTG 782 (1113)
Q Consensus 763 n~~~kp~~~~~C~LCp~~gG 782 (1113)
-.|.+|.+..|
T Consensus 71 ---------CnCs~Crrk~g 81 (105)
T PF10497_consen 71 ---------CNCSFCRRKRG 81 (105)
T ss_pred ---------eCCHhhhccCC
Confidence 46888877654
No 132
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=24.40 E-value=29 Score=32.93 Aligned_cols=33 Identities=42% Similarity=1.092 Sum_probs=26.3
Q ss_pred cccccccCc-CCceeecCC------------CCcccccchhhhhhc
Q 001260 825 DVCCICRHK-HGICIKCNY------------GNCQTTFHPTCARSA 857 (1113)
Q Consensus 825 ~~C~iC~~~-~GA~IqCs~------------~~C~~~FHvtCA~~a 857 (1113)
..|.||+.. .|.|++|.. +.|..+||.-|-.+-
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rW 66 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRW 66 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHH
Confidence 378899875 688888876 468899999998654
No 133
>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=24.39 E-value=28 Score=28.33 Aligned_cols=30 Identities=20% Similarity=0.458 Sum_probs=22.9
Q ss_pred cCcccCCCCCCCCCeEEccccCccccccccc
Q 001260 704 SCDICRRSETILNPILICSGCKVAVHLDCYR 734 (1113)
Q Consensus 704 ~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYG 734 (1113)
.|.||.+.-..++.++... |+-.+|..|..
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 5999998533356666666 99999999974
No 134
>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=23.91 E-value=34 Score=29.18 Aligned_cols=23 Identities=22% Similarity=0.521 Sum_probs=19.4
Q ss_pred CCcchhhhhhhhcCChhhhhhcc
Q 001260 232 GKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 232 gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
.+++|.|+|.++|+++..|-..|
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 46899999999999999998887
No 135
>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=23.60 E-value=58 Score=31.22 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=24.5
Q ss_pred HHHHHHhhhCCcchhhhhhhhcCChhhhhh
Q 001260 223 LILKKLIDRGKVNVKDIASDIGISPDLLKT 252 (1113)
Q Consensus 223 ~~lkkli~~gkv~~~~~a~~~g~s~~~~~a 252 (1113)
.-+.+|+++|+ +.++||..+|||.-++.-
T Consensus 41 ~~I~~ll~~G~-S~~eIA~~LgISrsTIyR 69 (88)
T TIGR02531 41 LQVAKMLKQGK-TYSDIEAETGASTATISR 69 (88)
T ss_pred HHHHHHHHCCC-CHHHHHHHHCcCHHHHHH
Confidence 44566788886 999999999999998875
No 136
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=23.40 E-value=53 Score=34.28 Aligned_cols=33 Identities=21% Similarity=0.433 Sum_probs=29.5
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
--||..|.+-|..+..+||.++|+|+-++..-+
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 567889999999999999999999999987764
No 137
>PLN02195 cellulose synthase A
Probab=22.83 E-value=54 Score=43.35 Aligned_cols=49 Identities=16% Similarity=0.384 Sum_probs=39.0
Q ss_pred CCcCcccCCCC--C-CCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 702 PRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 702 ~~~CsVC~~~E--~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
...|.||++.- + +++..|-|.-|+..|-+.||- .+..+|.=-|..|+.-
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 45799999842 2 467889999999999999993 3355888899999653
No 138
>PLN02436 cellulose synthase A
Probab=22.19 E-value=56 Score=43.56 Aligned_cols=49 Identities=27% Similarity=0.626 Sum_probs=38.6
Q ss_pred CCcCcccCCCC--C-CCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 702 PRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 702 ~~~CsVC~~~E--~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
...|.||++.- + +++..|-|.-|+..|-..||- .+..+|.=.|..|+..
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 35799999852 2 467788999999999999993 3345788899999653
No 139
>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=22.13 E-value=78 Score=27.67 Aligned_cols=33 Identities=21% Similarity=0.407 Sum_probs=28.5
Q ss_pred HHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 223 ~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
.+|.-|++.+..+++++|..+|+|.-+|..-+.
T Consensus 9 ~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 9 KLLELLLKNKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 467888999999999999999999999987764
No 140
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.10 E-value=70 Score=27.89 Aligned_cols=42 Identities=17% Similarity=0.306 Sum_probs=28.6
Q ss_pred CcchhhhhhhhcCChhhhhhccccc-cccchhh------HHHHHHhhhc
Q 001260 233 KVNVKDIASDIGISPDLLKTTLADG-TFASDLQ------CKLVKWLSNH 274 (1113)
Q Consensus 233 kv~~~~~a~~~g~s~~~~~a~l~~~-~~~~~~~------~k~~~wl~~~ 274 (1113)
++++++||.++|+|+..|...+... .++|.-- .+++.||.++
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~r~~~a~~~l~~~ 49 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDT 49 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHcC
Confidence 4689999999999999999887632 2333211 2456666655
No 141
>PRK10072 putative transcriptional regulator; Provisional
Probab=21.78 E-value=1.1e+02 Score=29.75 Aligned_cols=52 Identities=17% Similarity=0.256 Sum_probs=40.2
Q ss_pred HHHHHhhhCCcchhhhhhhhcCChhhhhhccccccccchhhHHHHHHhhhcc
Q 001260 224 ILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSNHA 275 (1113)
Q Consensus 224 ~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~~~~~~~~~~k~~~wl~~~~ 275 (1113)
=+|.|..+-+.+-+++|..+|||.-+|..-.........--..++++|+.+.
T Consensus 37 eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~Ll~~L~~~P 88 (96)
T PRK10072 37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANP 88 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhhCH
Confidence 3788888899999999999999998887776544443444467888887665
No 142
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=21.76 E-value=65 Score=36.11 Aligned_cols=33 Identities=24% Similarity=0.404 Sum_probs=29.4
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
..||..|-.+|+|+++|+|..+|+|++++..-|
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL 40 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQYFDTTGTTIRKDL 40 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHH
Confidence 467777888999999999999999999998876
No 143
>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=21.75 E-value=86 Score=28.95 Aligned_cols=42 Identities=29% Similarity=0.414 Sum_probs=32.6
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhccccccccchhhHHHHHHhhh
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLSN 273 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~~~~~~~~~~~k~~~wl~~ 273 (1113)
-.+++-|+..+.+++.++|.+++||.-++...+ .+|-+||+.
T Consensus 19 ~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i----------~~l~~~l~~ 60 (87)
T PF05043_consen 19 YQLLKLLLNNEYVSIEDLAEELFISRSTIYRDI----------KKLNKYLKK 60 (87)
T ss_dssp HHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHH----------HHHHHHHHC
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHH----------HHHHHHHHH
Confidence 457788889999999999999999999998876 466777774
No 144
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=21.62 E-value=70 Score=30.48 Aligned_cols=32 Identities=22% Similarity=0.560 Sum_probs=28.7
Q ss_pred HHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 223 LILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 223 ~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
-||+.|-+.|.++..++|.++|+|+.++...|
T Consensus 7 ~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l 38 (108)
T smart00344 7 KILEELQKDARISLAELAKKVGLSPSTVHNRV 38 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHH
Confidence 57788888899999999999999999998775
No 145
>PF13551 HTH_29: Winged helix-turn helix
Probab=21.61 E-value=1.1e+02 Score=28.93 Aligned_cols=50 Identities=20% Similarity=0.331 Sum_probs=37.5
Q ss_pred HhhhCCcchhhhhhhhcCChhhhhhccc-----------c--------cc-ccchhhHHHHHHhhhcccc
Q 001260 228 LIDRGKVNVKDIASDIGISPDLLKTTLA-----------D--------GT-FASDLQCKLVKWLSNHAYL 277 (1113)
Q Consensus 228 li~~gkv~~~~~a~~~g~s~~~~~a~l~-----------~--------~~-~~~~~~~k~~~wl~~~~~~ 277 (1113)
|+.+|.-++.+||..+|+|+.++..-+. . .. +.+.....|+.|+..+...
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 4556766899999999999999865544 1 12 6677778888888887655
No 146
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=21.05 E-value=74 Score=34.11 Aligned_cols=35 Identities=9% Similarity=0.159 Sum_probs=31.5
Q ss_pred hHHHHHHHhhhCCcchhhhhhhhcCChhhhhhccc
Q 001260 221 FTLILKKLIDRGKVNVKDIASDIGISPDLLKTTLA 255 (1113)
Q Consensus 221 ~~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l~ 255 (1113)
...||..|-.+|.++++|+|..+|+|.+++.--|.
T Consensus 9 ~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 9 QKALQELIEENPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 46788889999999999999999999999998764
No 147
>PHA02862 5L protein; Provisional
Probab=20.84 E-value=35 Score=35.69 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=25.0
Q ss_pred CCcCcccCCCCCCCCCeEEccccCccccccccc
Q 001260 702 PRSCDICRRSETILNPILICSGCKVAVHLDCYR 734 (1113)
Q Consensus 702 ~~~CsVC~~~E~~~N~IV~Cd~C~laVHq~CYG 734 (1113)
+..|=||++.+.....-=.|.|-..-|||.|..
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~ 34 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQ 34 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHH
Confidence 357999998754444445788889999999974
No 148
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=20.72 E-value=52 Score=29.99 Aligned_cols=33 Identities=27% Similarity=0.535 Sum_probs=13.7
Q ss_pred cccccccCc---CC--ceeecCCCCcccccchhhhhhc
Q 001260 825 DVCCICRHK---HG--ICIKCNYGNCQTTFHPTCARSA 857 (1113)
Q Consensus 825 ~~C~iC~~~---~G--A~IqCs~~~C~~~FHvtCA~~a 857 (1113)
..|.||... .+ ..+.|....|...||..|-...
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~w 40 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEW 40 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHH
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHH
Confidence 468888863 22 3467999999999999997554
No 149
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.70 E-value=67 Score=28.02 Aligned_cols=29 Identities=21% Similarity=0.479 Sum_probs=23.6
Q ss_pred HHHhhhCCcchhhhhhhhcC-Chhhhhhcc
Q 001260 226 KKLIDRGKVNVKDIASDIGI-SPDLLKTTL 254 (1113)
Q Consensus 226 kkli~~gkv~~~~~a~~~g~-s~~~~~a~l 254 (1113)
..+|..+..++.|||.+.|+ |+..+....
T Consensus 43 ~~~l~~~~~~~~~ia~~~g~~s~~~f~r~F 72 (84)
T smart00342 43 RRLLRDTDLSVTEIALRVGFSSQSYFSRAF 72 (84)
T ss_pred HHHHHcCCCCHHHHHHHhCCCChHHHHHHH
Confidence 45566779999999999999 888776654
No 150
>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=20.42 E-value=82 Score=35.24 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=42.9
Q ss_pred cchhhhhhhhcCChhhhhhcccc-ccccchhhHHHHHHhhhcccccccc
Q 001260 234 VNVKDIASDIGISPDLLKTTLAD-GTFASDLQCKLVKWLSNHAYLGGLL 281 (1113)
Q Consensus 234 v~~~~~a~~~g~s~~~~~a~l~~-~~~~~~~~~k~~~wl~~~~~~~~~~ 281 (1113)
++++|||.+.|+|.-+|--+|+. ...++....||.+=.+..-|.+...
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~~ 50 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNAV 50 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCHH
Confidence 68999999999999999999994 5689999999999999999977554
No 151
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=20.26 E-value=62 Score=31.29 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=28.7
Q ss_pred hCCcchhhhhhhhcCChhhhhhccccccccchhhHHHHHHhh
Q 001260 231 RGKVNVKDIASDIGISPDLLKTTLADGTFASDLQCKLVKWLS 272 (1113)
Q Consensus 231 ~gkv~~~~~a~~~g~s~~~~~a~l~~~~~~~~~~~k~~~wl~ 272 (1113)
+=-++..+||.++|+|++-|+..|.-..-.|..=-.+-.+|-
T Consensus 21 ~~~ls~~~ia~dL~~s~~~le~vL~l~~~~~~~vW~lRdyL~ 62 (89)
T PF10078_consen 21 LSGLSLEQIAADLGTSPEHLEQVLNLKQPFPEDVWILRDYLN 62 (89)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCcccchHHHHHHH
Confidence 445899999999999999999998732222333334444443
No 152
>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=20.25 E-value=52 Score=29.03 Aligned_cols=37 Identities=19% Similarity=0.433 Sum_probs=30.4
Q ss_pred chHHHHHHH-hh---hCCcchhhhhhhhcCChhhhhhcccc
Q 001260 220 NFTLILKKL-ID---RGKVNVKDIASDIGISPDLLKTTLAD 256 (1113)
Q Consensus 220 ~~~~~lkkl-i~---~gkv~~~~~a~~~g~s~~~~~a~l~~ 256 (1113)
..+-|++|+ || -|+.++.+.+.+.||+++.|.+.|.+
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 346677775 55 58999999999999999999999853
No 153
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.13 E-value=64 Score=42.96 Aligned_cols=49 Identities=24% Similarity=0.618 Sum_probs=39.1
Q ss_pred CCcCcccCCCC--C-CCCCeEEccccCcccccccccCcccCCCcccccccccc
Q 001260 702 PRSCDICRRSE--T-ILNPILICSGCKVAVHLDCYRNAKESTGPWYCELCEEL 751 (1113)
Q Consensus 702 ~~~CsVC~~~E--~-~~N~IV~Cd~C~laVHq~CYGi~~ipeg~WlCd~C~~~ 751 (1113)
...|.||++.- + +++..|-|.-|+..|-..||- .+..+|.=.|..|+..
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye-ye~~~g~~~cp~c~t~ 66 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYE-YERSEGNQCCPQCNTR 66 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCCCccccchhh-hhhhcCCccCCccCCc
Confidence 46799999852 2 467889999999999999993 3455788899999653
No 154
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=20.10 E-value=78 Score=31.84 Aligned_cols=33 Identities=21% Similarity=0.246 Sum_probs=28.0
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
--||+.|.+.|.++|.+||..+|+++-++-.-|
T Consensus 19 l~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL 51 (117)
T PRK10141 19 LGIVLLLRESGELCVCDLCTALDQSQPKISRHL 51 (117)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 457888888899999999999999999886544
No 155
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=20.01 E-value=75 Score=32.70 Aligned_cols=33 Identities=21% Similarity=0.483 Sum_probs=29.2
Q ss_pred HHHHHHHhhhCCcchhhhhhhhcCChhhhhhcc
Q 001260 222 TLILKKLIDRGKVNVKDIASDIGISPDLLKTTL 254 (1113)
Q Consensus 222 ~~~lkkli~~gkv~~~~~a~~~g~s~~~~~a~l 254 (1113)
-.||..|-.-|..+..+||.++|+|+.++..-+
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 457788888999999999999999999988764
Done!