Query 019587
Match_columns 338
No_of_seqs 320 out of 2350
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 02:57:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019587.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019587hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.9 7.8E-27 1.7E-31 210.6 11.4 131 145-305 126-266 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.9 3.6E-23 7.7E-28 187.0 6.3 121 170-318 127-250 (279)
3 KOG3576 Ovo and related transc 99.7 7.4E-19 1.6E-23 152.1 2.8 111 172-310 116-240 (267)
4 KOG1074 Transcriptional repres 99.7 1.7E-18 3.8E-23 175.0 4.0 70 237-306 613-692 (958)
5 KOG1074 Transcriptional repres 99.7 2.5E-18 5.4E-23 173.9 3.9 69 258-326 880-953 (958)
6 KOG3608 Zn finger proteins [Ge 99.6 4.9E-17 1.1E-21 150.9 1.9 158 129-316 187-357 (467)
7 KOG3608 Zn finger proteins [Ge 99.5 3.4E-14 7.3E-19 132.2 4.3 117 174-318 178-299 (467)
8 KOG3576 Ovo and related transc 99.4 8.8E-14 1.9E-18 120.7 5.3 106 147-280 115-235 (267)
9 KOG3623 Homeobox transcription 99.4 7E-14 1.5E-18 139.9 1.0 106 174-305 211-332 (1007)
10 KOG3623 Homeobox transcription 99.3 3.4E-13 7.4E-18 135.1 3.1 66 237-302 902-970 (1007)
11 PLN03086 PRLI-interacting fact 99.1 1.2E-10 2.7E-15 117.2 8.3 102 172-307 452-565 (567)
12 PHA00733 hypothetical protein 99.1 8.6E-11 1.9E-15 97.6 3.9 80 215-307 38-124 (128)
13 PHA02768 hypothetical protein; 98.9 4.1E-10 8.9E-15 78.5 1.8 41 258-298 6-47 (55)
14 PLN03086 PRLI-interacting fact 98.8 8.8E-09 1.9E-13 103.9 8.8 82 218-318 454-548 (567)
15 PHA00733 hypothetical protein 98.8 5.2E-09 1.1E-13 86.9 3.7 83 170-279 37-121 (128)
16 KOG3993 Transcription factor ( 98.7 1.7E-09 3.7E-14 103.2 -1.1 148 149-308 267-484 (500)
17 PHA02768 hypothetical protein; 98.6 1.3E-08 2.7E-13 71.1 2.0 43 217-273 5-47 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.6 3.7E-08 8E-13 58.7 2.4 26 244-269 1-26 (26)
19 KOG3993 Transcription factor ( 98.3 1.4E-07 3E-12 90.4 -0.1 82 215-308 265-382 (500)
20 PHA00732 hypothetical protein 98.3 3.5E-07 7.7E-12 69.4 2.1 46 217-280 1-47 (79)
21 PHA00616 hypothetical protein 98.1 1.4E-06 3.1E-11 58.0 1.4 33 283-316 1-34 (44)
22 PHA00732 hypothetical protein 97.8 2.1E-05 4.5E-10 59.7 3.1 46 257-305 1-47 (79)
23 PF13465 zf-H2C2_2: Zinc-finge 97.7 9.1E-06 2E-10 48.3 0.6 25 161-185 2-26 (26)
24 PF00096 zf-C2H2: Zinc finger, 97.7 3.1E-05 6.7E-10 44.3 2.2 22 284-305 1-23 (23)
25 PHA00616 hypothetical protein 97.6 2.5E-05 5.4E-10 52.1 1.4 40 217-268 1-40 (44)
26 COG5189 SFP1 Putative transcri 97.5 2.3E-05 5E-10 72.9 0.0 51 254-304 346-420 (423)
27 PF00096 zf-C2H2: Zinc finger, 97.5 7.4E-05 1.6E-09 42.7 1.9 23 258-280 1-23 (23)
28 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00011 2.4E-09 41.9 2.3 23 284-306 1-24 (24)
29 PF12756 zf-C2H2_2: C2H2 type 97.4 0.00012 2.7E-09 57.0 3.0 72 219-306 1-74 (100)
30 PF05605 zf-Di19: Drought indu 97.3 0.00032 6.9E-09 49.2 3.9 25 242-266 14-40 (54)
31 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00015 3.1E-09 43.2 1.2 24 283-306 1-25 (27)
32 PF05605 zf-Di19: Drought indu 97.1 0.00051 1.1E-08 48.2 3.3 53 173-254 2-54 (54)
33 PF12756 zf-C2H2_2: C2H2 type 97.0 0.00042 9.2E-09 53.9 2.5 73 175-280 1-73 (100)
34 PF13894 zf-C2H2_4: C2H2-type 96.9 0.00074 1.6E-08 38.4 2.0 23 258-280 1-23 (24)
35 PF13912 zf-C2H2_6: C2H2-type 96.7 0.00079 1.7E-08 39.9 1.5 24 257-280 1-24 (27)
36 smart00355 ZnF_C2H2 zinc finge 96.4 0.0021 4.6E-08 36.9 1.8 22 284-305 1-23 (26)
37 COG5189 SFP1 Putative transcri 96.4 0.0009 2E-08 62.5 0.1 55 214-278 346-419 (423)
38 smart00355 ZnF_C2H2 zinc finge 96.2 0.0039 8.6E-08 35.7 2.1 24 258-281 1-24 (26)
39 PRK04860 hypothetical protein; 95.6 0.0053 1.2E-07 52.9 1.4 31 241-271 127-157 (160)
40 PF09237 GAGA: GAGA factor; I 95.5 0.013 2.9E-07 40.1 2.8 32 214-257 21-52 (54)
41 PF12874 zf-met: Zinc-finger o 95.5 0.0069 1.5E-07 35.1 1.1 22 284-305 1-23 (25)
42 PF13909 zf-H2C2_5: C2H2-type 95.1 0.016 3.6E-07 33.2 1.8 22 284-306 1-23 (24)
43 KOG2231 Predicted E3 ubiquitin 95.0 0.032 6.9E-07 57.8 5.0 126 150-306 100-236 (669)
44 PF09237 GAGA: GAGA factor; I 95.0 0.014 3E-07 40.1 1.6 26 281-306 22-48 (54)
45 PF12874 zf-met: Zinc-finger o 94.9 0.012 2.5E-07 34.1 1.0 23 174-196 1-23 (25)
46 COG5048 FOG: Zn-finger [Genera 94.4 0.015 3.2E-07 56.4 0.8 48 149-196 289-346 (467)
47 PF12171 zf-C2H2_jaz: Zinc-fin 94.3 0.025 5.4E-07 33.5 1.4 24 173-196 1-24 (27)
48 KOG1146 Homeobox protein [Gene 94.1 0.021 4.6E-07 62.6 1.3 79 216-306 464-613 (1406)
49 PRK04860 hypothetical protein; 94.1 0.021 4.5E-07 49.2 1.0 35 257-295 119-156 (160)
50 PF12171 zf-C2H2_jaz: Zinc-fin 94.0 0.0095 2.1E-07 35.4 -0.9 21 284-304 2-23 (27)
51 COG5236 Uncharacterized conser 91.9 0.075 1.6E-06 50.5 1.4 68 237-307 228-306 (493)
52 PF13909 zf-H2C2_5: C2H2-type 91.6 0.14 3E-06 29.2 1.8 21 258-279 1-21 (24)
53 KOG2482 Predicted C2H2-type Zn 91.4 0.21 4.6E-06 47.5 3.8 22 173-194 195-216 (423)
54 PF13913 zf-C2HC_2: zinc-finge 90.8 0.2 4.3E-06 29.3 2.0 20 259-279 4-23 (25)
55 KOG1146 Homeobox protein [Gene 90.8 0.052 1.1E-06 59.6 -1.0 108 174-310 1229-1356(1406)
56 KOG2186 Cell growth-regulating 90.8 0.16 3.5E-06 46.4 2.3 46 258-305 4-51 (276)
57 smart00451 ZnF_U1 U1-like zinc 90.8 0.19 4.1E-06 31.3 2.0 22 283-304 3-25 (35)
58 COG5048 FOG: Zn-finger [Genera 89.9 0.054 1.2E-06 52.4 -1.7 69 172-268 288-364 (467)
59 PF13913 zf-C2HC_2: zinc-finge 89.0 0.29 6.2E-06 28.6 1.6 20 284-304 3-23 (25)
60 KOG2893 Zn finger protein [Gen 88.8 0.15 3.3E-06 46.2 0.5 36 237-276 18-53 (341)
61 KOG2785 C2H2-type Zn-finger pr 88.5 1.4 2.9E-05 42.8 6.7 55 258-312 167-250 (390)
62 smart00451 ZnF_U1 U1-like zinc 87.2 0.4 8.8E-06 29.7 1.6 23 257-279 3-25 (35)
63 TIGR00622 ssl1 transcription f 87.1 0.55 1.2E-05 37.9 2.7 24 282-305 80-104 (112)
64 KOG2231 Predicted E3 ubiquitin 84.3 0.99 2.2E-05 47.1 3.6 80 219-315 184-275 (669)
65 KOG2482 Predicted C2H2-type Zn 83.5 2.7 5.9E-05 40.2 5.9 63 243-305 129-218 (423)
66 KOG2893 Zn finger protein [Gen 83.3 0.36 7.7E-06 43.8 -0.0 49 254-305 8-58 (341)
67 KOG4173 Alpha-SNAP protein [In 82.4 0.78 1.7E-05 40.8 1.7 79 216-307 78-171 (253)
68 TIGR00622 ssl1 transcription f 77.7 2.9 6.4E-05 33.7 3.5 101 150-280 2-104 (112)
69 PF02892 zf-BED: BED zinc fing 76.9 2.3 4.9E-05 28.0 2.3 24 282-305 15-43 (45)
70 PF05443 ROS_MUCR: ROS/MUCR tr 71.3 2.2 4.8E-05 35.5 1.4 24 281-307 70-94 (132)
71 cd00350 rubredoxin_like Rubred 70.6 1.9 4E-05 26.8 0.6 10 256-265 16-25 (33)
72 COG1198 PriA Primosomal protei 69.9 3.5 7.6E-05 43.9 2.8 13 254-266 472-484 (730)
73 COG4049 Uncharacterized protei 69.3 2.3 5E-05 29.8 0.9 27 252-278 12-38 (65)
74 COG4957 Predicted transcriptio 68.2 3.3 7.1E-05 34.4 1.7 23 282-307 75-98 (148)
75 smart00614 ZnF_BED BED zinc fi 67.4 4.8 0.0001 27.4 2.2 19 285-303 20-44 (50)
76 KOG4167 Predicted DNA-binding 67.2 3.2 7E-05 43.5 1.8 25 173-197 792-816 (907)
77 COG5236 Uncharacterized conser 65.3 9.5 0.00021 36.7 4.4 48 259-306 222-275 (493)
78 KOG2186 Cell growth-regulating 65.0 3.6 7.7E-05 37.8 1.5 46 218-278 4-49 (276)
79 PF09986 DUF2225: Uncharacteri 61.9 4.3 9.3E-05 36.6 1.4 55 171-226 3-57 (214)
80 PF09986 DUF2225: Uncharacteri 61.5 1.3 2.9E-05 40.0 -2.0 41 255-295 3-61 (214)
81 KOG4167 Predicted DNA-binding 61.4 2.3 5E-05 44.5 -0.5 24 257-280 792-815 (907)
82 COG1997 RPL43A Ribosomal prote 60.5 3.3 7.2E-05 31.8 0.3 31 256-294 34-65 (89)
83 COG4049 Uncharacterized protei 60.2 4 8.7E-05 28.6 0.7 27 280-306 14-41 (65)
84 PF13717 zinc_ribbon_4: zinc-r 59.5 7.6 0.00016 24.6 1.8 33 151-184 4-36 (36)
85 PF09538 FYDLN_acid: Protein o 59.4 4.6 0.0001 32.4 1.1 14 282-295 25-39 (108)
86 PF15269 zf-C2H2_7: Zinc-finge 57.9 8.1 0.00018 25.9 1.8 21 284-304 21-42 (54)
87 COG2888 Predicted Zn-ribbon RN 57.7 8.1 0.00018 27.5 1.9 7 218-224 28-34 (61)
88 TIGR02098 MJ0042_CXXC MJ0042 f 57.7 6.1 0.00013 25.0 1.2 34 150-184 3-36 (38)
89 KOG4377 Zn-finger protein [Gen 56.2 5.1 0.00011 39.3 0.9 44 284-336 402-448 (480)
90 smart00531 TFIIE Transcription 53.6 8.1 0.00018 32.6 1.7 20 171-190 97-116 (147)
91 PRK09678 DNA-binding transcrip 52.7 3.2 7E-05 30.8 -0.8 14 255-268 25-40 (72)
92 KOG3408 U1-like Zn-finger-cont 51.6 7.3 0.00016 31.8 1.0 25 281-305 55-80 (129)
93 PF13719 zinc_ribbon_5: zinc-r 50.1 12 0.00027 23.8 1.7 33 151-184 4-36 (37)
94 PF04959 ARS2: Arsenite-resist 49.6 13 0.00028 33.6 2.4 27 281-307 75-102 (214)
95 smart00531 TFIIE Transcription 47.9 15 0.00032 31.0 2.3 37 254-293 96-134 (147)
96 PF08790 zf-LYAR: LYAR-type C2 47.0 4.4 9.6E-05 24.3 -0.7 20 284-304 1-21 (28)
97 KOG4173 Alpha-SNAP protein [In 46.5 10 0.00023 33.8 1.3 78 173-281 79-171 (253)
98 TIGR00373 conserved hypothetic 46.4 18 0.00038 31.0 2.6 34 252-292 104-138 (158)
99 COG1592 Rubrerythrin [Energy p 45.8 9.5 0.00021 33.1 0.9 13 252-264 144-156 (166)
100 COG5151 SSL1 RNA polymerase II 44.4 13 0.00029 35.2 1.7 46 260-305 365-411 (421)
101 KOG2785 C2H2-type Zn-finger pr 44.2 25 0.00055 34.3 3.5 51 217-279 166-242 (390)
102 cd00729 rubredoxin_SM Rubredox 43.8 9.9 0.00021 23.8 0.5 10 256-265 17-26 (34)
103 PHA00626 hypothetical protein 41.9 5.8 0.00013 27.9 -0.8 14 256-269 22-35 (59)
104 PF12013 DUF3505: Protein of u 41.8 50 0.0011 26.1 4.5 26 282-307 79-109 (109)
105 PF09538 FYDLN_acid: Protein o 41.0 21 0.00045 28.7 2.1 32 147-186 7-39 (108)
106 PF14353 CpXC: CpXC protein 40.5 9.8 0.00021 31.1 0.2 46 151-196 3-61 (128)
107 PF09845 DUF2072: Zn-ribbon co 40.0 14 0.00031 30.6 1.0 15 257-271 1-15 (131)
108 PRK06266 transcription initiat 39.2 21 0.00046 31.2 2.1 34 254-294 114-148 (178)
109 PRK14873 primosome assembly pr 38.7 21 0.00045 37.9 2.3 10 257-266 422-431 (665)
110 smart00734 ZnF_Rad18 Rad18-lik 38.5 25 0.00054 20.5 1.6 19 259-278 3-21 (26)
111 TIGR00595 priA primosomal prot 38.4 22 0.00047 36.4 2.3 6 219-224 255-260 (505)
112 COG3677 Transposase and inacti 37.4 19 0.00042 29.8 1.4 36 150-186 31-66 (129)
113 PF09723 Zn-ribbon_8: Zinc rib 36.7 15 0.00034 24.0 0.6 30 149-181 5-34 (42)
114 TIGR00373 conserved hypothetic 36.6 17 0.00038 31.1 1.1 34 214-268 106-139 (158)
115 COG1592 Rubrerythrin [Energy p 36.3 19 0.0004 31.3 1.2 25 148-181 133-157 (166)
116 PF04959 ARS2: Arsenite-resist 36.1 22 0.00048 32.1 1.7 25 255-279 75-99 (214)
117 PF04606 Ogr_Delta: Ogr/Delta- 36.1 6.2 0.00014 26.5 -1.4 35 260-294 2-39 (47)
118 PRK00464 nrdR transcriptional 35.8 15 0.00032 31.4 0.6 11 217-227 28-38 (154)
119 PRK00398 rpoP DNA-directed RNA 34.0 22 0.00048 23.6 1.1 30 149-184 3-32 (46)
120 PF05443 ROS_MUCR: ROS/MUCR tr 33.7 20 0.00044 29.8 1.0 26 217-257 72-97 (132)
121 PRK14890 putative Zn-ribbon RN 33.4 26 0.00057 24.9 1.4 7 218-224 26-32 (59)
122 KOG4124 Putative transcription 33.3 5 0.00011 38.6 -3.0 51 255-305 347-421 (442)
123 PF13878 zf-C2H2_3: zinc-finge 33.2 37 0.00081 22.1 2.0 22 259-280 15-38 (41)
124 PRK06266 transcription initiat 33.0 20 0.00044 31.4 0.9 32 216-268 116-147 (178)
125 PF12907 zf-met2: Zinc-binding 31.8 9.4 0.0002 25.0 -1.0 28 284-311 2-33 (40)
126 TIGR02605 CxxC_CxxC_SSSS putat 31.5 22 0.00047 24.1 0.7 30 149-181 5-34 (52)
127 KOG2593 Transcription initiati 31.4 49 0.0011 33.0 3.3 39 253-292 124-163 (436)
128 smart00834 CxxC_CXXC_SSSS Puta 30.5 24 0.00053 22.3 0.8 31 149-182 5-35 (41)
129 PRK05580 primosome assembly pr 30.4 33 0.00072 36.4 2.2 6 219-224 410-415 (679)
130 PF01096 TFIIS_C: Transcriptio 29.8 27 0.00058 22.5 0.9 33 151-183 2-38 (39)
131 PF01780 Ribosomal_L37ae: Ribo 29.7 12 0.00025 29.1 -1.0 30 256-293 34-64 (90)
132 PF15135 UPF0515: Uncharacteri 29.5 41 0.00089 31.0 2.3 15 172-186 154-168 (278)
133 PTZ00255 60S ribosomal protein 29.1 17 0.00038 28.1 -0.1 30 256-293 35-65 (90)
134 KOG4124 Putative transcription 29.0 16 0.00035 35.3 -0.4 55 254-308 175-238 (442)
135 PF06524 NOA36: NOA36 protein; 28.7 22 0.00048 33.0 0.4 26 255-280 207-232 (314)
136 PF09416 UPF1_Zn_bind: RNA hel 28.5 15 0.00031 31.4 -0.7 59 151-224 2-67 (152)
137 KOG2593 Transcription initiati 28.4 30 0.00065 34.4 1.3 35 171-224 126-160 (436)
138 PRK04023 DNA polymerase II lar 28.4 44 0.00095 36.9 2.6 44 174-290 627-671 (1121)
139 COG1996 RPC10 DNA-directed RNA 28.3 25 0.00054 24.1 0.5 9 216-224 5-13 (49)
140 KOG0717 Molecular chaperone (D 28.2 40 0.00086 33.9 2.1 22 284-305 293-315 (508)
141 PF12760 Zn_Tnp_IS1595: Transp 28.2 17 0.00037 24.2 -0.3 10 281-290 35-45 (46)
142 TIGR00280 L37a ribosomal prote 27.0 18 0.00038 28.2 -0.4 30 256-293 34-64 (91)
143 TIGR02300 FYDLN_acid conserved 27.0 51 0.0011 27.2 2.2 37 147-190 7-43 (129)
144 PF06524 NOA36: NOA36 protein; 26.3 49 0.0011 30.8 2.2 25 281-305 207-232 (314)
145 COG5112 UFD2 U1-like Zn-finger 26.0 25 0.00053 28.1 0.2 23 282-304 54-77 (126)
146 smart00440 ZnF_C2C2 C2C2 Zinc 25.9 54 0.0012 21.2 1.8 11 174-184 29-39 (40)
147 COG1198 PriA Primosomal protei 25.7 62 0.0013 34.7 3.2 9 216-224 474-482 (730)
148 PF02176 zf-TRAF: TRAF-type zi 25.6 24 0.00051 24.4 0.1 25 244-268 25-53 (60)
149 COG1779 C4-type Zn-finger prot 24.9 14 0.0003 32.9 -1.5 10 284-293 44-54 (201)
150 KOG2807 RNA polymerase II tran 24.7 87 0.0019 30.1 3.6 24 282-305 344-368 (378)
151 KOG1280 Uncharacterized conser 24.4 83 0.0018 30.5 3.4 36 217-264 79-116 (381)
152 KOG2071 mRNA cleavage and poly 24.3 56 0.0012 33.8 2.5 25 256-280 417-441 (579)
153 KOG3408 U1-like Zn-finger-cont 24.3 44 0.00096 27.3 1.4 26 254-279 54-79 (129)
154 KOG2807 RNA polymerase II tran 24.2 98 0.0021 29.8 3.8 26 255-280 343-368 (378)
155 PF12013 DUF3505: Protein of u 24.2 62 0.0013 25.5 2.3 18 237-254 92-109 (109)
156 PHA02998 RNA polymerase subuni 24.0 51 0.0011 28.9 1.8 37 149-185 143-183 (195)
157 PF10013 DUF2256: Uncharacteri 23.3 45 0.00097 22.1 1.0 17 259-275 10-26 (42)
158 smart00659 RPOLCX RNA polymera 22.7 58 0.0013 21.6 1.5 26 150-182 3-28 (44)
159 PF07754 DUF1610: Domain of un 21.9 36 0.00078 19.7 0.3 8 217-224 16-23 (24)
160 PF13451 zf-trcl: Probable zin 21.7 38 0.00083 23.2 0.5 21 281-301 2-23 (49)
161 PRK03976 rpl37ae 50S ribosomal 21.5 24 0.00051 27.4 -0.6 30 256-293 35-65 (90)
162 PF10571 UPF0547: Uncharacteri 21.3 42 0.00091 19.7 0.5 10 259-268 16-25 (26)
163 KOG0978 E3 ubiquitin ligase in 21.0 35 0.00076 36.2 0.3 23 254-276 675-697 (698)
164 KOG0782 Predicted diacylglycer 20.8 26 0.00057 36.1 -0.7 50 244-296 240-290 (1004)
165 PF10263 SprT-like: SprT-like 20.6 24 0.00052 29.6 -0.9 10 258-267 124-133 (157)
166 PF04780 DUF629: Protein of un 20.4 67 0.0015 32.5 2.1 28 282-309 56-84 (466)
167 COG1998 RPS31 Ribosomal protei 20.0 69 0.0015 22.0 1.4 10 257-266 37-46 (51)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.94 E-value=7.8e-27 Score=210.64 Aligned_cols=131 Identities=31% Similarity=0.513 Sum_probs=120.1
Q ss_pred CCCCCCCCCCCCcccc----CccchhhhcC---CCceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcc
Q 019587 145 ASGRGGGCSLNKGQYW----IPTPAQILIG---PTQFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLR 217 (338)
Q Consensus 145 ~~~~~~~c~~c~~~~~----l~~h~~~h~~---~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~ 217 (338)
.....+.|..|+++|. |.+|.|.|.. ++.+.|++|+|.|.+...|++|+++| + .+
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH----------------~--l~ 187 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTH----------------T--LP 187 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhcc----------------C--CC
Confidence 3455788999999887 7889999874 67799999999999999999999999 3 56
Q ss_pred cccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHhc--CCCeee-eCCcccCC
Q 019587 218 LPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKH 294 (338)
Q Consensus 218 ~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~ 294 (338)
+.|.+|| |.|...=-|+.|+|+|+|||||.|.+|+|+|+.+++|+.||++| .|+|+| .|+|.|..
T Consensus 188 c~C~iCG------------KaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 188 CECGICG------------KAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred ccccccc------------ccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 8999999 99999999999999999999999999999999999999999998 599999 99999999
Q ss_pred hHHHHHHHHHh
Q 019587 295 KRSLKDHIKAF 305 (338)
Q Consensus 295 ~s~L~~H~r~h 305 (338)
++.|.+|...-
T Consensus 256 ~SyLnKH~ES~ 266 (279)
T KOG2462|consen 256 KSYLNKHSESA 266 (279)
T ss_pred HHHHHHhhhhc
Confidence 99999998654
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.88 E-value=3.6e-23 Score=186.99 Aligned_cols=121 Identities=22% Similarity=0.455 Sum_probs=110.2
Q ss_pred CCCceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHH
Q 019587 170 GPTQFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHY 249 (338)
Q Consensus 170 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~ 249 (338)
....|+|..|||.+....+|.+|..+|-.- ...+.+.|..|+ |.|..-.+|+.|+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------------~s~ka~~C~~C~------------K~YvSmpALkMHi 181 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSL-------------DSKKAFSCKYCG------------KVYVSMPALKMHI 181 (279)
T ss_pred cCCceeccccccccccccccchhhcccccc-------------cccccccCCCCC------------ceeeehHHHhhHh
Confidence 345699999999999999999999999321 234668999999 9999999999999
Q ss_pred HHhcCCCcccccccccccCChHHHHHHHHhc--CCCeee-eCCcccCChHHHHHHHHHhCCCCCCccCCCCC
Q 019587 250 KRKHGIKPFMCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKHKRSLKDHIKAFGNGHASCGIDTFE 318 (338)
Q Consensus 250 r~H~gekp~~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~s~L~~H~r~hh~~~~~~~C~~~~ 318 (338)
|+|+ -+++|.+|||+|.+.+-|+.|+|+| ||||.| .|+|+|..+++|+.||++| .+.|+|+|+++-
T Consensus 182 rTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTH-S~~K~~qC~~C~ 250 (279)
T KOG2462|consen 182 RTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTH-SDVKKHQCPRCG 250 (279)
T ss_pred hccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhh-cCCccccCcchh
Confidence 9997 7899999999999999999999986 899999 9999999999999999999 899999998654
No 3
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.74 E-value=7.4e-19 Score=152.07 Aligned_cols=111 Identities=28% Similarity=0.536 Sum_probs=102.7
Q ss_pred CceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHH
Q 019587 172 TQFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKR 251 (338)
Q Consensus 172 ~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~ 251 (338)
..|.|.+|+|.|.....|.+||+.| ...+++.|..|| |.|.+...|++|+|+
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch----------------~~vkr~lct~cg------------kgfndtfdlkrh~rt 167 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCH----------------SDVKRHLCTFCG------------KGFNDTFDLKRHTRT 167 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhc----------------cHHHHHHHhhcc------------Ccccchhhhhhhhcc
Confidence 3599999999999999999999999 788999999999 899999999999999
Q ss_pred hcCCCcccccccccccCChHHHHHHHH-hc------------CCCeee-eCCcccCChHHHHHHHHHhCCCCC
Q 019587 252 KHGIKPFMCRKCSKAFAVRGDWRTHEK-NC------------GKLWYC-TCGSDFKHKRSLKDHIKAFGNGHA 310 (338)
Q Consensus 252 H~gekp~~C~~CgksF~~~~~L~~H~k-~h------------~k~~~C-~Cgk~F~~~s~L~~H~r~hh~~~~ 310 (338)
|+|.+||+|..|+|+|+++..|..|.+ +| .|.|.| .||..-.....+..|++.||....
T Consensus 168 htgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 168 HTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred ccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 999999999999999999999999987 34 478999 999999999999999999987654
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.72 E-value=1.7e-18 Score=175.03 Aligned_cols=70 Identities=29% Similarity=0.623 Sum_probs=65.1
Q ss_pred ccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHhcC------CCeee----eCCcccCChHHHHHHHHHhC
Q 019587 237 KPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNCG------KLWYC----TCGSDFKHKRSLKDHIKAFG 306 (338)
Q Consensus 237 k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h~------k~~~C----~Cgk~F~~~s~L~~H~r~hh 306 (338)
+++.-.++|+.|+|+|+||+||+|.+||++|+.|++|+.||-+|. -+|.| +|-+.|...-.|..|+|+|-
T Consensus 613 rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 613 RVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred ecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccceEEeec
Confidence 888899999999999999999999999999999999999999983 45778 39999999999999999995
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.72 E-value=2.5e-18 Score=173.91 Aligned_cols=69 Identities=22% Similarity=0.427 Sum_probs=59.0
Q ss_pred ccccccccccCChHHHHHHHHhc--CCCeee-eCCcccCChHHHHHHHHHhCCCC--CCccCCCCCCCCccchh
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKHKRSLKDHIKAFGNGH--ASCGIDTFEDDEPASEI 326 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~s~L~~H~r~hh~~~--~~~~C~~~~~~~~~~~~ 326 (338)
+.|.+|||.|...++|..|+++| +|||.| .|++.|..+..||.||.+|+-.. .+.+|..|+...+.+..
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srrG~~~~~~~~~vs~~ 953 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRRGPSPFIGSTGVSPF 953 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccCCCCcccCCCCCCcc
Confidence 67999999999999999999998 799999 99999999999999999996322 23588888877666543
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.64 E-value=4.9e-17 Score=150.90 Aligned_cols=158 Identities=18% Similarity=0.348 Sum_probs=113.3
Q ss_pred ccCCCCCcccccccccCCCCCCCCCCCCccccCccchhhh------cCCCceecCcccccccCchHHHhcccccCCCCcC
Q 019587 129 SDYNNDNNNKEEVVTIASGRGGGCSLNKGQYWIPTPAQIL------IGPTQFSCPLCFKTFNRYNNMQMHMWGHGSQYRK 202 (338)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~l~~h~~~h------~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~ 202 (338)
..+.+...+.+|++++.+.+...|..|++.|...+-+-.| ....+|.|..|.|.|.....|..|++.|..
T Consensus 187 ~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn---- 262 (467)
T KOG3608|consen 187 KHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN---- 262 (467)
T ss_pred hhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh----
Confidence 3444555577888999999999999999888754433222 234579999999999999999999998832
Q ss_pred CCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHH-hcCCCcccccccccccCChHHHHHHHHhcC
Q 019587 203 GPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKR-KHGIKPFMCRKCSKAFAVRGDWRTHEKNCG 281 (338)
Q Consensus 203 ~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~-H~gekp~~C~~CgksF~~~~~L~~H~k~h~ 281 (338)
-|+|+.|. .+....+.|.+|+|. |...|||+|..|++.|.+.++|.+|..+|.
T Consensus 263 --------------~ykCplCd------------mtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 263 --------------CYKCPLCD------------MTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred --------------cccccccc------------cCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 27788887 666677788888775 777788888888888888888888877763
Q ss_pred -CCeee-e--CCcccCChHHHHHHHHHhCCCCC--CccCCC
Q 019587 282 -KLWYC-T--CGSDFKHKRSLKDHIKAFGNGHA--SCGIDT 316 (338)
Q Consensus 282 -k~~~C-~--Cgk~F~~~s~L~~H~r~hh~~~~--~~~C~~ 316 (338)
-.|.| . |..+|++...|++|++.||.|.. +|.|-.
T Consensus 317 ~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~ 357 (467)
T KOG3608|consen 317 KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHC 357 (467)
T ss_pred ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeec
Confidence 34666 3 66666666666666666665443 355443
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.46 E-value=3.4e-14 Score=132.20 Aligned_cols=117 Identities=21% Similarity=0.402 Sum_probs=108.3
Q ss_pred eecC--cccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHH
Q 019587 174 FSCP--LCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKR 251 (338)
Q Consensus 174 ~~C~--~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~ 251 (338)
+.|. .|-+.|..+..|..|++.| ++++..-|+.|| ..|..+..|..|.++
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~H----------------s~eKvvACp~Cg------------~~F~~~tkl~DH~rR 229 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTH----------------SNEKVVACPHCG------------ELFRTKTKLFDHLRR 229 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhc----------------CCCeEEecchHH------------HHhccccHHHHHHHh
Confidence 5564 4999999999999999999 888999999999 899999999999987
Q ss_pred hc--CCCcccccccccccCChHHHHHHHHhcCCCeee-eCCcccCChHHHHHHHHHhCCCCCCccCCCCC
Q 019587 252 KH--GIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKHKRSLKDHIKAFGNGHASCGIDTFE 318 (338)
Q Consensus 252 H~--gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~s~L~~H~r~hh~~~~~~~C~~~~ 318 (338)
.+ ...+|+|..|-|.|+....|+.|+..|..-|+| .|+......++|.+|||.-|...+||+||++|
T Consensus 230 qt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd 299 (467)
T KOG3608|consen 230 QTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECD 299 (467)
T ss_pred hhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchh
Confidence 65 467899999999999999999999999999999 99999999999999999999999999999988
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.44 E-value=8.8e-14 Score=120.73 Aligned_cols=106 Identities=21% Similarity=0.365 Sum_probs=96.6
Q ss_pred CCCCCCCCCCcccc----CccchhhhcCCCceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCC
Q 019587 147 GRGGGCSLNKGQYW----IPTPAQILIGPTQFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYC 222 (338)
Q Consensus 147 ~~~~~c~~c~~~~~----l~~h~~~h~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~ 222 (338)
...+.|++|++.|. |.+|++.|...+.|.|..|||.|+....|++|+|+| +|.+||+|..
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rth----------------tgvrpykc~~ 178 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTH----------------TGVRPYKCSL 178 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccc----------------cCccccchhh
Confidence 44788999999998 567888899999999999999999999999999999 9999999999
Q ss_pred CCCCCCCCCCCCCCccCCCHHHHHHHHHHhcC-----------CCcccccccccccCChHHHHHHHHhc
Q 019587 223 CAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHG-----------IKPFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 223 C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~g-----------ekp~~C~~CgksF~~~~~L~~H~k~h 280 (338)
|+ |.|+++-.|..|.+.-+| .|-|.|..||..-.....+..|++.|
T Consensus 179 c~------------kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 179 CE------------KAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred hh------------HHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhc
Confidence 99 999999999999876555 46799999999999999999999976
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.39 E-value=7e-14 Score=139.94 Aligned_cols=106 Identities=22% Similarity=0.527 Sum_probs=93.6
Q ss_pred eecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhc
Q 019587 174 FSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKH 253 (338)
Q Consensus 174 ~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~ 253 (338)
..|++|.+.+.+...|+.|++.-+. ..+-.|.|..|. .+|..+..|.+||.+|.
T Consensus 211 ltcpycdrgykrltslkeHikyrhe--------------kne~nfsC~lCs------------ytFAyRtQLErhm~~hk 264 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHE--------------KNEPNFSCMLCS------------YTFAYRTQLERHMQLHK 264 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHh--------------hCCCCCcchhhh------------hhhhhHHHHHHHHHhhc
Confidence 6899999999999999999984321 344568999999 89999999999999885
Q ss_pred C-------------CCcccccccccccCChHHHHHHHHhc--CCCeee-eCCcccCChHHHHHHHHHh
Q 019587 254 G-------------IKPFMCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 254 g-------------ekp~~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
- .+.|+|.+|||+|..+-.|+.|+|+| +|||.| .|+|+|.+..++..||...
T Consensus 265 pg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSK 332 (1007)
T KOG3623|consen 265 PGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSK 332 (1007)
T ss_pred CCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccccc
Confidence 2 46799999999999999999999997 899999 9999999999999998654
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.35 E-value=3.4e-13 Score=135.07 Aligned_cols=66 Identities=27% Similarity=0.561 Sum_probs=34.6
Q ss_pred ccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHhc--CCCeee-eCCcccCChHHHHHHH
Q 019587 237 KPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKHKRSLKDHI 302 (338)
Q Consensus 237 k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~s~L~~H~ 302 (338)
|.|.-.+.|.+|.--|+|.+||+|.+|.|+|..+-.|..|+|.| +|||.| .|+|+|.+..+...||
T Consensus 902 K~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 902 KAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred HHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 55555555555555555555555555555555555555555543 455555 5555555555555544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.12 E-value=1.2e-10 Score=117.15 Aligned_cols=102 Identities=23% Similarity=0.419 Sum_probs=73.7
Q ss_pred CceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHH
Q 019587 172 TQFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKR 251 (338)
Q Consensus 172 ~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~ 251 (338)
+.+.|+.|++.|. ...|..|++.|+ +++.|. |+ +.+ .+..|..|+++
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H------------------kpv~Cp-Cg------------~~~-~R~~L~~H~~t 498 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH------------------EPLQCP-CG------------VVL-EKEQMVQHQAS 498 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC------------------CCccCC-CC------------CCc-chhHHHhhhhc
Confidence 4467888888875 567788887762 357787 76 544 45788888888
Q ss_pred hcCCCcccccccccccCC----------hHHHHHHHHhc-CCCeee-eCCcccCChHHHHHHHHHhCC
Q 019587 252 KHGIKPFMCRKCSKAFAV----------RGDWRTHEKNC-GKLWYC-TCGSDFKHKRSLKDHIKAFGN 307 (338)
Q Consensus 252 H~gekp~~C~~CgksF~~----------~~~L~~H~k~h-~k~~~C-~Cgk~F~~~s~L~~H~r~hh~ 307 (338)
|.+.+++.|..|++.|.. ...|..|+.++ .+++.| .||+.|..+ .|..|+...|.
T Consensus 499 hCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 499 TCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred cCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 888888888888888742 34677887775 478888 888887776 67778776654
No 12
>PHA00733 hypothetical protein
Probab=99.08 E-value=8.6e-11 Score=97.56 Aligned_cols=80 Identities=20% Similarity=0.361 Sum_probs=66.4
Q ss_pred CcccccCCCCCCCCCCCCCCCCccCCCHHH------HHHHHHHhcCCCcccccccccccCChHHHHHHHHhcCCCeee-e
Q 019587 215 MLRLPCYCCAPGCRNNIDHPRSKPLKDFRT------LQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-T 287 (338)
Q Consensus 215 ~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~------L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~ 287 (338)
.+++.|.+|. +.|..... |..|+. +++.+||.|..||+.|.....|..|++.+.++|.| .
T Consensus 38 ~~~~~~~~~~------------~~~~~~~~l~~~~~l~~~~~-~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~ 104 (128)
T PHA00733 38 QKRLIRAVVK------------TLIYNPQLLDESSYLYKLLT-SKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPV 104 (128)
T ss_pred hhhHHHHHHh------------hhccChhhhcchHHHHhhcc-cCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCC
Confidence 3568899987 55554444 444433 34589999999999999999999999988889999 9
Q ss_pred CCcccCChHHHHHHHHHhCC
Q 019587 288 CGSDFKHKRSLKDHIKAFGN 307 (338)
Q Consensus 288 Cgk~F~~~s~L~~H~r~hh~ 307 (338)
|++.|.....|.+|++..|+
T Consensus 105 CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 105 CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCHHHHHHHHHHhcC
Confidence 99999999999999998875
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.92 E-value=4.1e-10 Score=78.54 Aligned_cols=41 Identities=15% Similarity=0.247 Sum_probs=26.3
Q ss_pred ccccccccccCChHHHHHHHHhcCCCeee-eCCcccCChHHH
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKHKRSL 298 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~s~L 298 (338)
|+|+.|||.|++...|..|+++|.++|+| .|+|.|.+.+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCcccceeccccee
Confidence 56666666666666666666666666666 666666665554
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.84 E-value=8.8e-09 Score=103.93 Aligned_cols=82 Identities=21% Similarity=0.478 Sum_probs=70.2
Q ss_pred cccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHhc--CCCeee-eCCcccCC
Q 019587 218 LPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKH 294 (338)
Q Consensus 218 ~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~ 294 (338)
+.|..|+ +.|. ...|..|+++|+ +++.|+ ||+.+ .+..|..|+.+| .+++.| .|++.|..
T Consensus 454 ~~C~~Cg------------k~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~ 516 (567)
T PLN03086 454 VHCEKCG------------QAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQA 516 (567)
T ss_pred ccCCCCC------------Cccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcccc
Confidence 6799999 8885 678999999986 899999 99765 678999999876 799999 99999962
Q ss_pred ----------hHHHHHHHHHhCCCCCCccCCCCC
Q 019587 295 ----------KRSLKDHIKAFGNGHASCGIDTFE 318 (338)
Q Consensus 295 ----------~s~L~~H~r~hh~~~~~~~C~~~~ 318 (338)
.+.|..|.++. |.+++.|+.+.
T Consensus 517 g~~~~d~~d~~s~Lt~HE~~C--G~rt~~C~~Cg 548 (567)
T PLN03086 517 GGSAMDVRDRLRGMSEHESIC--GSRTAPCDSCG 548 (567)
T ss_pred CccccchhhhhhhHHHHHHhc--CCcceEccccC
Confidence 46899999986 88889998665
No 15
>PHA00733 hypothetical protein
Probab=98.76 E-value=5.2e-09 Score=86.88 Aligned_cols=83 Identities=13% Similarity=0.199 Sum_probs=68.4
Q ss_pred CCCceecCcccccccCchHHHhc--ccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHH
Q 019587 170 GPTQFSCPLCFKTFNRYNNMQMH--MWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQT 247 (338)
Q Consensus 170 ~~~~~~C~~C~k~F~~~~~L~~H--~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~ 247 (338)
.++++.|.+|.+.|.....|..+ ++.|.. ..+.++|.|..|+ +.|.....|..
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~-------------~~~~kPy~C~~Cg------------k~Fss~s~L~~ 91 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLT-------------SKAVSPYVCPLCL------------MPFSSSVSLKQ 91 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcc-------------cCCCCCccCCCCC------------CcCCCHHHHHH
Confidence 35789999999999988877766 222210 1346789999999 99999999999
Q ss_pred HHHHhcCCCcccccccccccCChHHHHHHHHh
Q 019587 248 HYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKN 279 (338)
Q Consensus 248 H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~ 279 (338)
|++.| +++|.|.+|++.|.....|..|+..
T Consensus 92 H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 92 HIRYT--EHSKVCPVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred HHhcC--CcCccCCCCCCccCCHHHHHHHHHH
Confidence 99987 4679999999999999999999875
No 16
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.71 E-value=1.7e-09 Score=103.22 Aligned_cols=148 Identities=19% Similarity=0.246 Sum_probs=100.5
Q ss_pred CCCCCCCCcccc----CccchhhhcCCCceecCcccccccCchHHHhcccccCCCCc-----CCCC------------Cc
Q 019587 149 GGGCSLNKGQYW----IPTPAQILIGPTQFSCPLCFKTFNRYNNMQMHMWGHGSQYR-----KGPE------------SL 207 (338)
Q Consensus 149 ~~~c~~c~~~~~----l~~h~~~h~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~-----~~~~------------~~ 207 (338)
.|.|.+|+..|. |..|.-..+..-.|+|+.|+|.|+...+|..|.|+|...-. ..+. ..
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 678999998765 77787665655669999999999999999999999942111 0110 11
Q ss_pred CCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCC---C--------------cc------------
Q 019587 208 RGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGI---K--------------PF------------ 258 (338)
Q Consensus 208 ~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~ge---k--------------p~------------ 258 (338)
+........-|.|..|+ |.|.....|+.|+.+|+.. + .+
T Consensus 347 rsg~dss~gi~~C~~C~------------KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~ 414 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCG------------KKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSAS 414 (500)
T ss_pred ccCCcccCceeecHHhh------------hhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccc
Confidence 11111233469999999 9999999999998887631 0 01
Q ss_pred -----------------cccccccccCChHHHHHHHHhc--CCCeee-eCCcccCChHHHHHHHHHhCCC
Q 019587 259 -----------------MCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKHKRSLKDHIKAFGNG 308 (338)
Q Consensus 259 -----------------~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~s~L~~H~r~hh~~ 308 (338)
.|..||-.+..+..--.|.+.+ +.-|.| +|...|.....|.+|+.+.|-.
T Consensus 415 ~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 415 DSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred cccccceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChH
Confidence 2333443333333322232221 456899 9999999999999999888743
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.64 E-value=1.3e-08 Score=71.10 Aligned_cols=43 Identities=14% Similarity=0.404 Sum_probs=39.9
Q ss_pred ccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHH
Q 019587 217 RLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDW 273 (338)
Q Consensus 217 ~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L 273 (338)
-|.|..|| +.|.....|+.|+++|+ ++|+|..|++.|.+.+.|
T Consensus 5 ~y~C~~CG------------K~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICG------------EIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhC------------CeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 38999999 99999999999999998 899999999999987765
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.57 E-value=3.7e-08 Score=58.69 Aligned_cols=26 Identities=35% Similarity=0.812 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCCcccccccccccCC
Q 019587 244 TLQTHYKRKHGIKPFMCRKCSKAFAV 269 (338)
Q Consensus 244 ~L~~H~r~H~gekp~~C~~CgksF~~ 269 (338)
+|..|+++|+|+|||+|+.|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 48899999999999999999999974
No 19
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.29 E-value=1.4e-07 Score=90.41 Aligned_cols=82 Identities=21% Similarity=0.456 Sum_probs=68.5
Q ss_pred CcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHhcC-------------
Q 019587 215 MLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNCG------------- 281 (338)
Q Consensus 215 ~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h~------------- 281 (338)
...|.|..|. ..|.+...|.+|.-.-.----|+|++|+|.|.-..+|..|.|.|.
T Consensus 265 iGdyiCqLCK------------~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~ 332 (500)
T KOG3993|consen 265 IGDYICQLCK------------EKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPP 332 (500)
T ss_pred HHHHHHHHHH------------HhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCCh
Confidence 3459999998 789999999999643332345999999999999999999998661
Q ss_pred ----------------------CCeee-eCCcccCChHHHHHHHHHhCCC
Q 019587 282 ----------------------KLWYC-TCGSDFKHKRSLKDHIKAFGNG 308 (338)
Q Consensus 282 ----------------------k~~~C-~Cgk~F~~~s~L~~H~r~hh~~ 308 (338)
-.|.| .|+|.|++...|++|+.+||..
T Consensus 333 k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 333 KQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred hhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 13899 9999999999999999999853
No 20
>PHA00732 hypothetical protein
Probab=98.28 E-value=3.5e-07 Score=69.38 Aligned_cols=46 Identities=20% Similarity=0.372 Sum_probs=32.9
Q ss_pred ccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHH-hcCCCcccccccccccCChHHHHHHHHhc
Q 019587 217 RLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKR-KHGIKPFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 217 ~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~-H~gekp~~C~~CgksF~~~~~L~~H~k~h 280 (338)
+|.|..|+ +.|.+...|+.|++. |. ++.|++||+.|. .|..|.++.
T Consensus 1 py~C~~Cg------------k~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICG------------FTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCC------------CccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 46777777 778888888888774 44 357888888887 466777665
No 21
>PHA00616 hypothetical protein
Probab=98.08 E-value=1.4e-06 Score=58.00 Aligned_cols=33 Identities=18% Similarity=0.607 Sum_probs=27.2
Q ss_pred Ceee-eCCcccCChHHHHHHHHHhCCCCCCccCCC
Q 019587 283 LWYC-TCGSDFKHKRSLKDHIKAFGNGHASCGIDT 316 (338)
Q Consensus 283 ~~~C-~Cgk~F~~~s~L~~H~r~hh~~~~~~~C~~ 316 (338)
||+| .||+.|..++.|.+|++.| .|++++.|+-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~-hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSV-HKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHh-cCCCccceeE
Confidence 5889 8999999999999999888 4668887763
No 22
>PHA00732 hypothetical protein
Probab=97.76 E-value=2.1e-05 Score=59.70 Aligned_cols=46 Identities=20% Similarity=0.422 Sum_probs=41.0
Q ss_pred cccccccccccCChHHHHHHHHhcCCCeee-eCCcccCChHHHHHHHHHh
Q 019587 257 PFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 257 p~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
||.|..||+.|.+...|+.|++.+..++.| .||+.|. .|..|++++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhccc
Confidence 689999999999999999999964456899 9999998 589999776
No 23
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.74 E-value=9.1e-06 Score=48.29 Aligned_cols=25 Identities=24% Similarity=0.638 Sum_probs=22.5
Q ss_pred CccchhhhcCCCceecCcccccccC
Q 019587 161 IPTPAQILIGPTQFSCPLCFKTFNR 185 (338)
Q Consensus 161 l~~h~~~h~~~~~~~C~~C~k~F~~ 185 (338)
|..|+++|+++++|.|+.|++.|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 4679999999999999999999963
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.67 E-value=3.1e-05 Score=44.33 Aligned_cols=22 Identities=36% Similarity=0.905 Sum_probs=14.7
Q ss_pred eee-eCCcccCChHHHHHHHHHh
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
|.| .|++.|..+..|++|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 566 6777777777777776653
No 25
>PHA00616 hypothetical protein
Probab=97.61 E-value=2.5e-05 Score=52.07 Aligned_cols=40 Identities=13% Similarity=0.192 Sum_probs=31.0
Q ss_pred ccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccC
Q 019587 217 RLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFA 268 (338)
Q Consensus 217 ~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~ 268 (338)
+|+|..|| +.|.+.+.|..|++.|+|++++.|+.--..|.
T Consensus 1 pYqC~~CG------------~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f~ 40 (44)
T PHA00616 1 MYQCLRCG------------GIFRKKKEVIEHLLSVHKQNKLTLEYFYIYFR 40 (44)
T ss_pred CCccchhh------------HHHhhHHHHHHHHHHhcCCCccceeEEEEEEE
Confidence 47788888 88888888888888888888888875444443
No 26
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.50 E-value=2.3e-05 Score=72.92 Aligned_cols=51 Identities=27% Similarity=0.554 Sum_probs=42.6
Q ss_pred CCCcccccc--cccccCChHHHHHHHHhc---------------------CCCeee-eCCcccCChHHHHHHHHH
Q 019587 254 GIKPFMCRK--CSKAFAVRGDWRTHEKNC---------------------GKLWYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 254 gekp~~C~~--CgksF~~~~~L~~H~k~h---------------------~k~~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
++|||+|++ |.|.+....-|+.|++-+ .|||+| .|+|+++....|+-|+..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 358899987 889888888888888721 489999 999999999999999653
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.47 E-value=7.4e-05 Score=42.72 Aligned_cols=23 Identities=22% Similarity=0.700 Sum_probs=17.9
Q ss_pred ccccccccccCChHHHHHHHHhc
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~h 280 (338)
|+|+.|++.|..+..|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 57888888888888888887754
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.42 E-value=0.00011 Score=41.90 Aligned_cols=23 Identities=30% Similarity=0.899 Sum_probs=15.3
Q ss_pred eee-eCCcccCChHHHHHHHHHhC
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKAFG 306 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~hh 306 (338)
|.| .|++.|..+..|+.|+++||
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 567 77777777777777777765
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.39 E-value=0.00012 Score=57.01 Aligned_cols=72 Identities=19% Similarity=0.424 Sum_probs=22.1
Q ss_pred ccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHhc-CCCeee-eCCcccCChH
Q 019587 219 PCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNC-GKLWYC-TCGSDFKHKR 296 (338)
Q Consensus 219 ~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h-~k~~~C-~Cgk~F~~~s 296 (338)
.|..|+ ..|.+...|..|+...++...- ..+.+.....+..+.+.- ...|.| .|++.|....
T Consensus 1 ~C~~C~------------~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~ 64 (100)
T PF12756_consen 1 QCLFCD------------ESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSRE 64 (100)
T ss_dssp ----------------------------------------------------------------SSEEBSSSS-EESSHH
T ss_pred Cccccc------------cccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHH
Confidence 488888 8899999999999876653211 122223344444454432 347999 9999999999
Q ss_pred HHHHHHHHhC
Q 019587 297 SLKDHIKAFG 306 (338)
Q Consensus 297 ~L~~H~r~hh 306 (338)
.|..||+.++
T Consensus 65 ~l~~Hm~~~~ 74 (100)
T PF12756_consen 65 ALQEHMRSKH 74 (100)
T ss_dssp HHHHHHHHTT
T ss_pred HHHHHHcCcc
Confidence 9999999874
No 30
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.30 E-value=0.00032 Score=49.19 Aligned_cols=25 Identities=24% Similarity=0.424 Sum_probs=10.6
Q ss_pred HHHHHHHHHH-hcC-CCcccccccccc
Q 019587 242 FRTLQTHYKR-KHG-IKPFMCRKCSKA 266 (338)
Q Consensus 242 ~~~L~~H~r~-H~g-ekp~~C~~Cgks 266 (338)
...|..|... |.. .+.+.|++|...
T Consensus 14 ~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 14 ESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred HHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 3445555443 222 133455555443
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.22 E-value=0.00015 Score=43.20 Aligned_cols=24 Identities=25% Similarity=0.679 Sum_probs=16.4
Q ss_pred Ceee-eCCcccCChHHHHHHHHHhC
Q 019587 283 LWYC-TCGSDFKHKRSLKDHIKAFG 306 (338)
Q Consensus 283 ~~~C-~Cgk~F~~~s~L~~H~r~hh 306 (338)
+|.| .|++.|.....|..|++.|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4667 67777777777777776664
No 32
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.11 E-value=0.00051 Score=48.15 Aligned_cols=53 Identities=21% Similarity=0.413 Sum_probs=39.2
Q ss_pred ceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHh
Q 019587 173 QFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRK 252 (338)
Q Consensus 173 ~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H 252 (338)
.|.|++|++. .+...|..|....+. ...+.+.|++|. ..+. ..|..|++.+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~--------------~~~~~v~CPiC~------------~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHR--------------SESKNVVCPICS------------SRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCc--------------CCCCCccCCCch------------hhhh--hHHHHHHHHh
Confidence 4899999995 567889999875432 223468999998 5443 4899999887
Q ss_pred cC
Q 019587 253 HG 254 (338)
Q Consensus 253 ~g 254 (338)
++
T Consensus 53 H~ 54 (54)
T PF05605_consen 53 HR 54 (54)
T ss_pred cC
Confidence 64
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.02 E-value=0.00042 Score=53.92 Aligned_cols=73 Identities=23% Similarity=0.373 Sum_probs=19.9
Q ss_pred ecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcC
Q 019587 175 SCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHG 254 (338)
Q Consensus 175 ~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~g 254 (338)
+|..|+..|.....|..||...++. .... . ..+.....|..+++...
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~-------------------~~~~-~------------~~l~~~~~~~~~~~~~~- 47 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGF-------------------DIPD-Q------------KYLVDPNRLLNYLRKKV- 47 (100)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Ccccccccccccccccccccccccc-------------------cccc-c------------ccccccccccccccccc-
Confidence 4899999999999999999754321 1110 0 22223334444443322
Q ss_pred CCcccccccccccCChHHHHHHHHhc
Q 019587 255 IKPFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 255 ekp~~C~~CgksF~~~~~L~~H~k~h 280 (338)
...+.|..|++.|.....|..|++.+
T Consensus 48 ~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 48 KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 22688999999999999999998863
No 34
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.86 E-value=0.00074 Score=38.39 Aligned_cols=23 Identities=30% Similarity=0.751 Sum_probs=17.0
Q ss_pred ccccccccccCChHHHHHHHHhc
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~h 280 (338)
|.|++|++.|..+..|..|++++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 67888888888888888888764
No 35
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.74 E-value=0.00079 Score=39.95 Aligned_cols=24 Identities=33% Similarity=0.821 Sum_probs=21.1
Q ss_pred cccccccccccCChHHHHHHHHhc
Q 019587 257 PFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 257 p~~C~~CgksF~~~~~L~~H~k~h 280 (338)
+|+|.+|++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 588999999999999999998866
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.40 E-value=0.0021 Score=36.90 Aligned_cols=22 Identities=41% Similarity=0.979 Sum_probs=17.4
Q ss_pred eee-eCCcccCChHHHHHHHHHh
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
|.| .|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 567 7888888888888888766
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.37 E-value=0.0009 Score=62.52 Aligned_cols=55 Identities=22% Similarity=0.333 Sum_probs=45.4
Q ss_pred CCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHH-hc------------------CCCcccccccccccCChHHHH
Q 019587 214 AMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKR-KH------------------GIKPFMCRKCSKAFAVRGDWR 274 (338)
Q Consensus 214 ~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~-H~------------------gekp~~C~~CgksF~~~~~L~ 274 (338)
++++|+|++-||. |.|+....|+-|+.- |- ..|||+|++|+|.+....-|+
T Consensus 346 d~KpykCpV~gC~----------K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLK 415 (423)
T COG5189 346 DGKPYKCPVEGCN----------KKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLK 415 (423)
T ss_pred cCceecCCCCCch----------hhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccce
Confidence 3589999986644 999999999999874 31 248999999999999998898
Q ss_pred HHHH
Q 019587 275 THEK 278 (338)
Q Consensus 275 ~H~k 278 (338)
.|.+
T Consensus 416 YHr~ 419 (423)
T COG5189 416 YHRK 419 (423)
T ss_pred eccc
Confidence 8864
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.15 E-value=0.0039 Score=35.72 Aligned_cols=24 Identities=21% Similarity=0.637 Sum_probs=19.7
Q ss_pred ccccccccccCChHHHHHHHHhcC
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKNCG 281 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~h~ 281 (338)
|+|..|+++|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578888888888888888887653
No 39
>PRK04860 hypothetical protein; Provisional
Probab=95.60 E-value=0.0053 Score=52.89 Aligned_cols=31 Identities=23% Similarity=0.588 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHhcCCCcccccccccccCChH
Q 019587 241 DFRTLQTHYKRKHGIKPFMCRKCSKAFAVRG 271 (338)
Q Consensus 241 ~~~~L~~H~r~H~gekp~~C~~CgksF~~~~ 271 (338)
....+..|.++|+|+++|.|..|++.|....
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 4567788888888888888888888876543
No 40
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.54 E-value=0.013 Score=40.15 Aligned_cols=32 Identities=25% Similarity=0.456 Sum_probs=17.2
Q ss_pred CCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCc
Q 019587 214 AMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKP 257 (338)
Q Consensus 214 ~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp 257 (338)
.+.+..|+.|+ ..+.+..+|.+|+..+++.||
T Consensus 21 S~~PatCP~C~------------a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICG------------AVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--------------EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcch------------hhccchhhHHHHHHHHhcccC
Confidence 34456677776 666666777777766666654
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.48 E-value=0.0069 Score=35.07 Aligned_cols=22 Identities=32% Similarity=0.943 Sum_probs=14.5
Q ss_pred eee-eCCcccCChHHHHHHHHHh
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
|.| .|++.|.....|+.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 566 6777777777777776543
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.06 E-value=0.016 Score=33.22 Aligned_cols=22 Identities=32% Similarity=0.641 Sum_probs=14.5
Q ss_pred eee-eCCcccCChHHHHHHHHHhC
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKAFG 306 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~hh 306 (338)
|+| .|+.... +..|.+|++.||
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 567 7777776 777777777765
No 43
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.02 E-value=0.032 Score=57.83 Aligned_cols=126 Identities=16% Similarity=0.294 Sum_probs=61.6
Q ss_pred CCCCCCCccccCccchhhhcCCCceecCcccccccCchHHHhccc-ccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCC
Q 019587 150 GGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFNRYNNMQMHMW-GHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCR 228 (338)
Q Consensus 150 ~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~~~L~~H~~-~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~ 228 (338)
+.|.+|...+.... ....|..| ..|.....|+.||+ .| +.+.|..|-.+-.
T Consensus 100 ~~C~~C~~~~~~~~--------~~~~~~~c-~~~~s~~~Lk~H~~~~H-------------------~~~~c~lC~~~~k 151 (669)
T KOG2231|consen 100 HSCHICDRRFRALY--------NKKECLHC-TEFKSVENLKNHMRDQH-------------------KLHLCSLCLQNLK 151 (669)
T ss_pred hhcCccccchhhhc--------ccCCCccc-cchhHHHHHHHHHHHhh-------------------hhhccccccccce
Confidence 45777765542111 11357777 77778888899985 44 1245555542210
Q ss_pred CCCCCCCCccCCCHHHHHHHHHH-hcCCCc----ccccccccccCChHHHHHHHHh-cCCCeeee----CCcccCChHHH
Q 019587 229 NNIDHPRSKPLKDFRTLQTHYKR-KHGIKP----FMCRKCSKAFAVRGDWRTHEKN-CGKLWYCT----CGSDFKHKRSL 298 (338)
Q Consensus 229 ~~~~h~~~k~F~~~~~L~~H~r~-H~gekp----~~C~~CgksF~~~~~L~~H~k~-h~k~~~C~----Cgk~F~~~s~L 298 (338)
.+.-. ...-....|+.|++. -.+++. -.|..|...|.....|.+|++. |+--.-|. ++.-|.....|
T Consensus 152 -if~~e--~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dL 228 (669)
T KOG2231|consen 152 -IFINE--RKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDL 228 (669)
T ss_pred -eeeee--eehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHH
Confidence 00000 111233456666553 111221 3566777777777777777663 22211220 23344455555
Q ss_pred HHHHHHhC
Q 019587 299 KDHIKAFG 306 (338)
Q Consensus 299 ~~H~r~hh 306 (338)
..|.|.+|
T Consensus 229 e~HfR~~H 236 (669)
T KOG2231|consen 229 EEHFRKGH 236 (669)
T ss_pred HHHhhhcC
Confidence 55555544
No 44
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.00 E-value=0.014 Score=40.07 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=13.0
Q ss_pred CCCeee-eCCcccCChHHHHHHHHHhC
Q 019587 281 GKLWYC-TCGSDFKHKRSLKDHIKAFG 306 (338)
Q Consensus 281 ~k~~~C-~Cgk~F~~~s~L~~H~r~hh 306 (338)
++|-.| .|+..+.+..+|++|+..+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHh
Confidence 456666 66666666666666665554
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.93 E-value=0.012 Score=34.10 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=21.3
Q ss_pred eecCcccccccCchHHHhccccc
Q 019587 174 FSCPLCFKTFNRYNNMQMHMWGH 196 (338)
Q Consensus 174 ~~C~~C~k~F~~~~~L~~H~~~H 196 (338)
|.|.+|++.|.....|+.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999865
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.37 E-value=0.015 Score=56.38 Aligned_cols=48 Identities=25% Similarity=0.322 Sum_probs=37.7
Q ss_pred CCCCCCCCcc----ccCccchh--hhcCC--CceecC--cccccccCchHHHhccccc
Q 019587 149 GGGCSLNKGQ----YWIPTPAQ--ILIGP--TQFSCP--LCFKTFNRYNNMQMHMWGH 196 (338)
Q Consensus 149 ~~~c~~c~~~----~~l~~h~~--~h~~~--~~~~C~--~C~k~F~~~~~L~~H~~~H 196 (338)
.+.|..|... +++..|.+ .|.++ +++.|+ .|++.|.+...+..|...|
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc
Confidence 4555555543 34778888 78888 899999 7999999999999998888
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.33 E-value=0.025 Score=33.54 Aligned_cols=24 Identities=38% Similarity=0.643 Sum_probs=21.2
Q ss_pred ceecCcccccccCchHHHhccccc
Q 019587 173 QFSCPLCFKTFNRYNNMQMHMWGH 196 (338)
Q Consensus 173 ~~~C~~C~k~F~~~~~L~~H~~~H 196 (338)
.|.|..|++.|.....|..|+++.
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 378999999999999999999754
No 48
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=94.11 E-value=0.021 Score=62.55 Aligned_cols=79 Identities=29% Similarity=0.522 Sum_probs=64.2
Q ss_pred cccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhc-------------------------CCCcccccccccccCCh
Q 019587 216 LRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKH-------------------------GIKPFMCRKCSKAFAVR 270 (338)
Q Consensus 216 ~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~-------------------------gekp~~C~~CgksF~~~ 270 (338)
+-++|+.|+ ..|+....|..|||..+ +.++|.|..|..++..+
T Consensus 464 kt~~cpkc~------------~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttn 531 (1406)
T KOG1146|consen 464 KTLKCPKCN------------WHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTN 531 (1406)
T ss_pred ccccCCccc------------hhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecc
Confidence 568999999 88999999999999832 13689999999999999
Q ss_pred HHHHHHHHh--c-------------------------------------------CCCeee-eCCcccCChHHHHHHHHH
Q 019587 271 GDWRTHEKN--C-------------------------------------------GKLWYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 271 ~~L~~H~k~--h-------------------------------------------~k~~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
..|.+|++. | .-.|.| .|+..-.-..+|+.||..
T Consensus 532 g~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 532 GNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred hHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 999999861 0 013889 999988888889888866
Q ss_pred hC
Q 019587 305 FG 306 (338)
Q Consensus 305 hh 306 (338)
-+
T Consensus 612 s~ 613 (1406)
T KOG1146|consen 612 SP 613 (1406)
T ss_pred CC
Confidence 54
No 49
>PRK04860 hypothetical protein; Provisional
Probab=94.05 E-value=0.021 Score=49.23 Aligned_cols=35 Identities=26% Similarity=0.747 Sum_probs=27.4
Q ss_pred cccccccccccCChHHHHHHHHhc--CCCeee-eCCcccCCh
Q 019587 257 PFMCRKCSKAFAVRGDWRTHEKNC--GKLWYC-TCGSDFKHK 295 (338)
Q Consensus 257 p~~C~~CgksF~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~ 295 (338)
+|.|. |++ ....+++|.++| +++|.| .|++.|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 68887 887 566788888876 678888 888888654
No 50
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.02 E-value=0.0095 Score=35.38 Aligned_cols=21 Identities=38% Similarity=0.982 Sum_probs=13.6
Q ss_pred eee-eCCcccCChHHHHHHHHH
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
|.| .|++.|.....|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 566 666666666666666543
No 51
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.93 E-value=0.075 Score=50.52 Aligned_cols=68 Identities=24% Similarity=0.417 Sum_probs=43.1
Q ss_pred ccCCCHHHHHHHHHHhcCCCcccccccc----cccCChHHHHHHHHhcCCCeee-e--C--C--cccCChHHHHHHHHHh
Q 019587 237 KPLKDFRTLQTHYKRKHGIKPFMCRKCS----KAFAVRGDWRTHEKNCGKLWYC-T--C--G--SDFKHKRSLKDHIKAF 305 (338)
Q Consensus 237 k~F~~~~~L~~H~r~H~gekp~~C~~Cg----ksF~~~~~L~~H~k~h~k~~~C-~--C--g--k~F~~~s~L~~H~r~h 305 (338)
+.|-+...|..|+|..+ ++-|.|..-+ ..|..-.+|.+|.+. .-|.| . | | ..|.....|..|+...
T Consensus 228 ~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~--~hy~ct~qtc~~~k~~vf~~~~el~~h~~~~ 304 (493)
T COG5236 228 IYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRN--AHYCCTFQTCRVGKCYVFPYHTELLEHLTRF 304 (493)
T ss_pred ceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhc--CceEEEEEEEecCcEEEeccHHHHHHHHHHH
Confidence 67777778888887654 3444443322 236666677777663 22455 2 3 2 3589999999998877
Q ss_pred CC
Q 019587 306 GN 307 (338)
Q Consensus 306 h~ 307 (338)
|.
T Consensus 305 h~ 306 (493)
T COG5236 305 HK 306 (493)
T ss_pred hh
Confidence 64
No 52
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.60 E-value=0.14 Score=29.22 Aligned_cols=21 Identities=24% Similarity=0.640 Sum_probs=15.3
Q ss_pred ccccccccccCChHHHHHHHHh
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKN 279 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~ 279 (338)
|+|..|+.... +..|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 67888887777 7788888876
No 53
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=91.44 E-value=0.21 Score=47.51 Aligned_cols=22 Identities=32% Similarity=0.650 Sum_probs=20.7
Q ss_pred ceecCcccccccCchHHHhccc
Q 019587 173 QFSCPLCFKTFNRYNNMQMHMW 194 (338)
Q Consensus 173 ~~~C~~C~k~F~~~~~L~~H~~ 194 (338)
.+.|-.|.|.|..+..|+.|||
T Consensus 195 r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred hheeeeeccccCCcHHHHHHHH
Confidence 4899999999999999999997
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.85 E-value=0.2 Score=29.25 Aligned_cols=20 Identities=30% Similarity=0.564 Sum_probs=12.3
Q ss_pred cccccccccCChHHHHHHHHh
Q 019587 259 MCRKCSKAFAVRGDWRTHEKN 279 (338)
Q Consensus 259 ~C~~CgksF~~~~~L~~H~k~ 279 (338)
.|+.||+.| ....|..|+++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 566666666 35566666654
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.82 E-value=0.052 Score=59.62 Aligned_cols=108 Identities=13% Similarity=0.192 Sum_probs=75.7
Q ss_pred eecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhc
Q 019587 174 FSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKH 253 (338)
Q Consensus 174 ~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~ 253 (338)
..|..|...|.....+..|-+.-.. . ......+.|..|. +.|.-...+. |+-
T Consensus 1229 l~~~~~e~~f~~~~~~~~~a~~~~~----------~--~~~sGe~~c~~~~------------~~~~~~~~~~-~l~--- 1280 (1406)
T KOG1146|consen 1229 LLPNALEQPFPQEPEPTATAPPKPP----------E--LPASGEGECGAVD------------ELLTPSFGIS-TLD--- 1280 (1406)
T ss_pred ccHHhhhcCccCcccccccCCCCCC----------c--CcCCCcchhhhcc------------ccccCcccee-ecc---
Confidence 6688889999888777766543210 0 0222346788887 5555544444 332
Q ss_pred CCCcccccccccccCChHHHHHHHHhc------------------C-CCeee-eCCcccCChHHHHHHHHHhCCCCC
Q 019587 254 GIKPFMCRKCSKAFAVRGDWRTHEKNC------------------G-KLWYC-TCGSDFKHKRSLKDHIKAFGNGHA 310 (338)
Q Consensus 254 gekp~~C~~CgksF~~~~~L~~H~k~h------------------~-k~~~C-~Cgk~F~~~s~L~~H~r~hh~~~~ 310 (338)
-..+|.|.+|...|.....|..|.+.. . ++| | .|...|.....|..|||..+...+
T Consensus 1281 ~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~~k 1356 (1406)
T KOG1146|consen 1281 VTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAHRRK 1356 (1406)
T ss_pred cchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhhccc
Confidence 235689999999999999999998631 1 345 9 999999999999999998865443
No 56
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=90.81 E-value=0.16 Score=46.39 Aligned_cols=46 Identities=28% Similarity=0.740 Sum_probs=24.6
Q ss_pred ccccccccccCChHHHHHHHHhc-CCCeee-eCCcccCChHHHHHHHHHh
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKNC-GKLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~h-~k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
|.|.+||.+.. +..+.+|+-.+ ...|.| .|++.|-. .+.+.|.+.-
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhhhhc
Confidence 45555655544 23445555543 455566 56666655 4555555544
No 57
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=90.78 E-value=0.19 Score=31.29 Aligned_cols=22 Identities=32% Similarity=0.785 Sum_probs=16.7
Q ss_pred Ceee-eCCcccCChHHHHHHHHH
Q 019587 283 LWYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 283 ~~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
+|.| .|++.|.....|..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 5778 888888888888887654
No 58
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.91 E-value=0.054 Score=52.38 Aligned_cols=69 Identities=20% Similarity=0.347 Sum_probs=57.2
Q ss_pred CceecCcccccccCchHHHhccc--ccCCCCcCCCCCcCCCCCCCC--cccccC--CCCCCCCCCCCCCCCccCCCHHHH
Q 019587 172 TQFSCPLCFKTFNRYNNMQMHMW--GHGSQYRKGPESLRGSQPTAM--LRLPCY--CCAPGCRNNIDHPRSKPLKDFRTL 245 (338)
Q Consensus 172 ~~~~C~~C~k~F~~~~~L~~H~~--~H~~~~~~~~~~~~~~~~~~~--~~~~C~--~C~~~c~~~~~h~~~k~F~~~~~L 245 (338)
.++.|..|...|.+...|..|.+ .| .++ +++.|. .|+ +.|.....+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h----------------~~~~~~~~~~p~~~~~------------~~~~~~~~~ 339 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNH----------------SGESLKPFSCPYSLCG------------KLFSRNDAL 339 (467)
T ss_pred cCCCCccccCCcccccccccccccccc----------------ccccCCceeeeccCCC------------ccccccccc
Confidence 57899999999999999999999 67 666 889999 788 889999999
Q ss_pred HHHHHHhcCCCcccccc--cccccC
Q 019587 246 QTHYKRKHGIKPFMCRK--CSKAFA 268 (338)
Q Consensus 246 ~~H~r~H~gekp~~C~~--CgksF~ 268 (338)
..|...|.+.+++.|.. |.+.+.
T Consensus 340 ~~~~~~~~~~~~~~~~~~~~~~~~~ 364 (467)
T COG5048 340 KRHILLHTSISPAKEKLLNSSSKFS 364 (467)
T ss_pred cCCcccccCCCccccccccCccccc
Confidence 99999998888777643 444444
No 59
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=89.00 E-value=0.29 Score=28.57 Aligned_cols=20 Identities=35% Similarity=0.702 Sum_probs=17.1
Q ss_pred eee-eCCcccCChHHHHHHHHH
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
..| .||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 579 999999 77799999875
No 60
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=88.82 E-value=0.15 Score=46.18 Aligned_cols=36 Identities=28% Similarity=0.456 Sum_probs=16.8
Q ss_pred ccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHH
Q 019587 237 KPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTH 276 (338)
Q Consensus 237 k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H 276 (338)
+.|-+..-|.+|++.. .|+|-+|-|.....--|..|
T Consensus 18 refddekiliqhqkak----hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 18 REFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred cccchhhhhhhhhhhc----cceeeeehhhhccCCCceee
Confidence 5555555555555432 25555555443333333333
No 61
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=88.47 E-value=1.4 Score=42.81 Aligned_cols=55 Identities=18% Similarity=0.317 Sum_probs=45.4
Q ss_pred ccccccccccCChHHHHHHHHh-c------------------------CCCeee-eCC---cccCChHHHHHHHHHhCCC
Q 019587 258 FMCRKCSKAFAVRGDWRTHEKN-C------------------------GKLWYC-TCG---SDFKHKRSLKDHIKAFGNG 308 (338)
Q Consensus 258 ~~C~~CgksF~~~~~L~~H~k~-h------------------------~k~~~C-~Cg---k~F~~~s~L~~H~r~hh~~ 308 (338)
-.|-.|++.|..-..-..||.. | +..|.| .|+ +.|..-.+.+.||+.....
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~HC 246 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKGHC 246 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhccCc
Confidence 4588899999999999999974 2 245889 999 9999999999999887555
Q ss_pred CCCc
Q 019587 309 HASC 312 (338)
Q Consensus 309 ~~~~ 312 (338)
.-+|
T Consensus 247 kl~y 250 (390)
T KOG2785|consen 247 KLPY 250 (390)
T ss_pred ccCC
Confidence 5666
No 62
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=87.23 E-value=0.4 Score=29.74 Aligned_cols=23 Identities=26% Similarity=0.507 Sum_probs=20.0
Q ss_pred cccccccccccCChHHHHHHHHh
Q 019587 257 PFMCRKCSKAFAVRGDWRTHEKN 279 (338)
Q Consensus 257 p~~C~~CgksF~~~~~L~~H~k~ 279 (338)
+|.|..|++.|.....|..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57899999999999999999763
No 63
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.11 E-value=0.55 Score=37.90 Aligned_cols=24 Identities=17% Similarity=0.279 Sum_probs=13.7
Q ss_pred CCeee-eCCcccCChHHHHHHHHHh
Q 019587 282 KLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 282 k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
..|+| .|.+.|-..-.+-.|-..|
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cceeCCCCCCccccccchhhhhhcc
Confidence 34666 6666666555555555444
No 64
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.29 E-value=0.99 Score=47.10 Aligned_cols=80 Identities=21% Similarity=0.345 Sum_probs=49.1
Q ss_pred ccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCccccccc------ccccCChHHHHHHHHhcCCCe---eeeCC
Q 019587 219 PCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKC------SKAFAVRGDWRTHEKNCGKLW---YCTCG 289 (338)
Q Consensus 219 ~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~C------gksF~~~~~L~~H~k~h~k~~---~C~Cg 289 (338)
.|..|. ..|-....|..|++.++ |.|..| +..|..-.+|..|.+.+...- .|.|+
T Consensus 184 ~C~~C~------------~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~HflCE~~~C~~~ 247 (669)
T KOG2231|consen 184 LCKFCH------------ERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHFLCEEEFCRTK 247 (669)
T ss_pred cchhhh------------hhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcCccccccccccc
Confidence 577777 77888888888887665 556555 455667778888877643211 12333
Q ss_pred ---cccCChHHHHHHHHHhCCCCCCccCC
Q 019587 290 ---SDFKHKRSLKDHIKAFGNGHASCGID 315 (338)
Q Consensus 290 ---k~F~~~s~L~~H~r~hh~~~~~~~C~ 315 (338)
..|.....|++|.+ ++.-++.|.|+
T Consensus 248 ~f~~~~~~ei~lk~~~~-~~~~e~~~~~~ 275 (669)
T KOG2231|consen 248 KFYVAFELEIELKAHNR-FIQHEKCYICR 275 (669)
T ss_pred eeeehhHHHHHHHhhcc-ccchheeccCC
Confidence 33455566666665 33445667775
No 65
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=83.54 E-value=2.7 Score=40.22 Aligned_cols=63 Identities=24% Similarity=0.414 Sum_probs=45.1
Q ss_pred HHHHHHHHHhcC-CCcccccccccccC-ChHHHHHHHH-hc----C-------------------CCeee-eCCcccCCh
Q 019587 243 RTLQTHYKRKHG-IKPFMCRKCSKAFA-VRGDWRTHEK-NC----G-------------------KLWYC-TCGSDFKHK 295 (338)
Q Consensus 243 ~~L~~H~r~H~g-ekp~~C~~CgksF~-~~~~L~~H~k-~h----~-------------------k~~~C-~Cgk~F~~~ 295 (338)
..|++|++--.+ .+..+|-.|..-+. .++.+..|+- .| + ..+.| .|.|.|+.+
T Consensus 129 eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdk 208 (423)
T KOG2482|consen 129 EALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDK 208 (423)
T ss_pred HHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCc
Confidence 356666654432 34568999986664 6777777764 23 1 24799 999999999
Q ss_pred HHHHHHHHHh
Q 019587 296 RSLKDHIKAF 305 (338)
Q Consensus 296 s~L~~H~r~h 305 (338)
..|+.|||..
T Consensus 209 ntLkeHMrkK 218 (423)
T KOG2482|consen 209 NTLKEHMRKK 218 (423)
T ss_pred HHHHHHHHhc
Confidence 9999999876
No 66
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=83.28 E-value=0.36 Score=43.82 Aligned_cols=49 Identities=24% Similarity=0.473 Sum_probs=40.3
Q ss_pred CCCcccccccccccCChHHHHHHHHhcCCCeee-eCCcccCChHHHHHH-HHHh
Q 019587 254 GIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKHKRSLKDH-IKAF 305 (338)
Q Consensus 254 gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~s~L~~H-~r~h 305 (338)
..||| |-.|++-|-...-|..|++ .|-|+| +|.|..-+-..|..| |++|
T Consensus 8 ~~kpw-cwycnrefddekiliqhqk--akhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 8 VDKPW-CWYCNREFDDEKILIQHQK--AKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred cCCce-eeecccccchhhhhhhhhh--hccceeeeehhhhccCCCceeehhhhh
Confidence 34565 8899999999999999998 577999 999998777788877 4555
No 67
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.41 E-value=0.78 Score=40.79 Aligned_cols=79 Identities=23% Similarity=0.466 Sum_probs=60.1
Q ss_pred cccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHh-c-----------CCC
Q 019587 216 LRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKN-C-----------GKL 283 (338)
Q Consensus 216 ~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~-h-----------~k~ 283 (338)
..+.|..-||- ..|........|+-+-+| -.|.+|.+.|...--|..|+.- | .-.
T Consensus 78 ~~~~cqvagc~----------~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dM 144 (253)
T KOG4173|consen 78 PAFACQVAGCC----------QVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDM 144 (253)
T ss_pred ccccccccchH----------HHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccH
Confidence 45778775532 667777777778766444 3699999999999999999762 3 345
Q ss_pred eee---eCCcccCChHHHHHHHHHhCC
Q 019587 284 WYC---TCGSDFKHKRSLKDHIKAFGN 307 (338)
Q Consensus 284 ~~C---~Cgk~F~~~s~L~~H~r~hh~ 307 (338)
|.| .|+-.|++...-++|+-..|.
T Consensus 145 y~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 145 YQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 999 399999999999999766654
No 68
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.71 E-value=2.9 Score=33.73 Aligned_cols=101 Identities=16% Similarity=0.262 Sum_probs=57.4
Q ss_pred CCCCCCCccccCccchhhhcCCCceecCcccccccCchHHHhccc--ccCCCCcCCCCCcCCCCCCCCcccccCCCCCCC
Q 019587 150 GGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFNRYNNMQMHMW--GHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGC 227 (338)
Q Consensus 150 ~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~~~L~~H~~--~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c 227 (338)
|.|..|+...- +-|-.|++||-+.-....|.+--. --...|..-++. .......|.-|.
T Consensus 2 Y~CPrC~skvC----------~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~------~~~~~~~C~~C~--- 62 (112)
T TIGR00622 2 YFCPQCRAKVC----------ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLE------EYNGSRFCFGCQ--- 62 (112)
T ss_pred ccCCCCCCCcc----------CCCCcCCcCCCEEeccchHHHhhhccCCCccccccccc------ccCCCCcccCcC---
Confidence 56777764421 236789999998877777765311 001112111111 011112488887
Q ss_pred CCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHHhc
Q 019587 228 RNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 228 ~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h 280 (338)
+.|....... ...-.....|+|..|...|-..-+.-.|...|
T Consensus 63 ---------~~f~~~~~~~--~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 63 ---------GPFPKPPVSP--FDELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ---------CCCCCccccc--ccccccccceeCCCCCCccccccchhhhhhcc
Confidence 6676432111 00022345799999999999999998886655
No 69
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=76.91 E-value=2.3 Score=28.03 Aligned_cols=24 Identities=38% Similarity=0.533 Sum_probs=11.0
Q ss_pred CCeee-eCCcccCCh----HHHHHHHHHh
Q 019587 282 KLWYC-TCGSDFKHK----RSLKDHIKAF 305 (338)
Q Consensus 282 k~~~C-~Cgk~F~~~----s~L~~H~r~h 305 (338)
+..+| .|++.+... +.|.+|++..
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 34556 666666553 5666666443
No 70
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=71.33 E-value=2.2 Score=35.52 Aligned_cols=24 Identities=33% Similarity=0.754 Sum_probs=15.7
Q ss_pred CCCeee-eCCcccCChHHHHHHHHHhCC
Q 019587 281 GKLWYC-TCGSDFKHKRSLKDHIKAFGN 307 (338)
Q Consensus 281 ~k~~~C-~Cgk~F~~~s~L~~H~r~hh~ 307 (338)
+.-..| .|||.|+. |++|++.||+
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-
T ss_pred cCeeEEccCCcccch---HHHHHHHccC
Confidence 455789 99999986 5999999963
No 71
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=70.63 E-value=1.9 Score=26.83 Aligned_cols=10 Identities=30% Similarity=1.092 Sum_probs=5.9
Q ss_pred Cccccccccc
Q 019587 256 KPFMCRKCSK 265 (338)
Q Consensus 256 kp~~C~~Cgk 265 (338)
.++.|++||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5566666653
No 72
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=69.88 E-value=3.5 Score=43.89 Aligned_cols=13 Identities=23% Similarity=0.562 Sum_probs=9.4
Q ss_pred CCCcccccccccc
Q 019587 254 GIKPFMCRKCSKA 266 (338)
Q Consensus 254 gekp~~C~~Cgks 266 (338)
...|..|+.||..
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 4567888888754
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=69.26 E-value=2.3 Score=29.79 Aligned_cols=27 Identities=26% Similarity=0.589 Sum_probs=22.4
Q ss_pred hcCCCcccccccccccCChHHHHHHHH
Q 019587 252 KHGIKPFMCRKCSKAFAVRGDWRTHEK 278 (338)
Q Consensus 252 H~gekp~~C~~CgksF~~~~~L~~H~k 278 (338)
.-|+--+.|+-||+.|....+..+|..
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 346777899999999999889999875
No 74
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=68.25 E-value=3.3 Score=34.41 Aligned_cols=23 Identities=35% Similarity=0.559 Sum_probs=18.9
Q ss_pred CCeee-eCCcccCChHHHHHHHHHhCC
Q 019587 282 KLWYC-TCGSDFKHKRSLKDHIKAFGN 307 (338)
Q Consensus 282 k~~~C-~Cgk~F~~~s~L~~H~r~hh~ 307 (338)
--..| .|||.|+ +|++|+.+|+.
T Consensus 75 D~IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 75 DYIICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred CeEEEeccCcchH---HHHHHHhcccC
Confidence 34689 9999997 68999999863
No 75
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=67.42 E-value=4.8 Score=27.36 Aligned_cols=19 Identities=26% Similarity=0.835 Sum_probs=11.5
Q ss_pred ee-eCCcccCCh-----HHHHHHHH
Q 019587 285 YC-TCGSDFKHK-----RSLKDHIK 303 (338)
Q Consensus 285 ~C-~Cgk~F~~~-----s~L~~H~r 303 (338)
.| .|++.+... +.|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 45 566666554 46666666
No 76
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=67.18 E-value=3.2 Score=43.48 Aligned_cols=25 Identities=32% Similarity=0.526 Sum_probs=23.3
Q ss_pred ceecCcccccccCchHHHhcccccC
Q 019587 173 QFSCPLCFKTFNRYNNMQMHMWGHG 197 (338)
Q Consensus 173 ~~~C~~C~k~F~~~~~L~~H~~~H~ 197 (338)
-|.|..|+|.|.....+..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999993
No 77
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=65.34 E-value=9.5 Score=36.70 Aligned_cols=48 Identities=21% Similarity=0.314 Sum_probs=30.6
Q ss_pred cccccccccCChHHHHHHHHh-cCCCeee-eC----CcccCChHHHHHHHHHhC
Q 019587 259 MCRKCSKAFAVRGDWRTHEKN-CGKLWYC-TC----GSDFKHKRSLKDHIKAFG 306 (338)
Q Consensus 259 ~C~~CgksF~~~~~L~~H~k~-h~k~~~C-~C----gk~F~~~s~L~~H~r~hh 306 (338)
+|..|.+.|-.-..|..|++. |++-|.| .= .+-|+....|.+|.+.-|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h 275 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAH 275 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCc
Confidence 477777777777777777764 6666665 32 233666677777766544
No 78
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=65.03 E-value=3.6 Score=37.85 Aligned_cols=46 Identities=24% Similarity=0.572 Sum_probs=36.6
Q ss_pred cccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccCChHHHHHHHH
Q 019587 218 LPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEK 278 (338)
Q Consensus 218 ~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k 278 (338)
|.|..||..+ -+..|-.|+-+-+| .-|.|-.||+.|.+ .+.+.|.+
T Consensus 4 FtCnvCgEsv-------------KKp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESV-------------KKPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhc-------------cccchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 7899998433 13467789988777 78999999999998 78888865
No 79
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=61.89 E-value=4.3 Score=36.64 Aligned_cols=55 Identities=16% Similarity=0.251 Sum_probs=31.3
Q ss_pred CCceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCC
Q 019587 171 PTQFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPG 226 (338)
Q Consensus 171 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 226 (338)
.+.+.|++|++.|.....+....+.-...... .....+..|.--....|+.||-.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~-~~~Y~~vnP~~Y~V~vCP~CgyA 57 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDF-CPRYKGVNPLFYEVWVCPHCGYA 57 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCC-ccccCCCCCeeeeEEECCCCCCc
Confidence 35689999999999887776666542111000 01112223332234689999943
No 80
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=61.48 E-value=1.3 Score=39.96 Aligned_cols=41 Identities=22% Similarity=0.479 Sum_probs=28.3
Q ss_pred CCcccccccccccCChHHHHHHHHhc------------C-----CCeee-eCCcccCCh
Q 019587 255 IKPFMCRKCSKAFAVRGDWRTHEKNC------------G-----KLWYC-TCGSDFKHK 295 (338)
Q Consensus 255 ekp~~C~~CgksF~~~~~L~~H~k~h------------~-----k~~~C-~Cgk~F~~~ 295 (338)
+|.+.|++|++.|..+.-+....+.- . ..+.| .||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 46688999999998776555555421 1 23689 999988655
No 81
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=61.44 E-value=2.3 Score=44.55 Aligned_cols=24 Identities=33% Similarity=0.560 Sum_probs=22.6
Q ss_pred cccccccccccCChHHHHHHHHhc
Q 019587 257 PFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 257 p~~C~~CgksF~~~~~L~~H~k~h 280 (338)
-|.|.+|+|.|.....+..|||+|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 489999999999999999999998
No 82
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=60.49 E-value=3.3 Score=31.77 Aligned_cols=31 Identities=26% Similarity=0.799 Sum_probs=20.0
Q ss_pred CcccccccccccCChHHHHHHHHhcCCCeee-eCCcccCC
Q 019587 256 KPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKH 294 (338)
Q Consensus 256 kp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~ 294 (338)
..|.|+.|++. .+.+..-.-|.| .||..|.-
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccCeEEcCCCCCeecc
Confidence 45778888754 233444567888 78877753
No 83
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=60.15 E-value=4 Score=28.63 Aligned_cols=27 Identities=19% Similarity=0.527 Sum_probs=23.6
Q ss_pred cCCCeee-eCCcccCChHHHHHHHHHhC
Q 019587 280 CGKLWYC-TCGSDFKHKRSLKDHIKAFG 306 (338)
Q Consensus 280 h~k~~~C-~Cgk~F~~~s~L~~H~r~hh 306 (338)
++--+.| .||+.|...-+..+|+...|
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4677999 99999999999999987665
No 84
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=59.46 E-value=7.6 Score=24.64 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=24.5
Q ss_pred CCCCCCccccCccchhhhcCCCceecCccccccc
Q 019587 151 GCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFN 184 (338)
Q Consensus 151 ~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~ 184 (338)
.|..|...|.+.... +-......+|..|+..|.
T Consensus 4 ~Cp~C~~~y~i~d~~-ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-IPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHH-CCCCCcEEECCCCCCEeC
Confidence 588899888877764 333345699999998873
No 85
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=59.44 E-value=4.6 Score=32.44 Aligned_cols=14 Identities=29% Similarity=0.850 Sum_probs=6.7
Q ss_pred CCeee-eCCcccCCh
Q 019587 282 KLWYC-TCGSDFKHK 295 (338)
Q Consensus 282 k~~~C-~Cgk~F~~~ 295 (338)
.|..| .||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 34445 555555444
No 86
>PF15269 zf-C2H2_7: Zinc-finger
Probab=57.89 E-value=8.1 Score=25.86 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=15.8
Q ss_pred eee-eCCcccCChHHHHHHHHH
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
|+| +|.....-++.|-.||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 567 787777778888888764
No 87
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=57.68 E-value=8.1 Score=27.49 Aligned_cols=7 Identities=43% Similarity=1.341 Sum_probs=3.5
Q ss_pred cccCCCC
Q 019587 218 LPCYCCA 224 (338)
Q Consensus 218 ~~C~~C~ 224 (338)
|+|+.||
T Consensus 28 F~CPnCG 34 (61)
T COG2888 28 FPCPNCG 34 (61)
T ss_pred eeCCCCC
Confidence 5555554
No 88
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=57.67 E-value=6.1 Score=25.03 Aligned_cols=34 Identities=12% Similarity=0.178 Sum_probs=23.3
Q ss_pred CCCCCCCccccCccchhhhcCCCceecCccccccc
Q 019587 150 GGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFN 184 (338)
Q Consensus 150 ~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~ 184 (338)
..|..|+..|.+..-... .......|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-CCCCEEECCCCCCEEE
Confidence 458889988887654322 2223688999998874
No 89
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=56.17 E-value=5.1 Score=39.32 Aligned_cols=44 Identities=25% Similarity=0.388 Sum_probs=29.4
Q ss_pred eee-e--CCcccCChHHHHHHHHHhCCCCCCccCCCCCCCCccchhhccCcccccC
Q 019587 284 WYC-T--CGSDFKHKRSLKDHIKAFGNGHASCGIDTFEDDEPASEIEQDNNESSRD 336 (338)
Q Consensus 284 ~~C-~--Cgk~F~~~s~L~~H~r~hh~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~ 336 (338)
|.| . |+..|...+.+..|.|.|... ...|++.+......|+|.|
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheRq---------eqgepaa~~~~~~pesSlD 448 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHERQ---------EQGEPAATGPRLAPESSLD 448 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhhh---------hhccccccCCCCCCCCCcc
Confidence 557 2 999999999999999999322 3444454444444455544
No 90
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=53.59 E-value=8.1 Score=32.63 Aligned_cols=20 Identities=20% Similarity=0.532 Sum_probs=14.7
Q ss_pred CCceecCcccccccCchHHH
Q 019587 171 PTQFSCPLCFKTFNRYNNMQ 190 (338)
Q Consensus 171 ~~~~~C~~C~k~F~~~~~L~ 190 (338)
..-|.|+.|+..|.....+.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~ 116 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQ 116 (147)
T ss_pred CcEEECcCCCCEeeHHHHHH
Confidence 34599999999998655443
No 91
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=52.68 E-value=3.2 Score=30.80 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=7.1
Q ss_pred CCccccc--ccccccC
Q 019587 255 IKPFMCR--KCSKAFA 268 (338)
Q Consensus 255 ekp~~C~--~CgksF~ 268 (338)
++.++|. .||.+|.
T Consensus 25 ~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 25 ERYHQCQNVNCSATFI 40 (72)
T ss_pred eeeeecCCCCCCCEEE
Confidence 3445554 5555554
No 92
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=51.63 E-value=7.3 Score=31.79 Aligned_cols=25 Identities=36% Similarity=0.788 Sum_probs=19.5
Q ss_pred CCCeee-eCCcccCChHHHHHHHHHh
Q 019587 281 GKLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 281 ~k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
.-.|+| .|.+-|.....|+.|.++.
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhcc
Confidence 345888 8888888888888887654
No 93
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=50.08 E-value=12 Score=23.76 Aligned_cols=33 Identities=21% Similarity=0.587 Sum_probs=24.6
Q ss_pred CCCCCCccccCccchhhhcCCCceecCccccccc
Q 019587 151 GCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFN 184 (338)
Q Consensus 151 ~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~ 184 (338)
.|..|...|.+.... +..+.+..+|+.|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~-l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHH-cccCCcEEECCCCCcEee
Confidence 588898888877654 334455799999998884
No 94
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=49.58 E-value=13 Score=33.61 Aligned_cols=27 Identities=30% Similarity=0.568 Sum_probs=21.5
Q ss_pred CCCeee-eCCcccCChHHHHHHHHHhCC
Q 019587 281 GKLWYC-TCGSDFKHKRSLKDHIKAFGN 307 (338)
Q Consensus 281 ~k~~~C-~Cgk~F~~~s~L~~H~r~hh~ 307 (338)
+..|.| .|+|.|+-..-.++||...|.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 346999 999999999999999988874
No 95
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=47.86 E-value=15 Score=31.04 Aligned_cols=37 Identities=14% Similarity=0.477 Sum_probs=24.6
Q ss_pred CCCcccccccccccCChHHHHH-HHHhcCCCeee-eCCcccC
Q 019587 254 GIKPFMCRKCSKAFAVRGDWRT-HEKNCGKLWYC-TCGSDFK 293 (338)
Q Consensus 254 gekp~~C~~CgksF~~~~~L~~-H~k~h~k~~~C-~Cgk~F~ 293 (338)
+..-|.|+.|++.|.....+.. + . ...|.| .||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d--~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLD--M-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcC--C-CCcEECCCCCCEEE
Confidence 4456899999998886544433 2 1 334999 8987653
No 96
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=46.98 E-value=4.4 Score=24.34 Aligned_cols=20 Identities=35% Similarity=0.796 Sum_probs=9.1
Q ss_pred eee-eCCcccCChHHHHHHHHH
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
|.| .|++.| .....+.|.+-
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~C 21 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSC 21 (28)
T ss_dssp EEETTTTEEE-EGGGTTT----
T ss_pred CeeecCCCCc-CcCCcCCCCcc
Confidence 456 666666 33445555443
No 97
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.52 E-value=10 Score=33.82 Aligned_cols=78 Identities=19% Similarity=0.468 Sum_probs=51.7
Q ss_pred ceecCc--ccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHH
Q 019587 173 QFSCPL--CFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYK 250 (338)
Q Consensus 173 ~~~C~~--C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r 250 (338)
.|.|++ |-+.|........|-.+.+ + -.|..|. +.|.....|..|+.
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h---------------~----~sCs~C~------------r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLH---------------G----NSCSFCK------------RAFPTGHLLDAHIL 127 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcc---------------c----chhHHHH------------HhCCchhhhhHHHH
Confidence 356655 6666766666666653221 1 2577777 77777777777764
Q ss_pred H----------hcCCCcccccc--cccccCChHHHHHHHH-hcC
Q 019587 251 R----------KHGIKPFMCRK--CSKAFAVRGDWRTHEK-NCG 281 (338)
Q Consensus 251 ~----------H~gekp~~C~~--CgksF~~~~~L~~H~k-~h~ 281 (338)
- -.|.-.|+|-+ |+..|....+.+.|+- +|.
T Consensus 128 E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 128 EWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 3 23556789954 9999998888888975 464
No 98
>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=46.35 E-value=18 Score=31.04 Aligned_cols=34 Identities=18% Similarity=0.427 Sum_probs=25.1
Q ss_pred hcCCCcccccccccccCChHHHHHHHHhcCCCeee-eCCccc
Q 019587 252 KHGIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDF 292 (338)
Q Consensus 252 H~gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F 292 (338)
..+..-|.|+.|+..|+.-.++. .-|.| .||...
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~-------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME-------LNFTCPRCGAML 138 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH-------cCCcCCCCCCEe
Confidence 34456688888888888777775 36888 888764
No 99
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=45.77 E-value=9.5 Score=33.05 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=10.3
Q ss_pred hcCCCcccccccc
Q 019587 252 KHGIKPFMCRKCS 264 (338)
Q Consensus 252 H~gekp~~C~~Cg 264 (338)
+.|+-|-+|++||
T Consensus 144 ~~ge~P~~CPiCg 156 (166)
T COG1592 144 HEGEAPEVCPICG 156 (166)
T ss_pred ccCCCCCcCCCCC
Confidence 4567888888888
No 100
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=44.37 E-value=13 Score=35.20 Aligned_cols=46 Identities=20% Similarity=0.276 Sum_probs=24.7
Q ss_pred ccccccccCChHHHHHHHHhcCCCeee-eCCcccCChHHHHHHHHHh
Q 019587 260 CRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 260 C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
|-.|.-.|.....-..-..+-.-.|.| .|...|-..-..-.|-..|
T Consensus 365 Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 365 CFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 666666665332211111112345777 7777777776666666655
No 101
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=44.18 E-value=25 Score=34.29 Aligned_cols=51 Identities=25% Similarity=0.547 Sum_probs=43.3
Q ss_pred ccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCC-----------------------Ccccccccc---cccCCh
Q 019587 217 RLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGI-----------------------KPFMCRKCS---KAFAVR 270 (338)
Q Consensus 217 ~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~ge-----------------------kp~~C~~Cg---ksF~~~ 270 (338)
|-.|-.|+ +.+++.-....||..+||- .-|.|-.|+ +.|..-
T Consensus 166 Pt~CLfC~------------~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sl 233 (390)
T KOG2785|consen 166 PTDCLFCD------------KKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSL 233 (390)
T ss_pred CcceeecC------------CCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCccccc
Confidence 35688898 8899999999999998872 347898898 999999
Q ss_pred HHHHHHHHh
Q 019587 271 GDWRTHEKN 279 (338)
Q Consensus 271 ~~L~~H~k~ 279 (338)
...+.||..
T Consensus 234 eavr~HM~~ 242 (390)
T KOG2785|consen 234 EAVRAHMRD 242 (390)
T ss_pred HHHHHHHhh
Confidence 999999984
No 102
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=43.81 E-value=9.9 Score=23.79 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=5.7
Q ss_pred Cccccccccc
Q 019587 256 KPFMCRKCSK 265 (338)
Q Consensus 256 kp~~C~~Cgk 265 (338)
.|..|++||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3556666663
No 103
>PHA00626 hypothetical protein
Probab=41.92 E-value=5.8 Score=27.86 Aligned_cols=14 Identities=14% Similarity=0.494 Sum_probs=8.9
Q ss_pred CcccccccccccCC
Q 019587 256 KPFMCRKCSKAFAV 269 (338)
Q Consensus 256 kp~~C~~CgksF~~ 269 (338)
..|+|..||..|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 45677777766663
No 104
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=41.79 E-value=50 Score=26.08 Aligned_cols=26 Identities=19% Similarity=0.479 Sum_probs=21.9
Q ss_pred CCeee-----eCCcccCChHHHHHHHHHhCC
Q 019587 282 KLWYC-----TCGSDFKHKRSLKDHIKAFGN 307 (338)
Q Consensus 282 k~~~C-----~Cgk~F~~~s~L~~H~r~hh~ 307 (338)
..|.| .|+..+.....+++|++.+|.
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 34788 399999999999999999873
No 105
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=41.01 E-value=21 Score=28.68 Aligned_cols=32 Identities=19% Similarity=0.503 Sum_probs=24.4
Q ss_pred CCCCCCCCCCcccc-CccchhhhcCCCceecCcccccccCc
Q 019587 147 GRGGGCSLNKGQYW-IPTPAQILIGPTQFSCPLCFKTFNRY 186 (338)
Q Consensus 147 ~~~~~c~~c~~~~~-l~~h~~~h~~~~~~~C~~C~k~F~~~ 186 (338)
|.-..|.-|+..|+ |. +.|..|+.||..|.-.
T Consensus 7 GtKR~Cp~CG~kFYDLn--------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLN--------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccCC--------CCCccCCCCCCccCcc
Confidence 34557999998877 33 3578899999999766
No 106
>PF14353 CpXC: CpXC protein
Probab=40.51 E-value=9.8 Score=31.12 Aligned_cols=46 Identities=22% Similarity=0.320 Sum_probs=27.7
Q ss_pred CCCCCCccccCccchh------------hhcCC-CceecCcccccccCchHHHhccccc
Q 019587 151 GCSLNKGQYWIPTPAQ------------ILIGP-TQFSCPLCFKTFNRYNNMQMHMWGH 196 (338)
Q Consensus 151 ~c~~c~~~~~l~~h~~------------~h~~~-~~~~C~~C~k~F~~~~~L~~H~~~H 196 (338)
.|..|+..|....... +..|. -.|.|+.||..|.-...+.-|-..+
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCCC
Confidence 5888887765332222 22222 2489999999987666665554433
No 107
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=39.99 E-value=14 Score=30.63 Aligned_cols=15 Identities=33% Similarity=0.871 Sum_probs=11.6
Q ss_pred cccccccccccCChH
Q 019587 257 PFMCRKCSKAFAVRG 271 (338)
Q Consensus 257 p~~C~~CgksF~~~~ 271 (338)
||+|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678888888888554
No 108
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.15 E-value=21 Score=31.20 Aligned_cols=34 Identities=21% Similarity=0.514 Sum_probs=24.3
Q ss_pred CCCcccccccccccCChHHHHHHHHhcCCCeee-eCCcccCC
Q 019587 254 GIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKH 294 (338)
Q Consensus 254 gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~ 294 (338)
...-|.|+.|++.|+.-..+. ..|.| .||.....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~-------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME-------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh-------cCCcCCCCCCCCee
Confidence 345688888888888776653 36888 88876543
No 109
>PRK14873 primosome assembly protein PriA; Provisional
Probab=38.69 E-value=21 Score=37.87 Aligned_cols=10 Identities=20% Similarity=0.873 Sum_probs=6.2
Q ss_pred cccccccccc
Q 019587 257 PFMCRKCSKA 266 (338)
Q Consensus 257 p~~C~~Cgks 266 (338)
++.|+.||..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 5667777643
No 110
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=38.50 E-value=25 Score=20.55 Aligned_cols=19 Identities=16% Similarity=0.319 Sum_probs=11.4
Q ss_pred cccccccccCChHHHHHHHH
Q 019587 259 MCRKCSKAFAVRGDWRTHEK 278 (338)
Q Consensus 259 ~C~~CgksF~~~~~L~~H~k 278 (338)
.|++|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466676666 3456666654
No 111
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.36 E-value=22 Score=36.39 Aligned_cols=6 Identities=33% Similarity=1.004 Sum_probs=2.8
Q ss_pred ccCCCC
Q 019587 219 PCYCCA 224 (338)
Q Consensus 219 ~C~~C~ 224 (338)
.|+.|+
T Consensus 255 ~Cp~C~ 260 (505)
T TIGR00595 255 TCPQCG 260 (505)
T ss_pred CCCCCC
Confidence 444444
No 112
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.44 E-value=19 Score=29.79 Aligned_cols=36 Identities=22% Similarity=0.351 Sum_probs=24.1
Q ss_pred CCCCCCCccccCccchhhhcCCCceecCcccccccCc
Q 019587 150 GGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFNRY 186 (338)
Q Consensus 150 ~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~ 186 (338)
-.|..|+... ....-..-.|...|+|..|++.|...
T Consensus 31 ~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccc-eeeECCccccccccccCCcCcceeee
Confidence 4577777554 44444444445679999999999765
No 113
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=36.65 E-value=15 Score=23.96 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=21.1
Q ss_pred CCCCCCCCccccCccchhhhcCCCceecCcccc
Q 019587 149 GGGCSLNKGQYWIPTPAQILIGPTQFSCPLCFK 181 (338)
Q Consensus 149 ~~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k 181 (338)
.|.|..|+..|.....+.. ...-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE---DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC---CCCCcCCCCCC
Confidence 5778888888775554433 45678888887
No 114
>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=36.59 E-value=17 Score=31.09 Aligned_cols=34 Identities=12% Similarity=0.289 Sum_probs=25.9
Q ss_pred CCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccC
Q 019587 214 AMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFA 268 (338)
Q Consensus 214 ~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~ 268 (338)
...-|.|+.|+ ..|+..-++. .-|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~------------~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMC------------VRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCC------------cEeeHHHHHH---------cCCcCCCCCCEee
Confidence 33458999998 8888777764 2599999997754
No 115
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=36.27 E-value=19 Score=31.28 Aligned_cols=25 Identities=20% Similarity=0.309 Sum_probs=20.4
Q ss_pred CCCCCCCCCccccCccchhhhcCCCceecCcccc
Q 019587 148 RGGGCSLNKGQYWIPTPAQILIGPTQFSCPLCFK 181 (338)
Q Consensus 148 ~~~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k 181 (338)
..|.|.+|+- ++.|+.|-.|++||.
T Consensus 133 ~~~vC~vCGy---------~~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGY---------THEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCC---------cccCCCCCcCCCCCC
Confidence 3799999984 356788999999994
No 116
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=36.09 E-value=22 Score=32.15 Aligned_cols=25 Identities=28% Similarity=0.329 Sum_probs=20.1
Q ss_pred CCcccccccccccCChHHHHHHHHh
Q 019587 255 IKPFMCRKCSKAFAVRGDWRTHEKN 279 (338)
Q Consensus 255 ekp~~C~~CgksF~~~~~L~~H~k~ 279 (338)
+..|.|..|+|.|.-...++.|+.+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhh
Confidence 4469999999999999999999874
No 117
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=36.05 E-value=6.2 Score=26.54 Aligned_cols=35 Identities=20% Similarity=0.477 Sum_probs=17.2
Q ss_pred ccccccccCChHHHHHHHHhcCCCeee-e--CCcccCC
Q 019587 260 CRKCSKAFAVRGDWRTHEKNCGKLWYC-T--CGSDFKH 294 (338)
Q Consensus 260 C~~CgksF~~~~~L~~H~k~h~k~~~C-~--Cgk~F~~ 294 (338)
|+.||..-.-+.....+...-+.-|.| . ||..|..
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVA 39 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEE
Confidence 666665444333333333333455666 2 6666643
No 118
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=35.85 E-value=15 Score=31.45 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=7.5
Q ss_pred ccccCCCCCCC
Q 019587 217 RLPCYCCAPGC 227 (338)
Q Consensus 217 ~~~C~~C~~~c 227 (338)
.+.|..||+.|
T Consensus 28 ~~~c~~c~~~f 38 (154)
T PRK00464 28 RRECLACGKRF 38 (154)
T ss_pred eeeccccCCcc
Confidence 37888888444
No 119
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=34.05 E-value=22 Score=23.55 Aligned_cols=30 Identities=17% Similarity=0.211 Sum_probs=20.6
Q ss_pred CCCCCCCCccccCccchhhhcCCCceecCccccccc
Q 019587 149 GGGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFN 184 (338)
Q Consensus 149 ~~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~ 184 (338)
.|.|..|+..+.+.... ..+.|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~~------~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYG------TGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCC------CceECCCCCCeEE
Confidence 46788888776654332 1688999997653
No 120
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=33.74 E-value=20 Score=29.81 Aligned_cols=26 Identities=35% Similarity=0.823 Sum_probs=16.5
Q ss_pred ccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCc
Q 019587 217 RLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKP 257 (338)
Q Consensus 217 ~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp 257 (338)
-..|-.|| |.|+. |.+|++.|+|..|
T Consensus 72 ~i~clecG------------k~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECG------------KKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--------------EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCC------------cccch---HHHHHHHccCCCH
Confidence 36899999 87765 6899999988765
No 121
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=33.42 E-value=26 Score=24.92 Aligned_cols=7 Identities=29% Similarity=0.871 Sum_probs=4.0
Q ss_pred cccCCCC
Q 019587 218 LPCYCCA 224 (338)
Q Consensus 218 ~~C~~C~ 224 (338)
|.|+.||
T Consensus 26 F~CPnCG 32 (59)
T PRK14890 26 FLCPNCG 32 (59)
T ss_pred eeCCCCC
Confidence 5555555
No 122
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=33.34 E-value=5 Score=38.60 Aligned_cols=51 Identities=27% Similarity=0.564 Sum_probs=40.6
Q ss_pred CCcccccc--cccccCChHHHHHHHHh---------------c------CCCeee-eCCcccCChHHHHHHHHHh
Q 019587 255 IKPFMCRK--CSKAFAVRGDWRTHEKN---------------C------GKLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 255 ekp~~C~~--CgksF~~~~~L~~H~k~---------------h------~k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
.++|+|.+ |.+.......|+.|... | .|+|+| +|.|+++....|+-|...-
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~~~ 421 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRTHS 421 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceeehh
Confidence 58899976 99999988888888652 1 389999 9999999888887775443
No 123
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=33.23 E-value=37 Score=22.10 Aligned_cols=22 Identities=23% Similarity=0.492 Sum_probs=11.2
Q ss_pred cccccccccC--ChHHHHHHHHhc
Q 019587 259 MCRKCSKAFA--VRGDWRTHEKNC 280 (338)
Q Consensus 259 ~C~~CgksF~--~~~~L~~H~k~h 280 (338)
.|+.||..|. ...+-..|.+-|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 5666665554 344445555443
No 124
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.03 E-value=20 Score=31.36 Aligned_cols=32 Identities=16% Similarity=0.405 Sum_probs=24.6
Q ss_pred cccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCcccccccccccC
Q 019587 216 LRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKPFMCRKCSKAFA 268 (338)
Q Consensus 216 ~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp~~C~~CgksF~ 268 (338)
.-|.|+.|+ +.|+..-++. .-|.|+.||....
T Consensus 116 ~~Y~Cp~C~------------~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCH------------IRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCC------------cEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 458999998 7787766652 3699999997765
No 125
>PF12907 zf-met2: Zinc-binding
Probab=31.82 E-value=9.4 Score=24.97 Aligned_cols=28 Identities=21% Similarity=0.414 Sum_probs=15.4
Q ss_pred eee-eCCcccC---ChHHHHHHHHHhCCCCCC
Q 019587 284 WYC-TCGSDFK---HKRSLKDHIKAFGNGHAS 311 (338)
Q Consensus 284 ~~C-~Cgk~F~---~~s~L~~H~r~hh~~~~~ 311 (338)
+.| +|-..|. ....|+.|....|.+...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~ 33 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTF 33 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCH
Confidence 456 6665553 334577776665555433
No 126
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=31.55 E-value=22 Score=24.08 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=20.4
Q ss_pred CCCCCCCCccccCccchhhhcCCCceecCcccc
Q 019587 149 GGGCSLNKGQYWIPTPAQILIGPTQFSCPLCFK 181 (338)
Q Consensus 149 ~~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k 181 (338)
.|.|..|+..|.+...+.. ...-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSD---DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCC---CCCCCCCCCCC
Confidence 5678888887776544322 34567999986
No 127
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.40 E-value=49 Score=32.95 Aligned_cols=39 Identities=18% Similarity=0.562 Sum_probs=26.4
Q ss_pred cCCCcccccccccccCChHHHHHHHHhcCCCeee-eCCccc
Q 019587 253 HGIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDF 292 (338)
Q Consensus 253 ~gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F 292 (338)
+...-|.|+.|.+.|..-..++.= -.-.--|.| .|+-..
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L~-~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQLL-DNETGEFHCENCGGEL 163 (436)
T ss_pred cccccccCCccccchhhhHHHHhh-cccCceEEEecCCCch
Confidence 455679999999999866554431 111356899 887554
No 128
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=30.47 E-value=24 Score=22.33 Aligned_cols=31 Identities=13% Similarity=0.139 Sum_probs=20.3
Q ss_pred CCCCCCCCccccCccchhhhcCCCceecCccccc
Q 019587 149 GGGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKT 182 (338)
Q Consensus 149 ~~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~ 182 (338)
.|.|..|+..|.+...... ...-.|+.||..
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD---DPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEecCC---CCCCCCCCCCCc
Confidence 4678888887765544322 345678888873
No 129
>PRK05580 primosome assembly protein PriA; Validated
Probab=30.41 E-value=33 Score=36.43 Aligned_cols=6 Identities=33% Similarity=1.060 Sum_probs=2.6
Q ss_pred ccCCCC
Q 019587 219 PCYCCA 224 (338)
Q Consensus 219 ~C~~C~ 224 (338)
.|..||
T Consensus 410 ~Ch~Cg 415 (679)
T PRK05580 410 RCHHCG 415 (679)
T ss_pred ECCCCc
Confidence 444444
No 130
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=29.77 E-value=27 Score=22.49 Aligned_cols=33 Identities=12% Similarity=0.126 Sum_probs=16.7
Q ss_pred CCCCCCccccCccchhhhcCCCc----eecCcccccc
Q 019587 151 GCSLNKGQYWIPTPAQILIGPTQ----FSCPLCFKTF 183 (338)
Q Consensus 151 ~c~~c~~~~~l~~h~~~h~~~~~----~~C~~C~k~F 183 (338)
.|..|+..-..-...|+..+..+ |.|..|+..|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 46667654333233344333322 8899999876
No 131
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=29.69 E-value=12 Score=29.12 Aligned_cols=30 Identities=30% Similarity=0.830 Sum_probs=17.4
Q ss_pred CcccccccccccCChHHHHHHHHhcCCCeee-eCCcccC
Q 019587 256 KPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFK 293 (338)
Q Consensus 256 kp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~ 293 (338)
..|.|+.||+.-..+ ...-.|.| .|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vkR--------~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR--------VATGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEEE--------EETTEEEETTTTEEEE
T ss_pred CCCcCCCCCCceeEE--------eeeEEeecCCCCCEEe
Confidence 457788887643322 12344788 7887774
No 132
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=29.47 E-value=41 Score=31.03 Aligned_cols=15 Identities=33% Similarity=1.041 Sum_probs=11.4
Q ss_pred CceecCcccccccCc
Q 019587 172 TQFSCPLCFKTFNRY 186 (338)
Q Consensus 172 ~~~~C~~C~k~F~~~ 186 (338)
..|.|+.|+..|.-.
T Consensus 154 aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 154 AEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeecccccccchhh
Confidence 348899999888644
No 133
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.08 E-value=17 Score=28.14 Aligned_cols=30 Identities=23% Similarity=0.675 Sum_probs=16.8
Q ss_pred CcccccccccccCChHHHHHHHHhcCCCeee-eCCcccC
Q 019587 256 KPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFK 293 (338)
Q Consensus 256 kp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~ 293 (338)
..|.|+.||+.-..+ ...-.|.| .|++.|.
T Consensus 35 a~y~CpfCgk~~vkR--------~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR--------QAVGIWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCceee--------eeeEEEEcCCCCCEEe
Confidence 457777777432211 12345777 7777764
No 134
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=29.02 E-value=16 Score=35.25 Aligned_cols=55 Identities=13% Similarity=-0.008 Sum_probs=36.5
Q ss_pred CCCcccccc--cccccCChHHHHHHHH-------hcCCCeeeeCCcccCChHHHHHHHHHhCCC
Q 019587 254 GIKPFMCRK--CSKAFAVRGDWRTHEK-------NCGKLWYCTCGSDFKHKRSLKDHIKAFGNG 308 (338)
Q Consensus 254 gekp~~C~~--CgksF~~~~~L~~H~k-------~h~k~~~C~Cgk~F~~~s~L~~H~r~hh~~ 308 (338)
.|+++.|.+ |.++..--.....|-+ +-.+||+|.|++...++..|+.|--..|.+
T Consensus 175 EE~~~S~~vp~~~~~~~~~Ns~~~~S~~~~~T~~t~~~p~k~~~~~~~~T~~~l~~HS~N~~~~ 238 (442)
T KOG4124|consen 175 EEYRVSVVVPAAAAAAAAANSSDMSSDEASSTAETTGTPKKMPESLVMDTSSPLSDHSMNIDVG 238 (442)
T ss_pred ccccccccCchhhhhhhccccccccccccccccccccCCccCcccccccccchhhhccccCCCC
Confidence 467777766 6555543333333332 236899999999999999998885554444
No 135
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=28.68 E-value=22 Score=32.96 Aligned_cols=26 Identities=23% Similarity=0.362 Sum_probs=20.6
Q ss_pred CCcccccccccccCChHHHHHHHHhc
Q 019587 255 IKPFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 255 ekp~~C~~CgksF~~~~~L~~H~k~h 280 (338)
.+++.|+.||.-...-.+|..-.|+|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 48999999998888777777666655
No 136
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=28.50 E-value=15 Score=31.41 Aligned_cols=59 Identities=22% Similarity=0.390 Sum_probs=23.8
Q ss_pred CCCCCCccccCccchhhhcCCCceecCcccccccCc------hHHHhccc-ccCCCCcCCCCCcCCCCCCCCcccccCCC
Q 019587 151 GCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFNRY------NNMQMHMW-GHGSQYRKGPESLRGSQPTAMLRLPCYCC 223 (338)
Q Consensus 151 ~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~------~~L~~H~~-~H~~~~~~~~~~~~~~~~~~~~~~~C~~C 223 (338)
.|.+|+ +|......+|..|+|-|-.. +.+..|+. ..+.+.. +-...+.+...+.|+.|
T Consensus 2 aC~YCG----------~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~-----LH~~s~lgdt~leCy~C 66 (152)
T PF09416_consen 2 ACAYCG----------IHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVS-----LHPDSPLGDTVLECYNC 66 (152)
T ss_dssp S-TTT--------------CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EE-----E-TTSTT-S-B---TTT
T ss_pred CccccC----------CCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCcee-----eCCCCCCCCcEEEEEec
Confidence 477776 33445567899998887543 33444532 1121111 11222345556899999
Q ss_pred C
Q 019587 224 A 224 (338)
Q Consensus 224 ~ 224 (338)
|
T Consensus 67 g 67 (152)
T PF09416_consen 67 G 67 (152)
T ss_dssp -
T ss_pred C
Confidence 8
No 137
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.38 E-value=30 Score=34.36 Aligned_cols=35 Identities=20% Similarity=0.489 Sum_probs=26.1
Q ss_pred CCceecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCC
Q 019587 171 PTQFSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCA 224 (338)
Q Consensus 171 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~ 224 (338)
..-|.|+.|.++|.....++.--. ....|.|..|+
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~-------------------~~~~F~C~~C~ 160 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDN-------------------ETGEFHCENCG 160 (436)
T ss_pred cccccCCccccchhhhHHHHhhcc-------------------cCceEEEecCC
Confidence 456999999999988877765421 22358999998
No 138
>PRK04023 DNA polymerase II large subunit; Validated
Probab=28.37 E-value=44 Score=36.90 Aligned_cols=44 Identities=25% Similarity=0.526 Sum_probs=0.0
Q ss_pred eecCcccccccCchHHHhcccccCCCCcCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhc
Q 019587 174 FSCPLCFKTFNRYNNMQMHMWGHGSQYRKGPESLRGSQPTAMLRLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKH 253 (338)
Q Consensus 174 ~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~ 253 (338)
..|+.||... .. +.|+.|| ..
T Consensus 627 RfCpsCG~~t-----------~~---------------------frCP~CG------------~~--------------- 647 (1121)
T PRK04023 627 RKCPSCGKET-----------FY---------------------RRCPFCG------------TH--------------- 647 (1121)
T ss_pred ccCCCCCCcC-----------Cc---------------------ccCCCCC------------CC---------------
Q ss_pred CCCcccccccccccCChHHHHHHHHhcCCCeee-eCCc
Q 019587 254 GIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGS 290 (338)
Q Consensus 254 gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk 290 (338)
.+..+.|+.||+.... +.| .||.
T Consensus 648 Te~i~fCP~CG~~~~~--------------y~CPKCG~ 671 (1121)
T PRK04023 648 TEPVYRCPRCGIEVEE--------------DECEKCGR 671 (1121)
T ss_pred CCcceeCccccCcCCC--------------CcCCCCCC
No 139
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.33 E-value=25 Score=24.09 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=5.4
Q ss_pred cccccCCCC
Q 019587 216 LRLPCYCCA 224 (338)
Q Consensus 216 ~~~~C~~C~ 224 (338)
..|.|-.||
T Consensus 5 ~~Y~C~~Cg 13 (49)
T COG1996 5 MEYKCARCG 13 (49)
T ss_pred EEEEhhhcC
Confidence 346666666
No 140
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=28.24 E-value=40 Score=33.91 Aligned_cols=22 Identities=36% Similarity=0.856 Sum_probs=19.3
Q ss_pred eee-eCCcccCChHHHHHHHHHh
Q 019587 284 WYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 284 ~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
+.| .|.|.|++.-.|+.|....
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSK 315 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSK 315 (508)
T ss_pred eEEeeccccccchHHHHhhHHHH
Confidence 899 9999999999999996443
No 141
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=28.19 E-value=17 Score=24.19 Aligned_cols=10 Identities=20% Similarity=0.690 Sum_probs=6.5
Q ss_pred CCCeee-eCCc
Q 019587 281 GKLWYC-TCGS 290 (338)
Q Consensus 281 ~k~~~C-~Cgk 290 (338)
...|+| .|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 466777 7764
No 142
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=26.97 E-value=18 Score=28.16 Aligned_cols=30 Identities=30% Similarity=0.887 Sum_probs=17.8
Q ss_pred CcccccccccccCChHHHHHHHHhcCCCeee-eCCcccC
Q 019587 256 KPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFK 293 (338)
Q Consensus 256 kp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~ 293 (338)
..|.|+.||+.-..+ ..--.|.| .|++.|.
T Consensus 34 a~y~CpfCgk~~vkR--------~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVKR--------GSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceEE--------EeeEEEEcCCCCCEEe
Confidence 457788887532211 22356788 7887774
No 143
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.95 E-value=51 Score=27.24 Aligned_cols=37 Identities=11% Similarity=0.178 Sum_probs=25.8
Q ss_pred CCCCCCCCCCccccCccchhhhcCCCceecCcccccccCchHHH
Q 019587 147 GRGGGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKTFNRYNNMQ 190 (338)
Q Consensus 147 ~~~~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~~~L~ 190 (338)
|.-..|..|+++|+=. ++.|..|+.||..|.....+.
T Consensus 7 GtKr~Cp~cg~kFYDL-------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 7 GTKRICPNTGSKFYDL-------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CccccCCCcCcccccc-------CCCCccCCCcCCccCcchhhc
Confidence 3455799999887721 235789999999987664443
No 144
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=26.34 E-value=49 Score=30.76 Aligned_cols=25 Identities=24% Similarity=0.535 Sum_probs=21.2
Q ss_pred CCCeee-eCCcccCChHHHHHHHHHh
Q 019587 281 GKLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 281 ~k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
.+++.| .||..-..-..|..-.|+|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 589999 9999888888888777777
No 145
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=25.96 E-value=25 Score=28.08 Aligned_cols=23 Identities=30% Similarity=0.684 Sum_probs=19.1
Q ss_pred CCeee-eCCcccCChHHHHHHHHH
Q 019587 282 KLWYC-TCGSDFKHKRSLKDHIKA 304 (338)
Q Consensus 282 k~~~C-~Cgk~F~~~s~L~~H~r~ 304 (338)
-.|+| .|.+-|.+.-.|..|.+.
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhcc
Confidence 34788 999999999999999754
No 146
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=25.89 E-value=54 Score=21.20 Aligned_cols=11 Identities=18% Similarity=0.733 Sum_probs=9.1
Q ss_pred eecCccccccc
Q 019587 174 FSCPLCFKTFN 184 (338)
Q Consensus 174 ~~C~~C~k~F~ 184 (338)
|.|..|+..|.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 88999998764
No 147
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.66 E-value=62 Score=34.74 Aligned_cols=9 Identities=22% Similarity=0.670 Sum_probs=7.0
Q ss_pred cccccCCCC
Q 019587 216 LRLPCYCCA 224 (338)
Q Consensus 216 ~~~~C~~C~ 224 (338)
.+..|+.||
T Consensus 474 ~p~~Cp~Cg 482 (730)
T COG1198 474 IPQSCPECG 482 (730)
T ss_pred CCCCCCCCC
Confidence 457888888
No 148
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=25.56 E-value=24 Score=24.42 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=10.5
Q ss_pred HHHHHHHHhcCCCcccccc----cccccC
Q 019587 244 TLQTHYKRKHGIKPFMCRK----CSKAFA 268 (338)
Q Consensus 244 ~L~~H~r~H~gekp~~C~~----CgksF~ 268 (338)
.|..|....=..++..|.. |+..+.
T Consensus 25 ~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred HHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 4555555433344445555 555444
No 149
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=24.91 E-value=14 Score=32.86 Aligned_cols=10 Identities=30% Similarity=0.647 Sum_probs=5.3
Q ss_pred eee-eCCcccC
Q 019587 284 WYC-TCGSDFK 293 (338)
Q Consensus 284 ~~C-~Cgk~F~ 293 (338)
+.| .||.++.
T Consensus 44 ~~C~~CgYR~~ 54 (201)
T COG1779 44 GVCERCGYRST 54 (201)
T ss_pred EEccccCCccc
Confidence 356 5665554
No 150
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=24.65 E-value=87 Score=30.12 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=16.2
Q ss_pred CCeee-eCCcccCChHHHHHHHHHh
Q 019587 282 KLWYC-TCGSDFKHKRSLKDHIKAF 305 (338)
Q Consensus 282 k~~~C-~Cgk~F~~~s~L~~H~r~h 305 (338)
-.|.| .|...|-.--..-.|-..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 45777 7777777666666666655
No 151
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=24.43 E-value=83 Score=30.49 Aligned_cols=36 Identities=22% Similarity=0.403 Sum_probs=19.3
Q ss_pred ccccCCCCCCCCCCCCCCCCccCCCHHHHHHHHHHhcCCCc--ccccccc
Q 019587 217 RLPCYCCAPGCRNNIDHPRSKPLKDFRTLQTHYKRKHGIKP--FMCRKCS 264 (338)
Q Consensus 217 ~~~C~~C~~~c~~~~~h~~~k~F~~~~~L~~H~r~H~gekp--~~C~~Cg 264 (338)
-|.|++|+ +.-.....|+.|....+-+-+ ..|++|+
T Consensus 79 SftCPyC~------------~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 79 SFTCPYCG------------IMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccCCccc------------ccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 46777776 444445567777665443322 2345554
No 152
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=24.32 E-value=56 Score=33.80 Aligned_cols=25 Identities=20% Similarity=0.419 Sum_probs=14.3
Q ss_pred CcccccccccccCChHHHHHHHHhc
Q 019587 256 KPFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 256 kp~~C~~CgksF~~~~~L~~H~k~h 280 (338)
+|.+|..||++|........||-.|
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CcchhcccccccccchhhhhHhhhh
Confidence 4455666666666555555555544
No 153
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=24.27 E-value=44 Score=27.35 Aligned_cols=26 Identities=31% Similarity=0.547 Sum_probs=22.0
Q ss_pred CCCcccccccccccCChHHHHHHHHh
Q 019587 254 GIKPFMCRKCSKAFAVRGDWRTHEKN 279 (338)
Q Consensus 254 gekp~~C~~CgksF~~~~~L~~H~k~ 279 (338)
|-..|-|-+|.+.|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44558899999999999999999874
No 154
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=24.22 E-value=98 Score=29.78 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=19.9
Q ss_pred CCcccccccccccCChHHHHHHHHhc
Q 019587 255 IKPFMCRKCSKAFAVRGDWRTHEKNC 280 (338)
Q Consensus 255 ekp~~C~~CgksF~~~~~L~~H~k~h 280 (338)
...|+|..|.-.|-.-.+.-.|...|
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CCcEEchhccceeeccchHHHHhhhh
Confidence 34589999999998888877775554
No 155
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=24.19 E-value=62 Score=25.53 Aligned_cols=18 Identities=22% Similarity=0.608 Sum_probs=14.1
Q ss_pred ccCCCHHHHHHHHHHhcC
Q 019587 237 KPLKDFRTLQTHYKRKHG 254 (338)
Q Consensus 237 k~F~~~~~L~~H~r~H~g 254 (338)
....+...+..|++.++|
T Consensus 92 y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 92 YITRSKKTMRKHWRKEHG 109 (109)
T ss_pred cEeccHHHHHHHHHHhcC
Confidence 667778888888887765
No 156
>PHA02998 RNA polymerase subunit; Provisional
Probab=24.00 E-value=51 Score=28.88 Aligned_cols=37 Identities=22% Similarity=0.293 Sum_probs=23.0
Q ss_pred CCCCCCCCccccCccchhhhcCCCc----eecCcccccccC
Q 019587 149 GGGCSLNKGQYWIPTPAQILIGPTQ----FSCPLCFKTFNR 185 (338)
Q Consensus 149 ~~~c~~c~~~~~l~~h~~~h~~~~~----~~C~~C~k~F~~ 185 (338)
.-.|..|+..-.....+|+..+..| |.|..||..|.-
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 3457778754433334455544333 899999998753
No 157
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.33 E-value=45 Score=22.05 Aligned_cols=17 Identities=29% Similarity=0.956 Sum_probs=12.8
Q ss_pred cccccccccCChHHHHH
Q 019587 259 MCRKCSKAFAVRGDWRT 275 (338)
Q Consensus 259 ~C~~CgksF~~~~~L~~ 275 (338)
.|.+||+.|+.+..+..
T Consensus 10 ~C~~C~rpf~WRKKW~~ 26 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWAR 26 (42)
T ss_pred cCcccCCcchHHHHHHH
Confidence 58888888887766654
No 158
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.69 E-value=58 Score=21.64 Aligned_cols=26 Identities=15% Similarity=0.081 Sum_probs=17.5
Q ss_pred CCCCCCCccccCccchhhhcCCCceecCccccc
Q 019587 150 GGCSLNKGQYWIPTPAQILIGPTQFSCPLCFKT 182 (338)
Q Consensus 150 ~~c~~c~~~~~l~~h~~~h~~~~~~~C~~C~k~ 182 (338)
|.|..|+..+.+. ...+..|+.||-.
T Consensus 3 Y~C~~Cg~~~~~~-------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-------CCCceECCCCCce
Confidence 5678888766654 2346888888753
No 159
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=21.86 E-value=36 Score=19.70 Aligned_cols=8 Identities=38% Similarity=1.136 Sum_probs=3.9
Q ss_pred ccccCCCC
Q 019587 217 RLPCYCCA 224 (338)
Q Consensus 217 ~~~C~~C~ 224 (338)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 44555444
No 160
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=21.65 E-value=38 Score=23.18 Aligned_cols=21 Identities=24% Similarity=0.588 Sum_probs=14.4
Q ss_pred CCCeee-eCCcccCChHHHHHH
Q 019587 281 GKLWYC-TCGSDFKHKRSLKDH 301 (338)
Q Consensus 281 ~k~~~C-~Cgk~F~~~s~L~~H 301 (338)
++.+.| .||+.|.--..=...
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~f 23 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKF 23 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHH
Confidence 467889 899988766544443
No 161
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.50 E-value=24 Score=27.40 Aligned_cols=30 Identities=27% Similarity=0.777 Sum_probs=16.8
Q ss_pred CcccccccccccCChHHHHHHHHhcCCCeee-eCCcccC
Q 019587 256 KPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFK 293 (338)
Q Consensus 256 kp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~ 293 (338)
..|.|+.||+.-..+ ..--.|.| .|++.|.
T Consensus 35 a~y~CpfCgk~~vkR--------~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKVKR--------VGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCceEE--------EEEEEEEcCCCCCEEe
Confidence 357777776442211 12345777 7777764
No 162
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=21.28 E-value=42 Score=19.69 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=6.0
Q ss_pred cccccccccC
Q 019587 259 MCRKCSKAFA 268 (338)
Q Consensus 259 ~C~~CgksF~ 268 (338)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666664
No 163
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=20.97 E-value=35 Score=36.17 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=15.0
Q ss_pred CCCcccccccccccCChHHHHHH
Q 019587 254 GIKPFMCRKCSKAFAVRGDWRTH 276 (338)
Q Consensus 254 gekp~~C~~CgksF~~~~~L~~H 276 (338)
+.+.-+||.|+.+|....-+..|
T Consensus 675 etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 675 ETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HHhcCCCCCCCCCCCcccccccC
Confidence 33455788888888866554443
No 164
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=20.80 E-value=26 Score=36.05 Aligned_cols=50 Identities=18% Similarity=0.252 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCCcccccccccccCChHHHHHHHHhcCCCeee-eCCcccCChH
Q 019587 244 TLQTHYKRKHGIKPFMCRKCSKAFAVRGDWRTHEKNCGKLWYC-TCGSDFKHKR 296 (338)
Q Consensus 244 ~L~~H~r~H~gekp~~C~~CgksF~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~s 296 (338)
.|.+|-.+|....-=+|..|||.|.++-.+..-. --...| .|...|-.+-
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~FhsKE---ivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHSKE---IVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheeecccc---EEEEEehHHHHHhhcch
Confidence 5556655555444457999999998876543311 124678 8888776664
No 165
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=20.62 E-value=24 Score=29.60 Aligned_cols=10 Identities=20% Similarity=1.125 Sum_probs=5.3
Q ss_pred cccccccccc
Q 019587 258 FMCRKCSKAF 267 (338)
Q Consensus 258 ~~C~~CgksF 267 (338)
|.|..|+..+
T Consensus 124 ~~C~~C~~~~ 133 (157)
T PF10263_consen 124 YRCPSCGREY 133 (157)
T ss_pred EEcCCCCCEe
Confidence 4555555444
No 166
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=20.40 E-value=67 Score=32.51 Aligned_cols=28 Identities=21% Similarity=0.608 Sum_probs=23.6
Q ss_pred CCeee-eCCcccCChHHHHHHHHHhCCCC
Q 019587 282 KLWYC-TCGSDFKHKRSLKDHIKAFGNGH 309 (338)
Q Consensus 282 k~~~C-~Cgk~F~~~s~L~~H~r~hh~~~ 309 (338)
+-|.| .|.+.|.....++.|+...|.+.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 45788 89999999999999998777553
No 167
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=20.02 E-value=69 Score=21.99 Aligned_cols=10 Identities=30% Similarity=0.870 Sum_probs=6.0
Q ss_pred cccccccccc
Q 019587 257 PFMCRKCSKA 266 (338)
Q Consensus 257 p~~C~~Cgks 266 (338)
.+.|..||..
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 4666666643
Done!