Query 020075
Match_columns 331
No_of_seqs 358 out of 3460
Neff 9.0
Searched_HMMs 46136
Date Fri Mar 29 06:49:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020075.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020075hhsearch_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 9.1E-28 2E-32 205.1 6.9 130 96-257 129-263 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.9 2.5E-27 5.4E-32 202.5 3.9 134 122-284 127-262 (279)
3 KOG1074 Transcriptional repres 99.8 3.4E-22 7.3E-27 192.1 4.4 79 172-261 605-692 (958)
4 KOG1074 Transcriptional repres 99.8 1E-20 2.2E-25 182.0 3.8 58 211-269 880-939 (958)
5 KOG3576 Ovo and related transc 99.7 1.4E-17 3.1E-22 136.0 2.7 116 122-267 114-242 (267)
6 KOG3608 Zn finger proteins [Ge 99.7 2.6E-17 5.6E-22 144.7 4.0 159 101-277 183-364 (467)
7 KOG3608 Zn finger proteins [Ge 99.7 1.7E-16 3.7E-21 139.6 6.8 176 60-276 189-397 (467)
8 KOG3576 Ovo and related transc 99.5 1.8E-15 3.9E-20 123.7 1.3 100 170-280 115-227 (267)
9 KOG3623 Homeobox transcription 99.5 3.1E-15 6.7E-20 142.4 2.4 107 125-259 210-331 (1007)
10 KOG3623 Homeobox transcription 99.5 6.7E-15 1.5E-19 140.1 2.3 68 190-258 902-971 (1007)
11 PHA00733 hypothetical protein 99.1 6.6E-11 1.4E-15 93.3 5.9 87 121-262 36-124 (128)
12 PLN03086 PRLI-interacting fact 99.0 4.9E-10 1.1E-14 107.7 7.9 127 126-279 408-555 (567)
13 PLN03086 PRLI-interacting fact 99.0 6.4E-10 1.4E-14 107.0 6.8 101 123-259 451-562 (567)
14 PHA02768 hypothetical protein; 99.0 2.3E-10 4.9E-15 74.8 1.4 41 211-254 6-48 (55)
15 PF13465 zf-H2C2_2: Zinc-finge 98.6 1.3E-08 2.8E-13 56.9 1.8 24 226-249 1-26 (26)
16 PHA02768 hypothetical protein; 98.6 2.9E-08 6.2E-13 65.0 3.1 42 238-281 5-47 (55)
17 PHA00616 hypothetical protein 98.5 3.5E-08 7.6E-13 61.4 1.8 33 238-270 1-34 (44)
18 PHA00733 hypothetical protein 98.5 4.6E-08 1E-12 77.2 3.0 71 208-281 38-115 (128)
19 KOG3993 Transcription factor ( 98.4 8.6E-08 1.9E-12 87.2 1.5 107 125-262 267-381 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.4 1E-07 2.3E-12 53.2 1.2 25 113-137 2-26 (26)
21 PHA00732 hypothetical protein 98.3 6.6E-07 1.4E-11 64.2 2.8 45 210-260 1-47 (79)
22 PHA00616 hypothetical protein 98.2 3.6E-07 7.8E-12 56.9 1.0 32 210-242 1-33 (44)
23 KOG3993 Transcription factor ( 98.2 2.1E-07 4.6E-12 84.7 -0.8 151 98-259 268-480 (500)
24 PF00096 zf-C2H2: Zinc finger, 97.9 9.2E-06 2E-10 43.8 2.4 22 239-260 1-23 (23)
25 PF00096 zf-C2H2: Zinc finger, 97.9 7.3E-06 1.6E-10 44.2 1.7 23 126-148 1-23 (23)
26 PF05605 zf-Di19: Drought indu 97.9 2.2E-05 4.8E-10 52.1 4.1 49 210-262 2-54 (54)
27 PHA00732 hypothetical protein 97.8 1.6E-05 3.6E-10 57.0 2.6 23 125-147 1-23 (79)
28 COG5189 SFP1 Putative transcri 97.5 2.6E-05 5.6E-10 68.8 0.1 50 208-258 347-419 (423)
29 PF13912 zf-C2H2_6: C2H2-type 97.5 7E-05 1.5E-09 42.0 1.8 24 238-261 1-25 (27)
30 PF13894 zf-C2H2_4: C2H2-type 97.4 9.3E-05 2E-09 39.9 2.1 24 126-149 1-24 (24)
31 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00012 2.7E-09 39.4 2.6 23 239-261 1-24 (24)
32 COG5189 SFP1 Putative transcri 97.4 7E-05 1.5E-09 66.1 2.1 72 122-233 346-420 (423)
33 PF13912 zf-C2H2_6: C2H2-type 97.3 0.0001 2.2E-09 41.3 0.8 26 125-150 1-26 (27)
34 PF05605 zf-Di19: Drought indu 97.1 0.00043 9.2E-09 45.9 2.5 46 173-232 3-50 (54)
35 PF12756 zf-C2H2_2: C2H2 type 96.9 0.00067 1.4E-08 50.8 2.8 72 174-260 1-73 (100)
36 PF09237 GAGA: GAGA factor; I 96.9 0.00093 2E-08 42.7 2.8 38 228-265 12-52 (54)
37 smart00355 ZnF_C2H2 zinc finge 96.9 0.00094 2E-08 36.4 2.4 23 239-261 1-24 (26)
38 smart00355 ZnF_C2H2 zinc finge 96.8 0.0011 2.3E-08 36.2 2.3 25 126-150 1-25 (26)
39 PF12756 zf-C2H2_2: C2H2 type 96.7 0.00097 2.1E-08 49.9 2.3 71 127-232 1-71 (100)
40 PF09237 GAGA: GAGA factor; I 96.4 0.0035 7.6E-08 40.1 2.6 30 122-151 21-50 (54)
41 KOG2231 Predicted E3 ubiquitin 96.3 0.0044 9.5E-08 61.2 4.2 71 190-269 190-275 (669)
42 PF12874 zf-met: Zinc-finger o 96.0 0.0045 9.7E-08 33.7 1.8 22 239-260 1-23 (25)
43 PF12874 zf-met: Zinc-finger o 96.0 0.0031 6.7E-08 34.4 0.9 23 126-148 1-23 (25)
44 PRK04860 hypothetical protein; 96.0 0.0041 9E-08 50.9 2.0 36 210-250 119-156 (160)
45 PF13909 zf-H2C2_5: C2H2-type 95.7 0.0099 2.1E-07 32.1 2.3 22 239-261 1-23 (24)
46 COG5048 FOG: Zn-finger [Genera 95.7 0.0032 6.9E-08 59.8 0.2 153 97-272 289-453 (467)
47 KOG1146 Homeobox protein [Gene 95.6 0.011 2.4E-07 61.9 3.7 50 102-151 441-491 (1406)
48 PF13909 zf-H2C2_5: C2H2-type 95.3 0.012 2.6E-07 31.7 1.6 24 126-150 1-24 (24)
49 PRK04860 hypothetical protein; 95.1 0.013 2.8E-07 48.1 2.0 35 124-170 118-152 (160)
50 PF12171 zf-C2H2_jaz: Zinc-fin 94.9 0.0068 1.5E-07 33.8 -0.2 21 239-259 2-23 (27)
51 PF06524 NOA36: NOA36 protein; 93.9 0.083 1.8E-06 45.8 4.3 26 236-261 207-233 (314)
52 PF12171 zf-C2H2_jaz: Zinc-fin 93.6 0.036 7.8E-07 30.8 1.1 21 211-232 2-22 (27)
53 PF13913 zf-C2HC_2: zinc-finge 92.9 0.072 1.6E-06 29.1 1.6 21 126-147 3-23 (25)
54 PF13913 zf-C2HC_2: zinc-finge 92.4 0.12 2.7E-06 28.2 2.0 19 240-259 4-23 (25)
55 KOG4173 Alpha-SNAP protein [In 92.2 0.086 1.9E-06 44.1 1.8 79 171-261 78-171 (253)
56 smart00451 ZnF_U1 U1-like zinc 91.8 0.14 3E-06 30.2 2.0 22 238-259 3-25 (35)
57 KOG1146 Homeobox protein [Gene 91.7 0.15 3.3E-06 53.9 3.3 54 205-259 460-540 (1406)
58 smart00451 ZnF_U1 U1-like zinc 89.4 0.29 6.3E-06 28.7 1.9 22 210-232 3-24 (35)
59 COG5048 FOG: Zn-finger [Genera 88.2 0.25 5.4E-06 46.7 1.6 62 209-271 288-357 (467)
60 KOG2231 Predicted E3 ubiquitin 87.1 0.57 1.2E-05 46.8 3.3 46 211-261 183-236 (669)
61 KOG2482 Predicted C2H2-type Zn 86.6 0.52 1.1E-05 42.7 2.5 48 211-259 280-356 (423)
62 COG5236 Uncharacterized conser 86.6 1.3 2.7E-05 40.4 4.9 27 125-151 151-179 (493)
63 COG4049 Uncharacterized protei 86.5 0.35 7.6E-06 31.5 1.0 26 234-259 13-39 (65)
64 COG1198 PriA Primosomal protei 85.8 0.64 1.4E-05 47.3 3.0 58 152-246 426-484 (730)
65 KOG2186 Cell growth-regulating 84.4 0.57 1.2E-05 40.7 1.7 44 211-258 4-49 (276)
66 KOG2893 Zn finger protein [Gen 84.3 0.43 9.2E-06 41.0 0.9 30 128-169 13-42 (341)
67 PF12013 DUF3505: Protein of u 83.3 2 4.3E-05 32.7 4.1 24 239-262 81-109 (109)
68 TIGR00595 priA primosomal prot 83.1 0.87 1.9E-05 44.7 2.6 58 152-246 204-262 (505)
69 COG4049 Uncharacterized protei 83.1 0.78 1.7E-05 30.0 1.5 32 119-150 11-42 (65)
70 PF09538 FYDLN_acid: Protein o 83.0 1.9 4.2E-05 32.8 3.9 30 210-250 9-39 (108)
71 PRK14873 primosome assembly pr 81.4 1.2 2.5E-05 45.3 2.8 56 153-246 375-431 (665)
72 PRK00464 nrdR transcriptional 81.3 0.51 1.1E-05 38.4 0.2 12 239-250 29-41 (154)
73 PF06524 NOA36: NOA36 protein; 79.8 5.3 0.00012 35.0 5.8 70 204-276 136-220 (314)
74 KOG2893 Zn finger protein [Gen 79.6 0.53 1.1E-05 40.5 -0.3 47 209-260 10-58 (341)
75 PF09986 DUF2225: Uncharacteri 79.2 0.76 1.6E-05 39.7 0.6 41 209-250 4-61 (214)
76 PRK14890 putative Zn-ribbon RN 77.8 1.2 2.7E-05 29.6 1.1 10 209-218 47-56 (59)
77 PHA00626 hypothetical protein 77.0 2.3 5E-05 27.9 2.2 14 209-223 22-35 (59)
78 cd00350 rubredoxin_like Rubred 76.2 1.5 3.3E-05 25.5 1.1 10 209-218 16-25 (33)
79 COG2888 Predicted Zn-ribbon RN 72.5 1.6 3.5E-05 29.0 0.6 10 209-218 49-58 (61)
80 TIGR00622 ssl1 transcription f 72.3 7 0.00015 29.9 4.1 47 212-261 57-105 (112)
81 smart00531 TFIIE Transcription 72.3 2.3 5.1E-05 34.3 1.7 22 121-142 95-116 (147)
82 COG5236 Uncharacterized conser 72.2 2.6 5.5E-05 38.4 2.0 125 101-260 157-304 (493)
83 smart00614 ZnF_BED BED zinc fi 72.0 3.1 6.7E-05 26.7 1.9 19 240-258 20-44 (50)
84 PF09538 FYDLN_acid: Protein o 71.9 2.4 5.2E-05 32.3 1.6 14 123-136 24-37 (108)
85 PF09986 DUF2225: Uncharacteri 71.9 0.69 1.5E-05 40.0 -1.6 17 123-139 3-19 (214)
86 PF02892 zf-BED: BED zinc fing 71.7 3.9 8.5E-05 25.4 2.3 21 237-257 15-40 (45)
87 PRK05580 primosome assembly pr 71.4 3.1 6.7E-05 42.5 2.7 22 156-179 376-397 (679)
88 COG1997 RPL43A Ribosomal prote 68.6 2.8 6.1E-05 30.2 1.2 31 209-249 34-65 (89)
89 TIGR02098 MJ0042_CXXC MJ0042 f 68.4 4 8.7E-05 24.4 1.7 33 211-248 3-36 (38)
90 PF05443 ROS_MUCR: ROS/MUCR tr 67.4 2.7 5.8E-05 33.3 1.0 26 238-266 72-98 (132)
91 COG1592 Rubrerythrin [Energy p 67.3 4.2 9.1E-05 33.5 2.2 11 207-217 146-156 (166)
92 TIGR00373 conserved hypothetic 66.9 4.4 9.6E-05 33.2 2.3 24 119-142 103-126 (158)
93 cd00729 rubredoxin_SM Rubredox 66.9 5.1 0.00011 23.5 1.9 10 209-218 17-26 (34)
94 KOG1280 Uncharacterized conser 65.8 7.4 0.00016 35.6 3.6 26 209-235 78-105 (381)
95 KOG4173 Alpha-SNAP protein [In 65.7 2.2 4.8E-05 35.9 0.3 82 125-239 79-176 (253)
96 COG1592 Rubrerythrin [Energy p 61.1 5.2 0.00011 33.0 1.6 23 209-244 133-156 (166)
97 PRK06266 transcription initiat 60.6 6.2 0.00013 33.0 2.0 21 121-141 113-133 (178)
98 PTZ00255 60S ribosomal protein 60.3 4.1 8.8E-05 29.8 0.8 31 209-249 35-66 (90)
99 PF13717 zinc_ribbon_4: zinc-r 60.0 8.7 0.00019 22.9 2.1 32 211-247 3-35 (36)
100 smart00734 ZnF_Rad18 Rad18-lik 59.4 6.8 0.00015 21.5 1.4 20 126-146 2-21 (26)
101 PF13719 zinc_ribbon_5: zinc-r 58.7 8.7 0.00019 23.0 1.9 32 212-248 4-36 (37)
102 COG1198 PriA Primosomal protei 58.3 12 0.00025 38.5 3.9 40 209-274 443-484 (730)
103 TIGR02300 FYDLN_acid conserved 57.9 6.8 0.00015 30.5 1.7 31 98-139 10-40 (129)
104 smart00531 TFIIE Transcription 57.1 7 0.00015 31.5 1.7 35 209-247 98-133 (147)
105 TIGR00280 L37a ribosomal prote 56.4 4.9 0.00011 29.4 0.7 31 209-249 34-65 (91)
106 PRK09678 DNA-binding transcrip 55.2 3.9 8.4E-05 28.7 -0.0 16 234-249 23-41 (72)
107 KOG3362 Predicted BBOX Zn-fing 54.9 4.6 0.0001 32.0 0.3 31 163-203 120-150 (156)
108 KOG4167 Predicted DNA-binding 54.5 4.9 0.00011 40.4 0.5 27 124-150 791-817 (907)
109 PF04438 zf-HIT: HIT zinc fing 54.5 11 0.00023 21.5 1.7 17 163-179 4-20 (30)
110 PF05443 ROS_MUCR: ROS/MUCR tr 54.3 7.9 0.00017 30.6 1.6 26 123-151 70-95 (132)
111 TIGR02300 FYDLN_acid conserved 53.6 10 0.00022 29.5 2.0 34 210-254 9-43 (129)
112 KOG4167 Predicted DNA-binding 53.5 3.7 8.1E-05 41.2 -0.5 24 238-261 792-816 (907)
113 KOG2785 C2H2-type Zn-finger pr 53.5 20 0.00044 33.3 4.2 24 236-259 66-90 (390)
114 PF01780 Ribosomal_L37ae: Ribo 52.2 6.1 0.00013 28.9 0.6 29 209-248 34-64 (90)
115 KOG2593 Transcription initiati 51.1 9.9 0.00021 36.0 1.9 24 120-143 123-146 (436)
116 PRK03976 rpl37ae 50S ribosomal 50.2 6.5 0.00014 28.8 0.4 31 209-249 35-66 (90)
117 PF09416 UPF1_Zn_bind: RNA hel 49.8 9.7 0.00021 30.8 1.4 21 211-232 15-41 (152)
118 COG4957 Predicted transcriptio 49.7 10 0.00022 29.8 1.5 28 239-269 77-105 (148)
119 PF15269 zf-C2H2_7: Zinc-finge 49.4 13 0.00029 23.1 1.7 21 239-259 21-42 (54)
120 PRK04023 DNA polymerase II lar 48.4 15 0.00033 38.7 2.8 9 210-218 663-671 (1121)
121 TIGR00622 ssl1 transcription f 45.0 29 0.00063 26.6 3.3 64 209-275 14-91 (112)
122 KOG2482 Predicted C2H2-type Zn 44.9 22 0.00047 32.6 3.0 57 209-265 143-225 (423)
123 PRK14714 DNA polymerase II lar 44.6 20 0.00043 38.8 3.1 9 210-218 692-700 (1337)
124 PF03833 PolC_DP2: DNA polymer 44.5 7.4 0.00016 40.0 0.0 18 162-179 656-674 (900)
125 KOG0320 Predicted E3 ubiquitin 44.3 12 0.00025 31.1 1.1 27 192-224 154-180 (187)
126 TIGR00595 priA primosomal prot 44.2 23 0.00049 34.9 3.3 39 209-273 221-261 (505)
127 PF14353 CpXC: CpXC protein 44.0 23 0.00051 27.6 2.8 18 239-256 39-57 (128)
128 PF12013 DUF3505: Protein of u 42.7 18 0.00039 27.4 1.9 26 125-150 80-109 (109)
129 KOG2785 C2H2-type Zn-finger pr 42.2 28 0.0006 32.5 3.3 50 209-259 165-242 (390)
130 smart00440 ZnF_C2C2 C2C2 Zinc 41.4 7.2 0.00016 23.8 -0.4 9 239-247 29-38 (40)
131 PRK00398 rpoP DNA-directed RNA 39.8 18 0.0004 22.6 1.3 8 211-218 22-29 (46)
132 PRK14873 primosome assembly pr 39.6 28 0.0006 35.6 3.2 39 209-274 391-431 (665)
133 COG4957 Predicted transcriptio 38.6 15 0.00032 29.0 0.8 24 125-151 76-99 (148)
134 COG4530 Uncharacterized protei 37.2 20 0.00044 27.1 1.3 27 100-137 12-38 (129)
135 KOG4124 Putative transcription 36.9 13 0.00028 34.1 0.3 24 234-257 209-232 (442)
136 PF12907 zf-met2: Zinc-binding 36.2 15 0.00033 22.5 0.4 25 211-236 2-31 (40)
137 KOG2857 Predicted MYND Zn-fing 35.6 19 0.00041 28.6 1.0 32 162-203 6-38 (157)
138 TIGR00244 transcriptional regu 35.3 13 0.00028 29.9 0.1 18 210-228 28-45 (147)
139 PRK06266 transcription initiat 35.1 29 0.00063 29.0 2.2 8 211-218 137-144 (178)
140 PF05495 zf-CHY: CHY zinc fing 34.5 19 0.00041 25.1 0.8 58 172-247 10-71 (71)
141 COG3364 Zn-ribbon containing p 33.8 26 0.00056 26.2 1.4 15 125-139 2-16 (112)
142 PF04959 ARS2: Arsenite-resist 33.8 16 0.00035 31.5 0.4 22 210-232 77-98 (214)
143 smart00659 RPOLCX RNA polymera 33.6 31 0.00067 21.6 1.6 10 209-218 18-27 (44)
144 KOG3408 U1-like Zn-finger-cont 32.9 28 0.00061 26.9 1.5 26 234-259 53-79 (129)
145 COG1996 RPC10 DNA-directed RNA 32.3 25 0.00055 22.6 1.0 8 211-218 25-32 (49)
146 PF04959 ARS2: Arsenite-resist 32.1 24 0.00052 30.4 1.2 7 173-179 78-84 (214)
147 PF07800 DUF1644: Protein of u 31.5 87 0.0019 25.5 4.2 56 210-268 80-140 (162)
148 KOG2186 Cell growth-regulating 31.4 20 0.00044 31.4 0.6 25 125-150 3-27 (276)
149 PF01096 TFIIS_C: Transcriptio 31.3 4.4 9.6E-05 24.6 -2.5 9 239-247 29-38 (39)
150 KOG2907 RNA polymerase I trans 30.9 32 0.00069 26.2 1.5 36 211-249 75-114 (116)
151 KOG0696 Serine/threonine prote 30.8 31 0.00068 32.9 1.8 90 132-244 26-128 (683)
152 PF09723 Zn-ribbon_8: Zinc rib 30.4 24 0.00052 21.7 0.7 28 239-273 6-34 (42)
153 smart00731 SprT SprT homologue 30.3 28 0.00061 27.9 1.3 32 210-248 112-144 (146)
154 COG1327 Predicted transcriptio 30.1 18 0.0004 29.1 0.1 17 210-227 28-44 (156)
155 PF11672 DUF3268: Protein of u 29.9 33 0.00071 25.8 1.5 9 210-218 2-10 (102)
156 PF04216 FdhE: Protein involve 29.5 20 0.00044 32.4 0.4 35 210-247 211-248 (290)
157 KOG2807 RNA polymerase II tran 29.1 91 0.002 28.6 4.3 52 208-260 288-368 (378)
158 PRK05580 primosome assembly pr 29.0 56 0.0012 33.5 3.5 13 234-246 417-430 (679)
159 smart00834 CxxC_CXXC_SSSS Puta 28.9 27 0.00058 20.9 0.7 29 238-273 5-34 (41)
160 PRK04023 DNA polymerase II lar 28.9 37 0.0008 35.9 2.1 20 160-179 625-645 (1121)
161 COG4640 Predicted membrane pro 28.6 40 0.00086 31.7 2.0 17 211-228 16-32 (465)
162 PF13451 zf-trcl: Probable zin 28.6 26 0.00056 22.5 0.6 36 236-272 2-40 (49)
163 PF10621 FpoO: F420H2 dehydrog 28.5 36 0.00078 25.8 1.4 14 164-177 4-17 (119)
164 PF01363 FYVE: FYVE zinc finge 28.3 28 0.0006 23.7 0.8 9 212-221 11-19 (69)
165 TIGR00373 conserved hypothetic 28.3 56 0.0012 26.7 2.7 15 239-253 110-125 (158)
166 KOG4124 Putative transcription 28.1 17 0.00036 33.5 -0.4 24 123-146 347-372 (442)
167 smart00154 ZnF_AN1 AN1-like Zi 28.1 30 0.00065 20.9 0.8 11 238-248 12-23 (39)
168 KOG2071 mRNA cleavage and poly 27.9 88 0.0019 31.1 4.3 31 120-150 413-443 (579)
169 PF13878 zf-C2H2_3: zinc-finge 27.6 51 0.0011 20.2 1.8 25 125-149 13-39 (41)
170 PF07754 DUF1610: Domain of un 27.3 47 0.001 17.9 1.4 10 209-218 15-24 (24)
171 PF10083 DUF2321: Uncharacteri 26.9 14 0.0003 29.9 -1.0 19 235-253 65-84 (158)
172 PF08271 TF_Zn_Ribbon: TFIIB z 26.9 36 0.00078 20.9 1.1 8 211-218 20-27 (43)
173 PHA02998 RNA polymerase subuni 26.6 21 0.00045 29.6 -0.1 10 239-248 172-182 (195)
174 COG3091 SprT Zn-dependent meta 26.3 41 0.00089 27.2 1.5 32 209-246 116-149 (156)
175 PRK03824 hypA hydrogenase nick 25.9 29 0.00062 27.6 0.6 13 210-223 70-82 (135)
176 KOG2593 Transcription initiati 25.6 47 0.001 31.6 2.0 39 205-246 123-162 (436)
177 PF01428 zf-AN1: AN1-like Zinc 25.5 29 0.00062 21.4 0.4 12 237-248 12-24 (43)
178 PF12760 Zn_Tnp_IS1595: Transp 24.6 55 0.0012 20.4 1.6 8 210-217 37-44 (46)
179 cd00065 FYVE FYVE domain; Zinc 24.5 42 0.00092 21.7 1.1 6 213-218 5-10 (57)
180 COG4888 Uncharacterized Zn rib 24.1 34 0.00074 25.5 0.6 8 211-218 47-54 (104)
181 PF05502 Dynactin_p62: Dynacti 24.0 54 0.0012 32.1 2.2 38 209-247 51-96 (483)
182 KOG4377 Zn-finger protein [Gen 23.2 61 0.0013 30.6 2.2 25 239-263 402-429 (480)
183 TIGR02605 CxxC_CxxC_SSSS putat 22.6 40 0.00086 21.5 0.7 28 239-273 6-34 (52)
184 PF03107 C1_2: C1 domain; Int 22.5 83 0.0018 17.6 1.9 8 211-218 1-8 (30)
185 COG1594 RPB9 DNA-directed RNA 22.2 32 0.0007 26.4 0.2 11 238-248 100-111 (113)
186 PF09845 DUF2072: Zn-ribbon co 22.0 38 0.00082 26.7 0.5 14 238-251 1-15 (131)
187 smart00064 FYVE Protein presen 22.0 51 0.0011 22.3 1.2 10 212-222 12-21 (68)
188 PF10571 UPF0547: Uncharacteri 21.5 54 0.0012 17.9 1.0 11 211-222 15-25 (26)
189 PF07282 OrfB_Zn_ribbon: Putat 21.5 71 0.0015 21.7 1.8 10 238-247 46-56 (69)
190 KOG2071 mRNA cleavage and poly 21.5 54 0.0012 32.5 1.6 27 235-261 415-442 (579)
191 PF11931 DUF3449: Domain of un 21.3 31 0.00068 29.2 0.0 25 208-232 99-123 (196)
192 smart00661 RPOL9 RNA polymeras 21.2 64 0.0014 20.4 1.5 10 238-247 20-30 (52)
193 KOG3002 Zn finger protein [Gen 20.6 39 0.00086 30.7 0.5 25 243-269 116-140 (299)
194 KOG0402 60S ribosomal protein 20.4 48 0.001 23.8 0.8 29 210-248 36-65 (92)
195 COG1571 Predicted DNA-binding 20.2 60 0.0013 31.0 1.6 28 212-250 352-380 (421)
196 COG4896 Uncharacterized protei 20.1 45 0.00097 22.4 0.5 40 211-250 3-44 (68)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.94 E-value=9.1e-28 Score=205.14 Aligned_cols=130 Identities=25% Similarity=0.422 Sum_probs=66.2
Q ss_pred CCCCCCCCCCCCCCchhhhhhhhhhc---CCCccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccc
Q 020075 96 KNPEIGSEHDIESDCEIVEIDAVELL---AEHIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTR 172 (331)
Q Consensus 96 ~~~~~~~~~~~~~~~~~l~~h~~~h~---~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~ 172 (331)
..+.|..|++.+.....|..|...|- ..+.+.|++|||.|..-..|+.|+|+|+- +
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l---------------------~ 187 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL---------------------P 187 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC---------------------C
Confidence 34444455555555555555555442 23445555555555555555555555542 2
Q ss_pred eeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCH
Q 020075 173 FSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRK 250 (331)
Q Consensus 173 ~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~ 250 (331)
+.|.+|| |.|...--|+.|+|+|+|||||.|..|+| .|..+++|+.||+ |.+.|+|.|. |+|+|+.+
T Consensus 188 c~C~iCG----------KaFSRPWLLQGHiRTHTGEKPF~C~hC~k-AFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 188 CECGICG----------KAFSRPWLLQGHIRTHTGEKPFSCPHCGK-AFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred ccccccc----------ccccchHHhhcccccccCCCCccCCcccc-hhcchHHHHHHHHhhcCCccccCcchhhHHHHH
Confidence 4444554 55555555555555555555555555555 5555555555555 5555555555 55555555
Q ss_pred HHHHHHH
Q 020075 251 DKLFGHV 257 (331)
Q Consensus 251 ~~L~~H~ 257 (331)
+.|.+|.
T Consensus 257 SyLnKH~ 263 (279)
T KOG2462|consen 257 SYLNKHS 263 (279)
T ss_pred HHHHHhh
Confidence 5555554
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.93 E-value=2.5e-27 Score=202.48 Aligned_cols=134 Identities=24% Similarity=0.408 Sum_probs=122.0
Q ss_pred CCCccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhcc
Q 020075 122 AEHIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNH 201 (331)
Q Consensus 122 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H 201 (331)
....|+|..|||.+.+.++|.+|..+|..- ...+.|.|++|+ |.|.....|+.|
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~----------------~s~ka~~C~~C~----------K~YvSmpALkMH 180 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSL----------------DSKKAFSCKYCG----------KVYVSMPALKMH 180 (279)
T ss_pred cCCceeccccccccccccccchhhcccccc----------------cccccccCCCCC----------ceeeehHHHhhH
Confidence 455799999999999999999999999653 112568999999 999999999999
Q ss_pred cccccCCCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhhcCCCCccCccccccCCccc
Q 020075 202 FKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKMKHHDQD 279 (331)
Q Consensus 202 ~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~~~~~~~ 279 (331)
+|+|+ -+++|.+||| .|.+.+.|+-|+| |||||||.|. |+|+|+.+++|+.||++|.+.|+|.|..|.+.+....
T Consensus 181 irTH~--l~c~C~iCGK-aFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 181 IRTHT--LPCECGICGK-AFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKS 257 (279)
T ss_pred hhccC--CCcccccccc-cccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHH
Confidence 99998 6899999999 9999999999999 9999999999 9999999999999999999999999999999887776
Q ss_pred ccccC
Q 020075 280 VVVVG 284 (331)
Q Consensus 280 ~~~~~ 284 (331)
.+..+
T Consensus 258 yLnKH 262 (279)
T KOG2462|consen 258 YLNKH 262 (279)
T ss_pred HHHHh
Confidence 66544
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.85 E-value=3.4e-22 Score=192.10 Aligned_cols=79 Identities=18% Similarity=0.458 Sum_probs=67.7
Q ss_pred ceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHhh-ccCCC----ceecc----
Q 020075 172 RFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGES----RWKCS---- 242 (331)
Q Consensus 172 ~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ek----p~~C~---- 242 (331)
+-.|-+|. |...|...|+.|+|+|+|||||+|.+||+ .|.++.+|+.|+- |...- +|.|+
T Consensus 605 PNqCiiC~----------rVlSC~saLqmHyrtHtGERPFkCKiCgR-AFtTkGNLkaH~~vHka~p~~R~q~ScP~~~i 673 (958)
T KOG1074|consen 605 PNQCIICL----------RVLSCPSALQMHYRTHTGERPFKCKICGR-AFTTKGNLKAHMSVHKAKPPARVQFSCPSTFI 673 (958)
T ss_pred ccceeeee----------ecccchhhhhhhhhcccCcCccccccccc-hhccccchhhcccccccCccccccccCCchhh
Confidence 56788877 88999999999999999999999999999 9999999999998 75443 36674
Q ss_pred CCcccCCHHHHHHHHHhhc
Q 020075 243 CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 243 C~k~F~~~~~L~~H~~~H~ 261 (331)
|-+.|...-.|..|+|+|.
T Consensus 674 c~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 674 CQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred hcccccccccccceEEeec
Confidence 8899999999999999997
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.81 E-value=1e-20 Score=181.95 Aligned_cols=58 Identities=24% Similarity=0.473 Sum_probs=54.4
Q ss_pred ccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhhcCCCCccCc
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEV 269 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~ 269 (331)
..|.+||+ .|...+.|..|+| |+|+|||.|. |++.|..+.+|+.||.+|....|+.-.
T Consensus 880 h~C~vCgk-~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 880 HVCNVCGK-QFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhccchh-cccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 68999999 9999999999999 9999999999 999999999999999999988776544
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.68 E-value=1.4e-17 Score=135.95 Aligned_cols=116 Identities=26% Similarity=0.566 Sum_probs=104.5
Q ss_pred CCCccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhcc
Q 020075 122 AEHIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNH 201 (331)
Q Consensus 122 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H 201 (331)
+...|.|.+|+|.|.-..-|.+|++.|... +.+-|.+|| |.|.....|++|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~v-------------------kr~lct~cg----------kgfndtfdlkrh 164 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDV-------------------KRHLCTFCG----------KGFNDTFDLKRH 164 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHH-------------------HHHHHhhcc----------Ccccchhhhhhh
Confidence 456799999999999999999999999887 778899999 889999999999
Q ss_pred cccccCCCCccCCCCCCCccCChhHhHHHhh--cc----------CCCceecc-CCcccCCHHHHHHHHHhhcCCCCcc
Q 020075 202 FKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK--NC----------GESRWKCS-CGTSFSRKDKLFGHVALFEGHMPEV 267 (331)
Q Consensus 202 ~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~--H~----------~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~ 267 (331)
+|+|+|.+||+|..|+| +|+.+-.|..|++ |. ..|.|.|+ ||.+-.+...+..|++.|+.-.|+.
T Consensus 165 ~rthtgvrpykc~~c~k-aftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spal 242 (267)
T KOG3576|consen 165 TRTHTGVRPYKCSLCEK-AFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPAL 242 (267)
T ss_pred hccccCccccchhhhhH-HHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHHH
Confidence 99999999999999999 9999999999998 53 35789999 9999999999999999988666543
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.67 E-value=2.6e-17 Score=144.72 Aligned_cols=159 Identities=16% Similarity=0.236 Sum_probs=132.1
Q ss_pred CCCCCCCCCchhhhhhhhhhcCCCccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCcc---------
Q 020075 101 GSEHDIESDCEIVEIDAVELLAEHIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKT--------- 171 (331)
Q Consensus 101 ~~~~~~~~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~--------- 171 (331)
..|.+.+.+...|+.|.+.|+++|...|+.||.-|.++..|-.|.+.-+.- ...+|.|..|-|.+
T Consensus 183 ~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l------~~n~fqC~~C~KrFaTeklL~~H 256 (467)
T KOG3608|consen 183 AMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTEL------NTNSFQCAQCFKRFATEKLLKSH 256 (467)
T ss_pred hhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhh------cCCchHHHHHHHHHhHHHHHHHH
Confidence 457778899999999999999999999999999999999999999876643 23688998887643
Q ss_pred ------ceeCCCCCCccccccCCccccccHHHHhcccc-cccCCCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-
Q 020075 172 ------RFSCPYDGCNRNKKHKKFRALKSVICVKNHFK-RSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS- 242 (331)
Q Consensus 172 ------~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~-~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~- 242 (331)
-|+|++|. -...+...|.+|++ +|...|||+|+.|++ .|.+.+.|..|.. |. +-.|.|.
T Consensus 257 v~rHvn~ykCplCd----------mtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~-~c~~esdL~kH~~~HS-~~~y~C~h 324 (467)
T KOG3608|consen 257 VVRHVNCYKCPLCD----------MTCSSASSLTTHIRYRHSKDKPFKCDECDT-RCVRESDLAKHVQVHS-KTVYQCEH 324 (467)
T ss_pred HHHhhhcccccccc----------cCCCChHHHHHHHHhhhccCCCccccchhh-hhccHHHHHHHHHhcc-ccceecCC
Confidence 38888888 77888888999987 455679999999999 8999999999998 87 6679995
Q ss_pred --CCcccCCHHHHHHHHHhhc-CCC--CccCccccccCCc
Q 020075 243 --CGTSFSRKDKLFGHVALFE-GHM--PEVEVDEKMKHHD 277 (331)
Q Consensus 243 --C~k~F~~~~~L~~H~~~H~-~e~--p~~c~~~~~~~~~ 277 (331)
|..+|++...|++|++.++ |.. +|.|-.|..-+..
T Consensus 325 ~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~ 364 (467)
T KOG3608|consen 325 PDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTS 364 (467)
T ss_pred CCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhcc
Confidence 9999999999999988754 544 5899888875543
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.65 E-value=1.7e-16 Score=139.64 Aligned_cols=176 Identities=17% Similarity=0.259 Sum_probs=123.7
Q ss_pred cchhhhhhhhHhhhcCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhhhh--cCCCccccccchhhccC
Q 020075 60 VSSEIASAIHQVIVNGSALLACSPQQPTLQQLPPDPKNPEIGSEHDIESDCEIVEIDAVEL--LAEHIHFCDICGKGFKR 137 (331)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~h~~~h--~~~~~~~C~~C~k~F~~ 137 (331)
+.+......|.+.|++++.+.|..+.. -|.....|-.|.+.. ....+|+|..|.|.|.+
T Consensus 189 ~~~k~~LreH~r~Hs~eKvvACp~Cg~-------------------~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaT 249 (467)
T KOG3608|consen 189 MGNKYRLREHIRTHSNEKVVACPHCGE-------------------LFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFAT 249 (467)
T ss_pred hccHHHHHHHHHhcCCCeEEecchHHH-------------------HhccccHHHHHHHhhhhhcCCchHHHHHHHHHhH
Confidence 455677788999999999999985444 344444444444422 22335555555555555
Q ss_pred HHHHHHHHHHhcCCCCCchhccCCcccccCC------------------CccceeCCCCCCccccccCCccccccHHHHh
Q 020075 138 DANLRMHMRAHGDEFKTPQALAKPEKGSVSG------------------RKTRFSCPYDGCNRNKKHKKFRALKSVICVK 199 (331)
Q Consensus 138 ~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~------------------~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~ 199 (331)
...|+.|++.|- ..|+|..|+ +.+||+|..|. +.|...+.|.
T Consensus 250 eklL~~Hv~rHv----------n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd----------~~c~~esdL~ 309 (467)
T KOG3608|consen 250 EKLLKSHVVRHV----------NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECD----------TRCVRESDLA 309 (467)
T ss_pred HHHHHHHHHHhh----------hcccccccccCCCChHHHHHHHHhhhccCCCccccchh----------hhhccHHHHH
Confidence 555555555553 345555443 23677777777 7788888899
Q ss_pred cccccccCCCCccCCC--CCCCccCChhHhHHHhh--ccC--CCceecc-CCcccCCHHHHHHHHHh-h-----cCCCCc
Q 020075 200 NHFKRSHCPKMYSCDK--CHKKSFSVVSDLRSHYK--NCG--ESRWKCS-CGTSFSRKDKLFGHVAL-F-----EGHMPE 266 (331)
Q Consensus 200 ~H~~~h~~~k~~~C~~--C~k~~f~~~~~L~~H~~--H~~--ekp~~C~-C~k~F~~~~~L~~H~~~-H-----~~e~p~ 266 (331)
+|...|. +-.|.|+. |.. +|.+...|++|++ |-| +-+|.|. |++.|++-.+|.+|++. | .|.+.|
T Consensus 310 kH~~~HS-~~~y~C~h~~C~~-s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~RF 387 (467)
T KOG3608|consen 310 KHVQVHS-KTVYQCEHPDCHY-SVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGHKRF 387 (467)
T ss_pred HHHHhcc-ccceecCCCCCcH-HHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCCCce
Confidence 9999888 67899988 999 9999999999999 434 5679999 99999999999999865 4 355566
Q ss_pred cCccccccCC
Q 020075 267 VEVDEKMKHH 276 (331)
Q Consensus 267 ~c~~~~~~~~ 276 (331)
...++...+-
T Consensus 388 tYk~~edG~m 397 (467)
T KOG3608|consen 388 TYKVDEDGFM 397 (467)
T ss_pred eeeeccCcee
Confidence 6666655443
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.53 E-value=1.8e-15 Score=123.71 Aligned_cols=100 Identities=24% Similarity=0.383 Sum_probs=89.0
Q ss_pred ccceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCccc
Q 020075 170 KTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSF 247 (331)
Q Consensus 170 ~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F 247 (331)
...|.|.+|+ |.|.-..-|.+|+++|...|.|-|..||| .|...-.|++|+| |+|.+||+|. |+|+|
T Consensus 115 ~d~ftCrvCg----------K~F~lQRmlnrh~kch~~vkr~lct~cgk-gfndtfdlkrh~rthtgvrpykc~~c~kaf 183 (267)
T KOG3576|consen 115 QDSFTCRVCG----------KKFGLQRMLNRHLKCHSDVKRHLCTFCGK-GFNDTFDLKRHTRTHTGVRPYKCSLCEKAF 183 (267)
T ss_pred CCeeeeehhh----------hhhhHHHHHHHHhhhccHHHHHHHhhccC-cccchhhhhhhhccccCccccchhhhhHHH
Confidence 3569999999 99999999999999999999999999999 9999999999999 9999999999 99999
Q ss_pred CCHHHHHHHHHhhc-----------CCCCccCccccccCCcccc
Q 020075 248 SRKDKLFGHVALFE-----------GHMPEVEVDEKMKHHDQDV 280 (331)
Q Consensus 248 ~~~~~L~~H~~~H~-----------~e~p~~c~~~~~~~~~~~~ 280 (331)
+++..|..|++.-+ +++.|+|++|.-.....++
T Consensus 184 tqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~ 227 (267)
T KOG3576|consen 184 TQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEV 227 (267)
T ss_pred HhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhH
Confidence 99999999987533 4678999999875544443
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.52 E-value=3.1e-15 Score=142.37 Aligned_cols=107 Identities=22% Similarity=0.563 Sum_probs=93.1
Q ss_pred ccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhccccc
Q 020075 125 IHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKR 204 (331)
Q Consensus 125 ~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~ 204 (331)
...|++|.+.+.+...|+.|++.-+.. . ...|.|.+|. ..|..+.-|.+|+..
T Consensus 210 lltcpycdrgykrltslkeHikyrhek--------n---------e~nfsC~lCs----------ytFAyRtQLErhm~~ 262 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEK--------N---------EPNFSCMLCS----------YTFAYRTQLERHMQL 262 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhh--------C---------CCCCcchhhh----------hhhhhHHHHHHHHHh
Confidence 468999999999999999999853321 0 1347888888 899999999999988
Q ss_pred ccC-------------CCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHh
Q 020075 205 SHC-------------PKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 205 h~~-------------~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
|.. -+.|+|..||| .|..+.+|+.|+| |.|||||.|+ |+|.|++...+..||..
T Consensus 263 hkpg~dqa~sltqsa~lRKFKCtECgK-AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 263 HKPGGDQAISLTQSALLRKFKCTECGK-AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hcCCCcccccccchhhhccccccccch-hhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 864 26799999999 9999999999999 9999999999 99999999999999853
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.49 E-value=6.7e-15 Score=140.11 Aligned_cols=68 Identities=24% Similarity=0.484 Sum_probs=56.9
Q ss_pred cccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHH
Q 020075 190 RALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVA 258 (331)
Q Consensus 190 k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~ 258 (331)
|.|.-...|-+|.-.|+|.+||+|.+|.| .|..+.+|..|+| |.|||||.|+ |+|.|++...+.+||.
T Consensus 902 K~FqKqSSLaRHKYEHsGqRPyqC~iCkK-AFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 902 KAFQKQSSLARHKYEHSGQRPYQCIICKK-AFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred HHHHhhHHHHHhhhhhcCCCCcccchhhH-hhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 44444444455555555558999999999 9999999999999 9999999999 9999999999999985
No 11
>PHA00733 hypothetical protein
Probab=99.15 E-value=6.6e-11 Score=93.35 Aligned_cols=87 Identities=18% Similarity=0.280 Sum_probs=68.6
Q ss_pred cCCCccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhc
Q 020075 121 LAEHIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKN 200 (331)
Q Consensus 121 ~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~ 200 (331)
...+++.|.+|.+.|.....|..|... .+
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l---------------------------------------------------~~ 64 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYL---------------------------------------------------YK 64 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHH---------------------------------------------------Hh
Confidence 446778888888888887777766321 22
Q ss_pred ccccccCCCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhhcC
Q 020075 201 HFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALFEG 262 (331)
Q Consensus 201 H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~ 262 (331)
|+.. ++.+||.|+.|++ .|.....|..|++ | +.+|.|. |++.|.....|..|++..++
T Consensus 65 ~~~~-~~~kPy~C~~Cgk-~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 65 LLTS-KAVSPYVCPLCLM-PFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred hccc-CCCCCccCCCCCC-cCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3222 3358999999999 9999999999999 7 4679999 99999999999999987654
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.04 E-value=4.9e-10 Score=107.74 Aligned_cols=127 Identities=17% Similarity=0.245 Sum_probs=96.8
Q ss_pred cccccchhhccCHHHHHHHHHHhcCCCCCchhccCCccccc--CCC-------ccceeCCCCCCccccccCCccccccHH
Q 020075 126 HFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSV--SGR-------KTRFSCPYDGCNRNKKHKKFRALKSVI 196 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~--C~~-------~~~~~C~~c~~~~~~~h~~~k~f~~~~ 196 (331)
-.|+.|.+... ..+|..|...-.- ....|.. |+. ...+.|+.|+ +.|. ..
T Consensus 408 V~C~NC~~~i~-l~~l~lHe~~C~r---------~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cg----------k~f~-~s 466 (567)
T PLN03086 408 VECRNCKHYIP-SRSIALHEAYCSR---------HNVVCPHDGCGIVLRVEEAKNHVHCEKCG----------QAFQ-QG 466 (567)
T ss_pred EECCCCCCccc-hhHHHHHHhhCCC---------cceeCCcccccceeeccccccCccCCCCC----------Cccc-hH
Confidence 46888876544 4556677653321 2334553 553 3457888888 7775 56
Q ss_pred HHhcccccccCCCCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccC----------CHHHHHHHHHhhcCCC
Q 020075 197 CVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFS----------RKDKLFGHVALFEGHM 264 (331)
Q Consensus 197 ~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~----------~~~~L~~H~~~H~~e~ 264 (331)
.|+.|++.+| ++|.|+ ||+ .+ .+..|..|+. |...+|+.|. |++.|. ....|..|+.++ |.+
T Consensus 467 ~LekH~~~~H--kpv~Cp-Cg~-~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~r 540 (567)
T PLN03086 467 EMEKHMKVFH--EPLQCP-CGV-VL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSR 540 (567)
T ss_pred HHHHHHHhcC--CCccCC-CCC-Cc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCc
Confidence 6899999987 899999 998 66 6789999999 9999999999 999995 346899999995 999
Q ss_pred CccCccccccCCccc
Q 020075 265 PEVEVDEKMKHHDQD 279 (331)
Q Consensus 265 p~~c~~~~~~~~~~~ 279 (331)
++.|..|.......+
T Consensus 541 t~~C~~Cgk~Vrlrd 555 (567)
T PLN03086 541 TAPCDSCGRSVMLKE 555 (567)
T ss_pred ceEccccCCeeeehh
Confidence 999999988766554
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.00 E-value=6.4e-10 Score=106.96 Aligned_cols=101 Identities=22% Similarity=0.473 Sum_probs=81.2
Q ss_pred CCccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhccc
Q 020075 123 EHIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHF 202 (331)
Q Consensus 123 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~ 202 (331)
++.+.|+.|++.|. ...|..|+++|+ +++.|+ |+ +.+ ....|..|.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H---------------------kpv~Cp-Cg----------~~~-~R~~L~~H~ 496 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH---------------------EPLQCP-CG----------VVL-EKEQMVQHQ 496 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC---------------------CCccCC-CC----------CCc-chhHHHhhh
Confidence 55679999999996 688999999975 246777 76 433 446789999
Q ss_pred ccccCCCCccCCCCCCCccC----------ChhHhHHHhhccCCCceecc-CCcccCCHHHHHHHHHh
Q 020075 203 KRSHCPKMYSCDKCHKKSFS----------VVSDLRSHYKNCGESRWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 203 ~~h~~~k~~~C~~C~k~~f~----------~~~~L~~H~~H~~ekp~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
+.|...+++.|..|++ .|. ..+.|..|....|.+++.|. ||+.|..+. |..|+..
T Consensus 497 ~thCp~Kpi~C~fC~~-~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlrd-m~~H~~~ 562 (567)
T PLN03086 497 ASTCPLRLITCRFCGD-MVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLKE-MDIHQIA 562 (567)
T ss_pred hccCCCCceeCCCCCC-ccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeehh-HHHHHHH
Confidence 9999999999999999 884 24589999985599999999 999998764 5677654
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.95 E-value=2.3e-10 Score=74.80 Aligned_cols=41 Identities=20% Similarity=0.424 Sum_probs=34.6
Q ss_pred ccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHH
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLF 254 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~ 254 (331)
|.|+.||+ .|+..++|..|++ |+ +||+|. |+|.|.+.+.|.
T Consensus 6 y~C~~CGK-~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGE-IYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCC-eeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 78888888 8888888888888 88 688888 888888777663
No 15
>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=98.65 E-value=1.3e-08 Score=56.88 Aligned_cols=24 Identities=50% Similarity=1.088 Sum_probs=18.9
Q ss_pred HhHHHhh-ccCCCceecc-CCcccCC
Q 020075 226 DLRSHYK-NCGESRWKCS-CGTSFSR 249 (331)
Q Consensus 226 ~L~~H~~-H~~ekp~~C~-C~k~F~~ 249 (331)
+|..|++ |+|+|||.|+ |+++|.+
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 4778888 8888888888 8888863
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.62 E-value=2.9e-08 Score=64.96 Aligned_cols=42 Identities=12% Similarity=0.270 Sum_probs=36.4
Q ss_pred ceecc-CCcccCCHHHHHHHHHhhcCCCCccCccccccCCccccc
Q 020075 238 RWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKMKHHDQDVV 281 (331)
Q Consensus 238 p~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~~~~~~~~~ 281 (331)
-|.|+ |||.|++.++|..|+++|+ +|+.|..|.+.+.....+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 38999 9999999999999999999 799999999877655443
No 17
>PHA00616 hypothetical protein
Probab=98.55 E-value=3.5e-08 Score=61.39 Aligned_cols=33 Identities=18% Similarity=0.374 Sum_probs=26.6
Q ss_pred ceecc-CCcccCCHHHHHHHHHhhcCCCCccCcc
Q 020075 238 RWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVD 270 (331)
Q Consensus 238 p~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~ 270 (331)
||.|. ||+.|..++.|.+|++.|+|++|+.|+-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 67888 8888888888888888888888877653
No 18
>PHA00733 hypothetical protein
Probab=98.54 E-value=4.6e-08 Score=77.19 Aligned_cols=71 Identities=15% Similarity=0.091 Sum_probs=59.2
Q ss_pred CCCccCCCCCCCccCChhHhHHH--h----hccCCCceecc-CCcccCCHHHHHHHHHhhcCCCCccCccccccCCcccc
Q 020075 208 PKMYSCDKCHKKSFSVVSDLRSH--Y----KNCGESRWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKMKHHDQDV 280 (331)
Q Consensus 208 ~k~~~C~~C~k~~f~~~~~L~~H--~----~H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~~~~~~~~ 280 (331)
.+++.|.+|.+ .|.....|..| + .+.+.+||.|. |++.|.+...|..|++.| +.+|.|..|...+.....
T Consensus 38 ~~~~~~~~~~~-~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 38 QKRLIRAVVKT-LIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhHHHHHHhh-hccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 47899999998 88887777766 2 24568999999 999999999999999987 468999999988776554
Q ss_pred c
Q 020075 281 V 281 (331)
Q Consensus 281 ~ 281 (331)
+
T Consensus 115 L 115 (128)
T PHA00733 115 T 115 (128)
T ss_pred H
Confidence 3
No 19
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.41 E-value=8.6e-08 Score=87.16 Aligned_cols=107 Identities=15% Similarity=0.294 Sum_probs=69.4
Q ss_pred ccccccchhhccCHHHHHHHHH--HhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhccc
Q 020075 125 IHFCDICGKGFKRDANLRMHMR--AHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHF 202 (331)
Q Consensus 125 ~~~C~~C~k~F~~~~~L~~H~~--~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~ 202 (331)
-|.|..|...|.....|-+|.- +-+-+ |+|+.|+ |.|.|..+|..|.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vE---------------------YrCPEC~----------KVFsCPANLASHR 315 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVE---------------------YRCPECD----------KVFSCPANLASHR 315 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEee---------------------ecCCccc----------ccccCchhhhhhh
Confidence 3999999999999999999973 33333 8888888 8999999999998
Q ss_pred ccccCCCCcc--CCCCCCCccCChhHhHHHhh---ccCCCceecc-CCcccCCHHHHHHHHHhhcC
Q 020075 203 KRSHCPKMYS--CDKCHKKSFSVVSDLRSHYK---NCGESRWKCS-CGTSFSRKDKLFGHVALFEG 262 (331)
Q Consensus 203 ~~h~~~k~~~--C~~C~k~~f~~~~~L~~H~~---H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~ 262 (331)
|.|--..--. =..=.+....+....+.=.| -..+-.|.|. |+|.|.+...|+.|+.+|..
T Consensus 316 RWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 316 RWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 8874311000 00000001001100001011 1223479999 99999999999999998863
No 20
>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=98.40 E-value=1e-07 Score=53.16 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=21.8
Q ss_pred hhhhhhhhcCCCccccccchhhccC
Q 020075 113 VEIDAVELLAEHIHFCDICGKGFKR 137 (331)
Q Consensus 113 l~~h~~~h~~~~~~~C~~C~k~F~~ 137 (331)
|..|+++|++++||+|++|++.|.+
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 6789999999999999999998864
No 21
>PHA00732 hypothetical protein
Probab=98.25 E-value=6.6e-07 Score=64.16 Aligned_cols=45 Identities=27% Similarity=0.498 Sum_probs=36.9
Q ss_pred CccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhh
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALF 260 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H 260 (331)
||.|..|++ .|.+...|..|++ ++. ++.|+ |++.|. .|..|++++
T Consensus 1 py~C~~Cgk-~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGF-TTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCC-ccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhccc
Confidence 588999999 9999999999997 432 36899 999998 588888664
No 22
>PHA00616 hypothetical protein
Probab=98.24 E-value=3.6e-07 Score=56.89 Aligned_cols=32 Identities=19% Similarity=0.399 Sum_probs=30.3
Q ss_pred CccCCCCCCCccCChhHhHHHhh-ccCCCceecc
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS 242 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~ 242 (331)
||.|..||+ .|..++.|..|++ |+|++|+.|+
T Consensus 1 pYqC~~CG~-~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGG-IFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhH-HHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999 9999999999999 9999999886
No 23
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.20 E-value=2.1e-07 Score=84.70 Aligned_cols=151 Identities=19% Similarity=0.175 Sum_probs=100.8
Q ss_pred CCCCCCCCCCCCchhhhhhhhhhcCCCccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcc-----------ccc
Q 020075 98 PEIGSEHDIESDCEIVEIDAVELLAEHIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEK-----------GSV 166 (331)
Q Consensus 98 ~~~~~~~~~~~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~-----------c~~ 166 (331)
+.|..|...|.....|-+|.-...-..-|+|+.|+|.|.-..||-.|.|+|.........-..|-+ -..
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 445556667777778888877665566799999999999999999999999643100000001100 000
Q ss_pred C---CCccceeCCCCCCccccccCCccccccHHHHhcccccccCC---C-------------------------------
Q 020075 167 S---GRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCP---K------------------------------- 209 (331)
Q Consensus 167 C---~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~---k------------------------------- 209 (331)
. .....|.|.+|+ |.|....-|++|..+|+.. +
T Consensus 348 sg~dss~gi~~C~~C~----------KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~ 417 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCG----------KKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSH 417 (500)
T ss_pred cCCcccCceeecHHhh----------hhhHHHHHHHHhHHhhhccccchhcccCcchhhccccccccccccccccccccc
Confidence 0 112368999999 8888888888887777641 0
Q ss_pred ------------CccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHh
Q 020075 210 ------------MYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 210 ------------~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
...|++|+- .+..+..--.|.+ -..+.-|.|. |.-.|.....|.+|+..
T Consensus 418 g~~vl~~a~sael~~pp~~~~-ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 418 GDEVLYVAGSAELELPPYDGS-PPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred ccceeeeeccccccCCCCCCC-CcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhh
Confidence 123555665 5555554444444 3344559999 99999999999999876
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=97.91 E-value=9.2e-06 Score=43.80 Aligned_cols=22 Identities=45% Similarity=0.871 Sum_probs=18.2
Q ss_pred eecc-CCcccCCHHHHHHHHHhh
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALF 260 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H 260 (331)
|.|+ |++.|.++..|..|++.|
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 6788 888888888888888775
No 25
>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=97.88 E-value=7.3e-06 Score=44.21 Aligned_cols=23 Identities=52% Similarity=0.995 Sum_probs=21.8
Q ss_pred cccccchhhccCHHHHHHHHHHh
Q 020075 126 HFCDICGKGFKRDANLRMHMRAH 148 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~~H 148 (331)
|+|++|++.|.++..|..|++.|
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 78999999999999999999976
No 26
>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=97.86 E-value=2.2e-05 Score=52.14 Aligned_cols=49 Identities=29% Similarity=0.572 Sum_probs=38.7
Q ss_pred CccCCCCCCCccCChhHhHHHhh--ccCC-Cceecc-CCcccCCHHHHHHHHHhhcC
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYK--NCGE-SRWKCS-CGTSFSRKDKLFGHVALFEG 262 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~--H~~e-kp~~C~-C~k~F~~~~~L~~H~~~H~~ 262 (331)
.|.|++|++ .|. ...|..|.. |..+ +.+.|+ |...+. .+|.+|+..+++
T Consensus 2 ~f~CP~C~~-~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFS-ESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccC-HHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 489999999 665 567999987 7654 579999 998765 499999988653
No 27
>PHA00732 hypothetical protein
Probab=97.78 E-value=1.6e-05 Score=56.96 Aligned_cols=23 Identities=30% Similarity=0.465 Sum_probs=19.5
Q ss_pred ccccccchhhccCHHHHHHHHHH
Q 020075 125 IHFCDICGKGFKRDANLRMHMRA 147 (331)
Q Consensus 125 ~~~C~~C~k~F~~~~~L~~H~~~ 147 (331)
||.|..||+.|.+...|..|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhc
Confidence 57888888888888888888874
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.48 E-value=2.6e-05 Score=68.80 Aligned_cols=50 Identities=22% Similarity=0.518 Sum_probs=43.8
Q ss_pred CCCccCCC--CCCCccCChhHhHHHhh--cc------------------CCCceecc-CCcccCCHHHHHHHHH
Q 020075 208 PKMYSCDK--CHKKSFSVVSDLRSHYK--NC------------------GESRWKCS-CGTSFSRKDKLFGHVA 258 (331)
Q Consensus 208 ~k~~~C~~--C~k~~f~~~~~L~~H~~--H~------------------~ekp~~C~-C~k~F~~~~~L~~H~~ 258 (331)
+|||+|++ |.| .|+....|+-|+. |- ..|||.|+ |+|.|.....|+-|+.
T Consensus 347 ~KpykCpV~gC~K-~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNK-KYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchh-hhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 59999976 999 9999999999998 51 24899999 9999999999998854
No 29
>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=97.47 E-value=7e-05 Score=42.00 Aligned_cols=24 Identities=29% Similarity=0.571 Sum_probs=18.8
Q ss_pred ceecc-CCcccCCHHHHHHHHHhhc
Q 020075 238 RWKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 238 p~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
||.|. |++.|.+...|..|++.|.
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 57788 8888888888888887764
No 30
>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=97.45 E-value=9.3e-05 Score=39.95 Aligned_cols=24 Identities=50% Similarity=1.023 Sum_probs=20.4
Q ss_pred cccccchhhccCHHHHHHHHHHhc
Q 020075 126 HFCDICGKGFKRDANLRMHMRAHG 149 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~~H~ 149 (331)
|.|++|++.|.+...|+.|++.|+
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 789999999999999999999874
No 31
>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=97.44 E-value=0.00012 Score=39.43 Aligned_cols=23 Identities=35% Similarity=0.792 Sum_probs=15.6
Q ss_pred eecc-CCcccCCHHHHHHHHHhhc
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
|.|+ |++.|.+...|..|+++|+
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 5677 7777777777777777653
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.42 E-value=7e-05 Score=66.14 Aligned_cols=72 Identities=26% Similarity=0.473 Sum_probs=47.2
Q ss_pred CCCcccccc--chhhccCHHHHHHHHHH-hcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHH
Q 020075 122 AEHIHFCDI--CGKGFKRDANLRMHMRA-HGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICV 198 (331)
Q Consensus 122 ~~~~~~C~~--C~k~F~~~~~L~~H~~~-H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l 198 (331)
++|||+|++ |.|.|+....|+-|+.- |... +. ..-+. +
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~--------~~-----------~~~p~-------------p------- 386 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQ--------KL-----------HENPS-------------P------- 386 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCc--------cc-----------CCCCC-------------c-------
Confidence 469999998 99999999999999863 2211 00 00000 0
Q ss_pred hcccccccCCCCccCCCCCCCccCChhHhHHHhhc
Q 020075 199 KNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYKN 233 (331)
Q Consensus 199 ~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~H 233 (331)
..|.-.....|||+|++|+| .|..-..|+-|+.|
T Consensus 387 ~~~~~F~~~~KPYrCevC~K-RYKNlNGLKYHr~H 420 (423)
T COG5189 387 EKMNIFSAKDKPYRCEVCDK-RYKNLNGLKYHRKH 420 (423)
T ss_pred cccccccccCCceeccccch-hhccCccceecccc
Confidence 01111122348899999998 88888888888774
No 33
>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=97.27 E-value=0.0001 Score=41.33 Aligned_cols=26 Identities=42% Similarity=0.672 Sum_probs=23.8
Q ss_pred ccccccchhhccCHHHHHHHHHHhcC
Q 020075 125 IHFCDICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 125 ~~~C~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
||.|..|++.|.+...|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999988753
No 34
>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=97.08 E-value=0.00043 Score=45.93 Aligned_cols=46 Identities=28% Similarity=0.546 Sum_probs=36.1
Q ss_pred eeCCCCCCccccccCCccccccHHHHhcccccccC--CCCccCCCCCCCccCChhHhHHHhh
Q 020075 173 FSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHC--PKMYSCDKCHKKSFSVVSDLRSHYK 232 (331)
Q Consensus 173 ~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~--~k~~~C~~C~k~~f~~~~~L~~H~~ 232 (331)
|.|++|+ + ......|..|....|. .+.+.|++|.. .+. .+|..|+.
T Consensus 3 f~CP~C~----------~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~-~~~--~~l~~Hl~ 50 (54)
T PF05605_consen 3 FTCPYCG----------K-GFSESSLVEHCEDEHRSESKNVVCPICSS-RVT--DNLIRHLN 50 (54)
T ss_pred cCCCCCC----------C-ccCHHHHHHHHHhHCcCCCCCccCCCchh-hhh--hHHHHHHH
Confidence 8899999 7 4556678999766554 36799999998 655 48999998
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.93 E-value=0.00067 Score=50.81 Aligned_cols=72 Identities=18% Similarity=0.313 Sum_probs=21.1
Q ss_pred eCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCCHHH
Q 020075 174 SCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSRKDK 252 (331)
Q Consensus 174 ~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~~~~ 252 (331)
.|.+|+ ..|.....|..|+...|+-. .+ ... .+.....+..+++..-...+.|. |++.|.+...
T Consensus 1 ~C~~C~----------~~f~~~~~l~~H~~~~H~~~---~~-~~~-~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~ 65 (100)
T PF12756_consen 1 QCLFCD----------ESFSSVDDLLQHMKKKHGFD---IP-DQK-YLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREA 65 (100)
T ss_dssp ---------------------------------------------------------------SSEEBSSSS-EESSHHH
T ss_pred Cccccc----------cccccccccccccccccccc---cc-ccc-ccccccccccccccccCCCCCCCccCCCCcCHHH
Confidence 377777 77777777778876666421 11 111 23333344444442222379999 9999999999
Q ss_pred HHHHHHhh
Q 020075 253 LFGHVALF 260 (331)
Q Consensus 253 L~~H~~~H 260 (331)
|..|++.+
T Consensus 66 l~~Hm~~~ 73 (100)
T PF12756_consen 66 LQEHMRSK 73 (100)
T ss_dssp HHHHHHHT
T ss_pred HHHHHcCc
Confidence 99999975
No 36
>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=96.91 E-value=0.00093 Score=42.65 Aligned_cols=38 Identities=21% Similarity=0.357 Sum_probs=22.5
Q ss_pred HHHhh--ccCCCceecc-CCcccCCHHHHHHHHHhhcCCCC
Q 020075 228 RSHYK--NCGESRWKCS-CGTSFSRKDKLFGHVALFEGHMP 265 (331)
Q Consensus 228 ~~H~~--H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p 265 (331)
..+.+ +..+.|-.|+ |+..+.+..+|++|+.++++.+|
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 44554 4667888888 88888888888888888777765
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.87 E-value=0.00094 Score=36.45 Aligned_cols=23 Identities=30% Similarity=0.755 Sum_probs=16.4
Q ss_pred eecc-CCcccCCHHHHHHHHHhhc
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
|.|. |++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 4677 7777777777777777654
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.80 E-value=0.0011 Score=36.23 Aligned_cols=25 Identities=44% Similarity=0.773 Sum_probs=22.6
Q ss_pred cccccchhhccCHHHHHHHHHHhcC
Q 020075 126 HFCDICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998753
No 39
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.73 E-value=0.00097 Score=49.89 Aligned_cols=71 Identities=20% Similarity=0.400 Sum_probs=20.5
Q ss_pred ccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhccccccc
Q 020075 127 FCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSH 206 (331)
Q Consensus 127 ~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~ 206 (331)
+|..|+..|.....|..|+...++- .+... ..+.....+..+.+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~--------------------~~~~~-------------~~l~~~~~~~~~~~~~- 46 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGF--------------------DIPDQ-------------KYLVDPNRLLNYLRKK- 46 (100)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Ccccccccccccccccccccccccc--------------------ccccc-------------cccccccccccccccc-
Confidence 5999999999999999999765542 00000 0001111111222211
Q ss_pred CCCCccCCCCCCCccCChhHhHHHhh
Q 020075 207 CPKMYSCDKCHKKSFSVVSDLRSHYK 232 (331)
Q Consensus 207 ~~k~~~C~~C~k~~f~~~~~L~~H~~ 232 (331)
....+.|.+|++ .|.+...|..|++
T Consensus 47 ~~~~~~C~~C~~-~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 47 VKESFRCPYCNK-TFRSREALQEHMR 71 (100)
T ss_dssp --SSEEBSSSS--EESSHHHHHHHHH
T ss_pred cCCCCCCCccCC-CCcCHHHHHHHHc
Confidence 113699999999 9999999999999
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=96.36 E-value=0.0035 Score=40.06 Aligned_cols=30 Identities=30% Similarity=0.553 Sum_probs=22.4
Q ss_pred CCCccccccchhhccCHHHHHHHHHHhcCC
Q 020075 122 AEHIHFCDICGKGFKRDANLRMHMRAHGDE 151 (331)
Q Consensus 122 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~ 151 (331)
.+.|..|++|+..+.+..+|++|+.++++.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 477999999999999999999999887764
No 41
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.27 E-value=0.0044 Score=61.21 Aligned_cols=71 Identities=15% Similarity=0.263 Sum_probs=47.4
Q ss_pred cccccHHHHhcccccccCCCCccCCCCC------CCccCChhHhHHHhh-ccCCCceecc--------CCcccCCHHHHH
Q 020075 190 RALKSVICVKNHFKRSHCPKMYSCDKCH------KKSFSVVSDLRSHYK-NCGESRWKCS--------CGTSFSRKDKLF 254 (331)
Q Consensus 190 k~f~~~~~l~~H~~~h~~~k~~~C~~C~------k~~f~~~~~L~~H~~-H~~ekp~~C~--------C~k~F~~~~~L~ 254 (331)
..|-+..+|.+|++.+| |.|..|. . .|.....|..|.+ ++ |.|. +-..|.....|.
T Consensus 190 ~~fld~~el~rH~~~~h----~~chfC~~~~~~ne-yy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 190 ERFLDDDELYRHLRFDH----EFCHFCDYKTGQNE-YYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred hhhccHHHHHHhhccce----eheeecCcccccch-hcccchHHHHHhhhcC----ccccccccccceeeehhHHHHHHH
Confidence 78888899999998776 6676663 4 5777888999988 43 3342 223334455666
Q ss_pred HHHHhhcCCCCccCc
Q 020075 255 GHVALFEGHMPEVEV 269 (331)
Q Consensus 255 ~H~~~H~~e~p~~c~ 269 (331)
+|.+.+.-++-|.|.
T Consensus 261 ~~~~~~~~e~~~~~~ 275 (669)
T KOG2231|consen 261 AHNRFIQHEKCYICR 275 (669)
T ss_pred hhccccchheeccCC
Confidence 666555556666664
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.03 E-value=0.0045 Score=33.74 Aligned_cols=22 Identities=32% Similarity=0.634 Sum_probs=16.8
Q ss_pred eecc-CCcccCCHHHHHHHHHhh
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALF 260 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H 260 (331)
|.|. |++.|.+...|..|++.+
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 5688 888888888888887654
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.96 E-value=0.0031 Score=34.42 Aligned_cols=23 Identities=43% Similarity=1.068 Sum_probs=21.0
Q ss_pred cccccchhhccCHHHHHHHHHHh
Q 020075 126 HFCDICGKGFKRDANLRMHMRAH 148 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~~H 148 (331)
|.|.+|++.|.+...|+.|++.+
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 67999999999999999999754
No 44
>PRK04860 hypothetical protein; Provisional
Probab=95.96 E-value=0.0041 Score=50.94 Aligned_cols=36 Identities=31% Similarity=0.765 Sum_probs=27.7
Q ss_pred CccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCH
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRK 250 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~ 250 (331)
+|.|. |++ ....+++|.+ |+++++|.|. |++.|...
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 58887 875 3456788888 8888888888 88888654
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.72 E-value=0.0099 Score=32.06 Aligned_cols=22 Identities=36% Similarity=0.623 Sum_probs=13.1
Q ss_pred eecc-CCcccCCHHHHHHHHHhhc
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
|.|+ |+.... ...|.+|++.|+
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 5666 776666 666777766654
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.66 E-value=0.0032 Score=59.79 Aligned_cols=153 Identities=21% Similarity=0.240 Sum_probs=93.2
Q ss_pred CCCCCCCCCCCCCchhhhhhhh--hhcCC--Cccccc--cchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCc
Q 020075 97 NPEIGSEHDIESDCEIVEIDAV--ELLAE--HIHFCD--ICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRK 170 (331)
Q Consensus 97 ~~~~~~~~~~~~~~~~l~~h~~--~h~~~--~~~~C~--~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~ 170 (331)
...+..|...+.....+..|.+ .|.++ +++.|+ .|++.|.+...+..|...|++. .++.+......
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~ 360 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI--------SPAKEKLLNSS 360 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC--------CccccccccCc
Confidence 4566778888888888999999 79999 899999 7999999999999999998886 33333222111
Q ss_pred cceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCC--CCCCCccCChhHhHHHhh-ccCCCc--eecc-CC
Q 020075 171 TRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCD--KCHKKSFSVVSDLRSHYK-NCGESR--WKCS-CG 244 (331)
Q Consensus 171 ~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~--~C~k~~f~~~~~L~~H~~-H~~ekp--~~C~-C~ 244 (331)
..+.-..-. .. .. ...........+.+.|. .|-. .+.....+..|.. |...++ +.|. |.
T Consensus 361 ~~~~~~~~~----------~~---~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 425 (467)
T COG5048 361 SKFSPLLNN----------EP---PQ-SLQQYKDLKNDKKSETLSNSCIR-NFKRDSNLSLHIITHLSFRPYNCKNPPCS 425 (467)
T ss_pred cccccccCC----------CC---cc-chhhccCccCCccccccccchhh-hhccccccccccccccccCCcCCCCCcch
Confidence 100000000 00 00 00011111112344442 3555 6777777777777 665554 3445 88
Q ss_pred cccCCHHHHHHHHHhhcCCCCccCcccc
Q 020075 245 TSFSRKDKLFGHVALFEGHMPEVEVDEK 272 (331)
Q Consensus 245 k~F~~~~~L~~H~~~H~~e~p~~c~~~~ 272 (331)
+.|.....|..|++.|....+..|....
T Consensus 426 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 453 (467)
T COG5048 426 KSFNRHYNLIPHKKIHTNHAPLLCSILK 453 (467)
T ss_pred hhccCcccccccccccccCCceeecccc
Confidence 8888888888888887766665554433
No 47
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.57 E-value=0.011 Score=61.91 Aligned_cols=50 Identities=20% Similarity=0.192 Sum_probs=35.3
Q ss_pred CCCCCCCCchhhhhhhh-hhcCCCccccccchhhccCHHHHHHHHHHhcCC
Q 020075 102 SEHDIESDCEIVEIDAV-ELLAEHIHFCDICGKGFKRDANLRMHMRAHGDE 151 (331)
Q Consensus 102 ~~~~~~~~~~~l~~h~~-~h~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~ 151 (331)
++.-.+.....+..+++ .+.-.+.|+|+.|+..|+....|..|||.-+.+
T Consensus 441 ~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~ 491 (1406)
T KOG1146|consen 441 KAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPE 491 (1406)
T ss_pred chhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccc
Confidence 34444444444555544 445568999999999999999999999974433
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.29 E-value=0.012 Score=31.71 Aligned_cols=24 Identities=25% Similarity=0.506 Sum_probs=19.0
Q ss_pred cccccchhhccCHHHHHHHHHHhcC
Q 020075 126 HFCDICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
|+|+.|+-... ...|..|++.|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 78999998888 8899999998753
No 49
>PRK04860 hypothetical protein; Provisional
Probab=95.10 E-value=0.013 Score=48.08 Aligned_cols=35 Identities=20% Similarity=0.300 Sum_probs=27.3
Q ss_pred CccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCc
Q 020075 124 HIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRK 170 (331)
Q Consensus 124 ~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~ 170 (331)
-+|.|. |++ ....+++|.++|+++ ++|.|..|++.
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~--------~~YrC~~C~~~ 152 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGE--------AVYRCRRCGET 152 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCC--------ccEECCCCCce
Confidence 479998 987 777899999999998 55555555543
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=94.87 E-value=0.0068 Score=33.81 Aligned_cols=21 Identities=29% Similarity=0.667 Sum_probs=12.9
Q ss_pred eecc-CCcccCCHHHHHHHHHh
Q 020075 239 WKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
|.|. |++.|.+...|..|+++
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 5566 66666666666666543
No 51
>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=93.91 E-value=0.083 Score=45.85 Aligned_cols=26 Identities=15% Similarity=0.254 Sum_probs=16.4
Q ss_pred CCceecc-CCcccCCHHHHHHHHHhhc
Q 020075 236 ESRWKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 236 ekp~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
.+++.|+ ||........|..-.|+|.
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecch
Confidence 3667777 7766666666666556553
No 52
>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=93.65 E-value=0.036 Score=30.80 Aligned_cols=21 Identities=43% Similarity=0.891 Sum_probs=19.3
Q ss_pred ccCCCCCCCccCChhHhHHHhh
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYK 232 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~ 232 (331)
|.|..|++ .|.+...|..|++
T Consensus 2 ~~C~~C~k-~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDK-YFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTB-BBSSHHHHHCCTT
T ss_pred CCcccCCC-CcCCHHHHHHHHc
Confidence 78999999 9999999999987
No 53
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.93 E-value=0.072 Score=29.09 Aligned_cols=21 Identities=33% Similarity=0.702 Sum_probs=17.7
Q ss_pred cccccchhhccCHHHHHHHHHH
Q 020075 126 HFCDICGKGFKRDANLRMHMRA 147 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~~ 147 (331)
..|+.||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5799999999 67889999764
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.35 E-value=0.12 Score=28.16 Aligned_cols=19 Identities=37% Similarity=0.857 Sum_probs=11.0
Q ss_pred ecc-CCcccCCHHHHHHHHHh
Q 020075 240 KCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 240 ~C~-C~k~F~~~~~L~~H~~~ 259 (331)
.|+ ||+.| ....|..|+++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 466 66666 45556666543
No 55
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.16 E-value=0.086 Score=44.14 Aligned_cols=79 Identities=22% Similarity=0.537 Sum_probs=58.7
Q ss_pred cceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHhh--cc---------CCCce
Q 020075 171 TRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK--NC---------GESRW 239 (331)
Q Consensus 171 ~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~--H~---------~ekp~ 239 (331)
..|.|++-||- ..|........|..+-|+ -.|..|.+ .|.+...|..|+. |- |..-|
T Consensus 78 ~~~~cqvagc~--------~~~d~lD~~E~hY~~~h~---~sCs~C~r-~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy 145 (253)
T KOG4173|consen 78 PAFACQVAGCC--------QVFDALDDYEHHYHTLHG---NSCSFCKR-AFPTGHLLDAHILEWHDSLFQALVERGQDMY 145 (253)
T ss_pred ccccccccchH--------HHHhhhhhHHHhhhhccc---chhHHHHH-hCCchhhhhHHHHHHHHHHHHHHHHcCccHH
Confidence 45778776654 555555555666544443 47999999 9999999999997 52 45569
Q ss_pred ec--c-CCcccCCHHHHHHHHH-hhc
Q 020075 240 KC--S-CGTSFSRKDKLFGHVA-LFE 261 (331)
Q Consensus 240 ~C--~-C~k~F~~~~~L~~H~~-~H~ 261 (331)
.| . |+-.|.+...-..|+- +|.
T Consensus 146 ~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 146 QCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 99 4 9999999999999975 453
No 56
>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=91.77 E-value=0.14 Score=30.16 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=18.0
Q ss_pred ceecc-CCcccCCHHHHHHHHHh
Q 020075 238 RWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 238 p~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
+|.|. |++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57888 88888888888888754
No 57
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.68 E-value=0.15 Score=53.89 Aligned_cols=54 Identities=20% Similarity=0.393 Sum_probs=46.5
Q ss_pred ccCCCCccCCCCCCCccCChhHhHHHhh--cc------------------------CCCceecc-CCcccCCHHHHHHHH
Q 020075 205 SHCPKMYSCDKCHKKSFSVVSDLRSHYK--NC------------------------GESRWKCS-CGTSFSRKDKLFGHV 257 (331)
Q Consensus 205 h~~~k~~~C~~C~k~~f~~~~~L~~H~~--H~------------------------~ekp~~C~-C~k~F~~~~~L~~H~ 257 (331)
+...|.|+|+.|++ .|.....|-.|+| |. +.+||.|. |..+|+.+.+|..|+
T Consensus 460 ~S~~kt~~cpkc~~-~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNW-HYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred ecccccccCCccch-hhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 33447899999999 9999999999998 53 23689999 999999999999999
Q ss_pred Hh
Q 020075 258 AL 259 (331)
Q Consensus 258 ~~ 259 (331)
..
T Consensus 539 qS 540 (1406)
T KOG1146|consen 539 QS 540 (1406)
T ss_pred HH
Confidence 75
No 58
>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=89.44 E-value=0.29 Score=28.71 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=20.0
Q ss_pred CccCCCCCCCccCChhHhHHHhh
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYK 232 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~ 232 (331)
+|.|++|++ .|.....+..|++
T Consensus 3 ~~~C~~C~~-~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNV-TFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCC-ccCCHHHHHHHHC
Confidence 588999999 9999999999987
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.23 E-value=0.25 Score=46.73 Aligned_cols=62 Identities=34% Similarity=0.540 Sum_probs=42.6
Q ss_pred CCccCCCCCCCccCChhHhHHHhh---ccCC--Cceecc---CCcccCCHHHHHHHHHhhcCCCCccCccc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK---NCGE--SRWKCS---CGTSFSRKDKLFGHVALFEGHMPEVEVDE 271 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~---H~~e--kp~~C~---C~k~F~~~~~L~~H~~~H~~e~p~~c~~~ 271 (331)
.++.|..|.. .|.....|..|.+ |+++ +|+.|. |++.|.+...+..|..+|++-+++.+...
T Consensus 288 ~~~~~~~~~~-~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (467)
T COG5048 288 LPIKSKQCNI-SFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLL 357 (467)
T ss_pred cCCCCccccC-CccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccc
Confidence 3566777777 6777777777766 6666 777776 77777777777777777776666655433
No 60
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.05 E-value=0.57 Score=46.75 Aligned_cols=46 Identities=24% Similarity=0.408 Sum_probs=31.0
Q ss_pred ccCCCCCCCccCChhHhHHHhh-ccCCCceecc-C------CcccCCHHHHHHHHHhhc
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-C------GTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C------~k~F~~~~~L~~H~~~H~ 261 (331)
-.|..|.. .|.....|.+|++ ++ |.|. | +.-|.....|..|-|.++
T Consensus 183 p~C~~C~~-~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHE-RFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhh-hhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 35777877 7777777777777 33 3344 4 456777777888877654
No 61
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=86.63 E-value=0.52 Score=42.73 Aligned_cols=48 Identities=23% Similarity=0.364 Sum_probs=38.0
Q ss_pred ccCCCCCCCccCChhHhHHHhh--ccC-------C-------------------Cceecc-CCcccCCHHHHHHHHHh
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYK--NCG-------E-------------------SRWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~--H~~-------e-------------------kp~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
.+|-.|.. ..-+...|..||+ |-= + +.-.|- |.-.|.....|..||.-
T Consensus 280 v~CLfC~~-~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 280 VVCLFCTN-FYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeecc-chhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 58999999 8888999999998 620 1 124566 99999999999999864
No 62
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.61 E-value=1.3 Score=40.36 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=20.2
Q ss_pred cccccc--chhhccCHHHHHHHHHHhcCC
Q 020075 125 IHFCDI--CGKGFKRDANLRMHMRAHGDE 151 (331)
Q Consensus 125 ~~~C~~--C~k~F~~~~~L~~H~~~H~~~ 151 (331)
.|.|+. |..+......|+.|.+.-++.
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~ 179 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF 179 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc
Confidence 478876 777777788899998876553
No 63
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=86.51 E-value=0.35 Score=31.54 Aligned_cols=26 Identities=35% Similarity=0.726 Sum_probs=19.7
Q ss_pred cCCCceecc-CCcccCCHHHHHHHHHh
Q 020075 234 CGESRWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 234 ~~ekp~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
-||--+.|+ ||+.|.....+.+|+..
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 466667888 88888888888888755
No 64
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=85.83 E-value=0.64 Score=47.32 Aligned_cols=58 Identities=17% Similarity=0.292 Sum_probs=34.4
Q ss_pred CCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHh
Q 020075 152 FKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHY 231 (331)
Q Consensus 152 ~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~ 231 (331)
|.++.....-..|..||-. +.|+.|. -+ +..|...+...|.+||.
T Consensus 426 flnRRGys~~l~C~~Cg~v--~~Cp~Cd----------~~----------lt~H~~~~~L~CH~Cg~------------- 470 (730)
T COG1198 426 FLNRRGYAPLLLCRDCGYI--AECPNCD----------SP----------LTLHKATGQLRCHYCGY------------- 470 (730)
T ss_pred EEccCCccceeecccCCCc--ccCCCCC----------cc----------eEEecCCCeeEeCCCCC-------------
Confidence 4444444455667777744 7777776 21 22333335577777776
Q ss_pred hccCCCceecc-CCcc
Q 020075 232 KNCGESRWKCS-CGTS 246 (331)
Q Consensus 232 ~H~~ekp~~C~-C~k~ 246 (331)
....|..|+ ||..
T Consensus 471 --~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 471 --QEPIPQSCPECGSE 484 (730)
T ss_pred --CCCCCCCCCCCCCC
Confidence 244678888 8854
No 65
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=84.41 E-value=0.57 Score=40.69 Aligned_cols=44 Identities=23% Similarity=0.598 Sum_probs=28.8
Q ss_pred ccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHH
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVA 258 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~ 258 (331)
|.|..||. .. -+..+.+|+- -++ .-|.|- |++.|.+ ..+..|..
T Consensus 4 FtCnvCgE-sv-KKp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGE-SV-KKPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhh-hc-cccchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 67777776 33 3455667776 455 557777 8888877 56666754
No 66
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=84.34 E-value=0.43 Score=41.02 Aligned_cols=30 Identities=27% Similarity=0.451 Sum_probs=23.2
Q ss_pred cccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCC
Q 020075 128 CDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGR 169 (331)
Q Consensus 128 C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~ 169 (331)
|-+|++.|....-|.+|++. |+|+|++|.+
T Consensus 13 cwycnrefddekiliqhqka------------khfkchichk 42 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA------------KHFKCHICHK 42 (341)
T ss_pred eeecccccchhhhhhhhhhh------------ccceeeeehh
Confidence 78889999888888888764 6666666655
No 67
>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=83.33 E-value=2 Score=32.75 Aligned_cols=24 Identities=25% Similarity=0.509 Sum_probs=22.1
Q ss_pred eec----c-CCcccCCHHHHHHHHHhhcC
Q 020075 239 WKC----S-CGTSFSRKDKLFGHVALFEG 262 (331)
Q Consensus 239 ~~C----~-C~k~F~~~~~L~~H~~~H~~ 262 (331)
|.| . |+..+.+...+.+|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 8 99999999999999998765
No 68
>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=83.10 E-value=0.87 Score=44.75 Aligned_cols=58 Identities=17% Similarity=0.305 Sum_probs=35.3
Q ss_pred CCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHh
Q 020075 152 FKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHY 231 (331)
Q Consensus 152 ~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~ 231 (331)
|.+.........|..||.. ..|+.|+ ..+..|.......|..||. ..
T Consensus 204 flnrrGya~~~~C~~Cg~~--~~C~~C~--------------------~~l~~h~~~~~l~Ch~Cg~-~~---------- 250 (505)
T TIGR00595 204 FLNRRGYSKNLLCRSCGYI--LCCPNCD--------------------VSLTYHKKEGKLRCHYCGY-QE---------- 250 (505)
T ss_pred EEeCCcCCCeeEhhhCcCc--cCCCCCC--------------------CceEEecCCCeEEcCCCcC-cC----------
Confidence 3444444455678888854 7788876 2233444445677888876 22
Q ss_pred hccCCCceecc-CCcc
Q 020075 232 KNCGESRWKCS-CGTS 246 (331)
Q Consensus 232 ~H~~ekp~~C~-C~k~ 246 (331)
.-|..|+ |+..
T Consensus 251 ----~~~~~Cp~C~s~ 262 (505)
T TIGR00595 251 ----PIPKTCPQCGSE 262 (505)
T ss_pred ----CCCCCCCCCCCC
Confidence 2467788 8763
No 69
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=83.05 E-value=0.78 Score=29.97 Aligned_cols=32 Identities=22% Similarity=0.375 Sum_probs=27.2
Q ss_pred hhcCCCccccccchhhccCHHHHHHHHHHhcC
Q 020075 119 ELLAEHIHFCDICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 119 ~h~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
...|+..+.|+-||..|.......+|...-++
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 45678899999999999999999999975443
No 70
>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=82.99 E-value=1.9 Score=32.79 Aligned_cols=30 Identities=27% Similarity=0.643 Sum_probs=22.9
Q ss_pred CccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCCH
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSRK 250 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~~ 250 (331)
...|+.||+ .|.. .+..|-.|+ ||..|.-.
T Consensus 9 KR~Cp~CG~-kFYD----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGA-KFYD----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcc-hhcc----------CCCCCccCCCCCCccCcc
Confidence 368999998 6642 344788999 99999765
No 71
>PRK14873 primosome assembly protein PriA; Provisional
Probab=81.39 E-value=1.2 Score=45.32 Aligned_cols=56 Identities=13% Similarity=0.337 Sum_probs=34.0
Q ss_pred CCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCCCccCChhHhHHHhh
Q 020075 153 KTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK 232 (331)
Q Consensus 153 ~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~ 232 (331)
.++.....-..|..||.. ..|+.|+ ..+..|...+...|..||. .
T Consensus 375 lnRrGyap~l~C~~Cg~~--~~C~~C~--------------------~~L~~h~~~~~l~Ch~CG~-~------------ 419 (665)
T PRK14873 375 VPRRGYVPSLACARCRTP--ARCRHCT--------------------GPLGLPSAGGTPRCRWCGR-A------------ 419 (665)
T ss_pred ecCCCCCCeeEhhhCcCe--eECCCCC--------------------CceeEecCCCeeECCCCcC-C------------
Confidence 344444444578888854 7888887 1223333345677888876 2
Q ss_pred ccCCCceecc-CCcc
Q 020075 233 NCGESRWKCS-CGTS 246 (331)
Q Consensus 233 H~~ekp~~C~-C~k~ 246 (331)
. .|+.|+ ||..
T Consensus 420 --~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 420 --A-PDWRCPRCGSD 431 (665)
T ss_pred --C-cCccCCCCcCC
Confidence 1 367888 8864
No 72
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.34 E-value=0.51 Score=38.38 Aligned_cols=12 Identities=33% Similarity=0.888 Sum_probs=7.0
Q ss_pred eecc-CCcccCCH
Q 020075 239 WKCS-CGTSFSRK 250 (331)
Q Consensus 239 ~~C~-C~k~F~~~ 250 (331)
|.|+ ||++|.+.
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5666 66666543
No 73
>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=79.81 E-value=5.3 Score=35.01 Aligned_cols=70 Identities=20% Similarity=0.332 Sum_probs=41.9
Q ss_pred cccCCCCccCCCCCCCccCChhHhHHHhh---ccCCCceecc-CCcccCCHHHH-------HHHHHh----hcCCCCccC
Q 020075 204 RSHCPKMYSCDKCHKKSFSVVSDLRSHYK---NCGESRWKCS-CGTSFSRKDKL-------FGHVAL----FEGHMPEVE 268 (331)
Q Consensus 204 ~h~~~k~~~C~~C~k~~f~~~~~L~~H~~---H~~ekp~~C~-C~k~F~~~~~L-------~~H~~~----H~~e~p~~c 268 (331)
..||++.|+|.+|.. |.-...--.|+. -...-.|+|. |.+. .+.+-| -.|+|. ....+++.|
T Consensus 136 w~hGGrif~CsfC~~--flCEDDQFEHQAsCQvLe~E~~KC~SCNrl-Gq~sCLRCK~cfCddHvrrKg~ky~k~k~~PC 212 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDN--FLCEDDQFEHQASCQVLESETFKCQSCNRL-GQYSCLRCKICFCDDHVRRKGFKYEKGKPIPC 212 (314)
T ss_pred ccCCCeEEEeecCCC--eeeccchhhhhhhhhhhhcccccccccccc-cchhhhheeeeehhhhhhhcccccccCCCCCC
Confidence 345668899999986 554444456665 2344457777 7642 222322 245543 345688999
Q ss_pred ccccccCC
Q 020075 269 VDEKMKHH 276 (331)
Q Consensus 269 ~~~~~~~~ 276 (331)
+.|.-...
T Consensus 213 PKCg~et~ 220 (314)
T PF06524_consen 213 PKCGYETQ 220 (314)
T ss_pred CCCCCccc
Confidence 98876443
No 74
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=79.61 E-value=0.53 Score=40.48 Aligned_cols=47 Identities=26% Similarity=0.455 Sum_probs=35.7
Q ss_pred CCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCCHHHHHHH-HHhh
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSRKDKLFGH-VALF 260 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~~~~L~~H-~~~H 260 (331)
|+| |.+|++ .|.....|.+|++ .|-|+|. |-|...+-..|.-| |.+|
T Consensus 10 kpw-cwycnr-efddekiliqhqk---akhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 10 KPW-CWYCNR-EFDDEKILIQHQK---AKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred Cce-eeeccc-ccchhhhhhhhhh---hccceeeeehhhhccCCCceeehhhhh
Confidence 443 889999 9999999988877 2338999 99888777777776 3344
No 75
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.17 E-value=0.76 Score=39.71 Aligned_cols=41 Identities=24% Similarity=0.583 Sum_probs=27.5
Q ss_pred CCccCCCCCCCccCChhHhHHHhh--c--c-------CCCc-----eecc-CCcccCCH
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK--N--C-------GESR-----WKCS-CGTSFSRK 250 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~--H--~-------~ekp-----~~C~-C~k~F~~~ 250 (331)
|.+.|++|++ .|.++.-+....+ . + +..| ..|+ ||.+|...
T Consensus 4 k~~~CPvC~~-~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGK-EFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCC-eeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 5688899998 8887755554443 1 1 2333 5799 99988654
No 76
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.77 E-value=1.2 Score=29.59 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=7.8
Q ss_pred CCccCCCCCC
Q 020075 209 KMYSCDKCHK 218 (331)
Q Consensus 209 k~~~C~~C~k 218 (331)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 6788888875
No 77
>PHA00626 hypothetical protein
Probab=76.99 E-value=2.3 Score=27.88 Aligned_cols=14 Identities=29% Similarity=0.429 Sum_probs=10.2
Q ss_pred CCccCCCCCCCccCC
Q 020075 209 KMYSCDKCHKKSFSV 223 (331)
Q Consensus 209 k~~~C~~C~k~~f~~ 223 (331)
..|+|+.||. .|+.
T Consensus 22 nrYkCkdCGY-~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGY-NDSK 35 (59)
T ss_pred cceEcCCCCC-eech
Confidence 4588888888 6653
No 78
>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=76.17 E-value=1.5 Score=25.53 Aligned_cols=10 Identities=20% Similarity=0.637 Sum_probs=5.1
Q ss_pred CCccCCCCCC
Q 020075 209 KMYSCDKCHK 218 (331)
Q Consensus 209 k~~~C~~C~k 218 (331)
.++.|++||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4455555553
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.54 E-value=1.6 Score=29.02 Aligned_cols=10 Identities=40% Similarity=0.892 Sum_probs=8.4
Q ss_pred CCccCCCCCC
Q 020075 209 KMYSCDKCHK 218 (331)
Q Consensus 209 k~~~C~~C~k 218 (331)
.+|.|+.||.
T Consensus 49 ~~Y~Cp~CGF 58 (61)
T COG2888 49 NPYRCPKCGF 58 (61)
T ss_pred CceECCCcCc
Confidence 7899999985
No 80
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.28 E-value=7 Score=29.88 Aligned_cols=47 Identities=21% Similarity=0.409 Sum_probs=30.9
Q ss_pred cCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhhc
Q 020075 212 SCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 212 ~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
.|--|.+ .|....... .. -.....|.|. |...|=-.-..-.|...|.
T Consensus 57 ~C~~C~~-~f~~~~~~~--~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQG-PFPKPPVSP--FDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCC-CCCCccccc--ccccccccceeCCCCCCccccccchhhhhhccC
Confidence 4888888 787543111 01 2334568999 9998887777777877664
No 81
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=72.28 E-value=2.3 Score=34.31 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=16.5
Q ss_pred cCCCccccccchhhccCHHHHH
Q 020075 121 LAEHIHFCDICGKGFKRDANLR 142 (331)
Q Consensus 121 ~~~~~~~C~~C~k~F~~~~~L~ 142 (331)
.....|.|+.|+..|.....+.
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~ 116 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQ 116 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHH
Confidence 3456799999999999655443
No 82
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.16 E-value=2.6 Score=38.44 Aligned_cols=125 Identities=19% Similarity=0.300 Sum_probs=71.6
Q ss_pred CCCCCCCCCchhhhhhhhhhcCC----------CccccccchhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCc
Q 020075 101 GSEHDIESDCEIVEIDAVELLAE----------HIHFCDICGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRK 170 (331)
Q Consensus 101 ~~~~~~~~~~~~l~~h~~~h~~~----------~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~ 170 (331)
..|...+.....|+.|.+...+. +.|.|.+ ..-++..|+.|...-..+ .-|+
T Consensus 157 skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~---~lF~~~~Lr~H~~~G~~e--------~GFK------- 218 (493)
T COG5236 157 SKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEI---RLFRSSTLRDHKNGGLEE--------EGFK------- 218 (493)
T ss_pred hhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccce---eeeecccccccccCCccc--------cCcC-------
Confidence 34555555566677887754432 3344433 233445666665432211 1111
Q ss_pred cceeCCCCCCccccccCCccccccHHHHhcccccccCCCCccCCCCCC------CccCChhHhHHHhhccCCCceecc--
Q 020075 171 TRFSCPYDGCNRNKKHKKFRALKSVICVKNHFKRSHCPKMYSCDKCHK------KSFSVVSDLRSHYKNCGESRWKCS-- 242 (331)
Q Consensus 171 ~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~~h~~~k~~~C~~C~k------~~f~~~~~L~~H~~H~~ekp~~C~-- 242 (331)
..-.|.+|. +.|-...-|.+|+|..|. .|-+|++ .-|.....|..|.+|. -|.|.
T Consensus 219 GHP~C~FC~----------~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~---hy~ct~q 281 (493)
T COG5236 219 GHPLCIFCK----------IYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNA---HYCCTFQ 281 (493)
T ss_pred CCchhhhcc----------ceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcC---ceEEEEE
Confidence 224577777 777777777888776552 3444443 0366777788877732 26663
Q ss_pred -CC----cccCCHHHHHHHHHhh
Q 020075 243 -CG----TSFSRKDKLFGHVALF 260 (331)
Q Consensus 243 -C~----k~F~~~~~L~~H~~~H 260 (331)
|- ..|.....|..|+-.-
T Consensus 282 tc~~~k~~vf~~~~el~~h~~~~ 304 (493)
T COG5236 282 TCRVGKCYVFPYHTELLEHLTRF 304 (493)
T ss_pred EEecCcEEEeccHHHHHHHHHHH
Confidence 43 3688889999998653
No 83
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=72.00 E-value=3.1 Score=26.74 Aligned_cols=19 Identities=42% Similarity=0.884 Sum_probs=10.7
Q ss_pred ecc-CCcccCCH-----HHHHHHHH
Q 020075 240 KCS-CGTSFSRK-----DKLFGHVA 258 (331)
Q Consensus 240 ~C~-C~k~F~~~-----~~L~~H~~ 258 (331)
.|. |++.+... ++|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455 55555443 46666666
No 84
>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=71.92 E-value=2.4 Score=32.28 Aligned_cols=14 Identities=29% Similarity=0.700 Sum_probs=6.6
Q ss_pred CCccccccchhhcc
Q 020075 123 EHIHFCDICGKGFK 136 (331)
Q Consensus 123 ~~~~~C~~C~k~F~ 136 (331)
..|..|+.||..|.
T Consensus 24 k~PivCP~CG~~~~ 37 (108)
T PF09538_consen 24 KDPIVCPKCGTEFP 37 (108)
T ss_pred CCCccCCCCCCccC
Confidence 34444555554444
No 85
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=71.90 E-value=0.69 Score=39.98 Aligned_cols=17 Identities=35% Similarity=0.810 Sum_probs=11.0
Q ss_pred CCccccccchhhccCHH
Q 020075 123 EHIHFCDICGKGFKRDA 139 (331)
Q Consensus 123 ~~~~~C~~C~k~F~~~~ 139 (331)
++.+.|++|++.|.++.
T Consensus 3 ~k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKK 19 (214)
T ss_pred CCceECCCCCCeeeeeE
Confidence 34566777777777654
No 86
>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=71.70 E-value=3.9 Score=25.40 Aligned_cols=21 Identities=29% Similarity=0.626 Sum_probs=10.2
Q ss_pred Cceecc-CCcccCCH----HHHHHHH
Q 020075 237 SRWKCS-CGTSFSRK----DKLFGHV 257 (331)
Q Consensus 237 kp~~C~-C~k~F~~~----~~L~~H~ 257 (331)
.-..|. |++.+... +.|.+|+
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 445666 66666553 5666666
No 87
>PRK05580 primosome assembly protein PriA; Validated
Probab=71.41 E-value=3.1 Score=42.52 Aligned_cols=22 Identities=18% Similarity=0.080 Sum_probs=14.0
Q ss_pred hhccCCcccccCCCccceeCCCCC
Q 020075 156 QALAKPEKGSVSGRKTRFSCPYDG 179 (331)
Q Consensus 156 ~~~~~~~~c~~C~~~~~~~C~~c~ 179 (331)
.....-..|..||.. ..|+.|+
T Consensus 376 rGy~~~~~C~~Cg~~--~~C~~C~ 397 (679)
T PRK05580 376 RGYAPFLLCRDCGWV--AECPHCD 397 (679)
T ss_pred CCCCCceEhhhCcCc--cCCCCCC
Confidence 333445667778744 7777776
No 88
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=68.60 E-value=2.8 Score=30.25 Aligned_cols=31 Identities=26% Similarity=0.740 Sum_probs=19.7
Q ss_pred CCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSR 249 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~ 249 (331)
.+|.|+.|++ . .+.| .+-.-+.|. ||..|.-
T Consensus 34 ~~~~Cp~C~~-~--------~VkR-~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGR-T--------TVKR-IATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCC-c--------ceee-eccCeEEcCCCCCeecc
Confidence 4688888887 2 1222 223457888 8888864
No 89
>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=68.36 E-value=4 Score=24.39 Aligned_cols=33 Identities=27% Similarity=0.712 Sum_probs=16.6
Q ss_pred ccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccC
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFS 248 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~ 248 (331)
+.|+.|+. .|.-.... .........|+ |+..|.
T Consensus 3 ~~CP~C~~-~~~v~~~~----~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKT-SFRVVDSQ----LGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCC-EEEeCHHH----cCCCCCEEECCCCCCEEE
Confidence 45777776 55443321 01122246677 776663
No 90
>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=67.37 E-value=2.7 Score=33.26 Aligned_cols=26 Identities=35% Similarity=0.643 Sum_probs=13.9
Q ss_pred ceecc-CCcccCCHHHHHHHHHhhcCCCCc
Q 020075 238 RWKCS-CGTSFSRKDKLFGHVALFEGHMPE 266 (331)
Q Consensus 238 p~~C~-C~k~F~~~~~L~~H~~~H~~e~p~ 266 (331)
-..|- |||.|.. |.+|++.|+|-.|-
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp~ 98 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTPE 98 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-HH
T ss_pred eeEEccCCcccch---HHHHHHHccCCCHH
Confidence 35677 8887764 57888888776653
No 91
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=67.32 E-value=4.2 Score=33.48 Aligned_cols=11 Identities=18% Similarity=0.298 Sum_probs=6.6
Q ss_pred CCCCccCCCCC
Q 020075 207 CPKMYSCDKCH 217 (331)
Q Consensus 207 ~~k~~~C~~C~ 217 (331)
++-|-+|++||
T Consensus 146 ge~P~~CPiCg 156 (166)
T COG1592 146 GEAPEVCPICG 156 (166)
T ss_pred CCCCCcCCCCC
Confidence 34566666666
No 92
>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=66.94 E-value=4.4 Score=33.16 Aligned_cols=24 Identities=8% Similarity=0.066 Sum_probs=19.1
Q ss_pred hhcCCCccccccchhhccCHHHHH
Q 020075 119 ELLAEHIHFCDICGKGFKRDANLR 142 (331)
Q Consensus 119 ~h~~~~~~~C~~C~k~F~~~~~L~ 142 (331)
...+..-|.|+.|+..|+...++.
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~~ 126 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAME 126 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHHH
Confidence 344566799999999999888874
No 93
>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=66.91 E-value=5.1 Score=23.53 Aligned_cols=10 Identities=20% Similarity=0.434 Sum_probs=5.8
Q ss_pred CCccCCCCCC
Q 020075 209 KMYSCDKCHK 218 (331)
Q Consensus 209 k~~~C~~C~k 218 (331)
.|..|++|+.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3556666654
No 94
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=65.77 E-value=7.4 Score=35.60 Aligned_cols=26 Identities=12% Similarity=0.199 Sum_probs=21.1
Q ss_pred CCccCCCCCCCccCChhHhHHHhh--ccC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK--NCG 235 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~--H~~ 235 (331)
.-|.|++|++ .-.+...|..|.. |..
T Consensus 78 qSftCPyC~~-~Gfte~~f~~Hv~s~Hpd 105 (381)
T KOG1280|consen 78 QSFTCPYCGI-MGFTERQFGTHVLSQHPE 105 (381)
T ss_pred ccccCCcccc-cccchhHHHHHhhhcCcc
Confidence 4699999999 7778888999987 643
No 95
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=65.75 E-value=2.2 Score=35.95 Aligned_cols=82 Identities=20% Similarity=0.409 Sum_probs=49.7
Q ss_pred cccccc--chhhccCHHHHHHHHHHhcCCCCCchhccCCcccccCCCccceeCCCCCCccccccCCccccccHHHHhccc
Q 020075 125 IHFCDI--CGKGFKRDANLRMHMRAHGDEFKTPQALAKPEKGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHF 202 (331)
Q Consensus 125 ~~~C~~--C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~ 202 (331)
.|.|++ |-+.|........|..+-++ -.|.+|. +.|.....|..|+
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~----------------------~sCs~C~----------r~~Pt~hLLd~HI 126 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG----------------------NSCSFCK----------RAFPTGHLLDAHI 126 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc----------------------chhHHHH----------HhCCchhhhhHHH
Confidence 355665 66666666656666544333 2455555 5555555555553
Q ss_pred cc----------ccCCCCccC--CCCCCCccCChhHhHHHhh--ccCCCce
Q 020075 203 KR----------SHCPKMYSC--DKCHKKSFSVVSDLRSHYK--NCGESRW 239 (331)
Q Consensus 203 ~~----------h~~~k~~~C--~~C~k~~f~~~~~L~~H~~--H~~ekp~ 239 (331)
.. ..|.-.|.| ..|+. .|.+...-..|+. |.=.-.|
T Consensus 127 ~E~HDs~Fqa~veRG~dMy~ClvEgCt~-KFkT~r~RkdH~I~~Hk~Pa~f 176 (253)
T KOG4173|consen 127 LEWHDSLFQALVERGQDMYQCLVEGCTE-KFKTSRDRKDHMIRMHKYPADF 176 (253)
T ss_pred HHHHHHHHHHHHHcCccHHHHHHHhhhh-hhhhhhhhhhHHHHhccCCcce
Confidence 32 223456899 56999 8999999999987 6433333
No 96
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.10 E-value=5.2 Score=32.96 Aligned_cols=23 Identities=35% Similarity=0.856 Sum_probs=19.0
Q ss_pred CCccCCCCCCCccCChhHhHHHhhccCCCceecc-CC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CG 244 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~ 244 (331)
+.|.|++||. . |-|+-|-+|+ ||
T Consensus 133 ~~~vC~vCGy-~------------~~ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGY-T------------HEGEAPEVCPICG 156 (166)
T ss_pred CEEEcCCCCC-c------------ccCCCCCcCCCCC
Confidence 3699999998 3 5668899999 99
No 97
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=60.65 E-value=6.2 Score=33.02 Aligned_cols=21 Identities=24% Similarity=0.485 Sum_probs=16.9
Q ss_pred cCCCccccccchhhccCHHHH
Q 020075 121 LAEHIHFCDICGKGFKRDANL 141 (331)
Q Consensus 121 ~~~~~~~C~~C~k~F~~~~~L 141 (331)
....-|.|+.|+..|+...++
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAM 133 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHh
Confidence 345679999999999988765
No 98
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=60.27 E-value=4.1 Score=29.81 Aligned_cols=31 Identities=26% Similarity=0.633 Sum_probs=20.8
Q ss_pred CCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSR 249 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~ 249 (331)
..|.|+.|++ .- ++-.+.-.+.|. |++.|+-
T Consensus 35 a~y~CpfCgk-~~---------vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGK-HA---------VKRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCC-Cc---------eeeeeeEEEEcCCCCCEEeC
Confidence 5689999987 21 122333568899 9998864
No 99
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=60.05 E-value=8.7 Score=22.85 Aligned_cols=32 Identities=22% Similarity=0.662 Sum_probs=17.6
Q ss_pred ccCCCCCCCccCChhHhHHHhhccCCCceecc-CCccc
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSF 247 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F 247 (331)
..|+.|+. .|.-.... .-.+.+..+|. |+..|
T Consensus 3 i~Cp~C~~-~y~i~d~~----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQA-KYEIDDEK----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCC-EEeCCHHH----CCCCCcEEECCCCCCEe
Confidence 45777776 66544321 12233456777 77666
No 100
>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=59.42 E-value=6.8 Score=21.46 Aligned_cols=20 Identities=15% Similarity=0.439 Sum_probs=16.1
Q ss_pred cccccchhhccCHHHHHHHHH
Q 020075 126 HFCDICGKGFKRDANLRMHMR 146 (331)
Q Consensus 126 ~~C~~C~k~F~~~~~L~~H~~ 146 (331)
..|++|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 6677888875
No 101
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=58.71 E-value=8.7 Score=22.97 Aligned_cols=32 Identities=31% Similarity=0.818 Sum_probs=16.9
Q ss_pred cCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccC
Q 020075 212 SCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFS 248 (331)
Q Consensus 212 ~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~ 248 (331)
.|+.|+. .|.-.... .-.+.+..+|. |+..|.
T Consensus 4 ~CP~C~~-~f~v~~~~----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQT-RFRVPDDK----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCc-eEEcCHHH----cccCCcEEECCCCCcEee
Confidence 5666766 66543321 12333456777 776663
No 102
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=58.28 E-value=12 Score=38.46 Aligned_cols=40 Identities=15% Similarity=0.533 Sum_probs=30.7
Q ss_pred CCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhhcCCCCccCcccccc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKMK 274 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~~ 274 (331)
-.+.|+.|+- . +. |...+-..|. || |....|..|+.|...
T Consensus 443 ~v~~Cp~Cd~-~----------lt~H~~~~~L~CH~Cg---------------~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 443 YIAECPNCDS-P----------LTLHKATGQLRCHYCG---------------YQEPIPQSCPECGSE 484 (730)
T ss_pred CcccCCCCCc-c----------eEEecCCCeeEeCCCC---------------CCCCCCCCCCCCCCC
Confidence 6688999987 4 24 6666778999 99 345679999999865
No 103
>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=57.92 E-value=6.8 Score=30.52 Aligned_cols=31 Identities=13% Similarity=0.056 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCchhhhhhhhhhcCCCccccccchhhccCHH
Q 020075 98 PEIGSEHDIESDCEIVEIDAVELLAEHIHFCDICGKGFKRDA 139 (331)
Q Consensus 98 ~~~~~~~~~~~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~~~ 139 (331)
..|..|+..|+. .+..|-.|+.||..|....
T Consensus 10 r~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccCCCcCccccc-----------cCCCCccCCCcCCccCcch
Confidence 346677777776 4456777777777766543
No 104
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=57.10 E-value=7 Score=31.53 Aligned_cols=35 Identities=17% Similarity=0.710 Sum_probs=16.7
Q ss_pred CCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCccc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSF 247 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F 247 (331)
.-|.|+.|+. .|.....+.. ... ...|.|+ ||...
T Consensus 98 ~~Y~Cp~C~~-~y~~~ea~~~--~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQS-KYTFLEANQL--LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCC-EeeHHHHHHh--cCC-CCcEECCCCCCEE
Confidence 3466666666 5654332211 011 2236666 66544
No 105
>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=56.45 E-value=4.9 Score=29.42 Aligned_cols=31 Identities=32% Similarity=0.794 Sum_probs=20.5
Q ss_pred CCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSR 249 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~ 249 (331)
..|.|+.|++ .- ++-.+.-.+.|. |++.|.-
T Consensus 34 a~y~CpfCgk-~~---------vkR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGK-KT---------VKRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCC-Cc---------eEEEeeEEEEcCCCCCEEeC
Confidence 5689999987 21 122233468899 9998864
No 106
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=55.20 E-value=3.9 Score=28.65 Aligned_cols=16 Identities=25% Similarity=0.654 Sum_probs=8.6
Q ss_pred cCCCceecc---CCcccCC
Q 020075 234 CGESRWKCS---CGTSFSR 249 (331)
Q Consensus 234 ~~ekp~~C~---C~k~F~~ 249 (331)
+.++-+.|. ||.+|..
T Consensus 23 ~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 23 TKERYHQCQNVNCSATFIT 41 (72)
T ss_pred hheeeeecCCCCCCCEEEE
Confidence 334445663 6666654
No 107
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=54.89 E-value=4.6 Score=32.02 Aligned_cols=31 Identities=32% Similarity=0.524 Sum_probs=26.0
Q ss_pred ccccCCCccceeCCCCCCccccccCCccccccHHHHhcccc
Q 020075 163 KGSVSGRKTRFSCPYDGCNRNKKHKKFRALKSVICVKNHFK 203 (331)
Q Consensus 163 ~c~~C~~~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~ 203 (331)
-|.+||-...|.|.-|| ..|.+..|++.|.-
T Consensus 120 fCaVCG~~S~ysC~~CG----------~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 120 FCAVCGYDSKYSCVNCG----------TKYCSVRCLKTHNE 150 (156)
T ss_pred hhhhcCCCchhHHHhcC----------Cceeechhhhhccc
Confidence 48999988889999999 88888888888753
No 108
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=54.51 E-value=4.9 Score=40.38 Aligned_cols=27 Identities=33% Similarity=0.559 Sum_probs=24.6
Q ss_pred CccccccchhhccCHHHHHHHHHHhcC
Q 020075 124 HIHFCDICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 124 ~~~~C~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
..|.|..|+|.|-....+..||++|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 459999999999999999999999964
No 109
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=54.48 E-value=11 Score=21.48 Aligned_cols=17 Identities=35% Similarity=0.722 Sum_probs=10.4
Q ss_pred ccccCCCccceeCCCCC
Q 020075 163 KGSVSGRKTRFSCPYDG 179 (331)
Q Consensus 163 ~c~~C~~~~~~~C~~c~ 179 (331)
.|..|+....|.|+.|+
T Consensus 4 ~C~vC~~~~kY~Cp~C~ 20 (30)
T PF04438_consen 4 LCSVCGNPAKYRCPRCG 20 (30)
T ss_dssp EETSSSSEESEE-TTT-
T ss_pred CCccCcCCCEEECCCcC
Confidence 46667776667777776
No 110
>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=54.31 E-value=7.9 Score=30.62 Aligned_cols=26 Identities=38% Similarity=0.692 Sum_probs=17.7
Q ss_pred CCccccccchhhccCHHHHHHHHHHhcCC
Q 020075 123 EHIHFCDICGKGFKRDANLRMHMRAHGDE 151 (331)
Q Consensus 123 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~ 151 (331)
+....|-+||+.|.. |++|++.|+|-
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred cCeeEEccCCcccch---HHHHHHHccCC
Confidence 456789999999996 59999999775
No 111
>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=53.60 E-value=10 Score=29.55 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=24.6
Q ss_pred CccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCCHHHHH
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSRKDKLF 254 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~~~~L~ 254 (331)
...|+.||+ .|.. .+..|-.|+ ||..|.-...++
T Consensus 9 Kr~Cp~cg~-kFYD----------Lnk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGS-KFYD----------LNRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCc-cccc----------cCCCCccCCCcCCccCcchhhc
Confidence 468999998 6642 344789999 999987664443
No 112
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=53.54 E-value=3.7 Score=41.16 Aligned_cols=24 Identities=21% Similarity=0.499 Sum_probs=22.4
Q ss_pred ceecc-CCcccCCHHHHHHHHHhhc
Q 020075 238 RWKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 238 p~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
-|-|. |+|.|-...+++.||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 49999 9999999999999999995
No 113
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=53.50 E-value=20 Score=33.34 Aligned_cols=24 Identities=29% Similarity=0.450 Sum_probs=19.6
Q ss_pred CCceecc-CCcccCCHHHHHHHHHh
Q 020075 236 ESRWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 236 ekp~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
+-++.|. |.|.|....+...|+..
T Consensus 66 ~~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 66 ESVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred ccceehHHhhccccChhhHHHHHHH
Confidence 3468899 99999998888888864
No 114
>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=52.24 E-value=6.1 Score=28.89 Aligned_cols=29 Identities=38% Similarity=0.981 Sum_probs=19.2
Q ss_pred CCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFS 248 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~ 248 (331)
..|.|+.||+ .-. .+ -+| -+.|. |++.|.
T Consensus 34 ~ky~Cp~Cgk-~~v--------kR~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGK-TSV--------KRVATG--IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSS-SEE--------EEEETT--EEEETTTTEEEE
T ss_pred CCCcCCCCCC-cee--------EEeeeE--EeecCCCCCEEe
Confidence 5699999998 221 12 344 48999 999885
No 115
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=51.09 E-value=9.9 Score=35.95 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=18.1
Q ss_pred hcCCCccccccchhhccCHHHHHH
Q 020075 120 LLAEHIHFCDICGKGFKRDANLRM 143 (331)
Q Consensus 120 h~~~~~~~C~~C~k~F~~~~~L~~ 143 (331)
-+...-|.|+.|.+.|+....++.
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L 146 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQL 146 (436)
T ss_pred ccccccccCCccccchhhhHHHHh
Confidence 345567999999999997766543
No 116
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=50.18 E-value=6.5 Score=28.76 Aligned_cols=31 Identities=29% Similarity=0.829 Sum_probs=20.4
Q ss_pred CCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSR 249 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~ 249 (331)
..|.|+.|++..+ +-.+.-.+.|. |++.|.-
T Consensus 35 a~y~CpfCgk~~v----------kR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKV----------KRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCce----------EEEEEEEEEcCCCCCEEeC
Confidence 5689999987211 12233468899 9998864
No 117
>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=49.79 E-value=9.7 Score=30.80 Aligned_cols=21 Identities=29% Similarity=0.607 Sum_probs=10.9
Q ss_pred ccCCCCCCCcc------CChhHhHHHhh
Q 020075 211 YSCDKCHKKSF------SVVSDLRSHYK 232 (331)
Q Consensus 211 ~~C~~C~k~~f------~~~~~L~~H~~ 232 (331)
.+|..|+| .| +..+++..|+.
T Consensus 15 v~C~~c~k-WFCNg~~~~s~SHIv~HLv 41 (152)
T PF09416_consen 15 VKCNTCNK-WFCNGRGNTSGSHIVNHLV 41 (152)
T ss_dssp EEETTTTE-EEES--TTSSS-HHHHHHH
T ss_pred eEcCCCCc-EeecCCCCCcccHHHHHHH
Confidence 45555555 44 35566677754
No 118
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=49.74 E-value=10 Score=29.79 Aligned_cols=28 Identities=25% Similarity=0.336 Sum_probs=19.0
Q ss_pred eecc-CCcccCCHHHHHHHHHhhcCCCCccCc
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALFEGHMPEVEV 269 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~ 269 (331)
..|- +||.|. +|++|+.+|.|-.|-...
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTPd~YR 105 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTPDEYR 105 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCHHHHH
Confidence 4677 777775 677888887766654443
No 119
>PF15269 zf-C2H2_7: Zinc-finger
Probab=49.41 E-value=13 Score=23.13 Aligned_cols=21 Identities=33% Similarity=0.771 Sum_probs=16.2
Q ss_pred eecc-CCcccCCHHHHHHHHHh
Q 020075 239 WKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
|+|- |..+..-++.|-.||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6777 88888888888888764
No 120
>PRK04023 DNA polymerase II large subunit; Validated
Probab=48.37 E-value=15 Score=38.65 Aligned_cols=9 Identities=33% Similarity=0.948 Sum_probs=6.0
Q ss_pred CccCCCCCC
Q 020075 210 MYSCDKCHK 218 (331)
Q Consensus 210 ~~~C~~C~k 218 (331)
++.|+.||.
T Consensus 663 ~y~CPKCG~ 671 (1121)
T PRK04023 663 EDECEKCGR 671 (1121)
T ss_pred CCcCCCCCC
Confidence 466777775
No 121
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.98 E-value=29 Score=26.55 Aligned_cols=64 Identities=14% Similarity=0.143 Sum_probs=37.6
Q ss_pred CCccCCCCCCCccCChhHhHHHhhc-cCCCce------------ecc-CCcccCCHHHHHHHHHhhcCCCCccCcccccc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYKN-CGESRW------------KCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKMK 274 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~H-~~ekp~------------~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~~ 274 (331)
-|-.|++||- ......+|.+-..| ---++| .|- |.+.|........= .-.....|.|+.|...
T Consensus 14 LP~~CpiCgL-tLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 14 LPVECPICGL-TLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--ELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCcCCcCCC-EEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccccc--ccccccceeCCCCCCc
Confidence 6788999998 88877777764433 112222 399 99999765321100 0122345777777654
Q ss_pred C
Q 020075 275 H 275 (331)
Q Consensus 275 ~ 275 (331)
+
T Consensus 91 F 91 (112)
T TIGR00622 91 F 91 (112)
T ss_pred c
Confidence 4
No 122
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=44.89 E-value=22 Score=32.64 Aligned_cols=57 Identities=23% Similarity=0.405 Sum_probs=39.5
Q ss_pred CCccCCCCCCCccCChhHhHHHhh--cc---CC------------------Cceecc-CCcccCCHHHHHHHHHh--hcC
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK--NC---GE------------------SRWKCS-CGTSFSRKDKLFGHVAL--FEG 262 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~--H~---~e------------------kp~~C~-C~k~F~~~~~L~~H~~~--H~~ 262 (331)
....|-.|..-.-..++.+..|+- |. |- ..+.|- |.|.|..+..|+.|||. |..
T Consensus 143 fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 143 FSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred eeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCcc
Confidence 345788887623345677777776 42 11 138899 99999999999999986 544
Q ss_pred CCC
Q 020075 263 HMP 265 (331)
Q Consensus 263 e~p 265 (331)
-.|
T Consensus 223 inP 225 (423)
T KOG2482|consen 223 INP 225 (423)
T ss_pred cCC
Confidence 434
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=44.60 E-value=20 Score=38.76 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=4.8
Q ss_pred CccCCCCCC
Q 020075 210 MYSCDKCHK 218 (331)
Q Consensus 210 ~~~C~~C~k 218 (331)
+|.|+.||.
T Consensus 692 vy~CPsCGa 700 (1337)
T PRK14714 692 VYVCPDCGA 700 (1337)
T ss_pred ceeCccCCC
Confidence 355555554
No 124
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=44.51 E-value=7.4 Score=40.04 Aligned_cols=18 Identities=22% Similarity=0.425 Sum_probs=0.0
Q ss_pred cccccCCCc-cceeCCCCC
Q 020075 162 EKGSVSGRK-TRFSCPYDG 179 (331)
Q Consensus 162 ~~c~~C~~~-~~~~C~~c~ 179 (331)
.+|..||.. ....|+.||
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG 674 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECG 674 (900)
T ss_dssp -------------------
T ss_pred ccCcccCCcchhhcCcccC
Confidence 557777653 335577777
No 125
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.28 E-value=12 Score=31.06 Aligned_cols=27 Identities=22% Similarity=0.545 Sum_probs=15.8
Q ss_pred cccHHHHhcccccccCCCCccCCCCCCCccCCh
Q 020075 192 LKSVICVKNHFKRSHCPKMYSCDKCHKKSFSVV 224 (331)
Q Consensus 192 f~~~~~l~~H~~~h~~~k~~~C~~C~k~~f~~~ 224 (331)
..|..|++.-.+ +..+|+.|+| ....+
T Consensus 154 vFC~~Cik~alk-----~~~~CP~C~k-kIt~k 180 (187)
T KOG0320|consen 154 VFCSQCIKDALK-----NTNKCPTCRK-KITHK 180 (187)
T ss_pred hHHHHHHHHHHH-----hCCCCCCccc-ccchh
Confidence 346666665544 3457888887 44433
No 126
>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=44.21 E-value=23 Score=34.94 Aligned_cols=39 Identities=21% Similarity=0.473 Sum_probs=28.2
Q ss_pred CCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhhcCCCCccCccccc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKM 273 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~ 273 (331)
....|+.|+- . +. |.......|. ||... .-|..|+.|..
T Consensus 221 ~~~~C~~C~~-~----------l~~h~~~~~l~Ch~Cg~~~---------------~~~~~Cp~C~s 261 (505)
T TIGR00595 221 YILCCPNCDV-S----------LTYHKKEGKLRCHYCGYQE---------------PIPKTCPQCGS 261 (505)
T ss_pred CccCCCCCCC-c----------eEEecCCCeEEcCCCcCcC---------------CCCCCCCCCCC
Confidence 6788999986 2 34 6667788999 99544 35777888865
No 127
>PF14353 CpXC: CpXC protein
Probab=43.97 E-value=23 Score=27.57 Aligned_cols=18 Identities=33% Similarity=0.813 Sum_probs=10.1
Q ss_pred eecc-CCcccCCHHHHHHH
Q 020075 239 WKCS-CGTSFSRKDKLFGH 256 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H 256 (331)
|.|+ ||+.|.-...+.-|
T Consensus 39 ~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 39 FTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred EECCCCCCceecCCCEEEE
Confidence 6666 66666544444433
No 128
>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=42.71 E-value=18 Score=27.40 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=23.1
Q ss_pred cccc----ccchhhccCHHHHHHHHHHhcC
Q 020075 125 IHFC----DICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 125 ~~~C----~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
=|.| ..|+..+.+...|+.|.+.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4889 9999999999999999998764
No 129
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=42.16 E-value=28 Score=32.46 Aligned_cols=50 Identities=20% Similarity=0.306 Sum_probs=41.9
Q ss_pred CCccCCCCCCCccCChhHhHHHhh-ccCC-----------------------Cceecc-CC---cccCCHHHHHHHHHh
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK-NCGE-----------------------SRWKCS-CG---TSFSRKDKLFGHVAL 259 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~-H~~e-----------------------kp~~C~-C~---k~F~~~~~L~~H~~~ 259 (331)
-|-.|-.|++ .+.+-..-..||. ++|- .-|.|- |. +.|.+..+.+.||..
T Consensus 165 ~Pt~CLfC~~-~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDK-KSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCC-CcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 3577999999 8999988999998 6542 238898 99 999999999999975
No 130
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=41.35 E-value=7.2 Score=23.82 Aligned_cols=9 Identities=33% Similarity=1.353 Sum_probs=5.3
Q ss_pred eecc-CCccc
Q 020075 239 WKCS-CGTSF 247 (331)
Q Consensus 239 ~~C~-C~k~F 247 (331)
|.|. |+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5666 66554
No 131
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.79 E-value=18 Score=22.59 Aligned_cols=8 Identities=25% Similarity=0.642 Sum_probs=3.9
Q ss_pred ccCCCCCC
Q 020075 211 YSCDKCHK 218 (331)
Q Consensus 211 ~~C~~C~k 218 (331)
+.|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 44555544
No 132
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.62 E-value=28 Score=35.59 Aligned_cols=39 Identities=13% Similarity=0.201 Sum_probs=27.6
Q ss_pred CCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCHHHHHHHHHhhcCCCCccCcccccc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKMK 274 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~~ 274 (331)
....|+.|+- . +. |.......|. ||.. ..|..|+.|...
T Consensus 391 ~~~~C~~C~~-~----------L~~h~~~~~l~Ch~CG~~----------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 391 TPARCRHCTG-P----------LGLPSAGGTPRCRWCGRA----------------APDWRCPRCGSD 431 (665)
T ss_pred CeeECCCCCC-c----------eeEecCCCeeECCCCcCC----------------CcCccCCCCcCC
Confidence 7788999986 2 23 6666778999 9932 147788888754
No 133
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=38.60 E-value=15 Score=28.96 Aligned_cols=24 Identities=33% Similarity=0.459 Sum_probs=20.8
Q ss_pred ccccccchhhccCHHHHHHHHHHhcCC
Q 020075 125 IHFCDICGKGFKRDANLRMHMRAHGDE 151 (331)
Q Consensus 125 ~~~C~~C~k~F~~~~~L~~H~~~H~~~ 151 (331)
-..|-.+||.|. .|++|+.+|.|-
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCC
Confidence 567999999998 699999999874
No 134
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.19 E-value=20 Score=27.08 Aligned_cols=27 Identities=19% Similarity=0.101 Sum_probs=19.7
Q ss_pred CCCCCCCCCCchhhhhhhhhhcCCCccccccchhhccC
Q 020075 100 IGSEHDIESDCEIVEIDAVELLAEHIHFCDICGKGFKR 137 (331)
Q Consensus 100 ~~~~~~~~~~~~~l~~h~~~h~~~~~~~C~~C~k~F~~ 137 (331)
++.|++.|+. ....|..|++||++|..
T Consensus 12 dPetg~KFYD-----------LNrdPiVsPytG~s~P~ 38 (129)
T COG4530 12 DPETGKKFYD-----------LNRDPIVSPYTGKSYPR 38 (129)
T ss_pred Cccccchhhc-----------cCCCccccCcccccchH
Confidence 4566666766 44678899999999843
No 135
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=36.95 E-value=13 Score=34.14 Aligned_cols=24 Identities=13% Similarity=0.012 Sum_probs=16.6
Q ss_pred cCCCceeccCCcccCCHHHHHHHH
Q 020075 234 CGESRWKCSCGTSFSRKDKLFGHV 257 (331)
Q Consensus 234 ~~ekp~~C~C~k~F~~~~~L~~H~ 257 (331)
+..+||+|.|++.+.++..|+.|-
T Consensus 209 t~~~p~k~~~~~~~~T~~~l~~HS 232 (442)
T KOG4124|consen 209 TTGTPKKMPESLVMDTSSPLSDHS 232 (442)
T ss_pred cccCCccCcccccccccchhhhcc
Confidence 445677777777777777776663
No 136
>PF12907 zf-met2: Zinc-binding
Probab=36.21 E-value=15 Score=22.50 Aligned_cols=25 Identities=20% Similarity=0.507 Sum_probs=11.6
Q ss_pred ccCCCCCCCcc---CChhHhHHHhh--ccCC
Q 020075 211 YSCDKCHKKSF---SVVSDLRSHYK--NCGE 236 (331)
Q Consensus 211 ~~C~~C~k~~f---~~~~~L~~H~~--H~~e 236 (331)
+.|.+|.. .| .....|..|.. |...
T Consensus 2 i~C~iC~q-tF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQ-TFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhH-HHHhcCCHHHHHHHHHccCCCC
Confidence 34555553 23 23344555554 5443
No 137
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=35.60 E-value=19 Score=28.57 Aligned_cols=32 Identities=19% Similarity=0.314 Sum_probs=23.3
Q ss_pred cccccCCCcc-ceeCCCCCCccccccCCccccccHHHHhcccc
Q 020075 162 EKGSVSGRKT-RFSCPYDGCNRNKKHKKFRALKSVICVKNHFK 203 (331)
Q Consensus 162 ~~c~~C~~~~-~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H~~ 203 (331)
..|.+|.+.. .|+|+.|. -+|....|++.|..
T Consensus 6 ~tC~ic~e~~~KYKCpkC~----------vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 6 TTCVICLESEIKYKCPKCS----------VPYCSLPCFKIHKS 38 (157)
T ss_pred eeehhhhcchhhccCCCCC----------CccccchhhhhccC
Confidence 3466676543 58888888 78888888888854
No 138
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=35.29 E-value=13 Score=29.87 Aligned_cols=18 Identities=22% Similarity=0.586 Sum_probs=12.2
Q ss_pred CccCCCCCCCccCChhHhH
Q 020075 210 MYSCDKCHKKSFSVVSDLR 228 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~ 228 (331)
.=.|..|++ .|++...+.
T Consensus 28 RReC~~C~~-RFTTyErve 45 (147)
T TIGR00244 28 RRECLECHE-RFTTFERAE 45 (147)
T ss_pred cccCCccCC-ccceeeecc
Confidence 356888888 787765443
No 139
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=35.08 E-value=29 Score=28.98 Aligned_cols=8 Identities=25% Similarity=1.186 Sum_probs=3.9
Q ss_pred ccCCCCCC
Q 020075 211 YSCDKCHK 218 (331)
Q Consensus 211 ~~C~~C~k 218 (331)
|.|+.||.
T Consensus 137 F~Cp~Cg~ 144 (178)
T PRK06266 137 FRCPQCGE 144 (178)
T ss_pred CcCCCCCC
Confidence 45555543
No 140
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=34.52 E-value=19 Score=25.07 Aligned_cols=58 Identities=24% Similarity=0.540 Sum_probs=30.3
Q ss_pred ceeCCCCCCccccccCCccccccHHH---HhcccccccCCCCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCccc
Q 020075 172 RFSCPYDGCNRNKKHKKFRALKSVIC---VKNHFKRSHCPKMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSF 247 (331)
Q Consensus 172 ~~~C~~c~~~~~~~h~~~k~f~~~~~---l~~H~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F 247 (331)
.++++-|+ +.|.|..| +..|.......+...|..|+. .+..... ..+ ..|.|+ |+-.|
T Consensus 10 ~~~~~cC~----------~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~-~~~~~~~------~c~-~~~~C~~C~~~~ 71 (71)
T PF05495_consen 10 AIRFPCCG----------KYYPCRFCHDELEDHPFDRWPVKRVICGKCRT-EQPIDEY------SCG-ADYFCPICGLYF 71 (71)
T ss_dssp EEEETTTT----------EEESSHHHHHHCSSS---TTT--EEEETTT---EEES-SB------TT---SEEETTTTEEE
T ss_pred EEECCccc----------CeecHHHHHHHhccCccccccccCeECCCCCC-ccChhhh------hcC-CCccCcCcCCCC
Confidence 36677777 88887776 334443333345678888887 5544332 112 568888 87554
No 141
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.84 E-value=26 Score=26.16 Aligned_cols=15 Identities=33% Similarity=0.762 Sum_probs=12.0
Q ss_pred ccccccchhhccCHH
Q 020075 125 IHFCDICGKGFKRDA 139 (331)
Q Consensus 125 ~~~C~~C~k~F~~~~ 139 (331)
|+.|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 688888998888753
No 142
>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=33.80 E-value=16 Score=31.50 Aligned_cols=22 Identities=27% Similarity=0.436 Sum_probs=12.3
Q ss_pred CccCCCCCCCccCChhHhHHHhh
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYK 232 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~ 232 (331)
.|.|..|+| .|.-....+.|+.
T Consensus 77 K~~C~lc~K-lFkg~eFV~KHI~ 98 (214)
T PF04959_consen 77 KWRCPLCGK-LFKGPEFVRKHIF 98 (214)
T ss_dssp EEEE-SSS--EESSHHHHHHHHH
T ss_pred EECCCCCCc-ccCChHHHHHHHh
Confidence 466666666 6666666666665
No 143
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.55 E-value=31 Score=21.57 Aligned_cols=10 Identities=20% Similarity=0.707 Sum_probs=5.3
Q ss_pred CCccCCCCCC
Q 020075 209 KMYSCDKCHK 218 (331)
Q Consensus 209 k~~~C~~C~k 218 (331)
.+..|+.||.
T Consensus 18 ~~irC~~CG~ 27 (44)
T smart00659 18 DVVRCRECGY 27 (44)
T ss_pred CceECCCCCc
Confidence 3455555554
No 144
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=32.90 E-value=28 Score=26.88 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=22.3
Q ss_pred cCCCceecc-CCcccCCHHHHHHHHHh
Q 020075 234 CGESRWKCS-CGTSFSRKDKLFGHVAL 259 (331)
Q Consensus 234 ~~ekp~~C~-C~k~F~~~~~L~~H~~~ 259 (331)
.|.-.|.|- |.+-|.....|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 344569999 99999999999999876
No 145
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=32.28 E-value=25 Score=22.56 Aligned_cols=8 Identities=25% Similarity=0.750 Sum_probs=3.8
Q ss_pred ccCCCCCC
Q 020075 211 YSCDKCHK 218 (331)
Q Consensus 211 ~~C~~C~k 218 (331)
..|+.||.
T Consensus 25 irCp~Cg~ 32 (49)
T COG1996 25 IRCPYCGS 32 (49)
T ss_pred eeCCCCCc
Confidence 44555543
No 146
>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=32.12 E-value=24 Score=30.44 Aligned_cols=7 Identities=43% Similarity=1.231 Sum_probs=3.5
Q ss_pred eeCCCCC
Q 020075 173 FSCPYDG 179 (331)
Q Consensus 173 ~~C~~c~ 179 (331)
|.|++|+
T Consensus 78 ~~C~lc~ 84 (214)
T PF04959_consen 78 WRCPLCG 84 (214)
T ss_dssp EEE-SSS
T ss_pred ECCCCCC
Confidence 5555555
No 147
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=31.51 E-value=87 Score=25.54 Aligned_cols=56 Identities=16% Similarity=0.219 Sum_probs=36.2
Q ss_pred CccCCCCCCCccCChhHhHHHhh-ccCCCceecc---CCcccCCHHHHHHHHHh-hcCCCCccC
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS---CGTSFSRKDKLFGHVAL-FEGHMPEVE 268 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~---C~k~F~~~~~L~~H~~~-H~~e~p~~c 268 (331)
...|+.|.- ...-... ..--| +.+.|+=.|. |... .+...|++|.|. |...+|-.-
T Consensus 80 ~L~CPLCRG-~V~GWtv-ve~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~~v 140 (162)
T PF07800_consen 80 ELACPLCRG-EVKGWTV-VEPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPSEV 140 (162)
T ss_pred cccCccccC-ceeceEE-chHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCccC
Confidence 478999965 3332222 23355 7788887885 6532 456789999987 777776543
No 148
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=31.44 E-value=20 Score=31.41 Aligned_cols=25 Identities=24% Similarity=0.699 Sum_probs=18.2
Q ss_pred ccccccchhhccCHHHHHHHHHHhcC
Q 020075 125 IHFCDICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 125 ~~~C~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
.|.|..||....- ..|..|+..-++
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn 27 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN 27 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC
Confidence 4789999988664 456778876555
No 149
>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=31.34 E-value=4.4 Score=24.60 Aligned_cols=9 Identities=33% Similarity=1.302 Sum_probs=5.4
Q ss_pred eecc-CCccc
Q 020075 239 WKCS-CGTSF 247 (331)
Q Consensus 239 ~~C~-C~k~F 247 (331)
|.|. |+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5666 66554
No 150
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=30.92 E-value=32 Score=26.23 Aligned_cols=36 Identities=22% Similarity=0.537 Sum_probs=18.3
Q ss_pred ccCCCCCCCccCChhHhHHHhhccCC---Cceecc-CCcccCC
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYKNCGE---SRWKCS-CGTSFSR 249 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~H~~e---kp~~C~-C~k~F~~ 249 (331)
.+|+.||. .=.....|+ +|-..| --|.|. |++.|+.
T Consensus 75 ~kCpkCgh-e~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGH-EEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCC-chhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 56777776 333222222 221222 237887 8877753
No 151
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=30.77 E-value=31 Score=32.90 Aligned_cols=90 Identities=23% Similarity=0.275 Sum_probs=49.0
Q ss_pred hhhccCHHHHHH---HH-HHhcCCCCCchhccCCcccccCCC------ccceeCCCCCCccccccCCccccccHHHHhcc
Q 020075 132 GKGFKRDANLRM---HM-RAHGDEFKTPQALAKPEKGSVSGR------KTRFSCPYDGCNRNKKHKKFRALKSVICVKNH 201 (331)
Q Consensus 132 ~k~F~~~~~L~~---H~-~~H~~~~~~~~~~~~~~~c~~C~~------~~~~~C~~c~~~~~~~h~~~k~f~~~~~l~~H 201 (331)
.+.|.++.+|++ |+ +.|.= ...-...|.-|.+|.- ...|+|.+|. +..|
T Consensus 26 ~~~f~RkGAlrqKnvhevk~HkF---~aRFFKqPTfCsHCkDFiwGfgKQGfQCqvC~------------------fvvH 84 (683)
T KOG0696|consen 26 MKRFLRKGALRQKNVHEVKSHKF---IARFFKQPTFCSHCKDFIWGFGKQGFQCQVCC------------------FVVH 84 (683)
T ss_pred HHHHHhhhhhhhcchhhhcccee---eehhccCCchhhhhhhheeccccCceeeeEEe------------------ehhh
Confidence 566777777765 22 12210 0111124556777742 2246666654 4566
Q ss_pred cccccCCCCccCCCCCCCccCChhHhHHHhh--ccCCCceecc-CC
Q 020075 202 FKRSHCPKMYSCDKCHKKSFSVVSDLRSHYK--NCGESRWKCS-CG 244 (331)
Q Consensus 202 ~~~h~~~k~~~C~~C~k~~f~~~~~L~~H~~--H~~ekp~~C~-C~ 244 (331)
.|+|.- -.|.|+-=++ .+.+-..-..|.- |+-..|--|. ||
T Consensus 85 krChef-VtF~CPGadk-g~dtDdpr~kHkf~~~tYssPTFCDhCG 128 (683)
T KOG0696|consen 85 KRCHEF-VTFSCPGADK-GPDTDDPRSKHKFKIHTYSSPTFCDHCG 128 (683)
T ss_pred hhhcce-EEEECCCCCC-CCCCCCcccccceeeeecCCCchhhhHH
Confidence 666643 3477777666 6666555556653 6666666677 76
No 152
>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=30.44 E-value=24 Score=21.69 Aligned_cols=28 Identities=21% Similarity=0.452 Sum_probs=19.3
Q ss_pred eecc-CCcccCCHHHHHHHHHhhcCCCCccCccccc
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKM 273 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~ 273 (331)
|.|. ||..|..... ... ..+-.|+.|..
T Consensus 6 y~C~~Cg~~fe~~~~------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEE------cCC-CCCCcCCCCCC
Confidence 8999 9999964332 223 56677888875
No 153
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.27 E-value=28 Score=27.88 Aligned_cols=32 Identities=25% Similarity=0.721 Sum_probs=20.4
Q ss_pred CccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccC
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFS 248 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~ 248 (331)
.|.|..|+. .+. .|.+|.....|.|. |+-.|.
T Consensus 112 ~y~C~~C~~-~~~------~~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQ-RYL------RVRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCC-CCc------eEccccCcceEEcCCCCCEEE
Confidence 588888887 553 33345444668888 886653
No 154
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=30.09 E-value=18 Score=29.10 Aligned_cols=17 Identities=18% Similarity=0.468 Sum_probs=11.5
Q ss_pred CccCCCCCCCccCChhHh
Q 020075 210 MYSCDKCHKKSFSVVSDL 227 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L 227 (331)
.=.|..|++ .|++-...
T Consensus 28 RReC~~C~~-RFTTfE~~ 44 (156)
T COG1327 28 RRECLECGE-RFTTFERA 44 (156)
T ss_pred hhccccccc-ccchhhee
Confidence 356888888 78775443
No 155
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.87 E-value=33 Score=25.82 Aligned_cols=9 Identities=22% Similarity=0.475 Sum_probs=4.5
Q ss_pred CccCCCCCC
Q 020075 210 MYSCDKCHK 218 (331)
Q Consensus 210 ~~~C~~C~k 218 (331)
|-.|++||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 344555554
No 156
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=29.50 E-value=20 Score=32.41 Aligned_cols=35 Identities=17% Similarity=0.304 Sum_probs=13.1
Q ss_pred CccCCCCCCCccCChhHhHHH-hh-ccCCCceecc-CCccc
Q 020075 210 MYSCDKCHKKSFSVVSDLRSH-YK-NCGESRWKCS-CGTSF 247 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H-~~-H~~ekp~~C~-C~k~F 247 (331)
...|+.||. .-..+ |... .. -.+.+-+.|. |+..+
T Consensus 211 R~~Cp~Cg~-~~~~~--l~~~~~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 211 RIKCPYCGN-TDHEK--LEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp TTS-TTT----SS-E--EE--------SEEEEEETTTTEEE
T ss_pred CCCCcCCCC-CCCcc--eeeEecCCCCcEEEEECCcccchH
Confidence 356888876 32221 1111 11 2344557787 77544
No 157
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=29.11 E-value=91 Score=28.59 Aligned_cols=52 Identities=21% Similarity=0.464 Sum_probs=34.2
Q ss_pred CCCccCCCCCCCccCChhHhHHHhhcc------C----------------------CCceecc-CCcccCCHHHHHHHHH
Q 020075 208 PKMYSCDKCHKKSFSVVSDLRSHYKNC------G----------------------ESRWKCS-CGTSFSRKDKLFGHVA 258 (331)
Q Consensus 208 ~k~~~C~~C~k~~f~~~~~L~~H~~H~------~----------------------ekp~~C~-C~k~F~~~~~L~~H~~ 258 (331)
.-|-.|++|+- ......+|.+-.+|. . .-.|.|. |.-.|=.--..--|..
T Consensus 288 sLP~eCpiC~l-tLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 288 SLPIECPICSL-TLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred cCCccCCccce-eEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhh
Confidence 46788899988 777777776544331 1 1237777 8877776666666766
Q ss_pred hh
Q 020075 259 LF 260 (331)
Q Consensus 259 ~H 260 (331)
.|
T Consensus 367 Lh 368 (378)
T KOG2807|consen 367 LH 368 (378)
T ss_pred hh
Confidence 55
No 158
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.03 E-value=56 Score=33.50 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=8.6
Q ss_pred cCCCceecc-CCcc
Q 020075 234 CGESRWKCS-CGTS 246 (331)
Q Consensus 234 ~~ekp~~C~-C~k~ 246 (331)
+...|..|+ ||..
T Consensus 417 ~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 417 QEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCCCcCC
Confidence 344567888 8764
No 159
>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=28.93 E-value=27 Score=20.91 Aligned_cols=29 Identities=17% Similarity=0.398 Sum_probs=18.8
Q ss_pred ceecc-CCcccCCHHHHHHHHHhhcCCCCccCccccc
Q 020075 238 RWKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKM 273 (331)
Q Consensus 238 p~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~ 273 (331)
-|.|. ||+.|...... .....-.|+.|..
T Consensus 5 ~y~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI-------SDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEec-------CCCCCCCCCCCCC
Confidence 38899 99988643322 1145667888876
No 160
>PRK04023 DNA polymerase II large subunit; Validated
Probab=28.93 E-value=37 Score=35.92 Aligned_cols=20 Identities=25% Similarity=0.497 Sum_probs=14.0
Q ss_pred CCcccccCCCc-cceeCCCCC
Q 020075 160 KPEKGSVSGRK-TRFSCPYDG 179 (331)
Q Consensus 160 ~~~~c~~C~~~-~~~~C~~c~ 179 (331)
....|..||.. ..+.|+.||
T Consensus 625 g~RfCpsCG~~t~~frCP~CG 645 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCG 645 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCC
Confidence 45678888865 446788887
No 161
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.62 E-value=40 Score=31.66 Aligned_cols=17 Identities=18% Similarity=0.528 Sum_probs=8.4
Q ss_pred ccCCCCCCCccCChhHhH
Q 020075 211 YSCDKCHKKSFSVVSDLR 228 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~ 228 (331)
+.|+.||. .|.....+.
T Consensus 16 ~qC~qCG~-~~t~~~sqa 32 (465)
T COG4640 16 VQCTQCGH-KFTSRQSQA 32 (465)
T ss_pred ccccccCC-cCCchhhhh
Confidence 33555555 555444433
No 162
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=28.61 E-value=26 Score=22.51 Aligned_cols=36 Identities=19% Similarity=0.327 Sum_probs=22.8
Q ss_pred CCceecc-CCcccCCHHHHHHHHHhhcC--CCCccCcccc
Q 020075 236 ESRWKCS-CGTSFSRKDKLFGHVALFEG--HMPEVEVDEK 272 (331)
Q Consensus 236 ekp~~C~-C~k~F~~~~~L~~H~~~H~~--e~p~~c~~~~ 272 (331)
++.+.|. ||+.|.-...=+....- .| ..|-.|..|-
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~e-Kgf~n~p~RC~~CR 40 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAE-KGFDNEPKRCPSCR 40 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHh-cCCcCCCccCHHHH
Confidence 5789999 99999876665544433 22 2355566554
No 163
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=28.47 E-value=36 Score=25.75 Aligned_cols=14 Identities=29% Similarity=0.586 Sum_probs=11.4
Q ss_pred cccCCCccceeCCC
Q 020075 164 GSVSGRKTRFSCPY 177 (331)
Q Consensus 164 c~~C~~~~~~~C~~ 177 (331)
|..||+..|-.|++
T Consensus 4 CdLCg~~~Pt~~Pv 17 (119)
T PF10621_consen 4 CDLCGRAIPTVCPV 17 (119)
T ss_pred cchhcCcCCceeEE
Confidence 78888888887776
No 164
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=28.32 E-value=28 Score=23.72 Aligned_cols=9 Identities=44% Similarity=1.025 Sum_probs=2.6
Q ss_pred cCCCCCCCcc
Q 020075 212 SCDKCHKKSF 221 (331)
Q Consensus 212 ~C~~C~k~~f 221 (331)
.|..|++ .|
T Consensus 11 ~C~~C~~-~F 19 (69)
T PF01363_consen 11 NCMICGK-KF 19 (69)
T ss_dssp B-TTT---B-
T ss_pred cCcCcCC-cC
Confidence 4555555 55
No 165
>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=28.27 E-value=56 Score=26.66 Aligned_cols=15 Identities=13% Similarity=0.479 Sum_probs=7.4
Q ss_pred eecc-CCcccCCHHHH
Q 020075 239 WKCS-CGTSFSRKDKL 253 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L 253 (331)
|.|+ |+..|+.-.++
T Consensus 110 Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 110 FICPNMCVRFTFNEAM 125 (158)
T ss_pred EECCCCCcEeeHHHHH
Confidence 4555 55555444444
No 166
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=28.13 E-value=17 Score=33.45 Aligned_cols=24 Identities=25% Similarity=0.596 Sum_probs=20.1
Q ss_pred CCcccccc--chhhccCHHHHHHHHH
Q 020075 123 EHIHFCDI--CGKGFKRDANLRMHMR 146 (331)
Q Consensus 123 ~~~~~C~~--C~k~F~~~~~L~~H~~ 146 (331)
.++|+|.+ |.+.+.....|+.|..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~ 372 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKL 372 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccc
Confidence 57899976 9999998888888764
No 167
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=28.06 E-value=30 Score=20.94 Aligned_cols=11 Identities=45% Similarity=1.232 Sum_probs=8.2
Q ss_pred ceecc-CCcccC
Q 020075 238 RWKCS-CGTSFS 248 (331)
Q Consensus 238 p~~C~-C~k~F~ 248 (331)
||.|. |++.|=
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 67788 887774
No 168
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=27.86 E-value=88 Score=31.08 Aligned_cols=31 Identities=29% Similarity=0.561 Sum_probs=25.9
Q ss_pred hcCCCccccccchhhccCHHHHHHHHHHhcC
Q 020075 120 LLAEHIHFCDICGKGFKRDANLRMHMRAHGD 150 (331)
Q Consensus 120 h~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~ 150 (331)
.....|.+|..||.+|........||..|..
T Consensus 413 Ly~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 413 LYKDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred hccCCcchhcccccccccchhhhhHhhhhhh
Confidence 3456789999999999999988888887754
No 169
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=27.65 E-value=51 Score=20.16 Aligned_cols=25 Identities=20% Similarity=0.519 Sum_probs=19.0
Q ss_pred ccccccchhhccC--HHHHHHHHHHhc
Q 020075 125 IHFCDICGKGFKR--DANLRMHMRAHG 149 (331)
Q Consensus 125 ~~~C~~C~k~F~~--~~~L~~H~~~H~ 149 (331)
.-.|+.||..|.. ...-..|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 3589999999886 455777888774
No 170
>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=27.27 E-value=47 Score=17.85 Aligned_cols=10 Identities=20% Similarity=0.660 Sum_probs=5.6
Q ss_pred CCccCCCCCC
Q 020075 209 KMYSCDKCHK 218 (331)
Q Consensus 209 k~~~C~~C~k 218 (331)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3466666653
No 171
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.94 E-value=14 Score=29.92 Aligned_cols=19 Identities=21% Similarity=0.538 Sum_probs=13.4
Q ss_pred CCCceecc-CCcccCCHHHH
Q 020075 235 GESRWKCS-CGTSFSRKDKL 253 (331)
Q Consensus 235 ~ekp~~C~-C~k~F~~~~~L 253 (331)
-+.|.-|. ||+.|.+...-
T Consensus 65 ~~~PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTENA 84 (158)
T ss_pred CCCChhHHhCCCCCchHHHH
Confidence 34678888 88888766543
No 172
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (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 seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=26.93 E-value=36 Score=20.91 Aligned_cols=8 Identities=25% Similarity=0.775 Sum_probs=3.8
Q ss_pred ccCCCCCC
Q 020075 211 YSCDKCHK 218 (331)
Q Consensus 211 ~~C~~C~k 218 (331)
+.|..||.
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 55555554
No 173
>PHA02998 RNA polymerase subunit; Provisional
Probab=26.64 E-value=21 Score=29.58 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=7.2
Q ss_pred eecc-CCcccC
Q 020075 239 WKCS-CGTSFS 248 (331)
Q Consensus 239 ~~C~-C~k~F~ 248 (331)
|.|. ||+.|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 6777 777764
No 174
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=26.32 E-value=41 Score=27.17 Aligned_cols=32 Identities=31% Similarity=0.884 Sum_probs=17.6
Q ss_pred CCccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTS 246 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~ 246 (331)
.+|.|. |+. .|.+. ++|-. -.|+ .|.|. |+-.
T Consensus 116 ~~Y~C~-C~q-~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQ-HYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCC-ccchh---hhcccccccc-eEEeccCCce
Confidence 457777 777 55432 23333 3444 67777 7643
No 175
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.89 E-value=29 Score=27.56 Aligned_cols=13 Identities=23% Similarity=0.830 Sum_probs=8.1
Q ss_pred CccCCCCCCCccCC
Q 020075 210 MYSCDKCHKKSFSV 223 (331)
Q Consensus 210 ~~~C~~C~k~~f~~ 223 (331)
.+.|..||. .|..
T Consensus 70 ~~~C~~CG~-~~~~ 82 (135)
T PRK03824 70 VLKCRNCGN-EWSL 82 (135)
T ss_pred EEECCCCCC-EEec
Confidence 466777776 5544
No 176
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.64 E-value=47 Score=31.58 Aligned_cols=39 Identities=21% Similarity=0.591 Sum_probs=26.2
Q ss_pred ccCCCCccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcc
Q 020075 205 SHCPKMYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTS 246 (331)
Q Consensus 205 h~~~k~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~ 246 (331)
-+...-|.|+.|.+ .|+.-..++. .-...-.|.|. |+-.
T Consensus 123 ~t~~~~Y~Cp~C~k-kyt~Lea~~L--~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQK-KYTSLEALQL--LDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccccCCcccc-chhhhHHHHh--hcccCceEEEecCCCc
Confidence 33446799999999 8987655432 13334469999 9854
No 177
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=25.50 E-value=29 Score=21.42 Aligned_cols=12 Identities=50% Similarity=1.190 Sum_probs=6.8
Q ss_pred Cceecc-CCcccC
Q 020075 237 SRWKCS-CGTSFS 248 (331)
Q Consensus 237 kp~~C~-C~k~F~ 248 (331)
-||.|. |++.|=
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 477888 888774
No 178
>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=24.59 E-value=55 Score=20.41 Aligned_cols=8 Identities=38% Similarity=1.232 Sum_probs=3.7
Q ss_pred CccCCCCC
Q 020075 210 MYSCDKCH 217 (331)
Q Consensus 210 ~~~C~~C~ 217 (331)
.|.|..|+
T Consensus 37 ~~~C~~C~ 44 (46)
T PF12760_consen 37 RYRCKACR 44 (46)
T ss_pred eEECCCCC
Confidence 34444444
No 179
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=24.49 E-value=42 Score=21.70 Aligned_cols=6 Identities=50% Similarity=1.148 Sum_probs=2.7
Q ss_pred CCCCCC
Q 020075 213 CDKCHK 218 (331)
Q Consensus 213 C~~C~k 218 (331)
|..|++
T Consensus 5 C~~C~~ 10 (57)
T cd00065 5 CMGCGK 10 (57)
T ss_pred CcccCc
Confidence 444444
No 180
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=24.10 E-value=34 Score=25.50 Aligned_cols=8 Identities=25% Similarity=0.717 Sum_probs=4.9
Q ss_pred ccCCCCCC
Q 020075 211 YSCDKCHK 218 (331)
Q Consensus 211 ~~C~~C~k 218 (331)
..|..||.
T Consensus 47 ~~Cg~CGl 54 (104)
T COG4888 47 AVCGNCGL 54 (104)
T ss_pred EEcccCcc
Confidence 45666665
No 181
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=23.96 E-value=54 Score=32.09 Aligned_cols=38 Identities=24% Similarity=0.511 Sum_probs=20.6
Q ss_pred CCccCCCCCCCccCChhHhHHHh----h-ccCCCce--ecc-CCccc
Q 020075 209 KMYSCDKCHKKSFSVVSDLRSHY----K-NCGESRW--KCS-CGTSF 247 (331)
Q Consensus 209 k~~~C~~C~k~~f~~~~~L~~H~----~-H~~ekp~--~C~-C~k~F 247 (331)
.-|.|+.|.- .......-..-. . -++.++| .|. |..+.
T Consensus 51 ~Cf~CP~C~~-~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss 96 (483)
T PF05502_consen 51 NCFDCPICFS-PLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSS 96 (483)
T ss_pred ccccCCCCCC-cceeEecccccccccccccCCCCCEEEECCCceeec
Confidence 4599999987 444332111000 0 2345665 898 88754
No 182
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=23.25 E-value=61 Score=30.60 Aligned_cols=25 Identities=16% Similarity=0.473 Sum_probs=21.4
Q ss_pred eecc---CCcccCCHHHHHHHHHhhcCC
Q 020075 239 WKCS---CGTSFSRKDKLFGHVALFEGH 263 (331)
Q Consensus 239 ~~C~---C~k~F~~~~~L~~H~~~H~~e 263 (331)
|.|. |+..|...+.+..|.|.|.+.
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhhh
Confidence 6675 999999999999999998643
No 183
>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=22.65 E-value=40 Score=21.51 Aligned_cols=28 Identities=18% Similarity=0.398 Sum_probs=18.9
Q ss_pred eecc-CCcccCCHHHHHHHHHhhcCCCCccCccccc
Q 020075 239 WKCS-CGTSFSRKDKLFGHVALFEGHMPEVEVDEKM 273 (331)
Q Consensus 239 ~~C~-C~k~F~~~~~L~~H~~~H~~e~p~~c~~~~~ 273 (331)
|.|. ||..|.....+ +. ..+-.|+.|..
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 8999 99999743221 11 45567888886
No 184
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=22.52 E-value=83 Score=17.61 Aligned_cols=8 Identities=38% Similarity=1.294 Sum_probs=4.5
Q ss_pred ccCCCCCC
Q 020075 211 YSCDKCHK 218 (331)
Q Consensus 211 ~~C~~C~k 218 (331)
|.|.+|++
T Consensus 1 ~~C~~C~~ 8 (30)
T PF03107_consen 1 FWCDVCRR 8 (30)
T ss_pred CCCCCCCC
Confidence 35666655
No 185
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.17 E-value=32 Score=26.38 Aligned_cols=11 Identities=36% Similarity=1.105 Sum_probs=8.3
Q ss_pred ceecc-CCcccC
Q 020075 238 RWKCS-CGTSFS 248 (331)
Q Consensus 238 p~~C~-C~k~F~ 248 (331)
-|.|. ||..|+
T Consensus 100 Fy~C~~Cg~~wr 111 (113)
T COG1594 100 FYKCTRCGYRWR 111 (113)
T ss_pred EEEecccCCEee
Confidence 38888 887765
No 186
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=21.99 E-value=38 Score=26.67 Aligned_cols=14 Identities=29% Similarity=0.857 Sum_probs=11.9
Q ss_pred ceecc-CCcccCCHH
Q 020075 238 RWKCS-CGTSFSRKD 251 (331)
Q Consensus 238 p~~C~-C~k~F~~~~ 251 (331)
|++|. ||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 68999 999998655
No 187
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=21.49 E-value=54 Score=17.93 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=7.3
Q ss_pred ccCCCCCCCccC
Q 020075 211 YSCDKCHKKSFS 222 (331)
Q Consensus 211 ~~C~~C~k~~f~ 222 (331)
-.|+.||. .|.
T Consensus 15 ~~Cp~CG~-~F~ 25 (26)
T PF10571_consen 15 KFCPHCGY-DFE 25 (26)
T ss_pred CcCCCCCC-CCc
Confidence 45777777 664
No 189
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.46 E-value=71 Score=21.65 Aligned_cols=10 Identities=30% Similarity=1.042 Sum_probs=4.6
Q ss_pred ceecc-CCccc
Q 020075 238 RWKCS-CGTSF 247 (331)
Q Consensus 238 p~~C~-C~k~F 247 (331)
-|.|+ ||..+
T Consensus 46 ~~~C~~Cg~~~ 56 (69)
T PF07282_consen 46 VFTCPNCGFEM 56 (69)
T ss_pred eEEcCCCCCEE
Confidence 34455 54443
No 190
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=21.46 E-value=54 Score=32.51 Aligned_cols=27 Identities=22% Similarity=0.578 Sum_probs=22.8
Q ss_pred CCCceecc-CCcccCCHHHHHHHHHhhc
Q 020075 235 GESRWKCS-CGTSFSRKDKLFGHVALFE 261 (331)
Q Consensus 235 ~ekp~~C~-C~k~F~~~~~L~~H~~~H~ 261 (331)
..+|..|. ||+.|........||-.|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 45778999 9999999998888887763
No 191
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=21.31 E-value=31 Score=29.22 Aligned_cols=25 Identities=20% Similarity=0.589 Sum_probs=0.0
Q ss_pred CCCccCCCCCCCccCChhHhHHHhh
Q 020075 208 PKMYSCDKCHKKSFSVVSDLRSHYK 232 (331)
Q Consensus 208 ~k~~~C~~C~k~~f~~~~~L~~H~~ 232 (331)
.+.|.|.+||-.+|.-+..+.+|..
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcC
Confidence 4679999999756777778888765
No 192
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.25 E-value=64 Score=20.39 Aligned_cols=10 Identities=40% Similarity=1.012 Sum_probs=5.6
Q ss_pred ceecc-CCccc
Q 020075 238 RWKCS-CGTSF 247 (331)
Q Consensus 238 p~~C~-C~k~F 247 (331)
.|.|+ ||..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 46666 66443
No 193
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=20.59 E-value=39 Score=30.74 Aligned_cols=25 Identities=28% Similarity=0.260 Sum_probs=11.4
Q ss_pred CCcccCCHHHHHHHHHhhcCCCCccCc
Q 020075 243 CGTSFSRKDKLFGHVALFEGHMPEVEV 269 (331)
Q Consensus 243 C~k~F~~~~~L~~H~~~H~~e~p~~c~ 269 (331)
|.+.|.+... ..|.+.-.. +|+.|+
T Consensus 116 C~~~~~Y~~~-~~HE~~C~f-~~~~CP 140 (299)
T KOG3002|consen 116 CTKSFPYGEK-SKHEKVCEF-RPCSCP 140 (299)
T ss_pred Cceeeccccc-ccccccccc-CCcCCC
Confidence 5555555444 344444333 444443
No 194
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=20.39 E-value=48 Score=23.76 Aligned_cols=29 Identities=31% Similarity=0.736 Sum_probs=16.2
Q ss_pred CccCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccC
Q 020075 210 MYSCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFS 248 (331)
Q Consensus 210 ~~~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~ 248 (331)
.|.|..||| .- ++-...--+.|. |.|.|.
T Consensus 36 ky~CsfCGK-~~---------vKR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 36 KYTCSFCGK-KT---------VKRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhcch-hh---------hhhhceeEEecCCccceec
Confidence 477888887 21 111122347777 877764
No 195
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.18 E-value=60 Score=30.96 Aligned_cols=28 Identities=29% Similarity=0.829 Sum_probs=0.0
Q ss_pred cCCCCCCCccCChhHhHHHhhccCCCceecc-CCcccCCH
Q 020075 212 SCDKCHKKSFSVVSDLRSHYKNCGESRWKCS-CGTSFSRK 250 (331)
Q Consensus 212 ~C~~C~k~~f~~~~~L~~H~~H~~ekp~~C~-C~k~F~~~ 250 (331)
.|+.||. +|+-.|.+=|+|+ ||..+...
T Consensus 352 ~Cp~Cg~-----------~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGG-----------RMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCC-----------chhhcCCCCcccccccccCCcc
No 196
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.07 E-value=45 Score=22.39 Aligned_cols=40 Identities=15% Similarity=0.277 Sum_probs=22.1
Q ss_pred ccCCCCCCCccCChhHhHHHhh-ccCCCceecc-CCcccCCH
Q 020075 211 YSCDKCHKKSFSVVSDLRSHYK-NCGESRWKCS-CGTSFSRK 250 (331)
Q Consensus 211 ~~C~~C~k~~f~~~~~L~~H~~-H~~ekp~~C~-C~k~F~~~ 250 (331)
.+|-+|++..+.....+..-.. ..--+.|.|+ |.-....+
T Consensus 3 vkCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~k 44 (68)
T COG4896 3 VKCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAIK 44 (68)
T ss_pred ceEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhchh
Confidence 3566777634444444443333 4455668888 87655443
Done!