Query psy4576
Match_columns 400
No_of_seqs 530 out of 2511
Neff 10.4
Searched_HMMs 46136
Date Fri Aug 16 20:30:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4576hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074|consensus 100.0 2.1E-32 4.5E-37 255.8 4.0 242 155-397 603-937 (958)
2 KOG2462|consensus 100.0 7.7E-30 1.7E-34 211.3 5.3 138 242-389 128-265 (279)
3 KOG3608|consensus 99.9 3.3E-27 7.2E-32 200.4 13.4 192 162-396 184-381 (467)
4 KOG3608|consensus 99.9 6.1E-26 1.3E-30 192.7 14.3 198 187-396 135-351 (467)
5 KOG3623|consensus 99.9 3.1E-26 6.7E-31 211.2 8.7 116 92-208 210-331 (1007)
6 KOG2462|consensus 99.9 6.3E-25 1.4E-29 182.2 6.4 138 118-265 127-264 (279)
7 KOG1074|consensus 99.9 2.2E-25 4.8E-30 209.1 2.5 134 217-358 606-776 (958)
8 KOG3623|consensus 99.8 1.6E-21 3.5E-26 180.3 5.7 76 313-388 896-971 (1007)
9 KOG3576|consensus 99.8 2E-19 4.2E-24 141.7 1.8 117 280-396 114-241 (267)
10 KOG3576|consensus 99.6 6.1E-17 1.3E-21 127.8 3.0 124 185-310 116-239 (267)
11 PLN03086 PRLI-interacting fact 99.4 6.7E-13 1.5E-17 124.8 9.5 147 217-393 408-566 (567)
12 PHA00733 hypothetical protein 99.2 7.2E-12 1.6E-16 96.2 4.5 79 312-393 41-125 (128)
13 PLN03086 PRLI-interacting fact 99.1 1.5E-10 3.2E-15 109.2 8.9 147 121-308 407-565 (567)
14 PHA00733 hypothetical protein 99.0 2.3E-10 4.9E-15 88.0 4.5 82 281-364 38-124 (128)
15 PHA02768 hypothetical protein; 99.0 1.4E-10 3E-15 72.7 1.5 44 339-384 5-48 (55)
16 KOG3993|consensus 99.0 4.9E-11 1.1E-15 105.1 -0.9 177 217-393 268-484 (500)
17 KOG3993|consensus 99.0 5E-11 1.1E-15 105.0 -1.4 55 91-146 266-320 (500)
18 PHA02768 hypothetical protein; 98.8 1.4E-09 3.1E-14 68.1 2.1 44 311-356 5-48 (55)
19 PF13465 zf-H2C2_2: Zinc-finge 98.7 6.2E-09 1.3E-13 55.7 1.8 24 355-378 2-25 (26)
20 PF13465 zf-H2C2_2: Zinc-finge 98.7 1.6E-08 3.5E-13 54.1 2.5 26 326-351 1-26 (26)
21 PHA00616 hypothetical protein 98.5 3.3E-08 7.2E-13 58.9 1.3 33 339-371 1-33 (44)
22 PHA00732 hypothetical protein 98.4 1.3E-07 2.8E-12 65.6 2.7 45 312-362 2-47 (79)
23 PHA00616 hypothetical protein 98.3 2.4E-07 5.2E-12 55.2 1.8 31 367-397 1-31 (44)
24 PF05605 zf-Di19: Drought indu 98.3 1.5E-06 3.3E-11 56.0 4.4 52 92-146 2-54 (54)
25 PF05605 zf-Di19: Drought indu 98.3 2.2E-06 4.7E-11 55.3 5.0 50 158-210 3-53 (54)
26 PHA00732 hypothetical protein 98.1 2.1E-06 4.5E-11 59.6 3.0 45 339-389 1-46 (79)
27 PF00096 zf-C2H2: Zinc finger, 97.9 5.5E-06 1.2E-10 43.0 1.6 22 368-389 1-22 (23)
28 PF13894 zf-C2H2_4: C2H2-type 97.9 7.1E-06 1.5E-10 43.1 2.0 24 368-391 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 97.9 8.4E-06 1.8E-10 42.3 1.8 23 340-362 1-23 (23)
30 PF13912 zf-C2H2_6: C2H2-type 97.8 1.2E-05 2.6E-10 43.6 1.5 26 367-392 1-26 (27)
31 PF12756 zf-C2H2_2: C2H2 type 97.7 1.7E-05 3.6E-10 58.9 2.3 22 368-389 51-72 (100)
32 KOG1146|consensus 97.7 4.9E-06 1.1E-10 84.5 -1.1 226 159-389 438-791 (1406)
33 PF12756 zf-C2H2_2: C2H2 type 97.7 2.9E-05 6.2E-10 57.6 2.4 72 286-362 2-73 (100)
34 COG5236 Uncharacterized conser 97.6 0.00013 2.8E-09 63.5 5.2 131 121-271 151-308 (493)
35 PF13912 zf-C2H2_6: C2H2-type 97.5 6.1E-05 1.3E-09 40.7 2.1 26 339-364 1-26 (27)
36 PF13894 zf-C2H2_4: C2H2-type 97.5 7E-05 1.5E-09 39.1 1.9 23 122-144 1-23 (24)
37 KOG1146|consensus 97.5 3.7E-05 8.1E-10 78.3 0.9 84 94-177 438-538 (1406)
38 KOG2231|consensus 97.4 0.00042 9E-09 67.1 7.7 47 188-240 184-236 (669)
39 PF13909 zf-H2C2_5: C2H2-type 97.4 8E-05 1.7E-09 39.0 1.3 24 368-392 1-24 (24)
40 KOG2231|consensus 97.4 0.0004 8.7E-09 67.2 6.8 125 187-335 100-236 (669)
41 COG5189 SFP1 Putative transcri 97.4 5E-05 1.1E-09 65.3 0.4 23 155-177 396-418 (423)
42 COG5189 SFP1 Putative transcri 97.1 0.00012 2.6E-09 63.0 0.0 62 242-303 347-418 (423)
43 KOG2482|consensus 97.1 0.0017 3.6E-08 56.8 6.7 61 119-179 142-217 (423)
44 PF09237 GAGA: GAGA factor; I 97.0 0.00063 1.4E-08 41.6 2.6 32 364-395 21-52 (54)
45 COG5236 Uncharacterized conser 97.0 0.00066 1.4E-08 59.2 3.8 72 313-392 222-306 (493)
46 smart00355 ZnF_C2H2 zinc finge 96.9 0.00078 1.7E-08 35.7 2.0 23 368-390 1-23 (26)
47 PF13909 zf-H2C2_5: C2H2-type 96.8 0.0008 1.7E-08 35.1 1.7 23 122-145 1-23 (24)
48 PF09237 GAGA: GAGA factor; I 96.8 0.0013 2.7E-08 40.3 2.5 30 337-366 22-51 (54)
49 smart00355 ZnF_C2H2 zinc finge 96.8 0.0011 2.3E-08 35.1 2.0 23 340-362 1-23 (26)
50 KOG2482|consensus 96.7 0.0076 1.7E-07 52.8 7.6 50 284-333 280-356 (423)
51 PF12874 zf-met: Zinc-finger o 96.6 0.0011 2.3E-08 35.0 1.4 22 368-389 1-22 (25)
52 PF12874 zf-met: Zinc-finger o 96.6 0.0014 3E-08 34.5 1.7 23 340-362 1-23 (25)
53 PRK04860 hypothetical protein; 96.6 0.0011 2.4E-08 53.1 1.5 38 339-380 119-156 (160)
54 KOG2785|consensus 96.4 0.0084 1.8E-07 53.6 6.4 166 216-396 3-250 (390)
55 KOG2785|consensus 96.2 0.028 6.1E-07 50.4 8.3 49 313-361 168-242 (390)
56 KOG4173|consensus 95.8 0.0042 9.1E-08 50.2 1.2 49 93-145 80-130 (253)
57 PF12171 zf-C2H2_jaz: Zinc-fin 95.7 0.0042 9.2E-08 33.4 0.8 22 340-361 2-23 (27)
58 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0058 1.3E-07 32.8 1.0 21 122-142 2-22 (27)
59 PRK04860 hypothetical protein; 95.4 0.0071 1.5E-07 48.4 1.2 38 311-352 119-156 (160)
60 PF13913 zf-C2HC_2: zinc-finge 94.7 0.025 5.4E-07 29.6 1.8 19 369-388 4-22 (25)
61 KOG4173|consensus 94.7 0.013 2.8E-07 47.5 0.9 81 120-211 78-171 (253)
62 PF13913 zf-C2HC_2: zinc-finge 94.0 0.042 9.1E-07 28.8 1.6 19 341-360 4-22 (25)
63 COG4049 Uncharacterized protei 93.4 0.039 8.5E-07 34.4 1.1 30 88-117 13-42 (65)
64 COG5048 FOG: Zn-finger [Genera 93.3 0.022 4.8E-07 54.5 -0.3 149 217-376 290-455 (467)
65 smart00451 ZnF_U1 U1-like zinc 93.2 0.075 1.6E-06 30.4 2.0 22 339-360 3-24 (35)
66 smart00451 ZnF_U1 U1-like zinc 92.9 0.068 1.5E-06 30.6 1.6 23 367-389 3-25 (35)
67 COG5048 FOG: Zn-finger [Genera 92.9 0.026 5.7E-07 54.0 -0.3 155 91-251 288-453 (467)
68 cd00350 rubredoxin_like Rubred 92.8 0.063 1.4E-06 30.3 1.3 24 340-375 2-25 (33)
69 PF12013 DUF3505: Protein of u 91.5 0.28 6E-06 36.8 3.8 26 367-392 80-109 (109)
70 KOG2893|consensus 91.4 0.054 1.2E-06 45.1 -0.2 47 218-268 12-58 (341)
71 COG4049 Uncharacterized protei 91.3 0.092 2E-06 32.8 0.8 30 363-392 13-42 (65)
72 TIGR00622 ssl1 transcription f 90.7 0.59 1.3E-05 34.6 4.7 86 120-208 14-103 (112)
73 PF12013 DUF3505: Protein of u 89.7 0.66 1.4E-05 34.7 4.5 23 159-182 13-35 (109)
74 KOG2893|consensus 89.7 0.14 2.9E-06 42.8 0.7 42 188-235 12-53 (341)
75 TIGR00622 ssl1 transcription f 88.4 0.75 1.6E-05 34.1 3.8 77 282-362 14-104 (112)
76 cd00729 rubredoxin_SM Rubredox 87.0 0.37 8E-06 27.4 1.2 25 339-375 2-26 (34)
77 PF02892 zf-BED: BED zinc fing 86.0 0.46 9.9E-06 28.9 1.3 27 365-391 14-44 (45)
78 COG2879 Uncharacterized small 84.4 0.92 2E-05 29.3 2.1 20 378-397 23-42 (65)
79 PF09538 FYDLN_acid: Protein o 84.0 0.5 1.1E-05 35.1 1.0 12 339-350 26-37 (108)
80 PF09986 DUF2225: Uncharacteri 83.8 0.27 5.9E-06 41.8 -0.5 43 338-380 4-61 (214)
81 PF13719 zinc_ribbon_5: zinc-r 83.6 0.82 1.8E-05 26.5 1.6 32 94-131 4-35 (37)
82 PF13717 zinc_ribbon_4: zinc-r 82.8 0.97 2.1E-05 26.0 1.7 32 94-131 4-35 (36)
83 PF10571 UPF0547: Uncharacteri 82.3 0.79 1.7E-05 24.2 1.1 10 218-227 16-25 (26)
84 TIGR02098 MJ0042_CXXC MJ0042 f 81.5 0.66 1.4E-05 27.0 0.7 32 94-131 4-35 (38)
85 COG2888 Predicted Zn-ribbon RN 80.0 1.1 2.4E-05 28.7 1.3 32 92-129 27-58 (61)
86 PF12907 zf-met2: Zinc-binding 80.0 1.2 2.5E-05 26.3 1.3 28 368-395 2-32 (40)
87 TIGR00373 conserved hypothetic 78.9 2.2 4.8E-05 34.3 3.1 32 336-376 106-137 (158)
88 smart00659 RPOLCX RNA polymera 78.9 1.4 3E-05 26.8 1.4 26 340-376 3-28 (44)
89 COG1592 Rubrerythrin [Energy p 77.9 1.4 3.1E-05 35.4 1.7 23 339-374 134-156 (166)
90 smart00614 ZnF_BED BED zinc fi 77.5 1.9 4E-05 27.0 1.9 25 368-392 19-48 (50)
91 PF09538 FYDLN_acid: Protein o 76.5 1.2 2.7E-05 33.0 0.9 29 218-257 11-39 (108)
92 PF12907 zf-met2: Zinc-binding 75.5 1.8 4E-05 25.5 1.3 31 93-123 2-35 (40)
93 PF09986 DUF2225: Uncharacteri 74.9 0.72 1.6E-05 39.2 -0.7 12 187-198 49-60 (214)
94 PF06524 NOA36: NOA36 protein; 74.8 1.2 2.7E-05 37.9 0.6 25 338-362 208-232 (314)
95 smart00531 TFIIE Transcription 74.6 3.6 7.8E-05 32.7 3.2 37 337-377 97-133 (147)
96 PRK06266 transcription initiat 74.5 2.8 6.1E-05 34.5 2.6 30 338-376 116-145 (178)
97 COG1996 RPC10 DNA-directed RNA 74.5 1.8 3.9E-05 26.8 1.1 28 339-376 6-33 (49)
98 TIGR02300 FYDLN_acid conserved 73.4 1.7 3.8E-05 32.8 1.0 12 338-349 25-36 (129)
99 smart00734 ZnF_Rad18 Rad18-lik 73.0 3 6.4E-05 22.0 1.6 19 369-388 3-21 (26)
100 KOG2186|consensus 72.8 2.2 4.8E-05 36.3 1.6 46 312-360 4-49 (276)
101 PRK14890 putative Zn-ribbon RN 72.3 2.6 5.5E-05 27.2 1.5 10 92-101 25-34 (59)
102 smart00834 CxxC_CXXC_SSSS Puta 71.9 1.2 2.6E-05 26.3 -0.1 30 340-376 6-35 (41)
103 PHA00626 hypothetical protein 71.6 2.1 4.5E-05 27.0 0.9 15 119-133 21-35 (59)
104 PF04959 ARS2: Arsenite-resist 71.6 1.3 2.9E-05 37.3 0.1 27 367-393 77-103 (214)
105 KOG2186|consensus 71.3 3 6.4E-05 35.6 2.1 49 187-240 4-52 (276)
106 TIGR02605 CxxC_CxxC_SSSS putat 71.0 1.3 2.8E-05 27.9 -0.0 29 340-375 6-34 (52)
107 PRK00398 rpoP DNA-directed RNA 70.5 2.1 4.6E-05 26.2 0.8 8 245-252 22-29 (46)
108 PF02176 zf-TRAF: TRAF-type zi 70.0 2.6 5.7E-05 27.3 1.3 40 338-378 8-53 (60)
109 PRK00464 nrdR transcriptional 69.7 1.1 2.4E-05 35.7 -0.7 17 121-137 28-44 (154)
110 TIGR00373 conserved hypothetic 69.6 5.1 0.00011 32.2 3.1 16 217-232 110-125 (158)
111 KOG1280|consensus 69.4 4.3 9.4E-05 36.3 2.7 40 185-224 78-117 (381)
112 PF09723 Zn-ribbon_8: Zinc rib 69.2 2.1 4.5E-05 25.7 0.6 30 283-319 5-34 (42)
113 PF03604 DNA_RNApol_7kD: DNA d 68.6 2.7 5.9E-05 23.4 0.9 26 340-376 1-26 (32)
114 PF06524 NOA36: NOA36 protein; 68.0 2.8 6E-05 35.9 1.2 26 309-334 207-232 (314)
115 PF07800 DUF1644: Protein of u 66.7 7.4 0.00016 30.8 3.2 40 359-399 99-140 (162)
116 PF15269 zf-C2H2_7: Zinc-finge 65.9 6.8 0.00015 23.4 2.2 26 212-237 16-41 (54)
117 smart00531 TFIIE Transcription 65.2 4.1 8.9E-05 32.3 1.7 12 93-104 100-111 (147)
118 PRK06266 transcription initiat 64.7 6.8 0.00015 32.2 2.9 15 217-231 118-132 (178)
119 KOG2807|consensus 64.0 14 0.0003 32.9 4.7 25 216-240 345-369 (378)
120 PF05443 ROS_MUCR: ROS/MUCR tr 62.8 4 8.7E-05 31.5 1.2 22 368-392 73-94 (132)
121 PRK09678 DNA-binding transcrip 62.7 1.2 2.6E-05 30.3 -1.5 41 340-382 2-44 (72)
122 KOG4118|consensus 62.0 5.5 0.00012 26.0 1.5 30 368-397 39-68 (74)
123 COG1592 Rubrerythrin [Energy p 61.6 7.1 0.00015 31.5 2.4 23 311-346 134-156 (166)
124 PF08274 PhnA_Zn_Ribbon: PhnA 61.2 2.9 6.3E-05 22.9 0.1 9 367-375 19-27 (30)
125 PF15269 zf-C2H2_7: Zinc-finge 60.9 5.9 0.00013 23.7 1.3 21 122-142 21-41 (54)
126 TIGR02300 FYDLN_acid conserved 59.8 5.2 0.00011 30.3 1.3 29 218-257 11-39 (129)
127 PF05443 ROS_MUCR: ROS/MUCR tr 58.3 5.4 0.00012 30.8 1.2 27 120-149 71-97 (132)
128 KOG2593|consensus 57.0 10 0.00022 35.3 2.9 16 338-353 127-142 (436)
129 COG1198 PriA Primosomal protei 56.5 8.7 0.00019 39.0 2.6 26 159-195 446-471 (730)
130 PF04959 ARS2: Arsenite-resist 56.2 4 8.7E-05 34.5 0.2 29 120-148 76-104 (214)
131 PRK04023 DNA polymerase II lar 55.8 11 0.00024 39.2 3.1 49 283-378 626-674 (1121)
132 PF04328 DUF466: Protein of un 54.0 11 0.00025 25.0 2.0 20 379-398 24-43 (65)
133 COG5188 PRP9 Splicing factor 3 53.6 16 0.00035 32.8 3.5 24 121-144 238-261 (470)
134 COG1198 PriA Primosomal protei 51.6 10 0.00022 38.5 2.2 10 187-196 436-445 (730)
135 KOG1280|consensus 51.3 14 0.0003 33.2 2.7 36 283-318 79-116 (381)
136 COG5151 SSL1 RNA polymerase II 50.8 16 0.00034 32.3 2.9 24 185-208 387-410 (421)
137 TIGR01384 TFS_arch transcripti 49.9 2.9 6.3E-05 30.9 -1.4 13 121-133 16-28 (104)
138 PF00301 Rubredoxin: Rubredoxi 49.8 6.3 0.00014 24.3 0.3 10 159-168 3-12 (47)
139 KOG2272|consensus 49.4 7.1 0.00015 33.2 0.6 13 284-296 222-234 (332)
140 KOG2593|consensus 49.3 9.9 0.00022 35.4 1.6 18 120-137 127-144 (436)
141 COG0068 HypF Hydrogenase matur 49.0 1.9 4.2E-05 42.6 -3.1 56 285-347 125-181 (750)
142 PF05290 Baculo_IE-1: Baculovi 48.9 12 0.00027 28.6 1.8 24 171-200 112-135 (140)
143 COG0068 HypF Hydrogenase matur 47.5 1.6 3.5E-05 43.1 -3.8 80 283-376 101-182 (750)
144 PRK04023 DNA polymerase II lar 47.4 21 0.00045 37.3 3.5 9 187-195 627-635 (1121)
145 KOG2807|consensus 46.9 30 0.00064 31.0 4.0 36 215-264 275-310 (378)
146 PF07754 DUF1610: Domain of un 46.8 8.8 0.00019 19.8 0.5 8 367-374 16-23 (24)
147 KOG2071|consensus 46.7 15 0.00033 35.7 2.4 23 313-335 420-442 (579)
148 PF14353 CpXC: CpXC protein 46.2 11 0.00024 29.0 1.3 21 244-264 38-58 (128)
149 PF12760 Zn_Tnp_IS1595: Transp 46.1 18 0.00038 22.1 1.9 10 366-375 36-45 (46)
150 COG5151 SSL1 RNA polymerase II 45.3 14 0.00031 32.6 1.8 25 338-362 387-411 (421)
151 PF05191 ADK_lid: Adenylate ki 44.6 13 0.00029 21.3 1.1 12 367-378 21-32 (36)
152 cd00730 rubredoxin Rubredoxin; 42.9 9.8 0.00021 23.8 0.4 11 284-294 2-12 (50)
153 PRK03824 hypA hydrogenase nick 41.4 11 0.00024 29.3 0.6 11 340-350 71-81 (135)
154 PF08790 zf-LYAR: LYAR-type C2 41.3 6.5 0.00014 21.1 -0.5 9 246-254 2-10 (28)
155 COG5188 PRP9 Splicing factor 3 41.3 25 0.00054 31.7 2.7 22 216-237 238-259 (470)
156 PF04780 DUF629: Protein of un 41.3 16 0.00035 34.8 1.7 26 368-393 58-83 (466)
157 PF09845 DUF2072: Zn-ribbon co 40.0 15 0.00032 28.2 1.0 13 122-134 2-14 (131)
158 PF13451 zf-trcl: Probable zin 39.0 22 0.00047 22.1 1.4 16 92-107 4-19 (49)
159 PF13878 zf-C2H2_3: zinc-finge 38.2 27 0.00059 20.7 1.8 24 93-117 14-39 (41)
160 KOG4167|consensus 38.1 8.8 0.00019 38.1 -0.5 25 339-363 792-816 (907)
161 COG1997 RPL43A Ribosomal prote 38.0 20 0.00042 25.3 1.3 10 245-254 54-63 (89)
162 TIGR00595 priA primosomal prot 37.1 21 0.00046 34.9 1.9 18 179-196 233-250 (505)
163 COG3357 Predicted transcriptio 36.6 20 0.00043 25.4 1.1 11 94-104 60-70 (97)
164 COG1571 Predicted DNA-binding 35.6 21 0.00044 33.5 1.4 33 310-353 349-381 (421)
165 PRK00432 30S ribosomal protein 35.1 19 0.00041 22.5 0.8 12 338-349 36-47 (50)
166 KOG4167|consensus 35.0 9.5 0.00021 37.9 -0.8 25 367-391 792-816 (907)
167 PRK14714 DNA polymerase II lar 34.4 38 0.00083 36.5 3.2 12 186-197 692-703 (1337)
168 TIGR00100 hypA hydrogenase nic 33.7 20 0.00043 27.1 0.8 11 340-350 71-81 (115)
169 KOG3408|consensus 33.6 25 0.00055 26.4 1.3 25 337-361 55-79 (129)
170 PRK12380 hydrogenase nickel in 33.5 21 0.00046 26.8 1.0 11 340-350 71-81 (113)
171 PF07295 DUF1451: Protein of u 32.8 15 0.00032 29.1 0.0 33 280-322 109-141 (146)
172 COG3091 SprT Zn-dependent meta 32.4 22 0.00048 28.0 0.9 34 338-376 116-149 (156)
173 COG4530 Uncharacterized protei 32.0 21 0.00046 26.1 0.7 12 338-349 25-36 (129)
174 PF04780 DUF629: Protein of un 31.8 28 0.00061 33.3 1.7 26 159-184 59-84 (466)
175 TIGR01206 lysW lysine biosynth 31.6 15 0.00032 23.5 -0.1 10 217-226 3-12 (54)
176 PF08271 TF_Zn_Ribbon: TFIIB z 31.1 24 0.00051 21.1 0.7 8 122-129 20-27 (43)
177 PF07975 C1_4: TFIIH C1-like d 31.1 20 0.00043 22.5 0.4 25 338-362 20-44 (51)
178 PF01363 FYVE: FYVE zinc finge 30.9 27 0.00058 23.3 1.1 25 313-349 11-35 (69)
179 PF10013 DUF2256: Uncharacteri 30.0 30 0.00065 20.6 1.0 12 341-352 10-21 (42)
180 COG3364 Zn-ribbon containing p 29.7 32 0.00069 24.9 1.3 11 94-104 4-14 (112)
181 KOG1842|consensus 29.3 30 0.00064 32.4 1.3 28 157-184 15-42 (505)
182 PF14446 Prok-RING_1: Prokaryo 29.2 30 0.00064 22.0 0.9 25 218-254 7-31 (54)
183 COG4888 Uncharacterized Zn rib 28.7 16 0.00035 26.4 -0.3 11 368-378 47-57 (104)
184 PF01155 HypA: Hydrogenase exp 28.6 20 0.00044 26.9 0.2 14 216-229 70-83 (113)
185 PF04810 zf-Sec23_Sec24: Sec23 28.5 27 0.00059 20.5 0.7 31 93-130 3-33 (40)
186 COG1655 Uncharacterized protei 27.9 16 0.00034 30.9 -0.6 39 338-376 18-71 (267)
187 KOG4124|consensus 27.9 9.3 0.0002 34.3 -2.0 28 89-116 346-375 (442)
188 PRK00564 hypA hydrogenase nick 27.7 28 0.00061 26.4 0.8 11 340-350 72-82 (117)
189 COG4957 Predicted transcriptio 27.6 37 0.0008 26.1 1.4 23 340-365 77-99 (148)
190 PF08209 Sgf11: Sgf11 (transcr 27.5 45 0.00097 18.8 1.4 21 368-389 5-25 (33)
191 PF13453 zf-TFIIB: Transcripti 27.4 28 0.00062 20.5 0.6 16 159-174 21-36 (41)
192 smart00154 ZnF_AN1 AN1-like Zi 27.2 28 0.00061 20.4 0.6 13 367-379 12-24 (39)
193 PF13821 DUF4187: Domain of un 26.6 75 0.0016 20.3 2.5 18 159-176 29-46 (55)
194 PF07649 C1_3: C1-like domain; 26.3 31 0.00067 18.7 0.6 10 367-376 15-24 (30)
195 PRK14873 primosome assembly pr 26.2 43 0.00092 34.1 2.0 14 181-194 405-418 (665)
196 TIGR00595 priA primosomal prot 25.7 40 0.00087 33.0 1.6 13 336-348 237-249 (505)
197 smart00440 ZnF_C2C2 C2C2 Zinc 25.6 11 0.00024 22.2 -1.4 10 368-377 29-38 (40)
198 cd00065 FYVE FYVE domain; Zinc 25.0 46 0.001 21.0 1.4 13 338-350 17-29 (57)
199 PRK05580 primosome assembly pr 24.9 43 0.00093 34.2 1.8 15 181-195 403-417 (679)
200 PF13824 zf-Mss51: Zinc-finger 24.6 52 0.0011 21.0 1.4 10 367-376 14-23 (55)
201 PF05129 Elf1: Transcription e 24.5 17 0.00037 25.4 -0.8 10 90-99 20-29 (81)
202 PF14311 DUF4379: Domain of un 24.4 54 0.0012 20.8 1.6 11 340-350 29-39 (55)
203 PTZ00255 60S ribosomal protein 24.3 41 0.00089 24.0 1.0 10 245-254 55-64 (90)
204 PF12773 DZR: Double zinc ribb 24.0 44 0.00096 20.5 1.1 10 218-227 14-23 (50)
205 PRK03681 hypA hydrogenase nick 24.0 29 0.00062 26.2 0.3 10 340-349 71-80 (114)
206 KOG3408|consensus 23.9 46 0.001 25.1 1.3 26 364-389 54-79 (129)
207 KOG0717|consensus 23.9 42 0.0009 31.8 1.3 22 122-143 293-314 (508)
208 KOG2907|consensus 23.5 40 0.00088 25.0 0.9 10 245-254 103-112 (116)
209 PF13248 zf-ribbon_3: zinc-rib 23.5 36 0.00078 17.8 0.5 7 218-224 18-24 (26)
210 PF09332 Mcm10: Mcm10 replicat 23.3 6.8 0.00015 35.7 -3.8 42 157-198 252-297 (344)
211 COG1773 Rubredoxin [Energy pro 23.2 35 0.00075 21.8 0.5 12 367-378 3-14 (55)
212 KOG2636|consensus 23.1 54 0.0012 30.8 1.8 27 333-359 395-422 (497)
213 PF01428 zf-AN1: AN1-like Zinc 23.1 30 0.00064 20.7 0.1 14 366-379 12-25 (43)
214 PF07282 OrfB_Zn_ribbon: Putat 23.0 50 0.0011 22.0 1.3 12 338-349 45-56 (69)
215 KOG2636|consensus 23.0 64 0.0014 30.4 2.3 31 113-143 393-424 (497)
216 smart00661 RPOL9 RNA polymeras 22.8 41 0.00089 20.8 0.8 10 368-377 21-30 (52)
217 PF01780 Ribosomal_L37ae: Ribo 22.7 24 0.00051 25.2 -0.4 10 245-254 54-63 (90)
218 PF10263 SprT-like: SprT-like 22.6 28 0.0006 27.8 -0.1 10 368-377 144-153 (157)
219 TIGR00280 L37a ribosomal prote 21.7 39 0.00084 24.2 0.5 11 244-254 53-63 (91)
220 KOG4377|consensus 21.7 39 0.00085 31.3 0.7 129 97-239 257-426 (480)
221 PF05495 zf-CHY: CHY zinc fing 21.6 19 0.00041 24.4 -1.0 13 339-351 41-53 (71)
222 smart00064 FYVE Protein presen 21.5 49 0.0011 21.9 1.0 26 313-350 12-37 (68)
223 PRK04351 hypothetical protein; 21.4 42 0.00092 26.7 0.7 10 284-293 113-122 (149)
224 COG1571 Predicted DNA-binding 20.8 53 0.0011 30.9 1.3 30 341-381 352-381 (421)
225 TIGR00686 phnA alkylphosphonat 20.7 39 0.00086 24.9 0.4 11 340-350 20-30 (109)
226 KOG0978|consensus 20.4 39 0.00085 34.0 0.4 13 369-381 680-692 (698)
227 PF03811 Zn_Tnp_IS1: InsA N-te 20.2 30 0.00064 19.9 -0.3 18 356-373 18-35 (36)
No 1
>KOG1074|consensus
Probab=99.97 E-value=2.1e-32 Score=255.82 Aligned_cols=242 Identities=25% Similarity=0.502 Sum_probs=179.8
Q ss_pred CCccccccccccccCHHHHHHhHhhcCCCCCcccCCCCCCccCCHHHHHHHHHhhcCCCC--CCcccC---cCccccCCH
Q psy4576 155 KTKCVCHYCNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQQRTKCRFYYHLRDKHLSKP--ANLSCE---FCSRIFTKK 229 (400)
Q Consensus 155 ~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~--~~~~C~---~C~~~f~~~ 229 (400)
..+-.|-+|.++..-++.|+.|. +.|++++||+|.+||+.|.++.+|+.||..|-...+ ..+.|+ +|.+.|...
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHy-rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHY-RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred CCccceeeeeecccchhhhhhhh-hcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccc
Confidence 34568999999999999999998 899999999999999999999999999988765433 357999 999999999
Q ss_pred HHHHHHHHHcCCCC-------------ceecccccccccChhHHhhhHhhhcchh-----hHHHHhhhcCC----ccccc
Q psy4576 230 ELLRSHLAVHKIGK-------------NYQCYYCRKTYCHKPNLTNHIQNVHLKS-----ELEKRTAILKR----EFICD 287 (400)
Q Consensus 230 ~~l~~H~~~h~~~~-------------~~~C~~C~~~f~~~~~l~~H~~~~h~~~-----~~~~~~~~~~~----~~~C~ 287 (400)
-.|..|+++|.+.. .-+|..|.+.|.....+..++..+-+.. ....+..+.+. +..+.
T Consensus 682 V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~ 761 (958)
T KOG1074|consen 682 VTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPEN 761 (958)
T ss_pred ccccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCcccc
Confidence 99999999987421 2479999999999999999886663222 11122333322 56788
Q ss_pred cccccccChhhHHHHHhhh-----------------------cCCCCC-cccccccccCCHHHHHHHHH-----------
Q psy4576 288 VCGKSYVRKGALTEHHQRE-----------------------HQGKKP-VCTICGKMLIDKRSLANHMN----------- 332 (400)
Q Consensus 288 ~C~~~f~~~~~l~~H~~~~-----------------------h~~~~~-~C~~C~~~f~~~~~l~~H~~----------- 332 (400)
.|+..+.....+..+-... ..++.. .+.+++..-...-...--+.
T Consensus 762 ~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~ 841 (958)
T KOG1074|consen 762 SCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGL 841 (958)
T ss_pred ccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccccccccccc
Confidence 8988888776665542111 011223 45555543322211100000
Q ss_pred -------HhcC------------------------CCCeecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCch
Q psy4576 333 -------THTG------------------------LKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQRS 381 (400)
Q Consensus 333 -------~h~~------------------------~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~ 381 (400)
++.+ .....|..|++.|...++|..|+++|+++|||.|.+|++.|..+.
T Consensus 842 ~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrg 921 (958)
T KOG1074|consen 842 ATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRG 921 (958)
T ss_pred ccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhh
Confidence 0000 012689999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhCCCCCCC
Q psy4576 382 SYTLHYKTHHPGVIPP 397 (400)
Q Consensus 382 ~l~~H~~~hh~~~~~~ 397 (400)
+|+.||.+|+...++.
T Consensus 922 nLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 922 NLKVHMGTHMWVQPPS 937 (958)
T ss_pred hhhhhhccccccCCCc
Confidence 9999999999776653
No 2
>KOG2462|consensus
Probab=99.96 E-value=7.7e-30 Score=211.28 Aligned_cols=138 Identities=35% Similarity=0.654 Sum_probs=124.5
Q ss_pred CCceecccccccccChhHHhhhHhhhcchhhHHHHhhhcCCccccccccccccChhhHHHHHhhhcCCCCCccccccccc
Q psy4576 242 GKNYQCYYCRKTYCHKPNLTNHIQNVHLKSELEKRTAILKREFICDVCGKSYVRKGALTEHHQREHQGKKPVCTICGKML 321 (400)
Q Consensus 242 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f 321 (400)
...|+|+.|++.+.+.++|.+|.+.|-. ....+.+.|.+|++.|.+...|..|+ +.|. -+.+|.+||+.|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~--------~~s~ka~~C~~C~K~YvSmpALkMHi-rTH~-l~c~C~iCGKaF 197 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRS--------LDSKKAFSCKYCGKVYVSMPALKMHI-RTHT-LPCECGICGKAF 197 (279)
T ss_pred CCceeccccccccccccccchhhccccc--------ccccccccCCCCCceeeehHHHhhHh-hccC-CCcccccccccc
Confidence 3458888888888888888888876643 33367799999999999999999998 6665 566999999999
Q ss_pred CCHHHHHHHHHHhcCCCCeecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCchHHHHHHhh
Q psy4576 322 IDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 322 ~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
.....|+.|+|+|+|||||.|+.|+++|.++++|+.||++|.+.|+|+|..|+++|+..+.|.+|...
T Consensus 198 SRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 198 SRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999865
No 3
>KOG3608|consensus
Probab=99.95 E-value=3.3e-27 Score=200.37 Aligned_cols=192 Identities=30% Similarity=0.574 Sum_probs=98.6
Q ss_pred cccccccCHHHHHHhHhhcCCCCCcccCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHHcCC
Q psy4576 162 YCNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAVHKI 241 (400)
Q Consensus 162 ~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 241 (400)
.|.+.|.+++.|++|+ +.|++++...|+.||..|+++..|..|++.........|.|..|.+.|.+...|..|+..|.
T Consensus 184 ~Ct~~~~~k~~LreH~-r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv- 261 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHI-RTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV- 261 (467)
T ss_pred hhhhhhccHHHHHHHH-HhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh-
Confidence 4555555555555555 45555555555555555555555555555544444444555555555555555555555443
Q ss_pred CCceecccccccccChhHHhhhHhhhcchhhHHHHhhhcCCccccccccccccChhhHHHHHhhhcCCCCC-cccccccc
Q psy4576 242 GKNYQCYYCRKTYCHKPNLTNHIQNVHLKSELEKRTAILKREFICDVCGKSYVRKGALTEHHQREHQGKKP-VCTICGKM 320 (400)
Q Consensus 242 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-~C~~C~~~ 320 (400)
.-|+|+.|+.+....++|..|+ +..|...++ +|+.|++.
T Consensus 262 -n~ykCplCdmtc~~~ssL~~H~---------------------------------------r~rHs~dkpfKCd~Cd~~ 301 (467)
T KOG3608|consen 262 -NCYKCPLCDMTCSSASSLTTHI---------------------------------------RYRHSKDKPFKCDECDTR 301 (467)
T ss_pred -hcccccccccCCCChHHHHHHH---------------------------------------HhhhccCCCccccchhhh
Confidence 2345555555555555555554 444433322 55555555
Q ss_pred cCCHHHHHHHHHHhcCCCCeeccc--ccccccChhhHHHHHhhcC-C--CCcccCCCCccccCCchHHHHHHhhhCCCCC
Q psy4576 321 LIDKRSLANHMNTHTGLKPHCCEI--CGRSYSTAAYLKVHMSCHT-G--ETSHTCHLCPQKFRQRSSYTLHYKTHHPGVI 395 (400)
Q Consensus 321 f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~L~~H~~~h~-~--~~~~~C~~C~~~f~~~~~l~~H~~~hh~~~~ 395 (400)
|...+.|.+|+..|. +..|+|.. |.++|.+..+|.+|++.++ | ..+|.|..|.+.|++..+|.+|++..|+-+.
T Consensus 302 c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~ 380 (467)
T KOG3608|consen 302 CVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRL 380 (467)
T ss_pred hccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccC
Confidence 555555555555444 34455555 5555555555555554433 2 2235555555555555555555555554443
Q ss_pred C
Q psy4576 396 P 396 (400)
Q Consensus 396 ~ 396 (400)
|
T Consensus 381 P 381 (467)
T KOG3608|consen 381 P 381 (467)
T ss_pred C
Confidence 3
No 4
>KOG3608|consensus
Probab=99.94 E-value=6.1e-26 Score=192.74 Aligned_cols=198 Identities=23% Similarity=0.457 Sum_probs=169.2
Q ss_pred ccCCC--CCCccCCHHHHHHHHHhhcC-----------CCCCCccc--CcCccccCCHHHHHHHHHHcCCCCceeccccc
Q psy4576 187 YQCDF--CGSQQRTKCRFYYHLRDKHL-----------SKPANLSC--EFCSRIFTKKELLRSHLAVHKIGKNYQCYYCR 251 (400)
Q Consensus 187 ~~C~~--C~~~f~~~~~l~~H~~~~~~-----------~~~~~~~C--~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 251 (400)
|.|.+ |+..|.+...+..|+..|.. .+...+.| ..|.+.+.++..|++|++.|++++...|+.|+
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg 214 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCG 214 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHH
Confidence 55543 77788888888777766542 11123455 45999999999999999999999999999999
Q ss_pred ccccChhHHhhhHhhhcchhhHHHHhhhcCCccccccccccccChhhHHHHHhhhcCCCCCcccccccccCCHHHHHHHH
Q psy4576 252 KTYCHKPNLTNHIQNVHLKSELEKRTAILKREFICDVCGKSYVRKGALTEHHQREHQGKKPVCTICGKMLIDKRSLANHM 331 (400)
Q Consensus 252 ~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~ 331 (400)
..|++...|..|++. ++.....+|.|..|.+.|.+...|..|+ ..| ..-|+|+.|+.+....++|..|+
T Consensus 215 ~~F~~~tkl~DH~rR---------qt~l~~n~fqC~~C~KrFaTeklL~~Hv-~rH-vn~ykCplCdmtc~~~ssL~~H~ 283 (467)
T KOG3608|consen 215 ELFRTKTKLFDHLRR---------QTELNTNSFQCAQCFKRFATEKLLKSHV-VRH-VNCYKCPLCDMTCSSASSLTTHI 283 (467)
T ss_pred HHhccccHHHHHHHh---------hhhhcCCchHHHHHHHHHhHHHHHHHHH-HHh-hhcccccccccCCCChHHHHHHH
Confidence 999999999999965 4455567899999999999999999998 444 24679999999999999999999
Q ss_pred HH-hcCCCCeecccccccccChhhHHHHHhhcCCCCcccCCC--CccccCCchHHHHHHhhhCCC-CCC
Q psy4576 332 NT-HTGLKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHL--CPQKFRQRSSYTLHYKTHHPG-VIP 396 (400)
Q Consensus 332 ~~-h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~hh~~-~~~ 396 (400)
+. |...+||+|..|++.|...+.|.+|+.+|+ +..|+|.. |.++|.+..+|.+|++.+|.+ .|+
T Consensus 284 r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~ 351 (467)
T KOG3608|consen 284 RYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPI 351 (467)
T ss_pred HhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCC
Confidence 85 888999999999999999999999999998 66799998 999999999999999999944 444
No 5
>KOG3623|consensus
Probab=99.93 E-value=3.1e-26 Score=211.16 Aligned_cols=116 Identities=22% Similarity=0.361 Sum_probs=100.8
Q ss_pred ccccCcccccccChhHHHHHHhhhcCC-CCcccccccccccCChHHHHHHhhhhcCCccc-----ccCCCCccccccccc
Q psy4576 92 EERCRSCGLLSGSITQTYIHYLECKNR-GKLYECSLCNESFENKKVLFRHLRGKHGMKIK-----LSRHKTKCVCHYCNR 165 (400)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~~h~~-~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-----~~~~~~~~~C~~C~~ 165 (400)
...|++|...+.....|..|.+-.|.. +..|.|.+|.++|..+..|.+||..|...... ......+|+|..|++
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 468999999999999999997666643 56699999999999999999999998764432 112256899999999
Q ss_pred cccCHHHHHHhHhhcCCCCCcccCCCCCCccCCHHHHHHHHHh
Q psy4576 166 TFDSKAKIQEHIISSHMHEKLYQCDFCGSQQRTKCRFYYHLRD 208 (400)
Q Consensus 166 ~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~ 208 (400)
.|..+..|+.|+ ++|.|++||.|+.|++.|.....+..||..
T Consensus 290 AFKfKHHLKEHl-RIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 290 AFKFKHHLKEHL-RIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhhHHHHHhhh-eeecCCCCcCCcccccccccCCcccccccc
Confidence 999999999999 999999999999999999999998888764
No 6
>KOG2462|consensus
Probab=99.91 E-value=6.3e-25 Score=182.20 Aligned_cols=138 Identities=28% Similarity=0.573 Sum_probs=99.1
Q ss_pred CCCcccccccccccCChHHHHHHhhhhcCCcccccCCCCccccccccccccCHHHHHHhHhhcCCCCCcccCCCCCCccC
Q psy4576 118 RGKLYECSLCNESFENKKVLFRHLRGKHGMKIKLSRHKTKCVCHYCNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQQR 197 (400)
Q Consensus 118 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~ 197 (400)
....|+|+.|++.+.+.+.|.+|.+.|-.... ...+.|++|+++|.+...|+.|+ +.|+ -++.|.+||+.|.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s-----~ka~~C~~C~K~YvSmpALkMHi-rTH~--l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDS-----KKAFSCKYCGKVYVSMPALKMHI-RTHT--LPCECGICGKAFS 198 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccc-----cccccCCCCCceeeehHHHhhHh-hccC--CCccccccccccc
Confidence 34567888888888888888888777765432 33446777777777777777777 5564 5677777777777
Q ss_pred CHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHHcCCCCceecccccccccChhHHhhhHh
Q psy4576 198 TKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHKPNLTNHIQ 265 (400)
Q Consensus 198 ~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 265 (400)
..+.|.-|+|+|.+++|+ .|+.|++.|.+++.|+.|+++|.+.++|.|..|+++|...+-|.+|..
T Consensus 199 RPWLLQGHiRTHTGEKPF--~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 199 RPWLLQGHIRTHTGEKPF--SCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred chHHhhcccccccCCCCc--cCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 777777777777777764 777777777777777777777777777777777777777777777753
No 7
>KOG1074|consensus
Probab=99.91 E-value=2.2e-25 Score=209.08 Aligned_cols=134 Identities=24% Similarity=0.505 Sum_probs=104.7
Q ss_pred cccCcCccccCCHHHHHHHHHHcCCCCceecccccccccChhHHhhhHhhhcchhhHHHHhhhcCCccccc---cccccc
Q psy4576 217 LSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHKPNLTNHIQNVHLKSELEKRTAILKREFICD---VCGKSY 293 (400)
Q Consensus 217 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~C~---~C~~~f 293 (400)
-.|-+|.++..-.+.|+-|++.|+|++||+|.+|++.|.++.+|+.|+-.|- ......-.|.|+ +|.+.|
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk-------a~p~~R~q~ScP~~~ic~~kf 678 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK-------AKPPARVQFSCPSTFICQKKF 678 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc-------cCccccccccCCchhhhcccc
Confidence 5799999999999999999999999999999999999999999999985443 223334568999 999999
Q ss_pred cChhhHHHHHhhhcCC-CC-------------CcccccccccCCHHHHHHHHHHhcC----------------CC----C
Q psy4576 294 VRKGALTEHHQREHQG-KK-------------PVCTICGKMLIDKRSLANHMNTHTG----------------LK----P 339 (400)
Q Consensus 294 ~~~~~l~~H~~~~h~~-~~-------------~~C~~C~~~f~~~~~l~~H~~~h~~----------------~~----~ 339 (400)
.+...|..|+ +.|.+ .. -+|..|.+.|.....+..++-.|.+ +. +
T Consensus 679 tn~V~lpQhI-riH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~ 757 (958)
T KOG1074|consen 679 TNAVTLPQHI-RIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPP 757 (958)
T ss_pred cccccccceE-EeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCC
Confidence 9999999998 66542 11 1799999999888888888766621 12 4
Q ss_pred eecccccccccChhhHHHH
Q psy4576 340 HCCEICGRSYSTAAYLKVH 358 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H 358 (400)
..+..|+..+.....+..+
T Consensus 758 ~~e~~~~~~~~~e~~i~~~ 776 (958)
T KOG1074|consen 758 PPENSCGRELEGEMAISVR 776 (958)
T ss_pred ccccccccccCcccccccc
Confidence 5677777766555554444
No 8
>KOG3623|consensus
Probab=99.84 E-value=1.6e-21 Score=180.25 Aligned_cols=76 Identities=32% Similarity=0.682 Sum_probs=74.0
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCeecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCchHHHHHHh
Q psy4576 313 VCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQRSSYTLHYK 388 (400)
Q Consensus 313 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 388 (400)
.|+.|+++|...++|.+|.--|+|.+||+|.+|.|+|..+-.|..|+|.|.|+|||+|+.|+++|+....+..||.
T Consensus 896 aCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 896 ACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred hHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 3999999999999999999999999999999999999999999999999999999999999999999999999985
No 9
>KOG3576|consensus
Probab=99.75 E-value=2e-19 Score=141.72 Aligned_cols=117 Identities=31% Similarity=0.590 Sum_probs=104.2
Q ss_pred cCCccccccccccccChhhHHHHHhhhcCCCCCcccccccccCCHHHHHHHHHHhcCCCCeecccccccccChhhHHHHH
Q psy4576 280 LKREFICDVCGKSYVRKGALTEHHQREHQGKKPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYLKVHM 359 (400)
Q Consensus 280 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~ 359 (400)
+...|.|.+|++.|.-...|.+|+.-+...+++-|..||+.|.+...|++|+++|+|.+||+|..|+++|++.-+|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 35668999999999999999999844445566799999999999999999999999999999999999999999999999
Q ss_pred hhcCC-----------CCcccCCCCccccCCchHHHHHHhhhCCCCCC
Q psy4576 360 SCHTG-----------ETSHTCHLCPQKFRQRSSYTLHYKTHHPGVIP 396 (400)
Q Consensus 360 ~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~hh~~~~~ 396 (400)
+..+| .+.|.|..||++-.....+..|++.||+..|+
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHH
Confidence 76554 36799999999999999999999999998654
No 10
>KOG3576|consensus
Probab=99.65 E-value=6.1e-17 Score=127.76 Aligned_cols=124 Identities=22% Similarity=0.419 Sum_probs=89.2
Q ss_pred CcccCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHHcCCCCceecccccccccChhHHhhhH
Q psy4576 185 KLYQCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHKPNLTNHI 264 (400)
Q Consensus 185 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 264 (400)
..|.|.+|++.|.-...|.+|++-|...+ .+.|..||+.|.+.-+|++|++.|++.+||+|..|++.|...-+|..|+
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vk--r~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVK--RHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHH--HHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 34555555555555555555555544322 2478888888888888888888888888899999999998888899998
Q ss_pred hhhcchhhHHHHhhhcCCccccccccccccChhhHHHHHhhhcCCC
Q psy4576 265 QNVHLKSELEKRTAILKREFICDVCGKSYVRKGALTEHHQREHQGK 310 (400)
Q Consensus 265 ~~~h~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 310 (400)
+..|+....-.-.....+.|.|..||..-.....+..|+..+|...
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 8888775443334445567888888888888888888876666543
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.42 E-value=6.7e-13 Score=124.78 Aligned_cols=147 Identities=22% Similarity=0.479 Sum_probs=116.6
Q ss_pred cccCcCccccCCHHHHHHHHHHcCCCCceeccc--ccccccChhHHhhhHhhhcchhhHHHHhhhcCCcccccccccccc
Q psy4576 217 LSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYY--CRKTYCHKPNLTNHIQNVHLKSELEKRTAILKREFICDVCGKSYV 294 (400)
Q Consensus 217 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~C~~C~~~f~ 294 (400)
..|+.|....... .|..|..... .....|+. |+..|. ...+..| +.|+.|++.|.
T Consensus 408 V~C~NC~~~i~l~-~l~lHe~~C~-r~~V~Cp~~~Cg~v~~-r~el~~H--------------------~~C~~Cgk~f~ 464 (567)
T PLN03086 408 VECRNCKHYIPSR-SIALHEAYCS-RHNVVCPHDGCGIVLR-VEEAKNH--------------------VHCEKCGQAFQ 464 (567)
T ss_pred EECCCCCCccchh-HHHHHHhhCC-CcceeCCcccccceee-ccccccC--------------------ccCCCCCCccc
Confidence 3788888876654 4667875443 35567885 999884 4445555 57999999996
Q ss_pred ChhhHHHHHhhhcCCCCCcccccccccCCHHHHHHHHHHhcCCCCeeccccccccc----------ChhhHHHHHhhcCC
Q psy4576 295 RKGALTEHHQREHQGKKPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYS----------TAAYLKVHMSCHTG 364 (400)
Q Consensus 295 ~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~L~~H~~~h~~ 364 (400)
...|..|+...| .++.|+ |++.+ .+..|..|+.+|.+.+++.|..|++.|. ..+.|..|.... |
T Consensus 465 -~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G 538 (567)
T PLN03086 465 -QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-G 538 (567)
T ss_pred -hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-C
Confidence 678999986655 678999 99755 6789999999999999999999999995 245899999885 8
Q ss_pred CCcccCCCCccccCCchHHHHHHhhhCCC
Q psy4576 365 ETSHTCHLCPQKFRQRSSYTLHYKTHHPG 393 (400)
Q Consensus 365 ~~~~~C~~C~~~f~~~~~l~~H~~~hh~~ 393 (400)
.+++.|..||+.+..+ .|..|+...|..
T Consensus 539 ~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 539 SRTAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred CcceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 9999999999998766 489999887753
No 12
>PHA00733 hypothetical protein
Probab=99.24 E-value=7.2e-12 Score=96.20 Aligned_cols=79 Identities=22% Similarity=0.439 Sum_probs=61.8
Q ss_pred CcccccccccCCHHHHHH------HHHHhcCCCCeecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCchHHHH
Q psy4576 312 PVCTICGKMLIDKRSLAN------HMNTHTGLKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQRSSYTL 385 (400)
Q Consensus 312 ~~C~~C~~~f~~~~~l~~------H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 385 (400)
+.|.+|...|.....|.. |+. +.+.+||.|+.|++.|.....|..|++.| +.+|.|+.|++.|.....|..
T Consensus 41 ~~~~~~~~~~~~~~~l~~~~~l~~~~~-~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 41 LIRAVVKTLIYNPQLLDESSYLYKLLT-SKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred HHHHHHhhhccChhhhcchHHHHhhcc-cCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHH
Confidence 355566555555544444 333 34578999999999999999999999876 357999999999999999999
Q ss_pred HHhhhCCC
Q psy4576 386 HYKTHHPG 393 (400)
Q Consensus 386 H~~~hh~~ 393 (400)
|+...|+-
T Consensus 118 H~~~~h~~ 125 (128)
T PHA00733 118 HVCKKHNI 125 (128)
T ss_pred HHHHhcCc
Confidence 99998863
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.14 E-value=1.5e-10 Score=109.24 Aligned_cols=147 Identities=22% Similarity=0.419 Sum_probs=100.2
Q ss_pred cccccccccccCChHHHHHHhhhhcCCcccccCCCCcccccc--ccccccCHHHHHHhHhhcCCCCCcccCCCCCCccCC
Q psy4576 121 LYECSLCNESFENKKVLFRHLRGKHGMKIKLSRHKTKCVCHY--CNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQQRT 198 (400)
Q Consensus 121 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~ 198 (400)
.-.|+.|.+.... ..|..|....--.. . .|+. |+..|. +..+..| +.|+.|++.|.
T Consensus 407 ~V~C~NC~~~i~l-~~l~lHe~~C~r~~-V--------~Cp~~~Cg~v~~-r~el~~H----------~~C~~Cgk~f~- 464 (567)
T PLN03086 407 TVECRNCKHYIPS-RSIALHEAYCSRHN-V--------VCPHDGCGIVLR-VEEAKNH----------VHCEKCGQAFQ- 464 (567)
T ss_pred eEECCCCCCccch-hHHHHHHhhCCCcc-e--------eCCcccccceee-ccccccC----------ccCCCCCCccc-
Confidence 4568888776654 34556764432211 1 5774 888873 3444444 47888888885
Q ss_pred HHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHHcCCCCceecccccccccC----------hhHHhhhHhhhc
Q psy4576 199 KCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCH----------KPNLTNHIQNVH 268 (400)
Q Consensus 199 ~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~----------~~~l~~H~~~~h 268 (400)
...|..|+..+| . .+.|+ |+..+ ....|..|+..|.+.+++.|.+|++.|.. ...|..|.
T Consensus 465 ~s~LekH~~~~H--k--pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE---- 534 (567)
T PLN03086 465 QGEMEKHMKVFH--E--PLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHE---- 534 (567)
T ss_pred hHHHHHHHHhcC--C--CccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHH----
Confidence 577888888875 2 35888 88655 55788888888888888888888888741 34677775
Q ss_pred chhhHHHHhhhcCCccccccccccccChhhHHHHHhhhcC
Q psy4576 269 LKSELEKRTAILKREFICDVCGKSYVRKGALTEHHQREHQ 308 (400)
Q Consensus 269 ~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 308 (400)
.. .+.+++.|..||+.+..+ .|..|+...|.
T Consensus 535 -------~~-CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 535 -------SI-CGSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred -------Hh-cCCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 22 467788888888887655 57778777665
No 14
>PHA00733 hypothetical protein
Probab=99.04 E-value=2.3e-10 Score=87.96 Aligned_cols=82 Identities=17% Similarity=0.292 Sum_probs=62.3
Q ss_pred CCccccccccccccChhhHHHH-----HhhhcCCCCCcccccccccCCHHHHHHHHHHhcCCCCeecccccccccChhhH
Q psy4576 281 KREFICDVCGKSYVRKGALTEH-----HQREHQGKKPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYL 355 (400)
Q Consensus 281 ~~~~~C~~C~~~f~~~~~l~~H-----~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L 355 (400)
++++.|.+|+..|.+...|..+ ....++..+|.|+.|++.|.+...|..|++.| ..+|.|..|+++|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4556677777666665555443 12455667779999999999999999998876 3579999999999999999
Q ss_pred HHHHhhcCC
Q psy4576 356 KVHMSCHTG 364 (400)
Q Consensus 356 ~~H~~~h~~ 364 (400)
..|+...++
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 999877654
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.00 E-value=1.4e-10 Score=72.70 Aligned_cols=44 Identities=23% Similarity=0.398 Sum_probs=33.0
Q ss_pred CeecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCchHHH
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQRSSYT 384 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 384 (400)
.|+|+.||+.|+..++|..|+++|+ ++|+|..|++.|...+.|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3677788888888888888887777 5777888887777766654
No 16
>KOG3993|consensus
Probab=98.99 E-value=4.9e-11 Score=105.07 Aligned_cols=177 Identities=19% Similarity=0.314 Sum_probs=105.2
Q ss_pred cccCcCccccCCHHHHHHHHHHcCCCCceecccccccccChhHHhhhHhhhcchhhHH--------H-------------
Q psy4576 217 LSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHKPNLTNHIQNVHLKSELE--------K------------- 275 (400)
Q Consensus 217 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~--------~------------- 275 (400)
|.|..|...|.+.-.|.+|.-.-....-|+|+.|++.|.-..+|..|.++|.+..... +
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 5566666666666556555432222234666666666666666666655554432111 0
Q ss_pred -HhhhcCCccccccccccccChhhHHHHHhhhcCCCCC-----------------cccccccccCCHHHHHHHHHHhcC-
Q psy4576 276 -RTAILKREFICDVCGKSYVRKGALTEHHQREHQGKKP-----------------VCTICGKMLIDKRSLANHMNTHTG- 336 (400)
Q Consensus 276 -~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-----------------~C~~C~~~f~~~~~l~~H~~~h~~- 336 (400)
-.......|.|..|++.|.....|+.|+..+|..... -|..|.-.+.....-..+...+.+
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~s 427 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGS 427 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeecc
Confidence 0012234689999999999999999997565543221 233333333322221112111111
Q ss_pred CCCeecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCchHHHHHHhhhCCC
Q psy4576 337 LKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQRSSYTLHYKTHHPG 393 (400)
Q Consensus 337 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~hh~~ 393 (400)
..-..|+.|+-.+..+..--.+.+.-..+..|.|.+|.-.|.+...|.+|+..-|+.
T Consensus 428 ael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 428 AELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred ccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChH
Confidence 122457778877777766666666666677799999999999999999999998874
No 17
>KOG3993|consensus
Probab=98.98 E-value=5e-11 Score=105.00 Aligned_cols=55 Identities=18% Similarity=0.196 Sum_probs=47.4
Q ss_pred cccccCcccccccChhHHHHHHhhhcCCCCcccccccccccCChHHHHHHhhhhcC
Q psy4576 91 DEERCRSCGLLSGSITQTYIHYLECKNRGKLYECSLCNESFENKKVLFRHLRGKHG 146 (400)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 146 (400)
..|.|.+|...|.+...|.+| .-.......|+|+.|++.|+-..+|..|.+.|-.
T Consensus 266 GdyiCqLCK~kYeD~F~LAQH-rC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQH-RCPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhc-cCCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 349999999999999999999 4444444569999999999999999999998864
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.84 E-value=1.4e-09 Score=68.14 Aligned_cols=44 Identities=23% Similarity=0.436 Sum_probs=37.9
Q ss_pred CCcccccccccCCHHHHHHHHHHhcCCCCeecccccccccChhhHH
Q psy4576 311 KPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYLK 356 (400)
Q Consensus 311 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~ 356 (400)
.|+|+.||+.|...+.|..|+++|+ ++|+|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3689999999999999999999988 6899999999998777664
No 19
>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=98.72 E-value=6.2e-09 Score=55.74 Aligned_cols=24 Identities=42% Similarity=0.834 Sum_probs=12.2
Q ss_pred HHHHHhhcCCCCcccCCCCccccC
Q psy4576 355 LKVHMSCHTGETSHTCHLCPQKFR 378 (400)
Q Consensus 355 L~~H~~~h~~~~~~~C~~C~~~f~ 378 (400)
|.+|+++|++++||.|++|+++|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 445555555555555555555543
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=98.67 E-value=1.6e-08 Score=54.11 Aligned_cols=26 Identities=54% Similarity=0.985 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCCCeecccccccccC
Q psy4576 326 SLANHMNTHTGLKPHCCEICGRSYST 351 (400)
Q Consensus 326 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 351 (400)
+|.+|+++|++++||.|+.|+++|.+
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 48899999999999999999999964
No 21
>PHA00616 hypothetical protein
Probab=98.52 E-value=3.3e-08 Score=58.87 Aligned_cols=33 Identities=15% Similarity=0.195 Sum_probs=20.5
Q ss_pred CeecccccccccChhhHHHHHhhcCCCCcccCC
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHTGETSHTCH 371 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~ 371 (400)
||+|+.||+.|...+.|..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 456666666666666666666666666666554
No 22
>PHA00732 hypothetical protein
Probab=98.44 E-value=1.3e-07 Score=65.60 Aligned_cols=45 Identities=31% Similarity=0.606 Sum_probs=22.9
Q ss_pred CcccccccccCCHHHHHHHHHH-hcCCCCeecccccccccChhhHHHHHhhc
Q psy4576 312 PVCTICGKMLIDKRSLANHMNT-HTGLKPHCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 312 ~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
|.|+.|++.|.+...|..|++. |. ++.|+.|+++|. .|..|++++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 3455555555555555555553 32 235555555554 355555433
No 23
>PHA00616 hypothetical protein
Probab=98.34 E-value=2.4e-07 Score=55.23 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=29.1
Q ss_pred cccCCCCccccCCchHHHHHHhhhCCCCCCC
Q psy4576 367 SHTCHLCPQKFRQRSSYTLHYKTHHPGVIPP 397 (400)
Q Consensus 367 ~~~C~~C~~~f~~~~~l~~H~~~hh~~~~~~ 397 (400)
||+|+.||+.|..+++|.+|+++||+.+++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 6999999999999999999999999998764
No 24
>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=98.26 E-value=1.5e-06 Score=55.95 Aligned_cols=52 Identities=25% Similarity=0.411 Sum_probs=36.5
Q ss_pred ccccCcccccccChhHHHHHHhhhcCCC-CcccccccccccCChHHHHHHhhhhcC
Q psy4576 92 EERCRSCGLLSGSITQTYIHYLECKNRG-KLYECSLCNESFENKKVLFRHLRGKHG 146 (400)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~h~ 146 (400)
.|.||+|++ ..+..+|..|+...|..+ +.+.|++|...+. .+|..|+...|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 367888888 455677888877777664 4678888877544 377777776663
No 25
>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=98.25 E-value=2.2e-06 Score=55.26 Aligned_cols=50 Identities=30% Similarity=0.538 Sum_probs=22.8
Q ss_pred cccccccccccCHHHHHHhHhhcCCCC-CcccCCCCCCccCCHHHHHHHHHhhc
Q psy4576 158 CVCHYCNRTFDSKAKIQEHIISSHMHE-KLYQCDFCGSQQRTKCRFYYHLRDKH 210 (400)
Q Consensus 158 ~~C~~C~~~f~~~~~l~~H~~~~H~~~-~~~~C~~C~~~f~~~~~l~~H~~~~~ 210 (400)
|.|++|++ ..+...|..|+...|..+ +.+.|++|...+. .+|..|+...|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 44555555 333445555554445433 2345555544322 24444444433
No 26
>PHA00732 hypothetical protein
Probab=98.12 E-value=2.1e-06 Score=59.65 Aligned_cols=45 Identities=31% Similarity=0.580 Sum_probs=26.2
Q ss_pred CeecccccccccChhhHHHHHhh-cCCCCcccCCCCccccCCchHHHHHHhh
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSC-HTGETSHTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
||.|..|++.|.+.+.|..|++. |. ++.|+.|++.|. .|..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 45666666666666666666653 33 245666666665 35566544
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.92 E-value=5.5e-06 Score=42.98 Aligned_cols=22 Identities=23% Similarity=0.631 Sum_probs=12.4
Q ss_pred ccCCCCccccCCchHHHHHHhh
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
|+|++|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4555555555555555555554
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.91 E-value=7.1e-06 Score=43.05 Aligned_cols=24 Identities=38% Similarity=0.872 Sum_probs=16.3
Q ss_pred ccCCCCccccCCchHHHHHHhhhC
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKTHH 391 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~hh 391 (400)
|.|++|++.|.+...|..|++++|
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 567777777777777777777765
No 29
>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=97.87 E-value=8.4e-06 Score=42.28 Aligned_cols=23 Identities=48% Similarity=0.872 Sum_probs=16.4
Q ss_pred eecccccccccChhhHHHHHhhc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
|+|+.|++.|.+...|..|++.|
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 56777777777777777777653
No 30
>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=97.78 E-value=1.2e-05 Score=43.58 Aligned_cols=26 Identities=23% Similarity=0.502 Sum_probs=16.2
Q ss_pred cccCCCCccccCCchHHHHHHhhhCC
Q psy4576 367 SHTCHLCPQKFRQRSSYTLHYKTHHP 392 (400)
Q Consensus 367 ~~~C~~C~~~f~~~~~l~~H~~~hh~ 392 (400)
||+|..|++.|.+...|..|++.|++
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 45666666666666666666666554
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.74 E-value=1.7e-05 Score=58.90 Aligned_cols=22 Identities=27% Similarity=0.718 Sum_probs=10.7
Q ss_pred ccCCCCccccCCchHHHHHHhh
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
+.|.+|++.|.+...|..|++.
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCccCCCCcCHHHHHHHHcC
Confidence 4555555555555555555543
No 32
>KOG1146|consensus
Probab=97.72 E-value=4.9e-06 Score=84.46 Aligned_cols=226 Identities=20% Similarity=0.272 Sum_probs=143.6
Q ss_pred ccccccccccCHHHHHHhHhhcCCCCCcccCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHH
Q psy4576 159 VCHYCNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAV 238 (400)
Q Consensus 159 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 238 (400)
.|..|+..+.+...+..|+...|...+.|.|+.|+..|.....|..|||..|.+-.. .+|.. +.....+.+-...
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~----~~c~~-gq~~~~~arg~~~ 512 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS----AYCKA-GQNHPRLARGEVY 512 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch----hHhHh-ccccccccccccc
Confidence 466677778888888888878888889999999999999999999999998865432 22211 1111111111112
Q ss_pred cCCCCceecccccccccChhHHhhhHhhhcchhhHHHHh--------------------------------hhcCCcccc
Q psy4576 239 HKIGKNYQCYYCRKTYCHKPNLTNHIQNVHLKSELEKRT--------------------------------AILKREFIC 286 (400)
Q Consensus 239 h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~--------------------------------~~~~~~~~C 286 (400)
-.+.++|.|..|...+....+|..|++..-....++... ......+.|
T Consensus 513 ~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C 592 (1406)
T KOG1146|consen 513 RCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRC 592 (1406)
T ss_pred cCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcch
Confidence 234578999999999999999999986543222111100 111234889
Q ss_pred ccccccccChhhHHHHHhhhcCCCCC-cccccccccCCHHHHHHHHHHh-c-----------------------------
Q psy4576 287 DVCGKSYVRKGALTEHHQREHQGKKP-VCTICGKMLIDKRSLANHMNTH-T----------------------------- 335 (400)
Q Consensus 287 ~~C~~~f~~~~~l~~H~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~~~h-~----------------------------- 335 (400)
..|++...-..+|..|+...+....+ .+..++-.+.....+..+-+.+ +
T Consensus 593 ~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~lp~tps~~~~s~~~l~qkl~l~~~~~e~~a~~a 672 (1406)
T KOG1146|consen 593 EVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRLPFTPSSPPSSDYELSQKLELPDLSLEVAAKPA 672 (1406)
T ss_pred hhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCCCCCCCCCCccccchhhhhhcccccccccccccc
Confidence 99999999999999997655543332 3333333333333222222222 0
Q ss_pred ----------------------------------------------------------CCCCeeccccccc-ccChhhHH
Q psy4576 336 ----------------------------------------------------------GLKPHCCEICGRS-YSTAAYLK 356 (400)
Q Consensus 336 ----------------------------------------------------------~~~~~~C~~C~~~-f~~~~~L~ 356 (400)
..|.|.|-.|+.- ..+...|.
T Consensus 673 s~~~~~~~~~~~~~~~aPt~s~~g~~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~ 752 (1406)
T KOG1146|consen 673 SGLDGQLQLIRADPFLAPTGSEVGGGESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLW 752 (1406)
T ss_pred ccccchhhhccCCcccCCCCCCCCCCCCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHh
Confidence 0144889999854 34455666
Q ss_pred HHHhhc------CCCCcccCCCCccccCCchHHHHHHhh
Q psy4576 357 VHMSCH------TGETSHTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 357 ~H~~~h------~~~~~~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
.|..+- .....|.|.+|.+....+.++..|.++
T Consensus 753 ~h~~~~rs~ke~v~g~~~~c~l~~y~t~~kanfqlh~Kt 791 (1406)
T KOG1146|consen 753 FHNTRERSRKEQVPGDVPSCKLKPYATNTKANFQLHNKT 791 (1406)
T ss_pred hcchhhhhhhhcccCCCCcceecccccccchhhhhhccc
Confidence 675322 122459999999999999999998765
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.65 E-value=2.9e-05 Score=57.60 Aligned_cols=72 Identities=24% Similarity=0.491 Sum_probs=16.1
Q ss_pred cccccccccChhhHHHHHhhhcCCCCCcccccccccCCHHHHHHHHHHhcCCCCeecccccccccChhhHHHHHhhc
Q psy4576 286 CDVCGKSYVRKGALTEHHQREHQGKKPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 286 C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
|..|+..|.+...|..|+...|.-... ....+.....+..+++.-.. ..+.|.+|++.|.+...|..|++.+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~-~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVK-ESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccc----cccccccccccccccccccC-CCCCCCccCCCCcCHHHHHHHHcCc
Confidence 555555565555566665555543222 11111123333333332211 2567777777777777777777653
No 34
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.55 E-value=0.00013 Score=63.52 Aligned_cols=131 Identities=24% Similarity=0.493 Sum_probs=93.6
Q ss_pred cccccc--cccccCChHHHHHHhhhhcCCcccccCCCCcccccccc---ccc------cCHHHHHHhHhhcCCCC---Cc
Q psy4576 121 LYECSL--CNESFENKKVLFRHLRGKHGMKIKLSRHKTKCVCHYCN---RTF------DSKAKIQEHIISSHMHE---KL 186 (400)
Q Consensus 121 ~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~C~~C~---~~f------~~~~~l~~H~~~~H~~~---~~ 186 (400)
.|.|+. |.........|..|++..|+.. .|.+|- +.| -+...|+.|....-.++ .-
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~~----------~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGH 220 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFV----------LCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGH 220 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcE----------EhHhhhcCcccCccceeeeecccccccccCCccccCcCCC
Confidence 377875 7777777888888988877643 566663 333 34567788863222221 12
Q ss_pred ccCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCcc-------ccCCHHHHHHHHHHcCCCCceeccc--cc----cc
Q psy4576 187 YQCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSR-------IFTKKELLRSHLAVHKIGKNYQCYY--CR----KT 253 (400)
Q Consensus 187 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~-------~f~~~~~l~~H~~~h~~~~~~~C~~--C~----~~ 253 (400)
=.|.+|...|.+...|..|++..|. .|.+|++ -|.+..+|..|.+..+ |.|.. |- ..
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~v 290 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYV 290 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhh------hhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEE
Confidence 3699999999999999999998885 7888875 4888888999987544 55544 32 47
Q ss_pred ccChhHHhhhHhhhcchh
Q psy4576 254 YCHKPNLTNHIQNVHLKS 271 (400)
Q Consensus 254 f~~~~~l~~H~~~~h~~~ 271 (400)
|.....|..|+...|+..
T Consensus 291 f~~~~el~~h~~~~h~~~ 308 (493)
T COG5236 291 FPYHTELLEHLTRFHKVN 308 (493)
T ss_pred eccHHHHHHHHHHHhhcc
Confidence 889999999998888653
No 35
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.54 E-value=6.1e-05 Score=40.73 Aligned_cols=26 Identities=31% Similarity=0.769 Sum_probs=21.8
Q ss_pred CeecccccccccChhhHHHHHhhcCC
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHTG 364 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~~ 364 (400)
||+|..|++.|.+...|..|++.|.+
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 58889999999999999999887753
No 36
>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=97.50 E-value=7e-05 Score=39.12 Aligned_cols=23 Identities=35% Similarity=0.895 Sum_probs=10.0
Q ss_pred ccccccccccCChHHHHHHhhhh
Q psy4576 122 YECSLCNESFENKKVLFRHLRGK 144 (400)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~~~ 144 (400)
|.|++|++.|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34444555555544444444443
No 37
>KOG1146|consensus
Probab=97.46 E-value=3.7e-05 Score=78.33 Aligned_cols=84 Identities=18% Similarity=0.202 Sum_probs=63.2
Q ss_pred ccCcccccccChhHHHHHHhhhcCCCCcccccccccccCChHHHHHHhhhhcCCccc-----------------ccCCCC
Q psy4576 94 RCRSCGLLSGSITQTYIHYLECKNRGKLYECSLCNESFENKKVLFRHLRGKHGMKIK-----------------LSRHKT 156 (400)
Q Consensus 94 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-----------------~~~~~~ 156 (400)
.|.-|.-.+.+...+.-|+...+...+.|+|+.|++.|+....|..||+..|.+... ......
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~ 517 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGK 517 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCC
Confidence 566677777777777777777777788899999999999999999999986654311 122256
Q ss_pred ccccccccccccCHHHHHHhH
Q psy4576 157 KCVCHYCNRTFDSKAKIQEHI 177 (400)
Q Consensus 157 ~~~C~~C~~~f~~~~~l~~H~ 177 (400)
+|.|..|...+.....|.+|+
T Consensus 518 p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 518 PYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred cccceeeeeeeecchHHHHHH
Confidence 677888888888888888877
No 38
>KOG2231|consensus
Probab=97.45 E-value=0.00042 Score=67.09 Aligned_cols=47 Identities=28% Similarity=0.596 Sum_probs=25.8
Q ss_pred cCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCc------cccCCHHHHHHHHHHcC
Q psy4576 188 QCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCS------RIFTKKELLRSHLAVHK 240 (400)
Q Consensus 188 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~------~~f~~~~~l~~H~~~h~ 240 (400)
.|..|...|-....|.+|++..| |.|..|. ..|.....|..|.+..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h------~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce------eheeecCcccccchhcccchHHHHHhhhcC
Confidence 45566666666666666665555 2444442 34555555666655544
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.40 E-value=8e-05 Score=38.96 Aligned_cols=24 Identities=33% Similarity=0.647 Sum_probs=16.7
Q ss_pred ccCCCCccccCCchHHHHHHhhhCC
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKTHHP 392 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~hh~ 392 (400)
|+|+.|++... ...|.+|++.+||
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 67788887777 7778888877765
No 40
>KOG2231|consensus
Probab=97.39 E-value=0.0004 Score=67.21 Aligned_cols=125 Identities=19% Similarity=0.356 Sum_probs=70.4
Q ss_pred ccCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHHcCCCCceeccccc---------ccccCh
Q psy4576 187 YQCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCR---------KTYCHK 257 (400)
Q Consensus 187 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~---------~~f~~~ 257 (400)
+.|.+|+..|.-.. ..-.|..| ..|.+...|+.|+..-+ +.+.|.+|- ....+.
T Consensus 100 ~~C~~C~~~~~~~~--------------~~~~~~~c-~~~~s~~~Lk~H~~~~H--~~~~c~lC~~~~kif~~e~k~Yt~ 162 (669)
T KOG2231|consen 100 HSCHICDRRFRALY--------------NKKECLHC-TEFKSVENLKNHMRDQH--KLHLCSLCLQNLKIFINERKLYTR 162 (669)
T ss_pred hhcCccccchhhhc--------------ccCCCccc-cchhHHHHHHHHHHHhh--hhhccccccccceeeeeeeehehH
Confidence 68888887764210 11278888 88888899999985433 234455542 233345
Q ss_pred hHHhhhHhhhcchhhHHHHhhhcCCccccccccccccChhhHHHHHhhhcCCCCCcc---cccccccCCHHHHHHHHHHh
Q psy4576 258 PNLTNHIQNVHLKSELEKRTAILKREFICDVCGKSYVRKGALTEHHQREHQGKKPVC---TICGKMLIDKRSLANHMNTH 334 (400)
Q Consensus 258 ~~l~~H~~~~h~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C---~~C~~~f~~~~~l~~H~~~h 334 (400)
..|..|++.--... ....+ --.|..|...|.....|.+|+...|.-..+ | +.++.-|.....|..|.+.+
T Consensus 163 ~el~~h~~~gd~d~----~s~rG--hp~C~~C~~~fld~~el~rH~~~~h~~chf-C~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 163 AELNLHLMFGDPDD----ESCRG--HPLCKFCHERFLDDDELYRHLRFDHEFCHF-CDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred HHHHHHHhcCCCcc----ccccC--CccchhhhhhhccHHHHHHhhccceeheee-cCcccccchhcccchHHHHHhhhc
Confidence 56667764332211 11111 235777777777777777776554432221 2 22344566666777776654
Q ss_pred c
Q psy4576 335 T 335 (400)
Q Consensus 335 ~ 335 (400)
+
T Consensus 236 H 236 (669)
T KOG2231|consen 236 H 236 (669)
T ss_pred C
Confidence 4
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.36 E-value=5e-05 Score=65.26 Aligned_cols=23 Identities=13% Similarity=0.475 Sum_probs=15.7
Q ss_pred CCccccccccccccCHHHHHHhH
Q psy4576 155 KTKCVCHYCNRTFDSKAKIQEHI 177 (400)
Q Consensus 155 ~~~~~C~~C~~~f~~~~~l~~H~ 177 (400)
.++|+|++|++.|.+...|+-|.
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CCceeccccchhhccCccceecc
Confidence 45667777777777777777664
No 42
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.11 E-value=0.00012 Score=63.00 Aligned_cols=62 Identities=29% Similarity=0.600 Sum_probs=46.3
Q ss_pred CCceeccc--ccccccChhHHhhhHhhhcchhhHH--------HHhhhcCCccccccccccccChhhHHHHH
Q psy4576 242 GKNYQCYY--CRKTYCHKPNLTNHIQNVHLKSELE--------KRTAILKREFICDVCGKSYVRKGALTEHH 303 (400)
Q Consensus 242 ~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~--------~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 303 (400)
++||+|+. |.+.|.+...|+.|+..-|...... .......+||+|++|++.+.+...|+.|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 58999998 9999999999999997766332111 11123457888888888888888888874
No 43
>KOG2482|consensus
Probab=97.08 E-value=0.0017 Score=56.76 Aligned_cols=61 Identities=28% Similarity=0.573 Sum_probs=43.1
Q ss_pred CCccccccccccc-CChHHHHHHhhhhcCCcccccCC--------------CCccccccccccccCHHHHHHhHhh
Q psy4576 119 GKLYECSLCNESF-ENKKVLFRHLRGKHGMKIKLSRH--------------KTKCVCHYCNRTFDSKAKIQEHIIS 179 (400)
Q Consensus 119 ~~~~~C~~C~~~f-~~~~~l~~H~~~~h~~~~~~~~~--------------~~~~~C~~C~~~f~~~~~l~~H~~~ 179 (400)
....+|-+|...+ .+++.+..|+...|+....+... -..+.|-+|.+.|.++..|+.||+.
T Consensus 142 ~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 142 IFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 3456788887655 67778888888888755433222 3345788888888888888888843
No 44
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.03 E-value=0.00063 Score=41.57 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=18.9
Q ss_pred CCCcccCCCCccccCCchHHHHHHhhhCCCCC
Q psy4576 364 GETSHTCHLCPQKFRQRSSYTLHYKTHHPGVI 395 (400)
Q Consensus 364 ~~~~~~C~~C~~~f~~~~~l~~H~~~hh~~~~ 395 (400)
.+.|-.|++|+..+.+..+|.+|+...|..+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34567777777777777777777777777665
No 45
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.03 E-value=0.00066 Score=59.21 Aligned_cols=72 Identities=21% Similarity=0.477 Sum_probs=39.3
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCeecccccc-------cccChhhHHHHHhhcCCCCcccCCC--Cc----cccCC
Q psy4576 313 VCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGR-------SYSTAAYLKVHMSCHTGETSHTCHL--CP----QKFRQ 379 (400)
Q Consensus 313 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~-------~f~~~~~L~~H~~~h~~~~~~~C~~--C~----~~f~~ 379 (400)
.|..|...|.+...|..|++..+. +|.+|++ -|.+..+|..|.+.-+ |.|.+ |- +.|..
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~~ 293 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFPY 293 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEecc
Confidence 566666666666666666654332 3555543 3555556666654322 44432 32 45666
Q ss_pred chHHHHHHhhhCC
Q psy4576 380 RSSYTLHYKTHHP 392 (400)
Q Consensus 380 ~~~l~~H~~~hh~ 392 (400)
...|..|+...|+
T Consensus 294 ~~el~~h~~~~h~ 306 (493)
T COG5236 294 HTELLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHHHHhh
Confidence 6666666666554
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.87 E-value=0.00078 Score=35.69 Aligned_cols=23 Identities=30% Similarity=0.654 Sum_probs=17.6
Q ss_pred ccCCCCccccCCchHHHHHHhhh
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKTH 390 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~h 390 (400)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 56788888888888888887754
No 47
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.82 E-value=0.0008 Score=35.07 Aligned_cols=23 Identities=43% Similarity=0.778 Sum_probs=13.2
Q ss_pred ccccccccccCChHHHHHHhhhhc
Q psy4576 122 YECSLCNESFENKKVLFRHLRGKH 145 (400)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~~~h 145 (400)
|+|+.|++... ...|..|++.+|
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 45666666665 666666666655
No 48
>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=96.77 E-value=0.0013 Score=40.27 Aligned_cols=30 Identities=23% Similarity=0.486 Sum_probs=13.0
Q ss_pred CCCeecccccccccChhhHHHHHhhcCCCC
Q psy4576 337 LKPHCCEICGRSYSTAAYLKVHMSCHTGET 366 (400)
Q Consensus 337 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~ 366 (400)
+.|-.|++|+..+.+..+|.+|+.++++.+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 344555555555555555555555544443
No 49
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.76 E-value=0.0011 Score=35.12 Aligned_cols=23 Identities=35% Similarity=0.722 Sum_probs=14.5
Q ss_pred eecccccccccChhhHHHHHhhc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666666666666666666654
No 50
>KOG2482|consensus
Probab=96.69 E-value=0.0076 Score=52.79 Aligned_cols=50 Identities=28% Similarity=0.433 Sum_probs=36.8
Q ss_pred cccccccccccChhhHHHHHhhhcC---------------------------CCCCcccccccccCCHHHHHHHHHH
Q psy4576 284 FICDVCGKSYVRKGALTEHHQREHQ---------------------------GKKPVCTICGKMLIDKRSLANHMNT 333 (400)
Q Consensus 284 ~~C~~C~~~f~~~~~l~~H~~~~h~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~~ 333 (400)
..|-.|.....+...|..|+...|. .....|-.|...|.....|..||.-
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 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 4777777777777777777766662 1223788899999999999999864
No 51
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.63 E-value=0.0011 Score=34.95 Aligned_cols=22 Identities=23% Similarity=0.664 Sum_probs=11.7
Q ss_pred ccCCCCccccCCchHHHHHHhh
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
|.|.+|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 3455555555555555555543
No 52
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.61 E-value=0.0014 Score=34.53 Aligned_cols=23 Identities=30% Similarity=0.804 Sum_probs=18.4
Q ss_pred eecccccccccChhhHHHHHhhc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
|.|.+|++.|.+...|..|++.+
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 67888888888888888888653
No 53
>PRK04860 hypothetical protein; Provisional
Probab=96.55 E-value=0.0011 Score=53.05 Aligned_cols=38 Identities=21% Similarity=0.494 Sum_probs=27.7
Q ss_pred CeecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCc
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQR 380 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~ 380 (400)
+|.|. |+. ....+.+|.++|.++++|.|..|+..|...
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 57777 776 556677788888877778888887776543
No 54
>KOG2785|consensus
Probab=96.44 E-value=0.0084 Score=53.61 Aligned_cols=166 Identities=18% Similarity=0.278 Sum_probs=98.8
Q ss_pred CcccCcCccccCCHHHHHHHHHHcCCCCceecccccccccChhHHhhhHhhhcchh-------------hHHHHhhhcCC
Q psy4576 216 NLSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHKPNLTNHIQNVHLKS-------------ELEKRTAILKR 282 (400)
Q Consensus 216 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~-------------~~~~~~~~~~~ 282 (400)
.|+|.-|...|.+....+.|+++-- ...+|++-+....+.. ...........
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdW---------------HRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~ 67 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDW---------------HRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAES 67 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhH---------------HHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhccc
Confidence 3688888888888888888876421 0112222222211111 01111244566
Q ss_pred ccccccccccccChhhHHHHHhhhcCC-----------------CCCc-------------ccccccccCCHHHHHHHHH
Q psy4576 283 EFICDVCGKSYVRKGALTEHHQREHQG-----------------KKPV-------------CTICGKMLIDKRSLANHMN 332 (400)
Q Consensus 283 ~~~C~~C~~~f~~~~~l~~H~~~~h~~-----------------~~~~-------------C~~C~~~f~~~~~l~~H~~ 332 (400)
++.|..|.+.|.+......|+...-.. .... +..+............+..
T Consensus 68 ~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~~E~~~~~d~~~e~~~ 147 (390)
T KOG2785|consen 68 VVYCEACNKSFASPKAHENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKWYEVDSDEDSSEEEEE 147 (390)
T ss_pred ceehHHhhccccChhhHHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccchhhcccccccchhhcc
Confidence 788999999999888888886432110 0011 2333333333222222211
Q ss_pred H------------hcCCCCeecccccccccChhhHHHHHhhcCCC-----------------------CcccCCCCc---
Q psy4576 333 T------------HTGLKPHCCEICGRSYSTAAYLKVHMSCHTGE-----------------------TSHTCHLCP--- 374 (400)
Q Consensus 333 ~------------h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~-----------------------~~~~C~~C~--- 374 (400)
. -...-|-.|-.|++.+.+...-..||..+||- .-|.|-.|+
T Consensus 148 dd~~Edi~~d~~~e~e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~ 227 (390)
T KOG2785|consen 148 DDEEEDIEEDGDDEDELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELG 227 (390)
T ss_pred CcchhhhhhccchhcccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEecccc
Confidence 1 11124578999999999999999999988762 247899999
Q ss_pred cccCCchHHHHHHhh-hCCCCCC
Q psy4576 375 QKFRQRSSYTLHYKT-HHPGVIP 396 (400)
Q Consensus 375 ~~f~~~~~l~~H~~~-hh~~~~~ 396 (400)
+.|.+....+.||.. -|-..++
T Consensus 228 ~~f~sleavr~HM~~K~HCkl~y 250 (390)
T KOG2785|consen 228 RPFSSLEAVRAHMRDKGHCKLPY 250 (390)
T ss_pred CcccccHHHHHHHhhccCcccCC
Confidence 999999999999965 3444443
No 55
>KOG2785|consensus
Probab=96.20 E-value=0.028 Score=50.38 Aligned_cols=49 Identities=24% Similarity=0.462 Sum_probs=40.6
Q ss_pred cccccccccCCHHHHHHHHHHhcCC-----------------------CCeeccccc---ccccChhhHHHHHhh
Q psy4576 313 VCTICGKMLIDKRSLANHMNTHTGL-----------------------KPHCCEICG---RSYSTAAYLKVHMSC 361 (400)
Q Consensus 313 ~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~L~~H~~~ 361 (400)
.|-.|++.+.+...-..||..++|- .-|.|-.|+ +.|.+..+.+.||..
T Consensus 168 ~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 168 DCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred ceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 6888888888888888888877652 337899999 999999999999954
No 56
>KOG4173|consensus
Probab=95.75 E-value=0.0042 Score=50.24 Aligned_cols=49 Identities=22% Similarity=0.472 Sum_probs=24.4
Q ss_pred cccCc--ccccccChhHHHHHHhhhcCCCCcccccccccccCChHHHHHHhhhhc
Q psy4576 93 ERCRS--CGLLSGSITQTYIHYLECKNRGKLYECSLCNESFENKKVLFRHLRGKH 145 (400)
Q Consensus 93 ~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 145 (400)
|.|+. |..+|.+...+..|+...|.. .|.+|.+.|.+...|..|+..-|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~----sCs~C~r~~Pt~hLLd~HI~E~H 130 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN----SCSFCKRAFPTGHLLDAHILEWH 130 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc----hhHHHHHhCCchhhhhHHHHHHH
Confidence 34544 555555555555554444432 45555555555555555544433
No 57
>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=95.75 E-value=0.0042 Score=33.35 Aligned_cols=22 Identities=32% Similarity=0.730 Sum_probs=14.1
Q ss_pred eecccccccccChhhHHHHHhh
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSC 361 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~ 361 (400)
|.|..|++.|.+...|..|++.
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 5566666666666666666643
No 58
>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=95.61 E-value=0.0058 Score=32.82 Aligned_cols=21 Identities=24% Similarity=0.770 Sum_probs=11.4
Q ss_pred ccccccccccCChHHHHHHhh
Q psy4576 122 YECSLCNESFENKKVLFRHLR 142 (400)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~ 142 (400)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 445555555555555555554
No 59
>PRK04860 hypothetical protein; Provisional
Probab=95.36 E-value=0.0071 Score=48.42 Aligned_cols=38 Identities=18% Similarity=0.398 Sum_probs=31.4
Q ss_pred CCcccccccccCCHHHHHHHHHHhcCCCCeecccccccccCh
Q psy4576 311 KPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTA 352 (400)
Q Consensus 311 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 352 (400)
+|.|. |+. ....+.+|.++|+++++|.|..|+..|...
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 45887 887 666788999999999999999999888654
No 60
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.73 E-value=0.025 Score=29.64 Aligned_cols=19 Identities=32% Similarity=0.690 Sum_probs=11.1
Q ss_pred cCCCCccccCCchHHHHHHh
Q psy4576 369 TCHLCPQKFRQRSSYTLHYK 388 (400)
Q Consensus 369 ~C~~C~~~f~~~~~l~~H~~ 388 (400)
.|++||+.| ..+.|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 4555666654
No 61
>KOG4173|consensus
Probab=94.66 E-value=0.013 Score=47.47 Aligned_cols=81 Identities=25% Similarity=0.542 Sum_probs=70.1
Q ss_pred Ccccccc--cccccCChHHHHHHhhhhcCCcccccCCCCccccccccccccCHHHHHHhHhhcC---------CCCCccc
Q psy4576 120 KLYECSL--CNESFENKKVLFRHLRGKHGMKIKLSRHKTKCVCHYCNRTFDSKAKIQEHIISSH---------MHEKLYQ 188 (400)
Q Consensus 120 ~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~H---------~~~~~~~ 188 (400)
..|.|.+ |-..|.+......|+..-|+. .|..|.+.|.+...|..|+...| .|...|+
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~-----------sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ 146 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN-----------SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQ 146 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc-----------hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHH
Confidence 4578876 889999999999999988876 59999999999999999998777 3567899
Q ss_pred CCC--CCCccCCHHHHHHHHHhhcC
Q psy4576 189 CDF--CGSQQRTKCRFYYHLRDKHL 211 (400)
Q Consensus 189 C~~--C~~~f~~~~~l~~H~~~~~~ 211 (400)
|-. |+..|.+...-..|+-..|.
T Consensus 147 ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 147 CLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 965 99999999999999888774
No 62
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.97 E-value=0.042 Score=28.79 Aligned_cols=19 Identities=37% Similarity=0.810 Sum_probs=11.6
Q ss_pred ecccccccccChhhHHHHHh
Q psy4576 341 CCEICGRSYSTAAYLKVHMS 360 (400)
Q Consensus 341 ~C~~C~~~f~~~~~L~~H~~ 360 (400)
.|+.||+.| ..+.|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 566666666 4556666654
No 63
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.44 E-value=0.039 Score=34.37 Aligned_cols=30 Identities=20% Similarity=0.281 Sum_probs=21.9
Q ss_pred CcccccccCcccccccChhHHHHHHhhhcC
Q psy4576 88 DVWDEERCRSCGLLSGSITQTYIHYLECKN 117 (400)
Q Consensus 88 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 117 (400)
+++..+.||-|+..|....+..+|+.+.|.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 456667788888888887777777666663
No 64
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.25 E-value=0.022 Score=54.48 Aligned_cols=149 Identities=18% Similarity=0.257 Sum_probs=93.7
Q ss_pred cccCcCccccCCHHHHHHHHH--HcCCC--Cceecc--cccccccChhHHhhhHhhhcchhhHHHHhhhcCCcccccc--
Q psy4576 217 LSCEFCSRIFTKKELLRSHLA--VHKIG--KNYQCY--YCRKTYCHKPNLTNHIQNVHLKSELEKRTAILKREFICDV-- 288 (400)
Q Consensus 217 ~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~C~~-- 288 (400)
+.|..|...|.....|..|.. .|.++ +++.|+ .|++.|.....+..|...+.. ..++.+..
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~ 358 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS-----------ISPAKEKLLN 358 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccC-----------CCcccccccc
Confidence 678888888888888888888 78888 788888 688888888888888744332 22233222
Q ss_pred ccccccChhh-----HHHHHhhhcCCCCCccc--ccccccCCHHHHHHHHHHhcCCC--CeecccccccccChhhHHHHH
Q psy4576 289 CGKSYVRKGA-----LTEHHQREHQGKKPVCT--ICGKMLIDKRSLANHMNTHTGLK--PHCCEICGRSYSTAAYLKVHM 359 (400)
Q Consensus 289 C~~~f~~~~~-----l~~H~~~~h~~~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~L~~H~ 359 (400)
+...+..... ........+......+. .|...+.....+..|...|.... .+.+..|.+.|.....+..|+
T Consensus 359 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 (467)
T COG5048 359 SSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHK 438 (467)
T ss_pred CccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccc
Confidence 2222222111 11111122222223332 36666666667777766666554 577788999999888899998
Q ss_pred hhcCCCCcccCCCCccc
Q psy4576 360 SCHTGETSHTCHLCPQK 376 (400)
Q Consensus 360 ~~h~~~~~~~C~~C~~~ 376 (400)
+.|....++.|..++..
T Consensus 439 ~~~~~~~~~~~~~~~~~ 455 (467)
T COG5048 439 KIHTNHAPLLCSILKSF 455 (467)
T ss_pred cccccCCceeecccccc
Confidence 88887777666555443
No 65
>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=93.20 E-value=0.075 Score=30.39 Aligned_cols=22 Identities=14% Similarity=0.616 Sum_probs=13.9
Q ss_pred CeecccccccccChhhHHHHHh
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMS 360 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~ 360 (400)
+|.|.+|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4666666666666666666653
No 66
>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=92.94 E-value=0.068 Score=30.57 Aligned_cols=23 Identities=30% Similarity=0.550 Sum_probs=21.0
Q ss_pred cccCCCCccccCCchHHHHHHhh
Q psy4576 367 SHTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 367 ~~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
+|.|.+|+..|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999865
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.92 E-value=0.026 Score=53.97 Aligned_cols=155 Identities=15% Similarity=0.196 Sum_probs=93.8
Q ss_pred cccccCcccccccChhHHHHHHhh-hcCCC--Cccccc--ccccccCChHHHHHHhhhhcCCcccccCCCCccccccccc
Q psy4576 91 DEERCRSCGLLSGSITQTYIHYLE-CKNRG--KLYECS--LCNESFENKKVLFRHLRGKHGMKIKLSRHKTKCVCHYCNR 165 (400)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~-~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~C~~C~~ 165 (400)
.++.|..|...|.....+..|... .|..+ +++.|+ .|++.|.....+..|...+.+...... .=..+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~ 361 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE------KLLNSSS 361 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc------ccccCcc
Confidence 467888888888888888888332 78888 888888 788888888888888888877654411 0112232
Q ss_pred cccCHHHH----HHhHhhcCCCCCcccCCC--CCCccCCHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHHc
Q psy4576 166 TFDSKAKI----QEHIISSHMHEKLYQCDF--CGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAVH 239 (400)
Q Consensus 166 ~f~~~~~l----~~H~~~~H~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 239 (400)
.+.....- .......-.....+.+.. |...+.....+..|...+-...+..+.+..|...+.....+..|++.+
T Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 441 (467)
T COG5048 362 KFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIH 441 (467)
T ss_pred ccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCccccccccccc
Confidence 22222110 111101111222333322 445555555566665555555555667777888888777777777777
Q ss_pred CCCCceeccccc
Q psy4576 240 KIGKNYQCYYCR 251 (400)
Q Consensus 240 ~~~~~~~C~~C~ 251 (400)
....++.|..+.
T Consensus 442 ~~~~~~~~~~~~ 453 (467)
T COG5048 442 TNHAPLLCSILK 453 (467)
T ss_pred ccCCceeecccc
Confidence 766655554433
No 68
>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=92.78 E-value=0.063 Score=30.31 Aligned_cols=24 Identities=25% Similarity=0.773 Sum_probs=14.7
Q ss_pred eecccccccccChhhHHHHHhhcCCCCcccCCCCcc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQ 375 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~ 375 (400)
|.|..||..+.... .++.|++||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 56777776654322 5567777764
No 69
>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=91.45 E-value=0.28 Score=36.79 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=24.1
Q ss_pred cccC----CCCccccCCchHHHHHHhhhCC
Q psy4576 367 SHTC----HLCPQKFRQRSSYTLHYKTHHP 392 (400)
Q Consensus 367 ~~~C----~~C~~~f~~~~~l~~H~~~hh~ 392 (400)
-|.| +.|++.+.+...|.+|++.+|+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999999986
No 70
>KOG2893|consensus
Probab=91.37 E-value=0.054 Score=45.07 Aligned_cols=47 Identities=32% Similarity=0.706 Sum_probs=30.2
Q ss_pred ccCcCccccCCHHHHHHHHHHcCCCCceecccccccccChhHHhhhHhhhc
Q psy4576 218 SCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHKPNLTNHIQNVH 268 (400)
Q Consensus 218 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 268 (400)
.|-+|++.|.+...|..|++. +-|+|-+|-+...+-..|..|-..+|
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhh
Confidence 566677777777767666654 33777777666666666666655544
No 71
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.31 E-value=0.092 Score=32.78 Aligned_cols=30 Identities=33% Similarity=0.595 Sum_probs=18.1
Q ss_pred CCCCcccCCCCccccCCchHHHHHHhhhCC
Q psy4576 363 TGETSHTCHLCPQKFRQRSSYTLHYKTHHP 392 (400)
Q Consensus 363 ~~~~~~~C~~C~~~f~~~~~l~~H~~~hh~ 392 (400)
.|+..++||-|+..|....++.+|+..-|+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 345556666666666666666666655553
No 72
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.68 E-value=0.59 Score=34.65 Aligned_cols=86 Identities=16% Similarity=0.261 Sum_probs=39.0
Q ss_pred CcccccccccccCChHHHHHHhhhhcCCccccc----CCCCccccccccccccCHHHHHHhHhhcCCCCCcccCCCCCCc
Q psy4576 120 KLYECSLCNESFENKKVLFRHLRGKHGMKIKLS----RHKTKCVCHYCNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQ 195 (400)
Q Consensus 120 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~----~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~ 195 (400)
-|..|++|+.+.-+...|.+-..---+..++.. .....-.|--|...|........ ..-.....|+|+.|...
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~---~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF---DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc---cccccccceeCCCCCCc
Confidence 356666666666555555443211111111100 01111247777777765421110 00122345667777666
Q ss_pred cCCHHHHHHHHHh
Q psy4576 196 QRTKCRFYYHLRD 208 (400)
Q Consensus 196 f~~~~~l~~H~~~ 208 (400)
|--.-++..|-..
T Consensus 91 FC~dCD~fiHe~L 103 (112)
T TIGR00622 91 FCVDCDVFVHESL 103 (112)
T ss_pred cccccchhhhhhc
Confidence 6666666666433
No 73
>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=89.75 E-value=0.66 Score=34.73 Aligned_cols=23 Identities=17% Similarity=0.641 Sum_probs=14.8
Q ss_pred ccccccccccCHHHHHHhHhhcCC
Q psy4576 159 VCHYCNRTFDSKAKIQEHIISSHM 182 (400)
Q Consensus 159 ~C~~C~~~f~~~~~l~~H~~~~H~ 182 (400)
.|..|...... +.+..|+...|.
T Consensus 13 IC~~C~~av~~-~~v~~HL~~~H~ 35 (109)
T PF12013_consen 13 ICRQCQYAVQP-SEVESHLRKRHH 35 (109)
T ss_pred EeCCCCcccCc-hHHHHHHHHhcc
Confidence 67777766554 677777754553
No 74
>KOG2893|consensus
Probab=89.66 E-value=0.14 Score=42.78 Aligned_cols=42 Identities=21% Similarity=0.474 Sum_probs=32.7
Q ss_pred cCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHH
Q psy4576 188 QCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSH 235 (400)
Q Consensus 188 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 235 (400)
.|-+|++.|.....|.+|++..| |+|.+|.+..-+--.|..|
T Consensus 12 wcwycnrefddekiliqhqkakh------fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH------FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc------ceeeeehhhhccCCCceee
Confidence 58888888888888888877666 6888888777666666666
No 75
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.40 E-value=0.75 Score=34.12 Aligned_cols=77 Identities=18% Similarity=0.291 Sum_probs=36.5
Q ss_pred CccccccccccccChhhHHHHHhhhcC--CCCC------------cccccccccCCHHHHHHHHHHhcCCCCeecccccc
Q psy4576 282 REFICDVCGKSYVRKGALTEHHQREHQ--GKKP------------VCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGR 347 (400)
Q Consensus 282 ~~~~C~~C~~~f~~~~~l~~H~~~~h~--~~~~------------~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 347 (400)
-|-.|+.||....+...|.+.. +|- -..| .|-.|...|........ ..-.....|+|+.|..
T Consensus 14 LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~ 89 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKN 89 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCC
Confidence 3556777777766666666542 221 0101 25556665554321100 0011123466666666
Q ss_pred cccChhhHHHHHhhc
Q psy4576 348 SYSTAAYLKVHMSCH 362 (400)
Q Consensus 348 ~f~~~~~L~~H~~~h 362 (400)
.|-..-.+-.|...|
T Consensus 90 ~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 90 VFCVDCDVFVHESLH 104 (112)
T ss_pred ccccccchhhhhhcc
Confidence 665555555555444
No 76
>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=86.99 E-value=0.37 Score=27.38 Aligned_cols=25 Identities=24% Similarity=0.679 Sum_probs=15.3
Q ss_pred CeecccccccccChhhHHHHHhhcCCCCcccCCCCcc
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQ 375 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~ 375 (400)
.|.|..||..+... +.|-.|++||.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 36777777665432 14567777775
No 77
>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=85.98 E-value=0.46 Score=28.94 Aligned_cols=27 Identities=22% Similarity=0.509 Sum_probs=14.7
Q ss_pred CCcccCCCCccccCC----chHHHHHHhhhC
Q psy4576 365 ETSHTCHLCPQKFRQ----RSSYTLHYKTHH 391 (400)
Q Consensus 365 ~~~~~C~~C~~~f~~----~~~l~~H~~~hh 391 (400)
....+|.+|++.+.. .+.|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 344567777766555 366777776555
No 78
>COG2879 Uncharacterized small protein [Function unknown]
Probab=84.40 E-value=0.92 Score=29.32 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=17.6
Q ss_pred CCchHHHHHHhhhCCCCCCC
Q psy4576 378 RQRSSYTLHYKTHHPGVIPP 397 (400)
Q Consensus 378 ~~~~~l~~H~~~hh~~~~~~ 397 (400)
...++...||+.+||++|++
T Consensus 23 pdYdnYVehmr~~hPd~p~m 42 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKPPM 42 (65)
T ss_pred CcHHHHHHHHHHhCcCCCcc
Confidence 46788999999999999986
No 79
>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=84.04 E-value=0.5 Score=35.06 Aligned_cols=12 Identities=33% Similarity=1.052 Sum_probs=5.1
Q ss_pred Ceeccccccccc
Q psy4576 339 PHCCEICGRSYS 350 (400)
Q Consensus 339 ~~~C~~C~~~f~ 350 (400)
|..|+.||..|.
T Consensus 26 PivCP~CG~~~~ 37 (108)
T PF09538_consen 26 PIVCPKCGTEFP 37 (108)
T ss_pred CccCCCCCCccC
Confidence 444444444443
No 80
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=83.82 E-value=0.27 Score=41.82 Aligned_cols=43 Identities=19% Similarity=0.419 Sum_probs=28.0
Q ss_pred CCeecccccccccChhhHHHHHhhc----------CCCCc-----ccCCCCccccCCc
Q psy4576 338 KPHCCEICGRSYSTAAYLKVHMSCH----------TGETS-----HTCHLCPQKFRQR 380 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~~L~~H~~~h----------~~~~~-----~~C~~C~~~f~~~ 380 (400)
+.+.||+|+..|.....+....+.- .+..| ..||.||++|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 5677888888887766555554431 12233 4799999987754
No 81
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=83.56 E-value=0.82 Score=26.54 Aligned_cols=32 Identities=19% Similarity=0.450 Sum_probs=17.9
Q ss_pred ccCcccccccChhHHHHHHhhhcCCCCccccccccccc
Q psy4576 94 RCRSCGLLSGSITQTYIHYLECKNRGKLYECSLCNESF 131 (400)
Q Consensus 94 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 131 (400)
.||.|+..|.-..+- .-......+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~~------l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK------LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHH------cccCCcEEECCCCCcEe
Confidence 577777766554421 11234556677776655
No 82
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=82.75 E-value=0.97 Score=26.04 Aligned_cols=32 Identities=22% Similarity=0.506 Sum_probs=16.2
Q ss_pred ccCcccccccChhHHHHHHhhhcCCCCccccccccccc
Q psy4576 94 RCRSCGLLSGSITQTYIHYLECKNRGKLYECSLCNESF 131 (400)
Q Consensus 94 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 131 (400)
.|+.|+..|.-.... +-......+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~------ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK------IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHH------CCCCCcEEECCCCCCEe
Confidence 466666666544321 22234456666666554
No 83
>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=82.32 E-value=0.79 Score=24.19 Aligned_cols=10 Identities=30% Similarity=0.710 Sum_probs=5.8
Q ss_pred ccCcCccccC
Q psy4576 218 SCEFCSRIFT 227 (400)
Q Consensus 218 ~C~~C~~~f~ 227 (400)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5666666553
No 84
>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=81.51 E-value=0.66 Score=27.04 Aligned_cols=32 Identities=16% Similarity=0.432 Sum_probs=16.0
Q ss_pred ccCcccccccChhHHHHHHhhhcCCCCccccccccccc
Q psy4576 94 RCRSCGLLSGSITQTYIHYLECKNRGKLYECSLCNESF 131 (400)
Q Consensus 94 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 131 (400)
.|+.|+..|.-..+... .......|+.|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~------~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLG------ANGGKVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcC------CCCCEEECCCCCCEE
Confidence 56666666654433211 122345666666554
No 85
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.01 E-value=1.1 Score=28.69 Aligned_cols=32 Identities=25% Similarity=0.634 Sum_probs=17.9
Q ss_pred ccccCcccccccChhHHHHHHhhhcCCCCccccccccc
Q psy4576 92 EERCRSCGLLSGSITQTYIHYLECKNRGKLYECSLCNE 129 (400)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~ 129 (400)
.|.||.||..-...-. +......+|.|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~------~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCA------KCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhh------hHHHcCCceECCCcCc
Confidence 4678888755443322 1222356777777764
No 86
>PF12907 zf-met2: Zinc-binding
Probab=80.00 E-value=1.2 Score=26.32 Aligned_cols=28 Identities=25% Similarity=0.561 Sum_probs=18.6
Q ss_pred ccCCCCcccc---CCchHHHHHHhhhCCCCC
Q psy4576 368 HTCHLCPQKF---RQRSSYTLHYKTHHPGVI 395 (400)
Q Consensus 368 ~~C~~C~~~f---~~~~~l~~H~~~hh~~~~ 395 (400)
++|.+|..+| .+...|..|....|+..+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~ 32 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNT 32 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCC
Confidence 5677777443 444568888887777753
No 87
>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=78.95 E-value=2.2 Score=34.33 Aligned_cols=32 Identities=13% Similarity=0.194 Sum_probs=20.6
Q ss_pred CCCCeecccccccccChhhHHHHHhhcCCCCcccCCCCccc
Q psy4576 336 GLKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQK 376 (400)
Q Consensus 336 ~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~ 376 (400)
+..-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 344577777777777666664 24777777754
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.86 E-value=1.4 Score=26.76 Aligned_cols=26 Identities=23% Similarity=0.566 Sum_probs=16.0
Q ss_pred eecccccccccChhhHHHHHhhcCCCCcccCCCCccc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQK 376 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~ 376 (400)
|.|..||..|... ...+.+|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 6777777766532 2345677777754
No 89
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=77.85 E-value=1.4 Score=35.41 Aligned_cols=23 Identities=30% Similarity=0.894 Sum_probs=15.6
Q ss_pred CeecccccccccChhhHHHHHhhcCCCCcccCCCCc
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCP 374 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~ 374 (400)
.|.|++||+.+ -|+.|-+||+||
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 57777777553 345677777777
No 90
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=77.54 E-value=1.9 Score=26.99 Aligned_cols=25 Identities=28% Similarity=0.700 Sum_probs=16.4
Q ss_pred ccCCCCccccCCc-----hHHHHHHhhhCC
Q psy4576 368 HTCHLCPQKFRQR-----SSYTLHYKTHHP 392 (400)
Q Consensus 368 ~~C~~C~~~f~~~-----~~l~~H~~~hh~ 392 (400)
-.|.+|++.++.. +.|.+|++..|+
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 4577777666554 578888875554
No 91
>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=76.46 E-value=1.2 Score=33.02 Aligned_cols=29 Identities=17% Similarity=0.443 Sum_probs=17.8
Q ss_pred ccCcCccccCCHHHHHHHHHHcCCCCceecccccccccCh
Q psy4576 218 SCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHK 257 (400)
Q Consensus 218 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 257 (400)
.|+.||..|.... ..|..|+.||..|.-.
T Consensus 11 ~Cp~CG~kFYDLn-----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLN-----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCC-----------CCCccCCCCCCccCcc
Confidence 6666666666542 3566677777666544
No 92
>PF12907 zf-met2: Zinc-binding
Probab=75.50 E-value=1.8 Score=25.50 Aligned_cols=31 Identities=16% Similarity=0.118 Sum_probs=15.7
Q ss_pred cccCcccccc---cChhHHHHHHhhhcCCCCccc
Q psy4576 93 ERCRSCGLLS---GSITQTYIHYLECKNRGKLYE 123 (400)
Q Consensus 93 ~~C~~C~~~f---~~~~~l~~H~~~~h~~~~~~~ 123 (400)
+.|.+|-..| .+...|..|....|.+..+-.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~ 35 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEE 35 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHH
Confidence 3566666333 334456666555555543333
No 93
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=74.91 E-value=0.72 Score=39.24 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=7.1
Q ss_pred ccCCCCCCccCC
Q psy4576 187 YQCDFCGSQQRT 198 (400)
Q Consensus 187 ~~C~~C~~~f~~ 198 (400)
..||.||+++..
T Consensus 49 ~vCP~CgyA~~~ 60 (214)
T PF09986_consen 49 WVCPHCGYAAFE 60 (214)
T ss_pred EECCCCCCcccc
Confidence 356666666543
No 94
>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=74.77 E-value=1.2 Score=37.90 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=14.0
Q ss_pred CCeecccccccccChhhHHHHHhhc
Q psy4576 338 KPHCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
++++|+.|++.......|..-.|+|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecc
Confidence 5666666666655555554444443
No 95
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.58 E-value=3.6 Score=32.69 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=20.3
Q ss_pred CCCeecccccccccChhhHHHHHhhcCCCCcccCCCCcccc
Q psy4576 337 LKPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKF 377 (400)
Q Consensus 337 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f 377 (400)
..-|.|+.|+..|+....+.. . .. ...|.|+.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~-~--d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL-L--DM-DGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh-c--CC-CCcEECCCCCCEE
Confidence 345777777777765443332 0 11 2237777777654
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=74.49 E-value=2.8 Score=34.46 Aligned_cols=30 Identities=13% Similarity=0.364 Sum_probs=17.3
Q ss_pred CCeecccccccccChhhHHHHHhhcCCCCcccCCCCccc
Q psy4576 338 KPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQK 376 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~ 376 (400)
.-|.|+.|+..|+...++. .-|.|+.||-.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 3466666666666555542 24666666644
No 97
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=74.46 E-value=1.8 Score=26.79 Aligned_cols=28 Identities=21% Similarity=0.527 Sum_probs=16.8
Q ss_pred CeecccccccccChhhHHHHHhhcCCCCcccCCCCccc
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQK 376 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~ 376 (400)
.|.|..||+.|... ......+|+.||..
T Consensus 6 ~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELD----------QETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehh----------hccCceeCCCCCcE
Confidence 47788888777211 12244678888754
No 98
>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=73.35 E-value=1.7 Score=32.82 Aligned_cols=12 Identities=17% Similarity=0.562 Sum_probs=5.3
Q ss_pred CCeecccccccc
Q psy4576 338 KPHCCEICGRSY 349 (400)
Q Consensus 338 ~~~~C~~C~~~f 349 (400)
.|..|+.||..|
T Consensus 25 ~p~vcP~cg~~~ 36 (129)
T TIGR02300 25 RPAVSPYTGEQF 36 (129)
T ss_pred CCccCCCcCCcc
Confidence 344444444444
No 99
>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=72.97 E-value=3 Score=22.01 Aligned_cols=19 Identities=16% Similarity=0.455 Sum_probs=13.5
Q ss_pred cCCCCccccCCchHHHHHHh
Q psy4576 369 TCHLCPQKFRQRSSYTLHYK 388 (400)
Q Consensus 369 ~C~~C~~~f~~~~~l~~H~~ 388 (400)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 578888777 5566777765
No 100
>KOG2186|consensus
Probab=72.82 E-value=2.2 Score=36.35 Aligned_cols=46 Identities=22% Similarity=0.543 Sum_probs=31.0
Q ss_pred CcccccccccCCHHHHHHHHHHhcCCCCeecccccccccChhhHHHHHh
Q psy4576 312 PVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYLKVHMS 360 (400)
Q Consensus 312 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~ 360 (400)
|.|..||....- ..+.+|+-..++ .-|.|-.|++.|.. ..+..|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 467777776654 345667777666 45778788888776 56666754
No 101
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=72.33 E-value=2.6 Score=27.16 Aligned_cols=10 Identities=30% Similarity=0.790 Sum_probs=6.5
Q ss_pred ccccCccccc
Q psy4576 92 EERCRSCGLL 101 (400)
Q Consensus 92 ~~~C~~C~~~ 101 (400)
.|.|+.||..
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 3667777665
No 102
>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=71.87 E-value=1.2 Score=26.34 Aligned_cols=30 Identities=23% Similarity=0.571 Sum_probs=17.1
Q ss_pred eecccccccccChhhHHHHHhhcCCCCcccCCCCccc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQK 376 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~ 376 (400)
|+|..||..|....... ....-.|+.||..
T Consensus 6 y~C~~Cg~~fe~~~~~~-------~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS-------DDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEecC-------CCCCCCCCCCCCc
Confidence 67777777775433221 1234567777763
No 103
>PHA00626 hypothetical protein
Probab=71.56 E-value=2.1 Score=27.03 Aligned_cols=15 Identities=20% Similarity=0.379 Sum_probs=9.3
Q ss_pred CCcccccccccccCC
Q psy4576 119 GKLYECSLCNESFEN 133 (400)
Q Consensus 119 ~~~~~C~~C~~~f~~ 133 (400)
...|.|+.|++.|+.
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 345777777766653
No 104
>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=71.56 E-value=1.3 Score=37.29 Aligned_cols=27 Identities=26% Similarity=0.501 Sum_probs=13.5
Q ss_pred cccCCCCccccCCchHHHHHHhhhCCC
Q psy4576 367 SHTCHLCPQKFRQRSSYTLHYKTHHPG 393 (400)
Q Consensus 367 ~~~C~~C~~~f~~~~~l~~H~~~hh~~ 393 (400)
.|.|+.|+|.|.-..-+.+|+...|++
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHH
Confidence 455555555555555555555555543
No 105
>KOG2186|consensus
Probab=71.30 E-value=3 Score=35.59 Aligned_cols=49 Identities=20% Similarity=0.497 Sum_probs=28.0
Q ss_pred ccCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCccccCCHHHHHHHHHHcC
Q psy4576 187 YQCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSRIFTKKELLRSHLAVHK 240 (400)
Q Consensus 187 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 240 (400)
|.|..||-...-+ .+.+|+...++ ..|.|-.|+..|.. .++..|..--+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn---~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN---AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC---CeeEEeeccccccc-chhhhhhhhcc
Confidence 6677776655433 34556665554 33566667766666 45666654433
No 106
>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=71.03 E-value=1.3 Score=27.91 Aligned_cols=29 Identities=21% Similarity=0.557 Sum_probs=15.8
Q ss_pred eecccccccccChhhHHHHHhhcCCCCcccCCCCcc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQ 375 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~ 375 (400)
|+|..||..|.....+. ...+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~-------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS-------DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC-------CCCCCCCCCCCC
Confidence 67777777666432111 123345777775
No 107
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=70.52 E-value=2.1 Score=26.19 Aligned_cols=8 Identities=38% Similarity=1.040 Sum_probs=3.6
Q ss_pred eecccccc
Q psy4576 245 YQCYYCRK 252 (400)
Q Consensus 245 ~~C~~C~~ 252 (400)
+.|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 44444443
No 108
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=69.96 E-value=2.6 Score=27.33 Aligned_cols=40 Identities=18% Similarity=0.433 Sum_probs=21.1
Q ss_pred CCeeccc--ccccccChhhHHHHHhhcCCCCcccCCC----CccccC
Q psy4576 338 KPHCCEI--CGRSYSTAAYLKVHMSCHTGETSHTCHL----CPQKFR 378 (400)
Q Consensus 338 ~~~~C~~--C~~~f~~~~~L~~H~~~h~~~~~~~C~~----C~~~f~ 378 (400)
.+..|+. |...+. ...|..|+...-...+..|++ |+..+.
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 3456666 434343 456777777666666677777 776654
No 109
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=69.70 E-value=1.1 Score=35.69 Aligned_cols=17 Identities=24% Similarity=0.507 Sum_probs=11.8
Q ss_pred cccccccccccCChHHH
Q psy4576 121 LYECSLCNESFENKKVL 137 (400)
Q Consensus 121 ~~~C~~C~~~f~~~~~l 137 (400)
.++|+.||++|.+...+
T Consensus 28 ~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RRECLACGKRFTTFERV 44 (154)
T ss_pred eeeccccCCcceEeEec
Confidence 37888888887765443
No 110
>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=69.61 E-value=5.1 Score=32.23 Aligned_cols=16 Identities=25% Similarity=0.316 Sum_probs=7.4
Q ss_pred cccCcCccccCCHHHH
Q psy4576 217 LSCEFCSRIFTKKELL 232 (400)
Q Consensus 217 ~~C~~C~~~f~~~~~l 232 (400)
|.|+.|+..|+...++
T Consensus 110 Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 110 FICPNMCVRFTFNEAM 125 (158)
T ss_pred EECCCCCcEeeHHHHH
Confidence 4444444444444443
No 111
>KOG1280|consensus
Probab=69.38 E-value=4.3 Score=36.34 Aligned_cols=40 Identities=23% Similarity=0.614 Sum_probs=27.4
Q ss_pred CcccCCCCCCccCCHHHHHHHHHhhcCCCCCCcccCcCcc
Q psy4576 185 KLYQCDFCGSQQRTKCRFYYHLRDKHLSKPANLSCEFCSR 224 (400)
Q Consensus 185 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~ 224 (400)
..|.|++|+..-.+...|..|+...|.+......|+.|+-
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 3577777777777777777777777766665556666653
No 112
>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=69.23 E-value=2.1 Score=25.65 Aligned_cols=30 Identities=23% Similarity=0.641 Sum_probs=16.8
Q ss_pred ccccccccccccChhhHHHHHhhhcCCCCCccccccc
Q psy4576 283 EFICDVCGKSYVRKGALTEHHQREHQGKKPVCTICGK 319 (400)
Q Consensus 283 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~ 319 (400)
.|.|..||..|.... .........|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~-------~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ-------SISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEE-------EcCCCCCCcCCCCCC
Confidence 367777777765442 222233446777765
No 113
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=68.57 E-value=2.7 Score=23.43 Aligned_cols=26 Identities=19% Similarity=0.473 Sum_probs=14.0
Q ss_pred eecccccccccChhhHHHHHhhcCCCCcccCCCCccc
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQK 376 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~ 376 (400)
|.|..|+..+... ...+.+|+.||..
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCe
Confidence 5677777666521 1234677777754
No 114
>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=68.03 E-value=2.8 Score=35.87 Aligned_cols=26 Identities=27% Similarity=0.526 Sum_probs=13.7
Q ss_pred CCCCcccccccccCCHHHHHHHHHHh
Q psy4576 309 GKKPVCTICGKMLIDKRSLANHMNTH 334 (400)
Q Consensus 309 ~~~~~C~~C~~~f~~~~~l~~H~~~h 334 (400)
++++.||.|+........|..-.++|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 34446666666655555554444433
No 115
>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=66.66 E-value=7.4 Score=30.81 Aligned_cols=40 Identities=18% Similarity=0.382 Sum_probs=27.8
Q ss_pred HhhcCCCCcccCCC--CccccCCchHHHHHHhhhCCCCCCCCC
Q psy4576 359 MSCHTGETSHTCHL--CPQKFRQRSSYTLHYKTHHPGVIPPKL 399 (400)
Q Consensus 359 ~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~hh~~~~~~~~ 399 (400)
.|.+...|+-.|.. |.+. .+...|.+|.+..||...|.++
T Consensus 99 AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~~v 140 (162)
T PF07800_consen 99 ARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPSEV 140 (162)
T ss_pred HHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCccC
Confidence 44444556666654 7666 3567799999999998887764
No 116
>PF15269 zf-C2H2_7: Zinc-finger
Probab=65.87 E-value=6.8 Score=23.40 Aligned_cols=26 Identities=27% Similarity=0.455 Sum_probs=16.4
Q ss_pred CCCCCcccCcCccccCCHHHHHHHHH
Q psy4576 212 SKPANLSCEFCSRIFTKKELLRSHLA 237 (400)
Q Consensus 212 ~~~~~~~C~~C~~~f~~~~~l~~H~~ 237 (400)
.+|+.|+|-.|.....-.+.|-.||+
T Consensus 16 gkp~~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 16 GKPFKYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred CCCccceeecCCcccchHHHHHHHHH
Confidence 44556666666666666666666654
No 117
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=65.16 E-value=4.1 Score=32.34 Aligned_cols=12 Identities=17% Similarity=0.335 Sum_probs=5.9
Q ss_pred cccCcccccccC
Q psy4576 93 ERCRSCGLLSGS 104 (400)
Q Consensus 93 ~~C~~C~~~f~~ 104 (400)
|.||.|+..|..
T Consensus 100 Y~Cp~C~~~y~~ 111 (147)
T smart00531 100 YKCPNCQSKYTF 111 (147)
T ss_pred EECcCCCCEeeH
Confidence 455555544443
No 118
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=64.72 E-value=6.8 Score=32.20 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=7.4
Q ss_pred cccCcCccccCCHHH
Q psy4576 217 LSCEFCSRIFTKKEL 231 (400)
Q Consensus 217 ~~C~~C~~~f~~~~~ 231 (400)
|.|+.|+..|+...+
T Consensus 118 Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 118 FFCPNCHIRFTFDEA 132 (178)
T ss_pred EECCCCCcEEeHHHH
Confidence 455555555544443
No 119
>KOG2807|consensus
Probab=63.96 E-value=14 Score=32.95 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=15.0
Q ss_pred CcccCcCccccCCHHHHHHHHHHcC
Q psy4576 216 NLSCEFCSRIFTKKELLRSHLAVHK 240 (400)
Q Consensus 216 ~~~C~~C~~~f~~~~~l~~H~~~h~ 240 (400)
.|.|..|...|-..-+.-.|...|.
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred cEEchhccceeeccchHHHHhhhhc
Confidence 3566666666666655556655543
No 120
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=62.81 E-value=4 Score=31.53 Aligned_cols=22 Identities=36% Similarity=0.724 Sum_probs=10.9
Q ss_pred ccCCCCccccCCchHHHHHHhhhCC
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKTHHP 392 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~hh~ 392 (400)
..|-+||+.|.. |.+|+++||+
T Consensus 73 i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-
T ss_pred eEEccCCcccch---HHHHHHHccC
Confidence 556666666642 4666666665
No 121
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=62.73 E-value=1.2 Score=30.26 Aligned_cols=41 Identities=22% Similarity=0.436 Sum_probs=19.2
Q ss_pred eecccccccccChhhHHHHHhhcCCCCcccCC--CCccccCCchH
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCHTGETSHTCH--LCPQKFRQRSS 382 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~--~C~~~f~~~~~ 382 (400)
+.|+.||.......+-..+.. ..+.-++|. .||.+|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCCEEEEEEE
Confidence 456666654422222221111 234446666 67776665443
No 122
>KOG4118|consensus
Probab=62.05 E-value=5.5 Score=25.98 Aligned_cols=30 Identities=23% Similarity=0.676 Sum_probs=26.6
Q ss_pred ccCCCCccccCCchHHHHHHhhhCCCCCCC
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKTHHPGVIPP 397 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~hh~~~~~~ 397 (400)
|+|.+|-........+..|....||..|.|
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~~~P 68 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKEPLP 68 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCCCCC
Confidence 789999988888899999999999988776
No 123
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.63 E-value=7.1 Score=31.46 Aligned_cols=23 Identities=43% Similarity=1.003 Sum_probs=13.9
Q ss_pred CCcccccccccCCHHHHHHHHHHhcCCCCeeccccc
Q psy4576 311 KPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICG 346 (400)
Q Consensus 311 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 346 (400)
.+.|+.||..+ .++-|-+||+||
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 45666666542 345666777776
No 124
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=61.16 E-value=2.9 Score=22.91 Aligned_cols=9 Identities=22% Similarity=0.545 Sum_probs=4.6
Q ss_pred cccCCCCcc
Q psy4576 367 SHTCHLCPQ 375 (400)
Q Consensus 367 ~~~C~~C~~ 375 (400)
.|.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 355555543
No 125
>PF15269 zf-C2H2_7: Zinc-finger
Probab=60.87 E-value=5.9 Score=23.66 Aligned_cols=21 Identities=33% Similarity=0.784 Sum_probs=12.6
Q ss_pred ccccccccccCChHHHHHHhh
Q psy4576 122 YECSLCNESFENKKVLFRHLR 142 (400)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~ 142 (400)
|+|-.|..+...++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 556666666666666666654
No 126
>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=59.75 E-value=5.2 Score=30.32 Aligned_cols=29 Identities=10% Similarity=0.095 Sum_probs=17.8
Q ss_pred ccCcCccccCCHHHHHHHHHHcCCCCceecccccccccCh
Q psy4576 218 SCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHK 257 (400)
Q Consensus 218 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 257 (400)
.|+.||..|... +..|..|+.||..|.-.
T Consensus 11 ~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 666677666553 23566677777666544
No 127
>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=58.27 E-value=5.4 Score=30.81 Aligned_cols=27 Identities=37% Similarity=0.717 Sum_probs=15.0
Q ss_pred CcccccccccccCChHHHHHHhhhhcCCcc
Q psy4576 120 KLYECSLCNESFENKKVLFRHLRGKHGMKI 149 (400)
Q Consensus 120 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 149 (400)
....|-+||+.|+. |.+|++.|||..+
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34677777877775 4788888877664
No 128
>KOG2593|consensus
Probab=57.04 E-value=10 Score=35.33 Aligned_cols=16 Identities=19% Similarity=0.561 Sum_probs=7.8
Q ss_pred CCeecccccccccChh
Q psy4576 338 KPHCCEICGRSYSTAA 353 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~ 353 (400)
..|.|+.|.+.|+...
T Consensus 127 ~~Y~Cp~C~kkyt~Le 142 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLE 142 (436)
T ss_pred ccccCCccccchhhhH
Confidence 3455555555554433
No 129
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.47 E-value=8.7 Score=39.05 Aligned_cols=26 Identities=27% Similarity=0.775 Sum_probs=16.5
Q ss_pred ccccccccccCHHHHHHhHhhcCCCCCcccCCCCCCc
Q psy4576 159 VCHYCNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQ 195 (400)
Q Consensus 159 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~ 195 (400)
.|+.|+..+ ..|...+...|.+||+.
T Consensus 446 ~Cp~Cd~~l-----------t~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 446 ECPNCDSPL-----------TLHKATGQLRCHYCGYQ 471 (730)
T ss_pred cCCCCCcce-----------EEecCCCeeEeCCCCCC
Confidence 477777652 34555567788888753
No 130
>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=56.19 E-value=4 Score=34.50 Aligned_cols=29 Identities=28% Similarity=0.635 Sum_probs=17.9
Q ss_pred CcccccccccccCChHHHHHHhhhhcCCc
Q psy4576 120 KLYECSLCNESFENKKVLFRHLRGKHGMK 148 (400)
Q Consensus 120 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 148 (400)
..|.|++|+|.|.-..-...|+...|.+.
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 34777777777777777777777777654
No 131
>PRK04023 DNA polymerase II large subunit; Validated
Probab=55.80 E-value=11 Score=39.20 Aligned_cols=49 Identities=24% Similarity=0.526 Sum_probs=29.9
Q ss_pred ccccccccccccChhhHHHHHhhhcCCCCCcccccccccCCHHHHHHHHHHhcCCCCeecccccccccChhhHHHHHhhc
Q psy4576 283 EFICDVCGKSYVRKGALTEHHQREHQGKKPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 283 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
...|+.||... ..+.|+.||.. .+..+.|+.|+...
T Consensus 626 ~RfCpsCG~~t----------------~~frCP~CG~~---------------Te~i~fCP~CG~~~------------- 661 (1121)
T PRK04023 626 RRKCPSCGKET----------------FYRRCPFCGTH---------------TEPVYRCPRCGIEV------------- 661 (1121)
T ss_pred CccCCCCCCcC----------------CcccCCCCCCC---------------CCcceeCccccCcC-------------
Confidence 45788887662 22477778765 23457777774332
Q ss_pred CCCCcccCCCCccccC
Q psy4576 363 TGETSHTCHLCPQKFR 378 (400)
Q Consensus 363 ~~~~~~~C~~C~~~f~ 378 (400)
.++.|+.||..-.
T Consensus 662 ---~~y~CPKCG~El~ 674 (1121)
T PRK04023 662 ---EEDECEKCGREPT 674 (1121)
T ss_pred ---CCCcCCCCCCCCC
Confidence 2366888876533
No 132
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=53.99 E-value=11 Score=25.01 Aligned_cols=20 Identities=30% Similarity=0.549 Sum_probs=16.1
Q ss_pred CchHHHHHHhhhCCCCCCCC
Q psy4576 379 QRSSYTLHYKTHHPGVIPPK 398 (400)
Q Consensus 379 ~~~~l~~H~~~hh~~~~~~~ 398 (400)
....+..|++.+||+.|++.
T Consensus 24 ~Ye~Yv~H~~~~HP~~p~ms 43 (65)
T PF04328_consen 24 DYERYVEHMRRHHPDEPPMS 43 (65)
T ss_pred HHHHHHHHHHHHCcCCCCCC
Confidence 34667889999999998863
No 133
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=53.56 E-value=16 Score=32.84 Aligned_cols=24 Identities=38% Similarity=0.635 Sum_probs=17.0
Q ss_pred cccccccccccCChHHHHHHhhhh
Q psy4576 121 LYECSLCNESFENKKVLFRHLRGK 144 (400)
Q Consensus 121 ~~~C~~C~~~f~~~~~l~~H~~~~ 144 (400)
.+-|..|++.|.....+..|+...
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~gK 261 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLEGK 261 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHhhh
Confidence 366777887777777777777543
No 134
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=51.61 E-value=10 Score=38.53 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=5.5
Q ss_pred ccCCCCCCcc
Q psy4576 187 YQCDFCGSQQ 196 (400)
Q Consensus 187 ~~C~~C~~~f 196 (400)
..|..||..+
T Consensus 436 l~C~~Cg~v~ 445 (730)
T COG1198 436 LLCRDCGYIA 445 (730)
T ss_pred eecccCCCcc
Confidence 3566666543
No 135
>KOG1280|consensus
Probab=51.28 E-value=14 Score=33.24 Aligned_cols=36 Identities=22% Similarity=0.610 Sum_probs=21.1
Q ss_pred ccccccccccccChhhHHHHHhhhcCCCCC--cccccc
Q psy4576 283 EFICDVCGKSYVRKGALTEHHQREHQGKKP--VCTICG 318 (400)
Q Consensus 283 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~--~C~~C~ 318 (400)
.|.|++|+..=.+...|..|+...|..-.+ .|++|+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 466666666655666666666666655444 455554
No 136
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=50.77 E-value=16 Score=32.35 Aligned_cols=24 Identities=29% Similarity=0.665 Sum_probs=13.4
Q ss_pred CcccCCCCCCccCCHHHHHHHHHh
Q psy4576 185 KLYQCDFCGSQQRTKCRFYYHLRD 208 (400)
Q Consensus 185 ~~~~C~~C~~~f~~~~~l~~H~~~ 208 (400)
..|+|+.|...|-...+...|-..
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~L 410 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETL 410 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHH
Confidence 346666666666555555555433
No 137
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=49.92 E-value=2.9 Score=30.90 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=9.2
Q ss_pred cccccccccccCC
Q psy4576 121 LYECSLCNESFEN 133 (400)
Q Consensus 121 ~~~C~~C~~~f~~ 133 (400)
.+.|+.|+..+..
T Consensus 16 ~~~C~~C~~~~~~ 28 (104)
T TIGR01384 16 VYVCPSCGYEKEK 28 (104)
T ss_pred eEECcCCCCcccc
Confidence 5778888876553
No 138
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=49.81 E-value=6.3 Score=24.28 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=4.7
Q ss_pred cccccccccc
Q psy4576 159 VCHYCNRTFD 168 (400)
Q Consensus 159 ~C~~C~~~f~ 168 (400)
+|..|+.++.
T Consensus 3 ~C~~CgyvYd 12 (47)
T PF00301_consen 3 QCPVCGYVYD 12 (47)
T ss_dssp EETTTSBEEE
T ss_pred CCCCCCEEEc
Confidence 4444444443
No 139
>KOG2272|consensus
Probab=49.39 E-value=7.1 Score=33.24 Aligned_cols=13 Identities=31% Similarity=1.035 Sum_probs=9.5
Q ss_pred cccccccccccCh
Q psy4576 284 FICDVCGKSYVRK 296 (400)
Q Consensus 284 ~~C~~C~~~f~~~ 296 (400)
|.|..|.+.|...
T Consensus 222 FvCa~CekPFlGH 234 (332)
T KOG2272|consen 222 FVCAKCEKPFLGH 234 (332)
T ss_pred eeehhcCCcccch
Confidence 7788887777654
No 140
>KOG2593|consensus
Probab=49.28 E-value=9.9 Score=35.37 Aligned_cols=18 Identities=22% Similarity=0.604 Sum_probs=11.1
Q ss_pred CcccccccccccCChHHH
Q psy4576 120 KLYECSLCNESFENKKVL 137 (400)
Q Consensus 120 ~~~~C~~C~~~f~~~~~l 137 (400)
..|.|+.|.+.|.....+
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~ 144 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEAL 144 (436)
T ss_pred ccccCCccccchhhhHHH
Confidence 456666666666665544
No 141
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=49.05 E-value=1.9 Score=42.61 Aligned_cols=56 Identities=25% Similarity=0.496 Sum_probs=33.5
Q ss_pred ccccccccccChhhHHHHHhhhcCCCCC-cccccccccCCHHHHHHHHHHhcCCCCeecccccc
Q psy4576 285 ICDVCGKSYVRKGALTEHHQREHQGKKP-VCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGR 347 (400)
Q Consensus 285 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 347 (400)
.|..||-.|+-...|-.-. .......| .|+.|.+.|.+..+-+-|. .|..|+.||=
T Consensus 125 ~CT~CGPRfTIi~alPYDR-~nTsM~~F~lC~~C~~EY~dP~nRRfHA------Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDR-ENTSMADFPLCPFCDKEYKDPLNRRFHA------QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCc-ccCccccCcCCHHHHHHhcCcccccccc------ccccCcccCC
Confidence 4777777777666554442 22223333 7888877777665533332 4677888874
No 142
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=48.92 E-value=12 Score=28.56 Aligned_cols=24 Identities=13% Similarity=0.290 Sum_probs=15.4
Q ss_pred HHHHHhHhhcCCCCCcccCCCCCCccCCHH
Q psy4576 171 AKIQEHIISSHMHEKLYQCDFCGSQQRTKC 200 (400)
Q Consensus 171 ~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~ 200 (400)
..|+.|- ..|+ +||.|.-+|.+..
T Consensus 112 a~LWK~~-~~yp-----vCPvCkTSFKss~ 135 (140)
T PF05290_consen 112 ANLWKFC-NLYP-----VCPVCKTSFKSSS 135 (140)
T ss_pred HHHHHHc-ccCC-----CCCcccccccccc
Confidence 5666665 4555 6777777776643
No 143
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=47.54 E-value=1.6 Score=43.08 Aligned_cols=80 Identities=18% Similarity=0.369 Sum_probs=54.2
Q ss_pred ccccccccccccChhhHHHHHhhhcCCCCC-cccccccccCCHHHHHHHHHHhcCCCCe-ecccccccccChhhHHHHHh
Q psy4576 283 EFICDVCGKSYVRKGALTEHHQREHQGKKP-VCTICGKMLIDKRSLANHMNTHTGLKPH-CCEICGRSYSTAAYLKVHMS 360 (400)
Q Consensus 283 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~-~C~~C~~~f~~~~~L~~H~~ 360 (400)
.-.|+.|-+.+.++.+-+.+. +| .|..||-.|+-...|-.- |-++.-..| -|+.|.+.|.+..+-+-|.
T Consensus 101 ~a~C~~Cl~Ei~dp~~rrY~Y-------PF~~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfHA- 171 (750)
T COG0068 101 AATCEDCLEEIFDPNSRRYLY-------PFINCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFHA- 171 (750)
T ss_pred hhhhHHHHHHhcCCCCcceec-------cccccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCcccccccc-
Confidence 357888887766665433222 34 899999999876655322 123333444 4999999999988876664
Q ss_pred hcCCCCcccCCCCccc
Q psy4576 361 CHTGETSHTCHLCPQK 376 (400)
Q Consensus 361 ~h~~~~~~~C~~C~~~ 376 (400)
.|..|+.||=.
T Consensus 172 -----Qp~aCp~CGP~ 182 (750)
T COG0068 172 -----QPIACPKCGPH 182 (750)
T ss_pred -----ccccCcccCCC
Confidence 46789999953
No 144
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.39 E-value=21 Score=37.33 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=4.8
Q ss_pred ccCCCCCCc
Q psy4576 187 YQCDFCGSQ 195 (400)
Q Consensus 187 ~~C~~C~~~ 195 (400)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 455555544
No 145
>KOG2807|consensus
Probab=46.92 E-value=30 Score=31.00 Aligned_cols=36 Identities=19% Similarity=0.422 Sum_probs=24.3
Q ss_pred CCcccCcCccccCCHHHHHHHHHHcCCCCceecccccccccChhHHhhhH
Q psy4576 215 ANLSCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTYCHKPNLTNHI 264 (400)
Q Consensus 215 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 264 (400)
..|.|+.|....- .-|..|+.|+-+......|.+-.
T Consensus 275 ~Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 275 GGYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred CceeCCcccCeee--------------cCCccCCccceeEecchHHHHHH
Confidence 4577777765432 25678888888887777776544
No 146
>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=46.84 E-value=8.8 Score=19.81 Aligned_cols=8 Identities=25% Similarity=0.737 Sum_probs=4.4
Q ss_pred cccCCCCc
Q psy4576 367 SHTCHLCP 374 (400)
Q Consensus 367 ~~~C~~C~ 374 (400)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45555555
No 147
>KOG2071|consensus
Probab=46.71 E-value=15 Score=35.74 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=20.0
Q ss_pred cccccccccCCHHHHHHHHHHhc
Q psy4576 313 VCTICGKMLIDKRSLANHMNTHT 335 (400)
Q Consensus 313 ~C~~C~~~f~~~~~l~~H~~~h~ 335 (400)
+|..||..|........||..|.
T Consensus 420 qC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 420 QCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred hhcccccccccchhhhhHhhhhh
Confidence 89999999999988888887664
No 148
>PF14353 CpXC: CpXC protein
Probab=46.23 E-value=11 Score=28.97 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=13.0
Q ss_pred ceecccccccccChhHHhhhH
Q psy4576 244 NYQCYYCRKTYCHKPNLTNHI 264 (400)
Q Consensus 244 ~~~C~~C~~~f~~~~~l~~H~ 264 (400)
.+.|+.||..|.-...+.-|-
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred EEECCCCCCceecCCCEEEEc
Confidence 466777776666555555553
No 149
>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=46.13 E-value=18 Score=22.06 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=5.3
Q ss_pred CcccCCCCcc
Q psy4576 366 TSHTCHLCPQ 375 (400)
Q Consensus 366 ~~~~C~~C~~ 375 (400)
..|+|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 4455655543
No 150
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=45.30 E-value=14 Score=32.56 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=17.1
Q ss_pred CCeecccccccccChhhHHHHHhhc
Q psy4576 338 KPHCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
..|+|+.|...|-..-....|...|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 4577777777777666666676555
No 151
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=44.64 E-value=13 Score=21.32 Aligned_cols=12 Identities=17% Similarity=0.495 Sum_probs=6.4
Q ss_pred cccCCCCccccC
Q psy4576 367 SHTCHLCPQKFR 378 (400)
Q Consensus 367 ~~~C~~C~~~f~ 378 (400)
.=.|+.||-.+.
T Consensus 21 ~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 21 EGVCDNCGGELV 32 (36)
T ss_dssp TTBCTTTTEBEB
T ss_pred CCccCCCCCeeE
Confidence 345666665443
No 152
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=42.87 E-value=9.8 Score=23.79 Aligned_cols=11 Identities=36% Similarity=1.084 Sum_probs=5.4
Q ss_pred ccccccccccc
Q psy4576 284 FICDVCGKSYV 294 (400)
Q Consensus 284 ~~C~~C~~~f~ 294 (400)
|+|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 44555554444
No 153
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.37 E-value=11 Score=29.34 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=6.0
Q ss_pred eeccccccccc
Q psy4576 340 HCCEICGRSYS 350 (400)
Q Consensus 340 ~~C~~C~~~f~ 350 (400)
+.|..||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 55555555554
No 154
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=41.28 E-value=6.5 Score=21.11 Aligned_cols=9 Identities=33% Similarity=1.028 Sum_probs=3.9
Q ss_pred ecccccccc
Q psy4576 246 QCYYCRKTY 254 (400)
Q Consensus 246 ~C~~C~~~f 254 (400)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344444444
No 155
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=41.28 E-value=25 Score=31.73 Aligned_cols=22 Identities=27% Similarity=0.692 Sum_probs=18.9
Q ss_pred CcccCcCccccCCHHHHHHHHH
Q psy4576 216 NLSCEFCSRIFTKKELLRSHLA 237 (400)
Q Consensus 216 ~~~C~~C~~~f~~~~~l~~H~~ 237 (400)
.+.|+.|++-|.....+..|+.
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHh
Confidence 3689999999999888988874
No 156
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=41.28 E-value=16 Score=34.79 Aligned_cols=26 Identities=31% Similarity=0.648 Sum_probs=13.3
Q ss_pred ccCCCCccccCCchHHHHHHhhhCCC
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKTHHPG 393 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~hh~~ 393 (400)
..|+.|.+.|.....+..|+...|.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 34555555555555555555544443
No 157
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=40.04 E-value=15 Score=28.20 Aligned_cols=13 Identities=31% Similarity=0.856 Sum_probs=7.4
Q ss_pred ccccccccccCCh
Q psy4576 122 YECSLCNESFENK 134 (400)
Q Consensus 122 ~~C~~C~~~f~~~ 134 (400)
++|..|++.|.+.
T Consensus 2 H~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 2 HQCTKCGRVFEDG 14 (131)
T ss_pred cccCcCCCCcCCC
Confidence 4566666666543
No 158
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=39.04 E-value=22 Score=22.13 Aligned_cols=16 Identities=19% Similarity=0.331 Sum_probs=8.6
Q ss_pred ccccCcccccccChhH
Q psy4576 92 EERCRSCGLLSGSITQ 107 (400)
Q Consensus 92 ~~~C~~C~~~f~~~~~ 107 (400)
.+.|..||..|.-...
T Consensus 4 ~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAG 19 (49)
T ss_pred eEEcccCCCeEEEehh
Confidence 4556666666544433
No 159
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=38.17 E-value=27 Score=20.71 Aligned_cols=24 Identities=21% Similarity=0.581 Sum_probs=17.4
Q ss_pred cccCcccccccC--hhHHHHHHhhhcC
Q psy4576 93 ERCRSCGLLSGS--ITQTYIHYLECKN 117 (400)
Q Consensus 93 ~~C~~C~~~f~~--~~~l~~H~~~~h~ 117 (400)
-.|+.|+..|.. ..+-..| .+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H-~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLH-KKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHH-HHHHh
Confidence 489999999854 5666777 66553
No 160
>KOG4167|consensus
Probab=38.07 E-value=8.8 Score=38.12 Aligned_cols=25 Identities=24% Similarity=0.493 Sum_probs=23.3
Q ss_pred CeecccccccccChhhHHHHHhhcC
Q psy4576 339 PHCCEICGRSYSTAAYLKVHMSCHT 363 (400)
Q Consensus 339 ~~~C~~C~~~f~~~~~L~~H~~~h~ 363 (400)
-|.|..|++.|....++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3999999999999999999999985
No 161
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=37.98 E-value=20 Score=25.26 Aligned_cols=10 Identities=20% Similarity=0.949 Sum_probs=4.3
Q ss_pred eecccccccc
Q psy4576 245 YQCYYCRKTY 254 (400)
Q Consensus 245 ~~C~~C~~~f 254 (400)
+.|..|+..|
T Consensus 54 W~C~kCg~~f 63 (89)
T COG1997 54 WKCRKCGAKF 63 (89)
T ss_pred EEcCCCCCee
Confidence 4444444443
No 162
>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=37.10 E-value=21 Score=34.92 Aligned_cols=18 Identities=33% Similarity=0.820 Sum_probs=11.2
Q ss_pred hcCCCCCcccCCCCCCcc
Q psy4576 179 SSHMHEKLYQCDFCGSQQ 196 (400)
Q Consensus 179 ~~H~~~~~~~C~~C~~~f 196 (400)
..|.......|.+||+..
T Consensus 233 ~~h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 233 TYHKKEGKLRCHYCGYQE 250 (505)
T ss_pred EEecCCCeEEcCCCcCcC
Confidence 344555667788887543
No 163
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=36.55 E-value=20 Score=25.36 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=5.9
Q ss_pred ccCcccccccC
Q psy4576 94 RCRSCGLLSGS 104 (400)
Q Consensus 94 ~C~~C~~~f~~ 104 (400)
.|..||+.|.+
T Consensus 60 ~CkkCGfef~~ 70 (97)
T COG3357 60 RCKKCGFEFRD 70 (97)
T ss_pred hhcccCccccc
Confidence 55555555544
No 164
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.59 E-value=21 Score=33.55 Aligned_cols=33 Identities=27% Similarity=0.626 Sum_probs=22.3
Q ss_pred CCCcccccccccCCHHHHHHHHHHhcCCCCeecccccccccChh
Q psy4576 310 KKPVCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSYSTAA 353 (400)
Q Consensus 310 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 353 (400)
..|.|+.||.+..+. |..-|+|+.||+.+....
T Consensus 349 ~~p~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 349 VNPVCPRCGGRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred cCCCCCccCCchhhc-----------CCCCcccccccccCCccc
Confidence 456788888764332 334788888888876544
No 165
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=35.05 E-value=19 Score=22.54 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=6.8
Q ss_pred CCeecccccccc
Q psy4576 338 KPHCCEICGRSY 349 (400)
Q Consensus 338 ~~~~C~~C~~~f 349 (400)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 346666666554
No 166
>KOG4167|consensus
Probab=35.00 E-value=9.5 Score=37.89 Aligned_cols=25 Identities=32% Similarity=0.507 Sum_probs=23.2
Q ss_pred cccCCCCccccCCchHHHHHHhhhC
Q psy4576 367 SHTCHLCPQKFRQRSSYTLHYKTHH 391 (400)
Q Consensus 367 ~~~C~~C~~~f~~~~~l~~H~~~hh 391 (400)
.|.|..|++.|.....+..||++|-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999984
No 167
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.41 E-value=38 Score=36.47 Aligned_cols=12 Identities=33% Similarity=0.913 Sum_probs=7.6
Q ss_pred cccCCCCCCccC
Q psy4576 186 LYQCDFCGSQQR 197 (400)
Q Consensus 186 ~~~C~~C~~~f~ 197 (400)
.|.|+.||....
T Consensus 692 vy~CPsCGaev~ 703 (1337)
T PRK14714 692 VYVCPDCGAEVP 703 (1337)
T ss_pred ceeCccCCCccC
Confidence 467777776543
No 168
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=33.70 E-value=20 Score=27.10 Aligned_cols=11 Identities=36% Similarity=0.625 Sum_probs=5.4
Q ss_pred eeccccccccc
Q psy4576 340 HCCEICGRSYS 350 (400)
Q Consensus 340 ~~C~~C~~~f~ 350 (400)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 44555554443
No 169
>KOG3408|consensus
Probab=33.56 E-value=25 Score=26.39 Aligned_cols=25 Identities=28% Similarity=0.429 Sum_probs=19.9
Q ss_pred CCCeecccccccccChhhHHHHHhh
Q psy4576 337 LKPHCCEICGRSYSTAAYLKVHMSC 361 (400)
Q Consensus 337 ~~~~~C~~C~~~f~~~~~L~~H~~~ 361 (400)
...|.|-.|.+-|.+...|..|.++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 3558888888888888888888754
No 170
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=33.52 E-value=21 Score=26.82 Aligned_cols=11 Identities=18% Similarity=0.398 Sum_probs=5.4
Q ss_pred eeccccccccc
Q psy4576 340 HCCEICGRSYS 350 (400)
Q Consensus 340 ~~C~~C~~~f~ 350 (400)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 45555554443
No 171
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=32.84 E-value=15 Score=29.08 Aligned_cols=33 Identities=24% Similarity=0.625 Sum_probs=20.9
Q ss_pred cCCccccccccccccChhhHHHHHhhhcCCCCCcccccccccC
Q psy4576 280 LKREFICDVCGKSYVRKGALTEHHQREHQGKKPVCTICGKMLI 322 (400)
Q Consensus 280 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~ 322 (400)
+...|.|..||.... ..+.+.-+.|+.|+....
T Consensus 109 g~G~l~C~~Cg~~~~----------~~~~~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE----------LTHPERLPPCPKCGHTEF 141 (146)
T ss_pred cCceEecccCCCEEE----------ecCCCcCCCCCCCCCCee
Confidence 445688888886542 234555668888886543
No 172
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=32.38 E-value=22 Score=28.00 Aligned_cols=34 Identities=29% Similarity=0.664 Sum_probs=20.6
Q ss_pred CCeecccccccccChhhHHHHHhhcCCCCcccCCCCccc
Q psy4576 338 KPHCCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQK 376 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~ 376 (400)
-+|.|. |+..|.+ .++|-.+-.|+ .|.|..|+-.
T Consensus 116 ~~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccch---hhhcccccccc-eEEeccCCce
Confidence 457777 7776543 33454444555 6778777643
No 173
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.02 E-value=21 Score=26.13 Aligned_cols=12 Identities=33% Similarity=0.656 Sum_probs=5.1
Q ss_pred CCeecccccccc
Q psy4576 338 KPHCCEICGRSY 349 (400)
Q Consensus 338 ~~~~C~~C~~~f 349 (400)
.|..|+.||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 344444444444
No 174
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=31.82 E-value=28 Score=33.26 Aligned_cols=26 Identities=19% Similarity=0.517 Sum_probs=21.7
Q ss_pred ccccccccccCHHHHHHhHhhcCCCC
Q psy4576 159 VCHYCNRTFDSKAKIQEHIISSHMHE 184 (400)
Q Consensus 159 ~C~~C~~~f~~~~~l~~H~~~~H~~~ 184 (400)
.|+.|.+.|.+...+..|+...|.+.
T Consensus 59 iCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 59 ICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eCCcccceeCCHHHHHHHHHHhhhhh
Confidence 78888888888888888888788654
No 175
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=31.63 E-value=15 Score=23.45 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=5.5
Q ss_pred cccCcCcccc
Q psy4576 217 LSCEFCSRIF 226 (400)
Q Consensus 217 ~~C~~C~~~f 226 (400)
+.|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 3566666544
No 176
>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=31.15 E-value=24 Score=21.09 Aligned_cols=8 Identities=25% Similarity=0.671 Sum_probs=3.3
Q ss_pred cccccccc
Q psy4576 122 YECSLCNE 129 (400)
Q Consensus 122 ~~C~~C~~ 129 (400)
+.|+.||.
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 44555543
No 177
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=31.11 E-value=20 Score=22.51 Aligned_cols=25 Identities=16% Similarity=0.372 Sum_probs=12.6
Q ss_pred CCeecccccccccChhhHHHHHhhc
Q psy4576 338 KPHCCEICGRSYSTAAYLKVHMSCH 362 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~~L~~H~~~h 362 (400)
..|+|+.|+..|=..=.+-.|..+|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 4577888777777666666665554
No 178
>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=30.88 E-value=27 Score=23.30 Aligned_cols=25 Identities=40% Similarity=0.769 Sum_probs=9.2
Q ss_pred cccccccccCCHHHHHHHHHHhcCCCCeecccccccc
Q psy4576 313 VCTICGKMLIDKRSLANHMNTHTGLKPHCCEICGRSY 349 (400)
Q Consensus 313 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 349 (400)
.|..|++.|.. -.+.+.|..||..|
T Consensus 11 ~C~~C~~~F~~------------~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 11 NCMICGKKFSL------------FRRRHHCRNCGRVV 35 (69)
T ss_dssp B-TTT--B-BS------------SS-EEE-TTT--EE
T ss_pred cCcCcCCcCCC------------ceeeEccCCCCCEE
Confidence 56667776642 12455666666554
No 179
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.03 E-value=30 Score=20.61 Aligned_cols=12 Identities=33% Similarity=1.074 Sum_probs=5.7
Q ss_pred ecccccccccCh
Q psy4576 341 CCEICGRSYSTA 352 (400)
Q Consensus 341 ~C~~C~~~f~~~ 352 (400)
.|..|++.|+..
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 345555555443
No 180
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=29.68 E-value=32 Score=24.93 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=5.5
Q ss_pred ccCcccccccC
Q psy4576 94 RCRSCGLLSGS 104 (400)
Q Consensus 94 ~C~~C~~~f~~ 104 (400)
+|..||..|.+
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 45555555544
No 181
>KOG1842|consensus
Probab=29.26 E-value=30 Score=32.45 Aligned_cols=28 Identities=18% Similarity=0.462 Sum_probs=19.9
Q ss_pred ccccccccccccCHHHHHHhHhhcCCCC
Q psy4576 157 KCVCHYCNRTFDSKAKIQEHIISSHMHE 184 (400)
Q Consensus 157 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 184 (400)
.|.||+|...|.+...|..|+...|.++
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 4567777777777777777776677654
No 182
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=29.25 E-value=30 Score=22.02 Aligned_cols=25 Identities=24% Similarity=0.655 Sum_probs=14.0
Q ss_pred ccCcCccccCCHHHHHHHHHHcCCCCceecccccccc
Q psy4576 218 SCEFCSRIFTKKELLRSHLAVHKIGKNYQCYYCRKTY 254 (400)
Q Consensus 218 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 254 (400)
.|+.|+..|... +....|+.|+..+
T Consensus 7 ~C~~Cg~~~~~~------------dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKKFKDG------------DDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCcccCC------------CCEEECCCCCCcc
Confidence 566666666542 2345666666554
No 183
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.70 E-value=16 Score=26.37 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=6.3
Q ss_pred ccCCCCccccC
Q psy4576 368 HTCHLCPQKFR 378 (400)
Q Consensus 368 ~~C~~C~~~f~ 378 (400)
..|..||.+|.
T Consensus 47 ~~Cg~CGls~e 57 (104)
T COG4888 47 AVCGNCGLSFE 57 (104)
T ss_pred EEcccCcceEE
Confidence 45666665554
No 184
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=28.61 E-value=20 Score=26.93 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=7.3
Q ss_pred CcccCcCccccCCH
Q psy4576 216 NLSCEFCSRIFTKK 229 (400)
Q Consensus 216 ~~~C~~C~~~f~~~ 229 (400)
.+.|..|+..|...
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 70 RARCRDCGHEFEPD 83 (113)
T ss_dssp EEEETTTS-EEECH
T ss_pred cEECCCCCCEEecC
Confidence 34566666666544
No 185
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=28.53 E-value=27 Score=20.53 Aligned_cols=31 Identities=26% Similarity=0.700 Sum_probs=12.6
Q ss_pred cccCcccccccChhHHHHHHhhhcCCCCcccccccccc
Q psy4576 93 ERCRSCGLLSGSITQTYIHYLECKNRGKLYECSLCNES 130 (400)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~ 130 (400)
.+|..|+..++-. .....+.+.+.|.+|+..
T Consensus 3 ~rC~~C~aylNp~-------~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPF-------CQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TT-------SEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCc-------ceEcCCCCEEECcCCCCc
Confidence 4566665544433 222234556777777653
No 186
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.91 E-value=16 Score=30.91 Aligned_cols=39 Identities=15% Similarity=0.428 Sum_probs=21.3
Q ss_pred CCeecccccccccChhhHHHHHhhcCCC----------Cc-----ccCCCCccc
Q psy4576 338 KPHCCEICGRSYSTAAYLKVHMSCHTGE----------TS-----HTCHLCPQK 376 (400)
Q Consensus 338 ~~~~C~~C~~~f~~~~~L~~H~~~h~~~----------~~-----~~C~~C~~~ 376 (400)
+.+.||+|+..|.....+.--.|+-.|+ .| ..||.|.++
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yA 71 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYA 71 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHH
Confidence 4566777776666544433333333222 12 379999865
No 187
>KOG4124|consensus
Probab=27.88 E-value=9.3 Score=34.31 Aligned_cols=28 Identities=18% Similarity=0.196 Sum_probs=20.9
Q ss_pred cccccccC--cccccccChhHHHHHHhhhc
Q psy4576 89 VWDEERCR--SCGLLSGSITQTYIHYLECK 116 (400)
Q Consensus 89 ~~~~~~C~--~C~~~f~~~~~l~~H~~~~h 116 (400)
..++|+|+ .|.+.++...+|..|....|
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h 375 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGH 375 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCc
Confidence 45778885 48898888888888855555
No 188
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.70 E-value=28 Score=26.36 Aligned_cols=11 Identities=18% Similarity=0.628 Sum_probs=5.2
Q ss_pred eeccccccccc
Q psy4576 340 HCCEICGRSYS 350 (400)
Q Consensus 340 ~~C~~C~~~f~ 350 (400)
+.|..||..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 44555554443
No 189
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=27.61 E-value=37 Score=26.07 Aligned_cols=23 Identities=30% Similarity=0.509 Sum_probs=13.1
Q ss_pred eecccccccccChhhHHHHHhhcCCC
Q psy4576 340 HCCEICGRSYSTAAYLKVHMSCHTGE 365 (400)
Q Consensus 340 ~~C~~C~~~f~~~~~L~~H~~~h~~~ 365 (400)
..|-.+|+.|. +|.+|+.+|.|-
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCC
Confidence 45666666664 356666665543
No 190
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=27.51 E-value=45 Score=18.77 Aligned_cols=21 Identities=19% Similarity=0.441 Sum_probs=11.3
Q ss_pred ccCCCCccccCCchHHHHHHhh
Q psy4576 368 HTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 368 ~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
+.|+.|++... .+.+..|+..
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLek 25 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLEK 25 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHHH
T ss_pred EECCCCcCCcc-hhhhHHHHHH
Confidence 56666666543 3446666544
No 191
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=27.37 E-value=28 Score=20.50 Aligned_cols=16 Identities=19% Similarity=0.576 Sum_probs=8.1
Q ss_pred ccccccccccCHHHHH
Q psy4576 159 VCHYCNRTFDSKAKIQ 174 (400)
Q Consensus 159 ~C~~C~~~f~~~~~l~ 174 (400)
.|+.|+-.+.+..+|.
T Consensus 21 ~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 21 VCPSCGGIWFDAGELE 36 (41)
T ss_pred ECCCCCeEEccHHHHH
Confidence 4555555555444443
No 192
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=27.24 E-value=28 Score=20.38 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=9.8
Q ss_pred cccCCCCccccCC
Q psy4576 367 SHTCHLCPQKFRQ 379 (400)
Q Consensus 367 ~~~C~~C~~~f~~ 379 (400)
||+|..|+..|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 6888888877754
No 193
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=26.65 E-value=75 Score=20.33 Aligned_cols=18 Identities=17% Similarity=0.820 Sum_probs=10.5
Q ss_pred ccccccccccCHHHHHHh
Q psy4576 159 VCHYCNRTFDSKAKIQEH 176 (400)
Q Consensus 159 ~C~~C~~~f~~~~~l~~H 176 (400)
-|-.|+..|.+...|..+
T Consensus 29 YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDLERN 46 (55)
T ss_pred eeeeeCCccCCHHHHHhC
Confidence 466666666666665543
No 194
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=26.30 E-value=31 Score=18.67 Aligned_cols=10 Identities=20% Similarity=0.401 Sum_probs=3.4
Q ss_pred cccCCCCccc
Q psy4576 367 SHTCHLCPQK 376 (400)
Q Consensus 367 ~~~C~~C~~~ 376 (400)
.|.|.+|++.
T Consensus 15 ~Y~C~~Cdf~ 24 (30)
T PF07649_consen 15 FYRCSECDFD 24 (30)
T ss_dssp EEE-TTT---
T ss_pred eEECccCCCc
Confidence 4556666544
No 195
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.22 E-value=43 Score=34.06 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=8.9
Q ss_pred CCCCCcccCCCCCC
Q psy4576 181 HMHEKLYQCDFCGS 194 (400)
Q Consensus 181 H~~~~~~~C~~C~~ 194 (400)
|.......|.+||+
T Consensus 405 h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 405 PSAGGTPRCRWCGR 418 (665)
T ss_pred ecCCCeeECCCCcC
Confidence 34445677888875
No 196
>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=25.66 E-value=40 Score=33.03 Aligned_cols=13 Identities=23% Similarity=0.462 Sum_probs=6.7
Q ss_pred CCCCeeccccccc
Q psy4576 336 GLKPHCCEICGRS 348 (400)
Q Consensus 336 ~~~~~~C~~C~~~ 348 (400)
......|..||+.
T Consensus 237 ~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 237 KEGKLRCHYCGYQ 249 (505)
T ss_pred CCCeEEcCCCcCc
Confidence 3344556666544
No 197
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=25.65 E-value=11 Score=22.23 Aligned_cols=10 Identities=20% Similarity=0.810 Sum_probs=6.5
Q ss_pred ccCCCCcccc
Q psy4576 368 HTCHLCPQKF 377 (400)
Q Consensus 368 ~~C~~C~~~f 377 (400)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6676676654
No 198
>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=25.02 E-value=46 Score=21.04 Aligned_cols=13 Identities=38% Similarity=1.071 Sum_probs=7.0
Q ss_pred CCeeccccccccc
Q psy4576 338 KPHCCEICGRSYS 350 (400)
Q Consensus 338 ~~~~C~~C~~~f~ 350 (400)
+.+.|..||+.|-
T Consensus 17 rk~~Cr~Cg~~~C 29 (57)
T cd00065 17 RRHHCRNCGRIFC 29 (57)
T ss_pred cccccCcCcCCcC
Confidence 3455666665543
No 199
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.91 E-value=43 Score=34.23 Aligned_cols=15 Identities=33% Similarity=0.857 Sum_probs=8.7
Q ss_pred CCCCCcccCCCCCCc
Q psy4576 181 HMHEKLYQCDFCGSQ 195 (400)
Q Consensus 181 H~~~~~~~C~~C~~~ 195 (400)
|.......|..||+.
T Consensus 403 h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 403 HRFQRRLRCHHCGYQ 417 (679)
T ss_pred ECCCCeEECCCCcCC
Confidence 334455667777654
No 200
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.60 E-value=52 Score=21.02 Aligned_cols=10 Identities=20% Similarity=0.484 Sum_probs=4.8
Q ss_pred cccCCCCccc
Q psy4576 367 SHTCHLCPQK 376 (400)
Q Consensus 367 ~~~C~~C~~~ 376 (400)
.|.|+.||..
T Consensus 14 ~~~Cp~cGip 23 (55)
T PF13824_consen 14 NFECPDCGIP 23 (55)
T ss_pred CCcCCCCCCc
Confidence 3455555543
No 201
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.52 E-value=17 Score=25.42 Aligned_cols=10 Identities=20% Similarity=0.305 Sum_probs=2.9
Q ss_pred ccccccCccc
Q psy4576 90 WDEERCRSCG 99 (400)
Q Consensus 90 ~~~~~C~~C~ 99 (400)
++.|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 3456666666
No 202
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.40 E-value=54 Score=20.76 Aligned_cols=11 Identities=27% Similarity=0.860 Sum_probs=5.0
Q ss_pred eeccccccccc
Q psy4576 340 HCCEICGRSYS 350 (400)
Q Consensus 340 ~~C~~C~~~f~ 350 (400)
++|+.||..|.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 44444444443
No 203
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=24.33 E-value=41 Score=24.00 Aligned_cols=10 Identities=40% Similarity=0.992 Sum_probs=4.5
Q ss_pred eecccccccc
Q psy4576 245 YQCYYCRKTY 254 (400)
Q Consensus 245 ~~C~~C~~~f 254 (400)
+.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PTZ00255 55 WRCKGCKKTV 64 (90)
T ss_pred EEcCCCCCEE
Confidence 4444444444
No 204
>PF12773 DZR: Double zinc ribbon
Probab=24.04 E-value=44 Score=20.52 Aligned_cols=10 Identities=20% Similarity=0.643 Sum_probs=5.0
Q ss_pred ccCcCccccC
Q psy4576 218 SCEFCSRIFT 227 (400)
Q Consensus 218 ~C~~C~~~f~ 227 (400)
.|+.||....
T Consensus 14 fC~~CG~~l~ 23 (50)
T PF12773_consen 14 FCPHCGTPLP 23 (50)
T ss_pred CChhhcCChh
Confidence 4555555443
No 205
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.99 E-value=29 Score=26.15 Aligned_cols=10 Identities=30% Similarity=0.707 Sum_probs=4.9
Q ss_pred eecccccccc
Q psy4576 340 HCCEICGRSY 349 (400)
Q Consensus 340 ~~C~~C~~~f 349 (400)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4455555443
No 206
>KOG3408|consensus
Probab=23.90 E-value=46 Score=25.07 Aligned_cols=26 Identities=27% Similarity=0.543 Sum_probs=22.9
Q ss_pred CCCcccCCCCccccCCchHHHHHHhh
Q psy4576 364 GETSHTCHLCPQKFRQRSSYTLHYKT 389 (400)
Q Consensus 364 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 389 (400)
|...|-|-.|.+-|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 34469999999999999999999876
No 207
>KOG0717|consensus
Probab=23.88 E-value=42 Score=31.78 Aligned_cols=22 Identities=36% Similarity=0.685 Sum_probs=16.2
Q ss_pred ccccccccccCChHHHHHHhhh
Q psy4576 122 YECSLCNESFENKKVLFRHLRG 143 (400)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~~ 143 (400)
+.|.+|+++|.+...|..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6777777777777777777654
No 208
>KOG2907|consensus
Probab=23.53 E-value=40 Score=24.99 Aligned_cols=10 Identities=30% Similarity=1.045 Sum_probs=4.6
Q ss_pred eecccccccc
Q psy4576 245 YQCYYCRKTY 254 (400)
Q Consensus 245 ~~C~~C~~~f 254 (400)
|.|+.|++.|
T Consensus 103 YTC~kC~~k~ 112 (116)
T KOG2907|consen 103 YTCPKCKYKF 112 (116)
T ss_pred EEcCccceee
Confidence 4444444444
No 209
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.49 E-value=36 Score=17.75 Aligned_cols=7 Identities=29% Similarity=0.781 Sum_probs=3.6
Q ss_pred ccCcCcc
Q psy4576 218 SCEFCSR 224 (400)
Q Consensus 218 ~C~~C~~ 224 (400)
.|+.||.
T Consensus 18 fC~~CG~ 24 (26)
T PF13248_consen 18 FCPNCGA 24 (26)
T ss_pred cChhhCC
Confidence 4555554
No 210
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=23.32 E-value=6.8 Score=35.74 Aligned_cols=42 Identities=19% Similarity=0.449 Sum_probs=17.5
Q ss_pred ccccccccccccCHHHHH---HhHhhcCCC-CCcccCCCCCCccCC
Q psy4576 157 KCVCHYCNRTFDSKAKIQ---EHIISSHMH-EKLYQCDFCGSQQRT 198 (400)
Q Consensus 157 ~~~C~~C~~~f~~~~~l~---~H~~~~H~~-~~~~~C~~C~~~f~~ 198 (400)
.+.|..|.+........- .|....|.. .+-|+|..|++...+
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEE
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeee
Confidence 346888877766555443 233233322 344778888776544
No 211
>COG1773 Rubredoxin [Energy production and conversion]
Probab=23.20 E-value=35 Score=21.79 Aligned_cols=12 Identities=17% Similarity=0.645 Sum_probs=7.0
Q ss_pred cccCCCCccccC
Q psy4576 367 SHTCHLCPQKFR 378 (400)
Q Consensus 367 ~~~C~~C~~~f~ 378 (400)
.|+|..||+.|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 356666666553
No 212
>KOG2636|consensus
Probab=23.10 E-value=54 Score=30.84 Aligned_cols=27 Identities=30% Similarity=0.429 Sum_probs=22.6
Q ss_pred HhcCCCCeeccccc-ccccChhhHHHHH
Q psy4576 333 THTGLKPHCCEICG-RSYSTAAYLKVHM 359 (400)
Q Consensus 333 ~h~~~~~~~C~~C~-~~f~~~~~L~~H~ 359 (400)
.|.=...|.|.+|| +++.-+..+.+|.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHh
Confidence 35556779999999 8999999999995
No 213
>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=23.06 E-value=30 Score=20.71 Aligned_cols=14 Identities=21% Similarity=0.572 Sum_probs=8.1
Q ss_pred CcccCCCCccccCC
Q psy4576 366 TSHTCHLCPQKFRQ 379 (400)
Q Consensus 366 ~~~~C~~C~~~f~~ 379 (400)
.||.|+.|+..|=.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 46888888887743
No 214
>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=23.04 E-value=50 Score=21.98 Aligned_cols=12 Identities=25% Similarity=0.650 Sum_probs=6.9
Q ss_pred CCeecccccccc
Q psy4576 338 KPHCCEICGRSY 349 (400)
Q Consensus 338 ~~~~C~~C~~~f 349 (400)
+.|.|+.||..+
T Consensus 45 r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 45 RVFTCPNCGFEM 56 (69)
T ss_pred ceEEcCCCCCEE
Confidence 446666666553
No 215
>KOG2636|consensus
Probab=23.03 E-value=64 Score=30.38 Aligned_cols=31 Identities=19% Similarity=0.511 Sum_probs=25.7
Q ss_pred hhhcCCCCcccccccc-cccCChHHHHHHhhh
Q psy4576 113 LECKNRGKLYECSLCN-ESFENKKVLFRHLRG 143 (400)
Q Consensus 113 ~~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~~ 143 (400)
-+.|.-+..|.|.+|| +++.-+..+.+|...
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~E 424 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHFNE 424 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHhHH
Confidence 5567778889999998 889999999998763
No 216
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.75 E-value=41 Score=20.83 Aligned_cols=10 Identities=20% Similarity=0.514 Sum_probs=4.7
Q ss_pred ccCCCCcccc
Q psy4576 368 HTCHLCPQKF 377 (400)
Q Consensus 368 ~~C~~C~~~f 377 (400)
|.|+.||+.+
T Consensus 21 ~vC~~Cg~~~ 30 (52)
T smart00661 21 FVCRKCGYEE 30 (52)
T ss_pred EECCcCCCeE
Confidence 4444444443
No 217
>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=22.73 E-value=24 Score=25.18 Aligned_cols=10 Identities=30% Similarity=1.059 Sum_probs=4.3
Q ss_pred eecccccccc
Q psy4576 245 YQCYYCRKTY 254 (400)
Q Consensus 245 ~~C~~C~~~f 254 (400)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (90)
T PF01780_consen 54 WKCKKCGKKF 63 (90)
T ss_dssp EEETTTTEEE
T ss_pred eecCCCCCEE
Confidence 4444444433
No 218
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=22.62 E-value=28 Score=27.79 Aligned_cols=10 Identities=20% Similarity=0.527 Sum_probs=5.8
Q ss_pred ccCCCCcccc
Q psy4576 368 HTCHLCPQKF 377 (400)
Q Consensus 368 ~~C~~C~~~f 377 (400)
|.|..|+-.+
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 6666666444
No 219
>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=21.72 E-value=39 Score=24.18 Aligned_cols=11 Identities=18% Similarity=0.733 Sum_probs=5.1
Q ss_pred ceecccccccc
Q psy4576 244 NYQCYYCRKTY 254 (400)
Q Consensus 244 ~~~C~~C~~~f 254 (400)
.+.|..|++.|
T Consensus 53 IW~C~~C~~~~ 63 (91)
T TIGR00280 53 IWTCRKCGAKF 63 (91)
T ss_pred EEEcCCCCCEE
Confidence 34444454444
No 220
>KOG4377|consensus
Probab=21.66 E-value=39 Score=31.29 Aligned_cols=129 Identities=19% Similarity=0.375 Sum_probs=0.0
Q ss_pred cccccccChhHHHHHHhhhcCCCCcccc--cccccccCChHHHHHHhhhhcCCcccccCC----CCcccc--cccccccc
Q psy4576 97 SCGLLSGSITQTYIHYLECKNRGKLYEC--SLCNESFENKKVLFRHLRGKHGMKIKLSRH----KTKCVC--HYCNRTFD 168 (400)
Q Consensus 97 ~C~~~f~~~~~l~~H~~~~h~~~~~~~C--~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~----~~~~~C--~~C~~~f~ 168 (400)
.|+..--...++..| |.| +.|+..+-.+.++.+|++.|--....+... ...|.| ..|.+
T Consensus 257 ~c~~~~c~~e~~rEh----------yhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k--- 323 (480)
T KOG4377|consen 257 KCSFFGCHVEAGREH----------YHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK--- 323 (480)
T ss_pred hhccccceeeccchh----------hcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---
Q ss_pred CHHHHHHhHhhcCCCCCc-------ccCCCCC--CccCCHHHHHHHHHhhcCCCCC----------------------Cc
Q psy4576 169 SKAKIQEHIISSHMHEKL-------YQCDFCG--SQQRTKCRFYYHLRDKHLSKPA----------------------NL 217 (400)
Q Consensus 169 ~~~~l~~H~~~~H~~~~~-------~~C~~C~--~~f~~~~~l~~H~~~~~~~~~~----------------------~~ 217 (400)
+-++...|- ..|+...- |.|..|+ ..|.....-..|++.+..+... .|
T Consensus 324 sTsdV~~h~-nFht~~~n~GfrrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhf 402 (480)
T KOG4377|consen 324 STSDVLLHD-NFHTDKRNNGFRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHF 402 (480)
T ss_pred ccccccccC-ccccccccCceecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeee
Q ss_pred ccCc--CccccCCHHHHHHHHHHc
Q psy4576 218 SCEF--CSRIFTKKELLRSHLAVH 239 (400)
Q Consensus 218 ~C~~--C~~~f~~~~~l~~H~~~h 239 (400)
-|.. |+..+.+.+.+..|.+.|
T Consensus 403 hc~r~Gc~~tl~s~sqm~shkrkh 426 (480)
T KOG4377|consen 403 HCDRLGCEATLYSVSQMASHKRKH 426 (480)
T ss_pred eecccCCceEEEehhhhhhhhhhh
No 221
>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=21.62 E-value=19 Score=24.43 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=5.5
Q ss_pred CeecccccccccC
Q psy4576 339 PHCCEICGRSYST 351 (400)
Q Consensus 339 ~~~C~~C~~~f~~ 351 (400)
+..|..|+...+.
T Consensus 41 ~v~Cg~C~~~~~~ 53 (71)
T PF05495_consen 41 RVICGKCRTEQPI 53 (71)
T ss_dssp EEEETTT--EEES
T ss_pred CeECCCCCCccCh
Confidence 4555555554443
No 222
>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 PRK04351 hypothetical protein; Provisional
Probab=21.42 E-value=42 Score=26.66 Aligned_cols=10 Identities=40% Similarity=1.378 Sum_probs=4.8
Q ss_pred cccccccccc
Q psy4576 284 FICDVCGKSY 293 (400)
Q Consensus 284 ~~C~~C~~~f 293 (400)
|.|..|+..+
T Consensus 113 Y~C~~Cg~~~ 122 (149)
T PRK04351 113 YECQSCGQQY 122 (149)
T ss_pred EECCCCCCEe
Confidence 4555555433
No 224
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.82 E-value=53 Score=30.94 Aligned_cols=30 Identities=27% Similarity=0.681 Sum_probs=23.3
Q ss_pred ecccccccccChhhHHHHHhhcCCCCcccCCCCccccCCch
Q psy4576 341 CCEICGRSYSTAAYLKVHMSCHTGETSHTCHLCPQKFRQRS 381 (400)
Q Consensus 341 ~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~ 381 (400)
.|+.||.+..+. |.+-|+|+.||+.+....
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCccc
Confidence 699999876543 444799999999987654
No 225
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.68 E-value=39 Score=24.89 Aligned_cols=11 Identities=18% Similarity=0.507 Sum_probs=6.0
Q ss_pred eeccccccccc
Q psy4576 340 HCCEICGRSYS 350 (400)
Q Consensus 340 ~~C~~C~~~f~ 350 (400)
|.|+.|+..+.
T Consensus 20 ~iCpeC~~EW~ 30 (109)
T TIGR00686 20 LICPSCLYEWN 30 (109)
T ss_pred eECcccccccc
Confidence 55555555543
No 226
>KOG0978|consensus
Probab=20.38 E-value=39 Score=34.04 Aligned_cols=13 Identities=23% Similarity=0.641 Sum_probs=7.1
Q ss_pred cCCCCccccCCch
Q psy4576 369 TCHLCPQKFRQRS 381 (400)
Q Consensus 369 ~C~~C~~~f~~~~ 381 (400)
+||.|+.+|.-..
T Consensus 680 KCP~Cn~aFganD 692 (698)
T KOG0978|consen 680 KCPKCNAAFGAND 692 (698)
T ss_pred CCCCCCCCCCccc
Confidence 4666665555443
No 227
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=20.20 E-value=30 Score=19.92 Aligned_cols=18 Identities=22% Similarity=0.442 Sum_probs=8.4
Q ss_pred HHHHhhcCCCCcccCCCC
Q psy4576 356 KVHMSCHTGETSHTCHLC 373 (400)
Q Consensus 356 ~~H~~~h~~~~~~~C~~C 373 (400)
.+|=+...|...|.|..|
T Consensus 18 ~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 18 KKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCCEeEecCcC
Confidence 334334444445555555
Done!