Query psy4688
Match_columns 388
No_of_seqs 595 out of 2632
Neff 10.5
Searched_HMMs 46136
Date Fri Aug 16 23:21:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4688.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4688hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074|consensus 100.0 3E-31 6.6E-36 245.7 5.5 240 104-368 605-936 (958)
2 KOG1074|consensus 100.0 4.5E-31 9.8E-36 244.6 6.3 198 188-388 605-930 (958)
3 KOG2462|consensus 100.0 1.9E-30 4.1E-35 212.9 5.9 130 217-385 130-263 (279)
4 KOG2462|consensus 100.0 1E-28 2.2E-33 202.6 7.4 137 184-335 126-265 (279)
5 KOG3608|consensus 99.9 9.3E-28 2E-32 201.8 9.5 231 71-339 135-378 (467)
6 KOG3608|consensus 99.9 7.8E-27 1.7E-31 196.3 10.4 241 41-325 134-398 (467)
7 KOG3623|consensus 99.9 1.7E-26 3.6E-31 210.9 11.7 113 41-153 210-330 (1007)
8 KOG3576|consensus 99.8 1.2E-19 2.6E-24 141.5 1.6 122 214-341 114-240 (267)
9 KOG3576|consensus 99.7 1.1E-17 2.4E-22 130.6 1.2 111 251-367 117-240 (267)
10 KOG3623|consensus 99.6 9.4E-16 2E-20 141.3 3.7 112 188-299 210-329 (1007)
11 PLN03086 PRLI-interacting fact 99.4 5.6E-13 1.2E-17 124.1 5.5 138 218-385 408-560 (567)
12 PLN03086 PRLI-interacting fact 99.3 4.1E-12 8.8E-17 118.4 6.8 142 189-361 408-562 (567)
13 PHA00733 hypothetical protein 99.1 5E-11 1.1E-15 90.7 4.3 80 251-338 40-124 (128)
14 KOG3993|consensus 99.1 2.5E-11 5.5E-16 105.9 2.4 201 103-338 266-483 (500)
15 PHA00733 hypothetical protein 99.0 2.9E-10 6.3E-15 86.5 5.5 98 54-157 25-124 (128)
16 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.6E-10 3.4E-15 61.4 1.6 25 354-378 1-25 (26)
17 PHA02768 hypothetical protein; 99.0 3.4E-10 7.4E-15 70.2 2.7 44 251-296 5-48 (55)
18 KOG3993|consensus 98.9 2E-10 4.3E-15 100.4 -0.3 110 41-158 267-382 (500)
19 PHA02768 hypothetical protein; 98.9 1E-09 2.2E-14 68.1 2.0 43 104-148 5-47 (55)
20 PHA00616 hypothetical protein 98.7 6.8E-09 1.5E-13 61.2 1.4 34 313-346 1-34 (44)
21 PF13465 zf-H2C2_2: Zinc-finge 98.7 1E-08 2.2E-13 54.4 1.8 25 266-290 1-25 (26)
22 PHA00732 hypothetical protein 98.6 1.6E-08 3.5E-13 69.5 1.5 46 314-362 2-47 (79)
23 PHA00616 hypothetical protein 98.5 7.2E-08 1.6E-12 56.9 2.6 32 341-372 1-34 (44)
24 PF05605 zf-Di19: Drought indu 98.5 1.9E-07 4.2E-12 59.6 4.8 50 313-363 2-53 (54)
25 PHA00732 hypothetical protein 98.4 1.8E-07 3.9E-12 64.3 3.2 21 218-238 2-22 (79)
26 PF05605 zf-Di19: Drought indu 98.4 7.8E-07 1.7E-11 56.8 4.6 51 41-94 2-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.1 1.8E-06 3.9E-11 44.4 1.8 23 314-336 1-23 (23)
28 PF13894 zf-C2H2_4: C2H2-type 97.9 5.5E-06 1.2E-10 43.1 1.9 24 314-337 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 97.8 1.1E-05 2.4E-10 41.4 1.7 20 219-238 2-21 (23)
30 COG5189 SFP1 Putative transcri 97.8 5.8E-06 1.3E-10 70.2 0.9 58 277-334 347-419 (423)
31 PF13912 zf-C2H2_6: C2H2-type 97.7 1.8E-05 3.9E-10 42.4 1.6 26 313-338 1-26 (27)
32 PF12756 zf-C2H2_2: C2H2 type 97.7 2.3E-05 5E-10 57.6 2.2 24 132-155 50-73 (100)
33 PF12756 zf-C2H2_2: C2H2 type 97.6 2.6E-05 5.6E-10 57.3 2.0 72 191-274 2-73 (100)
34 PF13894 zf-C2H2_4: C2H2-type 97.6 3.8E-05 8.2E-10 39.8 2.0 22 219-240 2-23 (24)
35 PF09237 GAGA: GAGA factor; I 97.5 0.00014 3E-09 44.0 3.0 32 310-341 21-52 (54)
36 PF13912 zf-C2H2_6: C2H2-type 97.4 5.6E-05 1.2E-09 40.5 1.2 23 218-240 2-24 (27)
37 COG5189 SFP1 Putative transcri 97.3 9E-05 1.9E-09 63.2 1.4 24 276-299 395-418 (423)
38 PRK04860 hypothetical protein; 97.0 0.00028 6E-09 55.9 1.6 34 342-377 120-153 (160)
39 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00045 9.8E-09 35.7 1.9 24 314-338 1-24 (24)
40 KOG2231|consensus 97.0 0.00075 1.6E-08 64.8 4.6 147 189-371 100-275 (669)
41 smart00355 ZnF_C2H2 zinc finge 97.0 0.00059 1.3E-08 35.8 2.2 23 314-336 1-23 (26)
42 KOG2231|consensus 96.9 0.0019 4.1E-08 62.1 6.1 103 191-303 118-236 (669)
43 COG5236 Uncharacterized conser 96.9 0.0015 3.3E-08 56.5 4.8 24 71-94 152-177 (493)
44 PF12874 zf-met: Zinc-finger o 96.9 0.0006 1.3E-08 35.6 1.5 23 314-336 1-23 (25)
45 smart00355 ZnF_C2H2 zinc finge 96.9 0.00092 2E-08 35.0 2.2 21 253-273 2-22 (26)
46 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.001 2.2E-08 35.5 0.9 22 314-335 2-23 (27)
47 PF09237 GAGA: GAGA factor; I 96.5 0.0014 3E-08 39.7 1.5 33 212-244 19-51 (54)
48 PF12874 zf-met: Zinc-finger o 96.4 0.0016 3.6E-08 33.9 1.3 17 107-123 3-19 (25)
49 PRK04860 hypothetical protein; 96.3 0.002 4.4E-08 51.0 1.9 40 250-293 118-157 (160)
50 KOG2482|consensus 96.3 0.026 5.6E-07 49.2 8.5 77 189-274 280-357 (423)
51 COG5236 Uncharacterized conser 96.0 0.0031 6.7E-08 54.7 1.3 19 254-272 223-241 (493)
52 KOG1146|consensus 95.9 0.0012 2.6E-08 67.2 -1.6 189 43-240 438-641 (1406)
53 PF13909 zf-H2C2_5: C2H2-type 95.9 0.0066 1.4E-07 31.2 1.9 21 219-240 2-22 (24)
54 PF12171 zf-C2H2_jaz: Zinc-fin 95.8 0.0036 7.9E-08 33.3 0.7 22 252-273 2-23 (27)
55 KOG2785|consensus 95.6 0.038 8.3E-07 49.1 6.6 57 217-273 166-242 (390)
56 KOG2785|consensus 95.4 0.047 1E-06 48.6 6.4 53 188-240 166-243 (390)
57 PF13913 zf-C2HC_2: zinc-finge 95.3 0.014 3E-07 30.3 1.8 20 314-334 3-22 (25)
58 KOG4173|consensus 95.0 0.0079 1.7E-07 48.3 0.4 42 194-239 87-128 (253)
59 KOG4173|consensus 94.9 0.0066 1.4E-07 48.7 -0.2 113 6-125 47-167 (253)
60 COG5048 FOG: Zn-finger [Genera 94.9 0.0091 2E-07 56.6 0.6 157 216-377 288-456 (467)
61 PF13913 zf-C2HC_2: zinc-finge 94.7 0.031 6.7E-07 29.0 2.1 20 42-62 3-22 (25)
62 smart00451 ZnF_U1 U1-like zinc 94.0 0.035 7.6E-07 31.5 1.5 23 313-335 3-25 (35)
63 KOG2893|consensus 94.0 0.034 7.4E-07 45.8 1.9 47 254-304 13-59 (341)
64 TIGR00622 ssl1 transcription f 93.6 0.077 1.7E-06 38.9 3.0 47 315-363 57-105 (112)
65 smart00451 ZnF_U1 U1-like zinc 93.4 0.063 1.4E-06 30.4 1.9 23 251-273 3-25 (35)
66 KOG2482|consensus 93.2 0.13 2.8E-06 45.0 4.2 117 39-155 142-357 (423)
67 COG5048 FOG: Zn-finger [Genera 93.2 0.043 9.3E-07 52.0 1.5 154 187-350 288-455 (467)
68 TIGR00622 ssl1 transcription f 92.3 0.39 8.4E-06 35.3 5.0 21 216-236 14-34 (112)
69 KOG2893|consensus 92.0 0.048 1E-06 45.0 0.2 47 43-94 12-58 (341)
70 KOG1146|consensus 92.0 0.06 1.3E-06 55.6 0.9 83 190-272 438-539 (1406)
71 cd00350 rubredoxin_like Rubred 91.7 0.097 2.1E-06 29.3 1.1 7 281-287 3-9 (33)
72 COG4049 Uncharacterized protei 90.3 0.14 3.1E-06 31.6 1.0 29 310-338 14-42 (65)
73 COG4049 Uncharacterized protei 90.3 0.16 3.5E-06 31.4 1.2 28 67-94 14-41 (65)
74 PF00301 Rubredoxin: Rubredoxi 89.4 0.38 8.3E-06 29.3 2.4 42 280-322 2-43 (47)
75 PF01352 KRAB: KRAB box; Inte 87.5 0.047 1E-06 32.2 -2.4 23 3-25 18-40 (41)
76 cd00730 rubredoxin Rubredoxin; 87.2 0.43 9.4E-06 29.5 1.6 12 280-291 2-13 (50)
77 PF02176 zf-TRAF: TRAF-type zi 87.0 0.36 7.9E-06 31.2 1.4 46 312-358 8-60 (60)
78 PF09986 DUF2225: Uncharacteri 86.3 0.47 1E-05 40.0 2.0 13 314-326 49-61 (214)
79 PF12013 DUF3505: Protein of u 85.8 1 2.2E-05 33.4 3.3 26 313-338 80-109 (109)
80 cd00729 rubredoxin_SM Rubredox 85.7 0.45 9.7E-06 26.8 1.1 6 315-320 4-9 (34)
81 TIGR02098 MJ0042_CXXC MJ0042 f 84.0 0.67 1.5E-05 26.8 1.4 11 313-323 25-35 (38)
82 PF12013 DUF3505: Protein of u 83.7 1.9 4E-05 32.0 4.0 26 187-213 10-35 (109)
83 PHA00626 hypothetical protein 83.6 0.72 1.6E-05 28.8 1.4 14 312-325 22-35 (59)
84 COG1592 Rubrerythrin [Energy p 83.5 0.56 1.2E-05 37.3 1.1 11 364-374 146-156 (166)
85 PF13717 zinc_ribbon_4: zinc-r 83.4 0.88 1.9E-05 26.0 1.6 32 190-227 4-35 (36)
86 PF02176 zf-TRAF: TRAF-type zi 82.0 0.67 1.5E-05 29.9 0.9 46 339-384 7-60 (60)
87 KOG2186|consensus 81.6 0.7 1.5E-05 38.9 1.1 46 218-272 4-49 (276)
88 PF09538 FYDLN_acid: Protein o 81.4 0.99 2.1E-05 33.2 1.7 12 313-324 26-37 (108)
89 PF13719 zinc_ribbon_5: zinc-r 80.9 1.1 2.3E-05 25.8 1.4 33 190-228 4-36 (37)
90 PF09538 FYDLN_acid: Protein o 80.4 0.9 1.9E-05 33.4 1.2 28 313-351 9-36 (108)
91 PF09986 DUF2225: Uncharacteri 80.2 0.37 8.1E-06 40.6 -1.0 10 253-262 50-59 (214)
92 PRK00398 rpoP DNA-directed RNA 79.3 1.3 2.9E-05 26.8 1.5 12 279-290 3-14 (46)
93 PF10571 UPF0547: Uncharacteri 78.9 1.4 3E-05 23.0 1.3 11 314-324 15-25 (26)
94 TIGR00373 conserved hypothetic 78.5 1.1 2.3E-05 35.8 1.1 29 313-350 109-137 (158)
95 smart00734 ZnF_Rad18 Rad18-lik 77.9 2 4.4E-05 22.4 1.7 19 315-334 3-21 (26)
96 PRK06266 transcription initiat 77.2 1.1 2.5E-05 36.4 1.0 29 313-350 117-145 (178)
97 TIGR00373 conserved hypothetic 76.7 1.8 4E-05 34.5 2.1 16 252-267 110-125 (158)
98 smart00531 TFIIE Transcription 75.2 1.6 3.4E-05 34.4 1.3 12 279-290 99-110 (147)
99 PF09723 Zn-ribbon_8: Zinc rib 75.1 1.7 3.7E-05 25.8 1.1 11 280-290 6-16 (42)
100 PF02892 zf-BED: BED zinc fing 75.0 2.6 5.7E-05 25.2 2.0 24 312-335 15-42 (45)
101 COG4957 Predicted transcriptio 74.4 1.7 3.7E-05 32.7 1.2 22 314-338 77-98 (148)
102 smart00531 TFIIE Transcription 73.3 3.3 7.2E-05 32.6 2.7 35 251-289 99-133 (147)
103 PRK00464 nrdR transcriptional 73.3 1 2.2E-05 35.6 -0.2 16 280-295 29-44 (154)
104 PRK14890 putative Zn-ribbon RN 73.2 2.2 4.7E-05 27.2 1.3 9 313-321 48-56 (59)
105 COG1773 Rubredoxin [Energy pro 73.1 3 6.5E-05 26.2 1.9 13 279-291 3-15 (55)
106 KOG2186|consensus 73.0 1.2 2.7E-05 37.5 0.2 54 280-342 4-57 (276)
107 PRK06266 transcription initiat 72.6 2.6 5.6E-05 34.4 2.0 13 279-291 117-129 (178)
108 COG1592 Rubrerythrin [Energy p 72.4 2.2 4.8E-05 34.0 1.5 12 275-286 145-156 (166)
109 TIGR01384 TFS_arch transcripti 72.1 1.3 2.8E-05 32.5 0.1 9 314-322 63-71 (104)
110 smart00834 CxxC_CXXC_SSSS Puta 71.1 1.4 3.1E-05 25.8 0.1 11 280-290 6-16 (41)
111 PF04959 ARS2: Arsenite-resist 71.0 1.6 3.5E-05 36.5 0.4 30 311-340 75-104 (214)
112 PRK00464 nrdR transcriptional 70.5 2.4 5.2E-05 33.5 1.3 18 313-330 28-45 (154)
113 smart00659 RPOLCX RNA polymera 70.1 2.8 6.2E-05 25.1 1.3 10 280-289 3-12 (44)
114 TIGR02605 CxxC_CxxC_SSSS putat 69.2 1.6 3.6E-05 27.2 0.1 11 280-290 6-16 (52)
115 COG2888 Predicted Zn-ribbon RN 69.1 2.9 6.3E-05 26.6 1.2 8 313-320 50-57 (61)
116 smart00614 ZnF_BED BED zinc fi 68.6 4.1 9E-05 25.2 1.9 23 313-335 18-45 (50)
117 TIGR02300 FYDLN_acid conserved 68.3 2.9 6.4E-05 31.3 1.3 10 315-324 11-20 (129)
118 TIGR02300 FYDLN_acid conserved 67.0 4.3 9.2E-05 30.5 1.9 30 252-292 10-39 (129)
119 PF03604 DNA_RNApol_7kD: DNA d 65.6 4.9 0.00011 22.2 1.5 10 313-322 17-26 (32)
120 KOG2593|consensus 65.3 4.4 9.5E-05 37.3 2.0 35 41-79 128-162 (436)
121 COG2331 Uncharacterized protei 64.8 5.4 0.00012 26.8 1.8 38 310-355 9-47 (82)
122 PRK09678 DNA-binding transcrip 64.6 2.9 6.4E-05 28.1 0.6 42 252-295 2-45 (72)
123 PRK04023 DNA polymerase II lar 63.8 5.2 0.00011 41.0 2.4 8 342-349 664-671 (1121)
124 PF08274 PhnA_Zn_Ribbon: PhnA 63.3 3.4 7.3E-05 22.5 0.6 8 313-320 19-26 (30)
125 PF09845 DUF2072: Zn-ribbon co 63.2 3.8 8.3E-05 31.0 1.1 13 314-326 2-14 (131)
126 PF12907 zf-met2: Zinc-binding 62.3 4.6 0.0001 23.6 1.1 23 72-94 3-28 (40)
127 COG1996 RPC10 DNA-directed RNA 61.8 3.6 7.9E-05 25.2 0.6 11 313-323 6-16 (49)
128 PF14353 CpXC: CpXC protein 61.5 7.7 0.00017 29.6 2.6 24 278-301 37-60 (128)
129 PF13451 zf-trcl: Probable zin 61.1 5 0.00011 24.6 1.1 15 40-54 3-17 (49)
130 PF05443 ROS_MUCR: ROS/MUCR tr 59.9 5.1 0.00011 30.7 1.3 27 312-341 71-97 (132)
131 COG5151 SSL1 RNA polymerase II 59.8 11 0.00023 33.0 3.3 12 340-351 387-398 (421)
132 TIGR01206 lysW lysine biosynth 58.9 5.9 0.00013 25.0 1.2 9 314-322 23-31 (54)
133 PF07754 DUF1610: Domain of un 58.8 3.8 8.2E-05 20.9 0.3 8 367-374 16-23 (24)
134 KOG2272|consensus 57.3 7 0.00015 33.0 1.7 18 217-234 99-116 (332)
135 KOG2807|consensus 55.5 20 0.00044 31.7 4.2 33 251-297 276-308 (378)
136 PF15269 zf-C2H2_7: Zinc-finge 54.5 15 0.00032 21.8 2.2 23 250-272 19-41 (54)
137 COG1997 RPL43A Ribosomal prote 54.2 7.7 0.00017 27.0 1.3 13 313-325 53-65 (89)
138 KOG2593|consensus 53.7 9.1 0.0002 35.3 2.0 19 276-294 125-143 (436)
139 COG1198 PriA Primosomal protei 52.6 3.1 6.8E-05 41.7 -1.2 40 314-376 445-484 (730)
140 PF04959 ARS2: Arsenite-resist 52.2 9.3 0.0002 32.1 1.7 29 68-96 75-103 (214)
141 PF07503 zf-HYPF: HypF finger; 52.1 5.3 0.00011 22.6 0.2 31 282-324 2-32 (35)
142 KOG2807|consensus 50.4 29 0.00062 30.8 4.4 13 46-58 138-150 (378)
143 PF14446 Prok-RING_1: Prokaryo 50.1 9.2 0.0002 24.0 1.0 9 253-261 7-15 (54)
144 KOG4124|consensus 49.8 5 0.00011 35.6 -0.2 51 102-153 176-233 (442)
145 PRK04023 DNA polymerase II lar 49.5 17 0.00037 37.6 3.3 10 217-226 626-635 (1121)
146 KOG4124|consensus 49.2 6.6 0.00014 34.9 0.4 26 278-303 348-375 (442)
147 PF11789 zf-Nse: Zinc-finger o 49.1 11 0.00024 24.0 1.4 29 341-372 24-53 (57)
148 COG1198 PriA Primosomal protei 48.6 13 0.00028 37.6 2.3 10 313-322 475-484 (730)
149 KOG4167|consensus 48.0 4.5 9.8E-05 39.7 -0.8 26 313-338 792-817 (907)
150 PF08790 zf-LYAR: LYAR-type C2 47.6 6.2 0.00013 21.0 0.0 9 281-289 2-10 (28)
151 PF05443 ROS_MUCR: ROS/MUCR tr 47.6 6.5 0.00014 30.1 0.1 26 341-367 72-97 (132)
152 TIGR00595 priA primosomal prot 45.2 12 0.00026 36.3 1.6 13 275-287 236-248 (505)
153 KOG1280|consensus 44.2 17 0.00036 32.5 2.1 37 312-348 78-116 (381)
154 PF04216 FdhE: Protein involve 43.9 2 4.3E-05 38.2 -3.7 9 314-322 212-220 (290)
155 COG4957 Predicted transcriptio 43.5 11 0.00025 28.5 0.9 17 280-299 77-93 (148)
156 COG4530 Uncharacterized protei 42.4 14 0.0003 26.8 1.1 11 313-323 26-36 (129)
157 PF05191 ADK_lid: Adenylate ki 42.2 10 0.00022 21.6 0.4 30 106-143 3-32 (36)
158 smart00504 Ubox Modified RING 42.1 25 0.00054 22.6 2.3 26 347-377 19-45 (63)
159 PF01286 XPA_N: XPA protein N- 41.9 14 0.00029 20.8 0.8 11 281-291 5-15 (34)
160 PRK00432 30S ribosomal protein 41.9 17 0.00036 22.5 1.3 6 315-320 39-44 (50)
161 TIGR00595 priA primosomal prot 40.9 16 0.00036 35.4 1.7 9 313-321 240-248 (505)
162 PF01780 Ribosomal_L37ae: Ribo 40.9 13 0.00028 26.2 0.8 13 313-325 53-65 (90)
163 COG0068 HypF Hydrogenase matur 40.7 8.3 0.00018 38.1 -0.3 37 188-232 101-138 (750)
164 PF01363 FYVE: FYVE zinc finge 40.4 13 0.00027 24.7 0.6 9 315-323 11-19 (69)
165 PF06524 NOA36: NOA36 protein; 40.4 12 0.00025 32.0 0.5 25 131-155 208-232 (314)
166 PF13639 zf-RING_2: Ring finge 40.1 20 0.00042 21.2 1.4 29 339-373 14-43 (44)
167 COG1655 Uncharacterized protei 38.6 12 0.00025 31.4 0.3 7 343-349 64-70 (267)
168 COG0068 HypF Hydrogenase matur 38.4 11 0.00024 37.3 0.1 56 253-321 125-181 (750)
169 PF09963 DUF2197: Uncharacteri 38.3 9.1 0.0002 24.2 -0.3 37 42-80 3-41 (56)
170 KOG4167|consensus 38.2 12 0.00025 37.0 0.3 25 69-93 791-815 (907)
171 COG5151 SSL1 RNA polymerase II 38.0 28 0.00061 30.5 2.5 99 39-156 306-412 (421)
172 PRK14873 primosome assembly pr 37.8 17 0.00037 36.5 1.4 9 281-289 385-393 (665)
173 PF14445 Prok-RING_2: Prokaryo 37.8 9.4 0.0002 23.3 -0.3 14 312-325 6-19 (57)
174 PF04780 DUF629: Protein of un 37.7 21 0.00046 33.7 1.9 28 69-96 56-83 (466)
175 TIGR03831 YgiT_finger YgiT-typ 36.9 17 0.00036 21.6 0.7 13 313-325 32-44 (46)
176 TIGR00100 hypA hydrogenase nic 36.8 16 0.00034 27.4 0.7 14 313-326 70-83 (115)
177 PF05290 Baculo_IE-1: Baculovi 36.7 33 0.00072 26.1 2.4 58 213-294 76-136 (140)
178 PRK14714 DNA polymerase II lar 36.3 38 0.00082 36.2 3.5 8 280-287 693-700 (1337)
179 KOG1280|consensus 36.2 31 0.00067 30.9 2.5 27 70-96 79-105 (381)
180 TIGR00280 L37a ribosomal prote 36.1 18 0.00039 25.6 0.8 13 313-325 53-65 (91)
181 COG4888 Uncharacterized Zn rib 35.9 19 0.0004 25.8 0.9 10 251-260 22-31 (104)
182 cd00162 RING RING-finger (Real 35.8 46 0.001 19.0 2.7 27 346-376 17-44 (45)
183 PF04780 DUF629: Protein of un 35.5 24 0.00051 33.4 1.8 27 42-68 58-84 (466)
184 PRK03824 hypA hydrogenase nick 34.9 15 0.00033 28.4 0.4 11 280-290 71-81 (135)
185 PF12760 Zn_Tnp_IS1595: Transp 34.6 69 0.0015 19.2 3.2 10 312-321 36-45 (46)
186 PF08271 TF_Zn_Ribbon: TFIIB z 34.6 14 0.0003 21.9 0.1 10 70-79 19-28 (43)
187 PRK05452 anaerobic nitric oxid 34.5 25 0.00054 33.9 1.9 12 279-290 425-436 (479)
188 COG1571 Predicted DNA-binding 34.5 16 0.00036 33.9 0.6 27 315-352 352-378 (421)
189 smart00154 ZnF_AN1 AN1-like Zi 34.4 19 0.00041 20.9 0.6 14 313-326 12-25 (39)
190 PRK12380 hydrogenase nickel in 34.2 19 0.0004 26.9 0.8 13 313-325 70-82 (113)
191 PF13878 zf-C2H2_3: zinc-finge 34.2 29 0.00062 20.4 1.4 12 314-325 14-25 (41)
192 PF06524 NOA36: NOA36 protein; 34.1 33 0.00071 29.4 2.2 12 214-225 139-150 (314)
193 PTZ00255 60S ribosomal protein 33.9 21 0.00047 25.2 1.0 13 313-325 54-66 (90)
194 COG5188 PRP9 Splicing factor 3 33.5 84 0.0018 28.3 4.6 22 104-125 238-259 (470)
195 cd00065 FYVE FYVE domain; Zinc 33.1 23 0.0005 22.3 1.0 9 316-324 5-13 (57)
196 KOG3408|consensus 32.9 26 0.00056 26.1 1.3 27 129-155 54-80 (129)
197 PF07649 C1_3: C1-like domain; 32.1 18 0.00039 19.4 0.3 9 341-349 15-23 (30)
198 smart00249 PHD PHD zinc finger 31.8 64 0.0014 18.7 2.8 11 279-289 14-24 (47)
199 PF07282 OrfB_Zn_ribbon: Putat 31.3 17 0.00036 24.1 0.1 27 315-351 30-56 (69)
200 PF01927 Mut7-C: Mut7-C RNAse 31.3 45 0.00098 26.1 2.6 19 313-331 124-142 (147)
201 PF08209 Sgf11: Sgf11 (transcr 30.6 23 0.00049 19.7 0.5 10 368-377 5-14 (33)
202 KOG3214|consensus 30.6 17 0.00037 25.9 0.1 41 39-84 21-61 (109)
203 PRK03976 rpl37ae 50S ribosomal 30.2 25 0.00055 24.8 0.9 13 313-325 54-66 (90)
204 KOG3408|consensus 30.1 41 0.0009 25.1 1.9 29 98-126 51-79 (129)
205 PF02591 DUF164: Putative zinc 29.9 46 0.001 21.0 2.0 31 43-78 24-54 (56)
206 KOG0717|consensus 29.3 27 0.00058 32.7 1.0 22 314-335 293-314 (508)
207 KOG1842|consensus 29.2 28 0.00062 32.3 1.2 29 40-68 14-42 (505)
208 PF01428 zf-AN1: AN1-like Zinc 29.2 20 0.00043 21.3 0.2 15 312-326 12-26 (43)
209 PRK00564 hypA hydrogenase nick 29.1 24 0.00051 26.5 0.6 13 313-325 71-83 (117)
210 PF15135 UPF0515: Uncharacteri 28.8 37 0.00081 28.9 1.7 15 216-230 154-168 (278)
211 KOG0717|consensus 28.4 28 0.0006 32.6 1.0 25 39-63 290-314 (508)
212 PRK05580 primosome assembly pr 28.3 33 0.00071 34.8 1.6 9 341-349 421-429 (679)
213 KOG0978|consensus 28.2 29 0.00064 34.6 1.2 11 368-378 679-689 (698)
214 PF14311 DUF4379: Domain of un 28.0 40 0.00086 21.2 1.4 13 314-326 29-41 (55)
215 PRK12496 hypothetical protein; 27.6 30 0.00065 27.8 1.0 10 314-323 128-137 (164)
216 PF09416 UPF1_Zn_bind: RNA hel 27.5 64 0.0014 25.4 2.7 10 340-349 59-68 (152)
217 PF10013 DUF2256: Uncharacteri 27.5 35 0.00076 20.1 1.0 17 314-330 9-25 (42)
218 COG3091 SprT Zn-dependent meta 27.5 27 0.00059 27.3 0.7 32 251-287 117-148 (156)
219 COG3364 Zn-ribbon containing p 27.4 29 0.00062 24.9 0.7 14 251-264 2-15 (112)
220 PF12230 PRP21_like_P: Pre-mRN 27.2 21 0.00045 30.5 0.0 19 342-360 169-188 (229)
221 smart00064 FYVE Protein presen 27.2 29 0.00063 22.9 0.7 10 315-324 12-21 (68)
222 COG1675 TFA1 Transcription ini 27.2 47 0.001 26.9 2.0 15 276-290 110-124 (176)
223 COG3880 Modulator of heat shoc 26.5 39 0.00083 26.9 1.3 35 313-357 74-108 (176)
224 PF13453 zf-TFIIB: Transcripti 26.1 37 0.00081 19.8 1.0 18 217-234 19-36 (41)
225 PF01096 TFIIS_C: Transcriptio 26.1 29 0.00064 20.1 0.5 11 313-323 28-38 (39)
226 PF04423 Rad50_zn_hook: Rad50 25.8 27 0.00058 21.9 0.3 13 315-327 22-34 (54)
227 PF05741 zf-nanos: Nanos RNA b 25.8 23 0.0005 22.4 0.0 10 367-376 33-42 (55)
228 PF05495 zf-CHY: CHY zinc fing 25.5 20 0.00044 24.1 -0.3 13 313-325 41-53 (71)
229 COG4896 Uncharacterized protei 25.3 41 0.00088 21.6 1.0 12 277-288 29-40 (68)
230 PTZ00303 phosphatidylinositol 25.1 22 0.00048 35.5 -0.2 12 106-117 462-473 (1374)
231 PF15227 zf-C3HC4_4: zinc fing 24.8 33 0.0007 20.2 0.5 6 368-373 37-42 (42)
232 KOG0562|consensus 24.6 54 0.0012 26.0 1.8 30 37-66 149-178 (184)
233 KOG1842|consensus 24.5 38 0.00082 31.5 1.1 29 311-339 13-41 (505)
234 KOG2636|consensus 24.5 50 0.0011 30.8 1.9 26 65-90 396-422 (497)
235 smart00440 ZnF_C2C2 C2C2 Zinc 24.4 52 0.0011 19.2 1.3 12 313-324 28-39 (40)
236 PF01155 HypA: Hydrogenase exp 24.3 27 0.00059 26.0 0.2 12 314-325 71-82 (113)
237 smart00132 LIM Zinc-binding do 23.9 53 0.0011 18.2 1.4 11 313-323 27-37 (39)
238 PF03833 PolC_DP2: DNA polymer 23.9 26 0.00056 35.6 0.0 8 280-287 656-663 (900)
239 PF04606 Ogr_Delta: Ogr/Delta- 23.3 28 0.00061 21.1 0.1 12 314-325 26-39 (47)
240 PRK03681 hypA hydrogenase nick 23.1 30 0.00065 25.8 0.2 10 314-323 71-80 (114)
241 PF11931 DUF3449: Domain of un 22.9 28 0.0006 28.7 0.0 24 39-62 99-123 (196)
242 PF05129 Elf1: Transcription e 22.9 35 0.00077 23.6 0.5 10 314-323 47-56 (81)
243 PF12230 PRP21_like_P: Pre-mRN 22.8 28 0.00061 29.7 0.0 29 312-341 167-195 (229)
244 COG4306 Uncharacterized protei 22.1 30 0.00065 25.8 0.0 12 70-81 68-79 (160)
245 PF14803 Nudix_N_2: Nudix N-te 21.9 51 0.0011 18.5 0.9 12 311-322 20-31 (34)
246 TIGR03830 CxxCG_CxxCG_HTH puta 21.8 50 0.0011 24.8 1.2 22 312-333 30-51 (127)
247 KOG2817|consensus 21.7 62 0.0013 29.7 1.9 24 27-50 358-383 (394)
248 PF09332 Mcm10: Mcm10 replicat 21.5 14 0.0003 33.5 -2.2 14 312-325 284-297 (344)
249 PF14634 zf-RING_5: zinc-RING 20.9 1.3E+02 0.0028 17.7 2.7 11 365-375 34-44 (44)
250 PRK14559 putative protein seri 20.3 88 0.0019 31.4 2.8 11 281-291 43-53 (645)
251 PRK05978 hypothetical protein; 20.3 55 0.0012 25.7 1.2 7 253-259 35-41 (148)
252 PF06220 zf-U1: U1 zinc finger 20.2 77 0.0017 18.2 1.5 11 313-323 3-13 (38)
253 PF04810 zf-Sec23_Sec24: Sec23 20.2 70 0.0015 18.6 1.3 10 312-321 23-32 (40)
254 PF06397 Desulfoferrod_N: Desu 20.1 38 0.00083 19.3 0.2 10 367-376 6-15 (36)
No 1
>KOG1074|consensus
Probab=99.97 E-value=3e-31 Score=245.71 Aligned_cols=240 Identities=24% Similarity=0.402 Sum_probs=173.2
Q ss_pred ccccccchhccCCchHHHHHHhhcCCCCCccCCccccccCChHHHHHHHhhhcccccccccCceeeecCCCCCccccchh
Q psy4688 104 HFECNYCHAKFSNKSLLSDHISSHTGLKNYKCHVCDKAYSCRKALKTHTLLHEQEKVIKSSKKEFIIDTGDCTLDEWNDF 183 (388)
Q Consensus 104 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (388)
|.+|-+|-++.+-++.|+.|.++|+|++||+|.+|++.|+++.+|+.||-+|......
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~---------------------- 662 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA---------------------- 662 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccc----------------------
Confidence 5789999999999999999999999999999999999999999999999998654322
Q ss_pred hccCCCccc---ccccccCCchHHHHhHHhhhCC-CC------------cccCCCCcccCCChhHHHHHHHHhccCCc--
Q psy4688 184 IKRRVTVCP---KCNRDYRNPRNMRKHLRRVHTS-VR------------KYGCDECGKMLKSRDSLNTHKKIQHEGKK-- 245 (388)
Q Consensus 184 ~~~~~~~C~---~C~~~f~~~~~l~~H~~~~h~~-~~------------~~~C~~C~~~f~~~~~l~~H~~~~~~~~~-- 245 (388)
+..+.|+ +|-+.|.+.-.|..|++ .|.+ .. .-+|..|.+.|.....+..++..+-....
T Consensus 663 --R~q~ScP~~~ic~~kftn~V~lpQhIr-iH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~ 739 (958)
T KOG1074|consen 663 --RVQFSCPSTFICQKKFTNAVTLPQHIR-IHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEP 739 (958)
T ss_pred --cccccCCchhhhcccccccccccceEE-eecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCC
Confidence 2346799 99999999999999974 5652 11 24699999999999999988877632111
Q ss_pred ------------ccccCcccccccCCcCCChhHHHHHHh-----------------------hcCCCCCc-ccccccccc
Q psy4688 246 ------------VKVKYEYECDYCGAKYPNKYTLSDHIS-----------------------GHTGIPNH-ICKICNKGY 289 (388)
Q Consensus 246 ------------~~~~~~~~C~~C~~~f~~~~~L~~H~~-----------------------~H~~~~~~-~C~~C~k~f 289 (388)
....-+..+..|+..+.....+..+-. .++++++. .+.+++-.-
T Consensus 740 ~~~~~~~t~t~~~~~tp~~~e~~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~ 819 (958)
T KOG1074|consen 740 DEQMDERTETEELDVTPPPPENSCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEIL 819 (958)
T ss_pred cccccccccccccccCCCccccccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCC
Confidence 111225678889998887766655421 23345555 555555433
Q ss_pred ccccccc----hh-------------hccccc-------cc------------cCCCCCccccCCCcccccChhhHHhHH
Q psy4688 290 ACAASLK----IH-------------NIKTHL-------QF------------TGVPIEKFKCDLCDKEFFEKKKLNKHK 333 (388)
Q Consensus 290 ~~~~~L~----~H-------------~~~~H~-------~~------------~~~~~~~~~C~~C~k~F~~~~~L~~H~ 333 (388)
...-... .- +...+. +. .........|.+||+.|.+.++|+.|+
T Consensus 820 ~~~v~~~pvl~~~~~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~ 899 (958)
T KOG1074|consen 820 APSVNMDPVLWNQETSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHM 899 (958)
T ss_pred ccccccCchhhcccccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhh
Confidence 2111000 00 000000 00 000012378999999999999999999
Q ss_pred hhhcCCCcccCCcchhhH--HhHHHHHHHHhcCCCCc
Q psy4688 334 NWAHGDKFHLCKVCGAKI--KGSLKQHMITHTGERKY 368 (388)
Q Consensus 334 ~~hh~~~~~~C~~C~~~f--~~~L~~H~~~H~~~~~~ 368 (388)
++|.|+|||.|.+|++.| +++|+.||.+|....|+
T Consensus 900 rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 900 RTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred hcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCC
Confidence 999999999999999998 78899999999876654
No 2
>KOG1074|consensus
Probab=99.97 E-value=4.5e-31 Score=244.57 Aligned_cols=198 Identities=27% Similarity=0.532 Sum_probs=146.4
Q ss_pred CCcccccccccCCchHHHHhHHhhhCCCCcccCCCCcccCCChhHHHHHHHHhccCCcccccCccccc---ccCCcCCCh
Q psy4688 188 VTVCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECD---YCGAKYPNK 264 (388)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~---~C~~~f~~~ 264 (388)
+..|-+|-++..-++.|+.|+ +.|+|+|||+|.+||+.|.++.+|+.|+-+|-.....+ ..+.|+ +|-+.|.+.
T Consensus 605 PNqCiiC~rVlSC~saLqmHy-rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R--~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHY-RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPAR--VQFSCPSTFICQKKFTNA 681 (958)
T ss_pred ccceeeeeecccchhhhhhhh-hcccCcCccccccccchhccccchhhcccccccCcccc--ccccCCchhhhccccccc
Confidence 346999999999999999997 67999999999999999999999999999886554433 479999 999999999
Q ss_pred hHHHHHHhhcCCC-C------------Cccccccccccccccccchhhccc-------ccccc---CCC----CCccccC
Q psy4688 265 YTLSDHISGHTGI-P------------NHICKICNKGYACAASLKIHNIKT-------HLQFT---GVP----IEKFKCD 317 (388)
Q Consensus 265 ~~L~~H~~~H~~~-~------------~~~C~~C~k~f~~~~~L~~H~~~~-------H~~~~---~~~----~~~~~C~ 317 (388)
..|..|+++|.+. . .-+|..|.+.|.....+..++... +.+.. ..+ ..+..+.
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 9999999999832 1 247999999998888777774332 11000 000 0123333
Q ss_pred CCcccccChhhHHhHHhhh-------------------------------------------------------------
Q psy4688 318 LCDKEFFEKKKLNKHKNWA------------------------------------------------------------- 336 (388)
Q Consensus 318 ~C~k~F~~~~~L~~H~~~h------------------------------------------------------------- 336 (388)
.|+..+.....+..+-..+
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 3433333222111110000
Q ss_pred -----------------------cC--------C--CcccCCcchhhH--HhHHHHHHHHhcCCCCccccccchhh--Hh
Q psy4688 337 -----------------------HG--------D--KFHLCKVCGAKI--KGSLKQHMITHTGERKYCCHICGKKL--RG 379 (388)
Q Consensus 337 -----------------------h~--------~--~~~~C~~C~~~f--~~~L~~H~~~H~~~~~~~C~~C~k~f--~~ 379 (388)
.. . ..+.|.+||+.| .+.|..||++|+|++||.|.+|++.| ++
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 00 0 127799999999 45699999999999999999999999 78
Q ss_pred hhhhhhccC
Q psy4688 380 KLKEHMLNT 388 (388)
Q Consensus 380 ~l~~H~~~~ 388 (388)
+||+||+.|
T Consensus 922 nLKvHMgtH 930 (958)
T KOG1074|consen 922 NLKVHMGTH 930 (958)
T ss_pred hhhhhhccc
Confidence 899999987
No 3
>KOG2462|consensus
Probab=99.96 E-value=1.9e-30 Score=212.85 Aligned_cols=130 Identities=33% Similarity=0.648 Sum_probs=78.0
Q ss_pred cccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCCcCCChhHHHHHHhhcCCCCCccccccccccccccccc
Q psy4688 217 KYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAASLK 296 (388)
Q Consensus 217 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~ 296 (388)
.|+|+.||+.+.+.+.|.+|.++|-.... ++.+.|.+|||.|.+...|..|+++|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s---~ka~~C~~C~K~YvSmpALkMHirTH~--------------------- 185 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDS---KKAFSCKYCGKVYVSMPALKMHIRTHT--------------------- 185 (279)
T ss_pred ceeccccccccccccccchhhcccccccc---cccccCCCCCceeeehHHHhhHhhccC---------------------
Confidence 45555555555555555555555543221 223555555555555555555555554
Q ss_pred hhhccccccccCCCCCccccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhH--HhHHHHHHHHhcCCCCccccccc
Q psy4688 297 IHNIKTHLQFTGVPIEKFKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKI--KGSLKQHMITHTGERKYCCHICG 374 (388)
Q Consensus 297 ~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f--~~~L~~H~~~H~~~~~~~C~~C~ 374 (388)
-+++|.+|||.|.+.-.|+-|+|+|+|||||.|++|+++| +++|+.||++|++.++|+|+.|+
T Consensus 186 ---------------l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~ 250 (279)
T KOG2462|consen 186 ---------------LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCG 250 (279)
T ss_pred ---------------CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchh
Confidence 2456666666666666666677777777777777777776 56677777777777777777777
Q ss_pred hhhH--hhhhhhh
Q psy4688 375 KKLR--GKLKEHM 385 (388)
Q Consensus 375 k~f~--~~l~~H~ 385 (388)
|+|. +-|.+|.
T Consensus 251 KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 251 KSFALKSYLNKHS 263 (279)
T ss_pred hHHHHHHHHHHhh
Confidence 7773 3366664
No 4
>KOG2462|consensus
Probab=99.95 E-value=1e-28 Score=202.64 Aligned_cols=137 Identities=32% Similarity=0.672 Sum_probs=111.9
Q ss_pred hccCCCcccccccccCCchHHHHhHHhhhC---CCCcccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCCc
Q psy4688 184 IKRRVTVCPKCNRDYRNPRNMRKHLRRVHT---SVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAK 260 (388)
Q Consensus 184 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~---~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~ 260 (388)
.....+.|+.|++.+.+..+|.+| +..|- ..+.+.|++||+.|.+..+|..|+++|.. +++|.+|||.
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrH-kQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l--------~c~C~iCGKa 196 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRH-KQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL--------PCECGICGKA 196 (279)
T ss_pred ccCCceeccccccccccccccchh-hcccccccccccccCCCCCceeeehHHHhhHhhccCC--------Cccccccccc
Confidence 455678999999999999999999 45664 35679999999999999999999999973 6899999999
Q ss_pred CCChhHHHHHHhhcCCCCCccccccccccccccccchhhccccccccCCCCCccccCCCcccccChhhHHhHHhh
Q psy4688 261 YPNKYTLSDHISGHTGIPNHICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFFEKKKLNKHKNW 335 (388)
Q Consensus 261 f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~ 335 (388)
|...+.|+.|+|+|+||+||.|+.|+|.|+.+++|+.| +.+|. ..++|+|+.|+|.|..++.|.+|...
T Consensus 197 FSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAH-mQTHS-----~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 197 FSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAH-MQTHS-----DVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccchHHhhcccccccCCCCccCCcccchhcchHHHHHH-HHhhc-----CCccccCcchhhHHHHHHHHHHhhhh
Confidence 99999999999999999988888777777777777766 33332 24567777777777777777777653
No 5
>KOG3608|consensus
Probab=99.95 E-value=9.3e-28 Score=201.83 Aligned_cols=231 Identities=23% Similarity=0.464 Sum_probs=195.0
Q ss_pred ccc--ccchhcccChhhHHHHHHhhccCCCc-----CC-C-Cccccc--cchhccCCchHHHHHHhhcCCCCCccCCccc
Q psy4688 71 TTC--TMCKKTFRNKATFQKHMQRAHVGLKI-----SV-S-KHFECN--YCHAKFSNKSLLSDHISSHTGLKNYKCHVCD 139 (388)
Q Consensus 71 ~~C--~~C~~~f~~~~~l~~H~~~~h~~~~~-----~~-~-~~~~C~--~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~ 139 (388)
|.| ..|+..|.+...+..|+..+-..... .. . ..+.|. .|-+.|.+++.|++|++.|++++...|+.|+
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 456 45999999999999998644332111 11 1 235565 5999999999999999999999999999999
Q ss_pred cccCChHHHHHHHhhhcccccccccCceeeecCCCCCccccchhhccCCCcccccccccCCchHHHHhHHhhhCCCCccc
Q psy4688 140 KAYSCRKALKTHTLLHEQEKVIKSSKKEFIIDTGDCTLDEWNDFIKRRVTVCPKCNRDYRNPRNMRKHLRRVHTSVRKYG 219 (388)
Q Consensus 140 ~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~ 219 (388)
..|.++..|-.|.+.-... ...+|.|..|.|.|.+...|..|+.+ |. .-|+
T Consensus 215 ~~F~~~tkl~DH~rRqt~l--------------------------~~n~fqC~~C~KrFaTeklL~~Hv~r-Hv--n~yk 265 (467)
T KOG3608|consen 215 ELFRTKTKLFDHLRRQTEL--------------------------NTNSFQCAQCFKRFATEKLLKSHVVR-HV--NCYK 265 (467)
T ss_pred HHhccccHHHHHHHhhhhh--------------------------cCCchHHHHHHHHHhHHHHHHHHHHH-hh--hccc
Confidence 9999999999998754321 22468899999999999999999754 44 3599
Q ss_pred CCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCCcCCChhHHHHHHhhcCCCCCccccc--cccccccccccch
Q psy4688 220 CDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAKYPNKYTLSDHISGHTGIPNHICKI--CNKGYACAASLKI 297 (388)
Q Consensus 220 C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~--C~k~f~~~~~L~~ 297 (388)
|+.|+.+....++|..|++..|... +||+|+.|++.|.+.+.|.+|..+|+ +..|.|+. |..+|.+..+|++
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~d-----kpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~ 339 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKD-----KPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRR 339 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccC-----CCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHH
Confidence 9999999999999999999988654 38999999999999999999999999 67899988 9999999999999
Q ss_pred hhccccccccCCCCCccccCCCcccccChhhHHhHHhhhcCC
Q psy4688 298 HNIKTHLQFTGVPIEKFKCDLCDKEFFEKKKLNKHKNWAHGD 339 (388)
Q Consensus 298 H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~hh~~ 339 (388)
|.+.+| .+....+|.|-.|++.|++-.+|..|++..|+-
T Consensus 340 H~~evh---Eg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 340 HFLEVH---EGNNPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred HHHHhc---cCCCCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 988888 344457899999999999999999999888763
No 6
>KOG3608|consensus
Probab=99.94 E-value=7.8e-27 Score=196.31 Aligned_cols=241 Identities=23% Similarity=0.496 Sum_probs=202.7
Q ss_pred cCCC--CCcCCcCCCcHHHHHHHHhhcc------------C-CCccccc--cchhcccChhhHHHHHHhhccCCCcCCCC
Q psy4688 41 TKTC--PICNKSYPGARNMRKHLRLVHD------------K-NSTTTCT--MCKKTFRNKATFQKHMQRAHVGLKISVSK 103 (388)
Q Consensus 41 ~~~C--~~C~~~f~~~~~l~~H~~~~h~------------~-~~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~~~~~~~ 103 (388)
.|.| +.|+..|.+...+..|+.. |. + ...+.|. .|-+.|.+++.|++|++ .|.+ ++
T Consensus 134 ~f~C~WedCe~~F~s~~ef~dHV~~-H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r-~Hs~-----eK 206 (467)
T KOG3608|consen 134 NFRCGWEDCEREFVSIVEFQDHVVK-HALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIR-THSN-----EK 206 (467)
T ss_pred hhccChhhcCCcccCHHHHHHHHHH-hhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHH-hcCC-----Ce
Confidence 4667 5799999999999999854 42 1 1346675 59999999999999986 5544 57
Q ss_pred ccccccchhccCCchHHHHHHhhcC--CCCCccCCccccccCChHHHHHHHhhhcccccccccCceeeecCCCCCccccc
Q psy4688 104 HFECNYCHAKFSNKSLLSDHISSHT--GLKNYKCHVCDKAYSCRKALKTHTLLHEQEKVIKSSKKEFIIDTGDCTLDEWN 181 (388)
Q Consensus 104 ~~~C~~C~~~f~~~~~L~~H~~~h~--~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~ 181 (388)
...|+.||..|.++..|-.|++.-+ ...+|.|..|.+.|.+...|..|+..|-.
T Consensus 207 vvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn------------------------ 262 (467)
T KOG3608|consen 207 VVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN------------------------ 262 (467)
T ss_pred EEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh------------------------
Confidence 8899999999999999999987644 45789999999999999999999998853
Q ss_pred hhhccCCCcccccccccCCchHHHHhHHhhhCCCCcccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccc--cCC
Q psy4688 182 DFIKRRVTVCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDY--CGA 259 (388)
Q Consensus 182 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~--C~~ 259 (388)
-|+|+.|+......++|..||+..|..++||+|+.|++.|.+.+.|.+|..+|... .|.|+. |..
T Consensus 263 ------~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~-------~y~C~h~~C~~ 329 (467)
T KOG3608|consen 263 ------CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKT-------VYQCEHPDCHY 329 (467)
T ss_pred ------cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcccc-------ceecCCCCCcH
Confidence 46799999999999999999999999999999999999999999999999988732 499998 999
Q ss_pred cCCChhHHHHHHhhcC-C--CCCccccccccccccccccchhhccccccccCCCCCccccCCCcccccC
Q psy4688 260 KYPNKYTLSDHISGHT-G--IPNHICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFFE 325 (388)
Q Consensus 260 ~f~~~~~L~~H~~~H~-~--~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~ 325 (388)
+|++...|.+|++.+. | +.+|.|..|++.|++-.+|..|.++.|.-....+-+.|.=..|.-.|.+
T Consensus 330 s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~RFtYk~~edG~mR 398 (467)
T KOG3608|consen 330 SVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGHKRFTYKVDEDGFMR 398 (467)
T ss_pred HHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCCCceeeeeccCceee
Confidence 9999999999998765 4 4579999999999999999999998886544444445555555555543
No 7
>KOG3623|consensus
Probab=99.94 E-value=1.7e-26 Score=210.93 Aligned_cols=113 Identities=27% Similarity=0.656 Sum_probs=99.1
Q ss_pred cCCCCCcCCcCCCcHHHHHHHHhhccC-CCccccccchhcccChhhHHHHHHhhccCCCc-------CCCCccccccchh
Q psy4688 41 TKTCPICNKSYPGARNMRKHLRLVHDK-NSTTTCTMCKKTFRNKATFQKHMQRAHVGLKI-------SVSKHFECNYCHA 112 (388)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~~h~~-~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-------~~~~~~~C~~C~~ 112 (388)
..+|++|.+.+.....|+.|++..|.. +..|.|.+|..+|..+..|.+||..+-.+... ...+.|+|..||+
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 479999999999999999999887754 45699999999999999999999866544221 1236799999999
Q ss_pred ccCCchHHHHHHhhcCCCCCccCCccccccCChHHHHHHHh
Q psy4688 113 KFSNKSLLSDHISSHTGLKNYKCHVCDKAYSCRKALKTHTL 153 (388)
Q Consensus 113 ~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 153 (388)
.|..+-.|+.|+++|.|++||.|+.|++.|+....+..||-
T Consensus 290 AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 99999999999999999999999999999999999988874
No 8
>KOG3576|consensus
Probab=99.76 E-value=1.2e-19 Score=141.55 Aligned_cols=122 Identities=24% Similarity=0.424 Sum_probs=106.6
Q ss_pred CCCcccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCCcCCChhHHHHHHhhcCCCCCcccccccccccccc
Q psy4688 214 SVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAA 293 (388)
Q Consensus 214 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~ 293 (388)
+...|.|.+|+|.|.....|++|++-|...+ .|.|..||+.|.....|++|+++|+|.+||+|..|++.|+..-
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vk------r~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrc 187 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVK------RHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRC 187 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHH------HHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhc
Confidence 3456999999999999999999999988665 5899999999999999999999999999999999999999999
Q ss_pred ccchhhcccccccc-----CCCCCccccCCCcccccChhhHHhHHhhhcCCCc
Q psy4688 294 SLKIHNIKTHLQFT-----GVPIEKFKCDLCDKEFFEKKKLNKHKNWAHGDKF 341 (388)
Q Consensus 294 ~L~~H~~~~H~~~~-----~~~~~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~ 341 (388)
+|..|..++|.... ....+.|.|+.||.+-.....+..|++.||..-|
T Consensus 188 sleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 188 SLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred cHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 99999888885422 1224569999999999999999999999987654
No 9
>KOG3576|consensus
Probab=99.67 E-value=1.1e-17 Score=130.65 Aligned_cols=111 Identities=31% Similarity=0.655 Sum_probs=97.8
Q ss_pred cccccccCCcCCChhHHHHHHhhcCCCCCccccccccccccccccchhhccccccccCCCCCccccCCCcccccChhhHH
Q psy4688 251 EYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFFEKKKLN 330 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~ 330 (388)
.|.|.+|+|.|.-+..|.+|++-|...+.|-|..||++|.....|++| .++| + .++||+|..|+|.|...-.|.
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh-~rth---t--gvrpykc~~c~kaftqrcsle 190 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRH-TRTH---T--GVRPYKCSLCEKAFTQRCSLE 190 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhh-hccc---c--CccccchhhhhHHHHhhccHH
Confidence 599999999999999999999999999999999999999999999999 4555 3 478999999999999999999
Q ss_pred hHHhhhcCC-----------CcccCCcchhhH--HhHHHHHHHHhcCCCC
Q psy4688 331 KHKNWAHGD-----------KFHLCKVCGAKI--KGSLKQHMITHTGERK 367 (388)
Q Consensus 331 ~H~~~hh~~-----------~~~~C~~C~~~f--~~~L~~H~~~H~~~~~ 367 (388)
.|++..||. +.|.|+.||.+- ...+..|+..|...-|
T Consensus 191 shl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 191 SHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 999999984 679999999865 3457788888765544
No 10
>KOG3623|consensus
Probab=99.57 E-value=9.4e-16 Score=141.28 Aligned_cols=112 Identities=23% Similarity=0.576 Sum_probs=99.3
Q ss_pred CCcccccccccCCchHHHHhHHhhhC-CCCcccCCCCcccCCChhHHHHHHHHhccCCccc-------ccCcccccccCC
Q psy4688 188 VTVCPKCNRDYRNPRNMRKHLRRVHT-SVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVK-------VKYEYECDYCGA 259 (388)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~~h~-~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~-------~~~~~~C~~C~~ 259 (388)
...|++|.+.+.....|+.|++..|. .+..|.|.+|..+|..+..|.+|+.+|..+.... ..+.|+|..|||
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 45799999999999999999987775 4567999999999999999999999987654321 234699999999
Q ss_pred cCCChhHHHHHHhhcCCCCCccccccccccccccccchhh
Q psy4688 260 KYPNKYTLSDHISGHTGIPNHICKICNKGYACAASLKIHN 299 (388)
Q Consensus 260 ~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~~H~ 299 (388)
.|..+..|+.|+|+|+|++||.|+-|+|+|.-..+...|+
T Consensus 290 AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred hhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccc
Confidence 9999999999999999999999999999999999998884
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.37 E-value=5.6e-13 Score=124.07 Aligned_cols=138 Identities=21% Similarity=0.500 Sum_probs=93.8
Q ss_pred ccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccc--cCCcCCChhHHHHHHhhcCCCCCcccccccccccccccc
Q psy4688 218 YGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDY--CGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAASL 295 (388)
Q Consensus 218 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~--C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L 295 (388)
-.|+.|...... ..|..|...-... .-.|+. ||..|. +..|..| +.|+.|++.|. ...|
T Consensus 408 V~C~NC~~~i~l-~~l~lHe~~C~r~-------~V~Cp~~~Cg~v~~-r~el~~H---------~~C~~Cgk~f~-~s~L 468 (567)
T PLN03086 408 VECRNCKHYIPS-RSIALHEAYCSRH-------NVVCPHDGCGIVLR-VEEAKNH---------VHCEKCGQAFQ-QGEM 468 (567)
T ss_pred EECCCCCCccch-hHHHHHHhhCCCc-------ceeCCcccccceee-ccccccC---------ccCCCCCCccc-hHHH
Confidence 467777765543 3455676433211 235763 887773 3344444 37888888885 5667
Q ss_pred chhhccccccccCCCCCccccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhHH------------hHHHHHHHHhc
Q psy4688 296 KIHNIKTHLQFTGVPIEKFKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKIK------------GSLKQHMITHT 363 (388)
Q Consensus 296 ~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f~------------~~L~~H~~~H~ 363 (388)
..|....| .++.|+ ||+.+ .+..|..|+.+|.+.+++.|+.|++.|. +.|..|+.+.
T Consensus 469 ekH~~~~H--------kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C- 537 (567)
T PLN03086 469 EKHMKVFH--------EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC- 537 (567)
T ss_pred HHHHHhcC--------CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-
Confidence 77754433 468888 88654 5688888888888888888888888773 2588888875
Q ss_pred CCCCccccccchhhH-hhhhhhh
Q psy4688 364 GERKYCCHICGKKLR-GKLKEHM 385 (388)
Q Consensus 364 ~~~~~~C~~C~k~f~-~~l~~H~ 385 (388)
|.+++.|..||+.|. .-|..|+
T Consensus 538 G~rt~~C~~Cgk~Vrlrdm~~H~ 560 (567)
T PLN03086 538 GSRTAPCDSCGRSVMLKEMDIHQ 560 (567)
T ss_pred CCcceEccccCCeeeehhHHHHH
Confidence 888888888888884 4477775
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.29 E-value=4.1e-12 Score=118.43 Aligned_cols=142 Identities=19% Similarity=0.477 Sum_probs=108.0
Q ss_pred CcccccccccCCchHHHHhHHhhhCCCCcccCCC--CcccCCChhHHHHHHHHhccCCcccccCcccccccCCcCCChhH
Q psy4688 189 TVCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDE--CGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAKYPNKYT 266 (388)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~ 266 (388)
..|+.|..... ..+|..|.. +-.-..-.|+. ||..|. +..+..| +.|+.|++.|. ...
T Consensus 408 V~C~NC~~~i~-l~~l~lHe~--~C~r~~V~Cp~~~Cg~v~~-r~el~~H---------------~~C~~Cgk~f~-~s~ 467 (567)
T PLN03086 408 VECRNCKHYIP-SRSIALHEA--YCSRHNVVCPHDGCGIVLR-VEEAKNH---------------VHCEKCGQAFQ-QGE 467 (567)
T ss_pred EECCCCCCccc-hhHHHHHHh--hCCCcceeCCcccccceee-ccccccC---------------ccCCCCCCccc-hHH
Confidence 36999988775 456668852 33334567884 999884 3334443 57999999996 678
Q ss_pred HHHHHhhcCCCCCccccccccccccccccchhhccccccccCCCCCccccCCCccccc----------ChhhHHhHHhhh
Q psy4688 267 LSDHISGHTGIPNHICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFF----------EKKKLNKHKNWA 336 (388)
Q Consensus 267 L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~----------~~~~L~~H~~~h 336 (388)
|..|+..|+ .++.|+ ||+.+ ....|..|. .. ..+.+++.|+.|++.|. ..+.|..|...
T Consensus 468 LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~-~t-----hCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~- 536 (567)
T PLN03086 468 MEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQ-AS-----TCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI- 536 (567)
T ss_pred HHHHHHhcC--CCccCC-CCCCc-chhHHHhhh-hc-----cCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh-
Confidence 999999985 789999 99755 567888883 33 34578999999999995 24589999987
Q ss_pred cCCCcccCCcchhhH-HhHHHHHHHH
Q psy4688 337 HGDKFHLCKVCGAKI-KGSLKQHMIT 361 (388)
Q Consensus 337 h~~~~~~C~~C~~~f-~~~L~~H~~~ 361 (388)
.|.+++.|..||+.+ ...|..|+..
T Consensus 537 CG~rt~~C~~Cgk~Vrlrdm~~H~~~ 562 (567)
T PLN03086 537 CGSRTAPCDSCGRSVMLKEMDIHQIA 562 (567)
T ss_pred cCCcceEccccCCeeeehhHHHHHHH
Confidence 599999999999998 4568888763
No 13
>PHA00733 hypothetical protein
Probab=99.13 E-value=5e-11 Score=90.66 Aligned_cols=80 Identities=19% Similarity=0.259 Sum_probs=50.4
Q ss_pred cccccccCCcCCChhHHHHH--Hh---hcCCCCCccccccccccccccccchhhccccccccCCCCCccccCCCcccccC
Q psy4688 251 EYECDYCGAKYPNKYTLSDH--IS---GHTGIPNHICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFFE 325 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H--~~---~H~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~ 325 (388)
++.|.+|++.|.+...|..+ ++ .+.+.+||.|+.||+.|.+...|..|.. .| ..+|.|+.|++.|..
T Consensus 40 ~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r-~h-------~~~~~C~~CgK~F~~ 111 (128)
T PHA00733 40 RLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIR-YT-------EHSKVCPVCGKEFRN 111 (128)
T ss_pred hHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHh-cC-------CcCccCCCCCCccCC
Confidence 57788887777776666555 11 2233566777777777777777766633 22 124677777777777
Q ss_pred hhhHHhHHhhhcC
Q psy4688 326 KKKLNKHKNWAHG 338 (388)
Q Consensus 326 ~~~L~~H~~~hh~ 338 (388)
...|..|+...|+
T Consensus 112 ~~sL~~H~~~~h~ 124 (128)
T PHA00733 112 TDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHHhcC
Confidence 7777777766665
No 14
>KOG3993|consensus
Probab=99.11 E-value=2.5e-11 Score=105.86 Aligned_cols=201 Identities=19% Similarity=0.324 Sum_probs=120.7
Q ss_pred CccccccchhccCCchHHHHHHhhcCCCCCccCCccccccCChHHHHHHHhhhcccccccc--cCc-eeeecCCCCCccc
Q psy4688 103 KHFECNYCHAKFSNKSLLSDHISSHTGLKNYKCHVCDKAYSCRKALKTHTLLHEQEKVIKS--SKK-EFIIDTGDCTLDE 179 (388)
Q Consensus 103 ~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~--~~~-~~~~~~~~~~~~~ 179 (388)
..|.|..|...|.+...|.+|.-.-.-...|+|+.|+++|+...+|..|.++|........ ... ...+++++
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ra----- 340 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRA----- 340 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhh-----
Confidence 3599999999999999999996433333469999999999999999999999975433221 000 00011000
Q ss_pred cchhhccCCCcccccccccCCchHHHHhHH--hhhCCCCcccCCCCcccCCChhHHHHHHHHhccCCccccc--------
Q psy4688 180 WNDFIKRRVTVCPKCNRDYRNPRNMRKHLR--RVHTSVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVK-------- 249 (388)
Q Consensus 180 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~--~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~-------- 249 (388)
+.+-.. .....+..|.|.+|++.|.+...|+.|+.+|+.....+..
T Consensus 341 ------------------------e~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~ 396 (500)
T KOG3993|consen 341 ------------------------EVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSR 396 (500)
T ss_pred ------------------------hhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhh
Confidence 000000 0012233577777777777777777777777654333211
Q ss_pred ---CcccccccCCcCCChhHHHHHHhhcCC-CCCccccccccccccccccchhhccccccccCCCCCccccCCCcccccC
Q psy4688 250 ---YEYECDYCGAKYPNKYTLSDHISGHTG-IPNHICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFFE 325 (388)
Q Consensus 250 ---~~~~C~~C~~~f~~~~~L~~H~~~H~~-~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~ 325 (388)
.-+-|+.|+-.+.....-..+...+.+ .....|++||-.+.++..--.+.. .+.....|.|.+|.-.|.+
T Consensus 397 ~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~r------lg~~~q~f~~ky~~atfys 470 (500)
T KOG3993|consen 397 VIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGR------LGIAEQGFTCKYCPATFYS 470 (500)
T ss_pred cccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCcccc------ccchhhccccccchHhhhc
Confidence 113455555555443333333322222 123457778877766555444421 1223456889999999999
Q ss_pred hhhHHhHHhhhcC
Q psy4688 326 KKKLNKHKNWAHG 338 (388)
Q Consensus 326 ~~~L~~H~~~hh~ 338 (388)
...|.+|+...|.
T Consensus 471 s~~ltrhin~~Hp 483 (500)
T KOG3993|consen 471 SPGLTRHINKCHP 483 (500)
T ss_pred CcchHhHhhhcCh
Confidence 9999999876553
No 15
>PHA00733 hypothetical protein
Probab=99.05 E-value=2.9e-10 Score=86.49 Aligned_cols=98 Identities=15% Similarity=0.291 Sum_probs=70.6
Q ss_pred cHHHHHHHHhhccCCCccccccchhcccChhhHHHH--HHhhccCCCcCCCCccccccchhccCCchHHHHHHhhcCCCC
Q psy4688 54 ARNMRKHLRLVHDKNSTTTCTMCKKTFRNKATFQKH--MQRAHVGLKISVSKHFECNYCHAKFSNKSLLSDHISSHTGLK 131 (388)
Q Consensus 54 ~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H--~~~~h~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~ 131 (388)
...|.++-.+ -...+++.|.+|++.|.....|..+ +.++ . .....++|.|+.|++.|.+...|..|++.| +.
T Consensus 25 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~-~--~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~ 98 (128)
T PHA00733 25 LEELKRYHSL-TPEQKRLIRAVVKTLIYNPQLLDESSYLYKL-L--TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EH 98 (128)
T ss_pred HHHhhhhhcC-ChhhhhHHHHHHhhhccChhhhcchHHHHhh-c--ccCCCCCccCCCCCCcCCCHHHHHHHHhcC--Cc
Confidence 4445444221 2335678888888888887777766 2221 1 112357899999999999999999998876 35
Q ss_pred CccCCccccccCChHHHHHHHhhhcc
Q psy4688 132 NYKCHVCDKAYSCRKALKTHTLLHEQ 157 (388)
Q Consensus 132 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 157 (388)
+|.|+.|++.|.....|..|+...++
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 78999999999999999999876654
No 16
>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=99.00 E-value=1.6e-10 Score=61.38 Aligned_cols=25 Identities=52% Similarity=1.042 Sum_probs=22.7
Q ss_pred HHHHHHHHhcCCCCccccccchhhH
Q psy4688 354 SLKQHMITHTGERKYCCHICGKKLR 378 (388)
Q Consensus 354 ~L~~H~~~H~~~~~~~C~~C~k~f~ 378 (388)
+|.+||++|+|++||.|++|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 5889999999999999999999984
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.97 E-value=3.4e-10 Score=70.25 Aligned_cols=44 Identities=23% Similarity=0.455 Sum_probs=37.1
Q ss_pred cccccccCCcCCChhHHHHHHhhcCCCCCccccccccccccccccc
Q psy4688 251 EYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAASLK 296 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~ 296 (388)
.|+|+.||+.|.....|..|+++|+ ++|+|..|++.|...+.|.
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 4789999999999899999998888 5888888888888777764
No 18
>KOG3993|consensus
Probab=98.90 E-value=2e-10 Score=100.36 Aligned_cols=110 Identities=22% Similarity=0.442 Sum_probs=68.6
Q ss_pred cCCCCCcCCcCCCcHHHHHHH--HhhccCCCccccccchhcccChhhHHHHHHhhccCCCcC--CCCccccccchhccCC
Q psy4688 41 TKTCPICNKSYPGARNMRKHL--RLVHDKNSTTTCTMCKKTFRNKATFQKHMQRAHVGLKIS--VSKHFECNYCHAKFSN 116 (388)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~--~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~--~~~~~~C~~C~~~f~~ 116 (388)
.|.|..|...|.+...|.+|. +++| ..|+|+.|+|+|.-..+|..|.+.|-...... ...+=+ +.-.+
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~---vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k-----~~~~~ 338 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVH---VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPK-----QAVET 338 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEE---eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChh-----hhhhh
Confidence 599999999999999999994 3334 35999999999999999999976543221111 001100 00000
Q ss_pred chHHHHHHhh--cCCCCCccCCccccccCChHHHHHHHhhhccc
Q psy4688 117 KSLLSDHISS--HTGLKNYKCHVCDKAYSCRKALKTHTLLHEQE 158 (388)
Q Consensus 117 ~~~L~~H~~~--h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 158 (388)
....+.=.+. ...+.-|.|.+|++.|.+...|+.|+.+|+..
T Consensus 339 rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 339 RAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred hhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 0000000000 02234688888888888888888888887654
No 19
>PHA02768 hypothetical protein; Provisional
Probab=98.87 E-value=1e-09 Score=68.14 Aligned_cols=43 Identities=19% Similarity=0.434 Sum_probs=36.6
Q ss_pred ccccccchhccCCchHHHHHHhhcCCCCCccCCccccccCChHHH
Q psy4688 104 HFECNYCHAKFSNKSLLSDHISSHTGLKNYKCHVCDKAYSCRKAL 148 (388)
Q Consensus 104 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l 148 (388)
.|.|+.||+.|+..+.|..|+++|+ ++|+|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3789999999999999999999987 688999999988876655
No 20
>PHA00616 hypothetical protein
Probab=98.69 E-value=6.8e-09 Score=61.19 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=25.0
Q ss_pred ccccCCCcccccChhhHHhHHhhhcCCCcccCCc
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKV 346 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~ 346 (388)
||+|+.||+.|..++.|.+|++.|||++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4677777777777777777777777777776653
No 21
>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=98.68 E-value=1e-08 Score=54.40 Aligned_cols=25 Identities=32% Similarity=0.663 Sum_probs=22.1
Q ss_pred HHHHHHhhcCCCCCccccccccccc
Q psy4688 266 TLSDHISGHTGIPNHICKICNKGYA 290 (388)
Q Consensus 266 ~L~~H~~~H~~~~~~~C~~C~k~f~ 290 (388)
+|..|+++|+|++||.|++|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4788999999999999999999886
No 22
>PHA00732 hypothetical protein
Probab=98.60 E-value=1.6e-08 Score=69.47 Aligned_cols=46 Identities=28% Similarity=0.606 Sum_probs=24.3
Q ss_pred cccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhHHhHHHHHHHHh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKIKGSLKQHMITH 362 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f~~~L~~H~~~H 362 (388)
|.|+.||+.|.+...|+.|++.+|. ++.|+.||+.|. .|..|++++
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 5556666666666666666553222 235666665554 355555443
No 23
>PHA00616 hypothetical protein
Probab=98.52 E-value=7.2e-08 Score=56.90 Aligned_cols=32 Identities=19% Similarity=0.407 Sum_probs=29.7
Q ss_pred cccCCcchhhH--HhHHHHHHHHhcCCCCccccc
Q psy4688 341 FHLCKVCGAKI--KGSLKQHMITHTGERKYCCHI 372 (388)
Q Consensus 341 ~~~C~~C~~~f--~~~L~~H~~~H~~~~~~~C~~ 372 (388)
||+|+.||+.| +++|..|++.|+|++|+.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 68999999999 678999999999999999975
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=98.52 E-value=1.9e-07 Score=59.57 Aligned_cols=50 Identities=26% Similarity=0.595 Sum_probs=35.8
Q ss_pred ccccCCCcccccChhhHHhHHhhhcCC--CcccCCcchhhHHhHHHHHHHHhc
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHGD--KFHLCKVCGAKIKGSLKQHMITHT 363 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~~--~~~~C~~C~~~f~~~L~~H~~~H~ 363 (388)
.|.||+|++ ..+...|..|....|.. +.+.|++|...+..+|..||..+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhc
Confidence 477888888 45567788887766542 457788888777777888877654
No 25
>PHA00732 hypothetical protein
Probab=98.43 E-value=1.8e-07 Score=64.31 Aligned_cols=21 Identities=24% Similarity=0.513 Sum_probs=10.0
Q ss_pred ccCCCCcccCCChhHHHHHHH
Q psy4688 218 YGCDECGKMLKSRDSLNTHKK 238 (388)
Q Consensus 218 ~~C~~C~~~f~~~~~l~~H~~ 238 (388)
|.|++||+.|.+..+|..|++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh
Confidence 444444444444444444444
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.36 E-value=7.8e-07 Score=56.79 Aligned_cols=51 Identities=22% Similarity=0.520 Sum_probs=33.5
Q ss_pred cCCCCCcCCcCCCcHHHHHHHHhhccCC-CccccccchhcccChhhHHHHHHhhc
Q psy4688 41 TKTCPICNKSYPGARNMRKHLRLVHDKN-STTTCTMCKKTFRNKATFQKHMQRAH 94 (388)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~h 94 (388)
.|+||+|++ ..+...|..|+...|..+ ..+.|++|...+. .+|..|+...|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 477777777 445667777776666554 3577777776544 36777776554
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=98.10 E-value=1.8e-06 Score=44.44 Aligned_cols=23 Identities=35% Similarity=0.803 Sum_probs=19.8
Q ss_pred cccCCCcccccChhhHHhHHhhh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWA 336 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~h 336 (388)
|+|++|++.|.++..|..|++.|
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 67999999999999999998873
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=97.95 E-value=5.5e-06 Score=43.09 Aligned_cols=24 Identities=38% Similarity=0.805 Sum_probs=19.3
Q ss_pred cccCCCcccccChhhHHhHHhhhc
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWAH 337 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~hh 337 (388)
|.|++|++.|.+...|+.|++++|
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 679999999999999999998875
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=97.82 E-value=1.1e-05 Score=41.39 Aligned_cols=20 Identities=35% Similarity=0.786 Sum_probs=9.1
Q ss_pred cCCCCcccCCChhHHHHHHH
Q psy4688 219 GCDECGKMLKSRDSLNTHKK 238 (388)
Q Consensus 219 ~C~~C~~~f~~~~~l~~H~~ 238 (388)
.|++|++.|.++..|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHh
Confidence 34444444444444444444
No 30
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.82 E-value=5.8e-06 Score=70.19 Aligned_cols=58 Identities=26% Similarity=0.552 Sum_probs=35.0
Q ss_pred CCCccccc--cccccccccccchhhcccccc-------------ccCCCCCccccCCCcccccChhhHHhHHh
Q psy4688 277 IPNHICKI--CNKGYACAASLKIHNIKTHLQ-------------FTGVPIEKFKCDLCDKEFFEKKKLNKHKN 334 (388)
Q Consensus 277 ~~~~~C~~--C~k~f~~~~~L~~H~~~~H~~-------------~~~~~~~~~~C~~C~k~F~~~~~L~~H~~ 334 (388)
++||+|++ |+|.|+....|+.|++.-|.. .-....+||.|++|+|+|+....|+.|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 36677765 677777777777665544411 01112366777777777777777777654
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.71 E-value=1.8e-05 Score=42.43 Aligned_cols=26 Identities=35% Similarity=0.612 Sum_probs=22.0
Q ss_pred ccccCCCcccccChhhHHhHHhhhcC
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHG 338 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~ 338 (388)
+|+|+.|++.|.+...|..|++.|++
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 57899999999999999999987753
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.68 E-value=2.3e-05 Score=57.58 Aligned_cols=24 Identities=29% Similarity=0.776 Sum_probs=12.8
Q ss_pred CccCCccccccCChHHHHHHHhhh
Q psy4688 132 NYKCHVCDKAYSCRKALKTHTLLH 155 (388)
Q Consensus 132 ~~~C~~C~~~f~~~~~l~~H~~~h 155 (388)
.+.|..|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 455555555555555555555543
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.64 E-value=2.6e-05 Score=57.28 Aligned_cols=72 Identities=19% Similarity=0.468 Sum_probs=17.8
Q ss_pred ccccccccCCchHHHHhHHhhhCCCCcccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCCcCCChhHHHHH
Q psy4688 191 CPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAKYPNKYTLSDH 270 (388)
Q Consensus 191 C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H 270 (388)
|..|+..|.+...|..||...|.-..+ ....+.....+..+.+.. +...+.|.+|++.|.+...|..|
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~-------~~~~~~C~~C~~~f~s~~~l~~H 69 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKK-------VKESFRCPYCNKTFRSREALQEH 69 (100)
T ss_dssp -----------------------------------------------------------SSEEBSSSS-EESSHHHHHHH
T ss_pred ccccccccccccccccccccccccccc-----cccccccccccccccccc-------cCCCCCCCccCCCCcCHHHHHHH
Confidence 777888888888888887766653322 111122333333333221 11147788888888888888888
Q ss_pred Hhhc
Q psy4688 271 ISGH 274 (388)
Q Consensus 271 ~~~H 274 (388)
|+.+
T Consensus 70 m~~~ 73 (100)
T PF12756_consen 70 MRSK 73 (100)
T ss_dssp HHHT
T ss_pred HcCc
Confidence 8764
No 34
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.63 E-value=3.8e-05 Score=39.78 Aligned_cols=22 Identities=32% Similarity=0.750 Sum_probs=10.2
Q ss_pred cCCCCcccCCChhHHHHHHHHh
Q psy4688 219 GCDECGKMLKSRDSLNTHKKIQ 240 (388)
Q Consensus 219 ~C~~C~~~f~~~~~l~~H~~~~ 240 (388)
.|++|++.|.+...|..|+.++
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHhh
Confidence 4555555555555555555444
No 35
>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=97.47 E-value=0.00014 Score=43.96 Aligned_cols=32 Identities=19% Similarity=0.342 Sum_probs=23.4
Q ss_pred CCCccccCCCcccccChhhHHhHHhhhcCCCc
Q psy4688 310 PIEKFKCDLCDKEFFEKKKLNKHKNWAHGDKF 341 (388)
Q Consensus 310 ~~~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~ 341 (388)
.+.|-.|++|+..+.+..+|++|+...|+.+|
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 35688999999999999999999999998876
No 36
>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=97.45 E-value=5.6e-05 Score=40.47 Aligned_cols=23 Identities=43% Similarity=0.927 Sum_probs=10.8
Q ss_pred ccCCCCcccCCChhHHHHHHHHh
Q psy4688 218 YGCDECGKMLKSRDSLNTHKKIQ 240 (388)
Q Consensus 218 ~~C~~C~~~f~~~~~l~~H~~~~ 240 (388)
|.|+.|++.|.+...|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 44444444444444444444433
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.32 E-value=9e-05 Score=63.16 Aligned_cols=24 Identities=29% Similarity=0.528 Sum_probs=20.2
Q ss_pred CCCCccccccccccccccccchhh
Q psy4688 276 GIPNHICKICNKGYACAASLKIHN 299 (388)
Q Consensus 276 ~~~~~~C~~C~k~f~~~~~L~~H~ 299 (388)
..+||.|++|+|+|+....|+.|.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 357899999999999988888883
No 38
>PRK04860 hypothetical protein; Provisional
Probab=97.05 E-value=0.00028 Score=55.88 Aligned_cols=34 Identities=32% Similarity=0.677 Sum_probs=18.1
Q ss_pred ccCCcchhhHHhHHHHHHHHhcCCCCccccccchhh
Q psy4688 342 HLCKVCGAKIKGSLKQHMITHTGERKYCCHICGKKL 377 (388)
Q Consensus 342 ~~C~~C~~~f~~~L~~H~~~H~~~~~~~C~~C~k~f 377 (388)
|.|. |+. ...++++|+++|+|+++|.|..|+..|
T Consensus 120 Y~C~-C~~-~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 120 YRCK-CQE-HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEcC-CCC-eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 4444 444 333455555555555555555555554
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.04 E-value=0.00045 Score=35.68 Aligned_cols=24 Identities=29% Similarity=0.565 Sum_probs=17.8
Q ss_pred cccCCCcccccChhhHHhHHhhhcC
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWAHG 338 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~hh~ 338 (388)
|+|+.|+.... +..|.+|++.+|+
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 67888888887 8888888888774
No 40
>KOG2231|consensus
Probab=97.03 E-value=0.00075 Score=64.78 Aligned_cols=147 Identities=27% Similarity=0.467 Sum_probs=90.4
Q ss_pred CcccccccccCCchHHHHhHHhhhCCCCcccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCC---------
Q psy4688 189 TVCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGA--------- 259 (388)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~--------- 259 (388)
..|.+|++.|.... ..-.|..| -.|.+...|+.|+...|.. +.|.+|-.
T Consensus 100 ~~C~~C~~~~~~~~-------------~~~~~~~c-~~~~s~~~Lk~H~~~~H~~--------~~c~lC~~~~kif~~e~ 157 (669)
T KOG2231|consen 100 HSCHICDRRFRALY-------------NKKECLHC-TEFKSVENLKNHMRDQHKL--------HLCSLCLQNLKIFINER 157 (669)
T ss_pred hhcCccccchhhhc-------------ccCCCccc-cchhHHHHHHHHHHHhhhh--------hccccccccceeeeeee
Confidence 56888877763210 11357777 6777888888888766642 44544422
Q ss_pred cCCChhHHHHHHhhcCC-CC----CccccccccccccccccchhhccccccccCCCCCccccCCC------cccccChhh
Q psy4688 260 KYPNKYTLSDHISGHTG-IP----NHICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLC------DKEFFEKKK 328 (388)
Q Consensus 260 ~f~~~~~L~~H~~~H~~-~~----~~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C------~k~F~~~~~ 328 (388)
...++..|..|+..-.. +. --.|..|...|-....|..|....| |.|-.| +..|.....
T Consensus 158 k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h----------~~chfC~~~~~~neyy~~~~d 227 (669)
T KOG2231|consen 158 KLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH----------EFCHFCDYKTGQNEYYNDYDD 227 (669)
T ss_pred ehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce----------eheeecCcccccchhcccchH
Confidence 22345677777653211 11 2358888888888888888866555 445555 456778888
Q ss_pred HHhHHhhhcCCCcccCC--cchh-hH------HhHHHHHHHHhcCCCCcccc
Q psy4688 329 LNKHKNWAHGDKFHLCK--VCGA-KI------KGSLKQHMITHTGERKYCCH 371 (388)
Q Consensus 329 L~~H~~~hh~~~~~~C~--~C~~-~f------~~~L~~H~~~H~~~~~~~C~ 371 (388)
|..|.+..| |.|+ .|.. .| ...|+.|.+.+.-++-|.|.
T Consensus 228 Le~HfR~~H----flCE~~~C~~~~f~~~~~~ei~lk~~~~~~~~e~~~~~~ 275 (669)
T KOG2231|consen 228 LEEHFRKGH----FLCEEEFCRTKKFYVAFELEIELKAHNRFIQHEKCYICR 275 (669)
T ss_pred HHHHhhhcC----ccccccccccceeeehhHHHHHHHhhccccchheeccCC
Confidence 999988766 6777 6642 23 22355555444445555553
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.00 E-value=0.00059 Score=35.81 Aligned_cols=23 Identities=30% Similarity=0.611 Sum_probs=17.7
Q ss_pred cccCCCcccccChhhHHhHHhhh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWA 336 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~h 336 (388)
|.|+.|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46888888888888888887754
No 42
>KOG2231|consensus
Probab=96.91 E-value=0.0019 Score=62.10 Aligned_cols=103 Identities=24% Similarity=0.513 Sum_probs=65.2
Q ss_pred ccccccccCCchHHHHhHHhhhCCCCcccCCCCc---------ccCCChhHHHHHHHHhcc-CCcccccCcccccccCCc
Q psy4688 191 CPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECG---------KMLKSRDSLNTHKKIQHE-GKKVKVKYEYECDYCGAK 260 (388)
Q Consensus 191 C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~---------~~f~~~~~l~~H~~~~~~-~~~~~~~~~~~C~~C~~~ 260 (388)
|..| ..|.+...|+.|+...|.. +.|.+|- ...-+...|..|+..--. ++..++ --.|..|...
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rG--hp~C~~C~~~ 191 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRG--HPLCKFCHER 191 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccC--Cccchhhhhh
Confidence 7777 7777888888887766643 4455442 222356677777765433 222111 2368888888
Q ss_pred CCChhHHHHHHhhcCCCCCcccccc------ccccccccccchhhcccc
Q psy4688 261 YPNKYTLSDHISGHTGIPNHICKIC------NKGYACAASLKIHNIKTH 303 (388)
Q Consensus 261 f~~~~~L~~H~~~H~~~~~~~C~~C------~k~f~~~~~L~~H~~~~H 303 (388)
|.....|..|++.++ |.|..| +.-|.....|..|-...|
T Consensus 192 fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 192 FLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 888888888887654 345555 445666677887766666
No 43
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.89 E-value=0.0015 Score=56.49 Aligned_cols=24 Identities=21% Similarity=0.534 Sum_probs=15.4
Q ss_pred ccccc--chhcccChhhHHHHHHhhc
Q psy4688 71 TTCTM--CKKTFRNKATFQKHMQRAH 94 (388)
Q Consensus 71 ~~C~~--C~~~f~~~~~l~~H~~~~h 94 (388)
|.|+. |..+......|..|.+..|
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H 177 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQH 177 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhc
Confidence 56654 6666666667777766555
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.88 E-value=0.0006 Score=35.61 Aligned_cols=23 Identities=35% Similarity=0.779 Sum_probs=19.2
Q ss_pred cccCCCcccccChhhHHhHHhhh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWA 336 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~h 336 (388)
|.|++|++.|.+...|+.|++.+
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 57889999999999999988753
No 45
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.86 E-value=0.00092 Score=35.05 Aligned_cols=21 Identities=29% Similarity=0.727 Sum_probs=9.7
Q ss_pred cccccCCcCCChhHHHHHHhh
Q psy4688 253 ECDYCGAKYPNKYTLSDHISG 273 (388)
Q Consensus 253 ~C~~C~~~f~~~~~L~~H~~~ 273 (388)
.|+.|++.|.+...|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHH
Confidence 344444444444444444443
No 46
>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=96.55 E-value=0.001 Score=35.49 Aligned_cols=22 Identities=41% Similarity=0.801 Sum_probs=18.3
Q ss_pred cccCCCcccccChhhHHhHHhh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNW 335 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~ 335 (388)
|.|++|++.|.+...|..|++.
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 6788888888888888888875
No 47
>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=96.54 E-value=0.0014 Score=39.72 Aligned_cols=33 Identities=27% Similarity=0.507 Sum_probs=19.2
Q ss_pred hCCCCcccCCCCcccCCChhHHHHHHHHhccCC
Q psy4688 212 HTSVRKYGCDECGKMLKSRDSLNTHKKIQHEGK 244 (388)
Q Consensus 212 h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 244 (388)
+.++.|-.|++|+..+.+..+|++|+.+.|..+
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 445567777777777777777777777766543
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.42 E-value=0.0016 Score=33.90 Aligned_cols=17 Identities=35% Similarity=0.905 Sum_probs=6.4
Q ss_pred cccchhccCCchHHHHH
Q psy4688 107 CNYCHAKFSNKSLLSDH 123 (388)
Q Consensus 107 C~~C~~~f~~~~~L~~H 123 (388)
|++|++.|.+...|..|
T Consensus 3 C~~C~~~f~s~~~~~~H 19 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQH 19 (25)
T ss_dssp ETTTTEEESSHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHH
Confidence 33333333333333333
No 49
>PRK04860 hypothetical protein; Provisional
Probab=96.34 E-value=0.002 Score=51.04 Aligned_cols=40 Identities=20% Similarity=0.500 Sum_probs=34.0
Q ss_pred CcccccccCCcCCChhHHHHHHhhcCCCCCcccccccccccccc
Q psy4688 250 YEYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAA 293 (388)
Q Consensus 250 ~~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~ 293 (388)
.+|.|. |+. ....+.+|.++|+++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 479998 987 6778899999999999999999999886543
No 50
>KOG2482|consensus
Probab=96.33 E-value=0.026 Score=49.17 Aligned_cols=77 Identities=22% Similarity=0.288 Sum_probs=44.5
Q ss_pred CcccccccccCCchHHHHhHHhhhCCCC-cccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCCcCCChhHH
Q psy4688 189 TVCPKCNRDYRNPRNMRKHLRRVHTSVR-KYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAKYPNKYTL 267 (388)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~-~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L 267 (388)
.+|-.|.....+...|..||..+|.-+- +-+ ..=+-.|-.+-.+..=++.. .+.-.|-.|.-.|.....|
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~-sd~~Ln~YqrvrviNyiRkq--------~~~~~c~~cd~~F~~e~~l 350 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQ-SDYSLNFYQRVRVINYIRKQ--------KKKSRCAECDLSFWKEPGL 350 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhc-cccccchhhhhhHHHHHHHH--------hhccccccccccccCcchh
Confidence 5788888888888889999888874210 000 00011111121121111111 1124588888999999999
Q ss_pred HHHHhhc
Q psy4688 268 SDHISGH 274 (388)
Q Consensus 268 ~~H~~~H 274 (388)
..||..+
T Consensus 351 ~~hm~e~ 357 (423)
T KOG2482|consen 351 LIHMVED 357 (423)
T ss_pred hhhcccc
Confidence 9998654
No 51
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.96 E-value=0.0031 Score=54.69 Aligned_cols=19 Identities=21% Similarity=0.532 Sum_probs=9.4
Q ss_pred ccccCCcCCChhHHHHHHh
Q psy4688 254 CDYCGAKYPNKYTLSDHIS 272 (388)
Q Consensus 254 C~~C~~~f~~~~~L~~H~~ 272 (388)
|..|...|.+-..|..|++
T Consensus 223 C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhccceecChHHHHHHHH
Confidence 4445555554445555544
No 52
>KOG1146|consensus
Probab=95.90 E-value=0.0012 Score=67.24 Aligned_cols=189 Identities=15% Similarity=0.185 Sum_probs=107.2
Q ss_pred CCCCcCCcCCCcHHHHHHHHhhccCCCccccccchhcccChhhHHHHHHhhccCCCcCCCCccccccchhccCCchHHHH
Q psy4688 43 TCPICNKSYPGARNMRKHLRLVHDKNSTTTCTMCKKTFRNKATFQKHMQRAHVGLKISVSKHFECNYCHAKFSNKSLLSD 122 (388)
Q Consensus 43 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~C~~C~~~f~~~~~L~~ 122 (388)
.|.-|+..+.+...+..|+...+.-.+.+.|+.|+..|.....|..||+..|..... .+|.. +.+...+.+
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--------~~c~~-gq~~~~~ar 508 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--------AYCKA-GQNHPRLAR 508 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch--------hHhHh-ccccccccc
Confidence 455566667777777777777777778899999999999999999999877654210 12211 000000000
Q ss_pred HHhhcCCCCCccCCccccccCChHHHHHHHhhhccccccc---ccCc------------eeeecCCCCCccccchhhccC
Q psy4688 123 HISSHTGLKNYKCHVCDKAYSCRKALKTHTLLHEQEKVIK---SSKK------------EFIIDTGDCTLDEWNDFIKRR 187 (388)
Q Consensus 123 H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~---~~~~------------~~~~~~~~~~~~~~~~~~~~~ 187 (388)
=...-.+.++|.|..|..+++++.+|..|+..-......+ .... ......+-.......+-....
T Consensus 509 g~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP 588 (1406)
T KOG1146|consen 509 GEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKP 588 (1406)
T ss_pred cccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCC
Confidence 0001123467777777777777777777775321110000 0000 000000000000000112234
Q ss_pred CCcccccccccCCchHHHHhHHhhhCCCCcccCCCCcccCCChhHHHHHHHHh
Q psy4688 188 VTVCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLKSRDSLNTHKKIQ 240 (388)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 240 (388)
.+.|.+|+..-.-..+|+.|+...+....|..+..++-.+.....+..+.+.+
T Consensus 589 ~~~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 589 SWRCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred CcchhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCCCC
Confidence 56799999999999999999876666555577777777666665555554444
No 53
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.88 E-value=0.0066 Score=31.22 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=8.6
Q ss_pred cCCCCcccCCChhHHHHHHHHh
Q psy4688 219 GCDECGKMLKSRDSLNTHKKIQ 240 (388)
Q Consensus 219 ~C~~C~~~f~~~~~l~~H~~~~ 240 (388)
+|+.|+.... ...|.+|++.+
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHhh
Confidence 4444444443 44444444443
No 54
>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=95.80 E-value=0.0036 Score=33.29 Aligned_cols=22 Identities=23% Similarity=0.693 Sum_probs=14.4
Q ss_pred ccccccCCcCCChhHHHHHHhh
Q psy4688 252 YECDYCGAKYPNKYTLSDHISG 273 (388)
Q Consensus 252 ~~C~~C~~~f~~~~~L~~H~~~ 273 (388)
|.|+.|++.|.+...|..|+++
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 5566777777776666666654
No 55
>KOG2785|consensus
Probab=95.62 E-value=0.038 Score=49.11 Aligned_cols=57 Identities=19% Similarity=0.266 Sum_probs=42.8
Q ss_pred cccCCCCcccCCChhHHHHHHHHhccCCccc-----------------ccCcccccccC---CcCCChhHHHHHHhh
Q psy4688 217 KYGCDECGKMLKSRDSLNTHKKIQHEGKKVK-----------------VKYEYECDYCG---AKYPNKYTLSDHISG 273 (388)
Q Consensus 217 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~-----------------~~~~~~C~~C~---~~f~~~~~L~~H~~~ 273 (388)
|-.|-.|++.+.+...-..||..+|+---+. +...|.|-.|+ +.|.+-.+.+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4668888888888888888888877643221 23457899998 899999999999864
No 56
>KOG2785|consensus
Probab=95.39 E-value=0.047 Score=48.55 Aligned_cols=53 Identities=19% Similarity=0.327 Sum_probs=43.4
Q ss_pred CCcccccccccCCchHHHHhHHhhhCC----------------------CCcccCCCCc---ccCCChhHHHHHHHHh
Q psy4688 188 VTVCPKCNRDYRNPRNMRKHLRRVHTS----------------------VRKYGCDECG---KMLKSRDSLNTHKKIQ 240 (388)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~~h~~----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~~ 240 (388)
+..|-.|++.+.+...-..||...|.- ..-+.|-.|+ +.|.+..+.+.||...
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 467999999999999999999776642 1236788888 9999999999999753
No 57
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.30 E-value=0.014 Score=30.31 Aligned_cols=20 Identities=30% Similarity=0.919 Sum_probs=13.1
Q ss_pred cccCCCcccccChhhHHhHHh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKN 334 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~ 334 (388)
.+|+.||+.| ..+.|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3577777777 5666666654
No 58
>KOG4173|consensus
Probab=94.96 E-value=0.0079 Score=48.27 Aligned_cols=42 Identities=17% Similarity=0.413 Sum_probs=19.2
Q ss_pred cccccCCchHHHHhHHhhhCCCCcccCCCCcccCCChhHHHHHHHH
Q psy4688 194 CNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLKSRDSLNTHKKI 239 (388)
Q Consensus 194 C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 239 (388)
|.+.|.+......|....|+ -.|..|.+.|.+..-|..|+..
T Consensus 87 c~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E 128 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILE 128 (253)
T ss_pred hHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHH
Confidence 44444444444444333332 2355555555555555555443
No 59
>KOG4173|consensus
Probab=94.90 E-value=0.0066 Score=48.69 Aligned_cols=113 Identities=19% Similarity=0.396 Sum_probs=74.8
Q ss_pred cceeeecccccCCCCCceeeeceehhHHHHHhhCCcCCCCC--cCCcCCCcHHHHHHHHhhccCCCccccccchhcccCh
Q psy4688 6 AEVFLSQNVQMSNLSGSCVVDVITADKWRALIKNKTKTCPI--CNKSYPGARNMRKHLRLVHDKNSTTTCTMCKKTFRNK 83 (388)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~ 83 (388)
...|-..||+-.-+.....+++... ...+....|.|++ |...|.+...+..|....|.. .|.+|.+.|.+.
T Consensus 47 ~pFf~~G~v~r~l~~~~V~~d~~d~---~~~~~~~~~~cqvagc~~~~d~lD~~E~hY~~~h~~----sCs~C~r~~Pt~ 119 (253)
T KOG4173|consen 47 HPFFEDGDVQRHLYLQDVIMDVADV---PEKPRVPAFACQVAGCCQVFDALDDYEHHYHTLHGN----SCSFCKRAFPTG 119 (253)
T ss_pred CcchhcccHHHHHhHhhheeecccc---ccccccccccccccchHHHHhhhhhHHHhhhhcccc----hhHHHHHhCCch
Confidence 3445555666555555555554222 2244556788887 778899988888888766643 699999999999
Q ss_pred hhHHHHHHhhccCC----CcCCCCccccc--cchhccCCchHHHHHHh
Q psy4688 84 ATFQKHMQRAHVGL----KISVSKHFECN--YCHAKFSNKSLLSDHIS 125 (388)
Q Consensus 84 ~~l~~H~~~~h~~~----~~~~~~~~~C~--~C~~~f~~~~~L~~H~~ 125 (388)
..|..|+...|... ...+...|+|- -|+..|.+...-+.|+.
T Consensus 120 hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 120 HLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred hhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHH
Confidence 99999987766421 01123457774 47777777777777754
No 60
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.86 E-value=0.0091 Score=56.60 Aligned_cols=157 Identities=16% Similarity=0.149 Sum_probs=101.2
Q ss_pred CcccCCCCcccCCChhHHHHHHH--HhccCCcccccCccccc--ccCCcCCChhHHHHHHhhcCCCCCcccccc--cccc
Q psy4688 216 RKYGCDECGKMLKSRDSLNTHKK--IQHEGKKVKVKYEYECD--YCGAKYPNKYTLSDHISGHTGIPNHICKIC--NKGY 289 (388)
Q Consensus 216 ~~~~C~~C~~~f~~~~~l~~H~~--~~~~~~~~~~~~~~~C~--~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C--~k~f 289 (388)
.++.|..|...|.....|..|.+ .|.... ..++.|+ .|++.|.+...+..|...|.+..++.+..- ...+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~----~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 363 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGES----LKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKF 363 (467)
T ss_pred cCCCCccccCCcccccccccccccccccccc----CCceeeeccCCCccccccccccCCcccccCCCccccccccCcccc
Confidence 36788888888888888888888 455441 1368888 799999888888888888888877776553 3333
Q ss_pred ccccccchhhccccccccCCCCCccccCC--CcccccChhhHHhHHhhhcCCC--cccCCcchhhHH--hHHHHHHHHhc
Q psy4688 290 ACAASLKIHNIKTHLQFTGVPIEKFKCDL--CDKEFFEKKKLNKHKNWAHGDK--FHLCKVCGAKIK--GSLKQHMITHT 363 (388)
Q Consensus 290 ~~~~~L~~H~~~~H~~~~~~~~~~~~C~~--C~k~F~~~~~L~~H~~~hh~~~--~~~C~~C~~~f~--~~L~~H~~~H~ 363 (388)
.....-..+ ..............+.+.. |-..+.+...+..|...+-..+ .+.+..|.+.+. ..|..|++.|.
T Consensus 364 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (467)
T COG5048 364 SPLLNNEPP-QSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHT 442 (467)
T ss_pred ccccCCCCc-cchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccc
Confidence 222221101 0000000111122333333 6777788888888877776655 466778887773 34778888888
Q ss_pred CCCCccccccchhh
Q psy4688 364 GERKYCCHICGKKL 377 (388)
Q Consensus 364 ~~~~~~C~~C~k~f 377 (388)
...++.|..++...
T Consensus 443 ~~~~~~~~~~~~~~ 456 (467)
T COG5048 443 NHAPLLCSILKSFR 456 (467)
T ss_pred cCCceeeccccccc
Confidence 88887776666554
No 61
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.73 E-value=0.031 Score=29.00 Aligned_cols=20 Identities=30% Similarity=0.904 Sum_probs=11.5
Q ss_pred CCCCCcCCcCCCcHHHHHHHH
Q psy4688 42 KTCPICNKSYPGARNMRKHLR 62 (388)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~ 62 (388)
..|++||+.| ....|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4566666666 4455666653
No 62
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.98 E-value=0.035 Score=31.49 Aligned_cols=23 Identities=26% Similarity=0.600 Sum_probs=19.9
Q ss_pred ccccCCCcccccChhhHHhHHhh
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNW 335 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~ 335 (388)
+|.|++|++.|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57899999999999999999874
No 63
>KOG2893|consensus
Probab=93.95 E-value=0.034 Score=45.81 Aligned_cols=47 Identities=28% Similarity=0.625 Sum_probs=34.6
Q ss_pred ccccCCcCCChhHHHHHHhhcCCCCCccccccccccccccccchhhccccc
Q psy4688 254 CDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAASLKIHNIKTHL 304 (388)
Q Consensus 254 C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 304 (388)
|-+|++.|.....|.+|++. +-|+|.+|.|...+--.|.+|-+.+|.
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 77888888888888777653 457888888777777777777666553
No 64
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.56 E-value=0.077 Score=38.85 Aligned_cols=47 Identities=17% Similarity=0.190 Sum_probs=25.4
Q ss_pred ccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhH--HhHHHHHHHHhc
Q psy4688 315 KCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKI--KGSLKQHMITHT 363 (388)
Q Consensus 315 ~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f--~~~L~~H~~~H~ 363 (388)
.|--|...|........ ........|.|+.|...| .-..-.|...|+
T Consensus 57 ~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccc--cccccccceeCCCCCCccccccchhhhhhccC
Confidence 37778887765431110 001223457788887777 334555655554
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=93.35 E-value=0.063 Score=30.40 Aligned_cols=23 Identities=17% Similarity=0.758 Sum_probs=16.3
Q ss_pred cccccccCCcCCChhHHHHHHhh
Q psy4688 251 EYECDYCGAKYPNKYTLSDHISG 273 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H~~~ 273 (388)
+|.|++|++.|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777777777777653
No 66
>KOG2482|consensus
Probab=93.20 E-value=0.13 Score=44.99 Aligned_cols=117 Identities=26% Similarity=0.489 Sum_probs=82.5
Q ss_pred CCcCCCCCcCCcCCC-cHHHHHHHHhhccCC---------------------CccccccchhcccChhhHHHHHHhh-cc
Q psy4688 39 NKTKTCPICNKSYPG-ARNMRKHLRLVHDKN---------------------STTTCTMCKKTFRNKATFQKHMQRA-HV 95 (388)
Q Consensus 39 ~~~~~C~~C~~~f~~-~~~l~~H~~~~h~~~---------------------~~~~C~~C~~~f~~~~~l~~H~~~~-h~ 95 (388)
.....|-.|+..+.. ++....|+-.+|.-+ ..+.|-+|.+.|.++..|+.||+.. |.
T Consensus 142 ~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hr 221 (423)
T KOG2482|consen 142 IFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHR 221 (423)
T ss_pred eeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCc
Confidence 345789999988754 556667765445311 2468999999999999999999743 21
Q ss_pred CCCc-----------------------------------------------CCCCc--cccccchhccCCchHHHHHHhh
Q psy4688 96 GLKI-----------------------------------------------SVSKH--FECNYCHAKFSNKSLLSDHISS 126 (388)
Q Consensus 96 ~~~~-----------------------------------------------~~~~~--~~C~~C~~~f~~~~~L~~H~~~ 126 (388)
.+.. ....+ ..|-.|.....+...|..||..
T Consensus 222 rinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~ 301 (423)
T KOG2482|consen 222 RINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKI 301 (423)
T ss_pred ccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHH
Confidence 1100 00112 5899999999999999999975
Q ss_pred cCC---------------------------CCCccCCccccccCChHHHHHHHhhh
Q psy4688 127 HTG---------------------------LKNYKCHVCDKAYSCRKALKTHTLLH 155 (388)
Q Consensus 127 h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~~h 155 (388)
-+. ...-.|-.|+-.|.....|..||..+
T Consensus 302 vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 302 VHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred HHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 321 01236888999999999999999754
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.16 E-value=0.043 Score=51.98 Aligned_cols=154 Identities=19% Similarity=0.308 Sum_probs=105.3
Q ss_pred CCCcccccccccCCchHHHHhHHh-hhCCC--CcccCC--CCcccCCChhHHHHHHHHhccCCcccccCccccc--ccCC
Q psy4688 187 RVTVCPKCNRDYRNPRNMRKHLRR-VHTSV--RKYGCD--ECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECD--YCGA 259 (388)
Q Consensus 187 ~~~~C~~C~~~f~~~~~l~~H~~~-~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~--~C~~ 259 (388)
..+.|..|...|.....|..|... .|.++ +++.|+ .|++.|.....+..|...+..... +.+. .+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~ 361 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP------AKEKLLNSSS 361 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc------cccccccCcc
Confidence 367899999999999999999764 89999 999999 899999999999999999886552 2222 2333
Q ss_pred cCCChhH-----HHHHHhhcCCCCCcccc--ccccccccccccchhhccccccccCCCCCccccCCCcccccChhhHHhH
Q psy4688 260 KYPNKYT-----LSDHISGHTGIPNHICK--ICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFFEKKKLNKH 332 (388)
Q Consensus 260 ~f~~~~~-----L~~H~~~H~~~~~~~C~--~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H 332 (388)
.+..... .......-.....+.+. .|...+.....+..|. ..|.. .....+.+..|.+.|.....|..|
T Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~ 437 (467)
T COG5048 362 KFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHI-ITHLS---FRPYNCKNPPCSKSFNRHYNLIPH 437 (467)
T ss_pred ccccccCCCCccchhhccCccCCccccccccchhhhhcccccccccc-ccccc---cCCcCCCCCcchhhccCccccccc
Confidence 3332222 11111111222333332 2556666666666663 33322 123468899999999999999999
Q ss_pred HhhhcCCCcccCCcchhh
Q psy4688 333 KNWAHGDKFHLCKVCGAK 350 (388)
Q Consensus 333 ~~~hh~~~~~~C~~C~~~ 350 (388)
++.+....++.|..++..
T Consensus 438 ~~~~~~~~~~~~~~~~~~ 455 (467)
T COG5048 438 KKIHTNHAPLLCSILKSF 455 (467)
T ss_pred ccccccCCceeecccccc
Confidence 999887777766655543
No 68
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.26 E-value=0.39 Score=35.29 Aligned_cols=21 Identities=24% Similarity=0.343 Sum_probs=16.1
Q ss_pred CcccCCCCcccCCChhHHHHH
Q psy4688 216 RKYGCDECGKMLKSRDSLNTH 236 (388)
Q Consensus 216 ~~~~C~~C~~~f~~~~~l~~H 236 (388)
-|..|++||-+..+...|.+-
T Consensus 14 LP~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARS 34 (112)
T ss_pred CCCcCCcCCCEEeccchHHHh
Confidence 477888888888887777654
No 69
>KOG2893|consensus
Probab=92.02 E-value=0.048 Score=44.97 Aligned_cols=47 Identities=21% Similarity=0.523 Sum_probs=30.8
Q ss_pred CCCCcCCcCCCcHHHHHHHHhhccCCCccccccchhcccChhhHHHHHHhhc
Q psy4688 43 TCPICNKSYPGARNMRKHLRLVHDKNSTTTCTMCKKTFRNKATFQKHMQRAH 94 (388)
Q Consensus 43 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 94 (388)
-|-+|++.|.+..-|..|.+..| |+|.+|.+...+--.|..|....|
T Consensus 12 wcwycnrefddekiliqhqkakh-----fkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH-----FKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc-----ceeeeehhhhccCCCceeehhhhh
Confidence 47777777777777777765433 677777776666666666654444
No 70
>KOG1146|consensus
Probab=92.01 E-value=0.06 Score=55.57 Aligned_cols=83 Identities=18% Similarity=0.294 Sum_probs=64.6
Q ss_pred cccccccccCCchHHHHhHHhhhCCCCcccCCCCcccCCChhHHHHHHHHhccCCcc-------------------cccC
Q psy4688 190 VCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKV-------------------KVKY 250 (388)
Q Consensus 190 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~-------------------~~~~ 250 (388)
.|..|+..+.....+..|+...+.-.+.|.|+.|+..|+....|..|++..|..... ....
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 355666677777777777777788788999999999999999999999985432110 1234
Q ss_pred cccccccCCcCCChhHHHHHHh
Q psy4688 251 EYECDYCGAKYPNKYTLSDHIS 272 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H~~ 272 (388)
+|.|..|...+..+..|..|+.
T Consensus 518 p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 518 PYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred cccceeeeeeeecchHHHHHHH
Confidence 7899999999999999999974
No 71
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.71 E-value=0.097 Score=29.27 Aligned_cols=7 Identities=29% Similarity=1.279 Sum_probs=3.0
Q ss_pred ccccccc
Q psy4688 281 ICKICNK 287 (388)
Q Consensus 281 ~C~~C~k 287 (388)
+|.+||.
T Consensus 3 ~C~~CGy 9 (33)
T cd00350 3 VCPVCGY 9 (33)
T ss_pred ECCCCCC
Confidence 3444443
No 72
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.31 E-value=0.14 Score=31.64 Aligned_cols=29 Identities=34% Similarity=0.549 Sum_probs=24.7
Q ss_pred CCCccccCCCcccccChhhHHhHHhhhcC
Q psy4688 310 PIEKFKCDLCDKEFFEKKKLNKHKNWAHG 338 (388)
Q Consensus 310 ~~~~~~C~~C~k~F~~~~~L~~H~~~hh~ 338 (388)
++.-+.||-||..|....++.+|....|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 34568899999999999999999988776
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.27 E-value=0.16 Score=31.42 Aligned_cols=28 Identities=25% Similarity=0.653 Sum_probs=17.0
Q ss_pred CCCccccccchhcccChhhHHHHHHhhc
Q psy4688 67 KNSTTTCTMCKKTFRNKATFQKHMQRAH 94 (388)
Q Consensus 67 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h 94 (388)
++.-+.|+-|+..|....++.+|+...|
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 3444566666666666666666665555
No 74
>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=89.37 E-value=0.38 Score=29.31 Aligned_cols=42 Identities=19% Similarity=0.481 Sum_probs=20.3
Q ss_pred ccccccccccccccccchhhccccccccCCCCCccccCCCccc
Q psy4688 280 HICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKE 322 (388)
Q Consensus 280 ~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~ 322 (388)
|+|.+|+..|.....-..+.+..-..+...+ ..|.|++|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp-~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLP-DDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS--TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCC-CCCcCcCCCCc
Confidence 6788888777655544333322222222222 34788888753
No 75
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=87.50 E-value=0.047 Score=32.24 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=17.7
Q ss_pred ccccceeeecccccCCCCCceee
Q psy4688 3 FDRAEVFLSQNVQMSNLSGSCVV 25 (388)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~ 25 (388)
||++|+.||.+++.+|+.+..++
T Consensus 18 L~~~Qk~ly~dvm~Eny~~l~sl 40 (41)
T PF01352_consen 18 LDPAQKNLYRDVMLENYRNLVSL 40 (41)
T ss_dssp S-HHHHHHHHHHHHHTTTS---S
T ss_pred ccceecccchhHHHHhhcccEec
Confidence 99999999999999999886443
No 76
>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=87.15 E-value=0.43 Score=29.52 Aligned_cols=12 Identities=33% Similarity=0.639 Sum_probs=8.1
Q ss_pred cccccccccccc
Q psy4688 280 HICKICNKGYAC 291 (388)
Q Consensus 280 ~~C~~C~k~f~~ 291 (388)
|+|.+||..|..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 567777776654
No 77
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=87.01 E-value=0.36 Score=31.23 Aligned_cols=46 Identities=20% Similarity=0.477 Sum_probs=23.6
Q ss_pred CccccCC--CcccccChhhHHhHHhhhcCCCcccCCc----chhhH-HhHHHHH
Q psy4688 312 EKFKCDL--CDKEFFEKKKLNKHKNWAHGDKFHLCKV----CGAKI-KGSLKQH 358 (388)
Q Consensus 312 ~~~~C~~--C~k~F~~~~~L~~H~~~hh~~~~~~C~~----C~~~f-~~~L~~H 358 (388)
.+..|+. |...+. +..|..|+...-..++..|++ |+..+ +..|..|
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 4566776 444443 556777777555556666776 66655 3344443
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.31 E-value=0.47 Score=39.99 Aligned_cols=13 Identities=31% Similarity=0.764 Sum_probs=9.9
Q ss_pred cccCCCcccccCh
Q psy4688 314 FKCDLCDKEFFEK 326 (388)
Q Consensus 314 ~~C~~C~k~F~~~ 326 (388)
..||.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5788888887754
No 79
>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=85.77 E-value=1 Score=33.43 Aligned_cols=26 Identities=31% Similarity=0.538 Sum_probs=24.1
Q ss_pred cccc----CCCcccccChhhHHhHHhhhcC
Q psy4688 313 KFKC----DLCDKEFFEKKKLNKHKNWAHG 338 (388)
Q Consensus 313 ~~~C----~~C~k~F~~~~~L~~H~~~hh~ 338 (388)
-|.| +.|+..+.+...|.+|.+.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4899 9999999999999999999886
No 80
>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=85.67 E-value=0.45 Score=26.77 Aligned_cols=6 Identities=33% Similarity=1.248 Sum_probs=2.3
Q ss_pred ccCCCc
Q psy4688 315 KCDLCD 320 (388)
Q Consensus 315 ~C~~C~ 320 (388)
.|.+||
T Consensus 4 ~C~~CG 9 (34)
T cd00729 4 VCPVCG 9 (34)
T ss_pred ECCCCC
Confidence 333333
No 81
>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=84.04 E-value=0.67 Score=26.75 Aligned_cols=11 Identities=27% Similarity=0.890 Sum_probs=6.6
Q ss_pred ccccCCCcccc
Q psy4688 313 KFKCDLCDKEF 323 (388)
Q Consensus 313 ~~~C~~C~k~F 323 (388)
...|+.|+..|
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 35666666655
No 82
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=83.74 E-value=1.9 Score=31.97 Aligned_cols=26 Identities=31% Similarity=0.712 Sum_probs=18.6
Q ss_pred CCCcccccccccCCchHHHHhHHhhhC
Q psy4688 187 RVTVCPKCNRDYRNPRNMRKHLRRVHT 213 (388)
Q Consensus 187 ~~~~C~~C~~~f~~~~~l~~H~~~~h~ 213 (388)
+...|..|+..... +++..|++..|.
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~ 35 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHH 35 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcc
Confidence 34568888877655 788888876654
No 83
>PHA00626 hypothetical protein
Probab=83.63 E-value=0.72 Score=28.76 Aligned_cols=14 Identities=14% Similarity=0.363 Sum_probs=8.4
Q ss_pred CccccCCCcccccC
Q psy4688 312 EKFKCDLCDKEFFE 325 (388)
Q Consensus 312 ~~~~C~~C~k~F~~ 325 (388)
..|.|+.||..|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 34666666666643
No 84
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=83.48 E-value=0.56 Score=37.33 Aligned_cols=11 Identities=55% Similarity=1.174 Sum_probs=5.4
Q ss_pred CCCCccccccc
Q psy4688 364 GERKYCCHICG 374 (388)
Q Consensus 364 ~~~~~~C~~C~ 374 (388)
|+.|-+||+||
T Consensus 146 ge~P~~CPiCg 156 (166)
T COG1592 146 GEAPEVCPICG 156 (166)
T ss_pred CCCCCcCCCCC
Confidence 34445555554
No 85
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.36 E-value=0.88 Score=25.96 Aligned_cols=32 Identities=28% Similarity=0.792 Sum_probs=18.4
Q ss_pred cccccccccCCchHHHHhHHhhhCCCCcccCCCCcccC
Q psy4688 190 VCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKML 227 (388)
Q Consensus 190 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 227 (388)
.|+.|+..|.-.... +-......+|+.|+..|
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 477777777655432 22333456777777665
No 86
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=81.98 E-value=0.67 Score=29.94 Aligned_cols=46 Identities=26% Similarity=0.519 Sum_probs=31.6
Q ss_pred CCcccCCc--chhhH-HhHHHHHHHHhcCCCCccccc----cchhh-Hhhhhhh
Q psy4688 339 DKFHLCKV--CGAKI-KGSLKQHMITHTGERKYCCHI----CGKKL-RGKLKEH 384 (388)
Q Consensus 339 ~~~~~C~~--C~~~f-~~~L~~H~~~H~~~~~~~C~~----C~k~f-~~~l~~H 384 (388)
..+-.|+. |...+ +..|..|+..-=..++-.|++ |+..+ ...|..|
T Consensus 7 ~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp TSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 45678988 65656 778999999766777889999 99998 5567766
No 87
>KOG2186|consensus
Probab=81.65 E-value=0.7 Score=38.87 Aligned_cols=46 Identities=20% Similarity=0.589 Sum_probs=21.4
Q ss_pred ccCCCCcccCCChhHHHHHHHHhccCCcccccCcccccccCCcCCChhHHHHHHh
Q psy4688 218 YGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYECDYCGAKYPNKYTLSDHIS 272 (388)
Q Consensus 218 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~ 272 (388)
|.|..||....-+ .+.+|+..-++. -|.|-.|++.|.. .....|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn~-------~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRNA-------YFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccCC-------eeEEeeccccccc-chhhhhhh
Confidence 4555555544332 344455444331 2555555555544 44444443
No 88
>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=81.45 E-value=0.99 Score=33.21 Aligned_cols=12 Identities=33% Similarity=0.719 Sum_probs=5.4
Q ss_pred ccccCCCccccc
Q psy4688 313 KFKCDLCDKEFF 324 (388)
Q Consensus 313 ~~~C~~C~k~F~ 324 (388)
|..|+.||..|.
T Consensus 26 PivCP~CG~~~~ 37 (108)
T PF09538_consen 26 PIVCPKCGTEFP 37 (108)
T ss_pred CccCCCCCCccC
Confidence 344444444443
No 89
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.93 E-value=1.1 Score=25.79 Aligned_cols=33 Identities=30% Similarity=0.893 Sum_probs=19.2
Q ss_pred cccccccccCCchHHHHhHHhhhCCCCcccCCCCcccCC
Q psy4688 190 VCPKCNRDYRNPRNMRKHLRRVHTSVRKYGCDECGKMLK 228 (388)
Q Consensus 190 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~ 228 (388)
.||.|+..|.-..+. .-.+.....|+.|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~------l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK------LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHH------cccCCcEEECCCCCcEee
Confidence 477777777655431 123344567777776663
No 90
>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=80.44 E-value=0.9 Score=33.43 Aligned_cols=28 Identities=25% Similarity=0.729 Sum_probs=18.9
Q ss_pred ccccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhH
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKI 351 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f 351 (388)
+..|+.||++|... +..|-.|+.||..|
T Consensus 9 KR~Cp~CG~kFYDL-----------nk~PivCP~CG~~~ 36 (108)
T PF09538_consen 9 KRTCPSCGAKFYDL-----------NKDPIVCPKCGTEF 36 (108)
T ss_pred cccCCCCcchhccC-----------CCCCccCCCCCCcc
Confidence 35688888888653 23566777777776
No 91
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=80.24 E-value=0.37 Score=40.58 Aligned_cols=10 Identities=30% Similarity=0.541 Sum_probs=5.6
Q ss_pred cccccCCcCC
Q psy4688 253 ECDYCGAKYP 262 (388)
Q Consensus 253 ~C~~C~~~f~ 262 (388)
.|+.||.+|.
T Consensus 50 vCP~CgyA~~ 59 (214)
T PF09986_consen 50 VCPHCGYAAF 59 (214)
T ss_pred ECCCCCCccc
Confidence 4666665554
No 92
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.35 E-value=1.3 Score=26.84 Aligned_cols=12 Identities=17% Similarity=0.501 Sum_probs=6.7
Q ss_pred Cccccccccccc
Q psy4688 279 NHICKICNKGYA 290 (388)
Q Consensus 279 ~~~C~~C~k~f~ 290 (388)
.|.|+.||..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 356666665553
No 93
>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=78.93 E-value=1.4 Score=23.03 Aligned_cols=11 Identities=27% Similarity=0.534 Sum_probs=7.4
Q ss_pred cccCCCccccc
Q psy4688 314 FKCDLCDKEFF 324 (388)
Q Consensus 314 ~~C~~C~k~F~ 324 (388)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35777777764
No 94
>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=78.48 E-value=1.1 Score=35.83 Aligned_cols=29 Identities=24% Similarity=0.364 Sum_probs=15.5
Q ss_pred ccccCCCcccccChhhHHhHHhhhcCCCcccCCcchhh
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAK 350 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~ 350 (388)
-|.|+.|+..|+.-.++. -.|.|+.||..
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred eEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 355666665555555553 13556666543
No 95
>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=77.88 E-value=2 Score=22.43 Aligned_cols=19 Identities=26% Similarity=0.697 Sum_probs=12.6
Q ss_pred ccCCCcccccChhhHHhHHh
Q psy4688 315 KCDLCDKEFFEKKKLNKHKN 334 (388)
Q Consensus 315 ~C~~C~k~F~~~~~L~~H~~ 334 (388)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777777 5566666664
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.21 E-value=1.1 Score=36.40 Aligned_cols=29 Identities=24% Similarity=0.470 Sum_probs=17.4
Q ss_pred ccccCCCcccccChhhHHhHHhhhcCCCcccCCcchhh
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAK 350 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~ 350 (388)
-|.|+.|+..|+.-.++. -.|.|+.||..
T Consensus 117 ~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred EEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 466666666666665552 24667777653
No 97
>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=76.72 E-value=1.8 Score=34.45 Aligned_cols=16 Identities=6% Similarity=0.320 Sum_probs=8.0
Q ss_pred ccccccCCcCCChhHH
Q psy4688 252 YECDYCGAKYPNKYTL 267 (388)
Q Consensus 252 ~~C~~C~~~f~~~~~L 267 (388)
|.|+.|+..|+...++
T Consensus 110 Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 110 FICPNMCVRFTFNEAM 125 (158)
T ss_pred EECCCCCcEeeHHHHH
Confidence 4555555555444444
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.21 E-value=1.6 Score=34.37 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=5.4
Q ss_pred Cccccccccccc
Q psy4688 279 NHICKICNKGYA 290 (388)
Q Consensus 279 ~~~C~~C~k~f~ 290 (388)
-|.|+.|+..|.
T Consensus 99 ~Y~Cp~C~~~y~ 110 (147)
T smart00531 99 YYKCPNCQSKYT 110 (147)
T ss_pred EEECcCCCCEee
Confidence 344444444444
No 99
>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=75.10 E-value=1.7 Score=25.79 Aligned_cols=11 Identities=18% Similarity=0.673 Sum_probs=5.6
Q ss_pred ccccccccccc
Q psy4688 280 HICKICNKGYA 290 (388)
Q Consensus 280 ~~C~~C~k~f~ 290 (388)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 45555555553
No 100
>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=75.04 E-value=2.6 Score=25.23 Aligned_cols=24 Identities=29% Similarity=0.486 Sum_probs=12.7
Q ss_pred CccccCCCcccccCh----hhHHhHHhh
Q psy4688 312 EKFKCDLCDKEFFEK----KKLNKHKNW 335 (388)
Q Consensus 312 ~~~~C~~C~k~F~~~----~~L~~H~~~ 335 (388)
...+|.+|++.+... +.|.+|++.
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 346677777777653 667777643
No 101
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=74.38 E-value=1.7 Score=32.74 Aligned_cols=22 Identities=27% Similarity=0.317 Sum_probs=11.3
Q ss_pred cccCCCcccccChhhHHhHHhhhcC
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWAHG 338 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~hh~ 338 (388)
..|-.+||.|++ |++|+.+|+|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccC
Confidence 345555555532 5555555544
No 102
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=73.29 E-value=3.3 Score=32.56 Aligned_cols=35 Identities=20% Similarity=0.402 Sum_probs=17.6
Q ss_pred cccccccCCcCCChhHHHHHHhhcCCCCCcccccccccc
Q psy4688 251 EYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGY 289 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f 289 (388)
.|.|+.|+..|.....+.. . .. ...|.||.||...
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~-~--d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQL-L--DM-DGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCCEeeHHHHHHh-c--CC-CCcEECCCCCCEE
Confidence 4667777766664333221 0 11 2236666666544
No 103
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=73.26 E-value=1 Score=35.57 Aligned_cols=16 Identities=19% Similarity=0.524 Sum_probs=9.3
Q ss_pred cccccccccccccccc
Q psy4688 280 HICKICNKGYACAASL 295 (388)
Q Consensus 280 ~~C~~C~k~f~~~~~L 295 (388)
++|+-||++|.+...+
T Consensus 29 ~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLACGKRFTTFERV 44 (154)
T ss_pred eeccccCCcceEeEec
Confidence 5666666666554443
No 104
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=73.16 E-value=2.2 Score=27.21 Aligned_cols=9 Identities=22% Similarity=0.800 Sum_probs=4.4
Q ss_pred ccccCCCcc
Q psy4688 313 KFKCDLCDK 321 (388)
Q Consensus 313 ~~~C~~C~k 321 (388)
+|.|+.||.
T Consensus 48 ~Y~CP~CGF 56 (59)
T PRK14890 48 PYTCPKCGF 56 (59)
T ss_pred ceECCCCCC
Confidence 355555543
No 105
>COG1773 Rubredoxin [Energy production and conversion]
Probab=73.07 E-value=3 Score=26.24 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=7.4
Q ss_pred Ccccccccccccc
Q psy4688 279 NHICKICNKGYAC 291 (388)
Q Consensus 279 ~~~C~~C~k~f~~ 291 (388)
.|+|.+||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4566666666543
No 106
>KOG2186|consensus
Probab=73.05 E-value=1.2 Score=37.47 Aligned_cols=54 Identities=17% Similarity=0.334 Sum_probs=33.5
Q ss_pred ccccccccccccccccchhhccccccccCCCCCccccCCCcccccChhhHHhHHhhhcCCCcc
Q psy4688 280 HICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFFEKKKLNKHKNWAHGDKFH 342 (388)
Q Consensus 280 ~~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~ 342 (388)
|.|.+||..-.- ..+.+|+-+-+ ..-|.|-.|++.|.. ..+..|..--+....|
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCr-------n~~fSCIDC~k~F~~-~sYknH~kCITEaQKY 57 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCR-------NAYFSCIDCGKTFER-VSYKNHTKCITEAQKY 57 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhcc-------CCeeEEeeccccccc-chhhhhhhhcchHHHh
Confidence 678888876653 34555643333 245788888888877 6777777655544333
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.61 E-value=2.6 Score=34.36 Aligned_cols=13 Identities=15% Similarity=0.524 Sum_probs=6.2
Q ss_pred Ccccccccccccc
Q psy4688 279 NHICKICNKGYAC 291 (388)
Q Consensus 279 ~~~C~~C~k~f~~ 291 (388)
-|.|+.|+..|+.
T Consensus 117 ~Y~Cp~C~~rytf 129 (178)
T PRK06266 117 FFFCPNCHIRFTF 129 (178)
T ss_pred EEECCCCCcEEeH
Confidence 3445555544443
No 108
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=72.38 E-value=2.2 Score=34.00 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=6.9
Q ss_pred CCCCCccccccc
Q psy4688 275 TGIPNHICKICN 286 (388)
Q Consensus 275 ~~~~~~~C~~C~ 286 (388)
.|+.|-+||+||
T Consensus 145 ~ge~P~~CPiCg 156 (166)
T COG1592 145 EGEAPEVCPICG 156 (166)
T ss_pred cCCCCCcCCCCC
Confidence 345566666665
No 109
>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=72.05 E-value=1.3 Score=32.47 Aligned_cols=9 Identities=22% Similarity=0.866 Sum_probs=5.2
Q ss_pred cccCCCccc
Q psy4688 314 FKCDLCDKE 322 (388)
Q Consensus 314 ~~C~~C~k~ 322 (388)
.+|+.||..
T Consensus 63 ~~Cp~Cg~~ 71 (104)
T TIGR01384 63 VECPKCGHK 71 (104)
T ss_pred CCCCCCCCC
Confidence 566666643
No 110
>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=71.11 E-value=1.4 Score=25.76 Aligned_cols=11 Identities=18% Similarity=0.631 Sum_probs=6.9
Q ss_pred ccccccccccc
Q psy4688 280 HICKICNKGYA 290 (388)
Q Consensus 280 ~~C~~C~k~f~ 290 (388)
|.|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 56666666664
No 111
>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=70.95 E-value=1.6 Score=36.50 Aligned_cols=30 Identities=33% Similarity=0.544 Sum_probs=23.4
Q ss_pred CCccccCCCcccccChhhHHhHHhhhcCCC
Q psy4688 311 IEKFKCDLCDKEFFEKKKLNKHKNWAHGDK 340 (388)
Q Consensus 311 ~~~~~C~~C~k~F~~~~~L~~H~~~hh~~~ 340 (388)
...|.|++|+|.|.-..-..+|+...|.++
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 457999999999999999999999888764
No 112
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=70.51 E-value=2.4 Score=33.48 Aligned_cols=18 Identities=22% Similarity=0.560 Sum_probs=14.4
Q ss_pred ccccCCCcccccChhhHH
Q psy4688 313 KFKCDLCDKEFFEKKKLN 330 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~ 330 (388)
.++|+.||++|.+...+.
T Consensus 28 ~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 28 RRECLACGKRFTTFERVE 45 (154)
T ss_pred eeeccccCCcceEeEecc
Confidence 489999999998765544
No 113
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=70.10 E-value=2.8 Score=25.14 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=4.5
Q ss_pred cccccccccc
Q psy4688 280 HICKICNKGY 289 (388)
Q Consensus 280 ~~C~~C~k~f 289 (388)
|.|..||..|
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 4444444433
No 114
>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=69.22 E-value=1.6 Score=27.18 Aligned_cols=11 Identities=18% Similarity=0.691 Sum_probs=6.4
Q ss_pred ccccccccccc
Q psy4688 280 HICKICNKGYA 290 (388)
Q Consensus 280 ~~C~~C~k~f~ 290 (388)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 55666665554
No 115
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=69.14 E-value=2.9 Score=26.59 Aligned_cols=8 Identities=25% Similarity=1.144 Sum_probs=3.5
Q ss_pred ccccCCCc
Q psy4688 313 KFKCDLCD 320 (388)
Q Consensus 313 ~~~C~~C~ 320 (388)
+|.|+.||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 34444444
No 116
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=68.63 E-value=4.1 Score=25.15 Aligned_cols=23 Identities=26% Similarity=0.606 Sum_probs=16.1
Q ss_pred ccccCCCcccccCh-----hhHHhHHhh
Q psy4688 313 KFKCDLCDKEFFEK-----KKLNKHKNW 335 (388)
Q Consensus 313 ~~~C~~C~k~F~~~-----~~L~~H~~~ 335 (388)
.-.|..|++.++.. +.|.+|++.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 45688888877655 577777763
No 117
>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=68.33 E-value=2.9 Score=31.34 Aligned_cols=10 Identities=20% Similarity=0.624 Sum_probs=4.8
Q ss_pred ccCCCccccc
Q psy4688 315 KCDLCDKEFF 324 (388)
Q Consensus 315 ~C~~C~k~F~ 324 (388)
.|+.||++|.
T Consensus 11 ~Cp~cg~kFY 20 (129)
T TIGR02300 11 ICPNTGSKFY 20 (129)
T ss_pred cCCCcCcccc
Confidence 4455554443
No 118
>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=67.01 E-value=4.3 Score=30.50 Aligned_cols=30 Identities=10% Similarity=0.192 Sum_probs=19.4
Q ss_pred ccccccCCcCCChhHHHHHHhhcCCCCCccccccccccccc
Q psy4688 252 YECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACA 292 (388)
Q Consensus 252 ~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~ 292 (388)
..|+.||++|... +..|-.|+.||..|...
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 5677777777542 22467777777777544
No 119
>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=65.59 E-value=4.9 Score=22.20 Aligned_cols=10 Identities=20% Similarity=0.790 Sum_probs=5.6
Q ss_pred ccccCCCccc
Q psy4688 313 KFKCDLCDKE 322 (388)
Q Consensus 313 ~~~C~~C~k~ 322 (388)
+.+|+.||..
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 4567777643
No 120
>KOG2593|consensus
Probab=65.26 E-value=4.4 Score=37.28 Aligned_cols=35 Identities=23% Similarity=0.633 Sum_probs=21.6
Q ss_pred cCCCCCcCCcCCCcHHHHHHHHhhccCCCccccccchhc
Q psy4688 41 TKTCPICNKSYPGARNMRKHLRLVHDKNSTTTCTMCKKT 79 (388)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~ 79 (388)
.|.|+.|++.|.....++ +.-.....|.|..|+-.
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~----L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQ----LLDNETGEFHCENCGGE 162 (436)
T ss_pred cccCCccccchhhhHHHH----hhcccCceEEEecCCCc
Confidence 477777777777666553 22333456777777543
No 121
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.81 E-value=5.4 Score=26.76 Aligned_cols=38 Identities=29% Similarity=0.685 Sum_probs=23.8
Q ss_pred CCCccccCCCcccccChhhHHhHHhhhcCCCcc-cCCcchhhHHhHH
Q psy4688 310 PIEKFKCDLCDKEFFEKKKLNKHKNWAHGDKFH-LCKVCGAKIKGSL 355 (388)
Q Consensus 310 ~~~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~-~C~~C~~~f~~~L 355 (388)
|.-.|.|..|+..| .+.+||. +.|+ .|+.||.+++..|
T Consensus 9 PtY~Y~c~~cg~~~----dvvq~~~----ddplt~ce~c~a~~kk~l 47 (82)
T COG2331 9 PTYSYECTECGNRF----DVVQAMT----DDPLTTCEECGARLKKLL 47 (82)
T ss_pred cceEEeecccchHH----HHHHhcc----cCccccChhhChHHHHhh
Confidence 44568888888766 3444443 3444 5888887775444
No 122
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=64.58 E-value=2.9 Score=28.12 Aligned_cols=42 Identities=17% Similarity=0.313 Sum_probs=22.2
Q ss_pred ccccccCCcCCChhHHHHHHhhcCCCCCcccc--cccccccccccc
Q psy4688 252 YECDYCGAKYPNKYTLSDHISGHTGIPNHICK--ICNKGYACAASL 295 (388)
Q Consensus 252 ~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~--~C~k~f~~~~~L 295 (388)
+.|+.||..-....+-.... -..+.-+.|. .||.+|....++
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheeeeecCCCCCCCEEEEEEEE
Confidence 45777776653322221111 1334456776 777777765544
No 123
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.76 E-value=5.2 Score=41.03 Aligned_cols=8 Identities=38% Similarity=1.086 Sum_probs=4.6
Q ss_pred ccCCcchh
Q psy4688 342 HLCKVCGA 349 (388)
Q Consensus 342 ~~C~~C~~ 349 (388)
+.|+.||.
T Consensus 664 y~CPKCG~ 671 (1121)
T PRK04023 664 DECEKCGR 671 (1121)
T ss_pred CcCCCCCC
Confidence 45666654
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=63.29 E-value=3.4 Score=22.46 Aligned_cols=8 Identities=25% Similarity=0.742 Sum_probs=3.8
Q ss_pred ccccCCCc
Q psy4688 313 KFKCDLCD 320 (388)
Q Consensus 313 ~~~C~~C~ 320 (388)
.|.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34455554
No 125
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=63.15 E-value=3.8 Score=31.00 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=6.6
Q ss_pred cccCCCcccccCh
Q psy4688 314 FKCDLCDKEFFEK 326 (388)
Q Consensus 314 ~~C~~C~k~F~~~ 326 (388)
++|..||+.|..-
T Consensus 2 H~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 2 HQCTKCGRVFEDG 14 (131)
T ss_pred cccCcCCCCcCCC
Confidence 4455555555443
No 126
>PF12907 zf-met2: Zinc-binding
Probab=62.34 E-value=4.6 Score=23.60 Aligned_cols=23 Identities=30% Similarity=0.889 Sum_probs=10.1
Q ss_pred ccccchhcc---cChhhHHHHHHhhc
Q psy4688 72 TCTMCKKTF---RNKATFQKHMQRAH 94 (388)
Q Consensus 72 ~C~~C~~~f---~~~~~l~~H~~~~h 94 (388)
.|.+|-.+| .+...|..|....|
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~enKH 28 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAENKH 28 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHHccC
Confidence 455554333 22334555544444
No 127
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.84 E-value=3.6 Score=25.21 Aligned_cols=11 Identities=36% Similarity=1.105 Sum_probs=6.3
Q ss_pred ccccCCCcccc
Q psy4688 313 KFKCDLCDKEF 323 (388)
Q Consensus 313 ~~~C~~C~k~F 323 (388)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35566666655
No 128
>PF14353 CpXC: CpXC protein
Probab=61.52 E-value=7.7 Score=29.61 Aligned_cols=24 Identities=17% Similarity=0.364 Sum_probs=15.7
Q ss_pred CCccccccccccccccccchhhcc
Q psy4688 278 PNHICKICNKGYACAASLKIHNIK 301 (388)
Q Consensus 278 ~~~~C~~C~k~f~~~~~L~~H~~~ 301 (388)
..|.||.||..|.-...+..|...
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCC
Confidence 356777777777766666666443
No 129
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=61.14 E-value=5 Score=24.65 Aligned_cols=15 Identities=33% Similarity=0.525 Sum_probs=7.9
Q ss_pred CcCCCCCcCCcCCCc
Q psy4688 40 KTKTCPICNKSYPGA 54 (388)
Q Consensus 40 ~~~~C~~C~~~f~~~ 54 (388)
+++.|..||..|.-.
T Consensus 3 k~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFT 17 (49)
T ss_pred eeEEcccCCCeEEEe
Confidence 345566666555443
No 130
>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=59.91 E-value=5.1 Score=30.67 Aligned_cols=27 Identities=30% Similarity=0.447 Sum_probs=17.3
Q ss_pred CccccCCCcccccChhhHHhHHhhhcCCCc
Q psy4688 312 EKFKCDLCDKEFFEKKKLNKHKNWAHGDKF 341 (388)
Q Consensus 312 ~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~ 341 (388)
....|-+||+.|.. |++|++.|||-.|
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 35789999999976 5999999988654
No 131
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=59.80 E-value=11 Score=33.00 Aligned_cols=12 Identities=17% Similarity=0.528 Sum_probs=7.4
Q ss_pred CcccCCcchhhH
Q psy4688 340 KFHLCKVCGAKI 351 (388)
Q Consensus 340 ~~~~C~~C~~~f 351 (388)
..|.|+.|...|
T Consensus 387 ~rY~Ce~CK~~F 398 (421)
T COG5151 387 GRYQCELCKSTF 398 (421)
T ss_pred cceechhhhhhh
Confidence 346666666666
No 132
>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=58.94 E-value=5.9 Score=24.96 Aligned_cols=9 Identities=44% Similarity=0.970 Sum_probs=4.0
Q ss_pred cccCCCccc
Q psy4688 314 FKCDLCDKE 322 (388)
Q Consensus 314 ~~C~~C~k~ 322 (388)
..|+.||..
T Consensus 23 V~Cp~CGae 31 (54)
T TIGR01206 23 VICDECGAE 31 (54)
T ss_pred EeCCCCCCE
Confidence 344444443
No 133
>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=58.82 E-value=3.8 Score=20.93 Aligned_cols=8 Identities=38% Similarity=1.128 Sum_probs=4.8
Q ss_pred Cccccccc
Q psy4688 367 KYCCHICG 374 (388)
Q Consensus 367 ~~~C~~C~ 374 (388)
+|.||.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 46666665
No 134
>KOG2272|consensus
Probab=57.35 E-value=7 Score=33.02 Aligned_cols=18 Identities=28% Similarity=0.588 Sum_probs=13.1
Q ss_pred cccCCCCcccCCChhHHH
Q psy4688 217 KYGCDECGKMLKSRDSLN 234 (388)
Q Consensus 217 ~~~C~~C~~~f~~~~~l~ 234 (388)
-|.|++|.+...+...++
T Consensus 99 CF~Cd~Cn~~Lad~gf~r 116 (332)
T KOG2272|consen 99 CFRCDLCNKHLADQGFYR 116 (332)
T ss_pred cchhHHHHHHHhhhhhHh
Confidence 478888888777666554
No 135
>KOG2807|consensus
Probab=55.54 E-value=20 Score=31.73 Aligned_cols=33 Identities=27% Similarity=0.413 Sum_probs=22.9
Q ss_pred cccccccCCcCCChhHHHHHHhhcCCCCCccccccccccccccccch
Q psy4688 251 EYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGYACAASLKI 297 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f~~~~~L~~ 297 (388)
.|.|+.|....- .-|-.|++|+-+......|.+
T Consensus 276 Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLAR 308 (378)
T KOG2807|consen 276 GYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLAR 308 (378)
T ss_pred ceeCCcccCeee--------------cCCccCCccceeEecchHHHH
Confidence 588888875432 237788888888777666654
No 136
>PF15269 zf-C2H2_7: Zinc-finger
Probab=54.48 E-value=15 Score=21.82 Aligned_cols=23 Identities=26% Similarity=0.592 Sum_probs=16.5
Q ss_pred CcccccccCCcCCChhHHHHHHh
Q psy4688 250 YEYECDYCGAKYPNKYTLSDHIS 272 (388)
Q Consensus 250 ~~~~C~~C~~~f~~~~~L~~H~~ 272 (388)
..|+|-.|..+...++.|-.||.
T Consensus 19 ~~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 19 FKYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ccceeecCCcccchHHHHHHHHH
Confidence 34677777777777777777775
No 137
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=54.25 E-value=7.7 Score=26.95 Aligned_cols=13 Identities=31% Similarity=0.772 Sum_probs=8.4
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
-+.|..||..|.-
T Consensus 53 IW~C~kCg~~fAG 65 (89)
T COG1997 53 IWKCRKCGAKFAG 65 (89)
T ss_pred eEEcCCCCCeecc
Confidence 4667777776654
No 138
>KOG2593|consensus
Probab=53.71 E-value=9.1 Score=35.29 Aligned_cols=19 Identities=21% Similarity=0.630 Sum_probs=9.4
Q ss_pred CCCCccccccccccccccc
Q psy4688 276 GIPNHICKICNKGYACAAS 294 (388)
Q Consensus 276 ~~~~~~C~~C~k~f~~~~~ 294 (388)
....|.|+.|++.|+.-..
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEA 143 (436)
T ss_pred ccccccCCccccchhhhHH
Confidence 3344555555555554333
No 139
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.59 E-value=3.1 Score=41.73 Aligned_cols=40 Identities=28% Similarity=0.601 Sum_probs=24.6
Q ss_pred cccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhHHhHHHHHHHHhcCCCCccccccchh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKIKGSLKQHMITHTGERKYCCHICGKK 376 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f~~~L~~H~~~H~~~~~~~C~~C~k~ 376 (388)
++|+.|+-.+ ..|+. .....|.+||. ....|..|+.||..
T Consensus 445 ~~Cp~Cd~~l------t~H~~----~~~L~CH~Cg~-------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPL------TLHKA----TGQLRCHYCGY-------------QEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcce------EEecC----CCeeEeCCCCC-------------CCCCCCCCCCCCCC
Confidence 4677776543 23332 34456777764 34578899999865
No 140
>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=52.20 E-value=9.3 Score=32.05 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=20.5
Q ss_pred CCccccccchhcccChhhHHHHHHhhccC
Q psy4688 68 NSTTTCTMCKKTFRNKATFQKHMQRAHVG 96 (388)
Q Consensus 68 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 96 (388)
+..|.|++|+|.|.-..-..+|+...|..
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 34688888888888888888888877753
No 141
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=52.11 E-value=5.3 Score=22.60 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=15.2
Q ss_pred ccccccccccccccchhhccccccccCCCCCccccCCCccccc
Q psy4688 282 CKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDKEFF 324 (388)
Q Consensus 282 C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~ 324 (388)
|+.|.+.+....+.+.| ..+..|..||-.++
T Consensus 2 C~~C~~Ey~~p~~RR~~------------~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFH------------YQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-------------TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCCCccc------------CcCccCCCCCCCEE
Confidence 66666666555543333 13456888876654
No 142
>KOG2807|consensus
Probab=50.39 E-value=29 Score=30.81 Aligned_cols=13 Identities=8% Similarity=0.340 Sum_probs=8.7
Q ss_pred CcCCcCCCcHHHH
Q psy4688 46 ICNKSYPGARNMR 58 (388)
Q Consensus 46 ~C~~~f~~~~~l~ 58 (388)
.|+..|+-...|.
T Consensus 138 ~~~g~fSLqNaLe 150 (378)
T KOG2807|consen 138 ECSGDFSLQNALE 150 (378)
T ss_pred ccCCChHHHHHHH
Confidence 6777777666654
No 143
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=50.11 E-value=9.2 Score=24.03 Aligned_cols=9 Identities=44% Similarity=1.364 Sum_probs=4.4
Q ss_pred cccccCCcC
Q psy4688 253 ECDYCGAKY 261 (388)
Q Consensus 253 ~C~~C~~~f 261 (388)
.|+.||+.|
T Consensus 7 ~C~~Cg~~~ 15 (54)
T PF14446_consen 7 KCPVCGKKF 15 (54)
T ss_pred cChhhCCcc
Confidence 345555444
No 144
>KOG4124|consensus
Probab=49.77 E-value=5 Score=35.62 Aligned_cols=51 Identities=10% Similarity=-0.024 Sum_probs=31.2
Q ss_pred CCcccccc--chhccCCchHHHHH-----HhhcCCCCCccCCccccccCChHHHHHHHh
Q psy4688 102 SKHFECNY--CHAKFSNKSLLSDH-----ISSHTGLKNYKCHVCDKAYSCRKALKTHTL 153 (388)
Q Consensus 102 ~~~~~C~~--C~~~f~~~~~L~~H-----~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 153 (388)
++++.|.. |.+.+........| +..-+..+||+|. |++++.+...|..|..
T Consensus 176 E~~~S~~vp~~~~~~~~~Ns~~~~S~~~~~T~~t~~~p~k~~-~~~~~~T~~~l~~HS~ 233 (442)
T KOG4124|consen 176 EYRVSVVVPAAAAAAAAANSSDMSSDEASSTAETTGTPKKMP-ESLVMDTSSPLSDHSM 233 (442)
T ss_pred cccccccCchhhhhhhccccccccccccccccccccCCccCc-ccccccccchhhhccc
Confidence 45666654 55555444333333 2223345788885 8888888888888854
No 145
>PRK04023 DNA polymerase II large subunit; Validated
Probab=49.48 E-value=17 Score=37.56 Aligned_cols=10 Identities=40% Similarity=1.002 Sum_probs=6.2
Q ss_pred cccCCCCccc
Q psy4688 217 KYGCDECGKM 226 (388)
Q Consensus 217 ~~~C~~C~~~ 226 (388)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 3567777665
No 146
>KOG4124|consensus
Probab=49.24 E-value=6.6 Score=34.92 Aligned_cols=26 Identities=31% Similarity=0.676 Sum_probs=18.8
Q ss_pred CCccccc--cccccccccccchhhcccc
Q psy4688 278 PNHICKI--CNKGYACAASLKIHNIKTH 303 (388)
Q Consensus 278 ~~~~C~~--C~k~f~~~~~L~~H~~~~H 303 (388)
++|+|++ |.+.+.....|+.|+...|
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h 375 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGH 375 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCc
Confidence 5677754 8888888778887766555
No 147
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=49.13 E-value=11 Score=24.04 Aligned_cols=29 Identities=21% Similarity=0.318 Sum_probs=11.8
Q ss_pred cccCCcchhhH-HhHHHHHHHHhcCCCCccccc
Q psy4688 341 FHLCKVCGAKI-KGSLKQHMITHTGERKYCCHI 372 (388)
Q Consensus 341 ~~~C~~C~~~f-~~~L~~H~~~H~~~~~~~C~~ 372 (388)
|+....||-.| +.++...+ .+.+..+||+
T Consensus 24 PV~s~~C~H~fek~aI~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEAILQYI---QRNGSKRCPV 53 (57)
T ss_dssp EEEESSS--EEEHHHHHHHC---TTTS-EE-SC
T ss_pred CcCcCCCCCeecHHHHHHHH---HhcCCCCCCC
Confidence 44445555555 44444444 2334455655
No 148
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.59 E-value=13 Score=37.55 Aligned_cols=10 Identities=30% Similarity=0.674 Sum_probs=5.5
Q ss_pred ccccCCCccc
Q psy4688 313 KFKCDLCDKE 322 (388)
Q Consensus 313 ~~~C~~C~k~ 322 (388)
|..|+.||-.
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 4556666543
No 149
>KOG4167|consensus
Probab=48.00 E-value=4.5 Score=39.68 Aligned_cols=26 Identities=35% Similarity=0.563 Sum_probs=23.8
Q ss_pred ccccCCCcccccChhhHHhHHhhhcC
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHG 338 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~ 338 (388)
-|.|..|+|.|.....+..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 49999999999999999999999853
No 150
>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=47.64 E-value=6.2 Score=20.99 Aligned_cols=9 Identities=33% Similarity=0.910 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy4688 281 ICKICNKGY 289 (388)
Q Consensus 281 ~C~~C~k~f 289 (388)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344455555
No 151
>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=47.61 E-value=6.5 Score=30.12 Aligned_cols=26 Identities=42% Similarity=0.814 Sum_probs=16.8
Q ss_pred cccCCcchhhHHhHHHHHHHHhcCCCC
Q psy4688 341 FHLCKVCGAKIKGSLKQHMITHTGERK 367 (388)
Q Consensus 341 ~~~C~~C~~~f~~~L~~H~~~H~~~~~ 367 (388)
.-.|-+||+.|+. |++|++.|.|-.|
T Consensus 72 ~i~clecGk~~k~-LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT-LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB-HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch-HHHHHHHccCCCH
Confidence 3579999999975 5999999987654
No 152
>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=45.23 E-value=12 Score=36.25 Aligned_cols=13 Identities=15% Similarity=0.319 Sum_probs=7.1
Q ss_pred CCCCCcccccccc
Q psy4688 275 TGIPNHICKICNK 287 (388)
Q Consensus 275 ~~~~~~~C~~C~k 287 (388)
.......|..||.
T Consensus 236 ~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 236 KKEGKLRCHYCGY 248 (505)
T ss_pred cCCCeEEcCCCcC
Confidence 3344556666664
No 153
>KOG1280|consensus
Probab=44.16 E-value=17 Score=32.50 Aligned_cols=37 Identities=22% Similarity=0.592 Sum_probs=27.2
Q ss_pred CccccCCCcccccChhhHHhHHhhhcCCCcc--cCCcch
Q psy4688 312 EKFKCDLCDKEFFEKKKLNKHKNWAHGDKFH--LCKVCG 348 (388)
Q Consensus 312 ~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~--~C~~C~ 348 (388)
..|.|++|++.=.+...|..|....|.+-++ .|++|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 4578888888888888888888777766543 477775
No 154
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=43.89 E-value=2 Score=38.24 Aligned_cols=9 Identities=33% Similarity=1.010 Sum_probs=2.6
Q ss_pred cccCCCccc
Q psy4688 314 FKCDLCDKE 322 (388)
Q Consensus 314 ~~C~~C~k~ 322 (388)
..|+.||..
T Consensus 212 ~~Cp~Cg~~ 220 (290)
T PF04216_consen 212 IKCPYCGNT 220 (290)
T ss_dssp TS-TTT---
T ss_pred CCCcCCCCC
Confidence 345555544
No 155
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=43.54 E-value=11 Score=28.46 Aligned_cols=17 Identities=41% Similarity=0.442 Sum_probs=11.4
Q ss_pred ccccccccccccccccchhh
Q psy4688 280 HICKICNKGYACAASLKIHN 299 (388)
Q Consensus 280 ~~C~~C~k~f~~~~~L~~H~ 299 (388)
..|-.+|+.|. +|++|.
T Consensus 77 IicLEDGkkfK---SLKRHL 93 (148)
T COG4957 77 IICLEDGKKFK---SLKRHL 93 (148)
T ss_pred EEEeccCcchH---HHHHHH
Confidence 45777777775 466773
No 156
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.43 E-value=14 Score=26.83 Aligned_cols=11 Identities=9% Similarity=0.190 Sum_probs=6.4
Q ss_pred ccccCCCcccc
Q psy4688 313 KFKCDLCDKEF 323 (388)
Q Consensus 313 ~~~C~~C~k~F 323 (388)
|..|++||++|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 45556666655
No 157
>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=42.16 E-value=10 Score=21.59 Aligned_cols=30 Identities=13% Similarity=0.257 Sum_probs=14.7
Q ss_pred ccccchhccCCchHHHHHHhhcCCCCCccCCccccccC
Q psy4688 106 ECNYCHAKFSNKSLLSDHISSHTGLKNYKCHVCDKAYS 143 (388)
Q Consensus 106 ~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~ 143 (388)
.|+.||+.|.. ..-....+-.|+.||..+.
T Consensus 3 ~C~~Cg~~Yh~--------~~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 3 ICPKCGRIYHI--------EFNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EETTTTEEEET--------TTB--SSTTBCTTTTEBEB
T ss_pred CcCCCCCcccc--------ccCCCCCCCccCCCCCeeE
Confidence 46666666632 2222334456666665443
No 158
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=42.07 E-value=25 Score=22.55 Aligned_cols=26 Identities=12% Similarity=0.340 Sum_probs=13.2
Q ss_pred chhhH-HhHHHHHHHHhcCCCCccccccchhh
Q psy4688 347 CGAKI-KGSLKQHMITHTGERKYCCHICGKKL 377 (388)
Q Consensus 347 C~~~f-~~~L~~H~~~H~~~~~~~C~~C~k~f 377 (388)
||..| +..+..++.. ...|++|++.+
T Consensus 19 ~G~v~~~~~i~~~~~~-----~~~cP~~~~~~ 45 (63)
T smart00504 19 SGQTYERRAIEKWLLS-----HGTDPVTGQPL 45 (63)
T ss_pred CCCEEeHHHHHHHHHH-----CCCCCCCcCCC
Confidence 34444 4445555443 12566666665
No 159
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=41.95 E-value=14 Score=20.79 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=4.2
Q ss_pred ccccccccccc
Q psy4688 281 ICKICNKGYAC 291 (388)
Q Consensus 281 ~C~~C~k~f~~ 291 (388)
.|..|++.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 46666666654
No 160
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=41.86 E-value=17 Score=22.54 Aligned_cols=6 Identities=33% Similarity=1.204 Sum_probs=2.3
Q ss_pred ccCCCc
Q psy4688 315 KCDLCD 320 (388)
Q Consensus 315 ~C~~C~ 320 (388)
.|..||
T Consensus 39 ~C~~Cg 44 (50)
T PRK00432 39 HCGKCG 44 (50)
T ss_pred ECCCcC
Confidence 333333
No 161
>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=40.88 E-value=16 Score=35.35 Aligned_cols=9 Identities=33% Similarity=1.084 Sum_probs=5.1
Q ss_pred ccccCCCcc
Q psy4688 313 KFKCDLCDK 321 (388)
Q Consensus 313 ~~~C~~C~k 321 (388)
...|..||.
T Consensus 240 ~l~Ch~Cg~ 248 (505)
T TIGR00595 240 KLRCHYCGY 248 (505)
T ss_pred eEEcCCCcC
Confidence 355666664
No 162
>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=40.88 E-value=13 Score=26.22 Aligned_cols=13 Identities=38% Similarity=0.884 Sum_probs=8.9
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
-+.|..|++.|.-
T Consensus 53 IW~C~~C~~~~AG 65 (90)
T PF01780_consen 53 IWKCKKCGKKFAG 65 (90)
T ss_dssp EEEETTTTEEEE-
T ss_pred EeecCCCCCEEeC
Confidence 4778888877754
No 163
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=40.72 E-value=8.3 Score=38.08 Aligned_cols=37 Identities=19% Similarity=0.567 Sum_probs=18.5
Q ss_pred CCcccccccccCCchHHHHhHHhhhCCCCcc-cCCCCcccCCChhH
Q psy4688 188 VTVCPKCNRDYRNPRNMRKHLRRVHTSVRKY-GCDECGKMLKSRDS 232 (388)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~-~C~~C~~~f~~~~~ 232 (388)
.-.|+.|-+...++.+-+-+ -|| .|..||-.|+--.+
T Consensus 101 ~a~C~~Cl~Ei~dp~~rrY~--------YPF~~CT~CGPRfTIi~a 138 (750)
T COG0068 101 AATCEDCLEEIFDPNSRRYL--------YPFINCTNCGPRFTIIEA 138 (750)
T ss_pred hhhhHHHHHHhcCCCCccee--------ccccccCCCCcceeeecc
Confidence 34577776655444332221 122 36666666655433
No 164
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=40.38 E-value=13 Score=24.72 Aligned_cols=9 Identities=44% Similarity=1.298 Sum_probs=2.7
Q ss_pred ccCCCcccc
Q psy4688 315 KCDLCDKEF 323 (388)
Q Consensus 315 ~C~~C~k~F 323 (388)
.|.+|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 355555555
No 165
>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=40.36 E-value=12 Score=31.98 Aligned_cols=25 Identities=28% Similarity=0.331 Sum_probs=15.4
Q ss_pred CCccCCccccccCChHHHHHHHhhh
Q psy4688 131 KNYKCHVCDKAYSCRKALKTHTLLH 155 (388)
Q Consensus 131 ~~~~C~~C~~~f~~~~~l~~H~~~h 155 (388)
+++.|+.|+........|..-.+.|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecc
Confidence 6777777776665555555444444
No 166
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=40.05 E-value=20 Score=21.22 Aligned_cols=29 Identities=21% Similarity=0.597 Sum_probs=13.0
Q ss_pred CCcccCCcchhhH-HhHHHHHHHHhcCCCCcccccc
Q psy4688 339 DKFHLCKVCGAKI-KGSLKQHMITHTGERKYCCHIC 373 (388)
Q Consensus 339 ~~~~~C~~C~~~f-~~~L~~H~~~H~~~~~~~C~~C 373 (388)
+.....+ ||-.| .+=|...++.+ ..||+|
T Consensus 14 ~~~~~l~-C~H~fh~~Ci~~~~~~~-----~~CP~C 43 (44)
T PF13639_consen 14 EKVVKLP-CGHVFHRSCIKEWLKRN-----NSCPVC 43 (44)
T ss_dssp SCEEEET-TSEEEEHHHHHHHHHHS-----SB-TTT
T ss_pred CeEEEcc-CCCeeCHHHHHHHHHhC-----CcCCcc
Confidence 3334444 55555 33344444432 266666
No 167
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.57 E-value=12 Score=31.37 Aligned_cols=7 Identities=29% Similarity=1.004 Sum_probs=4.9
Q ss_pred cCCcchh
Q psy4688 343 LCKVCGA 349 (388)
Q Consensus 343 ~C~~C~~ 349 (388)
.||.|+.
T Consensus 64 vCP~C~y 70 (267)
T COG1655 64 VCPICYY 70 (267)
T ss_pred EcchhhH
Confidence 4777775
No 168
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=38.38 E-value=11 Score=37.31 Aligned_cols=56 Identities=21% Similarity=0.616 Sum_probs=30.8
Q ss_pred cccccCCcCCChhHHHHHHhhcCCCCCc-cccccccccccccccchhhccccccccCCCCCccccCCCcc
Q psy4688 253 ECDYCGAKYPNKYTLSDHISGHTGIPNH-ICKICNKGYACAASLKIHNIKTHLQFTGVPIEKFKCDLCDK 321 (388)
Q Consensus 253 ~C~~C~~~f~~~~~L~~H~~~H~~~~~~-~C~~C~k~f~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k 321 (388)
.|..||-+|+--..|=.= |.++.-..| .|+.|.+.|....+.+-| ..|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfH------------AQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFH------------AQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccccc------------cccccCcccCC
Confidence 577777777654333211 222333333 377777777666655544 24566777765
No 169
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=38.26 E-value=9.1 Score=24.23 Aligned_cols=37 Identities=27% Similarity=0.464 Sum_probs=16.8
Q ss_pred CCCCCcCCcCCCc--HHHHHHHHhhccCCCccccccchhcc
Q psy4688 42 KTCPICNKSYPGA--RNMRKHLRLVHDKNSTTTCTMCKKTF 80 (388)
Q Consensus 42 ~~C~~C~~~f~~~--~~l~~H~~~~h~~~~~~~C~~C~~~f 80 (388)
.+|-+|++.+.-. ..+.+=++ -.....|.|+.|...-
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLr--nrPi~tYmC~eC~~RI 41 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLR--NRPIHTYMCDECKERI 41 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhh--cCCCcceeChhHHHHH
Confidence 3566666655322 11112122 2334456677765543
No 170
>KOG4167|consensus
Probab=38.22 E-value=12 Score=37.03 Aligned_cols=25 Identities=24% Similarity=0.429 Sum_probs=18.5
Q ss_pred CccccccchhcccChhhHHHHHHhh
Q psy4688 69 STTTCTMCKKTFRNKATFQKHMQRA 93 (388)
Q Consensus 69 ~~~~C~~C~~~f~~~~~l~~H~~~~ 93 (388)
..|.|.+|++.|....++..||++|
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHH
Confidence 4577888888887777777777654
No 171
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=38.00 E-value=28 Score=30.54 Aligned_cols=99 Identities=19% Similarity=0.451 Sum_probs=53.0
Q ss_pred CCcCCCCCcCCcCCCcHHHHHHHHhhccCCCccccccchhcccChhhHHHHHHhhcc-CCCc-------CCCCccccccc
Q psy4688 39 NKTKTCPICNKSYPGARNMRKHLRLVHDKNSTTTCTMCKKTFRNKATFQKHMQRAHV-GLKI-------SVSKHFECNYC 110 (388)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~-~~~~-------~~~~~~~C~~C 110 (388)
...|.||.|...- . ..|..|+.|.-..-....|.+-. +|. .++. ...+.--|-.|
T Consensus 306 ~gGy~CP~CktkV-------------C--sLPi~CP~Csl~LilsthLarSy--hhL~PLk~f~E~p~~~~~ks~~Cf~C 368 (421)
T COG5151 306 GGGYECPVCKTKV-------------C--SLPISCPICSLQLILSTHLARSY--HHLYPLKPFVEKPEGTNPKSTHCFVC 368 (421)
T ss_pred cCceeCCccccee-------------e--cCCccCcchhHHHHHHHHHHHHH--HhhccCcccccccCCCCCCCccceec
Confidence 4568888884321 1 23677888877665555554432 221 1110 11122337777
Q ss_pred hhccCCchHHHHHHhhcCCCCCccCCccccccCChHHHHHHHhhhc
Q psy4688 111 HAKFSNKSLLSDHISSHTGLKNYKCHVCDKAYSCRKALKTHTLLHE 156 (388)
Q Consensus 111 ~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 156 (388)
.-.|.....-..- .-+....|.|+.|...|-.--+.-.|...|.
T Consensus 369 Q~~fp~~~~~~~~--~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 369 QGPFPKPPVSPFD--ESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cCCCCCCCCCccc--ccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 7666543211100 0122346888888888887777777776664
No 172
>PRK14873 primosome assembly protein PriA; Provisional
Probab=37.84 E-value=17 Score=36.45 Aligned_cols=9 Identities=22% Similarity=0.593 Sum_probs=5.5
Q ss_pred ccccccccc
Q psy4688 281 ICKICNKGY 289 (388)
Q Consensus 281 ~C~~C~k~f 289 (388)
.|..||..+
T Consensus 385 ~C~~Cg~~~ 393 (665)
T PRK14873 385 ACARCRTPA 393 (665)
T ss_pred EhhhCcCee
Confidence 577776544
No 173
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=37.83 E-value=9.4 Score=23.29 Aligned_cols=14 Identities=29% Similarity=0.850 Sum_probs=9.4
Q ss_pred CccccCCCcccccC
Q psy4688 312 EKFKCDLCDKEFFE 325 (388)
Q Consensus 312 ~~~~C~~C~k~F~~ 325 (388)
..|.|++|.-+|+-
T Consensus 6 sry~CDLCn~~~p~ 19 (57)
T PF14445_consen 6 SRYSCDLCNSSHPI 19 (57)
T ss_pred hhHhHHhhcccCcH
Confidence 35777777777654
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=37.71 E-value=21 Score=33.74 Aligned_cols=28 Identities=25% Similarity=0.528 Sum_probs=22.7
Q ss_pred CccccccchhcccChhhHHHHHHhhccC
Q psy4688 69 STTTCTMCKKTFRNKATFQKHMQRAHVG 96 (388)
Q Consensus 69 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 96 (388)
.-+.|+.|.+.|.+...+..|+...|.+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 3467888888888888888888877765
No 175
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=36.95 E-value=17 Score=21.63 Aligned_cols=13 Identities=23% Similarity=0.905 Sum_probs=9.3
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
.+.|+.||..+.+
T Consensus 32 ~~~C~~CGE~~~~ 44 (46)
T TIGR03831 32 ALVCPQCGEEYLD 44 (46)
T ss_pred ccccccCCCEeeC
Confidence 4678888877654
No 176
>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=36.76 E-value=16 Score=27.39 Aligned_cols=14 Identities=21% Similarity=0.634 Sum_probs=8.7
Q ss_pred ccccCCCcccccCh
Q psy4688 313 KFKCDLCDKEFFEK 326 (388)
Q Consensus 313 ~~~C~~C~k~F~~~ 326 (388)
.+.|..|+..|...
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (115)
T TIGR00100 70 ECECEDCSEEVSPE 83 (115)
T ss_pred EEEcccCCCEEecC
Confidence 36677777666543
No 177
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=36.74 E-value=33 Score=26.11 Aligned_cols=58 Identities=22% Similarity=0.523 Sum_probs=32.9
Q ss_pred CCCCcccCCCCcccCCChhHHHHHHHHhccCCcccccCcccc---cccCCcCCChhHHHHHHhhcCCCCCcccccccccc
Q psy4688 213 TSVRKYGCDECGKMLKSRDSLNTHKKIQHEGKKVKVKYEYEC---DYCGAKYPNKYTLSDHISGHTGIPNHICKICNKGY 289 (388)
Q Consensus 213 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~C---~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f 289 (388)
.+.+-|+|++|..+.....-|+ |-+| .+|+.-+ ..|.+|-..|. +||+|..+|
T Consensus 76 ~d~~lYeCnIC~etS~ee~FLK----------------PneCCgY~iCn~Cy---a~LWK~~~~yp-----vCPvCkTSF 131 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERFLK----------------PNECCGYSICNACY---ANLWKFCNLYP-----VCPVCKTSF 131 (140)
T ss_pred cCCCceeccCcccccchhhcCC----------------cccccchHHHHHHH---HHHHHHcccCC-----CCCcccccc
Confidence 3456788888877655433221 2233 1233322 45666665543 588888888
Q ss_pred ccccc
Q psy4688 290 ACAAS 294 (388)
Q Consensus 290 ~~~~~ 294 (388)
++.+.
T Consensus 132 Kss~~ 136 (140)
T PF05290_consen 132 KSSSS 136 (140)
T ss_pred ccccc
Confidence 76553
No 178
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.33 E-value=38 Score=36.20 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=3.5
Q ss_pred cccccccc
Q psy4688 280 HICKICNK 287 (388)
Q Consensus 280 ~~C~~C~k 287 (388)
|.|+.||.
T Consensus 693 y~CPsCGa 700 (1337)
T PRK14714 693 YVCPDCGA 700 (1337)
T ss_pred eeCccCCC
Confidence 34444443
No 179
>KOG1280|consensus
Probab=36.24 E-value=31 Score=30.91 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=18.6
Q ss_pred ccccccchhcccChhhHHHHHHhhccC
Q psy4688 70 TTTCTMCKKTFRNKATFQKHMQRAHVG 96 (388)
Q Consensus 70 ~~~C~~C~~~f~~~~~l~~H~~~~h~~ 96 (388)
.|.|++|+..=.+...|..|+...|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpd 105 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPE 105 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcc
Confidence 467777777766777777777666654
No 180
>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=36.05 E-value=18 Score=25.59 Aligned_cols=13 Identities=23% Similarity=0.692 Sum_probs=8.5
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
.+.|..|++.|.-
T Consensus 53 IW~C~~C~~~~AG 65 (91)
T TIGR00280 53 IWTCRKCGAKFAG 65 (91)
T ss_pred EEEcCCCCCEEeC
Confidence 4677777776653
No 181
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.89 E-value=19 Score=25.84 Aligned_cols=10 Identities=30% Similarity=1.079 Sum_probs=4.9
Q ss_pred cccccccCCc
Q psy4688 251 EYECDYCGAK 260 (388)
Q Consensus 251 ~~~C~~C~~~ 260 (388)
.|.|+.||..
T Consensus 22 ~FtCp~Cghe 31 (104)
T COG4888 22 TFTCPRCGHE 31 (104)
T ss_pred eEecCccCCe
Confidence 3555555543
No 182
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=35.84 E-value=46 Score=18.99 Aligned_cols=27 Identities=19% Similarity=0.589 Sum_probs=13.2
Q ss_pred cchhhH-HhHHHHHHHHhcCCCCccccccchh
Q psy4688 346 VCGAKI-KGSLKQHMITHTGERKYCCHICGKK 376 (388)
Q Consensus 346 ~C~~~f-~~~L~~H~~~H~~~~~~~C~~C~k~ 376 (388)
.||-.| ..-|...+.. ....|++|...
T Consensus 17 ~C~H~~c~~C~~~~~~~----~~~~Cp~C~~~ 44 (45)
T cd00162 17 PCGHVFCRSCIDKWLKS----GKNTCPLCRTP 44 (45)
T ss_pred CCCChhcHHHHHHHHHh----CcCCCCCCCCc
Confidence 355555 3334443332 23468877653
No 183
>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=35.47 E-value=24 Score=33.44 Aligned_cols=27 Identities=26% Similarity=0.564 Sum_probs=24.1
Q ss_pred CCCCCcCCcCCCcHHHHHHHHhhccCC
Q psy4688 42 KTCPICNKSYPGARNMRKHLRLVHDKN 68 (388)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~~h~~~ 68 (388)
+.|+.|.+.|.+...+..|+...|.+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 679999999999999999998888654
No 184
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.90 E-value=15 Score=28.38 Aligned_cols=11 Identities=18% Similarity=0.742 Sum_probs=5.4
Q ss_pred ccccccccccc
Q psy4688 280 HICKICNKGYA 290 (388)
Q Consensus 280 ~~C~~C~k~f~ 290 (388)
+.|..||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 44555554443
No 185
>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=34.60 E-value=69 Score=19.22 Aligned_cols=10 Identities=30% Similarity=1.162 Sum_probs=6.6
Q ss_pred CccccCCCcc
Q psy4688 312 EKFKCDLCDK 321 (388)
Q Consensus 312 ~~~~C~~C~k 321 (388)
..|+|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 4577777764
No 186
>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=34.59 E-value=14 Score=21.92 Aligned_cols=10 Identities=20% Similarity=0.544 Sum_probs=4.5
Q ss_pred ccccccchhc
Q psy4688 70 TTTCTMCKKT 79 (388)
Q Consensus 70 ~~~C~~C~~~ 79 (388)
.+.|+.||..
T Consensus 19 ~~vC~~CG~V 28 (43)
T PF08271_consen 19 ELVCPNCGLV 28 (43)
T ss_dssp EEEETTT-BB
T ss_pred eEECCCCCCE
Confidence 4455555544
No 187
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=34.52 E-value=25 Score=33.87 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=6.7
Q ss_pred Cccccccccccc
Q psy4688 279 NHICKICNKGYA 290 (388)
Q Consensus 279 ~~~C~~C~k~f~ 290 (388)
.|+|..||..|.
T Consensus 425 ~~~c~~c~~~yd 436 (479)
T PRK05452 425 RMQCSVCQWIYD 436 (479)
T ss_pred eEEECCCCeEEC
Confidence 455666655554
No 188
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=34.47 E-value=16 Score=33.86 Aligned_cols=27 Identities=26% Similarity=0.640 Sum_probs=15.9
Q ss_pred ccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhHH
Q psy4688 315 KCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKIK 352 (388)
Q Consensus 315 ~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f~ 352 (388)
.|+.||.+..++ |..-|.|+.||.++.
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~ 378 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRAR 378 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCC
Confidence 577777654442 333567777776653
No 189
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=34.42 E-value=19 Score=20.93 Aligned_cols=14 Identities=36% Similarity=0.823 Sum_probs=11.6
Q ss_pred ccccCCCcccccCh
Q psy4688 313 KFKCDLCDKEFFEK 326 (388)
Q Consensus 313 ~~~C~~C~k~F~~~ 326 (388)
||+|+.|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78999999988664
No 190
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=34.25 E-value=19 Score=26.87 Aligned_cols=13 Identities=15% Similarity=0.082 Sum_probs=7.6
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
.+.|..||..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PRK12380 70 QAWCWDCSQVVEI 82 (113)
T ss_pred EEEcccCCCEEec
Confidence 3566666655544
No 191
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=34.15 E-value=29 Score=20.41 Aligned_cols=12 Identities=17% Similarity=0.462 Sum_probs=7.1
Q ss_pred cccCCCcccccC
Q psy4688 314 FKCDLCDKEFFE 325 (388)
Q Consensus 314 ~~C~~C~k~F~~ 325 (388)
-+|+.||..|..
T Consensus 14 ~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 14 TTCPTCGMLYSP 25 (41)
T ss_pred cCCCCCCCEECC
Confidence 456666666543
No 192
>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=34.08 E-value=33 Score=29.40 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=7.2
Q ss_pred CCCcccCCCCcc
Q psy4688 214 SVRKYGCDECGK 225 (388)
Q Consensus 214 ~~~~~~C~~C~~ 225 (388)
|.+.|+|..|..
T Consensus 139 GGrif~CsfC~~ 150 (314)
T PF06524_consen 139 GGRIFKCSFCDN 150 (314)
T ss_pred CCeEEEeecCCC
Confidence 445666666654
No 193
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=33.91 E-value=21 Score=25.16 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=8.2
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
.+.|..|++.|.-
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PTZ00255 54 IWRCKGCKKTVAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4667777766653
No 194
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=33.47 E-value=84 Score=28.32 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=17.1
Q ss_pred ccccccchhccCCchHHHHHHh
Q psy4688 104 HFECNYCHAKFSNKSLLSDHIS 125 (388)
Q Consensus 104 ~~~C~~C~~~f~~~~~L~~H~~ 125 (388)
.+-|..|++-|....-+..|..
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHh
Confidence 4668888888888888877764
No 195
>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=33.05 E-value=23 Score=22.26 Aligned_cols=9 Identities=44% Similarity=0.859 Sum_probs=4.2
Q ss_pred cCCCccccc
Q psy4688 316 CDLCDKEFF 324 (388)
Q Consensus 316 C~~C~k~F~ 324 (388)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 444444444
No 196
>KOG3408|consensus
Probab=32.88 E-value=26 Score=26.09 Aligned_cols=27 Identities=33% Similarity=0.491 Sum_probs=19.8
Q ss_pred CCCCccCCccccccCChHHHHHHHhhh
Q psy4688 129 GLKNYKCHVCDKAYSCRKALKTHTLLH 155 (388)
Q Consensus 129 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 155 (388)
|...|.|-.|.+-|.+...|..|.++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 344577888888888888888887654
No 197
>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=32.10 E-value=18 Score=19.42 Aligned_cols=9 Identities=33% Similarity=0.800 Sum_probs=2.8
Q ss_pred cccCCcchh
Q psy4688 341 FHLCKVCGA 349 (388)
Q Consensus 341 ~~~C~~C~~ 349 (388)
.|.|..|+.
T Consensus 15 ~Y~C~~Cdf 23 (30)
T PF07649_consen 15 FYRCSECDF 23 (30)
T ss_dssp EEE-TTT--
T ss_pred eEECccCCC
Confidence 344555443
No 198
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=31.28 E-value=17 Score=24.14 Aligned_cols=27 Identities=19% Similarity=0.571 Sum_probs=14.2
Q ss_pred ccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhH
Q psy4688 315 KCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKI 351 (388)
Q Consensus 315 ~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f 351 (388)
.|+.||..-.. --..+.|.|+.||..+
T Consensus 30 ~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 30 TCPRCGHRNKK----------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccccccc----------ccccceEEcCCCCCEE
Confidence 46677654433 1123456666666544
No 200
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=31.26 E-value=45 Score=26.15 Aligned_cols=19 Identities=21% Similarity=0.627 Sum_probs=13.3
Q ss_pred ccccCCCcccccChhhHHh
Q psy4688 313 KFKCDLCDKEFFEKKKLNK 331 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~ 331 (388)
-+.|+.||+.|..-+..++
T Consensus 124 f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred EEECCCCCCEecccccHHH
Confidence 4678888888876655443
No 201
>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=30.63 E-value=23 Score=19.75 Aligned_cols=10 Identities=30% Similarity=0.849 Sum_probs=5.1
Q ss_pred ccccccchhh
Q psy4688 368 YCCHICGKKL 377 (388)
Q Consensus 368 ~~C~~C~k~f 377 (388)
+.|+.|++.+
T Consensus 5 ~~C~nC~R~v 14 (33)
T PF08209_consen 5 VECPNCGRPV 14 (33)
T ss_dssp EE-TTTSSEE
T ss_pred EECCCCcCCc
Confidence 4566666554
No 202
>KOG3214|consensus
Probab=30.63 E-value=17 Score=25.87 Aligned_cols=41 Identities=17% Similarity=0.529 Sum_probs=19.2
Q ss_pred CCcCCCCCcCCcCCCcHHHHHHHHhhccCCCccccccchhcccChh
Q psy4688 39 NKTKTCPICNKSYPGARNMRKHLRLVHDKNSTTTCTMCKKTFRNKA 84 (388)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~ 84 (388)
...|.|+.|+-.-.-.-.|.+ -...+...|.+|+.+|.+..
T Consensus 21 dt~FnClfcnHek~v~~~~Dk-----~~~iG~~sC~iC~esFqt~i 61 (109)
T KOG3214|consen 21 DTQFNCLFCNHEKSVSCTLDK-----KHNIGKASCRICEESFQTTI 61 (109)
T ss_pred heeeccCccccccceeeeehh-----hcCcceeeeeehhhhhccch
Confidence 445777777643322222211 01123456666666665543
No 203
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=30.24 E-value=25 Score=24.79 Aligned_cols=13 Identities=23% Similarity=0.720 Sum_probs=8.4
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
.+.|..|++.|.-
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PRK03976 54 IWECRKCGAKFAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4667777776653
No 204
>KOG3408|consensus
Probab=30.08 E-value=41 Score=25.07 Aligned_cols=29 Identities=21% Similarity=0.436 Sum_probs=23.5
Q ss_pred CcCCCCccccccchhccCCchHHHHHHhh
Q psy4688 98 KISVSKHFECNYCHAKFSNKSLLSDHISS 126 (388)
Q Consensus 98 ~~~~~~~~~C~~C~~~f~~~~~L~~H~~~ 126 (388)
...+...|.|-.|.+-|.+...|..|.++
T Consensus 51 dlPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 51 DLPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 34455678999999999999999999764
No 205
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.88 E-value=46 Score=21.00 Aligned_cols=31 Identities=23% Similarity=0.558 Sum_probs=13.9
Q ss_pred CCCCcCCcCCCcHHHHHHHHhhccCCCccccccchh
Q psy4688 43 TCPICNKSYPGARNMRKHLRLVHDKNSTTTCTMCKK 78 (388)
Q Consensus 43 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~ 78 (388)
.|.-|+...+...... ++ ..+....|+.|++
T Consensus 24 ~C~gC~~~l~~~~~~~--i~---~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNE--IR---KGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHH--HH---cCCCeEECcCCCc
Confidence 4555655554332221 11 1234556666654
No 206
>KOG0717|consensus
Probab=29.28 E-value=27 Score=32.73 Aligned_cols=22 Identities=36% Similarity=0.765 Sum_probs=19.4
Q ss_pred cccCCCcccccChhhHHhHHhh
Q psy4688 314 FKCDLCDKEFFEKKKLNKHKNW 335 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~~H~~~ 335 (388)
+-|.+|+|+|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999999999999765
No 207
>KOG1842|consensus
Probab=29.19 E-value=28 Score=32.28 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=25.7
Q ss_pred CcCCCCCcCCcCCCcHHHHHHHHhhccCC
Q psy4688 40 KTKTCPICNKSYPGARNMRKHLRLVHDKN 68 (388)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 68 (388)
..|.||+|...|.+...|..|+...|..+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 35899999999999999999998888654
No 208
>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=29.18 E-value=20 Score=21.25 Aligned_cols=15 Identities=47% Similarity=0.855 Sum_probs=9.3
Q ss_pred CccccCCCcccccCh
Q psy4688 312 EKFKCDLCDKEFFEK 326 (388)
Q Consensus 312 ~~~~C~~C~k~F~~~ 326 (388)
-+|.|+.|++.|=.+
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 378899999988654
No 209
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.06 E-value=24 Score=26.52 Aligned_cols=13 Identities=23% Similarity=0.674 Sum_probs=7.8
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
.+.|..||..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 3566666665544
No 210
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=28.79 E-value=37 Score=28.86 Aligned_cols=15 Identities=13% Similarity=0.603 Sum_probs=9.1
Q ss_pred CcccCCCCcccCCCh
Q psy4688 216 RKYGCDECGKMLKSR 230 (388)
Q Consensus 216 ~~~~C~~C~~~f~~~ 230 (388)
..|.|+.|+..|...
T Consensus 154 aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 154 AEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeecccccccchhh
Confidence 346666666666644
No 211
>KOG0717|consensus
Probab=28.38 E-value=28 Score=32.63 Aligned_cols=25 Identities=24% Similarity=0.628 Sum_probs=21.7
Q ss_pred CCcCCCCCcCCcCCCcHHHHHHHHh
Q psy4688 39 NKTKTCPICNKSYPGARNMRKHLRL 63 (388)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~ 63 (388)
+..+.|.+|+++|.+...|..|...
T Consensus 290 ge~lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 290 GEVLYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred CCceEEeeccccccchHHHHhhHHH
Confidence 4448999999999999999999764
No 212
>PRK05580 primosome assembly protein PriA; Validated
Probab=28.31 E-value=33 Score=34.76 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=5.2
Q ss_pred cccCCcchh
Q psy4688 341 FHLCKVCGA 349 (388)
Q Consensus 341 ~~~C~~C~~ 349 (388)
|..|+.||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 445666654
No 213
>KOG0978|consensus
Probab=28.24 E-value=29 Score=34.58 Aligned_cols=11 Identities=18% Similarity=0.480 Sum_probs=9.3
Q ss_pred ccccccchhhH
Q psy4688 368 YCCHICGKKLR 378 (388)
Q Consensus 368 ~~C~~C~k~f~ 378 (388)
=+||.|+.+|.
T Consensus 679 RKCP~Cn~aFg 689 (698)
T KOG0978|consen 679 RKCPKCNAAFG 689 (698)
T ss_pred CCCCCCCCCCC
Confidence 37999999994
No 214
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=27.96 E-value=40 Score=21.18 Aligned_cols=13 Identities=31% Similarity=0.813 Sum_probs=6.9
Q ss_pred cccCCCcccccCh
Q psy4688 314 FKCDLCDKEFFEK 326 (388)
Q Consensus 314 ~~C~~C~k~F~~~ 326 (388)
++|+.||-.|...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 4555555555443
No 215
>PRK12496 hypothetical protein; Provisional
Probab=27.65 E-value=30 Score=27.76 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=6.9
Q ss_pred cccCCCcccc
Q psy4688 314 FKCDLCDKEF 323 (388)
Q Consensus 314 ~~C~~C~k~F 323 (388)
|.|+-|++.|
T Consensus 128 ~~C~gC~~~~ 137 (164)
T PRK12496 128 KVCKGCKKKY 137 (164)
T ss_pred EECCCCCccc
Confidence 6677777665
No 216
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=27.53 E-value=64 Score=25.41 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=2.3
Q ss_pred CcccCCcchh
Q psy4688 340 KFHLCKVCGA 349 (388)
Q Consensus 340 ~~~~C~~C~~ 349 (388)
....|-.||.
T Consensus 59 t~leCy~Cg~ 68 (152)
T PF09416_consen 59 TVLECYNCGS 68 (152)
T ss_dssp -B---TTT--
T ss_pred cEEEEEecCC
Confidence 3455666653
No 217
>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=27.49 E-value=35 Score=20.13 Aligned_cols=17 Identities=29% Similarity=0.581 Sum_probs=12.6
Q ss_pred cccCCCcccccChhhHH
Q psy4688 314 FKCDLCDKEFFEKKKLN 330 (388)
Q Consensus 314 ~~C~~C~k~F~~~~~L~ 330 (388)
-.|++||+.|+......
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 46889999888766554
No 218
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=27.48 E-value=27 Score=27.28 Aligned_cols=32 Identities=25% Similarity=0.544 Sum_probs=15.3
Q ss_pred cccccccCCcCCChhHHHHHHhhcCCCCCcccccccc
Q psy4688 251 EYECDYCGAKYPNKYTLSDHISGHTGIPNHICKICNK 287 (388)
Q Consensus 251 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~k 287 (388)
+|.|. |+..|.+. .+|-..-.|+ .|.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCc
Confidence 56666 66555433 2333333333 455555553
No 219
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.42 E-value=29 Score=24.94 Aligned_cols=14 Identities=21% Similarity=0.729 Sum_probs=9.5
Q ss_pred cccccccCCcCCCh
Q psy4688 251 EYECDYCGAKYPNK 264 (388)
Q Consensus 251 ~~~C~~C~~~f~~~ 264 (388)
|++|.-||..|.+-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 45677777777664
No 220
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=27.20 E-value=21 Score=30.50 Aligned_cols=19 Identities=26% Similarity=0.634 Sum_probs=0.0
Q ss_pred ccCCcchhhH-HhHHHHHHH
Q psy4688 342 HLCKVCGAKI-KGSLKQHMI 360 (388)
Q Consensus 342 ~~C~~C~~~f-~~~L~~H~~ 360 (388)
..|++||... -+.|..||+
T Consensus 169 ~~cPitGe~IP~~e~~eHmR 188 (229)
T PF12230_consen 169 IICPITGEMIPADEMDEHMR 188 (229)
T ss_dssp --------------------
T ss_pred cccccccccccccccccccc
Confidence 4455555544 233445544
No 221
>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 COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.16 E-value=47 Score=26.92 Aligned_cols=15 Identities=20% Similarity=0.487 Sum_probs=7.3
Q ss_pred CCCCccccccccccc
Q psy4688 276 GIPNHICKICNKGYA 290 (388)
Q Consensus 276 ~~~~~~C~~C~k~f~ 290 (388)
+..-|.|+.|.-.|+
T Consensus 110 ~~~~y~C~~~~~r~s 124 (176)
T COG1675 110 ENNYYVCPNCHVKYS 124 (176)
T ss_pred cCCceeCCCCCCccc
Confidence 334455555554443
No 223
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=26.49 E-value=39 Score=26.91 Aligned_cols=35 Identities=17% Similarity=0.382 Sum_probs=22.0
Q ss_pred ccccCCCcccccChhhHHhHHhhhcCCCcccCCcchhhHHhHHHH
Q psy4688 313 KFKCDLCDKEFFEKKKLNKHKNWAHGDKFHLCKVCGAKIKGSLKQ 357 (388)
Q Consensus 313 ~~~C~~C~k~F~~~~~L~~H~~~hh~~~~~~C~~C~~~f~~~L~~ 357 (388)
...|+.|+.+|..... .+.|-|..|=+.|.+.|..
T Consensus 74 ~l~C~~C~~Tfk~f~~----------~g~fGCaeCY~tf~~~i~p 108 (176)
T COG3880 74 LLGCHNCGMTFKEFIQ----------SGLFGCAECYKTFESQISP 108 (176)
T ss_pred HhcCccccccHHHHHH----------hcccchHHHHHHHHHHhhH
Confidence 3568888887755321 2457788888877655443
No 224
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=26.13 E-value=37 Score=19.79 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=9.6
Q ss_pred cccCCCCcccCCChhHHH
Q psy4688 217 KYGCDECGKMLKSRDSLN 234 (388)
Q Consensus 217 ~~~C~~C~~~f~~~~~l~ 234 (388)
-+.|+.|+-.+-....|.
T Consensus 19 id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEECCCCCeEEccHHHHH
Confidence 345666665555554443
No 225
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=26.08 E-value=29 Score=20.07 Aligned_cols=11 Identities=18% Similarity=0.655 Sum_probs=8.2
Q ss_pred ccccCCCcccc
Q psy4688 313 KFKCDLCDKEF 323 (388)
Q Consensus 313 ~~~C~~C~k~F 323 (388)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 37888888765
No 226
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=25.79 E-value=27 Score=21.88 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=6.7
Q ss_pred ccCCCcccccChh
Q psy4688 315 KCDLCDKEFFEKK 327 (388)
Q Consensus 315 ~C~~C~k~F~~~~ 327 (388)
.||+|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 7999999887643
No 227
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.76 E-value=23 Score=22.40 Aligned_cols=10 Identities=60% Similarity=1.438 Sum_probs=2.8
Q ss_pred Cccccccchh
Q psy4688 367 KYCCHICGKK 376 (388)
Q Consensus 367 ~~~C~~C~k~ 376 (388)
.|.|++||.+
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 4677777765
No 228
>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=25.47 E-value=20 Score=24.08 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=4.7
Q ss_pred ccccCCCcccccC
Q psy4688 313 KFKCDLCDKEFFE 325 (388)
Q Consensus 313 ~~~C~~C~k~F~~ 325 (388)
...|..|+..++-
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 3444444444433
No 229
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.29 E-value=41 Score=21.60 Aligned_cols=12 Identities=25% Similarity=0.670 Sum_probs=5.7
Q ss_pred CCCccccccccc
Q psy4688 277 IPNHICKICNKG 288 (388)
Q Consensus 277 ~~~~~C~~C~k~ 288 (388)
.+.|.|+.|.-.
T Consensus 29 IrtymC~eC~~R 40 (68)
T COG4896 29 IRTYMCPECEHR 40 (68)
T ss_pred ceeEechhhHhh
Confidence 344555555433
No 230
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=25.07 E-value=22 Score=35.52 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=7.7
Q ss_pred ccccchhccCCc
Q psy4688 106 ECNYCHAKFSNK 117 (388)
Q Consensus 106 ~C~~C~~~f~~~ 117 (388)
.|..|++.|...
T Consensus 462 tC~~C~kkFfSl 473 (1374)
T PTZ00303 462 SCPSCGRAFISL 473 (1374)
T ss_pred cccCcCCccccc
Confidence 477777777543
No 231
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=24.76 E-value=33 Score=20.23 Aligned_cols=6 Identities=33% Similarity=1.353 Sum_probs=1.8
Q ss_pred cccccc
Q psy4688 368 YCCHIC 373 (388)
Q Consensus 368 ~~C~~C 373 (388)
+.|+.|
T Consensus 37 ~~CP~C 42 (42)
T PF15227_consen 37 FSCPEC 42 (42)
T ss_dssp ---SSS
T ss_pred CCCcCC
Confidence 666655
No 232
>KOG0562|consensus
Probab=24.65 E-value=54 Score=26.05 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=20.1
Q ss_pred hhCCcCCCCCcCCcCCCcHHHHHHHHhhcc
Q psy4688 37 IKNKTKTCPICNKSYPGARNMRKHLRLVHD 66 (388)
Q Consensus 37 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 66 (388)
+.+....|-.|+..-+....|+.|++..++
T Consensus 149 llk~dLrC~~Cq~~~~~~~kLK~Hl~~~~~ 178 (184)
T KOG0562|consen 149 LLKEDLRCWRCQTFGPHFPKLKAHLREEYD 178 (184)
T ss_pred hhccceeehhhhhcccccHHHHHHHHHHHh
Confidence 345667888888444666778888776543
No 233
>KOG1842|consensus
Probab=24.52 E-value=38 Score=31.53 Aligned_cols=29 Identities=28% Similarity=0.505 Sum_probs=22.2
Q ss_pred CCccccCCCcccccChhhHHhHHhhhcCC
Q psy4688 311 IEKFKCDLCDKEFFEKKKLNKHKNWAHGD 339 (388)
Q Consensus 311 ~~~~~C~~C~k~F~~~~~L~~H~~~hh~~ 339 (388)
.+.|-||+|.+.|.+-..|..|...-|++
T Consensus 13 ~egflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 13 LEGFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred hhcccCchHhhhhhhHHHHHHHHhhhccc
Confidence 35688888888888888888888776653
No 234
>KOG2636|consensus
Probab=24.46 E-value=50 Score=30.78 Aligned_cols=26 Identities=19% Similarity=0.698 Sum_probs=17.1
Q ss_pred ccCCCccccccch-hcccChhhHHHHH
Q psy4688 65 HDKNSTTTCTMCK-KTFRNKATFQKHM 90 (388)
Q Consensus 65 h~~~~~~~C~~C~-~~f~~~~~l~~H~ 90 (388)
|.-+..|.|.+|| .++.....+.+|.
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHh
Confidence 4555567777776 6666666677665
No 235
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=24.41 E-value=52 Score=19.18 Aligned_cols=12 Identities=17% Similarity=0.625 Sum_probs=8.2
Q ss_pred ccccCCCccccc
Q psy4688 313 KFKCDLCDKEFF 324 (388)
Q Consensus 313 ~~~C~~C~k~F~ 324 (388)
-|.|..|+..|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 477777777654
No 236
>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=24.29 E-value=27 Score=25.99 Aligned_cols=12 Identities=33% Similarity=0.722 Sum_probs=5.9
Q ss_pred cccCCCcccccC
Q psy4688 314 FKCDLCDKEFFE 325 (388)
Q Consensus 314 ~~C~~C~k~F~~ 325 (388)
+.|..||..|.-
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 455555555543
No 237
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=23.92 E-value=53 Score=18.19 Aligned_cols=11 Identities=45% Similarity=1.017 Sum_probs=7.1
Q ss_pred ccccCCCcccc
Q psy4688 313 KFKCDLCDKEF 323 (388)
Q Consensus 313 ~~~C~~C~k~F 323 (388)
=|.|..|++.+
T Consensus 27 Cf~C~~C~~~L 37 (39)
T smart00132 27 CFKCSKCGKPL 37 (39)
T ss_pred CCCCcccCCcC
Confidence 36777777655
No 238
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=23.87 E-value=26 Score=35.58 Aligned_cols=8 Identities=38% Similarity=0.920 Sum_probs=0.0
Q ss_pred cccccccc
Q psy4688 280 HICKICNK 287 (388)
Q Consensus 280 ~~C~~C~k 287 (388)
+.|+.||.
T Consensus 656 r~Cp~Cg~ 663 (900)
T PF03833_consen 656 RRCPKCGK 663 (900)
T ss_dssp --------
T ss_pred ccCcccCC
Confidence 44555553
No 239
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=23.28 E-value=28 Score=21.10 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=6.1
Q ss_pred cccCC--CcccccC
Q psy4688 314 FKCDL--CDKEFFE 325 (388)
Q Consensus 314 ~~C~~--C~k~F~~ 325 (388)
++|.. ||..|..
T Consensus 26 ~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 26 CQCTNPECGHTFVA 39 (47)
T ss_pred EEECCCcCCCEEEE
Confidence 45544 5555543
No 240
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.14 E-value=30 Score=25.83 Aligned_cols=10 Identities=20% Similarity=0.664 Sum_probs=5.5
Q ss_pred cccCCCcccc
Q psy4688 314 FKCDLCDKEF 323 (388)
Q Consensus 314 ~~C~~C~k~F 323 (388)
+.|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5566665544
No 241
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=22.95 E-value=28 Score=28.74 Aligned_cols=24 Identities=33% Similarity=0.798 Sum_probs=0.0
Q ss_pred CCcCCCCCcC-CcCCCcHHHHHHHH
Q psy4688 39 NKTKTCPICN-KSYPGARNMRKHLR 62 (388)
Q Consensus 39 ~~~~~C~~C~-~~f~~~~~l~~H~~ 62 (388)
+..|+|.+|| .+|..+..+.+|..
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcC
Confidence 4568899997 56677777877753
No 242
>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=22.87 E-value=35 Score=23.63 Aligned_cols=10 Identities=30% Similarity=1.168 Sum_probs=3.5
Q ss_pred cccCCCcccc
Q psy4688 314 FKCDLCDKEF 323 (388)
Q Consensus 314 ~~C~~C~k~F 323 (388)
..|..||..|
T Consensus 47 ~~C~~Cg~~~ 56 (81)
T PF05129_consen 47 LSCRVCGESF 56 (81)
T ss_dssp EEESSS--EE
T ss_pred EEecCCCCeE
Confidence 3444444444
No 243
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=22.85 E-value=28 Score=29.70 Aligned_cols=29 Identities=10% Similarity=0.157 Sum_probs=0.0
Q ss_pred CccccCCCcccccChhhHHhHHhhhcCCCc
Q psy4688 312 EKFKCDLCDKEFFEKKKLNKHKNWAHGDKF 341 (388)
Q Consensus 312 ~~~~C~~C~k~F~~~~~L~~H~~~hh~~~~ 341 (388)
....|++||.... .+.|..|||+...+-.
T Consensus 167 ~~~~cPitGe~IP-~~e~~eHmRi~LlDP~ 195 (229)
T PF12230_consen 167 KMIICPITGEMIP-ADEMDEHMRIELLDPR 195 (229)
T ss_dssp ------------------------------
T ss_pred ccccccccccccc-cccccccccccccccc
Confidence 4578999998875 4789999998766543
No 244
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.07 E-value=30 Score=25.79 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=5.6
Q ss_pred ccccccchhccc
Q psy4688 70 TTTCTMCKKTFR 81 (388)
Q Consensus 70 ~~~C~~C~~~f~ 81 (388)
|--|..||..|.
T Consensus 68 psfchncgs~fp 79 (160)
T COG4306 68 PSFCHNCGSRFP 79 (160)
T ss_pred cchhhcCCCCCC
Confidence 334444554444
No 245
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.94 E-value=51 Score=18.49 Aligned_cols=12 Identities=25% Similarity=0.539 Sum_probs=7.4
Q ss_pred CCccccCCCccc
Q psy4688 311 IEKFKCDLCDKE 322 (388)
Q Consensus 311 ~~~~~C~~C~k~ 322 (388)
...+.|+.||..
T Consensus 20 r~R~vC~~Cg~I 31 (34)
T PF14803_consen 20 RERLVCPACGFI 31 (34)
T ss_dssp S-EEEETTTTEE
T ss_pred ccceECCCCCCE
Confidence 455777777754
No 246
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.83 E-value=50 Score=24.85 Aligned_cols=22 Identities=14% Similarity=0.563 Sum_probs=16.0
Q ss_pred CccccCCCcccccChhhHHhHH
Q psy4688 312 EKFKCDLCDKEFFEKKKLNKHK 333 (388)
Q Consensus 312 ~~~~C~~C~k~F~~~~~L~~H~ 333 (388)
.-+.|+.||..|.+......-.
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~~~ 51 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKRNS 51 (127)
T ss_pred eeeECCCCCCEEEcHHHHHHHH
Confidence 4578999998888877665543
No 247
>KOG2817|consensus
Probab=21.66 E-value=62 Score=29.72 Aligned_cols=24 Identities=38% Similarity=0.635 Sum_probs=18.1
Q ss_pred ceehhHHHHHhhCCc--CCCCCcCCc
Q psy4688 27 VITADKWRALIKNKT--KTCPICNKS 50 (388)
Q Consensus 27 ~~~~~~~~~~~~~~~--~~C~~C~~~ 50 (388)
||+.|....+.++.. |+||+|+..
T Consensus 358 VISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 358 VISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 577777777777776 888888764
No 248
>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=21.49 E-value=14 Score=33.50 Aligned_cols=14 Identities=29% Similarity=0.645 Sum_probs=6.2
Q ss_pred CccccCCCcccccC
Q psy4688 312 EKFKCDLCDKEFFE 325 (388)
Q Consensus 312 ~~~~C~~C~k~F~~ 325 (388)
+-|+|..|++...+
T Consensus 284 RFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 284 RFFKCKDCGNRTIS 297 (344)
T ss_dssp EEEE-T-TS-EEEE
T ss_pred eeEECCCCCCeeee
Confidence 44666666665544
No 249
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=20.86 E-value=1.3e+02 Score=17.66 Aligned_cols=11 Identities=36% Similarity=0.794 Sum_probs=7.3
Q ss_pred CCCccccccch
Q psy4688 365 ERKYCCHICGK 375 (388)
Q Consensus 365 ~~~~~C~~C~k 375 (388)
.....|++|++
T Consensus 34 ~~~~~CP~C~k 44 (44)
T PF14634_consen 34 GKSVKCPICRK 44 (44)
T ss_pred CCCCCCcCCCC
Confidence 45567888764
No 250
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.35 E-value=88 Score=31.40 Aligned_cols=11 Identities=18% Similarity=0.446 Sum_probs=6.1
Q ss_pred ccccccccccc
Q psy4688 281 ICKICNKGYAC 291 (388)
Q Consensus 281 ~C~~C~k~f~~ 291 (388)
.|+.||.....
T Consensus 43 fC~~CG~~~~~ 53 (645)
T PRK14559 43 HCPNCGAETGT 53 (645)
T ss_pred cccccCCcccc
Confidence 46666655443
No 251
>PRK05978 hypothetical protein; Provisional
Probab=20.30 E-value=55 Score=25.69 Aligned_cols=7 Identities=43% Similarity=1.289 Sum_probs=3.2
Q ss_pred cccccCC
Q psy4688 253 ECDYCGA 259 (388)
Q Consensus 253 ~C~~C~~ 259 (388)
.|+.||+
T Consensus 35 rCP~CG~ 41 (148)
T PRK05978 35 RCPACGE 41 (148)
T ss_pred cCCCCCC
Confidence 3444443
No 252
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=20.24 E-value=77 Score=18.24 Aligned_cols=11 Identities=36% Similarity=1.102 Sum_probs=3.9
Q ss_pred ccccCCCcccc
Q psy4688 313 KFKCDLCDKEF 323 (388)
Q Consensus 313 ~~~C~~C~k~F 323 (388)
.|-|+.|+..|
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 35677777766
No 253
>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=20.17 E-value=70 Score=18.58 Aligned_cols=10 Identities=20% Similarity=1.006 Sum_probs=5.0
Q ss_pred CccccCCCcc
Q psy4688 312 EKFKCDLCDK 321 (388)
Q Consensus 312 ~~~~C~~C~k 321 (388)
+.+.|++|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 4566666664
No 254
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=20.08 E-value=38 Score=19.31 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=4.9
Q ss_pred Cccccccchh
Q psy4688 367 KYCCHICGKK 376 (388)
Q Consensus 367 ~~~C~~C~k~ 376 (388)
-|+|.+||.-
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4788888753
Done!