Query psy6751
Match_columns 392
No_of_seqs 156 out of 2405
Neff 10.8
Searched_HMMs 46136
Date Fri Aug 16 17:32:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6751.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6751hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074|consensus 100.0 6E-31 1.3E-35 240.8 9.1 173 188-360 605-939 (958)
2 KOG2462|consensus 100.0 3.6E-29 7.8E-34 202.5 5.6 134 216-351 130-266 (279)
3 KOG2462|consensus 99.9 3.6E-27 7.8E-32 191.0 5.4 133 188-322 130-265 (279)
4 KOG3608|consensus 99.9 3.3E-25 7.1E-30 184.1 9.8 199 150-362 178-386 (467)
5 KOG3608|consensus 99.9 4.1E-24 8.8E-29 177.7 11.4 235 149-391 134-382 (467)
6 KOG3623|consensus 99.9 8.6E-25 1.9E-29 197.5 6.9 109 148-265 209-330 (1007)
7 KOG1074|consensus 99.9 5.6E-23 1.2E-27 189.0 6.4 172 148-330 604-937 (958)
8 KOG3623|consensus 99.8 1.8E-19 3.9E-24 163.5 9.6 78 244-321 894-971 (1007)
9 KOG3576|consensus 99.7 2E-18 4.3E-23 132.9 2.9 84 186-269 115-198 (267)
10 KOG3576|consensus 99.7 1.8E-18 3.9E-23 133.2 2.6 114 213-326 114-238 (267)
11 PLN03086 PRLI-interacting fact 99.4 1E-12 2.2E-17 120.9 8.4 147 189-354 408-566 (567)
12 PLN03086 PRLI-interacting fact 99.4 1.7E-12 3.8E-17 119.4 8.8 146 149-324 407-564 (567)
13 PHA00733 hypothetical protein 99.2 7.4E-12 1.6E-16 93.9 3.8 85 270-356 38-127 (128)
14 PHA00733 hypothetical protein 99.1 1.7E-10 3.7E-15 86.6 5.8 53 270-324 71-123 (128)
15 KOG3993|consensus 99.1 1.3E-11 2.8E-16 106.3 -0.5 167 188-355 267-485 (500)
16 PHA02768 hypothetical protein; 98.9 9.8E-10 2.1E-14 67.2 2.0 44 300-345 5-48 (55)
17 KOG3993|consensus 98.8 7.7E-10 1.7E-14 95.6 0.4 165 149-324 267-482 (500)
18 PHA02768 hypothetical protein; 98.8 3E-09 6.4E-14 65.1 2.2 41 273-315 6-46 (55)
19 PF13465 zf-H2C2_2: Zinc-finge 98.6 2.7E-08 5.8E-13 51.9 2.0 24 316-339 2-25 (26)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 8.7E-08 1.9E-12 50.0 2.1 24 288-311 2-25 (26)
21 PHA00616 hypothetical protein 98.5 8.5E-08 1.8E-12 55.7 1.7 31 301-331 2-32 (44)
22 PHA00616 hypothetical protein 98.4 1.2E-07 2.6E-12 55.1 1.6 35 272-306 1-35 (44)
23 PHA00732 hypothetical protein 98.3 4.2E-07 9.1E-12 61.6 2.8 45 272-322 1-46 (79)
24 PHA00732 hypothetical protein 98.2 1.2E-06 2.6E-11 59.4 3.0 47 300-352 1-48 (79)
25 PF05605 zf-Di19: Drought indu 98.2 3.9E-06 8.5E-11 52.8 4.6 20 273-293 3-22 (54)
26 KOG1146|consensus 98.1 8E-07 1.7E-11 88.2 1.6 53 1-53 464-540 (1406)
27 PF05605 zf-Di19: Drought indu 98.1 5.2E-06 1.1E-10 52.2 4.2 51 300-353 2-54 (54)
28 KOG1146|consensus 98.0 3.6E-06 7.8E-11 83.7 3.3 160 5-229 439-631 (1406)
29 PF00096 zf-C2H2: Zinc finger, 97.7 2.2E-05 4.8E-10 39.7 1.8 18 275-292 3-20 (23)
30 PF12756 zf-C2H2_2: C2H2 type 97.7 2E-05 4.4E-10 57.2 2.2 75 274-353 1-75 (100)
31 PF00096 zf-C2H2: Zinc finger, 97.7 2.3E-05 5.1E-10 39.6 1.8 21 302-322 2-22 (23)
32 PF13894 zf-C2H2_4: C2H2-type 97.6 3.3E-05 7.2E-10 39.4 1.3 24 329-352 1-24 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.6 6.1E-05 1.3E-09 54.7 3.0 71 191-266 2-72 (100)
34 PF13894 zf-C2H2_4: C2H2-type 97.5 7.7E-05 1.7E-09 38.0 2.3 19 275-293 3-21 (24)
35 PF13912 zf-C2H2_6: C2H2-type 97.5 5.8E-05 1.3E-09 39.8 1.3 26 328-353 1-26 (27)
36 COG5189 SFP1 Putative transcri 97.3 7.7E-05 1.7E-09 62.8 1.2 28 325-352 395-422 (423)
37 PF13912 zf-C2H2_6: C2H2-type 97.3 0.00012 2.7E-09 38.6 1.4 25 300-324 1-25 (27)
38 KOG2231|consensus 97.3 0.00055 1.2E-08 65.0 5.9 138 189-349 100-260 (669)
39 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00015 3.3E-09 37.0 1.0 24 329-353 1-24 (24)
40 KOG2231|consensus 97.2 0.0018 3.9E-08 61.6 8.4 161 189-360 116-309 (669)
41 KOG2785|consensus 97.1 0.0022 4.8E-08 56.0 7.2 52 272-323 166-243 (390)
42 KOG2482|consensus 97.0 0.00032 7E-09 59.8 1.5 52 3-54 145-218 (423)
43 KOG2785|consensus 96.9 0.00077 1.7E-08 58.8 3.4 54 2-55 3-92 (390)
44 COG5189 SFP1 Putative transcri 96.9 0.00022 4.7E-09 60.1 -0.1 67 214-292 347-418 (423)
45 COG5236 Uncharacterized conser 96.8 0.0014 3E-08 56.1 4.2 22 275-296 223-244 (493)
46 PF13909 zf-H2C2_5: C2H2-type 96.7 0.0012 2.5E-08 33.6 1.9 23 301-324 1-23 (24)
47 KOG2482|consensus 96.7 0.0061 1.3E-07 52.3 6.9 150 202-351 129-357 (423)
48 PF09237 GAGA: GAGA factor; I 96.6 0.0026 5.5E-08 38.0 3.0 22 245-266 25-46 (54)
49 smart00355 ZnF_C2H2 zinc finge 96.6 0.0022 4.8E-08 33.0 2.6 18 303-320 3-20 (26)
50 COG5236 Uncharacterized conser 96.5 0.0017 3.7E-08 55.6 2.6 114 245-360 152-313 (493)
51 smart00355 ZnF_C2H2 zinc finge 96.5 0.0033 7.1E-08 32.4 2.7 23 273-295 1-23 (26)
52 PF09237 GAGA: GAGA factor; I 96.4 0.0037 8E-08 37.4 2.8 29 299-327 23-51 (54)
53 PF12874 zf-met: Zinc-finger o 96.2 0.0028 6.1E-08 32.5 1.5 21 190-210 2-22 (25)
54 PF12874 zf-met: Zinc-finger o 96.2 0.0026 5.7E-08 32.6 1.4 20 302-321 2-21 (25)
55 PF12171 zf-C2H2_jaz: Zinc-fin 96.2 0.0023 5E-08 33.6 1.0 22 3-24 2-23 (27)
56 PRK04860 hypothetical protein; 96.1 0.0038 8.2E-08 48.9 2.1 36 272-311 119-154 (160)
57 PF12171 zf-C2H2_jaz: Zinc-fin 96.0 0.0033 7.1E-08 33.0 1.0 22 329-350 2-23 (27)
58 PRK04860 hypothetical protein; 96.0 0.0032 7E-08 49.3 1.3 36 244-283 119-154 (160)
59 KOG2893|consensus 95.1 0.0054 1.2E-07 49.7 -0.1 49 5-58 13-61 (341)
60 TIGR00622 ssl1 transcription f 94.4 0.066 1.4E-06 38.7 3.9 54 274-335 57-110 (112)
61 COG4049 Uncharacterized protei 94.1 0.021 4.5E-07 34.7 0.8 33 324-356 13-45 (65)
62 KOG4173|consensus 93.8 0.073 1.6E-06 42.4 3.4 75 244-321 79-167 (253)
63 PF12013 DUF3505: Protein of u 93.6 0.13 2.8E-06 37.8 4.3 25 329-353 81-109 (109)
64 PF13913 zf-C2HC_2: zinc-finge 93.3 0.079 1.7E-06 27.0 2.0 17 303-320 5-21 (25)
65 PF12013 DUF3505: Protein of u 93.2 0.21 4.5E-06 36.7 4.8 25 301-325 81-109 (109)
66 smart00451 ZnF_U1 U1-like zinc 93.1 0.03 6.5E-07 31.3 0.2 21 3-23 4-24 (35)
67 PF13913 zf-C2HC_2: zinc-finge 93.0 0.11 2.4E-06 26.5 2.2 20 273-293 3-22 (25)
68 COG5048 FOG: Zn-finger [Genera 93.0 0.015 3.2E-07 54.8 -1.9 55 2-57 33-89 (467)
69 COG4049 Uncharacterized protei 92.7 0.056 1.2E-06 32.9 1.0 30 268-297 13-42 (65)
70 smart00451 ZnF_U1 U1-like zinc 92.4 0.077 1.7E-06 29.6 1.3 22 329-350 4-25 (35)
71 PF09986 DUF2225: Uncharacteri 91.9 0.087 1.9E-06 43.9 1.6 44 1-44 4-61 (214)
72 COG5048 FOG: Zn-finger [Genera 90.9 0.041 8.8E-07 51.8 -1.5 28 29-57 31-58 (467)
73 KOG4173|consensus 90.6 0.15 3.1E-06 40.8 1.5 48 149-210 79-128 (253)
74 TIGR00622 ssl1 transcription f 90.6 0.3 6.4E-06 35.4 3.0 92 189-296 2-105 (112)
75 KOG2893|consensus 88.9 0.13 2.9E-06 41.9 0.2 41 275-319 13-53 (341)
76 PF10571 UPF0547: Uncharacteri 87.0 0.38 8.2E-06 24.8 1.1 9 274-282 16-24 (26)
77 PRK09678 DNA-binding transcrip 85.1 0.25 5.4E-06 32.8 -0.2 64 301-372 2-67 (72)
78 PF13719 zinc_ribbon_5: zinc-r 84.1 0.86 1.9E-05 25.8 1.8 8 273-280 26-33 (37)
79 smart00659 RPOLCX RNA polymera 82.3 0.73 1.6E-05 27.3 1.0 28 2-41 2-29 (44)
80 cd00729 rubredoxin_SM Rubredox 82.0 1.2 2.6E-05 24.7 1.8 7 274-280 4-10 (34)
81 PF09538 FYDLN_acid: Protein o 81.8 1.1 2.3E-05 32.6 2.0 30 3-44 10-39 (108)
82 PF13717 zinc_ribbon_4: zinc-r 81.1 1.3 2.9E-05 24.9 1.8 9 273-281 26-34 (36)
83 TIGR02098 MJ0042_CXXC MJ0042 f 80.6 1.2 2.6E-05 25.3 1.6 6 274-279 27-32 (38)
84 PF09538 FYDLN_acid: Protein o 80.0 1.5 3.2E-05 31.9 2.1 31 188-229 9-39 (108)
85 PRK00464 nrdR transcriptional 79.7 0.28 6.1E-06 38.2 -1.7 13 273-285 29-41 (154)
86 KOG2186|consensus 79.0 1.2 2.5E-05 37.2 1.5 46 273-321 4-49 (276)
87 KOG2807|consensus 78.9 3.7 7.9E-05 35.7 4.4 26 271-296 344-369 (378)
88 PF03604 DNA_RNApol_7kD: DNA d 78.6 1.3 2.9E-05 24.1 1.2 27 3-41 1-27 (32)
89 KOG2186|consensus 78.1 1.5 3.3E-05 36.5 2.0 46 189-237 4-49 (276)
90 PHA00626 hypothetical protein 78.1 1.1 2.5E-05 27.5 0.9 14 29-42 21-34 (59)
91 PRK00464 nrdR transcriptional 77.1 1.1 2.4E-05 35.0 0.8 43 3-51 1-48 (154)
92 PF09986 DUF2225: Uncharacteri 75.6 0.44 9.6E-06 39.7 -1.8 19 271-289 4-22 (214)
93 TIGR00373 conserved hypothetic 75.4 3.2 7E-05 32.7 3.1 33 295-336 104-136 (158)
94 PF02892 zf-BED: BED zinc fing 75.3 2 4.3E-05 25.5 1.5 24 329-352 17-44 (45)
95 COG2888 Predicted Zn-ribbon RN 74.4 2.7 5.9E-05 26.3 1.9 7 245-251 28-34 (61)
96 PRK00398 rpoP DNA-directed RNA 74.0 1.5 3.3E-05 26.2 0.7 7 273-279 22-28 (46)
97 smart00531 TFIIE Transcription 74.0 4 8.7E-05 31.8 3.3 13 188-200 99-111 (147)
98 TIGR02605 CxxC_CxxC_SSSS putat 73.9 1.4 2.9E-05 27.2 0.5 29 3-39 6-34 (52)
99 TIGR02300 FYDLN_acid conserved 72.9 2.9 6.3E-05 31.0 2.1 35 2-48 9-43 (129)
100 COG1996 RPC10 DNA-directed RNA 72.4 1.8 3.8E-05 26.2 0.7 28 2-40 6-33 (49)
101 PF02176 zf-TRAF: TRAF-type zi 72.3 1.8 3.9E-05 27.5 0.8 19 259-277 25-43 (60)
102 PRK06266 transcription initiat 72.0 3.4 7.3E-05 33.3 2.5 31 297-336 114-144 (178)
103 TIGR00373 conserved hypothetic 71.8 4.2 9E-05 32.1 2.9 16 189-204 110-125 (158)
104 PF05443 ROS_MUCR: ROS/MUCR tr 70.8 2 4.3E-05 32.5 0.9 24 329-355 73-96 (132)
105 KOG2807|consensus 70.7 7.2 0.00016 34.0 4.2 25 299-323 344-368 (378)
106 PRK04023 DNA polymerase II lar 70.5 4.4 9.6E-05 41.2 3.3 49 188-283 626-674 (1121)
107 COG5151 SSL1 RNA polymerase II 70.5 5.9 0.00013 34.2 3.6 26 271-296 387-412 (421)
108 PF12907 zf-met2: Zinc-binding 70.4 1.2 2.6E-05 25.6 -0.3 26 3-28 2-30 (40)
109 smart00531 TFIIE Transcription 70.0 4.5 9.8E-05 31.5 2.8 14 299-312 98-111 (147)
110 PF09723 Zn-ribbon_8: Zinc rib 69.7 1.4 3.1E-05 25.8 -0.1 29 3-39 6-34 (42)
111 COG1997 RPL43A Ribosomal prote 69.5 2.7 5.8E-05 28.7 1.2 14 298-311 51-64 (89)
112 smart00834 CxxC_CXXC_SSSS Puta 69.0 2 4.3E-05 24.8 0.4 30 3-40 6-35 (41)
113 PF06524 NOA36: NOA36 protein; 68.6 3 6.4E-05 35.0 1.5 20 326-345 207-226 (314)
114 PF04959 ARS2: Arsenite-resist 67.5 1.4 3E-05 36.4 -0.6 31 28-58 74-104 (214)
115 PRK14890 putative Zn-ribbon RN 67.3 6.1 0.00013 24.9 2.3 8 217-224 26-33 (59)
116 PF04959 ARS2: Arsenite-resist 66.9 2.5 5.5E-05 34.9 0.8 28 299-326 76-103 (214)
117 PRK06266 transcription initiat 66.6 5.8 0.00013 32.0 2.8 15 189-203 118-132 (178)
118 COG1198 PriA Primosomal protei 66.6 4.4 9.6E-05 40.3 2.5 11 271-281 474-484 (730)
119 PF14353 CpXC: CpXC protein 66.3 2.3 5.1E-05 32.1 0.5 50 3-53 2-60 (128)
120 COG1592 Rubrerythrin [Energy p 65.7 3.8 8.3E-05 32.3 1.5 23 300-335 134-156 (166)
121 TIGR02300 FYDLN_acid conserved 65.4 4.9 0.00011 29.8 1.9 31 188-229 9-39 (129)
122 smart00734 ZnF_Rad18 Rad18-lik 64.7 7.2 0.00016 20.0 2.0 19 302-321 3-21 (26)
123 PRK04023 DNA polymerase II lar 63.8 7.2 0.00016 39.8 3.3 10 328-337 663-672 (1121)
124 COG1198 PriA Primosomal protei 63.7 4.6 0.0001 40.2 2.0 25 297-336 459-483 (730)
125 COG5188 PRP9 Splicing factor 3 63.3 5.4 0.00012 35.1 2.1 28 294-321 368-396 (470)
126 COG1592 Rubrerythrin [Energy p 63.3 4.4 9.5E-05 32.0 1.5 23 188-223 134-156 (166)
127 smart00614 ZnF_BED BED zinc fi 63.1 4.7 0.0001 24.6 1.3 11 342-352 37-47 (50)
128 PF06524 NOA36: NOA36 protein; 62.8 2.3 5E-05 35.6 -0.2 26 298-323 207-232 (314)
129 PRK14714 DNA polymerase II lar 59.6 10 0.00022 39.9 3.6 53 188-282 667-719 (1337)
130 PF02176 zf-TRAF: TRAF-type zi 59.6 6.9 0.00015 24.8 1.7 37 217-254 10-52 (60)
131 PF00301 Rubredoxin: Rubredoxi 59.3 5.1 0.00011 24.1 0.9 39 2-40 1-43 (47)
132 COG5151 SSL1 RNA polymerase II 57.2 13 0.00028 32.2 3.3 24 300-323 388-411 (421)
133 PF15269 zf-C2H2_7: Zinc-finge 56.2 9.6 0.00021 22.2 1.6 22 245-266 21-42 (54)
134 COG4888 Uncharacterized Zn rib 55.8 3.9 8.4E-05 28.8 0.0 37 1-42 21-57 (104)
135 COG5188 PRP9 Splicing factor 3 55.2 17 0.00037 32.1 3.8 39 265-303 367-406 (470)
136 PF13240 zinc_ribbon_2: zinc-r 54.6 5.7 0.00012 19.7 0.5 7 191-197 16-22 (23)
137 cd00730 rubredoxin Rubredoxin; 52.8 2.7 5.8E-05 25.7 -1.0 13 150-162 2-14 (50)
138 KOG2593|consensus 52.7 17 0.00037 33.3 3.5 14 215-228 127-140 (436)
139 TIGR00595 priA primosomal prot 51.8 9.9 0.00021 36.5 2.1 15 267-281 235-249 (505)
140 KOG4124|consensus 51.1 8 0.00017 34.0 1.2 52 1-52 348-419 (442)
141 PF08274 PhnA_Zn_Ribbon: PhnA 50.0 6.2 0.00013 21.1 0.2 10 327-336 18-27 (30)
142 KOG2593|consensus 49.7 21 0.00046 32.7 3.6 36 271-309 127-162 (436)
143 KOG3408|consensus 49.4 9.9 0.00021 27.9 1.2 26 297-322 54-79 (129)
144 KOG4167|consensus 49.1 5.2 0.00011 38.9 -0.3 26 187-212 791-816 (907)
145 PTZ00255 60S ribosomal protein 49.0 6.9 0.00015 27.2 0.4 13 299-311 53-65 (90)
146 PF12760 Zn_Tnp_IS1595: Transp 48.8 15 0.00033 21.8 1.9 8 300-307 37-44 (46)
147 KOG1280|consensus 48.4 8.9 0.00019 33.8 1.1 37 2-38 79-116 (381)
148 PRK14714 DNA polymerase II lar 48.3 21 0.00046 37.6 3.8 11 300-310 692-702 (1337)
149 KOG2071|consensus 48.3 14 0.0003 35.3 2.4 24 29-52 416-439 (579)
150 PRK03824 hypA hydrogenase nick 46.4 7.7 0.00017 29.6 0.4 11 217-227 71-81 (135)
151 PF13453 zf-TFIIB: Transcripti 45.6 9 0.0002 22.1 0.5 19 271-289 18-36 (41)
152 COG3357 Predicted transcriptio 45.5 15 0.00032 25.4 1.5 13 31-43 58-70 (97)
153 TIGR00280 L37a ribosomal prote 45.3 7 0.00015 27.2 0.0 13 299-311 52-64 (91)
154 COG3364 Zn-ribbon containing p 45.0 14 0.00029 26.2 1.3 15 188-202 2-16 (112)
155 KOG1280|consensus 44.7 21 0.00046 31.6 2.7 22 149-170 79-100 (381)
156 PF07975 C1_4: TFIIH C1-like d 44.7 4.4 9.5E-05 24.8 -0.9 16 189-204 22-37 (51)
157 KOG3408|consensus 44.3 12 0.00025 27.5 1.0 35 144-178 52-86 (129)
158 COG4530 Uncharacterized protei 44.0 14 0.00031 26.4 1.4 27 4-42 11-37 (129)
159 PF04780 DUF629: Protein of un 43.7 12 0.00025 35.1 1.1 30 327-356 56-85 (466)
160 PF05443 ROS_MUCR: ROS/MUCR tr 43.2 12 0.00026 28.3 1.0 25 301-328 73-97 (132)
161 PF13248 zf-ribbon_3: zinc-rib 42.8 13 0.00029 18.9 0.8 9 150-158 3-11 (26)
162 PF15135 UPF0515: Uncharacteri 42.5 16 0.00035 30.6 1.7 58 187-257 111-168 (278)
163 PF01780 Ribosomal_L37ae: Ribo 42.4 5.9 0.00013 27.5 -0.7 13 299-311 52-64 (90)
164 PF07754 DUF1610: Domain of un 42.2 12 0.00026 18.8 0.5 8 272-279 16-23 (24)
165 PRK14873 primosome assembly pr 41.6 13 0.00028 37.0 1.2 8 301-308 423-430 (665)
166 PF08790 zf-LYAR: LYAR-type C2 41.2 7.3 0.00016 20.4 -0.3 17 33-50 2-18 (28)
167 KOG2636|consensus 40.8 37 0.00079 31.3 3.7 42 189-236 250-291 (497)
168 PF07503 zf-HYPF: HypF finger; 40.5 7.1 0.00015 21.8 -0.4 32 4-42 1-32 (35)
169 KOG4377|consensus 39.5 21 0.00045 32.4 2.0 26 329-354 402-429 (480)
170 PF14446 Prok-RING_1: Prokaryo 39.0 18 0.00038 22.5 1.0 27 3-42 6-32 (54)
171 KOG4377|consensus 38.4 12 0.00025 33.9 0.3 22 304-325 407-428 (480)
172 PRK03976 rpl37ae 50S ribosomal 38.1 10 0.00022 26.4 -0.1 13 299-311 53-65 (90)
173 PF05495 zf-CHY: CHY zinc fing 37.7 5.8 0.00013 26.4 -1.3 14 216-229 41-54 (71)
174 TIGR00244 transcriptional regu 37.5 6.6 0.00014 30.1 -1.2 18 299-316 27-44 (147)
175 PF03811 Zn_Tnp_IS1: InsA N-te 37.4 5.7 0.00012 22.3 -1.1 11 296-306 25-35 (36)
176 COG1773 Rubredoxin [Energy pro 37.3 12 0.00027 23.2 0.2 13 2-14 3-15 (55)
177 KOG1842|consensus 36.6 31 0.00067 31.7 2.6 28 328-355 15-42 (505)
178 PF13451 zf-trcl: Probable zin 35.9 20 0.00044 21.7 1.0 14 299-312 3-16 (49)
179 KOG0782|consensus 35.9 14 0.00031 34.9 0.4 50 287-342 240-290 (1004)
180 COG4957 Predicted transcriptio 35.8 20 0.00043 26.9 1.1 26 329-357 77-102 (148)
181 COG1327 Predicted transcriptio 35.4 9.3 0.0002 29.4 -0.7 15 300-314 28-42 (156)
182 PRK12380 hydrogenase nickel in 34.8 22 0.00047 26.2 1.2 13 188-200 70-82 (113)
183 PRK05580 primosome assembly pr 34.8 27 0.00059 35.0 2.2 11 299-309 420-430 (679)
184 COG0068 HypF Hydrogenase matur 33.9 3.6 7.8E-05 40.1 -3.8 56 190-252 125-181 (750)
185 PF05290 Baculo_IE-1: Baculovi 33.8 33 0.00072 25.8 2.0 13 243-255 79-91 (140)
186 TIGR00595 priA primosomal prot 33.1 15 0.00032 35.3 0.1 28 239-281 235-262 (505)
187 PF15135 UPF0515: Uncharacteri 32.9 39 0.00084 28.5 2.4 75 200-287 91-170 (278)
188 KOG1044|consensus 32.7 11 0.00023 35.9 -0.9 35 301-342 193-232 (670)
189 PF08271 TF_Zn_Ribbon: TFIIB z 32.7 16 0.00035 21.3 0.2 6 302-307 21-26 (43)
190 TIGR01206 lysW lysine biosynth 32.6 28 0.00062 21.7 1.3 10 189-198 23-32 (54)
191 COG1655 Uncharacterized protei 32.5 19 0.00042 29.8 0.7 18 1-18 18-35 (267)
192 KOG4317|consensus 32.3 23 0.00049 30.9 1.0 20 32-51 20-39 (383)
193 KOG2272|consensus 31.9 25 0.00054 29.5 1.2 68 188-257 99-176 (332)
194 PF07649 C1_3: C1-like domain; 31.2 23 0.00051 18.7 0.6 11 188-198 15-25 (30)
195 KOG1842|consensus 31.0 15 0.00032 33.7 -0.2 30 30-59 14-43 (505)
196 PF13821 DUF4187: Domain of un 30.7 15 0.00033 23.0 -0.2 29 17-50 18-46 (55)
197 PF11789 zf-Nse: Zinc-finger o 30.7 32 0.00069 21.7 1.3 30 272-305 24-53 (57)
198 COG3091 SprT Zn-dependent meta 30.5 21 0.00047 27.5 0.6 10 272-282 117-126 (156)
199 PF01363 FYVE: FYVE zinc finge 30.3 18 0.00038 23.7 0.1 9 303-311 12-20 (69)
200 PF07282 OrfB_Zn_ribbon: Putat 30.2 39 0.00084 22.1 1.7 13 215-227 45-57 (69)
201 PF05129 Elf1: Transcription e 30.1 15 0.00032 25.2 -0.3 38 2-44 22-59 (81)
202 COG1571 Predicted DNA-binding 29.8 31 0.00067 31.8 1.6 29 274-313 352-380 (421)
203 COG1779 C4-type Zn-finger prot 29.7 28 0.00062 28.2 1.1 40 3-48 15-60 (201)
204 PF13824 zf-Mss51: Zinc-finger 29.5 39 0.00084 21.1 1.4 11 328-338 14-24 (55)
205 COG1571 Predicted DNA-binding 29.3 34 0.00073 31.6 1.7 30 302-342 352-381 (421)
206 PF12773 DZR: Double zinc ribb 29.0 37 0.0008 20.4 1.4 9 191-199 15-23 (50)
207 PF11931 DUF3449: Domain of un 29.0 18 0.0004 29.4 0.0 29 148-176 100-129 (196)
208 smart00154 ZnF_AN1 AN1-like Zi 28.6 28 0.0006 19.9 0.7 14 2-15 12-25 (39)
209 PF01155 HypA: Hydrogenase exp 28.5 24 0.00053 25.9 0.6 14 188-201 70-83 (113)
210 KOG0978|consensus 28.4 24 0.00052 34.9 0.6 14 273-286 644-657 (698)
211 PF13878 zf-C2H2_3: zinc-finge 28.3 68 0.0015 18.6 2.3 22 246-267 15-38 (41)
212 KOG4167|consensus 28.2 14 0.0003 36.2 -0.9 25 272-296 792-816 (907)
213 PF03107 C1_2: C1 domain; Int 28.0 30 0.00064 18.4 0.7 9 189-197 16-24 (30)
214 TIGR00100 hypA hydrogenase nic 27.7 34 0.00074 25.3 1.2 13 188-200 70-82 (115)
215 COG2331 Uncharacterized protei 27.6 23 0.0005 23.6 0.3 53 300-367 12-65 (82)
216 PRK00432 30S ribosomal protein 27.6 33 0.00072 20.9 0.9 12 30-41 36-47 (50)
217 PRK14559 putative protein seri 27.5 37 0.0008 33.7 1.7 12 246-257 43-54 (645)
218 PF10013 DUF2256: Uncharacteri 26.8 32 0.0007 20.0 0.7 14 330-343 10-23 (42)
219 COG1656 Uncharacterized conser 26.6 53 0.0012 25.9 2.1 16 272-287 130-145 (165)
220 KOG4118|consensus 26.6 25 0.00054 22.5 0.3 28 32-59 39-66 (74)
221 COG4896 Uncharacterized protei 26.5 36 0.00079 21.5 1.0 12 213-224 28-39 (68)
222 PRK00564 hypA hydrogenase nick 26.5 39 0.00085 25.1 1.4 13 188-200 71-83 (117)
223 PF04780 DUF629: Protein of un 26.4 49 0.0011 31.2 2.2 27 271-297 56-82 (466)
224 PRK10220 hypothetical protein; 26.3 39 0.00084 24.4 1.2 29 190-229 5-33 (111)
225 PF14311 DUF4379: Domain of un 25.7 58 0.0013 20.2 1.8 11 273-283 29-39 (55)
226 cd00065 FYVE FYVE domain; Zinc 25.5 37 0.0008 21.0 0.9 9 303-311 5-13 (57)
227 TIGR00686 phnA alkylphosphonat 25.4 35 0.00075 24.6 0.8 28 191-229 5-32 (109)
228 PRK03681 hypA hydrogenase nick 25.4 28 0.0006 25.7 0.4 13 148-160 69-81 (114)
229 PRK03564 formate dehydrogenase 25.2 24 0.00053 31.2 0.1 36 189-227 188-223 (309)
230 smart00661 RPOL9 RNA polymeras 24.9 42 0.00091 20.3 1.1 13 328-340 20-32 (52)
231 PF04810 zf-Sec23_Sec24: Sec23 24.2 38 0.00081 19.5 0.7 33 2-41 2-34 (40)
232 PF05741 zf-nanos: Nanos RNA b 24.0 28 0.0006 21.8 0.1 40 5-44 1-46 (55)
233 smart00440 ZnF_C2C2 C2C2 Zinc 23.8 6.4 0.00014 22.7 -2.6 7 301-307 29-35 (40)
234 PF06220 zf-U1: U1 zinc finger 23.7 32 0.00069 19.6 0.3 11 2-12 3-13 (38)
235 KOG0717|consensus 23.6 45 0.00097 31.0 1.4 26 150-175 293-318 (508)
236 TIGR03826 YvyF flagellar opero 23.4 58 0.0013 24.9 1.8 11 190-200 5-15 (137)
237 PRK14873 primosome assembly pr 23.1 24 0.00052 35.2 -0.4 26 240-281 406-431 (665)
238 COG0068 HypF Hydrogenase matur 23.0 11 0.00024 36.9 -2.6 30 274-309 153-182 (750)
239 PF01927 Mut7-C: Mut7-C RNAse 22.4 39 0.00085 26.2 0.7 16 272-287 124-139 (147)
240 smart00064 FYVE Protein presen 22.0 47 0.001 21.5 1.0 10 274-283 12-21 (68)
241 KOG3214|consensus 21.9 34 0.00074 24.1 0.3 38 2-44 23-60 (109)
242 PF09332 Mcm10: Mcm10 replicat 21.7 22 0.00048 31.9 -0.9 43 3-45 253-299 (344)
243 COG5112 UFD2 U1-like Zn-finger 21.6 37 0.00081 24.2 0.4 24 298-321 53-76 (126)
244 PRK14892 putative transcriptio 21.4 42 0.00091 24.0 0.6 12 32-43 43-54 (99)
245 TIGR00340 zpr1_rel ZPR1-relate 21.1 29 0.00062 27.5 -0.3 19 30-48 27-45 (163)
246 PF14369 zf-RING_3: zinc-finge 20.9 54 0.0012 18.2 0.9 8 247-254 24-31 (35)
247 PF15288 zf-CCHC_6: Zinc knuck 20.8 89 0.0019 18.1 1.7 37 330-374 3-39 (40)
248 COG1675 TFA1 Transcription ini 20.5 1.2E+02 0.0025 24.5 3.0 18 296-313 109-126 (176)
249 KOG2907|consensus 20.5 41 0.00089 24.4 0.4 9 273-281 75-83 (116)
250 TIGR00515 accD acetyl-CoA carb 20.4 48 0.001 29.1 0.9 32 150-201 27-58 (285)
251 PF01428 zf-AN1: AN1-like Zinc 20.3 32 0.0007 20.1 -0.1 16 327-342 12-27 (43)
252 PRK12496 hypothetical protein; 20.1 66 0.0014 25.6 1.6 27 189-227 128-154 (164)
No 1
>KOG1074|consensus
Probab=99.97 E-value=6e-31 Score=240.85 Aligned_cols=173 Identities=30% Similarity=0.608 Sum_probs=151.4
Q ss_pred cccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCC----CCeecC---ccccccCChHHH
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGI----HPFTCH---FCNKSFTQKIGL 260 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~----~~~~C~---~C~~~~~~~~~l 260 (392)
+-.|-+|.++..-+..|+.|.+.|++++||+|++|++.|.++-+|+.||..|... .++.|+ +|-+.|.+...|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 5689999999999999999999999999999999999999999999999998765 457899 999999999999
Q ss_pred HHHHHHhcCC-------------CCccCCCCcCcccCHHHHHHHHHHhcCC-----------------------------
Q psy6751 261 VKHLNIHNGT-------------KKYQCHLCGKGFIHHTSYKFHQLVHSGE----------------------------- 298 (392)
Q Consensus 261 ~~H~~~h~~~-------------~~~~C~~C~~~f~~~~~l~~H~~~~~~~----------------------------- 298 (392)
..|++.|.+. ..-+|..|.+.|.....+..++..+-+.
T Consensus 685 pQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~~ 764 (958)
T KOG1074|consen 685 PQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSCG 764 (958)
T ss_pred cceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCccccccc
Confidence 9999998732 1357899999998887787777655111
Q ss_pred --------------------------------------------------------------------------------
Q psy6751 299 -------------------------------------------------------------------------------- 298 (392)
Q Consensus 299 -------------------------------------------------------------------------------- 298 (392)
T Consensus 765 ~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~ 844 (958)
T KOG1074|consen 765 RELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLATK 844 (958)
T ss_pred cccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhcccccccccccccc
Confidence
Q ss_pred ---------------------------------CccccccCcccCCChHHHHHHHHHhcCCCccccCccchhccCchHHH
Q psy6751 299 ---------------------------------RNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNAQ 345 (392)
Q Consensus 299 ---------------------------------~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 345 (392)
....|.+|++.|.+.++|..|+++|++.+||.|.+|++.|..+..|+
T Consensus 845 ~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLK 924 (958)
T KOG1074|consen 845 TNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLK 924 (958)
T ss_pred cccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhh
Confidence 00569999999999999999999999999999999999999999999
Q ss_pred hhhhhccCCCCCCCc
Q psy6751 346 VHKKKVHGLDVPGTT 360 (392)
Q Consensus 346 ~H~~~~H~~~~~~~~ 360 (392)
.||.+|+....+.-+
T Consensus 925 vHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 925 VHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhccccccCCCccC
Confidence 999999887765544
No 2
>KOG2462|consensus
Probab=99.95 E-value=3.6e-29 Score=202.54 Aligned_cols=134 Identities=31% Similarity=0.642 Sum_probs=114.2
Q ss_pred CcccccccccccCHHHHHHHHhhhcC---CCCeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCcccCHHHHHHHH
Q psy6751 216 PFVCEICGQGYKMKKALLVHVGMHSG---IHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQ 292 (392)
Q Consensus 216 ~~~C~~C~~~~~~~~~l~~H~~~h~~---~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 292 (392)
.|+|+.|++.+.+..+|..|.+.|.. .+.+.|++||+.+.+...|+.|+++|. -+..|..||+.|.+...|+-|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 36666677777777677777666643 456788888888888888888998886 5689999999999999999999
Q ss_pred HHhcCCCccccccCcccCCChHHHHHHHHHhcCCCccccCccchhccCchHHHhhhhhc
Q psy6751 293 LVHSGERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNAQVHKKKV 351 (392)
Q Consensus 293 ~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 351 (392)
|+|+|+|||.|+.|++.|...++|+.||++|.+.++|+|..|++.|+.++.|.+|....
T Consensus 208 RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 208 RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred ccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 99999999999999999999999999999999999999999999999999999997653
No 3
>KOG2462|consensus
Probab=99.93 E-value=3.6e-27 Score=190.99 Aligned_cols=133 Identities=35% Similarity=0.713 Sum_probs=108.3
Q ss_pred cccccccccccCCHHHHHHHHhhcC---CCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHH
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHS---DLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHL 264 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~---~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~ 264 (392)
.|.|+.|++.+.+..+|.+|.+.|- ..+.+.|++|++.|.+--.|..|+++|. -+..|.+||+.|...+.|+-|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 5788888888888888888887774 3456788888888888888888888877 5677888888888888888888
Q ss_pred HHhcCCCCccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHHHHH
Q psy6751 265 NIHNGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLV 322 (392)
Q Consensus 265 ~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~ 322 (392)
|+|+|||||.|+.|+++|.+++.|+.||.+|.+.|+|+|..|++.|...+.|.+|...
T Consensus 208 RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 208 RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 8888888888888888888888888888888888888888888888888888888643
No 4
>KOG3608|consensus
Probab=99.92 E-value=3.3e-25 Score=184.13 Aligned_cols=199 Identities=24% Similarity=0.528 Sum_probs=175.1
Q ss_pred ccc--ccccccccChhhHHHHHHHhhccccccccccCCCCcccccccccccCCHHHHHHHHhhcC--CCCCccccccccc
Q psy6751 150 WKC--FICDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGKKWRTVSELNAHIQTHS--DLRPFVCEICGQG 225 (392)
Q Consensus 150 ~~C--~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~--~~~~~~C~~C~~~ 225 (392)
+.| ..|.+.+.+...|++|.+..+... ...|+.|+..|.+...|..|++..+ ...+|.|..|.+.
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs~eK-----------vvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~Kr 246 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHSNEK-----------VVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKR 246 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcCCCe-----------EEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHH
Confidence 445 469999999999999955443332 5789999999999999999998764 4468999999999
Q ss_pred ccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHH-hcCCCCccCCCCcCcccCHHHHHHHHHHhcCCCccccc
Q psy6751 226 YKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNI-HNGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCD 304 (392)
Q Consensus 226 ~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~ 304 (392)
|.++..|..|+..|-.. |+|+.|+.+....+.|.+|++. |...+||+|..|++.|.+.++|.+|...|. +-.|+|.
T Consensus 247 FaTeklL~~Hv~rHvn~--ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~ 323 (467)
T KOG3608|consen 247 FATEKLLKSHVVRHVNC--YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCE 323 (467)
T ss_pred HhHHHHHHHHHHHhhhc--ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecC
Confidence 99999999999999754 8999999999999999999997 778899999999999999999999999887 6779998
Q ss_pred c--CcccCCChHHHHHHHHHhc-CC--CccccCccchhccCchHHHhhhhhccCCCCCCCccc
Q psy6751 305 I--CGLALTTKSHLNRHMLVHT-GD--RPHECSVCGKRFAKKWNAQVHKKKVHGLDVPGTTHR 362 (392)
Q Consensus 305 ~--C~~~~~~~~~l~~H~~~h~-~~--~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~~ 362 (392)
. |.+++.+...|++|++.++ |. .+|.|..|++.|++...|-.|+...|+-.+|.--++
T Consensus 324 h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~R 386 (467)
T KOG3608|consen 324 HPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGHKR 386 (467)
T ss_pred CCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCCCc
Confidence 8 9999999999999998766 44 459999999999999999999999999876654443
No 5
>KOG3608|consensus
Probab=99.91 E-value=4.1e-24 Score=177.68 Aligned_cols=235 Identities=21% Similarity=0.359 Sum_probs=185.6
Q ss_pred Cccc--ccccccccChhhHHHHHHHhhccccc---cccccCCC-Ccccc--cccccccCCHHHHHHHHhhcCCCCCcccc
Q psy6751 149 GWKC--FICDAQLTTETSYSVFYTMLSQSGVL---LSERACMP-LIHEC--PTCGKKWRTVSELNAHIQTHSDLRPFVCE 220 (392)
Q Consensus 149 ~~~C--~~C~~~f~~~~~l~~H~~~~~~~~~~---~~~~~~~~-~~~~C--~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 220 (392)
.|.| ..|+..|.+...|..| ...|..-. ....+... ..+.| ..|-..+.++..|++|++.|.+++...|+
T Consensus 134 ~f~C~WedCe~~F~s~~ef~dH--V~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp 211 (467)
T KOG3608|consen 134 NFRCGWEDCEREFVSIVEFQDH--VVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACP 211 (467)
T ss_pred hhccChhhcCCcccCHHHHHHH--HHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecc
Confidence 3667 4799999999999999 44443221 01111111 24667 56999999999999999999999999999
Q ss_pred cccccccCHHHHHHHHhhh--cCCCCeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCcccCHHHHHHHHHH-hcC
Q psy6751 221 ICGQGYKMKKALLVHVGMH--SGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQLV-HSG 297 (392)
Q Consensus 221 ~C~~~~~~~~~l~~H~~~h--~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~-~~~ 297 (392)
.|+..|.+..-|..|.++- ....+|.|..|.+.|.+...|..|++.|-.. |+|++|+-+....++|..||+. |..
T Consensus 212 ~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~--ykCplCdmtc~~~ssL~~H~r~rHs~ 289 (467)
T KOG3608|consen 212 HCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNC--YKCPLCDMTCSSASSLTTHIRYRHSK 289 (467)
T ss_pred hHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhc--ccccccccCCCChHHHHHHHHhhhcc
Confidence 9999999999999999764 4567899999999999999999999988554 9999999999999999999986 567
Q ss_pred CCccccccCcccCCChHHHHHHHHHhcCCCccccCc--cchhccCchHHHhhhhhccCC-CCCCCcccccccCCCCCCCc
Q psy6751 298 ERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSV--CGKRFAKKWNAQVHKKKVHGL-DVPGTTHRVMPVPPIGGGEK 374 (392)
Q Consensus 298 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~~H~~-~~~~~~~~~~~~~~~~~~~~ 374 (392)
++||+|..|++.|.+.+.|.+|+..|. +..|+|.. |.++|.+..+++.|++.+|.. .++....-+=..-. ..-
T Consensus 290 dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~f---t~G 365 (467)
T KOG3608|consen 290 DKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFF---TSG 365 (467)
T ss_pred CCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhh---ccc
Confidence 899999999999999999999999988 66799988 999999999999999999954 33333321111000 011
Q ss_pred hhHHHHHHHHHhhcCCC
Q psy6751 375 EEDVAVMIKQRLMQKPY 391 (392)
Q Consensus 375 ~~~~~~~~~~~~~~~~~ 391 (392)
..-++-+.+|+-.++||
T Consensus 366 ~~L~~HL~kkH~f~~Ps 382 (467)
T KOG3608|consen 366 KSLSAHLMKKHGFRLPS 382 (467)
T ss_pred hhHHHHHHHhhcccCCC
Confidence 22344566666667776
No 6
>KOG3623|consensus
Probab=99.91 E-value=8.6e-25 Score=197.48 Aligned_cols=109 Identities=29% Similarity=0.558 Sum_probs=96.2
Q ss_pred cCcccccccccccChhhHHHHHHHhhccccccccccCCCCcccccccccccCCHHHHHHHHhhcCC-------------C
Q psy6751 148 LGWKCFICDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGKKWRTVSELNAHIQTHSD-------------L 214 (392)
Q Consensus 148 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-------------~ 214 (392)
....|..|++.+.....|+.|.+..+... +. .|.|..|.+.|..+..|.+||..|.. .
T Consensus 209 qlltcpycdrgykrltslkeHikyrhekn----e~-----nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~l 279 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRHEKN----EP-----NFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALL 279 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHHhhC----CC-----CCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhh
Confidence 34799999999999999999987665552 22 58999999999999999999998843 2
Q ss_pred CCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHH
Q psy6751 215 RPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLN 265 (392)
Q Consensus 215 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~ 265 (392)
+.|+|..|++.|..+.+|+.|+++|.|++||.|+-|++.|+....+..||.
T Consensus 280 RKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 280 RKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 569999999999999999999999999999999999999999988888885
No 7
>KOG1074|consensus
Probab=99.87 E-value=5.6e-23 Score=189.02 Aligned_cols=172 Identities=26% Similarity=0.555 Sum_probs=146.5
Q ss_pred cCcccccccccccChhhHHHHHHHhhccccccccccCCCCcccccccccccCCHHHHHHHHhhcCCC----CCcccc---
Q psy6751 148 LGWKCFICDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGKKWRTVSELNAHIQTHSDL----RPFVCE--- 220 (392)
Q Consensus 148 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~----~~~~C~--- 220 (392)
-+..|-+|.+.+.-...|+.|++ +|. +++ +|+|.+|++.|.++.+|+.||..|... -.+.|+
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyr--tHt----GER-----PFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYR--THT----GER-----PFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred Cccceeeeeecccchhhhhhhhh--ccc----CcC-----ccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 35789999999999999999954 343 555 899999999999999999999998654 347899
Q ss_pred cccccccCHHHHHHHHhhhcCCC-------------CeecCccccccCChHHHHHHHHHhcCCC----------------
Q psy6751 221 ICGQGYKMKKALLVHVGMHSGIH-------------PFTCHFCNKSFTQKIGLVKHLNIHNGTK---------------- 271 (392)
Q Consensus 221 ~C~~~~~~~~~l~~H~~~h~~~~-------------~~~C~~C~~~~~~~~~l~~H~~~h~~~~---------------- 271 (392)
+|.+.|.+.-.|..|++.|.+.. .-+|..|.+.|.+...+..++.+|....
T Consensus 673 ic~~kftn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~ 752 (958)
T KOG1074|consen 673 ICQKKFTNAVTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEEL 752 (958)
T ss_pred hhcccccccccccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCccccccccccccc
Confidence 99999999999999999987321 1468889999988888888877661100
Q ss_pred --------------------------------------------------------------------------------
Q psy6751 272 -------------------------------------------------------------------------------- 271 (392)
Q Consensus 272 -------------------------------------------------------------------------------- 271 (392)
T Consensus 753 ~~tp~~~e~~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~ 832 (958)
T KOG1074|consen 753 DVTPPPPENSCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQ 832 (958)
T ss_pred ccCCCccccccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhcc
Confidence
Q ss_pred ----------------------------------------------CccCCCCcCcccCHHHHHHHHHHhcCCCcccccc
Q psy6751 272 ----------------------------------------------KYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDI 305 (392)
Q Consensus 272 ----------------------------------------------~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~ 305 (392)
...|..||+.|.+.+.|..|+++|+++|||.|.+
T Consensus 833 ~~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~f 912 (958)
T KOG1074|consen 833 ETSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHF 912 (958)
T ss_pred cccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchh
Confidence 2679999999999999999999999999999999
Q ss_pred CcccCCChHHHHHHHHHhcCCCccc
Q psy6751 306 CGLALTTKSHLNRHMLVHTGDRPHE 330 (392)
Q Consensus 306 C~~~~~~~~~l~~H~~~h~~~~~~~ 330 (392)
|++.|..+..|+.||..|++..++.
T Consensus 913 C~~aFttrgnLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 913 CEEAFTTRGNLKVHMGTHMWVQPPS 937 (958)
T ss_pred hhhhhhhhhhhhhhhccccccCCCc
Confidence 9999999999999999999987654
No 8
>KOG3623|consensus
Probab=99.80 E-value=1.8e-19 Score=163.45 Aligned_cols=78 Identities=32% Similarity=0.709 Sum_probs=74.7
Q ss_pred CeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHHHH
Q psy6751 244 PFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHML 321 (392)
Q Consensus 244 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 321 (392)
+|.|..|++.|.-.+.|.+|.-.|.|.+||+|.+|.++|..+--|..|+|.|.|+|||+|..|++.|+-......||.
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 599999999999999999999999999999999999999999999999999999999999999999998888888874
No 9
>KOG3576|consensus
Probab=99.72 E-value=2e-18 Score=132.95 Aligned_cols=84 Identities=36% Similarity=0.776 Sum_probs=63.1
Q ss_pred CCcccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHH
Q psy6751 186 PLIHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLN 265 (392)
Q Consensus 186 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~ 265 (392)
...|.|.+|++.|..+..|.+||+.|...+.+.|..||+.|...-.|++|++.|+|.+||+|..|++.|.....|..|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 33578888888888888888888887777777777777777777777777777777777777777777777777777776
Q ss_pred HhcC
Q psy6751 266 IHNG 269 (392)
Q Consensus 266 ~h~~ 269 (392)
..++
T Consensus 195 kvhg 198 (267)
T KOG3576|consen 195 KVHG 198 (267)
T ss_pred HHcC
Confidence 5544
No 10
>KOG3576|consensus
Probab=99.72 E-value=1.8e-18 Score=133.19 Aligned_cols=114 Identities=28% Similarity=0.622 Sum_probs=93.5
Q ss_pred CCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCcccCHHHHHHHH
Q psy6751 213 DLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQ 292 (392)
Q Consensus 213 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 292 (392)
+...|.|.+|++.|.....|.+|++-|...+.+-|..||+.|.+.-+|++|+++|++.+||+|..|+++|..+-+|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 44568999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHhcCC-----------CccccccCcccCCChHHHHHHHHHhcCC
Q psy6751 293 LVHSGE-----------RNVKCDICGLALTTKSHLNRHMLVHTGD 326 (392)
Q Consensus 293 ~~~~~~-----------~~~~C~~C~~~~~~~~~l~~H~~~h~~~ 326 (392)
+.-||. +.|.|..||+.-.....+..|+..|+..
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 877664 3455666666666666666666555543
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.38 E-value=1e-12 Score=120.95 Aligned_cols=147 Identities=23% Similarity=0.485 Sum_probs=116.5
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCccccc--ccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHH
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEI--CGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNI 266 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~ 266 (392)
-.|+.|...... ..|..|.....- ..-.|+. |+..|... .+..| +.|+.|+..|. ...|..|+..
T Consensus 408 V~C~NC~~~i~l-~~l~lHe~~C~r-~~V~Cp~~~Cg~v~~r~-el~~H---------~~C~~Cgk~f~-~s~LekH~~~ 474 (567)
T PLN03086 408 VECRNCKHYIPS-RSIALHEAYCSR-HNVVCPHDGCGIVLRVE-EAKNH---------VHCEKCGQAFQ-QGEMEKHMKV 474 (567)
T ss_pred EECCCCCCccch-hHHHHHHhhCCC-cceeCCcccccceeecc-ccccC---------ccCCCCCCccc-hHHHHHHHHh
Confidence 469999887665 455688765432 3356884 99988433 24444 58999999995 6889999999
Q ss_pred hcCCCCccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCC----------ChHHHHHHHHHhcCCCccccCccch
Q psy6751 267 HNGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALT----------TKSHLNRHMLVHTGDRPHECSVCGK 336 (392)
Q Consensus 267 h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~----------~~~~l~~H~~~h~~~~~~~C~~C~~ 336 (392)
++ +++.|+ ||..+ .+..|..|+..|-+.+++.|.+|++.+. ..+.|..|...+ |.+++.|..|++
T Consensus 475 ~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk 549 (567)
T PLN03086 475 FH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGR 549 (567)
T ss_pred cC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCC
Confidence 86 789999 99755 6789999999999999999999999985 245899998885 889999999998
Q ss_pred hccCchHHHhhhhhccCC
Q psy6751 337 RFAKKWNAQVHKKKVHGL 354 (392)
Q Consensus 337 ~f~~~~~l~~H~~~~H~~ 354 (392)
.+. ...|..|+-..|..
T Consensus 550 ~Vr-lrdm~~H~~~~h~~ 566 (567)
T PLN03086 550 SVM-LKEMDIHQIAVHQK 566 (567)
T ss_pred eee-ehhHHHHHHHhhcC
Confidence 866 55788899998874
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.37 E-value=1.7e-12 Score=119.43 Aligned_cols=146 Identities=24% Similarity=0.521 Sum_probs=114.1
Q ss_pred CcccccccccccChhhHHHHHHHhhccccccccccCCCCcccccc--cccccCCHHHHHHHHhhcCCCCCcccccccccc
Q psy6751 149 GWKCFICDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPT--CGKKWRTVSELNAHIQTHSDLRPFVCEICGQGY 226 (392)
Q Consensus 149 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~ 226 (392)
...|..|...... ..|..|....... .-.|+. |+..|. ...|..| +.|+.|++.|
T Consensus 407 ~V~C~NC~~~i~l-~~l~lHe~~C~r~------------~V~Cp~~~Cg~v~~-r~el~~H---------~~C~~Cgk~f 463 (567)
T PLN03086 407 TVECRNCKHYIPS-RSIALHEAYCSRH------------NVVCPHDGCGIVLR-VEEAKNH---------VHCEKCGQAF 463 (567)
T ss_pred eEECCCCCCccch-hHHHHHHhhCCCc------------ceeCCcccccceee-ccccccC---------ccCCCCCCcc
Confidence 4589999987765 3444664433222 356885 999994 3444555 5899999999
Q ss_pred cCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCccc----------CHHHHHHHHHHhc
Q psy6751 227 KMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFI----------HHTSYKFHQLVHS 296 (392)
Q Consensus 227 ~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~l~~H~~~~~ 296 (392)
. ...|..|+..++ .++.|+ |+..+ ....|..|+..|.+.+++.|++|+..|. ....|..|....
T Consensus 464 ~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C- 537 (567)
T PLN03086 464 Q-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC- 537 (567)
T ss_pred c-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-
Confidence 6 577999999986 789999 99765 6799999999999999999999999985 245799998885
Q ss_pred CCCccccccCcccCCChHHHHHHHHHhc
Q psy6751 297 GERNVKCDICGLALTTKSHLNRHMLVHT 324 (392)
Q Consensus 297 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~ 324 (392)
|.+++.|..|++.+.. ..|..|+..-|
T Consensus 538 G~rt~~C~~Cgk~Vrl-rdm~~H~~~~h 564 (567)
T PLN03086 538 GSRTAPCDSCGRSVML-KEMDIHQIAVH 564 (567)
T ss_pred CCcceEccccCCeeee-hhHHHHHHHhh
Confidence 9999999999988864 45888876433
No 13
>PHA00733 hypothetical protein
Probab=99.23 E-value=7.4e-12 Score=93.95 Aligned_cols=85 Identities=19% Similarity=0.311 Sum_probs=61.8
Q ss_pred CCCccCCCCcCcccCHHHHHHH--H---HHhcCCCccccccCcccCCChHHHHHHHHHhcCCCccccCccchhccCchHH
Q psy6751 270 TKKYQCHLCGKGFIHHTSYKFH--Q---LVHSGERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNA 344 (392)
Q Consensus 270 ~~~~~C~~C~~~f~~~~~l~~H--~---~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 344 (392)
.+++.|..|...|.....|..| + ..+++.+||.|+.|++.|.+...|..|++.| ..+|.|..|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4456666666555555444443 1 1234578888888888888888888888865 3568899999999999999
Q ss_pred HhhhhhccCCCC
Q psy6751 345 QVHKKKVHGLDV 356 (392)
Q Consensus 345 ~~H~~~~H~~~~ 356 (392)
..|+.+.|+|-+
T Consensus 116 ~~H~~~~h~~~~ 127 (128)
T PHA00733 116 LDHVCKKHNICV 127 (128)
T ss_pred HHHHHHhcCccc
Confidence 999999988753
No 14
>PHA00733 hypothetical protein
Probab=99.09 E-value=1.7e-10 Score=86.61 Aligned_cols=53 Identities=25% Similarity=0.421 Sum_probs=25.7
Q ss_pred CCCccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHHHHHhc
Q psy6751 270 TKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLVHT 324 (392)
Q Consensus 270 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~ 324 (392)
.++|.|+.|++.|.+...|..|++.+ ..+|.|..|++.|.....|..|+...|
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 44455555555555555555554433 233455555555555555555554443
No 15
>KOG3993|consensus
Probab=99.09 E-value=1.3e-11 Score=106.29 Aligned_cols=167 Identities=17% Similarity=0.215 Sum_probs=101.2
Q ss_pred cccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHHh
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIH 267 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h 267 (392)
.|.|..|...|.+...|.+|.-..-..-.|+|+.|+++|....+|..|.++|....-.-=.. +.--.....-+.-.+..
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~-~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAG-SPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcC-CCChhhhhhhhhhhhhc
Confidence 38899999999999999999755444445899999999999999999998885421100000 00000000000000000
Q ss_pred ------cCCCCccCCCCcCcccCHHHHHHHHHHhcCC-------------------------------------------
Q psy6751 268 ------NGTKKYQCHLCGKGFIHHTSYKFHQLVHSGE------------------------------------------- 298 (392)
Q Consensus 268 ------~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~------------------------------------------- 298 (392)
..+.-|.|.+|++.|.+..-|++|+.+|+..
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a 425 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVA 425 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeee
Confidence 0112355555555555555555554444211
Q ss_pred ---CccccccCcccCCChHHHHHHHHHhcCCCccccCccchhccCchHHHhhhhhccCCC
Q psy6751 299 ---RNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNAQVHKKKVHGLD 355 (392)
Q Consensus 299 ---~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 355 (392)
-...|++|+..+.++..-..+.+--.....|.|.+|.-.|.....|.+|+...|...
T Consensus 426 ~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse 485 (500)
T KOG3993|consen 426 GSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSE 485 (500)
T ss_pred ccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChHH
Confidence 113377777666665554444444444556999999999999999999999999753
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.87 E-value=9.8e-10 Score=67.20 Aligned_cols=44 Identities=18% Similarity=0.320 Sum_probs=32.7
Q ss_pred ccccccCcccCCChHHHHHHHHHhcCCCccccCccchhccCchHHH
Q psy6751 300 NVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNAQ 345 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 345 (392)
.|.|+.||+.|+..+.|..|+++|+ ++|+|..|++.|...+.|.
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 3677777777777777777777777 5777777777777666554
No 17
>KOG3993|consensus
Probab=98.82 E-value=7.7e-10 Score=95.59 Aligned_cols=165 Identities=15% Similarity=0.201 Sum_probs=110.2
Q ss_pred CcccccccccccChhhHHHHHHHhhccccccccccCCCCcccccccccccCCHHHHHHHHhhcCCC--------------
Q psy6751 149 GWKCFICDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGKKWRTVSELNAHIQTHSDL-------------- 214 (392)
Q Consensus 149 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-------------- 214 (392)
.|-|.+|...|.+.-.|..| .....- -..|+|+.|+++|+-..+|..|.+.|...
T Consensus 267 dyiCqLCK~kYeD~F~LAQH--rC~RIV---------~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~ 335 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQH--RCPRIV---------HVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQA 335 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhc--cCCeeE---------EeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhh
Confidence 39999999999999999888 433321 12699999999999999999999988321
Q ss_pred -------------------CCcccccccccccCHHHHHHHHhhhcCCCC-----------------eecCccccccCChH
Q psy6751 215 -------------------RPFVCEICGQGYKMKKALLVHVGMHSGIHP-----------------FTCHFCNKSFTQKI 258 (392)
Q Consensus 215 -------------------~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~-----------------~~C~~C~~~~~~~~ 258 (392)
..|.|.+|++.|.....|+.|+..|+.... +-|..|...+....
T Consensus 336 ~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~ 415 (500)
T KOG3993|consen 336 VETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASD 415 (500)
T ss_pred hhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhccccccccccccccccccc
Confidence 237788888888888888888776653211 22333433333222
Q ss_pred HHHHHHHHhcCC-CCccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHHHHHhc
Q psy6751 259 GLVKHLNIHNGT-KKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLVHT 324 (392)
Q Consensus 259 ~l~~H~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~ 324 (392)
.-..+..++.+. ..-.|++|+..+.++..=-.+.+.-...+.|-|.+|--.|.+...|.+|+...|
T Consensus 416 ~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 416 SHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred ccccceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcC
Confidence 212222222211 134577777777666554455555556677889999999999999999886543
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.79 E-value=3e-09 Score=65.11 Aligned_cols=41 Identities=27% Similarity=0.509 Sum_probs=23.7
Q ss_pred ccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHH
Q psy6751 273 YQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSH 315 (392)
Q Consensus 273 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~ 315 (392)
|.|+.||+.|.....|..|+++|+ ++|+|..|++.|...+.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGE 46 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccce
Confidence 556666666666666666666655 45556666665554443
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.60 E-value=2.7e-08 Score=51.94 Aligned_cols=24 Identities=54% Similarity=1.168 Sum_probs=15.1
Q ss_pred HHHHHHHhcCCCccccCccchhcc
Q psy6751 316 LNRHMLVHTGDRPHECSVCGKRFA 339 (392)
Q Consensus 316 l~~H~~~h~~~~~~~C~~C~~~f~ 339 (392)
|..||+.|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 556666666666666666666654
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.49 E-value=8.7e-08 Score=49.99 Aligned_cols=24 Identities=33% Similarity=0.758 Sum_probs=13.5
Q ss_pred HHHHHHHhcCCCccccccCcccCC
Q psy6751 288 YKFHQLVHSGERNVKCDICGLALT 311 (392)
Q Consensus 288 l~~H~~~~~~~~~~~C~~C~~~~~ 311 (392)
|.+|+++|+|++||.|++|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 455555555555555555555553
No 21
>PHA00616 hypothetical protein
Probab=98.45 E-value=8.5e-08 Score=55.72 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=14.1
Q ss_pred cccccCcccCCChHHHHHHHHHhcCCCcccc
Q psy6751 301 VKCDICGLALTTKSHLNRHMLVHTGDRPHEC 331 (392)
Q Consensus 301 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C 331 (392)
|+|+.||+.|..++.|..|++.|++++++.|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 4444444444444444444444444444443
No 22
>PHA00616 hypothetical protein
Probab=98.41 E-value=1.2e-07 Score=55.14 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=27.7
Q ss_pred CccCCCCcCcccCHHHHHHHHHHhcCCCccccccC
Q psy6751 272 KYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDIC 306 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C 306 (392)
||+|+.||..|...+.|..|++.|||++++.|+.=
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 57888888888888888888888888888777653
No 23
>PHA00732 hypothetical protein
Probab=98.32 E-value=4.2e-07 Score=61.61 Aligned_cols=45 Identities=27% Similarity=0.598 Sum_probs=24.1
Q ss_pred CccCCCCcCcccCHHHHHHHHHH-hcCCCccccccCcccCCChHHHHHHHHH
Q psy6751 272 KYQCHLCGKGFIHHTSYKFHQLV-HSGERNVKCDICGLALTTKSHLNRHMLV 322 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~l~~H~~~-~~~~~~~~C~~C~~~~~~~~~l~~H~~~ 322 (392)
||.|..|++.|.+...|..|++. |. ++.|+.|++.|. .|..|+.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 35566666666666666666553 32 235666665554 34455543
No 24
>PHA00732 hypothetical protein
Probab=98.20 E-value=1.2e-06 Score=59.43 Aligned_cols=47 Identities=32% Similarity=0.544 Sum_probs=27.5
Q ss_pred ccccccCcccCCChHHHHHHHHH-hcCCCccccCccchhccCchHHHhhhhhcc
Q psy6751 300 NVKCDICGLALTTKSHLNRHMLV-HTGDRPHECSVCGKRFAKKWNAQVHKKKVH 352 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~~H 352 (392)
||.|..|++.|.+...|..|++. |. ++.|..|++.|. .|..|+++.-
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 35666666666666666666653 33 245666666665 3556664443
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.16 E-value=3.9e-06 Score=52.80 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=8.5
Q ss_pred ccCCCCcCcccCHHHHHHHHH
Q psy6751 273 YQCHLCGKGFIHHTSYKFHQL 293 (392)
Q Consensus 273 ~~C~~C~~~f~~~~~l~~H~~ 293 (392)
|.||+|++ ..+...|..|+.
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~ 22 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCE 22 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHH
Confidence 44444444 233344444443
No 26
>KOG1146|consensus
Probab=98.14 E-value=8e-07 Score=88.21 Aligned_cols=53 Identities=23% Similarity=0.481 Sum_probs=47.2
Q ss_pred CCccCccccccCCCchhhhccceeccc------------------------CCCCcccCcccccccccchhhhhhcc
Q psy6751 1 KKYTCDYCTRLFRRPGEVKNHVLVKHL------------------------GKNPNQCTFCEKKFNSRNGLYVHLKK 53 (392)
Q Consensus 1 k~~~C~~C~~~f~~~~~l~~H~~~~H~------------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 53 (392)
|.|+|..|++.|.....|..||+..|. ..++|.|..|.+++.....|..||++
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 468999999999999999999999762 24569999999999999999999984
No 27
>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=98.09 E-value=5.2e-06 Score=52.22 Aligned_cols=51 Identities=25% Similarity=0.477 Sum_probs=41.1
Q ss_pred ccccccCcccCCChHHHHHHHHH-hcCC-CccccCccchhccCchHHHhhhhhccC
Q psy6751 300 NVKCDICGLALTTKSHLNRHMLV-HTGD-RPHECSVCGKRFAKKWNAQVHKKKVHG 353 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~H~ 353 (392)
.|.|++|++. -+...|..|+.. |..+ +.+.|++|...+. ..|..|+...|+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4889999995 567889999865 4433 4699999998755 499999999986
No 28
>KOG1146|consensus
Probab=98.01 E-value=3.6e-06 Score=83.74 Aligned_cols=160 Identities=14% Similarity=0.144 Sum_probs=101.7
Q ss_pred CccccccCCCchhhhccceecccCCCCcccCcccccccccchhhhhhccccccccccchhhccCcCCCcccchhhhhhhh
Q psy6751 5 CDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSRNGLYVHLKKVHNVEYSERIELVSNIPLDEDITDAALLVDK 84 (392)
Q Consensus 5 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (392)
|.-|+..+.+...+.-|+...|.-.+.|.|+.|++.|+....|..||+..|.+.... .|..
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~----------~c~~--------- 499 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSA----------YCKA--------- 499 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchh----------HhHh---------
Confidence 344566677777888888888888899999999999999999999999888754321 0000
Q ss_pred hhccCCCcccccCCCCCCCCCCCCCCCCCCccccccchhhhcccccCccCCCCCcchhhcccccCcccccccccccChhh
Q psy6751 85 ALTIKPKESEQSSQSEDEGMDEGGRDSSGSEWTEETDVFKADKANLDLQGLEMSPEDRAESEVLGWKCFICDAQLTTETS 164 (392)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~ 164 (392)
......+. .......+..+|.|..|+..+++...
T Consensus 500 ---gq~~~~~a-------------------------------------------rg~~~~~~~~p~~C~~C~~stttng~ 533 (1406)
T KOG1146|consen 500 ---GQNHPRLA-------------------------------------------RGEVYRCPGKPYPCRACNYSTTTNGN 533 (1406)
T ss_pred ---cccccccc-------------------------------------------ccccccCCCCcccceeeeeeeecchH
Confidence 00000000 00112223457999999999999999
Q ss_pred HHHHHHHhhccccc------cc----------------c---------c-cCCCCcccccccccccCCHHHHHHHHhhcC
Q psy6751 165 YSVFYTMLSQSGVL------LS----------------E---------R-ACMPLIHECPTCGKKWRTVSELNAHIQTHS 212 (392)
Q Consensus 165 l~~H~~~~~~~~~~------~~----------------~---------~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 212 (392)
|-+|++..-+.... .+ + . ......+.|..|++..+-..+|+-||....
T Consensus 534 LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~ 613 (1406)
T KOG1146|consen 534 LSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASP 613 (1406)
T ss_pred HHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCC
Confidence 99997765543320 00 0 0 011124789999999999999999987643
Q ss_pred CCCC-cccccccccccCH
Q psy6751 213 DLRP-FVCEICGQGYKMK 229 (392)
Q Consensus 213 ~~~~-~~C~~C~~~~~~~ 229 (392)
.-.+ .-|-.|+..+...
T Consensus 614 ~s~~p~~~Lq~~it~~l~ 631 (1406)
T KOG1146|consen 614 SSSPPSLVLQQNITSSLA 631 (1406)
T ss_pred CCCChHHHhhhcchhhcc
Confidence 3332 4444444444333
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=97.72 E-value=2.2e-05 Score=39.66 Aligned_cols=18 Identities=39% Similarity=0.886 Sum_probs=6.6
Q ss_pred CCCCcCcccCHHHHHHHH
Q psy6751 275 CHLCGKGFIHHTSYKFHQ 292 (392)
Q Consensus 275 C~~C~~~f~~~~~l~~H~ 292 (392)
|+.|++.|.++..|..|+
T Consensus 3 C~~C~~~f~~~~~l~~H~ 20 (23)
T PF00096_consen 3 CPICGKSFSSKSNLKRHM 20 (23)
T ss_dssp ETTTTEEESSHHHHHHHH
T ss_pred CCCCCCccCCHHHHHHHH
Confidence 333333333333333333
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.70 E-value=2e-05 Score=57.22 Aligned_cols=75 Identities=20% Similarity=0.272 Sum_probs=18.6
Q ss_pred cCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHHHHHhcCCCccccCccchhccCchHHHhhhhhccC
Q psy6751 274 QCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNAQVHKKKVHG 353 (392)
Q Consensus 274 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~ 353 (392)
+|..|+..|.+...|..|+...|+...- ....+.....+..++..... ..+.|.+|++.|.+...|..|++.++.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~-~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVK-ESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred Cccccccccccccccccccccccccccc----cccccccccccccccccccC-CCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 3666777777777777777665543211 11111123333333332211 257777777777777777777776543
No 31
>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=97.70 E-value=2.3e-05 Score=39.57 Aligned_cols=21 Identities=52% Similarity=0.988 Sum_probs=10.3
Q ss_pred ccccCcccCCChHHHHHHHHH
Q psy6751 302 KCDICGLALTTKSHLNRHMLV 322 (392)
Q Consensus 302 ~C~~C~~~~~~~~~l~~H~~~ 322 (392)
.|+.|++.|.+...|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhH
Confidence 445555555555555555443
No 32
>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=97.58 E-value=3.3e-05 Score=39.44 Aligned_cols=24 Identities=33% Similarity=0.766 Sum_probs=11.2
Q ss_pred cccCccchhccCchHHHhhhhhcc
Q psy6751 329 HECSVCGKRFAKKWNAQVHKKKVH 352 (392)
Q Consensus 329 ~~C~~C~~~f~~~~~l~~H~~~~H 352 (392)
|.|++|++.|.+...|..|+.++|
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 345555555555555555555443
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.56 E-value=6.1e-05 Score=54.66 Aligned_cols=71 Identities=21% Similarity=0.431 Sum_probs=12.6
Q ss_pred ccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHH
Q psy6751 191 CPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNI 266 (392)
Q Consensus 191 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~ 266 (392)
|..|+..|.+...|..||...|+-.. + ....+.....+..++..-. ...+.|..|+..|.+...|..|++.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~---~-~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDI---P-DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred cccccccccccccccccccccccccc---c-ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcC
Confidence 56666666666666666655443211 1 1111112222322322211 1135555555555555555555554
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=97.52 E-value=7.7e-05 Score=38.02 Aligned_cols=19 Identities=32% Similarity=0.781 Sum_probs=6.6
Q ss_pred CCCCcCcccCHHHHHHHHH
Q psy6751 275 CHLCGKGFIHHTSYKFHQL 293 (392)
Q Consensus 275 C~~C~~~f~~~~~l~~H~~ 293 (392)
|+.|++.|.+...|..|+.
T Consensus 3 C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 3 CPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp -SSTS-EESSHHHHHHHHH
T ss_pred CcCCCCcCCcHHHHHHHHH
Confidence 3333333333333333333
No 35
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.46 E-value=5.8e-05 Score=39.81 Aligned_cols=26 Identities=35% Similarity=0.671 Sum_probs=15.9
Q ss_pred ccccCccchhccCchHHHhhhhhccC
Q psy6751 328 PHECSVCGKRFAKKWNAQVHKKKVHG 353 (392)
Q Consensus 328 ~~~C~~C~~~f~~~~~l~~H~~~~H~ 353 (392)
||.|..|++.|.....|..|++.+++
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 45666666666666666666655543
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.34 E-value=7.7e-05 Score=62.78 Aligned_cols=28 Identities=36% Similarity=0.757 Sum_probs=22.2
Q ss_pred CCCccccCccchhccCchHHHhhhhhcc
Q psy6751 325 GDRPHECSVCGKRFAKKWNAQVHKKKVH 352 (392)
Q Consensus 325 ~~~~~~C~~C~~~f~~~~~l~~H~~~~H 352 (392)
..+||+|++|++.|.+...|..|...-|
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~Hsh 422 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRKHSH 422 (423)
T ss_pred cCCceeccccchhhccCccceecccccC
Confidence 3588999999999998888888865443
No 37
>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=97.31 E-value=0.00012 Score=38.55 Aligned_cols=25 Identities=32% Similarity=0.619 Sum_probs=15.5
Q ss_pred ccccccCcccCCChHHHHHHHHHhc
Q psy6751 300 NVKCDICGLALTTKSHLNRHMLVHT 324 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~~l~~H~~~h~ 324 (392)
||.|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 3566666666666666666665553
No 38
>KOG2231|consensus
Probab=97.25 E-value=0.00055 Score=64.99 Aligned_cols=138 Identities=19% Similarity=0.443 Sum_probs=96.8
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccc---------cccCChHH
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCN---------KSFTQKIG 259 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~---------~~~~~~~~ 259 (392)
+.|..|+..|.... ..-.|..| ..|.....|+.|+..-|.. +.|.+|- ....+...
T Consensus 100 ~~C~~C~~~~~~~~------------~~~~~~~c-~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~e 164 (669)
T KOG2231|consen 100 HSCHICDRRFRALY------------NKKECLHC-TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAE 164 (669)
T ss_pred hhcCccccchhhhc------------ccCCCccc-cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHH
Confidence 78999998775321 12368899 8889999999999765432 4455443 23357788
Q ss_pred HHHHHHHhcC-CC----CccCCCCcCcccCHHHHHHHHHHhcCCCccccccC------cccCCChHHHHHHHHHhcCCCc
Q psy6751 260 LVKHLNIHNG-TK----KYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDIC------GLALTTKSHLNRHMLVHTGDRP 328 (392)
Q Consensus 260 l~~H~~~h~~-~~----~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C------~~~~~~~~~l~~H~~~h~~~~~ 328 (392)
|..|++.-.. ++ --.|..|...|.....|.+|++.+| |.|-+| +..|.....|..|.+.+|
T Consensus 165 l~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H---- 236 (669)
T KOG2231|consen 165 LNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH---- 236 (669)
T ss_pred HHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----
Confidence 8889886443 22 2579999999999999999998876 556666 456778899999998876
Q ss_pred cccC--ccch-hccCchHHHhhhh
Q psy6751 329 HECS--VCGK-RFAKKWNAQVHKK 349 (392)
Q Consensus 329 ~~C~--~C~~-~f~~~~~l~~H~~ 349 (392)
|.|. .|.- .|..-..+..|++
T Consensus 237 flCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 237 FLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred ccccccccccceeeehhHHHHHHH
Confidence 5676 5654 3333335555555
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.20 E-value=0.00015 Score=36.96 Aligned_cols=24 Identities=29% Similarity=0.440 Sum_probs=13.5
Q ss_pred cccCccchhccCchHHHhhhhhccC
Q psy6751 329 HECSVCGKRFAKKWNAQVHKKKVHG 353 (392)
Q Consensus 329 ~~C~~C~~~f~~~~~l~~H~~~~H~ 353 (392)
|+|+.|++... ...|.+|++.+|+
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 45666666655 6666666666554
No 40
>KOG2231|consensus
Probab=97.17 E-value=0.0018 Score=61.61 Aligned_cols=161 Identities=19% Similarity=0.376 Sum_probs=100.1
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCcccccccc---------cccCHHHHHHHHhh-hcCCC----CeecCcccccc
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQ---------GYKMKKALLVHVGM-HSGIH----PFTCHFCNKSF 254 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~---------~~~~~~~l~~H~~~-h~~~~----~~~C~~C~~~~ 254 (392)
-.|.+| -.|.+...|+.|+..-|.. +.|..|-. ..-+...|..|++. -.++. --.|..|...|
T Consensus 116 ~~~~~c-~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~f 192 (669)
T KOG2231|consen 116 KECLHC-TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERF 192 (669)
T ss_pred CCCccc-cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhh
Confidence 579999 8899999999999665532 56665543 22345567777654 22222 24699999999
Q ss_pred CChHHHHHHHHHhcCCCCccCCCC------cCcccCHHHHHHHHHHhcCCCccccc--cCc-ccCCChHHHHHHHHHhc-
Q psy6751 255 TQKIGLVKHLNIHNGTKKYQCHLC------GKGFIHHTSYKFHQLVHSGERNVKCD--ICG-LALTTKSHLNRHMLVHT- 324 (392)
Q Consensus 255 ~~~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~~~~~~~~~C~--~C~-~~~~~~~~l~~H~~~h~- 324 (392)
-....|.+|++.++ |.|..| +.-|.....|..|.+.+| |.|. .|. ..|...-.+..|+..|.
T Consensus 193 ld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~~ei~lk~~~~ 264 (669)
T KOG2231|consen 193 LDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFELEIELKAHNR 264 (669)
T ss_pred ccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccceeeehhHHHHHHHhhcc
Confidence 99999999998753 666666 455778899999998877 5565 454 23333334555555333
Q ss_pred ---CCCccccC--c---cc-hhccCchHHHhhhhhccCCCCCCCc
Q psy6751 325 ---GDRPHECS--V---CG-KRFAKKWNAQVHKKKVHGLDVPGTT 360 (392)
Q Consensus 325 ---~~~~~~C~--~---C~-~~f~~~~~l~~H~~~~H~~~~~~~~ 360 (392)
-++-|.|. . +. ..+.....+..|.+..++.....+.
T Consensus 265 ~~~~e~~~~~~~~r~Gr~s~~~r~~~~~~~~~~~~~~~~~~~~t~ 309 (669)
T KOG2231|consen 265 FIQHEKCYICRPSRPGRPSSRYRGPYRRLESHFRVSDEARDGSTA 309 (669)
T ss_pred ccchheeccCCcccCCCCcccccCCcccccccccccccccCcccc
Confidence 23334442 1 11 2334455666666665554333333
No 41
>KOG2785|consensus
Probab=97.06 E-value=0.0022 Score=56.03 Aligned_cols=52 Identities=17% Similarity=0.273 Sum_probs=43.3
Q ss_pred CccCCCCcCcccCHHHHHHHHHHhcCC-----------------------CccccccCc---ccCCChHHHHHHHHHh
Q psy6751 272 KYQCHLCGKGFIHHTSYKFHQLVHSGE-----------------------RNVKCDICG---LALTTKSHLNRHMLVH 323 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~l~~H~~~~~~~-----------------------~~~~C~~C~---~~~~~~~~l~~H~~~h 323 (392)
|-.|-+|++.+.+......||..+||- ..|.|-.|+ +.|.+..+.+.||...
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 577899999999999999999998874 237788888 8899999999998753
No 42
>KOG2482|consensus
Probab=96.97 E-value=0.00032 Score=59.78 Aligned_cols=52 Identities=27% Similarity=0.503 Sum_probs=42.1
Q ss_pred ccCccccccCC-CchhhhccceecccC--C-------------------CCcccCcccccccccchhhhhhccc
Q psy6751 3 YTCDYCTRLFR-RPGEVKNHVLVKHLG--K-------------------NPNQCTFCEKKFNSRNGLYVHLKKV 54 (392)
Q Consensus 3 ~~C~~C~~~f~-~~~~l~~H~~~~H~~--~-------------------~~~~C~~C~~~f~~~~~l~~H~~~~ 54 (392)
..|-+|+..+. +.+.+..|+...|.- . ..+.|-.|.+.|+++..|+.||++.
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhc
Confidence 36899998875 778888898877731 1 1388999999999999999999854
No 43
>KOG2785|consensus
Probab=96.93 E-value=0.00077 Score=58.76 Aligned_cols=54 Identities=26% Similarity=0.450 Sum_probs=44.8
Q ss_pred CccCccccccCCCchhhhccceeccc------------------------------------CCCCcccCcccccccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHL------------------------------------GKNPNQCTFCEKKFNSRN 45 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~------------------------------------~~~~~~C~~C~~~f~~~~ 45 (392)
.|+|.-|...|.+...-+.|+++... ...++.|.+|.++|.+..
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 48999999999999889999988431 123589999999999999
Q ss_pred hhhhhhcccc
Q psy6751 46 GLYVHLKKVH 55 (392)
Q Consensus 46 ~l~~H~~~~H 55 (392)
....|+.+.-
T Consensus 83 a~~~hl~Sk~ 92 (390)
T KOG2785|consen 83 AHENHLKSKK 92 (390)
T ss_pred hHHHHHHHhh
Confidence 9999997543
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.90 E-value=0.00022 Score=60.15 Aligned_cols=67 Identities=24% Similarity=0.528 Sum_probs=34.5
Q ss_pred CCCccccc--ccccccCHHHHHHHHhh-hcCCCCe--ecCccccccCChHHHHHHHHHhcCCCCccCCCCcCcccCHHHH
Q psy6751 214 LRPFVCEI--CGQGYKMKKALLVHVGM-HSGIHPF--TCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSY 288 (392)
Q Consensus 214 ~~~~~C~~--C~~~~~~~~~l~~H~~~-h~~~~~~--~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 288 (392)
++||+|++ |.+.|.+...|+-|+.- |...+.. .-++=-..| -...|||+|+.|++.+.....|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F------------~~~~KPYrCevC~KRYKNlNGL 414 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF------------SAKDKPYRCEVCDKRYKNLNGL 414 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc------------cccCCceeccccchhhccCccc
Confidence 46677765 77777777777766643 2110000 000000001 1234677777777777777766
Q ss_pred HHHH
Q psy6751 289 KFHQ 292 (392)
Q Consensus 289 ~~H~ 292 (392)
+.|.
T Consensus 415 KYHr 418 (423)
T COG5189 415 KYHR 418 (423)
T ss_pred eecc
Confidence 6664
No 45
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.85 E-value=0.0014 Score=56.12 Aligned_cols=22 Identities=18% Similarity=0.395 Sum_probs=11.2
Q ss_pred CCCCcCcccCHHHHHHHHHHhc
Q psy6751 275 CHLCGKGFIHHTSYKFHQLVHS 296 (392)
Q Consensus 275 C~~C~~~f~~~~~l~~H~~~~~ 296 (392)
|..|...|-+-..|..|++..|
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhccceecChHHHHHHHHhhh
Confidence 5555555555555555554443
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.73 E-value=0.0012 Score=33.61 Aligned_cols=23 Identities=39% Similarity=0.730 Sum_probs=11.3
Q ss_pred cccccCcccCCChHHHHHHHHHhc
Q psy6751 301 VKCDICGLALTTKSHLNRHMLVHT 324 (392)
Q Consensus 301 ~~C~~C~~~~~~~~~l~~H~~~h~ 324 (392)
|+|..|++... ...|..|+..|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 44555555555 555555555543
No 47
>KOG2482|consensus
Probab=96.70 E-value=0.0061 Score=52.27 Aligned_cols=150 Identities=17% Similarity=0.265 Sum_probs=86.1
Q ss_pred HHHHHHHhhcCC-CCCcccccccccc-cCHHHHHHHHhhhcCC----------------------CCeecCccccccCCh
Q psy6751 202 SELNAHIQTHSD-LRPFVCEICGQGY-KMKKALLVHVGMHSGI----------------------HPFTCHFCNKSFTQK 257 (392)
Q Consensus 202 ~~l~~H~~~h~~-~~~~~C~~C~~~~-~~~~~l~~H~~~h~~~----------------------~~~~C~~C~~~~~~~ 257 (392)
..|.+|++...+ ....+|-.|...+ .+.+....|+-.-|+- ..++|-+|.+.|.++
T Consensus 129 eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdk 208 (423)
T KOG2482|consen 129 EALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDK 208 (423)
T ss_pred HHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCc
Confidence 344455544322 1234688887765 4566677777543321 136788888888888
Q ss_pred HHHHHHHHHh--cCCCCccCCC-------CcCcccCHHHHHHHH--HH--h-------------cCCCc--cccccCccc
Q psy6751 258 IGLVKHLNIH--NGTKKYQCHL-------CGKGFIHHTSYKFHQ--LV--H-------------SGERN--VKCDICGLA 309 (392)
Q Consensus 258 ~~l~~H~~~h--~~~~~~~C~~-------C~~~f~~~~~l~~H~--~~--~-------------~~~~~--~~C~~C~~~ 309 (392)
..|+.||+.- ..-.|-.=.+ -.....++.....|. .+ . .+..+ ..|-.|...
T Consensus 209 ntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~ 288 (423)
T KOG2482|consen 209 NTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNF 288 (423)
T ss_pred HHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccc
Confidence 8888888752 2111100000 000011111111111 00 0 11112 689999999
Q ss_pred CCChHHHHHHHHHhcC---------------------------CCccccCccchhccCchHHHhhhhhc
Q psy6751 310 LTTKSHLNRHMLVHTG---------------------------DRPHECSVCGKRFAKKWNAQVHKKKV 351 (392)
Q Consensus 310 ~~~~~~l~~H~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~~~ 351 (392)
..+...|..||..-|. .+.-.|..|+..|-....|..|+..+
T Consensus 289 ~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 289 YENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred hhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 9999999999974332 12357899999999999999999764
No 48
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.62 E-value=0.0026 Score=38.02 Aligned_cols=22 Identities=36% Similarity=0.656 Sum_probs=7.3
Q ss_pred eecCccccccCChHHHHHHHHH
Q psy6751 245 FTCHFCNKSFTQKIGLVKHLNI 266 (392)
Q Consensus 245 ~~C~~C~~~~~~~~~l~~H~~~ 266 (392)
-.|++|+..+.+..+|++|+..
T Consensus 25 atCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp EE-TTT--EESSHHHHHHHHHH
T ss_pred CCCCcchhhccchhhHHHHHHH
Confidence 3333333333333333333333
No 49
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.61 E-value=0.0022 Score=33.03 Aligned_cols=18 Identities=44% Similarity=0.887 Sum_probs=6.9
Q ss_pred cccCcccCCChHHHHHHH
Q psy6751 303 CDICGLALTTKSHLNRHM 320 (392)
Q Consensus 303 C~~C~~~~~~~~~l~~H~ 320 (392)
|..|++.|.....|..|+
T Consensus 3 C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 3 CPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCcchhCCHHHHHHHH
Confidence 333333333333333333
No 50
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.52 E-value=0.0017 Score=55.55 Aligned_cols=114 Identities=18% Similarity=0.339 Sum_probs=71.3
Q ss_pred eecCc--cccccCChHHHHHHHHHhcCCCCccCCCC---------cCcccCHHHHHHHHHHhcCCCcc----ccccCccc
Q psy6751 245 FTCHF--CNKSFTQKIGLVKHLNIHNGTKKYQCHLC---------GKGFIHHTSYKFHQLVHSGERNV----KCDICGLA 309 (392)
Q Consensus 245 ~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~C---------~~~f~~~~~l~~H~~~~~~~~~~----~C~~C~~~ 309 (392)
|.|+. |..+...+..|..|.+..|+. +-|..| .-...+...|+.|...-..+-.| .|..|+..
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 55653 555555566666666654443 344443 22344556677776554333223 49999999
Q ss_pred CCChHHHHHHHHHhcCC---------------------------CccccCc--cc----hhccCchHHHhhhhhccCCCC
Q psy6751 310 LTTKSHLNRHMLVHTGD---------------------------RPHECSV--CG----KRFAKKWNAQVHKKKVHGLDV 356 (392)
Q Consensus 310 ~~~~~~l~~H~~~h~~~---------------------------~~~~C~~--C~----~~f~~~~~l~~H~~~~H~~~~ 356 (392)
|-....|..|++..|.. ..|-|.+ |- +.|.....|..|+...||...
T Consensus 230 FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~~~~el~~h~~~~h~~~~ 309 (493)
T COG5236 230 FYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPYHTELLEHLTRFHKVNA 309 (493)
T ss_pred ecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEeccHHHHHHHHHHHhhccc
Confidence 99999999999864431 1245533 33 367888889999999998764
Q ss_pred CCCc
Q psy6751 357 PGTT 360 (392)
Q Consensus 357 ~~~~ 360 (392)
.+.+
T Consensus 310 ~~~~ 313 (493)
T COG5236 310 RLSE 313 (493)
T ss_pred ccCc
Confidence 4433
No 51
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.49 E-value=0.0033 Score=32.36 Aligned_cols=23 Identities=39% Similarity=0.738 Sum_probs=13.4
Q ss_pred ccCCCCcCcccCHHHHHHHHHHh
Q psy6751 273 YQCHLCGKGFIHHTSYKFHQLVH 295 (392)
Q Consensus 273 ~~C~~C~~~f~~~~~l~~H~~~~ 295 (392)
|.|..|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666666666666666665543
No 52
>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=96.42 E-value=0.0037 Score=37.36 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=11.7
Q ss_pred CccccccCcccCCChHHHHHHHHHhcCCC
Q psy6751 299 RNVKCDICGLALTTKSHLNRHMLVHTGDR 327 (392)
Q Consensus 299 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~ 327 (392)
.|-.|++|+..+.+..+|++|+...|+.+
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 44445555555555555555554444433
No 53
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.23 E-value=0.0028 Score=32.49 Aligned_cols=21 Identities=24% Similarity=0.678 Sum_probs=11.1
Q ss_pred cccccccccCCHHHHHHHHhh
Q psy6751 190 ECPTCGKKWRTVSELNAHIQT 210 (392)
Q Consensus 190 ~C~~C~~~f~~~~~l~~H~~~ 210 (392)
.|..|+..|.+...|..|++.
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCcCCHHHHHHHHCc
Confidence 455555555555555555543
No 54
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.23 E-value=0.0026 Score=32.61 Aligned_cols=20 Identities=30% Similarity=0.805 Sum_probs=9.1
Q ss_pred ccccCcccCCChHHHHHHHH
Q psy6751 302 KCDICGLALTTKSHLNRHML 321 (392)
Q Consensus 302 ~C~~C~~~~~~~~~l~~H~~ 321 (392)
.|.+|++.|.+...|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 34444444444444444443
No 55
>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=96.17 E-value=0.0023 Score=33.57 Aligned_cols=22 Identities=27% Similarity=0.754 Sum_probs=14.3
Q ss_pred ccCccccccCCCchhhhcccee
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLV 24 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~ 24 (392)
|.|.+|++.|.+...|..|++.
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 5666666666666666666653
No 56
>PRK04860 hypothetical protein; Provisional
Probab=96.05 E-value=0.0038 Score=48.89 Aligned_cols=36 Identities=33% Similarity=0.756 Sum_probs=19.4
Q ss_pred CccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCC
Q psy6751 272 KYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALT 311 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~ 311 (392)
+|.|. |+. ....+.+|.+++.++++|.|..|+..|.
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 45555 554 3444455555555555555555555544
No 57
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.98 E-value=0.0033 Score=32.97 Aligned_cols=22 Identities=27% Similarity=0.539 Sum_probs=16.1
Q ss_pred cccCccchhccCchHHHhhhhh
Q psy6751 329 HECSVCGKRFAKKWNAQVHKKK 350 (392)
Q Consensus 329 ~~C~~C~~~f~~~~~l~~H~~~ 350 (392)
|.|..|++.|.+...|..|+++
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 5677777777777777777765
No 58
>PRK04860 hypothetical protein; Provisional
Probab=95.96 E-value=0.0032 Score=49.29 Aligned_cols=36 Identities=25% Similarity=0.893 Sum_probs=20.2
Q ss_pred CeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCccc
Q psy6751 244 PFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFI 283 (392)
Q Consensus 244 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 283 (392)
+|.|. |+. ....+++|.++|.++++|.|..|+..|.
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 45565 554 4445555666666666666666655543
No 59
>KOG2893|consensus
Probab=95.13 E-value=0.0054 Score=49.71 Aligned_cols=49 Identities=37% Similarity=0.646 Sum_probs=43.8
Q ss_pred CccccccCCCchhhhccceecccCCCCcccCcccccccccchhhhhhccccccc
Q psy6751 5 CDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSRNGLYVHLKKVHNVE 58 (392)
Q Consensus 5 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 58 (392)
|=+|++.|.+..-|..|.+..| |+|-+|-++..+-..|..|-..+|.+.
T Consensus 13 cwycnrefddekiliqhqkakh-----fkchichkkl~sgpglsihcmqvhket 61 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH-----FKCHICHKKLFSGPGLSIHCMQVHKET 61 (341)
T ss_pred eeecccccchhhhhhhhhhhcc-----ceeeeehhhhccCCCceeehhhhhhhh
Confidence 8899999999999999998866 999999999999999999988787643
No 60
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.42 E-value=0.066 Score=38.70 Aligned_cols=54 Identities=19% Similarity=0.348 Sum_probs=28.9
Q ss_pred cCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHHHHHhcCCCccccCccc
Q psy6751 274 QCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCG 335 (392)
Q Consensus 274 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~ 335 (392)
.|-.|+..|........ ..-.....|+|+.|+..|-..-.+..|-..|. |+.|.
T Consensus 57 ~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~------CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLHC------CPGCI 110 (112)
T ss_pred cccCcCCCCCCcccccc--cccccccceeCCCCCCccccccchhhhhhccC------CcCCC
Confidence 36666666654321100 00112345777777777777666666654443 66554
No 61
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.15 E-value=0.021 Score=34.70 Aligned_cols=33 Identities=27% Similarity=0.504 Sum_probs=28.0
Q ss_pred cCCCccccCccchhccCchHHHhhhhhccCCCC
Q psy6751 324 TGDRPHECSVCGKRFAKKWNAQVHKKKVHGLDV 356 (392)
Q Consensus 324 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~ 356 (392)
.|+..++|+.|+..|.......+|+...||-..
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~~~ 45 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHGWLF 45 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhhhhh
Confidence 456678999999999999999999999998543
No 62
>KOG4173|consensus
Probab=93.83 E-value=0.073 Score=42.40 Aligned_cols=75 Identities=23% Similarity=0.507 Sum_probs=43.1
Q ss_pred CeecCc--cccccCChHHHHHHHHHhcCCCCccCCCCcCcccCHHHHHHHHHHh----------cCCCcccc--ccCccc
Q psy6751 244 PFTCHF--CNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQLVH----------SGERNVKC--DICGLA 309 (392)
Q Consensus 244 ~~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~----------~~~~~~~C--~~C~~~ 309 (392)
.+.|+. |...|.+......|+..-|+. .|..|.++|.+.-.|..|+..- -|..-|+| ..|+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 355654 666666666666666554443 5677777777777676666432 23334555 335555
Q ss_pred CCChHHHHHHHH
Q psy6751 310 LTTKSHLNRHML 321 (392)
Q Consensus 310 ~~~~~~l~~H~~ 321 (392)
|.+...-..|+.
T Consensus 156 FkT~r~RkdH~I 167 (253)
T KOG4173|consen 156 FKTSRDRKDHMI 167 (253)
T ss_pred hhhhhhhhhHHH
Confidence 555555555554
No 63
>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=93.62 E-value=0.13 Score=37.79 Aligned_cols=25 Identities=32% Similarity=0.500 Sum_probs=17.0
Q ss_pred ccc----CccchhccCchHHHhhhhhccC
Q psy6751 329 HEC----SVCGKRFAKKWNAQVHKKKVHG 353 (392)
Q Consensus 329 ~~C----~~C~~~f~~~~~l~~H~~~~H~ 353 (392)
|.| ..|++.+.+...+.+|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 566 6666666666677777666665
No 64
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.31 E-value=0.079 Score=27.04 Aligned_cols=17 Identities=35% Similarity=0.880 Sum_probs=7.6
Q ss_pred cccCcccCCChHHHHHHH
Q psy6751 303 CDICGLALTTKSHLNRHM 320 (392)
Q Consensus 303 C~~C~~~~~~~~~l~~H~ 320 (392)
|+.|++.| ....|..|+
T Consensus 5 C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 5 CPICGRKF-NPDRLEKHE 21 (25)
T ss_pred CCCCCCEE-CHHHHHHHH
Confidence 44444444 333444443
No 65
>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=93.16 E-value=0.21 Score=36.67 Aligned_cols=25 Identities=24% Similarity=0.589 Sum_probs=16.5
Q ss_pred ccc----ccCcccCCChHHHHHHHHHhcC
Q psy6751 301 VKC----DICGLALTTKSHLNRHMLVHTG 325 (392)
Q Consensus 301 ~~C----~~C~~~~~~~~~l~~H~~~h~~ 325 (392)
|.| ..|++.+.+...|..|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 666 6666666666667777666553
No 66
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.13 E-value=0.03 Score=31.34 Aligned_cols=21 Identities=24% Similarity=0.566 Sum_probs=10.5
Q ss_pred ccCccccccCCCchhhhccce
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVL 23 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~ 23 (392)
|.|.+|++.|.+...+..|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 445555555555555544443
No 67
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.02 E-value=0.11 Score=26.52 Aligned_cols=20 Identities=25% Similarity=0.700 Sum_probs=11.8
Q ss_pred ccCCCCcCcccCHHHHHHHHH
Q psy6751 273 YQCHLCGKGFIHHTSYKFHQL 293 (392)
Q Consensus 273 ~~C~~C~~~f~~~~~l~~H~~ 293 (392)
..|+.||+.| ....|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566666666 4445666654
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.98 E-value=0.015 Score=54.79 Aligned_cols=55 Identities=33% Similarity=0.623 Sum_probs=45.1
Q ss_pred CccCccccccCCCchhhhccceecccCCCCcccCccc--ccccccchhhhhhcccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCE--KKFNSRNGLYVHLKKVHNV 57 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~--~~f~~~~~l~~H~~~~H~~ 57 (392)
.+.|..|...|.....+..|... |....++.|...+ ..+.+...+..|.+.++..
T Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (467)
T COG5048 33 PDSCPNCTDSFSRLEHLTRHIRS-HTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89 (467)
T ss_pred hhhcccccccccccchhhhhccc-ccccCCccccccccccccCCcchhhhhccccccc
Confidence 46799999999999999999988 9999999998876 5566777777777755543
No 69
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.69 E-value=0.056 Score=32.90 Aligned_cols=30 Identities=27% Similarity=0.490 Sum_probs=21.8
Q ss_pred cCCCCccCCCCcCcccCHHHHHHHHHHhcC
Q psy6751 268 NGTKKYQCHLCGKGFIHHTSYKFHQLVHSG 297 (392)
Q Consensus 268 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 297 (392)
.++.-++|+.|+..|....++.+|.+..|+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 355567788888888888888888776554
No 70
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.38 E-value=0.077 Score=29.61 Aligned_cols=22 Identities=23% Similarity=0.560 Sum_probs=11.8
Q ss_pred cccCccchhccCchHHHhhhhh
Q psy6751 329 HECSVCGKRFAKKWNAQVHKKK 350 (392)
Q Consensus 329 ~~C~~C~~~f~~~~~l~~H~~~ 350 (392)
|.|.+|+..|.....+..|++.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred eEccccCCccCCHHHHHHHHCh
Confidence 4555555555555555555543
No 71
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.90 E-value=0.087 Score=43.87 Aligned_cols=44 Identities=27% Similarity=0.455 Sum_probs=31.2
Q ss_pred CCccCccccccCCCchhhhccceeccc---------CCCC-----cccCccccccccc
Q psy6751 1 KKYTCDYCTRLFRRPGEVKNHVLVKHL---------GKNP-----NQCTFCEKKFNSR 44 (392)
Q Consensus 1 k~~~C~~C~~~f~~~~~l~~H~~~~H~---------~~~~-----~~C~~C~~~f~~~ 44 (392)
|.++|++|+..|.+........+.... +.+| ..|+.||+++...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 568999999999988666666544221 2233 5799999998754
No 72
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.92 E-value=0.041 Score=51.76 Aligned_cols=28 Identities=25% Similarity=0.584 Sum_probs=19.8
Q ss_pred CCCcccCcccccccccchhhhhhcccccc
Q psy6751 29 KNPNQCTFCEKKFNSRNGLYVHLKKVHNV 57 (392)
Q Consensus 29 ~~~~~C~~C~~~f~~~~~l~~H~~~~H~~ 57 (392)
...+.|..|...|.....+..|.+ .+..
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 58 (467)
T COG5048 31 PRPDSCPNCTDSFSRLEHLTRHIR-SHTG 58 (467)
T ss_pred Cchhhcccccccccccchhhhhcc-cccc
Confidence 345778888888888888888877 4433
No 73
>KOG4173|consensus
Probab=90.55 E-value=0.15 Score=40.76 Aligned_cols=48 Identities=25% Similarity=0.539 Sum_probs=29.2
Q ss_pred Cccccc--ccccccChhhHHHHHHHhhccccccccccCCCCcccccccccccCCHHHHHHHHhh
Q psy6751 149 GWKCFI--CDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGKKWRTVSELNAHIQT 210 (392)
Q Consensus 149 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 210 (392)
.+.|.+ |.+.|.+.+.+..|+...+.. .|..|.+.|++...|..|+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~--------------sCs~C~r~~Pt~hLLd~HI~E 128 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN--------------SCSFCKRAFPTGHLLDAHILE 128 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc--------------hhHHHHHhCCchhhhhHHHHH
Confidence 355654 666777766666665433222 477777777777777766654
No 74
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.55 E-value=0.3 Score=35.41 Aligned_cols=92 Identities=21% Similarity=0.358 Sum_probs=51.3
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCC------------CCeecCccccccCC
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGI------------HPFTCHFCNKSFTQ 256 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~------------~~~~C~~C~~~~~~ 256 (392)
|.|+.|+...-. -|..|++|+.......+|.+-..---+- ....|-.|...|..
T Consensus 2 Y~CPrC~skvC~--------------LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~ 67 (112)
T TIGR00622 2 YFCPQCRAKVCE--------------LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPK 67 (112)
T ss_pred ccCCCCCCCccC--------------CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCC
Confidence 667777664422 4677888888777776665432110011 11237777777755
Q ss_pred hHHHHHHHHHhcCCCCccCCCCcCcccCHHHHHHHHHHhc
Q psy6751 257 KIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQLVHS 296 (392)
Q Consensus 257 ~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 296 (392)
...... ........|+|+.|...|-..-+...|...|.
T Consensus 68 ~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 68 PPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccccc--cccccccceeCCCCCCccccccchhhhhhccC
Confidence 321110 00122345778888877777777777766654
No 75
>KOG2893|consensus
Probab=88.86 E-value=0.13 Score=41.93 Aligned_cols=41 Identities=29% Similarity=0.563 Sum_probs=24.9
Q ss_pred CCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHH
Q psy6751 275 CHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRH 319 (392)
Q Consensus 275 C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H 319 (392)
|.+|++.|.+...|.+|++. +-|+|-+|-+..-+--.|..|
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 66777777777777666644 336666666555444445444
No 76
>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=86.97 E-value=0.38 Score=24.79 Aligned_cols=9 Identities=44% Similarity=1.073 Sum_probs=4.5
Q ss_pred cCCCCcCcc
Q psy6751 274 QCHLCGKGF 282 (392)
Q Consensus 274 ~C~~C~~~f 282 (392)
.|+.||+.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455555544
No 77
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=85.06 E-value=0.25 Score=32.76 Aligned_cols=64 Identities=25% Similarity=0.419 Sum_probs=37.1
Q ss_pred cccccCcccCCChHHHHHHHHHhcCCCccccC--ccchhccCchHHHhhhhhccCCCCCCCcccccccCCCCCC
Q psy6751 301 VKCDICGLALTTKSHLNRHMLVHTGDRPHECS--VCGKRFAKKWNAQVHKKKVHGLDVPGTTHRVMPVPPIGGG 372 (392)
Q Consensus 301 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~--~C~~~f~~~~~l~~H~~~~H~~~~~~~~~~~~~~~~~~~~ 372 (392)
+.|+.|+.......+-..+ ....+.-++|. .||..|.... .-.|-+..++.....+|.|...+.
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~e------s~s~tis~p~~~~~~~~~~~~~~~ 67 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYE------SVQRYIVKPGEVHAVRPHPLPSGQ 67 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEE------EEEEEEcCCCCCCCCCCCCCcccc
Confidence 4677787654322221111 12334557887 8998888544 345566667767667777755443
No 78
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.10 E-value=0.86 Score=25.81 Aligned_cols=8 Identities=38% Similarity=1.140 Sum_probs=3.0
Q ss_pred ccCCCCcC
Q psy6751 273 YQCHLCGK 280 (392)
Q Consensus 273 ~~C~~C~~ 280 (392)
.+|+.|+.
T Consensus 26 vrC~~C~~ 33 (37)
T PF13719_consen 26 VRCPKCGH 33 (37)
T ss_pred EECCCCCc
Confidence 33333333
No 79
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.27 E-value=0.73 Score=27.28 Aligned_cols=28 Identities=25% Similarity=0.520 Sum_probs=21.6
Q ss_pred CccCccccccCCCchhhhccceecccCCCCcccCcccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKF 41 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f 41 (392)
.|.|..|+..|... ...+..|+.||..-
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 48999999988633 24679999999653
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=82.01 E-value=1.2 Score=24.66 Aligned_cols=7 Identities=43% Similarity=1.270 Sum_probs=2.6
Q ss_pred cCCCCcC
Q psy6751 274 QCHLCGK 280 (392)
Q Consensus 274 ~C~~C~~ 280 (392)
.|..||.
T Consensus 4 ~C~~CG~ 10 (34)
T cd00729 4 VCPVCGY 10 (34)
T ss_pred ECCCCCC
Confidence 3333333
No 81
>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=81.83 E-value=1.1 Score=32.64 Aligned_cols=30 Identities=30% Similarity=0.625 Sum_probs=24.5
Q ss_pred ccCccccccCCCchhhhccceecccCCCCcccCccccccccc
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSR 44 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~ 44 (392)
..|..||+.|-.. +..|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL------------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL------------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC------------CCCCccCCCCCCccCcc
Confidence 5799999999542 44789999999999865
No 82
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=81.15 E-value=1.3 Score=24.86 Aligned_cols=9 Identities=33% Similarity=0.925 Sum_probs=3.8
Q ss_pred ccCCCCcCc
Q psy6751 273 YQCHLCGKG 281 (392)
Q Consensus 273 ~~C~~C~~~ 281 (392)
.+|+.|+..
T Consensus 26 v~C~~C~~~ 34 (36)
T PF13717_consen 26 VRCSKCGHV 34 (36)
T ss_pred EECCCCCCE
Confidence 444444443
No 83
>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=80.61 E-value=1.2 Score=25.29 Aligned_cols=6 Identities=50% Similarity=1.531 Sum_probs=2.3
Q ss_pred cCCCCc
Q psy6751 274 QCHLCG 279 (392)
Q Consensus 274 ~C~~C~ 279 (392)
+|+.|+
T Consensus 27 ~C~~C~ 32 (38)
T TIGR02098 27 RCGKCG 32 (38)
T ss_pred ECCCCC
Confidence 333333
No 84
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=80.00 E-value=1.5 Score=31.94 Aligned_cols=31 Identities=32% Similarity=0.869 Sum_probs=20.7
Q ss_pred cccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCH
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMK 229 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 229 (392)
...|+.||..|-. .+..|..|+.||..|.-.
T Consensus 9 KR~Cp~CG~kFYD-----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYD-----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhcc-----------CCCCCccCCCCCCccCcc
Confidence 4567788777765 233566777777777655
No 85
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.69 E-value=0.28 Score=38.17 Aligned_cols=13 Identities=38% Similarity=0.887 Sum_probs=6.4
Q ss_pred ccCCCCcCcccCH
Q psy6751 273 YQCHLCGKGFIHH 285 (392)
Q Consensus 273 ~~C~~C~~~f~~~ 285 (392)
++|+.||+.|.+.
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 4555555555443
No 86
>KOG2186|consensus
Probab=78.95 E-value=1.2 Score=37.19 Aligned_cols=46 Identities=17% Similarity=0.414 Sum_probs=31.7
Q ss_pred ccCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCChHHHHHHHH
Q psy6751 273 YQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHML 321 (392)
Q Consensus 273 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 321 (392)
|.|..||....-.. +.+|+...++ .-|.|-.|+..|.. .....|..
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 67777887776543 5667777766 55778888888766 55666654
No 87
>KOG2807|consensus
Probab=78.86 E-value=3.7 Score=35.74 Aligned_cols=26 Identities=23% Similarity=0.563 Sum_probs=20.2
Q ss_pred CCccCCCCcCcccCHHHHHHHHHHhc
Q psy6751 271 KKYQCHLCGKGFIHHTSYKFHQLVHS 296 (392)
Q Consensus 271 ~~~~C~~C~~~f~~~~~l~~H~~~~~ 296 (392)
..|+|+.|...|-..-+...|...|.
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhc
Confidence 35889999998888777778876663
No 88
>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=78.61 E-value=1.3 Score=24.08 Aligned_cols=27 Identities=22% Similarity=0.609 Sum_probs=18.4
Q ss_pred ccCccccccCCCchhhhccceecccCCCCcccCcccccc
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKF 41 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f 41 (392)
|.|..|+..+... ...+..|+.||..-
T Consensus 1 Y~C~~Cg~~~~~~------------~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELK------------PGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BS------------TSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcC------------CCCcEECCcCCCeE
Confidence 7899999888621 13468999999753
No 89
>KOG2186|consensus
Probab=78.11 E-value=1.5 Score=36.51 Aligned_cols=46 Identities=20% Similarity=0.521 Sum_probs=21.7
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHh
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVG 237 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~ 237 (392)
|.|..||...... .+..|+...++ .-|.|-.|+..|.. ..+..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 5555555544432 23335555444 33555555555554 33444433
No 90
>PHA00626 hypothetical protein
Probab=78.08 E-value=1.1 Score=27.52 Aligned_cols=14 Identities=14% Similarity=0.263 Sum_probs=12.1
Q ss_pred CCCcccCccccccc
Q psy6751 29 KNPNQCTFCEKKFN 42 (392)
Q Consensus 29 ~~~~~C~~C~~~f~ 42 (392)
...|.|+.||+.|+
T Consensus 21 snrYkCkdCGY~ft 34 (59)
T PHA00626 21 SDDYVCCDCGYNDS 34 (59)
T ss_pred CcceEcCCCCCeec
Confidence 35699999999987
No 91
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=77.07 E-value=1.1 Score=34.99 Aligned_cols=43 Identities=14% Similarity=0.388 Sum_probs=27.4
Q ss_pred ccCccccccCC---Cchhhhc--cceecccCCCCcccCcccccccccchhhhhh
Q psy6751 3 YTCDYCTRLFR---RPGEVKN--HVLVKHLGKNPNQCTFCEKKFNSRNGLYVHL 51 (392)
Q Consensus 3 ~~C~~C~~~f~---~~~~l~~--H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~ 51 (392)
++|++|+-.+. +...+.. +++ +.++|+.||++|.+.+.+..=+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~------~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIR------RRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCcee------eeeeccccCCcceEeEeccCcc
Confidence 57999996552 2222222 222 2399999999999877655433
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=75.58 E-value=0.44 Score=39.71 Aligned_cols=19 Identities=37% Similarity=0.719 Sum_probs=10.6
Q ss_pred CCccCCCCcCcccCHHHHH
Q psy6751 271 KKYQCHLCGKGFIHHTSYK 289 (392)
Q Consensus 271 ~~~~C~~C~~~f~~~~~l~ 289 (392)
+.+.||.|+..|.+...+.
T Consensus 4 k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CceECCCCCCeeeeeEEEc
Confidence 3456666666666554433
No 93
>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=75.42 E-value=3.2 Score=32.72 Aligned_cols=33 Identities=15% Similarity=0.337 Sum_probs=19.5
Q ss_pred hcCCCccccccCcccCCChHHHHHHHHHhcCCCccccCccch
Q psy6751 295 HSGERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGK 336 (392)
Q Consensus 295 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 336 (392)
..+..-|.|+.|+..|+...++. .-|.|+.||.
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~ 136 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGA 136 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCC
Confidence 33445566666666666666553 1466777765
No 94
>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=75.30 E-value=2 Score=25.47 Aligned_cols=24 Identities=38% Similarity=0.587 Sum_probs=10.3
Q ss_pred cccCccchhccC----chHHHhhhhhcc
Q psy6751 329 HECSVCGKRFAK----KWNAQVHKKKVH 352 (392)
Q Consensus 329 ~~C~~C~~~f~~----~~~l~~H~~~~H 352 (392)
..|.+|++.+.. ...|.+|++..|
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 445555544433 245555554443
No 95
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.38 E-value=2.7 Score=26.34 Aligned_cols=7 Identities=43% Similarity=1.251 Sum_probs=2.7
Q ss_pred eecCccc
Q psy6751 245 FTCHFCN 251 (392)
Q Consensus 245 ~~C~~C~ 251 (392)
|.|+-||
T Consensus 28 F~CPnCG 34 (61)
T COG2888 28 FPCPNCG 34 (61)
T ss_pred eeCCCCC
Confidence 3333333
No 96
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=73.98 E-value=1.5 Score=26.22 Aligned_cols=7 Identities=43% Similarity=1.374 Sum_probs=2.8
Q ss_pred ccCCCCc
Q psy6751 273 YQCHLCG 279 (392)
Q Consensus 273 ~~C~~C~ 279 (392)
..|+.||
T Consensus 22 ~~Cp~CG 28 (46)
T PRK00398 22 VRCPYCG 28 (46)
T ss_pred eECCCCC
Confidence 3344443
No 97
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=73.97 E-value=4 Score=31.76 Aligned_cols=13 Identities=31% Similarity=0.856 Sum_probs=6.8
Q ss_pred cccccccccccCC
Q psy6751 188 IHECPTCGKKWRT 200 (392)
Q Consensus 188 ~~~C~~C~~~f~~ 200 (392)
.|.|+.|+..|..
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 3555555555553
No 98
>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=73.87 E-value=1.4 Score=27.22 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=20.0
Q ss_pred ccCccccccCCCchhhhccceecccCCCCcccCcccc
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEK 39 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~ 39 (392)
|+|..|+..|.....+ . ......|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~-------~-~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM-------S-DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec-------C-CCCCCCCCCCCC
Confidence 7899999988743221 1 135577999986
No 99
>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=72.91 E-value=2.9 Score=30.98 Aligned_cols=35 Identities=17% Similarity=0.335 Sum_probs=26.4
Q ss_pred CccCccccccCCCchhhhccceecccCCCCcccCcccccccccchhh
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSRNGLY 48 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~ 48 (392)
...|.-|++.|-.. +..|..|+.||..|.....++
T Consensus 9 Kr~Cp~cg~kFYDL------------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGSKFYDL------------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCcccccc------------CCCCccCCCcCCccCcchhhc
Confidence 35799999999542 457899999999987664433
No 100
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.39 E-value=1.8 Score=26.19 Aligned_cols=28 Identities=21% Similarity=0.653 Sum_probs=20.7
Q ss_pred CccCccccccCCCchhhhccceecccCCCCcccCccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKK 40 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~ 40 (392)
.|+|.-|++.|.. -.....+.|+.||..
T Consensus 6 ~Y~C~~Cg~~~~~-----------~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVEL-----------DQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeeh-----------hhccCceeCCCCCcE
Confidence 4889999999831 123566899999975
No 101
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=72.28 E-value=1.8 Score=27.54 Aligned_cols=19 Identities=21% Similarity=0.303 Sum_probs=7.1
Q ss_pred HHHHHHHHhcCCCCccCCC
Q psy6751 259 GLVKHLNIHNGTKKYQCHL 277 (392)
Q Consensus 259 ~l~~H~~~h~~~~~~~C~~ 277 (392)
.|..|+...-..++..|++
T Consensus 25 ~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHccCCCCcEECCC
Confidence 3444444333333344444
No 102
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.03 E-value=3.4 Score=33.30 Aligned_cols=31 Identities=19% Similarity=0.496 Sum_probs=17.2
Q ss_pred CCCccccccCcccCCChHHHHHHHHHhcCCCccccCccch
Q psy6751 297 GERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGK 336 (392)
Q Consensus 297 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 336 (392)
...-|.|+.|+..|+...++. .-|.|+.||.
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~ 144 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGE 144 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCC
Confidence 334466666666666555442 2466666664
No 103
>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=71.82 E-value=4.2 Score=32.09 Aligned_cols=16 Identities=13% Similarity=0.353 Sum_probs=8.7
Q ss_pred ccccccccccCCHHHH
Q psy6751 189 HECPTCGKKWRTVSEL 204 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l 204 (392)
|.|+.|+..|+....+
T Consensus 110 Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 110 FICPNMCVRFTFNEAM 125 (158)
T ss_pred EECCCCCcEeeHHHHH
Confidence 5555555555555444
No 104
>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=70.84 E-value=2 Score=32.48 Aligned_cols=24 Identities=38% Similarity=0.740 Sum_probs=14.4
Q ss_pred cccCccchhccCchHHHhhhhhccCCC
Q psy6751 329 HECSVCGKRFAKKWNAQVHKKKVHGLD 355 (392)
Q Consensus 329 ~~C~~C~~~f~~~~~l~~H~~~~H~~~ 355 (392)
..|-.||+.|. .|.+|+.++||..
T Consensus 73 i~clecGk~~k---~LkrHL~~~~glt 96 (132)
T PF05443_consen 73 IICLECGKKFK---TLKRHLRTHHGLT 96 (132)
T ss_dssp EE-TBT--EES---BHHHHHHHTT-S-
T ss_pred eEEccCCcccc---hHHHHHHHccCCC
Confidence 57888888776 4578888888875
No 105
>KOG2807|consensus
Probab=70.72 E-value=7.2 Score=34.01 Aligned_cols=25 Identities=16% Similarity=0.375 Sum_probs=15.8
Q ss_pred CccccccCcccCCChHHHHHHHHHh
Q psy6751 299 RNVKCDICGLALTTKSHLNRHMLVH 323 (392)
Q Consensus 299 ~~~~C~~C~~~~~~~~~l~~H~~~h 323 (392)
..|.|..|+..|...-....|-..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 3477777777777666666664444
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=70.48 E-value=4.4 Score=41.15 Aligned_cols=49 Identities=27% Similarity=0.661 Sum_probs=30.6
Q ss_pred cccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHHh
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIH 267 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h 267 (392)
...|+.||... ..+.|+.||.. ....+.|+.|+....
T Consensus 626 ~RfCpsCG~~t----------------~~frCP~CG~~---------------Te~i~fCP~CG~~~~------------ 662 (1121)
T PRK04023 626 RRKCPSCGKET----------------FYRRCPFCGTH---------------TEPVYRCPRCGIEVE------------ 662 (1121)
T ss_pred CccCCCCCCcC----------------CcccCCCCCCC---------------CCcceeCccccCcCC------------
Confidence 45688888763 22678888775 233467777754432
Q ss_pred cCCCCccCCCCcCccc
Q psy6751 268 NGTKKYQCHLCGKGFI 283 (392)
Q Consensus 268 ~~~~~~~C~~C~~~f~ 283 (392)
++.|+.||....
T Consensus 663 ----~y~CPKCG~El~ 674 (1121)
T PRK04023 663 ----EDECEKCGREPT 674 (1121)
T ss_pred ----CCcCCCCCCCCC
Confidence 266888877544
No 107
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=70.46 E-value=5.9 Score=34.18 Aligned_cols=26 Identities=31% Similarity=0.660 Sum_probs=20.4
Q ss_pred CCccCCCCcCcccCHHHHHHHHHHhc
Q psy6751 271 KKYQCHLCGKGFIHHTSYKFHQLVHS 296 (392)
Q Consensus 271 ~~~~C~~C~~~f~~~~~l~~H~~~~~ 296 (392)
..|+|+.|...|-..-....|...|.
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHhh
Confidence 45889999888888888888876653
No 108
>PF12907 zf-met2: Zinc-binding
Probab=70.40 E-value=1.2 Score=25.64 Aligned_cols=26 Identities=27% Similarity=0.526 Sum_probs=11.5
Q ss_pred ccCccccccC---CCchhhhccceecccC
Q psy6751 3 YTCDYCTRLF---RRPGEVKNHVLVKHLG 28 (392)
Q Consensus 3 ~~C~~C~~~f---~~~~~l~~H~~~~H~~ 28 (392)
++|.+|...| .+...|..|....|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 3455555332 2334455555444443
No 109
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=69.98 E-value=4.5 Score=31.45 Aligned_cols=14 Identities=29% Similarity=0.392 Sum_probs=7.4
Q ss_pred CccccccCcccCCC
Q psy6751 299 RNVKCDICGLALTT 312 (392)
Q Consensus 299 ~~~~C~~C~~~~~~ 312 (392)
.-|.|+.|+..|+.
T Consensus 98 ~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 98 AYYKCPNCQSKYTF 111 (147)
T ss_pred cEEECcCCCCEeeH
Confidence 34555555555553
No 110
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=69.68 E-value=1.4 Score=25.77 Aligned_cols=29 Identities=24% Similarity=0.691 Sum_probs=20.8
Q ss_pred ccCccccccCCCchhhhccceecccCCCCcccCcccc
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEK 39 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~ 39 (392)
|+|..||..|.....+.. ..+..|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~--------~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE--------DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC--------CCCCcCCCCCC
Confidence 789999988875433221 45688999987
No 111
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=69.48 E-value=2.7 Score=28.73 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=8.4
Q ss_pred CCccccccCcccCC
Q psy6751 298 ERNVKCDICGLALT 311 (392)
Q Consensus 298 ~~~~~C~~C~~~~~ 311 (392)
...|.|..|+..|.
T Consensus 51 ~GIW~C~kCg~~fA 64 (89)
T COG1997 51 TGIWKCRKCGAKFA 64 (89)
T ss_pred cCeEEcCCCCCeec
Confidence 34566666666654
No 112
>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=68.98 E-value=2 Score=24.80 Aligned_cols=30 Identities=20% Similarity=0.557 Sum_probs=20.4
Q ss_pred ccCccccccCCCchhhhccceecccCCCCcccCccccc
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKK 40 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~ 40 (392)
|+|..|+..|....... ......|+.||..
T Consensus 6 y~C~~Cg~~fe~~~~~~--------~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS--------DDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEecC--------CCCCCCCCCCCCc
Confidence 78999999886432221 1456789999873
No 113
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=68.63 E-value=3 Score=34.98 Aligned_cols=20 Identities=20% Similarity=0.516 Sum_probs=12.2
Q ss_pred CCccccCccchhccCchHHH
Q psy6751 326 DRPHECSVCGKRFAKKWNAQ 345 (392)
Q Consensus 326 ~~~~~C~~C~~~f~~~~~l~ 345 (392)
.+++.|+.|++.......|.
T Consensus 207 ~k~~PCPKCg~et~eTkdLS 226 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLS 226 (314)
T ss_pred CCCCCCCCCCCcccccccce
Confidence 35677777776655555444
No 114
>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=67.52 E-value=1.4 Score=36.43 Aligned_cols=31 Identities=19% Similarity=0.394 Sum_probs=24.3
Q ss_pred CCCCcccCcccccccccchhhhhhccccccc
Q psy6751 28 GKNPNQCTFCEKKFNSRNGLYVHLKKVHNVE 58 (392)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 58 (392)
.+..|.|++|+|.|...+-+.+|+.+.|...
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 3456999999999999999999999999754
No 115
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=67.25 E-value=6.1 Score=24.90 Aligned_cols=8 Identities=50% Similarity=1.530 Sum_probs=3.8
Q ss_pred cccccccc
Q psy6751 217 FVCEICGQ 224 (392)
Q Consensus 217 ~~C~~C~~ 224 (392)
|.|+.||.
T Consensus 26 F~CPnCG~ 33 (59)
T PRK14890 26 FLCPNCGE 33 (59)
T ss_pred eeCCCCCC
Confidence 44555544
No 116
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=66.86 E-value=2.5 Score=34.94 Aligned_cols=28 Identities=14% Similarity=0.524 Sum_probs=15.2
Q ss_pred CccccccCcccCCChHHHHHHHHHhcCC
Q psy6751 299 RNVKCDICGLALTTKSHLNRHMLVHTGD 326 (392)
Q Consensus 299 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~ 326 (392)
..|.|.+|++.|.-......|+...|.+
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 3366666666666666666666666654
No 117
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=66.64 E-value=5.8 Score=31.97 Aligned_cols=15 Identities=20% Similarity=0.552 Sum_probs=7.2
Q ss_pred ccccccccccCCHHH
Q psy6751 189 HECPTCGKKWRTVSE 203 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~ 203 (392)
|.|+.|+..|.....
T Consensus 118 Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 118 FFCPNCHIRFTFDEA 132 (178)
T ss_pred EECCCCCcEEeHHHH
Confidence 445555554444443
No 118
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.62 E-value=4.4 Score=40.33 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=6.2
Q ss_pred CCccCCCCcCc
Q psy6751 271 KKYQCHLCGKG 281 (392)
Q Consensus 271 ~~~~C~~C~~~ 281 (392)
.|..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 35566666554
No 119
>PF14353 CpXC: CpXC protein
Probab=66.29 E-value=2.3 Score=32.14 Aligned_cols=50 Identities=20% Similarity=0.184 Sum_probs=33.6
Q ss_pred ccCccccccCCCchhhhccceecc---------cCCCCcccCcccccccccchhhhhhcc
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVKH---------LGKNPNQCTFCEKKFNSRNGLYVHLKK 53 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~H---------~~~~~~~C~~C~~~f~~~~~l~~H~~~ 53 (392)
.+|+.|+..|............ . .....|.|+.||..|.-...+..|-..
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~-~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADE-DPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcC-CHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence 4799999998754333222211 1 123358999999999988888887663
No 120
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=65.69 E-value=3.8 Score=32.30 Aligned_cols=23 Identities=35% Similarity=1.042 Sum_probs=15.6
Q ss_pred ccccccCcccCCChHHHHHHHHHhcCCCccccCccc
Q psy6751 300 NVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCG 335 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~ 335 (392)
.|.|++||+.+ -++.|-+|++||
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 57777777654 335677777777
No 121
>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=65.41 E-value=4.9 Score=29.84 Aligned_cols=31 Identities=26% Similarity=0.505 Sum_probs=19.8
Q ss_pred cccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCH
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMK 229 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 229 (392)
...|+.|++.|-. .+..|..|+.||..|.-.
T Consensus 9 Kr~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCccccc-----------cCCCCccCCCcCCccCcc
Confidence 3567777777764 233566777777776555
No 122
>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=64.74 E-value=7.2 Score=20.03 Aligned_cols=19 Identities=21% Similarity=0.576 Sum_probs=9.2
Q ss_pred ccccCcccCCChHHHHHHHH
Q psy6751 302 KCDICGLALTTKSHLNRHML 321 (392)
Q Consensus 302 ~C~~C~~~~~~~~~l~~H~~ 321 (392)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 355555554 3344445543
No 123
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.84 E-value=7.2 Score=39.76 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=6.3
Q ss_pred ccccCccchh
Q psy6751 328 PHECSVCGKR 337 (392)
Q Consensus 328 ~~~C~~C~~~ 337 (392)
++.|+.|+..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 4667777753
No 124
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=63.68 E-value=4.6 Score=40.21 Aligned_cols=25 Identities=28% Similarity=0.893 Sum_probs=16.0
Q ss_pred CCCccccccCcccCCChHHHHHHHHHhcCCCccccCccch
Q psy6751 297 GERNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGK 336 (392)
Q Consensus 297 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 336 (392)
..+...|-+||+. ...|..|+.||-
T Consensus 459 ~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs 483 (730)
T COG1198 459 ATGQLRCHYCGYQ---------------EPIPQSCPECGS 483 (730)
T ss_pred CCCeeEeCCCCCC---------------CCCCCCCCCCCC
Confidence 4456777777754 235677888874
No 125
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=63.31 E-value=5.4 Score=35.06 Aligned_cols=28 Identities=25% Similarity=0.681 Sum_probs=21.7
Q ss_pred HhcCCCccccccCc-ccCCChHHHHHHHH
Q psy6751 294 VHSGERNVKCDICG-LALTTKSHLNRHML 321 (392)
Q Consensus 294 ~~~~~~~~~C~~C~-~~~~~~~~l~~H~~ 321 (392)
.|--++-|.|.+|| +.+.-...+.+|..
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 34445679999999 88888888888874
No 126
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=63.29 E-value=4.4 Score=31.98 Aligned_cols=23 Identities=43% Similarity=1.044 Sum_probs=14.2
Q ss_pred cccccccccccCCHHHHHHHHhhcCCCCCccccccc
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICG 223 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 223 (392)
.|.|+.||..+. ++.|-.||+|+
T Consensus 134 ~~vC~vCGy~~~-------------ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHE-------------GEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCccc-------------CCCCCcCCCCC
Confidence 467777766544 34566677776
No 127
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=63.10 E-value=4.7 Score=24.58 Aligned_cols=11 Identities=27% Similarity=0.377 Sum_probs=5.6
Q ss_pred hHHHhhhhhcc
Q psy6751 342 WNAQVHKKKVH 352 (392)
Q Consensus 342 ~~l~~H~~~~H 352 (392)
+.|.+|+...|
T Consensus 37 s~L~rHl~~~h 47 (50)
T smart00614 37 SNLRRHLRRKH 47 (50)
T ss_pred HHHHHHHHhHC
Confidence 35555555433
No 128
>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=62.80 E-value=2.3 Score=35.60 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=15.8
Q ss_pred CCccccccCcccCCChHHHHHHHHHh
Q psy6751 298 ERNVKCDICGLALTTKSHLNRHMLVH 323 (392)
Q Consensus 298 ~~~~~C~~C~~~~~~~~~l~~H~~~h 323 (392)
.+++.|+.|++....-..|..-.++|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 36777888877766555554444443
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=59.59 E-value=10 Score=39.86 Aligned_cols=53 Identities=23% Similarity=0.599 Sum_probs=31.7
Q ss_pred cccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHHh
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIH 267 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h 267 (392)
.+.|+.|+..... ..|+.||... +.+|.|+.||.......
T Consensus 667 ~rkCPkCG~~t~~----------------~fCP~CGs~t---------------e~vy~CPsCGaev~~de--------- 706 (1337)
T PRK14714 667 RRRCPSCGTETYE----------------NRCPDCGTHT---------------EPVYVCPDCGAEVPPDE--------- 706 (1337)
T ss_pred EEECCCCCCcccc----------------ccCcccCCcC---------------CCceeCccCCCccCCCc---------
Confidence 3678888874321 3688887764 22467888887643311
Q ss_pred cCCCCccCCCCcCcc
Q psy6751 268 NGTKKYQCHLCGKGF 282 (392)
Q Consensus 268 ~~~~~~~C~~C~~~f 282 (392)
+. ...|+.|+.-.
T Consensus 707 s~--a~~CP~CGtpl 719 (1337)
T PRK14714 707 SG--RVECPRCDVEL 719 (1337)
T ss_pred cc--cccCCCCCCcc
Confidence 11 34688887543
No 130
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=59.56 E-value=6.9 Score=24.77 Aligned_cols=37 Identities=22% Similarity=0.516 Sum_probs=16.4
Q ss_pred ccccc--ccccccCHHHHHHHHhhhcCCCCeecCc----ccccc
Q psy6751 217 FVCEI--CGQGYKMKKALLVHVGMHSGIHPFTCHF----CNKSF 254 (392)
Q Consensus 217 ~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~----C~~~~ 254 (392)
..|+. |...+. ...|..|+...-..++..|++ |+..+
T Consensus 10 v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 10 VPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERV 52 (60)
T ss_dssp EE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EE
T ss_pred eeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCcc
Confidence 44555 333333 234566666555555666666 65554
No 131
>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=59.25 E-value=5.1 Score=24.11 Aligned_cols=39 Identities=15% Similarity=0.307 Sum_probs=20.3
Q ss_pred CccCccccccCCCchhhhccceecc----cCCCCcccCccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKH----LGKNPNQCTFCEKK 40 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H----~~~~~~~C~~C~~~ 40 (392)
.|.|.+|++.|.....-..+-...- ....-|.|+.|+..
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 4889999999875433222211100 01233899999864
No 132
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=57.22 E-value=13 Score=32.22 Aligned_cols=24 Identities=17% Similarity=0.520 Sum_probs=13.4
Q ss_pred ccccccCcccCCChHHHHHHHHHh
Q psy6751 300 NVKCDICGLALTTKSHLNRHMLVH 323 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~~l~~H~~~h 323 (392)
.|+|+.|+..|...-....|-..|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 366666666666555555554443
No 133
>PF15269 zf-C2H2_7: Zinc-finger
Probab=56.19 E-value=9.6 Score=22.23 Aligned_cols=22 Identities=23% Similarity=0.576 Sum_probs=15.8
Q ss_pred eecCccccccCChHHHHHHHHH
Q psy6751 245 FTCHFCNKSFTQKIGLVKHLNI 266 (392)
Q Consensus 245 ~~C~~C~~~~~~~~~l~~H~~~ 266 (392)
|+|=.|.++...++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5677777777777777777764
No 134
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=55.79 E-value=3.9 Score=28.78 Aligned_cols=37 Identities=22% Similarity=0.388 Sum_probs=22.0
Q ss_pred CCccCccccccCCCchhhhccceecccCCCCcccCccccccc
Q psy6751 1 KKYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFN 42 (392)
Q Consensus 1 k~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~ 42 (392)
|.|.|+.||..-.+.-.+ +. -.+..-..|..||.+|.
T Consensus 21 k~FtCp~Cghe~vs~ctv----kk-~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTV----KK-TVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ceEecCccCCeeeeEEEE----Ee-cCceeEEEcccCcceEE
Confidence 357788888765543332 22 23344567888887775
No 135
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=55.15 E-value=17 Score=32.08 Aligned_cols=39 Identities=15% Similarity=0.451 Sum_probs=26.7
Q ss_pred HHhcCCCCccCCCCc-CcccCHHHHHHHHHHhcCCCcccc
Q psy6751 265 NIHNGTKKYQCHLCG-KGFIHHTSYKFHQLVHSGERNVKC 303 (392)
Q Consensus 265 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~~~~~~~~~~C 303 (392)
+.|.-.+.|.|..|| +++..+..+.+|..-.......+|
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF~E~rHiygl~c 406 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHFEEDRHIYGLEC 406 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhhhhhhhhhheee
Confidence 446566789999998 788888888888754333333444
No 136
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=54.64 E-value=5.7 Score=19.71 Aligned_cols=7 Identities=57% Similarity=1.768 Sum_probs=4.0
Q ss_pred ccccccc
Q psy6751 191 CPTCGKK 197 (392)
Q Consensus 191 C~~C~~~ 197 (392)
|+.||..
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 6666543
No 137
>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=52.77 E-value=2.7 Score=25.70 Aligned_cols=13 Identities=23% Similarity=0.646 Sum_probs=9.6
Q ss_pred cccccccccccCh
Q psy6751 150 WKCFICDAQLTTE 162 (392)
Q Consensus 150 ~~C~~C~~~f~~~ 162 (392)
|.|..|+..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6788888877743
No 138
>KOG2593|consensus
Probab=52.69 E-value=17 Score=33.31 Aligned_cols=14 Identities=29% Similarity=0.759 Sum_probs=6.2
Q ss_pred CCcccccccccccC
Q psy6751 215 RPFVCEICGQGYKM 228 (392)
Q Consensus 215 ~~~~C~~C~~~~~~ 228 (392)
..|.|+.|.+.|..
T Consensus 127 ~~Y~Cp~C~kkyt~ 140 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTS 140 (436)
T ss_pred ccccCCccccchhh
Confidence 33444444444443
No 139
>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=51.81 E-value=9.9 Score=36.53 Aligned_cols=15 Identities=40% Similarity=0.926 Sum_probs=8.4
Q ss_pred hcCCCCccCCCCcCc
Q psy6751 267 HNGTKKYQCHLCGKG 281 (392)
Q Consensus 267 h~~~~~~~C~~C~~~ 281 (392)
|.......|.+||+.
T Consensus 235 h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 235 HKKEGKLRCHYCGYQ 249 (505)
T ss_pred ecCCCeEEcCCCcCc
Confidence 334445667777643
No 140
>KOG4124|consensus
Probab=51.11 E-value=8 Score=34.04 Aligned_cols=52 Identities=31% Similarity=0.714 Sum_probs=42.5
Q ss_pred CCccCcc--ccccCCCchhhhccceeccc------------------CCCCcccCcccccccccchhhhhhc
Q psy6751 1 KKYTCDY--CTRLFRRPGEVKNHVLVKHL------------------GKNPNQCTFCEKKFNSRNGLYVHLK 52 (392)
Q Consensus 1 k~~~C~~--C~~~f~~~~~l~~H~~~~H~------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 52 (392)
++|+|.+ |.+.+.+...|..|....|. .-++|.|++|.+++.....|..|..
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 5788887 99999999999988776552 2456999999999998888888765
No 141
>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=49.97 E-value=6.2 Score=21.12 Aligned_cols=10 Identities=30% Similarity=0.767 Sum_probs=5.1
Q ss_pred CccccCccch
Q psy6751 327 RPHECSVCGK 336 (392)
Q Consensus 327 ~~~~C~~C~~ 336 (392)
..|.|+.|+.
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 3455555543
No 142
>KOG2593|consensus
Probab=49.68 E-value=21 Score=32.72 Aligned_cols=36 Identities=22% Similarity=0.571 Sum_probs=18.7
Q ss_pred CCccCCCCcCcccCHHHHHHHHHHhcCCCccccccCccc
Q psy6751 271 KKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLA 309 (392)
Q Consensus 271 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 309 (392)
.-|.|+.|++.|.+...+. ..-.....|.|..|+-.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccCCccccchhhhHHHH---hhcccCceEEEecCCCc
Confidence 4566666666665544432 22223345666666543
No 143
>KOG3408|consensus
Probab=49.42 E-value=9.9 Score=27.86 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=22.0
Q ss_pred CCCccccccCcccCCChHHHHHHHHH
Q psy6751 297 GERNVKCDICGLALTTKSHLNRHMLV 322 (392)
Q Consensus 297 ~~~~~~C~~C~~~~~~~~~l~~H~~~ 322 (392)
|...|.|-.|-+.|.+...|..|.+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 34559999999999999999999864
No 144
>KOG4167|consensus
Probab=49.08 E-value=5.2 Score=38.93 Aligned_cols=26 Identities=38% Similarity=0.709 Sum_probs=22.2
Q ss_pred CcccccccccccCCHHHHHHHHhhcC
Q psy6751 187 LIHECPTCGKKWRTVSELNAHIQTHS 212 (392)
Q Consensus 187 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 212 (392)
-.|.|..|+++|.....+..||+.|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 46889999999999999999998874
No 145
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.99 E-value=6.9 Score=27.22 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=6.8
Q ss_pred CccccccCcccCC
Q psy6751 299 RNVKCDICGLALT 311 (392)
Q Consensus 299 ~~~~C~~C~~~~~ 311 (392)
..|.|..|++.|.
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PTZ00255 53 GIWRCKGCKKTVA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 4455555555544
No 146
>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=48.80 E-value=15 Score=21.83 Aligned_cols=8 Identities=25% Similarity=0.982 Sum_probs=3.4
Q ss_pred ccccccCc
Q psy6751 300 NVKCDICG 307 (392)
Q Consensus 300 ~~~C~~C~ 307 (392)
.|+|..|+
T Consensus 37 ~~~C~~C~ 44 (46)
T PF12760_consen 37 RYRCKACR 44 (46)
T ss_pred eEECCCCC
Confidence 34444443
No 147
>KOG1280|consensus
Probab=48.40 E-value=8.9 Score=33.79 Aligned_cols=37 Identities=27% Similarity=0.603 Sum_probs=23.9
Q ss_pred CccCccccccCCCchhhhccceecccCCC-CcccCccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKN-PNQCTFCE 38 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~-~~~C~~C~ 38 (392)
.|+|++|+..=.+...|..|+...|..-. ...|++|+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 47788887665567778888777775432 24456654
No 148
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=48.34 E-value=21 Score=37.62 Aligned_cols=11 Identities=27% Similarity=0.628 Sum_probs=6.9
Q ss_pred ccccccCcccC
Q psy6751 300 NVKCDICGLAL 310 (392)
Q Consensus 300 ~~~C~~C~~~~ 310 (392)
+|.|+.|+...
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 45677777654
No 149
>KOG2071|consensus
Probab=48.33 E-value=14 Score=35.32 Aligned_cols=24 Identities=29% Similarity=0.677 Sum_probs=21.1
Q ss_pred CCCcccCcccccccccchhhhhhc
Q psy6751 29 KNPNQCTFCEKKFNSRNGLYVHLK 52 (392)
Q Consensus 29 ~~~~~C~~C~~~f~~~~~l~~H~~ 52 (392)
..+-.|..||.+|.+.+....||.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md 439 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMD 439 (579)
T ss_pred CCcchhcccccccccchhhhhHhh
Confidence 456899999999999999888887
No 150
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.36 E-value=7.7 Score=29.64 Aligned_cols=11 Identities=27% Similarity=0.957 Sum_probs=5.1
Q ss_pred ccccccccccc
Q psy6751 217 FVCEICGQGYK 227 (392)
Q Consensus 217 ~~C~~C~~~~~ 227 (392)
+.|..||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 44555544443
No 151
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=45.56 E-value=9 Score=22.15 Aligned_cols=19 Identities=16% Similarity=0.354 Sum_probs=11.5
Q ss_pred CCccCCCCcCcccCHHHHH
Q psy6751 271 KKYQCHLCGKGFIHHTSYK 289 (392)
Q Consensus 271 ~~~~C~~C~~~f~~~~~l~ 289 (392)
.-+.|+.|+-.+.+...|.
T Consensus 18 ~id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEEECCCCCeEEccHHHHH
Confidence 3455666666666666554
No 152
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=45.49 E-value=15 Score=25.40 Aligned_cols=13 Identities=31% Similarity=0.858 Sum_probs=7.7
Q ss_pred CcccCcccccccc
Q psy6751 31 PNQCTFCEKKFNS 43 (392)
Q Consensus 31 ~~~C~~C~~~f~~ 43 (392)
|-.|..||+.|.+
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4556666666654
No 153
>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=45.28 E-value=7 Score=27.22 Aligned_cols=13 Identities=23% Similarity=0.562 Sum_probs=6.8
Q ss_pred CccccccCcccCC
Q psy6751 299 RNVKCDICGLALT 311 (392)
Q Consensus 299 ~~~~C~~C~~~~~ 311 (392)
..|.|..|++.|.
T Consensus 52 GIW~C~~C~~~~A 64 (91)
T TIGR00280 52 GIWTCRKCGAKFA 64 (91)
T ss_pred EEEEcCCCCCEEe
Confidence 4455555555544
No 154
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=45.00 E-value=14 Score=26.18 Aligned_cols=15 Identities=33% Similarity=0.807 Sum_probs=9.4
Q ss_pred cccccccccccCCHH
Q psy6751 188 IHECPTCGKKWRTVS 202 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~ 202 (392)
++.|..||..|.+.+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 456777777776643
No 155
>KOG1280|consensus
Probab=44.73 E-value=21 Score=31.58 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=12.4
Q ss_pred CcccccccccccChhhHHHHHH
Q psy6751 149 GWKCFICDAQLTTETSYSVFYT 170 (392)
Q Consensus 149 ~~~C~~C~~~f~~~~~l~~H~~ 170 (392)
.|.|+.|+..-.+...|..|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccCCcccccccchhHHHHHhh
Confidence 4566666655555555555543
No 156
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=44.72 E-value=4.4 Score=24.83 Aligned_cols=16 Identities=19% Similarity=0.661 Sum_probs=4.7
Q ss_pred ccccccccccCCHHHH
Q psy6751 189 HECPTCGKKWRTVSEL 204 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l 204 (392)
|+|+.|...|=..-++
T Consensus 22 y~C~~C~~~FC~dCD~ 37 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDV 37 (51)
T ss_dssp E--TTTT--B-HHHHH
T ss_pred EECCCCCCccccCcCh
Confidence 4444444444433333
No 157
>KOG3408|consensus
Probab=44.32 E-value=12 Score=27.50 Aligned_cols=35 Identities=6% Similarity=0.121 Sum_probs=28.0
Q ss_pred cccccCcccccccccccChhhHHHHHHHhhccccc
Q psy6751 144 ESEVLGWKCFICDAQLTTETSYSVFYTMLSQSGVL 178 (392)
Q Consensus 144 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 178 (392)
-++...|+|-.|.+-|.+...|..|++..-|...+
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRv 86 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRV 86 (129)
T ss_pred CCCCceeehhhhhhhhcchHHHHHHHhccHHHHHH
Confidence 34455699999999999999999998877665543
No 158
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.95 E-value=14 Score=26.39 Aligned_cols=27 Identities=15% Similarity=0.258 Sum_probs=21.1
Q ss_pred cCccccccCCCchhhhccceecccCCCCcccCccccccc
Q psy6751 4 TCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFN 42 (392)
Q Consensus 4 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~ 42 (392)
+|+.|++.|-. .+..|..|++||++|+
T Consensus 11 idPetg~KFYD------------LNrdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYD------------LNRDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhc------------cCCCccccCcccccch
Confidence 57788888753 2457899999999995
No 159
>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=43.71 E-value=12 Score=35.09 Aligned_cols=30 Identities=23% Similarity=0.427 Sum_probs=22.0
Q ss_pred CccccCccchhccCchHHHhhhhhccCCCC
Q psy6751 327 RPHECSVCGKRFAKKWNAQVHKKKVHGLDV 356 (392)
Q Consensus 327 ~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~ 356 (392)
+-..|+.|.+.|.....+..|+...|....
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 345777788888888888888887776643
No 160
>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=43.20 E-value=12 Score=28.32 Aligned_cols=25 Identities=40% Similarity=0.770 Sum_probs=14.4
Q ss_pred cccccCcccCCChHHHHHHHHHhcCCCc
Q psy6751 301 VKCDICGLALTTKSHLNRHMLVHTGDRP 328 (392)
Q Consensus 301 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~ 328 (392)
..|-+||+.|.. |++|+..|+|..|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 668888887754 4788888877544
No 161
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=42.78 E-value=13 Score=18.92 Aligned_cols=9 Identities=33% Similarity=0.604 Sum_probs=5.2
Q ss_pred ccccccccc
Q psy6751 150 WKCFICDAQ 158 (392)
Q Consensus 150 ~~C~~C~~~ 158 (392)
..|..|+..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 356666653
No 162
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=42.47 E-value=16 Score=30.58 Aligned_cols=58 Identities=21% Similarity=0.474 Sum_probs=26.1
Q ss_pred CcccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCCh
Q psy6751 187 LIHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQK 257 (392)
Q Consensus 187 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 257 (392)
..|.|..|+..+-. +.-.....-.|..|.+.|.-.-. ...=|..-|.|+.|+..|...
T Consensus 111 rqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rYDPVP~-----dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 111 RQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRYDPVPC-----DKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeeccccchHHHh--------ccCcccccccccccccccCCCcc-----ccccceeeeecccccccchhh
Confidence 35777777654332 11111223456666665532210 001133345666666666544
No 163
>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=42.37 E-value=5.9 Score=27.54 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=6.4
Q ss_pred CccccccCcccCC
Q psy6751 299 RNVKCDICGLALT 311 (392)
Q Consensus 299 ~~~~C~~C~~~~~ 311 (392)
..|.|..|++.|.
T Consensus 52 GIW~C~~C~~~~A 64 (90)
T PF01780_consen 52 GIWKCKKCGKKFA 64 (90)
T ss_dssp TEEEETTTTEEEE
T ss_pred EEeecCCCCCEEe
Confidence 3355555555443
No 164
>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=42.20 E-value=12 Score=18.85 Aligned_cols=8 Identities=38% Similarity=1.240 Sum_probs=4.5
Q ss_pred CccCCCCc
Q psy6751 272 KYQCHLCG 279 (392)
Q Consensus 272 ~~~C~~C~ 279 (392)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35565555
No 165
>PRK14873 primosome assembly protein PriA; Provisional
Probab=41.60 E-value=13 Score=36.96 Aligned_cols=8 Identities=38% Similarity=1.020 Sum_probs=3.8
Q ss_pred cccccCcc
Q psy6751 301 VKCDICGL 308 (392)
Q Consensus 301 ~~C~~C~~ 308 (392)
+.|+.|+.
T Consensus 423 ~~Cp~Cgs 430 (665)
T PRK14873 423 WRCPRCGS 430 (665)
T ss_pred ccCCCCcC
Confidence 44555543
No 166
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=41.19 E-value=7.3 Score=20.41 Aligned_cols=17 Identities=29% Similarity=0.667 Sum_probs=6.9
Q ss_pred ccCcccccccccchhhhh
Q psy6751 33 QCTFCEKKFNSRNGLYVH 50 (392)
Q Consensus 33 ~C~~C~~~f~~~~~l~~H 50 (392)
.|-.|++.| .....+.|
T Consensus 2 sCiDC~~~F-~~~~y~~H 18 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSH 18 (28)
T ss_dssp EETTTTEEE-EGGGTTT-
T ss_pred eeecCCCCc-CcCCcCCC
Confidence 344455444 33333334
No 167
>KOG2636|consensus
Probab=40.78 E-value=37 Score=31.32 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=25.1
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCcccccccccccCHHHHHHHH
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHV 236 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~ 236 (392)
+.|..|++.+.....|..|.. ...|..|++.|.++..-..|+
T Consensus 250 l~~~g~erlk~al~alglk~g------Gt~~~ra~rlf~Tk~~~l~~L 291 (497)
T KOG2636|consen 250 LYCLGCERLKSALTALGLKCG------GTLHERAQRLFSTKSKSLSHL 291 (497)
T ss_pred HHhhchhHHHHHHHHHHHhcC------CeecHHHHhhhhhcCcchhhh
Confidence 456666666666666666642 245666777776665554443
No 168
>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=40.53 E-value=7.1 Score=21.77 Aligned_cols=32 Identities=25% Similarity=0.617 Sum_probs=18.4
Q ss_pred cCccccccCCCchhhhccceecccCCCCcccCccccccc
Q psy6751 4 TCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFN 42 (392)
Q Consensus 4 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~ 42 (392)
.|+.|.+.+.+..+-+-|. .+..|+.||-.+.
T Consensus 1 lC~~C~~Ey~~p~~RR~~~-------~~isC~~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHY-------QFISCTNCGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT--------TT--BTTCC-SCC
T ss_pred CCHHHHHHHcCCCCCcccC-------cCccCCCCCCCEE
Confidence 3778888887776644443 3478999997654
No 169
>KOG4377|consensus
Probab=39.48 E-value=21 Score=32.37 Aligned_cols=26 Identities=19% Similarity=0.272 Sum_probs=19.1
Q ss_pred ccc--CccchhccCchHHHhhhhhccCC
Q psy6751 329 HEC--SVCGKRFAKKWNAQVHKKKVHGL 354 (392)
Q Consensus 329 ~~C--~~C~~~f~~~~~l~~H~~~~H~~ 354 (392)
|.| .-|+..+...+++.-|.+.+-.+
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhhh
Confidence 456 34888999999998887776443
No 170
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.98 E-value=18 Score=22.49 Aligned_cols=27 Identities=19% Similarity=0.595 Sum_probs=18.6
Q ss_pred ccCccccccCCCchhhhccceecccCCCCcccCccccccc
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFN 42 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~ 42 (392)
-+|..|++.|... +..+.|+.|+..+.
T Consensus 6 ~~C~~Cg~~~~~~-------------dDiVvCp~CgapyH 32 (54)
T PF14446_consen 6 CKCPVCGKKFKDG-------------DDIVVCPECGAPYH 32 (54)
T ss_pred ccChhhCCcccCC-------------CCEEECCCCCCccc
Confidence 4688888888643 33477888876654
No 171
>KOG4377|consensus
Probab=38.42 E-value=12 Score=33.93 Aligned_cols=22 Identities=23% Similarity=0.226 Sum_probs=16.9
Q ss_pred ccCcccCCChHHHHHHHHHhcC
Q psy6751 304 DICGLALTTKSHLNRHMLVHTG 325 (392)
Q Consensus 304 ~~C~~~~~~~~~l~~H~~~h~~ 325 (392)
.-|+..+.+.+.+..|.+.|-.
T Consensus 407 ~Gc~~tl~s~sqm~shkrkheR 428 (480)
T KOG4377|consen 407 LGCEATLYSVSQMASHKRKHER 428 (480)
T ss_pred cCCceEEEehhhhhhhhhhhhh
Confidence 3488888888888888877753
No 172
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=38.15 E-value=10 Score=26.45 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=6.6
Q ss_pred CccccccCcccCC
Q psy6751 299 RNVKCDICGLALT 311 (392)
Q Consensus 299 ~~~~C~~C~~~~~ 311 (392)
..|.|..|++.|.
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PRK03976 53 GIWECRKCGAKFA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 4455555555443
No 173
>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=37.72 E-value=5.8 Score=26.37 Aligned_cols=14 Identities=14% Similarity=0.508 Sum_probs=5.7
Q ss_pred CcccccccccccCH
Q psy6751 216 PFVCEICGQGYKMK 229 (392)
Q Consensus 216 ~~~C~~C~~~~~~~ 229 (392)
...|..|+......
T Consensus 41 ~v~Cg~C~~~~~~~ 54 (71)
T PF05495_consen 41 RVICGKCRTEQPID 54 (71)
T ss_dssp EEEETTT--EEES-
T ss_pred CeECCCCCCccChh
Confidence 44555555554443
No 174
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=37.54 E-value=6.6 Score=30.12 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=10.8
Q ss_pred CccccccCcccCCChHHH
Q psy6751 299 RNVKCDICGLALTTKSHL 316 (392)
Q Consensus 299 ~~~~C~~C~~~~~~~~~l 316 (392)
+.-.|..|++.|++...+
T Consensus 27 RRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 27 RRRECLECHERFTTFERA 44 (147)
T ss_pred ecccCCccCCccceeeec
Confidence 335577777777665443
No 175
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=37.43 E-value=5.7 Score=22.31 Aligned_cols=11 Identities=36% Similarity=0.978 Sum_probs=4.9
Q ss_pred cCCCccccccC
Q psy6751 296 SGERNVKCDIC 306 (392)
Q Consensus 296 ~~~~~~~C~~C 306 (392)
.|...|.|..|
T Consensus 25 ~G~qryrC~~C 35 (36)
T PF03811_consen 25 SGHQRYRCKDC 35 (36)
T ss_pred CCCEeEecCcC
Confidence 34444444444
No 176
>COG1773 Rubredoxin [Energy production and conversion]
Probab=37.31 E-value=12 Score=23.22 Aligned_cols=13 Identities=15% Similarity=0.815 Sum_probs=8.5
Q ss_pred CccCccccccCCC
Q psy6751 2 KYTCDYCTRLFRR 14 (392)
Q Consensus 2 ~~~C~~C~~~f~~ 14 (392)
.|+|..|++.|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4667777777654
No 177
>KOG1842|consensus
Probab=36.56 E-value=31 Score=31.73 Aligned_cols=28 Identities=14% Similarity=0.129 Sum_probs=25.3
Q ss_pred ccccCccchhccCchHHHhhhhhccCCC
Q psy6751 328 PHECSVCGKRFAKKWNAQVHKKKVHGLD 355 (392)
Q Consensus 328 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 355 (392)
-|.|++|...|.....|..|+...|+..
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 4899999999999999999999999854
No 178
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=35.91 E-value=20 Score=21.74 Aligned_cols=14 Identities=21% Similarity=0.714 Sum_probs=6.6
Q ss_pred CccccccCcccCCC
Q psy6751 299 RNVKCDICGLALTT 312 (392)
Q Consensus 299 ~~~~C~~C~~~~~~ 312 (392)
+.+.|..||..|..
T Consensus 3 k~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 3 KTLTCKDCGAEFVF 16 (49)
T ss_pred eeEEcccCCCeEEE
Confidence 33445555554443
No 179
>KOG0782|consensus
Probab=35.89 E-value=14 Score=34.93 Aligned_cols=50 Identities=26% Similarity=0.535 Sum_probs=31.7
Q ss_pred HHHHHHHHhcCCCccccccCcccCCChHHHHHHHHHhcCCC-ccccCccchhccCch
Q psy6751 287 SYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLVHTGDR-PHECSVCGKRFAKKW 342 (392)
Q Consensus 287 ~l~~H~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~-~~~C~~C~~~f~~~~ 342 (392)
.|.+|.=+|.-...-+|..|++.|.++-. .|..+. ...|.+|...|..+.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~------FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFF------FHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhhee------eccccEEEEEehHHHHHhhcch
Confidence 45566555544445568888888865532 333332 368899988888776
No 180
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=35.75 E-value=20 Score=26.91 Aligned_cols=26 Identities=27% Similarity=0.331 Sum_probs=19.6
Q ss_pred cccCccchhccCchHHHhhhhhccCCCCC
Q psy6751 329 HECSVCGKRFAKKWNAQVHKKKVHGLDVP 357 (392)
Q Consensus 329 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~ 357 (392)
..|..+|+.|. .|.+|+.+++|.-+.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTPd 102 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTPD 102 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCHH
Confidence 46888888775 788888888887543
No 181
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=35.44 E-value=9.3 Score=29.36 Aligned_cols=15 Identities=33% Similarity=0.510 Sum_probs=8.8
Q ss_pred ccccccCcccCCChH
Q psy6751 300 NVKCDICGLALTTKS 314 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~ 314 (392)
.-.|..|+..|++..
T Consensus 28 RReC~~C~~RFTTfE 42 (156)
T COG1327 28 RRECLECGERFTTFE 42 (156)
T ss_pred hhcccccccccchhh
Confidence 345666666666544
No 182
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=34.78 E-value=22 Score=26.21 Aligned_cols=13 Identities=15% Similarity=0.217 Sum_probs=8.9
Q ss_pred cccccccccccCC
Q psy6751 188 IHECPTCGKKWRT 200 (392)
Q Consensus 188 ~~~C~~C~~~f~~ 200 (392)
.+.|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PRK12380 70 QAWCWDCSQVVEI 82 (113)
T ss_pred EEEcccCCCEEec
Confidence 4677777776664
No 183
>PRK05580 primosome assembly protein PriA; Validated
Probab=34.77 E-value=27 Score=35.03 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=6.3
Q ss_pred CccccccCccc
Q psy6751 299 RNVKCDICGLA 309 (392)
Q Consensus 299 ~~~~C~~C~~~ 309 (392)
.|..|+.|+..
T Consensus 420 ~~~~Cp~Cg~~ 430 (679)
T PRK05580 420 IPKACPECGST 430 (679)
T ss_pred CCCCCCCCcCC
Confidence 34557777643
No 184
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=33.93 E-value=3.6 Score=40.09 Aligned_cols=56 Identities=25% Similarity=0.635 Sum_probs=32.8
Q ss_pred cccccccccCCHHHHHHHHhhcCCCCCc-ccccccccccCHHHHHHHHhhhcCCCCeecCcccc
Q psy6751 190 ECPTCGKKWRTVSELNAHIQTHSDLRPF-VCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNK 252 (392)
Q Consensus 190 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~-~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 252 (392)
.|..||-.|+-...|=--.....- +.| .|+.|.+.|.+....+-|. .|.-|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM-~~F~lC~~C~~EY~dP~nRRfHA------Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSM-ADFPLCPFCDKEYKDPLNRRFHA------QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCcc-ccCcCCHHHHHHhcCcccccccc------ccccCcccCC
Confidence 488888888766554322111111 112 4888888777776555442 4566888875
No 185
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=33.81 E-value=33 Score=25.79 Aligned_cols=13 Identities=15% Similarity=0.764 Sum_probs=6.0
Q ss_pred CCeecCccccccC
Q psy6751 243 HPFTCHFCNKSFT 255 (392)
Q Consensus 243 ~~~~C~~C~~~~~ 255 (392)
+.|.|.+|..++.
T Consensus 79 ~lYeCnIC~etS~ 91 (140)
T PF05290_consen 79 KLYECNICKETSA 91 (140)
T ss_pred CceeccCcccccc
Confidence 3445555544443
No 186
>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=33.12 E-value=15 Score=35.33 Aligned_cols=28 Identities=25% Similarity=0.623 Sum_probs=18.1
Q ss_pred hcCCCCeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCc
Q psy6751 239 HSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKG 281 (392)
Q Consensus 239 h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 281 (392)
|.......|.+||... ..+..|+.|+..
T Consensus 235 h~~~~~l~Ch~Cg~~~---------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 235 HKKEGKLRCHYCGYQE---------------PIPKTCPQCGSE 262 (505)
T ss_pred ecCCCeEEcCCCcCcC---------------CCCCCCCCCCCC
Confidence 3445567788887663 335678888764
No 187
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=32.93 E-value=39 Score=28.46 Aligned_cols=75 Identities=19% Similarity=0.386 Sum_probs=47.2
Q ss_pred CHHHHHHHHhhcCCC-----CCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCChHHHHHHHHHhcCCCCcc
Q psy6751 200 TVSELNAHIQTHSDL-----RPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQ 274 (392)
Q Consensus 200 ~~~~l~~H~~~h~~~-----~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~ 274 (392)
+..+|+..-..+.+. +.|.|..|+...=. +.-..+..-+|..|.+.|.-... ...-|-..|.
T Consensus 91 Te~Nlrm~d~a~~~~ip~~drqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rYDPVP~-----dkmwG~aef~ 157 (278)
T PF15135_consen 91 TEENLRMFDDAQENLIPSVDRQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRYDPVPC-----DKMWGIAEFH 157 (278)
T ss_pred hHHHHHHhhhhhhccccccceeeeccccchHHHh--------ccCcccccccccccccccCCCcc-----ccccceeeee
Confidence 556777666655444 67999999653211 22223344579999888754321 1223445699
Q ss_pred CCCCcCcccCHHH
Q psy6751 275 CHLCGKGFIHHTS 287 (392)
Q Consensus 275 C~~C~~~f~~~~~ 287 (392)
|+.|+..|.....
T Consensus 158 C~~C~h~F~G~~q 170 (278)
T PF15135_consen 158 CPKCRHNFRGFAQ 170 (278)
T ss_pred cccccccchhhhh
Confidence 9999999987754
No 188
>KOG1044|consensus
Probab=32.71 E-value=11 Score=35.87 Aligned_cols=35 Identities=34% Similarity=0.722 Sum_probs=19.7
Q ss_pred cccccCcccCCChHHHHHHHHHhcCCCcc-----ccCccchhccCch
Q psy6751 301 VKCDICGLALTTKSHLNRHMLVHTGDRPH-----ECSVCGKRFAKKW 342 (392)
Q Consensus 301 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~-----~C~~C~~~f~~~~ 342 (392)
.+|..|.+.++.+.. ..|.+.| +|..|+..|....
T Consensus 193 vkc~~c~~fisgkvL-------qag~kh~HPtCARCsRCgqmF~eGE 232 (670)
T KOG1044|consen 193 VKCEECEKFISGKVL-------QAGDKHFHPTCARCSRCGQMFGEGE 232 (670)
T ss_pred eehHHhhhhhhhhhh-------hccCcccCcchhhhhhhccccccch
Confidence 457777766554331 1222333 6777888887555
No 189
>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=32.66 E-value=16 Score=21.34 Aligned_cols=6 Identities=50% Similarity=1.353 Sum_probs=2.0
Q ss_pred ccccCc
Q psy6751 302 KCDICG 307 (392)
Q Consensus 302 ~C~~C~ 307 (392)
.|+.||
T Consensus 21 vC~~CG 26 (43)
T PF08271_consen 21 VCPNCG 26 (43)
T ss_dssp EETTT-
T ss_pred ECCCCC
Confidence 333333
No 190
>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=32.64 E-value=28 Score=21.65 Aligned_cols=10 Identities=30% Similarity=0.807 Sum_probs=5.9
Q ss_pred cccccccccc
Q psy6751 189 HECPTCGKKW 198 (392)
Q Consensus 189 ~~C~~C~~~f 198 (392)
..|+.|+..+
T Consensus 23 V~Cp~CGael 32 (54)
T TIGR01206 23 VICDECGAEL 32 (54)
T ss_pred EeCCCCCCEE
Confidence 4566666554
No 191
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.50 E-value=19 Score=29.80 Aligned_cols=18 Identities=22% Similarity=0.545 Sum_probs=13.1
Q ss_pred CCccCccccccCCCchhh
Q psy6751 1 KKYTCDYCTRLFRRPGEV 18 (392)
Q Consensus 1 k~~~C~~C~~~f~~~~~l 18 (392)
+.+.|++|+..|.....+
T Consensus 18 k~ieCPvC~tkFkkeev~ 35 (267)
T COG1655 18 KTIECPVCNTKFKKEEVK 35 (267)
T ss_pred ceeccCcccchhhhhhee
Confidence 356899999999765433
No 192
>KOG4317|consensus
Probab=32.28 E-value=23 Score=30.88 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=17.6
Q ss_pred cccCcccccccccchhhhhh
Q psy6751 32 NQCTFCEKKFNSRNGLYVHL 51 (392)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~H~ 51 (392)
|+|+.|+..|-+..-++.|-
T Consensus 20 YtCPRCn~~YCsl~CYr~h~ 39 (383)
T KOG4317|consen 20 YTCPRCNLLYCSLKCYRNHK 39 (383)
T ss_pred ccCCCCCccceeeeeecCCC
Confidence 99999999999888888883
No 193
>KOG2272|consensus
Probab=31.95 E-value=25 Score=29.53 Aligned_cols=68 Identities=18% Similarity=0.327 Sum_probs=37.5
Q ss_pred cccccccccccCCHHHHHHHHh----------hcCCCCCcccccccccccCHHHHHHHHhhhcCCCCeecCccccccCCh
Q psy6751 188 IHECPTCGKKWRTVSELNAHIQ----------THSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQK 257 (392)
Q Consensus 188 ~~~C~~C~~~f~~~~~l~~H~~----------~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 257 (392)
-|.|+.|++.+.+...++.--+ ...+...|.|..|...... +.|.---..-|+ --|+|..|++...+.
T Consensus 99 CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~-~~l~fr~d~yH~-yHFkCt~C~keL~sd 176 (332)
T KOG2272|consen 99 CFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDE-QPLTFRGDPYHP-YHFKCTTCGKELTSD 176 (332)
T ss_pred cchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccc-ccccccCCCCCc-cceecccccccccch
Confidence 5899999998888776653211 1112235778877665444 222111011111 126888888877553
No 194
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=31.25 E-value=23 Score=18.69 Aligned_cols=11 Identities=18% Similarity=0.579 Sum_probs=4.4
Q ss_pred ccccccccccc
Q psy6751 188 IHECPTCGKKW 198 (392)
Q Consensus 188 ~~~C~~C~~~f 198 (392)
.|.|..|++.+
T Consensus 15 ~Y~C~~Cdf~l 25 (30)
T PF07649_consen 15 FYRCSECDFDL 25 (30)
T ss_dssp EEE-TTT----
T ss_pred eEECccCCCcc
Confidence 57788877654
No 195
>KOG1842|consensus
Probab=31.00 E-value=15 Score=33.67 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=24.6
Q ss_pred CCcccCcccccccccchhhhhhcccccccc
Q psy6751 30 NPNQCTFCEKKFNSRNGLYVHLKKVHNVEY 59 (392)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~ 59 (392)
.-|.|++|...|.+...|..|+...|..+.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 468888998888888888888887787654
No 196
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=30.67 E-value=15 Score=22.97 Aligned_cols=29 Identities=21% Similarity=0.497 Sum_probs=21.0
Q ss_pred hhhccceecccCCCCcccCcccccccccchhhhh
Q psy6751 17 EVKNHVLVKHLGKNPNQCTFCEKKFNSRNGLYVH 50 (392)
Q Consensus 17 ~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H 50 (392)
.|...++..| +-|-.||..|.+...|..+
T Consensus 18 ~l~~YLR~~~-----~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 18 KLLSYLREEH-----NYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred HHHHHHHhhC-----ceeeeeCCccCCHHHHHhC
Confidence 3445555545 7899999999988887655
No 197
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=30.66 E-value=32 Score=21.70 Aligned_cols=30 Identities=13% Similarity=0.305 Sum_probs=11.8
Q ss_pred CccCCCCcCcccCHHHHHHHHHHhcCCCcccccc
Q psy6751 272 KYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDI 305 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~ 305 (392)
|++...|+..|.... +...+ ...+..+|++
T Consensus 24 PV~s~~C~H~fek~a-I~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEA-ILQYI---QRNGSKRCPV 53 (57)
T ss_dssp EEEESSS--EEEHHH-HHHHC---TTTS-EE-SC
T ss_pred CcCcCCCCCeecHHH-HHHHH---HhcCCCCCCC
Confidence 455556666664443 22333 2234455555
No 198
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=30.48 E-value=21 Score=27.50 Aligned_cols=10 Identities=30% Similarity=1.235 Sum_probs=5.2
Q ss_pred CccCCCCcCcc
Q psy6751 272 KYQCHLCGKGF 282 (392)
Q Consensus 272 ~~~C~~C~~~f 282 (392)
+|.|. |+..|
T Consensus 117 ~Y~C~-C~q~~ 126 (156)
T COG3091 117 PYRCQ-CQQHY 126 (156)
T ss_pred eEEee-cCCcc
Confidence 45555 55554
No 199
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=30.28 E-value=18 Score=23.69 Aligned_cols=9 Identities=44% Similarity=1.169 Sum_probs=2.5
Q ss_pred cccCcccCC
Q psy6751 303 CDICGLALT 311 (392)
Q Consensus 303 C~~C~~~~~ 311 (392)
|..|++.|.
T Consensus 12 C~~C~~~F~ 20 (69)
T PF01363_consen 12 CMICGKKFS 20 (69)
T ss_dssp -TTT--B-B
T ss_pred CcCcCCcCC
Confidence 555555553
No 200
>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=30.23 E-value=39 Score=22.07 Aligned_cols=13 Identities=38% Similarity=0.848 Sum_probs=6.7
Q ss_pred CCccccccccccc
Q psy6751 215 RPFVCEICGQGYK 227 (392)
Q Consensus 215 ~~~~C~~C~~~~~ 227 (392)
+.|.|+.||..+.
T Consensus 45 r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 45 RVFTCPNCGFEMD 57 (69)
T ss_pred ceEEcCCCCCEEC
Confidence 3455555555543
No 201
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=30.13 E-value=15 Score=25.17 Aligned_cols=38 Identities=16% Similarity=0.517 Sum_probs=14.4
Q ss_pred CccCccccccCCCchhhhccceecccCCCCcccCccccccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSR 44 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~ 44 (392)
-|.|++|+..=.-.-.|..- .+.....|..|+..|...
T Consensus 22 ~F~CPfC~~~~sV~v~idkk-----~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKK-----EGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ----TTT--SS-EEEEEETT-----TTEEEEEESSS--EEEEE
T ss_pred eEcCCcCCCCCeEEEEEEcc-----CCEEEEEecCCCCeEEEc
Confidence 47888888432222222111 233447888888777543
No 202
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.82 E-value=31 Score=31.81 Aligned_cols=29 Identities=24% Similarity=0.649 Sum_probs=17.9
Q ss_pred cCCCCcCcccCHHHHHHHHHHhcCCCccccccCcccCCCh
Q psy6751 274 QCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTK 313 (392)
Q Consensus 274 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~ 313 (392)
.|+.||....+. |...|+|..|++.+...
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCcc
Confidence 577777655443 33367777777776644
No 203
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=29.67 E-value=28 Score=28.23 Aligned_cols=40 Identities=20% Similarity=0.428 Sum_probs=24.9
Q ss_pred ccCccccccCCCchhhhccceec---ccC---CCCcccCcccccccccchhh
Q psy6751 3 YTCDYCTRLFRRPGEVKNHVLVK---HLG---KNPNQCTFCEKKFNSRNGLY 48 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~~---H~~---~~~~~C~~C~~~f~~~~~l~ 48 (392)
..|+.|+. .|..|+... |-+ ...+.|..||+++++...+.
T Consensus 15 ~~CPvCg~------~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e 60 (201)
T COG1779 15 IDCPVCGG------TLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLE 60 (201)
T ss_pred ecCCcccc------eeeEEEeeecCCccceEEEEEEEccccCCcccceeecc
Confidence 36999997 444555440 111 22367999999998765443
No 204
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.49 E-value=39 Score=21.13 Aligned_cols=11 Identities=36% Similarity=0.742 Sum_probs=5.8
Q ss_pred ccccCccchhc
Q psy6751 328 PHECSVCGKRF 338 (392)
Q Consensus 328 ~~~C~~C~~~f 338 (392)
.|.|+.||..+
T Consensus 14 ~~~Cp~cGipt 24 (55)
T PF13824_consen 14 NFECPDCGIPT 24 (55)
T ss_pred CCcCCCCCCcC
Confidence 45555555543
No 205
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.28 E-value=34 Score=31.61 Aligned_cols=30 Identities=27% Similarity=0.662 Sum_probs=20.5
Q ss_pred ccccCcccCCChHHHHHHHHHhcCCCccccCccchhccCch
Q psy6751 302 KCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKW 342 (392)
Q Consensus 302 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 342 (392)
.|+.||....+. |..-|+|+.|++.+....
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCccc
Confidence 599998765433 223789999998776544
No 206
>PF12773 DZR: Double zinc ribbon
Probab=29.04 E-value=37 Score=20.44 Aligned_cols=9 Identities=44% Similarity=1.287 Sum_probs=3.8
Q ss_pred ccccccccC
Q psy6751 191 CPTCGKKWR 199 (392)
Q Consensus 191 C~~C~~~f~ 199 (392)
|+.|+..+.
T Consensus 15 C~~CG~~l~ 23 (50)
T PF12773_consen 15 CPHCGTPLP 23 (50)
T ss_pred ChhhcCChh
Confidence 444444333
No 207
>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=29.02 E-value=18 Score=29.44 Aligned_cols=29 Identities=14% Similarity=0.416 Sum_probs=0.0
Q ss_pred cCccccccc-ccccChhhHHHHHHHhhccc
Q psy6751 148 LGWKCFICD-AQLTTETSYSVFYTMLSQSG 176 (392)
Q Consensus 148 ~~~~C~~C~-~~f~~~~~l~~H~~~~~~~~ 176 (392)
..|+|.+|| .+|.....+..||....|..
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~E~rH~~ 129 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQEWRHAY 129 (196)
T ss_dssp ------------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcChhHHHc
Confidence 458999998 78889999999998776653
No 208
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=28.63 E-value=28 Score=19.95 Aligned_cols=14 Identities=29% Similarity=0.740 Sum_probs=9.6
Q ss_pred CccCccccccCCCc
Q psy6751 2 KYTCDYCTRLFRRP 15 (392)
Q Consensus 2 ~~~C~~C~~~f~~~ 15 (392)
||+|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 56777777777644
No 209
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=28.45 E-value=24 Score=25.94 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=8.4
Q ss_pred cccccccccccCCH
Q psy6751 188 IHECPTCGKKWRTV 201 (392)
Q Consensus 188 ~~~C~~C~~~f~~~ 201 (392)
.+.|..|+..|...
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 70 RARCRDCGHEFEPD 83 (113)
T ss_dssp EEEETTTS-EEECH
T ss_pred cEECCCCCCEEecC
Confidence 45677777777653
No 210
>KOG0978|consensus
Probab=28.35 E-value=24 Score=34.88 Aligned_cols=14 Identities=14% Similarity=0.636 Sum_probs=8.7
Q ss_pred ccCCCCcCcccCHH
Q psy6751 273 YQCHLCGKGFIHHT 286 (392)
Q Consensus 273 ~~C~~C~~~f~~~~ 286 (392)
.+|+.|+..+.+..
T Consensus 644 LkCs~Cn~R~Kd~v 657 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAV 657 (698)
T ss_pred eeCCCccCchhhHH
Confidence 66777775555543
No 211
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=28.33 E-value=68 Score=18.57 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=10.2
Q ss_pred ecCcccccc--CChHHHHHHHHHh
Q psy6751 246 TCHFCNKSF--TQKIGLVKHLNIH 267 (392)
Q Consensus 246 ~C~~C~~~~--~~~~~l~~H~~~h 267 (392)
.|+.||..+ ....+...|.+.|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 455555444 2344444454444
No 212
>KOG4167|consensus
Probab=28.20 E-value=14 Score=36.20 Aligned_cols=25 Identities=32% Similarity=0.590 Sum_probs=22.5
Q ss_pred CccCCCCcCcccCHHHHHHHHHHhc
Q psy6751 272 KYQCHLCGKGFIHHTSYKFHQLVHS 296 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~l~~H~~~~~ 296 (392)
-|.|..|++.|....++..||+.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999884
No 213
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=28.02 E-value=30 Score=18.36 Aligned_cols=9 Identities=22% Similarity=0.604 Sum_probs=5.6
Q ss_pred ccccccccc
Q psy6751 189 HECPTCGKK 197 (392)
Q Consensus 189 ~~C~~C~~~ 197 (392)
|.|..|++.
T Consensus 16 Y~C~~c~f~ 24 (30)
T PF03107_consen 16 YHCSECCFT 24 (30)
T ss_pred EEeCCCCCe
Confidence 667666643
No 214
>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=27.72 E-value=34 Score=25.28 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=8.9
Q ss_pred cccccccccccCC
Q psy6751 188 IHECPTCGKKWRT 200 (392)
Q Consensus 188 ~~~C~~C~~~f~~ 200 (392)
...|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 70 ECECEDCSEEVSP 82 (115)
T ss_pred EEEcccCCCEEec
Confidence 4677777776664
No 215
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.60 E-value=23 Score=23.57 Aligned_cols=53 Identities=25% Similarity=0.511 Sum_probs=28.8
Q ss_pred ccccccCcccCCChHHHHHHHHHhcCCCc-cccCccchhccCchHHHhhhhhccCCCCCCCcccccccC
Q psy6751 300 NVKCDICGLALTTKSHLNRHMLVHTGDRP-HECSVCGKRFAKKWNAQVHKKKVHGLDVPGTTHRVMPVP 367 (392)
Q Consensus 300 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~-~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~~~~~~~ 367 (392)
.|+|..|+..|. +..||. +.| -.|+.|+-.+ ++ +...-|+...|+.+-+....
T Consensus 12 ~Y~c~~cg~~~d----vvq~~~----ddplt~ce~c~a~~------kk-~l~~vgi~fKGSGfYvtDsR 65 (82)
T COG2331 12 SYECTECGNRFD----VVQAMT----DDPLTTCEECGARL------KK-LLNAVGIVFKGSGFYVTDSR 65 (82)
T ss_pred EEeecccchHHH----HHHhcc----cCccccChhhChHH------HH-hhccceEEEecceEEEeccc
Confidence 477888876654 333332 233 3677777532 22 22344666666666555554
No 216
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.60 E-value=33 Score=20.94 Aligned_cols=12 Identities=17% Similarity=0.302 Sum_probs=9.0
Q ss_pred CCcccCcccccc
Q psy6751 30 NPNQCTFCEKKF 41 (392)
Q Consensus 30 ~~~~C~~C~~~f 41 (392)
..+.|..|++.+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 458888888765
No 217
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.47 E-value=37 Score=33.67 Aligned_cols=12 Identities=17% Similarity=0.371 Sum_probs=7.3
Q ss_pred ecCccccccCCh
Q psy6751 246 TCHFCNKSFTQK 257 (392)
Q Consensus 246 ~C~~C~~~~~~~ 257 (392)
-|+.||......
T Consensus 43 fC~~CG~~~~~~ 54 (645)
T PRK14559 43 HCPNCGAETGTI 54 (645)
T ss_pred cccccCCcccch
Confidence 477777665443
No 218
>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=26.75 E-value=32 Score=20.01 Aligned_cols=14 Identities=36% Similarity=0.871 Sum_probs=8.4
Q ss_pred ccCccchhccCchH
Q psy6751 330 ECSVCGKRFAKKWN 343 (392)
Q Consensus 330 ~C~~C~~~f~~~~~ 343 (392)
.|..|+..|+.+..
T Consensus 10 ~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 10 ICPVCGRPFTWRKK 23 (42)
T ss_pred cCcccCCcchHHHH
Confidence 46666666665543
No 219
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=26.64 E-value=53 Score=25.88 Aligned_cols=16 Identities=31% Similarity=0.727 Sum_probs=9.7
Q ss_pred CccCCCCcCcccCHHH
Q psy6751 272 KYQCHLCGKGFIHHTS 287 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~ 287 (392)
-|.|+.||+.|.--+.
T Consensus 130 f~~C~~CgkiYW~GsH 145 (165)
T COG1656 130 FYRCPKCGKIYWKGSH 145 (165)
T ss_pred eeECCCCcccccCchH
Confidence 3667777776665443
No 220
>KOG4118|consensus
Probab=26.60 E-value=25 Score=22.55 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=24.8
Q ss_pred cccCcccccccccchhhhhhcccccccc
Q psy6751 32 NQCTFCEKKFNSRNGLYVHLKKVHNVEY 59 (392)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~ 59 (392)
|+|.+|-..-++...+..|+.+.|+...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~~ 66 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKEP 66 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCCC
Confidence 8999999999999999999998887654
No 221
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.50 E-value=36 Score=21.51 Aligned_cols=12 Identities=25% Similarity=0.938 Sum_probs=5.3
Q ss_pred CCCCcccccccc
Q psy6751 213 DLRPFVCEICGQ 224 (392)
Q Consensus 213 ~~~~~~C~~C~~ 224 (392)
..+.|.|+.|.-
T Consensus 28 PIrtymC~eC~~ 39 (68)
T COG4896 28 PIRTYMCPECEH 39 (68)
T ss_pred CceeEechhhHh
Confidence 333444554443
No 222
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.50 E-value=39 Score=25.05 Aligned_cols=13 Identities=23% Similarity=0.695 Sum_probs=8.3
Q ss_pred cccccccccccCC
Q psy6751 188 IHECPTCGKKWRT 200 (392)
Q Consensus 188 ~~~C~~C~~~f~~ 200 (392)
.+.|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 4667777766654
No 223
>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=26.41 E-value=49 Score=31.16 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=21.9
Q ss_pred CCccCCCCcCcccCHHHHHHHHHHhcC
Q psy6751 271 KKYQCHLCGKGFIHHTSYKFHQLVHSG 297 (392)
Q Consensus 271 ~~~~C~~C~~~f~~~~~l~~H~~~~~~ 297 (392)
+-|.|+.|.+.|.+...+..|+...|.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhh
Confidence 357899999999999999999876543
No 224
>PRK10220 hypothetical protein; Provisional
Probab=26.34 E-value=39 Score=24.43 Aligned_cols=29 Identities=21% Similarity=0.708 Sum_probs=16.4
Q ss_pred cccccccccCCHHHHHHHHhhcCCCCCcccccccccccCH
Q psy6751 190 ECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMK 229 (392)
Q Consensus 190 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 229 (392)
.||.|+..|... ....|.|+.|+..+...
T Consensus 5 ~CP~C~seytY~-----------d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYE-----------DNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEc-----------CCCeEECCcccCcCCcc
Confidence 367776665541 22346677777666544
No 225
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=25.66 E-value=58 Score=20.16 Aligned_cols=11 Identities=27% Similarity=1.008 Sum_probs=4.8
Q ss_pred ccCCCCcCccc
Q psy6751 273 YQCHLCGKGFI 283 (392)
Q Consensus 273 ~~C~~C~~~f~ 283 (392)
++|+.||..|.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 44444444443
No 226
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=25.48 E-value=37 Score=21.03 Aligned_cols=9 Identities=44% Similarity=0.918 Sum_probs=4.5
Q ss_pred cccCcccCC
Q psy6751 303 CDICGLALT 311 (392)
Q Consensus 303 C~~C~~~~~ 311 (392)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 445555554
No 227
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=25.42 E-value=35 Score=24.64 Aligned_cols=28 Identities=21% Similarity=0.654 Sum_probs=15.3
Q ss_pred ccccccccCCHHHHHHHHhhcCCCCCcccccccccccCH
Q psy6751 191 CPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMK 229 (392)
Q Consensus 191 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 229 (392)
||.|+..|... ....|.|+.|+..+...
T Consensus 5 CP~C~seytY~-----------dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEYTYH-----------DGTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcceEe-----------cCCeeECcccccccccc
Confidence 66666655542 12236666666665443
No 228
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.38 E-value=28 Score=25.70 Aligned_cols=13 Identities=23% Similarity=0.393 Sum_probs=9.6
Q ss_pred cCccccccccccc
Q psy6751 148 LGWKCFICDAQLT 160 (392)
Q Consensus 148 ~~~~C~~C~~~f~ 160 (392)
..++|..|+..|.
T Consensus 69 ~~~~C~~Cg~~~~ 81 (114)
T PRK03681 69 AECWCETCQQYVT 81 (114)
T ss_pred cEEEcccCCCeee
Confidence 3478999997665
No 229
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.22 E-value=24 Score=31.18 Aligned_cols=36 Identities=31% Similarity=0.645 Sum_probs=17.0
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCccccccccccc
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYK 227 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~ 227 (392)
-.||.||..=. .+.+ +.....+.+-..|..|+....
T Consensus 188 ~~CPvCGs~P~-~s~v--~~~~~~G~RyL~CslC~teW~ 223 (309)
T PRK03564 188 QFCPVCGSMPV-SSVV--QIGTTQGLRYLHCNLCESEWH 223 (309)
T ss_pred CCCCCCCCcch-hhee--eccCCCCceEEEcCCCCCccc
Confidence 45777776422 1111 122223444456777765543
No 230
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.86 E-value=42 Score=20.31 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=7.0
Q ss_pred ccccCccchhccC
Q psy6751 328 PHECSVCGKRFAK 340 (392)
Q Consensus 328 ~~~C~~C~~~f~~ 340 (392)
.|.|+.||+.+..
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 4556666655443
No 231
>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=24.17 E-value=38 Score=19.46 Aligned_cols=33 Identities=21% Similarity=0.433 Sum_probs=14.9
Q ss_pred CccCccccccCCCchhhhccceecccCCCCcccCcccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKF 41 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f 41 (392)
|.+|..|+.-..-...+ ....+.+.|++|+...
T Consensus 2 p~rC~~C~aylNp~~~~-------~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQF-------DDGGKTWICNFCGTKN 34 (40)
T ss_dssp S-B-TTT--BS-TTSEE-------ETTTTEEEETTT--EE
T ss_pred ccccCCCCCEECCcceE-------cCCCCEEECcCCCCcC
Confidence 45677776554433222 2234569999998753
No 232
>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=24.03 E-value=28 Score=21.78 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=14.5
Q ss_pred CccccccCCCchhhhccceecc------cCCCCcccCccccccccc
Q psy6751 5 CDYCTRLFRRPGEVKNHVLVKH------LGKNPNQCTFCEKKFNSR 44 (392)
Q Consensus 5 C~~C~~~f~~~~~l~~H~~~~H------~~~~~~~C~~C~~~f~~~ 44 (392)
|.+|..-=.....+..|..+.- ...+.|.|++|+.+-...
T Consensus 1 C~FC~~n~e~~~~y~sH~lk~~~G~v~CPvLr~y~Cp~CgAtGd~A 46 (55)
T PF05741_consen 1 CVFCRNNGESREVYSSHTLKDPDGRVTCPVLRKYVCPICGATGDNA 46 (55)
T ss_dssp -HHHHHTT--HHHHTSB-SB-TTS-B--TTGGG---TTT---GGG-
T ss_pred CcCCCCCCCCCceEcccEEECCCCCEeCHHHhcCcCCCCcCcCccc
Confidence 4445433334555666766411 123458999999775443
No 233
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.82 E-value=6.4 Score=22.72 Aligned_cols=7 Identities=43% Similarity=1.175 Sum_probs=2.7
Q ss_pred cccccCc
Q psy6751 301 VKCDICG 307 (392)
Q Consensus 301 ~~C~~C~ 307 (392)
|.|..|+
T Consensus 29 y~C~~C~ 35 (40)
T smart00440 29 YVCTKCG 35 (40)
T ss_pred EEeCCCC
Confidence 3333333
No 234
>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=23.67 E-value=32 Score=19.58 Aligned_cols=11 Identities=45% Similarity=1.479 Sum_probs=3.1
Q ss_pred CccCccccccC
Q psy6751 2 KYTCDYCTRLF 12 (392)
Q Consensus 2 ~~~C~~C~~~f 12 (392)
.|-|++|+..|
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 34555555555
No 235
>KOG0717|consensus
Probab=23.64 E-value=45 Score=31.03 Aligned_cols=26 Identities=12% Similarity=0.340 Sum_probs=23.1
Q ss_pred cccccccccccChhhHHHHHHHhhcc
Q psy6751 150 WKCFICDAQLTTETSYSVFYTMLSQS 175 (392)
Q Consensus 150 ~~C~~C~~~f~~~~~l~~H~~~~~~~ 175 (392)
+.|.+|+++|.+...+.+|-....|.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHk 318 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHK 318 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHH
Confidence 89999999999999999997766665
No 236
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=23.43 E-value=58 Score=24.94 Aligned_cols=11 Identities=36% Similarity=1.226 Sum_probs=7.6
Q ss_pred cccccccccCC
Q psy6751 190 ECPTCGKKWRT 200 (392)
Q Consensus 190 ~C~~C~~~f~~ 200 (392)
-|+.|++.|..
T Consensus 5 nC~~CgklF~~ 15 (137)
T TIGR03826 5 NCPKCGRLFVK 15 (137)
T ss_pred cccccchhhhh
Confidence 47777777763
No 237
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.12 E-value=24 Score=35.17 Aligned_cols=26 Identities=23% Similarity=0.692 Sum_probs=17.5
Q ss_pred cCCCCeecCccccccCChHHHHHHHHHhcCCCCccCCCCcCc
Q psy6751 240 SGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKG 281 (392)
Q Consensus 240 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 281 (392)
......+|.+||... .++.|+.||..
T Consensus 406 ~~~~~l~Ch~CG~~~----------------~p~~Cp~Cgs~ 431 (665)
T PRK14873 406 SAGGTPRCRWCGRAA----------------PDWRCPRCGSD 431 (665)
T ss_pred cCCCeeECCCCcCCC----------------cCccCCCCcCC
Confidence 344567788887642 25788888875
No 238
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=22.97 E-value=11 Score=36.89 Aligned_cols=30 Identities=27% Similarity=0.749 Sum_probs=15.6
Q ss_pred cCCCCcCcccCHHHHHHHHHHhcCCCccccccCccc
Q psy6751 274 QCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLA 309 (392)
Q Consensus 274 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 309 (392)
.|+.|.+.+.+....+-|. +|..|+.||-.
T Consensus 153 lC~~C~~EY~dP~nRRfHA------Qp~aCp~CGP~ 182 (750)
T COG0068 153 LCPFCDKEYKDPLNRRFHA------QPIACPKCGPH 182 (750)
T ss_pred CCHHHHHHhcCcccccccc------ccccCcccCCC
Confidence 3555555555555433332 45556666643
No 239
>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=22.45 E-value=39 Score=26.24 Aligned_cols=16 Identities=25% Similarity=0.598 Sum_probs=10.4
Q ss_pred CccCCCCcCcccCHHH
Q psy6751 272 KYQCHLCGKGFIHHTS 287 (392)
Q Consensus 272 ~~~C~~C~~~f~~~~~ 287 (392)
-|.|+.||+.|..-+-
T Consensus 124 f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSH 139 (147)
T ss_pred EEECCCCCCEeccccc
Confidence 4677777777765443
No 240
>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 KOG3214|consensus
Probab=21.89 E-value=34 Score=24.12 Aligned_cols=38 Identities=21% Similarity=0.556 Sum_probs=22.8
Q ss_pred CccCccccccCCCchhhhccceecccCCCCcccCccccccccc
Q psy6751 2 KYTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSR 44 (392)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~ 44 (392)
.|.|.+|+-.-.-.-.| -+.| +.+-..|.+|+.+|.+.
T Consensus 23 ~FnClfcnHek~v~~~~----Dk~~-~iG~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 23 QFNCLFCNHEKSVSCTL----DKKH-NIGKASCRICEESFQTT 60 (109)
T ss_pred eeccCccccccceeeee----hhhc-Ccceeeeeehhhhhccc
Confidence 37888887554322222 2212 34557899999998754
No 242
>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=21.66 E-value=22 Score=31.93 Aligned_cols=43 Identities=23% Similarity=0.366 Sum_probs=21.4
Q ss_pred ccCccccccCCCchhh---hccceecccCCCC-cccCcccccccccc
Q psy6751 3 YTCDYCTRLFRRPGEV---KNHVLVKHLGKNP-NQCTFCEKKFNSRN 45 (392)
Q Consensus 3 ~~C~~C~~~f~~~~~l---~~H~~~~H~~~~~-~~C~~C~~~f~~~~ 45 (392)
+.|..|++.+...... ..|-...|...+. |+|..|++++.+..
T Consensus 253 v~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl~ 299 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISLE 299 (344)
T ss_dssp EEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEESS
T ss_pred EEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeecc
Confidence 6799998776655444 3455554544444 78999999876554
No 243
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.62 E-value=37 Score=24.20 Aligned_cols=24 Identities=21% Similarity=0.203 Sum_probs=20.3
Q ss_pred CCccccccCcccCCChHHHHHHHH
Q psy6751 298 ERNVKCDICGLALTTKSHLNRHML 321 (392)
Q Consensus 298 ~~~~~C~~C~~~~~~~~~l~~H~~ 321 (392)
-..+.|-+|.+.|.+...|..|.+
T Consensus 53 lGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhc
Confidence 345889999999999999999864
No 244
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.38 E-value=42 Score=24.01 Aligned_cols=12 Identities=17% Similarity=0.194 Sum_probs=7.9
Q ss_pred cccCcccccccc
Q psy6751 32 NQCTFCEKKFNS 43 (392)
Q Consensus 32 ~~C~~C~~~f~~ 43 (392)
..|+.||..+..
T Consensus 43 ~~C~~CG~y~~~ 54 (99)
T PRK14892 43 ITCGNCGLYTEF 54 (99)
T ss_pred EECCCCCCccCE
Confidence 667777766553
No 245
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=21.06 E-value=29 Score=27.52 Aligned_cols=19 Identities=16% Similarity=0.216 Sum_probs=14.2
Q ss_pred CCcccCcccccccccchhh
Q psy6751 30 NPNQCTFCEKKFNSRNGLY 48 (392)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~ 48 (392)
..|.|+.||++........
T Consensus 27 ~sf~C~~CGyr~~ev~~~~ 45 (163)
T TIGR00340 27 STYICEKCGYRSTDVYQLE 45 (163)
T ss_pred EEEECCCCCCchhheeEcC
Confidence 4589999999987654443
No 246
>PF14369 zf-RING_3: zinc-finger
Probab=20.94 E-value=54 Score=18.22 Aligned_cols=8 Identities=38% Similarity=1.090 Sum_probs=3.8
Q ss_pred cCcccccc
Q psy6751 247 CHFCNKSF 254 (392)
Q Consensus 247 C~~C~~~~ 254 (392)
|+.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 44444444
No 247
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=20.84 E-value=89 Score=18.07 Aligned_cols=37 Identities=22% Similarity=0.240 Sum_probs=22.8
Q ss_pred ccCccchhccCchHHHhhhhhccCCCCCCCcccccccCCCCCCCc
Q psy6751 330 ECSVCGKRFAKKWNAQVHKKKVHGLDVPGTTHRVMPVPPIGGGEK 374 (392)
Q Consensus 330 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~~~~~~~~~~~~~~ 374 (392)
+|.-||.- -|+++.-.-+.-.....++|+|.....++
T Consensus 3 kC~~CG~~--------GH~~t~k~CP~~~~~~a~~p~~~g~~~ek 39 (40)
T PF15288_consen 3 KCKNCGAF--------GHMRTNKRCPMYCWSGALAPQPVGMTKEK 39 (40)
T ss_pred cccccccc--------cccccCccCCCCCCCCCCCCccccccccc
Confidence 56677742 36665555566666666777777666543
No 248
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.54 E-value=1.2e+02 Score=24.47 Aligned_cols=18 Identities=11% Similarity=0.316 Sum_probs=9.3
Q ss_pred cCCCccccccCcccCCCh
Q psy6751 296 SGERNVKCDICGLALTTK 313 (392)
Q Consensus 296 ~~~~~~~C~~C~~~~~~~ 313 (392)
.+..-|.|+.|...|+..
T Consensus 109 ~~~~~y~C~~~~~r~sfd 126 (176)
T COG1675 109 TENNYYVCPNCHVKYSFD 126 (176)
T ss_pred ccCCceeCCCCCCcccHH
Confidence 344445665565555433
No 249
>KOG2907|consensus
Probab=20.53 E-value=41 Score=24.43 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=5.4
Q ss_pred ccCCCCcCc
Q psy6751 273 YQCHLCGKG 281 (392)
Q Consensus 273 ~~C~~C~~~ 281 (392)
.+|+.||..
T Consensus 75 ~kCpkCghe 83 (116)
T KOG2907|consen 75 HKCPKCGHE 83 (116)
T ss_pred ccCcccCCc
Confidence 566666643
No 250
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.43 E-value=48 Score=29.10 Aligned_cols=32 Identities=28% Similarity=0.493 Sum_probs=21.8
Q ss_pred cccccccccccChhhHHHHHHHhhccccccccccCCCCcccccccccccCCH
Q psy6751 150 WKCFICDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGKKWRTV 201 (392)
Q Consensus 150 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 201 (392)
.+|+.|+..+.......+ -+.|+.|+..|.-.
T Consensus 27 ~~c~~c~~~~~~~~l~~~--------------------~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERN--------------------LEVCPKCDHHMRMD 58 (285)
T ss_pred eECCCCcchhhHHHHHhh--------------------CCCCCCCCCcCcCC
Confidence 588999987665433222 37899999987643
No 251
>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=20.34 E-value=32 Score=20.08 Aligned_cols=16 Identities=44% Similarity=0.937 Sum_probs=9.8
Q ss_pred CccccCccchhccCch
Q psy6751 327 RPHECSVCGKRFAKKW 342 (392)
Q Consensus 327 ~~~~C~~C~~~f~~~~ 342 (392)
.||.|..|+..|-..-
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 4789999999887543
No 252
>PRK12496 hypothetical protein; Provisional
Probab=20.15 E-value=66 Score=25.57 Aligned_cols=27 Identities=44% Similarity=0.843 Sum_probs=17.3
Q ss_pred ccccccccccCCHHHHHHHHhhcCCCCCccccccccccc
Q psy6751 189 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYK 227 (392)
Q Consensus 189 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~ 227 (392)
|.|..|++.|.. +...-.|++||....
T Consensus 128 ~~C~gC~~~~~~------------~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPE------------DYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccC------------CCCCCcCCCCCChhh
Confidence 778889888863 111135888886543
Done!