Query psy11588
Match_columns 459
No_of_seqs 505 out of 3200
Neff 10.6
Searched_HMMs 46136
Date Fri Aug 16 22:32:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11588.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11588hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074|consensus 100.0 8.7E-30 1.9E-34 242.2 2.8 242 182-458 606-933 (958)
2 KOG2462|consensus 99.9 1E-28 2.2E-33 207.5 5.5 135 318-454 128-265 (279)
3 KOG3608|consensus 99.9 4.9E-26 1.1E-30 196.0 13.7 233 182-443 135-397 (467)
4 KOG3608|consensus 99.9 1.7E-25 3.7E-30 192.7 13.2 282 90-404 69-381 (467)
5 KOG2462|consensus 99.9 1.4E-25 3.1E-30 188.7 5.3 133 262-425 129-264 (279)
6 KOG1074|consensus 99.9 3.3E-25 7.1E-30 211.3 6.2 295 89-433 604-936 (958)
7 KOG3623|consensus 99.9 1.6E-23 3.4E-28 196.4 6.7 117 182-312 211-330 (1007)
8 KOG3623|consensus 99.8 1.1E-21 2.4E-26 184.2 7.8 80 289-369 892-971 (1007)
9 KOG3576|consensus 99.6 1.1E-16 2.5E-21 127.8 3.4 116 317-432 114-240 (267)
10 KOG3576|consensus 99.6 2.8E-16 6.1E-21 125.6 3.9 110 290-400 116-237 (267)
11 PLN03086 PRLI-interacting fact 99.2 2.7E-11 5.9E-16 116.1 8.4 146 291-456 407-564 (567)
12 PLN03086 PRLI-interacting fact 99.1 1.8E-10 4E-15 110.5 8.4 96 322-425 455-561 (567)
13 PHA00733 hypothetical protein 99.1 8E-11 1.7E-15 91.8 3.7 55 401-457 70-124 (128)
14 PHA02768 hypothetical protein; 99.0 2.7E-10 5.8E-15 72.2 2.0 44 404-449 5-48 (55)
15 PHA00733 hypothetical protein 98.9 1E-09 2.3E-14 85.6 4.7 54 346-400 71-124 (128)
16 KOG3993|consensus 98.8 5.9E-10 1.3E-14 99.9 -2.2 190 263-453 267-479 (500)
17 PF13465 zf-H2C2_2: Zinc-finge 98.7 7.6E-09 1.7E-13 56.0 2.6 26 419-444 1-26 (26)
18 KOG3993|consensus 98.7 4E-09 8.6E-14 94.7 -0.0 159 262-426 294-480 (500)
19 PHA02768 hypothetical protein; 98.6 2.3E-08 5E-13 63.5 2.3 42 321-364 6-47 (55)
20 PHA00616 hypothetical protein 98.5 4.6E-08 1E-12 58.8 2.0 34 404-437 1-34 (44)
21 PHA00732 hypothetical protein 98.4 2.1E-07 4.6E-12 65.4 2.4 46 376-427 2-47 (79)
22 PF13465 zf-H2C2_2: Zinc-finge 98.4 2.6E-07 5.6E-12 49.9 2.2 25 335-359 1-25 (26)
23 KOG1146|consensus 98.3 7.7E-07 1.7E-11 91.7 5.8 76 376-457 1261-1353(1406)
24 PF05605 zf-Di19: Drought indu 98.2 3.1E-06 6.7E-11 55.3 5.0 36 376-412 3-39 (54)
25 PHA00616 hypothetical protein 98.2 1.3E-06 2.8E-11 52.7 2.4 34 56-95 1-34 (44)
26 PF05605 zf-Di19: Drought indu 98.1 3.8E-06 8.2E-11 54.9 4.3 51 404-457 2-54 (54)
27 PHA00732 hypothetical protein 98.1 2.2E-06 4.7E-11 60.3 2.9 44 404-453 1-45 (79)
28 PF00096 zf-C2H2: Zinc finger, 98.0 5.5E-06 1.2E-10 43.5 2.1 23 433-455 1-23 (23)
29 PF00096 zf-C2H2: Zinc finger, 97.9 7.3E-06 1.6E-10 43.0 1.8 23 405-427 1-23 (23)
30 PF12756 zf-C2H2_2: C2H2 type 97.7 1.7E-05 3.7E-10 59.9 2.5 73 350-427 1-73 (100)
31 PF13894 zf-C2H2_4: C2H2-type 97.7 3.5E-05 7.5E-10 40.9 2.2 23 433-455 1-23 (24)
32 PF13894 zf-C2H2_4: C2H2-type 97.6 4.6E-05 1E-09 40.4 2.0 24 405-428 1-24 (24)
33 PF13912 zf-C2H2_6: C2H2-type 97.6 3.9E-05 8.5E-10 42.0 1.5 25 432-456 1-25 (27)
34 PF12756 zf-C2H2_2: C2H2 type 97.5 5.9E-05 1.3E-09 57.0 2.3 71 323-397 2-72 (100)
35 PF13912 zf-C2H2_6: C2H2-type 97.4 6.2E-05 1.3E-09 41.2 1.3 26 404-429 1-26 (27)
36 COG5189 SFP1 Putative transcri 97.4 4.1E-05 8.9E-10 66.7 0.4 51 403-453 348-419 (423)
37 PF09237 GAGA: GAGA factor; I 97.0 0.00049 1.1E-08 42.4 2.0 35 398-432 18-52 (54)
38 KOG1146|consensus 97.0 0.00023 4.9E-09 74.2 0.9 155 182-341 437-639 (1406)
39 smart00355 ZnF_C2H2 zinc finge 96.9 0.00079 1.7E-08 36.2 2.4 23 433-455 1-23 (26)
40 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00078 1.7E-08 35.5 2.0 23 433-456 1-23 (24)
41 COG5189 SFP1 Putative transcri 96.9 0.00042 9.1E-09 60.6 1.2 60 53-113 346-420 (423)
42 smart00355 ZnF_C2H2 zinc finge 96.8 0.0012 2.5E-08 35.5 2.4 24 405-428 1-24 (26)
43 PF09237 GAGA: GAGA factor; I 96.8 0.00075 1.6E-08 41.7 1.5 35 314-348 18-52 (54)
44 KOG2231|consensus 96.6 0.0053 1.2E-07 60.8 6.7 110 182-315 116-236 (669)
45 PF12874 zf-met: Zinc-finger o 96.5 0.0016 3.4E-08 34.7 1.4 22 433-454 1-22 (25)
46 PF13909 zf-H2C2_5: C2H2-type 96.4 0.0019 4E-08 34.1 1.4 23 405-428 1-23 (24)
47 KOG2231|consensus 96.4 0.0075 1.6E-07 59.7 6.6 103 293-399 117-236 (669)
48 PF12874 zf-met: Zinc-finger o 96.3 0.002 4.4E-08 34.3 1.2 22 405-426 1-22 (25)
49 PRK04860 hypothetical protein; 96.3 0.0019 4.1E-08 52.5 1.4 40 403-446 118-157 (160)
50 KOG2482|consensus 96.1 0.017 3.6E-07 51.5 6.4 65 278-342 130-217 (423)
51 PF12171 zf-C2H2_jaz: Zinc-fin 96.0 0.0013 2.9E-08 35.8 -0.4 23 3-25 2-24 (27)
52 COG5236 Uncharacterized conser 95.9 0.013 2.9E-07 52.1 5.0 129 292-428 152-305 (493)
53 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0063 1.4E-07 33.1 1.0 22 182-203 2-23 (27)
54 KOG2482|consensus 95.3 0.017 3.7E-07 51.4 3.4 109 263-371 195-357 (423)
55 PRK04860 hypothetical protein; 94.4 0.022 4.8E-07 46.4 1.7 39 319-361 118-156 (160)
56 PF13913 zf-C2HC_2: zinc-finge 94.3 0.036 7.8E-07 29.4 1.8 18 406-424 4-21 (25)
57 PF13913 zf-C2HC_2: zinc-finge 94.0 0.047 1E-06 28.9 1.9 21 433-454 3-23 (25)
58 KOG2785|consensus 93.7 0.14 3.1E-06 46.8 5.5 51 403-453 165-241 (390)
59 COG5236 Uncharacterized conser 93.0 0.1 2.2E-06 46.8 3.4 132 263-401 151-307 (493)
60 smart00451 ZnF_U1 U1-like zinc 92.7 0.081 1.8E-06 30.7 1.7 22 432-453 3-24 (35)
61 KOG2785|consensus 92.5 0.49 1.1E-05 43.4 7.1 52 375-426 166-242 (390)
62 KOG2893|consensus 92.1 0.051 1.1E-06 45.8 0.4 41 378-423 13-53 (341)
63 smart00451 ZnF_U1 U1-like zinc 92.0 0.1 2.2E-06 30.2 1.5 22 404-425 3-24 (35)
64 KOG4173|consensus 90.9 0.13 2.9E-06 42.4 1.7 74 349-424 80-166 (253)
65 TIGR00622 ssl1 transcription f 90.0 0.39 8.4E-06 36.1 3.3 77 346-427 13-104 (112)
66 cd00350 rubredoxin_like Rubred 90.0 0.16 3.4E-06 29.0 1.0 9 431-439 16-24 (33)
67 COG4049 Uncharacterized protei 89.3 0.32 7E-06 30.7 2.0 29 53-81 14-42 (65)
68 COG5048 FOG: Zn-finger [Genera 88.9 0.18 4E-06 49.3 1.3 156 55-217 288-454 (467)
69 PF00301 Rubredoxin: Rubredoxi 88.8 0.39 8.4E-06 30.0 2.1 43 2-44 1-43 (47)
70 KOG4173|consensus 88.5 0.39 8.5E-06 39.8 2.6 78 262-342 78-168 (253)
71 KOG2893|consensus 88.4 0.13 2.8E-06 43.5 -0.2 48 403-455 10-58 (341)
72 COG5048 FOG: Zn-finger [Genera 88.3 0.079 1.7E-06 51.9 -1.8 150 290-440 288-454 (467)
73 PF12013 DUF3505: Protein of u 87.8 0.95 2.1E-05 34.5 4.3 25 433-457 81-109 (109)
74 PF09723 Zn-ribbon_8: Zinc rib 86.5 0.29 6.2E-06 29.8 0.6 28 36-63 6-33 (42)
75 PF12013 DUF3505: Protein of u 86.5 1.2 2.6E-05 34.0 4.1 54 375-429 11-109 (109)
76 smart00834 CxxC_CXXC_SSSS Puta 84.8 0.39 8.5E-06 28.9 0.6 29 36-64 6-34 (41)
77 PF03604 DNA_RNApol_7kD: DNA d 83.5 0.54 1.2E-05 26.6 0.8 7 57-63 18-24 (32)
78 cd00730 rubredoxin Rubredoxin; 82.9 0.5 1.1E-05 29.9 0.5 15 3-17 2-16 (50)
79 PHA00626 hypothetical protein 82.6 0.58 1.2E-05 29.8 0.7 13 55-67 22-34 (59)
80 PF09538 FYDLN_acid: Protein o 81.5 1.1 2.3E-05 33.8 2.0 13 403-415 25-37 (108)
81 TIGR00622 ssl1 transcription f 80.9 0.92 2E-05 34.2 1.4 22 56-77 81-102 (112)
82 cd00729 rubredoxin_SM Rubredox 80.5 0.83 1.8E-05 26.3 0.8 10 405-414 3-12 (34)
83 TIGR02098 MJ0042_CXXC MJ0042 f 80.1 0.46 9.9E-06 28.1 -0.3 8 38-45 5-12 (38)
84 PRK00398 rpoP DNA-directed RNA 79.3 0.6 1.3E-05 29.1 -0.0 7 37-43 5-11 (46)
85 COG4049 Uncharacterized protei 78.9 1 2.2E-05 28.5 0.9 30 400-429 13-42 (65)
86 COG1773 Rubredoxin [Energy pro 78.6 1.2 2.6E-05 28.6 1.2 18 2-19 3-20 (55)
87 PF10571 UPF0547: Uncharacteri 76.5 0.83 1.8E-05 24.4 0.0 8 59-66 17-24 (26)
88 smart00659 RPOLCX RNA polymera 75.9 1.2 2.6E-05 27.4 0.6 11 57-67 3-13 (44)
89 TIGR01206 lysW lysine biosynth 75.7 1 2.2E-05 29.0 0.3 9 37-45 4-12 (54)
90 COG1996 RPC10 DNA-directed RNA 75.6 1.1 2.4E-05 28.0 0.4 10 57-66 7-16 (49)
91 PF09986 DUF2225: Uncharacteri 73.2 1.4 3E-05 38.2 0.6 27 1-27 4-30 (214)
92 KOG2186|consensus 72.3 2.6 5.6E-05 36.5 2.0 45 321-368 4-48 (276)
93 PF13717 zinc_ribbon_4: zinc-r 70.5 1.2 2.7E-05 25.9 -0.2 9 57-65 26-34 (36)
94 COG2888 Predicted Zn-ribbon RN 70.2 2.8 6E-05 27.3 1.3 8 404-411 50-57 (61)
95 PF13719 zinc_ribbon_5: zinc-r 70.2 1.2 2.7E-05 26.1 -0.3 10 57-66 26-35 (37)
96 COG1592 Rubrerythrin [Energy p 69.1 2.8 6.2E-05 34.3 1.5 10 402-411 147-156 (166)
97 TIGR02300 FYDLN_acid conserved 68.8 3.9 8.4E-05 31.5 2.0 11 375-385 26-36 (129)
98 smart00734 ZnF_Rad18 Rad18-lik 68.4 4.1 8.8E-05 21.7 1.5 19 406-425 3-21 (26)
99 PF09538 FYDLN_acid: Protein o 66.8 3.2 6.9E-05 31.4 1.3 12 375-386 26-37 (108)
100 PRK00464 nrdR transcriptional 66.5 2.1 4.7E-05 34.6 0.3 14 91-105 29-42 (154)
101 TIGR00373 conserved hypothetic 65.7 5.5 0.00012 32.6 2.6 30 403-441 108-137 (158)
102 PF02892 zf-BED: BED zinc fing 65.7 5.1 0.00011 24.6 1.8 20 433-452 17-40 (45)
103 PRK06266 transcription initiat 65.4 2.8 6E-05 35.1 0.8 14 376-389 118-131 (178)
104 PF12907 zf-met2: Zinc-binding 64.0 4.9 0.00011 24.0 1.4 27 292-318 2-31 (40)
105 smart00614 ZnF_BED BED zinc fi 63.9 5.6 0.00012 25.2 1.8 21 405-425 19-44 (50)
106 KOG4167|consensus 63.3 4.1 8.8E-05 41.0 1.6 29 54-82 790-818 (907)
107 PF09986 DUF2225: Uncharacteri 63.2 3.7 8.1E-05 35.6 1.2 56 90-146 5-60 (214)
108 PF06524 NOA36: NOA36 protein; 62.9 5.3 0.00011 34.8 2.0 13 287-299 138-150 (314)
109 KOG1280|consensus 62.7 14 0.00031 33.7 4.7 36 181-216 79-116 (381)
110 TIGR00373 conserved hypothetic 60.7 8.4 0.00018 31.6 2.8 32 317-357 106-137 (158)
111 smart00531 TFIIE Transcription 59.7 5.2 0.00011 32.3 1.4 11 376-386 100-110 (147)
112 PRK14890 putative Zn-ribbon RN 59.5 3.2 6.9E-05 27.1 0.1 9 90-98 48-56 (59)
113 KOG2186|consensus 59.4 6.6 0.00014 34.1 2.0 46 349-396 4-49 (276)
114 PF15269 zf-C2H2_7: Zinc-finge 59.2 5.3 0.00011 24.1 1.0 24 56-79 20-43 (54)
115 PF08790 zf-LYAR: LYAR-type C2 58.3 4.2 9.1E-05 22.1 0.4 20 3-23 1-20 (28)
116 PRK09678 DNA-binding transcrip 53.1 2.9 6.2E-05 28.8 -0.9 15 402-416 25-41 (72)
117 PF12760 Zn_Tnp_IS1595: Transp 52.8 7.1 0.00015 24.2 0.9 27 36-64 19-45 (46)
118 smart00531 TFIIE Transcription 51.8 14 0.00031 29.8 2.7 36 319-358 98-133 (147)
119 PRK06266 transcription initiat 50.4 14 0.0003 31.0 2.5 30 319-357 116-145 (178)
120 COG1997 RPL43A Ribosomal prote 49.9 6.5 0.00014 27.9 0.4 10 90-99 53-62 (89)
121 COG1198 PriA Primosomal protei 49.4 10 0.00022 39.3 1.9 28 182-219 445-472 (730)
122 PF07754 DUF1610: Domain of un 49.3 11 0.00024 19.7 1.1 10 133-142 15-24 (24)
123 KOG1280|consensus 49.0 14 0.00031 33.7 2.5 58 90-153 79-138 (381)
124 COG1198 PriA Primosomal protei 48.4 11 0.00024 39.1 1.9 40 292-357 445-484 (730)
125 PF13240 zinc_ribbon_2: zinc-r 48.1 6.9 0.00015 20.2 0.2 8 38-45 2-9 (23)
126 PF05191 ADK_lid: Adenylate ki 47.7 13 0.00028 21.7 1.4 32 3-47 2-33 (36)
127 PF08274 PhnA_Zn_Ribbon: PhnA 47.0 8.1 0.00018 21.5 0.4 9 90-98 19-27 (30)
128 COG5151 SSL1 RNA polymerase II 46.6 38 0.00083 30.5 4.6 77 133-219 321-398 (421)
129 COG2331 Uncharacterized protei 46.5 6.7 0.00015 26.9 0.0 14 54-67 10-23 (82)
130 KOG4167|consensus 46.1 5.6 0.00012 40.0 -0.5 28 2-29 792-819 (907)
131 PF07649 C1_3: C1-like domain; 44.3 11 0.00024 20.7 0.7 22 122-143 3-24 (30)
132 PF06524 NOA36: NOA36 protein; 44.2 9.2 0.0002 33.3 0.5 14 204-217 137-150 (314)
133 KOG3507|consensus 43.0 21 0.00045 23.2 1.8 33 35-71 20-52 (62)
134 PF01096 TFIIS_C: Transcriptio 41.8 7.6 0.00017 23.1 -0.2 8 57-64 29-36 (39)
135 COG1592 Rubrerythrin [Energy p 41.8 12 0.00026 30.7 0.8 10 90-99 134-143 (166)
136 PF13453 zf-TFIIB: Transcripti 41.2 10 0.00023 22.7 0.3 18 56-73 19-36 (41)
137 PF07503 zf-HYPF: HypF finger; 40.7 14 0.00031 21.3 0.8 32 4-46 1-32 (35)
138 COG4530 Uncharacterized protei 40.4 15 0.00033 27.3 1.1 13 402-414 24-36 (129)
139 PF02176 zf-TRAF: TRAF-type zi 39.9 13 0.00028 24.4 0.6 41 403-443 8-53 (60)
140 COG5188 PRP9 Splicing factor 3 39.8 44 0.00096 30.7 4.0 71 349-423 239-394 (470)
141 PF14353 CpXC: CpXC protein 39.4 24 0.00051 27.7 2.2 22 348-369 38-59 (128)
142 KOG2272|consensus 39.3 14 0.0003 32.1 0.8 22 178-199 96-117 (332)
143 KOG2807|consensus 39.1 50 0.0011 30.1 4.2 21 290-310 289-309 (378)
144 PF01286 XPA_N: XPA protein N- 38.9 15 0.00033 21.1 0.7 10 38-47 6-15 (34)
145 PF03107 C1_2: C1 domain; Int 38.8 14 0.00029 20.5 0.5 21 37-63 2-22 (30)
146 COG4888 Uncharacterized Zn rib 38.5 9.4 0.0002 27.9 -0.2 10 90-99 46-55 (104)
147 PF05443 ROS_MUCR: ROS/MUCR tr 37.7 20 0.00044 28.2 1.5 20 434-456 74-93 (132)
148 PF04959 ARS2: Arsenite-resist 36.6 14 0.0003 31.9 0.5 26 375-400 77-102 (214)
149 PF04959 ARS2: Arsenite-resist 36.3 23 0.00051 30.5 1.8 28 345-372 74-101 (214)
150 PRK04023 DNA polymerase II lar 36.2 30 0.00064 36.9 2.7 9 321-329 627-635 (1121)
151 KOG2807|consensus 36.2 47 0.001 30.3 3.6 24 404-427 345-368 (378)
152 PRK04023 DNA polymerase II lar 35.8 34 0.00073 36.5 3.1 48 348-442 626-673 (1121)
153 PF14446 Prok-RING_1: Prokaryo 35.6 15 0.00032 23.7 0.3 8 38-45 8-15 (54)
154 PF05443 ROS_MUCR: ROS/MUCR tr 35.5 21 0.00045 28.1 1.2 25 405-432 73-97 (132)
155 TIGR00595 priA primosomal prot 35.1 22 0.00048 35.5 1.7 14 206-219 237-250 (505)
156 KOG2593|consensus 34.6 39 0.00084 32.2 3.0 36 289-328 126-161 (436)
157 PF04810 zf-Sec23_Sec24: Sec23 34.5 23 0.00049 21.2 1.0 27 37-63 4-31 (40)
158 COG3357 Predicted transcriptio 34.3 21 0.00046 25.6 1.0 13 35-47 58-70 (97)
159 PF01363 FYVE: FYVE zinc finge 34.2 17 0.00036 24.8 0.5 24 36-64 10-33 (69)
160 KOG0696|consensus 33.5 21 0.00045 33.9 1.1 59 345-411 70-128 (683)
161 KOG1842|consensus 33.1 24 0.00052 33.6 1.4 34 175-208 9-42 (505)
162 TIGR01384 TFS_arch transcripti 31.9 15 0.00031 27.6 -0.1 38 182-219 63-100 (104)
163 smart00440 ZnF_C2C2 C2C2 Zinc 31.9 18 0.00038 21.7 0.3 7 57-63 29-35 (40)
164 smart00661 RPOL9 RNA polymeras 31.7 19 0.00042 22.7 0.4 9 91-99 21-29 (52)
165 PF15135 UPF0515: Uncharacteri 31.3 26 0.00056 30.5 1.2 69 18-104 95-168 (278)
166 PF13878 zf-C2H2_3: zinc-finge 31.3 51 0.0011 19.8 2.2 10 406-415 15-24 (41)
167 KOG2593|consensus 31.1 55 0.0012 31.3 3.4 17 403-419 127-143 (436)
168 PF13248 zf-ribbon_3: zinc-rib 30.5 21 0.00046 18.9 0.4 6 38-43 5-10 (26)
169 COG0068 HypF Hydrogenase matur 30.5 21 0.00046 36.3 0.7 51 37-99 125-182 (750)
170 PF00412 LIM: LIM domain; Int 29.3 27 0.00059 22.5 0.9 29 34-62 25-53 (58)
171 PF05290 Baculo_IE-1: Baculovi 28.9 43 0.00093 26.2 1.9 58 33-105 78-135 (140)
172 PF05495 zf-CHY: CHY zinc fing 28.2 14 0.0003 25.5 -0.8 28 35-63 41-68 (71)
173 KOG4124|consensus 28.0 11 0.00023 34.5 -1.6 49 403-451 348-417 (442)
174 PRK12380 hydrogenase nickel in 27.7 24 0.00053 27.0 0.4 12 56-67 70-81 (113)
175 cd00065 FYVE FYVE domain; Zinc 27.4 25 0.00055 22.7 0.5 9 38-46 5-13 (57)
176 COG3677 Transposase and inacti 27.2 25 0.00054 27.6 0.5 33 36-68 31-65 (129)
177 PRK00432 30S ribosomal protein 26.8 21 0.00045 22.7 -0.1 10 90-99 37-46 (50)
178 smart00154 ZnF_AN1 AN1-like Zi 26.3 27 0.00058 20.8 0.4 14 2-15 12-25 (39)
179 PRK03824 hypA hydrogenase nick 25.8 29 0.00064 27.5 0.6 14 55-68 69-82 (135)
180 TIGR00595 priA primosomal prot 25.7 45 0.00097 33.4 2.0 9 209-217 253-261 (505)
181 KOG1842|consensus 25.6 39 0.00084 32.2 1.4 26 375-400 15-40 (505)
182 KOG3408|consensus 25.2 41 0.00089 25.7 1.2 21 405-425 58-78 (129)
183 PF04780 DUF629: Protein of un 25.0 51 0.0011 32.2 2.2 26 376-401 58-83 (466)
184 COG3364 Zn-ribbon containing p 24.7 29 0.00063 25.5 0.4 17 1-17 1-17 (112)
185 PF05129 Elf1: Transcription e 24.4 24 0.00051 25.1 -0.1 10 90-99 46-55 (81)
186 PF07975 C1_4: TFIIH C1-like d 24.0 24 0.00052 22.5 -0.1 25 55-79 20-44 (51)
187 COG0068 HypF Hydrogenase matur 23.8 29 0.00064 35.4 0.3 30 183-218 153-182 (750)
188 TIGR00100 hypA hydrogenase nic 23.6 32 0.0007 26.4 0.5 11 57-67 71-81 (115)
189 TIGR03826 YvyF flagellar opero 23.6 1.1E+02 0.0024 24.3 3.5 24 37-66 5-28 (137)
190 KOG0782|consensus 23.4 36 0.00078 33.5 0.8 50 16-70 239-290 (1004)
191 PF14311 DUF4379: Domain of un 23.2 34 0.00073 22.1 0.4 11 57-67 29-39 (55)
192 KOG3408|consensus 22.9 48 0.001 25.3 1.2 30 84-114 51-80 (129)
193 COG4957 Predicted transcriptio 22.8 50 0.0011 25.8 1.3 20 434-456 78-97 (148)
194 COG4896 Uncharacterized protei 22.3 64 0.0014 21.2 1.5 6 349-354 32-37 (68)
195 COG5151 SSL1 RNA polymerase II 22.3 73 0.0016 28.8 2.4 26 54-79 386-411 (421)
196 PRK05580 primosome assembly pr 21.5 57 0.0012 34.1 1.9 13 207-219 406-418 (679)
197 PF12773 DZR: Double zinc ribb 21.4 47 0.001 20.7 0.8 8 38-45 15-22 (50)
198 PF06689 zf-C4_ClpX: ClpX C4-t 21.3 43 0.00094 20.1 0.6 31 37-67 3-35 (41)
199 cd02341 ZZ_ZZZ3 Zinc finger, Z 21.0 56 0.0012 20.5 1.1 21 121-141 2-22 (48)
200 PF01155 HypA: Hydrogenase exp 21.0 26 0.00056 26.8 -0.5 11 57-67 71-81 (113)
201 PF14803 Nudix_N_2: Nudix N-te 20.9 33 0.00071 19.7 0.0 11 262-272 21-31 (34)
202 PF14445 Prok-RING_2: Prokaryo 20.5 18 0.00039 22.6 -1.1 13 35-47 7-19 (57)
203 PF13451 zf-trcl: Probable zin 20.4 64 0.0014 20.4 1.2 9 264-272 5-13 (49)
204 PF04780 DUF629: Protein of un 20.2 70 0.0015 31.3 2.1 21 264-284 58-78 (466)
205 KOG3214|consensus 20.1 52 0.0011 24.1 0.9 8 92-99 49-56 (109)
No 1
>KOG1074|consensus
Probab=99.95 E-value=8.7e-30 Score=242.22 Aligned_cols=242 Identities=21% Similarity=0.416 Sum_probs=158.4
Q ss_pred cccccchhhccChhHHHHhhhhhcCCCccccCCCCCCCchhhHhHHHHHHHHHHhccccCCcccchhhcccceeeecCCC
Q psy11588 182 HSCQKCEESFDNCNNLWSHMFIKHENSDFVCNLCPSHSKVLVRYVHSAVRHMKKHHKLQLSIPKAHNYFRKKTVIHVNKK 261 (459)
Q Consensus 182 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~ 261 (459)
-.|-+|-++..-.+.|+.|.++|.|++||+|.+|++.| ..+.+|+.||-.|.... .-.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAF----tTkGNLkaH~~vHka~p------------------~~R 663 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAF----TTKGNLKAHMSVHKAKP------------------PAR 663 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchh----ccccchhhcccccccCc------------------ccc
Confidence 68999999999999999999999999999999999999 88888999988875422 003
Q ss_pred cccccc---cChhcccCHHHHHHHHhhccCCC-------------CccccccccccCCHHHHHHHHHHHcCCCCcccccc
Q psy11588 262 VNYKCP---DCSAILLSYGGFTSHLDIHSGEK-------------DHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSV 325 (459)
Q Consensus 262 ~~~~C~---~C~~~f~~~~~l~~H~~~h~~~~-------------~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~ 325 (459)
..+.|+ +|-+.|...-.|..|+++|.+.. .-+|..|.+.|.....+..++. .|.+...
T Consensus 664 ~q~ScP~~~ic~~kftn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~s-e~~~~~s----- 737 (958)
T KOG1074|consen 664 VQFSCPSTFICQKKFTNAVTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQIS-EQPSPES----- 737 (958)
T ss_pred ccccCCchhhhcccccccccccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhh-ccCCccc-----
Confidence 468888 89999999888999988887421 1346667777766666666655 2321110
Q ss_pred ccccccChHHHHHHHHHcCCCC----CcccccccccccccchHHHHHhh-----------------------hCCC-Cc-
Q psy11588 326 CGKAFADITNMKVHMRIHTGEK----KYVCETCGASFVQWGSLNQHNLV-----------------------HTAV-NV- 376 (459)
Q Consensus 326 C~~~f~~~~~l~~H~~~h~~~~----~~~C~~C~~~f~~~~~l~~H~~~-----------------------h~~~-~~- 376 (459)
.-....+.+.+.++. +..+..|+..+.....+..+-.. .+.. +.
T Consensus 738 -------~~~~~~~~~t~t~~~~~tp~~~e~~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~ 810 (958)
T KOG1074|consen 738 -------EPDEQMDERTETEELDVTPPPPENSCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQ 810 (958)
T ss_pred -------CCcccccccccccccccCCCccccccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcc
Confidence 001111111122222 34455555555544443333111 1111 22
Q ss_pred ccCCCCCcCCChHHHH----H-HHHh------------hcC------------------------CCCccccccchhccC
Q psy11588 377 VCSYCGNTYKNPKSLE----S-HIRY------------AHT------------------------IRQKSICDVCGKEFK 415 (459)
Q Consensus 377 ~C~~C~~~f~~~~~l~----~-H~~~------------~H~------------------------~~~~~~C~~C~~~f~ 415 (459)
.+..++..-....... . -... .+. ......|.+||+.|.
T Consensus 811 ~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~Fs 890 (958)
T KOG1074|consen 811 ASSFPGEILAPSVNMDPVLWNQETSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFS 890 (958)
T ss_pred cccCCCcCCccccccCchhhcccccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhccc
Confidence 3444443322211000 0 0000 000 011267999999999
Q ss_pred ChHHHHHHHHHhCCCCCcccCccccccCChHHHHHHHHHhcCC
Q psy11588 416 MKKRLKEHMAVHTTDRPFVCDMCPSAFKLKKHLQQHYKVHLKK 458 (459)
Q Consensus 416 ~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~ 458 (459)
..++|..|+++|+++|||.|.+|++.|+.+.+|+.||.+|+..
T Consensus 891 SSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~ 933 (958)
T KOG1074|consen 891 SSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWV 933 (958)
T ss_pred chHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhcccccc
Confidence 9999999999999999999999999999999999999999853
No 2
>KOG2462|consensus
Probab=99.95 E-value=1e-28 Score=207.53 Aligned_cols=135 Identities=31% Similarity=0.660 Sum_probs=120.9
Q ss_pred CCccccccccccccChHHHHHHHHHcCC---CCCcccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHH
Q psy11588 318 VRDHQCSVCGKAFADITNMKVHMRIHTG---EKKYVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESH 394 (459)
Q Consensus 318 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~---~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H 394 (459)
...|+|+.||+.+.+..+|.+|..+|-. .+.+.|+.|++.+.+...|..|+++|+ .+.+|.+||+.|...+.|+.|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~-l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT-LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC-CCcccccccccccchHHhhcc
Confidence 3457777777777777777777777743 567899999999999999999999998 478999999999999999999
Q ss_pred HHhhcCCCCccccccchhccCChHHHHHHHHHhCCCCCcccCccccccCChHHHHHHHHH
Q psy11588 395 IRYAHTIRQKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSAFKLKKHLQQHYKV 454 (459)
Q Consensus 395 ~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~ 454 (459)
+| .|+|++||.|+.|+|.|..+++|+.||++|.+.++|+|..|+|+|..++.|.+|...
T Consensus 207 iR-THTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 207 IR-THTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cc-cccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 99 999999999999999999999999999999999999999999999999999999763
No 3
>KOG3608|consensus
Probab=99.94 E-value=4.9e-26 Score=195.96 Aligned_cols=233 Identities=21% Similarity=0.434 Sum_probs=158.8
Q ss_pred ccc--ccchhhccChhHHHHhhhhhcCC-------------CccccC--CCCCCCchhhHhHHHHHHHHHHhccccCCcc
Q psy11588 182 HSC--QKCEESFDNCNNLWSHMFIKHEN-------------SDFVCN--LCPSHSKVLVRYVHSAVRHMKKHHKLQLSIP 244 (459)
Q Consensus 182 ~~C--~~C~~~f~~~~~l~~H~~~~~~~-------------~~~~C~--~C~~~f~~~~~~~~~l~~H~~~h~~~~~~~~ 244 (459)
|.| ..|+..|.+...|..|+..|..- ..+.|. .|.+.+ .++..|++|++.|.+
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~----~~k~~LreH~r~Hs~------ 204 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHM----GNKYRLREHIRTHSN------ 204 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhh----ccHHHHHHHHHhcCC------
Confidence 566 46999999999999998766421 113344 355665 667777777777765
Q ss_pred cchhhcccceeeecCCCcccccccChhcccCHHHHHHHHhhc--cCCCCccccccccccCCHHHHHHHHHHHcCCCCccc
Q psy11588 245 KAHNYFRKKTVIHVNKKVNYKCPDCSAILLSYGGFTSHLDIH--SGEKDHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQ 322 (459)
Q Consensus 245 ~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h--~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~ 322 (459)
++...|+.|+..|.+...|..|++.. ....+|+|..|.+.|.++..|..|+. .|. ..|+
T Consensus 205 ----------------eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~-rHv--n~yk 265 (467)
T KOG3608|consen 205 ----------------EKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVV-RHV--NCYK 265 (467)
T ss_pred ----------------CeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHH-Hhh--hccc
Confidence 44567777777777777777776533 33456777777777777777777776 343 3477
Q ss_pred cccccccccChHHHHHHHHH-cCCCCCcccccccccccccchHHHHHhhhCCCCcccCC--CCCcCCChHHHHHHHHhhc
Q psy11588 323 CSVCGKAFADITNMKVHMRI-HTGEKKYVCETCGASFVQWGSLNQHNLVHTAVNVVCSY--CGNTYKNPKSLESHIRYAH 399 (459)
Q Consensus 323 C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~~H 399 (459)
|+.|+.+....++|..|++. |..++||+|+.|++.|.+.++|.+|..+|+...|.|+. |.++|.+...|.+|++.+|
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 77777777777777777664 55667777777777777777777777777766777766 7777777777777777666
Q ss_pred CCC--CccccccchhccCChHHHHHHHHHhC------CCCCcccCccccccC
Q psy11588 400 TIR--QKSICDVCGKEFKMKKRLKEHMAVHT------TDRPFVCDMCPSAFK 443 (459)
Q Consensus 400 ~~~--~~~~C~~C~~~f~~~~~l~~H~~~H~------~~~~~~C~~C~~~f~ 443 (459)
.+. .+|.|-.|++.|.+-.+|..|+...+ |-+.|.-.+|.-+|.
T Consensus 346 Eg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~RFtYk~~edG~m 397 (467)
T KOG3608|consen 346 EGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGHKRFTYKVDEDGFM 397 (467)
T ss_pred cCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCCCceeeeeccCcee
Confidence 443 35777777777777777777765433 233455555555554
No 4
>KOG3608|consensus
Probab=99.93 E-value=1.7e-25 Score=192.69 Aligned_cols=282 Identities=21% Similarity=0.373 Sum_probs=219.8
Q ss_pred eeeccc--CCcceeeehhHHhhhhhhccc------------cccccccccccccc-------cceeecC--ccchhhhhh
Q psy11588 90 WFVCKM--CGHRLFMRLSDLRRHMQDYHC------------EFHFDVESCAVSRL-------QDITFPC--EECKELCVL 146 (459)
Q Consensus 90 ~~~C~~--C~~~~f~~~~~l~~H~~~h~~------------~~~~~~~~c~~~~~-------~~~~~~C--~~C~~~f~~ 146 (459)
.++|.. |++..-++..+|.+|.-.|-- ........|...|. ....|.| +.|+..|.+
T Consensus 69 e~qC~w~~C~f~~~~~s~~l~RHvy~H~y~~~l~q~G~~al~~~~dig~c~~~f~~~~~ip~~g~~f~C~WedCe~~F~s 148 (467)
T KOG3608|consen 69 EHQCTWNSCDFRTENSSADLIRHVYFHCYHTKLKQQGKLALDLHPDIGACTAPFRLMEKIPALGQNFRCGWEDCEREFVS 148 (467)
T ss_pred ceeEEeccCCccccchHHHHHhhhhhhhhHHHHHHHHHHHHhcCCCcCcccCCcchhhccccchhhhccChhhcCCcccC
Confidence 466654 776634557899999765420 00111222322222 1134666 789999999
Q ss_pred hhhhhhhccccCCCCCCCCCCccccccccCCCCCCcccc--cchhhccChhHHHHhhhhhcCCCccccCCCCCCCchhhH
Q psy11588 147 SKYCIKHQDCSKAMSTPAPSSESVCIKHSNLIPKCHSCQ--KCEESFDNCNNLWSHMFIKHENSDFVCNLCPSHSKVLVR 224 (459)
Q Consensus 147 ~~~l~~H~~c~~~~~~~~~l~~~~~~~h~~~~~~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~ 224 (459)
...+..|..-..-+- ... ...+..+++|. +.|. .|-+.+.+++.|++|++.|.+++...|+.||.-| +
T Consensus 149 ~~ef~dHV~~H~l~c-eyd----~~~~~~D~~pv-~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F----~ 218 (467)
T KOG3608|consen 149 IVEFQDHVVKHALFC-EYD----IQKTPEDERPV-TMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELF----R 218 (467)
T ss_pred HHHHHHHHHHhhhhh-hhh----hhhCCCCCCce-eeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHh----c
Confidence 999998873211111 000 01111122221 4564 5899999999999999999999999999999999 8
Q ss_pred hHHHHHHHHHHhccccCCcccchhhcccceeeecCCCcccccccChhcccCHHHHHHHHhhccCCCCccccccccccCCH
Q psy11588 225 YVHSAVRHMKKHHKLQLSIPKAHNYFRKKTVIHVNKKVNYKCPDCSAILLSYGGFTSHLDIHSGEKDHCCHICKKVFLRY 304 (459)
Q Consensus 225 ~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 304 (459)
.+..|..|++..+... ..+|.|..|.+.|.+...|..|+..|.. .|+|+.|+.+....
T Consensus 219 ~~tkl~DH~rRqt~l~--------------------~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ 276 (467)
T KOG3608|consen 219 TKTKLFDHLRRQTELN--------------------TNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSA 276 (467)
T ss_pred cccHHHHHHHhhhhhc--------------------CCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCCh
Confidence 8889999987654322 4589999999999999999999998864 59999999999999
Q ss_pred HHHHHHHHHHcCCCCccccccccccccChHHHHHHHHHcCCCCCccccc--ccccccccchHHHHHhhhC-CC---Cccc
Q psy11588 305 RNLVCHIKAVHEKVRDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCET--CGASFVQWGSLNQHNLVHT-AV---NVVC 378 (459)
Q Consensus 305 ~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-~~---~~~C 378 (459)
++|..|++..|...+||+|..|+..|...++|..|...|. +..|.|+. |..+|.+...+.+|.+.++ +. +|.|
T Consensus 277 ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~C 355 (467)
T KOG3608|consen 277 SSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYAC 355 (467)
T ss_pred HHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceee
Confidence 9999999999999999999999999999999999999887 77899988 9999999999999988765 33 7999
Q ss_pred CCCCCcCCChHHHHHHHHhhcCCCCc
Q psy11588 379 SYCGNTYKNPKSLESHIRYAHTIRQK 404 (459)
Q Consensus 379 ~~C~~~f~~~~~l~~H~~~~H~~~~~ 404 (459)
..|++.|++-.+|.+|+...|.-.-|
T Consensus 356 H~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 356 HCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred ecchhhhccchhHHHHHHHhhcccCC
Confidence 99999999999999999988875544
No 5
>KOG2462|consensus
Probab=99.92 E-value=1.4e-25 Score=188.72 Aligned_cols=133 Identities=34% Similarity=0.736 Sum_probs=77.8
Q ss_pred cccccccChhcccCHHHHHHHHhhccC---CCCccccccccccCCHHHHHHHHHHHcCCCCccccccccccccChHHHHH
Q psy11588 262 VNYKCPDCSAILLSYGGFTSHLDIHSG---EKDHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSVCGKAFADITNMKV 338 (459)
Q Consensus 262 ~~~~C~~C~~~f~~~~~l~~H~~~h~~---~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~ 338 (459)
..|+|+.|++.|.+..+|.+|.++|.. .+.+.|++|++.|.+...|..|++ .|. -++.|.+||+.|...+.|+-
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHir-TH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIR-THT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhh-ccC--CCcccccccccccchHHhhc
Confidence 357777777777777777777777643 234555555555555555555555 343 34555555555555555555
Q ss_pred HHHHcCCCCCcccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccCChH
Q psy11588 339 HMRIHTGEKKYVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKK 418 (459)
Q Consensus 339 H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~ 418 (459)
|+++|+||+||.|+.|++.|.+. ++|+.||+ .|.+.++|+|+.|+|+|..++
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADR---------------------------SNLRAHmQ-THS~~K~~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADR---------------------------SNLRAHMQ-THSDVKKHQCPRCGKSFALKS 257 (279)
T ss_pred ccccccCCCCccCCcccchhcch---------------------------HHHHHHHH-hhcCCccccCcchhhHHHHHH
Confidence 55555555555555555555554 55555555 555555566666666666666
Q ss_pred HHHHHHH
Q psy11588 419 RLKEHMA 425 (459)
Q Consensus 419 ~l~~H~~ 425 (459)
.|.+|..
T Consensus 258 yLnKH~E 264 (279)
T KOG2462|consen 258 YLNKHSE 264 (279)
T ss_pred HHHHhhh
Confidence 6665544
No 6
>KOG1074|consensus
Probab=99.91 E-value=3.3e-25 Score=211.33 Aligned_cols=295 Identities=18% Similarity=0.194 Sum_probs=154.1
Q ss_pred ceeecccCCcceeeehhHHhhhhhhccccccccccccccccccceeecCccchhhhhhhhhhhhhccccCCCCCCCCCCc
Q psy11588 89 HWFVCKMCGHRLFMRLSDLRRHMQDYHCEFHFDVESCAVSRLQDITFPCEECKELCVLSKYCIKHQDCSKAMSTPAPSSE 168 (459)
Q Consensus 89 ~~~~C~~C~~~~f~~~~~l~~H~~~h~~~~~~~~~~c~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~c~~~~~~~~~l~~ 168 (459)
.+-+|-+|-+. .+-.+.|+-|.|+|+||+ +|+|.+|++.|.++.+|+.|+..
T Consensus 604 dPNqCiiC~rV-lSC~saLqmHyrtHtGER---------------PFkCKiCgRAFtTkGNLkaH~~v------------ 655 (958)
T KOG1074|consen 604 DPNQCIICLRV-LSCPSALQMHYRTHTGER---------------PFKCKICGRAFTTKGNLKAHMSV------------ 655 (958)
T ss_pred Cccceeeeeec-ccchhhhhhhhhcccCcC---------------ccccccccchhccccchhhcccc------------
Confidence 35789999977 999999999999999986 47788888899999999999843
Q ss_pred cccccccCCCCCCcccc---cchhhccChhHHHHhhhhhcCCCc-------------cccCCCCCCCchhhHhHHHHHHH
Q psy11588 169 SVCIKHSNLIPKCHSCQ---KCEESFDNCNNLWSHMFIKHENSD-------------FVCNLCPSHSKVLVRYVHSAVRH 232 (459)
Q Consensus 169 ~~~~~h~~~~~~~~~C~---~C~~~f~~~~~l~~H~~~~~~~~~-------------~~C~~C~~~f~~~~~~~~~l~~H 232 (459)
|..++.-... +.|+ +|-+.|.+...|..|+++|.+... -+|..|.+.| .....+..+
T Consensus 656 -Hka~p~~R~q--~ScP~~~ic~~kftn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~----~~a~~f~~~ 728 (958)
T KOG1074|consen 656 -HKAKPPARVQ--FSCPSTFICQKKFTNAVTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTF----SDARSFSQQ 728 (958)
T ss_pred -cccCcccccc--ccCCchhhhcccccccccccceEEeecCCCCCCCcccccccchhcccchhhhcc----cccccchhh
Confidence 2223332333 8899 999999999999999999884321 2344454444 333333333
Q ss_pred HHHhccccCCcccchhhcccceeeecC---CCcccccccChhcccCHHHHHHHHhhccCCCCccccccccccCCHHHHHH
Q psy11588 233 MKKHHKLQLSIPKAHNYFRKKTVIHVN---KKVNYKCPDCSAILLSYGGFTSHLDIHSGEKDHCCHICKKVFLRYRNLVC 309 (459)
Q Consensus 233 ~~~h~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 309 (459)
+..+.+..... ........... ...+..+..|+..+.....+..+-..+... .+. +.++.....-..
T Consensus 729 ~se~~~~~s~~-----~~~~~~~t~t~~~~~tp~~~e~~~~~~~~~e~~i~~~g~te~as---a~~--~~vg~~s~~~~~ 798 (958)
T KOG1074|consen 729 ISEQPSPESEP-----DEQMDERTETEELDVTPPPPENSCGRELEGEMAISVRGSTEEAS---ANL--DEVGTVSAAGEA 798 (958)
T ss_pred hhccCCcccCC-----cccccccccccccccCCCccccccccccCcccccccccchhhhh---cCh--hhhcCccccchh
Confidence 33222111000 00000000000 001233334444433333332221111000 000 000000000000
Q ss_pred HHHHHcCCCCcc-ccccccccccChHHHHH-HHHHc---CCCCCcccccccccccc---cchHHHHHhhhC-----C---
Q psy11588 310 HIKAVHEKVRDH-QCSVCGKAFADITNMKV-HMRIH---TGEKKYVCETCGASFVQ---WGSLNQHNLVHT-----A--- 373 (459)
Q Consensus 310 H~~~~h~~~~~~-~C~~C~~~f~~~~~l~~-H~~~h---~~~~~~~C~~C~~~f~~---~~~l~~H~~~h~-----~--- 373 (459)
+ ...++++++. .+..++......-...- =+... .++..- =. -..+.. ...+..--.+-. +
T Consensus 799 ~-~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~-t~--~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~ 874 (958)
T KOG1074|consen 799 G-EEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLA-TK--TNEITPEGPADSVIQSGGVPTLEPSLGRPG 874 (958)
T ss_pred h-hhcccCCCCcccccCCCcCCccccccCchhhcccccccccccc-cc--cccccCCCcchhhhhhccccccCCCCCCCC
Confidence 1 1122333444 44444433222110000 00000 000000 00 000000 000000000000 0
Q ss_pred ---CCcccCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccCChHHHHHHHHHhCCCCCc
Q psy11588 374 ---VNVVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHMAVHTTDRPF 433 (459)
Q Consensus 374 ---~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~ 433 (459)
....|..|++.|.+.+.|+.|++ .|++++||.|.+|++.|..+..|+.||.+|....|+
T Consensus 875 pvnn~h~C~vCgk~FsSSsALqiH~r-THtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 875 PVNNAHVCNVCGKQFSSSAALEIHMR-THTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred cccchhhhccchhcccchHHHHHhhh-cCCCCCCccchhhhhhhhhhhhhhhhhccccccCCC
Confidence 02469999999999999999999 999999999999999999999999999999887654
No 7
>KOG3623|consensus
Probab=99.89 E-value=1.6e-23 Score=196.44 Aligned_cols=117 Identities=26% Similarity=0.474 Sum_probs=95.7
Q ss_pred cccccchhhccChhHHHHhhhhhcCCCcc---ccCCCCCCCchhhHhHHHHHHHHHHhccccCCcccchhhcccceeeec
Q psy11588 182 HSCQKCEESFDNCNNLWSHMFIKHENSDF---VCNLCPSHSKVLVRYVHSAVRHMKKHHKLQLSIPKAHNYFRKKTVIHV 258 (459)
Q Consensus 182 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~---~C~~C~~~f~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~ 258 (459)
..|++|+..+.....|+.|++..|. +.- .|.+|.+.| .++..|.+||.+|....-. . . .....
T Consensus 211 ltcpycdrgykrltslkeHikyrhe-kne~nfsC~lCsytF----AyRtQLErhm~~hkpg~dq----a----~-sltqs 276 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHE-KNEPNFSCMLCSYTF----AYRTQLERHMQLHKPGGDQ----A----I-SLTQS 276 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHh-hCCCCCcchhhhhhh----hhHHHHHHHHHhhcCCCcc----c----c-cccch
Confidence 5799999999999999999987653 223 299999999 9999999999999753200 0 0 00111
Q ss_pred CCCcccccccChhcccCHHHHHHHHhhccCCCCccccccccccCCHHHHHHHHH
Q psy11588 259 NKKVNYKCPDCSAILLSYGGFTSHLDIHSGEKDHCCHICKKVFLRYRNLVCHIK 312 (459)
Q Consensus 259 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 312 (459)
...+.|+|..|++.|.-+-.|+.|+++|.|++||.|+-|++.|....+...||.
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 277 ALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 124579999999999999999999999999999999999999999999999974
No 8
>KOG3623|consensus
Probab=99.85 E-value=1.1e-21 Score=184.19 Aligned_cols=80 Identities=34% Similarity=0.620 Sum_probs=76.7
Q ss_pred CCCccccccccccCCHHHHHHHHHHHcCCCCccccccccccccChHHHHHHHHHcCCCCCcccccccccccccchHHHHH
Q psy11588 289 EKDHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLNQHN 368 (459)
Q Consensus 289 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 368 (459)
+.+|.|+.|++.|.-.++|.+|.- .|+|.+||+|.+|.+.|..+-.|..|++.|.|++||+|+.|+++|....++..||
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKY-EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKY-EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhh-hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 457999999999999999999976 8999999999999999999999999999999999999999999999999999998
Q ss_pred h
Q psy11588 369 L 369 (459)
Q Consensus 369 ~ 369 (459)
.
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 5
No 9
>KOG3576|consensus
Probab=99.63 E-value=1.1e-16 Score=127.81 Aligned_cols=116 Identities=28% Similarity=0.568 Sum_probs=88.9
Q ss_pred CCCccccccccccccChHHHHHHHHHcCCCCCcccccccccccccchHHHHHhhhCCC-CcccCCCCCcCCChHHHHHHH
Q psy11588 317 KVRDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLNQHNLVHTAV-NVVCSYCGNTYKNPKSLESHI 395 (459)
Q Consensus 317 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~ 395 (459)
+...|.|.+|++.|.....|.+|++-|...+.+.|..||+.|....+|.+|+++|++. ||+|..|++.|+..-+|..|+
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 3455788888888888888888888888888888888888888888888888888877 788888888888888888888
Q ss_pred HhhcCCC----------CccccccchhccCChHHHHHHHHHhCCCCC
Q psy11588 396 RYAHTIR----------QKSICDVCGKEFKMKKRLKEHMAVHTTDRP 432 (459)
Q Consensus 396 ~~~H~~~----------~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 432 (459)
+.+|... +.|.|..||.+-.....+..|++.|+..-|
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 7777542 346777777777777777777777665543
No 10
>KOG3576|consensus
Probab=99.62 E-value=2.8e-16 Score=125.58 Aligned_cols=110 Identities=36% Similarity=0.669 Sum_probs=68.3
Q ss_pred CCccccccccccCCHHHHHHHHHHHcCCCCccccccccccccChHHHHHHHHHcCCCCCcccccccccccccchHHHHHh
Q psy11588 290 KDHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLNQHNL 369 (459)
Q Consensus 290 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 369 (459)
..|.|.+|++.|.-...|.+|++ -|...+.+.|..||+.|.+.-+|++|+++|+|.+||+|..|++.|++.-+|..|++
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~k-ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLK-CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhh-hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 34556666666666666666665 55555666666666666666666666666666666666666666666666666654
Q ss_pred hhCCC------------CcccCCCCCcCCChHHHHHHHHhhcC
Q psy11588 370 VHTAV------------NVVCSYCGNTYKNPKSLESHIRYAHT 400 (459)
Q Consensus 370 ~h~~~------------~~~C~~C~~~f~~~~~l~~H~~~~H~ 400 (459)
.-++. .|+|+.||.+-.....+..|++.+|.
T Consensus 195 kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 195 KVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 33322 25677777777777777777775443
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.22 E-value=2.7e-11 Score=116.09 Aligned_cols=146 Identities=22% Similarity=0.438 Sum_probs=112.1
Q ss_pred CccccccccccCCHHHHHHHHHHHcCCCCcccccc--ccccccChHHHHHHHHHcCCCCCcccccccccccccchHHHHH
Q psy11588 291 DHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSV--CGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLNQHN 368 (459)
Q Consensus 291 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 368 (459)
...|+.|..... ..+|..|.. +-......|+. |+..|. ...+.. .+.|+.|++.|. ...|..|+
T Consensus 407 ~V~C~NC~~~i~-l~~l~lHe~--~C~r~~V~Cp~~~Cg~v~~-r~el~~---------H~~C~~Cgk~f~-~s~LekH~ 472 (567)
T PLN03086 407 TVECRNCKHYIP-SRSIALHEA--YCSRHNVVCPHDGCGIVLR-VEEAKN---------HVHCEKCGQAFQ-QGEMEKHM 472 (567)
T ss_pred eEECCCCCCccc-hhHHHHHHh--hCCCcceeCCcccccceee-cccccc---------CccCCCCCCccc-hHHHHHHH
Confidence 356888888765 456678864 33334567874 998884 233333 368999999995 67899999
Q ss_pred hhhCCCCcccCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccC----------ChHHHHHHHHHhCCCCCcccCcc
Q psy11588 369 LVHTAVNVVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFK----------MKKRLKEHMAVHTTDRPFVCDMC 438 (459)
Q Consensus 369 ~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~----------~~~~l~~H~~~H~~~~~~~C~~C 438 (459)
..++ .++.|+ |+..+ ....|..|+. .|...+++.|++|++.|. ..+.|..|..+. |.+++.|..|
T Consensus 473 ~~~H-kpv~Cp-Cg~~~-~R~~L~~H~~-thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~C 547 (567)
T PLN03086 473 KVFH-EPLQCP-CGVVL-EKEQMVQHQA-STCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSC 547 (567)
T ss_pred HhcC-CCccCC-CCCCc-chhHHHhhhh-ccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEcccc
Confidence 9985 689999 99755 6789999987 789999999999999995 245899999885 9999999999
Q ss_pred ccccCChHHHHHHHHHhc
Q psy11588 439 PSAFKLKKHLQQHYKVHL 456 (459)
Q Consensus 439 ~~~f~~~~~l~~H~~~H~ 456 (459)
|+.+. ...|..|+..-+
T Consensus 548 gk~Vr-lrdm~~H~~~~h 564 (567)
T PLN03086 548 GRSVM-LKEMDIHQIAVH 564 (567)
T ss_pred CCeee-ehhHHHHHHHhh
Confidence 98865 456888876544
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.11 E-value=1.8e-10 Score=110.52 Aligned_cols=96 Identities=24% Similarity=0.617 Sum_probs=47.8
Q ss_pred ccccccccccChHHHHHHHHHcCCCCCcccccccccccccchHHHHHhhhCCC-CcccCCCCCcCC----------ChHH
Q psy11588 322 QCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLNQHNLVHTAV-NVVCSYCGNTYK----------NPKS 390 (459)
Q Consensus 322 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~f~----------~~~~ 390 (459)
.|+.|+..|. ...|..|+.+++ .++.|+ |++.+ ....|..|+.+|.+. ++.|+.|++.|. ....
T Consensus 455 ~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~ 529 (567)
T PLN03086 455 HCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRG 529 (567)
T ss_pred cCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhh
Confidence 4555555553 344555555543 445555 55433 334555555555444 455555555553 1235
Q ss_pred HHHHHHhhcCCCCccccccchhccCChHHHHHHHH
Q psy11588 391 LESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHMA 425 (459)
Q Consensus 391 l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~ 425 (459)
|..|.. . .+.+++.|..||+.+..+ .|..|+.
T Consensus 530 Lt~HE~-~-CG~rt~~C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 530 MSEHES-I-CGSRTAPCDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred HHHHHH-h-cCCcceEccccCCeeeeh-hHHHHHH
Confidence 555555 2 245556666666555432 3445543
No 13
>PHA00733 hypothetical protein
Probab=99.08 E-value=8e-11 Score=91.81 Aligned_cols=55 Identities=20% Similarity=0.403 Sum_probs=42.4
Q ss_pred CCCccccccchhccCChHHHHHHHHHhCCCCCcccCccccccCChHHHHHHHHHhcC
Q psy11588 401 IRQKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSAFKLKKHLQQHYKVHLK 457 (459)
Q Consensus 401 ~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 457 (459)
+.+||.|+.||+.|.+...|..|++.| +.+|.|++|+++|.....|..|+...++
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 367788888888888888888888766 3568888888888888888888776554
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.97 E-value=2.7e-10 Score=72.16 Aligned_cols=44 Identities=16% Similarity=0.320 Sum_probs=36.3
Q ss_pred ccccccchhccCChHHHHHHHHHhCCCCCcccCccccccCChHHHH
Q psy11588 404 KSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSAFKLKKHLQ 449 (459)
Q Consensus 404 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~ 449 (459)
-|+|+.||+.|...+.|..|+++|+ +||+|..|++.|.+.+.|.
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 3788888888888888888888887 6888888888888777653
No 15
>PHA00733 hypothetical protein
Probab=98.93 E-value=1e-09 Score=85.58 Aligned_cols=54 Identities=31% Similarity=0.532 Sum_probs=28.6
Q ss_pred CCCcccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHHhhcC
Q psy11588 346 EKKYVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRYAHT 400 (459)
Q Consensus 346 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~H~ 400 (459)
++||.|+.|++.|.+...|..|++.+ ..++.|+.|++.|.....|..|+...|.
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 44555555555555555555555543 1245555566666665666666554443
No 16
>KOG3993|consensus
Probab=98.76 E-value=5.9e-10 Score=99.85 Aligned_cols=190 Identities=18% Similarity=0.255 Sum_probs=97.0
Q ss_pred ccccccChhcccCHHHHHHHHhhccCCCCccccccccccCCHHHHHHHHHHHcCCCCcccc---ccccccccChHHHHHH
Q psy11588 263 NYKCPDCSAILLSYGGFTSHLDIHSGEKDHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQC---SVCGKAFADITNMKVH 339 (459)
Q Consensus 263 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C---~~C~~~f~~~~~l~~H 339 (459)
.|.|..|...|.+.-.|.+|.-...-...|.|+.|+++|+-..+|..|.+ -|.-...-.= +-=..........+.=
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRR-WHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRR-WHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhc-ccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 48888898888888888888643222334888888888888888888877 3421110000 0000000000000000
Q ss_pred HHH--cCCCCCcccccccccccccchHHHHHhhhCCCC------------------cccCCCCCcCCChHHHHHHHHhhc
Q psy11588 340 MRI--HTGEKKYVCETCGASFVQWGSLNQHNLVHTAVN------------------VVCSYCGNTYKNPKSLESHIRYAH 399 (459)
Q Consensus 340 ~~~--h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~------------------~~C~~C~~~f~~~~~l~~H~~~~H 399 (459)
.+. ...+..|.|..|++.|..+.-|+.|+.+|.... +.+..++-.+...+.--.+...+-
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 000 011234667777777777777777766654321 123333322222111111111000
Q ss_pred CCCCccccccchhccCChHHHHHHHHHhCCCCCcccCccccccCChHHHHHHHH
Q psy11588 400 TIRQKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSAFKLKKHLQQHYK 453 (459)
Q Consensus 400 ~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~ 453 (459)
.....-.+++|+-.+.++..---+.+.-..+..|.|.+|...|.+...|.+|+.
T Consensus 426 ~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin 479 (500)
T KOG3993|consen 426 GSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHIN 479 (500)
T ss_pred ccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhh
Confidence 011123466666666665555555554455556777777777777777777764
No 17
>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=98.74 E-value=7.6e-09 Score=55.97 Aligned_cols=26 Identities=35% Similarity=0.855 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCCCcccCccccccCC
Q psy11588 419 RLKEHMAVHTTDRPFVCDMCPSAFKL 444 (459)
Q Consensus 419 ~l~~H~~~H~~~~~~~C~~C~~~f~~ 444 (459)
+|..|+++|++++||.|++|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47888888888888888888888864
No 18
>KOG3993|consensus
Probab=98.66 E-value=4e-09 Score=94.66 Aligned_cols=159 Identities=18% Similarity=0.246 Sum_probs=96.5
Q ss_pred cccccccChhcccCHHHHHHHHhhccCCCCccccccccccCCH----HHHHHHHHHHc-----CCCCccccccccccccC
Q psy11588 262 VNYKCPDCSAILLSYGGFTSHLDIHSGEKDHCCHICKKVFLRY----RNLVCHIKAVH-----EKVRDHQCSVCGKAFAD 332 (459)
Q Consensus 262 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~----~~l~~H~~~~h-----~~~~~~~C~~C~~~f~~ 332 (459)
..|+|+.|++.|.-..+|..|.++|.....-- +.-... ..-..-.++.- ..+..|.|.+|++.|..
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa-----~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrR 368 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHKPRPEAA-----KAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRR 368 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccCCchhhh-----hcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHH
Confidence 46999999999999999999999985432110 000000 00001111111 22346999999999999
Q ss_pred hHHHHHHHHHcCCCCC-----------------cccccccccccccchHHHHHhhhCCC--CcccCCCCCcCCChHHHHH
Q psy11588 333 ITNMKVHMRIHTGEKK-----------------YVCETCGASFVQWGSLNQHNLVHTAV--NVVCSYCGNTYKNPKSLES 393 (459)
Q Consensus 333 ~~~l~~H~~~h~~~~~-----------------~~C~~C~~~f~~~~~l~~H~~~h~~~--~~~C~~C~~~f~~~~~l~~ 393 (459)
...|+.|+.+|+.... +.+..++-.+.....--.+...+.+. ...+++++..+.++..--.
T Consensus 369 qAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg 448 (500)
T KOG3993|consen 369 QAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGG 448 (500)
T ss_pred HHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCc
Confidence 9999999887753211 23444444333333222222222222 2457888877776654444
Q ss_pred HHHhhcCCCCccccccchhccCChHHHHHHHHH
Q psy11588 394 HIRYAHTIRQKSICDVCGKEFKMKKRLKEHMAV 426 (459)
Q Consensus 394 H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~ 426 (459)
+.+ .-...+.|.|.+|.-.|.+...|.+|+..
T Consensus 449 ~~r-lg~~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 449 YGR-LGIAEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred ccc-ccchhhccccccchHhhhcCcchHhHhhh
Confidence 443 12224568999999999999999999874
No 19
>PHA02768 hypothetical protein; Provisional
Probab=98.61 E-value=2.3e-08 Score=63.46 Aligned_cols=42 Identities=21% Similarity=0.530 Sum_probs=26.5
Q ss_pred cccccccccccChHHHHHHHHHcCCCCCcccccccccccccchH
Q psy11588 321 HQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSL 364 (459)
Q Consensus 321 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 364 (459)
|.|+.||+.|.....|..|+++|+ ++|+|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 566666666666666666666665 456666666666655443
No 20
>PHA00616 hypothetical protein
Probab=98.53 E-value=4.6e-08 Score=58.85 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=30.9
Q ss_pred ccccccchhccCChHHHHHHHHHhCCCCCcccCc
Q psy11588 404 KSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDM 437 (459)
Q Consensus 404 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~ 437 (459)
||+|+.||+.|..++.|..|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999988874
No 21
>PHA00732 hypothetical protein
Probab=98.37 E-value=2.1e-07 Score=65.42 Aligned_cols=46 Identities=35% Similarity=0.671 Sum_probs=27.1
Q ss_pred cccCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccCChHHHHHHHHHh
Q psy11588 376 VVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHMAVH 427 (459)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H 427 (459)
|.|+.|++.|.+...|..|++..|. ++.|+.||+.|. .|..|+.++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 5566666666666666666653343 245666666665 355665444
No 22
>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=98.37 E-value=2.6e-07 Score=49.95 Aligned_cols=25 Identities=60% Similarity=1.120 Sum_probs=18.3
Q ss_pred HHHHHHHHcCCCCCccccccccccc
Q psy11588 335 NMKVHMRIHTGEKKYVCETCGASFV 359 (459)
Q Consensus 335 ~l~~H~~~h~~~~~~~C~~C~~~f~ 359 (459)
+|..|+++|.+++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3667777777777777777777775
No 23
>KOG1146|consensus
Probab=98.31 E-value=7.7e-07 Score=91.67 Aligned_cols=76 Identities=14% Similarity=0.266 Sum_probs=58.7
Q ss_pred cccCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccCChHHHHHHHHHh-----------------CCCCCcccCcc
Q psy11588 376 VVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHMAVH-----------------TTDRPFVCDMC 438 (459)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H-----------------~~~~~~~C~~C 438 (459)
+.|..|++.|...-.+. |+-. ..+|.|..|...|.....|..|.+.- ..-.+| |..|
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~----~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c 1334 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDV----THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLAC 1334 (1406)
T ss_pred chhhhccccccCcccee-eccc----chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHH
Confidence 45888888887776666 5542 35699999999999999999998532 122446 9999
Q ss_pred ccccCChHHHHHHHHHhcC
Q psy11588 439 PSAFKLKKHLQQHYKVHLK 457 (459)
Q Consensus 439 ~~~f~~~~~l~~H~~~H~~ 457 (459)
...|.....|+.||++-++
T Consensus 1335 ~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1335 EVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred HhhcchhHHHHHHHHHhhh
Confidence 9999999999999986543
No 24
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.20 E-value=3.1e-06 Score=55.27 Aligned_cols=36 Identities=28% Similarity=0.682 Sum_probs=15.4
Q ss_pred cccCCCCCcCCChHHHHHHHHhhcCCC-Cccccccchh
Q psy11588 376 VVCSYCGNTYKNPKSLESHIRYAHTIR-QKSICDVCGK 412 (459)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~~H~~~-~~~~C~~C~~ 412 (459)
|.||+|++ ..+...|..|+...|..+ +.+.||+|..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 44444444 233344444444444432 2344444444
No 25
>PHA00616 hypothetical protein
Probab=98.17 E-value=1.3e-06 Score=52.70 Aligned_cols=34 Identities=29% Similarity=0.482 Sum_probs=28.1
Q ss_pred ccccchhhHhhhhHHHHHHHHhhhccCCCCCCCceeeccc
Q psy11588 56 VYHCADCEQVFLDKFVLELHLKIEHKDNMFPKSHWFVCKM 95 (459)
Q Consensus 56 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~ 95 (459)
+|+|..||+.|..+.+|..|++.|++++ ++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~------~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQN------KLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCC------ccceeE
Confidence 5889999999999999999999998887 566654
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.14 E-value=3.8e-06 Score=54.86 Aligned_cols=51 Identities=27% Similarity=0.539 Sum_probs=41.2
Q ss_pred ccccccchhccCChHHHHHHHHH-hCCC-CCcccCccccccCChHHHHHHHHHhcC
Q psy11588 404 KSICDVCGKEFKMKKRLKEHMAV-HTTD-RPFVCDMCPSAFKLKKHLQQHYKVHLK 457 (459)
Q Consensus 404 ~~~C~~C~~~f~~~~~l~~H~~~-H~~~-~~~~C~~C~~~f~~~~~l~~H~~~H~~ 457 (459)
.|.||+|++ -.+...|..|+.. |..+ +.+.|++|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 489999999 5667899999875 5443 5799999998755 499999988764
No 27
>PHA00732 hypothetical protein
Probab=98.11 E-value=2.2e-06 Score=60.35 Aligned_cols=44 Identities=30% Similarity=0.566 Sum_probs=23.2
Q ss_pred ccccccchhccCChHHHHHHHHH-hCCCCCcccCccccccCChHHHHHHHH
Q psy11588 404 KSICDVCGKEFKMKKRLKEHMAV-HTTDRPFVCDMCPSAFKLKKHLQQHYK 453 (459)
Q Consensus 404 ~~~C~~C~~~f~~~~~l~~H~~~-H~~~~~~~C~~C~~~f~~~~~l~~H~~ 453 (459)
||.|+.||+.|.+...|..|++. |. ++.|+.|+++|. .|..|++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhc
Confidence 35555555555555555555553 33 235555555554 3445543
No 28
>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=97.96 E-value=5.5e-06 Score=43.48 Aligned_cols=23 Identities=30% Similarity=0.823 Sum_probs=12.8
Q ss_pred cccCccccccCChHHHHHHHHHh
Q psy11588 433 FVCDMCPSAFKLKKHLQQHYKVH 455 (459)
Q Consensus 433 ~~C~~C~~~f~~~~~l~~H~~~H 455 (459)
|.|+.|++.|.+...|..|+++|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 45555555555555555555543
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=97.89 E-value=7.3e-06 Score=43.01 Aligned_cols=23 Identities=48% Similarity=0.898 Sum_probs=17.3
Q ss_pred cccccchhccCChHHHHHHHHHh
Q psy11588 405 SICDVCGKEFKMKKRLKEHMAVH 427 (459)
Q Consensus 405 ~~C~~C~~~f~~~~~l~~H~~~H 427 (459)
|.|++|++.|.++..|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 56777777777777777777764
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.75 E-value=1.7e-05 Score=59.93 Aligned_cols=73 Identities=25% Similarity=0.444 Sum_probs=17.8
Q ss_pred ccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccCChHHHHHHHHHh
Q psy11588 350 VCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHMAVH 427 (459)
Q Consensus 350 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H 427 (459)
+|..|+..|.+...|..|+...++..+. ....+.....+..+++. .....+.|.+|++.|.+...|..||+.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~---~~~~l~~~~~~~~~~~~--~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP---DQKYLVDPNRLLNYLRK--KVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc---ccccccccccccccccc--ccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 4777777777777777777655543221 11222234444444431 1223577888888888888888887754
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.67 E-value=3.5e-05 Score=40.86 Aligned_cols=23 Identities=39% Similarity=0.925 Sum_probs=11.5
Q ss_pred cccCccccccCChHHHHHHHHHh
Q psy11588 433 FVCDMCPSAFKLKKHLQQHYKVH 455 (459)
Q Consensus 433 ~~C~~C~~~f~~~~~l~~H~~~H 455 (459)
|.|++|++.|.+...|..|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 44555555555555555555544
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=97.59 E-value=4.6e-05 Score=40.37 Aligned_cols=24 Identities=42% Similarity=0.923 Sum_probs=15.7
Q ss_pred cccccchhccCChHHHHHHHHHhC
Q psy11588 405 SICDVCGKEFKMKKRLKEHMAVHT 428 (459)
Q Consensus 405 ~~C~~C~~~f~~~~~l~~H~~~H~ 428 (459)
|.|++|++.|.+...|..|+++|+
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 567777777777777777777653
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.56 E-value=3.9e-05 Score=42.02 Aligned_cols=25 Identities=36% Similarity=0.760 Sum_probs=14.7
Q ss_pred CcccCccccccCChHHHHHHHHHhc
Q psy11588 432 PFVCDMCPSAFKLKKHLQQHYKVHL 456 (459)
Q Consensus 432 ~~~C~~C~~~f~~~~~l~~H~~~H~ 456 (459)
||.|..|++.|.+...|..|++.|.
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 4556666666666666666665554
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.50 E-value=5.9e-05 Score=56.96 Aligned_cols=71 Identities=21% Similarity=0.437 Sum_probs=14.3
Q ss_pred cccccccccChHHHHHHHHHcCCCCCcccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHHh
Q psy11588 323 CSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRY 397 (459)
Q Consensus 323 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~ 397 (459)
|..|+..|.+...|..|+...++...- ....+.....+..+.+.-....+.|..|++.|.+...|..|++.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp ---------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred ccccccccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 566666666666666666544432110 11112233333333333223346666666666666666666663
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=97.45 E-value=6.2e-05 Score=41.21 Aligned_cols=26 Identities=38% Similarity=0.677 Sum_probs=21.0
Q ss_pred ccccccchhccCChHHHHHHHHHhCC
Q psy11588 404 KSICDVCGKEFKMKKRLKEHMAVHTT 429 (459)
Q Consensus 404 ~~~C~~C~~~f~~~~~l~~H~~~H~~ 429 (459)
||.|..|++.|.+..+|..|++.|.+
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 57888888888888888888877753
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.40 E-value=4.1e-05 Score=66.68 Aligned_cols=51 Identities=35% Similarity=0.726 Sum_probs=36.9
Q ss_pred Ccccccc--chhccCChHHHHHHHHH-h------------------CCCCCcccCccccccCChHHHHHHHH
Q psy11588 403 QKSICDV--CGKEFKMKKRLKEHMAV-H------------------TTDRPFVCDMCPSAFKLKKHLQQHYK 453 (459)
Q Consensus 403 ~~~~C~~--C~~~f~~~~~l~~H~~~-H------------------~~~~~~~C~~C~~~f~~~~~l~~H~~ 453 (459)
+||+|++ |.|.+.+...|+.|+.- | ...|||+|++|+|.|.+...|+.|..
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 5666665 66666666666666542 2 23589999999999999999998854
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.00 E-value=0.00049 Score=42.44 Aligned_cols=35 Identities=20% Similarity=0.610 Sum_probs=17.5
Q ss_pred hcCCCCccccccchhccCChHHHHHHHHHhCCCCC
Q psy11588 398 AHTIRQKSICDVCGKEFKMKKRLKEHMAVHTTDRP 432 (459)
Q Consensus 398 ~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 432 (459)
....+.|-.|++|+..+....+|.+|+.++++.+|
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34445566666666666666666666666655544
No 38
>KOG1146|consensus
Probab=97.00 E-value=0.00023 Score=74.20 Aligned_cols=155 Identities=16% Similarity=0.182 Sum_probs=98.4
Q ss_pred cccccchhhccChhHHHHhhhhhc-CCCccccCCCCCCCchhhHhHHHHHHHHHHhccccCCcccchh--hcc--cceee
Q psy11588 182 HSCQKCEESFDNCNNLWSHMFIKH-ENSDFVCNLCPSHSKVLVRYVHSAVRHMKKHHKLQLSIPKAHN--YFR--KKTVI 256 (459)
Q Consensus 182 ~~C~~C~~~f~~~~~l~~H~~~~~-~~~~~~C~~C~~~f~~~~~~~~~l~~H~~~h~~~~~~~~~~~~--~~~--~~~~~ 256 (459)
..|.-|+..+.+...+..|+..-+ ..+.|.|+.|+..| .....|..||+..+.+.-. ..|.. ... .....
T Consensus 437 ~e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~y----k~a~~L~vhmRskhp~~~~-~~c~~gq~~~~~arg~~ 511 (1406)
T KOG1146|consen 437 VELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHY----KLAQTLGVHMRSKHPESQS-AYCKAGQNHPRLARGEV 511 (1406)
T ss_pred ccccchhhhhhhhcccccceeeeecccccccCCccchhh----hhHHHhhhcccccccccch-hHhHhcccccccccccc
Confidence 457777777877777777775433 34678888888888 8888888888874433211 11111 100 11111
Q ss_pred ecCCCcccccccChhcccCHHHHHHHHhhc--cC-----------------------------------------CCCcc
Q psy11588 257 HVNKKVNYKCPDCSAILLSYGGFTSHLDIH--SG-----------------------------------------EKDHC 293 (459)
Q Consensus 257 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h--~~-----------------------------------------~~~~~ 293 (459)
-.....+|.|..|...+....+|.+|++.- .. ...|.
T Consensus 512 ~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~ 591 (1406)
T KOG1146|consen 512 YRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWR 591 (1406)
T ss_pred ccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcc
Confidence 222356899999999999999999998531 10 11378
Q ss_pred ccccccccCCHHHHHHHHHHHcCCCCccccccccccccChHHHHHHHH
Q psy11588 294 CHICKKVFLRYRNLVCHIKAVHEKVRDHQCSVCGKAFADITNMKVHMR 341 (459)
Q Consensus 294 C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 341 (459)
|.+|++..+-..+|..|+...+....+..+..++..+.....+..+.+
T Consensus 592 C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~ 639 (1406)
T KOG1146|consen 592 CEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGR 639 (1406)
T ss_pred hhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCC
Confidence 888888888888888888765554444555555555554444444433
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.94 E-value=0.00079 Score=36.16 Aligned_cols=23 Identities=35% Similarity=0.787 Sum_probs=12.0
Q ss_pred cccCccccccCChHHHHHHHHHh
Q psy11588 433 FVCDMCPSAFKLKKHLQQHYKVH 455 (459)
Q Consensus 433 ~~C~~C~~~f~~~~~l~~H~~~H 455 (459)
|.|+.|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34555555555555555555544
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.89 E-value=0.00078 Score=35.53 Aligned_cols=23 Identities=30% Similarity=0.648 Sum_probs=13.6
Q ss_pred cccCccccccCChHHHHHHHHHhc
Q psy11588 433 FVCDMCPSAFKLKKHLQQHYKVHL 456 (459)
Q Consensus 433 ~~C~~C~~~f~~~~~l~~H~~~H~ 456 (459)
|+|+.|+.... ...|.+|+++|+
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 56666666665 666666666654
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.85 E-value=0.00042 Score=60.59 Aligned_cols=60 Identities=23% Similarity=0.551 Sum_probs=47.9
Q ss_pred cCCccccch--hhHhhhhHHHHHHHHhhhcc-----CCCC--------CCCceeecccCCcceeeehhHHhhhhhh
Q psy11588 53 TKDVYHCAD--CEQVFLDKFVLELHLKIEHK-----DNMF--------PKSHWFVCKMCGHRLFMRLSDLRRHMQD 113 (459)
Q Consensus 53 ~~~~~~C~~--C~~~f~~~~~L~~H~~~h~~-----~~~~--------~~~~~~~C~~C~~~~f~~~~~l~~H~~~ 113 (459)
.++||+|++ |+|.+++...|+-|+.-=|. +.|. ...+||.|++|+++ |.....|+.|...
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KR-YKNlNGLKYHr~H 420 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR-YKNLNGLKYHRKH 420 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchh-hccCccceecccc
Confidence 458999997 99999999999999874331 1111 24479999999999 9999999999764
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.81 E-value=0.0012 Score=35.47 Aligned_cols=24 Identities=54% Similarity=0.811 Sum_probs=15.9
Q ss_pred cccccchhccCChHHHHHHHHHhC
Q psy11588 405 SICDVCGKEFKMKKRLKEHMAVHT 428 (459)
Q Consensus 405 ~~C~~C~~~f~~~~~l~~H~~~H~ 428 (459)
|.|+.|++.|.+...|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 456677777777777777766553
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.77 E-value=0.00075 Score=41.67 Aligned_cols=35 Identities=20% Similarity=0.472 Sum_probs=17.9
Q ss_pred HcCCCCccccccccccccChHHHHHHHHHcCCCCC
Q psy11588 314 VHEKVRDHQCSVCGKAFADITNMKVHMRIHTGEKK 348 (459)
Q Consensus 314 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 348 (459)
.+..+.|..|++|+..+.+..+|++|+.+.++.+|
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34455566666666666666666666666555543
No 44
>KOG2231|consensus
Probab=96.58 E-value=0.0053 Score=60.77 Aligned_cols=110 Identities=23% Similarity=0.423 Sum_probs=67.7
Q ss_pred cccccchhhccChhHHHHhhhhhcCCCccccCCCCCCCch-----hhHhHHHHHHHHHHhccccCCcccchhhcccceee
Q psy11588 182 HSCQKCEESFDNCNNLWSHMFIKHENSDFVCNLCPSHSKV-----LVRYVHSAVRHMKKHHKLQLSIPKAHNYFRKKTVI 256 (459)
Q Consensus 182 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~-----~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~ 256 (459)
..|..| ..|.+...|+.|+...| +.+.|.+|-..-+. .......|..|++.-.... .+
T Consensus 116 ~~~~~c-~~~~s~~~Lk~H~~~~H--~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~-------~s------- 178 (669)
T KOG2231|consen 116 KECLHC-TEFKSVENLKNHMRDQH--KLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDD-------ES------- 178 (669)
T ss_pred CCCccc-cchhHHHHHHHHHHHhh--hhhccccccccceeeeeeeehehHHHHHHHHhcCCCcc-------cc-------
Confidence 358888 88889999999997666 35667777432111 1134556666665422100 00
Q ss_pred ecCCCcccccccChhcccCHHHHHHHHhhccCCCCccccccc------cccCCHHHHHHHHHHHc
Q psy11588 257 HVNKKVNYKCPDCSAILLSYGGFTSHLDIHSGEKDHCCHICK------KVFLRYRNLVCHIKAVH 315 (459)
Q Consensus 257 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~------~~f~~~~~l~~H~~~~h 315 (459)
. ...-.|..|...|....+|.+|++.++ |.|..|+ ..|.....|..|.+..|
T Consensus 179 ~---rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 179 C---RGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred c---cCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 0 112468888888888888888887654 4465553 45666777888877655
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.49 E-value=0.0016 Score=34.74 Aligned_cols=22 Identities=36% Similarity=0.895 Sum_probs=13.7
Q ss_pred cccCccccccCChHHHHHHHHH
Q psy11588 433 FVCDMCPSAFKLKKHLQQHYKV 454 (459)
Q Consensus 433 ~~C~~C~~~f~~~~~l~~H~~~ 454 (459)
|.|++|++.|.+...|+.|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566666666666666666653
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.41 E-value=0.0019 Score=34.06 Aligned_cols=23 Identities=30% Similarity=0.522 Sum_probs=14.2
Q ss_pred cccccchhccCChHHHHHHHHHhC
Q psy11588 405 SICDVCGKEFKMKKRLKEHMAVHT 428 (459)
Q Consensus 405 ~~C~~C~~~f~~~~~l~~H~~~H~ 428 (459)
|+|+.|+.... ...|..|+++|+
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 56777777666 667777776654
No 47
>KOG2231|consensus
Probab=96.40 E-value=0.0075 Score=59.74 Aligned_cols=103 Identities=23% Similarity=0.467 Sum_probs=54.3
Q ss_pred cccccccccCCHHHHHHHHHHHcCCCCcccccccc---------ccccChHHHHHHHHHcCC-CC----Ccccccccccc
Q psy11588 293 CCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSVCG---------KAFADITNMKVHMRIHTG-EK----KYVCETCGASF 358 (459)
Q Consensus 293 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~---------~~f~~~~~l~~H~~~h~~-~~----~~~C~~C~~~f 358 (459)
.|..| ..|.+...|+.|+...|.. +.|.+|- ...-+..+|..|+..-.. ++ .-.|..|...|
T Consensus 117 ~~~~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 117 ECLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERF 192 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhh
Confidence 35555 5555666666666545532 2333321 112234555555543211 11 13577777777
Q ss_pred cccchHHHHHhhhCCCCccc---CCCCCcCCChHHHHHHHHhhc
Q psy11588 359 VQWGSLNQHNLVHTAVNVVC---SYCGNTYKNPKSLESHIRYAH 399 (459)
Q Consensus 359 ~~~~~l~~H~~~h~~~~~~C---~~C~~~f~~~~~l~~H~~~~H 399 (459)
.....|.+|++.++..-..| +.++..|.+...|..|.+..|
T Consensus 193 ld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 193 LDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 77777777776655332223 223455677777777777544
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.30 E-value=0.002 Score=34.31 Aligned_cols=22 Identities=32% Similarity=0.821 Sum_probs=16.5
Q ss_pred cccccchhccCChHHHHHHHHH
Q psy11588 405 SICDVCGKEFKMKKRLKEHMAV 426 (459)
Q Consensus 405 ~~C~~C~~~f~~~~~l~~H~~~ 426 (459)
|.|++|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4677788888888888777764
No 49
>PRK04860 hypothetical protein; Provisional
Probab=96.26 E-value=0.0019 Score=52.52 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=30.6
Q ss_pred CccccccchhccCChHHHHHHHHHhCCCCCcccCccccccCChH
Q psy11588 403 QKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSAFKLKK 446 (459)
Q Consensus 403 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~ 446 (459)
-+|.|. |+. ....+..|.++|.++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 368887 876 6677788888888888888888888776543
No 50
>KOG2482|consensus
Probab=96.09 E-value=0.017 Score=51.49 Aligned_cols=65 Identities=23% Similarity=0.372 Sum_probs=41.8
Q ss_pred HHHHHHhhccC-CCCccccccccccCC-HHHHHHHHHHHcCC---------------------CCccccccccccccChH
Q psy11588 278 GFTSHLDIHSG-EKDHCCHICKKVFLR-YRNLVCHIKAVHEK---------------------VRDHQCSVCGKAFADIT 334 (459)
Q Consensus 278 ~l~~H~~~h~~-~~~~~C~~C~~~f~~-~~~l~~H~~~~h~~---------------------~~~~~C~~C~~~f~~~~ 334 (459)
.|..+++...+ ....+|-.|+..+.- .+....|+-..|.- -..+.|-.|.+.|.++.
T Consensus 130 aLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkn 209 (423)
T KOG2482|consen 130 ALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKN 209 (423)
T ss_pred HHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcH
Confidence 44555544322 234679999877654 56677787666631 12367888888888888
Q ss_pred HHHHHHHH
Q psy11588 335 NMKVHMRI 342 (459)
Q Consensus 335 ~l~~H~~~ 342 (459)
.|+.||+.
T Consensus 210 tLkeHMrk 217 (423)
T KOG2482|consen 210 TLKEHMRK 217 (423)
T ss_pred HHHHHHHh
Confidence 88888765
No 51
>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=96.02 E-value=0.0013 Score=35.80 Aligned_cols=23 Identities=26% Similarity=0.553 Sum_probs=21.0
Q ss_pred eeecccchhhccccccchhhhhc
Q psy11588 3 WTCCKCIAKYTSRSHLSLHLLSH 25 (459)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~h 25 (459)
|.|..|++.|.+...|..|+++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999998753
No 52
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.92 E-value=0.013 Score=52.11 Aligned_cols=129 Identities=25% Similarity=0.382 Sum_probs=72.4
Q ss_pred ccccc--cccccCCHHHHHHHHHHHcCCCCccccccccc---ccc------ChHHHHHHHHHcCCCCC----cccccccc
Q psy11588 292 HCCHI--CKKVFLRYRNLVCHIKAVHEKVRDHQCSVCGK---AFA------DITNMKVHMRIHTGEKK----YVCETCGA 356 (459)
Q Consensus 292 ~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~---~f~------~~~~l~~H~~~h~~~~~----~~C~~C~~ 356 (459)
|.|+. |..+......|..|.+..|. .+.|.+|-. .|. +...|..|...-..+.- -.|..|..
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~~ 228 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG---FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC---cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 66765 66666667788888886664 356666632 232 23445555433222211 24777777
Q ss_pred cccccchHHHHHhhhCCCCcccCCC----CCcCCChHHHHHHHHhhcCCCCcccccc--ch----hccCChHHHHHHHHH
Q psy11588 357 SFVQWGSLNQHNLVHTAVNVVCSYC----GNTYKNPKSLESHIRYAHTIRQKSICDV--CG----KEFKMKKRLKEHMAV 426 (459)
Q Consensus 357 ~f~~~~~l~~H~~~h~~~~~~C~~C----~~~f~~~~~l~~H~~~~H~~~~~~~C~~--C~----~~f~~~~~l~~H~~~ 426 (459)
.|.+-..|..|.+..+..-+.|+.= ...|.+..+|..|.+..| |.|.+ |- ..|.....|..|+..
T Consensus 229 ~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h-----y~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 229 YFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAH-----YCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred eecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCc-----eEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 7777777777776655433333221 234666777777776433 43432 21 356677777777654
Q ss_pred hC
Q psy11588 427 HT 428 (459)
Q Consensus 427 H~ 428 (459)
-+
T Consensus 304 ~h 305 (493)
T COG5236 304 FH 305 (493)
T ss_pred Hh
Confidence 43
No 53
>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=95.52 E-value=0.0063 Score=33.06 Aligned_cols=22 Identities=32% Similarity=0.596 Sum_probs=20.2
Q ss_pred cccccchhhccChhHHHHhhhh
Q psy11588 182 HSCQKCEESFDNCNNLWSHMFI 203 (459)
Q Consensus 182 ~~C~~C~~~f~~~~~l~~H~~~ 203 (459)
|.|..|++.|.+...|..|++.
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 7899999999999999999865
No 54
>KOG2482|consensus
Probab=95.29 E-value=0.017 Score=51.42 Aligned_cols=109 Identities=17% Similarity=0.236 Sum_probs=62.2
Q ss_pred ccccccChhcccCHHHHHHHHhh--ccCCCC--------cccc--ccccccCC-HHHHHHHHHHHc------------CC
Q psy11588 263 NYKCPDCSAILLSYGGFTSHLDI--HSGEKD--------HCCH--ICKKVFLR-YRNLVCHIKAVH------------EK 317 (459)
Q Consensus 263 ~~~C~~C~~~f~~~~~l~~H~~~--h~~~~~--------~~C~--~C~~~f~~-~~~l~~H~~~~h------------~~ 317 (459)
.+.|-.|.+.|..+..|+.||+. |....| |.=. .=+++... .+.+.+-....+ .+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 57999999999999999999974 322222 0000 00111100 011100000000 01
Q ss_pred CC--ccccccccccccChHHHHHHHHHcCC---------------------------CCCcccccccccccccchHHHHH
Q psy11588 318 VR--DHQCSVCGKAFADITNMKVHMRIHTG---------------------------EKKYVCETCGASFVQWGSLNQHN 368 (459)
Q Consensus 318 ~~--~~~C~~C~~~f~~~~~l~~H~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~ 368 (459)
.. ...|-.|.....+...|..||.+-+. ...-.|-.|...|.....|..|+
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 11 15777787777777778888765432 01235788888999999999998
Q ss_pred hhh
Q psy11588 369 LVH 371 (459)
Q Consensus 369 ~~h 371 (459)
..+
T Consensus 355 ~e~ 357 (423)
T KOG2482|consen 355 VED 357 (423)
T ss_pred ccc
Confidence 754
No 55
>PRK04860 hypothetical protein; Provisional
Probab=94.38 E-value=0.022 Score=46.39 Aligned_cols=39 Identities=28% Similarity=0.621 Sum_probs=27.3
Q ss_pred CccccccccccccChHHHHHHHHHcCCCCCccccccccccccc
Q psy11588 319 RDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQW 361 (459)
Q Consensus 319 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 361 (459)
-+|.|. |+. ....+..|.++|.++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 357776 776 556677777777777777777777766543
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.29 E-value=0.036 Score=29.38 Aligned_cols=18 Identities=39% Similarity=0.983 Sum_probs=8.2
Q ss_pred ccccchhccCChHHHHHHH
Q psy11588 406 ICDVCGKEFKMKKRLKEHM 424 (459)
Q Consensus 406 ~C~~C~~~f~~~~~l~~H~ 424 (459)
.|+.||+.| ....|..|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 344444444 344444443
No 57
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.03 E-value=0.047 Score=28.94 Aligned_cols=21 Identities=29% Similarity=0.670 Sum_probs=18.6
Q ss_pred cccCccccccCChHHHHHHHHH
Q psy11588 433 FVCDMCPSAFKLKKHLQQHYKV 454 (459)
Q Consensus 433 ~~C~~C~~~f~~~~~l~~H~~~ 454 (459)
.+|+.||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5799999999 88899999875
No 58
>KOG2785|consensus
Probab=93.73 E-value=0.14 Score=46.82 Aligned_cols=51 Identities=22% Similarity=0.361 Sum_probs=43.4
Q ss_pred CccccccchhccCChHHHHHHHHHhCCC-----------------------CCcccCccc---cccCChHHHHHHHH
Q psy11588 403 QKSICDVCGKEFKMKKRLKEHMAVHTTD-----------------------RPFVCDMCP---SAFKLKKHLQQHYK 453 (459)
Q Consensus 403 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~ 453 (459)
.|-.|-.|++.+.+...-..||..+||- .-|.|-.|+ +.|.+....++||.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 3577999999999999999999888762 237899999 99999999999986
No 59
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.01 E-value=0.1 Score=46.78 Aligned_cols=132 Identities=23% Similarity=0.428 Sum_probs=87.5
Q ss_pred cccccc--ChhcccCHHHHHHHHhhccCCCCcccccccc---cc------CCHHHHHHHHHHHcCCCCc----ccccccc
Q psy11588 263 NYKCPD--CSAILLSYGGFTSHLDIHSGEKDHCCHICKK---VF------LRYRNLVCHIKAVHEKVRD----HQCSVCG 327 (459)
Q Consensus 263 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~---~f------~~~~~l~~H~~~~h~~~~~----~~C~~C~ 327 (459)
.|.||. |......+..|..|.+..++. +.|.+|-. .| .+...|..|.. .-..+.. -.|..|.
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~-~G~~e~GFKGHP~C~FC~ 227 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKN-GGLEEEGFKGHPLCIFCK 227 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeeccccccccc-CCccccCcCCCchhhhcc
Confidence 578864 777777788999999876653 67777742 23 34556777753 2222212 3699999
Q ss_pred ccccChHHHHHHHHHcCCCCCcccccc----cccccccchHHHHHhhhCCCCcccCC--C--C--CcCCChHHHHHHHHh
Q psy11588 328 KAFADITNMKVHMRIHTGEKKYVCETC----GASFVQWGSLNQHNLVHTAVNVVCSY--C--G--NTYKNPKSLESHIRY 397 (459)
Q Consensus 328 ~~f~~~~~l~~H~~~h~~~~~~~C~~C----~~~f~~~~~l~~H~~~h~~~~~~C~~--C--~--~~f~~~~~l~~H~~~ 397 (459)
..|-+-..|..|++..+ ++-|.|+.- ...|.+..+|..|.+.-+ |.|.. | + ..|.....|+.|+..
T Consensus 228 ~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h---y~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 228 IYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRNAH---YCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred ceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhcCc---eEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 99999999999998755 233333322 245778888888876433 44422 2 1 468889999999987
Q ss_pred hcCC
Q psy11588 398 AHTI 401 (459)
Q Consensus 398 ~H~~ 401 (459)
.|..
T Consensus 304 ~h~~ 307 (493)
T COG5236 304 FHKV 307 (493)
T ss_pred Hhhc
Confidence 7753
No 60
>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=92.65 E-value=0.081 Score=30.66 Aligned_cols=22 Identities=27% Similarity=0.664 Sum_probs=16.7
Q ss_pred CcccCccccccCChHHHHHHHH
Q psy11588 432 PFVCDMCPSAFKLKKHLQQHYK 453 (459)
Q Consensus 432 ~~~C~~C~~~f~~~~~l~~H~~ 453 (459)
+|.|++|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5778888888887777777764
No 61
>KOG2785|consensus
Probab=92.51 E-value=0.49 Score=43.45 Aligned_cols=52 Identities=21% Similarity=0.386 Sum_probs=42.8
Q ss_pred CcccCCCCCcCCChHHHHHHHHhhcCCCC----------------------ccccccch---hccCChHHHHHHHHH
Q psy11588 375 NVVCSYCGNTYKNPKSLESHIRYAHTIRQ----------------------KSICDVCG---KEFKMKKRLKEHMAV 426 (459)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~----------------------~~~C~~C~---~~f~~~~~l~~H~~~ 426 (459)
|-.|-.|+..+.+...-..||...|+--- -+.|-.|+ +.|.+..+.+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 35688899999999999999987775322 37899999 999999999999974
No 62
>KOG2893|consensus
Probab=92.08 E-value=0.051 Score=45.83 Aligned_cols=41 Identities=27% Similarity=0.583 Sum_probs=30.8
Q ss_pred cCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccCChHHHHHH
Q psy11588 378 CSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEH 423 (459)
Q Consensus 378 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H 423 (459)
|.+|++.|.+...|..|++. +-|+|.+|-|..-+-..|..|
T Consensus 13 cwycnrefddekiliqhqka-----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA-----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh-----ccceeeeehhhhccCCCceee
Confidence 77888888888888877763 447888887777777777766
No 63
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=91.96 E-value=0.1 Score=30.22 Aligned_cols=22 Identities=18% Similarity=0.511 Sum_probs=17.6
Q ss_pred ccccccchhccCChHHHHHHHH
Q psy11588 404 KSICDVCGKEFKMKKRLKEHMA 425 (459)
Q Consensus 404 ~~~C~~C~~~f~~~~~l~~H~~ 425 (459)
+|.|++|++.|.+..++..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5778888888888888888875
No 64
>KOG4173|consensus
Probab=90.93 E-value=0.13 Score=42.44 Aligned_cols=74 Identities=26% Similarity=0.542 Sum_probs=32.8
Q ss_pred ccccc--ccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHHhhcC---------CCCcccccc--chhccC
Q psy11588 349 YVCET--CGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRYAHT---------IRQKSICDV--CGKEFK 415 (459)
Q Consensus 349 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~H~---------~~~~~~C~~--C~~~f~ 415 (459)
|.|++ |...|.+...+..|-..-++ -.|..|.+.|.+...|..|+...|. |...|+|-+ |+..|.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~--~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFk 157 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG--NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFK 157 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc--chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhh
Confidence 44544 44444444444444322211 2355555555555555555543331 233344432 555555
Q ss_pred ChHHHHHHH
Q psy11588 416 MKKRLKEHM 424 (459)
Q Consensus 416 ~~~~l~~H~ 424 (459)
+..+-..|+
T Consensus 158 T~r~RkdH~ 166 (253)
T KOG4173|consen 158 TSRDRKDHM 166 (253)
T ss_pred hhhhhhhHH
Confidence 555444444
No 65
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.01 E-value=0.39 Score=36.13 Aligned_cols=77 Identities=19% Similarity=0.373 Sum_probs=38.6
Q ss_pred CCCcccccccccccccchHHHHHhhhCCC---C------------cccCCCCCcCCChHHHHHHHHhhcCCCCccccccc
Q psy11588 346 EKKYVCETCGASFVQWGSLNQHNLVHTAV---N------------VVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVC 410 (459)
Q Consensus 346 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~---~------------~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C 410 (459)
+-|..|++||-+..+...|.+-- |+-- + -.|--|...|....... ...-.....|+|+.|
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~---~~~~~~~~~y~C~~C 87 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSP---FDELKDSHRYVCAVC 87 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCccccc---ccccccccceeCCCC
Confidence 35777888887777776666531 2110 1 12666666665432100 000111234666666
Q ss_pred hhccCChHHHHHHHHHh
Q psy11588 411 GKEFKMKKRLKEHMAVH 427 (459)
Q Consensus 411 ~~~f~~~~~l~~H~~~H 427 (459)
...|-..=++..|...|
T Consensus 88 ~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 88 KNVFCVDCDVFVHESLH 104 (112)
T ss_pred CCccccccchhhhhhcc
Confidence 66666555555555544
No 66
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=89.97 E-value=0.16 Score=29.04 Aligned_cols=9 Identities=44% Similarity=1.342 Sum_probs=4.6
Q ss_pred CCcccCccc
Q psy11588 431 RPFVCDMCP 439 (459)
Q Consensus 431 ~~~~C~~C~ 439 (459)
.++.|++|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 444555554
No 67
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.29 E-value=0.32 Score=30.74 Aligned_cols=29 Identities=21% Similarity=0.410 Sum_probs=24.3
Q ss_pred cCCccccchhhHhhhhHHHHHHHHhhhcc
Q psy11588 53 TKDVYHCADCEQVFLDKFVLELHLKIEHK 81 (459)
Q Consensus 53 ~~~~~~C~~C~~~f~~~~~L~~H~~~h~~ 81 (459)
++..++|+-|++.|....++.+|...-|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 55678999999999999999999876543
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.93 E-value=0.18 Score=49.33 Aligned_cols=156 Identities=19% Similarity=0.206 Sum_probs=94.3
Q ss_pred CccccchhhHhhhhHHHHHHHHh--hhccCCCCCCCceeecc--cCCcceeeehhHHhhhhhhccccccccccccccc--
Q psy11588 55 DVYHCADCEQVFLDKFVLELHLK--IEHKDNMFPKSHWFVCK--MCGHRLFMRLSDLRRHMQDYHCEFHFDVESCAVS-- 128 (459)
Q Consensus 55 ~~~~C~~C~~~f~~~~~L~~H~~--~h~~~~~~~~~~~~~C~--~C~~~~f~~~~~l~~H~~~h~~~~~~~~~~c~~~-- 128 (459)
.++.|..|...|.....|..|.+ .|..+. ..++.|+ .|++. |.....+..|...|.+..+..+..-...
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~----~~~~~~p~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 362 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGES----LKPFSCPYSLCGKL-FSRNDALKRHILLHTSISPAKEKLLNSSSK 362 (467)
T ss_pred cCCCCccccCCcccccccccccccccccccc----CCceeeeccCCCcc-ccccccccCCcccccCCCccccccccCccc
Confidence 46899999999999999999999 787771 1278999 89999 9999999999999987655443322111
Q ss_pred ccccee-----ecCccchhhhhhhhhhhhhccccCCCCCCCCCCccccccccCCCCCCcccccchhhccChhHHHHhhhh
Q psy11588 129 RLQDIT-----FPCEECKELCVLSKYCIKHQDCSKAMSTPAPSSESVCIKHSNLIPKCHSCQKCEESFDNCNNLWSHMFI 203 (459)
Q Consensus 129 ~~~~~~-----~~C~~C~~~f~~~~~l~~H~~c~~~~~~~~~l~~~~~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 203 (459)
+..... ..-..-+.. ...........+...+.....+.. +...+....+..+.+..|.+.|.....+..|++.
T Consensus 363 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 (467)
T COG5048 363 FSPLLNNEPPQSLQQYKDLK-NDKKSETLSNSCIRNFKRDSNLSL-HIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKI 440 (467)
T ss_pred cccccCCCCccchhhccCcc-CCccccccccchhhhhcccccccc-ccccccccCCcCCCCCcchhhccCcccccccccc
Confidence 100000 000000000 000000000022223333333333 3344444444447788899999999999999988
Q ss_pred hcCCCccccCCCCC
Q psy11588 204 KHENSDFVCNLCPS 217 (459)
Q Consensus 204 ~~~~~~~~C~~C~~ 217 (459)
+....++.|..+..
T Consensus 441 ~~~~~~~~~~~~~~ 454 (467)
T COG5048 441 HTNHAPLLCSILKS 454 (467)
T ss_pred cccCCceeeccccc
Confidence 88777766665544
No 69
>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=88.76 E-value=0.39 Score=29.96 Aligned_cols=43 Identities=14% Similarity=0.380 Sum_probs=21.4
Q ss_pred ceeecccchhhccccccchhhhhccccccccccccccchhccc
Q psy11588 2 VWTCCKCIAKYTSRSHLSLHLLSHSSDADEIKQELSCEQCGCS 44 (459)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~C~~C~~~ 44 (459)
.|.|.+|+.++.-...-...-..-....++....|.|++|+..
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 3789999988887666544322221112222334666666653
No 70
>KOG4173|consensus
Probab=88.45 E-value=0.39 Score=39.77 Aligned_cols=78 Identities=24% Similarity=0.459 Sum_probs=58.3
Q ss_pred ccccccc--ChhcccCHHHHHHHHhhccCCCCccccccccccCCHHHHHHHHHHHcC---------CCCccccc--cccc
Q psy11588 262 VNYKCPD--CSAILLSYGGFTSHLDIHSGEKDHCCHICKKVFLRYRNLVCHIKAVHE---------KVRDHQCS--VCGK 328 (459)
Q Consensus 262 ~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~---------~~~~~~C~--~C~~ 328 (459)
..+.|++ |...|.+...+..|..+-++. .|..|.+.|.+..-|..|+.+.|. +...|.|- .|+.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 3467765 788888888888888765553 699999999999999999987773 34457773 4777
Q ss_pred cccChHHHHHHHHH
Q psy11588 329 AFADITNMKVHMRI 342 (459)
Q Consensus 329 ~f~~~~~l~~H~~~ 342 (459)
.|.+...-..|+-.
T Consensus 155 KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 155 KFKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhhHHHH
Confidence 77777777777543
No 71
>KOG2893|consensus
Probab=88.41 E-value=0.13 Score=43.48 Aligned_cols=48 Identities=29% Similarity=0.552 Sum_probs=40.0
Q ss_pred CccccccchhccCChHHHHHHHHHhCCCCCcccCccccccCChHHHHHHH-HHh
Q psy11588 403 QKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSAFKLKKHLQQHY-KVH 455 (459)
Q Consensus 403 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~-~~H 455 (459)
++| |.+|++.|....-|.+|++. +-|+|.+|.+...+--.|..|- .+|
T Consensus 10 kpw-cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred Cce-eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhh
Confidence 443 99999999999999999875 4599999999998888888884 444
No 72
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.34 E-value=0.079 Score=51.94 Aligned_cols=150 Identities=22% Similarity=0.349 Sum_probs=98.6
Q ss_pred CCccccccccccCCHHHHHHHHHH-HcCCC--Cccccc--cccccccChHHHHHHHHHcCCCCCccccc--ccccccccc
Q psy11588 290 KDHCCHICKKVFLRYRNLVCHIKA-VHEKV--RDHQCS--VCGKAFADITNMKVHMRIHTGEKKYVCET--CGASFVQWG 362 (459)
Q Consensus 290 ~~~~C~~C~~~f~~~~~l~~H~~~-~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~ 362 (459)
.++.|..|...|.....|..|.+. .|.++ .++.|+ .|++.|.....+..|...|.+..++.+.. +...+....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 357788888888888888888774 67777 788888 68888888888888888887777766644 333333222
Q ss_pred hH------HHHHhhhCCCCccc--CCCCCcCCChHHHHHHHHhhcCCCC--ccccccchhccCChHHHHHHHHHhCCCCC
Q psy11588 363 SL------NQHNLVHTAVNVVC--SYCGNTYKNPKSLESHIRYAHTIRQ--KSICDVCGKEFKMKKRLKEHMAVHTTDRP 432 (459)
Q Consensus 363 ~l------~~H~~~h~~~~~~C--~~C~~~f~~~~~l~~H~~~~H~~~~--~~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 432 (459)
.- .............+ ..|...+.....+..|.. .|.... .+.+..|.+.|.....+..|++.|....+
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHII-THLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAP 446 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccc-cccccCCcCCCCCcchhhccCcccccccccccccCCc
Confidence 21 11111112222333 235556666666666665 554444 46778899999999999999998888777
Q ss_pred cccCcccc
Q psy11588 433 FVCDMCPS 440 (459)
Q Consensus 433 ~~C~~C~~ 440 (459)
+.|..+..
T Consensus 447 ~~~~~~~~ 454 (467)
T COG5048 447 LLCSILKS 454 (467)
T ss_pred eeeccccc
Confidence 76665543
No 73
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=87.78 E-value=0.95 Score=34.46 Aligned_cols=25 Identities=20% Similarity=0.515 Sum_probs=19.5
Q ss_pred ccc----CccccccCChHHHHHHHHHhcC
Q psy11588 433 FVC----DMCPSAFKLKKHLQQHYKVHLK 457 (459)
Q Consensus 433 ~~C----~~C~~~f~~~~~l~~H~~~H~~ 457 (459)
|.| ..|++.+.+...|.+|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 778 7888888888888888777664
No 74
>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=86.49 E-value=0.29 Score=29.80 Aligned_cols=28 Identities=25% Similarity=0.774 Sum_probs=12.7
Q ss_pred cccchhccccccccccccCCccccchhh
Q psy11588 36 LSCEQCGCSLDFHSALYTKDVYHCADCE 63 (459)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~~~~~~C~~C~ 63 (459)
|.|..||..|.....+.....-.|+.|+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECG 33 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCC
Confidence 4455555444444443333344444444
No 75
>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=86.48 E-value=1.2 Score=33.95 Aligned_cols=54 Identities=26% Similarity=0.488 Sum_probs=43.6
Q ss_pred CcccCCCCCcCCChHHHHHHHHhhcCCC-----------------------------------------Ccccc----cc
Q psy11588 375 NVVCSYCGNTYKNPKSLESHIRYAHTIR-----------------------------------------QKSIC----DV 409 (459)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~-----------------------------------------~~~~C----~~ 409 (459)
...|..|+..... +++..|++..|... .-|.| +.
T Consensus 11 vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~~ 89 (109)
T PF12013_consen 11 VLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPPH 89 (109)
T ss_pred EEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCCC
Confidence 3579999988766 88999998665211 11889 99
Q ss_pred chhccCChHHHHHHHHHhCC
Q psy11588 410 CGKEFKMKKRLKEHMAVHTT 429 (459)
Q Consensus 410 C~~~f~~~~~l~~H~~~H~~ 429 (459)
|+..+.+...+..|++.++|
T Consensus 90 C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 90 CGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCcEeccHHHHHHHHHHhcC
Confidence 99999999999999998775
No 76
>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=84.76 E-value=0.39 Score=28.94 Aligned_cols=29 Identities=21% Similarity=0.701 Sum_probs=12.3
Q ss_pred cccchhccccccccccccCCccccchhhH
Q psy11588 36 LSCEQCGCSLDFHSALYTKDVYHCADCEQ 64 (459)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~~~~~~C~~C~~ 64 (459)
|.|..||..|...........-.|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 44555555444333332233344555543
No 77
>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=83.52 E-value=0.54 Score=26.55 Aligned_cols=7 Identities=29% Similarity=1.194 Sum_probs=3.0
Q ss_pred cccchhh
Q psy11588 57 YHCADCE 63 (459)
Q Consensus 57 ~~C~~C~ 63 (459)
.+|+.||
T Consensus 18 irC~~CG 24 (32)
T PF03604_consen 18 IRCPECG 24 (32)
T ss_dssp SSBSSSS
T ss_pred EECCcCC
Confidence 3444444
No 78
>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=82.85 E-value=0.5 Score=29.92 Aligned_cols=15 Identities=20% Similarity=0.452 Sum_probs=10.7
Q ss_pred eeecccchhhccccc
Q psy11588 3 WTCCKCIAKYTSRSH 17 (459)
Q Consensus 3 ~~C~~C~~~f~~~~~ 17 (459)
|.|.+||.++.-...
T Consensus 2 y~C~~CgyiYd~~~G 16 (50)
T cd00730 2 YECRICGYIYDPAEG 16 (50)
T ss_pred cCCCCCCeEECCCCC
Confidence 678888888776443
No 79
>PHA00626 hypothetical protein
Probab=82.62 E-value=0.58 Score=29.80 Aligned_cols=13 Identities=38% Similarity=0.628 Sum_probs=7.2
Q ss_pred CccccchhhHhhh
Q psy11588 55 DVYHCADCEQVFL 67 (459)
Q Consensus 55 ~~~~C~~C~~~f~ 67 (459)
..|+|+.|+..|+
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 4455666655554
No 80
>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=81.55 E-value=1.1 Score=33.84 Aligned_cols=13 Identities=38% Similarity=0.997 Sum_probs=5.6
Q ss_pred CccccccchhccC
Q psy11588 403 QKSICDVCGKEFK 415 (459)
Q Consensus 403 ~~~~C~~C~~~f~ 415 (459)
.|..|+.||..|.
T Consensus 25 ~PivCP~CG~~~~ 37 (108)
T PF09538_consen 25 DPIVCPKCGTEFP 37 (108)
T ss_pred CCccCCCCCCccC
Confidence 3444444444443
No 81
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.93 E-value=0.92 Score=34.16 Aligned_cols=22 Identities=32% Similarity=0.516 Sum_probs=9.5
Q ss_pred ccccchhhHhhhhHHHHHHHHh
Q psy11588 56 VYHCADCEQVFLDKFVLELHLK 77 (459)
Q Consensus 56 ~~~C~~C~~~f~~~~~L~~H~~ 77 (459)
.|+|+.|...|=..-+.-.|..
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred ceeCCCCCCccccccchhhhhh
Confidence 3444444444444444444433
No 82
>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=80.52 E-value=0.83 Score=26.27 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=5.0
Q ss_pred cccccchhcc
Q psy11588 405 SICDVCGKEF 414 (459)
Q Consensus 405 ~~C~~C~~~f 414 (459)
|.|.+||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 4455555443
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=80.14 E-value=0.46 Score=28.13 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=3.2
Q ss_pred cchhcccc
Q psy11588 38 CEQCGCSL 45 (459)
Q Consensus 38 C~~C~~~f 45 (459)
|+.|+..|
T Consensus 5 CP~C~~~~ 12 (38)
T TIGR02098 5 CPNCKTSF 12 (38)
T ss_pred CCCCCCEE
Confidence 34444433
No 84
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.31 E-value=0.6 Score=29.07 Aligned_cols=7 Identities=43% Similarity=1.379 Sum_probs=2.6
Q ss_pred ccchhcc
Q psy11588 37 SCEQCGC 43 (459)
Q Consensus 37 ~C~~C~~ 43 (459)
.|+.||.
T Consensus 5 ~C~~CG~ 11 (46)
T PRK00398 5 KCARCGR 11 (46)
T ss_pred ECCCCCC
Confidence 3333333
No 85
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.93 E-value=1 Score=28.53 Aligned_cols=30 Identities=20% Similarity=0.320 Sum_probs=19.6
Q ss_pred CCCCccccccchhccCChHHHHHHHHHhCC
Q psy11588 400 TIRQKSICDVCGKEFKMKKRLKEHMAVHTT 429 (459)
Q Consensus 400 ~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 429 (459)
.++.-+.||.||..|.......+|+..-++
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 345556777777777777777777764443
No 86
>COG1773 Rubredoxin [Energy production and conversion]
Probab=78.62 E-value=1.2 Score=28.62 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=12.6
Q ss_pred ceeecccchhhccccccc
Q psy11588 2 VWTCCKCIAKYTSRSHLS 19 (459)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~ 19 (459)
.|+|.+||.+|.-...-.
T Consensus 3 ~~~C~~CG~vYd~e~Gdp 20 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDP 20 (55)
T ss_pred ceEecCCceEeccccCCc
Confidence 578888888887654443
No 87
>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=76.52 E-value=0.83 Score=24.39 Aligned_cols=8 Identities=38% Similarity=1.053 Sum_probs=4.3
Q ss_pred cchhhHhh
Q psy11588 59 CADCEQVF 66 (459)
Q Consensus 59 C~~C~~~f 66 (459)
|+.||..|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 55555554
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=75.86 E-value=1.2 Score=27.39 Aligned_cols=11 Identities=27% Similarity=0.749 Sum_probs=5.9
Q ss_pred cccchhhHhhh
Q psy11588 57 YHCADCEQVFL 67 (459)
Q Consensus 57 ~~C~~C~~~f~ 67 (459)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55555555544
No 89
>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=75.67 E-value=1 Score=29.00 Aligned_cols=9 Identities=33% Similarity=1.246 Sum_probs=3.9
Q ss_pred ccchhcccc
Q psy11588 37 SCEQCGCSL 45 (459)
Q Consensus 37 ~C~~C~~~f 45 (459)
+|+.||..+
T Consensus 4 ~CP~CG~~i 12 (54)
T TIGR01206 4 ECPDCGAEI 12 (54)
T ss_pred CCCCCCCEE
Confidence 344444443
No 90
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=75.63 E-value=1.1 Score=28.00 Aligned_cols=10 Identities=40% Similarity=1.079 Sum_probs=5.3
Q ss_pred cccchhhHhh
Q psy11588 57 YHCADCEQVF 66 (459)
Q Consensus 57 ~~C~~C~~~f 66 (459)
|.|..|++.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555555554
No 91
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=73.23 E-value=1.4 Score=38.22 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=19.8
Q ss_pred Cceeecccchhhccccccchhhhhccc
Q psy11588 1 MVWTCCKCIAKYTSRSHLSLHLLSHSS 27 (459)
Q Consensus 1 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 27 (459)
|.++|++|++.|.+..-.....+.-..
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~ 30 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRR 30 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeee
Confidence 356888888888888877777765433
No 92
>KOG2186|consensus
Probab=72.27 E-value=2.6 Score=36.49 Aligned_cols=45 Identities=27% Similarity=0.651 Sum_probs=22.6
Q ss_pred cccccccccccChHHHHHHHHHcCCCCCcccccccccccccchHHHHH
Q psy11588 321 HQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLNQHN 368 (459)
Q Consensus 321 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 368 (459)
|.|..||.+..- ..+..|+..-++ .-|.|..|+..|.. .++..|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 455555554432 234445555544 44555555555555 4455553
No 93
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=70.49 E-value=1.2 Score=25.93 Aligned_cols=9 Identities=33% Similarity=1.032 Sum_probs=3.7
Q ss_pred cccchhhHh
Q psy11588 57 YHCADCEQV 65 (459)
Q Consensus 57 ~~C~~C~~~ 65 (459)
.+|+.|+.+
T Consensus 26 v~C~~C~~~ 34 (36)
T PF13717_consen 26 VRCSKCGHV 34 (36)
T ss_pred EECCCCCCE
Confidence 344444433
No 94
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=70.23 E-value=2.8 Score=27.26 Aligned_cols=8 Identities=38% Similarity=0.928 Sum_probs=3.8
Q ss_pred ccccccch
Q psy11588 404 KSICDVCG 411 (459)
Q Consensus 404 ~~~C~~C~ 411 (459)
+|.|+.||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 44444444
No 95
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=70.18 E-value=1.2 Score=26.15 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=4.2
Q ss_pred cccchhhHhh
Q psy11588 57 YHCADCEQVF 66 (459)
Q Consensus 57 ~~C~~C~~~f 66 (459)
.+|+.|+..|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4444444333
No 96
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=69.11 E-value=2.8 Score=34.26 Aligned_cols=10 Identities=30% Similarity=1.162 Sum_probs=6.0
Q ss_pred CCccccccch
Q psy11588 402 RQKSICDVCG 411 (459)
Q Consensus 402 ~~~~~C~~C~ 411 (459)
+.|-+||+||
T Consensus 147 e~P~~CPiCg 156 (166)
T COG1592 147 EAPEVCPICG 156 (166)
T ss_pred CCCCcCCCCC
Confidence 4556666665
No 97
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=68.75 E-value=3.9 Score=31.45 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=5.0
Q ss_pred CcccCCCCCcC
Q psy11588 375 NVVCSYCGNTY 385 (459)
Q Consensus 375 ~~~C~~C~~~f 385 (459)
|..|+.||..|
T Consensus 26 p~vcP~cg~~~ 36 (129)
T TIGR02300 26 PAVSPYTGEQF 36 (129)
T ss_pred CccCCCcCCcc
Confidence 34444444444
No 98
>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=68.42 E-value=4.1 Score=21.75 Aligned_cols=19 Identities=26% Similarity=0.609 Sum_probs=10.1
Q ss_pred ccccchhccCChHHHHHHHH
Q psy11588 406 ICDVCGKEFKMKKRLKEHMA 425 (459)
Q Consensus 406 ~C~~C~~~f~~~~~l~~H~~ 425 (459)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 456666555 4445555543
No 99
>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=66.83 E-value=3.2 Score=31.35 Aligned_cols=12 Identities=33% Similarity=1.065 Sum_probs=5.3
Q ss_pred CcccCCCCCcCC
Q psy11588 375 NVVCSYCGNTYK 386 (459)
Q Consensus 375 ~~~C~~C~~~f~ 386 (459)
|..||.||..|.
T Consensus 26 PivCP~CG~~~~ 37 (108)
T PF09538_consen 26 PIVCPKCGTEFP 37 (108)
T ss_pred CccCCCCCCccC
Confidence 344444444443
No 100
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=66.47 E-value=2.1 Score=34.63 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=6.4
Q ss_pred eecccCCcceeeehh
Q psy11588 91 FVCKMCGHRLFMRLS 105 (459)
Q Consensus 91 ~~C~~C~~~~f~~~~ 105 (459)
++|+.||.+ |.+..
T Consensus 29 ~~c~~c~~~-f~~~e 42 (154)
T PRK00464 29 RECLACGKR-FTTFE 42 (154)
T ss_pred eeccccCCc-ceEeE
Confidence 344455544 44443
No 101
>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=65.70 E-value=5.5 Score=32.61 Aligned_cols=30 Identities=20% Similarity=0.431 Sum_probs=15.4
Q ss_pred CccccccchhccCChHHHHHHHHHhCCCCCcccCccccc
Q psy11588 403 QKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSA 441 (459)
Q Consensus 403 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~ 441 (459)
.-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 3455555555555555553 13555555544
No 102
>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=65.67 E-value=5.1 Score=24.58 Aligned_cols=20 Identities=25% Similarity=0.609 Sum_probs=7.9
Q ss_pred cccCccccccCCh----HHHHHHH
Q psy11588 433 FVCDMCPSAFKLK----KHLQQHY 452 (459)
Q Consensus 433 ~~C~~C~~~f~~~----~~l~~H~ 452 (459)
..|.+|++.+... +.|.+|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4455555444432 4455554
No 103
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.35 E-value=2.8 Score=35.12 Aligned_cols=14 Identities=14% Similarity=0.487 Sum_probs=6.8
Q ss_pred cccCCCCCcCCChH
Q psy11588 376 VVCSYCGNTYKNPK 389 (459)
Q Consensus 376 ~~C~~C~~~f~~~~ 389 (459)
|.|+.|+..|+...
T Consensus 118 Y~Cp~C~~rytf~e 131 (178)
T PRK06266 118 FFCPNCHIRFTFDE 131 (178)
T ss_pred EECCCCCcEEeHHH
Confidence 44555555544443
No 104
>PF12907 zf-met2: Zinc-binding
Probab=64.02 E-value=4.9 Score=24.03 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=14.1
Q ss_pred cccccccc---ccCCHHHHHHHHHHHcCCC
Q psy11588 292 HCCHICKK---VFLRYRNLVCHIKAVHEKV 318 (459)
Q Consensus 292 ~~C~~C~~---~f~~~~~l~~H~~~~h~~~ 318 (459)
++|.+|.. ...+...|..|..+.|+..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 34566653 3334455666666555543
No 105
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=63.89 E-value=5.6 Score=25.18 Aligned_cols=21 Identities=29% Similarity=0.771 Sum_probs=11.2
Q ss_pred cccccchhccCCh-----HHHHHHHH
Q psy11588 405 SICDVCGKEFKMK-----KRLKEHMA 425 (459)
Q Consensus 405 ~~C~~C~~~f~~~-----~~l~~H~~ 425 (459)
-.|..|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3466666655443 35555555
No 106
>KOG4167|consensus
Probab=63.33 E-value=4.1 Score=41.00 Aligned_cols=29 Identities=21% Similarity=0.597 Sum_probs=25.5
Q ss_pred CCccccchhhHhhhhHHHHHHHHhhhccC
Q psy11588 54 KDVYHCADCEQVFLDKFVLELHLKIEHKD 82 (459)
Q Consensus 54 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~ 82 (459)
...|.|.+|+++|....++..||+.|.-.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 34699999999999999999999999643
No 107
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=63.24 E-value=3.7 Score=35.59 Aligned_cols=56 Identities=16% Similarity=0.245 Sum_probs=28.5
Q ss_pred eeecccCCcceeeehhHHhhhhhhccccccccccccccccccceeecCccchhhhhh
Q psy11588 90 WFVCKMCGHRLFMRLSDLRRHMQDYHCEFHFDVESCAVSRLQDITFPCEECKELCVL 146 (459)
Q Consensus 90 ~~~C~~C~~~~f~~~~~l~~H~~~h~~~~~~~~~~c~~~~~~~~~~~C~~C~~~f~~ 146 (459)
.+.|++|+.. |.+..-+....+.-.-+.-+.-.+-+....-=....||.|+..+..
T Consensus 5 ~~~CPvC~~~-F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 5 KITCPVCGKE-FKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred ceECCCCCCe-eeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 5789999988 8777655555543211111111111100000145689999886543
No 108
>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=62.86 E-value=5.3 Score=34.77 Aligned_cols=13 Identities=23% Similarity=0.685 Sum_probs=6.7
Q ss_pred cCCCCcccccccc
Q psy11588 287 SGEKDHCCHICKK 299 (459)
Q Consensus 287 ~~~~~~~C~~C~~ 299 (459)
++.+.|.|..|+.
T Consensus 138 hGGrif~CsfC~~ 150 (314)
T PF06524_consen 138 HGGRIFKCSFCDN 150 (314)
T ss_pred CCCeEEEeecCCC
Confidence 3444555555543
No 109
>KOG1280|consensus
Probab=62.69 E-value=14 Score=33.73 Aligned_cols=36 Identities=19% Similarity=0.487 Sum_probs=25.1
Q ss_pred CcccccchhhccChhHHHHhhhhhcCCCc--cccCCCC
Q psy11588 181 CHSCQKCEESFDNCNNLWSHMFIKHENSD--FVCNLCP 216 (459)
Q Consensus 181 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~--~~C~~C~ 216 (459)
.|.|++|+..=.+...|..|....|.+.+ ..|++|+
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 47888888877777778888777666544 3466664
No 110
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=60.71 E-value=8.4 Score=31.55 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=17.5
Q ss_pred CCCccccccccccccChHHHHHHHHHcCCCCCccccccccc
Q psy11588 317 KVRDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGAS 357 (459)
Q Consensus 317 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 357 (459)
+...|.|+.|+..|+....+. ..|.|+.||..
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 334466666666665555553 13666666544
No 111
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=59.71 E-value=5.2 Score=32.33 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=5.6
Q ss_pred cccCCCCCcCC
Q psy11588 376 VVCSYCGNTYK 386 (459)
Q Consensus 376 ~~C~~C~~~f~ 386 (459)
|.|+.|+..|.
T Consensus 100 Y~Cp~C~~~y~ 110 (147)
T smart00531 100 YKCPNCQSKYT 110 (147)
T ss_pred EECcCCCCEee
Confidence 44555555544
No 112
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=59.45 E-value=3.2 Score=27.09 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=6.9
Q ss_pred eeecccCCc
Q psy11588 90 WFVCKMCGH 98 (459)
Q Consensus 90 ~~~C~~C~~ 98 (459)
+|.|+.||.
T Consensus 48 ~Y~CP~CGF 56 (59)
T PRK14890 48 PYTCPKCGF 56 (59)
T ss_pred ceECCCCCC
Confidence 688888873
No 113
>KOG2186|consensus
Probab=59.35 E-value=6.6 Score=34.09 Aligned_cols=46 Identities=24% Similarity=0.593 Sum_probs=35.0
Q ss_pred cccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHH
Q psy11588 349 YVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIR 396 (459)
Q Consensus 349 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 396 (459)
|.|..||....- ..+.+|+-.-.+..|.|-.|++.|.. .+...|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhh
Confidence 678888877654 45677888877777888888888877 67777764
No 114
>PF15269 zf-C2H2_7: Zinc-finger
Probab=59.24 E-value=5.3 Score=24.10 Aligned_cols=24 Identities=29% Similarity=0.433 Sum_probs=20.4
Q ss_pred ccccchhhHhhhhHHHHHHHHhhh
Q psy11588 56 VYHCADCEQVFLDKFVLELHLKIE 79 (459)
Q Consensus 56 ~~~C~~C~~~f~~~~~L~~H~~~h 79 (459)
.|+|-.|+.+...++.|-.||+--
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 378999999999999999998643
No 115
>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=58.27 E-value=4.2 Score=22.08 Aligned_cols=20 Identities=15% Similarity=0.522 Sum_probs=13.5
Q ss_pred eeecccchhhccccccchhhh
Q psy11588 3 WTCCKCIAKYTSRSHLSLHLL 23 (459)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~ 23 (459)
|+|-.|++.| .......|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 6788999999 6666777754
No 116
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=53.15 E-value=2.9 Score=28.85 Aligned_cols=15 Identities=20% Similarity=0.525 Sum_probs=8.2
Q ss_pred CCccccc--cchhccCC
Q psy11588 402 RQKSICD--VCGKEFKM 416 (459)
Q Consensus 402 ~~~~~C~--~C~~~f~~ 416 (459)
+.-++|. .||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 3445565 56666654
No 117
>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=52.80 E-value=7.1 Score=24.19 Aligned_cols=27 Identities=33% Similarity=0.875 Sum_probs=16.0
Q ss_pred cccchhccccccccccccCCccccchhhH
Q psy11588 36 LSCEQCGCSLDFHSALYTKDVYHCADCEQ 64 (459)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~~~~~~C~~C~~ 64 (459)
+.|+.||.. ....+.....|+|..|.+
T Consensus 19 ~~CP~Cg~~--~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCCCCeEECCCCCC
Confidence 567777765 333333456677777753
No 118
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.78 E-value=14 Score=29.83 Aligned_cols=36 Identities=14% Similarity=0.539 Sum_probs=17.6
Q ss_pred CccccccccccccChHHHHHHHHHcCCCCCcccccccccc
Q psy11588 319 RDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASF 358 (459)
Q Consensus 319 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 358 (459)
..|.|+.|+..|.....+.. . . ....|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~-~--d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL-L--D-MDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh-c--C-CCCcEECCCCCCEE
Confidence 45666666666664333221 0 0 12236666666543
No 119
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=50.36 E-value=14 Score=30.98 Aligned_cols=30 Identities=23% Similarity=0.448 Sum_probs=15.8
Q ss_pred CccccccccccccChHHHHHHHHHcCCCCCccccccccc
Q psy11588 319 RDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGAS 357 (459)
Q Consensus 319 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 357 (459)
..|.|+.|+..|+....+. ..|.|+.||..
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 4466666666655554432 23556665543
No 120
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=49.86 E-value=6.5 Score=27.91 Aligned_cols=10 Identities=30% Similarity=1.095 Sum_probs=5.6
Q ss_pred eeecccCCcc
Q psy11588 90 WFVCKMCGHR 99 (459)
Q Consensus 90 ~~~C~~C~~~ 99 (459)
.+.|..|+..
T Consensus 53 IW~C~kCg~~ 62 (89)
T COG1997 53 IWKCRKCGAK 62 (89)
T ss_pred eEEcCCCCCe
Confidence 4556666555
No 121
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.41 E-value=10 Score=39.28 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=16.8
Q ss_pred cccccchhhccChhHHHHhhhhhcCCCccccCCCCCCC
Q psy11588 182 HSCQKCEESFDNCNNLWSHMFIKHENSDFVCNLCPSHS 219 (459)
Q Consensus 182 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 219 (459)
..|+.|+.. |..|+ ......|.+||..-
T Consensus 445 ~~Cp~Cd~~------lt~H~----~~~~L~CH~Cg~~~ 472 (730)
T COG1198 445 AECPNCDSP------LTLHK----ATGQLRCHYCGYQE 472 (730)
T ss_pred ccCCCCCcc------eEEec----CCCeeEeCCCCCCC
Confidence 457777654 33333 33567888888753
No 122
>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=49.26 E-value=11 Score=19.67 Aligned_cols=10 Identities=40% Similarity=1.205 Sum_probs=7.4
Q ss_pred eeecCccchh
Q psy11588 133 ITFPCEECKE 142 (459)
Q Consensus 133 ~~~~C~~C~~ 142 (459)
..|.|+.|++
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4688888874
No 123
>KOG1280|consensus
Probab=49.01 E-value=14 Score=33.71 Aligned_cols=58 Identities=16% Similarity=0.080 Sum_probs=38.9
Q ss_pred eeecccCCcceeeehhHHhhhhhhcccccccc--ccccccccccceeecCccchhhhhhhhhhhhh
Q psy11588 90 WFVCKMCGHRLFMRLSDLRRHMQDYHCEFHFD--VESCAVSRLQDITFPCEECKELCVLSKYCIKH 153 (459)
Q Consensus 90 ~~~C~~C~~~~f~~~~~l~~H~~~h~~~~~~~--~~~c~~~~~~~~~~~C~~C~~~f~~~~~l~~H 153 (459)
.|.|++|+.. -.+...|..|....|.+..+. |+.|+. .++.++.+.+.-........|
T Consensus 79 SftCPyC~~~-Gfte~~f~~Hv~s~Hpda~~~~icp~c~~-----~~~~qp~~~~~~~~~~~~~~~ 138 (381)
T KOG1280|consen 79 SFTCPYCGIM-GFTERQFGTHVLSQHPEASTSVICPLCAA-----NPEMQPIHSKETENLSVHWTE 138 (381)
T ss_pred cccCCccccc-ccchhHHHHHhhhcCcccCcceeeecccc-----CcccCchhhhhhhhhhhhhhh
Confidence 5889999977 567788888988877766543 455544 567777777655444444444
No 124
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.41 E-value=11 Score=39.08 Aligned_cols=40 Identities=23% Similarity=0.605 Sum_probs=26.0
Q ss_pred ccccccccccCCHHHHHHHHHHHcCCCCccccccccccccChHHHHHHHHHcCCCCCccccccccc
Q psy11588 292 HCCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGAS 357 (459)
Q Consensus 292 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 357 (459)
..|+.|+.... .|...+...|.+||.. ...|..|+.||..
T Consensus 445 ~~Cp~Cd~~lt-----------~H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT-----------LHKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE-----------EecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 34666665532 4555666788888764 3457788888755
No 125
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=48.10 E-value=6.9 Score=20.16 Aligned_cols=8 Identities=38% Similarity=1.385 Sum_probs=3.3
Q ss_pred cchhcccc
Q psy11588 38 CEQCGCSL 45 (459)
Q Consensus 38 C~~C~~~f 45 (459)
|+.||...
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 34444433
No 126
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=47.72 E-value=13 Score=21.67 Aligned_cols=32 Identities=31% Similarity=0.479 Sum_probs=17.4
Q ss_pred eeecccchhhccccccchhhhhccccccccccccccchhcccccc
Q psy11588 3 WTCCKCIAKYTSRSHLSLHLLSHSSDADEIKQELSCEQCGCSLDF 47 (459)
Q Consensus 3 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~C~~C~~~f~~ 47 (459)
+.|+.||++|.-...- . +.+-.|+.||..+..
T Consensus 2 r~C~~Cg~~Yh~~~~p--------P-----~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNP--------P-----KVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTTB---------------SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccccCC--------C-----CCCCccCCCCCeeEe
Confidence 5677777777632111 1 344557777765543
No 127
>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=46.99 E-value=8.1 Score=21.46 Aligned_cols=9 Identities=56% Similarity=1.394 Sum_probs=4.8
Q ss_pred eeecccCCc
Q psy11588 90 WFVCKMCGH 98 (459)
Q Consensus 90 ~~~C~~C~~ 98 (459)
.|.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 355665553
No 128
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=46.55 E-value=38 Score=30.50 Aligned_cols=77 Identities=21% Similarity=0.373 Sum_probs=39.1
Q ss_pred eeecCccchhhhhhhhhhhhhccccCCCCCCCCCCccccccccCCCCCCcccccchhhccChhHHHHhhh-hhcCCCccc
Q psy11588 133 ITFPCEECKELCVLSKYCIKHQDCSKAMSTPAPSSESVCIKHSNLIPKCHSCQKCEESFDNCNNLWSHMF-IKHENSDFV 211 (459)
Q Consensus 133 ~~~~C~~C~~~f~~~~~l~~H~~c~~~~~~~~~l~~~~~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~-~~~~~~~~~ 211 (459)
.|..|+.|+-.......|.+-.. ...+|.. ...+..+..|+.--|-.|.-.|.... .|.. .-.....|+
T Consensus 321 LPi~CP~Csl~LilsthLarSyh------hL~PLk~-f~E~p~~~~~ks~~Cf~CQ~~fp~~~---~~~~~~~~ss~rY~ 390 (421)
T COG5151 321 LPISCPICSLQLILSTHLARSYH------HLYPLKP-FVEKPEGTNPKSTHCFVCQGPFPKPP---VSPFDESTSSGRYQ 390 (421)
T ss_pred CCccCcchhHHHHHHHHHHHHHH------hhccCcc-cccccCCCCCCCccceeccCCCCCCC---CCccccccccccee
Confidence 36789999988877777765321 1111211 11222334444445666666665432 1111 111234577
Q ss_pred cCCCCCCC
Q psy11588 212 CNLCPSHS 219 (459)
Q Consensus 212 C~~C~~~f 219 (459)
|+.|...|
T Consensus 391 Ce~CK~~F 398 (421)
T COG5151 391 CELCKSTF 398 (421)
T ss_pred chhhhhhh
Confidence 77776666
No 129
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.45 E-value=6.7 Score=26.91 Aligned_cols=14 Identities=29% Similarity=0.755 Sum_probs=8.9
Q ss_pred CCccccchhhHhhh
Q psy11588 54 KDVYHCADCEQVFL 67 (459)
Q Consensus 54 ~~~~~C~~C~~~f~ 67 (459)
.-.|+|..|+..|.
T Consensus 10 tY~Y~c~~cg~~~d 23 (82)
T COG2331 10 TYSYECTECGNRFD 23 (82)
T ss_pred ceEEeecccchHHH
Confidence 34577777776654
No 130
>KOG4167|consensus
Probab=46.06 E-value=5.6 Score=40.05 Aligned_cols=28 Identities=14% Similarity=0.421 Sum_probs=25.5
Q ss_pred ceeecccchhhccccccchhhhhccccc
Q psy11588 2 VWTCCKCIAKYTSRSHLSLHLLSHSSDA 29 (459)
Q Consensus 2 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 29 (459)
.|.|..|+++|....++..||++|....
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 5899999999999999999999998743
No 131
>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=44.29 E-value=11 Score=20.75 Aligned_cols=22 Identities=18% Similarity=0.407 Sum_probs=6.8
Q ss_pred ccccccccccceeecCccchhh
Q psy11588 122 VESCAVSRLQDITFPCEECKEL 143 (459)
Q Consensus 122 ~~~c~~~~~~~~~~~C~~C~~~ 143 (459)
|..|+........|.|+.|+..
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDFD 24 (30)
T ss_dssp -TTTS----S--EEE-TTT---
T ss_pred CCcCCCcCCCCceEECccCCCc
Confidence 3334333333356888888764
No 132
>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=44.16 E-value=9.2 Score=33.34 Aligned_cols=14 Identities=29% Similarity=0.797 Sum_probs=10.2
Q ss_pred hcCCCccccCCCCC
Q psy11588 204 KHENSDFVCNLCPS 217 (459)
Q Consensus 204 ~~~~~~~~C~~C~~ 217 (459)
.||.+.|+|.+|..
T Consensus 137 ~hGGrif~CsfC~~ 150 (314)
T PF06524_consen 137 DHGGRIFKCSFCDN 150 (314)
T ss_pred cCCCeEEEeecCCC
Confidence 46777888888864
No 133
>KOG3507|consensus
Probab=43.03 E-value=21 Score=23.19 Aligned_cols=33 Identities=30% Similarity=0.505 Sum_probs=21.0
Q ss_pred ccccchhccccccccccccCCccccchhhHhhhhHHH
Q psy11588 35 ELSCEQCGCSLDFHSALYTKDVYHCADCEQVFLDKFV 71 (459)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~~~~~~C~~C~~~f~~~~~ 71 (459)
.|.|..|+... .|....+++|.+||..-..+..
T Consensus 20 iYiCgdC~~en----~lk~~D~irCReCG~RIlyKkR 52 (62)
T KOG3507|consen 20 IYICGDCGQEN----TLKRGDVIRCRECGYRILYKKR 52 (62)
T ss_pred EEEeccccccc----cccCCCcEehhhcchHHHHHHH
Confidence 47777777643 3445567888888876554443
No 134
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=41.82 E-value=7.6 Score=23.09 Aligned_cols=8 Identities=38% Similarity=1.327 Sum_probs=3.6
Q ss_pred cccchhhH
Q psy11588 57 YHCADCEQ 64 (459)
Q Consensus 57 ~~C~~C~~ 64 (459)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (39)
T PF01096_consen 29 YVCCNCGH 36 (39)
T ss_dssp EEESSSTE
T ss_pred EEeCCCCC
Confidence 44444443
No 135
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=41.76 E-value=12 Score=30.70 Aligned_cols=10 Identities=40% Similarity=1.085 Sum_probs=7.4
Q ss_pred eeecccCCcc
Q psy11588 90 WFVCKMCGHR 99 (459)
Q Consensus 90 ~~~C~~C~~~ 99 (459)
.|.|++||+.
T Consensus 134 ~~vC~vCGy~ 143 (166)
T COG1592 134 VWVCPVCGYT 143 (166)
T ss_pred EEEcCCCCCc
Confidence 5788888855
No 136
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=41.22 E-value=10 Score=22.73 Aligned_cols=18 Identities=28% Similarity=0.626 Sum_probs=9.7
Q ss_pred ccccchhhHhhhhHHHHH
Q psy11588 56 VYHCADCEQVFLDKFVLE 73 (459)
Q Consensus 56 ~~~C~~C~~~f~~~~~L~ 73 (459)
.+.|+.|+=.+.+..+|.
T Consensus 19 id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEECCCCCeEEccHHHHH
Confidence 455666655555555544
No 137
>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=40.74 E-value=14 Score=21.34 Aligned_cols=32 Identities=31% Similarity=0.686 Sum_probs=17.4
Q ss_pred eecccchhhccccccchhhhhccccccccccccccchhccccc
Q psy11588 4 TCCKCIAKYTSRSHLSLHLLSHSSDADEIKQELSCEQCGCSLD 46 (459)
Q Consensus 4 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~C~~C~~~f~ 46 (459)
.|+.|.+.+.+..+=..| -....|..||-.+.
T Consensus 1 lC~~C~~Ey~~p~~RR~~-----------~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFH-----------YQFISCTNCGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT------------TT--BTTCC-SCC
T ss_pred CCHHHHHHHcCCCCCccc-----------CcCccCCCCCCCEE
Confidence 377788888777764333 23556888886654
No 138
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.44 E-value=15 Score=27.25 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=7.8
Q ss_pred CCccccccchhcc
Q psy11588 402 RQKSICDVCGKEF 414 (459)
Q Consensus 402 ~~~~~C~~C~~~f 414 (459)
+.|..|++||++|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 4556666666666
No 139
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=39.91 E-value=13 Score=24.41 Aligned_cols=41 Identities=24% Similarity=0.559 Sum_probs=19.8
Q ss_pred Ccccccc-chhccCChHHHHHHHHHhCCCCCcccCc----cccccC
Q psy11588 403 QKSICDV-CGKEFKMKKRLKEHMAVHTTDRPFVCDM----CPSAFK 443 (459)
Q Consensus 403 ~~~~C~~-C~~~f~~~~~l~~H~~~H~~~~~~~C~~----C~~~f~ 443 (459)
.+..|+. |+..-..+..|..|+..-=..++..|+. |+..+.
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 3455666 3333223556677776555556667777 666554
No 140
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=39.81 E-value=44 Score=30.71 Aligned_cols=71 Identities=18% Similarity=0.351 Sum_probs=0.0
Q ss_pred cccccccccccccchHHHHHhhh---------------------------------------------------------
Q psy11588 349 YVCETCGASFVQWGSLNQHNLVH--------------------------------------------------------- 371 (459)
Q Consensus 349 ~~C~~C~~~f~~~~~l~~H~~~h--------------------------------------------------------- 371 (459)
+.|+.|++.|....-+..|+...
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~~v~~Ey~l~r~~kyl~d~~s~trs~V~r~la~ta~ER~aei~~l~r 318 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEEFVYSEYVLHRYLKYLGDPVSETRSLVLRSLAITAKERKAEISLLSR 318 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHhCChhHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q ss_pred ---------------------------CCCCcccCCCCCcCCChHHHHHHHHhhcCCCCccccccch-hccCChHHHHHH
Q psy11588 372 ---------------------------TAVNVVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCG-KEFKMKKRLKEH 423 (459)
Q Consensus 372 ---------------------------~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~-~~f~~~~~l~~H 423 (459)
.+.+|.=|.=.-..+-+..|-. .|.-...|.|.+|| +.+..+..+.+|
T Consensus 319 ~~~~~at~S~e~EGaeq~d~eQ~DE~~~~k~fdmPLG~DG~PmP~WL~k----lhgLd~ef~CEICgNyvy~GR~~FdrH 394 (470)
T COG5188 319 RKKQPATKSSEKEGAEQVDGEQRDEHVSGKSFDMPLGPDGLPMPRWLCK----LHGLDIEFECEICGNYVYYGRDRFDRH 394 (470)
T ss_pred HhhccCCCchhhcccccccccccchhhccCcccCCCCCCCCCCchHHHH----hcCCCcceeeeecccccccchHHHHhh
No 141
>PF14353 CpXC: CpXC protein
Probab=39.43 E-value=24 Score=27.68 Aligned_cols=22 Identities=27% Similarity=0.543 Sum_probs=11.9
Q ss_pred CcccccccccccccchHHHHHh
Q psy11588 348 KYVCETCGASFVQWGSLNQHNL 369 (459)
Q Consensus 348 ~~~C~~C~~~f~~~~~l~~H~~ 369 (459)
.|.|+.||..|.-...+..|-.
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred EEECCCCCCceecCCCEEEEcC
Confidence 3566666666655555444433
No 142
>KOG2272|consensus
Probab=39.26 E-value=14 Score=32.06 Aligned_cols=22 Identities=18% Similarity=0.576 Sum_probs=17.3
Q ss_pred CCCCcccccchhhccChhHHHH
Q psy11588 178 IPKCHSCQKCEESFDNCNNLWS 199 (459)
Q Consensus 178 ~~~~~~C~~C~~~f~~~~~l~~ 199 (459)
-|.+|.|++|++...+...++.
T Consensus 96 Hp~CF~Cd~Cn~~Lad~gf~rn 117 (332)
T KOG2272|consen 96 HPACFRCDLCNKHLADQGFYRN 117 (332)
T ss_pred CcccchhHHHHHHHhhhhhHhh
Confidence 3456999999999888777665
No 143
>KOG2807|consensus
Probab=39.12 E-value=50 Score=30.12 Aligned_cols=21 Identities=19% Similarity=0.313 Sum_probs=12.9
Q ss_pred CCccccccccccCCHHHHHHH
Q psy11588 290 KDHCCHICKKVFLRYRNLVCH 310 (459)
Q Consensus 290 ~~~~C~~C~~~f~~~~~l~~H 310 (459)
-|..|++|+-+......|.+-
T Consensus 289 LP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred CCccCCccceeEecchHHHHH
Confidence 356677777666666666554
No 144
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=38.90 E-value=15 Score=21.09 Aligned_cols=10 Identities=30% Similarity=0.869 Sum_probs=3.1
Q ss_pred cchhcccccc
Q psy11588 38 CEQCGCSLDF 47 (459)
Q Consensus 38 C~~C~~~f~~ 47 (459)
|..|++.|..
T Consensus 6 C~eC~~~f~d 15 (34)
T PF01286_consen 6 CDECGKPFMD 15 (34)
T ss_dssp -TTT--EES-
T ss_pred HhHhCCHHHH
Confidence 5555555544
No 145
>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=38.78 E-value=14 Score=20.45 Aligned_cols=21 Identities=33% Similarity=0.885 Sum_probs=10.4
Q ss_pred ccchhccccccccccccCCccccchhh
Q psy11588 37 SCEQCGCSLDFHSALYTKDVYHCADCE 63 (459)
Q Consensus 37 ~C~~C~~~f~~~~~l~~~~~~~C~~C~ 63 (459)
+|+.|++...... .|.|..|+
T Consensus 2 ~C~~C~~~~~~~~------~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY------FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE------eEEeCCCC
Confidence 4555555443322 36666665
No 146
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=38.48 E-value=9.4 Score=27.93 Aligned_cols=10 Identities=40% Similarity=0.727 Sum_probs=5.9
Q ss_pred eeecccCCcc
Q psy11588 90 WFVCKMCGHR 99 (459)
Q Consensus 90 ~~~C~~C~~~ 99 (459)
...|..||.+
T Consensus 46 ~~~Cg~CGls 55 (104)
T COG4888 46 TAVCGNCGLS 55 (104)
T ss_pred EEEcccCcce
Confidence 3456666655
No 147
>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=37.66 E-value=20 Score=28.16 Aligned_cols=20 Identities=35% Similarity=0.781 Sum_probs=7.6
Q ss_pred ccCccccccCChHHHHHHHHHhc
Q psy11588 434 VCDMCPSAFKLKKHLQQHYKVHL 456 (459)
Q Consensus 434 ~C~~C~~~f~~~~~l~~H~~~H~ 456 (459)
.|-.||+.|.. |.+|++.|+
T Consensus 74 ~clecGk~~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 74 ICLECGKKFKT---LKRHLRTHH 93 (132)
T ss_dssp E-TBT--EESB---HHHHHHHTT
T ss_pred EEccCCcccch---HHHHHHHcc
Confidence 44445544432 245554443
No 148
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=36.62 E-value=14 Score=31.87 Aligned_cols=26 Identities=31% Similarity=0.690 Sum_probs=15.5
Q ss_pred CcccCCCCCcCCChHHHHHHHHhhcC
Q psy11588 375 NVVCSYCGNTYKNPKSLESHIRYAHT 400 (459)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~~H~ 400 (459)
.|.|+.|++.|.-..-+..|+...|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 56677777777777667777666665
No 149
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=36.33 E-value=23 Score=30.51 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=21.1
Q ss_pred CCCCcccccccccccccchHHHHHhhhC
Q psy11588 345 GEKKYVCETCGASFVQWGSLNQHNLVHT 372 (459)
Q Consensus 345 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 372 (459)
.+..|.|+.|++.|.-..-...|+...+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 3456999999999999999999987654
No 150
>PRK04023 DNA polymerase II large subunit; Validated
Probab=36.24 E-value=30 Score=36.92 Aligned_cols=9 Identities=44% Similarity=1.269 Sum_probs=5.2
Q ss_pred ccccccccc
Q psy11588 321 HQCSVCGKA 329 (459)
Q Consensus 321 ~~C~~C~~~ 329 (459)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 456666654
No 151
>KOG2807|consensus
Probab=36.20 E-value=47 Score=30.32 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=12.9
Q ss_pred ccccccchhccCChHHHHHHHHHh
Q psy11588 404 KSICDVCGKEFKMKKRLKEHMAVH 427 (459)
Q Consensus 404 ~~~C~~C~~~f~~~~~l~~H~~~H 427 (459)
.|.|..|.-.|-.--+...|-..|
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh
Confidence 355666655555555555554444
No 152
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.84 E-value=34 Score=36.53 Aligned_cols=48 Identities=25% Similarity=0.637 Sum_probs=31.0
Q ss_pred CcccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHHhhcCCCCccccccchhccCChHHHHHHHHHh
Q psy11588 348 KYVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHMAVH 427 (459)
Q Consensus 348 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H 427 (459)
...|+.||... ..+.|+.||.. ....+.|+.|+...
T Consensus 626 ~RfCpsCG~~t---------------~~frCP~CG~~----------------Te~i~fCP~CG~~~------------- 661 (1121)
T PRK04023 626 RRKCPSCGKET---------------FYRRCPFCGTH----------------TEPVYRCPRCGIEV------------- 661 (1121)
T ss_pred CccCCCCCCcC---------------CcccCCCCCCC----------------CCcceeCccccCcC-------------
Confidence 46788888762 23678888865 13457788885432
Q ss_pred CCCCCcccCcccccc
Q psy11588 428 TTDRPFVCDMCPSAF 442 (459)
Q Consensus 428 ~~~~~~~C~~C~~~f 442 (459)
.++.|+.||..-
T Consensus 662 ---~~y~CPKCG~El 673 (1121)
T PRK04023 662 ---EEDECEKCGREP 673 (1121)
T ss_pred ---CCCcCCCCCCCC
Confidence 346788887543
No 153
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=35.62 E-value=15 Score=23.69 Aligned_cols=8 Identities=38% Similarity=1.120 Sum_probs=3.6
Q ss_pred cchhcccc
Q psy11588 38 CEQCGCSL 45 (459)
Q Consensus 38 C~~C~~~f 45 (459)
|+.||+.|
T Consensus 8 C~~Cg~~~ 15 (54)
T PF14446_consen 8 CPVCGKKF 15 (54)
T ss_pred ChhhCCcc
Confidence 44444444
No 154
>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=35.53 E-value=21 Score=28.15 Aligned_cols=25 Identities=48% Similarity=0.849 Sum_probs=15.1
Q ss_pred cccccchhccCChHHHHHHHHHhCCCCC
Q psy11588 405 SICDVCGKEFKMKKRLKEHMAVHTTDRP 432 (459)
Q Consensus 405 ~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 432 (459)
..|-+||+.|.. |.+|++.|+|-.|
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 568888888866 4888888877543
No 155
>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=35.11 E-value=22 Score=35.49 Aligned_cols=14 Identities=14% Similarity=0.598 Sum_probs=9.3
Q ss_pred CCCccccCCCCCCC
Q psy11588 206 ENSDFVCNLCPSHS 219 (459)
Q Consensus 206 ~~~~~~C~~C~~~f 219 (459)
......|.+||...
T Consensus 237 ~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 237 KEGKLRCHYCGYQE 250 (505)
T ss_pred CCCeEEcCCCcCcC
Confidence 34567788887654
No 156
>KOG2593|consensus
Probab=34.59 E-value=39 Score=32.22 Aligned_cols=36 Identities=19% Similarity=0.519 Sum_probs=19.9
Q ss_pred CCCccccccccccCCHHHHHHHHHHHcCCCCccccccccc
Q psy11588 289 EKDHCCHICKKVFLRYRNLVCHIKAVHEKVRDHQCSVCGK 328 (459)
Q Consensus 289 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~ 328 (459)
...|.|+.|.+.|.....++. .-.....|.|..|+-
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L----~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQL----LDNETGEFHCENCGG 161 (436)
T ss_pred cccccCCccccchhhhHHHHh----hcccCceEEEecCCC
Confidence 345777777777765554432 222334567777764
No 157
>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=34.53 E-value=23 Score=21.17 Aligned_cols=27 Identities=19% Similarity=0.511 Sum_probs=9.3
Q ss_pred ccchhccccccccccc-cCCccccchhh
Q psy11588 37 SCEQCGCSLDFHSALY-TKDVYHCADCE 63 (459)
Q Consensus 37 ~C~~C~~~f~~~~~l~-~~~~~~C~~C~ 63 (459)
.|..|+.-++-...+. +.+.+.|..|+
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~ 31 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCG 31 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT-
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCC
Confidence 4555554444433333 22344455444
No 158
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.30 E-value=21 Score=25.56 Aligned_cols=13 Identities=23% Similarity=0.692 Sum_probs=5.9
Q ss_pred ccccchhcccccc
Q psy11588 35 ELSCEQCGCSLDF 47 (459)
Q Consensus 35 ~~~C~~C~~~f~~ 47 (459)
|-.|..||..|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 3344444444443
No 159
>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=34.24 E-value=17 Score=24.78 Aligned_cols=24 Identities=25% Similarity=0.773 Sum_probs=8.1
Q ss_pred cccchhccccccccccccCCccccchhhH
Q psy11588 36 LSCEQCGCSLDFHSALYTKDVYHCADCEQ 64 (459)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~~~~~~C~~C~~ 64 (459)
-.|..|++.|... .+.+.|..||.
T Consensus 10 ~~C~~C~~~F~~~-----~rrhhCr~CG~ 33 (69)
T PF01363_consen 10 SNCMICGKKFSLF-----RRRHHCRNCGR 33 (69)
T ss_dssp SB-TTT--B-BSS-----S-EEE-TTT--
T ss_pred CcCcCcCCcCCCc-----eeeEccCCCCC
Confidence 3466666666331 33455666664
No 160
>KOG0696|consensus
Probab=33.47 E-value=21 Score=33.94 Aligned_cols=59 Identities=24% Similarity=0.499 Sum_probs=37.0
Q ss_pred CCCCcccccccccccccchHHHHHhhhCCCCcccCCCCCcCCChHHHHHHHHhhcCCCCccccccch
Q psy11588 345 GEKKYVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCG 411 (459)
Q Consensus 345 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~ 411 (459)
|.+-|+|.+|. +..|.+-|.-..|.|+-=++.+.+...-..|.-..|+-..|--|+.||
T Consensus 70 gKQGfQCqvC~--------fvvHkrChefVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCG 128 (683)
T KOG0696|consen 70 GKQGFQCQVCC--------FVVHKRCHEFVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCG 128 (683)
T ss_pred ccCceeeeEEe--------ehhhhhhcceEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHH
Confidence 44556666663 345666666666777776666666666666655566655666677776
No 161
>KOG1842|consensus
Probab=33.13 E-value=24 Score=33.59 Aligned_cols=34 Identities=24% Similarity=0.305 Sum_probs=27.6
Q ss_pred cCCCCCCcccccchhhccChhHHHHhhhhhcCCC
Q psy11588 175 SNLIPKCHSCQKCEESFDNCNNLWSHMFIKHENS 208 (459)
Q Consensus 175 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 208 (459)
++.....|.|++|...|.+...|..|....|++.
T Consensus 9 s~~i~egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 9 SGEILEGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cchhhhcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 4444444999999999999999999998877653
No 162
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=31.91 E-value=15 Score=27.63 Aligned_cols=38 Identities=18% Similarity=0.197 Sum_probs=19.2
Q ss_pred cccccchhhccChhHHHHhhhhhcCCCccccCCCCCCC
Q psy11588 182 HSCQKCEESFDNCNNLWSHMFIKHENSDFVCNLCPSHS 219 (459)
Q Consensus 182 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 219 (459)
..|+.||..-.....++.--.......-|.|..|+..+
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred CCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCee
Confidence 67999986543322221110001111348898898765
No 163
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=31.89 E-value=18 Score=21.68 Aligned_cols=7 Identities=43% Similarity=1.383 Sum_probs=2.8
Q ss_pred cccchhh
Q psy11588 57 YHCADCE 63 (459)
Q Consensus 57 ~~C~~C~ 63 (459)
|.|..|+
T Consensus 29 y~C~~C~ 35 (40)
T smart00440 29 YVCTKCG 35 (40)
T ss_pred EEeCCCC
Confidence 3344443
No 164
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=31.67 E-value=19 Score=22.73 Aligned_cols=9 Identities=56% Similarity=1.460 Sum_probs=4.4
Q ss_pred eecccCCcc
Q psy11588 91 FVCKMCGHR 99 (459)
Q Consensus 91 ~~C~~C~~~ 99 (459)
+.|+.||+.
T Consensus 21 ~vC~~Cg~~ 29 (52)
T smart00661 21 FVCRKCGYE 29 (52)
T ss_pred EECCcCCCe
Confidence 445555544
No 165
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=31.34 E-value=26 Score=30.51 Aligned_cols=69 Identities=19% Similarity=0.392 Sum_probs=35.3
Q ss_pred cchhhhhccccccccccccccchhccccccccccccCCccccchhhHhhhhHHHHHHHHhhhccCCCCCCC-----ceee
Q psy11588 18 LSLHLLSHSSDADEIKQELSCEQCGCSLDFHSALYTKDVYHCADCEQVFLDKFVLELHLKIEHKDNMFPKS-----HWFV 92 (459)
Q Consensus 18 l~~H~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~-----~~~~ 92 (459)
|.+.-+.+...-..++..|.|..|+...-... -..++.-+|..|.+.|. |.|.+ .-|.
T Consensus 95 lrm~d~a~~~~ip~~drqFaC~~Cd~~WwRrv-p~rKeVSRCr~C~~rYD----------------PVP~dkmwG~aef~ 157 (278)
T PF15135_consen 95 LRMFDDAQENLIPSVDRQFACSSCDHMWWRRV-PQRKEVSRCRKCRKRYD----------------PVPCDKMWGIAEFH 157 (278)
T ss_pred HHHhhhhhhccccccceeeeccccchHHHhcc-CcccccccccccccccC----------------CCccccccceeeee
Confidence 34443333333233356788888876432211 11234456777776653 22222 2477
Q ss_pred cccCCcceeeeh
Q psy11588 93 CKMCGHRLFMRL 104 (459)
Q Consensus 93 C~~C~~~~f~~~ 104 (459)
|+.|+.. |...
T Consensus 158 C~~C~h~-F~G~ 168 (278)
T PF15135_consen 158 CPKCRHN-FRGF 168 (278)
T ss_pred ccccccc-chhh
Confidence 8888877 6654
No 166
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=31.28 E-value=51 Score=19.83 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=4.6
Q ss_pred ccccchhccC
Q psy11588 406 ICDVCGKEFK 415 (459)
Q Consensus 406 ~C~~C~~~f~ 415 (459)
.|+.||..|.
T Consensus 15 ~C~~CgM~Y~ 24 (41)
T PF13878_consen 15 TCPTCGMLYS 24 (41)
T ss_pred CCCCCCCEEC
Confidence 4445544443
No 167
>KOG2593|consensus
Probab=31.09 E-value=55 Score=31.26 Aligned_cols=17 Identities=18% Similarity=0.505 Sum_probs=8.2
Q ss_pred CccccccchhccCChHH
Q psy11588 403 QKSICDVCGKEFKMKKR 419 (459)
Q Consensus 403 ~~~~C~~C~~~f~~~~~ 419 (459)
.-|.|+.|.+.|....+
T Consensus 127 ~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEA 143 (436)
T ss_pred ccccCCccccchhhhHH
Confidence 34555555555544333
No 168
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.48 E-value=21 Score=18.90 Aligned_cols=6 Identities=50% Similarity=1.680 Sum_probs=2.7
Q ss_pred cchhcc
Q psy11588 38 CEQCGC 43 (459)
Q Consensus 38 C~~C~~ 43 (459)
|+.||+
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 444444
No 169
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.47 E-value=21 Score=36.33 Aligned_cols=51 Identities=24% Similarity=0.573 Sum_probs=37.8
Q ss_pred ccchhccccccccccccC------Ccc-ccchhhHhhhhHHHHHHHHhhhccCCCCCCCceeecccCCcc
Q psy11588 37 SCEQCGCSLDFHSALYTK------DVY-HCADCEQVFLDKFVLELHLKIEHKDNMFPKSHWFVCKMCGHR 99 (459)
Q Consensus 37 ~C~~C~~~f~~~~~l~~~------~~~-~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~ 99 (459)
.|+.||-.|+-..+|--+ ..| .|+.|.+.+.+..+-+-|. + +..|+.||-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHA------Q------p~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHA------Q------PIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcccccccc------c------cccCcccCCC
Confidence 499999999888777422 223 4999999999887766553 2 4679999965
No 170
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=29.31 E-value=27 Score=22.51 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=16.3
Q ss_pred cccccchhccccccccccccCCccccchh
Q psy11588 34 QELSCEQCGCSLDFHSALYTKDVYHCADC 62 (459)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~~~~~~C~~C 62 (459)
.=|.|..|++.+.....+..+...-|..|
T Consensus 25 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c 53 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGDFYEKDGKPYCKDC 53 (58)
T ss_dssp TTSBETTTTCBTTTSSEEEETTEEEEHHH
T ss_pred cccccCCCCCccCCCeeEeECCEEECHHH
Confidence 34778888877766653333333444443
No 171
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=28.85 E-value=43 Score=26.16 Aligned_cols=58 Identities=17% Similarity=0.287 Sum_probs=38.8
Q ss_pred ccccccchhccccccccccccCCccccchhhHhhhhHHHHHHHHhhhccCCCCCCCceeecccCCcceeeehh
Q psy11588 33 KQELSCEQCGCSLDFHSALYTKDVYHCADCEQVFLDKFVLELHLKIEHKDNMFPKSHWFVCKMCGHRLFMRLS 105 (459)
Q Consensus 33 ~~~~~C~~C~~~f~~~~~l~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~~f~~~~ 105 (459)
.+.|.|++|..+.....-|.+.+--.=.+|+.-+ +.|-.|-..|- +|++|..+ |.+.+
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cy---a~LWK~~~~yp-----------vCPvCkTS-FKss~ 135 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACY---ANLWKFCNLYP-----------VCPVCKTS-FKSSS 135 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHH---HHHHHHcccCC-----------CCCccccc-ccccc
Confidence 4678999999998888888665433333465554 34666655441 59999877 86654
No 172
>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=28.17 E-value=14 Score=25.55 Aligned_cols=28 Identities=18% Similarity=0.470 Sum_probs=11.6
Q ss_pred ccccchhccccccccccccCCccccchhh
Q psy11588 35 ELSCEQCGCSLDFHSALYTKDVYHCADCE 63 (459)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~~~~~~C~~C~ 63 (459)
+..|..|+..+......-+ ..|.|+.|+
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~-~~~~C~~C~ 68 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCG-ADYFCPICG 68 (71)
T ss_dssp EEEETTT--EEES-SBTT---SEEETTTT
T ss_pred CeECCCCCCccChhhhhcC-CCccCcCcC
Confidence 5556666665544433222 335555554
No 173
>KOG4124|consensus
Probab=28.04 E-value=11 Score=34.48 Aligned_cols=49 Identities=29% Similarity=0.630 Sum_probs=32.3
Q ss_pred Ccccccc--chhccCChHHHHHHHHHhC-------------------CCCCcccCccccccCChHHHHHH
Q psy11588 403 QKSICDV--CGKEFKMKKRLKEHMAVHT-------------------TDRPFVCDMCPSAFKLKKHLQQH 451 (459)
Q Consensus 403 ~~~~C~~--C~~~f~~~~~l~~H~~~H~-------------------~~~~~~C~~C~~~f~~~~~l~~H 451 (459)
++|+|++ |.+.+.....|..|...-+ ..|+|+|++|.+++.....|.-|
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 4566654 6666666666666644211 24789999999988877666555
No 174
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=27.66 E-value=24 Score=26.96 Aligned_cols=12 Identities=42% Similarity=0.645 Sum_probs=6.4
Q ss_pred ccccchhhHhhh
Q psy11588 56 VYHCADCEQVFL 67 (459)
Q Consensus 56 ~~~C~~C~~~f~ 67 (459)
...|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (113)
T PRK12380 70 QAWCWDCSQVVE 81 (113)
T ss_pred EEEcccCCCEEe
Confidence 355666665543
No 175
>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=27.43 E-value=25 Score=22.68 Aligned_cols=9 Identities=33% Similarity=0.970 Sum_probs=3.8
Q ss_pred cchhccccc
Q psy11588 38 CEQCGCSLD 46 (459)
Q Consensus 38 C~~C~~~f~ 46 (459)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 344444443
No 176
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.16 E-value=25 Score=27.63 Aligned_cols=33 Identities=21% Similarity=0.490 Sum_probs=16.8
Q ss_pred cccchhcccccc--ccccccCCccccchhhHhhhh
Q psy11588 36 LSCEQCGCSLDF--HSALYTKDVYHCADCEQVFLD 68 (459)
Q Consensus 36 ~~C~~C~~~f~~--~~~l~~~~~~~C~~C~~~f~~ 68 (459)
..|+.|+..... .....+...|+|..|+++|..
T Consensus 31 ~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccceeeECCccccccccccCCcCcceee
Confidence 446666665411 112223455666666666653
No 177
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=26.77 E-value=21 Score=22.67 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=5.8
Q ss_pred eeecccCCcc
Q psy11588 90 WFVCKMCGHR 99 (459)
Q Consensus 90 ~~~C~~C~~~ 99 (459)
.+.|..|+..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 3566666654
No 178
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=26.33 E-value=27 Score=20.76 Aligned_cols=14 Identities=14% Similarity=0.484 Sum_probs=9.1
Q ss_pred ceeecccchhhccc
Q psy11588 2 VWTCCKCIAKYTSR 15 (459)
Q Consensus 2 ~~~C~~C~~~f~~~ 15 (459)
+|.|..|+..|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 56677777766543
No 179
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.76 E-value=29 Score=27.52 Aligned_cols=14 Identities=21% Similarity=0.567 Sum_probs=8.1
Q ss_pred CccccchhhHhhhh
Q psy11588 55 DVYHCADCEQVFLD 68 (459)
Q Consensus 55 ~~~~C~~C~~~f~~ 68 (459)
..+.|..||..|..
T Consensus 69 ~~~~C~~CG~~~~~ 82 (135)
T PRK03824 69 AVLKCRNCGNEWSL 82 (135)
T ss_pred eEEECCCCCCEEec
Confidence 34666666665543
No 180
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.75 E-value=45 Score=33.38 Aligned_cols=9 Identities=33% Similarity=0.634 Sum_probs=6.0
Q ss_pred ccccCCCCC
Q psy11588 209 DFVCNLCPS 217 (459)
Q Consensus 209 ~~~C~~C~~ 217 (459)
|..|+.|+.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 456777764
No 181
>KOG1842|consensus
Probab=25.59 E-value=39 Score=32.25 Aligned_cols=26 Identities=23% Similarity=0.466 Sum_probs=14.1
Q ss_pred CcccCCCCCcCCChHHHHHHHHhhcC
Q psy11588 375 NVVCSYCGNTYKNPKSLESHIRYAHT 400 (459)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~~H~ 400 (459)
.|.||+|...|.+...|..|....|.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcc
Confidence 35555555555555555555554553
No 182
>KOG3408|consensus
Probab=25.16 E-value=41 Score=25.68 Aligned_cols=21 Identities=33% Similarity=0.520 Sum_probs=11.2
Q ss_pred cccccchhccCChHHHHHHHH
Q psy11588 405 SICDVCGKEFKMKKRLKEHMA 425 (459)
Q Consensus 405 ~~C~~C~~~f~~~~~l~~H~~ 425 (459)
|.|-.|.+-|.+...|..|.+
T Consensus 58 fyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eehhhhhhhhcchHHHHHHHh
Confidence 455555555555555555543
No 183
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=25.03 E-value=51 Score=32.18 Aligned_cols=26 Identities=23% Similarity=0.576 Sum_probs=19.1
Q ss_pred cccCCCCCcCCChHHHHHHHHhhcCC
Q psy11588 376 VVCSYCGNTYKNPKSLESHIRYAHTI 401 (459)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~~H~~ 401 (459)
+.|+.|.+.|.+...+..|+...|.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 46777777777777777777766754
No 184
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=24.67 E-value=29 Score=25.47 Aligned_cols=17 Identities=24% Similarity=0.548 Sum_probs=11.9
Q ss_pred Cceeecccchhhccccc
Q psy11588 1 MVWTCCKCIAKYTSRSH 17 (459)
Q Consensus 1 ~~~~C~~C~~~f~~~~~ 17 (459)
+|..|..||.+|.+-+.
T Consensus 1 MpH~CtrCG~vf~~g~~ 17 (112)
T COG3364 1 MPHQCTRCGEVFDDGSE 17 (112)
T ss_pred CCceecccccccccccH
Confidence 46778888888877543
No 185
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.40 E-value=24 Score=25.14 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=4.5
Q ss_pred eeecccCCcc
Q psy11588 90 WFVCKMCGHR 99 (459)
Q Consensus 90 ~~~C~~C~~~ 99 (459)
...|.+|+..
T Consensus 46 ~~~C~~Cg~~ 55 (81)
T PF05129_consen 46 ILSCRVCGES 55 (81)
T ss_dssp EEEESSS--E
T ss_pred EEEecCCCCe
Confidence 3456666655
No 186
>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=23.96 E-value=24 Score=22.48 Aligned_cols=25 Identities=20% Similarity=0.485 Sum_probs=11.1
Q ss_pred CccccchhhHhhhhHHHHHHHHhhh
Q psy11588 55 DVYHCADCEQVFLDKFVLELHLKIE 79 (459)
Q Consensus 55 ~~~~C~~C~~~f~~~~~L~~H~~~h 79 (459)
..|+|+.|...|=-.-++-.|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 3466666666665555555555544
No 187
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=23.78 E-value=29 Score=35.39 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=24.3
Q ss_pred ccccchhhccChhHHHHhhhhhcCCCccccCCCCCC
Q psy11588 183 SCQKCEESFDNCNNLWSHMFIKHENSDFVCNLCPSH 218 (459)
Q Consensus 183 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 218 (459)
.|+.|.+.|.+..+=+-|. .+..|+.||-.
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 6999999999987766664 57889999853
No 188
>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=23.64 E-value=32 Score=26.39 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=6.1
Q ss_pred cccchhhHhhh
Q psy11588 57 YHCADCEQVFL 67 (459)
Q Consensus 57 ~~C~~C~~~f~ 67 (459)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 55666665554
No 189
>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=23.64 E-value=1.1e+02 Score=24.29 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=16.3
Q ss_pred ccchhccccccccccccCCccccchhhHhh
Q psy11588 37 SCEQCGCSLDFHSALYTKDVYHCADCEQVF 66 (459)
Q Consensus 37 ~C~~C~~~f~~~~~l~~~~~~~C~~C~~~f 66 (459)
.|+.||+.|... . ...|+.|.+.-
T Consensus 5 nC~~CgklF~~~--~----~~iCp~C~~~~ 28 (137)
T TIGR03826 5 NCPKCGRLFVKT--G----RDVCPSCYEEE 28 (137)
T ss_pred cccccchhhhhc--C----CccCHHHhHHH
Confidence 588888888762 1 13499997643
No 190
>KOG0782|consensus
Probab=23.39 E-value=36 Score=33.49 Aligned_cols=50 Identities=26% Similarity=0.474 Sum_probs=38.9
Q ss_pred cccchhhhhccccccccccccccchhccccccccccccCCc--cccchhhHhhhhHH
Q psy11588 16 SHLSLHLLSHSSDADEIKQELSCEQCGCSLDFHSALYTKDV--YHCADCEQVFLDKF 70 (459)
Q Consensus 16 ~~l~~H~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~~~~--~~C~~C~~~f~~~~ 70 (459)
+.|.+|-=+|.. ...-+|..||++|..+-.+.+++. ..|..|...|-.+.
T Consensus 239 ~~fvrHHWVHrr-----RqeGkC~~CgKgFQQKf~FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHWVHRR-----RQEGKCNTCGKGFQQKFFFHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhHhhHh-----hhccccchhhhhhhhheeeccccEEEEEehHHHHHhhcch
Confidence 367788777766 456789999999988777776653 57999999998776
No 191
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=23.24 E-value=34 Score=22.09 Aligned_cols=11 Identities=18% Similarity=0.863 Sum_probs=4.9
Q ss_pred cccchhhHhhh
Q psy11588 57 YHCADCEQVFL 67 (459)
Q Consensus 57 ~~C~~C~~~f~ 67 (459)
.+|+.|+..|.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 34444444443
No 192
>KOG3408|consensus
Probab=22.90 E-value=48 Score=25.34 Aligned_cols=30 Identities=23% Similarity=0.525 Sum_probs=25.2
Q ss_pred CCCCCceeecccCCcceeeehhHHhhhhhhc
Q psy11588 84 MFPKSHWFVCKMCGHRLFMRLSDLRRHMQDY 114 (459)
Q Consensus 84 ~~~~~~~~~C~~C~~~~f~~~~~l~~H~~~h 114 (459)
..|+...|.|-.|... |.+...|..|.++-
T Consensus 51 dlPG~GqfyCi~CaRy-Fi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 51 DLPGGGQFYCIECARY-FIDAKALKTHFKTK 80 (129)
T ss_pred CCCCCceeehhhhhhh-hcchHHHHHHHhcc
Confidence 3467778999999977 99999999999763
No 193
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=22.84 E-value=50 Score=25.77 Aligned_cols=20 Identities=30% Similarity=0.544 Sum_probs=9.3
Q ss_pred ccCccccccCChHHHHHHHHHhc
Q psy11588 434 VCDMCPSAFKLKKHLQQHYKVHL 456 (459)
Q Consensus 434 ~C~~C~~~f~~~~~l~~H~~~H~ 456 (459)
.|-.+|+.|. +|++|+.+|.
T Consensus 78 icLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEeccCcchH---HHHHHHhccc
Confidence 3444444442 4445555444
No 194
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.32 E-value=64 Score=21.22 Aligned_cols=6 Identities=50% Similarity=1.763 Sum_probs=2.6
Q ss_pred cccccc
Q psy11588 349 YVCETC 354 (459)
Q Consensus 349 ~~C~~C 354 (459)
|.|+.|
T Consensus 32 ymC~eC 37 (68)
T COG4896 32 YMCPEC 37 (68)
T ss_pred Eechhh
Confidence 444444
No 195
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=22.29 E-value=73 Score=28.79 Aligned_cols=26 Identities=19% Similarity=0.483 Sum_probs=14.7
Q ss_pred CCccccchhhHhhhhHHHHHHHHhhh
Q psy11588 54 KDVYHCADCEQVFLDKFVLELHLKIE 79 (459)
Q Consensus 54 ~~~~~C~~C~~~f~~~~~L~~H~~~h 79 (459)
...|+|..|...|-.--+.-.|...|
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHh
Confidence 34566666666665555555555444
No 196
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.55 E-value=57 Score=34.09 Aligned_cols=13 Identities=15% Similarity=0.524 Sum_probs=8.5
Q ss_pred CCccccCCCCCCC
Q psy11588 207 NSDFVCNLCPSHS 219 (459)
Q Consensus 207 ~~~~~C~~C~~~f 219 (459)
.....|..||...
T Consensus 406 ~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 406 QRRLRCHHCGYQE 418 (679)
T ss_pred CCeEECCCCcCCC
Confidence 3456777887654
No 197
>PF12773 DZR: Double zinc ribbon
Probab=21.38 E-value=47 Score=20.75 Aligned_cols=8 Identities=50% Similarity=1.423 Sum_probs=3.4
Q ss_pred cchhcccc
Q psy11588 38 CEQCGCSL 45 (459)
Q Consensus 38 C~~C~~~f 45 (459)
|+.||..+
T Consensus 15 C~~CG~~l 22 (50)
T PF12773_consen 15 CPHCGTPL 22 (50)
T ss_pred ChhhcCCh
Confidence 44444433
No 198
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=21.27 E-value=43 Score=20.13 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=17.5
Q ss_pred ccchhccccccccccc-cC-CccccchhhHhhh
Q psy11588 37 SCEQCGCSLDFHSALY-TK-DVYHCADCEQVFL 67 (459)
Q Consensus 37 ~C~~C~~~f~~~~~l~-~~-~~~~C~~C~~~f~ 67 (459)
.|..||++-.....|. +. ..|.|+.|=....
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~~ 35 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQAY 35 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHHH
Confidence 4777777776665554 22 4788888865543
No 199
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.02 E-value=56 Score=20.50 Aligned_cols=21 Identities=24% Similarity=0.841 Sum_probs=11.7
Q ss_pred cccccccccccceeecCccch
Q psy11588 121 DVESCAVSRLQDITFPCEECK 141 (459)
Q Consensus 121 ~~~~c~~~~~~~~~~~C~~C~ 141 (459)
.|+.|+........|+|..|.
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~ 22 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECD 22 (48)
T ss_pred CCCCCCCCccccceEECCCCC
Confidence 344454433344567777776
No 200
>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=21.00 E-value=26 Score=26.80 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=4.7
Q ss_pred cccchhhHhhh
Q psy11588 57 YHCADCEQVFL 67 (459)
Q Consensus 57 ~~C~~C~~~f~ 67 (459)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 44555554443
No 201
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.87 E-value=33 Score=19.72 Aligned_cols=11 Identities=36% Similarity=0.881 Sum_probs=6.1
Q ss_pred cccccccChhc
Q psy11588 262 VNYKCPDCSAI 272 (459)
Q Consensus 262 ~~~~C~~C~~~ 272 (459)
..+.|+.|+.+
T Consensus 21 ~R~vC~~Cg~I 31 (34)
T PF14803_consen 21 ERLVCPACGFI 31 (34)
T ss_dssp -EEEETTTTEE
T ss_pred cceECCCCCCE
Confidence 34567766654
No 202
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=20.51 E-value=18 Score=22.58 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=7.5
Q ss_pred ccccchhcccccc
Q psy11588 35 ELSCEQCGCSLDF 47 (459)
Q Consensus 35 ~~~C~~C~~~f~~ 47 (459)
+|.|+.|+-++..
T Consensus 7 ry~CDLCn~~~p~ 19 (57)
T PF14445_consen 7 RYSCDLCNSSHPI 19 (57)
T ss_pred hHhHHhhcccCcH
Confidence 4566666665543
No 203
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=20.43 E-value=64 Score=20.39 Aligned_cols=9 Identities=44% Similarity=1.010 Sum_probs=3.8
Q ss_pred cccccChhc
Q psy11588 264 YKCPDCSAI 272 (459)
Q Consensus 264 ~~C~~C~~~ 272 (459)
+.|..||..
T Consensus 5 l~C~dCg~~ 13 (49)
T PF13451_consen 5 LTCKDCGAE 13 (49)
T ss_pred EEcccCCCe
Confidence 344444443
No 204
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=20.22 E-value=70 Score=31.25 Aligned_cols=21 Identities=29% Similarity=0.657 Sum_probs=12.4
Q ss_pred cccccChhcccCHHHHHHHHh
Q psy11588 264 YKCPDCSAILLSYGGFTSHLD 284 (459)
Q Consensus 264 ~~C~~C~~~f~~~~~l~~H~~ 284 (459)
+.|+.|++.|.+...+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 455666666666666666654
No 205
>KOG3214|consensus
Probab=20.08 E-value=52 Score=24.12 Aligned_cols=8 Identities=25% Similarity=1.107 Sum_probs=4.1
Q ss_pred ecccCCcc
Q psy11588 92 VCKMCGHR 99 (459)
Q Consensus 92 ~C~~C~~~ 99 (459)
.|.+|+..
T Consensus 49 sC~iC~es 56 (109)
T KOG3214|consen 49 SCRICEES 56 (109)
T ss_pred eeeehhhh
Confidence 45555544
Done!