Query psy6525
Match_columns 360
No_of_seqs 475 out of 2584
Neff 10.2
Searched_HMMs 46136
Date Fri Aug 16 20:18:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6525.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6525hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3608|consensus 100.0 1.9E-28 4.1E-33 206.7 14.4 247 99-347 69-378 (467)
2 KOG2462|consensus 100.0 6.6E-30 1.4E-34 210.4 5.4 131 184-315 130-264 (279)
3 KOG1074|consensus 100.0 4.5E-30 9.7E-35 238.3 4.7 191 157-347 606-933 (958)
4 KOG2462|consensus 100.0 3.4E-29 7.3E-34 206.2 6.4 130 211-342 130-264 (279)
5 KOG3608|consensus 99.9 7.2E-27 1.6E-31 197.2 12.3 230 129-360 69-364 (467)
6 KOG1074|consensus 99.9 7.1E-28 1.5E-32 223.8 2.4 175 185-359 606-918 (958)
7 KOG3623|consensus 99.9 2.3E-25 5E-30 203.9 8.4 107 100-206 211-331 (1007)
8 KOG3623|consensus 99.9 9.2E-23 2E-27 187.0 6.4 104 129-232 210-330 (1007)
9 KOG3576|consensus 99.8 2.5E-19 5.5E-24 140.4 3.6 110 238-347 117-238 (267)
10 KOG3576|consensus 99.7 3E-17 6.4E-22 128.9 2.5 109 211-319 117-237 (267)
11 PLN03086 PRLI-interacting fact 99.5 1E-13 2.2E-18 129.0 8.4 145 184-344 407-563 (567)
12 PLN03086 PRLI-interacting fact 99.4 4.3E-13 9.3E-18 124.9 6.3 133 211-359 407-552 (567)
13 PHA00733 hypothetical protein 99.3 3.7E-12 8.1E-17 97.1 4.5 82 264-346 38-124 (128)
14 PHA00733 hypothetical protein 99.0 1.7E-10 3.7E-15 88.0 3.8 80 238-319 40-124 (128)
15 PHA02768 hypothetical protein; 99.0 1.4E-10 3E-15 72.5 1.5 42 295-337 6-47 (55)
16 KOG3993|consensus 99.0 7.3E-11 1.6E-15 103.3 -0.8 49 130-178 268-317 (500)
17 KOG3993|consensus 98.9 2E-10 4.3E-15 100.6 -1.2 189 99-289 267-481 (500)
18 PHA02768 hypothetical protein; 98.9 6.5E-10 1.4E-14 69.5 1.3 42 267-310 6-47 (55)
19 PF13465 zf-H2C2_2: Zinc-finge 98.7 1E-08 2.2E-13 54.8 1.4 24 282-305 2-25 (26)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 6.9E-08 1.5E-12 51.5 2.2 26 253-278 1-26 (26)
21 PHA00616 hypothetical protein 98.4 9E-08 1.9E-12 56.9 1.5 25 295-319 2-26 (44)
22 PHA00616 hypothetical protein 98.4 1.9E-07 4.1E-12 55.5 2.4 33 266-298 1-33 (44)
23 PHA00732 hypothetical protein 98.4 1.5E-07 3.3E-12 64.9 2.2 47 266-318 1-48 (79)
24 PF05605 zf-Di19: Drought indu 98.3 7.8E-07 1.7E-11 57.0 4.0 50 294-346 2-54 (54)
25 PHA00732 hypothetical protein 98.3 4.6E-07 1E-11 62.5 2.1 36 295-332 2-38 (79)
26 PF00096 zf-C2H2: Zinc finger, 98.0 3.2E-06 6.9E-11 43.7 1.9 23 322-344 1-23 (23)
27 PF12756 zf-C2H2_2: C2H2 type 97.9 5.2E-06 1.1E-10 61.0 2.4 71 269-343 2-72 (100)
28 PF05605 zf-Di19: Drought indu 97.9 1.5E-05 3.2E-10 51.0 4.1 49 100-151 3-51 (54)
29 PF00096 zf-C2H2: Zinc finger, 97.8 8.2E-06 1.8E-10 42.2 1.4 22 295-316 1-22 (23)
30 PF13894 zf-C2H2_4: C2H2-type 97.8 1.8E-05 3.8E-10 41.3 2.1 24 322-345 1-24 (24)
31 PF12756 zf-C2H2_2: C2H2 type 97.7 2.7E-05 5.7E-10 57.2 2.7 22 159-180 2-23 (100)
32 PF13912 zf-C2H2_6: C2H2-type 97.6 2.7E-05 5.9E-10 42.0 1.5 25 321-345 1-25 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.6 3.8E-05 8.2E-10 40.0 1.8 23 295-317 1-23 (24)
34 PF13912 zf-C2H2_6: C2H2-type 97.5 4.6E-05 9.9E-10 41.1 1.2 25 294-318 1-25 (27)
35 COG5189 SFP1 Putative transcri 97.4 4.2E-05 9.1E-10 65.3 0.4 27 154-180 347-375 (423)
36 KOG1146|consensus 97.3 4.1E-05 8.9E-10 77.3 -0.6 50 293-342 733-790 (1406)
37 COG5189 SFP1 Putative transcri 97.3 6.1E-05 1.3E-09 64.3 0.2 51 292-342 347-419 (423)
38 KOG2231|consensus 97.1 0.001 2.2E-08 63.9 6.1 23 158-181 117-139 (669)
39 smart00355 ZnF_C2H2 zinc finge 97.0 0.00051 1.1E-08 36.2 2.2 24 322-345 1-24 (26)
40 KOG2231|consensus 97.0 0.0017 3.6E-08 62.4 6.8 97 108-215 123-240 (669)
41 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00053 1.1E-08 35.6 1.6 24 322-346 1-24 (24)
42 smart00355 ZnF_C2H2 zinc finge 96.8 0.0011 2.4E-08 34.9 2.4 23 295-317 1-23 (26)
43 PF09237 GAGA: GAGA factor; I 96.8 0.00062 1.3E-08 41.5 1.1 28 320-347 23-50 (54)
44 COG5236 Uncharacterized conser 96.7 0.0021 4.5E-08 55.9 4.2 127 99-236 151-306 (493)
45 PF12874 zf-met: Zinc-finger o 96.5 0.0013 2.9E-08 34.4 1.4 22 322-343 1-22 (25)
46 PRK04860 hypothetical protein; 96.4 0.0016 3.5E-08 51.7 1.8 34 321-358 119-153 (160)
47 PF09237 GAGA: GAGA factor; I 96.4 0.0025 5.5E-08 38.9 2.2 19 296-314 26-44 (54)
48 KOG2785|consensus 96.4 0.0086 1.9E-07 53.1 6.4 23 129-151 3-25 (390)
49 PF13909 zf-H2C2_5: C2H2-type 96.4 0.0021 4.4E-08 33.4 1.5 23 295-318 1-23 (24)
50 PF12874 zf-met: Zinc-finger o 96.2 0.0025 5.5E-08 33.3 1.3 20 296-315 2-21 (25)
51 PRK04860 hypothetical protein; 96.1 0.0029 6.2E-08 50.2 1.7 26 279-304 128-153 (160)
52 KOG2785|consensus 96.1 0.018 3.9E-07 51.1 6.7 50 294-343 166-242 (390)
53 KOG2482|consensus 95.8 0.012 2.5E-07 51.3 4.0 137 98-234 143-357 (423)
54 COG5236 Uncharacterized conser 95.7 0.021 4.6E-07 49.8 5.3 127 156-288 151-303 (493)
55 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0034 7.5E-08 33.6 0.0 21 322-342 2-22 (27)
56 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0054 1.2E-07 32.8 0.8 22 267-288 2-23 (27)
57 KOG2482|consensus 95.3 0.062 1.3E-06 47.0 6.8 147 114-261 130-357 (423)
58 PF13913 zf-C2HC_2: zinc-finge 94.8 0.025 5.3E-07 29.6 1.9 21 322-343 3-23 (25)
59 KOG1146|consensus 94.6 0.004 8.6E-08 63.6 -2.6 24 210-233 517-540 (1406)
60 PF13913 zf-C2HC_2: zinc-finge 93.7 0.051 1.1E-06 28.4 1.6 18 268-286 4-21 (25)
61 COG5048 FOG: Zn-finger [Genera 93.3 0.014 3E-07 55.0 -1.5 116 238-353 289-451 (467)
62 smart00451 ZnF_U1 U1-like zinc 93.0 0.066 1.4E-06 30.4 1.6 22 321-342 3-24 (35)
63 KOG4173|consensus 92.5 0.13 2.7E-06 41.7 3.0 78 98-180 78-170 (253)
64 smart00451 ZnF_U1 U1-like zinc 92.4 0.085 1.8E-06 30.0 1.5 23 294-316 3-25 (35)
65 COG5048 FOG: Zn-finger [Genera 91.8 0.026 5.7E-07 53.0 -1.8 49 272-320 394-444 (467)
66 KOG2893|consensus 91.7 0.06 1.3E-06 44.5 0.5 42 158-203 12-53 (341)
67 KOG4173|consensus 89.9 0.12 2.6E-06 41.9 0.6 76 157-235 80-170 (253)
68 cd00350 rubredoxin_like Rubred 89.8 0.17 3.7E-06 28.4 1.0 6 241-246 4-9 (33)
69 TIGR00622 ssl1 transcription f 89.4 0.35 7.7E-06 35.6 2.7 48 297-345 58-105 (112)
70 PF12013 DUF3505: Protein of u 89.1 0.59 1.3E-05 34.7 3.8 25 322-346 81-109 (109)
71 KOG2893|consensus 88.9 0.11 2.3E-06 43.1 -0.3 46 132-180 13-58 (341)
72 TIGR00622 ssl1 transcription f 88.7 0.39 8.4E-06 35.4 2.5 17 129-145 15-31 (112)
73 PF12013 DUF3505: Protein of u 88.3 0.75 1.6E-05 34.1 3.9 25 295-319 81-109 (109)
74 KOG2186|consensus 87.1 0.37 8.1E-06 40.5 1.7 46 295-342 4-49 (276)
75 COG4049 Uncharacterized protei 84.4 0.69 1.5E-05 28.9 1.5 27 290-316 13-39 (65)
76 COG4049 Uncharacterized protei 84.0 0.45 9.7E-06 29.7 0.6 27 321-347 17-43 (65)
77 PF09538 FYDLN_acid: Protein o 82.3 0.8 1.7E-05 33.7 1.5 11 130-140 10-20 (108)
78 KOG2186|consensus 82.1 0.75 1.6E-05 38.8 1.4 46 185-232 4-49 (276)
79 cd00729 rubredoxin_SM Rubredox 79.4 0.94 2E-05 25.6 0.8 6 241-246 5-10 (34)
80 PF10571 UPF0547: Uncharacteri 78.2 1.4 3.1E-05 23.1 1.2 8 241-248 17-24 (26)
81 COG2888 Predicted Zn-ribbon RN 77.1 1.8 3.9E-05 27.6 1.6 32 294-329 27-58 (61)
82 PF09986 DUF2225: Uncharacteri 76.6 0.34 7.3E-06 40.8 -2.3 42 293-334 4-61 (214)
83 TIGR00373 conserved hypothetic 75.6 3.8 8.2E-05 32.7 3.6 17 184-200 109-125 (158)
84 COG1592 Rubrerythrin [Energy p 74.9 1.8 3.9E-05 34.5 1.5 11 263-273 146-156 (166)
85 smart00531 TFIIE Transcription 74.6 2.1 4.6E-05 33.6 1.9 14 294-307 99-112 (147)
86 PF09538 FYDLN_acid: Protein o 73.8 2.5 5.4E-05 31.2 1.9 11 266-276 26-36 (108)
87 TIGR00373 conserved hypothetic 73.0 2.9 6.3E-05 33.3 2.3 30 293-330 108-137 (158)
88 PF06524 NOA36: NOA36 protein; 72.8 1.2 2.5E-05 37.8 0.0 26 292-317 207-232 (314)
89 PF13717 zinc_ribbon_4: zinc-r 72.3 3.3 7.1E-05 23.7 1.8 33 100-139 3-35 (36)
90 smart00659 RPOLCX RNA polymera 72.2 2 4.4E-05 25.9 1.0 25 295-329 3-27 (44)
91 PF13719 zinc_ribbon_5: zinc-r 71.4 2.3 4.9E-05 24.5 1.0 6 268-273 27-32 (37)
92 PF02892 zf-BED: BED zinc fing 71.4 2.8 6E-05 25.2 1.5 20 322-341 17-40 (45)
93 PRK00464 nrdR transcriptional 71.1 0.83 1.8E-05 36.1 -1.1 12 267-278 29-40 (154)
94 smart00614 ZnF_BED BED zinc fi 70.9 3.3 7.1E-05 25.7 1.8 10 296-305 20-29 (50)
95 PF09986 DUF2225: Uncharacteri 70.8 1 2.2E-05 37.9 -0.8 43 265-307 4-61 (214)
96 smart00734 ZnF_Rad18 Rad18-lik 70.0 3.8 8.3E-05 21.5 1.6 19 323-342 3-21 (26)
97 COG1592 Rubrerythrin [Energy p 69.8 2.7 5.8E-05 33.6 1.4 24 266-302 134-157 (166)
98 KOG2272|consensus 69.7 4.6 0.0001 34.1 2.8 125 154-280 97-235 (332)
99 TIGR02300 FYDLN_acid conserved 69.1 3.1 6.7E-05 31.3 1.5 12 156-167 26-37 (129)
100 PRK06266 transcription initiat 68.8 6 0.00013 32.2 3.3 16 184-199 117-132 (178)
101 smart00531 TFIIE Transcription 68.7 6 0.00013 31.1 3.2 14 156-169 99-112 (147)
102 smart00834 CxxC_CXXC_SSSS Puta 67.8 1.3 2.7E-05 26.1 -0.6 29 295-329 6-34 (41)
103 TIGR02098 MJ0042_CXXC MJ0042 f 67.6 3.4 7.4E-05 23.8 1.3 10 185-194 26-35 (38)
104 PRK06266 transcription initiat 66.9 3.8 8.2E-05 33.4 1.8 16 295-310 118-133 (178)
105 PF03604 DNA_RNApol_7kD: DNA d 65.8 3.8 8.3E-05 22.8 1.1 8 321-328 17-24 (32)
106 PHA00626 hypothetical protein 64.6 1.7 3.8E-05 27.3 -0.4 12 129-140 23-34 (59)
107 KOG4167|consensus 63.9 11 0.00024 37.1 4.4 25 129-153 792-816 (907)
108 TIGR02605 CxxC_CxxC_SSSS putat 63.7 2.3 4.9E-05 26.6 -0.0 11 185-195 6-16 (52)
109 PF05443 ROS_MUCR: ROS/MUCR tr 63.4 4.3 9.3E-05 31.1 1.4 25 320-347 71-95 (132)
110 PF14353 CpXC: CpXC protein 63.0 6.2 0.00013 30.1 2.3 12 157-168 39-50 (128)
111 PF06524 NOA36: NOA36 protein; 62.8 2.3 5.1E-05 36.0 -0.1 100 157-289 126-232 (314)
112 COG5151 SSL1 RNA polymerase II 61.5 5.5 0.00012 34.8 1.8 24 238-261 388-411 (421)
113 COG1996 RPC10 DNA-directed RNA 61.5 2.9 6.2E-05 25.8 0.1 10 295-304 7-16 (49)
114 KOG2807|consensus 61.3 15 0.00033 32.5 4.5 24 211-234 345-368 (378)
115 PRK14890 putative Zn-ribbon RN 61.3 5.2 0.00011 25.6 1.3 10 99-108 25-34 (59)
116 PF09723 Zn-ribbon_8: Zinc rib 60.2 2.4 5.2E-05 25.2 -0.3 11 185-195 6-16 (42)
117 PF02176 zf-TRAF: TRAF-type zi 58.7 6.4 0.00014 25.3 1.5 6 172-177 26-31 (60)
118 PF08274 PhnA_Zn_Ribbon: PhnA 57.9 3.4 7.4E-05 22.6 0.0 9 320-328 18-26 (30)
119 PF15269 zf-C2H2_7: Zinc-finge 57.3 7.6 0.00017 23.1 1.4 21 322-342 21-41 (54)
120 COG3091 SprT Zn-dependent meta 57.1 4.1 8.8E-05 31.7 0.3 31 321-355 117-147 (156)
121 COG1997 RPL43A Ribosomal prote 56.9 3.4 7.4E-05 28.7 -0.1 10 295-304 54-63 (89)
122 PRK09678 DNA-binding transcrip 56.5 2.5 5.3E-05 28.6 -0.8 7 299-305 34-40 (72)
123 TIGR02300 FYDLN_acid conserved 56.3 9 0.0002 28.9 2.0 11 266-276 26-36 (129)
124 PRK00398 rpoP DNA-directed RNA 55.4 4.4 9.4E-05 24.6 0.2 11 100-110 4-14 (46)
125 PRK04023 DNA polymerase II lar 54.0 10 0.00022 39.0 2.5 9 267-275 627-635 (1121)
126 KOG1280|consensus 53.2 16 0.00034 32.7 3.3 38 99-136 79-116 (381)
127 PRK04023 DNA polymerase II lar 51.3 12 0.00026 38.5 2.6 10 185-194 664-673 (1121)
128 TIGR01206 lysW lysine biosynth 50.5 5.3 0.00011 25.3 0.0 10 321-330 22-31 (54)
129 COG4957 Predicted transcriptio 50.2 8.9 0.00019 29.1 1.2 23 322-347 77-99 (148)
130 PF12760 Zn_Tnp_IS1595: Transp 46.8 15 0.00032 22.2 1.6 7 267-273 19-25 (46)
131 cd00730 rubredoxin Rubredoxin; 45.8 12 0.00025 23.3 1.0 11 100-110 2-12 (50)
132 KOG2807|consensus 45.6 33 0.00071 30.5 4.0 86 184-301 276-374 (378)
133 KOG3408|consensus 44.3 16 0.00035 27.2 1.7 26 291-316 54-79 (129)
134 PF04959 ARS2: Arsenite-resist 44.2 16 0.00034 30.7 1.9 27 155-181 76-102 (214)
135 KOG2593|consensus 42.8 23 0.00049 32.8 2.8 35 128-164 127-161 (436)
136 COG5188 PRP9 Splicing factor 3 42.8 21 0.00045 31.9 2.5 91 97-187 236-406 (470)
137 COG1198 PriA Primosomal protei 42.7 8.7 0.00019 38.6 0.2 8 240-247 437-444 (730)
138 PF05290 Baculo_IE-1: Baculovi 42.1 15 0.00033 27.9 1.3 56 263-335 77-135 (140)
139 PF05443 ROS_MUCR: ROS/MUCR tr 42.1 19 0.0004 27.7 1.8 25 97-124 70-94 (132)
140 PF09845 DUF2072: Zn-ribbon co 42.0 14 0.00031 28.1 1.2 11 240-250 3-13 (131)
141 KOG2593|consensus 42.0 24 0.00053 32.6 2.8 11 239-249 129-139 (436)
142 COG5151 SSL1 RNA polymerase II 41.8 9.2 0.0002 33.5 0.2 24 321-344 388-411 (421)
143 KOG4167|consensus 41.7 9.6 0.00021 37.5 0.3 26 294-319 792-817 (907)
144 TIGR00595 priA primosomal prot 39.2 19 0.00042 34.7 2.0 9 266-274 253-261 (505)
145 PF04959 ARS2: Arsenite-resist 39.0 13 0.00029 31.1 0.7 25 321-345 77-101 (214)
146 COG1198 PriA Primosomal protei 38.6 7.3 0.00016 39.1 -1.0 10 130-139 436-445 (730)
147 KOG3408|consensus 37.9 33 0.00072 25.6 2.5 31 91-121 49-79 (129)
148 PRK14714 DNA polymerase II lar 37.9 25 0.00053 37.4 2.5 11 294-304 692-702 (1337)
149 PF12907 zf-met2: Zinc-binding 37.1 25 0.00055 20.6 1.5 26 157-182 2-30 (40)
150 PF07754 DUF1610: Domain of un 36.9 13 0.00028 19.1 0.2 8 294-301 16-23 (24)
151 PTZ00255 60S ribosomal protein 36.1 7.7 0.00017 27.4 -0.9 10 295-304 55-64 (90)
152 PF14446 Prok-RING_1: Prokaryo 36.1 21 0.00047 22.5 1.1 11 100-110 6-16 (54)
153 TIGR00280 L37a ribosomal prote 34.7 6.9 0.00015 27.7 -1.3 10 322-331 54-63 (91)
154 KOG4124|consensus 34.1 6.2 0.00013 35.1 -2.0 22 320-341 397-418 (442)
155 KOG1280|consensus 33.6 44 0.00095 30.0 3.0 23 266-288 79-101 (381)
156 COG5112 UFD2 U1-like Zn-finger 32.2 29 0.00063 25.1 1.4 33 88-120 44-76 (126)
157 PRK14873 primosome assembly pr 32.1 28 0.0006 34.9 1.8 10 294-303 422-431 (665)
158 PRK14714 DNA polymerase II lar 31.5 37 0.00081 36.1 2.6 11 184-194 692-702 (1337)
159 PLN02294 cytochrome c oxidase 31.4 15 0.00032 29.3 -0.2 18 341-358 134-151 (174)
160 KOG4377|consensus 31.1 13 0.00027 34.0 -0.7 24 295-318 402-427 (480)
161 PF05191 ADK_lid: Adenylate ki 30.4 6.9 0.00015 22.4 -1.6 8 241-248 4-11 (36)
162 PF01780 Ribosomal_L37ae: Ribo 30.1 5.4 0.00012 28.1 -2.5 10 295-304 54-63 (90)
163 PF06220 zf-U1: U1 zinc finger 29.1 38 0.00081 19.6 1.3 10 267-276 4-13 (38)
164 KOG4124|consensus 28.8 7.6 0.00016 34.6 -2.3 26 155-180 348-375 (442)
165 cd00924 Cyt_c_Oxidase_Vb Cytoc 28.8 15 0.00034 26.4 -0.4 8 348-355 79-86 (97)
166 PF13878 zf-C2H2_3: zinc-finge 28.7 46 0.001 19.6 1.7 9 268-276 15-23 (41)
167 PRK03824 hypA hydrogenase nick 28.6 20 0.00043 27.7 0.1 10 239-248 71-80 (135)
168 smart00154 ZnF_AN1 AN1-like Zi 28.6 24 0.00053 20.5 0.5 13 321-333 12-24 (39)
169 COG3364 Zn-ribbon containing p 28.3 37 0.00079 24.5 1.4 11 268-278 4-14 (112)
170 PRK03976 rpl37ae 50S ribosomal 28.0 9.8 0.00021 26.9 -1.5 10 322-331 55-64 (90)
171 COG4530 Uncharacterized protei 27.8 30 0.00066 25.2 0.9 12 155-166 25-36 (129)
172 PF01363 FYVE: FYVE zinc finge 27.6 40 0.00087 22.2 1.5 8 132-139 12-19 (69)
173 PF05495 zf-CHY: CHY zinc fing 26.3 11 0.00024 25.4 -1.5 12 294-305 41-52 (71)
174 PRK12380 hydrogenase nickel in 26.2 34 0.00073 25.5 1.0 13 129-141 70-82 (113)
175 TIGR00100 hypA hydrogenase nic 25.9 34 0.00074 25.5 1.0 11 157-167 71-81 (115)
176 KOG2636|consensus 25.8 44 0.00096 31.1 1.8 29 259-287 394-423 (497)
177 PF14311 DUF4379: Domain of un 25.7 41 0.00089 21.2 1.2 7 268-274 30-36 (55)
178 PRK00432 30S ribosomal protein 25.4 31 0.00068 21.4 0.6 10 238-247 37-46 (50)
179 COG3357 Predicted transcriptio 25.1 31 0.00067 24.3 0.5 26 99-136 58-83 (97)
180 PF03145 Sina: Seven in absent 25.1 37 0.00079 28.1 1.1 37 309-346 32-72 (198)
181 PF07503 zf-HYPF: HypF finger; 24.7 11 0.00023 21.5 -1.5 10 130-139 22-31 (35)
182 KOG2636|consensus 24.3 47 0.001 30.9 1.7 22 156-177 401-423 (497)
183 COG5112 UFD2 U1-like Zn-finger 24.2 49 0.0011 24.0 1.4 23 293-315 54-76 (126)
184 KOG0402|consensus 24.0 49 0.0011 22.9 1.3 10 294-303 36-45 (92)
185 PF10263 SprT-like: SprT-like 23.8 16 0.00035 28.8 -1.2 10 295-304 124-133 (157)
186 PRK04351 hypothetical protein; 23.7 28 0.0006 27.4 0.1 12 320-331 131-142 (149)
187 KOG0717|consensus 23.7 39 0.00085 31.6 1.1 22 295-316 293-314 (508)
188 COG1998 RPS31 Ribosomal protei 23.4 49 0.0011 20.4 1.1 10 238-247 37-46 (51)
189 PF07282 OrfB_Zn_ribbon: Putat 23.3 39 0.00084 22.3 0.8 10 321-330 46-55 (69)
190 PF13451 zf-trcl: Probable zin 23.1 61 0.0013 20.1 1.5 7 101-107 6-12 (49)
191 KOG3507|consensus 22.6 32 0.0007 22.0 0.2 11 320-330 36-46 (62)
192 PF10276 zf-CHCC: Zinc-finger 22.2 32 0.0007 20.2 0.2 11 321-331 29-39 (40)
193 PF01155 HypA: Hydrogenase exp 22.1 32 0.00069 25.6 0.2 12 157-168 71-82 (113)
194 COG1327 Predicted transcriptio 21.9 21 0.00045 27.9 -0.9 11 268-278 30-40 (156)
195 COG0068 HypF Hydrogenase matur 21.6 16 0.00035 36.1 -1.8 28 269-302 154-181 (750)
196 PF01428 zf-AN1: AN1-like Zinc 21.5 29 0.00062 20.6 -0.1 12 321-332 13-24 (43)
197 KOG2907|consensus 21.5 50 0.0011 24.3 1.0 12 184-195 102-113 (116)
198 KOG1842|consensus 21.3 55 0.0012 30.5 1.5 20 130-149 16-35 (505)
199 COG1675 TFA1 Transcription ini 21.0 1.2E+02 0.0026 24.7 3.2 14 182-195 111-124 (176)
200 smart00440 ZnF_C2C2 C2C2 Zinc 20.6 13 0.00028 21.8 -1.8 10 185-194 29-38 (40)
201 COG4888 Uncharacterized Zn rib 20.1 19 0.00041 25.9 -1.3 7 267-273 23-29 (104)
202 PRK00564 hypA hydrogenase nick 20.0 54 0.0012 24.6 1.0 13 129-141 71-83 (117)
No 1
>KOG3608|consensus
Probab=99.96 E-value=1.9e-28 Score=206.69 Aligned_cols=247 Identities=24% Similarity=0.482 Sum_probs=214.4
Q ss_pred ceecc--cchhccCC-hHHHHHHHhhccC--------------------------------CCCCcccc--ccccccccC
Q psy6525 99 NVLCY--ICDEILKD-IDDLRYHGLLHAT--------------------------------PLGTQFQC--NVCFLMLNN 141 (360)
Q Consensus 99 ~~~C~--~C~~~f~~-~~~l~~H~~~~~~--------------------------------~~~~~~~C--~~C~~~f~~ 141 (360)
.+.|. .|++...+ ..+|.+|.-.|-- ..+..|.| ..|+..|.+
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 46776 48877766 5789999765511 11234566 479999999
Q ss_pred hHHHHHHHHHcCC--------------ccccccc--ccccccCHHHHHHHHHHcCCCceeecccccccccChhHHHHHHH
Q psy6525 142 RCYTRFHLLKHNW--------------VRFKCDL--CSRTFNSQSYLQQHKKHDHEGVKYKCKECGKCYTQNTNLKQHML 205 (360)
Q Consensus 142 ~~~l~~H~~~h~~--------------~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 205 (360)
...+..|+..|.. ..+.|.. |-+.|.++..|++|++.|.+++...|+.||.-|.++..|-.|++
T Consensus 149 ~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~r 228 (467)
T KOG3608|consen 149 IVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLR 228 (467)
T ss_pred HHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHH
Confidence 9999999988831 1255655 99999999999999999999999999999999999999999988
Q ss_pred hcCC---CCCcCccccccccCHHHHHHHHhhcCCCCcccCCCCCccCCHHHHHHHHH-HhcCCCcccccccccccCChhH
Q psy6525 206 SHKG---IFFICFHCNKNFTHRALLVRHMQKHSSERFKCDLCGKVTPYYQHYLRHMR-IHQGLEVHECNLCAKLFACKRS 281 (360)
Q Consensus 206 ~h~~---~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~~ 281 (360)
..+. .+|.|..|.+.|.++..|..|+..|..- |+|+.|+.+....+.|..|++ .|...+||+|..|++.|.+.+.
T Consensus 229 Rqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~-ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esd 307 (467)
T KOG3608|consen 229 RQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNC-YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESD 307 (467)
T ss_pred hhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhc-ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHH
Confidence 7653 4899999999999999999999987654 999999999999999999998 5888999999999999999999
Q ss_pred HHHhHhhhcCCCcccccc--chhhhcCHHHHHHHHhhhc-C---CcccccccccccCChHHHHHHHHHhCCC
Q psy6525 282 LQDHMQRHEEPNKYQCAM--CKKQYASKKMLEKHIRRHE-G---QDYKCYICGNRYATQKYLEEHIRLHQGH 347 (360)
Q Consensus 282 l~~H~~~h~~~~~~~C~~--C~~~f~~~~~L~~H~~~h~-~---~~~~C~~C~~~f~~~~~l~~H~~~h~g~ 347 (360)
|.+|..+|. +..|+|+. |..+|.+...|++|++.++ | -+|.|-.|++.|++-.+|..|+...+|.
T Consensus 308 L~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 308 LAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred HHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 999999988 77899988 9999999999999999866 4 3799999999999999999999877775
No 2
>KOG2462|consensus
Probab=99.96 E-value=6.6e-30 Score=210.39 Aligned_cols=131 Identities=36% Similarity=0.692 Sum_probs=91.8
Q ss_pred eeecccccccccChhHHHHHHHhcCC----CCCcCccccccccCHHHHHHHHhhcCCCCcccCCCCCccCCHHHHHHHHH
Q psy6525 184 KYKCKECGKCYTQNTNLKQHMLSHKG----IFFICFHCNKNFTHRALLVRHMQKHSSERFKCDLCGKVTPYYQHYLRHMR 259 (360)
Q Consensus 184 ~~~C~~C~~~f~~~~~l~~H~~~h~~----~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 259 (360)
.|+|+.||+.+.+..+|.+|.++|.. ..+.|++|++.|.+...|..|+++|. -+..|.+||+.|...+.|+.|+|
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~-l~c~C~iCGKaFSRPWLLQGHiR 208 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT-LPCECGICGKAFSRPWLLQGHIR 208 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC-CCcccccccccccchHHhhcccc
Confidence 57888888888888888888877754 25667777777777777777776665 34666677777766666666777
Q ss_pred HhcCCCcccccccccccCChhHHHHhHhhhcCCCccccccchhhhcCHHHHHHHHh
Q psy6525 260 IHQGLEVHECNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKKQYASKKMLEKHIR 315 (360)
Q Consensus 260 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~ 315 (360)
+|+|||||.|++|+++|+++++|+.|+++|.+.++|+|..|+|+|+..+.|.+|..
T Consensus 209 THTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 209 THTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 77777777777777777777777777776666666667667666666666666654
No 3
>KOG1074|consensus
Probab=99.96 E-value=4.5e-30 Score=238.31 Aligned_cols=191 Identities=27% Similarity=0.496 Sum_probs=159.9
Q ss_pred cccccccccccCHHHHHHHHHHcCCCceeecccccccccChhHHHHHHHhcCCC-----CCcCc---cccccccCHHHHH
Q psy6525 157 FKCDLCSRTFNSQSYLQQHKKHDHEGVKYKCKECGKCYTQNTNLKQHMLSHKGI-----FFICF---HCNKNFTHRALLV 228 (360)
Q Consensus 157 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-----~~~C~---~C~~~f~~~~~l~ 228 (360)
-+|-+|.++..-.+.|+.|++.|.+++||+|.+||+.|.++.+|+.|+-.|... .+.|+ +|-+.|.+.-.|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lp 685 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLP 685 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccccc
Confidence 589999999999999999999999999999999999999999999999999764 68999 9999999999999
Q ss_pred HHHhhcCCC--------------CcccCCCCCccCCHHHHHHHHHHhcCC----------------C----ccccccccc
Q psy6525 229 RHMQKHSSE--------------RFKCDLCGKVTPYYQHYLRHMRIHQGL----------------E----VHECNLCAK 274 (360)
Q Consensus 229 ~H~~~h~~~--------------~~~C~~C~~~f~~~~~l~~H~~~h~~~----------------~----~~~C~~C~~ 274 (360)
.|++.|.+. .-+|..|.+.|.....+..++..|.+. . +..+..|+.
T Consensus 686 QhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~~~ 765 (958)
T KOG1074|consen 686 QHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSCGR 765 (958)
T ss_pred ceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCcccccccc
Confidence 999998743 247999999998888888887666321 1 355666777
Q ss_pred ccCChhHHHHhHhhh-----------------------cC----------------------------------------
Q psy6525 275 LFACKRSLQDHMQRH-----------------------EE---------------------------------------- 291 (360)
Q Consensus 275 ~f~~~~~l~~H~~~h-----------------------~~---------------------------------------- 291 (360)
.+.....+..+-..+ ++
T Consensus 766 ~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~~ 845 (958)
T KOG1074|consen 766 ELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLATKT 845 (958)
T ss_pred ccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccccccccccccccc
Confidence 666655444332111 00
Q ss_pred -------------------------------CCccccccchhhhcCHHHHHHHHhhhcC-CcccccccccccCChHHHHH
Q psy6525 292 -------------------------------PNKYQCAMCKKQYASKKMLEKHIRRHEG-QDYKCYICGNRYATQKYLEE 339 (360)
Q Consensus 292 -------------------------------~~~~~C~~C~~~f~~~~~L~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~ 339 (360)
.....|.+||+.|.+.++|..|+|+|++ +||.|.+|++.|..+.+|+.
T Consensus 846 n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKv 925 (958)
T KOG1074|consen 846 NEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKV 925 (958)
T ss_pred ccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhh
Confidence 0126799999999999999999999999 79999999999999999999
Q ss_pred HHHHhCCC
Q psy6525 340 HIRLHQGH 347 (360)
Q Consensus 340 H~~~h~g~ 347 (360)
||.+|...
T Consensus 926 HMgtH~w~ 933 (958)
T KOG1074|consen 926 HMGTHMWV 933 (958)
T ss_pred hhcccccc
Confidence 99999876
No 4
>KOG2462|consensus
Probab=99.95 E-value=3.4e-29 Score=206.22 Aligned_cols=130 Identities=32% Similarity=0.675 Sum_probs=110.9
Q ss_pred CCcCccccccccCHHHHHHHHhhcCC----CCcccCCCCCccCCHHHHHHHHHHhcCCCcccccccccccCChhHHHHhH
Q psy6525 211 FFICFHCNKNFTHRALLVRHMQKHSS----ERFKCDLCGKVTPYYQHYLRHMRIHQGLEVHECNLCAKLFACKRSLQDHM 286 (360)
Q Consensus 211 ~~~C~~C~~~f~~~~~l~~H~~~h~~----~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 286 (360)
.|.|+.||+.+.+.++|.+|.++|-. +.+.|+.|++.|.+...|..|+++|+ -+++|.+||+.|.+..-|+-|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 67888888888888888888888753 35788888888888888888888887 5688888888888888888888
Q ss_pred hhhcCCCccccccchhhhcCHHHHHHHHhhhcC-CcccccccccccCChHHHHHHHH
Q psy6525 287 QRHEEPNKYQCAMCKKQYASKKMLEKHIRRHEG-QDYKCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 287 ~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~ 342 (360)
|+|+||+||.|+.|+++|..+++|+.||++|.+ ++|+|..|+|+|..++.|..|..
T Consensus 208 RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 208 RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred ccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 888888888888888888888888888888888 78888888888888888888864
No 5
>KOG3608|consensus
Probab=99.94 E-value=7.2e-27 Score=197.16 Aligned_cols=230 Identities=23% Similarity=0.456 Sum_probs=198.9
Q ss_pred ccccc--cccccccC-hHHHHHHHHHcCCc-----------------------------------cccccc--ccccccC
Q psy6525 129 QFQCN--VCFLMLNN-RCYTRFHLLKHNWV-----------------------------------RFKCDL--CSRTFNS 168 (360)
Q Consensus 129 ~~~C~--~C~~~f~~-~~~l~~H~~~h~~~-----------------------------------~~~C~~--C~~~f~~ 168 (360)
.++|. .|+....+ ...|.+|...|... .|.|.. |+..|.+
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 56775 48777666 57899998776310 166765 9999999
Q ss_pred HHHHHHHHHHcCCC-------------ceeec--ccccccccChhHHHHHHHhcCCC-CCcCccccccccCHHHHHHHHh
Q psy6525 169 QSYLQQHKKHDHEG-------------VKYKC--KECGKCYTQNTNLKQHMLSHKGI-FFICFHCNKNFTHRALLVRHMQ 232 (360)
Q Consensus 169 ~~~l~~H~~~~h~~-------------~~~~C--~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~ 232 (360)
...|..|...|.-. ..+.| ..|.+.|.++..|+.|+++|.+. ...|+.||..|+++..|..|++
T Consensus 149 ~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~r 228 (467)
T KOG3608|consen 149 IVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLR 228 (467)
T ss_pred HHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHH
Confidence 99999998775421 13455 57999999999999999999986 6789999999999999999998
Q ss_pred hcCC---CCcccCCCCCccCCHHHHHHHHHHhcCCCcccccccccccCChhHHHHhHhh-hcCCCccccccchhhhcCHH
Q psy6525 233 KHSS---ERFKCDLCGKVTPYYQHYLRHMRIHQGLEVHECNLCAKLFACKRSLQDHMQR-HEEPNKYQCAMCKKQYASKK 308 (360)
Q Consensus 233 ~h~~---~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~ 308 (360)
.-+. .+|.|..|.+.|.+...|..|+..|.. -|+|+.|+.+....++|.+|++. |...+||+|+.|.+.|.+.+
T Consensus 229 Rqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~es 306 (467)
T KOG3608|consen 229 RQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRES 306 (467)
T ss_pred hhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHH
Confidence 6543 489999999999999999999999864 59999999999999999999995 88899999999999999999
Q ss_pred HHHHHHhhhcCCcccccc--cccccCChHHHHHHHHHhC-CC---CccCCCcccccCC
Q psy6525 309 MLEKHIRRHEGQDYKCYI--CGNRYATQKYLEEHIRLHQ-GH---TYMCNAKFSFNEQ 360 (360)
Q Consensus 309 ~L~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-g~---~~~C~~c~~~f~~ 360 (360)
.|.+|..+|..-.|+|.. |..+|.+..+|..|++.++ |. +|.|..|.+.|++
T Consensus 307 dL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~ 364 (467)
T KOG3608|consen 307 DLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTS 364 (467)
T ss_pred HHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhcc
Confidence 999999999977899998 9999999999999999776 65 6999999999964
No 6
>KOG1074|consensus
Probab=99.94 E-value=7.1e-28 Score=223.80 Aligned_cols=175 Identities=24% Similarity=0.487 Sum_probs=124.4
Q ss_pred eecccccccccChhHHHHHHHhcCCC-CCcCccccccccCHHHHHHHHhhcCCC-----CcccC---CCCCccCCHHHHH
Q psy6525 185 YKCKECGKCYTQNTNLKQHMLSHKGI-FFICFHCNKNFTHRALLVRHMQKHSSE-----RFKCD---LCGKVTPYYQHYL 255 (360)
Q Consensus 185 ~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~-----~~~C~---~C~~~f~~~~~l~ 255 (360)
-+|-+|.++..-++.|+.|.++|+|. ||+|.+||+.|.++.+|+.|+-.|..+ .+.|+ +|.+.|...-.|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lp 685 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLP 685 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccccc
Confidence 57777888888888888888887774 778888888888888888887777654 46777 7777777777777
Q ss_pred HHHHHhcCCC-------------cccccccccccCChhHHHHhHhhhc----------------CCC----ccccccchh
Q psy6525 256 RHMRIHQGLE-------------VHECNLCAKLFACKRSLQDHMQRHE----------------EPN----KYQCAMCKK 302 (360)
Q Consensus 256 ~H~~~h~~~~-------------~~~C~~C~~~f~~~~~l~~H~~~h~----------------~~~----~~~C~~C~~ 302 (360)
.|+++|.+.. .-+|..|.+.|.....+..++-.|. ++. +..+..|+.
T Consensus 686 QhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~~~ 765 (958)
T KOG1074|consen 686 QHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSCGR 765 (958)
T ss_pred ceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCcccccccc
Confidence 7777776321 1357777777777777766665542 112 345556666
Q ss_pred hhcCHHHHHHHHhhh-----------------------cC-C--------------------------------------
Q psy6525 303 QYASKKMLEKHIRRH-----------------------EG-Q-------------------------------------- 320 (360)
Q Consensus 303 ~f~~~~~L~~H~~~h-----------------------~~-~-------------------------------------- 320 (360)
.+.....+..+-..+ ++ +
T Consensus 766 ~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~~ 845 (958)
T KOG1074|consen 766 ELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLATKT 845 (958)
T ss_pred ccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccccccccccccccc
Confidence 555544443332111 00 0
Q ss_pred ---------------------------------cccccccccccCChHHHHHHHHHhCCC-CccCCCcccccC
Q psy6525 321 ---------------------------------DYKCYICGNRYATQKYLEEHIRLHQGH-TYMCNAKFSFNE 359 (360)
Q Consensus 321 ---------------------------------~~~C~~C~~~f~~~~~l~~H~~~h~g~-~~~C~~c~~~f~ 359 (360)
...|..||+.|...++|..|+|+|+|+ ||.|.+|++.|.
T Consensus 846 n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFt 918 (958)
T KOG1074|consen 846 NEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFT 918 (958)
T ss_pred ccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhh
Confidence 067999999999999999999999999 999999999985
No 7
>KOG3623|consensus
Probab=99.92 E-value=2.3e-25 Score=203.86 Aligned_cols=107 Identities=23% Similarity=0.479 Sum_probs=98.2
Q ss_pred eecccchhccCChHHHHHHHhhccCCCCCccccccccccccChHHHHHHHHHcCC--------------ccccccccccc
Q psy6525 100 VLCYICDEILKDIDDLRYHGLLHATPLGTQFQCNVCFLMLNNRCYTRFHLLKHNW--------------VRFKCDLCSRT 165 (360)
Q Consensus 100 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~--------------~~~~C~~C~~~ 165 (360)
+.|++|+..++.+..|+.|++..+......|.|..|...|..+..|.+|+..|.. +.|+|..|+|.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 6799999999999999999886665557789999999999999999999998842 45999999999
Q ss_pred ccCHHHHHHHHHHcCCCceeecccccccccChhHHHHHHHh
Q psy6525 166 FNSQSYLQQHKKHDHEGVKYKCKECGKCYTQNTNLKQHMLS 206 (360)
Q Consensus 166 f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~ 206 (360)
|+.+..|+.|++.|.|++||.|+.|+++|....++..||.+
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999999999999854
No 8
>KOG3623|consensus
Probab=99.87 E-value=9.2e-23 Score=186.99 Aligned_cols=104 Identities=32% Similarity=0.597 Sum_probs=94.1
Q ss_pred ccccccccccccChHHHHHHHHHcC---CcccccccccccccCHHHHHHHHHHcCCC-------------ceeecccccc
Q psy6525 129 QFQCNVCFLMLNNRCYTRFHLLKHN---WVRFKCDLCSRTFNSQSYLQQHKKHDHEG-------------VKYKCKECGK 192 (360)
Q Consensus 129 ~~~C~~C~~~f~~~~~l~~H~~~h~---~~~~~C~~C~~~f~~~~~l~~H~~~~h~~-------------~~~~C~~C~~ 192 (360)
..+|++|.+.+.....|+.|+..-+ +..|.|.+|.++|..+..|.+||..|... +.|+|..||+
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 4689999999999999999987543 66799999999999999999999987532 3699999999
Q ss_pred cccChhHHHHHHHhcCCC-CCcCccccccccCHHHHHHHHh
Q psy6525 193 CYTQNTNLKQHMLSHKGI-FFICFHCNKNFTHRALLVRHMQ 232 (360)
Q Consensus 193 ~f~~~~~l~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~ 232 (360)
.|..+..|+.|+++|.|. ||.|+.|++.|.....+..||.
T Consensus 290 AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 999999999999999985 9999999999999999999984
No 9
>KOG3576|consensus
Probab=99.76 E-value=2.5e-19 Score=140.43 Aligned_cols=110 Identities=28% Similarity=0.629 Sum_probs=93.5
Q ss_pred CcccCCCCCccCCHHHHHHHHHHhcCCCcccccccccccCChhHHHHhHhhhcCCCccccccchhhhcCHHHHHHHHhhh
Q psy6525 238 RFKCDLCGKVTPYYQHYLRHMRIHQGLEVHECNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKKQYASKKMLEKHIRRH 317 (360)
Q Consensus 238 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h 317 (360)
.|.|.+|++.|.....|.+|++-|...+.+-|..||+.|.....|++|+|+|+|.+||+|..|+++|+..-.|..|++.-
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 57888888888888888888888888888888888888888888888888888888888888888888888888888764
Q ss_pred cC------------CcccccccccccCChHHHHHHHHHhCCC
Q psy6525 318 EG------------QDYKCYICGNRYATQKYLEEHIRLHQGH 347 (360)
Q Consensus 318 ~~------------~~~~C~~C~~~f~~~~~l~~H~~~h~g~ 347 (360)
+| +.|.|+.||.+-.....+..|++.|+..
T Consensus 197 hgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 197 HGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred cCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 43 2588999999999999999999988754
No 10
>KOG3576|consensus
Probab=99.66 E-value=3e-17 Score=128.92 Aligned_cols=109 Identities=30% Similarity=0.577 Sum_probs=83.4
Q ss_pred CCcCccccccccCHHHHHHHHhhcCCC-CcccCCCCCccCCHHHHHHHHHHhcCCCcccccccccccCChhHHHHhHhhh
Q psy6525 211 FFICFHCNKNFTHRALLVRHMQKHSSE-RFKCDLCGKVTPYYQHYLRHMRIHQGLEVHECNLCAKLFACKRSLQDHMQRH 289 (360)
Q Consensus 211 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 289 (360)
.|.|.+|++.|.-...|.+|++.|..- ++-|..||+.|.+..+|++|+++|+|.+||+|..|+++|..+-+|..|++.-
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 345555555555555555555555433 5678888888888888888888888888888888888888888888888764
Q ss_pred cC-----------CCccccccchhhhcCHHHHHHHHhhhcC
Q psy6525 290 EE-----------PNKYQCAMCKKQYASKKMLEKHIRRHEG 319 (360)
Q Consensus 290 ~~-----------~~~~~C~~C~~~f~~~~~L~~H~~~h~~ 319 (360)
+| .+.|.|+.||.+-.....+..|+..|+.
T Consensus 197 hgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 197 HGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred cCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 44 3568899999998888889999988765
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.47 E-value=1e-13 Score=128.98 Aligned_cols=145 Identities=17% Similarity=0.363 Sum_probs=113.2
Q ss_pred eeecccccccccChhHHHHHHHhcCCCCCcCcc--ccccccCHHHHHHHHhhcCCCCcccCCCCCccCCHHHHHHHHHHh
Q psy6525 184 KYKCKECGKCYTQNTNLKQHMLSHKGIFFICFH--CNKNFTHRALLVRHMQKHSSERFKCDLCGKVTPYYQHYLRHMRIH 261 (360)
Q Consensus 184 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h 261 (360)
...|+.|.+.... ..|..|.....-....|+. |+..|. +..+..| +.|+.|++.|. ...|..|+.++
T Consensus 407 ~V~C~NC~~~i~l-~~l~lHe~~C~r~~V~Cp~~~Cg~v~~-r~el~~H--------~~C~~Cgk~f~-~s~LekH~~~~ 475 (567)
T PLN03086 407 TVECRNCKHYIPS-RSIALHEAYCSRHNVVCPHDGCGIVLR-VEEAKNH--------VHCEKCGQAFQ-QGEMEKHMKVF 475 (567)
T ss_pred eEECCCCCCccch-hHHHHHHhhCCCcceeCCcccccceee-ccccccC--------ccCCCCCCccc-hHHHHHHHHhc
Confidence 4578888877654 4566888776656667884 998884 3333444 58999999995 67889999987
Q ss_pred cCCCcccccccccccCChhHHHHhHhhhcCCCccccccchhhhc----------CHHHHHHHHhhhcCCccccccccccc
Q psy6525 262 QGLEVHECNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKKQYA----------SKKMLEKHIRRHEGQDYKCYICGNRY 331 (360)
Q Consensus 262 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~L~~H~~~h~~~~~~C~~C~~~f 331 (360)
+ .++.|+ ||+.+ .+..|..|+.+|.+.+++.|++|++.|. ....|..|...+..+++.|..||+.+
T Consensus 476 H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~V 551 (567)
T PLN03086 476 H--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSV 551 (567)
T ss_pred C--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCee
Confidence 5 789999 99654 6789999999999999999999999985 24579999998866899999999888
Q ss_pred CChHHHHHHHHHh
Q psy6525 332 ATQKYLEEHIRLH 344 (360)
Q Consensus 332 ~~~~~l~~H~~~h 344 (360)
..+ .|..|+-.-
T Consensus 552 rlr-dm~~H~~~~ 563 (567)
T PLN03086 552 MLK-EMDIHQIAV 563 (567)
T ss_pred eeh-hHHHHHHHh
Confidence 765 577886543
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.39 E-value=4.3e-13 Score=124.91 Aligned_cols=133 Identities=19% Similarity=0.349 Sum_probs=107.7
Q ss_pred CCcCccccccccCHHHHHHHHhhcCCCCcccCC--CCCccCCHHHHHHHHHHhcCCCcccccccccccCChhHHHHhHhh
Q psy6525 211 FFICFHCNKNFTHRALLVRHMQKHSSERFKCDL--CGKVTPYYQHYLRHMRIHQGLEVHECNLCAKLFACKRSLQDHMQR 288 (360)
Q Consensus 211 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 288 (360)
...|+.|..... ...|..|.....-....|+. |+..|. +..+. +.+.|+.|++.|. ...|..|++.
T Consensus 407 ~V~C~NC~~~i~-l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~-r~el~---------~H~~C~~Cgk~f~-~s~LekH~~~ 474 (567)
T PLN03086 407 TVECRNCKHYIP-SRSIALHEAYCSRHNVVCPHDGCGIVLR-VEEAK---------NHVHCEKCGQAFQ-QGEMEKHMKV 474 (567)
T ss_pred eEECCCCCCccc-hhHHHHHHhhCCCcceeCCcccccceee-ccccc---------cCccCCCCCCccc-hHHHHHHHHh
Confidence 457999988766 45666888776666677985 999884 33333 3368999999996 6889999999
Q ss_pred hcCCCccccccchhhhcCHHHHHHHHhhhcC-CcccccccccccC----------ChHHHHHHHHHhCCCCccCCCcccc
Q psy6525 289 HEEPNKYQCAMCKKQYASKKMLEKHIRRHEG-QDYKCYICGNRYA----------TQKYLEEHIRLHQGHTYMCNAKFSF 357 (360)
Q Consensus 289 h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~-~~~~C~~C~~~f~----------~~~~l~~H~~~h~g~~~~C~~c~~~ 357 (360)
|+ .++.|+ ||+.+ .+..|..|+++|.+ +++.|.+|++.|. ..+.|..|..+..+.++.|..|++.
T Consensus 475 ~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~ 550 (567)
T PLN03086 475 FH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRS 550 (567)
T ss_pred cC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCe
Confidence 86 789999 99755 67899999999887 7999999999995 2458999999986669999999998
Q ss_pred cC
Q psy6525 358 NE 359 (360)
Q Consensus 358 f~ 359 (360)
|+
T Consensus 551 Vr 552 (567)
T PLN03086 551 VM 552 (567)
T ss_pred ee
Confidence 75
No 13
>PHA00733 hypothetical protein
Probab=99.28 E-value=3.7e-12 Score=97.08 Aligned_cols=82 Identities=17% Similarity=0.368 Sum_probs=62.0
Q ss_pred CCcccccccccccCChhHHHHh--Hh---hhcCCCccccccchhhhcCHHHHHHHHhhhcCCcccccccccccCChHHHH
Q psy6525 264 LEVHECNLCAKLFACKRSLQDH--MQ---RHEEPNKYQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGNRYATQKYLE 338 (360)
Q Consensus 264 ~~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l~ 338 (360)
.+++.|.+|...|.....|..| ++ .+.+.+||.|+.|++.|.+...|..|++.| ..+|.|..|++.|.....|.
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL~ 116 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDSTL 116 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHHH
Confidence 4567777777777766666555 21 234577888888888888888888888876 35788888888888888888
Q ss_pred HHHHHhCC
Q psy6525 339 EHIRLHQG 346 (360)
Q Consensus 339 ~H~~~h~g 346 (360)
.|++..||
T Consensus 117 ~H~~~~h~ 124 (128)
T PHA00733 117 DHVCKKHN 124 (128)
T ss_pred HHHHHhcC
Confidence 88887766
No 14
>PHA00733 hypothetical protein
Probab=99.04 E-value=1.7e-10 Score=88.00 Aligned_cols=80 Identities=16% Similarity=0.308 Sum_probs=59.0
Q ss_pred CcccCCCCCccCCHHHHHHH--HH---HhcCCCcccccccccccCChhHHHHhHhhhcCCCccccccchhhhcCHHHHHH
Q psy6525 238 RFKCDLCGKVTPYYQHYLRH--MR---IHQGLEVHECNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKKQYASKKMLEK 312 (360)
Q Consensus 238 ~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~ 312 (360)
++.|.+|...|.....|..+ +. .+.+.+||.|+.|++.|.+...|..|++.| ..+|.|+.|++.|.....|..
T Consensus 40 ~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 40 RLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred hHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHH
Confidence 56666666666655555444 11 234577888999999999988888888876 356899999999999999998
Q ss_pred HHhhhcC
Q psy6525 313 HIRRHEG 319 (360)
Q Consensus 313 H~~~h~~ 319 (360)
|+...++
T Consensus 118 H~~~~h~ 124 (128)
T PHA00733 118 HVCKKHN 124 (128)
T ss_pred HHHHhcC
Confidence 8887554
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.00 E-value=1.4e-10 Score=72.50 Aligned_cols=42 Identities=24% Similarity=0.547 Sum_probs=26.5
Q ss_pred cccccchhhhcCHHHHHHHHhhhcCCcccccccccccCChHHH
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGNRYATQKYL 337 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l 337 (360)
|.|+.||+.|+..++|..|+++|+ ++|+|..|++.|.+.+.|
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 466666666666655544
No 16
>KOG3993|consensus
Probab=98.97 E-value=7.3e-11 Score=103.26 Aligned_cols=49 Identities=18% Similarity=0.490 Sum_probs=22.6
Q ss_pred cccccccccccChHHHHHHHHHc-CCcccccccccccccCHHHHHHHHHH
Q psy6525 130 FQCNVCFLMLNNRCYTRFHLLKH-NWVRFKCDLCSRTFNSQSYLQQHKKH 178 (360)
Q Consensus 130 ~~C~~C~~~f~~~~~l~~H~~~h-~~~~~~C~~C~~~f~~~~~l~~H~~~ 178 (360)
|.|.+|...|.+...|..|.-.- -..-|+|+.|+|+|.-..+|..|.++
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRW 317 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRW 317 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcc
Confidence 45555555555555554442110 01234555555555555555555544
No 17
>KOG3993|consensus
Probab=98.88 E-value=2e-10 Score=100.61 Aligned_cols=189 Identities=14% Similarity=0.213 Sum_probs=119.8
Q ss_pred ceecccchhccCChHHHHHHHhhccCCCCCccccccccccccChHHHHHHHHHcCCcccccccc----cccccCHHHHHH
Q psy6525 99 NVLCYICDEILKDIDDLRYHGLLHATPLGTQFQCNVCFLMLNNRCYTRFHLLKHNWVRFKCDLC----SRTFNSQSYLQQ 174 (360)
Q Consensus 99 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C----~~~f~~~~~l~~ 174 (360)
.|+|.+|...|.+.-.|.+|.-.... .-.|+|+.|+++|+-..+|..|.+-|..++--=.-= .+...+....+.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV--~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIV--HVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeE--EeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 48999999999999999999632222 235999999999999999999999996443111000 000011111110
Q ss_pred HHHH--cCCCceeecccccccccChhHHHHHHHhcCCC------------------CCcCccccccccCHHHHHHHHhhc
Q psy6525 175 HKKH--DHEGVKYKCKECGKCYTQNTNLKQHMLSHKGI------------------FFICFHCNKNFTHRALLVRHMQKH 234 (360)
Q Consensus 175 H~~~--~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~------------------~~~C~~C~~~f~~~~~l~~H~~~h 234 (360)
--+. .....-|.|..|++.|.+..-|+.|+.+|+.. .+-|..|.-.+...+.-..+...+
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~ 424 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYV 424 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeee
Confidence 0000 01122688999999999999999998877532 134555655554443322332222
Q ss_pred CCC--CcccCCCCCccCCHHHHHHHHHHhcCCCcccccccccccCChhHHHHhHhhh
Q psy6525 235 SSE--RFKCDLCGKVTPYYQHYLRHMRIHQGLEVHECNLCAKLFACKRSLQDHMQRH 289 (360)
Q Consensus 235 ~~~--~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 289 (360)
.+. .-.|+.|+..+.+...-..+.+.-..+..|.|.+|..+|.+...|.+|+...
T Consensus 425 a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~ 481 (500)
T KOG3993|consen 425 AGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKC 481 (500)
T ss_pred eccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhc
Confidence 221 3457778877766555444444444456689999999999999999998763
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.87 E-value=6.5e-10 Score=69.49 Aligned_cols=42 Identities=19% Similarity=0.557 Sum_probs=30.3
Q ss_pred ccccccccccCChhHHHHhHhhhcCCCccccccchhhhcCHHHH
Q psy6525 267 HECNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKKQYASKKML 310 (360)
Q Consensus 267 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L 310 (360)
|.|+.||+.|+..++|..|+++|+ ++|+|..|++.|...+.|
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 677777777777777777777776 567777777777766554
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.66 E-value=1e-08 Score=54.80 Aligned_cols=24 Identities=33% Similarity=0.868 Sum_probs=12.4
Q ss_pred HHHhHhhhcCCCccccccchhhhc
Q psy6525 282 LQDHMQRHEEPNKYQCAMCKKQYA 305 (360)
Q Consensus 282 l~~H~~~h~~~~~~~C~~C~~~f~ 305 (360)
|.+|+++|+|++||.|++|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 445555555555555555555543
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.51 E-value=6.9e-08 Score=51.52 Aligned_cols=26 Identities=38% Similarity=0.722 Sum_probs=23.4
Q ss_pred HHHHHHHHhcCCCcccccccccccCC
Q psy6525 253 HYLRHMRIHQGLEVHECNLCAKLFAC 278 (360)
Q Consensus 253 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 278 (360)
+|.+|+++|+|++||.|+.|++.|.+
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 47899999999999999999999864
No 21
>PHA00616 hypothetical protein
Probab=98.43 E-value=9e-08 Score=56.90 Aligned_cols=25 Identities=28% Similarity=0.527 Sum_probs=10.6
Q ss_pred cccccchhhhcCHHHHHHHHhhhcC
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRHEG 319 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h~~ 319 (360)
|+|+.||+.|...+.|..|+++|+|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg 26 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHK 26 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcC
Confidence 3444444444444444444444433
No 22
>PHA00616 hypothetical protein
Probab=98.40 E-value=1.9e-07 Score=55.52 Aligned_cols=33 Identities=21% Similarity=0.459 Sum_probs=19.5
Q ss_pred cccccccccccCChhHHHHhHhhhcCCCccccc
Q psy6525 266 VHECNLCAKLFACKRSLQDHMQRHEEPNKYQCA 298 (360)
Q Consensus 266 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 298 (360)
||+|+.||+.|..++.|..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 355666666666666666666666666555554
No 23
>PHA00732 hypothetical protein
Probab=98.40 E-value=1.5e-07 Score=64.95 Aligned_cols=47 Identities=26% Similarity=0.586 Sum_probs=28.8
Q ss_pred cccccccccccCChhHHHHhHhh-hcCCCccccccchhhhcCHHHHHHHHhhhc
Q psy6525 266 VHECNLCAKLFACKRSLQDHMQR-HEEPNKYQCAMCKKQYASKKMLEKHIRRHE 318 (360)
Q Consensus 266 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~ 318 (360)
||.|..|++.|.+..+|..|++. |. ++.|+.|++.|. .|..|.++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 45667777777777777777663 43 246666666666 3566665443
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=98.32 E-value=7.8e-07 Score=57.02 Aligned_cols=50 Identities=26% Similarity=0.539 Sum_probs=31.3
Q ss_pred ccccccchhhhcCHHHHHHHHhh-hcC--CcccccccccccCChHHHHHHHHHhCC
Q psy6525 294 KYQCAMCKKQYASKKMLEKHIRR-HEG--QDYKCYICGNRYATQKYLEEHIRLHQG 346 (360)
Q Consensus 294 ~~~C~~C~~~f~~~~~L~~H~~~-h~~--~~~~C~~C~~~f~~~~~l~~H~~~h~g 346 (360)
.|.|++|++ ..+...|..|... |.+ +.+.|++|...++ .+|..|+..++|
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 366777777 4455667777664 333 3567777776544 377777776654
No 25
>PHA00732 hypothetical protein
Probab=98.26 E-value=4.6e-07 Score=62.53 Aligned_cols=36 Identities=31% Similarity=0.716 Sum_probs=17.4
Q ss_pred cccccchhhhcCHHHHHHHHhh-hcCCcccccccccccC
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRR-HEGQDYKCYICGNRYA 332 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~-h~~~~~~C~~C~~~f~ 332 (360)
|.|+.|++.|.+...|..|++. |. ++.|+.||+.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC
Confidence 4455555555555555555542 32 234555555554
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.03 E-value=3.2e-06 Score=43.74 Aligned_cols=23 Identities=43% Similarity=1.051 Sum_probs=15.6
Q ss_pred ccccccccccCChHHHHHHHHHh
Q psy6525 322 YKCYICGNRYATQKYLEEHIRLH 344 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~~h 344 (360)
|+|++|++.|.++..|..|++.|
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 56777777777777777776654
No 27
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.94 E-value=5.2e-06 Score=61.02 Aligned_cols=71 Identities=21% Similarity=0.481 Sum_probs=13.4
Q ss_pred ccccccccCChhHHHHhHhhhcCCCccccccchhhhcCHHHHHHHHhhhcCCcccccccccccCChHHHHHHHHH
Q psy6525 269 CNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGNRYATQKYLEEHIRL 343 (360)
Q Consensus 269 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~ 343 (360)
|.+|+..|.+...|..|+...++...- ....+.....+..+++.-....+.|.+|++.|.+...|..||+.
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 555555555555555555443321100 11111222333333332222345566666666666666666554
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.93 E-value=1.5e-05 Score=51.04 Aligned_cols=49 Identities=16% Similarity=0.139 Sum_probs=26.0
Q ss_pred eecccchhccCChHHHHHHHhhccCCCCCccccccccccccChHHHHHHHHH
Q psy6525 100 VLCYICDEILKDIDDLRYHGLLHATPLGTQFQCNVCFLMLNNRCYTRFHLLK 151 (360)
Q Consensus 100 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 151 (360)
|.|++|++ .-+...|..|....|....+.+.||+|...+. ..|..|+..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 56666666 34455666665554444344566666655333 245555543
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=97.84 E-value=8.2e-06 Score=42.17 Aligned_cols=22 Identities=45% Similarity=1.100 Sum_probs=12.5
Q ss_pred cccccchhhhcCHHHHHHHHhh
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRR 316 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~ 316 (360)
|.|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4555555555555555555554
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.77 E-value=1.8e-05 Score=41.27 Aligned_cols=24 Identities=33% Similarity=0.941 Sum_probs=13.2
Q ss_pred ccccccccccCChHHHHHHHHHhC
Q psy6525 322 YKCYICGNRYATQKYLEEHIRLHQ 345 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~~h~ 345 (360)
|.|++|++.|.+...|..|+++|+
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 456666666666666666666553
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.69 E-value=2.7e-05 Score=57.18 Aligned_cols=22 Identities=41% Similarity=0.753 Sum_probs=0.0
Q ss_pred cccccccccCHHHHHHHHHHcC
Q psy6525 159 CDLCSRTFNSQSYLQQHKKHDH 180 (360)
Q Consensus 159 C~~C~~~f~~~~~l~~H~~~~h 180 (360)
|.+|+..|.+...|..||...|
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H 23 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKH 23 (100)
T ss_dssp ----------------------
T ss_pred cccccccccccccccccccccc
Confidence 4444444444444444444433
No 32
>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=97.64 E-value=2.7e-05 Score=41.95 Aligned_cols=25 Identities=32% Similarity=0.699 Sum_probs=15.7
Q ss_pred cccccccccccCChHHHHHHHHHhC
Q psy6525 321 DYKCYICGNRYATQKYLEEHIRLHQ 345 (360)
Q Consensus 321 ~~~C~~C~~~f~~~~~l~~H~~~h~ 345 (360)
||+|..|++.|.+...|..|++.|.
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 4566666666666666666666554
No 33
>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=97.61 E-value=3.8e-05 Score=39.98 Aligned_cols=23 Identities=43% Similarity=0.996 Sum_probs=13.6
Q ss_pred cccccchhhhcCHHHHHHHHhhh
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRH 317 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h 317 (360)
|.|++|++.|.+...|..|+++|
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 45666666666666666666654
No 34
>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=97.50 E-value=4.6e-05 Score=41.05 Aligned_cols=25 Identities=32% Similarity=0.689 Sum_probs=16.1
Q ss_pred ccccccchhhhcCHHHHHHHHhhhc
Q psy6525 294 KYQCAMCKKQYASKKMLEKHIRRHE 318 (360)
Q Consensus 294 ~~~C~~C~~~f~~~~~L~~H~~~h~ 318 (360)
||.|..|++.|.+...|..|++.|.
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 4666666666666666666666553
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.40 E-value=4.2e-05 Score=65.27 Aligned_cols=27 Identities=30% Similarity=0.670 Sum_probs=22.5
Q ss_pred Cccccccc--ccccccCHHHHHHHHHHcC
Q psy6525 154 WVRFKCDL--CSRTFNSQSYLQQHKKHDH 180 (360)
Q Consensus 154 ~~~~~C~~--C~~~f~~~~~l~~H~~~~h 180 (360)
.+||+|++ |+|.|.+...|+.|+..-|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH 375 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGH 375 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccc
Confidence 57888887 8899999999998887755
No 36
>KOG1146|consensus
Probab=97.32 E-value=4.1e-05 Score=77.25 Aligned_cols=50 Identities=18% Similarity=0.263 Sum_probs=35.9
Q ss_pred Cccccccchhhhc-CHHHHHHHHhhh-------cCCcccccccccccCChHHHHHHHH
Q psy6525 293 NKYQCAMCKKQYA-SKKMLEKHIRRH-------EGQDYKCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 293 ~~~~C~~C~~~f~-~~~~L~~H~~~h-------~~~~~~C~~C~~~f~~~~~l~~H~~ 342 (360)
+.+.|-+|..--. +...|+.|..+- .|..|.|.+|.+.-..+.++..|.+
T Consensus 733 k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~~~~c~l~~y~t~~kanfqlh~K 790 (1406)
T KOG1146|consen 733 KVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGDVPSCKLKPYATNTKANFQLHNK 790 (1406)
T ss_pred HHHHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCCCCcceecccccccchhhhhhcc
Confidence 3477888876443 566777786543 2356899999988888888888854
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.29 E-value=6.1e-05 Score=64.29 Aligned_cols=51 Identities=29% Similarity=0.751 Sum_probs=41.0
Q ss_pred CCcccccc--chhhhcCHHHHHHHHhh-h-------------------cCCcccccccccccCChHHHHHHHH
Q psy6525 292 PNKYQCAM--CKKQYASKKMLEKHIRR-H-------------------EGQDYKCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 292 ~~~~~C~~--C~~~f~~~~~L~~H~~~-h-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 342 (360)
++||+|++ |.|.|.+...|+.|+.- | ..+||+|++|+|.+++...|+.|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 58888877 88888888888888763 3 1258999999999999999998864
No 38
>KOG2231|consensus
Probab=97.09 E-value=0.001 Score=63.86 Aligned_cols=23 Identities=30% Similarity=0.686 Sum_probs=13.6
Q ss_pred ccccccccccCHHHHHHHHHHcCC
Q psy6525 158 KCDLCSRTFNSQSYLQQHKKHDHE 181 (360)
Q Consensus 158 ~C~~C~~~f~~~~~l~~H~~~~h~ 181 (360)
.|..| -.|.+...|+.|+...|.
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~ 139 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHK 139 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhh
Confidence 45566 556666666666655443
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.05 E-value=0.00051 Score=36.21 Aligned_cols=24 Identities=38% Similarity=0.908 Sum_probs=14.1
Q ss_pred ccccccccccCChHHHHHHHHHhC
Q psy6525 322 YKCYICGNRYATQKYLEEHIRLHQ 345 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~~h~ 345 (360)
|+|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 356666666666666666665543
No 40
>KOG2231|consensus
Probab=97.02 E-value=0.0017 Score=62.45 Aligned_cols=97 Identities=24% Similarity=0.484 Sum_probs=59.0
Q ss_pred ccCChHHHHHHHhhccCCCCCcccccccc---------ccccChHHHHHHHHHcCC------cccccccccccccCHHHH
Q psy6525 108 ILKDIDDLRYHGLLHATPLGTQFQCNVCF---------LMLNNRCYTRFHLLKHNW------VRFKCDLCSRTFNSQSYL 172 (360)
Q Consensus 108 ~f~~~~~l~~H~~~~~~~~~~~~~C~~C~---------~~f~~~~~l~~H~~~h~~------~~~~C~~C~~~f~~~~~l 172 (360)
.|+++..|+.|+...|. .+.|.+|- ....++..|..|+..-.. ..-.|..|...|-....|
T Consensus 123 ~~~s~~~Lk~H~~~~H~----~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el 198 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQHK----LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDEL 198 (669)
T ss_pred chhHHHHHHHHHHHhhh----hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHH
Confidence 33477788888765443 35555552 223455566666654321 124677788778777888
Q ss_pred HHHHHHcCCCceeecccc------cccccChhHHHHHHHhcCCCCCcCc
Q psy6525 173 QQHKKHDHEGVKYKCKEC------GKCYTQNTNLKQHMLSHKGIFFICF 215 (360)
Q Consensus 173 ~~H~~~~h~~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~~~~C~ 215 (360)
..|++..| |.|..| +..|.....|..|.+.++ |.|.
T Consensus 199 ~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H---flCE 240 (669)
T KOG2231|consen 199 YRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH---FLCE 240 (669)
T ss_pred HHhhccce----eheeecCcccccchhcccchHHHHHhhhcC---cccc
Confidence 87777755 445555 344666777777777765 4555
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.93 E-value=0.00053 Score=35.64 Aligned_cols=24 Identities=29% Similarity=0.659 Sum_probs=13.6
Q ss_pred ccccccccccCChHHHHHHHHHhCC
Q psy6525 322 YKCYICGNRYATQKYLEEHIRLHQG 346 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~~h~g 346 (360)
|+|+.|+.... ...|..|++.|+|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 45666666665 6666666666543
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.83 E-value=0.0011 Score=34.88 Aligned_cols=23 Identities=43% Similarity=0.957 Sum_probs=15.1
Q ss_pred cccccchhhhcCHHHHHHHHhhh
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRH 317 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h 317 (360)
|.|+.|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666666666666666666654
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=96.76 E-value=0.00062 Score=41.49 Aligned_cols=28 Identities=25% Similarity=0.504 Sum_probs=15.7
Q ss_pred CcccccccccccCChHHHHHHHHHhCCC
Q psy6525 320 QDYKCYICGNRYATQKYLEEHIRLHQGH 347 (360)
Q Consensus 320 ~~~~C~~C~~~f~~~~~l~~H~~~h~g~ 347 (360)
.|-.|++|+..+.+..+|++|+.++|+.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 4666777777777777777777666553
No 44
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.70 E-value=0.0021 Score=55.85 Aligned_cols=127 Identities=19% Similarity=0.353 Sum_probs=79.2
Q ss_pred ceeccc--chhccCChHHHHHHHhhccCCCCCcccccccc---ccc------cChHHHHHHHHHcCC-----cccccccc
Q psy6525 99 NVLCYI--CDEILKDIDDLRYHGLLHATPLGTQFQCNVCF---LML------NNRCYTRFHLLKHNW-----VRFKCDLC 162 (360)
Q Consensus 99 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~---~~f------~~~~~l~~H~~~h~~-----~~~~C~~C 162 (360)
.|.|+. |......+..|..|....|+ .+.|.+|- +.| .+...|+.|...-.. ..-.|..|
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 226 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHG----FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFC 226 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC----cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhc
Confidence 367875 77777778899999887665 36787772 223 234455555443221 12358888
Q ss_pred cccccCHHHHHHHHHHcCCCceeeccccccc-------ccChhHHHHHHHhcCCCCCcCcc--cc----ccccCHHHHHH
Q psy6525 163 SRTFNSQSYLQQHKKHDHEGVKYKCKECGKC-------YTQNTNLKQHMLSHKGIFFICFH--CN----KNFTHRALLVR 229 (360)
Q Consensus 163 ~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~-------f~~~~~l~~H~~~h~~~~~~C~~--C~----~~f~~~~~l~~ 229 (360)
...|-+...|.+|++..|. .|.+|++. |.+...|..|.+.-+ |.|.. |- .+|.....|..
T Consensus 227 ~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h---y~ct~qtc~~~k~~vf~~~~el~~ 299 (493)
T COG5236 227 KIYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAH---YCCTFQTCRVGKCYVFPYHTELLE 299 (493)
T ss_pred cceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcCc---eEEEEEEEecCcEEEeccHHHHHH
Confidence 8888888888888887664 35555433 667777777766532 33332 21 35677777777
Q ss_pred HHhhcCC
Q psy6525 230 HMQKHSS 236 (360)
Q Consensus 230 H~~~h~~ 236 (360)
|+..-|+
T Consensus 300 h~~~~h~ 306 (493)
T COG5236 300 HLTRFHK 306 (493)
T ss_pred HHHHHhh
Confidence 7665443
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.54 E-value=0.0013 Score=34.42 Aligned_cols=22 Identities=27% Similarity=0.818 Sum_probs=15.0
Q ss_pred ccccccccccCChHHHHHHHHH
Q psy6525 322 YKCYICGNRYATQKYLEEHIRL 343 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~~ 343 (360)
|.|.+|++.|.+...|..|++.
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 4577777777777777777654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.44 E-value=0.0016 Score=51.68 Aligned_cols=34 Identities=26% Similarity=0.512 Sum_probs=17.4
Q ss_pred cccccccccccCChHHHHHHHHHhCCC-CccCCCccccc
Q psy6525 321 DYKCYICGNRYATQKYLEEHIRLHQGH-TYMCNAKFSFN 358 (360)
Q Consensus 321 ~~~C~~C~~~f~~~~~l~~H~~~h~g~-~~~C~~c~~~f 358 (360)
+|.|. |+. ....+..|.++|+|+ +|.|..|+..|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 45554 544 444455555555554 45555555544
No 47
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.43 E-value=0.0025 Score=38.87 Aligned_cols=19 Identities=21% Similarity=0.670 Sum_probs=5.9
Q ss_pred ccccchhhhcCHHHHHHHH
Q psy6525 296 QCAMCKKQYASKKMLEKHI 314 (360)
Q Consensus 296 ~C~~C~~~f~~~~~L~~H~ 314 (360)
.|++|+..+.+..+|++|+
T Consensus 26 tCP~C~a~~~~srnLrRHl 44 (54)
T PF09237_consen 26 TCPICGAVIRQSRNLRRHL 44 (54)
T ss_dssp E-TTT--EESSHHHHHHHH
T ss_pred CCCcchhhccchhhHHHHH
Confidence 3333333333333333333
No 48
>KOG2785|consensus
Probab=96.43 E-value=0.0086 Score=53.12 Aligned_cols=23 Identities=26% Similarity=0.520 Sum_probs=19.7
Q ss_pred ccccccccccccChHHHHHHHHH
Q psy6525 129 QFQCNVCFLMLNNRCYTRFHLLK 151 (360)
Q Consensus 129 ~~~C~~C~~~f~~~~~l~~H~~~ 151 (360)
-|.|.-|...|.+....+.|+++
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKS 25 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKS 25 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhh
Confidence 48899999999998888888865
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.39 E-value=0.0021 Score=33.35 Aligned_cols=23 Identities=35% Similarity=0.873 Sum_probs=12.0
Q ss_pred cccccchhhhcCHHHHHHHHhhhc
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRHE 318 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h~ 318 (360)
|+|+.|+.... ...|..|++.|+
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 45666665555 556666665543
No 50
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.23 E-value=0.0025 Score=33.35 Aligned_cols=20 Identities=35% Similarity=0.934 Sum_probs=8.6
Q ss_pred ccccchhhhcCHHHHHHHHh
Q psy6525 296 QCAMCKKQYASKKMLEKHIR 315 (360)
Q Consensus 296 ~C~~C~~~f~~~~~L~~H~~ 315 (360)
.|++|++.|.+...|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 34444444444444444443
No 51
>PRK04860 hypothetical protein; Provisional
Probab=96.13 E-value=0.0029 Score=50.24 Aligned_cols=26 Identities=15% Similarity=0.415 Sum_probs=12.0
Q ss_pred hhHHHHhHhhhcCCCccccccchhhh
Q psy6525 279 KRSLQDHMQRHEEPNKYQCAMCKKQY 304 (360)
Q Consensus 279 ~~~l~~H~~~h~~~~~~~C~~C~~~f 304 (360)
...+++|.++|+++++|.|..|+..|
T Consensus 128 ~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 128 QLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred eCHHHHHHHHhcCCccEECCCCCcee
Confidence 33444444444444444444444444
No 52
>KOG2785|consensus
Probab=96.11 E-value=0.018 Score=51.14 Aligned_cols=50 Identities=22% Similarity=0.523 Sum_probs=36.5
Q ss_pred ccccccchhhhcCHHHHHHHHhhhcC------------------------Ccccccccc---cccCChHHHHHHHHH
Q psy6525 294 KYQCAMCKKQYASKKMLEKHIRRHEG------------------------QDYKCYICG---NRYATQKYLEEHIRL 343 (360)
Q Consensus 294 ~~~C~~C~~~f~~~~~L~~H~~~h~~------------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 343 (360)
|-.|-.|++.+.+...-..||..+|| ..|.|-.|+ +.|.+..+.+.||..
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 45566677777776666677766654 127788888 888999999999864
No 53
>KOG2482|consensus
Probab=95.76 E-value=0.012 Score=51.28 Aligned_cols=137 Identities=18% Similarity=0.300 Sum_probs=78.6
Q ss_pred Cceecccchhcc-CChHHHHHHHh-hccCCCCC-------------------ccccccccccccChHHHHHHHHHcCCc-
Q psy6525 98 KNVLCYICDEIL-KDIDDLRYHGL-LHATPLGT-------------------QFQCNVCFLMLNNRCYTRFHLLKHNWV- 155 (360)
Q Consensus 98 ~~~~C~~C~~~f-~~~~~l~~H~~-~~~~~~~~-------------------~~~C~~C~~~f~~~~~l~~H~~~h~~~- 155 (360)
....|-.|...+ .+++....|+. .|.-..+. .+.|-.|.+.|.++..|+.||+.-+.+
T Consensus 143 fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 143 FSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred eeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCcc
Confidence 346799998888 55666777764 33322221 357888888888888888888764211
Q ss_pred --c-------c-c--cccccccccCH-HHHHHHHHHc-------------CCCc--eeecccccccccChhHHHHHHHhc
Q psy6525 156 --R-------F-K--CDLCSRTFNSQ-SYLQQHKKHD-------------HEGV--KYKCKECGKCYTQNTNLKQHMLSH 207 (360)
Q Consensus 156 --~-------~-~--C~~C~~~f~~~-~~l~~H~~~~-------------h~~~--~~~C~~C~~~f~~~~~l~~H~~~h 207 (360)
| | . -..=+++.... ..+.+-.... ++.. ...|-.|.....+...|..||...
T Consensus 223 inPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~v 302 (423)
T KOG2482|consen 223 INPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIV 302 (423)
T ss_pred cCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHH
Confidence 1 0 0 00011111100 0000000000 0111 147888888888788888887753
Q ss_pred CC----------------------------CCCcCccccccccCHHHHHHHHhhc
Q psy6525 208 KG----------------------------IFFICFHCNKNFTHRALLVRHMQKH 234 (360)
Q Consensus 208 ~~----------------------------~~~~C~~C~~~f~~~~~l~~H~~~h 234 (360)
+. ....|-.|...|.....|..||..+
T Consensus 303 He~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 303 HEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred HHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 21 0245888999999999999998754
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.70 E-value=0.021 Score=49.79 Aligned_cols=127 Identities=26% Similarity=0.479 Sum_probs=78.8
Q ss_pred cccccc--ccccccCHHHHHHHHHHcCCCceeecccccc---ccc------ChhHHHHHHHhcCCC-----CCcCccccc
Q psy6525 156 RFKCDL--CSRTFNSQSYLQQHKKHDHEGVKYKCKECGK---CYT------QNTNLKQHMLSHKGI-----FFICFHCNK 219 (360)
Q Consensus 156 ~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~---~f~------~~~~l~~H~~~h~~~-----~~~C~~C~~ 219 (360)
.|.|+. |..+......|..|.+..|+. +.|.+|-. .|. +...|..|...-... --.|..|..
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~~ 228 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 388877 777777788899999887753 66777632 232 334555554432111 136888888
Q ss_pred cccCHHHHHHHHhhcCCCCcccCCCC----CccCCHHHHHHHHHHhcCCCcccccc--cc----cccCChhHHHHhHhh
Q psy6525 220 NFTHRALLVRHMQKHSSERFKCDLCG----KVTPYYQHYLRHMRIHQGLEVHECNL--CA----KLFACKRSLQDHMQR 288 (360)
Q Consensus 220 ~f~~~~~l~~H~~~h~~~~~~C~~C~----~~f~~~~~l~~H~~~h~~~~~~~C~~--C~----~~f~~~~~l~~H~~~ 288 (360)
.|..-..|..|++..|..-+.|+.-+ .-|.+...|..|.+.-+ |.|.+ |. ..|.....|..|+..
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 88888888888887776534443322 23666677777765432 44433 32 356677777777654
No 55
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.56 E-value=0.0034 Score=33.57 Aligned_cols=21 Identities=19% Similarity=0.763 Sum_probs=13.0
Q ss_pred ccccccccccCChHHHHHHHH
Q psy6525 322 YKCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~ 342 (360)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666666666654
No 56
>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=95.54 E-value=0.0054 Score=32.79 Aligned_cols=22 Identities=32% Similarity=0.788 Sum_probs=12.6
Q ss_pred ccccccccccCChhHHHHhHhh
Q psy6525 267 HECNLCAKLFACKRSLQDHMQR 288 (360)
Q Consensus 267 ~~C~~C~~~f~~~~~l~~H~~~ 288 (360)
|.|..|++.|.+...|..|+++
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 4555666666666666555543
No 57
>KOG2482|consensus
Probab=95.34 E-value=0.062 Score=46.98 Aligned_cols=147 Identities=20% Similarity=0.306 Sum_probs=91.2
Q ss_pred HHHHHHhhccCCCCCccccccccccc-cChHHHHHHHH-HcC---Cc-------------------ccccccccccccCH
Q psy6525 114 DLRYHGLLHATPLGTQFQCNVCFLML-NNRCYTRFHLL-KHN---WV-------------------RFKCDLCSRTFNSQ 169 (360)
Q Consensus 114 ~l~~H~~~~~~~~~~~~~C~~C~~~f-~~~~~l~~H~~-~h~---~~-------------------~~~C~~C~~~f~~~ 169 (360)
.|+.|++.-.+ .....+|-.|+..+ .+++....|+. .|+ .. .+.|-.|.+.|+++
T Consensus 130 aLeqqQ~Ered-t~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdk 208 (423)
T KOG2482|consen 130 ALEQQQKERED-TIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDK 208 (423)
T ss_pred HHHHHHHHhcC-CeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCc
Confidence 34455543322 24567899998765 45677777774 343 11 37899999999999
Q ss_pred HHHHHHHHHcCCCc--e--------eecc--cccccccCh-hHHH-----HHHH---------hcCCC--CCcCcccccc
Q psy6525 170 SYLQQHKKHDHEGV--K--------YKCK--ECGKCYTQN-TNLK-----QHML---------SHKGI--FFICFHCNKN 220 (360)
Q Consensus 170 ~~l~~H~~~~h~~~--~--------~~C~--~C~~~f~~~-~~l~-----~H~~---------~h~~~--~~~C~~C~~~ 220 (360)
..|+.||+.....+ | |.=. .=|++.... +.+. .+.. .+... ...|-.|...
T Consensus 209 ntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~ 288 (423)
T KOG2482|consen 209 NTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNF 288 (423)
T ss_pred HHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccc
Confidence 99999998643221 1 1110 011211110 0010 0000 00111 2589999999
Q ss_pred ccCHHHHHHHHhhcCCC----------------------------CcccCCCCCccCCHHHHHHHHHHh
Q psy6525 221 FTHRALLVRHMQKHSSE----------------------------RFKCDLCGKVTPYYQHYLRHMRIH 261 (360)
Q Consensus 221 f~~~~~l~~H~~~h~~~----------------------------~~~C~~C~~~f~~~~~l~~H~~~h 261 (360)
..+...|..||+..|.- ...|-.|...|.....|..||..+
T Consensus 289 ~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 289 YENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred hhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 99999999999865520 135889999999999999998743
No 58
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.79 E-value=0.025 Score=29.58 Aligned_cols=21 Identities=33% Similarity=0.849 Sum_probs=13.0
Q ss_pred ccccccccccCChHHHHHHHHH
Q psy6525 322 YKCYICGNRYATQKYLEEHIRL 343 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~~ 343 (360)
..|+.||+.| ..+.|..|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3566777776 55566666653
No 59
>KOG1146|consensus
Probab=94.59 E-value=0.004 Score=63.59 Aligned_cols=24 Identities=29% Similarity=0.393 Sum_probs=16.5
Q ss_pred CCCcCccccccccCHHHHHHHHhh
Q psy6525 210 IFFICFHCNKNFTHRALLVRHMQK 233 (360)
Q Consensus 210 ~~~~C~~C~~~f~~~~~l~~H~~~ 233 (360)
.+|.|..|...+....+|..|++.
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHH
Confidence 466777777777777777777653
No 60
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.66 E-value=0.051 Score=28.36 Aligned_cols=18 Identities=28% Similarity=0.737 Sum_probs=8.1
Q ss_pred cccccccccCChhHHHHhH
Q psy6525 268 ECNLCAKLFACKRSLQDHM 286 (360)
Q Consensus 268 ~C~~C~~~f~~~~~l~~H~ 286 (360)
.|+.||+.| ....|.+|+
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 334444443
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.34 E-value=0.014 Score=54.96 Aligned_cols=116 Identities=24% Similarity=0.449 Sum_probs=65.6
Q ss_pred CcccCCCCCccCCHHHHHHHHH--HhcCC--Cccccc--ccccccCChhHHHHhHhhhcCCCccc---------------
Q psy6525 238 RFKCDLCGKVTPYYQHYLRHMR--IHQGL--EVHECN--LCAKLFACKRSLQDHMQRHEEPNKYQ--------------- 296 (360)
Q Consensus 238 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~--------------- 296 (360)
++.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.+...+..|...|.+..++.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLN 368 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccccC
Confidence 3455555555555555555555 45555 555555 45555555555555555554433322
Q ss_pred --------------------ccc--chhhhcCHHHHHHHHhhhcC---CcccccccccccCChHHHHHHHHHhCCC-Ccc
Q psy6525 297 --------------------CAM--CKKQYASKKMLEKHIRRHEG---QDYKCYICGNRYATQKYLEEHIRLHQGH-TYM 350 (360)
Q Consensus 297 --------------------C~~--C~~~f~~~~~L~~H~~~h~~---~~~~C~~C~~~f~~~~~l~~H~~~h~g~-~~~ 350 (360)
+.. |...+.+...+..|...|.. ..+.+..|.+.|.....+..|++.|.-. +..
T Consensus 369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 448 (467)
T COG5048 369 NEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448 (467)
T ss_pred CCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCcee
Confidence 211 44444444445555444433 2466778888888888888888887766 333
Q ss_pred CCC
Q psy6525 351 CNA 353 (360)
Q Consensus 351 C~~ 353 (360)
|..
T Consensus 449 ~~~ 451 (467)
T COG5048 449 CSI 451 (467)
T ss_pred ecc
Confidence 433
No 62
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.96 E-value=0.066 Score=30.42 Aligned_cols=22 Identities=18% Similarity=0.683 Sum_probs=16.5
Q ss_pred cccccccccccCChHHHHHHHH
Q psy6525 321 DYKCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 321 ~~~C~~C~~~f~~~~~l~~H~~ 342 (360)
+|.|.+|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4677888888887777777765
No 63
>KOG4173|consensus
Probab=92.45 E-value=0.13 Score=41.71 Aligned_cols=78 Identities=18% Similarity=0.391 Sum_probs=59.1
Q ss_pred Cceeccc--chhccCChHHHHHHHhhccCCCCCccccccccccccChHHHHHHHHHcC-----------Cccccccc--c
Q psy6525 98 KNVLCYI--CDEILKDIDDLRYHGLLHATPLGTQFQCNVCFLMLNNRCYTRFHLLKHN-----------WVRFKCDL--C 162 (360)
Q Consensus 98 ~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~-----------~~~~~C~~--C 162 (360)
..+.|.+ |...|........|...-|+ -.|.+|.+.|.+...|..|+...+ ...|.|-+ |
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~-----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG-----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc-----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 4577886 89999999999999876665 359999999999999999986532 23466754 7
Q ss_pred cccccCHHHHHHHHHHcC
Q psy6525 163 SRTFNSQSYLQQHKKHDH 180 (360)
Q Consensus 163 ~~~f~~~~~l~~H~~~~h 180 (360)
+..|.+...-..||-..|
T Consensus 153 t~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhhhhhHHHHhc
Confidence 777777777777776555
No 64
>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=92.42 E-value=0.085 Score=29.96 Aligned_cols=23 Identities=17% Similarity=0.670 Sum_probs=17.7
Q ss_pred ccccccchhhhcCHHHHHHHHhh
Q psy6525 294 KYQCAMCKKQYASKKMLEKHIRR 316 (360)
Q Consensus 294 ~~~C~~C~~~f~~~~~L~~H~~~ 316 (360)
+|.|++|++.|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57788888888888888888763
No 65
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.78 E-value=0.026 Score=53.03 Aligned_cols=49 Identities=20% Similarity=0.333 Sum_probs=34.0
Q ss_pred cccccCChhHHHHhHhhhcCCC--ccccccchhhhcCHHHHHHHHhhhcCC
Q psy6525 272 CAKLFACKRSLQDHMQRHEEPN--KYQCAMCKKQYASKKMLEKHIRRHEGQ 320 (360)
Q Consensus 272 C~~~f~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~L~~H~~~h~~~ 320 (360)
|...+.....+..|...|...+ .+.+..|.+.+.....+..|++.|...
T Consensus 394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (467)
T COG5048 394 CIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNH 444 (467)
T ss_pred hhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccC
Confidence 5566666666777766666555 355667888888877787887777664
No 66
>KOG2893|consensus
Probab=91.74 E-value=0.06 Score=44.51 Aligned_cols=42 Identities=36% Similarity=0.691 Sum_probs=23.7
Q ss_pred ccccccccccCHHHHHHHHHHcCCCceeecccccccccChhHHHHH
Q psy6525 158 KCDLCSRTFNSQSYLQQHKKHDHEGVKYKCKECGKCYTQNTNLKQH 203 (360)
Q Consensus 158 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H 203 (360)
.|-.|++.|.+..-|..|++..| |+|.+|.+..-+--.|..|
T Consensus 12 wcwycnrefddekiliqhqkakh----fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceee
Confidence 45566666666666666655533 5566666555555455444
No 67
>KOG4173|consensus
Probab=89.92 E-value=0.12 Score=41.86 Aligned_cols=76 Identities=21% Similarity=0.542 Sum_probs=41.0
Q ss_pred ccccc--ccccccCHHHHHHHHHHcCCCceeecccccccccChhHHHHHHHhcCC-----------CCCcCcc--ccccc
Q psy6525 157 FKCDL--CSRTFNSQSYLQQHKKHDHEGVKYKCKECGKCYTQNTNLKQHMLSHKG-----------IFFICFH--CNKNF 221 (360)
Q Consensus 157 ~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-----------~~~~C~~--C~~~f 221 (360)
|.|++ |...|.+...+..|+..-|+. .|..|.+.|.+...|..|+...+. ..|.|-. |+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 55555 555666666666666555543 366666666666666666544321 1344433 55555
Q ss_pred cCHHHHHHHHhhcC
Q psy6525 222 THRALLVRHMQKHS 235 (360)
Q Consensus 222 ~~~~~l~~H~~~h~ 235 (360)
.+...-..|+...|
T Consensus 157 kT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhHHHHhc
Confidence 55555555554433
No 68
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=89.75 E-value=0.17 Score=28.40 Aligned_cols=6 Identities=50% Similarity=1.586 Sum_probs=2.3
Q ss_pred cCCCCC
Q psy6525 241 CDLCGK 246 (360)
Q Consensus 241 C~~C~~ 246 (360)
|..||.
T Consensus 4 C~~CGy 9 (33)
T cd00350 4 CPVCGY 9 (33)
T ss_pred CCCCCC
Confidence 333333
No 69
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.42 E-value=0.35 Score=35.57 Aligned_cols=48 Identities=19% Similarity=0.389 Sum_probs=25.8
Q ss_pred cccchhhhcCHHHHHHHHhhhcCCcccccccccccCChHHHHHHHHHhC
Q psy6525 297 CAMCKKQYASKKMLEKHIRRHEGQDYKCYICGNRYATQKYLEEHIRLHQ 345 (360)
Q Consensus 297 C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 345 (360)
|--|...|........=. .-....|+|+.|...|=-.-++-.|..+|.
T Consensus 58 C~~C~~~f~~~~~~~~~~-~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPFDE-LKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccCcCCCCCCcccccccc-cccccceeCCCCCCccccccchhhhhhccC
Confidence 666777666543111000 011135777777777766666666665554
No 70
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=89.09 E-value=0.59 Score=34.67 Aligned_cols=25 Identities=32% Similarity=0.696 Sum_probs=23.3
Q ss_pred ccc----cccccccCChHHHHHHHHHhCC
Q psy6525 322 YKC----YICGNRYATQKYLEEHIRLHQG 346 (360)
Q Consensus 322 ~~C----~~C~~~f~~~~~l~~H~~~h~g 346 (360)
|.| ..|++...+...|..|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999998886
No 71
>KOG2893|consensus
Probab=88.88 E-value=0.11 Score=43.06 Aligned_cols=46 Identities=24% Similarity=0.400 Sum_probs=27.4
Q ss_pred cccccccccChHHHHHHHHHcCCcccccccccccccCHHHHHHHHHHcC
Q psy6525 132 CNVCFLMLNNRCYTRFHLLKHNWVRFKCDLCSRTFNSQSYLQQHKKHDH 180 (360)
Q Consensus 132 C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~h 180 (360)
|=+|++.|.+...|..|++.- .|+|-+|-+...+--.|..|....|
T Consensus 13 cwycnrefddekiliqhqkak---hfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK---HFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhhhc---cceeeeehhhhccCCCceeehhhhh
Confidence 556666666666666665432 2667777666665666666654444
No 72
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.74 E-value=0.39 Score=35.36 Aligned_cols=17 Identities=24% Similarity=0.374 Sum_probs=8.4
Q ss_pred ccccccccccccChHHH
Q psy6525 129 QFQCNVCFLMLNNRCYT 145 (360)
Q Consensus 129 ~~~C~~C~~~f~~~~~l 145 (360)
|..|++|+...-+...|
T Consensus 15 P~~CpiCgLtLVss~HL 31 (112)
T TIGR00622 15 PVECPICGLTLILSTHL 31 (112)
T ss_pred CCcCCcCCCEEeccchH
Confidence 45555555555444333
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=88.32 E-value=0.75 Score=34.10 Aligned_cols=25 Identities=40% Similarity=0.761 Sum_probs=23.0
Q ss_pred ccc----ccchhhhcCHHHHHHHHhhhcC
Q psy6525 295 YQC----AMCKKQYASKKMLEKHIRRHEG 319 (360)
Q Consensus 295 ~~C----~~C~~~f~~~~~L~~H~~~h~~ 319 (360)
|.| ..|++.+.+...+..|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999998765
No 74
>KOG2186|consensus
Probab=87.05 E-value=0.37 Score=40.49 Aligned_cols=46 Identities=22% Similarity=0.632 Sum_probs=24.6
Q ss_pred cccccchhhhcCHHHHHHHHhhhcCCcccccccccccCChHHHHHHHH
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 342 (360)
|.|..||....-. .+.+|+.+.++.-|.|-.|++.|.+ ..+..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccCCeeEEeeccccccc-chhhhhhh
Confidence 4555555554332 3444655555555666666666655 44555543
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.37 E-value=0.69 Score=28.89 Aligned_cols=27 Identities=15% Similarity=0.463 Sum_probs=16.0
Q ss_pred cCCCccccccchhhhcCHHHHHHHHhh
Q psy6525 290 EEPNKYQCAMCKKQYASKKMLEKHIRR 316 (360)
Q Consensus 290 ~~~~~~~C~~C~~~f~~~~~L~~H~~~ 316 (360)
.|+.-+.|+.|+..|.......+|+..
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 344555666666666666666666554
No 76
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.03 E-value=0.45 Score=29.70 Aligned_cols=27 Identities=22% Similarity=0.439 Sum_probs=23.8
Q ss_pred cccccccccccCChHHHHHHHHHhCCC
Q psy6525 321 DYKCYICGNRYATQKYLEEHIRLHQGH 347 (360)
Q Consensus 321 ~~~C~~C~~~f~~~~~l~~H~~~h~g~ 347 (360)
-++|+-||..|....++.+|+..-||-
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 579999999999999999999876653
No 77
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.34 E-value=0.8 Score=33.74 Aligned_cols=11 Identities=18% Similarity=0.325 Sum_probs=5.4
Q ss_pred ccccccccccc
Q psy6525 130 FQCNVCFLMLN 140 (360)
Q Consensus 130 ~~C~~C~~~f~ 140 (360)
..|+.||..|.
T Consensus 10 R~Cp~CG~kFY 20 (108)
T PF09538_consen 10 RTCPSCGAKFY 20 (108)
T ss_pred ccCCCCcchhc
Confidence 44555555544
No 78
>KOG2186|consensus
Probab=82.12 E-value=0.75 Score=38.76 Aligned_cols=46 Identities=24% Similarity=0.722 Sum_probs=27.3
Q ss_pred eecccccccccChhHHHHHHHhcCCCCCcCccccccccCHHHHHHHHh
Q psy6525 185 YKCKECGKCYTQNTNLKQHMLSHKGIFFICFHCNKNFTHRALLVRHMQ 232 (360)
Q Consensus 185 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 232 (360)
|.|..||..... ..+.+|+...++..|.|--|++.|.. ..+..|..
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 566666666543 33455666666666666666666665 45555554
No 79
>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=79.36 E-value=0.94 Score=25.59 Aligned_cols=6 Identities=50% Similarity=1.586 Sum_probs=2.2
Q ss_pred cCCCCC
Q psy6525 241 CDLCGK 246 (360)
Q Consensus 241 C~~C~~ 246 (360)
|..||.
T Consensus 5 C~~CG~ 10 (34)
T cd00729 5 CPVCGY 10 (34)
T ss_pred CCCCCC
Confidence 333333
No 80
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=78.15 E-value=1.4 Score=23.15 Aligned_cols=8 Identities=38% Similarity=0.825 Sum_probs=3.6
Q ss_pred cCCCCCcc
Q psy6525 241 CDLCGKVT 248 (360)
Q Consensus 241 C~~C~~~f 248 (360)
|+.||..|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 44444444
No 81
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.07 E-value=1.8 Score=27.61 Aligned_cols=32 Identities=28% Similarity=0.607 Sum_probs=16.1
Q ss_pred ccccccchhhhcCHHHHHHHHhhhcCCccccccccc
Q psy6525 294 KYQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGN 329 (360)
Q Consensus 294 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~ 329 (360)
.|.|+.||..-..+..- -+-.+.+|+|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~~----CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCAK----CRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhhh----HHHcCCceECCCcCc
Confidence 36677777544433221 112345666666664
No 82
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=76.56 E-value=0.34 Score=40.84 Aligned_cols=42 Identities=29% Similarity=0.615 Sum_probs=22.9
Q ss_pred CccccccchhhhcCHHHHHHHHhh-h--c-------C-C-----cccccccccccCCh
Q psy6525 293 NKYQCAMCKKQYASKKMLEKHIRR-H--E-------G-Q-----DYKCYICGNRYATQ 334 (360)
Q Consensus 293 ~~~~C~~C~~~f~~~~~L~~H~~~-h--~-------~-~-----~~~C~~C~~~f~~~ 334 (360)
+.+.||+|++.|.+...+....+. . . + . ...|+.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 345666666666655444444332 1 1 1 1 25688888877644
No 83
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=75.60 E-value=3.8 Score=32.66 Aligned_cols=17 Identities=18% Similarity=0.313 Sum_probs=8.3
Q ss_pred eeecccccccccChhHH
Q psy6525 184 KYKCKECGKCYTQNTNL 200 (360)
Q Consensus 184 ~~~C~~C~~~f~~~~~l 200 (360)
-|.|+.|+..|+...++
T Consensus 109 ~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAM 125 (158)
T ss_pred eEECCCCCcEeeHHHHH
Confidence 45555555555444444
No 84
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.87 E-value=1.8 Score=34.55 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=6.6
Q ss_pred CCCcccccccc
Q psy6525 263 GLEVHECNLCA 273 (360)
Q Consensus 263 ~~~~~~C~~C~ 273 (360)
|+.|-+||+||
T Consensus 146 ge~P~~CPiCg 156 (166)
T COG1592 146 GEAPEVCPICG 156 (166)
T ss_pred CCCCCcCCCCC
Confidence 45566666665
No 85
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.63 E-value=2.1 Score=33.64 Aligned_cols=14 Identities=29% Similarity=0.831 Sum_probs=7.3
Q ss_pred ccccccchhhhcCH
Q psy6525 294 KYQCAMCKKQYASK 307 (360)
Q Consensus 294 ~~~C~~C~~~f~~~ 307 (360)
-|.|+.|+..|...
T Consensus 99 ~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 99 YYKCPNCQSKYTFL 112 (147)
T ss_pred EEECcCCCCEeeHH
Confidence 35555555555543
No 86
>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=73.77 E-value=2.5 Score=31.18 Aligned_cols=11 Identities=27% Similarity=0.573 Sum_probs=4.5
Q ss_pred ccccccccccc
Q psy6525 266 VHECNLCAKLF 276 (360)
Q Consensus 266 ~~~C~~C~~~f 276 (360)
|..|+.||..|
T Consensus 26 PivCP~CG~~~ 36 (108)
T PF09538_consen 26 PIVCPKCGTEF 36 (108)
T ss_pred CccCCCCCCcc
Confidence 33444444433
No 87
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=73.02 E-value=2.9 Score=33.32 Aligned_cols=30 Identities=17% Similarity=0.466 Sum_probs=15.6
Q ss_pred CccccccchhhhcCHHHHHHHHhhhcCCcccccccccc
Q psy6525 293 NKYQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGNR 330 (360)
Q Consensus 293 ~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~ 330 (360)
.-|.|+.|+..|+.-.++. ..|.|+.||..
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 13556666554
No 88
>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=72.84 E-value=1.2 Score=37.79 Aligned_cols=26 Identities=23% Similarity=0.373 Sum_probs=16.3
Q ss_pred CCccccccchhhhcCHHHHHHHHhhh
Q psy6525 292 PNKYQCAMCKKQYASKKMLEKHIRRH 317 (360)
Q Consensus 292 ~~~~~C~~C~~~f~~~~~L~~H~~~h 317 (360)
.+++.|+.|+........|..-.|+|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 35677777777666666665555554
No 89
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.28 E-value=3.3 Score=23.71 Aligned_cols=33 Identities=21% Similarity=0.486 Sum_probs=17.7
Q ss_pred eecccchhccCChHHHHHHHhhccCCCCCccccccccccc
Q psy6525 100 VLCYICDEILKDIDDLRYHGLLHATPLGTQFQCNVCFLML 139 (360)
Q Consensus 100 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~~~f 139 (360)
+.|+.|+..|.-..+.. ...+...+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-------p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-------PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-------CCCCcEEECCCCCCEe
Confidence 45777776665444421 1123456666666655
No 90
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=72.19 E-value=2 Score=25.86 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=13.1
Q ss_pred cccccchhhhcCHHHHHHHHhhhcCCccccccccc
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGN 329 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~ 329 (360)
|.|..||..|.-. .+.+.+|+.||.
T Consensus 3 Y~C~~Cg~~~~~~----------~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIK----------SKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecC----------CCCceECCCCCc
Confidence 5566666655422 224556666654
No 91
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=71.39 E-value=2.3 Score=24.53 Aligned_cols=6 Identities=33% Similarity=1.160 Sum_probs=2.2
Q ss_pred cccccc
Q psy6525 268 ECNLCA 273 (360)
Q Consensus 268 ~C~~C~ 273 (360)
+|+.|+
T Consensus 27 rC~~C~ 32 (37)
T PF13719_consen 27 RCPKCG 32 (37)
T ss_pred ECCCCC
Confidence 333333
No 92
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=71.37 E-value=2.8 Score=25.20 Aligned_cols=20 Identities=30% Similarity=0.615 Sum_probs=8.6
Q ss_pred ccccccccccCCh----HHHHHHH
Q psy6525 322 YKCYICGNRYATQ----KYLEEHI 341 (360)
Q Consensus 322 ~~C~~C~~~f~~~----~~l~~H~ 341 (360)
.+|.+|++.+... +.|..|+
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 4455555555432 4555555
No 93
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=71.13 E-value=0.83 Score=36.08 Aligned_cols=12 Identities=42% Similarity=0.877 Sum_probs=5.5
Q ss_pred ccccccccccCC
Q psy6525 267 HECNLCAKLFAC 278 (360)
Q Consensus 267 ~~C~~C~~~f~~ 278 (360)
++|+-||++|.+
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 444444444443
No 94
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=70.93 E-value=3.3 Score=25.68 Aligned_cols=10 Identities=30% Similarity=0.952 Sum_probs=4.8
Q ss_pred ccccchhhhc
Q psy6525 296 QCAMCKKQYA 305 (360)
Q Consensus 296 ~C~~C~~~f~ 305 (360)
.|..|++.++
T Consensus 20 ~C~~C~~~l~ 29 (50)
T smart00614 20 KCKYCGKKLS 29 (50)
T ss_pred EecCCCCEee
Confidence 4555555443
No 95
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.76 E-value=1 Score=37.94 Aligned_cols=43 Identities=19% Similarity=0.420 Sum_probs=26.7
Q ss_pred CcccccccccccCChhHHHHhHhh---h-------cCCCc-----cccccchhhhcCH
Q psy6525 265 EVHECNLCAKLFACKRSLQDHMQR---H-------EEPNK-----YQCAMCKKQYASK 307 (360)
Q Consensus 265 ~~~~C~~C~~~f~~~~~l~~H~~~---h-------~~~~~-----~~C~~C~~~f~~~ 307 (360)
+.+.||+|+..|..+.-+....+. . .+..| ..|+.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 456777777777766544444432 1 22334 4699999988754
No 96
>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=69.97 E-value=3.8 Score=21.48 Aligned_cols=19 Identities=16% Similarity=0.595 Sum_probs=12.6
Q ss_pred cccccccccCChHHHHHHHH
Q psy6525 323 KCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 323 ~C~~C~~~f~~~~~l~~H~~ 342 (360)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 5566666664
No 97
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=69.80 E-value=2.7 Score=33.59 Aligned_cols=24 Identities=25% Similarity=0.599 Sum_probs=18.1
Q ss_pred cccccccccccCChhHHHHhHhhhcCCCccccccchh
Q psy6525 266 VHECNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKK 302 (360)
Q Consensus 266 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 302 (360)
.|.|++||..+ .|+.|-+||+||.
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 68888888654 3567888888873
No 98
>KOG2272|consensus
Probab=69.70 E-value=4.6 Score=34.10 Aligned_cols=125 Identities=22% Similarity=0.423 Sum_probs=56.2
Q ss_pred CcccccccccccccCHHHHHHH---H------HHcC-CCceeecccccccccChhHHHHHHHhcCCCCCcCccccccccC
Q psy6525 154 WVRFKCDLCSRTFNSQSYLQQH---K------KHDH-EGVKYKCKECGKCYTQNTNLKQHMLSHKGIFFICFHCNKNFTH 223 (360)
Q Consensus 154 ~~~~~C~~C~~~f~~~~~l~~H---~------~~~h-~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~ 223 (360)
+.-|.|++|++...+...++.- + +... +...|.|..|..-... ..|.---..-++--|.|..|++...+
T Consensus 97 p~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~-~~l~fr~d~yH~yHFkCt~C~keL~s 175 (332)
T KOG2272|consen 97 PACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDE-QPLTFRGDPYHPYHFKCTTCGKELTS 175 (332)
T ss_pred cccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccc-ccccccCCCCCccceecccccccccc
Confidence 5567888888776666555421 1 1001 1125777777655443 22211111122234678888777665
Q ss_pred HHHHHHHHh---hcCCCCcccCCCCCccCCH-HHHHHHHHHhcCCCcccccccccccCChh
Q psy6525 224 RALLVRHMQ---KHSSERFKCDLCGKVTPYY-QHYLRHMRIHQGLEVHECNLCAKLFACKR 280 (360)
Q Consensus 224 ~~~l~~H~~---~h~~~~~~C~~C~~~f~~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 280 (360)
.+.-..--. ..+ ..+.+++|+.--+-. .....-|..|....-|.|..|.+-|..-.
T Consensus 176 daRevk~eLyClrCh-D~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHr 235 (332)
T KOG2272|consen 176 DAREVKGELYCLRCH-DKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHR 235 (332)
T ss_pred hhhhhccceeccccc-cccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchh
Confidence 432111000 000 124455554321111 11111222333444577888877776543
No 99
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=69.08 E-value=3.1 Score=31.31 Aligned_cols=12 Identities=8% Similarity=0.027 Sum_probs=5.7
Q ss_pred cccccccccccc
Q psy6525 156 RFKCDLCSRTFN 167 (360)
Q Consensus 156 ~~~C~~C~~~f~ 167 (360)
|..|+.||..|.
T Consensus 26 p~vcP~cg~~~~ 37 (129)
T TIGR02300 26 PAVSPYTGEQFP 37 (129)
T ss_pred CccCCCcCCccC
Confidence 444555554443
No 100
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=68.75 E-value=6 Score=32.21 Aligned_cols=16 Identities=19% Similarity=0.478 Sum_probs=8.2
Q ss_pred eeecccccccccChhH
Q psy6525 184 KYKCKECGKCYTQNTN 199 (360)
Q Consensus 184 ~~~C~~C~~~f~~~~~ 199 (360)
-|.|+.|+..|+....
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 4555555555554444
No 101
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=68.66 E-value=6 Score=31.10 Aligned_cols=14 Identities=21% Similarity=0.645 Sum_probs=7.7
Q ss_pred ccccccccccccCH
Q psy6525 156 RFKCDLCSRTFNSQ 169 (360)
Q Consensus 156 ~~~C~~C~~~f~~~ 169 (360)
-|.|+.|+..|...
T Consensus 99 ~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 99 YYKCPNCQSKYTFL 112 (147)
T ss_pred EEECcCCCCEeeHH
Confidence 45566666555543
No 102
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=67.75 E-value=1.3 Score=26.08 Aligned_cols=29 Identities=21% Similarity=0.628 Sum_probs=14.4
Q ss_pred cccccchhhhcCHHHHHHHHhhhcCCccccccccc
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRRHEGQDYKCYICGN 329 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~ 329 (360)
|+|..||..|.-..... .+..-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS------DDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecC------CCCCCCCCCCCC
Confidence 56666666655332221 134455666665
No 103
>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=67.60 E-value=3.4 Score=23.80 Aligned_cols=10 Identities=30% Similarity=1.198 Sum_probs=4.2
Q ss_pred eecccccccc
Q psy6525 185 YKCKECGKCY 194 (360)
Q Consensus 185 ~~C~~C~~~f 194 (360)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 3444444433
No 104
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=66.89 E-value=3.8 Score=33.39 Aligned_cols=16 Identities=13% Similarity=0.632 Sum_probs=7.7
Q ss_pred cccccchhhhcCHHHH
Q psy6525 295 YQCAMCKKQYASKKML 310 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L 310 (360)
|.|+.|+..|+.-.++
T Consensus 118 Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 118 FFCPNCHIRFTFDEAM 133 (178)
T ss_pred EECCCCCcEEeHHHHh
Confidence 4455555544444443
No 105
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=65.83 E-value=3.8 Score=22.76 Aligned_cols=8 Identities=38% Similarity=1.045 Sum_probs=3.7
Q ss_pred cccccccc
Q psy6525 321 DYKCYICG 328 (360)
Q Consensus 321 ~~~C~~C~ 328 (360)
+.+|+.||
T Consensus 17 ~irC~~CG 24 (32)
T PF03604_consen 17 PIRCPECG 24 (32)
T ss_dssp TSSBSSSS
T ss_pred cEECCcCC
Confidence 34444444
No 106
>PHA00626 hypothetical protein
Probab=64.58 E-value=1.7 Score=27.26 Aligned_cols=12 Identities=17% Similarity=0.343 Sum_probs=5.9
Q ss_pred cccccccccccc
Q psy6525 129 QFQCNVCFLMLN 140 (360)
Q Consensus 129 ~~~C~~C~~~f~ 140 (360)
.|.|+.||..|+
T Consensus 23 rYkCkdCGY~ft 34 (59)
T PHA00626 23 DYVCCDCGYNDS 34 (59)
T ss_pred ceEcCCCCCeec
Confidence 355555554443
No 107
>KOG4167|consensus
Probab=63.94 E-value=11 Score=37.14 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=14.1
Q ss_pred ccccccccccccChHHHHHHHHHcC
Q psy6525 129 QFQCNVCFLMLNNRCYTRFHLLKHN 153 (360)
Q Consensus 129 ~~~C~~C~~~f~~~~~l~~H~~~h~ 153 (360)
.|.|..|+++|....++..||+.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3555555555555555555555553
No 108
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=63.68 E-value=2.3 Score=26.59 Aligned_cols=11 Identities=36% Similarity=1.319 Sum_probs=5.5
Q ss_pred eeccccccccc
Q psy6525 185 YKCKECGKCYT 195 (360)
Q Consensus 185 ~~C~~C~~~f~ 195 (360)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44555555444
No 109
>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=63.40 E-value=4.3 Score=31.11 Aligned_cols=25 Identities=36% Similarity=0.834 Sum_probs=16.3
Q ss_pred CcccccccccccCChHHHHHHHHHhCCC
Q psy6525 320 QDYKCYICGNRYATQKYLEEHIRLHQGH 347 (360)
Q Consensus 320 ~~~~C~~C~~~f~~~~~l~~H~~~h~g~ 347 (360)
.-..|-+||+.|+. |.+|++.|+|-
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred CeeEEccCCcccch---HHHHHHHccCC
Confidence 34679999999984 58999999885
No 110
>PF14353 CpXC: CpXC protein
Probab=63.04 E-value=6.2 Score=30.13 Aligned_cols=12 Identities=33% Similarity=0.933 Sum_probs=5.4
Q ss_pred cccccccccccC
Q psy6525 157 FKCDLCSRTFNS 168 (360)
Q Consensus 157 ~~C~~C~~~f~~ 168 (360)
|.|+.||..|.-
T Consensus 39 ~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 39 FTCPSCGHKFRL 50 (128)
T ss_pred EECCCCCCceec
Confidence 444444444433
No 111
>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=62.82 E-value=2.3 Score=36.03 Aligned_cols=100 Identities=23% Similarity=0.388 Sum_probs=55.4
Q ss_pred cccccccccccCHHHHHHHHHHcCCCceeecccccccccChhHHHHHHHhc---CCCCCcCccccccccCHHHHHHHHhh
Q psy6525 157 FKCDLCSRTFNSQSYLQQHKKHDHEGVKYKCKECGKCYTQNTNLKQHMLSH---KGIFFICFHCNKNFTHRALLVRHMQK 233 (360)
Q Consensus 157 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h---~~~~~~C~~C~~~f~~~~~l~~H~~~ 233 (360)
-.|..|.+..- .|+++.|+|..|.. |.-...--.|+.+- ....|+|.-|++.=
T Consensus 126 a~C~EC~R~vw-----------~hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrlG------------ 181 (314)
T PF06524_consen 126 AVCIECERGVW-----------DHGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRLG------------ 181 (314)
T ss_pred cEeeeeecccc-----------cCCCeEEEeecCCC-eeeccchhhhhhhhhhhhccccccccccccc------------
Confidence 45667776532 47888999999975 33444444555443 23467777776531
Q ss_pred cCCCCcccCCCCCccCCHHHHHHHHHHh----cCCCcccccccccccCChhHHHHhHhhh
Q psy6525 234 HSSERFKCDLCGKVTPYYQHYLRHMRIH----QGLEVHECNLCAKLFACKRSLQDHMQRH 289 (360)
Q Consensus 234 h~~~~~~C~~C~~~f~~~~~l~~H~~~h----~~~~~~~C~~C~~~f~~~~~l~~H~~~h 289 (360)
.|.|..|...|-. .|.+.. ...+++.|+.|+........|..-.|+|
T Consensus 182 ----q~sCLRCK~cfCd-----dHvrrKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 182 ----QYSCLRCKICFCD-----DHVRRKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred ----chhhhheeeeehh-----hhhhhcccccccCCCCCCCCCCCcccccccceeeeecc
Confidence 1444444444432 233221 2235677777776666655555555544
No 112
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=61.54 E-value=5.5 Score=34.79 Aligned_cols=24 Identities=25% Similarity=0.544 Sum_probs=15.4
Q ss_pred CcccCCCCCccCCHHHHHHHHHHh
Q psy6525 238 RFKCDLCGKVTPYYQHYLRHMRIH 261 (360)
Q Consensus 238 ~~~C~~C~~~f~~~~~l~~H~~~h 261 (360)
+|.|+.|...|-..-+.-.|-..|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 577777777776666666665544
No 113
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.46 E-value=2.9 Score=25.76 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=4.8
Q ss_pred cccccchhhh
Q psy6525 295 YQCAMCKKQY 304 (360)
Q Consensus 295 ~~C~~C~~~f 304 (360)
|.|..||+.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 4444444444
No 114
>KOG2807|consensus
Probab=61.32 E-value=15 Score=32.49 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=14.6
Q ss_pred CCcCccccccccCHHHHHHHHhhc
Q psy6525 211 FFICFHCNKNFTHRALLVRHMQKH 234 (360)
Q Consensus 211 ~~~C~~C~~~f~~~~~l~~H~~~h 234 (360)
.|.|+.|...|-.--..-.|-..|
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh
Confidence 466777777776665555554443
No 115
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=61.28 E-value=5.2 Score=25.65 Aligned_cols=10 Identities=40% Similarity=0.959 Sum_probs=5.4
Q ss_pred ceecccchhc
Q psy6525 99 NVLCYICDEI 108 (360)
Q Consensus 99 ~~~C~~C~~~ 108 (360)
.|.|+.|++.
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 4556666543
No 116
>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=60.17 E-value=2.4 Score=25.21 Aligned_cols=11 Identities=45% Similarity=1.437 Sum_probs=5.4
Q ss_pred eeccccccccc
Q psy6525 185 YKCKECGKCYT 195 (360)
Q Consensus 185 ~~C~~C~~~f~ 195 (360)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 44555554444
No 117
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=58.75 E-value=6.4 Score=25.25 Aligned_cols=6 Identities=33% Similarity=0.606 Sum_probs=2.3
Q ss_pred HHHHHH
Q psy6525 172 LQQHKK 177 (360)
Q Consensus 172 l~~H~~ 177 (360)
|..|..
T Consensus 26 l~~H~~ 31 (60)
T PF02176_consen 26 LDDHLE 31 (60)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 333333
No 118
>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=57.92 E-value=3.4 Score=22.57 Aligned_cols=9 Identities=33% Similarity=0.733 Sum_probs=4.5
Q ss_pred Ccccccccc
Q psy6525 320 QDYKCYICG 328 (360)
Q Consensus 320 ~~~~C~~C~ 328 (360)
..|.|+.|+
T Consensus 18 ~~~vCp~C~ 26 (30)
T PF08274_consen 18 ELLVCPECG 26 (30)
T ss_dssp SSEEETTTT
T ss_pred CEEeCCccc
Confidence 445555554
No 119
>PF15269 zf-C2H2_7: Zinc-finger
Probab=57.25 E-value=7.6 Score=23.12 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=14.4
Q ss_pred ccccccccccCChHHHHHHHH
Q psy6525 322 YKCYICGNRYATQKYLEEHIR 342 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~ 342 (360)
|+|-.|..+..-++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 567777777667777777765
No 120
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=57.13 E-value=4.1 Score=31.71 Aligned_cols=31 Identities=26% Similarity=0.648 Sum_probs=13.9
Q ss_pred cccccccccccCChHHHHHHHHHhCCCCccCCCcc
Q psy6525 321 DYKCYICGNRYATQKYLEEHIRLHQGHTYMCNAKF 355 (360)
Q Consensus 321 ~~~C~~C~~~f~~~~~l~~H~~~h~g~~~~C~~c~ 355 (360)
+|.|. |+..|-+. ++|-.+-.|+.|.|..|+
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~~YrC~~C~ 147 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGEVYRCGKCG 147 (156)
T ss_pred eEEee-cCCccchh---hhcccccccceEEeccCC
Confidence 45555 55443322 233334444455555554
No 121
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=56.94 E-value=3.4 Score=28.73 Aligned_cols=10 Identities=20% Similarity=1.055 Sum_probs=4.6
Q ss_pred cccccchhhh
Q psy6525 295 YQCAMCKKQY 304 (360)
Q Consensus 295 ~~C~~C~~~f 304 (360)
+.|..|+..|
T Consensus 54 W~C~kCg~~f 63 (89)
T COG1997 54 WKCRKCGAKF 63 (89)
T ss_pred EEcCCCCCee
Confidence 4444444444
No 122
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=56.51 E-value=2.5 Score=28.57 Aligned_cols=7 Identities=14% Similarity=0.634 Sum_probs=2.9
Q ss_pred cchhhhc
Q psy6525 299 MCKKQYA 305 (360)
Q Consensus 299 ~C~~~f~ 305 (360)
.||.+|.
T Consensus 34 eCg~tF~ 40 (72)
T PRK09678 34 NCSATFI 40 (72)
T ss_pred CCCCEEE
Confidence 3444443
No 123
>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=56.30 E-value=9 Score=28.88 Aligned_cols=11 Identities=9% Similarity=0.042 Sum_probs=4.6
Q ss_pred ccccccccccc
Q psy6525 266 VHECNLCAKLF 276 (360)
Q Consensus 266 ~~~C~~C~~~f 276 (360)
|..|+.||..|
T Consensus 26 p~vcP~cg~~~ 36 (129)
T TIGR02300 26 PAVSPYTGEQF 36 (129)
T ss_pred CccCCCcCCcc
Confidence 34444444443
No 124
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=55.43 E-value=4.4 Score=24.61 Aligned_cols=11 Identities=18% Similarity=0.486 Sum_probs=6.2
Q ss_pred eecccchhccC
Q psy6525 100 VLCYICDEILK 110 (360)
Q Consensus 100 ~~C~~C~~~f~ 110 (360)
|.|+.|+..|.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 55666665543
No 125
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.99 E-value=10 Score=39.04 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=5.0
Q ss_pred ccccccccc
Q psy6525 267 HECNLCAKL 275 (360)
Q Consensus 267 ~~C~~C~~~ 275 (360)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 456666654
No 126
>KOG1280|consensus
Probab=53.15 E-value=16 Score=32.67 Aligned_cols=38 Identities=18% Similarity=0.303 Sum_probs=28.1
Q ss_pred ceecccchhccCChHHHHHHHhhccCCCCCcccccccc
Q psy6525 99 NVLCYICDEILKDIDDLRYHGLLHATPLGTQFQCNVCF 136 (360)
Q Consensus 99 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~ 136 (360)
.|.|++|+..=-+...|..|....|.+......|++|+
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 68888888888888888888776666555556677775
No 127
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.33 E-value=12 Score=38.54 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=5.2
Q ss_pred eecccccccc
Q psy6525 185 YKCKECGKCY 194 (360)
Q Consensus 185 ~~C~~C~~~f 194 (360)
+.|+.||..-
T Consensus 664 y~CPKCG~El 673 (1121)
T PRK04023 664 DECEKCGREP 673 (1121)
T ss_pred CcCCCCCCCC
Confidence 4455555443
No 128
>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=50.47 E-value=5.3 Score=25.28 Aligned_cols=10 Identities=30% Similarity=0.567 Sum_probs=4.7
Q ss_pred cccccccccc
Q psy6525 321 DYKCYICGNR 330 (360)
Q Consensus 321 ~~~C~~C~~~ 330 (360)
...|+.||..
T Consensus 22 iV~Cp~CGae 31 (54)
T TIGR01206 22 LVICDECGAE 31 (54)
T ss_pred EEeCCCCCCE
Confidence 3445555443
No 129
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=50.20 E-value=8.9 Score=29.10 Aligned_cols=23 Identities=26% Similarity=0.545 Sum_probs=19.5
Q ss_pred ccccccccccCChHHHHHHHHHhCCC
Q psy6525 322 YKCYICGNRYATQKYLEEHIRLHQGH 347 (360)
Q Consensus 322 ~~C~~C~~~f~~~~~l~~H~~~h~g~ 347 (360)
..|-.+|+.|+ +|++|+.+|+|-
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCC
Confidence 46999999986 788999999885
No 130
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=46.80 E-value=15 Score=22.25 Aligned_cols=7 Identities=29% Similarity=0.890 Sum_probs=3.1
Q ss_pred ccccccc
Q psy6525 267 HECNLCA 273 (360)
Q Consensus 267 ~~C~~C~ 273 (360)
+.|+.||
T Consensus 19 ~~CP~Cg 25 (46)
T PF12760_consen 19 FVCPHCG 25 (46)
T ss_pred CCCCCCC
Confidence 3344444
No 131
>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=45.76 E-value=12 Score=23.31 Aligned_cols=11 Identities=36% Similarity=0.703 Sum_probs=7.1
Q ss_pred eecccchhccC
Q psy6525 100 VLCYICDEILK 110 (360)
Q Consensus 100 ~~C~~C~~~f~ 110 (360)
|+|.+|+..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56677766664
No 132
>KOG2807|consensus
Probab=45.58 E-value=33 Score=30.47 Aligned_cols=86 Identities=19% Similarity=0.361 Sum_probs=50.1
Q ss_pred eeecccccccccChhHHHHHHHhcCCCCCcCccccccccCHHHHHHHHhhcCC-CC------------cccCCCCCccCC
Q psy6525 184 KYKCKECGKCYTQNTNLKQHMLSHKGIFFICFHCNKNFTHRALLVRHMQKHSS-ER------------FKCDLCGKVTPY 250 (360)
Q Consensus 184 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-~~------------~~C~~C~~~f~~ 250 (360)
.|.|+.|+...-+ .|..|++|+.+......|.+-..---+ ++ -.|-.|+-.
T Consensus 276 Gy~CP~CkakvCs-------------LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~--- 339 (378)
T KOG2807|consen 276 GYFCPQCKAKVCS-------------LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGE--- 339 (378)
T ss_pred ceeCCcccCeeec-------------CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccc---
Confidence 4667776554322 367788888877776666543221100 00 115555211
Q ss_pred HHHHHHHHHHhcCCCcccccccccccCChhHHHHhHhhhcCCCccccccch
Q psy6525 251 YQHYLRHMRIHQGLEVHECNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCK 301 (360)
Q Consensus 251 ~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 301 (360)
-.+...|.|..|...|-.--+.-.|...|. |+.|.
T Consensus 340 ----------~~~~~~y~C~~Ck~~FCldCDv~iHesLh~------CpgCe 374 (378)
T KOG2807|consen 340 ----------LLSSGRYRCESCKNVFCLDCDVFIHESLHN------CPGCE 374 (378)
T ss_pred ----------cCCCCcEEchhccceeeccchHHHHhhhhc------CCCcC
Confidence 123345889999988887777777877663 66664
No 133
>KOG3408|consensus
Probab=44.27 E-value=16 Score=27.20 Aligned_cols=26 Identities=19% Similarity=0.583 Sum_probs=20.2
Q ss_pred CCCccccccchhhhcCHHHHHHHHhh
Q psy6525 291 EPNKYQCAMCKKQYASKKMLEKHIRR 316 (360)
Q Consensus 291 ~~~~~~C~~C~~~f~~~~~L~~H~~~ 316 (360)
|...|.|-.|.+-|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 33458888888888888888888774
No 134
>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=44.18 E-value=16 Score=30.73 Aligned_cols=27 Identities=22% Similarity=0.742 Sum_probs=14.4
Q ss_pred cccccccccccccCHHHHHHHHHHcCC
Q psy6525 155 VRFKCDLCSRTFNSQSYLQQHKKHDHE 181 (360)
Q Consensus 155 ~~~~C~~C~~~f~~~~~l~~H~~~~h~ 181 (360)
..|.|.+|+|.|.-..-..+|+...|.
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCH
Confidence 346666666666666666666665554
No 135
>KOG2593|consensus
Probab=42.83 E-value=23 Score=32.80 Aligned_cols=35 Identities=17% Similarity=0.412 Sum_probs=18.9
Q ss_pred CccccccccccccChHHHHHHHHHcCCcccccccccc
Q psy6525 128 TQFQCNVCFLMLNNRCYTRFHLLKHNWVRFKCDLCSR 164 (360)
Q Consensus 128 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~ 164 (360)
..|.|+.|++.|+....++. ..-....|.|..|+-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L--~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQL--LDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHh--hcccCceEEEecCCC
Confidence 34677777776665544431 111234566777654
No 136
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=42.80 E-value=21 Score=31.93 Aligned_cols=91 Identities=14% Similarity=0.185 Sum_probs=0.0
Q ss_pred CCceecccchhccCChHHHHHHHhhccCCCCCccccc-------------cccccccChHHHHHHHHHcCCcc-------
Q psy6525 97 TKNVLCYICDEILKDIDDLRYHGLLHATPLGTQFQCN-------------VCFLMLNNRCYTRFHLLKHNWVR------- 156 (360)
Q Consensus 97 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~-------------~C~~~f~~~~~l~~H~~~h~~~~------- 156 (360)
...+-|..|+..|.+..-+..|...........-.=. .|+..++...++..-...-...-
T Consensus 236 ~~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~~v~~Ey~l~r~~kyl~d~~s~trs~V~r~la~ta~ER~aei~~ 315 (470)
T COG5188 236 FPKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEEFVYSEYVLHRYLKYLGDPVSETRSLVLRSLAITAKERKAEISL 315 (470)
T ss_pred ccceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHhCChhHHHHHHHHHHHHHHHHHHHHHhHH
Q ss_pred -----------------------------------------------------------ccccccc-ccccCHHHHHHHH
Q psy6525 157 -----------------------------------------------------------FKCDLCS-RTFNSQSYLQQHK 176 (360)
Q Consensus 157 -----------------------------------------------------------~~C~~C~-~~f~~~~~l~~H~ 176 (360)
|.|.+|+ +++.-+..+.+|.
T Consensus 316 l~r~~~~~at~S~e~EGaeq~d~eQ~DE~~~~k~fdmPLG~DG~PmP~WL~klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 316 LSRRKKQPATKSSEKEGAEQVDGEQRDEHVSGKSFDMPLGPDGLPMPRWLCKLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred HHHHhhccCCCchhhcccccccccccchhhccCcccCCCCCCCCCCchHHHHhcCCCcceeeeecccccccchHHHHhhh
Q ss_pred HHcCCCceeec
Q psy6525 177 KHDHEGVKYKC 187 (360)
Q Consensus 177 ~~~h~~~~~~C 187 (360)
..........|
T Consensus 396 ~E~rHiygl~c 406 (470)
T COG5188 396 EEDRHIYGLEC 406 (470)
T ss_pred hhhhhhhheee
No 137
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.71 E-value=8.7 Score=38.60 Aligned_cols=8 Identities=38% Similarity=1.007 Sum_probs=4.4
Q ss_pred ccCCCCCc
Q psy6525 240 KCDLCGKV 247 (360)
Q Consensus 240 ~C~~C~~~ 247 (360)
.|..||..
T Consensus 437 ~C~~Cg~v 444 (730)
T COG1198 437 LCRDCGYI 444 (730)
T ss_pred ecccCCCc
Confidence 46666554
No 138
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=42.06 E-value=15 Score=27.91 Aligned_cols=56 Identities=23% Similarity=0.459 Sum_probs=30.7
Q ss_pred CCCcccccccccccCChhHHHHhHhhhcCCCcccc---ccchhhhcCHHHHHHHHhhhcCCcccccccccccCChH
Q psy6525 263 GLEVHECNLCAKLFACKRSLQDHMQRHEEPNKYQC---AMCKKQYASKKMLEKHIRRHEGQDYKCYICGNRYATQK 335 (360)
Q Consensus 263 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C---~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~ 335 (360)
..+.|+|.+|..+.....-| +|-.| .+|+.- -..|+.|-..| -+|+.|.-+|++..
T Consensus 77 d~~lYeCnIC~etS~ee~FL----------KPneCCgY~iCn~C---ya~LWK~~~~y----pvCPvCkTSFKss~ 135 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFL----------KPNECCGYSICNAC---YANLWKFCNLY----PVCPVCKTSFKSSS 135 (140)
T ss_pred CCCceeccCcccccchhhcC----------CcccccchHHHHHH---HHHHHHHcccC----CCCCcccccccccc
Confidence 44667888887776655443 23333 123222 24555554433 25888887777654
No 139
>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=42.05 E-value=19 Score=27.68 Aligned_cols=25 Identities=20% Similarity=0.477 Sum_probs=16.1
Q ss_pred CCceecccchhccCChHHHHHHHhhccC
Q psy6525 97 TKNVLCYICDEILKDIDDLRYHGLLHAT 124 (360)
Q Consensus 97 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 124 (360)
.+.+.|-+||+.|+.. ++|...|++
T Consensus 70 ~d~i~clecGk~~k~L---krHL~~~~g 94 (132)
T PF05443_consen 70 PDYIICLECGKKFKTL---KRHLRTHHG 94 (132)
T ss_dssp SS-EE-TBT--EESBH---HHHHHHTT-
T ss_pred cCeeEEccCCcccchH---HHHHHHccC
Confidence 3457899999998765 889988877
No 140
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=42.03 E-value=14 Score=28.07 Aligned_cols=11 Identities=36% Similarity=0.896 Sum_probs=5.0
Q ss_pred ccCCCCCccCC
Q psy6525 240 KCDLCGKVTPY 250 (360)
Q Consensus 240 ~C~~C~~~f~~ 250 (360)
+|..||+.|.+
T Consensus 3 ~Ct~Cg~~f~d 13 (131)
T PF09845_consen 3 QCTKCGRVFED 13 (131)
T ss_pred ccCcCCCCcCC
Confidence 44444444443
No 141
>KOG2593|consensus
Probab=41.99 E-value=24 Score=32.62 Aligned_cols=11 Identities=27% Similarity=0.649 Sum_probs=5.0
Q ss_pred cccCCCCCccC
Q psy6525 239 FKCDLCGKVTP 249 (360)
Q Consensus 239 ~~C~~C~~~f~ 249 (360)
|.|+.|.+.|.
T Consensus 129 Y~Cp~C~kkyt 139 (436)
T KOG2593|consen 129 YVCPNCQKKYT 139 (436)
T ss_pred ccCCccccchh
Confidence 44444444443
No 142
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=41.83 E-value=9.2 Score=33.45 Aligned_cols=24 Identities=25% Similarity=0.589 Sum_probs=16.7
Q ss_pred cccccccccccCChHHHHHHHHHh
Q psy6525 321 DYKCYICGNRYATQKYLEEHIRLH 344 (360)
Q Consensus 321 ~~~C~~C~~~f~~~~~l~~H~~~h 344 (360)
.|+|+.|...|-...+.-.|...|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 577777777777666666665554
No 143
>KOG4167|consensus
Probab=41.68 E-value=9.6 Score=37.50 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=23.7
Q ss_pred ccccccchhhhcCHHHHHHHHhhhcC
Q psy6525 294 KYQCAMCKKQYASKKMLEKHIRRHEG 319 (360)
Q Consensus 294 ~~~C~~C~~~f~~~~~L~~H~~~h~~ 319 (360)
-|.|..|+|.|-....+..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48999999999999999999999864
No 144
>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=39.24 E-value=19 Score=34.73 Aligned_cols=9 Identities=22% Similarity=0.733 Sum_probs=4.9
Q ss_pred ccccccccc
Q psy6525 266 VHECNLCAK 274 (360)
Q Consensus 266 ~~~C~~C~~ 274 (360)
|..|+.|+.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 445666654
No 145
>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=39.04 E-value=13 Score=31.15 Aligned_cols=25 Identities=20% Similarity=0.719 Sum_probs=11.7
Q ss_pred cccccccccccCChHHHHHHHHHhC
Q psy6525 321 DYKCYICGNRYATQKYLEEHIRLHQ 345 (360)
Q Consensus 321 ~~~C~~C~~~f~~~~~l~~H~~~h~ 345 (360)
.|.|+.|+|.|+-..-...|+...|
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred EECCCCCCcccCChHHHHHHHhhcC
Confidence 3555555555555555555555433
No 146
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.57 E-value=7.3 Score=39.10 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=6.6
Q ss_pred cccccccccc
Q psy6525 130 FQCNVCFLML 139 (360)
Q Consensus 130 ~~C~~C~~~f 139 (360)
..|..||..+
T Consensus 436 l~C~~Cg~v~ 445 (730)
T COG1198 436 LLCRDCGYIA 445 (730)
T ss_pred eecccCCCcc
Confidence 4588887554
No 147
>KOG3408|consensus
Probab=37.93 E-value=33 Score=25.60 Aligned_cols=31 Identities=23% Similarity=0.424 Sum_probs=25.4
Q ss_pred CCCccCCCceecccchhccCChHHHHHHHhh
Q psy6525 91 DPEIMDTKNVLCYICDEILKDIDDLRYHGLL 121 (360)
Q Consensus 91 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 121 (360)
++.+-+...|.|-.|...|.+...|..|.++
T Consensus 49 D~dlPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 49 DPDLPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 4555566779999999999999999999764
No 148
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.86 E-value=25 Score=37.40 Aligned_cols=11 Identities=27% Similarity=0.727 Sum_probs=6.6
Q ss_pred ccccccchhhh
Q psy6525 294 KYQCAMCKKQY 304 (360)
Q Consensus 294 ~~~C~~C~~~f 304 (360)
+|.|+.||...
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 45666666643
No 149
>PF12907 zf-met2: Zinc-binding
Probab=37.07 E-value=25 Score=20.65 Aligned_cols=26 Identities=27% Similarity=0.742 Sum_probs=12.6
Q ss_pred cccccccccc---cCHHHHHHHHHHcCCC
Q psy6525 157 FKCDLCSRTF---NSQSYLQQHKKHDHEG 182 (360)
Q Consensus 157 ~~C~~C~~~f---~~~~~l~~H~~~~h~~ 182 (360)
+.|.+|..+| .+...|..|....|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 3455555333 3334455565554443
No 150
>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=36.91 E-value=13 Score=19.11 Aligned_cols=8 Identities=25% Similarity=1.012 Sum_probs=4.0
Q ss_pred ccccccch
Q psy6525 294 KYQCAMCK 301 (360)
Q Consensus 294 ~~~C~~C~ 301 (360)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35555554
No 151
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=36.15 E-value=7.7 Score=27.41 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=4.3
Q ss_pred cccccchhhh
Q psy6525 295 YQCAMCKKQY 304 (360)
Q Consensus 295 ~~C~~C~~~f 304 (360)
+.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PTZ00255 55 WRCKGCKKTV 64 (90)
T ss_pred EEcCCCCCEE
Confidence 4444444443
No 152
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=36.08 E-value=21 Score=22.50 Aligned_cols=11 Identities=27% Similarity=0.766 Sum_probs=6.9
Q ss_pred eecccchhccC
Q psy6525 100 VLCYICDEILK 110 (360)
Q Consensus 100 ~~C~~C~~~f~ 110 (360)
-.|+.|++.|.
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 45666766664
No 153
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=34.72 E-value=6.9 Score=27.66 Aligned_cols=10 Identities=30% Similarity=1.245 Sum_probs=4.4
Q ss_pred cccccccccc
Q psy6525 322 YKCYICGNRY 331 (360)
Q Consensus 322 ~~C~~C~~~f 331 (360)
++|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 4444444444
No 154
>KOG4124|consensus
Probab=34.10 E-value=6.2 Score=35.11 Aligned_cols=22 Identities=32% Similarity=0.754 Sum_probs=15.0
Q ss_pred CcccccccccccCChHHHHHHH
Q psy6525 320 QDYKCYICGNRYATQKYLEEHI 341 (360)
Q Consensus 320 ~~~~C~~C~~~f~~~~~l~~H~ 341 (360)
++|+|++|.+.++....|..|+
T Consensus 397 k~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 397 KPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred CcccChhhhhhhccCCCCCcee
Confidence 4677888887777666565553
No 155
>KOG1280|consensus
Probab=33.59 E-value=44 Score=29.98 Aligned_cols=23 Identities=17% Similarity=0.392 Sum_probs=11.7
Q ss_pred cccccccccccCChhHHHHhHhh
Q psy6525 266 VHECNLCAKLFACKRSLQDHMQR 288 (360)
Q Consensus 266 ~~~C~~C~~~f~~~~~l~~H~~~ 288 (360)
.|.|++|+.+-.+...|..|+..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s 101 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLS 101 (381)
T ss_pred cccCCcccccccchhHHHHHhhh
Confidence 34555555555555555555443
No 156
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=32.22 E-value=29 Score=25.10 Aligned_cols=33 Identities=24% Similarity=0.356 Sum_probs=27.2
Q ss_pred CCCCCCccCCCceecccchhccCChHHHHHHHh
Q psy6525 88 SPSDPEIMDTKNVLCYICDEILKDIDDLRYHGL 120 (360)
Q Consensus 88 ~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 120 (360)
.+-+|...+-..+.|-.|...|.+...|..|.+
T Consensus 44 lp~Dp~lPGlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 44 LPYDPELPGLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCCCCCCCCCceeeeehhHHHHHHHHHHHHHhc
Confidence 345666667778999999999999999999965
No 157
>PRK14873 primosome assembly protein PriA; Provisional
Probab=32.13 E-value=28 Score=34.93 Aligned_cols=10 Identities=20% Similarity=0.919 Sum_probs=5.7
Q ss_pred ccccccchhh
Q psy6525 294 KYQCAMCKKQ 303 (360)
Q Consensus 294 ~~~C~~C~~~ 303 (360)
|..|+.||-.
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 4566666543
No 158
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.51 E-value=37 Score=36.14 Aligned_cols=11 Identities=36% Similarity=0.957 Sum_probs=5.9
Q ss_pred eeecccccccc
Q psy6525 184 KYKCKECGKCY 194 (360)
Q Consensus 184 ~~~C~~C~~~f 194 (360)
+|.|+.||...
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 35566665543
No 159
>PLN02294 cytochrome c oxidase subunit Vb
Probab=31.43 E-value=15 Score=29.31 Aligned_cols=18 Identities=17% Similarity=0.464 Sum_probs=11.4
Q ss_pred HHHhCCCCccCCCccccc
Q psy6525 341 IRLHQGHTYMCNAKFSFN 358 (360)
Q Consensus 341 ~~~h~g~~~~C~~c~~~f 358 (360)
+..+.|+|++|+.||..|
T Consensus 134 f~L~kGkp~RCpeCG~~f 151 (174)
T PLN02294 134 FWLEKGKSFECPVCTQYF 151 (174)
T ss_pred EEecCCCceeCCCCCCEE
Confidence 445666666677776665
No 160
>KOG4377|consensus
Probab=31.06 E-value=13 Score=34.05 Aligned_cols=24 Identities=29% Similarity=0.685 Sum_probs=17.0
Q ss_pred ccccc--chhhhcCHHHHHHHHhhhc
Q psy6525 295 YQCAM--CKKQYASKKMLEKHIRRHE 318 (360)
Q Consensus 295 ~~C~~--C~~~f~~~~~L~~H~~~h~ 318 (360)
|-|.. |+.++.+.+.+..|.|.|.
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkhe 427 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHE 427 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhh
Confidence 44544 7778888888888877764
No 161
>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=30.36 E-value=6.9 Score=22.41 Aligned_cols=8 Identities=38% Similarity=1.277 Sum_probs=3.4
Q ss_pred cCCCCCcc
Q psy6525 241 CDLCGKVT 248 (360)
Q Consensus 241 C~~C~~~f 248 (360)
|+.||.+|
T Consensus 4 C~~Cg~~Y 11 (36)
T PF05191_consen 4 CPKCGRIY 11 (36)
T ss_dssp ETTTTEEE
T ss_pred cCCCCCcc
Confidence 44444443
No 162
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=30.06 E-value=5.4 Score=28.15 Aligned_cols=10 Identities=30% Similarity=1.182 Sum_probs=4.2
Q ss_pred cccccchhhh
Q psy6525 295 YQCAMCKKQY 304 (360)
Q Consensus 295 ~~C~~C~~~f 304 (360)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (90)
T PF01780_consen 54 WKCKKCGKKF 63 (90)
T ss_dssp EEETTTTEEE
T ss_pred eecCCCCCEE
Confidence 3444444433
No 163
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=29.09 E-value=38 Score=19.62 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=3.0
Q ss_pred cccccccccc
Q psy6525 267 HECNLCAKLF 276 (360)
Q Consensus 267 ~~C~~C~~~f 276 (360)
|-|..|...|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 5566666655
No 164
>KOG4124|consensus
Probab=28.84 E-value=7.6 Score=34.55 Aligned_cols=26 Identities=35% Similarity=0.807 Sum_probs=20.6
Q ss_pred ccccccc--ccccccCHHHHHHHHHHcC
Q psy6525 155 VRFKCDL--CSRTFNSQSYLQQHKKHDH 180 (360)
Q Consensus 155 ~~~~C~~--C~~~f~~~~~l~~H~~~~h 180 (360)
++|+|.+ |++.+....+|..|....|
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h 375 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGH 375 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCc
Confidence 4588866 9999999999988876554
No 165
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=28.82 E-value=15 Score=26.43 Aligned_cols=8 Identities=13% Similarity=-0.043 Sum_probs=2.9
Q ss_pred CccCCCcc
Q psy6525 348 TYMCNAKF 355 (360)
Q Consensus 348 ~~~C~~c~ 355 (360)
|++|..||
T Consensus 79 ~~rC~eCG 86 (97)
T cd00924 79 PKRCPECG 86 (97)
T ss_pred ceeCCCCC
Confidence 33333333
No 166
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=28.74 E-value=46 Score=19.58 Aligned_cols=9 Identities=33% Similarity=1.069 Sum_probs=4.0
Q ss_pred ccccccccc
Q psy6525 268 ECNLCAKLF 276 (360)
Q Consensus 268 ~C~~C~~~f 276 (360)
.|+.||..|
T Consensus 15 ~C~~CgM~Y 23 (41)
T PF13878_consen 15 TCPTCGMLY 23 (41)
T ss_pred CCCCCCCEE
Confidence 444444443
No 167
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.58 E-value=20 Score=27.73 Aligned_cols=10 Identities=40% Similarity=0.896 Sum_probs=4.6
Q ss_pred cccCCCCCcc
Q psy6525 239 FKCDLCGKVT 248 (360)
Q Consensus 239 ~~C~~C~~~f 248 (360)
+.|..||..|
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 4444444444
No 168
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=28.57 E-value=24 Score=20.54 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=9.9
Q ss_pred cccccccccccCC
Q psy6525 321 DYKCYICGNRYAT 333 (360)
Q Consensus 321 ~~~C~~C~~~f~~ 333 (360)
||+|..|+..|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7888888887743
No 169
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=28.27 E-value=37 Score=24.48 Aligned_cols=11 Identities=27% Similarity=0.908 Sum_probs=4.5
Q ss_pred cccccccccCC
Q psy6525 268 ECNLCAKLFAC 278 (360)
Q Consensus 268 ~C~~C~~~f~~ 278 (360)
+|..||..|..
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 34444444433
No 170
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=27.96 E-value=9.8 Score=26.89 Aligned_cols=10 Identities=30% Similarity=1.281 Sum_probs=4.4
Q ss_pred cccccccccc
Q psy6525 322 YKCYICGNRY 331 (360)
Q Consensus 322 ~~C~~C~~~f 331 (360)
+.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PRK03976 55 WECRKCGAKF 64 (90)
T ss_pred EEcCCCCCEE
Confidence 4444444444
No 171
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.77 E-value=30 Score=25.22 Aligned_cols=12 Identities=0% Similarity=0.116 Sum_probs=5.8
Q ss_pred cccccccccccc
Q psy6525 155 VRFKCDLCSRTF 166 (360)
Q Consensus 155 ~~~~C~~C~~~f 166 (360)
.|..|+.||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 344455555544
No 172
>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=27.59 E-value=40 Score=22.23 Aligned_cols=8 Identities=25% Similarity=0.716 Sum_probs=1.7
Q ss_pred cccccccc
Q psy6525 132 CNVCFLML 139 (360)
Q Consensus 132 C~~C~~~f 139 (360)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 44444444
No 173
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=26.30 E-value=11 Score=25.38 Aligned_cols=12 Identities=17% Similarity=0.692 Sum_probs=4.5
Q ss_pred ccccccchhhhc
Q psy6525 294 KYQCAMCKKQYA 305 (360)
Q Consensus 294 ~~~C~~C~~~f~ 305 (360)
...|..|+...+
T Consensus 41 ~v~Cg~C~~~~~ 52 (71)
T PF05495_consen 41 RVICGKCRTEQP 52 (71)
T ss_dssp EEEETTT--EEE
T ss_pred CeECCCCCCccC
Confidence 344555544443
No 174
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.22 E-value=34 Score=25.49 Aligned_cols=13 Identities=23% Similarity=0.291 Sum_probs=7.2
Q ss_pred ccccccccccccC
Q psy6525 129 QFQCNVCFLMLNN 141 (360)
Q Consensus 129 ~~~C~~C~~~f~~ 141 (360)
.+.|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PRK12380 70 QAWCWDCSQVVEI 82 (113)
T ss_pred EEEcccCCCEEec
Confidence 4556666655543
No 175
>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=25.87 E-value=34 Score=25.54 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=5.9
Q ss_pred ccccccccccc
Q psy6525 157 FKCDLCSRTFN 167 (360)
Q Consensus 157 ~~C~~C~~~f~ 167 (360)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 45555555544
No 176
>KOG2636|consensus
Probab=25.82 E-value=44 Score=31.09 Aligned_cols=29 Identities=14% Similarity=0.497 Sum_probs=23.9
Q ss_pred HHhcCCCcccccccc-cccCChhHHHHhHh
Q psy6525 259 RIHQGLEVHECNLCA-KLFACKRSLQDHMQ 287 (360)
Q Consensus 259 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 287 (360)
+.|.-...|.|.+|| +++..+.++.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 445556779999999 89999999999975
No 177
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=25.73 E-value=41 Score=21.15 Aligned_cols=7 Identities=29% Similarity=1.061 Sum_probs=2.6
Q ss_pred ccccccc
Q psy6525 268 ECNLCAK 274 (360)
Q Consensus 268 ~C~~C~~ 274 (360)
+|+.||.
T Consensus 30 ~C~~Cgh 36 (55)
T PF14311_consen 30 KCPKCGH 36 (55)
T ss_pred ECCCCCC
Confidence 3333333
No 178
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.39 E-value=31 Score=21.38 Aligned_cols=10 Identities=40% Similarity=1.145 Sum_probs=4.4
Q ss_pred CcccCCCCCc
Q psy6525 238 RFKCDLCGKV 247 (360)
Q Consensus 238 ~~~C~~C~~~ 247 (360)
.+.|..||.+
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 3444444443
No 179
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=25.15 E-value=31 Score=24.29 Aligned_cols=26 Identities=19% Similarity=0.407 Sum_probs=16.2
Q ss_pred ceecccchhccCChHHHHHHHhhccCCCCCcccccccc
Q psy6525 99 NVLCYICDEILKDIDDLRYHGLLHATPLGTQFQCNVCF 136 (360)
Q Consensus 99 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~C~~C~ 136 (360)
|-.|..||+.|.+. ....+-.|+.|.
T Consensus 58 Pa~CkkCGfef~~~------------~ik~pSRCP~CK 83 (97)
T COG3357 58 PARCKKCGFEFRDD------------KIKKPSRCPKCK 83 (97)
T ss_pred ChhhcccCcccccc------------ccCCcccCCcch
Confidence 45688888777652 114566777774
No 180
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=25.09 E-value=37 Score=28.13 Aligned_cols=37 Identities=19% Similarity=0.234 Sum_probs=15.3
Q ss_pred HHHHHHhhhcCCcccccc----cccccCChHHHHHHHHHhCC
Q psy6525 309 MLEKHIRRHEGQDYKCYI----CGNRYATQKYLEEHIRLHQG 346 (360)
Q Consensus 309 ~L~~H~~~h~~~~~~C~~----C~~~f~~~~~l~~H~~~h~g 346 (360)
.+..|.....-+|+.|+. |+..= ....|..|....|+
T Consensus 32 ~~~~HE~~C~~~p~~CP~~~~~C~~~G-~~~~l~~Hl~~~H~ 72 (198)
T PF03145_consen 32 EKREHEEECPFRPCSCPFPGSGCDWQG-SYKELLDHLRDKHS 72 (198)
T ss_dssp GHHHHHHT-TTSEEE-SSSSTT---EE-ECCCHHHHHHHHTT
T ss_pred ChhhHhccCCCcCCcCCCCCCCccccC-CHHHHHHHHHHHCC
Confidence 444555555445555555 43322 22345555554443
No 181
>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=24.74 E-value=11 Score=21.50 Aligned_cols=10 Identities=20% Similarity=0.444 Sum_probs=3.5
Q ss_pred cccccccccc
Q psy6525 130 FQCNVCFLML 139 (360)
Q Consensus 130 ~~C~~C~~~f 139 (360)
..|+.||-.+
T Consensus 22 isC~~CGPr~ 31 (35)
T PF07503_consen 22 ISCTNCGPRY 31 (35)
T ss_dssp --BTTCC-SC
T ss_pred ccCCCCCCCE
Confidence 4455555443
No 182
>KOG2636|consensus
Probab=24.29 E-value=47 Score=30.90 Aligned_cols=22 Identities=14% Similarity=0.712 Sum_probs=12.1
Q ss_pred cccccccc-ccccCHHHHHHHHH
Q psy6525 156 RFKCDLCS-RTFNSQSYLQQHKK 177 (360)
Q Consensus 156 ~~~C~~C~-~~f~~~~~l~~H~~ 177 (360)
-|.|.+|| +++.-+..+.+|..
T Consensus 401 ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 401 EYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred ccceeeccCccccCcHHHHHHhH
Confidence 35555555 55555555555543
No 183
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=24.19 E-value=49 Score=24.00 Aligned_cols=23 Identities=22% Similarity=0.553 Sum_probs=19.0
Q ss_pred CccccccchhhhcCHHHHHHHHh
Q psy6525 293 NKYQCAMCKKQYASKKMLEKHIR 315 (360)
Q Consensus 293 ~~~~C~~C~~~f~~~~~L~~H~~ 315 (360)
..+.|-.|.+-|.+...|..|.+
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhc
Confidence 44778889999999888888876
No 184
>KOG0402|consensus
Probab=24.00 E-value=49 Score=22.86 Aligned_cols=10 Identities=50% Similarity=1.341 Sum_probs=5.9
Q ss_pred ccccccchhh
Q psy6525 294 KYQCAMCKKQ 303 (360)
Q Consensus 294 ~~~C~~C~~~ 303 (360)
.|.|+.||+.
T Consensus 36 ky~CsfCGK~ 45 (92)
T KOG0402|consen 36 KYTCSFCGKK 45 (92)
T ss_pred hhhhhhcchh
Confidence 3666666654
No 185
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=23.81 E-value=16 Score=28.83 Aligned_cols=10 Identities=40% Similarity=1.408 Sum_probs=5.2
Q ss_pred cccccchhhh
Q psy6525 295 YQCAMCKKQY 304 (360)
Q Consensus 295 ~~C~~C~~~f 304 (360)
|.|..|+..+
T Consensus 124 ~~C~~C~~~~ 133 (157)
T PF10263_consen 124 YRCPSCGREY 133 (157)
T ss_pred EEcCCCCCEe
Confidence 4555555444
No 186
>PRK04351 hypothetical protein; Provisional
Probab=23.68 E-value=28 Score=27.44 Aligned_cols=12 Identities=25% Similarity=0.852 Sum_probs=6.2
Q ss_pred Cccccccccccc
Q psy6525 320 QDYKCYICGNRY 331 (360)
Q Consensus 320 ~~~~C~~C~~~f 331 (360)
..|.|..|+-.+
T Consensus 131 ~~yrCg~C~g~L 142 (149)
T PRK04351 131 KRYRCGKCRGKL 142 (149)
T ss_pred CcEEeCCCCcEe
Confidence 445555555443
No 187
>KOG0717|consensus
Probab=23.66 E-value=39 Score=31.64 Aligned_cols=22 Identities=32% Similarity=0.711 Sum_probs=0.0
Q ss_pred cccccchhhhcCHHHHHHHHhh
Q psy6525 295 YQCAMCKKQYASKKMLEKHIRR 316 (360)
Q Consensus 295 ~~C~~C~~~f~~~~~L~~H~~~ 316 (360)
+.|.+|+++|.+..+|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
No 188
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=23.38 E-value=49 Score=20.41 Aligned_cols=10 Identities=40% Similarity=1.112 Sum_probs=5.1
Q ss_pred CcccCCCCCc
Q psy6525 238 RFKCDLCGKV 247 (360)
Q Consensus 238 ~~~C~~C~~~ 247 (360)
++.|.-||++
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 4555555543
No 189
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.32 E-value=39 Score=22.34 Aligned_cols=10 Identities=30% Similarity=0.776 Sum_probs=4.6
Q ss_pred cccccccccc
Q psy6525 321 DYKCYICGNR 330 (360)
Q Consensus 321 ~~~C~~C~~~ 330 (360)
.|.|+.||..
T Consensus 46 ~~~C~~Cg~~ 55 (69)
T PF07282_consen 46 VFTCPNCGFE 55 (69)
T ss_pred eEEcCCCCCE
Confidence 3444444444
No 190
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=23.07 E-value=61 Score=20.06 Aligned_cols=7 Identities=29% Similarity=0.757 Sum_probs=2.6
Q ss_pred ecccchh
Q psy6525 101 LCYICDE 107 (360)
Q Consensus 101 ~C~~C~~ 107 (360)
.|..|+.
T Consensus 6 ~C~dCg~ 12 (49)
T PF13451_consen 6 TCKDCGA 12 (49)
T ss_pred EcccCCC
Confidence 3333333
No 191
>KOG3507|consensus
Probab=22.60 E-value=32 Score=21.95 Aligned_cols=11 Identities=36% Similarity=0.860 Sum_probs=7.1
Q ss_pred Ccccccccccc
Q psy6525 320 QDYKCYICGNR 330 (360)
Q Consensus 320 ~~~~C~~C~~~ 330 (360)
..++|..||..
T Consensus 36 D~irCReCG~R 46 (62)
T KOG3507|consen 36 DVIRCRECGYR 46 (62)
T ss_pred CcEehhhcchH
Confidence 46667777654
No 192
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=22.19 E-value=32 Score=20.21 Aligned_cols=11 Identities=45% Similarity=1.068 Sum_probs=6.0
Q ss_pred ccccccccccc
Q psy6525 321 DYKCYICGNRY 331 (360)
Q Consensus 321 ~~~C~~C~~~f 331 (360)
+-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 34566665554
No 193
>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=22.14 E-value=32 Score=25.61 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=5.7
Q ss_pred cccccccccccC
Q psy6525 157 FKCDLCSRTFNS 168 (360)
Q Consensus 157 ~~C~~C~~~f~~ 168 (360)
+.|..|+..|.-
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 455555555543
No 194
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=21.91 E-value=21 Score=27.90 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=5.6
Q ss_pred cccccccccCC
Q psy6525 268 ECNLCAKLFAC 278 (360)
Q Consensus 268 ~C~~C~~~f~~ 278 (360)
.|+.|+..|++
T Consensus 30 eC~~C~~RFTT 40 (156)
T COG1327 30 ECLECGERFTT 40 (156)
T ss_pred cccccccccch
Confidence 45555555544
No 195
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.60 E-value=16 Score=36.12 Aligned_cols=28 Identities=21% Similarity=0.516 Sum_probs=14.9
Q ss_pred ccccccccCChhHHHHhHhhhcCCCccccccchh
Q psy6525 269 CNLCAKLFACKRSLQDHMQRHEEPNKYQCAMCKK 302 (360)
Q Consensus 269 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 302 (360)
|+.|.+.|.+..+.+-|. .|..|+.||-
T Consensus 154 C~~C~~EY~dP~nRRfHA------Qp~aCp~CGP 181 (750)
T COG0068 154 CPFCDKEYKDPLNRRFHA------QPIACPKCGP 181 (750)
T ss_pred CHHHHHHhcCcccccccc------ccccCcccCC
Confidence 666666655555544332 3455666654
No 196
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=21.47 E-value=29 Score=20.63 Aligned_cols=12 Identities=33% Similarity=1.085 Sum_probs=7.0
Q ss_pred cccccccccccC
Q psy6525 321 DYKCYICGNRYA 332 (360)
Q Consensus 321 ~~~C~~C~~~f~ 332 (360)
|+.|..|+..|=
T Consensus 13 ~~~C~~C~~~FC 24 (43)
T PF01428_consen 13 PFKCKHCGKSFC 24 (43)
T ss_dssp HEE-TTTS-EE-
T ss_pred CeECCCCCcccC
Confidence 677888887774
No 197
>KOG2907|consensus
Probab=21.45 E-value=50 Score=24.35 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=6.6
Q ss_pred eeeccccccccc
Q psy6525 184 KYKCKECGKCYT 195 (360)
Q Consensus 184 ~~~C~~C~~~f~ 195 (360)
-|.|+.|++.|.
T Consensus 102 FYTC~kC~~k~~ 113 (116)
T KOG2907|consen 102 FYTCPKCKYKFT 113 (116)
T ss_pred EEEcCccceeee
Confidence 355555555554
No 198
>KOG1842|consensus
Probab=21.26 E-value=55 Score=30.50 Aligned_cols=20 Identities=40% Similarity=0.678 Sum_probs=10.0
Q ss_pred cccccccccccChHHHHHHH
Q psy6525 130 FQCNVCFLMLNNRCYTRFHL 149 (360)
Q Consensus 130 ~~C~~C~~~f~~~~~l~~H~ 149 (360)
|.||+|...|.+...|..|+
T Consensus 16 flCPiC~~dl~~~~~L~~H~ 35 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHL 35 (505)
T ss_pred ccCchHhhhhhhHHHHHHHH
Confidence 44555555555555555444
No 199
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.98 E-value=1.2e+02 Score=24.68 Aligned_cols=14 Identities=29% Similarity=0.688 Sum_probs=6.5
Q ss_pred Cceeeccccccccc
Q psy6525 182 GVKYKCKECGKCYT 195 (360)
Q Consensus 182 ~~~~~C~~C~~~f~ 195 (360)
..-|.|+.|...|+
T Consensus 111 ~~~y~C~~~~~r~s 124 (176)
T COG1675 111 NNYYVCPNCHVKYS 124 (176)
T ss_pred CCceeCCCCCCccc
Confidence 33455555544443
No 200
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=20.55 E-value=13 Score=21.82 Aligned_cols=10 Identities=40% Similarity=1.315 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy6525 185 YKCKECGKCY 194 (360)
Q Consensus 185 ~~C~~C~~~f 194 (360)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 4455554443
No 201
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=20.11 E-value=19 Score=25.88 Aligned_cols=7 Identities=29% Similarity=0.961 Sum_probs=2.8
Q ss_pred ccccccc
Q psy6525 267 HECNLCA 273 (360)
Q Consensus 267 ~~C~~C~ 273 (360)
|.|+.|+
T Consensus 23 FtCp~Cg 29 (104)
T COG4888 23 FTCPRCG 29 (104)
T ss_pred EecCccC
Confidence 3344443
No 202
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.03 E-value=54 Score=24.57 Aligned_cols=13 Identities=15% Similarity=0.644 Sum_probs=7.4
Q ss_pred ccccccccccccC
Q psy6525 129 QFQCNVCFLMLNN 141 (360)
Q Consensus 129 ~~~C~~C~~~f~~ 141 (360)
.+.|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 4566666655543
Done!