Query psy3485
Match_columns 304
No_of_seqs 162 out of 2734
Neff 9.7
Searched_HMMs 46136
Date Fri Aug 16 17:54:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3485.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3485hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 3.8E-33 8.3E-38 227.7 6.4 131 150-298 129-264 (279)
2 KOG2462|consensus 99.9 3.6E-27 7.8E-32 192.8 5.6 112 181-302 126-240 (279)
3 KOG1074|consensus 99.9 4.8E-23 1E-27 189.8 3.2 53 247-301 879-931 (958)
4 KOG1074|consensus 99.8 1.8E-22 4E-27 186.0 0.7 83 214-302 606-693 (958)
5 KOG3576|consensus 99.8 2.4E-21 5.3E-26 151.0 2.8 118 149-273 115-238 (267)
6 KOG3608|consensus 99.8 1.5E-20 3.2E-25 158.0 7.6 166 129-301 184-376 (467)
7 KOG3576|consensus 99.8 1.3E-20 2.9E-25 146.8 4.3 117 179-301 111-236 (267)
8 KOG3608|consensus 99.8 4.6E-19 9.9E-24 149.1 5.5 140 152-301 178-345 (467)
9 KOG3623|consensus 99.7 2.9E-18 6.3E-23 156.1 3.3 111 185-298 210-330 (1007)
10 KOG3623|consensus 99.7 7.3E-18 1.6E-22 153.6 2.3 80 182-267 891-970 (1007)
11 PLN03086 PRLI-interacting fact 99.6 1.1E-14 2.3E-19 133.7 9.5 133 151-298 407-561 (567)
12 PHA00733 hypothetical protein 99.4 1.9E-13 4.1E-18 103.2 5.6 86 210-302 37-124 (128)
13 PHA00733 hypothetical protein 99.3 2.2E-12 4.7E-17 97.4 4.8 85 181-273 36-125 (128)
14 PHA02768 hypothetical protein; 99.3 1.1E-12 2.3E-17 81.7 1.8 44 247-294 5-48 (55)
15 PLN03086 PRLI-interacting fact 99.2 2.4E-11 5.2E-16 111.9 7.3 102 152-272 454-565 (567)
16 PHA02768 hypothetical protein; 99.1 1.6E-11 3.4E-16 76.6 1.5 40 186-227 6-45 (55)
17 KOG3993|consensus 99.0 1.2E-10 2.5E-15 101.1 1.7 135 152-299 268-480 (500)
18 PF13465 zf-H2C2_2: Zinc-finge 98.9 1E-09 2.2E-14 58.6 2.2 26 262-289 1-26 (26)
19 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.3E-09 2.7E-14 58.2 1.9 24 201-224 2-25 (26)
20 PHA00732 hypothetical protein 98.8 2.6E-09 5.7E-14 73.2 3.2 50 213-273 1-50 (79)
21 PHA00616 hypothetical protein 98.7 5.9E-09 1.3E-13 61.9 1.6 39 247-287 1-39 (44)
22 PHA00732 hypothetical protein 98.7 9E-09 2E-13 70.5 2.7 36 186-224 2-38 (79)
23 KOG3993|consensus 98.7 3.7E-09 8E-14 91.9 0.1 88 184-274 266-383 (500)
24 PHA00616 hypothetical protein 98.6 1.8E-08 3.9E-13 59.8 1.7 35 185-219 1-35 (44)
25 PF05605 zf-Di19: Drought indu 98.6 1.2E-07 2.6E-12 60.4 4.6 51 214-271 3-53 (54)
26 PF05605 zf-Di19: Drought indu 98.5 2.6E-07 5.5E-12 58.9 4.5 52 247-301 2-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.3 2.8E-07 6.1E-12 47.7 1.5 22 248-269 1-22 (23)
28 PF00096 zf-C2H2: Zinc finger, 98.3 5E-07 1.1E-11 46.7 1.9 23 278-300 1-23 (23)
29 PF12756 zf-C2H2_2: C2H2 type 98.1 1.3E-06 2.8E-11 63.3 2.3 75 187-272 1-75 (100)
30 PF13894 zf-C2H2_4: C2H2-type 98.1 2.1E-06 4.5E-11 44.7 2.1 24 248-271 1-24 (24)
31 COG5189 SFP1 Putative transcri 98.0 1.3E-06 2.9E-11 73.6 0.5 59 210-268 346-419 (423)
32 PF13912 zf-C2H2_6: C2H2-type 98.0 3.3E-06 7.1E-11 45.4 1.5 24 248-271 2-25 (27)
33 PF12756 zf-C2H2_2: C2H2 type 98.0 4.2E-06 9E-11 60.6 2.4 73 215-300 1-73 (100)
34 PF13894 zf-C2H2_4: C2H2-type 97.9 5.6E-06 1.2E-10 43.0 1.8 24 278-301 1-24 (24)
35 COG5189 SFP1 Putative transcri 97.9 2.2E-06 4.7E-11 72.3 0.2 52 183-234 347-419 (423)
36 PF13912 zf-C2H2_6: C2H2-type 97.9 6.2E-06 1.3E-10 44.3 1.5 25 277-301 1-25 (27)
37 smart00355 ZnF_C2H2 zinc finge 97.6 5.4E-05 1.2E-09 39.9 2.1 23 278-300 1-23 (26)
38 smart00355 ZnF_C2H2 zinc finge 97.5 0.0001 2.3E-09 38.7 2.6 24 248-271 1-24 (26)
39 PF09237 GAGA: GAGA factor; I 97.4 6.1E-05 1.3E-09 45.8 1.4 32 243-274 20-51 (54)
40 PRK04860 hypothetical protein; 97.2 0.00024 5.1E-09 55.8 2.2 38 247-290 119-156 (160)
41 PF12874 zf-met: Zinc-finger o 97.1 0.00027 5.9E-09 37.0 1.5 22 248-269 1-22 (25)
42 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00053 1.1E-08 35.5 2.1 23 248-271 1-23 (24)
43 PRK04860 hypothetical protein; 96.9 0.00055 1.2E-08 53.7 2.0 38 213-260 119-156 (160)
44 PF12874 zf-met: Zinc-finger o 96.9 0.00053 1.1E-08 35.9 1.3 23 278-300 1-23 (25)
45 PF09237 GAGA: GAGA factor; I 96.8 0.0014 3E-08 39.9 3.0 30 208-237 19-48 (54)
46 KOG2231|consensus 96.8 0.0032 6.8E-08 59.8 6.9 89 194-298 158-260 (669)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.00041 8.9E-09 37.1 0.2 22 248-269 2-23 (27)
48 COG5048 FOG: Zn-finger [Genera 96.6 0.00026 5.6E-09 65.0 -1.9 117 185-302 289-443 (467)
49 PF13909 zf-H2C2_5: C2H2-type 96.6 0.0016 3.5E-08 33.6 1.7 24 278-302 1-24 (24)
50 KOG2482|consensus 96.5 0.01 2.3E-07 51.1 6.9 23 185-207 195-217 (423)
51 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.0011 2.4E-08 35.4 0.7 23 277-299 1-23 (27)
52 COG5236 Uncharacterized conser 96.0 0.026 5.7E-07 48.8 7.1 74 187-274 222-308 (493)
53 KOG1146|consensus 96.0 0.0029 6.2E-08 63.6 1.5 111 188-298 439-610 (1406)
54 KOG2231|consensus 95.7 0.028 6E-07 53.6 6.4 105 187-301 117-236 (669)
55 PF01352 KRAB: KRAB box; Inte 95.7 0.0063 1.4E-07 36.0 1.4 38 21-58 2-39 (41)
56 KOG1146|consensus 95.6 0.0041 8.9E-08 62.6 0.9 80 215-299 438-540 (1406)
57 PF13913 zf-C2HC_2: zinc-finge 95.6 0.01 2.3E-07 30.9 1.9 20 278-298 3-22 (25)
58 smart00451 ZnF_U1 U1-like zinc 95.6 0.0095 2E-07 33.8 1.9 22 277-298 3-24 (35)
59 smart00451 ZnF_U1 U1-like zinc 95.3 0.013 2.7E-07 33.3 1.9 23 247-269 3-25 (35)
60 PF13913 zf-C2HC_2: zinc-finge 95.1 0.019 4.2E-07 29.9 2.0 19 249-268 4-22 (25)
61 KOG2785|consensus 94.8 0.1 2.3E-06 46.0 6.8 116 181-298 64-241 (390)
62 KOG2785|consensus 94.5 0.08 1.7E-06 46.6 5.5 57 213-269 166-242 (390)
63 TIGR00622 ssl1 transcription f 94.3 0.059 1.3E-06 39.3 3.6 84 212-301 14-105 (112)
64 PF09538 FYDLN_acid: Protein o 94.2 0.038 8.3E-07 40.3 2.5 32 246-290 8-39 (108)
65 COG5236 Uncharacterized conser 94.0 0.049 1.1E-06 47.2 3.1 122 152-299 152-303 (493)
66 COG5048 FOG: Zn-finger [Genera 93.8 0.012 2.7E-07 53.8 -0.9 70 212-288 288-364 (467)
67 smart00868 zf-AD Zinc-finger a 93.3 0.13 2.7E-06 34.0 3.6 22 22-43 38-59 (73)
68 KOG4173|consensus 93.2 0.048 1E-06 43.7 1.5 51 187-237 108-170 (253)
69 COG4049 Uncharacterized protei 92.2 0.067 1.5E-06 33.2 0.9 31 243-273 13-43 (65)
70 PF07776 zf-AD: Zinc-finger as 92.1 0.056 1.2E-06 36.2 0.6 23 21-43 39-61 (75)
71 KOG4173|consensus 91.8 0.15 3.3E-06 40.9 2.8 84 184-271 78-170 (253)
72 COG2888 Predicted Zn-ribbon RN 91.4 0.14 3E-06 32.4 1.7 9 185-193 27-35 (61)
73 KOG2186|consensus 91.1 0.12 2.7E-06 42.8 1.7 25 184-209 28-52 (276)
74 cd00350 rubredoxin_like Rubred 91.1 0.12 2.6E-06 28.9 1.1 24 186-221 2-25 (33)
75 KOG2893|consensus 90.9 0.055 1.2E-06 44.4 -0.5 49 184-237 10-58 (341)
76 TIGR02300 FYDLN_acid conserved 90.6 0.2 4.4E-06 37.1 2.3 33 246-291 8-40 (129)
77 PF12013 DUF3505: Protein of u 89.4 0.63 1.4E-05 34.1 4.1 26 247-272 80-109 (109)
78 KOG2186|consensus 89.3 0.17 3.7E-06 42.0 1.1 47 185-234 3-49 (276)
79 PF09986 DUF2225: Uncharacteri 89.3 0.073 1.6E-06 44.2 -1.1 45 246-290 4-61 (214)
80 PF12013 DUF3505: Protein of u 88.9 0.99 2.1E-05 33.0 4.9 25 278-302 81-109 (109)
81 PF13719 zinc_ribbon_5: zinc-r 88.2 0.32 6.9E-06 28.0 1.4 32 187-223 4-35 (37)
82 TIGR02098 MJ0042_CXXC MJ0042 f 88.0 0.3 6.5E-06 28.2 1.3 12 187-198 4-15 (38)
83 PF13717 zinc_ribbon_4: zinc-r 88.0 0.35 7.6E-06 27.6 1.5 12 187-198 4-15 (36)
84 cd00729 rubredoxin_SM Rubredox 87.8 0.42 9E-06 26.9 1.7 26 247-286 2-27 (34)
85 PF10571 UPF0547: Uncharacteri 87.5 0.42 9.1E-06 25.1 1.5 11 278-288 15-25 (26)
86 PF09538 FYDLN_acid: Protein o 87.2 0.34 7.4E-06 35.3 1.4 15 212-226 25-39 (108)
87 KOG2893|consensus 86.7 0.16 3.5E-06 41.8 -0.6 41 216-266 13-53 (341)
88 PRK14890 putative Zn-ribbon RN 86.7 0.49 1.1E-05 30.1 1.7 8 247-254 48-55 (59)
89 smart00659 RPOLCX RNA polymera 86.7 0.4 8.6E-06 28.8 1.3 27 247-286 2-28 (44)
90 smart00614 ZnF_BED BED zinc fi 85.0 0.67 1.4E-05 28.6 1.8 21 248-268 19-44 (50)
91 PF02892 zf-BED: BED zinc fing 84.8 0.85 1.8E-05 27.3 2.1 12 248-259 17-28 (45)
92 COG4049 Uncharacterized protei 84.5 0.62 1.3E-05 29.0 1.4 28 210-237 14-41 (65)
93 TIGR00373 conserved hypothetic 84.2 0.52 1.1E-05 37.1 1.2 37 177-222 101-137 (158)
94 PF02892 zf-BED: BED zinc fing 84.2 0.8 1.7E-05 27.4 1.8 27 211-237 14-44 (45)
95 PF09986 DUF2225: Uncharacteri 83.7 0.14 3E-06 42.5 -2.3 13 248-260 49-61 (214)
96 TIGR00373 conserved hypothetic 83.3 1.4 3.1E-05 34.6 3.4 34 243-287 105-138 (158)
97 COG4530 Uncharacterized protei 82.9 1.4 3E-05 31.7 2.8 28 248-288 10-37 (129)
98 PF07754 DUF1610: Domain of un 82.7 0.72 1.6E-05 23.7 1.0 8 185-192 16-23 (24)
99 TIGR00622 ssl1 transcription f 82.6 1.1 2.5E-05 32.7 2.3 23 245-267 79-101 (112)
100 PRK06266 transcription initiat 82.3 0.66 1.4E-05 37.3 1.2 34 243-287 113-146 (178)
101 COG1996 RPC10 DNA-directed RNA 82.2 0.66 1.4E-05 28.4 0.9 30 245-286 4-33 (49)
102 PRK06266 transcription initiat 81.8 0.74 1.6E-05 37.0 1.3 36 179-223 111-146 (178)
103 smart00614 ZnF_BED BED zinc fi 81.8 1.1 2.4E-05 27.6 1.8 25 277-301 18-48 (50)
104 smart00531 TFIIE Transcription 81.7 0.75 1.6E-05 35.7 1.2 15 246-260 98-112 (147)
105 PF05443 ROS_MUCR: ROS/MUCR tr 81.4 0.81 1.8E-05 34.7 1.3 27 245-274 70-96 (132)
106 smart00834 CxxC_CXXC_SSSS Puta 80.3 0.4 8.6E-06 28.1 -0.6 30 248-286 6-35 (41)
107 COG1592 Rubrerythrin [Energy p 79.1 1.2 2.6E-05 35.1 1.6 8 277-284 149-156 (166)
108 TIGR02300 FYDLN_acid conserved 79.0 1.2 2.6E-05 33.2 1.4 29 187-226 11-39 (129)
109 COG1997 RPL43A Ribosomal prote 78.8 1.2 2.5E-05 30.8 1.2 31 246-288 34-64 (89)
110 smart00531 TFIIE Transcription 78.8 1.2 2.6E-05 34.6 1.5 39 181-223 95-133 (147)
111 PF08274 PhnA_Zn_Ribbon: PhnA 78.6 0.83 1.8E-05 24.9 0.4 26 249-287 4-29 (30)
112 smart00734 ZnF_Rad18 Rad18-lik 78.1 2.1 4.5E-05 22.4 1.8 18 249-267 3-20 (26)
113 PRK00464 nrdR transcriptional 78.1 0.36 7.9E-06 37.6 -1.5 12 248-259 29-40 (154)
114 PF15269 zf-C2H2_7: Zinc-finge 78.0 1.5 3.2E-05 26.0 1.4 21 214-234 21-41 (54)
115 KOG2482|consensus 77.3 4.3 9.4E-05 35.6 4.5 23 247-269 195-217 (423)
116 COG1592 Rubrerythrin [Energy p 76.6 1.5 3.3E-05 34.6 1.5 12 209-220 145-156 (166)
117 TIGR02605 CxxC_CxxC_SSSS putat 76.6 0.61 1.3E-05 29.0 -0.6 13 248-260 6-18 (52)
118 KOG2071|consensus 76.4 2 4.4E-05 40.4 2.5 27 183-209 416-442 (579)
119 PF03604 DNA_RNApol_7kD: DNA d 76.1 1.8 4E-05 23.9 1.3 26 248-286 1-26 (32)
120 PRK09678 DNA-binding transcrip 75.9 0.72 1.6E-05 30.9 -0.4 15 211-225 25-41 (72)
121 KOG2907|consensus 75.1 0.54 1.2E-05 34.0 -1.2 29 170-198 10-38 (116)
122 COG5151 SSL1 RNA polymerase II 75.1 1.7 3.8E-05 37.4 1.6 84 212-301 321-412 (421)
123 PF09723 Zn-ribbon_8: Zinc rib 74.9 1 2.2E-05 26.7 0.1 29 248-285 6-34 (42)
124 COG1198 PriA Primosomal protei 74.3 1.7 3.6E-05 42.8 1.5 27 243-286 458-484 (730)
125 PRK09678 DNA-binding transcrip 73.9 0.47 1E-05 31.8 -1.7 12 278-289 28-41 (72)
126 KOG2272|consensus 73.1 2.7 5.8E-05 35.1 2.2 62 186-260 164-234 (332)
127 KOG4167|consensus 71.1 1.2 2.6E-05 42.9 -0.3 28 246-273 791-818 (907)
128 PHA00626 hypothetical protein 70.2 2.4 5.1E-05 26.6 1.0 14 212-225 22-35 (59)
129 PF14353 CpXC: CpXC protein 69.5 0.37 7.9E-06 36.5 -3.4 14 277-290 38-51 (128)
130 PF06524 NOA36: NOA36 protein; 69.3 1.1 2.3E-05 37.6 -0.9 24 276-299 208-231 (314)
131 PF04959 ARS2: Arsenite-resist 66.9 3.7 8E-05 33.9 1.8 26 212-237 76-101 (214)
132 KOG1280|consensus 66.7 4.2 9.2E-05 35.7 2.1 72 177-254 45-116 (381)
133 PF01363 FYVE: FYVE zinc finge 66.5 2.8 6E-05 27.7 0.8 28 247-288 9-36 (69)
134 PRK00398 rpoP DNA-directed RNA 66.2 3.3 7.2E-05 24.9 1.1 13 185-197 3-15 (46)
135 COG0068 HypF Hydrogenase matur 65.8 1.4 3.1E-05 42.5 -1.0 56 187-255 125-181 (750)
136 PF15269 zf-C2H2_7: Zinc-finge 64.4 5.4 0.00012 23.7 1.6 33 237-269 9-42 (54)
137 KOG4124|consensus 63.8 1.3 2.8E-05 38.7 -1.4 28 211-238 347-376 (442)
138 COG1997 RPL43A Ribosomal prote 63.7 3 6.6E-05 28.8 0.6 15 182-196 50-64 (89)
139 COG4957 Predicted transcriptio 62.8 3.4 7.5E-05 31.0 0.8 24 248-274 77-100 (148)
140 smart00661 RPOL9 RNA polymeras 62.7 3.8 8.3E-05 25.2 0.9 13 185-197 20-32 (52)
141 TIGR01206 lysW lysine biosynth 61.9 2.9 6.4E-05 26.3 0.2 30 248-287 3-32 (54)
142 PF04959 ARS2: Arsenite-resist 61.8 3.8 8.2E-05 33.9 0.9 32 243-274 73-104 (214)
143 PF08790 zf-LYAR: LYAR-type C2 61.3 1.5 3.2E-05 23.4 -1.0 19 249-268 2-20 (28)
144 PF09416 UPF1_Zn_bind: RNA hel 60.7 7.8 0.00017 30.0 2.4 44 243-286 10-69 (152)
145 PF15135 UPF0515: Uncharacteri 60.3 18 0.0004 30.3 4.6 20 146-165 107-126 (278)
146 TIGR00595 priA primosomal prot 59.4 4.6 9.9E-05 38.3 1.2 27 243-286 236-262 (505)
147 PF04216 FdhE: Protein involve 58.6 1.1 2.5E-05 39.0 -2.8 14 182-195 194-207 (290)
148 KOG2593|consensus 58.6 8.3 0.00018 35.1 2.5 18 183-200 126-143 (436)
149 cd00065 FYVE FYVE domain; Zinc 58.4 7.4 0.00016 24.4 1.7 26 249-288 4-29 (57)
150 PRK04023 DNA polymerase II lar 57.9 8 0.00017 39.1 2.5 10 185-194 626-635 (1121)
151 COG3091 SprT Zn-dependent meta 57.4 4.4 9.6E-05 31.2 0.6 32 247-285 117-148 (156)
152 KOG4167|consensus 57.3 3.3 7.3E-05 40.0 -0.1 24 213-237 792-815 (907)
153 COG1198 PriA Primosomal protei 56.4 6.4 0.00014 38.8 1.6 34 152-192 436-469 (730)
154 KOG3408|consensus 55.2 9.2 0.0002 28.2 1.9 27 243-269 53-79 (129)
155 PF02176 zf-TRAF: TRAF-type zi 55.1 5.3 0.00011 25.4 0.6 41 184-225 8-54 (60)
156 smart00064 FYVE Protein presen 54.6 8.7 0.00019 25.1 1.6 27 248-288 11-37 (68)
157 PF07975 C1_4: TFIIH C1-like d 54.4 3.5 7.7E-05 25.5 -0.3 25 277-301 21-45 (51)
158 PF14311 DUF4379: Domain of un 54.2 8.6 0.00019 24.1 1.5 18 248-265 29-46 (55)
159 PRK14873 primosome assembly pr 53.5 3.5 7.6E-05 40.4 -0.7 47 215-286 385-431 (665)
160 PRK04023 DNA polymerase II lar 53.1 13 0.00028 37.7 3.1 9 186-194 639-647 (1121)
161 PF07282 OrfB_Zn_ribbon: Putat 52.9 6.9 0.00015 25.7 0.9 16 182-197 43-58 (69)
162 KOG1280|consensus 52.7 14 0.00031 32.5 2.9 42 244-285 76-117 (381)
163 PF14369 zf-RING_3: zinc-finge 52.1 9.5 0.00021 21.5 1.2 10 187-196 23-32 (35)
164 PF05443 ROS_MUCR: ROS/MUCR tr 52.0 8.8 0.00019 29.1 1.4 23 277-302 72-94 (132)
165 KOG0978|consensus 51.7 5.4 0.00012 38.8 0.3 49 152-203 644-696 (698)
166 COG1645 Uncharacterized Zn-fin 51.6 7.9 0.00017 29.2 1.1 27 168-196 29-55 (131)
167 COG5151 SSL1 RNA polymerase II 50.3 6.3 0.00014 34.1 0.5 77 184-268 321-409 (421)
168 COG2331 Uncharacterized protei 49.4 7.9 0.00017 26.0 0.7 18 152-169 13-31 (82)
169 TIGR03826 YvyF flagellar opero 48.9 8.7 0.00019 29.3 1.0 23 153-176 5-27 (137)
170 PF13878 zf-C2H2_3: zinc-finge 48.7 18 0.00038 21.2 2.1 25 185-209 13-39 (41)
171 PF07295 DUF1451: Protein of u 48.5 7.4 0.00016 30.1 0.6 10 247-256 112-121 (146)
172 PF09332 Mcm10: Mcm10 replicat 48.2 3.3 7.1E-05 36.9 -1.6 65 213-294 252-320 (344)
173 smart00154 ZnF_AN1 AN1-like Zi 47.7 9 0.0002 22.2 0.7 13 277-289 12-24 (39)
174 KOG4124|consensus 47.6 2.3 5E-05 37.3 -2.5 52 183-234 347-419 (442)
175 PF09297 zf-NADH-PPase: NADH p 47.6 11 0.00023 20.7 1.0 26 170-195 6-31 (32)
176 PF04423 Rad50_zn_hook: Rad50 46.6 6.4 0.00014 24.6 -0.1 20 279-298 22-43 (54)
177 KOG2593|consensus 46.4 20 0.00043 32.7 2.9 20 209-228 124-143 (436)
178 PF12760 Zn_Tnp_IS1595: Transp 46.4 4.7 0.0001 24.3 -0.7 9 277-285 37-45 (46)
179 PF06524 NOA36: NOA36 protein; 46.3 7.3 0.00016 32.8 0.2 25 245-269 207-231 (314)
180 smart00440 ZnF_C2C2 C2C2 Zinc 45.8 1.8 4E-05 25.3 -2.4 10 248-257 29-38 (40)
181 PF06220 zf-U1: U1 zinc finger 45.8 15 0.00033 21.1 1.4 12 247-258 3-14 (38)
182 PF09845 DUF2072: Zn-ribbon co 45.8 6.3 0.00014 29.6 -0.2 25 151-175 1-27 (131)
183 PRK12380 hydrogenase nickel in 45.5 9.3 0.0002 28.1 0.7 12 248-259 71-82 (113)
184 PRK03564 formate dehydrogenase 45.4 11 0.00024 33.1 1.2 77 184-289 186-264 (309)
185 PRK14873 primosome assembly pr 45.2 12 0.00025 36.9 1.4 35 152-193 384-418 (665)
186 KOG3408|consensus 45.2 13 0.00028 27.5 1.3 28 180-207 52-79 (129)
187 PRK14714 DNA polymerase II lar 44.7 12 0.00026 39.0 1.4 36 152-196 668-703 (1337)
188 KOG0782|consensus 44.4 4.3 9.4E-05 38.1 -1.5 35 187-227 255-290 (1004)
189 COG4888 Uncharacterized Zn rib 44.2 2.1 4.6E-05 30.3 -2.7 37 245-287 20-56 (104)
190 PTZ00255 60S ribosomal protein 44.0 6.1 0.00013 27.7 -0.5 15 182-196 51-65 (90)
191 PF01780 Ribosomal_L37ae: Ribo 43.5 3.3 7.2E-05 29.0 -1.8 27 170-196 38-64 (90)
192 KOG4727|consensus 43.2 12 0.00026 29.4 1.0 22 277-298 75-96 (193)
193 PRK03824 hypA hydrogenase nick 43.1 7.7 0.00017 29.6 -0.1 10 152-161 71-80 (135)
194 PF12907 zf-met2: Zinc-binding 43.0 24 0.00053 20.6 2.0 7 187-193 3-9 (40)
195 KOG0717|consensus 42.9 14 0.0003 34.1 1.4 22 248-269 293-314 (508)
196 PF13240 zinc_ribbon_2: zinc-r 42.4 12 0.00025 18.9 0.5 6 188-193 16-21 (23)
197 PF05290 Baculo_IE-1: Baculovi 42.1 6.8 0.00015 29.5 -0.5 18 150-167 79-96 (140)
198 KOG2636|consensus 41.9 16 0.00036 33.3 1.8 27 208-234 396-423 (497)
199 TIGR00244 transcriptional regu 41.8 11 0.00024 29.1 0.5 19 184-202 27-45 (147)
200 COG0068 HypF Hydrogenase matur 41.7 4.3 9.3E-05 39.3 -2.0 57 215-286 125-182 (750)
201 PF01428 zf-AN1: AN1-like Zinc 40.8 8.5 0.00018 22.8 -0.1 11 277-287 13-23 (43)
202 PF08792 A2L_zn_ribbon: A2L zi 40.6 11 0.00025 20.9 0.4 12 184-195 20-31 (33)
203 TIGR01562 FdhE formate dehydro 40.5 14 0.0003 32.4 1.1 77 185-289 184-264 (305)
204 TIGR00280 L37a ribosomal prote 40.1 7.2 0.00016 27.3 -0.6 15 182-196 50-64 (91)
205 TIGR00686 phnA alkylphosphonat 39.5 14 0.00031 26.7 0.8 28 249-289 4-31 (109)
206 PF10263 SprT-like: SprT-like 39.0 8.4 0.00018 29.9 -0.4 32 247-288 123-154 (157)
207 TIGR01053 LSD1 zinc finger dom 38.6 18 0.00039 19.8 1.0 24 170-193 4-27 (31)
208 TIGR00595 priA primosomal prot 38.4 18 0.0004 34.3 1.6 36 152-194 214-249 (505)
209 KOG0717|consensus 38.1 18 0.00038 33.4 1.4 22 186-207 293-314 (508)
210 PTZ00448 hypothetical protein; 37.9 23 0.00049 31.8 2.0 23 247-269 314-336 (373)
211 KOG0402|consensus 37.6 17 0.00037 24.8 0.9 27 170-196 39-65 (92)
212 PRK05580 primosome assembly pr 37.5 17 0.00036 35.9 1.2 27 243-286 404-430 (679)
213 PF01286 XPA_N: XPA protein N- 37.4 13 0.00027 20.9 0.2 14 278-291 4-17 (34)
214 COG4306 Uncharacterized protei 37.3 10 0.00022 28.1 -0.2 39 187-225 41-80 (160)
215 PRK10220 hypothetical protein; 37.0 21 0.00045 25.9 1.3 29 249-290 5-33 (111)
216 COG1675 TFA1 Transcription ini 36.6 21 0.00047 28.5 1.5 19 181-199 109-127 (176)
217 PF14445 Prok-RING_2: Prokaryo 36.2 7.6 0.00016 23.7 -0.8 16 152-167 8-23 (57)
218 PRK14892 putative transcriptio 35.9 11 0.00023 27.1 -0.3 36 246-290 20-55 (99)
219 PF13451 zf-trcl: Probable zin 35.6 20 0.00043 22.0 0.9 12 185-196 4-15 (49)
220 KOG2071|consensus 35.6 23 0.00049 33.7 1.7 31 244-274 415-445 (579)
221 COG1571 Predicted DNA-binding 35.5 19 0.00042 32.9 1.2 14 247-260 367-380 (421)
222 COG1594 RPB9 DNA-directed RNA 35.4 7.3 0.00016 28.7 -1.2 15 184-198 21-35 (113)
223 PF10276 zf-CHCC: Zinc-finger 35.1 13 0.00029 21.7 0.1 11 247-257 29-39 (40)
224 PRK03976 rpl37ae 50S ribosomal 34.9 9.1 0.0002 26.8 -0.7 16 181-196 50-65 (90)
225 TIGR00100 hypA hydrogenase nic 34.5 15 0.00032 27.2 0.2 15 183-197 68-82 (115)
226 smart00731 SprT SprT homologue 34.4 18 0.00038 27.9 0.7 32 213-257 112-143 (146)
227 PF08209 Sgf11: Sgf11 (transcr 34.0 20 0.00044 20.0 0.7 16 152-167 5-24 (33)
228 KOG2461|consensus 33.6 13 0.00029 33.9 -0.1 87 191-285 309-395 (396)
229 PRK00432 30S ribosomal protein 33.2 21 0.00046 22.0 0.8 9 213-221 37-45 (50)
230 PF05495 zf-CHY: CHY zinc fing 32.9 5.6 0.00012 26.6 -2.0 14 247-260 41-54 (71)
231 PF13453 zf-TFIIB: Transcripti 32.9 21 0.00045 20.8 0.7 21 277-297 19-39 (41)
232 COG1656 Uncharacterized conser 32.8 36 0.00078 26.8 2.1 11 278-288 131-141 (165)
233 COG4640 Predicted membrane pro 32.7 27 0.00059 31.4 1.7 19 247-265 15-33 (465)
234 COG1327 Predicted transcriptio 32.4 17 0.00038 28.0 0.3 17 183-199 26-42 (156)
235 PF15135 UPF0515: Uncharacteri 32.3 22 0.00047 29.9 0.9 18 209-226 151-168 (278)
236 PF13821 DUF4187: Domain of un 32.1 51 0.0011 20.7 2.4 29 228-266 18-46 (55)
237 PF10013 DUF2256: Uncharacteri 31.9 26 0.00057 20.6 1.0 17 215-231 10-26 (42)
238 KOG0696|consensus 31.5 13 0.00029 34.0 -0.4 47 202-254 82-128 (683)
239 PF11931 DUF3449: Domain of un 31.5 16 0.00034 29.8 0.0 8 185-192 101-108 (196)
240 PRK04351 hypothetical protein; 31.5 22 0.00048 27.6 0.8 32 247-288 112-143 (149)
241 PF04931 DNA_pol_phi: DNA poly 31.4 38 0.00083 34.1 2.7 13 27-39 606-618 (784)
242 PRK12496 hypothetical protein; 31.3 29 0.00063 27.4 1.5 10 248-257 128-137 (164)
243 COG1998 RPS31 Ribosomal protei 31.2 11 0.00023 23.1 -0.7 16 152-167 20-36 (51)
244 KOG2807|consensus 31.0 44 0.00096 29.3 2.6 73 212-301 289-369 (378)
245 KOG0320|consensus 30.8 27 0.00058 27.8 1.2 53 182-260 128-180 (187)
246 PRK01343 zinc-binding protein; 30.7 28 0.00061 22.1 1.0 13 246-258 8-20 (57)
247 COG5112 UFD2 U1-like Zn-finger 30.5 26 0.00056 25.2 0.9 26 243-268 51-76 (126)
248 KOG0782|consensus 30.2 17 0.00036 34.4 -0.1 57 228-297 240-298 (1004)
249 COG5152 Uncharacterized conser 30.0 27 0.0006 28.2 1.1 17 183-199 194-210 (259)
250 PF01096 TFIIS_C: Transcriptio 29.9 28 0.0006 20.1 0.8 9 214-222 29-37 (39)
251 KOG0957|consensus 29.8 32 0.00069 32.0 1.6 45 152-197 545-601 (707)
252 PF04780 DUF629: Protein of un 29.8 33 0.00072 31.9 1.8 32 180-211 52-84 (466)
253 PF04810 zf-Sec23_Sec24: Sec23 29.6 21 0.00046 20.7 0.3 9 212-220 23-31 (40)
254 PF05191 ADK_lid: Adenylate ki 29.3 27 0.00058 19.8 0.7 10 187-196 3-12 (36)
255 KOG3214|consensus 29.0 16 0.00035 25.9 -0.3 42 245-292 21-62 (109)
256 COG1571 Predicted DNA-binding 28.5 29 0.00063 31.8 1.1 30 187-227 352-381 (421)
257 PF14787 zf-CCHC_5: GAG-polypr 28.2 29 0.00062 19.7 0.7 13 277-289 2-14 (36)
258 PF07295 DUF1451: Protein of u 28.1 22 0.00048 27.5 0.3 9 152-160 113-121 (146)
259 PRK05580 primosome assembly pr 27.9 34 0.00073 33.8 1.6 36 152-194 382-417 (679)
260 COG5112 UFD2 U1-like Zn-finger 27.9 22 0.00047 25.5 0.2 22 277-298 55-76 (126)
261 COG3364 Zn-ribbon containing p 27.4 35 0.00076 24.4 1.1 14 247-260 2-15 (112)
262 TIGR00143 hypF [NiFe] hydrogen 27.1 9.7 0.00021 37.7 -2.3 39 187-226 92-131 (711)
263 KOG2807|consensus 27.0 79 0.0017 27.9 3.4 22 183-204 288-309 (378)
264 PRK11827 hypothetical protein; 26.7 34 0.00073 22.0 0.9 28 170-197 11-38 (60)
265 COG1773 Rubredoxin [Energy pro 26.6 28 0.0006 22.0 0.5 11 277-287 3-13 (55)
266 PF09963 DUF2197: Uncharacteri 26.5 19 0.00042 22.7 -0.2 9 187-195 4-12 (56)
267 PRK00564 hypA hydrogenase nick 26.4 26 0.00056 26.0 0.4 14 184-197 70-83 (117)
268 COG3677 Transposase and inacti 26.4 29 0.00064 26.2 0.7 36 247-289 30-65 (129)
269 PTZ00303 phosphatidylinositol 26.3 20 0.00044 35.3 -0.3 12 215-226 462-473 (1374)
270 PF13824 zf-Mss51: Zinc-finger 26.2 46 0.00099 21.0 1.4 10 185-194 14-23 (55)
271 PF00628 PHD: PHD-finger; Int 26.1 40 0.00088 20.3 1.2 20 179-198 8-27 (51)
272 PF04780 DUF629: Protein of un 25.4 69 0.0015 29.9 3.0 22 248-269 58-79 (466)
273 PF05741 zf-nanos: Nanos RNA b 25.4 24 0.00053 22.2 0.1 10 277-286 33-42 (55)
274 smart00132 LIM Zinc-binding do 25.4 11 0.00023 21.1 -1.5 10 278-287 28-37 (39)
275 PTZ00448 hypothetical protein; 25.2 49 0.0011 29.7 1.9 24 184-207 313-336 (373)
276 PF03833 PolC_DP2: DNA polymer 25.2 24 0.00051 35.2 0.0 36 152-196 656-691 (900)
277 KOG1729|consensus 25.1 19 0.00042 31.2 -0.6 8 152-159 169-176 (288)
278 KOG2636|consensus 25.0 47 0.001 30.5 1.8 29 178-206 394-423 (497)
279 PF09082 DUF1922: Domain of un 24.8 25 0.00055 23.2 0.1 23 173-196 8-30 (68)
280 PF12647 RNHCP: RNHCP domain; 24.5 14 0.00031 25.9 -1.2 29 150-178 3-35 (92)
281 COG4896 Uncharacterized protei 24.3 39 0.00085 21.7 0.8 16 244-259 28-43 (68)
282 PF06397 Desulfoferrod_N: Desu 24.1 31 0.00066 19.7 0.3 11 277-287 6-16 (36)
283 PF14255 Cys_rich_CPXG: Cystei 24.1 36 0.00078 21.2 0.6 11 278-288 1-11 (52)
284 COG5188 PRP9 Splicing factor 3 24.1 49 0.0011 29.4 1.7 28 207-234 368-396 (470)
285 cd00924 Cyt_c_Oxidase_Vb Cytoc 23.5 30 0.00066 24.7 0.3 12 212-223 78-89 (97)
286 KOG1842|consensus 23.4 43 0.00094 30.7 1.3 11 279-289 81-91 (505)
287 PLN02294 cytochrome c oxidase 23.3 25 0.00053 27.8 -0.2 12 277-288 141-152 (174)
288 COG4391 Uncharacterized protei 23.3 33 0.00072 22.1 0.4 12 277-288 48-59 (62)
289 PF09332 Mcm10: Mcm10 replicat 23.3 10 0.00022 33.8 -2.7 45 245-290 250-298 (344)
290 PF01155 HypA: Hydrogenase exp 23.3 29 0.00062 25.5 0.1 10 152-161 71-80 (113)
291 COG5188 PRP9 Splicing factor 3 22.9 37 0.00081 30.1 0.8 24 245-268 236-259 (470)
292 COG3464 Transposase and inacti 22.8 21 0.00045 32.8 -0.8 10 214-223 39-48 (402)
293 PRK11032 hypothetical protein; 22.4 30 0.00065 27.2 0.1 31 152-198 125-155 (160)
294 PF14803 Nudix_N_2: Nudix N-te 22.4 40 0.00088 18.9 0.6 11 184-194 21-31 (34)
295 CHL00174 accD acetyl-CoA carbo 22.0 58 0.0013 28.5 1.7 11 278-288 58-68 (296)
296 TIGR00515 accD acetyl-CoA carb 22.0 54 0.0012 28.5 1.6 11 248-258 46-56 (285)
297 KOG1842|consensus 21.9 59 0.0013 29.9 1.8 28 184-211 14-42 (505)
298 PRK03681 hypA hydrogenase nick 21.8 26 0.00057 25.8 -0.3 9 152-160 71-79 (114)
299 KOG2330|consensus 21.7 32 0.00068 31.4 0.1 55 1-55 284-353 (500)
300 COG1779 C4-type Zn-finger prot 21.3 18 0.00039 29.4 -1.4 11 248-258 44-54 (201)
301 PRK05978 hypothetical protein; 21.2 26 0.00057 27.2 -0.5 10 249-258 54-63 (148)
302 PF01844 HNH: HNH endonuclease 21.0 14 0.00031 21.8 -1.6 11 280-290 1-11 (47)
303 KOG0978|consensus 20.4 34 0.00075 33.5 0.1 21 277-297 678-698 (698)
304 PF10083 DUF2321: Uncharacteri 20.3 19 0.00041 28.0 -1.4 40 187-226 41-81 (158)
305 PF11494 Ta0938: Ta0938; Inte 20.1 58 0.0013 23.0 1.1 36 152-198 15-50 (105)
No 1
>KOG2462|consensus
Probab=99.98 E-value=3.8e-33 Score=227.70 Aligned_cols=131 Identities=20% Similarity=0.338 Sum_probs=122.8
Q ss_pred CccccCCCchHH-----HHHHHHHHhhhhccccccCCCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhcc
Q psy3485 150 DQFFCIHCNGCV-----LYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224 (304)
Q Consensus 150 ~~~~C~~C~~~f-----l~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~ 224 (304)
.+|+|..||+.+ |.+|.+.||. -...+.|.|++|||.|.+.-+|..|+|+|+ -+++|.+|||.|.
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~--------~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRS--------LDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFS 198 (279)
T ss_pred Cceeccccccccccccccchhhccccc--------ccccccccCCCCCceeeehHHHhhHhhccC--CCccccccccccc
Confidence 459999999999 9999998832 334678999999999999999999999998 7799999999999
Q ss_pred CHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHHHHHh
Q psy3485 225 SKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYFIWIS 298 (304)
Q Consensus 225 ~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~~h~~ 298 (304)
..+.|+.|+| .| ||||||.|..|+|+|+.+++|+.||+||.+.+ +|+|+.|+|+|+.++.|-.|..
T Consensus 199 RPWLLQGHiR-TH-----TGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K--~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 199 RPWLLQGHIR-TH-----TGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK--KHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred chHHhhcccc-cc-----cCCCCccCCcccchhcchHHHHHHHHhhcCCc--cccCcchhhHHHHHHHHHHhhh
Confidence 9999999999 99 99999999999999999999999999999997 9999999999999999999975
No 2
>KOG2462|consensus
Probab=99.94 E-value=3.6e-27 Score=192.80 Aligned_cols=112 Identities=21% Similarity=0.402 Sum_probs=104.6
Q ss_pred CCCCCcccCCCcccccChHHHHHHHHhhCC---CCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccC
Q psy3485 181 PMRRNFMCFACPYYCRYGSSMAIHLRTHTK---EKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTS 257 (304)
Q Consensus 181 ~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~---~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F 257 (304)
.....|+|+.||+.+.+.++|.+|..+|.. .+.+.|.+|||.|.+..+|..|+| +| + -+++|.+|||.|
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHir-TH-----~--l~c~C~iCGKaF 197 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIR-TH-----T--LPCECGICGKAF 197 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhh-cc-----C--CCcccccccccc
Confidence 345679999999999999999999999963 577999999999999999999999 77 4 689999999999
Q ss_pred CChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHHHHHhhccc
Q psy3485 258 PTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYFIWISVDVN 302 (304)
Q Consensus 258 ~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~~h~~~~~~ 302 (304)
.+.+-|.-|+|+|+|++ ||.|++|+|.|+.++||+.||++|++
T Consensus 198 SRPWLLQGHiRTHTGEK--PF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 198 SRPWLLQGHIRTHTGEK--PFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred cchHHhhcccccccCCC--CccCCcccchhcchHHHHHHHHhhcC
Confidence 99999999999999997 99999999999999999999999986
No 3
>KOG1074|consensus
Probab=99.86 E-value=4.8e-23 Score=189.79 Aligned_cols=53 Identities=11% Similarity=0.135 Sum_probs=51.0
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHHHHHhhcc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~~h~~~~~ 301 (304)
...|..||+.|.+.++|..|||+|++++ ||.|.+|++.|.++.+|.+|+.+|.
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~K--PF~C~fC~~aFttrgnLKvHMgtH~ 931 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPK--PFFCHFCEEAFTTRGNLKVHMGTHM 931 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCC--Cccchhhhhhhhhhhhhhhhhcccc
Confidence 3899999999999999999999999997 9999999999999999999999985
No 4
>KOG1074|consensus
Probab=99.84 E-value=1.8e-22 Score=186.00 Aligned_cols=83 Identities=20% Similarity=0.329 Sum_probs=76.8
Q ss_pred cccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCCC--CCcccC---CCccccc
Q psy3485 214 FACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTS--GPTIQP---ECIKILW 288 (304)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~--~~~~C~---~C~k~F~ 288 (304)
-+|-+|.++..-++.|+.|.| .| +|||||+|.+||+.|.++.+|+.||-+|.-.-. -+|.|+ +|-+-|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyr-tH-----tGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYR-TH-----TGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred cceeeeeecccchhhhhhhhh-cc-----cCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccc
Confidence 479999999999999999999 88 999999999999999999999999988877641 258999 9999999
Q ss_pred chhHHHHHHhhccc
Q psy3485 289 SFLSYFIWISVDVN 302 (304)
Q Consensus 289 ~~~~l~~h~~~~~~ 302 (304)
+.-.|-+|||+|.+
T Consensus 680 n~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 680 NAVTLPQHIRIHLG 693 (958)
T ss_pred ccccccceEEeecC
Confidence 99999999999984
No 5
>KOG3576|consensus
Probab=99.82 E-value=2.4e-21 Score=150.97 Aligned_cols=118 Identities=23% Similarity=0.406 Sum_probs=89.4
Q ss_pred CCccccCCCchHH-HHHHHHHHhhhhccccccCCCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHH
Q psy3485 149 DDQFFCIHCNGCV-LYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKI 227 (304)
Q Consensus 149 ~~~~~C~~C~~~f-l~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~ 227 (304)
+..|.|.+|||.| |++=+.+| ++-|...+.+-|..|||.|.....|.+|+|+|+|.+||+|..|+|.|+.+.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh-------~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrc 187 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRH-------LKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRC 187 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHH-------hhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhc
Confidence 3458888888888 66666666 667777788888888888888888888888888888888888888888888
Q ss_pred HHHHHHHhhcCCC-----CCCCCCccccccCCccCCChHHHHHHHHhhcCC
Q psy3485 228 AIYAHMRTTHIMP-----DTSEERRYHCAFCNFTSPTQWAINRHTKYTHMN 273 (304)
Q Consensus 228 ~L~~H~~~~H~~~-----~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~ 273 (304)
.|..|.+.+|+++ ....++.|+|+.||.+-.....+-.|.+.||.-
T Consensus 188 sleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 188 SLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred cHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 8888887777543 112346677777777777777777777777765
No 6
>KOG3608|consensus
Probab=99.82 E-value=1.5e-20 Score=158.00 Aligned_cols=166 Identities=23% Similarity=0.451 Sum_probs=134.5
Q ss_pred hhhHhHHHHHHhhcCCCCCCCCc-cccCCCchHH-----HHHHHHHH---------hhhhccc------cccCCC--CCC
Q psy3485 129 KQLMAIEEKIKAARHPLFSPDDQ-FFCIHCNGCV-----LYADLLDH---------CKLCLRR------KRKNPM--RRN 185 (304)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~~~~~~-~~C~~C~~~f-----l~~H~~~h---------C~~C~~~------~~~h~~--~~~ 185 (304)
.+...++.+..+.+|.+.|+++. ..|+.||..| |.-|+++- |..|.|+ +..|.. ..-
T Consensus 184 ~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ 263 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNC 263 (467)
T ss_pred hhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhc
Confidence 34556677788899988888775 7899999999 66676655 8888776 222211 245
Q ss_pred cccCCCcccccChHHHHHHHHh-hCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCcccccc--CCccCCChHH
Q psy3485 186 FMCFACPYYCRYGSSMAIHLRT-HTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAF--CNFTSPTQWA 262 (304)
Q Consensus 186 ~~C~~C~k~f~~~~~l~~H~~~-H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~--C~k~F~~~~~ 262 (304)
|.|+.|+.+....++|..|++. |...|||+|+.|++.|.+.+.|.+|.. +| + +-.|.|.. |..+|++...
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~-~H-----S-~~~y~C~h~~C~~s~r~~~q 336 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ-VH-----S-KTVYQCEHPDCHYSVRTYTQ 336 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH-hc-----c-ccceecCCCCCcHHHHHHHH
Confidence 8999999999999999999885 899999999999999999999999999 88 5 56799988 9999999999
Q ss_pred HHHHHHhhc-CCCCCCcccCCCcccccchhHHHHHHhhcc
Q psy3485 263 INRHTKYTH-MNTSGPTIQPECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 263 L~~H~r~h~-~~~~~~~~C~~C~k~F~~~~~l~~h~~~~~ 301 (304)
|++|++-|| |....+|.|..|.+.|.+-.+|-+|.+-.+
T Consensus 337 ~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 337 MRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred HHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhh
Confidence 999998888 555567999999999999999999986443
No 7
>KOG3576|consensus
Probab=99.81 E-value=1.3e-20 Score=146.85 Aligned_cols=117 Identities=19% Similarity=0.360 Sum_probs=109.1
Q ss_pred cCCCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCC
Q psy3485 179 KNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSP 258 (304)
Q Consensus 179 ~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~ 258 (304)
.-.+...|.|.+|+|.|.....|.+|++.|...++|-|..|||.|.....|++|+| +| +|.+||+|..|+|+|.
T Consensus 111 sssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~r-th-----tgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 111 SSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTR-TH-----TGVRPYKCSLCEKAFT 184 (267)
T ss_pred CCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhc-cc-----cCccccchhhhhHHHH
Confidence 33456779999999999999999999999999999999999999999999999999 88 9999999999999999
Q ss_pred ChHHHHHHHHhhcCCC---------CCCcccCCCcccccchhHHHHHHhhcc
Q psy3485 259 TQWAINRHTKYTHMNT---------SGPTIQPECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 259 ~~~~L~~H~r~h~~~~---------~~~~~C~~C~k~F~~~~~l~~h~~~~~ 301 (304)
.+-+|..|.+..||.. .+.|.|+.||.+-...--++.|+.+|+
T Consensus 185 qrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 185 QRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred hhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcC
Confidence 9999999999999986 246999999999999999999999875
No 8
>KOG3608|consensus
Probab=99.76 E-value=4.6e-19 Score=149.14 Aligned_cols=140 Identities=16% Similarity=0.350 Sum_probs=102.0
Q ss_pred cccCC--CchHH-----HHHHHHHH-------hhhhccc------------cccCCCCCCcccCCCcccccChHHHHHHH
Q psy3485 152 FFCIH--CNGCV-----LYADLLDH-------CKLCLRR------------KRKNPMRRNFMCFACPYYCRYGSSMAIHL 205 (304)
Q Consensus 152 ~~C~~--C~~~f-----l~~H~~~h-------C~~C~~~------------~~~h~~~~~~~C~~C~k~f~~~~~l~~H~ 205 (304)
+.|.. |.+.| |++|++.| |+.|+.. ...-....+|+|.+|-|.|.+..+|..|+
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv 257 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHV 257 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHH
Confidence 67764 77777 88888877 7777654 22223345677777777777777777777
Q ss_pred HhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCC--C
Q psy3485 206 RTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPE--C 283 (304)
Q Consensus 206 ~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~--C 283 (304)
++|-+- |+|+.|+.+....+.|..||+..| ...|||+|+.|+++|.+-+.|.+|..+|+.. -|.|+. |
T Consensus 258 ~rHvn~--ykCplCdmtc~~~ssL~~H~r~rH-----s~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~---~y~C~h~~C 327 (467)
T KOG3608|consen 258 VRHVNC--YKCPLCDMTCSSASSLTTHIRYRH-----SKDKPFKCDECDTRCVRESDLAKHVQVHSKT---VYQCEHPDC 327 (467)
T ss_pred HHhhhc--ccccccccCCCChHHHHHHHHhhh-----ccCCCccccchhhhhccHHHHHHHHHhcccc---ceecCCCCC
Confidence 777543 777777777777777777777777 7777788887888887778888887777743 577777 7
Q ss_pred cccccchhHHHHHHhhcc
Q psy3485 284 IKILWSFLSYFIWISVDV 301 (304)
Q Consensus 284 ~k~F~~~~~l~~h~~~~~ 301 (304)
..+|.+..+|+.|++-|.
T Consensus 328 ~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 328 HYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred cHHHHHHHHHHHHHHHhc
Confidence 777777777777776544
No 9
>KOG3623|consensus
Probab=99.71 E-value=2.9e-18 Score=156.13 Aligned_cols=111 Identities=23% Similarity=0.376 Sum_probs=96.8
Q ss_pred CcccCCCcccccChHHHHHHHHh-h-CCCCccccccchhhccCHHHHHHHHHhhcCCCCC--------CCCCccccccCC
Q psy3485 185 NFMCFACPYYCRYGSSMAIHLRT-H-TKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDT--------SEERRYHCAFCN 254 (304)
Q Consensus 185 ~~~C~~C~k~f~~~~~l~~H~~~-H-~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~--------~~~~~~~C~~C~ 254 (304)
...|++|++.+.+...|+.|++. | .++..|.|..|..+|..+..|.+||. .|...++ .+-|+|+|+.||
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~-~hkpg~dqa~sltqsa~lRKFKCtECg 288 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQ-LHKPGGDQAISLTQSALLRKFKCTECG 288 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHH-hhcCCCcccccccchhhhccccccccc
Confidence 36899999999999999999764 5 46677999999999999999999999 7753322 235889999999
Q ss_pred ccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHHHHHh
Q psy3485 255 FTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYFIWIS 298 (304)
Q Consensus 255 k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~~h~~ 298 (304)
|.|+.+..|+.|.|+|.|++ ||.|+-|+|.|+...++-.||+
T Consensus 289 KAFKfKHHLKEHlRIHSGEK--PfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 289 KAFKFKHHLKEHLRIHSGEK--PFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhhhHHHHHhhheeecCCC--CcCCcccccccccCCccccccc
Confidence 99999999999999999997 9999999999999999999986
No 10
>KOG3623|consensus
Probab=99.68 E-value=7.3e-18 Score=153.58 Aligned_cols=80 Identities=24% Similarity=0.431 Sum_probs=65.3
Q ss_pred CCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChH
Q psy3485 182 MRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQW 261 (304)
Q Consensus 182 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~ 261 (304)
...+|.|++|+|.|...++|.+|...|+|.|||+|.+|.|.|+.+..|..|+| .| .|||||+|+.|+|+|.+..
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkR-LH-----SGEKPfQCdKClKRFSHSG 964 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKR-LH-----SGEKPFQCDKCLKRFSHSG 964 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhh-hc-----cCCCcchhhhhhhhccccc
Confidence 35678888888888888888888888888888888888888888888888888 77 8888888888888888888
Q ss_pred HHHHHH
Q psy3485 262 AINRHT 267 (304)
Q Consensus 262 ~L~~H~ 267 (304)
++.+||
T Consensus 965 SYSQHM 970 (1007)
T KOG3623|consen 965 SYSQHM 970 (1007)
T ss_pred chHhhh
Confidence 888887
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.56 E-value=1.1e-14 Score=133.73 Aligned_cols=133 Identities=17% Similarity=0.285 Sum_probs=110.3
Q ss_pred ccccCCCchHHHHHHHHHH----------hhh--hccccccCCCCCCcccCCCcccccChHHHHHHHHhhCCCCcccccc
Q psy3485 151 QFFCIHCNGCVLYADLLDH----------CKL--CLRRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEM 218 (304)
Q Consensus 151 ~~~C~~C~~~fl~~H~~~h----------C~~--C~~~~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~ 218 (304)
.-.|..|......+++..| |+. |+.......-+..+.|+.|++.|. ...|..|++.|+ +++.|+
T Consensus 407 ~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp- 482 (567)
T PLN03086 407 TVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP- 482 (567)
T ss_pred eEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-
Confidence 3689999998855555555 653 888877777788899999999996 678999999975 889999
Q ss_pred chhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCC----------ChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 219 CNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSP----------TQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 219 C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~----------~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
||+.| .+..|..|+. .| ...+++.|..|++.|. ..+.|..|..+. |.. ++.|..||+.|.
T Consensus 483 Cg~~~-~R~~L~~H~~-th-----Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~r--t~~C~~Cgk~Vr 552 (567)
T PLN03086 483 CGVVL-EKEQMVQHQA-ST-----CPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSR--TAPCDSCGRSVM 552 (567)
T ss_pred CCCCc-chhHHHhhhh-cc-----CCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCc--ceEccccCCeee
Confidence 99755 6799999998 88 9999999999999995 246899999986 664 999999999998
Q ss_pred chhHHHHHHh
Q psy3485 289 SFLSYFIWIS 298 (304)
Q Consensus 289 ~~~~l~~h~~ 298 (304)
.+. |..|+.
T Consensus 553 lrd-m~~H~~ 561 (567)
T PLN03086 553 LKE-MDIHQI 561 (567)
T ss_pred ehh-HHHHHH
Confidence 775 555543
No 12
>PHA00733 hypothetical protein
Probab=99.43 E-value=1.9e-13 Score=103.18 Aligned_cols=86 Identities=14% Similarity=0.234 Sum_probs=59.7
Q ss_pred CCCccccccchhhccCHHHHHHH--HHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccc
Q psy3485 210 KEKPFACEMCNYRAASKIAIYAH--MRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287 (304)
Q Consensus 210 ~~~~~~C~~C~k~F~~~~~L~~H--~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F 287 (304)
..+++.|.+|.+.|.+...|..| ++ .|. ...+.+||.|+.||+.|.+.++|..|++.| .. +|.|+.|++.|
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~-~~~--~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~--~~~C~~CgK~F 109 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLY-KLL--TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EH--SKVCPVCGKEF 109 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHH-hhc--ccCCCCCccCCCCCCcCCCHHHHHHHHhcC--Cc--CccCCCCCCcc
Confidence 35667777777777777666665 22 110 114577888888888888888888888776 22 68888888888
Q ss_pred cchhHHHHHHhhccc
Q psy3485 288 WSFLSYFIWISVDVN 302 (304)
Q Consensus 288 ~~~~~l~~h~~~~~~ 302 (304)
...++|..|+.-.+|
T Consensus 110 ~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 110 RNTDSTLDHVCKKHN 124 (128)
T ss_pred CCHHHHHHHHHHhcC
Confidence 888888888775544
No 13
>PHA00733 hypothetical protein
Probab=99.31 E-value=2.2e-12 Score=97.44 Aligned_cols=85 Identities=14% Similarity=0.230 Sum_probs=70.6
Q ss_pred CCCCCcccCCCcccccChHHHHHH--HHh---hCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCc
Q psy3485 181 PMRRNFMCFACPYYCRYGSSMAIH--LRT---HTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNF 255 (304)
Q Consensus 181 ~~~~~~~C~~C~k~f~~~~~l~~H--~~~---H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k 255 (304)
...+++.|.+|.+.|.....|..| ++. +.+.+||.|+.||+.|.+.+.|..|++ .| + .+|.|..|++
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r-~h-----~--~~~~C~~CgK 107 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIR-YT-----E--HSKVCPVCGK 107 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHh-cC-----C--cCccCCCCCC
Confidence 345778999999999888777776 332 445889999999999999999999999 55 3 4799999999
Q ss_pred cCCChHHHHHHHHhhcCC
Q psy3485 256 TSPTQWAINRHTKYTHMN 273 (304)
Q Consensus 256 ~F~~~~~L~~H~r~h~~~ 273 (304)
+|.....|.+|++..|+.
T Consensus 108 ~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 108 EFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred ccCCHHHHHHHHHHhcCc
Confidence 999999999999988874
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.29 E-value=1.1e-12 Score=81.72 Aligned_cols=44 Identities=18% Similarity=0.314 Sum_probs=38.8
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHH
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYF 294 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~ 294 (304)
.|.|+.||+.|...++|..|||+|+ + +|+|..|++.|+.++.|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k--~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--T--NLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--C--cccCCcccceecccceeE
Confidence 4899999999999999999999988 3 899999999999888775
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.21 E-value=2.4e-11 Score=111.90 Aligned_cols=102 Identities=15% Similarity=0.279 Sum_probs=79.6
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhcc-------
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA------- 224 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~------- 224 (304)
+.|+.|++.|....+..| +..|. .++.|+ ||+.| .+..|..|+.+|.+.+++.|..|++.|.
T Consensus 454 ~~C~~Cgk~f~~s~LekH-------~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d 522 (567)
T PLN03086 454 VHCEKCGQAFQQGEMEKH-------MKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMD 522 (567)
T ss_pred ccCCCCCCccchHHHHHH-------HHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccc
Confidence 567777777722222232 23332 789999 99765 6789999999999999999999999995
Q ss_pred ---CHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcC
Q psy3485 225 ---SKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHM 272 (304)
Q Consensus 225 ---~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~ 272 (304)
..+.|..|.. . .|.+++.|..||+.|..+ .|..|+...|.
T Consensus 523 ~~d~~s~Lt~HE~-~------CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 523 VRDRLRGMSEHES-I------CGSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred hhhhhhhHHHHHH-h------cCCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 2468999998 6 588999999999998776 78889877665
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.14 E-value=1.6e-11 Score=76.57 Aligned_cols=40 Identities=23% Similarity=0.316 Sum_probs=19.0
Q ss_pred cccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHH
Q psy3485 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKI 227 (304)
Q Consensus 186 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~ 227 (304)
|.|+.||+.|+...+|..|+++|+ ++|+|..|++.|...+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTG 45 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccc
Confidence 444444444444444444444444 3444444444444433
No 17
>KOG3993|consensus
Probab=99.00 E-value=1.2e-10 Score=101.09 Aligned_cols=135 Identities=13% Similarity=0.160 Sum_probs=101.2
Q ss_pred cccCCCchHH-----HHHHHHHHhhhhccccccCCCCCCcccCCCcccccChHHHHHHHHhhC--------CC-------
Q psy3485 152 FFCIHCNGCV-----LYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHT--------KE------- 211 (304)
Q Consensus 152 ~~C~~C~~~f-----l~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~--------~~------- 211 (304)
|.|..|...| |.+|.=- .-+| .-|+|+.|+|.|+-.++|..|.|.|. +.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~--------RIV~---vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~ 336 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCP--------RIVH---VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAV 336 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCC--------eeEE---eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhh
Confidence 9999999888 6666421 2233 34999999999999999999999983 11
Q ss_pred ------------------CccccccchhhccCHHHHHHHHHhhcCCCCC-------------------------------
Q psy3485 212 ------------------KPFACEMCNYRAASKIAIYAHMRTTHIMPDT------------------------------- 242 (304)
Q Consensus 212 ------------------~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~------------------------------- 242 (304)
..|.|.+|+|.|+....|+.|+.++|..+..
T Consensus 337 ~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~ 416 (500)
T KOG3993|consen 337 ETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDS 416 (500)
T ss_pred hhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccc
Confidence 2389999999999999999999866642100
Q ss_pred -C--------CCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHHHHHhh
Q psy3485 243 -S--------EERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYFIWISV 299 (304)
Q Consensus 243 -~--------~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~~h~~~ 299 (304)
. ..-...|++||-.|.++..=-.|.|.-+-.+ -|.|.+|.-+|.+...|-+||..
T Consensus 417 ~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q--~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 417 HGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQ--GFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred cccceeeeeccccccCCCCCCCCcccCCCCCccccccchhh--ccccccchHhhhcCcchHhHhhh
Confidence 0 0122456777777777766666665555554 69999999999999999999975
No 18
>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=98.89 E-value=1e-09 Score=58.60 Aligned_cols=26 Identities=23% Similarity=0.318 Sum_probs=17.1
Q ss_pred HHHHHHHhhcCCCCCCcccCCCcccccc
Q psy3485 262 AINRHTKYTHMNTSGPTIQPECIKILWS 289 (304)
Q Consensus 262 ~L~~H~r~h~~~~~~~~~C~~C~k~F~~ 289 (304)
+|++|+++|++++ ||.|++|++.|++
T Consensus 1 ~l~~H~~~H~~~k--~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEK--PYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSS--SEEESSSSEEESS
T ss_pred CHHHHhhhcCCCC--CCCCCCCcCeeCc
Confidence 4666777766665 6777777776653
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=98.86 E-value=1.3e-09 Score=58.21 Aligned_cols=24 Identities=42% Similarity=0.854 Sum_probs=11.2
Q ss_pred HHHHHHhhCCCCccccccchhhcc
Q psy3485 201 MAIHLRTHTKEKPFACEMCNYRAA 224 (304)
Q Consensus 201 l~~H~~~H~~~~~~~C~~C~k~F~ 224 (304)
|..|+++|+|++||+|++|++.|.
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 444444444444444444444443
No 20
>PHA00732 hypothetical protein
Probab=98.83 E-value=2.6e-09 Score=73.20 Aligned_cols=50 Identities=24% Similarity=0.499 Sum_probs=35.0
Q ss_pred ccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCC
Q psy3485 213 PFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMN 273 (304)
Q Consensus 213 ~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~ 273 (304)
||+|..||+.|.+...|..|++.+| . ++.|+.||++|. .|..|.+++.+-
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H-----~---~~~C~~CgKsF~---~l~~H~~~~~~~ 50 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH-----T---LTKCPVCNKSYR---RLNQHFYSQYDI 50 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc-----C---CCccCCCCCEeC---ChhhhhcccCCc
Confidence 4777888888888888888877445 3 356788888777 467777665553
No 21
>PHA00616 hypothetical protein
Probab=98.71 E-value=5.9e-09 Score=61.86 Aligned_cols=39 Identities=13% Similarity=0.109 Sum_probs=30.2
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F 287 (304)
||+|..||+.|..+++|+.|++.||+.. ++.|++=-..|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~--~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQN--KLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCC--ccceeEEEEEE
Confidence 5788888888888888888888888886 88777644333
No 22
>PHA00732 hypothetical protein
Probab=98.71 E-value=9e-09 Score=70.55 Aligned_cols=36 Identities=28% Similarity=0.478 Sum_probs=17.4
Q ss_pred cccCCCcccccChHHHHHHHHh-hCCCCccccccchhhcc
Q psy3485 186 FMCFACPYYCRYGSSMAIHLRT-HTKEKPFACEMCNYRAA 224 (304)
Q Consensus 186 ~~C~~C~k~f~~~~~l~~H~~~-H~~~~~~~C~~C~k~F~ 224 (304)
|.|+.|++.|.+..+|..|++. |.+ +.|+.||+.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 4455555555555555555442 332 34555555554
No 23
>KOG3993|consensus
Probab=98.67 E-value=3.7e-09 Score=91.93 Aligned_cols=88 Identities=17% Similarity=0.319 Sum_probs=71.1
Q ss_pred CCcccCCCcccccChHHHHHHHH--h-hCCCCccccccchhhccCHHHHHHHHHhhcCCCCC------------------
Q psy3485 184 RNFMCFACPYYCRYGSSMAIHLR--T-HTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDT------------------ 242 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~~H~~--~-H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~------------------ 242 (304)
.-|.|..|--.|-....|.+|.- + |- -|+|..|+|.|+-..+|-.|.|||-.-+..
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~v---EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~ 342 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHV---EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEV 342 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEe---eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhh
Confidence 45999999999999999999943 3 43 399999999999999999999954321100
Q ss_pred ---------CCCCccccccCCccCCChHHHHHHHHhhcCCC
Q psy3485 243 ---------SEERRYHCAFCNFTSPTQWAINRHTKYTHMNT 274 (304)
Q Consensus 243 ---------~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~ 274 (304)
.....|.|.+|+|.|++...|+.|+.+|+...
T Consensus 343 ~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 343 QEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 12246999999999999999999999988754
No 24
>PHA00616 hypothetical protein
Probab=98.61 E-value=1.8e-08 Score=59.77 Aligned_cols=35 Identities=20% Similarity=0.334 Sum_probs=23.8
Q ss_pred CcccCCCcccccChHHHHHHHHhhCCCCccccccc
Q psy3485 185 NFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMC 219 (304)
Q Consensus 185 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C 219 (304)
||+|..||+.|..++.|..|++.|+|+++++|+.-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 46677777777777777777777777777666643
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.56 E-value=1.2e-07 Score=60.40 Aligned_cols=51 Identities=25% Similarity=0.496 Sum_probs=22.1
Q ss_pred cccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhc
Q psy3485 214 FACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTH 271 (304)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~ 271 (304)
|.|++|++ ..+...|..|....|. .+.+.+.|++|...+. .+|.+|++.+|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~----~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHR----SESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCc----CCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 44555555 2333445555444441 1123345555554333 24455544444
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.47 E-value=2.6e-07 Score=58.87 Aligned_cols=52 Identities=13% Similarity=0.293 Sum_probs=35.6
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHHHHHhhcc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~~h~~~~~ 301 (304)
.|.|++|++ ..+..+|..|....|....+.+.||+|...+. .+|+.||..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 377888888 45566788886665555445678888887654 37788877665
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.32 E-value=2.8e-07 Score=47.67 Aligned_cols=22 Identities=23% Similarity=0.650 Sum_probs=10.7
Q ss_pred cccccCCccCCChHHHHHHHHh
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
|.|+.|++.|.++.+|++|++.
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 3444455555555555544444
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.28 E-value=5e-07 Score=46.71 Aligned_cols=23 Identities=17% Similarity=-0.034 Sum_probs=15.9
Q ss_pred cccCCCcccccchhHHHHHHhhc
Q psy3485 278 TIQPECIKILWSFLSYFIWISVD 300 (304)
Q Consensus 278 ~~C~~C~k~F~~~~~l~~h~~~~ 300 (304)
|.|+.|++.|+++++|..||++|
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 56777777777777777777654
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.13 E-value=1.3e-06 Score=63.33 Aligned_cols=75 Identities=15% Similarity=0.280 Sum_probs=21.4
Q ss_pred ccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHH
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRH 266 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H 266 (304)
+|..|+..|.+...|..|+...++-. .. ....+.....+..+++ . .-...+.|..|++.|.+...|..|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~---~~-~~~~l~~~~~~~~~~~-~------~~~~~~~C~~C~~~f~s~~~l~~H 69 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD---IP-DQKYLVDPNRLLNYLR-K------KVKESFRCPYCNKTFRSREALQEH 69 (100)
T ss_dssp -----------------------------------------------------------SSEEBSSSS-EESSHHHHHHH
T ss_pred Cccccccccccccccccccccccccc---cc-cccccccccccccccc-c------ccCCCCCCCccCCCCcCHHHHHHH
Confidence 47888888888888888886633321 11 2222334444444544 1 112368999999999999999999
Q ss_pred HHhhcC
Q psy3485 267 TKYTHM 272 (304)
Q Consensus 267 ~r~h~~ 272 (304)
|+.++.
T Consensus 70 m~~~~H 75 (100)
T PF12756_consen 70 MRSKHH 75 (100)
T ss_dssp HHHTTT
T ss_pred HcCccC
Confidence 987543
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=98.10 E-value=2.1e-06 Score=44.68 Aligned_cols=24 Identities=17% Similarity=0.580 Sum_probs=11.6
Q ss_pred cccccCCccCCChHHHHHHHHhhc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTH 271 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~ 271 (304)
|.|++|++.|.+...|+.|+++||
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 345555555555555555555543
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.02 E-value=1.3e-06 Score=73.56 Aligned_cols=59 Identities=22% Similarity=0.521 Sum_probs=43.3
Q ss_pred CCCcccccc--chhhccCHHHHHHHHHhhcCCC--------CC-----CCCCccccccCCccCCChHHHHHHHH
Q psy3485 210 KEKPFACEM--CNYRAASKIAIYAHMRTTHIMP--------DT-----SEERRYHCAFCNFTSPTQWAINRHTK 268 (304)
Q Consensus 210 ~~~~~~C~~--C~k~F~~~~~L~~H~~~~H~~~--------~~-----~~~~~~~C~~C~k~F~~~~~L~~H~r 268 (304)
++|||+|++ |.|.|++...|+.||+--|--+ .+ ...|||.|++|+|+|+.-..|+.|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 358899987 8899999999999988545211 11 12388888888888888888888853
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=97.98 E-value=3.3e-06 Score=45.44 Aligned_cols=24 Identities=21% Similarity=0.408 Sum_probs=12.0
Q ss_pred cccccCCccCCChHHHHHHHHhhc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTH 271 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~ 271 (304)
|.|..|++.|.+..+|..|++.|+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 445555555555555555554443
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.98 E-value=4.2e-06 Score=60.59 Aligned_cols=73 Identities=14% Similarity=0.052 Sum_probs=20.2
Q ss_pred ccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHH
Q psy3485 215 ACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYF 294 (304)
Q Consensus 215 ~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~ 294 (304)
+|..|+..|.+...|..||...|. - .-. ....+.....|..+.+.-... .+.|.+|++.|.+...|.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~-----~----~~~-~~~~l~~~~~~~~~~~~~~~~---~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHG-----F----DIP-DQKYLVDPNRLLNYLRKKVKE---SFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp ----------------------------------------------------------S---SEEBSSSS-EESSHHHHH
T ss_pred Cccccccccccccccccccccccc-----c----ccc-cccccccccccccccccccCC---CCCCCccCCCCcCHHHHH
Confidence 488899999999999999987882 1 111 222333555555565543333 589999999999999999
Q ss_pred HHHhhc
Q psy3485 295 IWISVD 300 (304)
Q Consensus 295 ~h~~~~ 300 (304)
.|++.+
T Consensus 68 ~Hm~~~ 73 (100)
T PF12756_consen 68 EHMRSK 73 (100)
T ss_dssp HHHHHT
T ss_pred HHHcCc
Confidence 999854
No 34
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.93 E-value=5.6e-06 Score=42.99 Aligned_cols=24 Identities=17% Similarity=-0.011 Sum_probs=20.5
Q ss_pred cccCCCcccccchhHHHHHHhhcc
Q psy3485 278 TIQPECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 278 ~~C~~C~k~F~~~~~l~~h~~~~~ 301 (304)
|.|++|++.|.++..|..|+++|+
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 689999999999999999999874
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.93 E-value=2.2e-06 Score=72.34 Aligned_cols=52 Identities=23% Similarity=0.561 Sum_probs=45.9
Q ss_pred CCCcccCC--CcccccChHHHHHHHHh-hC------------------CCCccccccchhhccCHHHHHHHHH
Q psy3485 183 RRNFMCFA--CPYYCRYGSSMAIHLRT-HT------------------KEKPFACEMCNYRAASKIAIYAHMR 234 (304)
Q Consensus 183 ~~~~~C~~--C~k~f~~~~~l~~H~~~-H~------------------~~~~~~C~~C~k~F~~~~~L~~H~~ 234 (304)
++||+|++ |+|.|.....|+.|+.- |. ..|||+|++|+|.|++...|+.|..
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 59999987 99999999999999765 51 3489999999999999999999987
No 36
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.89 E-value=6.2e-06 Score=44.34 Aligned_cols=25 Identities=20% Similarity=0.070 Sum_probs=23.6
Q ss_pred CcccCCCcccccchhHHHHHHhhcc
Q psy3485 277 PTIQPECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~~~~~ 301 (304)
+|.|..|++.|.+..+|+.|++.|.
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 6899999999999999999999885
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.56 E-value=5.4e-05 Score=39.87 Aligned_cols=23 Identities=22% Similarity=0.148 Sum_probs=12.5
Q ss_pred cccCCCcccccchhHHHHHHhhc
Q psy3485 278 TIQPECIKILWSFLSYFIWISVD 300 (304)
Q Consensus 278 ~~C~~C~k~F~~~~~l~~h~~~~ 300 (304)
|.|+.|++.|.+..+|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34555555555555555555544
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.49 E-value=0.0001 Score=38.71 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=15.2
Q ss_pred cccccCCccCCChHHHHHHHHhhc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTH 271 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~ 271 (304)
|.|..|+++|.+...|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 456666666666666666666543
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.45 E-value=6.1e-05 Score=45.76 Aligned_cols=32 Identities=19% Similarity=0.432 Sum_probs=20.4
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCCC
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMNT 274 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~ 274 (304)
..+.|-.|++|+..+.+..+|++|+..+|+.+
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 55667778888888888888888887777764
No 40
>PRK04860 hypothetical protein; Provisional
Probab=97.16 E-value=0.00024 Score=55.77 Aligned_cols=38 Identities=21% Similarity=0.334 Sum_probs=31.5
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccch
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSF 290 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~ 290 (304)
+|.|. |++ ....+++|.++|++++ +|.|..|++.|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~--~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEA--VYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCc--cEECCCCCceeEEe
Confidence 68898 887 7778899999999886 89999999888643
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.11 E-value=0.00027 Score=36.99 Aligned_cols=22 Identities=18% Similarity=0.561 Sum_probs=11.0
Q ss_pred cccccCCccCCChHHHHHHHHh
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
|.|.+|++.|.+...|+.|++.
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 3455555555555555555443
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.03 E-value=0.00053 Score=35.51 Aligned_cols=23 Identities=30% Similarity=0.854 Sum_probs=10.7
Q ss_pred cccccCCccCCChHHHHHHHHhhc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTH 271 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~ 271 (304)
|.|+.|+.+.. ...|.+|++.||
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 34555555544 555555555544
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.89 E-value=0.00055 Score=53.74 Aligned_cols=38 Identities=26% Similarity=0.599 Sum_probs=24.6
Q ss_pred ccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCCh
Q psy3485 213 PFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQ 260 (304)
Q Consensus 213 ~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~ 260 (304)
+|.|. |++ ....+.+|++ .| +++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~r-i~-----~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNR-VV-----RGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHH-Hh-----cCCccEECCCCCceeEEe
Confidence 46776 765 4555666777 55 677777777777766543
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.88 E-value=0.00053 Score=35.87 Aligned_cols=23 Identities=17% Similarity=-0.087 Sum_probs=21.1
Q ss_pred cccCCCcccccchhHHHHHHhhc
Q psy3485 278 TIQPECIKILWSFLSYFIWISVD 300 (304)
Q Consensus 278 ~~C~~C~k~F~~~~~l~~h~~~~ 300 (304)
|.|.+|++.|++...|..|++-+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999854
No 45
>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=96.84 E-value=0.0014 Score=39.94 Aligned_cols=30 Identities=20% Similarity=0.480 Sum_probs=15.9
Q ss_pred hCCCCccccccchhhccCHHHHHHHHHhhc
Q psy3485 208 HTKEKPFACEMCNYRAASKIAIYAHMRTTH 237 (304)
Q Consensus 208 H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H 237 (304)
+..+.|-+|++|+..+....+|++|+.+.|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHh
Confidence 344566666666666666666666666565
No 46
>KOG2231|consensus
Probab=96.84 E-value=0.0032 Score=59.77 Aligned_cols=89 Identities=18% Similarity=0.336 Sum_probs=57.4
Q ss_pred cccChHHHHHHHHh-hCCCCc----cccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCC------ccCCChHH
Q psy3485 194 YCRYGSSMAIHLRT-HTKEKP----FACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCN------FTSPTQWA 262 (304)
Q Consensus 194 ~f~~~~~l~~H~~~-H~~~~~----~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~------k~F~~~~~ 262 (304)
...++..|+.|+.. -.+++. -.|..|...|.....|.+|++..| |.|..|. .-|..-..
T Consensus 158 k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h----------~~chfC~~~~~~neyy~~~~d 227 (669)
T KOG2231|consen 158 KLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH----------EFCHFCDYKTGQNEYYNDYDD 227 (669)
T ss_pred ehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce----------eheeecCcccccchhcccchH
Confidence 34456677777664 223333 358888888888888888888666 6777774 34777778
Q ss_pred HHHHHHhhcCCCCCCcccC--CCccc-ccchhHHHHHHh
Q psy3485 263 INRHTKYTHMNTSGPTIQP--ECIKI-LWSFLSYFIWIS 298 (304)
Q Consensus 263 L~~H~r~h~~~~~~~~~C~--~C~k~-F~~~~~l~~h~~ 298 (304)
|..|.|.+|- .|+ .|--. |..--.+.++++
T Consensus 228 Le~HfR~~Hf------lCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 228 LEEHFRKGHF------LCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred HHHHhhhcCc------cccccccccceeeehhHHHHHHH
Confidence 8888877664 366 45433 333335555555
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.73 E-value=0.00041 Score=37.11 Aligned_cols=22 Identities=18% Similarity=0.442 Sum_probs=13.0
Q ss_pred cccccCCccCCChHHHHHHHHh
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
|.|..|++.|.+...|..|+++
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 4566666666666666666543
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.62 E-value=0.00026 Score=65.05 Aligned_cols=117 Identities=19% Similarity=0.259 Sum_probs=71.6
Q ss_pred CcccCCCcccccChHHHHHHHH--hhCCC--Cccccc--cchhhccCHHHHHHHHHhhcCCC------------------
Q psy3485 185 NFMCFACPYYCRYGSSMAIHLR--THTKE--KPFACE--MCNYRAASKIAIYAHMRTTHIMP------------------ 240 (304)
Q Consensus 185 ~~~C~~C~k~f~~~~~l~~H~~--~H~~~--~~~~C~--~C~k~F~~~~~L~~H~~~~H~~~------------------ 240 (304)
++.|..|...|+....|..|.+ .|.++ +++.|. .|++.|.....+..|.. .|...
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHIL-LHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcc-cccCCCccccccccCcccccccc
Confidence 4566666666666666666666 56666 666666 56666666666666666 33100
Q ss_pred ------------CCCCCCcccccc--CCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhHHHHHHhhccc
Q psy3485 241 ------------DTSEERRYHCAF--CNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLSYFIWISVDVN 302 (304)
Q Consensus 241 ------------~~~~~~~~~C~~--C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~l~~h~~~~~~ 302 (304)
.....+.+.|.. |-..+.....+..|...|-......+.+..|.+.|.....+..|++.|..
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTN 443 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCccccccccccccc
Confidence 001223344432 66666666666667666666554457778888888888888888887765
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.56 E-value=0.0016 Score=33.62 Aligned_cols=24 Identities=8% Similarity=-0.133 Sum_probs=19.7
Q ss_pred cccCCCcccccchhHHHHHHhhccc
Q psy3485 278 TIQPECIKILWSFLSYFIWISVDVN 302 (304)
Q Consensus 278 ~~C~~C~k~F~~~~~l~~h~~~~~~ 302 (304)
|+|+.|+.... ++.|..|+++|++
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 78999999998 9999999999764
No 50
>KOG2482|consensus
Probab=96.47 E-value=0.01 Score=51.11 Aligned_cols=23 Identities=22% Similarity=0.519 Sum_probs=19.0
Q ss_pred CcccCCCcccccChHHHHHHHHh
Q psy3485 185 NFMCFACPYYCRYGSSMAIHLRT 207 (304)
Q Consensus 185 ~~~C~~C~k~f~~~~~l~~H~~~ 207 (304)
.++|-.|-+.|..+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 37888888888888888888875
No 51
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.45 E-value=0.0011 Score=35.38 Aligned_cols=23 Identities=13% Similarity=-0.087 Sum_probs=20.7
Q ss_pred CcccCCCcccccchhHHHHHHhh
Q psy3485 277 PTIQPECIKILWSFLSYFIWISV 299 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~~~ 299 (304)
.|.|..|++.|.+...|..|++.
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCCcccCCCCcCCHHHHHHHHcc
Confidence 38899999999999999999874
No 52
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.02 E-value=0.026 Score=48.79 Aligned_cols=74 Identities=27% Similarity=0.551 Sum_probs=51.7
Q ss_pred ccCCCcccccChHHHHHHHHhhCCCCccccccchh-------hccCHHHHHHHHHhhcCCCCCCCCCcccccc--CC---
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNY-------RAASKIAIYAHMRTTHIMPDTSEERRYHCAF--CN--- 254 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k-------~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~--C~--- 254 (304)
.|..|...|..-..|..|+|.-+ -+|-+|++ .|.+-..|..|-+..| |.|.. |-
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H----E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----------y~ct~qtc~~~k 287 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH----EACHICDMVGPIRYQYFKSYEDLEAHFRNAH----------YCCTFQTCRVGK 287 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh----hhhhhhhccCccchhhhhCHHHHHHHhhcCc----------eEEEEEEEecCc
Confidence 68888888888888888877632 24555554 3777777888887555 66754 32
Q ss_pred -ccCCChHHHHHHHHhhcCCC
Q psy3485 255 -FTSPTQWAINRHTKYTHMNT 274 (304)
Q Consensus 255 -k~F~~~~~L~~H~r~h~~~~ 274 (304)
..|+....|..|....|++.
T Consensus 288 ~~vf~~~~el~~h~~~~h~~~ 308 (493)
T COG5236 288 CYVFPYHTELLEHLTRFHKVN 308 (493)
T ss_pred EEEeccHHHHHHHHHHHhhcc
Confidence 24788888888887777765
No 53
>KOG1146|consensus
Probab=96.01 E-value=0.0029 Score=63.63 Aligned_cols=111 Identities=16% Similarity=0.180 Sum_probs=81.1
Q ss_pred cCCCcccccChHHHHHHHHh-hCCCCccccccchhhccCHHHHHHHHHhhcCCC-------------------CCCCCCc
Q psy3485 188 CFACPYYCRYGSSMAIHLRT-HTKEKPFACEMCNYRAASKIAIYAHMRTTHIMP-------------------DTSEERR 247 (304)
Q Consensus 188 C~~C~k~f~~~~~l~~H~~~-H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~-------------------~~~~~~~ 247 (304)
|.-|+..+.++..+..|+.. |+-.+.|+|+.|+..|+....|-.|||..|... -..+.++
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p 518 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP 518 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc
Confidence 34455666666667777654 666688888888888888888888888756422 1134588
Q ss_pred cccccCCccCCChHHHHHHHHh--hcCC--------------------------------------C-CCCcccCCCccc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKY--THMN--------------------------------------T-SGPTIQPECIKI 286 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~--h~~~--------------------------------------~-~~~~~C~~C~k~ 286 (304)
|.|..|..+|..+.+|..|+.. |-.+ + .+.+.|..|+..
T Consensus 519 ~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~ye 598 (1406)
T KOG1146|consen 519 YPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYE 598 (1406)
T ss_pred ccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcch
Confidence 9999999999999999999853 1111 0 135899999998
Q ss_pred ccchhHHHHHHh
Q psy3485 287 LWSFLSYFIWIS 298 (304)
Q Consensus 287 F~~~~~l~~h~~ 298 (304)
-+-..+|.+|+.
T Consensus 599 tniarnlrihmt 610 (1406)
T KOG1146|consen 599 TNIARNLRIHMT 610 (1406)
T ss_pred hhhhhccccccc
Confidence 888888888874
No 54
>KOG2231|consensus
Probab=95.68 E-value=0.028 Score=53.61 Aligned_cols=105 Identities=15% Similarity=0.205 Sum_probs=73.6
Q ss_pred ccCCCcccccChHHHHHHHHh-hCCCCcccccc----------chhhccCHHHHHHHHHhhcCCCCCCCCCc-cccccCC
Q psy3485 187 MCFACPYYCRYGSSMAIHLRT-HTKEKPFACEM----------CNYRAASKIAIYAHMRTTHIMPDTSEERR-YHCAFCN 254 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~-H~~~~~~~C~~----------C~k~F~~~~~L~~H~~~~H~~~~~~~~~~-~~C~~C~ 254 (304)
.|..| -.|.+...|..|++. |.. +.|.. +.|.| +...|+.|+. .- .+.....+- -.|..|.
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Y-t~~el~~h~~-~g-d~d~~s~rGhp~C~~C~ 189 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLY-TRAELNLHLM-FG-DPDDESCRGHPLCKFCH 189 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehe-hHHHHHHHHh-cC-CCccccccCCccchhhh
Confidence 67888 888899999999965 643 33333 33444 4566778877 32 111122233 5899999
Q ss_pred ccCCChHHHHHHHHhhcCCCCCCccc---CCCcccccchhHHHHHHhhcc
Q psy3485 255 FTSPTQWAINRHTKYTHMNTSGPTIQ---PECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 255 k~F~~~~~L~~H~r~h~~~~~~~~~C---~~C~k~F~~~~~l~~h~~~~~ 301 (304)
..|-....|.+|++.+|.. -+.| +.++.-|..-..|-+|.+-++
T Consensus 190 ~~fld~~el~rH~~~~h~~---chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 190 ERFLDDDELYRHLRFDHEF---CHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hhhccHHHHHHhhccceeh---eeecCcccccchhcccchHHHHHhhhcC
Confidence 9999999999999998876 4555 334566888889999998654
No 55
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=95.66 E-value=0.0063 Score=35.98 Aligned_cols=38 Identities=11% Similarity=0.176 Sum_probs=25.0
Q ss_pred ccCCchHHHHHHHHHHHhhhhhhhhhhhhhhhhhcccc
Q psy3485 21 KKVNYPIIVARKMWTKLKKNHQNRNQKKMKSKTAKYWT 58 (304)
Q Consensus 21 ~~~~~p~~iC~~C~~~l~~f~~~~~~~~~~~~~~~~~~ 58 (304)
.+.|++..|.++.|..|+..+++++.++++++..+..+
T Consensus 2 tf~Dvav~fs~eEW~~L~~~Qk~ly~dvm~Eny~~l~s 39 (41)
T PF01352_consen 2 TFEDVAVYFSQEEWELLDPAQKNLYRDVMLENYRNLVS 39 (41)
T ss_dssp -----TT---HHHHHTS-HHHHHHHHHHHHHTTTS---
T ss_pred eEEEEEEEcChhhcccccceecccchhHHHHhhcccEe
Confidence 46789999999999999999999999999998887654
No 56
>KOG1146|consensus
Probab=95.65 E-value=0.0041 Score=62.58 Aligned_cols=80 Identities=15% Similarity=0.120 Sum_probs=68.0
Q ss_pred ccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCC--------------------
Q psy3485 215 ACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNT-------------------- 274 (304)
Q Consensus 215 ~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~-------------------- 274 (304)
.|.-|+..|..+..+..|+...| ...+.|+|+.|+-.|+....|-.|||..|-+-
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~-----S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~ 512 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLH-----SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVY 512 (1406)
T ss_pred cccchhhhhhhhcccccceeeee-----cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccc
Confidence 35567778888888999999888 77899999999999999999999999833221
Q ss_pred ---CCCcccCCCcccccchhHHHHHHhh
Q psy3485 275 ---SGPTIQPECIKILWSFLSYFIWISV 299 (304)
Q Consensus 275 ---~~~~~C~~C~k~F~~~~~l~~h~~~ 299 (304)
..+|.|..|..+|..+.+|.+|++-
T Consensus 513 ~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 513 RCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cCCCCcccceeeeeeeecchHHHHHHHH
Confidence 1479999999999999999999874
No 57
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.58 E-value=0.01 Score=30.93 Aligned_cols=20 Identities=10% Similarity=-0.114 Sum_probs=11.4
Q ss_pred cccCCCcccccchhHHHHHHh
Q psy3485 278 TIQPECIKILWSFLSYFIWIS 298 (304)
Q Consensus 278 ~~C~~C~k~F~~~~~l~~h~~ 298 (304)
..|+.||+.| ..++|-.|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566666666 4555555554
No 58
>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=95.55 E-value=0.0095 Score=33.80 Aligned_cols=22 Identities=9% Similarity=-0.111 Sum_probs=15.2
Q ss_pred CcccCCCcccccchhHHHHHHh
Q psy3485 277 PTIQPECIKILWSFLSYFIWIS 298 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~~ 298 (304)
+|.|++|++.|.+..++..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5667777777777777766664
No 59
>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=95.33 E-value=0.013 Score=33.27 Aligned_cols=23 Identities=26% Similarity=0.559 Sum_probs=19.4
Q ss_pred ccccccCCccCCChHHHHHHHHh
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
+|.|.+|++.|.+..++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999988888888754
No 60
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.14 E-value=0.019 Score=29.92 Aligned_cols=19 Identities=21% Similarity=0.487 Sum_probs=11.6
Q ss_pred ccccCCccCCChHHHHHHHH
Q psy3485 249 HCAFCNFTSPTQWAINRHTK 268 (304)
Q Consensus 249 ~C~~C~k~F~~~~~L~~H~r 268 (304)
.|+.||++| ....|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 566666666 5556666654
No 61
>KOG2785|consensus
Probab=94.79 E-value=0.1 Score=45.95 Aligned_cols=116 Identities=15% Similarity=0.055 Sum_probs=75.2
Q ss_pred CCCCCcccCCCcccccChHHHHHHHHh--hCCC--C-------------ccc-------------cccchhhccCHHHHH
Q psy3485 181 PMRRNFMCFACPYYCRYGSSMAIHLRT--HTKE--K-------------PFA-------------CEMCNYRAASKIAIY 230 (304)
Q Consensus 181 ~~~~~~~C~~C~k~f~~~~~l~~H~~~--H~~~--~-------------~~~-------------C~~C~k~F~~~~~L~ 230 (304)
.+.-++.|.+|+++|....+...|+.. |... + ... +..+-..+.......
T Consensus 64 ~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~~E~~~~~d~~~ 143 (390)
T KOG2785|consen 64 EAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKWYEVDSDEDSSE 143 (390)
T ss_pred hcccceehHHhhccccChhhHHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccchhhcccccccch
Confidence 345678999999999999999999764 4211 0 011 222222222211111
Q ss_pred HHHHhhcCCC--------CCCCCCccccccCCccCCChHHHHHHHHhhcCCC---------------------CCCcccC
Q psy3485 231 AHMRTTHIMP--------DTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNT---------------------SGPTIQP 281 (304)
Q Consensus 231 ~H~~~~H~~~--------~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~---------------------~~~~~C~ 281 (304)
.+.. - +.+ .....-|-.|-.|++.|.+--.-..||..+||-. ..-|.|=
T Consensus 144 e~~~-d-d~~Edi~~d~~~e~e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL 221 (390)
T KOG2785|consen 144 EEEE-D-DEEEDIEEDGDDEDELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICL 221 (390)
T ss_pred hhcc-C-cchhhhhhccchhcccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEE
Confidence 1111 0 000 0012345789999999999999999999999864 1248899
Q ss_pred CCc---ccccchhHHHHHHh
Q psy3485 282 ECI---KILWSFLSYFIWIS 298 (304)
Q Consensus 282 ~C~---k~F~~~~~l~~h~~ 298 (304)
.|+ +.|++--+...|+.
T Consensus 222 ~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 222 FCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred EeccccCcccccHHHHHHHh
Confidence 999 99999999999986
No 62
>KOG2785|consensus
Probab=94.54 E-value=0.08 Score=46.65 Aligned_cols=57 Identities=26% Similarity=0.457 Sum_probs=46.4
Q ss_pred ccccccchhhccCHHHHHHHHHhhcC--CCCC---------------CCCCccccccCC---ccCCChHHHHHHHHh
Q psy3485 213 PFACEMCNYRAASKIAIYAHMRTTHI--MPDT---------------SEERRYHCAFCN---FTSPTQWAINRHTKY 269 (304)
Q Consensus 213 ~~~C~~C~k~F~~~~~L~~H~~~~H~--~~~~---------------~~~~~~~C~~C~---k~F~~~~~L~~H~r~ 269 (304)
|-.|-.|++.|.+.-.-..||-..|+ +|+. .-..-|.|-.|+ +.|.+-.+.+.||+.
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 46799999999999999999998886 2211 012558999999 999999999999975
No 63
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.34 E-value=0.059 Score=39.25 Aligned_cols=84 Identities=13% Similarity=0.175 Sum_probs=51.2
Q ss_pred CccccccchhhccCHHHHHHHHHhhcCCCCC-C-------CCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCC
Q psy3485 212 KPFACEMCNYRAASKIAIYAHMRTTHIMPDT-S-------EERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPEC 283 (304)
Q Consensus 212 ~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~-~-------~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C 283 (304)
-|..|++||-+......|.+.- +|+.|-+ - ..+.-.|--|++.|........ ..-... ..|.|+.|
T Consensus 14 LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~--~~y~C~~C 87 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDS--HRYVCAVC 87 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccc--cceeCCCC
Confidence 4566777776666666665542 4543311 0 1111248889999876532110 001122 36999999
Q ss_pred cccccchhHHHHHHhhcc
Q psy3485 284 IKILWSFLSYFIWISVDV 301 (304)
Q Consensus 284 ~k~F~~~~~l~~h~~~~~ 301 (304)
.+.|=---..++|-.+|+
T Consensus 88 ~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 88 KNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCccccccchhhhhhccC
Confidence 999999999999988886
No 64
>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=94.22 E-value=0.038 Score=40.28 Aligned_cols=32 Identities=19% Similarity=0.314 Sum_probs=24.8
Q ss_pred CccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccch
Q psy3485 246 RRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSF 290 (304)
Q Consensus 246 ~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~ 290 (304)
.+..|+.||+.|.-- ++ .|..|+.||..|.-.
T Consensus 8 tKR~Cp~CG~kFYDL------------nk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL------------NK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccC------------CC-CCccCCCCCCccCcc
Confidence 456899999998754 33 489999999999654
No 65
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.03 E-value=0.049 Score=47.19 Aligned_cols=122 Identities=16% Similarity=0.198 Sum_probs=79.1
Q ss_pred cccCC------CchHH-HHHHHHHHhhhhccccccCCCCCCcccCCCcc---cc------cChHHHHHHHHhhCCCCcc-
Q psy3485 152 FFCIH------CNGCV-LYADLLDHCKLCLRRKRKNPMRRNFMCFACPY---YC------RYGSSMAIHLRTHTKEKPF- 214 (304)
Q Consensus 152 ~~C~~------C~~~f-l~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k---~f------~~~~~l~~H~~~H~~~~~~- 214 (304)
|.|+. |+-.| |..|+... +| .+-|.+|-+ .| -++..|..|...-..+.-|
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~---------H~----~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFK 218 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQ---------HG----FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFK 218 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhh---------cC----cEEhHhhhcCcccCccceeeeecccccccccCCccccCcC
Confidence 88864 55544 88888742 22 367777753 33 3455677776553333234
Q ss_pred ---ccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCc----cCCChHHHHHHHHhhcCCCCCCcccCC--C--
Q psy3485 215 ---ACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNF----TSPTQWAINRHTKYTHMNTSGPTIQPE--C-- 283 (304)
Q Consensus 215 ---~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k----~F~~~~~L~~H~r~h~~~~~~~~~C~~--C-- 283 (304)
.|..|...|..-..|.+|+|..| |+-|.|+.-+. -|+.-.+|.+|.+.- -|.|++ |
T Consensus 219 GHP~C~FC~~~FYdDDEL~~HcR~~H-------E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~------hy~ct~qtc~~ 285 (493)
T COG5236 219 GHPLCIFCKIYFYDDDELRRHCRLRH-------EACHICDMVGPIRYQYFKSYEDLEAHFRNA------HYCCTFQTCRV 285 (493)
T ss_pred CCchhhhccceecChHHHHHHHHhhh-------hhhhhhhccCccchhhhhCHHHHHHHhhcC------ceEEEEEEEec
Confidence 59999999999999999999777 44344433332 278888888886532 366765 4
Q ss_pred cc--cccchhHHHHHHhh
Q psy3485 284 IK--ILWSFLSYFIWISV 299 (304)
Q Consensus 284 ~k--~F~~~~~l~~h~~~ 299 (304)
|| .|...--|+.||.-
T Consensus 286 ~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 286 GKCYVFPYHTELLEHLTR 303 (493)
T ss_pred CcEEEeccHHHHHHHHHH
Confidence 33 37788888888853
No 66
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.81 E-value=0.012 Score=53.84 Aligned_cols=70 Identities=20% Similarity=0.361 Sum_probs=54.4
Q ss_pred CccccccchhhccCHHHHHHHHHh-hcCCCCCCCC--Cccccc--cCCccCCChHHHHHHHHhhcCCCCCCcccCC--Cc
Q psy3485 212 KPFACEMCNYRAASKIAIYAHMRT-THIMPDTSEE--RRYHCA--FCNFTSPTQWAINRHTKYTHMNTSGPTIQPE--CI 284 (304)
Q Consensus 212 ~~~~C~~C~k~F~~~~~L~~H~~~-~H~~~~~~~~--~~~~C~--~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~--C~ 284 (304)
.++.|..|...|.....|..|.+. .| +++ +++.|+ .|++.|.+...+..|..+|++.. ++.|.. |.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h-----~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 360 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNH-----SGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSIS--PAKEKLLNSS 360 (467)
T ss_pred cCCCCccccCCcccccccccccccccc-----ccccCCceeeeccCCCccccccccccCCcccccCCC--ccccccccCc
Confidence 468888888888888888888884 56 777 888888 78888888888888888888885 666655 44
Q ss_pred cccc
Q psy3485 285 KILW 288 (304)
Q Consensus 285 k~F~ 288 (304)
+.+.
T Consensus 361 ~~~~ 364 (467)
T COG5048 361 SKFS 364 (467)
T ss_pred cccc
Confidence 4443
No 67
>smart00868 zf-AD Zinc-finger associated domain (zf-AD). The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA.
Probab=93.27 E-value=0.13 Score=34.01 Aligned_cols=22 Identities=14% Similarity=0.096 Sum_probs=19.3
Q ss_pred cCCchHHHHHHHHHHHhhhhhh
Q psy3485 22 KVNYPIIVARKMWTKLKKNHQN 43 (304)
Q Consensus 22 ~~~~p~~iC~~C~~~l~~f~~~ 43 (304)
.+++|..||..||..|+.|+..
T Consensus 38 ~~~~p~~iC~~C~~~l~~~~~f 59 (73)
T smart00868 38 DDDLPKKICGDCLEKLESFYKF 59 (73)
T ss_pred CCCCcHHHHHHHHHHHHHHHHH
Confidence 4559999999999999999955
No 68
>KOG4173|consensus
Probab=93.16 E-value=0.048 Score=43.72 Aligned_cols=51 Identities=20% Similarity=0.374 Sum_probs=28.4
Q ss_pred ccCCCcccccChHHHHHHHHh-h---------CCCCcccccc--chhhccCHHHHHHHHHhhc
Q psy3485 187 MCFACPYYCRYGSSMAIHLRT-H---------TKEKPFACEM--CNYRAASKIAIYAHMRTTH 237 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~-H---------~~~~~~~C~~--C~k~F~~~~~L~~H~~~~H 237 (304)
.|..|.+.|.+.-.|-.|+-. | .|..-|.|-+ |+..|.+...-+.||-+.|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 566666666666666666443 3 2334455543 5555555555555555555
No 69
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.22 E-value=0.067 Score=33.23 Aligned_cols=31 Identities=19% Similarity=0.243 Sum_probs=22.6
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCC
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMN 273 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~ 273 (304)
.||--+.|+.||+-|..+.++.+|...-|+=
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 5677777888888888888888777655543
No 70
>PF07776 zf-AD: Zinc-finger associated domain (zf-AD) ; InterPro: IPR012934 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 zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 1PZW_A.
Probab=92.10 E-value=0.056 Score=36.19 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=19.3
Q ss_pred ccCCchHHHHHHHHHHHhhhhhh
Q psy3485 21 KKVNYPIIVARKMWTKLKKNHQN 43 (304)
Q Consensus 21 ~~~~~p~~iC~~C~~~l~~f~~~ 43 (304)
..+++|..||..||..|+.|+..
T Consensus 39 ~~~~lp~~IC~~C~~~l~~~~~F 61 (75)
T PF07776_consen 39 PDDDLPQQICSSCWEKLQQFYRF 61 (75)
T ss_dssp SS-SS-SEEEHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHH
Confidence 77889999999999999999955
No 71
>KOG4173|consensus
Probab=91.83 E-value=0.15 Score=40.92 Aligned_cols=84 Identities=20% Similarity=0.280 Sum_probs=55.1
Q ss_pred CCcccCC--CcccccChHHHHHHHHh-hCCCCccccccchhhccCHHHHHHHHHhhcCC----CCCCCCCcccccc--CC
Q psy3485 184 RNFMCFA--CPYYCRYGSSMAIHLRT-HTKEKPFACEMCNYRAASKIAIYAHMRTTHIM----PDTSEERRYHCAF--CN 254 (304)
Q Consensus 184 ~~~~C~~--C~k~f~~~~~l~~H~~~-H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~----~~~~~~~~~~C~~--C~ 254 (304)
+.|.|.+ |...|.....+..|..+ |+ -.|..|.+.|.+...|-.|+..-|.. .-..|.--|.|-. |+
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt 153 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCT 153 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhh
Confidence 4466665 66777777777777655 54 35888888888888888887765520 0002344578844 88
Q ss_pred ccCCChHHHHHHHHhhc
Q psy3485 255 FTSPTQWAINRHTKYTH 271 (304)
Q Consensus 255 k~F~~~~~L~~H~r~h~ 271 (304)
-.|.+...-++|+..-|
T Consensus 154 ~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 154 EKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhhhhHHHHhc
Confidence 88888888888875433
No 72
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.39 E-value=0.14 Score=32.39 Aligned_cols=9 Identities=33% Similarity=0.740 Sum_probs=4.3
Q ss_pred CcccCCCcc
Q psy3485 185 NFMCFACPY 193 (304)
Q Consensus 185 ~~~C~~C~k 193 (304)
.|.|+.||.
T Consensus 27 ~F~CPnCGe 35 (61)
T COG2888 27 KFPCPNCGE 35 (61)
T ss_pred EeeCCCCCc
Confidence 345555553
No 73
>KOG2186|consensus
Probab=91.14 E-value=0.12 Score=42.84 Aligned_cols=25 Identities=24% Similarity=0.328 Sum_probs=12.5
Q ss_pred CCcccCCCcccccChHHHHHHHHhhC
Q psy3485 184 RNFMCFACPYYCRYGSSMAIHLRTHT 209 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~~H~~~H~ 209 (304)
..|.|.-|++.|.. ..+..|...-+
T Consensus 28 ~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 28 AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred CeeEEeeccccccc-chhhhhhhhcc
Confidence 34555555555555 44555544443
No 74
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.08 E-value=0.12 Score=28.91 Aligned_cols=24 Identities=25% Similarity=0.823 Sum_probs=14.1
Q ss_pred cccCCCcccccChHHHHHHHHhhCCCCccccccchh
Q psy3485 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNY 221 (304)
Q Consensus 186 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k 221 (304)
|+|.+||..+.... .++.|++||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 56666666554432 5566666663
No 75
>KOG2893|consensus
Probab=90.95 E-value=0.055 Score=44.39 Aligned_cols=49 Identities=18% Similarity=0.415 Sum_probs=31.2
Q ss_pred CCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhc
Q psy3485 184 RNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTH 237 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H 237 (304)
++ .|=.|++.|....-|.+|++.-+ |+|.+|.|..-+--.|..|-..+|
T Consensus 10 kp-wcwycnrefddekiliqhqkakh----fkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 10 KP-WCWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred Cc-eeeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceeehhhhh
Confidence 44 35567777777777777766522 777777766555555655633355
No 76
>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=90.64 E-value=0.2 Score=37.14 Aligned_cols=33 Identities=12% Similarity=0.012 Sum_probs=24.1
Q ss_pred CccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchh
Q psy3485 246 RRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFL 291 (304)
Q Consensus 246 ~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~ 291 (304)
.+..|+.||+.|.-- ++ .|..|+.||..|.-..
T Consensus 8 tKr~Cp~cg~kFYDL------------nk-~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 8 TKRICPNTGSKFYDL------------NR-RPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccccCCCcCcccccc------------CC-CCccCCCcCCccCcch
Confidence 356899999888643 22 4889999999885553
No 77
>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=89.37 E-value=0.63 Score=34.05 Aligned_cols=26 Identities=19% Similarity=0.606 Sum_probs=23.8
Q ss_pred cccc----ccCCccCCChHHHHHHHHhhcC
Q psy3485 247 RYHC----AFCNFTSPTQWAINRHTKYTHM 272 (304)
Q Consensus 247 ~~~C----~~C~k~F~~~~~L~~H~r~h~~ 272 (304)
-|.| ..|+..+.+...+++|++.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999999886
No 78
>KOG2186|consensus
Probab=89.32 E-value=0.17 Score=42.04 Aligned_cols=47 Identities=17% Similarity=0.357 Sum_probs=29.1
Q ss_pred CcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHH
Q psy3485 185 NFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMR 234 (304)
Q Consensus 185 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~ 234 (304)
.|.|..||-+..-.. +.+|+.+-+| ..|.|-.|++.|-. .....|.+
T Consensus 3 ~FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 366777776655443 5556666555 55677777777766 55566665
No 79
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=89.29 E-value=0.073 Score=44.17 Aligned_cols=45 Identities=11% Similarity=0.153 Sum_probs=26.4
Q ss_pred CccccccCCccCCChHHHHHHHHh----------hcCCCC---CCcccCCCcccccch
Q psy3485 246 RRYHCAFCNFTSPTQWAINRHTKY----------THMNTS---GPTIQPECIKILWSF 290 (304)
Q Consensus 246 ~~~~C~~C~k~F~~~~~L~~H~r~----------h~~~~~---~~~~C~~C~k~F~~~ 290 (304)
+.+.|++|++.|.++.-+....|. ..+..+ ....||.||.+|...
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 456777777777776555544433 112210 125899999987654
No 80
>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=88.94 E-value=0.99 Score=33.01 Aligned_cols=25 Identities=16% Similarity=-0.041 Sum_probs=22.1
Q ss_pred ccc----CCCcccccchhHHHHHHhhccc
Q psy3485 278 TIQ----PECIKILWSFLSYFIWISVDVN 302 (304)
Q Consensus 278 ~~C----~~C~k~F~~~~~l~~h~~~~~~ 302 (304)
|.| ..|+..+.+..+|..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999988764
No 81
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.23 E-value=0.32 Score=27.97 Aligned_cols=32 Identities=16% Similarity=0.337 Sum_probs=14.2
Q ss_pred ccCCCcccccChHHHHHHHHhhCCCCccccccchhhc
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRA 223 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F 223 (304)
.|+.|+..|.-... +.-.+.+..+|..|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 45555555544432 122233345555555444
No 82
>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=88.01 E-value=0.3 Score=28.17 Aligned_cols=12 Identities=25% Similarity=0.362 Sum_probs=5.8
Q ss_pred ccCCCcccccCh
Q psy3485 187 MCFACPYYCRYG 198 (304)
Q Consensus 187 ~C~~C~k~f~~~ 198 (304)
.|+.|+..|.-.
T Consensus 4 ~CP~C~~~~~v~ 15 (38)
T TIGR02098 4 QCPNCKTSFRVV 15 (38)
T ss_pred ECCCCCCEEEeC
Confidence 455555554444
No 83
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=87.96 E-value=0.35 Score=27.61 Aligned_cols=12 Identities=17% Similarity=0.365 Sum_probs=5.5
Q ss_pred ccCCCcccccCh
Q psy3485 187 MCFACPYYCRYG 198 (304)
Q Consensus 187 ~C~~C~k~f~~~ 198 (304)
.|+.|+..|.-.
T Consensus 4 ~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 4 TCPNCQAKYEID 15 (36)
T ss_pred ECCCCCCEEeCC
Confidence 344444444443
No 84
>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=87.80 E-value=0.42 Score=26.92 Aligned_cols=26 Identities=19% Similarity=0.511 Sum_probs=17.3
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
.|.|..||..+.. .. .|..|++||..
T Consensus 2 ~~~C~~CG~i~~g-------------~~-~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEG-------------EE-APEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeEC-------------Cc-CCCcCcCCCCc
Confidence 4788888865332 22 37788888863
No 85
>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=87.52 E-value=0.42 Score=25.09 Aligned_cols=11 Identities=18% Similarity=0.169 Sum_probs=7.6
Q ss_pred cccCCCccccc
Q psy3485 278 TIQPECIKILW 288 (304)
Q Consensus 278 ~~C~~C~k~F~ 288 (304)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 45777777774
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=87.20 E-value=0.34 Score=35.34 Aligned_cols=15 Identities=20% Similarity=0.640 Sum_probs=7.6
Q ss_pred CccccccchhhccCH
Q psy3485 212 KPFACEMCNYRAASK 226 (304)
Q Consensus 212 ~~~~C~~C~k~F~~~ 226 (304)
.|..|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 445555555555443
No 87
>KOG2893|consensus
Probab=86.72 E-value=0.16 Score=41.78 Aligned_cols=41 Identities=20% Similarity=0.470 Sum_probs=24.8
Q ss_pred cccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHH
Q psy3485 216 CEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRH 266 (304)
Q Consensus 216 C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H 266 (304)
|=+|.+.|....-|..|++..| |+|.+|.|...+--.|.-|
T Consensus 13 cwycnrefddekiliqhqkakh----------fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH----------FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhhcc----------ceeeeehhhhccCCCceee
Confidence 5556666666666666666555 6666666665555555555
No 88
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.67 E-value=0.49 Score=30.06 Aligned_cols=8 Identities=38% Similarity=1.123 Sum_probs=4.0
Q ss_pred ccccccCC
Q psy3485 247 RYHCAFCN 254 (304)
Q Consensus 247 ~~~C~~C~ 254 (304)
+|.|+.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 45555554
No 89
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.65 E-value=0.4 Score=28.78 Aligned_cols=27 Identities=19% Similarity=0.240 Sum_probs=18.8
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
.|.|..||..|... .. .+.+|+.||..
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~--~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------SK--DVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------CC--CceECCCCCce
Confidence 37888888887744 22 27888888864
No 90
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=84.99 E-value=0.67 Score=28.60 Aligned_cols=21 Identities=19% Similarity=0.528 Sum_probs=13.5
Q ss_pred cccccCCccCCCh-----HHHHHHHH
Q psy3485 248 YHCAFCNFTSPTQ-----WAINRHTK 268 (304)
Q Consensus 248 ~~C~~C~k~F~~~-----~~L~~H~r 268 (304)
-.|.+|++.+... ++|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4677777766554 46666666
No 91
>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=84.77 E-value=0.85 Score=27.27 Aligned_cols=12 Identities=17% Similarity=0.526 Sum_probs=4.3
Q ss_pred cccccCCccCCC
Q psy3485 248 YHCAFCNFTSPT 259 (304)
Q Consensus 248 ~~C~~C~k~F~~ 259 (304)
..|.+|++.+..
T Consensus 17 a~C~~C~~~~~~ 28 (45)
T PF02892_consen 17 AKCKYCGKVIKY 28 (45)
T ss_dssp EEETTTTEE---
T ss_pred EEeCCCCeEEee
Confidence 344444444443
No 92
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.50 E-value=0.62 Score=29.03 Aligned_cols=28 Identities=18% Similarity=0.360 Sum_probs=13.6
Q ss_pred CCCccccccchhhccCHHHHHHHHHhhc
Q psy3485 210 KEKPFACEMCNYRAASKIAIYAHMRTTH 237 (304)
Q Consensus 210 ~~~~~~C~~C~k~F~~~~~L~~H~~~~H 237 (304)
|+--++|+.||..|.......+|....|
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4444455555555555555555544333
No 93
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=84.18 E-value=0.52 Score=37.08 Aligned_cols=37 Identities=16% Similarity=0.283 Sum_probs=29.2
Q ss_pred cccCCCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhh
Q psy3485 177 KRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYR 222 (304)
Q Consensus 177 ~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~ 222 (304)
+....+...|.|+.|+.+|+...++. ..|.|+.||..
T Consensus 101 l~~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 101 LEFETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred HhhccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 34455667899999999999988875 25999999966
No 94
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=84.16 E-value=0.8 Score=27.39 Aligned_cols=27 Identities=19% Similarity=0.422 Sum_probs=12.0
Q ss_pred CCccccccchhhccCH----HHHHHHHHhhc
Q psy3485 211 EKPFACEMCNYRAASK----IAIYAHMRTTH 237 (304)
Q Consensus 211 ~~~~~C~~C~k~F~~~----~~L~~H~~~~H 237 (304)
....+|..|++.+... +.|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3445566666665543 55666664343
No 95
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=83.73 E-value=0.14 Score=42.51 Aligned_cols=13 Identities=15% Similarity=0.777 Sum_probs=10.6
Q ss_pred cccccCCccCCCh
Q psy3485 248 YHCAFCNFTSPTQ 260 (304)
Q Consensus 248 ~~C~~C~k~F~~~ 260 (304)
.+|+.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5899999987754
No 96
>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=83.30 E-value=1.4 Score=34.59 Aligned_cols=34 Identities=15% Similarity=0.180 Sum_probs=25.6
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccc
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F 287 (304)
++..-|.|+.|+..|+.--++. . .|.|+.||...
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~--~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------L--NFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------c--CCcCCCCCCEe
Confidence 4556688888888888888775 1 58888888764
No 97
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.86 E-value=1.4 Score=31.69 Aligned_cols=28 Identities=14% Similarity=-0.132 Sum_probs=20.9
Q ss_pred cccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
-.|+.||+.|.-- ++ +|..|++||++|.
T Consensus 10 ridPetg~KFYDL------------Nr-dPiVsPytG~s~P 37 (129)
T COG4530 10 RIDPETGKKFYDL------------NR-DPIVSPYTGKSYP 37 (129)
T ss_pred ccCccccchhhcc------------CC-CccccCcccccch
Confidence 4688888888643 22 5899999999983
No 98
>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=82.73 E-value=0.72 Score=23.66 Aligned_cols=8 Identities=38% Similarity=0.874 Sum_probs=3.7
Q ss_pred CcccCCCc
Q psy3485 185 NFMCFACP 192 (304)
Q Consensus 185 ~~~C~~C~ 192 (304)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 44444444
No 99
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.62 E-value=1.1 Score=32.68 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=13.7
Q ss_pred CCccccccCCccCCChHHHHHHH
Q psy3485 245 ERRYHCAFCNFTSPTQWAINRHT 267 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~~H~ 267 (304)
...|.|+.|..-|=-.=+.-.|.
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ccceeCCCCCCccccccchhhhh
Confidence 34677777777666555554443
No 100
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.35 E-value=0.66 Score=37.26 Aligned_cols=34 Identities=18% Similarity=0.347 Sum_probs=24.0
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccc
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F 287 (304)
....-|.|+.|++.|+.--++. . .|.|+.||-..
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~---------~--~F~Cp~Cg~~L 146 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME---------Y--GFRCPQCGEML 146 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh---------c--CCcCCCCCCCC
Confidence 3445678888888888777663 2 58888888764
No 101
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.19 E-value=0.66 Score=28.38 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=18.2
Q ss_pred CCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 245 ERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
..-|.|..||+.|.. -... +...|++||..
T Consensus 4 ~~~Y~C~~Cg~~~~~----------~~~~--~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVEL----------DQET--RGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeeh----------hhcc--CceeCCCCCcE
Confidence 345888888888711 1111 36788888753
No 102
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.83 E-value=0.74 Score=36.99 Aligned_cols=36 Identities=19% Similarity=0.442 Sum_probs=27.5
Q ss_pred cCCCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhc
Q psy3485 179 KNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRA 223 (304)
Q Consensus 179 ~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F 223 (304)
.-.....|.|+.|+..|+...++. ..|.|+.||...
T Consensus 111 ~e~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 111 EEENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred hccCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 334456799999999999888763 359999999653
No 103
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=81.81 E-value=1.1 Score=27.59 Aligned_cols=25 Identities=12% Similarity=-0.136 Sum_probs=20.8
Q ss_pred CcccCCCcccccch-----hHHHHHHh-hcc
Q psy3485 277 PTIQPECIKILWSF-----LSYFIWIS-VDV 301 (304)
Q Consensus 277 ~~~C~~C~k~F~~~-----~~l~~h~~-~~~ 301 (304)
.-.|.+|++.++.. ++|..|+. +|-
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 46899999999665 79999999 664
No 104
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.73 E-value=0.75 Score=35.73 Aligned_cols=15 Identities=20% Similarity=0.414 Sum_probs=8.3
Q ss_pred CccccccCCccCCCh
Q psy3485 246 RRYHCAFCNFTSPTQ 260 (304)
Q Consensus 246 ~~~~C~~C~k~F~~~ 260 (304)
.-|.|+.|+..|..-
T Consensus 98 ~~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 98 AYYKCPNCQSKYTFL 112 (147)
T ss_pred cEEECcCCCCEeeHH
Confidence 345666666665543
No 105
>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=81.36 E-value=0.81 Score=34.65 Aligned_cols=27 Identities=26% Similarity=0.246 Sum_probs=17.3
Q ss_pred CCccccccCCccCCChHHHHHHHHhhcCCC
Q psy3485 245 ERRYHCAFCNFTSPTQWAINRHTKYTHMNT 274 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~ 274 (304)
..-..|-+|||.|+.- ++|.++|||-.
T Consensus 70 ~d~i~clecGk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EESBH---HHHHHHTT-S-
T ss_pred cCeeEEccCCcccchH---HHHHHHccCCC
Confidence 3447899999999874 99999998876
No 106
>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=80.30 E-value=0.4 Score=28.05 Aligned_cols=30 Identities=27% Similarity=0.354 Sum_probs=17.2
Q ss_pred cccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
|.|..||+.|.-.... ... ..-.|+.||..
T Consensus 6 y~C~~Cg~~fe~~~~~-------~~~--~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKI-------SDD--PLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEec-------CCC--CCCCCCCCCCc
Confidence 6777777776544222 112 25667777763
No 107
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=79.14 E-value=1.2 Score=35.10 Aligned_cols=8 Identities=38% Similarity=0.837 Sum_probs=5.1
Q ss_pred CcccCCCc
Q psy3485 277 PTIQPECI 284 (304)
Q Consensus 277 ~~~C~~C~ 284 (304)
|-+||+||
T Consensus 149 P~~CPiCg 156 (166)
T COG1592 149 PEVCPICG 156 (166)
T ss_pred CCcCCCCC
Confidence 66666666
No 108
>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=78.96 E-value=1.2 Score=33.17 Aligned_cols=29 Identities=7% Similarity=0.014 Sum_probs=15.5
Q ss_pred ccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCH
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASK 226 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~ 226 (304)
.|+.||++|+.. +..|..|+.||..|...
T Consensus 11 ~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 555666665543 23455566666555444
No 109
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=78.83 E-value=1.2 Score=30.80 Aligned_cols=31 Identities=16% Similarity=0.187 Sum_probs=19.8
Q ss_pred CccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 246 RRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 246 ~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
.+|.|+.|++. .+.|.-+| .+.|..||..|.
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~G----IW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATG----IWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccC----eEEcCCCCCeec
Confidence 45788888864 22334444 578888888874
No 110
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=78.77 E-value=1.2 Score=34.60 Aligned_cols=39 Identities=13% Similarity=0.353 Sum_probs=24.0
Q ss_pred CCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhc
Q psy3485 181 PMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRA 223 (304)
Q Consensus 181 ~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F 223 (304)
.....|.|+.|+..|+...++..- +. +..|.|+.||...
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEE
Confidence 345568888888888765443321 11 3348888888654
No 111
>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=78.61 E-value=0.83 Score=24.88 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=12.0
Q ss_pred ccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccc
Q psy3485 249 HCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287 (304)
Q Consensus 249 ~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F 287 (304)
+|+.|+-.+.. +... .|.|+.|+..+
T Consensus 4 ~Cp~C~se~~y-----------~D~~--~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGE--LLVCPECGHEW 29 (30)
T ss_dssp --TTT-----E-----------E-SS--SEEETTTTEEE
T ss_pred CCCCCCCccee-----------ccCC--EEeCCcccccC
Confidence 57778777666 3332 68888887643
No 112
>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=78.10 E-value=2.1 Score=22.41 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=9.9
Q ss_pred ccccCCccCCChHHHHHHH
Q psy3485 249 HCAFCNFTSPTQWAINRHT 267 (304)
Q Consensus 249 ~C~~C~k~F~~~~~L~~H~ 267 (304)
.|++|++.+ ....++.|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 456666665 445555554
No 113
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=78.10 E-value=0.36 Score=37.65 Aligned_cols=12 Identities=25% Similarity=0.412 Sum_probs=6.3
Q ss_pred cccccCCccCCC
Q psy3485 248 YHCAFCNFTSPT 259 (304)
Q Consensus 248 ~~C~~C~k~F~~ 259 (304)
++|+.||++|.+
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 455555555544
No 114
>PF15269 zf-C2H2_7: Zinc-finger
Probab=78.02 E-value=1.5 Score=26.00 Aligned_cols=21 Identities=24% Similarity=0.768 Sum_probs=19.0
Q ss_pred cccccchhhccCHHHHHHHHH
Q psy3485 214 FACEMCNYRAASKIAIYAHMR 234 (304)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~ 234 (304)
|+|-+|.-+..-++.|..||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 789999988888999999998
No 115
>KOG2482|consensus
Probab=77.32 E-value=4.3 Score=35.55 Aligned_cols=23 Identities=17% Similarity=0.494 Sum_probs=18.6
Q ss_pred ccccccCCccCCChHHHHHHHHh
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
.+.|-.|.|.|+.+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 57888888888888888888864
No 116
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=76.58 E-value=1.5 Score=34.57 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=5.6
Q ss_pred CCCCccccccch
Q psy3485 209 TKEKPFACEMCN 220 (304)
Q Consensus 209 ~~~~~~~C~~C~ 220 (304)
-|+.|-.|++||
T Consensus 145 ~ge~P~~CPiCg 156 (166)
T COG1592 145 EGEAPEVCPICG 156 (166)
T ss_pred cCCCCCcCCCCC
Confidence 334444555554
No 117
>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=76.58 E-value=0.61 Score=28.97 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=8.4
Q ss_pred cccccCCccCCCh
Q psy3485 248 YHCAFCNFTSPTQ 260 (304)
Q Consensus 248 ~~C~~C~k~F~~~ 260 (304)
|.|..||..|.-.
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 6677777766643
No 118
>KOG2071|consensus
Probab=76.36 E-value=2 Score=40.43 Aligned_cols=27 Identities=15% Similarity=0.249 Sum_probs=20.7
Q ss_pred CCCcccCCCcccccChHHHHHHHHhhC
Q psy3485 183 RRNFMCFACPYYCRYGSSMAIHLRTHT 209 (304)
Q Consensus 183 ~~~~~C~~C~k~f~~~~~l~~H~~~H~ 209 (304)
..+.+|..||++|........||..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456788888888888877777777663
No 119
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=76.08 E-value=1.8 Score=23.93 Aligned_cols=26 Identities=27% Similarity=0.462 Sum_probs=14.6
Q ss_pred cccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
|.|..||..+.-. .+ .+.+|+.||..
T Consensus 1 Y~C~~Cg~~~~~~----------~~---~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK----------PG---DPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS----------TS---STSSBSSSS-S
T ss_pred CCCCcCCCeeEcC----------CC---CcEECCcCCCe
Confidence 5677777776522 12 26778887753
No 120
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=75.89 E-value=0.72 Score=30.89 Aligned_cols=15 Identities=20% Similarity=0.496 Sum_probs=7.7
Q ss_pred CCccccc--cchhhccC
Q psy3485 211 EKPFACE--MCNYRAAS 225 (304)
Q Consensus 211 ~~~~~C~--~C~k~F~~ 225 (304)
++.+.|. .||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 3445555 55555554
No 121
>KOG2907|consensus
Probab=75.06 E-value=0.54 Score=34.02 Aligned_cols=29 Identities=14% Similarity=0.376 Sum_probs=18.2
Q ss_pred hhhhccccccCCCCCCcccCCCcccccCh
Q psy3485 170 CKLCLRRKRKNPMRRNFMCFACPYYCRYG 198 (304)
Q Consensus 170 C~~C~~~~~~h~~~~~~~C~~C~k~f~~~ 198 (304)
|..||-.+..-...-.+.|..|...|..+
T Consensus 10 C~~CG~ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116)
T KOG2907|consen 10 CSDCGSLLEEPSAQSTVLCIRCKIEYPVS 38 (116)
T ss_pred hhhhhhhcccccccCceEeccccccCCHH
Confidence 55555555555555566688888776543
No 122
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=75.06 E-value=1.7 Score=37.36 Aligned_cols=84 Identities=17% Similarity=0.311 Sum_probs=52.9
Q ss_pred CccccccchhhccCHHHHHHHHHhhcCCC------CCCCC--CccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCC
Q psy3485 212 KPFACEMCNYRAASKIAIYAHMRTTHIMP------DTSEE--RRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPEC 283 (304)
Q Consensus 212 ~~~~C~~C~k~F~~~~~L~~H~~~~H~~~------~~~~~--~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C 283 (304)
-|..|+.|.-.......|.+-. +|++| .++++ |--.|-.|.-.|... ..|.---.... ..|.|+.|
T Consensus 321 LPi~CP~Csl~LilsthLarSy--hhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~---~~~~~~~~~ss-~rY~Ce~C 394 (421)
T COG5151 321 LPISCPICSLQLILSTHLARSY--HHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKP---PVSPFDESTSS-GRYQCELC 394 (421)
T ss_pred CCccCcchhHHHHHHHHHHHHH--HhhccCcccccccCCCCCCCccceeccCCCCCC---CCCcccccccc-cceechhh
Confidence 3567888887766666655433 45544 22333 334588888888765 22221111111 36999999
Q ss_pred cccccchhHHHHHHhhcc
Q psy3485 284 IKILWSFLSYFIWISVDV 301 (304)
Q Consensus 284 ~k~F~~~~~l~~h~~~~~ 301 (304)
-..|-+--..++|-..|.
T Consensus 395 K~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 395 KSTFCSDCDVFIHETLHF 412 (421)
T ss_pred hhhhhhhhHHHHHHHHhh
Confidence 999999999999988874
No 123
>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=74.85 E-value=1 Score=26.71 Aligned_cols=29 Identities=28% Similarity=0.532 Sum_probs=16.1
Q ss_pred cccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIK 285 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k 285 (304)
|.|..||..|.....+ +.. .+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~-------~~~--~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI-------SED--DPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc-------CCC--CCCcCCCCCC
Confidence 6677777666554221 112 2566777776
No 124
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.30 E-value=1.7 Score=42.77 Aligned_cols=27 Identities=22% Similarity=0.539 Sum_probs=20.8
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
...+...|.+|| |+... |..|+.||-.
T Consensus 458 ~~~~~L~CH~Cg---------------~~~~~--p~~Cp~Cgs~ 484 (730)
T COG1198 458 KATGQLRCHYCG---------------YQEPI--PQSCPECGSE 484 (730)
T ss_pred cCCCeeEeCCCC---------------CCCCC--CCCCCCCCCC
Confidence 445578999999 44444 9999999976
No 125
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=73.90 E-value=0.47 Score=31.78 Aligned_cols=12 Identities=8% Similarity=0.183 Sum_probs=5.7
Q ss_pred cccC--CCcccccc
Q psy3485 278 TIQP--ECIKILWS 289 (304)
Q Consensus 278 ~~C~--~C~k~F~~ 289 (304)
+.|. .||.+|.+
T Consensus 28 ~qC~N~eCg~tF~t 41 (72)
T PRK09678 28 HQCQNVNCSATFIT 41 (72)
T ss_pred eecCCCCCCCEEEE
Confidence 4454 45555543
No 126
>KOG2272|consensus
Probab=73.14 E-value=2.7 Score=35.13 Aligned_cols=62 Identities=21% Similarity=0.361 Sum_probs=31.7
Q ss_pred cccCCCcccccChHHHHH-H---HHhhCCCCccccccchhhccC-----HHHHHHHHHhhcCCCCCCCCCccccccCCcc
Q psy3485 186 FMCFACPYYCRYGSSMAI-H---LRTHTKEKPFACEMCNYRAAS-----KIAIYAHMRTTHIMPDTSEERRYHCAFCNFT 256 (304)
Q Consensus 186 ~~C~~C~k~f~~~~~l~~-H---~~~H~~~~~~~C~~C~k~F~~-----~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~ 256 (304)
|.|..|++...+.+.-.. - ++.| ..+.|++||-.=+. -.+|..||-+-| |.|..|.|-
T Consensus 164 FkCt~C~keL~sdaRevk~eLyClrCh---D~mgipiCgaC~rpIeervi~amgKhWHveH----------FvCa~CekP 230 (332)
T KOG2272|consen 164 FKCTTCGKELTSDAREVKGELYCLRCH---DKMGIPICGACRRPIEERVIFAMGKHWHVEH----------FVCAKCEKP 230 (332)
T ss_pred eecccccccccchhhhhccceeccccc---cccCCcccccccCchHHHHHHHhccccchhh----------eeehhcCCc
Confidence 677778877665532111 0 0111 12455555532211 244666666444 777777777
Q ss_pred CCCh
Q psy3485 257 SPTQ 260 (304)
Q Consensus 257 F~~~ 260 (304)
|---
T Consensus 231 FlGH 234 (332)
T KOG2272|consen 231 FLGH 234 (332)
T ss_pred ccch
Confidence 6543
No 127
>KOG4167|consensus
Probab=71.15 E-value=1.2 Score=42.87 Aligned_cols=28 Identities=18% Similarity=0.156 Sum_probs=23.3
Q ss_pred CccccccCCccCCChHHHHHHHHhhcCC
Q psy3485 246 RRYHCAFCNFTSPTQWAINRHTKYTHMN 273 (304)
Q Consensus 246 ~~~~C~~C~k~F~~~~~L~~H~r~h~~~ 273 (304)
..|.|..|+|.|-...+++.||++|...
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 4688999999998888899999888654
No 128
>PHA00626 hypothetical protein
Probab=70.20 E-value=2.4 Score=26.59 Aligned_cols=14 Identities=21% Similarity=0.748 Sum_probs=7.7
Q ss_pred CccccccchhhccC
Q psy3485 212 KPFACEMCNYRAAS 225 (304)
Q Consensus 212 ~~~~C~~C~k~F~~ 225 (304)
..|.|..||..|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 34666666655554
No 129
>PF14353 CpXC: CpXC protein
Probab=69.55 E-value=0.37 Score=36.45 Aligned_cols=14 Identities=14% Similarity=0.071 Sum_probs=7.6
Q ss_pred CcccCCCcccccch
Q psy3485 277 PTIQPECIKILWSF 290 (304)
Q Consensus 277 ~~~C~~C~k~F~~~ 290 (304)
.|.|+.||+.|.-.
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 35666666655433
No 130
>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=69.34 E-value=1.1 Score=37.65 Aligned_cols=24 Identities=13% Similarity=-0.013 Sum_probs=14.5
Q ss_pred CCcccCCCcccccchhHHHHHHhh
Q psy3485 276 GPTIQPECIKILWSFLSYFIWISV 299 (304)
Q Consensus 276 ~~~~C~~C~k~F~~~~~l~~h~~~ 299 (304)
+++.||-||........|-...|.
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRS 231 (314)
T ss_pred CCCCCCCCCCcccccccceeeeec
Confidence 367777777766655555444443
No 131
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=66.92 E-value=3.7 Score=33.94 Aligned_cols=26 Identities=15% Similarity=0.375 Sum_probs=16.1
Q ss_pred CccccccchhhccCHHHHHHHHHhhc
Q psy3485 212 KPFACEMCNYRAASKIAIYAHMRTTH 237 (304)
Q Consensus 212 ~~~~C~~C~k~F~~~~~L~~H~~~~H 237 (304)
..|.|..|+|.|.......+|+...|
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CEECCCCCCcccCChHHHHHHHhhcC
Confidence 34777777777777777777777666
No 132
>KOG1280|consensus
Probab=66.66 E-value=4.2 Score=35.68 Aligned_cols=72 Identities=13% Similarity=0.225 Sum_probs=42.6
Q ss_pred cccCCCCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCC
Q psy3485 177 KRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCN 254 (304)
Q Consensus 177 ~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~ 254 (304)
..+|.-+.|.+|..=...|..... .-.-.|-...-|.|++|++.=.+...|..|....|.++. --..|++|+
T Consensus 45 t~~H~~dHPmqcil~~~dfeL~f~--Ge~i~~y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~----~~~icp~c~ 116 (381)
T KOG1280|consen 45 TPIHDEDHPMQCILSRVDFELYFG--GEPISHYDPQSFTCPYCGIMGFTERQFGTHVLSQHPEAS----TSVICPLCA 116 (381)
T ss_pred CcccCCCCceeEEeeccceeeEec--CccccccccccccCCcccccccchhHHHHHhhhcCcccC----cceeeeccc
Confidence 567777777777433333322110 001124455578999999888888888888887884321 124566665
No 133
>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=66.53 E-value=2.8 Score=27.66 Aligned_cols=28 Identities=11% Similarity=0.290 Sum_probs=13.0
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
.-.|..|++.|.. .. +.|.|..||..|=
T Consensus 9 ~~~C~~C~~~F~~------------~~--rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKFSL------------FR--RRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B-BS------------SS---EEE-TTT--EEE
T ss_pred CCcCcCcCCcCCC------------ce--eeEccCCCCCEEC
Confidence 3478889988853 12 4788888888773
No 134
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=66.21 E-value=3.3 Score=24.92 Aligned_cols=13 Identities=15% Similarity=0.488 Sum_probs=7.2
Q ss_pred CcccCCCcccccC
Q psy3485 185 NFMCFACPYYCRY 197 (304)
Q Consensus 185 ~~~C~~C~k~f~~ 197 (304)
.|.|+.||..|..
T Consensus 3 ~y~C~~CG~~~~~ 15 (46)
T PRK00398 3 EYKCARCGREVEL 15 (46)
T ss_pred EEECCCCCCEEEE
Confidence 3556666665544
No 135
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=65.84 E-value=1.4 Score=42.47 Aligned_cols=56 Identities=18% Similarity=0.361 Sum_probs=29.7
Q ss_pred ccCCCcccccChHHHHHHHHhhCCCCcc-ccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCc
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKEKPF-ACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNF 255 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~-~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k 255 (304)
.|..||=+|+--.+|-.= |.+|.-+.| -|+.|.+.|....+-+ .| ..|..|+.||=
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRR-----fH-------AQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRR-----FH-------AQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccc-----cc-------cccccCcccCC
Confidence 566677766654333221 224444445 3777777666655422 33 22566777764
No 136
>PF15269 zf-C2H2_7: Zinc-finger
Probab=64.44 E-value=5.4 Score=23.71 Aligned_cols=33 Identities=30% Similarity=0.642 Sum_probs=24.7
Q ss_pred cCCCCCCCC-CccccccCCccCCChHHHHHHHHh
Q psy3485 237 HIMPDTSEE-RRYHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 237 H~~~~~~~~-~~~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
|.+|++.|. -.|+|-.|+.+-.-++.|-+||+.
T Consensus 9 hyiprp~gkp~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 9 HYIPRPPGKPFKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred CcCCCCCCCCccceeecCCcccchHHHHHHHHHH
Confidence 444444432 347999999999999999999975
No 137
>KOG4124|consensus
Probab=63.81 E-value=1.3 Score=38.73 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=23.4
Q ss_pred CCcccccc--chhhccCHHHHHHHHHhhcC
Q psy3485 211 EKPFACEM--CNYRAASKIAIYAHMRTTHI 238 (304)
Q Consensus 211 ~~~~~C~~--C~k~F~~~~~L~~H~~~~H~ 238 (304)
.++|+|.+ |++.+++...|+.|....|-
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~ 376 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHC 376 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcC
Confidence 36789976 99999999999999886664
No 138
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=63.72 E-value=3 Score=28.79 Aligned_cols=15 Identities=13% Similarity=0.215 Sum_probs=8.4
Q ss_pred CCCCcccCCCccccc
Q psy3485 182 MRRNFMCFACPYYCR 196 (304)
Q Consensus 182 ~~~~~~C~~C~k~f~ 196 (304)
+..-+.|.-||..|.
T Consensus 50 a~GIW~C~kCg~~fA 64 (89)
T COG1997 50 ATGIWKCRKCGAKFA 64 (89)
T ss_pred ccCeEEcCCCCCeec
Confidence 334566666666654
No 139
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=62.75 E-value=3.4 Score=31.00 Aligned_cols=24 Identities=17% Similarity=0.007 Sum_probs=20.5
Q ss_pred cccccCCccCCChHHHHHHHHhhcCCC
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTHMNT 274 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~~~~ 274 (304)
..|-++||.|++ |++|.++|++-.
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmT 100 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLT 100 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCC
Confidence 589999999975 799999999876
No 140
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=62.75 E-value=3.8 Score=25.19 Aligned_cols=13 Identities=31% Similarity=0.697 Sum_probs=7.8
Q ss_pred CcccCCCcccccC
Q psy3485 185 NFMCFACPYYCRY 197 (304)
Q Consensus 185 ~~~C~~C~k~f~~ 197 (304)
.+.|+.||..+.-
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 5667777655543
No 141
>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=61.89 E-value=2.9 Score=26.25 Aligned_cols=30 Identities=20% Similarity=0.253 Sum_probs=17.1
Q ss_pred cccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccc
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F 287 (304)
|.|+.||..+.-... .-|+ ...|+.||..|
T Consensus 3 ~~CP~CG~~iev~~~-------~~Ge---iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENP-------ELGE---LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCC-------ccCC---EEeCCCCCCEE
Confidence 567777776533211 1133 46777777765
No 142
>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=61.82 E-value=3.8 Score=33.89 Aligned_cols=32 Identities=16% Similarity=0.365 Sum_probs=24.9
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCCC
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMNT 274 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~ 274 (304)
.++..|.|..|+|.|+-..-.++|+..-|.++
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 35678999999999999999999998877764
No 143
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=61.33 E-value=1.5 Score=23.42 Aligned_cols=19 Identities=21% Similarity=0.277 Sum_probs=6.9
Q ss_pred ccccCCccCCChHHHHHHHH
Q psy3485 249 HCAFCNFTSPTQWAINRHTK 268 (304)
Q Consensus 249 ~C~~C~k~F~~~~~L~~H~r 268 (304)
.|--|++.| .....+.|..
T Consensus 2 sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEE-EGGGTTT---
T ss_pred eeecCCCCc-CcCCcCCCCc
Confidence 344444444 3334444433
No 144
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=60.71 E-value=7.8 Score=30.05 Aligned_cols=44 Identities=16% Similarity=0.070 Sum_probs=20.4
Q ss_pred CCCCccccccCCccC------CChHHHHHHHH-hhcCCC---------CCCcccCCCccc
Q psy3485 243 SEERRYHCAFCNFTS------PTQWAINRHTK-YTHMNT---------SGPTIQPECIKI 286 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F------~~~~~L~~H~r-~h~~~~---------~~~~~C~~C~k~ 286 (304)
...--..|..|+|+| ++.+.+..|+. +.|.+. -...+|-.||-.
T Consensus 10 ~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 10 DPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp -CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT---
T ss_pred CcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCC
Confidence 445567888888887 35566777753 333321 024788888754
No 145
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=60.25 E-value=18 Score=30.31 Aligned_cols=20 Identities=30% Similarity=0.346 Sum_probs=14.0
Q ss_pred CCCCCccccCCCchHHHHHH
Q psy3485 146 FSPDDQFFCIHCNGCVLYAD 165 (304)
Q Consensus 146 ~~~~~~~~C~~C~~~fl~~H 165 (304)
......|.|..|...+.++.
T Consensus 107 p~~drqFaC~~Cd~~WwRrv 126 (278)
T PF15135_consen 107 PSVDRQFACSSCDHMWWRRV 126 (278)
T ss_pred cccceeeeccccchHHHhcc
Confidence 34456699999988775544
No 146
>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=59.42 E-value=4.6 Score=38.26 Aligned_cols=27 Identities=22% Similarity=0.678 Sum_probs=16.1
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
.......|..||.. ... |..|+.||..
T Consensus 236 ~~~~~l~Ch~Cg~~---------------~~~--~~~Cp~C~s~ 262 (505)
T TIGR00595 236 KKEGKLRCHYCGYQ---------------EPI--PKTCPQCGSE 262 (505)
T ss_pred cCCCeEEcCCCcCc---------------CCC--CCCCCCCCCC
Confidence 44456677777732 232 6677777653
No 147
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=58.60 E-value=1.1 Score=39.01 Aligned_cols=14 Identities=21% Similarity=0.358 Sum_probs=5.8
Q ss_pred CCCCcccCCCcccc
Q psy3485 182 MRRNFMCFACPYYC 195 (304)
Q Consensus 182 ~~~~~~C~~C~k~f 195 (304)
|.|...|..|+-.+
T Consensus 194 G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 194 GKRYLHCSLCGTEW 207 (290)
T ss_dssp -EEEEEETTT--EE
T ss_pred ccEEEEcCCCCCee
Confidence 34555565555443
No 148
>KOG2593|consensus
Probab=58.56 E-value=8.3 Score=35.06 Aligned_cols=18 Identities=11% Similarity=0.248 Sum_probs=8.9
Q ss_pred CCCcccCCCcccccChHH
Q psy3485 183 RRNFMCFACPYYCRYGSS 200 (304)
Q Consensus 183 ~~~~~C~~C~k~f~~~~~ 200 (304)
..-|.|+.|.+.|+.-.+
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEA 143 (436)
T ss_pred cccccCCccccchhhhHH
Confidence 344555555555554433
No 149
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=58.37 E-value=7.4 Score=24.37 Aligned_cols=26 Identities=15% Similarity=0.229 Sum_probs=15.3
Q ss_pred ccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 249 HCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 249 ~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
.|..|++.|.. .. +.+.|..||+.|-
T Consensus 4 ~C~~C~~~F~~------------~~--rk~~Cr~Cg~~~C 29 (57)
T cd00065 4 SCMGCGKPFTL------------TR--RRHHCRNCGRIFC 29 (57)
T ss_pred cCcccCccccC------------Cc--cccccCcCcCCcC
Confidence 46667776664 11 3566666666663
No 150
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.95 E-value=8 Score=39.12 Aligned_cols=10 Identities=20% Similarity=0.321 Sum_probs=5.5
Q ss_pred CcccCCCccc
Q psy3485 185 NFMCFACPYY 194 (304)
Q Consensus 185 ~~~C~~C~k~ 194 (304)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 3455556555
No 151
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=57.38 E-value=4.4 Score=31.22 Aligned_cols=32 Identities=19% Similarity=0.284 Sum_probs=15.1
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIK 285 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k 285 (304)
+|.|. |+..|-+. ++|-+.-.|+ .|.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~---~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE---VYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc---eEEeccCCc
Confidence 45555 55554444 3443333333 355555543
No 152
>KOG4167|consensus
Probab=57.30 E-value=3.3 Score=39.96 Aligned_cols=24 Identities=33% Similarity=0.486 Sum_probs=22.2
Q ss_pred ccccccchhhccCHHHHHHHHHhhc
Q psy3485 213 PFACEMCNYRAASKIAIYAHMRTTH 237 (304)
Q Consensus 213 ~~~C~~C~k~F~~~~~L~~H~~~~H 237 (304)
-|.|..|+|.|-.-..++.||+ .|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK-~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMK-TH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHH-HH
Confidence 4999999999999999999999 66
No 153
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.40 E-value=6.4 Score=38.85 Aligned_cols=34 Identities=18% Similarity=0.486 Sum_probs=16.9
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCc
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACP 192 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~ 192 (304)
..|..||..+ -|+.|+..+..|...+...|..||
T Consensus 436 l~C~~Cg~v~-------~Cp~Cd~~lt~H~~~~~L~CH~Cg 469 (730)
T COG1198 436 LLCRDCGYIA-------ECPNCDSPLTLHKATGQLRCHYCG 469 (730)
T ss_pred eecccCCCcc-------cCCCCCcceEEecCCCeeEeCCCC
Confidence 3466666542 244444444444444455555554
No 154
>KOG3408|consensus
Probab=55.17 E-value=9.2 Score=28.22 Aligned_cols=27 Identities=19% Similarity=0.210 Sum_probs=20.3
Q ss_pred CCCCccccccCCccCCChHHHHHHHHh
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
.|...|.|-.|.+-|.+...|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 455568888888888888888888764
No 155
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=55.05 E-value=5.3 Score=25.35 Aligned_cols=41 Identities=22% Similarity=0.489 Sum_probs=21.7
Q ss_pred CCcccCC--CcccccChHHHHHHHHhhCCCCcccccc----chhhccC
Q psy3485 184 RNFMCFA--CPYYCRYGSSMAIHLRTHTKEKPFACEM----CNYRAAS 225 (304)
Q Consensus 184 ~~~~C~~--C~k~f~~~~~l~~H~~~H~~~~~~~C~~----C~k~F~~ 225 (304)
.+..|+. |...+. +..|..|+..--..++..|.. |+..+..
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 4556766 334344 445777777655566777777 7766543
No 156
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=54.37 E-value=3.5 Score=25.53 Aligned_cols=25 Identities=16% Similarity=0.146 Sum_probs=15.2
Q ss_pred CcccCCCcccccchhHHHHHHhhcc
Q psy3485 277 PTIQPECIKILWSFLSYFIWISVDV 301 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~~~~~ 301 (304)
.|.|+.|++.|=---.+++|-++|+
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-S
T ss_pred eEECCCCCCccccCcChhhhccccC
Confidence 6888888888888888888877775
No 158
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=54.20 E-value=8.6 Score=24.08 Aligned_cols=18 Identities=11% Similarity=0.283 Sum_probs=12.9
Q ss_pred cccccCCccCCChHHHHH
Q psy3485 248 YHCAFCNFTSPTQWAINR 265 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~ 265 (304)
+.|+.||..|..+...+.
T Consensus 29 W~C~~Cgh~w~~~v~~R~ 46 (55)
T PF14311_consen 29 WKCPKCGHEWKASVNDRT 46 (55)
T ss_pred EECCCCCCeeEccHhhhc
Confidence 688888888777755554
No 159
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.51 E-value=3.5 Score=40.38 Aligned_cols=47 Identities=19% Similarity=0.315 Sum_probs=27.3
Q ss_pred ccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 215 ACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 215 ~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
.|..||..+.-..- ...+. .| .......|..||.. . . +..|+.||..
T Consensus 385 ~C~~Cg~~~~C~~C-~~~L~-~h-----~~~~~l~Ch~CG~~---------------~-~--p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHC-TGPLG-LP-----SAGGTPRCRWCGRA---------------A-P--DWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCC-CCcee-Ee-----cCCCeeECCCCcCC---------------C-c--CccCCCCcCC
Confidence 56666655443210 01222 44 44457889999932 2 2 7899999875
No 160
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.15 E-value=13 Score=37.72 Aligned_cols=9 Identities=22% Similarity=0.235 Sum_probs=5.6
Q ss_pred cccCCCccc
Q psy3485 186 FMCFACPYY 194 (304)
Q Consensus 186 ~~C~~C~k~ 194 (304)
+.|+.||..
T Consensus 639 frCP~CG~~ 647 (1121)
T PRK04023 639 RRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCC
Confidence 566666655
No 161
>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=52.87 E-value=6.9 Score=25.72 Aligned_cols=16 Identities=25% Similarity=0.484 Sum_probs=8.8
Q ss_pred CCCCcccCCCcccccC
Q psy3485 182 MRRNFMCFACPYYCRY 197 (304)
Q Consensus 182 ~~~~~~C~~C~k~f~~ 197 (304)
..+.|.|+.||..+..
T Consensus 43 ~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMDR 58 (69)
T ss_pred ccceEEcCCCCCEECc
Confidence 3455666666665443
No 162
>KOG1280|consensus
Probab=52.74 E-value=14 Score=32.54 Aligned_cols=42 Identities=21% Similarity=0.501 Sum_probs=33.8
Q ss_pred CCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcc
Q psy3485 244 EERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIK 285 (304)
Q Consensus 244 ~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k 285 (304)
...-|.|++|+++=.+-..|..|...-|.+......|++|+-
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 345799999999999999999999888887644457777763
No 163
>PF14369 zf-RING_3: zinc-finger
Probab=52.07 E-value=9.5 Score=21.54 Aligned_cols=10 Identities=20% Similarity=0.202 Sum_probs=5.9
Q ss_pred ccCCCccccc
Q psy3485 187 MCFACPYYCR 196 (304)
Q Consensus 187 ~C~~C~k~f~ 196 (304)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 3666666553
No 164
>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=52.05 E-value=8.8 Score=29.11 Aligned_cols=23 Identities=17% Similarity=0.063 Sum_probs=15.2
Q ss_pred CcccCCCcccccchhHHHHHHhhccc
Q psy3485 277 PTIQPECIKILWSFLSYFIWISVDVN 302 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~~~~~~ 302 (304)
-..|=+|||.|.+- .+|++.|+|
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~g 94 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHG 94 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-
T ss_pred eeEEccCCcccchH---HHHHHHccC
Confidence 47999999999875 789888854
No 165
>KOG0978|consensus
Probab=51.70 E-value=5.4 Score=38.77 Aligned_cols=49 Identities=18% Similarity=0.295 Sum_probs=30.5
Q ss_pred cccCCCchHH----HHHHHHHHhhhhccccccCCCCCCcccCCCcccccChHHHHH
Q psy3485 152 FFCIHCNGCV----LYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCRYGSSMAI 203 (304)
Q Consensus 152 ~~C~~C~~~f----l~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~~~~~l~~ 203 (304)
.+|+.|...| +..=+...|..|-+++..+ |.-.||.||..|....-+..
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~et---RqRKCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYET---RQRKCPKCNAAFGANDVHRI 696 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHH---hcCCCCCCCCCCCccccccc
Confidence 6899999777 2222222377776654333 34489999999986654433
No 166
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=51.55 E-value=7.9 Score=29.18 Aligned_cols=27 Identities=22% Similarity=0.453 Sum_probs=17.5
Q ss_pred HHhhhhccccccCCCCCCcccCCCccccc
Q psy3485 168 DHCKLCLRRKRKNPMRRNFMCFACPYYCR 196 (304)
Q Consensus 168 ~hC~~C~~~~~~h~~~~~~~C~~C~k~f~ 196 (304)
.||+.|+-.+-.++| ..-|++|+..+.
T Consensus 29 ~hCp~Cg~PLF~KdG--~v~CPvC~~~~~ 55 (131)
T COG1645 29 KHCPKCGTPLFRKDG--EVFCPVCGYREV 55 (131)
T ss_pred hhCcccCCcceeeCC--eEECCCCCceEE
Confidence 347777766555555 367888886554
No 167
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=50.27 E-value=6.3 Score=34.06 Aligned_cols=77 Identities=16% Similarity=0.280 Sum_probs=43.3
Q ss_pred CCcccCCCcccccChHHHHHHHHhh----------CCC--CccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccc
Q psy3485 184 RNFMCFACPYYCRYGSSMAIHLRTH----------TKE--KPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCA 251 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~~H~~~H----------~~~--~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~ 251 (304)
-|..|+.|.........|.+-..-- ++. +.--|-.|.-.|.... .|+-...+....|.|+
T Consensus 321 LPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~--------~~~~~~~~ss~rY~Ce 392 (421)
T COG5151 321 LPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPP--------VSPFDESTSSGRYQCE 392 (421)
T ss_pred CCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCC--------CCcccccccccceech
Confidence 4667777776655444444322110 111 2223788887776532 2322222455678999
Q ss_pred cCCccCCChHHHHHHHH
Q psy3485 252 FCNFTSPTQWAINRHTK 268 (304)
Q Consensus 252 ~C~k~F~~~~~L~~H~r 268 (304)
.|...|-.--+.--|..
T Consensus 393 ~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 393 LCKSTFCSDCDVFIHET 409 (421)
T ss_pred hhhhhhhhhhHHHHHHH
Confidence 99888877766655543
No 168
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.38 E-value=7.9 Score=25.96 Aligned_cols=18 Identities=17% Similarity=0.547 Sum_probs=14.7
Q ss_pred cccCCCchHH-HHHHHHHH
Q psy3485 152 FFCIHCNGCV-LYADLLDH 169 (304)
Q Consensus 152 ~~C~~C~~~f-l~~H~~~h 169 (304)
|.|..||..| +-++|...
T Consensus 13 Y~c~~cg~~~dvvq~~~dd 31 (82)
T COG2331 13 YECTECGNRFDVVQAMTDD 31 (82)
T ss_pred EeecccchHHHHHHhcccC
Confidence 8999999999 77777643
No 169
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=48.88 E-value=8.7 Score=29.34 Aligned_cols=23 Identities=22% Similarity=0.485 Sum_probs=12.3
Q ss_pred ccCCCchHHHHHHHHHHhhhhccc
Q psy3485 153 FCIHCNGCVLYADLLDHCKLCLRR 176 (304)
Q Consensus 153 ~C~~C~~~fl~~H~~~hC~~C~~~ 176 (304)
-|+.||+.|... ....|+.|.+.
T Consensus 5 nC~~CgklF~~~-~~~iCp~C~~~ 27 (137)
T TIGR03826 5 NCPKCGRLFVKT-GRDVCPSCYEE 27 (137)
T ss_pred cccccchhhhhc-CCccCHHHhHH
Confidence 377777777442 33335555543
No 170
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=48.65 E-value=18 Score=21.22 Aligned_cols=25 Identities=20% Similarity=0.394 Sum_probs=16.6
Q ss_pred CcccCCCcccccCh--HHHHHHHHhhC
Q psy3485 185 NFMCFACPYYCRYG--SSMAIHLRTHT 209 (304)
Q Consensus 185 ~~~C~~C~k~f~~~--~~l~~H~~~H~ 209 (304)
...|+.||..|..- ..-..|.+-|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 35788888887643 55566766663
No 171
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=48.50 E-value=7.4 Score=30.12 Aligned_cols=10 Identities=20% Similarity=0.597 Sum_probs=5.6
Q ss_pred ccccccCCcc
Q psy3485 247 RYHCAFCNFT 256 (304)
Q Consensus 247 ~~~C~~C~k~ 256 (304)
.|.|..||..
T Consensus 112 ~l~C~~Cg~~ 121 (146)
T PF07295_consen 112 TLVCENCGHE 121 (146)
T ss_pred eEecccCCCE
Confidence 3666666644
No 172
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=48.19 E-value=3.3 Score=36.85 Aligned_cols=65 Identities=17% Similarity=0.312 Sum_probs=24.2
Q ss_pred ccccccchhhccCHHHH---HHHHHhhcCCCCCCCC-CccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 213 PFACEMCNYRAASKIAI---YAHMRTTHIMPDTSEE-RRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 213 ~~~C~~C~k~F~~~~~L---~~H~~~~H~~~~~~~~-~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
-+.|.+|.+.+-..... ..|....| ... |-|.|..|++... +.+.-+...|+.||..=.
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~-----~a~KRFFkC~~C~~Rt~------------sl~r~P~~~C~~Cg~~~w 314 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWH-----DAVKRFFKCKDCGNRTI------------SLERLPKKHCSNCGSSKW 314 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEE-----EEE-EEEE-T-TS-EEE------------ESSSS--S--TTT-S---
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEe-----eeeeeeEECCCCCCeee------------ecccCCCCCCCcCCcCce
Confidence 36777787665444332 34544444 343 4468888886532 222223467888886544
Q ss_pred chhHHH
Q psy3485 289 SFLSYF 294 (304)
Q Consensus 289 ~~~~l~ 294 (304)
.+.+|+
T Consensus 315 er~~M~ 320 (344)
T PF09332_consen 315 ERTGML 320 (344)
T ss_dssp EEE---
T ss_pred eehhhh
Confidence 444443
No 173
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=47.69 E-value=9 Score=22.21 Aligned_cols=13 Identities=8% Similarity=0.084 Sum_probs=9.4
Q ss_pred CcccCCCcccccc
Q psy3485 277 PTIQPECIKILWS 289 (304)
Q Consensus 277 ~~~C~~C~k~F~~ 289 (304)
+|.|..|++.|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 6778888877743
No 174
>KOG4124|consensus
Probab=47.62 E-value=2.3 Score=37.26 Aligned_cols=52 Identities=21% Similarity=0.480 Sum_probs=36.4
Q ss_pred CCCcccCC--CcccccChHHHHHHHHh-hC------------------CCCccccccchhhccCHHHHHHHHH
Q psy3485 183 RRNFMCFA--CPYYCRYGSSMAIHLRT-HT------------------KEKPFACEMCNYRAASKIAIYAHMR 234 (304)
Q Consensus 183 ~~~~~C~~--C~k~f~~~~~l~~H~~~-H~------------------~~~~~~C~~C~k~F~~~~~L~~H~~ 234 (304)
.+++.|.+ |.+.+.....|..|... |. ..|+|+|++|.+.++....|..|..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 46789965 99999999888888654 52 2356677777777666655555544
No 175
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=47.58 E-value=11 Score=20.69 Aligned_cols=26 Identities=19% Similarity=0.316 Sum_probs=15.0
Q ss_pred hhhhccccccCCCCCCcccCCCcccc
Q psy3485 170 CKLCLRRKRKNPMRRNFMCFACPYYC 195 (304)
Q Consensus 170 C~~C~~~~~~h~~~~~~~C~~C~k~f 195 (304)
|..|+-.+....+...-+|+.|+..+
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred cCcCCccccCCCCcCEeECCCCcCEe
Confidence 66777777777777778888888643
No 176
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=46.61 E-value=6.4 Score=24.61 Aligned_cols=20 Identities=15% Similarity=-0.037 Sum_probs=8.5
Q ss_pred ccCCCcccccc--hhHHHHHHh
Q psy3485 279 IQPECIKILWS--FLSYFIWIS 298 (304)
Q Consensus 279 ~C~~C~k~F~~--~~~l~~h~~ 298 (304)
.||+|+..|.. +..|+.+++
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~ 43 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYK 43 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHH
Confidence 67777777743 344444444
No 177
>KOG2593|consensus
Probab=46.39 E-value=20 Score=32.74 Aligned_cols=20 Identities=25% Similarity=0.408 Sum_probs=9.9
Q ss_pred CCCCccccccchhhccCHHH
Q psy3485 209 TKEKPFACEMCNYRAASKIA 228 (304)
Q Consensus 209 ~~~~~~~C~~C~k~F~~~~~ 228 (304)
+...-|.|+.|.+.|+..-.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEA 143 (436)
T ss_pred cccccccCCccccchhhhHH
Confidence 34444555555555554443
No 178
>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=46.36 E-value=4.7 Score=24.30 Aligned_cols=9 Identities=22% Similarity=0.154 Sum_probs=5.9
Q ss_pred CcccCCCcc
Q psy3485 277 PTIQPECIK 285 (304)
Q Consensus 277 ~~~C~~C~k 285 (304)
.|+|..|++
T Consensus 37 ~~~C~~C~~ 45 (46)
T PF12760_consen 37 RYRCKACRK 45 (46)
T ss_pred eEECCCCCC
Confidence 577777664
No 179
>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=46.29 E-value=7.3 Score=32.84 Aligned_cols=25 Identities=12% Similarity=0.363 Sum_probs=13.1
Q ss_pred CCccccccCCccCCChHHHHHHHHh
Q psy3485 245 ERRYHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
.+++.|+.||..-.-...|..=.|+
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRS 231 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeec
Confidence 3566666666555444444433333
No 180
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=45.85 E-value=1.8 Score=25.28 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=5.1
Q ss_pred cccccCCccC
Q psy3485 248 YHCAFCNFTS 257 (304)
Q Consensus 248 ~~C~~C~k~F 257 (304)
|.|..||..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5555555444
No 181
>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=45.80 E-value=15 Score=21.14 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=4.6
Q ss_pred ccccccCCccCC
Q psy3485 247 RYHCAFCNFTSP 258 (304)
Q Consensus 247 ~~~C~~C~k~F~ 258 (304)
.|-|+.|++.|.
T Consensus 3 ryyCdyC~~~~~ 14 (38)
T PF06220_consen 3 RYYCDYCKKYLT 14 (38)
T ss_dssp S-B-TTT--B-S
T ss_pred Ceecccccceec
Confidence 467777777773
No 182
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=45.79 E-value=6.3 Score=29.62 Aligned_cols=25 Identities=20% Similarity=0.477 Sum_probs=16.8
Q ss_pred ccccCCCchHH--HHHHHHHHhhhhcc
Q psy3485 151 QFFCIHCNGCV--LYADLLDHCKLCLR 175 (304)
Q Consensus 151 ~~~C~~C~~~f--l~~H~~~hC~~C~~ 175 (304)
++.|..||+.| -...++.-|+.||-
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCC
Confidence 36799999999 44456655666553
No 183
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.54 E-value=9.3 Score=28.14 Aligned_cols=12 Identities=17% Similarity=0.227 Sum_probs=7.4
Q ss_pred cccccCCccCCC
Q psy3485 248 YHCAFCNFTSPT 259 (304)
Q Consensus 248 ~~C~~C~k~F~~ 259 (304)
+.|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 566666665544
No 184
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=45.37 E-value=11 Score=33.11 Aligned_cols=77 Identities=17% Similarity=0.305 Sum_probs=45.1
Q ss_pred CCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHH
Q psy3485 184 RNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAI 263 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L 263 (304)
..-.|++||..=. .++ .+.....|.|...|..|+-. +|+. .-.|+.||.. ..|
T Consensus 186 ~~~~CPvCGs~P~--~s~-v~~~~~~G~RyL~CslC~te--------W~~~------------R~~C~~Cg~~----~~l 238 (309)
T PRK03564 186 QRQFCPVCGSMPV--SSV-VQIGTTQGLRYLHCNLCESE--------WHVV------------RVKCSNCEQS----GKL 238 (309)
T ss_pred CCCCCCCCCCcch--hhe-eeccCCCCceEEEcCCCCCc--------cccc------------CccCCCCCCC----Cce
Confidence 4468999997522 111 13344567888999999933 2333 4579999963 122
Q ss_pred HHHHHhhcCC--CCCCcccCCCcccccc
Q psy3485 264 NRHTKYTHMN--TSGPTIQPECIKILWS 289 (304)
Q Consensus 264 ~~H~r~h~~~--~~~~~~C~~C~k~F~~ 289 (304)
..+ +..++ ..+-..|..|+--++.
T Consensus 239 ~y~--~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 239 HYW--SLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred eee--eecCCCcceEeeeccccccccee
Confidence 211 11221 1145799999876654
No 185
>PRK14873 primosome assembly protein PriA; Provisional
Probab=45.22 E-value=12 Score=36.86 Aligned_cols=35 Identities=17% Similarity=0.375 Sum_probs=20.2
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCcc
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPY 193 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k 193 (304)
..|..||..+ .|+.|+-.+..|.......|..||.
T Consensus 384 l~C~~Cg~~~-------~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 384 LACARCRTPA-------RCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eEhhhCcCee-------ECCCCCCceeEecCCCeeECCCCcC
Confidence 4677777652 3555555555555555556666663
No 186
>KOG3408|consensus
Probab=45.21 E-value=13 Score=27.51 Aligned_cols=28 Identities=25% Similarity=0.567 Sum_probs=23.7
Q ss_pred CCCCCCcccCCCcccccChHHHHHHHHh
Q psy3485 180 NPMRRNFMCFACPYYCRYGSSMAIHLRT 207 (304)
Q Consensus 180 h~~~~~~~C~~C~k~f~~~~~l~~H~~~ 207 (304)
-.|-..|-|-.|.+-|.+..+|..|.++
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 3456779999999999999999999875
No 187
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=44.66 E-value=12 Score=38.97 Aligned_cols=36 Identities=17% Similarity=0.373 Sum_probs=22.7
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCccccc
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCR 196 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~ 196 (304)
+.|+.||..-.. .-|+.|+..+. .+|.|+.||....
T Consensus 668 rkCPkCG~~t~~----~fCP~CGs~te-----~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYE----NRCPDCGTHTE-----PVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCcccc----ccCcccCCcCC-----CceeCccCCCccC
Confidence 789999974211 14777776653 2467777777644
No 188
>KOG0782|consensus
Probab=44.40 E-value=4.3 Score=38.09 Aligned_cols=35 Identities=23% Similarity=0.367 Sum_probs=22.0
Q ss_pred ccCCCcccccChHHHHHHHHhhCCC-CccccccchhhccCHH
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKE-KPFACEMCNYRAASKI 227 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~-~~~~C~~C~k~F~~~~ 227 (304)
+|.+|||.|.++.. -|..+ -...|..|...|-.+.
T Consensus 255 kC~~CgKgFQQKf~------FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 255 KCNTCGKGFQQKFF------FHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchhhhhhhhhee------eccccEEEEEehHHHHHhhcch
Confidence 67788888776632 23322 2367788887777665
No 189
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=44.25 E-value=2.1 Score=30.34 Aligned_cols=37 Identities=14% Similarity=0.430 Sum_probs=18.4
Q ss_pred CCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccc
Q psy3485 245 ERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F 287 (304)
.+.|.|+.||..-.+.-.++ -+.+. -...|..||.+|
T Consensus 20 ~k~FtCp~Cghe~vs~ctvk-----k~~~~-g~~~Cg~CGls~ 56 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVK-----KTVNI-GTAVCGNCGLSF 56 (104)
T ss_pred CceEecCccCCeeeeEEEEE-----ecCce-eEEEcccCcceE
Confidence 35577777776544332211 01111 135677777776
No 190
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=44.04 E-value=6.1 Score=27.68 Aligned_cols=15 Identities=13% Similarity=0.233 Sum_probs=8.9
Q ss_pred CCCCcccCCCccccc
Q psy3485 182 MRRNFMCFACPYYCR 196 (304)
Q Consensus 182 ~~~~~~C~~C~k~f~ 196 (304)
+...+.|.-|++.|.
T Consensus 51 a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 51 AVGIWRCKGCKKTVA 65 (90)
T ss_pred eeEEEEcCCCCCEEe
Confidence 334566666666664
No 191
>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=43.48 E-value=3.3 Score=28.96 Aligned_cols=27 Identities=19% Similarity=0.395 Sum_probs=13.0
Q ss_pred hhhhccccccCCCCCCcccCCCccccc
Q psy3485 170 CKLCLRRKRKNPMRRNFMCFACPYYCR 196 (304)
Q Consensus 170 C~~C~~~~~~h~~~~~~~C~~C~k~f~ 196 (304)
|+.|++......+..-|.|.-|++.|.
T Consensus 38 Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 38 CPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp ESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 333333333333334466666766664
No 192
>KOG4727|consensus
Probab=43.16 E-value=12 Score=29.40 Aligned_cols=22 Identities=9% Similarity=0.092 Sum_probs=18.2
Q ss_pred CcccCCCcccccchhHHHHHHh
Q psy3485 277 PTIQPECIKILWSFLSYFIWIS 298 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~~ 298 (304)
-|.|.+|.-.|...-+++.||-
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 3888888888888888888873
No 193
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.13 E-value=7.7 Score=29.61 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=4.6
Q ss_pred cccCCCchHH
Q psy3485 152 FFCIHCNGCV 161 (304)
Q Consensus 152 ~~C~~C~~~f 161 (304)
+.|..||..|
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 4444444444
No 194
>PF12907 zf-met2: Zinc-binding
Probab=43.00 E-value=24 Score=20.61 Aligned_cols=7 Identities=29% Similarity=0.894 Sum_probs=3.3
Q ss_pred ccCCCcc
Q psy3485 187 MCFACPY 193 (304)
Q Consensus 187 ~C~~C~k 193 (304)
+|.+|..
T Consensus 3 ~C~iC~q 9 (40)
T PF12907_consen 3 ICKICRQ 9 (40)
T ss_pred CcHHhhH
Confidence 4444443
No 195
>KOG0717|consensus
Probab=42.92 E-value=14 Score=34.05 Aligned_cols=22 Identities=18% Similarity=0.422 Sum_probs=19.3
Q ss_pred cccccCCccCCChHHHHHHHHh
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
+-|.+|+|+|++...|.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999754
No 196
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=42.44 E-value=12 Score=18.93 Aligned_cols=6 Identities=33% Similarity=0.855 Sum_probs=2.9
Q ss_pred cCCCcc
Q psy3485 188 CFACPY 193 (304)
Q Consensus 188 C~~C~k 193 (304)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444544
No 197
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=42.12 E-value=6.8 Score=29.47 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=13.3
Q ss_pred CccccCCCchHHHHHHHH
Q psy3485 150 DQFFCIHCNGCVLYADLL 167 (304)
Q Consensus 150 ~~~~C~~C~~~fl~~H~~ 167 (304)
+-|.|.+|..+...+|..
T Consensus 79 ~lYeCnIC~etS~ee~FL 96 (140)
T PF05290_consen 79 KLYECNICKETSAEERFL 96 (140)
T ss_pred CceeccCcccccchhhcC
Confidence 349999999887665554
No 198
>KOG2636|consensus
Probab=41.90 E-value=16 Score=33.32 Aligned_cols=27 Identities=26% Similarity=0.609 Sum_probs=19.7
Q ss_pred hCCCCccccccch-hhccCHHHHHHHHH
Q psy3485 208 HTKEKPFACEMCN-YRAASKIAIYAHMR 234 (304)
Q Consensus 208 H~~~~~~~C~~C~-k~F~~~~~L~~H~~ 234 (304)
|-=...|.|.+|| ++|..+.++.+|-.
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 4445568888888 88888888888843
No 199
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=41.76 E-value=11 Score=29.05 Aligned_cols=19 Identities=16% Similarity=0.184 Sum_probs=14.1
Q ss_pred CCcccCCCcccccChHHHH
Q psy3485 184 RNFMCFACPYYCRYGSSMA 202 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~ 202 (304)
+.=.|..||+.|++.....
T Consensus 27 RRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 27 RRRECLECHERFTTFERAE 45 (147)
T ss_pred ecccCCccCCccceeeecc
Confidence 4568999999998875443
No 200
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=41.71 E-value=4.3 Score=39.32 Aligned_cols=57 Identities=19% Similarity=0.371 Sum_probs=42.0
Q ss_pred ccccchhhccCHHHHHHHHHhhcCCCCCCCCCcc-ccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 215 ACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRY-HCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 215 ~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~-~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
.|..||=.|+--..|-.-.. + |.-+.| -|+.|.+.|....+ |.+|-+ |..|+.||=.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~--n-----TsM~~F~lC~~C~~EY~dP~n-----RRfHAQ---p~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRE--N-----TSMADFPLCPFCDKEYKDPLN-----RRFHAQ---PIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcc--c-----CccccCcCCHHHHHHhcCccc-----cccccc---cccCcccCCC
Confidence 59999999998766644333 3 555666 79999999888755 334454 8999999964
No 201
>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=40.83 E-value=8.5 Score=22.78 Aligned_cols=11 Identities=27% Similarity=0.338 Sum_probs=6.8
Q ss_pred CcccCCCcccc
Q psy3485 277 PTIQPECIKIL 287 (304)
Q Consensus 277 ~~~C~~C~k~F 287 (304)
++.|+.|++.|
T Consensus 13 ~~~C~~C~~~F 23 (43)
T PF01428_consen 13 PFKCKHCGKSF 23 (43)
T ss_dssp HEE-TTTS-EE
T ss_pred CeECCCCCccc
Confidence 67777777777
No 202
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=40.59 E-value=11 Score=20.93 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=6.2
Q ss_pred CCcccCCCcccc
Q psy3485 184 RNFMCFACPYYC 195 (304)
Q Consensus 184 ~~~~C~~C~k~f 195 (304)
-.+.|..|+.+|
T Consensus 20 ~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 20 DYEVCIFCGSSF 31 (33)
T ss_pred CeEEcccCCcEe
Confidence 344555555554
No 203
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=40.52 E-value=14 Score=32.44 Aligned_cols=77 Identities=18% Similarity=0.260 Sum_probs=42.4
Q ss_pred CcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHH
Q psy3485 185 NFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAIN 264 (304)
Q Consensus 185 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~ 264 (304)
.-.|++||..=. .++...-....|.|...|..|+-. +|+. .-.|+.||.+- .|.
T Consensus 184 ~~~CPvCGs~P~--~s~~~~~~~~~G~RyL~CslC~te--------W~~~------------R~~C~~Cg~~~----~l~ 237 (305)
T TIGR01562 184 RTLCPACGSPPV--ASMVRQGGKETGLRYLSCSLCATE--------WHYV------------RVKCSHCEESK----HLA 237 (305)
T ss_pred CCcCCCCCChhh--hhhhcccCCCCCceEEEcCCCCCc--------cccc------------CccCCCCCCCC----cee
Confidence 348999997521 111111112567788899999933 2333 45799999741 122
Q ss_pred HHHHhhcC--CC--CCCcccCCCcccccc
Q psy3485 265 RHTKYTHM--NT--SGPTIQPECIKILWS 289 (304)
Q Consensus 265 ~H~r~h~~--~~--~~~~~C~~C~k~F~~ 289 (304)
.. +..+ +. .+-..|..|+--++.
T Consensus 238 y~--~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 238 YL--SLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred eE--eecCCCCCcceEEeeccccccchhh
Confidence 11 1111 11 135689999865544
No 204
>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=40.08 E-value=7.2 Score=27.35 Aligned_cols=15 Identities=13% Similarity=0.217 Sum_probs=9.1
Q ss_pred CCCCcccCCCccccc
Q psy3485 182 MRRNFMCFACPYYCR 196 (304)
Q Consensus 182 ~~~~~~C~~C~k~f~ 196 (304)
+...+.|.-|++.|.
T Consensus 50 a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 50 STGIWTCRKCGAKFA 64 (91)
T ss_pred eeEEEEcCCCCCEEe
Confidence 344566666666664
No 205
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=39.52 E-value=14 Score=26.67 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=17.8
Q ss_pred ccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccc
Q psy3485 249 HCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWS 289 (304)
Q Consensus 249 ~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~ 289 (304)
.|+.|+..|.+. -+. .|.|+.|+..++.
T Consensus 4 ~CP~C~seytY~----------dg~---~~iCpeC~~EW~~ 31 (109)
T TIGR00686 4 PCPKCNSEYTYH----------DGT---QLICPSCLYEWNE 31 (109)
T ss_pred cCCcCCCcceEe----------cCC---eeECccccccccc
Confidence 477777766543 233 6788888777653
No 206
>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=39.03 E-value=8.4 Score=29.94 Aligned_cols=32 Identities=22% Similarity=0.292 Sum_probs=17.7
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
.|.|..|+..+ .+|.+. .. ..|.|..|+-.|.
T Consensus 123 ~~~C~~C~~~~------~r~~~~--~~--~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREY------KRHRRS--KR--KRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEe------eeeccc--ch--hhEECCCCCCEEE
Confidence 46777777665 233333 11 1477777776553
No 207
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=38.60 E-value=18 Score=19.81 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=15.0
Q ss_pred hhhhccccccCCCCCCcccCCCcc
Q psy3485 170 CKLCLRRKRKNPMRRNFMCFACPY 193 (304)
Q Consensus 170 C~~C~~~~~~h~~~~~~~C~~C~k 193 (304)
|..|+..+..-.+...++|..|..
T Consensus 4 C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 4 CGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred cCCCCcEeecCCCCCeEECCCCCe
Confidence 444555566666677777777754
No 208
>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=38.43 E-value=18 Score=34.27 Aligned_cols=36 Identities=19% Similarity=0.446 Sum_probs=22.6
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCccc
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPYY 194 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~ 194 (304)
..|..||.. .-|+.|+-.+..|.......|..||..
T Consensus 214 ~~C~~Cg~~-------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 214 LLCRSCGYI-------LCCPNCDVSLTYHKKEGKLRCHYCGYQ 249 (505)
T ss_pred eEhhhCcCc-------cCCCCCCCceEEecCCCeEEcCCCcCc
Confidence 467777765 236666666666666666667666643
No 209
>KOG0717|consensus
Probab=38.12 E-value=18 Score=33.38 Aligned_cols=22 Identities=14% Similarity=0.368 Sum_probs=20.3
Q ss_pred cccCCCcccccChHHHHHHHHh
Q psy3485 186 FMCFACPYYCRYGSSMAIHLRT 207 (304)
Q Consensus 186 ~~C~~C~k~f~~~~~l~~H~~~ 207 (304)
+-|.+|+|+|.+..+|..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999765
No 210
>PTZ00448 hypothetical protein; Provisional
Probab=37.91 E-value=23 Score=31.76 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=20.7
Q ss_pred ccccccCCccCCChHHHHHHHHh
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
.|.|..|+-.|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999999999999986
No 211
>KOG0402|consensus
Probab=37.57 E-value=17 Score=24.84 Aligned_cols=27 Identities=19% Similarity=0.461 Sum_probs=13.8
Q ss_pred hhhhccccccCCCCCCcccCCCccccc
Q psy3485 170 CKLCLRRKRKNPMRRNFMCFACPYYCR 196 (304)
Q Consensus 170 C~~C~~~~~~h~~~~~~~C~~C~k~f~ 196 (304)
|+.|++.........-|.|.-|.+.|.
T Consensus 39 CsfCGK~~vKR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 39 CSFCGKKTVKRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhcchhhhhhhceeEEecCCccceec
Confidence 333333333333445577777776664
No 212
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.46 E-value=17 Score=35.95 Aligned_cols=27 Identities=30% Similarity=0.666 Sum_probs=18.1
Q ss_pred CCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccc
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKI 286 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~ 286 (304)
...+...|..||.. ... +..|+.||..
T Consensus 404 ~~~~~l~Ch~Cg~~---------------~~~--~~~Cp~Cg~~ 430 (679)
T PRK05580 404 RFQRRLRCHHCGYQ---------------EPI--PKACPECGST 430 (679)
T ss_pred CCCCeEECCCCcCC---------------CCC--CCCCCCCcCC
Confidence 44556788888833 333 6788888765
No 213
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=37.41 E-value=13 Score=20.94 Aligned_cols=14 Identities=21% Similarity=0.116 Sum_probs=6.9
Q ss_pred cccCCCcccccchh
Q psy3485 278 TIQPECIKILWSFL 291 (304)
Q Consensus 278 ~~C~~C~k~F~~~~ 291 (304)
-.|..||+.|..++
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 46888888886654
No 214
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.33 E-value=10 Score=28.07 Aligned_cols=39 Identities=23% Similarity=0.237 Sum_probs=16.8
Q ss_pred ccCCCcccccChHHHHHHHHh-hCCCCccccccchhhccC
Q psy3485 187 MCFACPYYCRYGSSMAIHLRT-HTKEKPFACEMCNYRAAS 225 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~-H~~~~~~~C~~C~k~F~~ 225 (304)
+|+.|+.+........-=+.. |.=+-|--|..||+.|.+
T Consensus 41 qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpw 80 (160)
T COG4306 41 QCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPW 80 (160)
T ss_pred cCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCc
Confidence 566666554443211111111 222334446666666655
No 215
>PRK10220 hypothetical protein; Provisional
Probab=36.95 E-value=21 Score=25.92 Aligned_cols=29 Identities=28% Similarity=0.398 Sum_probs=17.8
Q ss_pred ccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccch
Q psy3485 249 HCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSF 290 (304)
Q Consensus 249 ~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~ 290 (304)
.|+.|+..|.+. -+. .|.|+.|+..++..
T Consensus 5 ~CP~C~seytY~----------d~~---~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYE----------DNG---MYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEc----------CCC---eEECCcccCcCCcc
Confidence 477777666532 222 57788777777543
No 216
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.65 E-value=21 Score=28.50 Aligned_cols=19 Identities=11% Similarity=0.410 Sum_probs=10.3
Q ss_pred CCCCCcccCCCcccccChH
Q psy3485 181 PMRRNFMCFACPYYCRYGS 199 (304)
Q Consensus 181 ~~~~~~~C~~C~k~f~~~~ 199 (304)
.....|.|+.|...|+.-.
T Consensus 109 ~~~~~y~C~~~~~r~sfde 127 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDE 127 (176)
T ss_pred ccCCceeCCCCCCcccHHH
Confidence 3344566666665555443
No 217
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=36.16 E-value=7.6 Score=23.74 Aligned_cols=16 Identities=25% Similarity=0.511 Sum_probs=9.0
Q ss_pred cccCCCchHHHHHHHH
Q psy3485 152 FFCIHCNGCVLYADLL 167 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~ 167 (304)
|.|+.|..+|....++
T Consensus 8 y~CDLCn~~~p~~~LR 23 (57)
T PF14445_consen 8 YSCDLCNSSHPISELR 23 (57)
T ss_pred HhHHhhcccCcHHHHH
Confidence 6666666666444433
No 218
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.86 E-value=11 Score=27.11 Aligned_cols=36 Identities=11% Similarity=0.067 Sum_probs=19.4
Q ss_pred CccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccch
Q psy3485 246 RRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSF 290 (304)
Q Consensus 246 ~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~ 290 (304)
..|.|+.||. ..-...+.+ +. .-..|+.||..|...
T Consensus 20 t~f~CP~Cge-~~v~v~~~k------~~--~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRCGK-VSISVKIKK------NI--AIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCCCC-eEeeeecCC------Cc--ceEECCCCCCccCEE
Confidence 4578888882 222111211 22 245788888877543
No 219
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=35.59 E-value=20 Score=22.01 Aligned_cols=12 Identities=17% Similarity=0.335 Sum_probs=5.3
Q ss_pred CcccCCCccccc
Q psy3485 185 NFMCFACPYYCR 196 (304)
Q Consensus 185 ~~~C~~C~k~f~ 196 (304)
.+.|..||..|.
T Consensus 4 ~l~C~dCg~~Fv 15 (49)
T PF13451_consen 4 TLTCKDCGAEFV 15 (49)
T ss_pred eEEcccCCCeEE
Confidence 344444444444
No 220
>KOG2071|consensus
Probab=35.58 E-value=23 Score=33.72 Aligned_cols=31 Identities=10% Similarity=0.180 Sum_probs=24.0
Q ss_pred CCCccccccCCccCCChHHHHHHHHhhcCCC
Q psy3485 244 EERRYHCAFCNFTSPTQWAINRHTKYTHMNT 274 (304)
Q Consensus 244 ~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~ 274 (304)
...+-.|..||++|........||-.|-..+
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~dwh 445 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDDWH 445 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhhhh
Confidence 3456889999999998888888887776543
No 221
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.50 E-value=19 Score=32.88 Aligned_cols=14 Identities=14% Similarity=0.527 Sum_probs=8.2
Q ss_pred ccccccCCccCCCh
Q psy3485 247 RYHCAFCNFTSPTQ 260 (304)
Q Consensus 247 ~~~C~~C~k~F~~~ 260 (304)
-|.|+.||..+.+.
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 56666666655544
No 222
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=35.37 E-value=7.3 Score=28.70 Aligned_cols=15 Identities=20% Similarity=0.487 Sum_probs=8.8
Q ss_pred CCcccCCCcccccCh
Q psy3485 184 RNFMCFACPYYCRYG 198 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~ 198 (304)
..+.|.-||..+...
T Consensus 21 ~~l~C~kCgye~~~~ 35 (113)
T COG1594 21 GKLVCRKCGYEEEAS 35 (113)
T ss_pred cEEECCCCCcchhcc
Confidence 356666666655444
No 223
>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=35.10 E-value=13 Score=21.70 Aligned_cols=11 Identities=18% Similarity=0.621 Sum_probs=5.6
Q ss_pred ccccccCCccC
Q psy3485 247 RYHCAFCNFTS 257 (304)
Q Consensus 247 ~~~C~~C~k~F 257 (304)
+-.|++||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 34555555544
No 224
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.89 E-value=9.1 Score=26.81 Aligned_cols=16 Identities=13% Similarity=0.094 Sum_probs=9.4
Q ss_pred CCCCCcccCCCccccc
Q psy3485 181 PMRRNFMCFACPYYCR 196 (304)
Q Consensus 181 ~~~~~~~C~~C~k~f~ 196 (304)
.+-..+.|.-|++.|.
T Consensus 50 ~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 50 VGTGIWECRKCGAKFA 65 (90)
T ss_pred EEEEEEEcCCCCCEEe
Confidence 3344566666666664
No 225
>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=34.51 E-value=15 Score=27.20 Aligned_cols=15 Identities=13% Similarity=0.129 Sum_probs=7.7
Q ss_pred CCCcccCCCcccccC
Q psy3485 183 RRNFMCFACPYYCRY 197 (304)
Q Consensus 183 ~~~~~C~~C~k~f~~ 197 (304)
.-.+.|..|+..|..
T Consensus 68 p~~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 68 PVECECEDCSEEVSP 82 (115)
T ss_pred CcEEEcccCCCEEec
Confidence 334555555555544
No 226
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=34.44 E-value=18 Score=27.94 Aligned_cols=32 Identities=28% Similarity=0.621 Sum_probs=17.4
Q ss_pred ccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccC
Q psy3485 213 PFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTS 257 (304)
Q Consensus 213 ~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F 257 (304)
.|.|..|+..+. +|.| + .....|.|..|+-.|
T Consensus 112 ~y~C~~C~~~~~------~~rr-~------~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYL------RVRR-S------NNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCc------eEcc-c------cCcceEEcCCCCCEE
Confidence 467776776553 2333 2 222457777776554
No 227
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=34.00 E-value=20 Score=19.96 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=8.9
Q ss_pred cccCCCchHH----HHHHHH
Q psy3485 152 FFCIHCNGCV----LYADLL 167 (304)
Q Consensus 152 ~~C~~C~~~f----l~~H~~ 167 (304)
|.|+.|++.+ +..|+.
T Consensus 5 ~~C~nC~R~v~a~RfA~HLe 24 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPHLE 24 (33)
T ss_dssp EE-TTTSSEEEGGGHHHHHH
T ss_pred EECCCCcCCcchhhhHHHHH
Confidence 5666666655 555554
No 228
>KOG2461|consensus
Probab=33.60 E-value=13 Score=33.89 Aligned_cols=87 Identities=6% Similarity=-0.217 Sum_probs=57.9
Q ss_pred CcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhh
Q psy3485 191 CPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYT 270 (304)
Q Consensus 191 C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h 270 (304)
++..+.....+..|...+++..+.-+.++.+.+.....+..|.. .| ..+.++.+..+...+.+...+..+..+|
T Consensus 309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 382 (396)
T KOG2461|consen 309 ARLSLPKQLVLDQSEVPATVSVWTGETIPVRTPAGQLIYTQSHS-ME-----VAEPTDMAPNQIWKIYHTGVLGFLIITT 382 (396)
T ss_pred cCcccccccccccccccccccccCcCcccccccccccchhhhhh-cc-----cCCCCcccccccccceeccccceeeeec
Confidence 44555556666667777777777777777777777777777777 66 5666666665555555555566666666
Q ss_pred cCCCCCCcccCCCcc
Q psy3485 271 HMNTSGPTIQPECIK 285 (304)
Q Consensus 271 ~~~~~~~~~C~~C~k 285 (304)
+... .+.+..|++
T Consensus 383 ~~~~--~~~~~~~~~ 395 (396)
T KOG2461|consen 383 DESE--CNNMSFVCK 395 (396)
T ss_pred cccc--cccccccCC
Confidence 6665 677766654
No 229
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=33.16 E-value=21 Score=21.97 Aligned_cols=9 Identities=33% Similarity=1.143 Sum_probs=4.1
Q ss_pred ccccccchh
Q psy3485 213 PFACEMCNY 221 (304)
Q Consensus 213 ~~~C~~C~k 221 (304)
.+.|..||.
T Consensus 37 r~~C~~Cgy 45 (50)
T PRK00432 37 RWHCGKCGY 45 (50)
T ss_pred cEECCCcCC
Confidence 344444443
No 230
>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=32.89 E-value=5.6 Score=26.58 Aligned_cols=14 Identities=29% Similarity=0.660 Sum_probs=4.7
Q ss_pred ccccccCCccCCCh
Q psy3485 247 RYHCAFCNFTSPTQ 260 (304)
Q Consensus 247 ~~~C~~C~k~F~~~ 260 (304)
...|..|++.+...
T Consensus 41 ~v~Cg~C~~~~~~~ 54 (71)
T PF05495_consen 41 RVICGKCRTEQPID 54 (71)
T ss_dssp EEEETTT--EEES-
T ss_pred CeECCCCCCccChh
Confidence 34444444444333
No 231
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.86 E-value=21 Score=20.79 Aligned_cols=21 Identities=14% Similarity=0.142 Sum_probs=13.9
Q ss_pred CcccCCCcccccchhHHHHHH
Q psy3485 277 PTIQPECIKILWSFLSYFIWI 297 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~ 297 (304)
-+.|+.|+=.|-....|-..+
T Consensus 19 id~C~~C~G~W~d~~el~~~~ 39 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEKLL 39 (41)
T ss_pred EEECCCCCeEEccHHHHHHHH
Confidence 567777777776666665544
No 232
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=32.85 E-value=36 Score=26.81 Aligned_cols=11 Identities=45% Similarity=0.924 Sum_probs=5.2
Q ss_pred cccCCCccccc
Q psy3485 278 TIQPECIKILW 288 (304)
Q Consensus 278 ~~C~~C~k~F~ 288 (304)
+.|+.||+-|.
T Consensus 131 ~~C~~CgkiYW 141 (165)
T COG1656 131 YRCPKCGKIYW 141 (165)
T ss_pred eECCCCccccc
Confidence 44555544443
No 233
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.73 E-value=27 Score=31.45 Aligned_cols=19 Identities=11% Similarity=0.317 Sum_probs=12.0
Q ss_pred ccccccCCccCCChHHHHH
Q psy3485 247 RYHCAFCNFTSPTQWAINR 265 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~ 265 (304)
-++|+.||..|..+.++-+
T Consensus 15 ~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 15 DVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred cccccccCCcCCchhhhhh
Confidence 3447777777776665544
No 234
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=32.43 E-value=17 Score=28.04 Aligned_cols=17 Identities=24% Similarity=0.305 Sum_probs=12.4
Q ss_pred CCCcccCCCcccccChH
Q psy3485 183 RRNFMCFACPYYCRYGS 199 (304)
Q Consensus 183 ~~~~~C~~C~k~f~~~~ 199 (304)
.+.=.|..||..|++..
T Consensus 26 RRRReC~~C~~RFTTfE 42 (156)
T COG1327 26 RRRRECLECGERFTTFE 42 (156)
T ss_pred hhhhcccccccccchhh
Confidence 34558888888888764
No 235
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=32.31 E-value=22 Score=29.90 Aligned_cols=18 Identities=17% Similarity=0.218 Sum_probs=12.1
Q ss_pred CCCCccccccchhhccCH
Q psy3485 209 TKEKPFACEMCNYRAASK 226 (304)
Q Consensus 209 ~~~~~~~C~~C~k~F~~~ 226 (304)
+|-..|.|..|+..|+.-
T Consensus 151 wG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 151 WGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred cceeeeecccccccchhh
Confidence 444557788888777754
No 236
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=32.09 E-value=51 Score=20.75 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=18.4
Q ss_pred HHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHH
Q psy3485 228 AIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRH 266 (304)
Q Consensus 228 ~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H 266 (304)
.|...+|..| +-|-.||..|.+...|.++
T Consensus 18 ~l~~YLR~~~----------~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 18 KLLSYLREEH----------NYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred HHHHHHHhhC----------ceeeeeCCccCCHHHHHhC
Confidence 4555556455 6677777777777666543
No 237
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.91 E-value=26 Score=20.63 Aligned_cols=17 Identities=12% Similarity=0.229 Sum_probs=10.5
Q ss_pred ccccchhhccCHHHHHH
Q psy3485 215 ACEMCNYRAASKIAIYA 231 (304)
Q Consensus 215 ~C~~C~k~F~~~~~L~~ 231 (304)
.|.+||+.|+.+-...+
T Consensus 10 ~C~~C~rpf~WRKKW~~ 26 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWAR 26 (42)
T ss_pred cCcccCCcchHHHHHHH
Confidence 46777777766655443
No 238
>KOG0696|consensus
Probab=31.51 E-value=13 Score=33.96 Aligned_cols=47 Identities=19% Similarity=0.335 Sum_probs=20.3
Q ss_pred HHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCC
Q psy3485 202 AIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCN 254 (304)
Q Consensus 202 ~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~ 254 (304)
..|.|.|.= -.|.|+-=++.+.+-..-..|.-..| +-..|--|.+||
T Consensus 82 vvHkrChef-VtF~CPGadkg~dtDdpr~kHkf~~~-----tYssPTFCDhCG 128 (683)
T KOG0696|consen 82 VVHKRCHEF-VTFSCPGADKGPDTDDPRSKHKFKIH-----TYSSPTFCDHCG 128 (683)
T ss_pred hhhhhhcce-EEEECCCCCCCCCCCCcccccceeee-----ecCCCchhhhHH
Confidence 345454421 22444444444444444444433344 444444444444
No 239
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=31.50 E-value=16 Score=29.77 Aligned_cols=8 Identities=25% Similarity=0.887 Sum_probs=0.0
Q ss_pred CcccCCCc
Q psy3485 185 NFMCFACP 192 (304)
Q Consensus 185 ~~~C~~C~ 192 (304)
.|.|.+||
T Consensus 101 ey~CEICG 108 (196)
T PF11931_consen 101 EYKCEICG 108 (196)
T ss_dssp --------
T ss_pred eeeeEeCC
Confidence 35555555
No 240
>PRK04351 hypothetical protein; Provisional
Probab=31.48 E-value=22 Score=27.63 Aligned_cols=32 Identities=16% Similarity=0.201 Sum_probs=18.9
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCccccc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILW 288 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~ 288 (304)
.|.|..||..+.+. |.|.. ..|.|..|+-.+.
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~n~---~~yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRINT---KRYRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeeee-------eecCC---CcEEeCCCCcEee
Confidence 47777777666443 22222 2678888776654
No 241
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=31.43 E-value=38 Score=34.11 Aligned_cols=13 Identities=8% Similarity=0.135 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHhh
Q psy3485 27 IIVARKMWTKLKK 39 (304)
Q Consensus 27 ~~iC~~C~~~l~~ 39 (304)
..++..=|..+..
T Consensus 606 R~~~~~vf~~~~~ 618 (784)
T PF04931_consen 606 RKVSEQVFEAFCP 618 (784)
T ss_pred HHHHHHHHHHHHh
Confidence 3444444554443
No 242
>PRK12496 hypothetical protein; Provisional
Probab=31.35 E-value=29 Score=27.43 Aligned_cols=10 Identities=20% Similarity=0.301 Sum_probs=5.1
Q ss_pred cccccCCccC
Q psy3485 248 YHCAFCNFTS 257 (304)
Q Consensus 248 ~~C~~C~k~F 257 (304)
|.|.-|++.|
T Consensus 128 ~~C~gC~~~~ 137 (164)
T PRK12496 128 KVCKGCKKKY 137 (164)
T ss_pred EECCCCCccc
Confidence 4455555444
No 243
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=31.21 E-value=11 Score=23.06 Aligned_cols=16 Identities=19% Similarity=0.382 Sum_probs=12.1
Q ss_pred cccCCCch-HHHHHHHH
Q psy3485 152 FFCIHCNG-CVLYADLL 167 (304)
Q Consensus 152 ~~C~~C~~-~fl~~H~~ 167 (304)
-.|+-||- +|+..|..
T Consensus 20 ~~CPrCG~gvfmA~H~d 36 (51)
T COG1998 20 RFCPRCGPGVFMADHKD 36 (51)
T ss_pred ccCCCCCCcchhhhcCc
Confidence 46999996 77887764
No 244
>KOG2807|consensus
Probab=31.01 E-value=44 Score=29.34 Aligned_cols=73 Identities=19% Similarity=0.316 Sum_probs=47.8
Q ss_pred CccccccchhhccCHHHHHHHHHhhcCCCC------CCCC--CccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCC
Q psy3485 212 KPFACEMCNYRAASKIAIYAHMRTTHIMPD------TSEE--RRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPEC 283 (304)
Q Consensus 212 ~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~------~~~~--~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C 283 (304)
-|..|++|+-+......|.+-.+ |+.|- +.++ +--.|-.|+-. -.+. ..|.|..|
T Consensus 289 LP~eCpiC~ltLVss~hLARSyh--hL~PL~~F~Eip~~~~~~~~~Cf~C~~~-------------~~~~--~~y~C~~C 351 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYH--HLFPLKPFVEIPETEYNGSRFCFACQGE-------------LLSS--GRYRCESC 351 (378)
T ss_pred CCccCCccceeEecchHHHHHHH--hhcCCcchhhccccccCCCcceeeeccc-------------cCCC--CcEEchhc
Confidence 46788999988888888766544 55441 1122 11126666111 1112 26999999
Q ss_pred cccccchhHHHHHHhhcc
Q psy3485 284 IKILWSFLSYFIWISVDV 301 (304)
Q Consensus 284 ~k~F~~~~~l~~h~~~~~ 301 (304)
...|=.--..++|-+.|.
T Consensus 352 k~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 352 KNVFCLDCDVFIHESLHN 369 (378)
T ss_pred cceeeccchHHHHhhhhc
Confidence 999999999999998885
No 245
>KOG0320|consensus
Probab=30.78 E-value=27 Score=27.84 Aligned_cols=53 Identities=13% Similarity=0.238 Sum_probs=30.2
Q ss_pred CCCCcccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHHHHHHHHHhhcCCCCCCCCCccccccCCccCCCh
Q psy3485 182 MRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQ 260 (304)
Q Consensus 182 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~ 260 (304)
.+..|.|++|--.|..+.- --..||..|-..-. +.-.+.. .+|+.|+|....+
T Consensus 128 ~~~~~~CPiCl~~~sek~~--------------vsTkCGHvFC~~Ci-k~alk~~-----------~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVP--------------VSTKCGHVFCSQCI-KDALKNT-----------NKCPTCRKKITHK 180 (187)
T ss_pred cccccCCCceecchhhccc--------------cccccchhHHHHHH-HHHHHhC-----------CCCCCcccccchh
Confidence 3445888888877766542 11347777765433 2333323 3688888754433
No 246
>PRK01343 zinc-binding protein; Provisional
Probab=30.68 E-value=28 Score=22.10 Aligned_cols=13 Identities=23% Similarity=0.383 Sum_probs=8.6
Q ss_pred CccccccCCccCC
Q psy3485 246 RRYHCAFCNFTSP 258 (304)
Q Consensus 246 ~~~~C~~C~k~F~ 258 (304)
....|++|+|.|.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3456777777764
No 247
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=30.48 E-value=26 Score=25.18 Aligned_cols=26 Identities=23% Similarity=0.179 Sum_probs=20.3
Q ss_pred CCCCccccccCCccCCChHHHHHHHH
Q psy3485 243 SEERRYHCAFCNFTSPTQWAINRHTK 268 (304)
Q Consensus 243 ~~~~~~~C~~C~k~F~~~~~L~~H~r 268 (304)
.|-..|-|-.|.+-|.+...|..|.+
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhc
Confidence 45556788888888888888888875
No 248
>KOG0782|consensus
Probab=30.16 E-value=17 Score=34.41 Aligned_cols=57 Identities=11% Similarity=0.105 Sum_probs=35.6
Q ss_pred HHHHHHHhhcCCCCCCCCCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchh--HHHHHH
Q psy3485 228 AIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFL--SYFIWI 297 (304)
Q Consensus 228 ~L~~H~~~~H~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~--~l~~h~ 297 (304)
.|.+|-- +| ....-=+|..|||.|..+-. .|..+. --..|.-|-..|.++- .|+.||
T Consensus 240 ~fvrHHW-VH-----rrRqeGkC~~CgKgFQQKf~------FhsKEi-vAisCSWCKqayH~KvtCFml~~i 298 (1004)
T KOG0782|consen 240 GFVRHHW-VH-----RRRQEGKCNTCGKGFQQKFF------FHSKEI-VAISCSWCKQAYHLKVTCFMLDKI 298 (1004)
T ss_pred cchHHhH-hh-----Hhhhccccchhhhhhhhhee------eccccE-EEEEehHHHHHhhcchhhhhhhhh
Confidence 5555554 44 32223479999999877633 344443 3478999999997776 344444
No 249
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=29.99 E-value=27 Score=28.20 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=11.4
Q ss_pred CCCcccCCCcccccChH
Q psy3485 183 RRNFMCFACPYYCRYGS 199 (304)
Q Consensus 183 ~~~~~C~~C~k~f~~~~ 199 (304)
.-||.|-+|-+.|....
T Consensus 194 ~IPF~C~iCKkdy~spv 210 (259)
T COG5152 194 KIPFLCGICKKDYESPV 210 (259)
T ss_pred CCceeehhchhhccchh
Confidence 35677777777776653
No 250
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=29.85 E-value=28 Score=20.10 Aligned_cols=9 Identities=33% Similarity=0.958 Sum_probs=3.8
Q ss_pred cccccchhh
Q psy3485 214 FACEMCNYR 222 (304)
Q Consensus 214 ~~C~~C~k~ 222 (304)
|.|..||+.
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 344444433
No 251
>KOG0957|consensus
Probab=29.77 E-value=32 Score=32.03 Aligned_cols=45 Identities=20% Similarity=0.387 Sum_probs=31.4
Q ss_pred cccCCCchHHHHHHHHHHhhhhccc------------cccCCCCCCcccCCCcccccC
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRR------------KRKNPMRRNFMCFACPYYCRY 197 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~------------~~~h~~~~~~~C~~C~k~f~~ 197 (304)
|.|-+|.++ ..+|++..|..|... +......--|+|..|++.=++
T Consensus 545 ysCgiCkks-~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~esS 601 (707)
T KOG0957|consen 545 YSCGICKKS-TDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKNESS 601 (707)
T ss_pred eeeeeeccc-hhhHHHhhcchhhceeeccccCCccccCcccccCcceeecccccccCc
Confidence 899999988 788988888888776 122222234788888765443
No 252
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=29.77 E-value=33 Score=31.94 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=22.6
Q ss_pred CCCCCCcccCCCcccccChHHHHHHHHh-hCCC
Q psy3485 180 NPMRRNFMCFACPYYCRYGSSMAIHLRT-HTKE 211 (304)
Q Consensus 180 h~~~~~~~C~~C~k~f~~~~~l~~H~~~-H~~~ 211 (304)
+..=+-+.|+.|.+.|.....+..|+.. |.+.
T Consensus 52 n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 52 NKSWRFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred cCceeEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 3334567888888888888888888764 6543
No 253
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=29.61 E-value=21 Score=20.70 Aligned_cols=9 Identities=33% Similarity=1.184 Sum_probs=3.7
Q ss_pred Cccccccch
Q psy3485 212 KPFACEMCN 220 (304)
Q Consensus 212 ~~~~C~~C~ 220 (304)
+.+.|..|+
T Consensus 23 ~~w~C~~C~ 31 (40)
T PF04810_consen 23 KTWICNFCG 31 (40)
T ss_dssp TEEEETTT-
T ss_pred CEEECcCCC
Confidence 344444444
No 254
>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=29.34 E-value=27 Score=19.84 Aligned_cols=10 Identities=20% Similarity=0.577 Sum_probs=5.1
Q ss_pred ccCCCccccc
Q psy3485 187 MCFACPYYCR 196 (304)
Q Consensus 187 ~C~~C~k~f~ 196 (304)
.|+.||+.|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4555555554
No 255
>KOG3214|consensus
Probab=29.00 E-value=16 Score=25.92 Aligned_cols=42 Identities=14% Similarity=0.392 Sum_probs=21.1
Q ss_pred CCccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccchhH
Q psy3485 245 ERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWSFLS 292 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~~~~ 292 (304)
+..|.|..|+..-.-.-.|. .-+... ...|.+|+.+|.+.-+
T Consensus 21 dt~FnClfcnHek~v~~~~D----k~~~iG--~~sC~iC~esFqt~it 62 (109)
T KOG3214|consen 21 DTQFNCLFCNHEKSVSCTLD----KKHNIG--KASCRICEESFQTTIT 62 (109)
T ss_pred heeeccCccccccceeeeeh----hhcCcc--eeeeeehhhhhccchH
Confidence 34577777765432221111 112221 4677777777766544
No 256
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.55 E-value=29 Score=31.79 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=17.3
Q ss_pred ccCCCcccccChHHHHHHHHhhCCCCccccccchhhccCHH
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKI 227 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~ 227 (304)
.|+.||.+..+. |..-|+|..||..+....
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCccc
Confidence 666777664333 223577777776665543
No 257
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.15 E-value=29 Score=19.70 Aligned_cols=13 Identities=31% Similarity=0.475 Sum_probs=7.4
Q ss_pred CcccCCCcccccc
Q psy3485 277 PTIQPECIKILWS 289 (304)
Q Consensus 277 ~~~C~~C~k~F~~ 289 (304)
+-.|+-|+|+|--
T Consensus 2 ~~~CprC~kg~Hw 14 (36)
T PF14787_consen 2 PGLCPRCGKGFHW 14 (36)
T ss_dssp --C-TTTSSSCS-
T ss_pred CccCcccCCCcch
Confidence 4568999998843
No 258
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=28.08 E-value=22 Score=27.52 Aligned_cols=9 Identities=22% Similarity=0.726 Sum_probs=6.5
Q ss_pred cccCCCchH
Q psy3485 152 FFCIHCNGC 160 (304)
Q Consensus 152 ~~C~~C~~~ 160 (304)
|.|..||..
T Consensus 113 l~C~~Cg~~ 121 (146)
T PF07295_consen 113 LVCENCGHE 121 (146)
T ss_pred EecccCCCE
Confidence 777777755
No 259
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.92 E-value=34 Score=33.84 Aligned_cols=36 Identities=22% Similarity=0.631 Sum_probs=20.1
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCccc
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPYY 194 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~ 194 (304)
..|..||.. .-|+.|+-.+..|.......|..||..
T Consensus 382 ~~C~~Cg~~-------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 382 LLCRDCGWV-------AECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred eEhhhCcCc-------cCCCCCCCceeEECCCCeEECCCCcCC
Confidence 457777755 225555555555555555566666543
No 260
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=27.89 E-value=22 Score=25.55 Aligned_cols=22 Identities=9% Similarity=0.048 Sum_probs=20.6
Q ss_pred CcccCCCcccccchhHHHHHHh
Q psy3485 277 PTIQPECIKILWSFLSYFIWIS 298 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~~ 298 (304)
.|.|-.|.+-|-+...|+.|.+
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 5999999999999999999986
No 261
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.37 E-value=35 Score=24.39 Aligned_cols=14 Identities=14% Similarity=0.252 Sum_probs=9.8
Q ss_pred ccccccCCccCCCh
Q psy3485 247 RYHCAFCNFTSPTQ 260 (304)
Q Consensus 247 ~~~C~~C~k~F~~~ 260 (304)
|+.|..||..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 56777777777764
No 262
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=27.11 E-value=9.7 Score=37.70 Aligned_cols=39 Identities=18% Similarity=0.308 Sum_probs=20.1
Q ss_pred ccCCCcccccChHHHHHHHHhhCCCCcc-ccccchhhccCH
Q psy3485 187 MCFACPYYCRYGSSMAIHLRTHTKEKPF-ACEMCNYRAASK 226 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~-~C~~C~k~F~~~ 226 (304)
.|..||=+|+-...|-.- |.++.-+.| -|+.|-+.|.+.
T Consensus 92 nCt~CGPr~~i~~~lpyd-r~~t~m~~f~~C~~C~~ey~~p 131 (711)
T TIGR00143 92 SCTHCGPRFTIIEALPYD-RENTSMADFPLCPDCAKEYKDP 131 (711)
T ss_pred cccCCCCCeEEeecCCCC-CCCcCCCCCcCCHHHHHHhcCC
Confidence 566677666644433221 123333334 477777666654
No 263
>KOG2807|consensus
Probab=27.03 E-value=79 Score=27.87 Aligned_cols=22 Identities=14% Similarity=0.159 Sum_probs=16.3
Q ss_pred CCCcccCCCcccccChHHHHHH
Q psy3485 183 RRNFMCFACPYYCRYGSSMAIH 204 (304)
Q Consensus 183 ~~~~~C~~C~k~f~~~~~l~~H 204 (304)
.-|..|++|+.+......|.+-
T Consensus 288 sLP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 288 SLPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred cCCccCCccceeEecchHHHHH
Confidence 3567888888888777776653
No 264
>PRK11827 hypothetical protein; Provisional
Probab=26.74 E-value=34 Score=22.04 Aligned_cols=28 Identities=14% Similarity=0.326 Sum_probs=13.0
Q ss_pred hhhhccccccCCCCCCcccCCCcccccC
Q psy3485 170 CKLCLRRKRKNPMRRNFMCFACPYYCRY 197 (304)
Q Consensus 170 C~~C~~~~~~h~~~~~~~C~~C~k~f~~ 197 (304)
|+.|.-.+....+.....|..|+..|.-
T Consensus 11 CP~ckg~L~~~~~~~~Lic~~~~laYPI 38 (60)
T PRK11827 11 CPVCNGKLWYNQEKQELICKLDNLAFPL 38 (60)
T ss_pred CCCCCCcCeEcCCCCeEECCccCeeccc
Confidence 3333333333333344556666666543
No 265
>COG1773 Rubredoxin [Energy production and conversion]
Probab=26.64 E-value=28 Score=21.96 Aligned_cols=11 Identities=9% Similarity=-0.079 Sum_probs=7.1
Q ss_pred CcccCCCcccc
Q psy3485 277 PTIQPECIKIL 287 (304)
Q Consensus 277 ~~~C~~C~k~F 287 (304)
.|+|..||..|
T Consensus 3 ~~~C~~CG~vY 13 (55)
T COG1773 3 RWRCSVCGYVY 13 (55)
T ss_pred ceEecCCceEe
Confidence 46677776655
No 266
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=26.51 E-value=19 Score=22.74 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=4.2
Q ss_pred ccCCCcccc
Q psy3485 187 MCFACPYYC 195 (304)
Q Consensus 187 ~C~~C~k~f 195 (304)
+|-.|++.+
T Consensus 4 kC~lCdk~~ 12 (56)
T PF09963_consen 4 KCILCDKKE 12 (56)
T ss_pred EEEecCCEE
Confidence 444455444
No 267
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.42 E-value=26 Score=25.97 Aligned_cols=14 Identities=14% Similarity=0.339 Sum_probs=6.5
Q ss_pred CCcccCCCcccccC
Q psy3485 184 RNFMCFACPYYCRY 197 (304)
Q Consensus 184 ~~~~C~~C~k~f~~ 197 (304)
-.+.|..||..|..
T Consensus 70 ~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 70 VELECKDCSHVFKP 83 (117)
T ss_pred CEEEhhhCCCcccc
Confidence 33455555544433
No 268
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.37 E-value=29 Score=26.20 Aligned_cols=36 Identities=8% Similarity=0.107 Sum_probs=20.7
Q ss_pred ccccccCCccCCChHHHHHHHHhhcCCCCCCcccCCCcccccc
Q psy3485 247 RYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKILWS 289 (304)
Q Consensus 247 ~~~C~~C~k~F~~~~~L~~H~r~h~~~~~~~~~C~~C~k~F~~ 289 (304)
+-.|+.|+.....+ +-..-.+. ..|+|+.|+++|..
T Consensus 30 ~~~cP~C~s~~~~k-----~g~~~~~~--qRyrC~~C~~tf~~ 65 (129)
T COG3677 30 KVNCPRCKSSNVVK-----IGGIRRGH--QRYKCKSCGSTFTV 65 (129)
T ss_pred cCcCCCCCccceee-----ECCccccc--cccccCCcCcceee
Confidence 35788888553111 11111122 37999999999954
No 269
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=26.27 E-value=20 Score=35.31 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=7.9
Q ss_pred ccccchhhccCH
Q psy3485 215 ACEMCNYRAASK 226 (304)
Q Consensus 215 ~C~~C~k~F~~~ 226 (304)
.|..|++.|.+.
T Consensus 462 tC~~C~kkFfSl 473 (1374)
T PTZ00303 462 SCPSCGRAFISL 473 (1374)
T ss_pred cccCcCCccccc
Confidence 477777777554
No 270
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=26.21 E-value=46 Score=21.00 Aligned_cols=10 Identities=40% Similarity=0.743 Sum_probs=4.5
Q ss_pred CcccCCCccc
Q psy3485 185 NFMCFACPYY 194 (304)
Q Consensus 185 ~~~C~~C~k~ 194 (304)
.|.|+.||-.
T Consensus 14 ~~~Cp~cGip 23 (55)
T PF13824_consen 14 NFECPDCGIP 23 (55)
T ss_pred CCcCCCCCCc
Confidence 3444444443
No 271
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=26.14 E-value=40 Score=20.31 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=13.9
Q ss_pred cCCCCCCcccCCCcccccCh
Q psy3485 179 KNPMRRNFMCFACPYYCRYG 198 (304)
Q Consensus 179 ~h~~~~~~~C~~C~k~f~~~ 198 (304)
.........|+.|+..|...
T Consensus 8 ~~~~~~~i~C~~C~~~~H~~ 27 (51)
T PF00628_consen 8 SDDDGDMIQCDSCNRWYHQE 27 (51)
T ss_dssp SCTTSSEEEBSTTSCEEETT
T ss_pred cCCCCCeEEcCCCChhhCcc
Confidence 34456678888888877654
No 272
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=25.44 E-value=69 Score=29.92 Aligned_cols=22 Identities=14% Similarity=0.222 Sum_probs=12.3
Q ss_pred cccccCCccCCChHHHHHHHHh
Q psy3485 248 YHCAFCNFTSPTQWAINRHTKY 269 (304)
Q Consensus 248 ~~C~~C~k~F~~~~~L~~H~r~ 269 (304)
..|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 4555555555555555555553
No 273
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.36 E-value=24 Score=22.23 Aligned_cols=10 Identities=20% Similarity=0.305 Sum_probs=2.6
Q ss_pred CcccCCCccc
Q psy3485 277 PTIQPECIKI 286 (304)
Q Consensus 277 ~~~C~~C~k~ 286 (304)
.|.|++||.+
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 4667777654
No 274
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=25.35 E-value=11 Score=21.08 Aligned_cols=10 Identities=30% Similarity=0.218 Sum_probs=5.6
Q ss_pred cccCCCcccc
Q psy3485 278 TIQPECIKIL 287 (304)
Q Consensus 278 ~~C~~C~k~F 287 (304)
|.|..|++.+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5555555554
No 275
>PTZ00448 hypothetical protein; Provisional
Probab=25.23 E-value=49 Score=29.72 Aligned_cols=24 Identities=17% Similarity=0.350 Sum_probs=21.2
Q ss_pred CCcccCCCcccccChHHHHHHHHh
Q psy3485 184 RNFMCFACPYYCRYGSSMAIHLRT 207 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~~H~~~ 207 (304)
..|.|..|+..|.+....+.|+++
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CCccccccccccCCHHHHHHHhhh
Confidence 368899999999988999999987
No 276
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=25.21 E-value=24 Score=35.24 Aligned_cols=36 Identities=17% Similarity=0.461 Sum_probs=0.0
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCccccc
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCR 196 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~ 196 (304)
+.|+.||..-+ ...|+.|+-... ..|.|+.|+....
T Consensus 656 r~Cp~Cg~~t~----~~~Cp~CG~~T~-----~~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 656 RRCPKCGKETF----YNRCPECGSHTE-----PVYVCPDCGIEVE 691 (900)
T ss_dssp ---------------------------------------------
T ss_pred ccCcccCCcch----hhcCcccCCccc-----cceeccccccccC
Confidence 67888885421 122555543322 2356666666543
No 277
>KOG1729|consensus
Probab=25.07 E-value=19 Score=31.24 Aligned_cols=8 Identities=25% Similarity=0.658 Sum_probs=4.2
Q ss_pred cccCCCch
Q psy3485 152 FFCIHCNG 159 (304)
Q Consensus 152 ~~C~~C~~ 159 (304)
-.|..|++
T Consensus 169 ~~C~~C~~ 176 (288)
T KOG1729|consen 169 TECMVCGC 176 (288)
T ss_pred eecccCCC
Confidence 44555555
No 278
>KOG2636|consensus
Probab=25.04 E-value=47 Score=30.53 Aligned_cols=29 Identities=14% Similarity=0.382 Sum_probs=24.3
Q ss_pred ccCCCCCCcccCCCc-ccccChHHHHHHHH
Q psy3485 178 RKNPMRRNFMCFACP-YYCRYGSSMAIHLR 206 (304)
Q Consensus 178 ~~h~~~~~~~C~~C~-k~f~~~~~l~~H~~ 206 (304)
+.|.=...|.|.+|| +++..+.++.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 345556779999999 99999999999966
No 279
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=24.84 E-value=25 Score=23.16 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=11.3
Q ss_pred hccccccCCCCCCcccCCCccccc
Q psy3485 173 CLRRKRKNPMRRNFMCFACPYYCR 196 (304)
Q Consensus 173 C~~~~~~h~~~~~~~C~~C~k~f~ 196 (304)
|++.+-...+.+.-.| .||+...
T Consensus 8 Cgr~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 8 CGRYLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp TS--EEEETT-SEEEE-TTTEEEE
T ss_pred CCCEEEecCCcceeEe-cCCCeee
Confidence 4444555555566666 6666543
No 280
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=24.52 E-value=14 Score=25.90 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=20.1
Q ss_pred CccccCCCchHH----HHHHHHHHhhhhccccc
Q psy3485 150 DQFFCIHCNGCV----LYADLLDHCKLCLRRKR 178 (304)
Q Consensus 150 ~~~~C~~C~~~f----l~~H~~~hC~~C~~~~~ 178 (304)
..|.|..||... -....+.||+.|...+.
T Consensus 3 ~~F~C~~CG~~V~p~~~g~~~RNHCP~CL~S~H 35 (92)
T PF12647_consen 3 ESFTCVHCGLTVSPLAAGSAHRNHCPSCLSSLH 35 (92)
T ss_pred cccCccccCCCcccCCCCCCccCcCcccccccc
Confidence 358999999877 33445677888876643
No 281
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.27 E-value=39 Score=21.65 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=8.6
Q ss_pred CCCccccccCCccCCC
Q psy3485 244 EERRYHCAFCNFTSPT 259 (304)
Q Consensus 244 ~~~~~~C~~C~k~F~~ 259 (304)
.-+.|-|+.|......
T Consensus 28 PIrtymC~eC~~Rva~ 43 (68)
T COG4896 28 PIRTYMCPECEHRVAI 43 (68)
T ss_pred CceeEechhhHhhhch
Confidence 3445666666554433
No 282
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=24.12 E-value=31 Score=19.68 Aligned_cols=11 Identities=18% Similarity=0.102 Sum_probs=5.8
Q ss_pred CcccCCCcccc
Q psy3485 277 PTIQPECIKIL 287 (304)
Q Consensus 277 ~~~C~~C~k~F 287 (304)
.|+|.+||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 58888888653
No 283
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.11 E-value=36 Score=21.20 Aligned_cols=11 Identities=18% Similarity=0.127 Sum_probs=7.7
Q ss_pred cccCCCccccc
Q psy3485 278 TIQPECIKILW 288 (304)
Q Consensus 278 ~~C~~C~k~F~ 288 (304)
+.||+||..|.
T Consensus 1 i~CPyCge~~~ 11 (52)
T PF14255_consen 1 IQCPYCGEPIE 11 (52)
T ss_pred CCCCCCCCeeE
Confidence 36888887763
No 284
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=24.07 E-value=49 Score=29.36 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=19.4
Q ss_pred hhCCCCccccccch-hhccCHHHHHHHHH
Q psy3485 207 THTKEKPFACEMCN-YRAASKIAIYAHMR 234 (304)
Q Consensus 207 ~H~~~~~~~C~~C~-k~F~~~~~L~~H~~ 234 (304)
.|--.+.|.|++|| +++..+..+-+|--
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 35555668888888 77777777777743
No 285
>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=23.48 E-value=30 Score=24.67 Aligned_cols=12 Identities=33% Similarity=0.592 Sum_probs=6.2
Q ss_pred Cccccccchhhc
Q psy3485 212 KPFACEMCNYRA 223 (304)
Q Consensus 212 ~~~~C~~C~k~F 223 (304)
++++|..||..|
T Consensus 78 ~~~rC~eCG~~f 89 (97)
T cd00924 78 KPKRCPECGHVF 89 (97)
T ss_pred CceeCCCCCcEE
Confidence 455555555444
No 286
>KOG1842|consensus
Probab=23.39 E-value=43 Score=30.73 Aligned_cols=11 Identities=27% Similarity=0.326 Sum_probs=7.7
Q ss_pred ccCCCcccccc
Q psy3485 279 IQPECIKILWS 289 (304)
Q Consensus 279 ~C~~C~k~F~~ 289 (304)
.|+.||+.|+.
T Consensus 81 ~~s~~g~~~n~ 91 (505)
T KOG1842|consen 81 HDSMCGKLLNE 91 (505)
T ss_pred ccccccccccc
Confidence 57778887754
No 287
>PLN02294 cytochrome c oxidase subunit Vb
Probab=23.32 E-value=25 Score=27.82 Aligned_cols=12 Identities=17% Similarity=0.230 Sum_probs=8.7
Q ss_pred CcccCCCccccc
Q psy3485 277 PTIQPECIKILW 288 (304)
Q Consensus 277 ~~~C~~C~k~F~ 288 (304)
++.|+.||.-|.
T Consensus 141 p~RCpeCG~~fk 152 (174)
T PLN02294 141 SFECPVCTQYFE 152 (174)
T ss_pred ceeCCCCCCEEE
Confidence 677777777764
No 288
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.32 E-value=33 Score=22.05 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=7.2
Q ss_pred CcccCCCccccc
Q psy3485 277 PTIQPECIKILW 288 (304)
Q Consensus 277 ~~~C~~C~k~F~ 288 (304)
...|++|+..|+
T Consensus 48 ev~CPYC~t~y~ 59 (62)
T COG4391 48 EVVCPYCSTRYR 59 (62)
T ss_pred cEecCccccEEE
Confidence 456666666554
No 289
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=23.28 E-value=10 Score=33.83 Aligned_cols=45 Identities=16% Similarity=0.167 Sum_probs=24.3
Q ss_pred CCccccccCCccCCChHHHH---HHH-HhhcCCCCCCcccCCCcccccch
Q psy3485 245 ERRYHCAFCNFTSPTQWAIN---RHT-KYTHMNTSGPTIQPECIKILWSF 290 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~---~H~-r~h~~~~~~~~~C~~C~k~F~~~ 290 (304)
-+-|.|..|.++.-..+..= .|- ..|...+ |-|+|..|++...+-
T Consensus 250 ~kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~K-RFFkC~~C~~Rt~sl 298 (344)
T PF09332_consen 250 CKAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVK-RFFKCKDCGNRTISL 298 (344)
T ss_dssp EEEEEETTT--EESS--HHHHHTT--EEEEEEE--EEEE-T-TS-EEEES
T ss_pred EEEEEcCCCCCcccCcchhHHhcCCceEEeeeee-eeEECCCCCCeeeec
Confidence 35689999998877666653 443 3344444 779999999986653
No 290
>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=23.27 E-value=29 Score=25.52 Aligned_cols=10 Identities=20% Similarity=0.388 Sum_probs=5.0
Q ss_pred cccCCCchHH
Q psy3485 152 FFCIHCNGCV 161 (304)
Q Consensus 152 ~~C~~C~~~f 161 (304)
+.|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PF01155_consen 71 ARCRDCGHEF 80 (113)
T ss_dssp EEETTTS-EE
T ss_pred EECCCCCCEE
Confidence 5555555554
No 291
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.94 E-value=37 Score=30.09 Aligned_cols=24 Identities=13% Similarity=0.164 Sum_probs=21.3
Q ss_pred CCccccccCCccCCChHHHHHHHH
Q psy3485 245 ERRYHCAFCNFTSPTQWAINRHTK 268 (304)
Q Consensus 245 ~~~~~C~~C~k~F~~~~~L~~H~r 268 (304)
...+-|..|++.|.+.+.+..|..
T Consensus 236 ~~~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 236 FPKVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ccceeeHhhhhHhhhhHHHHHHHh
Confidence 356899999999999999999985
No 292
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.80 E-value=21 Score=32.77 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=5.8
Q ss_pred cccccchhhc
Q psy3485 214 FACEMCNYRA 223 (304)
Q Consensus 214 ~~C~~C~k~F 223 (304)
..|+.||...
T Consensus 39 ~~CP~Cg~~~ 48 (402)
T COG3464 39 HRCPECGQRT 48 (402)
T ss_pred CCCCCCCCcc
Confidence 5566666544
No 293
>PRK11032 hypothetical protein; Provisional
Probab=22.41 E-value=30 Score=27.20 Aligned_cols=31 Identities=13% Similarity=0.111 Sum_probs=17.5
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCcccccCh
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCRYG 198 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~~~ 198 (304)
+.|..||.. +.......--.|+.||....++
T Consensus 125 LvC~~Cg~~----------------~~~~~p~~i~pCp~C~~~~F~R 155 (160)
T PRK11032 125 LVCEKCHHH----------------LAFYTPEVLPLCPKCGHDQFQR 155 (160)
T ss_pred EEecCCCCE----------------EEecCCCcCCCCCCCCCCeeee
Confidence 777777765 2222223334788888654443
No 294
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=22.40 E-value=40 Score=18.87 Aligned_cols=11 Identities=27% Similarity=0.869 Sum_probs=6.1
Q ss_pred CCcccCCCccc
Q psy3485 184 RNFMCFACPYY 194 (304)
Q Consensus 184 ~~~~C~~C~k~ 194 (304)
..+.|+.||..
T Consensus 21 ~R~vC~~Cg~I 31 (34)
T PF14803_consen 21 ERLVCPACGFI 31 (34)
T ss_dssp -EEEETTTTEE
T ss_pred cceECCCCCCE
Confidence 44566666654
No 295
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.97 E-value=58 Score=28.46 Aligned_cols=11 Identities=27% Similarity=0.199 Sum_probs=5.4
Q ss_pred cccCCCccccc
Q psy3485 278 TIQPECIKILW 288 (304)
Q Consensus 278 ~~C~~C~k~F~ 288 (304)
+.|+.||..|.
T Consensus 58 ~vcp~c~~h~r 68 (296)
T CHL00174 58 NICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCcC
Confidence 44555555444
No 296
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=21.96 E-value=54 Score=28.53 Aligned_cols=11 Identities=18% Similarity=0.449 Sum_probs=5.2
Q ss_pred cccccCCccCC
Q psy3485 248 YHCAFCNFTSP 258 (304)
Q Consensus 248 ~~C~~C~k~F~ 258 (304)
+.|+.||.-|+
T Consensus 46 ~vc~~c~~h~r 56 (285)
T TIGR00515 46 EVCPKCDHHMR 56 (285)
T ss_pred CCCCCCCCcCc
Confidence 44555554443
No 297
>KOG1842|consensus
Probab=21.86 E-value=59 Score=29.89 Aligned_cols=28 Identities=29% Similarity=0.430 Sum_probs=20.7
Q ss_pred CCcccCCCcccccChHHHHHHHHh-hCCC
Q psy3485 184 RNFMCFACPYYCRYGSSMAIHLRT-HTKE 211 (304)
Q Consensus 184 ~~~~C~~C~k~f~~~~~l~~H~~~-H~~~ 211 (304)
.-|.|++|.+.|.+..+|..|... |.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 347888888888888888888765 6543
No 298
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.81 E-value=26 Score=25.78 Aligned_cols=9 Identities=22% Similarity=0.814 Sum_probs=4.4
Q ss_pred cccCCCchH
Q psy3485 152 FFCIHCNGC 160 (304)
Q Consensus 152 ~~C~~C~~~ 160 (304)
+.|..||..
T Consensus 71 ~~C~~Cg~~ 79 (114)
T PRK03681 71 CWCETCQQY 79 (114)
T ss_pred EEcccCCCe
Confidence 455555543
No 299
>KOG2330|consensus
Probab=21.67 E-value=32 Score=31.38 Aligned_cols=55 Identities=13% Similarity=0.204 Sum_probs=32.3
Q ss_pred CCCCCCchh--hHHHHh-----hCcccccCCchHHHHHHH--------HHHHhhhhhhhhhhhhhhhhhc
Q psy3485 1 MKLTPKIPN--LQQIQK-----TNPKLKKVNYPIIVARKM--------WTKLKKNHQNRNQKKMKSKTAK 55 (304)
Q Consensus 1 ~~~~~~~~~--l~~~~~-----~~~~~~~~~~p~~iC~~C--------~~~l~~f~~~~~~~~~~~~~~~ 55 (304)
|||++.+|+ |..||. .|+.|+..+|..-|=..| |.-+++|..-++.++.-.....
T Consensus 284 Lgmp~g~pPPWl~aMqryGpPpsYPdlkIpGLNapIPeg~s~Gyh~gGWGpVDe~g~PLygDVfG~~~p~ 353 (500)
T KOG2330|consen 284 LGMPVGTPPPWLIAMQRYGPPPSYPDLKIPGLNAPIPEGCSFGYHAGGWGPVDEFGKPLYGDVFGLNIPE 353 (500)
T ss_pred hCCCCCCCChHHHHhhhcCCCCCCCcccCCCCCCCCCcccccccccCCCccccccCCccchhcccccccc
Confidence 345544443 555554 355565555544444455 8889999887777665444443
No 300
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=21.28 E-value=18 Score=29.36 Aligned_cols=11 Identities=27% Similarity=0.649 Sum_probs=6.4
Q ss_pred cccccCCccCC
Q psy3485 248 YHCAFCNFTSP 258 (304)
Q Consensus 248 ~~C~~C~k~F~ 258 (304)
+.|..||.+++
T Consensus 44 ~~C~~CgYR~~ 54 (201)
T COG1779 44 GVCERCGYRST 54 (201)
T ss_pred EEccccCCccc
Confidence 45666665544
No 301
>PRK05978 hypothetical protein; Provisional
Probab=21.23 E-value=26 Score=27.16 Aligned_cols=10 Identities=40% Similarity=0.763 Sum_probs=5.3
Q ss_pred ccccCCccCC
Q psy3485 249 HCAFCNFTSP 258 (304)
Q Consensus 249 ~C~~C~k~F~ 258 (304)
.|+.||-.|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 3555555544
No 302
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=21.02 E-value=14 Score=21.84 Aligned_cols=11 Identities=18% Similarity=-0.239 Sum_probs=4.5
Q ss_pred cCCCcccccch
Q psy3485 280 QPECIKILWSF 290 (304)
Q Consensus 280 C~~C~k~F~~~ 290 (304)
|.+||+.|...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 77888887665
No 303
>KOG0978|consensus
Probab=20.39 E-value=34 Score=33.50 Aligned_cols=21 Identities=14% Similarity=0.050 Sum_probs=15.4
Q ss_pred CcccCCCcccccchhHHHHHH
Q psy3485 277 PTIQPECIKILWSFLSYFIWI 297 (304)
Q Consensus 277 ~~~C~~C~k~F~~~~~l~~h~ 297 (304)
.=+||.||..|....-+.+||
T Consensus 678 qRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 678 QRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred cCCCCCCCCCCCcccccccCC
Confidence 456888888888777666654
No 304
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.27 E-value=19 Score=27.98 Aligned_cols=40 Identities=18% Similarity=0.177 Sum_probs=19.9
Q ss_pred ccCCCcccccChHHHHHHHH-hhCCCCccccccchhhccCH
Q psy3485 187 MCFACPYYCRYGSSMAIHLR-THTKEKPFACEMCNYRAASK 226 (304)
Q Consensus 187 ~C~~C~k~f~~~~~l~~H~~-~H~~~~~~~C~~C~k~F~~~ 226 (304)
.|+.|+.........-.=.- ..+-+.|.-|..||+.|.+.
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWT 81 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchH
Confidence 67777665544421100000 12334666677777777664
No 305
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=20.11 E-value=58 Score=23.05 Aligned_cols=36 Identities=17% Similarity=0.122 Sum_probs=11.5
Q ss_pred cccCCCchHHHHHHHHHHhhhhccccccCCCCCCcccCCCcccccCh
Q psy3485 152 FFCIHCNGCVLYADLLDHCKLCLRRKRKNPMRRNFMCFACPYYCRYG 198 (304)
Q Consensus 152 ~~C~~C~~~fl~~H~~~hC~~C~~~~~~h~~~~~~~C~~C~k~f~~~ 198 (304)
--|..||.++-..+. .+-.....|.|+.|.+-|.+.
T Consensus 15 ~~CalCG~tWg~~y~-----------Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 15 MGCALCGATWGDYYE-----------EVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp GS-SS---S---SS------------B-TT--BSSS--SSSS-TTS-
T ss_pred ccccccCCcHHHHHH-----------hhcCCEEEEEcHHHHHHHHHH
Confidence 456666666632222 222334456667777777655
Done!