Query psy2238
Match_columns 311
No_of_seqs 290 out of 2903
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 19:41:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2238.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2238hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06524 NOA36: NOA36 protein; 100.0 4.6E-35 1E-39 244.0 8.0 241 1-242 1-241 (314)
2 KOG2462|consensus 99.9 7.8E-27 1.7E-31 198.2 4.9 134 61-232 127-265 (279)
3 KOG1074|consensus 99.9 5.4E-23 1.2E-27 196.2 3.9 60 183-242 879-939 (958)
4 KOG2462|consensus 99.9 5.7E-22 1.2E-26 168.7 5.8 124 37-202 128-263 (279)
5 KOG3623|consensus 99.8 9.1E-21 2E-25 178.3 3.9 78 141-231 892-971 (1007)
6 KOG3623|consensus 99.8 1.8E-20 3.9E-25 176.4 5.2 105 64-181 210-318 (1007)
7 KOG3608|consensus 99.8 6.5E-19 1.4E-23 153.8 6.7 160 59-241 202-384 (467)
8 KOG3608|consensus 99.7 6.9E-18 1.5E-22 147.4 5.6 175 39-234 134-345 (467)
9 KOG1074|consensus 99.6 4.4E-17 9.6E-22 156.1 1.5 60 182-241 604-664 (958)
10 KOG3576|consensus 99.4 6.2E-14 1.4E-18 114.2 3.7 109 97-238 116-240 (267)
11 KOG3576|consensus 99.4 5.1E-14 1.1E-18 114.7 1.0 82 140-234 114-198 (267)
12 PLN03086 PRLI-interacting fact 99.0 8.6E-10 1.9E-14 105.3 8.0 123 99-242 408-545 (567)
13 PLN03086 PRLI-interacting fact 98.9 2.7E-09 5.9E-14 102.0 7.9 138 39-232 407-562 (567)
14 PHA00733 hypothetical protein 98.9 1.5E-09 3.3E-14 85.0 4.2 82 141-235 38-124 (128)
15 PHA02768 hypothetical protein; 98.9 6.3E-10 1.4E-14 72.4 1.7 42 184-227 6-48 (55)
16 PF13465 zf-H2C2_2: Zinc-finge 98.6 1.6E-08 3.5E-13 56.2 2.0 26 197-222 1-26 (26)
17 PHA02768 hypothetical protein; 98.4 9.6E-08 2.1E-12 62.2 1.8 39 143-196 5-44 (55)
18 PHA00733 hypothetical protein 98.4 1.9E-07 4.1E-12 73.2 3.8 52 141-207 71-124 (128)
19 KOG3993|consensus 98.4 1.7E-07 3.8E-12 84.7 3.5 81 143-236 267-382 (500)
20 PHA00616 hypothetical protein 98.3 2.2E-07 4.8E-12 57.6 1.7 32 210-241 1-32 (44)
21 PF13465 zf-H2C2_2: Zinc-finge 98.2 7.5E-07 1.6E-11 49.5 2.0 25 157-194 1-25 (26)
22 PF05605 zf-Di19: Drought indu 98.2 1.8E-06 3.9E-11 57.1 4.0 49 184-234 3-53 (54)
23 PHA00732 hypothetical protein 98.2 1E-06 2.3E-11 62.8 2.6 46 183-233 1-47 (79)
24 PF00096 zf-C2H2: Zinc finger, 98.0 4E-06 8.6E-11 45.0 1.7 23 211-233 1-23 (23)
25 PHA00616 hypothetical protein 97.9 5.1E-06 1.1E-10 51.6 1.4 34 64-103 1-34 (44)
26 KOG3993|consensus 97.8 7.9E-06 1.7E-10 74.2 1.5 174 39-234 267-482 (500)
27 PF05605 zf-Di19: Drought indu 97.7 8E-05 1.7E-09 49.2 4.7 52 143-207 2-54 (54)
28 PHA00732 hypothetical protein 97.7 2.5E-05 5.4E-10 55.7 2.3 46 64-119 1-48 (79)
29 PF13894 zf-C2H2_4: C2H2-type 97.6 5.2E-05 1.1E-09 40.7 2.2 24 211-234 1-24 (24)
30 PF13912 zf-C2H2_6: C2H2-type 97.4 6.6E-05 1.4E-09 41.9 1.1 25 210-234 1-25 (27)
31 PF00096 zf-C2H2: Zinc finger, 97.3 0.00016 3.5E-09 38.6 1.5 23 65-90 1-23 (23)
32 PF12756 zf-C2H2_2: C2H2 type 97.2 0.00019 4.2E-09 53.3 2.5 72 145-234 1-74 (100)
33 smart00355 ZnF_C2H2 zinc finge 97.0 0.00062 1.3E-08 37.0 2.5 24 211-234 1-24 (26)
34 COG5189 SFP1 Putative transcri 96.9 0.00032 6.9E-09 61.7 0.6 52 170-230 347-418 (423)
35 PF09237 GAGA: GAGA factor; I 96.8 0.00099 2.1E-08 42.4 2.5 33 206-238 20-52 (54)
36 PF13894 zf-C2H2_4: C2H2-type 96.8 0.00087 1.9E-08 35.8 1.7 24 65-91 1-24 (24)
37 KOG2231|consensus 96.7 0.005 1.1E-07 60.4 7.2 131 66-231 117-260 (669)
38 PF13912 zf-C2H2_6: C2H2-type 96.4 0.0016 3.4E-08 36.2 1.3 25 64-91 1-25 (27)
39 PF13909 zf-H2C2_5: C2H2-type 96.3 0.0028 6E-08 34.1 1.7 23 211-234 1-23 (24)
40 PF12874 zf-met: Zinc-finger o 96.2 0.0021 4.6E-08 34.9 1.0 23 211-233 1-23 (25)
41 COG5189 SFP1 Putative transcri 96.2 0.0026 5.6E-08 56.1 1.7 62 140-202 346-418 (423)
42 PRK04860 hypothetical protein; 96.0 0.003 6.6E-08 51.4 1.4 38 183-223 119-156 (160)
43 PF09237 GAGA: GAGA factor; I 95.9 0.0076 1.7E-07 38.4 2.5 31 140-172 21-52 (54)
44 smart00355 ZnF_C2H2 zinc finge 95.5 0.012 2.7E-07 31.6 2.3 24 65-91 1-24 (26)
45 PF12756 zf-C2H2_2: C2H2 type 95.3 0.011 2.4E-07 43.6 2.2 72 66-165 1-73 (100)
46 KOG2893|consensus 95.2 0.0071 1.5E-07 51.3 0.6 46 186-235 13-60 (341)
47 PF12171 zf-C2H2_jaz: Zinc-fin 94.8 0.0064 1.4E-07 33.8 -0.3 22 211-232 2-23 (27)
48 PF12874 zf-met: Zinc-finger o 94.5 0.021 4.5E-07 30.8 1.3 23 65-90 1-23 (25)
49 PF13909 zf-H2C2_5: C2H2-type 94.5 0.027 5.9E-07 30.1 1.8 21 144-165 1-22 (24)
50 PF13913 zf-C2HC_2: zinc-finge 94.5 0.034 7.3E-07 30.3 2.0 21 211-232 3-23 (25)
51 PF06524 NOA36: NOA36 protein; 94.4 0.04 8.7E-07 47.5 3.3 45 174-218 127-179 (314)
52 KOG2231|consensus 94.3 0.064 1.4E-06 52.9 5.0 98 127-234 100-236 (669)
53 PRK04860 hypothetical protein; 93.7 0.055 1.2E-06 44.1 2.7 36 142-193 118-153 (160)
54 KOG2785|consensus 93.5 0.22 4.8E-06 45.4 6.5 58 182-239 165-250 (390)
55 PF12171 zf-C2H2_jaz: Zinc-fin 92.6 0.062 1.3E-06 29.7 1.1 22 65-89 2-23 (27)
56 PF13913 zf-C2HC_2: zinc-finge 92.2 0.1 2.2E-06 28.3 1.5 20 185-204 4-23 (25)
57 smart00451 ZnF_U1 U1-like zinc 91.9 0.1 2.3E-06 30.5 1.5 23 210-232 3-25 (35)
58 PF09538 FYDLN_acid: Protein o 91.7 0.11 2.3E-06 39.4 1.8 29 127-155 10-39 (108)
59 COG5236 Uncharacterized conser 89.8 2.2 4.8E-05 38.6 8.4 116 98-232 151-303 (493)
60 KOG1146|consensus 89.5 0.19 4.1E-06 52.8 1.8 71 141-232 463-540 (1406)
61 COG5048 FOG: Zn-finger [Genera 89.3 0.096 2.1E-06 49.0 -0.4 60 183-242 289-355 (467)
62 PRK14890 putative Zn-ribbon RN 88.9 0.33 7.2E-06 32.1 2.0 9 128-136 9-17 (59)
63 PRK00398 rpoP DNA-directed RNA 87.8 0.33 7.2E-06 30.6 1.5 27 126-152 3-31 (46)
64 cd00350 rubredoxin_like Rubred 87.1 0.28 6.1E-06 28.5 0.8 24 184-218 2-25 (33)
65 TIGR02300 FYDLN_acid conserved 87.0 0.41 8.8E-06 36.9 1.8 29 127-155 10-39 (129)
66 smart00451 ZnF_U1 U1-like zinc 86.9 0.54 1.2E-05 27.4 2.0 23 143-165 3-26 (35)
67 PRK14890 putative Zn-ribbon RN 86.1 0.38 8.2E-06 31.8 1.1 33 171-218 24-56 (59)
68 KOG2893|consensus 86.1 0.14 2.9E-06 43.7 -1.3 49 38-91 10-59 (341)
69 PF03604 DNA_RNApol_7kD: DNA d 85.5 0.56 1.2E-05 27.1 1.4 25 127-151 1-26 (32)
70 COG5048 FOG: Zn-finger [Genera 85.1 0.22 4.8E-06 46.6 -0.6 55 63-123 288-351 (467)
71 TIGR00622 ssl1 transcription f 84.7 1.5 3.3E-05 33.2 3.9 102 127-234 2-105 (112)
72 smart00659 RPOLCX RNA polymera 84.2 0.71 1.5E-05 28.8 1.6 25 127-151 3-28 (44)
73 PF12013 DUF3505: Protein of u 84.1 1.5 3.3E-05 33.1 3.8 25 211-235 81-109 (109)
74 PHA00626 hypothetical protein 83.1 0.88 1.9E-05 29.7 1.7 14 209-222 22-35 (59)
75 PF11596 DUF3246: Protein of u 81.6 0.94 2E-05 38.4 1.8 26 285-310 213-238 (241)
76 KOG2186|consensus 81.4 0.77 1.7E-05 39.7 1.3 49 144-206 4-52 (276)
77 KOG1146|consensus 81.3 0.49 1.1E-05 49.9 0.1 29 205-234 1324-1352(1406)
78 PF10571 UPF0547: Uncharacteri 81.0 1 2.3E-05 24.6 1.3 8 186-193 17-24 (26)
79 KOG2785|consensus 80.3 3 6.6E-05 38.3 4.8 80 143-232 3-90 (390)
80 COG4049 Uncharacterized protei 79.4 0.91 2E-05 29.6 0.8 27 206-232 13-39 (65)
81 COG2888 Predicted Zn-ribbon RN 79.1 1.1 2.4E-05 29.7 1.1 23 128-150 11-34 (61)
82 KOG2186|consensus 78.0 0.9 2E-05 39.3 0.7 47 184-232 4-50 (276)
83 KOG2023|consensus 77.6 1.3 2.8E-05 43.7 1.7 27 273-299 343-369 (885)
84 COG1996 RPC10 DNA-directed RNA 77.3 1.3 2.8E-05 28.2 1.1 26 126-151 6-33 (49)
85 cd00729 rubredoxin_SM Rubredox 77.2 1.4 3.1E-05 25.8 1.2 23 127-150 3-25 (34)
86 COG1997 RPL43A Ribosomal prote 76.4 1.6 3.4E-05 31.3 1.4 23 171-193 34-63 (89)
87 smart00614 ZnF_BED BED zinc fi 76.1 2.3 5E-05 27.2 2.0 24 211-234 19-48 (50)
88 PF09723 Zn-ribbon_8: Zinc rib 74.8 1.6 3.4E-05 26.9 0.9 25 126-150 5-33 (42)
89 COG5236 Uncharacterized conser 74.1 2.3 5E-05 38.5 2.2 35 143-181 151-188 (493)
90 COG1198 PriA Primosomal protei 73.7 2.2 4.8E-05 43.2 2.2 46 127-192 436-484 (730)
91 COG4049 Uncharacterized protei 73.6 2 4.2E-05 28.0 1.2 22 186-207 20-42 (65)
92 PF01780 Ribosomal_L37ae: Ribo 72.8 2.3 4.9E-05 30.9 1.5 23 171-193 34-63 (90)
93 COG1592 Rubrerythrin [Energy p 72.0 2 4.4E-05 35.1 1.2 23 126-150 134-156 (166)
94 PF09538 FYDLN_acid: Protein o 71.9 2.9 6.3E-05 31.6 2.0 26 40-73 10-35 (108)
95 smart00834 CxxC_CXXC_SSSS Puta 71.4 2.7 5.9E-05 25.3 1.5 30 40-73 6-35 (41)
96 TIGR00622 ssl1 transcription f 71.2 6.8 0.00015 29.8 3.8 52 173-224 2-69 (112)
97 PF02892 zf-BED: BED zinc fing 71.0 3.1 6.7E-05 25.7 1.7 24 208-231 14-41 (45)
98 PF09845 DUF2072: Zn-ribbon co 70.6 1.8 4E-05 33.7 0.7 30 126-155 1-33 (131)
99 PF09986 DUF2225: Uncharacteri 70.6 1.1 2.4E-05 38.3 -0.5 41 183-223 5-61 (214)
100 PRK14873 primosome assembly pr 69.7 3.1 6.7E-05 41.9 2.2 46 127-192 384-431 (665)
101 TIGR00595 priA primosomal prot 69.7 3 6.5E-05 40.6 2.1 46 127-192 214-262 (505)
102 TIGR02605 CxxC_CxxC_SSSS putat 69.4 3 6.6E-05 26.7 1.5 29 40-72 6-34 (52)
103 smart00734 ZnF_Rad18 Rad18-lik 67.8 4.6 0.0001 22.0 1.7 21 211-232 2-22 (26)
104 PF13719 zinc_ribbon_5: zinc-r 67.3 4 8.7E-05 24.3 1.5 8 143-150 25-32 (37)
105 TIGR02098 MJ0042_CXXC MJ0042 f 66.9 2.7 5.9E-05 25.0 0.8 32 40-73 3-34 (38)
106 TIGR00280 L37a ribosomal prote 66.8 5.7 0.00012 28.9 2.5 23 171-193 34-63 (91)
107 KOG2482|consensus 66.8 13 0.00028 33.9 5.2 57 184-240 145-227 (423)
108 COG5151 SSL1 RNA polymerase II 66.3 8.4 0.00018 34.5 3.9 81 64-165 308-411 (421)
109 PF09986 DUF2225: Uncharacteri 65.9 1.3 2.8E-05 38.0 -1.1 11 184-194 49-59 (214)
110 PTZ00255 60S ribosomal protein 65.3 3.4 7.4E-05 30.0 1.1 24 170-193 34-64 (90)
111 PRK03976 rpl37ae 50S ribosomal 65.3 5 0.00011 29.2 2.0 23 171-193 35-64 (90)
112 COG4530 Uncharacterized protei 63.2 3.9 8.4E-05 30.7 1.1 27 127-153 10-37 (129)
113 smart00531 TFIIE Transcription 62.2 5.3 0.00011 32.0 1.8 35 184-221 100-134 (147)
114 COG1592 Rubrerythrin [Energy p 62.0 4.4 9.5E-05 33.1 1.3 8 143-150 134-141 (166)
115 COG1198 PriA Primosomal protei 61.3 5.5 0.00012 40.4 2.1 44 40-105 436-482 (730)
116 PF13717 zinc_ribbon_4: zinc-r 60.2 7 0.00015 23.1 1.7 8 143-150 25-32 (36)
117 PRK04023 DNA polymerase II lar 59.9 7.3 0.00016 40.6 2.7 45 127-193 627-673 (1121)
118 PRK00464 nrdR transcriptional 59.8 4.9 0.00011 32.5 1.2 8 186-193 31-38 (154)
119 COG3357 Predicted transcriptio 59.5 4.9 0.00011 29.1 1.1 27 124-150 56-83 (97)
120 KOG2482|consensus 59.4 10 0.00023 34.4 3.3 92 142-233 194-357 (423)
121 TIGR02300 FYDLN_acid conserved 59.3 7.3 0.00016 30.2 2.0 12 97-108 25-37 (129)
122 PF08274 PhnA_Zn_Ribbon: PhnA 59.2 4.6 0.0001 22.9 0.7 23 128-150 4-26 (30)
123 COG1997 RPL43A Ribosomal prote 58.5 6.7 0.00015 28.2 1.6 27 127-153 36-64 (89)
124 PF11789 zf-Nse: Zinc-finger o 58.3 10 0.00022 25.0 2.4 43 170-215 9-53 (57)
125 smart00531 TFIIE Transcription 58.0 10 0.00022 30.3 2.8 13 38-50 98-110 (147)
126 PRK05580 primosome assembly pr 56.8 7 0.00015 39.6 2.1 46 127-192 382-430 (679)
127 COG3364 Zn-ribbon containing p 55.9 3.1 6.7E-05 30.7 -0.5 29 126-154 2-33 (112)
128 PF15017 AF1Q: Drug resistance 55.5 11 0.00025 27.2 2.4 16 285-300 61-76 (87)
129 TIGR00373 conserved hypothetic 54.3 8.5 0.00018 31.3 1.8 26 186-220 112-138 (158)
130 KOG2807|consensus 53.1 18 0.0004 32.7 3.8 74 127-205 277-368 (378)
131 TIGR00373 conserved hypothetic 52.8 9.7 0.00021 30.9 1.9 33 35-73 105-137 (158)
132 PF02176 zf-TRAF: TRAF-type zi 52.6 7.1 0.00015 25.6 0.9 16 186-201 41-60 (60)
133 PF05290 Baculo_IE-1: Baculovi 52.5 8.7 0.00019 30.0 1.5 56 33-109 74-133 (140)
134 PRK06266 transcription initiat 52.3 8.5 0.00018 31.9 1.5 31 184-222 118-148 (178)
135 PRK06266 transcription initiat 52.1 12 0.00025 31.1 2.3 31 37-73 115-145 (178)
136 KOG4173|consensus 49.9 9.4 0.0002 32.1 1.4 77 142-234 78-171 (253)
137 PF14353 CpXC: CpXC protein 49.6 8.5 0.00018 29.9 1.1 21 209-229 37-57 (128)
138 KOG2807|consensus 48.8 22 0.00047 32.2 3.6 64 171-234 275-369 (378)
139 PRK03824 hypA hydrogenase nick 48.5 9.1 0.0002 30.2 1.1 10 127-136 71-80 (135)
140 KOG4167|consensus 47.7 4.4 9.5E-05 40.4 -1.0 26 210-235 792-817 (907)
141 PF05443 ROS_MUCR: ROS/MUCR tr 47.0 9.9 0.00021 29.9 1.1 27 208-237 70-96 (132)
142 PRK00464 nrdR transcriptional 47.0 8.3 0.00018 31.2 0.7 34 40-73 1-37 (154)
143 PRK03681 hypA hydrogenase nick 46.6 10 0.00022 28.9 1.1 25 126-150 70-94 (114)
144 smart00154 ZnF_AN1 AN1-like Zi 46.5 12 0.00027 22.5 1.2 11 183-193 12-22 (39)
145 KOG2272|consensus 46.5 19 0.00042 31.3 2.8 13 38-50 39-51 (332)
146 PF13878 zf-C2H2_3: zinc-finge 46.4 23 0.00049 21.6 2.4 26 65-91 14-39 (41)
147 COG4957 Predicted transcriptio 45.9 12 0.00026 29.3 1.3 25 211-238 77-101 (148)
148 PRK09678 DNA-binding transcrip 45.4 6.6 0.00014 27.3 -0.1 41 184-226 2-45 (72)
149 PF15269 zf-C2H2_7: Zinc-finge 44.2 15 0.00033 22.8 1.3 22 211-232 21-42 (54)
150 cd00730 rubredoxin Rubredoxin; 44.1 14 0.00029 23.8 1.2 10 184-193 2-11 (50)
151 KOG1940|consensus 42.9 53 0.0012 29.2 5.1 27 211-238 197-223 (276)
152 COG0068 HypF Hydrogenase matur 41.2 4.8 0.00011 40.2 -1.8 75 127-219 102-182 (750)
153 TIGR00595 priA primosomal prot 40.1 18 0.00038 35.3 1.9 44 40-105 214-260 (505)
154 smart00504 Ubox Modified RING 40.1 45 0.00097 21.8 3.4 32 186-222 16-47 (63)
155 PF01286 XPA_N: XPA protein N- 39.3 21 0.00045 20.9 1.3 25 41-72 5-29 (34)
156 PRK00564 hypA hydrogenase nick 39.3 15 0.00033 28.2 1.0 25 126-150 71-95 (117)
157 COG2331 Uncharacterized protei 39.1 17 0.00038 25.4 1.2 9 65-73 13-21 (82)
158 PF04438 zf-HIT: HIT zinc fing 39.1 9.3 0.0002 21.6 -0.1 20 174-193 4-23 (30)
159 PF00301 Rubredoxin: Rubredoxi 38.9 11 0.00025 23.8 0.2 10 184-193 2-11 (47)
160 PF13240 zinc_ribbon_2: zinc-r 38.1 17 0.00037 19.1 0.8 6 186-191 16-21 (23)
161 PF04216 FdhE: Protein involve 37.9 1.6 3.5E-05 39.2 -5.3 46 171-217 196-245 (290)
162 COG1773 Rubredoxin [Energy pro 37.8 24 0.00051 23.2 1.6 13 126-138 3-15 (55)
163 PF08790 zf-LYAR: LYAR-type C2 37.7 7.4 0.00016 21.7 -0.7 19 185-203 2-20 (28)
164 PF05191 ADK_lid: Adenylate ki 37.1 24 0.00052 20.9 1.4 10 41-50 3-12 (36)
165 KOG3362|consensus 36.9 13 0.00027 29.5 0.2 22 64-88 129-150 (156)
166 PRK14714 DNA polymerase II lar 36.7 39 0.00084 36.4 3.7 20 174-193 681-702 (1337)
167 COG5151 SSL1 RNA polymerase II 36.0 39 0.00085 30.4 3.2 25 210-234 388-412 (421)
168 PRK03564 formate dehydrogenase 36.0 17 0.00037 32.9 1.0 68 142-217 186-259 (309)
169 TIGR00686 phnA alkylphosphonat 35.6 22 0.00048 26.7 1.4 28 128-155 4-32 (109)
170 PRK14873 primosome assembly pr 35.5 21 0.00045 36.1 1.6 32 41-73 385-419 (665)
171 PF01155 HypA: Hydrogenase exp 35.1 11 0.00024 28.7 -0.3 24 126-150 70-93 (113)
172 TIGR00244 transcriptional regu 35.1 23 0.0005 28.3 1.4 8 186-193 31-38 (147)
173 PF01153 Glypican: Glypican; 34.8 14 0.0003 36.5 0.3 20 282-301 471-490 (557)
174 COG4957 Predicted transcriptio 34.7 22 0.00048 27.8 1.3 24 185-210 78-101 (148)
175 PRK10220 hypothetical protein; 34.7 29 0.00063 26.1 1.8 28 128-155 5-33 (111)
176 PF05443 ROS_MUCR: ROS/MUCR tr 34.5 20 0.00044 28.1 1.0 24 62-91 70-93 (132)
177 PF15387 DUF4611: Domain of un 34.1 35 0.00077 24.8 2.1 19 278-296 63-81 (96)
178 PF11781 RRN7: RNA polymerase 34.1 25 0.00055 20.8 1.2 24 127-150 9-32 (36)
179 PF08271 TF_Zn_Ribbon: TFIIB z 34.1 28 0.0006 21.3 1.4 9 142-150 18-26 (43)
180 TIGR01206 lysW lysine biosynth 34.0 21 0.00046 23.3 0.9 10 211-220 23-32 (54)
181 PF07649 C1_3: C1-like domain; 33.2 26 0.00056 19.5 1.1 21 128-150 2-22 (30)
182 COG1512 Beta-propeller domains 33.2 27 0.00058 31.1 1.7 12 299-310 257-268 (271)
183 PF15135 UPF0515: Uncharacteri 32.6 29 0.00064 30.2 1.8 13 183-195 155-167 (278)
184 KOG3362|consensus 32.2 18 0.00039 28.6 0.4 28 175-202 121-149 (156)
185 PF01363 FYVE: FYVE zinc finge 32.1 25 0.00053 23.8 1.1 22 128-150 11-32 (69)
186 PF09963 DUF2197: Uncharacteri 31.5 16 0.00034 24.1 -0.0 37 185-221 4-42 (56)
187 KOG2593|consensus 31.4 25 0.00054 33.1 1.3 32 184-217 129-160 (436)
188 KOG2023|consensus 31.3 27 0.00059 34.9 1.6 13 285-297 352-364 (885)
189 KOG1819|consensus 30.9 70 0.0015 30.8 4.1 24 281-304 425-448 (990)
190 PF12013 DUF3505: Protein of u 30.9 37 0.0008 25.4 2.0 26 63-91 79-108 (109)
191 TIGR01562 FdhE formate dehydro 30.8 24 0.00053 31.9 1.1 66 145-217 186-259 (305)
192 PF13453 zf-TFIIB: Transcripti 30.6 41 0.00088 20.3 1.7 21 140-160 16-37 (41)
193 PF15135 UPF0515: Uncharacteri 30.5 71 0.0015 27.9 3.7 67 80-155 92-168 (278)
194 PRK12380 hydrogenase nickel in 30.2 26 0.00057 26.6 1.0 24 126-150 70-93 (113)
195 COG1571 Predicted DNA-binding 30.0 28 0.00062 32.8 1.4 29 128-156 352-381 (421)
196 PF09332 Mcm10: Mcm10 replicat 29.4 13 0.00028 34.2 -1.0 51 98-150 252-310 (344)
197 PF09416 UPF1_Zn_bind: RNA hel 29.2 17 0.00037 29.2 -0.2 19 175-193 3-24 (152)
198 PRK14714 DNA polymerase II lar 29.1 41 0.00089 36.2 2.5 22 172-193 667-689 (1337)
199 KOG1280|consensus 28.5 41 0.00088 30.8 2.0 60 171-230 22-139 (381)
200 PF04959 ARS2: Arsenite-resist 28.5 37 0.0008 29.1 1.7 26 207-232 74-99 (214)
201 KOG2907|consensus 28.4 34 0.00074 25.9 1.3 38 98-137 74-113 (116)
202 COG4888 Uncharacterized Zn rib 28.2 26 0.00056 26.0 0.6 12 211-222 47-58 (104)
203 KOG4167|consensus 27.6 19 0.0004 36.2 -0.2 25 182-206 791-816 (907)
204 KOG0402|consensus 27.6 30 0.00065 24.6 0.8 23 171-193 35-64 (92)
205 PF03107 C1_2: C1 domain; Int 27.6 42 0.00091 18.7 1.3 21 128-150 2-22 (30)
206 PRK03564 formate dehydrogenase 26.6 30 0.00065 31.4 0.9 47 98-150 187-233 (309)
207 PRK00420 hypothetical protein; 26.5 42 0.00092 25.5 1.6 24 127-150 24-47 (112)
208 KOG2593|consensus 26.4 34 0.00074 32.3 1.2 36 61-105 125-160 (436)
209 smart00661 RPOL9 RNA polymeras 26.2 38 0.00081 21.4 1.1 14 210-223 20-33 (52)
210 PF12223 DUF3602: Protein of u 26.2 1.1E+02 0.0025 21.5 3.7 9 303-311 73-81 (81)
211 PF00130 C1_1: Phorbol esters/ 26.0 63 0.0014 20.4 2.2 25 126-150 11-35 (53)
212 PRK04023 DNA polymerase II lar 25.7 54 0.0012 34.5 2.6 14 209-222 662-675 (1121)
213 PF01096 TFIIS_C: Transcriptio 25.4 26 0.00055 21.1 0.2 10 211-220 29-38 (39)
214 smart00440 ZnF_C2C2 C2C2 Zinc 25.3 34 0.00074 20.7 0.7 10 211-220 29-38 (40)
215 PF12907 zf-met2: Zinc-binding 25.2 38 0.00083 20.6 0.9 25 65-89 2-26 (40)
216 PRK05580 primosome assembly pr 25.2 42 0.00092 34.1 1.8 33 40-73 382-417 (679)
217 PF05129 Elf1: Transcription e 25.1 27 0.00059 24.9 0.3 10 184-193 47-56 (81)
218 PF15539 CAF1-p150_C2: CAF1 co 25.1 66 0.0014 28.4 2.7 11 81-91 70-80 (292)
219 PF08911 NUP50: NUP50 (Nucleop 25.0 33 0.00071 23.8 0.7 13 279-291 7-19 (72)
220 PF13824 zf-Mss51: Zinc-finger 24.8 48 0.001 21.7 1.4 13 209-221 13-25 (55)
221 PF03833 PolC_DP2: DNA polymer 24.7 25 0.00053 36.2 0.0 8 212-219 694-701 (900)
222 smart00249 PHD PHD zinc finger 24.4 41 0.00089 20.0 1.0 12 185-196 16-27 (47)
223 KOG3507|consensus 24.4 33 0.00072 22.7 0.5 27 127-153 21-48 (62)
224 PF12773 DZR: Double zinc ribb 24.3 64 0.0014 20.1 1.9 11 209-219 28-38 (50)
225 PF07975 C1_4: TFIIH C1-like d 24.2 43 0.00093 21.6 1.1 19 186-204 24-43 (51)
226 PF12760 Zn_Tnp_IS1595: Transp 24.2 60 0.0013 20.1 1.7 7 99-105 19-25 (46)
227 COG1675 TFA1 Transcription ini 23.8 49 0.0011 27.4 1.6 33 35-73 109-141 (176)
228 COG1327 Predicted transcriptio 23.7 44 0.00095 26.8 1.2 8 186-193 31-38 (156)
229 KOG2071|consensus 23.4 54 0.0012 32.2 2.0 29 207-235 415-443 (579)
230 KOG0320|consensus 23.1 54 0.0012 27.1 1.7 33 187-224 149-181 (187)
231 TIGR00100 hypA hydrogenase nic 22.0 47 0.001 25.3 1.1 24 126-150 70-93 (115)
232 COG1656 Uncharacterized conser 21.5 39 0.00084 27.6 0.5 7 99-105 98-104 (165)
233 COG4306 Uncharacterized protei 21.3 21 0.00045 27.6 -1.0 49 175-223 31-81 (160)
234 KOG1701|consensus 20.9 12 0.00026 35.1 -2.7 12 210-221 427-438 (468)
235 PF01428 zf-AN1: AN1-like Zinc 20.8 33 0.00071 21.0 -0.0 15 209-223 12-26 (43)
236 PRK00762 hypA hydrogenase nick 20.7 50 0.0011 25.6 1.0 10 127-137 71-80 (124)
237 COG3091 SprT Zn-dependent meta 20.6 40 0.00087 27.0 0.5 9 64-73 117-125 (156)
238 PRK12496 hypothetical protein; 20.3 57 0.0012 26.6 1.3 25 125-150 126-150 (164)
No 1
>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=100.00 E-value=4.6e-35 Score=244.05 Aligned_cols=241 Identities=83% Similarity=1.567 Sum_probs=223.0
Q ss_pred CCcchhhhHHHHHHHHHHHHHhhhhhccccccccCCCCccccCcCccccccccchhhcccCCCCccccccccccccCCCH
Q psy2238 1 MPKKKTGQRKKAEKMKLRQKEIRSARDKMSVAEFPCNANMECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKIKCMLKTG 80 (311)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~~~~f~~~ 80 (311)
|||+|+|+|||+|++++||+++|+. ...++..||.+..++|..|++..+|++.|||+.+.++...|..||+.-+|..+.
T Consensus 1 MPkKKtG~rKKaEkqk~rqk~ir~~-~~~dl~~~pcN~~MeCdkC~r~QKnRAFCYFC~s~qrlp~Ca~Cgk~KCm~k~g 79 (314)
T PF06524_consen 1 MPKKKTGQRKKAEKQKERQKEIRSA-EEVDLAKHPCNALMECDKCQRKQKNRAFCYFCQSVQRLPMCAHCGKTKCMLKTG 79 (314)
T ss_pred CCCcccchhhHHHHHHHHHHHHHhc-cccccccCCCCccccchhhhhhccccceeehhhhhhcCchhhhcCCeeeeccCC
Confidence 8999999999999999999999999 778899999999999999999999999999999999999999999998889999
Q ss_pred HHHHHhHhhhccCCCcCcccCCCChhhHHhHHHHHHhhcCcCCCCcccccccccccccCCCceeecCCCCCCCChHHHHH
Q psy2238 81 DCVIKHAGVFSTGMGMVGAICDFCEAWICHGRKCLQTHACTCPLQDAVCLECERGVWDHGGRVYKCCFCEGFLCEDDQFE 160 (311)
Q Consensus 81 ~~L~~H~~~h~~~~~~~~~~C~~C~~f~~~~~~H~~~H~~~~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~f~~~~~L~~ 160 (311)
..++.|.-+++++.+.....|++|.+|+.+.+.-|.+|....|++...|.+|.+..|.++.+.|+|.+|..|.-...-..
T Consensus 80 dCvvkH~g~~~tGl~mvGaiCDfCEawvCHgrkCl~~HaC~Cpl~da~C~EC~R~vw~hGGrif~CsfC~~flCEDDQFE 159 (314)
T PF06524_consen 80 DCVVKHPGVFTTGLGMVGAICDFCEAWVCHGRKCLSTHACTCPLQDAVCIECERGVWDHGGRIFKCSFCDNFLCEDDQFE 159 (314)
T ss_pred CeEEecCceeecccchhhhhhccchhheeccccccccccccCcCCCcEeeeeecccccCCCeEEEeecCCCeeeccchhh
Confidence 99999999998888888899999999999999899999999999999999999999999999999999998887777889
Q ss_pred HHHHhcccCCCCccCCCCCCCCCcccCCCchhcchHHHHHHhhhhcCCCCccCCCCCccccCchHHHHHHHHhcCCCCCC
Q psy2238 161 HQASCQVLESENYKCKSCNKLGQYSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETSQTKDLSMSTRSHKFGRQQL 240 (311)
Q Consensus 161 H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~ 240 (311)
|+...++++...|+|..|.+...|.|..|--.|-..+.++.-......+|++||.|+........|..-.|+|.-+++..
T Consensus 160 HQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~hkyGRQ~~ 239 (314)
T PF06524_consen 160 HQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSHKYGRQGQ 239 (314)
T ss_pred hhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCCCcccccccceeeeecchhccccC
Confidence 99888778889999999999999999999999977776666666677799999999999999999999999998887766
Q ss_pred CC
Q psy2238 241 NG 242 (311)
Q Consensus 241 ~~ 242 (311)
..
T Consensus 240 ~~ 241 (314)
T PF06524_consen 240 AD 241 (314)
T ss_pred CC
Confidence 64
No 2
>KOG2462|consensus
Probab=99.93 E-value=7.8e-27 Score=198.25 Aligned_cols=134 Identities=19% Similarity=0.339 Sum_probs=117.8
Q ss_pred CCCCccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-hhHHh--HHHHHHhhcCcCCCCcccccccccccc
Q psy2238 61 VQRLPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-AWICH--GRKCLQTHACTCPLQDAVCLECERGVW 137 (311)
Q Consensus 61 ~~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~f~~~--~~~H~~~H~~~~~~~~~~C~~C~~~f~ 137 (311)
..-.|+|..||+. +.+..+|.+|.++|-.....+-+.|++|+ .|+.. +++|+|+|+-
T Consensus 127 ~~~r~~c~eCgk~---ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l----------------- 186 (279)
T KOG2462|consen 127 KHPRYKCPECGKS---YSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL----------------- 186 (279)
T ss_pred cCCceeccccccc---cccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC-----------------
Confidence 3447999999999 89999999999999855455679999999 66643 4799999972
Q ss_pred cCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhc-chHHHHHHhhhhcCCCCccCCC
Q psy2238 138 DHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPK 215 (311)
Q Consensus 138 ~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~ 215 (311)
+++|.+|| .|...+.|+-|+|+| +|||||. |+.|+|+| .+++|+.|+++|.+.|+|+|..
T Consensus 187 -----~c~C~iCGKaFSRPWLLQGHiRTH--TGEKPF~-----------C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~ 248 (279)
T KOG2462|consen 187 -----PCECGICGKAFSRPWLLQGHIRTH--TGEKPFS-----------CPHCGKAFADRSNLRAHMQTHSDVKKHQCPR 248 (279)
T ss_pred -----CcccccccccccchHHhhcccccc--cCCCCcc-----------CCcccchhcchHHHHHHHHhhcCCccccCcc
Confidence 45677777 788889999999999 9999999 99999999 7779999999999999999999
Q ss_pred CCccccCchHHHHHHHH
Q psy2238 216 CGFETSQTKDLSMSTRS 232 (311)
Q Consensus 216 C~k~f~~~~~L~~H~~~ 232 (311)
|+|.|...+.|.+|...
T Consensus 249 C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 249 CGKSFALKSYLNKHSES 265 (279)
T ss_pred hhhHHHHHHHHHHhhhh
Confidence 99999999999999765
No 3
>KOG1074|consensus
Probab=99.87 E-value=5.4e-23 Score=196.15 Aligned_cols=60 Identities=15% Similarity=0.182 Sum_probs=55.7
Q ss_pred CcccCCCchhc-chHHHHHHhhhhcCCCCccCCCCCccccCchHHHHHHHHhcCCCCCCCC
Q psy2238 183 QYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPKCGFETSQTKDLSMSTRSHKFGRQQLNG 242 (311)
Q Consensus 183 ~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~~~ 242 (311)
.+.|.+|++.| ++..|..|+++|+++|||.|.+|++.|+.+.+|+.||.+|+...+....
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 37799999999 6669999999999999999999999999999999999999998887764
No 4
>KOG2462|consensus
Probab=99.85 E-value=5.7e-22 Score=168.70 Aligned_cols=124 Identities=16% Similarity=0.384 Sum_probs=102.9
Q ss_pred CCccccCcCccccccccchhhcc-------cCCCCccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-hhH
Q psy2238 37 NANMECDKCKRKQKNRAFCYFCQ-------SVQRLPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-AWI 108 (311)
Q Consensus 37 ~~~~~C~~C~~~f~~~~~c~~~h-------~~~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~f~ 108 (311)
...|.|.+|++.+.+... +-+| ..++.+.|++|+|. |.+..+|+.|+++|+ -+++|.+|| +|.
T Consensus 128 ~~r~~c~eCgk~ysT~sn-LsrHkQ~H~~~~s~ka~~C~~C~K~---YvSmpALkMHirTH~-----l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSN-LSRHKQTHRSLDSKKAFSCKYCGKV---YVSMPALKMHIRTHT-----LPCECGICGKAFS 198 (279)
T ss_pred CCceeccccccccccccc-cchhhcccccccccccccCCCCCce---eeehHHHhhHhhccC-----CCccccccccccc
Confidence 445899999999985543 2222 23677999999999 899999999999998 699999999 787
Q ss_pred H--hHHHHHHhhcCcCCCCcccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcc
Q psy2238 109 C--HGRKCLQTHACTCPLQDAVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYS 185 (311)
Q Consensus 109 ~--~~~~H~~~H~~~~~~~~~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~ 185 (311)
. .++-|+|+|+|| |||.|+.|+ .|+.+++|+.||++| .+.|+|+
T Consensus 199 RPWLLQGHiRTHTGE--------------------KPF~C~hC~kAFADRSNLRAHmQTH--S~~K~~q----------- 245 (279)
T KOG2462|consen 199 RPWLLQGHIRTHTGE--------------------KPFSCPHCGKAFADRSNLRAHMQTH--SDVKKHQ----------- 245 (279)
T ss_pred chHHhhcccccccCC--------------------CCccCCcccchhcchHHHHHHHHhh--cCCcccc-----------
Confidence 4 337999999999 467778888 799999999999999 8899999
Q ss_pred cCCCchhcchHH-HHHHh
Q psy2238 186 CLRCKICFCEDH-ARRKG 202 (311)
Q Consensus 186 C~~C~k~F~~~~-l~~H~ 202 (311)
|..|+|+|...+ |.+|.
T Consensus 246 C~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 246 CPRCGKSFALKSYLNKHS 263 (279)
T ss_pred CcchhhHHHHHHHHHHhh
Confidence 999999997664 45554
No 5
>KOG3623|consensus
Probab=99.81 E-value=9.1e-21 Score=178.34 Aligned_cols=78 Identities=23% Similarity=0.430 Sum_probs=62.1
Q ss_pred CceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchH-HHHHHhhhhcCCCCccCCCCCc
Q psy2238 141 GRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCED-HARRKGFKYEKNKPIPCPKCGF 218 (311)
Q Consensus 141 ~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~-~l~~H~~~h~~~k~~~C~~C~k 218 (311)
+.+|.|+.|. .|...++|.+|.-.| +|.+||+ |.+|.|+|..+ +|..|+|.|.|+|||+|..|+|
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEH--sGqRPyq-----------C~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClK 958 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEH--SGQRPYQ-----------CIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLK 958 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhh--cCCCCcc-----------cchhhHhhhhhhhhhhhhhhccCCCcchhhhhhh
Confidence 4567888888 788888888888777 8888887 88888888666 7888888888888888888888
Q ss_pred cccCchHHHHHHH
Q psy2238 219 ETSQTKDLSMSTR 231 (311)
Q Consensus 219 ~f~~~~~L~~H~~ 231 (311)
+|+...++.+||-
T Consensus 959 RFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 959 RFSHSGSYSQHMN 971 (1007)
T ss_pred hcccccchHhhhc
Confidence 8888888888873
No 6
>KOG3623|consensus
Probab=99.81 E-value=1.8e-20 Score=176.36 Aligned_cols=105 Identities=18% Similarity=0.266 Sum_probs=78.8
Q ss_pred CccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-hhHHhH--HHHHHhhcCcCCCCcccccccccccccCC
Q psy2238 64 LPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-AWICHG--RKCLQTHACTCPLQDAVCLECERGVWDHG 140 (311)
Q Consensus 64 ~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~f~~~~--~~H~~~H~~~~~~~~~~C~~C~~~f~~~~ 140 (311)
...|+.|.+. +.....|+.|++.-+ ...+..|.|.+|. +|.... -+|+.+|..-.+ -. -..-....
T Consensus 210 lltcpycdrg---ykrltslkeHikyrh-ekne~nfsC~lCsytFAyRtQLErhm~~hkpg~d---qa----~sltqsa~ 278 (1007)
T KOG3623|consen 210 LLTCPYCDRG---YKRLTSLKEHIKYRH-EKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGD---QA----ISLTQSAL 278 (1007)
T ss_pred hhcchhHHHH---HHHHHHHHHHHHHHH-hhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCc---cc----ccccchhh
Confidence 4689999999 889999999998543 1134579999999 776544 599999875422 00 00001124
Q ss_pred CceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCC
Q psy2238 141 GRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKL 181 (311)
Q Consensus 141 ~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~ 181 (311)
.+-|+|..|+ .|..+..|+.|+|+| .|||||.|+.|.|.
T Consensus 279 lRKFKCtECgKAFKfKHHLKEHlRIH--SGEKPfeCpnCkKR 318 (1007)
T KOG3623|consen 279 LRKFKCTECGKAFKFKHHLKEHLRIH--SGEKPFECPNCKKR 318 (1007)
T ss_pred hccccccccchhhhhHHHHHhhheee--cCCCCcCCcccccc
Confidence 5678899999 799999999999998 99999999999998
No 7
>KOG3608|consensus
Probab=99.76 E-value=6.5e-19 Score=153.82 Aligned_cols=160 Identities=19% Similarity=0.330 Sum_probs=100.6
Q ss_pred ccCCCCccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-hhHHh--HHHHHHhhcCcCCCCcccccccccc
Q psy2238 59 QSVQRLPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-AWICH--GRKCLQTHACTCPLQDAVCLECERG 135 (311)
Q Consensus 59 h~~~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~f~~~--~~~H~~~H~~~~~~~~~~C~~C~~~ 135 (311)
|+++|...|+.||.. |.++..|-.|++..+.. ...+|.|.+|- .|... ++.|++.|..- |+|+.|+.+
T Consensus 202 Hs~eKvvACp~Cg~~---F~~~tkl~DH~rRqt~l-~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~-----ykCplCdmt 272 (467)
T KOG3608|consen 202 HSNEKVVACPHCGEL---FRTKTKLFDHLRRQTEL-NTNSFQCAQCFKRFATEKLLKSHVVRHVNC-----YKCPLCDMT 272 (467)
T ss_pred cCCCeEEecchHHHH---hccccHHHHHHHhhhhh-cCCchHHHHHHHHHhHHHHHHHHHHHhhhc-----ccccccccC
Confidence 444444444444444 44444444444433311 12344444444 33321 13444444433 444444443
Q ss_pred cc------------cCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCC--Cchhc-chHHHH
Q psy2238 136 VW------------DHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLR--CKICF-CEDHAR 199 (311)
Q Consensus 136 f~------------~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~--C~k~F-~~~~l~ 199 (311)
.. +...+||+|+.|. .|...+.|.+|..+| + +-.|. |+. |...| +...++
T Consensus 273 c~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H--S-~~~y~-----------C~h~~C~~s~r~~~q~~ 338 (467)
T KOG3608|consen 273 CSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH--S-KTVYQ-----------CEHPDCHYSVRTYTQMR 338 (467)
T ss_pred CCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc--c-cccee-----------cCCCCCcHHHHHHHHHH
Confidence 22 1245788888899 889999999999987 4 66788 655 99999 445999
Q ss_pred HHhhhhc-CC--CCccCCCCCccccCchHHHHHH-HHhcCCCCCCC
Q psy2238 200 RKGFKYE-KN--KPIPCPKCGFETSQTKDLSMST-RSHKFGRQQLN 241 (311)
Q Consensus 200 ~H~~~h~-~~--k~~~C~~C~k~f~~~~~L~~H~-~~H~~~~~~~~ 241 (311)
+|++.++ |. -+|.|-.|++.|++..+|..|+ +.|.-.-|+.-
T Consensus 339 ~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh 384 (467)
T KOG3608|consen 339 RHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGH 384 (467)
T ss_pred HHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCC
Confidence 9998876 43 6799999999999999999996 55655555443
No 8
>KOG3608|consensus
Probab=99.71 E-value=6.9e-18 Score=147.45 Aligned_cols=175 Identities=15% Similarity=0.272 Sum_probs=140.7
Q ss_pred cccc--CcCccccccccchhhcc----c------------CCCC-ccc--cccccccccCCCHHHHHHhHhhhccCCCcC
Q psy2238 39 NMEC--DKCKRKQKNRAFCYFCQ----S------------VQRL-PQC--GHCGKIKCMLKTGDCVIKHAGVFSTGMGMV 97 (311)
Q Consensus 39 ~~~C--~~C~~~f~~~~~c~~~h----~------------~~k~-~~C--~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~ 97 (311)
.|.| ++|++.|.+-.. ++.| + .++| +.| ..|.+. |.++..|+.|++.|+ +++
T Consensus 134 ~f~C~WedCe~~F~s~~e-f~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~---~~~k~~LreH~r~Hs---~eK 206 (467)
T KOG3608|consen 134 NFRCGWEDCEREFVSIVE-FQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKH---MGNKYRLREHIRTHS---NEK 206 (467)
T ss_pred hhccChhhcCCcccCHHH-HHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhh---hccHHHHHHHHHhcC---CCe
Confidence 3556 789999985433 3331 1 1222 344 568888 899999999999999 889
Q ss_pred cccCCCCh-hhHHhH--HHHHHhhcCcCCCCcccccccccccccC---------CCceeecCCCC-CCCChHHHHHHHHH
Q psy2238 98 GAICDFCE-AWICHG--RKCLQTHACTCPLQDAVCLECERGVWDH---------GGRVYKCCFCE-GFLCEDDQFEHQAS 164 (311)
Q Consensus 98 ~~~C~~C~-~f~~~~--~~H~~~H~~~~~~~~~~C~~C~~~f~~~---------~~~~~~C~~C~-~f~~~~~L~~H~~~ 164 (311)
...|+.|+ .|.... -.|++..+.... .+|.|..|.|.|.+. ...-|+|+.|. .....++|.+||+.
T Consensus 207 vvACp~Cg~~F~~~tkl~DH~rRqt~l~~-n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~ 285 (467)
T KOG3608|consen 207 VVACPHCGELFRTKTKLFDHLRRQTELNT-NSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRY 285 (467)
T ss_pred EEecchHHHHhccccHHHHHHHhhhhhcC-CchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHh
Confidence 99999999 676554 388886664432 579999999999763 45679999999 99999999999987
Q ss_pred hcccCCCCccCCCCCCCCCcccCCCchhc-chHHHHHHhhhhcCCCCccCCC--CCccccCchHHHHHHHHhc
Q psy2238 165 CQVLESENYKCKSCNKLGQYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPK--CGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 165 h~~~~~k~~~C~~C~~~~~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~--C~k~f~~~~~L~~H~~~H~ 234 (311)
- |...|||+ |+.|++.| +-+.|.+|...|. +..|.|.. |..+|.+...|++|++.++
T Consensus 286 r-Hs~dkpfK-----------Cd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 286 R-HSKDKPFK-----------CDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred h-hccCCCcc-----------ccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 5 37789999 99999999 5669999999877 88899966 9999999999999988765
No 9
>KOG1074|consensus
Probab=99.64 E-value=4.4e-17 Score=156.13 Aligned_cols=60 Identities=17% Similarity=0.314 Sum_probs=54.2
Q ss_pred CCcccCCCchhc-chHHHHHHhhhhcCCCCccCCCCCccccCchHHHHHHHHhcCCCCCCC
Q psy2238 182 GQYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPKCGFETSQTKDLSMSTRSHKFGRQQLN 241 (311)
Q Consensus 182 ~~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~~ 241 (311)
-|.+|.+|-++. ..++|+.|.++|+||+||+|.+|+++|+++.+|+.||-+|...-++..
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~ 664 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARV 664 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccc
Confidence 468899999999 666999999999999999999999999999999999999987665543
No 10
>KOG3576|consensus
Probab=99.44 E-value=6.2e-14 Score=114.18 Aligned_cols=109 Identities=20% Similarity=0.357 Sum_probs=79.2
Q ss_pred CcccCCCCh-hhHHhH--HHHHHhhcCcCCCCcccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCC
Q psy2238 97 VGAICDFCE-AWICHG--RKCLQTHACTCPLQDAVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESEN 172 (311)
Q Consensus 97 ~~~~C~~C~-~f~~~~--~~H~~~H~~~~~~~~~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~ 172 (311)
..|.|.+|+ +|.... .+|++-|... +.|.|..|| .|.....|++|+++| +|.+|
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~v--------------------kr~lct~cgkgfndtfdlkrh~rth--tgvrp 173 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDV--------------------KRHLCTFCGKGFNDTFDLKRHTRTH--TGVRP 173 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHH--------------------HHHHHhhccCcccchhhhhhhhccc--cCccc
Confidence 457777777 565332 5777777655 234444555 455666788899888 88888
Q ss_pred ccCCCCCCCCCcccCCCchhcchH-HHHHHhhhhcC-----------CCCccCCCCCccccCchHHHHHHHHhcCCCC
Q psy2238 173 YKCKSCNKLGQYSCLRCKICFCED-HARRKGFKYEK-----------NKPIPCPKCGFETSQTKDLSMSTRSHKFGRQ 238 (311)
Q Consensus 173 ~~C~~C~~~~~~~C~~C~k~F~~~-~l~~H~~~h~~-----------~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~ 238 (311)
|+ |..|+|+|++. +|..|.+..|| +|.|.|..||..-.....+..|++.|+...|
T Consensus 174 yk-----------c~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 174 YK-----------CSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred cc-----------hhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 88 88888888766 88888765554 3778999999888888888888888876544
No 11
>KOG3576|consensus
Probab=99.40 E-value=5.1e-14 Score=114.70 Aligned_cols=82 Identities=17% Similarity=0.282 Sum_probs=74.8
Q ss_pred CCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchH-HHHHHhhhhcCCCCccCCCCC
Q psy2238 140 GGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCED-HARRKGFKYEKNKPIPCPKCG 217 (311)
Q Consensus 140 ~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~-~l~~H~~~h~~~k~~~C~~C~ 217 (311)
+...|.|.+|+ +|.....|.+|++-| ...+.|. |..|||.|... .|.+|+++|+|-+||+|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch--~~vkr~l-----------ct~cgkgfndtfdlkrh~rthtgvrpykc~~c~ 180 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCH--SDVKRHL-----------CTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCE 180 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhc--cHHHHHH-----------HhhccCcccchhhhhhhhccccCccccchhhhh
Confidence 56789999999 899999999999998 7788888 99999999555 999999999999999999999
Q ss_pred ccccCchHHHHHHH-Hhc
Q psy2238 218 FETSQTKDLSMSTR-SHK 234 (311)
Q Consensus 218 k~f~~~~~L~~H~~-~H~ 234 (311)
|+|++..+|..|++ +|.
T Consensus 181 kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 181 KAFTQRCSLESHLKKVHG 198 (267)
T ss_pred HHHHhhccHHHHHHHHcC
Confidence 99999999999975 453
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.00 E-value=8.6e-10 Score=105.32 Aligned_cols=123 Identities=16% Similarity=0.296 Sum_probs=87.6
Q ss_pred ccCCCCh-hhHHhHHHHHHhhcCcCCCCcccccc--cccccccC-CCceeecCCCC-CCCChHHHHHHHHHhcccCCCCc
Q psy2238 99 AICDFCE-AWICHGRKCLQTHACTCPLQDAVCLE--CERGVWDH-GGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENY 173 (311)
Q Consensus 99 ~~C~~C~-~f~~~~~~H~~~H~~~~~~~~~~C~~--C~~~f~~~-~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~ 173 (311)
-.|+.|. .... .++..|..........|+. |+..|... -++.+.|+.|+ .|. ...|..|+++| + +++
T Consensus 408 V~C~NC~~~i~l---~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~--H--kpv 479 (567)
T PLN03086 408 VECRNCKHYIPS---RSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVF--H--EPL 479 (567)
T ss_pred EECCCCCCccch---hHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhc--C--CCc
Confidence 4798888 3221 1233444444323457874 99988654 56778999999 785 67799999997 3 778
Q ss_pred cCCCCCCCCCcccCCCchhcchHHHHHHhhhhcCCCCccCCCCCccccC----------chHHHHHHHHhcCCCCCCCC
Q psy2238 174 KCKSCNKLGQYSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETSQ----------TKDLSMSTRSHKFGRQQLNG 242 (311)
Q Consensus 174 ~C~~C~~~~~~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~~----------~~~L~~H~~~H~~~~~~~~~ 242 (311)
. |+ |++.+.+..|..|..+|.+.+|+.|+.|++.|.. .+.|..|+.++ +.+++.|.
T Consensus 480 ~-----------Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~ 545 (567)
T PLN03086 480 Q-----------CP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCD 545 (567)
T ss_pred c-----------CC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEcc
Confidence 8 77 8876666688888888888888888888888852 35788888875 67777774
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.92 E-value=2.7e-09 Score=101.95 Aligned_cols=138 Identities=20% Similarity=0.347 Sum_probs=92.8
Q ss_pred ccccCcCccccccccchhhcccCCC---Cccccc--cccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-hhHH-hH
Q psy2238 39 NMECDKCKRKQKNRAFCYFCQSVQR---LPQCGH--CGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-AWIC-HG 111 (311)
Q Consensus 39 ~~~C~~C~~~f~~~~~c~~~h~~~k---~~~C~~--C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~f~~-~~ 111 (311)
.-.|..|.+....+. +..|...= .-.|+. |+.. |.. .. .+.++.|+.|+ .|.. .+
T Consensus 407 ~V~C~NC~~~i~l~~--l~lHe~~C~r~~V~Cp~~~Cg~v---~~r----------~e---l~~H~~C~~Cgk~f~~s~L 468 (567)
T PLN03086 407 TVECRNCKHYIPSRS--IALHEAYCSRHNVVCPHDGCGIV---LRV----------EE---AKNHVHCEKCGQAFQQGEM 468 (567)
T ss_pred eEECCCCCCccchhH--HHHHHhhCCCcceeCCcccccce---eec----------cc---cccCccCCCCCCccchHHH
Confidence 346999988877332 22344332 345774 8888 522 11 23456899999 6643 23
Q ss_pred HHHHHhhcCcCCCCcccccccccccccCCCceeecCCCCCCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCch
Q psy2238 112 RKCLQTHACTCPLQDAVCLECERGVWDHGGRVYKCCFCEGFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKI 191 (311)
Q Consensus 112 ~~H~~~H~~~~~~~~~~C~~C~~~f~~~~~~~~~C~~C~~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k 191 (311)
..|+++|+ +++.|+ |+.+..+..|..|+.+| ..++++. |..|++
T Consensus 469 ekH~~~~H----------------------kpv~Cp-Cg~~~~R~~L~~H~~th--Cp~Kpi~-----------C~fC~~ 512 (567)
T PLN03086 469 EKHMKVFH----------------------EPLQCP-CGVVLEKEQMVQHQAST--CPLRLIT-----------CRFCGD 512 (567)
T ss_pred HHHHHhcC----------------------CCccCC-CCCCcchhHHHhhhhcc--CCCCcee-----------CCCCCC
Confidence 57877764 235555 66222457899999988 8889999 777877
Q ss_pred hcc-----------hHHHHHHhhhhcCCCCccCCCCCccccCchHHHHHHHH
Q psy2238 192 CFC-----------EDHARRKGFKYEKNKPIPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 192 ~F~-----------~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
.|. ...|..|... .+.+++.|..|++.|..+ .|..|+..
T Consensus 513 ~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 513 MVQAGGSAMDVRDRLRGMSEHESI-CGSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred ccccCccccchhhhhhhHHHHHHh-cCCcceEccccCCeeeeh-hHHHHHHH
Confidence 773 2377888777 599999999999988876 46678654
No 14
>PHA00733 hypothetical protein
Probab=98.89 E-value=1.5e-09 Score=85.04 Aligned_cols=82 Identities=13% Similarity=0.072 Sum_probs=58.9
Q ss_pred CceeecCCCC-CCCChHHHHHH--HHHhc-ccCCCCccCCCCCCCCCcccCCCchhc-chHHHHHHhhhhcCCCCccCCC
Q psy2238 141 GRVYKCCFCE-GFLCEDDQFEH--QASCQ-VLESENYKCKSCNKLGQYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPK 215 (311)
Q Consensus 141 ~~~~~C~~C~-~f~~~~~L~~H--~~~h~-~~~~k~~~C~~C~~~~~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~ 215 (311)
.+++.|.+|. .|.....|..| ++.|. +.+++||. |+.|++.| ....|..|++.| +.+|.|+.
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~-----------C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~ 104 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYV-----------CPLCLMPFSSSVSLKQHIRYT--EHSKVCPV 104 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCcc-----------CCCCCCcCCCHHHHHHHHhcC--CcCccCCC
Confidence 3555666666 45555555444 22211 13467888 99999999 555899998876 46899999
Q ss_pred CCccccCchHHHHHHHHhcC
Q psy2238 216 CGFETSQTKDLSMSTRSHKF 235 (311)
Q Consensus 216 C~k~f~~~~~L~~H~~~H~~ 235 (311)
|++.|.....|.+|+...++
T Consensus 105 CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 105 CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCHHHHHHHHHHhcC
Confidence 99999999999999877553
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.89 E-value=6.3e-10 Score=72.39 Aligned_cols=42 Identities=14% Similarity=0.199 Sum_probs=37.7
Q ss_pred cccCCCchhc-chHHHHHHhhhhcCCCCccCCCCCccccCchHHH
Q psy2238 184 YSCLRCKICF-CEDHARRKGFKYEKNKPIPCPKCGFETSQTKDLS 227 (311)
Q Consensus 184 ~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~ 227 (311)
|.|+.||+.| ...+|..|+++|+ +||+|..|++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 5699999999 5559999999999 7999999999999988874
No 16
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.64 E-value=1.6e-08 Score=56.24 Aligned_cols=26 Identities=35% Similarity=0.553 Sum_probs=19.2
Q ss_pred HHHHHhhhhcCCCCccCCCCCccccC
Q psy2238 197 HARRKGFKYEKNKPIPCPKCGFETSQ 222 (311)
Q Consensus 197 ~l~~H~~~h~~~k~~~C~~C~k~f~~ 222 (311)
+|.+|+++|++++||+|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 46777777777777777777777753
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.43 E-value=9.6e-08 Score=62.25 Aligned_cols=39 Identities=21% Similarity=0.328 Sum_probs=34.0
Q ss_pred eeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchH
Q psy2238 143 VYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCED 196 (311)
Q Consensus 143 ~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~ 196 (311)
-|+|+.|| .|...++|..|+++| + ++|+ |..|++.|.+.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H--~--k~~k-----------c~~C~k~f~~~ 44 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH--N--TNLK-----------LSNCKRISLRT 44 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc--C--Cccc-----------CCcccceeccc
Confidence 47899999 899999999999998 4 6888 88999998544
No 18
>PHA00733 hypothetical protein
Probab=98.43 E-value=1.9e-07 Score=73.22 Aligned_cols=52 Identities=19% Similarity=0.228 Sum_probs=43.5
Q ss_pred CceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcc-hHHHHHHhhhhcC
Q psy2238 141 GRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFC-EDHARRKGFKYEK 207 (311)
Q Consensus 141 ~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~-~~~l~~H~~~h~~ 207 (311)
.+||.|+.|+ .|.....|..|++.| +.+|. |.+|++.|. ...|..|+...|+
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h----~~~~~-----------C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYT----EHSKV-----------CPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcC----CcCcc-----------CCCCCCccCCHHHHHHHHHHhcC
Confidence 5678889999 899999999999976 35677 999999994 4599999887764
No 19
>KOG3993|consensus
Probab=98.41 E-value=1.7e-07 Score=84.69 Aligned_cols=81 Identities=16% Similarity=0.307 Sum_probs=53.3
Q ss_pred eeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchH-HHHHHhhhhc--------CC----
Q psy2238 143 VYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCED-HARRKGFKYE--------KN---- 208 (311)
Q Consensus 143 ~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~-~l~~H~~~h~--------~~---- 208 (311)
.|.|..|. +|.....|-+|.-.- .---.|+ |++|+|+|+-. +|..|.|.|- +.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~R--IV~vEYr-----------CPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k 333 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPR--IVHVEYR-----------CPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPK 333 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCe--eEEeeec-----------CCcccccccCchhhhhhhcccCCchhhhhcCCCChh
Confidence 36677777 676666666664322 1112244 66677777333 6666666551 11
Q ss_pred ---------------------CCccCCCCCccccCchHHHHHHHHhcCC
Q psy2238 209 ---------------------KPIPCPKCGFETSQTKDLSMSTRSHKFG 236 (311)
Q Consensus 209 ---------------------k~~~C~~C~k~f~~~~~L~~H~~~H~~~ 236 (311)
--|.|.+|+|.|.+...|++|+.+|+..
T Consensus 334 ~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 334 QAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred hhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 2489999999999999999999998754
No 20
>PHA00616 hypothetical protein
Probab=98.34 E-value=2.2e-07 Score=57.61 Aligned_cols=32 Identities=16% Similarity=0.112 Sum_probs=20.6
Q ss_pred CccCCCCCccccCchHHHHHHHHhcCCCCCCC
Q psy2238 210 PIPCPKCGFETSQTKDLSMSTRSHKFGRQQLN 241 (311)
Q Consensus 210 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~~ 241 (311)
||+|+.||+.|..+++|.+|+++|++++++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 46666666666666666666666666665544
No 21
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.22 E-value=7.5e-07 Score=49.46 Aligned_cols=25 Identities=24% Similarity=0.463 Sum_probs=22.0
Q ss_pred HHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcc
Q psy2238 157 DQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFC 194 (311)
Q Consensus 157 ~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~ 194 (311)
+|.+|+++| ++++||+ |++|+++|.
T Consensus 1 ~l~~H~~~H--~~~k~~~-----------C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTH--TGEKPYK-----------CPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHH--SSSSSEE-----------ESSSSEEES
T ss_pred CHHHHhhhc--CCCCCCC-----------CCCCcCeeC
Confidence 589999999 9999999 888888874
No 22
>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=98.21 E-value=1.8e-06 Score=57.10 Aligned_cols=49 Identities=20% Similarity=0.427 Sum_probs=40.0
Q ss_pred cccCCCchhcchHHHHHHhhhhcCC--CCccCCCCCccccCchHHHHHHHHhc
Q psy2238 184 YSCLRCKICFCEDHARRKGFKYEKN--KPIPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 184 ~~C~~C~k~F~~~~l~~H~~~h~~~--k~~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
|.|++|++.|+...|..|....|.. +.+.||+|...+. .+|.+|+..++
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 6699999977888999998765543 6799999998765 48999998765
No 23
>PHA00732 hypothetical protein
Probab=98.18 E-value=1e-06 Score=62.76 Aligned_cols=46 Identities=15% Similarity=0.271 Sum_probs=36.5
Q ss_pred CcccCCCchhc-chHHHHHHhhhhcCCCCccCCCCCccccCchHHHHHHHHh
Q psy2238 183 QYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPKCGFETSQTKDLSMSTRSH 233 (311)
Q Consensus 183 ~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~H 233 (311)
||.|+.|++.| ...+|..|++.++. ++.|+.|++.|. .|..|+++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhccc
Confidence 46699999999 55599999985332 468999999998 588887553
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.97 E-value=4e-06 Score=45.04 Aligned_cols=23 Identities=35% Similarity=0.658 Sum_probs=20.0
Q ss_pred ccCCCCCccccCchHHHHHHHHh
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRSH 233 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~H 233 (311)
|+|+.|++.|.++..|.+|+++|
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 67899999999999999998875
No 25
>PHA00616 hypothetical protein
Probab=97.90 E-value=5.1e-06 Score=51.55 Aligned_cols=34 Identities=24% Similarity=0.386 Sum_probs=30.5
Q ss_pred CccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCC
Q psy2238 64 LPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDF 103 (311)
Q Consensus 64 ~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~ 103 (311)
||+|..||+. |..+..|..|++.|+ +++++.|+.
T Consensus 1 pYqC~~CG~~---F~~~s~l~~H~r~~h---g~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGI---FRKKKEVIEHLLSVH---KQNKLTLEY 34 (44)
T ss_pred CCccchhhHH---HhhHHHHHHHHHHhc---CCCccceeE
Confidence 6899999999 899999999999999 888988864
No 26
>KOG3993|consensus
Probab=97.80 E-value=7.9e-06 Score=74.20 Aligned_cols=174 Identities=14% Similarity=0.098 Sum_probs=100.8
Q ss_pred ccccCcCccccccccchhhc-ccC----CCCccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-h-hHHhH
Q psy2238 39 NMECDKCKRKQKNRAFCYFC-QSV----QRLPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-A-WICHG 111 (311)
Q Consensus 39 ~~~C~~C~~~f~~~~~c~~~-h~~----~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~-f~~~~ 111 (311)
.|.|..|...|. ... .|. |.- .-.|+|++|+|. |+...+|..|.|.|. ...+ .-+ -+ . -....
T Consensus 267 dyiCqLCK~kYe-D~F-~LAQHrC~RIV~vEYrCPEC~KV---FsCPANLASHRRWHK-PR~e-aa~---a~~~P~k~~~ 336 (500)
T KOG3993|consen 267 DYICQLCKEKYE-DAF-ALAQHRCPRIVHVEYRCPECDKV---FSCPANLASHRRWHK-PRPE-AAK---AGSPPPKQAV 336 (500)
T ss_pred HHHHHHHHHhhh-hHH-HHhhccCCeeEEeeecCCccccc---ccCchhhhhhhcccC-Cchh-hhh---cCCCChhhhh
Confidence 377888888777 333 333 332 336888888888 888888888888776 1110 000 00 0 00000
Q ss_pred HHHHHhhcCcCCCCcccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCC-C---C-----------ccC
Q psy2238 112 RKCLQTHACTCPLQDAVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLES-E---N-----------YKC 175 (311)
Q Consensus 112 ~~H~~~H~~~~~~~~~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~-k---~-----------~~C 175 (311)
. -+.-..+ -.+.=....+..|.|.+|+ +|.....|+.|+.+|+.... + + +-|
T Consensus 337 ~--~rae~~e----------a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~ 404 (500)
T KOG3993|consen 337 E--TRAEVQE----------AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFN 404 (500)
T ss_pred h--hhhhhhh----------ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccc
Confidence 0 0000000 0000011234589999999 89999999999999842221 1 0 112
Q ss_pred CCCCCC------------------CCcccCCCchhcchH-HHHHHhhhhcCCCCccCCCCCccccCchHHHHHHHHhc
Q psy2238 176 KSCNKL------------------GQYSCLRCKICFCED-HARRKGFKYEKNKPIPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 176 ~~C~~~------------------~~~~C~~C~k~F~~~-~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
..|.-. .-..|++|+-.+..+ .--.+-+.-+.+.-|.|.+|--.|.....|.+|+...+
T Consensus 405 ~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 405 QAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred cccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcC
Confidence 222222 124477777777444 33344444455677999999999999999999976644
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.69 E-value=8e-05 Score=49.16 Aligned_cols=52 Identities=25% Similarity=0.427 Sum_probs=37.8
Q ss_pred eeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchHHHHHHhhhhcC
Q psy2238 143 VYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCEDHARRKGFKYEK 207 (311)
Q Consensus 143 ~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~~l~~H~~~h~~ 207 (311)
.|.|++|+ .|. ...|..|....+..+.+.+. |++|...+.. +|..|+..+|+
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~~~~~v~-----------CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRSESKNVV-----------CPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcCCCCCcc-----------CCCchhhhhh-HHHHHHHHhcC
Confidence 47899999 544 57899998776333346677 8888877643 88899887764
No 28
>PHA00732 hypothetical protein
Probab=97.68 E-value=2.5e-05 Score=55.70 Aligned_cols=46 Identities=17% Similarity=0.285 Sum_probs=36.5
Q ss_pred CccccccccccccCCCHHHHHHhHhh-hccCCCcCcccCCCCh-hhHHhHHHHHHhhc
Q psy2238 64 LPQCGHCGKIKCMLKTGDCVIKHAGV-FSTGMGMVGAICDFCE-AWICHGRKCLQTHA 119 (311)
Q Consensus 64 ~~~C~~C~k~~~~f~~~~~L~~H~~~-h~~~~~~~~~~C~~C~-~f~~~~~~H~~~H~ 119 (311)
||.|.+|++. |.+..+|..|++. |. ++.|+.|+ .|. .+..|++++.
T Consensus 1 py~C~~Cgk~---F~s~s~Lk~H~r~~H~------~~~C~~CgKsF~-~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFT---TVTLFALKQHARRNHT------LTKCPVCNKSYR-RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCc---cCCHHHHHHHhhcccC------CCccCCCCCEeC-ChhhhhcccC
Confidence 6889999999 8999999999985 54 46899999 776 4567775443
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.58 E-value=5.2e-05 Score=40.74 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=18.3
Q ss_pred ccCCCCCccccCchHHHHHHHHhc
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
|.|++|++.|.+...|..|+++|+
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 678888888888888888888763
No 30
>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=97.40 E-value=6.6e-05 Score=41.90 Aligned_cols=25 Identities=36% Similarity=0.604 Sum_probs=19.8
Q ss_pred CccCCCCCccccCchHHHHHHHHhc
Q psy2238 210 PIPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 210 ~~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
||+|..|++.|.....|..|++.|.
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 5778888888888888888887765
No 31
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.25 E-value=0.00016 Score=38.61 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=21.1
Q ss_pred ccccccccccccCCCHHHHHHhHhhh
Q psy2238 65 PQCGHCGKIKCMLKTGDCVIKHAGVF 90 (311)
Q Consensus 65 ~~C~~C~k~~~~f~~~~~L~~H~~~h 90 (311)
|.|++|++. |.+...|..|++.|
T Consensus 1 y~C~~C~~~---f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKS---FSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEE---ESSHHHHHHHHHHH
T ss_pred CCCCCCCCc---cCCHHHHHHHHhHC
Confidence 689999999 99999999999875
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.25 E-value=0.00019 Score=53.33 Aligned_cols=72 Identities=19% Similarity=0.284 Sum_probs=22.6
Q ss_pred ecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhc-chHHHHHHhhhhcCCCCccCCCCCccccC
Q psy2238 145 KCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPKCGFETSQ 222 (311)
Q Consensus 145 ~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~C~k~f~~ 222 (311)
+|.+|+ .|.....|..|+... ++-.. + ....+ ....++.+.... -...+.|..|++.|..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~--H~~~~--------------~-~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s 62 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKK--HGFDI--------------P-DQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRS 62 (100)
T ss_dssp ------------------------------------------------------------------SSEEBSSSS-EESS
T ss_pred Cccccccccccccccccccccc--ccccc--------------c-cccccccccccccccccc-cCCCCCCCccCCCCcC
Confidence 589999 899999999999765 22110 0 00111 112344433322 1237999999999999
Q ss_pred chHHHHHHHHhc
Q psy2238 223 TKDLSMSTRSHK 234 (311)
Q Consensus 223 ~~~L~~H~~~H~ 234 (311)
...|..||+.+.
T Consensus 63 ~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 63 REALQEHMRSKH 74 (100)
T ss_dssp HHHHHHHHHHTT
T ss_pred HHHHHHHHcCcc
Confidence 999999999754
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.02 E-value=0.00062 Score=36.98 Aligned_cols=24 Identities=29% Similarity=0.589 Sum_probs=19.7
Q ss_pred ccCCCCCccccCchHHHHHHHHhc
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
|.|+.|++.|.....|..|+++|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578888888888888888888764
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.86 E-value=0.00032 Score=61.71 Aligned_cols=52 Identities=19% Similarity=0.401 Sum_probs=40.1
Q ss_pred CCCccCCCCCCCCCcccCCCchhc-chHHHHHHhhhhc-------------------CCCCccCCCCCccccCchHHHHH
Q psy2238 170 SENYKCKSCNKLGQYSCLRCKICF-CEDHARRKGFKYE-------------------KNKPIPCPKCGFETSQTKDLSMS 229 (311)
Q Consensus 170 ~k~~~C~~C~~~~~~~C~~C~k~F-~~~~l~~H~~~h~-------------------~~k~~~C~~C~k~f~~~~~L~~H 229 (311)
+|||+|+ -.-|.|++ .+..|+.|+.-=| .+|||.|++|+|+|.....|+-|
T Consensus 347 ~KpykCp---------V~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 347 GKPYKCP---------VEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred CceecCC---------CCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceec
Confidence 4777755 45699999 4558888876211 24999999999999999999988
Q ss_pred H
Q psy2238 230 T 230 (311)
Q Consensus 230 ~ 230 (311)
.
T Consensus 418 r 418 (423)
T COG5189 418 R 418 (423)
T ss_pred c
Confidence 4
No 35
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.84 E-value=0.00099 Score=42.37 Aligned_cols=33 Identities=24% Similarity=0.597 Sum_probs=22.7
Q ss_pred cCCCCccCCCCCccccCchHHHHHHHHhcCCCC
Q psy2238 206 EKNKPIPCPKCGFETSQTKDLSMSTRSHKFGRQ 238 (311)
Q Consensus 206 ~~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~ 238 (311)
..+.|-.|++|+..+.+..+|++|+.++++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 456888999999999999999999988877765
No 36
>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=96.77 E-value=0.00087 Score=35.76 Aligned_cols=24 Identities=25% Similarity=0.468 Sum_probs=19.7
Q ss_pred ccccccccccccCCCHHHHHHhHhhhc
Q psy2238 65 PQCGHCGKIKCMLKTGDCVIKHAGVFS 91 (311)
Q Consensus 65 ~~C~~C~k~~~~f~~~~~L~~H~~~h~ 91 (311)
|.|++|++. |.+...|+.|++.|+
T Consensus 1 ~~C~~C~~~---~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKS---FRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-E---ESSHHHHHHHHHHHS
T ss_pred CCCcCCCCc---CCcHHHHHHHHHhhC
Confidence 679999999 899999999998764
No 37
>KOG2231|consensus
Probab=96.67 E-value=0.005 Score=60.36 Aligned_cols=131 Identities=19% Similarity=0.262 Sum_probs=74.3
Q ss_pred cccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh----hhHHhH----HHHHHhhcCcCCCCcccccccccccc
Q psy2238 66 QCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE----AWICHG----RKCLQTHACTCPLQDAVCLECERGVW 137 (311)
Q Consensus 66 ~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~----~f~~~~----~~H~~~H~~~~~~~~~~C~~C~~~f~ 137 (311)
.|..| .. |.+...|+.|+..-+ +.+.|.+|- .|.... +.-++.|... -|. +.+.|.
T Consensus 117 ~~~~c-~~---~~s~~~Lk~H~~~~H-----~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~------gd~-d~~s~r 180 (669)
T KOG2231|consen 117 ECLHC-TE---FKSVENLKNHMRDQH-----KLHLCSLCLQNLKIFINERKLYTRAELNLHLMF------GDP-DDESCR 180 (669)
T ss_pred CCccc-cc---hhHHHHHHHHHHHhh-----hhhccccccccceeeeeeeehehHHHHHHHHhc------CCC-cccccc
Confidence 35555 44 568889999997555 367788776 233211 1223333221 111 233332
Q ss_pred cCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhc-chHHHHHHhhhhcCCCCccCC-
Q psy2238 138 DHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICF-CEDHARRKGFKYEKNKPIPCP- 214 (311)
Q Consensus 138 ~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~- 214 (311)
- --.|.+|. .|.....|.+|++.+ + |.|-.|++. +.++..| ....|..|-+.+| |.|.
T Consensus 181 G----hp~C~~C~~~fld~~el~rH~~~~--h----~~chfC~~~-----~~~neyy~~~~dLe~HfR~~H----flCE~ 241 (669)
T KOG2231|consen 181 G----HPLCKFCHERFLDDDELYRHLRFD--H----EFCHFCDYK-----TGQNEYYNDYDDLEEHFRKGH----FLCEE 241 (669)
T ss_pred C----CccchhhhhhhccHHHHHHhhccc--e----eheeecCcc-----cccchhcccchHHHHHhhhcC----ccccc
Confidence 2 34699999 899999999999876 2 333332210 1223344 4458888888777 7776
Q ss_pred -CCC-ccccCchHHHHHHH
Q psy2238 215 -KCG-FETSQTKDLSMSTR 231 (311)
Q Consensus 215 -~C~-k~f~~~~~L~~H~~ 231 (311)
.|. +.|.....+..|++
T Consensus 242 ~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 242 EFCRTKKFYVAFELEIELK 260 (669)
T ss_pred cccccceeeehhHHHHHHH
Confidence 564 45555444444444
No 38
>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=96.44 E-value=0.0016 Score=36.19 Aligned_cols=25 Identities=20% Similarity=0.437 Sum_probs=22.9
Q ss_pred CccccccccccccCCCHHHHHHhHhhhc
Q psy2238 64 LPQCGHCGKIKCMLKTGDCVIKHAGVFS 91 (311)
Q Consensus 64 ~~~C~~C~k~~~~f~~~~~L~~H~~~h~ 91 (311)
+|.|.+|++. |.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~---F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKT---FSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEE---ESSHHHHHHHHCTTT
T ss_pred CCCCCccCCc---cCChhHHHHHhHHhc
Confidence 6899999999 999999999998876
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.30 E-value=0.0028 Score=34.13 Aligned_cols=23 Identities=30% Similarity=0.764 Sum_probs=16.5
Q ss_pred ccCCCCCccccCchHHHHHHHHhc
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
|+|+.|+.... ...|.+|+++|+
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 67888888887 778888887764
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.19 E-value=0.0021 Score=34.88 Aligned_cols=23 Identities=26% Similarity=0.372 Sum_probs=18.9
Q ss_pred ccCCCCCccccCchHHHHHHHHh
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRSH 233 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~H 233 (311)
|.|.+|++.|.....|..|++.+
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 57888888888888888888654
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.15 E-value=0.0026 Score=56.15 Aligned_cols=62 Identities=18% Similarity=0.254 Sum_probs=41.1
Q ss_pred CCceeecCC--CC-CCCChHHHHHHHHHhcccCCCCccCCCCCC-------CCCcccCCCchhcchH-HHHHHh
Q psy2238 140 GGRVYKCCF--CE-GFLCEDDQFEHQASCQVLESENYKCKSCNK-------LGQYSCLRCKICFCED-HARRKG 202 (311)
Q Consensus 140 ~~~~~~C~~--C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~-------~~~~~C~~C~k~F~~~-~l~~H~ 202 (311)
.++||+|++ |. ++.....|+-|+.-- |-..+...-+.-.+ .+||.|++|+|++... .|+.|.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhG-H~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHG-HQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhcc-ccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 569999988 66 699999999997543 22222222211111 1788899999999666 666653
No 42
>PRK04860 hypothetical protein; Provisional
Probab=96.00 E-value=0.003 Score=51.36 Aligned_cols=38 Identities=21% Similarity=0.411 Sum_probs=28.2
Q ss_pred CcccCCCchhcchHHHHHHhhhhcCCCCccCCCCCccccCc
Q psy2238 183 QYSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETSQT 223 (311)
Q Consensus 183 ~~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~ 223 (311)
+|.|. |+. ....+.+|.++|+++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~--~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE--HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC--eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 45576 776 444777888888888888888888877654
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.89 E-value=0.0076 Score=38.39 Aligned_cols=31 Identities=10% Similarity=0.036 Sum_probs=22.3
Q ss_pred CCceeecCCCC-CCCChHHHHHHHHHhcccCCCC
Q psy2238 140 GGRVYKCCFCE-GFLCEDDQFEHQASCQVLESEN 172 (311)
Q Consensus 140 ~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~ 172 (311)
.+.|..|++|+ .+.+..+|++|+.++ ++.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~--H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIR--HFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHH--TTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHH--hcccC
Confidence 56789999999 899999999999887 66554
No 44
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.53 E-value=0.012 Score=31.57 Aligned_cols=24 Identities=25% Similarity=0.631 Sum_probs=21.3
Q ss_pred ccccccccccccCCCHHHHHHhHhhhc
Q psy2238 65 PQCGHCGKIKCMLKTGDCVIKHAGVFS 91 (311)
Q Consensus 65 ~~C~~C~k~~~~f~~~~~L~~H~~~h~ 91 (311)
|.|..|++. |.....|..|++.|.
T Consensus 1 ~~C~~C~~~---f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKV---FKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcch---hCCHHHHHHHHHHhc
Confidence 679999999 899999999998775
No 45
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.35 E-value=0.011 Score=43.64 Aligned_cols=72 Identities=19% Similarity=0.293 Sum_probs=21.2
Q ss_pred cccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCChhhHHhHHHHHHhhcCcCCCCcccccccccccccCCCceee
Q psy2238 66 QCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCEAWICHGRKCLQTHACTCPLQDAVCLECERGVWDHGGRVYK 145 (311)
Q Consensus 66 ~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~~f~~~~~~H~~~H~~~~~~~~~~C~~C~~~f~~~~~~~~~ 145 (311)
+|..|+.. |.+...|..|+...+ +.. .+....+..... +..+... .....+.
T Consensus 1 ~C~~C~~~---f~~~~~l~~H~~~~H---~~~---~~~~~~l~~~~~--~~~~~~~-----------------~~~~~~~ 52 (100)
T PF12756_consen 1 QCLFCDES---FSSVDDLLQHMKKKH---GFD---IPDQKYLVDPNR--LLNYLRK-----------------KVKESFR 52 (100)
T ss_dssp ----------------------------------------------------------------------------SSEE
T ss_pred Cccccccc---ccccccccccccccc---ccc---cccccccccccc--ccccccc-----------------ccCCCCC
Confidence 48899999 888999999998655 211 000000110000 0000001 1123688
Q ss_pred cCCCC-CCCChHHHHHHHHHh
Q psy2238 146 CCFCE-GFLCEDDQFEHQASC 165 (311)
Q Consensus 146 C~~C~-~f~~~~~L~~H~~~h 165 (311)
|.+|+ .|.....|..||+.+
T Consensus 53 C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 53 CPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp BSSSS-EESSHHHHHHHHHHT
T ss_pred CCccCCCCcCHHHHHHHHcCc
Confidence 99999 899999999999986
No 46
>KOG2893|consensus
Probab=95.15 E-value=0.0071 Score=51.31 Aligned_cols=46 Identities=24% Similarity=0.309 Sum_probs=37.8
Q ss_pred cCCCchhc-chHHHHHHhhhhcCCCCccCCCCCccccCchHHHHH-HHHhcC
Q psy2238 186 CLRCKICF-CEDHARRKGFKYEKNKPIPCPKCGFETSQTKDLSMS-TRSHKF 235 (311)
Q Consensus 186 C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H-~~~H~~ 235 (311)
|.+|++-| .-+-|.+|++. |-|+|-+|.|...+--.|..| |.+|..
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhhh
Confidence 99999999 44578877664 559999999998888889888 777753
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=94.82 E-value=0.0064 Score=33.75 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=16.1
Q ss_pred ccCCCCCccccCchHHHHHHHH
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
|.|..|++.|.+...|..|+++
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 6677777777777777777654
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.54 E-value=0.021 Score=30.84 Aligned_cols=23 Identities=17% Similarity=0.330 Sum_probs=20.4
Q ss_pred ccccccccccccCCCHHHHHHhHhhh
Q psy2238 65 PQCGHCGKIKCMLKTGDCVIKHAGVF 90 (311)
Q Consensus 65 ~~C~~C~k~~~~f~~~~~L~~H~~~h 90 (311)
|.|.+|++. |.+...|..|++.+
T Consensus 1 ~~C~~C~~~---f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKS---FSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEE---ESSHHHHHHHHTTH
T ss_pred CCCCCCCCC---cCCHHHHHHHHCcC
Confidence 579999999 89999999999865
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.53 E-value=0.027 Score=30.12 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=17.5
Q ss_pred eecCCCC-CCCChHHHHHHHHHh
Q psy2238 144 YKCCFCE-GFLCEDDQFEHQASC 165 (311)
Q Consensus 144 ~~C~~C~-~f~~~~~L~~H~~~h 165 (311)
|+|+.|. ... ...|.+|+++|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 7899999 776 88999999986
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.47 E-value=0.034 Score=30.28 Aligned_cols=21 Identities=29% Similarity=0.730 Sum_probs=12.1
Q ss_pred ccCCCCCccccCchHHHHHHHH
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
.+|+.|++.| ....|.+|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3566666666 55556666543
No 51
>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=94.39 E-value=0.04 Score=47.47 Aligned_cols=45 Identities=20% Similarity=0.539 Sum_probs=22.1
Q ss_pred cCCCCCCC------CCcccCCCchhcchHHHHHHhhhh--cCCCCccCCCCCc
Q psy2238 174 KCKSCNKL------GQYSCLRCKICFCEDHARRKGFKY--EKNKPIPCPKCGF 218 (311)
Q Consensus 174 ~C~~C~~~------~~~~C~~C~k~F~~~~l~~H~~~h--~~~k~~~C~~C~k 218 (311)
.|-+|.+. +.|+|..|....--.....|+..- .....|+|.-|.+
T Consensus 127 ~C~EC~R~vw~hGGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNr 179 (314)
T PF06524_consen 127 VCIECERGVWDHGGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNR 179 (314)
T ss_pred EeeeeecccccCCCeEEEeecCCCeeeccchhhhhhhhhhhhccccccccccc
Confidence 35555554 556677777655333333444321 1123455655543
No 52
>KOG2231|consensus
Probab=94.33 E-value=0.064 Score=52.87 Aligned_cols=98 Identities=19% Similarity=0.250 Sum_probs=57.2
Q ss_pred ccccccccccccCCCceeecCCCCCCCChHHHHHHHH-HhcccCCCCccCCCCCCC-C----------------------
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCEGFLCEDDQFEHQA-SCQVLESENYKCKSCNKL-G---------------------- 182 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~~f~~~~~L~~H~~-~h~~~~~k~~~C~~C~~~-~---------------------- 182 (311)
+.|.+|+..|...- .-..|..|-.|.....|+.|++ .| +.+.|.+|-.. +
T Consensus 100 ~~C~~C~~~~~~~~-~~~~~~~c~~~~s~~~Lk~H~~~~H-----~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd 173 (669)
T KOG2231|consen 100 HSCHICDRRFRALY-NKKECLHCTEFKSVENLKNHMRDQH-----KLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGD 173 (669)
T ss_pred hhcCccccchhhhc-ccCCCccccchhHHHHHHHHHHHhh-----hhhccccccccceeeeeeeehehHHHHHHHHhcCC
Confidence 67888888774321 1124777755777888888884 44 56677776555 1
Q ss_pred --------CcccCCCchhc-chHHHHHHhhhhcCCCCccCCCC------CccccCchHHHHHHHHhc
Q psy2238 183 --------QYSCLRCKICF-CEDHARRKGFKYEKNKPIPCPKC------GFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 183 --------~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~~C------~k~f~~~~~L~~H~~~H~ 234 (311)
--.|..|...| ....|.+|++.+| |.|-.| ..-|.....|..|-|.++
T Consensus 174 ~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 174 PDDESCRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred CccccccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 12356666666 4446666666555 444444 234455566666655443
No 53
>PRK04860 hypothetical protein; Provisional
Probab=93.66 E-value=0.055 Score=44.07 Aligned_cols=36 Identities=22% Similarity=0.487 Sum_probs=29.0
Q ss_pred ceeecCCCCCCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhc
Q psy2238 142 RVYKCCFCEGFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICF 193 (311)
Q Consensus 142 ~~~~C~~C~~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F 193 (311)
-+|.|. |+. ....+.+|.++| +++++|. |..|+..|
T Consensus 118 ~~Y~C~-C~~--~~~~~rrH~ri~--~g~~~Yr-----------C~~C~~~l 153 (160)
T PRK04860 118 FPYRCK-CQE--HQLTVRRHNRVV--RGEAVYR-----------CRRCGETL 153 (160)
T ss_pred EEEEcC-CCC--eeCHHHHHHHHh--cCCccEE-----------CCCCCcee
Confidence 579998 985 456689999999 9999999 66666665
No 54
>KOG2785|consensus
Probab=93.50 E-value=0.22 Score=45.44 Aligned_cols=58 Identities=16% Similarity=0.112 Sum_probs=44.4
Q ss_pred CCcccCCCchhcch-HHHHHHhhhhcCC-----------------------CCccCCCCC---ccccCchHHHHHHHH-h
Q psy2238 182 GQYSCLRCKICFCE-DHARRKGFKYEKN-----------------------KPIPCPKCG---FETSQTKDLSMSTRS-H 233 (311)
Q Consensus 182 ~~~~C~~C~k~F~~-~~l~~H~~~h~~~-----------------------k~~~C~~C~---k~f~~~~~L~~H~~~-H 233 (311)
-|-.|-.|++.|.. ...+.||..+|+- .-|.|-.|. +.|.+-.+.+.||.. -
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~ 244 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKG 244 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhcc
Confidence 35789999999954 4889999988873 126788888 999999999999864 2
Q ss_pred cCCCCC
Q psy2238 234 KFGRQQ 239 (311)
Q Consensus 234 ~~~~~~ 239 (311)
+-.-+|
T Consensus 245 HCkl~y 250 (390)
T KOG2785|consen 245 HCKLPY 250 (390)
T ss_pred CcccCC
Confidence 224455
No 55
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=92.63 E-value=0.062 Score=29.68 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=19.7
Q ss_pred ccccccccccccCCCHHHHHHhHhh
Q psy2238 65 PQCGHCGKIKCMLKTGDCVIKHAGV 89 (311)
Q Consensus 65 ~~C~~C~k~~~~f~~~~~L~~H~~~ 89 (311)
|.|.+|++. |.+...|..|++.
T Consensus 2 ~~C~~C~k~---f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKY---FSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBB---BSSHHHHHCCTTS
T ss_pred CCcccCCCC---cCCHHHHHHHHcc
Confidence 679999999 8999999999875
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.16 E-value=0.1 Score=28.35 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=17.0
Q ss_pred ccCCCchhcchHHHHHHhhh
Q psy2238 185 SCLRCKICFCEDHARRKGFK 204 (311)
Q Consensus 185 ~C~~C~k~F~~~~l~~H~~~ 204 (311)
.|+.|++.|....|.+|..+
T Consensus 4 ~C~~CgR~F~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKFNPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEECHHHHHHHHHh
Confidence 49999999988899998753
No 57
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=91.88 E-value=0.1 Score=30.52 Aligned_cols=23 Identities=9% Similarity=0.268 Sum_probs=19.0
Q ss_pred CccCCCCCccccCchHHHHHHHH
Q psy2238 210 PIPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 210 ~~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
+|.|.+|++.|.....|..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57899999999988888888753
No 58
>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=91.71 E-value=0.11 Score=39.37 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=25.1
Q ss_pred ccccccccccccCCCceeecCCCC-CCCCh
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCE 155 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~ 155 (311)
..|+.||+.|...+..|..|+.|| .|.-.
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 679999999999888999999999 67654
No 59
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.77 E-value=2.2 Score=38.61 Aligned_cols=116 Identities=18% Similarity=0.346 Sum_probs=71.0
Q ss_pred cccCCC--Ch---hhHHhHHHHHHhhcCcCCCCccccccccc---ccccC--------------------CCc-eeecCC
Q psy2238 98 GAICDF--CE---AWICHGRKCLQTHACTCPLQDAVCLECER---GVWDH--------------------GGR-VYKCCF 148 (311)
Q Consensus 98 ~~~C~~--C~---~f~~~~~~H~~~H~~~~~~~~~~C~~C~~---~f~~~--------------------~~~-~~~C~~ 148 (311)
.|.|+. |. .+...++.|.+..++. +-|.+|-. .|+.. |-+ .-.|.+
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~-----~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~F 225 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF-----VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIF 225 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc-----EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhh
Confidence 377875 44 2334456777776665 77887753 45531 111 236999
Q ss_pred CC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhc-chHHHHHHhhhhcCCCCccCC--CCC----ccc
Q psy2238 149 CE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICF-CEDHARRKGFKYEKNKPIPCP--KCG----FET 220 (311)
Q Consensus 149 C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~--~C~----k~f 220 (311)
|. .|-....|.+|+|.. + |+ |-+|+++.|- =...| ....|..|.+.-| |.|. .|. ..|
T Consensus 226 C~~~FYdDDEL~~HcR~~--H-E~---ChICD~v~p~----~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf 291 (493)
T COG5236 226 CKIYFYDDDELRRHCRLR--H-EA---CHICDMVGPI----RYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVF 291 (493)
T ss_pred ccceecChHHHHHHHHhh--h-hh---hhhhhccCcc----chhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEe
Confidence 99 899999999999875 2 33 4444444221 12345 3447777766444 6663 242 478
Q ss_pred cCchHHHHHHHH
Q psy2238 221 SQTKDLSMSTRS 232 (311)
Q Consensus 221 ~~~~~L~~H~~~ 232 (311)
.....|..|+..
T Consensus 292 ~~~~el~~h~~~ 303 (493)
T COG5236 292 PYHTELLEHLTR 303 (493)
T ss_pred ccHHHHHHHHHH
Confidence 889999999754
No 60
>KOG1146|consensus
Probab=89.51 E-value=0.19 Score=52.76 Aligned_cols=71 Identities=21% Similarity=0.323 Sum_probs=46.3
Q ss_pred CceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchHHHHHHhh------hhcCCCCccC
Q psy2238 141 GRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCEDHARRKGF------KYEKNKPIPC 213 (311)
Q Consensus 141 ~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~~l~~H~~------~h~~~k~~~C 213 (311)
.+.|+|+.|+ .|.....|-.|||.-++..+-.|. ..-..|.+ .--+.+||.|
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c---------------------~~gq~~~~~arg~~~~~~~~p~~C 521 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYC---------------------KAGQNHPRLARGEVYRCPGKPYPC 521 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHh---------------------HhccccccccccccccCCCCcccc
Confidence 4678888888 788888888888874222222111 01111111 1123488999
Q ss_pred CCCCccccCchHHHHHHHH
Q psy2238 214 PKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 214 ~~C~k~f~~~~~L~~H~~~ 232 (311)
..|..+|+.+.+|.+|+..
T Consensus 522 ~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 522 RACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred eeeeeeeecchHHHHHHHH
Confidence 9999999999999999763
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.31 E-value=0.096 Score=49.03 Aligned_cols=60 Identities=22% Similarity=0.299 Sum_probs=53.4
Q ss_pred CcccCCCchhcchH-HHHHHhh--hhcCC--CCccCC--CCCccccCchHHHHHHHHhcCCCCCCCC
Q psy2238 183 QYSCLRCKICFCED-HARRKGF--KYEKN--KPIPCP--KCGFETSQTKDLSMSTRSHKFGRQQLNG 242 (311)
Q Consensus 183 ~~~C~~C~k~F~~~-~l~~H~~--~h~~~--k~~~C~--~C~k~f~~~~~L~~H~~~H~~~~~~~~~ 242 (311)
++.|..|...|+.. .|..|.+ .|+++ +|+.|+ .|++.|.+...|..|..+|....++...
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 57899999999555 8999999 89999 999999 8999999999999999999988766653
No 62
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.88 E-value=0.33 Score=32.11 Aligned_cols=9 Identities=22% Similarity=0.715 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy2238 128 VCLECERGV 136 (311)
Q Consensus 128 ~C~~C~~~f 136 (311)
.|..|+...
T Consensus 9 ~CtSCg~~i 17 (59)
T PRK14890 9 KCTSCGIEI 17 (59)
T ss_pred cccCCCCcc
Confidence 344444433
No 63
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.80 E-value=0.33 Score=30.56 Aligned_cols=27 Identities=22% Similarity=0.459 Sum_probs=19.6
Q ss_pred cccccccccccccCCC-ceeecCCCC-CC
Q psy2238 126 DAVCLECERGVWDHGG-RVYKCCFCE-GF 152 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~-~~~~C~~C~-~f 152 (311)
.|.|..||..|.-... ..+.|+.|| .+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 4888899888755422 278999999 54
No 64
>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=87.14 E-value=0.28 Score=28.53 Aligned_cols=24 Identities=33% Similarity=0.883 Sum_probs=15.2
Q ss_pred cccCCCchhcchHHHHHHhhhhcCCCCccCCCCCc
Q psy2238 184 YSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGF 218 (311)
Q Consensus 184 ~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k 218 (311)
|.|.+||..+.... .|+.||+|+.
T Consensus 2 ~~C~~CGy~y~~~~-----------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-----------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-----------CCCcCcCCCC
Confidence 45777776662221 6778888864
No 65
>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=87.01 E-value=0.41 Score=36.94 Aligned_cols=29 Identities=17% Similarity=0.236 Sum_probs=25.5
Q ss_pred ccccccccccccCCCceeecCCCC-CCCCh
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCE 155 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~ 155 (311)
..|+.||+.|...+..|..|+.|| .|.-.
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 689999999999999999999999 77554
No 66
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=86.92 E-value=0.54 Score=27.36 Aligned_cols=23 Identities=22% Similarity=0.302 Sum_probs=19.6
Q ss_pred eeecCCCC-CCCChHHHHHHHHHh
Q psy2238 143 VYKCCFCE-GFLCEDDQFEHQASC 165 (311)
Q Consensus 143 ~~~C~~C~-~f~~~~~L~~H~~~h 165 (311)
+|.|++|+ .|.....+..|+...
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 57899999 899999999998653
No 67
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.14 E-value=0.38 Score=31.85 Aligned_cols=33 Identities=36% Similarity=1.079 Sum_probs=18.5
Q ss_pred CCccCCCCCCCCCcccCCCchhcchHHHHHHhhhhcCCCCccCCCCCc
Q psy2238 171 ENYKCKSCNKLGQYSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGF 218 (311)
Q Consensus 171 k~~~C~~C~~~~~~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k 218 (311)
-.|.|+.||..-.+.|..|.+. ..+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~~CRk~---------------~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKCRKQ---------------SNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechhHHhc---------------CCceECCCCCC
Confidence 3466555555544444444322 26788888874
No 68
>KOG2893|consensus
Probab=86.13 E-value=0.14 Score=43.73 Aligned_cols=49 Identities=20% Similarity=0.323 Sum_probs=34.3
Q ss_pred CccccCcCccccccccchhhcccCCCCccccccccccccCCCHHHHHHhHh-hhc
Q psy2238 38 ANMECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKIKCMLKTGDCVIKHAG-VFS 91 (311)
Q Consensus 38 ~~~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~~~~f~~~~~L~~H~~-~h~ 91 (311)
|+| |..|++-|..... ++.|...+.|+|.+|.|. +.+--.|..|.. +|.
T Consensus 10 kpw-cwycnrefddeki-liqhqkakhfkchichkk---l~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKI-LIQHQKAKHFKCHICHKK---LFSGPGLSIHCMQVHK 59 (341)
T ss_pred Cce-eeecccccchhhh-hhhhhhhccceeeeehhh---hccCCCceeehhhhhh
Confidence 444 8888888886666 666877888888888887 555555666643 443
No 69
>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=85.54 E-value=0.56 Score=27.13 Aligned_cols=25 Identities=28% Similarity=0.477 Sum_probs=17.9
Q ss_pred ccccccccccccCCCceeecCCCC-C
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-G 151 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~ 151 (311)
|.|..|+..+......+.+|+.|| .
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCe
Confidence 567788887776666677888888 5
No 70
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=85.12 E-value=0.22 Score=46.55 Aligned_cols=55 Identities=15% Similarity=0.293 Sum_probs=43.7
Q ss_pred CCccccccccccccCCCHHHHHHhHh--hhccCCCc--CcccCC--CCh-hhHHhH--HHHHHhhcCcCC
Q psy2238 63 RLPQCGHCGKIKCMLKTGDCVIKHAG--VFSTGMGM--VGAICD--FCE-AWICHG--RKCLQTHACTCP 123 (311)
Q Consensus 63 k~~~C~~C~k~~~~f~~~~~L~~H~~--~h~~~~~~--~~~~C~--~C~-~f~~~~--~~H~~~H~~~~~ 123 (311)
.++.|..|... |.....|..|.+ .|. ++ +++.|+ .|+ .|.... ..|..+|.+..+
T Consensus 288 ~~~~~~~~~~~---~s~~~~l~~~~~~~~h~---~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 288 LPIKSKQCNIS---FSRSSPLTRHLRSVNHS---GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred cCCCCccccCC---ccccccccccccccccc---cccCCceeeeccCCCccccccccccCCcccccCCCc
Confidence 46889999999 888899999999 788 77 899999 798 665444 477888877743
No 71
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.66 E-value=1.5 Score=33.20 Aligned_cols=102 Identities=13% Similarity=0.185 Sum_probs=57.2
Q ss_pred ccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCC-CCCCCCCcccCCCchhcchHHHHHHhhh
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCK-SCNKLGQYSCLRCKICFCEDHARRKGFK 204 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~-~C~~~~~~~C~~C~k~F~~~~l~~H~~~ 204 (311)
|.|+.|+... -+.|..|++|+ .......|.+-. |+--.-++|.=- .=.......|--|...|....... ...
T Consensus 2 Y~CPrC~skv---C~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~-~~~ 75 (112)
T TIGR00622 2 YFCPQCRAKV---CELPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSP-FDE 75 (112)
T ss_pred ccCCCCCCCc---cCCCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCccccc-ccc
Confidence 5666665432 24678899999 776666666542 311122334200 000001223888888884331100 000
Q ss_pred hcCCCCccCCCCCccccCchHHHHHHHHhc
Q psy2238 205 YEKNKPIPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 205 h~~~k~~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
......|.|+.|...|-..-.+-.|...|.
T Consensus 76 ~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 76 LKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccccceeCCCCCCccccccchhhhhhccC
Confidence 223356899999999988888888877775
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.21 E-value=0.71 Score=28.83 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=19.3
Q ss_pred ccccccccccccCCCceeecCCCC-C
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-G 151 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~ 151 (311)
|.|..||..|......+..|+.|| .
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCce
Confidence 778888887776666778888888 5
No 73
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=84.09 E-value=1.5 Score=33.08 Aligned_cols=25 Identities=28% Similarity=0.567 Sum_probs=22.5
Q ss_pred ccC----CCCCccccCchHHHHHHHHhcC
Q psy2238 211 IPC----PKCGFETSQTKDLSMSTRSHKF 235 (311)
Q Consensus 211 ~~C----~~C~k~f~~~~~L~~H~~~H~~ 235 (311)
|.| +.|+..+.+...|.+|.+.+++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 9999999999999999988764
No 74
>PHA00626 hypothetical protein
Probab=83.09 E-value=0.88 Score=29.66 Aligned_cols=14 Identities=29% Similarity=0.809 Sum_probs=7.7
Q ss_pred CCccCCCCCccccC
Q psy2238 209 KPIPCPKCGFETSQ 222 (311)
Q Consensus 209 k~~~C~~C~k~f~~ 222 (311)
..|+|+.|+..|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 34566666655553
No 75
>PF11596 DUF3246: Protein of unknown function (DUF3246); InterPro: IPR021642 This is a small family of fungal proteins one of whose members, A3LUS4 from SWISSPROT from Pichia stipitis is described as being an extremely serine rich protein-mucin-like protein.
Probab=81.63 E-value=0.94 Score=38.39 Aligned_cols=26 Identities=38% Similarity=0.418 Sum_probs=19.8
Q ss_pred CCCCCCCCcCCCCCCCCCccCCCCCC
Q psy2238 285 DYDDEDDDYDVGGGYSGFSYGGGGAT 310 (311)
Q Consensus 285 ~~dd~ddd~d~~~~~~~~~~~~g~~~ 310 (311)
.+|.+||+++.+|+++|+++++|.|+
T Consensus 213 p~d~edD~y~~~gsGsGssgs~~SgS 238 (241)
T PF11596_consen 213 PDDWEDDGYEGEGSGSGSSGSGSSGS 238 (241)
T ss_pred cccccCCcceeecccccCCCCCCCcC
Confidence 55677888888888888777777654
No 76
>KOG2186|consensus
Probab=81.38 E-value=0.77 Score=39.66 Aligned_cols=49 Identities=14% Similarity=0.373 Sum_probs=24.8
Q ss_pred eecCCCCCCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchHHHHHHhhhhc
Q psy2238 144 YKCCFCEGFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCEDHARRKGFKYE 206 (311)
Q Consensus 144 ~~C~~C~~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~~l~~H~~~h~ 206 (311)
|.|.+||-...+-.|.+|+-.. ++ .-|. |-.|++.|.+.....|....+
T Consensus 4 FtCnvCgEsvKKp~vekH~srC--rn-~~fS-----------CIDC~k~F~~~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRC--RN-AYFS-----------CIDCGKTFERVSYKNHTKCIT 52 (276)
T ss_pred EehhhhhhhccccchHHHHHhc--cC-CeeE-----------Eeecccccccchhhhhhhhcc
Confidence 4555555555555555555554 33 3333 555555554455555544443
No 77
>KOG1146|consensus
Probab=81.33 E-value=0.49 Score=49.90 Aligned_cols=29 Identities=21% Similarity=0.249 Sum_probs=23.6
Q ss_pred hcCCCCccCCCCCccccCchHHHHHHHHhc
Q psy2238 205 YEKNKPIPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 205 h~~~k~~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
+-..++| |+.|...|.....|..||++-.
T Consensus 1324 ~~d~~~~-c~~c~~~~~~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1324 VPDCTYH-CLACEVLLSGREALQIHMRSSA 1352 (1406)
T ss_pred Ccccccc-chHHHhhcchhHHHHHHHHHhh
Confidence 3334667 9999999999999999998743
No 78
>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=81.01 E-value=1 Score=24.64 Aligned_cols=8 Identities=38% Similarity=0.970 Sum_probs=4.5
Q ss_pred cCCCchhc
Q psy2238 186 CLRCKICF 193 (311)
Q Consensus 186 C~~C~k~F 193 (311)
|+.||..|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 55555555
No 79
>KOG2785|consensus
Probab=80.33 E-value=3 Score=38.29 Aligned_cols=80 Identities=18% Similarity=0.113 Sum_probs=47.6
Q ss_pred eeecCCCC-CCCChHHHHHHHHHhcccCC---CCccCCCCCCCCCcccCCCchhcchHHHHH--Hhhh--hcCCCCccCC
Q psy2238 143 VYKCCFCE-GFLCEDDQFEHQASCQVLES---ENYKCKSCNKLGQYSCLRCKICFCEDHARR--KGFK--YEKNKPIPCP 214 (311)
Q Consensus 143 ~~~C~~C~-~f~~~~~L~~H~~~h~~~~~---k~~~C~~C~~~~~~~C~~C~k~F~~~~l~~--H~~~--h~~~k~~~C~ 214 (311)
-|.|..|. .|......+.|+++-.|.=. +.+.= =++=-..|....+.. -... -..+-++.|.
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~l----------PPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~ 72 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASL----------PPITAEEFNEKVLSDDSEKEENLEEAESVVYCE 72 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcC----------CCcCHHHHhHHHhhhhhhhhhhhhhcccceehH
Confidence 37788888 78888888888876421110 11110 122233342221111 1111 2445789999
Q ss_pred CCCccccCchHHHHHHHH
Q psy2238 215 KCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 215 ~C~k~f~~~~~L~~H~~~ 232 (311)
+|.|.|....+...|+..
T Consensus 73 ~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 73 ACNKSFASPKAHENHLKS 90 (390)
T ss_pred HhhccccChhhHHHHHHH
Confidence 999999999999999864
No 80
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=79.36 E-value=0.91 Score=29.55 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=18.5
Q ss_pred cCCCCccCCCCCccccCchHHHHHHHH
Q psy2238 206 EKNKPIPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 206 ~~~k~~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
.||--+.||-|+..|.....+.+|+-.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 455667777777777777777777543
No 81
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=79.12 E-value=1.1 Score=29.65 Aligned_cols=23 Identities=26% Similarity=0.626 Sum_probs=11.2
Q ss_pred ccccccccc-ccCCCceeecCCCC
Q psy2238 128 VCLECERGV-WDHGGRVYKCCFCE 150 (311)
Q Consensus 128 ~C~~C~~~f-~~~~~~~~~C~~C~ 150 (311)
.|..|+... ....--.|.|+.||
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCG 34 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCG 34 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCC
Confidence 455555544 22233445566665
No 82
>KOG2186|consensus
Probab=78.02 E-value=0.9 Score=39.26 Aligned_cols=47 Identities=13% Similarity=0.314 Sum_probs=31.3
Q ss_pred cccCCCchhcchHHHHHHhhhhcCCCCccCCCCCccccCchHHHHHHHH
Q psy2238 184 YSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 184 ~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
|.|.+||.......+-+|+.+-++ .-|.|=.|++.|.. ..+..|..=
T Consensus 4 FtCnvCgEsvKKp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EehhhhhhhccccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 457777777766666666665554 56777777777777 555667543
No 83
>KOG2023|consensus
Probab=77.61 E-value=1.3 Score=43.71 Aligned_cols=27 Identities=41% Similarity=0.522 Sum_probs=14.1
Q ss_pred cccccCCCCCCCCCCCCCCCcCCCCCC
Q psy2238 273 SHKFGRQQLNGDDYDDEDDDYDVGGGY 299 (311)
Q Consensus 273 ~~~~~~~~~~~d~~dd~ddd~d~~~~~ 299 (311)
.+..+..+.++||+||||||+|..+.|
T Consensus 343 ~~~~~~~~~~eDdddDe~DDdD~~~dW 369 (885)
T KOG2023|consen 343 EHGNGEDADDEDDDDDEDDDDDAFSDW 369 (885)
T ss_pred hccCccccccccccccccccccccccc
Confidence 333344443555555566666666555
No 84
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=77.27 E-value=1.3 Score=28.25 Aligned_cols=26 Identities=27% Similarity=0.579 Sum_probs=18.6
Q ss_pred ccccccccccccc-CCCceeecCCCC-C
Q psy2238 126 DAVCLECERGVWD-HGGRVYKCCFCE-G 151 (311)
Q Consensus 126 ~~~C~~C~~~f~~-~~~~~~~C~~C~-~ 151 (311)
.|.|..||+.|.. .......|+.|| +
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 4788888888753 355667888888 5
No 85
>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=77.18 E-value=1.4 Score=25.77 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=13.9
Q ss_pred ccccccccccccCCCceeecCCCC
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
|.|..||..+.. ...|-.|++|+
T Consensus 3 ~~C~~CG~i~~g-~~~p~~CP~Cg 25 (34)
T cd00729 3 WVCPVCGYIHEG-EEAPEKCPICG 25 (34)
T ss_pred EECCCCCCEeEC-CcCCCcCcCCC
Confidence 667777765532 23456777776
No 86
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.41 E-value=1.6 Score=31.34 Aligned_cols=23 Identities=26% Similarity=0.768 Sum_probs=16.1
Q ss_pred CCccCCCCCCC-------CCcccCCCchhc
Q psy2238 171 ENYKCKSCNKL-------GQYSCLRCKICF 193 (311)
Q Consensus 171 k~~~C~~C~~~-------~~~~C~~C~k~F 193 (311)
.+|.|+.|++. ..+.|..|+..|
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 57887777766 456677777776
No 87
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=76.12 E-value=2.3 Score=27.19 Aligned_cols=24 Identities=29% Similarity=0.562 Sum_probs=16.7
Q ss_pred ccCCCCCccccCc-----hHHHHHHH-Hhc
Q psy2238 211 IPCPKCGFETSQT-----KDLSMSTR-SHK 234 (311)
Q Consensus 211 ~~C~~C~k~f~~~-----~~L~~H~~-~H~ 234 (311)
-.|..|++.++.. ++|.+|++ +|.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 4677777777655 58888877 553
No 88
>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=74.75 E-value=1.6 Score=26.92 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=13.6
Q ss_pred cccccccccccccC----CCceeecCCCC
Q psy2238 126 DAVCLECERGVWDH----GGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~----~~~~~~C~~C~ 150 (311)
.|.|..||..|... ...+..|+.||
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECG 33 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCC
Confidence 46666666666321 23445566665
No 89
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.13 E-value=2.3 Score=38.49 Aligned_cols=35 Identities=17% Similarity=0.239 Sum_probs=19.1
Q ss_pred eeecCC--CC-CCCChHHHHHHHHHhcccCCCCccCCCCCCC
Q psy2238 143 VYKCCF--CE-GFLCEDDQFEHQASCQVLESENYKCKSCNKL 181 (311)
Q Consensus 143 ~~~C~~--C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~ 181 (311)
.|.|+. |. .......|+.|.+.. + ..+-|.+|-.-
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~--H--~~~~C~~C~~n 188 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQ--H--GFVLCSECIGN 188 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhh--c--CcEEhHhhhcC
Confidence 355653 55 444456677787764 1 24556665444
No 90
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.69 E-value=2.2 Score=43.21 Aligned_cols=46 Identities=20% Similarity=0.509 Sum_probs=32.4
Q ss_pred ccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCC--CCcccCCCchh
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKL--GQYSCLRCKIC 192 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~--~~~~C~~C~k~ 192 (311)
..|..||. .++|+.|+ .+. .| .......|.+|++. .|..|+.||..
T Consensus 436 l~C~~Cg~--------v~~Cp~Cd~~lt----------~H--~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGY--------IAECPNCDSPLT----------LH--KATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eecccCCC--------cccCCCCCcceE----------Ee--cCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 46888884 46799998 532 23 33467788888877 67788888766
No 91
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=73.62 E-value=2 Score=28.03 Aligned_cols=22 Identities=27% Similarity=0.418 Sum_probs=18.0
Q ss_pred cCCCchhc-chHHHHHHhhhhcC
Q psy2238 186 CLRCKICF-CEDHARRKGFKYEK 207 (311)
Q Consensus 186 C~~C~k~F-~~~~l~~H~~~h~~ 207 (311)
|+.|+..| .++...+|....|+
T Consensus 20 CPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 20 CPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCchhHHHHHhHHHHHHhhHHhh
Confidence 99999999 66689999876554
No 92
>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=72.82 E-value=2.3 Score=30.93 Aligned_cols=23 Identities=35% Similarity=0.928 Sum_probs=18.6
Q ss_pred CCccCCCCCCC-------CCcccCCCchhc
Q psy2238 171 ENYKCKSCNKL-------GQYSCLRCKICF 193 (311)
Q Consensus 171 k~~~C~~C~~~-------~~~~C~~C~k~F 193 (311)
..|.|+.|++. ..+.|..|++.|
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 78999999888 568888888887
No 93
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=72.05 E-value=2 Score=35.09 Aligned_cols=23 Identities=22% Similarity=0.267 Sum_probs=15.3
Q ss_pred cccccccccccccCCCceeecCCCC
Q psy2238 126 DAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.|.|.+||.++.. +.|-+||+||
T Consensus 134 ~~vC~vCGy~~~g--e~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHEG--EAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcccC--CCCCcCCCCC
Confidence 3777777765544 6677777776
No 94
>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=71.93 E-value=2.9 Score=31.65 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=14.6
Q ss_pred cccCcCccccccccchhhcccCCCCccccccccc
Q psy2238 40 MECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKI 73 (311)
Q Consensus 40 ~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~ 73 (311)
..|+.||..|. ..++.|..|+.||..
T Consensus 10 R~Cp~CG~kFY--------DLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 10 RTCPSCGAKFY--------DLNKDPIVCPKCGTE 35 (108)
T ss_pred ccCCCCcchhc--------cCCCCCccCCCCCCc
Confidence 35666666665 122355666666666
No 95
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=71.39 E-value=2.7 Score=25.29 Aligned_cols=30 Identities=23% Similarity=0.467 Sum_probs=15.6
Q ss_pred cccCcCccccccccchhhcccCCCCccccccccc
Q psy2238 40 MECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKI 73 (311)
Q Consensus 40 ~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~ 73 (311)
|+|..|+..|..... -.....-.|+.||..
T Consensus 6 y~C~~Cg~~fe~~~~----~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQK----ISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEe----cCCCCCCCCCCCCCc
Confidence 567777776652111 111345567776654
No 96
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.24 E-value=6.8 Score=29.77 Aligned_cols=52 Identities=19% Similarity=0.311 Sum_probs=32.5
Q ss_pred ccCCCCCCC---CCcccCCCchhc-chHHHHH--HhhhhcC---C-------CCccCCCCCccccCch
Q psy2238 173 YKCKSCNKL---GQYSCLRCKICF-CEDHARR--KGFKYEK---N-------KPIPCPKCGFETSQTK 224 (311)
Q Consensus 173 ~~C~~C~~~---~~~~C~~C~k~F-~~~~l~~--H~~~h~~---~-------k~~~C~~C~k~f~~~~ 224 (311)
|.|+.|.-. -|..|++|+-+. .+.+|.+ |+..-.. + ..-.|-.|.+.|....
T Consensus 2 Y~CPrC~skvC~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~ 69 (112)
T TIGR00622 2 YFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPP 69 (112)
T ss_pred ccCCCCCCCccCCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcc
Confidence 556666555 566799999999 5557755 3321110 1 1124999999998654
No 97
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=71.01 E-value=3.1 Score=25.71 Aligned_cols=24 Identities=21% Similarity=0.402 Sum_probs=13.1
Q ss_pred CCCccCCCCCccccCc----hHHHHHHH
Q psy2238 208 NKPIPCPKCGFETSQT----KDLSMSTR 231 (311)
Q Consensus 208 ~k~~~C~~C~k~f~~~----~~L~~H~~ 231 (311)
..-..|..|++.+... ++|.+|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3456777777776663 67777773
No 98
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=70.64 E-value=1.8 Score=33.66 Aligned_cols=30 Identities=23% Similarity=0.365 Sum_probs=20.9
Q ss_pred cccccccccccccCC-CceeecCCCC--CCCCh
Q psy2238 126 DAVCLECERGVWDHG-GRVYKCCFCE--GFLCE 155 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~-~~~~~C~~C~--~f~~~ 155 (311)
|++|..||+.|.... +..--|+.|| +|...
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~yv 33 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGGNKFQYV 33 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCCcceEEc
Confidence 478888888887653 4455688888 46543
No 99
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.58 E-value=1.1 Score=38.33 Aligned_cols=41 Identities=22% Similarity=0.439 Sum_probs=24.8
Q ss_pred CcccCCCchhcchHHH-HHHhhh---hc-------CCCC-----ccCCCCCccccCc
Q psy2238 183 QYSCLRCKICFCEDHA-RRKGFK---YE-------KNKP-----IPCPKCGFETSQT 223 (311)
Q Consensus 183 ~~~C~~C~k~F~~~~l-~~H~~~---h~-------~~k~-----~~C~~C~k~f~~~ 223 (311)
...|++|++.|....+ ....+. .+ +-.| ..||.||.+|...
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3459999999955422 222221 11 1233 3899999998865
No 100
>PRK14873 primosome assembly protein PriA; Provisional
Probab=69.71 E-value=3.1 Score=41.94 Aligned_cols=46 Identities=20% Similarity=0.550 Sum_probs=33.8
Q ss_pred ccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCC-CCcccCCCchh
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKL-GQYSCLRCKIC 192 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~-~~~~C~~C~k~ 192 (311)
..|..|| ...+|+.|+ ... .| .......|.+||+. .|+.|+.|+..
T Consensus 384 l~C~~Cg--------~~~~C~~C~~~L~----------~h--~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCR--------TPARCRHCTGPLG----------LP--SAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eEhhhCc--------CeeECCCCCCcee----------Ee--cCCCeeECCCCcCCCcCccCCCCcCC
Confidence 4788887 467899998 533 23 33567889999886 67889999875
No 101
>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=69.68 E-value=3 Score=40.64 Aligned_cols=46 Identities=17% Similarity=0.494 Sum_probs=33.8
Q ss_pred ccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCC--CCcccCCCchh
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKL--GQYSCLRCKIC 192 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~--~~~~C~~C~k~ 192 (311)
..|..|| ...+|+.|+ ... .| .......|..|+.. .|..|+.|+..
T Consensus 214 ~~C~~Cg--------~~~~C~~C~~~l~----------~h--~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCG--------YILCCPNCDVSLT----------YH--KKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCc--------CccCCCCCCCceE----------Ee--cCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4788887 456799998 422 23 44567899999988 57889999874
No 102
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=69.44 E-value=3 Score=26.72 Aligned_cols=29 Identities=24% Similarity=0.525 Sum_probs=15.3
Q ss_pred cccCcCccccccccchhhcccCCCCcccccccc
Q psy2238 40 MECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGK 72 (311)
Q Consensus 40 ~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k 72 (311)
|.|..|+..|..... -....+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~----~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQK----MSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEe----cCCCCCCCCCCCCC
Confidence 567777776662211 11134455777765
No 103
>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=67.77 E-value=4.6 Score=22.01 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=15.0
Q ss_pred ccCCCCCccccCchHHHHHHHH
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
..||+|.+.+ ....+..|+..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3688888887 55677777653
No 104
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=67.29 E-value=4 Score=24.31 Aligned_cols=8 Identities=25% Similarity=0.654 Sum_probs=3.7
Q ss_pred eeecCCCC
Q psy2238 143 VYKCCFCE 150 (311)
Q Consensus 143 ~~~C~~C~ 150 (311)
..+|+.|+
T Consensus 25 ~vrC~~C~ 32 (37)
T PF13719_consen 25 KVRCPKCG 32 (37)
T ss_pred EEECCCCC
Confidence 34444444
No 105
>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=66.95 E-value=2.7 Score=24.98 Aligned_cols=32 Identities=22% Similarity=0.576 Sum_probs=16.3
Q ss_pred cccCcCccccccccchhhcccCCCCccccccccc
Q psy2238 40 MECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKI 73 (311)
Q Consensus 40 ~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~ 73 (311)
+.|+.|+..|..... .+.. ......|+.|+..
T Consensus 3 ~~CP~C~~~~~v~~~-~~~~-~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS-QLGA-NGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHH-HcCC-CCCEEECCCCCCE
Confidence 456777776663332 1111 1224567777665
No 106
>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=66.81 E-value=5.7 Score=28.94 Aligned_cols=23 Identities=35% Similarity=0.928 Sum_probs=18.7
Q ss_pred CCccCCCCCCC-------CCcccCCCchhc
Q psy2238 171 ENYKCKSCNKL-------GQYSCLRCKICF 193 (311)
Q Consensus 171 k~~~C~~C~~~-------~~~~C~~C~k~F 193 (311)
..|.|+.|++. ..+.|..|++.|
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 68998888776 468888888888
No 107
>KOG2482|consensus
Probab=66.80 E-value=13 Score=33.85 Aligned_cols=57 Identities=16% Similarity=0.167 Sum_probs=39.5
Q ss_pred cccCCCchhc-chH-HHHHHhhhhcCC----------------------CCccCCCCCccccCchHHHHHHHH--hcCCC
Q psy2238 184 YSCLRCKICF-CED-HARRKGFKYEKN----------------------KPIPCPKCGFETSQTKDLSMSTRS--HKFGR 237 (311)
Q Consensus 184 ~~C~~C~k~F-~~~-~l~~H~~~h~~~----------------------k~~~C~~C~k~f~~~~~L~~H~~~--H~~~~ 237 (311)
.+|-.|..-+ ... ..+.|+..-|+- ..+.|-.|.|.|..+..|+.|||. |..-.
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrrin 224 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRIN 224 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCcccC
Confidence 4499999888 444 555555422221 237899999999999999999986 55444
Q ss_pred CCC
Q psy2238 238 QQL 240 (311)
Q Consensus 238 ~~~ 240 (311)
|-.
T Consensus 225 Pkn 227 (423)
T KOG2482|consen 225 PKN 227 (423)
T ss_pred CCc
Confidence 433
No 108
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=66.27 E-value=8.4 Score=34.49 Aligned_cols=81 Identities=25% Similarity=0.461 Sum_probs=51.4
Q ss_pred CccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-hhH--HhHH---HHHH-------hhcCcCCCCccccc
Q psy2238 64 LPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-AWI--CHGR---KCLQ-------THACTCPLQDAVCL 130 (311)
Q Consensus 64 ~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~f~--~~~~---~H~~-------~H~~~~~~~~~~C~ 130 (311)
-|.|+.|... +.+ -|..|+.|. ... .++. .|+. .-.+++| +.-.|-
T Consensus 308 Gy~CP~Cktk---------------VCs-----LPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~-ks~~Cf 366 (421)
T COG5151 308 GYECPVCKTK---------------VCS-----LPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNP-KSTHCF 366 (421)
T ss_pred ceeCCcccce---------------eec-----CCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCC-CCccce
Confidence 5888888765 222 478899998 433 2221 3332 1223333 334577
Q ss_pred cccccccc---------CCCceeecCCCC-CCCChHHHHHHHHHh
Q psy2238 131 ECERGVWD---------HGGRVYKCCFCE-GFLCEDDQFEHQASC 165 (311)
Q Consensus 131 ~C~~~f~~---------~~~~~~~C~~C~-~f~~~~~L~~H~~~h 165 (311)
.|.-.|.. +....|+|+.|. .|-..-....|...|
T Consensus 367 ~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 367 VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 78777753 245679999999 888888888887776
No 109
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=65.92 E-value=1.3 Score=37.96 Aligned_cols=11 Identities=18% Similarity=0.606 Sum_probs=8.1
Q ss_pred cccCCCchhcc
Q psy2238 184 YSCLRCKICFC 194 (311)
Q Consensus 184 ~~C~~C~k~F~ 194 (311)
..|+.||.+|.
T Consensus 49 ~vCP~CgyA~~ 59 (214)
T PF09986_consen 49 WVCPHCGYAAF 59 (214)
T ss_pred EECCCCCCccc
Confidence 45888888873
No 110
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=65.30 E-value=3.4 Score=30.03 Aligned_cols=24 Identities=33% Similarity=0.772 Sum_probs=18.5
Q ss_pred CCCccCCCCCCC-------CCcccCCCchhc
Q psy2238 170 SENYKCKSCNKL-------GQYSCLRCKICF 193 (311)
Q Consensus 170 ~k~~~C~~C~~~-------~~~~C~~C~k~F 193 (311)
...|.|+.|++. ..+.|..|++.|
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred hCCccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 368898888766 457788888887
No 111
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=65.26 E-value=5 Score=29.16 Aligned_cols=23 Identities=26% Similarity=0.781 Sum_probs=18.9
Q ss_pred CCccCCCCCCC-------CCcccCCCchhc
Q psy2238 171 ENYKCKSCNKL-------GQYSCLRCKICF 193 (311)
Q Consensus 171 k~~~C~~C~~~-------~~~~C~~C~k~F 193 (311)
..|.|+.|++. ..+.|..|++.|
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 78999999776 568888888888
No 112
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.19 E-value=3.9 Score=30.66 Aligned_cols=27 Identities=7% Similarity=0.086 Sum_probs=23.8
Q ss_pred ccccccccccccCCCceeecCCCC-CCC
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFL 153 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~ 153 (311)
-.|+.|++.|......|..|++|| +|.
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s~P 37 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKSYP 37 (129)
T ss_pred ccCccccchhhccCCCccccCcccccch
Confidence 468899999999999999999999 784
No 113
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.23 E-value=5.3 Score=32.01 Aligned_cols=35 Identities=26% Similarity=0.529 Sum_probs=21.4
Q ss_pred cccCCCchhcchHHHHHHhhhhcCCCCccCCCCCcccc
Q psy2238 184 YSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETS 221 (311)
Q Consensus 184 ~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~ 221 (311)
|.|+.|+..|+........- ....|.||.||....
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d---~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLD---MDGTFTCPRCGEELE 134 (147)
T ss_pred EECcCCCCEeeHHHHHHhcC---CCCcEECCCCCCEEE
Confidence 33999999996542221111 134499999997654
No 114
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=62.05 E-value=4.4 Score=33.13 Aligned_cols=8 Identities=38% Similarity=1.040 Sum_probs=4.2
Q ss_pred eeecCCCC
Q psy2238 143 VYKCCFCE 150 (311)
Q Consensus 143 ~~~C~~C~ 150 (311)
.|.|++||
T Consensus 134 ~~vC~vCG 141 (166)
T COG1592 134 VWVCPVCG 141 (166)
T ss_pred EEEcCCCC
Confidence 45555555
No 115
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=61.28 E-value=5.5 Score=40.44 Aligned_cols=44 Identities=18% Similarity=0.387 Sum_probs=26.8
Q ss_pred cccCcCccccccccchhhc---ccCCCCccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh
Q psy2238 40 MECDKCKRKQKNRAFCYFC---QSVQRLPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE 105 (311)
Q Consensus 40 ~~C~~C~~~f~~~~~c~~~---h~~~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~ 105 (311)
..|..||..+. =..|... |...+...|..||.. ...|..|+.|+
T Consensus 436 l~C~~Cg~v~~-Cp~Cd~~lt~H~~~~~L~CH~Cg~~---------------------~~~p~~Cp~Cg 482 (730)
T COG1198 436 LLCRDCGYIAE-CPNCDSPLTLHKATGQLRCHYCGYQ---------------------EPIPQSCPECG 482 (730)
T ss_pred eecccCCCccc-CCCCCcceEEecCCCeeEeCCCCCC---------------------CCCCCCCCCCC
Confidence 45888877766 1111111 555556666666655 33688999999
No 116
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=60.22 E-value=7 Score=23.12 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=3.8
Q ss_pred eeecCCCC
Q psy2238 143 VYKCCFCE 150 (311)
Q Consensus 143 ~~~C~~C~ 150 (311)
..+|+.|+
T Consensus 25 ~v~C~~C~ 32 (36)
T PF13717_consen 25 KVRCSKCG 32 (36)
T ss_pred EEECCCCC
Confidence 34444444
No 117
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.91 E-value=7.3 Score=40.55 Aligned_cols=45 Identities=22% Similarity=0.575 Sum_probs=25.6
Q ss_pred ccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCC-CCcccCCCchhc
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKL-GQYSCLRCKICF 193 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~-~~~~C~~C~k~F 193 (311)
..|+.||... -.+.|+.|| . .+..+.|+.|+.. .++.|+.|+..-
T Consensus 627 RfCpsCG~~t-----~~frCP~CG~~-----------------Te~i~fCP~CG~~~~~y~CPKCG~El 673 (1121)
T PRK04023 627 RKCPSCGKET-----FYRRCPFCGTH-----------------TEPVYRCPRCGIEVEEDECEKCGREP 673 (1121)
T ss_pred ccCCCCCCcC-----CcccCCCCCCC-----------------CCcceeCccccCcCCCCcCCCCCCCC
Confidence 4666776553 335677776 3 1344566666655 446666666544
No 118
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=59.80 E-value=4.9 Score=32.51 Aligned_cols=8 Identities=50% Similarity=1.165 Sum_probs=4.2
Q ss_pred cCCCchhc
Q psy2238 186 CLRCKICF 193 (311)
Q Consensus 186 C~~C~k~F 193 (311)
|+.||++|
T Consensus 31 c~~c~~~f 38 (154)
T PRK00464 31 CLACGKRF 38 (154)
T ss_pred ccccCCcc
Confidence 55555555
No 119
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=59.49 E-value=4.9 Score=29.05 Aligned_cols=27 Identities=22% Similarity=0.468 Sum_probs=21.2
Q ss_pred CCcccccccccccccC-CCceeecCCCC
Q psy2238 124 LQDAVCLECERGVWDH-GGRVYKCCFCE 150 (311)
Q Consensus 124 ~~~~~C~~C~~~f~~~-~~~~~~C~~C~ 150 (311)
++|-.|..||..|... -.+|-.|+.|-
T Consensus 56 v~Pa~CkkCGfef~~~~ik~pSRCP~CK 83 (97)
T COG3357 56 VRPARCKKCGFEFRDDKIKKPSRCPKCK 83 (97)
T ss_pred ecChhhcccCccccccccCCcccCCcch
Confidence 3568899999999874 44588999987
No 120
>KOG2482|consensus
Probab=59.45 E-value=10 Score=34.40 Aligned_cols=92 Identities=15% Similarity=0.195 Sum_probs=61.5
Q ss_pred ceeecCCCC-CCCChHHHHHHHHHhcccCCCCcc--------CC--CCCCC-----------------------------
Q psy2238 142 RVYKCCFCE-GFLCEDDQFEHQASCQVLESENYK--------CK--SCNKL----------------------------- 181 (311)
Q Consensus 142 ~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~--------C~--~C~~~----------------------------- 181 (311)
..+.|-+|. .|..+..|+.||+.-.|-.-.|-. -. .=+++
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed 273 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNED 273 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcC
Confidence 457899999 899999999999875322222210 00 00111
Q ss_pred --CC--cccCCCchhcc-hHHHHHHhhhhcCC---------------------------CCccCCCCCccccCchHHHHH
Q psy2238 182 --GQ--YSCLRCKICFC-EDHARRKGFKYEKN---------------------------KPIPCPKCGFETSQTKDLSMS 229 (311)
Q Consensus 182 --~~--~~C~~C~k~F~-~~~l~~H~~~h~~~---------------------------k~~~C~~C~k~f~~~~~L~~H 229 (311)
-+ -.|-.|....- ...|..||.+.|.= +.-.|-.|.-.|-....|..|
T Consensus 274 ~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~h 353 (423)
T KOG2482|consen 274 DAEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIH 353 (423)
T ss_pred CCCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhh
Confidence 12 47999998884 55899998754321 113688899999999999999
Q ss_pred HHHh
Q psy2238 230 TRSH 233 (311)
Q Consensus 230 ~~~H 233 (311)
|.-+
T Consensus 354 m~e~ 357 (423)
T KOG2482|consen 354 MVED 357 (423)
T ss_pred cccc
Confidence 8643
No 121
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=59.34 E-value=7.3 Score=30.18 Aligned_cols=12 Identities=8% Similarity=0.166 Sum_probs=7.7
Q ss_pred CcccCCCCh-hhH
Q psy2238 97 VGAICDFCE-AWI 108 (311)
Q Consensus 97 ~~~~C~~C~-~f~ 108 (311)
.|..|+.|| .|.
T Consensus 25 ~p~vcP~cg~~~~ 37 (129)
T TIGR02300 25 RPAVSPYTGEQFP 37 (129)
T ss_pred CCccCCCcCCccC
Confidence 467777777 443
No 122
>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=59.18 E-value=4.6 Score=22.92 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=8.5
Q ss_pred cccccccccccCCCceeecCCCC
Q psy2238 128 VCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 128 ~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
+|+.|+..+.......|.|+.|+
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECG 26 (30)
T ss_dssp --TTT-----EE-SSSEEETTTT
T ss_pred CCCCCCCcceeccCCEEeCCccc
Confidence 45555555555555555666655
No 123
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=58.54 E-value=6.7 Score=28.19 Aligned_cols=27 Identities=30% Similarity=0.584 Sum_probs=14.4
Q ss_pred ccccccccccc-cCCCceeecCCCC-CCC
Q psy2238 127 AVCLECERGVW-DHGGRVYKCCFCE-GFL 153 (311)
Q Consensus 127 ~~C~~C~~~f~-~~~~~~~~C~~C~-~f~ 153 (311)
|.|+.|++.-. ..+...+.|..|+ +|.
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 56666665421 1244556666666 554
No 124
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=58.32 E-value=10 Score=25.01 Aligned_cols=43 Identities=16% Similarity=0.280 Sum_probs=26.1
Q ss_pred CCCccCCCCCCC--CCcccCCCchhcchHHHHHHhhhhcCCCCccCCC
Q psy2238 170 SENYKCKSCNKL--GQYSCLRCKICFCEDHARRKGFKYEKNKPIPCPK 215 (311)
Q Consensus 170 ~k~~~C~~C~~~--~~~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~ 215 (311)
...+.|++..+. .|+....|+-+|...+++... ...+...||+
T Consensus 9 ~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYI---QRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHC---TTTS-EE-SC
T ss_pred EeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHH---HhcCCCCCCC
Confidence 345666666555 677789999999888777766 3457788887
No 125
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.02 E-value=10 Score=30.34 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=7.1
Q ss_pred CccccCcCccccc
Q psy2238 38 ANMECDKCKRKQK 50 (311)
Q Consensus 38 ~~~~C~~C~~~f~ 50 (311)
..|.|+.|+..|.
T Consensus 98 ~~Y~Cp~C~~~y~ 110 (147)
T smart00531 98 AYYKCPNCQSKYT 110 (147)
T ss_pred cEEECcCCCCEee
Confidence 3455555555554
No 126
>PRK05580 primosome assembly protein PriA; Validated
Probab=56.80 E-value=7 Score=39.60 Aligned_cols=46 Identities=20% Similarity=0.536 Sum_probs=34.0
Q ss_pred ccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCC--CCcccCCCchh
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKL--GQYSCLRCKIC 192 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~--~~~~C~~C~k~ 192 (311)
..|..|| ...+|+.|+ ... .| .......|..|++. .|..|+.|+..
T Consensus 382 ~~C~~Cg--------~~~~C~~C~~~l~----------~h--~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 382 LLCRDCG--------WVAECPHCDASLT----------LH--RFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred eEhhhCc--------CccCCCCCCCcee----------EE--CCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 5688887 456799998 532 23 34567889999988 57889999776
No 127
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=55.94 E-value=3.1 Score=30.74 Aligned_cols=29 Identities=24% Similarity=0.387 Sum_probs=18.3
Q ss_pred cccccccccccccC-CCceeecCCCC--CCCC
Q psy2238 126 DAVCLECERGVWDH-GGRVYKCCFCE--GFLC 154 (311)
Q Consensus 126 ~~~C~~C~~~f~~~-~~~~~~C~~C~--~f~~ 154 (311)
|++|..||..|..- .+..--|+.|| +|..
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~nkF~y 33 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGCNKFLY 33 (112)
T ss_pred CceecccccccccccHHHHccCccccchheEe
Confidence 36777788777663 33344577777 4654
No 128
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=55.48 E-value=11 Score=27.17 Aligned_cols=16 Identities=31% Similarity=0.796 Sum_probs=9.0
Q ss_pred CCCCCCCCcCCCCCCC
Q psy2238 285 DYDDEDDDYDVGGGYS 300 (311)
Q Consensus 285 ~~dd~ddd~d~~~~~~ 300 (311)
++++++|++|.||||=
T Consensus 61 Ee~eee~~ddD~gGWI 76 (87)
T PF15017_consen 61 EEEEEEEEDDDGGGWI 76 (87)
T ss_pred cccccccccCCCCccc
Confidence 3444555566677763
No 129
>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=54.33 E-value=8.5 Score=31.26 Aligned_cols=26 Identities=23% Similarity=0.549 Sum_probs=19.0
Q ss_pred cCCCchhcchH-HHHHHhhhhcCCCCccCCCCCccc
Q psy2238 186 CLRCKICFCED-HARRKGFKYEKNKPIPCPKCGFET 220 (311)
Q Consensus 186 C~~C~k~F~~~-~l~~H~~~h~~~k~~~C~~C~k~f 220 (311)
|+.|+..|+.. ++. .-|.||.||-..
T Consensus 112 Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 112 CPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 88888888666 442 259999998654
No 130
>KOG2807|consensus
Probab=53.11 E-value=18 Score=32.68 Aligned_cols=74 Identities=20% Similarity=0.467 Sum_probs=40.1
Q ss_pred ccccccccccccCCCceeecCCCC-CCCChHHHHHHHHHhcccCCCCc------------cCCCC-CCC---CCcccCCC
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFLCEDDQFEHQASCQVLESENY------------KCKSC-NKL---GQYSCLRC 189 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~------------~C~~C-~~~---~~~~C~~C 189 (311)
|.|++|.... -.-|..|++|+ ......+|.+-.+-- -.-++| -|-.| +.. ..|.|..|
T Consensus 277 y~CP~Ckakv---CsLP~eCpiC~ltLVss~hLARSyhhL--~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~C 351 (378)
T KOG2807|consen 277 YFCPQCKAKV---CSLPIECPICSLTLVSSPHLARSYHHL--FPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESC 351 (378)
T ss_pred eeCCcccCee---ecCCccCCccceeEecchHHHHHHHhh--cCCcchhhccccccCCCcceeeeccccCCCCcEEchhc
Confidence 5666665432 34688899999 766666666443211 111222 15555 222 45777777
Q ss_pred chhcc-hHHHHHHhhhh
Q psy2238 190 KICFC-EDHARRKGFKY 205 (311)
Q Consensus 190 ~k~F~-~~~l~~H~~~h 205 (311)
-..|- .=....|...|
T Consensus 352 k~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 352 KNVFCLDCDVFIHESLH 368 (378)
T ss_pred cceeeccchHHHHhhhh
Confidence 77773 33555554443
No 131
>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=52.81 E-value=9.7 Score=30.92 Aligned_cols=33 Identities=15% Similarity=0.236 Sum_probs=18.9
Q ss_pred CCCCccccCcCccccccccchhhcccCCCCccccccccc
Q psy2238 35 PCNANMECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKI 73 (311)
Q Consensus 35 ~~~~~~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~ 73 (311)
....-|.|+.|+..|+.... .+.-|.|+.||..
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA------~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEA------MELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECCCCCcEeeHHHH------HHcCCcCCCCCCE
Confidence 34455777777766652211 2345777777765
No 132
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=52.56 E-value=7.1 Score=25.62 Aligned_cols=16 Identities=19% Similarity=0.374 Sum_probs=7.4
Q ss_pred cCC----CchhcchHHHHHH
Q psy2238 186 CLR----CKICFCEDHARRK 201 (311)
Q Consensus 186 C~~----C~k~F~~~~l~~H 201 (311)
|+. |...+....|..|
T Consensus 41 C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 41 CPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp -SS----S--EEEHHHHHHC
T ss_pred CCCCCCCCCCccchhHHhCC
Confidence 666 6666655555544
No 133
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=52.54 E-value=8.7 Score=29.99 Aligned_cols=56 Identities=20% Similarity=0.520 Sum_probs=32.5
Q ss_pred ccCCCCccccCcCccccccccchhhcccCCCCccc---cccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh-hhH
Q psy2238 33 EFPCNANMECDKCKRKQKNRAFCYFCQSVQRLPQC---GHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE-AWI 108 (311)
Q Consensus 33 ~~~~~~~~~C~~C~~~f~~~~~c~~~h~~~k~~~C---~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~-~f~ 108 (311)
+....+.|+|.+|..+...... -||-.| .+|+.- -.+|++|-..|. +||.|. +|.
T Consensus 74 vF~d~~lYeCnIC~etS~ee~F-------LKPneCCgY~iCn~C------ya~LWK~~~~yp--------vCPvCkTSFK 132 (140)
T PF05290_consen 74 VFLDPKLYECNICKETSAEERF-------LKPNECCGYSICNAC------YANLWKFCNLYP--------VCPVCKTSFK 132 (140)
T ss_pred eecCCCceeccCcccccchhhc-------CCcccccchHHHHHH------HHHHHHHcccCC--------CCCccccccc
Confidence 3344578999999887662221 234333 233333 345777766555 688887 665
Q ss_pred H
Q psy2238 109 C 109 (311)
Q Consensus 109 ~ 109 (311)
.
T Consensus 133 s 133 (140)
T PF05290_consen 133 S 133 (140)
T ss_pred c
Confidence 4
No 134
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.29 E-value=8.5 Score=31.94 Aligned_cols=31 Identities=32% Similarity=0.697 Sum_probs=20.7
Q ss_pred cccCCCchhcchHHHHHHhhhhcCCCCccCCCCCccccC
Q psy2238 184 YSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETSQ 222 (311)
Q Consensus 184 ~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~~ 222 (311)
|.|+.|+..|+..... +.-|.||.||-....
T Consensus 118 Y~Cp~C~~rytf~eA~--------~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 118 FFCPNCHIRFTFDEAM--------EYGFRCPQCGEMLEE 148 (178)
T ss_pred EECCCCCcEEeHHHHh--------hcCCcCCCCCCCCee
Confidence 3388899888666322 136999999865443
No 135
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.10 E-value=12 Score=31.10 Aligned_cols=31 Identities=19% Similarity=0.480 Sum_probs=15.5
Q ss_pred CCccccCcCccccccccchhhcccCCCCccccccccc
Q psy2238 37 NANMECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKI 73 (311)
Q Consensus 37 ~~~~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~ 73 (311)
..-|.|+.|+..|+... +.+.-|.|+.||..
T Consensus 115 ~~~Y~Cp~C~~rytf~e------A~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDE------AMEYGFRCPQCGEM 145 (178)
T ss_pred CCEEECCCCCcEEeHHH------HhhcCCcCCCCCCC
Confidence 34566666666555111 12234666666654
No 136
>KOG4173|consensus
Probab=49.93 E-value=9.4 Score=32.11 Aligned_cols=77 Identities=19% Similarity=0.274 Sum_probs=47.7
Q ss_pred ceeecCCCC---CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchH-HHHHHhhhh----------cC
Q psy2238 142 RVYKCCFCE---GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCED-HARRKGFKY----------EK 207 (311)
Q Consensus 142 ~~~~C~~C~---~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~-~l~~H~~~h----------~~ 207 (311)
..|.|++-| .|.....+..|..+- |.. . |.+|.+.|... -|-.|+.-. -|
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~-h~~----s-----------Cs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG 141 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTL-HGN----S-----------CSFCKRAFPTGHLLDAHILEWHDSLFQALVERG 141 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhc-ccc----h-----------hHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC
Confidence 345555533 365555566666443 122 2 88888888544 344454322 23
Q ss_pred CCCccC--CCCCccccCchHHHHHH-HHhc
Q psy2238 208 NKPIPC--PKCGFETSQTKDLSMST-RSHK 234 (311)
Q Consensus 208 ~k~~~C--~~C~k~f~~~~~L~~H~-~~H~ 234 (311)
.--|+| ..|+..|.+.-.-+.|+ ++|.
T Consensus 142 ~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 142 QDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred ccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 456899 67999999999999996 5564
No 137
>PF14353 CpXC: CpXC protein
Probab=49.65 E-value=8.5 Score=29.87 Aligned_cols=21 Identities=24% Similarity=0.496 Sum_probs=12.6
Q ss_pred CCccCCCCCccccCchHHHHH
Q psy2238 209 KPIPCPKCGFETSQTKDLSMS 229 (311)
Q Consensus 209 k~~~C~~C~k~f~~~~~L~~H 229 (311)
-.|.||.||..|.-...|.-|
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred CEEECCCCCCceecCCCEEEE
Confidence 456777777766655554444
No 138
>KOG2807|consensus
Probab=48.82 E-value=22 Score=32.20 Aligned_cols=64 Identities=19% Similarity=0.352 Sum_probs=45.5
Q ss_pred CCccCCCCCCC---CCcccCCCchhc-chHHHHH--Hhhhh--------c-----------------CCCCccCCCCCcc
Q psy2238 171 ENYKCKSCNKL---GQYSCLRCKICF-CEDHARR--KGFKY--------E-----------------KNKPIPCPKCGFE 219 (311)
Q Consensus 171 k~~~C~~C~~~---~~~~C~~C~k~F-~~~~l~~--H~~~h--------~-----------------~~k~~~C~~C~k~ 219 (311)
.-|.|+.|.-. -|-.|++|+-+. ...+|.+ |+..- . +.-.|.|..|...
T Consensus 275 ~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~ 354 (378)
T KOG2807|consen 275 GGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNV 354 (378)
T ss_pred CceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccce
Confidence 45888888777 788899999999 5556644 33210 1 1123788899999
Q ss_pred ccCchHHHHHHHHhc
Q psy2238 220 TSQTKDLSMSTRSHK 234 (311)
Q Consensus 220 f~~~~~L~~H~~~H~ 234 (311)
|-.-...-.|...|.
T Consensus 355 FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 355 FCLDCDVFIHESLHN 369 (378)
T ss_pred eeccchHHHHhhhhc
Confidence 988888888877664
No 139
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.54 E-value=9.1 Score=30.21 Aligned_cols=10 Identities=20% Similarity=0.498 Sum_probs=4.5
Q ss_pred cccccccccc
Q psy2238 127 AVCLECERGV 136 (311)
Q Consensus 127 ~~C~~C~~~f 136 (311)
+.|..||..|
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 4444444444
No 140
>KOG4167|consensus
Probab=47.69 E-value=4.4 Score=40.40 Aligned_cols=26 Identities=23% Similarity=0.485 Sum_probs=23.7
Q ss_pred CccCCCCCccccCchHHHHHHHHhcC
Q psy2238 210 PIPCPKCGFETSQTKDLSMSTRSHKF 235 (311)
Q Consensus 210 ~~~C~~C~k~f~~~~~L~~H~~~H~~ 235 (311)
-|.|.+|+|.|-.-.++..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48999999999999999999999964
No 141
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=47.04 E-value=9.9 Score=29.86 Aligned_cols=27 Identities=26% Similarity=0.324 Sum_probs=15.6
Q ss_pred CCCccCCCCCccccCchHHHHHHHHhcCCC
Q psy2238 208 NKPIPCPKCGFETSQTKDLSMSTRSHKFGR 237 (311)
Q Consensus 208 ~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~ 237 (311)
+.-..|-+|||.|.. |++|+++|+|-.
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCC
Confidence 344678888888874 588888886654
No 142
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=47.02 E-value=8.3 Score=31.18 Aligned_cols=34 Identities=24% Similarity=0.420 Sum_probs=18.7
Q ss_pred cccCcCcccccc-ccchhhc--ccCCCCccccccccc
Q psy2238 40 MECDKCKRKQKN-RAFCYFC--QSVQRLPQCGHCGKI 73 (311)
Q Consensus 40 ~~C~~C~~~f~~-~~~c~~~--h~~~k~~~C~~C~k~ 73 (311)
+.|+.|+-.+.. ...=++. ....+.++|+.||+.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~ 37 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKR 37 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCc
Confidence 468888865521 1110111 123445888888888
No 143
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=46.61 E-value=10 Score=28.94 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=17.9
Q ss_pred cccccccccccccCCCceeecCCCC
Q psy2238 126 DAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.+.|..|+..|.......+.||.||
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcC
Confidence 4788888877765544446788888
No 144
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=46.48 E-value=12 Score=22.50 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=6.9
Q ss_pred CcccCCCchhc
Q psy2238 183 QYSCLRCKICF 193 (311)
Q Consensus 183 ~~~C~~C~k~F 193 (311)
|+.|..|++.|
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 45566666666
No 145
>KOG2272|consensus
Probab=46.48 E-value=19 Score=31.28 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=8.6
Q ss_pred CccccCcCccccc
Q psy2238 38 ANMECDKCKRKQK 50 (311)
Q Consensus 38 ~~~~C~~C~~~f~ 50 (311)
.-|.|..|-+.|.
T Consensus 39 ~CFvCAQCf~pf~ 51 (332)
T KOG2272|consen 39 QCFVCAQCFRPFP 51 (332)
T ss_pred HHHHHHHhcCcCC
Confidence 3466777777666
No 146
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=46.41 E-value=23 Score=21.61 Aligned_cols=26 Identities=15% Similarity=0.269 Sum_probs=17.9
Q ss_pred ccccccccccccCCCHHHHHHhHhhhc
Q psy2238 65 PQCGHCGKIKCMLKTGDCVIKHAGVFS 91 (311)
Q Consensus 65 ~~C~~C~k~~~~f~~~~~L~~H~~~h~ 91 (311)
-.|+.||..|. .........|.+.|.
T Consensus 14 ~~C~~CgM~Y~-~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYS-PGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEEC-CCCHHHHHHHHHHHh
Confidence 47888888753 345666777877764
No 147
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=45.90 E-value=12 Score=29.25 Aligned_cols=25 Identities=20% Similarity=0.103 Sum_probs=19.6
Q ss_pred ccCCCCCccccCchHHHHHHHHhcCCCC
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRSHKFGRQ 238 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~ 238 (311)
..|-.+||.|. +|++|+.+|.+--|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 46888888887 68899988876554
No 148
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=45.42 E-value=6.6 Score=27.34 Aligned_cols=41 Identities=12% Similarity=0.293 Sum_probs=26.3
Q ss_pred cccCCCchhc-chHHHHHHhhhhcCCCCccCC--CCCccccCchHH
Q psy2238 184 YSCLRCKICF-CEDHARRKGFKYEKNKPIPCP--KCGFETSQTKDL 226 (311)
Q Consensus 184 ~~C~~C~k~F-~~~~l~~H~~~h~~~k~~~C~--~C~k~f~~~~~L 226 (311)
+.|+.|+... ...+-... .-..+.-++|. .||..|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEEEE
Confidence 3488888776 33322111 12556778997 999999987665
No 149
>PF15269 zf-C2H2_7: Zinc-finger
Probab=44.18 E-value=15 Score=22.80 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=16.8
Q ss_pred ccCCCCCccccCchHHHHHHHH
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
|+|-.|......++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5777787777778888888764
No 150
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=44.11 E-value=14 Score=23.78 Aligned_cols=10 Identities=30% Similarity=0.952 Sum_probs=6.2
Q ss_pred cccCCCchhc
Q psy2238 184 YSCLRCKICF 193 (311)
Q Consensus 184 ~~C~~C~k~F 193 (311)
|+|.+||..+
T Consensus 2 y~C~~CgyiY 11 (50)
T cd00730 2 YECRICGYIY 11 (50)
T ss_pred cCCCCCCeEE
Confidence 4466666666
No 151
>KOG1940|consensus
Probab=42.85 E-value=53 Score=29.24 Aligned_cols=27 Identities=15% Similarity=0.281 Sum_probs=20.6
Q ss_pred ccCCCCCccccCchHHHHHHHHhcCCCC
Q psy2238 211 IPCPKCGFETSQTKDLSMSTRSHKFGRQ 238 (311)
Q Consensus 211 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~ 238 (311)
|.||+|.+ -...+.+.++.-.+-...|
T Consensus 197 y~CP~C~~-~~d~~~~~~~~d~~l~~~~ 223 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRKLDKELAGSP 223 (276)
T ss_pred CCCCcccc-hHHHHHHHHHHHHHHhcCC
Confidence 99999999 8888888888766555444
No 152
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=41.17 E-value=4.8 Score=40.17 Aligned_cols=75 Identities=27% Similarity=0.592 Sum_probs=41.1
Q ss_pred ccccccccccccCCCcee-----ecCCCC-CCCChHHHHHHHHHhcccCCCCccCCCCCCCCCcccCCCchhcchHHHHH
Q psy2238 127 AVCLECERGVWDHGGRVY-----KCCFCE-GFLCEDDQFEHQASCQVLESENYKCKSCNKLGQYSCLRCKICFCEDHARR 200 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~-----~C~~C~-~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~~~~~C~~C~k~F~~~~l~~ 200 (311)
-.|+.|-+-+.....+.| .|..|| +|+-...|---... +.-+.|. .|+.|.+-|.....++
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~n---TsM~~F~----------lC~~C~~EY~dP~nRR 168 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDREN---TSMADFP----------LCPFCDKEYKDPLNRR 168 (750)
T ss_pred hhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCccc---CccccCc----------CCHHHHHHhcCccccc
Confidence 456666666555555544 478888 77765444322211 2223332 1777877775553333
Q ss_pred HhhhhcCCCCccCCCCCcc
Q psy2238 201 KGFKYEKNKPIPCPKCGFE 219 (311)
Q Consensus 201 H~~~h~~~k~~~C~~C~k~ 219 (311)
.| ..|.-|+.||-.
T Consensus 169 fH-----AQp~aCp~CGP~ 182 (750)
T COG0068 169 FH-----AQPIACPKCGPH 182 (750)
T ss_pred cc-----cccccCcccCCC
Confidence 22 256778888753
No 153
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.15 E-value=18 Score=35.33 Aligned_cols=44 Identities=18% Similarity=0.402 Sum_probs=25.3
Q ss_pred cccCcCccccccccchhhc---ccCCCCccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh
Q psy2238 40 MECDKCKRKQKNRAFCYFC---QSVQRLPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE 105 (311)
Q Consensus 40 ~~C~~C~~~f~~~~~c~~~---h~~~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~ 105 (311)
..|..||.... =..|... |.......|..||.. ...|..|+.|+
T Consensus 214 ~~C~~Cg~~~~-C~~C~~~l~~h~~~~~l~Ch~Cg~~---------------------~~~~~~Cp~C~ 260 (505)
T TIGR00595 214 LLCRSCGYILC-CPNCDVSLTYHKKEGKLRCHYCGYQ---------------------EPIPKTCPQCG 260 (505)
T ss_pred eEhhhCcCccC-CCCCCCceEEecCCCeEEcCCCcCc---------------------CCCCCCCCCCC
Confidence 36777776655 1111111 555556667777765 22477888888
No 154
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=40.06 E-value=45 Score=21.78 Aligned_cols=32 Identities=9% Similarity=-0.017 Sum_probs=22.6
Q ss_pred cCCCchhcchHHHHHHhhhhcCCCCccCCCCCccccC
Q psy2238 186 CLRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETSQ 222 (311)
Q Consensus 186 C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~~ 222 (311)
...||.+|....+..+.+. ...||.|++.++.
T Consensus 16 ~~~~G~v~~~~~i~~~~~~-----~~~cP~~~~~~~~ 47 (63)
T smart00504 16 ILPSGQTYERRAIEKWLLS-----HGTDPVTGQPLTH 47 (63)
T ss_pred ECCCCCEEeHHHHHHHHHH-----CCCCCCCcCCCCh
Confidence 3467888877777766654 2479999988754
No 155
>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=39.34 E-value=21 Score=20.93 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=10.5
Q ss_pred ccCcCccccccccchhhcccCCCCcccccccc
Q psy2238 41 ECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGK 72 (311)
Q Consensus 41 ~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k 72 (311)
.|.+|++.|..... -..|.+.+|.+
T Consensus 5 ~C~eC~~~f~dSyL-------~~~F~~~VCD~ 29 (34)
T PF01286_consen 5 KCDECGKPFMDSYL-------LNNFDLPVCDK 29 (34)
T ss_dssp E-TTT--EES-SSC-------CCCTS-S--TT
T ss_pred hHhHhCCHHHHHHH-------HHhCCcccccc
Confidence 58888888874332 33455666654
No 156
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.30 E-value=15 Score=28.16 Aligned_cols=25 Identities=16% Similarity=0.320 Sum_probs=16.1
Q ss_pred cccccccccccccCCCceeecCCCC
Q psy2238 126 DAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.+.|..|+..|.......+.||.||
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cg 95 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCH 95 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCC
Confidence 4678888877655433333588888
No 157
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.11 E-value=17 Score=25.37 Aligned_cols=9 Identities=33% Similarity=0.958 Sum_probs=5.8
Q ss_pred ccccccccc
Q psy2238 65 PQCGHCGKI 73 (311)
Q Consensus 65 ~~C~~C~k~ 73 (311)
|+|..|+..
T Consensus 13 Y~c~~cg~~ 21 (82)
T COG2331 13 YECTECGNR 21 (82)
T ss_pred EeecccchH
Confidence 566666665
No 158
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=39.10 E-value=9.3 Score=21.63 Aligned_cols=20 Identities=30% Similarity=0.914 Sum_probs=11.2
Q ss_pred cCCCCCCCCCcccCCCchhc
Q psy2238 174 KCKSCNKLGQYSCLRCKICF 193 (311)
Q Consensus 174 ~C~~C~~~~~~~C~~C~k~F 193 (311)
.|.+|+....|.|+.|+..+
T Consensus 4 ~C~vC~~~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 4 LCSVCGNPAKYRCPRCGARY 23 (30)
T ss_dssp EETSSSSEESEE-TTT--EE
T ss_pred CCccCcCCCEEECCCcCCce
Confidence 35666666667777777666
No 159
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=38.94 E-value=11 Score=23.80 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=6.2
Q ss_pred cccCCCchhc
Q psy2238 184 YSCLRCKICF 193 (311)
Q Consensus 184 ~~C~~C~k~F 193 (311)
|+|.+|+..+
T Consensus 2 y~C~~CgyvY 11 (47)
T PF00301_consen 2 YQCPVCGYVY 11 (47)
T ss_dssp EEETTTSBEE
T ss_pred cCCCCCCEEE
Confidence 4466666666
No 160
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.05 E-value=17 Score=19.11 Aligned_cols=6 Identities=33% Similarity=1.071 Sum_probs=2.7
Q ss_pred cCCCch
Q psy2238 186 CLRCKI 191 (311)
Q Consensus 186 C~~C~k 191 (311)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 161
>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=37.92 E-value=1.6 Score=39.22 Aligned_cols=46 Identities=17% Similarity=0.261 Sum_probs=16.6
Q ss_pred CCccCCCCCCC---CCcccCCCchhcchH-HHHHHhhhhcCCCCccCCCCC
Q psy2238 171 ENYKCKSCNKL---GQYSCLRCKICFCED-HARRKGFKYEKNKPIPCPKCG 217 (311)
Q Consensus 171 k~~~C~~C~~~---~~~~C~~C~k~F~~~-~l~~H~~~h~~~k~~~C~~C~ 217 (311)
+-..|..|+.. ....|+.||..-... .... ...-.+.+.+.|..|+
T Consensus 196 R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 196 RYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEEEETTT--EEE--TTS-TTT---SS-EEE---------SEEEEEETTTT
T ss_pred EEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEe-cCCCCcEEEEECCccc
Confidence 33444444444 334488887665222 1110 0111233667888886
No 162
>COG1773 Rubredoxin [Energy production and conversion]
Probab=37.77 E-value=24 Score=23.17 Aligned_cols=13 Identities=15% Similarity=0.008 Sum_probs=8.6
Q ss_pred ccccccccccccc
Q psy2238 126 DAVCLECERGVWD 138 (311)
Q Consensus 126 ~~~C~~C~~~f~~ 138 (311)
.|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4777777777643
No 163
>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=37.70 E-value=7.4 Score=21.69 Aligned_cols=19 Identities=26% Similarity=0.474 Sum_probs=9.6
Q ss_pred ccCCCchhcchHHHHHHhh
Q psy2238 185 SCLRCKICFCEDHARRKGF 203 (311)
Q Consensus 185 ~C~~C~k~F~~~~l~~H~~ 203 (311)
.|-.|++.|.......|-.
T Consensus 2 sCiDC~~~F~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEEEGGGTTT---
T ss_pred eeecCCCCcCcCCcCCCCc
Confidence 4666777775555555543
No 164
>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=37.14 E-value=24 Score=20.87 Aligned_cols=10 Identities=40% Similarity=0.773 Sum_probs=5.9
Q ss_pred ccCcCccccc
Q psy2238 41 ECDKCKRKQK 50 (311)
Q Consensus 41 ~C~~C~~~f~ 50 (311)
.|+.|+++|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4566666655
No 165
>KOG3362|consensus
Probab=36.89 E-value=13 Score=29.48 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=15.8
Q ss_pred CccccccccccccCCCHHHHHHhHh
Q psy2238 64 LPQCGHCGKIKCMLKTGDCVIKHAG 88 (311)
Q Consensus 64 ~~~C~~C~k~~~~f~~~~~L~~H~~ 88 (311)
+|.|.-||.. +-+...|..|.-
T Consensus 129 ~ysC~~CG~k---yCsv~C~~~Hne 150 (156)
T KOG3362|consen 129 KYSCVNCGTK---YCSVRCLKTHNE 150 (156)
T ss_pred hhHHHhcCCc---eeechhhhhccc
Confidence 5678888888 566677777643
No 166
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.72 E-value=39 Score=36.43 Aligned_cols=20 Identities=25% Similarity=0.725 Sum_probs=9.5
Q ss_pred cCCCCCCC--CCcccCCCchhc
Q psy2238 174 KCKSCNKL--GQYSCLRCKICF 193 (311)
Q Consensus 174 ~C~~C~~~--~~~~C~~C~k~F 193 (311)
.|+.||.. .+|.|+.||...
T Consensus 681 fCP~CGs~te~vy~CPsCGaev 702 (1337)
T PRK14714 681 RCPDCGTHTEPVYVCPDCGAEV 702 (1337)
T ss_pred cCcccCCcCCCceeCccCCCcc
Confidence 34444444 234466665543
No 167
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=36.04 E-value=39 Score=30.38 Aligned_cols=25 Identities=16% Similarity=0.218 Sum_probs=20.0
Q ss_pred CccCCCCCccccCchHHHHHHHHhc
Q psy2238 210 PIPCPKCGFETSQTKDLSMSTRSHK 234 (311)
Q Consensus 210 ~~~C~~C~k~f~~~~~L~~H~~~H~ 234 (311)
.|.|+.|...|-.....-.|...|.
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHhh
Confidence 3788888888888888888877764
No 168
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.95 E-value=17 Score=32.92 Aligned_cols=68 Identities=15% Similarity=0.283 Sum_probs=39.2
Q ss_pred ceeecCCCCCCCChHHHHHHHHHhcccCCCCccCCCCCCC---CCcccCCCchhcchHHHHHHhhhh---cCCCCccCCC
Q psy2238 142 RVYKCCFCEGFLCEDDQFEHQASCQVLESENYKCKSCNKL---GQYSCLRCKICFCEDHARRKGFKY---EKNKPIPCPK 215 (311)
Q Consensus 142 ~~~~C~~C~~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~---~~~~C~~C~k~F~~~~l~~H~~~h---~~~k~~~C~~ 215 (311)
..-.|++||.....+-+ +.... .|.+-..|..|+-. ....|+.||.. ..|... .+- ...+...|..
T Consensus 186 ~~~~CPvCGs~P~~s~v--~~~~~--~G~RyL~CslC~teW~~~R~~C~~Cg~~---~~l~y~-~~~~~~~~~r~e~C~~ 257 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVV--QIGTT--QGLRYLHCNLCESEWHVVRVKCSNCEQS---GKLHYW-SLDSEQAAVKAESCGD 257 (309)
T ss_pred CCCCCCCCCCcchhhee--eccCC--CCceEEEcCCCCCcccccCccCCCCCCC---Cceeee-eecCCCcceEeeeccc
Confidence 34568999944333322 22222 56677788888877 56779999962 222111 111 1236678888
Q ss_pred CC
Q psy2238 216 CG 217 (311)
Q Consensus 216 C~ 217 (311)
|+
T Consensus 258 C~ 259 (309)
T PRK03564 258 CG 259 (309)
T ss_pred cc
Confidence 86
No 169
>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=35.58 E-value=22 Score=26.69 Aligned_cols=28 Identities=21% Similarity=0.400 Sum_probs=20.5
Q ss_pred cccccccccccCCCceeecCCCC-CCCCh
Q psy2238 128 VCLECERGVWDHGGRVYKCCFCE-GFLCE 155 (311)
Q Consensus 128 ~C~~C~~~f~~~~~~~~~C~~C~-~f~~~ 155 (311)
.|+.|+..|.......|.|+.|+ .+...
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccccc
Confidence 57788877777766678888888 66544
No 170
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.53 E-value=21 Score=36.11 Aligned_cols=32 Identities=25% Similarity=0.686 Sum_probs=16.8
Q ss_pred ccCcCccccccccchhhc---ccCCCCccccccccc
Q psy2238 41 ECDKCKRKQKNRAFCYFC---QSVQRLPQCGHCGKI 73 (311)
Q Consensus 41 ~C~~C~~~f~~~~~c~~~---h~~~k~~~C~~C~k~ 73 (311)
.|..|+..+. =..|... |.......|..||..
T Consensus 385 ~C~~Cg~~~~-C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 385 ACARCRTPAR-CRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred EhhhCcCeeE-CCCCCCceeEecCCCeeECCCCcCC
Confidence 6888877765 1111111 444455666666654
No 171
>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=35.10 E-value=11 Score=28.69 Aligned_cols=24 Identities=21% Similarity=0.458 Sum_probs=14.5
Q ss_pred cccccccccccccCCCceeecCCCC
Q psy2238 126 DAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.+.|..|+..|.-.... +.||.|+
T Consensus 70 ~~~C~~Cg~~~~~~~~~-~~CP~Cg 93 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFD-FSCPRCG 93 (113)
T ss_dssp EEEETTTS-EEECHHCC-HH-SSSS
T ss_pred cEECCCCCCEEecCCCC-CCCcCCc
Confidence 36788888777654333 6688887
No 172
>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=35.06 E-value=23 Score=28.28 Aligned_cols=8 Identities=50% Similarity=1.252 Sum_probs=5.8
Q ss_pred cCCCchhc
Q psy2238 186 CLRCKICF 193 (311)
Q Consensus 186 C~~C~k~F 193 (311)
|..|++.|
T Consensus 31 C~~C~~RF 38 (147)
T TIGR00244 31 CLECHERF 38 (147)
T ss_pred CCccCCcc
Confidence 77777777
No 173
>PF01153 Glypican: Glypican; InterPro: IPR001863 Glypicans [, ] are a family of heparan sulphate proteoglycans which are anchored to cell membranes by a glycosylphosphatidylinositol (GPI) linkage. Six members (GPC1-6) are known in vertebrates []. Structurally, these proteins consist of three separate domains: A signal sequence; An extracellular domain of about 500 residues that contains 12 conserved cysteines probably involved in disulphide bonds and which also contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A C-terminal hydrophobic region which is post-translationally removed after formation of the GPI-anchor. ; GO: 0043395 heparan sulfate proteoglycan binding, 0005578 proteinaceous extracellular matrix, 0016020 membrane; PDB: 3ODN_A 4AD7_A 4ACR_C.
Probab=34.79 E-value=14 Score=36.49 Aligned_cols=20 Identities=50% Similarity=0.669 Sum_probs=1.1
Q ss_pred CCCCCCCCCCCcCCCCCCCC
Q psy2238 282 NGDDYDDEDDDYDVGGGYSG 301 (311)
Q Consensus 282 ~~d~~dd~ddd~d~~~~~~~ 301 (311)
+++|.|.+|+|+|..|.+||
T Consensus 471 ~G~d~d~~D~~dd~sGsGSG 490 (557)
T PF01153_consen 471 SGNDVDFQDDDDDGSGSGSG 490 (557)
T ss_dssp TT------------------
T ss_pred CCCCCCCCCCCcCCCCCCCC
Confidence 55666655555555443344
No 174
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=34.69 E-value=22 Score=27.80 Aligned_cols=24 Identities=21% Similarity=0.157 Sum_probs=19.3
Q ss_pred ccCCCchhcchHHHHHHhhhhcCCCC
Q psy2238 185 SCLRCKICFCEDHARRKGFKYEKNKP 210 (311)
Q Consensus 185 ~C~~C~k~F~~~~l~~H~~~h~~~k~ 210 (311)
.|-++|+.| ++|.+|..+|.+-.|
T Consensus 78 icLEDGkkf--KSLKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKF--KSLKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcch--HHHHHHHhcccCCCH
Confidence 399999999 678899999877544
No 175
>PRK10220 hypothetical protein; Provisional
Probab=34.66 E-value=29 Score=26.13 Aligned_cols=28 Identities=18% Similarity=0.384 Sum_probs=20.8
Q ss_pred cccccccccccCCCceeecCCCC-CCCCh
Q psy2238 128 VCLECERGVWDHGGRVYKCCFCE-GFLCE 155 (311)
Q Consensus 128 ~C~~C~~~f~~~~~~~~~C~~C~-~f~~~ 155 (311)
.|+.|+..|.......|.|+.|+ .+...
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 57888888777766778888888 65543
No 176
>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=34.45 E-value=20 Score=28.14 Aligned_cols=24 Identities=29% Similarity=0.491 Sum_probs=16.3
Q ss_pred CCCccccccccccccCCCHHHHHHhHhhhc
Q psy2238 62 QRLPQCGHCGKIKCMLKTGDCVIKHAGVFS 91 (311)
Q Consensus 62 ~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~ 91 (311)
..-..|-+||+. |.. |++|++.|+
T Consensus 70 ~d~i~clecGk~---~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 70 PDYIICLECGKK---FKT---LKRHLRTHH 93 (132)
T ss_dssp SS-EE-TBT--E---ESB---HHHHHHHTT
T ss_pred cCeeEEccCCcc---cch---HHHHHHHcc
Confidence 345689999999 676 799999997
No 177
>PF15387 DUF4611: Domain of unknown function (DUF4611)
Probab=34.12 E-value=35 Score=24.85 Aligned_cols=19 Identities=37% Similarity=0.776 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCCCCCcCCC
Q psy2238 278 RQQLNGDDYDDEDDDYDVG 296 (311)
Q Consensus 278 ~~~~~~d~~dd~ddd~d~~ 296 (311)
...++++|+||.+||.++.
T Consensus 63 ~E~ldg~deddaede~n~~ 81 (96)
T PF15387_consen 63 DEALDGDDEDDAEDENNID 81 (96)
T ss_pred hhhccCccccccccccCcc
Confidence 3445666665555555543
No 178
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=34.09 E-value=25 Score=20.77 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=16.0
Q ss_pred ccccccccccccCCCceeecCCCC
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
..|.+|+..+....+--|-|..||
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCG 32 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCc
Confidence 347777776666666667777666
No 179
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=34.06 E-value=28 Score=21.28 Aligned_cols=9 Identities=22% Similarity=0.423 Sum_probs=3.7
Q ss_pred ceeecCCCC
Q psy2238 142 RVYKCCFCE 150 (311)
Q Consensus 142 ~~~~C~~C~ 150 (311)
..+.|..||
T Consensus 18 g~~vC~~CG 26 (43)
T PF08271_consen 18 GELVCPNCG 26 (43)
T ss_dssp TEEEETTT-
T ss_pred CeEECCCCC
Confidence 334455554
No 180
>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=34.02 E-value=21 Score=23.28 Aligned_cols=10 Identities=40% Similarity=1.019 Sum_probs=4.8
Q ss_pred ccCCCCCccc
Q psy2238 211 IPCPKCGFET 220 (311)
Q Consensus 211 ~~C~~C~k~f 220 (311)
..|+.||..|
T Consensus 23 V~Cp~CGael 32 (54)
T TIGR01206 23 VICDECGAEL 32 (54)
T ss_pred EeCCCCCCEE
Confidence 3555555443
No 181
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=33.16 E-value=26 Score=19.54 Aligned_cols=21 Identities=29% Similarity=0.838 Sum_probs=6.2
Q ss_pred cccccccccccCCCceeecCCCC
Q psy2238 128 VCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 128 ~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.|..|++.... ...|.|..|.
T Consensus 2 ~C~~C~~~~~~--~~~Y~C~~Cd 22 (30)
T PF07649_consen 2 RCDACGKPIDG--GWFYRCSECD 22 (30)
T ss_dssp --TTTS----S----EEE-TTT-
T ss_pred cCCcCCCcCCC--CceEECccCC
Confidence 35555544332 3556666665
No 182
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=33.15 E-value=27 Score=31.06 Aligned_cols=12 Identities=58% Similarity=0.789 Sum_probs=8.2
Q ss_pred CCCCccCCCCCC
Q psy2238 299 YSGFSYGGGGAT 310 (311)
Q Consensus 299 ~~~~~~~~g~~~ 310 (311)
++|+|+|||||+
T Consensus 257 gGGgS~GGGGas 268 (271)
T COG1512 257 GGGGSSGGGGAS 268 (271)
T ss_pred CCCCCCCCCCCC
Confidence 556777777775
No 183
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=32.62 E-value=29 Score=30.15 Aligned_cols=13 Identities=23% Similarity=0.838 Sum_probs=9.1
Q ss_pred CcccCCCchhcch
Q psy2238 183 QYSCLRCKICFCE 195 (311)
Q Consensus 183 ~~~C~~C~k~F~~ 195 (311)
.|.|+.|+..|+-
T Consensus 155 ef~C~~C~h~F~G 167 (278)
T PF15135_consen 155 EFHCPKCRHNFRG 167 (278)
T ss_pred eeecccccccchh
Confidence 4778888777743
No 184
>KOG3362|consensus
Probab=32.22 E-value=18 Score=28.60 Aligned_cols=28 Identities=21% Similarity=0.624 Sum_probs=20.6
Q ss_pred CCCCCCCCCcccCCCchhc-chHHHHHHh
Q psy2238 175 CKSCNKLGQYSCLRCKICF-CEDHARRKG 202 (311)
Q Consensus 175 C~~C~~~~~~~C~~C~k~F-~~~~l~~H~ 202 (311)
|.+||...+|.|.-||..+ +-.-+..|.
T Consensus 121 CaVCG~~S~ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 121 CAVCGYDSKYSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred hhhcCCCchhHHHhcCCceeechhhhhcc
Confidence 7788877888888888888 555666554
No 185
>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=32.10 E-value=25 Score=23.82 Aligned_cols=22 Identities=23% Similarity=0.431 Sum_probs=7.6
Q ss_pred cccccccccccCCCceeecCCCC
Q psy2238 128 VCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 128 ~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.|..|++.|. .-.+.+.|..||
T Consensus 11 ~C~~C~~~F~-~~~rrhhCr~CG 32 (69)
T PF01363_consen 11 NCMICGKKFS-LFRRRHHCRNCG 32 (69)
T ss_dssp B-TTT--B-B-SSS-EEE-TTT-
T ss_pred cCcCcCCcCC-CceeeEccCCCC
Confidence 4556666663 234555555555
No 186
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=31.52 E-value=16 Score=24.09 Aligned_cols=37 Identities=14% Similarity=0.341 Sum_probs=24.6
Q ss_pred ccCCCchhc-chH-HHHHHhhhhcCCCCccCCCCCcccc
Q psy2238 185 SCLRCKICF-CED-HARRKGFKYEKNKPIPCPKCGFETS 221 (311)
Q Consensus 185 ~C~~C~k~F-~~~-~l~~H~~~h~~~k~~~C~~C~k~f~ 221 (311)
+|..|++.+ -.. ++.....+...-..|-|..|.-...
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~ 42 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIR 42 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHh
Confidence 488999988 333 5555544445567799999964433
No 187
>KOG2593|consensus
Probab=31.36 E-value=25 Score=33.10 Aligned_cols=32 Identities=22% Similarity=0.576 Sum_probs=19.7
Q ss_pred cccCCCchhcchHHHHHHhhhhcCCCCccCCCCC
Q psy2238 184 YSCLRCKICFCEDHARRKGFKYEKNKPIPCPKCG 217 (311)
Q Consensus 184 ~~C~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~ 217 (311)
|.|+.|.+.|+....++ ..-...-.|.|..|+
T Consensus 129 Y~Cp~C~kkyt~Lea~~--L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQ--LLDNETGEFHCENCG 160 (436)
T ss_pred ccCCccccchhhhHHHH--hhcccCceEEEecCC
Confidence 44999999996662222 122223558898885
No 188
>KOG2023|consensus
Probab=31.34 E-value=27 Score=34.91 Aligned_cols=13 Identities=46% Similarity=0.652 Sum_probs=6.3
Q ss_pred CCCCCCCCcCCCC
Q psy2238 285 DYDDEDDDYDVGG 297 (311)
Q Consensus 285 ~~dd~ddd~d~~~ 297 (311)
++||+|||+|.+.
T Consensus 352 ~eDdddDe~DDdD 364 (885)
T KOG2023|consen 352 DEDDDDDEDDDDD 364 (885)
T ss_pred ccccccccccccc
Confidence 4455555555433
No 189
>KOG1819|consensus
Probab=30.90 E-value=70 Score=30.80 Aligned_cols=24 Identities=38% Similarity=0.404 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCcCCCCCCCCCcc
Q psy2238 281 LNGDDYDDEDDDYDVGGGYSGFSY 304 (311)
Q Consensus 281 ~~~d~~dd~ddd~d~~~~~~~~~~ 304 (311)
.++||++++|||.|++-....++.
T Consensus 425 ~dgdde~eddddidvdeediessd 448 (990)
T KOG1819|consen 425 EDGDDEAEDDDDIDVDEEDIESSD 448 (990)
T ss_pred ccCcccccCccccccccccccccc
Confidence 455666666666666555444443
No 190
>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=30.88 E-value=37 Score=25.42 Aligned_cols=26 Identities=27% Similarity=0.378 Sum_probs=22.6
Q ss_pred CCccc----cccccccccCCCHHHHHHhHhhhc
Q psy2238 63 RLPQC----GHCGKIKCMLKTGDCVIKHAGVFS 91 (311)
Q Consensus 63 k~~~C----~~C~k~~~~f~~~~~L~~H~~~h~ 91 (311)
.-|.| ..|+.. ..+...+..|++.++
T Consensus 79 ~G~~C~~~~~~C~y~---~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYI---TRSKKTMRKHWRKEH 108 (109)
T ss_pred CCeeeecCCCCCCcE---eccHHHHHHHHHHhc
Confidence 34789 999998 899999999999876
No 191
>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=30.84 E-value=24 Score=31.90 Aligned_cols=66 Identities=15% Similarity=0.197 Sum_probs=35.6
Q ss_pred ecCCCCCCCChHHHHHHHHHhcccCCCCccCCCCCCC---CCcccCCCchhcchHHHHHHhhhhc-----CCCCccCCCC
Q psy2238 145 KCCFCEGFLCEDDQFEHQASCQVLESENYKCKSCNKL---GQYSCLRCKICFCEDHARRKGFKYE-----KNKPIPCPKC 216 (311)
Q Consensus 145 ~C~~C~~f~~~~~L~~H~~~h~~~~~k~~~C~~C~~~---~~~~C~~C~k~F~~~~l~~H~~~h~-----~~k~~~C~~C 216 (311)
.|++||.....+.+. .-... .|.+-..|..|+-. ...+|+.|+.. ..|.. ...-. +.+...|..|
T Consensus 186 ~CPvCGs~P~~s~~~-~~~~~--~G~RyL~CslC~teW~~~R~~C~~Cg~~---~~l~y-~~~e~~~~~~~~r~e~C~~C 258 (305)
T TIGR01562 186 LCPACGSPPVASMVR-QGGKE--TGLRYLSCSLCATEWHYVRVKCSHCEES---KHLAY-LSLEHDAEKAVLKAETCDSC 258 (305)
T ss_pred cCCCCCChhhhhhhc-ccCCC--CCceEEEcCCCCCcccccCccCCCCCCC---Cceee-EeecCCCCCcceEEeecccc
Confidence 688888433222211 00011 45567788888777 55679999864 22211 11111 2266788888
Q ss_pred C
Q psy2238 217 G 217 (311)
Q Consensus 217 ~ 217 (311)
+
T Consensus 259 ~ 259 (305)
T TIGR01562 259 Q 259 (305)
T ss_pred c
Confidence 6
No 192
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=30.58 E-value=41 Score=20.30 Aligned_cols=21 Identities=10% Similarity=0.137 Sum_probs=14.0
Q ss_pred CCceeecCCCC-CCCChHHHHH
Q psy2238 140 GGRVYKCCFCE-GFLCEDDQFE 160 (311)
Q Consensus 140 ~~~~~~C~~C~-~f~~~~~L~~ 160 (311)
+...+.|+.|+ .|.....|.+
T Consensus 16 ~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 16 DVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CEEEEECCCCCeEEccHHHHHH
Confidence 34567788888 7666666653
No 193
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=30.51 E-value=71 Score=27.88 Aligned_cols=67 Identities=13% Similarity=0.215 Sum_probs=36.6
Q ss_pred HHHHHHhHhhhcc--CCCcCcccCCCCh-hhHHhHHHHHHhhcCcCCCCccccccccccccc------CCCceeecCCCC
Q psy2238 80 GDCVIKHAGVFST--GMGMVGAICDFCE-AWICHGRKCLQTHACTCPLQDAVCLECERGVWD------HGGRVYKCCFCE 150 (311)
Q Consensus 80 ~~~L~~H~~~h~~--~~~~~~~~C~~C~-~f~~~~~~H~~~H~~~~~~~~~~C~~C~~~f~~------~~~~~~~C~~C~ 150 (311)
..+|+.+.+.+.. +.-.+.|.|..|. .|-.. ....| ..-.|..|.+.|.- .|...|.|+.|+
T Consensus 92 e~Nlrm~d~a~~~~ip~~drqFaC~~Cd~~WwRr-------vp~rK--eVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~ 162 (278)
T PF15135_consen 92 EENLRMFDDAQENLIPSVDRQFACSSCDHMWWRR-------VPQRK--EVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCR 162 (278)
T ss_pred HHHHHHhhhhhhccccccceeeeccccchHHHhc-------cCccc--ccccccccccccCCCccccccceeeeeccccc
Confidence 4455555554431 0012568888887 43221 11112 13567777777632 256678888888
Q ss_pred -CCCCh
Q psy2238 151 -GFLCE 155 (311)
Q Consensus 151 -~f~~~ 155 (311)
.|...
T Consensus 163 h~F~G~ 168 (278)
T PF15135_consen 163 HNFRGF 168 (278)
T ss_pred ccchhh
Confidence 77754
No 194
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.16 E-value=26 Score=26.63 Aligned_cols=24 Identities=29% Similarity=0.578 Sum_probs=15.6
Q ss_pred cccccccccccccCCCceeecCCCC
Q psy2238 126 DAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.+.|..|+..|... ...+.||.||
T Consensus 70 ~~~C~~Cg~~~~~~-~~~~~CP~Cg 93 (113)
T PRK12380 70 QAWCWDCSQVVEIH-QHDAQCPHCH 93 (113)
T ss_pred EEEcccCCCEEecC-CcCccCcCCC
Confidence 46788888666543 2345588887
No 195
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.00 E-value=28 Score=32.82 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=22.7
Q ss_pred cccccccccccCCCceeecCCCC-CCCChH
Q psy2238 128 VCLECERGVWDHGGRVYKCCFCE-GFLCED 156 (311)
Q Consensus 128 ~C~~C~~~f~~~~~~~~~C~~C~-~f~~~~ 156 (311)
.|+.||....+.|..-|+|+.|| ++....
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccCCccc
Confidence 68888888888877788888888 666543
No 196
>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=29.37 E-value=13 Score=34.24 Aligned_cols=51 Identities=16% Similarity=0.267 Sum_probs=23.6
Q ss_pred cccCCCCh--hhHHhH----HHHHH-hhcCcCCCCcccccccccccccCCCce-eecCCCC
Q psy2238 98 GAICDFCE--AWICHG----RKCLQ-THACTCPLQDAVCLECERGVWDHGGRV-YKCCFCE 150 (311)
Q Consensus 98 ~~~C~~C~--~f~~~~----~~H~~-~H~~~~~~~~~~C~~C~~~f~~~~~~~-~~C~~C~ 150 (311)
-+.|..|. .|.... ..|.. .|.+.+ +.|+|..|+........-| -.|..||
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~K--RFFkC~~C~~Rt~sl~r~P~~~C~~Cg 310 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVK--RFFKCKDCGNRTISLERLPKKHCSNCG 310 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE---EEEE-T-TS-EEEESSSS--S--TTT-
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeee--eeEECCCCCCeeeecccCCCCCCCcCC
Confidence 47788888 343322 13432 444555 6788998988766554445 5688888
No 197
>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=29.24 E-value=17 Score=29.21 Aligned_cols=19 Identities=26% Similarity=0.651 Sum_probs=10.2
Q ss_pred CCCCCCC---CCcccCCCchhc
Q psy2238 175 CKSCNKL---GQYSCLRCKICF 193 (311)
Q Consensus 175 C~~C~~~---~~~~C~~C~k~F 193 (311)
|.+||-. -..+|..|+|.|
T Consensus 3 C~YCG~~~p~~vv~C~~c~kWF 24 (152)
T PF09416_consen 3 CAYCGIHDPSCVVKCNTCNKWF 24 (152)
T ss_dssp -TTT----CCCEEEETTTTEEE
T ss_pred ccccCCCCcccEeEcCCCCcEe
Confidence 4455533 234588888888
No 198
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=29.09 E-value=41 Score=36.23 Aligned_cols=22 Identities=23% Similarity=0.528 Sum_probs=17.4
Q ss_pred CccCCCCCCC-CCcccCCCchhc
Q psy2238 172 NYKCKSCNKL-GQYSCLRCKICF 193 (311)
Q Consensus 172 ~~~C~~C~~~-~~~~C~~C~k~F 193 (311)
.++|+.|+.. ....|+.||...
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCccccccCcccCCcC
Confidence 4789999987 446899999765
No 199
>KOG1280|consensus
Probab=28.50 E-value=41 Score=30.78 Aligned_cols=60 Identities=20% Similarity=0.296 Sum_probs=0.0
Q ss_pred CCccCCCCCCC---------------------------------------------CCcccCCCchhc-chHHHHHHhhh
Q psy2238 171 ENYKCKSCNKL---------------------------------------------GQYSCLRCKICF-CEDHARRKGFK 204 (311)
Q Consensus 171 k~~~C~~C~~~---------------------------------------------~~~~C~~C~k~F-~~~~l~~H~~~ 204 (311)
+.|+|-.|... ..|.|++|+..= +-..+..|...
T Consensus 22 rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~dfeL~f~Ge~i~~y~~qSftCPyC~~~Gfte~~f~~Hv~s 101 (381)
T KOG1280|consen 22 RRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVDFELYFGGEPISHYDPQSFTCPYCGIMGFTERQFGTHVLS 101 (381)
T ss_pred eeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccceeeEecCccccccccccccCCcccccccchhHHHHHhhh
Q ss_pred hcCC------------CCccCCCCCccccCchHHHHHH
Q psy2238 205 YEKN------------KPIPCPKCGFETSQTKDLSMST 230 (311)
Q Consensus 205 h~~~------------k~~~C~~C~k~f~~~~~L~~H~ 230 (311)
.|.+ .++.|+.|.+.-.....++.|.
T Consensus 102 ~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~~~~~ 139 (381)
T KOG1280|consen 102 QHPEASTSVICPLCAANPEMQPIHSKETENLSVHWTEI 139 (381)
T ss_pred cCcccCcceeeeccccCcccCchhhhhhhhhhhhhhhh
No 200
>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=28.50 E-value=37 Score=29.07 Aligned_cols=26 Identities=15% Similarity=0.238 Sum_probs=19.6
Q ss_pred CCCCccCCCCCccccCchHHHHHHHH
Q psy2238 207 KNKPIPCPKCGFETSQTKDLSMSTRS 232 (311)
Q Consensus 207 ~~k~~~C~~C~k~f~~~~~L~~H~~~ 232 (311)
.+..|.|++|+|.|.-..-..+|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 34569999999999999988999764
No 201
>KOG2907|consensus
Probab=28.37 E-value=34 Score=25.91 Aligned_cols=38 Identities=18% Similarity=0.198 Sum_probs=18.8
Q ss_pred cccCCCCh--hhHHhHHHHHHhhcCcCCCCcccccccccccc
Q psy2238 98 GAICDFCE--AWICHGRKCLQTHACTCPLQDAVCLECERGVW 137 (311)
Q Consensus 98 ~~~C~~C~--~f~~~~~~H~~~H~~~~~~~~~~C~~C~~~f~ 137 (311)
..+|+.|| ....+.. .+|. ..|.....|.|..|+..|.
T Consensus 74 ~~kCpkCghe~m~Y~T~-QlRS-ADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTL-QLRS-ADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred hccCcccCCchhhhhhh-hccc-ccCCceEEEEcCccceeee
Confidence 36788888 3333222 1222 2222224567777766654
No 202
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.25 E-value=26 Score=25.98 Aligned_cols=12 Identities=25% Similarity=0.667 Sum_probs=8.2
Q ss_pred ccCCCCCccccC
Q psy2238 211 IPCPKCGFETSQ 222 (311)
Q Consensus 211 ~~C~~C~k~f~~ 222 (311)
..|..||.+|--
T Consensus 47 ~~Cg~CGls~e~ 58 (104)
T COG4888 47 AVCGNCGLSFEC 58 (104)
T ss_pred EEcccCcceEEE
Confidence 567778777653
No 203
>KOG4167|consensus
Probab=27.61 E-value=19 Score=36.22 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=21.2
Q ss_pred CCcccCCCchhc-chHHHHHHhhhhc
Q psy2238 182 GQYSCLRCKICF-CEDHARRKGFKYE 206 (311)
Q Consensus 182 ~~~~C~~C~k~F-~~~~l~~H~~~h~ 206 (311)
..|.|.+|+|.| .-+++..||++|-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 458899999999 6679999999884
No 204
>KOG0402|consensus
Probab=27.58 E-value=30 Score=24.65 Aligned_cols=23 Identities=35% Similarity=0.855 Sum_probs=16.1
Q ss_pred CCccCCCCCCC-------CCcccCCCchhc
Q psy2238 171 ENYKCKSCNKL-------GQYSCLRCKICF 193 (311)
Q Consensus 171 k~~~C~~C~~~-------~~~~C~~C~k~F 193 (311)
-.|.|+.||+. ..+.|.-|.++|
T Consensus 35 aky~CsfCGK~~vKR~AvGiW~C~~C~kv~ 64 (92)
T KOG0402|consen 35 AKYTCSFCGKKTVKRKAVGIWKCGSCKKVV 64 (92)
T ss_pred hhhhhhhcchhhhhhhceeEEecCCcccee
Confidence 56887777776 456677777666
No 205
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=27.56 E-value=42 Score=18.74 Aligned_cols=21 Identities=29% Similarity=0.589 Sum_probs=9.9
Q ss_pred cccccccccccCCCceeecCCCC
Q psy2238 128 VCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 128 ~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.|..|++...... -|.|..|.
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 4555554433221 55555554
No 206
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.55 E-value=30 Score=31.39 Aligned_cols=47 Identities=21% Similarity=0.315 Sum_probs=26.0
Q ss_pred cccCCCChhhHHhHHHHHHhhcCcCCCCcccccccccccccCCCceeecCCCC
Q psy2238 98 GAICDFCEAWICHGRKCLQTHACTCPLQDAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 98 ~~~C~~C~~f~~~~~~H~~~H~~~~~~~~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
.-.|++||+....+..++....|. +...|..|+..... ...+|+.||
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~---RyL~CslC~teW~~---~R~~C~~Cg 233 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGL---RYLHCNLCESEWHV---VRVKCSNCE 233 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCc---eEEEcCCCCCcccc---cCccCCCCC
Confidence 356888883322221122223344 55778888754322 356788888
No 207
>PRK00420 hypothetical protein; Validated
Probab=26.52 E-value=42 Score=25.54 Aligned_cols=24 Identities=13% Similarity=0.247 Sum_probs=15.4
Q ss_pred ccccccccccccCCCceeecCCCC
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
-.|+.||..+.........|+.||
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCC
Confidence 457777766554344566777777
No 208
>KOG2593|consensus
Probab=26.43 E-value=34 Score=32.26 Aligned_cols=36 Identities=14% Similarity=0.144 Sum_probs=22.6
Q ss_pred CCCCccccccccccccCCCHHHHHHhHhhhccCCCcCcccCCCCh
Q psy2238 61 VQRLPQCGHCGKIKCMLKTGDCVIKHAGVFSTGMGMVGAICDFCE 105 (311)
Q Consensus 61 ~~k~~~C~~C~k~~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~ 105 (311)
....|.|+.|.+. |+....|+ ..-. ..-.|.|..|+
T Consensus 125 ~~~~Y~Cp~C~kk---yt~Lea~~---L~~~---~~~~F~C~~C~ 160 (436)
T KOG2593|consen 125 NVAGYVCPNCQKK---YTSLEALQ---LLDN---ETGEFHCENCG 160 (436)
T ss_pred ccccccCCccccc---hhhhHHHH---hhcc---cCceEEEecCC
Confidence 3456888888888 66655444 2222 12368888888
No 209
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.25 E-value=38 Score=21.36 Aligned_cols=14 Identities=36% Similarity=0.885 Sum_probs=8.8
Q ss_pred CccCCCCCccccCc
Q psy2238 210 PIPCPKCGFETSQT 223 (311)
Q Consensus 210 ~~~C~~C~k~f~~~ 223 (311)
.|.|+.|+..+...
T Consensus 20 ~~vC~~Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRKCGYEEPIE 33 (52)
T ss_pred EEECCcCCCeEECC
Confidence 56777777655543
No 210
>PF12223 DUF3602: Protein of unknown function (DUF3602); InterPro: IPR022024 This domain family is found in eukaryotes, and is typically between 78 and 89 amino acids in length.
Probab=26.16 E-value=1.1e+02 Score=21.55 Aligned_cols=9 Identities=56% Similarity=0.837 Sum_probs=5.8
Q ss_pred ccCCCCCCC
Q psy2238 303 SYGGGGATN 311 (311)
Q Consensus 303 ~~~~g~~~~ 311 (311)
..|.|||.|
T Consensus 73 ~vGRGGaGN 81 (81)
T PF12223_consen 73 HVGRGGAGN 81 (81)
T ss_pred cccccccCC
Confidence 566677666
No 211
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=26.04 E-value=63 Score=20.39 Aligned_cols=25 Identities=28% Similarity=0.909 Sum_probs=16.5
Q ss_pred cccccccccccccCCCceeecCCCC
Q psy2238 126 DAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
+-.|..|++..+......|.|..|+
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~ 35 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCG 35 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT
T ss_pred CCCCcccCcccCCCCCCeEEECCCC
Confidence 4667777777655566677777776
No 212
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.74 E-value=54 Score=34.52 Aligned_cols=14 Identities=36% Similarity=0.726 Sum_probs=9.5
Q ss_pred CCccCCCCCccccC
Q psy2238 209 KPIPCPKCGFETSQ 222 (311)
Q Consensus 209 k~~~C~~C~k~f~~ 222 (311)
.++.|+.|+..-..
T Consensus 662 ~~y~CPKCG~El~~ 675 (1121)
T PRK04023 662 EEDECEKCGREPTP 675 (1121)
T ss_pred CCCcCCCCCCCCCc
Confidence 34779999865544
No 213
>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=25.40 E-value=26 Score=21.08 Aligned_cols=10 Identities=30% Similarity=0.720 Sum_probs=4.9
Q ss_pred ccCCCCCccc
Q psy2238 211 IPCPKCGFET 220 (311)
Q Consensus 211 ~~C~~C~k~f 220 (311)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 4555555443
No 214
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=25.27 E-value=34 Score=20.68 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=5.1
Q ss_pred ccCCCCCccc
Q psy2238 211 IPCPKCGFET 220 (311)
Q Consensus 211 ~~C~~C~k~f 220 (311)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 4555555444
No 215
>PF12907 zf-met2: Zinc-binding
Probab=25.24 E-value=38 Score=20.61 Aligned_cols=25 Identities=16% Similarity=0.157 Sum_probs=15.7
Q ss_pred ccccccccccccCCCHHHHHHhHhh
Q psy2238 65 PQCGHCGKIKCMLKTGDCVIKHAGV 89 (311)
Q Consensus 65 ~~C~~C~k~~~~f~~~~~L~~H~~~ 89 (311)
+.|.+|-..|....+...|..|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 4677777554334556677777764
No 216
>PRK05580 primosome assembly protein PriA; Validated
Probab=25.17 E-value=42 Score=34.06 Aligned_cols=33 Identities=27% Similarity=0.607 Sum_probs=16.3
Q ss_pred cccCcCccccccccchhhc---ccCCCCccccccccc
Q psy2238 40 MECDKCKRKQKNRAFCYFC---QSVQRLPQCGHCGKI 73 (311)
Q Consensus 40 ~~C~~C~~~f~~~~~c~~~---h~~~k~~~C~~C~k~ 73 (311)
..|..|+.... =..|... |.......|..||..
T Consensus 382 ~~C~~Cg~~~~-C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 382 LLCRDCGWVAE-CPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred eEhhhCcCccC-CCCCCCceeEECCCCeEECCCCcCC
Confidence 45777776654 1111111 444455566666655
No 217
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=25.13 E-value=27 Score=24.86 Aligned_cols=10 Identities=40% Similarity=0.810 Sum_probs=4.9
Q ss_pred cccCCCchhc
Q psy2238 184 YSCLRCKICF 193 (311)
Q Consensus 184 ~~C~~C~k~F 193 (311)
..|.+|+..|
T Consensus 47 ~~C~~Cg~~~ 56 (81)
T PF05129_consen 47 LSCRVCGESF 56 (81)
T ss_dssp EEESSS--EE
T ss_pred EEecCCCCeE
Confidence 4466666666
No 218
>PF15539 CAF1-p150_C2: CAF1 complex subunit p150, region binding to CAF1-p60 at C-term
Probab=25.07 E-value=66 Score=28.37 Aligned_cols=11 Identities=0% Similarity=-0.007 Sum_probs=4.6
Q ss_pred HHHHHhHhhhc
Q psy2238 81 DCVIKHAGVFS 91 (311)
Q Consensus 81 ~~L~~H~~~h~ 91 (311)
..|..-++.-|
T Consensus 70 qlL~QLlpLlH 80 (292)
T PF15539_consen 70 QLLQQLLPLLH 80 (292)
T ss_pred HHHHHHHHHhc
Confidence 33444444434
No 219
>PF08911 NUP50: NUP50 (Nucleoporin 50 kDa); InterPro: IPR015007 This entry represents a domain found in Nup2, 50 and 61, which are components of the nuclear pore complex. Nucleoporin 50 kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localisation signals from importin-alpha []. NUP2 encodes a non-essential nuclear pore protein that has a central domain similar to those of Nsp1 and Nup1[, ]. Transport of macromolecules between the nucleus and the cytoplasm of eukaryotic cells occurs through the nuclear pore complex (NPC), a large macromolecular complex that spans the nuclear envelope [, , ]. The structure of the vertebrate NPC has been studied extensively; recent reviews include [, , , ]. The yeast NPC shares several features with the vertebrate NPC, despite being smaller and less elaborate [, ]. Many yeast nuclear pore proteins, or nucleoporins, have been identified by a variety of genetic approaches [, , , ]. nup2 mutants show genetic interactions with nsp1 and nup1 conditional alleles [, ]. Nup1 interacts with the nuclear import factor Srp1 [] and with the small GTPase Ran (encoded by GSP1) [].; GO: 0005643 nuclear pore; PDB: 3TJ3_D 1UN0_D 2C1T_D 2C1M_B.
Probab=24.98 E-value=33 Score=23.82 Aligned_cols=13 Identities=46% Similarity=0.918 Sum_probs=4.1
Q ss_pred CCCCCCCCCCCCC
Q psy2238 279 QQLNGDDYDDEDD 291 (311)
Q Consensus 279 ~~~~~d~~dd~dd 291 (311)
.|++.|+.|+||+
T Consensus 7 ~qlt~dn~d~ed~ 19 (72)
T PF08911_consen 7 SQLTRDNWDEEDE 19 (72)
T ss_dssp S---TTTSSS---
T ss_pred ccccccCcccccc
Confidence 4566666654433
No 220
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.79 E-value=48 Score=21.74 Aligned_cols=13 Identities=38% Similarity=0.984 Sum_probs=6.4
Q ss_pred CCccCCCCCcccc
Q psy2238 209 KPIPCPKCGFETS 221 (311)
Q Consensus 209 k~~~C~~C~k~f~ 221 (311)
-.|.|+.||..+.
T Consensus 13 v~~~Cp~cGipth 25 (55)
T PF13824_consen 13 VNFECPDCGIPTH 25 (55)
T ss_pred cCCcCCCCCCcCc
Confidence 3455555554443
No 221
>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=24.69 E-value=25 Score=36.16 Aligned_cols=8 Identities=75% Similarity=1.676 Sum_probs=0.0
Q ss_pred cCCCCCcc
Q psy2238 212 PCPKCGFE 219 (311)
Q Consensus 212 ~C~~C~k~ 219 (311)
.|+.|+..
T Consensus 694 ~C~~C~~~ 701 (900)
T PF03833_consen 694 ECPKCGRE 701 (900)
T ss_dssp --------
T ss_pred cccccccc
Confidence 44444443
No 222
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG3507|consensus
Probab=24.38 E-value=33 Score=22.69 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=15.9
Q ss_pred ccccccccccccCCCceeecCCCC-CCC
Q psy2238 127 AVCLECERGVWDHGGRVYKCCFCE-GFL 153 (311)
Q Consensus 127 ~~C~~C~~~f~~~~~~~~~C~~C~-~f~ 153 (311)
|.|..|+..-.-...-++.|..|| ...
T Consensus 21 YiCgdC~~en~lk~~D~irCReCG~RIl 48 (62)
T KOG3507|consen 21 YICGDCGQENTLKRGDVIRCRECGYRIL 48 (62)
T ss_pred EEeccccccccccCCCcEehhhcchHHH
Confidence 666666654444444567777777 543
No 224
>PF12773 DZR: Double zinc ribbon
Probab=24.33 E-value=64 Score=20.14 Aligned_cols=11 Identities=45% Similarity=1.032 Sum_probs=6.7
Q ss_pred CCccCCCCCcc
Q psy2238 209 KPIPCPKCGFE 219 (311)
Q Consensus 209 k~~~C~~C~k~ 219 (311)
....|+.|+..
T Consensus 28 ~~~~C~~Cg~~ 38 (50)
T PF12773_consen 28 SKKICPNCGAE 38 (50)
T ss_pred CCCCCcCCcCC
Confidence 44567777654
No 225
>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=24.25 E-value=43 Score=21.59 Aligned_cols=19 Identities=32% Similarity=0.586 Sum_probs=7.6
Q ss_pred cCCCchhcchH-HHHHHhhh
Q psy2238 186 CLRCKICFCED-HARRKGFK 204 (311)
Q Consensus 186 C~~C~k~F~~~-~l~~H~~~ 204 (311)
|+.|...|--. ....|...
T Consensus 24 C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 24 CPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp -TTTT--B-HHHHHTTTTTS
T ss_pred CCCCCCccccCcChhhhccc
Confidence 66666666333 55555433
No 226
>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=24.23 E-value=60 Score=20.11 Aligned_cols=7 Identities=29% Similarity=1.056 Sum_probs=3.9
Q ss_pred ccCCCCh
Q psy2238 99 AICDFCE 105 (311)
Q Consensus 99 ~~C~~C~ 105 (311)
+.|+.|+
T Consensus 19 ~~CP~Cg 25 (46)
T PF12760_consen 19 FVCPHCG 25 (46)
T ss_pred CCCCCCC
Confidence 4455555
No 227
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.81 E-value=49 Score=27.37 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=20.4
Q ss_pred CCCCccccCcCccccccccchhhcccCCCCccccccccc
Q psy2238 35 PCNANMECDKCKRKQKNRAFCYFCQSVQRLPQCGHCGKI 73 (311)
Q Consensus 35 ~~~~~~~C~~C~~~f~~~~~c~~~h~~~k~~~C~~C~k~ 73 (311)
..+.-|.|+.|...|+-..+ .+..|.|+.||-.
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA------~~~~F~Cp~Cg~~ 141 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEA------MELGFTCPKCGED 141 (176)
T ss_pred ccCCceeCCCCCCcccHHHH------HHhCCCCCCCCch
Confidence 44566888888776652221 2334888888865
No 228
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=23.71 E-value=44 Score=26.82 Aligned_cols=8 Identities=50% Similarity=1.182 Sum_probs=6.0
Q ss_pred cCCCchhc
Q psy2238 186 CLRCKICF 193 (311)
Q Consensus 186 C~~C~k~F 193 (311)
|..|+..|
T Consensus 31 C~~C~~RF 38 (156)
T COG1327 31 CLECGERF 38 (156)
T ss_pred cccccccc
Confidence 77777777
No 229
>KOG2071|consensus
Probab=23.39 E-value=54 Score=32.25 Aligned_cols=29 Identities=24% Similarity=0.505 Sum_probs=24.6
Q ss_pred CCCCccCCCCCccccCchHHHHHHHHhcC
Q psy2238 207 KNKPIPCPKCGFETSQTKDLSMSTRSHKF 235 (311)
Q Consensus 207 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~ 235 (311)
...|-+|..||.+|.......+||-.|..
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhh
Confidence 45778999999999999999888887753
No 230
>KOG0320|consensus
Probab=23.15 E-value=54 Score=27.08 Aligned_cols=33 Identities=18% Similarity=0.549 Sum_probs=19.6
Q ss_pred CCCchhcchHHHHHHhhhhcCCCCccCCCCCccccCch
Q psy2238 187 LRCKICFCEDHARRKGFKYEKNKPIPCPKCGFETSQTK 224 (311)
Q Consensus 187 ~~C~k~F~~~~l~~H~~~h~~~k~~~C~~C~k~f~~~~ 224 (311)
..||-.|-..-+..-. ....+||.|+|..+.+.
T Consensus 149 TkCGHvFC~~Cik~al-----k~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKDAL-----KNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cccchhHHHHHHHHHH-----HhCCCCCCcccccchhh
Confidence 5677788554332221 14468999998665443
No 231
>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=22.04 E-value=47 Score=25.32 Aligned_cols=24 Identities=25% Similarity=0.671 Sum_probs=15.4
Q ss_pred cccccccccccccCCCceeecCCCC
Q psy2238 126 DAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 126 ~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
...|..|+..|.... ..+.||.||
T Consensus 70 ~~~C~~Cg~~~~~~~-~~~~CP~Cg 93 (115)
T TIGR00100 70 ECECEDCSEEVSPEI-DLYRCPKCH 93 (115)
T ss_pred EEEcccCCCEEecCC-cCccCcCCc
Confidence 467778876665432 246688887
No 232
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=21.50 E-value=39 Score=27.56 Aligned_cols=7 Identities=29% Similarity=0.857 Sum_probs=5.4
Q ss_pred ccCCCCh
Q psy2238 99 AICDFCE 105 (311)
Q Consensus 99 ~~C~~C~ 105 (311)
-.|+.|+
T Consensus 98 ~RCp~CN 104 (165)
T COG1656 98 SRCPECN 104 (165)
T ss_pred ccCcccC
Confidence 4688888
No 233
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.27 E-value=21 Score=27.55 Aligned_cols=49 Identities=20% Similarity=0.366 Sum_probs=24.5
Q ss_pred CCCCCCCCCcccCCCchhcchHHHHHHhh--hhcCCCCccCCCCCccccCc
Q psy2238 175 CKSCNKLGQYSCLRCKICFCEDHARRKGF--KYEKNKPIPCPKCGFETSQT 223 (311)
Q Consensus 175 C~~C~~~~~~~C~~C~k~F~~~~l~~H~~--~h~~~k~~~C~~C~k~f~~~ 223 (311)
|..||..-...|+.|....+-.....-.. -+.-+-|--|..||+.|.+.
T Consensus 31 cskcgeati~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwt 81 (160)
T COG4306 31 CSKCGEATITQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWT 81 (160)
T ss_pred HhhhchHHHhcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcH
Confidence 44444444444777765543321111111 12223556688888888774
No 234
>KOG1701|consensus
Probab=20.93 E-value=12 Score=35.05 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=8.3
Q ss_pred CccCCCCCcccc
Q psy2238 210 PIPCPKCGFETS 221 (311)
Q Consensus 210 ~~~C~~C~k~f~ 221 (311)
=|+|..|+...+
T Consensus 427 CY~CEDCg~~LS 438 (468)
T KOG1701|consen 427 CYKCEDCGLLLS 438 (468)
T ss_pred ceehhhcCcccc
Confidence 367788876655
No 235
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=20.77 E-value=33 Score=21.02 Aligned_cols=15 Identities=27% Similarity=0.640 Sum_probs=9.6
Q ss_pred CCccCCCCCccccCc
Q psy2238 209 KPIPCPKCGFETSQT 223 (311)
Q Consensus 209 k~~~C~~C~k~f~~~ 223 (311)
-||.|+.|++.|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 578999999988754
No 236
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.68 E-value=50 Score=25.58 Aligned_cols=10 Identities=30% Similarity=0.488 Sum_probs=5.7
Q ss_pred ccccccccccc
Q psy2238 127 AVCLECERGVW 137 (311)
Q Consensus 127 ~~C~~C~~~f~ 137 (311)
+.| .|+..|.
T Consensus 71 ~~C-~Cg~~~~ 80 (124)
T PRK00762 71 IEC-ECGYEGV 80 (124)
T ss_pred EEe-eCcCccc
Confidence 556 6665554
No 237
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=20.60 E-value=40 Score=27.05 Aligned_cols=9 Identities=22% Similarity=0.608 Sum_probs=5.3
Q ss_pred Cccccccccc
Q psy2238 64 LPQCGHCGKI 73 (311)
Q Consensus 64 ~~~C~~C~k~ 73 (311)
+|.|. |+..
T Consensus 117 ~Y~C~-C~q~ 125 (156)
T COG3091 117 PYRCQ-CQQH 125 (156)
T ss_pred eEEee-cCCc
Confidence 55666 6655
No 238
>PRK12496 hypothetical protein; Provisional
Probab=20.34 E-value=57 Score=26.63 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=15.8
Q ss_pred CcccccccccccccCCCceeecCCCC
Q psy2238 125 QDAVCLECERGVWDHGGRVYKCCFCE 150 (311)
Q Consensus 125 ~~~~C~~C~~~f~~~~~~~~~C~~C~ 150 (311)
+.|.|.-|++.|....+. -.|++||
T Consensus 126 w~~~C~gC~~~~~~~~~~-~~C~~CG 150 (164)
T PRK12496 126 WRKVCKGCKKKYPEDYPD-DVCEICG 150 (164)
T ss_pred eeEECCCCCccccCCCCC-CcCCCCC
Confidence 347788888887543211 2588888
Done!