Query psy4796
Match_columns 274
No_of_seqs 173 out of 2166
Neff 10.9
Searched_HMMs 46136
Date Fri Aug 16 17:51:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4796.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4796hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 3.1E-30 6.8E-35 193.6 4.2 133 91-269 129-264 (279)
2 KOG2462|consensus 99.9 3.6E-28 7.7E-33 182.6 6.6 136 61-242 127-265 (279)
3 KOG1074|consensus 99.9 3.3E-28 7.3E-33 206.3 5.1 169 93-273 606-932 (958)
4 KOG3608|consensus 99.9 3.8E-26 8.2E-31 176.3 8.7 229 26-273 132-377 (467)
5 KOG3623|consensus 99.9 3.8E-26 8.2E-31 191.1 6.1 81 189-269 891-971 (1007)
6 KOG3608|consensus 99.9 1.5E-24 3.1E-29 167.6 8.3 191 65-272 135-345 (467)
7 KOG1074|consensus 99.9 2E-22 4.3E-27 171.6 5.5 219 21-248 598-935 (958)
8 KOG3623|consensus 99.8 3E-21 6.6E-26 162.0 2.6 80 157-242 893-972 (1007)
9 KOG3576|consensus 99.8 2.9E-19 6.3E-24 128.2 5.2 113 25-145 114-237 (267)
10 KOG3576|consensus 99.7 3.8E-19 8.3E-24 127.6 2.5 114 154-273 113-237 (267)
11 PHA00733 hypothetical protein 99.4 3.1E-13 6.7E-18 93.9 4.4 100 167-273 20-124 (128)
12 PLN03086 PRLI-interacting fact 99.4 3.9E-12 8.4E-17 108.1 9.7 146 93-273 408-565 (567)
13 PLN03086 PRLI-interacting fact 99.3 1.2E-11 2.6E-16 105.1 11.0 148 24-213 403-561 (567)
14 PHA02768 hypothetical protein; 99.1 2.7E-11 5.9E-16 69.2 1.9 42 221-264 6-47 (55)
15 KOG3993|consensus 99.1 8.3E-12 1.8E-16 99.8 -0.5 111 27-145 266-381 (500)
16 KOG3993|consensus 99.1 4E-11 8.6E-16 96.0 1.9 26 92-117 356-381 (500)
17 PHA00733 hypothetical protein 99.1 2.3E-10 4.9E-15 79.6 5.4 83 59-143 35-122 (128)
18 PHA02768 hypothetical protein; 98.9 5.7E-10 1.2E-14 63.8 2.4 43 192-236 5-47 (55)
19 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.6E-09 3.4E-14 53.0 2.3 25 235-259 1-25 (26)
20 PF13465 zf-H2C2_2: Zinc-finge 98.7 1.1E-08 2.4E-13 50.0 2.1 26 207-232 1-26 (26)
21 PHA00616 hypothetical protein 98.6 9.7E-09 2.1E-13 55.8 1.1 33 220-252 1-33 (44)
22 PF05605 zf-Di19: Drought indu 98.6 1E-07 2.2E-12 55.8 3.8 51 220-273 2-54 (54)
23 PHA00616 hypothetical protein 98.5 3.4E-08 7.3E-13 53.7 1.0 27 248-274 1-27 (44)
24 PHA00732 hypothetical protein 98.5 7.8E-08 1.7E-12 60.6 2.6 48 192-245 1-49 (79)
25 PHA00732 hypothetical protein 98.4 2.8E-07 6E-12 58.1 3.6 45 220-270 1-46 (79)
26 PF05605 zf-Di19: Drought indu 98.2 4.6E-06 1E-10 48.8 4.7 50 192-244 2-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.1 1.5E-06 3.3E-11 41.1 1.7 22 249-270 1-22 (23)
28 PF13894 zf-C2H2_4: C2H2-type 98.1 2E-06 4.3E-11 41.2 2.0 24 249-272 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 98.1 2.1E-06 4.5E-11 40.6 1.4 23 221-243 1-23 (23)
30 PF13912 zf-C2H2_6: C2H2-type 97.9 6.6E-06 1.4E-10 40.6 1.7 25 248-272 1-25 (27)
31 PF12756 zf-C2H2_2: C2H2 type 97.8 1.2E-05 2.7E-10 53.9 2.4 23 248-270 50-72 (100)
32 PF13894 zf-C2H2_4: C2H2-type 97.8 1.7E-05 3.7E-10 37.8 1.8 23 221-243 1-23 (24)
33 PF13912 zf-C2H2_6: C2H2-type 97.7 1.8E-05 3.8E-10 39.0 1.5 25 220-244 1-25 (27)
34 PF12756 zf-C2H2_2: C2H2 type 97.7 2.3E-05 4.9E-10 52.5 2.3 73 30-115 1-73 (100)
35 COG5189 SFP1 Putative transcri 97.7 1.6E-05 3.5E-10 62.1 1.2 53 218-270 347-420 (423)
36 PF13909 zf-H2C2_5: C2H2-type 97.6 5E-05 1.1E-09 36.2 1.9 24 249-273 1-24 (24)
37 COG5189 SFP1 Putative transcri 97.6 2.2E-05 4.7E-10 61.4 0.7 24 62-85 347-372 (423)
38 smart00355 ZnF_C2H2 zinc finge 97.2 0.00031 6.6E-09 33.9 2.1 20 250-269 2-21 (26)
39 PF09237 GAGA: GAGA factor; I 97.2 0.00033 7.1E-09 39.1 2.3 28 218-245 22-49 (54)
40 smart00355 ZnF_C2H2 zinc finge 97.2 0.00032 6.8E-09 33.8 1.9 23 221-243 1-23 (26)
41 PRK04860 hypothetical protein; 97.1 0.00046 1E-08 50.0 2.7 37 220-260 119-155 (160)
42 KOG2231|consensus 97.0 0.0021 4.6E-08 56.5 7.0 48 193-244 183-236 (669)
43 KOG1146|consensus 97.0 0.00062 1.3E-08 63.4 3.9 108 29-143 437-612 (1406)
44 PF09237 GAGA: GAGA factor; I 97.0 0.00051 1.1E-08 38.3 2.0 37 237-273 12-49 (54)
45 PF12874 zf-met: Zinc-finger o 96.9 0.00044 9.5E-09 33.2 1.2 18 223-240 3-20 (25)
46 PF12874 zf-met: Zinc-finger o 96.9 0.00061 1.3E-08 32.7 1.6 23 249-271 1-23 (25)
47 PF13909 zf-H2C2_5: C2H2-type 96.6 0.0011 2.5E-08 31.4 1.2 23 221-244 1-23 (24)
48 KOG2785|consensus 96.5 0.01 2.2E-07 48.3 6.9 51 192-242 166-242 (390)
49 PRK04860 hypothetical protein; 96.5 0.0014 3E-08 47.6 1.5 40 191-234 118-157 (160)
50 KOG2785|consensus 96.5 0.0085 1.8E-07 48.7 5.9 52 219-270 165-242 (390)
51 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.0012 2.6E-08 32.3 0.2 21 249-269 2-22 (27)
52 COG5236 Uncharacterized conser 96.3 0.008 1.7E-07 48.1 4.7 72 194-273 222-306 (493)
53 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0033 7.1E-08 30.7 0.8 21 193-213 2-22 (27)
54 KOG2482|consensus 95.9 0.067 1.5E-06 42.9 8.3 78 121-215 280-357 (423)
55 PF13913 zf-C2HC_2: zinc-finge 95.9 0.0049 1.1E-07 29.5 1.3 20 29-50 3-22 (25)
56 PF13913 zf-C2HC_2: zinc-finge 95.6 0.01 2.3E-07 28.3 1.7 19 250-269 4-22 (25)
57 KOG1146|consensus 95.6 0.009 2E-07 56.1 2.7 168 67-243 439-641 (1406)
58 KOG2231|consensus 95.4 0.027 5.9E-07 49.9 5.0 45 94-142 184-234 (669)
59 KOG2482|consensus 95.4 0.021 4.7E-07 45.7 3.8 90 28-117 144-304 (423)
60 PF12013 DUF3505: Protein of u 95.2 0.036 7.8E-07 37.7 4.0 85 188-273 7-109 (109)
61 KOG2893|consensus 95.1 0.0056 1.2E-07 46.3 -0.1 42 30-83 12-53 (341)
62 cd00350 rubredoxin_like Rubred 94.9 0.018 3.8E-07 29.7 1.5 24 221-256 2-25 (33)
63 COG5236 Uncharacterized conser 94.8 0.055 1.2E-06 43.5 4.5 19 31-50 223-241 (493)
64 smart00451 ZnF_U1 U1-like zinc 94.4 0.037 7.9E-07 28.8 2.0 22 248-269 3-24 (35)
65 smart00451 ZnF_U1 U1-like zinc 93.7 0.047 1E-06 28.3 1.6 23 220-242 3-25 (35)
66 COG4049 Uncharacterized protei 93.6 0.028 6.1E-07 32.0 0.6 26 217-242 14-39 (65)
67 COG5048 FOG: Zn-finger [Genera 93.0 0.029 6.3E-07 48.1 0.1 151 92-257 289-455 (467)
68 TIGR00622 ssl1 transcription f 92.8 0.32 7E-06 32.8 4.8 54 194-255 57-110 (112)
69 KOG2893|consensus 92.8 0.028 6E-07 42.7 -0.3 47 194-244 12-59 (341)
70 cd00729 rubredoxin_SM Rubredox 92.2 0.093 2E-06 27.1 1.3 24 221-256 3-26 (34)
71 COG5048 FOG: Zn-finger [Genera 92.1 0.14 3E-06 43.9 3.1 153 64-227 289-453 (467)
72 PF09538 FYDLN_acid: Protein o 91.5 0.12 2.6E-06 34.8 1.6 14 219-232 25-38 (108)
73 KOG4173|consensus 91.1 0.075 1.6E-06 39.4 0.4 47 194-240 108-166 (253)
74 TIGR00622 ssl1 transcription f 91.0 0.88 1.9E-05 30.7 5.3 50 159-216 56-105 (112)
75 TIGR00373 conserved hypothetic 91.0 0.23 4.9E-06 36.2 2.8 36 216-260 105-140 (158)
76 PHA00626 hypothetical protein 90.9 0.14 3.1E-06 29.3 1.3 17 189-205 20-36 (59)
77 COG2888 Predicted Zn-ribbon RN 90.8 0.36 7.9E-06 28.1 2.8 33 191-228 26-58 (61)
78 COG4049 Uncharacterized protei 90.7 0.097 2.1E-06 29.9 0.5 31 187-217 12-42 (65)
79 PF10571 UPF0547: Uncharacteri 90.3 0.21 4.5E-06 24.1 1.4 10 250-259 16-25 (26)
80 PRK06266 transcription initiat 89.7 0.3 6.6E-06 36.3 2.6 35 217-260 114-148 (178)
81 PF12013 DUF3505: Protein of u 89.5 0.77 1.7E-05 31.1 4.3 25 221-245 81-109 (109)
82 TIGR02098 MJ0042_CXXC MJ0042 f 89.4 0.26 5.7E-06 26.1 1.6 11 248-258 25-35 (38)
83 PF04959 ARS2: Arsenite-resist 89.0 0.15 3.3E-06 38.9 0.6 28 247-274 76-103 (214)
84 PF06524 NOA36: NOA36 protein; 88.9 0.2 4.3E-06 38.8 1.1 97 114-243 136-232 (314)
85 PF09986 DUF2225: Uncharacteri 88.8 0.14 3E-06 39.4 0.2 24 26-50 3-26 (214)
86 smart00531 TFIIE Transcription 88.7 0.47 1E-05 34.2 2.9 38 217-258 96-133 (147)
87 PRK14890 putative Zn-ribbon RN 88.4 0.72 1.6E-05 27.0 2.9 11 191-201 24-34 (59)
88 PF13719 zinc_ribbon_5: zinc-r 88.1 0.42 9.2E-06 25.2 1.8 11 194-204 4-14 (37)
89 KOG2186|consensus 87.7 0.32 7E-06 37.5 1.6 45 65-112 4-48 (276)
90 PF02892 zf-BED: BED zinc fing 87.6 0.43 9.2E-06 26.4 1.7 27 246-272 14-44 (45)
91 PF13717 zinc_ribbon_4: zinc-r 87.4 0.51 1.1E-05 24.7 1.8 6 222-227 27-32 (36)
92 smart00659 RPOLCX RNA polymera 87.4 0.46 1E-05 26.2 1.7 11 193-203 3-13 (44)
93 COG1592 Rubrerythrin [Energy p 87.4 0.36 7.9E-06 35.2 1.6 24 220-256 134-157 (166)
94 PF09538 FYDLN_acid: Protein o 87.1 0.34 7.5E-06 32.6 1.3 30 221-261 10-39 (108)
95 KOG2186|consensus 86.9 0.34 7.5E-06 37.4 1.3 46 193-241 4-49 (276)
96 KOG4173|consensus 86.6 0.31 6.6E-06 36.3 0.9 75 65-142 80-168 (253)
97 smart00734 ZnF_Rad18 Rad18-lik 85.4 0.76 1.7E-05 22.1 1.7 19 250-269 3-21 (26)
98 TIGR02300 FYDLN_acid conserved 85.1 0.6 1.3E-05 32.1 1.6 30 193-233 10-39 (129)
99 PF02176 zf-TRAF: TRAF-type zi 85.0 0.78 1.7E-05 27.1 2.0 47 219-267 8-60 (60)
100 TIGR02605 CxxC_CxxC_SSSS putat 84.9 0.28 6.1E-06 28.1 0.0 11 221-231 6-16 (52)
101 PRK00398 rpoP DNA-directed RNA 83.7 0.43 9.4E-06 26.6 0.4 11 221-231 4-14 (46)
102 PF03604 DNA_RNApol_7kD: DNA d 83.2 0.86 1.9E-05 23.1 1.4 8 221-228 18-25 (32)
103 smart00614 ZnF_BED BED zinc fi 82.3 1.1 2.5E-05 25.4 1.8 24 249-272 19-47 (50)
104 PF09723 Zn-ribbon_8: Zinc rib 82.0 0.54 1.2E-05 25.6 0.4 12 159-170 6-17 (42)
105 PF09986 DUF2225: Uncharacteri 80.9 0.25 5.5E-06 38.0 -1.6 11 221-231 49-59 (214)
106 TIGR00373 conserved hypothetic 80.7 1.9 4.1E-05 31.5 2.9 34 88-130 105-138 (158)
107 PF05443 ROS_MUCR: ROS/MUCR tr 80.6 0.88 1.9E-05 31.9 1.1 22 249-273 73-94 (132)
108 smart00834 CxxC_CXXC_SSSS Puta 79.5 0.84 1.8E-05 24.5 0.6 11 159-169 6-16 (41)
109 smart00531 TFIIE Transcription 79.5 3.7 8E-05 29.5 4.1 38 89-130 96-133 (147)
110 COG1996 RPC10 DNA-directed RNA 79.1 0.98 2.1E-05 25.4 0.8 10 221-230 7-16 (49)
111 PRK04023 DNA polymerase II lar 78.4 3.2 6.9E-05 39.1 4.2 12 249-260 664-675 (1121)
112 COG5188 PRP9 Splicing factor 3 78.3 3.1 6.7E-05 34.0 3.6 28 241-268 367-395 (470)
113 TIGR02300 FYDLN_acid conserved 77.9 1.6 3.4E-05 30.1 1.6 31 65-106 10-40 (129)
114 PF02176 zf-TRAF: TRAF-type zi 77.4 1.6 3.5E-05 25.7 1.5 10 41-50 22-31 (60)
115 COG1592 Rubrerythrin [Energy p 76.9 1.7 3.7E-05 31.8 1.7 23 192-227 134-156 (166)
116 PRK06266 transcription initiat 76.6 2.8 6.1E-05 31.2 2.9 34 89-131 114-147 (178)
117 PF04959 ARS2: Arsenite-resist 75.6 3.1 6.8E-05 31.9 2.9 30 120-149 77-106 (214)
118 PRK00464 nrdR transcriptional 75.1 1.6 3.5E-05 31.5 1.2 12 193-204 29-40 (154)
119 PRK09678 DNA-binding transcrip 75.0 0.66 1.4E-05 28.6 -0.7 15 218-232 25-41 (72)
120 PF08274 PhnA_Zn_Ribbon: PhnA 74.9 1.5 3.3E-05 21.9 0.7 11 246-256 17-27 (30)
121 PF13240 zinc_ribbon_2: zinc-r 73.5 2 4.3E-05 19.9 0.9 6 251-256 16-21 (23)
122 PF02148 zf-UBP: Zn-finger in 72.4 2.7 5.9E-05 25.2 1.6 49 25-74 8-59 (63)
123 PF14353 CpXC: CpXC protein 72.1 4.6 0.0001 28.2 2.9 15 221-235 39-53 (128)
124 PF06524 NOA36: NOA36 protein; 71.4 2.9 6.4E-05 32.6 1.9 22 118-139 207-228 (314)
125 COG2331 Uncharacterized protei 69.6 2 4.4E-05 26.5 0.6 10 29-38 13-22 (82)
126 KOG3408|consensus 68.5 6 0.00013 27.0 2.6 33 18-51 47-79 (129)
127 PRK14714 DNA polymerase II lar 67.5 7.8 0.00017 37.7 4.0 29 220-259 692-720 (1337)
128 PRK04023 DNA polymerase II lar 67.0 7.5 0.00016 36.8 3.8 10 193-202 664-673 (1121)
129 PF12907 zf-met2: Zinc-binding 67.0 3 6.5E-05 22.4 0.8 25 249-273 2-29 (40)
130 PF15269 zf-C2H2_7: Zinc-finge 66.6 3.8 8.3E-05 22.3 1.2 22 221-242 21-42 (54)
131 COG4530 Uncharacterized protei 66.6 3.4 7.3E-05 27.5 1.1 13 218-230 24-36 (129)
132 PF13878 zf-C2H2_3: zinc-finge 66.3 5.6 0.00012 21.5 1.8 23 221-243 14-38 (41)
133 PF05443 ROS_MUCR: ROS/MUCR tr 65.8 3.5 7.5E-05 29.0 1.2 25 220-247 72-96 (132)
134 COG4957 Predicted transcriptio 64.2 5.2 0.00011 27.8 1.8 20 221-243 77-96 (148)
135 PF08209 Sgf11: Sgf11 (transcr 64.2 3.9 8.4E-05 20.9 0.9 22 28-51 4-25 (33)
136 KOG4602|consensus 63.0 12 0.00025 29.3 3.6 56 20-76 225-280 (318)
137 COG1997 RPL43A Ribosomal prote 62.6 6.5 0.00014 25.1 1.8 12 192-203 53-64 (89)
138 PF15135 UPF0515: Uncharacteri 62.1 6.1 0.00013 30.7 2.0 14 191-204 154-167 (278)
139 PRK03824 hypA hydrogenase nick 62.0 3.1 6.6E-05 29.5 0.4 13 26-38 68-80 (135)
140 PRK00432 30S ribosomal protein 61.6 5.5 0.00012 22.6 1.3 9 221-229 38-46 (50)
141 PF12760 Zn_Tnp_IS1595: Transp 61.4 12 0.00025 20.7 2.6 11 246-256 35-45 (46)
142 PF07754 DUF1610: Domain of un 61.3 4.6 9.9E-05 19.0 0.8 7 249-255 17-23 (24)
143 PF08790 zf-LYAR: LYAR-type C2 60.2 2.8 6.1E-05 20.5 -0.0 19 29-49 1-19 (28)
144 COG3091 SprT Zn-dependent meta 60.1 4.5 9.8E-05 28.9 0.9 33 220-257 117-149 (156)
145 PF08271 TF_Zn_Ribbon: TFIIB z 60.0 6.3 0.00014 21.4 1.4 9 65-73 20-28 (43)
146 KOG2593|consensus 59.8 6.8 0.00015 33.2 2.0 41 59-102 123-163 (436)
147 PF14446 Prok-RING_1: Prokaryo 59.5 7.5 0.00016 22.5 1.6 10 194-203 7-16 (54)
148 COG5151 SSL1 RNA polymerase II 58.4 4.2 9.2E-05 32.6 0.6 23 221-243 389-411 (421)
149 KOG1280|consensus 57.9 9 0.00019 31.4 2.3 41 216-256 75-117 (381)
150 smart00440 ZnF_C2C2 C2C2 Zinc 57.8 2.4 5.1E-05 22.8 -0.6 10 249-258 29-38 (40)
151 COG1198 PriA Primosomal protei 57.8 8.1 0.00018 35.7 2.3 11 218-228 473-483 (730)
152 cd00730 rubredoxin Rubredoxin; 56.6 10 0.00022 21.6 1.8 8 193-200 35-42 (50)
153 PF05191 ADK_lid: Adenylate ki 56.3 5.4 0.00012 20.9 0.6 29 66-102 3-31 (36)
154 KOG2636|consensus 56.1 13 0.00028 31.7 3.0 23 62-84 399-422 (497)
155 TIGR00686 phnA alkylphosphonat 54.6 7.7 0.00017 25.9 1.3 11 249-259 20-30 (109)
156 PF13453 zf-TFIIB: Transcripti 54.6 9.3 0.0002 20.5 1.4 20 247-266 18-37 (41)
157 PRK10220 hypothetical protein; 54.5 9.1 0.0002 25.6 1.6 11 249-259 21-31 (111)
158 COG1198 PriA Primosomal protei 54.3 4.9 0.00011 37.0 0.4 15 243-257 470-484 (730)
159 PF09845 DUF2072: Zn-ribbon co 53.9 11 0.00023 26.3 1.9 11 121-131 2-12 (131)
160 COG4888 Uncharacterized Zn rib 53.2 4.6 0.0001 26.5 0.1 12 190-201 20-31 (104)
161 KOG2593|consensus 52.9 15 0.00033 31.2 3.0 41 87-130 123-163 (436)
162 PRK00464 nrdR transcriptional 52.6 7.5 0.00016 28.2 1.1 15 65-79 29-43 (154)
163 KOG2071|consensus 52.3 12 0.00025 33.2 2.3 17 118-134 511-527 (579)
164 TIGR01206 lysW lysine biosynth 51.7 11 0.00025 21.8 1.5 10 193-202 23-32 (54)
165 KOG4124|consensus 50.2 2.7 5.9E-05 34.3 -1.6 50 219-268 348-418 (442)
166 KOG2807|consensus 50.2 29 0.00063 28.4 4.0 20 249-268 346-365 (378)
167 KOG3507|consensus 50.1 25 0.00053 20.6 2.6 15 24-38 16-30 (62)
168 PF01927 Mut7-C: Mut7-C RNAse 49.5 11 0.00024 27.1 1.6 16 220-235 124-139 (147)
169 KOG2807|consensus 49.2 28 0.0006 28.5 3.8 20 121-140 346-365 (378)
170 PTZ00255 60S ribosomal protein 48.6 23 0.0005 23.0 2.7 12 192-203 54-65 (90)
171 PF05290 Baculo_IE-1: Baculovi 47.7 21 0.00046 25.0 2.5 13 250-262 123-135 (140)
172 PRK12380 hydrogenase nickel in 47.4 9.7 0.00021 26.0 0.9 11 193-203 71-81 (113)
173 smart00661 RPOL9 RNA polymeras 47.3 17 0.00038 20.4 1.9 12 192-203 20-31 (52)
174 PF00301 Rubredoxin: Rubredoxi 46.9 11 0.00024 21.1 0.9 8 193-200 35-42 (47)
175 COG3364 Zn-ribbon containing p 46.8 14 0.00031 24.3 1.6 13 158-170 2-14 (112)
176 PF13248 zf-ribbon_3: zinc-rib 46.4 13 0.00028 17.7 1.0 7 222-228 4-10 (26)
177 KOG1280|consensus 46.3 21 0.00045 29.4 2.7 42 187-228 74-117 (381)
178 TIGR00100 hypA hydrogenase nic 46.0 10 0.00022 25.9 0.9 13 192-204 70-82 (115)
179 TIGR00280 L37a ribosomal prote 45.7 22 0.00048 23.1 2.3 12 192-203 53-64 (91)
180 KOG2907|consensus 45.1 11 0.00025 25.3 0.9 11 221-231 103-113 (116)
181 KOG2272|consensus 45.1 16 0.00035 28.5 1.9 20 91-110 98-117 (332)
182 PF14311 DUF4379: Domain of un 45.0 14 0.0003 21.3 1.2 12 193-204 29-40 (55)
183 KOG4167|consensus 44.8 15 0.00033 33.5 1.9 27 23-50 787-813 (907)
184 COG5151 SSL1 RNA polymerase II 44.6 39 0.00084 27.4 3.9 50 159-216 363-412 (421)
185 KOG3408|consensus 44.3 14 0.0003 25.3 1.3 27 188-214 53-79 (129)
186 PF14369 zf-RING_3: zinc-finge 44.1 19 0.0004 18.7 1.5 10 65-74 3-12 (35)
187 PF01363 FYVE: FYVE zinc finge 44.1 13 0.00028 22.6 1.0 11 193-203 10-20 (69)
188 PF01780 Ribosomal_L37ae: Ribo 43.8 8.2 0.00018 25.0 0.1 11 193-203 54-64 (90)
189 KOG1701|consensus 43.6 4.8 0.0001 33.9 -1.2 43 66-108 276-318 (468)
190 COG0068 HypF Hydrogenase matur 43.4 2.7 5.8E-05 37.9 -2.8 88 22-130 95-183 (750)
191 COG3357 Predicted transcriptio 43.3 43 0.00092 21.7 3.2 13 192-204 58-70 (97)
192 KOG4167|consensus 43.0 6 0.00013 35.8 -0.8 26 191-216 791-816 (907)
193 KOG3002|consensus 42.8 43 0.00094 27.4 4.1 79 190-273 78-164 (299)
194 COG0068 HypF Hydrogenase matur 42.3 4 8.7E-05 36.9 -1.9 58 94-167 125-182 (750)
195 PF05495 zf-CHY: CHY zinc fing 42.0 9.2 0.0002 23.6 0.1 13 92-104 41-53 (71)
196 PF04780 DUF629: Protein of un 41.5 18 0.00039 31.4 1.9 21 221-241 58-78 (466)
197 PRK00564 hypA hydrogenase nick 40.7 14 0.0003 25.4 0.9 12 192-203 71-82 (117)
198 COG1655 Uncharacterized protei 40.5 8.2 0.00018 29.7 -0.3 24 26-50 17-40 (267)
199 PRK04351 hypothetical protein; 40.2 18 0.00038 26.1 1.4 30 221-258 113-142 (149)
200 CHL00174 accD acetyl-CoA carbo 40.2 35 0.00075 27.8 3.1 40 28-84 38-77 (296)
201 cd00065 FYVE FYVE domain; Zinc 39.8 21 0.00045 20.6 1.4 11 194-204 4-14 (57)
202 COG1656 Uncharacterized conser 39.7 20 0.00044 26.2 1.6 14 221-234 131-144 (165)
203 PRK03976 rpl37ae 50S ribosomal 39.5 31 0.00068 22.4 2.3 12 192-203 54-65 (90)
204 PRK03681 hypA hydrogenase nick 38.0 20 0.00043 24.5 1.3 12 64-75 70-81 (114)
205 PRK00420 hypothetical protein; 37.9 22 0.00049 24.2 1.5 27 66-103 25-51 (112)
206 KOG2636|consensus 37.9 25 0.00053 30.1 2.0 31 212-242 393-424 (497)
207 PF14803 Nudix_N_2: Nudix N-te 37.7 14 0.00031 19.0 0.4 14 188-201 18-31 (34)
208 PF07282 OrfB_Zn_ribbon: Putat 37.6 48 0.001 20.0 2.9 11 120-130 46-56 (69)
209 PF01096 TFIIS_C: Transcriptio 37.6 4.5 9.8E-05 21.6 -1.5 10 65-74 29-38 (39)
210 PF03833 PolC_DP2: DNA polymer 37.4 11 0.00024 35.0 0.0 12 220-231 680-691 (900)
211 PF06220 zf-U1: U1 zinc finger 37.1 33 0.00072 18.1 1.8 11 192-202 3-13 (38)
212 PF12773 DZR: Double zinc ribb 37.0 43 0.00093 18.6 2.4 10 194-203 14-23 (50)
213 PF03145 Sina: Seven in absent 36.9 31 0.00068 26.1 2.4 52 192-246 14-73 (198)
214 PF07503 zf-HYPF: HypF finger; 36.8 3.9 8.5E-05 21.2 -1.7 9 66-74 23-31 (35)
215 PF03811 Zn_Tnp_IS1: InsA N-te 36.7 11 0.00023 19.8 -0.1 11 244-254 25-35 (36)
216 PRK03564 formate dehydrogenase 36.4 29 0.00064 28.4 2.2 75 158-260 187-264 (309)
217 COG5112 UFD2 U1-like Zn-finger 36.4 26 0.00056 23.3 1.6 32 18-50 45-76 (126)
218 COG1594 RPB9 DNA-directed RNA 36.4 7.1 0.00015 26.7 -1.1 11 221-231 101-111 (113)
219 smart00154 ZnF_AN1 AN1-like Zi 36.3 21 0.00045 19.0 1.0 14 248-261 12-25 (39)
220 PF13824 zf-Mss51: Zinc-finger 36.2 32 0.00069 20.0 1.7 10 92-101 14-23 (55)
221 PF10263 SprT-like: SprT-like 36.0 11 0.00025 27.2 -0.1 8 249-256 144-151 (157)
222 PF01155 HypA: Hydrogenase exp 35.8 14 0.00029 25.3 0.2 14 192-205 70-83 (113)
223 COG1998 RPS31 Ribosomal protei 35.7 24 0.00051 19.9 1.1 10 64-73 37-46 (51)
224 TIGR00244 transcriptional regu 35.7 6.3 0.00014 28.1 -1.4 19 92-110 28-46 (147)
225 PF09788 Tmemb_55A: Transmembr 35.4 46 0.00099 26.3 3.0 35 25-75 62-96 (256)
226 KOG0717|consensus 34.4 23 0.00049 30.6 1.3 21 29-50 293-313 (508)
227 PRK14559 putative protein seri 34.3 57 0.0012 30.0 3.9 7 122-128 3-9 (645)
228 COG3677 Transposase and inacti 34.0 49 0.0011 23.2 2.8 15 190-204 51-65 (129)
229 TIGR00595 priA primosomal prot 33.8 42 0.00091 29.8 3.0 28 186-228 234-261 (505)
230 KOG0978|consensus 33.4 14 0.0003 33.7 -0.0 11 28-38 643-653 (698)
231 PF08792 A2L_zn_ribbon: A2L zi 33.2 28 0.0006 17.8 1.1 13 62-74 19-31 (33)
232 PF13451 zf-trcl: Probable zin 33.0 21 0.00046 20.2 0.7 12 27-38 3-14 (49)
233 PF10013 DUF2256: Uncharacteri 32.7 31 0.00068 18.7 1.3 17 193-209 9-25 (42)
234 COG1327 Predicted transcriptio 32.3 12 0.00025 26.8 -0.5 16 93-108 29-44 (156)
235 PRK14873 primosome assembly pr 32.3 37 0.00081 31.3 2.4 9 160-168 385-393 (665)
236 PF07800 DUF1644: Protein of u 32.0 65 0.0014 23.4 3.1 57 191-248 79-137 (162)
237 COG1675 TFA1 Transcription ini 31.9 57 0.0012 24.3 2.9 35 87-130 108-142 (176)
238 PRK12496 hypothetical protein; 31.7 29 0.00063 25.5 1.4 11 221-231 128-138 (164)
239 PF07975 C1_4: TFIIH C1-like d 31.1 28 0.0006 19.9 1.0 23 27-50 20-42 (51)
240 COG4896 Uncharacterized protei 30.9 30 0.00064 20.5 1.0 37 194-230 4-41 (68)
241 PF05741 zf-nanos: Nanos RNA b 30.9 17 0.00038 21.1 0.1 11 64-74 33-43 (55)
242 PF01428 zf-AN1: AN1-like Zinc 30.9 19 0.00042 19.5 0.3 15 247-261 12-26 (43)
243 PF04423 Rad50_zn_hook: Rad50 30.3 19 0.00041 20.7 0.2 11 250-260 22-32 (54)
244 KOG4727|consensus 30.3 37 0.00081 24.8 1.7 27 187-213 70-96 (193)
245 PF11781 RRN7: RNA polymerase 30.1 33 0.00071 17.9 1.1 12 189-200 22-33 (36)
246 PF04810 zf-Sec23_Sec24: Sec23 29.7 39 0.00085 18.0 1.4 13 189-201 21-33 (40)
247 COG1571 Predicted DNA-binding 29.4 37 0.00081 29.1 1.8 11 221-231 368-378 (421)
248 COG1773 Rubredoxin [Energy pro 29.2 25 0.00053 20.5 0.5 10 29-38 4-13 (55)
249 PF05129 Elf1: Transcription e 28.9 11 0.00023 24.0 -1.1 14 64-77 46-59 (81)
250 PF11931 DUF3449: Domain of un 28.9 19 0.0004 27.3 0.0 20 29-49 102-122 (196)
251 PF14205 Cys_rich_KTR: Cystein 28.1 19 0.00041 20.8 -0.0 10 219-228 27-36 (55)
252 PF14690 zf-ISL3: zinc-finger 27.9 10 0.00023 20.8 -1.2 10 28-37 2-11 (47)
253 PF10276 zf-CHCC: Zinc-finger 27.7 22 0.00048 19.1 0.2 11 248-258 29-39 (40)
254 PF09963 DUF2197: Uncharacteri 27.4 15 0.00033 21.4 -0.5 7 221-227 32-38 (56)
255 PF07295 DUF1451: Protein of u 27.4 30 0.00064 24.9 0.8 9 221-229 113-121 (146)
256 smart00731 SprT SprT homologue 27.3 41 0.00089 24.1 1.5 33 192-231 112-144 (146)
257 KOG4727|consensus 27.2 35 0.00075 25.0 1.1 22 247-268 74-95 (193)
258 smart00064 FYVE Protein presen 27.1 55 0.0012 19.6 1.9 10 160-169 12-21 (68)
259 TIGR03830 CxxCG_CxxCG_HTH puta 26.7 37 0.00081 23.3 1.2 14 65-78 32-45 (127)
260 PF04216 FdhE: Protein involve 26.6 8.9 0.00019 31.1 -2.2 56 189-259 194-249 (290)
261 PF04780 DUF629: Protein of un 26.5 90 0.0019 27.3 3.6 31 187-217 52-83 (466)
262 cd00924 Cyt_c_Oxidase_Vb Cytoc 26.4 34 0.00075 22.6 0.9 16 217-232 76-91 (97)
263 KOG4377|consensus 26.3 44 0.00095 28.4 1.7 23 249-271 402-426 (480)
264 TIGR01562 FdhE formate dehydro 26.3 64 0.0014 26.5 2.6 54 188-260 206-264 (305)
265 PF10083 DUF2321: Uncharacteri 26.0 57 0.0012 23.6 2.0 19 189-207 65-83 (158)
266 TIGR01384 TFS_arch transcripti 25.9 47 0.001 22.1 1.6 27 194-232 2-28 (104)
267 PRK00762 hypA hydrogenase nick 25.7 33 0.00071 23.9 0.8 10 28-38 70-79 (124)
268 KOG2906|consensus 25.5 5 0.00011 26.2 -3.0 12 120-131 21-32 (105)
269 KOG0717|consensus 25.4 42 0.0009 29.0 1.4 21 249-269 293-313 (508)
270 PRK05452 anaerobic nitric oxid 25.1 60 0.0013 28.7 2.4 17 22-38 419-435 (479)
271 COG5188 PRP9 Splicing factor 3 25.1 81 0.0017 26.2 2.9 27 59-85 369-396 (470)
272 PLN02294 cytochrome c oxidase 24.9 38 0.00083 24.9 1.0 18 216-233 137-154 (174)
273 TIGR00515 accD acetyl-CoA carb 24.7 78 0.0017 25.7 2.8 41 28-85 26-66 (285)
274 KOG1842|consensus 24.5 48 0.001 28.5 1.6 30 23-53 10-39 (505)
275 KOG4118|consensus 24.5 33 0.00072 20.5 0.5 25 249-273 39-63 (74)
276 KOG2071|consensus 24.4 48 0.001 29.6 1.7 27 218-244 416-442 (579)
277 PHA02998 RNA polymerase subuni 23.8 25 0.00053 26.0 -0.1 11 221-231 172-182 (195)
278 PRK05654 acetyl-CoA carboxylas 23.8 79 0.0017 25.8 2.7 41 28-85 27-67 (292)
279 PF04606 Ogr_Delta: Ogr/Delta- 23.3 27 0.00058 19.4 -0.0 8 31-38 2-9 (47)
280 PF09416 UPF1_Zn_bind: RNA hel 23.1 52 0.0011 23.8 1.4 14 25-38 11-24 (152)
281 PF06397 Desulfoferrod_N: Desu 22.9 41 0.00089 17.6 0.6 10 248-257 6-15 (36)
282 KOG1994|consensus 22.4 42 0.0009 25.9 0.8 23 190-212 237-259 (268)
283 COG1439 Predicted nucleic acid 21.7 38 0.00083 25.1 0.5 11 28-38 139-149 (177)
284 PRK05580 primosome assembly pr 21.5 51 0.0011 30.6 1.3 7 94-100 423-429 (679)
285 KOG3214|consensus 20.7 46 0.00099 21.9 0.6 13 65-77 48-60 (109)
286 KOG2747|consensus 20.6 53 0.0012 27.9 1.2 29 24-53 154-182 (396)
287 PF13696 zf-CCHC_2: Zinc knuck 20.6 89 0.0019 15.9 1.5 12 26-37 6-17 (32)
288 PRK05978 hypothetical protein; 20.6 39 0.00084 24.4 0.3 11 66-76 54-64 (148)
289 PTZ00448 hypothetical protein; 20.1 69 0.0015 26.9 1.7 23 248-270 314-336 (373)
No 1
>KOG2462|consensus
Probab=99.96 E-value=3.1e-30 Score=193.59 Aligned_cols=133 Identities=29% Similarity=0.573 Sum_probs=117.0
Q ss_pred CcccCCCCCcccCChhHHHHHHhhhcC---CCCccCCCCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCC
Q psy4796 91 KPYKCPHCDHCFTQKVVLQRHLLTHTG---EKPFACHLCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEP 167 (274)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~h~~---~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 167 (274)
..|+|..|++.|.+..+|.+|.++|.. .+.+.|+.|++.|.+-..|+.|+++
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirT------------------------- 183 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRT------------------------- 183 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhc-------------------------
Confidence 458899999999999999999888744 4567888888888877777777665
Q ss_pred CCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHHHhhhCCCC
Q psy4796 168 ISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTHLRIHKTER 247 (274)
Q Consensus 168 ~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 247 (274)
|+ -+.+|.+||+.|...+.|+.|+++|+|||||.|+.|++.|.++++|+.||++|.+.|
T Consensus 184 -------------------H~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 184 -------------------HT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred -------------------cC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 22 347899999999999999999999999999999999999999999999999999999
Q ss_pred ceecCCCCccCCChhHHHHHHh
Q psy4796 248 EYACGKCAYRTAALPDLKLHLK 269 (274)
Q Consensus 248 ~~~C~~C~~~f~~~~~l~~H~~ 269 (274)
+|+|+.|+|+|..++.|.+|..
T Consensus 243 ~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 243 KHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cccCcchhhHHHHHHHHHHhhh
Confidence 9999999999999999999975
No 2
>KOG2462|consensus
Probab=99.95 E-value=3.6e-28 Score=182.56 Aligned_cols=136 Identities=25% Similarity=0.480 Sum_probs=123.8
Q ss_pred CCcceecccccccccChHHHHHHHhhcCC---CCcccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCccccHHHHH
Q psy4796 61 AKLQFLCLFCSYVATARIAIKNHLSSHLG---WKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRASRKYYIT 137 (274)
Q Consensus 61 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~---~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 137 (274)
....|+|+.||+.+.+..+|.+|...|-. .+.+.|+.|+++|.+...|+.|+++|. -+++|.+||+.|...+.|.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhh
Confidence 34468999999999999999999998853 467999999999999999999999997 6799999999999999988
Q ss_pred HHHHHHHHHHHHHhHhhcCCCccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhccC
Q psy4796 138 AHLNSLLSALLLQHFLASQPRRKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHTG 217 (274)
Q Consensus 138 ~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 217 (274)
-|+ ++|++++||.|+.|++.|.++++|+.|+++|.+
T Consensus 205 GHi--------------------------------------------RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 205 GHI--------------------------------------------RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred ccc--------------------------------------------ccccCCCCccCCcccchhcchHHHHHHHHhhcC
Confidence 884 457899999999999999999999999999999
Q ss_pred CCCcccCcCccccCCchhHHHHHhh
Q psy4796 218 DKPFACSYCDYTCNQSSNLQTHLRI 242 (274)
Q Consensus 218 ~~~~~C~~C~~~f~~~~~l~~H~~~ 242 (274)
.|+|+|..|+++|...+.|.+|...
T Consensus 241 ~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 241 VKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred CccccCcchhhHHHHHHHHHHhhhh
Confidence 9999999999999999999999765
No 3
>KOG1074|consensus
Probab=99.94 E-value=3.3e-28 Score=206.25 Aligned_cols=169 Identities=21% Similarity=0.401 Sum_probs=139.3
Q ss_pred ccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCC---CCCCCCC
Q psy4796 93 YKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCV---HCSEPIS 169 (274)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~---~c~~~~~ 169 (274)
-.|-+|.++......|+-|.++|++++||+|.+|++.|.++.+|+.|+-.|... + ....+++|+ +|-+.|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~----p--~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK----P--PARVQFSCPSTFICQKKFT 679 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccC----c--cccccccCCchhhhccccc
Confidence 689999999999999999999999999999999999999999999999773210 1 222568898 8999998
Q ss_pred CChhhhhhhccCCCCCcccC-------------CCccccCCCCccccCHHHHHHHHhhccCC------------------
Q psy4796 170 SDMSEIIEHCLVCPNATRTD-------------KKKFVCFACPYATQYACYIKTHVMTHTGD------------------ 218 (274)
Q Consensus 170 ~~~~~l~~h~~~~~~~~~~~-------------~~~~~C~~C~~~f~~~~~l~~H~~~h~~~------------------ 218 (274)
. .-.|-.| ...|.+ ...-.|..|.+.|.....+..++..|.+.
T Consensus 680 n-~V~lpQh-----IriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~ 753 (958)
T KOG1074|consen 680 N-AVTLPQH-----IRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELD 753 (958)
T ss_pred c-cccccce-----EEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccc
Confidence 8 6666666 444331 11246888888888887777777776210
Q ss_pred --------------------------------------------------------------------------------
Q psy4796 219 -------------------------------------------------------------------------------- 218 (274)
Q Consensus 219 -------------------------------------------------------------------------------- 218 (274)
T Consensus 754 ~tp~~~e~~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~ 833 (958)
T KOG1074|consen 754 VTPPPPENSCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQE 833 (958)
T ss_pred cCCCccccccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccc
Confidence
Q ss_pred --------------------------------------------CCcccCcCccccCCchhHHHHHhhhCCCCceecCCC
Q psy4796 219 --------------------------------------------KPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKC 254 (274)
Q Consensus 219 --------------------------------------------~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C 254 (274)
....|.+||+.|...++|..|+++|+++|||.|.+|
T Consensus 834 ~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC 913 (958)
T KOG1074|consen 834 TSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFC 913 (958)
T ss_pred ccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhh
Confidence 116799999999999999999999999999999999
Q ss_pred CccCCChhHHHHHHhhhcC
Q psy4796 255 AYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 255 ~~~f~~~~~l~~H~~~~H~ 273 (274)
++.|..+.+|+.|+..|+.
T Consensus 914 ~~aFttrgnLKvHMgtH~w 932 (958)
T KOG1074|consen 914 EEAFTTRGNLKVHMGTHMW 932 (958)
T ss_pred hhhhhhhhhhhhhhccccc
Confidence 9999999999999998874
No 4
>KOG3608|consensus
Probab=99.93 E-value=3.8e-26 Score=176.31 Aligned_cols=229 Identities=22% Similarity=0.395 Sum_probs=193.9
Q ss_pred CCCeeecc--ccCCcchhhHHHHHhhhcc----ccccccccC-Cc-ceeccc--ccccccChHHHHHHHhhcCCCCcccC
Q psy4796 26 PADVTCLH--CSLTTPCVMKDMIRHGRLC----EFNSVVTSA-KL-QFLCLF--CSYVATARIAIKNHLSSHLGWKPYKC 95 (274)
Q Consensus 26 ~~~~~C~~--C~~~f~~~~~~l~~H~~~~----~~~~~~h~~-~~-~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C 95 (274)
+..|.|.. |+..| .++..|..|+..+ +-+.....+ ++ .+.|.+ |-+.+.++..|++|++.|++++...|
T Consensus 132 g~~f~C~WedCe~~F-~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvAC 210 (467)
T KOG3608|consen 132 GQNFRCGWEDCEREF-VSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVAC 210 (467)
T ss_pred hhhhccChhhcCCcc-cCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEec
Confidence 34478865 99999 9999999998622 111111111 21 255666 88999999999999999999999999
Q ss_pred CCCCcccCChhHHHHHHhh--hcCCCCccCCCCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCCCCCChh
Q psy4796 96 PHCDHCFTQKVVLQRHLLT--HTGEKPFACHLCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEPISSDMS 173 (274)
Q Consensus 96 ~~C~~~f~~~~~l~~H~~~--h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~ 173 (274)
+.|+.-|.++..|..|.+. -....+|.|..|.+.|.++..|..|+..| ..-|+|+.|+.+.+. .+
T Consensus 211 p~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rH------------vn~ykCplCdmtc~~-~s 277 (467)
T KOG3608|consen 211 PHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRH------------VNCYKCPLCDMTCSS-AS 277 (467)
T ss_pred chHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHh------------hhcccccccccCCCC-hH
Confidence 9999999999999999864 34456899999999999999999998862 356999999999999 99
Q ss_pred hhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCc--CccccCCchhHHHHHhhhC-CC--Cc
Q psy4796 174 EIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSY--CDYTCNQSSNLQTHLRIHK-TE--RE 248 (274)
Q Consensus 174 ~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-~~--~~ 248 (274)
+|..|+ +..|...++|+|..|.+.|...+.|.+|...|. +..|+|.. |...|.+..++++|++.++ +. .+
T Consensus 278 sL~~H~----r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~ 352 (467)
T KOG3608|consen 278 SLTTHI----RYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPIL 352 (467)
T ss_pred HHHHHH----HhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCc
Confidence 999995 456778999999999999999999999999998 77799988 9999999999999998754 44 45
Q ss_pred eecCCCCccCCChhHHHHHHhhhcC
Q psy4796 249 YACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
|.|-.|.+.|.+-.+|.+|+.+.|+
T Consensus 353 Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 353 YACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred eeeecchhhhccchhHHHHHHHhhc
Confidence 9999999999999999999998886
No 5
>KOG3623|consensus
Probab=99.92 E-value=3.8e-26 Score=191.06 Aligned_cols=81 Identities=25% Similarity=0.577 Sum_probs=77.5
Q ss_pred CCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCCChhHHHHHH
Q psy4796 189 DKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTAALPDLKLHL 268 (274)
Q Consensus 189 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 268 (274)
....|.|+.|++.|...+.|.+|.-.|+|.+||+|.+|.+.|.-+..|..|+|.|.|+|||+|..|+|.|....+...||
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 45579999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred h
Q psy4796 269 K 269 (274)
Q Consensus 269 ~ 269 (274)
.
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 3
No 6
>KOG3608|consensus
Probab=99.91 E-value=1.5e-24 Score=167.61 Aligned_cols=191 Identities=25% Similarity=0.515 Sum_probs=170.0
Q ss_pred eeccc--ccccccChHHHHHHHhhcCC------------CC-cccCCC--CCcccCChhHHHHHHhhhcCCCCccCCCCC
Q psy4796 65 FLCLF--CSYVATARIAIKNHLSSHLG------------WK-PYKCPH--CDHCFTQKVVLQRHLLTHTGEKPFACHLCP 127 (274)
Q Consensus 65 ~~C~~--C~~~f~~~~~l~~H~~~h~~------------~~-~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 127 (274)
|.|.+ |+..|.+...+..|+..|.- ++ -+.|.+ |-+.|.++..|+.|++.|.+++...|+.|+
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg 214 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCG 214 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHH
Confidence 55655 99999999999999887742 12 256776 999999999999999999999999999999
Q ss_pred CccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHH
Q psy4796 128 YRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACY 207 (274)
Q Consensus 128 ~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~ 207 (274)
.-|.++..|-+|++. .......+|.|..|.+.|.. ...|..| ...|. +-|+|+.|..+....+.
T Consensus 215 ~~F~~~tkl~DH~rR--------qt~l~~n~fqC~~C~KrFaT-eklL~~H-----v~rHv--n~ykCplCdmtc~~~ss 278 (467)
T KOG3608|consen 215 ELFRTKTKLFDHLRR--------QTELNTNSFQCAQCFKRFAT-EKLLKSH-----VVRHV--NCYKCPLCDMTCSSASS 278 (467)
T ss_pred HHhccccHHHHHHHh--------hhhhcCCchHHHHHHHHHhH-HHHHHHH-----HHHhh--hcccccccccCCCChHH
Confidence 999999999999987 44466779999999999999 8888888 44444 45999999999999999
Q ss_pred HHHHHh-hccCCCCcccCcCccccCCchhHHHHHhhhCCCCceecCC--CCccCCChhHHHHHHhhhc
Q psy4796 208 IKTHVM-THTGDKPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGK--CAYRTAALPDLKLHLKNMH 272 (274)
Q Consensus 208 l~~H~~-~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~~H 272 (274)
|..|++ .|...|||.|..|++.|...++|.+|+.+|. +-.|.|.. |..+|..+..|.+|++.+|
T Consensus 279 L~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 279 LTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred HHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 999998 7889999999999999999999999999999 66799977 9999999999999999998
No 7
>KOG1074|consensus
Probab=99.86 E-value=2e-22 Score=171.57 Aligned_cols=219 Identities=22% Similarity=0.362 Sum_probs=157.7
Q ss_pred CCCCCCCCeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHhhcCCC----CcccCC
Q psy4796 21 SPGPPPADVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLSSHLGW----KPYKCP 96 (274)
Q Consensus 21 ~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~----~~~~C~ 96 (274)
.......+-+|.+|.++. .-+..|+.|++ .|+++++|+|.+||+.|.++.+|+.||..|... .+|.|+
T Consensus 598 ~~~~~TdPNqCiiC~rVl-SC~saLqmHyr-------tHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP 669 (958)
T KOG1074|consen 598 SENKRTDPNQCIICLRVL-SCPSALQMHYR-------THTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCP 669 (958)
T ss_pred cccccCCccceeeeeecc-cchhhhhhhhh-------cccCcCccccccccchhccccchhhcccccccCccccccccCC
Confidence 344555678999999999 99999999999 999999999999999999999999999988543 458999
Q ss_pred ---CCCcccCChhHHHHHHhhhcCC-CC------------ccCCCCCCccccHHHHHHHHHHHHHHHHHHh---------
Q psy4796 97 ---HCDHCFTQKVVLQRHLLTHTGE-KP------------FACHLCPYRASRKYYITAHLNSLLSALLLQH--------- 151 (274)
Q Consensus 97 ---~C~~~f~~~~~l~~H~~~h~~~-~~------------~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~--------- 151 (274)
+|.+.|.....|..|++.|.+. .+ =.|..|.+.|.....+..++..+........
T Consensus 670 ~~~ic~~kftn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t 749 (958)
T KOG1074|consen 670 STFICQKKFTNAVTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTET 749 (958)
T ss_pred chhhhcccccccccccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccc
Confidence 9999999999999999999843 21 3588899988777777777655411000000
Q ss_pred -HhhcCCCccCCCCCCCCCCChhhhhhh----------------------------------------------------
Q psy4796 152 -FLASQPRRKCVHCSEPISSDMSEIIEH---------------------------------------------------- 178 (274)
Q Consensus 152 -~~~~~~~~~c~~c~~~~~~~~~~l~~h---------------------------------------------------- 178 (274)
......+..+..|+..+.. ...+..+
T Consensus 750 ~~~~~tp~~~e~~~~~~~~~-e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pv 828 (958)
T KOG1074|consen 750 EELDVTPPPPENSCGRELEG-EMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPV 828 (958)
T ss_pred cccccCCCccccccccccCc-ccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCch
Confidence 0000011122222222211 0000000
Q ss_pred -------ccC-----------------------------C-CCCcccCCCccccCCCCccccCHHHHHHHHhhccCCCCc
Q psy4796 179 -------CLV-----------------------------C-PNATRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPF 221 (274)
Q Consensus 179 -------~~~-----------------------------~-~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 221 (274)
++. + ....-...+...|..||+.|...+.|.+|+++|+++|||
T Consensus 829 l~~~~~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF 908 (958)
T KOG1074|consen 829 LWNQETSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPF 908 (958)
T ss_pred hhcccccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCc
Confidence 000 0 000001123478999999999999999999999999999
Q ss_pred ccCcCccccCCchhHHHHHhhhCCCCc
Q psy4796 222 ACSYCDYTCNQSSNLQTHLRIHKTERE 248 (274)
Q Consensus 222 ~C~~C~~~f~~~~~l~~H~~~h~~~~~ 248 (274)
.|.+|++.|+.+.+|+.||..|....+
T Consensus 909 ~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 909 FCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred cchhhhhhhhhhhhhhhhhccccccCC
Confidence 999999999999999999999987654
No 8
>KOG3623|consensus
Probab=99.82 E-value=3e-21 Score=162.01 Aligned_cols=80 Identities=21% Similarity=0.494 Sum_probs=76.5
Q ss_pred CCccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhH
Q psy4796 157 PRRKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNL 236 (274)
Q Consensus 157 ~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 236 (274)
..|.|+.|++.|.. .+.|.+| .-.|++.+||.|.+|.++|..+..|..|.+.|.|+|||+|..|+++|+-...+
T Consensus 893 gmyaCDqCDK~FqK-qSSLaRH-----KYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSY 966 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQK-QSSLARH-----KYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSY 966 (1007)
T ss_pred ccchHHHHHHHHHh-hHHHHHh-----hhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccch
Confidence 45899999999999 9999999 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhh
Q psy4796 237 QTHLRI 242 (274)
Q Consensus 237 ~~H~~~ 242 (274)
.+||..
T Consensus 967 SQHMNH 972 (1007)
T KOG3623|consen 967 SQHMNH 972 (1007)
T ss_pred Hhhhcc
Confidence 999853
No 9
>KOG3576|consensus
Probab=99.77 E-value=2.9e-19 Score=128.18 Aligned_cols=113 Identities=29% Similarity=0.542 Sum_probs=103.1
Q ss_pred CCCCeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHhhcCCCCcccCCCCCcccCC
Q psy4796 25 PPADVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCFTQ 104 (274)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 104 (274)
+...|.|.+|++.| ....-|.+|++ -|+.-+.+.|..||+.|.+..+|.+|+++|++.+||+|..|++.|+.
T Consensus 114 d~d~ftCrvCgK~F-~lQRmlnrh~k-------ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKF-GLQRMLNRHLK-------CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCCeeeeehhhhhh-hHHHHHHHHhh-------hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 34569999999999 99999999999 99999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHhhhcC-----------CCCccCCCCCCccccHHHHHHHHHHHHH
Q psy4796 105 KVVLQRHLLTHTG-----------EKPFACHLCPYRASRKYYITAHLNSLLS 145 (274)
Q Consensus 105 ~~~l~~H~~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 145 (274)
.-.|..|.+.-++ .+.|.|+.||..-.....+..|++.++.
T Consensus 186 rcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 186 RCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred hccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 9999999875444 4669999999999999999999988654
No 10
>KOG3576|consensus
Probab=99.75 E-value=3.8e-19 Score=127.56 Aligned_cols=114 Identities=28% Similarity=0.527 Sum_probs=103.4
Q ss_pred hcCCCccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCc
Q psy4796 154 ASQPRRKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQS 233 (274)
Q Consensus 154 ~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 233 (274)
.+.-.+.|.+|++.|.- ..+|.+| .+-|..-+.|.|..||+.|.+...|.+|+++|+|.+||.|..|++.|+.+
T Consensus 113 sd~d~ftCrvCgK~F~l-QRmlnrh-----~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqr 186 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGL-QRMLNRH-----LKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQR 186 (267)
T ss_pred CCCCeeeeehhhhhhhH-HHHHHHH-----hhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhh
Confidence 34556889999999988 8999999 89999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHhh-hCC----------CCceecCCCCccCCChhHHHHHHhhhcC
Q psy4796 234 SNLQTHLRI-HKT----------EREYACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 234 ~~l~~H~~~-h~~----------~~~~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
-.|..|++. |.. .+.|+|..||.+-.....+..|++.+|+
T Consensus 187 csleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 187 CSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred ccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 999999865 542 3569999999999999999999999986
No 11
>PHA00733 hypothetical protein
Probab=99.39 E-value=3.1e-13 Score=93.90 Aligned_cols=100 Identities=16% Similarity=0.269 Sum_probs=79.4
Q ss_pred CCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHH--Hh---hccCCCCcccCcCccccCCchhHHHHHh
Q psy4796 167 PISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTH--VM---THTGDKPFACSYCDYTCNQSSNLQTHLR 241 (274)
Q Consensus 167 ~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 241 (274)
.|.-..+.|.++ .......+++.|.+|+..|.....|..+ +. .+.+.+||.|+.|++.|.+...|..|++
T Consensus 20 ~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 20 FIHVTLEELKRY-----HSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred EEecCHHHhhhh-----hcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHh
Confidence 333335555554 3344456789999999998887777666 22 3345889999999999999999999999
Q ss_pred hhCCCCceecCCCCccCCChhHHHHHHhhhcC
Q psy4796 242 IHKTEREYACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 242 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
.| ..+|.|+.|++.|.....|.+|+...|+
T Consensus 95 ~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 95 YT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 87 3579999999999999999999999986
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.36 E-value=3.9e-12 Score=108.07 Aligned_cols=146 Identities=16% Similarity=0.348 Sum_probs=108.1
Q ss_pred ccCCCCCcccCChhHHHHHHhhhcCCCCccCCC--CCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCCCCC
Q psy4796 93 YKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHL--CPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEPISS 170 (274)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~ 170 (274)
-.|+.|...... ..|..|.... ......|+. |+..|... .+ ...+.|+.|++.|.
T Consensus 408 V~C~NC~~~i~l-~~l~lHe~~C-~r~~V~Cp~~~Cg~v~~r~-el-------------------~~H~~C~~Cgk~f~- 464 (567)
T PLN03086 408 VECRNCKHYIPS-RSIALHEAYC-SRHNVVCPHDGCGIVLRVE-EA-------------------KNHVHCEKCGQAFQ- 464 (567)
T ss_pred EECCCCCCccch-hHHHHHHhhC-CCcceeCCcccccceeecc-cc-------------------ccCccCCCCCCccc-
Confidence 468888877554 3455776543 334567874 88777322 22 22357888888884
Q ss_pred ChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCC----------chhHHHHH
Q psy4796 171 DMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQ----------SSNLQTHL 240 (274)
Q Consensus 171 ~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~----------~~~l~~H~ 240 (274)
...|..| ...+. .++.|+ ||+.+ .+..|..|+.+|.+++++.|..|++.|.. ...|..|.
T Consensus 465 -~s~LekH-----~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE 534 (567)
T PLN03086 465 -QGEMEKH-----MKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHE 534 (567)
T ss_pred -hHHHHHH-----HHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHH
Confidence 4567777 44442 679999 99755 67899999999999999999999999852 34799998
Q ss_pred hhhCCCCceecCCCCccCCChhHHHHHHhhhcC
Q psy4796 241 RIHKTEREYACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 241 ~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
... +.+++.|..||+.+. ..+|..|+-.+|.
T Consensus 535 ~~C-G~rt~~C~~Cgk~Vr-lrdm~~H~~~~h~ 565 (567)
T PLN03086 535 SIC-GSRTAPCDSCGRSVM-LKEMDIHQIAVHQ 565 (567)
T ss_pred Hhc-CCcceEccccCCeee-ehhHHHHHHHhhc
Confidence 885 899999999999875 5569999998886
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.33 E-value=1.2e-11 Score=105.11 Aligned_cols=148 Identities=18% Similarity=0.411 Sum_probs=104.2
Q ss_pred CCCCCeeeccccCCcchhhHHHHHhhhccccccccccCCcceeccc--ccccccChHHHHHHHhhcCCCCcccCCCCCcc
Q psy4796 24 PPPADVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLF--CSYVATARIAIKNHLSSHLGWKPYKCPHCDHC 101 (274)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 101 (274)
.......|..|.+.. ....|..|...|.. ..-.|+. |+..|... .+. ..+.|+.|++.
T Consensus 403 ~~~~~V~C~NC~~~i--~l~~l~lHe~~C~r--------~~V~Cp~~~Cg~v~~r~-el~---------~H~~C~~Cgk~ 462 (567)
T PLN03086 403 MDVDTVECRNCKHYI--PSRSIALHEAYCSR--------HNVVCPHDGCGIVLRVE-EAK---------NHVHCEKCGQA 462 (567)
T ss_pred CCCCeEECCCCCCcc--chhHHHHHHhhCCC--------cceeCCcccccceeecc-ccc---------cCccCCCCCCc
Confidence 344567899999998 77778899874442 2345774 88877422 222 23578888888
Q ss_pred cCChhHHHHHHhhhcCCCCccCCCCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCCCCCC---------h
Q psy4796 102 FTQKVVLQRHLLTHTGEKPFACHLCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEPISSD---------M 172 (274)
Q Consensus 102 f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~---------~ 172 (274)
|. ...|..|+..++ .++.|+ |+..+ .+..|..|+.. + ...+++.|+.|+..+... .
T Consensus 463 f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~t--------h--Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~ 527 (567)
T PLN03086 463 FQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQAS--------T--CPLRLITCRFCGDMVQAGGSAMDVRDRL 527 (567)
T ss_pred cc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhc--------c--CCCCceeCCCCCCccccCccccchhhhh
Confidence 85 577888888764 678888 88654 56788888765 3 677888888888877421 3
Q ss_pred hhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHh
Q psy4796 173 SEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVM 213 (274)
Q Consensus 173 ~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 213 (274)
+.|..| .... +.+++.|..||+.+..+ .+..|+.
T Consensus 528 s~Lt~H-----E~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 528 RGMSEH-----ESIC-GSRTAPCDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred hhHHHH-----HHhc-CCcceEccccCCeeeeh-hHHHHHH
Confidence 467777 5554 77889999999888855 4667765
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.12 E-value=2.7e-11 Score=69.15 Aligned_cols=42 Identities=19% Similarity=0.420 Sum_probs=28.6
Q ss_pred cccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCCChhHH
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTAALPDL 264 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 264 (274)
|.|+.||+.|...++|..|+++|. ++|+|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 567777777777777777777766 566777777776665544
No 15
>KOG3993|consensus
Probab=99.11 E-value=8.3e-12 Score=99.79 Aligned_cols=111 Identities=16% Similarity=0.248 Sum_probs=72.1
Q ss_pred CCeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHhhcCCCCcccC---CCCCcccC
Q psy4796 27 ADVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLSSHLGWKPYKC---PHCDHCFT 103 (274)
Q Consensus 27 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C---~~C~~~f~ 103 (274)
..|.|.+|...| .+...|.+|.- .---...|+|++|+|+|..-.+|..|.++|.....--= +-=.+...
T Consensus 266 GdyiCqLCK~kY-eD~F~LAQHrC-------~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~ 337 (500)
T KOG3993|consen 266 GDYICQLCKEKY-EDAFALAQHRC-------PRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVE 337 (500)
T ss_pred HHHHHHHHHHhh-hhHHHHhhccC-------CeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhh
Confidence 358899999999 99999999975 33334568999999999999999999999854321100 00000011
Q ss_pred ChhHHHHHHh--hhcCCCCccCCCCCCccccHHHHHHHHHHHHH
Q psy4796 104 QKVVLQRHLL--THTGEKPFACHLCPYRASRKYYITAHLNSLLS 145 (274)
Q Consensus 104 ~~~~l~~H~~--~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 145 (274)
+....+.-.+ ....+..|.|..|+++|.....|+.|+.+++.
T Consensus 338 ~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 338 TRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred hhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 1111111110 01223469999999999999999999887654
No 16
>KOG3993|consensus
Probab=99.08 E-value=4e-11 Score=95.97 Aligned_cols=26 Identities=31% Similarity=0.705 Sum_probs=17.9
Q ss_pred cccCCCCCcccCChhHHHHHHhhhcC
Q psy4796 92 PYKCPHCDHCFTQKVVLQRHLLTHTG 117 (274)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 117 (274)
-|.|..|++.|.....|+.|+.+|..
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 57777777777777777777666543
No 17
>PHA00733 hypothetical protein
Probab=99.08 E-value=2.3e-10 Score=79.65 Aligned_cols=83 Identities=18% Similarity=0.303 Sum_probs=59.7
Q ss_pred ccCCcceecccccccccChHHHHHH--Hh---hcCCCCcccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCccccH
Q psy4796 59 TSAKLQFLCLFCSYVATARIAIKNH--LS---SHLGWKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRASRK 133 (274)
Q Consensus 59 h~~~~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 133 (274)
-..++++.|.+|...|.....|..+ +. .+.+.+||.|..|++.|.+...|..|++.+ ..+|.|+.|++.|...
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 3446677888888777766555544 11 223467888888888888888888888765 3468888888888888
Q ss_pred HHHHHHHHHH
Q psy4796 134 YYITAHLNSL 143 (274)
Q Consensus 134 ~~l~~H~~~~ 143 (274)
..|..|+...
T Consensus 113 ~sL~~H~~~~ 122 (128)
T PHA00733 113 DSTLDHVCKK 122 (128)
T ss_pred HHHHHHHHHh
Confidence 8888887763
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.94 E-value=5.7e-10 Score=63.78 Aligned_cols=43 Identities=16% Similarity=0.241 Sum_probs=39.4
Q ss_pred ccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhH
Q psy4796 192 KFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNL 236 (274)
Q Consensus 192 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 236 (274)
.|.|+.||+.|.....|..|+++|+ ++|.|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3899999999999999999999999 689999999999977665
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.87 E-value=1.6e-09 Score=53.02 Aligned_cols=25 Identities=36% Similarity=0.755 Sum_probs=18.2
Q ss_pred hHHHHHhhhCCCCceecCCCCccCC
Q psy4796 235 NLQTHLRIHKTEREYACGKCAYRTA 259 (274)
Q Consensus 235 ~l~~H~~~h~~~~~~~C~~C~~~f~ 259 (274)
+|.+|+++|++++||.|++|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3667777777777777777777765
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.69 E-value=1.1e-08 Score=49.97 Aligned_cols=26 Identities=38% Similarity=0.988 Sum_probs=23.6
Q ss_pred HHHHHHhhccCCCCcccCcCccccCC
Q psy4796 207 YIKTHVMTHTGDKPFACSYCDYTCNQ 232 (274)
Q Consensus 207 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 232 (274)
+|..|+++|++++||.|+.|++.|..
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 47899999999999999999999863
No 21
>PHA00616 hypothetical protein
Probab=98.64 E-value=9.7e-09 Score=55.80 Aligned_cols=33 Identities=12% Similarity=0.256 Sum_probs=21.9
Q ss_pred CcccCcCccccCCchhHHHHHhhhCCCCceecC
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRIHKTEREYACG 252 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 252 (274)
||+|+.||+.|..+++|.+|++.|++++++.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 466666666666666666666666666666554
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=98.55 E-value=1e-07 Score=55.83 Aligned_cols=51 Identities=31% Similarity=0.621 Sum_probs=36.7
Q ss_pred CcccCcCccccCCchhHHHHHhh-hCCC-CceecCCCCccCCChhHHHHHHhhhcC
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRI-HKTE-REYACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
.|.|+.|++ ..+...|..|... |..+ +.+.||+|...+. .+|.+|+...|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 477888888 4456778888765 5443 4588888887655 488888888775
No 23
>PHA00616 hypothetical protein
Probab=98.51 E-value=3.4e-08 Score=53.70 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=25.9
Q ss_pred ceecCCCCccCCChhHHHHHHhhhcCC
Q psy4796 248 EYACGKCAYRTAALPDLKLHLKNMHLY 274 (274)
Q Consensus 248 ~~~C~~C~~~f~~~~~l~~H~~~~H~~ 274 (274)
||+|+.||+.|.++++|.+|+++|||+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCC
Confidence 689999999999999999999999986
No 24
>PHA00732 hypothetical protein
Probab=98.50 E-value=7.8e-08 Score=60.61 Aligned_cols=48 Identities=25% Similarity=0.454 Sum_probs=36.6
Q ss_pred ccccCCCCccccCHHHHHHHHhh-ccCCCCcccCcCccccCCchhHHHHHhhhCC
Q psy4796 192 KFVCFACPYATQYACYIKTHVMT-HTGDKPFACSYCDYTCNQSSNLQTHLRIHKT 245 (274)
Q Consensus 192 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 245 (274)
+|.|..|++.|.....|..|++. |++ +.|+.|++.|. .|..|++.+.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---ChhhhhcccCC
Confidence 47788888888888888888874 543 57888888887 47778866554
No 25
>PHA00732 hypothetical protein
Probab=98.42 E-value=2.8e-07 Score=58.13 Aligned_cols=45 Identities=27% Similarity=0.490 Sum_probs=34.7
Q ss_pred CcccCcCccccCCchhHHHHHhh-hCCCCceecCCCCccCCChhHHHHHHhh
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRI-HKTEREYACGKCAYRTAALPDLKLHLKN 270 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 270 (274)
||.|..|++.|.+..+|+.|++. |.+ +.|+.|++.|. .+..|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhcc
Confidence 57888888888888888888874 543 57888888886 46677654
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.17 E-value=4.6e-06 Score=48.80 Aligned_cols=50 Identities=24% Similarity=0.450 Sum_probs=39.4
Q ss_pred ccccCCCCccccCHHHHHHHHh-hccCC-CCcccCcCccccCCchhHHHHHhhhC
Q psy4796 192 KFVCFACPYATQYACYIKTHVM-THTGD-KPFACSYCDYTCNQSSNLQTHLRIHK 244 (274)
Q Consensus 192 ~~~C~~C~~~f~~~~~l~~H~~-~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~ 244 (274)
.|.||.|++ ..+...|..|.. .|..+ +.+.|++|...+. .+|.+|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 489999999 455788999987 55543 5699999998755 48999998754
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.13 E-value=1.5e-06 Score=41.13 Aligned_cols=22 Identities=27% Similarity=0.640 Sum_probs=14.6
Q ss_pred eecCCCCccCCChhHHHHHHhh
Q psy4796 249 YACGKCAYRTAALPDLKLHLKN 270 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~~ 270 (274)
|.|++|++.|.+...|.+|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5666666666666666666665
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.12 E-value=2e-06 Score=41.17 Aligned_cols=24 Identities=21% Similarity=0.605 Sum_probs=16.3
Q ss_pred eecCCCCccCCChhHHHHHHhhhc
Q psy4796 249 YACGKCAYRTAALPDLKLHLKNMH 272 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~~~H 272 (274)
|.|++|++.|.+...|..|++.+|
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 567777777777777777777765
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.06 E-value=2.1e-06 Score=40.65 Aligned_cols=23 Identities=35% Similarity=0.807 Sum_probs=13.9
Q ss_pred cccCcCccccCCchhHHHHHhhh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIH 243 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h 243 (274)
|.|+.|++.|.++..|.+|++.|
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 45666666666666666666543
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=97.91 E-value=6.6e-06 Score=40.61 Aligned_cols=25 Identities=20% Similarity=0.534 Sum_probs=16.3
Q ss_pred ceecCCCCccCCChhHHHHHHhhhc
Q psy4796 248 EYACGKCAYRTAALPDLKLHLKNMH 272 (274)
Q Consensus 248 ~~~C~~C~~~f~~~~~l~~H~~~~H 272 (274)
+|.|..|++.|.+...|..|++.|+
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 4666666666666666666666555
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.82 E-value=1.2e-05 Score=53.85 Aligned_cols=23 Identities=17% Similarity=0.462 Sum_probs=11.9
Q ss_pred ceecCCCCccCCChhHHHHHHhh
Q psy4796 248 EYACGKCAYRTAALPDLKLHLKN 270 (274)
Q Consensus 248 ~~~C~~C~~~f~~~~~l~~H~~~ 270 (274)
.+.|.+|++.|.+...|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 35555555555555555555553
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.77 E-value=1.7e-05 Score=37.78 Aligned_cols=23 Identities=35% Similarity=0.816 Sum_probs=13.7
Q ss_pred cccCcCccccCCchhHHHHHhhh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIH 243 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h 243 (274)
|.|++|++.|.+...|+.|+..|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 45666666666666666666654
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.72 E-value=1.8e-05 Score=39.04 Aligned_cols=25 Identities=40% Similarity=0.686 Sum_probs=17.0
Q ss_pred CcccCcCccccCCchhHHHHHhhhC
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRIHK 244 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~h~ 244 (274)
+|.|..|++.|.+...|..|++.|.
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 4667777777777777777776654
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.70 E-value=2.3e-05 Score=52.55 Aligned_cols=73 Identities=19% Similarity=0.440 Sum_probs=17.5
Q ss_pred eeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHhhcCCCCcccCCCCCcccCChhHHH
Q psy4796 30 TCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCFTQKVVLQ 109 (274)
Q Consensus 30 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 109 (274)
+|..|+..| .+...|..|+.. .|.-..+ ....+.....+..+..... ...+.|..|++.|.+...|.
T Consensus 1 ~C~~C~~~f-~~~~~l~~H~~~------~H~~~~~-----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESF-SSVDDLLQHMKK------KHGFDIP-----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Ccccccccc-cccccccccccc------ccccccc-----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHH
Confidence 477888888 778888888763 3332211 1111112223333332211 12577777777777777777
Q ss_pred HHHhhh
Q psy4796 110 RHLLTH 115 (274)
Q Consensus 110 ~H~~~h 115 (274)
.|++.+
T Consensus 68 ~Hm~~~ 73 (100)
T PF12756_consen 68 EHMRSK 73 (100)
T ss_dssp HHHHHT
T ss_pred HHHcCc
Confidence 777754
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.67 E-value=1.6e-05 Score=62.11 Aligned_cols=53 Identities=30% Similarity=0.674 Sum_probs=42.0
Q ss_pred CCCcccCc--CccccCCchhHHHHHhh-hC------------------CCCceecCCCCccCCChhHHHHHHhh
Q psy4796 218 DKPFACSY--CDYTCNQSSNLQTHLRI-HK------------------TEREYACGKCAYRTAALPDLKLHLKN 270 (274)
Q Consensus 218 ~~~~~C~~--C~~~f~~~~~l~~H~~~-h~------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 270 (274)
+|||.|++ |.+.|.....|+.|+.. |- ..|||.|.+|+|.+.+...|+-|+.-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 58888866 88888888888888754 31 34789999999999999999888543
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.59 E-value=5e-05 Score=36.19 Aligned_cols=24 Identities=46% Similarity=0.876 Sum_probs=18.0
Q ss_pred eecCCCCccCCChhHHHHHHhhhcC
Q psy4796 249 YACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
|.|+.|+.... ...|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 67888888887 8888888888875
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.57 E-value=2.2e-05 Score=61.43 Aligned_cols=24 Identities=17% Similarity=0.357 Sum_probs=17.5
Q ss_pred Ccceeccc--ccccccChHHHHHHHh
Q psy4796 62 KLQFLCLF--CSYVATARIAIKNHLS 85 (274)
Q Consensus 62 ~~~~~C~~--C~~~f~~~~~l~~H~~ 85 (274)
+++|+|++ |+++|.++..|.-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhh
Confidence 47777777 7777777777777764
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.20 E-value=0.00031 Score=33.88 Aligned_cols=20 Identities=25% Similarity=0.514 Sum_probs=8.6
Q ss_pred ecCCCCccCCChhHHHHHHh
Q psy4796 250 ACGKCAYRTAALPDLKLHLK 269 (274)
Q Consensus 250 ~C~~C~~~f~~~~~l~~H~~ 269 (274)
.|+.|++.|.+...|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 34444444444444444443
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.19 E-value=0.00033 Score=39.09 Aligned_cols=28 Identities=36% Similarity=0.680 Sum_probs=10.3
Q ss_pred CCCcccCcCccccCCchhHHHHHhhhCC
Q psy4796 218 DKPFACSYCDYTCNQSSNLQTHLRIHKT 245 (274)
Q Consensus 218 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 245 (274)
+.|-.|++|+..+.+..+|++|+.++++
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 3344444444444444444444444333
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.15 E-value=0.00032 Score=33.83 Aligned_cols=23 Identities=30% Similarity=0.720 Sum_probs=21.0
Q ss_pred cccCcCccccCCchhHHHHHhhh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIH 243 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h 243 (274)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 68999999999999999999865
No 41
>PRK04860 hypothetical protein; Provisional
Probab=97.05 E-value=0.00046 Score=49.97 Aligned_cols=37 Identities=24% Similarity=0.665 Sum_probs=23.0
Q ss_pred CcccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCCC
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTAA 260 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 260 (274)
+|.|. |+. ....+++|.++|.++++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 46665 665 44556666666666666666666666543
No 42
>KOG2231|consensus
Probab=97.04 E-value=0.0021 Score=56.52 Aligned_cols=48 Identities=21% Similarity=0.313 Sum_probs=31.7
Q ss_pred cccCCCCccccCHHHHHHHHhhccCCCCcccCcCc------cccCCchhHHHHHhhhC
Q psy4796 193 FVCFACPYATQYACYIKTHVMTHTGDKPFACSYCD------YTCNQSSNLQTHLRIHK 244 (274)
Q Consensus 193 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~------~~f~~~~~l~~H~~~h~ 244 (274)
-.|..|...|-....|..|++.++ |.|..|. ..|...+.|..|.+.++
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 457777777777777777777665 4555553 45556667777776655
No 43
>KOG1146|consensus
Probab=97.03 E-value=0.00062 Score=63.41 Aligned_cols=108 Identities=19% Similarity=0.324 Sum_probs=80.0
Q ss_pred eeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHhhcC--------------------
Q psy4796 29 VTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLSSHL-------------------- 88 (274)
Q Consensus 29 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~-------------------- 88 (274)
..|.-|+..+ .....+..|+.. .++..+.|+|+.|+..|.....|..||+..+
T Consensus 437 ~e~~~~e~~~-~s~r~~~~~t~~------L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg 509 (1406)
T KOG1146|consen 437 VELTKAEPLL-ESKRSLEGQTVV------LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARG 509 (1406)
T ss_pred ccccchhhhh-hhhcccccceee------eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcccccccccc
Confidence 4456666666 666666666553 6666778888888888888888888887621
Q ss_pred -----CCCcccCCCCCcccCChhHHHHHHhh--hcC-----------------------------------------CCC
Q psy4796 89 -----GWKPYKCPHCDHCFTQKVVLQRHLLT--HTG-----------------------------------------EKP 120 (274)
Q Consensus 89 -----~~~~~~C~~C~~~f~~~~~l~~H~~~--h~~-----------------------------------------~~~ 120 (274)
+.++|.|..|...+.++.+|-+|++. |.. ...
T Consensus 510 ~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~ 589 (1406)
T KOG1146|consen 510 EVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPS 589 (1406)
T ss_pred ccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCC
Confidence 23578999999999999999999753 111 122
Q ss_pred ccCCCCCCccccHHHHHHHHHHH
Q psy4796 121 FACHLCPYRASRKYYITAHLNSL 143 (274)
Q Consensus 121 ~~C~~C~~~f~~~~~l~~H~~~~ 143 (274)
|.|..|+++..-..+|+.|+...
T Consensus 590 ~~C~vc~yetniarnlrihmtss 612 (1406)
T KOG1146|consen 590 WRCEVCSYETNIARNLRIHMTAS 612 (1406)
T ss_pred cchhhhcchhhhhhccccccccC
Confidence 88999999998888899888653
No 44
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.03 E-value=0.00051 Score=38.33 Aligned_cols=37 Identities=19% Similarity=0.348 Sum_probs=23.9
Q ss_pred HHHHhhh-CCCCceecCCCCccCCChhHHHHHHhhhcC
Q psy4796 237 QTHLRIH-KTEREYACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 237 ~~H~~~h-~~~~~~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
..+.+.+ ..+.|-.||+|+..+....+|.+|+...|+
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred hhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 4444443 456789999999999999999999998886
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.94 E-value=0.00044 Score=33.20 Aligned_cols=18 Identities=28% Similarity=0.781 Sum_probs=7.5
Q ss_pred cCcCccccCCchhHHHHH
Q psy4796 223 CSYCDYTCNQSSNLQTHL 240 (274)
Q Consensus 223 C~~C~~~f~~~~~l~~H~ 240 (274)
|.+|++.|.+...|+.|+
T Consensus 3 C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHL 20 (25)
T ss_dssp ETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHHH
Confidence 444444444444444443
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.92 E-value=0.00061 Score=32.67 Aligned_cols=23 Identities=22% Similarity=0.514 Sum_probs=21.0
Q ss_pred eecCCCCccCCChhHHHHHHhhh
Q psy4796 249 YACGKCAYRTAALPDLKLHLKNM 271 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~~~ 271 (274)
|.|.+|++.|.+...|..|++.+
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 68999999999999999999754
No 47
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.60 E-value=0.0011 Score=31.37 Aligned_cols=23 Identities=39% Similarity=0.933 Sum_probs=13.7
Q ss_pred cccCcCccccCCchhHHHHHhhhC
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIHK 244 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h~ 244 (274)
|.|+.|+.... ...|.+|++.|+
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 56777776666 667777776643
No 48
>KOG2785|consensus
Probab=96.55 E-value=0.01 Score=48.25 Aligned_cols=51 Identities=18% Similarity=0.363 Sum_probs=37.6
Q ss_pred ccccCCCCccccCHHHHHHHHhhccCC-----------------------CCcccCcCc---cccCCchhHHHHHhh
Q psy4796 192 KFVCFACPYATQYACYIKTHVMTHTGD-----------------------KPFACSYCD---YTCNQSSNLQTHLRI 242 (274)
Q Consensus 192 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 242 (274)
|-.|-.|+..+.+......||..+++- .-+.|..|. +.|.+..+.++||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 466888888888888888888877652 236677777 777777777777765
No 49
>PRK04860 hypothetical protein; Provisional
Probab=96.49 E-value=0.0014 Score=47.58 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=34.6
Q ss_pred CccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCch
Q psy4796 191 KKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSS 234 (274)
Q Consensus 191 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 234 (274)
-+|.|. |+. ....+..|.++|+++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 369998 997 6677899999999999999999999887654
No 50
>KOG2785|consensus
Probab=96.46 E-value=0.0085 Score=48.72 Aligned_cols=52 Identities=17% Similarity=0.383 Sum_probs=43.6
Q ss_pred CCcccCcCccccCCchhHHHHHhhhCCCC-----------------------ceecCCCC---ccCCChhHHHHHHhh
Q psy4796 219 KPFACSYCDYTCNQSSNLQTHLRIHKTER-----------------------EYACGKCA---YRTAALPDLKLHLKN 270 (274)
Q Consensus 219 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-----------------------~~~C~~C~---~~f~~~~~l~~H~~~ 270 (274)
-|-.|..|++.+.+...-..||..+++-. -+.|-.|. +.|.+...+..||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 35789999999999999999998876531 27888888 999999999999964
No 51
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.30 E-value=0.0012 Score=32.34 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=12.9
Q ss_pred eecCCCCccCCChhHHHHHHh
Q psy4796 249 YACGKCAYRTAALPDLKLHLK 269 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~ 269 (274)
|.|.+|++.|.+...+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666666666654
No 52
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.26 E-value=0.008 Score=48.09 Aligned_cols=72 Identities=25% Similarity=0.476 Sum_probs=53.8
Q ss_pred ccCCCCccccCHHHHHHHHhhccCCCCcccCcCcc-------ccCCchhHHHHHhhhCCCCceecCC--CC----ccCCC
Q psy4796 194 VCFACPYATQYACYIKTHVMTHTGDKPFACSYCDY-------TCNQSSNLQTHLRIHKTEREYACGK--CA----YRTAA 260 (274)
Q Consensus 194 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~-------~f~~~~~l~~H~~~h~~~~~~~C~~--C~----~~f~~ 260 (274)
.|..|...|-+...|.+|++.-+. .|-+|++ -|.+..+|.+|.+. .-|.|.+ |. ..|++
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~~~k~~vf~~ 293 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCRVGKCYVFPY 293 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEecCcEEEecc
Confidence 699999999999999999986552 3555543 45666777777653 3377755 54 37999
Q ss_pred hhHHHHHHhhhcC
Q psy4796 261 LPDLKLHLKNMHL 273 (274)
Q Consensus 261 ~~~l~~H~~~~H~ 273 (274)
...|..|+-+-|+
T Consensus 294 ~~el~~h~~~~h~ 306 (493)
T COG5236 294 HTELLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999988776
No 53
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.93 E-value=0.0033 Score=30.75 Aligned_cols=21 Identities=29% Similarity=0.423 Sum_probs=13.2
Q ss_pred cccCCCCccccCHHHHHHHHh
Q psy4796 193 FVCFACPYATQYACYIKTHVM 213 (274)
Q Consensus 193 ~~C~~C~~~f~~~~~l~~H~~ 213 (274)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 556666666666666666654
No 54
>KOG2482|consensus
Probab=95.90 E-value=0.067 Score=42.95 Aligned_cols=78 Identities=18% Similarity=0.244 Sum_probs=46.4
Q ss_pred ccCCCCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCc
Q psy4796 121 FACHLCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPY 200 (274)
Q Consensus 121 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~ 200 (274)
..|-.|.....+...+..||+..|.-.+.+- ...+. -.|-. .-.++. -...+.....|..|.-
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki----~sd~~-----Ln~Yq-rvrviN-------yiRkq~~~~~c~~cd~ 342 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKI----QSDYS-----LNFYQ-RVRVIN-------YIRKQKKKSRCAECDL 342 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhh----ccccc-----cchhh-hhhHHH-------HHHHHhhccccccccc
Confidence 5899999999999999999998776443322 11110 00000 000100 1112233456788888
Q ss_pred cccCHHHHHHHHhhc
Q psy4796 201 ATQYACYIKTHVMTH 215 (274)
Q Consensus 201 ~f~~~~~l~~H~~~h 215 (274)
.|-....|..|+..+
T Consensus 343 ~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 343 SFWKEPGLLIHMVED 357 (423)
T ss_pred cccCcchhhhhcccc
Confidence 888888888888643
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.89 E-value=0.0049 Score=29.47 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=11.3
Q ss_pred eeeccccCCcchhhHHHHHhhh
Q psy4796 29 VTCLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 29 ~~C~~C~~~f~~~~~~l~~H~~ 50 (274)
..|+.||+.| ..+.|..|+.
T Consensus 3 ~~C~~CgR~F--~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF--NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE--CHHHHHHHHH
Confidence 3456666666 5555555554
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.56 E-value=0.01 Score=28.32 Aligned_cols=19 Identities=26% Similarity=0.434 Sum_probs=11.1
Q ss_pred ecCCCCccCCChhHHHHHHh
Q psy4796 250 ACGKCAYRTAALPDLKLHLK 269 (274)
Q Consensus 250 ~C~~C~~~f~~~~~l~~H~~ 269 (274)
.|+.||..| ....|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 4555666654
No 57
>KOG1146|consensus
Probab=95.56 E-value=0.009 Score=56.12 Aligned_cols=168 Identities=20% Similarity=0.301 Sum_probs=104.7
Q ss_pred cccccccccChHHHHHHHh-hcCCCCcccCCCCCcccCChhHHHHHHhhhcC-------------------------CCC
Q psy4796 67 CLFCSYVATARIAIKNHLS-SHLGWKPYKCPHCDHCFTQKVVLQRHLLTHTG-------------------------EKP 120 (274)
Q Consensus 67 C~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-------------------------~~~ 120 (274)
|..|+..+.....+.-|+. .+...+.++|+.|+..|+....|..||+..+. .++
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p 518 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP 518 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc
Confidence 3444444444444433332 23445789999999999999999999987221 366
Q ss_pred ccCCCCCCccccHHHHHHHHHHHHHHHHHHhHh--hcC----CCc-cCCCCCCCCCCChhhhhhhccCCCCCc-ccCCCc
Q psy4796 121 FACHLCPYRASRKYYITAHLNSLLSALLLQHFL--ASQ----PRR-KCVHCSEPISSDMSEIIEHCLVCPNAT-RTDKKK 192 (274)
Q Consensus 121 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~--~~~----~~~-~c~~c~~~~~~~~~~l~~h~~~~~~~~-~~~~~~ 192 (274)
|.|..|..++..+..|..|++............ .+. .+- .+..+...-+...+. -.. ....-.
T Consensus 519 ~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~a---------gs~~pktkP~ 589 (1406)
T KOG1146|consen 519 YPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSA---------GSSGPKTKPS 589 (1406)
T ss_pred ccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCC---------CCCCCCCCCC
Confidence 899999999999999999998644322211100 110 000 021222111110000 011 122335
Q ss_pred cccCCCCccccCHHHHHHHHh-hccCCCCcccCcCccccCCchhHHHHHhhh
Q psy4796 193 FVCFACPYATQYACYIKTHVM-THTGDKPFACSYCDYTCNQSSNLQTHLRIH 243 (274)
Q Consensus 193 ~~C~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 243 (274)
+.|..|+..-.-..+|+.|+. .++...|..+..+.-.+.....+..+.+.+
T Consensus 590 ~~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 590 WRCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred cchhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCCCC
Confidence 889999999999999999987 556566678888888887777776666665
No 58
>KOG2231|consensus
Probab=95.43 E-value=0.027 Score=49.86 Aligned_cols=45 Identities=24% Similarity=0.408 Sum_probs=29.2
Q ss_pred cCCCCCcccCChhHHHHHHhhhcCCCCccCCCC------CCccccHHHHHHHHHH
Q psy4796 94 KCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLC------PYRASRKYYITAHLNS 142 (274)
Q Consensus 94 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~ 142 (274)
.|..|...|-....|.+|++.++ |.|..| +.-|.....|..|.+.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~ 234 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK 234 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh
Confidence 57777777777777777777654 445555 2345666667777655
No 59
>KOG2482|consensus
Probab=95.36 E-value=0.021 Score=45.65 Aligned_cols=90 Identities=17% Similarity=0.332 Sum_probs=63.3
Q ss_pred CeeeccccCCcchhhHHHHHhhhcccccc------cc-------cc--CCcceecccccccccChHHHHHHHhhc--CC-
Q psy4796 28 DVTCLHCSLTTPCVMKDMIRHGRLCEFNS------VV-------TS--AKLQFLCLFCSYVATARIAIKNHLSSH--LG- 89 (274)
Q Consensus 28 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~------~~-------h~--~~~~~~C~~C~~~f~~~~~l~~H~~~h--~~- 89 (274)
-..|..|+..+..++.....|+...++-. -+ |. .-..+.|-.|.+.|.++..|+.||+.. ..
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 36799998888677788888876433210 00 00 111377999999999999999999752 10
Q ss_pred ---------------------------------------------------CCc--ccCCCCCcccCChhHHHHHHhhhc
Q psy4796 90 ---------------------------------------------------WKP--YKCPHCDHCFTQKVVLQRHLLTHT 116 (274)
Q Consensus 90 ---------------------------------------------------~~~--~~C~~C~~~f~~~~~l~~H~~~h~ 116 (274)
..+ .+|-.|.....+...|..||...+
T Consensus 224 nPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 224 NPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 011 489999999999999999998644
Q ss_pred C
Q psy4796 117 G 117 (274)
Q Consensus 117 ~ 117 (274)
.
T Consensus 304 e 304 (423)
T KOG2482|consen 304 E 304 (423)
T ss_pred H
Confidence 3
No 60
>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=95.15 E-value=0.036 Score=37.67 Aligned_cols=85 Identities=22% Similarity=0.365 Sum_probs=48.2
Q ss_pred cCCCccccCCCCccccCHHHHHHHHh-hccCCCCcccCcCccccCCchhHH---HHHhh-hCCC---------Cceec--
Q psy4796 188 TDKKKFVCFACPYATQYACYIKTHVM-THTGDKPFACSYCDYTCNQSSNLQ---THLRI-HKTE---------REYAC-- 251 (274)
Q Consensus 188 ~~~~~~~C~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~~l~---~H~~~-h~~~---------~~~~C-- 251 (274)
...+...|..|+..... +.+..|++ .|+..+...-..=...+.....|. ..+.. ..+. ..|.|
T Consensus 7 ~~~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~ 85 (109)
T PF12013_consen 7 PEYRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQC 85 (109)
T ss_pred CcCCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeec
Confidence 34456789999988876 78899988 444321110000000000000000 00000 0000 23899
Q ss_pred --CCCCccCCChhHHHHHHhhhcC
Q psy4796 252 --GKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 252 --~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
+.|++.+.+...|.+|.+.+||
T Consensus 86 ~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 86 DPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCCCcEeccHHHHHHHHHHhcC
Confidence 9999999999999999999997
No 61
>KOG2893|consensus
Probab=95.11 E-value=0.0056 Score=46.27 Aligned_cols=42 Identities=21% Similarity=0.340 Sum_probs=24.7
Q ss_pred eeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHH
Q psy4796 30 TCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNH 83 (274)
Q Consensus 30 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H 83 (274)
.|+.|++.| .+...|+.|++ .+-|+|.+|-++..+--.|.+|
T Consensus 12 wcwycnref-ddekiliqhqk-----------akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREF-DDEKILIQHQK-----------AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeeccccc-chhhhhhhhhh-----------hccceeeeehhhhccCCCceee
Confidence 366777777 66666666666 3446666666554444444433
No 62
>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=94.93 E-value=0.018 Score=29.67 Aligned_cols=24 Identities=21% Similarity=0.791 Sum_probs=13.6
Q ss_pred cccCcCccccCCchhHHHHHhhhCCCCceecCCCCc
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAY 256 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 256 (274)
|.|..||..+.... .+..||+|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 56666665554322 5566666664
No 63
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.76 E-value=0.055 Score=43.49 Aligned_cols=19 Identities=26% Similarity=0.616 Sum_probs=12.0
Q ss_pred eccccCCcchhhHHHHHhhh
Q psy4796 31 CLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 31 C~~C~~~f~~~~~~l~~H~~ 50 (274)
|..|+..| .+.++|..|++
T Consensus 223 C~FC~~~F-YdDDEL~~HcR 241 (493)
T COG5236 223 CIFCKIYF-YDDDELRRHCR 241 (493)
T ss_pred hhhcccee-cChHHHHHHHH
Confidence 66666666 66666666665
No 64
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.40 E-value=0.037 Score=28.77 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=16.5
Q ss_pred ceecCCCCccCCChhHHHHHHh
Q psy4796 248 EYACGKCAYRTAALPDLKLHLK 269 (274)
Q Consensus 248 ~~~C~~C~~~f~~~~~l~~H~~ 269 (274)
+|.|.+|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4678888888877777777764
No 65
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.72 E-value=0.047 Score=28.34 Aligned_cols=23 Identities=26% Similarity=0.611 Sum_probs=16.3
Q ss_pred CcccCcCccccCCchhHHHHHhh
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRI 242 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~ 242 (274)
+|.|..|+..|.+..++..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777777777777654
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.61 E-value=0.028 Score=31.98 Aligned_cols=26 Identities=15% Similarity=0.470 Sum_probs=15.3
Q ss_pred CCCCcccCcCccccCCchhHHHHHhh
Q psy4796 217 GDKPFACSYCDYTCNQSSNLQTHLRI 242 (274)
Q Consensus 217 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 242 (274)
|+..+.|+.||..|....++.+|+..
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhH
Confidence 44456666666666666666666543
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.00 E-value=0.029 Score=48.13 Aligned_cols=151 Identities=25% Similarity=0.374 Sum_probs=85.2
Q ss_pred cccCCCCCcccCChhHHHHHHh--hhcCC--CCccCC--CCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCC--C
Q psy4796 92 PYKCPHCDHCFTQKVVLQRHLL--THTGE--KPFACH--LCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCV--H 163 (274)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~--~ 163 (274)
++.|..|...|.....+..|.+ .|..+ +++.|+ .|++.|.....+..|...+ ....+..+. .
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~ 358 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH----------TSISPAKEKLLN 358 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc----------cCCCcccccccc
Confidence 4666777777777777777776 56666 677777 5777776666666665542 222222221 1
Q ss_pred CCCCCCCChh----hhhhhccCCCCCcccCCCcccc--CCCCccccCHHHHHHHHhhccCCC--CcccCcCccccCCchh
Q psy4796 164 CSEPISSDMS----EIIEHCLVCPNATRTDKKKFVC--FACPYATQYACYIKTHVMTHTGDK--PFACSYCDYTCNQSSN 235 (274)
Q Consensus 164 c~~~~~~~~~----~l~~h~~~~~~~~~~~~~~~~C--~~C~~~f~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~ 235 (274)
+...+..... ..... .........+.+ ..|...+.....+..|...+.... .+.+..|...|.....
T Consensus 359 ~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 433 (467)
T COG5048 359 SSSKFSPLLNNEPPQSLQQ-----YKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYN 433 (467)
T ss_pred CccccccccCCCCccchhh-----ccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCccc
Confidence 2222221000 00110 112222233333 235566666666667766666555 3556778888888888
Q ss_pred HHHHHhhhCCCCceecCCCCcc
Q psy4796 236 LQTHLRIHKTEREYACGKCAYR 257 (274)
Q Consensus 236 l~~H~~~h~~~~~~~C~~C~~~ 257 (274)
+..|++.|....++.|..++..
T Consensus 434 ~~~~~~~~~~~~~~~~~~~~~~ 455 (467)
T COG5048 434 LIPHKKIHTNHAPLLCSILKSF 455 (467)
T ss_pred ccccccccccCCceeecccccc
Confidence 8888888877776666555533
No 68
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.82 E-value=0.32 Score=32.78 Aligned_cols=54 Identities=17% Similarity=0.403 Sum_probs=31.4
Q ss_pred ccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHHHhhhCCCCceecCCCC
Q psy4796 194 VCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCA 255 (274)
Q Consensus 194 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 255 (274)
.|-.|+..|....... ...-.....|+|+.|...|=..-+...|...|. |+-|.
T Consensus 57 ~C~~C~~~f~~~~~~~--~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~------CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSP--FDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC------CPGCI 110 (112)
T ss_pred cccCcCCCCCCccccc--ccccccccceeCCCCCCccccccchhhhhhccC------CcCCC
Confidence 4777777776542110 000112335788888888777777777776664 66554
No 69
>KOG2893|consensus
Probab=92.80 E-value=0.028 Score=42.65 Aligned_cols=47 Identities=21% Similarity=0.471 Sum_probs=35.7
Q ss_pred ccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHH-HhhhC
Q psy4796 194 VCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTH-LRIHK 244 (274)
Q Consensus 194 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H-~~~h~ 244 (274)
.|..|++.|.+..-|..|++..+ |.|.+|.+..-+-..|..| +++|.
T Consensus 12 wcwycnrefddekiliqhqkakh----fkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceeehhhhhh
Confidence 58999999999988888876544 8899998776666667666 45553
No 70
>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=92.22 E-value=0.093 Score=27.15 Aligned_cols=24 Identities=25% Similarity=0.682 Sum_probs=14.2
Q ss_pred cccCcCccccCCchhHHHHHhhhCCCCceecCCCCc
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAY 256 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 256 (274)
|.|..||..+... +.|..||+|+.
T Consensus 3 ~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECC------------cCCCcCcCCCC
Confidence 6677777654432 14556777775
No 71
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.06 E-value=0.14 Score=43.94 Aligned_cols=153 Identities=21% Similarity=0.308 Sum_probs=73.8
Q ss_pred ceecccccccccChHHHHHHHh--hcCCC--CcccCC--CCCcccCChhHHHHHHhhhcCCCCccCCCC--CCccccHHH
Q psy4796 64 QFLCLFCSYVATARIAIKNHLS--SHLGW--KPYKCP--HCDHCFTQKVVLQRHLLTHTGEKPFACHLC--PYRASRKYY 135 (274)
Q Consensus 64 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C--~~~f~~~~~ 135 (274)
++.|..|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...|....++.+..- ...+.....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLN 368 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccccC
Confidence 4555555555555555555555 45555 555565 466666666666666555555544443222 222211111
Q ss_pred HHHHHHHHHHHHHHHhHhhcCCCccCC--CCCCCCCCChhhhhhhccCCCCCcccCCC--ccccCCCCccccCHHHHHHH
Q psy4796 136 ITAHLNSLLSALLLQHFLASQPRRKCV--HCSEPISSDMSEIIEHCLVCPNATRTDKK--KFVCFACPYATQYACYIKTH 211 (274)
Q Consensus 136 l~~H~~~~~~~~~~~~~~~~~~~~~c~--~c~~~~~~~~~~l~~h~~~~~~~~~~~~~--~~~C~~C~~~f~~~~~l~~H 211 (274)
-..+..... ...........+. .|...+.. ...+..+ ...+.... .+.+..|...+.....+..|
T Consensus 369 ~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (467)
T COG5048 369 NEPPQSLQQ-----YKDLKNDKKSETLSNSCIRNFKR-DSNLSLH-----IITHLSFRPYNCKNPPCSKSFNRHYNLIPH 437 (467)
T ss_pred CCCccchhh-----ccCccCCccccccccchhhhhcc-ccccccc-----cccccccCCcCCCCCcchhhccCccccccc
Confidence 000000000 0000111111111 12222222 2222222 33333333 46678899999999999999
Q ss_pred HhhccCCCCcccCcCc
Q psy4796 212 VMTHTGDKPFACSYCD 227 (274)
Q Consensus 212 ~~~h~~~~~~~C~~C~ 227 (274)
.+.+....++.|..++
T Consensus 438 ~~~~~~~~~~~~~~~~ 453 (467)
T COG5048 438 KKIHTNHAPLLCSILK 453 (467)
T ss_pred ccccccCCceeecccc
Confidence 9988877776665544
No 72
>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=91.51 E-value=0.12 Score=34.80 Aligned_cols=14 Identities=21% Similarity=0.636 Sum_probs=6.9
Q ss_pred CCcccCcCccccCC
Q psy4796 219 KPFACSYCDYTCNQ 232 (274)
Q Consensus 219 ~~~~C~~C~~~f~~ 232 (274)
.|..|+.||..|.-
T Consensus 25 ~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 25 DPIVCPKCGTEFPP 38 (108)
T ss_pred CCccCCCCCCccCc
Confidence 44455555555443
No 73
>KOG4173|consensus
Probab=91.08 E-value=0.075 Score=39.44 Aligned_cols=47 Identities=19% Similarity=0.468 Sum_probs=24.2
Q ss_pred ccCCCCccccCHHHHHHHHhhcc----------CCCCccc--CcCccccCCchhHHHHH
Q psy4796 194 VCFACPYATQYACYIKTHVMTHT----------GDKPFAC--SYCDYTCNQSSNLQTHL 240 (274)
Q Consensus 194 ~C~~C~~~f~~~~~l~~H~~~h~----------~~~~~~C--~~C~~~f~~~~~l~~H~ 240 (274)
.|.+|.+.|.+...|..|+...+ |.-.|+| ..|+..|....+.+.|+
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 45666666666666666654222 2233555 23555555555555554
No 74
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.97 E-value=0.88 Score=30.72 Aligned_cols=50 Identities=22% Similarity=0.430 Sum_probs=33.6
Q ss_pred ccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhcc
Q psy4796 159 RKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHT 216 (274)
Q Consensus 159 ~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 216 (274)
..|-.|...|...... . .........|.|+.|...|-..-....|...|.
T Consensus 56 ~~C~~C~~~f~~~~~~-~-------~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVS-P-------FDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CcccCcCCCCCCcccc-c-------ccccccccceeCCCCCCccccccchhhhhhccC
Confidence 3488888888752110 0 011234557999999999998888888887775
No 75
>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=90.97 E-value=0.23 Score=36.22 Aligned_cols=36 Identities=14% Similarity=0.324 Sum_probs=27.1
Q ss_pred cCCCCcccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCCC
Q psy4796 216 TGDKPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTAA 260 (274)
Q Consensus 216 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 260 (274)
....-|.|+.|+..|+...++. ..|.||.||.....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 3456688999999888888774 36899999986543
No 76
>PHA00626 hypothetical protein
Probab=90.94 E-value=0.14 Score=29.28 Aligned_cols=17 Identities=24% Similarity=0.589 Sum_probs=11.5
Q ss_pred CCCccccCCCCccccCH
Q psy4796 189 DKKKFVCFACPYATQYA 205 (274)
Q Consensus 189 ~~~~~~C~~C~~~f~~~ 205 (274)
....|.|+.||..|+..
T Consensus 20 ~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 20 WSDDYVCCDCGYNDSKD 36 (59)
T ss_pred cCcceEcCCCCCeechh
Confidence 35567777777777643
No 77
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.75 E-value=0.36 Score=28.11 Aligned_cols=33 Identities=27% Similarity=0.675 Sum_probs=17.0
Q ss_pred CccccCCCCccccCHHHHHHHHhhccCCCCcccCcCcc
Q psy4796 191 KKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDY 228 (274)
Q Consensus 191 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 228 (274)
..|.|+.||.....+..-- -.-..+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~~C-----Rk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKC-----RKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhhH-----HHcCCceECCCcCc
Confidence 3477888886544332111 11134577777663
No 78
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.66 E-value=0.097 Score=29.86 Aligned_cols=31 Identities=19% Similarity=0.237 Sum_probs=20.5
Q ss_pred ccCCCccccCCCCccccCHHHHHHHHhhccC
Q psy4796 187 RTDKKKFVCFACPYATQYACYIKTHVMTHTG 217 (274)
Q Consensus 187 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 217 (274)
..++.-+.|+-||..|+.......|...-++
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3455566777777777777777777764443
No 79
>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=90.33 E-value=0.21 Score=24.05 Aligned_cols=10 Identities=30% Similarity=0.849 Sum_probs=5.7
Q ss_pred ecCCCCccCC
Q psy4796 250 ACGKCAYRTA 259 (274)
Q Consensus 250 ~C~~C~~~f~ 259 (274)
.|+.||+.|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666553
No 80
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.74 E-value=0.3 Score=36.31 Aligned_cols=35 Identities=14% Similarity=0.431 Sum_probs=24.6
Q ss_pred CCCCcccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCCC
Q psy4796 217 GDKPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTAA 260 (274)
Q Consensus 217 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 260 (274)
....|.|+.|+..|+...++. ..|.||.||.....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 345688888888888777652 35888888875543
No 81
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=89.52 E-value=0.77 Score=31.10 Aligned_cols=25 Identities=20% Similarity=0.612 Sum_probs=22.3
Q ss_pred ccc----CcCccccCCchhHHHHHhhhCC
Q psy4796 221 FAC----SYCDYTCNQSSNLQTHLRIHKT 245 (274)
Q Consensus 221 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 245 (274)
|.| ..|+..+.+...+.+|++.+++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999988664
No 82
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.43 E-value=0.26 Score=26.10 Aligned_cols=11 Identities=36% Similarity=0.761 Sum_probs=5.8
Q ss_pred ceecCCCCccC
Q psy4796 248 EYACGKCAYRT 258 (274)
Q Consensus 248 ~~~C~~C~~~f 258 (274)
...|+.|+..|
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 35555555544
No 83
>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=89.03 E-value=0.15 Score=38.88 Aligned_cols=28 Identities=18% Similarity=0.261 Sum_probs=17.0
Q ss_pred CceecCCCCccCCChhHHHHHHhhhcCC
Q psy4796 247 REYACGKCAYRTAALPDLKLHLKNMHLY 274 (274)
Q Consensus 247 ~~~~C~~C~~~f~~~~~l~~H~~~~H~~ 274 (274)
..|.|++|+|.|.-..-+.+||...|+|
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 3477777777777777777777766653
No 84
>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=88.86 E-value=0.2 Score=38.76 Aligned_cols=97 Identities=20% Similarity=0.379 Sum_probs=54.3
Q ss_pred hhcCCCCccCCCCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCCCCCChhhhhhhccCCCCCcccCCCcc
Q psy4796 114 THTGEKPFACHLCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKF 193 (274)
Q Consensus 114 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~ 193 (274)
+.++.+.|+|..|.. |.-...--.|+++ -.......|+|..|++. ..|
T Consensus 136 w~hGGrif~CsfC~~-flCEDDQFEHQAs--------CQvLe~E~~KC~SCNrl-----------------------Gq~ 183 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDN-FLCEDDQFEHQAS--------CQVLESETFKCQSCNRL-----------------------GQY 183 (314)
T ss_pred ccCCCeEEEeecCCC-eeeccchhhhhhh--------hhhhhcccccccccccc-----------------------cch
Confidence 456778899999965 4334444455544 22355667888777642 115
Q ss_pred ccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHHHhhh
Q psy4796 194 VCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTHLRIH 243 (274)
Q Consensus 194 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 243 (274)
.|-.|...|-.....+.=.+ -...+++.|+.|+.....-..|..-.+.|
T Consensus 184 sCLRCK~cfCddHvrrKg~k-y~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 184 SCLRCKICFCDDHVRRKGFK-YEKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred hhhheeeeehhhhhhhcccc-cccCCCCCCCCCCCcccccccceeeeecc
Confidence 55555555553322111111 12347788888887766655555544444
No 85
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.84 E-value=0.14 Score=39.44 Aligned_cols=24 Identities=21% Similarity=0.170 Sum_probs=17.1
Q ss_pred CCCeeeccccCCcchhhHHHHHhhh
Q psy4796 26 PADVTCLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~~l~~H~~ 50 (274)
++.+.||+|+..| .+..-.....+
T Consensus 3 ~k~~~CPvC~~~F-~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEF-KTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCee-eeeEEEcCCce
Confidence 4568899999998 66665555555
No 86
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.68 E-value=0.47 Score=34.17 Aligned_cols=38 Identities=16% Similarity=0.445 Sum_probs=24.4
Q ss_pred CCCCcccCcCccccCCchhHHHHHhhhCCCCceecCCCCccC
Q psy4796 217 GDKPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRT 258 (274)
Q Consensus 217 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 258 (274)
....|.|+.|+..|.....+.- . . ....|.||.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~-~--d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL-L--D-MDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh-c--C-CCCcEECCCCCCEE
Confidence 4456888888888886544322 0 1 23448888888765
No 87
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.45 E-value=0.72 Score=26.98 Aligned_cols=11 Identities=36% Similarity=0.757 Sum_probs=7.9
Q ss_pred CccccCCCCcc
Q psy4796 191 KKFVCFACPYA 201 (274)
Q Consensus 191 ~~~~C~~C~~~ 201 (274)
..|.|+.||..
T Consensus 24 ~~F~CPnCG~~ 34 (59)
T PRK14890 24 VKFLCPNCGEV 34 (59)
T ss_pred CEeeCCCCCCe
Confidence 34788888866
No 88
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.14 E-value=0.42 Score=25.21 Aligned_cols=11 Identities=18% Similarity=0.437 Sum_probs=5.1
Q ss_pred ccCCCCccccC
Q psy4796 194 VCFACPYATQY 204 (274)
Q Consensus 194 ~C~~C~~~f~~ 204 (274)
.|+.|+..|.-
T Consensus 4 ~CP~C~~~f~v 14 (37)
T PF13719_consen 4 TCPNCQTRFRV 14 (37)
T ss_pred ECCCCCceEEc
Confidence 34445444443
No 89
>KOG2186|consensus
Probab=87.73 E-value=0.32 Score=37.53 Aligned_cols=45 Identities=22% Similarity=0.559 Sum_probs=22.6
Q ss_pred eecccccccccChHHHHHHHhhcCCCCcccCCCCCcccCChhHHHHHH
Q psy4796 65 FLCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCFTQKVVLQRHL 112 (274)
Q Consensus 65 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 112 (274)
|.|.+||.... +..+.+|+..-++ ..|.|-.|+..|.. ..+..|.
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 45555555443 3334445555444 34555555555555 4445553
No 90
>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=87.55 E-value=0.43 Score=26.35 Aligned_cols=27 Identities=30% Similarity=0.500 Sum_probs=14.5
Q ss_pred CCceecCCCCccCCC----hhHHHHHHhhhc
Q psy4796 246 EREYACGKCAYRTAA----LPDLKLHLKNMH 272 (274)
Q Consensus 246 ~~~~~C~~C~~~f~~----~~~l~~H~~~~H 272 (274)
.....|.+|++.+.. .+.|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 344567777776654 356777775554
No 91
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=87.45 E-value=0.51 Score=24.75 Aligned_cols=6 Identities=50% Similarity=1.254 Sum_probs=2.3
Q ss_pred ccCcCc
Q psy4796 222 ACSYCD 227 (274)
Q Consensus 222 ~C~~C~ 227 (274)
+|+.|+
T Consensus 27 ~C~~C~ 32 (36)
T PF13717_consen 27 RCSKCG 32 (36)
T ss_pred ECCCCC
Confidence 333333
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.43 E-value=0.46 Score=26.20 Aligned_cols=11 Identities=18% Similarity=0.751 Sum_probs=5.2
Q ss_pred cccCCCCcccc
Q psy4796 193 FVCFACPYATQ 203 (274)
Q Consensus 193 ~~C~~C~~~f~ 203 (274)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 44455554444
No 93
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=87.38 E-value=0.36 Score=35.18 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=16.9
Q ss_pred CcccCcCccccCCchhHHHHHhhhCCCCceecCCCCc
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAY 256 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 256 (274)
.|.|++||..+ .++.|-+||+||.
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 58888887653 3456777888874
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=87.11 E-value=0.34 Score=32.64 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=19.4
Q ss_pred cccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCCCh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTAAL 261 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 261 (274)
..|+.||..|-... ..|.+||.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLn-----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN-----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC-----------CCCccCCCCCCccCcc
Confidence 46777777776532 2667777777776544
No 95
>KOG2186|consensus
Probab=86.92 E-value=0.34 Score=37.37 Aligned_cols=46 Identities=20% Similarity=0.476 Sum_probs=29.0
Q ss_pred cccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHHHh
Q psy4796 193 FVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTHLR 241 (274)
Q Consensus 193 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 241 (274)
|.|..||...... .+..|+...++ .-|.|.-|++.|.. .++..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 6677777665533 45557766665 44777777777766 55666643
No 96
>KOG4173|consensus
Probab=86.62 E-value=0.31 Score=36.34 Aligned_cols=75 Identities=24% Similarity=0.506 Sum_probs=38.5
Q ss_pred eeccc--ccccccChHHHHHHHhhcCCCCcccCCCCCcccCChhHHHHHHhh-h---------cCCCCccC--CCCCCcc
Q psy4796 65 FLCLF--CSYVATARIAIKNHLSSHLGWKPYKCPHCDHCFTQKVVLQRHLLT-H---------TGEKPFAC--HLCPYRA 130 (274)
Q Consensus 65 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~-h---------~~~~~~~C--~~C~~~f 130 (274)
+.|++ |.+.|.+.+....|...-++ -.|..|.+.|.+...|..|+.. | -+...|.| ..|+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 45555 55556555555555432222 2466666666666666666432 2 12233555 4455566
Q ss_pred ccHHHHHHHHHH
Q psy4796 131 SRKYYITAHLNS 142 (274)
Q Consensus 131 ~~~~~l~~H~~~ 142 (274)
.+......|+-.
T Consensus 157 kT~r~RkdH~I~ 168 (253)
T KOG4173|consen 157 KTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhHHHH
Confidence 555555555443
No 97
>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=85.39 E-value=0.76 Score=22.06 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=14.6
Q ss_pred ecCCCCccCCChhHHHHHHh
Q psy4796 250 ACGKCAYRTAALPDLKLHLK 269 (274)
Q Consensus 250 ~C~~C~~~f~~~~~l~~H~~ 269 (274)
.||+|++.+ ....+.+|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 588888887 5677888875
No 98
>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=85.07 E-value=0.6 Score=32.08 Aligned_cols=30 Identities=10% Similarity=0.077 Sum_probs=16.5
Q ss_pred cccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCc
Q psy4796 193 FVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQS 233 (274)
Q Consensus 193 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 233 (274)
..|+.||+.|... ++.|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 4566666666543 23455666666665443
No 99
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=85.03 E-value=0.78 Score=27.08 Aligned_cols=47 Identities=28% Similarity=0.550 Sum_probs=25.7
Q ss_pred CCcccCc--CccccCCchhHHHHHhhhCCCCceecCC----CCccCCChhHHHHH
Q psy4796 219 KPFACSY--CDYTCNQSSNLQTHLRIHKTEREYACGK----CAYRTAALPDLKLH 267 (274)
Q Consensus 219 ~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~~~l~~H 267 (274)
.+..|+. |...+ .+..|..|+..--..++..|+. |+..+. ...|.+|
T Consensus 8 ~~v~C~~~cc~~~i-~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~-~~~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMI-PRKELDDHLENECPKRPVPCPYSPYGCKERVP-REDLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEE-ECCCHHHHHHTTSTTSEEE-SS----S--EEE-HHHHHHC
T ss_pred CEeeCCCCCcccce-eHHHHHHHHHccCCCCcEECCCCCCCCCCccc-hhHHhCC
Confidence 4566766 43333 4557788888777777778888 777653 3334433
No 100
>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=84.87 E-value=0.28 Score=28.12 Aligned_cols=11 Identities=18% Similarity=0.745 Sum_probs=5.7
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45555555554
No 101
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.73 E-value=0.43 Score=26.58 Aligned_cols=11 Identities=18% Similarity=0.791 Sum_probs=5.8
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
|.|+.||..|.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 55555555444
No 102
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=83.22 E-value=0.86 Score=23.15 Aligned_cols=8 Identities=25% Similarity=0.791 Sum_probs=3.2
Q ss_pred cccCcCcc
Q psy4796 221 FACSYCDY 228 (274)
Q Consensus 221 ~~C~~C~~ 228 (274)
.+|+.||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 34444443
No 103
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=82.29 E-value=1.1 Score=25.37 Aligned_cols=24 Identities=25% Similarity=0.558 Sum_probs=13.3
Q ss_pred eecCCCCccCCCh-----hHHHHHHhhhc
Q psy4796 249 YACGKCAYRTAAL-----PDLKLHLKNMH 272 (274)
Q Consensus 249 ~~C~~C~~~f~~~-----~~l~~H~~~~H 272 (274)
-.|..|++.+... +.|.+|++..|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 3456666655443 46777766433
No 104
>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=81.97 E-value=0.54 Score=25.63 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=6.0
Q ss_pred ccCCCCCCCCCC
Q psy4796 159 RKCVHCSEPISS 170 (274)
Q Consensus 159 ~~c~~c~~~~~~ 170 (274)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 445555554443
No 105
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=80.91 E-value=0.25 Score=38.01 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=5.6
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
..|+.||..|.
T Consensus 49 ~vCP~CgyA~~ 59 (214)
T PF09986_consen 49 WVCPHCGYAAF 59 (214)
T ss_pred EECCCCCCccc
Confidence 44555555444
No 106
>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=80.70 E-value=1.9 Score=31.46 Aligned_cols=34 Identities=21% Similarity=0.328 Sum_probs=24.0
Q ss_pred CCCCcccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCcc
Q psy4796 88 LGWKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRA 130 (274)
Q Consensus 88 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 130 (274)
.+..-|.|+.|+..|+.-..+. ..|.||.||...
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 4455678888888877777664 258888888755
No 107
>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=80.58 E-value=0.88 Score=31.89 Aligned_cols=22 Identities=32% Similarity=0.544 Sum_probs=9.0
Q ss_pred eecCCCCccCCChhHHHHHHhhhcC
Q psy4796 249 YACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
..|-+||+.|.. |.+|++.|||
T Consensus 73 i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-
T ss_pred eEEccCCcccch---HHHHHHHccC
Confidence 455555555532 3455555554
No 108
>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=79.54 E-value=0.84 Score=24.49 Aligned_cols=11 Identities=18% Similarity=0.742 Sum_probs=5.0
Q ss_pred ccCCCCCCCCC
Q psy4796 159 RKCVHCSEPIS 169 (274)
Q Consensus 159 ~~c~~c~~~~~ 169 (274)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 34444444443
No 109
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.48 E-value=3.7 Score=29.52 Aligned_cols=38 Identities=29% Similarity=0.504 Sum_probs=21.4
Q ss_pred CCCcccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCcc
Q psy4796 89 GWKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRA 130 (274)
Q Consensus 89 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 130 (274)
+..-|.|+.|+..|.....+.. . . ....|.||.|+...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~-~--d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL-L--D-MDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh-c--C-CCCcEECCCCCCEE
Confidence 3445777777777775443321 0 1 12337777777755
No 110
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=79.14 E-value=0.98 Score=25.44 Aligned_cols=10 Identities=20% Similarity=0.839 Sum_probs=4.8
Q ss_pred cccCcCcccc
Q psy4796 221 FACSYCDYTC 230 (274)
Q Consensus 221 ~~C~~C~~~f 230 (274)
|.|..||+.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 4444444444
No 111
>PRK04023 DNA polymerase II large subunit; Validated
Probab=78.42 E-value=3.2 Score=39.07 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=7.7
Q ss_pred eecCCCCccCCC
Q psy4796 249 YACGKCAYRTAA 260 (274)
Q Consensus 249 ~~C~~C~~~f~~ 260 (274)
|.|+.|+..-..
T Consensus 664 y~CPKCG~El~~ 675 (1121)
T PRK04023 664 DECEKCGREPTP 675 (1121)
T ss_pred CcCCCCCCCCCc
Confidence 667777765443
No 112
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=78.33 E-value=3.1 Score=33.99 Aligned_cols=28 Identities=21% Similarity=0.548 Sum_probs=20.2
Q ss_pred hhhCCCCceecCCCC-ccCCChhHHHHHH
Q psy4796 241 RIHKTEREYACGKCA-YRTAALPDLKLHL 268 (274)
Q Consensus 241 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~ 268 (274)
+.|.-.+.|.|.+|| +++.-...+.+|.
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhh
Confidence 344445569999999 6777777788776
No 113
>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=77.93 E-value=1.6 Score=30.11 Aligned_cols=31 Identities=13% Similarity=0.108 Sum_probs=19.2
Q ss_pred eecccccccccChHHHHHHHhhcCCCCcccCCCCCcccCChh
Q psy4796 65 FLCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCFTQKV 106 (274)
Q Consensus 65 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 106 (274)
..|+.||+.|... +..|..|+.||..|....
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcCCccCcch
Confidence 3577777777532 335677777777765553
No 114
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=77.37 E-value=1.6 Score=25.70 Aligned_cols=10 Identities=20% Similarity=0.106 Sum_probs=4.8
Q ss_pred hhHHHHHhhh
Q psy4796 41 VMKDMIRHGR 50 (274)
Q Consensus 41 ~~~~l~~H~~ 50 (274)
.+..|..|+.
T Consensus 22 ~r~~l~~H~~ 31 (60)
T PF02176_consen 22 PRKELDDHLE 31 (60)
T ss_dssp ECCCHHHHHH
T ss_pred eHHHHHHHHH
Confidence 3445555554
No 115
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=76.92 E-value=1.7 Score=31.75 Aligned_cols=23 Identities=39% Similarity=1.054 Sum_probs=17.3
Q ss_pred ccccCCCCccccCHHHHHHHHhhccCCCCcccCcCc
Q psy4796 192 KFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCD 227 (274)
Q Consensus 192 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 227 (274)
.|.|++||.. +.++-|-.||+||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 6888888865 4456778888887
No 116
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=76.58 E-value=2.8 Score=31.22 Aligned_cols=34 Identities=24% Similarity=0.465 Sum_probs=24.6
Q ss_pred CCCcccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCccc
Q psy4796 89 GWKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRAS 131 (274)
Q Consensus 89 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 131 (274)
+..-|.|+.|+..|+.-..+. ..|.|+.||....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 445688888888887776653 2588999988653
No 117
>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=75.58 E-value=3.1 Score=31.90 Aligned_cols=30 Identities=13% Similarity=0.262 Sum_probs=21.3
Q ss_pred CccCCCCCCccccHHHHHHHHHHHHHHHHH
Q psy4796 120 PFACHLCPYRASRKYYITAHLNSLLSALLL 149 (274)
Q Consensus 120 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 149 (274)
.|.|+.|++.|.-...+..||...|.+.+.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e~ve 106 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPEKVE 106 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HHHHH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHHHHH
Confidence 488888888888888888888887775544
No 118
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=75.14 E-value=1.6 Score=31.55 Aligned_cols=12 Identities=25% Similarity=0.387 Sum_probs=5.7
Q ss_pred cccCCCCccccC
Q psy4796 193 FVCFACPYATQY 204 (274)
Q Consensus 193 ~~C~~C~~~f~~ 204 (274)
+.|+.||+.|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 444445444443
No 119
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=75.04 E-value=0.66 Score=28.65 Aligned_cols=15 Identities=20% Similarity=0.467 Sum_probs=8.1
Q ss_pred CCCcccC--cCccccCC
Q psy4796 218 DKPFACS--YCDYTCNQ 232 (274)
Q Consensus 218 ~~~~~C~--~C~~~f~~ 232 (274)
+..++|. .||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 4445554 56665554
No 120
>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=74.93 E-value=1.5 Score=21.86 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=6.4
Q ss_pred CCceecCCCCc
Q psy4796 246 EREYACGKCAY 256 (274)
Q Consensus 246 ~~~~~C~~C~~ 256 (274)
...|.|+.|+.
T Consensus 17 ~~~~vCp~C~~ 27 (30)
T PF08274_consen 17 GELLVCPECGH 27 (30)
T ss_dssp SSSEEETTTTE
T ss_pred CCEEeCCcccc
Confidence 34466666664
No 121
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.51 E-value=2 Score=19.92 Aligned_cols=6 Identities=33% Similarity=1.154 Sum_probs=2.9
Q ss_pred cCCCCc
Q psy4796 251 CGKCAY 256 (274)
Q Consensus 251 C~~C~~ 256 (274)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 454543
No 122
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=72.43 E-value=2.7 Score=25.17 Aligned_cols=49 Identities=16% Similarity=0.294 Sum_probs=31.9
Q ss_pred CCCCeeeccccCCcchhh---HHHHHhhhccccccccccCCcceecccccccc
Q psy4796 25 PPADVTCLHCSLTTPCVM---KDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVA 74 (274)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~---~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f 74 (274)
+...|.|..|+..+ -.. .....|.+..++...+........|-.|+...
T Consensus 8 ~~~lw~CL~Cg~~~-C~~~~~~Ha~~H~~~~~H~l~v~~~~~~i~C~~C~~~v 59 (63)
T PF02148_consen 8 NSNLWLCLTCGYVG-CGRYSNGHALKHYKETGHPLAVSLSTGSIWCYACDDYV 59 (63)
T ss_dssp SSSEEEETTTS-EE-ETTTSTSHHHHHHHHHT--EEEETTTTCEEETTTTEEE
T ss_pred CCceEEeCCCCccc-ccCCcCcHHHHhhcccCCeEEEECCCCeEEEcCCCcEE
Confidence 35578899998877 553 56777777666666666666667777776543
No 123
>PF14353 CpXC: CpXC protein
Probab=72.10 E-value=4.6 Score=28.20 Aligned_cols=15 Identities=20% Similarity=0.498 Sum_probs=8.0
Q ss_pred cccCcCccccCCchh
Q psy4796 221 FACSYCDYTCNQSSN 235 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~ 235 (274)
|.|+.||..|.-...
T Consensus 39 ~~CP~Cg~~~~~~~p 53 (128)
T PF14353_consen 39 FTCPSCGHKFRLEYP 53 (128)
T ss_pred EECCCCCCceecCCC
Confidence 556666655554433
No 124
>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=71.36 E-value=2.9 Score=32.60 Aligned_cols=22 Identities=23% Similarity=0.569 Sum_probs=13.4
Q ss_pred CCCccCCCCCCccccHHHHHHH
Q psy4796 118 EKPFACHLCPYRASRKYYITAH 139 (274)
Q Consensus 118 ~~~~~C~~C~~~f~~~~~l~~H 139 (274)
.+++.||.|+........|..-
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmS 228 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMS 228 (314)
T ss_pred CCCCCCCCCCCcccccccceee
Confidence 4667777777766555544433
No 125
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.63 E-value=2 Score=26.45 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=6.3
Q ss_pred eeeccccCCc
Q psy4796 29 VTCLHCSLTT 38 (274)
Q Consensus 29 ~~C~~C~~~f 38 (274)
|.|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 6666666655
No 126
>KOG3408|consensus
Probab=68.49 E-value=6 Score=27.00 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=26.8
Q ss_pred CCCCCCCCCCCeeeccccCCcchhhHHHHHhhhc
Q psy4796 18 DKASPGPPPADVTCLHCSLTTPCVMKDMIRHGRL 51 (274)
Q Consensus 18 ~~~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~ 51 (274)
+.++..++..-|-|..|.+.| .+...|..|.+.
T Consensus 47 ~~D~dlPG~GqfyCi~CaRyF-i~~~~l~~H~kt 79 (129)
T KOG3408|consen 47 EIDPDLPGGGQFYCIECARYF-IDAKALKTHFKT 79 (129)
T ss_pred cCCCCCCCCceeehhhhhhhh-cchHHHHHHHhc
Confidence 445566666679999999999 999999999873
No 127
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=67.47 E-value=7.8 Score=37.67 Aligned_cols=29 Identities=14% Similarity=0.485 Sum_probs=15.4
Q ss_pred CcccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCC
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTA 259 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 259 (274)
+|.|+.||....... ++ ...|+.|+....
T Consensus 692 vy~CPsCGaev~~de---------s~--a~~CP~CGtplv 720 (1337)
T PRK14714 692 VYVCPDCGAEVPPDE---------SG--RVECPRCDVELT 720 (1337)
T ss_pred ceeCccCCCccCCCc---------cc--cccCCCCCCccc
Confidence 467777776543211 11 345777775443
No 128
>PRK04023 DNA polymerase II large subunit; Validated
Probab=66.98 E-value=7.5 Score=36.80 Aligned_cols=10 Identities=20% Similarity=0.301 Sum_probs=5.6
Q ss_pred cccCCCCccc
Q psy4796 193 FVCFACPYAT 202 (274)
Q Consensus 193 ~~C~~C~~~f 202 (274)
+.|+.||...
T Consensus 664 y~CPKCG~El 673 (1121)
T PRK04023 664 DECEKCGREP 673 (1121)
T ss_pred CcCCCCCCCC
Confidence 4566666543
No 129
>PF12907 zf-met2: Zinc-binding
Probab=66.97 E-value=3 Score=22.42 Aligned_cols=25 Identities=32% Similarity=0.466 Sum_probs=14.5
Q ss_pred eecCCCCccCCC---hhHHHHHHhhhcC
Q psy4796 249 YACGKCAYRTAA---LPDLKLHLKNMHL 273 (274)
Q Consensus 249 ~~C~~C~~~f~~---~~~l~~H~~~~H~ 273 (274)
+.|.+|..+|.. ...|..|....|.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHp 29 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHP 29 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCC
Confidence 456777744433 3457777666554
No 130
>PF15269 zf-C2H2_7: Zinc-finger
Probab=66.63 E-value=3.8 Score=22.30 Aligned_cols=22 Identities=36% Similarity=0.958 Sum_probs=17.1
Q ss_pred cccCcCccccCCchhHHHHHhh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRI 242 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~ 242 (274)
|.|-.|..+..-++.|..||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 7788888888778888877764
No 131
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.59 E-value=3.4 Score=27.52 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=7.0
Q ss_pred CCCcccCcCcccc
Q psy4796 218 DKPFACSYCDYTC 230 (274)
Q Consensus 218 ~~~~~C~~C~~~f 230 (274)
..|..|+.||++|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 3445555555555
No 132
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=66.29 E-value=5.6 Score=21.50 Aligned_cols=23 Identities=17% Similarity=0.447 Sum_probs=12.7
Q ss_pred cccCcCccccCC--chhHHHHHhhh
Q psy4796 221 FACSYCDYTCNQ--SSNLQTHLRIH 243 (274)
Q Consensus 221 ~~C~~C~~~f~~--~~~l~~H~~~h 243 (274)
-.|+.||..|.. ..+-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 456666666553 34445555555
No 133
>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=65.79 E-value=3.5 Score=28.96 Aligned_cols=25 Identities=28% Similarity=0.472 Sum_probs=13.5
Q ss_pred CcccCcCccccCCchhHHHHHhhhCCCC
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRIHKTER 247 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 247 (274)
...|-+||+.|.. |++|++.|+|..
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred eeEEccCCcccch---HHHHHHHccCCC
Confidence 3677778877764 477887776553
No 134
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=64.23 E-value=5.2 Score=27.83 Aligned_cols=20 Identities=25% Similarity=0.388 Sum_probs=10.1
Q ss_pred cccCcCccccCCchhHHHHHhhh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIH 243 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h 243 (274)
..|-++|+.|. .|++|+.+|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~ 96 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTH 96 (148)
T ss_pred EEEeccCcchH---HHHHHHhcc
Confidence 44555555554 245555554
No 135
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=64.16 E-value=3.9 Score=20.94 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=16.4
Q ss_pred CeeeccccCCcchhhHHHHHhhhc
Q psy4796 28 DVTCLHCSLTTPCVMKDMIRHGRL 51 (274)
Q Consensus 28 ~~~C~~C~~~f~~~~~~l~~H~~~ 51 (274)
.+.|+.|++.+ ....+..|+..
T Consensus 4 ~~~C~nC~R~v--~a~RfA~HLek 25 (33)
T PF08209_consen 4 YVECPNCGRPV--AASRFAPHLEK 25 (33)
T ss_dssp EEE-TTTSSEE--EGGGHHHHHHH
T ss_pred eEECCCCcCCc--chhhhHHHHHH
Confidence 47899998887 77778888764
No 136
>KOG4602|consensus
Probab=63.02 E-value=12 Score=29.29 Aligned_cols=56 Identities=16% Similarity=0.336 Sum_probs=34.3
Q ss_pred CCCCCCCCCeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccC
Q psy4796 20 ASPGPPPADVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATA 76 (274)
Q Consensus 20 ~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~ 76 (274)
..++....++.|..|--.- .....+..|...-+...|.-...+.|.|++||-+-.+
T Consensus 225 P~pg~Q~r~l~CvFC~nN~-E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGATgDn 280 (318)
T KOG4602|consen 225 PPPGNQPRPLCCVFCFNNA-EEFARYHTHPLKDKDGRVLCPKLRSYVCPICGATGDN 280 (318)
T ss_pred CCCCCCCCceeEEeecCCC-chhhheecccccCCCCcEechhHhhhcCccccccCCc
Confidence 3445555668899996555 5556667777643333333344456778888876543
No 137
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.61 E-value=6.5 Score=25.11 Aligned_cols=12 Identities=17% Similarity=0.351 Sum_probs=5.7
Q ss_pred ccccCCCCcccc
Q psy4796 192 KFVCFACPYATQ 203 (274)
Q Consensus 192 ~~~C~~C~~~f~ 203 (274)
.+.|..||..|.
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 344555555443
No 138
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=62.07 E-value=6.1 Score=30.69 Aligned_cols=14 Identities=21% Similarity=0.394 Sum_probs=7.8
Q ss_pred CccccCCCCccccC
Q psy4796 191 KKFVCFACPYATQY 204 (274)
Q Consensus 191 ~~~~C~~C~~~f~~ 204 (274)
..|.|+.|+..|+.
T Consensus 154 aef~C~~C~h~F~G 167 (278)
T PF15135_consen 154 AEFHCPKCRHNFRG 167 (278)
T ss_pred eeeecccccccchh
Confidence 34556666666554
No 139
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.01 E-value=3.1 Score=29.47 Aligned_cols=13 Identities=23% Similarity=0.429 Sum_probs=10.1
Q ss_pred CCCeeeccccCCc
Q psy4796 26 PADVTCLHCSLTT 38 (274)
Q Consensus 26 ~~~~~C~~C~~~f 38 (274)
+..+.|..||..|
T Consensus 68 p~~~~C~~CG~~~ 80 (135)
T PRK03824 68 EAVLKCRNCGNEW 80 (135)
T ss_pred ceEEECCCCCCEE
Confidence 3458899998888
No 140
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=61.62 E-value=5.5 Score=22.65 Aligned_cols=9 Identities=44% Similarity=1.276 Sum_probs=4.5
Q ss_pred cccCcCccc
Q psy4796 221 FACSYCDYT 229 (274)
Q Consensus 221 ~~C~~C~~~ 229 (274)
+.|..||.+
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 455555543
No 141
>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=61.44 E-value=12 Score=20.73 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=6.3
Q ss_pred CCceecCCCCc
Q psy4796 246 EREYACGKCAY 256 (274)
Q Consensus 246 ~~~~~C~~C~~ 256 (274)
...|.|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 34566666654
No 142
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=61.29 E-value=4.6 Score=18.98 Aligned_cols=7 Identities=29% Similarity=1.336 Sum_probs=3.5
Q ss_pred eecCCCC
Q psy4796 249 YACGKCA 255 (274)
Q Consensus 249 ~~C~~C~ 255 (274)
|.||.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4555554
No 143
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=60.21 E-value=2.8 Score=20.50 Aligned_cols=19 Identities=21% Similarity=0.399 Sum_probs=10.7
Q ss_pred eeeccccCCcchhhHHHHHhh
Q psy4796 29 VTCLHCSLTTPCVMKDMIRHG 49 (274)
Q Consensus 29 ~~C~~C~~~f~~~~~~l~~H~ 49 (274)
|.|..|++.| ....+..|.
T Consensus 1 ~sCiDC~~~F--~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF--DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE--EGGGTTT--
T ss_pred CeeecCCCCc--CcCCcCCCC
Confidence 4577777777 555555554
No 144
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=60.08 E-value=4.5 Score=28.89 Aligned_cols=33 Identities=30% Similarity=0.815 Sum_probs=18.9
Q ss_pred CcccCcCccccCCchhHHHHHhhhCCCCceecCCCCcc
Q psy4796 220 PFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYR 257 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 257 (274)
+|.|. |+..|.+. ++|-.+-.|+ .|.|..|+-.
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 46776 76665443 3444444455 6777777654
No 145
>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=60.04 E-value=6.3 Score=21.43 Aligned_cols=9 Identities=33% Similarity=0.933 Sum_probs=3.7
Q ss_pred eeccccccc
Q psy4796 65 FLCLFCSYV 73 (274)
Q Consensus 65 ~~C~~C~~~ 73 (274)
+.|+.||..
T Consensus 20 ~vC~~CG~V 28 (43)
T PF08271_consen 20 LVCPNCGLV 28 (43)
T ss_dssp EEETTT-BB
T ss_pred EECCCCCCE
Confidence 345555443
No 146
>KOG2593|consensus
Probab=59.81 E-value=6.8 Score=33.16 Aligned_cols=41 Identities=15% Similarity=0.285 Sum_probs=27.7
Q ss_pred ccCCcceecccccccccChHHHHHHHhhcCCCCcccCCCCCccc
Q psy4796 59 TSAKLQFLCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCF 102 (274)
Q Consensus 59 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 102 (274)
-+....|.|+.|.++|....+++. .-.....|.|..|+-..
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccccCCccccchhhhHHHHh---hcccCceEEEecCCCch
Confidence 344556899999999987766543 22223468999998654
No 147
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=59.46 E-value=7.5 Score=22.46 Aligned_cols=10 Identities=20% Similarity=0.428 Sum_probs=4.9
Q ss_pred ccCCCCcccc
Q psy4796 194 VCFACPYATQ 203 (274)
Q Consensus 194 ~C~~C~~~f~ 203 (274)
.|+.||+.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 4555555443
No 148
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=58.40 E-value=4.2 Score=32.63 Aligned_cols=23 Identities=22% Similarity=0.580 Sum_probs=12.2
Q ss_pred cccCcCccccCCchhHHHHHhhh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIH 243 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h 243 (274)
|+|+.|...|-..-+...|...|
T Consensus 389 Y~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 389 YQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred eechhhhhhhhhhhHHHHHHHHh
Confidence 55555555555555555554444
No 149
>KOG1280|consensus
Probab=57.93 E-value=9 Score=31.41 Aligned_cols=41 Identities=24% Similarity=0.510 Sum_probs=30.7
Q ss_pred cCCCCcccCcCccccCCchhHHHHHhhhCCCCc--eecCCCCc
Q psy4796 216 TGDKPFACSYCDYTCNQSSNLQTHLRIHKTERE--YACGKCAY 256 (274)
Q Consensus 216 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~--~~C~~C~~ 256 (274)
-....|.|+.|+..=.....|..|+..-+.+.+ -.|++|+.
T Consensus 75 y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 75 YDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred cccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 345579999999977788899999987555544 35788774
No 150
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=57.85 E-value=2.4 Score=22.80 Aligned_cols=10 Identities=50% Similarity=1.082 Sum_probs=6.4
Q ss_pred eecCCCCccC
Q psy4796 249 YACGKCAYRT 258 (274)
Q Consensus 249 ~~C~~C~~~f 258 (274)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6666666654
No 151
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.81 E-value=8.1 Score=35.65 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.6
Q ss_pred CCCcccCcCcc
Q psy4796 218 DKPFACSYCDY 228 (274)
Q Consensus 218 ~~~~~C~~C~~ 228 (274)
..|..|+.||.
T Consensus 473 ~~p~~Cp~Cgs 483 (730)
T COG1198 473 PIPQSCPECGS 483 (730)
T ss_pred CCCCCCCCCCC
Confidence 34455555553
No 152
>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=56.56 E-value=10 Score=21.58 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=4.4
Q ss_pred cccCCCCc
Q psy4796 193 FVCFACPY 200 (274)
Q Consensus 193 ~~C~~C~~ 200 (274)
|.|+.|+.
T Consensus 35 w~CP~C~a 42 (50)
T cd00730 35 WVCPVCGA 42 (50)
T ss_pred CCCCCCCC
Confidence 55555553
No 153
>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=56.28 E-value=5.4 Score=20.86 Aligned_cols=29 Identities=14% Similarity=0.269 Sum_probs=14.3
Q ss_pred ecccccccccChHHHHHHHhhcCCCCcccCCCCCccc
Q psy4796 66 LCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCF 102 (274)
Q Consensus 66 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 102 (274)
.|+.||..|... ......+-.|..|+..+
T Consensus 3 ~C~~Cg~~Yh~~--------~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIE--------FNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETT--------TB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccc--------cCCCCCCCccCCCCCee
Confidence 466666666422 12233345566666544
No 154
>KOG2636|consensus
Probab=56.10 E-value=13 Score=31.73 Aligned_cols=23 Identities=30% Similarity=0.769 Sum_probs=13.0
Q ss_pred Ccceeccccc-ccccChHHHHHHH
Q psy4796 62 KLQFLCLFCS-YVATARIAIKNHL 84 (274)
Q Consensus 62 ~~~~~C~~C~-~~f~~~~~l~~H~ 84 (274)
...|.|.+|| +++....++.+|.
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred CcccceeeccCccccCcHHHHHHh
Confidence 4456666665 5555555555554
No 155
>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=54.61 E-value=7.7 Score=25.94 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=5.8
Q ss_pred eecCCCCccCC
Q psy4796 249 YACGKCAYRTA 259 (274)
Q Consensus 249 ~~C~~C~~~f~ 259 (274)
|.||.|+....
T Consensus 20 ~iCpeC~~EW~ 30 (109)
T TIGR00686 20 LICPSCLYEWN 30 (109)
T ss_pred eECcccccccc
Confidence 55555555443
No 156
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=54.58 E-value=9.3 Score=20.51 Aligned_cols=20 Identities=15% Similarity=0.127 Sum_probs=11.4
Q ss_pred CceecCCCCccCCChhHHHH
Q psy4796 247 REYACGKCAYRTAALPDLKL 266 (274)
Q Consensus 247 ~~~~C~~C~~~f~~~~~l~~ 266 (274)
..+.|+.|+-.+-+..+|.+
T Consensus 18 ~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEECCCCCeEEccHHHHHH
Confidence 34566666666666555543
No 157
>PRK10220 hypothetical protein; Provisional
Probab=54.47 E-value=9.1 Score=25.62 Aligned_cols=11 Identities=36% Similarity=0.800 Sum_probs=5.7
Q ss_pred eecCCCCccCC
Q psy4796 249 YACGKCAYRTA 259 (274)
Q Consensus 249 ~~C~~C~~~f~ 259 (274)
|.|+.|+..+.
T Consensus 21 ~vCpeC~hEW~ 31 (111)
T PRK10220 21 YICPECAHEWN 31 (111)
T ss_pred EECCcccCcCC
Confidence 55555555443
No 158
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=54.30 E-value=4.9 Score=36.98 Aligned_cols=15 Identities=13% Similarity=0.374 Sum_probs=11.5
Q ss_pred hCCCCceecCCCCcc
Q psy4796 243 HKTEREYACGKCAYR 257 (274)
Q Consensus 243 h~~~~~~~C~~C~~~ 257 (274)
+....|..|+.||-.
T Consensus 470 ~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 470 YQEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCCC
Confidence 445678899999965
No 159
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=53.92 E-value=11 Score=26.33 Aligned_cols=11 Identities=18% Similarity=0.389 Sum_probs=5.0
Q ss_pred ccCCCCCCccc
Q psy4796 121 FACHLCPYRAS 131 (274)
Q Consensus 121 ~~C~~C~~~f~ 131 (274)
++|..|++.|.
T Consensus 2 H~Ct~Cg~~f~ 12 (131)
T PF09845_consen 2 HQCTKCGRVFE 12 (131)
T ss_pred cccCcCCCCcC
Confidence 34444444443
No 160
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=53.20 E-value=4.6 Score=26.49 Aligned_cols=12 Identities=33% Similarity=0.681 Sum_probs=6.5
Q ss_pred CCccccCCCCcc
Q psy4796 190 KKKFVCFACPYA 201 (274)
Q Consensus 190 ~~~~~C~~C~~~ 201 (274)
++.|.|+.||..
T Consensus 20 ~k~FtCp~Cghe 31 (104)
T COG4888 20 PKTFTCPRCGHE 31 (104)
T ss_pred CceEecCccCCe
Confidence 344566666644
No 161
>KOG2593|consensus
Probab=52.94 E-value=15 Score=31.21 Aligned_cols=41 Identities=27% Similarity=0.516 Sum_probs=29.8
Q ss_pred cCCCCcccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCcc
Q psy4796 87 HLGWKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRA 130 (274)
Q Consensus 87 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 130 (274)
-+....|.|+.|.+.|+....++ ..-...-.|.|..|+-..
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccccCCccccchhhhHHHH---hhcccCceEEEecCCCch
Confidence 34556799999999998776553 233334569999999865
No 162
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=52.63 E-value=7.5 Score=28.17 Aligned_cols=15 Identities=27% Similarity=0.208 Sum_probs=9.1
Q ss_pred eecccccccccChHH
Q psy4796 65 FLCLFCSYVATARIA 79 (274)
Q Consensus 65 ~~C~~C~~~f~~~~~ 79 (274)
++|+.||+.|.....
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 566666666665543
No 163
>KOG2071|consensus
Probab=52.32 E-value=12 Score=33.22 Aligned_cols=17 Identities=18% Similarity=0.563 Sum_probs=13.2
Q ss_pred CCCccCCCCCCccccHH
Q psy4796 118 EKPFACHLCPYRASRKY 134 (274)
Q Consensus 118 ~~~~~C~~C~~~f~~~~ 134 (274)
+....|++|+..|...+
T Consensus 511 e~~~~C~IC~EkFe~v~ 527 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVF 527 (579)
T ss_pred ccccCCcccccccceee
Confidence 56688999999886554
No 164
>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=51.68 E-value=11 Score=21.78 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=5.2
Q ss_pred cccCCCCccc
Q psy4796 193 FVCFACPYAT 202 (274)
Q Consensus 193 ~~C~~C~~~f 202 (274)
..|+.||..+
T Consensus 23 V~Cp~CGael 32 (54)
T TIGR01206 23 VICDECGAEL 32 (54)
T ss_pred EeCCCCCCEE
Confidence 4555555543
No 165
>KOG4124|consensus
Probab=50.17 E-value=2.7 Score=34.26 Aligned_cols=50 Identities=32% Similarity=0.639 Sum_probs=28.1
Q ss_pred CCcccCc--CccccCCchhHHHHHhh-hC------------------CCCceecCCCCccCCChhHHHHHH
Q psy4796 219 KPFACSY--CDYTCNQSSNLQTHLRI-HK------------------TEREYACGKCAYRTAALPDLKLHL 268 (274)
Q Consensus 219 ~~~~C~~--C~~~f~~~~~l~~H~~~-h~------------------~~~~~~C~~C~~~f~~~~~l~~H~ 268 (274)
++|.|++ |++.+.....|+.|... |. ..|+|.|++|.+....-..|.-|+
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 4566633 66666655555555332 21 246677888777776655554443
No 166
>KOG2807|consensus
Probab=50.16 E-value=29 Score=28.37 Aligned_cols=20 Identities=25% Similarity=0.416 Sum_probs=14.8
Q ss_pred eecCCCCccCCChhHHHHHH
Q psy4796 249 YACGKCAYRTAALPDLKLHL 268 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~ 268 (274)
|.|..|...|..--+...|-
T Consensus 346 y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred EEchhccceeeccchHHHHh
Confidence 88888888887766655554
No 167
>KOG3507|consensus
Probab=50.06 E-value=25 Score=20.61 Aligned_cols=15 Identities=13% Similarity=0.279 Sum_probs=9.5
Q ss_pred CCCCCeeeccccCCc
Q psy4796 24 PPPADVTCLHCSLTT 38 (274)
Q Consensus 24 ~~~~~~~C~~C~~~f 38 (274)
.....|.|..|+..-
T Consensus 16 ~~~miYiCgdC~~en 30 (62)
T KOG3507|consen 16 TATMIYICGDCGQEN 30 (62)
T ss_pred cccEEEEeccccccc
Confidence 344457777777665
No 168
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=49.52 E-value=11 Score=27.07 Aligned_cols=16 Identities=19% Similarity=0.364 Sum_probs=8.4
Q ss_pred CcccCcCccccCCchh
Q psy4796 220 PFACSYCDYTCNQSSN 235 (274)
Q Consensus 220 ~~~C~~C~~~f~~~~~ 235 (274)
.|.|+.||+.|..-++
T Consensus 124 f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSH 139 (147)
T ss_pred EEECCCCCCEeccccc
Confidence 4555555555554443
No 169
>KOG2807|consensus
Probab=49.23 E-value=28 Score=28.48 Aligned_cols=20 Identities=15% Similarity=0.300 Sum_probs=10.8
Q ss_pred ccCCCCCCccccHHHHHHHH
Q psy4796 121 FACHLCPYRASRKYYITAHL 140 (274)
Q Consensus 121 ~~C~~C~~~f~~~~~l~~H~ 140 (274)
|.|+.|...|-..-+.-.|-
T Consensus 346 y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred EEchhccceeeccchHHHHh
Confidence 55666665555555544443
No 170
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.59 E-value=23 Score=22.96 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=6.3
Q ss_pred ccccCCCCcccc
Q psy4796 192 KFVCFACPYATQ 203 (274)
Q Consensus 192 ~~~C~~C~~~f~ 203 (274)
.+.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PTZ00255 54 IWRCKGCKKTVA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 355555555554
No 171
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=47.73 E-value=21 Score=24.97 Aligned_cols=13 Identities=15% Similarity=0.363 Sum_probs=7.5
Q ss_pred ecCCCCccCCChh
Q psy4796 250 ACGKCAYRTAALP 262 (274)
Q Consensus 250 ~C~~C~~~f~~~~ 262 (274)
+||.|..+|.+.+
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 5666666665543
No 172
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=47.43 E-value=9.7 Score=25.98 Aligned_cols=11 Identities=18% Similarity=0.664 Sum_probs=5.7
Q ss_pred cccCCCCcccc
Q psy4796 193 FVCFACPYATQ 203 (274)
Q Consensus 193 ~~C~~C~~~f~ 203 (274)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 55555554444
No 173
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=47.31 E-value=17 Score=20.42 Aligned_cols=12 Identities=42% Similarity=1.065 Sum_probs=6.9
Q ss_pred ccccCCCCcccc
Q psy4796 192 KFVCFACPYATQ 203 (274)
Q Consensus 192 ~~~C~~C~~~f~ 203 (274)
.+.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 466666665543
No 174
>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=46.91 E-value=11 Score=21.10 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=3.2
Q ss_pred cccCCCCc
Q psy4796 193 FVCFACPY 200 (274)
Q Consensus 193 ~~C~~C~~ 200 (274)
|.|+.|+.
T Consensus 35 w~CP~C~a 42 (47)
T PF00301_consen 35 WVCPVCGA 42 (47)
T ss_dssp -B-TTTSS
T ss_pred CcCcCCCC
Confidence 55555553
No 175
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=46.82 E-value=14 Score=24.32 Aligned_cols=13 Identities=23% Similarity=0.744 Sum_probs=7.9
Q ss_pred CccCCCCCCCCCC
Q psy4796 158 RRKCVHCSEPISS 170 (274)
Q Consensus 158 ~~~c~~c~~~~~~ 170 (274)
+..|..||..|..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 4456666666665
No 176
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.40 E-value=13 Score=17.67 Aligned_cols=7 Identities=29% Similarity=0.838 Sum_probs=3.4
Q ss_pred ccCcCcc
Q psy4796 222 ACSYCDY 228 (274)
Q Consensus 222 ~C~~C~~ 228 (274)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3455554
No 177
>KOG1280|consensus
Probab=46.31 E-value=21 Score=29.44 Aligned_cols=42 Identities=21% Similarity=0.431 Sum_probs=30.1
Q ss_pred ccCCCccccCCCCccccCHHHHHHHHhhccCCCC--cccCcCcc
Q psy4796 187 RTDKKKFVCFACPYATQYACYIKTHVMTHTGDKP--FACSYCDY 228 (274)
Q Consensus 187 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~--~~C~~C~~ 228 (274)
+-...-|.|+.|++.=.....|..|+..-+.+-+ ..|++|+-
T Consensus 74 ~y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 74 HYDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 3445579999999998888889999875444433 45677753
No 178
>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=45.95 E-value=10 Score=25.94 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=7.0
Q ss_pred ccccCCCCccccC
Q psy4796 192 KFVCFACPYATQY 204 (274)
Q Consensus 192 ~~~C~~C~~~f~~ 204 (274)
...|..||..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 70 ECECEDCSEEVSP 82 (115)
T ss_pred EEEcccCCCEEec
Confidence 3556666655543
No 179
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=45.67 E-value=22 Score=23.11 Aligned_cols=12 Identities=17% Similarity=0.398 Sum_probs=6.2
Q ss_pred ccccCCCCcccc
Q psy4796 192 KFVCFACPYATQ 203 (274)
Q Consensus 192 ~~~C~~C~~~f~ 203 (274)
.+.|..|++.|.
T Consensus 53 IW~C~~C~~~~A 64 (91)
T TIGR00280 53 IWTCRKCGAKFA 64 (91)
T ss_pred EEEcCCCCCEEe
Confidence 355555555544
No 180
>KOG2907|consensus
Probab=45.08 E-value=11 Score=25.32 Aligned_cols=11 Identities=27% Similarity=1.062 Sum_probs=5.7
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
|.|+.|++.|+
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 55555555443
No 181
>KOG2272|consensus
Probab=45.07 E-value=16 Score=28.52 Aligned_cols=20 Identities=10% Similarity=0.497 Sum_probs=13.4
Q ss_pred CcccCCCCCcccCChhHHHH
Q psy4796 91 KPYKCPHCDHCFTQKVVLQR 110 (274)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~ 110 (274)
.-|.|.+|++...+...++.
T Consensus 98 ~CF~Cd~Cn~~Lad~gf~rn 117 (332)
T KOG2272|consen 98 ACFRCDLCNKHLADQGFYRN 117 (332)
T ss_pred ccchhHHHHHHHhhhhhHhh
Confidence 35788888877766665543
No 182
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=44.95 E-value=14 Score=21.30 Aligned_cols=12 Identities=17% Similarity=0.354 Sum_probs=6.3
Q ss_pred cccCCCCccccC
Q psy4796 193 FVCFACPYATQY 204 (274)
Q Consensus 193 ~~C~~C~~~f~~ 204 (274)
+.|+.||-.|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 455555555443
No 183
>KOG4167|consensus
Probab=44.76 E-value=15 Score=33.46 Aligned_cols=27 Identities=19% Similarity=0.297 Sum_probs=20.0
Q ss_pred CCCCCCeeeccccCCcchhhHHHHHhhh
Q psy4796 23 GPPPADVTCLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 23 ~~~~~~~~C~~C~~~f~~~~~~l~~H~~ 50 (274)
......|.|-.|++.| .....+-.||+
T Consensus 787 ~~~~giFpCreC~kvF-~KiKSrNAHMK 813 (907)
T KOG4167|consen 787 TDPTGIFPCRECGKVF-FKIKSRNAHMK 813 (907)
T ss_pred CCCCceeehHHHHHHH-HHHhhhhHHHH
Confidence 3445568888888888 77788888887
No 184
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=44.63 E-value=39 Score=27.45 Aligned_cols=50 Identities=20% Similarity=0.410 Sum_probs=34.6
Q ss_pred ccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhcc
Q psy4796 159 RKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHT 216 (274)
Q Consensus 159 ~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 216 (274)
-.|..|...|...+.. +....+....|.|+.|...|-..-..-.|...|.
T Consensus 363 ~~Cf~CQ~~fp~~~~~--------~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 363 THCFVCQGPFPKPPVS--------PFDESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ccceeccCCCCCCCCC--------cccccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 3477787777662111 1233345667999999999999988888877664
No 185
>KOG3408|consensus
Probab=44.29 E-value=14 Score=25.29 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=23.0
Q ss_pred cCCCccccCCCCccccCHHHHHHHHhh
Q psy4796 188 TDKKKFVCFACPYATQYACYIKTHVMT 214 (274)
Q Consensus 188 ~~~~~~~C~~C~~~f~~~~~l~~H~~~ 214 (274)
.+...|.|-.|.+-|.+...|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 345569999999999999999999874
No 186
>PF14369 zf-RING_3: zinc-finger
Probab=44.14 E-value=19 Score=18.70 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=4.5
Q ss_pred eecccccccc
Q psy4796 65 FLCLFCSYVA 74 (274)
Q Consensus 65 ~~C~~C~~~f 74 (274)
|+|-.|.+.+
T Consensus 3 ywCh~C~~~V 12 (35)
T PF14369_consen 3 YWCHQCNRFV 12 (35)
T ss_pred EeCccCCCEe
Confidence 4444444443
No 187
>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=44.10 E-value=13 Score=22.57 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=4.3
Q ss_pred cccCCCCcccc
Q psy4796 193 FVCFACPYATQ 203 (274)
Q Consensus 193 ~~C~~C~~~f~ 203 (274)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 35677777775
No 188
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=43.80 E-value=8.2 Score=24.99 Aligned_cols=11 Identities=18% Similarity=0.446 Sum_probs=6.2
Q ss_pred cccCCCCcccc
Q psy4796 193 FVCFACPYATQ 203 (274)
Q Consensus 193 ~~C~~C~~~f~ 203 (274)
+.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (90)
T PF01780_consen 54 WKCKKCGKKFA 64 (90)
T ss_dssp EEETTTTEEEE
T ss_pred eecCCCCCEEe
Confidence 55666655553
No 189
>KOG1701|consensus
Probab=43.56 E-value=4.8 Score=33.93 Aligned_cols=43 Identities=12% Similarity=0.388 Sum_probs=22.4
Q ss_pred ecccccccccChHHHHHHHhhcCCCCcccCCCCCcccCChhHH
Q psy4796 66 LCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCFTQKVVL 108 (274)
Q Consensus 66 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 108 (274)
.|..|++...-...--.-|..---..-|+|..|+++..-+.-+
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY 318 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFY 318 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhcccccc
Confidence 5777877654433222222211112357888888776555443
No 190
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=43.44 E-value=2.7 Score=37.94 Aligned_cols=88 Identities=20% Similarity=0.317 Sum_probs=55.9
Q ss_pred CCCCCCCeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHhhcCCCCcc-cCCCCCc
Q psy4796 22 PGPPPADVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLSSHLGWKPY-KCPHCDH 100 (274)
Q Consensus 22 ~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~-~C~~C~~ 100 (274)
...+...-.|+.|-+.+ .++..-+-++- --.|..||-.|+-..+|---. ..+.-..| -|+.|.+
T Consensus 95 ~~I~pD~a~C~~Cl~Ei-~dp~~rrY~YP-------------F~~CT~CGPRfTIi~alPYDR-~nTsM~~F~lC~~C~~ 159 (750)
T COG0068 95 TQIPPDAATCEDCLEEI-FDPNSRRYLYP-------------FINCTNCGPRFTIIEALPYDR-ENTSMADFPLCPFCDK 159 (750)
T ss_pred cccCCchhhhHHHHHHh-cCCCCcceecc-------------ccccCCCCcceeeeccCCCCc-ccCccccCcCCHHHHH
Confidence 44455668899998888 66655544432 014999999997655442211 12222334 4999999
Q ss_pred ccCChhHHHHHHhhhcCCCCccCCCCCCcc
Q psy4796 101 CFTQKVVLQRHLLTHTGEKPFACHLCPYRA 130 (274)
Q Consensus 101 ~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 130 (274)
.|.+..+-+-|. .+..|+.||-..
T Consensus 160 EY~dP~nRRfHA------Qp~aCp~CGP~~ 183 (750)
T COG0068 160 EYKDPLNRRFHA------QPIACPKCGPHL 183 (750)
T ss_pred HhcCcccccccc------ccccCcccCCCe
Confidence 888887644443 368899999744
No 191
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=43.33 E-value=43 Score=21.69 Aligned_cols=13 Identities=15% Similarity=0.370 Sum_probs=7.5
Q ss_pred ccccCCCCccccC
Q psy4796 192 KFVCFACPYATQY 204 (274)
Q Consensus 192 ~~~C~~C~~~f~~ 204 (274)
|-.|..||..|.+
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 3456666666655
No 192
>KOG4167|consensus
Probab=43.00 E-value=6 Score=35.84 Aligned_cols=26 Identities=23% Similarity=0.249 Sum_probs=21.5
Q ss_pred CccccCCCCccccCHHHHHHHHhhcc
Q psy4796 191 KKFVCFACPYATQYACYIKTHVMTHT 216 (274)
Q Consensus 191 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 216 (274)
..|.|.+|++.|.....+..|+++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 45888888888888888888888885
No 193
>KOG3002|consensus
Probab=42.84 E-value=43 Score=27.37 Aligned_cols=79 Identities=19% Similarity=0.339 Sum_probs=44.8
Q ss_pred CCccccCCCCccccCHHHHHHHHhhccCCCCcccC----cCccccCCchhHHHHHhhhCCCCceecCC----CCccCCCh
Q psy4796 190 KKKFVCFACPYATQYACYIKTHVMTHTGDKPFACS----YCDYTCNQSSNLQTHLRIHKTEREYACGK----CAYRTAAL 261 (274)
Q Consensus 190 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~----~C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~ 261 (274)
+....|+.|...+..... .++..-.......|+ -|.+.|..... ..|.+.-.. ++|.||. |... ...
T Consensus 78 ~~~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~p~~~C~~~-G~~ 152 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPVPGAECKYT-GSY 152 (299)
T ss_pred hhcccCCccccccccHHH--HHHHHHHHhceecccccccCCceeeccccc-ccccccccc-CCcCCCCCcccCCcc-CcH
Confidence 344678888887775432 223222333445564 37777776554 445544333 6677754 5543 456
Q ss_pred hHHHHHHhhhcC
Q psy4796 262 PDLKLHLKNMHL 273 (274)
Q Consensus 262 ~~l~~H~~~~H~ 273 (274)
..|..|...-|.
T Consensus 153 ~~l~~H~~~~hk 164 (299)
T KOG3002|consen 153 KDLYAHLNDTHK 164 (299)
T ss_pred HHHHHHHHhhCh
Confidence 677778776554
No 194
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=42.29 E-value=4 Score=36.91 Aligned_cols=58 Identities=17% Similarity=0.269 Sum_probs=42.4
Q ss_pred cCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCccccHHHHHHHHHHHHHHHHHHhHhhcCCCccCCCCCCC
Q psy4796 94 KCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRASRKYYITAHLNSLLSALLLQHFLASQPRRKCVHCSEP 167 (274)
Q Consensus 94 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 167 (274)
.|..||-.|+....|-......+...--.|+.|.++|.+..+.+.|. .+..|+.||-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHA----------------Qp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHA----------------QPIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcccccccc----------------ccccCcccCCC
Confidence 59999999998887744443333333357999999999988877763 35779999864
No 195
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=42.00 E-value=9.2 Score=23.59 Aligned_cols=13 Identities=15% Similarity=0.255 Sum_probs=5.0
Q ss_pred cccCCCCCcccCC
Q psy4796 92 PYKCPHCDHCFTQ 104 (274)
Q Consensus 92 ~~~C~~C~~~f~~ 104 (274)
...|..|+..+..
T Consensus 41 ~v~Cg~C~~~~~~ 53 (71)
T PF05495_consen 41 RVICGKCRTEQPI 53 (71)
T ss_dssp EEEETTT--EEES
T ss_pred CeECCCCCCccCh
Confidence 3445555544433
No 196
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=41.53 E-value=18 Score=31.38 Aligned_cols=21 Identities=14% Similarity=0.536 Sum_probs=10.2
Q ss_pred cccCcCccccCCchhHHHHHh
Q psy4796 221 FACSYCDYTCNQSSNLQTHLR 241 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~ 241 (274)
+.|+.|.+.|.+...+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 444445555555555555443
No 197
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.67 E-value=14 Score=25.44 Aligned_cols=12 Identities=17% Similarity=0.509 Sum_probs=6.5
Q ss_pred ccccCCCCcccc
Q psy4796 192 KFVCFACPYATQ 203 (274)
Q Consensus 192 ~~~C~~C~~~f~ 203 (274)
.+.|..||..|.
T Consensus 71 ~~~C~~Cg~~~~ 82 (117)
T PRK00564 71 ELECKDCSHVFK 82 (117)
T ss_pred EEEhhhCCCccc
Confidence 355666665544
No 198
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.53 E-value=8.2 Score=29.70 Aligned_cols=24 Identities=13% Similarity=0.099 Sum_probs=16.0
Q ss_pred CCCeeeccccCCcchhhHHHHHhhh
Q psy4796 26 PADVTCLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 26 ~~~~~C~~C~~~f~~~~~~l~~H~~ 50 (274)
.+...||+|+..| ....-+..-.+
T Consensus 17 kk~ieCPvC~tkF-kkeev~tgsiR 40 (267)
T COG1655 17 KKTIECPVCNTKF-KKEEVKTGSIR 40 (267)
T ss_pred hceeccCcccchh-hhhheecccee
Confidence 4567899999999 65554444444
No 199
>PRK04351 hypothetical protein; Provisional
Probab=40.20 E-value=18 Score=26.14 Aligned_cols=30 Identities=27% Similarity=0.703 Sum_probs=15.0
Q ss_pred cccCcCccccCCchhHHHHHhhhCCCCceecCCCCccC
Q psy4796 221 FACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRT 258 (274)
Q Consensus 221 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 258 (274)
|.|..|+..+... +.+ +...|.|..|+-.+
T Consensus 113 Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L 142 (149)
T PRK04351 113 YECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKL 142 (149)
T ss_pred EECCCCCCEeeee-------eec-CCCcEEeCCCCcEe
Confidence 6666666544321 112 23446666666544
No 200
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=40.20 E-value=35 Score=27.80 Aligned_cols=40 Identities=20% Similarity=0.260 Sum_probs=27.6
Q ss_pred CeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHH
Q psy4796 28 DVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHL 84 (274)
Q Consensus 28 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 84 (274)
-.+|+.|+... ....|..... .|+.|+.-|.-...-+...
T Consensus 38 w~kc~~C~~~~--~~~~l~~~~~---------------vcp~c~~h~rltAreRI~~ 77 (296)
T CHL00174 38 WVQCENCYGLN--YKKFLKSKMN---------------ICEQCGYHLKMSSSDRIEL 77 (296)
T ss_pred eeECCCccchh--hHHHHHHcCC---------------CCCCCCCCcCCCHHHHHHH
Confidence 46799999888 4555655543 6999999887555444443
No 201
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=39.82 E-value=21 Score=20.56 Aligned_cols=11 Identities=18% Similarity=0.561 Sum_probs=6.7
Q ss_pred ccCCCCccccC
Q psy4796 194 VCFACPYATQY 204 (274)
Q Consensus 194 ~C~~C~~~f~~ 204 (274)
.|..|++.|..
T Consensus 4 ~C~~C~~~F~~ 14 (57)
T cd00065 4 SCMGCGKPFTL 14 (57)
T ss_pred cCcccCccccC
Confidence 46666666664
No 202
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.66 E-value=20 Score=26.15 Aligned_cols=14 Identities=21% Similarity=0.553 Sum_probs=6.6
Q ss_pred cccCcCccccCCch
Q psy4796 221 FACSYCDYTCNQSS 234 (274)
Q Consensus 221 ~~C~~C~~~f~~~~ 234 (274)
|.|+.||+.|.--+
T Consensus 131 ~~C~~CgkiYW~Gs 144 (165)
T COG1656 131 YRCPKCGKIYWKGS 144 (165)
T ss_pred eECCCCcccccCch
Confidence 44555555544333
No 203
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=39.51 E-value=31 Score=22.39 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=6.2
Q ss_pred ccccCCCCcccc
Q psy4796 192 KFVCFACPYATQ 203 (274)
Q Consensus 192 ~~~C~~C~~~f~ 203 (274)
.+.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PRK03976 54 IWECRKCGAKFA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 355555555544
No 204
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.03 E-value=20 Score=24.52 Aligned_cols=12 Identities=25% Similarity=0.506 Sum_probs=6.9
Q ss_pred ceeccccccccc
Q psy4796 64 QFLCLFCSYVAT 75 (274)
Q Consensus 64 ~~~C~~C~~~f~ 75 (274)
..+|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (114)
T PRK03681 70 ECWCETCQQYVT 81 (114)
T ss_pred EEEcccCCCeee
Confidence 355666666554
No 205
>PRK00420 hypothetical protein; Validated
Probab=37.92 E-value=22 Score=24.16 Aligned_cols=27 Identities=15% Similarity=0.276 Sum_probs=14.8
Q ss_pred ecccccccccChHHHHHHHhhcCCCCcccCCCCCcccC
Q psy4796 66 LCLFCSYVATARIAIKNHLSSHLGWKPYKCPHCDHCFT 103 (274)
Q Consensus 66 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 103 (274)
.||.||..+... ......|+.|+....
T Consensus 25 ~CP~Cg~pLf~l-----------k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFEL-----------KDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCcceec-----------CCCceECCCCCCeee
Confidence 577777654320 112456777777544
No 206
>KOG2636|consensus
Probab=37.86 E-value=25 Score=30.11 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=25.7
Q ss_pred HhhccCCCCcccCcCc-cccCCchhHHHHHhh
Q psy4796 212 VMTHTGDKPFACSYCD-YTCNQSSNLQTHLRI 242 (274)
Q Consensus 212 ~~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~~ 242 (274)
.+.|.-...|.|.+|| +++.-+.++.+|...
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~E 424 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHFNE 424 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHhHH
Confidence 3556667889999999 788899999999885
No 207
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=37.74 E-value=14 Score=19.02 Aligned_cols=14 Identities=36% Similarity=0.975 Sum_probs=8.0
Q ss_pred cCCCccccCCCCcc
Q psy4796 188 TDKKKFVCFACPYA 201 (274)
Q Consensus 188 ~~~~~~~C~~C~~~ 201 (274)
.+...+.|+.||..
T Consensus 18 d~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 18 DDRERLVCPACGFI 31 (34)
T ss_dssp -SS-EEEETTTTEE
T ss_pred CCccceECCCCCCE
Confidence 34455778887754
No 208
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=37.62 E-value=48 Score=19.98 Aligned_cols=11 Identities=27% Similarity=0.845 Sum_probs=5.2
Q ss_pred CccCCCCCCcc
Q psy4796 120 PFACHLCPYRA 130 (274)
Q Consensus 120 ~~~C~~C~~~f 130 (274)
.|.|+.|+..+
T Consensus 46 ~~~C~~Cg~~~ 56 (69)
T PF07282_consen 46 VFTCPNCGFEM 56 (69)
T ss_pred eEEcCCCCCEE
Confidence 34555554443
No 209
>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=37.58 E-value=4.5 Score=21.56 Aligned_cols=10 Identities=20% Similarity=0.597 Sum_probs=5.3
Q ss_pred eecccccccc
Q psy4796 65 FLCLFCSYVA 74 (274)
Q Consensus 65 ~~C~~C~~~f 74 (274)
|.|..|+..|
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 5555555543
No 210
>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=37.42 E-value=11 Score=35.02 Aligned_cols=12 Identities=17% Similarity=0.672 Sum_probs=0.0
Q ss_pred CcccCcCccccC
Q psy4796 220 PFACSYCDYTCN 231 (274)
Q Consensus 220 ~~~C~~C~~~f~ 231 (274)
.|.|+.|+....
T Consensus 680 ~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 680 VYVCPDCGIEVE 691 (900)
T ss_dssp ------------
T ss_pred ceeccccccccC
Confidence 377777776543
No 211
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=37.11 E-value=33 Score=18.13 Aligned_cols=11 Identities=18% Similarity=0.510 Sum_probs=3.8
Q ss_pred ccccCCCCccc
Q psy4796 192 KFVCFACPYAT 202 (274)
Q Consensus 192 ~~~C~~C~~~f 202 (274)
.|.|+.|+..|
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 36666777666
No 212
>PF12773 DZR: Double zinc ribbon
Probab=37.01 E-value=43 Score=18.63 Aligned_cols=10 Identities=20% Similarity=0.461 Sum_probs=5.3
Q ss_pred ccCCCCcccc
Q psy4796 194 VCFACPYATQ 203 (274)
Q Consensus 194 ~C~~C~~~f~ 203 (274)
.|+.||..+.
T Consensus 14 fC~~CG~~l~ 23 (50)
T PF12773_consen 14 FCPHCGTPLP 23 (50)
T ss_pred CChhhcCChh
Confidence 4555555544
No 213
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=36.90 E-value=31 Score=26.12 Aligned_cols=52 Identities=27% Similarity=0.535 Sum_probs=22.3
Q ss_pred ccccCC----CCccccCHHHHHHHHhhccCCCCcccCc----CccccCCchhHHHHHhhhCCC
Q psy4796 192 KFVCFA----CPYATQYACYIKTHVMTHTGDKPFACSY----CDYTCNQSSNLQTHLRIHKTE 246 (274)
Q Consensus 192 ~~~C~~----C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~~~l~~H~~~h~~~ 246 (274)
.+.|.. |...+... ....|..... -+||.|+. |+..= ....|..|....+..
T Consensus 14 ~~pC~~~~~GC~~~~~~~-~~~~HE~~C~-~~p~~CP~~~~~C~~~G-~~~~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 14 KFPCKNAKYGCTETFPYS-EKREHEEECP-FRPCSCPFPGSGCDWQG-SYKELLDHLRDKHSW 73 (198)
T ss_dssp -EE-CCGGGT---EE-GG-GHHHHHHT-T-TSEEE-SSSSTT---EE-ECCCHHHHHHHHTTT
T ss_pred eecCCCCCCCCccccccc-ChhhHhccCC-CcCCcCCCCCCCccccC-CHHHHHHHHHHHCCC
Confidence 356654 66665433 4455554433 45677766 54332 345677777764444
No 214
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=36.76 E-value=3.9 Score=21.25 Aligned_cols=9 Identities=22% Similarity=0.357 Sum_probs=4.2
Q ss_pred ecccccccc
Q psy4796 66 LCLFCSYVA 74 (274)
Q Consensus 66 ~C~~C~~~f 74 (274)
.|+.||-.+
T Consensus 23 sC~~CGPr~ 31 (35)
T PF07503_consen 23 SCTNCGPRY 31 (35)
T ss_dssp -BTTCC-SC
T ss_pred cCCCCCCCE
Confidence 466666544
No 215
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=36.73 E-value=11 Score=19.78 Aligned_cols=11 Identities=27% Similarity=0.936 Sum_probs=4.9
Q ss_pred CCCCceecCCC
Q psy4796 244 KTEREYACGKC 254 (274)
Q Consensus 244 ~~~~~~~C~~C 254 (274)
.|...|.|..|
T Consensus 25 ~G~qryrC~~C 35 (36)
T PF03811_consen 25 SGHQRYRCKDC 35 (36)
T ss_pred CCCEeEecCcC
Confidence 33344555444
No 216
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.43 E-value=29 Score=28.42 Aligned_cols=75 Identities=19% Similarity=0.410 Sum_probs=38.3
Q ss_pred CccCCCCCCCCCCChhhhhhhccCCCCCcccCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHH
Q psy4796 158 RRKCVHCSEPISSDMSEIIEHCLVCPNATRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQ 237 (274)
Q Consensus 158 ~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 237 (274)
.-.|+.||..-.. .+. + .....+.+...|..|+-.... +...|+.||.. ..|.
T Consensus 187 ~~~CPvCGs~P~~---s~v-~-----~~~~~G~RyL~CslC~teW~~--------------~R~~C~~Cg~~----~~l~ 239 (309)
T PRK03564 187 RQFCPVCGSMPVS---SVV-Q-----IGTTQGLRYLHCNLCESEWHV--------------VRVKCSNCEQS----GKLH 239 (309)
T ss_pred CCCCCCCCCcchh---hee-e-----ccCCCCceEEEcCCCCCcccc--------------cCccCCCCCCC----Ccee
Confidence 4568888865322 111 1 112345555677777754432 12578888852 1121
Q ss_pred HHHhhh---CCCCceecCCCCccCCC
Q psy4796 238 THLRIH---KTEREYACGKCAYRTAA 260 (274)
Q Consensus 238 ~H~~~h---~~~~~~~C~~C~~~f~~ 260 (274)
. ...- ...+-..|..|+.-++.
T Consensus 240 y-~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 240 Y-WSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred e-eeecCCCcceEeeeccccccccee
Confidence 1 1111 12355789988876554
No 217
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=36.42 E-value=26 Score=23.29 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCeeeccccCCcchhhHHHHHhhh
Q psy4796 18 DKASPGPPPADVTCLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 18 ~~~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~ 50 (274)
..++..++..-+-|..|.+.| .+...|..|.+
T Consensus 45 p~Dp~lPGlGqhYCieCaryf-~t~~aL~~Hkk 76 (126)
T COG5112 45 PYDPELPGLGQHYCIECARYF-ITEKALMEHKK 76 (126)
T ss_pred CCCCCCCCCceeeeehhHHHH-HHHHHHHHHhc
Confidence 345556666678899999999 99999999976
No 218
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=36.39 E-value=7.1 Score=26.66 Aligned_cols=11 Identities=27% Similarity=1.041 Sum_probs=6.5
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
|.|..||..|.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 66666665553
No 219
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=36.29 E-value=21 Score=19.01 Aligned_cols=14 Identities=14% Similarity=0.463 Sum_probs=11.5
Q ss_pred ceecCCCCccCCCh
Q psy4796 248 EYACGKCAYRTAAL 261 (274)
Q Consensus 248 ~~~C~~C~~~f~~~ 261 (274)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999888654
No 220
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=36.17 E-value=32 Score=20.01 Aligned_cols=10 Identities=30% Similarity=1.039 Sum_probs=4.4
Q ss_pred cccCCCCCcc
Q psy4796 92 PYKCPHCDHC 101 (274)
Q Consensus 92 ~~~C~~C~~~ 101 (274)
.|.|+.||..
T Consensus 14 ~~~Cp~cGip 23 (55)
T PF13824_consen 14 NFECPDCGIP 23 (55)
T ss_pred CCcCCCCCCc
Confidence 3444444443
No 221
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=36.05 E-value=11 Score=27.18 Aligned_cols=8 Identities=50% Similarity=1.497 Sum_probs=4.1
Q ss_pred eecCCCCc
Q psy4796 249 YACGKCAY 256 (274)
Q Consensus 249 ~~C~~C~~ 256 (274)
|.|+.|+.
T Consensus 144 ~~C~~C~~ 151 (157)
T PF10263_consen 144 YRCGRCGG 151 (157)
T ss_pred EECCCCCC
Confidence 55555553
No 222
>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=35.79 E-value=14 Score=25.26 Aligned_cols=14 Identities=14% Similarity=0.244 Sum_probs=7.2
Q ss_pred ccccCCCCccccCH
Q psy4796 192 KFVCFACPYATQYA 205 (274)
Q Consensus 192 ~~~C~~C~~~f~~~ 205 (274)
...|..||..|...
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 70 RARCRDCGHEFEPD 83 (113)
T ss_dssp EEEETTTS-EEECH
T ss_pred cEECCCCCCEEecC
Confidence 35566666665543
No 223
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=35.74 E-value=24 Score=19.91 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=5.0
Q ss_pred ceeccccccc
Q psy4796 64 QFLCLFCSYV 73 (274)
Q Consensus 64 ~~~C~~C~~~ 73 (274)
.+.|..||.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 3455555543
No 224
>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=35.65 E-value=6.3 Score=28.09 Aligned_cols=19 Identities=21% Similarity=0.331 Sum_probs=13.5
Q ss_pred cccCCCCCcccCChhHHHH
Q psy4796 92 PYKCPHCDHCFTQKVVLQR 110 (274)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~ 110 (274)
.-.|..|++.|++...+..
T Consensus 28 RReC~~C~~RFTTyErve~ 46 (147)
T TIGR00244 28 RRECLECHERFTTFERAEL 46 (147)
T ss_pred cccCCccCCccceeeeccc
Confidence 3568888888888776543
No 225
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=35.42 E-value=46 Score=26.26 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=25.6
Q ss_pred CCCCeeeccccCCcchhhHHHHHhhhccccccccccCCcceeccccccccc
Q psy4796 25 PPADVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVAT 75 (274)
Q Consensus 25 ~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~ 75 (274)
+.....|.+|+... .-...+.+|+. +|..|+....
T Consensus 62 ~~p~v~CrVCq~~I-~i~gk~~QhVV---------------kC~~CnEATP 96 (256)
T PF09788_consen 62 GAPVVTCRVCQSLI-DIEGKMHQHVV---------------KCSVCNEATP 96 (256)
T ss_pred CCceEEeecCCcee-cccCccceeeE---------------ECCCCCcccc
Confidence 33457899999988 77777777876 5777776543
No 226
>KOG0717|consensus
Probab=34.37 E-value=23 Score=30.55 Aligned_cols=21 Identities=19% Similarity=0.407 Sum_probs=19.4
Q ss_pred eeeccccCCcchhhHHHHHhhh
Q psy4796 29 VTCLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 29 ~~C~~C~~~f~~~~~~l~~H~~ 50 (274)
+-|.+|++.| .+...|..|..
T Consensus 293 lyC~vCnKsF-KseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSF-KSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccc-cchHHHHhhHH
Confidence 8899999999 99999999975
No 227
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=34.33 E-value=57 Score=29.95 Aligned_cols=7 Identities=29% Similarity=1.160 Sum_probs=3.5
Q ss_pred cCCCCCC
Q psy4796 122 ACHLCPY 128 (274)
Q Consensus 122 ~C~~C~~ 128 (274)
.|+.|+.
T Consensus 3 ~Cp~Cg~ 9 (645)
T PRK14559 3 ICPQCQF 9 (645)
T ss_pred cCCCCCC
Confidence 3555544
No 228
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.01 E-value=49 Score=23.23 Aligned_cols=15 Identities=13% Similarity=0.507 Sum_probs=9.8
Q ss_pred CCccccCCCCccccC
Q psy4796 190 KKKFVCFACPYATQY 204 (274)
Q Consensus 190 ~~~~~C~~C~~~f~~ 204 (274)
...|.|..|++.|..
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 455777777777654
No 229
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.75 E-value=42 Score=29.80 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=16.4
Q ss_pred cccCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCcc
Q psy4796 186 TRTDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDY 228 (274)
Q Consensus 186 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 228 (274)
.|...+...|..||... ..|..|+.|+.
T Consensus 234 ~h~~~~~l~Ch~Cg~~~---------------~~~~~Cp~C~s 261 (505)
T TIGR00595 234 YHKKEGKLRCHYCGYQE---------------PIPKTCPQCGS 261 (505)
T ss_pred EecCCCeEEcCCCcCcC---------------CCCCCCCCCCC
Confidence 34445556777777432 33467777765
No 230
>KOG0978|consensus
Probab=33.39 E-value=14 Score=33.74 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=8.4
Q ss_pred CeeeccccCCc
Q psy4796 28 DVTCLHCSLTT 38 (274)
Q Consensus 28 ~~~C~~C~~~f 38 (274)
.+.|+.|+.++
T Consensus 643 ~LkCs~Cn~R~ 653 (698)
T KOG0978|consen 643 LLKCSVCNTRW 653 (698)
T ss_pred ceeCCCccCch
Confidence 47799998666
No 231
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.24 E-value=28 Score=17.77 Aligned_cols=13 Identities=23% Similarity=0.531 Sum_probs=6.3
Q ss_pred Ccceecccccccc
Q psy4796 62 KLQFLCLFCSYVA 74 (274)
Q Consensus 62 ~~~~~C~~C~~~f 74 (274)
..-+.|..|+..|
T Consensus 19 ~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 19 DDYEVCIFCGSSF 31 (33)
T ss_pred CCeEEcccCCcEe
Confidence 3334555555544
No 232
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=33.01 E-value=21 Score=20.17 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=6.4
Q ss_pred CCeeeccccCCc
Q psy4796 27 ADVTCLHCSLTT 38 (274)
Q Consensus 27 ~~~~C~~C~~~f 38 (274)
+++.|..||..|
T Consensus 3 k~l~C~dCg~~F 14 (49)
T PF13451_consen 3 KTLTCKDCGAEF 14 (49)
T ss_pred eeEEcccCCCeE
Confidence 345555555554
No 233
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=32.73 E-value=31 Score=18.70 Aligned_cols=17 Identities=12% Similarity=0.202 Sum_probs=12.2
Q ss_pred cccCCCCccccCHHHHH
Q psy4796 193 FVCFACPYATQYACYIK 209 (274)
Q Consensus 193 ~~C~~C~~~f~~~~~l~ 209 (274)
-.|+.||+.|..+....
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 36888888888765544
No 234
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=32.26 E-value=12 Score=26.85 Aligned_cols=16 Identities=25% Similarity=0.416 Sum_probs=11.1
Q ss_pred ccCCCCCcccCChhHH
Q psy4796 93 YKCPHCDHCFTQKVVL 108 (274)
Q Consensus 93 ~~C~~C~~~f~~~~~l 108 (274)
-.|..|+..|++....
T Consensus 29 ReC~~C~~RFTTfE~~ 44 (156)
T COG1327 29 RECLECGERFTTFERA 44 (156)
T ss_pred hcccccccccchhhee
Confidence 4677777777777654
No 235
>PRK14873 primosome assembly protein PriA; Provisional
Probab=32.25 E-value=37 Score=31.29 Aligned_cols=9 Identities=33% Similarity=1.102 Sum_probs=5.1
Q ss_pred cCCCCCCCC
Q psy4796 160 KCVHCSEPI 168 (274)
Q Consensus 160 ~c~~c~~~~ 168 (274)
.|..|+..+
T Consensus 385 ~C~~Cg~~~ 393 (665)
T PRK14873 385 ACARCRTPA 393 (665)
T ss_pred EhhhCcCee
Confidence 466666543
No 236
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=31.96 E-value=65 Score=23.43 Aligned_cols=57 Identities=19% Similarity=0.257 Sum_probs=30.9
Q ss_pred CccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccC-CchhHHHHHhh-hCCCCc
Q psy4796 191 KKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCN-QSSNLQTHLRI-HKTERE 248 (274)
Q Consensus 191 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~~l~~H~~~-h~~~~~ 248 (274)
....|++|--........ .-.+.+-..|+-.|..=+=.|. +..+|++|.+. |-..+|
T Consensus 79 ~~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~rP 137 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSARP 137 (162)
T ss_pred ccccCccccCceeceEEc-hHHHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCCC
Confidence 347788886554332222 2244555566666755222333 55678888876 544443
No 237
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.87 E-value=57 Score=24.31 Aligned_cols=35 Identities=20% Similarity=0.487 Sum_probs=24.0
Q ss_pred cCCCCcccCCCCCcccCChhHHHHHHhhhcCCCCccCCCCCCcc
Q psy4796 87 HLGWKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRA 130 (274)
Q Consensus 87 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 130 (274)
-.++.-|.|+.|...|+.-..+. ..|.||.||...
T Consensus 108 ~~~~~~y~C~~~~~r~sfdeA~~---------~~F~Cp~Cg~~L 142 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDEAME---------LGFTCPKCGEDL 142 (176)
T ss_pred hccCCceeCCCCCCcccHHHHHH---------hCCCCCCCCchh
Confidence 35566789988888776554432 129999999854
No 238
>PRK12496 hypothetical protein; Provisional
Probab=31.74 E-value=29 Score=25.50 Aligned_cols=11 Identities=18% Similarity=0.395 Sum_probs=7.1
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
|.|.-|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 56777776664
No 239
>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=31.13 E-value=28 Score=19.90 Aligned_cols=23 Identities=22% Similarity=0.495 Sum_probs=9.8
Q ss_pred CCeeeccccCCcchhhHHHHHhhh
Q psy4796 27 ADVTCLHCSLTTPCVMKDMIRHGR 50 (274)
Q Consensus 27 ~~~~C~~C~~~f~~~~~~l~~H~~ 50 (274)
..|.|+.|+..| --.-.+-.|..
T Consensus 20 ~~y~C~~C~~~F-C~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHF-CIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B--HHHHHTTTTT
T ss_pred CeEECCCCCCcc-ccCcChhhhcc
Confidence 346666666666 55555555544
No 240
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.93 E-value=30 Score=20.45 Aligned_cols=37 Identities=16% Similarity=0.379 Sum_probs=17.7
Q ss_pred ccCCCCcc-ccCHHHHHHHHhhccCCCCcccCcCcccc
Q psy4796 194 VCFACPYA-TQYACYIKTHVMTHTGDKPFACSYCDYTC 230 (274)
Q Consensus 194 ~C~~C~~~-f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 230 (274)
.|..|.+. +.+...+..-......-+.|-|+.|....
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rv 41 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRV 41 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhh
Confidence 45555553 33333444333333444456666665443
No 241
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=30.91 E-value=17 Score=21.09 Aligned_cols=11 Identities=18% Similarity=0.872 Sum_probs=2.9
Q ss_pred ceecccccccc
Q psy4796 64 QFLCLFCSYVA 74 (274)
Q Consensus 64 ~~~C~~C~~~f 74 (274)
.|.|++||.+-
T Consensus 33 ~y~Cp~CgAtG 43 (55)
T PF05741_consen 33 KYVCPICGATG 43 (55)
T ss_dssp G---TTT---G
T ss_pred cCcCCCCcCcC
Confidence 46677776653
No 242
>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=30.85 E-value=19 Score=19.53 Aligned_cols=15 Identities=13% Similarity=0.394 Sum_probs=9.3
Q ss_pred CceecCCCCccCCCh
Q psy4796 247 REYACGKCAYRTAAL 261 (274)
Q Consensus 247 ~~~~C~~C~~~f~~~ 261 (274)
-++.|..|++.|-..
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 478899999888654
No 243
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=30.29 E-value=19 Score=20.67 Aligned_cols=11 Identities=18% Similarity=0.486 Sum_probs=6.0
Q ss_pred ecCCCCccCCC
Q psy4796 250 ACGKCAYRTAA 260 (274)
Q Consensus 250 ~C~~C~~~f~~ 260 (274)
.||+|+..|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999998875
No 244
>KOG4727|consensus
Probab=30.27 E-value=37 Score=24.85 Aligned_cols=27 Identities=19% Similarity=0.405 Sum_probs=22.9
Q ss_pred ccCCCccccCCCCccccCHHHHHHHHh
Q psy4796 187 RTDKKKFVCFACPYATQYACYIKTHVM 213 (274)
Q Consensus 187 ~~~~~~~~C~~C~~~f~~~~~l~~H~~ 213 (274)
......|.|.+|+-+|.+.-++.-|+.
T Consensus 70 ~sq~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 70 RSQKGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ccccCceeeeecceeehhhHHHHHHhc
Confidence 344556999999999999999999986
No 245
>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=30.13 E-value=33 Score=17.91 Aligned_cols=12 Identities=25% Similarity=0.525 Sum_probs=6.4
Q ss_pred CCCccccCCCCc
Q psy4796 189 DKKKFVCFACPY 200 (274)
Q Consensus 189 ~~~~~~C~~C~~ 200 (274)
.+..|.|..||-
T Consensus 22 ~dG~~yC~~cG~ 33 (36)
T PF11781_consen 22 DDGFYYCDRCGH 33 (36)
T ss_pred cCCEEEhhhCce
Confidence 334466666653
No 246
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=29.73 E-value=39 Score=17.99 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=6.4
Q ss_pred CCCccccCCCCcc
Q psy4796 189 DKKKFVCFACPYA 201 (274)
Q Consensus 189 ~~~~~~C~~C~~~ 201 (274)
+.+.+.|.+|+..
T Consensus 21 ~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 21 GGKTWICNFCGTK 33 (40)
T ss_dssp TTTEEEETTT--E
T ss_pred CCCEEECcCCCCc
Confidence 3445667776653
No 247
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.43 E-value=37 Score=29.06 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=5.4
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
|+|+.||..+.
T Consensus 368 ~rC~kCg~~~~ 378 (421)
T COG1571 368 FRCKKCGTRAR 378 (421)
T ss_pred cccccccccCC
Confidence 45555554444
No 248
>COG1773 Rubredoxin [Energy production and conversion]
Probab=29.23 E-value=25 Score=20.46 Aligned_cols=10 Identities=20% Similarity=0.487 Sum_probs=5.0
Q ss_pred eeeccccCCc
Q psy4796 29 VTCLHCSLTT 38 (274)
Q Consensus 29 ~~C~~C~~~f 38 (274)
|+|.+||..|
T Consensus 4 ~~C~~CG~vY 13 (55)
T COG1773 4 WRCSVCGYVY 13 (55)
T ss_pred eEecCCceEe
Confidence 4455555544
No 249
>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=28.95 E-value=11 Score=24.00 Aligned_cols=14 Identities=14% Similarity=0.396 Sum_probs=7.6
Q ss_pred ceecccccccccCh
Q psy4796 64 QFLCLFCSYVATAR 77 (274)
Q Consensus 64 ~~~C~~C~~~f~~~ 77 (274)
...|..|+..|...
T Consensus 46 ~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 46 ILSCRVCGESFQTK 59 (81)
T ss_dssp EEEESSS--EEEEE
T ss_pred EEEecCCCCeEEEc
Confidence 45688887776543
No 250
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=28.87 E-value=19 Score=27.29 Aligned_cols=20 Identities=20% Similarity=0.217 Sum_probs=0.0
Q ss_pred eeecccc-CCcchhhHHHHHhh
Q psy4796 29 VTCLHCS-LTTPCVMKDMIRHG 49 (274)
Q Consensus 29 ~~C~~C~-~~f~~~~~~l~~H~ 49 (274)
|.|.+|| ..| ..+..+.+|.
T Consensus 102 y~CEICGN~~Y-~GrkaFekHF 122 (196)
T PF11931_consen 102 YKCEICGNQSY-KGRKAFEKHF 122 (196)
T ss_dssp ----------------------
T ss_pred eeeEeCCCcce-ecHHHHHHhc
Confidence 4455552 344 4444444443
No 251
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=28.09 E-value=19 Score=20.75 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=5.6
Q ss_pred CCcccCcCcc
Q psy4796 219 KPFACSYCDY 228 (274)
Q Consensus 219 ~~~~C~~C~~ 228 (274)
-|+.|+.|.+
T Consensus 27 fPlyCpKCK~ 36 (55)
T PF14205_consen 27 FPLYCPKCKQ 36 (55)
T ss_pred ccccCCCCCc
Confidence 3555666654
No 252
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=27.87 E-value=10 Score=20.84 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=6.3
Q ss_pred CeeeccccCC
Q psy4796 28 DVTCLHCSLT 37 (274)
Q Consensus 28 ~~~C~~C~~~ 37 (274)
+..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 4567777743
No 253
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=27.73 E-value=22 Score=19.13 Aligned_cols=11 Identities=27% Similarity=0.582 Sum_probs=6.6
Q ss_pred ceecCCCCccC
Q psy4796 248 EYACGKCAYRT 258 (274)
Q Consensus 248 ~~~C~~C~~~f 258 (274)
+-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45666666554
No 254
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=27.45 E-value=15 Score=21.40 Aligned_cols=7 Identities=29% Similarity=1.222 Sum_probs=3.3
Q ss_pred cccCcCc
Q psy4796 221 FACSYCD 227 (274)
Q Consensus 221 ~~C~~C~ 227 (274)
|-|..|.
T Consensus 32 YmC~eC~ 38 (56)
T PF09963_consen 32 YMCDECK 38 (56)
T ss_pred eeChhHH
Confidence 4444444
No 255
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=27.42 E-value=30 Score=24.89 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=5.3
Q ss_pred cccCcCccc
Q psy4796 221 FACSYCDYT 229 (274)
Q Consensus 221 ~~C~~C~~~ 229 (274)
|.|..||..
T Consensus 113 l~C~~Cg~~ 121 (146)
T PF07295_consen 113 LVCENCGHE 121 (146)
T ss_pred EecccCCCE
Confidence 666666643
No 256
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.29 E-value=41 Score=24.07 Aligned_cols=33 Identities=12% Similarity=0.276 Sum_probs=18.8
Q ss_pred ccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccC
Q psy4796 192 KFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCN 231 (274)
Q Consensus 192 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 231 (274)
.|.|..|+..+... . .+.....|.|..|+-.+.
T Consensus 112 ~y~C~~C~~~~~~~------r-r~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLRV------R-RSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCceE------c-cccCcceEEcCCCCCEEE
Confidence 57787787766432 1 122224478888876543
No 257
>KOG4727|consensus
Probab=27.21 E-value=35 Score=25.02 Aligned_cols=22 Identities=18% Similarity=0.363 Sum_probs=19.2
Q ss_pred CceecCCCCccCCChhHHHHHH
Q psy4796 247 REYACGKCAYRTAALPDLKLHL 268 (274)
Q Consensus 247 ~~~~C~~C~~~f~~~~~l~~H~ 268 (274)
..|.|.+|.-+|.+..++..|+
T Consensus 74 ~GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred CceeeeecceeehhhHHHHHHh
Confidence 3489999999999999998887
No 258
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=26.70 E-value=37 Score=23.35 Aligned_cols=14 Identities=14% Similarity=0.273 Sum_probs=6.8
Q ss_pred eecccccccccChH
Q psy4796 65 FLCLFCSYVATARI 78 (274)
Q Consensus 65 ~~C~~C~~~f~~~~ 78 (274)
+.|+.||..+.+..
T Consensus 32 ~~C~~CGe~~~~~e 45 (127)
T TIGR03830 32 WYCPACGEELLDPE 45 (127)
T ss_pred eECCCCCCEEEcHH
Confidence 34555555544443
No 260
>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=26.62 E-value=8.9 Score=31.15 Aligned_cols=56 Identities=20% Similarity=0.395 Sum_probs=24.3
Q ss_pred CCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHHHhhhCCCCceecCCCCccCC
Q psy4796 189 DKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTHLRIHKTEREYACGKCAYRTA 259 (274)
Q Consensus 189 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 259 (274)
+.+...|..|+-.+... ...|+.||..-...-.+.. ...-.+.+-+.|..|+..++
T Consensus 194 G~R~L~Cs~C~t~W~~~--------------R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 194 GKRYLHCSLCGTEWRFV--------------RIKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp -EEEEEETTT--EEE----------------TTS-TTT---SS-EEE---------SEEEEEETTTTEEEE
T ss_pred ccEEEEcCCCCCeeeec--------------CCCCcCCCCCCCcceeeEe-cCCCCcEEEEECCcccchHH
Confidence 45667788888665422 2579999876433322210 11122345578999986544
No 261
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=26.52 E-value=90 Score=27.32 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=24.8
Q ss_pred ccCCCccccCCCCccccCHHHHHHHHh-hccC
Q psy4796 187 RTDKKKFVCFACPYATQYACYIKTHVM-THTG 217 (274)
Q Consensus 187 ~~~~~~~~C~~C~~~f~~~~~l~~H~~-~h~~ 217 (274)
+...+-+.|+.|.+.|.+...+..|+. .|.+
T Consensus 52 n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 52 NKSWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred cCceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 444556889999999999999999987 5654
No 262
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=26.42 E-value=34 Score=22.61 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=12.8
Q ss_pred CCCCcccCcCccccCC
Q psy4796 217 GDKPFACSYCDYTCNQ 232 (274)
Q Consensus 217 ~~~~~~C~~C~~~f~~ 232 (274)
..++++|..||..|..
T Consensus 76 ~g~~~rC~eCG~~fkL 91 (97)
T cd00924 76 KGKPKRCPECGHVFKL 91 (97)
T ss_pred CCCceeCCCCCcEEEE
Confidence 3478999999988864
No 263
>KOG4377|consensus
Probab=26.33 E-value=44 Score=28.35 Aligned_cols=23 Identities=13% Similarity=0.505 Sum_probs=18.0
Q ss_pred eecCC--CCccCCChhHHHHHHhhh
Q psy4796 249 YACGK--CAYRTAALPDLKLHLKNM 271 (274)
Q Consensus 249 ~~C~~--C~~~f~~~~~l~~H~~~~ 271 (274)
|.|.. |+..+.+.+.+..|.+.|
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkh 426 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKH 426 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhh
Confidence 56644 888999999998887765
No 264
>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=26.29 E-value=64 Score=26.47 Aligned_cols=54 Identities=20% Similarity=0.426 Sum_probs=29.0
Q ss_pred cCCCccccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCCchhHHHHHhhh-----CCCCceecCCCCccCCC
Q psy4796 188 TDKKKFVCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQSSNLQTHLRIH-----KTEREYACGKCAYRTAA 260 (274)
Q Consensus 188 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h-----~~~~~~~C~~C~~~f~~ 260 (274)
.+.+...|..|+-.+.. +...|+.||.. ..|.. +.+- .+.+-..|..|+...+.
T Consensus 206 ~G~RyL~CslC~teW~~--------------~R~~C~~Cg~~----~~l~y-~~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 206 TGLRYLSCSLCATEWHY--------------VRVKCSHCEES----KHLAY-LSLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred CCceEEEcCCCCCcccc--------------cCccCCCCCCC----Cceee-EeecCCCCCcceEEeeccccccchhh
Confidence 44555667777754332 22578888864 11211 1111 12345789999876554
No 265
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.02 E-value=57 Score=23.62 Aligned_cols=19 Identities=11% Similarity=0.193 Sum_probs=13.3
Q ss_pred CCCccccCCCCccccCHHH
Q psy4796 189 DKKKFVCFACPYATQYACY 207 (274)
Q Consensus 189 ~~~~~~C~~C~~~f~~~~~ 207 (274)
...|..|..||+.|..-..
T Consensus 65 ~~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCCChhHHhCCCCCchHHH
Confidence 3467788888888876543
No 266
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=25.88 E-value=47 Score=22.06 Aligned_cols=27 Identities=19% Similarity=0.538 Sum_probs=15.4
Q ss_pred ccCCCCccccCHHHHHHHHhhccCCCCcccCcCccccCC
Q psy4796 194 VCFACPYATQYACYIKTHVMTHTGDKPFACSYCDYTCNQ 232 (274)
Q Consensus 194 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 232 (274)
.|+.||..+... ...+.|+.|+..+..
T Consensus 2 fC~~Cg~~l~~~------------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------------CCeEECcCCCCcccc
Confidence 367777666321 124677777766543
No 267
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.67 E-value=33 Score=23.86 Aligned_cols=10 Identities=20% Similarity=0.943 Sum_probs=6.0
Q ss_pred CeeeccccCCc
Q psy4796 28 DVTCLHCSLTT 38 (274)
Q Consensus 28 ~~~C~~C~~~f 38 (274)
.+.| .|+..|
T Consensus 70 ~~~C-~Cg~~~ 79 (124)
T PRK00762 70 EIEC-ECGYEG 79 (124)
T ss_pred eEEe-eCcCcc
Confidence 3556 666665
No 268
>KOG2906|consensus
Probab=25.48 E-value=5 Score=26.17 Aligned_cols=12 Identities=42% Similarity=1.137 Sum_probs=6.7
Q ss_pred CccCCCCCCccc
Q psy4796 120 PFACHLCPYRAS 131 (274)
Q Consensus 120 ~~~C~~C~~~f~ 131 (274)
.|.|+.|++.|.
T Consensus 21 rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 21 RFSCRTCPYVFP 32 (105)
T ss_pred eEEcCCCCceee
Confidence 355666666553
No 269
>KOG0717|consensus
Probab=25.44 E-value=42 Score=29.03 Aligned_cols=21 Identities=24% Similarity=0.278 Sum_probs=16.6
Q ss_pred eecCCCCccCCChhHHHHHHh
Q psy4796 249 YACGKCAYRTAALPDLKLHLK 269 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~ 269 (274)
+.|.+|.++|.+...+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 778888888888887777764
No 270
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=25.07 E-value=60 Score=28.66 Aligned_cols=17 Identities=12% Similarity=0.266 Sum_probs=11.4
Q ss_pred CCCCCCCeeeccccCCc
Q psy4796 22 PGPPPADVTCLHCSLTT 38 (274)
Q Consensus 22 ~~~~~~~~~C~~C~~~f 38 (274)
.....+.|.|..|+..|
T Consensus 419 ~~~~~~~~~c~~c~~~y 435 (479)
T PRK05452 419 TADLGPRMQCSVCQWIY 435 (479)
T ss_pred ccCCCCeEEECCCCeEE
Confidence 34455568888888777
No 271
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=25.05 E-value=81 Score=26.22 Aligned_cols=27 Identities=26% Similarity=0.588 Sum_probs=17.7
Q ss_pred ccCCcceeccccc-ccccChHHHHHHHh
Q psy4796 59 TSAKLQFLCLFCS-YVATARIAIKNHLS 85 (274)
Q Consensus 59 h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 85 (274)
|.-...|.|.+|| +++.....+.+|..
T Consensus 369 hgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 369 HGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred cCCCcceeeeecccccccchHHHHhhhh
Confidence 3446667788887 66666666766654
No 272
>PLN02294 cytochrome c oxidase subunit Vb
Probab=24.93 E-value=38 Score=24.89 Aligned_cols=18 Identities=22% Similarity=0.499 Sum_probs=14.0
Q ss_pred cCCCCcccCcCccccCCc
Q psy4796 216 TGDKPFACSYCDYTCNQS 233 (274)
Q Consensus 216 ~~~~~~~C~~C~~~f~~~ 233 (274)
+..++++|++||..|..+
T Consensus 137 ~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 137 EKGKSFECPVCTQYFELE 154 (174)
T ss_pred cCCCceeCCCCCCEEEEE
Confidence 446789999999988743
No 273
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=24.74 E-value=78 Score=25.72 Aligned_cols=41 Identities=15% Similarity=0.209 Sum_probs=27.9
Q ss_pred CeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHh
Q psy4796 28 DVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLS 85 (274)
Q Consensus 28 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 85 (274)
-.+|+.|+... ....|..... .|+.|+.-|.-...-+....
T Consensus 26 ~~~c~~c~~~~--~~~~l~~~~~---------------vc~~c~~h~rl~areRi~~L 66 (285)
T TIGR00515 26 WTKCPKCGQVL--YTKELERNLE---------------VCPKCDHHMRMDARERIESL 66 (285)
T ss_pred eeECCCCcchh--hHHHHHhhCC---------------CCCCCCCcCcCCHHHHHHHc
Confidence 46799999988 4444555443 69999998876554444443
No 274
>KOG1842|consensus
Probab=24.48 E-value=48 Score=28.47 Aligned_cols=30 Identities=17% Similarity=0.187 Sum_probs=24.6
Q ss_pred CCCCCCeeeccccCCcchhhHHHHHhhhccc
Q psy4796 23 GPPPADVTCLHCSLTTPCVMKDMIRHGRLCE 53 (274)
Q Consensus 23 ~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~ 53 (274)
+.....|.||+|...| ...+.|..|+...|
T Consensus 10 ~~i~egflCPiC~~dl-~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 10 GEILEGFLCPICLLDL-PNLSALNDHLDVEH 39 (505)
T ss_pred chhhhcccCchHhhhh-hhHHHHHHHHhhhc
Confidence 3444569999999999 99999999998633
No 275
>KOG4118|consensus
Probab=24.46 E-value=33 Score=20.54 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=17.4
Q ss_pred eecCCCCccCCChhHHHHHHhhhcC
Q psy4796 249 YACGKCAYRTAALPDLKLHLKNMHL 273 (274)
Q Consensus 249 ~~C~~C~~~f~~~~~l~~H~~~~H~ 273 (274)
|+|.+|-...++.-.+..|....|+
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCC
Confidence 6777777777777777777666554
No 276
>KOG2071|consensus
Probab=24.37 E-value=48 Score=29.59 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=19.3
Q ss_pred CCCcccCcCccccCCchhHHHHHhhhC
Q psy4796 218 DKPFACSYCDYTCNQSSNLQTHLRIHK 244 (274)
Q Consensus 218 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 244 (274)
..+-+|..||.+|.+......||..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 455778888888887777777776664
No 277
>PHA02998 RNA polymerase subunit; Provisional
Probab=23.84 E-value=25 Score=26.00 Aligned_cols=11 Identities=27% Similarity=0.618 Sum_probs=5.8
Q ss_pred cccCcCccccC
Q psy4796 221 FACSYCDYTCN 231 (274)
Q Consensus 221 ~~C~~C~~~f~ 231 (274)
|.|..||..|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 55555555543
No 278
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=23.77 E-value=79 Score=25.81 Aligned_cols=41 Identities=15% Similarity=0.197 Sum_probs=27.8
Q ss_pred CeeeccccCCcchhhHHHHHhhhccccccccccCCcceecccccccccChHHHHHHHh
Q psy4796 28 DVTCLHCSLTTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCLFCSYVATARIAIKNHLS 85 (274)
Q Consensus 28 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 85 (274)
-.+|+.|+... ....|..... .|+.|+.-|.-...-+..+.
T Consensus 27 ~~~c~~c~~~~--~~~~l~~~~~---------------vc~~c~~h~rl~areRi~~L 67 (292)
T PRK05654 27 WTKCPSCGQVL--YRKELEANLN---------------VCPKCGHHMRISARERLDLL 67 (292)
T ss_pred eeECCCccchh--hHHHHHhcCC---------------CCCCCCCCeeCCHHHHHHHH
Confidence 46799999888 4445555443 69999998875554444443
No 279
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=23.25 E-value=27 Score=19.41 Aligned_cols=8 Identities=38% Similarity=1.070 Sum_probs=4.5
Q ss_pred eccccCCc
Q psy4796 31 CLHCSLTT 38 (274)
Q Consensus 31 C~~C~~~f 38 (274)
|+.||...
T Consensus 2 CP~Cg~~a 9 (47)
T PF04606_consen 2 CPHCGSKA 9 (47)
T ss_pred cCCCCCee
Confidence 55665544
No 280
>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=23.13 E-value=52 Score=23.79 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=9.0
Q ss_pred CCCCeeeccccCCc
Q psy4796 25 PPADVTCLHCSLTT 38 (274)
Q Consensus 25 ~~~~~~C~~C~~~f 38 (274)
+....+|..|++.|
T Consensus 11 p~~vv~C~~c~kWF 24 (152)
T PF09416_consen 11 PSCVVKCNTCNKWF 24 (152)
T ss_dssp CCCEEEETTTTEEE
T ss_pred cccEeEcCCCCcEe
Confidence 33456777777766
No 281
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=22.91 E-value=41 Score=17.62 Aligned_cols=10 Identities=30% Similarity=0.766 Sum_probs=5.0
Q ss_pred ceecCCCCcc
Q psy4796 248 EYACGKCAYR 257 (274)
Q Consensus 248 ~~~C~~C~~~ 257 (274)
.|+|..||..
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4788888764
No 282
>KOG1994|consensus
Probab=22.38 E-value=42 Score=25.91 Aligned_cols=23 Identities=17% Similarity=0.414 Sum_probs=20.2
Q ss_pred CCccccCCCCccccCHHHHHHHH
Q psy4796 190 KKKFVCFACPYATQYACYIKTHV 212 (274)
Q Consensus 190 ~~~~~C~~C~~~f~~~~~l~~H~ 212 (274)
...|.|-+||..|.+...|..|.
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhC
Confidence 34599999999999999999885
No 283
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=21.74 E-value=38 Score=25.12 Aligned_cols=11 Identities=18% Similarity=0.489 Sum_probs=9.4
Q ss_pred CeeeccccCCc
Q psy4796 28 DVTCLHCSLTT 38 (274)
Q Consensus 28 ~~~C~~C~~~f 38 (274)
.|.|..|.+.|
T Consensus 139 ~~rC~GC~~~f 149 (177)
T COG1439 139 RLRCHGCKRIF 149 (177)
T ss_pred eEEEecCceec
Confidence 37899999999
No 284
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.48 E-value=51 Score=30.58 Aligned_cols=7 Identities=43% Similarity=1.450 Sum_probs=3.1
Q ss_pred cCCCCCc
Q psy4796 94 KCPHCDH 100 (274)
Q Consensus 94 ~C~~C~~ 100 (274)
.|+.|+.
T Consensus 423 ~Cp~Cg~ 429 (679)
T PRK05580 423 ACPECGS 429 (679)
T ss_pred CCCCCcC
Confidence 4444433
No 285
>KOG3214|consensus
Probab=20.68 E-value=46 Score=21.94 Aligned_cols=13 Identities=15% Similarity=0.309 Sum_probs=7.3
Q ss_pred eecccccccccCh
Q psy4796 65 FLCLFCSYVATAR 77 (274)
Q Consensus 65 ~~C~~C~~~f~~~ 77 (274)
..|.+|+..|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 3466666666544
No 286
>KOG2747|consensus
Probab=20.65 E-value=53 Score=27.87 Aligned_cols=29 Identities=17% Similarity=0.224 Sum_probs=20.7
Q ss_pred CCCCCeeeccccCCcchhhHHHHHhhhccc
Q psy4796 24 PPPADVTCLHCSLTTPCVMKDMIRHGRLCE 53 (274)
Q Consensus 24 ~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~ 53 (274)
.....|.|..|-+.+ .....|.+|+..|.
T Consensus 154 ~~~~lYiCEfCLkY~-~s~~~l~rH~~kC~ 182 (396)
T KOG2747|consen 154 KLDKLYICEFCLKYM-KSRTSLQRHLKKCK 182 (396)
T ss_pred cCCeEEEehHHHhHh-chHHHHHHHHHhcC
Confidence 334557788888777 77888888877554
No 287
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.57 E-value=89 Score=15.89 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=6.7
Q ss_pred CCCeeeccccCC
Q psy4796 26 PADVTCLHCSLT 37 (274)
Q Consensus 26 ~~~~~C~~C~~~ 37 (274)
...|.|..|++.
T Consensus 6 P~~Y~C~~C~~~ 17 (32)
T PF13696_consen 6 PPGYVCHRCGQK 17 (32)
T ss_pred CCCCEeecCCCC
Confidence 334666666543
No 288
>PRK05978 hypothetical protein; Provisional
Probab=20.56 E-value=39 Score=24.35 Aligned_cols=11 Identities=27% Similarity=0.359 Sum_probs=7.7
Q ss_pred ecccccccccC
Q psy4796 66 LCLFCSYVATA 76 (274)
Q Consensus 66 ~C~~C~~~f~~ 76 (274)
.|+.||..|..
T Consensus 54 ~C~~CG~~~~~ 64 (148)
T PRK05978 54 HCAACGEDFTH 64 (148)
T ss_pred CccccCCcccc
Confidence 48888877753
No 289
>PTZ00448 hypothetical protein; Provisional
Probab=20.08 E-value=69 Score=26.91 Aligned_cols=23 Identities=22% Similarity=0.440 Sum_probs=18.8
Q ss_pred ceecCCCCccCCChhHHHHHHhh
Q psy4796 248 EYACGKCAYRTAALPDLKLHLKN 270 (274)
Q Consensus 248 ~~~C~~C~~~f~~~~~l~~H~~~ 270 (274)
.|.|..|+..|.+......|++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888764
Done!