Query psy11318
Match_columns 263
No_of_seqs 174 out of 2217
Neff 10.4
Searched_HMMs 46136
Date Fri Aug 16 15:20:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11318.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11318hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 5E-31 1.1E-35 202.1 6.6 134 29-166 130-266 (279)
2 KOG2462|consensus 100.0 5.1E-30 1.1E-34 196.6 3.7 133 57-193 130-265 (279)
3 KOG1074|consensus 100.0 1.2E-29 2.7E-34 218.9 1.3 142 58-201 606-937 (958)
4 KOG3608|consensus 99.9 5.3E-24 1.1E-28 167.9 8.6 183 6-193 183-374 (467)
5 KOG3623|consensus 99.9 9.1E-25 2E-29 186.3 4.5 78 114-193 895-972 (1007)
6 KOG3608|consensus 99.9 5.7E-23 1.2E-27 162.1 6.7 185 6-195 140-345 (467)
7 KOG1074|consensus 99.9 1.6E-23 3.4E-28 181.5 3.7 170 2-173 605-937 (958)
8 KOG3623|consensus 99.8 8.2E-22 1.8E-26 168.5 3.2 77 86-164 895-971 (1007)
9 KOG3576|consensus 99.8 1.5E-19 3.3E-24 132.5 3.6 108 2-109 117-236 (267)
10 KOG3576|consensus 99.7 2.9E-19 6.4E-24 131.0 0.9 111 84-196 116-237 (267)
11 PLN03086 PRLI-interacting fact 99.4 3.4E-13 7.4E-18 116.4 8.9 96 59-163 455-560 (567)
12 PLN03086 PRLI-interacting fact 99.3 4.9E-12 1.1E-16 109.4 7.5 143 29-192 407-561 (567)
13 PHA00733 hypothetical protein 99.1 3.7E-11 8.1E-16 85.2 4.2 82 27-110 38-124 (128)
14 PHA00733 hypothetical protein 99.1 6.5E-11 1.4E-15 84.0 4.4 81 84-168 39-124 (128)
15 KOG3993|consensus 99.1 1.1E-11 2.5E-16 100.9 -0.7 188 3-193 268-480 (500)
16 PHA02768 hypothetical protein; 99.1 4.4E-11 9.5E-16 70.0 1.7 43 3-46 6-48 (55)
17 PHA02768 hypothetical protein; 99.0 4.4E-10 9.4E-15 65.8 3.1 45 143-189 5-49 (55)
18 KOG3993|consensus 98.6 3.2E-09 7E-14 86.9 -1.2 52 30-81 268-319 (500)
19 PHA00732 hypothetical protein 98.6 2.4E-08 5.3E-13 64.3 2.8 49 2-55 1-50 (79)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 3.4E-08 7.3E-13 49.4 1.5 23 159-181 2-24 (26)
21 PHA00616 hypothetical protein 98.5 6.3E-08 1.4E-12 54.0 2.2 33 143-175 1-33 (44)
22 PF13465 zf-H2C2_2: Zinc-finge 98.5 5.2E-08 1.1E-12 48.8 1.7 26 130-155 1-26 (26)
23 PF05605 zf-Di19: Drought indu 98.4 4.6E-07 1E-11 54.2 4.3 48 3-53 3-53 (54)
24 PHA00616 hypothetical protein 98.4 1.2E-07 2.7E-12 52.8 1.6 33 30-62 2-34 (44)
25 PF05605 zf-Di19: Drought indu 98.3 9.2E-07 2E-11 52.9 4.5 50 29-81 2-53 (54)
26 PHA00732 hypothetical protein 98.3 4.7E-07 1E-11 58.3 2.2 44 29-77 1-44 (79)
27 PF00096 zf-C2H2: Zinc finger, 98.2 1.1E-06 2.4E-11 42.6 1.9 22 3-24 1-22 (23)
28 KOG2231|consensus 98.1 4.5E-05 9.8E-10 67.7 12.1 134 31-175 117-275 (669)
29 PF00096 zf-C2H2: Zinc finger, 98.0 4.9E-06 1.1E-10 40.3 2.1 22 30-51 1-22 (23)
30 PF13894 zf-C2H2_4: C2H2-type 97.9 7E-06 1.5E-10 40.0 2.1 23 3-25 1-23 (24)
31 PF12756 zf-C2H2_2: C2H2 type 97.9 6.5E-06 1.4E-10 56.1 2.7 23 5-27 2-24 (100)
32 PF13894 zf-C2H2_4: C2H2-type 97.9 1E-05 2.2E-10 39.4 2.3 24 30-53 1-24 (24)
33 PF13912 zf-C2H2_6: C2H2-type 97.7 2.1E-05 4.5E-10 39.7 1.8 25 2-26 1-25 (27)
34 PF12756 zf-C2H2_2: C2H2 type 97.7 2.2E-05 4.8E-10 53.4 2.4 73 31-108 1-73 (100)
35 COG5236 Uncharacterized conser 97.6 0.0003 6.5E-09 56.9 7.2 130 29-168 151-306 (493)
36 PF13912 zf-C2H2_6: C2H2-type 97.6 3.5E-05 7.6E-10 38.8 1.3 25 29-53 1-25 (27)
37 COG5189 SFP1 Putative transcri 97.6 4.5E-05 9.7E-10 60.8 2.3 53 140-192 346-419 (423)
38 KOG1146|consensus 97.6 2.4E-05 5.3E-10 73.3 1.0 80 1-80 464-612 (1406)
39 COG5189 SFP1 Putative transcri 97.5 2.6E-05 5.7E-10 62.1 0.8 54 111-164 347-419 (423)
40 smart00355 ZnF_C2H2 zinc finge 97.4 0.00017 3.7E-09 35.6 2.3 23 3-25 1-23 (26)
41 KOG2231|consensus 97.2 0.0011 2.3E-08 59.2 6.8 134 3-146 100-274 (669)
42 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00027 5.9E-09 34.4 1.5 22 3-25 1-22 (24)
43 PF09237 GAGA: GAGA factor; I 97.1 0.0004 8.7E-09 39.7 1.9 29 28-56 23-51 (54)
44 KOG1146|consensus 97.1 0.00017 3.8E-09 67.9 0.6 129 60-193 439-611 (1406)
45 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00053 1.1E-08 33.3 2.0 23 30-53 1-23 (24)
46 smart00355 ZnF_C2H2 zinc finge 97.0 0.00086 1.9E-08 32.9 2.5 23 30-52 1-23 (26)
47 PF09237 GAGA: GAGA factor; I 96.9 0.00059 1.3E-08 39.0 1.9 31 141-171 22-52 (54)
48 PF12874 zf-met: Zinc-finger o 96.9 0.00056 1.2E-08 33.6 1.6 22 3-24 1-22 (25)
49 PF12874 zf-met: Zinc-finger o 96.8 0.00076 1.6E-08 33.1 1.3 22 30-51 1-22 (25)
50 COG5236 Uncharacterized conser 96.7 0.0023 4.9E-08 52.0 4.2 130 2-140 151-306 (493)
51 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.00084 1.8E-08 33.7 0.5 22 3-24 2-23 (27)
52 KOG2785|consensus 96.4 0.0084 1.8E-07 49.6 6.0 49 3-51 4-90 (390)
53 PRK04860 hypothetical protein; 96.3 0.0018 4E-08 47.8 1.4 39 143-185 119-157 (160)
54 KOG2785|consensus 96.2 0.0079 1.7E-07 49.7 4.4 51 143-193 166-242 (390)
55 PF12171 zf-C2H2_jaz: Zinc-fin 96.1 0.0013 2.9E-08 32.9 -0.2 22 30-51 2-23 (27)
56 PRK04860 hypothetical protein; 95.9 0.0043 9.3E-08 45.9 1.8 34 30-67 120-153 (160)
57 COG5048 FOG: Zn-finger [Genera 95.5 0.0017 3.6E-08 56.4 -2.0 60 29-88 289-354 (467)
58 KOG2482|consensus 95.5 0.033 7.1E-07 45.5 5.2 134 3-138 145-357 (423)
59 KOG2893|consensus 95.4 0.003 6.5E-08 48.6 -0.6 50 30-83 11-60 (341)
60 KOG2482|consensus 95.3 0.042 9.1E-07 44.8 5.4 50 144-193 280-356 (423)
61 KOG4173|consensus 95.1 0.011 2.4E-07 44.5 1.5 105 38-165 48-168 (253)
62 smart00451 ZnF_U1 U1-like zinc 95.0 0.019 4E-07 30.6 1.8 21 3-23 4-24 (35)
63 COG5048 FOG: Zn-finger [Genera 94.8 0.0059 1.3E-07 52.9 -0.9 142 56-197 288-444 (467)
64 cd00350 rubredoxin_like Rubred 94.2 0.024 5.3E-07 29.8 1.1 24 3-37 2-25 (33)
65 PF13913 zf-C2HC_2: zinc-finge 94.2 0.045 9.8E-07 26.7 1.9 19 4-23 4-22 (25)
66 PF13913 zf-C2HC_2: zinc-finge 94.2 0.048 1E-06 26.6 2.0 21 30-51 3-23 (25)
67 smart00451 ZnF_U1 U1-like zinc 94.1 0.035 7.7E-07 29.4 1.6 23 29-51 3-25 (35)
68 TIGR02098 MJ0042_CXXC MJ0042 f 94.0 0.024 5.2E-07 30.9 0.9 36 1-40 1-36 (38)
69 KOG2893|consensus 94.0 0.016 3.4E-07 44.8 0.1 51 2-55 10-60 (341)
70 TIGR00622 ssl1 transcription f 93.2 0.11 2.5E-06 35.6 3.2 49 115-167 57-105 (112)
71 KOG2186|consensus 92.8 0.047 1E-06 42.7 1.0 54 3-58 4-57 (276)
72 PF12013 DUF3505: Protein of u 92.7 0.2 4.4E-06 34.5 4.0 26 143-168 80-109 (109)
73 PF13717 zinc_ribbon_4: zinc-r 92.6 0.06 1.3E-06 28.9 1.0 35 1-39 1-35 (36)
74 TIGR00622 ssl1 transcription f 92.4 0.2 4.4E-06 34.4 3.6 24 113-138 81-104 (112)
75 PF09986 DUF2225: Uncharacteri 92.1 0.022 4.8E-07 44.5 -1.6 23 1-23 4-26 (214)
76 COG4049 Uncharacterized protei 91.9 0.094 2E-06 30.6 1.3 30 139-168 13-42 (65)
77 PF12013 DUF3505: Protein of u 91.7 0.4 8.7E-06 33.1 4.5 25 86-110 81-109 (109)
78 KOG4173|consensus 91.5 0.1 2.3E-06 39.5 1.5 79 29-110 79-171 (253)
79 cd00729 rubredoxin_SM Rubredox 90.5 0.13 2.8E-06 27.2 0.8 25 2-37 2-26 (34)
80 COG4049 Uncharacterized protei 90.1 0.15 3.1E-06 29.8 0.9 26 84-109 16-41 (65)
81 PF13719 zinc_ribbon_5: zinc-r 89.6 0.19 4.2E-06 27.1 1.1 36 1-40 1-36 (37)
82 smart00659 RPOLCX RNA polymera 87.7 0.31 6.6E-06 27.5 1.1 28 1-38 1-28 (44)
83 PF06524 NOA36: NOA36 protein; 87.7 0.23 4.9E-06 39.1 0.8 92 80-192 137-230 (314)
84 PF09538 FYDLN_acid: Protein o 86.3 0.56 1.2E-05 32.2 2.0 13 85-97 26-38 (108)
85 PF06524 NOA36: NOA36 protein; 85.7 0.72 1.6E-05 36.4 2.5 94 52-166 137-232 (314)
86 smart00834 CxxC_CXXC_SSSS Puta 85.1 0.17 3.7E-06 27.9 -0.8 11 3-13 6-16 (41)
87 smart00531 TFIIE Transcription 85.1 0.44 9.4E-06 34.9 1.1 36 28-67 98-133 (147)
88 COG1592 Rubrerythrin [Energy p 83.2 0.67 1.5E-05 34.4 1.4 24 143-179 134-157 (166)
89 TIGR02605 CxxC_CxxC_SSSS putat 82.5 0.27 5.9E-06 28.7 -0.7 11 3-13 6-16 (52)
90 PF09538 FYDLN_acid: Protein o 82.1 1.1 2.4E-05 30.8 2.0 30 144-184 10-39 (108)
91 PF15269 zf-C2H2_7: Zinc-finge 82.1 1 2.2E-05 25.1 1.5 21 30-50 21-41 (54)
92 PRK00398 rpoP DNA-directed RNA 82.0 0.32 7E-06 27.7 -0.5 12 2-13 3-14 (46)
93 PRK00464 nrdR transcriptional 82.0 0.18 3.9E-06 37.0 -2.0 16 30-45 29-44 (154)
94 PF02892 zf-BED: BED zinc fing 81.7 1.3 2.7E-05 24.9 1.9 23 29-51 16-42 (45)
95 PF09986 DUF2225: Uncharacteri 81.4 0.24 5.2E-06 38.7 -1.6 22 29-50 5-26 (214)
96 smart00734 ZnF_Rad18 Rad18-lik 81.2 1.5 3.3E-05 21.5 1.8 19 4-23 3-21 (26)
97 COG1996 RPC10 DNA-directed RNA 79.6 0.75 1.6E-05 26.5 0.4 11 2-12 6-16 (49)
98 PF15269 zf-C2H2_7: Zinc-finge 79.5 1.3 2.9E-05 24.6 1.4 21 2-22 20-40 (54)
99 PF14353 CpXC: CpXC protein 78.9 0.19 4E-06 35.9 -2.7 20 29-48 38-57 (128)
100 TIGR00373 conserved hypothetic 78.4 2.3 5E-05 31.5 2.9 34 139-181 105-138 (158)
101 TIGR00373 conserved hypothetic 77.5 3 6.5E-05 30.9 3.3 18 84-101 108-125 (158)
102 COG2888 Predicted Zn-ribbon RN 77.5 2.3 5E-05 25.4 2.1 8 113-120 50-57 (61)
103 PF02176 zf-TRAF: TRAF-type zi 77.4 1.7 3.7E-05 26.1 1.6 21 42-62 23-43 (60)
104 smart00614 ZnF_BED BED zinc fi 77.0 2.5 5.3E-05 24.5 2.1 23 29-51 18-45 (50)
105 PF05443 ROS_MUCR: ROS/MUCR tr 76.1 1.1 2.4E-05 31.9 0.6 26 143-171 72-97 (132)
106 PF08274 PhnA_Zn_Ribbon: PhnA 75.7 1.1 2.3E-05 23.0 0.3 24 4-37 4-27 (30)
107 PF03604 DNA_RNApol_7kD: DNA d 75.5 1.9 4.1E-05 22.4 1.2 26 3-38 1-26 (32)
108 TIGR02300 FYDLN_acid conserved 75.1 2.4 5.1E-05 29.8 1.9 30 86-128 10-39 (129)
109 PF09723 Zn-ribbon_8: Zinc rib 74.0 0.53 1.2E-05 26.2 -1.2 11 3-13 6-16 (42)
110 PRK06266 transcription initiat 73.2 4.3 9.3E-05 30.8 3.1 13 58-70 118-130 (178)
111 PF05443 ROS_MUCR: ROS/MUCR tr 73.2 2.1 4.6E-05 30.5 1.4 26 29-57 72-97 (132)
112 PRK06266 transcription initiat 73.1 3.3 7.2E-05 31.3 2.5 35 140-183 114-148 (178)
113 KOG1280|consensus 72.9 1.2 2.7E-05 36.7 0.2 36 58-93 80-117 (381)
114 COG4957 Predicted transcriptio 72.1 1.9 4.2E-05 30.4 1.0 25 144-171 77-101 (148)
115 COG5151 SSL1 RNA polymerase II 71.7 1.8 3.9E-05 35.2 0.9 26 142-167 387-412 (421)
116 PF10571 UPF0547: Uncharacteri 71.4 2.7 5.9E-05 20.6 1.2 6 115-120 16-21 (26)
117 PRK04023 DNA polymerase II lar 70.4 4.5 9.9E-05 38.6 3.2 9 86-94 664-672 (1121)
118 PF07754 DUF1610: Domain of un 70.3 1.7 3.7E-05 20.9 0.3 9 2-10 16-24 (24)
119 PF06220 zf-U1: U1 zinc finger 69.9 3.7 7.9E-05 22.3 1.6 12 1-12 2-13 (38)
120 KOG2186|consensus 69.7 2.8 6E-05 33.2 1.4 48 30-80 4-51 (276)
121 smart00531 TFIIE Transcription 69.3 6.1 0.00013 28.9 3.2 37 141-181 97-133 (147)
122 TIGR01206 lysW lysine biosynth 69.1 2.1 4.6E-05 25.3 0.6 11 2-12 2-12 (54)
123 COG1592 Rubrerythrin [Energy p 69.0 3.3 7.1E-05 30.9 1.6 23 85-120 134-156 (166)
124 PRK09678 DNA-binding transcrip 68.6 1.4 3.1E-05 27.7 -0.2 12 58-69 28-41 (72)
125 PHA00626 hypothetical protein 68.2 2.2 4.8E-05 25.1 0.5 12 2-13 23-34 (59)
126 KOG2807|consensus 67.8 8.8 0.00019 31.7 3.9 25 143-167 345-369 (378)
127 COG1198 PriA Primosomal protei 67.3 3.4 7.4E-05 38.5 1.8 29 137-180 456-484 (730)
128 COG5188 PRP9 Splicing factor 3 67.1 8.1 0.00018 32.2 3.7 29 107-136 368-396 (470)
129 KOG4124|consensus 67.0 0.66 1.4E-05 38.3 -2.5 49 1-49 348-418 (442)
130 COG1198 PriA Primosomal protei 66.6 3.7 8E-05 38.2 1.8 9 112-120 474-482 (730)
131 KOG2593|consensus 65.9 5.7 0.00012 34.1 2.7 37 141-180 126-162 (436)
132 PF04959 ARS2: Arsenite-resist 65.9 2.5 5.3E-05 33.0 0.5 27 29-55 77-103 (214)
133 KOG2807|consensus 65.7 9.5 0.00021 31.5 3.7 31 112-150 344-374 (378)
134 KOG1280|consensus 64.7 5.7 0.00012 33.0 2.4 23 3-25 80-102 (381)
135 PF13878 zf-C2H2_3: zinc-finge 64.5 9.5 0.00021 21.0 2.6 26 114-139 14-39 (41)
136 PRK14890 putative Zn-ribbon RN 62.3 7.3 0.00016 23.4 1.9 8 113-120 48-55 (59)
137 COG1997 RPL43A Ribosomal prote 62.0 3.3 7.2E-05 26.9 0.5 11 144-154 54-64 (89)
138 COG3357 Predicted transcriptio 59.0 4.7 0.0001 26.4 0.8 27 84-120 57-83 (97)
139 COG5188 PRP9 Splicing factor 3 58.4 13 0.00028 31.1 3.3 22 86-107 239-260 (470)
140 PF09963 DUF2197: Uncharacteri 57.8 4 8.6E-05 24.2 0.3 37 1-37 1-39 (56)
141 KOG2593|consensus 56.9 5.1 0.00011 34.4 0.9 35 29-66 128-162 (436)
142 KOG4377|consensus 56.4 3.5 7.7E-05 35.0 -0.1 25 144-168 402-428 (480)
143 KOG4377|consensus 55.8 4.4 9.4E-05 34.5 0.3 22 176-197 408-429 (480)
144 KOG4167|consensus 55.3 3.2 6.8E-05 38.0 -0.6 22 4-25 794-815 (907)
145 PRK14873 primosome assembly pr 53.1 8.3 0.00018 35.8 1.7 7 59-65 385-391 (665)
146 COG1773 Rubredoxin [Energy pro 52.9 6 0.00013 23.4 0.5 13 2-14 3-15 (55)
147 COG4530 Uncharacterized protei 52.3 9.7 0.00021 25.9 1.5 11 85-95 26-36 (129)
148 PF05191 ADK_lid: Adenylate ki 52.3 5.4 0.00012 21.3 0.2 29 145-181 3-31 (36)
149 PF08790 zf-LYAR: LYAR-type C2 51.6 3.3 7.1E-05 20.7 -0.6 8 32-39 3-10 (28)
150 PF14446 Prok-RING_1: Prokaryo 51.5 12 0.00026 22.0 1.6 10 4-13 7-16 (54)
151 TIGR00595 priA primosomal prot 50.7 8.7 0.00019 34.4 1.4 13 138-150 235-247 (505)
152 PRK14714 DNA polymerase II lar 50.3 15 0.00032 36.4 2.8 11 57-67 692-702 (1337)
153 KOG4167|consensus 50.1 5.6 0.00012 36.5 0.1 26 58-83 793-818 (907)
154 PF04959 ARS2: Arsenite-resist 49.7 8.1 0.00018 30.2 0.9 29 84-112 76-104 (214)
155 PF14445 Prok-RING_2: Prokaryo 49.3 5.3 0.00012 22.9 -0.1 20 2-22 7-26 (57)
156 PF15135 UPF0515: Uncharacteri 48.4 14 0.00031 29.2 2.1 26 41-66 91-121 (278)
157 TIGR00595 priA primosomal prot 48.3 11 0.00024 33.7 1.7 8 113-120 253-260 (505)
158 COG1655 Uncharacterized protei 47.7 3.4 7.3E-05 32.2 -1.4 27 29-55 19-45 (267)
159 PF05290 Baculo_IE-1: Baculovi 47.1 3.8 8.3E-05 29.0 -1.1 54 28-99 79-135 (140)
160 PF00301 Rubredoxin: Rubredoxi 46.5 6.9 0.00015 22.4 0.1 15 2-16 1-15 (47)
161 KOG1044|consensus 45.2 2.7 5.8E-05 37.3 -2.5 28 172-199 219-248 (670)
162 PF13453 zf-TFIIB: Transcripti 44.8 11 0.00023 20.7 0.7 19 29-47 19-37 (41)
163 KOG0717|consensus 44.7 12 0.00027 32.5 1.3 22 3-24 293-314 (508)
164 COG2331 Uncharacterized protei 44.5 9.5 0.00021 24.1 0.5 31 30-67 13-43 (82)
165 PRK12380 hydrogenase nickel in 44.5 8.9 0.00019 26.6 0.4 25 29-65 70-94 (113)
166 PF03833 PolC_DP2: DNA polymer 44.4 7.4 0.00016 36.5 0.0 8 30-37 656-663 (900)
167 PF12760 Zn_Tnp_IS1595: Transp 44.0 17 0.00036 20.5 1.4 7 144-150 19-25 (46)
168 PF13824 zf-Mss51: Zinc-finger 43.8 28 0.0006 20.7 2.3 14 29-42 14-27 (55)
169 PF09416 UPF1_Zn_bind: RNA hel 43.8 33 0.00072 25.2 3.2 17 53-69 10-26 (152)
170 PF08271 TF_Zn_Ribbon: TFIIB z 43.8 7.6 0.00016 21.5 -0.0 9 3-11 1-9 (43)
171 PF07282 OrfB_Zn_ribbon: Putat 43.8 17 0.00036 22.4 1.6 29 31-69 30-58 (69)
172 PF01363 FYVE: FYVE zinc finge 43.0 14 0.0003 22.8 1.1 9 31-39 11-19 (69)
173 KOG4124|consensus 43.0 9.4 0.0002 31.8 0.4 51 142-192 348-419 (442)
174 PF03884 DUF329: Domain of unk 42.8 7.9 0.00017 23.1 -0.0 13 1-13 1-13 (57)
175 KOG3408|consensus 42.5 13 0.00028 25.9 0.9 23 29-51 57-79 (129)
176 PRK03824 hypA hydrogenase nick 40.4 10 0.00022 27.3 0.2 12 58-69 71-82 (135)
177 KOG2907|consensus 39.6 10 0.00022 26.0 0.1 11 144-154 103-113 (116)
178 TIGR00100 hypA hydrogenase nic 39.2 11 0.00024 26.2 0.2 26 29-66 70-95 (115)
179 PRK00432 30S ribosomal protein 38.1 14 0.00031 21.4 0.5 11 57-67 37-47 (50)
180 cd00730 rubredoxin Rubredoxin; 37.8 15 0.00033 21.3 0.6 12 3-14 2-13 (50)
181 smart00154 ZnF_AN1 AN1-like Zi 37.5 15 0.00032 20.0 0.5 13 2-14 12-24 (39)
182 smart00661 RPOL9 RNA polymeras 36.8 13 0.00028 21.4 0.2 11 29-39 20-30 (52)
183 KOG2636|consensus 36.3 23 0.0005 30.7 1.7 23 29-51 401-424 (497)
184 PF13451 zf-trcl: Probable zin 36.1 22 0.00048 20.5 1.1 12 58-69 5-16 (49)
185 COG1571 Predicted DNA-binding 35.8 22 0.00048 30.8 1.5 32 145-187 352-383 (421)
186 PF06397 Desulfoferrod_N: Desu 35.5 13 0.00029 19.8 0.1 9 3-11 7-15 (36)
187 PF04780 DUF629: Protein of un 35.3 22 0.00048 31.3 1.5 25 143-167 57-81 (466)
188 PTZ00255 60S ribosomal protein 35.1 11 0.00024 24.9 -0.3 10 144-153 55-64 (90)
189 KOG0782|consensus 34.9 9.9 0.00022 33.9 -0.7 55 17-76 240-296 (1004)
190 KOG3408|consensus 34.6 28 0.00062 24.3 1.6 27 140-166 54-80 (129)
191 PRK05978 hypothetical protein; 34.1 13 0.00028 27.2 -0.1 32 29-69 33-64 (148)
192 smart00440 ZnF_C2C2 C2C2 Zinc 34.1 3.6 7.9E-05 22.5 -2.3 9 172-180 29-37 (40)
193 PRK00564 hypA hydrogenase nick 34.1 21 0.00045 25.0 0.9 14 29-42 71-84 (117)
194 PF11672 DUF3268: Protein of u 34.0 16 0.00035 24.8 0.4 10 1-10 1-10 (102)
195 COG1571 Predicted DNA-binding 33.7 22 0.00048 30.8 1.2 30 115-157 352-381 (421)
196 PRK03681 hypA hydrogenase nick 32.9 22 0.00047 24.7 0.9 13 29-41 70-82 (114)
197 KOG2071|consensus 32.6 27 0.00058 31.5 1.6 23 30-52 419-441 (579)
198 PF04780 DUF629: Protein of un 32.1 34 0.00073 30.2 2.1 27 30-56 58-84 (466)
199 COG4896 Uncharacterized protei 32.1 33 0.00071 20.7 1.4 9 2-10 2-10 (68)
200 PF14369 zf-RING_3: zinc-finge 31.9 30 0.00065 18.3 1.1 11 2-12 2-12 (35)
201 PF01428 zf-AN1: AN1-like Zinc 31.5 15 0.00032 20.4 -0.1 13 2-14 13-25 (43)
202 KOG0717|consensus 31.4 26 0.00056 30.6 1.2 22 30-51 293-314 (508)
203 CHL00174 accD acetyl-CoA carbo 31.2 31 0.00068 28.4 1.6 34 29-71 38-71 (296)
204 COG1656 Uncharacterized conser 30.9 48 0.001 24.6 2.4 18 143-160 130-147 (165)
205 TIGR00515 accD acetyl-CoA carb 30.8 33 0.00072 28.2 1.7 34 29-71 26-59 (285)
206 KOG1940|consensus 30.7 38 0.00083 27.6 2.0 46 58-104 197-253 (276)
207 PF01155 HypA: Hydrogenase exp 29.9 18 0.00038 25.1 0.0 15 29-43 70-84 (113)
208 cd00065 FYVE FYVE domain; Zinc 29.8 37 0.00079 19.8 1.4 9 32-40 5-13 (57)
209 COG3677 Transposase and inacti 29.7 18 0.00039 25.8 0.0 11 3-13 54-64 (129)
210 KOG1842|consensus 29.6 30 0.00065 30.0 1.3 28 29-56 15-42 (505)
211 PF04438 zf-HIT: HIT zinc fing 29.5 21 0.00046 18.1 0.3 11 2-12 13-23 (30)
212 COG3364 Zn-ribbon containing p 29.4 33 0.00072 23.1 1.2 14 29-42 2-15 (112)
213 PF14690 zf-ISL3: zinc-finger 29.4 5.4 0.00012 22.5 -2.2 10 2-11 2-11 (47)
214 PF12907 zf-met2: Zinc-binding 28.8 57 0.0012 17.9 1.9 26 144-169 2-30 (40)
215 PF14311 DUF4379: Domain of un 28.5 36 0.00079 19.9 1.2 19 29-47 28-46 (55)
216 COG4888 Uncharacterized Zn rib 28.4 6.5 0.00014 26.3 -2.2 36 29-68 22-57 (104)
217 TIGR00310 ZPR1_znf ZPR1 zinc f 28.0 8.3 0.00018 29.6 -2.0 10 30-39 31-40 (192)
218 cd02341 ZZ_ZZZ3 Zinc finger, Z 27.7 40 0.00088 19.3 1.3 10 27-36 13-22 (48)
219 PF07975 C1_4: TFIIH C1-like d 27.4 13 0.00029 21.6 -0.7 26 142-167 20-45 (51)
220 PRK05654 acetyl-CoA carboxylas 27.0 38 0.00082 28.0 1.5 33 29-70 27-59 (292)
221 PF03145 Sina: Seven in absent 27.0 59 0.0013 24.9 2.5 19 16-34 31-49 (198)
222 PF14255 Cys_rich_CPXG: Cystei 26.1 29 0.00062 20.3 0.5 8 4-11 2-9 (52)
223 PF07295 DUF1451: Protein of u 25.6 25 0.00054 25.7 0.2 32 143-184 112-143 (146)
224 PF11789 zf-Nse: Zinc-finger o 25.5 50 0.0011 19.7 1.4 14 57-70 24-37 (57)
225 KOG1842|consensus 25.5 43 0.00092 29.2 1.5 26 58-83 16-41 (505)
226 COG1779 C4-type Zn-finger prot 24.9 10 0.00023 28.9 -1.9 12 58-69 44-55 (201)
227 COG3091 SprT Zn-dependent meta 24.7 23 0.00051 25.8 -0.1 32 143-179 117-148 (156)
228 PF04810 zf-Sec23_Sec24: Sec23 24.3 12 0.00025 20.5 -1.4 13 140-152 21-33 (40)
229 PF01780 Ribosomal_L37ae: Ribo 24.1 33 0.00071 22.7 0.5 10 2-11 35-44 (90)
230 TIGR01562 FdhE formate dehydro 24.1 16 0.00036 30.2 -1.1 11 84-94 209-219 (305)
231 PF04606 Ogr_Delta: Ogr/Delta- 24.1 13 0.00029 21.1 -1.2 8 5-12 2-9 (47)
232 COG1326 Uncharacterized archae 24.0 74 0.0016 24.4 2.4 11 85-95 30-40 (201)
233 PF08209 Sgf11: Sgf11 (transcr 23.9 54 0.0012 17.1 1.2 21 3-24 5-25 (33)
234 PRK12860 transcriptional activ 23.7 45 0.00098 25.5 1.2 47 123-178 115-161 (189)
235 TIGR03830 CxxCG_CxxCG_HTH puta 23.5 32 0.0007 24.0 0.4 18 30-47 32-49 (127)
236 KOG4727|consensus 23.5 40 0.00086 25.1 0.9 23 29-51 75-97 (193)
237 smart00064 FYVE Protein presen 23.2 53 0.0011 20.0 1.3 10 31-40 12-21 (68)
238 KOG2636|consensus 23.0 67 0.0015 28.0 2.2 18 32-49 274-291 (497)
239 PTZ00448 hypothetical protein; 22.5 58 0.0013 27.7 1.7 23 29-51 314-336 (373)
240 KOG4118|consensus 22.1 68 0.0015 19.7 1.5 29 144-172 39-67 (74)
241 KOG3214|consensus 22.1 40 0.00087 22.6 0.6 38 29-70 23-60 (109)
242 PF13248 zf-ribbon_3: zinc-rib 22.0 43 0.00093 16.2 0.6 9 2-10 2-10 (26)
243 PRK10220 hypothetical protein; 22.0 45 0.00097 22.9 0.8 30 145-185 5-34 (111)
244 COG1675 TFA1 Transcription ini 21.7 1.5E+02 0.0033 22.4 3.6 16 83-98 111-126 (176)
245 PF03811 Zn_Tnp_IS1: InsA N-te 21.3 12 0.00025 20.1 -1.7 7 143-149 29-35 (36)
246 PLN02294 cytochrome c oxidase 21.2 31 0.00067 25.8 -0.1 15 26-40 138-152 (174)
247 TIGR00686 phnA alkylphosphonat 21.1 38 0.00082 23.2 0.4 30 145-185 4-33 (109)
248 cd00924 Cyt_c_Oxidase_Vb Cytoc 21.1 29 0.00062 23.4 -0.2 16 25-40 75-90 (97)
249 KOG2857|consensus 20.9 48 0.001 23.9 0.8 21 2-22 17-37 (157)
250 PF10013 DUF2256: Uncharacteri 20.5 60 0.0013 18.0 1.0 16 4-19 10-25 (42)
251 PF05495 zf-CHY: CHY zinc fing 20.4 8.8 0.00019 24.1 -2.6 8 58-65 42-49 (71)
252 KOG3990|consensus 20.0 1.5E+02 0.0032 23.8 3.4 37 58-94 38-79 (305)
No 1
>KOG2462|consensus
Probab=99.97 E-value=5e-31 Score=202.11 Aligned_cols=134 Identities=28% Similarity=0.554 Sum_probs=99.3
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCC---CceecccccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRG---IRFQCNKCFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRHSLKNHI 105 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~---~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 105 (263)
.|+|..||+.|.+..+|-+|..+|... +.+.|..|++.|.+...|..|++.|. .+.+|.+||+.|.+.+.|+.|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 567777777777777777777665432 23666666666666666666665555 4577888888888888888888
Q ss_pred HHhcCCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHHHHHHHhhc
Q psy11318 106 LKIHKAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHMAVH 166 (263)
Q Consensus 106 ~~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 166 (263)
|.|+|||||.|+.|+ ++|...++|+.|+.+|.+.|+|.|..|++.|++.+-|.+|...-
T Consensus 208 RTHTGEKPF~C~hC~--kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 208 RTHTGEKPFSCPHCG--KAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred ccccCCCCccCCccc--chhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 888888888888888 88888888888888888888888888888888888888886543
No 2
>KOG2462|consensus
Probab=99.96 E-value=5.1e-30 Score=196.58 Aligned_cols=133 Identities=25% Similarity=0.443 Sum_probs=127.1
Q ss_pred ceecccccccccchHHHHHHHHHhcCC---CcccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCHHHHHH
Q psy11318 57 RFQCNKCFRAYKLKKDLLAHTMLEHFG---IRHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTKRDLRR 133 (263)
Q Consensus 57 ~~~C~~C~~~f~~~~~l~~H~~~~~~~---~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~~~l~~ 133 (263)
.|+|+.|++.+.+..+|.+|.+.|..- +-+.|++|++.+.+...|.+|++.|. -+.+|.+|| +.|...+.|+.
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCG--KaFSRPWLLQG 205 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICG--KAFSRPWLLQG 205 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCccccccc--ccccchHHhhc
Confidence 499999999999999999999988764 67999999999999999999999987 578999999 99999999999
Q ss_pred HHHHhCCCCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccccceeeeccCC
Q psy11318 134 HMKLHFNGKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGVRELRHVGF 193 (263)
Q Consensus 134 H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~~l~~H~~~ 193 (263)
|+++|+|||||.|+.|++.|+++++|+.||++|.+.+.|.|..|++.|...+-|-+|...
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 999999999999999999999999999999999999999999999999999999999875
No 3
>KOG1074|consensus
Probab=99.95 E-value=1.2e-29 Score=218.91 Aligned_cols=142 Identities=23% Similarity=0.379 Sum_probs=125.6
Q ss_pred eecccccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHHHHHHHHHHhcCC----ccccCC---CCCCCcccCCHHH
Q psy11318 58 FQCNKCFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRHSLKNHILKIHKA----VLYQCN---ECSTSKDYLTKRD 130 (263)
Q Consensus 58 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~----~~~~C~---~C~~~~~f~~~~~ 130 (263)
-.|=+|.+...-...|+.|.+.|.+++||+|.+|++.|.++.+|+.||..|... ..+.|+ +|. +.|...-.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~--~kftn~V~ 683 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQ--KKFTNAVT 683 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhc--cccccccc
Confidence 358899999999999999999999999999999999999999999999887643 347788 888 88888888
Q ss_pred HHHHHHHhCCCC--------------------------------------------------------------------
Q psy11318 131 LRRHMKLHFNGK-------------------------------------------------------------------- 142 (263)
Q Consensus 131 l~~H~~~h~~~~-------------------------------------------------------------------- 142 (263)
|..|+++|.+..
T Consensus 684 lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~ 763 (958)
T KOG1074|consen 684 LPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSC 763 (958)
T ss_pred ccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCcccccc
Confidence 888888886321
Q ss_pred --------------------------------------------------------------------------------
Q psy11318 143 -------------------------------------------------------------------------------- 142 (263)
Q Consensus 143 -------------------------------------------------------------------------------- 142 (263)
T Consensus 764 ~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t 843 (958)
T KOG1074|consen 764 GRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLAT 843 (958)
T ss_pred ccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccccccccccccc
Confidence
Q ss_pred -----------------------------------CccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCccccccccee
Q psy11318 143 -----------------------------------RYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGVRE 187 (263)
Q Consensus 143 -----------------------------------~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~~l 187 (263)
...|.+|++.|...+.|.+|+++|+++|+|.|..|++.|..+.+|
T Consensus 844 ~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnL 923 (958)
T KOG1074|consen 844 KTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNL 923 (958)
T ss_pred ccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhh
Confidence 378999999999999999999999999999999999999999999
Q ss_pred eeccCCCcccccCC
Q psy11318 188 LRHVGFPMKTDHWS 201 (263)
Q Consensus 188 ~~H~~~~~~~~~~~ 201 (263)
..||.+|+.....+
T Consensus 924 KvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 924 KVHMGTHMWVQPPS 937 (958)
T ss_pred hhhhccccccCCCc
Confidence 99999999755443
No 4
>KOG3608|consensus
Probab=99.90 E-value=5.3e-24 Score=167.93 Aligned_cols=183 Identities=25% Similarity=0.408 Sum_probs=164.2
Q ss_pred cccccccCChHHHHHHHHhhCCc-ccccCCCccccCChhHHHHHHHHh--cCCCceecccccccccchHHHHHHHHHhcC
Q psy11318 6 NACSKNFSAKDTLNKHMDIHKGV-RYQCEECPKDFSTRKYLTQHQNAI--HRGIRFQCNKCFRAYKLKKDLLAHTMLEHF 82 (263)
Q Consensus 6 ~~C~~~f~~~~~L~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~~--~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 82 (263)
.-|-+.|.+++.|++|+++|+++ ...|+.||.-|.++..|..|++.. ....+|.|..|.+.|.+...|..|+..|-.
T Consensus 183 ~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn 262 (467)
T KOG3608|consen 183 AMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN 262 (467)
T ss_pred hhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 46888999999999999999995 789999999999999999998753 344579999999999999999999977764
Q ss_pred CCcccCCcCCCcCCCHHHHHHHHHHhc-CCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCc--chhhhcChHHH
Q psy11318 83 GIRHPCSECPKTFASRHSLKNHILKIH-KAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQ--CSKFYIQESDL 159 (263)
Q Consensus 83 ~~~~~C~~C~~~f~~~~~l~~H~~~~~-~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l 159 (263)
-|+|+.|+.+....+.|..|++..| ..+||+|..|. ..|.+.++|.+|+..|. +-.|.|.. |.+.|....++
T Consensus 263 --~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd--~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~ 337 (467)
T KOG3608|consen 263 --CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECD--TRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQM 337 (467)
T ss_pred --cccccccccCCCChHHHHHHHHhhhccCCCccccchh--hhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHH
Confidence 3899999999999999999998766 67999999999 99999999999999887 66799988 99999999999
Q ss_pred HHHHhhcc-CCCC--CcCCCCcccccccceeeeccCC
Q psy11318 160 MEHMAVHS-GVRK--LTTGPIKTEQTFGVRELRHVGF 193 (263)
Q Consensus 160 ~~H~~~h~-~~~~--~~c~~c~~~~~~~~~l~~H~~~ 193 (263)
++|++.++ |..| |.|..|++-|++..+|..|+..
T Consensus 338 ~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~k 374 (467)
T KOG3608|consen 338 RRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMK 374 (467)
T ss_pred HHHHHHhccCCCCCceeeecchhhhccchhHHHHHHH
Confidence 99998766 5554 9999999999999999999765
No 5
>KOG3623|consensus
Probab=99.90 E-value=9.1e-25 Score=186.33 Aligned_cols=78 Identities=24% Similarity=0.505 Sum_probs=75.8
Q ss_pred ccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccccceeeeccCC
Q psy11318 114 YQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGVRELRHVGF 193 (263)
Q Consensus 114 ~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~~l~~H~~~ 193 (263)
|.|..|. +.|.-.+.|.+|.-.|+|.+||.|..|.+.|..+..|..|+|.|.|++||.|..|++.|+...++-.||.-
T Consensus 895 yaCDqCD--K~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMNH 972 (1007)
T KOG3623|consen 895 YACDQCD--KAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMNH 972 (1007)
T ss_pred chHHHHH--HHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhcc
Confidence 9999999 99999999999999999999999999999999999999999999999999999999999999999999973
No 6
>KOG3608|consensus
Probab=99.88 E-value=5.7e-23 Score=162.15 Aligned_cols=185 Identities=22% Similarity=0.379 Sum_probs=167.8
Q ss_pred cccccccCChHHHHHHHHhhCCc----------------ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccc
Q psy11318 6 NACSKNFSAKDTLNKHMDIHKGV----------------RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKL 69 (263)
Q Consensus 6 ~~C~~~f~~~~~L~~H~~~h~~~----------------~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 69 (263)
..|+..|.+...|..|+..|..- +..+..|-+.+.++..|++|+++|.+++...|+.|+..|.+
T Consensus 140 edCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~ 219 (467)
T KOG3608|consen 140 EDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRT 219 (467)
T ss_pred hhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhcc
Confidence 68999999999999999887331 35567799999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhcCC--CcccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCHHHHHHHHHH-hCCCCCccC
Q psy11318 70 KKDLLAHTMLEHFG--IRHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTKRDLRRHMKL-HFNGKRYHC 146 (263)
Q Consensus 70 ~~~l~~H~~~~~~~--~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~-h~~~~~~~C 146 (263)
...|-.|++....- .+|.|..|.+.|.+...|..|+..|-. -|+|+.|. -+....+.|..|++. |...+||+|
T Consensus 220 ~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCd--mtc~~~ssL~~H~r~rHs~dkpfKC 295 (467)
T KOG3608|consen 220 KTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCD--MTCSSASSLTTHIRYRHSKDKPFKC 295 (467)
T ss_pred ccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccc--cCCCChHHHHHHHHhhhccCCCccc
Confidence 99999999776643 689999999999999999999998854 68999999 889999999999986 778899999
Q ss_pred CcchhhhcChHHHHHHHhhccCCCCCcCCC--CcccccccceeeeccCCCc
Q psy11318 147 TQCSKFYIQESDLMEHMAVHSGVRKLTTGP--IKTEQTFGVRELRHVGFPM 195 (263)
Q Consensus 147 ~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~--c~~~~~~~~~l~~H~~~~~ 195 (263)
..|++.|.+.++|.+|..+|. +-.|.|.. |.+++.+...+++|++.+.
T Consensus 296 d~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 296 DECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred cchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 999999999999999999887 77899988 9999999999999998655
No 7
>KOG1074|consensus
Probab=99.88 E-value=1.6e-23 Score=181.50 Aligned_cols=170 Identities=25% Similarity=0.492 Sum_probs=149.2
Q ss_pred CccccccccccCChHHHHHHHHhhCCc-ccccCCCccccCChhHHHHHHHHhcCCCc----eecc---cccccccchHHH
Q psy11318 2 RYYCNACSKNFSAKDTLNKHMDIHKGV-RYQCEECPKDFSTRKYLTQHQNAIHRGIR----FQCN---KCFRAYKLKKDL 73 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~~~~~~~----~~C~---~C~~~f~~~~~l 73 (263)
+.+|.+|.++...+..|+.|+++|+|+ ||+|++||++|.++++|+.||-.|...-+ |.|+ +|-+.|...-.|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 568999999999999999999999995 99999999999999999999998554433 8999 999999999999
Q ss_pred HHHHHHhcCCC-------------cccCCcCCCcCCCHHHHHHHHHHhcCCcc---------------------------
Q psy11318 74 LAHTMLEHFGI-------------RHPCSECPKTFASRHSLKNHILKIHKAVL--------------------------- 113 (263)
Q Consensus 74 ~~H~~~~~~~~-------------~~~C~~C~~~f~~~~~l~~H~~~~~~~~~--------------------------- 113 (263)
..|+++|.++. .-.|..|.+.|.....+..++..+.+...
T Consensus 685 pQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~~ 764 (958)
T KOG1074|consen 685 PQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSCG 764 (958)
T ss_pred cceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCccccccc
Confidence 99999887441 14688999999888777777776632100
Q ss_pred --------------------------------------------------------------------------------
Q psy11318 114 -------------------------------------------------------------------------------- 113 (263)
Q Consensus 114 -------------------------------------------------------------------------------- 113 (263)
T Consensus 765 ~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~ 844 (958)
T KOG1074|consen 765 RELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLATK 844 (958)
T ss_pred cccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhcccccccccccccc
Confidence
Q ss_pred -----------------------------------ccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHH
Q psy11318 114 -----------------------------------YQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESD 158 (263)
Q Consensus 114 -----------------------------------~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 158 (263)
..|.+|+ +.|.+.+.|..|+++|+++++|.|.+|++.|.++.+
T Consensus 845 ~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCg--k~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgn 922 (958)
T KOG1074|consen 845 TNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCG--KQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGN 922 (958)
T ss_pred cccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccch--hcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhh
Confidence 6799999 999999999999999999999999999999999999
Q ss_pred HHHHHhhccCCCCCc
Q psy11318 159 LMEHMAVHSGVRKLT 173 (263)
Q Consensus 159 l~~H~~~h~~~~~~~ 173 (263)
|+.||.+|.+..++.
T Consensus 923 LKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 923 LKVHMGTHMWVQPPS 937 (958)
T ss_pred hhhhhccccccCCCc
Confidence 999999999887754
No 8
>KOG3623|consensus
Probab=99.84 E-value=8.2e-22 Score=168.46 Aligned_cols=77 Identities=30% Similarity=0.610 Sum_probs=74.6
Q ss_pred ccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHHHHHHHh
Q psy11318 86 HPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHMA 164 (263)
Q Consensus 86 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 164 (263)
|.|..|++.|...+.|.+|.-.|.|.+||+|.+|. +.|..+..|..|.+.|.|+|||.|..|++.|....++..||.
T Consensus 895 yaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCk--KAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICK--KAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhh--HhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 45999999999999999999999999999999999 999999999999999999999999999999999999999984
No 9
>KOG3576|consensus
Probab=99.77 E-value=1.5e-19 Score=132.48 Aligned_cols=108 Identities=25% Similarity=0.431 Sum_probs=80.4
Q ss_pred CccccccccccCChHHHHHHHHhhCCc-ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccchHHHHHHHHHh
Q psy11318 2 RYYCNACSKNFSAKDTLNKHMDIHKGV-RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKKDLLAHTMLE 80 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 80 (263)
.+.|.+|+|.|+..-.|++|+..|..+ .|.|..||+.|++...|++|+++|++.+||+|..|++.|...-.|..|++..
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 367888888888888888888888774 7888888888888888888888888888888888888888888888888776
Q ss_pred cCC-----------CcccCCcCCCcCCCHHHHHHHHHHhc
Q psy11318 81 HFG-----------IRHPCSECPKTFASRHSLKNHILKIH 109 (263)
Q Consensus 81 ~~~-----------~~~~C~~C~~~f~~~~~l~~H~~~~~ 109 (263)
|+. +.|.|+.||.+-.....+..|++.++
T Consensus 197 hgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 197 HGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred cCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcC
Confidence 654 33445555555555555555555444
No 10
>KOG3576|consensus
Probab=99.74 E-value=2.9e-19 Score=131.00 Aligned_cols=111 Identities=22% Similarity=0.350 Sum_probs=100.2
Q ss_pred CcccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHHHHHHH
Q psy11318 84 IRHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHM 163 (263)
Q Consensus 84 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 163 (263)
..|.|.+|++.|.....|.+|++-|...+.+.|..|| ++|...-+|++|.++|+|.+||+|..|++.|+.+-+|..|+
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cg--kgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCG--KGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhcc--CcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 3478999999999999999999999999999999999 99999999999999999999999999999999999999999
Q ss_pred hhccCC-----------CCCcCCCCcccccccceeeeccCCCcc
Q psy11318 164 AVHSGV-----------RKLTTGPIKTEQTFGVRELRHVGFPMK 196 (263)
Q Consensus 164 ~~h~~~-----------~~~~c~~c~~~~~~~~~l~~H~~~~~~ 196 (263)
+.-+|. +-|+|+.||+.....+.+..|++.+..
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 877664 568999999999999999999887553
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.44 E-value=3.4e-13 Score=116.44 Aligned_cols=96 Identities=18% Similarity=0.423 Sum_probs=44.6
Q ss_pred ecccccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccC----------CH
Q psy11318 59 QCNKCFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYL----------TK 128 (263)
Q Consensus 59 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~----------~~ 128 (263)
.|+.|++.|. ...|..|++.+| .++.|+ |++.+ ....|..|+..|.+.+++.|..|+ ..+. ..
T Consensus 455 ~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~--~~v~~g~~~~d~~d~~ 527 (567)
T PLN03086 455 HCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCG--DMVQAGGSAMDVRDRL 527 (567)
T ss_pred cCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCC--CccccCccccchhhhh
Confidence 4555555553 344555554443 445555 55433 334555555555555555555555 4342 12
Q ss_pred HHHHHHHHHhCCCCCccCCcchhhhcChHHHHHHH
Q psy11318 129 RDLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHM 163 (263)
Q Consensus 129 ~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 163 (263)
+.|..|.... |.+++.|..||+.+..+ .+..|+
T Consensus 528 s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 528 RGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQ 560 (567)
T ss_pred hhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHH
Confidence 3444554443 44555555555444433 234443
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.31 E-value=4.9e-12 Score=109.39 Aligned_cols=143 Identities=16% Similarity=0.335 Sum_probs=111.3
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceeccc--ccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNK--CFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRHSLKNHIL 106 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 106 (263)
.-.|+.|..... ...|..|... .......|+. |+..|.. ..+..| +.|+.|++.|. ...|..|+.
T Consensus 407 ~V~C~NC~~~i~-l~~l~lHe~~-C~r~~V~Cp~~~Cg~v~~r-~el~~H---------~~C~~Cgk~f~-~s~LekH~~ 473 (567)
T PLN03086 407 TVECRNCKHYIP-SRSIALHEAY-CSRHNVVCPHDGCGIVLRV-EEAKNH---------VHCEKCGQAFQ-QGEMEKHMK 473 (567)
T ss_pred eEECCCCCCccc-hhHHHHHHhh-CCCcceeCCcccccceeec-cccccC---------ccCCCCCCccc-hHHHHHHHH
Confidence 357888877654 4456688865 5555678984 9998843 334444 59999999996 678999999
Q ss_pred HhcCCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhc----------ChHHHHHHHhhccCCCCCcCCC
Q psy11318 107 KIHKAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYI----------QESDLMEHMAVHSGVRKLTTGP 176 (263)
Q Consensus 107 ~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~l~~H~~~h~~~~~~~c~~ 176 (263)
.+| +++.|+ |+ ..+ ....|..|+.+|.+.+++.|.+|++.|. ....|..|.... +.+++.|..
T Consensus 474 ~~H--kpv~Cp-Cg--~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~ 546 (567)
T PLN03086 474 VFH--EPLQCP-CG--VVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDS 546 (567)
T ss_pred hcC--CCccCC-CC--CCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccc
Confidence 986 789999 98 655 6689999999999999999999999985 245899999885 999999999
Q ss_pred CcccccccceeeeccC
Q psy11318 177 IKTEQTFGVRELRHVG 192 (263)
Q Consensus 177 c~~~~~~~~~l~~H~~ 192 (263)
|++.+..+ .|..|+.
T Consensus 547 Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 547 CGRSVMLK-EMDIHQI 561 (567)
T ss_pred cCCeeeeh-hHHHHHH
Confidence 99877544 3444543
No 13
>PHA00733 hypothetical protein
Probab=99.15 E-value=3.7e-11 Score=85.23 Aligned_cols=82 Identities=17% Similarity=0.244 Sum_probs=65.3
Q ss_pred CcccccCCCccccCChhHHHHH--H---HHhcCCCceecccccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHHHH
Q psy11318 27 GVRYQCEECPKDFSTRKYLTQH--Q---NAIHRGIRFQCNKCFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRHSL 101 (263)
Q Consensus 27 ~~~~~C~~C~~~f~~~~~l~~H--~---~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l 101 (263)
..++.|.+|+..|.+...|..| + ..++++.+|.|..|++.|.+...|..|++.+ ..+|.|+.|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 3478888888887777666655 1 1335577899999999999999999998754 3568999999999999999
Q ss_pred HHHHHHhcC
Q psy11318 102 KNHILKIHK 110 (263)
Q Consensus 102 ~~H~~~~~~ 110 (263)
..|+...|+
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 999988876
No 14
>PHA00733 hypothetical protein
Probab=99.12 E-value=6.5e-11 Score=84.02 Aligned_cols=81 Identities=14% Similarity=0.292 Sum_probs=52.8
Q ss_pred CcccCCcCCCcCCCHHHHHHH--HH---HhcCCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHH
Q psy11318 84 IRHPCSECPKTFASRHSLKNH--IL---KIHKAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESD 158 (263)
Q Consensus 84 ~~~~C~~C~~~f~~~~~l~~H--~~---~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 158 (263)
+++.|.+|.+.|.....|..+ ++ .+++.++|.|+.|+ +.|.+...|..|++.+ +.+|.|..|++.|.....
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cg--k~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCL--MPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCC--CcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 455565555555554444443 11 22346677777777 7777777777777765 345778888888888888
Q ss_pred HHHHHhhccC
Q psy11318 159 LMEHMAVHSG 168 (263)
Q Consensus 159 l~~H~~~h~~ 168 (263)
|.+|+...|+
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 8887776665
No 15
>KOG3993|consensus
Probab=99.09 E-value=1.1e-11 Score=100.91 Aligned_cols=188 Identities=14% Similarity=0.102 Sum_probs=110.3
Q ss_pred ccccccccccCChHHHHHHHHhhCC-cccccCCCccccCChhHHHHHHHHhcCCCcee---cccccccccchHHHHHHHH
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIHKG-VRYQCEECPKDFSTRKYLTQHQNAIHRGIRFQ---CNKCFRAYKLKKDLLAHTM 78 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~---C~~C~~~f~~~~~l~~H~~ 78 (263)
|.|-+|...|.+...|.+|.=.... +.|+|+.|+|+|+.-.+|-.|.+.|.....-. -+.=.+. .....+.....
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~-~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQA-VETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhh-hhhhhhhhhcc
Confidence 7899999999999999999644333 37999999999999999999998865332110 0000000 00011111110
Q ss_pred H---hcCCCcccCCcCCCcCCCHHHHHHHHHHhcCCc-----------------cccCCCCCCCcccCCHHHHHHHHHHh
Q psy11318 79 L---EHFGIRHPCSECPKTFASRHSLKNHILKIHKAV-----------------LYQCNECSTSKDYLTKRDLRRHMKLH 138 (263)
Q Consensus 79 ~---~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~-----------------~~~C~~C~~~~~f~~~~~l~~H~~~h 138 (263)
. ...+-.|.|.+|++.|.+...|+.|+..|+... .+-|..+. -.+...+.--.+...+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a--~h~~a~~~~g~~vl~~ 424 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVA--THSSASDSHGDEVLYV 424 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccc--cccccccccccceeee
Confidence 0 011235777777777777777777766665211 02233333 1121111111111111
Q ss_pred CC-CCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccccceeeeccCC
Q psy11318 139 FN-GKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGVRELRHVGF 193 (263)
Q Consensus 139 ~~-~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~~l~~H~~~ 193 (263)
.+ .....|++|+..+..+..-..+.+.-.....|.|..|.-.|.+...|.+|+..
T Consensus 425 a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 425 AGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred eccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhh
Confidence 11 11245677777777666656666666667778888888888888888888775
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=4.4e-11 Score=69.98 Aligned_cols=43 Identities=14% Similarity=0.370 Sum_probs=32.7
Q ss_pred ccccccccccCChHHHHHHHHhhCCcccccCCCccccCChhHHH
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKDFSTRKYLT 46 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l~ 46 (263)
|.|++||+.|.....|..|+++|+ .+|+|..|++.|...+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeE
Confidence 678888888888888888888877 4778888888777666554
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.98 E-value=4.4e-10 Score=65.82 Aligned_cols=45 Identities=20% Similarity=0.432 Sum_probs=39.8
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccccceeee
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGVRELR 189 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~~l~~ 189 (263)
.|.|+.||+.|++.+.|.+|+++|+ ++++|..|++.|+..++|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 4889999999999999999999988 78999999999998887764
No 18
>KOG3993|consensus
Probab=98.64 E-value=3.2e-09 Score=86.89 Aligned_cols=52 Identities=19% Similarity=0.503 Sum_probs=31.4
Q ss_pred cccCCCccccCChhHHHHHHHHhcCCCceecccccccccchHHHHHHHHHhc
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKKDLLAHTMLEH 81 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 81 (263)
|.|..|...|.+.+.|-+|.-.---.++|+|++|+|.|+--.||..|.+-|.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccC
Confidence 6666666666666666666533222234666666666666666666665443
No 19
>PHA00732 hypothetical protein
Probab=98.63 E-value=2.4e-08 Score=64.26 Aligned_cols=49 Identities=22% Similarity=0.339 Sum_probs=38.8
Q ss_pred CccccccccccCChHHHHHHHHh-hCCcccccCCCccccCChhHHHHHHHHhcCC
Q psy11318 2 RYYCNACSKNFSAKDTLNKHMDI-HKGVRYQCEECPKDFSTRKYLTQHQNAIHRG 55 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~~~-h~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 55 (263)
+|.|.+||+.|.+...|..|++. |.+ +.|+.|++.|. .|..|++++.+-
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~--~~C~~CgKsF~---~l~~H~~~~~~~ 50 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL--TKCPVCNKSYR---RLNQHFYSQYDI 50 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC--CccCCCCCEeC---ChhhhhcccCCc
Confidence 58899999999999999999874 553 68899998887 588888775543
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=98.55 E-value=3.4e-08 Score=49.42 Aligned_cols=23 Identities=22% Similarity=0.250 Sum_probs=9.7
Q ss_pred HHHHHhhccCCCCCcCCCCcccc
Q psy11318 159 LMEHMAVHSGVRKLTTGPIKTEQ 181 (263)
Q Consensus 159 l~~H~~~h~~~~~~~c~~c~~~~ 181 (263)
|.+|+++|+++++|.|+.|++.|
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEE
T ss_pred HHHHhhhcCCCCCCCCCCCcCee
Confidence 33444444444444444444443
No 21
>PHA00616 hypothetical protein
Probab=98.52 E-value=6.3e-08 Score=53.97 Aligned_cols=33 Identities=24% Similarity=0.572 Sum_probs=27.4
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCCCCCcCC
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTG 175 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~ 175 (263)
+|.|+.||+.|...++|.+|++.|++.+++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 578888888888888888888888888887765
No 22
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.52 E-value=5.2e-08 Score=48.75 Aligned_cols=26 Identities=42% Similarity=0.866 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCCCccCCcchhhhcC
Q psy11318 130 DLRRHMKLHFNGKRYHCTQCSKFYIQ 155 (263)
Q Consensus 130 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (263)
+|.+|+++|+|+++|.|+.|++.|.+
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 48899999999999999999999964
No 23
>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=98.41 E-value=4.6e-07 Score=54.19 Aligned_cols=48 Identities=23% Similarity=0.452 Sum_probs=23.1
Q ss_pred ccccccccccCChHHHHHHHHhhCC---cccccCCCccccCChhHHHHHHHHhc
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIHKG---VRYQCEECPKDFSTRKYLTQHQNAIH 53 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h~~---~~~~C~~C~~~f~~~~~l~~H~~~~~ 53 (263)
|.||+|++ ..+...|..|....+. ..+.|++|...+. .+|..|++..|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 55555555 3344555555444332 1455555554332 25555555443
No 24
>PHA00616 hypothetical protein
Probab=98.41 E-value=1.2e-07 Score=52.78 Aligned_cols=33 Identities=24% Similarity=0.507 Sum_probs=17.0
Q ss_pred cccCCCccccCChhHHHHHHHHhcCCCceeccc
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNK 62 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~ 62 (263)
|+|+.||+.|...++|.+|++.+|++.++.|..
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 455555555555555555555555555544443
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.35 E-value=9.2e-07 Score=52.90 Aligned_cols=50 Identities=24% Similarity=0.440 Sum_probs=31.3
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCC--CceecccccccccchHHHHHHHHHhc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRG--IRFQCNKCFRAYKLKKDLLAHTMLEH 81 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~--~~~~C~~C~~~f~~~~~l~~H~~~~~ 81 (263)
.|.|++|++ ..+...|..|....|.. ..+.|++|...+. .+|..|+..+|
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 367777777 45566777777765553 2366777766433 36666665554
No 26
>PHA00732 hypothetical protein
Probab=98.28 E-value=4.7e-07 Score=58.33 Aligned_cols=44 Identities=27% Similarity=0.453 Sum_probs=31.8
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccchHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKKDLLAHT 77 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 77 (263)
||.|..|++.|.+...|+.|++.+|. ++.|+.|++.|. .+..|+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhh
Confidence 57788888888888888888874333 257888888776 366676
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=98.18 E-value=1.1e-06 Score=42.58 Aligned_cols=22 Identities=45% Similarity=0.925 Sum_probs=13.3
Q ss_pred ccccccccccCChHHHHHHHHh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDI 24 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~ 24 (263)
|.|+.|++.|.++..|..|++.
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 4566666666666666666554
No 28
>KOG2231|consensus
Probab=98.13 E-value=4.5e-05 Score=67.67 Aligned_cols=134 Identities=22% Similarity=0.422 Sum_probs=85.6
Q ss_pred ccCCCccccCChhHHHHHHHHhcCCCceeccccc---------ccccchHHHHHHHHHhcC-C---C-cccCCcCCCcCC
Q psy11318 31 QCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCF---------RAYKLKKDLLAHTMLEHF-G---I-RHPCSECPKTFA 96 (263)
Q Consensus 31 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~---------~~f~~~~~l~~H~~~~~~-~---~-~~~C~~C~~~f~ 96 (263)
.|.+| -.|.....|+.|+...|+. +.|.+|- ....+...|..|++.--. + + --.|..|...|.
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fl 193 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFL 193 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhc
Confidence 45555 5566888899999766653 5555543 233456778888764333 2 1 146899999999
Q ss_pred CHHHHHHHHHHhcCCccccCCCCC----CCcccCCHHHHHHHHHHhCCCCCccCC--cch-hhhcCh----HHHHHHHhh
Q psy11318 97 SRHSLKNHILKIHKAVLYQCNECS----TSKDYLTKRDLRRHMKLHFNGKRYHCT--QCS-KFYIQE----SDLMEHMAV 165 (263)
Q Consensus 97 ~~~~l~~H~~~~~~~~~~~C~~C~----~~~~f~~~~~l~~H~~~h~~~~~~~C~--~C~-~~f~~~----~~l~~H~~~ 165 (263)
....|..|++..|- .|-.|. ...-|....+|..|.+.+| |.|. .|. +.|... ..|++|.+.
T Consensus 194 d~~el~rH~~~~h~----~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~~ei~lk~~~~~ 265 (669)
T KOG2231|consen 194 DDDELYRHLRFDHE----FCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFELEIELKAHNRF 265 (669)
T ss_pred cHHHHHHhhcccee----heeecCcccccchhcccchHHHHHhhhcC----ccccccccccceeeehhHHHHHHHhhccc
Confidence 99999999998774 455552 2367888889999998766 6676 453 334444 344444433
Q ss_pred ccCCCCCcCC
Q psy11318 166 HSGVRKLTTG 175 (263)
Q Consensus 166 h~~~~~~~c~ 175 (263)
+.-++.|.|.
T Consensus 266 ~~~e~~~~~~ 275 (669)
T KOG2231|consen 266 IQHEKCYICR 275 (669)
T ss_pred cchheeccCC
Confidence 3334445553
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.99 E-value=4.9e-06 Score=40.28 Aligned_cols=22 Identities=36% Similarity=0.812 Sum_probs=15.7
Q ss_pred cccCCCccccCChhHHHHHHHH
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
|.|++|++.|.+...|+.|++.
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 5677777777777777777765
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.94 E-value=7e-06 Score=40.05 Aligned_cols=23 Identities=39% Similarity=0.896 Sum_probs=10.8
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIH 25 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h 25 (263)
|.|++|++.|.+...|+.|+++|
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 34555555555555555555443
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.94 E-value=6.5e-06 Score=56.09 Aligned_cols=23 Identities=39% Similarity=0.762 Sum_probs=0.0
Q ss_pred ccccccccCChHHHHHHHHhhCC
Q psy11318 5 CNACSKNFSAKDTLNKHMDIHKG 27 (263)
Q Consensus 5 C~~C~~~f~~~~~L~~H~~~h~~ 27 (263)
|..|+..|.+...|..||...++
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~ 24 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHG 24 (100)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 55555555555555555554444
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=97.90 E-value=1e-05 Score=39.44 Aligned_cols=24 Identities=38% Similarity=0.754 Sum_probs=17.0
Q ss_pred cccCCCccccCChhHHHHHHHHhc
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIH 53 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~ 53 (263)
|.|++|++.|.+...|+.|++++|
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 578888888888888888887764
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=97.73 E-value=2.1e-05 Score=39.66 Aligned_cols=25 Identities=32% Similarity=0.684 Sum_probs=14.4
Q ss_pred CccccccccccCChHHHHHHHHhhC
Q psy11318 2 RYYCNACSKNFSAKDTLNKHMDIHK 26 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~~~h~ 26 (263)
+|.|..|++.|.+...|..|++.|.
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 3556666666666666666655543
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.72 E-value=2.2e-05 Score=53.44 Aligned_cols=73 Identities=27% Similarity=0.296 Sum_probs=17.6
Q ss_pred ccCCCccccCChhHHHHHHHHhcCCCceecccccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHHHHHHHHHHh
Q psy11318 31 QCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRHSLKNHILKI 108 (263)
Q Consensus 31 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 108 (263)
+|..|+..|.+...|..||...|+-.. . ....+.....+..++... ....+.|..|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~---~-~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI---P-DQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccc---c-cccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 488888888888888888877665321 1 111111222333333221 122577777777777777777777764
No 35
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.57 E-value=0.0003 Score=56.91 Aligned_cols=130 Identities=22% Similarity=0.433 Sum_probs=90.8
Q ss_pred ccccCC--CccccCChhHHHHHHHHhcCCCceecccccc---ccc------chHHHHHHHHHhcCCCcc----cCCcCCC
Q psy11318 29 RYQCEE--CPKDFSTRKYLTQHQNAIHRGIRFQCNKCFR---AYK------LKKDLLAHTMLEHFGIRH----PCSECPK 93 (263)
Q Consensus 29 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~---~f~------~~~~l~~H~~~~~~~~~~----~C~~C~~ 93 (263)
.|.|+. |..+......|+.|.+..|+. +.|.+|-. .|. ++..|..|...--.+..| .|..|..
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~ 228 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 488876 777777788899999987764 77887752 343 344555555332223233 6999999
Q ss_pred cCCCHHHHHHHHHHhcCCccccCCCCCCC-----cccCCHHHHHHHHHHhCCCCCccCCc--ch----hhhcChHHHHHH
Q psy11318 94 TFASRHSLKNHILKIHKAVLYQCNECSTS-----KDYLTKRDLRRHMKLHFNGKRYHCTQ--CS----KFYIQESDLMEH 162 (263)
Q Consensus 94 ~f~~~~~l~~H~~~~~~~~~~~C~~C~~~-----~~f~~~~~l~~H~~~h~~~~~~~C~~--C~----~~f~~~~~l~~H 162 (263)
.|-+...|..|++..|. .|-+|... .-|.+...|.+|.+.-+ |.|.+ |- +.|.....|..|
T Consensus 229 ~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~~~~el~~h 300 (493)
T COG5236 229 YFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFPYHTELLEH 300 (493)
T ss_pred eecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEeccHHHHHHH
Confidence 99999999999998875 46555521 34778888888886432 67755 42 568888899999
Q ss_pred HhhccC
Q psy11318 163 MAVHSG 168 (263)
Q Consensus 163 ~~~h~~ 168 (263)
+...|+
T Consensus 301 ~~~~h~ 306 (493)
T COG5236 301 LTRFHK 306 (493)
T ss_pred HHHHhh
Confidence 866554
No 36
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.57 E-value=3.5e-05 Score=38.80 Aligned_cols=25 Identities=32% Similarity=0.721 Sum_probs=16.7
Q ss_pred ccccCCCccccCChhHHHHHHHHhc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIH 53 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~ 53 (263)
+|.|..|++.|.+...|..|++.|+
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 4667777777777777777766544
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.56 E-value=4.5e-05 Score=60.84 Aligned_cols=53 Identities=21% Similarity=0.222 Sum_probs=45.1
Q ss_pred CCCCccCCc--chhhhcChHHHHHHHhhcc-------------------CCCCCcCCCCcccccccceeeeccC
Q psy11318 140 NGKRYHCTQ--CSKFYIQESDLMEHMAVHS-------------------GVRKLTTGPIKTEQTFGVRELRHVG 192 (263)
Q Consensus 140 ~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-------------------~~~~~~c~~c~~~~~~~~~l~~H~~ 192 (263)
+++||+|++ |++.|+....|+-|+.--| ..+||+|++|++.+.....|..|..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 458999988 9999999999999986432 2389999999999999999998875
No 38
>KOG1146|consensus
Probab=97.56 E-value=2.4e-05 Score=73.34 Aligned_cols=80 Identities=23% Similarity=0.445 Sum_probs=64.5
Q ss_pred CCccccccccccCChHHHHHHHHhh--------------------------CCcccccCCCccccCChhHHHHHHHHhc-
Q psy11318 1 MRYYCNACSKNFSAKDTLNKHMDIH--------------------------KGVRYQCEECPKDFSTRKYLTQHQNAIH- 53 (263)
Q Consensus 1 ~~y~C~~C~~~f~~~~~L~~H~~~h--------------------------~~~~~~C~~C~~~f~~~~~l~~H~~~~~- 53 (263)
|-|+|+.|+..|.....|..|||.- .+.+|.|..|...+..+++|-+|++...
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h 543 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLH 543 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHhh
Confidence 4689999999999999999999981 1227999999999999999999997422
Q ss_pred CCC------------------------------------------ceecccccccccchHHHHHHHHHh
Q psy11318 54 RGI------------------------------------------RFQCNKCFRAYKLKKDLLAHTMLE 80 (263)
Q Consensus 54 ~~~------------------------------------------~~~C~~C~~~f~~~~~l~~H~~~~ 80 (263)
... .|.|.+|++.-.-..+|..|+...
T Consensus 544 ~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss 612 (1406)
T KOG1146|consen 544 RNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTAS 612 (1406)
T ss_pred HHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccC
Confidence 111 178999999888888888888543
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.54 E-value=2.6e-05 Score=62.14 Aligned_cols=54 Identities=28% Similarity=0.468 Sum_probs=44.0
Q ss_pred CccccCCCCCCCcccCCHHHHHHHHHHhC-------------------CCCCccCCcchhhhcChHHHHHHHh
Q psy11318 111 AVLYQCNECSTSKDYLTKRDLRRHMKLHF-------------------NGKRYHCTQCSKFYIQESDLMEHMA 164 (263)
Q Consensus 111 ~~~~~C~~C~~~~~f~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 164 (263)
++||+|++-||.+.|.+...|+-|+..-+ ..|||+|++|++.|.....|+-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 47888888888788888888888876422 1379999999999999999998854
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.36 E-value=0.00017 Score=35.55 Aligned_cols=23 Identities=43% Similarity=0.918 Sum_probs=13.6
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIH 25 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h 25 (263)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666666666666666666544
No 41
>KOG2231|consensus
Probab=97.19 E-value=0.0011 Score=59.23 Aligned_cols=134 Identities=23% Similarity=0.474 Sum_probs=88.8
Q ss_pred ccccccccccC---------------ChHHHHHHHHhhCCcccccCCC---------ccccCChhHHHHHHHHhcC-CC-
Q psy11318 3 YYCNACSKNFS---------------AKDTLNKHMDIHKGVRYQCEEC---------PKDFSTRKYLTQHQNAIHR-GI- 56 (263)
Q Consensus 3 y~C~~C~~~f~---------------~~~~L~~H~~~h~~~~~~C~~C---------~~~f~~~~~l~~H~~~~~~-~~- 56 (263)
+.|.+|+..|+ +...|+.|+...++ -+.|..| .....+...|.+|++.--. ++
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~-~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s 178 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHK-LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDES 178 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh-hhccccccccceeeeeeeehehHHHHHHHHhcCCCcccc
Confidence 56788887774 77889999966555 3455554 2334566778999876322 22
Q ss_pred ---ceecccccccccchHHHHHHHHHhcCCCcccCCcC------CCcCCCHHHHHHHHHHhcCCccccCC--CCCCCccc
Q psy11318 57 ---RFQCNKCFRAYKLKKDLLAHTMLEHFGIRHPCSEC------PKTFASRHSLKNHILKIHKAVLYQCN--ECSTSKDY 125 (263)
Q Consensus 57 ---~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~~~~~~~~~C~--~C~~~~~f 125 (263)
--.|..|...|.....|..|++.+| |.|..| +.-|.....|..|.+.+| |.|. .|.+. .|
T Consensus 179 ~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~-~f 249 (669)
T KOG2231|consen 179 CRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTK-KF 249 (669)
T ss_pred ccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccc-ee
Confidence 2579999999999999999998777 556665 345777899999999887 4665 56542 33
Q ss_pred CCH----HHHHHHHHHhCCCCCccC
Q psy11318 126 LTK----RDLRRHMKLHFNGKRYHC 146 (263)
Q Consensus 126 ~~~----~~l~~H~~~h~~~~~~~C 146 (263)
... -.|++|.+.+.-++.|.|
T Consensus 250 ~~~~~~ei~lk~~~~~~~~e~~~~~ 274 (669)
T KOG2231|consen 250 YVAFELEIELKAHNRFIQHEKCYIC 274 (669)
T ss_pred eehhHHHHHHHhhccccchheeccC
Confidence 333 344444433333444555
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.14 E-value=0.00027 Score=34.37 Aligned_cols=22 Identities=41% Similarity=0.797 Sum_probs=10.0
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIH 25 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h 25 (263)
|+|++|++... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 44555555554 44555555443
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.07 E-value=0.0004 Score=39.68 Aligned_cols=29 Identities=17% Similarity=0.222 Sum_probs=18.0
Q ss_pred cccccCCCccccCChhHHHHHHHHhcCCC
Q psy11318 28 VRYQCEECPKDFSTRKYLTQHQNAIHRGI 56 (263)
Q Consensus 28 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 56 (263)
.|..|++|+..+....+|++|+...|+.+
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 37778888888888888888877766654
No 44
>KOG1146|consensus
Probab=97.06 E-value=0.00017 Score=67.88 Aligned_cols=129 Identities=19% Similarity=0.235 Sum_probs=81.5
Q ss_pred cccccccccchHHHHHHHHHhc-CCCcccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCHHHHHHHHHHh
Q psy11318 60 CNKCFRAYKLKKDLLAHTMLEH-FGIRHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTKRDLRRHMKLH 138 (263)
Q Consensus 60 C~~C~~~f~~~~~l~~H~~~~~-~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~h 138 (263)
|.-|+..+.+...+.-|+...+ ..+.++|+.|+..|.....|..|+|..|.+-.- .+| +.+.....+.+-....
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c---~~gq~~~~~arg~~~~ 513 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYC---KAGQNHPRLARGEVYR 513 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch--hHh---Hhcccccccccccccc
Confidence 3344444555555555543333 337788999999998888899998886643211 223 2222222222212223
Q ss_pred CCCCCccCCcchhhhcChHHHHHHHhhc--c----------C-------------------------------CCCCcCC
Q psy11318 139 FNGKRYHCTQCSKFYIQESDLMEHMAVH--S----------G-------------------------------VRKLTTG 175 (263)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h--~----------~-------------------------------~~~~~c~ 175 (263)
.+.++|.|..|.+.++...+|.+|+..- - + .-.+.|.
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~ 593 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCE 593 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchh
Confidence 3556788888888888888888887421 1 0 0237899
Q ss_pred CCcccccccceeeeccCC
Q psy11318 176 PIKTEQTFGVRELRHVGF 193 (263)
Q Consensus 176 ~c~~~~~~~~~l~~H~~~ 193 (263)
+|++..+-..+|+.|+..
T Consensus 594 vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 594 VCSYETNIARNLRIHMTA 611 (1406)
T ss_pred hhcchhhhhhcccccccc
Confidence 999999999999999985
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.04 E-value=0.00053 Score=33.32 Aligned_cols=23 Identities=30% Similarity=0.673 Sum_probs=15.7
Q ss_pred cccCCCccccCChhHHHHHHHHhc
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIH 53 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~ 53 (263)
|+|+.|++... ...|.+|++.+|
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 57788887777 777888877765
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.97 E-value=0.00086 Score=32.90 Aligned_cols=23 Identities=35% Similarity=0.765 Sum_probs=16.7
Q ss_pred cccCCCccccCChhHHHHHHHHh
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAI 52 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~ 52 (263)
|.|..|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46777777777777777777753
No 47
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.95 E-value=0.00059 Score=39.01 Aligned_cols=31 Identities=16% Similarity=0.330 Sum_probs=17.0
Q ss_pred CCCccCCcchhhhcChHHHHHHHhhccCCCC
Q psy11318 141 GKRYHCTQCSKFYIQESDLMEHMAVHSGVRK 171 (263)
Q Consensus 141 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 171 (263)
+.|-.|+.|+..+.+.-+|++|+...|+.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4556677777777777777777766666554
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.93 E-value=0.00056 Score=33.56 Aligned_cols=22 Identities=36% Similarity=1.059 Sum_probs=11.1
Q ss_pred ccccccccccCChHHHHHHHHh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDI 24 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~ 24 (263)
|.|..|+..|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 3455555555555555555543
No 49
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.78 E-value=0.00076 Score=33.08 Aligned_cols=22 Identities=36% Similarity=0.780 Sum_probs=15.0
Q ss_pred cccCCCccccCChhHHHHHHHH
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
|.|.+|++.|.+...|+.|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4577777777777777777654
No 50
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.70 E-value=0.0023 Score=52.02 Aligned_cols=130 Identities=25% Similarity=0.419 Sum_probs=90.2
Q ss_pred Ccccc--ccccccCChHHHHHHHHhhCCcccccCCCc---cccC------ChhHHHHHHHHhcCCCc----eeccccccc
Q psy11318 2 RYYCN--ACSKNFSAKDTLNKHMDIHKGVRYQCEECP---KDFS------TRKYLTQHQNAIHRGIR----FQCNKCFRA 66 (263)
Q Consensus 2 ~y~C~--~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~---~~f~------~~~~l~~H~~~~~~~~~----~~C~~C~~~ 66 (263)
.|.|| .|..+......|+.|....++ .+.|.+|- +.|. +...|..|......+.= -.|..|...
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~-~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHG-FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC-cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 35664 366677778999999988877 46777772 3343 44557777654332222 469999999
Q ss_pred ccchHHHHHHHHHhcCCCcccCCcCCCc-------CCCHHHHHHHHHHhcCCccccCCCCC----CCcccCCHHHHHHHH
Q psy11318 67 YKLKKDLLAHTMLEHFGIRHPCSECPKT-------FASRHSLKNHILKIHKAVLYQCNECS----TSKDYLTKRDLRRHM 135 (263)
Q Consensus 67 f~~~~~l~~H~~~~~~~~~~~C~~C~~~-------f~~~~~l~~H~~~~~~~~~~~C~~C~----~~~~f~~~~~l~~H~ 135 (263)
|..-..|..|++..|. .|.+|++. |.+...|..|.+..| |.|.+=. ....|.....|..|+
T Consensus 230 FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~~~~el~~h~ 301 (493)
T COG5236 230 FYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFPYHTELLEHL 301 (493)
T ss_pred ecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEeccHHHHHHHH
Confidence 9999999999987773 46666553 778889999988655 4442211 126799999999999
Q ss_pred HHhCC
Q psy11318 136 KLHFN 140 (263)
Q Consensus 136 ~~h~~ 140 (263)
...++
T Consensus 302 ~~~h~ 306 (493)
T COG5236 302 TRFHK 306 (493)
T ss_pred HHHhh
Confidence 76554
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=96.53 E-value=0.00084 Score=33.67 Aligned_cols=22 Identities=45% Similarity=1.087 Sum_probs=12.8
Q ss_pred ccccccccccCChHHHHHHHHh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDI 24 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~ 24 (263)
|.|..|++.|.+...|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5566666666666666665543
No 52
>KOG2785|consensus
Probab=96.45 E-value=0.0084 Score=49.58 Aligned_cols=49 Identities=27% Similarity=0.561 Sum_probs=36.2
Q ss_pred ccccccccccCChHHHHHHHHhh--------------------------------------CCcccccCCCccccCChhH
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIH--------------------------------------KGVRYQCEECPKDFSTRKY 44 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h--------------------------------------~~~~~~C~~C~~~f~~~~~ 44 (263)
|+|.-|...|.+...-+.|+.+. .+.++.|.+|.+.|.....
T Consensus 4 ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a 83 (390)
T KOG2785|consen 4 FTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKA 83 (390)
T ss_pred ceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhh
Confidence 78999999999998899998763 0114677777777777777
Q ss_pred HHHHHHH
Q psy11318 45 LTQHQNA 51 (263)
Q Consensus 45 l~~H~~~ 51 (263)
...|+..
T Consensus 84 ~~~hl~S 90 (390)
T KOG2785|consen 84 HENHLKS 90 (390)
T ss_pred HHHHHHH
Confidence 7777654
No 53
>PRK04860 hypothetical protein; Provisional
Probab=96.31 E-value=0.0018 Score=47.79 Aligned_cols=39 Identities=18% Similarity=0.310 Sum_probs=30.4
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccccc
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGV 185 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~ 185 (263)
+|.|. |+. ....+.+|.++|.+.++|.|..|+..+....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 58887 876 6667788888888888888888888776544
No 54
>KOG2785|consensus
Probab=96.15 E-value=0.0079 Score=49.75 Aligned_cols=51 Identities=14% Similarity=0.018 Sum_probs=36.8
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCC-----------------------CCCcCCCCc---ccccccceeeeccCC
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGV-----------------------RKLTTGPIK---TEQTFGVRELRHVGF 193 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~c~~c~---~~~~~~~~l~~H~~~ 193 (263)
|-.|..|++.+.+...-..||..+||. ..|.|-.|+ +.|.+.+..+.||..
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 456777888888777777788777763 235666677 788888887888764
No 55
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.10 E-value=0.0013 Score=32.93 Aligned_cols=22 Identities=36% Similarity=0.798 Sum_probs=17.6
Q ss_pred cccCCCccccCChhHHHHHHHH
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
|.|..|++.|.+...|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788888888888888888764
No 56
>PRK04860 hypothetical protein; Provisional
Probab=95.94 E-value=0.0043 Score=45.85 Aligned_cols=34 Identities=18% Similarity=0.681 Sum_probs=16.0
Q ss_pred cccCCCccccCChhHHHHHHHHhcCCCceecccccccc
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAY 67 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 67 (263)
|.|. |+. ....+.+|.+++.++.+|.|..|+..|
T Consensus 120 Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 120 YRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 4444 444 344444454444444445554444444
No 57
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.53 E-value=0.0017 Score=56.36 Aligned_cols=60 Identities=20% Similarity=0.277 Sum_probs=31.6
Q ss_pred ccccCCCccccCChhHHHHHHH--HhcCC--Cceecc--cccccccchHHHHHHHHHhcCCCcccC
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQN--AIHRG--IRFQCN--KCFRAYKLKKDLLAHTMLEHFGIRHPC 88 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C 88 (263)
++.|..|...|.....|.+|.+ .|.++ +++.|. .|++.|.+...+..|...+.....+.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 3555555555555555555555 44555 455555 455555555555555544444443333
No 58
>KOG2482|consensus
Probab=95.46 E-value=0.033 Score=45.45 Aligned_cols=134 Identities=19% Similarity=0.310 Sum_probs=82.3
Q ss_pred ccccccccc-cCChHHHHHHHHhhCCc-----------------------ccccCCCccccCChhHHHHHHHHhc-CCCc
Q psy11318 3 YYCNACSKN-FSAKDTLNKHMDIHKGV-----------------------RYQCEECPKDFSTRKYLTQHQNAIH-RGIR 57 (263)
Q Consensus 3 y~C~~C~~~-f~~~~~L~~H~~~h~~~-----------------------~~~C~~C~~~f~~~~~l~~H~~~~~-~~~~ 57 (263)
.+|..|... -+.+...-.|+-.-++. .+.|-.|.+.|.++..|+.||+... ....
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrrin 224 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRIN 224 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCcccC
Confidence 468888875 34566666776443331 4899999999999999999998632 2221
Q ss_pred eecccccccc--------cchHHHHHHH----HHhcCC-------------Cc--ccCCcCCCcCCCHHHHHHHHHHhcC
Q psy11318 58 FQCNKCFRAY--------KLKKDLLAHT----MLEHFG-------------IR--HPCSECPKTFASRHSLKNHILKIHK 110 (263)
Q Consensus 58 ~~C~~C~~~f--------~~~~~l~~H~----~~~~~~-------------~~--~~C~~C~~~f~~~~~l~~H~~~~~~ 110 (263)
-+-...++.| .+......+. ....++ .+ ..|-.|.....+...|..||+..|.
T Consensus 225 PknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe 304 (423)
T KOG2482|consen 225 PKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIVHE 304 (423)
T ss_pred CCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHHHH
Confidence 1111111111 0111111111 001111 11 4788899888889999999988773
Q ss_pred C---------------------------ccccCCCCCCCcccCCHHHHHHHHHHh
Q psy11318 111 A---------------------------VLYQCNECSTSKDYLTKRDLRRHMKLH 138 (263)
Q Consensus 111 ~---------------------------~~~~C~~C~~~~~f~~~~~l~~H~~~h 138 (263)
- ....|-.|. ..|-....|..|+..+
T Consensus 305 ~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd--~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 305 FDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECD--LSFWKEPGLLIHMVED 357 (423)
T ss_pred hhHHhhccccccchhhhhhHHHHHHHHhhcccccccc--ccccCcchhhhhcccc
Confidence 1 124677787 7899999999999743
No 59
>KOG2893|consensus
Probab=95.43 E-value=0.003 Score=48.61 Aligned_cols=50 Identities=34% Similarity=0.548 Sum_probs=37.9
Q ss_pred cccCCCccccCChhHHHHHHHHhcCCCceecccccccccchHHHHHHHHHhcCC
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKKDLLAHTMLEHFG 83 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 83 (263)
-.|=+|++.|.+...|++|++..| |+|-+|.+...+--.|..|.+..|.+
T Consensus 11 pwcwycnrefddekiliqhqkakh----fkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred ceeeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceeehhhhhhh
Confidence 367789999999999999988866 88888888776666666665444433
No 60
>KOG2482|consensus
Probab=95.33 E-value=0.042 Score=44.83 Aligned_cols=50 Identities=22% Similarity=0.203 Sum_probs=41.4
Q ss_pred ccCCcchhhhcChHHHHHHHhhccC---------------------------CCCCcCCCCcccccccceeeeccCC
Q psy11318 144 YHCTQCSKFYIQESDLMEHMAVHSG---------------------------VRKLTTGPIKTEQTFGVRELRHVGF 193 (263)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~h~~---------------------------~~~~~c~~c~~~~~~~~~l~~H~~~ 193 (263)
.+|..|....-+...|..||..-|. .....|-.|...|.....|+.||..
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 5899999999989999999976542 1234788999999999999999975
No 61
>KOG4173|consensus
Probab=95.13 E-value=0.011 Score=44.53 Aligned_cols=105 Identities=23% Similarity=0.436 Sum_probs=52.5
Q ss_pred ccCChhHHHHHHHHhc-----CCC-------ceeccc--ccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHHHHHH
Q psy11318 38 DFSTRKYLTQHQNAIH-----RGI-------RFQCNK--CFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRHSLKN 103 (263)
Q Consensus 38 ~f~~~~~l~~H~~~~~-----~~~-------~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~ 103 (263)
.|.-.+++++|+...- .+. .|.|++ |-..|........|-..-|+ ..|..|.+.|++...|..
T Consensus 48 pFf~~G~v~r~l~~~~V~~d~~d~~~~~~~~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~ 124 (253)
T KOG4173|consen 48 PFFEDGDVQRHLYLQDVIMDVADVPEKPRVPAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDA 124 (253)
T ss_pred cchhcccHHHHHhHhhheeeccccccccccccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhH
Confidence 4556667777765321 000 145544 44555555544444333332 245555555555555555
Q ss_pred HHHHhcCCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCc--chhhhcChHHHHHHHhh
Q psy11318 104 HILKIHKAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQ--CSKFYIQESDLMEHMAV 165 (263)
Q Consensus 104 H~~~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~ 165 (263)
|+...|.. -|. .....|.-.|.|.+ |+..|.+.-.-++|+-.
T Consensus 125 HI~E~HDs------------~Fq--------a~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 125 HILEWHDS------------LFQ--------ALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred HHHHHHHH------------HHH--------HHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 55544420 000 00112344567755 77777777777777643
No 62
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.97 E-value=0.019 Score=30.57 Aligned_cols=21 Identities=24% Similarity=0.855 Sum_probs=10.9
Q ss_pred ccccccccccCChHHHHHHHH
Q psy11318 3 YYCNACSKNFSAKDTLNKHMD 23 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~ 23 (263)
|.|.+|+..|.+...+..|++
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 445555555555555555543
No 63
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.78 E-value=0.0059 Score=52.90 Aligned_cols=142 Identities=17% Similarity=0.201 Sum_probs=102.1
Q ss_pred CceecccccccccchHHHHHHHH--HhcCC--CcccCC--cCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCHH
Q psy11318 56 IRFQCNKCFRAYKLKKDLLAHTM--LEHFG--IRHPCS--ECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTKR 129 (263)
Q Consensus 56 ~~~~C~~C~~~f~~~~~l~~H~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~~ 129 (263)
..+.|..|...|.....|..|.. .|..+ +++.|+ .|++.|.+...+..|...|.+..++.+..-.+...+....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 35788999999999999999998 68888 899999 7999999999999999999888777775544334443333
Q ss_pred HHHHHH-----HHhCCCCCccCCc--chhhhcChHHHHHHHhhccCCC--CCcCCCCcccccccceeeeccCCCccc
Q psy11318 130 DLRRHM-----KLHFNGKRYHCTQ--CSKFYIQESDLMEHMAVHSGVR--KLTTGPIKTEQTFGVRELRHVGFPMKT 197 (263)
Q Consensus 130 ~l~~H~-----~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~--~~~c~~c~~~~~~~~~l~~H~~~~~~~ 197 (263)
.-..+. ..-...+.+.+.. |...+.+...+..|...|.... .+.+..|...+.....+..|++.+...
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNH 444 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccC
Confidence 311111 1112233455544 7777778878888877777665 467788889898888888888876543
No 64
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.21 E-value=0.024 Score=29.79 Aligned_cols=24 Identities=21% Similarity=0.761 Sum_probs=14.2
Q ss_pred ccccccccccCChHHHHHHHHhhCCcccccCCCcc
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPK 37 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~ 37 (263)
|.|..||..+.-.. .++.|++||.
T Consensus 2 ~~C~~CGy~y~~~~-----------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-----------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-----------CCCcCcCCCC
Confidence 56667776655432 4566666654
No 65
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.20 E-value=0.045 Score=26.73 Aligned_cols=19 Identities=37% Similarity=0.795 Sum_probs=11.6
Q ss_pred cccccccccCChHHHHHHHH
Q psy11318 4 YCNACSKNFSAKDTLNKHMD 23 (263)
Q Consensus 4 ~C~~C~~~f~~~~~L~~H~~ 23 (263)
.|+.||..| ..+.|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 566666666 3566666654
No 66
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.19 E-value=0.048 Score=26.65 Aligned_cols=21 Identities=24% Similarity=0.612 Sum_probs=14.5
Q ss_pred cccCCCccccCChhHHHHHHHH
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
..|+.||+.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4677888877 56667777653
No 67
>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=94.07 E-value=0.035 Score=29.44 Aligned_cols=23 Identities=17% Similarity=0.483 Sum_probs=18.5
Q ss_pred ccccCCCccccCChhHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
+|.|.+|++.|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57788888888888888888765
No 68
>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=94.04 E-value=0.024 Score=30.88 Aligned_cols=36 Identities=25% Similarity=0.582 Sum_probs=21.8
Q ss_pred CCccccccccccCChHHHHHHHHhhCCcccccCCCccccC
Q psy11318 1 MRYYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKDFS 40 (263)
Q Consensus 1 ~~y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~ 40 (263)
|.+.|+.|+..|.-...... ..+....|+.|+..|.
T Consensus 1 M~~~CP~C~~~~~v~~~~~~----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLG----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEEeCHHHcC----CCCCEEECCCCCCEEE
Confidence 56778888887765544321 1223567777777664
No 69
>KOG2893|consensus
Probab=94.01 E-value=0.016 Score=44.77 Aligned_cols=51 Identities=24% Similarity=0.555 Sum_probs=42.1
Q ss_pred CccccccccccCChHHHHHHHHhhCCcccccCCCccccCChhHHHHHHHHhcCC
Q psy11318 2 RYYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKDFSTRKYLTQHQNAIHRG 55 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 55 (263)
+-+|=+|+..|...+.|..|+ ..+-|+|.+|.|...+--.|..|-+..|.+
T Consensus 10 kpwcwycnrefddekiliqhq---kakhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQ---KAKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred Cceeeecccccchhhhhhhhh---hhccceeeeehhhhccCCCceeehhhhhhh
Confidence 348999999999999999998 445699999998888877788887765644
No 70
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.22 E-value=0.11 Score=35.59 Aligned_cols=49 Identities=18% Similarity=0.415 Sum_probs=29.9
Q ss_pred cCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHHHHHHHhhcc
Q psy11318 115 QCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHMAVHS 167 (263)
Q Consensus 115 ~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 167 (263)
.|-.|+ ..|........- .-.....|.|+.|...|-..-+...|...|.
T Consensus 57 ~C~~C~--~~f~~~~~~~~~--~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQ--GPFPKPPVSPFD--ELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcC--CCCCCccccccc--ccccccceeCCCCCCccccccchhhhhhccC
Confidence 477777 666543211100 0122345888888888888888888877775
No 71
>KOG2186|consensus
Probab=92.78 E-value=0.047 Score=42.65 Aligned_cols=54 Identities=24% Similarity=0.628 Sum_probs=40.9
Q ss_pred ccccccccccCChHHHHHHHHhhCCcccccCCCccccCChhHHHHHHHHhcCCCce
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKDFSTRKYLTQHQNAIHRGIRF 58 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 58 (263)
|.|..||.... +..|-.|+....+..|.|-.|++.|.. ..++.|..-......|
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCITEaQKY 57 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCITEAQKY 57 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhhhhcchHHHh
Confidence 67888888765 566777888888888888888888888 6678887655544433
No 72
>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=92.73 E-value=0.2 Score=34.54 Aligned_cols=26 Identities=19% Similarity=0.514 Sum_probs=20.8
Q ss_pred CccC----CcchhhhcChHHHHHHHhhccC
Q psy11318 143 RYHC----TQCSKFYIQESDLMEHMAVHSG 168 (263)
Q Consensus 143 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 168 (263)
.|.| ..|++.+.+...+.+|++.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3788 8888888888888888887764
No 73
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.59 E-value=0.06 Score=28.91 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=21.2
Q ss_pred CCccccccccccCChHHHHHHHHhhCCcccccCCCcccc
Q psy11318 1 MRYYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKDF 39 (263)
Q Consensus 1 ~~y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f 39 (263)
|...|+.|+..|.-.+... --.+...+|..|+..|
T Consensus 1 M~i~Cp~C~~~y~i~d~~i----p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKI----PPKGRKVRCSKCGHVF 35 (36)
T ss_pred CEEECCCCCCEEeCCHHHC----CCCCcEEECCCCCCEe
Confidence 4567777777776655432 1234456777777665
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=92.44 E-value=0.2 Score=34.38 Aligned_cols=24 Identities=29% Similarity=0.559 Sum_probs=13.3
Q ss_pred cccCCCCCCCcccCCHHHHHHHHHHh
Q psy11318 113 LYQCNECSTSKDYLTKRDLRRHMKLH 138 (263)
Q Consensus 113 ~~~C~~C~~~~~f~~~~~l~~H~~~h 138 (263)
.|+|+.|. ..|-..-++-.|...|
T Consensus 81 ~y~C~~C~--~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCK--NVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCC--Cccccccchhhhhhcc
Confidence 45666666 5555555555555444
No 75
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.07 E-value=0.022 Score=44.50 Aligned_cols=23 Identities=22% Similarity=0.540 Sum_probs=16.0
Q ss_pred CCccccccccccCChHHHHHHHH
Q psy11318 1 MRYYCNACSKNFSAKDTLNKHMD 23 (263)
Q Consensus 1 ~~y~C~~C~~~f~~~~~L~~H~~ 23 (263)
|.+.||+|++.|.++..+....+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCce
Confidence 56788888888887765555543
No 76
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.92 E-value=0.094 Score=30.61 Aligned_cols=30 Identities=17% Similarity=0.455 Sum_probs=24.8
Q ss_pred CCCCCccCCcchhhhcChHHHHHHHhhccC
Q psy11318 139 FNGKRYHCTQCSKFYIQESDLMEHMAVHSG 168 (263)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 168 (263)
.||.-++|+.||..|....++.+|....|+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 466778899999999999999999876654
No 77
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=91.69 E-value=0.4 Score=33.05 Aligned_cols=25 Identities=24% Similarity=0.458 Sum_probs=21.7
Q ss_pred ccC----CcCCCcCCCHHHHHHHHHHhcC
Q psy11318 86 HPC----SECPKTFASRHSLKNHILKIHK 110 (263)
Q Consensus 86 ~~C----~~C~~~f~~~~~l~~H~~~~~~ 110 (263)
|.| ..|+..+.+...|..|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 778 8899999999999999988875
No 78
>KOG4173|consensus
Probab=91.54 E-value=0.1 Score=39.45 Aligned_cols=79 Identities=25% Similarity=0.501 Sum_probs=59.5
Q ss_pred ccccCC--CccccCChhHHHHHHHHhcCCCceecccccccccchHHHHHHHHHhc----------CCCcccC--CcCCCc
Q psy11318 29 RYQCEE--CPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKKDLLAHTMLEH----------FGIRHPC--SECPKT 94 (263)
Q Consensus 29 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~----------~~~~~~C--~~C~~~ 94 (263)
.|.|++ |-..|.+...+..|-.+.|+ -.|..|.+.|.+..-|..|+..-| +...|.| ..|+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 467776 77788888888888777666 378888888888888888875443 3455788 458888
Q ss_pred CCCHHHHHHHHHHhcC
Q psy11318 95 FASRHSLKNHILKIHK 110 (263)
Q Consensus 95 f~~~~~l~~H~~~~~~ 110 (263)
|.+...-..|+-..|.
T Consensus 156 FkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 156 FKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhhHHHHhcc
Confidence 8888888888766653
No 79
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.51 E-value=0.13 Score=27.23 Aligned_cols=25 Identities=16% Similarity=0.474 Sum_probs=14.5
Q ss_pred CccccccccccCChHHHHHHHHhhCCcccccCCCcc
Q psy11318 2 RYYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPK 37 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~ 37 (263)
.|.|..||..+... ..|-.|++|+.
T Consensus 2 ~~~C~~CG~i~~g~-----------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE-----------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC-----------cCCCcCcCCCC
Confidence 46677777665432 13556777764
No 80
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.07 E-value=0.15 Score=29.85 Aligned_cols=26 Identities=27% Similarity=0.473 Sum_probs=14.4
Q ss_pred CcccCCcCCCcCCCHHHHHHHHHHhc
Q psy11318 84 IRHPCSECPKTFASRHSLKNHILKIH 109 (263)
Q Consensus 84 ~~~~C~~C~~~f~~~~~l~~H~~~~~ 109 (263)
..+.|+.|+..|...-.+.+|....|
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 44555555555555555555555544
No 81
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.60 E-value=0.19 Score=27.11 Aligned_cols=36 Identities=25% Similarity=0.523 Sum_probs=19.5
Q ss_pred CCccccccccccCChHHHHHHHHhhCCcccccCCCccccC
Q psy11318 1 MRYYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKDFS 40 (263)
Q Consensus 1 ~~y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~f~ 40 (263)
|...|+.|+..|.-...- ..-.+...+|+.|+..|.
T Consensus 1 M~i~CP~C~~~f~v~~~~----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDK----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred CEEECCCCCceEEcCHHH----cccCCcEEECCCCCcEee
Confidence 445677777766654431 112334566666666553
No 82
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.74 E-value=0.31 Score=27.49 Aligned_cols=28 Identities=29% Similarity=0.636 Sum_probs=17.9
Q ss_pred CCccccccccccCChHHHHHHHHhhCCcccccCCCccc
Q psy11318 1 MRYYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKD 38 (263)
Q Consensus 1 ~~y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~ 38 (263)
+.|.|..||..|... .+.+..|+.||..
T Consensus 1 ~~Y~C~~Cg~~~~~~----------~~~~irC~~CG~r 28 (44)
T smart00659 1 MIYICGECGRENEIK----------SKDVVRCRECGYR 28 (44)
T ss_pred CEEECCCCCCEeecC----------CCCceECCCCCce
Confidence 357777887776633 3346777777654
No 83
>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=87.71 E-value=0.23 Score=39.14 Aligned_cols=92 Identities=13% Similarity=0.257 Sum_probs=43.1
Q ss_pred hcCCCcccCCcCCCcCCCHHHHHHHHHHhc--CCccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChH
Q psy11318 80 EHFGIRHPCSECPKTFASRHSLKNHILKIH--KAVLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQES 157 (263)
Q Consensus 80 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~--~~~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 157 (263)
.|+++.|.|..|...+- ...-..|+.+-. ....|+|..|+ + + -.|.|..|...|-.-.
T Consensus 137 ~hGGrif~CsfC~~flC-EDDQFEHQAsCQvLe~E~~KC~SCN--r-l----------------Gq~sCLRCK~cfCddH 196 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFLC-EDDQFEHQASCQVLESETFKCQSCN--R-L----------------GQYSCLRCKICFCDDH 196 (314)
T ss_pred cCCCeEEEeecCCCeee-ccchhhhhhhhhhhhcccccccccc--c-c----------------cchhhhheeeeehhhh
Confidence 35777888888775332 222233433221 23457777775 2 1 1244554444443322
Q ss_pred HHHHHHhhccCCCCCcCCCCcccccccceeeeccC
Q psy11318 158 DLMEHMAVHSGVRKLTTGPIKTEQTFGVRELRHVG 192 (263)
Q Consensus 158 ~l~~H~~~h~~~~~~~c~~c~~~~~~~~~l~~H~~ 192 (263)
...+-.. ....+++.|+.|++....-..|--..+
T Consensus 197 vrrKg~k-y~k~k~~PCPKCg~et~eTkdLSmStR 230 (314)
T PF06524_consen 197 VRRKGFK-YEKGKPIPCPKCGYETQETKDLSMSTR 230 (314)
T ss_pred hhhcccc-cccCCCCCCCCCCCcccccccceeeee
Confidence 1111111 122356677777766654444443333
No 84
>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=86.26 E-value=0.56 Score=32.23 Aligned_cols=13 Identities=23% Similarity=0.662 Sum_probs=6.2
Q ss_pred cccCCcCCCcCCC
Q psy11318 85 RHPCSECPKTFAS 97 (263)
Q Consensus 85 ~~~C~~C~~~f~~ 97 (263)
|..|++||..|.-
T Consensus 26 PivCP~CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPKCGTEFPP 38 (108)
T ss_pred CccCCCCCCccCc
Confidence 4445555554443
No 85
>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=85.73 E-value=0.72 Score=36.44 Aligned_cols=94 Identities=21% Similarity=0.358 Sum_probs=55.0
Q ss_pred hcCCCceecccccccccchHHHHHHHHHhc--CCCcccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCHH
Q psy11318 52 IHRGIRFQCNKCFRAYKLKKDLLAHTMLEH--FGIRHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTKR 129 (263)
Q Consensus 52 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~--~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~~ 129 (263)
.|+++.|.|..|......-..+ .|+.+-. ....|+|..|++. ..|.|..|. .-|-...
T Consensus 137 ~hGGrif~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrl-----------------Gq~sCLRCK--~cfCddH 196 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRL-----------------GQYSCLRCK--ICFCDDH 196 (314)
T ss_pred cCCCeEEEeecCCCeeeccchh-hhhhhhhhhhcccccccccccc-----------------cchhhhhee--eeehhhh
Confidence 4677889999999865544443 3443322 2367899999863 124555554 3332221
Q ss_pred HHHHHHHHhCCCCCccCCcchhhhcChHHHHHHHhhc
Q psy11318 130 DLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHMAVH 166 (263)
Q Consensus 130 ~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 166 (263)
....-... ...+++.|+.|++.......|..-.+.|
T Consensus 197 vrrKg~ky-~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 197 VRRKGFKY-EKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred hhhccccc-ccCCCCCCCCCCCcccccccceeeeecc
Confidence 11111112 2347899999998887777776555555
No 86
>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=85.15 E-value=0.17 Score=27.87 Aligned_cols=11 Identities=36% Similarity=1.159 Sum_probs=6.5
Q ss_pred ccccccccccC
Q psy11318 3 YYCNACSKNFS 13 (263)
Q Consensus 3 y~C~~C~~~f~ 13 (263)
|+|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 55666666554
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.14 E-value=0.44 Score=34.89 Aligned_cols=36 Identities=17% Similarity=0.438 Sum_probs=24.4
Q ss_pred cccccCCCccccCChhHHHHHHHHhcCCCceecccccccc
Q psy11318 28 VRYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAY 67 (263)
Q Consensus 28 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 67 (263)
.-|.|+.|+..|.....+..- .....|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~----d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLL----DMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhc----CCCCcEECCCCCCEE
Confidence 379999999888865543320 123449999999765
No 88
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=83.19 E-value=0.67 Score=34.40 Aligned_cols=24 Identities=17% Similarity=0.257 Sum_probs=14.9
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcc
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKT 179 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~ 179 (263)
-|+|++||+. +-|+-|.+|++|+-
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 4777777654 33566677777763
No 89
>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=82.52 E-value=0.27 Score=28.75 Aligned_cols=11 Identities=45% Similarity=1.222 Sum_probs=5.7
Q ss_pred ccccccccccC
Q psy11318 3 YYCNACSKNFS 13 (263)
Q Consensus 3 y~C~~C~~~f~ 13 (263)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45555555444
No 90
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.14 E-value=1.1 Score=30.82 Aligned_cols=30 Identities=13% Similarity=0.170 Sum_probs=23.0
Q ss_pred ccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCccccccc
Q psy11318 144 YHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFG 184 (263)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~ 184 (263)
..|+.||..|... +..|.+|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 6788888888654 34778888888887665
No 91
>PF15269 zf-C2H2_7: Zinc-finger
Probab=82.11 E-value=1 Score=25.06 Aligned_cols=21 Identities=29% Similarity=0.687 Sum_probs=10.2
Q ss_pred cccCCCccccCChhHHHHHHH
Q psy11318 30 YQCEECPKDFSTRKYLTQHQN 50 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~ 50 (263)
|+|-+|..+..-++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 344444444444555555543
No 92
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.00 E-value=0.32 Score=27.67 Aligned_cols=12 Identities=25% Similarity=0.902 Sum_probs=6.8
Q ss_pred CccccccccccC
Q psy11318 2 RYYCNACSKNFS 13 (263)
Q Consensus 2 ~y~C~~C~~~f~ 13 (263)
.|.|+.||..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 456666666543
No 93
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.95 E-value=0.18 Score=37.02 Aligned_cols=16 Identities=31% Similarity=0.634 Sum_probs=10.9
Q ss_pred cccCCCccccCChhHH
Q psy11318 30 YQCEECPKDFSTRKYL 45 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l 45 (263)
++|+-||+.|.+...+
T Consensus 29 ~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLACGKRFTTFERV 44 (154)
T ss_pred eeccccCCcceEeEec
Confidence 6777777777766543
No 94
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=81.66 E-value=1.3 Score=24.90 Aligned_cols=23 Identities=22% Similarity=0.440 Sum_probs=13.3
Q ss_pred ccccCCCccccCCh----hHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTR----KYLTQHQNA 51 (263)
Q Consensus 29 ~~~C~~C~~~f~~~----~~l~~H~~~ 51 (263)
..+|.+|++.+... ..|++|++.
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 56788888777663 667777754
No 95
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=81.35 E-value=0.24 Score=38.72 Aligned_cols=22 Identities=27% Similarity=0.585 Sum_probs=14.6
Q ss_pred ccccCCCccccCChhHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQN 50 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~ 50 (263)
...||+|+..|.+........+
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCce
Confidence 4678888888877765544443
No 96
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=81.24 E-value=1.5 Score=21.52 Aligned_cols=19 Identities=26% Similarity=0.772 Sum_probs=10.1
Q ss_pred cccccccccCChHHHHHHHH
Q psy11318 4 YCNACSKNFSAKDTLNKHMD 23 (263)
Q Consensus 4 ~C~~C~~~f~~~~~L~~H~~ 23 (263)
.||+|++.+ ....++.|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 456666655 3445555553
No 97
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=79.59 E-value=0.75 Score=26.47 Aligned_cols=11 Identities=27% Similarity=0.978 Sum_probs=7.0
Q ss_pred Ccccccccccc
Q psy11318 2 RYYCNACSKNF 12 (263)
Q Consensus 2 ~y~C~~C~~~f 12 (263)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 36666666666
No 98
>PF15269 zf-C2H2_7: Zinc-finger
Probab=79.55 E-value=1.3 Score=24.62 Aligned_cols=21 Identities=33% Similarity=0.654 Sum_probs=17.3
Q ss_pred CccccccccccCChHHHHHHH
Q psy11318 2 RYYCNACSKNFSAKDTLNKHM 22 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~ 22 (263)
.|+|-+|.++...++.|-.||
T Consensus 20 ~ykcfqcpftc~~kshl~nhm 40 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHM 40 (54)
T ss_pred cceeecCCcccchHHHHHHHH
Confidence 478888888888888888887
No 99
>PF14353 CpXC: CpXC protein
Probab=78.94 E-value=0.19 Score=35.86 Aligned_cols=20 Identities=25% Similarity=0.580 Sum_probs=9.8
Q ss_pred ccccCCCccccCChhHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQH 48 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H 48 (263)
.|.|+.||..|.-...+.-|
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred EEECCCCCCceecCCCEEEE
Confidence 45555555555444444444
No 100
>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=78.44 E-value=2.3 Score=31.52 Aligned_cols=34 Identities=9% Similarity=0.054 Sum_probs=20.8
Q ss_pred CCCCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccc
Q psy11318 139 FNGKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQ 181 (263)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~ 181 (263)
.+..-|.|+.|+..|+....+. ..|.|+.||...
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 3444567777776666655553 257777777654
No 101
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=77.55 E-value=3 Score=30.89 Aligned_cols=18 Identities=11% Similarity=0.240 Sum_probs=8.0
Q ss_pred CcccCCcCCCcCCCHHHH
Q psy11318 84 IRHPCSECPKTFASRHSL 101 (263)
Q Consensus 84 ~~~~C~~C~~~f~~~~~l 101 (263)
..|.|+.|+..|.....+
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CeEECCCCCcEeeHHHHH
Confidence 344444444444444433
No 102
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.53 E-value=2.3 Score=25.40 Aligned_cols=8 Identities=38% Similarity=1.277 Sum_probs=3.9
Q ss_pred cccCCCCC
Q psy11318 113 LYQCNECS 120 (263)
Q Consensus 113 ~~~C~~C~ 120 (263)
+|+|+.||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 44454444
No 103
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=77.44 E-value=1.7 Score=26.07 Aligned_cols=21 Identities=24% Similarity=0.227 Sum_probs=9.6
Q ss_pred hhHHHHHHHHhcCCCceeccc
Q psy11318 42 RKYLTQHQNAIHRGIRFQCNK 62 (263)
Q Consensus 42 ~~~l~~H~~~~~~~~~~~C~~ 62 (263)
+..|..|+...-...+..|..
T Consensus 23 r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 23 RKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CCCHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHHHccCCCCcEECCC
Confidence 334555555334444455555
No 104
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=77.03 E-value=2.5 Score=24.46 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=16.0
Q ss_pred ccccCCCccccCCh-----hHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTR-----KYLTQHQNA 51 (263)
Q Consensus 29 ~~~C~~C~~~f~~~-----~~l~~H~~~ 51 (263)
.-.|.+|++.+... +.|.+|++.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 35688888777554 577777773
No 105
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=76.07 E-value=1.1 Score=31.94 Aligned_cols=26 Identities=23% Similarity=0.511 Sum_probs=16.6
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCCCC
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGVRK 171 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 171 (263)
...|..||+.|... ++|++.|+|..+
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eeEEccCCcccchH---HHHHHHccCCCH
Confidence 46899999999865 899999988654
No 106
>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=75.67 E-value=1.1 Score=22.96 Aligned_cols=24 Identities=25% Similarity=0.717 Sum_probs=8.8
Q ss_pred cccccccccCChHHHHHHHHhhCCcccccCCCcc
Q psy11318 4 YCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPK 37 (263)
Q Consensus 4 ~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~ 37 (263)
+|+.|+..+.. +.+..|.|+.|+.
T Consensus 4 ~Cp~C~se~~y----------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY----------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E----------E-SSSEEETTTTE
T ss_pred CCCCCCCccee----------ccCCEEeCCcccc
Confidence 56666665543 3444566666654
No 107
>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=75.53 E-value=1.9 Score=22.42 Aligned_cols=26 Identities=27% Similarity=0.755 Sum_probs=14.7
Q ss_pred ccccccccccCChHHHHHHHHhhCCcccccCCCccc
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIHKGVRYQCEECPKD 38 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h~~~~~~C~~C~~~ 38 (263)
|.|..||..+.. -.+.+.+|+.||..
T Consensus 1 Y~C~~Cg~~~~~----------~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVEL----------KPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-B----------STSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEc----------CCCCcEECCcCCCe
Confidence 667777776552 12345677777754
No 108
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=75.11 E-value=2.4 Score=29.81 Aligned_cols=30 Identities=7% Similarity=0.078 Sum_probs=17.4
Q ss_pred ccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCCCCcccCCH
Q psy11318 86 HPCSECPKTFASRHSLKNHILKIHKAVLYQCNECSTSKDYLTK 128 (263)
Q Consensus 86 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~f~~~ 128 (263)
..|+.|++.|... +..|..|+.|| ..|...
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg--~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTG--EQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcC--CccCcc
Confidence 4677777666543 23466777777 555443
No 109
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=74.01 E-value=0.53 Score=26.20 Aligned_cols=11 Identities=36% Similarity=1.180 Sum_probs=5.2
Q ss_pred ccccccccccC
Q psy11318 3 YYCNACSKNFS 13 (263)
Q Consensus 3 y~C~~C~~~f~ 13 (263)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 44555554443
No 110
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.22 E-value=4.3 Score=30.76 Aligned_cols=13 Identities=23% Similarity=0.817 Sum_probs=5.9
Q ss_pred eecccccccccch
Q psy11318 58 FQCNKCFRAYKLK 70 (263)
Q Consensus 58 ~~C~~C~~~f~~~ 70 (263)
|.|+.|+..|...
T Consensus 118 Y~Cp~C~~rytf~ 130 (178)
T PRK06266 118 FFCPNCHIRFTFD 130 (178)
T ss_pred EECCCCCcEEeHH
Confidence 4444444444443
No 111
>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=73.15 E-value=2.1 Score=30.53 Aligned_cols=26 Identities=31% Similarity=0.420 Sum_probs=16.4
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIR 57 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 57 (263)
-..|-+||+.|+.. ++|++.||+-.+
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eeEEccCCcccchH---HHHHHHccCCCH
Confidence 36799999988875 999999877554
No 112
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.12 E-value=3.3 Score=31.34 Aligned_cols=35 Identities=9% Similarity=0.144 Sum_probs=21.3
Q ss_pred CCCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccc
Q psy11318 140 NGKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTF 183 (263)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~ 183 (263)
+..-|.|+.|+..|+....+. ..|.|+.||.....
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 334577777777766555432 35777777765543
No 113
>KOG1280|consensus
Probab=72.88 E-value=1.2 Score=36.71 Aligned_cols=36 Identities=19% Similarity=0.351 Sum_probs=29.5
Q ss_pred eecccccccccchHHHHHHHHHhcCCCc--ccCCcCCC
Q psy11318 58 FQCNKCFRAYKLKKDLLAHTMLEHFGIR--HPCSECPK 93 (263)
Q Consensus 58 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~--~~C~~C~~ 93 (263)
|.|+.|+++-.+...|..|+...|.+.. ..|+.|.-
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 8899999998889999999988888744 45777765
No 114
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=72.11 E-value=1.9 Score=30.44 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=20.9
Q ss_pred ccCCcchhhhcChHHHHHHHhhccCCCC
Q psy11318 144 YHCTQCSKFYIQESDLMEHMAVHSGVRK 171 (263)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 171 (263)
..|..+|+.|. +|++|+.+|.+..|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 47999999987 68999999988655
No 115
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=71.70 E-value=1.8 Score=35.20 Aligned_cols=26 Identities=27% Similarity=0.691 Sum_probs=21.5
Q ss_pred CCccCCcchhhhcChHHHHHHHhhcc
Q psy11318 142 KRYHCTQCSKFYIQESDLMEHMAVHS 167 (263)
Q Consensus 142 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 167 (263)
..|.|+.|...|-.--+...|...|.
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHhh
Confidence 35899999999988888888877774
No 116
>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=71.45 E-value=2.7 Score=20.63 Aligned_cols=6 Identities=33% Similarity=1.126 Sum_probs=2.8
Q ss_pred cCCCCC
Q psy11318 115 QCNECS 120 (263)
Q Consensus 115 ~C~~C~ 120 (263)
.|+.||
T Consensus 16 ~Cp~CG 21 (26)
T PF10571_consen 16 FCPHCG 21 (26)
T ss_pred cCCCCC
Confidence 344454
No 117
>PRK04023 DNA polymerase II large subunit; Validated
Probab=70.38 E-value=4.5 Score=38.62 Aligned_cols=9 Identities=22% Similarity=0.936 Sum_probs=5.0
Q ss_pred ccCCcCCCc
Q psy11318 86 HPCSECPKT 94 (263)
Q Consensus 86 ~~C~~C~~~ 94 (263)
+.|+.|+..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 446666554
No 118
>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=70.33 E-value=1.7 Score=20.89 Aligned_cols=9 Identities=22% Similarity=0.741 Sum_probs=5.3
Q ss_pred Ccccccccc
Q psy11318 2 RYYCNACSK 10 (263)
Q Consensus 2 ~y~C~~C~~ 10 (263)
+|.||.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 356666664
No 119
>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=69.89 E-value=3.7 Score=22.28 Aligned_cols=12 Identities=50% Similarity=1.242 Sum_probs=4.2
Q ss_pred CCcccccccccc
Q psy11318 1 MRYYCNACSKNF 12 (263)
Q Consensus 1 ~~y~C~~C~~~f 12 (263)
++|-|+.|+..+
T Consensus 2 ~ryyCdyC~~~~ 13 (38)
T PF06220_consen 2 PRYYCDYCKKYL 13 (38)
T ss_dssp -S-B-TTT--B-
T ss_pred cCeeccccccee
Confidence 356777777766
No 120
>KOG2186|consensus
Probab=69.68 E-value=2.8 Score=33.17 Aligned_cols=48 Identities=17% Similarity=0.440 Sum_probs=30.9
Q ss_pred cccCCCccccCChhHHHHHHHHhcCCCceecccccccccchHHHHHHHHHh
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKKDLLAHTMLE 80 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 80 (263)
|.|.+||....-.. |-+|+...++ .-|.|=.|++.|.. ..+..|..-.
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhhhc
Confidence 67777877666544 5557766443 56777777777777 5566666433
No 121
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=69.34 E-value=6.1 Score=28.85 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=18.9
Q ss_pred CCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccc
Q psy11318 141 GKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQ 181 (263)
Q Consensus 141 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~ 181 (263)
..-|.|+.|+..|.....+.. . . ....|.|+.|+...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~-~--d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL-L--D-MDGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh-c--C-CCCcEECCCCCCEE
Confidence 345667777766664332221 0 1 12337777776654
No 122
>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=69.06 E-value=2.1 Score=25.28 Aligned_cols=11 Identities=18% Similarity=0.836 Sum_probs=5.9
Q ss_pred Ccccccccccc
Q psy11318 2 RYYCNACSKNF 12 (263)
Q Consensus 2 ~y~C~~C~~~f 12 (263)
.++|+.||..+
T Consensus 2 ~~~CP~CG~~i 12 (54)
T TIGR01206 2 QFECPDCGAEI 12 (54)
T ss_pred ccCCCCCCCEE
Confidence 34566666544
No 123
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=69.00 E-value=3.3 Score=30.86 Aligned_cols=23 Identities=22% Similarity=0.406 Sum_probs=14.4
Q ss_pred cccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCC
Q psy11318 85 RHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECS 120 (263)
Q Consensus 85 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 120 (263)
.|.|++||..+. ++.|.+|++||
T Consensus 134 ~~vC~vCGy~~~-------------ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHE-------------GEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCccc-------------CCCCCcCCCCC
Confidence 467777766532 35566777776
No 124
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=68.60 E-value=1.4 Score=27.73 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=5.7
Q ss_pred eecc--cccccccc
Q psy11318 58 FQCN--KCFRAYKL 69 (263)
Q Consensus 58 ~~C~--~C~~~f~~ 69 (263)
+.|. .|+..|..
T Consensus 28 ~qC~N~eCg~tF~t 41 (72)
T PRK09678 28 HQCQNVNCSATFIT 41 (72)
T ss_pred eecCCCCCCCEEEE
Confidence 4454 45554443
No 125
>PHA00626 hypothetical protein
Probab=68.18 E-value=2.2 Score=25.10 Aligned_cols=12 Identities=42% Similarity=0.753 Sum_probs=6.4
Q ss_pred CccccccccccC
Q psy11318 2 RYYCNACSKNFS 13 (263)
Q Consensus 2 ~y~C~~C~~~f~ 13 (263)
+|+|+.||+.|+
T Consensus 23 rYkCkdCGY~ft 34 (59)
T PHA00626 23 DYVCCDCGYNDS 34 (59)
T ss_pred ceEcCCCCCeec
Confidence 355555555544
No 126
>KOG2807|consensus
Probab=67.82 E-value=8.8 Score=31.68 Aligned_cols=25 Identities=28% Similarity=0.821 Sum_probs=21.6
Q ss_pred CccCCcchhhhcChHHHHHHHhhcc
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHS 167 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~ 167 (263)
.|.|..|.-.|-.--+...|-..|.
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred cEEchhccceeeccchHHHHhhhhc
Confidence 5899999999998888889987775
No 127
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=67.29 E-value=3.4 Score=38.47 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=19.1
Q ss_pred HhCCCCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCccc
Q psy11318 137 LHFNGKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTE 180 (263)
Q Consensus 137 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~ 180 (263)
.|...+...|.+|| +....|..|+.|+..
T Consensus 456 ~H~~~~~L~CH~Cg---------------~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 456 LHKATGQLRCHYCG---------------YQEPIPQSCPECGSE 484 (730)
T ss_pred EecCCCeeEeCCCC---------------CCCCCCCCCCCCCCC
Confidence 34455567777777 335567788888875
No 128
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=67.12 E-value=8.1 Score=32.18 Aligned_cols=29 Identities=17% Similarity=0.466 Sum_probs=16.8
Q ss_pred HhcCCccccCCCCCCCcccCCHHHHHHHHH
Q psy11318 107 KIHKAVLYQCNECSTSKDYLTKRDLRRHMK 136 (263)
Q Consensus 107 ~~~~~~~~~C~~C~~~~~f~~~~~l~~H~~ 136 (263)
.|.-.+.|.|.+|| ++.+.-...+.+|..
T Consensus 368 lhgLd~ef~CEICg-Nyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICG-NYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecc-cccccchHHHHhhhh
Confidence 34445667888887 244445555556653
No 129
>KOG4124|consensus
Probab=66.98 E-value=0.66 Score=38.27 Aligned_cols=49 Identities=27% Similarity=0.540 Sum_probs=31.8
Q ss_pred CCccc--cccccccCChHHHHHHHHhhCC--------------------cccccCCCccccCChhHHHHHH
Q psy11318 1 MRYYC--NACSKNFSAKDTLNKHMDIHKG--------------------VRYQCEECPKDFSTRKYLTQHQ 49 (263)
Q Consensus 1 ~~y~C--~~C~~~f~~~~~L~~H~~~h~~--------------------~~~~C~~C~~~f~~~~~l~~H~ 49 (263)
|+|+| +.|++.+....+|+.|-..-+. ++|.|++|.+.++..-.|+-|.
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 46777 5788888888888887543211 1567777777666665555554
No 130
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.55 E-value=3.7 Score=38.24 Aligned_cols=9 Identities=33% Similarity=0.940 Sum_probs=4.8
Q ss_pred ccccCCCCC
Q psy11318 112 VLYQCNECS 120 (263)
Q Consensus 112 ~~~~C~~C~ 120 (263)
.|..|+.||
T Consensus 474 ~p~~Cp~Cg 482 (730)
T COG1198 474 IPQSCPECG 482 (730)
T ss_pred CCCCCCCCC
Confidence 445555555
No 131
>KOG2593|consensus
Probab=65.86 E-value=5.7 Score=34.08 Aligned_cols=37 Identities=19% Similarity=0.290 Sum_probs=17.5
Q ss_pred CCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCccc
Q psy11318 141 GKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTE 180 (263)
Q Consensus 141 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~ 180 (263)
...|.|+.|.+.|+....+.. .-.....|.|..|+-.
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGGE 162 (436)
T ss_pred cccccCCccccchhhhHHHHh---hcccCceEEEecCCCc
Confidence 344666666666554443321 2222344555555543
No 132
>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=65.85 E-value=2.5 Score=32.98 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=22.0
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCC
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRG 55 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~ 55 (263)
.|.|+.|+|.|+-...++.|+...|.+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHH
Confidence 699999999999999999999988754
No 133
>KOG2807|consensus
Probab=65.65 E-value=9.5 Score=31.49 Aligned_cols=31 Identities=29% Similarity=0.699 Sum_probs=23.0
Q ss_pred ccccCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcch
Q psy11318 112 VLYQCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCS 150 (263)
Q Consensus 112 ~~~~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 150 (263)
..|+|..|. ..|-.--+.-.|...| .|+.|.
T Consensus 344 ~~y~C~~Ck--~~FCldCDv~iHesLh------~CpgCe 374 (378)
T KOG2807|consen 344 GRYRCESCK--NVFCLDCDVFIHESLH------NCPGCE 374 (378)
T ss_pred CcEEchhcc--ceeeccchHHHHhhhh------cCCCcC
Confidence 458899988 7888777777777666 576665
No 134
>KOG1280|consensus
Probab=64.74 E-value=5.7 Score=33.01 Aligned_cols=23 Identities=13% Similarity=0.265 Sum_probs=11.0
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDIH 25 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~h 25 (263)
|.|++|+.+=.+...|..|+...
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~ 102 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQ 102 (381)
T ss_pred ccCCcccccccchhHHHHHhhhc
Confidence 44555555444444455554443
No 135
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=64.46 E-value=9.5 Score=21.02 Aligned_cols=26 Identities=23% Similarity=0.280 Sum_probs=19.8
Q ss_pred ccCCCCCCCcccCCHHHHHHHHHHhC
Q psy11318 114 YQCNECSTSKDYLTKRDLRRHMKLHF 139 (263)
Q Consensus 114 ~~C~~C~~~~~f~~~~~l~~H~~~h~ 139 (263)
.+|+.||..+......+-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 57888887777777888888887764
No 136
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=62.33 E-value=7.3 Score=23.36 Aligned_cols=8 Identities=38% Similarity=1.215 Sum_probs=4.4
Q ss_pred cccCCCCC
Q psy11318 113 LYQCNECS 120 (263)
Q Consensus 113 ~~~C~~C~ 120 (263)
+|+|+.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 45555555
No 137
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.96 E-value=3.3 Score=26.91 Aligned_cols=11 Identities=18% Similarity=0.908 Sum_probs=5.5
Q ss_pred ccCCcchhhhc
Q psy11318 144 YHCTQCSKFYI 154 (263)
Q Consensus 144 ~~C~~C~~~f~ 154 (263)
|.|..|+..|+
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 45555554443
No 138
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=59.03 E-value=4.7 Score=26.42 Aligned_cols=27 Identities=19% Similarity=0.470 Sum_probs=17.4
Q ss_pred CcccCCcCCCcCCCHHHHHHHHHHhcCCccccCCCCC
Q psy11318 84 IRHPCSECPKTFASRHSLKNHILKIHKAVLYQCNECS 120 (263)
Q Consensus 84 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 120 (263)
.|-.|..||..|.+.- -.+|..|+.|.
T Consensus 57 ~Pa~CkkCGfef~~~~----------ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDDK----------IKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCccccccc----------cCCcccCCcch
Confidence 4567888888777621 23466777775
No 139
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=58.44 E-value=13 Score=31.08 Aligned_cols=22 Identities=18% Similarity=0.502 Sum_probs=12.8
Q ss_pred ccCCcCCCcCCCHHHHHHHHHH
Q psy11318 86 HPCSECPKTFASRHSLKNHILK 107 (263)
Q Consensus 86 ~~C~~C~~~f~~~~~l~~H~~~ 107 (263)
+.|..|++.|.....+..|+..
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~g 260 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLEG 260 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHhh
Confidence 4466666666666666666543
No 140
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=57.77 E-value=4 Score=24.24 Aligned_cols=37 Identities=27% Similarity=0.527 Sum_probs=21.2
Q ss_pred CCccccccccccCChHH--HHHHHHhhCCcccccCCCcc
Q psy11318 1 MRYYCNACSKNFSAKDT--LNKHMDIHKGVRYQCEECPK 37 (263)
Q Consensus 1 ~~y~C~~C~~~f~~~~~--L~~H~~~h~~~~~~C~~C~~ 37 (263)
|+.+|..|++.+.--.. +..-++...-..|-|..|..
T Consensus 1 m~vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~ 39 (56)
T PF09963_consen 1 MRVKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKE 39 (56)
T ss_pred CeeEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHH
Confidence 56788888887543332 33334443334677777744
No 141
>KOG2593|consensus
Probab=56.92 E-value=5.1 Score=34.35 Aligned_cols=35 Identities=23% Similarity=0.587 Sum_probs=26.8
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceeccccccc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRA 66 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 66 (263)
.|.|+.|++.|.....++.=- .....|.|..|+.-
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~---~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLD---NETGEFHCENCGGE 162 (436)
T ss_pred cccCCccccchhhhHHHHhhc---ccCceEEEecCCCc
Confidence 799999999999988776542 22345999999853
No 142
>KOG4377|consensus
Probab=56.39 E-value=3.5 Score=34.97 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=19.2
Q ss_pred ccCCc--chhhhcChHHHHHHHhhccC
Q psy11318 144 YHCTQ--CSKFYIQESDLMEHMAVHSG 168 (263)
Q Consensus 144 ~~C~~--C~~~f~~~~~l~~H~~~h~~ 168 (263)
+.|.+ |+..+...+....|.+.|..
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheR 428 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHER 428 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhh
Confidence 45544 88888888888888888864
No 143
>KOG4377|consensus
Probab=55.82 E-value=4.4 Score=34.45 Aligned_cols=22 Identities=5% Similarity=-0.207 Sum_probs=18.6
Q ss_pred CCcccccccceeeeccCCCccc
Q psy11318 176 PIKTEQTFGVRELRHVGFPMKT 197 (263)
Q Consensus 176 ~c~~~~~~~~~l~~H~~~~~~~ 197 (263)
.|+..+.+-+.+..|.+.|-+.
T Consensus 408 Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 408 GCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred CCceEEEehhhhhhhhhhhhhh
Confidence 4889999999999999887764
No 144
>KOG4167|consensus
Probab=55.28 E-value=3.2 Score=38.00 Aligned_cols=22 Identities=36% Similarity=0.647 Sum_probs=11.7
Q ss_pred cccccccccCChHHHHHHHHhh
Q psy11318 4 YCNACSKNFSAKDTLNKHMDIH 25 (263)
Q Consensus 4 ~C~~C~~~f~~~~~L~~H~~~h 25 (263)
-|-+|+|+|.-.++++.||.+|
T Consensus 794 pCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 794 PCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred ehHHHHHHHHHHhhhhHHHHHH
Confidence 3555555555555555555554
No 145
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.07 E-value=8.3 Score=35.78 Aligned_cols=7 Identities=29% Similarity=1.037 Sum_probs=3.4
Q ss_pred ecccccc
Q psy11318 59 QCNKCFR 65 (263)
Q Consensus 59 ~C~~C~~ 65 (263)
.|..|+.
T Consensus 385 ~C~~Cg~ 391 (665)
T PRK14873 385 ACARCRT 391 (665)
T ss_pred EhhhCcC
Confidence 4555544
No 146
>COG1773 Rubredoxin [Energy production and conversion]
Probab=52.91 E-value=6 Score=23.40 Aligned_cols=13 Identities=23% Similarity=0.846 Sum_probs=8.2
Q ss_pred CccccccccccCC
Q psy11318 2 RYYCNACSKNFSA 14 (263)
Q Consensus 2 ~y~C~~C~~~f~~ 14 (263)
+|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 5666666666654
No 147
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.32 E-value=9.7 Score=25.93 Aligned_cols=11 Identities=9% Similarity=0.021 Sum_probs=5.1
Q ss_pred cccCCcCCCcC
Q psy11318 85 RHPCSECPKTF 95 (263)
Q Consensus 85 ~~~C~~C~~~f 95 (263)
|..|++||+.|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 44444444444
No 148
>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=52.25 E-value=5.4 Score=21.32 Aligned_cols=29 Identities=17% Similarity=0.282 Sum_probs=13.4
Q ss_pred cCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccc
Q psy11318 145 HCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQ 181 (263)
Q Consensus 145 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~ 181 (263)
.|+.||..|... ..-....-.|..|+-.+
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 466666665321 22233345566665533
No 149
>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=51.58 E-value=3.3 Score=20.74 Aligned_cols=8 Identities=63% Similarity=1.593 Sum_probs=3.3
Q ss_pred cCCCcccc
Q psy11318 32 CEECPKDF 39 (263)
Q Consensus 32 C~~C~~~f 39 (263)
|-.|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 33444444
No 150
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=51.51 E-value=12 Score=22.05 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=4.6
Q ss_pred cccccccccC
Q psy11318 4 YCNACSKNFS 13 (263)
Q Consensus 4 ~C~~C~~~f~ 13 (263)
.|+.||+.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 3444444443
No 151
>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=50.67 E-value=8.7 Score=34.40 Aligned_cols=13 Identities=23% Similarity=0.674 Sum_probs=6.4
Q ss_pred hCCCCCccCCcch
Q psy11318 138 HFNGKRYHCTQCS 150 (263)
Q Consensus 138 h~~~~~~~C~~C~ 150 (263)
|...+...|.+||
T Consensus 235 h~~~~~l~Ch~Cg 247 (505)
T TIGR00595 235 HKKEGKLRCHYCG 247 (505)
T ss_pred ecCCCeEEcCCCc
Confidence 3334445555555
No 152
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=50.31 E-value=15 Score=36.36 Aligned_cols=11 Identities=18% Similarity=0.525 Sum_probs=6.7
Q ss_pred ceecccccccc
Q psy11318 57 RFQCNKCFRAY 67 (263)
Q Consensus 57 ~~~C~~C~~~f 67 (263)
.|.|+.|+...
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 46677776643
No 153
>KOG4167|consensus
Probab=50.08 E-value=5.6 Score=36.50 Aligned_cols=26 Identities=23% Similarity=0.354 Sum_probs=23.0
Q ss_pred eecccccccccchHHHHHHHHHhcCC
Q psy11318 58 FQCNKCFRAYKLKKDLLAHTMLEHFG 83 (263)
Q Consensus 58 ~~C~~C~~~f~~~~~l~~H~~~~~~~ 83 (263)
|.|.+|++.|.....+..||+.|...
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 99999999999999999999887643
No 154
>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=49.66 E-value=8.1 Score=30.17 Aligned_cols=29 Identities=24% Similarity=0.478 Sum_probs=21.4
Q ss_pred CcccCCcCCCcCCCHHHHHHHHHHhcCCc
Q psy11318 84 IRHPCSECPKTFASRHSLKNHILKIHKAV 112 (263)
Q Consensus 84 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 112 (263)
..|.|+.|+|.|....-...|+...|.++
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 34789999999999999999998887654
No 155
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=49.30 E-value=5.3 Score=22.92 Aligned_cols=20 Identities=25% Similarity=0.687 Sum_probs=13.9
Q ss_pred CccccccccccCChHHHHHHH
Q psy11318 2 RYYCNACSKNFSAKDTLNKHM 22 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~ 22 (263)
+|.|+.|+..|. ...|++-+
T Consensus 7 ry~CDLCn~~~p-~~~LRQCv 26 (57)
T PF14445_consen 7 RYSCDLCNSSHP-ISELRQCV 26 (57)
T ss_pred hHhHHhhcccCc-HHHHHHHh
Confidence 578888887765 56676654
No 156
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=48.40 E-value=14 Score=29.21 Aligned_cols=26 Identities=27% Similarity=0.475 Sum_probs=13.0
Q ss_pred ChhHHHHHHHHhcCCC-----ceeccccccc
Q psy11318 41 TRKYLTQHQNAIHRGI-----RFQCNKCFRA 66 (263)
Q Consensus 41 ~~~~l~~H~~~~~~~~-----~~~C~~C~~~ 66 (263)
+..+|+..-+.+...+ .|.|..|+..
T Consensus 91 Te~Nlrm~d~a~~~~ip~~drqFaC~~Cd~~ 121 (278)
T PF15135_consen 91 TEENLRMFDDAQENLIPSVDRQFACSSCDHM 121 (278)
T ss_pred hHHHHHHhhhhhhccccccceeeeccccchH
Confidence 3444555555444332 2666666553
No 157
>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=48.26 E-value=11 Score=33.71 Aligned_cols=8 Identities=25% Similarity=0.825 Sum_probs=4.5
Q ss_pred cccCCCCC
Q psy11318 113 LYQCNECS 120 (263)
Q Consensus 113 ~~~C~~C~ 120 (263)
+..|+.|+
T Consensus 253 ~~~Cp~C~ 260 (505)
T TIGR00595 253 PKTCPQCG 260 (505)
T ss_pred CCCCCCCC
Confidence 44566665
No 158
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.73 E-value=3.4 Score=32.25 Aligned_cols=27 Identities=19% Similarity=0.346 Sum_probs=15.8
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCC
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRG 55 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~ 55 (263)
.+.||+|+-.|.....+..-.++..++
T Consensus 19 ~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 19 TIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred eeccCcccchhhhhheeccceeEeccc
Confidence 567777777776665554444443333
No 159
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=47.12 E-value=3.8 Score=29.00 Aligned_cols=54 Identities=24% Similarity=0.576 Sum_probs=28.8
Q ss_pred cccccCCCccccCChhHHHHHHHHhcCCCceec---ccccccccchHHHHHHHHHhcCCCcccCCcCCCcCCCHH
Q psy11318 28 VRYQCEECPKDFSTRKYLTQHQNAIHRGIRFQC---NKCFRAYKLKKDLLAHTMLEHFGIRHPCSECPKTFASRH 99 (263)
Q Consensus 28 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C---~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 99 (263)
.-|+|.+|..+.....-|+ |=+| .+|+.-+ .+|+.|-..+ -.||.|...|.+..
T Consensus 79 ~lYeCnIC~etS~ee~FLK----------PneCCgY~iCn~Cy---a~LWK~~~~y-----pvCPvCkTSFKss~ 135 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLK----------PNECCGYSICNACY---ANLWKFCNLY-----PVCPVCKTSFKSSS 135 (140)
T ss_pred CceeccCcccccchhhcCC----------cccccchHHHHHHH---HHHHHHcccC-----CCCCcccccccccc
Confidence 4688999877665544332 2222 2333333 2344444322 27888877777653
No 160
>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=46.52 E-value=6.9 Score=22.37 Aligned_cols=15 Identities=20% Similarity=0.771 Sum_probs=9.0
Q ss_pred CccccccccccCChH
Q psy11318 2 RYYCNACSKNFSAKD 16 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~ 16 (263)
+|+|..|+..|.-..
T Consensus 1 ky~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEK 15 (47)
T ss_dssp EEEETTTSBEEETTT
T ss_pred CcCCCCCCEEEcCCc
Confidence 466666666665433
No 161
>KOG1044|consensus
Probab=45.18 E-value=2.7 Score=37.33 Aligned_cols=28 Identities=4% Similarity=-0.185 Sum_probs=19.6
Q ss_pred CcCCCCcccccccceeeeccC-C-Cccccc
Q psy11318 172 LTTGPIKTEQTFGVRELRHVG-F-PMKTDH 199 (263)
Q Consensus 172 ~~c~~c~~~~~~~~~l~~H~~-~-~~~~~~ 199 (263)
-+|..|+..|...+++-.--. + |..++.
T Consensus 219 ARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 219 ARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred hhhhhhccccccchheeeccccccCCcccc
Confidence 479999999999988875432 2 444443
No 162
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=44.84 E-value=11 Score=20.68 Aligned_cols=19 Identities=16% Similarity=0.200 Sum_probs=10.0
Q ss_pred ccccCCCccccCChhHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQ 47 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~ 47 (263)
.+.|+.|+-.+.+...|.+
T Consensus 19 id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEECCCCCeEEccHHHHHH
Confidence 3455555555555555443
No 163
>KOG0717|consensus
Probab=44.72 E-value=12 Score=32.48 Aligned_cols=22 Identities=32% Similarity=0.812 Sum_probs=16.1
Q ss_pred ccccccccccCChHHHHHHHHh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDI 24 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~ 24 (263)
+-|+.|+|+|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 4577777777777777777654
No 164
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.52 E-value=9.5 Score=24.09 Aligned_cols=31 Identities=26% Similarity=0.570 Sum_probs=15.9
Q ss_pred cccCCCccccCChhHHHHHHHHhcCCCceecccccccc
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAY 67 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 67 (263)
|.|..|+..| .+.+|| .++-...|..|+..+
T Consensus 13 Y~c~~cg~~~----dvvq~~---~ddplt~ce~c~a~~ 43 (82)
T COG2331 13 YECTECGNRF----DVVQAM---TDDPLTTCEECGARL 43 (82)
T ss_pred EeecccchHH----HHHHhc---ccCccccChhhChHH
Confidence 6666665533 344443 233345666666543
No 165
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=44.48 E-value=8.9 Score=26.60 Aligned_cols=25 Identities=20% Similarity=0.512 Sum_probs=15.0
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceecccccc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFR 65 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 65 (263)
.+.|..|+..|.... ..+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCC
Confidence 467777776665432 2255777774
No 166
>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=44.35 E-value=7.4 Score=36.53 Aligned_cols=8 Identities=38% Similarity=1.040 Sum_probs=0.0
Q ss_pred cccCCCcc
Q psy11318 30 YQCEECPK 37 (263)
Q Consensus 30 ~~C~~C~~ 37 (263)
+.|+.||.
T Consensus 656 r~Cp~Cg~ 663 (900)
T PF03833_consen 656 RRCPKCGK 663 (900)
T ss_dssp --------
T ss_pred ccCcccCC
Confidence 45555544
No 167
>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=44.04 E-value=17 Score=20.52 Aligned_cols=7 Identities=29% Similarity=1.322 Sum_probs=3.5
Q ss_pred ccCCcch
Q psy11318 144 YHCTQCS 150 (263)
Q Consensus 144 ~~C~~C~ 150 (263)
+.|+.||
T Consensus 19 ~~CP~Cg 25 (46)
T PF12760_consen 19 FVCPHCG 25 (46)
T ss_pred CCCCCCC
Confidence 4455555
No 168
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=43.85 E-value=28 Score=20.66 Aligned_cols=14 Identities=14% Similarity=0.591 Sum_probs=7.4
Q ss_pred ccccCCCccccCCh
Q psy11318 29 RYQCEECPKDFSTR 42 (263)
Q Consensus 29 ~~~C~~C~~~f~~~ 42 (263)
.|.|+.||..+...
T Consensus 14 ~~~Cp~cGipthcS 27 (55)
T PF13824_consen 14 NFECPDCGIPTHCS 27 (55)
T ss_pred CCcCCCCCCcCccC
Confidence 45566665554443
No 169
>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=43.82 E-value=33 Score=25.15 Aligned_cols=17 Identities=18% Similarity=0.405 Sum_probs=11.2
Q ss_pred cCCCceecccccccccc
Q psy11318 53 HRGIRFQCNKCFRAYKL 69 (263)
Q Consensus 53 ~~~~~~~C~~C~~~f~~ 69 (263)
...-..+|..|+++|..
T Consensus 10 ~p~~vv~C~~c~kWFCN 26 (152)
T PF09416_consen 10 DPSCVVKCNTCNKWFCN 26 (152)
T ss_dssp -CCCEEEETTTTEEEES
T ss_pred CcccEeEcCCCCcEeec
Confidence 34445788888888854
No 170
>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=43.79 E-value=7.6 Score=21.54 Aligned_cols=9 Identities=22% Similarity=0.770 Sum_probs=4.3
Q ss_pred ccccccccc
Q psy11318 3 YYCNACSKN 11 (263)
Q Consensus 3 y~C~~C~~~ 11 (263)
|.|+.||..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 345555543
No 171
>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=43.78 E-value=17 Score=22.45 Aligned_cols=29 Identities=21% Similarity=0.443 Sum_probs=18.4
Q ss_pred ccCCCccccCChhHHHHHHHHhcCCCceecccccccccc
Q psy11318 31 QCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKL 69 (263)
Q Consensus 31 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 69 (263)
.|+.||..-.. -.....|.|+.||..+..
T Consensus 30 ~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 30 TCPRCGHRNKK----------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccccccc----------ccccceEEcCCCCCEECc
Confidence 57777765554 133345888888877654
No 172
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=43.05 E-value=14 Score=22.82 Aligned_cols=9 Identities=44% Similarity=1.040 Sum_probs=2.6
Q ss_pred ccCCCcccc
Q psy11318 31 QCEECPKDF 39 (263)
Q Consensus 31 ~C~~C~~~f 39 (263)
.|.+|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 455555555
No 173
>KOG4124|consensus
Probab=43.03 E-value=9.4 Score=31.80 Aligned_cols=51 Identities=18% Similarity=0.144 Sum_probs=38.2
Q ss_pred CCccCCc--chhhhcChHHHHHHHhhcc-------------------CCCCCcCCCCcccccccceeeeccC
Q psy11318 142 KRYHCTQ--CSKFYIQESDLMEHMAVHS-------------------GVRKLTTGPIKTEQTFGVRELRHVG 192 (263)
Q Consensus 142 ~~~~C~~--C~~~f~~~~~l~~H~~~h~-------------------~~~~~~c~~c~~~~~~~~~l~~H~~ 192 (263)
++|+|++ |++.+.....|+.|...-| ..|+|+|++|.+.++-...|..|..
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 5788877 9999888888887754322 2478999999999887777666654
No 174
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=42.83 E-value=7.9 Score=23.14 Aligned_cols=13 Identities=31% Similarity=0.646 Sum_probs=4.5
Q ss_pred CCccccccccccC
Q psy11318 1 MRYYCNACSKNFS 13 (263)
Q Consensus 1 ~~y~C~~C~~~f~ 13 (263)
|...|++|++.+.
T Consensus 1 m~v~CP~C~k~~~ 13 (57)
T PF03884_consen 1 MTVKCPICGKPVE 13 (57)
T ss_dssp -EEE-TTT--EEE
T ss_pred CcccCCCCCCeec
Confidence 3445566655433
No 175
>KOG3408|consensus
Probab=42.53 E-value=13 Score=25.89 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=21.3
Q ss_pred ccccCCCccccCChhHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
.|-|-.|.+.|.+...|+.|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 48999999999999999999886
No 176
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.35 E-value=10 Score=27.26 Aligned_cols=12 Identities=25% Similarity=0.858 Sum_probs=7.1
Q ss_pred eecccccccccc
Q psy11318 58 FQCNKCFRAYKL 69 (263)
Q Consensus 58 ~~C~~C~~~f~~ 69 (263)
+.|..|+..|..
T Consensus 71 ~~C~~CG~~~~~ 82 (135)
T PRK03824 71 LKCRNCGNEWSL 82 (135)
T ss_pred EECCCCCCEEec
Confidence 566666655544
No 177
>KOG2907|consensus
Probab=39.58 E-value=10 Score=26.05 Aligned_cols=11 Identities=27% Similarity=0.948 Sum_probs=5.2
Q ss_pred ccCCcchhhhc
Q psy11318 144 YHCTQCSKFYI 154 (263)
Q Consensus 144 ~~C~~C~~~f~ 154 (263)
|.|+.|++.|+
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 44554544443
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=39.22 E-value=11 Score=26.24 Aligned_cols=26 Identities=27% Similarity=0.781 Sum_probs=17.0
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceeccccccc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRA 66 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 66 (263)
...|..|+..|..... .+.|+.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 4778888876665432 3678888753
No 179
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=38.14 E-value=14 Score=21.37 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=6.5
Q ss_pred ceecccccccc
Q psy11318 57 RFQCNKCFRAY 67 (263)
Q Consensus 57 ~~~C~~C~~~f 67 (263)
.+.|..|+..+
T Consensus 37 r~~C~~Cgyt~ 47 (50)
T PRK00432 37 RWHCGKCGYTE 47 (50)
T ss_pred cEECCCcCCEE
Confidence 46666666543
No 180
>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=37.83 E-value=15 Score=21.29 Aligned_cols=12 Identities=25% Similarity=0.805 Sum_probs=6.6
Q ss_pred ccccccccccCC
Q psy11318 3 YYCNACSKNFSA 14 (263)
Q Consensus 3 y~C~~C~~~f~~ 14 (263)
|.|..||..|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 555555555553
No 181
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=37.51 E-value=15 Score=20.00 Aligned_cols=13 Identities=23% Similarity=0.777 Sum_probs=8.0
Q ss_pred CccccccccccCC
Q psy11318 2 RYYCNACSKNFSA 14 (263)
Q Consensus 2 ~y~C~~C~~~f~~ 14 (263)
++.|..|++.|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 4566666666654
No 182
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=36.80 E-value=13 Score=21.38 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=5.6
Q ss_pred ccccCCCcccc
Q psy11318 29 RYQCEECPKDF 39 (263)
Q Consensus 29 ~~~C~~C~~~f 39 (263)
.+.|+.||+.+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45555555443
No 183
>KOG2636|consensus
Probab=36.34 E-value=23 Score=30.72 Aligned_cols=23 Identities=35% Similarity=0.677 Sum_probs=15.1
Q ss_pred ccccCCCc-cccCChhHHHHHHHH
Q psy11318 29 RYQCEECP-KDFSTRKYLTQHQNA 51 (263)
Q Consensus 29 ~~~C~~C~-~~f~~~~~l~~H~~~ 51 (263)
.|.|.+|| +++.-...+.+|...
T Consensus 401 ey~CEICGNy~Y~GrkaF~RHF~E 424 (497)
T KOG2636|consen 401 EYNCEICGNYVYKGRKAFDRHFNE 424 (497)
T ss_pred ccceeeccCccccCcHHHHHHhHH
Confidence 46777776 666666666666654
No 184
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=36.07 E-value=22 Score=20.51 Aligned_cols=12 Identities=17% Similarity=0.719 Sum_probs=5.5
Q ss_pred eecccccccccc
Q psy11318 58 FQCNKCFRAYKL 69 (263)
Q Consensus 58 ~~C~~C~~~f~~ 69 (263)
+.|..||..|..
T Consensus 5 l~C~dCg~~Fvf 16 (49)
T PF13451_consen 5 LTCKDCGAEFVF 16 (49)
T ss_pred EEcccCCCeEEE
Confidence 444455544433
No 185
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.76 E-value=22 Score=30.77 Aligned_cols=32 Identities=13% Similarity=0.168 Sum_probs=21.1
Q ss_pred cCCcchhhhcChHHHHHHHhhccCCCCCcCCCCccccccccee
Q psy11318 145 HCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGVRE 187 (263)
Q Consensus 145 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~~l 187 (263)
+|+.||....+. |.+.|+|..|++.+......
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCccccc
Confidence 688888654322 44488888888877665443
No 186
>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=35.51 E-value=13 Score=19.83 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy11318 3 YYCNACSKN 11 (263)
Q Consensus 3 y~C~~C~~~ 11 (263)
|+|..||..
T Consensus 7 YkC~~CGni 15 (36)
T PF06397_consen 7 YKCEHCGNI 15 (36)
T ss_dssp EE-TTT--E
T ss_pred EEccCCCCE
Confidence 666666664
No 187
>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=35.27 E-value=22 Score=31.29 Aligned_cols=25 Identities=24% Similarity=0.545 Sum_probs=21.5
Q ss_pred CccCCcchhhhcChHHHHHHHhhcc
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHS 167 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~ 167 (263)
-|.|+.|.+.|.....+..|+...|
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhh
Confidence 3689999999999999999998544
No 188
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=35.10 E-value=11 Score=24.88 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=4.1
Q ss_pred ccCCcchhhh
Q psy11318 144 YHCTQCSKFY 153 (263)
Q Consensus 144 ~~C~~C~~~f 153 (263)
|.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PTZ00255 55 WRCKGCKKTV 64 (90)
T ss_pred EEcCCCCCEE
Confidence 4444444333
No 189
>KOG0782|consensus
Probab=34.86 E-value=9.9 Score=33.95 Aligned_cols=55 Identities=22% Similarity=0.504 Sum_probs=31.3
Q ss_pred HHHHHHHhhCC-cccccCCCccccCChhHHHHHHHHhcCCCceecccccccccchH-HHHHH
Q psy11318 17 TLNKHMDIHKG-VRYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKK-DLLAH 76 (263)
Q Consensus 17 ~L~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~-~l~~H 76 (263)
.|.+|-=.|.. ..-+|..|+|.|..+..+..- ......|+.|...|-.+. .+..+
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~FhsK-----EivAisCSWCKqayH~KvtCFml~ 296 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHSK-----EIVAISCSWCKQAYHLKVTCFMLD 296 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheeeccc-----cEEEEEehHHHHHhhcchhhhhhh
Confidence 34444333322 134888999888776644221 123478888888876653 44333
No 190
>KOG3408|consensus
Probab=34.62 E-value=28 Score=24.28 Aligned_cols=27 Identities=22% Similarity=0.783 Sum_probs=22.8
Q ss_pred CCCCccCCcchhhhcChHHHHHHHhhc
Q psy11318 140 NGKRYHCTQCSKFYIQESDLMEHMAVH 166 (263)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 166 (263)
|.-.|-|..|.+-|.+...|..|.++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 445688999999999999999998654
No 191
>PRK05978 hypothetical protein; Provisional
Probab=34.10 E-value=13 Score=27.21 Aligned_cols=32 Identities=22% Similarity=0.473 Sum_probs=19.0
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKL 69 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 69 (263)
.-+|+.||+.=-....|+.+ -.|+.|+..|..
T Consensus 33 ~grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~ 64 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKPV---------DHCAACGEDFTH 64 (148)
T ss_pred cCcCCCCCCCcccccccccC---------CCccccCCcccc
Confidence 46788887654434433322 468888876644
No 192
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=34.08 E-value=3.6 Score=22.55 Aligned_cols=9 Identities=0% Similarity=-0.156 Sum_probs=4.1
Q ss_pred CcCCCCccc
Q psy11318 172 LTTGPIKTE 180 (263)
Q Consensus 172 ~~c~~c~~~ 180 (263)
|.|..|++.
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 444444443
No 193
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.06 E-value=21 Score=24.95 Aligned_cols=14 Identities=21% Similarity=0.823 Sum_probs=9.2
Q ss_pred ccccCCCccccCCh
Q psy11318 29 RYQCEECPKDFSTR 42 (263)
Q Consensus 29 ~~~C~~C~~~f~~~ 42 (263)
.+.|..||..|...
T Consensus 71 ~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 71 ELECKDCSHVFKPN 84 (117)
T ss_pred EEEhhhCCCccccC
Confidence 46777887666543
No 194
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=34.01 E-value=16 Score=24.81 Aligned_cols=10 Identities=20% Similarity=0.517 Sum_probs=5.5
Q ss_pred CCcccccccc
Q psy11318 1 MRYYCNACSK 10 (263)
Q Consensus 1 ~~y~C~~C~~ 10 (263)
||-.|++||.
T Consensus 1 ~p~~CpYCg~ 10 (102)
T PF11672_consen 1 KPIICPYCGG 10 (102)
T ss_pred CCcccCCCCC
Confidence 4455555555
No 195
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.71 E-value=22 Score=30.79 Aligned_cols=30 Identities=13% Similarity=0.451 Sum_probs=20.9
Q ss_pred cCCCCCCCcccCCHHHHHHHHHHhCCCCCccCCcchhhhcChH
Q psy11318 115 QCNECSTSKDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQES 157 (263)
Q Consensus 115 ~C~~C~~~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 157 (263)
.|+.|| .+..+. |.+-|+|+.||+.+....
T Consensus 352 ~Cp~Cg--~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCG--GRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccC--Cchhhc-----------CCCCcccccccccCCccc
Confidence 689998 433222 434899999998887654
No 196
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.88 E-value=22 Score=24.74 Aligned_cols=13 Identities=23% Similarity=0.577 Sum_probs=8.5
Q ss_pred ccccCCCccccCC
Q psy11318 29 RYQCEECPKDFST 41 (263)
Q Consensus 29 ~~~C~~C~~~f~~ 41 (263)
.+.|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (114)
T PRK03681 70 ECWCETCQQYVTL 82 (114)
T ss_pred EEEcccCCCeeec
Confidence 4777888765543
No 197
>KOG2071|consensus
Probab=32.56 E-value=27 Score=31.49 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=15.6
Q ss_pred cccCCCccccCChhHHHHHHHHh
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAI 52 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~ 52 (263)
.+|..||..|.+......||..|
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred chhcccccccccchhhhhHhhhh
Confidence 46777777777777777666664
No 198
>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=32.09 E-value=34 Score=30.20 Aligned_cols=27 Identities=26% Similarity=0.477 Sum_probs=23.5
Q ss_pred cccCCCccccCChhHHHHHHHHhcCCC
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNAIHRGI 56 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~~~~~~ 56 (263)
+.|+.|.+.|.+...++.|+...|...
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 689999999999999999999766543
No 199
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.08 E-value=33 Score=20.71 Aligned_cols=9 Identities=22% Similarity=0.730 Sum_probs=4.4
Q ss_pred Ccccccccc
Q psy11318 2 RYYCNACSK 10 (263)
Q Consensus 2 ~y~C~~C~~ 10 (263)
..+|.+|+.
T Consensus 2 ~vkCiiCd~ 10 (68)
T COG4896 2 NVKCIICDR 10 (68)
T ss_pred CceEEEecc
Confidence 344555554
No 200
>PF14369 zf-RING_3: zinc-finger
Probab=31.93 E-value=30 Score=18.29 Aligned_cols=11 Identities=36% Similarity=1.247 Sum_probs=5.8
Q ss_pred Ccccccccccc
Q psy11318 2 RYYCNACSKNF 12 (263)
Q Consensus 2 ~y~C~~C~~~f 12 (263)
+|.|-.|...+
T Consensus 2 ~ywCh~C~~~V 12 (35)
T PF14369_consen 2 RYWCHQCNRFV 12 (35)
T ss_pred CEeCccCCCEe
Confidence 35555555543
No 201
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=31.48 E-value=15 Score=20.43 Aligned_cols=13 Identities=31% Similarity=0.910 Sum_probs=5.8
Q ss_pred CccccccccccCC
Q psy11318 2 RYYCNACSKNFSA 14 (263)
Q Consensus 2 ~y~C~~C~~~f~~ 14 (263)
++.|..|++.|=.
T Consensus 13 ~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 13 PFKCKHCGKSFCL 25 (43)
T ss_dssp HEE-TTTS-EE-T
T ss_pred CeECCCCCcccCc
Confidence 4566666666544
No 202
>KOG0717|consensus
Probab=31.37 E-value=26 Score=30.61 Aligned_cols=22 Identities=36% Similarity=0.730 Sum_probs=20.8
Q ss_pred cccCCCccccCChhHHHHHHHH
Q psy11318 30 YQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
+-|.+|++.|.+...|+.|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999999876
No 203
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=31.22 E-value=31 Score=28.44 Aligned_cols=34 Identities=24% Similarity=0.328 Sum_probs=20.8
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccchH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKK 71 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 71 (263)
=.+|+.|+.....+. |. +..+.|+.|+..|.-..
T Consensus 38 w~kc~~C~~~~~~~~-l~--------~~~~vcp~c~~h~rltA 71 (296)
T CHL00174 38 WVQCENCYGLNYKKF-LK--------SKMNICEQCGYHLKMSS 71 (296)
T ss_pred eeECCCccchhhHHH-HH--------HcCCCCCCCCCCcCCCH
Confidence 367888877554433 11 12368888888777543
No 204
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=30.94 E-value=48 Score=24.64 Aligned_cols=18 Identities=33% Similarity=0.765 Sum_probs=12.8
Q ss_pred CccCCcchhhhcChHHHH
Q psy11318 143 RYHCTQCSKFYIQESDLM 160 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~ 160 (263)
-|.|+.||+.|..-+.+.
T Consensus 130 f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 130 FYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred eeECCCCcccccCchHHH
Confidence 467888888887666544
No 205
>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=30.80 E-value=33 Score=28.20 Aligned_cols=34 Identities=21% Similarity=0.454 Sum_probs=21.4
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccchH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLKK 71 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 71 (263)
=.+|+.|+.....+. |.. ..+.|+.|+..|.-..
T Consensus 26 ~~~c~~c~~~~~~~~-l~~--------~~~vc~~c~~h~rl~a 59 (285)
T TIGR00515 26 WTKCPKCGQVLYTKE-LER--------NLEVCPKCDHHMRMDA 59 (285)
T ss_pred eeECCCCcchhhHHH-HHh--------hCCCCCCCCCcCcCCH
Confidence 367888887654443 111 1268899998877543
No 206
>KOG1940|consensus
Probab=30.68 E-value=38 Score=27.60 Aligned_cols=46 Identities=15% Similarity=0.265 Sum_probs=30.6
Q ss_pred eecccccccccchHHHHHHHHHhcCCCc-----------ccCCcCCCcCCCHHHHHHH
Q psy11318 58 FQCNKCFRAYKLKKDLLAHTMLEHFGIR-----------HPCSECPKTFASRHSLKNH 104 (263)
Q Consensus 58 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~-----------~~C~~C~~~f~~~~~l~~H 104 (263)
|.|++|.+ -.....+..+......+.+ ..|+.|+..-..+.....|
T Consensus 197 y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~ 253 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYH 253 (276)
T ss_pred CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhh
Confidence 99999998 6666666666655444322 4688898877666555444
No 207
>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=29.87 E-value=18 Score=25.12 Aligned_cols=15 Identities=27% Similarity=0.888 Sum_probs=9.0
Q ss_pred ccccCCCccccCChh
Q psy11318 29 RYQCEECPKDFSTRK 43 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~ 43 (263)
.+.|..||+.|.-..
T Consensus 70 ~~~C~~Cg~~~~~~~ 84 (113)
T PF01155_consen 70 RARCRDCGHEFEPDE 84 (113)
T ss_dssp EEEETTTS-EEECHH
T ss_pred cEECCCCCCEEecCC
Confidence 467777777766544
No 208
>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=29.80 E-value=37 Score=19.81 Aligned_cols=9 Identities=44% Similarity=1.095 Sum_probs=4.0
Q ss_pred cCCCccccC
Q psy11318 32 CEECPKDFS 40 (263)
Q Consensus 32 C~~C~~~f~ 40 (263)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 444444444
No 209
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.69 E-value=18 Score=25.79 Aligned_cols=11 Identities=36% Similarity=1.213 Sum_probs=5.4
Q ss_pred ccccccccccC
Q psy11318 3 YYCNACSKNFS 13 (263)
Q Consensus 3 y~C~~C~~~f~ 13 (263)
|.|..|+++|.
T Consensus 54 yrC~~C~~tf~ 64 (129)
T COG3677 54 YKCKSCGSTFT 64 (129)
T ss_pred cccCCcCccee
Confidence 44555555444
No 210
>KOG1842|consensus
Probab=29.58 E-value=30 Score=30.01 Aligned_cols=28 Identities=21% Similarity=0.357 Sum_probs=24.1
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCC
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGI 56 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 56 (263)
.|.|++|..-|.+...|..|+...|.+.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 6899999999999999999998777654
No 211
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=29.49 E-value=21 Score=18.13 Aligned_cols=11 Identities=27% Similarity=1.077 Sum_probs=4.4
Q ss_pred Ccccccccccc
Q psy11318 2 RYYCNACSKNF 12 (263)
Q Consensus 2 ~y~C~~C~~~f 12 (263)
+|.|+.|+..|
T Consensus 13 kY~Cp~C~~~~ 23 (30)
T PF04438_consen 13 KYRCPRCGARY 23 (30)
T ss_dssp SEE-TTT--EE
T ss_pred EEECCCcCCce
Confidence 45666666554
No 212
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=29.36 E-value=33 Score=23.11 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=7.0
Q ss_pred ccccCCCccccCCh
Q psy11318 29 RYQCEECPKDFSTR 42 (263)
Q Consensus 29 ~~~C~~C~~~f~~~ 42 (263)
|+.|.-||..|.+-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 34455555555543
No 213
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=29.36 E-value=5.4 Score=22.45 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=6.2
Q ss_pred Cccccccccc
Q psy11318 2 RYYCNACSKN 11 (263)
Q Consensus 2 ~y~C~~C~~~ 11 (263)
+..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 5567777743
No 214
>PF12907 zf-met2: Zinc-binding
Probab=28.78 E-value=57 Score=17.90 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=15.2
Q ss_pred ccCCcchhhhc---ChHHHHHHHhhccCC
Q psy11318 144 YHCTQCSKFYI---QESDLMEHMAVHSGV 169 (263)
Q Consensus 144 ~~C~~C~~~f~---~~~~l~~H~~~h~~~ 169 (263)
+.|.+|-.+|. +...|..|....|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 46777774443 445677776654443
No 215
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=28.54 E-value=36 Score=19.90 Aligned_cols=19 Identities=11% Similarity=0.461 Sum_probs=13.3
Q ss_pred ccccCCCccccCChhHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQ 47 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~ 47 (263)
-++|+.||..|...-..+.
T Consensus 28 ~W~C~~Cgh~w~~~v~~R~ 46 (55)
T PF14311_consen 28 WWKCPKCGHEWKASVNDRT 46 (55)
T ss_pred EEECCCCCCeeEccHhhhc
Confidence 5788888887776654443
No 216
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.36 E-value=6.5 Score=26.33 Aligned_cols=36 Identities=11% Similarity=0.320 Sum_probs=17.1
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceeccccccccc
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYK 68 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 68 (263)
.|.|+.||..-...-.++.- .......|..||..|-
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~e 57 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSFE 57 (104)
T ss_pred eEecCccCCeeeeEEEEEec----CceeEEEcccCcceEE
Confidence 47777776544332222111 1112256666666553
No 217
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=28.01 E-value=8.3 Score=29.58 Aligned_cols=10 Identities=30% Similarity=0.547 Sum_probs=4.9
Q ss_pred cccCCCcccc
Q psy11318 30 YQCEECPKDF 39 (263)
Q Consensus 30 ~~C~~C~~~f 39 (263)
|.|+.||+..
T Consensus 31 f~C~~CGyr~ 40 (192)
T TIGR00310 31 TICEHCGYRS 40 (192)
T ss_pred EECCCCCCcc
Confidence 4555555443
No 218
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=27.71 E-value=40 Score=19.29 Aligned_cols=10 Identities=60% Similarity=1.544 Sum_probs=6.4
Q ss_pred CcccccCCCc
Q psy11318 27 GVRYQCEECP 36 (263)
Q Consensus 27 ~~~~~C~~C~ 36 (263)
|.+|+|..|.
T Consensus 13 G~R~~C~~C~ 22 (48)
T cd02341 13 GTRYHCSECD 22 (48)
T ss_pred cceEECCCCC
Confidence 4567777765
No 219
>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=27.45 E-value=13 Score=21.60 Aligned_cols=26 Identities=27% Similarity=0.797 Sum_probs=11.6
Q ss_pred CCccCCcchhhhcChHHHHHHHhhcc
Q psy11318 142 KRYHCTQCSKFYIQESDLMEHMAVHS 167 (263)
Q Consensus 142 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 167 (263)
..|+|+.|...|=.--++..|...|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CeEECCCCCCccccCcChhhhccccC
Confidence 34666666666666555666655543
No 220
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=26.97 E-value=38 Score=27.98 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=20.7
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccch
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLK 70 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 70 (263)
-.+|+.|+.....+. |.. ..+.|+.|+..|.-.
T Consensus 27 ~~~c~~c~~~~~~~~-l~~--------~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQVLYRKE-LEA--------NLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccchhhHHH-HHh--------cCCCCCCCCCCeeCC
Confidence 467888877544433 111 126889999888654
No 221
>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=26.96 E-value=59 Score=24.93 Aligned_cols=19 Identities=11% Similarity=0.013 Sum_probs=8.4
Q ss_pred HHHHHHHHhhCCcccccCC
Q psy11318 16 DTLNKHMDIHKGVRYQCEE 34 (263)
Q Consensus 16 ~~L~~H~~~h~~~~~~C~~ 34 (263)
.....|.....-.|+.|+.
T Consensus 31 ~~~~~HE~~C~~~p~~CP~ 49 (198)
T PF03145_consen 31 SEKREHEEECPFRPCSCPF 49 (198)
T ss_dssp GGHHHHHHT-TTSEEE-SS
T ss_pred cChhhHhccCCCcCCcCCC
Confidence 3444555554445555544
No 222
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=26.12 E-value=29 Score=20.34 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=3.7
Q ss_pred cccccccc
Q psy11318 4 YCNACSKN 11 (263)
Q Consensus 4 ~C~~C~~~ 11 (263)
.||+||..
T Consensus 2 ~CPyCge~ 9 (52)
T PF14255_consen 2 QCPYCGEP 9 (52)
T ss_pred CCCCCCCe
Confidence 34444443
No 223
>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=25.63 E-value=25 Score=25.70 Aligned_cols=32 Identities=9% Similarity=0.043 Sum_probs=15.8
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCccccccc
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFG 184 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~ 184 (263)
.|+|..||.... ..+...--.|+.|+.....+
T Consensus 112 ~l~C~~Cg~~~~----------~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 112 TLVCENCGHEVE----------LTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred eEecccCCCEEE----------ecCCCcCCCCCCCCCCeeee
Confidence 367777774422 11122345566676654433
No 224
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=25.53 E-value=50 Score=19.69 Aligned_cols=14 Identities=14% Similarity=0.422 Sum_probs=6.0
Q ss_pred ceecccccccccch
Q psy11318 57 RFQCNKCFRAYKLK 70 (263)
Q Consensus 57 ~~~C~~C~~~f~~~ 70 (263)
|+....|+-.|...
T Consensus 24 PV~s~~C~H~fek~ 37 (57)
T PF11789_consen 24 PVKSKKCGHTFEKE 37 (57)
T ss_dssp EEEESSS--EEEHH
T ss_pred CcCcCCCCCeecHH
Confidence 44555555555443
No 225
>KOG1842|consensus
Probab=25.49 E-value=43 Score=29.15 Aligned_cols=26 Identities=31% Similarity=0.501 Sum_probs=24.2
Q ss_pred eecccccccccchHHHHHHHHHhcCC
Q psy11318 58 FQCNKCFRAYKLKKDLLAHTMLEHFG 83 (263)
Q Consensus 58 ~~C~~C~~~f~~~~~l~~H~~~~~~~ 83 (263)
|.|++|...|.+...|..|....|.+
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhccc
Confidence 99999999999999999999887765
No 226
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=24.90 E-value=10 Score=28.93 Aligned_cols=12 Identities=17% Similarity=0.182 Sum_probs=8.5
Q ss_pred eecccccccccc
Q psy11318 58 FQCNKCFRAYKL 69 (263)
Q Consensus 58 ~~C~~C~~~f~~ 69 (263)
+.|..||+.+..
T Consensus 44 ~~C~~CgYR~~D 55 (201)
T COG1779 44 GVCERCGYRSTD 55 (201)
T ss_pred EEccccCCcccc
Confidence 568888876655
No 227
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=24.67 E-value=23 Score=25.83 Aligned_cols=32 Identities=25% Similarity=0.557 Sum_probs=13.9
Q ss_pred CccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcc
Q psy11318 143 RYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKT 179 (263)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~ 179 (263)
+|.|. |+..|-+. .+|-..-.|+ .|.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCc
Confidence 35555 55444332 2333333333 455555543
No 228
>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=24.25 E-value=12 Score=20.50 Aligned_cols=13 Identities=31% Similarity=0.769 Sum_probs=6.0
Q ss_pred CCCCccCCcchhh
Q psy11318 140 NGKRYHCTQCSKF 152 (263)
Q Consensus 140 ~~~~~~C~~C~~~ 152 (263)
+.+.|.|..|+..
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 3445666666543
No 229
>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=24.14 E-value=33 Score=22.70 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=6.0
Q ss_pred Cccccccccc
Q psy11318 2 RYYCNACSKN 11 (263)
Q Consensus 2 ~y~C~~C~~~ 11 (263)
+|.|+.||+.
T Consensus 35 ky~Cp~Cgk~ 44 (90)
T PF01780_consen 35 KYTCPFCGKT 44 (90)
T ss_dssp -BEESSSSSS
T ss_pred CCcCCCCCCc
Confidence 5667777664
No 230
>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=24.10 E-value=16 Score=30.23 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=6.0
Q ss_pred CcccCCcCCCc
Q psy11318 84 IRHPCSECPKT 94 (263)
Q Consensus 84 ~~~~C~~C~~~ 94 (263)
+...|..|+..
T Consensus 209 RyL~CslC~te 219 (305)
T TIGR01562 209 RYLSCSLCATE 219 (305)
T ss_pred eEEEcCCCCCc
Confidence 44556666554
No 231
>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=24.07 E-value=13 Score=21.05 Aligned_cols=8 Identities=25% Similarity=0.845 Sum_probs=4.0
Q ss_pred cccccccc
Q psy11318 5 CNACSKNF 12 (263)
Q Consensus 5 C~~C~~~f 12 (263)
||+||..-
T Consensus 2 CP~Cg~~a 9 (47)
T PF04606_consen 2 CPHCGSKA 9 (47)
T ss_pred cCCCCCee
Confidence 55555543
No 232
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.01 E-value=74 Score=24.36 Aligned_cols=11 Identities=27% Similarity=0.609 Sum_probs=5.8
Q ss_pred cccCCcCCCcC
Q psy11318 85 RHPCSECPKTF 95 (263)
Q Consensus 85 ~~~C~~C~~~f 95 (263)
.+.|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 44555555554
No 233
>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=23.86 E-value=54 Score=17.15 Aligned_cols=21 Identities=14% Similarity=0.505 Sum_probs=11.8
Q ss_pred ccccccccccCChHHHHHHHHh
Q psy11318 3 YYCNACSKNFSAKDTLNKHMDI 24 (263)
Q Consensus 3 y~C~~C~~~f~~~~~L~~H~~~ 24 (263)
+.|+.|+..+. ...+..|+..
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLek 25 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLEK 25 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHHH
T ss_pred EECCCCcCCcc-hhhhHHHHHH
Confidence 46777776544 4566666544
No 234
>PRK12860 transcriptional activator FlhC; Provisional
Probab=23.65 E-value=45 Score=25.51 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=33.5
Q ss_pred cccCCHHHHHHHHHHhCCCCCccCCcchhhhcChHHHHHHHhhccCCCCCcCCCCc
Q psy11318 123 KDYLTKRDLRRHMKLHFNGKRYHCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIK 178 (263)
Q Consensus 123 ~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~ 178 (263)
..|...+.|.+..... -.....|..||-.|.... |.....|+|+.|.
T Consensus 115 Ls~tRAw~LvRf~~s~-~L~l~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (189)
T PRK12860 115 LDLTRAWTLVRFFDAG-MLQLARCCRCGGKFVTHA--------HDLRHNFVCGLCQ 161 (189)
T ss_pred ecHHHHHHHHHHhcCC-CeeeccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 6677788888877654 345578999998887442 2344579999998
No 235
>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=23.52 E-value=32 Score=24.01 Aligned_cols=18 Identities=11% Similarity=0.449 Sum_probs=9.1
Q ss_pred cccCCCccccCChhHHHH
Q psy11318 30 YQCEECPKDFSTRKYLTQ 47 (263)
Q Consensus 30 ~~C~~C~~~f~~~~~l~~ 47 (263)
+.|+.||..+.+......
T Consensus 32 ~~C~~CGe~~~~~e~~~~ 49 (127)
T TIGR03830 32 WYCPACGEELLDPEESKR 49 (127)
T ss_pred eECCCCCCEEEcHHHHHH
Confidence 455555555555544333
No 236
>KOG4727|consensus
Probab=23.50 E-value=40 Score=25.14 Aligned_cols=23 Identities=22% Similarity=0.421 Sum_probs=21.2
Q ss_pred ccccCCCccccCChhHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
.|-|.+|+-++.+..++..|++.
T Consensus 75 GyyCdVCdcvvKDSinflDHiNg 97 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHING 97 (193)
T ss_pred ceeeeecceeehhhHHHHHHhcc
Confidence 59999999999999999999864
No 237
>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 KOG2636|consensus
Probab=22.99 E-value=67 Score=28.02 Aligned_cols=18 Identities=28% Similarity=0.285 Sum_probs=9.6
Q ss_pred cCCCccccCChhHHHHHH
Q psy11318 32 CEECPKDFSTRKYLTQHQ 49 (263)
Q Consensus 32 C~~C~~~f~~~~~l~~H~ 49 (263)
|+-|++.|.+++....|+
T Consensus 274 ~~ra~rlf~Tk~~~l~~L 291 (497)
T KOG2636|consen 274 HERAQRLFSTKSKSLSHL 291 (497)
T ss_pred cHHHHhhhhhcCcchhhh
Confidence 444556666665554444
No 239
>PTZ00448 hypothetical protein; Provisional
Probab=22.47 E-value=58 Score=27.68 Aligned_cols=23 Identities=17% Similarity=0.429 Sum_probs=21.3
Q ss_pred ccccCCCccccCChhHHHHHHHH
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNA 51 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~ 51 (263)
.|.|..|+..|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999999999999987
No 240
>KOG4118|consensus
Probab=22.11 E-value=68 Score=19.67 Aligned_cols=29 Identities=17% Similarity=0.266 Sum_probs=20.0
Q ss_pred ccCCcchhhhcChHHHHHHHhhccCCCCC
Q psy11318 144 YHCTQCSKFYIQESDLMEHMAVHSGVRKL 172 (263)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 172 (263)
|+|.+|-......-.++.|....|...++
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~~~ 67 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKEPL 67 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCCCC
Confidence 67777777777777777777666655543
No 241
>KOG3214|consensus
Probab=22.11 E-value=40 Score=22.62 Aligned_cols=38 Identities=18% Similarity=0.384 Sum_probs=19.5
Q ss_pred ccccCCCccccCChhHHHHHHHHhcCCCceecccccccccch
Q psy11318 29 RYQCEECPKDFSTRKYLTQHQNAIHRGIRFQCNKCFRAYKLK 70 (263)
Q Consensus 29 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 70 (263)
.|.|+.|+..-...-.|. ..+......|.+|+..|.+.
T Consensus 23 ~FnClfcnHek~v~~~~D----k~~~iG~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 23 QFNCLFCNHEKSVSCTLD----KKHNIGKASCRICEESFQTT 60 (109)
T ss_pred eeccCccccccceeeeeh----hhcCcceeeeeehhhhhccc
Confidence 477887754322222221 12333346777777777654
No 242
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.03 E-value=43 Score=16.16 Aligned_cols=9 Identities=22% Similarity=1.003 Sum_probs=4.8
Q ss_pred Ccccccccc
Q psy11318 2 RYYCNACSK 10 (263)
Q Consensus 2 ~y~C~~C~~ 10 (263)
...|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (26)
T PF13248_consen 2 EMFCPNCGA 10 (26)
T ss_pred cCCCcccCC
Confidence 345555555
No 243
>PRK10220 hypothetical protein; Provisional
Probab=22.00 E-value=45 Score=22.87 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=19.3
Q ss_pred cCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccccc
Q psy11318 145 HCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGV 185 (263)
Q Consensus 145 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~ 185 (263)
.|+.|+..|++. ...-|.|+.|++.++..+
T Consensus 5 ~CP~C~seytY~-----------d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTYE-----------DNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceEc-----------CCCeEECCcccCcCCccc
Confidence 477777666543 233477888888776654
No 244
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=21.70 E-value=1.5e+02 Score=22.45 Aligned_cols=16 Identities=13% Similarity=0.345 Sum_probs=8.0
Q ss_pred CCcccCCcCCCcCCCH
Q psy11318 83 GIRHPCSECPKTFASR 98 (263)
Q Consensus 83 ~~~~~C~~C~~~f~~~ 98 (263)
...|.|+.|...+...
T Consensus 111 ~~~y~C~~~~~r~sfd 126 (176)
T COG1675 111 NNYYVCPNCHVKYSFD 126 (176)
T ss_pred CCceeCCCCCCcccHH
Confidence 3445565555544433
No 245
>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=21.28 E-value=12 Score=20.07 Aligned_cols=7 Identities=57% Similarity=1.763 Sum_probs=3.0
Q ss_pred CccCCcc
Q psy11318 143 RYHCTQC 149 (263)
Q Consensus 143 ~~~C~~C 149 (263)
.|.|..|
T Consensus 29 ryrC~~C 35 (36)
T PF03811_consen 29 RYRCKDC 35 (36)
T ss_pred eEecCcC
Confidence 3444443
No 246
>PLN02294 cytochrome c oxidase subunit Vb
Probab=21.24 E-value=31 Score=25.76 Aligned_cols=15 Identities=33% Similarity=0.917 Sum_probs=8.1
Q ss_pred CCcccccCCCccccC
Q psy11318 26 KGVRYQCEECPKDFS 40 (263)
Q Consensus 26 ~~~~~~C~~C~~~f~ 40 (263)
.|++..|+.||..|.
T Consensus 138 kGkp~RCpeCG~~fk 152 (174)
T PLN02294 138 KGKSFECPVCTQYFE 152 (174)
T ss_pred CCCceeCCCCCCEEE
Confidence 344555666665553
No 247
>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=21.15 E-value=38 Score=23.17 Aligned_cols=30 Identities=17% Similarity=0.193 Sum_probs=18.0
Q ss_pred cCCcchhhhcChHHHHHHHhhccCCCCCcCCCCcccccccc
Q psy11318 145 HCTQCSKFYIQESDLMEHMAVHSGVRKLTTGPIKTEQTFGV 185 (263)
Q Consensus 145 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~ 185 (263)
.|+.|+..|++. ...-|.|+.|++.+....
T Consensus 4 ~CP~C~seytY~-----------dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYH-----------DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEe-----------cCCeeECccccccccccc
Confidence 466776665543 223477777777776543
No 248
>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=21.08 E-value=29 Score=23.38 Aligned_cols=16 Identities=38% Similarity=0.756 Sum_probs=9.2
Q ss_pred hCCcccccCCCccccC
Q psy11318 25 HKGVRYQCEECPKDFS 40 (263)
Q Consensus 25 h~~~~~~C~~C~~~f~ 40 (263)
+.+.++.|+.||..|.
T Consensus 75 ~~g~~~rC~eCG~~fk 90 (97)
T cd00924 75 EKGKPKRCPECGHVFK 90 (97)
T ss_pred eCCCceeCCCCCcEEE
Confidence 3445666666666554
No 249
>KOG2857|consensus
Probab=20.91 E-value=48 Score=23.86 Aligned_cols=21 Identities=24% Similarity=0.603 Sum_probs=11.1
Q ss_pred CccccccccccCChHHHHHHH
Q psy11318 2 RYYCNACSKNFSAKDTLNKHM 22 (263)
Q Consensus 2 ~y~C~~C~~~f~~~~~L~~H~ 22 (263)
+|+|+.|..-|-+...+++|.
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk 37 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHK 37 (157)
T ss_pred hccCCCCCCccccchhhhhcc
Confidence 455555555555555555554
No 250
>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=20.55 E-value=60 Score=18.01 Aligned_cols=16 Identities=19% Similarity=0.644 Sum_probs=10.9
Q ss_pred cccccccccCChHHHH
Q psy11318 4 YCNACSKNFSAKDTLN 19 (263)
Q Consensus 4 ~C~~C~~~f~~~~~L~ 19 (263)
.|+.||..|..+....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 4777777777666554
No 251
>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=20.44 E-value=8.8 Score=24.09 Aligned_cols=8 Identities=38% Similarity=0.891 Sum_probs=2.7
Q ss_pred eecccccc
Q psy11318 58 FQCNKCFR 65 (263)
Q Consensus 58 ~~C~~C~~ 65 (263)
..|..|+.
T Consensus 42 v~Cg~C~~ 49 (71)
T PF05495_consen 42 VICGKCRT 49 (71)
T ss_dssp EEETTT--
T ss_pred eECCCCCC
Confidence 44444443
No 252
>KOG3990|consensus
Probab=20.05 E-value=1.5e+02 Score=23.81 Aligned_cols=37 Identities=19% Similarity=0.476 Sum_probs=18.2
Q ss_pred eecccccccccchHHHH-----HHHHHhcCCCcccCCcCCCc
Q psy11318 58 FQCNKCFRAYKLKKDLL-----AHTMLEHFGIRHPCSECPKT 94 (263)
Q Consensus 58 ~~C~~C~~~f~~~~~l~-----~H~~~~~~~~~~~C~~C~~~ 94 (263)
-+|..|..-|-....-. --......+.|+.|..|...
T Consensus 38 gKctyCrse~q~askt~t~CkkCah~~~kfG~P~pC~~Ckii 79 (305)
T KOG3990|consen 38 GKCTYCRSEFQQASKTNTICKKCAHNVRKFGTPKPCQYCKII 79 (305)
T ss_pred cccchhHHHhhhhhhhhhHHHHHHHHHHhcCCCCcchhhhhh
Confidence 46777766554322111 11113334567777777654
Done!