Query psy4420
Match_columns 213
No_of_seqs 142 out of 1436
Neff 10.6
Searched_HMMs 46136
Date Fri Aug 16 16:39:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4420.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4420hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 2E-30 4.3E-35 187.9 4.9 135 39-178 129-268 (279)
2 KOG2462|consensus 99.9 5E-27 1.1E-31 170.3 6.2 136 7-149 127-265 (279)
3 KOG3608|consensus 99.9 7.6E-24 1.6E-28 158.1 7.7 175 2-185 199-384 (467)
4 KOG1074|consensus 99.9 7E-23 1.5E-27 167.5 3.9 53 69-121 606-658 (958)
5 KOG3608|consensus 99.8 6.3E-21 1.4E-25 142.6 7.3 155 17-180 189-348 (467)
6 KOG1074|consensus 99.8 2.4E-20 5.2E-25 152.9 0.7 81 97-180 606-695 (958)
7 KOG3623|consensus 99.8 4.7E-19 1E-23 143.5 4.5 106 10-118 210-331 (1007)
8 KOG3576|consensus 99.7 7.8E-18 1.7E-22 117.1 3.7 128 39-184 116-243 (267)
9 KOG3576|consensus 99.7 1.8E-17 3.8E-22 115.4 1.2 86 92-180 113-200 (267)
10 KOG3623|consensus 99.5 2E-14 4.3E-19 117.1 2.0 79 39-117 893-971 (1007)
11 PLN03086 PRLI-interacting fact 99.4 6.7E-13 1.5E-17 108.0 8.3 147 8-179 405-566 (567)
12 PHA00733 hypothetical protein 99.4 5.8E-13 1.3E-17 89.2 4.8 86 94-179 38-125 (128)
13 PHA02768 hypothetical protein; 99.1 2.7E-11 6E-16 67.3 2.0 45 126-170 4-48 (55)
14 PLN03086 PRLI-interacting fact 99.1 2.7E-10 5.8E-15 93.1 8.5 100 39-148 452-561 (567)
15 KOG3993|consensus 99.1 2E-11 4.3E-16 94.2 0.5 163 9-178 266-483 (500)
16 PHA00733 hypothetical protein 99.0 3.6E-10 7.7E-15 75.8 4.5 81 39-121 39-124 (128)
17 KOG3993|consensus 98.9 1.5E-10 3.3E-15 89.4 0.0 55 39-93 266-320 (500)
18 PHA02768 hypothetical protein; 98.8 2.6E-09 5.6E-14 59.4 1.7 42 40-83 5-46 (55)
19 PHA00732 hypothetical protein 98.7 2E-08 4.4E-13 61.2 2.9 46 127-175 1-46 (79)
20 PF13465 zf-H2C2_2: Zinc-finge 98.6 5.7E-08 1.2E-12 46.2 2.6 24 56-79 2-25 (26)
21 PHA00616 hypothetical protein 98.5 4E-08 8.6E-13 52.0 1.8 36 40-75 1-36 (44)
22 PHA00616 hypothetical protein 98.5 4.8E-08 1E-12 51.7 1.5 29 153-181 1-29 (44)
23 PF13465 zf-H2C2_2: Zinc-finge 98.4 2.1E-07 4.5E-12 44.2 2.6 24 84-107 2-25 (26)
24 PF05605 zf-Di19: Drought indu 98.3 6.8E-07 1.5E-11 50.6 3.5 48 128-178 3-54 (54)
25 PHA00732 hypothetical protein 98.1 1.9E-06 4E-11 52.6 2.6 46 40-91 1-47 (79)
26 PF00096 zf-C2H2: Zinc finger, 98.1 1.4E-06 2.9E-11 40.1 1.5 22 154-175 1-22 (23)
27 PF05605 zf-Di19: Drought indu 98.1 9.1E-06 2E-10 46.0 4.3 49 40-91 2-52 (54)
28 PF13894 zf-C2H2_4: C2H2-type 98.0 3.1E-06 6.8E-11 39.2 1.7 24 154-177 1-24 (24)
29 PF13912 zf-C2H2_6: C2H2-type 98.0 5.2E-06 1.1E-10 39.8 1.8 26 153-178 1-26 (27)
30 PF00096 zf-C2H2: Zinc finger, 97.9 8.7E-06 1.9E-10 37.4 2.4 23 41-63 1-23 (23)
31 PF12756 zf-C2H2_2: C2H2 type 97.8 1.2E-05 2.6E-10 51.6 2.6 72 98-176 1-73 (100)
32 COG5189 SFP1 Putative transcri 97.8 5.1E-06 1.1E-10 62.6 0.8 54 124-177 346-422 (423)
33 PF13894 zf-C2H2_4: C2H2-type 97.6 6.4E-05 1.4E-09 34.6 2.5 23 41-63 1-23 (24)
34 PF12756 zf-C2H2_2: C2H2 type 97.6 5.8E-05 1.3E-09 48.4 2.6 20 43-62 2-21 (100)
35 PF13912 zf-C2H2_6: C2H2-type 97.5 8.9E-05 1.9E-09 35.4 2.2 25 127-151 1-25 (27)
36 PF09237 GAGA: GAGA factor; I 97.4 0.00023 5E-09 38.7 3.0 30 39-68 23-52 (54)
37 PF09237 GAGA: GAGA factor; I 97.3 0.00022 4.7E-09 38.8 2.0 29 153-181 24-52 (54)
38 smart00355 ZnF_C2H2 zinc finge 97.3 0.00021 4.6E-09 33.4 1.8 23 154-176 1-23 (26)
39 COG5189 SFP1 Putative transcri 97.1 0.00015 3.3E-09 54.9 0.8 55 94-148 347-419 (423)
40 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00024 5.3E-09 32.8 1.2 24 154-178 1-24 (24)
41 PF12874 zf-met: Zinc-finger o 97.1 0.00033 7.3E-09 32.6 1.4 23 154-176 1-23 (25)
42 KOG2231|consensus 96.8 0.0062 1.4E-07 51.5 7.3 120 43-174 118-260 (669)
43 smart00355 ZnF_C2H2 zinc finge 96.7 0.0018 3.9E-08 30.0 2.4 23 41-63 1-23 (26)
44 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.0011 2.4E-08 31.5 1.1 22 154-175 2-23 (27)
45 PF12874 zf-met: Zinc-finger o 96.5 0.0024 5.1E-08 29.6 1.8 22 41-62 1-22 (25)
46 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0052 1.1E-07 28.2 2.3 23 41-64 1-23 (24)
47 KOG2231|consensus 96.2 0.016 3.4E-07 49.2 6.5 121 13-148 118-260 (669)
48 PRK04860 hypothetical protein; 96.1 0.0029 6.3E-08 44.2 1.6 38 68-109 119-156 (160)
49 KOG2785|consensus 95.6 0.099 2.1E-06 41.2 7.9 50 126-175 165-242 (390)
50 PF13913 zf-C2HC_2: zinc-finge 95.6 0.011 2.3E-07 27.5 1.7 19 155-174 4-22 (25)
51 PRK04860 hypothetical protein; 95.3 0.016 3.4E-07 40.6 2.6 39 95-140 118-156 (160)
52 COG5236 Uncharacterized conser 95.2 0.033 7.3E-07 43.1 4.4 133 40-180 151-308 (493)
53 PF12171 zf-C2H2_jaz: Zinc-fin 95.2 0.0049 1.1E-07 29.2 -0.1 22 41-62 2-23 (27)
54 KOG2482|consensus 95.1 0.12 2.7E-06 40.1 6.9 132 40-175 195-356 (423)
55 smart00451 ZnF_U1 U1-like zinc 95.0 0.019 4.1E-07 28.9 1.8 23 153-175 3-25 (35)
56 KOG1146|consensus 94.9 0.0088 1.9E-07 53.9 0.5 25 153-177 589-613 (1406)
57 COG4049 Uncharacterized protei 94.6 0.025 5.4E-07 31.3 1.6 35 153-187 17-51 (65)
58 KOG4173|consensus 94.5 0.014 2.9E-07 41.8 0.6 72 102-179 87-172 (253)
59 KOG2482|consensus 94.3 0.1 2.3E-06 40.4 4.9 76 69-150 280-357 (423)
60 smart00451 ZnF_U1 U1-like zinc 93.9 0.06 1.3E-06 27.0 2.2 24 39-62 2-25 (35)
61 KOG1146|consensus 93.7 0.021 4.6E-07 51.6 0.3 51 126-176 464-541 (1406)
62 TIGR00622 ssl1 transcription f 93.4 0.12 2.5E-06 33.7 3.2 54 98-160 57-110 (112)
63 COG5048 FOG: Zn-finger [Genera 93.2 0.012 2.6E-07 47.8 -1.9 141 40-180 289-445 (467)
64 cd00350 rubredoxin_like Rubred 93.0 0.058 1.3E-06 26.9 1.2 9 152-160 16-24 (33)
65 TIGR00622 ssl1 transcription f 92.8 0.13 2.7E-06 33.5 2.7 49 129-177 57-105 (112)
66 PF12013 DUF3505: Protein of u 91.1 0.5 1.1E-05 30.8 4.2 26 153-178 80-109 (109)
67 KOG2893|consensus 91.0 0.064 1.4E-06 39.4 -0.1 40 100-146 14-53 (341)
68 COG4049 Uncharacterized protei 90.5 0.14 3E-06 28.5 1.0 24 39-62 16-39 (65)
69 COG5236 Uncharacterized conser 90.5 0.25 5.5E-06 38.5 2.7 105 69-177 152-275 (493)
70 KOG2893|consensus 89.6 0.084 1.8E-06 38.8 -0.4 49 130-180 13-61 (341)
71 PF13719 zinc_ribbon_5: zinc-r 89.1 0.42 9E-06 24.5 2.1 11 42-52 4-14 (37)
72 PF09538 FYDLN_acid: Protein o 89.0 0.26 5.6E-06 32.1 1.5 30 41-81 10-39 (108)
73 PF09538 FYDLN_acid: Protein o 88.6 0.16 3.5E-06 33.0 0.4 29 70-109 11-39 (108)
74 COG2888 Predicted Zn-ribbon RN 88.5 0.43 9.4E-06 27.0 2.0 31 127-160 27-57 (61)
75 PF12013 DUF3505: Protein of u 88.1 1.3 2.8E-05 28.8 4.5 24 97-120 81-108 (109)
76 TIGR02098 MJ0042_CXXC MJ0042 f 87.3 0.57 1.2E-05 24.0 1.9 6 43-48 5-10 (38)
77 KOG4173|consensus 86.8 0.28 6.2E-06 35.3 0.8 101 48-151 47-170 (253)
78 PF09986 DUF2225: Uncharacteri 86.8 0.079 1.7E-06 39.1 -2.1 14 153-166 48-61 (214)
79 PF13717 zinc_ribbon_4: zinc-r 86.8 0.67 1.5E-05 23.5 2.0 9 43-51 5-13 (36)
80 PHA00626 hypothetical protein 86.7 0.22 4.7E-06 27.8 0.1 17 150-166 20-36 (59)
81 COG5048 FOG: Zn-finger [Genera 86.2 0.15 3.2E-06 41.5 -1.1 158 9-170 288-462 (467)
82 cd00729 rubredoxin_SM Rubredox 85.6 0.46 9.9E-06 23.8 1.0 10 128-137 3-12 (34)
83 PF06524 NOA36: NOA36 protein; 85.1 0.27 5.8E-06 36.8 -0.0 25 94-118 207-231 (314)
84 TIGR00373 conserved hypothetic 84.8 0.55 1.2E-05 32.9 1.4 33 39-80 108-140 (158)
85 PF02892 zf-BED: BED zinc fing 84.4 0.71 1.5E-05 24.6 1.5 22 154-175 17-42 (45)
86 PRK14890 putative Zn-ribbon RN 83.5 0.8 1.7E-05 26.0 1.4 31 127-160 25-55 (59)
87 smart00734 ZnF_Rad18 Rad18-lik 83.3 0.99 2.1E-05 21.0 1.5 20 154-174 2-21 (26)
88 COG1997 RPL43A Ribosomal prote 83.0 0.41 8.9E-06 29.4 0.2 32 126-165 34-65 (89)
89 PRK06266 transcription initiat 82.7 0.88 1.9E-05 32.6 1.8 33 39-80 116-148 (178)
90 PRK06266 transcription initiat 82.6 0.77 1.7E-05 32.9 1.4 34 125-165 115-148 (178)
91 smart00531 TFIIE Transcription 82.5 3.1 6.7E-05 28.8 4.4 14 67-80 98-111 (147)
92 smart00531 TFIIE Transcription 82.1 0.89 1.9E-05 31.4 1.6 35 126-162 98-132 (147)
93 smart00659 RPOLCX RNA polymera 82.1 0.91 2E-05 24.3 1.3 24 128-160 3-26 (44)
94 smart00834 CxxC_CXXC_SSSS Puta 81.7 0.3 6.6E-06 25.4 -0.7 12 128-139 6-17 (41)
95 TIGR00373 conserved hypothetic 81.3 2.7 5.8E-05 29.5 3.8 31 67-106 108-138 (158)
96 TIGR02605 CxxC_CxxC_SSSS putat 80.1 0.4 8.6E-06 26.5 -0.6 29 128-161 6-34 (52)
97 smart00614 ZnF_BED BED zinc fi 79.7 1.4 3E-05 24.2 1.5 20 155-174 20-44 (50)
98 PF09986 DUF2225: Uncharacteri 79.6 0.29 6.2E-06 36.2 -1.6 20 39-58 4-23 (214)
99 KOG2785|consensus 78.9 2.9 6.4E-05 33.3 3.6 74 69-150 167-243 (390)
100 KOG2186|consensus 77.9 1.9 4.2E-05 32.2 2.2 49 39-90 2-50 (276)
101 TIGR02300 FYDLN_acid conserved 77.9 1.7 3.7E-05 28.9 1.8 13 67-79 25-37 (129)
102 PF15269 zf-C2H2_7: Zinc-finge 77.7 1.5 3.3E-05 23.2 1.2 24 153-176 20-43 (54)
103 KOG2186|consensus 77.6 2 4.4E-05 32.1 2.3 47 11-64 4-52 (276)
104 COG1592 Rubrerythrin [Energy p 76.3 1.8 3.8E-05 30.5 1.6 10 40-49 134-143 (166)
105 PF09723 Zn-ribbon_8: Zinc rib 75.7 0.49 1.1E-05 25.0 -1.0 12 128-139 6-17 (42)
106 PF04959 ARS2: Arsenite-resist 75.4 1.1 2.4E-05 33.0 0.5 29 153-181 77-105 (214)
107 PF05443 ROS_MUCR: ROS/MUCR tr 74.2 2.6 5.6E-05 28.5 1.9 23 40-65 72-94 (132)
108 PF05443 ROS_MUCR: ROS/MUCR tr 74.1 1.8 3.8E-05 29.3 1.1 25 153-180 72-96 (132)
109 PF10571 UPF0547: Uncharacteri 70.9 2 4.4E-05 20.0 0.6 9 155-163 16-24 (26)
110 KOG2807|consensus 70.0 12 0.00026 29.4 4.8 32 125-160 343-374 (378)
111 PF14353 CpXC: CpXC protein 69.4 1.9 4.1E-05 28.9 0.5 24 153-176 38-61 (128)
112 PRK00464 nrdR transcriptional 67.0 2.1 4.6E-05 29.8 0.3 17 39-55 27-43 (154)
113 PRK09678 DNA-binding transcrip 65.7 1.3 2.9E-05 26.4 -0.7 41 128-168 2-44 (72)
114 KOG2907|consensus 65.4 5 0.00011 26.1 1.7 10 69-78 103-112 (116)
115 COG5151 SSL1 RNA polymerase II 64.7 2.6 5.7E-05 32.6 0.4 47 130-176 365-411 (421)
116 PF13453 zf-TFIIB: Transcripti 64.3 3 6.5E-05 21.7 0.5 16 41-56 20-35 (41)
117 PF02176 zf-TRAF: TRAF-type zi 64.1 7 0.00015 22.0 2.1 39 40-79 9-53 (60)
118 KOG2593|consensus 63.3 5.5 0.00012 32.4 2.0 35 39-76 127-161 (436)
119 COG1996 RPC10 DNA-directed RNA 63.1 4.8 0.0001 22.0 1.2 10 128-137 7-16 (49)
120 PF04780 DUF629: Protein of un 61.7 5.1 0.00011 33.2 1.6 27 154-180 58-84 (466)
121 KOG4167|consensus 61.2 2.7 5.8E-05 36.4 -0.0 27 39-65 791-817 (907)
122 PF07800 DUF1644: Protein of u 60.2 21 0.00045 25.0 4.1 9 11-19 3-11 (162)
123 PRK04023 DNA polymerase II lar 59.4 9.5 0.00021 34.7 2.9 8 41-48 627-634 (1121)
124 PF09845 DUF2072: Zn-ribbon co 58.7 4.8 0.0001 27.0 0.8 15 127-141 1-15 (131)
125 PF12907 zf-met2: Zinc-binding 57.7 8.7 0.00019 20.0 1.5 27 154-180 2-31 (40)
126 smart00440 ZnF_C2C2 C2C2 Zinc 57.0 3.9 8.5E-05 21.2 0.2 13 39-51 27-39 (40)
127 PF07754 DUF1610: Domain of un 56.0 6.6 0.00014 17.9 0.8 10 39-48 15-24 (24)
128 KOG3408|consensus 54.3 10 0.00022 25.0 1.8 27 36-62 53-79 (129)
129 PF14369 zf-RING_3: zinc-finge 53.6 6.3 0.00014 19.8 0.6 10 42-51 23-32 (35)
130 PF04959 ARS2: Arsenite-resist 53.4 11 0.00025 27.8 2.1 26 125-150 75-100 (214)
131 PF01096 TFIIS_C: Transcriptio 53.2 3.3 7.1E-05 21.4 -0.5 12 39-50 27-38 (39)
132 KOG4124|consensus 52.6 1.7 3.6E-05 34.2 -2.3 56 125-180 347-425 (442)
133 COG4957 Predicted transcriptio 52.0 10 0.00022 25.6 1.5 25 41-68 77-101 (148)
134 TIGR00280 L37a ribosomal prote 51.9 3.2 7E-05 26.0 -0.8 32 126-165 34-65 (91)
135 KOG2807|consensus 51.7 24 0.00052 27.8 3.6 25 95-119 344-368 (378)
136 PF15135 UPF0515: Uncharacteri 51.6 11 0.00025 28.2 1.9 58 39-109 111-168 (278)
137 KOG2593|consensus 51.0 26 0.00055 28.8 3.8 38 65-105 125-162 (436)
138 PF05191 ADK_lid: Adenylate ki 50.4 2.5 5.4E-05 21.5 -1.2 10 42-51 3-12 (36)
139 PF12760 Zn_Tnp_IS1595: Transp 50.0 6.5 0.00014 21.1 0.3 8 41-48 19-26 (46)
140 COG4530 Uncharacterized protei 49.9 6.4 0.00014 25.4 0.3 11 96-106 26-36 (129)
141 PRK03824 hypA hydrogenase nick 48.8 6.3 0.00014 26.8 0.2 15 39-53 69-83 (135)
142 COG3357 Predicted transcriptio 48.5 8.5 0.00018 24.0 0.7 13 96-108 58-70 (97)
143 COG1655 Uncharacterized protei 48.3 3.7 8.1E-05 30.4 -1.0 38 39-76 18-70 (267)
144 COG1594 RPB9 DNA-directed RNA 47.5 3.6 7.9E-05 27.0 -1.1 39 41-79 73-111 (113)
145 COG2331 Uncharacterized protei 47.3 7.3 0.00016 23.4 0.3 11 40-50 12-22 (82)
146 PF01780 Ribosomal_L37ae: Ribo 47.2 3.6 7.8E-05 25.7 -1.1 31 126-164 34-64 (90)
147 PRK00432 30S ribosomal protein 46.7 8.6 0.00019 21.1 0.5 12 152-163 36-47 (50)
148 PF07975 C1_4: TFIIH C1-like d 46.4 5 0.00011 22.2 -0.5 21 68-88 21-41 (51)
149 KOG3408|consensus 46.3 16 0.00034 24.2 1.7 27 124-150 54-80 (129)
150 KOG4377|consensus 45.9 13 0.00028 30.2 1.5 50 40-92 271-336 (480)
151 COG4896 Uncharacterized protei 44.7 12 0.00026 21.4 0.9 12 39-50 30-41 (68)
152 PRK03976 rpl37ae 50S ribosomal 42.9 4.9 0.00011 25.1 -1.0 32 126-165 35-66 (90)
153 PF07282 OrfB_Zn_ribbon: Putat 42.2 15 0.00032 21.5 1.1 14 125-138 44-57 (69)
154 COG3364 Zn-ribbon containing p 42.1 16 0.00035 23.3 1.3 15 127-141 2-16 (112)
155 PF08790 zf-LYAR: LYAR-type C2 41.1 6.8 0.00015 18.6 -0.4 19 154-173 1-19 (28)
156 KOG0978|consensus 40.6 16 0.00034 32.1 1.3 23 151-173 676-698 (698)
157 PF13878 zf-C2H2_3: zinc-finge 40.5 32 0.00069 17.9 2.1 10 41-50 14-23 (41)
158 PF01363 FYVE: FYVE zinc finge 40.4 18 0.0004 21.0 1.3 11 41-51 10-20 (69)
159 KOG1842|consensus 40.4 16 0.00034 30.0 1.3 29 153-181 15-43 (505)
160 PF13451 zf-trcl: Probable zin 40.2 21 0.00045 19.6 1.3 17 39-55 3-19 (49)
161 PF08271 TF_Zn_Ribbon: TFIIB z 39.9 17 0.00037 19.0 1.0 9 97-105 20-28 (43)
162 smart00154 ZnF_AN1 AN1-like Zi 39.4 14 0.0003 19.1 0.5 14 153-166 12-25 (39)
163 COG5188 PRP9 Splicing factor 3 39.2 29 0.00064 27.6 2.5 22 153-174 374-396 (470)
164 PRK12380 hydrogenase nickel in 37.0 16 0.00035 23.9 0.8 12 128-139 71-82 (113)
165 KOG4167|consensus 37.0 8.5 0.00018 33.6 -0.7 26 96-121 792-817 (907)
166 COG1675 TFA1 Transcription ini 36.8 25 0.00053 25.2 1.6 31 125-162 111-141 (176)
167 COG4888 Uncharacterized Zn rib 36.3 4.2 9.2E-05 25.8 -1.9 6 41-46 23-28 (104)
168 TIGR00100 hypA hydrogenase nic 36.0 16 0.00034 24.1 0.5 13 128-140 71-83 (115)
169 PF01428 zf-AN1: AN1-like Zinc 34.8 12 0.00026 19.7 -0.1 13 153-165 13-25 (43)
170 PTZ00255 60S ribosomal protein 34.6 22 0.00048 22.3 1.0 11 153-163 54-64 (90)
171 PF04423 Rad50_zn_hook: Rad50 34.5 15 0.00032 20.4 0.2 12 155-166 22-33 (54)
172 PRK03564 formate dehydrogenase 34.4 14 0.00029 29.1 0.1 14 126-139 251-264 (309)
173 PF14311 DUF4379: Domain of un 34.4 30 0.00066 19.2 1.5 11 128-138 29-39 (55)
174 PRK14714 DNA polymerase II lar 34.1 44 0.00095 31.6 3.1 8 41-48 668-675 (1337)
175 PF10058 DUF2296: Predicted in 34.0 30 0.00065 19.4 1.4 8 40-47 44-51 (54)
176 COG5151 SSL1 RNA polymerase II 33.9 42 0.00092 26.3 2.6 46 71-119 365-411 (421)
177 PHA02998 RNA polymerase subuni 33.6 18 0.00038 25.8 0.5 12 40-51 171-182 (195)
178 PF13824 zf-Mss51: Zinc-finger 32.5 34 0.00074 19.2 1.4 7 41-47 15-21 (55)
179 COG1779 C4-type Zn-finger prot 31.9 8 0.00017 28.0 -1.4 34 126-165 13-55 (201)
180 cd00065 FYVE FYVE domain; Zinc 31.7 32 0.0007 18.9 1.4 10 130-139 5-14 (57)
181 KOG1280|consensus 31.7 59 0.0013 25.9 3.0 25 68-92 79-103 (381)
182 KOG3002|consensus 30.8 54 0.0012 25.7 2.8 81 94-180 78-166 (299)
183 cd00730 rubredoxin Rubredoxin; 30.6 21 0.00046 19.6 0.4 14 153-166 1-14 (50)
184 KOG0320|consensus 30.6 9 0.00019 27.3 -1.3 11 68-78 167-177 (187)
185 PF14446 Prok-RING_1: Prokaryo 30.5 36 0.00077 19.1 1.3 11 98-108 7-17 (54)
186 KOG2272|consensus 30.1 30 0.00065 26.2 1.2 19 39-57 98-116 (332)
187 PF01155 HypA: Hydrogenase exp 29.7 25 0.00054 23.0 0.7 13 40-52 70-82 (113)
188 PF05290 Baculo_IE-1: Baculovi 29.6 41 0.00088 22.8 1.7 15 94-108 78-92 (140)
189 PF07503 zf-HYPF: HypF finger; 29.6 11 0.00025 18.9 -0.7 13 152-164 20-32 (35)
190 COG3091 SprT Zn-dependent meta 29.4 35 0.00075 23.7 1.3 33 96-136 117-149 (156)
191 KOG0717|consensus 29.3 29 0.00062 28.8 1.1 22 154-175 293-314 (508)
192 PF00301 Rubredoxin: Rubredoxi 28.8 22 0.00047 19.3 0.3 13 154-166 2-14 (47)
193 PF08209 Sgf11: Sgf11 (transcr 27.2 46 0.001 16.5 1.2 22 39-61 3-24 (33)
194 COG1656 Uncharacterized conser 27.1 53 0.0012 23.2 2.0 19 151-169 128-146 (165)
195 KOG0978|consensus 27.0 29 0.00063 30.5 0.8 17 96-112 678-694 (698)
196 PF10263 SprT-like: SprT-like 26.8 20 0.00043 24.8 -0.1 32 126-163 122-153 (157)
197 smart00064 FYVE Protein presen 26.7 39 0.00084 19.5 1.1 10 129-138 12-21 (68)
198 KOG4727|consensus 26.6 44 0.00095 23.7 1.5 24 38-61 73-96 (193)
199 COG1327 Predicted transcriptio 26.6 24 0.00051 24.5 0.2 15 40-54 28-42 (156)
200 COG1571 Predicted DNA-binding 26.6 30 0.00066 28.4 0.8 14 127-140 367-380 (421)
201 KOG0717|consensus 26.4 41 0.00089 28.0 1.5 22 128-149 293-314 (508)
202 PRK00564 hypA hydrogenase nick 26.3 26 0.00056 23.2 0.3 12 40-51 71-82 (117)
203 PF10276 zf-CHCC: Zinc-finger 26.0 36 0.00077 17.7 0.8 12 39-50 28-39 (40)
204 PRK12860 transcriptional activ 25.8 42 0.00092 24.3 1.3 30 49-79 116-145 (189)
205 COG1773 Rubredoxin [Energy pro 25.4 37 0.00081 19.1 0.8 12 40-51 3-14 (55)
206 COG0068 HypF Hydrogenase matur 25.1 7.4 0.00016 33.9 -2.9 14 98-111 153-166 (750)
207 PF02084 Bindin: Bindin; Inte 24.6 49 0.0011 24.6 1.5 21 167-187 131-151 (238)
208 KOG2071|consensus 24.2 43 0.00092 28.7 1.3 25 152-176 417-441 (579)
209 PF10013 DUF2256: Uncharacteri 24.0 52 0.0011 17.3 1.1 16 98-113 10-25 (42)
210 PRK03681 hypA hydrogenase nick 23.9 28 0.00061 22.9 0.2 10 128-137 71-80 (114)
211 PF06397 Desulfoferrod_N: Desu 23.8 31 0.00067 17.5 0.2 10 153-162 6-15 (36)
212 TIGR00244 transcriptional regu 23.7 31 0.00066 23.8 0.3 16 40-55 28-43 (147)
213 COG1998 RPS31 Ribosomal protei 23.2 33 0.00071 18.8 0.3 9 153-161 37-45 (51)
214 PTZ00448 hypothetical protein; 22.9 58 0.0013 26.3 1.7 24 153-176 314-337 (373)
215 PF01286 XPA_N: XPA protein N- 22.8 32 0.0007 17.2 0.2 8 130-137 6-13 (34)
216 PF04606 Ogr_Delta: Ogr/Delta- 22.2 11 0.00023 20.3 -1.7 7 99-105 2-8 (47)
217 cd00924 Cyt_c_Oxidase_Vb Cytoc 21.8 39 0.00084 21.6 0.5 13 152-164 78-90 (97)
218 smart00731 SprT SprT homologue 21.8 40 0.00088 23.1 0.6 31 127-163 112-143 (146)
219 PF05495 zf-CHY: CHY zinc fing 21.3 13 0.00029 22.0 -1.6 8 153-160 61-68 (71)
220 TIGR01385 TFSII transcription 21.2 21 0.00046 27.9 -0.9 10 39-48 257-266 (299)
221 PF02891 zf-MIZ: MIZ/SP-RING z 21.2 57 0.0012 17.8 1.0 7 69-75 42-48 (50)
222 PLN03238 probable histone acet 21.1 76 0.0016 24.7 2.0 33 9-41 47-82 (290)
223 COG0068 HypF Hydrogenase matur 21.1 12 0.00026 32.7 -2.4 56 98-161 125-181 (750)
224 PF03145 Sina: Seven in absent 21.1 57 0.0012 23.7 1.3 46 133-180 24-74 (198)
225 KOG1280|consensus 21.0 81 0.0018 25.2 2.1 36 125-160 77-116 (381)
226 COG4391 Uncharacterized protei 20.9 60 0.0013 18.7 1.1 15 94-108 46-60 (62)
227 PF04780 DUF629: Protein of un 20.6 94 0.002 26.1 2.5 26 96-121 57-82 (466)
228 PRK14873 primosome assembly pr 20.5 26 0.00057 30.8 -0.6 8 127-134 410-417 (665)
229 PF14255 Cys_rich_CPXG: Cystei 20.4 44 0.00095 18.6 0.4 11 154-164 1-11 (52)
230 PRK00762 hypA hydrogenase nick 20.4 58 0.0013 21.8 1.1 13 126-139 69-81 (124)
231 PRK05978 hypothetical protein; 20.1 39 0.00086 23.4 0.3 11 155-165 54-64 (148)
232 COG1198 PriA Primosomal protei 20.1 43 0.00094 29.8 0.6 11 39-49 474-484 (730)
No 1
>KOG2462|consensus
Probab=99.96 E-value=2e-30 Score=187.86 Aligned_cols=135 Identities=28% Similarity=0.530 Sum_probs=126.6
Q ss_pred CceecccccccccCHHHHHHHHHHhcC---CCceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQ---EKFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLRVH 115 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~---~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H 115 (213)
..|+|+.|++.+.+..+|.+|..+|.. .+.+.|+.||+.+.+...|.+|+++|+ -+.+|.+||+.|...|.|+.|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 579999999999999999999999864 567999999999999999999999998 579999999999999999999
Q ss_pred HHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCC--CccccccccccCChHHHHhHHhhcCC
Q psy4420 116 YKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNL--NYNCEVCEKVFDKIEEFENHLSDNHI 178 (213)
Q Consensus 116 ~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~--~~~C~~C~~~f~~~~~L~~H~~~~h~ 178 (213)
+++|++ ++||.|+.|+++|...++|+.|+++|.. +|+|..|+|.|+..+.|.+|.+....
T Consensus 207 iRTHTG---EKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C~ 268 (279)
T KOG2462|consen 207 IRTHTG---EKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESACL 268 (279)
T ss_pred cccccC---CCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhccc
Confidence 999996 9999999999999999999999999954 99999999999999999999987643
No 2
>KOG2462|consensus
Probab=99.94 E-value=5e-27 Score=170.30 Aligned_cols=136 Identities=29% Similarity=0.453 Sum_probs=125.3
Q ss_pred CCCccccCcc---chhhhhhhhhhhhcccccccCCCceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHH
Q psy4420 7 TPSKLICSFC---LEEVDNSALKMFEHNCDGVLNARKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYIND 83 (213)
Q Consensus 7 ~~~~~~C~~C---f~~~~~l~~h~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~ 83 (213)
....|+|+.| +...++|.+|...|...... +.+.|+.|++.|.....|+-|+++|. .++.|.+||+.|...=-
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~--ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWL 202 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSK--KAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWL 202 (279)
T ss_pred cCCceeccccccccccccccchhhccccccccc--ccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHH
Confidence 4567999999 88899999999999876442 78999999999999999999999995 68999999999998777
Q ss_pred HHHHHHhccCCCCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHhh
Q psy4420 84 VKKHTRKHTGEKPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNL 149 (213)
Q Consensus 84 l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 149 (213)
|+-|++.|+||+||.|+.|++.|.+++.|+.|+++|.. .+.|+|..|++.|...+.|..|...
T Consensus 203 LQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~---~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 203 LQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD---VKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcccccccCCCCccCCcccchhcchHHHHHHHHhhcC---CccccCcchhhHHHHHHHHHHhhhh
Confidence 88899999999999999999999999999999999996 7899999999999999999999754
No 3
>KOG3608|consensus
Probab=99.90 E-value=7.6e-24 Score=158.08 Aligned_cols=175 Identities=22% Similarity=0.501 Sum_probs=157.2
Q ss_pred CCCCCCCCccccCcc---chhhhhhhhhhhhcccccccCCCceecccccccccCHHHHHHHHHHhcCCCceecccCcccc
Q psy4420 2 LRSTDTPSKLICSFC---LEEVDNSALKMFEHNCDGVLNARKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKS 78 (213)
Q Consensus 2 ~~~~~~~~~~~C~~C---f~~~~~l~~h~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~ 78 (213)
+++|+++|-..|+.| |.....|-.|+++.+... .++|+|..|.+.|.+...|..|+..|- ..|.|+.|+.+.
T Consensus 199 ~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~---~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc 273 (467)
T KOG3608|consen 199 IRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELN---TNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTC 273 (467)
T ss_pred HHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhc---CCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCC
Confidence 478999999999999 899999999998877553 379999999999999999999999984 578999999999
Q ss_pred cCHHHHHHHHH-hccCCCCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCc--cccccCCHHHHHHHHhhCC-C--
Q psy4420 79 AYINDVKKHTR-KHTGEKPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTI--CSKRFYTKSKLDFHVNLHN-L-- 152 (213)
Q Consensus 79 ~~~~~l~~H~~-~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-~-- 152 (213)
...++|..|++ .|...+|++|+.|...+.....|..|..+|. +..|.|.. |..+|.+...+.+|.+.++ +
T Consensus 274 ~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS----~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~n 349 (467)
T KOG3608|consen 274 SSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS----KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNN 349 (467)
T ss_pred CChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc----ccceecCCCCCcHHHHHHHHHHHHHHHhccCCC
Confidence 99999999987 5777899999999999999999999999887 68899987 9999999999999997664 3
Q ss_pred --CccccccccccCChHHHHhHHhhcCCCCCCCCC
Q psy4420 153 --NYNCEVCEKVFDKIEEFENHLSDNHIFTYDHGT 185 (213)
Q Consensus 153 --~~~C~~C~~~f~~~~~L~~H~~~~h~~~~~~~~ 185 (213)
+|.|-.|++.|++..+|..|++..|+..++.+-
T Consensus 350 p~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh 384 (467)
T KOG3608|consen 350 PILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGH 384 (467)
T ss_pred CCceeeecchhhhccchhHHHHHHHhhcccCCCCC
Confidence 899999999999999999999999988765543
No 4
>KOG1074|consensus
Probab=99.87 E-value=7e-23 Score=167.52 Aligned_cols=53 Identities=34% Similarity=0.619 Sum_probs=49.3
Q ss_pred eecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHHHHHHHhhc
Q psy4420 69 FACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLRVHYKTHAK 121 (213)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 121 (213)
..|.+|.+.+...+.|+.|.+.|+|++||+|.+|+++|..+..|+.|+-.|-.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhccccccc
Confidence 48999999999999999999999999999999999999999999999987743
No 5
>KOG3608|consensus
Probab=99.84 E-value=6.3e-21 Score=142.61 Aligned_cols=155 Identities=21% Similarity=0.404 Sum_probs=143.3
Q ss_pred chhhhhhhhhhhhcccccccCCCceecccccccccCHHHHHHHHHH--hcCCCceecccCcccccCHHHHHHHHHhccCC
Q psy4420 17 LEEVDNSALKMFEHNCDGVLNARKYTCLLCKQKESQAWKIKRHYLK--HTQEKFFACSHCDYKSAYINDVKKHTRKHTGE 94 (213)
Q Consensus 17 f~~~~~l~~h~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~--h~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~ 94 (213)
+.....|..|++.|..+ +...|+.||..|.++..|-.|.+. .....+|.|..|.+.|.....|..|++.|..
T Consensus 189 ~~~k~~LreH~r~Hs~e-----KvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn- 262 (467)
T KOG3608|consen 189 MGNKYRLREHIRTHSNE-----KVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN- 262 (467)
T ss_pred hccHHHHHHHHHhcCCC-----eEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh-
Confidence 88899999999999999 888999999999999999999875 4467899999999999999999999998874
Q ss_pred CCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCC-Cccccc--cccccCChHHHHh
Q psy4420 95 KPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNL-NYNCEV--CEKVFDKIEEFEN 171 (213)
Q Consensus 95 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-~~~C~~--C~~~f~~~~~L~~ 171 (213)
.|+|+.|.......++|..|++.-+. ..+||+|..|...|...+.|..|..+|+. .|+|.. |..+|....++.+
T Consensus 263 -~ykCplCdmtc~~~ssL~~H~r~rHs--~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~ 339 (467)
T KOG3608|consen 263 -CYKCPLCDMTCSSASSLTTHIRYRHS--KDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRR 339 (467)
T ss_pred -cccccccccCCCChHHHHHHHHhhhc--cCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHH
Confidence 69999999999999999999998776 48999999999999999999999999987 899988 9999999999999
Q ss_pred HHhhcCCCC
Q psy4420 172 HLSDNHIFT 180 (213)
Q Consensus 172 H~~~~h~~~ 180 (213)
|++.+|+..
T Consensus 340 H~~evhEg~ 348 (467)
T KOG3608|consen 340 HFLEVHEGN 348 (467)
T ss_pred HHHHhccCC
Confidence 999999554
No 6
>KOG1074|consensus
Probab=99.78 E-value=2.4e-20 Score=152.88 Aligned_cols=81 Identities=28% Similarity=0.639 Sum_probs=75.7
Q ss_pred eecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCC------Ccccc---ccccccCChH
Q psy4420 97 FKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNL------NYNCE---VCEKVFDKIE 167 (213)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~------~~~C~---~C~~~f~~~~ 167 (213)
-.|-+|.++..-.++|+.|.++|++ ++||+|.+||+.|....+|+.|+.+|.. +++|+ +|.+.|...-
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtG---ERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V 682 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTG---ERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAV 682 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccC---cCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccc
Confidence 5899999999999999999999996 9999999999999999999999999942 79999 9999999999
Q ss_pred HHHhHHhhcCCCC
Q psy4420 168 EFENHLSDNHIFT 180 (213)
Q Consensus 168 ~L~~H~~~~h~~~ 180 (213)
.|..|++.|.+..
T Consensus 683 ~lpQhIriH~~~~ 695 (958)
T KOG1074|consen 683 TLPQHIRIHLGGQ 695 (958)
T ss_pred cccceEEeecCCC
Confidence 9999999998554
No 7
>KOG3623|consensus
Probab=99.76 E-value=4.7e-19 Score=143.47 Aligned_cols=106 Identities=25% Similarity=0.544 Sum_probs=90.8
Q ss_pred ccccCcc---chhhhhhhhhhhhcccccccCCCceecccccccccCHHHHHHHHHHhcCC-------------Cceeccc
Q psy4420 10 KLICSFC---LEEVDNSALKMFEHNCDGVLNARKYTCLLCKQKESQAWKIKRHYLKHTQE-------------KFFACSH 73 (213)
Q Consensus 10 ~~~C~~C---f~~~~~l~~h~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-------------~~~~C~~ 73 (213)
...|++| +..+..|..|+..-+.... ..|.|..|.++|..+..|.+||..|..- +-|.|.+
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne---~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtE 286 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNE---PNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTE 286 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCC---CCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccc
Confidence 4689999 7888888999876554432 5788999999999999999999887532 3489999
Q ss_pred CcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHHHHHHH
Q psy4420 74 CDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLRVHYKT 118 (213)
Q Consensus 74 C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 118 (213)
||+.|..+-.|+.|+++|.|++||.|+.|++.|+...++..|+..
T Consensus 287 CgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 287 CGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 999999999999999999999999999999999999999998754
No 8
>KOG3576|consensus
Probab=99.70 E-value=7.8e-18 Score=117.13 Aligned_cols=128 Identities=28% Similarity=0.449 Sum_probs=98.6
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHHHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLRVHYKT 118 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 118 (213)
..|+|.+|++.|....-|.+|++.|...+.+.|..||+.|...-+|++|.+.|+|.+||+|..|++.|...-+|..|++.
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~k 195 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKK 195 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHH
Confidence 56888888888888888888888888888888888888888888888888888888888888888888888888888766
Q ss_pred hhccCCCeeeecCccccccCCHHHHHHHHhhCCCCccccccccccCChHHHHhHHhhcCCCCCCCC
Q psy4420 119 HAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEFENHLSDNHIFTYDHG 184 (213)
Q Consensus 119 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L~~H~~~~h~~~~~~~ 184 (213)
-++ .. ....+. ..-.+.|.|..||.+-.....+..|++.+|......-
T Consensus 196 vhg---v~------------~~yayk---err~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spall 243 (267)
T KOG3576|consen 196 VHG---VQ------------HQYAYK---ERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPALL 243 (267)
T ss_pred HcC---ch------------HHHHHH---HhhhheeeecccCCCCCChhHHHHHHHhcCCCCHHHH
Confidence 553 10 000000 1113478999999888888888999999888764443
No 9
>KOG3576|consensus
Probab=99.66 E-value=1.8e-17 Score=115.36 Aligned_cols=86 Identities=29% Similarity=0.559 Sum_probs=79.2
Q ss_pred cCCCCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCC--CccccccccccCChHHH
Q psy4420 92 TGEKPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNL--NYNCEVCEKVFDKIEEF 169 (213)
Q Consensus 92 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~--~~~C~~C~~~f~~~~~L 169 (213)
.+...+.|.+|++.|.....|..|++.|.. .+.+.|..||+.|..-..|.+|+++|.+ ||+|..|+++|+++-+|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~---vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsl 189 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSD---VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSL 189 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccH---HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccH
Confidence 345679999999999999999999999985 7889999999999999999999999987 99999999999999999
Q ss_pred HhHHhhcCCCC
Q psy4420 170 ENHLSDNHIFT 180 (213)
Q Consensus 170 ~~H~~~~h~~~ 180 (213)
..|++..||..
T Consensus 190 eshl~kvhgv~ 200 (267)
T KOG3576|consen 190 ESHLKKVHGVQ 200 (267)
T ss_pred HHHHHHHcCch
Confidence 99999999874
No 10
>KOG3623|consensus
Probab=99.46 E-value=2e-14 Score=117.12 Aligned_cols=79 Identities=27% Similarity=0.539 Sum_probs=41.6
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLRVHYK 117 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 117 (213)
..|.|.+|+++|...+.|.+|-.-|.|.+||.|.+|.+.|.-+-.|..|.+.|.|++||.|+.|++.|+...++.+||.
T Consensus 893 gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred ccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 3455555555555555555555555555555555555555555555555555555555555555555555555555543
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.42 E-value=6.7e-13 Score=108.04 Aligned_cols=147 Identities=17% Similarity=0.331 Sum_probs=112.4
Q ss_pred CCccccCcc--chhhhhhhhhhhhcccccccCCCceeccc--ccccccCHHHHHHHHHHhcCCCceecccCcccccCHHH
Q psy4420 8 PSKLICSFC--LEEVDNSALKMFEHNCDGVLNARKYTCLL--CKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYIND 83 (213)
Q Consensus 8 ~~~~~C~~C--f~~~~~l~~h~~~h~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~ 83 (213)
.....|+.| ......|..|....... .-.|+. |+..|. +..+..| +.|+.|++.|. ...
T Consensus 405 ~~~V~C~NC~~~i~l~~l~lHe~~C~r~------~V~Cp~~~Cg~v~~-r~el~~H---------~~C~~Cgk~f~-~s~ 467 (567)
T PLN03086 405 VDTVECRNCKHYIPSRSIALHEAYCSRH------NVVCPHDGCGIVLR-VEEAKNH---------VHCEKCGQAFQ-QGE 467 (567)
T ss_pred CCeEECCCCCCccchhHHHHHHhhCCCc------ceeCCcccccceee-ccccccC---------ccCCCCCCccc-hHH
Confidence 345689999 55567788888665544 345874 998884 2333333 57999999986 577
Q ss_pred HHHHHHhccCCCCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCC----------HHHHHHHHhhCC-C
Q psy4420 84 VKKHTRKHTGEKPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYT----------KSKLDFHVNLHN-L 152 (213)
Q Consensus 84 l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~----------~~~l~~H~~~h~-~ 152 (213)
|..|+..++ .++.|+ |+..+ ....|..|+..+.+ .+++.|+.|++.|.. ...|..|..+.. +
T Consensus 468 LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp---~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~r 540 (567)
T PLN03086 468 MEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCP---LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSR 540 (567)
T ss_pred HHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCC---CCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCc
Confidence 999999876 789999 99755 66899999988885 899999999999852 357889988874 4
Q ss_pred CccccccccccCChHHHHhHHhhcCCC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHIF 179 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~~ 179 (213)
++.|..||+.+..+ .+..|+-..|..
T Consensus 541 t~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 541 TAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred ceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 99999999888655 677888877754
No 12
>PHA00733 hypothetical protein
Probab=99.38 E-value=5.8e-13 Score=89.23 Aligned_cols=86 Identities=17% Similarity=0.313 Sum_probs=69.3
Q ss_pred CCCeecCCCCcccCChhHHHHH--HHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCCCccccccccccCChHHHHh
Q psy4420 94 EKPFKCQICPYAAADSKSLRVH--YKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEFEN 171 (213)
Q Consensus 94 ~~~~~C~~C~~~f~~~~~l~~H--~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L~~ 171 (213)
.+++.|.+|...|.....|..+ +..+....+..+|.|+.|++.|.+...|..|++.+..+|.|++|++.|.....|.+
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHH
Confidence 4567787888777777666665 33332222478899999999999999999999988778999999999999999999
Q ss_pred HHhhcCCC
Q psy4420 172 HLSDNHIF 179 (213)
Q Consensus 172 H~~~~h~~ 179 (213)
|+...|+.
T Consensus 118 H~~~~h~~ 125 (128)
T PHA00733 118 HVCKKHNI 125 (128)
T ss_pred HHHHhcCc
Confidence 99998874
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.12 E-value=2.7e-11 Score=67.26 Aligned_cols=45 Identities=22% Similarity=0.503 Sum_probs=41.1
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCCCccccccccccCChHHHH
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEFE 170 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L~ 170 (213)
-.|+|+.||+.|...+.|..|+++|.++|+|..|++.|.+.+.|.
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceecccceeE
Confidence 348999999999999999999999999999999999999887774
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.12 E-value=2.7e-10 Score=93.11 Aligned_cols=100 Identities=17% Similarity=0.353 Sum_probs=83.3
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCC----------
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAAD---------- 108 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~---------- 108 (213)
+.+.|+.|++.|. ...|..|+..++ +++.|+ ||+.+ ....|..|+..+.+.+++.|+.|++.+..
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhh
Confidence 4568999999996 678999999975 789999 99755 56889999999999999999999999852
Q ss_pred hhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHh
Q psy4420 109 SKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVN 148 (213)
Q Consensus 109 ~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 148 (213)
...|..|.... +.+++.|..||+.+.... +..|+-
T Consensus 527 ~s~Lt~HE~~C----G~rt~~C~~Cgk~Vrlrd-m~~H~~ 561 (567)
T PLN03086 527 LRGMSEHESIC----GSRTAPCDSCGRSVMLKE-MDIHQI 561 (567)
T ss_pred hhhHHHHHHhc----CCcceEccccCCeeeehh-HHHHHH
Confidence 34788887775 489999999999998775 566653
No 15
>KOG3993|consensus
Probab=99.09 E-value=2e-11 Score=94.19 Aligned_cols=163 Identities=17% Similarity=0.198 Sum_probs=99.5
Q ss_pred CccccCcc---chhhhhhhhhhhhcccccccCCCceecccccccccCHHHHHHHHHHhcCC-------------------
Q psy4420 9 SKLICSFC---LEEVDNSALKMFEHNCDGVLNARKYTCLLCKQKESQAWKIKRHYLKHTQE------------------- 66 (213)
Q Consensus 9 ~~~~C~~C---f~~~~~l~~h~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~------------------- 66 (213)
..|.|..| |.+...|.+|.-.-... .-|.|++|++.|+-..||..|.+.|...
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~-----vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ra 340 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVH-----VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRA 340 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEE-----eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhh
Confidence 45899999 88888888775443333 6799999999999999999999887421
Q ss_pred --------------CceecccCcccccCHHHHHHHHHhccCCCC-----------------eecCCCCcccCChhHHHHH
Q psy4420 67 --------------KFFACSHCDYKSAYINDVKKHTRKHTGEKP-----------------FKCQICPYAAADSKSLRVH 115 (213)
Q Consensus 67 --------------~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~-----------------~~C~~C~~~f~~~~~l~~H 115 (213)
.-|.|..|+++|.....|+.|+..|+.... +.+..|.-.+.....--.+
T Consensus 341 e~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~ 420 (500)
T KOG3993|consen 341 EVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDE 420 (500)
T ss_pred hhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccc
Confidence 116777777777777777777665543211 1111111111111110000
Q ss_pred HHHhhccCCCeeeecCccccccCCHHHHHHHHhhC--CCCccccccccccCChHHHHhHHhhcCC
Q psy4420 116 YKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLH--NLNYNCEVCEKVFDKIEEFENHLSDNHI 178 (213)
Q Consensus 116 ~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h--~~~~~C~~C~~~f~~~~~L~~H~~~~h~ 178 (213)
.-.+.+ -..-..++.++..+.++..--.+.+.- ...|.|.+|.-.|.+...|.+|+..-|.
T Consensus 421 vl~~a~--sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hp 483 (500)
T KOG3993|consen 421 VLYVAG--SAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHP 483 (500)
T ss_pred eeeeec--cccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcCh
Confidence 000000 012245677886666654433333222 2268999999999999999999877664
No 16
>PHA00733 hypothetical protein
Probab=99.02 E-value=3.6e-10 Score=75.83 Aligned_cols=81 Identities=14% Similarity=0.184 Sum_probs=64.5
Q ss_pred CceecccccccccCHHHHHHH--HH---HhcCCCceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKRH--YL---KHTQEKFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLR 113 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~ 113 (213)
+++.|.+|.+.|.....|..+ +. .+.+++||.|+.||+.|.....|..|++.+ ..++.|+.|++.|.....|.
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~ 116 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTL 116 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHH
Confidence 678888888888877776655 22 234578899999999999999999998865 34689999999999999999
Q ss_pred HHHHHhhc
Q psy4420 114 VHYKTHAK 121 (213)
Q Consensus 114 ~H~~~~~~ 121 (213)
.|+...++
T Consensus 117 ~H~~~~h~ 124 (128)
T PHA00733 117 DHVCKKHN 124 (128)
T ss_pred HHHHHhcC
Confidence 99887764
No 17
>KOG3993|consensus
Probab=98.93 E-value=1.5e-10 Score=89.36 Aligned_cols=55 Identities=25% Similarity=0.503 Sum_probs=49.6
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHHHHHHHHhccC
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYINDVKKHTRKHTG 93 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~ 93 (213)
+.|.|..|...|.+...|.+|.-...-..-|.|++|++.|....+|..|.++|..
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 5699999999999999999998766666779999999999999999999999864
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.79 E-value=2.6e-09 Score=59.42 Aligned_cols=42 Identities=21% Similarity=0.363 Sum_probs=30.2
Q ss_pred ceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHH
Q psy4420 40 KYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYIND 83 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~ 83 (213)
.|.|+.||+.|....+|..|++.|. +++.|..|++.|...+.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGE 46 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccce
Confidence 5677777777777777777777776 56777777777765443
No 19
>PHA00732 hypothetical protein
Probab=98.65 E-value=2e-08 Score=61.21 Aligned_cols=46 Identities=24% Similarity=0.527 Sum_probs=27.7
Q ss_pred eeecCccccccCCHHHHHHHHhhCCCCccccccccccCChHHHHhHHhh
Q psy4420 127 VYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEFENHLSD 175 (213)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L~~H~~~ 175 (213)
||.|..|++.|.+...|..|++.++.++.|+.||+.|. .|..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhcc
Confidence 35666666666666666666664334556666666665 35555533
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=98.57 E-value=5.7e-08 Score=46.17 Aligned_cols=24 Identities=33% Similarity=0.649 Sum_probs=13.0
Q ss_pred HHHHHHHhcCCCceecccCccccc
Q psy4420 56 IKRHYLKHTQEKFFACSHCDYKSA 79 (213)
Q Consensus 56 l~~H~~~h~~~~~~~C~~C~~~~~ 79 (213)
|..|++.|.+++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 455555555555555555555543
No 21
>PHA00616 hypothetical protein
Probab=98.55 E-value=4e-08 Score=52.03 Aligned_cols=36 Identities=17% Similarity=0.252 Sum_probs=27.9
Q ss_pred ceecccccccccCHHHHHHHHHHhcCCCceecccCc
Q psy4420 40 KYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCD 75 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 75 (213)
||+|+.||+.|..+.+|..|++.|++++++.|+.--
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y 36 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFY 36 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEEE
Confidence 577888888888888888888888888887776543
No 22
>PHA00616 hypothetical protein
Probab=98.51 E-value=4.8e-08 Score=51.71 Aligned_cols=29 Identities=31% Similarity=0.489 Sum_probs=25.9
Q ss_pred CccccccccccCChHHHHhHHhhcCCCCC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHIFTY 181 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~~~~ 181 (213)
||+|+.||+.|.+.++|..|++.+|++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 68999999999999999999999998864
No 23
>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=98.44 E-value=2.1e-07 Score=44.21 Aligned_cols=24 Identities=46% Similarity=1.020 Sum_probs=14.5
Q ss_pred HHHHHHhccCCCCeecCCCCcccC
Q psy4420 84 VKKHTRKHTGEKPFKCQICPYAAA 107 (213)
Q Consensus 84 l~~H~~~~~~~~~~~C~~C~~~f~ 107 (213)
|.+|++.|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 555666666666666666666554
No 24
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.33 E-value=6.8e-07 Score=50.65 Aligned_cols=48 Identities=25% Similarity=0.546 Sum_probs=26.5
Q ss_pred eecCccccccCCHHHHHHHHhhCCC----CccccccccccCChHHHHhHHhhcCC
Q psy4420 128 YHCTICSKRFYTKSKLDFHVNLHNL----NYNCEVCEKVFDKIEEFENHLSDNHI 178 (213)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h~~----~~~C~~C~~~f~~~~~L~~H~~~~h~ 178 (213)
|.|+.|++ ..+...|..|....+. .+.||+|...+. .+|..|+...|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 55666666 3445556666544322 466666665433 366666666553
No 25
>PHA00732 hypothetical protein
Probab=98.14 E-value=1.9e-06 Score=52.62 Aligned_cols=46 Identities=20% Similarity=0.512 Sum_probs=33.8
Q ss_pred ceecccccccccCHHHHHHHHHH-hcCCCceecccCcccccCHHHHHHHHHhc
Q psy4420 40 KYTCLLCKQKESQAWKIKRHYLK-HTQEKFFACSHCDYKSAYINDVKKHTRKH 91 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~~~~~~~l~~H~~~~ 91 (213)
||.|..|++.|....+|..|++. |. ++.|+.||+.|. .+..|....
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 47788888888888888888874 54 346888888886 366676543
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.13 E-value=1.4e-06 Score=40.15 Aligned_cols=22 Identities=27% Similarity=0.818 Sum_probs=16.8
Q ss_pred ccccccccccCChHHHHhHHhh
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSD 175 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~ 175 (213)
|+|+.|++.|.....|..|++.
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 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.06 E-value=9.1e-06 Score=46.00 Aligned_cols=49 Identities=20% Similarity=0.491 Sum_probs=22.1
Q ss_pred ceecccccccccCHHHHHHHHHH-hcCC-CceecccCcccccCHHHHHHHHHhc
Q psy4420 40 KYTCLLCKQKESQAWKIKRHYLK-HTQE-KFFACSHCDYKSAYINDVKKHTRKH 91 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~-~~~~C~~C~~~~~~~~~l~~H~~~~ 91 (213)
.|.||.|++ ..+...|..|... |..+ +.+.|++|...+. .+|..|+..+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 355555555 2334455555543 2221 2355555554322 2455554443
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.03 E-value=3.1e-06 Score=39.21 Aligned_cols=24 Identities=29% Similarity=0.836 Sum_probs=17.5
Q ss_pred ccccccccccCChHHHHhHHhhcC
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSDNH 177 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~~h 177 (213)
|.|++|++.|.+...|..|++.+|
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 578888888888888888887765
No 29
>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=97.96 E-value=5.2e-06 Score=39.78 Aligned_cols=26 Identities=19% Similarity=0.609 Sum_probs=19.2
Q ss_pred CccccccccccCChHHHHhHHhhcCC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHI 178 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~ 178 (213)
+|+|..|++.|.....|..|++.+++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 46777777777777777777776654
No 30
>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=97.95 E-value=8.7e-06 Score=37.35 Aligned_cols=23 Identities=35% Similarity=0.732 Sum_probs=16.5
Q ss_pred eecccccccccCHHHHHHHHHHh
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLKH 63 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~h 63 (213)
|+|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 56777777777777777777653
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.84 E-value=1.2e-05 Score=51.64 Aligned_cols=72 Identities=18% Similarity=0.338 Sum_probs=20.0
Q ss_pred ecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCC-CccccccccccCChHHHHhHHhhc
Q psy4420 98 KCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNL-NYNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 98 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-~~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
.|..|+..|.+...|..|+...++ . ..+ ....+.....+..+.+..-. .+.|..|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~---~---~~~-~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHG---F---DIP-DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccc---c---ccc-cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 377777788778788888766553 1 111 11122233334444433322 688999999999999999999875
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.84 E-value=5.1e-06 Score=62.63 Aligned_cols=54 Identities=26% Similarity=0.744 Sum_probs=43.3
Q ss_pred CCeeeecCc--cccccCCHHHHHHHHhhC---------------------CCCccccccccccCChHHHHhHHhhcC
Q psy4420 124 GRRVYHCTI--CSKRFYTKSKLDFHVNLH---------------------NLNYNCEVCEKVFDKIEEFENHLSDNH 177 (213)
Q Consensus 124 ~~~~~~C~~--C~~~f~~~~~l~~H~~~h---------------------~~~~~C~~C~~~f~~~~~L~~H~~~~h 177 (213)
+++||+|++ |.+.|.....|+.|+..- .+||+|++|+|.|.....|+.|....|
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~Hsh 422 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHSH 422 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccccC
Confidence 358888886 888888888888886532 258999999999999999999976543
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.62 E-value=6.4e-05 Score=34.59 Aligned_cols=23 Identities=17% Similarity=0.571 Sum_probs=14.1
Q ss_pred eecccccccccCHHHHHHHHHHh
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLKH 63 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~h 63 (213)
|.|+.|+..|.....|..|+..+
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 45677777777777777776654
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.57 E-value=5.8e-05 Score=48.45 Aligned_cols=20 Identities=30% Similarity=0.572 Sum_probs=0.0
Q ss_pred cccccccccCHHHHHHHHHH
Q psy4420 43 CLLCKQKESQAWKIKRHYLK 62 (213)
Q Consensus 43 C~~C~~~f~~~~~l~~H~~~ 62 (213)
|..|+..|.....|..|+..
T Consensus 2 C~~C~~~f~~~~~l~~H~~~ 21 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKK 21 (100)
T ss_dssp --------------------
T ss_pred cccccccccccccccccccc
Confidence 55566666666666666544
No 35
>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=97.51 E-value=8.9e-05 Score=35.37 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=17.0
Q ss_pred eeecCccccccCCHHHHHHHHhhCC
Q psy4420 127 VYHCTICSKRFYTKSKLDFHVNLHN 151 (213)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~ 151 (213)
+|+|..|++.|.+...|..|++.|.
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 4667777777777777777766654
No 36
>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=97.39 E-value=0.00023 Score=38.65 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=17.6
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCc
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKF 68 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 68 (213)
.|-+|++|+..+....+|.+|+..+++.+|
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 567777777777777777777776666554
No 37
>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=97.27 E-value=0.00022 Score=38.76 Aligned_cols=29 Identities=21% Similarity=0.426 Sum_probs=21.3
Q ss_pred CccccccccccCChHHHHhHHhhcCCCCC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHIFTY 181 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~~~~ 181 (213)
|..|++|+..+.+..+|.+|++..|+.+.
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 78899999999999999999988888764
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.25 E-value=0.00021 Score=33.35 Aligned_cols=23 Identities=30% Similarity=0.784 Sum_probs=19.3
Q ss_pred ccccccccccCChHHHHhHHhhc
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
|+|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 57888999999999999998744
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.12 E-value=0.00015 Score=54.88 Aligned_cols=55 Identities=25% Similarity=0.664 Sum_probs=41.5
Q ss_pred CCCeecCC--CCcccCChhHHHHHHHHhhccC----------------CCeeeecCccccccCCHHHHHHHHh
Q psy4420 94 EKPFKCQI--CPYAAADSKSLRVHYKTHAKEN----------------GRRVYHCTICSKRFYTKSKLDFHVN 148 (213)
Q Consensus 94 ~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~----------------~~~~~~C~~C~~~f~~~~~l~~H~~ 148 (213)
++||+|++ |.+.|+....|.-|+..-+... ..+||.|++|+++|.....|+.|..
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 47888875 8888888888888865322100 3589999999999999999988754
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.11 E-value=0.00024 Score=32.78 Aligned_cols=24 Identities=25% Similarity=0.576 Sum_probs=17.8
Q ss_pred ccccccccccCChHHHHhHHhhcCC
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSDNHI 178 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~~h~ 178 (213)
|+|+.|+.... ...|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 67888888887 8888888888764
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.07 E-value=0.00033 Score=32.63 Aligned_cols=23 Identities=26% Similarity=0.808 Sum_probs=17.1
Q ss_pred ccccccccccCChHHHHhHHhhc
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
|.|.+|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 56778888888888888877653
No 42
>KOG2231|consensus
Probab=96.76 E-value=0.0062 Score=51.54 Aligned_cols=120 Identities=23% Similarity=0.379 Sum_probs=68.7
Q ss_pred cccccccccCHHHHHHHHHHhcCCCceecccCc---------ccccCHHHHHHHHHhccC-C----CCeecCCCCcccCC
Q psy4420 43 CLLCKQKESQAWKIKRHYLKHTQEKFFACSHCD---------YKSAYINDVKKHTRKHTG-E----KPFKCQICPYAAAD 108 (213)
Q Consensus 43 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~---------~~~~~~~~l~~H~~~~~~-~----~~~~C~~C~~~f~~ 108 (213)
|..| ..|..-..|+.|+..-+. .+.|.+|- ........|..|++.-.. + ..-.|..|...|..
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld 194 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLD 194 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhh--hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhcc
Confidence 4444 444566777888754221 22233321 223334557777663221 1 12467888888888
Q ss_pred hhHHHHHHHHhhccCCCeeeecCcc------ccccCCHHHHHHHHhhCCCCcccc--ccc-cccCChHHHHhHHh
Q psy4420 109 SKSLRVHYKTHAKENGRRVYHCTIC------SKRFYTKSKLDFHVNLHNLNYNCE--VCE-KVFDKIEEFENHLS 174 (213)
Q Consensus 109 ~~~l~~H~~~~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~~~C~--~C~-~~f~~~~~L~~H~~ 174 (213)
...|..|++.++ |.|..| ...|.....|..|.+..|. -|. .|- +.|.....+..+++
T Consensus 195 ~~el~rH~~~~h-------~~chfC~~~~~~neyy~~~~dLe~HfR~~Hf--lCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 195 DDELYRHLRFDH-------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHF--LCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred HHHHHHhhccce-------eheeecCcccccchhcccchHHHHHhhhcCc--cccccccccceeeehhHHHHHHH
Confidence 888888877665 455555 3556777788888877773 444 443 44555555555655
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.71 E-value=0.0018 Score=29.99 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=14.7
Q ss_pred eecccccccccCHHHHHHHHHHh
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLKH 63 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~h 63 (213)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666644
No 44
>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=96.58 E-value=0.0011 Score=31.49 Aligned_cols=22 Identities=23% Similarity=0.835 Sum_probs=18.3
Q ss_pred ccccccccccCChHHHHhHHhh
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSD 175 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~ 175 (213)
|.|..|++.|.+...|..|+++
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 6788888888888888888865
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.47 E-value=0.0024 Score=29.64 Aligned_cols=22 Identities=18% Similarity=0.505 Sum_probs=15.1
Q ss_pred eecccccccccCHHHHHHHHHH
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLK 62 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~ 62 (213)
|.|.+|+..|.....|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4577777777777777777654
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.24 E-value=0.0052 Score=28.16 Aligned_cols=23 Identities=35% Similarity=0.687 Sum_probs=13.4
Q ss_pred eecccccccccCHHHHHHHHHHhc
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLKHT 64 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~h~ 64 (213)
|+|+.|+.... ...|..|++.++
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 46677776665 666777766543
No 47
>KOG2231|consensus
Probab=96.23 E-value=0.016 Score=49.22 Aligned_cols=121 Identities=20% Similarity=0.395 Sum_probs=76.7
Q ss_pred cCcc--chhhhhhhhhhhhcccccccCCCceecccc---------cccccCHHHHHHHHHHhcC-CCc----eecccCcc
Q psy4420 13 CSFC--LEEVDNSALKMFEHNCDGVLNARKYTCLLC---------KQKESQAWKIKRHYLKHTQ-EKF----FACSHCDY 76 (213)
Q Consensus 13 C~~C--f~~~~~l~~h~~~h~~~~~~~~~~~~C~~C---------~~~f~~~~~l~~H~~~h~~-~~~----~~C~~C~~ 76 (213)
|..| |..+..|..|+...+ +.+.|..| .........|..|++.--. +.. -.|.+|..
T Consensus 118 ~~~c~~~~s~~~Lk~H~~~~H-------~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~ 190 (669)
T KOG2231|consen 118 CLHCTEFKSVENLKNHMRDQH-------KLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHE 190 (669)
T ss_pred CccccchhHHHHHHHHHHHhh-------hhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhh
Confidence 5555 456788888985443 33444443 2334567778888875322 221 36999999
Q ss_pred cccCHHHHHHHHHhccCCCCeec---CCCCcccCChhHHHHHHHHhhccCCCeeeecC--ccc-cccCCHHHHHHHHh
Q psy4420 77 KSAYINDVKKHTRKHTGEKPFKC---QICPYAAADSKSLRVHYKTHAKENGRRVYHCT--ICS-KRFYTKSKLDFHVN 148 (213)
Q Consensus 77 ~~~~~~~l~~H~~~~~~~~~~~C---~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~--~C~-~~f~~~~~l~~H~~ 148 (213)
.|.....|.+|++..+..- ..| +.++..|.....|..|.+..| |.|. .|. +.|.....+..+++
T Consensus 191 ~fld~~el~rH~~~~h~~c-hfC~~~~~~neyy~~~~dLe~HfR~~H-------flCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 191 RFLDDDELYRHLRFDHEFC-HFCDYKTGQNEYYNDYDDLEEHFRKGH-------FLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred hhccHHHHHHhhccceehe-eecCcccccchhcccchHHHHHhhhcC-------ccccccccccceeeehhHHHHHHH
Confidence 9999999999998766321 223 234567888899999998877 5666 455 23333334444444
No 48
>PRK04860 hypothetical protein; Provisional
Probab=96.13 E-value=0.0029 Score=44.20 Aligned_cols=38 Identities=24% Similarity=0.524 Sum_probs=27.8
Q ss_pred ceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCCh
Q psy4420 68 FFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADS 109 (213)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 109 (213)
+|.|. |+. ....+.+|.+++.++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 57786 776 345577788888888888888888777544
No 49
>KOG2785|consensus
Probab=95.58 E-value=0.099 Score=41.18 Aligned_cols=50 Identities=20% Similarity=0.407 Sum_probs=42.4
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCC-------------------------Cccccccc---cccCChHHHHhHHhh
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNL-------------------------NYNCEVCE---KVFDKIEEFENHLSD 175 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-------------------------~~~C~~C~---~~f~~~~~L~~H~~~ 175 (213)
.|-.|-.|++.+.+...-..|+..+|+ -+.|-.|+ +.|.+....+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 456788999999999999999987764 26788888 999999999999955
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.56 E-value=0.011 Score=27.51 Aligned_cols=19 Identities=26% Similarity=0.753 Sum_probs=10.6
Q ss_pred cccccccccCChHHHHhHHh
Q psy4420 155 NCEVCEKVFDKIEEFENHLS 174 (213)
Q Consensus 155 ~C~~C~~~f~~~~~L~~H~~ 174 (213)
.|+.||+.| ..+.|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 4455555543
No 51
>PRK04860 hypothetical protein; Provisional
Probab=95.30 E-value=0.016 Score=40.56 Aligned_cols=39 Identities=26% Similarity=0.659 Sum_probs=32.5
Q ss_pred CCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCH
Q psy4420 95 KPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTK 140 (213)
Q Consensus 95 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~ 140 (213)
-+|.|. |+. ....+..|.+++.+ +++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g---~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRG---EAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcC---CccEECCCCCceeEEe
Confidence 368998 987 66778999999985 8899999999988654
No 52
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.24 E-value=0.033 Score=43.13 Aligned_cols=133 Identities=22% Similarity=0.403 Sum_probs=90.1
Q ss_pred ceeccc--ccccccCHHHHHHHHHHhcCCCceecccCcc---------cccCHHHHHHHHHhccCC----CCeecCCCCc
Q psy4420 40 KYTCLL--CKQKESQAWKIKRHYLKHTQEKFFACSHCDY---------KSAYINDVKKHTRKHTGE----KPFKCQICPY 104 (213)
Q Consensus 40 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~---------~~~~~~~l~~H~~~~~~~----~~~~C~~C~~ 104 (213)
.|.||. |..+......|..|.+..++ .+.|.+|-. .......|..|...-..+ ..-.|..|..
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 SFKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 378875 66666667788999887554 345666642 222334466776543322 2246999999
Q ss_pred ccCChhHHHHHHHHhhccCCCeeeecCccc----cccCCHHHHHHHHhhCCCCccccc--c--c--cccCChHHHHhHHh
Q psy4420 105 AAADSKSLRVHYKTHAKENGRRVYHCTICS----KRFYTKSKLDFHVNLHNLNYNCEV--C--E--KVFDKIEEFENHLS 174 (213)
Q Consensus 105 ~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~----~~f~~~~~l~~H~~~h~~~~~C~~--C--~--~~f~~~~~L~~H~~ 174 (213)
.|-+...|..|++..+ ++-+.|..-+ .-|.....|..|.+..+. .|.+ | | ..|.....|..|+.
T Consensus 229 ~FYdDDEL~~HcR~~H----E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy--~ct~qtc~~~k~~vf~~~~el~~h~~ 302 (493)
T COG5236 229 YFYDDDELRRHCRLRH----EACHICDMVGPIRYQYFKSYEDLEAHFRNAHY--CCTFQTCRVGKCYVFPYHTELLEHLT 302 (493)
T ss_pred eecChHHHHHHHHhhh----hhhhhhhccCccchhhhhCHHHHHHHhhcCce--EEEEEEEecCcEEEeccHHHHHHHHH
Confidence 9999999999999877 4445554332 347888899999876653 3322 2 1 47889999999998
Q ss_pred hcCCCC
Q psy4420 175 DNHIFT 180 (213)
Q Consensus 175 ~~h~~~ 180 (213)
.-|+..
T Consensus 303 ~~h~~~ 308 (493)
T COG5236 303 RFHKVN 308 (493)
T ss_pred HHhhcc
Confidence 888765
No 53
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.19 E-value=0.0049 Score=29.21 Aligned_cols=22 Identities=23% Similarity=0.434 Sum_probs=15.9
Q ss_pred eecccccccccCHHHHHHHHHH
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLK 62 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~ 62 (213)
|.|..|++.|.+...+..|++.
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 5677777777777777777653
No 54
>KOG2482|consensus
Probab=95.07 E-value=0.12 Score=40.06 Aligned_cols=132 Identities=16% Similarity=0.228 Sum_probs=70.7
Q ss_pred ceecccccccccCHHHHHHHHHH--hcCCCc--------eeccc--CcccccC-HHHHHHHHHhc-------------cC
Q psy4420 40 KYTCLLCKQKESQAWKIKRHYLK--HTQEKF--------FACSH--CDYKSAY-INDVKKHTRKH-------------TG 93 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~l~~H~~~--h~~~~~--------~~C~~--C~~~~~~-~~~l~~H~~~~-------------~~ 93 (213)
.+.|..|.+.|+++..|..||+. |....| |.-.. =|+.... .+...+-...- .+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 47888888888888888888875 333222 22211 1111110 01110000100 01
Q ss_pred CC--CeecCCCCcccCChhHHHHHHHHhhccCCCeeee--cCccccccCCHHHHHHHHhhCCCCccccccccccCChHHH
Q psy4420 94 EK--PFKCQICPYAAADSKSLRVHYKTHAKENGRRVYH--CTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEF 169 (213)
Q Consensus 94 ~~--~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~--C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L 169 (213)
.. ..+|..|.....+...|..|++.-+. -.+. =..-+-.|-+.-.+..-.+.....-.|-.|...|-....|
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe----~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l 350 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHE----FDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGL 350 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHH----hhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchh
Confidence 11 25788888888888888888876542 1000 0001122223333333333333356788888999999999
Q ss_pred HhHHhh
Q psy4420 170 ENHLSD 175 (213)
Q Consensus 170 ~~H~~~ 175 (213)
..||..
T Consensus 351 ~~hm~e 356 (423)
T KOG2482|consen 351 LIHMVE 356 (423)
T ss_pred hhhccc
Confidence 999955
No 55
>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=94.99 E-value=0.019 Score=28.91 Aligned_cols=23 Identities=26% Similarity=0.655 Sum_probs=18.3
Q ss_pred CccccccccccCChHHHHhHHhh
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSD 175 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~ 175 (213)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57788888888888888888754
No 56
>KOG1146|consensus
Probab=94.86 E-value=0.0088 Score=53.90 Aligned_cols=25 Identities=20% Similarity=0.525 Sum_probs=20.5
Q ss_pred CccccccccccCChHHHHhHHhhcC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNH 177 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h 177 (213)
.|.|.+|++.-+-..+|..||...+
T Consensus 589 ~~~C~vc~yetniarnlrihmtss~ 613 (1406)
T KOG1146|consen 589 SWRCEVCSYETNIARNLRIHMTASP 613 (1406)
T ss_pred CcchhhhcchhhhhhccccccccCC
Confidence 5889999988888888999886643
No 57
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.60 E-value=0.025 Score=31.35 Aligned_cols=35 Identities=20% Similarity=0.549 Sum_probs=27.4
Q ss_pred CccccccccccCChHHHHhHHhhcCCCCCCCCCCc
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHIFTYDHGTKD 187 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~~~~~~~~~~ 187 (213)
-++||.||..|....++.+|....|+-........
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~~~~r~k~~ 51 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGWLFGRGKPK 51 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhhhhcCCchh
Confidence 57888899989888888899888888776555443
No 58
>KOG4173|consensus
Probab=94.50 E-value=0.014 Score=41.81 Aligned_cols=72 Identities=26% Similarity=0.504 Sum_probs=39.0
Q ss_pred CCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHh-hC---------CC--Cccc--cccccccCChH
Q psy4420 102 CPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVN-LH---------NL--NYNC--EVCEKVFDKIE 167 (213)
Q Consensus 102 C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~-~h---------~~--~~~C--~~C~~~f~~~~ 167 (213)
|-..|.+...+..|..+-++ -.|..|.+.|.+.-.|..|+. .| .+ +|+| ..|+..|....
T Consensus 87 c~~~~d~lD~~E~hY~~~h~------~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r 160 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHG------NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSR 160 (253)
T ss_pred hHHHHhhhhhHHHhhhhccc------chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhh
Confidence 44555555555555443332 355666666666555555543 12 11 5666 44777777666
Q ss_pred HHHhHHhhcCCC
Q psy4420 168 EFENHLSDNHIF 179 (213)
Q Consensus 168 ~L~~H~~~~h~~ 179 (213)
.-..|+-..|..
T Consensus 161 ~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 161 DRKDHMIRMHKY 172 (253)
T ss_pred hhhhHHHHhccC
Confidence 666666555543
No 59
>KOG2482|consensus
Probab=94.31 E-value=0.1 Score=40.44 Aligned_cols=76 Identities=11% Similarity=0.155 Sum_probs=46.1
Q ss_pred eecccCcccccCHHHHHHHHHhccCCC--CeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHH
Q psy4420 69 FACSHCDYKSAYINDVKKHTRKHTGEK--PFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFH 146 (213)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~H~~~~~~~~--~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 146 (213)
..|.+|.....+...+..|+..-+.-. ..+-+. +..|-..-.+..-.+.. ...-.|-.|.-.|-....|..|
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~-~Ln~YqrvrviNyiRkq-----~~~~~c~~cd~~F~~e~~l~~h 353 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDY-SLNFYQRVRVINYIRKQ-----KKKSRCAECDLSFWKEPGLLIH 353 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhcccc-ccchhhhhhHHHHHHHH-----hhccccccccccccCcchhhhh
Confidence 489999999998899999987544210 011110 11122223333333332 2234677788899999999999
Q ss_pred HhhC
Q psy4420 147 VNLH 150 (213)
Q Consensus 147 ~~~h 150 (213)
+..+
T Consensus 354 m~e~ 357 (423)
T KOG2482|consen 354 MVED 357 (423)
T ss_pred cccc
Confidence 8654
No 60
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.89 E-value=0.06 Score=27.00 Aligned_cols=24 Identities=17% Similarity=0.400 Sum_probs=18.0
Q ss_pred CceecccccccccCHHHHHHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLK 62 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~ 62 (213)
.+|.|.+|+..|.....+..|+..
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 467788888888877777777753
No 61
>KOG1146|consensus
Probab=93.67 E-value=0.021 Score=51.63 Aligned_cols=51 Identities=18% Similarity=0.443 Sum_probs=36.8
Q ss_pred eeeecCccccccCCHHHHHHHHhhC---------------------------CCCccccccccccCChHHHHhHHhhc
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLH---------------------------NLNYNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h---------------------------~~~~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
+.+.|+.|+..|.....|..|++.. .++|.|..|...++.+..|.+|++.-
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~ 541 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSD 541 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHH
Confidence 4455666666666666666665541 12799999999999999999999764
No 62
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.38 E-value=0.12 Score=33.69 Aligned_cols=54 Identities=20% Similarity=0.398 Sum_probs=29.3
Q ss_pred ecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCCCccccccc
Q psy4420 98 KCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCE 160 (213)
Q Consensus 98 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~ 160 (213)
.|-.|+..|....... .... .....|+|+.|...|--.-..-.|...|. |+.|.
T Consensus 57 ~C~~C~~~f~~~~~~~---~~~~--~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~----CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSP---FDEL--KDSHRYVCAVCKNVFCVDCDVFVHESLHC----CPGCI 110 (112)
T ss_pred cccCcCCCCCCccccc---cccc--ccccceeCCCCCCccccccchhhhhhccC----CcCCC
Confidence 4777777776542100 0000 02456788888888776666555554443 66664
No 63
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.16 E-value=0.012 Score=47.85 Aligned_cols=141 Identities=19% Similarity=0.251 Sum_probs=87.3
Q ss_pred ceecccccccccCHHHHHHHHH--HhcCC--Cceecc--cCcccccCHHHHHHHHHhccCCCCeecCC--CCcccCChhH
Q psy4420 40 KYTCLLCKQKESQAWKIKRHYL--KHTQE--KFFACS--HCDYKSAYINDVKKHTRKHTGEKPFKCQI--CPYAAADSKS 111 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~~~~~~~l~~H~~~~~~~~~~~C~~--C~~~f~~~~~ 111 (213)
++.|..|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...|.+..++.+.. +...+.....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLN 368 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccccC
Confidence 5778888888888888888888 78888 888888 78888888888888888887776665543 2222222211
Q ss_pred HHHH--HHHhhccCCCeeeecCc--cccccCCHHHHHHHHhhCC----CCccccccccccCChHHHHhHHhhcCCCC
Q psy4420 112 LRVH--YKTHAKENGRRVYHCTI--CSKRFYTKSKLDFHVNLHN----LNYNCEVCEKVFDKIEEFENHLSDNHIFT 180 (213)
Q Consensus 112 l~~H--~~~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~----~~~~C~~C~~~f~~~~~L~~H~~~~h~~~ 180 (213)
-..+ ..............+.. |...+.....+..|...+- ..+.+..|.+.|.....+..|++.+....
T Consensus 369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (467)
T COG5048 369 NEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHA 445 (467)
T ss_pred CCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCC
Confidence 0000 00010000123333322 4444444444455544442 26778888888888888888887775554
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=92.98 E-value=0.058 Score=26.87 Aligned_cols=9 Identities=33% Similarity=0.921 Sum_probs=5.2
Q ss_pred CCccccccc
Q psy4420 152 LNYNCEVCE 160 (213)
Q Consensus 152 ~~~~C~~C~ 160 (213)
.++.||+||
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 455666665
No 65
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.76 E-value=0.13 Score=33.52 Aligned_cols=49 Identities=24% Similarity=0.304 Sum_probs=33.4
Q ss_pred ecCccccccCCHHHHHHHHhhCCCCccccccccccCChHHHHhHHhhcC
Q psy4420 129 HCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEFENHLSDNH 177 (213)
Q Consensus 129 ~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L~~H~~~~h 177 (213)
.|--|...|........-...-...|+|+.|...|-..-++-.|...|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccC
Confidence 5888999887653111000111337999999999998888888877663
No 66
>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=91.07 E-value=0.5 Score=30.79 Aligned_cols=26 Identities=19% Similarity=0.470 Sum_probs=24.3
Q ss_pred Cccc----cccccccCChHHHHhHHhhcCC
Q psy4420 153 NYNC----EVCEKVFDKIEEFENHLSDNHI 178 (213)
Q Consensus 153 ~~~C----~~C~~~f~~~~~L~~H~~~~h~ 178 (213)
.|.| +.|+....+...+.+|++.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4899 9999999999999999999986
No 67
>KOG2893|consensus
Probab=90.96 E-value=0.064 Score=39.41 Aligned_cols=40 Identities=30% Similarity=0.613 Sum_probs=20.5
Q ss_pred CCCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHH
Q psy4420 100 QICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFH 146 (213)
Q Consensus 100 ~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 146 (213)
=+|++.|.+...|++|++..+ |+|.+|.+..-+...|..|
T Consensus 14 wycnrefddekiliqhqkakh-------fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 14 WYCNREFDDEKILIQHQKAKH-------FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eecccccchhhhhhhhhhhcc-------ceeeeehhhhccCCCceee
Confidence 345566666655555554333 5555555554444444444
No 68
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.52 E-value=0.14 Score=28.47 Aligned_cols=24 Identities=21% Similarity=0.174 Sum_probs=12.9
Q ss_pred CceecccccccccCHHHHHHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLK 62 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~ 62 (213)
..+.||.|+..|.......+|+..
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhhH
Confidence 345555555555555555555543
No 69
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.47 E-value=0.25 Score=38.49 Aligned_cols=105 Identities=28% Similarity=0.597 Sum_probs=65.0
Q ss_pred eeccc--CcccccCHHHHHHHHHhccCCCCeecCCCCc---------ccCChhHHHHHHHHhhccCCCe-eeecCccccc
Q psy4420 69 FACSH--CDYKSAYINDVKKHTRKHTGEKPFKCQICPY---------AAADSKSLRVHYKTHAKENGRR-VYHCTICSKR 136 (213)
Q Consensus 69 ~~C~~--C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~---------~f~~~~~l~~H~~~~~~~~~~~-~~~C~~C~~~ 136 (213)
|.|+. |...-...-.|..|....++ .+.|..|-. ...+...|..|...--.+.|-+ .-.|..|...
T Consensus 152 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 152 FKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 66764 55555556678888776665 356655432 2333445666644322211222 2358889999
Q ss_pred cCCHHHHHHHHhhCCCCccccccc-------cccCChHHHHhHHhhcC
Q psy4420 137 FYTKSKLDFHVNLHNLNYNCEVCE-------KVFDKIEEFENHLSDNH 177 (213)
Q Consensus 137 f~~~~~l~~H~~~h~~~~~C~~C~-------~~f~~~~~L~~H~~~~h 177 (213)
|.+.+.|..|.+..+. .|-+|+ .-|....+|-.|.+..|
T Consensus 230 FYdDDEL~~HcR~~HE--~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h 275 (493)
T COG5236 230 FYDDDELRRHCRLRHE--ACHICDMVGPIRYQYFKSYEDLEAHFRNAH 275 (493)
T ss_pred ecChHHHHHHHHhhhh--hhhhhhccCccchhhhhCHHHHHHHhhcCc
Confidence 9999999999886553 444444 45777888889987765
No 70
>KOG2893|consensus
Probab=89.63 E-value=0.084 Score=38.83 Aligned_cols=49 Identities=22% Similarity=0.406 Sum_probs=36.7
Q ss_pred cCccccccCCHHHHHHHHhhCCCCccccccccccCChHHHHhHHhhcCCCC
Q psy4420 130 CTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEFENHLSDNHIFT 180 (213)
Q Consensus 130 C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L~~H~~~~h~~~ 180 (213)
|=.|++.|-....|..|++..+ |+|-+|-|..-+...|..|-..+|.+.
T Consensus 13 cwycnrefddekiliqhqkakh--fkchichkkl~sgpglsihcmqvhket 61 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH--FKCHICHKKLFSGPGLSIHCMQVHKET 61 (341)
T ss_pred eeecccccchhhhhhhhhhhcc--ceeeeehhhhccCCCceeehhhhhhhh
Confidence 5567888888888877776655 688888877777777888777777664
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.07 E-value=0.42 Score=24.46 Aligned_cols=11 Identities=27% Similarity=0.570 Sum_probs=5.2
Q ss_pred ecccccccccC
Q psy4420 42 TCLLCKQKESQ 52 (213)
Q Consensus 42 ~C~~C~~~f~~ 52 (213)
+||.|+..|.-
T Consensus 4 ~CP~C~~~f~v 14 (37)
T PF13719_consen 4 TCPNCQTRFRV 14 (37)
T ss_pred ECCCCCceEEc
Confidence 34555544443
No 72
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.96 E-value=0.26 Score=32.06 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=15.8
Q ss_pred eecccccccccCHHHHHHHHHHhcCCCceecccCcccccCH
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYI 81 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 81 (213)
..|+.||+.|... +..|..|+.||..|...
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 3466666666541 22455566666555433
No 73
>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=88.58 E-value=0.16 Score=33.02 Aligned_cols=29 Identities=21% Similarity=0.502 Sum_probs=19.3
Q ss_pred ecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCCh
Q psy4420 70 ACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADS 109 (213)
Q Consensus 70 ~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 109 (213)
.|+.||++|.-. +..|..|++||..|.-.
T Consensus 11 ~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 577787777542 22567788887777655
No 74
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.50 E-value=0.43 Score=27.01 Aligned_cols=31 Identities=16% Similarity=0.427 Sum_probs=13.1
Q ss_pred eeecCccccccCCHHHHHHHHhhCCCCccccccc
Q psy4420 127 VYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCE 160 (213)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~ 160 (213)
.|.|+.||..-..... --+.+..+|+|+.||
T Consensus 27 ~F~CPnCGe~~I~Rc~---~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 27 KFPCPNCGEVEIYRCA---KCRKLGNPYRCPKCG 57 (61)
T ss_pred EeeCCCCCceeeehhh---hHHHcCCceECCCcC
Confidence 3555555544333321 112333455555555
No 75
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=88.08 E-value=1.3 Score=28.80 Aligned_cols=24 Identities=25% Similarity=0.797 Sum_probs=20.1
Q ss_pred eec----CCCCcccCChhHHHHHHHHhh
Q psy4420 97 FKC----QICPYAAADSKSLRVHYKTHA 120 (213)
Q Consensus 97 ~~C----~~C~~~f~~~~~l~~H~~~~~ 120 (213)
|.| ..|+....+...+..|++.++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 788 888888888888888888765
No 76
>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=87.30 E-value=0.57 Score=23.96 Aligned_cols=6 Identities=50% Similarity=1.159 Sum_probs=2.2
Q ss_pred cccccc
Q psy4420 43 CLLCKQ 48 (213)
Q Consensus 43 C~~C~~ 48 (213)
|+.|+.
T Consensus 5 CP~C~~ 10 (38)
T TIGR02098 5 CPNCKT 10 (38)
T ss_pred CCCCCC
Confidence 333333
No 77
>KOG4173|consensus
Probab=86.83 E-value=0.28 Score=35.29 Aligned_cols=101 Identities=22% Similarity=0.403 Sum_probs=71.2
Q ss_pred ccccCHHHHHHHHHHh------------cCCCceeccc--CcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHH
Q psy4420 48 QKESQAWKIKRHYLKH------------TQEKFFACSH--CDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLR 113 (213)
Q Consensus 48 ~~f~~~~~l~~H~~~h------------~~~~~~~C~~--C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~ 113 (213)
..|...++.++|+... .....+.|+. |...|.+..+...|...-++ ..|..|.++|.+...|.
T Consensus 47 ~pFf~~G~v~r~l~~~~V~~d~~d~~~~~~~~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd 123 (253)
T KOG4173|consen 47 HPFFEDGDVQRHLYLQDVIMDVADVPEKPRVPAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLD 123 (253)
T ss_pred CcchhcccHHHHHhHhhheeeccccccccccccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhh
Confidence 4455666677776422 1223367875 77888888888888766554 47999999999999999
Q ss_pred HHHHHhhc-------cCCCeeeecCc--cccccCCHHHHHHHHhhCC
Q psy4420 114 VHYKTHAK-------ENGRRVYHCTI--CSKRFYTKSKLDFHVNLHN 151 (213)
Q Consensus 114 ~H~~~~~~-------~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~ 151 (213)
.|+...+. +.|.-.|+|-+ |+..|.+......|+-.-+
T Consensus 124 ~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 124 AHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred HHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 99765432 11456699964 9999999988888875443
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.79 E-value=0.079 Score=39.10 Aligned_cols=14 Identities=14% Similarity=0.218 Sum_probs=11.0
Q ss_pred CccccccccccCCh
Q psy4420 153 NYNCEVCEKVFDKI 166 (213)
Q Consensus 153 ~~~C~~C~~~f~~~ 166 (213)
.+.||.||.++...
T Consensus 48 V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 48 VWVCPHCGYAAFEE 61 (214)
T ss_pred EEECCCCCCccccc
Confidence 46899999877654
No 79
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.76 E-value=0.67 Score=23.53 Aligned_cols=9 Identities=33% Similarity=0.730 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy4420 43 CLLCKQKES 51 (213)
Q Consensus 43 C~~C~~~f~ 51 (213)
|+.|+..|.
T Consensus 5 Cp~C~~~y~ 13 (36)
T PF13717_consen 5 CPNCQAKYE 13 (36)
T ss_pred CCCCCCEEe
Confidence 444444443
No 80
>PHA00626 hypothetical protein
Probab=86.71 E-value=0.22 Score=27.76 Aligned_cols=17 Identities=24% Similarity=0.223 Sum_probs=11.7
Q ss_pred CCCCccccccccccCCh
Q psy4420 150 HNLNYNCEVCEKVFDKI 166 (213)
Q Consensus 150 h~~~~~C~~C~~~f~~~ 166 (213)
+...|.|+.||..|+.-
T Consensus 20 ~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 20 WSDDYVCCDCGYNDSKD 36 (59)
T ss_pred cCcceEcCCCCCeechh
Confidence 34478888888777543
No 81
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.16 E-value=0.15 Score=41.47 Aligned_cols=158 Identities=18% Similarity=0.164 Sum_probs=98.1
Q ss_pred CccccCcc---chhhhhhhhhhh--hcccccccCCCceecc--cccccccCHHHHHHHHHHhcCCCceeccc--Cccccc
Q psy4420 9 SKLICSFC---LEEVDNSALKMF--EHNCDGVLNARKYTCL--LCKQKESQAWKIKRHYLKHTQEKFFACSH--CDYKSA 79 (213)
Q Consensus 9 ~~~~C~~C---f~~~~~l~~h~~--~h~~~~~~~~~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~~~ 79 (213)
..+.|..| |.....+..|.. .|..+. ..++.|+ .|++.|.....+..|...|.+..+..+.. +...+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~---~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 364 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGES---LKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFS 364 (467)
T ss_pred cCCCCccccCCcccccccccccccccccccc---CCceeeeccCCCccccccccccCCcccccCCCccccccccCccccc
Confidence 46778888 888888999998 566663 2689999 89999999999999999999888776644 333333
Q ss_pred CHHHHHHHHH-----hccCCCCeecC--CCCcccCChhHHHHHHHHhhccCCCeeeecCccccccCCHHHHHHHHhhCCC
Q psy4420 80 YINDVKKHTR-----KHTGEKPFKCQ--ICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKRFYTKSKLDFHVNLHNL 152 (213)
Q Consensus 80 ~~~~l~~H~~-----~~~~~~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 152 (213)
.......+.. .-.......+. .|...+.....+..|...+... +...+.+..|.+.+.....+..|.+.+..
T Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 (467)
T COG5048 365 PLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSF-RPYNCKNPPCSKSFNRHYNLIPHKKIHTN 443 (467)
T ss_pred cccCCCCccchhhccCccCCccccccccchhhhhcccccccccccccccc-CCcCCCCCcchhhccCccccccccccccc
Confidence 3222110111 11112223332 3555566666666665555431 12346677899999999888888888743
Q ss_pred -CccccccccccCChHHHH
Q psy4420 153 -NYNCEVCEKVFDKIEEFE 170 (213)
Q Consensus 153 -~~~C~~C~~~f~~~~~L~ 170 (213)
..-+..+-..|.....+.
T Consensus 444 ~~~~~~~~~~~~~~~~~~~ 462 (467)
T COG5048 444 HAPLLCSILKSFRRDLDLS 462 (467)
T ss_pred CCceeeccccccchhhhhh
Confidence 233333333444433333
No 82
>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=85.63 E-value=0.46 Score=23.81 Aligned_cols=10 Identities=20% Similarity=0.803 Sum_probs=4.6
Q ss_pred eecCcccccc
Q psy4420 128 YHCTICSKRF 137 (213)
Q Consensus 128 ~~C~~C~~~f 137 (213)
|.|..||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 4455555443
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=85.07 E-value=0.27 Score=36.76 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=13.7
Q ss_pred CCCeecCCCCcccCChhHHHHHHHH
Q psy4420 94 EKPFKCQICPYAAADSKSLRVHYKT 118 (213)
Q Consensus 94 ~~~~~C~~C~~~f~~~~~l~~H~~~ 118 (213)
.++++||.|+........|....++
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRS 231 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeec
Confidence 3566677776665555444443333
No 84
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=84.79 E-value=0.55 Score=32.91 Aligned_cols=33 Identities=15% Similarity=0.256 Sum_probs=25.6
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccC
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAY 80 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~ 80 (213)
..|.|+.|+..|.....+. ..|.|+.||.....
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 6789999998888777664 25899999976543
No 85
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=84.41 E-value=0.71 Score=24.55 Aligned_cols=22 Identities=27% Similarity=0.611 Sum_probs=9.2
Q ss_pred ccccccccccCCh----HHHHhHHhh
Q psy4420 154 YNCEVCEKVFDKI----EEFENHLSD 175 (213)
Q Consensus 154 ~~C~~C~~~f~~~----~~L~~H~~~ 175 (213)
.+|..|++.+... +.|.+|++.
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 4555555544442 455555533
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.51 E-value=0.8 Score=25.99 Aligned_cols=31 Identities=16% Similarity=0.474 Sum_probs=13.9
Q ss_pred eeecCccccccCCHHHHHHHHhhCCCCccccccc
Q psy4420 127 VYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCE 160 (213)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~ 160 (213)
.|.|+.||..-...- ..-+....+|.|+.||
T Consensus 25 ~F~CPnCG~~~I~RC---~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 25 KFLCPNCGEVIIYRC---EKCRKQSNPYTCPKCG 55 (59)
T ss_pred EeeCCCCCCeeEeec---hhHHhcCCceECCCCC
Confidence 355555554422221 1223334456666655
No 87
>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=83.32 E-value=0.99 Score=21.05 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=14.0
Q ss_pred ccccccccccCChHHHHhHHh
Q psy4420 154 YNCEVCEKVFDKIEEFENHLS 174 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~ 174 (213)
..||+|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3688888877 5567777764
No 88
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.99 E-value=0.41 Score=29.43 Aligned_cols=32 Identities=16% Similarity=0.412 Sum_probs=21.5
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCCCccccccccccCC
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDK 165 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~ 165 (213)
..|.|+.|++. .+.++-.+-|+|..||..|.-
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccCeEEcCCCCCeecc
Confidence 45778888754 234556667888888877753
No 89
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.73 E-value=0.88 Score=32.56 Aligned_cols=33 Identities=15% Similarity=0.260 Sum_probs=24.8
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccC
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAY 80 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~ 80 (213)
..|.|+.|+..|.....+. ..|.|+.||.....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 6788999998887766543 25889999976544
No 90
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.61 E-value=0.77 Score=32.87 Aligned_cols=34 Identities=18% Similarity=0.684 Sum_probs=25.9
Q ss_pred CeeeecCccccccCCHHHHHHHHhhCCCCccccccccccCC
Q psy4420 125 RRVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDK 165 (213)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~ 165 (213)
..-|.|+.|+..|+....+. ..|.|+.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~-------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME-------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh-------cCCcCCCCCCCCee
Confidence 45688999999998887764 37999999965433
No 91
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=82.49 E-value=3.1 Score=28.75 Aligned_cols=14 Identities=21% Similarity=0.951 Sum_probs=7.7
Q ss_pred CceecccCcccccC
Q psy4420 67 KFFACSHCDYKSAY 80 (213)
Q Consensus 67 ~~~~C~~C~~~~~~ 80 (213)
..|.|+.|+..|..
T Consensus 98 ~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 98 AYYKCPNCQSKYTF 111 (147)
T ss_pred cEEECcCCCCEeeH
Confidence 34556666655553
No 92
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=82.14 E-value=0.89 Score=31.42 Aligned_cols=35 Identities=14% Similarity=0.482 Sum_probs=16.5
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCCCccccccccc
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKV 162 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~ 162 (213)
.-|.|+.|+..|.....+..- . ..+.|.|+.||..
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~-d-~~~~f~Cp~Cg~~ 132 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLL-D-MDGTFTCPRCGEE 132 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhc-C-CCCcEECCCCCCE
Confidence 345566666665544332220 0 1334666666643
No 93
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.08 E-value=0.91 Score=24.26 Aligned_cols=24 Identities=25% Similarity=0.548 Sum_probs=12.4
Q ss_pred eecCccccccCCHHHHHHHHhhCCCCccccccc
Q psy4420 128 YHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCE 160 (213)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~ 160 (213)
|.|..||..|.-. -..+.+|+.||
T Consensus 3 Y~C~~Cg~~~~~~---------~~~~irC~~CG 26 (44)
T smart00659 3 YICGECGRENEIK---------SKDVVRCRECG 26 (44)
T ss_pred EECCCCCCEeecC---------CCCceECCCCC
Confidence 5566666555422 12355666665
No 94
>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=81.75 E-value=0.3 Score=25.39 Aligned_cols=12 Identities=33% Similarity=0.905 Sum_probs=6.7
Q ss_pred eecCccccccCC
Q psy4420 128 YHCTICSKRFYT 139 (213)
Q Consensus 128 ~~C~~C~~~f~~ 139 (213)
|.|+.||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 556666655543
No 95
>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=81.34 E-value=2.7 Score=29.46 Aligned_cols=31 Identities=19% Similarity=0.481 Sum_probs=15.6
Q ss_pred CceecccCcccccCHHHHHHHHHhccCCCCeecCCCCccc
Q psy4420 67 KFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAA 106 (213)
Q Consensus 67 ~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 106 (213)
..|.|+.|+..|.....+. ..|.|+.||...
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 4455655655555444432 135555555543
No 96
>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=80.09 E-value=0.4 Score=26.52 Aligned_cols=29 Identities=31% Similarity=0.657 Sum_probs=14.0
Q ss_pred eecCccccccCCHHHHHHHHhhCCCCcccccccc
Q psy4420 128 YHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEK 161 (213)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~ 161 (213)
|.|..||..|.....+.. .....|+.||-
T Consensus 6 y~C~~Cg~~fe~~~~~~~-----~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-----DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCC-----CCCCCCCCCCC
Confidence 556666665554322111 23445666663
No 97
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=79.65 E-value=1.4 Score=24.17 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=9.3
Q ss_pred cccccccccCCh-----HHHHhHHh
Q psy4420 155 NCEVCEKVFDKI-----EEFENHLS 174 (213)
Q Consensus 155 ~C~~C~~~f~~~-----~~L~~H~~ 174 (213)
.|..|++.++.. +.|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 444444444332 35555554
No 98
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.58 E-value=0.29 Score=36.18 Aligned_cols=20 Identities=20% Similarity=0.320 Sum_probs=13.5
Q ss_pred CceecccccccccCHHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKR 58 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~ 58 (213)
+..+||+|+..|..+.....
T Consensus 4 k~~~CPvC~~~F~~~~vrs~ 23 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSG 23 (214)
T ss_pred CceECCCCCCeeeeeEEEcC
Confidence 56778888888876654333
No 99
>KOG2785|consensus
Probab=78.95 E-value=2.9 Score=33.28 Aligned_cols=74 Identities=23% Similarity=0.307 Sum_probs=50.4
Q ss_pred eecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccc---cccCCHHHHHH
Q psy4420 69 FACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICS---KRFYTKSKLDF 145 (213)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~---~~f~~~~~l~~ 145 (213)
-.|.+|++.+........|+..++|- |..+. ....+...|..-+.... ...+.|-.|. +.|.+....+.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~Hgf--fIPdr--eYL~D~~GLl~YLgeKV----~~~~~CL~CN~~~~~f~sleavr~ 238 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGF--FIPDR--EYLTDEKGLLKYLGEKV----GIGFICLFCNELGRPFSSLEAVRA 238 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCC--cCCch--HhhhchhHHHHHHHHHh----ccCceEEEeccccCcccccHHHHH
Confidence 46999999999998899999988862 22221 12234455555555444 3556777777 77888888888
Q ss_pred HHhhC
Q psy4420 146 HVNLH 150 (213)
Q Consensus 146 H~~~h 150 (213)
|+...
T Consensus 239 HM~~K 243 (390)
T KOG2785|consen 239 HMRDK 243 (390)
T ss_pred HHhhc
Confidence 88654
No 100
>KOG2186|consensus
Probab=77.88 E-value=1.9 Score=32.24 Aligned_cols=49 Identities=20% Similarity=0.492 Sum_probs=34.2
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHHHHHHHHh
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYINDVKKHTRK 90 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~ 90 (213)
..|+|..||...+... +..|+..-++ .-|.|.-|++.|.. .++..|..-
T Consensus 2 V~FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 2 VFFTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred eEEehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 4578888888776544 6668766555 55788888888876 556677553
No 101
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=77.86 E-value=1.7 Score=28.91 Aligned_cols=13 Identities=0% Similarity=-0.230 Sum_probs=6.4
Q ss_pred CceecccCccccc
Q psy4420 67 KFFACSHCDYKSA 79 (213)
Q Consensus 67 ~~~~C~~C~~~~~ 79 (213)
.|..|+.||..|.
T Consensus 25 ~p~vcP~cg~~~~ 37 (129)
T TIGR02300 25 RPAVSPYTGEQFP 37 (129)
T ss_pred CCccCCCcCCccC
Confidence 3445555555443
No 102
>PF15269 zf-C2H2_7: Zinc-finger
Probab=77.73 E-value=1.5 Score=23.21 Aligned_cols=24 Identities=21% Similarity=0.462 Sum_probs=20.1
Q ss_pred CccccccccccCChHHHHhHHhhc
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
.|+|-.|.-+...++.|-.||+-.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 478999998999999999998653
No 103
>KOG2186|consensus
Probab=77.65 E-value=2 Score=32.14 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=30.2
Q ss_pred cccCcc--chhhhhhhhhhhhcccccccCCCceecccccccccCHHHHHHHHHHhc
Q psy4420 11 LICSFC--LEEVDNSALKMFEHNCDGVLNARKYTCLLCKQKESQAWKIKRHYLKHT 64 (213)
Q Consensus 11 ~~C~~C--f~~~~~l~~h~~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 64 (213)
|.|..| .--...+.+|+.+.+.. -|.|--|++.|.. .....|...-.
T Consensus 4 FtCnvCgEsvKKp~vekH~srCrn~------~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRCRNA------YFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred EehhhhhhhccccchHHHHHhccCC------eeEEeeccccccc-chhhhhhhhcc
Confidence 567777 23344567777766543 6778888888877 55666665433
No 104
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=76.31 E-value=1.8 Score=30.53 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.5
Q ss_pred ceeccccccc
Q psy4420 40 KYTCLLCKQK 49 (213)
Q Consensus 40 ~~~C~~C~~~ 49 (213)
-|.|++||.+
T Consensus 134 ~~vC~vCGy~ 143 (166)
T COG1592 134 VWVCPVCGYT 143 (166)
T ss_pred EEEcCCCCCc
Confidence 4556666554
No 105
>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=75.66 E-value=0.49 Score=24.97 Aligned_cols=12 Identities=33% Similarity=0.952 Sum_probs=5.9
Q ss_pred eecCccccccCC
Q psy4420 128 YHCTICSKRFYT 139 (213)
Q Consensus 128 ~~C~~C~~~f~~ 139 (213)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 455555544443
No 106
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=75.38 E-value=1.1 Score=32.97 Aligned_cols=29 Identities=24% Similarity=0.529 Sum_probs=19.9
Q ss_pred CccccccccccCChHHHHhHHhhcCCCCC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHIFTY 181 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~~~~ 181 (213)
.|.|+.|+|.|.-..-+.+|+...|.+..
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e~v 105 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPEKV 105 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HHHH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHHHH
Confidence 57888888888888888888877777653
No 107
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=74.19 E-value=2.6 Score=28.54 Aligned_cols=23 Identities=35% Similarity=0.579 Sum_probs=9.3
Q ss_pred ceecccccccccCHHHHHHHHHHhcC
Q psy4420 40 KYTCLLCKQKESQAWKIKRHYLKHTQ 65 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 65 (213)
...|.+||+.|+. |.+|++.|+|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-
T ss_pred eeEEccCCcccch---HHHHHHHccC
Confidence 3445555555554 3455555544
No 108
>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=74.14 E-value=1.8 Score=29.30 Aligned_cols=25 Identities=32% Similarity=0.563 Sum_probs=14.6
Q ss_pred CccccccccccCChHHHHhHHhhcCCCC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHIFT 180 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~~~ 180 (213)
-..|-+||+.|.. |.+|++.|||-.
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred eeEEccCCcccch---HHHHHHHccCCC
Confidence 4678888888865 478888887764
No 109
>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=70.89 E-value=2 Score=20.03 Aligned_cols=9 Identities=33% Similarity=0.689 Sum_probs=5.1
Q ss_pred ccccccccc
Q psy4420 155 NCEVCEKVF 163 (213)
Q Consensus 155 ~C~~C~~~f 163 (213)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455565555
No 110
>KOG2807|consensus
Probab=70.05 E-value=12 Score=29.38 Aligned_cols=32 Identities=34% Similarity=0.744 Sum_probs=21.9
Q ss_pred CeeeecCccccccCCHHHHHHHHhhCCCCccccccc
Q psy4420 125 RRVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCE 160 (213)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~ 160 (213)
...|.|..|...|-..-..-.|...| .|+.|.
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHesLh----~CpgCe 374 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHESLH----NCPGCE 374 (378)
T ss_pred CCcEEchhccceeeccchHHHHhhhh----cCCCcC
Confidence 45589999998887776655555444 566665
No 111
>PF14353 CpXC: CpXC protein
Probab=69.42 E-value=1.9 Score=28.93 Aligned_cols=24 Identities=17% Similarity=0.397 Sum_probs=17.1
Q ss_pred CccccccccccCChHHHHhHHhhc
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
.|.||.||..|.-...+..|-..+
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCC
Confidence 678888888777776666665554
No 112
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=67.00 E-value=2.1 Score=29.79 Aligned_cols=17 Identities=24% Similarity=0.552 Sum_probs=11.1
Q ss_pred CceecccccccccCHHH
Q psy4420 39 RKYTCLLCKQKESQAWK 55 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~ 55 (213)
+.++|+.||.+|...-.
T Consensus 27 ~~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 27 RRRECLACGKRFTTFER 43 (154)
T ss_pred eeeeccccCCcceEeEe
Confidence 34778888877765433
No 113
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=65.72 E-value=1.3 Score=26.40 Aligned_cols=41 Identities=17% Similarity=0.446 Sum_probs=19.7
Q ss_pred eecCccccccCCHHHHHHHHhhCCCCcccc--ccccccCChHH
Q psy4420 128 YHCTICSKRFYTKSKLDFHVNLHNLNYNCE--VCEKVFDKIEE 168 (213)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~--~C~~~f~~~~~ 168 (213)
+.|+.||.......+-.....+-..-++|. .||..|...-.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEEE
Confidence 456666655432222222222223346676 67777765433
No 114
>KOG2907|consensus
Probab=65.40 E-value=5 Score=26.07 Aligned_cols=10 Identities=40% Similarity=1.278 Sum_probs=5.7
Q ss_pred eecccCcccc
Q psy4420 69 FACSHCDYKS 78 (213)
Q Consensus 69 ~~C~~C~~~~ 78 (213)
|.|+-|+..|
T Consensus 103 YTC~kC~~k~ 112 (116)
T KOG2907|consen 103 YTCPKCKYKF 112 (116)
T ss_pred EEcCccceee
Confidence 5666665554
No 115
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=64.68 E-value=2.6 Score=32.59 Aligned_cols=47 Identities=21% Similarity=0.401 Sum_probs=29.2
Q ss_pred cCccccccCCHHHHHHHHhhCCCCccccccccccCChHHHHhHHhhc
Q psy4420 130 CTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 130 C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
|-.|...|.-...-..-..+....|+|+.|...|-.--..-.|...|
T Consensus 365 Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 365 CFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 66666666544321111112234789999988888888887887665
No 116
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=64.29 E-value=3 Score=21.72 Aligned_cols=16 Identities=19% Similarity=0.165 Sum_probs=6.8
Q ss_pred eecccccccccCHHHH
Q psy4420 41 YTCLLCKQKESQAWKI 56 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l 56 (213)
..|+.|+..|-+...|
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 3344444444444433
No 117
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=64.15 E-value=7 Score=22.01 Aligned_cols=39 Identities=13% Similarity=0.345 Sum_probs=17.4
Q ss_pred ceeccc--ccccccCHHHHHHHHHHhcCCCceeccc----Cccccc
Q psy4420 40 KYTCLL--CKQKESQAWKIKRHYLKHTQEKFFACSH----CDYKSA 79 (213)
Q Consensus 40 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~~~ 79 (213)
+..|+. |...+. +..|..|+...-...+..|++ |+..+.
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 445655 434333 234566665555555556666 555443
No 118
>KOG2593|consensus
Probab=63.27 E-value=5.5 Score=32.40 Aligned_cols=35 Identities=23% Similarity=0.510 Sum_probs=23.0
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcc
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDY 76 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 76 (213)
..|.||.|.+.|..-..++ ..-.....|.|..|+.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 6788888888886544333 3333455788888874
No 119
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.12 E-value=4.8 Score=22.02 Aligned_cols=10 Identities=30% Similarity=1.105 Sum_probs=4.2
Q ss_pred eecCcccccc
Q psy4420 128 YHCTICSKRF 137 (213)
Q Consensus 128 ~~C~~C~~~f 137 (213)
|.|..||+.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 3444444443
No 120
>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=61.70 E-value=5.1 Score=33.22 Aligned_cols=27 Identities=26% Similarity=0.527 Sum_probs=15.9
Q ss_pred ccccccccccCChHHHHhHHhhcCCCC
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSDNHIFT 180 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~~h~~~ 180 (213)
+.|+.|.+.|.....+..|+...|...
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 456666666666666666665555443
No 121
>KOG4167|consensus
Probab=61.25 E-value=2.7 Score=36.45 Aligned_cols=27 Identities=19% Similarity=0.242 Sum_probs=24.2
Q ss_pred CceecccccccccCHHHHHHHHHHhcC
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQ 65 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 65 (213)
.-|.|.+|++.|....++..||++|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 569999999999999999999999853
No 122
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=60.22 E-value=21 Score=24.96 Aligned_cols=9 Identities=33% Similarity=1.198 Sum_probs=5.9
Q ss_pred cccCccchh
Q psy4420 11 LICSFCLEE 19 (213)
Q Consensus 11 ~~C~~Cf~~ 19 (213)
..|++|+..
T Consensus 3 ~~CpICme~ 11 (162)
T PF07800_consen 3 VTCPICMEH 11 (162)
T ss_pred ccCceeccC
Confidence 468999433
No 123
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.44 E-value=9.5 Score=34.73 Aligned_cols=8 Identities=25% Similarity=0.721 Sum_probs=3.6
Q ss_pred eecccccc
Q psy4420 41 YTCLLCKQ 48 (213)
Q Consensus 41 ~~C~~C~~ 48 (213)
..|+.||.
T Consensus 627 RfCpsCG~ 634 (1121)
T PRK04023 627 RKCPSCGK 634 (1121)
T ss_pred ccCCCCCC
Confidence 34444444
No 124
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=58.68 E-value=4.8 Score=27.04 Aligned_cols=15 Identities=33% Similarity=0.603 Sum_probs=9.9
Q ss_pred eeecCccccccCCHH
Q psy4420 127 VYHCTICSKRFYTKS 141 (213)
Q Consensus 127 ~~~C~~C~~~f~~~~ 141 (213)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 356777777776654
No 125
>PF12907 zf-met2: Zinc-binding
Probab=57.66 E-value=8.7 Score=20.03 Aligned_cols=27 Identities=19% Similarity=0.552 Sum_probs=20.0
Q ss_pred cccccccccc---CChHHHHhHHhhcCCCC
Q psy4420 154 YNCEVCEKVF---DKIEEFENHLSDNHIFT 180 (213)
Q Consensus 154 ~~C~~C~~~f---~~~~~L~~H~~~~h~~~ 180 (213)
++|.+|-.+| .+...|..|....|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 6788898555 44567999988877664
No 126
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=57.00 E-value=3.9 Score=21.25 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=8.3
Q ss_pred Cceeccccccccc
Q psy4420 39 RKYTCLLCKQKES 51 (213)
Q Consensus 39 ~~~~C~~C~~~f~ 51 (213)
.-|.|..|+..|.
T Consensus 27 ~fy~C~~C~~~w~ 39 (40)
T smart00440 27 VFYVCTKCGHRWR 39 (40)
T ss_pred EEEEeCCCCCEeC
Confidence 4567777776654
No 127
>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=56.05 E-value=6.6 Score=17.94 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=7.7
Q ss_pred Cceecccccc
Q psy4420 39 RKYTCLLCKQ 48 (213)
Q Consensus 39 ~~~~C~~C~~ 48 (213)
..|.||.||.
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 5788888873
No 128
>KOG3408|consensus
Probab=54.26 E-value=10 Score=25.04 Aligned_cols=27 Identities=19% Similarity=0.407 Sum_probs=22.3
Q ss_pred cCCCceecccccccccCHHHHHHHHHH
Q psy4420 36 LNARKYTCLLCKQKESQAWKIKRHYLK 62 (213)
Q Consensus 36 ~~~~~~~C~~C~~~f~~~~~l~~H~~~ 62 (213)
++...|.|-.|.+-|.+...|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 445678899999999999999988875
No 129
>PF14369 zf-RING_3: zinc-finger
Probab=53.65 E-value=6.3 Score=19.82 Aligned_cols=10 Identities=20% Similarity=0.424 Sum_probs=7.3
Q ss_pred eccccccccc
Q psy4420 42 TCLLCKQKES 51 (213)
Q Consensus 42 ~C~~C~~~f~ 51 (213)
.||.|+..|-
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4888887763
No 130
>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=53.37 E-value=11 Score=27.78 Aligned_cols=26 Identities=19% Similarity=0.415 Sum_probs=13.5
Q ss_pred CeeeecCccccccCCHHHHHHHHhhC
Q psy4420 125 RRVYHCTICSKRFYTKSKLDFHVNLH 150 (213)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h 150 (213)
+..|.|+.|+|.|....-...|+...
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhc
Confidence 34466666666666665555665443
No 131
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=53.25 E-value=3.3 Score=21.39 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=8.4
Q ss_pred Cceecccccccc
Q psy4420 39 RKYTCLLCKQKE 50 (213)
Q Consensus 39 ~~~~C~~C~~~f 50 (213)
.-|.|..|+..|
T Consensus 27 ~fy~C~~C~~~w 38 (39)
T PF01096_consen 27 LFYVCCNCGHRW 38 (39)
T ss_dssp EEEEESSSTEEE
T ss_pred EEEEeCCCCCee
Confidence 457788887765
No 132
>KOG4124|consensus
Probab=52.65 E-value=1.7 Score=34.18 Aligned_cols=56 Identities=27% Similarity=0.684 Sum_probs=41.2
Q ss_pred CeeeecCc--cccccCCHHHHHHHHhhC---------------------CCCccccccccccCChHHHHhHHhhcCCCC
Q psy4420 125 RRVYHCTI--CSKRFYTKSKLDFHVNLH---------------------NLNYNCEVCEKVFDKIEEFENHLSDNHIFT 180 (213)
Q Consensus 125 ~~~~~C~~--C~~~f~~~~~l~~H~~~h---------------------~~~~~C~~C~~~f~~~~~L~~H~~~~h~~~ 180 (213)
.++|.|++ |.+.+.....|..|...- .++|+|++|.+.+.....|.-|....|-..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~~~~~~~ 425 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRTHSHLQV 425 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceeehhhhhh
Confidence 46788875 888888777777765422 247999999999998888877765555444
No 133
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=51.95 E-value=10 Score=25.61 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=15.2
Q ss_pred eecccccccccCHHHHHHHHHHhcCCCc
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLKHTQEKF 68 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 68 (213)
..|.++|+.|+ +|++|+.+|.+-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 55667777664 36667666665433
No 134
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=51.86 E-value=3.2 Score=25.96 Aligned_cols=32 Identities=22% Similarity=0.489 Sum_probs=18.1
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCCCccccccccccCC
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDK 165 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~ 165 (213)
..|.|+.|++.-. .+.-.+.|+|..|++.|.-
T Consensus 34 a~y~CpfCgk~~v--------kR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTV--------KRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCce--------EEEeeEEEEcCCCCCEEeC
Confidence 4477777764311 1233456777777776644
No 135
>KOG2807|consensus
Probab=51.69 E-value=24 Score=27.78 Aligned_cols=25 Identities=16% Similarity=0.388 Sum_probs=19.9
Q ss_pred CCeecCCCCcccCChhHHHHHHHHh
Q psy4420 95 KPFKCQICPYAAADSKSLRVHYKTH 119 (213)
Q Consensus 95 ~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (213)
..|.|..|...|-..-+.-.|-..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 4589999999998888877776655
No 136
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=51.61 E-value=11 Score=28.24 Aligned_cols=58 Identities=17% Similarity=0.352 Sum_probs=35.6
Q ss_pred CceecccccccccCHHHHHHHHHHhcCCCceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcccCCh
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYAAADS 109 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 109 (213)
..|.|..|...+.. ++-.......|..|.+.|..-. .....|...|.|+.|+..|...
T Consensus 111 rqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rYDPVP-----~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 111 RQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRYDPVP-----CDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeeccccchHHHh--------ccCcccccccccccccccCCCc-----cccccceeeeecccccccchhh
Confidence 56888888765432 2222333466888877765432 1234455568888888888754
No 137
>KOG2593|consensus
Probab=50.98 E-value=26 Score=28.76 Aligned_cols=38 Identities=16% Similarity=0.364 Sum_probs=22.6
Q ss_pred CCCceecccCcccccCHHHHHHHHHhccCCCCeecCCCCcc
Q psy4420 65 QEKFFACSHCDYKSAYINDVKKHTRKHTGEKPFKCQICPYA 105 (213)
Q Consensus 65 ~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 105 (213)
....|.|+.|.++|..... -+..-.....|.|..|+..
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea---~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEA---LQLLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccchhhhHH---HHhhcccCceEEEecCCCc
Confidence 4456888888888765443 2222222345778777654
No 138
>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=50.44 E-value=2.5 Score=21.47 Aligned_cols=10 Identities=20% Similarity=0.448 Sum_probs=5.3
Q ss_pred eccccccccc
Q psy4420 42 TCLLCKQKES 51 (213)
Q Consensus 42 ~C~~C~~~f~ 51 (213)
.|+.||..|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 3555555554
No 139
>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=49.97 E-value=6.5 Score=21.05 Aligned_cols=8 Identities=25% Similarity=0.957 Sum_probs=4.1
Q ss_pred eecccccc
Q psy4420 41 YTCLLCKQ 48 (213)
Q Consensus 41 ~~C~~C~~ 48 (213)
+.||.|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44555554
No 140
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.93 E-value=6.4 Score=25.44 Aligned_cols=11 Identities=9% Similarity=0.027 Sum_probs=5.4
Q ss_pred CeecCCCCccc
Q psy4420 96 PFKCQICPYAA 106 (213)
Q Consensus 96 ~~~C~~C~~~f 106 (213)
|..|++||+.|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 44455555444
No 141
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.83 E-value=6.3 Score=26.82 Aligned_cols=15 Identities=20% Similarity=0.275 Sum_probs=10.1
Q ss_pred CceecccccccccCH
Q psy4420 39 RKYTCLLCKQKESQA 53 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~ 53 (213)
..+.|+.||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 457788888777643
No 142
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=48.55 E-value=8.5 Score=23.99 Aligned_cols=13 Identities=31% Similarity=0.915 Sum_probs=7.1
Q ss_pred CeecCCCCcccCC
Q psy4420 96 PFKCQICPYAAAD 108 (213)
Q Consensus 96 ~~~C~~C~~~f~~ 108 (213)
|..|..||..|.+
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4455555555554
No 143
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.29 E-value=3.7 Score=30.38 Aligned_cols=38 Identities=16% Similarity=0.313 Sum_probs=24.8
Q ss_pred CceecccccccccCHHHHHHHHHHhcCC----------Cc-----eecccCcc
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYLKHTQE----------KF-----FACSHCDY 76 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~----------~~-----~~C~~C~~ 76 (213)
+.+.||+|+..|....-+..-.+.-.++ .| ..||.|+-
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 5788999999998766554444444433 22 46888873
No 144
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=47.50 E-value=3.6 Score=27.03 Aligned_cols=39 Identities=23% Similarity=0.732 Sum_probs=18.7
Q ss_pred eecccccccccCHHHHHHHHHHhcCCCceecccCccccc
Q psy4420 41 YTCLLCKQKESQAWKIKRHYLKHTQEKFFACSHCDYKSA 79 (213)
Q Consensus 41 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~ 79 (213)
..|+.|+..-.....++....--.....|.|..||..|.
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 457777654333333332222222333466777766553
No 145
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.28 E-value=7.3 Score=23.38 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=7.0
Q ss_pred ceecccccccc
Q psy4420 40 KYTCLLCKQKE 50 (213)
Q Consensus 40 ~~~C~~C~~~f 50 (213)
.|.|..|+..|
T Consensus 12 ~Y~c~~cg~~~ 22 (82)
T COG2331 12 SYECTECGNRF 22 (82)
T ss_pred EEeecccchHH
Confidence 36677777654
No 146
>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=47.24 E-value=3.6 Score=25.73 Aligned_cols=31 Identities=26% Similarity=0.608 Sum_probs=17.2
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCCCccccccccccC
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFD 164 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~ 164 (213)
..|.|+.|++.-. .+.-.+-|+|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~v--------kR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSV--------KRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEE--------EEEETTEEEETTTTEEEE
T ss_pred CCCcCCCCCCcee--------EEeeeEEeecCCCCCEEe
Confidence 4477777775421 123345677777776663
No 147
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.69 E-value=8.6 Score=21.13 Aligned_cols=12 Identities=17% Similarity=0.426 Sum_probs=6.8
Q ss_pred CCcccccccccc
Q psy4420 152 LNYNCEVCEKVF 163 (213)
Q Consensus 152 ~~~~C~~C~~~f 163 (213)
..+.|+.||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 456666666543
No 148
>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=46.38 E-value=5 Score=22.17 Aligned_cols=21 Identities=24% Similarity=0.398 Sum_probs=7.3
Q ss_pred ceecccCcccccCHHHHHHHH
Q psy4420 68 FFACSHCDYKSAYINDVKKHT 88 (213)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~H~ 88 (213)
.|.|+.|...|-..-++..|.
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTT
T ss_pred eEECCCCCCccccCcChhhhc
Confidence 345555555554444444443
No 149
>KOG3408|consensus
Probab=46.31 E-value=16 Score=24.19 Aligned_cols=27 Identities=22% Similarity=0.517 Sum_probs=22.3
Q ss_pred CCeeeecCccccccCCHHHHHHHHhhC
Q psy4420 124 GRRVYHCTICSKRFYTKSKLDFHVNLH 150 (213)
Q Consensus 124 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 150 (213)
|...|.|-.|.+-|.....|..|.++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 345688999999999999999998754
No 150
>KOG4377|consensus
Probab=45.94 E-value=13 Score=30.19 Aligned_cols=50 Identities=30% Similarity=0.518 Sum_probs=29.6
Q ss_pred ceec--ccccccccCHHHHHHHHHHhcCCC------------ceec--ccCcccccCHHHHHHHHHhcc
Q psy4420 40 KYTC--LLCKQKESQAWKIKRHYLKHTQEK------------FFAC--SHCDYKSAYINDVKKHTRKHT 92 (213)
Q Consensus 40 ~~~C--~~C~~~f~~~~~l~~H~~~h~~~~------------~~~C--~~C~~~~~~~~~l~~H~~~~~ 92 (213)
-|.| +.|+..+..+..+.+|+..|-... .|.| ..|.+ +.+++..|.+.|+
T Consensus 271 hyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht 336 (480)
T KOG4377|consen 271 HYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHT 336 (480)
T ss_pred hhcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCcccc
Confidence 4555 358877777888888887764221 1344 34555 4455666666553
No 151
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.67 E-value=12 Score=21.36 Aligned_cols=12 Identities=33% Similarity=0.919 Sum_probs=6.4
Q ss_pred Cceecccccccc
Q psy4420 39 RKYTCLLCKQKE 50 (213)
Q Consensus 39 ~~~~C~~C~~~f 50 (213)
..|.|+.|....
T Consensus 30 rtymC~eC~~Rv 41 (68)
T COG4896 30 RTYMCPECEHRV 41 (68)
T ss_pred eeEechhhHhhh
Confidence 455666665443
No 152
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=42.86 E-value=4.9 Score=25.15 Aligned_cols=32 Identities=16% Similarity=0.409 Sum_probs=16.5
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCCCccccccccccCC
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVFDK 165 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~ 165 (213)
..|.|+.|++.-. .+.-.+.|.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~v--------kR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKV--------KRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCce--------EEEEEEEEEcCCCCCEEeC
Confidence 3466666653311 1222346677777766643
No 153
>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=42.20 E-value=15 Score=21.46 Aligned_cols=14 Identities=29% Similarity=0.679 Sum_probs=8.1
Q ss_pred CeeeecCccccccC
Q psy4420 125 RRVYHCTICSKRFY 138 (213)
Q Consensus 125 ~~~~~C~~C~~~f~ 138 (213)
.+.|.|+.||..+.
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 45566666665543
No 154
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=42.14 E-value=16 Score=23.31 Aligned_cols=15 Identities=33% Similarity=0.561 Sum_probs=10.0
Q ss_pred eeecCccccccCCHH
Q psy4420 127 VYHCTICSKRFYTKS 141 (213)
Q Consensus 127 ~~~C~~C~~~f~~~~ 141 (213)
|..|..||..|...+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 456777777777643
No 155
>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=41.08 E-value=6.8 Score=18.62 Aligned_cols=19 Identities=26% Similarity=0.732 Sum_probs=10.6
Q ss_pred ccccccccccCChHHHHhHH
Q psy4420 154 YNCEVCEKVFDKIEEFENHL 173 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~ 173 (213)
|.|-.|++.| ....+..|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 4567777777 445555554
No 156
>KOG0978|consensus
Probab=40.60 E-value=16 Score=32.09 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=18.0
Q ss_pred CCCccccccccccCChHHHHhHH
Q psy4420 151 NLNYNCEVCEKVFDKIEEFENHL 173 (213)
Q Consensus 151 ~~~~~C~~C~~~f~~~~~L~~H~ 173 (213)
++.-+||.|+.+|+..+-+..|+
T Consensus 676 tRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred HhcCCCCCCCCCCCcccccccCC
Confidence 45679999999999887766653
No 157
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=40.53 E-value=32 Score=17.92 Aligned_cols=10 Identities=30% Similarity=0.438 Sum_probs=4.9
Q ss_pred eecccccccc
Q psy4420 41 YTCLLCKQKE 50 (213)
Q Consensus 41 ~~C~~C~~~f 50 (213)
-+|+.||..|
T Consensus 14 ~~C~~CgM~Y 23 (41)
T PF13878_consen 14 TTCPTCGMLY 23 (41)
T ss_pred cCCCCCCCEE
Confidence 3455555444
No 158
>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=40.43 E-value=18 Score=21.02 Aligned_cols=11 Identities=36% Similarity=0.881 Sum_probs=4.1
Q ss_pred eeccccccccc
Q psy4420 41 YTCLLCKQKES 51 (213)
Q Consensus 41 ~~C~~C~~~f~ 51 (213)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 34666666664
No 159
>KOG1842|consensus
Probab=40.40 E-value=16 Score=30.02 Aligned_cols=29 Identities=17% Similarity=0.452 Sum_probs=25.2
Q ss_pred CccccccccccCChHHHHhHHhhcCCCCC
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDNHIFTY 181 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~h~~~~ 181 (213)
.|.||+|.+.|.+.+.|..|+..-|++.-
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 68899999999999999999988887764
No 160
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=40.17 E-value=21 Score=19.55 Aligned_cols=17 Identities=18% Similarity=0.208 Sum_probs=9.1
Q ss_pred CceecccccccccCHHH
Q psy4420 39 RKYTCLLCKQKESQAWK 55 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~ 55 (213)
+.+.|..||..|-....
T Consensus 3 k~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAG 19 (49)
T ss_pred eeEEcccCCCeEEEehh
Confidence 45556666655554443
No 161
>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=39.94 E-value=17 Score=19.00 Aligned_cols=9 Identities=22% Similarity=0.696 Sum_probs=3.3
Q ss_pred eecCCCCcc
Q psy4420 97 FKCQICPYA 105 (213)
Q Consensus 97 ~~C~~C~~~ 105 (213)
+.|..||..
T Consensus 20 ~vC~~CG~V 28 (43)
T PF08271_consen 20 LVCPNCGLV 28 (43)
T ss_dssp EEETTT-BB
T ss_pred EECCCCCCE
Confidence 344444433
No 162
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=39.41 E-value=14 Score=19.09 Aligned_cols=14 Identities=21% Similarity=0.702 Sum_probs=10.2
Q ss_pred CccccccccccCCh
Q psy4420 153 NYNCEVCEKVFDKI 166 (213)
Q Consensus 153 ~~~C~~C~~~f~~~ 166 (213)
|++|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 67888888777543
No 163
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=39.24 E-value=29 Score=27.61 Aligned_cols=22 Identities=27% Similarity=0.866 Sum_probs=16.3
Q ss_pred Cccccccc-cccCChHHHHhHHh
Q psy4420 153 NYNCEVCE-KVFDKIEEFENHLS 174 (213)
Q Consensus 153 ~~~C~~C~-~~f~~~~~L~~H~~ 174 (213)
.|.|.+|| +.+.-+..+.+|..
T Consensus 374 ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 374 EFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred ceeeeecccccccchHHHHhhhh
Confidence 58888888 67777777777763
No 164
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=37.04 E-value=16 Score=23.94 Aligned_cols=12 Identities=25% Similarity=0.313 Sum_probs=6.7
Q ss_pred eecCccccccCC
Q psy4420 128 YHCTICSKRFYT 139 (213)
Q Consensus 128 ~~C~~C~~~f~~ 139 (213)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 556666655543
No 165
>KOG4167|consensus
Probab=36.99 E-value=8.5 Score=33.61 Aligned_cols=26 Identities=35% Similarity=0.489 Sum_probs=23.4
Q ss_pred CeecCCCCcccCChhHHHHHHHHhhc
Q psy4420 96 PFKCQICPYAAADSKSLRVHYKTHAK 121 (213)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 121 (213)
-|.|..|++.|.-..++.+|+++|..
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48999999999999999999999863
No 166
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.78 E-value=25 Score=25.18 Aligned_cols=31 Identities=16% Similarity=0.640 Sum_probs=18.4
Q ss_pred CeeeecCccccccCCHHHHHHHHhhCCCCccccccccc
Q psy4420 125 RRVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKV 162 (213)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~ 162 (213)
..-|.|+.|...|+...+... .|.||.||..
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~-------~F~Cp~Cg~~ 141 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMEL-------GFTCPKCGED 141 (176)
T ss_pred CCceeCCCCCCcccHHHHHHh-------CCCCCCCCch
Confidence 445777777666655544332 3777777743
No 167
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=36.30 E-value=4.2 Score=25.82 Aligned_cols=6 Identities=50% Similarity=1.447 Sum_probs=2.2
Q ss_pred eecccc
Q psy4420 41 YTCLLC 46 (213)
Q Consensus 41 ~~C~~C 46 (213)
|.|+.|
T Consensus 23 FtCp~C 28 (104)
T COG4888 23 FTCPRC 28 (104)
T ss_pred EecCcc
Confidence 333333
No 168
>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=36.01 E-value=16 Score=24.11 Aligned_cols=13 Identities=23% Similarity=0.572 Sum_probs=7.4
Q ss_pred eecCccccccCCH
Q psy4420 128 YHCTICSKRFYTK 140 (213)
Q Consensus 128 ~~C~~C~~~f~~~ 140 (213)
..|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (115)
T TIGR00100 71 CECEDCSEEVSPE 83 (115)
T ss_pred EEcccCCCEEecC
Confidence 5566666555443
No 169
>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=34.79 E-value=12 Score=19.65 Aligned_cols=13 Identities=31% Similarity=0.777 Sum_probs=7.7
Q ss_pred CccccccccccCC
Q psy4420 153 NYNCEVCEKVFDK 165 (213)
Q Consensus 153 ~~~C~~C~~~f~~ 165 (213)
++.|+.|++.|=.
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 6788888888754
No 170
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=34.58 E-value=22 Score=22.29 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=4.4
Q ss_pred Ccccccccccc
Q psy4420 153 NYNCEVCEKVF 163 (213)
Q Consensus 153 ~~~C~~C~~~f 163 (213)
.|.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 34444444333
No 171
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=34.47 E-value=15 Score=20.35 Aligned_cols=12 Identities=25% Similarity=0.772 Sum_probs=6.4
Q ss_pred cccccccccCCh
Q psy4420 155 NCEVCEKVFDKI 166 (213)
Q Consensus 155 ~C~~C~~~f~~~ 166 (213)
.||+|+..|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999888764
No 172
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.42 E-value=14 Score=29.10 Aligned_cols=14 Identities=14% Similarity=0.382 Sum_probs=7.7
Q ss_pred eeeecCccccccCC
Q psy4420 126 RVYHCTICSKRFYT 139 (213)
Q Consensus 126 ~~~~C~~C~~~f~~ 139 (213)
+...|..|+.-.+.
T Consensus 251 r~e~C~~C~~YlK~ 264 (309)
T PRK03564 251 KAESCGDCGTYLKI 264 (309)
T ss_pred Eeeeccccccccee
Confidence 44566666644433
No 173
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=34.40 E-value=30 Score=19.15 Aligned_cols=11 Identities=18% Similarity=0.866 Sum_probs=5.0
Q ss_pred eecCccccccC
Q psy4420 128 YHCTICSKRFY 138 (213)
Q Consensus 128 ~~C~~C~~~f~ 138 (213)
+.|+.||..|.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 44444444443
No 174
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.14 E-value=44 Score=31.63 Aligned_cols=8 Identities=25% Similarity=0.646 Sum_probs=4.0
Q ss_pred eecccccc
Q psy4420 41 YTCLLCKQ 48 (213)
Q Consensus 41 ~~C~~C~~ 48 (213)
++|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 44555554
No 175
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=34.05 E-value=30 Score=19.35 Aligned_cols=8 Identities=38% Similarity=1.194 Sum_probs=3.7
Q ss_pred ceeccccc
Q psy4420 40 KYTCLLCK 47 (213)
Q Consensus 40 ~~~C~~C~ 47 (213)
.|.|+.|+
T Consensus 44 ~y~C~~Cg 51 (54)
T PF10058_consen 44 QYRCPYCG 51 (54)
T ss_pred EEEcCCCC
Confidence 34444444
No 176
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=33.85 E-value=42 Score=26.28 Aligned_cols=46 Identities=15% Similarity=0.300 Sum_probs=27.7
Q ss_pred cccCcccccCHHHHHHHHH-hccCCCCeecCCCCcccCChhHHHHHHHHh
Q psy4420 71 CSHCDYKSAYINDVKKHTR-KHTGEKPFKCQICPYAAADSKSLRVHYKTH 119 (213)
Q Consensus 71 C~~C~~~~~~~~~l~~H~~-~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (213)
|-.|...|..... |.. ..+....|.|+.|...|-..-..-.|-..|
T Consensus 365 Cf~CQ~~fp~~~~---~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 365 CFVCQGPFPKPPV---SPFDESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceeccCCCCCCCC---CcccccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 6666666654321 111 122345688888888888887777776655
No 177
>PHA02998 RNA polymerase subunit; Provisional
Probab=33.57 E-value=18 Score=25.79 Aligned_cols=12 Identities=25% Similarity=0.539 Sum_probs=5.6
Q ss_pred ceeccccccccc
Q psy4420 40 KYTCLLCKQKES 51 (213)
Q Consensus 40 ~~~C~~C~~~f~ 51 (213)
.|.|..|+..|.
T Consensus 171 FYkC~~CG~~wk 182 (195)
T PHA02998 171 RHACRDCKKHFK 182 (195)
T ss_pred EEEcCCCCCccC
Confidence 344555554443
No 178
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=32.46 E-value=34 Score=19.25 Aligned_cols=7 Identities=29% Similarity=0.980 Sum_probs=2.7
Q ss_pred eeccccc
Q psy4420 41 YTCLLCK 47 (213)
Q Consensus 41 ~~C~~C~ 47 (213)
|.|+.||
T Consensus 15 ~~Cp~cG 21 (55)
T PF13824_consen 15 FECPDCG 21 (55)
T ss_pred CcCCCCC
Confidence 3333333
No 179
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=31.92 E-value=8 Score=28.01 Aligned_cols=34 Identities=24% Similarity=0.491 Sum_probs=20.2
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCC---------CccccccccccCC
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNL---------NYNCEVCEKVFDK 165 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~---------~~~C~~C~~~f~~ 165 (213)
....||.||. .|..|+....- .+.|..||+.++-
T Consensus 13 ~~~~CPvCg~------~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~D 55 (201)
T COG1779 13 TRIDCPVCGG------TLKAHMYLYDIPYFGEVLISTGVCERCGYRSTD 55 (201)
T ss_pred eeecCCcccc------eeeEEEeeecCCccceEEEEEEEccccCCcccc
Confidence 3456888875 33444444433 3578888876654
No 180
>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=31.71 E-value=32 Score=18.94 Aligned_cols=10 Identities=40% Similarity=0.813 Sum_probs=5.1
Q ss_pred cCccccccCC
Q psy4420 130 CTICSKRFYT 139 (213)
Q Consensus 130 C~~C~~~f~~ 139 (213)
|..|++.|..
T Consensus 5 C~~C~~~F~~ 14 (57)
T cd00065 5 CMGCGKPFTL 14 (57)
T ss_pred CcccCccccC
Confidence 4555555543
No 181
>KOG1280|consensus
Probab=31.70 E-value=59 Score=25.95 Aligned_cols=25 Identities=16% Similarity=0.303 Sum_probs=12.8
Q ss_pred ceecccCcccccCHHHHHHHHHhcc
Q psy4420 68 FFACSHCDYKSAYINDVKKHTRKHT 92 (213)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~H~~~~~ 92 (213)
.|.|++|++.-.+...+..|+...+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcC
Confidence 4555555555444555555544433
No 182
>KOG3002|consensus
Probab=30.81 E-value=54 Score=25.75 Aligned_cols=81 Identities=19% Similarity=0.326 Sum_probs=49.4
Q ss_pred CCCeecCCCCcccCChhHHHHHHHHhhccCCCeeeecC----ccccccCCHHHHHHHHhhCC-CCccccccccc--c-CC
Q psy4420 94 EKPFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCT----ICSKRFYTKSKLDFHVNLHN-LNYNCEVCEKV--F-DK 165 (213)
Q Consensus 94 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~----~C~~~f~~~~~l~~H~~~h~-~~~~C~~C~~~--f-~~ 165 (213)
+....|+.|...+.....+..-.-.. ...+.|+ -|.+.|..... ..|.+... .+|.||.-+-. + ..
T Consensus 78 ~~~~~CP~Cr~~~g~~R~~amEkV~e-----~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f~~~~CP~p~~~C~~~G~ 151 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNIRCRAMEKVAE-----AVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEFRPCSCPVPGAECKYTGS 151 (299)
T ss_pred hhcccCCccccccccHHHHHHHHHHH-----hceecccccccCCceeeccccc-cccccccccCCcCCCCCcccCCccCc
Confidence 34567888888887665544333222 3445666 37888877766 45555443 48888776322 2 34
Q ss_pred hHHHHhHHhhcCCCC
Q psy4420 166 IEEFENHLSDNHIFT 180 (213)
Q Consensus 166 ~~~L~~H~~~~h~~~ 180 (213)
...|..|.+.-|...
T Consensus 152 ~~~l~~H~~~~hk~~ 166 (299)
T KOG3002|consen 152 YKDLYAHLNDTHKSD 166 (299)
T ss_pred HHHHHHHHHhhChhh
Confidence 467888888776663
No 183
>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=30.63 E-value=21 Score=19.59 Aligned_cols=14 Identities=29% Similarity=1.061 Sum_probs=10.7
Q ss_pred CccccccccccCCh
Q psy4420 153 NYNCEVCEKVFDKI 166 (213)
Q Consensus 153 ~~~C~~C~~~f~~~ 166 (213)
.|+|.+||..|...
T Consensus 1 ~y~C~~CgyiYd~~ 14 (50)
T cd00730 1 KYECRICGYIYDPA 14 (50)
T ss_pred CcCCCCCCeEECCC
Confidence 37899999887653
No 184
>KOG0320|consensus
Probab=30.62 E-value=9 Score=27.26 Aligned_cols=11 Identities=27% Similarity=0.498 Sum_probs=6.6
Q ss_pred ceecccCcccc
Q psy4420 68 FFACSHCDYKS 78 (213)
Q Consensus 68 ~~~C~~C~~~~ 78 (213)
...|+.|++..
T Consensus 167 ~~~CP~C~kkI 177 (187)
T KOG0320|consen 167 TNKCPTCRKKI 177 (187)
T ss_pred CCCCCCccccc
Confidence 34577777644
No 185
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.53 E-value=36 Score=19.09 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=5.6
Q ss_pred ecCCCCcccCC
Q psy4420 98 KCQICPYAAAD 108 (213)
Q Consensus 98 ~C~~C~~~f~~ 108 (213)
.|+.|+..|..
T Consensus 7 ~C~~Cg~~~~~ 17 (54)
T PF14446_consen 7 KCPVCGKKFKD 17 (54)
T ss_pred cChhhCCcccC
Confidence 45555555543
No 186
>KOG2272|consensus
Probab=30.11 E-value=30 Score=26.18 Aligned_cols=19 Identities=16% Similarity=0.371 Sum_probs=12.1
Q ss_pred CceecccccccccCHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIK 57 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~ 57 (213)
.-|.|.+|++...+..-++
T Consensus 98 ~CF~Cd~Cn~~Lad~gf~r 116 (332)
T KOG2272|consen 98 ACFRCDLCNKHLADQGFYR 116 (332)
T ss_pred ccchhHHHHHHHhhhhhHh
Confidence 4577777777666555443
No 187
>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=29.66 E-value=25 Score=23.04 Aligned_cols=13 Identities=15% Similarity=0.373 Sum_probs=7.7
Q ss_pred ceecccccccccC
Q psy4420 40 KYTCLLCKQKESQ 52 (213)
Q Consensus 40 ~~~C~~C~~~f~~ 52 (213)
.+.|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 70 RARCRDCGHEFEP 82 (113)
T ss_dssp EEEETTTS-EEEC
T ss_pred cEECCCCCCEEec
Confidence 4667777777654
No 188
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=29.65 E-value=41 Score=22.80 Aligned_cols=15 Identities=33% Similarity=0.842 Sum_probs=8.4
Q ss_pred CCCeecCCCCcccCC
Q psy4420 94 EKPFKCQICPYAAAD 108 (213)
Q Consensus 94 ~~~~~C~~C~~~f~~ 108 (213)
.+-|+|.+|......
T Consensus 78 ~~lYeCnIC~etS~e 92 (140)
T PF05290_consen 78 PKLYECNICKETSAE 92 (140)
T ss_pred CCceeccCcccccch
Confidence 355666666655433
No 189
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=29.56 E-value=11 Score=18.92 Aligned_cols=13 Identities=15% Similarity=0.473 Sum_probs=5.9
Q ss_pred CCccccccccccC
Q psy4420 152 LNYNCEVCEKVFD 164 (213)
Q Consensus 152 ~~~~C~~C~~~f~ 164 (213)
.+..|..||-.++
T Consensus 20 ~~isC~~CGPr~~ 32 (35)
T PF07503_consen 20 QFISCTNCGPRYS 32 (35)
T ss_dssp TT--BTTCC-SCC
T ss_pred cCccCCCCCCCEE
Confidence 3566777775543
No 190
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=29.44 E-value=35 Score=23.71 Aligned_cols=33 Identities=30% Similarity=0.797 Sum_probs=15.9
Q ss_pred CeecCCCCcccCChhHHHHHHHHhhccCCCeeeecCccccc
Q psy4420 96 PFKCQICPYAAADSKSLRVHYKTHAKENGRRVYHCTICSKR 136 (213)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~C~~C~~~ 136 (213)
+|.|. |+..|.+.. .|-..-- |+ .|.|..|+..
T Consensus 117 ~Y~C~-C~q~~l~~R---Rhn~~~~---g~-~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRIR---RHNTVRR---GE-VYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchhh---hcccccc---cc-eEEeccCCce
Confidence 56666 666654432 1211111 23 5667766643
No 191
>KOG0717|consensus
Probab=29.33 E-value=29 Score=28.81 Aligned_cols=22 Identities=32% Similarity=0.691 Sum_probs=19.9
Q ss_pred ccccccccccCChHHHHhHHhh
Q psy4420 154 YNCEVCEKVFDKIEEFENHLSD 175 (213)
Q Consensus 154 ~~C~~C~~~f~~~~~L~~H~~~ 175 (213)
+-|.+|+++|.+.-.|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999999855
No 192
>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=28.79 E-value=22 Score=19.26 Aligned_cols=13 Identities=46% Similarity=1.060 Sum_probs=9.5
Q ss_pred ccccccccccCCh
Q psy4420 154 YNCEVCEKVFDKI 166 (213)
Q Consensus 154 ~~C~~C~~~f~~~ 166 (213)
|+|.+||..|...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 7888888777544
No 193
>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=27.22 E-value=46 Score=16.50 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=11.7
Q ss_pred CceecccccccccCHHHHHHHHH
Q psy4420 39 RKYTCLLCKQKESQAWKIKRHYL 61 (213)
Q Consensus 39 ~~~~C~~C~~~f~~~~~l~~H~~ 61 (213)
..+.|+.|++... ...+..|+.
T Consensus 3 ~~~~C~nC~R~v~-a~RfA~HLe 24 (33)
T PF08209_consen 3 PYVECPNCGRPVA-ASRFAPHLE 24 (33)
T ss_dssp -EEE-TTTSSEEE-GGGHHHHHH
T ss_pred CeEECCCCcCCcc-hhhhHHHHH
Confidence 4567777777654 233555554
No 194
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=27.08 E-value=53 Score=23.18 Aligned_cols=19 Identities=26% Similarity=0.566 Sum_probs=11.5
Q ss_pred CCCccccccccccCChHHH
Q psy4420 151 NLNYNCEVCEKVFDKIEEF 169 (213)
Q Consensus 151 ~~~~~C~~C~~~f~~~~~L 169 (213)
+.-|.|+.||+.|=..+++
T Consensus 128 ~~f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 128 EEFYRCPKCGKIYWKGSHW 146 (165)
T ss_pred cceeECCCCcccccCchHH
Confidence 3356677777776555444
No 195
>KOG0978|consensus
Probab=26.99 E-value=29 Score=30.51 Aligned_cols=17 Identities=24% Similarity=0.319 Sum_probs=12.1
Q ss_pred CeecCCCCcccCChhHH
Q psy4420 96 PFKCQICPYAAADSKSL 112 (213)
Q Consensus 96 ~~~C~~C~~~f~~~~~l 112 (213)
.-+||.|+..|+....+
T Consensus 678 qRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 678 QRKCPKCNAAFGANDVH 694 (698)
T ss_pred cCCCCCCCCCCCccccc
Confidence 34788888888776543
No 196
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=26.76 E-value=20 Score=24.75 Aligned_cols=32 Identities=22% Similarity=0.626 Sum_probs=17.9
Q ss_pred eeeecCccccccCCHHHHHHHHhhCCCCcccccccccc
Q psy4420 126 RVYHCTICSKRFYTKSKLDFHVNLHNLNYNCEVCEKVF 163 (213)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f 163 (213)
-.|.|+.|+..+... .+.....|.|+.|+-.+
T Consensus 122 ~~~~C~~C~~~~~r~------~~~~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 122 YVYRCPSCGREYKRH------RRSKRKRYRCGRCGGPL 153 (157)
T ss_pred eEEEcCCCCCEeeee------cccchhhEECCCCCCEE
Confidence 347777777665322 22222247777777544
No 197
>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 KOG4727|consensus
Probab=26.63 E-value=44 Score=23.67 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=21.4
Q ss_pred CCceecccccccccCHHHHHHHHH
Q psy4420 38 ARKYTCLLCKQKESQAWKIKRHYL 61 (213)
Q Consensus 38 ~~~~~C~~C~~~f~~~~~l~~H~~ 61 (213)
...|-|.+|+-++++..++..|+.
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhc
Confidence 357999999999999999999985
No 199
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=26.63 E-value=24 Score=24.46 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=10.0
Q ss_pred ceecccccccccCHH
Q psy4420 40 KYTCLLCKQKESQAW 54 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~ 54 (213)
.-.|+.|+..|.+.-
T Consensus 28 RReC~~C~~RFTTfE 42 (156)
T COG1327 28 RRECLECGERFTTFE 42 (156)
T ss_pred hhcccccccccchhh
Confidence 445888887776544
No 200
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.55 E-value=30 Score=28.39 Aligned_cols=14 Identities=21% Similarity=0.584 Sum_probs=7.7
Q ss_pred eeecCccccccCCH
Q psy4420 127 VYHCTICSKRFYTK 140 (213)
Q Consensus 127 ~~~C~~C~~~f~~~ 140 (213)
.|+|+.||..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 45666666555443
No 201
>KOG0717|consensus
Probab=26.42 E-value=41 Score=27.96 Aligned_cols=22 Identities=32% Similarity=0.670 Sum_probs=20.1
Q ss_pred eecCccccccCCHHHHHHHHhh
Q psy4420 128 YHCTICSKRFYTKSKLDFHVNL 149 (213)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~ 149 (213)
+.|.+|.++|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999999754
No 202
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.28 E-value=26 Score=23.16 Aligned_cols=12 Identities=17% Similarity=0.385 Sum_probs=6.5
Q ss_pred ceeccccccccc
Q psy4420 40 KYTCLLCKQKES 51 (213)
Q Consensus 40 ~~~C~~C~~~f~ 51 (213)
.+.|..|+..|.
T Consensus 71 ~~~C~~Cg~~~~ 82 (117)
T PRK00564 71 ELECKDCSHVFK 82 (117)
T ss_pred EEEhhhCCCccc
Confidence 355666665543
No 203
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=26.03 E-value=36 Score=17.74 Aligned_cols=12 Identities=17% Similarity=0.470 Sum_probs=9.2
Q ss_pred Cceecccccccc
Q psy4420 39 RKYTCLLCKQKE 50 (213)
Q Consensus 39 ~~~~C~~C~~~f 50 (213)
++-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 457899998876
No 204
>PRK12860 transcriptional activator FlhC; Provisional
Probab=25.77 E-value=42 Score=24.31 Aligned_cols=30 Identities=20% Similarity=0.440 Sum_probs=13.9
Q ss_pred cccCHHHHHHHHHHhcCCCceecccCccccc
Q psy4420 49 KESQAWKIKRHYLKHTQEKFFACSHCDYKSA 79 (213)
Q Consensus 49 ~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~ 79 (213)
.|...+.|.+.+... .-....|..||..|.
T Consensus 116 s~tRAw~LvRf~~s~-~L~l~~C~~Cgg~fv 145 (189)
T PRK12860 116 DLTRAWTLVRFFDAG-MLQLARCCRCGGKFV 145 (189)
T ss_pred cHHHHHHHHHHhcCC-CeeeccCCCCCCCee
Confidence 344445555544432 122244666665554
No 205
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.39 E-value=37 Score=19.09 Aligned_cols=12 Identities=17% Similarity=0.628 Sum_probs=7.3
Q ss_pred ceeccccccccc
Q psy4420 40 KYTCLLCKQKES 51 (213)
Q Consensus 40 ~~~C~~C~~~f~ 51 (213)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 456666666654
No 206
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=25.08 E-value=7.4 Score=33.94 Aligned_cols=14 Identities=21% Similarity=0.482 Sum_probs=7.1
Q ss_pred ecCCCCcccCChhH
Q psy4420 98 KCQICPYAAADSKS 111 (213)
Q Consensus 98 ~C~~C~~~f~~~~~ 111 (213)
.|+.|.+.|.+...
T Consensus 153 lC~~C~~EY~dP~n 166 (750)
T COG0068 153 LCPFCDKEYKDPLN 166 (750)
T ss_pred CCHHHHHHhcCccc
Confidence 35555555555433
No 207
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=24.63 E-value=49 Score=24.56 Aligned_cols=21 Identities=14% Similarity=0.184 Sum_probs=12.1
Q ss_pred HHHHhHHhhcCCCCCCCCCCc
Q psy4420 167 EEFENHLSDNHIFTYDHGTKD 187 (213)
Q Consensus 167 ~~L~~H~~~~h~~~~~~~~~~ 187 (213)
.-|.+|+|.|..-..+..+++
T Consensus 131 GLLLRhLRHHSNLLAnIgdP~ 151 (238)
T PF02084_consen 131 GLLLRHLRHHSNLLANIGDPE 151 (238)
T ss_pred HHHHHHHHHHHHHHhhcCCHH
Confidence 457788876655544444443
No 208
>KOG2071|consensus
Probab=24.23 E-value=43 Score=28.73 Aligned_cols=25 Identities=28% Similarity=0.490 Sum_probs=20.0
Q ss_pred CCccccccccccCChHHHHhHHhhc
Q psy4420 152 LNYNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 152 ~~~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
.+-+|..||..|........||-.|
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CcchhcccccccccchhhhhHhhhh
Confidence 3789999999999987777666554
No 209
>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=24.04 E-value=52 Score=17.32 Aligned_cols=16 Identities=19% Similarity=0.326 Sum_probs=11.2
Q ss_pred ecCCCCcccCChhHHH
Q psy4420 98 KCQICPYAAADSKSLR 113 (213)
Q Consensus 98 ~C~~C~~~f~~~~~l~ 113 (213)
.|+.|++.|.......
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5788888887765544
No 210
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.88 E-value=28 Score=22.87 Aligned_cols=10 Identities=20% Similarity=0.700 Sum_probs=5.3
Q ss_pred eecCcccccc
Q psy4420 128 YHCTICSKRF 137 (213)
Q Consensus 128 ~~C~~C~~~f 137 (213)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5555565444
No 211
>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=23.77 E-value=31 Score=17.52 Aligned_cols=10 Identities=40% Similarity=1.105 Sum_probs=4.9
Q ss_pred Cccccccccc
Q psy4420 153 NYNCEVCEKV 162 (213)
Q Consensus 153 ~~~C~~C~~~ 162 (213)
-|+|..||..
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4778888754
No 212
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=23.68 E-value=31 Score=23.85 Aligned_cols=16 Identities=19% Similarity=0.495 Sum_probs=11.0
Q ss_pred ceecccccccccCHHH
Q psy4420 40 KYTCLLCKQKESQAWK 55 (213)
Q Consensus 40 ~~~C~~C~~~f~~~~~ 55 (213)
.=.|..|++.|.+.-.
T Consensus 28 RReC~~C~~RFTTyEr 43 (147)
T TIGR00244 28 RRECLECHERFTTFER 43 (147)
T ss_pred cccCCccCCccceeee
Confidence 4568888888876544
No 213
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=23.20 E-value=33 Score=18.78 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=4.4
Q ss_pred Ccccccccc
Q psy4420 153 NYNCEVCEK 161 (213)
Q Consensus 153 ~~~C~~C~~ 161 (213)
.|.|..||.
T Consensus 37 R~~CGkCgy 45 (51)
T COG1998 37 RWACGKCGY 45 (51)
T ss_pred eeEeccccc
Confidence 445555553
No 214
>PTZ00448 hypothetical protein; Provisional
Probab=22.87 E-value=58 Score=26.27 Aligned_cols=24 Identities=17% Similarity=0.391 Sum_probs=21.5
Q ss_pred CccccccccccCChHHHHhHHhhc
Q psy4420 153 NYNCEVCEKVFDKIEEFENHLSDN 176 (213)
Q Consensus 153 ~~~C~~C~~~f~~~~~L~~H~~~~ 176 (213)
.|.|..|+..|......+.|+++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 689999999999999999999773
No 215
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=22.78 E-value=32 Score=17.19 Aligned_cols=8 Identities=50% Similarity=1.248 Sum_probs=1.9
Q ss_pred cCcccccc
Q psy4420 130 CTICSKRF 137 (213)
Q Consensus 130 C~~C~~~f 137 (213)
|..|++.|
T Consensus 6 C~eC~~~f 13 (34)
T PF01286_consen 6 CDECGKPF 13 (34)
T ss_dssp -TTT--EE
T ss_pred HhHhCCHH
Confidence 33333333
No 216
>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=22.20 E-value=11 Score=20.33 Aligned_cols=7 Identities=29% Similarity=0.795 Sum_probs=3.1
Q ss_pred cCCCCcc
Q psy4420 99 CQICPYA 105 (213)
Q Consensus 99 C~~C~~~ 105 (213)
||.||..
T Consensus 2 CP~Cg~~ 8 (47)
T PF04606_consen 2 CPHCGSK 8 (47)
T ss_pred cCCCCCe
Confidence 4444443
No 217
>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=21.80 E-value=39 Score=21.57 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.1
Q ss_pred CCccccccccccC
Q psy4420 152 LNYNCEVCEKVFD 164 (213)
Q Consensus 152 ~~~~C~~C~~~f~ 164 (213)
.+++|++||..|.
T Consensus 78 ~~~rC~eCG~~fk 90 (97)
T cd00924 78 KPKRCPECGHVFK 90 (97)
T ss_pred CceeCCCCCcEEE
Confidence 3888888887774
No 218
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=21.78 E-value=40 Score=23.11 Aligned_cols=31 Identities=29% Similarity=0.683 Sum_probs=17.7
Q ss_pred eeecCccccccCCHHHHHHHHhhCC-CCcccccccccc
Q psy4420 127 VYHCTICSKRFYTKSKLDFHVNLHN-LNYNCEVCEKVF 163 (213)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~-~~~~C~~C~~~f 163 (213)
.|.|..|+..+.. +.+... ..|.|..|+-.+
T Consensus 112 ~y~C~~C~~~~~~------~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------EccccCcceEEcCCCCCEE
Confidence 5778777766532 222222 457787777544
No 219
>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=21.27 E-value=13 Score=22.03 Aligned_cols=8 Identities=38% Similarity=1.319 Sum_probs=4.0
Q ss_pred Cccccccc
Q psy4420 153 NYNCEVCE 160 (213)
Q Consensus 153 ~~~C~~C~ 160 (213)
.|.|+.|+
T Consensus 61 ~~~C~~C~ 68 (71)
T PF05495_consen 61 DYFCPICG 68 (71)
T ss_dssp SEEETTTT
T ss_pred CccCcCcC
Confidence 44555554
No 220
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=21.21 E-value=21 Score=27.93 Aligned_cols=10 Identities=50% Similarity=0.919 Sum_probs=5.4
Q ss_pred Cceecccccc
Q psy4420 39 RKYTCLLCKQ 48 (213)
Q Consensus 39 ~~~~C~~C~~ 48 (213)
..|+|+.|+.
T Consensus 257 ~~~~C~~C~~ 266 (299)
T TIGR01385 257 DLFTCGKCKQ 266 (299)
T ss_pred ccccCCCCCC
Confidence 3456666653
No 221
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=21.18 E-value=57 Score=17.78 Aligned_cols=7 Identities=29% Similarity=1.265 Sum_probs=2.2
Q ss_pred eecccCc
Q psy4420 69 FACSHCD 75 (213)
Q Consensus 69 ~~C~~C~ 75 (213)
+.|+.|+
T Consensus 42 W~CPiC~ 48 (50)
T PF02891_consen 42 WKCPICN 48 (50)
T ss_dssp -B-TTT-
T ss_pred eECcCCc
Confidence 5555554
No 222
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=21.14 E-value=76 Score=24.71 Aligned_cols=33 Identities=12% Similarity=0.317 Sum_probs=17.3
Q ss_pred CccccCcc---chhhhhhhhhhhhcccccccCCCce
Q psy4420 9 SKLICSFC---LEEVDNSALKMFEHNCDGVLNARKY 41 (213)
Q Consensus 9 ~~~~C~~C---f~~~~~l~~h~~~h~~~~~~~~~~~ 41 (213)
.-|.|+.| |.....|.+|+.......+++..-|
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~~C~~r~PPG~eIY 82 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLAKCDIRQPPGGGIY 82 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHHhCCCCCCCcCEeE
Confidence 44666666 5555666666654443333333334
No 223
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.10 E-value=12 Score=32.72 Aligned_cols=56 Identities=16% Similarity=0.380 Sum_probs=31.6
Q ss_pred ecCCCCcccCChhHHHHHHHHhhccCCCeeee-cCccccccCCHHHHHHHHhhCCCCcccccccc
Q psy4420 98 KCQICPYAAADSKSLRVHYKTHAKENGRRVYH-CTICSKRFYTKSKLDFHVNLHNLNYNCEVCEK 161 (213)
Q Consensus 98 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~-C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~ 161 (213)
.|..||-.|+-..+|---+. .+. -+.|. |+.|.+.|....+.+ -|..|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR~-nTs---M~~F~lC~~C~~EY~dP~nRR----fHAQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRE-NTS---MADFPLCPFCDKEYKDPLNRR----FHAQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCcc-cCc---cccCcCCHHHHHHhcCccccc----cccccccCcccCC
Confidence 47777777766544332211 111 23333 778887777765433 3445777888874
No 224
>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=21.07 E-value=57 Score=23.66 Aligned_cols=46 Identities=24% Similarity=0.434 Sum_probs=24.6
Q ss_pred cccccCCHHHHHHHHhhCC-CCccccc----cccccCChHHHHhHHhhcCCCC
Q psy4420 133 CSKRFYTKSKLDFHVNLHN-LNYNCEV----CEKVFDKIEEFENHLSDNHIFT 180 (213)
Q Consensus 133 C~~~f~~~~~l~~H~~~h~-~~~~C~~----C~~~f~~~~~L~~H~~~~h~~~ 180 (213)
|...+.. .....|..... +|+.||. |+ ..+....|..|+...|...
T Consensus 24 C~~~~~~-~~~~~HE~~C~~~p~~CP~~~~~C~-~~G~~~~l~~Hl~~~H~~~ 74 (198)
T PF03145_consen 24 CTETFPY-SEKREHEEECPFRPCSCPFPGSGCD-WQGSYKELLDHLRDKHSWN 74 (198)
T ss_dssp ---EE-G-GGHHHHHHT-TTSEEE-SSSSTT----EEECCCHHHHHHHHTTTS
T ss_pred Ccccccc-cChhhHhccCCCcCCcCCCCCCCcc-ccCCHHHHHHHHHHHCCCc
Confidence 6666543 35667777764 4888877 54 2233457888888888764
No 225
>KOG1280|consensus
Probab=20.97 E-value=81 Score=25.22 Aligned_cols=36 Identities=19% Similarity=0.527 Sum_probs=25.4
Q ss_pred CeeeecCccccccCCHHHHHHHHhhCCC--Ccc--ccccc
Q psy4420 125 RRVYHCTICSKRFYTKSKLDFHVNLHNL--NYN--CEVCE 160 (213)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~--~~~--C~~C~ 160 (213)
..-|.|+.|+..=.....+..|....+. ++. |++|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 4568899998877777788888766554 342 56665
No 226
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.92 E-value=60 Score=18.68 Aligned_cols=15 Identities=20% Similarity=0.304 Sum_probs=10.3
Q ss_pred CCCeecCCCCcccCC
Q psy4420 94 EKPFKCQICPYAAAD 108 (213)
Q Consensus 94 ~~~~~C~~C~~~f~~ 108 (213)
+....|++|+..|..
T Consensus 46 ~gev~CPYC~t~y~l 60 (62)
T COG4391 46 EGEVVCPYCSTRYRL 60 (62)
T ss_pred CCcEecCccccEEEe
Confidence 445678888877753
No 227
>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=20.61 E-value=94 Score=26.12 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.4
Q ss_pred CeecCCCCcccCChhHHHHHHHHhhc
Q psy4420 96 PFKCQICPYAAADSKSLRVHYKTHAK 121 (213)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 121 (213)
-+.|+.|.+.|.+...+..|+...|.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhh
Confidence 46899999999999999999875543
No 228
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.48 E-value=26 Score=30.80 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=3.9
Q ss_pred eeecCccc
Q psy4420 127 VYHCTICS 134 (213)
Q Consensus 127 ~~~C~~C~ 134 (213)
...|..||
T Consensus 410 ~l~Ch~CG 417 (665)
T PRK14873 410 TPRCRWCG 417 (665)
T ss_pred eeECCCCc
Confidence 34455555
No 229
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.42 E-value=44 Score=18.56 Aligned_cols=11 Identities=18% Similarity=0.718 Sum_probs=7.3
Q ss_pred ccccccccccC
Q psy4420 154 YNCEVCEKVFD 164 (213)
Q Consensus 154 ~~C~~C~~~f~ 164 (213)
+.||.||..+.
T Consensus 1 i~CPyCge~~~ 11 (52)
T PF14255_consen 1 IQCPYCGEPIE 11 (52)
T ss_pred CCCCCCCCeeE
Confidence 46888886653
No 230
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.36 E-value=58 Score=21.76 Aligned_cols=13 Identities=15% Similarity=0.220 Sum_probs=7.6
Q ss_pred eeeecCccccccCC
Q psy4420 126 RVYHCTICSKRFYT 139 (213)
Q Consensus 126 ~~~~C~~C~~~f~~ 139 (213)
....| .|+..|..
T Consensus 69 ~~~~C-~Cg~~~~~ 81 (124)
T PRK00762 69 VEIEC-ECGYEGVV 81 (124)
T ss_pred eeEEe-eCcCcccc
Confidence 33667 77766544
No 231
>PRK05978 hypothetical protein; Provisional
Probab=20.11 E-value=39 Score=23.41 Aligned_cols=11 Identities=27% Similarity=0.890 Sum_probs=6.6
Q ss_pred cccccccccCC
Q psy4420 155 NCEVCEKVFDK 165 (213)
Q Consensus 155 ~C~~C~~~f~~ 165 (213)
.|+.||..|..
T Consensus 54 ~C~~CG~~~~~ 64 (148)
T PRK05978 54 HCAACGEDFTH 64 (148)
T ss_pred CccccCCcccc
Confidence 56667665543
No 232
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.08 E-value=43 Score=29.82 Aligned_cols=11 Identities=18% Similarity=0.455 Sum_probs=5.1
Q ss_pred Cceeccccccc
Q psy4420 39 RKYTCLLCKQK 49 (213)
Q Consensus 39 ~~~~C~~C~~~ 49 (213)
.|..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 34445555443
Done!