Query 010389
Match_columns 512
No_of_seqs 413 out of 3091
Neff 7.1
Searched_HMMs 46136
Date Thu Mar 28 23:57:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010389.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010389hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.9 4.3E-23 9.3E-28 200.0 8.6 133 31-185 129-266 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 8.2E-21 1.8E-25 184.2 6.3 126 55-199 125-252 (279)
3 KOG3576 Ovo and related transc 99.7 9.3E-19 2E-23 162.1 3.8 119 56-194 113-244 (267)
4 KOG1074 Transcriptional repres 99.5 1.5E-14 3.3E-19 157.1 4.9 49 138-186 607-657 (958)
5 KOG1074 Transcriptional repres 99.5 1.1E-14 2.3E-19 158.3 3.6 51 137-187 880-932 (958)
6 KOG3623 Homeobox transcription 99.5 6.5E-15 1.4E-19 157.3 1.4 107 60-184 210-331 (1007)
7 KOG3608 Zn finger proteins [Ge 99.5 2.4E-14 5.2E-19 142.5 4.1 131 55-193 232-383 (467)
8 KOG3623 Homeobox transcription 99.4 2.9E-14 6.2E-19 152.5 2.9 81 57-157 891-971 (1007)
9 KOG3608 Zn finger proteins [Ge 99.4 2.2E-13 4.8E-18 135.6 2.1 141 40-187 187-346 (467)
10 KOG3576 Ovo and related transc 99.3 2E-13 4.4E-18 126.8 1.5 89 98-193 114-204 (267)
11 PLN03086 PRLI-interacting fact 99.3 9.8E-12 2.1E-16 134.3 8.3 104 58-187 451-565 (567)
12 PHA00733 hypothetical protein 99.0 3.6E-10 7.9E-15 100.9 4.8 84 98-189 37-126 (128)
13 PHA00733 hypothetical protein 99.0 4E-10 8.8E-15 100.6 4.7 96 46-160 26-124 (128)
14 KOG3993 Transcription factor ( 98.7 5.7E-09 1.2E-13 106.8 1.1 136 49-191 284-487 (500)
15 PLN03086 PRLI-interacting fact 98.7 6.1E-08 1.3E-12 105.2 8.8 115 59-186 406-538 (567)
16 PHA02768 hypothetical protein; 98.5 5.2E-08 1.1E-12 73.2 1.8 44 101-153 5-48 (55)
17 KOG3993 Transcription factor ( 98.4 5.2E-08 1.1E-12 99.9 0.5 87 100-193 266-387 (500)
18 PHA02768 hypothetical protein; 98.4 1.2E-07 2.5E-12 71.3 2.2 44 60-125 5-48 (55)
19 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.2E-07 2.7E-12 60.7 1.3 26 123-148 1-26 (26)
20 COG5189 SFP1 Putative transcri 98.0 2.7E-06 5.9E-11 84.5 1.4 56 98-158 346-420 (423)
21 PHA00732 hypothetical protein 97.9 9.7E-06 2.1E-10 66.2 3.2 23 60-82 1-23 (79)
22 PHA00616 hypothetical protein 97.8 9.1E-06 2E-10 58.3 1.4 34 60-106 1-34 (44)
23 COG5189 SFP1 Putative transcri 97.8 2.4E-05 5.1E-10 78.0 4.4 67 57-130 346-420 (423)
24 PHA00616 hypothetical protein 97.8 7.9E-06 1.7E-10 58.6 0.8 35 101-142 1-35 (44)
25 PF05605 zf-Di19: Drought indu 97.8 3E-05 6.4E-10 58.7 3.9 52 60-132 2-53 (54)
26 PHA00732 hypothetical protein 97.7 2.7E-05 5.9E-10 63.6 2.9 45 101-158 1-46 (79)
27 PF00096 zf-C2H2: Zinc finger, 97.7 2.8E-05 6E-10 48.0 2.2 23 61-83 1-23 (23)
28 PF13465 zf-H2C2_2: Zinc-finge 97.6 3.4E-05 7.5E-10 49.3 1.9 26 75-120 1-26 (26)
29 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00014 3.1E-09 44.7 2.4 24 61-84 1-24 (24)
30 PF05605 zf-Di19: Drought indu 97.4 0.00019 4E-09 54.3 3.4 47 102-158 3-51 (54)
31 KOG2231 Predicted E3 ubiquitin 97.3 0.00023 4.9E-09 78.7 4.7 46 115-167 189-240 (669)
32 PF12756 zf-C2H2_2: C2H2 type 97.1 0.00025 5.4E-09 59.5 2.1 23 62-84 1-23 (100)
33 PF13912 zf-C2H2_6: C2H2-type 97.1 0.00033 7.2E-09 44.9 2.1 25 60-84 1-25 (27)
34 PF12756 zf-C2H2_2: C2H2 type 96.9 0.00077 1.7E-08 56.5 3.0 74 103-187 1-75 (100)
35 PF00096 zf-C2H2: Zinc finger, 96.7 0.00076 1.7E-08 41.4 1.4 16 115-130 7-22 (23)
36 PF13894 zf-C2H2_4: C2H2-type 96.5 0.0023 5.1E-08 39.1 2.6 23 164-186 1-24 (24)
37 smart00355 ZnF_C2H2 zinc finge 96.4 0.0021 4.6E-08 39.8 1.9 24 61-84 1-24 (26)
38 COG5236 Uncharacterized conser 96.3 0.013 2.9E-07 59.4 7.8 114 60-187 151-306 (493)
39 KOG1146 Homeobox protein [Gene 96.3 0.0025 5.4E-08 74.4 2.9 121 58-185 463-641 (1406)
40 PF09237 GAGA: GAGA factor; I 96.2 0.0029 6.4E-08 46.6 1.8 29 134-162 22-51 (54)
41 COG5048 FOG: Zn-finger [Genera 96.1 0.0075 1.6E-07 63.1 5.2 139 37-180 294-463 (467)
42 PF12874 zf-met: Zinc-finger o 95.9 0.005 1.1E-07 38.5 1.9 23 61-83 1-23 (25)
43 PF09237 GAGA: GAGA factor; I 95.9 0.0048 1E-07 45.5 1.7 33 97-136 20-52 (54)
44 PRK04860 hypothetical protein; 95.7 0.0047 1E-07 57.3 1.7 29 120-148 127-155 (160)
45 PF13912 zf-C2H2_6: C2H2-type 95.6 0.007 1.5E-07 38.6 1.7 25 101-132 1-25 (27)
46 COG5048 FOG: Zn-finger [Genera 95.6 0.0072 1.6E-07 63.2 2.5 107 59-185 288-411 (467)
47 KOG1146 Homeobox protein [Gene 95.4 0.01 2.2E-07 69.5 3.1 104 63-188 439-544 (1406)
48 PF12171 zf-C2H2_jaz: Zinc-fin 94.8 0.009 1.9E-07 38.3 0.2 23 61-83 2-24 (27)
49 PF13909 zf-H2C2_5: C2H2-type 94.5 0.024 5.3E-07 35.1 1.8 23 61-84 1-23 (24)
50 KOG4173 Alpha-SNAP protein [In 94.4 0.015 3.2E-07 55.1 0.8 82 98-187 76-171 (253)
51 PRK04860 hypothetical protein; 93.9 0.033 7E-07 51.8 2.1 39 59-121 118-156 (160)
52 PF13909 zf-H2C2_5: C2H2-type 93.9 0.034 7.3E-07 34.5 1.5 23 102-132 1-23 (24)
53 KOG2231 Predicted E3 ubiquitin 93.7 0.052 1.1E-06 60.5 3.3 83 62-166 184-274 (669)
54 smart00355 ZnF_C2H2 zinc finge 93.6 0.045 9.8E-07 33.6 1.7 17 115-131 7-23 (26)
55 PF12171 zf-C2H2_jaz: Zinc-fin 93.2 0.051 1.1E-06 34.8 1.5 22 137-158 2-23 (27)
56 PF12874 zf-met: Zinc-finger o 92.7 0.05 1.1E-06 33.9 0.9 20 138-157 2-21 (25)
57 KOG2482 Predicted C2H2-type Zn 91.9 0.24 5.1E-06 50.6 4.9 87 98-190 141-307 (423)
58 KOG2482 Predicted C2H2-type Zn 91.6 0.16 3.5E-06 51.8 3.4 25 59-83 194-218 (423)
59 PF13913 zf-C2HC_2: zinc-finge 90.9 0.21 4.5E-06 31.6 2.2 21 61-82 3-23 (25)
60 KOG4377 Zn-finger protein [Gen 90.8 0.22 4.7E-06 52.0 3.4 121 59-188 270-429 (480)
61 smart00451 ZnF_U1 U1-like zinc 90.1 0.23 4.9E-06 33.4 2.0 24 60-83 3-26 (35)
62 KOG2785 C2H2-type Zn-finger pr 90.1 0.47 1E-05 49.3 5.2 118 60-184 3-242 (390)
63 COG5236 Uncharacterized conser 89.5 0.29 6.2E-06 50.0 3.1 79 61-160 221-306 (493)
64 KOG4173 Alpha-SNAP protein [In 88.5 0.15 3.2E-06 48.6 0.2 81 56-159 75-170 (253)
65 KOG2785 C2H2-type Zn-finger pr 87.0 0.94 2E-05 47.2 5.0 51 101-158 166-242 (390)
66 KOG2071 mRNA cleavage and poly 87.0 1.4 2.9E-05 48.5 6.4 30 55-84 413-442 (579)
67 KOG2893 Zn finger protein [Gen 86.3 0.23 5E-06 48.3 0.2 22 63-84 13-34 (341)
68 KOG2893 Zn finger protein [Gen 86.2 0.25 5.5E-06 48.0 0.4 38 115-156 17-54 (341)
69 KOG2186 Cell growth-regulating 85.3 0.49 1.1E-05 46.5 1.9 44 137-182 4-48 (276)
70 smart00451 ZnF_U1 U1-like zinc 84.9 0.61 1.3E-05 31.3 1.7 23 136-158 3-25 (35)
71 PF13913 zf-C2HC_2: zinc-finge 84.5 0.66 1.4E-05 29.3 1.6 19 138-157 4-22 (25)
72 PF09986 DUF2225: Uncharacteri 79.2 0.59 1.3E-05 45.6 -0.1 25 58-82 3-27 (214)
73 TIGR00622 ssl1 transcription f 78.5 3.4 7.3E-05 36.0 4.3 24 162-185 80-104 (112)
74 COG4049 Uncharacterized protei 77.7 1.2 2.7E-05 33.5 1.3 30 55-84 12-41 (65)
75 PF12013 DUF3505: Protein of u 76.4 5.6 0.00012 34.2 5.2 26 58-84 9-34 (109)
76 KOG4124 Putative transcription 76.0 0.71 1.5E-05 47.4 -0.6 27 52-79 205-231 (442)
77 COG4049 Uncharacterized protei 75.2 1.3 2.8E-05 33.5 0.8 26 133-158 14-39 (65)
78 PF09986 DUF2225: Uncharacteri 73.4 1.3 2.8E-05 43.2 0.5 41 135-175 4-61 (214)
79 KOG4124 Putative transcription 72.8 0.81 1.7E-05 47.0 -1.1 29 55-83 344-374 (442)
80 PF09538 FYDLN_acid: Protein o 72.1 2.6 5.6E-05 36.6 2.0 15 135-149 25-39 (108)
81 PF02892 zf-BED: BED zinc fing 72.0 3.4 7.3E-05 29.4 2.3 26 57-82 13-42 (45)
82 PF12013 DUF3505: Protein of u 68.6 7.9 0.00017 33.3 4.3 25 163-187 80-109 (109)
83 PF04959 ARS2: Arsenite-resist 67.0 1.9 4E-05 42.0 0.1 29 133-161 74-103 (214)
84 cd00350 rubredoxin_like Rubred 66.5 4.3 9.3E-05 27.3 1.8 11 135-145 16-26 (33)
85 PRK00464 nrdR transcriptional 65.6 2.3 5E-05 39.3 0.4 19 136-154 28-46 (154)
86 PF09538 FYDLN_acid: Protein o 64.8 4 8.7E-05 35.4 1.7 31 60-121 9-39 (108)
87 COG1997 RPL43A Ribosomal prote 62.3 2.9 6.3E-05 34.6 0.4 11 137-147 54-64 (89)
88 KOG2932 E3 ubiquitin ligase in 61.7 35 0.00076 34.9 7.8 110 60-187 53-172 (389)
89 PF15135 UPF0515: Uncharacteri 61.3 8.5 0.00018 38.0 3.4 78 71-175 90-168 (278)
90 TIGR02300 FYDLN_acid conserved 61.0 6 0.00013 35.2 2.1 13 135-147 25-37 (129)
91 smart00614 ZnF_BED BED zinc fi 61.0 6.1 0.00013 29.1 1.9 24 60-83 18-47 (50)
92 PF04959 ARS2: Arsenite-resist 58.5 4.3 9.3E-05 39.6 0.9 34 95-135 71-104 (214)
93 PRK00464 nrdR transcriptional 58.2 3.8 8.2E-05 37.9 0.4 15 162-176 27-42 (154)
94 smart00531 TFIIE Transcription 58.1 6.9 0.00015 35.7 2.1 40 95-146 93-133 (147)
95 PF02892 zf-BED: BED zinc fing 57.2 5.9 0.00013 28.1 1.2 14 135-148 15-28 (45)
96 COG1592 Rubrerythrin [Energy p 56.6 7.5 0.00016 36.3 2.1 25 100-144 133-157 (166)
97 KOG0320 Predicted E3 ubiquitin 54.9 8.1 0.00017 36.4 2.0 13 97-109 127-139 (187)
98 KOG1280 Uncharacterized conser 54.4 5 0.00011 41.4 0.5 33 134-166 77-110 (381)
99 COG2888 Predicted Zn-ribbon RN 54.1 13 0.00028 28.6 2.6 14 60-73 27-40 (61)
100 PF05443 ROS_MUCR: ROS/MUCR tr 53.9 11 0.00024 33.9 2.6 26 56-84 68-93 (132)
101 PF06524 NOA36: NOA36 protein; 53.0 5.6 0.00012 39.5 0.7 12 57-68 139-150 (314)
102 COG1997 RPL43A Ribosomal prote 52.7 8.8 0.00019 31.8 1.6 32 135-175 34-66 (89)
103 TIGR02300 FYDLN_acid conserved 52.4 9.2 0.0002 34.0 1.8 24 60-107 9-32 (129)
104 PF06066 SepZ: SepZ; InterPro 51.9 5.2 0.00011 32.8 0.2 23 457-486 74-96 (99)
105 PRK06266 transcription initiat 51.7 8.9 0.00019 36.3 1.8 33 98-146 114-146 (178)
106 KOG2186 Cell growth-regulating 51.3 8.9 0.00019 38.0 1.7 49 61-132 4-52 (276)
107 COG1198 PriA Primosomal protei 51.2 12 0.00026 43.1 3.0 25 133-171 459-484 (730)
108 cd00729 rubredoxin_SM Rubredox 51.0 12 0.00027 25.3 1.9 10 135-144 17-26 (34)
109 PF02176 zf-TRAF: TRAF-type zi 50.5 8.6 0.00019 29.0 1.2 43 99-148 7-54 (60)
110 TIGR02098 MJ0042_CXXC MJ0042 f 49.4 11 0.00023 25.9 1.4 16 61-76 3-18 (38)
111 COG1198 PriA Primosomal protei 48.9 11 0.00024 43.3 2.2 14 132-145 471-484 (730)
112 COG5151 SSL1 RNA polymerase II 48.8 15 0.00033 37.4 2.9 46 138-186 364-412 (421)
113 PRK14873 primosome assembly pr 47.9 10 0.00022 43.3 1.8 26 131-171 405-431 (665)
114 TIGR00373 conserved hypothetic 47.7 12 0.00025 34.7 1.9 35 96-146 104-138 (158)
115 PRK14873 primosome assembly pr 47.6 7 0.00015 44.6 0.5 11 135-145 421-431 (665)
116 PF13717 zinc_ribbon_4: zinc-r 46.7 15 0.00032 25.3 1.8 13 138-150 4-16 (36)
117 KOG2593 Transcription initiati 46.7 17 0.00037 38.7 3.1 36 133-170 125-161 (436)
118 PTZ00255 60S ribosomal protein 46.6 10 0.00022 31.8 1.1 12 162-173 53-65 (90)
119 KOG4167 Predicted DNA-binding 46.5 5.2 0.00011 45.0 -0.7 27 58-84 790-816 (907)
120 smart00531 TFIIE Transcription 46.5 20 0.00043 32.7 3.2 39 133-174 96-135 (147)
121 PF07975 C1_4: TFIIH C1-like d 45.0 6.4 0.00014 29.4 -0.3 27 58-84 19-45 (51)
122 TIGR00280 L37a ribosomal prote 44.9 11 0.00023 31.7 1.0 12 162-173 52-64 (91)
123 PF01780 Ribosomal_L37ae: Ribo 44.1 8.9 0.00019 32.1 0.4 12 162-173 52-64 (90)
124 KOG2593 Transcription initiati 43.7 13 0.00028 39.7 1.6 38 54-107 122-159 (436)
125 smart00734 ZnF_Rad18 Rad18-lik 43.4 18 0.00039 23.0 1.7 20 61-81 2-21 (26)
126 TIGR00373 conserved hypothetic 43.2 19 0.00041 33.3 2.5 36 132-175 105-141 (158)
127 PRK00398 rpoP DNA-directed RNA 42.3 17 0.00036 26.2 1.6 13 60-72 3-15 (46)
128 PRK03564 formate dehydrogenase 42.2 16 0.00035 37.6 2.0 74 59-173 186-263 (309)
129 PF13719 zinc_ribbon_5: zinc-r 41.2 20 0.00043 24.7 1.8 11 136-146 25-35 (37)
130 PRK09678 DNA-binding transcrip 40.4 10 0.00023 30.4 0.3 14 162-175 26-42 (72)
131 TIGR01562 FdhE formate dehydro 40.4 18 0.0004 37.1 2.1 12 98-109 207-218 (305)
132 PF15269 zf-C2H2_7: Zinc-finge 40.1 49 0.0011 24.0 3.6 24 60-83 20-43 (54)
133 TIGR00595 priA primosomal prot 39.5 16 0.00034 40.3 1.6 29 129-171 233-262 (505)
134 PRK04023 DNA polymerase II lar 39.2 46 0.001 39.4 5.2 14 56-69 622-635 (1121)
135 PRK03976 rpl37ae 50S ribosomal 38.9 14 0.0003 31.0 0.8 12 162-173 53-65 (90)
136 KOG2807 RNA polymerase II tran 38.3 36 0.00077 35.1 3.7 25 162-186 344-369 (378)
137 COG1592 Rubrerythrin [Energy p 38.1 20 0.00043 33.5 1.8 23 60-108 134-156 (166)
138 COG4530 Uncharacterized protei 37.8 18 0.00038 31.3 1.3 13 134-146 24-36 (129)
139 PRK06266 transcription initiat 37.6 23 0.0005 33.5 2.2 36 133-176 114-150 (178)
140 COG1655 Uncharacterized protei 37.0 10 0.00022 37.1 -0.3 26 58-83 17-42 (267)
141 COG3091 SprT Zn-dependent meta 36.7 18 0.0004 33.2 1.3 32 135-171 116-149 (156)
142 COG4957 Predicted transcriptio 36.5 34 0.00074 30.7 2.9 22 60-84 76-97 (148)
143 PF02176 zf-TRAF: TRAF-type zi 36.0 25 0.00055 26.3 1.8 35 58-106 7-43 (60)
144 PF15269 zf-C2H2_7: Zinc-finge 35.9 22 0.00047 25.8 1.3 22 137-158 21-42 (54)
145 PF03833 PolC_DP2: DNA polymer 35.7 12 0.00027 43.1 0.0 9 60-68 655-663 (900)
146 COG2331 Uncharacterized protei 35.6 18 0.00038 29.3 0.9 23 55-81 7-29 (82)
147 TIGR00622 ssl1 transcription f 35.2 29 0.00063 30.3 2.2 29 56-84 77-105 (112)
148 COG3357 Predicted transcriptio 35.1 20 0.00043 30.0 1.1 15 58-72 56-70 (97)
149 PRK09678 DNA-binding transcrip 35.0 16 0.00035 29.3 0.6 21 132-152 23-45 (72)
150 TIGR00595 priA primosomal prot 34.8 16 0.00035 40.3 0.8 14 132-145 249-262 (505)
151 PRK14714 DNA polymerase II lar 32.1 43 0.00092 40.6 3.6 8 61-68 668-675 (1337)
152 PF04810 zf-Sec23_Sec24: Sec23 31.7 16 0.00035 25.6 0.1 22 125-146 13-34 (40)
153 COG1996 RPC10 DNA-directed RNA 31.5 25 0.00054 26.1 1.0 8 137-144 25-32 (49)
154 COG5151 SSL1 RNA polymerase II 30.8 62 0.0013 33.2 4.0 30 55-84 383-412 (421)
155 KOG4167 Predicted DNA-binding 30.6 10 0.00022 42.9 -1.6 25 136-160 792-816 (907)
156 PF09416 UPF1_Zn_bind: RNA hel 30.5 27 0.00058 32.2 1.3 23 136-158 14-42 (152)
157 PF12760 Zn_Tnp_IS1595: Transp 30.5 63 0.0014 23.2 3.1 8 137-144 19-26 (46)
158 KOG2636 Splicing factor 3a, su 30.5 53 0.0011 35.3 3.6 29 53-81 394-423 (497)
159 PRK14890 putative Zn-ribbon RN 29.5 44 0.00096 25.7 2.1 8 100-107 24-31 (59)
160 KOG1280 Uncharacterized conser 29.3 54 0.0012 34.1 3.4 22 60-81 79-100 (381)
161 COG3677 Transposase and inacti 29.2 22 0.00048 31.8 0.5 16 134-149 51-66 (129)
162 COG4888 Uncharacterized Zn rib 29.0 17 0.00036 31.0 -0.2 14 58-71 20-33 (104)
163 KOG3002 Zn finger protein [Gen 29.0 49 0.0011 34.0 3.1 79 99-188 78-165 (299)
164 KOG4602 Nanos and related prot 28.9 26 0.00055 34.8 0.9 24 132-155 277-300 (318)
165 PF03145 Sina: Seven in absent 27.7 47 0.001 31.6 2.5 55 60-135 14-74 (198)
166 PF05443 ROS_MUCR: ROS/MUCR tr 27.5 35 0.00075 30.8 1.5 17 115-134 79-95 (132)
167 COG4957 Predicted transcriptio 27.1 40 0.00087 30.3 1.8 18 138-158 78-95 (148)
168 PF09845 DUF2072: Zn-ribbon co 26.7 29 0.00063 31.1 0.8 15 60-74 1-15 (131)
169 PF13451 zf-trcl: Probable zin 26.5 34 0.00075 25.3 1.0 23 58-80 2-24 (49)
170 KOG1506 S-adenosylmethionine s 26.2 34 0.00073 34.5 1.2 11 499-509 266-276 (383)
171 PF09963 DUF2197: Uncharacteri 26.2 29 0.00062 26.5 0.6 35 61-107 3-37 (56)
172 PRK14892 putative transcriptio 26.2 30 0.00064 29.6 0.8 10 59-68 20-29 (99)
173 PF14353 CpXC: CpXC protein 25.4 8.6 0.00019 34.0 -2.8 22 136-157 38-59 (128)
174 KOG3408 U1-like Zn-finger-cont 25.3 58 0.0013 28.8 2.4 29 55-83 52-80 (129)
175 TIGR02605 CxxC_CxxC_SSSS putat 25.1 29 0.00064 25.4 0.5 10 135-144 25-34 (52)
176 PF05502 Dynactin_p62: Dynacti 25.0 67 0.0014 35.3 3.4 10 59-68 4-13 (483)
177 PF14446 Prok-RING_1: Prokaryo 24.7 67 0.0015 24.3 2.3 13 60-72 5-17 (54)
178 PRK04023 DNA polymerase II lar 24.5 69 0.0015 38.0 3.5 10 98-107 623-632 (1121)
179 PF09723 Zn-ribbon_8: Zinc rib 24.5 34 0.00074 24.2 0.7 10 135-144 25-34 (42)
180 PF15135 UPF0515: Uncharacteri 24.1 42 0.0009 33.3 1.4 14 136-149 155-168 (278)
181 PF03811 Zn_Tnp_IS1: InsA N-te 23.7 31 0.00068 23.8 0.4 19 124-142 17-35 (36)
182 PF07754 DUF1610: Domain of un 23.4 37 0.00081 21.3 0.6 10 59-68 15-24 (24)
183 smart00731 SprT SprT homologue 23.4 46 0.001 30.1 1.5 31 136-172 112-143 (146)
184 KOG0717 Molecular chaperone (D 23.3 44 0.00096 36.1 1.6 22 61-82 293-314 (508)
185 KOG2807 RNA polymerase II tran 23.1 99 0.0022 32.0 3.9 23 136-158 345-367 (378)
186 COG1571 Predicted DNA-binding 22.8 47 0.001 35.6 1.6 28 138-175 352-380 (421)
187 KOG4377 Zn-finger protein [Gen 22.7 2.4E+02 0.0052 30.2 6.6 68 98-173 268-360 (480)
188 KOG2385 Uncharacterized conser 22.7 27 0.00059 38.3 -0.1 14 423-436 239-252 (633)
189 smart00440 ZnF_C2C2 C2C2 Zinc 22.7 30 0.00065 24.3 0.1 9 137-145 29-37 (40)
190 PF13878 zf-C2H2_3: zinc-finge 22.4 59 0.0013 23.0 1.6 24 61-84 14-39 (41)
191 PF09788 Tmemb_55A: Transmembr 22.2 3.5E+02 0.0075 27.1 7.4 23 59-81 64-86 (256)
192 PF07295 DUF1451: Protein of u 22.0 35 0.00076 31.3 0.4 15 131-145 103-121 (146)
193 smart00834 CxxC_CXXC_SSSS Puta 21.7 43 0.00094 22.9 0.8 15 59-73 4-18 (41)
194 COG5188 PRP9 Splicing factor 3 21.7 1E+02 0.0022 32.2 3.6 30 52-81 366-396 (470)
195 PF11931 DUF3449: Domain of un 21.7 31 0.00066 33.2 0.0 27 53-79 94-121 (196)
196 PF05191 ADK_lid: Adenylate ki 21.5 43 0.00094 23.0 0.7 15 134-148 19-33 (36)
197 KOG0696 Serine/threonine prote 21.3 38 0.00083 36.3 0.6 8 76-83 81-88 (683)
198 PF10263 SprT-like: SprT-like 21.1 40 0.00087 30.5 0.7 29 137-172 124-153 (157)
199 PLN02748 tRNA dimethylallyltra 21.0 57 0.0012 35.7 1.9 26 58-83 416-442 (468)
200 PF08274 PhnA_Zn_Ribbon: PhnA 20.7 43 0.00094 22.2 0.6 22 62-107 4-25 (30)
201 COG0192 MetK S-adenosylmethion 20.7 50 0.0011 34.5 1.3 29 351-379 126-155 (388)
202 PTZ00448 hypothetical protein; 20.5 73 0.0016 33.6 2.4 22 163-184 314-336 (373)
203 PF06220 zf-U1: U1 zinc finger 20.5 70 0.0015 22.3 1.6 23 59-81 2-26 (38)
204 KOG2385 Uncharacterized conser 20.4 34 0.00074 37.5 0.0 9 489-497 288-296 (633)
205 PRK04351 hypothetical protein; 20.3 55 0.0012 30.0 1.4 32 136-174 112-144 (149)
206 KOG0978 E3 ubiquitin ligase in 20.2 34 0.00074 39.0 -0.0 18 138-155 680-697 (698)
207 PF10013 DUF2256: Uncharacteri 20.1 69 0.0015 23.0 1.5 16 138-153 10-25 (42)
208 PHA00626 hypothetical protein 20.1 57 0.0012 24.9 1.1 17 58-74 21-37 (59)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.88 E-value=4.3e-23 Score=199.96 Aligned_cols=133 Identities=23% Similarity=0.403 Sum_probs=110.3
Q ss_pred CCCCCCCCCCCCCchhhhhcCccccC---CCCCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCC
Q 010389 31 NKKKRSLPGTPDPDAEVIALSPKTLL---ATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEK 107 (512)
Q Consensus 31 ~kkk~~~~~~~~~~~~~~~~~~~~~~---~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C 107 (512)
.+-++.++++.-.....+..|++.|. +.+-|.|++|+|.|.....|+.|+|+|+ -+++|.+|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~---------------l~c~C~iC 193 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT---------------LPCECGIC 193 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC---------------CCcccccc
Confidence 33445555565555566666666665 4667888888888888888888888886 46778887
Q ss_pred CCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcccChHHHhhhhhh-cCCcceecc-CCCccCChhHHHHHHHHh
Q 010389 108 SCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSRRDSFITHRAFC 185 (512)
Q Consensus 108 ~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~~~~L~~H~~~h 185 (512)
||.|.+..-|+.|+|+|+|||||.|..|+|.|+.+++|+.||++ .+.|+|+|. |+|.|.++..|.+|....
T Consensus 194 -------GKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 194 -------GKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred -------cccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 99999999999999999999999999999999999999999999 567999999 999999999999997553
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.82 E-value=8.2e-21 Score=184.16 Aligned_cols=126 Identities=20% Similarity=0.428 Sum_probs=114.3
Q ss_pred cCCCCCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCC
Q 010389 55 LLATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGE 134 (512)
Q Consensus 55 ~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ge 134 (512)
.....+|+|..|+|.|.+..+|-+|..+|. ....++.+.|++| +|.|.....|+.|+++|+
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~----------~~~s~ka~~C~~C-------~K~YvSmpALkMHirTH~-- 185 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHR----------SLDSKKAFSCKYC-------GKVYVSMPALKMHIRTHT-- 185 (279)
T ss_pred cccCCceeccccccccccccccchhhcccc----------cccccccccCCCC-------CceeeehHHHhhHhhccC--
Confidence 335568999999999999999999999996 2234788999999 999999999999999997
Q ss_pred ccccccCCCCcccChHHHhhhhhh-cCCcceecc-CCCccCChhHHHHHHHHhcCcchhhhhhhcCC
Q 010389 135 KKWKCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSRRDSFITHRAFCDMLTKESAKVQSEE 199 (512)
Q Consensus 135 kp~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~~~~L~~H~~~hh~~~~~~~~~~~~~ 199 (512)
-+++|.+|||.|.+.+.|+.|+|+ +|||||.|. |+|.|..+.+|+.|+++|-...+.........
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhH
Confidence 789999999999999999999999 899999999 99999999999999999998888877666554
No 3
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.74 E-value=9.3e-19 Score=162.07 Aligned_cols=119 Identities=24% Similarity=0.499 Sum_probs=109.0
Q ss_pred CCCCCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCc
Q 010389 56 LATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEK 135 (512)
Q Consensus 56 ~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gek 135 (512)
.+...|.|.+|+|.|..+.-|.+|++.|. ..+.|.|..| +|.|.+...|++|+|+|+|.|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~-------------~vkr~lct~c-------gkgfndtfdlkrh~rthtgvr 172 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHS-------------DVKRHLCTFC-------GKGFNDTFDLKRHTRTHTGVR 172 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhcc-------------HHHHHHHhhc-------cCcccchhhhhhhhccccCcc
Confidence 35668999999999999999999999998 8899999999 999999999999999999999
Q ss_pred cccccCCCCcccChHHHhhhhhh-cC-----------Ccceecc-CCCccCChhHHHHHHHHhcCcchhhhh
Q 010389 136 KWKCDKCSKKYAVQSDYKAHSKV-CG-----------TKEYKCN-CGAVFSRRDSFITHRAFCDMLTKESAK 194 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~-h~-----------~kpy~C~-Cgk~F~~~~~L~~H~~~hh~~~~~~~~ 194 (512)
||+|..|+|.|..+..|..|++. |+ +|.|.|+ ||.+-.+...+..|++.||.......+
T Consensus 173 pykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~SpallK 244 (267)
T KOG3576|consen 173 PYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPALLK 244 (267)
T ss_pred ccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHHHHH
Confidence 99999999999999999999988 85 4779999 999999999999999999985544433
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.49 E-value=1.5e-14 Score=157.13 Aligned_cols=49 Identities=22% Similarity=0.623 Sum_probs=34.0
Q ss_pred cccCCCCcccChHHHhhhhhh-cCCcceecc-CCCccCChhHHHHHHHHhc
Q 010389 138 KCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSRRDSFITHRAFCD 186 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~~~~L~~H~~~hh 186 (512)
+|-+|-|....+..|+.|.|+ +|||||+|. |++.|.++.+|+.|+-.|.
T Consensus 607 qCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred ceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc
Confidence 477777777777777777777 566777777 7777777777777765554
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.49 E-value=1.1e-14 Score=158.29 Aligned_cols=51 Identities=22% Similarity=0.559 Sum_probs=48.2
Q ss_pred ccccCCCCcccChHHHhhhhhh-cCCcceecc-CCCccCChhHHHHHHHHhcC
Q 010389 137 WKCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSRRDSFITHRAFCDM 187 (512)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~~~~L~~H~~~hh~ 187 (512)
+.|.+|+|.|.....|..|+|+ .++|+|.|. |++.|..+.+|+.||.+|+-
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w 932 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMW 932 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccc
Confidence 5699999999999999999999 789999999 99999999999999998874
No 6
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.48 E-value=6.5e-15 Score=157.34 Aligned_cols=107 Identities=23% Similarity=0.547 Sum_probs=95.9
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccC------
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHG------ 133 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~g------ 133 (512)
...|++|.+.|++...|+.|++..+ +..+..|.|..| ...|.++..|.+||.+|.-
T Consensus 210 lltcpycdrgykrltslkeHikyrh-----------ekne~nfsC~lC-------sytFAyRtQLErhm~~hkpg~dqa~ 271 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRH-----------EKNEPNFSCMLC-------SYTFAYRTQLERHMQLHKPGGDQAI 271 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHH-----------hhCCCCCcchhh-------hhhhhhHHHHHHHHHhhcCCCcccc
Confidence 3689999999999999999998654 225567889999 9999999999999999842
Q ss_pred -------CccccccCCCCcccChHHHhhhhhh-cCCcceecc-CCCccCChhHHHHHHHH
Q 010389 134 -------EKKWKCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSRRDSFITHRAF 184 (512)
Q Consensus 134 -------ekp~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~~~~L~~H~~~ 184 (512)
.|.|+|..|+|.|+.+.+|+.|+|+ .|||||.|. |.|+|.....+..|+..
T Consensus 272 sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 272 SLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 4789999999999999999999999 699999999 99999999999999743
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.47 E-value=2.4e-14 Score=142.46 Aligned_cols=131 Identities=21% Similarity=0.328 Sum_probs=78.6
Q ss_pred cCCCCCeeccccCcccCChHHHHHHHHhcCCCchhh--------------cccccccCCcceeCCCCCCCCCCCCCccCC
Q 010389 55 LLATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLR--------------QRSNKEVKKRVYVCPEKSCVHHDPTRALGD 120 (512)
Q Consensus 55 ~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~--------------~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~ 120 (512)
...+++|.|.+|.|.|.++..|+.|++.|..-++|- .-+-.+...|+|+|+.| .+.|.+
T Consensus 232 ~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~C-------d~~c~~ 304 (467)
T KOG3608|consen 232 ELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDEC-------DTRCVR 304 (467)
T ss_pred hhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccch-------hhhhcc
Confidence 334455666666666666666666666665333321 11123344566666666 666666
Q ss_pred hhhHHhhhhhccCCccccccC--CCCcccChHHHhhhhhh-c---CCcceecc-CCCccCChhHHHHHHHHhcCcchhhh
Q 010389 121 LTGIKKHFCRKHGEKKWKCDK--CSKKYAVQSDYKAHSKV-C---GTKEYKCN-CGAVFSRRDSFITHRAFCDMLTKESA 193 (512)
Q Consensus 121 ~~~Lk~H~~~H~gekp~~C~~--C~k~F~~~~~L~~H~~~-h---~~kpy~C~-Cgk~F~~~~~L~~H~~~hh~~~~~~~ 193 (512)
...|.+|...|. +-.|.|.. |...|....++++|++. | .+-+|.|. |++.|.+-.+|.+|+++.|.......
T Consensus 305 esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsG 383 (467)
T KOG3608|consen 305 ESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSG 383 (467)
T ss_pred HHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCC
Confidence 666666666655 45566666 66666666666666666 3 23457777 77777777777777766666554443
No 8
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.44 E-value=2.9e-14 Score=152.47 Aligned_cols=81 Identities=28% Similarity=0.626 Sum_probs=71.4
Q ss_pred CCCCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCcc
Q 010389 57 ATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKK 136 (512)
Q Consensus 57 ~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp 136 (512)
+...|.|++|+|.|.....|.||.-.|. +++||+|.+| .|.|+.+..|..|+|.|.||||
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHs-------------GqRPyqC~iC-------kKAFKHKHHLtEHkRLHSGEKP 950 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHS-------------GQRPYQCIIC-------KKAFKHKHHLTEHKRLHSGEKP 950 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhc-------------CCCCcccchh-------hHhhhhhhhhhhhhhhccCCCc
Confidence 4567999999999999999999998887 8899999998 8999999999999999999999
Q ss_pred ccccCCCCcccChHHHhhhhh
Q 010389 137 WKCDKCSKKYAVQSDYKAHSK 157 (512)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~ 157 (512)
|+|+.|+|+|.....+-.||.
T Consensus 951 fQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 951 FQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chhhhhhhhcccccchHhhhc
Confidence 999999999988888888875
No 9
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.35 E-value=2.2e-13 Score=135.62 Aligned_cols=141 Identities=18% Similarity=0.288 Sum_probs=115.4
Q ss_pred CCCCchhhhhcCccccCCCCCeeccccCcccCChHHHHHHHHhcC----CCchhhccccc-----------ccCCcceeC
Q 010389 40 TPDPDAEVIALSPKTLLATNRFVCEICNKGFQRDQNLQLHRRGHN----LPWKLRQRSNK-----------EVKKRVYVC 104 (512)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~----~p~~~~~~~~~-----------~~~~k~~~C 104 (512)
....+...++.|.+.|..+|...|+.|+.-|.++..|-.|+|.-+ .++.|+...+. ......|+|
T Consensus 187 ~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykC 266 (467)
T KOG3608|consen 187 KHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKC 266 (467)
T ss_pred hhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccc
Confidence 334445567788899999999999999999999999999988765 34554433221 123356889
Q ss_pred CCCCCCCCCCCCccCChhhHHhhhhh-ccCCccccccCCCCcccChHHHhhhhhhcCCcceecc---CCCccCChhHHHH
Q 010389 105 PEKSCVHHDPTRALGDLTGIKKHFCR-KHGEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN---CGAVFSRRDSFIT 180 (512)
Q Consensus 105 ~~C~C~~~~~~k~F~~~~~Lk~H~~~-H~gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~---Cgk~F~~~~~L~~ 180 (512)
+.| .......+.|.+||+. |..+|||+|+.|++.|.+...|.+|..+|.+-.|+|+ |...|++...+++
T Consensus 267 plC-------dmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~ 339 (467)
T KOG3608|consen 267 PLC-------DMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRR 339 (467)
T ss_pred ccc-------ccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHH
Confidence 988 8888889999999884 6678999999999999999999999999888889997 9999999999999
Q ss_pred HHHHhcC
Q 010389 181 HRAFCDM 187 (512)
Q Consensus 181 H~~~hh~ 187 (512)
|++.+|.
T Consensus 340 H~~evhE 346 (467)
T KOG3608|consen 340 HFLEVHE 346 (467)
T ss_pred HHHHhcc
Confidence 9988884
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.35 E-value=2e-13 Score=126.82 Aligned_cols=89 Identities=22% Similarity=0.451 Sum_probs=83.1
Q ss_pred CCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcccChHHHhhhhhh-cCCcceecc-CCCccCCh
Q 010389 98 KKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSRR 175 (512)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~~ 175 (512)
....|.|.+| +|.|.-..-|.+||+-|...|.|.|..|||.|...-+|++|+|+ ++.|||+|. |+|.|..+
T Consensus 114 d~d~ftCrvC-------gK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqr 186 (267)
T KOG3576|consen 114 DQDSFTCRVC-------GKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQR 186 (267)
T ss_pred CCCeeeeehh-------hhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhh
Confidence 4678999999 99999999999999999999999999999999999999999999 789999999 99999999
Q ss_pred hHHHHHHHHhcCcchhhh
Q 010389 176 DSFITHRAFCDMLTKESA 193 (512)
Q Consensus 176 ~~L~~H~~~hh~~~~~~~ 193 (512)
-.|..|.++.|.......
T Consensus 187 csleshl~kvhgv~~~ya 204 (267)
T KOG3576|consen 187 CSLESHLKKVHGVQHQYA 204 (267)
T ss_pred ccHHHHHHHHcCchHHHH
Confidence 999999999888655544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.26 E-value=9.8e-12 Score=134.28 Aligned_cols=104 Identities=19% Similarity=0.437 Sum_probs=90.2
Q ss_pred CCCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccc
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKW 137 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~ 137 (512)
++.+.|++|++.|. ...|+.|+++|| ++|.|+ | ++.+ .+..|..|+.+|..+|++
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H---------------kpv~Cp-C-------g~~~-~R~~L~~H~~thCp~Kpi 505 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH---------------EPLQCP-C-------GVVL-EKEQMVQHQASTCPLRLI 505 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC---------------CCccCC-C-------CCCc-chhHHHhhhhccCCCCce
Confidence 45679999999996 688999999885 679998 8 8655 679999999999999999
Q ss_pred cccCCCCccc----------ChHHHhhhhhhcCCcceecc-CCCccCChhHHHHHHHHhcC
Q 010389 138 KCDKCSKKYA----------VQSDYKAHSKVCGTKEYKCN-CGAVFSRRDSFITHRAFCDM 187 (512)
Q Consensus 138 ~C~~C~k~F~----------~~~~L~~H~~~h~~kpy~C~-Cgk~F~~~~~L~~H~~~hh~ 187 (512)
.|.+|++.|. ....|..|+..++.+++.|. |++.|..++ |..|+..+|.
T Consensus 506 ~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlrd-m~~H~~~~h~ 565 (567)
T PLN03086 506 TCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLKE-MDIHQIAVHQ 565 (567)
T ss_pred eCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeehh-HHHHHHHhhc
Confidence 9999999995 24589999999999999999 999998775 8899888775
No 12
>PHA00733 hypothetical protein
Probab=98.99 E-value=3.6e-10 Score=100.88 Aligned_cols=84 Identities=13% Similarity=0.262 Sum_probs=69.9
Q ss_pred CCcceeCCCCCCCCCCCCCccCChhhHHhh--h---hhccCCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCc
Q 010389 98 KKRVYVCPEKSCVHHDPTRALGDLTGIKKH--F---CRKHGEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAV 171 (512)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H--~---~~H~gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~ 171 (512)
..+++.|.+| .+.|.+...|..| + ..++++++|.|..|++.|.....|+.|++.+ +.+|.|. |++.
T Consensus 37 ~~~~~~~~~~-------~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~ 108 (128)
T PHA00733 37 EQKRLIRAVV-------KTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKE 108 (128)
T ss_pred hhhhHHHHHH-------hhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCc
Confidence 5688999998 7777766555554 1 1334589999999999999999999999976 5679999 9999
Q ss_pred cCChhHHHHHHHHhcCcc
Q 010389 172 FSRRDSFITHRAFCDMLT 189 (512)
Q Consensus 172 F~~~~~L~~H~~~hh~~~ 189 (512)
|.+...|.+|+...|.+.
T Consensus 109 F~~~~sL~~H~~~~h~~~ 126 (128)
T PHA00733 109 FRNTDSTLDHVCKKHNIC 126 (128)
T ss_pred cCCHHHHHHHHHHhcCcc
Confidence 999999999999988764
No 13
>PHA00733 hypothetical protein
Probab=98.98 E-value=4e-10 Score=100.59 Aligned_cols=96 Identities=16% Similarity=0.155 Sum_probs=78.0
Q ss_pred hhhhcCccccCCCCCeeccccCcccCChHHHHHH--HHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhh
Q 010389 46 EVIALSPKTLLATNRFVCEICNKGFQRDQNLQLH--RRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTG 123 (512)
Q Consensus 46 ~~~~~~~~~~~~~k~f~C~~Cgk~F~~~~~L~~H--~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~ 123 (512)
+.+........+++++.|.+|.+.|.....|..| ++.|. .....++|+|+.| ++.|.+...
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~----------~~~~~kPy~C~~C-------gk~Fss~s~ 88 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLL----------TSKAVSPYVCPLC-------LMPFSSSVS 88 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhc----------ccCCCCCccCCCC-------CCcCCCHHH
Confidence 4444444445568899999999999998888877 33332 1125789999999 999999999
Q ss_pred HHhhhhhccCCccccccCCCCcccChHHHhhhhhh-cC
Q 010389 124 IKKHFCRKHGEKKWKCDKCSKKYAVQSDYKAHSKV-CG 160 (512)
Q Consensus 124 Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-h~ 160 (512)
|..|++.| +++|.|.+|++.|.....|++|+.. |+
T Consensus 89 L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 89 LKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 99999987 4679999999999999999999988 64
No 14
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.66 E-value=5.7e-09 Score=106.79 Aligned_cols=136 Identities=17% Similarity=0.241 Sum_probs=98.8
Q ss_pred hcCccccCCCCCeeccccCcccCChHHHHHHHHhcCCCchhh--------------------cccccccCCcceeCCCCC
Q 010389 49 ALSPKTLLATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLR--------------------QRSNKEVKKRVYVCPEKS 108 (512)
Q Consensus 49 ~~~~~~~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~--------------------~~~~~~~~~k~~~C~~C~ 108 (512)
+-|+=.....-.|+|+.|+|+|....||--|+|+|.-..... .+.........|.|.+|
T Consensus 284 AQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C- 362 (500)
T KOG3993|consen 284 AQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTC- 362 (500)
T ss_pred hhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHh-
Confidence 333333334456999999999999999999999997211111 11222234458999999
Q ss_pred CCCCCCCCccCChhhHHhhhhhccCC---c-------------------------------------------cccccCC
Q 010389 109 CVHHDPTRALGDLTGIKKHFCRKHGE---K-------------------------------------------KWKCDKC 142 (512)
Q Consensus 109 C~~~~~~k~F~~~~~Lk~H~~~H~ge---k-------------------------------------------p~~C~~C 142 (512)
+|.|.++..|++|..+|+.. | -..|.+|
T Consensus 363 ------~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~ 436 (500)
T KOG3993|consen 363 ------GKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYD 436 (500)
T ss_pred ------hhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCC
Confidence 99999999999998888531 0 0236667
Q ss_pred CCcccChHHHhhhhhh-cCCcceecc-CCCccCChhHHHHHHHHhcCcchh
Q 010389 143 SKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSRRDSFITHRAFCDMLTKE 191 (512)
Q Consensus 143 ~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~~~~L~~H~~~hh~~~~~ 191 (512)
+-.+..+..--.|.+. +.+..|.|. |..+|.....|.+|+.++|.-+..
T Consensus 437 ~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse~r 487 (500)
T KOG3993|consen 437 GSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSELR 487 (500)
T ss_pred CCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChHHhh
Confidence 7666666666666666 667789999 999999999999999999964433
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.66 E-value=6.1e-08 Score=105.22 Aligned_cols=115 Identities=18% Similarity=0.356 Sum_probs=87.3
Q ss_pred CCeeccccCcccCChHHHHHHHHhcC-----CC-chhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhcc
Q 010389 59 NRFVCEICNKGFQRDQNLQLHRRGHN-----LP-WKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKH 132 (512)
Q Consensus 59 k~f~C~~Cgk~F~~~~~L~~H~r~H~-----~p-~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ 132 (512)
..-.|..|.+... ..+|..|..... +| ..|...-.....++.+.|++| ++.|. ...|++|+++||
T Consensus 406 ~~V~C~NC~~~i~-l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~C-------gk~f~-~s~LekH~~~~H 476 (567)
T PLN03086 406 DTVECRNCKHYIP-SRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKC-------GQAFQ-QGEMEKHMKVFH 476 (567)
T ss_pred CeEECCCCCCccc-hhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCC-------CCccc-hHHHHHHHHhcC
Confidence 3457999998765 456888975442 11 123333344455677899998 89885 688999999986
Q ss_pred CCccccccCCCCcccChHHHhhhhhh-cCCcceecc-CCCccCC----------hhHHHHHHHHhc
Q 010389 133 GEKKWKCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAVFSR----------RDSFITHRAFCD 186 (512)
Q Consensus 133 gekp~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~F~~----------~~~L~~H~~~hh 186 (512)
++|.|. |++.+ .+..|..|+++ +.++++.|. |++.|.. ...|..|...+.
T Consensus 477 --kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG 538 (567)
T PLN03086 477 --EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICG 538 (567)
T ss_pred --CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcC
Confidence 899999 99865 67899999988 789999999 9999952 347889988764
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.49 E-value=5.2e-08 Score=73.16 Aligned_cols=44 Identities=16% Similarity=0.296 Sum_probs=34.4
Q ss_pred ceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcccChHHHh
Q 010389 101 VYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDYK 153 (512)
Q Consensus 101 ~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~ 153 (512)
-|.|++| ++.|....+|.+||++|+ ++|+|..|+|.|.+...|.
T Consensus 5 ~y~C~~C-------GK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPIC-------GEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchh-------CCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3678887 888888888888888887 6788888888887666554
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.42 E-value=5.2e-08 Score=99.88 Aligned_cols=87 Identities=17% Similarity=0.442 Sum_probs=73.8
Q ss_pred cceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcccChHHHhhhhhhcC-------------------
Q 010389 100 RVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDYKAHSKVCG------------------- 160 (512)
Q Consensus 100 k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~h~------------------- 160 (512)
.-|.|..| ...|.+...|.+|..--...-.|+|..|+|.|....+|..|.|+|.
T Consensus 266 GdyiCqLC-------K~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ 338 (500)
T KOG3993|consen 266 GDYICQLC-------KEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVET 338 (500)
T ss_pred HHHHHHHH-------HHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhh
Confidence 46899999 8999999999999875544456999999999999999999999972
Q ss_pred ---------------Ccceecc-CCCccCChhHHHHHHHHhcCcchhhh
Q 010389 161 ---------------TKEYKCN-CGAVFSRRDSFITHRAFCDMLTKESA 193 (512)
Q Consensus 161 ---------------~kpy~C~-Cgk~F~~~~~L~~H~~~hh~~~~~~~ 193 (512)
+..|.|. |+|.|.+...|+.|+..||.......
T Consensus 339 rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~ 387 (500)
T KOG3993|consen 339 RAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKE 387 (500)
T ss_pred hhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchh
Confidence 1248999 99999999999999999987555443
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.42 E-value=1.2e-07 Score=71.29 Aligned_cols=44 Identities=18% Similarity=0.264 Sum_probs=39.2
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHH
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIK 125 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk 125 (512)
.|+|+.|||.|.+..+|.+|+++|+ ++|+|..| ++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~---------------k~~kc~~C-------~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN---------------TNLKLSNC-------KRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC---------------CcccCCcc-------cceecccceeE
Confidence 5899999999999999999999995 58899999 99998777654
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.38 E-value=1.2e-07 Score=60.69 Aligned_cols=26 Identities=31% Similarity=0.796 Sum_probs=23.8
Q ss_pred hHHhhhhhccCCccccccCCCCcccC
Q 010389 123 GIKKHFCRKHGEKKWKCDKCSKKYAV 148 (512)
Q Consensus 123 ~Lk~H~~~H~gekp~~C~~C~k~F~~ 148 (512)
+|++||++|+++|||.|.+|++.|..
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 58999999999999999999999863
No 20
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.96 E-value=2.7e-06 Score=84.51 Aligned_cols=56 Identities=29% Similarity=0.688 Sum_probs=40.5
Q ss_pred CCcceeCCCCCCCCCCCCCccCChhhHHhhhhhcc-------------------CCccccccCCCCcccChHHHhhhhhh
Q 010389 98 KKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKH-------------------GEKKWKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~-------------------gekp~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
.+|||+|++-+| .|.|++...|+.||..-| ..|||+|.+|+|+|+....|+.|+..
T Consensus 346 d~KpykCpV~gC-----~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 346 DGKPYKCPVEGC-----NKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred cCceecCCCCCc-----hhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 458999998877 899999999999987533 13666676677666666666666543
No 21
>PHA00732 hypothetical protein
Probab=97.88 E-value=9.7e-06 Score=66.24 Aligned_cols=23 Identities=30% Similarity=0.411 Sum_probs=16.2
Q ss_pred CeeccccCcccCChHHHHHHHHh
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRG 82 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~ 82 (512)
+|.|.+|++.|.+..+|+.|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhc
Confidence 46677777777777777777764
No 22
>PHA00616 hypothetical protein
Probab=97.79 E-value=9.1e-06 Score=58.29 Aligned_cols=34 Identities=15% Similarity=0.252 Sum_probs=30.7
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCC
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPE 106 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~ 106 (512)
+|+|..||+.|..+.+|.+|++.|+ +++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h-------------g~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH-------------KQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc-------------CCCccceeE
Confidence 6899999999999999999999999 778887754
No 23
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.77 E-value=2.4e-05 Score=77.99 Aligned_cols=67 Identities=22% Similarity=0.417 Sum_probs=50.0
Q ss_pred CCCCeeccc--cCcccCChHHHHHHHHhcCCCchhh-----ccc-ccccCCcceeCCCCCCCCCCCCCccCChhhHHhhh
Q 010389 57 ATNRFVCEI--CNKGFQRDQNLQLHRRGHNLPWKLR-----QRS-NKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHF 128 (512)
Q Consensus 57 ~~k~f~C~~--Cgk~F~~~~~L~~H~r~H~~p~~~~-----~~~-~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~ 128 (512)
++|+|+|++ |+|.|+.+.-|+.|+..-|...++- ... .-....|||+|++| +|+|++...|+.|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC-------~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVC-------DKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceecccc-------chhhccCccceecc
Confidence 359999998 9999999999999986433111110 001 11346799999999 99999999999997
Q ss_pred hh
Q 010389 129 CR 130 (512)
Q Consensus 129 ~~ 130 (512)
..
T Consensus 419 ~H 420 (423)
T COG5189 419 KH 420 (423)
T ss_pred cc
Confidence 64
No 24
>PHA00616 hypothetical protein
Probab=97.76 E-value=7.9e-06 Score=58.61 Aligned_cols=35 Identities=14% Similarity=0.246 Sum_probs=29.3
Q ss_pred ceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCC
Q 010389 101 VYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKC 142 (512)
Q Consensus 101 ~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C 142 (512)
+|+|+.| ++.|..+..|.+|++.||++++|.|++-
T Consensus 1 pYqC~~C-------G~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRC-------GGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CCccchh-------hHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 5788888 8888888888888888888888888753
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.76 E-value=3e-05 Score=58.68 Aligned_cols=52 Identities=23% Similarity=0.505 Sum_probs=35.2
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhcc
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKH 132 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ 132 (512)
.|.|++|++. .+...|..|....|. ...+.++||+| ...+. .+|.+||+.+|
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~-----------~~~~~v~CPiC-------~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHR-----------SESKNVVCPIC-------SSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCc-----------CCCCCccCCCc-------hhhhh--hHHHHHHHHhc
Confidence 4888889884 556788888766551 13456888888 55433 37777777665
No 26
>PHA00732 hypothetical protein
Probab=97.69 E-value=2.7e-05 Score=63.61 Aligned_cols=45 Identities=27% Similarity=0.420 Sum_probs=37.9
Q ss_pred ceeCCCCCCCCCCCCCccCChhhHHhhhhh-ccCCccccccCCCCcccChHHHhhhhhh
Q 010389 101 VYVCPEKSCVHHDPTRALGDLTGIKKHFCR-KHGEKKWKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 101 ~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~-H~gekp~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
+|.|++| ++.|.+...|++|++. |. ++.|.+|++.|. .|..|.+.
T Consensus 1 py~C~~C-------gk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPIC-------GFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCC-------CCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 5788888 9999999999999985 54 368999999997 57888876
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.67 E-value=2.8e-05 Score=47.98 Aligned_cols=23 Identities=43% Similarity=0.908 Sum_probs=21.8
Q ss_pred eeccccCcccCChHHHHHHHHhc
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
|+|++|++.|.++.+|++|++.|
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 78999999999999999999975
No 28
>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=97.61 E-value=3.4e-05 Score=49.32 Aligned_cols=26 Identities=31% Similarity=0.635 Sum_probs=23.3
Q ss_pred HHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCC
Q 010389 75 NLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGD 120 (512)
Q Consensus 75 ~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~ 120 (512)
+|++|+++|+ ++++|.|++| ++.|.+
T Consensus 1 ~l~~H~~~H~-------------~~k~~~C~~C-------~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHT-------------GEKPYKCPYC-------GKSFSN 26 (26)
T ss_dssp HHHHHHHHHS-------------SSSSEEESSS-------SEEESS
T ss_pred CHHHHhhhcC-------------CCCCCCCCCC-------cCeeCc
Confidence 5899999998 9999999999 888853
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.36 E-value=0.00014 Score=44.71 Aligned_cols=24 Identities=42% Similarity=0.901 Sum_probs=20.7
Q ss_pred eeccccCcccCChHHHHHHHHhcC
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
|.|++|++.|.++..|+.|++.|+
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 789999999999999999999875
No 30
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.35 E-value=0.00019 Score=54.30 Aligned_cols=47 Identities=19% Similarity=0.349 Sum_probs=25.9
Q ss_pred eeCCCCCCCCCCCCCccCChhhHHhhhhhccC--CccccccCCCCcccChHHHhhhhhh
Q 010389 102 YVCPEKSCVHHDPTRALGDLTGIKKHFCRKHG--EKKWKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 102 ~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~g--ekp~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
|.||+| ++ ..+...|..|....|. .+.+.|++|...+. .+|.+|++.
T Consensus 3 f~CP~C-------~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYC-------GK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCC-------CC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 566666 66 4455666666554332 23466666665433 255555554
No 31
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.30 E-value=0.00023 Score=78.67 Aligned_cols=46 Identities=20% Similarity=0.362 Sum_probs=27.9
Q ss_pred CCccCChhhHHhhhhhccCCccccccCCC------CcccChHHHhhhhhhcCCcceecc
Q 010389 115 TRALGDLTGIKKHFCRKHGEKKWKCDKCS------KKYAVQSDYKAHSKVCGTKEYKCN 167 (512)
Q Consensus 115 ~k~F~~~~~Lk~H~~~H~gekp~~C~~C~------k~F~~~~~L~~H~~~h~~kpy~C~ 167 (512)
...|.+...|.+|++.+| |.|.+|. .-|.....|+.|.|. ..|.|+
T Consensus 189 ~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~---~HflCE 240 (669)
T KOG2231|consen 189 HERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK---GHFLCE 240 (669)
T ss_pred hhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh---cCcccc
Confidence 677777777777776654 5566663 234455666666665 125665
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.12 E-value=0.00025 Score=59.51 Aligned_cols=23 Identities=22% Similarity=0.569 Sum_probs=0.0
Q ss_pred eccccCcccCChHHHHHHHHhcC
Q 010389 62 VCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 62 ~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
+|..|+..|.....|..|+...|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H 23 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKH 23 (100)
T ss_dssp -----------------------
T ss_pred Ccccccccccccccccccccccc
Confidence 47788888888888888876554
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.10 E-value=0.00033 Score=44.86 Aligned_cols=25 Identities=36% Similarity=0.711 Sum_probs=23.6
Q ss_pred CeeccccCcccCChHHHHHHHHhcC
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
+|+|.+|++.|.+...|..|++.|+
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 5899999999999999999999885
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.87 E-value=0.00077 Score=56.49 Aligned_cols=74 Identities=15% Similarity=0.226 Sum_probs=22.0
Q ss_pred eCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCChhHHHHH
Q 010389 103 VCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSRRDSFITH 181 (512)
Q Consensus 103 ~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~~~~L~~H 181 (512)
+|.+| +..|.+...|..||...|+...- ....+.....+..+.+..-...+.|. |++.|.....|..|
T Consensus 1 ~C~~C-------~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~H 69 (100)
T PF12756_consen 1 QCLFC-------DESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEH 69 (100)
T ss_dssp -----------------------------------------------------------SSEEBSSSS-EESSHHHHHHH
T ss_pred Ccccc-------ccccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHH
Confidence 36667 99999999999999877753211 11222234444445444333479999 99999999999999
Q ss_pred HHHhcC
Q 010389 182 RAFCDM 187 (512)
Q Consensus 182 ~~~hh~ 187 (512)
++.++.
T Consensus 70 m~~~~H 75 (100)
T PF12756_consen 70 MRSKHH 75 (100)
T ss_dssp HHHTTT
T ss_pred HcCccC
Confidence 987643
No 35
>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=96.72 E-value=0.00076 Score=41.43 Aligned_cols=16 Identities=19% Similarity=0.505 Sum_probs=9.8
Q ss_pred CCccCChhhHHhhhhh
Q 010389 115 TRALGDLTGIKKHFCR 130 (512)
Q Consensus 115 ~k~F~~~~~Lk~H~~~ 130 (512)
++.|.++..|++||+.
T Consensus 7 ~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 7 GKSFSSKSNLKRHMRR 22 (23)
T ss_dssp TEEESSHHHHHHHHHH
T ss_pred CCccCCHHHHHHHHhH
Confidence 6666666666666654
No 36
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.50 E-value=0.0023 Score=39.09 Aligned_cols=23 Identities=22% Similarity=0.639 Sum_probs=11.0
Q ss_pred eecc-CCCccCChhHHHHHHHHhc
Q 010389 164 YKCN-CGAVFSRRDSFITHRAFCD 186 (512)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~hh 186 (512)
|.|+ |++.|.+...|+.|++.||
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 4455 5555555555555555443
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.41 E-value=0.0021 Score=39.82 Aligned_cols=24 Identities=33% Similarity=0.670 Sum_probs=22.3
Q ss_pred eeccccCcccCChHHHHHHHHhcC
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
|+|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999874
No 38
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.28 E-value=0.013 Score=59.40 Aligned_cols=114 Identities=21% Similarity=0.339 Sum_probs=70.5
Q ss_pred Ceeccc--cCcccCChHHHHHHHHhcCCCchhh----------------------ccccc---ccC-CcceeCCCCCCCC
Q 010389 60 RFVCEI--CNKGFQRDQNLQLHRRGHNLPWKLR----------------------QRSNK---EVK-KRVYVCPEKSCVH 111 (512)
Q Consensus 60 ~f~C~~--Cgk~F~~~~~L~~H~r~H~~p~~~~----------------------~~~~~---~~~-~k~~~C~~C~C~~ 111 (512)
.|.|+. |..+......|+.|.+..|..+-|. .+... +.+ +.--.|.+|
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---- 226 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFC---- 226 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhc----
Confidence 378876 7766666778999987655221111 00000 001 112357777
Q ss_pred CCCCCccCChhhHHhhhhhccCCccccccCCCC-------cccChHHHhhhhhhcCCcceecc---CC----CccCChhH
Q 010389 112 HDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSK-------KYAVQSDYKAHSKVCGTKEYKCN---CG----AVFSRRDS 177 (512)
Q Consensus 112 ~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k-------~F~~~~~L~~H~~~h~~kpy~C~---Cg----k~F~~~~~ 177 (512)
...|.+-..|.+|+|..| | +|.+|++ -|+.-..|.+|.+. ..|.|. |- ..|.....
T Consensus 227 ---~~~FYdDDEL~~HcR~~H-E---~ChICD~v~p~~~QYFK~Y~~Le~HF~~---~hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 227 ---KIYFYDDDELRRHCRLRH-E---ACHICDMVGPIRYQYFKSYEDLEAHFRN---AHYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred ---cceecChHHHHHHHHhhh-h---hhhhhhccCccchhhhhCHHHHHHHhhc---CceEEEEEEEecCcEEEeccHHH
Confidence 888888888888888655 3 4555554 36667777788765 227775 52 46788888
Q ss_pred HHHHHHHhcC
Q 010389 178 FITHRAFCDM 187 (512)
Q Consensus 178 L~~H~~~hh~ 187 (512)
|..|+...|.
T Consensus 297 l~~h~~~~h~ 306 (493)
T COG5236 297 LLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHhh
Confidence 8889766554
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.27 E-value=0.0025 Score=74.45 Aligned_cols=121 Identities=13% Similarity=0.217 Sum_probs=85.6
Q ss_pred CCCeeccccCcccCChHHHHHHHHhcCCCch---hhc---------ccccccCCcceeCCCCCCCCCCCCCccCChhhHH
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHRRGHNLPWK---LRQ---------RSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIK 125 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~---~~~---------~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk 125 (512)
.|.|+|+.|+..|+....|..|||..|-... |.. ........++|.|..| ...+..+.+|-
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C-------~~stttng~Ls 535 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRAC-------NYSTTTNGNLS 535 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceee-------eeeeecchHHH
Confidence 4789999999999999999999998541111 110 0112335577888877 99999999999
Q ss_pred hhhhh--ccC-----------------------------------------CccccccCCCCcccChHHHhhhhhh-cCC
Q 010389 126 KHFCR--KHG-----------------------------------------EKKWKCDKCSKKYAVQSDYKAHSKV-CGT 161 (512)
Q Consensus 126 ~H~~~--H~g-----------------------------------------ekp~~C~~C~k~F~~~~~L~~H~~~-h~~ 161 (512)
+|++. |.. +-.|.|.+|++...-..+|+.|+.. +..
T Consensus 536 ihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s 615 (1406)
T KOG1146|consen 536 IHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSS 615 (1406)
T ss_pred HHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCC
Confidence 99864 200 1138899999988888899999887 444
Q ss_pred cc-eecc-CCCccCChhHHHHHHHHh
Q 010389 162 KE-YKCN-CGAVFSRRDSFITHRAFC 185 (512)
Q Consensus 162 kp-y~C~-Cgk~F~~~~~L~~H~~~h 185 (512)
.+ ..|. |.-.+.....+..|.+.+
T Consensus 616 ~~p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 616 SPPSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred CChHHHhhhcchhhccccccCcCCCC
Confidence 43 7776 777776666666555544
No 40
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.17 E-value=0.0029 Score=46.60 Aligned_cols=29 Identities=17% Similarity=0.300 Sum_probs=11.5
Q ss_pred CccccccCCCCcccChHHHhhhhhh-cCCc
Q 010389 134 EKKWKCDKCSKKYAVQSDYKAHSKV-CGTK 162 (512)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~-h~~k 162 (512)
+.|..|.+|+..+.+..+|++|+.+ |+.|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 3444455555555555555555544 4433
No 41
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.08 E-value=0.0075 Score=63.06 Aligned_cols=139 Identities=14% Similarity=0.139 Sum_probs=87.1
Q ss_pred CCCCCCCchhhhhcCcc--ccCCC--CCeecc--ccCcccCChHHHHHHHHhcCCCc--hhh--c---------------
Q 010389 37 LPGTPDPDAEVIALSPK--TLLAT--NRFVCE--ICNKGFQRDQNLQLHRRGHNLPW--KLR--Q--------------- 91 (512)
Q Consensus 37 ~~~~~~~~~~~~~~~~~--~~~~~--k~f~C~--~Cgk~F~~~~~L~~H~r~H~~p~--~~~--~--------------- 91 (512)
...........+..+.+ .|..+ ++|.|+ .|++.|.+...+.+|...|.... .+. .
T Consensus 294 ~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 373 (467)
T COG5048 294 QCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQ 373 (467)
T ss_pred cccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccccCCCCcc
Confidence 33344444445555566 68888 999999 79999999999999999987211 110 0
Q ss_pred ---ccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCc--cccccCCCCcccChHHHhhhhhhcCCcceec
Q 010389 92 ---RSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEK--KWKCDKCSKKYAVQSDYKAHSKVCGTKEYKC 166 (512)
Q Consensus 92 ---~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gek--p~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C 166 (512)
........+.+.|..- .|.+.+.....+..|...|-..+ .+.|..|.+.|.....+..|++.|....+.|
T Consensus 374 ~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 448 (467)
T COG5048 374 SLQQYKDLKNDKKSETLSN-----SCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448 (467)
T ss_pred chhhccCccCCcccccccc-----chhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCcee
Confidence 0001112233344332 23677777777888877777655 4566778888888888888888854444444
Q ss_pred c-CCCccCChhHHHH
Q 010389 167 N-CGAVFSRRDSFIT 180 (512)
Q Consensus 167 ~-Cgk~F~~~~~L~~ 180 (512)
. +-+.|.....+..
T Consensus 449 ~~~~~~~~~~~~~~~ 463 (467)
T COG5048 449 CSILKSFRRDLDLSN 463 (467)
T ss_pred eccccccchhhhhhc
Confidence 3 5555555444433
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.93 E-value=0.005 Score=38.54 Aligned_cols=23 Identities=43% Similarity=0.980 Sum_probs=21.6
Q ss_pred eeccccCcccCChHHHHHHHHhc
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
|.|.+|++.|.++..|+.|++.+
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 78999999999999999999875
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.86 E-value=0.0048 Score=45.48 Aligned_cols=33 Identities=15% Similarity=0.286 Sum_probs=18.3
Q ss_pred cCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCcc
Q 010389 97 VKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKK 136 (512)
Q Consensus 97 ~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp 136 (512)
..+.|..|++| +..+....+|++|+.++|+.||
T Consensus 20 ~S~~PatCP~C-------~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPIC-------GAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT---------EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcc-------hhhccchhhHHHHHHHHhcccC
Confidence 34566677777 6777777777777776666654
No 44
>PRK04860 hypothetical protein; Provisional
Probab=95.75 E-value=0.0047 Score=57.34 Aligned_cols=29 Identities=17% Similarity=0.515 Sum_probs=18.6
Q ss_pred ChhhHHhhhhhccCCccccccCCCCcccC
Q 010389 120 DLTGIKKHFCRKHGEKKWKCDKCSKKYAV 148 (512)
Q Consensus 120 ~~~~Lk~H~~~H~gekp~~C~~C~k~F~~ 148 (512)
....+++|.++|+++++|+|..|++.|..
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 45566666666666666666666666553
No 45
>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=95.62 E-value=0.007 Score=38.61 Aligned_cols=25 Identities=16% Similarity=0.406 Sum_probs=15.0
Q ss_pred ceeCCCCCCCCCCCCCccCChhhHHhhhhhcc
Q 010389 101 VYVCPEKSCVHHDPTRALGDLTGIKKHFCRKH 132 (512)
Q Consensus 101 ~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ 132 (512)
+|+|.+| ++.|.+...|..|++.|+
T Consensus 1 ~~~C~~C-------~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDEC-------GKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTT-------TEEESSHHHHHHHHCTTT
T ss_pred CCCCCcc-------CCccCChhHHHHHhHHhc
Confidence 3556665 666666666666665554
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.57 E-value=0.0072 Score=63.17 Aligned_cols=107 Identities=20% Similarity=0.257 Sum_probs=74.8
Q ss_pred CCeeccccCcccCChHHHHHHHH--hcCCCchhhcccccccCC--cceeCC--CCCCCCCCCCCccCChhhHHhhhhhcc
Q 010389 59 NRFVCEICNKGFQRDQNLQLHRR--GHNLPWKLRQRSNKEVKK--RVYVCP--EKSCVHHDPTRALGDLTGIKKHFCRKH 132 (512)
Q Consensus 59 k~f~C~~Cgk~F~~~~~L~~H~r--~H~~p~~~~~~~~~~~~~--k~~~C~--~C~C~~~~~~k~F~~~~~Lk~H~~~H~ 132 (512)
.++.|..|.+.|.+...|.+|.+ .|. .+ +++.|+ .| ++.|.....+++|...|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-------------~~~~~~~~~p~~~~-------~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-------------GESLKPFSCPYSLC-------GKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-------------cccCCceeeeccCC-------CccccccccccCCccccc
Confidence 47899999999999999999999 676 66 899999 67 999999999999999999
Q ss_pred CCccccccC--CCCcccChHHHhhhh-----hh-cCCcceecc---CCCccCChhHHHHHHHHh
Q 010389 133 GEKKWKCDK--CSKKYAVQSDYKAHS-----KV-CGTKEYKCN---CGAVFSRRDSFITHRAFC 185 (512)
Q Consensus 133 gekp~~C~~--C~k~F~~~~~L~~H~-----~~-h~~kpy~C~---Cgk~F~~~~~L~~H~~~h 185 (512)
+.+++.|.. |.+.+.....-..+. .. +..+.+.|. |...+.+...+..|...|
T Consensus 348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 411 (467)
T COG5048 348 SISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITH 411 (467)
T ss_pred CCCccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccc
Confidence 888777755 555544333311111 11 334455554 555555555555554333
No 47
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.38 E-value=0.01 Score=69.49 Aligned_cols=104 Identities=13% Similarity=0.136 Sum_probs=66.7
Q ss_pred ccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCC
Q 010389 63 CEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKC 142 (512)
Q Consensus 63 C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C 142 (512)
|.-|+..|.++..+.-|+..-+ ...+.|+|+.| +..|+....|..|||..|-+-.- .+|
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~------------S~~kt~~cpkc-------~~~yk~a~~L~vhmRskhp~~~~--~~c 497 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLH------------SFFKTLKCPKC-------NWHYKLAQTLGVHMRSKHPESQS--AYC 497 (1406)
T ss_pred ccchhhhhhhhcccccceeeee------------cccccccCCcc-------chhhhhHHHhhhcccccccccch--hHh
Confidence 4445555555555555543322 35588999999 99999999999999985533211 444
Q ss_pred CCcccChHHHhh-hhhhcCCcceecc-CCCccCChhHHHHHHHHhcCc
Q 010389 143 SKKYAVQSDYKA-HSKVCGTKEYKCN-CGAVFSRRDSFITHRAFCDML 188 (512)
Q Consensus 143 ~k~F~~~~~L~~-H~~~h~~kpy~C~-Cgk~F~~~~~L~~H~~~hh~~ 188 (512)
... .....+.+ -....+.++|.|. |...|..+.+|.+|++.....
T Consensus 498 ~~g-q~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~ 544 (1406)
T KOG1146|consen 498 KAG-QNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHR 544 (1406)
T ss_pred Hhc-cccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHhhH
Confidence 222 11111111 1111566899999 999999999999998765443
No 48
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.76 E-value=0.009 Score=38.32 Aligned_cols=23 Identities=30% Similarity=0.800 Sum_probs=21.2
Q ss_pred eeccccCcccCChHHHHHHHHhc
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
|.|..|++.|.+...|+.|++.+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999998754
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.54 E-value=0.024 Score=35.10 Aligned_cols=23 Identities=26% Similarity=0.600 Sum_probs=19.2
Q ss_pred eeccccCcccCChHHHHHHHHhcC
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
|+|+.|+.... +.+|++|++.|+
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 78999999998 999999999875
No 50
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.39 E-value=0.015 Score=55.14 Aligned_cols=82 Identities=20% Similarity=0.437 Sum_probs=68.0
Q ss_pred CCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcccChHHHhhhhhh-c----------CCcceec
Q 010389 98 KKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDYKAHSKV-C----------GTKEYKC 166 (512)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-h----------~~kpy~C 166 (512)
....|.|++-+| ...|.....+..|..+-|+ -.|.+|.+.|.+...|..|+.- | |.-.|.|
T Consensus 76 ~~~~~~cqvagc-----~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~C 147 (253)
T KOG4173|consen 76 RVPAFACQVAGC-----CQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQC 147 (253)
T ss_pred ccccccccccch-----HHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHH
Confidence 446788999877 8889888888888766554 3799999999999999999876 6 4567999
Q ss_pred c---CCCccCChhHHHHHHHHhcC
Q 010389 167 N---CGAVFSRRDSFITHRAFCDM 187 (512)
Q Consensus 167 ~---Cgk~F~~~~~L~~H~~~hh~ 187 (512)
- |+..|.+...-++|+-..|.
T Consensus 148 lvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 148 LVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHhhhhhhhhhhhhhhHHHHhcc
Confidence 6 99999999999999866665
No 51
>PRK04860 hypothetical protein; Provisional
Probab=93.94 E-value=0.033 Score=51.78 Aligned_cols=39 Identities=21% Similarity=0.374 Sum_probs=32.8
Q ss_pred CCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCCh
Q 010389 59 NRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDL 121 (512)
Q Consensus 59 k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~ 121 (512)
-+|.|. |++ ....+++|.++|. ++++|+|..| +..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~-------------g~~~YrC~~C-------~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVR-------------GEAVYRCRRC-------GETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhc-------------CCccEECCCC-------CceeEEe
Confidence 479998 998 6778999999998 8999999999 6666543
No 52
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.93 E-value=0.034 Score=34.47 Aligned_cols=23 Identities=30% Similarity=0.691 Sum_probs=12.5
Q ss_pred eeCCCCCCCCCCCCCccCChhhHHhhhhhcc
Q 010389 102 YVCPEKSCVHHDPTRALGDLTGIKKHFCRKH 132 (512)
Q Consensus 102 ~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ 132 (512)
|+|++| ..... +..|++|+++|+
T Consensus 1 y~C~~C-------~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHC-------SYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSS-------S-EES-HHHHHHHHHHHH
T ss_pred CCCCCC-------CCcCC-HHHHHHHHHhhC
Confidence 456666 55555 566666666654
No 53
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.66 E-value=0.052 Score=60.52 Aligned_cols=83 Identities=28% Similarity=0.569 Sum_probs=53.0
Q ss_pred eccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCcccccc-
Q 010389 62 VCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCD- 140 (512)
Q Consensus 62 ~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~- 140 (512)
.|..|...|.....|.+|++.+| |.|.+|.- -..+..-|.+...|..|.+.+| |.|.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h-----------------~~chfC~~-~~~~neyy~~~~dLe~HfR~~H----flCE~ 241 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH-----------------EFCHFCDY-KTGQNEYYNDYDDLEEHFRKGH----FLCEE 241 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce-----------------eheeecCc-ccccchhcccchHHHHHhhhcC----ccccc
Confidence 47777777777777777776665 67777732 2334778888999999999887 6776
Q ss_pred -CCC-CcccC----hHHHhhhhhh-cCCcceec
Q 010389 141 -KCS-KKYAV----QSDYKAHSKV-CGTKEYKC 166 (512)
Q Consensus 141 -~C~-k~F~~----~~~L~~H~~~-h~~kpy~C 166 (512)
.|- +.|.. ...|++|.+. ..++-|.|
T Consensus 242 ~~C~~~~f~~~~~~ei~lk~~~~~~~~e~~~~~ 274 (669)
T KOG2231|consen 242 EFCRTKKFYVAFELEIELKAHNRFIQHEKCYIC 274 (669)
T ss_pred cccccceeeehhHHHHHHHhhccccchheeccC
Confidence 443 23333 3344444433 34555666
No 54
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.63 E-value=0.045 Score=33.58 Aligned_cols=17 Identities=12% Similarity=0.315 Sum_probs=8.9
Q ss_pred CCccCChhhHHhhhhhc
Q 010389 115 TRALGDLTGIKKHFCRK 131 (512)
Q Consensus 115 ~k~F~~~~~Lk~H~~~H 131 (512)
++.|.....|..|++.|
T Consensus 7 ~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 7 GKVFKSKSALKEHMRTH 23 (26)
T ss_pred cchhCCHHHHHHHHHHh
Confidence 55555555555555543
No 55
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.24 E-value=0.051 Score=34.78 Aligned_cols=22 Identities=32% Similarity=0.741 Sum_probs=13.2
Q ss_pred ccccCCCCcccChHHHhhhhhh
Q 010389 137 WKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
|.|.+|++.|.....|+.|++.
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 4566666666666666666553
No 56
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.73 E-value=0.05 Score=33.88 Aligned_cols=20 Identities=25% Similarity=0.752 Sum_probs=8.7
Q ss_pred cccCCCCcccChHHHhhhhh
Q 010389 138 KCDKCSKKYAVQSDYKAHSK 157 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~ 157 (512)
.|.+|++.|.....|+.|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 34444444444444444443
No 57
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=91.85 E-value=0.24 Score=50.60 Aligned_cols=87 Identities=17% Similarity=0.326 Sum_probs=63.4
Q ss_pred CCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccC----------------------CccccccCCCCcccChHHHhhh
Q 010389 98 KKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHG----------------------EKKWKCDKCSKKYAVQSDYKAH 155 (512)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~g----------------------ekp~~C~~C~k~F~~~~~L~~H 155 (512)
.....+|-+|- ......++.+-.|+-..|+ -..++|-+|.|.|..+..|+.|
T Consensus 141 t~fslqClFCn------~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeH 214 (423)
T KOG2482|consen 141 TIFSLQCLFCN------NEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEH 214 (423)
T ss_pred CeeeeEEEEec------chhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHH
Confidence 34556788872 3455667778888765443 1237899999999999999999
Q ss_pred hhh--cC-----------------------------------------------------Ccc--eecc-CCCccCChhH
Q 010389 156 SKV--CG-----------------------------------------------------TKE--YKCN-CGAVFSRRDS 177 (512)
Q Consensus 156 ~~~--h~-----------------------------------------------------~kp--y~C~-Cgk~F~~~~~ 177 (512)
||. |. ..+ .+|- |...+-....
T Consensus 215 MrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~ 294 (423)
T KOG2482|consen 215 MRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVF 294 (423)
T ss_pred HHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHH
Confidence 987 50 111 4788 9998888999
Q ss_pred HHHHHHHhcCcch
Q 010389 178 FITHRAFCDMLTK 190 (512)
Q Consensus 178 L~~H~~~hh~~~~ 190 (512)
|..||+..|...-
T Consensus 295 l~eHmk~vHe~Dl 307 (423)
T KOG2482|consen 295 LFEHMKIVHEFDL 307 (423)
T ss_pred HHHHHHHHHHhhH
Confidence 9999999886433
No 58
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=91.57 E-value=0.16 Score=51.77 Aligned_cols=25 Identities=32% Similarity=0.611 Sum_probs=22.5
Q ss_pred CCeeccccCcccCChHHHHHHHHhc
Q 010389 59 NRFVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 59 k~f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
.++.|-.|.|.|+.+..|+.|||..
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhc
Confidence 4689999999999999999999864
No 59
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.88 E-value=0.21 Score=31.56 Aligned_cols=21 Identities=29% Similarity=0.680 Sum_probs=18.1
Q ss_pred eeccccCcccCChHHHHHHHHh
Q 010389 61 FVCEICNKGFQRDQNLQLHRRG 82 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~ 82 (512)
..|++|++.| ....|.+|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5799999999 67789999864
No 60
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=90.77 E-value=0.22 Score=52.03 Aligned_cols=121 Identities=13% Similarity=0.232 Sum_probs=71.2
Q ss_pred CCeec--cccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCC--
Q 010389 59 NRFVC--EICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGE-- 134 (512)
Q Consensus 59 k~f~C--~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ge-- 134 (512)
.-|.| +.|+..+-.+.++.+|.++|.+..........+ -...|.|-.- +|.+ +-.....|-.-|+..
T Consensus 270 Ehyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~r-fs~syhC~~~-----~C~k---sTsdV~~h~nFht~~~n 340 (480)
T KOG4377|consen 270 EHYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHR-FSNSYHCTGQ-----ICEK---STSDVLLHDNFHTDKRN 340 (480)
T ss_pred hhhcccCccccccccchhhhHHHHHHHhhcccccccchhh-cCccchhhhc-----ccCc---ccccccccCcccccccc
Confidence 34777 459888888999999999996211100000000 0112455433 4466 556667776666532
Q ss_pred -----ccccccCCC--CcccChHHHhhhhhhc-----C--------------------Ccceecc---CCCccCChhHHH
Q 010389 135 -----KKWKCDKCS--KKYAVQSDYKAHSKVC-----G--------------------TKEYKCN---CGAVFSRRDSFI 179 (512)
Q Consensus 135 -----kp~~C~~C~--k~F~~~~~L~~H~~~h-----~--------------------~kpy~C~---Cgk~F~~~~~L~ 179 (512)
..|.|..|+ ..|+...+-..|.+-+ | -..|.|. |+.+|.....+.
T Consensus 341 ~GfrrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~ 420 (480)
T KOG4377|consen 341 NGFRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMA 420 (480)
T ss_pred CceecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhh
Confidence 237788877 5555333333333221 0 0235676 999999999999
Q ss_pred HHHHHhcCc
Q 010389 180 THRAFCDML 188 (512)
Q Consensus 180 ~H~~~hh~~ 188 (512)
.|.++|...
T Consensus 421 shkrkheRq 429 (480)
T KOG4377|consen 421 SHKRKHERQ 429 (480)
T ss_pred hhhhhhhhh
Confidence 999998754
No 61
>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=90.08 E-value=0.23 Score=33.43 Aligned_cols=24 Identities=29% Similarity=0.796 Sum_probs=21.7
Q ss_pred CeeccccCcccCChHHHHHHHHhc
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
+|.|++|++.|.....+..|++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 689999999999999999998754
No 62
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=90.06 E-value=0.47 Score=49.31 Aligned_cols=118 Identities=24% Similarity=0.418 Sum_probs=84.4
Q ss_pred CeeccccCcccCChHHHHHHHHh--cC---------CC-ch---hhcc---------cccccCCcceeCCCCCCCCCCCC
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRG--HN---------LP-WK---LRQR---------SNKEVKKRVYVCPEKSCVHHDPT 115 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~--H~---------~p-~~---~~~~---------~~~~~~~k~~~C~~C~C~~~~~~ 115 (512)
-|.|.-|...|.....-+.|+++ |. .| .. +..+ ...+...-++.|..| .
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c-------~ 75 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEAC-------N 75 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHh-------h
Confidence 48999999999999888889764 43 11 00 0000 012445678999999 9
Q ss_pred CccCChhhHHhhhhhcc---------------------------------C--C--------------------------
Q 010389 116 RALGDLTGIKKHFCRKH---------------------------------G--E-------------------------- 134 (512)
Q Consensus 116 k~F~~~~~Lk~H~~~H~---------------------------------g--e-------------------------- 134 (512)
|.|........|++... + +
T Consensus 76 k~~~s~~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~~E~~~~~d~~~e~~~dd~~Edi~ 155 (390)
T KOG2785|consen 76 KSFASPKAHENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKWYEVDSDEDSSEEEEEDDEEEDIE 155 (390)
T ss_pred ccccChhhHHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccchhhcccccccchhhccCcchhhhh
Confidence 99999888877765310 0 0
Q ss_pred ---------ccccccCCCCcccChHHHhhhhhh-cC-----------------------Ccceecc-CC---CccCChhH
Q 010389 135 ---------KKWKCDKCSKKYAVQSDYKAHSKV-CG-----------------------TKEYKCN-CG---AVFSRRDS 177 (512)
Q Consensus 135 ---------kp~~C~~C~k~F~~~~~L~~H~~~-h~-----------------------~kpy~C~-Cg---k~F~~~~~ 177 (512)
-|-.|-+|++.|........||.. |+ ..-|.|- |+ +.|..-..
T Consensus 156 ~d~~~e~e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~slea 235 (390)
T KOG2785|consen 156 EDGDDEDELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEA 235 (390)
T ss_pred hccchhcccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHH
Confidence 013489999999999999999988 74 2347888 88 89999999
Q ss_pred HHHHHHH
Q 010389 178 FITHRAF 184 (512)
Q Consensus 178 L~~H~~~ 184 (512)
.+.||..
T Consensus 236 vr~HM~~ 242 (390)
T KOG2785|consen 236 VRAHMRD 242 (390)
T ss_pred HHHHHhh
Confidence 9999854
No 63
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.55 E-value=0.29 Score=50.02 Aligned_cols=79 Identities=18% Similarity=0.336 Sum_probs=56.1
Q ss_pred eeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCcccccc
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCD 140 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~ 140 (512)
-.|..|.+.|.....|.+|+|..| ++.|.|+.- -..-..-|++...|.+|++.-| |.|.
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~H--------------E~ChICD~v---~p~~~QYFK~Y~~Le~HF~~~h----y~ct 279 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRH--------------EACHICDMV---GPIRYQYFKSYEDLEAHFRNAH----YCCT 279 (493)
T ss_pred chhhhccceecChHHHHHHHHhhh--------------hhhhhhhcc---CccchhhhhCHHHHHHHhhcCc----eEEE
Confidence 369999999999999999998764 444444332 2222345888899999997654 7776
Q ss_pred C--CC----CcccChHHHhhhhhh-cC
Q 010389 141 K--CS----KKYAVQSDYKAHSKV-CG 160 (512)
Q Consensus 141 ~--C~----k~F~~~~~L~~H~~~-h~ 160 (512)
+ |- ..|...-.|..|+.. |+
T Consensus 280 ~qtc~~~k~~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 280 FQTCRVGKCYVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEEEecCcEEEeccHHHHHHHHHHHhh
Confidence 5 32 357777788888766 64
No 64
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.53 E-value=0.15 Score=48.60 Aligned_cols=81 Identities=21% Similarity=0.377 Sum_probs=65.1
Q ss_pred CCCCCeeccc--cCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhcc-
Q 010389 56 LATNRFVCEI--CNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKH- 132 (512)
Q Consensus 56 ~~~k~f~C~~--Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~- 132 (512)
.....|.|.+ |-..|....++..|..+-| --.|.+| .+.|.+..-|..|+..-|
T Consensus 75 ~~~~~~~cqvagc~~~~d~lD~~E~hY~~~h----------------~~sCs~C-------~r~~Pt~hLLd~HI~E~HD 131 (253)
T KOG4173|consen 75 PRVPAFACQVAGCCQVFDALDDYEHHYHTLH----------------GNSCSFC-------KRAFPTGHLLDAHILEWHD 131 (253)
T ss_pred cccccccccccchHHHHhhhhhHHHhhhhcc----------------cchhHHH-------HHhCCchhhhhHHHHHHHH
Confidence 3456789998 8899998888888876544 2368888 999999999999987644
Q ss_pred ---------CCccccccC--CCCcccChHHHhhhhhh-c
Q 010389 133 ---------GEKKWKCDK--CSKKYAVQSDYKAHSKV-C 159 (512)
Q Consensus 133 ---------gekp~~C~~--C~k~F~~~~~L~~H~~~-h 159 (512)
|...|.|-+ |+..|.+....++|+-. |
T Consensus 132 s~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 132 SLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred HHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 344699966 99999999999999877 5
No 65
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=87.03 E-value=0.94 Score=47.15 Aligned_cols=51 Identities=20% Similarity=0.297 Sum_probs=43.2
Q ss_pred ceeCCCCCCCCCCCCCccCChhhHHhhhhhccCC-----------------------ccccccCCC---CcccChHHHhh
Q 010389 101 VYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGE-----------------------KKWKCDKCS---KKYAVQSDYKA 154 (512)
Q Consensus 101 ~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ge-----------------------kp~~C~~C~---k~F~~~~~L~~ 154 (512)
|-.|-+| .+.|.+...-.+||..||+- +-|.|-+|. +.|......+.
T Consensus 166 Pt~CLfC-------~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~ 238 (390)
T KOG2785|consen 166 PTDCLFC-------DKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRA 238 (390)
T ss_pred Ccceeec-------CCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHH
Confidence 3456666 99999999999999999871 337899999 99999999999
Q ss_pred hhhh
Q 010389 155 HSKV 158 (512)
Q Consensus 155 H~~~ 158 (512)
||..
T Consensus 239 HM~~ 242 (390)
T KOG2785|consen 239 HMRD 242 (390)
T ss_pred HHhh
Confidence 9987
No 66
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=86.96 E-value=1.4 Score=48.54 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=25.9
Q ss_pred cCCCCCeeccccCcccCChHHHHHHHHhcC
Q 010389 55 LLATNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 55 ~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
....++-+|..||+.|.+.....+||..|-
T Consensus 413 Ly~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 413 LYKDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred hccCCcchhcccccccccchhhhhHhhhhh
Confidence 345667899999999999999999999884
No 67
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=86.27 E-value=0.23 Score=48.26 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=15.6
Q ss_pred ccccCcccCChHHHHHHHHhcC
Q 010389 63 CEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 63 C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
|=.|++.|..+.-|..|++..|
T Consensus 13 cwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred eeecccccchhhhhhhhhhhcc
Confidence 6777777777777777766543
No 68
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=86.23 E-value=0.25 Score=47.99 Aligned_cols=38 Identities=26% Similarity=0.411 Sum_probs=28.2
Q ss_pred CCccCChhhHHhhhhhccCCccccccCCCCcccChHHHhhhh
Q 010389 115 TRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDYKAHS 156 (512)
Q Consensus 115 ~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~ 156 (512)
++.|.+..-|.+|.+.. .|+|.+|.|....--.|..|-
T Consensus 17 nrefddekiliqhqkak----hfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 17 NREFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred ccccchhhhhhhhhhhc----cceeeeehhhhccCCCceeeh
Confidence 88888888888887653 488888888766655666653
No 69
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=85.27 E-value=0.49 Score=46.53 Aligned_cols=44 Identities=25% Similarity=0.677 Sum_probs=23.8
Q ss_pred ccccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCChhHHHHHH
Q 010389 137 WKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSRRDSFITHR 182 (512)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~~~~L~~H~ 182 (512)
|.|.+||-.... ..+.+|+..+...-|.|. |++.|-+ ..++.|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhh
Confidence 556666655433 244556666333556666 6666655 4455553
No 70
>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=84.87 E-value=0.61 Score=31.30 Aligned_cols=23 Identities=22% Similarity=0.445 Sum_probs=16.8
Q ss_pred cccccCCCCcccChHHHhhhhhh
Q 010389 136 KWKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
+|.|.+|++.|.....++.|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46777777777777777777664
No 71
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=84.47 E-value=0.66 Score=29.26 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=9.5
Q ss_pred cccCCCCcccChHHHhhhhh
Q 010389 138 KCDKCSKKYAVQSDYKAHSK 157 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~ 157 (512)
.|.+|++.| ....|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455555555 4444555543
No 72
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.23 E-value=0.59 Score=45.56 Aligned_cols=25 Identities=20% Similarity=0.457 Sum_probs=19.4
Q ss_pred CCCeeccccCcccCChHHHHHHHHh
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHRRG 82 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~r~ 82 (512)
+|.+.|++|++.|.++.-+....|.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 4678999999999998766555544
No 73
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.46 E-value=3.4 Score=36.03 Aligned_cols=24 Identities=25% Similarity=0.600 Sum_probs=12.6
Q ss_pred cceecc-CCCccCChhHHHHHHHHh
Q 010389 162 KEYKCN-CGAVFSRRDSFITHRAFC 185 (512)
Q Consensus 162 kpy~C~-Cgk~F~~~~~L~~H~~~h 185 (512)
..|+|. |...|=-.-..-.|...|
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cceeCCCCCCccccccchhhhhhcc
Confidence 356666 666655554454554433
No 74
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=77.73 E-value=1.2 Score=33.53 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=25.2
Q ss_pred cCCCCCeeccccCcccCChHHHHHHHHhcC
Q 010389 55 LLATNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 55 ~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
..++.-+.|+-|++.|..+.++.+|.+..|
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 345567899999999999999999987655
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=76.43 E-value=5.6 Score=34.23 Aligned_cols=26 Identities=19% Similarity=0.459 Sum_probs=20.6
Q ss_pred CCCeeccccCcccCChHHHHHHHHhcC
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
-+...|..|.....- ..+..|++..+
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H 34 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRH 34 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhc
Confidence 456789999988776 78999998443
No 76
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=76.01 E-value=0.71 Score=47.36 Aligned_cols=27 Identities=7% Similarity=-0.114 Sum_probs=22.4
Q ss_pred ccccCCCCCeeccccCcccCChHHHHHH
Q 010389 52 PKTLLATNRFVCEICNKGFQRDQNLQLH 79 (512)
Q Consensus 52 ~~~~~~~k~f~C~~Cgk~F~~~~~L~~H 79 (512)
....+..++|+|. |++.+.++..|+.|
T Consensus 205 ~T~~t~~~p~k~~-~~~~~~T~~~l~~H 231 (442)
T KOG4124|consen 205 STAETTGTPKKMP-ESLVMDTSSPLSDH 231 (442)
T ss_pred cccccccCCccCc-ccccccccchhhhc
Confidence 4445566799997 99999999999998
No 77
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=75.24 E-value=1.3 Score=33.46 Aligned_cols=26 Identities=27% Similarity=0.646 Sum_probs=14.1
Q ss_pred CCccccccCCCCcccChHHHhhhhhh
Q 010389 133 GEKKWKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 133 gekp~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
||.-++|+.|++.|.....+.+|...
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhH
Confidence 44445555555555555555555544
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=73.38 E-value=1.3 Score=43.19 Aligned_cols=41 Identities=24% Similarity=0.534 Sum_probs=21.8
Q ss_pred ccccccCCCCcccChHHHhhhhhh-c----------CC-----cceecc-CCCccCCh
Q 010389 135 KKWKCDKCSKKYAVQSDYKAHSKV-C----------GT-----KEYKCN-CGAVFSRR 175 (512)
Q Consensus 135 kp~~C~~C~k~F~~~~~L~~H~~~-h----------~~-----kpy~C~-Cgk~F~~~ 175 (512)
|.+.|++|++.|..+.-+....+. . +. ....|+ |+..|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 445566666666555444444332 1 11 225788 88877655
No 79
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=72.81 E-value=0.81 Score=46.96 Aligned_cols=29 Identities=17% Similarity=0.651 Sum_probs=22.9
Q ss_pred cCCCCCeeccc--cCcccCChHHHHHHHHhc
Q 010389 55 LLATNRFVCEI--CNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 55 ~~~~k~f~C~~--Cgk~F~~~~~L~~H~r~H 83 (512)
..-.++|+|++ |.|.+.....|+.|...-
T Consensus 344 ~~~~~~~~~~vp~~~~~~~n~ng~~~~~~~~ 374 (442)
T KOG4124|consen 344 VVVDKPYKCPVPNCDKAYKNQNGLKYHKLHG 374 (442)
T ss_pred EEecCCCCCCCCcchhhcccCcceeeccccC
Confidence 34568899975 999999999898886543
No 80
>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=72.14 E-value=2.6 Score=36.59 Aligned_cols=15 Identities=20% Similarity=0.643 Sum_probs=8.5
Q ss_pred ccccccCCCCcccCh
Q 010389 135 KKWKCDKCSKKYAVQ 149 (512)
Q Consensus 135 kp~~C~~C~k~F~~~ 149 (512)
.|..|++||..|...
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 455566666665444
No 81
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=71.98 E-value=3.4 Score=29.42 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=17.6
Q ss_pred CCCCeeccccCcccCCh----HHHHHHHHh
Q 010389 57 ATNRFVCEICNKGFQRD----QNLQLHRRG 82 (512)
Q Consensus 57 ~~k~f~C~~Cgk~F~~~----~~L~~H~r~ 82 (512)
..+..+|.+|++.|... .+|.+|++.
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 45678999999999885 789999954
No 82
>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=68.61 E-value=7.9 Score=33.28 Aligned_cols=25 Identities=20% Similarity=0.469 Sum_probs=22.5
Q ss_pred ceec----c-CCCccCChhHHHHHHHHhcC
Q 010389 163 EYKC----N-CGAVFSRRDSFITHRAFCDM 187 (512)
Q Consensus 163 py~C----~-Cgk~F~~~~~L~~H~~~hh~ 187 (512)
-|.| . |++.+.....+.+|.+.+|+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 7 99999999999999998874
No 83
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=66.96 E-value=1.9 Score=42.04 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=17.9
Q ss_pred CCccccccCCCCcccChHHHhhhhhh-cCC
Q 010389 133 GEKKWKCDKCSKKYAVQSDYKAHSKV-CGT 161 (512)
Q Consensus 133 gekp~~C~~C~k~F~~~~~L~~H~~~-h~~ 161 (512)
.+..|.|..|+|.|+-..-.++|+.. |.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 34457777777777777777777766 543
No 84
>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=66.54 E-value=4.3 Score=27.26 Aligned_cols=11 Identities=27% Similarity=0.954 Sum_probs=8.1
Q ss_pred ccccccCCCCc
Q 010389 135 KKWKCDKCSKK 145 (512)
Q Consensus 135 kp~~C~~C~k~ 145 (512)
.++.|++|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 67888888753
No 85
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.57 E-value=2.3 Score=39.26 Aligned_cols=19 Identities=16% Similarity=0.511 Sum_probs=13.8
Q ss_pred cccccCCCCcccChHHHhh
Q 010389 136 KWKCDKCSKKYAVQSDYKA 154 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~ 154 (512)
.|+|+.|+++|.....+..
T Consensus 28 ~~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 28 RRECLACGKRFTTFERVEL 46 (154)
T ss_pred eeeccccCCcceEeEeccC
Confidence 3789999999876655443
No 86
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=64.75 E-value=4 Score=35.42 Aligned_cols=31 Identities=26% Similarity=0.493 Sum_probs=22.6
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCCh
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDL 121 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~ 121 (512)
...|+.||++|.- | .+.|.+||.| +..|.-.
T Consensus 9 KR~Cp~CG~kFYD---L---------------------nk~PivCP~C-------G~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYD---L---------------------NKDPIVCPKC-------GTEFPPE 39 (108)
T ss_pred cccCCCCcchhcc---C---------------------CCCCccCCCC-------CCccCcc
Confidence 3579999999953 2 3478899999 6666443
No 87
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.34 E-value=2.9 Score=34.59 Aligned_cols=11 Identities=64% Similarity=1.633 Sum_probs=6.7
Q ss_pred ccccCCCCccc
Q 010389 137 WKCDKCSKKYA 147 (512)
Q Consensus 137 ~~C~~C~k~F~ 147 (512)
|.|..|++.|+
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 56666666654
No 88
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=61.74 E-value=35 Score=34.89 Aligned_cols=110 Identities=13% Similarity=0.144 Sum_probs=57.8
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCC------CCCCccCChhhHHhhhhhccC
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHH------DPTRALGDLTGIKKHFCRKHG 133 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~------~~~k~F~~~~~Lk~H~~~H~g 133 (512)
.|.|.. .-.|+....+--|...-+ +...++.+....+.+-|+.|+-.-. -|...|..+.. +.| .
T Consensus 53 ~~~~~~-~p~f~~~~r~pphl~w~~---~V~~~gek~l~p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CA-----r~~-~ 122 (389)
T KOG2932|consen 53 HLVLAD-LPVFKGIGRVPPHLTWIK---PVGRRGEKQLGPRVHFCDRCDFPIAIYGRMIPCKHVFCLECA-----RSD-S 122 (389)
T ss_pred hhhhcC-CchhcccccCCCceeeee---ecccccccccCcceEeecccCCcceeeecccccchhhhhhhh-----hcC-c
Confidence 344433 334555444443332221 2334555667778899999953100 01122221111 111 1
Q ss_pred CccccccCCCCcccChHHHhhhhhhcCCcceecc----CCCccCChhHHHHHHHHhcC
Q 010389 134 EKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN----CGAVFSRRDSFITHRAFCDM 187 (512)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~----Cgk~F~~~~~L~~H~~~hh~ 187 (512)
+| .|..|.....+.++ +.-+..|.|. |.++|..+..|+.|+..-|.
T Consensus 123 dK--~Cp~C~d~VqrIeq------~~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 123 DK--ICPLCDDRVQRIEQ------IMMGGIFMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred cc--cCcCcccHHHHHHH------hcccceEEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 23 67777554322211 1345789996 99999999999999866554
No 89
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=61.28 E-value=8.5 Score=38.01 Aligned_cols=78 Identities=19% Similarity=0.399 Sum_probs=45.9
Q ss_pred CChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcccChH
Q 010389 71 QRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQS 150 (512)
Q Consensus 71 ~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F~~~~ 150 (512)
.++.+|+.+.+.+. .......+.|.|..|. .. -++ ++-.....-+|..|.+.|.---
T Consensus 90 LTe~Nlrm~d~a~~--------~~ip~~drqFaC~~Cd-------~~-----WwR---rvp~rKeVSRCr~C~~rYDPVP 146 (278)
T PF15135_consen 90 LTEENLRMFDDAQE--------NLIPSVDRQFACSSCD-------HM-----WWR---RVPQRKEVSRCRKCRKRYDPVP 146 (278)
T ss_pred chHHHHHHhhhhhh--------ccccccceeeeccccc-------hH-----HHh---ccCcccccccccccccccCCCc
Confidence 35678888777664 1122345889999992 11 111 1112233467999988875322
Q ss_pred HHhhhhhhcCCcceecc-CCCccCCh
Q 010389 151 DYKAHSKVCGTKEYKCN-CGAVFSRR 175 (512)
Q Consensus 151 ~L~~H~~~h~~kpy~C~-Cgk~F~~~ 175 (512)
. -+..|--.|.|. |++.|.-.
T Consensus 147 ~----dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 147 C----DKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred c----ccccceeeeecccccccchhh
Confidence 1 112455679998 99999754
No 90
>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=61.04 E-value=6 Score=35.17 Aligned_cols=13 Identities=0% Similarity=0.056 Sum_probs=6.4
Q ss_pred ccccccCCCCccc
Q 010389 135 KKWKCDKCSKKYA 147 (512)
Q Consensus 135 kp~~C~~C~k~F~ 147 (512)
.|..|.+||..|.
T Consensus 25 ~p~vcP~cg~~~~ 37 (129)
T TIGR02300 25 RPAVSPYTGEQFP 37 (129)
T ss_pred CCccCCCcCCccC
Confidence 3445555555543
No 91
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=60.97 E-value=6.1 Score=29.05 Aligned_cols=24 Identities=42% Similarity=0.761 Sum_probs=20.1
Q ss_pred CeeccccCcccCCh-----HHHHHHHH-hc
Q 010389 60 RFVCEICNKGFQRD-----QNLQLHRR-GH 83 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~-----~~L~~H~r-~H 83 (512)
.-.|.+|++.+... .+|.+|++ .|
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 46899999999877 58999998 45
No 92
>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=58.51 E-value=4.3 Score=39.55 Aligned_cols=34 Identities=29% Similarity=0.431 Sum_probs=26.1
Q ss_pred cccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCc
Q 010389 95 KEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEK 135 (512)
Q Consensus 95 ~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gek 135 (512)
.+..+..|.|++| +|.|+-..-+++|+...|.|+
T Consensus 71 ~e~~~~K~~C~lc-------~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 71 KEEDEDKWRCPLC-------GKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp -SSSSEEEEE-SS-------S-EESSHHHHHHHHHHH-HHH
T ss_pred HHHcCCEECCCCC-------CcccCChHHHHHHHhhcCHHH
Confidence 3456778999999 999999999999999888765
No 93
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=58.17 E-value=3.8 Score=37.88 Aligned_cols=15 Identities=27% Similarity=0.766 Sum_probs=10.7
Q ss_pred cceecc-CCCccCChh
Q 010389 162 KEYKCN-CGAVFSRRD 176 (512)
Q Consensus 162 kpy~C~-Cgk~F~~~~ 176 (512)
+.|+|. |+++|..-.
T Consensus 27 ~~~~c~~c~~~f~~~e 42 (154)
T PRK00464 27 RRRECLACGKRFTTFE 42 (154)
T ss_pred eeeeccccCCcceEeE
Confidence 348888 888887653
No 94
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.13 E-value=6.9 Score=35.70 Aligned_cols=40 Identities=18% Similarity=0.478 Sum_probs=24.0
Q ss_pred cccCCcceeCCCCCCCCCCCCCccCChhhHHh-hhhhccCCccccccCCCCcc
Q 010389 95 KEVKKRVYVCPEKSCVHHDPTRALGDLTGIKK-HFCRKHGEKKWKCDKCSKKY 146 (512)
Q Consensus 95 ~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~-H~~~H~gekp~~C~~C~k~F 146 (512)
......-|.|+.| +..|.....+.. ++ +..|.|+.|+...
T Consensus 93 ~e~~~~~Y~Cp~C-------~~~y~~~ea~~~~d~-----~~~f~Cp~Cg~~l 133 (147)
T smart00531 93 DETNNAYYKCPNC-------QSKYTFLEANQLLDM-----DGTFTCPRCGEEL 133 (147)
T ss_pred cccCCcEEECcCC-------CCEeeHHHHHHhcCC-----CCcEECCCCCCEE
Confidence 3345567888887 777765544332 21 2337888887754
No 95
>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=57.20 E-value=5.9 Score=28.14 Aligned_cols=14 Identities=43% Similarity=0.645 Sum_probs=5.1
Q ss_pred ccccccCCCCcccC
Q 010389 135 KKWKCDKCSKKYAV 148 (512)
Q Consensus 135 kp~~C~~C~k~F~~ 148 (512)
...+|.+|++.|..
T Consensus 15 ~~a~C~~C~~~~~~ 28 (45)
T PF02892_consen 15 KKAKCKYCGKVIKY 28 (45)
T ss_dssp S-EEETTTTEE---
T ss_pred CeEEeCCCCeEEee
Confidence 33455555555443
No 96
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=56.62 E-value=7.5 Score=36.33 Aligned_cols=25 Identities=32% Similarity=0.658 Sum_probs=19.6
Q ss_pred cceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCC
Q 010389 100 RVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSK 144 (512)
Q Consensus 100 k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k 144 (512)
+.|+|++| |. +|-++-|.+|++|+-
T Consensus 133 ~~~vC~vC-------Gy-------------~~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVC-------GY-------------THEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCC-------CC-------------cccCCCCCcCCCCCC
Confidence 38999999 43 336788999999984
No 97
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.95 E-value=8.1 Score=36.36 Aligned_cols=13 Identities=31% Similarity=0.406 Sum_probs=9.7
Q ss_pred cCCcceeCCCCCC
Q 010389 97 VKKRVYVCPEKSC 109 (512)
Q Consensus 97 ~~~k~~~C~~C~C 109 (512)
..+..|.|++|-|
T Consensus 127 ~~~~~~~CPiCl~ 139 (187)
T KOG0320|consen 127 RKEGTYKCPICLD 139 (187)
T ss_pred ccccccCCCceec
Confidence 3556699999955
No 98
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=54.39 E-value=5 Score=41.41 Aligned_cols=33 Identities=9% Similarity=0.199 Sum_probs=24.3
Q ss_pred CccccccCCCCcccChHHHhhhhhh-cCCcceec
Q 010389 134 EKKWKCDKCSKKYAVQSDYKAHSKV-CGTKEYKC 166 (512)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C 166 (512)
..-|.|.+|++.-.....|..|... |-+-.+.|
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~ 110 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSV 110 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcce
Confidence 3458888888888888888888877 76655433
No 99
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=54.15 E-value=13 Score=28.58 Aligned_cols=14 Identities=21% Similarity=0.430 Sum_probs=9.9
Q ss_pred CeeccccCcccCCh
Q 010389 60 RFVCEICNKGFQRD 73 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~ 73 (512)
.|.|+.||+.-..+
T Consensus 27 ~F~CPnCGe~~I~R 40 (61)
T COG2888 27 KFPCPNCGEVEIYR 40 (61)
T ss_pred EeeCCCCCceeeeh
Confidence 58899999755443
No 100
>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=53.86 E-value=11 Score=33.88 Aligned_cols=26 Identities=31% Similarity=0.695 Sum_probs=17.5
Q ss_pred CCCCCeeccccCcccCChHHHHHHHHhcC
Q 010389 56 LATNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 56 ~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
....-..|-+|||.|+. |++|++.||
T Consensus 68 I~~d~i~clecGk~~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 68 ITPDYIICLECGKKFKT---LKRHLRTHH 93 (132)
T ss_dssp B-SS-EE-TBT--EESB---HHHHHHHTT
T ss_pred cccCeeEEccCCcccch---HHHHHHHcc
Confidence 34556899999999975 699999996
No 101
>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=53.03 E-value=5.6 Score=39.46 Aligned_cols=12 Identities=25% Similarity=0.827 Sum_probs=7.0
Q ss_pred CCCCeeccccCc
Q 010389 57 ATNRFVCEICNK 68 (512)
Q Consensus 57 ~~k~f~C~~Cgk 68 (512)
+-+.|+|..|..
T Consensus 139 GGrif~CsfC~~ 150 (314)
T PF06524_consen 139 GGRIFKCSFCDN 150 (314)
T ss_pred CCeEEEeecCCC
Confidence 345566666654
No 102
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=52.70 E-value=8.8 Score=31.82 Aligned_cols=32 Identities=31% Similarity=0.731 Sum_probs=23.1
Q ss_pred ccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCCh
Q 010389 135 KKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSRR 175 (512)
Q Consensus 135 kp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~~ 175 (512)
.+|.|+.|++. .+.|+ ....|+|. |++.|.--
T Consensus 34 ~~~~Cp~C~~~--------~VkR~-a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRI-ATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc--------ceeee-ccCeEEcCCCCCeeccc
Confidence 45899999886 22333 45689999 99998753
No 103
>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=52.38 E-value=9.2 Score=34.01 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=18.9
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCC
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEK 107 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C 107 (512)
+..|+.|+++|.- | .+.|.+||.|
T Consensus 9 Kr~Cp~cg~kFYD---L---------------------nk~p~vcP~c 32 (129)
T TIGR02300 9 KRICPNTGSKFYD---L---------------------NRRPAVSPYT 32 (129)
T ss_pred cccCCCcCccccc---c---------------------CCCCccCCCc
Confidence 3589999999953 2 4578899999
No 104
>PF06066 SepZ: SepZ; InterPro: IPR009275 SepZ is a component of the type III secretion system use in bacteria. SepZ is a gene within the enterocyte effacement locus. SepZ mutants exhibit reduced invasion efficiency and lack of tyrosine phosphorylation of Hp90 [].
Probab=51.86 E-value=5.2 Score=32.81 Aligned_cols=23 Identities=52% Similarity=0.850 Sum_probs=16.6
Q ss_pred hhcccccCCCCCCCCCcccccccCCCccch
Q 010389 457 FLGLGMAAGGATPGVGRSALVPPAGGALDV 486 (512)
Q Consensus 457 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 486 (512)
||||||+++. =|| +|.+||+|-|
T Consensus 74 ~LgLGiaaGV---LGg----~T~vgg~LAM 96 (99)
T PF06066_consen 74 YLGLGIAAGV---LGG----VTAVGGGLAM 96 (99)
T ss_pred hcchhhhhhh---ccc----eeeecceeee
Confidence 9999999752 123 5667888876
No 105
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.65 E-value=8.9 Score=36.28 Aligned_cols=33 Identities=12% Similarity=0.432 Sum_probs=18.6
Q ss_pred CCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcc
Q 010389 98 KKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKY 146 (512)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F 146 (512)
...-|.|+.| +++|.....+. .-|.|+.||...
T Consensus 114 ~~~~Y~Cp~C-------~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNC-------HIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCC-------CcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 4455666666 55665555442 246666666544
No 106
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=51.35 E-value=8.9 Score=37.99 Aligned_cols=49 Identities=14% Similarity=0.406 Sum_probs=36.4
Q ss_pred eeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhcc
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKH 132 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ 132 (512)
|.|.+||....- ..|.+|+...+ ..-|.|-.| ++.|.. ..++.|..--+
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCr--------------n~~fSCIDC-------~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCR--------------NAYFSCIDC-------GKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhcc--------------CCeeEEeec-------cccccc-chhhhhhhhcc
Confidence 789999988764 46788987653 367888887 888887 77788865433
No 107
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=51.16 E-value=12 Score=43.05 Aligned_cols=25 Identities=20% Similarity=0.626 Sum_probs=15.5
Q ss_pred CCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCc
Q 010389 133 GEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAV 171 (512)
Q Consensus 133 gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~ 171 (512)
..+..+|.+|++. ...|..|+ |+-.
T Consensus 459 ~~~~L~CH~Cg~~--------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 459 ATGQLRCHYCGYQ--------------EPIPQSCPECGSE 484 (730)
T ss_pred CCCeeEeCCCCCC--------------CCCCCCCCCCCCC
Confidence 3345677777653 24677788 8754
No 108
>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=50.95 E-value=12 Score=25.32 Aligned_cols=10 Identities=30% Similarity=0.604 Sum_probs=7.2
Q ss_pred ccccccCCCC
Q 010389 135 KKWKCDKCSK 144 (512)
Q Consensus 135 kp~~C~~C~k 144 (512)
.|..|.+|+.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4678888875
No 109
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=50.46 E-value=8.6 Score=28.96 Aligned_cols=43 Identities=16% Similarity=0.417 Sum_probs=22.8
Q ss_pred CcceeCCC-CCCCCCCCCCccCChhhHHhhhhhccCCccccccC----CCCcccC
Q 010389 99 KRVYVCPE-KSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDK----CSKKYAV 148 (512)
Q Consensus 99 ~k~~~C~~-C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~----C~k~F~~ 148 (512)
..+..|+. | | ...+ .+..|..|+...-..++..|.+ |...+.+
T Consensus 7 ~~~v~C~~~c-c-----~~~i-~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 7 FRPVPCPNGC-C-----NEMI-PRKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp TSEEE-TT---S------BEE-ECCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred CCEeeCCCCC-c-----ccce-eHHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 34566766 2 0 3333 3556777777666667777877 7776643
No 110
>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=49.43 E-value=11 Score=25.89 Aligned_cols=16 Identities=19% Similarity=0.507 Sum_probs=12.8
Q ss_pred eeccccCcccCChHHH
Q 010389 61 FVCEICNKGFQRDQNL 76 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L 76 (512)
+.|+.|+..|.-....
T Consensus 3 ~~CP~C~~~~~v~~~~ 18 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ 18 (38)
T ss_pred EECCCCCCEEEeCHHH
Confidence 6899999998776543
No 111
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.88 E-value=11 Score=43.33 Aligned_cols=14 Identities=14% Similarity=0.472 Sum_probs=11.1
Q ss_pred cCCccccccCCCCc
Q 010389 132 HGEKKWKCDKCSKK 145 (512)
Q Consensus 132 ~gekp~~C~~C~k~ 145 (512)
+...|..|+.|+-.
T Consensus 471 ~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 471 QEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCC
Confidence 45678999999875
No 112
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=48.81 E-value=15 Score=37.40 Aligned_cols=46 Identities=15% Similarity=0.403 Sum_probs=31.9
Q ss_pred cccCCCCcccChHHHhhhhhh--cCCcceecc-CCCccCChhHHHHHHHHhc
Q 010389 138 KCDKCSKKYAVQSDYKAHSKV--CGTKEYKCN-CGAVFSRRDSFITHRAFCD 186 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~~--h~~kpy~C~-Cgk~F~~~~~L~~H~~~hh 186 (512)
.|-.|.-.|.... .|-.- .....|+|+ |...|-..-+.-.|...|.
T Consensus 364 ~Cf~CQ~~fp~~~---~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 364 HCFVCQGPFPKPP---VSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceeccCCCCCCC---CCcccccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 3888887776543 22221 344679999 9999988888888876664
No 113
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.95 E-value=10 Score=43.33 Aligned_cols=26 Identities=19% Similarity=0.691 Sum_probs=16.9
Q ss_pred ccCCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCc
Q 010389 131 KHGEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAV 171 (512)
Q Consensus 131 H~gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~ 171 (512)
|...+..+|.+||+. ..++.|. |+..
T Consensus 405 h~~~~~l~Ch~CG~~---------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 405 PSAGGTPRCRWCGRA---------------APDWRCPRCGSD 431 (665)
T ss_pred ecCCCeeECCCCcCC---------------CcCccCCCCcCC
Confidence 334456778888753 2467888 8764
No 114
>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=47.67 E-value=12 Score=34.72 Aligned_cols=35 Identities=14% Similarity=0.485 Sum_probs=22.6
Q ss_pred ccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccCCCCcc
Q 010389 96 EVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKKY 146 (512)
Q Consensus 96 ~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~C~k~F 146 (512)
+....-|.|+.| +.+|.....+. .-|.|+.||...
T Consensus 104 e~~~~~Y~Cp~c-------~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNM-------CVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred ccCCCeEECCCC-------CcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 345566777777 67776666664 247777777654
No 115
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.56 E-value=7 Score=44.55 Aligned_cols=11 Identities=27% Similarity=1.295 Sum_probs=9.4
Q ss_pred ccccccCCCCc
Q 010389 135 KKWKCDKCSKK 145 (512)
Q Consensus 135 kp~~C~~C~k~ 145 (512)
.++.|..|+..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 58999999875
No 116
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=46.74 E-value=15 Score=25.27 Aligned_cols=13 Identities=31% Similarity=0.986 Sum_probs=6.0
Q ss_pred cccCCCCcccChH
Q 010389 138 KCDKCSKKYAVQS 150 (512)
Q Consensus 138 ~C~~C~k~F~~~~ 150 (512)
.|+.|+..|....
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 3445555544433
No 117
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=46.71 E-value=17 Score=38.73 Aligned_cols=36 Identities=28% Similarity=0.674 Sum_probs=23.7
Q ss_pred CCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCC
Q 010389 133 GEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGA 170 (512)
Q Consensus 133 gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk 170 (512)
...-|.|..|.+.|.....+..-- ...-.|.|. |+-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L~~--~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQLLD--NETGEFHCENCGG 161 (436)
T ss_pred ccccccCCccccchhhhHHHHhhc--ccCceEEEecCCC
Confidence 345589999999988776655321 234568887 753
No 118
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=46.63 E-value=10 Score=31.81 Aligned_cols=12 Identities=17% Similarity=0.736 Sum_probs=5.6
Q ss_pred cceecc-CCCccC
Q 010389 162 KEYKCN-CGAVFS 173 (512)
Q Consensus 162 kpy~C~-Cgk~F~ 173 (512)
..|.|. |++.|.
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PTZ00255 53 GIWRCKGCKKTVA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 344554 544443
No 119
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=46.53 E-value=5.2 Score=45.02 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=24.5
Q ss_pred CCCeeccccCcccCChHHHHHHHHhcC
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
..-|.|..|+|.|.....+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 345999999999999999999999996
No 120
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=46.51 E-value=20 Score=32.66 Aligned_cols=39 Identities=21% Similarity=0.541 Sum_probs=27.1
Q ss_pred CCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCC
Q 010389 133 GEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSR 174 (512)
Q Consensus 133 gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~ 174 (512)
...-|.|+.|++.|.....+..- ..+..|.|+ |+.....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~---d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLL---DMDGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhc---CCCCcEECCCCCCEEEE
Confidence 34569999999999876554431 123459999 9987644
No 121
>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=45.03 E-value=6.4 Score=29.43 Aligned_cols=27 Identities=30% Similarity=0.631 Sum_probs=18.2
Q ss_pred CCCeeccccCcccCChHHHHHHHHhcC
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
..+|+|+.|.+.|-..-++-.|...|+
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 458999999999999999999988886
No 122
>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=44.89 E-value=11 Score=31.69 Aligned_cols=12 Identities=42% Similarity=1.085 Sum_probs=6.1
Q ss_pred cceecc-CCCccC
Q 010389 162 KEYKCN-CGAVFS 173 (512)
Q Consensus 162 kpy~C~-Cgk~F~ 173 (512)
..|.|. |++.|.
T Consensus 52 GIW~C~~C~~~~A 64 (91)
T TIGR00280 52 GIWTCRKCGAKFA 64 (91)
T ss_pred EEEEcCCCCCEEe
Confidence 445555 555543
No 123
>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=44.09 E-value=8.9 Score=32.10 Aligned_cols=12 Identities=42% Similarity=1.107 Sum_probs=6.2
Q ss_pred cceecc-CCCccC
Q 010389 162 KEYKCN-CGAVFS 173 (512)
Q Consensus 162 kpy~C~-Cgk~F~ 173 (512)
-.|+|. |++.|.
T Consensus 52 GIW~C~~C~~~~A 64 (90)
T PF01780_consen 52 GIWKCKKCGKKFA 64 (90)
T ss_dssp TEEEETTTTEEEE
T ss_pred EEeecCCCCCEEe
Confidence 345555 555543
No 124
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=43.74 E-value=13 Score=39.67 Aligned_cols=38 Identities=21% Similarity=0.403 Sum_probs=27.2
Q ss_pred ccCCCCCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCC
Q 010389 54 TLLATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEK 107 (512)
Q Consensus 54 ~~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C 107 (512)
......-|.|+.|.+.|.....++.--. ....|.|..|
T Consensus 122 d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~----------------~~~~F~C~~C 159 (436)
T KOG2593|consen 122 DDTNVAGYVCPNCQKKYTSLEALQLLDN----------------ETGEFHCENC 159 (436)
T ss_pred hccccccccCCccccchhhhHHHHhhcc----------------cCceEEEecC
Confidence 3445567999999999987766654321 4467889988
No 125
>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=43.39 E-value=18 Score=22.99 Aligned_cols=20 Identities=15% Similarity=0.459 Sum_probs=16.1
Q ss_pred eeccccCcccCChHHHHHHHH
Q 010389 61 FVCEICNKGFQRDQNLQLHRR 81 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r 81 (512)
..|++|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5677888875
No 126
>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=43.24 E-value=19 Score=33.31 Aligned_cols=36 Identities=14% Similarity=0.484 Sum_probs=28.0
Q ss_pred cCCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCCh
Q 010389 132 HGEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSRR 175 (512)
Q Consensus 132 ~gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~~ 175 (512)
....-|.|+.|+..|.....+. .-|.|+ ||......
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME--------LNFTCPRCGAMLDYL 141 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEeeec
Confidence 3456699999999999888875 369999 99875443
No 127
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.33 E-value=17 Score=26.19 Aligned_cols=13 Identities=15% Similarity=0.675 Sum_probs=10.5
Q ss_pred CeeccccCcccCC
Q 010389 60 RFVCEICNKGFQR 72 (512)
Q Consensus 60 ~f~C~~Cgk~F~~ 72 (512)
.|+|+.||..|..
T Consensus 3 ~y~C~~CG~~~~~ 15 (46)
T PRK00398 3 EYKCARCGREVEL 15 (46)
T ss_pred EEECCCCCCEEEE
Confidence 5889999988764
No 128
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.25 E-value=16 Score=37.62 Aligned_cols=74 Identities=19% Similarity=0.390 Sum_probs=39.7
Q ss_pred CCeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCcccc
Q 010389 59 NRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWK 138 (512)
Q Consensus 59 k~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~ 138 (512)
.+-.|++||..=. - .+ .|.... .+.+-..|..|++.++ -+.-+
T Consensus 186 ~~~~CPvCGs~P~-~-s~-v~~~~~-------------~G~RyL~CslC~teW~---------------------~~R~~ 228 (309)
T PRK03564 186 QRQFCPVCGSMPV-S-SV-VQIGTT-------------QGLRYLHCNLCESEWH---------------------VVRVK 228 (309)
T ss_pred CCCCCCCCCCcch-h-he-eeccCC-------------CCceEEEcCCCCCccc---------------------ccCcc
Confidence 4567999997421 1 11 122222 2678889999954221 13358
Q ss_pred ccCCCCcccChHHHhhhh-hh--cCCcceecc-CCCccC
Q 010389 139 CDKCSKKYAVQSDYKAHS-KV--CGTKEYKCN-CGAVFS 173 (512)
Q Consensus 139 C~~C~k~F~~~~~L~~H~-~~--h~~kpy~C~-Cgk~F~ 173 (512)
|.+|+.. ..|..+. .. -..|.+.|+ |+.=++
T Consensus 229 C~~Cg~~----~~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 229 CSNCEQS----GKLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred CCCCCCC----CceeeeeecCCCcceEeeecccccccce
Confidence 9999963 2222221 11 123668898 875433
No 129
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=41.18 E-value=20 Score=24.71 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=5.2
Q ss_pred cccccCCCCcc
Q 010389 136 KWKCDKCSKKY 146 (512)
Q Consensus 136 p~~C~~C~k~F 146 (512)
..+|..|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34455554444
No 130
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=40.40 E-value=10 Score=30.40 Aligned_cols=14 Identities=29% Similarity=0.691 Sum_probs=7.7
Q ss_pred cceecc---CCCccCCh
Q 010389 162 KEYKCN---CGAVFSRR 175 (512)
Q Consensus 162 kpy~C~---Cgk~F~~~ 175 (512)
+-|.|. |+.+|...
T Consensus 26 ~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 26 RYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeecCCCCCCCEEEEE
Confidence 445564 66666543
No 131
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=40.37 E-value=18 Score=37.15 Aligned_cols=12 Identities=17% Similarity=0.177 Sum_probs=9.6
Q ss_pred CCcceeCCCCCC
Q 010389 98 KKRVYVCPEKSC 109 (512)
Q Consensus 98 ~~k~~~C~~C~C 109 (512)
+.+-..|..|.+
T Consensus 207 G~RyL~CslC~t 218 (305)
T TIGR01562 207 GLRYLSCSLCAT 218 (305)
T ss_pred CceEEEcCCCCC
Confidence 678889999954
No 132
>PF15269 zf-C2H2_7: Zinc-finger
Probab=40.08 E-value=49 Score=24.03 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=21.3
Q ss_pred CeeccccCcccCChHHHHHHHHhc
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
.|+|-+|..+...+.+|-.||+.-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 589999999999999999999865
No 133
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.55 E-value=16 Score=40.32 Aligned_cols=29 Identities=24% Similarity=0.544 Sum_probs=18.0
Q ss_pred hhccCCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCc
Q 010389 129 CRKHGEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAV 171 (512)
Q Consensus 129 ~~H~gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~ 171 (512)
..|..++...|.+||+.. ..+..|+ |+..
T Consensus 233 ~~h~~~~~l~Ch~Cg~~~--------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 233 TYHKKEGKLRCHYCGYQE--------------PIPKTCPQCGSE 262 (505)
T ss_pred EEecCCCeEEcCCCcCcC--------------CCCCCCCCCCCC
Confidence 334445567788887652 3467788 8653
No 134
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.18 E-value=46 Score=39.39 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=10.5
Q ss_pred CCCCCeeccccCcc
Q 010389 56 LATNRFVCEICNKG 69 (512)
Q Consensus 56 ~~~k~f~C~~Cgk~ 69 (512)
.+.....|+.||+.
T Consensus 622 VEVg~RfCpsCG~~ 635 (1121)
T PRK04023 622 VEIGRRKCPSCGKE 635 (1121)
T ss_pred ecccCccCCCCCCc
Confidence 34556789999986
No 135
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=38.92 E-value=14 Score=30.99 Aligned_cols=12 Identities=42% Similarity=1.115 Sum_probs=5.6
Q ss_pred cceecc-CCCccC
Q 010389 162 KEYKCN-CGAVFS 173 (512)
Q Consensus 162 kpy~C~-Cgk~F~ 173 (512)
..|.|. |++.|.
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PRK03976 53 GIWECRKCGAKFA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 345555 544443
No 136
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=38.32 E-value=36 Score=35.11 Aligned_cols=25 Identities=24% Similarity=0.647 Sum_probs=18.2
Q ss_pred cceecc-CCCccCChhHHHHHHHHhc
Q 010389 162 KEYKCN-CGAVFSRRDSFITHRAFCD 186 (512)
Q Consensus 162 kpy~C~-Cgk~F~~~~~L~~H~~~hh 186 (512)
..|.|. |...|--.-+.-.|...|.
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhc
Confidence 458888 8888877777777765553
No 137
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=38.09 E-value=20 Score=33.53 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=18.3
Q ss_pred CeeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCCC
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEKS 108 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C~ 108 (512)
.|+|++||..+ . ++-|-+||+|+
T Consensus 134 ~~vC~vCGy~~-------------~-------------ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------E-------------GEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------c-------------CCCCCcCCCCC
Confidence 79999998643 2 67899999994
No 138
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.83 E-value=18 Score=31.32 Aligned_cols=13 Identities=15% Similarity=0.133 Sum_probs=8.5
Q ss_pred CccccccCCCCcc
Q 010389 134 EKKWKCDKCSKKY 146 (512)
Q Consensus 134 ekp~~C~~C~k~F 146 (512)
.+|..|++||+.|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 3566677777766
No 139
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.63 E-value=23 Score=33.47 Aligned_cols=36 Identities=17% Similarity=0.636 Sum_probs=27.6
Q ss_pred CCccccccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCChh
Q 010389 133 GEKKWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSRRD 176 (512)
Q Consensus 133 gekp~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~~~ 176 (512)
...-|.|+.|++.|.....+. .-|.|+ ||......+
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLEEYD 150 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCeecc
Confidence 345699999999998887764 369999 998765543
No 140
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.98 E-value=10 Score=37.08 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=18.8
Q ss_pred CCCeeccccCcccCChHHHHHHHHhc
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
++.+.|++|+..|..+.-+.--+|+-
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRii 42 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRII 42 (267)
T ss_pred hceeccCcccchhhhhheeccceeEe
Confidence 46799999999998776544444443
No 141
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=36.71 E-value=18 Score=33.16 Aligned_cols=32 Identities=31% Similarity=0.908 Sum_probs=20.9
Q ss_pred ccccccCCCCcccChHHHhhhhhh-cCCcceecc-CCCc
Q 010389 135 KKWKCDKCSKKYAVQSDYKAHSKV-CGTKEYKCN-CGAV 171 (512)
Q Consensus 135 kp~~C~~C~k~F~~~~~L~~H~~~-h~~kpy~C~-Cgk~ 171 (512)
.+|.|. |+..|-+. ++|-.+ -++ .|.|. |+-.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 468888 88876544 445444 455 78888 8644
No 142
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=36.52 E-value=34 Score=30.74 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=19.6
Q ss_pred CeeccccCcccCChHHHHHHHHhcC
Q 010389 60 RFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
-..|-.|||.|+ .|++|.++|+
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred eEEEeccCcchH---HHHHHHhccc
Confidence 468999999995 6999999987
No 143
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=36.03 E-value=25 Score=26.31 Aligned_cols=35 Identities=26% Similarity=0.408 Sum_probs=23.7
Q ss_pred CCCeeccc--cCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCC
Q 010389 58 TNRFVCEI--CNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPE 106 (512)
Q Consensus 58 ~k~f~C~~--Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~ 106 (512)
..+..|+. |.+.+. +..|..|+...- ..++..|++
T Consensus 7 ~~~v~C~~~cc~~~i~-r~~l~~H~~~~C-------------~~~~v~C~~ 43 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIP-RKELDDHLENEC-------------PKRPVPCPY 43 (60)
T ss_dssp TSEEE-TT--S-BEEE-CCCHHHHHHTTS-------------TTSEEE-SS
T ss_pred CCEeeCCCCCccccee-HHHHHHHHHccC-------------CCCcEECCC
Confidence 35678998 666666 457999998654 667888988
No 144
>PF15269 zf-C2H2_7: Zinc-finger
Probab=35.88 E-value=22 Score=25.79 Aligned_cols=22 Identities=27% Similarity=0.440 Sum_probs=17.7
Q ss_pred ccccCCCCcccChHHHhhhhhh
Q 010389 137 WKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
|+|-.|..++..+++|-.||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6788888888888888888764
No 145
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=35.68 E-value=12 Score=43.12 Aligned_cols=9 Identities=44% Similarity=0.870 Sum_probs=0.0
Q ss_pred CeeccccCc
Q 010389 60 RFVCEICNK 68 (512)
Q Consensus 60 ~f~C~~Cgk 68 (512)
.++|+.|++
T Consensus 655 ~r~Cp~Cg~ 663 (900)
T PF03833_consen 655 RRRCPKCGK 663 (900)
T ss_dssp ---------
T ss_pred cccCcccCC
Confidence 456777765
No 146
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.57 E-value=18 Score=29.28 Aligned_cols=23 Identities=22% Similarity=0.534 Sum_probs=16.6
Q ss_pred cCCCCCeeccccCcccCChHHHHHHHH
Q 010389 55 LLATNRFVCEICNKGFQRDQNLQLHRR 81 (512)
Q Consensus 55 ~~~~k~f~C~~Cgk~F~~~~~L~~H~r 81 (512)
....-.|+|..|+..| ++..||+
T Consensus 7 lMPtY~Y~c~~cg~~~----dvvq~~~ 29 (82)
T COG2331 7 LMPTYSYECTECGNRF----DVVQAMT 29 (82)
T ss_pred cccceEEeecccchHH----HHHHhcc
Confidence 3445679999999876 4666665
No 147
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.19 E-value=29 Score=30.29 Aligned_cols=29 Identities=28% Similarity=0.598 Sum_probs=25.9
Q ss_pred CCCCCeeccccCcccCChHHHHHHHHhcC
Q 010389 56 LATNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 56 ~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
....+|+|+.|.+.|-..-++-.|...|+
T Consensus 77 ~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 77 KDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccccceeCCCCCCccccccchhhhhhccC
Confidence 34568999999999999999999999986
No 148
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=35.08 E-value=20 Score=30.02 Aligned_cols=15 Identities=20% Similarity=0.483 Sum_probs=12.0
Q ss_pred CCCeeccccCcccCC
Q 010389 58 TNRFVCEICNKGFQR 72 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~ 72 (512)
-+|-.|..||..|..
T Consensus 56 v~Pa~CkkCGfef~~ 70 (97)
T COG3357 56 VRPARCKKCGFEFRD 70 (97)
T ss_pred ecChhhcccCccccc
Confidence 356789999999875
No 149
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=34.96 E-value=16 Score=29.31 Aligned_cols=21 Identities=19% Similarity=0.513 Sum_probs=15.9
Q ss_pred cCCcccccc--CCCCcccChHHH
Q 010389 132 HGEKKWKCD--KCSKKYAVQSDY 152 (512)
Q Consensus 132 ~gekp~~C~--~C~k~F~~~~~L 152 (512)
..++-|.|. .|+.+|.....+
T Consensus 23 ~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 23 TKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred hheeeeecCCCCCCCEEEEEEEE
Confidence 346778998 899999876544
No 150
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.83 E-value=16 Score=40.26 Aligned_cols=14 Identities=14% Similarity=0.461 Sum_probs=10.8
Q ss_pred cCCccccccCCCCc
Q 010389 132 HGEKKWKCDKCSKK 145 (512)
Q Consensus 132 ~gekp~~C~~C~k~ 145 (512)
....|+.|+.|+..
T Consensus 249 ~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 249 QEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCCCCCCC
Confidence 44568899999874
No 151
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.14 E-value=43 Score=40.62 Aligned_cols=8 Identities=25% Similarity=0.667 Sum_probs=6.0
Q ss_pred eeccccCc
Q 010389 61 FVCEICNK 68 (512)
Q Consensus 61 f~C~~Cgk 68 (512)
++|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 67777776
No 152
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=31.65 E-value=16 Score=25.59 Aligned_cols=22 Identities=27% Similarity=0.607 Sum_probs=11.8
Q ss_pred HhhhhhccCCccccccCCCCcc
Q 010389 125 KKHFCRKHGEKKWKCDKCSKKY 146 (512)
Q Consensus 125 k~H~~~H~gekp~~C~~C~k~F 146 (512)
.-+++...+.+.|.|.+|+..-
T Consensus 13 Np~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 13 NPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp -TTSEEETTTTEEEETTT--EE
T ss_pred CCcceEcCCCCEEECcCCCCcC
Confidence 3344444556778888887643
No 153
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.49 E-value=25 Score=26.06 Aligned_cols=8 Identities=25% Similarity=0.900 Sum_probs=4.0
Q ss_pred ccccCCCC
Q 010389 137 WKCDKCSK 144 (512)
Q Consensus 137 ~~C~~C~k 144 (512)
.+|++|+.
T Consensus 25 irCp~Cg~ 32 (49)
T COG1996 25 IRCPYCGS 32 (49)
T ss_pred eeCCCCCc
Confidence 45555544
No 154
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=30.82 E-value=62 Score=33.17 Aligned_cols=30 Identities=27% Similarity=0.586 Sum_probs=26.3
Q ss_pred cCCCCCeeccccCcccCChHHHHHHHHhcC
Q 010389 55 LLATNRFVCEICNKGFQRDQNLQLHRRGHN 84 (512)
Q Consensus 55 ~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 84 (512)
.+...+|.|+.|...|....+.-.|...|.
T Consensus 383 ~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 383 STSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 345568999999999999999999998886
No 155
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=30.58 E-value=10 Score=42.85 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=21.4
Q ss_pred cccccCCCCcccChHHHhhhhhhcC
Q 010389 136 KWKCDKCSKKYAVQSDYKAHSKVCG 160 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~h~ 160 (512)
-|.|..|+|+|.....+..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3899999999998888888888763
No 156
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=30.54 E-value=27 Score=32.20 Aligned_cols=23 Identities=26% Similarity=0.414 Sum_probs=12.8
Q ss_pred cccccCCCCccc------ChHHHhhhhhh
Q 010389 136 KWKCDKCSKKYA------VQSDYKAHSKV 158 (512)
Q Consensus 136 p~~C~~C~k~F~------~~~~L~~H~~~ 158 (512)
-.+|..|+|-|- ..+++..|+..
T Consensus 14 vv~C~~c~kWFCNg~~~~s~SHIv~HLv~ 42 (152)
T PF09416_consen 14 VVKCNTCNKWFCNGRGNTSGSHIVNHLVR 42 (152)
T ss_dssp EEEETTTTEEEES--TTSSS-HHHHHHHH
T ss_pred EeEcCCCCcEeecCCCCCcccHHHHHHHH
Confidence 356666666663 44566666554
No 157
>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=30.51 E-value=63 Score=23.19 Aligned_cols=8 Identities=25% Similarity=1.053 Sum_probs=4.0
Q ss_pred ccccCCCC
Q 010389 137 WKCDKCSK 144 (512)
Q Consensus 137 ~~C~~C~k 144 (512)
+.|+.|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44555544
No 158
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=30.46 E-value=53 Score=35.30 Aligned_cols=29 Identities=21% Similarity=0.355 Sum_probs=24.3
Q ss_pred cccCCCCCeeccccC-cccCChHHHHHHHH
Q 010389 53 KTLLATNRFVCEICN-KGFQRDQNLQLHRR 81 (512)
Q Consensus 53 ~~~~~~k~f~C~~Cg-k~F~~~~~L~~H~r 81 (512)
+-|.-...|.|++|| ++|.-+..+++|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456667789999999 88999999999954
No 159
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=29.55 E-value=44 Score=25.73 Aligned_cols=8 Identities=25% Similarity=0.850 Sum_probs=4.7
Q ss_pred cceeCCCC
Q 010389 100 RVYVCPEK 107 (512)
Q Consensus 100 k~~~C~~C 107 (512)
-.|.||.|
T Consensus 24 ~~F~CPnC 31 (59)
T PRK14890 24 VKFLCPNC 31 (59)
T ss_pred CEeeCCCC
Confidence 35666666
No 160
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=29.34 E-value=54 Score=34.09 Aligned_cols=22 Identities=18% Similarity=0.332 Sum_probs=11.0
Q ss_pred CeeccccCcccCChHHHHHHHH
Q 010389 60 RFVCEICNKGFQRDQNLQLHRR 81 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~~L~~H~r 81 (512)
-|.|+.|++.=-+...|..|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccCCcccccccchhHHHHHhh
Confidence 4555555554444455555543
No 161
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.21 E-value=22 Score=31.81 Aligned_cols=16 Identities=25% Similarity=0.976 Sum_probs=12.5
Q ss_pred CccccccCCCCcccCh
Q 010389 134 EKKWKCDKCSKKYAVQ 149 (512)
Q Consensus 134 ekp~~C~~C~k~F~~~ 149 (512)
.-.|+|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4568999999988754
No 162
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.99 E-value=17 Score=30.99 Aligned_cols=14 Identities=21% Similarity=0.553 Sum_probs=10.7
Q ss_pred CCCeeccccCcccC
Q 010389 58 TNRFVCEICNKGFQ 71 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~ 71 (512)
.+.|.|+.|+..-.
T Consensus 20 ~k~FtCp~Cghe~v 33 (104)
T COG4888 20 PKTFTCPRCGHEKV 33 (104)
T ss_pred CceEecCccCCeee
Confidence 46899999996543
No 163
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=28.97 E-value=49 Score=33.96 Aligned_cols=79 Identities=19% Similarity=0.345 Sum_probs=52.9
Q ss_pred CcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCCccccccC----CCCcccChHHHhhhhhhcCCcceecc-----CC
Q 010389 99 KRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGEKKWKCDK----CSKKYAVQSDYKAHSKVCGTKEYKCN-----CG 169 (512)
Q Consensus 99 ~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~gekp~~C~~----C~k~F~~~~~L~~H~~~h~~kpy~C~-----Cg 169 (512)
++..+||.| ...+... .-++|...-....+.|.. |.+.|..... ..|.+...-++|.|+ |.
T Consensus 78 ~~~~~CP~C-------r~~~g~~--R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f~~~~CP~p~~~C~ 147 (299)
T KOG3002|consen 78 KVSNKCPTC-------RLPIGNI--RCRAMEKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEFRPCSCPVPGAECK 147 (299)
T ss_pred hhcccCCcc-------ccccccH--HHHHHHHHHHhceecccccccCCceeeccccc-cccccccccCCcCCCCCcccCC
Confidence 567788888 5555533 445555555556678876 9999887776 678888555899997 54
Q ss_pred CccCChhHHHHHHHHhcCc
Q 010389 170 AVFSRRDSFITHRAFCDML 188 (512)
Q Consensus 170 k~F~~~~~L~~H~~~hh~~ 188 (512)
..=. -..|..|.+.-|..
T Consensus 148 ~~G~-~~~l~~H~~~~hk~ 165 (299)
T KOG3002|consen 148 YTGS-YKDLYAHLNDTHKS 165 (299)
T ss_pred ccCc-HHHHHHHHHhhChh
Confidence 4332 34577887666543
No 164
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=28.87 E-value=26 Score=34.85 Aligned_cols=24 Identities=13% Similarity=0.347 Sum_probs=12.3
Q ss_pred cCCccccccCCCCcccChHHHhhh
Q 010389 132 HGEKKWKCDKCSKKYAVQSDYKAH 155 (512)
Q Consensus 132 ~gekp~~C~~C~k~F~~~~~L~~H 155 (512)
+|++-+.=.+|.+.|........|
T Consensus 277 TgDnAHTiKyCPl~~~~~~s~~~~ 300 (318)
T KOG4602|consen 277 TGDNAHTIKYCPLAFGDDTSVYSH 300 (318)
T ss_pred cCCcccceecccccCCCCccccch
Confidence 455555555566655544443333
No 165
>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=27.66 E-value=47 Score=31.62 Aligned_cols=55 Identities=24% Similarity=0.484 Sum_probs=31.9
Q ss_pred Ceeccc----cCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCC--CCCCCCCCCCccCChhhHHhhhhhccC
Q 010389 60 RFVCEI----CNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPE--KSCVHHDPTRALGDLTGIKKHFCRKHG 133 (512)
Q Consensus 60 ~f~C~~----Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~--C~C~~~~~~k~F~~~~~Lk~H~~~H~g 133 (512)
.|.|.. |...|... .+..|.+.. .-+||.||. .+| +.. .....|..|....|.
T Consensus 14 ~~pC~~~~~GC~~~~~~~-~~~~HE~~C--------------~~~p~~CP~~~~~C-----~~~-G~~~~l~~Hl~~~H~ 72 (198)
T PF03145_consen 14 KFPCKNAKYGCTETFPYS-EKREHEEEC--------------PFRPCSCPFPGSGC-----DWQ-GSYKELLDHLRDKHS 72 (198)
T ss_dssp -EE-CCGGGT---EE-GG-GHHHHHHT---------------TTSEEE-SSSSTT--------E-EECCCHHHHHHHHTT
T ss_pred eecCCCCCCCCccccccc-ChhhHhccC--------------CCcCCcCCCCCCCc-----ccc-CCHHHHHHHHHHHCC
Confidence 578887 88887654 677788765 578999998 555 322 234579999998776
Q ss_pred Cc
Q 010389 134 EK 135 (512)
Q Consensus 134 ek 135 (512)
..
T Consensus 73 ~~ 74 (198)
T PF03145_consen 73 WN 74 (198)
T ss_dssp TS
T ss_pred Cc
Confidence 64
No 166
>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=27.48 E-value=35 Score=30.75 Aligned_cols=17 Identities=29% Similarity=0.550 Sum_probs=7.0
Q ss_pred CCccCChhhHHhhhhhccCC
Q 010389 115 TRALGDLTGIKKHFCRKHGE 134 (512)
Q Consensus 115 ~k~F~~~~~Lk~H~~~H~ge 134 (512)
|+.|+.. ++|.+.|||-
T Consensus 79 Gk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 79 GKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp --EESBH---HHHHHHTT-S
T ss_pred CcccchH---HHHHHHccCC
Confidence 5555432 5555555543
No 167
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=27.13 E-value=40 Score=30.33 Aligned_cols=18 Identities=28% Similarity=0.408 Sum_probs=8.8
Q ss_pred cccCCCCcccChHHHhhhhhh
Q 010389 138 KCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~~ 158 (512)
.|-+|||.|+ .|+||+.+
T Consensus 78 icLEDGkkfK---SLKRHL~t 95 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTT 95 (148)
T ss_pred EEeccCcchH---HHHHHHhc
Confidence 4555555542 34555544
No 168
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=26.67 E-value=29 Score=31.11 Aligned_cols=15 Identities=20% Similarity=0.596 Sum_probs=12.5
Q ss_pred CeeccccCcccCChH
Q 010389 60 RFVCEICNKGFQRDQ 74 (512)
Q Consensus 60 ~f~C~~Cgk~F~~~~ 74 (512)
|++|..||+.|..-.
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578999999998654
No 169
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=26.48 E-value=34 Score=25.35 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=17.4
Q ss_pred CCCeeccccCcccCChHHHHHHH
Q 010389 58 TNRFVCEICNKGFQRDQNLQLHR 80 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~~L~~H~ 80 (512)
.+.+.|..||..|..-..=+...
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy 24 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFY 24 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHH
Confidence 46789999999998766555443
No 170
>KOG1506 consensus S-adenosylmethionine synthetase [Coenzyme transport and metabolism]
Probab=26.22 E-value=34 Score=34.47 Aligned_cols=11 Identities=55% Similarity=0.990 Sum_probs=9.3
Q ss_pred CCcccccccCC
Q 010389 499 GGGEIAGKDIG 509 (512)
Q Consensus 499 ~~~~~~~~~~~ 509 (512)
|||.|||||.-
T Consensus 266 GGGAFSGKD~t 276 (383)
T KOG1506|consen 266 GGGAFSGKDPT 276 (383)
T ss_pred CCcccCCCCcc
Confidence 78899999963
No 171
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=26.21 E-value=29 Score=26.50 Aligned_cols=35 Identities=26% Similarity=0.468 Sum_probs=22.5
Q ss_pred eeccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCC
Q 010389 61 FVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEK 107 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C 107 (512)
-+|-+|++.+.-...-..-.+.-+ .....|.|++|
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrn------------rPi~tYmC~eC 37 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRN------------RPIHTYMCDEC 37 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhc------------CCCcceeChhH
Confidence 579999998876654333332222 15567899988
No 172
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.20 E-value=30 Score=29.60 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=8.4
Q ss_pred CCeeccccCc
Q 010389 59 NRFVCEICNK 68 (512)
Q Consensus 59 k~f~C~~Cgk 68 (512)
+.|.|+.|+.
T Consensus 20 t~f~CP~Cge 29 (99)
T PRK14892 20 KIFECPRCGK 29 (99)
T ss_pred cEeECCCCCC
Confidence 4699999994
No 173
>PF14353 CpXC: CpXC protein
Probab=25.36 E-value=8.6 Score=34.02 Aligned_cols=22 Identities=18% Similarity=0.567 Sum_probs=14.6
Q ss_pred cccccCCCCcccChHHHhhhhh
Q 010389 136 KWKCDKCSKKYAVQSDYKAHSK 157 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~ 157 (512)
.|.|+.||+.|.....+..|-.
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred EEECCCCCCceecCCCEEEEcC
Confidence 3778888887776665555543
No 174
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=25.34 E-value=58 Score=28.80 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=24.4
Q ss_pred cCCCCCeeccccCcccCChHHHHHHHHhc
Q 010389 55 LLATNRFVCEICNKGFQRDQNLQLHRRGH 83 (512)
Q Consensus 55 ~~~~k~f~C~~Cgk~F~~~~~L~~H~r~H 83 (512)
..+-.-|.|-+|.+-|.+...|+.|.++.
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 33445699999999999999999998764
No 175
>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=25.11 E-value=29 Score=25.39 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=5.7
Q ss_pred ccccccCCCC
Q 010389 135 KKWKCDKCSK 144 (512)
Q Consensus 135 kp~~C~~C~k 144 (512)
..-.|..|+.
T Consensus 25 ~~~~CP~Cg~ 34 (52)
T TIGR02605 25 PLATCPECGG 34 (52)
T ss_pred CCCCCCCCCC
Confidence 3345666664
No 176
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=25.01 E-value=67 Score=35.32 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=7.5
Q ss_pred CCeeccccCc
Q 010389 59 NRFVCEICNK 68 (512)
Q Consensus 59 k~f~C~~Cgk 68 (512)
.-|-|++|.+
T Consensus 4 ~L~fC~~C~~ 13 (483)
T PF05502_consen 4 ELYFCEHCHK 13 (483)
T ss_pred cceecccccc
Confidence 4688888876
No 177
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.69 E-value=67 Score=24.32 Aligned_cols=13 Identities=31% Similarity=0.841 Sum_probs=10.0
Q ss_pred CeeccccCcccCC
Q 010389 60 RFVCEICNKGFQR 72 (512)
Q Consensus 60 ~f~C~~Cgk~F~~ 72 (512)
..+|..|++.|..
T Consensus 5 ~~~C~~Cg~~~~~ 17 (54)
T PF14446_consen 5 GCKCPVCGKKFKD 17 (54)
T ss_pred CccChhhCCcccC
Confidence 4579999998854
No 178
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.49 E-value=69 Score=38.00 Aligned_cols=10 Identities=20% Similarity=0.305 Sum_probs=5.9
Q ss_pred CCcceeCCCC
Q 010389 98 KKRVYVCPEK 107 (512)
Q Consensus 98 ~~k~~~C~~C 107 (512)
......|+.|
T Consensus 623 EVg~RfCpsC 632 (1121)
T PRK04023 623 EIGRRKCPSC 632 (1121)
T ss_pred cccCccCCCC
Confidence 4445567776
No 179
>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=24.46 E-value=34 Score=24.22 Aligned_cols=10 Identities=20% Similarity=0.690 Sum_probs=5.9
Q ss_pred ccccccCCCC
Q 010389 135 KKWKCDKCSK 144 (512)
Q Consensus 135 kp~~C~~C~k 144 (512)
..-.|..|+.
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 4456666665
No 180
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=24.10 E-value=42 Score=33.34 Aligned_cols=14 Identities=21% Similarity=0.731 Sum_probs=10.7
Q ss_pred cccccCCCCcccCh
Q 010389 136 KWKCDKCSKKYAVQ 149 (512)
Q Consensus 136 p~~C~~C~k~F~~~ 149 (512)
.|.|..|+..|.-.
T Consensus 155 ef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 155 EFHCPKCRHNFRGF 168 (278)
T ss_pred eeecccccccchhh
Confidence 47888888888654
No 181
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=23.71 E-value=31 Score=23.79 Aligned_cols=19 Identities=26% Similarity=0.767 Sum_probs=11.6
Q ss_pred HHhhhhhccCCccccccCC
Q 010389 124 IKKHFCRKHGEKKWKCDKC 142 (512)
Q Consensus 124 Lk~H~~~H~gekp~~C~~C 142 (512)
+.+|=+...|...|.|..|
T Consensus 17 v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 17 VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred ceeCCCCCCCCEeEecCcC
Confidence 4555555555566777766
No 182
>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=23.44 E-value=37 Score=21.33 Aligned_cols=10 Identities=30% Similarity=0.630 Sum_probs=8.5
Q ss_pred CCeeccccCc
Q 010389 59 NRFVCEICNK 68 (512)
Q Consensus 59 k~f~C~~Cgk 68 (512)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4799999985
No 183
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=23.36 E-value=46 Score=30.12 Aligned_cols=31 Identities=23% Similarity=0.845 Sum_probs=18.6
Q ss_pred cccccCCCCcccChHHHhhhhhhcCCcceecc-CCCcc
Q 010389 136 KWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVF 172 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F 172 (512)
.|+|..|+..+. +|.|......|.|. |+-.|
T Consensus 112 ~y~C~~C~~~~~------~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYL------RVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCc------eEccccCcceEEcCCCCCEE
Confidence 577887877653 33332222668887 87655
No 184
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=23.35 E-value=44 Score=36.08 Aligned_cols=22 Identities=32% Similarity=0.837 Sum_probs=0.0
Q ss_pred eeccccCcccCChHHHHHHHHh
Q 010389 61 FVCEICNKGFQRDQNLQLHRRG 82 (512)
Q Consensus 61 f~C~~Cgk~F~~~~~L~~H~r~ 82 (512)
+-|.+|+|.|.+...|..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
No 185
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=23.11 E-value=99 Score=31.99 Aligned_cols=23 Identities=17% Similarity=0.732 Sum_probs=15.7
Q ss_pred cccccCCCCcccChHHHhhhhhh
Q 010389 136 KWKCDKCSKKYAVQSDYKAHSKV 158 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~ 158 (512)
.|+|..|...|-..-+.-.|...
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesL 367 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESL 367 (378)
T ss_pred cEEchhccceeeccchHHHHhhh
Confidence 47777777777776666666544
No 186
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.83 E-value=47 Score=35.63 Aligned_cols=28 Identities=25% Similarity=0.803 Sum_probs=19.8
Q ss_pred cccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCCh
Q 010389 138 KCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSRR 175 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~~ 175 (512)
+|..||.+ |+..|.+-|+|. |++++...
T Consensus 352 ~Cp~Cg~~----------m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGR----------MKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCc----------hhhcCCCCcccccccccCCcc
Confidence 58888876 334454578898 98888665
No 187
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=22.75 E-value=2.4e+02 Score=30.23 Aligned_cols=68 Identities=21% Similarity=0.505 Sum_probs=40.1
Q ss_pred CCcceeCCCCCCCCCCCCCccCChhhHHhhhhhccCC------------ccccccC--CCCcccChHHHhhhhhhcCC--
Q 010389 98 KKRVYVCPEKSCVHHDPTRALGDLTGIKKHFCRKHGE------------KKWKCDK--CSKKYAVQSDYKAHSKVCGT-- 161 (512)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~k~F~~~~~Lk~H~~~H~ge------------kp~~C~~--C~k~F~~~~~L~~H~~~h~~-- 161 (512)
....|.|-.-.| ...+..+..+.+|.++|... .-|.|.. |.|. -.+...|..-|.+
T Consensus 268 ~rEhyhcl~e~C-----~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~ks---TsdV~~h~nFht~~~ 339 (480)
T KOG4377|consen 268 GREHYHCLNEYC-----FYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEKS---TSDVLLHDNFHTDKR 339 (480)
T ss_pred cchhhcccCccc-----cccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCcc---cccccccCccccccc
Confidence 555677755433 65566699999999988532 1256754 8883 3344445443332
Q ss_pred ----c--ceecc-CC--CccC
Q 010389 162 ----K--EYKCN-CG--AVFS 173 (512)
Q Consensus 162 ----k--py~C~-Cg--k~F~ 173 (512)
+ -|.|. |+ ..|.
T Consensus 340 n~GfrrthfhC~r~gCTdtfK 360 (480)
T KOG4377|consen 340 NNGFRRTHFHCQRIGCTDTFK 360 (480)
T ss_pred cCceecceeEEeccCCccccc
Confidence 2 37787 55 5554
No 188
>KOG2385 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.73 E-value=27 Score=38.27 Aligned_cols=14 Identities=43% Similarity=0.563 Sum_probs=8.1
Q ss_pred CCCCCCCCCCCCCC
Q 010389 423 PGLGLGLPCEGSSG 436 (512)
Q Consensus 423 ~~~~~~~~~~~~~~ 436 (512)
||+|=|+-.+-..|
T Consensus 239 Ag~~GG~ligLTGG 252 (633)
T KOG2385|consen 239 AGLGGGLLIGLTGG 252 (633)
T ss_pred hhcccceeeeeccc
Confidence 67666665554444
No 189
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.69 E-value=30 Score=24.30 Aligned_cols=9 Identities=33% Similarity=1.195 Sum_probs=4.1
Q ss_pred ccccCCCCc
Q 010389 137 WKCDKCSKK 145 (512)
Q Consensus 137 ~~C~~C~k~ 145 (512)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 444444443
No 190
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=22.44 E-value=59 Score=22.97 Aligned_cols=24 Identities=21% Similarity=0.559 Sum_probs=18.8
Q ss_pred eeccccCcccCC--hHHHHHHHHhcC
Q 010389 61 FVCEICNKGFQR--DQNLQLHRRGHN 84 (512)
Q Consensus 61 f~C~~Cgk~F~~--~~~L~~H~r~H~ 84 (512)
-.|+.|+..|.. ..+-+.|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 589999998864 557788888774
No 191
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=22.21 E-value=3.5e+02 Score=27.14 Aligned_cols=23 Identities=13% Similarity=0.385 Sum_probs=17.6
Q ss_pred CCeeccccCcccCChHHHHHHHH
Q 010389 59 NRFVCEICNKGFQRDQNLQLHRR 81 (512)
Q Consensus 59 k~f~C~~Cgk~F~~~~~L~~H~r 81 (512)
....|.+|+....-...+.+|.-
T Consensus 64 p~v~CrVCq~~I~i~gk~~QhVV 86 (256)
T PF09788_consen 64 PVVTCRVCQSLIDIEGKMHQHVV 86 (256)
T ss_pred ceEEeecCCceecccCccceeeE
Confidence 45789999998887777776654
No 192
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=21.99 E-value=35 Score=31.27 Aligned_cols=15 Identities=27% Similarity=0.745 Sum_probs=9.0
Q ss_pred ccCCcc----ccccCCCCc
Q 010389 131 KHGEKK----WKCDKCSKK 145 (512)
Q Consensus 131 H~gekp----~~C~~C~k~ 145 (512)
|.||+. |.|..||..
T Consensus 103 ~sGE~~g~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 103 HSGEVVGPGTLVCENCGHE 121 (146)
T ss_pred ecCcEecCceEecccCCCE
Confidence 445543 677777664
No 193
>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=21.71 E-value=43 Score=22.94 Aligned_cols=15 Identities=27% Similarity=0.612 Sum_probs=12.0
Q ss_pred CCeeccccCcccCCh
Q 010389 59 NRFVCEICNKGFQRD 73 (512)
Q Consensus 59 k~f~C~~Cgk~F~~~ 73 (512)
-.|+|..|++.|...
T Consensus 4 Y~y~C~~Cg~~fe~~ 18 (41)
T smart00834 4 YEYRCEDCGHTFEVL 18 (41)
T ss_pred EEEEcCCCCCEEEEE
Confidence 358999999998643
No 194
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=21.70 E-value=1e+02 Score=32.25 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=23.8
Q ss_pred ccccCCCCCeeccccC-cccCChHHHHHHHH
Q 010389 52 PKTLLATNRFVCEICN-KGFQRDQNLQLHRR 81 (512)
Q Consensus 52 ~~~~~~~k~f~C~~Cg-k~F~~~~~L~~H~r 81 (512)
.+.|.-.+.|.|++|+ +++.-+..+.+|..
T Consensus 366 ~klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 366 CKLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred HHhcCCCcceeeeecccccccchHHHHhhhh
Confidence 3556777889999999 78877788888854
No 195
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=21.69 E-value=31 Score=33.20 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=0.0
Q ss_pred cccCCCCCeeccccC-cccCChHHHHHH
Q 010389 53 KTLLATNRFVCEICN-KGFQRDQNLQLH 79 (512)
Q Consensus 53 ~~~~~~k~f~C~~Cg-k~F~~~~~L~~H 79 (512)
+-|.-.+.|.|++|| ..|.=+..+.+|
T Consensus 94 KLhGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ----------------------------
T ss_pred HHhCCCCeeeeEeCCCcceecHHHHHHh
No 196
>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=21.46 E-value=43 Score=23.04 Aligned_cols=15 Identities=20% Similarity=0.503 Sum_probs=8.6
Q ss_pred CccccccCCCCcccC
Q 010389 134 EKKWKCDKCSKKYAV 148 (512)
Q Consensus 134 ekp~~C~~C~k~F~~ 148 (512)
...-+|+.|+-.+.+
T Consensus 19 ~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 19 KVEGVCDNCGGELVQ 33 (36)
T ss_dssp SSTTBCTTTTEBEBE
T ss_pred CCCCccCCCCCeeEe
Confidence 344567777765443
No 197
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=21.34 E-value=38 Score=36.34 Aligned_cols=8 Identities=38% Similarity=0.821 Sum_probs=4.8
Q ss_pred HHHHHHhc
Q 010389 76 LQLHRRGH 83 (512)
Q Consensus 76 L~~H~r~H 83 (512)
+..|.|.|
T Consensus 81 fvvHkrCh 88 (683)
T KOG0696|consen 81 FVVHKRCH 88 (683)
T ss_pred ehhhhhhc
Confidence 45666666
No 198
>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=21.09 E-value=40 Score=30.50 Aligned_cols=29 Identities=34% Similarity=1.090 Sum_probs=0.0
Q ss_pred ccccCCCCcccChHHHhhhhhhcCCcceecc-CCCcc
Q 010389 137 WKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVF 172 (512)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F 172 (512)
|.|..|+..+ .+|.+. ....|.|. |+..|
T Consensus 124 ~~C~~C~~~~------~r~~~~-~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 124 YRCPSCGREY------KRHRRS-KRKRYRCGRCGGPL 153 (157)
T ss_pred EEcCCCCCEe------eeeccc-chhhEECCCCCCEE
No 199
>PLN02748 tRNA dimethylallyltransferase
Probab=21.05 E-value=57 Score=35.67 Aligned_cols=26 Identities=23% Similarity=0.665 Sum_probs=22.6
Q ss_pred CCCeeccccCc-ccCChHHHHHHHHhc
Q 010389 58 TNRFVCEICNK-GFQRDQNLQLHRRGH 83 (512)
Q Consensus 58 ~k~f~C~~Cgk-~F~~~~~L~~H~r~H 83 (512)
.+.|.|++|++ .+.....+..|++..
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcch
Confidence 57899999997 899999999998654
No 200
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=20.69 E-value=43 Score=22.17 Aligned_cols=22 Identities=27% Similarity=0.794 Sum_probs=11.1
Q ss_pred eccccCcccCChHHHHHHHHhcCCCchhhcccccccCCcceeCCCC
Q 010389 62 VCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSNKEVKKRVYVCPEK 107 (512)
Q Consensus 62 ~C~~Cgk~F~~~~~L~~H~r~H~~p~~~~~~~~~~~~~k~~~C~~C 107 (512)
+|+.|+-.|.. . ....|+|+.|
T Consensus 4 ~Cp~C~se~~y-----------~-------------D~~~~vCp~C 25 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------E-------------DGELLVCPEC 25 (30)
T ss_dssp --TTT-----E-----------E--------------SSSEEETTT
T ss_pred CCCCCCCccee-----------c-------------cCCEEeCCcc
Confidence 58888877755 2 5678999998
No 201
>COG0192 MetK S-adenosylmethionine synthetase [Coenzyme metabolism]
Probab=20.69 E-value=50 Score=34.47 Aligned_cols=29 Identities=28% Similarity=0.440 Sum_probs=19.0
Q ss_pred CCCCCCCCCCcC-CCCCCChHHHHHHHHhc
Q 010389 351 IFGSGGQEPRQY-SQPAMSATALLQKAAQM 379 (512)
Q Consensus 351 ~~~~~~~~~~~f-~tP~lsa~~l~~ka~~~ 379 (512)
+|+-.-.|.-+| |-|=.-|..|++++++.
T Consensus 126 mFGyA~~ET~~lMPlpI~lAH~l~~r~a~~ 155 (388)
T COG0192 126 MFGYACNETPELMPLPISLAHRLLRRLAEV 155 (388)
T ss_pred EeeeecCCcccccChHHHHHHHHHHHHHHH
Confidence 344433343344 67777889999999884
No 202
>PTZ00448 hypothetical protein; Provisional
Probab=20.49 E-value=73 Score=33.56 Aligned_cols=22 Identities=18% Similarity=0.413 Sum_probs=11.5
Q ss_pred ceecc-CCCccCChhHHHHHHHH
Q 010389 163 EYKCN-CGAVFSRRDSFITHRAF 184 (512)
Q Consensus 163 py~C~-Cgk~F~~~~~L~~H~~~ 184 (512)
.|.|. |+..|......+.|.+.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 35555 55555555555555443
No 203
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=20.45 E-value=70 Score=22.26 Aligned_cols=23 Identities=26% Similarity=0.610 Sum_probs=9.7
Q ss_pred CCeeccccCcccCC-h-HHHHHHHH
Q 010389 59 NRFVCEICNKGFQR-D-QNLQLHRR 81 (512)
Q Consensus 59 k~f~C~~Cgk~F~~-~-~~L~~H~r 81 (512)
++|-|+.|.+.|.. . ..-+.|.+
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT-
T ss_pred cCeecccccceecCCChHHHHHhhc
Confidence 46899999999943 3 23366654
No 204
>KOG2385 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.36 E-value=34 Score=37.52 Aligned_cols=9 Identities=22% Similarity=0.512 Sum_probs=3.9
Q ss_pred hhcccCCCC
Q 010389 489 GAASLGGGG 497 (512)
Q Consensus 489 ~~~~~~~~~ 497 (512)
.+++||+++
T Consensus 288 v~ta~gaa~ 296 (633)
T KOG2385|consen 288 VITAFGAAG 296 (633)
T ss_pred HHHhhcccc
Confidence 334454433
No 205
>PRK04351 hypothetical protein; Provisional
Probab=20.27 E-value=55 Score=30.05 Aligned_cols=32 Identities=25% Similarity=0.766 Sum_probs=21.1
Q ss_pred cccccCCCCcccChHHHhhhhhhcCCcceecc-CCCccCC
Q 010389 136 KWKCDKCSKKYAVQSDYKAHSKVCGTKEYKCN-CGAVFSR 174 (512)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~h~~kpy~C~-Cgk~F~~ 174 (512)
.|.|..|+..+.+ + |.+..+.|.|. |+-.+..
T Consensus 112 ~Y~C~~Cg~~~~r------~-Rr~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLR------K-RRINTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeee------e-eecCCCcEEeCCCCcEeee
Confidence 4888888876532 2 23556789998 8766543
No 206
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=20.20 E-value=34 Score=38.96 Aligned_cols=18 Identities=28% Similarity=0.713 Sum_probs=11.9
Q ss_pred cccCCCCcccChHHHhhh
Q 010389 138 KCDKCSKKYAVQSDYKAH 155 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H 155 (512)
+|+.|+..|....-+..|
T Consensus 680 KCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCcccccccC
Confidence 677777777766555544
No 207
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.12 E-value=69 Score=22.96 Aligned_cols=16 Identities=13% Similarity=0.623 Sum_probs=11.6
Q ss_pred cccCCCCcccChHHHh
Q 010389 138 KCDKCSKKYAVQSDYK 153 (512)
Q Consensus 138 ~C~~C~k~F~~~~~L~ 153 (512)
.|.+|++.|.-+....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6888888887665544
No 208
>PHA00626 hypothetical protein
Probab=20.07 E-value=57 Score=24.88 Aligned_cols=17 Identities=24% Similarity=0.583 Sum_probs=13.8
Q ss_pred CCCeeccccCcccCChH
Q 010389 58 TNRFVCEICNKGFQRDQ 74 (512)
Q Consensus 58 ~k~f~C~~Cgk~F~~~~ 74 (512)
..+|+|+.||..|....
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 56899999999996543
Done!