Query 040791
Match_columns 465
No_of_seqs 450 out of 2691
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 11:51:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040791.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040791hhsearch_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 1E-27 2.2E-32 217.4 5.6 139 9-315 127-265 (279)
2 KOG1074 Transcriptional repres 99.9 3.1E-25 6.7E-30 226.0 7.4 83 170-259 603-692 (958)
3 KOG2462 C2H2-type Zn-finger pr 99.8 2.3E-22 4.9E-27 182.8 3.1 108 8-256 157-264 (279)
4 KOG3623 Homeobox transcription 99.8 1.8E-21 3.9E-26 195.3 2.3 103 13-115 211-315 (1007)
5 KOG1074 Transcriptional repres 99.8 6.6E-21 1.4E-25 194.7 6.3 245 9-263 602-935 (958)
6 KOG3608 Zn finger proteins [Ge 99.8 2.4E-21 5.2E-26 180.0 -0.4 197 11-317 176-377 (467)
7 KOG3608 Zn finger proteins [Ge 99.7 1.8E-18 3.9E-23 160.9 1.7 209 13-322 135-350 (467)
8 KOG3576 Ovo and related transc 99.7 2.1E-17 4.6E-22 142.8 1.1 97 205-320 143-239 (267)
9 KOG3576 Ovo and related transc 99.5 1.3E-15 2.9E-20 131.7 -0.6 85 5-103 110-195 (267)
10 KOG3623 Homeobox transcription 99.4 1.7E-13 3.6E-18 138.6 2.4 53 204-256 919-971 (1007)
11 PLN03086 PRLI-interacting fact 99.1 1.1E-10 2.4E-15 119.6 8.2 74 207-314 478-561 (567)
12 PHA00733 hypothetical protein 98.9 4.9E-10 1.1E-14 94.1 3.2 88 199-318 32-124 (128)
13 KOG3993 Transcription factor ( 98.8 1.1E-09 2.4E-14 105.2 1.6 53 13-106 268-320 (500)
14 PHA02768 hypothetical protein; 98.8 2.1E-09 4.6E-14 74.4 2.2 43 207-251 5-47 (55)
15 PHA02768 hypothetical protein; 98.7 5.9E-09 1.3E-13 72.2 0.7 38 12-52 5-42 (55)
16 PLN03086 PRLI-interacting fact 98.6 4.8E-08 1E-12 100.4 5.8 58 197-256 494-561 (567)
17 PHA00733 hypothetical protein 98.6 1.7E-08 3.7E-13 84.8 1.0 83 8-106 36-124 (128)
18 KOG3993 Transcription factor ( 98.4 1.3E-07 2.8E-12 91.2 3.5 84 12-105 295-380 (500)
19 PHA00732 hypothetical protein 98.2 5.7E-07 1.2E-11 68.5 2.4 25 207-231 1-26 (79)
20 PHA00616 hypothetical protein 98.2 4.7E-07 1E-11 59.7 1.1 34 207-240 1-34 (44)
21 PF13465 zf-H2C2_2: Zinc-finge 98.2 5.7E-07 1.2E-11 53.1 1.0 25 222-246 1-25 (26)
22 PF13465 zf-H2C2_2: Zinc-finge 98.1 7.6E-07 1.7E-11 52.6 0.8 21 285-305 6-26 (26)
23 PHA00732 hypothetical protein 97.9 4E-06 8.6E-11 63.9 1.9 24 12-35 1-25 (79)
24 PF00096 zf-C2H2: Zinc finger, 97.9 3.5E-06 7.7E-11 48.2 0.9 23 294-316 1-23 (23)
25 PHA00616 hypothetical protein 97.9 2.5E-06 5.5E-11 56.2 -0.4 33 12-45 1-33 (44)
26 PF00096 zf-C2H2: Zinc finger, 97.8 8.8E-06 1.9E-10 46.5 1.1 23 208-230 1-23 (23)
27 PF13912 zf-C2H2_6: C2H2-type 97.7 1.8E-05 4E-10 47.2 1.3 26 293-318 1-26 (27)
28 PF05605 zf-Di19: Drought indu 97.6 4.1E-05 8.8E-10 54.1 2.8 24 292-317 30-53 (54)
29 PF13894 zf-C2H2_4: C2H2-type 97.5 4.3E-05 9.4E-10 43.9 1.2 24 294-317 1-24 (24)
30 PF13912 zf-C2H2_6: C2H2-type 97.5 5.9E-05 1.3E-09 44.9 1.5 26 207-232 1-26 (27)
31 PF12756 zf-C2H2_2: C2H2 type 97.4 8E-05 1.7E-09 59.7 1.7 26 292-317 49-74 (100)
32 COG5189 SFP1 Putative transcri 97.3 0.00015 3.2E-09 67.9 2.8 71 204-314 346-419 (423)
33 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00012 2.5E-09 42.0 1.2 24 208-231 1-24 (24)
34 PF05605 zf-Di19: Drought indu 97.2 0.00027 5.8E-09 49.9 2.5 51 12-105 2-53 (54)
35 PF12756 zf-C2H2_2: C2H2 type 97.1 0.00023 5E-09 57.0 2.0 73 14-104 1-73 (100)
36 smart00355 ZnF_C2H2 zinc finge 96.9 0.00037 7.9E-09 40.6 1.2 25 294-318 1-25 (26)
37 COG5189 SFP1 Putative transcri 96.9 0.00047 1E-08 64.6 2.3 68 10-102 347-419 (423)
38 smart00355 ZnF_C2H2 zinc finge 96.7 0.0009 2E-08 38.9 1.6 25 208-232 1-25 (26)
39 PF09237 GAGA: GAGA factor; I 96.7 0.0011 2.4E-08 44.8 1.9 30 289-318 20-49 (54)
40 PF12874 zf-met: Zinc-finger o 96.5 0.0011 2.3E-08 38.6 0.9 23 294-316 1-23 (25)
41 KOG2231 Predicted E3 ubiquitin 96.5 0.0028 6E-08 66.6 4.4 23 209-231 184-206 (669)
42 PF12874 zf-met: Zinc-finger o 96.3 0.0018 3.8E-08 37.6 1.0 23 208-230 1-23 (25)
43 COG5048 FOG: Zn-finger [Genera 96.1 0.0065 1.4E-07 62.0 4.5 58 11-109 288-351 (467)
44 PF12171 zf-C2H2_jaz: Zinc-fin 96.0 0.0031 6.6E-08 37.4 1.2 23 294-316 2-24 (27)
45 PF09237 GAGA: GAGA factor; I 95.9 0.0064 1.4E-07 41.2 2.5 33 203-235 20-52 (54)
46 PRK04860 hypothetical protein; 95.7 0.0046 1E-07 53.9 1.4 40 206-249 118-157 (160)
47 PF13909 zf-H2C2_5: C2H2-type 95.7 0.0045 9.7E-08 35.5 0.9 23 294-317 1-23 (24)
48 PF12171 zf-C2H2_jaz: Zinc-fin 95.7 0.0049 1.1E-07 36.5 1.1 23 208-230 2-24 (27)
49 PF13909 zf-H2C2_5: C2H2-type 94.5 0.011 2.5E-07 33.8 0.2 23 82-105 1-23 (24)
50 KOG1146 Homeobox protein [Gene 94.4 0.025 5.5E-07 63.1 2.6 24 80-103 517-540 (1406)
51 KOG2893 Zn finger protein [Gen 94.0 0.018 3.9E-07 52.1 0.5 29 291-319 32-61 (341)
52 PF13913 zf-C2HC_2: zinc-finge 93.9 0.027 5.9E-07 32.7 0.9 21 294-315 3-23 (25)
53 KOG2231 Predicted E3 ubiquitin 93.3 0.082 1.8E-06 55.9 3.9 46 212-258 155-205 (669)
54 COG5048 FOG: Zn-finger [Genera 92.5 0.079 1.7E-06 54.0 2.6 57 206-262 288-350 (467)
55 PF13913 zf-C2HC_2: zinc-finge 92.4 0.079 1.7E-06 30.7 1.4 21 208-229 3-23 (25)
56 smart00451 ZnF_U1 U1-like zinc 92.3 0.077 1.7E-06 33.3 1.4 23 207-229 3-25 (35)
57 PRK04860 hypothetical protein; 91.9 0.092 2E-06 45.9 1.8 41 234-308 118-158 (160)
58 smart00451 ZnF_U1 U1-like zinc 91.5 0.11 2.4E-06 32.6 1.4 23 293-315 3-25 (35)
59 KOG1146 Homeobox protein [Gene 90.0 0.17 3.7E-06 56.9 2.0 28 291-319 1327-1354(1406)
60 KOG2893 Zn finger protein [Gen 90.0 0.13 2.7E-06 46.8 0.9 25 208-232 35-60 (341)
61 COG5236 Uncharacterized conser 89.5 0.23 5E-06 47.6 2.2 74 208-319 221-307 (493)
62 KOG2785 C2H2-type Zn-finger pr 87.1 0.48 1E-05 46.4 2.8 65 235-314 166-241 (390)
63 PF09986 DUF2225: Uncharacteri 85.9 0.44 9.4E-06 44.0 1.8 25 10-34 3-27 (214)
64 TIGR00622 ssl1 transcription f 84.9 1.7 3.8E-05 35.2 4.5 27 291-317 79-105 (112)
65 KOG2785 C2H2-type Zn-finger pr 84.7 0.76 1.7E-05 45.0 2.9 51 206-256 165-241 (390)
66 COG5236 Uncharacterized conser 82.8 2.2 4.8E-05 41.1 5.0 21 83-103 222-242 (493)
67 COG4049 Uncharacterized protei 82.2 0.56 1.2E-05 32.4 0.6 26 203-228 13-38 (65)
68 PF02892 zf-BED: BED zinc fing 78.0 1.3 2.9E-05 29.4 1.4 26 291-316 14-44 (45)
69 cd00350 rubredoxin_like Rubred 76.5 1.4 3.1E-05 27.3 1.1 7 83-89 19-25 (33)
70 KOG2482 Predicted C2H2-type Zn 76.4 1.7 3.7E-05 41.9 2.1 26 207-232 195-222 (423)
71 TIGR00622 ssl1 transcription f 75.7 16 0.00034 29.8 7.1 27 205-231 79-105 (112)
72 PF10571 UPF0547: Uncharacteri 74.3 2.3 4.9E-05 24.9 1.5 10 83-92 16-25 (26)
73 smart00614 ZnF_BED BED zinc fi 74.1 1.6 3.4E-05 30.0 1.0 25 293-317 18-48 (50)
74 KOG2482 Predicted C2H2-type Zn 73.9 2.7 5.9E-05 40.6 2.7 51 208-258 280-357 (423)
75 PRK04023 DNA polymerase II lar 73.7 3.8 8.2E-05 45.5 4.1 16 292-307 662-677 (1121)
76 PF09538 FYDLN_acid: Protein o 72.8 2.2 4.9E-05 34.6 1.7 12 83-94 28-39 (108)
77 COG4049 Uncharacterized protei 72.7 1.3 2.9E-05 30.6 0.3 32 286-317 10-42 (65)
78 KOG2186 Cell growth-regulating 71.9 2.1 4.4E-05 39.7 1.4 22 83-105 31-52 (276)
79 PF09538 FYDLN_acid: Protein o 71.5 2.8 6E-05 34.0 1.9 33 10-54 7-39 (108)
80 PF09986 DUF2225: Uncharacteri 70.3 1.5 3.2E-05 40.5 0.1 42 205-246 3-59 (214)
81 PF02892 zf-BED: BED zinc fing 69.9 2.9 6.4E-05 27.7 1.5 24 204-227 13-40 (45)
82 cd00729 rubredoxin_SM Rubredox 69.2 2.7 5.9E-05 26.3 1.1 7 83-89 20-26 (34)
83 PHA00626 hypothetical protein 68.7 2.7 5.9E-05 29.2 1.1 16 205-220 21-36 (59)
84 PRK00464 nrdR transcriptional 68.2 1.8 3.9E-05 37.5 0.2 22 205-226 26-47 (154)
85 COG1198 PriA Primosomal protei 68.2 3.2 7E-05 45.2 2.1 12 291-302 473-484 (730)
86 smart00614 ZnF_BED BED zinc fi 67.2 3.3 7.1E-05 28.4 1.3 26 206-231 17-48 (50)
87 PRK00398 rpoP DNA-directed RNA 66.0 3.1 6.6E-05 28.0 1.0 10 83-92 23-32 (46)
88 PF13717 zinc_ribbon_4: zinc-r 64.2 2.7 5.9E-05 26.7 0.4 34 173-218 3-36 (36)
89 KOG2071 mRNA cleavage and poly 64.1 4.4 9.5E-05 42.3 2.1 30 7-36 413-442 (579)
90 KOG4167 Predicted DNA-binding 63.5 1.5 3.2E-05 46.5 -1.4 29 292-320 791-819 (907)
91 PF09723 Zn-ribbon_8: Zinc rib 63.5 2.2 4.7E-05 28.1 -0.1 30 172-215 5-34 (42)
92 smart00734 ZnF_Rad18 Rad18-lik 63.4 3.9 8.5E-05 23.9 0.9 21 294-315 2-22 (26)
93 TIGR02300 FYDLN_acid conserved 59.7 6 0.00013 32.7 1.7 14 83-96 28-41 (129)
94 PF05443 ROS_MUCR: ROS/MUCR tr 58.9 4.3 9.3E-05 34.2 0.8 26 291-319 70-95 (132)
95 smart00834 CxxC_CXXC_SSSS Puta 58.6 3.2 7E-05 26.8 0.0 12 173-184 6-17 (41)
96 TIGR02300 FYDLN_acid conserved 57.9 7.3 0.00016 32.2 2.0 33 10-54 7-39 (129)
97 KOG2071 mRNA cleavage and poly 57.7 7.9 0.00017 40.5 2.6 26 82-107 419-444 (579)
98 TIGR02605 CxxC_CxxC_SSSS putat 57.1 3.6 7.7E-05 28.3 0.0 11 173-183 6-16 (52)
99 COG1198 PriA Primosomal protei 56.6 6.5 0.00014 42.9 1.9 46 13-90 436-484 (730)
100 PF13719 zinc_ribbon_5: zinc-r 56.3 4 8.7E-05 26.0 0.2 34 173-218 3-36 (37)
101 PRK00464 nrdR transcriptional 56.1 6.9 0.00015 33.9 1.7 15 82-96 29-43 (154)
102 KOG1280 Uncharacterized conser 55.8 15 0.00033 35.7 4.0 40 204-243 76-117 (381)
103 PF06524 NOA36: NOA36 protein; 55.3 13 0.00028 34.7 3.3 41 207-252 182-226 (314)
104 PRK14890 putative Zn-ribbon RN 54.9 5.3 0.00011 28.3 0.6 52 10-90 5-57 (59)
105 TIGR02098 MJ0042_CXXC MJ0042 f 54.2 3.3 7.2E-05 26.4 -0.5 34 173-218 3-36 (38)
106 PRK14873 primosome assembly pr 53.2 6.8 0.00015 42.6 1.4 34 209-243 385-418 (665)
107 COG1997 RPL43A Ribosomal prote 51.9 9.3 0.0002 29.4 1.5 11 83-93 55-65 (89)
108 PF14353 CpXC: CpXC protein 51.0 3.3 7.1E-05 34.7 -1.2 58 173-230 2-61 (128)
109 PF12013 DUF3505: Protein of u 50.8 8.2 0.00018 31.3 1.2 26 293-318 80-109 (109)
110 TIGR00595 priA primosomal prot 50.7 8.6 0.00019 40.4 1.7 19 225-243 230-248 (505)
111 PRK06266 transcription initiat 50.6 7.4 0.00016 34.7 1.0 34 205-247 115-148 (178)
112 TIGR00373 conserved hypothetic 48.6 9.8 0.00021 33.2 1.4 32 204-244 106-137 (158)
113 PF15269 zf-C2H2_7: Zinc-finge 48.2 10 0.00022 25.1 1.1 24 81-104 20-43 (54)
114 COG4957 Predicted transcriptio 47.2 9.2 0.0002 31.9 0.9 24 293-319 76-99 (148)
115 KOG4173 Alpha-SNAP protein [In 47.1 2.6 5.7E-05 37.6 -2.3 29 290-318 141-172 (253)
116 TIGR00373 conserved hypothetic 46.9 11 0.00024 32.9 1.4 37 167-219 104-140 (158)
117 COG1996 RPC10 DNA-directed RNA 46.9 8.2 0.00018 26.3 0.5 7 83-89 26-32 (49)
118 KOG2186 Cell growth-regulating 46.3 12 0.00027 34.7 1.7 25 292-317 28-52 (276)
119 PRK06266 transcription initiat 46.1 7.1 0.00015 34.8 0.2 21 231-251 113-133 (178)
120 COG5151 SSL1 RNA polymerase II 46.1 30 0.00065 33.2 4.2 27 204-230 385-411 (421)
121 PF05443 ROS_MUCR: ROS/MUCR tr 46.0 9.7 0.00021 32.1 0.9 27 205-234 70-96 (132)
122 COG1592 Rubrerythrin [Energy p 45.8 12 0.00027 32.7 1.6 12 289-300 145-156 (166)
123 PF03604 DNA_RNApol_7kD: DNA d 45.2 13 0.00028 22.9 1.2 8 83-90 19-26 (32)
124 COG2888 Predicted Zn-ribbon RN 44.6 9.1 0.0002 27.1 0.5 50 12-90 9-59 (61)
125 smart00659 RPOLCX RNA polymera 44.3 7.8 0.00017 25.8 0.1 25 173-215 3-27 (44)
126 smart00531 TFIIE Transcription 44.0 10 0.00022 32.7 0.7 13 292-304 122-134 (147)
127 PF12013 DUF3505: Protein of u 43.6 15 0.00033 29.7 1.7 27 80-106 79-109 (109)
128 PF08790 zf-LYAR: LYAR-type C2 42.5 12 0.00026 22.3 0.6 22 294-316 1-22 (28)
129 PF15269 zf-C2H2_7: Zinc-finge 42.4 11 0.00023 25.0 0.5 26 10-35 18-43 (54)
130 smart00531 TFIIE Transcription 41.8 16 0.00035 31.4 1.7 37 204-245 96-133 (147)
131 PTZ00303 phosphatidylinositol 41.6 12 0.00026 40.3 1.0 12 83-94 462-473 (1374)
132 KOG4377 Zn-finger protein [Gen 41.3 37 0.00081 33.9 4.2 26 294-319 402-429 (480)
133 PF01780 Ribosomal_L37ae: Ribo 40.6 7.3 0.00016 30.3 -0.5 31 172-219 35-65 (90)
134 COG4957 Predicted transcriptio 40.6 15 0.00032 30.7 1.2 25 82-109 77-101 (148)
135 COG1592 Rubrerythrin [Energy p 40.3 16 0.00034 32.1 1.4 23 41-88 134-156 (166)
136 TIGR00280 L37a ribosomal prote 39.9 9.8 0.00021 29.6 0.1 32 171-219 34-65 (91)
137 PTZ00255 60S ribosomal protein 39.9 14 0.0003 28.8 0.9 32 40-93 35-66 (90)
138 PRK09678 DNA-binding transcrip 39.4 14 0.00031 27.5 0.8 19 291-309 25-45 (72)
139 KOG4173 Alpha-SNAP protein [In 39.3 15 0.00032 33.1 1.1 49 209-257 108-168 (253)
140 KOG1280 Uncharacterized conser 38.8 27 0.00059 34.1 2.8 25 81-105 79-103 (381)
141 PF09416 UPF1_Zn_bind: RNA hel 37.8 25 0.00055 30.3 2.2 15 205-219 12-26 (152)
142 COG4530 Uncharacterized protei 37.5 19 0.00042 28.8 1.3 15 83-98 28-42 (129)
143 PF04959 ARS2: Arsenite-resist 36.6 11 0.00025 34.5 -0.0 30 6-35 71-101 (214)
144 TIGR00244 transcriptional regu 35.5 14 0.0003 31.6 0.3 22 205-226 26-47 (147)
145 PF04959 ARS2: Arsenite-resist 35.4 20 0.00044 32.9 1.4 30 203-232 73-102 (214)
146 COG1773 Rubredoxin [Energy pro 35.4 17 0.00036 25.5 0.6 15 292-306 2-16 (55)
147 smart00440 ZnF_C2C2 C2C2 Zinc 35.0 25 0.00054 22.8 1.4 11 82-92 29-39 (40)
148 TIGR00595 priA primosomal prot 34.9 24 0.00053 37.1 2.1 36 13-50 214-249 (505)
149 PRK03976 rpl37ae 50S ribosomal 34.6 13 0.00028 29.0 -0.0 32 171-219 35-66 (90)
150 PF13878 zf-C2H2_3: zinc-finge 34.1 20 0.00044 23.4 0.8 25 293-317 13-39 (41)
151 COG3677 Transposase and inacti 32.4 20 0.00044 30.1 0.8 18 204-221 50-67 (129)
152 PF01096 TFIIS_C: Transcriptio 32.3 18 0.0004 23.3 0.4 11 82-92 29-39 (39)
153 COG4640 Predicted membrane pro 32.3 28 0.0006 34.6 1.8 21 291-311 13-33 (465)
154 PF01363 FYVE: FYVE zinc finge 32.1 24 0.00051 25.7 1.0 10 83-92 27-36 (69)
155 KOG1044 Actin-binding LIM Zn-f 32.1 37 0.00081 35.5 2.7 41 9-52 13-53 (670)
156 PF08274 PhnA_Zn_Ribbon: PhnA 32.0 19 0.0004 21.9 0.4 25 174-216 4-28 (30)
157 PF07754 DUF1610: Domain of un 32.0 22 0.00048 20.3 0.7 11 291-301 14-24 (24)
158 PRK05580 primosome assembly pr 31.9 25 0.00055 38.5 1.7 47 173-300 382-428 (679)
159 PF12760 Zn_Tnp_IS1595: Transp 31.8 23 0.0005 23.7 0.8 11 205-215 35-45 (46)
160 PF09845 DUF2072: Zn-ribbon co 31.8 21 0.00046 29.8 0.8 15 293-307 1-15 (131)
161 COG3357 Predicted transcriptio 31.8 30 0.00065 26.8 1.5 14 40-53 57-70 (97)
162 TIGR01206 lysW lysine biosynth 31.6 19 0.00042 25.1 0.5 30 173-217 3-32 (54)
163 COG2331 Uncharacterized protei 31.0 18 0.0004 26.9 0.3 33 171-217 11-43 (82)
164 smart00154 ZnF_AN1 AN1-like Zi 30.8 26 0.00055 22.6 0.9 15 293-307 12-26 (39)
165 PF14446 Prok-RING_1: Prokaryo 30.3 41 0.00088 23.5 1.9 9 83-91 23-31 (54)
166 PRK03824 hypA hydrogenase nick 30.0 37 0.00081 28.7 2.0 35 150-184 42-82 (135)
167 KOG3408 U1-like Zn-finger-cont 29.5 28 0.0006 28.6 1.1 27 203-229 53-79 (129)
168 COG1327 Predicted transcriptio 29.5 21 0.00046 30.6 0.4 21 204-224 25-45 (156)
169 COG5152 Uncharacterized conser 29.2 24 0.00051 31.5 0.7 16 206-221 195-210 (259)
170 cd00924 Cyt_c_Oxidase_Vb Cytoc 29.1 24 0.00051 28.0 0.6 20 285-305 72-91 (97)
171 PF11519 DUF3222: Protein of u 27.3 15 0.00033 26.2 -0.7 17 441-457 35-51 (74)
172 PF10013 DUF2256: Uncharacteri 27.3 41 0.0009 22.1 1.4 16 83-98 10-25 (42)
173 KOG2807 RNA polymerase II tran 26.9 44 0.00096 32.4 2.1 83 13-129 277-374 (378)
174 PRK03681 hypA hydrogenase nick 26.8 55 0.0012 26.8 2.4 16 148-163 40-55 (114)
175 cd00065 FYVE FYVE domain; Zinc 26.7 40 0.00088 23.3 1.5 11 83-93 20-30 (57)
176 COG1655 Uncharacterized protei 26.6 25 0.00054 32.3 0.4 29 205-233 17-45 (267)
177 PRK14873 primosome assembly pr 26.2 36 0.00078 37.1 1.6 31 14-49 385-418 (665)
178 PF07975 C1_4: TFIIH C1-like d 26.0 29 0.00063 23.9 0.6 25 11-35 20-44 (51)
179 PF09332 Mcm10: Mcm10 replicat 25.8 21 0.00046 35.2 -0.2 42 11-52 251-296 (344)
180 KOG2593 Transcription initiati 25.6 47 0.001 33.5 2.1 11 386-396 280-290 (436)
181 PLN02294 cytochrome c oxidase 25.4 32 0.0007 30.1 0.8 21 285-306 134-154 (174)
182 KOG2461 Transcription factor B 25.4 4E+02 0.0086 27.1 8.7 52 17-69 187-239 (396)
183 KOG0717 Molecular chaperone (D 25.2 32 0.00069 35.0 0.9 22 294-315 293-314 (508)
184 smart00661 RPOL9 RNA polymeras 24.9 50 0.0011 22.4 1.6 16 293-308 20-35 (52)
185 PRK12380 hydrogenase nickel in 24.9 32 0.00069 28.1 0.7 11 42-52 71-81 (113)
186 PF13240 zinc_ribbon_2: zinc-r 24.8 49 0.0011 18.6 1.2 8 83-90 15-22 (23)
187 COG3364 Zn-ribbon containing p 24.7 37 0.0008 26.9 0.9 17 293-309 2-18 (112)
188 KOG2636 Splicing factor 3a, su 24.2 39 0.00084 34.2 1.2 28 287-314 395-423 (497)
189 PRK14714 DNA polymerase II lar 24.2 63 0.0014 37.4 3.0 12 207-218 692-703 (1337)
190 PF06524 NOA36: NOA36 protein; 24.2 45 0.00099 31.2 1.6 90 7-105 137-233 (314)
191 PF05191 ADK_lid: Adenylate ki 24.1 43 0.00093 21.2 1.0 11 13-23 2-12 (36)
192 KOG4124 Putative transcription 23.9 34 0.00074 33.4 0.8 69 66-227 347-418 (442)
193 KOG3408 U1-like Zn-finger-cont 23.6 38 0.00082 27.8 0.9 27 289-315 53-79 (129)
194 smart00064 FYVE Protein presen 22.7 50 0.0011 23.9 1.4 10 83-92 28-37 (68)
195 PF01428 zf-AN1: AN1-like Zinc 22.7 32 0.0007 22.6 0.3 16 292-307 12-27 (43)
196 COG0068 HypF Hydrogenase matur 22.3 57 0.0012 35.3 2.1 80 14-132 103-183 (750)
197 TIGR00100 hypA hydrogenase nic 22.2 40 0.00087 27.6 0.8 11 42-52 71-81 (115)
198 COG5188 PRP9 Splicing factor 3 22.2 43 0.00094 32.7 1.1 27 287-313 368-395 (470)
199 PRK04023 DNA polymerase II lar 22.0 62 0.0014 36.5 2.4 12 11-22 625-636 (1121)
200 PF06220 zf-U1: U1 zinc finger 21.6 42 0.0009 21.5 0.6 23 11-33 2-26 (38)
201 PF07203 DUF1412: Protein of u 21.4 37 0.0008 23.1 0.4 13 442-454 26-40 (53)
202 PF13248 zf-ribbon_3: zinc-rib 21.3 61 0.0013 18.7 1.2 8 83-90 18-25 (26)
203 KOG0402 60S ribosomal protein 21.1 41 0.0009 25.5 0.6 31 172-219 36-66 (92)
204 KOG2636 Splicing factor 3a, su 21.0 50 0.0011 33.5 1.3 28 200-227 394-422 (497)
205 COG4640 Predicted membrane pro 21.0 60 0.0013 32.4 1.8 17 83-99 17-33 (465)
206 PF00301 Rubredoxin: Rubredoxi 20.5 42 0.00091 22.7 0.5 13 294-306 2-14 (47)
207 KOG3507 DNA-directed RNA polym 20.4 62 0.0013 22.9 1.3 16 291-306 35-50 (62)
208 KOG4226 Adaptor protein NCK/Do 20.3 93 0.002 29.4 2.8 86 358-457 103-197 (379)
209 PRK12496 hypothetical protein; 20.2 58 0.0013 28.6 1.4 11 42-52 128-138 (164)
210 PF04423 Rad50_zn_hook: Rad50 20.2 39 0.00085 23.4 0.3 13 295-307 22-34 (54)
211 COG1571 Predicted DNA-binding 20.2 55 0.0012 33.2 1.4 17 86-102 215-231 (421)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.94 E-value=1e-27 Score=217.43 Aligned_cols=139 Identities=24% Similarity=0.430 Sum_probs=124.8
Q ss_pred CCceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCccc
Q 040791 9 SNFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCG 88 (465)
Q Consensus 9 ~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cg 88 (465)
...+|+|..|||.+.+.++|.+|..+|. + + ...+.+ .|++||
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~--------~-----------~------~s~ka~-------------~C~~C~ 168 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHR--------S-----------L------DSKKAF-------------SCKYCG 168 (279)
T ss_pred cCCceeccccccccccccccchhhcccc--------c-----------c------cccccc-------------cCCCCC
Confidence 5677999999999999999999999994 1 0 123445 899999
Q ss_pred ccccChHHHHHhhhhCCCccCcCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCchhHHHHHHHHhhccCCCCCC
Q 040791 89 KEFLSWKSFLEHGKCSSEDAESLVSSPGSDGEDGTPRRGCGWSKRKRSLRAKVGNCPSSEEEDLANCLMMLSNATVDPLD 168 (465)
Q Consensus 89 k~F~~~~~L~~H~r~H~ge~~~~~~~~~~~~e~~~~c~~c~~~~~~~s~~~~~~~~~~~eee~~a~~l~~l~~~~~~~~~ 168 (465)
|.|.+...|+.|+|+|+
T Consensus 169 K~YvSmpALkMHirTH~--------------------------------------------------------------- 185 (279)
T KOG2462|consen 169 KVYVSMPALKMHIRTHT--------------------------------------------------------------- 185 (279)
T ss_pred ceeeehHHHhhHhhccC---------------------------------------------------------------
Confidence 99999999999999997
Q ss_pred CCCCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCCc
Q 040791 169 AEPEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDSL 248 (465)
Q Consensus 169 ~~~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~~ 248 (465)
-+++|.+|||.|.+...|++|+|+|+|||||.|+.|+++|...
T Consensus 186 -------------------------------------l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADR 228 (279)
T KOG2462|consen 186 -------------------------------------LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADR 228 (279)
T ss_pred -------------------------------------CCcccccccccccchHHhhcccccccCCCCccCCcccchhcch
Confidence 1489999999999999999999999999999999999999999
Q ss_pred chhhhhhhhcccccCCCcchhhHhhhcCCCCCCcccccccCCCCceecCccccccCCchhhhhhhhh
Q 040791 249 ADEDHDVITHEEFFPTKSTSAMQFDHGANNNNAPLASSSKRKSKVHECSICHRVFSSGQALGGHKRC 315 (465)
Q Consensus 249 ~~l~~H~~~H~~~~~~~~~s~~l~~H~~~~~~~~~~~~~h~~ekp~~C~~Cgk~F~~~~~L~~H~r~ 315 (465)
++|+.|+.+|.+ .|+|+|..|+|+|+.++.|.+|...
T Consensus 229 SNLRAHmQTHS~------------------------------~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 229 SNLRAHMQTHSD------------------------------VKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred HHHHHHHHhhcC------------------------------CccccCcchhhHHHHHHHHHHhhhh
Confidence 999999999866 6899999999999999999999764
No 2
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.91 E-value=3.1e-25 Score=225.96 Aligned_cols=83 Identities=13% Similarity=0.197 Sum_probs=73.8
Q ss_pred CCCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCChhhhhhhhhhcCCCC----cccCC---CCC
Q 040791 170 EPEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNSHQALGGHRASHKKVK----GCFAA---RLD 242 (465)
Q Consensus 170 ~~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k----~~~C~---~C~ 242 (465)
..+..|-+|-+...-++.|. .|++.|+|++||+|++||+.|.++.+|+.|+-+|+..- .+.|+ .|-
T Consensus 603 TdPNqCiiC~rVlSC~saLq-------mHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~ 675 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQ-------MHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQ 675 (958)
T ss_pred CCccceeeeeecccchhhhh-------hhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhc
Confidence 45788999999998888887 89999999999999999999999999999999997654 57788 899
Q ss_pred CcCCCcchhhhhhhhcc
Q 040791 243 HMDDSLADEDHDVITHE 259 (465)
Q Consensus 243 ~~f~~~~~l~~H~~~H~ 259 (465)
+.|...-.|..|+++|.
T Consensus 676 ~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 676 KKFTNAVTLPQHIRIHL 692 (958)
T ss_pred ccccccccccceEEeec
Confidence 99988888888988886
No 3
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.85 E-value=2.3e-22 Score=182.78 Aligned_cols=108 Identities=25% Similarity=0.321 Sum_probs=93.6
Q ss_pred CCCceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCcc
Q 040791 8 QSNFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENC 87 (465)
Q Consensus 8 ~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~C 87 (465)
+..+.+.|++|+|.|.+-.+|+.|+|+|+ .++ +|.+|
T Consensus 157 ~s~ka~~C~~C~K~YvSmpALkMHirTH~------------------------------l~c-------------~C~iC 193 (279)
T KOG2462|consen 157 DSKKAFSCKYCGKVYVSMPALKMHIRTHT------------------------------LPC-------------ECGIC 193 (279)
T ss_pred cccccccCCCCCceeeehHHHhhHhhccC------------------------------CCc-------------ccccc
Confidence 34778999999999999999999999994 456 89999
Q ss_pred cccccChHHHHHhhhhCCCccCcCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCchhHHHHHHHHhhccCCCCC
Q 040791 88 GKEFLSWKSFLEHGKCSSEDAESLVSSPGSDGEDGTPRRGCGWSKRKRSLRAKVGNCPSSEEEDLANCLMMLSNATVDPL 167 (465)
Q Consensus 88 gk~F~~~~~L~~H~r~H~ge~~~~~~~~~~~~e~~~~c~~c~~~~~~~s~~~~~~~~~~~eee~~a~~l~~l~~~~~~~~ 167 (465)
||.|...+.|+.|+|+|+|
T Consensus 194 GKaFSRPWLLQGHiRTHTG------------------------------------------------------------- 212 (279)
T KOG2462|consen 194 GKAFSRPWLLQGHIRTHTG------------------------------------------------------------- 212 (279)
T ss_pred cccccchHHhhcccccccC-------------------------------------------------------------
Confidence 9999999999999998884
Q ss_pred CCCCCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCC
Q 040791 168 DAEPEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDS 247 (465)
Q Consensus 168 ~~~~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~ 247 (465)
||||.|..|+|.|..+++|+.||++|.+.|.|.|..|++.|..
T Consensus 213 -------------------------------------EKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 213 -------------------------------------EKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred -------------------------------------CCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 4568888888888888889999888888888889889888888
Q ss_pred cchhhhhhh
Q 040791 248 LADEDHDVI 256 (465)
Q Consensus 248 ~~~l~~H~~ 256 (465)
++-|.+|..
T Consensus 256 ~SyLnKH~E 264 (279)
T KOG2462|consen 256 KSYLNKHSE 264 (279)
T ss_pred HHHHHHhhh
Confidence 888888765
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.82 E-value=1.8e-21 Score=195.31 Aligned_cols=103 Identities=17% Similarity=0.192 Sum_probs=76.7
Q ss_pred eccCcccCcCCCccchhhhhhh-cccCCcccCCCcCcccCcCcccCCCCCC-CCCCcceecccCCCCCCCcccCCccccc
Q 040791 13 HYCKICKKGFGCGRALGGHMRA-HGIGDESGHIDDDDQASDWEDKLGGNVP-PTNKRMYALRANPNRLKSCRVCENCGKE 90 (465)
Q Consensus 13 ~~C~~C~k~F~~~~~L~~H~r~-H~~~~~~~~C~~C~~~f~~~~~l~~h~~-~~~~~~~~lr~~~~~~~~~y~C~~Cgk~ 90 (465)
..|.+|.+++.....|+.|++. |--.+..|.|..|...|.+...|.+|+. |....+-+....-+...+-|+|.+|||.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 5799999999999999999774 5446677899999999998888888876 5443333222222223344699999999
Q ss_pred ccChHHHHHhhhhCCCccCcCCCCC
Q 040791 91 FLSWKSFLEHGKCSSEDAESLVSSP 115 (465)
Q Consensus 91 F~~~~~L~~H~r~H~ge~~~~~~~~ 115 (465)
|..+..|++|+|+|.||+++.|..|
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnC 315 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNC 315 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCccc
Confidence 9999999999999998887655444
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.82 E-value=6.6e-21 Score=194.66 Aligned_cols=245 Identities=18% Similarity=0.166 Sum_probs=157.4
Q ss_pred CCceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCC-CCCCcceecccCCCCCCCcccCC--
Q 040791 9 SNFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVP-PTNKRMYALRANPNRLKSCRVCE-- 85 (465)
Q Consensus 9 ~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~-~~~~~~~~lr~~~~~~~~~y~C~-- 85 (465)
...+-+|-+|-|+..++++|+.|.|+|+ ||+||+|.+|++.|..+-+|+.|+. |....++ +.++.|+
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHt-GERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~---------R~q~ScP~~ 671 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHT-GERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA---------RVQFSCPST 671 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhccc-CcCccccccccchhccccchhhcccccccCccc---------cccccCCch
Confidence 3456799999999999999999999998 9999999999999999999999998 7776666 3556999
Q ss_pred -cccccccChHHHHHhhhhCCCccCcCCCCCCCCCCCCCCCCCCCCCccccccccccCCCC--------------CCch-
Q 040791 86 -NCGKEFLSWKSFLEHGKCSSEDAESLVSSPGSDGEDGTPRRGCGWSKRKRSLRAKVGNCP--------------SSEE- 149 (465)
Q Consensus 86 -~Cgk~F~~~~~L~~H~r~H~ge~~~~~~~~~~~~e~~~~c~~c~~~~~~~s~~~~~~~~~--------------~~ee- 149 (465)
+|-+.|.....|..|+++|.+..-.--............|..|.+.|........++..+ ..++
T Consensus 672 ~ic~~kftn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~ 751 (958)
T KOG1074|consen 672 FICQKKFTNAVTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEE 751 (958)
T ss_pred hhhcccccccccccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccc
Confidence 999999999999999999995432211111222333446777777775444333333221 0000
Q ss_pred hHH------HHHHHHhh--------------cc----CCC----------CCCCCCCC-cccccchhhhhh---c-----
Q 040791 150 EDL------ANCLMMLS--------------NA----TVD----------PLDAEPEE-SCASASKEEERR---N----- 186 (465)
Q Consensus 150 e~~------a~~l~~l~--------------~~----~~~----------~~~~~~~~-~C~~c~k~f~~~---~----- 186 (465)
.++ ..|..++. .. ... ..+.+++. .+..++..-... .
T Consensus 752 ~~~tp~~~e~~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~ 831 (958)
T KOG1074|consen 752 LDVTPPPPENSCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWN 831 (958)
T ss_pred cccCCCccccccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhc
Confidence 000 01110000 00 000 01122232 333332211100 0
Q ss_pred ----cc----c----ccCCcc-------------cccccccc--CCCcccccccccccCChhhhhhhhhhcCCCCcccCC
Q 040791 187 ----SM----N----FIGPIS-------------MDKAKGVA--NKGLFECKACKKVFNSHQALGGHRASHKKVKGCFAA 239 (465)
Q Consensus 187 ----~l----~----~~~~~~-------------~~~~~~~~--~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~ 239 (465)
.| . ...+.. +....... ......|.+|||.|.+..+|..|+|+|+++|||+|.
T Consensus 832 ~~~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~ 911 (958)
T KOG1074|consen 832 QETSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCH 911 (958)
T ss_pred ccccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccch
Confidence 00 0 000000 00000001 112368999999999999999999999999999999
Q ss_pred CCCCcCCCcchhhhhhhhcccccC
Q 040791 240 RLDHMDDSLADEDHDVITHEEFFP 263 (465)
Q Consensus 240 ~C~~~f~~~~~l~~H~~~H~~~~~ 263 (465)
+|++.|....+|+.||.+|.-..+
T Consensus 912 fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 912 FCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhhhhhhhhhhhhhhccccccCC
Confidence 999999999999999999976433
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.81 E-value=2.4e-21 Score=179.96 Aligned_cols=197 Identities=17% Similarity=0.199 Sum_probs=152.5
Q ss_pred ceeccC--cccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCccc
Q 040791 11 FKHYCK--ICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCG 88 (465)
Q Consensus 11 ~~~~C~--~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cg 88 (465)
..+.|. .|-+.|.+++.|++|+|.|+ ++|...|+.|+..|.....|-.|.+ .-+.-..+.|.|..|.
T Consensus 176 pv~~C~W~~Ct~~~~~k~~LreH~r~Hs-~eKvvACp~Cg~~F~~~tkl~DH~r----------Rqt~l~~n~fqC~~C~ 244 (467)
T KOG3608|consen 176 PVTMCNWAMCTKHMGNKYRLREHIRTHS-NEKVVACPHCGELFRTKTKLFDHLR----------RQTELNTNSFQCAQCF 244 (467)
T ss_pred ceeeccchhhhhhhccHHHHHHHHHhcC-CCeEEecchHHHHhccccHHHHHHH----------hhhhhcCCchHHHHHH
Confidence 446776 59999999999999999998 9999999999999997766655544 1111112234999999
Q ss_pred ccccChHHHHHhhhhCCCccCcCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCchhHHHHHHHHhhccCCCCCC
Q 040791 89 KEFLSWKSFLEHGKCSSEDAESLVSSPGSDGEDGTPRRGCGWSKRKRSLRAKVGNCPSSEEEDLANCLMMLSNATVDPLD 168 (465)
Q Consensus 89 k~F~~~~~L~~H~r~H~ge~~~~~~~~~~~~e~~~~c~~c~~~~~~~s~~~~~~~~~~~eee~~a~~l~~l~~~~~~~~~ 168 (465)
|.|.+...|..|++.|.. -|.|+.|...-..++.+..|++
T Consensus 245 KrFaTeklL~~Hv~rHvn---------------~ykCplCdmtc~~~ssL~~H~r------------------------- 284 (467)
T KOG3608|consen 245 KRFATEKLLKSHVVRHVN---------------CYKCPLCDMTCSSASSLTTHIR------------------------- 284 (467)
T ss_pred HHHhHHHHHHHHHHHhhh---------------cccccccccCCCChHHHHHHHH-------------------------
Confidence 999999999999999862 2455555444444444433332
Q ss_pred CCCCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCChhhhhhhhhhcCCCCcccCCC--CCCcCC
Q 040791 169 AEPEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNSHQALGGHRASHKKVKGCFAAR--LDHMDD 246 (465)
Q Consensus 169 ~~~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~--C~~~f~ 246 (465)
-.|...++|+|+.|.+.|.+.+.|.+|..+|. +-.|.|.. |..++.
T Consensus 285 -------------------------------~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r 332 (467)
T KOG3608|consen 285 -------------------------------YRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVR 332 (467)
T ss_pred -------------------------------hhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHH
Confidence 13455789999999999999999999999998 66788887 999999
Q ss_pred CcchhhhhhhhcccccCCCcchhhHhhhcCCCCCCcccccccCCCCceecCccccccCCchhhhhhhh-hcc
Q 040791 247 SLADEDHDVITHEEFFPTKSTSAMQFDHGANNNNAPLASSSKRKSKVHECSICHRVFSSGQALGGHKR-CHW 317 (465)
Q Consensus 247 ~~~~l~~H~~~H~~~~~~~~~s~~l~~H~~~~~~~~~~~~~h~~ekp~~C~~Cgk~F~~~~~L~~H~r-~H~ 317 (465)
...++.+|++.+.+.+ .+-+|.|..|+|.|+++.+|.+|++ .|.
T Consensus 333 ~~~q~~~H~~evhEg~---------------------------np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 333 TYTQMRRHFLEVHEGN---------------------------NPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred HHHHHHHHHHHhccCC---------------------------CCCceeeecchhhhccchhHHHHHHHhhc
Confidence 9999999988654311 1457999999999999999999975 453
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.71 E-value=1.8e-18 Score=160.91 Aligned_cols=209 Identities=18% Similarity=0.203 Sum_probs=163.9
Q ss_pred eccC--cccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCC--ccc
Q 040791 13 HYCK--ICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCE--NCG 88 (465)
Q Consensus 13 ~~C~--~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~--~Cg 88 (465)
|.|. .|+..|.+...|..|...|. .-|++. ..|. ...++|- +.|. .|-
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~-----l~ceyd-~~~~----------~~D~~pv------------~~C~W~~Ct 186 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHA-----LFCEYD-IQKT----------PEDERPV------------TMCNWAMCT 186 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhh-----hhhhhh-hhhC----------CCCCCce------------eeccchhhh
Confidence 5554 69999999999999999984 112111 1111 0223232 2675 599
Q ss_pred ccccChHHHHHhhhhCCCccCcCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCchhHHHHHHHHhhccCCCCCC
Q 040791 89 KEFLSWKSFLEHGKCSSEDAESLVSSPGSDGEDGTPRRGCGWSKRKRSLRAKVGNCPSSEEEDLANCLMMLSNATVDPLD 168 (465)
Q Consensus 89 k~F~~~~~L~~H~r~H~ge~~~~~~~~~~~~e~~~~c~~c~~~~~~~s~~~~~~~~~~~eee~~a~~l~~l~~~~~~~~~ 168 (465)
+.|.++..|.+|.+.|++|+. ..|+.||.-|+.+..+--|.+.. ...
T Consensus 187 ~~~~~k~~LreH~r~Hs~eKv-------------vACp~Cg~~F~~~tkl~DH~rRq--------------------t~l 233 (467)
T KOG3608|consen 187 KHMGNKYRLREHIRTHSNEKV-------------VACPHCGELFRTKTKLFDHLRRQ--------------------TEL 233 (467)
T ss_pred hhhccHHHHHHHHHhcCCCeE-------------EecchHHHHhccccHHHHHHHhh--------------------hhh
Confidence 999999999999999997764 78999999999988877665422 112
Q ss_pred CCCCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCChhhhhhhhhh-cCCCCcccCCCCCCcCCC
Q 040791 169 AEPEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNSHQALGGHRAS-HKKVKGCFAARLDHMDDS 247 (465)
Q Consensus 169 ~~~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~~~~L~~H~~~-H~~~k~~~C~~C~~~f~~ 247 (465)
...+|.|..|.|.|.+...|. .|...|. .-|+|+.|..+-...+.|..|++. |.+.|||+|..|++.+..
T Consensus 234 ~~n~fqC~~C~KrFaTeklL~-------~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~ 304 (467)
T KOG3608|consen 234 NTNSFQCAQCFKRFATEKLLK-------SHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVR 304 (467)
T ss_pred cCCchHHHHHHHHHhHHHHHH-------HHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhcc
Confidence 345799999999998877665 4555553 359999999999999999999875 889999999999999999
Q ss_pred cchhhhhhhhcccccCCCcchhhHhhhcCCCCCCcccccccCCCCceecCc--cccccCCchhhhhhhhhccCCCCC
Q 040791 248 LADEDHDVITHEEFFPTKSTSAMQFDHGANNNNAPLASSSKRKSKVHECSI--CHRVFSSGQALGGHKRCHWITSNS 322 (465)
Q Consensus 248 ~~~l~~H~~~H~~~~~~~~~s~~l~~H~~~~~~~~~~~~~h~~ekp~~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~ 322 (465)
.++|.+|+.+|.+ -.|.|.. |..+|.+...|.+|++-|..+.+.
T Consensus 305 esdL~kH~~~HS~-------------------------------~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np 350 (467)
T KOG3608|consen 305 ESDLAKHVQVHSK-------------------------------TVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNP 350 (467)
T ss_pred HHHHHHHHHhccc-------------------------------cceecCCCCCcHHHHHHHHHHHHHHHhccCCCC
Confidence 9999999998853 5799999 999999999999999987755443
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.65 E-value=2.1e-17 Score=142.75 Aligned_cols=97 Identities=16% Similarity=0.135 Sum_probs=78.9
Q ss_pred CCcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCCcchhhhhhhhcccccCCCcchhhHhhhcCCCCCCccc
Q 040791 205 KGLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDSLADEDHDVITHEEFFPTKSTSAMQFDHGANNNNAPLA 284 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~~~s~~l~~H~~~~~~~~~~ 284 (465)
.+.|.|..|||.|.....|++|+|+|+|++||+|..|+++|.....|..|++.-.+... ....+
T Consensus 143 vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~----~yayk------------ 206 (267)
T KOG3576|consen 143 VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQH----QYAYK------------ 206 (267)
T ss_pred HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchH----HHHHH------------
Confidence 34689999999999999999999999999999999999999999999999764322110 01111
Q ss_pred ccccCCCCceecCccccccCCchhhhhhhhhccCCC
Q 040791 285 SSSKRKSKVHECSICHRVFSSGQALGGHKRCHWITS 320 (465)
Q Consensus 285 ~~~h~~ekp~~C~~Cgk~F~~~~~L~~H~r~H~~~~ 320 (465)
-..+|.|.|+.||.+-.....+..|++.|+..+
T Consensus 207 ---err~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 207 ---ERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred ---HhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 123789999999999999999999999997543
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.52 E-value=1.3e-15 Score=131.72 Aligned_cols=85 Identities=24% Similarity=0.299 Sum_probs=72.9
Q ss_pred cccCCCceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCC-CCCCcceecccCCCCCCCccc
Q 040791 5 VDQQSNFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVP-PTNKRMYALRANPNRLKSCRV 83 (465)
Q Consensus 5 ~~~~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~-~~~~~~~~lr~~~~~~~~~y~ 83 (465)
........|.|.+|+|.|.-..-|.+||+-|. .-+.|.|..||+.|.....|.+|.+ |++.+|| +
T Consensus 110 gsssd~d~ftCrvCgK~F~lQRmlnrh~kch~-~vkr~lct~cgkgfndtfdlkrh~rthtgvrpy-------------k 175 (267)
T KOG3576|consen 110 GSSSDQDSFTCRVCGKKFGLQRMLNRHLKCHS-DVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPY-------------K 175 (267)
T ss_pred cCCCCCCeeeeehhhhhhhHHHHHHHHhhhcc-HHHHHHHhhccCcccchhhhhhhhccccCcccc-------------c
Confidence 34456778999999999999999999999996 6678888888888888888888888 8888888 8
Q ss_pred CCcccccccChHHHHHhhhh
Q 040791 84 CENCGKEFLSWKSFLEHGKC 103 (465)
Q Consensus 84 C~~Cgk~F~~~~~L~~H~r~ 103 (465)
|..|+|.|+.+.+|..|.+.
T Consensus 176 c~~c~kaftqrcsleshl~k 195 (267)
T KOG3576|consen 176 CSLCEKAFTQRCSLESHLKK 195 (267)
T ss_pred hhhhhHHHHhhccHHHHHHH
Confidence 88888888888888888764
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.37 E-value=1.7e-13 Score=138.64 Aligned_cols=53 Identities=17% Similarity=0.248 Sum_probs=50.4
Q ss_pred CCCcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCCcchhhhhhh
Q 040791 204 NKGLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDSLADEDHDVI 256 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~~~~l~~H~~ 256 (465)
|.+||+|.+|.|.|+.+..|..|+|.|.|||||.|.+|+++|+.......||.
T Consensus 919 GqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 919 GQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred CCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 56789999999999999999999999999999999999999999999988886
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.13 E-value=1.1e-10 Score=119.59 Aligned_cols=74 Identities=18% Similarity=0.253 Sum_probs=58.5
Q ss_pred cccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCC----------cchhhhhhhhcccccCCCcchhhHhhhcC
Q 040791 207 LFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDS----------LADEDHDVITHEEFFPTKSTSAMQFDHGA 276 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~----------~~~l~~H~~~H~~~~~~~~~s~~l~~H~~ 276 (465)
+|.|+ ||+.| .+..|..|+++|...+++.|.+|++.+.. ...|..|..++
T Consensus 478 pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C------------------ 537 (567)
T PLN03086 478 PLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC------------------ 537 (567)
T ss_pred CccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc------------------
Confidence 58899 99765 66899999999999999999999998842 23555555544
Q ss_pred CCCCCcccccccCCCCceecCccccccCCchhhhhhhh
Q 040791 277 NNNNAPLASSSKRKSKVHECSICHRVFSSGQALGGHKR 314 (465)
Q Consensus 277 ~~~~~~~~~~~h~~ekp~~C~~Cgk~F~~~~~L~~H~r 314 (465)
|.+++.|..||+.|..+. |..|+-
T Consensus 538 -------------G~rt~~C~~Cgk~Vrlrd-m~~H~~ 561 (567)
T PLN03086 538 -------------GSRTAPCDSCGRSVMLKE-MDIHQI 561 (567)
T ss_pred -------------CCcceEccccCCeeeehh-HHHHHH
Confidence 479999999999998774 667754
No 12
>PHA00733 hypothetical protein
Probab=98.94 E-value=4.9e-10 Score=94.11 Aligned_cols=88 Identities=11% Similarity=0.036 Sum_probs=71.4
Q ss_pred cccccCCCcccccccccccCChhhhhhh--hh---hcCCCCcccCCCCCCcCCCcchhhhhhhhcccccCCCcchhhHhh
Q 040791 199 AKGVANKGLFECKACKKVFNSHQALGGH--RA---SHKKVKGCFAARLDHMDDSLADEDHDVITHEEFFPTKSTSAMQFD 273 (465)
Q Consensus 199 ~~~~~~~k~y~C~~Cgk~F~~~~~L~~H--~~---~H~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~~~s~~l~~ 273 (465)
+......+++.|.+|++.|.....|..| ++ .+.+.++|.|..|++.|.....|..|++.|
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--------------- 96 (128)
T PHA00733 32 HSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--------------- 96 (128)
T ss_pred hcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC---------------
Confidence 3333457789999999999988888776 22 334578999999999999999998888765
Q ss_pred hcCCCCCCcccccccCCCCceecCccccccCCchhhhhhhhhccC
Q 040791 274 HGANNNNAPLASSSKRKSKVHECSICHRVFSSGQALGGHKRCHWI 318 (465)
Q Consensus 274 H~~~~~~~~~~~~~h~~ekp~~C~~Cgk~F~~~~~L~~H~r~H~~ 318 (465)
+++|.|.+|++.|.....|..|++..++
T Consensus 97 -----------------~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 97 -----------------EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred -----------------CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3579999999999999999999987653
No 13
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.82 E-value=1.1e-09 Score=105.19 Aligned_cols=53 Identities=23% Similarity=0.422 Sum_probs=43.5
Q ss_pred eccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCccccccc
Q 040791 13 HYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGKEFL 92 (465)
Q Consensus 13 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk~F~ 92 (465)
|.|..|...|.....|.+|.-.- .-.-.| +|++|+|.|+
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R----------------------------IV~vEY-------------rCPEC~KVFs 306 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR----------------------------IVHVEY-------------RCPECDKVFS 306 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe----------------------------eEEeee-------------cCCccccccc
Confidence 88999999999999998885321 112345 9999999999
Q ss_pred ChHHHHHhhhhCCC
Q 040791 93 SWKSFLEHGKCSSE 106 (465)
Q Consensus 93 ~~~~L~~H~r~H~g 106 (465)
...+|..|+|+|.-
T Consensus 307 CPANLASHRRWHKP 320 (500)
T KOG3993|consen 307 CPANLASHRRWHKP 320 (500)
T ss_pred CchhhhhhhcccCC
Confidence 99999999999973
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.81 E-value=2.1e-09 Score=74.38 Aligned_cols=43 Identities=12% Similarity=0.277 Sum_probs=39.9
Q ss_pred cccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCCcchh
Q 040791 207 LFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDSLADE 251 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~~~~l 251 (465)
-|+|+.|||.|...++|..|+++|+ ++|+|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3899999999999999999999999 799999999999877766
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.66 E-value=5.9e-09 Score=72.18 Aligned_cols=38 Identities=18% Similarity=0.282 Sum_probs=29.6
Q ss_pred eeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCc
Q 040791 12 KHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASD 52 (465)
Q Consensus 12 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~ 52 (465)
-|.|++||+.|....+|..||++|. ++|+|..|++.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~---k~~kc~~C~k~f~ 42 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN---TNLKLSNCKRISL 42 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC---CcccCCcccceec
Confidence 3899999999999999999999994 3444444444444
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.60 E-value=4.8e-08 Score=100.38 Aligned_cols=58 Identities=10% Similarity=0.153 Sum_probs=39.7
Q ss_pred cccccccCCCcccccccccccC----------ChhhhhhhhhhcCCCCcccCCCCCCcCCCcchhhhhhh
Q 040791 197 DKAKGVANKGLFECKACKKVFN----------SHQALGGHRASHKKVKGCFAARLDHMDDSLADEDHDVI 256 (465)
Q Consensus 197 ~~~~~~~~~k~y~C~~Cgk~F~----------~~~~L~~H~~~H~~~k~~~C~~C~~~f~~~~~l~~H~~ 256 (465)
.|...|.+.+++.|..|++.|. ....|..|..++ +.+++.|..|++.+.. .++..|+.
T Consensus 494 ~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl-rdm~~H~~ 561 (567)
T PLN03086 494 QHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML-KEMDIHQI 561 (567)
T ss_pred hhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee-hhHHHHHH
Confidence 3334455677888888888885 235788888875 8888888888876653 34444543
No 17
>PHA00733 hypothetical protein
Probab=98.56 E-value=1.7e-08 Score=84.75 Aligned_cols=83 Identities=17% Similarity=0.066 Sum_probs=68.6
Q ss_pred CCCceeccCcccCcCCCccchhhh------hhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCc
Q 040791 8 QSNFKHYCKICKKGFGCGRALGGH------MRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSC 81 (465)
Q Consensus 8 ~~~~~~~C~~C~k~F~~~~~L~~H------~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~ 81 (465)
+..+++.|.+|++.|.....|..| +..| +++||.|+.|++.|.....|..|.+.. ..+|
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~--~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~------------ 100 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSK--AVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSK------------ 100 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccC--CCCCccCCCCCCcCCCHHHHHHHHhcC-CcCc------------
Confidence 346889999999999988877766 2333 688999999999999999998887621 3456
Q ss_pred ccCCcccccccChHHHHHhhhhCCC
Q 040791 82 RVCENCGKEFLSWKSFLEHGKCSSE 106 (465)
Q Consensus 82 y~C~~Cgk~F~~~~~L~~H~r~H~g 106 (465)
.|.+|++.|.....|..|+...++
T Consensus 101 -~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 101 -VCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred -cCCCCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999999987654
No 18
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.43 E-value=1.3e-07 Score=91.23 Aligned_cols=84 Identities=24% Similarity=0.296 Sum_probs=50.8
Q ss_pred eeccCcccCcCCCccchhhhhhhcccCCcccCCC--cCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCcccc
Q 040791 12 KHYCKICKKGFGCGRALGGHMRAHGIGDESGHID--DDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGK 89 (465)
Q Consensus 12 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~--~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk 89 (465)
-|+|..|+|+|.+..+|..|.|+|......-.-. .-.+. .....+.+ -.-|...+.....|.|..|+|
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~-~~~rae~~---------ea~rsg~dss~gi~~C~~C~K 364 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQA-VETRAEVQ---------EAERSGDDSSSGIFSCHTCGK 364 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhh-hhhhhhhh---------hccccCCcccCceeecHHhhh
Confidence 4999999999999999999999995221111100 00000 00000000 000011112233569999999
Q ss_pred cccChHHHHHhhhhCC
Q 040791 90 EFLSWKSFLEHGKCSS 105 (465)
Q Consensus 90 ~F~~~~~L~~H~r~H~ 105 (465)
.|.....|+.|+-.|.
T Consensus 365 kFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 365 KFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hhHHHHHHHHhHHhhh
Confidence 9999999999998876
No 19
>PHA00732 hypothetical protein
Probab=98.24 E-value=5.7e-07 Score=68.50 Aligned_cols=25 Identities=28% Similarity=0.478 Sum_probs=22.0
Q ss_pred cccccccccccCChhhhhhhhhh-cC
Q 040791 207 LFECKACKKVFNSHQALGGHRAS-HK 231 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~~-H~ 231 (465)
||.|..|++.|.+...|..|++. |.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC
Confidence 58899999999999999999984 54
No 20
>PHA00616 hypothetical protein
Probab=98.21 E-value=4.7e-07 Score=59.68 Aligned_cols=34 Identities=18% Similarity=0.343 Sum_probs=31.8
Q ss_pred cccccccccccCChhhhhhhhhhcCCCCcccCCC
Q 040791 207 LFECKACKKVFNSHQALGGHRASHKKVKGCFAAR 240 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~ 240 (465)
||+|..||+.|..++.|..|++.|++++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6999999999999999999999999999988764
No 21
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.18 E-value=5.7e-07 Score=53.12 Aligned_cols=25 Identities=16% Similarity=0.010 Sum_probs=21.8
Q ss_pred hhhhhhhhcCCCCcccCCCCCCcCC
Q 040791 222 ALGGHRASHKKVKGCFAARLDHMDD 246 (465)
Q Consensus 222 ~L~~H~~~H~~~k~~~C~~C~~~f~ 246 (465)
+|.+|+++|+++|||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 5788999999999999999998875
No 22
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.13 E-value=7.6e-07 Score=52.58 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=17.5
Q ss_pred ccccCCCCceecCccccccCC
Q 040791 285 SSSKRKSKVHECSICHRVFSS 305 (465)
Q Consensus 285 ~~~h~~ekp~~C~~Cgk~F~~ 305 (465)
+++|+++|||+|++|++.|.+
T Consensus 6 ~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 6 MRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHSSSSSEEESSSSEEESS
T ss_pred hhhcCCCCCCCCCCCcCeeCc
Confidence 445577999999999999974
No 23
>PHA00732 hypothetical protein
Probab=97.95 E-value=4e-06 Score=63.90 Aligned_cols=24 Identities=33% Similarity=0.326 Sum_probs=22.1
Q ss_pred eeccCcccCcCCCccchhhhhhh-c
Q 040791 12 KHYCKICKKGFGCGRALGGHMRA-H 35 (465)
Q Consensus 12 ~~~C~~C~k~F~~~~~L~~H~r~-H 35 (465)
+|.|.+|++.|.....|+.|++. |
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H 25 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH 25 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc
Confidence 58999999999999999999985 5
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.92 E-value=3.5e-06 Score=48.23 Aligned_cols=23 Identities=43% Similarity=0.752 Sum_probs=22.0
Q ss_pred eecCccccccCCchhhhhhhhhc
Q 040791 294 HECSICHRVFSSGQALGGHKRCH 316 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~H 316 (465)
|+|++|++.|.+...|..|++.|
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 78999999999999999999986
No 25
>PHA00616 hypothetical protein
Probab=97.86 E-value=2.5e-06 Score=56.23 Aligned_cols=33 Identities=12% Similarity=0.140 Sum_probs=29.8
Q ss_pred eeccCcccCcCCCccchhhhhhhcccCCcccCCC
Q 040791 12 KHYCKICKKGFGCGRALGGHMRAHGIGDESGHID 45 (465)
Q Consensus 12 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~ 45 (465)
+|+|..||+.|..++.|..|++.|+ +++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h-g~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH-KQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc-CCCcccee
Confidence 5899999999999999999999997 77777776
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.78 E-value=8.8e-06 Score=46.55 Aligned_cols=23 Identities=35% Similarity=0.739 Sum_probs=21.6
Q ss_pred ccccccccccCChhhhhhhhhhc
Q 040791 208 FECKACKKVFNSHQALGGHRASH 230 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~H 230 (465)
|+|++|++.|.+...|..|++.|
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 78999999999999999999875
No 27
>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=97.67 E-value=1.8e-05 Score=47.16 Aligned_cols=26 Identities=46% Similarity=0.677 Sum_probs=24.3
Q ss_pred ceecCccccccCCchhhhhhhhhccC
Q 040791 293 VHECSICHRVFSSGQALGGHKRCHWI 318 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~~L~~H~r~H~~ 318 (465)
||+|.+|++.|.+..+|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 69999999999999999999999964
No 28
>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=97.63 E-value=4.1e-05 Score=54.07 Aligned_cols=24 Identities=25% Similarity=0.383 Sum_probs=18.8
Q ss_pred CceecCccccccCCchhhhhhhhhcc
Q 040791 292 KVHECSICHRVFSSGQALGGHKRCHW 317 (465)
Q Consensus 292 kp~~C~~Cgk~F~~~~~L~~H~r~H~ 317 (465)
+.+.|++|...+. .+|..|++.++
T Consensus 30 ~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 30 KNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCccCCCchhhhh--hHHHHHHHHhc
Confidence 5688999988655 48889988765
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=97.49 E-value=4.3e-05 Score=43.89 Aligned_cols=24 Identities=38% Similarity=0.742 Sum_probs=20.5
Q ss_pred eecCccccccCCchhhhhhhhhcc
Q 040791 294 HECSICHRVFSSGQALGGHKRCHW 317 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~H~ 317 (465)
|.|++|++.|.+...|..|+++|+
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 789999999999999999999874
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.46 E-value=5.9e-05 Score=44.94 Aligned_cols=26 Identities=46% Similarity=0.775 Sum_probs=24.0
Q ss_pred cccccccccccCChhhhhhhhhhcCC
Q 040791 207 LFECKACKKVFNSHQALGGHRASHKK 232 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~~H~~ 232 (465)
+|+|..|++.|.+..+|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 58999999999999999999998864
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.37 E-value=8e-05 Score=59.71 Aligned_cols=26 Identities=31% Similarity=0.649 Sum_probs=22.6
Q ss_pred CceecCccccccCCchhhhhhhhhcc
Q 040791 292 KVHECSICHRVFSSGQALGGHKRCHW 317 (465)
Q Consensus 292 kp~~C~~Cgk~F~~~~~L~~H~r~H~ 317 (465)
..+.|.+|++.|.+...|..||+.+.
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 36999999999999999999999753
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.30 E-value=0.00015 Score=67.94 Aligned_cols=71 Identities=23% Similarity=0.444 Sum_probs=48.8
Q ss_pred CCCcccccc--cccccCChhhhhhhhh-hcCCCCcccCCCCCCcCCCcchhhhhhhhcccccCCCcchhhHhhhcCCCCC
Q 040791 204 NKGLFECKA--CKKVFNSHQALGGHRA-SHKKVKGCFAARLDHMDDSLADEDHDVITHEEFFPTKSTSAMQFDHGANNNN 280 (465)
Q Consensus 204 ~~k~y~C~~--Cgk~F~~~~~L~~H~~-~H~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~~~s~~l~~H~~~~~~ 280 (465)
++|||+|++ |.|+|++...|+-|+. -|...+. |....|-
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~----------------------~~~p~p~---------------- 387 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKL----------------------HENPSPE---------------- 387 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCccc----------------------CCCCCcc----------------
Confidence 359999987 9999999999999974 2433221 1000000
Q ss_pred CcccccccCCCCceecCccccccCCchhhhhhhh
Q 040791 281 APLASSSKRKSKVHECSICHRVFSSGQALGGHKR 314 (465)
Q Consensus 281 ~~~~~~~h~~ekp~~C~~Cgk~F~~~~~L~~H~r 314 (465)
.+...-.+.|||.|++|+|.|+....|+.|..
T Consensus 388 --~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 388 --KMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred --ccccccccCCceeccccchhhccCccceeccc
Confidence 01111234799999999999999999999864
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.27 E-value=0.00012 Score=42.02 Aligned_cols=24 Identities=38% Similarity=0.771 Sum_probs=20.0
Q ss_pred ccccccccccCChhhhhhhhhhcC
Q 040791 208 FECKACKKVFNSHQALGGHRASHK 231 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~H~ 231 (465)
|.|++|++.|.+...|..|+++|.
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 789999999999999999998763
No 34
>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=97.18 E-value=0.00027 Score=49.87 Aligned_cols=51 Identities=22% Similarity=0.441 Sum_probs=37.9
Q ss_pred eeccCcccCcCCCccchhhhhhh-cccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCccccc
Q 040791 12 KHYCKICKKGFGCGRALGGHMRA-HGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGKE 90 (465)
Q Consensus 12 ~~~C~~C~k~F~~~~~L~~H~r~-H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk~ 90 (465)
.|.|++|++. .+...|..|... |. ...+.+ .|++|...
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~---------------------------~~~~~v-------------~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHR---------------------------SESKNV-------------VCPICSSR 40 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCc---------------------------CCCCCc-------------cCCCchhh
Confidence 5899999995 556789999765 42 223345 89999987
Q ss_pred ccChHHHHHhhhhCC
Q 040791 91 FLSWKSFLEHGKCSS 105 (465)
Q Consensus 91 F~~~~~L~~H~r~H~ 105 (465)
+. .+|..|+..++
T Consensus 41 ~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 41 VT--DNLIRHLNSQH 53 (54)
T ss_pred hh--hHHHHHHHHhc
Confidence 65 49999998754
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.14 E-value=0.00023 Score=57.01 Aligned_cols=73 Identities=23% Similarity=0.330 Sum_probs=20.8
Q ss_pred ccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCcccccccC
Q 040791 14 YCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGKEFLS 93 (465)
Q Consensus 14 ~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk~F~~ 93 (465)
+|.+|+..|.+...|..||...+.-..+ ....+.....+...........+ .|..|++.|.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~~~~~-------------~C~~C~~~f~s 62 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKVKESF-------------RCPYCNKTFRS 62 (100)
T ss_dssp -----------------------------------------------------SSE-------------EBSSSS-EESS
T ss_pred Cccccccccccccccccccccccccccc-----cccccccccccccccccccCCCC-------------CCCccCCCCcC
Confidence 5999999999999999999754311111 00000011111111111111133 89999999999
Q ss_pred hHHHHHhhhhC
Q 040791 94 WKSFLEHGKCS 104 (465)
Q Consensus 94 ~~~L~~H~r~H 104 (465)
...|..||+.+
T Consensus 63 ~~~l~~Hm~~~ 73 (100)
T PF12756_consen 63 REALQEHMRSK 73 (100)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHcCc
Confidence 99999999965
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.95 E-value=0.00037 Score=40.60 Aligned_cols=25 Identities=40% Similarity=0.639 Sum_probs=22.9
Q ss_pred eecCccccccCCchhhhhhhhhccC
Q 040791 294 HECSICHRVFSSGQALGGHKRCHWI 318 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~H~~ 318 (465)
|+|.+|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998853
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.93 E-value=0.00047 Score=64.64 Aligned_cols=68 Identities=21% Similarity=0.366 Sum_probs=47.5
Q ss_pred CceeccCc--ccCcCCCccchhhhhhh-cccCCcccC--CCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccC
Q 040791 10 NFKHYCKI--CKKGFGCGRALGGHMRA-HGIGDESGH--IDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVC 84 (465)
Q Consensus 10 ~~~~~C~~--C~k~F~~~~~L~~H~r~-H~~~~~~~~--C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C 84 (465)
+|+|+|++ |.|.|.+...|+-||.- |. ..+... -++-...|. ...+|| .|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~-~~~~~~~p~p~~~~~F~-----------~~~KPY-------------rC 401 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQ-NQKLHENPSPEKMNIFS-----------AKDKPY-------------RC 401 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhcccc-CcccCCCCCcccccccc-----------ccCCce-------------ec
Confidence 59999998 99999999999999763 31 111111 111111221 445777 99
Q ss_pred CcccccccChHHHHHhhh
Q 040791 85 ENCGKEFLSWKSFLEHGK 102 (465)
Q Consensus 85 ~~Cgk~F~~~~~L~~H~r 102 (465)
++|+|.|+....|+.|+.
T Consensus 402 evC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 402 EVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cccchhhccCccceeccc
Confidence 999999999999999975
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.70 E-value=0.0009 Score=38.86 Aligned_cols=25 Identities=40% Similarity=0.780 Sum_probs=22.4
Q ss_pred ccccccccccCChhhhhhhhhhcCC
Q 040791 208 FECKACKKVFNSHQALGGHRASHKK 232 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~H~~ 232 (465)
|+|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998753
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.66 E-value=0.0011 Score=44.78 Aligned_cols=30 Identities=20% Similarity=0.423 Sum_probs=21.7
Q ss_pred CCCCceecCccccccCCchhhhhhhhhccC
Q 040791 289 RKSKVHECSICHRVFSSGQALGGHKRCHWI 318 (465)
Q Consensus 289 ~~ekp~~C~~Cgk~F~~~~~L~~H~r~H~~ 318 (465)
..+.|..|++|+..+.+..+|++|+.++++
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 447899999999999999999999977654
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.50 E-value=0.0011 Score=38.55 Aligned_cols=23 Identities=39% Similarity=0.743 Sum_probs=21.6
Q ss_pred eecCccccccCCchhhhhhhhhc
Q 040791 294 HECSICHRVFSSGQALGGHKRCH 316 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~H 316 (465)
|.|.+|++.|.+...|..|++.+
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 68999999999999999999876
No 41
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.48 E-value=0.0028 Score=66.63 Aligned_cols=23 Identities=26% Similarity=0.394 Sum_probs=13.6
Q ss_pred cccccccccCChhhhhhhhhhcC
Q 040791 209 ECKACKKVFNSHQALGGHRASHK 231 (465)
Q Consensus 209 ~C~~Cgk~F~~~~~L~~H~~~H~ 231 (465)
.|+.|...|-....|.+|++.++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce
Confidence 46666666666666666655443
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.30 E-value=0.0018 Score=37.63 Aligned_cols=23 Identities=39% Similarity=0.729 Sum_probs=21.3
Q ss_pred ccccccccccCChhhhhhhhhhc
Q 040791 208 FECKACKKVFNSHQALGGHRASH 230 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~H 230 (465)
|.|.+|++.|.+...|..|++++
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 68999999999999999999875
No 43
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.05 E-value=0.0065 Score=62.02 Aligned_cols=58 Identities=22% Similarity=0.398 Sum_probs=45.1
Q ss_pred ceeccCcccCcCCCccchhhhhh--hcccCCcccCCCcCcccCcCcccCCCCCCCCCC--cceecccCCCCCCCcccCC-
Q 040791 11 FKHYCKICKKGFGCGRALGGHMR--AHGIGDESGHIDDDDQASDWEDKLGGNVPPTNK--RMYALRANPNRLKSCRVCE- 85 (465)
Q Consensus 11 ~~~~C~~C~k~F~~~~~L~~H~r--~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~--~~~~lr~~~~~~~~~y~C~- 85 (465)
.++.|..|...|.....|..|.+ .| +++ +++ .|+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h----------------------------~~~~~~~~-------------~~p~ 326 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNH----------------------------SGESLKPF-------------SCPY 326 (467)
T ss_pred cCCCCccccCCcccccccccccccccc----------------------------ccccCCce-------------eeec
Confidence 46888888888888888888888 67 455 666 777
Q ss_pred -cccccccChHHHHHhhhhCCCccC
Q 040791 86 -NCGKEFLSWKSFLEHGKCSSEDAE 109 (465)
Q Consensus 86 -~Cgk~F~~~~~L~~H~r~H~ge~~ 109 (465)
.|++.|.+...|..|...|.+...
T Consensus 327 ~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 327 SLCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred cCCCccccccccccCCcccccCCCc
Confidence 688888888888888888876543
No 44
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.04 E-value=0.0031 Score=37.43 Aligned_cols=23 Identities=30% Similarity=0.622 Sum_probs=21.4
Q ss_pred eecCccccccCCchhhhhhhhhc
Q 040791 294 HECSICHRVFSSGQALGGHKRCH 316 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~H 316 (465)
|.|.+|++.|.+...|..|++++
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 78999999999999999999864
No 45
>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=95.94 E-value=0.0064 Score=41.15 Aligned_cols=33 Identities=18% Similarity=0.244 Sum_probs=23.9
Q ss_pred cCCCcccccccccccCChhhhhhhhhhcCCCCc
Q 040791 203 ANKGLFECKACKKVFNSHQALGGHRASHKKVKG 235 (465)
Q Consensus 203 ~~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~ 235 (465)
..+.|-.|++|+..+.+..+|++|+.++++.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 457789999999999999999999988877665
No 46
>PRK04860 hypothetical protein; Provisional
Probab=95.71 E-value=0.0046 Score=53.95 Aligned_cols=40 Identities=13% Similarity=0.114 Sum_probs=35.3
Q ss_pred CcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCCcc
Q 040791 206 GLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDSLA 249 (465)
Q Consensus 206 k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~~~ 249 (465)
-+|.|. |++ ....+.+|.++|+++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 479998 998 7788999999999999999999999886543
No 47
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.71 E-value=0.0045 Score=35.52 Aligned_cols=23 Identities=26% Similarity=0.400 Sum_probs=19.2
Q ss_pred eecCccccccCCchhhhhhhhhcc
Q 040791 294 HECSICHRVFSSGQALGGHKRCHW 317 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~H~ 317 (465)
|+|+.|+.... ...|..|++.|+
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 889999999875
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=95.69 E-value=0.0049 Score=36.52 Aligned_cols=23 Identities=43% Similarity=0.759 Sum_probs=21.0
Q ss_pred ccccccccccCChhhhhhhhhhc
Q 040791 208 FECKACKKVFNSHQALGGHRASH 230 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~H 230 (465)
|.|.+|++.|.+...|..|++++
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 78999999999999999999763
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.53 E-value=0.011 Score=33.79 Aligned_cols=23 Identities=17% Similarity=0.211 Sum_probs=18.3
Q ss_pred ccCCcccccccChHHHHHhhhhCC
Q 040791 82 RVCENCGKEFLSWKSFLEHGKCSS 105 (465)
Q Consensus 82 y~C~~Cgk~F~~~~~L~~H~r~H~ 105 (465)
|+|+.|+.... ...|.+|++.|+
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 48999999988 899999999764
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=94.35 E-value=0.025 Score=63.11 Aligned_cols=24 Identities=13% Similarity=0.135 Sum_probs=21.4
Q ss_pred CcccCCcccccccChHHHHHhhhh
Q 040791 80 SCRVCENCGKEFLSWKSFLEHGKC 103 (465)
Q Consensus 80 ~~y~C~~Cgk~F~~~~~L~~H~r~ 103 (465)
..|.|..|...|+.+.+|.+|++.
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHH
Confidence 445999999999999999999984
No 51
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=94.01 E-value=0.018 Score=52.09 Aligned_cols=29 Identities=38% Similarity=0.619 Sum_probs=22.7
Q ss_pred CCceecCccccccCCchhhhhh-hhhccCC
Q 040791 291 SKVHECSICHRVFSSGQALGGH-KRCHWIT 319 (465)
Q Consensus 291 ekp~~C~~Cgk~F~~~~~L~~H-~r~H~~~ 319 (465)
.|-|+|.||.|..-++-.|..| |++|..+
T Consensus 32 akhfkchichkkl~sgpglsihcmqvhket 61 (341)
T KOG2893|consen 32 AKHFKCHICHKKLFSGPGLSIHCMQVHKET 61 (341)
T ss_pred hccceeeeehhhhccCCCceeehhhhhhhh
Confidence 3558999999888888888888 7777644
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.87 E-value=0.027 Score=32.66 Aligned_cols=21 Identities=33% Similarity=0.699 Sum_probs=18.0
Q ss_pred eecCccccccCCchhhhhhhhh
Q 040791 294 HECSICHRVFSSGQALGGHKRC 315 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~ 315 (465)
.+|++||+.| ....|.+|+++
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 53
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.31 E-value=0.082 Score=55.91 Aligned_cols=46 Identities=9% Similarity=-0.073 Sum_probs=26.4
Q ss_pred ccccccCChhhhhhhhhhc-CCCC---c-ccCCCCCCcCCCcchhhhhhhhc
Q 040791 212 ACKKVFNSHQALGGHRASH-KKVK---G-CFAARLDHMDDSLADEDHDVITH 258 (465)
Q Consensus 212 ~Cgk~F~~~~~L~~H~~~H-~~~k---~-~~C~~C~~~f~~~~~l~~H~~~H 258 (465)
.|.|.|+.. .|..|+..- .+++ + -.|..|...|-....|.+|++.+
T Consensus 155 ~e~k~Yt~~-el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~ 205 (669)
T KOG2231|consen 155 NERKLYTRA-ELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFD 205 (669)
T ss_pred eeeehehHH-HHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccc
Confidence 345555543 455554431 1122 2 25778888888888888887753
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.55 E-value=0.079 Score=53.98 Aligned_cols=57 Identities=14% Similarity=0.138 Sum_probs=47.4
Q ss_pred CcccccccccccCChhhhhhhhh--hcCCC--CcccCC--CCCCcCCCcchhhhhhhhccccc
Q 040791 206 GLFECKACKKVFNSHQALGGHRA--SHKKV--KGCFAA--RLDHMDDSLADEDHDVITHEEFF 262 (465)
Q Consensus 206 k~y~C~~Cgk~F~~~~~L~~H~~--~H~~~--k~~~C~--~C~~~f~~~~~l~~H~~~H~~~~ 262 (465)
.++.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.....+..|..+|....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCC
Confidence 36888888888888888888888 78888 888888 78888888888888888887644
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.43 E-value=0.079 Score=30.72 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=17.9
Q ss_pred ccccccccccCChhhhhhhhhh
Q 040791 208 FECKACKKVFNSHQALGGHRAS 229 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~ 229 (465)
..|+.||+.| ....|..|+++
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 77889999764
No 56
>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=92.33 E-value=0.077 Score=33.33 Aligned_cols=23 Identities=26% Similarity=0.535 Sum_probs=20.7
Q ss_pred cccccccccccCChhhhhhhhhh
Q 040791 207 LFECKACKKVFNSHQALGGHRAS 229 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~~ 229 (465)
+|.|++|++.|.+..+|..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999854
No 57
>PRK04860 hypothetical protein; Provisional
Probab=91.85 E-value=0.092 Score=45.86 Aligned_cols=41 Identities=10% Similarity=0.011 Sum_probs=30.0
Q ss_pred CcccCCCCCCcCCCcchhhhhhhhcccccCCCcchhhHhhhcCCCCCCcccccccCCCCceecCccccccCCchh
Q 040791 234 KGCFAARLDHMDDSLADEDHDVITHEEFFPTKSTSAMQFDHGANNNNAPLASSSKRKSKVHECSICHRVFSSGQA 308 (465)
Q Consensus 234 k~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~~~s~~l~~H~~~~~~~~~~~~~h~~ekp~~C~~Cgk~F~~~~~ 308 (465)
-+|.|. |+. ....+..|.++| +++++|.|..|+..|.....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~------------------------------~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVV------------------------------RGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHh------------------------------cCCccEECCCCCceeEEecc
Confidence 379997 887 445555555555 56899999999999976543
No 58
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=91.49 E-value=0.11 Score=32.62 Aligned_cols=23 Identities=17% Similarity=0.472 Sum_probs=21.0
Q ss_pred ceecCccccccCCchhhhhhhhh
Q 040791 293 VHECSICHRVFSSGQALGGHKRC 315 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~~L~~H~r~ 315 (465)
+|.|.+|++.|....++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58999999999999999999864
No 59
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.02 E-value=0.17 Score=56.89 Aligned_cols=28 Identities=29% Similarity=0.415 Sum_probs=23.8
Q ss_pred CCceecCccccccCCchhhhhhhhhccCC
Q 040791 291 SKVHECSICHRVFSSGQALGGHKRCHWIT 319 (465)
Q Consensus 291 ekp~~C~~Cgk~F~~~~~L~~H~r~H~~~ 319 (465)
-++| |.+|...|....+|..|||+-...
T Consensus 1327 ~~~~-c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1327 CTYH-CLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred cccc-chHHHhhcchhHHHHHHHHHhhhc
Confidence 4667 999999999999999999974333
No 60
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=89.95 E-value=0.13 Score=46.76 Aligned_cols=25 Identities=36% Similarity=0.620 Sum_probs=18.9
Q ss_pred ccccccccccCChhhhhhh-hhhcCC
Q 040791 208 FECKACKKVFNSHQALGGH-RASHKK 232 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H-~~~H~~ 232 (465)
|+|.+|-|...+--.|..| +.+|+.
T Consensus 35 fkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 35 FKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred ceeeeehhhhccCCCceeehhhhhhh
Confidence 8888888887777778777 566653
No 61
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.45 E-value=0.23 Score=47.61 Aligned_cols=74 Identities=20% Similarity=0.198 Sum_probs=49.9
Q ss_pred ccccccccccCChhhhhhhhhhcCCCCcccCCCCCCc-------CCCcchhhhhhhhcccccCCCcchhhHhhhcCCCCC
Q 040791 208 FECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHM-------DDSLADEDHDVITHEEFFPTKSTSAMQFDHGANNNN 280 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~-------f~~~~~l~~H~~~H~~~~~~~~~s~~l~~H~~~~~~ 280 (465)
=.|..|.+.|-.-..|..|+|.-+. .|-.|++. |+...+|..|.+.
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~----------------------- 273 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRN----------------------- 273 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhc-----------------------
Confidence 3699999999999999999876443 46666653 4444455555431
Q ss_pred CcccccccCCCCceecCc--c----ccccCCchhhhhhhhhccCC
Q 040791 281 APLASSSKRKSKVHECSI--C----HRVFSSGQALGGHKRCHWIT 319 (465)
Q Consensus 281 ~~~~~~~h~~ekp~~C~~--C----gk~F~~~~~L~~H~r~H~~~ 319 (465)
--|.|.+ | -.+|.....|..|+-.-++.
T Consensus 274 -----------~hy~ct~qtc~~~k~~vf~~~~el~~h~~~~h~~ 307 (493)
T COG5236 274 -----------AHYCCTFQTCRVGKCYVFPYHTELLEHLTRFHKV 307 (493)
T ss_pred -----------CceEEEEEEEecCcEEEeccHHHHHHHHHHHhhc
Confidence 2266654 4 26899999999997543333
No 62
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=87.14 E-value=0.48 Score=46.36 Aligned_cols=65 Identities=22% Similarity=0.232 Sum_probs=46.0
Q ss_pred cccCCCCCCcCCCcchhhhhhhhcccccCCCc--------chhhHhhhcCCCCCCcccccccCCCCceecCccc---ccc
Q 040791 235 GCFAARLDHMDDSLADEDHDVITHEEFFPTKS--------TSAMQFDHGANNNNAPLASSSKRKSKVHECSICH---RVF 303 (465)
Q Consensus 235 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~~--------~s~~l~~H~~~~~~~~~~~~~h~~ekp~~C~~Cg---k~F 303 (465)
|-.|-+|++.+...-....||..+++++..-. +...|..- -..-|.|-.|. +.|
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeK---------------V~~~~~CL~CN~~~~~f 230 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEK---------------VGIGFICLFCNELGRPF 230 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHH---------------hccCceEEEeccccCcc
Confidence 46788888888888888888888777653211 11222111 03568999998 999
Q ss_pred CCchhhhhhhh
Q 040791 304 SSGQALGGHKR 314 (465)
Q Consensus 304 ~~~~~L~~H~r 314 (465)
.+-.+.+.||+
T Consensus 231 ~sleavr~HM~ 241 (390)
T KOG2785|consen 231 SSLEAVRAHMR 241 (390)
T ss_pred cccHHHHHHHh
Confidence 99999999995
No 63
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.93 E-value=0.44 Score=43.98 Aligned_cols=25 Identities=28% Similarity=0.595 Sum_probs=19.1
Q ss_pred CceeccCcccCcCCCccchhhhhhh
Q 040791 10 NFKHYCKICKKGFGCGRALGGHMRA 34 (465)
Q Consensus 10 ~~~~~C~~C~k~F~~~~~L~~H~r~ 34 (465)
.+...|++|++.|..+.-+....|.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 4678899999999888766666554
No 64
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.86 E-value=1.7 Score=35.23 Aligned_cols=27 Identities=26% Similarity=0.439 Sum_probs=22.8
Q ss_pred CCceecCccccccCCchhhhhhhhhcc
Q 040791 291 SKVHECSICHRVFSSGQALGGHKRCHW 317 (465)
Q Consensus 291 ekp~~C~~Cgk~F~~~~~L~~H~r~H~ 317 (465)
...|+|+.|...|--.-+.-.|...|.
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhccC
Confidence 347999999999998888888888875
No 65
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=84.73 E-value=0.76 Score=45.02 Aligned_cols=51 Identities=16% Similarity=0.034 Sum_probs=41.5
Q ss_pred CcccccccccccCChhhhhhhhhhcCCCC-----------------------cccCCCCC---CcCCCcchhhhhhh
Q 040791 206 GLFECKACKKVFNSHQALGGHRASHKKVK-----------------------GCFAARLD---HMDDSLADEDHDVI 256 (465)
Q Consensus 206 k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k-----------------------~~~C~~C~---~~f~~~~~l~~H~~ 256 (465)
-|-.|-.|++.|.+-..-..||..|++-. .+.|-.|. +.|.+......||.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 35789999999999999999998877532 46788888 88888888878876
No 66
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.76 E-value=2.2 Score=41.11 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=13.9
Q ss_pred cCCcccccccChHHHHHhhhh
Q 040791 83 VCENCGKEFLSWKSFLEHGKC 103 (465)
Q Consensus 83 ~C~~Cgk~F~~~~~L~~H~r~ 103 (465)
.|..|.+.|-.-..|.+|+|.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhhhccceecChHHHHHHHHh
Confidence 566666666666666666664
No 67
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=82.22 E-value=0.56 Score=32.40 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=23.8
Q ss_pred cCCCcccccccccccCChhhhhhhhh
Q 040791 203 ANKGLFECKACKKVFNSHQALGGHRA 228 (465)
Q Consensus 203 ~~~k~y~C~~Cgk~F~~~~~L~~H~~ 228 (465)
.|+-.+.|+-||..|.....+.+|..
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhh
Confidence 57888999999999999999999984
No 68
>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=78.01 E-value=1.3 Score=29.44 Aligned_cols=26 Identities=27% Similarity=0.517 Sum_probs=17.3
Q ss_pred CCceecCccccccCCc----hhhhhhh-hhc
Q 040791 291 SKVHECSICHRVFSSG----QALGGHK-RCH 316 (465)
Q Consensus 291 ekp~~C~~Cgk~F~~~----~~L~~H~-r~H 316 (465)
....+|.+|++.|... ..|.+|+ +.|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 5678999999999986 6899998 444
No 69
>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=76.54 E-value=1.4 Score=27.31 Aligned_cols=7 Identities=57% Similarity=1.421 Sum_probs=4.4
Q ss_pred cCCcccc
Q 040791 83 VCENCGK 89 (465)
Q Consensus 83 ~C~~Cgk 89 (465)
.|++||.
T Consensus 19 ~CP~Cg~ 25 (33)
T cd00350 19 VCPVCGA 25 (33)
T ss_pred cCcCCCC
Confidence 6666654
No 70
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=76.38 E-value=1.7 Score=41.88 Aligned_cols=26 Identities=27% Similarity=0.681 Sum_probs=22.6
Q ss_pred cccccccccccCChhhhhhhhh--hcCC
Q 040791 207 LFECKACKKVFNSHQALGGHRA--SHKK 232 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~--~H~~ 232 (465)
.++|-.|.|.|+.+..|+.||| .|.+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcc
Confidence 5899999999999999999996 3543
No 71
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.71 E-value=16 Score=29.79 Aligned_cols=27 Identities=26% Similarity=0.416 Sum_probs=22.0
Q ss_pred CCcccccccccccCChhhhhhhhhhcC
Q 040791 205 KGLFECKACKKVFNSHQALGGHRASHK 231 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H~~~H~ 231 (465)
...|+|+.|...|--.-+.-.|...|.
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhccC
Confidence 457999999999988888888877765
No 72
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=74.25 E-value=2.3 Score=24.89 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=8.6
Q ss_pred cCCccccccc
Q 040791 83 VCENCGKEFL 92 (465)
Q Consensus 83 ~C~~Cgk~F~ 92 (465)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 6999999885
No 73
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=74.10 E-value=1.6 Score=29.96 Aligned_cols=25 Identities=28% Similarity=0.448 Sum_probs=20.6
Q ss_pred ceecCccccccCCc-----hhhhhhhh-hcc
Q 040791 293 VHECSICHRVFSSG-----QALGGHKR-CHW 317 (465)
Q Consensus 293 p~~C~~Cgk~F~~~-----~~L~~H~r-~H~ 317 (465)
.-.|..|++.++.. ++|.+|++ +|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 46899999999876 58999998 663
No 74
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=73.87 E-value=2.7 Score=40.57 Aligned_cols=51 Identities=16% Similarity=0.091 Sum_probs=38.7
Q ss_pred ccccccccccCChhhhhhhhhh-cC--------------------------CCCcccCCCCCCcCCCcchhhhhhhhc
Q 040791 208 FECKACKKVFNSHQALGGHRAS-HK--------------------------KVKGCFAARLDHMDDSLADEDHDVITH 258 (465)
Q Consensus 208 y~C~~Cgk~F~~~~~L~~H~~~-H~--------------------------~~k~~~C~~C~~~f~~~~~l~~H~~~H 258 (465)
.+|-.|....-+...|..||.+ |. ..+...|..|+-.|.....|..||..+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 5899999988889999999864 32 112466888888888888888887644
No 75
>PRK04023 DNA polymerase II large subunit; Validated
Probab=73.73 E-value=3.8 Score=45.49 Aligned_cols=16 Identities=25% Similarity=0.420 Sum_probs=11.2
Q ss_pred CceecCccccccCCch
Q 040791 292 KVHECSICHRVFSSGQ 307 (465)
Q Consensus 292 kp~~C~~Cgk~F~~~~ 307 (465)
.++.|+.||..-...+
T Consensus 662 ~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 662 EEDECEKCGREPTPYS 677 (1121)
T ss_pred CCCcCCCCCCCCCccc
Confidence 4578999987665544
No 76
>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=72.84 E-value=2.2 Score=34.55 Aligned_cols=12 Identities=50% Similarity=1.049 Sum_probs=9.5
Q ss_pred cCCcccccccCh
Q 040791 83 VCENCGKEFLSW 94 (465)
Q Consensus 83 ~C~~Cgk~F~~~ 94 (465)
.|+.||..|.-.
T Consensus 28 vCP~CG~~~~~~ 39 (108)
T PF09538_consen 28 VCPKCGTEFPPE 39 (108)
T ss_pred cCCCCCCccCcc
Confidence 788888888755
No 77
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=72.73 E-value=1.3 Score=30.60 Aligned_cols=32 Identities=19% Similarity=0.327 Sum_probs=26.6
Q ss_pred cccCCCCceecCccccccCCchhhhhhhh-hcc
Q 040791 286 SSKRKSKVHECSICHRVFSSGQALGGHKR-CHW 317 (465)
Q Consensus 286 ~~h~~ekp~~C~~Cgk~F~~~~~L~~H~r-~H~ 317 (465)
....||--+.|+-||..|.....+.+|.. .|.
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 44567888999999999999999999975 453
No 78
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=71.91 E-value=2.1 Score=39.66 Aligned_cols=22 Identities=41% Similarity=0.892 Sum_probs=18.8
Q ss_pred cCCcccccccChHHHHHhhhhCC
Q 040791 83 VCENCGKEFLSWKSFLEHGKCSS 105 (465)
Q Consensus 83 ~C~~Cgk~F~~~~~L~~H~r~H~ 105 (465)
.|..|++.|.. ..+..|.++-+
T Consensus 31 SCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 31 SCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred EEeeccccccc-chhhhhhhhcc
Confidence 89999999987 77888888766
No 79
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=71.46 E-value=2.8 Score=34.04 Aligned_cols=33 Identities=15% Similarity=0.020 Sum_probs=26.7
Q ss_pred CceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCc
Q 040791 10 NFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWE 54 (465)
Q Consensus 10 ~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~ 54 (465)
..+..|..||+.|..- +..|..|+.||..|.-.
T Consensus 7 GtKR~Cp~CG~kFYDL------------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDL------------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccC------------CCCCccCCCCCCccCcc
Confidence 4567999999999753 44688999999998855
No 80
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.28 E-value=1.5 Score=40.51 Aligned_cols=42 Identities=17% Similarity=0.222 Sum_probs=30.2
Q ss_pred CCcccccccccccCChhhhhhhhhhc----------CCCCc-----ccCCCCCCcCC
Q 040791 205 KGLFECKACKKVFNSHQALGGHRASH----------KKVKG-----CFAARLDHMDD 246 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H~~~H----------~~~k~-----~~C~~C~~~f~ 246 (465)
++.+.|++|++.|....-+.+..++- .+..| ..|+.|+.++.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF 59 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc
Confidence 45688999999999887777776541 23333 36999999865
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=69.94 E-value=2.9 Score=27.72 Aligned_cols=24 Identities=33% Similarity=0.499 Sum_probs=16.3
Q ss_pred CCCcccccccccccCCh----hhhhhhh
Q 040791 204 NKGLFECKACKKVFNSH----QALGGHR 227 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~----~~L~~H~ 227 (465)
+....+|..|++.|... ..|.+|+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 45678999999999875 7899998
No 82
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=69.21 E-value=2.7 Score=26.28 Aligned_cols=7 Identities=43% Similarity=1.151 Sum_probs=4.0
Q ss_pred cCCcccc
Q 040791 83 VCENCGK 89 (465)
Q Consensus 83 ~C~~Cgk 89 (465)
.|++||.
T Consensus 20 ~CP~Cg~ 26 (34)
T cd00729 20 KCPICGA 26 (34)
T ss_pred cCcCCCC
Confidence 5666654
No 83
>PHA00626 hypothetical protein
Probab=68.74 E-value=2.7 Score=29.22 Aligned_cols=16 Identities=13% Similarity=0.227 Sum_probs=12.4
Q ss_pred CCcccccccccccCCh
Q 040791 205 KGLFECKACKKVFNSH 220 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~ 220 (465)
...|+|+.||..|+.-
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4579999999888754
No 84
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=68.23 E-value=1.8 Score=37.54 Aligned_cols=22 Identities=27% Similarity=0.424 Sum_probs=16.1
Q ss_pred CCcccccccccccCChhhhhhh
Q 040791 205 KGLFECKACKKVFNSHQALGGH 226 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H 226 (465)
++.|+|+.||++|.....+..=
T Consensus 26 ~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 26 RRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred eeeeeccccCCcceEeEeccCc
Confidence 3458999999999887665433
No 85
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=68.18 E-value=3.2 Score=45.21 Aligned_cols=12 Identities=17% Similarity=0.420 Sum_probs=9.9
Q ss_pred CCceecCccccc
Q 040791 291 SKVHECSICHRV 302 (465)
Q Consensus 291 ekp~~C~~Cgk~ 302 (465)
..|+.|+.||-.
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 478999999865
No 86
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=67.17 E-value=3.3 Score=28.38 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=20.5
Q ss_pred CcccccccccccCCh-----hhhhhhhh-hcC
Q 040791 206 GLFECKACKKVFNSH-----QALGGHRA-SHK 231 (465)
Q Consensus 206 k~y~C~~Cgk~F~~~-----~~L~~H~~-~H~ 231 (465)
..-.|..|++.+... +.|.+|++ .|.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 346899999999766 58999987 564
No 87
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.97 E-value=3.1 Score=27.96 Aligned_cols=10 Identities=40% Similarity=0.966 Sum_probs=6.8
Q ss_pred cCCccccccc
Q 040791 83 VCENCGKEFL 92 (465)
Q Consensus 83 ~C~~Cgk~F~ 92 (465)
.|+.||..+.
T Consensus 23 ~Cp~CG~~~~ 32 (46)
T PRK00398 23 RCPYCGYRIL 32 (46)
T ss_pred ECCCCCCeEE
Confidence 6888876543
No 88
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=64.20 E-value=2.7 Score=26.65 Aligned_cols=34 Identities=18% Similarity=0.323 Sum_probs=22.0
Q ss_pred CcccccchhhhhhccccccCCccccccccccCCCcccccccccccC
Q 040791 173 ESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFN 218 (465)
Q Consensus 173 ~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~ 218 (465)
..|+.|+..|.-.... +.......+|..|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~------------ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK------------IPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHH------------CCCCCcEEECCCCCCEeC
Confidence 4688888887543321 223445688999998874
No 89
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=64.10 E-value=4.4 Score=42.33 Aligned_cols=30 Identities=23% Similarity=0.361 Sum_probs=26.1
Q ss_pred cCCCceeccCcccCcCCCccchhhhhhhcc
Q 040791 7 QQSNFKHYCKICKKGFGCGRALGGHMRAHG 36 (465)
Q Consensus 7 ~~~~~~~~C~~C~k~F~~~~~L~~H~r~H~ 36 (465)
....++..|..||..|.+......||.+|.
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 445677899999999999999999999983
No 90
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=63.54 E-value=1.5 Score=46.51 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=26.3
Q ss_pred CceecCccccccCCchhhhhhhhhccCCC
Q 040791 292 KVHECSICHRVFSSGQALGGHKRCHWITS 320 (465)
Q Consensus 292 kp~~C~~Cgk~F~~~~~L~~H~r~H~~~~ 320 (465)
-.|.|.+|+|+|-.-..+..||++|....
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 45999999999999999999999998654
No 91
>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=63.54 E-value=2.2 Score=28.12 Aligned_cols=30 Identities=23% Similarity=0.440 Sum_probs=17.9
Q ss_pred CCcccccchhhhhhccccccCCccccccccccCCCccccccccc
Q 040791 172 EESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKK 215 (465)
Q Consensus 172 ~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk 215 (465)
.|.|..||..|.....+. ....-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~--------------~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS--------------EDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcC--------------CCCCCcCCCCCC
Confidence 367777777775444333 134566777775
No 92
>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=63.35 E-value=3.9 Score=23.85 Aligned_cols=21 Identities=19% Similarity=0.562 Sum_probs=16.7
Q ss_pred eecCccccccCCchhhhhhhhh
Q 040791 294 HECSICHRVFSSGQALGGHKRC 315 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~ 315 (465)
..|++|++.+ ....+..|+..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 4699999999 56778888763
No 93
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=59.74 E-value=6 Score=32.74 Aligned_cols=14 Identities=21% Similarity=0.328 Sum_probs=10.3
Q ss_pred cCCcccccccChHH
Q 040791 83 VCENCGKEFLSWKS 96 (465)
Q Consensus 83 ~C~~Cgk~F~~~~~ 96 (465)
.|+.||..|.-...
T Consensus 28 vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 28 VSPYTGEQFPPEEA 41 (129)
T ss_pred cCCCcCCccCcchh
Confidence 78889888865533
No 94
>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=58.88 E-value=4.3 Score=34.18 Aligned_cols=26 Identities=27% Similarity=0.395 Sum_probs=17.1
Q ss_pred CCceecCccccccCCchhhhhhhhhccCC
Q 040791 291 SKVHECSICHRVFSSGQALGGHKRCHWIT 319 (465)
Q Consensus 291 ekp~~C~~Cgk~F~~~~~L~~H~r~H~~~ 319 (465)
+.--.|-+|||.|.. |++|++.|+|-
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred cCeeEEccCCcccch---HHHHHHHccCC
Confidence 455799999999965 59999999643
No 95
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=58.61 E-value=3.2 Score=26.82 Aligned_cols=12 Identities=17% Similarity=0.230 Sum_probs=8.1
Q ss_pred Ccccccchhhhh
Q 040791 173 ESCASASKEEER 184 (465)
Q Consensus 173 ~~C~~c~k~f~~ 184 (465)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 677777777643
No 96
>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=57.93 E-value=7.3 Score=32.25 Aligned_cols=33 Identities=12% Similarity=-0.068 Sum_probs=25.9
Q ss_pred CceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCc
Q 040791 10 NFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWE 54 (465)
Q Consensus 10 ~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~ 54 (465)
..+..|..||+.|... +..|..|+.|+..|...
T Consensus 7 GtKr~Cp~cg~kFYDL------------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 7 GTKRICPNTGSKFYDL------------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred CccccCCCcCcccccc------------CCCCccCCCcCCccCcc
Confidence 3567999999999753 45689999999887644
No 97
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=57.66 E-value=7.9 Score=40.49 Aligned_cols=26 Identities=19% Similarity=0.335 Sum_probs=22.1
Q ss_pred ccCCcccccccChHHHHHhhhhCCCc
Q 040791 82 RVCENCGKEFLSWKSFLEHGKCSSED 107 (465)
Q Consensus 82 y~C~~Cgk~F~~~~~L~~H~r~H~ge 107 (465)
..|..||..|........||..|.+.
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred chhcccccccccchhhhhHhhhhhhh
Confidence 48999999999999888888888643
No 98
>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=57.13 E-value=3.6 Score=28.34 Aligned_cols=11 Identities=18% Similarity=0.362 Sum_probs=5.3
Q ss_pred Ccccccchhhh
Q 040791 173 ESCASASKEEE 183 (465)
Q Consensus 173 ~~C~~c~k~f~ 183 (465)
|.|..|+..|+
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44555555443
No 99
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.62 E-value=6.5 Score=42.95 Aligned_cols=46 Identities=20% Similarity=0.257 Sum_probs=33.0
Q ss_pred eccCcccCcCCCc---cchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCcccc
Q 040791 13 HYCKICKKGFGCG---RALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGK 89 (465)
Q Consensus 13 ~~C~~C~k~F~~~---~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk 89 (465)
-.|..||..|.+. ..|..|+..+ -..|..|+.. ...|. .|+.||-
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~~~-----~L~CH~Cg~~--------------~~~p~-------------~Cp~Cgs 483 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKATG-----QLRCHYCGYQ--------------EPIPQ-------------SCPECGS 483 (730)
T ss_pred eecccCCCcccCCCCCcceEEecCCC-----eeEeCCCCCC--------------CCCCC-------------CCCCCCC
Confidence 3699999988866 4566676554 5788888753 34566 8999987
Q ss_pred c
Q 040791 90 E 90 (465)
Q Consensus 90 ~ 90 (465)
.
T Consensus 484 ~ 484 (730)
T COG1198 484 E 484 (730)
T ss_pred C
Confidence 5
No 100
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=56.26 E-value=4 Score=26.04 Aligned_cols=34 Identities=21% Similarity=0.367 Sum_probs=21.0
Q ss_pred CcccccchhhhhhccccccCCccccccccccCCCcccccccccccC
Q 040791 173 ESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFN 218 (465)
Q Consensus 173 ~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~ 218 (465)
..|+.|+..|.-... ++..+.+..+|..|+-.|.
T Consensus 3 i~CP~C~~~f~v~~~------------~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD------------KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHH------------HcccCCcEEECCCCCcEee
Confidence 457788877743321 1223455788888887774
No 101
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=56.11 E-value=6.9 Score=33.94 Aligned_cols=15 Identities=40% Similarity=0.992 Sum_probs=11.8
Q ss_pred ccCCcccccccChHH
Q 040791 82 RVCENCGKEFLSWKS 96 (465)
Q Consensus 82 y~C~~Cgk~F~~~~~ 96 (465)
|+|+.||+.|.+...
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 489999999987544
No 102
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=55.82 E-value=15 Score=35.74 Aligned_cols=40 Identities=15% Similarity=0.282 Sum_probs=28.4
Q ss_pred CCCcccccccccccCChhhhhhhhh-hcCCCC-cccCCCCCC
Q 040791 204 NKGLFECKACKKVFNSHQALGGHRA-SHKKVK-GCFAARLDH 243 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~~~L~~H~~-~H~~~k-~~~C~~C~~ 243 (465)
....|.|++|++.=.+-..|+.|.. .|..-. ...|+.|.-
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 3457999999999999999999974 453322 345666653
No 103
>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=55.33 E-value=13 Score=34.69 Aligned_cols=41 Identities=20% Similarity=0.263 Sum_probs=25.0
Q ss_pred cccccccccccCChhhhhhhhhhc----CCCCcccCCCCCCcCCCcchhh
Q 040791 207 LFECKACKKVFNSHQALGGHRASH----KKVKGCFAARLDHMDDSLADED 252 (465)
Q Consensus 207 ~y~C~~Cgk~F~~~~~L~~H~~~H----~~~k~~~C~~C~~~f~~~~~l~ 252 (465)
.|.|-.|.-.|-. .|.|.- .+.+++.|++|++-.....+|.
T Consensus 182 q~sCLRCK~cfCd-----dHvrrKg~ky~k~k~~PCPKCg~et~eTkdLS 226 (314)
T PF06524_consen 182 QYSCLRCKICFCD-----DHVRRKGFKYEKGKPIPCPKCGYETQETKDLS 226 (314)
T ss_pred chhhhheeeeehh-----hhhhhcccccccCCCCCCCCCCCcccccccce
Confidence 4666666666644 344331 2347899999998766555553
No 104
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.92 E-value=5.3 Score=28.30 Aligned_cols=52 Identities=15% Similarity=0.155 Sum_probs=30.1
Q ss_pred CceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCccc-CcCcccCCCCCCCCCCcceecccCCCCCCCcccCCccc
Q 040791 10 NFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQA-SDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCG 88 (465)
Q Consensus 10 ~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~-f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cg 88 (465)
..+..|.-|+....-.. ....|.|+.||.. -.+...+++ ...+| +|+.||
T Consensus 5 ~~~~~CtSCg~~i~~~~-----------~~~~F~CPnCG~~~I~RC~~CRk-----~~~~Y-------------~CP~CG 55 (59)
T PRK14890 5 MEPPKCTSCGIEIAPRE-----------KAVKFLCPNCGEVIIYRCEKCRK-----QSNPY-------------TCPKCG 55 (59)
T ss_pred ccCccccCCCCcccCCC-----------ccCEeeCCCCCCeeEeechhHHh-----cCCce-------------ECCCCC
Confidence 34556777765432110 1346888888876 444444432 33456 999998
Q ss_pred cc
Q 040791 89 KE 90 (465)
Q Consensus 89 k~ 90 (465)
+.
T Consensus 56 F~ 57 (59)
T PRK14890 56 FE 57 (59)
T ss_pred Cc
Confidence 63
No 105
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=54.24 E-value=3.3 Score=26.41 Aligned_cols=34 Identities=24% Similarity=0.354 Sum_probs=18.7
Q ss_pred CcccccchhhhhhccccccCCccccccccccCCCcccccccccccC
Q 040791 173 ESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFN 218 (465)
Q Consensus 173 ~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~ 218 (465)
+.|+.|+..|.-.... .........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~------------~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------------LGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHH------------cCCCCCEEECCCCCCEEE
Confidence 4677777766433211 111223577888887764
No 106
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.20 E-value=6.8 Score=42.59 Aligned_cols=34 Identities=9% Similarity=0.064 Sum_probs=18.5
Q ss_pred cccccccccCChhhhhhhhhhcCCCCcccCCCCCC
Q 040791 209 ECKACKKVFNSHQALGGHRASHKKVKGCFAARLDH 243 (465)
Q Consensus 209 ~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~ 243 (465)
.|..||..+.-.. -...+..|.......|..|+.
T Consensus 385 ~C~~Cg~~~~C~~-C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 385 ACARCRTPARCRH-CTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred EhhhCcCeeECCC-CCCceeEecCCCeeECCCCcC
Confidence 5555555544321 122333455556778888886
No 107
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=51.94 E-value=9.3 Score=29.36 Aligned_cols=11 Identities=36% Similarity=1.093 Sum_probs=9.4
Q ss_pred cCCcccccccC
Q 040791 83 VCENCGKEFLS 93 (465)
Q Consensus 83 ~C~~Cgk~F~~ 93 (465)
.|..||..|.-
T Consensus 55 ~C~kCg~~fAG 65 (89)
T COG1997 55 KCRKCGAKFAG 65 (89)
T ss_pred EcCCCCCeecc
Confidence 89999998864
No 108
>PF14353 CpXC: CpXC protein
Probab=50.98 E-value=3.3 Score=34.71 Aligned_cols=58 Identities=16% Similarity=0.141 Sum_probs=33.5
Q ss_pred CcccccchhhhhhccccccCCc--cccccccccCCCcccccccccccCChhhhhhhhhhc
Q 040791 173 ESCASASKEEERRNSMNFIGPI--SMDKAKGVANKGLFECKACKKVFNSHQALGGHRASH 230 (465)
Q Consensus 173 ~~C~~c~k~f~~~~~l~~~~~~--~~~~~~~~~~~k~y~C~~Cgk~F~~~~~L~~H~~~H 230 (465)
..|+.|+..|...-...+.... .+.....-..-..|.|+.||..|.-...+.-|-..|
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCCC
Confidence 4799999988655322211111 011111111224689999999998887777775543
No 109
>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=50.78 E-value=8.2 Score=31.29 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=23.6
Q ss_pred ceec----CccccccCCchhhhhhhhhccC
Q 040791 293 VHEC----SICHRVFSSGQALGGHKRCHWI 318 (465)
Q Consensus 293 p~~C----~~Cgk~F~~~~~L~~H~r~H~~ 318 (465)
-|.| ..|++.+.+...+..|.+.+++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3999 9999999999999999998764
No 110
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.74 E-value=8.6 Score=40.44 Aligned_cols=19 Identities=16% Similarity=-0.157 Sum_probs=13.4
Q ss_pred hhhhhcCCCCcccCCCCCC
Q 040791 225 GHRASHKKVKGCFAARLDH 243 (465)
Q Consensus 225 ~H~~~H~~~k~~~C~~C~~ 243 (465)
..+..|.......|..|+.
T Consensus 230 ~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 230 VSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred CceEEecCCCeEEcCCCcC
Confidence 3445566667788999987
No 111
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=50.56 E-value=7.4 Score=34.72 Aligned_cols=34 Identities=21% Similarity=0.366 Sum_probs=26.9
Q ss_pred CCcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCC
Q 040791 205 KGLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDS 247 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~ 247 (465)
..-|.|+.|++.|+.-.++. ..|.|+.|+.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 45689999999999888874 37999999986544
No 112
>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=48.63 E-value=9.8 Score=33.22 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=20.6
Q ss_pred CCCcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCc
Q 040791 204 NKGLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHM 244 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~ 244 (465)
...-|.|+.|+..|+.-.++. ..|.|+.|+..
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 345577777777777777774 24666666653
No 113
>PF15269 zf-C2H2_7: Zinc-finger
Probab=48.22 E-value=10 Score=25.08 Aligned_cols=24 Identities=21% Similarity=0.191 Sum_probs=20.6
Q ss_pred cccCCcccccccChHHHHHhhhhC
Q 040791 81 CRVCENCGKEFLSWKSFLEHGKCS 104 (465)
Q Consensus 81 ~y~C~~Cgk~F~~~~~L~~H~r~H 104 (465)
-|+|-+|..+...++.|..||+.-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 368999999999999999999753
No 114
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=47.24 E-value=9.2 Score=31.88 Aligned_cols=24 Identities=21% Similarity=0.206 Sum_probs=20.3
Q ss_pred ceecCccccccCCchhhhhhhhhccCC
Q 040791 293 VHECSICHRVFSSGQALGGHKRCHWIT 319 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~~L~~H~r~H~~~ 319 (465)
-..|-+|||.|. .|++|+++|.+-
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCC
Confidence 368999999995 689999999754
No 115
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.09 E-value=2.6 Score=37.64 Aligned_cols=29 Identities=21% Similarity=0.377 Sum_probs=22.4
Q ss_pred CCCceecC--ccccccCCchhhhhhh-hhccC
Q 040791 290 KSKVHECS--ICHRVFSSGQALGGHK-RCHWI 318 (465)
Q Consensus 290 ~ekp~~C~--~Cgk~F~~~~~L~~H~-r~H~~ 318 (465)
|.-.|+|- -|+-.|.+..+-..|| ++|.-
T Consensus 141 G~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 141 GQDMYQCLVEGCTEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred CccHHHHHHHhhhhhhhhhhhhhhHHHHhccC
Confidence 35678884 4999999999999996 56653
No 116
>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=46.94 E-value=11 Score=32.94 Aligned_cols=37 Identities=14% Similarity=0.187 Sum_probs=27.3
Q ss_pred CCCCCCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCC
Q 040791 167 LDAEPEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNS 219 (465)
Q Consensus 167 ~~~~~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~ 219 (465)
.....-|.|+.|+..|.....+. .-|.|+.||.....
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~----------------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME----------------LNFTCPRCGAMLDY 140 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH----------------cCCcCCCCCCEeee
Confidence 34566799999999887665543 25999999977543
No 117
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=46.93 E-value=8.2 Score=26.34 Aligned_cols=7 Identities=43% Similarity=1.227 Sum_probs=4.4
Q ss_pred cCCcccc
Q 040791 83 VCENCGK 89 (465)
Q Consensus 83 ~C~~Cgk 89 (465)
.|+.||.
T Consensus 26 rCp~Cg~ 32 (49)
T COG1996 26 RCPYCGS 32 (49)
T ss_pred eCCCCCc
Confidence 5666664
No 118
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=46.27 E-value=12 Score=34.69 Aligned_cols=25 Identities=20% Similarity=0.505 Sum_probs=15.8
Q ss_pred CceecCccccccCCchhhhhhhhhcc
Q 040791 292 KVHECSICHRVFSSGQALGGHKRCHW 317 (465)
Q Consensus 292 kp~~C~~Cgk~F~~~~~L~~H~r~H~ 317 (465)
.-|.|-.|++.|.. ..+..|..+-+
T Consensus 28 ~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 28 AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred CeeEEeeccccccc-chhhhhhhhcc
Confidence 34677777777766 55666666544
No 119
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=46.13 E-value=7.1 Score=34.82 Aligned_cols=21 Identities=5% Similarity=-0.284 Sum_probs=15.0
Q ss_pred CCCCcccCCCCCCcCCCcchh
Q 040791 231 KKVKGCFAARLDHMDDSLADE 251 (465)
Q Consensus 231 ~~~k~~~C~~C~~~f~~~~~l 251 (465)
.....|.|+.|+..|+..-.+
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAM 133 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHh
Confidence 344679999999887755443
No 120
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=46.13 E-value=30 Score=33.16 Aligned_cols=27 Identities=30% Similarity=0.576 Sum_probs=23.1
Q ss_pred CCCcccccccccccCChhhhhhhhhhc
Q 040791 204 NKGLFECKACKKVFNSHQALGGHRASH 230 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~~~L~~H~~~H 230 (465)
....|.|+.|...|-...+.-.|...|
T Consensus 385 ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 385 SSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cccceechhhhhhhhhhhHHHHHHHHh
Confidence 356799999999999999988887766
No 121
>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=46.05 E-value=9.7 Score=32.08 Aligned_cols=27 Identities=26% Similarity=0.524 Sum_probs=17.5
Q ss_pred CCcccccccccccCChhhhhhhhhhcCCCC
Q 040791 205 KGLFECKACKKVFNSHQALGGHRASHKKVK 234 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k 234 (465)
+....|-+|||.|.. |++|++.|+|-.
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCC
Confidence 445789999999986 599999998754
No 122
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=45.82 E-value=12 Score=32.74 Aligned_cols=12 Identities=25% Similarity=0.606 Sum_probs=10.0
Q ss_pred CCCCceecCccc
Q 040791 289 RKSKVHECSICH 300 (465)
Q Consensus 289 ~~ekp~~C~~Cg 300 (465)
.|+-|-.|++||
T Consensus 145 ~ge~P~~CPiCg 156 (166)
T COG1592 145 EGEAPEVCPICG 156 (166)
T ss_pred cCCCCCcCCCCC
Confidence 347889999998
No 123
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=45.25 E-value=13 Score=22.91 Aligned_cols=8 Identities=38% Similarity=1.207 Sum_probs=5.0
Q ss_pred cCCccccc
Q 040791 83 VCENCGKE 90 (465)
Q Consensus 83 ~C~~Cgk~ 90 (465)
.|+.||..
T Consensus 19 rC~~CG~R 26 (32)
T PF03604_consen 19 RCPECGHR 26 (32)
T ss_dssp SBSSSS-S
T ss_pred ECCcCCCe
Confidence 67777754
No 124
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=44.55 E-value=9.1 Score=27.09 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=27.4
Q ss_pred eeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcC-cccCCCCCCCCCCcceecccCCCCCCCcccCCccccc
Q 040791 12 KHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDW-EDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGKE 90 (465)
Q Consensus 12 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~-~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk~ 90 (465)
+-.|.-||....-.. ....|.|+.||..-.+ ...++ ....+| +|+.||+.
T Consensus 9 ~~~CtSCg~~i~p~e-----------~~v~F~CPnCGe~~I~Rc~~CR-----k~g~~Y-------------~Cp~CGF~ 59 (61)
T COG2888 9 PPVCTSCGREIAPGE-----------TAVKFPCPNCGEVEIYRCAKCR-----KLGNPY-------------RCPKCGFE 59 (61)
T ss_pred CceeccCCCEeccCC-----------ceeEeeCCCCCceeeehhhhHH-----HcCCce-------------ECCCcCcc
Confidence 346777766542111 2345788888854332 22222 234566 99999863
No 125
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.29 E-value=7.8 Score=25.82 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=17.0
Q ss_pred CcccccchhhhhhccccccCCccccccccccCCCccccccccc
Q 040791 173 ESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKK 215 (465)
Q Consensus 173 ~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk 215 (465)
|.|..||..|... ...+..|+.||-
T Consensus 3 Y~C~~Cg~~~~~~------------------~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIK------------------SKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecC------------------CCCceECCCCCc
Confidence 7788888877433 123578888874
No 126
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=44.01 E-value=10 Score=32.71 Aligned_cols=13 Identities=15% Similarity=0.488 Sum_probs=10.0
Q ss_pred CceecCccccccC
Q 040791 292 KVHECSICHRVFS 304 (465)
Q Consensus 292 kp~~C~~Cgk~F~ 304 (465)
..|.|+.||....
T Consensus 122 ~~f~Cp~Cg~~l~ 134 (147)
T smart00531 122 GTFTCPRCGEELE 134 (147)
T ss_pred CcEECCCCCCEEE
Confidence 3499999997653
No 127
>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=43.60 E-value=15 Score=29.72 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=23.9
Q ss_pred CcccC----CcccccccChHHHHHhhhhCCC
Q 040791 80 SCRVC----ENCGKEFLSWKSFLEHGKCSSE 106 (465)
Q Consensus 80 ~~y~C----~~Cgk~F~~~~~L~~H~r~H~g 106 (465)
..|.| ..|+..+.+...+..|.+.++|
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 55799 9999999999999999997664
No 128
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=42.54 E-value=12 Score=22.31 Aligned_cols=22 Identities=27% Similarity=0.723 Sum_probs=14.6
Q ss_pred eecCccccccCCchhhhhhhhhc
Q 040791 294 HECSICHRVFSSGQALGGHKRCH 316 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~H 316 (465)
|.|-.|++.| .+...+.|...=
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~CI 22 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSCI 22 (28)
T ss_dssp EEETTTTEEE-EGGGTTT-----
T ss_pred CeeecCCCCc-CcCCcCCCCccc
Confidence 5799999999 777788887654
No 129
>PF15269 zf-C2H2_7: Zinc-finger
Probab=42.35 E-value=11 Score=24.96 Aligned_cols=26 Identities=27% Similarity=0.285 Sum_probs=22.4
Q ss_pred CceeccCcccCcCCCccchhhhhhhc
Q 040791 10 NFKHYCKICKKGFGCGRALGGHMRAH 35 (465)
Q Consensus 10 ~~~~~C~~C~k~F~~~~~L~~H~r~H 35 (465)
...|+|-.|......++.|-.||+.-
T Consensus 18 p~~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 18 PFKYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred CccceeecCCcccchHHHHHHHHHHH
Confidence 46689999999999999999999753
No 130
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.81 E-value=16 Score=31.38 Aligned_cols=37 Identities=14% Similarity=0.177 Sum_probs=23.5
Q ss_pred CCCcccccccccccCChhhhhh-hhhhcCCCCcccCCCCCCcC
Q 040791 204 NKGLFECKACKKVFNSHQALGG-HRASHKKVKGCFAARLDHMD 245 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~~~L~~-H~~~H~~~k~~~C~~C~~~f 245 (465)
....|.|+.|++.|..-.++.. + . ...|.|+.|+...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d----~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLD----M-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcC----C-CCcEECCCCCCEE
Confidence 3456888888888886555433 2 1 2338888888643
No 131
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=41.61 E-value=12 Score=40.33 Aligned_cols=12 Identities=42% Similarity=1.193 Sum_probs=9.0
Q ss_pred cCCcccccccCh
Q 040791 83 VCENCGKEFLSW 94 (465)
Q Consensus 83 ~C~~Cgk~F~~~ 94 (465)
.|..|++.|.+.
T Consensus 462 tC~~C~kkFfSl 473 (1374)
T PTZ00303 462 SCPSCGRAFISL 473 (1374)
T ss_pred cccCcCCccccc
Confidence 588888888654
No 132
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=41.28 E-value=37 Score=33.92 Aligned_cols=26 Identities=27% Similarity=0.441 Sum_probs=21.6
Q ss_pred eecCc--cccccCCchhhhhhhhhccCC
Q 040791 294 HECSI--CHRVFSSGQALGGHKRCHWIT 319 (465)
Q Consensus 294 ~~C~~--Cgk~F~~~~~L~~H~r~H~~~ 319 (465)
|-|.. |+.+|.+-+++..|+|.|-..
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhhh
Confidence 55644 999999999999999999754
No 133
>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=40.61 E-value=7.3 Score=30.30 Aligned_cols=31 Identities=29% Similarity=0.686 Sum_probs=21.7
Q ss_pred CCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCC
Q 040791 172 EESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNS 219 (465)
Q Consensus 172 ~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~ 219 (465)
.|.|+.|++.-..+. ..+-+.|..|+++|.-
T Consensus 35 ky~Cp~Cgk~~vkR~-----------------a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRV-----------------ATGIWKCKKCGKKFAG 65 (90)
T ss_dssp -BEESSSSSSEEEEE-----------------ETTEEEETTTTEEEE-
T ss_pred CCcCCCCCCceeEEe-----------------eeEEeecCCCCCEEeC
Confidence 488999988653322 3456999999999864
No 134
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=40.59 E-value=15 Score=30.71 Aligned_cols=25 Identities=24% Similarity=0.267 Sum_probs=20.9
Q ss_pred ccCCcccccccChHHHHHhhhhCCCccC
Q 040791 82 RVCENCGKEFLSWKSFLEHGKCSSEDAE 109 (465)
Q Consensus 82 y~C~~Cgk~F~~~~~L~~H~r~H~ge~~ 109 (465)
..|-+|||.|. +|++|+.+|.|-.+
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 38999999995 69999999987543
No 135
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=40.27 E-value=16 Score=32.08 Aligned_cols=23 Identities=17% Similarity=0.179 Sum_probs=18.2
Q ss_pred ccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCccc
Q 040791 41 SGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCG 88 (465)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cg 88 (465)
.|.|.+||..+. ++-|- +|++||
T Consensus 134 ~~vC~vCGy~~~------------ge~P~-------------~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHE------------GEAPE-------------VCPICG 156 (166)
T ss_pred EEEcCCCCCccc------------CCCCC-------------cCCCCC
Confidence 589999987664 36666 899998
No 136
>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=39.91 E-value=9.8 Score=29.65 Aligned_cols=32 Identities=22% Similarity=0.636 Sum_probs=22.9
Q ss_pred CCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCC
Q 040791 171 PEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNS 219 (465)
Q Consensus 171 ~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~ 219 (465)
..|.|+.|++.-..+. +.+.+.|..|+++|.-
T Consensus 34 a~y~CpfCgk~~vkR~-----------------a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRG-----------------STGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceEEE-----------------eeEEEEcCCCCCEEeC
Confidence 3588999987543322 3457999999999874
No 137
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=39.91 E-value=14 Score=28.78 Aligned_cols=32 Identities=9% Similarity=0.105 Sum_probs=21.8
Q ss_pred cccCCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCcccccccC
Q 040791 40 ESGHIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGKEFLS 93 (465)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk~F~~ 93 (465)
..|.|+.|++.-... .....+ .|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vkR---------~a~GIW-------------~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR---------QAVGIW-------------RCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceee---------eeeEEE-------------EcCCCCCEEeC
Confidence 578999997643221 333456 89999999864
No 138
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=39.41 E-value=14 Score=27.53 Aligned_cols=19 Identities=21% Similarity=0.639 Sum_probs=16.2
Q ss_pred CCceecC--ccccccCCchhh
Q 040791 291 SKVHECS--ICHRVFSSGQAL 309 (465)
Q Consensus 291 ekp~~C~--~Cgk~F~~~~~L 309 (465)
++-++|. .||.+|.....+
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeeecCCCCCCCEEEEEEEE
Confidence 6789999 999999887655
No 139
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.35 E-value=15 Score=33.07 Aligned_cols=49 Identities=18% Similarity=0.277 Sum_probs=39.2
Q ss_pred cccccccccCChhhhhhhhh-hc---------CCCCcccC--CCCCCcCCCcchhhhhhhh
Q 040791 209 ECKACKKVFNSHQALGGHRA-SH---------KKVKGCFA--ARLDHMDDSLADEDHDVIT 257 (465)
Q Consensus 209 ~C~~Cgk~F~~~~~L~~H~~-~H---------~~~k~~~C--~~C~~~f~~~~~l~~H~~~ 257 (465)
.|..|.+.|.+...|..|+. .| .|.--|.| ..|...|....+.+.|+..
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 89999999999999999984 34 24445666 6799999988888888654
No 140
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=38.81 E-value=27 Score=34.07 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=20.5
Q ss_pred cccCCcccccccChHHHHHhhhhCC
Q 040791 81 CRVCENCGKEFLSWKSFLEHGKCSS 105 (465)
Q Consensus 81 ~y~C~~Cgk~F~~~~~L~~H~r~H~ 105 (465)
.|.|++|++.=.+...|..|...-+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcC
Confidence 5699999998888889999986433
No 141
>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=37.80 E-value=25 Score=30.27 Aligned_cols=15 Identities=27% Similarity=0.736 Sum_probs=11.1
Q ss_pred CCcccccccccccCC
Q 040791 205 KGLFECKACKKVFNS 219 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~ 219 (465)
.-..+|..|+|-|-+
T Consensus 12 ~~vv~C~~c~kWFCN 26 (152)
T PF09416_consen 12 SCVVKCNTCNKWFCN 26 (152)
T ss_dssp CCEEEETTTTEEEES
T ss_pred ccEeEcCCCCcEeec
Confidence 345789999988854
No 142
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.50 E-value=19 Score=28.82 Aligned_cols=15 Identities=27% Similarity=0.328 Sum_probs=10.9
Q ss_pred cCCcccccccChHHHH
Q 040791 83 VCENCGKEFLSWKSFL 98 (465)
Q Consensus 83 ~C~~Cgk~F~~~~~L~ 98 (465)
.|+.||++|. .+.|.
T Consensus 28 VsPytG~s~P-~s~fe 42 (129)
T COG4530 28 VSPYTGKSYP-RSYFE 42 (129)
T ss_pred ccCcccccch-HHHHH
Confidence 8999999994 34443
No 143
>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=36.62 E-value=11 Score=34.48 Aligned_cols=30 Identities=23% Similarity=0.395 Sum_probs=22.8
Q ss_pred ccCCCceeccCcccCcCCCccchhhhhhh-c
Q 040791 6 DQQSNFKHYCKICKKGFGCGRALGGHMRA-H 35 (465)
Q Consensus 6 ~~~~~~~~~C~~C~k~F~~~~~L~~H~r~-H 35 (465)
.+..+.+|.|.+|+|.|.-..-...|+.. |
T Consensus 71 ~e~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 71 KEEDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp -SSSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HHHcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 34567889999999999999999999875 5
No 144
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=35.53 E-value=14 Score=31.61 Aligned_cols=22 Identities=18% Similarity=0.339 Sum_probs=17.1
Q ss_pred CCcccccccccccCChhhhhhh
Q 040791 205 KGLFECKACKKVFNSHQALGGH 226 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H 226 (465)
.+.-+|..||+.|++..-...-
T Consensus 26 RRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 26 RRRRECLECHERFTTFERAELL 47 (147)
T ss_pred eecccCCccCCccceeeecccc
Confidence 4667999999999998765443
No 145
>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=35.45 E-value=20 Score=32.89 Aligned_cols=30 Identities=17% Similarity=0.440 Sum_probs=22.7
Q ss_pred cCCCcccccccccccCChhhhhhhhhhcCC
Q 040791 203 ANKGLFECKACKKVFNSHQALGGHRASHKK 232 (465)
Q Consensus 203 ~~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~ 232 (465)
..+..|.|..|+|.|.-..-...|+..-+.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 356679999999999999999999875443
No 146
>COG1773 Rubredoxin [Energy production and conversion]
Probab=35.43 E-value=17 Score=25.51 Aligned_cols=15 Identities=33% Similarity=0.767 Sum_probs=12.1
Q ss_pred CceecCccccccCCc
Q 040791 292 KVHECSICHRVFSSG 306 (465)
Q Consensus 292 kp~~C~~Cgk~F~~~ 306 (465)
+.|+|.+||.+|.-.
T Consensus 2 ~~~~C~~CG~vYd~e 16 (55)
T COG1773 2 KRWRCSVCGYVYDPE 16 (55)
T ss_pred CceEecCCceEeccc
Confidence 469999999999643
No 147
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=34.96 E-value=25 Score=22.81 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=8.2
Q ss_pred ccCCccccccc
Q 040791 82 RVCENCGKEFL 92 (465)
Q Consensus 82 y~C~~Cgk~F~ 92 (465)
|.|..|+..|.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 48888887764
No 148
>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=34.92 E-value=24 Score=37.10 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=22.6
Q ss_pred eccCcccCcCCCccchhhhhhhcccCCcccCCCcCccc
Q 040791 13 HYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQA 50 (465)
Q Consensus 13 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~ 50 (465)
..|..||....+..- ...|..|. ......|..|+..
T Consensus 214 ~~C~~Cg~~~~C~~C-~~~l~~h~-~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 214 LLCRSCGYILCCPNC-DVSLTYHK-KEGKLRCHYCGYQ 249 (505)
T ss_pred eEhhhCcCccCCCCC-CCceEEec-CCCeEEcCCCcCc
Confidence 378888888876532 22344443 4446789988853
No 149
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.57 E-value=13 Score=28.96 Aligned_cols=32 Identities=22% Similarity=0.684 Sum_probs=22.8
Q ss_pred CCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCC
Q 040791 171 PEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNS 219 (465)
Q Consensus 171 ~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~ 219 (465)
..|.|+.|++.-..+. +.+.+.|..|+++|.-
T Consensus 35 a~y~CpfCgk~~vkR~-----------------a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKRV-----------------GTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEEE-----------------EEEEEEcCCCCCEEeC
Confidence 3588999977543332 3457999999999875
No 150
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=34.12 E-value=20 Score=23.42 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=19.3
Q ss_pred ceecCccccccCCch--hhhhhhhhcc
Q 040791 293 VHECSICHRVFSSGQ--ALGGHKRCHW 317 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~--~L~~H~r~H~ 317 (465)
.-.|+.||..|.... .-..|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 359999999998754 5677888774
No 151
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.39 E-value=20 Score=30.06 Aligned_cols=18 Identities=22% Similarity=0.691 Sum_probs=13.8
Q ss_pred CCCcccccccccccCChh
Q 040791 204 NKGLFECKACKKVFNSHQ 221 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~~ 221 (465)
+...|.|+.|+++|....
T Consensus 50 ~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 50 GHQRYKCKSCGSTFTVET 67 (129)
T ss_pred cccccccCCcCcceeeec
Confidence 466799999999887653
No 152
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=32.31 E-value=18 Score=23.29 Aligned_cols=11 Identities=45% Similarity=1.041 Sum_probs=8.4
Q ss_pred ccCCccccccc
Q 040791 82 RVCENCGKEFL 92 (465)
Q Consensus 82 y~C~~Cgk~F~ 92 (465)
|.|..||..|+
T Consensus 29 y~C~~C~~~wr 39 (39)
T PF01096_consen 29 YVCCNCGHRWR 39 (39)
T ss_dssp EEESSSTEEEE
T ss_pred EEeCCCCCeeC
Confidence 48888888763
No 153
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.30 E-value=28 Score=34.63 Aligned_cols=21 Identities=24% Similarity=0.483 Sum_probs=17.4
Q ss_pred CCceecCccccccCCchhhhh
Q 040791 291 SKVHECSICHRVFSSGQALGG 311 (465)
Q Consensus 291 ekp~~C~~Cgk~F~~~~~L~~ 311 (465)
|-.++|..||..|..++++..
T Consensus 13 Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 13 EDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred cccccccccCCcCCchhhhhh
Confidence 445669999999999998765
No 154
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=32.08 E-value=24 Score=25.75 Aligned_cols=10 Identities=40% Similarity=1.039 Sum_probs=3.9
Q ss_pred cCCccccccc
Q 040791 83 VCENCGKEFL 92 (465)
Q Consensus 83 ~C~~Cgk~F~ 92 (465)
.|..||..|=
T Consensus 27 hCr~CG~~vC 36 (69)
T PF01363_consen 27 HCRNCGRVVC 36 (69)
T ss_dssp E-TTT--EEE
T ss_pred ccCCCCCEEC
Confidence 4666666554
No 155
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=32.08 E-value=37 Score=35.50 Aligned_cols=41 Identities=12% Similarity=0.034 Sum_probs=22.6
Q ss_pred CCceeccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCc
Q 040791 9 SNFKHYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASD 52 (465)
Q Consensus 9 ~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~ 52 (465)
+...-.|..|++.-.- .-|+.+-. |- ...-|+|..|+....
T Consensus 13 ~~~~i~c~~c~~kc~g-evlrv~d~-~f-hi~cf~c~~cg~~la 53 (670)
T KOG1044|consen 13 GKQGIKCDKCRKKCSG-EVLRVNDN-HF-HINCFQCKKCGRNLA 53 (670)
T ss_pred cccceehhhhCCcccc-ceeEeecc-cc-ceeeeeccccCCCcc
Confidence 3445678888876542 23333322 11 234578888887644
No 156
>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=32.04 E-value=19 Score=21.88 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=12.0
Q ss_pred cccccchhhhhhccccccCCccccccccccCCCcccccccccc
Q 040791 174 SCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKV 216 (465)
Q Consensus 174 ~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~ 216 (465)
.|+.|+..+.... ...|.|+.|+..
T Consensus 4 ~Cp~C~se~~y~D------------------~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTYED------------------GELLVCPECGHE 28 (30)
T ss_dssp --TTT-----EE-------------------SSSEEETTTTEE
T ss_pred CCCCCCCcceecc------------------CCEEeCCccccc
Confidence 6888888775532 335899999854
No 157
>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=32.04 E-value=22 Score=20.34 Aligned_cols=11 Identities=18% Similarity=0.395 Sum_probs=9.0
Q ss_pred CCceecCcccc
Q 040791 291 SKVHECSICHR 301 (465)
Q Consensus 291 ekp~~C~~Cgk 301 (465)
.-+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35799999985
No 158
>PRK05580 primosome assembly protein PriA; Validated
Probab=31.87 E-value=25 Score=38.46 Aligned_cols=47 Identities=15% Similarity=0.292 Sum_probs=0.0
Q ss_pred CcccccchhhhhhccccccCCccccccccccCCCcccccccccccCChhhhhhhhhhcCCCCcccCCCCCCcCCCcchhh
Q 040791 173 ESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNSHQALGGHRASHKKVKGCFAARLDHMDDSLADED 252 (465)
Q Consensus 173 ~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~~~f~~~~~l~ 252 (465)
..|..||... +|+.|+ .-+..|.......|..|++
T Consensus 382 ~~C~~Cg~~~--------------------------~C~~C~----------~~l~~h~~~~~l~Ch~Cg~--------- 416 (679)
T PRK05580 382 LLCRDCGWVA--------------------------ECPHCD----------ASLTLHRFQRRLRCHHCGY--------- 416 (679)
T ss_pred eEhhhCcCcc--------------------------CCCCCC----------CceeEECCCCeEECCCCcC---------
Q ss_pred hhhhhcccccCCCcchhhHhhhcCCCCCCcccccccCCCCceecCccc
Q 040791 253 HDVITHEEFFPTKSTSAMQFDHGANNNNAPLASSSKRKSKVHECSICH 300 (465)
Q Consensus 253 ~H~~~H~~~~~~~~~s~~l~~H~~~~~~~~~~~~~h~~ekp~~C~~Cg 300 (465)
....|..|+.||
T Consensus 417 ------------------------------------~~~~~~~Cp~Cg 428 (679)
T PRK05580 417 ------------------------------------QEPIPKACPECG 428 (679)
T ss_pred ------------------------------------CCCCCCCCCCCc
No 159
>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=31.85 E-value=23 Score=23.68 Aligned_cols=11 Identities=55% Similarity=1.425 Sum_probs=8.4
Q ss_pred CCccccccccc
Q 040791 205 KGLFECKACKK 215 (465)
Q Consensus 205 ~k~y~C~~Cgk 215 (465)
.+.|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 56788888875
No 160
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=31.81 E-value=21 Score=29.81 Aligned_cols=15 Identities=47% Similarity=1.099 Sum_probs=13.9
Q ss_pred ceecCccccccCCch
Q 040791 293 VHECSICHRVFSSGQ 307 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~ 307 (465)
||+|.-||+.|..++
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 689999999999887
No 161
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=31.77 E-value=30 Score=26.82 Aligned_cols=14 Identities=0% Similarity=-0.287 Sum_probs=10.0
Q ss_pred cccCCCcCcccCcC
Q 040791 40 ESGHIDDDDQASDW 53 (465)
Q Consensus 40 ~~~~C~~C~~~f~~ 53 (465)
.|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 46677788777764
No 162
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=31.58 E-value=19 Score=25.14 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=17.3
Q ss_pred CcccccchhhhhhccccccCCccccccccccCCCccccccccccc
Q 040791 173 ESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVF 217 (465)
Q Consensus 173 ~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F 217 (465)
|.|+.|+..+.-..... |+ ...|+.||..|
T Consensus 3 ~~CP~CG~~iev~~~~~--------------Ge-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--------------GE-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc--------------CC-EEeCCCCCCEE
Confidence 67888877663322221 22 45788887655
No 163
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.01 E-value=18 Score=26.94 Aligned_cols=33 Identities=15% Similarity=0.364 Sum_probs=19.9
Q ss_pred CCCcccccchhhhhhccccccCCccccccccccCCCccccccccccc
Q 040791 171 PEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVF 217 (465)
Q Consensus 171 ~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F 217 (465)
-.|.|..|+..|.--+.+. ....-.|+.|+-.|
T Consensus 11 Y~Y~c~~cg~~~dvvq~~~--------------ddplt~ce~c~a~~ 43 (82)
T COG2331 11 YSYECTECGNRFDVVQAMT--------------DDPLTTCEECGARL 43 (82)
T ss_pred eEEeecccchHHHHHHhcc--------------cCccccChhhChHH
Confidence 3477888888776544443 22234688887544
No 164
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=30.82 E-value=26 Score=22.65 Aligned_cols=15 Identities=20% Similarity=0.600 Sum_probs=13.0
Q ss_pred ceecCccccccCCch
Q 040791 293 VHECSICHRVFSSGQ 307 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~ 307 (465)
||+|..|++.|=..-
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 899999999997653
No 165
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.26 E-value=41 Score=23.51 Aligned_cols=9 Identities=44% Similarity=1.390 Sum_probs=4.5
Q ss_pred cCCcccccc
Q 040791 83 VCENCGKEF 91 (465)
Q Consensus 83 ~C~~Cgk~F 91 (465)
.|+.|+..+
T Consensus 23 vCp~Cgapy 31 (54)
T PF14446_consen 23 VCPECGAPY 31 (54)
T ss_pred ECCCCCCcc
Confidence 455555443
No 166
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.05 E-value=37 Score=28.73 Aligned_cols=35 Identities=20% Similarity=0.112 Sum_probs=19.2
Q ss_pred hHHHHHHHHhhccCCCCC------CCCCCCcccccchhhhh
Q 040791 150 EDLANCLMMLSNATVDPL------DAEPEESCASASKEEER 184 (465)
Q Consensus 150 e~~a~~l~~l~~~~~~~~------~~~~~~~C~~c~k~f~~ 184 (465)
+.+..+...+.....-.. ..+..+.|..||..|..
T Consensus 42 e~L~fafe~l~~gt~~ega~L~i~~~p~~~~C~~CG~~~~~ 82 (135)
T PRK03824 42 EIVEFALNELLKGTILEGAEIIFEEEEAVLKCRNCGNEWSL 82 (135)
T ss_pred HHHHHHHHHHHcCCcccCCEEEEEecceEEECCCCCCEEec
Confidence 344455555555443222 23355788888877754
No 167
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=29.55 E-value=28 Score=28.56 Aligned_cols=27 Identities=30% Similarity=0.550 Sum_probs=24.2
Q ss_pred cCCCcccccccccccCChhhhhhhhhh
Q 040791 203 ANKGLFECKACKKVFNSHQALGGHRAS 229 (465)
Q Consensus 203 ~~~k~y~C~~Cgk~F~~~~~L~~H~~~ 229 (465)
.|-+.|-|-.|-+-|.+...|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 367789999999999999999999865
No 168
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.50 E-value=21 Score=30.56 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=16.2
Q ss_pred CCCcccccccccccCChhhhh
Q 040791 204 NKGLFECKACKKVFNSHQALG 224 (465)
Q Consensus 204 ~~k~y~C~~Cgk~F~~~~~L~ 224 (465)
..+.-+|..||+.|++..-..
T Consensus 25 IRRRReC~~C~~RFTTfE~~E 45 (156)
T COG1327 25 IRRRRECLECGERFTTFERAE 45 (156)
T ss_pred hhhhhcccccccccchhheee
Confidence 356778999999999886543
No 169
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=29.23 E-value=24 Score=31.54 Aligned_cols=16 Identities=38% Similarity=0.576 Sum_probs=13.4
Q ss_pred CcccccccccccCChh
Q 040791 206 GLFECKACKKVFNSHQ 221 (465)
Q Consensus 206 k~y~C~~Cgk~F~~~~ 221 (465)
-||.|.+|.+.|.+.-
T Consensus 195 IPF~C~iCKkdy~spv 210 (259)
T COG5152 195 IPFLCGICKKDYESPV 210 (259)
T ss_pred Cceeehhchhhccchh
Confidence 4899999999998764
No 170
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=29.14 E-value=24 Score=28.04 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=15.9
Q ss_pred ccccCCCCceecCccccccCC
Q 040791 285 SSSKRKSKVHECSICHRVFSS 305 (465)
Q Consensus 285 ~~~h~~ekp~~C~~Cgk~F~~ 305 (465)
...+.+ +|+.|..||..|.-
T Consensus 72 ~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCC-CceeCCCCCcEEEE
Confidence 455566 89999999999864
No 171
>PF11519 DUF3222: Protein of unknown function (DUF3222); InterPro: IPR021599 This family of proteins with unknown function appears to be restricted to Rhodopseudomonas. ; PDB: 2JS3_B.
Probab=27.32 E-value=15 Score=26.24 Aligned_cols=17 Identities=35% Similarity=0.659 Sum_probs=10.2
Q ss_pred cccCCCCCCceeeeecc
Q 040791 441 MNISGGSSPWLQVGIGS 457 (465)
Q Consensus 441 ~~~~~~~~~~~~~~~~~ 457 (465)
-.+-|-|-||||-|=.+
T Consensus 35 cklc~asvpwl~tgdei 51 (74)
T PF11519_consen 35 CKLCNASVPWLQTGDEI 51 (74)
T ss_dssp ETTSS-EEETTS--SS-
T ss_pred chhcCCcChhhhcCccc
Confidence 56778888999998544
No 172
>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=27.31 E-value=41 Score=22.08 Aligned_cols=16 Identities=31% Similarity=0.806 Sum_probs=13.4
Q ss_pred cCCcccccccChHHHH
Q 040791 83 VCENCGKEFLSWKSFL 98 (465)
Q Consensus 83 ~C~~Cgk~F~~~~~L~ 98 (465)
.|.+||+.|+.+....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 7999999999876554
No 173
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=26.90 E-value=44 Score=32.40 Aligned_cols=83 Identities=13% Similarity=0.108 Sum_probs=0.0
Q ss_pred eccCcccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCC-CCCCcceecccCCC--------------C
Q 040791 13 HYCKICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVP-PTNKRMYALRANPN--------------R 77 (465)
Q Consensus 13 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~-~~~~~~~~lr~~~~--------------~ 77 (465)
|.|+.|+-.. -+-|-.|+.|+-.......|.+... ---.++|....-.. .
T Consensus 277 y~CP~Ckakv---------------CsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~ 341 (378)
T KOG2807|consen 277 YFCPQCKAKV---------------CSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELL 341 (378)
T ss_pred eeCCcccCee---------------ecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccC
Q ss_pred CCCcccCCcccccccChHHHHHhhhhCCCccCcCCCCCCCCCCCCCCCCCCC
Q 040791 78 LKSCRVCENCGKEFLSWKSFLEHGKCSSEDAESLVSSPGSDGEDGTPRRGCG 129 (465)
Q Consensus 78 ~~~~y~C~~Cgk~F~~~~~L~~H~r~H~ge~~~~~~~~~~~~e~~~~c~~c~ 129 (465)
....|.|..|...|-.-.....|...|. |+.|.
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iHesLh~-------------------CpgCe 374 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIHESLHN-------------------CPGCE 374 (378)
T ss_pred CCCcEEchhccceeeccchHHHHhhhhc-------------------CCCcC
No 174
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.84 E-value=55 Score=26.81 Aligned_cols=16 Identities=31% Similarity=0.542 Sum_probs=8.7
Q ss_pred chhHHHHHHHHhhccC
Q 040791 148 EEEDLANCLMMLSNAT 163 (465)
Q Consensus 148 eee~~a~~l~~l~~~~ 163 (465)
+.+.+.+|...+....
T Consensus 40 ~p~~L~f~f~~~~~~t 55 (114)
T PRK03681 40 ETSSLAFCFDLVCRGT 55 (114)
T ss_pred CHHHHHHHHHHHhCCC
Confidence 3455566666655443
No 175
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=26.75 E-value=40 Score=23.31 Aligned_cols=11 Identities=55% Similarity=1.195 Sum_probs=6.6
Q ss_pred cCCcccccccC
Q 040791 83 VCENCGKEFLS 93 (465)
Q Consensus 83 ~C~~Cgk~F~~ 93 (465)
.|..||+.|-.
T Consensus 20 ~Cr~Cg~~~C~ 30 (57)
T cd00065 20 HCRNCGRIFCS 30 (57)
T ss_pred ccCcCcCCcCh
Confidence 56666666543
No 176
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.59 E-value=25 Score=32.29 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=23.0
Q ss_pred CCcccccccccccCChhhhhhhhhhcCCC
Q 040791 205 KGLFECKACKKVFNSHQALGGHRASHKKV 233 (465)
Q Consensus 205 ~k~y~C~~Cgk~F~~~~~L~~H~~~H~~~ 233 (465)
++.++|++|+-+|....-+..-.|+-.|+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred hceeccCcccchhhhhheeccceeEeccc
Confidence 56789999999999888777777766554
No 177
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.16 E-value=36 Score=37.12 Aligned_cols=31 Identities=16% Similarity=0.233 Sum_probs=21.6
Q ss_pred ccCcccCcCCCc---cchhhhhhhcccCCcccCCCcCcc
Q 040791 14 YCKICKKGFGCG---RALGGHMRAHGIGDESGHIDDDDQ 49 (465)
Q Consensus 14 ~C~~C~k~F~~~---~~L~~H~r~H~~~~~~~~C~~C~~ 49 (465)
.|..||..+.+. ..|..|. ......|..|+.
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~h~-----~~~~l~Ch~CG~ 418 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGLPS-----AGGTPRCRWCGR 418 (665)
T ss_pred EhhhCcCeeECCCCCCceeEec-----CCCeeECCCCcC
Confidence 799999888765 3455543 344678998884
No 178
>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=26.00 E-value=29 Score=23.94 Aligned_cols=25 Identities=24% Similarity=0.281 Sum_probs=14.3
Q ss_pred ceeccCcccCcCCCccchhhhhhhc
Q 040791 11 FKHYCKICKKGFGCGRALGGHMRAH 35 (465)
Q Consensus 11 ~~~~C~~C~k~F~~~~~L~~H~r~H 35 (465)
..|+|+.|+..|=---.+-.|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 5688888888887777777777776
No 179
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=25.75 E-value=21 Score=35.23 Aligned_cols=42 Identities=19% Similarity=0.041 Sum_probs=21.1
Q ss_pred ceeccCcccCcCCCccch---hhhh-hhcccCCcccCCCcCcccCc
Q 040791 11 FKHYCKICKKGFGCGRAL---GGHM-RAHGIGDESGHIDDDDQASD 52 (465)
Q Consensus 11 ~~~~C~~C~k~F~~~~~L---~~H~-r~H~~~~~~~~C~~C~~~f~ 52 (465)
+-+.|..|.+.+...... ..|. ..|..-.+-|.|..|++...
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~ 296 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTI 296 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEE
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeee
Confidence 458999998877666554 3453 34543445689999987644
No 180
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.64 E-value=47 Score=33.55 Aligned_cols=11 Identities=18% Similarity=0.537 Sum_probs=6.2
Q ss_pred ccccccccccC
Q 040791 386 DIYLQPWIGVD 396 (465)
Q Consensus 386 ~~~~~~~~~~~ 396 (465)
.-++|.|-.-+
T Consensus 280 ~~~~P~W~~~s 290 (436)
T KOG2593|consen 280 QKILPEWLAKS 290 (436)
T ss_pred hhcCChHHHhc
Confidence 34567775544
No 181
>PLN02294 cytochrome c oxidase subunit Vb
Probab=25.38 E-value=32 Score=30.11 Aligned_cols=21 Identities=24% Similarity=0.520 Sum_probs=15.6
Q ss_pred ccccCCCCceecCccccccCCc
Q 040791 285 SSSKRKSKVHECSICHRVFSSG 306 (465)
Q Consensus 285 ~~~h~~ekp~~C~~Cgk~F~~~ 306 (465)
...+. .+|+.|++||..|.-.
T Consensus 134 f~L~k-Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 134 FWLEK-GKSFECPVCTQYFELE 154 (174)
T ss_pred EEecC-CCceeCCCCCCEEEEE
Confidence 33444 4899999999999654
No 182
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=25.38 E-value=4e+02 Score=27.11 Aligned_cols=52 Identities=12% Similarity=0.111 Sum_probs=25.6
Q ss_pred cccCcCCCccchhhhhhhcccCCcccCCCcCcccCcCcccCCCCCC-CCCCcce
Q 040791 17 ICKKGFGCGRALGGHMRAHGIGDESGHIDDDDQASDWEDKLGGNVP-PTNKRMY 69 (465)
Q Consensus 17 ~C~k~F~~~~~L~~H~r~H~~~~~~~~C~~C~~~f~~~~~l~~h~~-~~~~~~~ 69 (465)
+|...+........++..+. .+....++.+...+.....+..+.. .++.+++
T Consensus 187 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 239 (396)
T KOG2461|consen 187 ICHISILTSAMSSNSAEVLD-SDSHNLADEESVSLKEQGQLLEPVEVASGPQPV 239 (396)
T ss_pred ccccccccccCCCcchhhcc-cccCCccccccccccccccccccccccCccccc
Confidence 34444444444444444443 4455566666655555555555444 4444444
No 183
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=25.25 E-value=32 Score=35.04 Aligned_cols=22 Identities=27% Similarity=0.668 Sum_probs=20.2
Q ss_pred eecCccccccCCchhhhhhhhh
Q 040791 294 HECSICHRVFSSGQALGGHKRC 315 (465)
Q Consensus 294 ~~C~~Cgk~F~~~~~L~~H~r~ 315 (465)
+-|.+|.|+|.+..+|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999999753
No 184
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.89 E-value=50 Score=22.36 Aligned_cols=16 Identities=19% Similarity=0.164 Sum_probs=12.9
Q ss_pred ceecCccccccCCchh
Q 040791 293 VHECSICHRVFSSGQA 308 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~~ 308 (465)
.|.|+.||..+.-...
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 6999999988776554
No 185
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=24.88 E-value=32 Score=28.13 Aligned_cols=11 Identities=18% Similarity=-0.000 Sum_probs=6.1
Q ss_pred cCCCcCcccCc
Q 040791 42 GHIDDDDQASD 52 (465)
Q Consensus 42 ~~C~~C~~~f~ 52 (465)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 45666665444
No 186
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=24.80 E-value=49 Score=18.60 Aligned_cols=8 Identities=50% Similarity=1.356 Sum_probs=5.7
Q ss_pred cCCccccc
Q 040791 83 VCENCGKE 90 (465)
Q Consensus 83 ~C~~Cgk~ 90 (465)
-|+.||..
T Consensus 15 fC~~CG~~ 22 (23)
T PF13240_consen 15 FCPNCGTP 22 (23)
T ss_pred chhhhCCc
Confidence 38888864
No 187
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=24.70 E-value=37 Score=26.93 Aligned_cols=17 Identities=35% Similarity=0.831 Sum_probs=14.4
Q ss_pred ceecCccccccCCchhh
Q 040791 293 VHECSICHRVFSSGQAL 309 (465)
Q Consensus 293 p~~C~~Cgk~F~~~~~L 309 (465)
||.|.-||..|...+.+
T Consensus 2 pH~CtrCG~vf~~g~~~ 18 (112)
T COG3364 2 PHQCTRCGEVFDDGSEE 18 (112)
T ss_pred CceecccccccccccHH
Confidence 68999999999997543
No 188
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=24.18 E-value=39 Score=34.24 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=23.7
Q ss_pred ccCCCCceecCccc-cccCCchhhhhhhh
Q 040791 287 SKRKSKVHECSICH-RVFSSGQALGGHKR 314 (465)
Q Consensus 287 ~h~~ekp~~C~~Cg-k~F~~~~~L~~H~r 314 (465)
.|-=...|.|.||| +++.-+.++.+|..
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 45567889999999 99999999999963
No 189
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.18 E-value=63 Score=37.37 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=7.4
Q ss_pred cccccccccccC
Q 040791 207 LFECKACKKVFN 218 (465)
Q Consensus 207 ~y~C~~Cgk~F~ 218 (465)
.|.|+.||....
T Consensus 692 vy~CPsCGaev~ 703 (1337)
T PRK14714 692 VYVCPDCGAEVP 703 (1337)
T ss_pred ceeCccCCCccC
Confidence 467777776543
No 190
>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=24.16 E-value=45 Score=31.22 Aligned_cols=90 Identities=13% Similarity=0.201 Sum_probs=53.4
Q ss_pred cCCCceeccCcccCcCCCccchhhhhhhccc-CCcccCCCcCcccCcCcc------cCCCCCCCCCCcceecccCCCCCC
Q 040791 7 QQSNFKHYCKICKKGFGCGRALGGHMRAHGI-GDESGHIDDDDQASDWED------KLGGNVPPTNKRMYALRANPNRLK 79 (465)
Q Consensus 7 ~~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~-~~~~~~C~~C~~~f~~~~------~l~~h~~~~~~~~~~lr~~~~~~~ 79 (465)
..+.+.|+|.+|.. |-....--.|+.+-.+ ....|+|..|.+.=.+.- .+..|++. +.|... ..
T Consensus 137 ~hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrr---Kg~ky~-----k~ 207 (314)
T PF06524_consen 137 DHGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRR---KGFKYE-----KG 207 (314)
T ss_pred cCCCeEEEeecCCC-eeeccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhh---cccccc-----cC
Confidence 45678899999975 4444444466654322 456788988876433210 22333321 111000 11
Q ss_pred CcccCCcccccccChHHHHHhhhhCC
Q 040791 80 SCRVCENCGKEFLSWKSFLEHGKCSS 105 (465)
Q Consensus 80 ~~y~C~~Cgk~F~~~~~L~~H~r~H~ 105 (465)
..++|+.||........|..-.|.|.
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecch
Confidence 23399999999988888888777775
No 191
>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=24.15 E-value=43 Score=21.21 Aligned_cols=11 Identities=18% Similarity=0.636 Sum_probs=6.8
Q ss_pred eccCcccCcCC
Q 040791 13 HYCKICKKGFG 23 (465)
Q Consensus 13 ~~C~~C~k~F~ 23 (465)
..|..||+.|.
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 45666766664
No 192
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=23.87 E-value=34 Score=33.40 Aligned_cols=69 Identities=19% Similarity=0.392 Sum_probs=0.0
Q ss_pred CcceecccCCCCCCCcccCCc--ccccccChHHHHHhhh-hCCCccCcCCCCCCCCCCCCCCCCCCCCCccccccccccC
Q 040791 66 KRMYALRANPNRLKSCRVCEN--CGKEFLSWKSFLEHGK-CSSEDAESLVSSPGSDGEDGTPRRGCGWSKRKRSLRAKVG 142 (465)
Q Consensus 66 ~~~~~lr~~~~~~~~~y~C~~--Cgk~F~~~~~L~~H~r-~H~ge~~~~~~~~~~~~e~~~~c~~c~~~~~~~s~~~~~~ 142 (465)
.++| +|.+ |.+.++....|+.|.- .|.
T Consensus 347 ~~~~-------------~~~vp~~~~~~~n~ng~~~~~~~~h~------------------------------------- 376 (442)
T KOG4124|consen 347 DKPY-------------KCPVPNCDKAYKNQNGLKYHKLHGHC------------------------------------- 376 (442)
T ss_pred cCCC-------------CCCCCcchhhcccCcceeeccccCcC-------------------------------------
Q ss_pred CCCCCchhHHHHHHHHhhccCCCCCCCCCCCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCChhh
Q 040791 143 NCPSSEEEDLANCLMMLSNATVDPLDAEPEESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNSHQA 222 (465)
Q Consensus 143 ~~~~~eee~~a~~l~~l~~~~~~~~~~~~~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~~~~ 222 (465)
+++....+..+.|.-.....|+|.|++|.+.++.-..
T Consensus 377 -------------------------------------------s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~ 413 (442)
T KOG4124|consen 377 -------------------------------------------SPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNG 413 (442)
T ss_pred -------------------------------------------CCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCC
Q ss_pred hhhhh
Q 040791 223 LGGHR 227 (465)
Q Consensus 223 L~~H~ 227 (465)
|.-|+
T Consensus 414 l~~~~ 418 (442)
T KOG4124|consen 414 LKYHR 418 (442)
T ss_pred CCcee
No 193
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=23.61 E-value=38 Score=27.80 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=23.4
Q ss_pred CCCCceecCccccccCCchhhhhhhhh
Q 040791 289 RKSKVHECSICHRVFSSGQALGGHKRC 315 (465)
Q Consensus 289 ~~ekp~~C~~Cgk~F~~~~~L~~H~r~ 315 (465)
.|.--|-|-.|.+-|....+|..|.|+
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 344569999999999999999999875
No 194
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=22.68 E-value=32 Score=22.60 Aligned_cols=16 Identities=19% Similarity=0.490 Sum_probs=10.7
Q ss_pred CceecCccccccCCch
Q 040791 292 KVHECSICHRVFSSGQ 307 (465)
Q Consensus 292 kp~~C~~Cgk~F~~~~ 307 (465)
-||+|+.|++.|=..-
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5899999999997654
No 196
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=22.33 E-value=57 Score=35.27 Aligned_cols=80 Identities=13% Similarity=0.085 Sum_probs=45.3
Q ss_pred ccCcccCcCCCccchhhhhhhcccCCccc-CCCcCcccCcCcccCCCCCCCCCCcceecccCCCCCCCcccCCccccccc
Q 040791 14 YCKICKKGFGCGRALGGHMRAHGIGDESG-HIDDDDQASDWEDKLGGNVPPTNKRMYALRANPNRLKSCRVCENCGKEFL 92 (465)
Q Consensus 14 ~C~~C~k~F~~~~~L~~H~r~H~~~~~~~-~C~~C~~~f~~~~~l~~h~~~~~~~~~~lr~~~~~~~~~y~C~~Cgk~F~ 92 (465)
.|+.|-+-+....+=+-| -|| .|..||..|+--..+.-....+....|. .|+.|.+.|.
T Consensus 103 ~C~~Cl~Ei~dp~~rrY~--------YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~------------lC~~C~~EY~ 162 (750)
T COG0068 103 TCEDCLEEIFDPNSRRYL--------YPFINCTNCGPRFTIIEALPYDRENTSMADFP------------LCPFCDKEYK 162 (750)
T ss_pred hhHHHHHHhcCCCCccee--------ccccccCCCCcceeeeccCCCCcccCccccCc------------CCHHHHHHhc
Confidence 577776655544332111 122 5888888887544443332233333332 6899988887
Q ss_pred ChHHHHHhhhhCCCccCcCCCCCCCCCCCCCCCCCCCCCc
Q 040791 93 SWKSFLEHGKCSSEDAESLVSSPGSDGEDGTPRRGCGWSK 132 (465)
Q Consensus 93 ~~~~L~~H~r~H~ge~~~~~~~~~~~~e~~~~c~~c~~~~ 132 (465)
...+ +|-|. .+..|+.||...
T Consensus 163 dP~n----RRfHA---------------Qp~aCp~CGP~~ 183 (750)
T COG0068 163 DPLN----RRFHA---------------QPIACPKCGPHL 183 (750)
T ss_pred Cccc----ccccc---------------ccccCcccCCCe
Confidence 7654 33343 346799998764
No 197
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=22.23 E-value=40 Score=27.64 Aligned_cols=11 Identities=9% Similarity=0.099 Sum_probs=6.1
Q ss_pred cCCCcCcccCc
Q 040791 42 GHIDDDDQASD 52 (465)
Q Consensus 42 ~~C~~C~~~f~ 52 (465)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 45666665444
No 198
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.18 E-value=43 Score=32.72 Aligned_cols=27 Identities=22% Similarity=0.365 Sum_probs=23.1
Q ss_pred ccCCCCceecCccc-cccCCchhhhhhh
Q 040791 287 SKRKSKVHECSICH-RVFSSGQALGGHK 313 (465)
Q Consensus 287 ~h~~ekp~~C~~Cg-k~F~~~~~L~~H~ 313 (465)
.|.-.+.|+|.||| +++.-+..+.+|.
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhh
Confidence 46668899999999 8888888888885
No 199
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.95 E-value=62 Score=36.47 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=8.7
Q ss_pred ceeccCcccCcC
Q 040791 11 FKHYCKICKKGF 22 (465)
Q Consensus 11 ~~~~C~~C~k~F 22 (465)
....|..||...
T Consensus 625 g~RfCpsCG~~t 636 (1121)
T PRK04023 625 GRRKCPSCGKET 636 (1121)
T ss_pred cCccCCCCCCcC
Confidence 346888888873
No 200
>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=21.61 E-value=42 Score=21.54 Aligned_cols=23 Identities=30% Similarity=0.576 Sum_probs=9.1
Q ss_pred ceeccCcccCcCCCcc-ch-hhhhh
Q 040791 11 FKHYCKICKKGFGCGR-AL-GGHMR 33 (465)
Q Consensus 11 ~~~~C~~C~k~F~~~~-~L-~~H~r 33 (465)
++|-|++|..-|..-+ .- +.|.+
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 4689999999995433 33 45544
No 201
>PF07203 DUF1412: Protein of unknown function (DUF1412); InterPro: IPR009853 This family consists of several Caenorhabditis elegans proteins of around 70-75 residues in length. The function of this family is unknown.
Probab=21.45 E-value=37 Score=23.07 Aligned_cols=13 Identities=46% Similarity=0.787 Sum_probs=8.7
Q ss_pred ccCCCC--CCceeee
Q 040791 442 NISGGS--SPWLQVG 454 (465)
Q Consensus 442 ~~~~~~--~~~~~~~ 454 (465)
+|.|+. .-|.||=
T Consensus 26 ~~~GgptslGWaQVp 40 (53)
T PF07203_consen 26 NLWGGPTSLGWAQVP 40 (53)
T ss_pred ccccCccccchhhCc
Confidence 566754 4499984
No 202
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.27 E-value=61 Score=18.67 Aligned_cols=8 Identities=50% Similarity=1.406 Sum_probs=5.7
Q ss_pred cCCccccc
Q 040791 83 VCENCGKE 90 (465)
Q Consensus 83 ~C~~Cgk~ 90 (465)
-|+.||..
T Consensus 18 fC~~CG~~ 25 (26)
T PF13248_consen 18 FCPNCGAK 25 (26)
T ss_pred cChhhCCC
Confidence 38888864
No 203
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=21.12 E-value=41 Score=25.55 Aligned_cols=31 Identities=29% Similarity=0.730 Sum_probs=22.3
Q ss_pred CCcccccchhhhhhccccccCCccccccccccCCCcccccccccccCC
Q 040791 172 EESCASASKEEERRNSMNFIGPISMDKAKGVANKGLFECKACKKVFNS 219 (465)
Q Consensus 172 ~~~C~~c~k~f~~~~~l~~~~~~~~~~~~~~~~~k~y~C~~Cgk~F~~ 219 (465)
.|.|+.||+.-..+.. .+.+.|..|.|+|.-
T Consensus 36 ky~CsfCGK~~vKR~A-----------------vGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRKA-----------------VGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhcchhhhhhhc-----------------eeEEecCCccceecc
Confidence 3889999987654443 336889999888854
No 204
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=21.03 E-value=50 Score=33.49 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=23.2
Q ss_pred ccccCCCcccccccc-cccCChhhhhhhh
Q 040791 200 KGVANKGLFECKACK-KVFNSHQALGGHR 227 (465)
Q Consensus 200 ~~~~~~k~y~C~~Cg-k~F~~~~~L~~H~ 227 (465)
+.|.-...|.|.+|| +++.-+.++.+|-
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHh
Confidence 445456679999999 9999999999995
No 205
>COG4640 Predicted membrane protein [Function unknown]
Probab=21.02 E-value=60 Score=32.37 Aligned_cols=17 Identities=35% Similarity=0.737 Sum_probs=14.2
Q ss_pred cCCcccccccChHHHHH
Q 040791 83 VCENCGKEFLSWKSFLE 99 (465)
Q Consensus 83 ~C~~Cgk~F~~~~~L~~ 99 (465)
.|+.||..|....++..
T Consensus 17 qC~qCG~~~t~~~sqan 33 (465)
T COG4640 17 QCTQCGHKFTSRQSQAN 33 (465)
T ss_pred cccccCCcCCchhhhhh
Confidence 79999999998877655
No 206
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=20.50 E-value=42 Score=22.71 Aligned_cols=13 Identities=23% Similarity=0.805 Sum_probs=10.5
Q ss_pred eecCccccccCCc
Q 040791 294 HECSICHRVFSSG 306 (465)
Q Consensus 294 ~~C~~Cgk~F~~~ 306 (465)
|+|.+||.+|.-.
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 8899999888544
No 207
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=20.40 E-value=62 Score=22.89 Aligned_cols=16 Identities=19% Similarity=0.279 Sum_probs=11.6
Q ss_pred CCceecCccccccCCc
Q 040791 291 SKVHECSICHRVFSSG 306 (465)
Q Consensus 291 ekp~~C~~Cgk~F~~~ 306 (465)
.-++.|..||...-.+
T Consensus 35 ~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 35 GDVIRCRECGYRILYK 50 (62)
T ss_pred CCcEehhhcchHHHHH
Confidence 4679999999765433
No 208
>KOG4226 consensus Adaptor protein NCK/Dock, contains SH2 and SH3 domains [Signal transduction mechanisms]
Probab=20.30 E-value=93 Score=29.44 Aligned_cols=86 Identities=26% Similarity=0.193 Sum_probs=52.4
Q ss_pred cccccCCCCCCccccCCCccccccccCcccc------cccccccCcccCCcccccccccccccccccccCcccchhhhh-
Q 040791 358 KLDLNLPAPEDDHARGGRREHVSMEVSTDIY------LQPWIGVDAKEKDIDHHQHNQEINCTTSIQNNNVDDEADSKV- 430 (465)
Q Consensus 358 ~~dlnlpa~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 430 (465)
..|||+||-..-...++|.+.++|.--..++ --||-|.. |..+|=-.+|-+++|.||++
T Consensus 103 ~~~~~t~AvVKf~Y~a~~eDELsLtKGtrv~vmEKssDGWWrG~~--------------ng~VGWFPSNYv~E~~ds~~g 168 (379)
T KOG4226|consen 103 IYDLNTPAVVKFNYVAEREDELSLTKGTRVTVMEKSSDGWWRGSY--------------NGQVGWFPSNYVTEEVDSAAG 168 (379)
T ss_pred hhhcCCceEEEEeeccccccccccccCcEEEEEEeccCcceeccc--------------CCeeccccccceehhcccccc
Confidence 7899999987777777777777766555554 35898876 33344444455666667762
Q ss_pred -hhhhcccccc-cccCCCCCCceeeeecc
Q 040791 431 -KLAKLSEIKD-MNISGGSSPWLQVGIGS 457 (465)
Q Consensus 431 -~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 457 (465)
.-.-|+.-+. |-..|-.+-=|||=.++
T Consensus 169 d~~s~~~~~~~A~a~n~~~s~vl~vVvaL 197 (379)
T KOG4226|consen 169 DSPSFLSLRKAASASNGQGSRVLHVVVAL 197 (379)
T ss_pred CCccceecchhhcccCCCCceEEEEEEEE
Confidence 2222443333 44455555677776654
No 209
>PRK12496 hypothetical protein; Provisional
Probab=20.17 E-value=58 Score=28.58 Aligned_cols=11 Identities=0% Similarity=-0.233 Sum_probs=9.0
Q ss_pred cCCCcCcccCc
Q 040791 42 GHIDDDDQASD 52 (465)
Q Consensus 42 ~~C~~C~~~f~ 52 (465)
|.|.-|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 77888888875
No 210
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=20.17 E-value=39 Score=23.38 Aligned_cols=13 Identities=23% Similarity=0.713 Sum_probs=7.4
Q ss_pred ecCccccccCCch
Q 040791 295 ECSICHRVFSSGQ 307 (465)
Q Consensus 295 ~C~~Cgk~F~~~~ 307 (465)
.|++|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 9999999998643
No 211
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.15 E-value=55 Score=33.24 Aligned_cols=17 Identities=12% Similarity=-0.150 Sum_probs=8.3
Q ss_pred cccccccChHHHHHhhh
Q 040791 86 NCGKEFLSWKSFLEHGK 102 (465)
Q Consensus 86 ~Cgk~F~~~~~L~~H~r 102 (465)
.=|-.|.....|..-+.
T Consensus 215 l~GIRg~~p~~l~~a~~ 231 (421)
T COG1571 215 LYGIRGAVPEVLLKAMS 231 (421)
T ss_pred EEEEecCCHHHHHHHHH
Confidence 34555555555544443
Done!