Query 048287
Match_columns 365
No_of_seqs 355 out of 2970
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 08:08:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048287hhsearch_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 3.3E-28 7.2E-33 219.4 4.9 134 29-184 127-265 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 4.6E-22 1E-26 179.8 5.0 124 57-199 127-252 (279)
3 KOG1074 Transcriptional repres 99.7 2.3E-19 4.9E-24 181.6 0.0 79 101-186 605-692 (958)
4 KOG3576 Ovo and related transc 99.7 3.5E-18 7.6E-23 147.5 6.1 114 56-189 113-239 (267)
5 KOG3608 Zn finger proteins [Ge 99.7 3.2E-17 6.9E-22 152.0 2.5 176 34-216 181-375 (467)
6 KOG1074 Transcriptional repres 99.6 3.6E-17 7.9E-22 165.8 2.7 55 30-84 603-657 (958)
7 KOG3576 Ovo and related transc 99.6 6.5E-16 1.4E-20 133.6 1.2 111 30-160 115-237 (267)
8 KOG3623 Homeobox transcription 99.5 1.5E-15 3.2E-20 151.9 1.6 107 60-184 210-331 (1007)
9 KOG3623 Homeobox transcription 99.5 7.8E-15 1.7E-19 146.8 1.8 120 32-158 210-331 (1007)
10 KOG3608 Zn finger proteins [Ge 99.4 3.9E-14 8.4E-19 131.7 1.9 159 22-188 197-378 (467)
11 PLN03086 PRLI-interacting fact 99.3 3.3E-12 7.1E-17 128.8 7.2 105 58-188 451-566 (567)
12 PHA00733 hypothetical protein 99.0 4.1E-10 8.9E-15 93.6 4.1 54 134-188 71-125 (128)
13 PHA00733 hypothetical protein 99.0 3.9E-10 8.5E-15 93.8 3.4 54 98-160 70-124 (128)
14 PLN03086 PRLI-interacting fact 98.9 9.9E-10 2.1E-14 111.0 5.9 104 30-160 451-565 (567)
15 KOG3993 Transcription factor ( 98.8 1.1E-09 2.3E-14 104.6 1.0 154 27-188 262-484 (500)
16 PHA02768 hypothetical protein; 98.6 2.9E-08 6.3E-13 69.0 2.3 43 102-153 6-48 (55)
17 PHA02768 hypothetical protein; 98.6 2.5E-08 5.5E-13 69.3 1.9 44 60-125 5-48 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.5 9.3E-08 2E-12 56.7 2.1 26 123-148 1-26 (26)
19 KOG3993 Transcription factor ( 98.2 1.8E-07 3.8E-12 89.7 -0.3 85 101-192 267-386 (500)
20 PHA00616 hypothetical protein 98.0 2.7E-06 5.8E-11 56.4 1.1 34 60-106 1-34 (44)
21 COG5189 SFP1 Putative transcri 97.9 8.2E-06 1.8E-10 75.7 3.5 71 58-158 347-420 (423)
22 PHA00732 hypothetical protein 97.9 1E-05 2.2E-10 61.4 2.7 23 60-82 1-23 (79)
23 PF13465 zf-H2C2_2: Zinc-finge 97.8 1.2E-05 2.5E-10 47.7 1.9 26 75-120 1-26 (26)
24 PHA00616 hypothetical protein 97.8 8.5E-06 1.8E-10 54.0 1.4 39 101-146 1-39 (44)
25 PF00096 zf-C2H2: Zinc finger, 97.8 1.5E-05 3.2E-10 45.6 2.0 23 61-83 1-23 (23)
26 PHA00732 hypothetical protein 97.7 3.4E-05 7.5E-10 58.5 2.8 45 101-158 1-46 (79)
27 PF05605 zf-Di19: Drought indu 97.6 7.6E-05 1.6E-09 52.4 3.9 52 60-132 2-53 (54)
28 COG5189 SFP1 Putative transcri 97.4 6.8E-05 1.5E-09 69.8 1.2 72 98-184 346-420 (423)
29 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00016 3.5E-09 41.2 2.1 24 61-84 1-24 (24)
30 PF00096 zf-C2H2: Zinc finger, 97.2 0.00021 4.5E-09 40.7 2.0 22 164-185 1-23 (23)
31 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00026 5.6E-09 42.0 1.9 25 60-84 1-25 (27)
32 PF05605 zf-Di19: Drought indu 97.1 0.0004 8.6E-09 48.7 2.8 47 102-158 3-51 (54)
33 PF13894 zf-C2H2_4: C2H2-type 96.9 0.00074 1.6E-08 38.4 2.2 23 164-186 1-24 (24)
34 PF13912 zf-C2H2_6: C2H2-type 96.8 0.00055 1.2E-08 40.6 1.3 24 163-186 1-25 (27)
35 PF12756 zf-C2H2_2: C2H2 type 96.7 0.00068 1.5E-08 53.1 1.4 19 63-81 2-20 (100)
36 PF12756 zf-C2H2_2: C2H2 type 96.7 0.0011 2.4E-08 51.9 2.6 68 115-186 6-74 (100)
37 COG5048 FOG: Zn-finger [Genera 96.6 0.0021 4.6E-08 63.1 4.6 54 31-84 288-347 (467)
38 smart00355 ZnF_C2H2 zinc finge 96.5 0.0015 3.2E-08 37.6 1.7 24 61-84 1-24 (26)
39 KOG2231 Predicted E3 ubiquitin 96.4 0.0042 9E-08 64.4 5.1 15 69-83 123-138 (669)
40 KOG1146 Homeobox protein [Gene 96.1 0.0053 1.1E-07 67.2 4.2 145 34-185 438-641 (1406)
41 PF12874 zf-met: Zinc-finger o 96.0 0.004 8.7E-08 36.0 1.6 23 61-83 1-23 (25)
42 PRK04860 hypothetical protein; 95.8 0.0056 1.2E-07 52.9 2.4 40 100-150 118-157 (160)
43 PF09237 GAGA: GAGA factor; I 95.7 0.011 2.4E-07 40.2 2.9 29 56-84 20-48 (54)
44 smart00355 ZnF_C2H2 zinc finge 95.5 0.011 2.4E-07 33.8 2.0 22 164-185 1-23 (26)
45 KOG2231 Predicted E3 ubiquitin 95.2 0.02 4.4E-07 59.4 4.4 125 32-184 115-261 (669)
46 PF12171 zf-C2H2_jaz: Zinc-fin 94.7 0.008 1.7E-07 35.6 -0.1 24 60-83 1-24 (27)
47 PF09237 GAGA: GAGA factor; I 94.7 0.045 9.7E-07 37.4 3.3 32 98-136 21-52 (54)
48 PF13909 zf-H2C2_5: C2H2-type 94.2 0.041 8.9E-07 31.4 2.1 22 164-186 1-23 (24)
49 PRK04860 hypothetical protein; 94.2 0.035 7.6E-07 47.9 2.6 39 59-121 118-156 (160)
50 PF12171 zf-C2H2_jaz: Zinc-fin 93.8 0.034 7.3E-07 32.9 1.3 22 137-158 2-23 (27)
51 COG5048 FOG: Zn-finger [Genera 93.8 0.036 7.9E-07 54.3 2.3 107 59-185 288-411 (467)
52 PF12874 zf-met: Zinc-finger o 93.8 0.036 7.9E-07 31.9 1.4 21 164-184 1-22 (25)
53 KOG1146 Homeobox protein [Gene 93.6 0.028 6.1E-07 61.8 1.1 78 98-185 462-541 (1406)
54 COG5236 Uncharacterized conser 93.5 0.042 9E-07 52.2 1.9 74 103-188 222-307 (493)
55 PF13909 zf-H2C2_5: C2H2-type 93.2 0.089 1.9E-06 30.0 2.4 23 102-132 1-23 (24)
56 PF13913 zf-C2HC_2: zinc-finge 91.8 0.12 2.7E-06 30.0 1.7 21 61-82 3-23 (25)
57 KOG2482 Predicted C2H2-type Zn 91.7 0.16 3.4E-06 48.3 3.3 113 59-186 194-358 (423)
58 smart00451 ZnF_U1 U1-like zinc 91.1 0.16 3.5E-06 31.6 1.9 25 59-83 2-26 (35)
59 PF13913 zf-C2HC_2: zinc-finge 90.5 0.21 4.5E-06 29.0 1.8 21 164-185 3-24 (25)
60 KOG4173 Alpha-SNAP protein [In 90.2 0.11 2.4E-06 45.9 0.7 83 98-188 76-172 (253)
61 KOG2785 C2H2-type Zn-finger pr 88.9 0.68 1.5E-05 44.9 5.0 48 137-184 167-242 (390)
62 KOG2893 Zn finger protein [Gen 88.6 0.12 2.5E-06 46.8 -0.3 47 34-84 12-59 (341)
63 smart00451 ZnF_U1 U1-like zinc 87.4 0.47 1E-05 29.4 2.0 23 163-185 3-26 (35)
64 COG4049 Uncharacterized protei 86.6 0.34 7.3E-06 33.7 1.1 29 159-187 13-42 (65)
65 KOG2893 Zn finger protein [Gen 86.0 0.28 6E-06 44.4 0.5 43 104-157 13-55 (341)
66 PRK00464 nrdR transcriptional 84.6 0.47 1E-05 40.7 1.2 44 33-77 1-45 (154)
67 PF09538 FYDLN_acid: Protein o 84.6 0.67 1.4E-05 37.3 2.0 33 30-73 7-39 (108)
68 KOG2186 Cell growth-regulating 84.3 0.57 1.2E-05 42.9 1.7 47 102-158 4-50 (276)
69 COG5236 Uncharacterized conser 82.4 1.1 2.4E-05 42.8 2.8 26 102-132 152-177 (493)
70 PHA00626 hypothetical protein 80.9 0.99 2.1E-05 31.5 1.4 36 34-74 2-37 (59)
71 TIGR00622 ssl1 transcription f 80.7 2.8 6.1E-05 33.8 4.2 46 139-185 58-104 (112)
72 KOG4173 Alpha-SNAP protein [In 75.8 1.1 2.4E-05 39.7 0.7 79 58-159 77-170 (253)
73 PF09986 DUF2225: Uncharacteri 75.6 1.3 2.9E-05 40.1 1.1 42 134-175 3-61 (214)
74 KOG2482 Predicted C2H2-type Zn 75.5 6.2 0.00013 37.9 5.5 83 100-188 143-305 (423)
75 cd00350 rubredoxin_like Rubred 75.4 2 4.4E-05 26.6 1.6 10 135-144 16-25 (33)
76 PF12013 DUF3505: Protein of u 74.4 3.6 7.8E-05 32.9 3.3 25 163-187 80-109 (109)
77 COG4049 Uncharacterized protei 74.3 0.99 2.1E-05 31.4 -0.0 29 132-160 13-42 (65)
78 TIGR02300 FYDLN_acid conserved 74.2 2.2 4.8E-05 35.0 2.0 37 30-77 7-43 (129)
79 COG2888 Predicted Zn-ribbon RN 74.1 1.3 2.9E-05 31.3 0.6 37 27-68 22-58 (61)
80 PF02892 zf-BED: BED zinc fing 73.6 3 6.5E-05 27.4 2.2 25 57-81 13-41 (45)
81 PRK00464 nrdR transcriptional 71.9 1.6 3.5E-05 37.4 0.7 18 136-153 28-45 (154)
82 PRK09678 DNA-binding transcrip 70.1 2 4.3E-05 31.9 0.7 42 33-76 2-45 (72)
83 smart00614 ZnF_BED BED zinc fi 68.1 3.6 7.9E-05 27.9 1.7 25 60-84 18-48 (50)
84 PF12013 DUF3505: Protein of u 67.3 11 0.00024 30.1 4.6 25 58-83 9-33 (109)
85 PF13719 zinc_ribbon_5: zinc-r 64.8 4.2 9.2E-05 25.9 1.4 12 135-146 24-35 (37)
86 KOG2186 Cell growth-regulating 64.5 3.1 6.8E-05 38.2 1.0 47 137-185 4-51 (276)
87 PF09986 DUF2225: Uncharacteri 64.0 2.7 5.8E-05 38.1 0.5 44 30-73 3-61 (214)
88 PRK03564 formate dehydrogenase 63.7 4.9 0.00011 38.5 2.2 12 98-109 209-220 (309)
89 KOG2071 mRNA cleavage and poly 62.4 4.6 0.0001 41.5 1.9 28 57-84 415-442 (579)
90 PF13717 zinc_ribbon_4: zinc-r 62.2 5.6 0.00012 25.2 1.6 34 33-71 3-36 (36)
91 TIGR00244 transcriptional regu 61.9 4.1 8.9E-05 34.5 1.2 44 34-77 2-45 (147)
92 KOG4124 Putative transcription 61.7 2.2 4.7E-05 41.0 -0.6 29 54-83 207-236 (442)
93 TIGR02098 MJ0042_CXXC MJ0042 f 61.2 4.3 9.2E-05 25.7 0.9 34 33-71 3-36 (38)
94 PF04959 ARS2: Arsenite-resist 61.1 2 4.3E-05 38.9 -0.9 31 159-189 73-104 (214)
95 PF09538 FYDLN_acid: Protein o 60.2 5.3 0.00011 32.1 1.5 14 162-175 25-39 (108)
96 COG1592 Rubrerythrin [Energy p 59.1 6.3 0.00014 34.2 1.9 23 101-143 134-156 (166)
97 PF10571 UPF0547: Uncharacteri 58.8 7 0.00015 22.9 1.5 25 33-71 1-25 (26)
98 KOG4377 Zn-finger protein [Gen 58.2 13 0.00028 36.6 4.0 121 59-188 270-429 (480)
99 COG1327 Predicted transcriptio 57.0 5.7 0.00012 33.7 1.2 44 34-77 2-45 (156)
100 COG4530 Uncharacterized protei 55.9 8.9 0.00019 30.6 2.1 37 30-78 7-43 (129)
101 KOG4167 Predicted DNA-binding 55.6 3.9 8.4E-05 43.0 -0.0 27 58-84 790-816 (907)
102 PRK14890 putative Zn-ribbon RN 55.4 6.4 0.00014 27.9 1.1 34 30-68 23-56 (59)
103 smart00531 TFIIE Transcription 55.0 12 0.00026 31.7 3.0 35 135-172 98-133 (147)
104 PRK04023 DNA polymerase II lar 54.8 11 0.00025 41.3 3.3 11 59-69 625-635 (1121)
105 KOG2907 RNA polymerase I trans 54.1 12 0.00025 30.2 2.4 45 28-72 70-114 (116)
106 TIGR00373 conserved hypothetic 53.9 11 0.00023 32.5 2.4 33 134-174 107-140 (158)
107 smart00734 ZnF_Rad18 Rad18-lik 50.9 11 0.00024 22.0 1.5 20 61-81 2-21 (26)
108 PRK06266 transcription initiat 50.6 13 0.00027 32.8 2.4 35 134-176 115-150 (178)
109 smart00659 RPOLCX RNA polymera 50.5 7.9 0.00017 25.7 0.9 28 32-70 2-29 (44)
110 TIGR01562 FdhE formate dehydro 50.2 14 0.0003 35.4 2.8 12 98-109 207-218 (305)
111 PF05443 ROS_MUCR: ROS/MUCR tr 50.0 10 0.00022 31.7 1.6 31 162-195 71-102 (132)
112 COG1997 RPL43A Ribosomal prote 49.9 8.6 0.00019 29.5 1.1 12 136-147 53-64 (89)
113 PF15135 UPF0515: Uncharacteri 49.8 21 0.00045 32.9 3.7 76 72-174 91-167 (278)
114 KOG2593 Transcription initiati 49.8 14 0.00031 36.7 2.8 37 133-171 125-162 (436)
115 TIGR00622 ssl1 transcription f 49.0 25 0.00054 28.4 3.7 51 32-84 55-105 (112)
116 PF04216 FdhE: Protein involve 48.5 2.9 6.3E-05 39.7 -2.1 54 98-172 194-248 (290)
117 PF04959 ARS2: Arsenite-resist 47.7 16 0.00034 33.2 2.6 30 133-162 74-104 (214)
118 cd00729 rubredoxin_SM Rubredox 47.3 14 0.00031 23.0 1.6 10 135-144 17-26 (34)
119 COG1996 RPC10 DNA-directed RNA 47.1 7.7 0.00017 26.5 0.4 29 31-69 5-33 (49)
120 TIGR00373 conserved hypothetic 47.1 22 0.00047 30.6 3.3 34 96-145 104-137 (158)
121 PRK00398 rpoP DNA-directed RNA 46.1 13 0.00029 24.6 1.5 14 59-72 2-15 (46)
122 COG5188 PRP9 Splicing factor 3 45.5 16 0.00035 35.2 2.4 26 59-84 237-264 (470)
123 smart00440 ZnF_C2C2 C2C2 Zinc 45.4 11 0.00023 24.5 0.8 37 33-71 1-39 (40)
124 PF06524 NOA36: NOA36 protein; 45.3 10 0.00022 35.1 1.0 26 160-185 206-232 (314)
125 TIGR02300 FYDLN_acid conserved 44.2 15 0.00033 30.2 1.8 29 137-175 10-39 (129)
126 PRK09678 DNA-binding transcrip 43.8 9.9 0.00022 28.2 0.6 14 161-174 25-41 (72)
127 PRK06266 transcription initiat 43.7 13 0.00028 32.6 1.5 34 97-146 113-146 (178)
128 PF13240 zinc_ribbon_2: zinc-r 43.5 14 0.00029 21.0 1.0 7 63-69 16-22 (23)
129 PF14353 CpXC: CpXC protein 43.1 5.5 0.00012 32.8 -1.0 51 33-83 2-61 (128)
130 PF01096 TFIIS_C: Transcriptio 43.0 5.9 0.00013 25.6 -0.6 13 59-71 27-39 (39)
131 smart00531 TFIIE Transcription 43.0 21 0.00046 30.2 2.6 40 96-146 94-133 (147)
132 KOG2636 Splicing factor 3a, su 42.5 15 0.00032 36.7 1.7 29 52-80 393-422 (497)
133 KOG2807 RNA polymerase II tran 40.7 81 0.0017 30.4 6.2 115 23-185 235-368 (378)
134 PF09845 DUF2072: Zn-ribbon co 39.7 19 0.0004 29.9 1.6 15 32-46 1-15 (131)
135 PF07282 OrfB_Zn_ribbon: Putat 39.3 23 0.0005 25.5 2.0 35 31-75 27-61 (69)
136 COG3677 Transposase and inacti 38.8 16 0.00035 30.3 1.2 38 32-74 30-67 (129)
137 KOG2785 C2H2-type Zn-finger pr 38.4 28 0.00061 34.0 2.9 50 102-158 167-242 (390)
138 KOG4167 Predicted DNA-binding 38.3 12 0.00026 39.6 0.4 27 163-189 792-819 (907)
139 cd00730 rubredoxin Rubredoxin; 38.1 18 0.00039 24.8 1.1 37 32-68 1-42 (50)
140 PRK04023 DNA polymerase II lar 37.7 53 0.0012 36.4 5.0 8 61-68 639-646 (1121)
141 PF02176 zf-TRAF: TRAF-type zi 36.8 19 0.00041 25.0 1.2 28 121-148 23-54 (60)
142 COG1198 PriA Primosomal protei 36.8 24 0.00051 38.0 2.3 18 90-107 464-481 (730)
143 PF11931 DUF3449: Domain of un 36.2 12 0.00026 33.4 0.0 29 52-80 93-122 (196)
144 COG5151 SSL1 RNA polymerase II 36.1 32 0.0007 32.7 2.8 48 138-186 364-412 (421)
145 TIGR02605 CxxC_CxxC_SSSS putat 35.9 12 0.00027 25.3 0.0 30 101-144 5-34 (52)
146 smart00661 RPOL9 RNA polymeras 35.6 29 0.00064 23.3 1.9 14 59-72 19-32 (52)
147 PF03811 Zn_Tnp_IS1: InsA N-te 35.4 27 0.00059 22.1 1.5 32 32-67 5-36 (36)
148 KOG4124 Putative transcription 34.6 8 0.00017 37.2 -1.4 23 58-80 347-371 (442)
149 PF09416 UPF1_Zn_bind: RNA hel 34.6 58 0.0013 27.8 3.9 49 59-109 13-68 (152)
150 PF12760 Zn_Tnp_IS1595: Transp 34.5 57 0.0012 21.6 3.1 26 137-170 19-45 (46)
151 COG1571 Predicted DNA-binding 34.2 22 0.00048 35.4 1.5 29 138-176 352-381 (421)
152 COG1592 Rubrerythrin [Energy p 34.1 22 0.00047 30.9 1.3 24 32-68 134-157 (166)
153 smart00834 CxxC_CXXC_SSSS Puta 33.8 14 0.0003 23.5 0.0 10 135-144 25-34 (41)
154 KOG3408 U1-like Zn-finger-cont 33.8 24 0.00053 28.8 1.4 28 56-83 53-80 (129)
155 PF08790 zf-LYAR: LYAR-type C2 33.6 19 0.00041 21.6 0.6 19 138-157 2-20 (28)
156 PF01780 Ribosomal_L37ae: Ribo 33.5 14 0.0003 28.6 0.0 10 136-145 35-44 (90)
157 PTZ00303 phosphatidylinositol 32.5 27 0.00058 37.4 1.8 13 102-121 461-473 (1374)
158 COG3357 Predicted transcriptio 31.8 23 0.0005 27.4 0.9 14 135-148 57-70 (97)
159 COG4957 Predicted transcriptio 31.4 30 0.00065 28.8 1.6 23 59-84 75-97 (148)
160 COG3091 SprT Zn-dependent meta 31.3 25 0.00053 30.0 1.1 32 135-171 116-149 (156)
161 PF09963 DUF2197: Uncharacteri 31.2 19 0.00042 25.2 0.4 10 138-147 4-13 (56)
162 PF08274 PhnA_Zn_Ribbon: PhnA 30.9 26 0.00056 21.3 0.9 25 34-69 4-28 (30)
163 PF10013 DUF2256: Uncharacteri 30.6 39 0.00084 22.3 1.7 16 62-77 10-25 (42)
164 PTZ00255 60S ribosomal protein 30.6 22 0.00047 27.6 0.6 12 136-147 54-65 (90)
165 smart00731 SprT SprT homologue 30.5 27 0.00058 29.4 1.2 32 136-173 112-144 (146)
166 PF07754 DUF1610: Domain of un 30.4 22 0.00047 20.5 0.4 10 59-68 15-24 (24)
167 PRK05978 hypothetical protein; 30.2 32 0.0007 29.3 1.7 33 32-73 33-65 (148)
168 COG5188 PRP9 Splicing factor 3 30.2 29 0.00062 33.6 1.5 29 52-80 366-395 (470)
169 PF13453 zf-TFIIB: Transcripti 29.9 35 0.00075 22.0 1.4 37 34-78 1-37 (41)
170 COG4957 Predicted transcriptio 29.6 32 0.0007 28.6 1.5 28 164-194 77-105 (148)
171 PF07975 C1_4: TFIIH C1-like d 29.3 15 0.00032 25.4 -0.5 27 58-84 19-45 (51)
172 KOG1280 Uncharacterized conser 29.0 28 0.0006 33.7 1.1 30 134-163 77-107 (381)
173 PF15135 UPF0515: Uncharacteri 28.9 24 0.00053 32.5 0.7 59 58-149 110-168 (278)
174 PF14446 Prok-RING_1: Prokaryo 28.6 34 0.00074 23.8 1.3 30 31-72 4-33 (54)
175 PF05443 ROS_MUCR: ROS/MUCR tr 28.4 40 0.00086 28.1 1.9 28 98-135 69-96 (132)
176 PF01927 Mut7-C: Mut7-C RNAse 28.3 51 0.0011 27.8 2.6 48 32-79 91-143 (147)
177 PRK04351 hypothetical protein; 28.1 30 0.00066 29.4 1.2 32 136-174 112-144 (149)
178 PRK03564 formate dehydrogenase 28.0 43 0.00093 32.1 2.3 39 29-70 184-222 (309)
179 TIGR00280 L37a ribosomal prote 27.9 23 0.00051 27.4 0.4 12 136-147 53-64 (91)
180 PF06220 zf-U1: U1 zinc finger 27.6 41 0.00089 21.5 1.4 22 59-80 2-25 (38)
181 PRK14714 DNA polymerase II lar 27.5 49 0.0011 37.5 2.9 10 60-69 667-676 (1337)
182 PF15269 zf-C2H2_7: Zinc-finge 27.4 61 0.0013 21.6 2.2 25 59-83 19-43 (54)
183 COG3364 Zn-ribbon containing p 27.0 39 0.00084 26.7 1.5 14 32-45 2-15 (112)
184 PF10263 SprT-like: SprT-like 26.7 26 0.00055 29.6 0.5 31 136-173 123-154 (157)
185 KOG2593 Transcription initiati 26.1 27 0.00058 34.8 0.6 39 97-145 124-162 (436)
186 PRK03824 hypA hydrogenase nick 26.0 25 0.00055 29.3 0.3 40 30-69 68-116 (135)
187 PF09723 Zn-ribbon_8: Zinc rib 25.8 30 0.00064 22.6 0.5 15 60-74 5-19 (42)
188 smart00154 ZnF_AN1 AN1-like Zi 24.7 34 0.00074 22.0 0.7 14 60-73 12-25 (39)
189 PF03604 DNA_RNApol_7kD: DNA d 24.6 46 0.00099 20.5 1.2 10 136-145 17-26 (32)
190 KOG0320 Predicted E3 ubiquitin 24.5 55 0.0012 28.7 2.1 14 96-109 126-139 (187)
191 PF09845 DUF2072: Zn-ribbon co 24.4 47 0.001 27.6 1.6 15 136-150 1-15 (131)
192 PF01363 FYVE: FYVE zinc finge 24.0 33 0.00072 24.6 0.6 30 31-72 8-37 (69)
193 PF06689 zf-C4_ClpX: ClpX C4-t 23.9 20 0.00042 23.4 -0.6 32 32-68 1-32 (41)
194 TIGR01206 lysW lysine biosynth 23.8 46 0.001 23.2 1.2 10 137-146 23-32 (54)
195 PF14803 Nudix_N_2: Nudix N-te 23.7 34 0.00075 21.4 0.5 30 35-70 3-32 (34)
196 PRK03976 rpl37ae 50S ribosomal 23.6 30 0.00064 26.8 0.3 12 136-147 54-65 (90)
197 PF05191 ADK_lid: Adenylate ki 23.0 33 0.0007 21.7 0.3 11 136-146 21-31 (36)
198 PRK14873 primosome assembly pr 22.9 30 0.00064 37.0 0.2 8 136-143 422-429 (665)
199 KOG2807 RNA polymerase II tran 22.9 1.4E+02 0.0031 28.7 4.6 35 31-79 275-309 (378)
200 COG1594 RPB9 DNA-directed RNA 22.7 52 0.0011 26.6 1.6 40 32-71 72-111 (113)
201 PF03833 PolC_DP2: DNA polymer 22.7 28 0.00061 37.7 0.0 12 58-69 653-664 (900)
202 COG1198 PriA Primosomal protei 22.3 30 0.00065 37.2 0.1 12 134-145 473-484 (730)
203 KOG3408 U1-like Zn-finger-cont 22.1 24 0.00052 28.8 -0.5 22 137-158 58-79 (129)
204 PF08209 Sgf11: Sgf11 (transcr 22.0 70 0.0015 19.9 1.7 24 163-187 4-28 (33)
205 PHA02998 RNA polymerase subuni 22.0 44 0.00094 29.3 1.0 40 31-72 142-183 (195)
206 TIGR00595 priA primosomal prot 21.8 57 0.0012 33.6 2.0 11 62-72 215-225 (505)
207 PF13878 zf-C2H2_3: zinc-finge 21.7 70 0.0015 20.8 1.7 24 61-84 14-39 (41)
208 TIGR00595 priA primosomal prot 21.6 35 0.00076 35.1 0.4 10 280-289 449-458 (505)
209 COG1571 Predicted DNA-binding 21.3 62 0.0013 32.3 2.0 36 30-76 348-383 (421)
210 PRK12380 hydrogenase nickel in 21.3 32 0.00069 27.8 0.0 27 30-68 68-94 (113)
211 COG2331 Uncharacterized protei 21.0 39 0.00084 25.3 0.4 16 56-71 8-23 (82)
212 KOG4317 Predicted Zn-finger pr 21.0 28 0.00061 33.1 -0.4 27 136-162 19-45 (383)
213 PRK14873 primosome assembly pr 20.4 68 0.0015 34.3 2.3 9 100-108 421-429 (665)
214 KOG2461 Transcription factor B 20.3 1.3E+02 0.0029 29.9 4.1 19 121-139 344-362 (396)
215 PF10276 zf-CHCC: Zinc-finger 20.2 52 0.0011 21.4 0.8 13 59-71 28-40 (40)
216 PF01428 zf-AN1: AN1-like Zinc 20.1 38 0.00082 22.1 0.2 15 59-73 12-26 (43)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.94 E-value=3.3e-28 Score=219.40 Aligned_cols=134 Identities=23% Similarity=0.419 Sum_probs=126.3
Q ss_pred CcCCCCCCCCCCCCCchhhhhcCccccCC---CCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCC
Q 048287 29 TAAKKKRNLPGTPDPEAEVIALSPKTLMA---TNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCP 105 (365)
Q Consensus 29 ~~~~~~c~~c~~~~~~~~~l~~h~k~~~~---~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~ 105 (365)
....++|+.||+.+.+...|.+|+.+|-. .+.+.|++|||.|.....|++|+|+|+ -+++|.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~---------------l~c~C~ 191 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT---------------LPCECG 191 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC---------------CCcccc
Confidence 45588999999999999999999999854 688999999999999999999999996 468899
Q ss_pred CCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcc-cCCcceecc-CCCccCChhHHHHHHH
Q 048287 106 EKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKT-CGTREYKCD-CGTVFSRRDSFITHRA 183 (365)
Q Consensus 106 ~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kpy~C~-Cgk~F~~~~~L~~H~~ 183 (365)
+| ||.|...-.|..|+|+|+|||||.|..|+|.|..+++|+.|+++ .+.|+|.|. |+|.|++++.|.+|.+
T Consensus 192 iC-------GKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 192 IC-------GKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cc-------cccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 98 99999999999999999999999999999999999999999999 778999999 9999999999999987
Q ss_pred H
Q 048287 184 F 184 (365)
Q Consensus 184 ~ 184 (365)
.
T Consensus 265 S 265 (279)
T KOG2462|consen 265 S 265 (279)
T ss_pred h
Confidence 6
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.85 E-value=4.6e-22 Score=179.75 Aligned_cols=124 Identities=21% Similarity=0.459 Sum_probs=112.9
Q ss_pred CCCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCc
Q 048287 57 ATNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKK 136 (365)
Q Consensus 57 ~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp 136 (365)
...+|+|..|||.|.+.++|.+|+++|.. -..++.+.|++| +|.|.....|+.|+|+|+ -+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~----------~~s~ka~~C~~C-------~K~YvSmpALkMHirTH~--l~ 187 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRS----------LDSKKAFSCKYC-------GKVYVSMPALKMHIRTHT--LP 187 (279)
T ss_pred cCCceeccccccccccccccchhhccccc----------ccccccccCCCC-------CceeeehHHHhhHhhccC--CC
Confidence 45789999999999999999999999961 114678999999 999999999999999998 58
Q ss_pred cccccccccccchhhhhhhhcc-cCCcceecc-CCCccCChhHHHHHHHHhhhhhhhhhhhcccc
Q 048287 137 WKCEKCSKRYAVQSDWKAHSKT-CGTREYKCD-CGTVFSRRDSFITHRAFCDALAEETARVNAAS 199 (365)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~-~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~~~~~~~~~~~~~~ 199 (365)
++|.+|||.|.+.+-|+.|+|+ +|||||.|. |+|.|..+++|+.|+++|.......+..|...
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhH
Confidence 9999999999999999999999 999999999 99999999999999999998887777766654
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.74 E-value=2.3e-19 Score=181.61 Aligned_cols=79 Identities=20% Similarity=0.455 Sum_probs=72.4
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcccCCcc-----eecc----CCCc
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKTCGTRE-----YKCD----CGTV 171 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp-----y~C~----Cgk~ 171 (365)
+-+|-+| .|.+..++.|+.|+|+|+|||||+|.+|++.|.++.+|+.|+-+|..+| |.|. |-+.
T Consensus 605 PNqCiiC-------~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~k 677 (958)
T KOG1074|consen 605 PNQCIIC-------LRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKK 677 (958)
T ss_pred ccceeee-------eecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccc
Confidence 4578888 9999999999999999999999999999999999999999999876654 7885 8999
Q ss_pred cCChhHHHHHHHHhh
Q 048287 172 FSRRDSFITHRAFCD 186 (365)
Q Consensus 172 F~~~~~L~~H~~~h~ 186 (365)
|...-.|..|++.|.
T Consensus 678 ftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 678 FTNAVTLPQHIRIHL 692 (958)
T ss_pred ccccccccceEEeec
Confidence 999999999999986
No 4
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.73 E-value=3.5e-18 Score=147.50 Aligned_cols=114 Identities=24% Similarity=0.554 Sum_probs=105.2
Q ss_pred CCCCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCC
Q 048287 56 MATNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEK 135 (365)
Q Consensus 56 ~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ek 135 (365)
.....|.|.+|+|.|.-..-|.+|++.|. .-|.|.|..| |+.|.+--.|++|+|+|+|.+
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~-------------~vkr~lct~c-------gkgfndtfdlkrh~rthtgvr 172 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHS-------------DVKRHLCTFC-------GKGFNDTFDLKRHTRTHTGVR 172 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhcc-------------HHHHHHHhhc-------cCcccchhhhhhhhccccCcc
Confidence 34577999999999999999999999998 7789999998 999999999999999999999
Q ss_pred ccccccccccccchhhhhhhhcc-cC-----------Ccceecc-CCCccCChhHHHHHHHHhhhhh
Q 048287 136 KWKCEKCSKRYAVQSDWKAHSKT-CG-----------TREYKCD-CGTVFSRRDSFITHRAFCDALA 189 (365)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~-~~-----------~kpy~C~-Cgk~F~~~~~L~~H~~~h~~~~ 189 (365)
||+|..|+|.|.++-.|..|++. |+ .|.|.|+ ||.+-.+...+..|++.||...
T Consensus 173 pykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 173 PYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred ccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 99999999999999999999987 75 4679999 9999999999999999998643
No 5
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.65 E-value=3.2e-17 Score=152.02 Aligned_cols=176 Identities=18% Similarity=0.259 Sum_probs=143.2
Q ss_pred CCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHHHHhcC----CCccccccccc---------cc--C
Q 048287 34 KRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHN----LPWKLKQRTSK---------EV--R 98 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~----~~~~~~~~~~~---------~~--~ 98 (365)
+-..|-+.+.++..|++|.++|+++|...|+.||.-|.++..|-.|++.-+ .++.|....++ |+ .
T Consensus 181 ~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rH 260 (467)
T KOG3608|consen 181 NWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRH 260 (467)
T ss_pred cchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHh
Confidence 445888999999999999999999999999999999999999999987654 33444322111 11 1
Q ss_pred CceeeCCCCCccCCCCCCccCChhHHHHHHh-hhcCCCccccccccccccchhhhhhhhcccCCcceecc---CCCccCC
Q 048287 99 KRVYVCPEKTCVHHHPSRALGDLTGIKKHFC-RKHGEKKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD---CGTVFSR 174 (365)
Q Consensus 99 ~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~-~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~---Cgk~F~~ 174 (365)
-..|+|+.| .......+.|..|++ +|..+|||+|+.|++.|.+.++|.+|..+|.+-.|.|+ |...|..
T Consensus 261 vn~ykCplC-------dmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~ 333 (467)
T KOG3608|consen 261 VNCYKCPLC-------DMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRT 333 (467)
T ss_pred hhccccccc-------ccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHH
Confidence 145888888 888888899999987 57778999999999999999999999999888889996 9999999
Q ss_pred hhHHHHHHHHhhhhhhhhhhhcccccccccCCCCcccccCCC
Q 048287 175 RDSFITHRAFCDALAEETARVNAASSMNSLANGSISYHFMGT 216 (365)
Q Consensus 175 ~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 (365)
...|++|++.+|....+..+.|-.+...+....+++.|++-.
T Consensus 334 ~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kk 375 (467)
T KOG3608|consen 334 YTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKK 375 (467)
T ss_pred HHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHh
Confidence 999999999999878888888888888887776666665543
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.65 E-value=3.6e-17 Score=165.81 Aligned_cols=55 Identities=20% Similarity=0.327 Sum_probs=52.4
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHHHHhcC
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
..+..|=+|-++....+.|+.|.++|++++||+|++||+.|.++.+|+.||-+|.
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred CCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc
Confidence 3577899999999999999999999999999999999999999999999999996
No 7
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.56 E-value=6.5e-16 Score=133.56 Aligned_cols=111 Identities=24% Similarity=0.394 Sum_probs=103.3
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCc
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTC 109 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C 109 (365)
...+.|.+|+|.|.-...|.+|+|-|...|+|.|..|||.|.....|++|+|+|+ +-+||+|..|
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rtht-------------gvrpykc~~c-- 179 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHT-------------GVRPYKCSLC-- 179 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcccc-------------Cccccchhhh--
Confidence 4678999999999999999999999999999999999999999999999999998 9999999999
Q ss_pred cCCCCCCccCChhHHHHHHhhhcC-----------CCccccccccccccchhhhhhhhcc-cC
Q 048287 110 VHHHPSRALGDLTGIKKHFCRKHG-----------EKKWKCEKCSKRYAVQSDWKAHSKT-CG 160 (365)
Q Consensus 110 ~~~~~~~~f~~~~~L~~H~~~H~~-----------ekp~~C~~C~k~F~~~~~L~~H~~~-~~ 160 (365)
+++|..+..|..|.+.-+| +|-|.|+.||.+-.+...+..|++. |.
T Consensus 180 -----~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 180 -----EKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred -----hHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 9999999999999875443 4679999999999999999999998 53
No 8
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.54 E-value=1.5e-15 Score=151.86 Aligned_cols=107 Identities=23% Similarity=0.523 Sum_probs=96.3
Q ss_pred ceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcC------
Q 048287 60 RFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHG------ 133 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~------ 133 (365)
...|++|.+.|.+...|+.|++..+ ...+.-|.|..| .+.|.++..|.+||.+|..
T Consensus 210 lltcpycdrgykrltslkeHikyrh-----------ekne~nfsC~lC-------sytFAyRtQLErhm~~hkpg~dqa~ 271 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRH-----------EKNEPNFSCMLC-------SYTFAYRTQLERHMQLHKPGGDQAI 271 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHH-----------hhCCCCCcchhh-------hhhhhhHHHHHHHHHhhcCCCcccc
Confidence 3789999999999999999987654 125566899999 9999999999999999852
Q ss_pred -------CCccccccccccccchhhhhhhhcc-cCCcceecc-CCCccCChhHHHHHHHH
Q 048287 134 -------EKKWKCEKCSKRYAVQSDWKAHSKT-CGTREYKCD-CGTVFSRRDSFITHRAF 184 (365)
Q Consensus 134 -------ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kpy~C~-Cgk~F~~~~~L~~H~~~ 184 (365)
-|+|+|..|+|.|..+.+|+.|+|+ .|+|||.|+ |+|.|+...++..||..
T Consensus 272 sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 272 SLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 4789999999999999999999999 899999999 99999999999999854
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.48 E-value=7.8e-15 Score=146.76 Aligned_cols=120 Identities=18% Similarity=0.278 Sum_probs=100.5
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCC--CCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCc
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMA--TNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTC 109 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~--~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C 109 (365)
.-.|+.|...+..-..|+.|.+.... +..|.|..|..+|..+..|.+||..|.-...-..........|.|+|.+|
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtEC-- 287 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTEC-- 287 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccccccc--
Confidence 45899999998888889999886543 45799999999999999999999999621111122222335688999999
Q ss_pred cCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcc
Q 048287 110 VHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKT 158 (365)
Q Consensus 110 ~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 158 (365)
+|+|+.+.+|+.|+|+|.|||||.|+.|+|+|.....+..|+..
T Consensus 288 -----gKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 288 -----GKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred -----chhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999999999999999865
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.42 E-value=3.9e-14 Score=131.70 Aligned_cols=159 Identities=17% Similarity=0.233 Sum_probs=135.8
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCchhhhhcCccccC--CCCceecccccccccChHhHHHHHHhcCCCcccc---------
Q 048287 22 GSNNPPNTAAKKKRNLPGTPDPEAEVIALSPKTLM--ATNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLK--------- 90 (365)
Q Consensus 22 ~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~k~~~--~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~--------- 90 (365)
++-...+.++--.|+.||.-|.....|..|.+..+ ..++|.|..|.|.|.+...|+.|++.|..-++|.
T Consensus 197 eH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ 276 (467)
T KOG3608|consen 197 EHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSA 276 (467)
T ss_pred HHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCCh
Confidence 34455667777899999999999999999877544 5679999999999999999999999997555442
Q ss_pred ----c-ccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcccccc--ccccccchhhhhhhhcc-c-C-
Q 048287 91 ----Q-RTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEK--CSKRYAVQSDWKAHSKT-C-G- 160 (365)
Q Consensus 91 ----~-~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~--C~k~F~~~~~L~~H~~~-~-~- 160 (365)
. -.-+|..+|||+|+.| .+.|...+.|.+|..+|. +--|.|+. |..+|.....+++|++. + +
T Consensus 277 ssL~~H~r~rHs~dkpfKCd~C-------d~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~ 348 (467)
T KOG3608|consen 277 SSLTTHIRYRHSKDKPFKCDEC-------DTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGN 348 (467)
T ss_pred HHHHHHHHhhhccCCCccccch-------hhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCC
Confidence 1 1245778999999999 999999999999999998 67899988 99999999999999998 5 2
Q ss_pred -Ccceecc-CCCccCChhHHHHHHHHhhhh
Q 048287 161 -TREYKCD-CGTVFSRRDSFITHRAFCDAL 188 (365)
Q Consensus 161 -~kpy~C~-Cgk~F~~~~~L~~H~~~h~~~ 188 (365)
.-+|.|. |++.|.+-.+|..|+.+-|+.
T Consensus 349 np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 349 NPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred CCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 3579999 999999999999999887764
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.30 E-value=3.3e-12 Score=128.76 Aligned_cols=105 Identities=22% Similarity=0.448 Sum_probs=89.7
Q ss_pred CCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcc
Q 048287 58 TNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKW 137 (365)
Q Consensus 58 ~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~ 137 (365)
++.+.|++|++.|. ...|..|++.|+ +++.|+ | ++.+ .+..|..|+.+|.++|++
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H---------------kpv~Cp-C-------g~~~-~R~~L~~H~~thCp~Kpi 505 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH---------------EPLQCP-C-------GVVL-EKEQMVQHQASTCPLRLI 505 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC---------------CCccCC-C-------CCCc-chhHHHhhhhccCCCCce
Confidence 35578999999996 688999999874 679998 7 8755 678999999999999999
Q ss_pred cccccccccc----------chhhhhhhhcccCCcceecc-CCCccCChhHHHHHHHHhhhh
Q 048287 138 KCEKCSKRYA----------VQSDWKAHSKTCGTREYKCD-CGTVFSRRDSFITHRAFCDAL 188 (365)
Q Consensus 138 ~C~~C~k~F~----------~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~~~ 188 (365)
.|..|++.|. ....|..|...++.+++.|. |++.|..+ .|..|+..+|+.
T Consensus 506 ~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 506 TCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred eCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 9999999995 24589999999999999999 99999765 678999887753
No 12
>PHA00733 hypothetical protein
Probab=98.98 E-value=4.1e-10 Score=93.64 Aligned_cols=54 Identities=20% Similarity=0.417 Sum_probs=28.6
Q ss_pred CCccccccccccccchhhhhhhhcccCCcceecc-CCCccCChhHHHHHHHHhhhh
Q 048287 134 EKKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRRDSFITHRAFCDAL 188 (365)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~~~ 188 (365)
++||.|+.|++.|.....|..|++.+ +.+|.|. |++.|.....|..|+...|++
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHHHHHHHHhcCc
Confidence 44555555555555555555555443 2345555 555555555555555555543
No 13
>PHA00733 hypothetical protein
Probab=98.96 E-value=3.9e-10 Score=93.76 Aligned_cols=54 Identities=20% Similarity=0.319 Sum_probs=49.1
Q ss_pred CCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcc-cC
Q 048287 98 RKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKT-CG 160 (365)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~-~~ 160 (365)
..++|.|+.| ++.|.....|..|++.| +.+|.|..|++.|.....|..|+.. |+
T Consensus 70 ~~kPy~C~~C-------gk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 70 AVSPYVCPLC-------LMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCCC-------CCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5789999999 99999999999999987 4679999999999999999999987 64
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.94 E-value=9.9e-10 Score=111.04 Aligned_cols=104 Identities=14% Similarity=0.275 Sum_probs=87.0
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCc
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTC 109 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C 109 (365)
+.-+.|+.|++.|. ...+..|.++++ ++|.|+ ||+.| .+..|..|++.|. .++++.|++|
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thC-------------p~Kpi~C~fC-- 510 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTC-------------PLRLITCRFC-- 510 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccC-------------CCCceeCCCC--
Confidence 34568999999996 577899999985 889999 99866 6689999999998 8999999999
Q ss_pred cCCCCCCccC----------ChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcc-cC
Q 048287 110 VHHHPSRALG----------DLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKT-CG 160 (365)
Q Consensus 110 ~~~~~~~~f~----------~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~-~~ 160 (365)
++.|. ....|..|.... |.+++.|..|++.|..+ +|..|+.. |.
T Consensus 511 -----~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 511 -----GDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred -----CCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 88884 246899999885 89999999999887655 67888776 53
No 15
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.81 E-value=1.1e-09 Score=104.63 Aligned_cols=154 Identities=18% Similarity=0.251 Sum_probs=115.0
Q ss_pred CCCcCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHHHHhcCCCcc-c--------c-------
Q 048287 27 PNTAAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHNLPWK-L--------K------- 90 (365)
Q Consensus 27 ~~~~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~-~--------~------- 90 (365)
+.....|.|.+|...|.+.-.|..|.-.-.-.--|+|++|+|.|....+|--|+|-|. |.. . +
T Consensus 262 ~n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHK-PR~eaa~a~~~P~k~~~~~ra 340 (500)
T KOG3993|consen 262 PNVIGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHK-PRPEAAKAGSPPPKQAVETRA 340 (500)
T ss_pred cccHHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccC-CchhhhhcCCCChhhhhhhhh
Confidence 4445678999999999999999999887777778999999999999999999999996 111 0 0
Q ss_pred -----cccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCC---C---------------------------
Q 048287 91 -----QRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGE---K--------------------------- 135 (365)
Q Consensus 91 -----~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~e---k--------------------------- 135 (365)
.+......+..|.|.+| ++.|.....|++|+.+|+.. +
T Consensus 341 e~~ea~rsg~dss~gi~~C~~C-------~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a 413 (500)
T KOG3993|consen 341 EVQEAERSGDDSSSGIFSCHTC-------GKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSA 413 (500)
T ss_pred hhhhccccCCcccCceeecHHh-------hhhhHHHHHHHHhHHhhhccccchhcccCcchhhccccccccccccccccc
Confidence 01112234458999999 99999999999999887521 0
Q ss_pred ----------------ccccccccccccchhhhhhhhcc-cCCcceecc-CCCccCChhHHHHHHHHhhhh
Q 048287 136 ----------------KWKCEKCSKRYAVQSDWKAHSKT-CGTREYKCD-CGTVFSRRDSFITHRAFCDAL 188 (365)
Q Consensus 136 ----------------p~~C~~C~k~F~~~~~L~~H~~~-~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~~~ 188 (365)
-..|+.|+-.+..+..--.|.+. +-+.-|.|. |.-.|.....|.+|+..+|-.
T Consensus 414 ~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 414 SDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred ccccccceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChH
Confidence 01234444444444444444444 445569999 999999999999999999864
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.58 E-value=2.9e-08 Score=69.03 Aligned_cols=43 Identities=14% Similarity=0.307 Sum_probs=35.3
Q ss_pred eeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhh
Q 048287 102 YVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWK 153 (365)
Q Consensus 102 ~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~ 153 (365)
|.|++| |+.|.....|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 6 y~C~~C-------GK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPIC-------GEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchh-------CCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 678888 888888888888888887 6888888888888777664
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.57 E-value=2.5e-08 Score=69.31 Aligned_cols=44 Identities=20% Similarity=0.304 Sum_probs=39.2
Q ss_pred ceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHH
Q 048287 60 RFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIK 125 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~ 125 (365)
-|+|++|||.|.+..+|..|+++|. ++|+|..| ++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~---------------k~~kc~~C-------~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN---------------TNLKLSNC-------KRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC---------------CcccCCcc-------cceecccceeE
Confidence 5899999999999999999999994 58999998 99998776654
No 18
>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=98.46 E-value=9.3e-08 Score=56.72 Aligned_cols=26 Identities=31% Similarity=0.795 Sum_probs=23.7
Q ss_pred HHHHHHhhhcCCCccccccccccccc
Q 048287 123 GIKKHFCRKHGEKKWKCEKCSKRYAV 148 (365)
Q Consensus 123 ~L~~H~~~H~~ekp~~C~~C~k~F~~ 148 (365)
+|.+|+++|+++|||+|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 48899999999999999999999963
No 19
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.25 E-value=1.8e-07 Score=89.68 Aligned_cols=85 Identities=18% Similarity=0.445 Sum_probs=70.5
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcccCC-------------------
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKTCGT------------------- 161 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~------------------- 161 (365)
.|.|..| ...|.+.-.|..|.......--|+|..|+|.|.-..+|..|.|+|.-
T Consensus 267 dyiCqLC-------K~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~r 339 (500)
T KOG3993|consen 267 DYICQLC-------KEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETR 339 (500)
T ss_pred HHHHHHH-------HHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhh
Confidence 3899998 89999999999998644444459999999999999999999987531
Q ss_pred ---------------cceecc-CCCccCChhHHHHHHHHhhhhhhhh
Q 048287 162 ---------------REYKCD-CGTVFSRRDSFITHRAFCDALAEET 192 (365)
Q Consensus 162 ---------------kpy~C~-Cgk~F~~~~~L~~H~~~h~~~~~~~ 192 (365)
.-|.|. |+|.|.+...|++|+..|+......
T Consensus 340 ae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 340 AEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred hhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 129999 9999999999999999998754443
No 20
>PHA00616 hypothetical protein
Probab=97.97 E-value=2.7e-06 Score=56.41 Aligned_cols=34 Identities=15% Similarity=0.306 Sum_probs=30.8
Q ss_pred ceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCC
Q 048287 60 RFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPE 106 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~ 106 (365)
+|+|..||+.|..++.|.+|++.|+ +++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h-------------g~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH-------------KQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc-------------CCCccceeE
Confidence 6899999999999999999999998 788888764
No 21
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.90 E-value=8.2e-06 Score=75.74 Aligned_cols=71 Identities=28% Similarity=0.578 Sum_probs=42.2
Q ss_pred CCceeccc--ccccccChHhHHHHHH-hcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCC
Q 048287 58 TNRFLCEI--CGKGFQRDQNLQLHRR-GHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGE 134 (365)
Q Consensus 58 ~k~~~C~~--Cgk~F~~~~~L~~H~~-~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~e 134 (365)
+|+|+|++ |.|.|+....|+.|+. .|..+.. .+.| -++. -..| -...
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~---------~~~p--~p~~-------~~~F------------~~~~ 396 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKL---------HENP--SPEK-------MNIF------------SAKD 396 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCccc---------CCCC--Cccc-------cccc------------cccC
Confidence 48888876 8888888888888863 3421100 0011 0111 1222 1235
Q ss_pred Cccccccccccccchhhhhhhhcc
Q 048287 135 KKWKCEKCSKRYAVQSDWKAHSKT 158 (365)
Q Consensus 135 kp~~C~~C~k~F~~~~~L~~H~~~ 158 (365)
|||+|++|+|+|.....|+-|++.
T Consensus 397 KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 397 KPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred CceeccccchhhccCccceecccc
Confidence 778888888888777777777654
No 22
>PHA00732 hypothetical protein
Probab=97.85 E-value=1e-05 Score=61.41 Aligned_cols=23 Identities=35% Similarity=0.495 Sum_probs=16.0
Q ss_pred ceecccccccccChHhHHHHHHh
Q 048287 60 RFLCEICGKGFQRDQNLQLHRRG 82 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~~L~~H~~~ 82 (365)
+|.|.+|++.|.+...|+.|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhc
Confidence 46677777777777777777764
No 23
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.82 E-value=1.2e-05 Score=47.65 Aligned_cols=26 Identities=31% Similarity=0.655 Sum_probs=23.4
Q ss_pred hHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCC
Q 048287 75 NLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGD 120 (365)
Q Consensus 75 ~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~ 120 (365)
+|.+|++.|+ ++++|.|++| ++.|..
T Consensus 1 ~l~~H~~~H~-------------~~k~~~C~~C-------~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHT-------------GEKPYKCPYC-------GKSFSN 26 (26)
T ss_dssp HHHHHHHHHS-------------SSSSEEESSS-------SEEESS
T ss_pred CHHHHhhhcC-------------CCCCCCCCCC-------cCeeCc
Confidence 5899999998 9999999999 998863
No 24
>PHA00616 hypothetical protein
Probab=97.81 E-value=8.5e-06 Score=54.04 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=31.5
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccc
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRY 146 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F 146 (365)
||+|+.| |+.|..+..|.+|++.|++++++.|+.--..|
T Consensus 1 pYqC~~C-------G~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRC-------GGIFRKKKEVIEHLLSVHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchh-------hHHHhhHHHHHHHHHHhcCCCccceeEEEEEE
Confidence 5788888 89999999999999999999988887543333
No 25
>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=1.5e-05 Score=45.59 Aligned_cols=23 Identities=48% Similarity=0.992 Sum_probs=21.7
Q ss_pred eecccccccccChHhHHHHHHhc
Q 048287 61 FLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 61 ~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
|+|++|++.|.++..|..|++.|
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 26
>PHA00732 hypothetical protein
Probab=97.65 E-value=3.4e-05 Score=58.48 Aligned_cols=45 Identities=27% Similarity=0.444 Sum_probs=36.8
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhh-hcCCCccccccccccccchhhhhhhhcc
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCR-KHGEKKWKCEKCSKRYAVQSDWKAHSKT 158 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~-H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 158 (365)
||.|+.| ++.|.....|+.|++. |. ++.|+.|++.|. .|..|.++
T Consensus 1 py~C~~C-------gk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPIC-------GFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCC-------CCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 4788888 9999999999999985 54 358999999997 57888866
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.61 E-value=7.6e-05 Score=52.38 Aligned_cols=52 Identities=27% Similarity=0.535 Sum_probs=33.8
Q ss_pred ceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhc
Q 048287 60 RFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKH 132 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~ 132 (365)
.|.|++|++. .+...|..|....+. ...+.+.|++| ...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~-----------~~~~~v~CPiC-------~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHR-----------SESKNVVCPIC-------SSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCc-----------CCCCCccCCCc-------hhhhh--hHHHHHHHHhc
Confidence 4788888884 456778888644431 13356888888 55443 37777877654
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.35 E-value=6.8e-05 Score=69.80 Aligned_cols=72 Identities=19% Similarity=0.476 Sum_probs=45.4
Q ss_pred CCceeeCCCCCccCCCCCCccCChhHHHHHHhhhc-CCCccccccccccccchhhhhhhhcc-cCCcceecc-CCCccCC
Q 048287 98 RKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKH-GEKKWKCEKCSKRYAVQSDWKAHSKT-CGTREYKCD-CGTVFSR 174 (365)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~-~ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kpy~C~-Cgk~F~~ 174 (365)
++|||+|++-+| .|.|+....|+-|+.--+ ..+...-+ .-..|.-. ...|||+|+ |+|.|..
T Consensus 346 d~KpykCpV~gC-----~K~YknqnGLKYH~lhGH~~~~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYKN 410 (423)
T COG5189 346 DGKPYKCPVEGC-----NKKYKNQNGLKYHMLHGHQNQKLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYKN 410 (423)
T ss_pred cCceecCCCCCc-----hhhhccccchhhhhhccccCcccCCCC----------CccccccccccCCceeccccchhhcc
Confidence 447788877777 777777777777765321 11111100 11111111 457999999 9999999
Q ss_pred hhHHHHHHHH
Q 048287 175 RDSFITHRAF 184 (365)
Q Consensus 175 ~~~L~~H~~~ 184 (365)
...|+-|++-
T Consensus 411 lNGLKYHr~H 420 (423)
T COG5189 411 LNGLKYHRKH 420 (423)
T ss_pred Cccceecccc
Confidence 9999888753
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=97.31 E-value=0.00016 Score=41.21 Aligned_cols=24 Identities=46% Similarity=0.985 Sum_probs=20.2
Q ss_pred eecccccccccChHhHHHHHHhcC
Q 048287 61 FLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 61 ~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
|.|++|++.|.+...|+.|++.|+
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 789999999999999999998773
No 30
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.24 E-value=0.00021 Score=40.71 Aligned_cols=22 Identities=36% Similarity=0.773 Sum_probs=15.5
Q ss_pred eecc-CCCccCChhHHHHHHHHh
Q 048287 164 YKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
|.|+ |++.|.++..|..|++.|
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 5677 777777777777777653
No 31
>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=97.16 E-value=0.00026 Score=42.02 Aligned_cols=25 Identities=40% Similarity=0.781 Sum_probs=23.5
Q ss_pred ceecccccccccChHhHHHHHHhcC
Q 048287 60 RFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
+|+|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999999885
No 32
>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=97.11 E-value=0.0004 Score=48.71 Aligned_cols=47 Identities=23% Similarity=0.422 Sum_probs=25.2
Q ss_pred eeCCCCCccCCCCCCccCChhHHHHHHhhhc-CC-Cccccccccccccchhhhhhhhcc
Q 048287 102 YVCPEKTCVHHHPSRALGDLTGIKKHFCRKH-GE-KKWKCEKCSKRYAVQSDWKAHSKT 158 (365)
Q Consensus 102 ~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~-~e-kp~~C~~C~k~F~~~~~L~~H~~~ 158 (365)
|.|++| ++ ..+...|..|....+ .+ +.+.|++|...+. .+|..|+..
T Consensus 3 f~CP~C-------~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYC-------GK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCC-------CC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 566666 66 344556666654433 22 3466666665433 255555554
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=96.90 E-value=0.00074 Score=38.37 Aligned_cols=23 Identities=22% Similarity=0.650 Sum_probs=15.1
Q ss_pred eecc-CCCccCChhHHHHHHHHhh
Q 048287 164 YKCD-CGTVFSRRDSFITHRAFCD 186 (365)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~h~ 186 (365)
|.|+ |++.|.+...|..|++.+|
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 5677 7777777777777777654
No 34
>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=96.84 E-value=0.00055 Score=40.56 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=15.5
Q ss_pred ceecc-CCCccCChhHHHHHHHHhh
Q 048287 163 EYKCD-CGTVFSRRDSFITHRAFCD 186 (365)
Q Consensus 163 py~C~-Cgk~F~~~~~L~~H~~~h~ 186 (365)
+|.|+ |++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 46666 6666666666666666554
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.71 E-value=0.00068 Score=53.09 Aligned_cols=19 Identities=26% Similarity=0.665 Sum_probs=0.0
Q ss_pred cccccccccChHhHHHHHH
Q 048287 63 CEICGKGFQRDQNLQLHRR 81 (365)
Q Consensus 63 C~~Cgk~F~~~~~L~~H~~ 81 (365)
|..|+..|.....|..|+.
T Consensus 2 C~~C~~~f~~~~~l~~H~~ 20 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMK 20 (100)
T ss_dssp -------------------
T ss_pred ccccccccccccccccccc
Confidence 5666666666666666653
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.71 E-value=0.0011 Score=51.89 Aligned_cols=68 Identities=15% Similarity=0.279 Sum_probs=21.6
Q ss_pred CCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcccCCcceecc-CCCccCChhHHHHHHHHhh
Q 048287 115 SRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRRDSFITHRAFCD 186 (365)
Q Consensus 115 ~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~ 186 (365)
+..|.....|..|+...++-.. . ....+.....+..+.+..-...+.|. |++.|.....|..|++.+.
T Consensus 6 ~~~f~~~~~l~~H~~~~H~~~~---~-~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 6 DESFSSVDDLLQHMKKKHGFDI---P-DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -----------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred cccccccccccccccccccccc---c-cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 9999999999999976665321 1 11222344445555544323479999 9999999999999999753
No 37
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.63 E-value=0.0021 Score=63.14 Aligned_cols=54 Identities=20% Similarity=0.293 Sum_probs=51.0
Q ss_pred CCCCCCCCCCCCCchhhhhcCcc--ccCCC--Cceecc--cccccccChHhHHHHHHhcC
Q 048287 31 AKKKRNLPGTPDPEAEVIALSPK--TLMAT--NRFLCE--ICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~k--~~~~~--k~~~C~--~Cgk~F~~~~~L~~H~~~H~ 84 (365)
..+.|..|...|.....+..|.+ .|..+ +++.|+ .|++.|.+...|..|...|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccccc
Confidence 46899999999999999999999 89999 999999 79999999999999999997
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.54 E-value=0.0015 Score=37.61 Aligned_cols=24 Identities=38% Similarity=0.753 Sum_probs=22.1
Q ss_pred eecccccccccChHhHHHHHHhcC
Q 048287 61 FLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 61 ~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999774
No 39
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.41 E-value=0.0042 Score=64.37 Aligned_cols=15 Identities=33% Similarity=0.481 Sum_probs=9.2
Q ss_pred cccChHhHHHHH-Hhc
Q 048287 69 GFQRDQNLQLHR-RGH 83 (365)
Q Consensus 69 ~F~~~~~L~~H~-~~H 83 (365)
.|.....|+.|+ ..|
T Consensus 123 ~~~s~~~Lk~H~~~~H 138 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQH 138 (669)
T ss_pred chhHHHHHHHHHHHhh
Confidence 334667788887 344
No 40
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.11 E-value=0.0053 Score=67.24 Aligned_cols=145 Identities=12% Similarity=0.149 Sum_probs=100.1
Q ss_pred CCCCCCCCCCchhhhhcCccc-cCCCCceecccccccccChHhHHHHHHhcC-CCcc--ccc---------ccccccCCc
Q 048287 34 KRNLPGTPDPEAEVIALSPKT-LMATNRFLCEICGKGFQRDQNLQLHRRGHN-LPWK--LKQ---------RTSKEVRKR 100 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~-~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~-~~~~--~~~---------~~~~~~~~k 100 (365)
.|..|+..+.....+..+... +...+.|+|+.|+..|+....|..|||.-+ .... +.. ........+
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~ 517 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGK 517 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCC
Confidence 344555555555555555443 344588999999999999999999998732 1110 100 011223457
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhh--hc-----------------------------------C------CCcc
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCR--KH-----------------------------------G------EKKW 137 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~--H~-----------------------------------~------ekp~ 137 (365)
+|.|..| ...+..+..|-.|+.. |. + +-+|
T Consensus 518 p~~C~~C-------~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~ 590 (1406)
T KOG1146|consen 518 PYPCRAC-------NYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSW 590 (1406)
T ss_pred cccceee-------eeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCc
Confidence 7888888 9999999999999864 10 0 1258
Q ss_pred ccccccccccchhhhhhhhcc--cCCcceecc-CCCccCChhHHHHHHHHh
Q 048287 138 KCEKCSKRYAVQSDWKAHSKT--CGTREYKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~~--~~~kpy~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
.|.+|++.-.-...|+.|+.. |...|..|. |...+.....|..+.+.+
T Consensus 591 ~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 591 RCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred chhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCCCC
Confidence 999999999999999999988 444448888 888887777666665554
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.03 E-value=0.004 Score=36.04 Aligned_cols=23 Identities=39% Similarity=0.947 Sum_probs=21.3
Q ss_pred eecccccccccChHhHHHHHHhc
Q 048287 61 FLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 61 ~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
|.|.+|++.|.....|+.|++.+
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 68999999999999999999765
No 42
>PRK04860 hypothetical protein; Provisional
Probab=95.84 E-value=0.0056 Score=52.85 Aligned_cols=40 Identities=18% Similarity=0.472 Sum_probs=27.2
Q ss_pred ceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchh
Q 048287 100 RVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQS 150 (365)
Q Consensus 100 k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~ 150 (365)
-+|.|. | ++ ....+.+|.++|.++++|+|..|+..|....
T Consensus 118 ~~Y~C~-C-------~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-C-------QE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-C-------CC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 457776 6 54 4566677777777777777777777765443
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.70 E-value=0.011 Score=40.24 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=21.0
Q ss_pred CCCCceecccccccccChHhHHHHHHhcC
Q 048287 56 MATNRFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 56 ~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
..+.|-.|++|+..+.+..+|++|+..++
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHh
Confidence 34689999999999999999999997665
No 44
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.48 E-value=0.011 Score=33.82 Aligned_cols=22 Identities=32% Similarity=0.819 Sum_probs=17.8
Q ss_pred eecc-CCCccCChhHHHHHHHHh
Q 048287 164 YKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
|.|. |++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 5788 888888888888888755
No 45
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.24 E-value=0.02 Score=59.44 Aligned_cols=125 Identities=19% Similarity=0.205 Sum_probs=77.1
Q ss_pred CCCCCCCCCCCCchhhhhcCcc-ccCCCCceeccc----------ccccccChHhHHHHHHhcCCCcccccccccccCCc
Q 048287 32 KKKRNLPGTPDPEAEVIALSPK-TLMATNRFLCEI----------CGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKR 100 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k-~~~~~k~~~C~~----------Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k 100 (365)
++.|..| ..|.....|+.|+. .|. .+.|.+ |.|.|. ...|..|++.-- + . ....+.
T Consensus 115 ~~~~~~c-~~~~s~~~Lk~H~~~~H~---~~~c~lC~~~~kif~~e~k~Yt-~~el~~h~~~gd-~--d-----~~s~rG 181 (669)
T KOG2231|consen 115 KKECLHC-TEFKSVENLKNHMRDQHK---LHLCSLCLQNLKIFINERKLYT-RAELNLHLMFGD-P--D-----DESCRG 181 (669)
T ss_pred cCCCccc-cchhHHHHHHHHHHHhhh---hhccccccccceeeeeeeeheh-HHHHHHHHhcCC-C--c-----cccccC
Confidence 4455555 55557788888883 342 233433 445554 456777775432 1 0 000111
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccc------cccccchhhhhhhhcc-cCCcceecc---CC-
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKC------SKRYAVQSDWKAHSKT-CGTREYKCD---CG- 169 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C------~k~F~~~~~L~~H~~~-~~~kpy~C~---Cg- 169 (365)
.-.|..| ...|.....|.+|++.++ |.|..| +..|....+|..|-+. | |.|. |.
T Consensus 182 hp~C~~C-------~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~ 246 (669)
T KOG2231|consen 182 HPLCKFC-------HERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRT 246 (669)
T ss_pred Cccchhh-------hhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----cccccccccc
Confidence 2457777 999999999999998765 566666 4568888899999887 5 7775 53
Q ss_pred CccCChhHHHHHHHH
Q 048287 170 TVFSRRDSFITHRAF 184 (365)
Q Consensus 170 k~F~~~~~L~~H~~~ 184 (365)
+.|.....+..|++.
T Consensus 247 ~~f~~~~~~ei~lk~ 261 (669)
T KOG2231|consen 247 KKFYVAFELEIELKA 261 (669)
T ss_pred ceeeehhHHHHHHHh
Confidence 445555455555553
No 46
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.74 E-value=0.008 Score=35.62 Aligned_cols=24 Identities=29% Similarity=0.773 Sum_probs=20.2
Q ss_pred ceecccccccccChHhHHHHHHhc
Q 048287 60 RFLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
.|.|..|++.|.+...|+.|++..
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 378999999999999999998653
No 47
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.66 E-value=0.045 Score=37.39 Aligned_cols=32 Identities=16% Similarity=0.323 Sum_probs=18.2
Q ss_pred CCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCc
Q 048287 98 RKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKK 136 (365)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp 136 (365)
.+.|-.|++| +..+....+|++|+.++++.||
T Consensus 21 S~~PatCP~C-------~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPIC-------GAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT---------EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcc-------hhhccchhhHHHHHHHHhcccC
Confidence 4566777777 7777777777777776666554
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.21 E-value=0.041 Score=31.43 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=14.4
Q ss_pred eecc-CCCccCChhHHHHHHHHhh
Q 048287 164 YKCD-CGTVFSRRDSFITHRAFCD 186 (365)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~h~ 186 (365)
|+|. |+.... ...|.+|++.+|
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 6777 777776 777777777765
No 49
>PRK04860 hypothetical protein; Provisional
Probab=94.17 E-value=0.035 Score=47.92 Aligned_cols=39 Identities=21% Similarity=0.371 Sum_probs=33.2
Q ss_pred CceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCCh
Q 048287 59 NRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDL 121 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~ 121 (365)
-+|.|. |++ ....+.+|.++|. ++++|.|..| +..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~-------------g~~~YrC~~C-------~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVR-------------GEAVYRCRRC-------GETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhc-------------CCccEECCCC-------CceeEEe
Confidence 479998 998 6678999999998 8999999999 7777543
No 50
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.82 E-value=0.034 Score=32.86 Aligned_cols=22 Identities=27% Similarity=0.742 Sum_probs=16.8
Q ss_pred cccccccccccchhhhhhhhcc
Q 048287 137 WKCEKCSKRYAVQSDWKAHSKT 158 (365)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~ 158 (365)
|.|..|++.|.....|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6677788888888888777765
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.82 E-value=0.036 Score=54.30 Aligned_cols=107 Identities=17% Similarity=0.249 Sum_probs=69.9
Q ss_pred CceecccccccccChHhHHHHHH--hcCCCcccccccccccCC--ceeeCC--CCCccCCCCCCccCChhHHHHHHhhhc
Q 048287 59 NRFLCEICGKGFQRDQNLQLHRR--GHNLPWKLKQRTSKEVRK--RVYVCP--EKTCVHHHPSRALGDLTGIKKHFCRKH 132 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~~L~~H~~--~H~~~~~~~~~~~~~~~~--k~~~C~--~C~C~~~~~~~~f~~~~~L~~H~~~H~ 132 (365)
.++.|..|.+.|.+...|..|.+ .|. .+ +++.|+ .| ++.|.....+..|..+|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-------------~~~~~~~~~p~~~~-------~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-------------GESLKPFSCPYSLC-------GKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-------------cccCCceeeeccCC-------CccccccccccCCccccc
Confidence 46888888888888888888888 676 66 888888 56 888888888888888888
Q ss_pred CCCcccccc--ccccccchhhhhhhh-----cc-cCCcceecc---CCCccCChhHHHHHHHHh
Q 048287 133 GEKKWKCEK--CSKRYAVQSDWKAHS-----KT-CGTREYKCD---CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 133 ~ekp~~C~~--C~k~F~~~~~L~~H~-----~~-~~~kpy~C~---Cgk~F~~~~~L~~H~~~h 185 (365)
+.++++|.. |.+.+.....-..+. .. ...+.+.|. |...+.+...+..|...+
T Consensus 348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 411 (467)
T COG5048 348 SISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITH 411 (467)
T ss_pred CCCccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccc
Confidence 877776633 444444443311111 11 334445553 555555555555554444
No 52
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.79 E-value=0.036 Score=31.89 Aligned_cols=21 Identities=33% Similarity=0.698 Sum_probs=13.1
Q ss_pred eecc-CCCccCChhHHHHHHHH
Q 048287 164 YKCD-CGTVFSRRDSFITHRAF 184 (365)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~ 184 (365)
|.|+ |++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566 66666666666666543
No 53
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.59 E-value=0.028 Score=61.82 Aligned_cols=78 Identities=15% Similarity=0.226 Sum_probs=54.9
Q ss_pred CCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhh-cccCCcceecc-CCCccCCh
Q 048287 98 RKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHS-KTCGTREYKCD-CGTVFSRR 175 (365)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~-~~~~~kpy~C~-Cgk~F~~~ 175 (365)
..+.|+|+.| +..|.....|..|||..+-+-.- .+|. .+.....+.+=. ...+.++|.|. |...|..+
T Consensus 462 ~~kt~~cpkc-------~~~yk~a~~L~vhmRskhp~~~~--~~c~-~gq~~~~~arg~~~~~~~~p~~C~~C~~stttn 531 (1406)
T KOG1146|consen 462 FFKTLKCPKC-------NWHYKLAQTLGVHMRSKHPESQS--AYCK-AGQNHPRLARGEVYRCPGKPYPCRACNYSTTTN 531 (1406)
T ss_pred ccccccCCcc-------chhhhhHHHhhhcccccccccch--hHhH-hccccccccccccccCCCCcccceeeeeeeecc
Confidence 5688999999 99999999999999975433211 3332 222222222211 11677999999 99999999
Q ss_pred hHHHHHHHHh
Q 048287 176 DSFITHRAFC 185 (365)
Q Consensus 176 ~~L~~H~~~h 185 (365)
..|..|++..
T Consensus 532 g~LsihlqS~ 541 (1406)
T KOG1146|consen 532 GNLSIHLQSD 541 (1406)
T ss_pred hHHHHHHHHH
Confidence 9999999874
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.46 E-value=0.042 Score=52.18 Aligned_cols=74 Identities=20% Similarity=0.371 Sum_probs=48.3
Q ss_pred eCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcccccccc----ccccchhhhhhhhcc-cCCcceecc---CC----C
Q 048287 103 VCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCS----KRYAVQSDWKAHSKT-CGTREYKCD---CG----T 170 (365)
Q Consensus 103 ~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~----k~F~~~~~L~~H~~~-~~~kpy~C~---Cg----k 170 (365)
.|..| ...|-+-..|..|+|..+ |+-|.|+.-+ .-|..-..|..|-+. | |.|. |. .
T Consensus 222 ~C~FC-------~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~ 289 (493)
T COG5236 222 LCIFC-------KIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCY 289 (493)
T ss_pred hhhhc-------cceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEE
Confidence 46666 888888888888887554 2333333222 346777777777766 4 6663 42 4
Q ss_pred ccCChhHHHHHHHHhhhh
Q 048287 171 VFSRRDSFITHRAFCDAL 188 (365)
Q Consensus 171 ~F~~~~~L~~H~~~h~~~ 188 (365)
.|.....|..|+..-|+.
T Consensus 290 vf~~~~el~~h~~~~h~~ 307 (493)
T COG5236 290 VFPYHTELLEHLTRFHKV 307 (493)
T ss_pred EeccHHHHHHHHHHHhhc
Confidence 588888888898776653
No 55
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.19 E-value=0.089 Score=29.98 Aligned_cols=23 Identities=35% Similarity=0.702 Sum_probs=13.7
Q ss_pred eeCCCCCccCCCCCCccCChhHHHHHHhhhc
Q 048287 102 YVCPEKTCVHHHPSRALGDLTGIKKHFCRKH 132 (365)
Q Consensus 102 ~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~ 132 (365)
|.|+.| ..... ...|.+|+++|+
T Consensus 1 y~C~~C-------~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHC-------SYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSS-------S-EES-HHHHHHHHHHHH
T ss_pred CCCCCC-------CCcCC-HHHHHHHHHhhC
Confidence 566666 66666 667777776654
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.76 E-value=0.12 Score=29.99 Aligned_cols=21 Identities=33% Similarity=0.770 Sum_probs=17.2
Q ss_pred eecccccccccChHhHHHHHHh
Q 048287 61 FLCEICGKGFQRDQNLQLHRRG 82 (365)
Q Consensus 61 ~~C~~Cgk~F~~~~~L~~H~~~ 82 (365)
.+|+.||+.| ....|.+|+..
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 56779999764
No 57
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=91.74 E-value=0.16 Score=48.32 Aligned_cols=113 Identities=19% Similarity=0.277 Sum_probs=65.4
Q ss_pred CceecccccccccChHhHHHHHHh--cC--CCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHh--hh-
Q 048287 59 NRFLCEICGKGFQRDQNLQLHRRG--HN--LPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFC--RK- 131 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~~L~~H~~~--H~--~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~--~H- 131 (365)
.++.|-.|.|.|+.+..|+.|||. |. .|+ .+.=++.|.-.+- ..-+.+.....|.. +-
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~HrrinPk-------nreYDkfyiINY~--------ev~ks~t~~~~e~dret~~ 258 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRRINPK-------NREYDKFYIINYL--------EVGKSWTIVHSEDDRETNE 258 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcccCCC-------ccccceEEEEeHh--------hcCCccchhhhhhhhhhhc
Confidence 468999999999999999999964 42 110 0011122332221 11111111122221 10
Q ss_pred --------------cCCCc--cccccccccccchhhhhhhhcc-cC---------------------------Ccceecc
Q 048287 132 --------------HGEKK--WKCEKCSKRYAVQSDWKAHSKT-CG---------------------------TREYKCD 167 (365)
Q Consensus 132 --------------~~ekp--~~C~~C~k~F~~~~~L~~H~~~-~~---------------------------~kpy~C~ 167 (365)
.+..+ .+|-.|...+.....|..|+++ |. .+.-.|-
T Consensus 259 d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~ 338 (423)
T KOG2482|consen 259 DINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCA 338 (423)
T ss_pred cccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccc
Confidence 01122 4788888888888888888876 52 0113355
Q ss_pred -CCCccCChhHHHHHHHHhh
Q 048287 168 -CGTVFSRRDSFITHRAFCD 186 (365)
Q Consensus 168 -Cgk~F~~~~~L~~H~~~h~ 186 (365)
|...|.....|..|+.-+.
T Consensus 339 ~cd~~F~~e~~l~~hm~e~k 358 (423)
T KOG2482|consen 339 ECDLSFWKEPGLLIHMVEDK 358 (423)
T ss_pred cccccccCcchhhhhccccc
Confidence 8888999999999986653
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=91.11 E-value=0.16 Score=31.60 Aligned_cols=25 Identities=24% Similarity=0.739 Sum_probs=21.5
Q ss_pred CceecccccccccChHhHHHHHHhc
Q 048287 59 NRFLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
.+|.|++|++.|.....+..|++..
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChH
Confidence 3688999999999999999998543
No 59
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.51 E-value=0.21 Score=29.03 Aligned_cols=21 Identities=33% Similarity=0.858 Sum_probs=13.9
Q ss_pred eecc-CCCccCChhHHHHHHHHh
Q 048287 164 YKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
..|. ||+.| ..+.|.+|++.|
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~C 24 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKIC 24 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHhc
Confidence 3566 77777 566777776654
No 60
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.16 E-value=0.11 Score=45.88 Aligned_cols=83 Identities=20% Similarity=0.435 Sum_probs=66.9
Q ss_pred CCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcc-c----------CCcceec
Q 048287 98 RKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKT-C----------GTREYKC 166 (365)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~-~----------~~kpy~C 166 (365)
..+.|.|++-+| -+.|.....+..|..+-++ -.|..|.+.|.+...|..|+.. | |.--|.|
T Consensus 76 ~~~~~~cqvagc-----~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~C 147 (253)
T KOG4173|consen 76 RVPAFACQVAGC-----CQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQC 147 (253)
T ss_pred ccccccccccch-----HHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHH
Confidence 446689999988 8899888888888865444 3799999999999999999865 4 3456999
Q ss_pred c---CCCccCChhHHHHHHHHhhhh
Q 048287 167 D---CGTVFSRRDSFITHRAFCDAL 188 (365)
Q Consensus 167 ~---Cgk~F~~~~~L~~H~~~h~~~ 188 (365)
- |+..|.+...-..|+-.-|..
T Consensus 148 lvEgCt~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 148 LVEGCTEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred HHHhhhhhhhhhhhhhhHHHHhccC
Confidence 4 999999998888887665543
No 61
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=88.93 E-value=0.68 Score=44.87 Aligned_cols=48 Identities=21% Similarity=0.293 Sum_probs=36.7
Q ss_pred cccccccccccchhhhhhhhcc-cCC-----------------------cceecc-CC---CccCChhHHHHHHHH
Q 048287 137 WKCEKCSKRYAVQSDWKAHSKT-CGT-----------------------REYKCD-CG---TVFSRRDSFITHRAF 184 (365)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~-~~~-----------------------kpy~C~-Cg---k~F~~~~~L~~H~~~ 184 (365)
-.|-.|++.|.....-..||.. |+- .-|.|- |. +.|.+....+.||..
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4578888888888888888877 641 337787 87 888888888888865
No 62
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=88.63 E-value=0.12 Score=46.79 Aligned_cols=47 Identities=19% Similarity=0.307 Sum_probs=39.6
Q ss_pred CCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHH-HHhcC
Q 048287 34 KRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLH-RRGHN 84 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H-~~~H~ 84 (365)
=|=.|...|.+...|+.|+|. |-|+|.+|-|..-+--.|..| |++|.
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 477899999999999999874 889999999888777888888 56664
No 63
>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=87.37 E-value=0.47 Score=29.43 Aligned_cols=23 Identities=22% Similarity=0.385 Sum_probs=19.2
Q ss_pred ceecc-CCCccCChhHHHHHHHHh
Q 048287 163 EYKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 163 py~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
+|.|+ |++.|.....+..|++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 58899 999999888888888653
No 64
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=86.64 E-value=0.34 Score=33.70 Aligned_cols=29 Identities=34% Similarity=0.714 Sum_probs=20.6
Q ss_pred cCCcceecc-CCCccCChhHHHHHHHHhhh
Q 048287 159 CGTREYKCD-CGTVFSRRDSFITHRAFCDA 187 (365)
Q Consensus 159 ~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~~ 187 (365)
-|+.-++|+ |++.|.....+.+|+..-|+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 456667777 77777777777777766553
No 65
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=86.03 E-value=0.28 Score=44.44 Aligned_cols=43 Identities=23% Similarity=0.354 Sum_probs=34.2
Q ss_pred CCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhc
Q 048287 104 CPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSK 157 (365)
Q Consensus 104 C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~ 157 (365)
|.+| ++.|.+..-|..|++. |.|+|.+|.|...+--.|..|.-
T Consensus 13 cwyc-------nrefddekiliqhqka----khfkchichkkl~sgpglsihcm 55 (341)
T KOG2893|consen 13 CWYC-------NREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCM 55 (341)
T ss_pred eeec-------ccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehh
Confidence 7787 9999998888888764 56999999988777777777743
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=84.56 E-value=0.47 Score=40.68 Aligned_cols=44 Identities=20% Similarity=0.353 Sum_probs=27.4
Q ss_pred CCCCCCCCCCCch-hhhhcCccccCCCCceecccccccccChHhHH
Q 048287 33 KKRNLPGTPDPEA-EVIALSPKTLMATNRFLCEICGKGFQRDQNLQ 77 (365)
Q Consensus 33 ~~c~~c~~~~~~~-~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~ 77 (365)
++|+.||.++... ..-......+ -.+.+.|+-||++|.+...+.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~-~~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNA-IRRRRECLACGKRFTTFERVE 45 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCc-eeeeeeccccCCcceEeEecc
Confidence 4899999887332 2222222112 224599999999999876544
No 67
>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=84.56 E-value=0.67 Score=37.29 Aligned_cols=33 Identities=18% Similarity=0.426 Sum_probs=27.5
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccCh
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRD 73 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~ 73 (365)
..|+.|+.||+.|=. ..+.|..|+.||..|.-.
T Consensus 7 GtKR~Cp~CG~kFYD-----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYD-----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhcc-----------CCCCCccCCCCCCccCcc
Confidence 469999999999855 334788999999999876
No 68
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=84.33 E-value=0.57 Score=42.86 Aligned_cols=47 Identities=21% Similarity=0.543 Sum_probs=28.8
Q ss_pred eeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcc
Q 048287 102 YVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKT 158 (365)
Q Consensus 102 ~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 158 (365)
|.|..| |..... ..+.+|+.+-++ ..|.|-.|++.|.+ .+++.|.+-
T Consensus 4 FtCnvC-------gEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVC-------GESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhh-------hhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 667666 554433 345557666555 55677777777766 566666655
No 69
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.35 E-value=1.1 Score=42.81 Aligned_cols=26 Identities=38% Similarity=0.930 Sum_probs=18.5
Q ss_pred eeCCCCCccCCCCCCccCChhHHHHHHhhhc
Q 048287 102 YVCPEKTCVHHHPSRALGDLTGIKKHFCRKH 132 (365)
Q Consensus 102 ~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~ 132 (365)
|.|+.-.| ......+..|+.|.+..+
T Consensus 152 F~CP~skc-----~~~C~~~k~lk~H~K~~H 177 (493)
T COG5236 152 FKCPKSKC-----HRRCGSLKELKKHYKAQH 177 (493)
T ss_pred hcCCchhh-----hhhhhhHHHHHHHHHhhc
Confidence 77887555 666666788888887654
No 70
>PHA00626 hypothetical protein
Probab=80.91 E-value=0.99 Score=31.46 Aligned_cols=36 Identities=17% Similarity=0.217 Sum_probs=22.9
Q ss_pred CCCCCCCCCCchhhhhcCccccCCCCceecccccccccChH
Q 048287 34 KRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQ 74 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~ 74 (365)
.|+.||........+ .-....+|+|+.||..|+...
T Consensus 2 ~CP~CGS~~Ivrcg~-----cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKT-----MRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeece-----ecccCcceEcCCCCCeechhh
Confidence 588888753322211 112247899999999997654
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=80.71 E-value=2.8 Score=33.84 Aligned_cols=46 Identities=17% Similarity=0.393 Sum_probs=22.4
Q ss_pred cccccccccchhhhhhhhcccCCcceecc-CCCccCChhHHHHHHHHh
Q 048287 139 CEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 139 C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
|--|.+.|........- .......|.|. |...|=..-....|...|
T Consensus 58 C~~C~~~f~~~~~~~~~-~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPFD-ELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ccCcCCCCCCccccccc-ccccccceeCCCCCCccccccchhhhhhcc
Confidence 66666666543211100 01223456666 666666555555555544
No 72
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=75.80 E-value=1.1 Score=39.74 Aligned_cols=79 Identities=22% Similarity=0.443 Sum_probs=61.8
Q ss_pred CCceeccc--ccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhc---
Q 048287 58 TNRFLCEI--CGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKH--- 132 (365)
Q Consensus 58 ~k~~~C~~--Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~--- 132 (365)
...|.|.+ |-..|.....+..|-.+-+ + -.|.+| .+.|.+...|..|+...+
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h-------------~---~sCs~C-------~r~~Pt~hLLd~HI~E~HDs~ 133 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLH-------------G---NSCSFC-------KRAFPTGHLLDAHILEWHDSL 133 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhcc-------------c---chhHHH-------HHhCCchhhhhHHHHHHHHHH
Confidence 35688987 8889988888887764433 1 368888 999999999999986443
Q ss_pred -------CCCcccc--ccccccccchhhhhhhhcc-c
Q 048287 133 -------GEKKWKC--EKCSKRYAVQSDWKAHSKT-C 159 (365)
Q Consensus 133 -------~ekp~~C--~~C~k~F~~~~~L~~H~~~-~ 159 (365)
|..-|.| +.|+-.|.+...-+.|+-. |
T Consensus 134 Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 134 FQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred HHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 4456999 5699999999999999876 5
No 73
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=75.62 E-value=1.3 Score=40.11 Aligned_cols=42 Identities=21% Similarity=0.521 Sum_probs=26.3
Q ss_pred CCccccccccccccchhhhhhhhcc-c----------CCcc-----eecc-CCCccCCh
Q 048287 134 EKKWKCEKCSKRYAVQSDWKAHSKT-C----------GTRE-----YKCD-CGTVFSRR 175 (365)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~-~----------~~kp-----y~C~-Cgk~F~~~ 175 (365)
+|.+.|++|++.|.++.-+....+. . +..| ..|+ ||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3566777777777777666555543 1 1122 5688 99887654
No 74
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=75.50 E-value=6.2 Score=37.89 Aligned_cols=83 Identities=17% Similarity=0.336 Sum_probs=57.3
Q ss_pred ceeeCCCCCccCCCCCCccCChhHHHHHHh-hhc---C------------------CCccccccccccccchhhhhhhhc
Q 048287 100 RVYVCPEKTCVHHHPSRALGDLTGIKKHFC-RKH---G------------------EKKWKCEKCSKRYAVQSDWKAHSK 157 (365)
Q Consensus 100 k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~-~H~---~------------------ekp~~C~~C~k~F~~~~~L~~H~~ 157 (365)
...+|-.|. ......++.+..|+- .|. | -..++|-.|.|.|..+..|+.||+
T Consensus 143 fslqClFCn------~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 143 FSLQCLFCN------NEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred eeeEEEEec------chhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHH
Confidence 445788872 233445666667764 332 1 124789999999999999999987
Q ss_pred c--cCC-----------------------------------------------------cc--eecc-CCCccCChhHHH
Q 048287 158 T--CGT-----------------------------------------------------RE--YKCD-CGTVFSRRDSFI 179 (365)
Q Consensus 158 ~--~~~-----------------------------------------------------kp--y~C~-Cgk~F~~~~~L~ 179 (365)
. |.+ .+ -.|- |...+-....|.
T Consensus 217 kK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~ 296 (423)
T KOG2482|consen 217 KKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLF 296 (423)
T ss_pred hccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHH
Confidence 5 421 11 3698 999888899999
Q ss_pred HHHHHhhhh
Q 048287 180 THRAFCDAL 188 (365)
Q Consensus 180 ~H~~~h~~~ 188 (365)
.||+..|..
T Consensus 297 eHmk~vHe~ 305 (423)
T KOG2482|consen 297 EHMKIVHEF 305 (423)
T ss_pred HHHHHHHHh
Confidence 999987754
No 75
>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=75.43 E-value=2 Score=26.56 Aligned_cols=10 Identities=30% Similarity=1.076 Sum_probs=7.6
Q ss_pred Cccccccccc
Q 048287 135 KKWKCEKCSK 144 (365)
Q Consensus 135 kp~~C~~C~k 144 (365)
.++.|++|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 6788888874
No 76
>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=74.36 E-value=3.6 Score=32.89 Aligned_cols=25 Identities=20% Similarity=0.529 Sum_probs=22.5
Q ss_pred ceec----c-CCCccCChhHHHHHHHHhhh
Q 048287 163 EYKC----D-CGTVFSRRDSFITHRAFCDA 187 (365)
Q Consensus 163 py~C----~-Cgk~F~~~~~L~~H~~~h~~ 187 (365)
-|.| . |+..+.+...+.+|.+.+|+
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 7 99999999999999998774
No 77
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=74.29 E-value=0.99 Score=31.42 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=19.4
Q ss_pred cCCCccccccccccccchhhhhhhhcc-cC
Q 048287 132 HGEKKWKCEKCSKRYAVQSDWKAHSKT-CG 160 (365)
Q Consensus 132 ~~ekp~~C~~C~k~F~~~~~L~~H~~~-~~ 160 (365)
.||--++|+.|+..|..+.++.+|... |+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 455666777777777777777777665 53
No 78
>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=74.20 E-value=2.2 Score=35.05 Aligned_cols=37 Identities=14% Similarity=0.213 Sum_probs=28.8
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHH
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQ 77 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~ 77 (365)
..|+.|+.||+.|=. ..+.|..|+.||..|.....++
T Consensus 7 GtKr~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 7 GTKRICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CccccCCCcCccccc-----------cCCCCccCCCcCCccCcchhhc
Confidence 468999999999855 3347889999999987664433
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.15 E-value=1.3 Score=31.25 Aligned_cols=37 Identities=24% Similarity=0.191 Sum_probs=24.8
Q ss_pred CCCcCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccc
Q 048287 27 PNTAAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGK 68 (365)
Q Consensus 27 ~~~~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk 68 (365)
-....++.|+.||+.... +-.+--....+|.|+.||-
T Consensus 22 ~e~~v~F~CPnCGe~~I~-----Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 22 GETAVKFPCPNCGEVEIY-----RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred CCceeEeeCCCCCceeee-----hhhhHHHcCCceECCCcCc
Confidence 334678999999975433 3333344458899999984
No 80
>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=73.58 E-value=3 Score=27.43 Aligned_cols=25 Identities=28% Similarity=0.586 Sum_probs=17.1
Q ss_pred CCCceecccccccccCh----HhHHHHHH
Q 048287 57 ATNRFLCEICGKGFQRD----QNLQLHRR 81 (365)
Q Consensus 57 ~~k~~~C~~Cgk~F~~~----~~L~~H~~ 81 (365)
......|.+|++.|... ++|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45778899999999875 78999984
No 81
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=71.92 E-value=1.6 Score=37.38 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=11.9
Q ss_pred ccccccccccccchhhhh
Q 048287 136 KWKCEKCSKRYAVQSDWK 153 (365)
Q Consensus 136 p~~C~~C~k~F~~~~~L~ 153 (365)
.++|..||++|.....+.
T Consensus 28 ~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 28 RRECLACGKRFTTFERVE 45 (154)
T ss_pred eeeccccCCcceEeEecc
Confidence 367777777777665543
No 82
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=70.07 E-value=2 Score=31.89 Aligned_cols=42 Identities=10% Similarity=0.106 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCchhhhhcCccccCCCCceecc--cccccccChHhH
Q 048287 33 KKRNLPGTPDPEAEVIALSPKTLMATNRFLCE--ICGKGFQRDQNL 76 (365)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~--~Cgk~F~~~~~L 76 (365)
.+|+.||....-...-..+.. ..+..+.|. .||.+|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCCEEEEEEEE
Confidence 479999998754444444433 567789998 999999876543
No 83
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=68.06 E-value=3.6 Score=27.95 Aligned_cols=25 Identities=44% Similarity=0.796 Sum_probs=19.8
Q ss_pred ceecccccccccCh-----HhHHHHHH-hcC
Q 048287 60 RFLCEICGKGFQRD-----QNLQLHRR-GHN 84 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~-----~~L~~H~~-~H~ 84 (365)
.-.|.+|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 45699999998766 58999997 553
No 84
>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=67.33 E-value=11 Score=30.07 Aligned_cols=25 Identities=20% Similarity=0.434 Sum_probs=19.8
Q ss_pred CCceecccccccccChHhHHHHHHhc
Q 048287 58 TNRFLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 58 ~k~~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
-+...|..|+..... ..+..|++..
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~ 33 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKR 33 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHh
Confidence 356789999988876 8899998743
No 85
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=64.83 E-value=4.2 Score=25.87 Aligned_cols=12 Identities=33% Similarity=0.994 Sum_probs=5.9
Q ss_pred Cccccccccccc
Q 048287 135 KKWKCEKCSKRY 146 (365)
Q Consensus 135 kp~~C~~C~k~F 146 (365)
+..+|..|+..|
T Consensus 24 ~~vrC~~C~~~f 35 (37)
T PF13719_consen 24 RKVRCPKCGHVF 35 (37)
T ss_pred cEEECCCCCcEe
Confidence 344555555444
No 86
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=64.47 E-value=3.1 Score=38.21 Aligned_cols=47 Identities=23% Similarity=0.604 Sum_probs=37.9
Q ss_pred cccccccccccchhhhhhhhcccCCcceecc-CCCccCChhHHHHHHHHh
Q 048287 137 WKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
|.|..||-.... ..+..|+..+...-|.|- |++.|.+ ..+..|.+-.
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhhhc
Confidence 789999987554 466779988666889998 9999998 7788897654
No 87
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=64.04 E-value=2.7 Score=38.09 Aligned_cols=44 Identities=16% Similarity=0.223 Sum_probs=31.6
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccC----------CCCc-----eecccccccccCh
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLM----------ATNR-----FLCEICGKGFQRD 73 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~----------~~k~-----~~C~~Cgk~F~~~ 73 (365)
.++..|+.|++.|....+.....+... +..| .+|+.||-.|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 467899999999999877766655321 1222 5799999887654
No 88
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=63.70 E-value=4.9 Score=38.46 Aligned_cols=12 Identities=17% Similarity=0.099 Sum_probs=9.5
Q ss_pred CCceeeCCCCCc
Q 048287 98 RKRVYVCPEKTC 109 (365)
Q Consensus 98 ~~k~~~C~~C~C 109 (365)
+.|...|..|++
T Consensus 209 G~RyL~CslC~t 220 (309)
T PRK03564 209 GLRYLHCNLCES 220 (309)
T ss_pred CceEEEcCCCCC
Confidence 678888999855
No 89
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=62.36 E-value=4.6 Score=41.53 Aligned_cols=28 Identities=21% Similarity=0.419 Sum_probs=24.6
Q ss_pred CCCceecccccccccChHhHHHHHHhcC
Q 048287 57 ATNRFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 57 ~~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
...+..|..||++|........||-.|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3567899999999999999999998885
No 90
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=62.21 E-value=5.6 Score=25.18 Aligned_cols=34 Identities=12% Similarity=0.037 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCchhhhhcCccccCCCCceeccccccccc
Q 048287 33 KKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQ 71 (365)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~ 71 (365)
-.|+.|++.|.-.+.... ......+|..|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~ip-----~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP-----PKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHCC-----CCCcEEECCCCCCEeC
Confidence 358899988876554332 3346788999998873
No 91
>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=61.94 E-value=4.1 Score=34.46 Aligned_cols=44 Identities=11% Similarity=0.053 Sum_probs=25.5
Q ss_pred CCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHH
Q 048287 34 KRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQ 77 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~ 77 (365)
+|+.|+..+...-.-.....-..=.++=+|..||+.|++...+.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAE 45 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecc
Confidence 68888876543221111111111135678999999999876544
No 92
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=61.71 E-value=2.2 Score=40.98 Aligned_cols=29 Identities=7% Similarity=-0.160 Sum_probs=22.7
Q ss_pred ccCCCCceecccccccccChHhHHHHH-Hhc
Q 048287 54 TLMATNRFLCEICGKGFQRDQNLQLHR-RGH 83 (365)
Q Consensus 54 ~~~~~k~~~C~~Cgk~F~~~~~L~~H~-~~H 83 (365)
..+-.++|+|. |++.+.++..|+.|- ..|
T Consensus 207 ~~t~~~p~k~~-~~~~~~T~~~l~~HS~N~~ 236 (442)
T KOG4124|consen 207 AETTGTPKKMP-ESLVMDTSSPLSDHSMNID 236 (442)
T ss_pred cccccCCccCc-ccccccccchhhhccccCC
Confidence 34456899996 999999999999884 444
No 93
>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=61.21 E-value=4.3 Score=25.75 Aligned_cols=34 Identities=12% Similarity=0.040 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCchhhhhcCccccCCCCceeccccccccc
Q 048287 33 KKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQ 71 (365)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~ 71 (365)
..|+.|+..|.-...... .......|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEEE
Confidence 579999998765543322 1223688999998875
No 94
>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=61.12 E-value=2 Score=38.89 Aligned_cols=31 Identities=16% Similarity=0.338 Sum_probs=21.7
Q ss_pred cCCcceecc-CCCccCChhHHHHHHHHhhhhh
Q 048287 159 CGTREYKCD-CGTVFSRRDSFITHRAFCDALA 189 (365)
Q Consensus 159 ~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~~~~ 189 (365)
..+..|.|. |+|.|.-..-.++|+..-|...
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 455678998 9999998888888987766543
No 95
>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=60.23 E-value=5.3 Score=32.14 Aligned_cols=14 Identities=36% Similarity=0.790 Sum_probs=7.6
Q ss_pred cceecc-CCCccCCh
Q 048287 162 REYKCD-CGTVFSRR 175 (365)
Q Consensus 162 kpy~C~-Cgk~F~~~ 175 (365)
.|-.|. ||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 455555 66655543
No 96
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=59.06 E-value=6.3 Score=34.18 Aligned_cols=23 Identities=35% Similarity=0.706 Sum_probs=18.7
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcccccccc
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCS 143 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~ 143 (365)
.|+|++| |. +|.|+-|.+|++|+
T Consensus 134 ~~vC~vC-------Gy-------------~~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVC-------GY-------------THEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCC-------CC-------------cccCCCCCcCCCCC
Confidence 7999999 65 34568899999998
No 97
>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=58.82 E-value=7 Score=22.90 Aligned_cols=25 Identities=32% Similarity=0.559 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCchhhhhcCccccCCCCceeccccccccc
Q 048287 33 KKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQ 71 (365)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~ 71 (365)
+.|+.|++.-+. ..-.|+.||..|.
T Consensus 1 K~CP~C~~~V~~--------------~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 1 KTCPECGAEVPE--------------SAKFCPHCGYDFE 25 (26)
T ss_pred CcCCCCcCCchh--------------hcCcCCCCCCCCc
Confidence 357777765422 2234888888874
No 98
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=58.19 E-value=13 Score=36.64 Aligned_cols=121 Identities=14% Similarity=0.286 Sum_probs=68.9
Q ss_pred Cceec--ccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCC--
Q 048287 59 NRFLC--EICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGE-- 134 (365)
Q Consensus 59 k~~~C--~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~e-- 134 (365)
.-|.| +.|+..+..+....+|...|.......... .+.=...|-|..-.| .+ .-+.+..|-.-|+..
T Consensus 270 Ehyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dg-f~rfs~syhC~~~~C-----~k---sTsdV~~h~nFht~~~n 340 (480)
T KOG4377|consen 270 EHYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDG-FHRFSNSYHCTGQIC-----EK---STSDVLLHDNFHTDKRN 340 (480)
T ss_pred hhhcccCccccccccchhhhHHHHHHHhhcccccccc-hhhcCccchhhhccc-----Cc---ccccccccCcccccccc
Confidence 44777 569877777999999998885211100000 000111256655444 66 234445555555421
Q ss_pred -----Ccccccccc--ccccchhhhhhhhcc-cCC------------------------cceecc---CCCccCChhHHH
Q 048287 135 -----KKWKCEKCS--KRYAVQSDWKAHSKT-CGT------------------------REYKCD---CGTVFSRRDSFI 179 (365)
Q Consensus 135 -----kp~~C~~C~--k~F~~~~~L~~H~~~-~~~------------------------kpy~C~---Cgk~F~~~~~L~ 179 (365)
..|.|..|+ ..|.....-.-|.+- .++ ..|.|+ |+..|...+.+.
T Consensus 341 ~GfrrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~ 420 (480)
T KOG4377|consen 341 NGFRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMA 420 (480)
T ss_pred CceecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhh
Confidence 247787776 555533322223221 100 126675 999999999999
Q ss_pred HHHHHhhhh
Q 048287 180 THRAFCDAL 188 (365)
Q Consensus 180 ~H~~~h~~~ 188 (365)
.|.+.|...
T Consensus 421 shkrkheRq 429 (480)
T KOG4377|consen 421 SHKRKHERQ 429 (480)
T ss_pred hhhhhhhhh
Confidence 999999865
No 99
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=57.03 E-value=5.7 Score=33.71 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=25.2
Q ss_pred CCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHH
Q 048287 34 KRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQ 77 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~ 77 (365)
+|+.|+-.+...-.-..-..-..=.++=.|+.|++.|++.....
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~E 45 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAE 45 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheee
Confidence 68888776543221111111112235678999999998876543
No 100
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.88 E-value=8.9 Score=30.64 Aligned_cols=37 Identities=11% Similarity=0.196 Sum_probs=27.8
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHH
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQL 78 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~ 78 (365)
..|+.|+.|++.|-. ....|..|++||+.|. .+.|..
T Consensus 7 GtKridPetg~KFYD-----------LNrdPiVsPytG~s~P-~s~fe~ 43 (129)
T COG4530 7 GTKRIDPETGKKFYD-----------LNRDPIVSPYTGKSYP-RSYFEE 43 (129)
T ss_pred cccccCccccchhhc-----------cCCCccccCcccccch-HHHHHh
Confidence 358889999998854 3457899999999994 444543
No 101
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=55.59 E-value=3.9 Score=43.02 Aligned_cols=27 Identities=33% Similarity=0.588 Sum_probs=24.7
Q ss_pred CCceecccccccccChHhHHHHHHhcC
Q 048287 58 TNRFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 58 ~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
...|.|.+|+|.|.....+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 356999999999999999999999996
No 102
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=55.42 E-value=6.4 Score=27.89 Aligned_cols=34 Identities=26% Similarity=0.217 Sum_probs=20.7
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccc
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGK 68 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk 68 (365)
..++.|+.||+.. +.+=.+--....+|+|+.||-
T Consensus 23 ~~~F~CPnCG~~~-----I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVI-----IYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCee-----EeechhHHhcCCceECCCCCC
Confidence 4678888888742 222333333447788888874
No 103
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.05 E-value=12 Score=31.68 Aligned_cols=35 Identities=20% Similarity=0.562 Sum_probs=17.6
Q ss_pred CccccccccccccchhhhhhhhcccCCcceecc-CCCcc
Q 048287 135 KKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVF 172 (365)
Q Consensus 135 kp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F 172 (365)
.-|.|+.|++.|.....+..- ..+..|.|+ ||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~---d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLL---DMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhc---CCCCcEECCCCCCEE
Confidence 346666666666654433210 012336666 66554
No 104
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.76 E-value=11 Score=41.26 Aligned_cols=11 Identities=45% Similarity=0.893 Sum_probs=6.6
Q ss_pred Cceeccccccc
Q 048287 59 NRFLCEICGKG 69 (365)
Q Consensus 59 k~~~C~~Cgk~ 69 (365)
....|+.||+.
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 44556666665
No 105
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=54.09 E-value=12 Score=30.18 Aligned_cols=45 Identities=18% Similarity=0.208 Sum_probs=30.4
Q ss_pred CCcCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccC
Q 048287 28 NTAAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQR 72 (365)
Q Consensus 28 ~~~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~ 72 (365)
.+..+++|+.||-..-....+..--.--...--|.|.-|+..|..
T Consensus 70 ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 70 GAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 455699999999875554444433323334456999999998864
No 106
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=53.93 E-value=11 Score=32.52 Aligned_cols=33 Identities=15% Similarity=0.546 Sum_probs=20.9
Q ss_pred CCccccccccccccchhhhhhhhcccCCcceecc-CCCccCC
Q 048287 134 EKKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSR 174 (365)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~ 174 (365)
..-|.|+.|+.+|.....+. .-|.|+ ||.....
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME--------LNFTCPRCGAMLDY 140 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEeee
Confidence 34577777777776666653 247777 7766443
No 107
>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=50.86 E-value=11 Score=21.95 Aligned_cols=20 Identities=15% Similarity=0.423 Sum_probs=15.5
Q ss_pred eecccccccccChHhHHHHHH
Q 048287 61 FLCEICGKGFQRDQNLQLHRR 81 (365)
Q Consensus 61 ~~C~~Cgk~F~~~~~L~~H~~ 81 (365)
..|++|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5577777864
No 108
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=50.60 E-value=13 Score=32.75 Aligned_cols=35 Identities=20% Similarity=0.668 Sum_probs=26.0
Q ss_pred CCccccccccccccchhhhhhhhcccCCcceecc-CCCccCChh
Q 048287 134 EKKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRRD 176 (365)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~ 176 (365)
..-|.|+.|++.|.....+. .-|.|+ ||......+
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLEEYD 150 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCeecc
Confidence 45688999998888877653 369999 998766543
No 109
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=50.52 E-value=7.9 Score=25.75 Aligned_cols=28 Identities=14% Similarity=0.180 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceecccccccc
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGF 70 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F 70 (365)
.|.|..||..+... ...+..|+.||-.-
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCceE
Confidence 57899999876532 34668899998643
No 110
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=50.17 E-value=14 Score=35.39 Aligned_cols=12 Identities=17% Similarity=0.166 Sum_probs=9.8
Q ss_pred CCceeeCCCCCc
Q 048287 98 RKRVYVCPEKTC 109 (365)
Q Consensus 98 ~~k~~~C~~C~C 109 (365)
+.|...|..|++
T Consensus 207 G~RyL~CslC~t 218 (305)
T TIGR01562 207 GLRYLSCSLCAT 218 (305)
T ss_pred CceEEEcCCCCC
Confidence 778889999955
No 111
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=50.00 E-value=10 Score=31.65 Aligned_cols=31 Identities=26% Similarity=0.384 Sum_probs=18.7
Q ss_pred cceecc-CCCccCChhHHHHHHHHhhhhhhhhhhh
Q 048287 162 REYKCD-CGTVFSRRDSFITHRAFCDALAEETARV 195 (365)
Q Consensus 162 kpy~C~-Cgk~F~~~~~L~~H~~~h~~~~~~~~~~ 195 (365)
.--.|- ||+.|.. |++|.+.||++..+..+.
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp~eYR~ 102 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTPEEYRA 102 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-HHHHHH
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCHHHHHH
Confidence 446777 9999975 589999999887665543
No 112
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=49.91 E-value=8.6 Score=29.47 Aligned_cols=12 Identities=50% Similarity=1.445 Sum_probs=6.5
Q ss_pred cccccccccccc
Q 048287 136 KWKCEKCSKRYA 147 (365)
Q Consensus 136 p~~C~~C~k~F~ 147 (365)
-|+|..|+..|.
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 355555555554
No 113
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=49.83 E-value=21 Score=32.92 Aligned_cols=76 Identities=21% Similarity=0.402 Sum_probs=44.1
Q ss_pred ChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhh
Q 048287 72 RDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSD 151 (365)
Q Consensus 72 ~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~ 151 (365)
+..+|+.+-+.+.. .....++.|.|..| .... . .+.-...+--+|..|.+.|.---.
T Consensus 91 Te~Nlrm~d~a~~~--------~ip~~drqFaC~~C-------d~~W------w--Rrvp~rKeVSRCr~C~~rYDPVP~ 147 (278)
T PF15135_consen 91 TEENLRMFDDAQEN--------LIPSVDRQFACSSC-------DHMW------W--RRVPQRKEVSRCRKCRKRYDPVPC 147 (278)
T ss_pred hHHHHHHhhhhhhc--------cccccceeeecccc-------chHH------H--hccCcccccccccccccccCCCcc
Confidence 45677777666541 11225588999998 3211 0 011112234579999888765432
Q ss_pred hhhhhcccCCcceecc-CCCccCC
Q 048287 152 WKAHSKTCGTREYKCD-CGTVFSR 174 (365)
Q Consensus 152 L~~H~~~~~~kpy~C~-Cgk~F~~ 174 (365)
-+..|.-.|.|. |+..|.-
T Consensus 148 ----dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 148 ----DKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred ----ccccceeeeecccccccchh
Confidence 122556679998 9999973
No 114
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=49.75 E-value=14 Score=36.67 Aligned_cols=37 Identities=24% Similarity=0.628 Sum_probs=25.8
Q ss_pred CCCccccccccccccchhhhhhhhcccCCcceecc-CCCc
Q 048287 133 GEKKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTV 171 (365)
Q Consensus 133 ~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~ 171 (365)
....|+|+.|.+.|.....++-- .-..-.|.|. |+-.
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L~--~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQLL--DNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccchhhhHHHHhh--cccCceEEEecCCCc
Confidence 34579999999999887776421 1334569998 8743
No 115
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.05 E-value=25 Score=28.44 Aligned_cols=51 Identities=22% Similarity=0.315 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHHHHhcC
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
...|--|.+.|+...... ........+|.|+.|.+.|-..-.+-.|...|.
T Consensus 55 ~~~C~~C~~~f~~~~~~~--~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSP--FDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCcccCcCCCCCCccccc--ccccccccceeCCCCCCccccccchhhhhhccC
Confidence 356999999987753211 111344568999999999999999999988885
No 116
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=48.46 E-value=2.9 Score=39.68 Aligned_cols=54 Identities=19% Similarity=0.300 Sum_probs=23.5
Q ss_pred CCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccccchhhhhhhhcccCCcceecc-CCCcc
Q 048287 98 RKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVF 172 (365)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F 172 (365)
|.|...|..|+..| .-+..+|..||..-...-.+..-...-+.+-+.|+ |+.-+
T Consensus 194 G~R~L~Cs~C~t~W---------------------~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 194 GKRYLHCSLCGTEW---------------------RFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp -EEEEEETTT--EE---------------------E--TTS-TTT---SS-EEE--------SEEEEEETTTTEEE
T ss_pred ccEEEEcCCCCCee---------------------eecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH
Confidence 56888999994321 12346899999764333222110111345678898 87433
No 117
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=47.73 E-value=16 Score=33.16 Aligned_cols=30 Identities=23% Similarity=0.488 Sum_probs=23.3
Q ss_pred CCCccccccccccccchhhhhhhhcc-cCCc
Q 048287 133 GEKKWKCEKCSKRYAVQSDWKAHSKT-CGTR 162 (365)
Q Consensus 133 ~ekp~~C~~C~k~F~~~~~L~~H~~~-~~~k 162 (365)
.+.+|.|..|+|.|.-..-++.|+.. |.++
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 56789999999999999999999988 7543
No 118
>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=47.30 E-value=14 Score=23.00 Aligned_cols=10 Identities=30% Similarity=0.611 Sum_probs=6.9
Q ss_pred Cccccccccc
Q 048287 135 KKWKCEKCSK 144 (365)
Q Consensus 135 kp~~C~~C~k 144 (365)
.|..|++|+.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4667877774
No 119
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.09 E-value=7.7 Score=26.46 Aligned_cols=29 Identities=21% Similarity=0.210 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCCchhhhhcCccccCCCCceeccccccc
Q 048287 31 AKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKG 69 (365)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~ 69 (365)
..|+|-.||+.+. .........|+.||-.
T Consensus 5 ~~Y~C~~Cg~~~~----------~~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVE----------LDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeee----------hhhccCceeCCCCCcE
Confidence 5789999999872 1233466789999854
No 120
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=47.05 E-value=22 Score=30.58 Aligned_cols=34 Identities=15% Similarity=0.499 Sum_probs=27.0
Q ss_pred ccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcccccccccc
Q 048287 96 EVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKR 145 (365)
Q Consensus 96 ~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~ 145 (365)
.....-|.|+.| +..|.....+. .-|.|+.||..
T Consensus 104 e~~~~~Y~Cp~c-------~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNM-------CVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCC-------CcEeeHHHHHH---------cCCcCCCCCCE
Confidence 346678999998 88888877764 26999999965
No 121
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=46.10 E-value=13 Score=24.63 Aligned_cols=14 Identities=21% Similarity=0.757 Sum_probs=10.0
Q ss_pred CceecccccccccC
Q 048287 59 NRFLCEICGKGFQR 72 (365)
Q Consensus 59 k~~~C~~Cgk~F~~ 72 (365)
..|.|+.||..|..
T Consensus 2 ~~y~C~~CG~~~~~ 15 (46)
T PRK00398 2 AEYKCARCGREVEL 15 (46)
T ss_pred CEEECCCCCCEEEE
Confidence 35788888887754
No 122
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=45.49 E-value=16 Score=35.23 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=21.8
Q ss_pred CceecccccccccChHhHHHHH--HhcC
Q 048287 59 NRFLCEICGKGFQRDQNLQLHR--RGHN 84 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~~L~~H~--~~H~ 84 (365)
..+-|+.|++.|.+..-+..|. +.|.
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~ 264 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHC 264 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhh
Confidence 4577999999999999999997 5564
No 123
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=45.35 E-value=11 Score=24.51 Aligned_cols=37 Identities=16% Similarity=0.371 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCchhhhhcCcccc--CCCCceeccccccccc
Q 048287 33 KKRNLPGTPDPEAEVIALSPKTL--MATNRFLCEICGKGFQ 71 (365)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~k~~--~~~k~~~C~~Cgk~F~ 71 (365)
.+|+.|+..... .+....+.- ....-|.|..|+..|.
T Consensus 1 ~~Cp~C~~~~a~--~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREAT--FFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEE--EEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 368888754322 222222221 1234699999998775
No 124
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=45.28 E-value=10 Score=35.08 Aligned_cols=26 Identities=12% Similarity=0.226 Sum_probs=17.4
Q ss_pred CCcceecc-CCCccCChhHHHHHHHHh
Q 048287 160 GTREYKCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 160 ~~kpy~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
..+++.|+ |+........|..-.+.|
T Consensus 206 k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 206 KGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred cCCCCCCCCCCCcccccccceeeeecc
Confidence 45788998 987776666665444444
No 125
>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=44.20 E-value=15 Score=30.24 Aligned_cols=29 Identities=14% Similarity=0.237 Sum_probs=16.2
Q ss_pred cccccccccccchhhhhhhhcccCCcceecc-CCCccCCh
Q 048287 137 WKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRR 175 (365)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~ 175 (365)
+.|..|+++|-.. ...|-.|. ||..|...
T Consensus 10 r~Cp~cg~kFYDL----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc----------CCCCccCCCcCCccCcc
Confidence 4566666665432 23556666 66666544
No 126
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=43.79 E-value=9.9 Score=28.19 Aligned_cols=14 Identities=29% Similarity=0.740 Sum_probs=7.4
Q ss_pred Ccceecc---CCCccCC
Q 048287 161 TREYKCD---CGTVFSR 174 (365)
Q Consensus 161 ~kpy~C~---Cgk~F~~ 174 (365)
++-|.|. ||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 3445553 6666653
No 127
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.72 E-value=13 Score=32.64 Aligned_cols=34 Identities=12% Similarity=0.396 Sum_probs=26.1
Q ss_pred cCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccc
Q 048287 97 VRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRY 146 (365)
Q Consensus 97 ~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F 146 (365)
....-|.|+.| ++.|.....+. .-|.|+.||...
T Consensus 113 ~~~~~Y~Cp~C-------~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 113 ENNMFFFCPNC-------HIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred cCCCEEECCCC-------CcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 35578999998 88887776653 369999999653
No 128
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.46 E-value=14 Score=20.95 Aligned_cols=7 Identities=43% Similarity=1.179 Sum_probs=5.1
Q ss_pred ccccccc
Q 048287 63 CEICGKG 69 (365)
Q Consensus 63 C~~Cgk~ 69 (365)
|+.||..
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 8888764
No 129
>PF14353 CpXC: CpXC protein
Probab=43.05 E-value=5.5 Score=32.76 Aligned_cols=51 Identities=20% Similarity=0.212 Sum_probs=31.6
Q ss_pred CCCCCCCCCCCchhhhhcCc--------cccCC-CCceecccccccccChHhHHHHHHhc
Q 048287 33 KKRNLPGTPDPEAEVIALSP--------KTLMA-TNRFLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~--------k~~~~-~k~~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
-.|+.|+..|.-.--..... +...+ -..|.|+.||+.|.-...|..|-..+
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 36999999875533222111 12222 25799999999998777666665444
No 130
>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=43.04 E-value=5.9 Score=25.56 Aligned_cols=13 Identities=23% Similarity=0.749 Sum_probs=10.5
Q ss_pred Cceeccccccccc
Q 048287 59 NRFLCEICGKGFQ 71 (365)
Q Consensus 59 k~~~C~~Cgk~F~ 71 (365)
.-|.|..||..|+
T Consensus 27 ~fy~C~~C~~~wr 39 (39)
T PF01096_consen 27 LFYVCCNCGHRWR 39 (39)
T ss_dssp EEEEESSSTEEEE
T ss_pred EEEEeCCCCCeeC
Confidence 4599999998873
No 131
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.03 E-value=21 Score=30.18 Aligned_cols=40 Identities=18% Similarity=0.407 Sum_probs=27.2
Q ss_pred ccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccccc
Q 048287 96 EVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKRY 146 (365)
Q Consensus 96 ~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~F 146 (365)
......|.|+.| +..|.....+.. .+ .+..|.|+.||...
T Consensus 94 e~~~~~Y~Cp~C-------~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 94 ETNNAYYKCPNC-------QSKYTFLEANQL---LD-MDGTFTCPRCGEEL 133 (147)
T ss_pred ccCCcEEECcCC-------CCEeeHHHHHHh---cC-CCCcEECCCCCCEE
Confidence 346678999998 888886543332 01 14459999999764
No 132
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=42.51 E-value=15 Score=36.70 Aligned_cols=29 Identities=24% Similarity=0.388 Sum_probs=25.2
Q ss_pred ccccCCCCceeccccc-ccccChHhHHHHH
Q 048287 52 PKTLMATNRFLCEICG-KGFQRDQNLQLHR 80 (365)
Q Consensus 52 ~k~~~~~k~~~C~~Cg-k~F~~~~~L~~H~ 80 (365)
-|.|.-..-|.|++|| ++|.-...+++|.
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHh
Confidence 4667788999999999 8999999999995
No 133
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=40.69 E-value=81 Score=30.37 Aligned_cols=115 Identities=18% Similarity=0.359 Sum_probs=61.0
Q ss_pred CCCCCCCcCCCCCCCCCCCCCchhhh------hcCccccCCCCceecccccccccChHhHHHHHHhcCCCcccccccccc
Q 048287 23 SNNPPNTAAKKKRNLPGTPDPEAEVI------ALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKE 96 (365)
Q Consensus 23 ~~~~~~~~~~~~c~~c~~~~~~~~~l------~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~ 96 (365)
+-.||+..+...|++-...|+..+.. .-|.. ....-|.|+.|+...
T Consensus 235 ~~~Pp~~~~~~~~sLvkmGFP~~~~e~~ps~C~CH~~--~~~~Gy~CP~Ckakv-------------------------- 286 (378)
T KOG2807|consen 235 HTHPPPANKSKECSLVKMGFPSRSPEDTPSFCACHSE--LSGGGYFCPQCKAKV-------------------------- 286 (378)
T ss_pred cCCCCCcccccCCceEEecCCCcccccCcchheeccc--cccCceeCCcccCee--------------------------
Confidence 33445544555677777777743321 22311 123458888886532
Q ss_pred cCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcc------------ccccccccccchhhhhhhhcccCCcce
Q 048287 97 VRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKW------------KCEKCSKRYAVQSDWKAHSKTCGTREY 164 (365)
Q Consensus 97 ~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~------------~C~~C~k~F~~~~~L~~H~~~~~~kpy 164 (365)
-.-|-.|++| +-......+|.+-.+---.-++| .|-.|+- . ..+...|
T Consensus 287 -CsLP~eCpiC-------~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~------~------~~~~~~y 346 (378)
T KOG2807|consen 287 -CSLPIECPIC-------SLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQG------E------LLSSGRY 346 (378)
T ss_pred -ecCCccCCcc-------ceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeecc------c------cCCCCcE
Confidence 3456678887 77766666665433211111111 1544510 0 1234558
Q ss_pred ecc-CCCccCChhHHHHHHHHh
Q 048287 165 KCD-CGTVFSRRDSFITHRAFC 185 (365)
Q Consensus 165 ~C~-Cgk~F~~~~~L~~H~~~h 185 (365)
.|. |...|-.--....|...|
T Consensus 347 ~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 347 RCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred EchhccceeeccchHHHHhhhh
Confidence 888 888887666666666655
No 134
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=39.73 E-value=19 Score=29.94 Aligned_cols=15 Identities=7% Similarity=-0.051 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCchh
Q 048287 32 KKKRNLPGTPDPEAE 46 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~ 46 (365)
+++|..||+.|.+-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 468899999988755
No 135
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=39.31 E-value=23 Score=25.49 Aligned_cols=35 Identities=23% Similarity=0.369 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHh
Q 048287 31 AKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQN 75 (365)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~ 75 (365)
....|+.||..... ....+.|.|+.||..+.+..+
T Consensus 27 TSq~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----------RRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred CccCccCccccccc----------ccccceEEcCCCCCEECcHHH
Confidence 45679999987544 234578999999998876654
No 136
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.77 E-value=16 Score=30.30 Aligned_cols=38 Identities=16% Similarity=0.294 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChH
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQ 74 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~ 74 (365)
+-.|+.|+-.. +.++-..-.+.-+|.|..|++.|....
T Consensus 30 ~~~cP~C~s~~-----~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 30 KVNCPRCKSSN-----VVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred cCcCCCCCccc-----eeeECCccccccccccCCcCcceeeec
Confidence 56788887654 122222233367899999999998654
No 137
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=38.41 E-value=28 Score=34.04 Aligned_cols=50 Identities=20% Similarity=0.333 Sum_probs=42.2
Q ss_pred eeCCCCCccCCCCCCccCChhHHHHHHhhhcCC-----------------------Ccccccccc---ccccchhhhhhh
Q 048287 102 YVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGE-----------------------KKWKCEKCS---KRYAVQSDWKAH 155 (365)
Q Consensus 102 ~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~e-----------------------kp~~C~~C~---k~F~~~~~L~~H 155 (365)
-.|-.| ++.|.+...-..||..+||- .-|.|-.|+ +.|......+.|
T Consensus 167 t~CLfC-------~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~H 239 (390)
T KOG2785|consen 167 TDCLFC-------DKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAH 239 (390)
T ss_pred cceeec-------CCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHH
Confidence 456666 99999999999999988761 347899999 999999999999
Q ss_pred hcc
Q 048287 156 SKT 158 (365)
Q Consensus 156 ~~~ 158 (365)
|.-
T Consensus 240 M~~ 242 (390)
T KOG2785|consen 240 MRD 242 (390)
T ss_pred Hhh
Confidence 987
No 138
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=38.30 E-value=12 Score=39.57 Aligned_cols=27 Identities=26% Similarity=0.429 Sum_probs=23.8
Q ss_pred ceecc-CCCccCChhHHHHHHHHhhhhh
Q 048287 163 EYKCD-CGTVFSRRDSFITHRAFCDALA 189 (365)
Q Consensus 163 py~C~-Cgk~F~~~~~L~~H~~~h~~~~ 189 (365)
-|-|. |+|.|-...++..||+.|....
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 39999 9999999999999999997544
No 139
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=38.05 E-value=18 Score=24.79 Aligned_cols=37 Identities=19% Similarity=0.227 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCchhhhh-----cCccccCCCCceecccccc
Q 048287 32 KKKRNLPGTPDPEAEVIA-----LSPKTLMATNRFLCEICGK 68 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~-----~h~k~~~~~k~~~C~~Cgk 68 (365)
+|+|..||..+.....-. ....--.-..-|.|+.|+.
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 477888888776543211 1111111124578888875
No 140
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.66 E-value=53 Score=36.39 Aligned_cols=8 Identities=38% Similarity=1.032 Sum_probs=3.6
Q ss_pred eecccccc
Q 048287 61 FLCEICGK 68 (365)
Q Consensus 61 ~~C~~Cgk 68 (365)
+.|+.||.
T Consensus 639 frCP~CG~ 646 (1121)
T PRK04023 639 RRCPFCGT 646 (1121)
T ss_pred ccCCCCCC
Confidence 34444444
No 141
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=36.81 E-value=19 Score=24.98 Aligned_cols=28 Identities=14% Similarity=0.337 Sum_probs=14.7
Q ss_pred hhHHHHHHhhhcCCCcccccc----ccccccc
Q 048287 121 LTGIKKHFCRKHGEKKWKCEK----CSKRYAV 148 (365)
Q Consensus 121 ~~~L~~H~~~H~~ekp~~C~~----C~k~F~~ 148 (365)
+..|..|+...-..++..|.. |...+.+
T Consensus 23 r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 23 RKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp CCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred HHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 445666666555556666666 6655443
No 142
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.77 E-value=24 Score=37.96 Aligned_cols=18 Identities=17% Similarity=0.124 Sum_probs=10.3
Q ss_pred ccccccccCCceeeCCCC
Q 048287 90 KQRTSKEVRKRVYVCPEK 107 (365)
Q Consensus 90 ~~~~~~~~~~k~~~C~~C 107 (365)
.++.+.+....|..|+.|
T Consensus 464 ~CH~Cg~~~~~p~~Cp~C 481 (730)
T COG1198 464 RCHYCGYQEPIPQSCPEC 481 (730)
T ss_pred EeCCCCCCCCCCCCCCCC
Confidence 333344445667777777
No 143
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=36.23 E-value=12 Score=33.40 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=0.0
Q ss_pred ccccCCCCceeccccc-ccccChHhHHHHH
Q 048287 52 PKTLMATNRFLCEICG-KGFQRDQNLQLHR 80 (365)
Q Consensus 52 ~k~~~~~k~~~C~~Cg-k~F~~~~~L~~H~ 80 (365)
-|.|.-.+.|.|++|| .+|.-+..+.+|.
T Consensus 93 YKLhGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 93 YKLHGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ------------------------------
T ss_pred HHHhCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 4566777899999997 4677778888885
No 144
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=36.08 E-value=32 Score=32.71 Aligned_cols=48 Identities=15% Similarity=0.387 Sum_probs=31.4
Q ss_pred ccccccccccchhhhhhhhcccCCcceecc-CCCccCChhHHHHHHHHhh
Q 048287 138 KCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRRDSFITHRAFCD 186 (365)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~~L~~H~~~h~ 186 (365)
.|-.|.-.|.....-..-.. ...-.|.|+ |...|-..-....|...|.
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~-~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDES-TSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceeccCCCCCCCCCccccc-ccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 37778777765433211111 334579999 9999988777777877764
No 145
>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=35.87 E-value=12 Score=25.33 Aligned_cols=30 Identities=17% Similarity=0.407 Sum_probs=15.5
Q ss_pred eeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCccccccccc
Q 048287 101 VYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSK 144 (365)
Q Consensus 101 ~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k 144 (365)
.|.|..| +..|.....+. .+..-.|+.|+.
T Consensus 5 ey~C~~C-------g~~fe~~~~~~-------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTAC-------GHRFEVLQKMS-------DDPLATCPECGG 34 (52)
T ss_pred EEEeCCC-------CCEeEEEEecC-------CCCCCCCCCCCC
Confidence 3667766 66665432111 133455777764
No 146
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.62 E-value=29 Score=23.29 Aligned_cols=14 Identities=36% Similarity=0.769 Sum_probs=10.9
Q ss_pred CceecccccccccC
Q 048287 59 NRFLCEICGKGFQR 72 (365)
Q Consensus 59 k~~~C~~Cgk~F~~ 72 (365)
..|.|+.||..+.-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 48999999976544
No 147
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=35.37 E-value=27 Score=22.14 Aligned_cols=32 Identities=16% Similarity=0.217 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceeccccc
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICG 67 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cg 67 (365)
.-+|+.|+.. ..+.+|-+...+..+|.|..|.
T Consensus 5 ~v~CP~C~s~----~~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQST----EGVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCC----CcceeCCCCCCCCEeEecCcCC
Confidence 3468888764 3467777888888899999883
No 148
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=34.62 E-value=8 Score=37.24 Aligned_cols=23 Identities=22% Similarity=0.803 Sum_probs=19.4
Q ss_pred CCceeccc--ccccccChHhHHHHH
Q 048287 58 TNRFLCEI--CGKGFQRDQNLQLHR 80 (365)
Q Consensus 58 ~k~~~C~~--Cgk~F~~~~~L~~H~ 80 (365)
.++|+|++ |.+.+.....|+.|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~ 371 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHK 371 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeecc
Confidence 47899964 999999988898885
No 149
>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=34.57 E-value=58 Score=27.81 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=22.0
Q ss_pred Cceeccccccccc------ChHhHHHHH-HhcCCCcccccccccccCCceeeCCCCCc
Q 048287 59 NRFLCEICGKGFQ------RDQNLQLHR-RGHNLPWKLKQRTSKEVRKRVYVCPEKTC 109 (365)
Q Consensus 59 k~~~C~~Cgk~F~------~~~~L~~H~-~~H~~~~~~~~~~~~~~~~k~~~C~~C~C 109 (365)
-..+|..|+|-|- ..+++..|+ +..+.+..+ +.....++..++|-.|++
T Consensus 13 ~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~L--H~~s~lgdt~leCy~Cg~ 68 (152)
T PF09416_consen 13 CVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSL--HPDSPLGDTVLECYNCGS 68 (152)
T ss_dssp CEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE---TTSTT-S-B---TTT--
T ss_pred cEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceee--CCCCCCCCcEEEEEecCC
Confidence 4567888888775 456677885 444422222 222234666778877755
No 150
>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=34.47 E-value=57 Score=21.59 Aligned_cols=26 Identities=23% Similarity=0.737 Sum_probs=13.8
Q ss_pred cccccccccccchhhhhhhhcccCCcceecc-CCC
Q 048287 137 WKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGT 170 (365)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk 170 (365)
+.|+.|+.. . +.+......|+|. |++
T Consensus 19 ~~CP~Cg~~--~------~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--K------HYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--e------eEEeCCCCeEECCCCCC
Confidence 667777753 1 1112224567777 764
No 151
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=34.24 E-value=22 Score=35.44 Aligned_cols=29 Identities=31% Similarity=0.796 Sum_probs=21.6
Q ss_pred ccccccccccchhhhhhhhcccCCcceecc-CCCccCChh
Q 048287 138 KCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSRRD 176 (365)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~~~ 176 (365)
+|+.||.+ ++..|..-|+|. ||+.+....
T Consensus 352 ~Cp~Cg~~----------m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGR----------MKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCc----------hhhcCCCCcccccccccCCccc
Confidence 79999876 334455589999 999987664
No 152
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=34.09 E-value=22 Score=30.89 Aligned_cols=24 Identities=21% Similarity=0.303 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceecccccc
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGK 68 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk 68 (365)
.|.|+.||... -++-|-+||+||-
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 78999998854 3357888999983
No 153
>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=33.81 E-value=14 Score=23.54 Aligned_cols=10 Identities=20% Similarity=0.561 Sum_probs=5.9
Q ss_pred Cccccccccc
Q 048287 135 KKWKCEKCSK 144 (365)
Q Consensus 135 kp~~C~~C~k 144 (365)
..-.|+.|+.
T Consensus 25 ~~~~CP~Cg~ 34 (41)
T smart00834 25 PLATCPECGG 34 (41)
T ss_pred CCCCCCCCCC
Confidence 3455666665
No 154
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=33.75 E-value=24 Score=28.76 Aligned_cols=28 Identities=21% Similarity=0.449 Sum_probs=23.8
Q ss_pred CCCCceecccccccccChHhHHHHHHhc
Q 048287 56 MATNRFLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 56 ~~~k~~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
-+...|-|-.|.+-|.+...|+.|.++-
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 3456799999999999999999998643
No 155
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=33.64 E-value=19 Score=21.56 Aligned_cols=19 Identities=32% Similarity=0.775 Sum_probs=8.4
Q ss_pred ccccccccccchhhhhhhhc
Q 048287 138 KCEKCSKRYAVQSDWKAHSK 157 (365)
Q Consensus 138 ~C~~C~k~F~~~~~L~~H~~ 157 (365)
.|-.|++.| ....++.|..
T Consensus 2 sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEE-EGGGTTT---
T ss_pred eeecCCCCc-CcCCcCCCCc
Confidence 455566666 3444455544
No 156
>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=33.53 E-value=14 Score=28.61 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=5.1
Q ss_pred cccccccccc
Q 048287 136 KWKCEKCSKR 145 (365)
Q Consensus 136 p~~C~~C~k~ 145 (365)
.|.|+.|++.
T Consensus 35 ky~Cp~Cgk~ 44 (90)
T PF01780_consen 35 KYTCPFCGKT 44 (90)
T ss_dssp -BEESSSSSS
T ss_pred CCcCCCCCCc
Confidence 4556666553
No 157
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=32.54 E-value=27 Score=37.44 Aligned_cols=13 Identities=38% Similarity=0.570 Sum_probs=9.5
Q ss_pred eeCCCCCccCCCCCCccCCh
Q 048287 102 YVCPEKTCVHHHPSRALGDL 121 (365)
Q Consensus 102 ~~C~~C~C~~~~~~~~f~~~ 121 (365)
-.|..| ++.|...
T Consensus 461 dtC~~C-------~kkFfSl 473 (1374)
T PTZ00303 461 DSCPSC-------GRAFISL 473 (1374)
T ss_pred CcccCc-------CCccccc
Confidence 457777 8998754
No 158
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=31.85 E-value=23 Score=27.36 Aligned_cols=14 Identities=21% Similarity=0.660 Sum_probs=7.3
Q ss_pred Cccccccccccccc
Q 048287 135 KKWKCEKCSKRYAV 148 (365)
Q Consensus 135 kp~~C~~C~k~F~~ 148 (365)
+|-+|..||+.|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 34455555555544
No 159
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=31.43 E-value=30 Score=28.83 Aligned_cols=23 Identities=30% Similarity=0.515 Sum_probs=19.6
Q ss_pred CceecccccccccChHhHHHHHHhcC
Q 048287 59 NRFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
.-..|-+|||.|+ .|++|+++|.
T Consensus 75 D~IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 75 DYIICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred CeEEEeccCcchH---HHHHHHhccc
Confidence 3467999999995 5999999987
No 160
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=31.34 E-value=25 Score=29.98 Aligned_cols=32 Identities=28% Similarity=0.861 Sum_probs=19.1
Q ss_pred Cccccccccccccchhhhhhhhcc-cCCcceecc-CCCc
Q 048287 135 KKWKCEKCSKRYAVQSDWKAHSKT-CGTREYKCD-CGTV 171 (365)
Q Consensus 135 kp~~C~~C~k~F~~~~~L~~H~~~-~~~kpy~C~-Cgk~ 171 (365)
-+|.|. |+..|.+. ++|-.. .|+ .|.|. |+-.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 367787 77766554 334344 444 68887 7644
No 161
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=31.21 E-value=19 Score=25.24 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=5.2
Q ss_pred cccccccccc
Q 048287 138 KCEKCSKRYA 147 (365)
Q Consensus 138 ~C~~C~k~F~ 147 (365)
+|-.|++.+.
T Consensus 4 kC~lCdk~~~ 13 (56)
T PF09963_consen 4 KCILCDKKEE 13 (56)
T ss_pred EEEecCCEEE
Confidence 4555555443
No 162
>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=30.89 E-value=26 Score=21.29 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=12.7
Q ss_pred CCCCCCCCCCchhhhhcCccccCCCCceeccccccc
Q 048287 34 KRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKG 69 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~ 69 (365)
+|++|+-.+.- .....|.|+.|+..
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-----------ccCCEEeCCccccc
Confidence 68888776544 34467999999864
No 163
>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=30.62 E-value=39 Score=22.25 Aligned_cols=16 Identities=25% Similarity=0.887 Sum_probs=10.6
Q ss_pred ecccccccccChHhHH
Q 048287 62 LCEICGKGFQRDQNLQ 77 (365)
Q Consensus 62 ~C~~Cgk~F~~~~~L~ 77 (365)
.|..||+.|.......
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 4777777777665544
No 164
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.61 E-value=22 Score=27.57 Aligned_cols=12 Identities=42% Similarity=1.174 Sum_probs=6.4
Q ss_pred cccccccccccc
Q 048287 136 KWKCEKCSKRYA 147 (365)
Q Consensus 136 p~~C~~C~k~F~ 147 (365)
-|.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PTZ00255 54 IWRCKGCKKTVA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 455555555554
No 165
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.48 E-value=27 Score=29.42 Aligned_cols=32 Identities=25% Similarity=0.823 Sum_probs=19.6
Q ss_pred ccccccccccccchhhhhhhhcccCCcceecc-CCCccC
Q 048287 136 KWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFS 173 (365)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~ 173 (365)
.|+|..|+..+. .|.+......|.|. |+-.|.
T Consensus 112 ~y~C~~C~~~~~------~~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYL------RVRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCc------eEccccCcceEEcCCCCCEEE
Confidence 678888887654 23333222668887 876553
No 166
>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=30.35 E-value=22 Score=20.49 Aligned_cols=10 Identities=40% Similarity=0.819 Sum_probs=7.0
Q ss_pred Cceecccccc
Q 048287 59 NRFLCEICGK 68 (365)
Q Consensus 59 k~~~C~~Cgk 68 (365)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4677887774
No 167
>PRK05978 hypothetical protein; Provisional
Probab=30.25 E-value=32 Score=29.26 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccCh
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRD 73 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~ 73 (365)
.-+|+.||+.---...++.+ -.|+.||..|...
T Consensus 33 ~grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKPV---------DHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCCCcccccccccC---------CCccccCCccccC
Confidence 55999998864433333333 2499999887643
No 168
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=30.16 E-value=29 Score=33.61 Aligned_cols=29 Identities=28% Similarity=0.376 Sum_probs=24.3
Q ss_pred ccccCCCCceeccccc-ccccChHhHHHHH
Q 048287 52 PKTLMATNRFLCEICG-KGFQRDQNLQLHR 80 (365)
Q Consensus 52 ~k~~~~~k~~~C~~Cg-k~F~~~~~L~~H~ 80 (365)
.|.|.-.+-|.|++|| +++.-+..+.+|.
T Consensus 366 ~klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 366 CKLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred HHhcCCCcceeeeecccccccchHHHHhhh
Confidence 3567778999999999 8888888888885
No 169
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.88 E-value=35 Score=22.00 Aligned_cols=37 Identities=19% Similarity=0.167 Sum_probs=24.9
Q ss_pred CCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHH
Q 048287 34 KRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQL 78 (365)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~ 78 (365)
+|+.|+........ .....+.|+.|+-.|.....|.+
T Consensus 1 ~CP~C~~~l~~~~~--------~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVRL--------GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEEE--------CCEEEEECCCCCeEEccHHHHHH
Confidence 57888764332211 33466889999999888887765
No 170
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=29.63 E-value=32 Score=28.63 Aligned_cols=28 Identities=25% Similarity=0.279 Sum_probs=22.1
Q ss_pred eecc-CCCccCChhHHHHHHHHhhhhhhhhhh
Q 048287 164 YKCD-CGTVFSRRDSFITHRAFCDALAEETAR 194 (365)
Q Consensus 164 y~C~-Cgk~F~~~~~L~~H~~~h~~~~~~~~~ 194 (365)
..|- |||.|. +|++|..+|+++..+..+
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTPd~YR 105 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTPDEYR 105 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCHHHHH
Confidence 5687 999996 689999999887665544
No 171
>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=29.29 E-value=15 Score=25.37 Aligned_cols=27 Identities=30% Similarity=0.605 Sum_probs=16.4
Q ss_pred CCceecccccccccChHhHHHHHHhcC
Q 048287 58 TNRFLCEICGKGFQRDQNLQLHRRGHN 84 (365)
Q Consensus 58 ~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 84 (365)
..+|.|+.|.+.|--.-.+-.|...|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 478999999999988888777777765
No 172
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=29.02 E-value=28 Score=33.67 Aligned_cols=30 Identities=10% Similarity=0.246 Sum_probs=17.9
Q ss_pred CCccccccccccccchhhhhhhhcc-cCCcc
Q 048287 134 EKKWKCEKCSKRYAVQSDWKAHSKT-CGTRE 163 (365)
Q Consensus 134 ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kp 163 (365)
+.-|.|+.|++.-.+...|..|... |.+-.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~ 107 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEAS 107 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccC
Confidence 3456666666666666666666655 54443
No 173
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=28.91 E-value=24 Score=32.47 Aligned_cols=59 Identities=22% Similarity=0.464 Sum_probs=36.7
Q ss_pred CCceecccccccccChHhHHHHHHhcCCCcccccccccccCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcc
Q 048287 58 TNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKW 137 (365)
Q Consensus 58 ~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~ 137 (365)
.+.|.|..|.....+ |.-. .+..-.|..| .+.|.---. ....|.--|
T Consensus 110 drqFaC~~Cd~~WwR--------rvp~-------------rKeVSRCr~C-------~~rYDPVP~-----dkmwG~aef 156 (278)
T PF15135_consen 110 DRQFACSSCDHMWWR--------RVPQ-------------RKEVSRCRKC-------RKRYDPVPC-----DKMWGIAEF 156 (278)
T ss_pred ceeeeccccchHHHh--------ccCc-------------cccccccccc-------ccccCCCcc-----ccccceeee
Confidence 478999999765432 2222 5566778887 666543211 112344568
Q ss_pred ccccccccccch
Q 048287 138 KCEKCSKRYAVQ 149 (365)
Q Consensus 138 ~C~~C~k~F~~~ 149 (365)
.|..|+..|.--
T Consensus 157 ~C~~C~h~F~G~ 168 (278)
T PF15135_consen 157 HCPKCRHNFRGF 168 (278)
T ss_pred ecccccccchhh
Confidence 999999988754
No 174
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=28.58 E-value=34 Score=23.85 Aligned_cols=30 Identities=20% Similarity=0.403 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccC
Q 048287 31 AKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQR 72 (365)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~ 72 (365)
...+|..||+.|.+. +..-.|+.||..+-+
T Consensus 4 ~~~~C~~Cg~~~~~~------------dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDG------------DDIVVCPECGAPYHR 33 (54)
T ss_pred cCccChhhCCcccCC------------CCEEECCCCCCcccH
Confidence 456899999987543 356679999987644
No 175
>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=28.42 E-value=40 Score=28.15 Aligned_cols=28 Identities=25% Similarity=0.475 Sum_probs=16.2
Q ss_pred CCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCC
Q 048287 98 RKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEK 135 (365)
Q Consensus 98 ~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ek 135 (365)
.+....|-+| |+.|... ++|++.|+|-.
T Consensus 69 ~~d~i~clec-------Gk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 69 TPDYIICLEC-------GKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp -SS-EE-TBT---------EESBH---HHHHHHTT-S-
T ss_pred ccCeeEEccC-------CcccchH---HHHHHHccCCC
Confidence 4455678888 9988654 89999997753
No 176
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=28.32 E-value=51 Score=27.77 Aligned_cols=48 Identities=13% Similarity=0.124 Sum_probs=30.2
Q ss_pred CCCCCCCCCCCCchhhhhc----Ccccc-CCCCceecccccccccChHhHHHH
Q 048287 32 KKKRNLPGTPDPEAEVIAL----SPKTL-MATNRFLCEICGKGFQRDQNLQLH 79 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~----h~k~~-~~~k~~~C~~Cgk~F~~~~~L~~H 79 (365)
-..|..|+......+.-.. ...+. ....-+.|+.|||.|..=+++++-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHH
Confidence 5689999886654432211 11121 123468899999999987776654
No 177
>PRK04351 hypothetical protein; Provisional
Probab=28.07 E-value=30 Score=29.43 Aligned_cols=32 Identities=22% Similarity=0.777 Sum_probs=20.7
Q ss_pred ccccccccccccchhhhhhhhcccCCcceecc-CCCccCC
Q 048287 136 KWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFSR 174 (365)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~~ 174 (365)
.|.|..|+..+.+. +.+..+.|.|. |+-.+..
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRINTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee-------eecCCCcEEeCCCCcEeee
Confidence 47888888665432 22445778888 8766643
No 178
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=28.02 E-value=43 Score=32.13 Aligned_cols=39 Identities=13% Similarity=0.249 Sum_probs=25.1
Q ss_pred CcCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccc
Q 048287 29 TAAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGF 70 (365)
Q Consensus 29 ~~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F 70 (365)
...+..|+.||..- ..+.+. .+...+.+-..|..|+-..
T Consensus 184 ~~~~~~CPvCGs~P-~~s~v~--~~~~~G~RyL~CslC~teW 222 (309)
T PRK03564 184 GEQRQFCPVCGSMP-VSSVVQ--IGTTQGLRYLHCNLCESEW 222 (309)
T ss_pred ccCCCCCCCCCCcc-hhheee--ccCCCCceEEEcCCCCCcc
Confidence 34578999999863 233332 2334566778899998754
No 179
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=27.94 E-value=23 Score=27.45 Aligned_cols=12 Identities=42% Similarity=1.359 Sum_probs=6.0
Q ss_pred cccccccccccc
Q 048287 136 KWKCEKCSKRYA 147 (365)
Q Consensus 136 p~~C~~C~k~F~ 147 (365)
-|+|..|++.|.
T Consensus 53 IW~C~~C~~~~A 64 (91)
T TIGR00280 53 IWTCRKCGAKFA 64 (91)
T ss_pred EEEcCCCCCEEe
Confidence 355555555443
No 180
>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=27.58 E-value=41 Score=21.53 Aligned_cols=22 Identities=27% Similarity=0.618 Sum_probs=9.1
Q ss_pred CceecccccccccChH--hHHHHH
Q 048287 59 NRFLCEICGKGFQRDQ--NLQLHR 80 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~--~L~~H~ 80 (365)
++|-|+.|.+.|.... .-+.|.
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~ 25 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHE 25 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT
T ss_pred cCeecccccceecCCChHHHHHhh
Confidence 5689999999995444 225554
No 181
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.53 E-value=49 Score=37.54 Aligned_cols=10 Identities=40% Similarity=0.863 Sum_probs=7.0
Q ss_pred ceeccccccc
Q 048287 60 RFLCEICGKG 69 (365)
Q Consensus 60 ~~~C~~Cgk~ 69 (365)
.+.|+.||..
T Consensus 667 ~rkCPkCG~~ 676 (1337)
T PRK14714 667 RRRCPSCGTE 676 (1337)
T ss_pred EEECCCCCCc
Confidence 3778888763
No 182
>PF15269 zf-C2H2_7: Zinc-finger
Probab=27.42 E-value=61 Score=21.61 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=19.4
Q ss_pred CceecccccccccChHhHHHHHHhc
Q 048287 59 NRFLCEICGKGFQRDQNLQLHRRGH 83 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~~~L~~H~~~H 83 (365)
-.|+|=+|.-+..-+++|-.||+.-
T Consensus 19 ~~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 19 FKYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred ccceeecCCcccchHHHHHHHHHHH
Confidence 4577888888888888888888654
No 183
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.02 E-value=39 Score=26.73 Aligned_cols=14 Identities=7% Similarity=-0.064 Sum_probs=10.4
Q ss_pred CCCCCCCCCCCCch
Q 048287 32 KKKRNLPGTPDPEA 45 (365)
Q Consensus 32 ~~~c~~c~~~~~~~ 45 (365)
++.|..||+.|.+-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 56788888888774
No 184
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=26.70 E-value=26 Score=29.59 Aligned_cols=31 Identities=26% Similarity=0.932 Sum_probs=19.2
Q ss_pred ccccccccccccchhhhhhhhcccCCcceecc-CCCccC
Q 048287 136 KWKCEKCSKRYAVQSDWKAHSKTCGTREYKCD-CGTVFS 173 (365)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~~~~kpy~C~-Cgk~F~ 173 (365)
.|.|..|+..+.+ |.+. ....|.|. |+..|.
T Consensus 123 ~~~C~~C~~~~~r------~~~~-~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS-KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeee------eccc-chhhEECCCCCCEEE
Confidence 5778888876633 2333 33458888 876654
No 185
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=26.10 E-value=27 Score=34.76 Aligned_cols=39 Identities=21% Similarity=0.532 Sum_probs=27.2
Q ss_pred cCCceeeCCCCCccCCCCCCccCChhHHHHHHhhhcCCCcccccccccc
Q 048287 97 VRKRVYVCPEKTCVHHHPSRALGDLTGIKKHFCRKHGEKKWKCEKCSKR 145 (365)
Q Consensus 97 ~~~k~~~C~~C~C~~~~~~~~f~~~~~L~~H~~~H~~ekp~~C~~C~k~ 145 (365)
+...-|.|+.| .+.|.....+. ..-...-.|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C-------~kkyt~Lea~~---L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNC-------QKKYTSLEALQ---LLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCcc-------ccchhhhHHHH---hhcccCceEEEecCCCc
Confidence 35567999999 99987765543 23333457999999743
No 186
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.04 E-value=25 Score=29.33 Aligned_cols=40 Identities=18% Similarity=0.127 Sum_probs=23.0
Q ss_pred cCCCCCCCCCCCCCchh---hhhc--Ccccc----CCCCceeccccccc
Q 048287 30 AAKKKRNLPGTPDPEAE---VIAL--SPKTL----MATNRFLCEICGKG 69 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~---~l~~--h~k~~----~~~k~~~C~~Cgk~ 69 (365)
+..+.|..||..|.... .|.. +..+| .....+.|+.||..
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 46789999998876541 1100 11111 11345779999964
No 187
>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=25.83 E-value=30 Score=22.58 Aligned_cols=15 Identities=40% Similarity=0.866 Sum_probs=12.2
Q ss_pred ceecccccccccChH
Q 048287 60 RFLCEICGKGFQRDQ 74 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~~ 74 (365)
.|.|..||..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEeCCCCCEEEEEE
Confidence 589999999997644
No 188
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=24.70 E-value=34 Score=21.99 Aligned_cols=14 Identities=36% Similarity=0.819 Sum_probs=12.1
Q ss_pred ceecccccccccCh
Q 048287 60 RFLCEICGKGFQRD 73 (365)
Q Consensus 60 ~~~C~~Cgk~F~~~ 73 (365)
+|+|..|++.|-.+
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999999653
No 189
>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=24.61 E-value=46 Score=20.52 Aligned_cols=10 Identities=30% Similarity=0.989 Sum_probs=5.8
Q ss_pred cccccccccc
Q 048287 136 KWKCEKCSKR 145 (365)
Q Consensus 136 p~~C~~C~k~ 145 (365)
+.+|..||.+
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 4567777654
No 190
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.54 E-value=55 Score=28.70 Aligned_cols=14 Identities=21% Similarity=0.318 Sum_probs=9.6
Q ss_pred ccCCceeeCCCCCc
Q 048287 96 EVRKRVYVCPEKTC 109 (365)
Q Consensus 96 ~~~~k~~~C~~C~C 109 (365)
+..+..|.|++|-+
T Consensus 126 ~~~~~~~~CPiCl~ 139 (187)
T KOG0320|consen 126 LRKEGTYKCPICLD 139 (187)
T ss_pred cccccccCCCceec
Confidence 33555699999944
No 191
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.41 E-value=47 Score=27.59 Aligned_cols=15 Identities=27% Similarity=0.682 Sum_probs=10.9
Q ss_pred ccccccccccccchh
Q 048287 136 KWKCEKCSKRYAVQS 150 (365)
Q Consensus 136 p~~C~~C~k~F~~~~ 150 (365)
|++|..||+.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567888888877654
No 192
>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=23.96 E-value=33 Score=24.58 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccC
Q 048287 31 AKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQR 72 (365)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~ 72 (365)
....|..|++.|.- -.+++.|..||+.|-.
T Consensus 8 ~~~~C~~C~~~F~~------------~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 8 EASNCMICGKKFSL------------FRRRHHCRNCGRVVCS 37 (69)
T ss_dssp G-SB-TTT--B-BS------------SS-EEE-TTT--EEEC
T ss_pred CCCcCcCcCCcCCC------------ceeeEccCCCCCEECC
Confidence 45678888888842 2467788888887754
No 193
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=23.89 E-value=20 Score=23.38 Aligned_cols=32 Identities=22% Similarity=0.622 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceecccccc
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGK 68 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk 68 (365)
+..|..||++......|.... ...|.|+.|=.
T Consensus 1 ~~~CSFCgr~~~~v~~li~g~-----~~~~IC~~Cv~ 32 (41)
T PF06689_consen 1 EKRCSFCGRPESEVGRLISGP-----NGAYICDECVE 32 (41)
T ss_dssp --B-TTT--BTTTSSSEEEES------SEEEEHHHHH
T ss_pred CCCccCCCCCHHHHhceecCC-----CCcEECHHHHH
Confidence 357999999887765554332 14889988843
No 194
>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=23.78 E-value=46 Score=23.19 Aligned_cols=10 Identities=20% Similarity=0.753 Sum_probs=4.9
Q ss_pred cccccccccc
Q 048287 137 WKCEKCSKRY 146 (365)
Q Consensus 137 ~~C~~C~k~F 146 (365)
..|+.||..|
T Consensus 23 V~Cp~CGael 32 (54)
T TIGR01206 23 VICDECGAEL 32 (54)
T ss_pred EeCCCCCCEE
Confidence 3555555443
No 195
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.73 E-value=34 Score=21.37 Aligned_cols=30 Identities=20% Similarity=0.219 Sum_probs=13.7
Q ss_pred CCCCCCCCCchhhhhcCccccCCCCceecccccccc
Q 048287 35 RNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGF 70 (365)
Q Consensus 35 c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F 70 (365)
|+.||.+... ..-.-....++.|+.||...
T Consensus 3 C~~CG~~l~~------~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 3 CPQCGGPLER------RIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -TTT--B-EE------E--TT-SS-EEEETTTTEEE
T ss_pred cccccChhhh------hcCCCCCccceECCCCCCEE
Confidence 6778775321 11111334679999998753
No 196
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=23.61 E-value=30 Score=26.84 Aligned_cols=12 Identities=42% Similarity=1.389 Sum_probs=6.1
Q ss_pred cccccccccccc
Q 048287 136 KWKCEKCSKRYA 147 (365)
Q Consensus 136 p~~C~~C~k~F~ 147 (365)
-|.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PRK03976 54 IWECRKCGAKFA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 355555555544
No 197
>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=22.97 E-value=33 Score=21.74 Aligned_cols=11 Identities=18% Similarity=0.658 Sum_probs=5.6
Q ss_pred ccccccccccc
Q 048287 136 KWKCEKCSKRY 146 (365)
Q Consensus 136 p~~C~~C~k~F 146 (365)
.-+|+.||-.+
T Consensus 21 ~~~Cd~cg~~L 31 (36)
T PF05191_consen 21 EGVCDNCGGEL 31 (36)
T ss_dssp TTBCTTTTEBE
T ss_pred CCccCCCCCee
Confidence 34565555443
No 198
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.92 E-value=30 Score=36.96 Aligned_cols=8 Identities=38% Similarity=1.788 Sum_probs=3.9
Q ss_pred cccccccc
Q 048287 136 KWKCEKCS 143 (365)
Q Consensus 136 p~~C~~C~ 143 (365)
++.|+.|+
T Consensus 422 p~~Cp~Cg 429 (665)
T PRK14873 422 DWRCPRCG 429 (665)
T ss_pred CccCCCCc
Confidence 44455554
No 199
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.89 E-value=1.4e+02 Score=28.73 Aligned_cols=35 Identities=11% Similarity=0.020 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhHHHH
Q 048287 31 AKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLH 79 (365)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L~~H 79 (365)
.=|-|+.|+...= .-|-+|++|+-......+|.+=
T Consensus 275 ~Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 275 GGYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred CceeCCcccCeee--------------cCCccCCccceeEecchHHHHH
Confidence 4577888865432 2578899999999888888753
No 200
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.72 E-value=52 Score=26.58 Aligned_cols=40 Identities=18% Similarity=0.216 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCCchhhhhcCccccCCCCceeccccccccc
Q 048287 32 KKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQ 71 (365)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~ 71 (365)
..+|+.||.....-..+..--.--....-|+|..||..|+
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 5689999875433322222222222335599999999875
No 201
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=22.71 E-value=28 Score=37.65 Aligned_cols=12 Identities=42% Similarity=0.791 Sum_probs=0.0
Q ss_pred CCceeccccccc
Q 048287 58 TNRFLCEICGKG 69 (365)
Q Consensus 58 ~k~~~C~~Cgk~ 69 (365)
-..+.|+.||+.
T Consensus 653 i~~r~Cp~Cg~~ 664 (900)
T PF03833_consen 653 IGRRRCPKCGKE 664 (900)
T ss_dssp ------------
T ss_pred eecccCcccCCc
Confidence 356788888874
No 202
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.29 E-value=30 Score=37.22 Aligned_cols=12 Identities=17% Similarity=0.523 Sum_probs=7.1
Q ss_pred CCcccccccccc
Q 048287 134 EKKWKCEKCSKR 145 (365)
Q Consensus 134 ekp~~C~~C~k~ 145 (365)
..|..|+.||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 456666666643
No 203
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=22.13 E-value=24 Score=28.82 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=12.9
Q ss_pred cccccccccccchhhhhhhhcc
Q 048287 137 WKCEKCSKRYAVQSDWKAHSKT 158 (365)
Q Consensus 137 ~~C~~C~k~F~~~~~L~~H~~~ 158 (365)
|-|-.|.+-|.....|..|.++
T Consensus 58 fyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhc
Confidence 5565666666666666555554
No 204
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.99 E-value=70 Score=19.88 Aligned_cols=24 Identities=25% Similarity=0.570 Sum_probs=15.4
Q ss_pred ceecc-CCCccCChhHHHHHHHHhhh
Q 048287 163 EYKCD-CGTVFSRRDSFITHRAFCDA 187 (365)
Q Consensus 163 py~C~-Cgk~F~~~~~L~~H~~~h~~ 187 (365)
-|.|. |++.+. ...|..|++.|-+
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLekCmg 28 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLEKCMG 28 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHHHHTC
T ss_pred eEECCCCcCCcc-hhhhHHHHHHHHc
Confidence 36777 877664 4567778777754
No 205
>PHA02998 RNA polymerase subunit; Provisional
Probab=21.97 E-value=44 Score=29.27 Aligned_cols=40 Identities=13% Similarity=0.183 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCCCchhhhhcCcccc--CCCCceecccccccccC
Q 048287 31 AKKKRNLPGTPDPEAEVIALSPKTL--MATNRFLCEICGKGFQR 72 (365)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~k~~--~~~k~~~C~~Cgk~F~~ 72 (365)
..-+|+.|+..... ......+.- ....-|.|..||+.|.-
T Consensus 142 t~v~CPkCg~~~A~--f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTT--PMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceE--EEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 46789999864322 222222221 12345999999998864
No 206
>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=21.76 E-value=57 Score=33.55 Aligned_cols=11 Identities=36% Similarity=0.697 Sum_probs=7.1
Q ss_pred ecccccccccC
Q 048287 62 LCEICGKGFQR 72 (365)
Q Consensus 62 ~C~~Cgk~F~~ 72 (365)
.|..||..+..
T Consensus 215 ~C~~Cg~~~~C 225 (505)
T TIGR00595 215 LCRSCGYILCC 225 (505)
T ss_pred EhhhCcCccCC
Confidence 57777766553
No 207
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=21.75 E-value=70 Score=20.76 Aligned_cols=24 Identities=25% Similarity=0.638 Sum_probs=16.4
Q ss_pred eecccccccccCh--HhHHHHHHhcC
Q 048287 61 FLCEICGKGFQRD--QNLQLHRRGHN 84 (365)
Q Consensus 61 ~~C~~Cgk~F~~~--~~L~~H~~~H~ 84 (365)
-.|+.||-.|... ..-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4799999887654 34556777663
No 208
>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=21.58 E-value=35 Score=35.11 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=5.2
Q ss_pred cccCCCCCCC
Q 048287 280 AMYGDHPPPS 289 (365)
Q Consensus 280 ~~~~~~p~~~ 289 (365)
.+.|+.|++.
T Consensus 449 ~~lgP~~~~~ 458 (505)
T TIGR00595 449 EVLGPSPAPI 458 (505)
T ss_pred EEeCCccccc
Confidence 4556655444
No 209
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.33 E-value=62 Score=32.35 Aligned_cols=36 Identities=17% Similarity=0.148 Sum_probs=25.7
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccccccChHhH
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNL 76 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk~F~~~~~L 76 (365)
..+-+|+.||..- +..... -|.|+.||..+......
T Consensus 348 ~~~p~Cp~Cg~~m----------~S~G~~-g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 348 RVNPVCPRCGGRM----------KSAGRN-GFRCKKCGTRARETLIK 383 (421)
T ss_pred EcCCCCCccCCch----------hhcCCC-CcccccccccCCccccc
Confidence 4566999999863 333333 89999999998876543
No 210
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.28 E-value=32 Score=27.77 Aligned_cols=27 Identities=11% Similarity=-0.052 Sum_probs=18.9
Q ss_pred cCCCCCCCCCCCCCchhhhhcCccccCCCCceecccccc
Q 048287 30 AAKKKRNLPGTPDPEAEVIALSPKTLMATNRFLCEICGK 68 (365)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~k~~~~~k~~~C~~Cgk 68 (365)
+....|..|+..|.... ..|.|+.||.
T Consensus 68 p~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred CcEEEcccCCCEEecCC------------cCccCcCCCC
Confidence 45678999997765532 4466999985
No 211
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.04 E-value=39 Score=25.26 Aligned_cols=16 Identities=38% Similarity=0.881 Sum_probs=12.3
Q ss_pred CCCCceeccccccccc
Q 048287 56 MATNRFLCEICGKGFQ 71 (365)
Q Consensus 56 ~~~k~~~C~~Cgk~F~ 71 (365)
+..-.|+|..||..|.
T Consensus 8 MPtY~Y~c~~cg~~~d 23 (82)
T COG2331 8 MPTYSYECTECGNRFD 23 (82)
T ss_pred ccceEEeecccchHHH
Confidence 4456799999998873
No 212
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.03 E-value=28 Score=33.12 Aligned_cols=27 Identities=19% Similarity=0.728 Sum_probs=19.8
Q ss_pred ccccccccccccchhhhhhhhcccCCc
Q 048287 136 KWKCEKCSKRYAVQSDWKAHSKTCGTR 162 (365)
Q Consensus 136 p~~C~~C~k~F~~~~~L~~H~~~~~~k 162 (365)
.|+|+.|+..|.+..-++.|...+.++
T Consensus 19 ~YtCPRCn~~YCsl~CYr~h~~~CsE~ 45 (383)
T KOG4317|consen 19 EYTCPRCNLLYCSLKCYRNHKHSCSEK 45 (383)
T ss_pred cccCCCCCccceeeeeecCCCccchHH
Confidence 488999988888877777776654444
No 213
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.38 E-value=68 Score=34.25 Aligned_cols=9 Identities=22% Similarity=0.516 Sum_probs=7.0
Q ss_pred ceeeCCCCC
Q 048287 100 RVYVCPEKT 108 (365)
Q Consensus 100 k~~~C~~C~ 108 (365)
.++.|+.|+
T Consensus 421 ~p~~Cp~Cg 429 (665)
T PRK14873 421 PDWRCPRCG 429 (665)
T ss_pred cCccCCCCc
Confidence 478899983
No 214
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=20.34 E-value=1.3e+02 Score=29.94 Aligned_cols=19 Identities=5% Similarity=-0.202 Sum_probs=7.9
Q ss_pred hhHHHHHHhhhcCCCcccc
Q 048287 121 LTGIKKHFCRKHGEKKWKC 139 (365)
Q Consensus 121 ~~~L~~H~~~H~~ekp~~C 139 (365)
...+..|...+.++.++.+
T Consensus 344 ~~~~~~~~~~~~~~~~~~~ 362 (396)
T KOG2461|consen 344 QLIYTQSHSMEVAEPTDMA 362 (396)
T ss_pred ccchhhhhhcccCCCCccc
Confidence 3334444444444444333
No 215
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=20.21 E-value=52 Score=21.41 Aligned_cols=13 Identities=23% Similarity=0.833 Sum_probs=10.8
Q ss_pred Cceeccccccccc
Q 048287 59 NRFLCEICGKGFQ 71 (365)
Q Consensus 59 k~~~C~~Cgk~F~ 71 (365)
++-.|++||..|.
T Consensus 28 ~~~~CpYCg~~yv 40 (40)
T PF10276_consen 28 GPVVCPYCGTRYV 40 (40)
T ss_dssp CEEEETTTTEEEE
T ss_pred CeEECCCCCCEEC
Confidence 4688999999883
No 216
>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=20.07 E-value=38 Score=22.13 Aligned_cols=15 Identities=40% Similarity=0.802 Sum_probs=10.0
Q ss_pred CceecccccccccCh
Q 048287 59 NRFLCEICGKGFQRD 73 (365)
Q Consensus 59 k~~~C~~Cgk~F~~~ 73 (365)
-+|.|+.|++.|-.+
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 589999999999754
Done!