Query 014041
Match_columns 432
No_of_seqs 341 out of 3175
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 01:17:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014041.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014041hhsearch_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 1.5E-28 3.3E-33 228.3 4.9 135 32-188 127-266 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.9 5.1E-25 1.1E-29 204.8 5.9 133 7-161 130-265 (279)
3 KOG1074 Transcriptional repres 99.8 6.1E-20 1.3E-24 191.2 0.2 80 104-190 605-693 (958)
4 KOG3576 Ovo and related transc 99.8 9.6E-19 2.1E-23 155.4 6.8 115 59-193 113-240 (267)
5 KOG3608 Zn finger proteins [Ge 99.7 1.7E-18 3.6E-23 165.1 0.4 160 11-192 183-348 (467)
6 KOG1074 Transcriptional repres 99.7 7.9E-18 1.7E-22 175.6 3.5 54 34-87 604-657 (958)
7 KOG3576 Ovo and related transc 99.6 3.1E-17 6.6E-22 145.8 0.7 113 31-163 113-237 (267)
8 KOG3608 Zn finger proteins [Ge 99.6 3.8E-16 8.2E-21 149.1 0.1 169 4-194 204-381 (467)
9 KOG3623 Homeobox transcription 99.5 8.6E-15 1.9E-19 150.7 2.4 106 63-186 210-330 (1007)
10 KOG3623 Homeobox transcription 99.5 9.4E-15 2E-19 150.4 1.9 81 60-160 891-971 (1007)
11 PLN03086 PRLI-interacting fact 99.2 1.1E-11 2.3E-16 129.0 7.6 103 62-190 452-565 (567)
12 PHA00733 hypothetical protein 99.1 7.6E-11 1.6E-15 101.1 4.6 114 31-163 7-124 (128)
13 PLN03086 PRLI-interacting fact 99.1 1.2E-10 2.5E-15 121.4 6.9 103 34-163 452-565 (567)
14 PHA00733 hypothetical protein 98.9 4.7E-10 1E-14 96.2 3.5 83 101-191 37-125 (128)
15 KOG3993 Transcription factor ( 98.9 1.6E-10 3.5E-15 113.4 0.4 151 34-191 266-484 (500)
16 PHA02768 hypothetical protein; 98.6 1.3E-08 2.9E-13 72.9 1.8 44 63-128 5-48 (55)
17 PHA02768 hypothetical protein; 98.5 4.6E-08 9.9E-13 70.1 2.2 44 104-156 5-48 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.5 8.9E-08 1.9E-12 58.5 2.1 26 126-151 1-26 (26)
19 KOG3993 Transcription factor ( 98.3 8.6E-08 1.9E-12 94.5 -0.6 85 103-194 266-385 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.2 3.9E-07 8.5E-12 55.7 0.2 26 50-75 1-26 (26)
21 PHA00616 hypothetical protein 98.1 1.2E-06 2.7E-11 59.8 1.3 34 63-109 1-34 (44)
22 PHA00732 hypothetical protein 98.0 5E-06 1.1E-10 65.0 2.7 49 63-136 1-49 (79)
23 PHA00616 hypothetical protein 97.9 7.2E-06 1.6E-10 56.1 1.6 36 104-146 1-36 (44)
24 PF00096 zf-C2H2: Zinc finger, 97.8 9.2E-06 2E-10 47.9 1.9 23 64-86 1-23 (23)
25 PHA00732 hypothetical protein 97.8 1.1E-05 2.3E-10 63.2 2.7 48 35-88 1-49 (79)
26 PF05605 zf-Di19: Drought indu 97.8 2.3E-05 4.9E-10 56.8 4.1 52 63-135 2-53 (54)
27 COG5189 SFP1 Putative transcri 97.8 6.8E-06 1.5E-10 78.5 1.5 28 101-133 346-373 (423)
28 COG5189 SFP1 Putative transcri 97.7 8.6E-06 1.9E-10 77.8 0.4 51 136-186 346-419 (423)
29 PF13894 zf-C2H2_4: C2H2-type 97.5 6.7E-05 1.5E-09 44.2 2.1 24 64-87 1-24 (24)
30 PF05605 zf-Di19: Drought indu 97.4 0.00021 4.6E-09 51.7 3.6 48 104-161 2-51 (54)
31 PF13912 zf-C2H2_6: C2H2-type 97.3 0.0001 2.2E-09 45.2 1.6 25 63-87 1-25 (27)
32 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00012 2.6E-09 59.3 1.6 23 65-87 1-23 (100)
33 COG5048 FOG: Zn-finger [Genera 97.2 0.00023 5E-09 72.4 3.7 143 34-181 288-461 (467)
34 KOG2231 Predicted E3 ubiquitin 97.1 0.00085 1.9E-08 71.5 6.2 22 65-87 117-138 (669)
35 KOG2231 Predicted E3 ubiquitin 96.9 0.0011 2.4E-08 70.7 4.8 125 34-186 114-260 (669)
36 PF00096 zf-C2H2: Zinc finger, 96.7 0.0013 2.8E-08 38.6 1.9 16 118-133 7-22 (23)
37 smart00355 ZnF_C2H2 zinc finge 96.6 0.0012 2.5E-08 39.3 1.8 24 64-87 1-24 (26)
38 PF12756 zf-C2H2_2: C2H2 type 96.6 0.0013 2.7E-08 53.2 2.5 73 106-189 1-74 (100)
39 KOG1146 Homeobox protein [Gene 96.5 0.00093 2E-08 75.0 1.2 145 37-188 438-641 (1406)
40 PF13912 zf-C2H2_6: C2H2-type 96.4 0.0016 3.4E-08 39.8 1.3 22 167-188 2-24 (27)
41 PF13894 zf-C2H2_4: C2H2-type 96.3 0.004 8.6E-08 36.4 2.5 24 105-135 1-24 (24)
42 PF12874 zf-met: Zinc-finger o 96.2 0.0024 5.2E-08 38.2 1.4 23 64-86 1-23 (25)
43 PF09237 GAGA: GAGA factor; I 96.1 0.0056 1.2E-07 43.0 2.8 34 54-87 14-48 (54)
44 PRK04860 hypothetical protein; 95.8 0.0047 1E-07 55.0 1.9 39 103-152 118-156 (160)
45 PF09237 GAGA: GAGA factor; I 95.5 0.012 2.5E-07 41.4 2.4 32 101-139 21-52 (54)
46 COG5048 FOG: Zn-finger [Genera 95.4 0.0067 1.5E-07 61.6 1.7 109 62-190 288-413 (467)
47 PF12171 zf-C2H2_jaz: Zinc-fin 95.2 0.0046 1E-07 37.8 -0.3 22 64-85 2-23 (27)
48 PRK04860 hypothetical protein; 94.9 0.014 3.1E-07 52.0 1.8 39 62-124 118-156 (160)
49 COG5236 Uncharacterized conser 94.4 0.025 5.5E-07 55.2 2.4 113 63-190 151-306 (493)
50 KOG1146 Homeobox protein [Gene 94.0 0.019 4.2E-07 64.9 0.7 77 101-188 462-541 (1406)
51 PF13909 zf-H2C2_5: C2H2-type 93.9 0.034 7.4E-07 32.8 1.5 23 64-87 1-23 (24)
52 KOG2785 C2H2-type Zn-finger pr 93.7 0.022 4.8E-07 56.5 0.5 171 7-187 3-242 (390)
53 smart00355 ZnF_C2H2 zinc finge 93.6 0.076 1.6E-06 31.1 2.6 17 118-134 7-23 (26)
54 PF13909 zf-H2C2_5: C2H2-type 93.5 0.071 1.5E-06 31.4 2.3 23 105-135 1-23 (24)
55 KOG4173 Alpha-SNAP protein [In 93.5 0.026 5.6E-07 51.3 0.5 82 101-190 76-171 (253)
56 PF12874 zf-met: Zinc-finger o 93.5 0.035 7.6E-07 33.0 0.9 21 140-160 1-21 (25)
57 PF12171 zf-C2H2_jaz: Zinc-fin 93.4 0.053 1.1E-06 33.1 1.7 22 140-161 2-23 (27)
58 PF09538 FYDLN_acid: Protein o 93.1 0.055 1.2E-06 44.9 1.9 33 33-76 7-39 (108)
59 COG5236 Uncharacterized conser 93.1 0.26 5.6E-06 48.4 6.7 42 118-163 258-306 (493)
60 KOG1280 Uncharacterized conser 93.0 0.19 4.2E-06 49.3 5.6 11 6-16 7-17 (381)
61 KOG3982 Runt and related trans 92.8 0.037 8.1E-07 54.4 0.6 10 409-418 104-113 (475)
62 smart00451 ZnF_U1 U1-like zinc 92.4 0.087 1.9E-06 34.0 1.7 24 63-86 3-26 (35)
63 PF13913 zf-C2HC_2: zinc-finge 92.4 0.095 2.1E-06 31.5 1.7 21 64-85 3-23 (25)
64 KOG2482 Predicted C2H2-type Zn 92.3 0.15 3.2E-06 50.0 3.9 24 63-86 195-218 (423)
65 KOG4377 Zn-finger protein [Gen 89.7 0.39 8.5E-06 48.2 4.1 121 62-191 270-429 (480)
66 PRK00464 nrdR transcriptional 89.7 0.12 2.6E-06 45.7 0.5 45 36-80 1-45 (154)
67 TIGR02300 FYDLN_acid conserved 89.5 0.23 5E-06 42.0 2.0 37 33-80 7-43 (129)
68 KOG2071 mRNA cleavage and poly 86.7 0.32 6.9E-06 51.3 1.4 30 58-87 413-442 (579)
69 smart00451 ZnF_U1 U1-like zinc 86.0 0.45 9.8E-06 30.5 1.4 23 139-161 3-25 (35)
70 KOG2893 Zn finger protein [Gen 85.7 0.26 5.6E-06 46.0 0.2 42 107-159 13-54 (341)
71 KOG1280 Uncharacterized conser 85.5 0.53 1.1E-05 46.3 2.2 33 137-169 77-110 (381)
72 KOG2893 Zn finger protein [Gen 85.3 0.21 4.6E-06 46.5 -0.5 43 65-131 12-54 (341)
73 KOG2482 Predicted C2H2-type Zn 85.2 1.8 3.8E-05 42.7 5.5 85 101-191 141-305 (423)
74 TIGR00622 ssl1 transcription f 85.1 1.5 3.2E-05 36.6 4.3 25 164-188 79-104 (112)
75 KOG4173 Alpha-SNAP protein [In 84.9 0.38 8.2E-06 43.9 0.8 78 61-161 77-168 (253)
76 PF12013 DUF3505: Protein of u 84.2 1 2.2E-05 37.3 3.1 24 167-190 81-109 (109)
77 cd00350 rubredoxin_like Rubred 83.3 0.52 1.1E-05 30.2 0.8 26 35-72 1-26 (33)
78 KOG2186 Cell growth-regulating 82.0 0.85 1.8E-05 43.1 1.9 44 140-185 4-48 (276)
79 PF09986 DUF2225: Uncharacteri 81.8 0.62 1.3E-05 43.6 1.0 42 137-178 3-61 (214)
80 KOG3982 Runt and related trans 81.4 0.99 2.1E-05 44.7 2.2 9 412-420 176-184 (475)
81 COG5151 SSL1 RNA polymerase II 80.9 2.3 5E-05 41.3 4.4 55 31-87 358-412 (421)
82 COG4049 Uncharacterized protei 80.9 0.87 1.9E-05 32.7 1.2 32 56-87 10-41 (65)
83 KOG1883 Cofactor required for 80.6 1.1 2.5E-05 50.4 2.6 32 280-311 1435-1466(1517)
84 COG4530 Uncharacterized protei 79.9 1.2 2.7E-05 36.5 1.9 36 33-80 7-42 (129)
85 TIGR00622 ssl1 transcription f 79.4 3.9 8.5E-05 34.1 4.8 79 7-87 15-105 (112)
86 PF09986 DUF2225: Uncharacteri 79.4 0.76 1.6E-05 43.0 0.7 44 33-76 3-61 (214)
87 KOG4167 Predicted DNA-binding 79.3 2 4.2E-05 46.4 3.7 26 62-87 791-816 (907)
88 PF10571 UPF0547: Uncharacteri 77.0 1.6 3.4E-05 26.5 1.3 25 36-74 1-25 (26)
89 COG4049 Uncharacterized protei 76.9 0.79 1.7E-05 32.9 0.0 24 138-161 16-39 (65)
90 PF02892 zf-BED: BED zinc fing 75.8 2.2 4.9E-05 29.0 2.1 26 60-85 13-42 (45)
91 KOG2186 Cell growth-regulating 75.5 1.6 3.6E-05 41.2 1.7 50 64-136 4-53 (276)
92 PHA00626 hypothetical protein 74.5 2 4.3E-05 30.9 1.5 17 61-77 21-37 (59)
93 KOG4124 Putative transcription 74.3 0.7 1.5E-05 45.5 -1.1 54 32-86 175-236 (442)
94 smart00531 TFIIE Transcription 74.0 1.7 3.7E-05 38.1 1.4 40 32-75 96-135 (147)
95 COG1198 PriA Primosomal protei 73.7 2.2 4.7E-05 47.1 2.4 14 135-148 471-484 (730)
96 KOG3598 Thyroid hormone recept 72.1 2 4.3E-05 49.6 1.6 10 65-74 1841-1850(2220)
97 KOG2907 RNA polymerase I trans 71.9 2.7 5.9E-05 34.7 2.0 44 32-75 71-114 (116)
98 PF13913 zf-C2HC_2: zinc-finge 71.7 4.1 8.8E-05 24.3 2.2 14 118-132 9-22 (25)
99 PRK09678 DNA-binding transcrip 71.5 1.6 3.4E-05 33.5 0.5 42 36-79 2-45 (72)
100 PF11179 DUF2967: Protein of u 71.2 2.6 5.6E-05 38.1 1.8 8 391-398 249-256 (258)
101 PRK04023 DNA polymerase II lar 70.5 4.2 9E-05 45.8 3.6 9 140-148 664-672 (1121)
102 PF04959 ARS2: Arsenite-resist 70.4 1 2.2E-05 42.0 -0.9 28 137-164 75-103 (214)
103 TIGR00373 conserved hypothetic 70.2 1.6 3.5E-05 38.8 0.3 36 32-76 106-141 (158)
104 cd00729 rubredoxin_SM Rubredox 70.0 1.9 4.2E-05 27.8 0.6 25 35-71 2-26 (34)
105 PRK00464 nrdR transcriptional 69.9 2.1 4.6E-05 37.8 1.0 48 8-55 1-48 (154)
106 KOG4407 Predicted Rho GTPase-a 69.4 2.8 6E-05 48.1 2.0 15 347-361 449-463 (1973)
107 PRK06266 transcription initiat 68.9 1.8 3.9E-05 39.3 0.4 37 32-77 114-150 (178)
108 PRK14890 putative Zn-ribbon RN 68.5 5 0.00011 29.3 2.5 33 34-71 24-56 (59)
109 PF09538 FYDLN_acid: Protein o 67.7 3.1 6.7E-05 34.6 1.5 16 137-152 24-39 (108)
110 TIGR02098 MJ0042_CXXC MJ0042 f 66.5 2.9 6.4E-05 27.4 0.9 34 36-74 3-36 (38)
111 PRK03564 formate dehydrogenase 65.2 4.1 9E-05 40.2 2.1 14 101-114 209-222 (309)
112 smart00614 ZnF_BED BED zinc fi 64.6 4.5 9.8E-05 28.4 1.7 25 63-87 18-48 (50)
113 PF12013 DUF3505: Protein of u 64.4 21 0.00046 29.3 5.9 24 62-86 10-33 (109)
114 PF13717 zinc_ribbon_4: zinc-r 64.4 2.7 5.8E-05 27.6 0.4 12 34-45 24-35 (36)
115 TIGR01384 TFS_arch transcripti 64.1 5.4 0.00012 32.6 2.3 41 35-75 62-102 (104)
116 TIGR01562 FdhE formate dehydro 64.0 4.3 9.4E-05 40.1 2.0 27 101-148 207-233 (305)
117 COG1996 RPC10 DNA-directed RNA 62.4 3.3 7.2E-05 29.2 0.6 30 33-72 4-33 (49)
118 KOG2785 C2H2-type Zn-finger pr 61.8 11 0.00024 37.9 4.3 23 139-161 217-242 (390)
119 COG1327 Predicted transcriptio 61.6 5.2 0.00011 35.0 1.8 48 8-55 1-48 (156)
120 COG1997 RPL43A Ribosomal prote 61.4 5.3 0.00012 31.6 1.6 33 33-75 33-65 (89)
121 COG1592 Rubrerythrin [Energy p 61.4 4.4 9.6E-05 36.3 1.4 24 35-71 134-157 (166)
122 smart00659 RPOLCX RNA polymera 61.3 4.4 9.6E-05 27.9 1.1 27 35-72 2-28 (44)
123 COG5151 SSL1 RNA polymerase II 61.0 9.4 0.0002 37.3 3.6 48 141-189 364-412 (421)
124 TIGR00244 transcriptional regu 60.9 3.5 7.6E-05 36.0 0.6 22 33-54 26-47 (147)
125 PF04216 FdhE: Protein involve 60.9 1.4 3E-05 43.2 -2.1 52 101-175 194-248 (290)
126 PRK00398 rpoP DNA-directed RNA 60.8 2.9 6.2E-05 28.9 0.1 31 34-74 2-32 (46)
127 TIGR00244 transcriptional regu 59.7 5.9 0.00013 34.6 1.8 46 37-82 2-47 (147)
128 COG1592 Rubrerythrin [Energy p 59.4 6.2 0.00013 35.3 1.9 25 103-147 133-157 (166)
129 COG1327 Predicted transcriptio 58.3 4.9 0.00011 35.1 1.1 44 37-80 2-45 (156)
130 KOG2807 RNA polymerase II tran 58.3 14 0.0003 36.5 4.2 34 35-82 276-309 (378)
131 smart00834 CxxC_CXXC_SSSS Puta 58.3 2.7 5.8E-05 27.9 -0.4 12 35-46 5-16 (41)
132 smart00440 ZnF_C2C2 C2C2 Zinc 58.1 4.3 9.3E-05 27.3 0.6 37 36-74 1-39 (40)
133 TIGR02605 CxxC_CxxC_SSSS putat 57.8 3 6.5E-05 29.4 -0.3 12 35-46 5-16 (52)
134 PF13719 zinc_ribbon_5: zinc-r 57.7 5.7 0.00012 26.1 1.1 11 63-73 25-35 (37)
135 smart00531 TFIIE Transcription 57.5 5.6 0.00012 34.8 1.4 40 100-150 95-134 (147)
136 PRK06266 transcription initiat 56.8 5.6 0.00012 36.1 1.3 35 100-150 113-147 (178)
137 PRK14873 primosome assembly pr 56.7 7.6 0.00016 42.7 2.5 11 138-148 421-431 (665)
138 COG1997 RPL43A Ribosomal prote 56.7 5.6 0.00012 31.4 1.1 13 139-151 53-65 (89)
139 KOG4124 Putative transcription 56.4 2.3 5.1E-05 42.0 -1.3 21 33-54 211-231 (442)
140 KOG2593 Transcription initiati 54.6 13 0.00027 38.2 3.4 36 137-174 126-162 (436)
141 PF05443 ROS_MUCR: ROS/MUCR tr 53.9 9.5 0.00021 32.8 2.1 24 61-87 70-93 (132)
142 TIGR02300 FYDLN_acid conserved 53.0 9.3 0.0002 32.5 1.9 16 137-152 24-39 (129)
143 TIGR00373 conserved hypothetic 53.0 16 0.00034 32.5 3.5 36 99-150 104-139 (158)
144 KOG0320 Predicted E3 ubiquitin 53.0 11 0.00024 33.9 2.5 13 100-112 127-139 (187)
145 PF14353 CpXC: CpXC protein 52.8 3.2 6.9E-05 35.3 -1.0 25 62-86 37-61 (128)
146 TIGR00595 priA primosomal prot 52.5 9.9 0.00021 40.4 2.5 49 64-148 214-262 (505)
147 smart00734 ZnF_Rad18 Rad18-lik 52.5 10 0.00022 22.9 1.5 20 64-84 2-21 (26)
148 COG3677 Transposase and inacti 52.4 7 0.00015 33.5 1.1 37 35-76 30-66 (129)
149 COG4957 Predicted transcriptio 51.7 8.8 0.00019 32.9 1.5 21 64-87 77-97 (148)
150 PF04959 ARS2: Arsenite-resist 51.5 8.9 0.00019 35.9 1.7 28 60-87 74-101 (214)
151 PF09723 Zn-ribbon_8: Zinc rib 51.0 5.3 0.00012 27.0 0.1 30 35-71 5-34 (42)
152 KOG0978 E3 ubiquitin ligase in 50.6 5.9 0.00013 43.2 0.4 50 104-158 643-697 (698)
153 PRK05978 hypothetical protein; 50.0 10 0.00022 33.4 1.7 34 34-76 32-65 (148)
154 PF01096 TFIIS_C: Transcriptio 49.7 3 6.5E-05 27.8 -1.3 12 63-74 28-39 (39)
155 COG2888 Predicted Zn-ribbon RN 49.6 10 0.00022 27.7 1.4 33 34-71 26-58 (61)
156 KOG3002 Zn finger protein [Gen 49.3 14 0.0003 36.5 2.7 16 33-48 78-93 (299)
157 PF08274 PhnA_Zn_Ribbon: PhnA 48.5 7.2 0.00016 24.5 0.4 25 37-72 4-28 (30)
158 PF07282 OrfB_Zn_ribbon: Putat 48.3 14 0.00031 27.5 2.1 35 34-78 27-61 (69)
159 PRK05580 primosome assembly pr 48.1 12 0.00026 41.3 2.4 26 101-148 405-430 (679)
160 KOG2593 Transcription initiati 47.5 10 0.00022 38.8 1.5 38 33-73 126-163 (436)
161 PF13240 zinc_ribbon_2: zinc-r 47.3 10 0.00023 22.1 1.0 11 37-47 1-11 (23)
162 COG2331 Uncharacterized protei 47.3 7.8 0.00017 29.8 0.5 23 58-84 7-29 (82)
163 PF11789 zf-Nse: Zinc-finger o 47.2 16 0.00035 26.5 2.2 49 32-112 8-56 (57)
164 KOG2807 RNA polymerase II tran 46.3 20 0.00044 35.3 3.2 24 165-188 344-368 (378)
165 PF14446 Prok-RING_1: Prokaryo 45.6 17 0.00038 26.1 2.0 29 34-74 4-32 (54)
166 cd00730 rubredoxin Rubredoxin; 45.5 12 0.00025 26.6 1.1 7 64-70 35-41 (50)
167 PF15135 UPF0515: Uncharacteri 44.8 24 0.00051 33.6 3.3 76 75-177 91-167 (278)
168 PF02166 Androgen_recep: Andro 44.7 7.3 0.00016 38.4 0.0 11 316-326 137-147 (423)
169 PHA02998 RNA polymerase subuni 44.6 12 0.00026 33.7 1.3 46 31-76 139-184 (195)
170 PF01363 FYVE: FYVE zinc finge 43.7 11 0.00024 28.0 0.9 32 32-75 6-37 (69)
171 PF02166 Androgen_recep: Andro 43.0 8 0.00017 38.1 0.0 6 339-344 168-173 (423)
172 PF14803 Nudix_N_2: Nudix N-te 43.0 10 0.00022 24.5 0.5 28 38-73 3-32 (34)
173 COG4530 Uncharacterized protei 42.1 17 0.00038 29.9 1.8 20 136-156 23-42 (129)
174 PRK03824 hypA hydrogenase nick 40.8 11 0.00023 32.6 0.5 41 32-72 67-116 (135)
175 PF01780 Ribosomal_L37ae: Ribo 39.9 9.5 0.00021 30.5 -0.0 32 33-74 33-64 (90)
176 PF01927 Mut7-C: Mut7-C RNAse 39.7 24 0.00052 30.8 2.5 49 34-82 90-143 (147)
177 PF03604 DNA_RNApol_7kD: DNA d 39.5 15 0.00032 23.5 0.8 26 36-72 1-26 (32)
178 COG0068 HypF Hydrogenase matur 39.5 11 0.00023 41.2 0.2 55 38-111 126-180 (750)
179 COG3091 SprT Zn-dependent meta 39.5 16 0.00034 32.1 1.2 34 137-175 115-150 (156)
180 COG1655 Uncharacterized protei 39.4 13 0.00029 34.8 0.9 39 33-71 17-70 (267)
181 PF09963 DUF2197: Uncharacteri 39.0 15 0.00032 26.7 0.8 36 63-110 2-37 (56)
182 PF09416 UPF1_Zn_bind: RNA hel 38.9 41 0.00088 29.7 3.7 50 61-112 12-68 (152)
183 PF05443 ROS_MUCR: ROS/MUCR tr 38.6 20 0.00044 30.8 1.8 29 100-138 68-96 (132)
184 COG1594 RPB9 DNA-directed RNA 38.1 13 0.00028 31.1 0.5 40 35-74 72-111 (113)
185 PTZ00255 60S ribosomal protein 37.8 20 0.00044 28.7 1.5 14 138-151 53-66 (90)
186 smart00661 RPOL9 RNA polymeras 37.6 26 0.00057 24.4 2.0 13 63-75 20-32 (52)
187 COG3357 Predicted transcriptio 37.1 20 0.00043 28.6 1.4 35 62-119 57-91 (97)
188 PF06524 NOA36: NOA36 protein; 36.2 18 0.00039 34.5 1.2 12 60-71 139-150 (314)
189 PF07800 DUF1644: Protein of u 36.2 61 0.0013 28.8 4.3 48 37-88 4-51 (162)
190 PF03833 PolC_DP2: DNA polymer 36.1 12 0.00026 41.6 0.0 11 62-72 654-664 (900)
191 PF11494 Ta0938: Ta0938; Inte 35.8 24 0.00053 28.4 1.7 43 31-78 10-52 (105)
192 PF13878 zf-C2H2_3: zinc-finge 35.7 28 0.0006 23.4 1.8 24 64-87 14-39 (41)
193 TIGR00280 L37a ribosomal prote 35.3 20 0.00044 28.7 1.2 13 139-151 53-65 (91)
194 KOG2636 Splicing factor 3a, su 35.1 22 0.00048 36.6 1.7 27 57-83 395-422 (497)
195 PF13824 zf-Mss51: Zinc-finger 34.5 28 0.0006 25.2 1.6 19 59-77 10-28 (55)
196 PF05290 Baculo_IE-1: Baculovi 34.3 23 0.0005 30.4 1.4 55 33-125 78-135 (140)
197 KOG3362 Predicted BBOX Zn-fing 34.3 18 0.0004 31.3 0.8 38 31-85 114-151 (156)
198 TIGR01206 lysW lysine biosynth 33.9 20 0.00043 25.9 0.8 11 63-73 22-32 (54)
199 PRK14714 DNA polymerase II lar 33.6 37 0.0008 39.6 3.3 8 36-43 668-675 (1337)
200 PF03811 Zn_Tnp_IS1: InsA N-te 33.5 29 0.00062 22.8 1.5 31 35-69 5-35 (36)
201 PRK03976 rpl37ae 50S ribosomal 33.1 22 0.00047 28.5 1.0 13 139-151 54-66 (90)
202 PF04810 zf-Sec23_Sec24: Sec23 33.0 25 0.00054 23.4 1.2 32 36-73 3-34 (40)
203 COG1571 Predicted DNA-binding 32.9 24 0.00052 36.3 1.5 29 141-179 352-381 (421)
204 PF02176 zf-TRAF: TRAF-type zi 32.3 33 0.00071 24.5 1.9 35 61-109 7-43 (60)
205 smart00064 FYVE Protein presen 32.2 43 0.00093 24.7 2.5 29 35-75 10-38 (68)
206 PF07754 DUF1610: Domain of un 32.1 19 0.00042 21.4 0.4 10 62-71 15-24 (24)
207 KOG0801 Predicted E3 ubiquitin 32.0 9 0.0002 33.8 -1.4 37 126-166 128-164 (205)
208 PF07975 C1_4: TFIIH C1-like d 31.8 7.4 0.00016 27.7 -1.6 27 61-87 19-45 (51)
209 PRK03564 formate dehydrogenase 31.7 31 0.00067 34.2 2.0 37 32-71 184-220 (309)
210 PRK12380 hydrogenase nickel in 31.4 18 0.00039 30.2 0.3 27 33-71 68-94 (113)
211 PF15269 zf-C2H2_7: Zinc-finge 31.4 25 0.00053 24.2 0.9 22 140-161 21-42 (54)
212 PRK12496 hypothetical protein; 31.0 26 0.00057 31.3 1.3 30 35-76 127-156 (164)
213 PF10263 SprT-like: SprT-like 30.4 19 0.00041 31.4 0.3 35 32-74 120-154 (157)
214 PF10013 DUF2256: Uncharacteri 30.3 29 0.00063 23.6 1.1 16 65-80 10-25 (42)
215 COG5624 TAF61 Transcription in 29.7 23 0.00049 36.0 0.8 20 271-290 230-249 (505)
216 PF13453 zf-TFIIB: Transcripti 29.7 33 0.00072 22.9 1.4 37 37-81 1-37 (41)
217 COG5188 PRP9 Splicing factor 3 29.6 29 0.00064 34.6 1.5 28 57-84 368-396 (470)
218 smart00154 ZnF_AN1 AN1-like Zi 29.5 24 0.00053 23.5 0.7 14 63-76 12-25 (39)
219 COG5432 RAD18 RING-finger-cont 29.0 27 0.00058 33.9 1.1 39 104-148 25-68 (391)
220 PF11931 DUF3449: Domain of un 28.3 19 0.00042 33.1 0.0 26 58-83 96-122 (196)
221 smart00132 LIM Zinc-binding do 28.3 34 0.00073 21.6 1.2 11 64-74 28-38 (39)
222 PRK14714 DNA polymerase II lar 28.2 49 0.0011 38.7 3.1 10 63-72 667-676 (1337)
223 COG1655 Uncharacterized protei 28.2 20 0.00043 33.7 0.1 25 137-161 17-41 (267)
224 KOG2071 mRNA cleavage and poly 28.1 39 0.00084 36.1 2.2 29 101-136 415-443 (579)
225 PF06689 zf-C4_ClpX: ClpX C4-t 27.8 16 0.00035 24.6 -0.4 33 35-72 1-33 (41)
226 KOG3408 U1-like Zn-finger-cont 27.6 39 0.00085 28.5 1.7 29 58-86 52-80 (129)
227 PF08792 A2L_zn_ribbon: A2L zi 27.5 39 0.00085 21.6 1.3 29 35-74 3-32 (33)
228 KOG3507 DNA-directed RNA polym 27.5 48 0.001 24.2 1.9 35 30-75 15-49 (62)
229 PRK04023 DNA polymerase II lar 27.5 47 0.001 37.9 2.8 13 63-75 663-675 (1121)
230 PF03249 TSA: Type specific an 27.4 36 0.00078 34.2 1.7 8 301-308 329-336 (503)
231 TIGR00100 hypA hydrogenase nic 27.4 22 0.00049 29.7 0.2 28 33-72 68-95 (115)
232 COG1198 PriA Primosomal protei 27.3 45 0.00097 37.1 2.6 48 9-72 437-484 (730)
233 cd00924 Cyt_c_Oxidase_Vb Cytoc 26.7 29 0.00062 28.2 0.7 43 28-75 49-91 (97)
234 PLN02294 cytochrome c oxidase 26.7 51 0.0011 29.6 2.3 46 28-76 109-154 (174)
235 COG1571 Predicted DNA-binding 26.6 39 0.00085 34.8 1.9 36 33-79 348-383 (421)
236 COG4896 Uncharacterized protei 25.9 51 0.0011 24.3 1.8 34 64-110 3-37 (68)
237 PF15135 UPF0515: Uncharacteri 25.7 27 0.00058 33.2 0.4 14 59-72 108-121 (278)
238 PF08271 TF_Zn_Ribbon: TFIIB z 25.5 41 0.00089 22.6 1.2 30 36-74 1-30 (43)
239 PF09332 Mcm10: Mcm10 replicat 25.2 8.6 0.00019 38.6 -3.1 43 101-150 249-296 (344)
240 PF03107 C1_2: C1 domain; Int 25.1 62 0.0014 20.0 1.9 21 36-70 1-22 (30)
241 TIGR03831 YgiT_finger YgiT-typ 25.0 30 0.00064 23.2 0.5 16 60-75 29-44 (46)
242 smart00731 SprT SprT homologue 24.6 38 0.00083 29.4 1.2 32 139-176 112-144 (146)
243 KOG4369 RTK signaling protein 24.2 2.4E+02 0.0052 33.1 7.3 15 295-309 1880-1894(2131)
244 PF01428 zf-AN1: AN1-like Zinc 23.9 28 0.00062 23.5 0.2 15 62-76 12-26 (43)
245 PRK00564 hypA hydrogenase nick 23.9 31 0.00068 28.9 0.5 29 32-72 68-97 (117)
246 PF14369 zf-RING_3: zinc-finge 23.5 51 0.0011 21.4 1.3 13 8-20 22-34 (35)
247 COG1656 Uncharacterized conser 23.5 56 0.0012 29.2 2.0 49 34-82 96-149 (165)
248 PF03145 Sina: Seven in absent 23.1 89 0.0019 28.5 3.4 56 62-138 13-74 (198)
249 PF06524 NOA36: NOA36 protein; 22.9 22 0.00048 33.9 -0.6 39 134-173 137-179 (314)
250 PF13451 zf-trcl: Probable zin 22.9 37 0.00081 23.9 0.6 18 61-78 2-19 (49)
251 KOG4167 Predicted DNA-binding 22.9 19 0.00042 39.2 -1.2 27 102-135 790-816 (907)
252 COG1773 Rubredoxin [Energy pro 22.8 36 0.00079 24.6 0.6 13 62-74 2-14 (55)
253 cd00065 FYVE FYVE domain; Zinc 22.6 56 0.0012 23.1 1.6 27 37-75 4-30 (57)
254 COG4888 Uncharacterized Zn rib 22.3 47 0.001 27.1 1.1 41 32-76 19-59 (104)
255 smart00731 SprT SprT homologue 21.7 53 0.0012 28.5 1.5 35 33-74 110-144 (146)
256 KOG1701 Focal adhesion adaptor 21.6 7.2 0.00016 39.7 -4.4 96 37-154 336-442 (468)
257 PF12760 Zn_Tnp_IS1595: Transp 21.6 95 0.0021 21.2 2.5 11 137-147 35-45 (46)
258 PRK03681 hypA hydrogenase nick 21.6 42 0.00091 28.0 0.8 30 32-72 67-96 (114)
259 PRK00432 30S ribosomal protein 21.4 60 0.0013 22.9 1.5 28 35-73 20-47 (50)
260 KOG3227 Calcium-responsive tra 21.3 56 0.0012 30.2 1.6 117 171-296 38-154 (231)
261 PRK00420 hypothetical protein; 21.3 69 0.0015 26.8 2.0 30 35-75 23-52 (112)
262 TIGR00515 accD acetyl-CoA carb 20.9 44 0.00096 32.7 0.9 36 34-78 25-60 (285)
263 PF05191 ADK_lid: Adenylate ki 20.7 25 0.00055 23.0 -0.5 13 137-149 19-31 (36)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.95 E-value=1.5e-28 Score=228.32 Aligned_cols=135 Identities=21% Similarity=0.395 Sum_probs=127.4
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCC---CCceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCC
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMA---TNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICP 108 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~---~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~ 108 (432)
...+|+|+.|||.|.+...|.+|+.+|-. .+.|.|++|||.|..-..|+.|+|+|+ -+++|.
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 46699999999999999999999999853 677999999999999999999999997 469999
Q ss_pred CCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcc-cCCcceeec-CCCccCCchHHHHHHH
Q 014041 109 EKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSRKDSFITHRA 186 (432)
Q Consensus 109 ~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-~~~k~~~C~-C~~~F~~~~~L~~H~~ 186 (432)
+| ||.|.+.+-|..|+|+|+|||||.|..|+|.|..+++|+.||++ .+.|+|.|. |+|+|..++.|.+|..
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 99 99999999999999999999999999999999999999999999 789999999 9999999999999987
Q ss_pred Hh
Q 014041 187 FC 188 (432)
Q Consensus 187 ~h 188 (432)
..
T Consensus 265 S~ 266 (279)
T KOG2462|consen 265 SA 266 (279)
T ss_pred hc
Confidence 53
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.91 E-value=5.1e-25 Score=204.82 Aligned_cols=133 Identities=23% Similarity=0.383 Sum_probs=125.8
Q ss_pred CCCCCCCCCcCcCCCCCCCCCCCCC---CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHH
Q 014041 7 GLSVPSTLKGFVQEPNSNPNPNPSS---NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHR 83 (432)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~ 83 (432)
.+.|++|+|.+.-.-++..|...|. ..+-+.|+.|||.|.....|+.|+++|+ -+++|.+|||.|.+...|+-|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 5899999999998888888886664 4678999999999999999999999998 6799999999999999999999
Q ss_pred HhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcc
Q 014041 84 RGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 84 r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~ 161 (432)
|+|+ |||||.|+.| +|+|.++++|+.||++|.+.|+|+|..|+|.|.+++.|.+|...
T Consensus 208 RTHT-------------GEKPF~C~hC-------~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 208 RTHT-------------GEKPFSCPHC-------GKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccc-------------CCCCccCCcc-------cchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 9999 9999999999 99999999999999999999999999999999999999999876
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.76 E-value=6.1e-20 Score=191.22 Aligned_cols=80 Identities=20% Similarity=0.469 Sum_probs=71.9
Q ss_pred ceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcccCCcc-----eeec----CCCc
Q 014041 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTRE-----YRCD----CGTL 174 (432)
Q Consensus 104 ~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~~~~k~-----~~C~----C~~~ 174 (432)
+-.|-+| -|.+..++.|+.|+|+|+|||||+|.+|++.|.++.+|+.||-+|.-+| |.|. |-+.
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 4567777 9999999999999999999999999999999999999999999976554 7785 8899
Q ss_pred cCCchHHHHHHHHhcc
Q 014041 175 FSRKDSFITHRAFCDA 190 (432)
Q Consensus 175 F~~~~~L~~H~~~h~~ 190 (432)
|...-.|..|++.|..
T Consensus 678 ftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 678 FTNAVTLPQHIRIHLG 693 (958)
T ss_pred ccccccccceEEeecC
Confidence 9999999999999864
No 4
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.76 E-value=9.6e-19 Score=155.36 Aligned_cols=115 Identities=23% Similarity=0.531 Sum_probs=106.2
Q ss_pred CCCCceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCC
Q 014041 59 MATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEK 138 (432)
Q Consensus 59 ~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gek 138 (432)
.+...|.|.+|+|.|.....|.+|++.|+ ..|.|.|..| ||.|.+...|++|+|+|+|.+
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 44567999999999999999999999999 8899999999 999999999999999999999
Q ss_pred cccccccccccCChHHhhhhhcc-cC-----------Ccceeec-CCCccCCchHHHHHHHHhccccc
Q 014041 139 KWKCEKCSKKYAVQSDWKAHSKI-CG-----------TREYRCD-CGTLFSRKDSFITHRAFCDALAE 193 (432)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~-~~-----------~k~~~C~-C~~~F~~~~~L~~H~~~h~~~~~ 193 (432)
||+|..|+|.|..+-.|..|++. || +|.|.|+ ||.+-.+...+..|++.|+....
T Consensus 173 pykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 173 PYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred ccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 99999999999999999999998 75 4679999 99999999999999999986443
No 5
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.70 E-value=1.7e-18 Score=165.08 Aligned_cols=160 Identities=18% Similarity=0.262 Sum_probs=134.5
Q ss_pred CCCCCcCcCCCCCCCCCCCCCCCCCcCCCCCCCCCCChhhhhcCccccC--CCCceecccccccccChHHHHHHHHhcCC
Q 014041 11 PSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSPKSLM--ATNRFLCEICNKGFQRDQNLQLHRRGHNL 88 (432)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~k~~c~~cg~~~~~~~~l~~h~~~h~--~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~ 88 (432)
..|.+.|....++..|.-.++++|-..|+.||..|.+...|-.|.+.-+ ...+|.|..|.|.|.++..|..|++.|-
T Consensus 183 ~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv- 261 (467)
T KOG3608|consen 183 AMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV- 261 (467)
T ss_pred hhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh-
Confidence 4566667777777778888888999999999999999988888877654 4568999999999999999999998886
Q ss_pred CcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhh-hcCCCcccccccccccCChHHhhhhhcccCCcce
Q 014041 89 PWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSR-KHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREY 167 (432)
Q Consensus 89 ~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~-H~gekp~~C~~C~k~F~~~~~L~~H~~~~~~k~~ 167 (432)
..|+|+.| +......+.|..|++. |..+|||+|+.|++.|.+.++|.+|..+|.+-.|
T Consensus 262 --------------n~ykCplC-------dmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y 320 (467)
T KOG3608|consen 262 --------------NCYKCPLC-------DMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVY 320 (467)
T ss_pred --------------hccccccc-------ccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccce
Confidence 46899998 8888889999999986 7788999999999999999999999888778888
Q ss_pred eec---CCCccCCchHHHHHHHHhcccc
Q 014041 168 RCD---CGTLFSRKDSFITHRAFCDALA 192 (432)
Q Consensus 168 ~C~---C~~~F~~~~~L~~H~~~h~~~~ 192 (432)
.|+ |.++|++...|++|++.++...
T Consensus 321 ~C~h~~C~~s~r~~~q~~~H~~evhEg~ 348 (467)
T KOG3608|consen 321 QCEHPDCHYSVRTYTQMRRHFLEVHEGN 348 (467)
T ss_pred ecCCCCCcHHHHHHHHHHHHHHHhccCC
Confidence 885 8888888888888988777433
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.69 E-value=7.9e-18 Score=175.61 Aligned_cols=54 Identities=17% Similarity=0.258 Sum_probs=50.9
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcC
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
-+-.|=+|.+.....+.|+.|.++|++|+||+|+|||+.|.++.+|+.||-+|.
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc
Confidence 467799999999999999999999999999999999999999999999999997
No 7
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.64 E-value=3.1e-17 Score=145.84 Aligned_cols=113 Identities=24% Similarity=0.393 Sum_probs=105.5
Q ss_pred CCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCC
Q 014041 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEK 110 (432)
Q Consensus 31 ~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C 110 (432)
...-.+.|.+|||.|.....|++|++.|...|+|.|..|||.|..-..|++|+|+|+ |.+||+|..|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rtht-------------gvrpykc~~c 179 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHT-------------GVRPYKCSLC 179 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcccc-------------Cccccchhhh
Confidence 345678999999999999999999999999999999999999999999999999999 9999999999
Q ss_pred CCCCCCCCCccCCHHHHHHHHhhhcC-----------CCcccccccccccCChHHhhhhhcc-cC
Q 014041 111 SCVHHDPSRALGDLTGIKKHFSRKHG-----------EKKWKCEKCSKKYAVQSDWKAHSKI-CG 163 (432)
Q Consensus 111 ~c~~~~c~k~f~~~~~L~~H~~~H~g-----------ekp~~C~~C~k~F~~~~~L~~H~~~-~~ 163 (432)
+|+|..+..|..|++.-+| +|-|.|..||.+-.+.+.+..|++. |.
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 9999999999999988665 4679999999999999999999998 54
No 8
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.56 E-value=3.8e-16 Score=149.12 Aligned_cols=169 Identities=14% Similarity=0.210 Sum_probs=143.5
Q ss_pred CCCCCCCCCCCCcCcCCCCCCCCCCCC--CCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHH
Q 014041 4 QDHGLSVPSTLKGFVQEPNSNPNPNPS--SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQL 81 (432)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~ 81 (432)
.|+-+.||.|+.-|.-...+-.|--+. -..-.|.|..|.|.|.++..|..|+..|.. -|+|+.|+......+.|.+
T Consensus 204 ~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~ 281 (467)
T KOG3608|consen 204 NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTT 281 (467)
T ss_pred CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHH
Confidence 566789999999888654443333221 123489999999999999999999998865 4999999999999999999
Q ss_pred HHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccc--cccccCChHHhhhhh
Q 014041 82 HRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEK--CSKKYAVQSDWKAHS 159 (432)
Q Consensus 82 H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~--C~k~F~~~~~L~~H~ 159 (432)
|+|.-+ ..+|||+|+.| ++.|.+.+.|.+|...|. +-.|.|+. |...|.....|++|+
T Consensus 282 H~r~rH------------s~dkpfKCd~C-------d~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~ 341 (467)
T KOG3608|consen 282 HIRYRH------------SKDKPFKCDEC-------DTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHF 341 (467)
T ss_pred HHHhhh------------ccCCCccccch-------hhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHH
Confidence 988755 37999999999 999999999999999997 77799988 999999999999999
Q ss_pred cc-c-C--Ccceeec-CCCccCCchHHHHHHHHhcccccc
Q 014041 160 KI-C-G--TREYRCD-CGTLFSRKDSFITHRAFCDALAEE 194 (432)
Q Consensus 160 ~~-~-~--~k~~~C~-C~~~F~~~~~L~~H~~~h~~~~~~ 194 (432)
+. | | .-+|.|. |.+.|.+-.+|..|+++-|+....
T Consensus 342 ~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 342 LEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred HHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCC
Confidence 98 5 3 4579999 999999999999998877765443
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.48 E-value=8.6e-15 Score=150.70 Aligned_cols=106 Identities=25% Similarity=0.563 Sum_probs=96.1
Q ss_pred ceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcC------
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHG------ 136 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~g------ 136 (432)
...|++|.+.+++...|+.|++.-+ +..+..|.|..| ...|..+..|.+||.+|..
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 4789999999999999999977654 125667999999 9999999999999998863
Q ss_pred -------CCcccccccccccCChHHhhhhhcc-cCCcceeec-CCCccCCchHHHHHHH
Q 014041 137 -------EKKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSRKDSFITHRA 186 (432)
Q Consensus 137 -------ekp~~C~~C~k~F~~~~~L~~H~~~-~~~k~~~C~-C~~~F~~~~~L~~H~~ 186 (432)
.|+|+|..|+|.|+.+-+|+.|+|+ .|||||.|+ |+|+|+....+..||.
T Consensus 272 sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 272 SLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred cccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 4789999999999999999999999 899999999 9999999999999985
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.48 E-value=9.4e-15 Score=150.44 Aligned_cols=81 Identities=25% Similarity=0.596 Sum_probs=67.5
Q ss_pred CCCceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCc
Q 014041 60 ATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKK 139 (432)
Q Consensus 60 ~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp 139 (432)
.+..|.|+.|+|+|.....|.+|.-.|+ |.+||.|.+| .|+|+.+.+|..|+|.|.||||
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHs-------------GqRPyqC~iC-------kKAFKHKHHLtEHkRLHSGEKP 950 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHS-------------GQRPYQCIIC-------KKAFKHKHHLTEHKRLHSGEKP 950 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhc-------------CCCCcccchh-------hHhhhhhhhhhhhhhhccCCCc
Confidence 3456888888888888888888888887 8888888888 8888888888888888888888
Q ss_pred ccccccccccCChHHhhhhhc
Q 014041 140 WKCEKCSKKYAVQSDWKAHSK 160 (432)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~ 160 (432)
|.|+.|+|+|.....+-.||.
T Consensus 951 fQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 951 FQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chhhhhhhhcccccchHhhhc
Confidence 888888888888887777776
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.25 E-value=1.1e-11 Score=128.98 Aligned_cols=103 Identities=23% Similarity=0.468 Sum_probs=88.3
Q ss_pred CceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCccc
Q 014041 62 NRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWK 141 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~ 141 (432)
+.+.|+.|++.|. ...|..|++.|+ ++|.|+ | ++.+ .+..|..|+++|.++|++.
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H---------------kpv~Cp-C-------g~~~-~R~~L~~H~~thCp~Kpi~ 506 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH---------------EPLQCP-C-------GVVL-EKEQMVQHQASTCPLRLIT 506 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC---------------CCccCC-C-------CCCc-chhHHHhhhhccCCCCcee
Confidence 4479999999996 678999999986 579999 8 8755 6789999999999999999
Q ss_pred ccccccccC----------ChHHhhhhhcccCCcceeec-CCCccCCchHHHHHHHHhcc
Q 014041 142 CEKCSKKYA----------VQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITHRAFCDA 190 (432)
Q Consensus 142 C~~C~k~F~----------~~~~L~~H~~~~~~k~~~C~-C~~~F~~~~~L~~H~~~h~~ 190 (432)
|.+|++.|. ....|..|..++|.+++.|+ |++.|..++ |..|+..+|+
T Consensus 507 C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlrd-m~~H~~~~h~ 565 (567)
T PLN03086 507 CRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLKE-MDIHQIAVHQ 565 (567)
T ss_pred CCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeehh-HHHHHHHhhc
Confidence 999999995 24589999999999999999 999987665 5788877665
No 12
>PHA00733 hypothetical protein
Probab=99.10 E-value=7.6e-11 Score=101.10 Aligned_cols=114 Identities=16% Similarity=0.115 Sum_probs=81.3
Q ss_pred CCCCCcCCCCCCCCC-CChhhhhcCccccCCCCceecccccccccChHHHHHH--HHhcCCCcccccccccccCCcceeC
Q 014041 31 SNQLKRKRNLPGTPD-PDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLH--RRGHNLPWKLKQRTNKEVRKKVYIC 107 (432)
Q Consensus 31 ~~~~k~~c~~cg~~~-~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H--~r~H~~~~~~~~~~~~~~~~k~y~C 107 (432)
++.++|-.+..|-.| ++.+.|..+...-.+.++++|.+|++.|.....|..| ++.|. .....++|.|
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~----------~~~~~kPy~C 76 (128)
T PHA00733 7 SGSKKYLSNHKGIFIHVTLEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLL----------TSKAVSPYVC 76 (128)
T ss_pred cchHhhcccCCCeEEecCHHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhc----------ccCCCCCccC
Confidence 345666655555433 3456666665555667889999999999888887776 33322 0124678888
Q ss_pred CCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcc-cC
Q 014041 108 PEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI-CG 163 (432)
Q Consensus 108 ~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-~~ 163 (432)
+.| ++.|.....|..|++.| +++|.|.+|++.|.....|..|+.. |+
T Consensus 77 ~~C-------gk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 77 PLC-------LMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCC-------CCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 888 88888888888888876 4568888888888888888888776 54
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.10 E-value=1.2e-10 Score=121.36 Aligned_cols=103 Identities=14% Similarity=0.241 Sum_probs=87.4
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCC
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCV 113 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~ 113 (432)
..+.|+.||+.|. ...|..|.++++ ++|.|+ ||+.| .+..|..|+++|. .++++.|++|
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thC-------------p~Kpi~C~fC--- 510 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTC-------------PLRLITCRFC--- 510 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccC-------------CCCceeCCCC---
Confidence 4469999999997 577999999985 789999 99866 6689999999998 8999999999
Q ss_pred CCCCCCccC----------CHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcc-cC
Q 014041 114 HHDPSRALG----------DLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI-CG 163 (432)
Q Consensus 114 ~~~c~k~f~----------~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-~~ 163 (432)
++.|. ....|..|...+ |.+++.|..|++.|..+ +|..|+.. |.
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 88874 356899999996 99999999999988766 67788776 53
No 14
>PHA00733 hypothetical protein
Probab=98.95 E-value=4.7e-10 Score=96.22 Aligned_cols=83 Identities=16% Similarity=0.275 Sum_probs=70.5
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHH--Hh---hhcCCCcccccccccccCChHHhhhhhcccCCcceeec-CCCc
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKH--FS---RKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTL 174 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H--~~---~H~gekp~~C~~C~k~F~~~~~L~~H~~~~~~k~~~C~-C~~~ 174 (432)
..+++.|.+| .+.|.....|..| ++ .+++++||.|+.|++.|.....|..|++.+ +.+|.|+ |++.
T Consensus 37 ~~~~~~~~~~-------~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~ 108 (128)
T PHA00733 37 EQKRLIRAVV-------KTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKE 108 (128)
T ss_pred hhhhHHHHHH-------hhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCc
Confidence 5688999999 8888777776665 22 344689999999999999999999999975 4679999 9999
Q ss_pred cCCchHHHHHHHHhccc
Q 014041 175 FSRKDSFITHRAFCDAL 191 (432)
Q Consensus 175 F~~~~~L~~H~~~h~~~ 191 (432)
|.....|.+|+...|.+
T Consensus 109 F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 109 FRNTDSTLDHVCKKHNI 125 (128)
T ss_pred cCCHHHHHHHHHHhcCc
Confidence 99999999999987764
No 15
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.94 E-value=1.6e-10 Score=113.36 Aligned_cols=151 Identities=16% Similarity=0.204 Sum_probs=113.8
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcC-CCccc--cc----------------
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHN-LPWKL--KQ---------------- 94 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~-~~~~~--~~---------------- 94 (432)
-.|.|.+|...|.+.-.|..|...-.--.-|+|++|+|+|.-..+|.-|+|+|. ++... ..
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 368999999999999999999877666566999999999999999999999997 11111 00
Q ss_pred -ccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCC-----------------------------------
Q 014041 95 -RTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEK----------------------------------- 138 (432)
Q Consensus 95 -~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gek----------------------------------- 138 (432)
+.-....+.-|.|.+| +|.|.+...|++|..+|+...
T Consensus 346 ~rsg~dss~gi~~C~~C-------~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g 418 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTC-------GKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHG 418 (500)
T ss_pred cccCCcccCceeecHHh-------hhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccc
Confidence 0001123447999999 999999999999988876310
Q ss_pred -----------cccccccccccCChHHhhhhhcc-cCCcceeec-CCCccCCchHHHHHHHHhccc
Q 014041 139 -----------KWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSRKDSFITHRAFCDAL 191 (432)
Q Consensus 139 -----------p~~C~~C~k~F~~~~~L~~H~~~-~~~k~~~C~-C~~~F~~~~~L~~H~~~h~~~ 191 (432)
-..|++|+-.+..+..--.|.+. +-+..|.|. |.-.|.....|.+|+..+|..
T Consensus 419 ~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 419 DEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred cceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChH
Confidence 01355566555555555555555 556669999 999999999999999988753
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.63 E-value=1.3e-08 Score=72.85 Aligned_cols=44 Identities=18% Similarity=0.257 Sum_probs=38.9
Q ss_pred ceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHH
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIK 128 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~ 128 (432)
-|+|++|||.|.+..+|..|+|+|+ ++|+|..| ++.|...+.|.
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 4899999999999999999999996 58999998 99998776654
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.52 E-value=4.6e-08 Score=70.13 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=37.0
Q ss_pred ceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhh
Q 014041 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWK 156 (432)
Q Consensus 104 ~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~ 156 (432)
-|.|+.| |+.|...+.|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~C-------GK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPIC-------GEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchh-------CCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4788888 899999999999999988 6888988998888777664
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=8.9e-08 Score=58.55 Aligned_cols=26 Identities=31% Similarity=0.824 Sum_probs=23.7
Q ss_pred HHHHHHhhhcCCCcccccccccccCC
Q 014041 126 GIKKHFSRKHGEKKWKCEKCSKKYAV 151 (432)
Q Consensus 126 ~L~~H~~~H~gekp~~C~~C~k~F~~ 151 (432)
+|.+|+++|+|+|||+|++|++.|..
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=98.32 E-value=8.6e-08 Score=94.50 Aligned_cols=85 Identities=19% Similarity=0.427 Sum_probs=71.3
Q ss_pred cceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcccCCc-----------------
Q 014041 103 KVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTR----------------- 165 (432)
Q Consensus 103 k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~~~~k----------------- 165 (432)
..|+|..| ...|.+...|..|.-.-.-.--|+|+.|+|.|.-..+|..|.|+|.-|
T Consensus 266 GdyiCqLC-------K~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ 338 (500)
T KOG3993|consen 266 GDYICQLC-------KEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVET 338 (500)
T ss_pred HHHHHHHH-------HHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhh
Confidence 46999999 999999999999975433333499999999999999999999986221
Q ss_pred -----------------ceeec-CCCccCCchHHHHHHHHhcccccc
Q 014041 166 -----------------EYRCD-CGTLFSRKDSFITHRAFCDALAEE 194 (432)
Q Consensus 166 -----------------~~~C~-C~~~F~~~~~L~~H~~~h~~~~~~ 194 (432)
.|.|. |++.|++...|++|...|+.....
T Consensus 339 rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~ 385 (500)
T KOG3993|consen 339 RAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLA 385 (500)
T ss_pred hhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccc
Confidence 28999 999999999999999999875443
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.17 E-value=3.9e-07 Score=55.69 Aligned_cols=26 Identities=15% Similarity=0.430 Sum_probs=23.8
Q ss_pred hhhcCccccCCCCceecccccccccC
Q 014041 50 VIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 50 ~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
.|..|+++|++++||+|++|++.|.+
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 47889999999999999999999974
No 21
>PHA00616 hypothetical protein
Probab=98.09 E-value=1.2e-06 Score=59.78 Aligned_cols=34 Identities=12% Similarity=0.245 Sum_probs=31.3
Q ss_pred ceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCC
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPE 109 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~ 109 (432)
||+|+.||+.|..+..|..|++.|+ +++++.|+.
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 6999999999999999999999999 788888865
No 22
>PHA00732 hypothetical protein
Probab=97.96 E-value=5e-06 Score=65.01 Aligned_cols=49 Identities=22% Similarity=0.412 Sum_probs=33.8
Q ss_pred ceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcC
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHG 136 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~g 136 (432)
||.|++||+.|.+...|+.|++.++ . ++.|+.| ++.|. .|..|++.+.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H-------------~--~~~C~~C-------gKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH-------------T--LTKCPVC-------NKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc-------------C--CCccCCC-------CCEeC---ChhhhhcccCC
Confidence 5778888888888888888877533 1 2467777 77776 46777765543
No 23
>PHA00616 hypothetical protein
Probab=97.85 E-value=7.2e-06 Score=56.06 Aligned_cols=36 Identities=17% Similarity=0.234 Sum_probs=30.3
Q ss_pred ceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccc
Q 014041 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCS 146 (432)
Q Consensus 104 ~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~ 146 (432)
||.|..| |+.|..+..|.+|++.|+|++++.|+.--
T Consensus 1 pYqC~~C-------G~~F~~~s~l~~H~r~~hg~~~~~~~~~y 36 (44)
T PHA00616 1 MYQCLRC-------GGIFRKKKEVIEHLLSVHKQNKLTLEYFY 36 (44)
T ss_pred CCccchh-------hHHHhhHHHHHHHHHHhcCCCccceeEEE
Confidence 5788888 89999999999999999999988887643
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.85 E-value=9.2e-06 Score=47.92 Aligned_cols=23 Identities=43% Similarity=0.902 Sum_probs=21.8
Q ss_pred eecccccccccChHHHHHHHHhc
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGH 86 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H 86 (432)
|+|++|++.|.+...|+.|++.|
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 79999999999999999999875
No 25
>PHA00732 hypothetical protein
Probab=97.84 E-value=1.1e-05 Score=63.16 Aligned_cols=48 Identities=17% Similarity=0.200 Sum_probs=41.9
Q ss_pred CcCCCCCCCCCCChhhhhcCccc-cCCCCceecccccccccChHHHHHHHHhcCC
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKS-LMATNRFLCEICNKGFQRDQNLQLHRRGHNL 88 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~-h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~ 88 (432)
+|+|..||+.|.....|..|++. |.+ +.|++||+.|. .|..|++++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---ChhhhhcccCC
Confidence 47899999999999999999984 653 68999999997 69999988763
No 26
>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=97.83 E-value=2.3e-05 Score=56.81 Aligned_cols=52 Identities=23% Similarity=0.439 Sum_probs=35.0
Q ss_pred ceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhc
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKH 135 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~ 135 (432)
.|.|++|++ ..+...|..|....+. ...+.+.|++| ...+. ..|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~-----------~~~~~v~CPiC-------~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHR-----------SESKNVVCPIC-------SSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCc-----------CCCCCccCCCc-------hhhhh--hHHHHHHHHhc
Confidence 478888888 4556778888555441 13456888888 55443 37888887765
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.82 E-value=6.8e-06 Score=78.53 Aligned_cols=28 Identities=29% Similarity=0.665 Sum_probs=23.9
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhh
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSR 133 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~ 133 (432)
++|||+|++-+| .|.|+...+|+.|+.-
T Consensus 346 d~KpykCpV~gC-----~K~YknqnGLKYH~lh 373 (423)
T COG5189 346 DGKPYKCPVEGC-----NKKYKNQNGLKYHMLH 373 (423)
T ss_pred cCceecCCCCCc-----hhhhccccchhhhhhc
Confidence 458999999877 9999999999999875
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.71 E-value=8.6e-06 Score=77.83 Aligned_cols=51 Identities=31% Similarity=0.635 Sum_probs=45.5
Q ss_pred CCCcccccc--cccccCChHHhhhhhcc-c-------------------CCcceeec-CCCccCCchHHHHHHH
Q 014041 136 GEKKWKCEK--CSKKYAVQSDWKAHSKI-C-------------------GTREYRCD-CGTLFSRKDSFITHRA 186 (432)
Q Consensus 136 gekp~~C~~--C~k~F~~~~~L~~H~~~-~-------------------~~k~~~C~-C~~~F~~~~~L~~H~~ 186 (432)
++|||+|++ |.|+|+....|+.|+.- | ..|||+|+ |+|+|+....|+-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 469999987 99999999999999886 5 34899999 9999999999998875
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=97.50 E-value=6.7e-05 Score=44.21 Aligned_cols=24 Identities=42% Similarity=0.899 Sum_probs=20.5
Q ss_pred eecccccccccChHHHHHHHHhcC
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
|+|++|++.|.+...|..|++.|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999999875
No 30
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.35 E-value=0.00021 Score=51.71 Aligned_cols=48 Identities=21% Similarity=0.387 Sum_probs=32.6
Q ss_pred ceeCCCCCCCCCCCCCccCCHHHHHHHHhhhc-CC-CcccccccccccCChHHhhhhhcc
Q 014041 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKH-GE-KKWKCEKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 104 ~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~-ge-kp~~C~~C~k~F~~~~~L~~H~~~ 161 (432)
.|.|++| ++ ..+...|..|....+ .+ +.+.|++|...+. .+|..|+..
T Consensus 2 ~f~CP~C-------~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 2 SFTCPYC-------GK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred CcCCCCC-------CC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 3778888 77 455677888877643 33 4688888887544 377777765
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=97.34 E-value=0.0001 Score=45.17 Aligned_cols=25 Identities=36% Similarity=0.699 Sum_probs=23.7
Q ss_pred ceecccccccccChHHHHHHHHhcC
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
+|+|++|++.|.+...|..|++.|.
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 6999999999999999999999886
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.26 E-value=0.00012 Score=59.27 Aligned_cols=23 Identities=22% Similarity=0.567 Sum_probs=0.0
Q ss_pred ecccccccccChHHHHHHHHhcC
Q 014041 65 LCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 65 ~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
+|.+|+..|.....|..|+...+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H 23 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKH 23 (100)
T ss_dssp -----------------------
T ss_pred Ccccccccccccccccccccccc
Confidence 58888888888888888876555
No 33
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=97.23 E-value=0.00023 Score=72.37 Aligned_cols=143 Identities=19% Similarity=0.227 Sum_probs=96.6
Q ss_pred CCcCCCCCCCCCCChhhhhcCcc--ccCCC--Cceecc--cccccccChHHHHHHHHhcCCCccccccc-----------
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPK--SLMAT--NRFLCE--ICNKGFQRDQNLQLHRRGHNLPWKLKQRT----------- 96 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~--~h~~~--k~f~C~--~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~----------- 96 (432)
.++.|..|...|.....+..|.+ .|.++ ++|.|+ .|++.|.+...|..|...|..........
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 57999999999999999999999 89999 999999 89999999999999999998322111000
Q ss_pred -----------ccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCC--cccccccccccCChHHhhhhhcc-c
Q 014041 97 -----------NKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEK--KWKCEKCSKKYAVQSDWKAHSKI-C 162 (432)
Q Consensus 97 -----------~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gek--p~~C~~C~k~F~~~~~L~~H~~~-~ 162 (432)
......+.+.|..-.| ...+.....+..|...|...+ .+.|..|.+.|.....+..|++. .
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSC-----IRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHT 442 (467)
T ss_pred CCCCccchhhccCccCCccccccccch-----hhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccc
Confidence 0001122233333222 566666666777777666655 35556788888888888887777 3
Q ss_pred CCcceeecCCCccCCchHH
Q 014041 163 GTREYRCDCGTLFSRKDSF 181 (432)
Q Consensus 163 ~~k~~~C~C~~~F~~~~~L 181 (432)
...++.|.+-+.|.....+
T Consensus 443 ~~~~~~~~~~~~~~~~~~~ 461 (467)
T COG5048 443 NHAPLLCSILKSFRRDLDL 461 (467)
T ss_pred cCCceeeccccccchhhhh
Confidence 3444444444444444433
No 34
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.08 E-value=0.00085 Score=71.48 Aligned_cols=22 Identities=32% Similarity=0.597 Sum_probs=13.9
Q ss_pred ecccccccccChHHHHHHHHhcC
Q 014041 65 LCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 65 ~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
+|.+| -.|.....|+.|++..|
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H 138 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQH 138 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhh
Confidence 34444 44457888999985544
No 35
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.88 E-value=0.0011 Score=70.70 Aligned_cols=125 Identities=19% Similarity=0.264 Sum_probs=78.6
Q ss_pred CCcCCCCCCCCCCChhhhhcCcc-ccCCCCceecccc----------cccccChHHHHHHHHhcCCCcccccccccccCC
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPK-SLMATNRFLCEIC----------NKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRK 102 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~-~h~~~k~f~C~~C----------gk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~ 102 (432)
.++.|..| ..|...+.|+.|+. .|.. +.|.+| .|.|. ...|..|++.=- + .....+
T Consensus 114 ~~~~~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt-~~el~~h~~~gd-~-------d~~s~r 180 (669)
T KOG2231|consen 114 NKKECLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYT-RAELNLHLMFGD-P-------DDESCR 180 (669)
T ss_pred ccCCCccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeeheh-HHHHHHHHhcCC-C-------cccccc
Confidence 35667777 77788999999984 3432 444444 44444 445667755321 0 000111
Q ss_pred cceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccc------cccCChHHhhhhhcc-cCCcceeec---CC
Q 014041 103 KVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCS------KKYAVQSDWKAHSKI-CGTREYRCD---CG 172 (432)
Q Consensus 103 k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~------k~F~~~~~L~~H~~~-~~~k~~~C~---C~ 172 (432)
.--.|..| ...|-....|.+|++.++ |.|..|. ..|..-++|..|.|. | |.|+ |.
T Consensus 181 Ghp~C~~C-------~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~ 245 (669)
T KOG2231|consen 181 GHPLCKFC-------HERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCR 245 (669)
T ss_pred CCccchhh-------hhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----ccccccccc
Confidence 23567777 899999999999999876 6777774 456777889999888 6 5564 54
Q ss_pred -CccCCchHHHHHHH
Q 014041 173 -TLFSRKDSFITHRA 186 (432)
Q Consensus 173 -~~F~~~~~L~~H~~ 186 (432)
+.|.....+..|++
T Consensus 246 ~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 246 TKKFYVAFELEIELK 260 (669)
T ss_pred cceeeehhHHHHHHH
Confidence 33444444555554
No 36
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.65 E-value=0.0013 Score=38.55 Aligned_cols=16 Identities=19% Similarity=0.578 Sum_probs=9.4
Q ss_pred CCccCCHHHHHHHHhh
Q 014041 118 SRALGDLTGIKKHFSR 133 (432)
Q Consensus 118 ~k~f~~~~~L~~H~~~ 133 (432)
++.|.++..|..|++.
T Consensus 7 ~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 7 GKSFSSKSNLKRHMRR 22 (23)
T ss_dssp TEEESSHHHHHHHHHH
T ss_pred CCccCCHHHHHHHHhH
Confidence 5566666666666554
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.64 E-value=0.0012 Score=39.31 Aligned_cols=24 Identities=33% Similarity=0.667 Sum_probs=22.2
Q ss_pred eecccccccccChHHHHHHHHhcC
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
|+|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999775
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.64 E-value=0.0013 Score=53.21 Aligned_cols=73 Identities=15% Similarity=0.238 Sum_probs=21.4
Q ss_pred eCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcccCCcceeec-CCCccCCchHHHHH
Q 014041 106 ICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITH 184 (432)
Q Consensus 106 ~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~~~~k~~~C~-C~~~F~~~~~L~~H 184 (432)
.|..| +..|.+...|..|+...++...- ..+.+.....+..+++..-...+.|. |++.|.+...|..|
T Consensus 1 ~C~~C-------~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~H 69 (100)
T PF12756_consen 1 QCLFC-------DESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEH 69 (100)
T ss_dssp -----------------------------------------------------------SSEEBSSSS-EESSHHHHHHH
T ss_pred Ccccc-------ccccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHH
Confidence 37777 99999999999999886663211 11223344445555554333479999 99999999999999
Q ss_pred HHHhc
Q 014041 185 RAFCD 189 (432)
Q Consensus 185 ~~~h~ 189 (432)
++.+.
T Consensus 70 m~~~~ 74 (100)
T PF12756_consen 70 MRSKH 74 (100)
T ss_dssp HHHTT
T ss_pred HcCcc
Confidence 99753
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.51 E-value=0.00093 Score=75.04 Aligned_cols=145 Identities=14% Similarity=0.160 Sum_probs=103.5
Q ss_pred CCCCCCCCCCChhhhhcCccc-cCCCCceecccccccccChHHHHHHHHhcCCCcc---cc--------cc-cccccCCc
Q 014041 37 KRNLPGTPDPDAEVIALSPKS-LMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWK---LK--------QR-TNKEVRKK 103 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~-h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~---~~--------~~-~~~~~~~k 103 (432)
.|..|+..+.....+.-|... +.-.|.|+|+.|+..|+....|..|||.-+-... ++ .+ .....+.+
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 355566666666666666554 4455789999999999999999999998441111 11 01 11224557
Q ss_pred ceeCCCCCCCCCCCCCccCCHHHHHHHHhh--hc-----------------------------------C------CCcc
Q 014041 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSR--KH-----------------------------------G------EKKW 140 (432)
Q Consensus 104 ~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~--H~-----------------------------------g------ekp~ 140 (432)
+|.|..| ...++....|-.|+.. |. | +-+|
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 8889888 9999999999999853 21 0 1259
Q ss_pred cccccccccCChHHhhhhhcc-cC-Ccceeec-CCCccCCchHHHHHHHHh
Q 014041 141 KCEKCSKKYAVQSDWKAHSKI-CG-TREYRCD-CGTLFSRKDSFITHRAFC 188 (432)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~-~~-~k~~~C~-C~~~F~~~~~L~~H~~~h 188 (432)
.|.+|+........|+.||.. +. .-|..|. |.-.+.....+..+.+.+
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 999999999999999999998 44 4447787 888877777776666655
No 40
>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=96.42 E-value=0.0016 Score=39.81 Aligned_cols=22 Identities=32% Similarity=0.767 Sum_probs=11.1
Q ss_pred eeec-CCCccCCchHHHHHHHHh
Q 014041 167 YRCD-CGTLFSRKDSFITHRAFC 188 (432)
Q Consensus 167 ~~C~-C~~~F~~~~~L~~H~~~h 188 (432)
|.|+ |++.|.+...|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 4454 555555555555555444
No 41
>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=96.27 E-value=0.004 Score=36.35 Aligned_cols=24 Identities=17% Similarity=0.582 Sum_probs=13.9
Q ss_pred eeCCCCCCCCCCCCCccCCHHHHHHHHhhhc
Q 014041 105 YICPEKSCVHHDPSRALGDLTGIKKHFSRKH 135 (432)
Q Consensus 105 y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~ 135 (432)
|.|++| ++.|.++..|+.|++.|+
T Consensus 1 ~~C~~C-------~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPIC-------GKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SST-------S-EESSHHHHHHHHHHHS
T ss_pred CCCcCC-------CCcCCcHHHHHHHHHhhC
Confidence 456666 666666666666666653
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.24 E-value=0.0024 Score=38.20 Aligned_cols=23 Identities=43% Similarity=0.996 Sum_probs=21.3
Q ss_pred eecccccccccChHHHHHHHHhc
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGH 86 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H 86 (432)
|.|++|++.|.+...|..|++.+
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 78999999999999999998865
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=96.10 E-value=0.0056 Score=42.97 Aligned_cols=34 Identities=26% Similarity=0.438 Sum_probs=22.7
Q ss_pred CccccC-CCCceecccccccccChHHHHHHHHhcC
Q 014041 54 SPKSLM-ATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 54 h~~~h~-~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
+.+.+. .+.|-.|++|+..+....+|++|+..++
T Consensus 14 ~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 14 KPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp --CCCCTTS--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred HHHHhhccCCCCCCCcchhhccchhhHHHHHHHHh
Confidence 344444 4678999999999999999999998777
No 44
>PRK04860 hypothetical protein; Provisional
Probab=95.82 E-value=0.0047 Score=55.03 Aligned_cols=39 Identities=18% Similarity=0.496 Sum_probs=28.1
Q ss_pred cceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCCh
Q 014041 103 KVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQ 152 (432)
Q Consensus 103 k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~ 152 (432)
-+|.|. | ++ ....+.+|.++|+++++|+|..|+..|...
T Consensus 118 ~~Y~C~-C-------~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-C-------QE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-C-------CC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 467776 6 55 566677888888888888888887777654
No 45
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.48 E-value=0.012 Score=41.40 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=16.1
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCc
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKK 139 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp 139 (432)
.+.|-.|++| +..+....+|++|+..+|+.||
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 4456666666 6666666666666666555554
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.44 E-value=0.0067 Score=61.57 Aligned_cols=109 Identities=18% Similarity=0.226 Sum_probs=79.6
Q ss_pred CceecccccccccChHHHHHHHH--hcCCCcccccccccccCC--cceeCC--CCCCCCCCCCCccCCHHHHHHHHhhhc
Q 014041 62 NRFLCEICNKGFQRDQNLQLHRR--GHNLPWKLKQRTNKEVRK--KVYICP--EKSCVHHDPSRALGDLTGIKKHFSRKH 135 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~~~L~~H~r--~H~~~~~~~~~~~~~~~~--k~y~C~--~C~c~~~~c~k~f~~~~~L~~H~~~H~ 135 (432)
.++.|..|.+.|.+...|..|.+ .|. ++ +++.|+ .| ++.|.+...+..|...|+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-------------~~~~~~~~~p~~~~-------~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-------------GESLKPFSCPYSLC-------GKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-------------cccCCceeeeccCC-------CccccccccccCCccccc
Confidence 57999999999999999999999 787 67 899999 67 999999999999999999
Q ss_pred CCCccccc--ccccccCChHHhh----hhhc-c-cCCcceeec---CCCccCCchHHHHHHHHhcc
Q 014041 136 GEKKWKCE--KCSKKYAVQSDWK----AHSK-I-CGTREYRCD---CGTLFSRKDSFITHRAFCDA 190 (432)
Q Consensus 136 gekp~~C~--~C~k~F~~~~~L~----~H~~-~-~~~k~~~C~---C~~~F~~~~~L~~H~~~h~~ 190 (432)
+.++++|. .|.+.+.....-. .+.. . ...+.+.|. |...+.+...+..|...+..
T Consensus 348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 413 (467)
T COG5048 348 SISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLS 413 (467)
T ss_pred CCCccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccc
Confidence 98887774 3655555444311 1111 1 445556663 66666666666666555544
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.20 E-value=0.0046 Score=37.84 Aligned_cols=22 Identities=32% Similarity=0.844 Sum_probs=19.5
Q ss_pred eecccccccccChHHHHHHHHh
Q 014041 64 FLCEICNKGFQRDQNLQLHRRG 85 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~ 85 (432)
|.|++|++.|.+...|..|++.
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 7899999999999999988765
No 48
>PRK04860 hypothetical protein; Provisional
Probab=94.86 E-value=0.014 Score=51.97 Aligned_cols=39 Identities=21% Similarity=0.384 Sum_probs=33.6
Q ss_pred CceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCH
Q 014041 62 NRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDL 124 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~ 124 (432)
-+|.|. |++ ....+.+|.++|+ ++++|.|..| +..|...
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 7788999999999 8999999999 7777543
No 49
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.38 E-value=0.025 Score=55.15 Aligned_cols=113 Identities=18% Similarity=0.299 Sum_probs=69.6
Q ss_pred ceeccc--ccccccChHHHHHHHHhcCCCccccc------------------ccccc--------cCCcceeCCCCCCCC
Q 014041 63 RFLCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQ------------------RTNKE--------VRKKVYICPEKSCVH 114 (432)
Q Consensus 63 ~f~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~~~------------------~~~~~--------~~~k~y~C~~C~c~~ 114 (432)
.|.|+. |..+-.....|+.|.+..+.-.-|.. -.+.+ .-+.--.|..|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC---- 226 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFC---- 226 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhc----
Confidence 488864 66665556788999766552221110 00111 11223357776
Q ss_pred CCCCCccCCHHHHHHHHhhhcCCCccccccccc-------ccCChHHhhhhhcc-cCCcceeec---CC----CccCCch
Q 014041 115 HDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSK-------KYAVQSDWKAHSKI-CGTREYRCD---CG----TLFSRKD 179 (432)
Q Consensus 115 ~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k-------~F~~~~~L~~H~~~-~~~k~~~C~---C~----~~F~~~~ 179 (432)
...|-+-+.|.+|+|..|. +|.+|++ -|+.-..|.+|.+. | |.|. |. ..|....
T Consensus 227 ---~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~~~~ 295 (493)
T COG5236 227 ---KIYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFPYHT 295 (493)
T ss_pred ---cceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEeccHH
Confidence 8888888888888887542 3555554 36667778888776 4 6674 54 4688888
Q ss_pred HHHHHHHHhcc
Q 014041 180 SFITHRAFCDA 190 (432)
Q Consensus 180 ~L~~H~~~h~~ 190 (432)
.|..|+..-|+
T Consensus 296 el~~h~~~~h~ 306 (493)
T COG5236 296 ELLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHHhh
Confidence 88999765554
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.96 E-value=0.019 Score=64.90 Aligned_cols=77 Identities=17% Similarity=0.248 Sum_probs=55.0
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCC-CcccccccccccCChHHhhhhhcc-cCCcceeec-CCCccCC
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGE-KKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSR 177 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~ge-kp~~C~~C~k~F~~~~~L~~H~~~-~~~k~~~C~-C~~~F~~ 177 (432)
..|.|+|+.| +..|.....|..|||..|.+ +- .+|. .+.....+-+=... .+.++|.|. |...+..
T Consensus 462 ~~kt~~cpkc-------~~~yk~a~~L~vhmRskhp~~~~---~~c~-~gq~~~~~arg~~~~~~~~p~~C~~C~~sttt 530 (1406)
T KOG1146|consen 462 FFKTLKCPKC-------NWHYKLAQTLGVHMRSKHPESQS---AYCK-AGQNHPRLARGEVYRCPGKPYPCRACNYSTTT 530 (1406)
T ss_pred ccccccCCcc-------chhhhhHHHhhhcccccccccch---hHhH-hccccccccccccccCCCCcccceeeeeeeec
Confidence 5688999999 99999999999999984433 22 3442 23323223221112 677899999 9999999
Q ss_pred chHHHHHHHHh
Q 014041 178 KDSFITHRAFC 188 (432)
Q Consensus 178 ~~~L~~H~~~h 188 (432)
+..|.+|+...
T Consensus 531 ng~LsihlqS~ 541 (1406)
T KOG1146|consen 531 NGNLSIHLQSD 541 (1406)
T ss_pred chHHHHHHHHH
Confidence 99999998754
No 51
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.93 E-value=0.034 Score=32.80 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=18.9
Q ss_pred eecccccccccChHHHHHHHHhcC
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
|+|+.|+-... +..|.+|++.|+
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 79999999888 889999999875
No 52
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=93.69 E-value=0.022 Score=56.49 Aligned_cols=171 Identities=18% Similarity=0.160 Sum_probs=92.6
Q ss_pred CCCCCCCCCcCcCCCCCCCCCCC--CC-CCCCcCCCCCCCCCCChhhhhcCccc---------cCCCCceeccccccccc
Q 014041 7 GLSVPSTLKGFVQEPNSNPNPNP--SS-NQLKRKRNLPGTPDPDAEVIALSPKS---------LMATNRFLCEICNKGFQ 74 (432)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~--~~-~~~k~~c~~cg~~~~~~~~l~~h~~~---------h~~~k~f~C~~Cgk~F~ 74 (432)
.|.|..|.-.|.....-..|.+. |. +-|++.-.+++ -+++.+..-..+ -.+..++.|.+|.|.|.
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPP---ItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~ 79 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPP---ITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFA 79 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCC---cCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhcccc
Confidence 57888888888866434444433 22 33333333333 233333222111 23345799999999999
Q ss_pred ChHHHHHHHHhcCCCcccccccc----------cc-------cCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhh----
Q 014041 75 RDQNLQLHRRGHNLPWKLKQRTN----------KE-------VRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSR---- 133 (432)
Q Consensus 75 ~~~~L~~H~r~H~~~~~~~~~~~----------~~-------~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~---- 133 (432)
.......|+..-..-...+...+ .. ...+.-.+..+ -..+........+...
T Consensus 80 s~~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~-------~E~~~~~d~~~e~~~dd~~E 152 (390)
T KOG2785|consen 80 SPKAHENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKW-------YEVDSDEDSSEEEEEDDEEE 152 (390)
T ss_pred ChhhHHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccch-------hhcccccccchhhccCcchh
Confidence 99999999644320000000000 00 00011012222 2222222222222211
Q ss_pred --------hcCCCcccccccccccCChHHhhhhhcc-cCCc-----------------------ceeec-CC---CccCC
Q 014041 134 --------KHGEKKWKCEKCSKKYAVQSDWKAHSKI-CGTR-----------------------EYRCD-CG---TLFSR 177 (432)
Q Consensus 134 --------H~gekp~~C~~C~k~F~~~~~L~~H~~~-~~~k-----------------------~~~C~-C~---~~F~~ 177 (432)
-..+-|--|-.|++.|........||.. ||-. -|.|- |. +.|.+
T Consensus 153 di~~d~~~e~e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~s 232 (390)
T KOG2785|consen 153 DIEEDGDDEDELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSS 232 (390)
T ss_pred hhhhccchhcccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccc
Confidence 1112356788899998888888888887 6432 27888 98 99999
Q ss_pred chHHHHHHHH
Q 014041 178 KDSFITHRAF 187 (432)
Q Consensus 178 ~~~L~~H~~~ 187 (432)
....+.||.-
T Consensus 233 leavr~HM~~ 242 (390)
T KOG2785|consen 233 LEAVRAHMRD 242 (390)
T ss_pred cHHHHHHHhh
Confidence 9999999973
No 53
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.60 E-value=0.076 Score=31.12 Aligned_cols=17 Identities=12% Similarity=0.384 Sum_probs=10.4
Q ss_pred CCccCCHHHHHHHHhhh
Q 014041 118 SRALGDLTGIKKHFSRK 134 (432)
Q Consensus 118 ~k~f~~~~~L~~H~~~H 134 (432)
++.|.....|..|++.|
T Consensus 7 ~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 7 GKVFKSKSALKEHMRTH 23 (26)
T ss_pred cchhCCHHHHHHHHHHh
Confidence 66666666666666544
No 54
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.48 E-value=0.071 Score=31.40 Aligned_cols=23 Identities=35% Similarity=0.738 Sum_probs=13.5
Q ss_pred eeCCCCCCCCCCCCCccCCHHHHHHHHhhhc
Q 014041 105 YICPEKSCVHHDPSRALGDLTGIKKHFSRKH 135 (432)
Q Consensus 105 y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~ 135 (432)
|.|+.| +.... ...|.+|++.|+
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 66665 666777776654
No 55
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.46 E-value=0.026 Score=51.33 Aligned_cols=82 Identities=21% Similarity=0.465 Sum_probs=68.2
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhhcc-c----------CCcceee
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI-C----------GTREYRC 169 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~-~----------~~k~~~C 169 (432)
..+.|.|++-+| ...|...+.+..|+.+-|+ -.|.+|.+.|.+.--|..|+.. | |.-.|.|
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 446688999877 8999999999999987555 3699999999999999999875 5 5556999
Q ss_pred --c-CCCccCCchHHHHHHHHhcc
Q 014041 170 --D-CGTLFSRKDSFITHRAFCDA 190 (432)
Q Consensus 170 --~-C~~~F~~~~~L~~H~~~h~~ 190 (432)
+ |+..|.+...-+.|+-..|.
T Consensus 148 lvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 148 LVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHhhhhhhhhhhhhhhHHHHhcc
Confidence 4 99999999999999765544
No 56
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.45 E-value=0.035 Score=32.99 Aligned_cols=21 Identities=19% Similarity=0.730 Sum_probs=11.9
Q ss_pred ccccccccccCChHHhhhhhc
Q 014041 140 WKCEKCSKKYAVQSDWKAHSK 160 (432)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~ 160 (432)
|.|.+|++.|.....|+.|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 445555555555555555554
No 57
>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=93.42 E-value=0.053 Score=33.07 Aligned_cols=22 Identities=27% Similarity=0.688 Sum_probs=18.8
Q ss_pred ccccccccccCChHHhhhhhcc
Q 014041 140 WKCEKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~ 161 (432)
|.|..|++.|.....|..|++.
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 6788888888888888888875
No 58
>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=93.11 E-value=0.055 Score=44.89 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=27.6
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
..|+.|+.||+.|.. ..+.|..|+.||..|.-.
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 468999999999988 334788999999999876
No 59
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.10 E-value=0.26 Score=48.35 Aligned_cols=42 Identities=14% Similarity=0.351 Sum_probs=30.2
Q ss_pred CCccCCHHHHHHHHhhhcCCCcccccc--cc----cccCChHHhhhhhcc-cC
Q 014041 118 SRALGDLTGIKKHFSRKHGEKKWKCEK--CS----KKYAVQSDWKAHSKI-CG 163 (432)
Q Consensus 118 ~k~f~~~~~L~~H~~~H~gekp~~C~~--C~----k~F~~~~~L~~H~~~-~~ 163 (432)
..-|.+...|..|++.-+ |.|.+ |. ..|.....|..|+.. |+
T Consensus 258 ~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 258 YQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFPYHTELLEHLTRFHK 306 (493)
T ss_pred hhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEeccHHHHHHHHHHHhh
Confidence 345888899999988744 77743 32 357888888888876 64
No 60
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=92.95 E-value=0.19 Score=49.29 Aligned_cols=11 Identities=27% Similarity=0.241 Sum_probs=8.3
Q ss_pred CCCCCCCCCCc
Q 014041 6 HGLSVPSTLKG 16 (432)
Q Consensus 6 ~~~~~~~~~~~ 16 (432)
++++|+.|+|.
T Consensus 7 e~v~CdgC~k~ 17 (381)
T KOG1280|consen 7 EGVSCDGCGKT 17 (381)
T ss_pred CCceecccccc
Confidence 47888888764
No 61
>KOG3982 consensus Runt and related transcription factors [Transcription]
Probab=92.80 E-value=0.037 Score=54.38 Aligned_cols=10 Identities=0% Similarity=0.162 Sum_probs=4.1
Q ss_pred CcHHHHHHhh
Q 014041 409 LSQQELAKFM 418 (432)
Q Consensus 409 ~~~~~~~~~~ 418 (432)
||.+.++|..
T Consensus 104 ~laehpgeLv 113 (475)
T KOG3982|consen 104 FLAEHPGELV 113 (475)
T ss_pred HHHhCcccee
Confidence 4444444433
No 62
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.38 E-value=0.087 Score=33.96 Aligned_cols=24 Identities=29% Similarity=0.811 Sum_probs=21.1
Q ss_pred ceecccccccccChHHHHHHHHhc
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGH 86 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H 86 (432)
+|.|++|++.|.....+..|++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 589999999999999999997543
No 63
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.36 E-value=0.095 Score=31.48 Aligned_cols=21 Identities=29% Similarity=0.672 Sum_probs=17.5
Q ss_pred eecccccccccChHHHHHHHHh
Q 014041 64 FLCEICNKGFQRDQNLQLHRRG 85 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~ 85 (432)
.+|++||+.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5899999999 67779999764
No 64
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=92.32 E-value=0.15 Score=49.99 Aligned_cols=24 Identities=33% Similarity=0.621 Sum_probs=22.0
Q ss_pred ceecccccccccChHHHHHHHHhc
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGH 86 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H 86 (432)
++.|-.|.|.|+.+..|+.|||..
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhc
Confidence 689999999999999999998754
No 65
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=89.72 E-value=0.39 Score=48.19 Aligned_cols=121 Identities=14% Similarity=0.289 Sum_probs=72.3
Q ss_pred Cceec--ccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCC--
Q 014041 62 NRFLC--EICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGE-- 137 (432)
Q Consensus 62 k~f~C--~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~ge-- 137 (432)
.-|.| +.|+..+..+....+|..+|-+-.. +...-.+.-...|.|-.-+| .+ +-+....|-..|+..
T Consensus 270 Ehyhcl~e~C~ykr~~k~DvirH~~~hkkrdn-sL~dgf~rfs~syhC~~~~C-----~k---sTsdV~~h~nFht~~~n 340 (480)
T KOG4377|consen 270 EHYHCLNEYCFYKRGQKNDVIRHVEIHKKRDN-SLIDGFHRFSNSYHCTGQIC-----EK---STSDVLLHDNFHTDKRN 340 (480)
T ss_pred hhhcccCccccccccchhhhHHHHHHHhhccc-ccccchhhcCccchhhhccc-----Cc---ccccccccCcccccccc
Confidence 34888 6799888889999999998862100 00000001112255554433 76 445556666666532
Q ss_pred -----Ccccccccc--cccCChHHhhhhhcc-c----CC--------------------cceeec---CCCccCCchHHH
Q 014041 138 -----KKWKCEKCS--KKYAVQSDWKAHSKI-C----GT--------------------REYRCD---CGTLFSRKDSFI 182 (432)
Q Consensus 138 -----kp~~C~~C~--k~F~~~~~L~~H~~~-~----~~--------------------k~~~C~---C~~~F~~~~~L~ 182 (432)
..|.|..|+ ..|+...+-..|.+- - |- .-|.|+ |+.+|...+.+.
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 247887766 555533333333331 1 11 116785 999999999999
Q ss_pred HHHHHhccc
Q 014041 183 THRAFCDAL 191 (432)
Q Consensus 183 ~H~~~h~~~ 191 (432)
.|.|.|.+.
T Consensus 421 shkrkheRq 429 (480)
T KOG4377|consen 421 SHKRKHERQ 429 (480)
T ss_pred hhhhhhhhh
Confidence 999999876
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.69 E-value=0.12 Score=45.72 Aligned_cols=45 Identities=18% Similarity=0.228 Sum_probs=21.7
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHH
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~ 80 (432)
++|+.||.++...-.-..-.....-++.|.|+.||+.|.+...+.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVE 45 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEecc
Confidence 367777766532211111111111123377777777777665543
No 67
>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=89.53 E-value=0.23 Score=42.00 Aligned_cols=37 Identities=16% Similarity=0.162 Sum_probs=29.0
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHH
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~ 80 (432)
..|+.|+.||+.|.. ..+.|..|+.||..|.....++
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 368999999999988 3357889999999987664443
No 68
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=86.65 E-value=0.32 Score=51.25 Aligned_cols=30 Identities=20% Similarity=0.365 Sum_probs=25.6
Q ss_pred cCCCCceecccccccccChHHHHHHHHhcC
Q 014041 58 LMATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 58 h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
.-..++-.|..||++|........||-.|-
T Consensus 413 Ly~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 413 LYKDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred hccCCcchhcccccccccchhhhhHhhhhh
Confidence 345677999999999999999998888885
No 69
>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=86.04 E-value=0.45 Score=30.50 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=16.1
Q ss_pred cccccccccccCChHHhhhhhcc
Q 014041 139 KWKCEKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~ 161 (432)
+|.|++|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777777777777664
No 70
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=85.70 E-value=0.26 Score=45.95 Aligned_cols=42 Identities=26% Similarity=0.400 Sum_probs=34.4
Q ss_pred CCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhhh
Q 014041 107 CPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHS 159 (432)
Q Consensus 107 C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~ 159 (432)
|++| .+.|....-|..|.+. |.|+|.+|-|.+-+--.|..|-
T Consensus 13 cwyc-------nrefddekiliqhqka----khfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 13 CWYC-------NREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeec-------ccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeeh
Confidence 7888 9999999999988765 3499999999887777777663
No 71
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=85.49 E-value=0.53 Score=46.33 Aligned_cols=33 Identities=9% Similarity=0.173 Sum_probs=26.0
Q ss_pred CCcccccccccccCChHHhhhhhcc-cCCcceee
Q 014041 137 EKKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRC 169 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~-~~~k~~~C 169 (432)
..-|.|++|+++-.+...|..|... |.+-.+.|
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~ 110 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSV 110 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcce
Confidence 3468999999998888899999888 77665543
No 72
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=85.35 E-value=0.21 Score=46.48 Aligned_cols=43 Identities=23% Similarity=0.486 Sum_probs=34.5
Q ss_pred ecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHH
Q 014041 65 LCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHF 131 (432)
Q Consensus 65 ~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~ 131 (432)
=|=+|++.|..+.-|.+|++..+ |+|.+| .|.+.+--.|..|-
T Consensus 12 wcwycnrefddekiliqhqkakh-----------------fkchic-------hkkl~sgpglsihc 54 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH-----------------FKCHIC-------HKKLFSGPGLSIHC 54 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc-----------------ceeeee-------hhhhccCCCceeeh
Confidence 48899999999999999988766 999999 66665656666663
No 73
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=85.20 E-value=1.8 Score=42.72 Aligned_cols=85 Identities=18% Similarity=0.341 Sum_probs=61.7
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCC----------------------CcccccccccccCChHHhhhh
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGE----------------------KKWKCEKCSKKYAVQSDWKAH 158 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~ge----------------------kp~~C~~C~k~F~~~~~L~~H 158 (432)
......|-.|. ......++.+..|+-.-|+- ..++|-+|.|.|..+..|+.|
T Consensus 141 t~fslqClFCn------~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeH 214 (423)
T KOG2482|consen 141 TIFSLQCLFCN------NEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEH 214 (423)
T ss_pred CeeeeEEEEec------chhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHH
Confidence 33456788883 34556777777777553321 247899999999999999999
Q ss_pred hcc--cCC-c----------------------------------------------------c--eeec-CCCccCCchH
Q 014041 159 SKI--CGT-R----------------------------------------------------E--YRCD-CGTLFSRKDS 180 (432)
Q Consensus 159 ~~~--~~~-k----------------------------------------------------~--~~C~-C~~~F~~~~~ 180 (432)
||. |.+ . + -+|- |...+-....
T Consensus 215 MrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~ 294 (423)
T KOG2482|consen 215 MRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVF 294 (423)
T ss_pred HHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHH
Confidence 997 411 0 0 3898 9998888999
Q ss_pred HHHHHHHhccc
Q 014041 181 FITHRAFCDAL 191 (432)
Q Consensus 181 L~~H~~~h~~~ 191 (432)
|..||+..|..
T Consensus 295 l~eHmk~vHe~ 305 (423)
T KOG2482|consen 295 LFEHMKIVHEF 305 (423)
T ss_pred HHHHHHHHHHh
Confidence 99999987753
No 74
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.09 E-value=1.5 Score=36.55 Aligned_cols=25 Identities=20% Similarity=0.592 Sum_probs=14.2
Q ss_pred Ccceeec-CCCccCCchHHHHHHHHh
Q 014041 164 TREYRCD-CGTLFSRKDSFITHRAFC 188 (432)
Q Consensus 164 ~k~~~C~-C~~~F~~~~~L~~H~~~h 188 (432)
...|.|+ |...|-..=+.-.|-..|
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhcc
Confidence 3456666 666666555555555444
No 75
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.93 E-value=0.38 Score=43.95 Aligned_cols=78 Identities=22% Similarity=0.435 Sum_probs=63.1
Q ss_pred CCceeccc--ccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhh-hc--
Q 014041 61 TNRFLCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSR-KH-- 135 (432)
Q Consensus 61 ~k~f~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~-H~-- 135 (432)
...|.|.+ |-..|.....+..|..+-+ + -.|.+| .+.|.+...|..|+.. |.
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 45688986 8899998888888854443 2 478888 9999999999999875 32
Q ss_pred -------CCCcccc--cccccccCChHHhhhhhcc
Q 014041 136 -------GEKKWKC--EKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 136 -------gekp~~C--~~C~k~F~~~~~L~~H~~~ 161 (432)
|...|.| ..|+.+|.+...-+.|+-.
T Consensus 134 Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 134 FQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred HHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 4557999 5599999999999999887
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=84.23 E-value=1 Score=37.31 Aligned_cols=24 Identities=29% Similarity=0.592 Sum_probs=21.9
Q ss_pred eee----c-CCCccCCchHHHHHHHHhcc
Q 014041 167 YRC----D-CGTLFSRKDSFITHRAFCDA 190 (432)
Q Consensus 167 ~~C----~-C~~~F~~~~~L~~H~~~h~~ 190 (432)
|.| . |++.+.+...+.+|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 7 99999999999999998764
No 77
>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=83.31 E-value=0.52 Score=30.24 Aligned_cols=26 Identities=19% Similarity=0.332 Sum_probs=18.1
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
.|+|.+||-.+.... .++.|++||..
T Consensus 1 ~~~C~~CGy~y~~~~------------~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDGEE------------APWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECCCc------------CCCcCcCCCCc
Confidence 378888987644322 67899999863
No 78
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=82.01 E-value=0.85 Score=43.06 Aligned_cols=44 Identities=25% Similarity=0.636 Sum_probs=18.4
Q ss_pred ccccccccccCChHHhhhhhcccCCcceeec-CCCccCCchHHHHHH
Q 014041 140 WKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITHR 185 (432)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~~~~k~~~C~-C~~~F~~~~~L~~H~ 185 (432)
|.|++||..... ..+.+|+..+...-|.|- |++.|-+ ..+..|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhh
Confidence 444444444332 233444444222444453 5555544 3334443
No 79
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=81.79 E-value=0.62 Score=43.64 Aligned_cols=42 Identities=21% Similarity=0.545 Sum_probs=27.2
Q ss_pred CCcccccccccccCChHHhhhhhcc-c----------CCcc-----eeec-CCCccCCc
Q 014041 137 EKKWKCEKCSKKYAVQSDWKAHSKI-C----------GTRE-----YRCD-CGTLFSRK 178 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~-~----------~~k~-----~~C~-C~~~F~~~ 178 (432)
+|.++|++|++.|.++.-+....|. . +..| ..|+ ||..|...
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 4567788888888777655555543 1 1222 5799 99887655
No 80
>KOG3982 consensus Runt and related transcription factors [Transcription]
Probab=81.43 E-value=0.99 Score=44.73 Aligned_cols=9 Identities=44% Similarity=0.770 Sum_probs=4.2
Q ss_pred HHHHHhhcc
Q 014041 412 QELAKFMNL 420 (432)
Q Consensus 412 ~~~~~~~~~ 420 (432)
...|||.-+
T Consensus 176 nQVAkFNDL 184 (475)
T KOG3982|consen 176 NQVAKFNDL 184 (475)
T ss_pred hhhhhhccc
Confidence 344555543
No 81
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=80.94 E-value=2.3 Score=41.34 Aligned_cols=55 Identities=22% Similarity=0.383 Sum_probs=40.7
Q ss_pred CCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcC
Q 014041 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 31 ~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
.+.|.-.|-+|..+|+...+-..-. .+...+|.|+.|...|-..-....|...|.
T Consensus 358 ~~~ks~~Cf~CQ~~fp~~~~~~~~~--~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 358 TNPKSTHCFVCQGPFPKPPVSPFDE--STSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred CCCCCccceeccCCCCCCCCCcccc--cccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 4556777999999998744322222 233457999999999999999999988775
No 82
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=80.88 E-value=0.87 Score=32.69 Aligned_cols=32 Identities=16% Similarity=0.291 Sum_probs=26.4
Q ss_pred cccCCCCceecccccccccChHHHHHHHHhcC
Q 014041 56 KSLMATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 56 ~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
.+-.+|.-+.|+-||+.|.....+.+|+..-+
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 34567888999999999999999999965433
No 83
>KOG1883 consensus Cofactor required for Sp1 transcriptional activation, subunit 3 [Transcription]
Probab=80.60 E-value=1.1 Score=50.36 Aligned_cols=32 Identities=22% Similarity=0.232 Sum_probs=18.3
Q ss_pred HHHHHHhhhhccccHHHHHHHHHHhcCCCCCC
Q 014041 280 QQQQQQQQGLAHMSATALLQKAAQMGSTRSNA 311 (432)
Q Consensus 280 QQQQQQQQqqq~~s~~~l~q~~~q~~s~~s~s 311 (432)
+|+|++||++.+..+++++++.-+++...+.+
T Consensus 1435 ~q~q~~Qqq~~~~~qqqlqhq~~n~~~vQt~s 1466 (1517)
T KOG1883|consen 1435 SQHQTIQQQSNHPTQQQLQHQIPNMSMVQTMS 1466 (1517)
T ss_pred hHHHHHHHHhcchHHHHHHHhccccceeeecC
Confidence 33333444444555566666777777766665
No 84
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.85 E-value=1.2 Score=36.49 Aligned_cols=36 Identities=14% Similarity=0.138 Sum_probs=27.9
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHH
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~ 80 (432)
..|++|+.||+.|..- ...|..|+.|||+|. .+.|.
T Consensus 7 GtKridPetg~KFYDL-----------NrdPiVsPytG~s~P-~s~fe 42 (129)
T COG4530 7 GTKRIDPETGKKFYDL-----------NRDPIVSPYTGKSYP-RSYFE 42 (129)
T ss_pred cccccCccccchhhcc-----------CCCccccCcccccch-HHHHH
Confidence 3589999999999873 357899999999994 33343
No 85
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.40 E-value=3.9 Score=34.07 Aligned_cols=79 Identities=18% Similarity=0.233 Sum_probs=50.7
Q ss_pred CCCCCCCCCcCcCCCCC-------CCCC--CC---CCCCCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 7 GLSVPSTLKGFVQEPNS-------NPNP--NP---SSNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 7 ~~~~~~~~~~~~~~~~~-------~~~~--~~---~~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
+..||.|+-..+..+.+ -|-+ .+ ....+...|-.|.+.|+....... .......+|+|+.|...|-
T Consensus 15 P~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC 92 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFC 92 (112)
T ss_pred CCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCccc
Confidence 56788887665544322 1111 11 112234569999999987532211 1134456899999999999
Q ss_pred ChHHHHHHHHhcC
Q 014041 75 RDQNLQLHRRGHN 87 (432)
Q Consensus 75 ~~~~L~~H~r~H~ 87 (432)
..-....|...|+
T Consensus 93 ~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 93 VDCDVFVHESLHC 105 (112)
T ss_pred cccchhhhhhccC
Confidence 9999999988886
No 86
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.36 E-value=0.76 Score=43.03 Aligned_cols=44 Identities=14% Similarity=0.114 Sum_probs=30.7
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccc---c-------CCCCc-----eecccccccccCh
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKS---L-------MATNR-----FLCEICNKGFQRD 76 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~---h-------~~~k~-----f~C~~Cgk~F~~~ 76 (432)
.++..|++|++.|....+.....+. . .+..| ..|+.||-+|...
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 3678899999999888776666543 1 12223 4799999988755
No 87
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=79.30 E-value=2 Score=46.43 Aligned_cols=26 Identities=27% Similarity=0.500 Sum_probs=24.3
Q ss_pred CceecccccccccChHHHHHHHHhcC
Q 014041 62 NRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
.-|.|.+|+|+|.....+..||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35999999999999999999999997
No 88
>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=77.02 E-value=1.6 Score=26.51 Aligned_cols=25 Identities=20% Similarity=0.458 Sum_probs=15.6
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
++|+.|++.-+. .--.|+.||..|.
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 357777775432 1246888888774
No 89
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=76.89 E-value=0.79 Score=32.89 Aligned_cols=24 Identities=17% Similarity=0.505 Sum_probs=10.1
Q ss_pred CcccccccccccCChHHhhhhhcc
Q 014041 138 KKWKCEKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 138 kp~~C~~C~k~F~~~~~L~~H~~~ 161 (432)
--++|+.|++.|....++.+|...
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhhH
Confidence 334444444444444444444433
No 90
>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=75.79 E-value=2.2 Score=29.01 Aligned_cols=26 Identities=23% Similarity=0.470 Sum_probs=17.3
Q ss_pred CCCceecccccccccCh----HHHHHHHHh
Q 014041 60 ATNRFLCEICNKGFQRD----QNLQLHRRG 85 (432)
Q Consensus 60 ~~k~f~C~~Cgk~F~~~----~~L~~H~r~ 85 (432)
+....+|.+|++.|... .+|.+|++.
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 45668999999999885 789999843
No 91
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=75.46 E-value=1.6 Score=41.20 Aligned_cols=50 Identities=14% Similarity=0.402 Sum_probs=30.4
Q ss_pred eecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcC
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHG 136 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~g 136 (432)
|.|.+||...+-. .|.+|+-..+ + ..|.|-.| ++.|.. ..++.|...-+.
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCr-------------n-~~fSCIDC-------~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCR-------------N-AYFSCIDC-------GKTFER-VSYKNHTKCITE 53 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhcc-------------C-CeeEEeec-------cccccc-chhhhhhhhcch
Confidence 6777777766544 3566765543 2 45666666 777766 556666655443
No 92
>PHA00626 hypothetical protein
Probab=74.53 E-value=2 Score=30.93 Aligned_cols=17 Identities=18% Similarity=0.552 Sum_probs=12.8
Q ss_pred CCceecccccccccChH
Q 014041 61 TNRFLCEICNKGFQRDQ 77 (432)
Q Consensus 61 ~k~f~C~~Cgk~F~~~~ 77 (432)
..+|+|+.||..|....
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 35699999999886543
No 93
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=74.30 E-value=0.7 Score=45.52 Aligned_cols=54 Identities=9% Similarity=0.009 Sum_probs=36.7
Q ss_pred CCCCcCCCCCCC--CCCChhhhhcCcc-----ccCCCCceecccccccccChHHHHHH-HHhc
Q 014041 32 NQLKRKRNLPGT--PDPDAEVIALSPK-----SLMATNRFLCEICNKGFQRDQNLQLH-RRGH 86 (432)
Q Consensus 32 ~~~k~~c~~cg~--~~~~~~~l~~h~~-----~h~~~k~f~C~~Cgk~F~~~~~L~~H-~r~H 86 (432)
+|++..|.+.+. .+........|.+ --+-.++|+|. |+++++++.-|..| +..|
T Consensus 175 EE~~~S~~vp~~~~~~~~~Ns~~~~S~~~~~T~~t~~~p~k~~-~~~~~~T~~~l~~HS~N~~ 236 (442)
T KOG4124|consen 175 EEYRVSVVVPAAAAAAAAANSSDMSSDEASSTAETTGTPKKMP-ESLVMDTSSPLSDHSMNID 236 (442)
T ss_pred ccccccccCchhhhhhhccccccccccccccccccccCCccCc-ccccccccchhhhccccCC
Confidence 677888887663 3444444444433 34456789997 89999999999888 5544
No 94
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.04 E-value=1.7 Score=38.10 Aligned_cols=40 Identities=20% Similarity=0.185 Sum_probs=29.9
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
+..-|.|+.|+..|...+.+..-. . ...|.|+.||.....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d---~-~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLD---M-DGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcC---C-CCcEECCCCCCEEEE
Confidence 456799999999999877766521 1 344999999987743
No 95
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.73 E-value=2.2 Score=47.08 Aligned_cols=14 Identities=14% Similarity=0.477 Sum_probs=10.5
Q ss_pred cCCCcccccccccc
Q 014041 135 HGEKKWKCEKCSKK 148 (432)
Q Consensus 135 ~gekp~~C~~C~k~ 148 (432)
....|..|+.||-.
T Consensus 471 ~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 471 QEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCC
Confidence 35678889888865
No 96
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=72.10 E-value=2 Score=49.64 Aligned_cols=10 Identities=10% Similarity=0.145 Sum_probs=4.3
Q ss_pred eccccccccc
Q 014041 65 LCEICNKGFQ 74 (432)
Q Consensus 65 ~C~~Cgk~F~ 74 (432)
.|..-++...
T Consensus 1841 ~~~r~~p~~~ 1850 (2220)
T KOG3598|consen 1841 KCKRASPKDD 1850 (2220)
T ss_pred CcccCCCCCC
Confidence 4444444333
No 97
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=71.89 E-value=2.7 Score=34.74 Aligned_cols=44 Identities=18% Similarity=0.238 Sum_probs=33.7
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
...+++|+.||..-.....+......-....-|.|+-|+..|..
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 45699999999977666666665555555567999999999864
No 98
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=71.75 E-value=4.1 Score=24.35 Aligned_cols=14 Identities=21% Similarity=0.358 Sum_probs=9.3
Q ss_pred CCccCCHHHHHHHHh
Q 014041 118 SRALGDLTGIKKHFS 132 (432)
Q Consensus 118 ~k~f~~~~~L~~H~~ 132 (432)
++.| ..+.|.+|++
T Consensus 9 gR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 9 GRKF-NPDRLEKHEK 22 (25)
T ss_pred CCEE-CHHHHHHHHH
Confidence 7777 5666777754
No 99
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=71.46 E-value=1.6 Score=33.45 Aligned_cols=42 Identities=10% Similarity=0.108 Sum_probs=28.4
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCCceecc--cccccccChHHH
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCE--ICNKGFQRDQNL 79 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~--~Cgk~F~~~~~L 79 (432)
.+|+.||....-..+-..+.. ..++.|.|. .||..|.....+
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 478999887644333333332 556779998 999999876654
No 100
>PF11179 DUF2967: Protein of unknown function (DUF2967); InterPro: IPR021349 This family of proteins with unknown function appears to be restricted to Drosophila.
Probab=71.18 E-value=2.6 Score=38.07 Aligned_cols=8 Identities=50% Similarity=0.899 Sum_probs=3.6
Q ss_pred hhcccccc
Q 014041 391 ERRLTRDF 398 (432)
Q Consensus 391 ~~~~~~~~ 398 (432)
|..|.-|+
T Consensus 249 erk~~adi 256 (258)
T PF11179_consen 249 ERKLSADI 256 (258)
T ss_pred hhhccccc
Confidence 34444444
No 101
>PRK04023 DNA polymerase II large subunit; Validated
Probab=70.46 E-value=4.2 Score=45.83 Aligned_cols=9 Identities=44% Similarity=1.114 Sum_probs=4.6
Q ss_pred ccccccccc
Q 014041 140 WKCEKCSKK 148 (432)
Q Consensus 140 ~~C~~C~k~ 148 (432)
+.|+.|+..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 445555543
No 102
>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=70.38 E-value=1 Score=42.02 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=15.1
Q ss_pred CCcccccccccccCChHHhhhhhcc-cCC
Q 014041 137 EKKWKCEKCSKKYAVQSDWKAHSKI-CGT 164 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~-~~~ 164 (432)
+..|.|..|+|.|+-...++.|+.. |.+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 3456666666666666666666665 543
No 103
>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=70.21 E-value=1.6 Score=38.83 Aligned_cols=36 Identities=17% Similarity=0.076 Sum_probs=29.4
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
+..=|.|+.|+..|+..+++.. -|.|+.||......
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~~---------~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAMEL---------NFTCPRCGAMLDYL 141 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHHc---------CCcCCCCCCEeeec
Confidence 4567999999999999998863 49999999876543
No 104
>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=70.02 E-value=1.9 Score=27.85 Aligned_cols=25 Identities=16% Similarity=0.161 Sum_probs=17.1
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk 71 (432)
.|+|.+||-.+... +.|..|++||.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 57889998753321 24678999986
No 105
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=69.91 E-value=2.1 Score=37.84 Aligned_cols=48 Identities=17% Similarity=0.128 Sum_probs=29.7
Q ss_pred CCCCCCCCcCcCCCCCCCCCCCCCCCCCcCCCCCCCCCCChhhhhcCc
Q 014041 8 LSVPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSP 55 (432)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~c~~cg~~~~~~~~l~~h~ 55 (432)
+.||.|+..+..-.....-+.-..-.+.|.|+.||+.|...+.+..-+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 579999875532222221111111234599999999999988776664
No 106
>KOG4407 consensus Predicted Rho GTPase-activating protein [General function prediction only]
Probab=69.44 E-value=2.8 Score=48.15 Aligned_cols=15 Identities=27% Similarity=-0.015 Sum_probs=6.8
Q ss_pred cccchhhhHhhhhcC
Q 014041 347 ADNDQNLNELIMNSF 361 (432)
Q Consensus 347 ~~~~~~~~~~~~~~~ 361 (432)
|.+..++--++..++
T Consensus 449 ~~q~le~~~L~s~~p 463 (1973)
T KOG4407|consen 449 MLQLLELHLLISTSP 463 (1973)
T ss_pred HHHHHhhhhhhccCc
Confidence 334444445554443
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=68.87 E-value=1.8 Score=39.31 Aligned_cols=37 Identities=14% Similarity=0.054 Sum_probs=29.3
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChH
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQ 77 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~ 77 (432)
...=|.|+.|+..|+..+++. .-|.|+.||.......
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEEYD 150 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCeecc
Confidence 345799999999999988874 2599999998776543
No 108
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.48 E-value=5 Score=29.34 Aligned_cols=33 Identities=21% Similarity=0.231 Sum_probs=19.2
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccc
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk 71 (432)
.++.|+.||+. .|.+=.+--....+|+|+.||-
T Consensus 24 ~~F~CPnCG~~-----~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEV-----IIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCe-----eEeechhHHhcCCceECCCCCC
Confidence 46777777763 1222222233346799999984
No 109
>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=67.75 E-value=3.1 Score=34.55 Aligned_cols=16 Identities=19% Similarity=0.632 Sum_probs=9.0
Q ss_pred CCcccccccccccCCh
Q 014041 137 EKKWKCEKCSKKYAVQ 152 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~ 152 (432)
..|..|++||..|...
T Consensus 24 k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 24 KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCccCCCCCCccCcc
Confidence 3555666666655544
No 110
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=66.50 E-value=2.9 Score=27.41 Aligned_cols=34 Identities=9% Similarity=-0.034 Sum_probs=17.9
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
.+|+.|+..|.-.+.... .....+.|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEEE
Confidence 457777766554332211 1122467777777664
No 111
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=65.22 E-value=4.1 Score=40.22 Aligned_cols=14 Identities=7% Similarity=-0.023 Sum_probs=10.4
Q ss_pred CCcceeCCCCCCCC
Q 014041 101 RKKVYICPEKSCVH 114 (432)
Q Consensus 101 ~~k~y~C~~C~c~~ 114 (432)
|.|-..|..|++.|
T Consensus 209 G~RyL~CslC~teW 222 (309)
T PRK03564 209 GLRYLHCNLCESEW 222 (309)
T ss_pred CceEEEcCCCCCcc
Confidence 67888888886543
No 112
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=64.64 E-value=4.5 Score=28.39 Aligned_cols=25 Identities=40% Similarity=0.713 Sum_probs=19.5
Q ss_pred ceecccccccccCh-----HHHHHHHH-hcC
Q 014041 63 RFLCEICNKGFQRD-----QNLQLHRR-GHN 87 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~-----~~L~~H~r-~H~ 87 (432)
.-.|..|++.+... .+|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 46788898888776 58999988 553
No 113
>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=64.40 E-value=21 Score=29.34 Aligned_cols=24 Identities=21% Similarity=0.502 Sum_probs=17.8
Q ss_pred CceecccccccccChHHHHHHHHhc
Q 014041 62 NRFLCEICNKGFQRDQNLQLHRRGH 86 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~~~L~~H~r~H 86 (432)
+-..|..|+....- ..+..|++..
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~ 33 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKR 33 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHh
Confidence 45688888887766 7788887743
No 114
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=64.37 E-value=2.7 Score=27.55 Aligned_cols=12 Identities=17% Similarity=-0.131 Sum_probs=5.8
Q ss_pred CCcCCCCCCCCC
Q 014041 34 LKRKRNLPGTPD 45 (432)
Q Consensus 34 ~k~~c~~cg~~~ 45 (432)
++.+|+.||..|
T Consensus 24 ~~v~C~~C~~~f 35 (36)
T PF13717_consen 24 RKVRCSKCGHVF 35 (36)
T ss_pred cEEECCCCCCEe
Confidence 345555555443
No 115
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=64.10 E-value=5.4 Score=32.57 Aligned_cols=41 Identities=10% Similarity=0.114 Sum_probs=24.7
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
..+|+.||........+......-....-|.|..|+..++.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 67899998754433333322222223345999999987753
No 116
>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=63.96 E-value=4.3 Score=40.05 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=19.6
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccc
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKK 148 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~ 148 (432)
|.|-..|..|.+.|+ -+.-+|..|+..
T Consensus 207 G~RyL~CslC~teW~---------------------~~R~~C~~Cg~~ 233 (305)
T TIGR01562 207 GLRYLSCSLCATEWH---------------------YVRVKCSHCEES 233 (305)
T ss_pred CceEEEcCCCCCccc---------------------ccCccCCCCCCC
Confidence 778899999966442 123679999974
No 117
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=62.43 E-value=3.3 Score=29.16 Aligned_cols=30 Identities=17% Similarity=0.135 Sum_probs=20.6
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
...|+|..||+.|.. ........|+.||-.
T Consensus 4 ~~~Y~C~~Cg~~~~~----------~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVEL----------DQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeeh----------hhccCceeCCCCCcE
Confidence 347899999998721 223456889999853
No 118
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=61.83 E-value=11 Score=37.91 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=18.9
Q ss_pred cccccccc---cccCChHHhhhhhcc
Q 014041 139 KWKCEKCS---KKYAVQSDWKAHSKI 161 (432)
Q Consensus 139 p~~C~~C~---k~F~~~~~L~~H~~~ 161 (432)
-|.|-.|. +.|.+....+.||..
T Consensus 217 ~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 217 GFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CceEEEeccccCcccccHHHHHHHhh
Confidence 37788888 888888888888886
No 119
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=61.62 E-value=5.2 Score=35.01 Aligned_cols=48 Identities=17% Similarity=0.092 Sum_probs=28.6
Q ss_pred CCCCCCCCcCcCCCCCCCCCCCCCCCCCcCCCCCCCCCCChhhhhcCc
Q 014041 8 LSVPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSP 55 (432)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~c~~cg~~~~~~~~l~~h~ 55 (432)
+.||.|.-.-.......+-.--..-.+++.|+.||+.|++.+.+..-+
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 468888654333322222222223356788999999998887776663
No 120
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.44 E-value=5.3 Score=31.56 Aligned_cols=33 Identities=18% Similarity=0.299 Sum_probs=22.6
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
..+|.|+.|++. .+.+.- ..-..|..||..|.-
T Consensus 33 ~~~~~Cp~C~~~--------~VkR~a--~GIW~C~kCg~~fAG 65 (89)
T COG1997 33 RAKHVCPFCGRT--------TVKRIA--TGIWKCRKCGAKFAG 65 (89)
T ss_pred hcCCcCCCCCCc--------ceeeec--cCeEEcCCCCCeecc
Confidence 357899999985 222222 334899999999864
No 121
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.40 E-value=4.4 Score=36.26 Aligned_cols=24 Identities=17% Similarity=0.212 Sum_probs=19.9
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk 71 (432)
-|+|++||-. +-++-|-+|++||.
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 7999999984 44578899999993
No 122
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.31 E-value=4.4 Score=27.85 Aligned_cols=27 Identities=11% Similarity=0.089 Sum_probs=19.2
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
.|+|..||..|.-. ...+..|+.||-.
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCce
Confidence 48899999876532 3456889999854
No 123
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=60.98 E-value=9.4 Score=37.27 Aligned_cols=48 Identities=15% Similarity=0.372 Sum_probs=32.3
Q ss_pred cccccccccCChHHhhhhhcccCCcceeec-CCCccCCchHHHHHHHHhc
Q 014041 141 KCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITHRAFCD 189 (432)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~~~~k~~~C~-C~~~F~~~~~L~~H~~~h~ 189 (432)
.|-.|.-.|.....-..-. .+....|.|+ |...|-..-..-.|-..|.
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~-~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDE-STSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceeccCCCCCCCCCcccc-cccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 3888888777553221111 1445679999 9999988888778877663
No 124
>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=60.89 E-value=3.5 Score=35.98 Aligned_cols=22 Identities=14% Similarity=-0.143 Sum_probs=15.3
Q ss_pred CCCcCCCCCCCCCCChhhhhcC
Q 014041 33 QLKRKRNLPGTPDPDAEVIALS 54 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h 54 (432)
.+++.|..||+.|++.|.+..-
T Consensus 26 RRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 26 RRRRECLECHERFTTFERAELL 47 (147)
T ss_pred eecccCCccCCccceeeecccc
Confidence 3567777888777777666554
No 125
>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=60.86 E-value=1.4 Score=43.22 Aligned_cols=52 Identities=17% Similarity=0.291 Sum_probs=23.6
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhh-hcc-cCCcceeec-CCCcc
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAH-SKI-CGTREYRCD-CGTLF 175 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H-~~~-~~~k~~~C~-C~~~F 175 (432)
|.|...|..|+..|+ -+..+|..||..-... |... ... -+.+.+.|+ |+.-+
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 GKRYLHCSLCGTEWR---------------------FVRIKCPYCGNTDHEK--LEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp -EEEEEETTT--EEE-----------------------TTS-TTT---SS-E--EE--------SEEEEEETTTTEEE
T ss_pred ccEEEEcCCCCCeee---------------------ecCCCCcCCCCCCCcc--eeeEecCCCCcEEEEECCcccchH
Confidence 568889999954331 1235799998763322 2111 111 355778898 97433
No 126
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.85 E-value=2.9 Score=28.87 Aligned_cols=31 Identities=16% Similarity=0.100 Sum_probs=19.0
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
..|+|+.||..+...+. ...+.|+.||-.+.
T Consensus 2 ~~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEY----------GTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCC----------CCceECCCCCCeEE
Confidence 35788888876544211 11578888886554
No 127
>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=59.71 E-value=5.9 Score=34.59 Aligned_cols=46 Identities=13% Similarity=0.091 Sum_probs=27.8
Q ss_pred CCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHH
Q 014041 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLH 82 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H 82 (432)
+|+.||......-.-....-.-.-.++=+|..||+.|.+......-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELL 47 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccc
Confidence 6888887655421111111111123557999999999998876544
No 128
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=59.38 E-value=6.2 Score=35.32 Aligned_cols=25 Identities=32% Similarity=0.694 Sum_probs=19.8
Q ss_pred cceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCccccccccc
Q 014041 103 KVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSK 147 (432)
Q Consensus 103 k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k 147 (432)
+.|+|++| |.. |.|+-|.+|++|+.
T Consensus 133 ~~~vC~vC-------Gy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVC-------GYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCC-------CCc-------------ccCCCCCcCCCCCC
Confidence 37999999 543 35788999999984
No 129
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=58.35 E-value=4.9 Score=35.15 Aligned_cols=44 Identities=16% Similarity=0.148 Sum_probs=27.7
Q ss_pred CCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHH
Q 014041 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~ 80 (432)
+|+.|+-..+..-.-....-...-.++=+|+.||+.|.+.....
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~E 45 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAE 45 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheee
Confidence 69999876654322222222222345679999999999887544
No 130
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=58.34 E-value=14 Score=36.46 Aligned_cols=34 Identities=12% Similarity=0.023 Sum_probs=24.2
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHH
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLH 82 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H 82 (432)
=|.|+.|+...= .-|.+|++|+-......+|.+-
T Consensus 276 Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 276 GYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred ceeCCcccCeee--------------cCCccCCccceeEecchHHHHH
Confidence 466777765322 2478899999999888888754
No 131
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=58.30 E-value=2.7 Score=27.89 Aligned_cols=12 Identities=8% Similarity=-0.133 Sum_probs=6.6
Q ss_pred CcCCCCCCCCCC
Q 014041 35 KRKRNLPGTPDP 46 (432)
Q Consensus 35 k~~c~~cg~~~~ 46 (432)
.|+|..||+.|.
T Consensus 5 ~y~C~~Cg~~fe 16 (41)
T smart00834 5 EYRCEDCGHTFE 16 (41)
T ss_pred EEEcCCCCCEEE
Confidence 355666666544
No 132
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=58.14 E-value=4.3 Score=27.25 Aligned_cols=37 Identities=16% Similarity=0.321 Sum_probs=20.1
Q ss_pred cCCCCCCCCCCChhhhhcCccccCC--CCceeccccccccc
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMA--TNRFLCEICNKGFQ 74 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~--~k~f~C~~Cgk~F~ 74 (432)
++|+.||..... .+....++-.+ ..-|+|..||..|+
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 367888753322 22333333221 23489999998775
No 133
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=57.80 E-value=3 Score=29.41 Aligned_cols=12 Identities=8% Similarity=-0.095 Sum_probs=6.4
Q ss_pred CcCCCCCCCCCC
Q 014041 35 KRKRNLPGTPDP 46 (432)
Q Consensus 35 k~~c~~cg~~~~ 46 (432)
.|+|..||..|.
T Consensus 5 ey~C~~Cg~~fe 16 (52)
T TIGR02605 5 EYRCTACGHRFE 16 (52)
T ss_pred EEEeCCCCCEeE
Confidence 355555555544
No 134
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=57.72 E-value=5.7 Score=26.13 Aligned_cols=11 Identities=27% Similarity=0.779 Sum_probs=5.6
Q ss_pred ceecccccccc
Q 014041 63 RFLCEICNKGF 73 (432)
Q Consensus 63 ~f~C~~Cgk~F 73 (432)
..+|..|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34555555544
No 135
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=57.49 E-value=5.6 Score=34.82 Aligned_cols=40 Identities=15% Similarity=0.382 Sum_probs=23.5
Q ss_pred cCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccC
Q 014041 100 VRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYA 150 (432)
Q Consensus 100 ~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~ 150 (432)
.....|.|+.| +..|.....+.. .+ .+..|.|+.||....
T Consensus 95 ~~~~~Y~Cp~C-------~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNC-------QSKYTFLEANQL---LD-MDGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCC-------CCEeeHHHHHHh---cC-CCCcEECCCCCCEEE
Confidence 45567888877 777765443332 01 133388888877643
No 136
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=56.85 E-value=5.6 Score=36.11 Aligned_cols=35 Identities=11% Similarity=0.399 Sum_probs=23.5
Q ss_pred cCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccC
Q 014041 100 VRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYA 150 (432)
Q Consensus 100 ~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~ 150 (432)
.....|.|+.| ++.|.....+. .-|.|+.||....
T Consensus 113 ~~~~~Y~Cp~C-------~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 113 ENNMFFFCPNC-------HIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred cCCCEEECCCC-------CcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 34567888887 77777766653 2488888877644
No 137
>PRK14873 primosome assembly protein PriA; Provisional
Probab=56.74 E-value=7.6 Score=42.68 Aligned_cols=11 Identities=27% Similarity=1.301 Sum_probs=8.3
Q ss_pred Ccccccccccc
Q 014041 138 KKWKCEKCSKK 148 (432)
Q Consensus 138 kp~~C~~C~k~ 148 (432)
.|+.|+.|+..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 47888888764
No 138
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=56.67 E-value=5.6 Score=31.43 Aligned_cols=13 Identities=54% Similarity=1.262 Sum_probs=8.1
Q ss_pred cccccccccccCC
Q 014041 139 KWKCEKCSKKYAV 151 (432)
Q Consensus 139 p~~C~~C~k~F~~ 151 (432)
-|.|..|+..|.-
T Consensus 53 IW~C~kCg~~fAG 65 (89)
T COG1997 53 IWKCRKCGAKFAG 65 (89)
T ss_pred eEEcCCCCCeecc
Confidence 3666666666653
No 139
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=56.39 E-value=2.3 Score=41.97 Aligned_cols=21 Identities=5% Similarity=-0.113 Sum_probs=14.9
Q ss_pred CCCcCCCCCCCCCCChhhhhcC
Q 014041 33 QLKRKRNLPGTPDPDAEVIALS 54 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h 54 (432)
.++|+|. |++.+.++..|..|
T Consensus 211 ~~p~k~~-~~~~~~T~~~l~~H 231 (442)
T KOG4124|consen 211 GTPKKMP-ESLVMDTSSPLSDH 231 (442)
T ss_pred cCCccCc-ccccccccchhhhc
Confidence 4566664 67777777777777
No 140
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=54.60 E-value=13 Score=38.18 Aligned_cols=36 Identities=28% Similarity=0.601 Sum_probs=25.1
Q ss_pred CCcccccccccccCChHHhhhhhcccCCcceeec-CCCc
Q 014041 137 EKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTL 174 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~~~~k~~~C~-C~~~ 174 (432)
..-|+|+.|.++|.....+.- -.-.+..|.|. |+.-
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L--~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQL--LDNETGEFHCENCGGE 162 (436)
T ss_pred cccccCCccccchhhhHHHHh--hcccCceEEEecCCCc
Confidence 456999999999988777642 11345678898 8744
No 141
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=53.88 E-value=9.5 Score=32.84 Aligned_cols=24 Identities=33% Similarity=0.701 Sum_probs=16.8
Q ss_pred CCceecccccccccChHHHHHHHHhcC
Q 014041 61 TNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 61 ~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
+.-..|-+|||.|+. |++|++.|+
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHH 93 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT
T ss_pred cCeeEEccCCcccch---HHHHHHHcc
Confidence 345899999999974 699999997
No 142
>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=53.02 E-value=9.3 Score=32.49 Aligned_cols=16 Identities=0% Similarity=0.057 Sum_probs=8.7
Q ss_pred CCcccccccccccCCh
Q 014041 137 EKKWKCEKCSKKYAVQ 152 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~ 152 (432)
..|..|++||..|...
T Consensus 24 k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 24 RRPAVSPYTGEQFPPE 39 (129)
T ss_pred CCCccCCCcCCccCcc
Confidence 3555566666555443
No 143
>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=53.01 E-value=16 Score=32.46 Aligned_cols=36 Identities=17% Similarity=0.482 Sum_probs=27.9
Q ss_pred ccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccC
Q 014041 99 EVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYA 150 (432)
Q Consensus 99 ~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~ 150 (432)
.....-|.|+.| +..|+....+. .-|.|+.||....
T Consensus 104 e~~~~~Y~Cp~c-------~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNM-------CVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCC-------CcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 346678999998 88888888775 2499999998643
No 144
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.99 E-value=11 Score=33.91 Aligned_cols=13 Identities=23% Similarity=0.381 Sum_probs=9.5
Q ss_pred cCCcceeCCCCCC
Q 014041 100 VRKKVYICPEKSC 112 (432)
Q Consensus 100 ~~~k~y~C~~C~c 112 (432)
..+..|+|++|.+
T Consensus 127 ~~~~~~~CPiCl~ 139 (187)
T KOG0320|consen 127 RKEGTYKCPICLD 139 (187)
T ss_pred ccccccCCCceec
Confidence 3455699999954
No 145
>PF14353 CpXC: CpXC protein
Probab=52.82 E-value=3.2 Score=35.35 Aligned_cols=25 Identities=24% Similarity=0.486 Sum_probs=16.9
Q ss_pred CceecccccccccChHHHHHHHHhc
Q 014041 62 NRFLCEICNKGFQRDQNLQLHRRGH 86 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~~~L~~H~r~H 86 (432)
..|.|+.||+.|.-...|.-|-..+
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCCC
Confidence 3588888888887666666554443
No 146
>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=52.49 E-value=9.9 Score=40.38 Aligned_cols=49 Identities=14% Similarity=0.285 Sum_probs=29.2
Q ss_pred eecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCccccc
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCE 143 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~ 143 (432)
..|..||..+.-... ...+..|. ......|.+| |. ....|+.|+
T Consensus 214 ~~C~~Cg~~~~C~~C-~~~l~~h~-------------~~~~l~Ch~C-------g~---------------~~~~~~~Cp 257 (505)
T TIGR00595 214 LLCRSCGYILCCPNC-DVSLTYHK-------------KEGKLRCHYC-------GY---------------QEPIPKTCP 257 (505)
T ss_pred eEhhhCcCccCCCCC-CCceEEec-------------CCCeEEcCCC-------cC---------------cCCCCCCCC
Confidence 367777776654331 12233333 4556788888 43 245678899
Q ss_pred ccccc
Q 014041 144 KCSKK 148 (432)
Q Consensus 144 ~C~k~ 148 (432)
.|+..
T Consensus 258 ~C~s~ 262 (505)
T TIGR00595 258 QCGSE 262 (505)
T ss_pred CCCCC
Confidence 99764
No 147
>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=52.47 E-value=10 Score=22.91 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=15.3
Q ss_pred eecccccccccChHHHHHHHH
Q 014041 64 FLCEICNKGFQRDQNLQLHRR 84 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r 84 (432)
..|++|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4699999998 5567777865
No 148
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.37 E-value=7 Score=33.55 Aligned_cols=37 Identities=14% Similarity=0.187 Sum_probs=19.9
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
+..|+.|+-.. .. .+...-.+..+|+|..|++.|...
T Consensus 30 ~~~cP~C~s~~--~~---k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 30 KVNCPRCKSSN--VV---KIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cCcCCCCCccc--ee---eECCccccccccccCCcCcceeee
Confidence 45677776543 11 122222235567777777777644
No 149
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=51.65 E-value=8.8 Score=32.88 Aligned_cols=21 Identities=29% Similarity=0.460 Sum_probs=19.3
Q ss_pred eecccccccccChHHHHHHHHhcC
Q 014041 64 FLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 64 f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
..|-+|||.|+ .|++|+++|.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEEeccCcchH---HHHHHHhccc
Confidence 78999999995 7999999998
No 150
>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=51.47 E-value=8.9 Score=35.86 Aligned_cols=28 Identities=18% Similarity=0.472 Sum_probs=21.9
Q ss_pred CCCceecccccccccChHHHHHHHHhcC
Q 014041 60 ATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 60 ~~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
++..|.|.+|+|.|+-..-...|+..-|
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 4556999999999999999999987766
No 151
>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=50.98 E-value=5.3 Score=27.03 Aligned_cols=30 Identities=13% Similarity=0.131 Sum_probs=15.4
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk 71 (432)
.|+|..||..|.....+ .. ...-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 46667776655432211 11 34456777765
No 152
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=50.57 E-value=5.9 Score=43.16 Aligned_cols=50 Identities=12% Similarity=0.304 Sum_probs=25.0
Q ss_pred ceeCCCCCCCCC-----CCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHHhhhh
Q 014041 104 VYICPEKSCVHH-----DPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAH 158 (432)
Q Consensus 104 ~y~C~~C~c~~~-----~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H 158 (432)
-.+|+.|.-.|. .|+-.|+.-. ++.-.+-|.-+||.|+..|..-+.+..|
T Consensus 643 ~LkCs~Cn~R~Kd~vI~kC~H~FC~~C-----vq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAVITKCGHVFCEEC-----VQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred ceeCCCccCchhhHHHHhcchHHHHHH-----HHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 467998843332 2333333222 1112223445677777777666555554
No 153
>PRK05978 hypothetical protein; Provisional
Probab=50.02 E-value=10 Score=33.37 Aligned_cols=34 Identities=12% Similarity=0.214 Sum_probs=24.7
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
-+-+|+.||+.---...|+.+ -.|+.||..|...
T Consensus 32 l~grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGEGKLFRAFLKPV---------DHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCCCcccccccccC---------CCccccCCccccC
Confidence 478899999865555555544 4899999988643
No 154
>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=49.70 E-value=3 Score=27.83 Aligned_cols=12 Identities=17% Similarity=0.722 Sum_probs=9.5
Q ss_pred ceeccccccccc
Q 014041 63 RFLCEICNKGFQ 74 (432)
Q Consensus 63 ~f~C~~Cgk~F~ 74 (432)
-|.|..||+.|+
T Consensus 28 fy~C~~C~~~wr 39 (39)
T PF01096_consen 28 FYVCCNCGHRWR 39 (39)
T ss_dssp EEEESSSTEEEE
T ss_pred EEEeCCCCCeeC
Confidence 489999998763
No 155
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=49.59 E-value=10 Score=27.72 Aligned_cols=33 Identities=21% Similarity=0.158 Sum_probs=20.2
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccc
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk 71 (432)
.++.|+.||+. .+.+-.+.-.-..+|+|+.||-
T Consensus 26 v~F~CPnCGe~-----~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEV-----EIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCce-----eeehhhhHHHcCCceECCCcCc
Confidence 46778888853 2223333333456799999984
No 156
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=49.34 E-value=14 Score=36.45 Aligned_cols=16 Identities=13% Similarity=0.017 Sum_probs=8.5
Q ss_pred CCCcCCCCCCCCCCCh
Q 014041 33 QLKRKRNLPGTPDPDA 48 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~ 48 (432)
++..+|+.|..++...
T Consensus 78 ~~~~~CP~Cr~~~g~~ 93 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNI 93 (299)
T ss_pred hhcccCCccccccccH
Confidence 4455555555555533
No 157
>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=48.46 E-value=7.2 Score=24.53 Aligned_cols=25 Identities=20% Similarity=0.297 Sum_probs=12.7
Q ss_pred CCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
+|+.|+-.+.. .+...|.|+.|+..
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 68888887766 33456999999854
No 158
>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=48.32 E-value=14 Score=27.53 Aligned_cols=35 Identities=20% Similarity=0.285 Sum_probs=25.1
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHH
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQN 78 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~ 78 (432)
.-..|+.||..... ....+.|.|+.||..+.+..+
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 45779999986444 234566999999998776543
No 159
>PRK05580 primosome assembly protein PriA; Validated
Probab=48.12 E-value=12 Score=41.29 Aligned_cols=26 Identities=12% Similarity=0.268 Sum_probs=18.1
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccc
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKK 148 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~ 148 (432)
..+...|.+| |. ....|+.|+.|+..
T Consensus 405 ~~~~l~Ch~C-------g~---------------~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 405 FQRRLRCHHC-------GY---------------QEPIPKACPECGST 430 (679)
T ss_pred CCCeEECCCC-------cC---------------CCCCCCCCCCCcCC
Confidence 4456788888 54 34567889999765
No 160
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=47.49 E-value=10 Score=38.79 Aligned_cols=38 Identities=18% Similarity=0.148 Sum_probs=23.9
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccc
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGF 73 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F 73 (432)
..-|+|+.|.+.|..-+.+.+-. .....|.|..|+-..
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~---~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLD---NETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHhhc---ccCceEEEecCCCch
Confidence 34577888877777766665432 234557777776543
No 161
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=47.34 E-value=10 Score=22.14 Aligned_cols=11 Identities=18% Similarity=-0.124 Sum_probs=6.3
Q ss_pred CCCCCCCCCCC
Q 014041 37 KRNLPGTPDPD 47 (432)
Q Consensus 37 ~c~~cg~~~~~ 47 (432)
.|+.||....+
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 36677765433
No 162
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.28 E-value=7.8 Score=29.77 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=15.3
Q ss_pred cCCCCceecccccccccChHHHHHHHH
Q 014041 58 LMATNRFLCEICNKGFQRDQNLQLHRR 84 (432)
Q Consensus 58 h~~~k~f~C~~Cgk~F~~~~~L~~H~r 84 (432)
.+....|+|..||..| .+.+||+
T Consensus 7 lMPtY~Y~c~~cg~~~----dvvq~~~ 29 (82)
T COG2331 7 LMPTYSYECTECGNRF----DVVQAMT 29 (82)
T ss_pred cccceEEeecccchHH----HHHHhcc
Confidence 3445678888888877 3555554
No 163
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=47.20 E-value=16 Score=26.52 Aligned_cols=49 Identities=16% Similarity=0.337 Sum_probs=27.7
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCC
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKS 111 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~ 111 (432)
....++|++..+.|. .|++...||-.|.+.. +..++ . ..+...|++-|
T Consensus 8 ~~~~~~CPiT~~~~~---------------~PV~s~~C~H~fek~a-I~~~i---~-------------~~~~~~CPv~G 55 (57)
T PF11789_consen 8 GTISLKCPITLQPFE---------------DPVKSKKCGHTFEKEA-ILQYI---Q-------------RNGSKRCPVAG 55 (57)
T ss_dssp SB--SB-TTTSSB-S---------------SEEEESSS--EEEHHH-HHHHC---T-------------TTS-EE-SCCC
T ss_pred cEeccCCCCcCChhh---------------CCcCcCCCCCeecHHH-HHHHH---H-------------hcCCCCCCCCC
Confidence 456788888887644 4788889999997655 44444 2 45678899865
Q ss_pred C
Q 014041 112 C 112 (432)
Q Consensus 112 c 112 (432)
|
T Consensus 56 C 56 (57)
T PF11789_consen 56 C 56 (57)
T ss_dssp -
T ss_pred C
Confidence 5
No 164
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=46.28 E-value=20 Score=35.33 Aligned_cols=24 Identities=25% Similarity=0.697 Sum_probs=18.7
Q ss_pred cceeec-CCCccCCchHHHHHHHHh
Q 014041 165 REYRCD-CGTLFSRKDSFITHRAFC 188 (432)
Q Consensus 165 k~~~C~-C~~~F~~~~~L~~H~~~h 188 (432)
..|.|. |...|-..-+.-.|-..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 348898 999998887777787666
No 165
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=45.64 E-value=17 Score=26.13 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=20.9
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
...+|.+||+.|.. ++..-.|+.||..+-
T Consensus 4 ~~~~C~~Cg~~~~~------------~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 4 EGCKCPVCGKKFKD------------GDDIVVCPECGAPYH 32 (54)
T ss_pred cCccChhhCCcccC------------CCCEEECCCCCCccc
Confidence 46789999998754 234478999988764
No 166
>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=45.52 E-value=12 Score=26.55 Aligned_cols=7 Identities=29% Similarity=1.493 Sum_probs=4.0
Q ss_pred eeccccc
Q 014041 64 FLCEICN 70 (432)
Q Consensus 64 f~C~~Cg 70 (432)
|.|++|+
T Consensus 35 w~CP~C~ 41 (50)
T cd00730 35 WVCPVCG 41 (50)
T ss_pred CCCCCCC
Confidence 5555555
No 167
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=44.83 E-value=24 Score=33.56 Aligned_cols=76 Identities=18% Similarity=0.397 Sum_probs=44.2
Q ss_pred ChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCCcccccccccccCChHH
Q 014041 75 RDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSD 154 (432)
Q Consensus 75 ~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~F~~~~~ 154 (432)
+..+|..+-+.+... .....+-|.|..|+-.| . .+.-.-..--+|..|.+.|.--..
T Consensus 91 Te~Nlrm~d~a~~~~--------ip~~drqFaC~~Cd~~W-------w--------Rrvp~rKeVSRCr~C~~rYDPVP~ 147 (278)
T PF15135_consen 91 TEENLRMFDDAQENL--------IPSVDRQFACSSCDHMW-------W--------RRVPQRKEVSRCRKCRKRYDPVPC 147 (278)
T ss_pred hHHHHHHhhhhhhcc--------ccccceeeeccccchHH-------H--------hccCcccccccccccccccCCCcc
Confidence 345677776665411 11245789999993211 0 112222334679999888875431
Q ss_pred hhhhhcccCCcceeec-CCCccCC
Q 014041 155 WKAHSKICGTREYRCD-CGTLFSR 177 (432)
Q Consensus 155 L~~H~~~~~~k~~~C~-C~~~F~~ 177 (432)
-+.-|.-.|.|. |+..|+-
T Consensus 148 ----dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 148 ----DKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred ----ccccceeeeecccccccchh
Confidence 112566779998 9999864
No 168
>PF02166 Androgen_recep: Androgen receptor; InterPro: IPR001103 Steroid or nuclear hormone receptors (NRs) constitute an important super-family of transcription regulators that are involved in diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members include the steroid hormone receptors and receptors for thyroid hormone, retinoids and 1,25-dihydroxy-vitamin D3. The proteins function as dimeric molecules in the nucleus to regulate the transcription of target genes in a ligand-responsive manner [, ]. NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes and hormone resistance syndromes. Many do not yet have a defined ligand and are accordingly termed "orphan" receptors. More than 300 NRs have been described to date and a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members. The androgen receptor (AR) consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain (IPR001628 from INTERPRO) that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain (NTD) is unique to the androgen receptors and spans approximately the first 530 residues; the highly-conserved DNA-binding domain is smaller (around 65 residues) and occupies the central portion of the protein; and the hormone ligand binding domain (LBD) lies at the receptor C terminus. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity. The LBDs of steroid hormone receptors fold into 12 helices that form a ligand-binding pocket. When an agonist is bound, helix 12 folds over the pocket to enclose the ligand []. When an antagonist is unbound, helix 12 is positioned away from the pocket in a way that interferes with the binding of coactivators to a groove in the hormone-binding domain formed after ligand binding. In AR, ligand binding that induces folding of helix 12 to overlie the pocket discloses a groove that binds a region of the NTD. Coactivator molecules can also bind to this groove, but the predominant site for coactivator binding to AR is in the NTD. AR ligand resides in a pocket and primarily contacts helices 4, 5, and 10. The DNA-binding region includes eight cysteine residues that form two coordination complexes, each composed of four cysteines and a Zn2+ ion. These two zinc fingers form the structure that binds to the major groove of DNA. The second zinc finger stabilises the binding complex by hydrophobic interactions with the first finger and contributes to specificity of receptor DNA binding. It is also necessary for receptor dimerisation that occurs during DNA binding Defects in the androgen receptor cause testicular feminisation syndrome, androgen insensibility syndrome (AIS) [, ]. AIS may be complete (CAIS), where external genitalia are phenotypically female; partial (PAIS), where genitalia are substantively ambiguous; or mild (MAIS), where external genitalia are normal male, or nearly so. Defects in the receptor also cause X-linked spinal and bulbar muscular atrophy (also known as Kennedy's disease).; GO: 0003677 DNA binding, 0004882 androgen receptor activity, 0005496 steroid binding, 0006355 regulation of transcription, DNA-dependent, 0030521 androgen receptor signaling pathway, 0005634 nucleus; PDB: 1XOW_B 2Q7K_B 2Q7I_B.
Probab=44.66 E-value=7.3 Score=38.42 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=0.0
Q ss_pred ccccccccccc
Q 014041 316 GFGLMSTSFNS 326 (432)
Q Consensus 316 ~~~~~~~~~n~ 326 (432)
++.++-..|-.
T Consensus 137 tlSllGptfp~ 147 (423)
T PF02166_consen 137 TLSLLGPTFPG 147 (423)
T ss_dssp -----------
T ss_pred ccccccccccc
Confidence 34455444444
No 169
>PHA02998 RNA polymerase subunit; Provisional
Probab=44.58 E-value=12 Score=33.68 Aligned_cols=46 Identities=13% Similarity=0.165 Sum_probs=26.9
Q ss_pred CCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 31 ~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
+.....+|+.|+..-...-.+......-....-|+|..||+.|.-.
T Consensus 139 pkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 139 DEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence 3336789999996533322222222222223459999999988643
No 170
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=43.68 E-value=11 Score=28.05 Aligned_cols=32 Identities=13% Similarity=0.122 Sum_probs=13.9
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
......|.+|++.|.- -.+++-|..||+.|-.
T Consensus 6 d~~~~~C~~C~~~F~~------------~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 6 DSEASNCMICGKKFSL------------FRRRHHCRNCGRVVCS 37 (69)
T ss_dssp GGG-SB-TTT--B-BS------------SS-EEE-TTT--EEEC
T ss_pred CCCCCcCcCcCCcCCC------------ceeeEccCCCCCEECC
Confidence 3445677778877742 2455777777777753
No 171
>PF02166 Androgen_recep: Androgen receptor; InterPro: IPR001103 Steroid or nuclear hormone receptors (NRs) constitute an important super-family of transcription regulators that are involved in diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members include the steroid hormone receptors and receptors for thyroid hormone, retinoids and 1,25-dihydroxy-vitamin D3. The proteins function as dimeric molecules in the nucleus to regulate the transcription of target genes in a ligand-responsive manner [, ]. NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes and hormone resistance syndromes. Many do not yet have a defined ligand and are accordingly termed "orphan" receptors. More than 300 NRs have been described to date and a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members. The androgen receptor (AR) consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain (IPR001628 from INTERPRO) that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain (NTD) is unique to the androgen receptors and spans approximately the first 530 residues; the highly-conserved DNA-binding domain is smaller (around 65 residues) and occupies the central portion of the protein; and the hormone ligand binding domain (LBD) lies at the receptor C terminus. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity. The LBDs of steroid hormone receptors fold into 12 helices that form a ligand-binding pocket. When an agonist is bound, helix 12 folds over the pocket to enclose the ligand []. When an antagonist is unbound, helix 12 is positioned away from the pocket in a way that interferes with the binding of coactivators to a groove in the hormone-binding domain formed after ligand binding. In AR, ligand binding that induces folding of helix 12 to overlie the pocket discloses a groove that binds a region of the NTD. Coactivator molecules can also bind to this groove, but the predominant site for coactivator binding to AR is in the NTD. AR ligand resides in a pocket and primarily contacts helices 4, 5, and 10. The DNA-binding region includes eight cysteine residues that form two coordination complexes, each composed of four cysteines and a Zn2+ ion. These two zinc fingers form the structure that binds to the major groove of DNA. The second zinc finger stabilises the binding complex by hydrophobic interactions with the first finger and contributes to specificity of receptor DNA binding. It is also necessary for receptor dimerisation that occurs during DNA binding Defects in the androgen receptor cause testicular feminisation syndrome, androgen insensibility syndrome (AIS) [, ]. AIS may be complete (CAIS), where external genitalia are phenotypically female; partial (PAIS), where genitalia are substantively ambiguous; or mild (MAIS), where external genitalia are normal male, or nearly so. Defects in the receptor also cause X-linked spinal and bulbar muscular atrophy (also known as Kennedy's disease).; GO: 0003677 DNA binding, 0004882 androgen receptor activity, 0005496 steroid binding, 0006355 regulation of transcription, DNA-dependent, 0030521 androgen receptor signaling pathway, 0005634 nucleus; PDB: 1XOW_B 2Q7K_B 2Q7I_B.
Probab=43.03 E-value=8 Score=38.15 Aligned_cols=6 Identities=33% Similarity=0.523 Sum_probs=0.0
Q ss_pred hcCccc
Q 014041 339 FKQPNQ 344 (432)
Q Consensus 339 ~~~~~~ 344 (432)
.+++.+
T Consensus 168 lqqqqq 173 (423)
T PF02166_consen 168 LQQQQQ 173 (423)
T ss_dssp ------
T ss_pred cccccc
Confidence 333333
No 172
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=43.02 E-value=10 Score=24.54 Aligned_cols=28 Identities=21% Similarity=0.326 Sum_probs=13.8
Q ss_pred CCCCCCCCCChhhhhcCcccc--CCCCceecccccccc
Q 014041 38 RNLPGTPDPDAEVIALSPKSL--MATNRFLCEICNKGF 73 (432)
Q Consensus 38 c~~cg~~~~~~~~l~~h~~~h--~~~k~f~C~~Cgk~F 73 (432)
|+.||.+ +..++. .+..++.|+.||..+
T Consensus 3 C~~CG~~--------l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 3 CPQCGGP--------LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -TTT--B---------EEE--TT-SS-EEEETTTTEEE
T ss_pred cccccCh--------hhhhcCCCCCccceECCCCCCEE
Confidence 7788875 122333 345679999998754
No 173
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.11 E-value=17 Score=29.94 Aligned_cols=20 Identities=15% Similarity=0.197 Sum_probs=13.1
Q ss_pred CCCcccccccccccCChHHhh
Q 014041 136 GEKKWKCEKCSKKYAVQSDWK 156 (432)
Q Consensus 136 gekp~~C~~C~k~F~~~~~L~ 156 (432)
..+|..|++||+.|. .+.|.
T Consensus 23 NrdPiVsPytG~s~P-~s~fe 42 (129)
T COG4530 23 NRDPIVSPYTGKSYP-RSYFE 42 (129)
T ss_pred CCCccccCcccccch-HHHHH
Confidence 456788888888883 34443
No 174
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.76 E-value=11 Score=32.61 Aligned_cols=41 Identities=15% Similarity=0.083 Sum_probs=23.1
Q ss_pred CCCCcCCCCCCCCCCChh---hh------hcCccccCCCCceeccccccc
Q 014041 32 NQLKRKRNLPGTPDPDAE---VI------ALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~---~l------~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
.+..++|..||..|.... .| ..|.-.-.....+.|+.||..
T Consensus 67 ~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 67 EEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred cceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 346799999998776541 11 111111111344779999853
No 175
>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=39.85 E-value=9.5 Score=30.50 Aligned_cols=32 Identities=25% Similarity=0.415 Sum_probs=20.3
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
..+|.|+.||+.-- .+. ...-..|..|++.|.
T Consensus 33 ~~ky~Cp~Cgk~~v--------kR~--a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 33 HAKYTCPFCGKTSV--------KRV--ATGIWKCKKCGKKFA 64 (90)
T ss_dssp HS-BEESSSSSSEE--------EEE--ETTEEEETTTTEEEE
T ss_pred hCCCcCCCCCCcee--------EEe--eeEEeecCCCCCEEe
Confidence 35788999998421 111 123389999999886
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=39.75 E-value=24 Score=30.81 Aligned_cols=49 Identities=8% Similarity=0.047 Sum_probs=30.4
Q ss_pred CCcCCCCCCCCCCChhhhhcCcccc-----CCCCceecccccccccChHHHHHH
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSL-----MATNRFLCEICNKGFQRDQNLQLH 82 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h-----~~~k~f~C~~Cgk~F~~~~~L~~H 82 (432)
.--+|..|+......+.-....+.. ..+.-+.|+.|||.|..-.++++-
T Consensus 90 ~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 90 IFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHH
Confidence 3578999998665443322221111 123468999999999877666543
No 177
>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=39.52 E-value=15 Score=23.48 Aligned_cols=26 Identities=12% Similarity=0.071 Sum_probs=15.2
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
|.|..||..+.. ....+..|+.||-.
T Consensus 1 Y~C~~Cg~~~~~-----------~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVEL-----------KPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-B-----------STSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEc-----------CCCCcEECCcCCCe
Confidence 577788876441 12335688888754
No 178
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=39.51 E-value=11 Score=41.20 Aligned_cols=55 Identities=20% Similarity=0.298 Sum_probs=39.9
Q ss_pred CCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCC
Q 014041 38 RNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKS 111 (432)
Q Consensus 38 c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~ 111 (432)
|--||..|+-.+.|..-..--+-..---|+.|.+.|....+- |-|- .+..|+.|+
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nR----RfHA---------------Qp~aCp~CG 180 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNR----RFHA---------------QPIACPKCG 180 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcccc----cccc---------------ccccCcccC
Confidence 999999999988888765443333333599999999887763 3333 468899994
No 179
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=39.47 E-value=16 Score=32.13 Aligned_cols=34 Identities=29% Similarity=0.875 Sum_probs=23.3
Q ss_pred CCcccccccccccCChHHhhhhhcc-cCCcceeec-CCCcc
Q 014041 137 EKKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLF 175 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~-~~~k~~~C~-C~~~F 175 (432)
..+|.|. |+..|.+. ++|-.+ -|+ .|.|. |+...
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred ceeEEee-cCCccchh---hhcccccccc-eEEeccCCceE
Confidence 3468888 88887655 455555 566 88888 87543
No 180
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.44 E-value=13 Score=34.78 Aligned_cols=39 Identities=18% Similarity=0.146 Sum_probs=30.4
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCC----------c-----eecccccc
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATN----------R-----FLCEICNK 71 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k----------~-----f~C~~Cgk 71 (432)
++...|++|+..|...+.+....|+..++- | ..|++|+-
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 457889999999999998888888765542 2 36999974
No 181
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=39.04 E-value=15 Score=26.71 Aligned_cols=36 Identities=28% Similarity=0.498 Sum_probs=23.2
Q ss_pred ceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCC
Q 014041 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEK 110 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C 110 (432)
.-+|-+|++.+.-......-.|.-++ ....|.|+.|
T Consensus 2 ~vkC~lCdk~~~Id~~~~~aKrLrnr------------Pi~tYmC~eC 37 (56)
T PF09963_consen 2 RVKCILCDKKEEIDEDTPEAKRLRNR------------PIHTYMCDEC 37 (56)
T ss_pred eeEEEecCCEEEeccCCHHHHHhhcC------------CCcceeChhH
Confidence 35899999988755543333333221 4567999999
No 182
>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=38.90 E-value=41 Score=29.67 Aligned_cols=50 Identities=18% Similarity=0.311 Sum_probs=23.0
Q ss_pred CCceeccccccccc------ChHHHHHH-HHhcCCCcccccccccccCCcceeCCCCCC
Q 014041 61 TNRFLCEICNKGFQ------RDQNLQLH-RRGHNLPWKLKQRTNKEVRKKVYICPEKSC 112 (432)
Q Consensus 61 ~k~f~C~~Cgk~F~------~~~~L~~H-~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c 112 (432)
.-..+|..|+|.|- ..+.+..| ++..+++ ...+.....++..+.|-.|++
T Consensus 12 ~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~e--v~LH~~s~lgdt~leCy~Cg~ 68 (152)
T PF09416_consen 12 SCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKE--VSLHPDSPLGDTVLECYNCGS 68 (152)
T ss_dssp CCEEEETTTTEEEES--TTSSS-HHHHHHHHHT-----EEE-TTSTT-S-B---TTT--
T ss_pred ccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCc--eeeCCCCCCCCcEEEEEecCC
Confidence 34589999999996 45567778 4444422 111222223555667766643
No 183
>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=38.65 E-value=20 Score=30.81 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=16.2
Q ss_pred cCCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcCCC
Q 014041 100 VRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEK 138 (432)
Q Consensus 100 ~~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~gek 138 (432)
..+....|-+| |+.|+.. ++|++.|+|-.
T Consensus 68 I~~d~i~clec-------Gk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 68 ITPDYIICLEC-------GKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp B-SS-EE-TBT---------EESBH---HHHHHHTT-S-
T ss_pred cccCeeEEccC-------CcccchH---HHHHHHccCCC
Confidence 34455778888 8888764 88888887753
No 184
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=38.15 E-value=13 Score=31.10 Aligned_cols=40 Identities=15% Similarity=0.161 Sum_probs=26.0
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
+.+|+.||..-.....+..-...-....-|+|..||..|+
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 4578888875444444444433344455699999999886
No 185
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=37.78 E-value=20 Score=28.67 Aligned_cols=14 Identities=36% Similarity=0.909 Sum_probs=8.2
Q ss_pred CcccccccccccCC
Q 014041 138 KKWKCEKCSKKYAV 151 (432)
Q Consensus 138 kp~~C~~C~k~F~~ 151 (432)
..|.|..|++.|.-
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PTZ00255 53 GIWRCKGCKKTVAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 34666666666553
No 186
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=37.64 E-value=26 Score=24.35 Aligned_cols=13 Identities=31% Similarity=0.662 Sum_probs=8.9
Q ss_pred ceecccccccccC
Q 014041 63 RFLCEICNKGFQR 75 (432)
Q Consensus 63 ~f~C~~Cgk~F~~ 75 (432)
.|.|+.||..+.-
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 6788888865543
No 187
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=37.12 E-value=20 Score=28.61 Aligned_cols=35 Identities=26% Similarity=0.436 Sum_probs=23.8
Q ss_pred CceecccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCCCCCCCCCCCC
Q 014041 62 NRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSR 119 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~c~~~~c~k 119 (432)
+|-.|.-||..|.... -++|-.|+.|...|....+
T Consensus 57 ~Pa~CkkCGfef~~~~-----------------------ik~pSRCP~CKSE~Ie~pr 91 (97)
T COG3357 57 RPARCKKCGFEFRDDK-----------------------IKKPSRCPKCKSEWIEEPR 91 (97)
T ss_pred cChhhcccCccccccc-----------------------cCCcccCCcchhhcccCCc
Confidence 4678999998886421 3468889998665554443
No 188
>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=36.20 E-value=18 Score=34.55 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=6.8
Q ss_pred CCCceecccccc
Q 014041 60 ATNRFLCEICNK 71 (432)
Q Consensus 60 ~~k~f~C~~Cgk 71 (432)
+.+.|+|.+|..
T Consensus 139 GGrif~CsfC~~ 150 (314)
T PF06524_consen 139 GGRIFKCSFCDN 150 (314)
T ss_pred CCeEEEeecCCC
Confidence 344566666655
No 189
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=36.19 E-value=61 Score=28.77 Aligned_cols=48 Identities=10% Similarity=0.277 Sum_probs=26.6
Q ss_pred CCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHhcCC
Q 014041 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNL 88 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H~~ 88 (432)
.|++|=. +|-..+|-+=.--..|-+||.| +-.|....-|.+=.+.+..
T Consensus 4 ~CpICme-~PHNAVLLlCSS~~kgcRpymc---~Ts~rhSNCLdqfkka~~~ 51 (162)
T PF07800_consen 4 TCPICME-HPHNAVLLLCSSHEKGCRPYMC---DTSYRHSNCLDQFKKAYGK 51 (162)
T ss_pred cCceecc-CCCceEEEEeccccCCcccccc---CCccchhHHHHHHHHHhcC
Confidence 4555543 2333333332223345566755 5678888888877777763
No 190
>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=36.12 E-value=12 Score=41.60 Aligned_cols=11 Identities=36% Similarity=0.694 Sum_probs=0.0
Q ss_pred Cceeccccccc
Q 014041 62 NRFLCEICNKG 72 (432)
Q Consensus 62 k~f~C~~Cgk~ 72 (432)
-.+.|+.||+.
T Consensus 654 ~~r~Cp~Cg~~ 664 (900)
T PF03833_consen 654 GRRRCPKCGKE 664 (900)
T ss_dssp -----------
T ss_pred ecccCcccCCc
Confidence 34677777763
No 191
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=35.85 E-value=24 Score=28.40 Aligned_cols=43 Identities=21% Similarity=0.176 Sum_probs=18.2
Q ss_pred CCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHH
Q 014041 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQN 78 (432)
Q Consensus 31 ~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~ 78 (432)
.+.+...|.+||++..+ .+.-+-...--|-|++|-+.|..--+
T Consensus 10 ag~ke~~CalCG~tWg~-----~y~Ev~G~rLfFCCd~ca~EF~nmi~ 52 (105)
T PF11494_consen 10 AGTKEMGCALCGATWGD-----YYEEVDGERLFFCCDDCAKEFKNMIN 52 (105)
T ss_dssp --SGGGS-SS---S--------SS-B-TT--BSSS--SSSS-TTS-TH
T ss_pred cccccccccccCCcHHH-----HHHhhcCCEEEEEcHHHHHHHHHHHH
Confidence 45678899999998664 22223333345889999999986543
No 192
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=35.69 E-value=28 Score=23.44 Aligned_cols=24 Identities=21% Similarity=0.541 Sum_probs=17.3
Q ss_pred eecccccccccC--hHHHHHHHHhcC
Q 014041 64 FLCEICNKGFQR--DQNLQLHRRGHN 87 (432)
Q Consensus 64 f~C~~Cgk~F~~--~~~L~~H~r~H~ 87 (432)
-+|+.||..|.. ...-+.|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 588888888874 445677877774
No 193
>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=35.29 E-value=20 Score=28.71 Aligned_cols=13 Identities=46% Similarity=1.183 Sum_probs=7.8
Q ss_pred cccccccccccCC
Q 014041 139 KWKCEKCSKKYAV 151 (432)
Q Consensus 139 p~~C~~C~k~F~~ 151 (432)
.|+|..|++.|.-
T Consensus 53 IW~C~~C~~~~AG 65 (91)
T TIGR00280 53 IWTCRKCGAKFAG 65 (91)
T ss_pred EEEcCCCCCEEeC
Confidence 4666666666543
No 194
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=35.05 E-value=22 Score=36.56 Aligned_cols=27 Identities=19% Similarity=0.330 Sum_probs=22.7
Q ss_pred ccCCCCceeccccc-ccccChHHHHHHH
Q 014041 57 SLMATNRFLCEICN-KGFQRDQNLQLHR 83 (432)
Q Consensus 57 ~h~~~k~f~C~~Cg-k~F~~~~~L~~H~ 83 (432)
.|.-..-|.|+||| +++.-+..+.+|.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHh
Confidence 35556779999999 9999999999994
No 195
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=34.51 E-value=28 Score=25.20 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=13.0
Q ss_pred CCCCceecccccccccChH
Q 014041 59 MATNRFLCEICNKGFQRDQ 77 (432)
Q Consensus 59 ~~~k~f~C~~Cgk~F~~~~ 77 (432)
.+...|.|+.||..+-...
T Consensus 10 ~~~v~~~Cp~cGipthcS~ 28 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTHCSE 28 (55)
T ss_pred ccccCCcCCCCCCcCccCH
Confidence 3345699999998775443
No 196
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=34.31 E-value=23 Score=30.37 Aligned_cols=55 Identities=16% Similarity=0.237 Sum_probs=33.3
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceec---ccccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCC
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLC---EICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPE 109 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C---~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~ 109 (432)
.+-|+|++|.....++.-|+ |-+| .+|+.-+ .+|..|-..| -+|+.
T Consensus 78 ~~lYeCnIC~etS~ee~FLK----------PneCCgY~iCn~Cy---a~LWK~~~~y------------------pvCPv 126 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLK----------PNECCGYSICNACY---ANLWKFCNLY------------------PVCPV 126 (140)
T ss_pred CCceeccCcccccchhhcCC----------cccccchHHHHHHH---HHHHHHcccC------------------CCCCc
Confidence 36788888887766644433 3344 3454444 4677775555 36888
Q ss_pred CCCCCCCCCCccCCHH
Q 014041 110 KSCVHHDPSRALGDLT 125 (432)
Q Consensus 110 C~c~~~~c~k~f~~~~ 125 (432)
| ...|++..
T Consensus 127 C-------kTSFKss~ 135 (140)
T PF05290_consen 127 C-------KTSFKSSS 135 (140)
T ss_pred c-------cccccccc
Confidence 8 77776543
No 197
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=34.28 E-value=18 Score=31.31 Aligned_cols=38 Identities=16% Similarity=0.330 Sum_probs=30.1
Q ss_pred CCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHHHHHh
Q 014041 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRG 85 (432)
Q Consensus 31 ~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~H~r~ 85 (432)
.++...-|.+||- . -.|.|.-||-.+-....|..|..+
T Consensus 114 ~KP~r~fCaVCG~--~---------------S~ysC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 114 FKPLRKFCAVCGY--D---------------SKYSCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred CCCcchhhhhcCC--C---------------chhHHHhcCCceeechhhhhcccc
Confidence 3455677999993 2 359999999999999999988544
No 198
>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=33.93 E-value=20 Score=25.85 Aligned_cols=11 Identities=18% Similarity=0.754 Sum_probs=6.6
Q ss_pred ceecccccccc
Q 014041 63 RFLCEICNKGF 73 (432)
Q Consensus 63 ~f~C~~Cgk~F 73 (432)
...|+.||..|
T Consensus 22 iV~Cp~CGael 32 (54)
T TIGR01206 22 LVICDECGAEL 32 (54)
T ss_pred EEeCCCCCCEE
Confidence 35666666655
No 199
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=33.62 E-value=37 Score=39.61 Aligned_cols=8 Identities=38% Similarity=0.343 Sum_probs=4.0
Q ss_pred cCCCCCCC
Q 014041 36 RKRNLPGT 43 (432)
Q Consensus 36 ~~c~~cg~ 43 (432)
++|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 44555554
No 200
>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=33.48 E-value=29 Score=22.76 Aligned_cols=31 Identities=19% Similarity=0.239 Sum_probs=19.0
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEIC 69 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~C 69 (432)
...|+.|+.. +.+..|-+...+..+|.|..|
T Consensus 5 ~v~CP~C~s~----~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQST----EGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCCCCCCC----CcceeCCCCCCCCEeEecCcC
Confidence 3456666653 224556666666677777776
No 201
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=33.08 E-value=22 Score=28.47 Aligned_cols=13 Identities=46% Similarity=1.211 Sum_probs=7.7
Q ss_pred cccccccccccCC
Q 014041 139 KWKCEKCSKKYAV 151 (432)
Q Consensus 139 p~~C~~C~k~F~~ 151 (432)
.|.|..|++.|.-
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PRK03976 54 IWECRKCGAKFAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4666666666543
No 202
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=32.96 E-value=25 Score=23.44 Aligned_cols=32 Identities=6% Similarity=0.061 Sum_probs=17.5
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCCceecccccccc
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGF 73 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F 73 (432)
-+|..|+. .|....+...+.+.++|.+|+..-
T Consensus 3 ~rC~~C~a------ylNp~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 3 VRCRRCRA------YLNPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp -B-TTT--------BS-TTSEEETTTTEEEETTT--EE
T ss_pred cccCCCCC------EECCcceEcCCCCEEECcCCCCcC
Confidence 45666654 455666666677789999998753
No 203
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.85 E-value=24 Score=36.31 Aligned_cols=29 Identities=31% Similarity=0.760 Sum_probs=21.2
Q ss_pred cccccccccCChHHhhhhhcccCCcceeec-CCCccCCch
Q 014041 141 KCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKD 179 (432)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~~~~k~~~C~-C~~~F~~~~ 179 (432)
+|+.||.+ |+..|.+-|+|. |++.+....
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 68888865 444555589998 998887654
No 204
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=32.32 E-value=33 Score=24.55 Aligned_cols=35 Identities=23% Similarity=0.374 Sum_probs=23.1
Q ss_pred CCceeccc--ccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCC
Q 014041 61 TNRFLCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPE 109 (432)
Q Consensus 61 ~k~f~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~ 109 (432)
..+..|+. |.+.+. +..|..|+...- ..++..|++
T Consensus 7 ~~~v~C~~~cc~~~i~-r~~l~~H~~~~C-------------~~~~v~C~~ 43 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIP-RKELDDHLENEC-------------PKRPVPCPY 43 (60)
T ss_dssp TSEEE-TT--S-BEEE-CCCHHHHHHTTS-------------TTSEEE-SS
T ss_pred CCEeeCCCCCccccee-HHHHHHHHHccC-------------CCCcEECCC
Confidence 45678988 556566 456999988655 667788888
No 205
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=32.13 E-value=19 Score=21.38 Aligned_cols=10 Identities=30% Similarity=0.614 Sum_probs=7.0
Q ss_pred Cceecccccc
Q 014041 62 NRFLCEICNK 71 (432)
Q Consensus 62 k~f~C~~Cgk 71 (432)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4578887774
No 207
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.03 E-value=9 Score=33.83 Aligned_cols=37 Identities=27% Similarity=0.497 Sum_probs=24.9
Q ss_pred HHHHHHhhhcCCCcccccccccccCChHHhhhhhcccCCcc
Q 014041 126 GIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTRE 166 (432)
Q Consensus 126 ~L~~H~~~H~gekp~~C~~C~k~F~~~~~L~~H~~~~~~k~ 166 (432)
.|-.|+..|.| ++|++|.| |...++...|+..+-.||
T Consensus 128 slP~hi~~~~g---~KCPvC~K-~V~sDd~e~HlvMCLtkP 164 (205)
T KOG0801|consen 128 SLPVHIMDHSG---MKCPVCHK-VVPSDDAEIHLVMCLTKP 164 (205)
T ss_pred ccceeeeccCC---ccCCcccc-ccCCCcceEEEEEEeccc
Confidence 45566666655 78999998 555677788877643333
No 208
>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=31.83 E-value=7.4 Score=27.69 Aligned_cols=27 Identities=30% Similarity=0.629 Sum_probs=15.9
Q ss_pred CCceecccccccccChHHHHHHHHhcC
Q 014041 61 TNRFLCEICNKGFQRDQNLQLHRRGHN 87 (432)
Q Consensus 61 ~k~f~C~~Cgk~F~~~~~L~~H~r~H~ 87 (432)
..+|+|+.|+..|--.-.+..|...|+
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 457999999999988777777777665
No 209
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=31.67 E-value=31 Score=34.18 Aligned_cols=37 Identities=14% Similarity=0.329 Sum_probs=23.6
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccc
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk 71 (432)
...+..|++||.. +..+.+ +.....|.+-..|..|+-
T Consensus 184 ~~~~~~CPvCGs~-P~~s~v--~~~~~~G~RyL~CslC~t 220 (309)
T PRK03564 184 GEQRQFCPVCGSM-PVSSVV--QIGTTQGLRYLHCNLCES 220 (309)
T ss_pred ccCCCCCCCCCCc-chhhee--eccCCCCceEEEcCCCCC
Confidence 4467889999974 333433 223345667788999875
No 210
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=31.39 E-value=18 Score=30.23 Aligned_cols=27 Identities=7% Similarity=-0.086 Sum_probs=19.2
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccc
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk 71 (432)
+...+|..||..|.... ..|.|+.||.
T Consensus 68 p~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred CcEEEcccCCCEEecCC------------cCccCcCCCC
Confidence 45788999997765522 3467999984
No 211
>PF15269 zf-C2H2_7: Zinc-finger
Probab=31.35 E-value=25 Score=24.22 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=17.3
Q ss_pred ccccccccccCChHHhhhhhcc
Q 014041 140 WKCEKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~ 161 (432)
|+|-.|..+...+++|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6777787777778888888875
No 212
>PRK12496 hypothetical protein; Provisional
Probab=30.99 E-value=26 Score=31.30 Aligned_cols=30 Identities=20% Similarity=0.336 Sum_probs=20.5
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
+|.|.-||+.|+... ..-.|++||...+++
T Consensus 127 ~~~C~gC~~~~~~~~------------~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 127 RKVCKGCKKKYPEDY------------PDDVCEICGSPVKRK 156 (164)
T ss_pred eEECCCCCccccCCC------------CCCcCCCCCChhhhc
Confidence 578999999886410 113699999765443
No 213
>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=30.41 E-value=19 Score=31.41 Aligned_cols=35 Identities=14% Similarity=0.224 Sum_probs=24.5
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
..-.|+|..|+..+ ..+.+. ....|.|..|+..|.
T Consensus 120 ~~~~~~C~~C~~~~------~r~~~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 120 KKYVYRCPSCGREY------KRHRRS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred cceEEEcCCCCCEe------eeeccc--chhhEECCCCCCEEE
Confidence 34588999999865 334443 445599999997764
No 214
>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=30.29 E-value=29 Score=23.57 Aligned_cols=16 Identities=19% Similarity=0.758 Sum_probs=11.0
Q ss_pred ecccccccccChHHHH
Q 014041 65 LCEICNKGFQRDQNLQ 80 (432)
Q Consensus 65 ~C~~Cgk~F~~~~~L~ 80 (432)
.|.+||+.|.-.....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6888888887554443
No 215
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=29.75 E-value=23 Score=35.98 Aligned_cols=20 Identities=25% Similarity=-0.042 Sum_probs=0.0
Q ss_pred CCCchhHHHHHHHHHhhhhc
Q 014041 271 SNQSGQQQQQQQQQQQQGLA 290 (432)
Q Consensus 271 qqqQQQQQQQQQQQQQQqqq 290 (432)
++++++|+||+|+|++++++
T Consensus 230 ~~~~~pQ~qq~q~q~~~pqq 249 (505)
T COG5624 230 LVDRYPQFQQGQKQVLSPQQ 249 (505)
T ss_pred HHhhhHHHHHHHHHhhChHh
No 216
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.72 E-value=33 Score=22.86 Aligned_cols=37 Identities=19% Similarity=0.129 Sum_probs=24.1
Q ss_pred CCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHHHH
Q 014041 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQL 81 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L~~ 81 (432)
+|+.|+....... ..+..-+.|+.|+-.|-....|.+
T Consensus 1 ~CP~C~~~l~~~~--------~~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVR--------LGDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEE--------ECCEEEEECCCCCeEEccHHHHHH
Confidence 4777877422211 133455889999988888887764
No 217
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=29.59 E-value=29 Score=34.56 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=22.6
Q ss_pred ccCCCCceeccccc-ccccChHHHHHHHH
Q 014041 57 SLMATNRFLCEICN-KGFQRDQNLQLHRR 84 (432)
Q Consensus 57 ~h~~~k~f~C~~Cg-k~F~~~~~L~~H~r 84 (432)
.|.-.+-|.|+||| +++.-+..+.+|..
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 35557789999999 88888888888853
No 218
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=29.49 E-value=24 Score=23.45 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=12.0
Q ss_pred ceecccccccccCh
Q 014041 63 RFLCEICNKGFQRD 76 (432)
Q Consensus 63 ~f~C~~Cgk~F~~~ 76 (432)
+|+|..|++.|-.+
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 79999999999643
No 219
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=28.95 E-value=27 Score=33.90 Aligned_cols=39 Identities=18% Similarity=0.445 Sum_probs=23.2
Q ss_pred ceeCCCCCCCCC-----CCCCccCCHHHHHHHHhhhcCCCcccccccccc
Q 014041 104 VYICPEKSCVHH-----DPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKK 148 (432)
Q Consensus 104 ~y~C~~C~c~~~-----~c~k~f~~~~~L~~H~~~H~gekp~~C~~C~k~ 148 (432)
...|.+|.|... .||-.|++.. +|.|-++.|| |+.|..-
T Consensus 25 ~lrC~IC~~~i~ip~~TtCgHtFCslC-----IR~hL~~qp~-CP~Cr~~ 68 (391)
T COG5432 25 MLRCRICDCRISIPCETTCGHTFCSLC-----IRRHLGTQPF-CPVCRED 68 (391)
T ss_pred HHHhhhhhheeecceecccccchhHHH-----HHHHhcCCCC-Ccccccc
Confidence 356777765433 5677777654 4455555554 7787654
No 220
>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=28.31 E-value=19 Score=33.11 Aligned_cols=26 Identities=19% Similarity=0.479 Sum_probs=0.0
Q ss_pred cCCCCceeccccc-ccccChHHHHHHH
Q 014041 58 LMATNRFLCEICN-KGFQRDQNLQLHR 83 (432)
Q Consensus 58 h~~~k~f~C~~Cg-k~F~~~~~L~~H~ 83 (432)
|.-.+.|+|+||| .+|.-+..+.+|.
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ---------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 4445679999997 6677777888884
No 221
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=28.31 E-value=34 Score=21.59 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=8.6
Q ss_pred eeccccccccc
Q 014041 64 FLCEICNKGFQ 74 (432)
Q Consensus 64 f~C~~Cgk~F~ 74 (432)
|.|..|++.+.
T Consensus 28 f~C~~C~~~L~ 38 (39)
T smart00132 28 FKCSKCGKPLG 38 (39)
T ss_pred CCCcccCCcCc
Confidence 88888888764
No 222
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.21 E-value=49 Score=38.71 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=7.3
Q ss_pred ceeccccccc
Q 014041 63 RFLCEICNKG 72 (432)
Q Consensus 63 ~f~C~~Cgk~ 72 (432)
.++|+.||..
T Consensus 667 ~rkCPkCG~~ 676 (1337)
T PRK14714 667 RRRCPSCGTE 676 (1337)
T ss_pred EEECCCCCCc
Confidence 3788888863
No 223
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.18 E-value=20 Score=33.66 Aligned_cols=25 Identities=20% Similarity=0.437 Sum_probs=16.9
Q ss_pred CCcccccccccccCChHHhhhhhcc
Q 014041 137 EKKWKCEKCSKKYAVQSDWKAHSKI 161 (432)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (432)
++.+.|++|+..|....-+..-.|+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRi 41 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRI 41 (267)
T ss_pred hceeccCcccchhhhhheeccceeE
Confidence 4557777777777777666655555
No 224
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=28.09 E-value=39 Score=36.12 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=23.2
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhcC
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHG 136 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~g 136 (432)
..++-.|..| |++|.+.....+||-.|..
T Consensus 415 ~~~pnqC~~C-------G~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSC-------GLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cCCcchhccc-------ccccccchhhhhHhhhhhh
Confidence 3566789999 9999999888888777753
No 225
>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=27.84 E-value=16 Score=24.58 Aligned_cols=33 Identities=12% Similarity=0.517 Sum_probs=17.1
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
+.+|+.||+.......|..- ....|.|+.|=..
T Consensus 1 ~~~CSFCgr~~~~v~~li~g-----~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 1 EKRCSFCGRPESEVGRLISG-----PNGAYICDECVEQ 33 (41)
T ss_dssp --B-TTT--BTTTSSSEEEE-----S-SEEEEHHHHHH
T ss_pred CCCccCCCCCHHHHhceecC-----CCCcEECHHHHHH
Confidence 46899999987665433211 1147999998543
No 226
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=27.60 E-value=39 Score=28.47 Aligned_cols=29 Identities=24% Similarity=0.470 Sum_probs=24.4
Q ss_pred cCCCCceecccccccccChHHHHHHHHhc
Q 014041 58 LMATNRFLCEICNKGFQRDQNLQLHRRGH 86 (432)
Q Consensus 58 h~~~k~f~C~~Cgk~F~~~~~L~~H~r~H 86 (432)
..|...|-|-.|.+-|.+...|+.|.++.
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 34556699999999999999999998754
No 227
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.50 E-value=39 Score=21.64 Aligned_cols=29 Identities=17% Similarity=0.322 Sum_probs=19.4
Q ss_pred CcCCCCCCCCCCChhhhhcCcccc-CCCCceeccccccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSL-MATNRFLCEICNKGFQ 74 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h-~~~k~f~C~~Cgk~F~ 74 (432)
.++|..|+..- .. +..--+.|..||.+|.
T Consensus 3 ~~~C~~C~~~~-----------i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSKCGGNG-----------IVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred ceEcCCCCCCe-----------EEEecCCeEEcccCCcEee
Confidence 46788887631 12 3445588999999885
No 228
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=27.50 E-value=48 Score=24.21 Aligned_cols=35 Identities=11% Similarity=0.137 Sum_probs=25.1
Q ss_pred CCCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 30 SSNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 30 ~~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
.+..-.|.|..||... +......+.|..||..-..
T Consensus 15 r~~~miYiCgdC~~en-----------~lk~~D~irCReCG~RIly 49 (62)
T KOG3507|consen 15 RTATMIYICGDCGQEN-----------TLKRGDVIRCRECGYRILY 49 (62)
T ss_pred CcccEEEEeccccccc-----------cccCCCcEehhhcchHHHH
Confidence 4456789999999842 3344567999999976543
No 229
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.49 E-value=47 Score=37.87 Aligned_cols=13 Identities=23% Similarity=0.391 Sum_probs=9.0
Q ss_pred ceecccccccccC
Q 014041 63 RFLCEICNKGFQR 75 (432)
Q Consensus 63 ~f~C~~Cgk~F~~ 75 (432)
+|+|+-||..-..
T Consensus 663 ~y~CPKCG~El~~ 675 (1121)
T PRK04023 663 EDECEKCGREPTP 675 (1121)
T ss_pred CCcCCCCCCCCCc
Confidence 4778888765543
No 230
>PF03249 TSA: Type specific antigen; InterPro: IPR004933 There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation [, ]. TSA proteins are probably integral membrane proteins. ; GO: 0016021 integral to membrane
Probab=27.42 E-value=36 Score=34.24 Aligned_cols=8 Identities=38% Similarity=0.426 Sum_probs=3.2
Q ss_pred HHHhcCCC
Q 014041 301 AAQMGSTR 308 (432)
Q Consensus 301 ~~q~~s~~ 308 (432)
++..++.+
T Consensus 329 a~aaaavr 336 (503)
T PF03249_consen 329 AAAAAAVR 336 (503)
T ss_pred HHHHHHHH
Confidence 33333444
No 231
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=27.38 E-value=22 Score=29.71 Aligned_cols=28 Identities=7% Similarity=0.016 Sum_probs=19.5
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
+...+|..||..|..... .|.|+.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 456889999987765321 4779999853
No 232
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.31 E-value=45 Score=37.05 Aligned_cols=48 Identities=10% Similarity=-0.020 Sum_probs=29.4
Q ss_pred CCCCCCCcCcCCCCCCCCCCCCCCCCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 9 SVPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
.|..|+-.+. .++.+....-|......+|..||.. ...|+.|+.||-.
T Consensus 437 ~C~~Cg~v~~-Cp~Cd~~lt~H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAE-CPNCDSPLTLHKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCccc-CCCCCcceEEecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 3555533332 2333333444555678889998873 3467899999875
No 233
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=26.71 E-value=29 Score=28.24 Aligned_cols=43 Identities=12% Similarity=-0.005 Sum_probs=26.2
Q ss_pred CCCCCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 28 NPSSNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 28 ~~~~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
-+....+++.--.|+.. +....-...+.+ +++.|+.||..|+-
T Consensus 49 VpS~~~~RiVGC~g~~~----~h~v~W~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 49 VPSAFDKRIVGCICEPD----SHDVIWMWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred ecCCCCCeEEeeeCCCC----CceEEEEEEeCC-CceeCCCCCcEEEE
Confidence 33344555555556554 222333444555 79999999999974
No 234
>PLN02294 cytochrome c oxidase subunit Vb
Probab=26.68 E-value=51 Score=29.55 Aligned_cols=46 Identities=13% Similarity=0.090 Sum_probs=26.7
Q ss_pred CCCCCCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 28 NPSSNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 28 ~~~~~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
-+....+++..-.||..--. ....-...+. .+++.|+.||..|+-+
T Consensus 109 VpS~~d~RiVGCtg~~~eDs--h~v~Wf~L~k-Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 109 VKSYYDKRIVGCPGGEGEDE--HDVVWFWLEK-GKSFECPVCTQYFELE 154 (174)
T ss_pred eccCCCceEEeeCCCCCCCC--ceeEEEEecC-CCceeCCCCCCEEEEE
Confidence 34445667777777532111 1122233333 4789999999999743
No 235
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.60 E-value=39 Score=34.77 Aligned_cols=36 Identities=17% Similarity=0.135 Sum_probs=25.8
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHHH
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNL 79 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~L 79 (432)
..+-+|+.||.. +++-... -|+|+-||..+......
T Consensus 348 ~~~p~Cp~Cg~~----------m~S~G~~-g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 348 RVNPVCPRCGGR----------MKSAGRN-GFRCKKCGTRARETLIK 383 (421)
T ss_pred EcCCCCCccCCc----------hhhcCCC-CcccccccccCCccccc
Confidence 445689999985 4443333 79999999999766543
No 236
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.87 E-value=51 Score=24.31 Aligned_cols=34 Identities=24% Similarity=0.571 Sum_probs=22.0
Q ss_pred eeccccccc-ccChHHHHHHHHhcCCCcccccccccccCCcceeCCCC
Q 014041 64 FLCEICNKG-FQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEK 110 (432)
Q Consensus 64 f~C~~Cgk~-F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C 110 (432)
-+|-+|++. |.....|+.-+..-. .-+.|.|++|
T Consensus 3 vkCiiCd~v~~iD~rt~~tKrLrN~-------------PIrtymC~eC 37 (68)
T COG4896 3 VKCIICDRVDEIDNRTFKTKRLRNK-------------PIRTYMCPEC 37 (68)
T ss_pred ceEEEecceeeecchhHHHHHhhCC-------------CceeEechhh
Confidence 578899854 555555655433322 5567999999
No 237
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=25.71 E-value=27 Score=33.19 Aligned_cols=14 Identities=21% Similarity=0.643 Sum_probs=10.3
Q ss_pred CCCCceeccccccc
Q 014041 59 MATNRFLCEICNKG 72 (432)
Q Consensus 59 ~~~k~f~C~~Cgk~ 72 (432)
...+.|.|..|...
T Consensus 108 ~~drqFaC~~Cd~~ 121 (278)
T PF15135_consen 108 SVDRQFACSSCDHM 121 (278)
T ss_pred ccceeeeccccchH
Confidence 33478999999654
No 238
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=25.53 E-value=41 Score=22.64 Aligned_cols=30 Identities=13% Similarity=0.133 Sum_probs=17.2
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
|+|+.||.... -.-....-+.|..||.+..
T Consensus 1 m~Cp~Cg~~~~---------~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKEI---------VFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp ESBTTTSSSEE---------EEETTTTEEEETTT-BBEE
T ss_pred CCCcCCcCCce---------EEcCCCCeEECCCCCCEee
Confidence 57888887431 1112334578999987654
No 239
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=25.17 E-value=8.6 Score=38.57 Aligned_cols=43 Identities=14% Similarity=0.303 Sum_probs=17.4
Q ss_pred CCcceeCCCCCCCCCCCCCccCCHHHH---HHHHhh-hcC-CCcccccccccccC
Q 014041 101 RKKVYICPEKSCVHHDPSRALGDLTGI---KKHFSR-KHG-EKKWKCEKCSKKYA 150 (432)
Q Consensus 101 ~~k~y~C~~C~c~~~~c~k~f~~~~~L---~~H~~~-H~g-ekp~~C~~C~k~F~ 150 (432)
.-+.+.|..| .+.+...... ..|... |.+ .|-|+|..|++.+.
T Consensus 249 k~kav~C~~C-------~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~ 296 (344)
T PF09332_consen 249 KCKAVTCKQC-------KYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTI 296 (344)
T ss_dssp EEEEEEETTT---------EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEE
T ss_pred EEEEEEcCCC-------CCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeee
Confidence 3456778887 4333333221 233222 333 34578888887644
No 240
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=25.14 E-value=62 Score=19.98 Aligned_cols=21 Identities=10% Similarity=0.006 Sum_probs=14.2
Q ss_pred cCCCCCCCCCCChhhhhcCccccCCCC-ceeccccc
Q 014041 36 RKRNLPGTPDPDAEVIALSPKSLMATN-RFLCEICN 70 (432)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k-~f~C~~Cg 70 (432)
+.|.+|++... .. .|.|+.|+
T Consensus 1 ~~C~~C~~~~~--------------~~~~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKID--------------GFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCCcC--------------CCEeEEeCCCC
Confidence 46888877422 22 68998887
No 241
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=25.03 E-value=30 Score=23.20 Aligned_cols=16 Identities=13% Similarity=0.555 Sum_probs=10.8
Q ss_pred CCCceecccccccccC
Q 014041 60 ATNRFLCEICNKGFQR 75 (432)
Q Consensus 60 ~~k~f~C~~Cgk~F~~ 75 (432)
...-+.|+.||..|-+
T Consensus 29 ~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 29 NVPALVCPQCGEEYLD 44 (46)
T ss_pred CCCccccccCCCEeeC
Confidence 3344778888887754
No 242
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.62 E-value=38 Score=29.41 Aligned_cols=32 Identities=25% Similarity=0.784 Sum_probs=19.0
Q ss_pred cccccccccccCChHHhhhhhcccCCcceeec-CCCccC
Q 014041 139 KWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFS 176 (432)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~~~~k~~~C~-C~~~F~ 176 (432)
.|+|..|+..+. +|.|......|.|. |+..+.
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 577877877654 33333222667887 876553
No 243
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=24.23 E-value=2.4e+02 Score=33.14 Aligned_cols=15 Identities=27% Similarity=0.149 Sum_probs=6.9
Q ss_pred HHHHHHHHHhcCCCC
Q 014041 295 TALLQKAAQMGSTRS 309 (432)
Q Consensus 295 ~~l~q~~~q~~s~~s 309 (432)
+++.++..|-.+..+
T Consensus 1880 qq~~~~~~q~~sq~~ 1894 (2131)
T KOG4369|consen 1880 QQFQQQYQQHQSQSS 1894 (2131)
T ss_pred HHHHHHHhcccCCCC
Confidence 344444455444443
No 244
>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=23.95 E-value=28 Score=23.52 Aligned_cols=15 Identities=33% Similarity=0.665 Sum_probs=10.0
Q ss_pred CceecccccccccCh
Q 014041 62 NRFLCEICNKGFQRD 76 (432)
Q Consensus 62 k~f~C~~Cgk~F~~~ 76 (432)
.+|+|+.|++.|-.+
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 589999999999644
No 245
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.88 E-value=31 Score=28.95 Aligned_cols=29 Identities=10% Similarity=0.190 Sum_probs=19.1
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCce-eccccccc
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRF-LCEICNKG 72 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f-~C~~Cgk~ 72 (432)
-+...+|..||..|+... ..| .|+.||..
T Consensus 68 vp~~~~C~~Cg~~~~~~~------------~~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHVFKPNA------------LDYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCccccCC------------ccCCcCcCCCCC
Confidence 345788999997766532 123 49999853
No 246
>PF14369 zf-RING_3: zinc-finger
Probab=23.54 E-value=51 Score=21.39 Aligned_cols=13 Identities=38% Similarity=0.746 Sum_probs=8.6
Q ss_pred CCCCCCCCcCcCC
Q 014041 8 LSVPSTLKGFVQE 20 (432)
Q Consensus 8 ~~~~~~~~~~~~~ 20 (432)
..||.|+.+|+.+
T Consensus 22 ~~CP~C~~gFvEe 34 (35)
T PF14369_consen 22 VACPRCHGGFVEE 34 (35)
T ss_pred cCCcCCCCcEeEe
Confidence 3477777777654
No 247
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=23.50 E-value=56 Score=29.20 Aligned_cols=49 Identities=8% Similarity=-0.006 Sum_probs=28.8
Q ss_pred CCcCCCCCCCCCCChhhhhcCccc-----cCCCCceecccccccccChHHHHHH
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKS-----LMATNRFLCEICNKGFQRDQNLQLH 82 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~-----h~~~k~f~C~~Cgk~F~~~~~L~~H 82 (432)
..-+|+.|+......+.-.+-.+. -..+.-|.|+.||+.|..-+++..=
T Consensus 96 e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 96 EFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred ccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCchHHHHH
Confidence 456899998754432221111111 1123458899999999887766544
No 248
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=23.11 E-value=89 Score=28.51 Aligned_cols=56 Identities=20% Similarity=0.407 Sum_probs=31.0
Q ss_pred Cceeccc----ccccccChHHHHHHHHhcCCCcccccccccccCCcceeCCC--CCCCCCCCCCccCCHHHHHHHHhhhc
Q 014041 62 NRFLCEI----CNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPE--KSCVHHDPSRALGDLTGIKKHFSRKH 135 (432)
Q Consensus 62 k~f~C~~----Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~--C~c~~~~c~k~f~~~~~L~~H~~~H~ 135 (432)
-.|.|.. |.+.|... ....|.+.. .-+||.|+. .+|.|.+ ....|..|+...|
T Consensus 13 ~~~pC~~~~~GC~~~~~~~-~~~~HE~~C--------------~~~p~~CP~~~~~C~~~G------~~~~l~~Hl~~~H 71 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYS-EKREHEEEC--------------PFRPCSCPFPGSGCDWQG------SYKELLDHLRDKH 71 (198)
T ss_dssp --EE-CCGGGT---EE-GG-GHHHHHHT---------------TTSEEE-SSSSTT---EE------ECCCHHHHHHHHT
T ss_pred ceecCCCCCCCCccccccc-ChhhHhccC--------------CCcCCcCCCCCCCccccC------CHHHHHHHHHHHC
Confidence 3578876 88886554 567787665 468999999 6664432 2346899999877
Q ss_pred CCC
Q 014041 136 GEK 138 (432)
Q Consensus 136 gek 138 (432)
...
T Consensus 72 ~~~ 74 (198)
T PF03145_consen 72 SWN 74 (198)
T ss_dssp TTS
T ss_pred CCc
Confidence 664
No 249
>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=22.94 E-value=22 Score=33.94 Aligned_cols=39 Identities=23% Similarity=0.693 Sum_probs=21.4
Q ss_pred hcCCCcccccccccccCChHHhhhhhcc---cCCcceeec-CCC
Q 014041 134 KHGEKKWKCEKCSKKYAVQSDWKAHSKI---CGTREYRCD-CGT 173 (432)
Q Consensus 134 H~gekp~~C~~C~k~F~~~~~L~~H~~~---~~~k~~~C~-C~~ 173 (432)
.+|.|.|+|.+|.. |.-..+--.|... .....|+|. |.+
T Consensus 137 ~hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNr 179 (314)
T PF06524_consen 137 DHGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNR 179 (314)
T ss_pred cCCCeEEEeecCCC-eeeccchhhhhhhhhhhhccccccccccc
Confidence 45777777777765 4444444455544 233455665 554
No 250
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=22.94 E-value=37 Score=23.94 Aligned_cols=18 Identities=17% Similarity=0.434 Sum_probs=14.2
Q ss_pred CCceecccccccccChHH
Q 014041 61 TNRFLCEICNKGFQRDQN 78 (432)
Q Consensus 61 ~k~f~C~~Cgk~F~~~~~ 78 (432)
++.+.|..||+.|.--..
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 467999999999975443
No 251
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=22.93 E-value=19 Score=39.22 Aligned_cols=27 Identities=11% Similarity=0.329 Sum_probs=23.4
Q ss_pred CcceeCCCCCCCCCCCCCccCCHHHHHHHHhhhc
Q 014041 102 KKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKH 135 (432)
Q Consensus 102 ~k~y~C~~C~c~~~~c~k~f~~~~~L~~H~~~H~ 135 (432)
...|.|++| +|.|.....+..||++|.
T Consensus 790 ~giFpCreC-------~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCREC-------GKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHH-------HHHHHHHhhhhHHHHHHH
Confidence 457999999 999999999999999885
No 252
>COG1773 Rubredoxin [Energy production and conversion]
Probab=22.79 E-value=36 Score=24.59 Aligned_cols=13 Identities=23% Similarity=0.876 Sum_probs=11.2
Q ss_pred Cceeccccccccc
Q 014041 62 NRFLCEICNKGFQ 74 (432)
Q Consensus 62 k~f~C~~Cgk~F~ 74 (432)
+.|+|.+||..|.
T Consensus 2 ~~~~C~~CG~vYd 14 (55)
T COG1773 2 KRWRCSVCGYVYD 14 (55)
T ss_pred CceEecCCceEec
Confidence 4699999999985
No 253
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=22.65 E-value=56 Score=23.06 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=15.1
Q ss_pred CCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
.|..|++.|.. ..+.+.|..||+.|-.
T Consensus 4 ~C~~C~~~F~~------------~~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 4 SCMGCGKPFTL------------TRRRHHCRNCGRIFCS 30 (57)
T ss_pred cCcccCccccC------------CccccccCcCcCCcCh
Confidence 45666665553 1234566666666653
No 254
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.28 E-value=47 Score=27.08 Aligned_cols=41 Identities=12% Similarity=0.118 Sum_probs=25.8
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccCh
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~ 76 (432)
-++.+.|+.||......-. .+.-.......|.+||.+|...
T Consensus 19 L~k~FtCp~Cghe~vs~ct----vkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCT----VKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CCceEecCccCCeeeeEEE----EEecCceeEEEcccCcceEEEe
Confidence 4678899999986443222 2222233447899999888643
No 255
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=21.67 E-value=53 Score=28.50 Aligned_cols=35 Identities=11% Similarity=0.153 Sum_probs=23.6
Q ss_pred CCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccccc
Q 014041 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (432)
Q Consensus 33 ~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~ 74 (432)
.-.|+|..|+..+.. .+.+.....|.|..|+-.|.
T Consensus 110 ~~~y~C~~C~~~~~~-------~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 110 KYPYRCTGCGQRYLR-------VRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred eEEEECCCCCCCCce-------EccccCcceEEcCCCCCEEE
Confidence 358999999987642 22222336799999987764
No 256
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=21.62 E-value=7.2 Score=39.74 Aligned_cols=96 Identities=20% Similarity=0.281 Sum_probs=0.0
Q ss_pred CCCCCCCCCCChhhhhcCccccCCCCceecccc-----cccccChHHHHHH-HHhcCCCcccccccccccCCcceeCCCC
Q 014041 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEIC-----NKGFQRDQNLQLH-RRGHNLPWKLKQRTNKEVRKKVYICPEK 110 (432)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~C-----gk~F~~~~~L~~H-~r~H~~~~~~~~~~~~~~~~k~y~C~~C 110 (432)
||.+||+...+.-.-..-+.-|.+- |.|-+| |..|.-...=+.| +.-.+ .+--=+|.+|
T Consensus 336 kC~~Cg~~I~d~iLrA~GkayHp~C--F~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh-------------~kfAPrCs~C 400 (468)
T KOG1701|consen 336 KCNKCGEPIMDRILRALGKAYHPGC--FTCVVCARCLDGIPFTVDSQNNVYCVPDFH-------------KKFAPRCSVC 400 (468)
T ss_pred HHhhhhhHHHHHHHHhcccccCCCc--eEEEEeccccCCccccccCCCceeeehhhh-------------hhcCcchhhc
Q ss_pred CCCCCCCCCccCCHHHHHHHHhhhcCCCc-----ccccccccccCChHH
Q 014041 111 SCVHHDPSRALGDLTGIKKHFSRKHGEKK-----WKCEKCSKKYAVQSD 154 (432)
Q Consensus 111 ~c~~~~c~k~f~~~~~L~~H~~~H~gekp-----~~C~~C~k~F~~~~~ 154 (432)
++-.-=...-+.-+|+-.-+|. |+|+.|+........
T Consensus 401 -------~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e 442 (468)
T KOG1701|consen 401 -------GNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEE 442 (468)
T ss_pred -------cCCccCCCCCcceEEEEEccccccccceehhhcCccccccCC
No 257
>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=21.61 E-value=95 Score=21.18 Aligned_cols=11 Identities=27% Similarity=1.078 Sum_probs=6.3
Q ss_pred CCccccccccc
Q 014041 137 EKKWKCEKCSK 147 (432)
Q Consensus 137 ekp~~C~~C~k 147 (432)
...|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 44566666654
No 258
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.56 E-value=42 Score=28.03 Aligned_cols=30 Identities=7% Similarity=-0.081 Sum_probs=19.3
Q ss_pred CCCCcCCCCCCCCCCChhhhhcCccccCCCCceeccccccc
Q 014041 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (432)
Q Consensus 32 ~~~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~ 72 (432)
-+...+|..||..|+... ...+.|+.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~-----------~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLLT-----------QRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecCC-----------ccCCcCcCcCCC
Confidence 345788999998655421 112679999853
No 259
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.43 E-value=60 Score=22.90 Aligned_cols=28 Identities=18% Similarity=0.240 Sum_probs=19.4
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccccc
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGF 73 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F 73 (432)
..-|+.||.. .+..|. .+|.|..||..+
T Consensus 20 ~~fCP~Cg~~-----~m~~~~------~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSG-----FMAEHL------DRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcc-----hheccC------CcEECCCcCCEE
Confidence 5579999863 333332 579999999765
No 260
>KOG3227 consensus Calcium-responsive transcription coactivator [Transcription]
Probab=21.32 E-value=56 Score=30.20 Aligned_cols=117 Identities=17% Similarity=0.137 Sum_probs=0.0
Q ss_pred CCCccCCchHHHHHHHHhcccccccccccCCCCCCccccccCCCCccccccCCCCCCCccccCCCCCCCCCCCCCCCCCC
Q 014041 171 CGTLFSRKDSFITHRAFCDALAEESARFTTISSTNPQAAAAIPQFSSVFRQQQQSAPGSELAGGANLSMSSSSSLPRGIP 250 (432)
Q Consensus 171 C~~~F~~~~~L~~H~~~h~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 250 (432)
|-..|-.+..|.+-...+..+.....-+..++...+......+. .......+..+...........-....
T Consensus 38 ~I~e~Qn~Gk~~EC~qyq~~LhrNL~YLA~iAD~qp~pps~~~~---------pptq~~~~gpg~~~~~q~pp~~~mQq~ 108 (231)
T KOG3227|consen 38 CIVESQNKGKLSECAQYQALLHRNLVYLATIADSQPTPPSLLPA---------PPTQNMGMGPGPGSQSQPPPQYFMQQH 108 (231)
T ss_pred HHHHhhccchHHHHHHHHHHHHHhHHHHHHHhhcCCCCCcCCCC---------CccccccCCCCCCCCCCCCCchhhhcc
Q ss_pred cchhhhhccccccccCCCCCCCCchhHHHHHHHHHhhhhccccHHH
Q 014041 251 KEEEENKAYNLSESMTSLYPSNQSGQQQQQQQQQQQQGLAHMSATA 296 (432)
Q Consensus 251 ~~~~~~~~~~~~~~~~~~~qqqqQQQQQQQQQQQQQQqqq~~s~~~ 296 (432)
................-...++.+++|+|+.+||++++++.+....
T Consensus 109 q~d~m~~glPpg~~~qrq~~q~~~~~q~q~pqQq~~~hQqa~~~~~ 154 (231)
T KOG3227|consen 109 QSDGMVGGLPPGIFAQRQPLQQGQPQQQQQPQQQQQQHQQAMTSHS 154 (231)
T ss_pred ccccccCCCCccccccccchhccCcccccchhhhhhHHHHHHHHhh
No 261
>PRK00420 hypothetical protein; Validated
Probab=21.30 E-value=69 Score=26.76 Aligned_cols=30 Identities=13% Similarity=0.293 Sum_probs=20.4
Q ss_pred CcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccC
Q 014041 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (432)
Q Consensus 35 k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~ 75 (432)
-..|++||.++-. .......|+.||+...-
T Consensus 23 ~~~CP~Cg~pLf~-----------lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGLPLFE-----------LKDGEVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCCccee-----------cCCCceECCCCCCeeee
Confidence 3679999976432 12345889999987664
No 262
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.89 E-value=44 Score=32.72 Aligned_cols=36 Identities=19% Similarity=0.190 Sum_probs=25.3
Q ss_pred CCcCCCCCCCCCCChhhhhcCccccCCCCceecccccccccChHH
Q 014041 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQN 78 (432)
Q Consensus 34 ~k~~c~~cg~~~~~~~~l~~h~~~h~~~k~f~C~~Cgk~F~~~~~ 78 (432)
.=.+|+.|++.....+.. +.-+.|+.||..|+-...
T Consensus 25 ~~~~c~~c~~~~~~~~l~---------~~~~vc~~c~~h~rl~ar 60 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELE---------RNLEVCPKCDHHMRMDAR 60 (285)
T ss_pred CeeECCCCcchhhHHHHH---------hhCCCCCCCCCcCcCCHH
Confidence 467899999976554422 223899999998875444
No 263
>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=20.68 E-value=25 Score=22.98 Aligned_cols=13 Identities=15% Similarity=0.565 Sum_probs=6.5
Q ss_pred CCccccccccccc
Q 014041 137 EKKWKCEKCSKKY 149 (432)
Q Consensus 137 ekp~~C~~C~k~F 149 (432)
...-+|+.||-.+
T Consensus 19 ~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 19 KVEGVCDNCGGEL 31 (36)
T ss_dssp SSTTBCTTTTEBE
T ss_pred CCCCccCCCCCee
Confidence 3345565555443
Done!