Query psy2288
Match_columns 247
No_of_seqs 169 out of 1467
Neff 10.8
Searched_HMMs 46136
Date Fri Aug 16 20:51:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2288.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2288hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 9.5E-32 2.1E-36 198.5 6.3 135 91-227 129-266 (279)
2 KOG2462|consensus 100.0 1.6E-29 3.5E-34 186.7 7.1 134 63-198 129-265 (279)
3 KOG1074|consensus 99.9 5.6E-29 1.2E-33 207.3 3.4 143 93-235 606-938 (958)
4 KOG3608|consensus 99.9 3.7E-25 7.9E-30 168.2 12.0 215 13-230 141-378 (467)
5 KOG3608|consensus 99.9 4.9E-25 1.1E-29 167.6 10.9 207 37-246 135-366 (467)
6 KOG3623|consensus 99.9 3.7E-26 8E-31 187.9 4.2 103 11-113 213-330 (1007)
7 KOG1074|consensus 99.9 8.8E-25 1.9E-29 182.5 3.0 142 64-205 605-936 (958)
8 KOG3623|consensus 99.9 2.7E-23 5.8E-28 171.2 3.9 107 35-141 209-330 (1007)
9 KOG3576|consensus 99.7 1.4E-18 3E-23 123.0 3.1 114 118-231 115-239 (267)
10 KOG3576|consensus 99.7 5.5E-17 1.2E-21 114.9 3.5 85 33-117 114-198 (267)
11 PLN03086 PRLI-interacting fact 99.4 9.2E-13 2E-17 109.8 9.9 144 64-226 407-562 (567)
12 PLN03086 PRLI-interacting fact 99.4 2.1E-12 4.6E-17 107.7 10.6 86 149-240 454-549 (567)
13 PHA00733 hypothetical protein 99.3 6.2E-12 1.3E-16 86.0 4.4 94 134-229 26-124 (128)
14 PHA00733 hypothetical protein 99.1 9.1E-11 2E-15 80.3 4.9 84 31-116 35-123 (128)
15 PHA02768 hypothetical protein; 99.1 4.5E-11 9.7E-16 67.4 1.8 44 176-221 5-48 (55)
16 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.2E-09 2.7E-14 52.7 2.4 26 191-216 1-26 (26)
17 PHA02768 hypothetical protein; 98.8 1.3E-09 2.9E-14 61.5 1.7 42 149-192 6-47 (55)
18 KOG3993|consensus 98.8 7.2E-10 1.6E-14 87.5 0.0 165 36-200 267-482 (500)
19 KOG3993|consensus 98.8 1.5E-09 3.2E-14 85.7 0.4 165 64-228 267-482 (500)
20 PHA00616 hypothetical protein 98.7 1.1E-08 2.3E-13 54.9 2.2 34 176-209 1-34 (44)
21 PHA00616 hypothetical protein 98.7 8.3E-09 1.8E-13 55.4 1.7 34 204-237 1-34 (44)
22 PF13465 zf-H2C2_2: Zinc-finge 98.6 3.3E-08 7.1E-13 47.7 2.2 25 163-187 1-25 (26)
23 PHA00732 hypothetical protein 98.5 1.1E-07 2.4E-12 59.0 2.6 36 177-215 2-38 (79)
24 PHA00732 hypothetical protein 98.3 6.9E-07 1.5E-11 55.5 2.7 48 148-201 1-49 (79)
25 PF05605 zf-Di19: Drought indu 98.3 1.9E-06 4E-11 49.7 4.1 49 177-228 3-53 (54)
26 PF05605 zf-Di19: Drought indu 98.2 3.2E-06 6.9E-11 48.7 4.4 49 36-87 2-52 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.1 1.7E-06 3.8E-11 40.4 2.1 22 205-226 1-22 (23)
28 PF13894 zf-C2H2_4: C2H2-type 98.0 6.3E-06 1.4E-10 38.8 2.2 24 205-228 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 97.9 6.3E-06 1.4E-10 38.4 1.7 22 177-198 1-22 (23)
30 PF12756 zf-C2H2_2: C2H2 type 97.9 9.7E-06 2.1E-10 53.3 3.0 73 150-227 1-73 (100)
31 PF13912 zf-C2H2_6: C2H2-type 97.9 8.7E-06 1.9E-10 39.6 1.8 25 204-228 1-25 (27)
32 PF13894 zf-C2H2_4: C2H2-type 97.7 3.5E-05 7.6E-10 36.1 2.2 23 177-199 1-23 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.6 4.2E-05 9.1E-10 50.3 2.7 72 38-114 1-72 (100)
34 PF13912 zf-C2H2_6: C2H2-type 97.6 4.1E-05 8.8E-10 37.2 1.7 25 176-200 1-25 (27)
35 PF09237 GAGA: GAGA factor; I 97.4 0.00018 4E-09 39.6 2.8 32 201-232 21-52 (54)
36 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00029 6.2E-09 33.0 2.0 23 205-228 1-23 (24)
37 smart00355 ZnF_C2H2 zinc finge 97.2 0.00032 7E-09 33.3 2.2 23 205-227 1-23 (26)
38 PF12874 zf-met: Zinc-finger o 97.1 0.00036 7.8E-09 33.0 1.6 23 205-227 1-23 (25)
39 PF09237 GAGA: GAGA factor; I 97.0 0.00075 1.6E-08 37.2 2.6 32 173-204 21-52 (54)
40 COG5189 SFP1 Putative transcri 97.0 0.00012 2.6E-09 56.5 -0.7 67 146-224 347-418 (423)
41 smart00355 ZnF_C2H2 zinc finge 97.0 0.00081 1.8E-08 31.8 2.5 23 177-199 1-23 (26)
42 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00068 1.5E-08 31.7 1.7 23 177-200 1-23 (24)
43 KOG1146|consensus 96.9 0.00026 5.5E-09 64.6 0.1 50 177-226 735-791 (1406)
44 PRK04860 hypothetical protein; 96.9 0.00063 1.4E-08 48.5 1.9 38 175-216 118-155 (160)
45 COG5189 SFP1 Putative transcri 96.8 0.00043 9.4E-09 53.5 0.8 68 62-141 347-419 (423)
46 PF12874 zf-met: Zinc-finger o 96.6 0.0014 3E-08 31.0 1.4 22 177-198 1-22 (25)
47 KOG1146|consensus 96.2 0.00049 1.1E-08 62.9 -2.5 28 63-90 464-491 (1406)
48 PF12171 zf-C2H2_jaz: Zinc-fin 96.2 0.0014 3E-08 31.7 0.1 22 205-226 2-23 (27)
49 PRK04860 hypothetical protein; 96.1 0.0031 6.7E-08 45.0 1.8 37 203-243 118-154 (160)
50 KOG2231|consensus 95.9 0.042 9.1E-07 47.9 7.7 103 95-208 118-240 (669)
51 KOG2231|consensus 95.9 0.036 7.8E-07 48.3 7.1 47 122-172 184-236 (669)
52 KOG2785|consensus 95.7 0.053 1.1E-06 43.6 6.9 52 176-227 166-243 (390)
53 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0031 6.7E-08 30.4 -0.1 22 37-58 2-23 (27)
54 KOG2482|consensus 95.5 0.092 2E-06 41.5 7.6 24 204-227 334-357 (423)
55 PF13913 zf-C2HC_2: zinc-finge 95.3 0.016 3.5E-07 27.3 1.9 20 205-225 3-22 (25)
56 COG5236 Uncharacterized conser 95.2 0.042 9.1E-07 43.4 4.8 126 93-228 152-305 (493)
57 KOG2785|consensus 95.2 0.093 2E-06 42.2 6.8 27 204-230 166-192 (390)
58 TIGR00622 ssl1 transcription f 94.8 0.062 1.3E-06 35.6 4.1 18 120-137 15-32 (112)
59 KOG4173|consensus 94.6 0.025 5.3E-07 41.3 2.2 74 148-224 79-166 (253)
60 KOG2893|consensus 94.6 0.0093 2E-07 44.5 -0.1 45 179-227 13-58 (341)
61 smart00451 ZnF_U1 U1-like zinc 94.5 0.033 7.1E-07 28.5 1.9 24 204-227 3-26 (35)
62 PF12013 DUF3505: Protein of u 93.8 0.13 2.9E-06 34.3 4.4 25 205-229 81-109 (109)
63 COG5048 FOG: Zn-finger [Genera 93.8 0.011 2.4E-07 49.6 -1.2 147 92-238 289-452 (467)
64 smart00451 ZnF_U1 U1-like zinc 93.6 0.072 1.6E-06 27.2 2.1 23 36-58 3-25 (35)
65 TIGR00622 ssl1 transcription f 93.3 0.2 4.3E-06 33.2 4.3 109 65-211 2-110 (112)
66 KOG2482|consensus 93.3 0.38 8.2E-06 38.2 6.5 134 36-170 144-356 (423)
67 COG5048 FOG: Zn-finger [Genera 93.1 0.019 4.2E-07 48.1 -0.8 149 64-212 289-454 (467)
68 COG5236 Uncharacterized conser 92.7 0.22 4.8E-06 39.5 4.5 77 37-115 152-243 (493)
69 cd00350 rubredoxin_like Rubred 92.6 0.091 2E-06 26.6 1.6 8 148-155 17-24 (33)
70 KOG2893|consensus 92.4 0.034 7.4E-07 41.5 -0.2 44 37-84 11-54 (341)
71 PF10571 UPF0547: Uncharacteri 92.4 0.072 1.6E-06 25.3 0.9 9 178-186 16-24 (26)
72 PF12013 DUF3505: Protein of u 92.1 0.33 7.2E-06 32.3 4.3 54 147-201 10-109 (109)
73 smart00659 RPOLCX RNA polymera 89.5 0.18 3.8E-06 27.5 0.9 11 177-187 3-13 (44)
74 PHA00626 hypothetical protein 89.5 0.1 2.3E-06 29.4 -0.0 13 203-215 22-34 (59)
75 COG4049 Uncharacterized protei 89.2 0.16 3.5E-06 28.6 0.6 31 31-61 12-42 (65)
76 COG4049 Uncharacterized protei 88.0 0.26 5.7E-06 27.8 0.9 24 201-224 14-37 (65)
77 KOG4173|consensus 87.6 0.28 6.1E-06 36.0 1.2 84 92-196 79-166 (253)
78 smart00531 TFIIE Transcription 87.6 0.68 1.5E-05 32.7 3.1 12 36-47 99-110 (147)
79 COG2888 Predicted Zn-ribbon RN 87.5 0.48 1E-05 27.3 1.8 32 176-212 27-58 (61)
80 cd00729 rubredoxin_SM Rubredox 87.4 0.38 8.3E-06 24.5 1.3 10 203-212 17-26 (34)
81 PF09538 FYDLN_acid: Protein o 86.8 0.3 6.4E-06 32.4 0.8 29 178-217 11-39 (108)
82 TIGR00373 conserved hypothetic 86.7 0.82 1.8E-05 32.7 3.1 35 171-214 104-138 (158)
83 smart00734 ZnF_Rad18 Rad18-lik 86.6 0.61 1.3E-05 22.1 1.6 20 205-225 2-21 (26)
84 PF09723 Zn-ribbon_8: Zinc rib 86.0 0.17 3.8E-06 27.2 -0.5 29 205-240 6-34 (42)
85 TIGR00373 conserved hypothetic 85.8 0.87 1.9E-05 32.6 2.9 31 34-73 107-137 (158)
86 PF13717 zinc_ribbon_4: zinc-r 85.7 0.94 2E-05 23.4 2.2 8 67-74 5-12 (36)
87 PF13719 zinc_ribbon_5: zinc-r 85.4 0.89 1.9E-05 23.6 2.1 8 39-46 5-12 (37)
88 PF06524 NOA36: NOA36 protein; 85.3 0.4 8.6E-06 36.6 1.0 27 202-228 207-233 (314)
89 KOG2186|consensus 85.1 0.63 1.4E-05 35.4 1.9 48 92-142 3-50 (276)
90 COG1996 RPC10 DNA-directed RNA 85.0 0.37 8.1E-06 26.7 0.5 10 177-186 7-16 (49)
91 PRK14890 putative Zn-ribbon RN 84.7 0.74 1.6E-05 26.6 1.6 9 149-157 26-34 (59)
92 smart00834 CxxC_CXXC_SSSS Puta 84.6 0.3 6.5E-06 25.9 0.1 11 205-215 6-16 (41)
93 PRK06266 transcription initiat 84.1 1.1 2.3E-05 32.8 2.8 33 173-214 114-146 (178)
94 PRK00464 nrdR transcriptional 83.2 0.17 3.7E-06 35.9 -1.6 14 177-190 29-42 (154)
95 KOG2807|consensus 82.8 1.8 4E-05 34.3 3.6 25 203-227 344-368 (378)
96 PRK06266 transcription initiat 82.8 1.2 2.6E-05 32.6 2.5 16 36-51 117-132 (178)
97 TIGR02098 MJ0042_CXXC MJ0042 f 82.3 1.2 2.7E-05 23.1 1.9 8 39-46 5-12 (38)
98 PF08274 PhnA_Zn_Ribbon: PhnA 82.1 0.7 1.5E-05 22.8 0.8 25 178-213 4-28 (30)
99 TIGR02605 CxxC_CxxC_SSSS putat 81.6 0.43 9.3E-06 26.9 -0.1 11 205-215 6-16 (52)
100 KOG2593|consensus 81.6 1.5 3.3E-05 36.2 2.9 37 203-242 127-163 (436)
101 PRK00398 rpoP DNA-directed RNA 81.0 1 2.2E-05 24.7 1.2 8 205-212 22-29 (46)
102 COG1592 Rubrerythrin [Energy p 80.9 1.1 2.3E-05 32.2 1.7 11 173-183 146-156 (166)
103 PF09986 DUF2225: Uncharacteri 79.5 0.24 5.2E-06 37.4 -2.1 20 34-53 3-22 (214)
104 PF09986 DUF2225: Uncharacteri 79.5 0.44 9.5E-06 36.0 -0.7 18 62-79 3-20 (214)
105 PF02176 zf-TRAF: TRAF-type zi 79.4 0.94 2E-05 26.3 0.9 25 190-214 24-52 (60)
106 PF02892 zf-BED: BED zinc fing 79.2 2.2 4.9E-05 23.0 2.3 25 202-226 14-42 (45)
107 COG1592 Rubrerythrin [Energy p 79.2 1.1 2.5E-05 32.1 1.4 25 175-212 133-157 (166)
108 KOG2186|consensus 78.4 2 4.3E-05 32.8 2.4 49 65-116 4-52 (276)
109 PF03604 DNA_RNApol_7kD: DNA d 78.3 1.9 4.2E-05 21.6 1.6 10 232-241 17-26 (32)
110 TIGR00595 priA primosomal prot 78.3 1.2 2.7E-05 38.4 1.6 9 150-158 215-223 (505)
111 PF05191 ADK_lid: Adenylate ki 77.4 0.85 1.9E-05 23.6 0.2 31 205-243 2-32 (36)
112 smart00531 TFIIE Transcription 76.1 7.3 0.00016 27.5 4.8 35 64-102 99-133 (147)
113 COG4896 Uncharacterized protei 76.0 1.2 2.6E-05 25.7 0.6 38 178-215 4-42 (68)
114 PF06524 NOA36: NOA36 protein; 75.4 0.99 2.2E-05 34.5 0.2 39 61-100 139-179 (314)
115 TIGR02300 FYDLN_acid conserved 74.6 1.5 3.3E-05 29.7 0.9 13 203-215 25-37 (129)
116 KOG2807|consensus 74.1 6.2 0.00013 31.5 4.2 88 91-211 275-374 (378)
117 smart00614 ZnF_BED BED zinc fi 73.8 3 6.5E-05 23.2 1.9 22 204-225 18-44 (50)
118 PF12907 zf-met2: Zinc-binding 71.1 2.8 6.1E-05 22.2 1.2 27 205-231 2-31 (40)
119 PRK14873 primosome assembly pr 68.5 2.7 5.9E-05 37.6 1.4 11 202-212 408-418 (665)
120 PF07754 DUF1610: Domain of un 67.5 2.5 5.3E-05 19.6 0.5 8 204-211 16-23 (24)
121 PRK09678 DNA-binding transcrip 67.2 1.1 2.3E-05 27.3 -1.0 19 202-220 25-45 (72)
122 KOG2593|consensus 66.9 7.7 0.00017 32.3 3.5 37 33-72 125-161 (436)
123 PRK14714 DNA polymerase II lar 66.1 7.9 0.00017 36.9 3.8 11 204-214 692-702 (1337)
124 PF05443 ROS_MUCR: ROS/MUCR tr 65.9 3.9 8.4E-05 28.3 1.4 23 205-230 73-95 (132)
125 COG1198 PriA Primosomal protei 65.5 1.5 3.3E-05 39.4 -0.7 10 149-158 436-445 (730)
126 PF14353 CpXC: CpXC protein 64.0 6.9 0.00015 26.8 2.4 10 38-47 3-12 (128)
127 PRK04023 DNA polymerase II lar 63.3 10 0.00023 35.3 3.9 9 149-157 627-635 (1121)
128 PRK04023 DNA polymerase II lar 63.1 8.5 0.00019 35.8 3.3 9 121-129 627-635 (1121)
129 PF13878 zf-C2H2_3: zinc-finge 63.1 10 0.00022 20.2 2.4 25 36-60 13-39 (41)
130 PF15269 zf-C2H2_7: Zinc-finge 62.7 6.1 0.00013 21.3 1.5 23 64-86 20-42 (54)
131 PF13240 zinc_ribbon_2: zinc-r 60.8 3.5 7.6E-05 18.8 0.3 6 207-212 16-21 (23)
132 PF05290 Baculo_IE-1: Baculovi 60.8 11 0.00023 26.0 2.7 57 32-106 76-135 (140)
133 KOG2071|consensus 60.5 7.4 0.00016 33.8 2.4 42 173-214 415-523 (579)
134 KOG4167|consensus 60.3 2.4 5.3E-05 37.5 -0.4 27 204-230 792-818 (907)
135 COG1997 RPL43A Ribosomal prote 60.2 4.5 9.7E-05 25.5 0.8 11 177-187 54-64 (89)
136 PF12760 Zn_Tnp_IS1595: Transp 59.2 8.8 0.00019 20.9 1.8 8 65-72 19-26 (46)
137 PF07295 DUF1451: Protein of u 58.2 4.3 9.4E-05 28.6 0.6 33 204-246 112-144 (146)
138 PF13453 zf-TFIIB: Transcripti 54.1 5.4 0.00012 21.1 0.4 21 202-222 17-37 (41)
139 PF09845 DUF2072: Zn-ribbon co 53.6 8.5 0.00018 26.4 1.4 14 120-133 1-14 (131)
140 PRK05580 primosome assembly pr 53.4 7.1 0.00015 35.2 1.3 8 150-157 383-390 (679)
141 COG3357 Predicted transcriptio 52.8 8.3 0.00018 24.5 1.1 12 120-131 58-69 (97)
142 COG4530 Uncharacterized protei 51.3 6.4 0.00014 25.9 0.5 12 203-214 25-36 (129)
143 TIGR00686 phnA alkylphosphonat 51.1 7.3 0.00016 25.6 0.7 29 178-217 4-32 (109)
144 KOG3408|consensus 50.9 10 0.00023 25.5 1.4 28 32-59 53-80 (129)
145 PF08271 TF_Zn_Ribbon: TFIIB z 50.3 3.2 7E-05 22.3 -0.8 29 177-214 1-29 (43)
146 PF12773 DZR: Double zinc ribb 49.4 10 0.00022 20.9 1.1 8 205-212 30-37 (50)
147 PF04959 ARS2: Arsenite-resist 48.5 13 0.00028 28.1 1.8 30 145-174 74-103 (214)
148 KOG4167|consensus 47.7 5.5 0.00012 35.4 -0.3 27 63-89 791-817 (907)
149 PRK03824 hypA hydrogenase nick 47.7 8.8 0.00019 26.7 0.8 11 177-187 71-81 (135)
150 COG3677 Transposase and inacti 46.7 5.8 0.00013 27.4 -0.2 15 174-188 51-65 (129)
151 KOG1280|consensus 46.5 20 0.00044 29.0 2.7 37 35-71 78-116 (381)
152 PF04959 ARS2: Arsenite-resist 46.5 17 0.00037 27.5 2.2 26 36-61 77-102 (214)
153 PF07975 C1_4: TFIIH C1-like d 46.4 8.9 0.00019 21.6 0.5 20 176-195 21-40 (51)
154 PRK10220 hypothetical protein; 46.3 11 0.00024 24.9 1.0 29 178-217 5-33 (111)
155 COG5151 SSL1 RNA polymerase II 46.0 11 0.00024 29.9 1.2 78 147-227 321-411 (421)
156 PF09963 DUF2197: Uncharacteri 45.1 11 0.00024 21.7 0.7 14 201-214 28-41 (56)
157 PF13248 zf-ribbon_3: zinc-rib 45.1 11 0.00023 17.7 0.6 7 150-156 4-10 (26)
158 KOG3408|consensus 44.9 15 0.00033 24.7 1.5 27 173-199 54-80 (129)
159 PF01363 FYVE: FYVE zinc finge 44.1 11 0.00023 22.5 0.7 9 150-158 11-19 (69)
160 KOG1701|consensus 44.0 6.6 0.00014 32.6 -0.3 42 122-163 276-317 (468)
161 KOG1280|consensus 43.6 24 0.00052 28.6 2.6 40 173-212 76-117 (381)
162 COG4957 Predicted transcriptio 42.2 18 0.00038 24.9 1.5 23 205-230 77-99 (148)
163 smart00154 ZnF_AN1 AN1-like Zi 42.0 13 0.00029 19.5 0.8 12 204-215 12-23 (39)
164 PF13451 zf-trcl: Probable zin 41.7 21 0.00045 19.9 1.5 38 34-71 2-40 (49)
165 PF01780 Ribosomal_L37ae: Ribo 39.4 9.3 0.0002 24.4 -0.1 9 149-157 36-44 (90)
166 COG1675 TFA1 Transcription ini 39.4 35 0.00075 25.0 2.8 33 172-213 109-141 (176)
167 PF14446 Prok-RING_1: Prokaryo 38.8 12 0.00025 21.4 0.2 9 66-74 7-15 (54)
168 PRK00432 30S ribosomal protein 38.3 14 0.00031 20.6 0.5 10 204-213 37-46 (50)
169 TIGR00100 hypA hydrogenase nic 38.0 19 0.0004 24.3 1.2 11 177-187 71-81 (115)
170 PRK12380 hydrogenase nickel in 37.5 21 0.00046 23.9 1.4 11 177-187 71-81 (113)
171 PF15135 UPF0515: Uncharacteri 37.3 19 0.00042 27.6 1.2 58 119-189 111-168 (278)
172 PF03811 Zn_Tnp_IS1: InsA N-te 36.9 5.3 0.00011 20.6 -1.2 11 200-210 25-35 (36)
173 PF07800 DUF1644: Protein of u 36.5 1.6E+02 0.0035 21.1 5.9 49 148-198 80-130 (162)
174 PF01155 HypA: Hydrogenase exp 36.2 16 0.00034 24.5 0.6 11 205-215 71-81 (113)
175 PF14311 DUF4379: Domain of un 36.0 23 0.00051 20.0 1.2 10 149-158 29-38 (55)
176 PF10276 zf-CHCC: Zinc-finger 35.3 14 0.00031 19.6 0.2 12 35-46 28-39 (40)
177 PTZ00255 60S ribosomal protein 35.2 17 0.00036 23.3 0.5 12 176-187 54-65 (90)
178 PF08209 Sgf11: Sgf11 (transcr 35.1 36 0.00077 17.2 1.6 22 205-227 5-26 (33)
179 PF05495 zf-CHY: CHY zinc fing 35.0 6.7 0.00014 23.8 -1.2 9 93-101 42-50 (71)
180 PF01428 zf-AN1: AN1-like Zinc 34.7 14 0.0003 19.8 0.1 13 203-215 12-24 (43)
181 KOG3214|consensus 34.5 11 0.00024 24.4 -0.4 14 204-217 47-60 (109)
182 cd00924 Cyt_c_Oxidase_Vb Cytoc 34.5 21 0.00046 23.2 0.9 16 199-215 75-90 (97)
183 PF14369 zf-RING_3: zinc-finge 34.3 25 0.00054 18.0 1.0 8 67-74 24-31 (35)
184 PF04780 DUF629: Protein of un 33.2 32 0.00068 29.4 2.0 26 203-228 56-81 (466)
185 KOG2907|consensus 33.1 20 0.00042 23.9 0.6 12 92-103 102-113 (116)
186 KOG2636|consensus 32.9 37 0.00081 28.6 2.3 29 197-225 394-423 (497)
187 cd00065 FYVE FYVE domain; Zinc 32.7 24 0.00052 19.9 0.9 9 151-159 5-13 (57)
188 PF06220 zf-U1: U1 zinc finger 32.6 35 0.00077 17.7 1.4 12 35-46 2-13 (38)
189 PRK00564 hypA hydrogenase nick 32.5 25 0.00053 23.8 1.1 10 177-186 72-81 (117)
190 PRK04351 hypothetical protein; 32.4 17 0.00037 25.8 0.3 33 175-215 111-143 (149)
191 TIGR00280 L37a ribosomal prote 32.0 17 0.00036 23.3 0.2 11 177-187 54-64 (91)
192 PF04423 Rad50_zn_hook: Rad50 31.8 43 0.00093 18.9 1.9 12 38-49 22-33 (54)
193 COG4391 Uncharacterized protei 31.5 25 0.00054 20.5 0.8 15 33-47 45-59 (62)
194 COG2879 Uncharacterized small 31.3 63 0.0014 19.0 2.4 20 215-234 23-42 (65)
195 COG1773 Rubredoxin [Energy pro 30.6 23 0.00051 20.2 0.6 14 204-217 3-16 (55)
196 COG2331 Uncharacterized protei 30.6 17 0.00038 22.2 0.1 32 176-214 12-43 (82)
197 PF07282 OrfB_Zn_ribbon: Putat 30.5 64 0.0014 19.1 2.6 6 94-99 48-53 (69)
198 COG3091 SprT Zn-dependent meta 30.1 20 0.00043 25.3 0.3 35 174-213 115-149 (156)
199 PF13824 zf-Mss51: Zinc-finger 29.9 45 0.00097 19.1 1.6 7 177-183 15-21 (55)
200 COG1198 PriA Primosomal protei 29.8 31 0.00067 31.5 1.5 13 173-185 472-484 (730)
201 COG1327 Predicted transcriptio 29.5 10 0.00022 26.7 -1.2 14 177-190 29-42 (156)
202 PF00301 Rubredoxin: Rubredoxi 29.1 25 0.00054 19.4 0.5 36 205-240 2-42 (47)
203 smart00064 FYVE Protein presen 28.7 31 0.00068 20.4 1.0 10 150-159 12-21 (68)
204 PF10263 SprT-like: SprT-like 28.5 16 0.00035 25.9 -0.4 10 205-214 144-153 (157)
205 PF14255 Cys_rich_CPXG: Cystei 28.4 23 0.0005 20.0 0.3 11 205-215 1-11 (52)
206 KOG2272|consensus 28.3 41 0.00088 26.0 1.7 19 142-160 215-233 (332)
207 COG1655 Uncharacterized protei 28.3 12 0.00027 28.3 -1.0 8 178-185 64-71 (267)
208 COG4888 Uncharacterized Zn rib 28.2 10 0.00022 24.6 -1.2 11 148-158 22-32 (104)
209 COG1571 Predicted DNA-binding 27.5 38 0.00082 28.5 1.5 29 150-189 352-380 (421)
210 KOG0717|consensus 27.4 40 0.00086 28.7 1.6 22 65-86 293-314 (508)
211 PLN02294 cytochrome c oxidase 27.2 33 0.00072 24.8 1.0 14 202-215 139-152 (174)
212 KOG0717|consensus 27.1 36 0.00077 28.9 1.3 22 177-198 293-314 (508)
213 KOG4118|consensus 26.4 34 0.00073 20.2 0.8 26 37-62 39-64 (74)
214 PF08790 zf-LYAR: LYAR-type C2 26.1 15 0.00033 17.7 -0.6 9 122-130 2-10 (28)
215 PRK03976 rpl37ae 50S ribosomal 25.9 24 0.00051 22.6 0.1 11 177-187 55-65 (90)
216 COG3364 Zn-ribbon containing p 25.8 35 0.00075 22.3 0.8 13 204-216 2-14 (112)
217 PRK00420 hypothetical protein; 25.6 42 0.0009 22.5 1.2 9 177-185 41-49 (112)
218 smart00440 ZnF_C2C2 C2C2 Zinc 25.5 5.1 0.00011 21.2 -2.5 7 65-71 29-35 (40)
219 cd00730 rubredoxin Rubredoxin; 24.9 29 0.00063 19.4 0.3 36 205-240 2-42 (50)
220 PF04780 DUF629: Protein of un 24.9 68 0.0015 27.5 2.6 21 65-85 58-78 (466)
221 COG1326 Uncharacterized archae 24.9 82 0.0018 23.4 2.7 11 64-74 30-40 (201)
222 KOG0978|consensus 24.9 27 0.00058 31.4 0.3 10 65-74 644-653 (698)
223 PRK03681 hypA hydrogenase nick 24.7 32 0.00069 23.1 0.5 10 177-186 71-80 (114)
224 PF02591 DUF164: Putative zinc 24.5 64 0.0014 18.3 1.7 31 38-72 24-54 (56)
225 COG5188 PRP9 Splicing factor 3 24.5 57 0.0012 26.6 1.9 30 197-226 367-397 (470)
226 PRK12496 hypothetical protein; 24.4 47 0.001 24.0 1.4 9 150-158 129-137 (164)
227 COG1594 RPB9 DNA-directed RNA 24.3 15 0.00033 24.6 -1.0 9 177-185 101-109 (113)
228 TIGR01206 lysW lysine biosynth 24.0 32 0.00068 19.7 0.4 30 204-241 2-31 (54)
229 PRK11032 hypothetical protein; 23.6 33 0.00072 24.6 0.5 34 203-246 123-156 (160)
230 PRK14559 putative protein seri 23.3 49 0.0011 29.8 1.5 13 205-217 42-54 (645)
231 cd01410 SIRT7 SIRT7: Eukaryoti 23.1 1.1E+02 0.0025 22.9 3.3 12 176-187 95-106 (206)
232 PRK14138 NAD-dependent deacety 23.0 86 0.0019 24.3 2.7 10 232-241 143-152 (244)
233 PRK00481 NAD-dependent deacety 23.0 77 0.0017 24.5 2.5 9 233-241 143-151 (242)
234 KOG1842|consensus 23.0 48 0.001 28.0 1.3 24 37-60 16-39 (505)
235 PF11789 zf-Nse: Zinc-finger o 22.9 57 0.0012 18.8 1.3 12 35-46 23-34 (57)
236 smart00661 RPOL9 RNA polymeras 22.4 74 0.0016 17.4 1.7 6 94-99 22-27 (52)
237 PF14205 Cys_rich_KTR: Cystein 22.2 28 0.00062 19.8 -0.1 9 147-155 27-35 (55)
238 PF08792 A2L_zn_ribbon: A2L zi 22.2 44 0.00096 16.8 0.6 10 205-214 22-31 (33)
239 PF11023 DUF2614: Protein of u 21.9 59 0.0013 21.7 1.3 12 175-186 68-79 (114)
240 KOG2636|consensus 21.0 70 0.0015 27.1 1.9 27 170-196 395-422 (497)
241 KOG1842|consensus 20.8 63 0.0014 27.3 1.6 22 149-170 16-37 (505)
242 PF04216 FdhE: Protein involve 20.6 9.1 0.0002 30.5 -3.2 14 145-158 194-207 (290)
243 COG0068 HypF Hydrogenase matur 20.6 18 0.00039 32.4 -1.5 29 178-212 153-181 (750)
244 TIGR00627 tfb4 transcription f 20.5 60 0.0013 25.8 1.4 11 205-215 256-266 (279)
245 cd01413 SIR2_Af2 SIR2_Af2: Arc 20.4 1.2E+02 0.0025 23.2 2.9 11 177-187 114-124 (222)
246 KOG4377|consensus 20.4 45 0.00096 27.8 0.7 25 65-89 272-298 (480)
247 COG5112 UFD2 U1-like Zn-finger 20.2 51 0.0011 21.6 0.8 25 34-58 53-77 (126)
No 1
>KOG2462|consensus
Probab=99.97 E-value=9.5e-32 Score=198.51 Aligned_cols=135 Identities=34% Similarity=0.662 Sum_probs=125.2
Q ss_pred CCeeCCCCCcccCChhHHHHHHHHhc---CCCCeecCcCcccccChhHHHHHHHHhCCCCccccCCCccccCChHHHHHH
Q psy2288 91 KPFRCSVCGKSFSQRGILSSHLAVHA---GVKPHICKQCGHAFTQKSQLRLHEMRHGNIRHFACNVCPFKFTTKSDLQRH 167 (247)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~~~---~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H 167 (247)
..|.|+.|++.+.+..+|.+|.++|- ..+.+.|.+|++.+.+...|.+|+++|. -+.+|.+||+.|...+.|+.|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 35889999999999999999988774 3677899999999999999999999986 689999999999999999999
Q ss_pred HHHhCCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccChHHHHHHHHhc
Q psy2288 168 QRSHEGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 168 ~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
+++|+|||||.|+.|+++|.++++|+.||++|.+.++|+|..|++.|..++-|.+|..+-
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 999999999999999999999999999999999999999999999999999999998764
No 2
>KOG2462|consensus
Probab=99.96 E-value=1.6e-29 Score=186.74 Aligned_cols=134 Identities=29% Similarity=0.640 Sum_probs=123.8
Q ss_pred CceeccccccccCChHHHHHHHhhccC---CCCeeCCCCCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHH
Q psy2288 63 GKFTCTVCKKVFNNIKSLKTHSRIHTG---EKPFRCSVCGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLH 139 (247)
Q Consensus 63 ~~~~C~~C~~~f~~~~~l~~H~~~~~~---~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h 139 (247)
..|+|+.|++.+.+...|.+|.++|-. .+.+.|++|++.+.+...|..|+++|+ .+++|.+||+.|...+.|.-|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 458999999999999999999988854 466889999999999999999999985 678999999999999999999
Q ss_pred HHHhCCCCccccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHHh
Q psy2288 140 EMRHGNIRHFACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLNR 198 (247)
Q Consensus 140 ~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 198 (247)
+++|++|+||.|+.|+++|++.++|+.|+++|.+.++|+|..|++.|...+.|.+|...
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999765
No 3
>KOG1074|consensus
Probab=99.95 E-value=5.6e-29 Score=207.25 Aligned_cols=143 Identities=31% Similarity=0.624 Sum_probs=125.2
Q ss_pred eeCCCCCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHHHhCCCC----ccccC---CCccccCChHHHH
Q psy2288 93 FRCSVCGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEMRHGNIR----HFACN---VCPFKFTTKSDLQ 165 (247)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~----~~~C~---~C~~~~~~~~~l~ 165 (247)
-.|-+|.+..+-.+.|+.|.++|++++||+|.+|++.|..+.+|+.|+..|.... .+.|+ +|.+.|.+.-.|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lp 685 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLP 685 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccccc
Confidence 5899999999999999999999999999999999999999999999998876543 36688 8888888888888
Q ss_pred HHHHHhCCC-CC--------------------------------------------------------------------
Q psy2288 166 RHQRSHEGV-KP-------------------------------------------------------------------- 176 (247)
Q Consensus 166 ~H~~~h~~~-~~-------------------------------------------------------------------- 176 (247)
.|+++|.+. .+
T Consensus 686 QhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~~~ 765 (958)
T KOG1074|consen 686 QHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSCGR 765 (958)
T ss_pred ceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCcccccccc
Confidence 888776521 00
Q ss_pred --------------------------------------------------------------------------------
Q psy2288 177 -------------------------------------------------------------------------------- 176 (247)
Q Consensus 177 -------------------------------------------------------------------------------- 176 (247)
T Consensus 766 ~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~~ 845 (958)
T KOG1074|consen 766 ELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLATKT 845 (958)
T ss_pred ccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccccccccccccccc
Confidence
Q ss_pred ----------------------------------cccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccChHHHHH
Q psy2288 177 ----------------------------------FRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDAQSLNK 222 (247)
Q Consensus 177 ----------------------------------~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 222 (247)
..|.+|++.|...++|..|+++|++++||.|-+|++.|.++..|..
T Consensus 846 n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKv 925 (958)
T KOG1074|consen 846 NEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKV 925 (958)
T ss_pred ccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhh
Confidence 6799999999999999999999999999999999999999999999
Q ss_pred HHHhccCCCCCCC
Q psy2288 223 HKLSHKTSADPIS 235 (247)
Q Consensus 223 H~~~h~~~~~~~c 235 (247)
||.+|+...++.=
T Consensus 926 HMgtH~w~q~~sr 938 (958)
T KOG1074|consen 926 HMGTHMWVQPPSR 938 (958)
T ss_pred hhccccccCCCcc
Confidence 9999988766543
No 4
>KOG3608|consensus
Probab=99.93 E-value=3.7e-25 Score=168.25 Aligned_cols=215 Identities=25% Similarity=0.491 Sum_probs=180.0
Q ss_pred CcccchhHHHHHhhhhhhhh------------cCC-ceecc--cccccccCHHHHHHHHHHhCCCCceeccccccccCCh
Q psy2288 13 DPVENASKILALCMRKETEA------------QQK-SLACN--ICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKKVFNNI 77 (247)
Q Consensus 13 ~~~~~~~~~~~l~~~~~~~~------------~~~-~~~C~--~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 77 (247)
++...|.+...+..|...|. +++ .+.|. -|-.++.+...|+.|++.|.+++...|+.|+..|.+.
T Consensus 141 dCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~ 220 (467)
T KOG3608|consen 141 DCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTK 220 (467)
T ss_pred hcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccc
Confidence 45555566655555554432 232 25565 4889999999999999999999999999999999999
Q ss_pred HHHHHHHhhcc--CCCCeeCCCCCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHHH-hCCCCccccCCC
Q psy2288 78 KSLKTHSRIHT--GEKPFRCSVCGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEMR-HGNIRHFACNVC 154 (247)
Q Consensus 78 ~~l~~H~~~~~--~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~C~~C 154 (247)
..|-.|++.-+ ...+|.|..|.+.|..+..|..|+..|- .-|+|+.|+-+....+.|..|++. |...+||+|..|
T Consensus 221 tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~C 298 (467)
T KOG3608|consen 221 TKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDEC 298 (467)
T ss_pred cHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccch
Confidence 99999986533 3458999999999999999999999884 458999999999999999999984 778899999999
Q ss_pred ccccCChHHHHHHHHHhCCCCCcccCc--CchhcccHHHHHHHHHhcC-CCC--CeecccccccccChHHHHHHHHhccC
Q psy2288 155 PFKFTTKSDLQRHQRSHEGVKPFRCEY--CDKTFTRQIIMKEHLNRHK-GVQ--PYSCSHCDKTFFDAQSLNKHKLSHKT 229 (247)
Q Consensus 155 ~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-~~~--~~~C~~C~~~f~~~~~l~~H~~~h~~ 229 (247)
++.+.+.+.|.+|..+|. +-.|+|.. |..++.+..+|++|++.++ |.. +|.|-.|.+.|.+-.+|.+|+...|+
T Consensus 299 d~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 299 DTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred hhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 999999999999999888 77799977 9999999999999997654 554 59999999999999999999866544
Q ss_pred C
Q psy2288 230 S 230 (247)
Q Consensus 230 ~ 230 (247)
=
T Consensus 378 f 378 (467)
T KOG3608|consen 378 F 378 (467)
T ss_pred c
Confidence 3
No 5
>KOG3608|consensus
Probab=99.92 E-value=4.9e-25 Score=167.56 Aligned_cols=207 Identities=26% Similarity=0.513 Sum_probs=182.1
Q ss_pred eecc--cccccccCHHHHHHHHHHhCC-----------CC-c-eecc--ccccccCChHHHHHHHhhccCCCCeeCCCCC
Q psy2288 37 LACN--ICSMVFCDEIVLNKHVEEHST-----------LG-K-FTCT--VCKKVFNNIKSLKTHSRIHTGEKPFRCSVCG 99 (247)
Q Consensus 37 ~~C~--~C~~~~~~~~~l~~H~~~~~~-----------~~-~-~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 99 (247)
+.|. .|++.|.+...|..|+..|.- ++ | +.|. -|.+++.++..|++|++.|.+++...|+.|+
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg 214 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCG 214 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHH
Confidence 5565 599999999999999877631 11 2 4454 4899999999999999999999999999999
Q ss_pred cccCChhHHHHHHHHhc--CCCCeecCcCcccccChhHHHHHHHHhCCCCccccCCCccccCChHHHHHHHHH-hCCCCC
Q psy2288 100 KSFSQRGILSSHLAVHA--GVKPHICKQCGHAFTQKSQLRLHEMRHGNIRHFACNVCPFKFTTKSDLQRHQRS-HEGVKP 176 (247)
Q Consensus 100 ~~f~~~~~l~~H~~~~~--~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~ 176 (247)
..|++...|-.|++..+ ...+|.|..|.+.|..+..|..|+..|. ..|+|+.|+-.....++|.+|++. |...+|
T Consensus 215 ~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkp 292 (467)
T KOG3608|consen 215 ELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKP 292 (467)
T ss_pred HHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCC
Confidence 99999999999976543 4578999999999999999999999875 679999999999999999999875 677899
Q ss_pred cccCcCchhcccHHHHHHHHHhcCCCCCeeccc--ccccccChHHHHHHHHhcc---CCCCCCCccccCCCcCCC
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSH--CDKTFFDAQSLNKHKLSHK---TSADPISSAKGSKLFGGI 246 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~---~~~~~~c~~c~~~~~~~~ 246 (247)
|+|..|.+.|.+.+.|.+|+.+|. +-.|+|.. |.++|.+..++.+|++.++ ++-+|.|..|+--+++|.
T Consensus 293 fKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~ 366 (467)
T KOG3608|consen 293 FKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGK 366 (467)
T ss_pred ccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccch
Confidence 999999999999999999999887 66799977 9999999999999998876 558899999988777774
No 6
>KOG3623|consensus
Probab=99.92 E-value=3.7e-26 Score=187.91 Aligned_cols=103 Identities=35% Similarity=0.632 Sum_probs=74.5
Q ss_pred CCCcccchhHHHHHhhhhhhhh--cCCceecccccccccCHHHHHHHHHHhCC-------------CCceeccccccccC
Q psy2288 11 TNDPVENASKILALCMRKETEA--QQKSLACNICSMVFCDEIVLNKHVEEHST-------------LGKFTCTVCKKVFN 75 (247)
Q Consensus 11 ~~~~~~~~~~~~~l~~~~~~~~--~~~~~~C~~C~~~~~~~~~l~~H~~~~~~-------------~~~~~C~~C~~~f~ 75 (247)
+..++..+.....|.+|.+... .+..+.|..|..+|.....|.+||.+|.. ...|+|..|++.|+
T Consensus 213 cpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFK 292 (1007)
T KOG3623|consen 213 CPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFK 292 (1007)
T ss_pred chhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhh
Confidence 4455566666667777765432 34457788888888888888888877642 12478888888888
Q ss_pred ChHHHHHHHhhccCCCCeeCCCCCcccCChhHHHHHHH
Q psy2288 76 NIKSLKTHSRIHTGEKPFRCSVCGKSFSQRGILSSHLA 113 (247)
Q Consensus 76 ~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 113 (247)
.+..|..|+++|.+++||.|+.|++.|+....+..||.
T Consensus 293 fKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 293 FKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 88888888888888888888888888888777777764
No 7
>KOG1074|consensus
Probab=99.90 E-value=8.8e-25 Score=182.46 Aligned_cols=142 Identities=36% Similarity=0.729 Sum_probs=123.3
Q ss_pred ceeccccccccCChHHHHHHHhhccCCCCeeCCCCCcccCChhHHHHHHHHhcCC----CCeecC---cCcccccChhHH
Q psy2288 64 KFTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQRGILSSHLAVHAGV----KPHICK---QCGHAFTQKSQL 136 (247)
Q Consensus 64 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~----~~~~C~---~C~~~f~~~~~l 136 (247)
+.+|.+|.++..-.+.|+.|+++|++++||+|.+|++.|..+.+|+.|+.+|... ..+.|+ +|-+.|.+...|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 4679999999999999999999999999999999999999999999999888543 346788 888888887777
Q ss_pred HHHHHHhCCC-Cc-------------------------------------------------------------------
Q psy2288 137 RLHEMRHGNI-RH------------------------------------------------------------------- 148 (247)
Q Consensus 137 ~~h~~~~~~~-~~------------------------------------------------------------------- 148 (247)
..|++.|.+. .+
T Consensus 685 pQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~~ 764 (958)
T KOG1074|consen 685 PQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSCG 764 (958)
T ss_pred cceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCccccccc
Confidence 7776665210 00
Q ss_pred --------------------------------------------------------------------------------
Q psy2288 149 -------------------------------------------------------------------------------- 148 (247)
Q Consensus 149 -------------------------------------------------------------------------------- 148 (247)
T Consensus 765 ~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~ 844 (958)
T KOG1074|consen 765 RELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLATK 844 (958)
T ss_pred cccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhcccccccccccccc
Confidence
Q ss_pred -----------------------------------cccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHH
Q psy2288 149 -----------------------------------FACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMK 193 (247)
Q Consensus 149 -----------------------------------~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 193 (247)
..|..|++.|.+.+.|..|+++|.+++||.|..|++.|..+..|+
T Consensus 845 ~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLK 924 (958)
T KOG1074|consen 845 TNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLK 924 (958)
T ss_pred cccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhh
Confidence 569999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCCe
Q psy2288 194 EHLNRHKGVQPY 205 (247)
Q Consensus 194 ~H~~~h~~~~~~ 205 (247)
.||.+|....++
T Consensus 925 vHMgtH~w~q~~ 936 (958)
T KOG1074|consen 925 VHMGTHMWVQPP 936 (958)
T ss_pred hhhccccccCCC
Confidence 999999876543
No 8
>KOG3623|consensus
Probab=99.87 E-value=2.7e-23 Score=171.25 Aligned_cols=107 Identities=27% Similarity=0.619 Sum_probs=95.7
Q ss_pred CceecccccccccCHHHHHHHHHHhCC--CCceeccccccccCChHHHHHHHhhccCC-------------CCeeCCCCC
Q psy2288 35 KSLACNICSMVFCDEIVLNKHVEEHST--LGKFTCTVCKKVFNNIKSLKTHSRIHTGE-------------KPFRCSVCG 99 (247)
Q Consensus 35 ~~~~C~~C~~~~~~~~~l~~H~~~~~~--~~~~~C~~C~~~f~~~~~l~~H~~~~~~~-------------~~~~C~~C~ 99 (247)
....|++|++.+.....|+.|++.-+. +..|.|+.|..+|.....|.+||..|... +-|+|.+|+
T Consensus 209 qlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECg 288 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECG 288 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccc
Confidence 347899999999999999999887443 44599999999999999999999988543 349999999
Q ss_pred cccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHH
Q psy2288 100 KSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEM 141 (247)
Q Consensus 100 ~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 141 (247)
+.|..+..|+.|+++|.|++||.|+.|++.|.....+..|+.
T Consensus 289 KAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 289 KAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 999999999999999999999999999999999999999974
No 9
>KOG3576|consensus
Probab=99.73 E-value=1.4e-18 Score=122.95 Aligned_cols=114 Identities=30% Similarity=0.656 Sum_probs=99.9
Q ss_pred CCCeecCcCcccccChhHHHHHHHHhCCCCccccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHH
Q psy2288 118 VKPHICKQCGHAFTQKSQLRLHEMRHGNIRHFACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLN 197 (247)
Q Consensus 118 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 197 (247)
...|.|.+|++.|....-|.+|++-|...+.+.|..||+.|.+...|.+|.++|+|.+||+|..|+++|+++-+|..|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 45588999999999998999999988888899999999999999999999999999999999999999999999999987
Q ss_pred hcCCC-----------CCeecccccccccChHHHHHHHHhccCCC
Q psy2288 198 RHKGV-----------QPYSCSHCDKTFFDAQSLNKHKLSHKTSA 231 (247)
Q Consensus 198 ~h~~~-----------~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 231 (247)
..+|. +.|.|..||.+-.....+..|+..|+..-
T Consensus 195 kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 195 KVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 76653 57999999999988889999998886543
No 10
>KOG3576|consensus
Probab=99.66 E-value=5.5e-17 Score=114.88 Aligned_cols=85 Identities=42% Similarity=0.807 Sum_probs=74.6
Q ss_pred cCCceecccccccccCHHHHHHHHHHhCCCCceeccccccccCChHHHHHHHhhccCCCCeeCCCCCcccCChhHHHHHH
Q psy2288 33 QQKSLACNICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQRGILSSHL 112 (247)
Q Consensus 33 ~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 112 (247)
++..+.|..|++.|.-+..|.+|++-|...+.+.|..|++.|.+..+|.+|+++|++.+||+|..|++.|...-+|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 45568899999999989999999999988888999999999999999999999999999999999999999999999998
Q ss_pred HHhcC
Q psy2288 113 AVHAG 117 (247)
Q Consensus 113 ~~~~~ 117 (247)
+..++
T Consensus 194 ~kvhg 198 (267)
T KOG3576|consen 194 KKVHG 198 (267)
T ss_pred HHHcC
Confidence 65544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.43 E-value=9.2e-13 Score=109.77 Aligned_cols=144 Identities=21% Similarity=0.480 Sum_probs=92.8
Q ss_pred ceeccccccccCChHHHHHHHhhccCCCCeeCCC--CCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHH
Q psy2288 64 KFTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSV--CGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEM 141 (247)
Q Consensus 64 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 141 (247)
...|+.|.+... ...|..|... .......|+. |+..|.. ..+ +..+.|+.|++.|. ...|..|+.
T Consensus 407 ~V~C~NC~~~i~-l~~l~lHe~~-C~r~~V~Cp~~~Cg~v~~r-~el---------~~H~~C~~Cgk~f~-~s~LekH~~ 473 (567)
T PLN03086 407 TVECRNCKHYIP-SRSIALHEAY-CSRHNVVCPHDGCGIVLRV-EEA---------KNHVHCEKCGQAFQ-QGEMEKHMK 473 (567)
T ss_pred eEECCCCCCccc-hhHHHHHHhh-CCCcceeCCcccccceeec-ccc---------ccCccCCCCCCccc-hHHHHHHHH
Confidence 356777776533 3445566543 2334456764 7776632 212 23346777877775 466777777
Q ss_pred HhCCCCccccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcc----------cHHHHHHHHHhcCCCCCeeccccc
Q psy2288 142 RHGNIRHFACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFT----------RQIIMKEHLNRHKGVQPYSCSHCD 211 (247)
Q Consensus 142 ~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~l~~H~~~h~~~~~~~C~~C~ 211 (247)
.++ .++.|+ |+..+ ....|..|+.+|.+.+++.|+.|+..+. ....|..|.... |.+++.|..||
T Consensus 474 ~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cg 548 (567)
T PLN03086 474 VFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCG 548 (567)
T ss_pred hcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccC
Confidence 764 677787 87544 4577777877777888888888887774 234777887774 77788888888
Q ss_pred ccccChHHHHHHHHh
Q psy2288 212 KTFFDAQSLNKHKLS 226 (247)
Q Consensus 212 ~~f~~~~~l~~H~~~ 226 (247)
+.+..+ .|..|+-.
T Consensus 549 k~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 549 RSVMLK-EMDIHQIA 562 (567)
T ss_pred Ceeeeh-hHHHHHHH
Confidence 777543 56667643
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.40 E-value=2.1e-12 Score=107.65 Aligned_cols=86 Identities=16% Similarity=0.433 Sum_probs=44.4
Q ss_pred cccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeeccccccccc----------ChH
Q psy2288 149 FACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFF----------DAQ 218 (247)
Q Consensus 149 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~ 218 (247)
+.|+.|+..|. ...|..|+.+++ .++.|+ |+..+ .+..|..|+.+|.+.+++.|+.|++.|. ...
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s 528 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLR 528 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhh
Confidence 45555555553 344555555543 455555 55433 3455555555555555555555555553 123
Q ss_pred HHHHHHHhccCCCCCCCccccC
Q psy2288 219 SLNKHKLSHKTSADPISSAKGS 240 (247)
Q Consensus 219 ~l~~H~~~h~~~~~~~c~~c~~ 240 (247)
.|..|..+. +.+++.|..|+.
T Consensus 529 ~Lt~HE~~C-G~rt~~C~~Cgk 549 (567)
T PLN03086 529 GMSEHESIC-GSRTAPCDSCGR 549 (567)
T ss_pred hHHHHHHhc-CCcceEccccCC
Confidence 455555443 555555555544
No 13
>PHA00733 hypothetical protein
Probab=99.26 E-value=6.2e-12 Score=86.01 Aligned_cols=94 Identities=17% Similarity=0.307 Sum_probs=65.0
Q ss_pred hHHHHHHHHhCCCCccccCCCccccCChHHHHHH--HH---HhCCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeecc
Q psy2288 134 SQLRLHEMRHGNIRHFACNVCPFKFTTKSDLQRH--QR---SHEGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCS 208 (247)
Q Consensus 134 ~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H--~~---~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 208 (247)
..|.++.......+++.|.+|...|.....|..+ +. .+.+.+||.|+.|++.|.+...|..|++.+ ..+|.|+
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~ 103 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP 103 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCC
Confidence 4444444444445667777777666665554444 11 234477888888888888888888888876 3568888
Q ss_pred cccccccChHHHHHHHHhccC
Q psy2288 209 HCDKTFFDAQSLNKHKLSHKT 229 (247)
Q Consensus 209 ~C~~~f~~~~~l~~H~~~h~~ 229 (247)
+|++.|.....|..|+...|+
T Consensus 104 ~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 104 VCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCHHHHHHHHHHhcC
Confidence 888888888888888876654
No 14
>PHA00733 hypothetical protein
Probab=99.12 E-value=9.1e-11 Score=80.28 Aligned_cols=84 Identities=24% Similarity=0.465 Sum_probs=48.8
Q ss_pred hhcCCceecccccccccCHHHHHHH--HHH---hCCCCceeccccccccCChHHHHHHHhhccCCCCeeCCCCCcccCCh
Q psy2288 31 EAQQKSLACNICSMVFCDEIVLNKH--VEE---HSTLGKFTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQR 105 (247)
Q Consensus 31 ~~~~~~~~C~~C~~~~~~~~~l~~H--~~~---~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 105 (247)
.+.++++.|.+|...|.+...|..+ +.. .+...+|.|+.|++.|.+...|..|+..+ ..++.|+.|++.|.+.
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 3446777788877777766555544 111 22344566666666666666666666543 2345666666666666
Q ss_pred hHHHHHHHHhc
Q psy2288 106 GILSSHLAVHA 116 (247)
Q Consensus 106 ~~l~~H~~~~~ 116 (247)
..|..|+...+
T Consensus 113 ~sL~~H~~~~h 123 (128)
T PHA00733 113 DSTLDHVCKKH 123 (128)
T ss_pred HHHHHHHHHhc
Confidence 66666655443
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.09 E-value=4.5e-11 Score=67.41 Aligned_cols=44 Identities=18% Similarity=0.487 Sum_probs=36.3
Q ss_pred CcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccChHHHH
Q psy2288 176 PFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDAQSLN 221 (247)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 221 (247)
.|+|+.||+.|....+|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4788888888888888888888887 6788888888888776653
No 16
>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=98.89 E-value=1.2e-09 Score=52.70 Aligned_cols=26 Identities=35% Similarity=0.925 Sum_probs=20.3
Q ss_pred HHHHHHHhcCCCCCeecccccccccC
Q psy2288 191 IMKEHLNRHKGVQPYSCSHCDKTFFD 216 (247)
Q Consensus 191 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 216 (247)
+|.+|+++|+|++||+|++|++.|.+
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 47788888888888888888888753
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.84 E-value=1.3e-09 Score=61.47 Aligned_cols=42 Identities=17% Similarity=0.445 Sum_probs=28.8
Q ss_pred cccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHH
Q psy2288 149 FACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIM 192 (247)
Q Consensus 149 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 192 (247)
|.|+.||+.|...+.|..|+++|. ++|+|..|++.|.+.+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 567777777777777777777766 566777777776655444
No 18
>KOG3993|consensus
Probab=98.81 E-value=7.2e-10 Score=87.49 Aligned_cols=165 Identities=21% Similarity=0.345 Sum_probs=99.1
Q ss_pred ceecccccccccCHHHHHHHHHHhCCCCceeccccccccCChHHHHHHHhhccCC-------------------------
Q psy2288 36 SLACNICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKKVFNNIKSLKTHSRIHTGE------------------------- 90 (247)
Q Consensus 36 ~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~------------------------- 90 (247)
.|.|.+|...|.+...|.+|.-.-.-...|+|+.|+++|.-...|..|.+.|...
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 4889999999999999999955433334699999999999999999998777432
Q ss_pred --------CCeeCCCCCcccCChhHHHHHHHHhcCCCC-----------------eecCcCcccccChhHHHHHHHHh-C
Q psy2288 91 --------KPFRCSVCGKSFSQRGILSSHLAVHAGVKP-----------------HICKQCGHAFTQKSQLRLHEMRH-G 144 (247)
Q Consensus 91 --------~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~-----------------~~C~~C~~~f~~~~~l~~h~~~~-~ 144 (247)
..|.|.+|++.|+....|+.|+.+|+.... +-+..++..+.....-..+..-+ .
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~ 426 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAG 426 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeec
Confidence 125666666666666666666554432110 11111211111110000000000 0
Q ss_pred CCCccccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHHhcC
Q psy2288 145 NIRHFACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLNRHK 200 (247)
Q Consensus 145 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 200 (247)
......++.++..+++...--.+.+.-..+..|.|.+|.-.|.....|.+|+..-|
T Consensus 427 sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 427 SAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred cccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcC
Confidence 00113466777666555443333333444566889999999999999999987643
No 19
>KOG3993|consensus
Probab=98.76 E-value=1.5e-09 Score=85.75 Aligned_cols=165 Identities=19% Similarity=0.292 Sum_probs=106.0
Q ss_pred ceeccccccccCChHHHHHHHhhccCCCCeeCCCCCcccCChhHHHHHHHHhcC--------------------------
Q psy2288 64 KFTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQRGILSSHLAVHAG-------------------------- 117 (247)
Q Consensus 64 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~-------------------------- 117 (247)
-|.|..|...|.+...|.+|.-.-+-...|.|+.|++.|+-..+|..|.++|.-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 489999999999999999997555555679999999999999999999998721
Q ss_pred -------CCCeecCcCcccccChhHHHHHHHHhCCCCc-----------------cccCCCccccCChHHHHHHHHHhC-
Q psy2288 118 -------VKPHICKQCGHAFTQKSQLRLHEMRHGNIRH-----------------FACNVCPFKFTTKSDLQRHQRSHE- 172 (247)
Q Consensus 118 -------~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~-----------------~~C~~C~~~~~~~~~l~~H~~~h~- 172 (247)
+..|.|.+|++.|.....|+.|+.+|..... +.+..+...+...+.--.+.-.+.
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~ 426 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAG 426 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeec
Confidence 1236677777777777777777655432110 112222222211111000000000
Q ss_pred CCCCcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccChHHHHHHHHhcc
Q psy2288 173 GVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDAQSLNKHKLSHK 228 (247)
Q Consensus 173 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 228 (247)
......++.++..+..+..--.+.+.-..+..|-|.+|-..|.+..+|.+|...-|
T Consensus 427 sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 427 SAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred cccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcC
Confidence 01123467777666665544444444444667999999999999999999976544
No 20
>PHA00616 hypothetical protein
Probab=98.69 E-value=1.1e-08 Score=54.94 Aligned_cols=34 Identities=18% Similarity=0.307 Sum_probs=19.9
Q ss_pred CcccCcCchhcccHHHHHHHHHhcCCCCCeeccc
Q psy2288 176 PFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSH 209 (247)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 209 (247)
||+|+.||+.|.+.++|..|++.|+|++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 3556666666666666666666666665555543
No 21
>PHA00616 hypothetical protein
Probab=98.69 E-value=8.3e-09 Score=55.38 Aligned_cols=34 Identities=21% Similarity=0.330 Sum_probs=31.9
Q ss_pred CeecccccccccChHHHHHHHHhccCCCCCCCcc
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSHKTSADPISSA 237 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~ 237 (247)
||+|+.||+.|.+.++|..|+++|+++.++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6999999999999999999999999999988764
No 22
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.60 E-value=3.3e-08 Score=47.69 Aligned_cols=25 Identities=52% Similarity=1.283 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCCCcccCcCchhcc
Q psy2288 163 DLQRHQRSHEGVKPFRCEYCDKTFT 187 (247)
Q Consensus 163 ~l~~H~~~h~~~~~~~C~~C~~~f~ 187 (247)
+|.+|+++|.+++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3667777777777777777777775
No 23
>PHA00732 hypothetical protein
Probab=98.47 E-value=1.1e-07 Score=59.03 Aligned_cols=36 Identities=31% Similarity=0.691 Sum_probs=16.7
Q ss_pred cccCcCchhcccHHHHHHHHHh-cCCCCCeeccccccccc
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNR-HKGVQPYSCSHCDKTFF 215 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~ 215 (247)
|.|..|++.|.+...|..|++. |.+ +.|++|++.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 4445555555555555555442 221 34555555544
No 24
>PHA00732 hypothetical protein
Probab=98.27 E-value=6.9e-07 Score=55.51 Aligned_cols=48 Identities=27% Similarity=0.654 Sum_probs=31.0
Q ss_pred ccccCCCccccCChHHHHHHHHH-hCCCCCcccCcCchhcccHHHHHHHHHhcCC
Q psy2288 148 HFACNVCPFKFTTKSDLQRHQRS-HEGVKPFRCEYCDKTFTRQIIMKEHLNRHKG 201 (247)
Q Consensus 148 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 201 (247)
||.|..|++.|.+.+.|..|++. |. ++.|+.|++.|. .|..|+.++.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCC
Confidence 46677777777777777777764 33 246777777776 35667655544
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.25 E-value=1.9e-06 Score=49.73 Aligned_cols=49 Identities=27% Similarity=0.521 Sum_probs=29.7
Q ss_pred cccCcCchhcccHHHHHHHHHh-cCCC-CCeecccccccccChHHHHHHHHhcc
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNR-HKGV-QPYSCSHCDKTFFDAQSLNKHKLSHK 228 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~-h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~ 228 (247)
|.||.|++ ..+...|..|... |..+ +.+.||+|...+. .+|..|+..+|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 66777777 3445667777654 3332 3577777776544 36777776654
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=98.20 E-value=3.2e-06 Score=48.74 Aligned_cols=49 Identities=22% Similarity=0.444 Sum_probs=26.6
Q ss_pred ceecccccccccCHHHHHHHHHHhCCC--CceeccccccccCChHHHHHHHhhc
Q psy2288 36 SLACNICSMVFCDEIVLNKHVEEHSTL--GKFTCTVCKKVFNNIKSLKTHSRIH 87 (247)
Q Consensus 36 ~~~C~~C~~~~~~~~~l~~H~~~~~~~--~~~~C~~C~~~f~~~~~l~~H~~~~ 87 (247)
.|.||+|++ ..+...|..|+...+.. +.+.||+|...+. ..|..|+...
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 356666666 34556666666554332 2466666665433 2555565544
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.14 E-value=1.7e-06 Score=40.39 Aligned_cols=22 Identities=32% Similarity=0.742 Sum_probs=14.8
Q ss_pred eecccccccccChHHHHHHHHh
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLS 226 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~ 226 (247)
|+|++|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5666677777777777666665
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.97 E-value=6.3e-06 Score=38.79 Aligned_cols=24 Identities=29% Similarity=0.721 Sum_probs=14.6
Q ss_pred eecccccccccChHHHHHHHHhcc
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSHK 228 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h~ 228 (247)
|+|++|++.|.+...|..|+.+|+
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 566677777777777777766653
No 29
>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=97.93 E-value=6.3e-06 Score=38.44 Aligned_cols=22 Identities=32% Similarity=0.905 Sum_probs=14.5
Q ss_pred cccCcCchhcccHHHHHHHHHh
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNR 198 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~ 198 (247)
|.|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666655
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.91 E-value=9.7e-06 Score=53.35 Aligned_cols=73 Identities=23% Similarity=0.435 Sum_probs=18.4
Q ss_pred ccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccChHHHHHHHHhc
Q psy2288 150 ACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 150 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
+|..|+..|.+...|..|+...++...- ....+.....+..+++.-. ...+.|.+|++.|.+...|..|++++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 3667777777777777777655543211 1111223333434433221 12578888888888888888888764
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=97.88 E-value=8.7e-06 Score=39.62 Aligned_cols=25 Identities=44% Similarity=0.870 Sum_probs=18.7
Q ss_pred CeecccccccccChHHHHHHHHhcc
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSHK 228 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~ 228 (247)
||+|..|++.|.+...|..|++.|.
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 5777777777777777777777664
No 32
>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=97.69 E-value=3.5e-05 Score=36.12 Aligned_cols=23 Identities=30% Similarity=0.881 Sum_probs=14.1
Q ss_pred cccCcCchhcccHHHHHHHHHhc
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNRH 199 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h 199 (247)
|.|+.|++.|.+...|..|+.+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 45667777777777777776655
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.63 E-value=4.2e-05 Score=50.27 Aligned_cols=72 Identities=24% Similarity=0.410 Sum_probs=12.4
Q ss_pred ecccccccccCHHHHHHHHHHhCCCCceeccccccccCChHHHHHHHhhccCCCCeeCCCCCcccCChhHHHHHHHH
Q psy2288 38 ACNICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQRGILSSHLAV 114 (247)
Q Consensus 38 ~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 114 (247)
+|..|+..|++...|..|+...++...- ....+.....+..+...... ..+.|..|+..|.+...|..|++.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~-~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVK-ESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc----cccccccccccccccccccC-CCCCCCccCCCCcCHHHHHHHHcC
Confidence 3666666666666666666554432110 11111122222222221111 135555555555555555555554
No 34
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.60 E-value=4.1e-05 Score=37.17 Aligned_cols=25 Identities=40% Similarity=0.856 Sum_probs=17.4
Q ss_pred CcccCcCchhcccHHHHHHHHHhcC
Q psy2288 176 PFRCEYCDKTFTRQIIMKEHLNRHK 200 (247)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~ 200 (247)
+|+|..|++.|.+...|..|++.|.
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 4667777777777777777776654
No 35
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.41 E-value=0.00018 Score=39.58 Aligned_cols=32 Identities=19% Similarity=0.371 Sum_probs=18.2
Q ss_pred CCCCeecccccccccChHHHHHHHHhccCCCC
Q psy2288 201 GVQPYSCSHCDKTFFDAQSLNKHKLSHKTSAD 232 (247)
Q Consensus 201 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 232 (247)
.+.|..||+|+..+.+..+|.+|+...|+.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45677777777777777777777766665554
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.22 E-value=0.00029 Score=33.04 Aligned_cols=23 Identities=30% Similarity=0.704 Sum_probs=12.3
Q ss_pred eecccccccccChHHHHHHHHhcc
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSHK 228 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h~ 228 (247)
|+|+.|+.... ...|.+|++.++
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 45666666555 556666665544
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.21 E-value=0.00032 Score=33.28 Aligned_cols=23 Identities=35% Similarity=0.807 Sum_probs=13.0
Q ss_pred eecccccccccChHHHHHHHHhc
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
|+|+.|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34555666666555565555544
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.09 E-value=0.00036 Score=33.04 Aligned_cols=23 Identities=35% Similarity=0.714 Sum_probs=17.3
Q ss_pred eecccccccccChHHHHHHHHhc
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
|.|.+|+..|.+...|..|++++
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 56777888888888888777654
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.02 E-value=0.00075 Score=37.20 Aligned_cols=32 Identities=19% Similarity=0.435 Sum_probs=18.4
Q ss_pred CCCCcccCcCchhcccHHHHHHHHHhcCCCCC
Q psy2288 173 GVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQP 204 (247)
Q Consensus 173 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 204 (247)
.+.|-.|++|+..+.+..+|++|+...|+.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45566777777777777777777777666553
No 40
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.01 E-value=0.00012 Score=56.48 Aligned_cols=67 Identities=25% Similarity=0.509 Sum_probs=37.4
Q ss_pred CCccccCC--CccccCChHHHHHHHHH-hCCCCCcccCc--CchhcccHHHHHHHHHhcCCCCCeecccccccccChHHH
Q psy2288 146 IRHFACNV--CPFKFTTKSDLQRHQRS-HEGVKPFRCEY--CDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDAQSL 220 (247)
Q Consensus 146 ~~~~~C~~--C~~~~~~~~~l~~H~~~-h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 220 (247)
++||+|++ |++.|.+...|+-|+.- |..++..+=+. =-..| -...+||.|++|+|.+.+..+|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F------------~~~~KPYrCevC~KRYKNlNGL 414 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF------------SAKDKPYRCEVCDKRYKNLNGL 414 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc------------cccCCceeccccchhhccCccc
Confidence 58888875 88888888888888753 32222222111 00111 1224566666666666666555
Q ss_pred HHHH
Q psy2288 221 NKHK 224 (247)
Q Consensus 221 ~~H~ 224 (247)
.-|.
T Consensus 415 KYHr 418 (423)
T COG5189 415 KYHR 418 (423)
T ss_pred eecc
Confidence 5553
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.00 E-value=0.00081 Score=31.82 Aligned_cols=23 Identities=39% Similarity=0.915 Sum_probs=15.2
Q ss_pred cccCcCchhcccHHHHHHHHHhc
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNRH 199 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h 199 (247)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666777777777777766654
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.91 E-value=0.00068 Score=31.73 Aligned_cols=23 Identities=30% Similarity=0.764 Sum_probs=15.0
Q ss_pred cccCcCchhcccHHHHHHHHHhcC
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNRHK 200 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~ 200 (247)
|+|+.|+.... ...|..|++.++
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 56777777776 777777777654
No 43
>KOG1146|consensus
Probab=96.87 E-value=0.00026 Score=64.64 Aligned_cols=50 Identities=22% Similarity=0.204 Sum_probs=33.8
Q ss_pred cccCcCchhcc-cHHHHHHHHHhcC------CCCCeecccccccccChHHHHHHHHh
Q psy2288 177 FRCEYCDKTFT-RQIIMKEHLNRHK------GVQPYSCSHCDKTFFDAQSLNKHKLS 226 (247)
Q Consensus 177 ~~C~~C~~~f~-~~~~l~~H~~~h~------~~~~~~C~~C~~~f~~~~~l~~H~~~ 226 (247)
+.|-+|+...+ +...|..|..+-. ....|+|.+|....+.+.++..|.++
T Consensus 735 ~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~~~~c~l~~y~t~~kanfqlh~Kt 791 (1406)
T KOG1146|consen 735 FDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGDVPSCKLKPYATNTKANFQLHNKT 791 (1406)
T ss_pred HHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCCCCcceecccccccchhhhhhccc
Confidence 77888876544 3344555543321 12349999999999999999888765
No 44
>PRK04860 hypothetical protein; Provisional
Probab=96.86 E-value=0.00063 Score=48.49 Aligned_cols=38 Identities=29% Similarity=0.769 Sum_probs=26.0
Q ss_pred CCcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccC
Q psy2288 175 KPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFD 216 (247)
Q Consensus 175 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 216 (247)
-+|.|. |+. ....+++|.++|+++++|.|..|+..|..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 357776 765 45566777777777777777777776653
No 45
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.80 E-value=0.00043 Score=53.53 Aligned_cols=68 Identities=25% Similarity=0.408 Sum_probs=46.1
Q ss_pred CCceeccc--cccccCChHHHHHHHhhcc-CCCCeeCC--CCCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHH
Q psy2288 62 LGKFTCTV--CKKVFNNIKSLKTHSRIHT-GEKPFRCS--VCGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQL 136 (247)
Q Consensus 62 ~~~~~C~~--C~~~f~~~~~l~~H~~~~~-~~~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l 136 (247)
.+||+|++ |++.|.+...|+-|+..-+ ..+...-+ .--..| ....+||.|.+|++.+.+...|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F------------~~~~KPYrCevC~KRYKNlNGL 414 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF------------SAKDKPYRCEVCDKRYKNLNGL 414 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc------------cccCCceeccccchhhccCccc
Confidence 37899987 9999999999999976433 22211111 011112 3467889999999998888888
Q ss_pred HHHHH
Q psy2288 137 RLHEM 141 (247)
Q Consensus 137 ~~h~~ 141 (247)
+.|+.
T Consensus 415 KYHr~ 419 (423)
T COG5189 415 KYHRK 419 (423)
T ss_pred eeccc
Confidence 87764
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.56 E-value=0.0014 Score=30.98 Aligned_cols=22 Identities=32% Similarity=0.905 Sum_probs=15.2
Q ss_pred cccCcCchhcccHHHHHHHHHh
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNR 198 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~ 198 (247)
|.|.+|+..|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4577777777777777777654
No 47
>KOG1146|consensus
Probab=96.20 E-value=0.00049 Score=62.88 Aligned_cols=28 Identities=21% Similarity=0.425 Sum_probs=20.3
Q ss_pred CceeccccccccCChHHHHHHHhhccCC
Q psy2288 63 GKFTCTVCKKVFNNIKSLKTHSRIHTGE 90 (247)
Q Consensus 63 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 90 (247)
+.++|+.|++.|.....|..||+..+.+
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~ 491 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPE 491 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccc
Confidence 5677888887777777777777775444
No 48
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.16 E-value=0.0014 Score=31.69 Aligned_cols=22 Identities=36% Similarity=0.735 Sum_probs=15.8
Q ss_pred eecccccccccChHHHHHHHHh
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLS 226 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~ 226 (247)
|-|..|++.|.+...|..|+++
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 5677777777777777777655
No 49
>PRK04860 hypothetical protein; Provisional
Probab=96.14 E-value=0.0031 Score=45.01 Aligned_cols=37 Identities=22% Similarity=0.430 Sum_probs=32.7
Q ss_pred CCeecccccccccChHHHHHHHHhccCCCCCCCccccCCCc
Q psy2288 203 QPYSCSHCDKTFFDAQSLNKHKLSHKTSADPISSAKGSKLF 243 (247)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~ 243 (247)
-+|.|. |+. ....+.+|.++|.++++|.|..|++.+.
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 479998 998 6678899999999999999999988764
No 50
>KOG2231|consensus
Probab=95.88 E-value=0.042 Score=47.86 Aligned_cols=103 Identities=25% Similarity=0.565 Sum_probs=60.3
Q ss_pred CCCCCcccCChhHHHHHHHHhcCCCCeecCcC---ccccc------ChhHHHHHHHHhCC-CC----ccccCCCccccCC
Q psy2288 95 CSVCGKSFSQRGILSSHLAVHAGVKPHICKQC---GHAFT------QKSQLRLHEMRHGN-IR----HFACNVCPFKFTT 160 (247)
Q Consensus 95 C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C---~~~f~------~~~~l~~h~~~~~~-~~----~~~C~~C~~~~~~ 160 (247)
|..| ..|.....|+.|+...+.. +.|..| .+.|. ....|..|++.--. +. .-.|..|...|..
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld 194 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLD 194 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhcc
Confidence 4444 3444667777787433221 233332 22332 24556666654221 11 2468888888888
Q ss_pred hHHHHHHHHHhCCCCCcccCcC------chhcccHHHHHHHHHhcCCCCCeecc
Q psy2288 161 KSDLQRHQRSHEGVKPFRCEYC------DKTFTRQIIMKEHLNRHKGVQPYSCS 208 (247)
Q Consensus 161 ~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~~~~~C~ 208 (247)
...|.+|++.++ |.|..| +..|.....|..|.+.+| |.|.
T Consensus 195 ~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE 240 (669)
T KOG2231|consen 195 DDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCE 240 (669)
T ss_pred HHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----cccc
Confidence 888888887766 455555 345667778888887766 5555
No 51
>KOG2231|consensus
Probab=95.85 E-value=0.036 Score=48.26 Aligned_cols=47 Identities=26% Similarity=0.460 Sum_probs=27.7
Q ss_pred ecCcCcccccChhHHHHHHHHhCCCCccccCCCc------cccCChHHHHHHHHHhC
Q psy2288 122 ICKQCGHAFTQKSQLRLHEMRHGNIRHFACNVCP------FKFTTKSDLQRHQRSHE 172 (247)
Q Consensus 122 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~------~~~~~~~~l~~H~~~h~ 172 (247)
.|..|...|.....|..|++..+ |.|..|. .-|.....|..|.+..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 46677777777777776666433 4555553 22445566666665555
No 52
>KOG2785|consensus
Probab=95.68 E-value=0.053 Score=43.55 Aligned_cols=52 Identities=21% Similarity=0.505 Sum_probs=36.7
Q ss_pred CcccCcCchhcccHHHHHHHHHhcCCC-----------------------CCeeccccc---ccccChHHHHHHHHhc
Q psy2288 176 PFRCEYCDKTFTRQIIMKEHLNRHKGV-----------------------QPYSCSHCD---KTFFDAQSLNKHKLSH 227 (247)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~h 227 (247)
|-.|-.|+..+.+...-..||..+||- .-|.|-.|+ +.|.+......||...
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 456666777777766666777666652 247888888 8888888888888653
No 53
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.56 E-value=0.0031 Score=30.42 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=14.6
Q ss_pred eecccccccccCHHHHHHHHHH
Q psy2288 37 LACNICSMVFCDEIVLNKHVEE 58 (247)
Q Consensus 37 ~~C~~C~~~~~~~~~l~~H~~~ 58 (247)
|.|..|++.|.+...+..|+++
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 4567777777777777666654
No 54
>KOG2482|consensus
Probab=95.51 E-value=0.092 Score=41.53 Aligned_cols=24 Identities=25% Similarity=0.599 Sum_probs=18.6
Q ss_pred CeecccccccccChHHHHHHHHhc
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
.-.|-.|.-.|-....|..||.-+
T Consensus 334 ~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 334 KSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred ccccccccccccCcchhhhhcccc
Confidence 356788888888888888887554
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.31 E-value=0.016 Score=27.30 Aligned_cols=20 Identities=30% Similarity=0.780 Sum_probs=11.9
Q ss_pred eecccccccccChHHHHHHHH
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKL 225 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~ 225 (247)
.+|+.||..| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566666666 4555666654
No 56
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.19 E-value=0.042 Score=43.44 Aligned_cols=126 Identities=25% Similarity=0.493 Sum_probs=78.6
Q ss_pred eeCCC--CCcccCChhHHHHHHHHhcCCCCeecCcCc---ccccC------hhHHHHHHHHhCCC----CccccCCCccc
Q psy2288 93 FRCSV--CGKSFSQRGILSSHLAVHAGVKPHICKQCG---HAFTQ------KSQLRLHEMRHGNI----RHFACNVCPFK 157 (247)
Q Consensus 93 ~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~---~~f~~------~~~l~~h~~~~~~~----~~~~C~~C~~~ 157 (247)
|.|+. |..+...-..|..|.++.++. +.|.+|- +.|+. +..|+.|...-..+ -.-.|..|...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 66765 555444455677887766543 4566553 44543 34455554432211 12368899988
Q ss_pred cCChHHHHHHHHHhCCCCCcccCcCch-------hcccHHHHHHHHHhcCCCCCeeccc--c--c--ccccChHHHHHHH
Q psy2288 158 FTTKSDLQRHQRSHEGVKPFRCEYCDK-------TFTRQIIMKEHLNRHKGVQPYSCSH--C--D--KTFFDAQSLNKHK 224 (247)
Q Consensus 158 ~~~~~~l~~H~~~h~~~~~~~C~~C~~-------~f~~~~~l~~H~~~h~~~~~~~C~~--C--~--~~f~~~~~l~~H~ 224 (247)
|.+-..|.+|++..+. .|-+|++ .|....+|..|.+.-+ |-|.+ | | ..|.....|..|+
T Consensus 230 FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~~~~el~~h~ 301 (493)
T COG5236 230 FYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFPYHTELLEHL 301 (493)
T ss_pred ecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEeccHHHHHHHH
Confidence 9999999999887664 4666654 3667778888876533 55543 3 2 3788888899997
Q ss_pred Hhcc
Q psy2288 225 LSHK 228 (247)
Q Consensus 225 ~~h~ 228 (247)
...|
T Consensus 302 ~~~h 305 (493)
T COG5236 302 TRFH 305 (493)
T ss_pred HHHh
Confidence 6543
No 57
>KOG2785|consensus
Probab=95.17 E-value=0.093 Score=42.21 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=22.6
Q ss_pred CeecccccccccChHHHHHHHHhccCC
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSHKTS 230 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~ 230 (247)
|-.|-.|++.+.+...-..||..+|+-
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~Hgf 192 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGF 192 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCC
Confidence 578888999999988888999887664
No 58
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.77 E-value=0.062 Score=35.59 Aligned_cols=18 Identities=28% Similarity=0.643 Sum_probs=8.8
Q ss_pred CeecCcCcccccChhHHH
Q psy2288 120 PHICKQCGHAFTQKSQLR 137 (247)
Q Consensus 120 ~~~C~~C~~~f~~~~~l~ 137 (247)
|..|++|+....+...|.
T Consensus 15 P~~CpiCgLtLVss~HLA 32 (112)
T TIGR00622 15 PVECPICGLTLILSTHLA 32 (112)
T ss_pred CCcCCcCCCEEeccchHH
Confidence 344555555554444444
No 59
>KOG4173|consensus
Probab=94.65 E-value=0.025 Score=41.29 Aligned_cols=74 Identities=27% Similarity=0.687 Sum_probs=42.1
Q ss_pred ccccCC--CccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHHh-c---------CCCCCeec--cccccc
Q psy2288 148 HFACNV--CPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLNR-H---------KGVQPYSC--SHCDKT 213 (247)
Q Consensus 148 ~~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~-h---------~~~~~~~C--~~C~~~ 213 (247)
.+.|+. |-..|.+...+..|..+-++. .|..|.+.|.+..-|..|+.- | .|.-.|+| ..|+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 344543 455566666666665554443 566666666666666666532 2 23344666 336666
Q ss_pred ccChHHHHHHH
Q psy2288 214 FFDAQSLNKHK 224 (247)
Q Consensus 214 f~~~~~l~~H~ 224 (247)
|-+...-..|+
T Consensus 156 FkT~r~RkdH~ 166 (253)
T KOG4173|consen 156 FKTSRDRKDHM 166 (253)
T ss_pred hhhhhhhhhHH
Confidence 66666666665
No 60
>KOG2893|consensus
Probab=94.59 E-value=0.0093 Score=44.46 Aligned_cols=45 Identities=29% Similarity=0.743 Sum_probs=33.5
Q ss_pred cCcCchhcccHHHHHHHHHhcCCCCCeecccccccccChHHHHHH-HHhc
Q psy2288 179 CEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDAQSLNKH-KLSH 227 (247)
Q Consensus 179 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H-~~~h 227 (247)
|..|++.|.....|..|++..+ |+|-+|.+...+--.|..| |++|
T Consensus 13 cwycnrefddekiliqhqkakh----fkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceeehhhhh
Confidence 7778888888888888876533 8888888877777777777 4555
No 61
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.49 E-value=0.033 Score=28.51 Aligned_cols=24 Identities=29% Similarity=0.566 Sum_probs=19.0
Q ss_pred CeecccccccccChHHHHHHHHhc
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
+|.|.+|+..|.+...+..|+...
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 477888888888888888887553
No 62
>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=93.85 E-value=0.13 Score=34.25 Aligned_cols=25 Identities=24% Similarity=0.517 Sum_probs=16.3
Q ss_pred eec----ccccccccChHHHHHHHHhccC
Q psy2288 205 YSC----SHCDKTFFDAQSLNKHKLSHKT 229 (247)
Q Consensus 205 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 229 (247)
|.| +.|++.+.+...+.+|++.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 666 6666666666666666666543
No 63
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.80 E-value=0.011 Score=49.59 Aligned_cols=147 Identities=25% Similarity=0.397 Sum_probs=69.5
Q ss_pred CeeCCCCCcccCChhHHHHHHH--HhcCC--CCeecC--cCcccccChhHHHHHHHHhCCCCccccCC--CccccCChHH
Q psy2288 92 PFRCSVCGKSFSQRGILSSHLA--VHAGV--KPHICK--QCGHAFTQKSQLRLHEMRHGNIRHFACNV--CPFKFTTKSD 163 (247)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~h~~~~~~~~~~~C~~--C~~~~~~~~~ 163 (247)
++.|..|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...+....+..+.. +...+.....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLN 368 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccccC
Confidence 3455555555555555555555 45555 556665 46666665555555555555444444332 1111111110
Q ss_pred -----HHHHHHHhCCCCCcccC--cCchhcccHHHHHHHHHhcCCCC--CeecccccccccChHHHHHHHHhccCCCCCC
Q psy2288 164 -----LQRHQRSHEGVKPFRCE--YCDKTFTRQIIMKEHLNRHKGVQ--PYSCSHCDKTFFDAQSLNKHKLSHKTSADPI 234 (247)
Q Consensus 164 -----l~~H~~~h~~~~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~ 234 (247)
.......-.....+.+. .|...+.....+..|...+-... .+.+..|.+.+.....+..|++.+....+..
T Consensus 369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 448 (467)
T COG5048 369 NEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448 (467)
T ss_pred CCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCcee
Confidence 00000011112222222 24444445555555555544433 3455556666666666666666665555554
Q ss_pred Cccc
Q psy2288 235 SSAK 238 (247)
Q Consensus 235 c~~c 238 (247)
|...
T Consensus 449 ~~~~ 452 (467)
T COG5048 449 CSIL 452 (467)
T ss_pred eccc
Confidence 4433
No 64
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.56 E-value=0.072 Score=27.19 Aligned_cols=23 Identities=30% Similarity=0.834 Sum_probs=14.5
Q ss_pred ceecccccccccCHHHHHHHHHH
Q psy2288 36 SLACNICSMVFCDEIVLNKHVEE 58 (247)
Q Consensus 36 ~~~C~~C~~~~~~~~~l~~H~~~ 58 (247)
++.|.+|+..|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 45666666666666666666554
No 65
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.33 E-value=0.2 Score=33.25 Aligned_cols=109 Identities=17% Similarity=0.315 Sum_probs=53.3
Q ss_pred eeccccccccCChHHHHHHHhhccCCCCeeCCCCCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHHHhC
Q psy2288 65 FTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEMRHG 144 (247)
Q Consensus 65 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~ 144 (247)
|.||.|+..+ -+.|..|+.|+-+..+...|.+....--.-++|.= .... .
T Consensus 2 Y~CPrC~skv--------------C~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~e------v~~~----------~ 51 (112)
T TIGR00622 2 YFCPQCRAKV--------------CELPVECPICGLTLILSTHLARSYHHLFPLKAFQE------IPLE----------E 51 (112)
T ss_pred ccCCCCCCCc--------------cCCCCcCCcCCCEEeccchHHHhhhccCCCccccc------cccc----------c
Confidence 5677776543 23567788888887776666554321111111210 0000 0
Q ss_pred CCCccccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeeccccc
Q psy2288 145 NIRHFACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCD 211 (247)
Q Consensus 145 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 211 (247)
......|-.|+..|........ ..-.....|+|+.|...|-..-++..|...| .|+.|.
T Consensus 52 ~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh------~CPGC~ 110 (112)
T TIGR00622 52 YNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLH------CCPGCI 110 (112)
T ss_pred cCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCccccccchhhhhhcc------CCcCCC
Confidence 0111236666666654321000 0011233577777777777777777775444 366664
No 66
>KOG2482|consensus
Probab=93.31 E-value=0.38 Score=38.24 Aligned_cols=134 Identities=19% Similarity=0.301 Sum_probs=79.6
Q ss_pred ceeccccccccc-CHHHHHHHHHHhCCC----------------------CceeccccccccCChHHHHHHHhhccCC--
Q psy2288 36 SLACNICSMVFC-DEIVLNKHVEEHSTL----------------------GKFTCTVCKKVFNNIKSLKTHSRIHTGE-- 90 (247)
Q Consensus 36 ~~~C~~C~~~~~-~~~~l~~H~~~~~~~----------------------~~~~C~~C~~~f~~~~~l~~H~~~~~~~-- 90 (247)
..+|-+|...+. ..+....|+..-|+- ..+.|-.|.+.|.++..|+.||+.....
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 478999987654 567777776654321 2478999999999999999999753211
Q ss_pred CC--------eeCCCCCcccCChhHHHHHH--HHh---------------cCCCC--eecCcCcccccChhHHHHHHHHh
Q psy2288 91 KP--------FRCSVCGKSFSQRGILSSHL--AVH---------------AGVKP--HICKQCGHAFTQKSQLRLHEMRH 143 (247)
Q Consensus 91 ~~--------~~C~~C~~~f~~~~~l~~H~--~~~---------------~~~~~--~~C~~C~~~f~~~~~l~~h~~~~ 143 (247)
.| |.-.+-..+-++.. ...+. .+- .+..+ ..|..|.....+...|..|+...
T Consensus 224 nPknreYDkfyiINY~ev~ks~t~-~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~v 302 (423)
T KOG2482|consen 224 NPKNREYDKFYIINYLEVGKSWTI-VHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIV 302 (423)
T ss_pred CCCccccceEEEEeHhhcCCccch-hhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHH
Confidence 11 11111111111110 01111 000 01112 47888888777777788887643
Q ss_pred CC---------------------------CCccccCCCccccCChHHHHHHHHH
Q psy2288 144 GN---------------------------IRHFACNVCPFKFTTKSDLQRHQRS 170 (247)
Q Consensus 144 ~~---------------------------~~~~~C~~C~~~~~~~~~l~~H~~~ 170 (247)
+. ...-.|-.|...|.....|..|+.-
T Consensus 303 He~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 303 HEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred HHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 21 1124578889999999999999854
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.09 E-value=0.019 Score=48.07 Aligned_cols=149 Identities=26% Similarity=0.429 Sum_probs=92.3
Q ss_pred ceeccccccccCChHHHHHHHh--hccCC--CCeeCC--CCCcccCChhHHHHHHHHhcCCCCeecCcCc--ccccChhH
Q psy2288 64 KFTCTVCKKVFNNIKSLKTHSR--IHTGE--KPFRCS--VCGKSFSQRGILSSHLAVHAGVKPHICKQCG--HAFTQKSQ 135 (247)
Q Consensus 64 ~~~C~~C~~~f~~~~~l~~H~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~--~~f~~~~~ 135 (247)
++.|..|...|.....+..|.. .|..+ .++.|+ .|++.|.+...+..|...+....++.+..-. ..+.....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLN 368 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccccC
Confidence 5778888888888888888888 67777 788888 6888888888888888877777666654422 22221111
Q ss_pred H-----HHHHHHhCCCCccccC--CCccccCChHHHHHHHHHhCCCC--CcccCcCchhcccHHHHHHHHHhcCCCCCee
Q psy2288 136 L-----RLHEMRHGNIRHFACN--VCPFKFTTKSDLQRHQRSHEGVK--PFRCEYCDKTFTRQIIMKEHLNRHKGVQPYS 206 (247)
Q Consensus 136 l-----~~h~~~~~~~~~~~C~--~C~~~~~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~ 206 (247)
- ............+.+. .|...+.....+..|...+.... .+.+..|...+.....+..|++.+.-..++.
T Consensus 369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 448 (467)
T COG5048 369 NEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448 (467)
T ss_pred CCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCcee
Confidence 0 0000011112222222 24444455555555555555544 3556778888888888888888887776666
Q ss_pred cccccc
Q psy2288 207 CSHCDK 212 (247)
Q Consensus 207 C~~C~~ 212 (247)
|..+..
T Consensus 449 ~~~~~~ 454 (467)
T COG5048 449 CSILKS 454 (467)
T ss_pred eccccc
Confidence 655544
No 68
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.71 E-value=0.22 Score=39.53 Aligned_cols=77 Identities=21% Similarity=0.305 Sum_probs=39.3
Q ss_pred eeccc--ccccccCHHHHHHHHHHhCCCCceecccccc---ccC------ChHHHHHHHhhccCCC----CeeCCCCCcc
Q psy2288 37 LACNI--CSMVFCDEIVLNKHVEEHSTLGKFTCTVCKK---VFN------NIKSLKTHSRIHTGEK----PFRCSVCGKS 101 (247)
Q Consensus 37 ~~C~~--C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~---~f~------~~~~l~~H~~~~~~~~----~~~C~~C~~~ 101 (247)
|.||. |..+......|..|.+..+. .+.|.+|-. .|. ++..|+.|...-..+. --.|..|...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 45653 55555556677777776555 456666632 232 2233444433221111 1235566666
Q ss_pred cCChhHHHHHHHHh
Q psy2288 102 FSQRGILSSHLAVH 115 (247)
Q Consensus 102 f~~~~~l~~H~~~~ 115 (247)
|.+.+.|..|++..
T Consensus 230 FYdDDEL~~HcR~~ 243 (493)
T COG5236 230 FYDDDELRRHCRLR 243 (493)
T ss_pred ecChHHHHHHHHhh
Confidence 66666666665543
No 69
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.59 E-value=0.091 Score=26.59 Aligned_cols=8 Identities=38% Similarity=1.103 Sum_probs=3.6
Q ss_pred ccccCCCc
Q psy2288 148 HFACNVCP 155 (247)
Q Consensus 148 ~~~C~~C~ 155 (247)
++.||.|+
T Consensus 17 ~~~CP~Cg 24 (33)
T cd00350 17 PWVCPVCG 24 (33)
T ss_pred CCcCcCCC
Confidence 34444444
No 70
>KOG2893|consensus
Probab=92.38 E-value=0.034 Score=41.55 Aligned_cols=44 Identities=30% Similarity=0.544 Sum_probs=36.4
Q ss_pred eecccccccccCHHHHHHHHHHhCCCCceeccccccccCChHHHHHHH
Q psy2288 37 LACNICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKKVFNNIKSLKTHS 84 (247)
Q Consensus 37 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 84 (247)
-+|=+|++.|.+...|.+|++..+ |+|.+|.+...+--.|..|-
T Consensus 11 pwcwycnrefddekiliqhqkakh----fkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred ceeeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceeeh
Confidence 469999999999999999988754 78999998877777777663
No 71
>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=92.35 E-value=0.072 Score=25.32 Aligned_cols=9 Identities=33% Similarity=0.818 Sum_probs=4.9
Q ss_pred ccCcCchhc
Q psy2288 178 RCEYCDKTF 186 (247)
Q Consensus 178 ~C~~C~~~f 186 (247)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455555554
No 72
>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=92.06 E-value=0.33 Score=32.34 Aligned_cols=54 Identities=22% Similarity=0.600 Sum_probs=42.3
Q ss_pred CccccCCCccccCChHHHHHHHHHhCCC------------------------------------------CCccc----C
Q psy2288 147 RHFACNVCPFKFTTKSDLQRHQRSHEGV------------------------------------------KPFRC----E 180 (247)
Q Consensus 147 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~------------------------------------------~~~~C----~ 180 (247)
+-..|..|+.++.- +.+..|++..+.. ..|.| +
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~ 88 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPP 88 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCC
Confidence 44679999988765 7888888743311 12889 9
Q ss_pred cCchhcccHHHHHHHHHhcCC
Q psy2288 181 YCDKTFTRQIIMKEHLNRHKG 201 (247)
Q Consensus 181 ~C~~~f~~~~~l~~H~~~h~~ 201 (247)
.|++.+.+...+.+|++.+||
T Consensus 89 ~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 89 HCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCcEeccHHHHHHHHHHhcC
Confidence 999999999999999998775
No 73
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.54 E-value=0.18 Score=27.45 Aligned_cols=11 Identities=18% Similarity=0.658 Sum_probs=5.0
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 44444444433
No 74
>PHA00626 hypothetical protein
Probab=89.48 E-value=0.1 Score=29.45 Aligned_cols=13 Identities=23% Similarity=0.557 Sum_probs=6.6
Q ss_pred CCeeccccccccc
Q psy2288 203 QPYSCSHCDKTFF 215 (247)
Q Consensus 203 ~~~~C~~C~~~f~ 215 (247)
..|+|+.||..|+
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 3455555555553
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.24 E-value=0.16 Score=28.63 Aligned_cols=31 Identities=26% Similarity=0.427 Sum_probs=20.6
Q ss_pred hhcCCceecccccccccCHHHHHHHHHHhCC
Q psy2288 31 EAQQKSLACNICSMVFCDEIVLNKHVEEHST 61 (247)
Q Consensus 31 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~ 61 (247)
..++.-+.||-|+..|........|+...++
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3455667777777777777777777665444
No 76
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.03 E-value=0.26 Score=27.78 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=12.1
Q ss_pred CCCCeecccccccccChHHHHHHH
Q psy2288 201 GVQPYSCSHCDKTFFDAQSLNKHK 224 (247)
Q Consensus 201 ~~~~~~C~~C~~~f~~~~~l~~H~ 224 (247)
|+..+.||-||..|....+..+|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHh
Confidence 344455555555555555555554
No 77
>KOG4173|consensus
Probab=87.63 E-value=0.28 Score=35.97 Aligned_cols=84 Identities=24% Similarity=0.453 Sum_probs=49.9
Q ss_pred CeeCCC--CCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHHHhCCCCccccCCCccccCChHHHHHHHH
Q psy2288 92 PFRCSV--CGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEMRHGNIRHFACNVCPFKFTTKSDLQRHQR 169 (247)
Q Consensus 92 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 169 (247)
.+.|+. |...|.+...+..|..+.++. .|..|.+.|++...|..|+...+. +.| ...
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HD----------------s~F--qa~ 137 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHD----------------SLF--QAL 137 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHH----------------HHH--HHH
Confidence 356665 556666666666666544443 477777777777777777654221 000 112
Q ss_pred HhCCCCCcccC--cCchhcccHHHHHHHH
Q psy2288 170 SHEGVKPFRCE--YCDKTFTRQIIMKEHL 196 (247)
Q Consensus 170 ~h~~~~~~~C~--~C~~~f~~~~~l~~H~ 196 (247)
+..|...|+|- .|+..|.+...-..|+
T Consensus 138 veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 138 VERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred HHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 33455667773 4777777777777776
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.58 E-value=0.68 Score=32.74 Aligned_cols=12 Identities=17% Similarity=0.520 Sum_probs=6.1
Q ss_pred ceeccccccccc
Q psy2288 36 SLACNICSMVFC 47 (247)
Q Consensus 36 ~~~C~~C~~~~~ 47 (247)
.|.|+.|+..|.
T Consensus 99 ~Y~Cp~C~~~y~ 110 (147)
T smart00531 99 YYKCPNCQSKYT 110 (147)
T ss_pred EEECcCCCCEee
Confidence 455555555544
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=87.50 E-value=0.48 Score=27.25 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=16.2
Q ss_pred CcccCcCchhcccHHHHHHHHHhcCCCCCeecccccc
Q psy2288 176 PFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDK 212 (247)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 212 (247)
.|.|+.||.....+..--+ .-..+|+|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~~CR-----k~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCAKCR-----KLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhhhHH-----HcCCceECCCcCc
Confidence 3667777755443322111 1135677777764
No 80
>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=87.38 E-value=0.38 Score=24.49 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=5.5
Q ss_pred CCeecccccc
Q psy2288 203 QPYSCSHCDK 212 (247)
Q Consensus 203 ~~~~C~~C~~ 212 (247)
.|-.||+||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3456666654
No 81
>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=86.76 E-value=0.3 Score=32.43 Aligned_cols=29 Identities=24% Similarity=0.638 Sum_probs=15.3
Q ss_pred ccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccCh
Q psy2288 178 RCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDA 217 (247)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 217 (247)
.|+.||..|... +..|..||+||..|.-.
T Consensus 11 ~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 466666555533 13455666666655433
No 82
>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=86.68 E-value=0.82 Score=32.75 Aligned_cols=35 Identities=20% Similarity=0.379 Sum_probs=23.4
Q ss_pred hCCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccc
Q psy2288 171 HEGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTF 214 (247)
Q Consensus 171 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 214 (247)
.....-|.|+.|+..|+...++. .-|.||.||...
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 34455577888887777776663 248888888643
No 83
>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=86.56 E-value=0.61 Score=22.11 Aligned_cols=20 Identities=20% Similarity=0.388 Sum_probs=14.2
Q ss_pred eecccccccccChHHHHHHHH
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKL 225 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~ 225 (247)
..||+|++.+ ....+..|+-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3688888887 5567777764
No 84
>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=86.00 E-value=0.17 Score=27.18 Aligned_cols=29 Identities=28% Similarity=0.473 Sum_probs=15.9
Q ss_pred eecccccccccChHHHHHHHHhccCCCCCCCccccC
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSHKTSADPISSAKGS 240 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~ 240 (247)
|+|..||..|.....+ .. ..+..|+.||+
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 6677777666432221 11 45666777766
No 85
>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=85.79 E-value=0.87 Score=32.61 Aligned_cols=31 Identities=19% Similarity=0.382 Sum_probs=17.1
Q ss_pred CCceecccccccccCHHHHHHHHHHhCCCCceeccccccc
Q psy2288 34 QKSLACNICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKKV 73 (247)
Q Consensus 34 ~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 73 (247)
..-|.|+.|+..|+...++. ..|.||.||..
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 34466666666665555553 14666666654
No 86
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.68 E-value=0.94 Score=23.38 Aligned_cols=8 Identities=25% Similarity=1.057 Sum_probs=3.2
Q ss_pred cccccccc
Q psy2288 67 CTVCKKVF 74 (247)
Q Consensus 67 C~~C~~~f 74 (247)
|+.|+..|
T Consensus 5 Cp~C~~~y 12 (36)
T PF13717_consen 5 CPNCQAKY 12 (36)
T ss_pred CCCCCCEE
Confidence 34444333
No 87
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.43 E-value=0.89 Score=23.62 Aligned_cols=8 Identities=38% Similarity=0.995 Sum_probs=3.1
Q ss_pred cccccccc
Q psy2288 39 CNICSMVF 46 (247)
Q Consensus 39 C~~C~~~~ 46 (247)
||.|+..|
T Consensus 5 CP~C~~~f 12 (37)
T PF13719_consen 5 CPNCQTRF 12 (37)
T ss_pred CCCCCceE
Confidence 33343333
No 88
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=85.31 E-value=0.4 Score=36.59 Aligned_cols=27 Identities=26% Similarity=0.501 Sum_probs=22.8
Q ss_pred CCCeecccccccccChHHHHHHHHhcc
Q psy2288 202 VQPYSCSHCDKTFFDAQSLNKHKLSHK 228 (247)
Q Consensus 202 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 228 (247)
.+++.||.||........|..-.++|.
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecch
Confidence 478999999999999888888777773
No 89
>KOG2186|consensus
Probab=85.13 E-value=0.63 Score=35.44 Aligned_cols=48 Identities=25% Similarity=0.562 Sum_probs=33.0
Q ss_pred CeeCCCCCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHHH
Q psy2288 92 PFRCSVCGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEMR 142 (247)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~ 142 (247)
.|.|..||....- ..+..|+..-.+ ..|.|..|++.|.. ..+..|..-
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 3678888876554 446667766655 66888888888876 566667653
No 90
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.04 E-value=0.37 Score=26.72 Aligned_cols=10 Identities=20% Similarity=1.059 Sum_probs=5.3
Q ss_pred cccCcCchhc
Q psy2288 177 FRCEYCDKTF 186 (247)
Q Consensus 177 ~~C~~C~~~f 186 (247)
|.|..|++.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 4555555554
No 91
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.70 E-value=0.74 Score=26.57 Aligned_cols=9 Identities=33% Similarity=0.685 Sum_probs=4.5
Q ss_pred cccCCCccc
Q psy2288 149 FACNVCPFK 157 (247)
Q Consensus 149 ~~C~~C~~~ 157 (247)
|.|+.||..
T Consensus 26 F~CPnCG~~ 34 (59)
T PRK14890 26 FLCPNCGEV 34 (59)
T ss_pred eeCCCCCCe
Confidence 455555544
No 92
>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=84.62 E-value=0.3 Score=25.88 Aligned_cols=11 Identities=45% Similarity=1.135 Sum_probs=5.6
Q ss_pred eeccccccccc
Q psy2288 205 YSCSHCDKTFF 215 (247)
Q Consensus 205 ~~C~~C~~~f~ 215 (247)
|+|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 45555555443
No 93
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=84.13 E-value=1.1 Score=32.83 Aligned_cols=33 Identities=24% Similarity=0.547 Sum_probs=21.3
Q ss_pred CCCCcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccc
Q psy2288 173 GVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTF 214 (247)
Q Consensus 173 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 214 (247)
...-|.|+.|+..|+...++. .-|.|+.||...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 344577777777777666542 247777777644
No 94
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=83.24 E-value=0.17 Score=35.89 Aligned_cols=14 Identities=36% Similarity=0.532 Sum_probs=8.5
Q ss_pred cccCcCchhcccHH
Q psy2288 177 FRCEYCDKTFTRQI 190 (247)
Q Consensus 177 ~~C~~C~~~f~~~~ 190 (247)
++|+.||..|.+..
T Consensus 29 ~~c~~c~~~f~~~e 42 (154)
T PRK00464 29 RECLACGKRFTTFE 42 (154)
T ss_pred eeccccCCcceEeE
Confidence 56666666666543
No 95
>KOG2807|consensus
Probab=82.76 E-value=1.8 Score=34.34 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=13.8
Q ss_pred CCeecccccccccChHHHHHHHHhc
Q psy2288 203 QPYSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
..|+|+.|...|=---+.-.|-..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 3466666666665555555554333
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.75 E-value=1.2 Score=32.61 Aligned_cols=16 Identities=19% Similarity=0.389 Sum_probs=8.1
Q ss_pred ceecccccccccCHHH
Q psy2288 36 SLACNICSMVFCDEIV 51 (247)
Q Consensus 36 ~~~C~~C~~~~~~~~~ 51 (247)
-|.|+.|+..|+...+
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 4555555555544443
No 97
>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=82.35 E-value=1.2 Score=23.08 Aligned_cols=8 Identities=38% Similarity=1.032 Sum_probs=3.2
Q ss_pred cccccccc
Q psy2288 39 CNICSMVF 46 (247)
Q Consensus 39 C~~C~~~~ 46 (247)
|+.|+..|
T Consensus 5 CP~C~~~~ 12 (38)
T TIGR02098 5 CPNCKTSF 12 (38)
T ss_pred CCCCCCEE
Confidence 44444433
No 98
>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=82.10 E-value=0.7 Score=22.76 Aligned_cols=25 Identities=20% Similarity=0.692 Sum_probs=10.2
Q ss_pred ccCcCchhcccHHHHHHHHHhcCCCCCeeccccccc
Q psy2288 178 RCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKT 213 (247)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 213 (247)
.|+.|+..+.+ .+...|.|+.|+..
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 46666655554 33445777777654
No 99
>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=81.58 E-value=0.43 Score=26.92 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=5.6
Q ss_pred eeccccccccc
Q psy2288 205 YSCSHCDKTFF 215 (247)
Q Consensus 205 ~~C~~C~~~f~ 215 (247)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45555555443
No 100
>KOG2593|consensus
Probab=81.57 E-value=1.5 Score=36.21 Aligned_cols=37 Identities=22% Similarity=0.473 Sum_probs=17.4
Q ss_pred CCeecccccccccChHHHHHHHHhccCCCCCCCccccCCC
Q psy2288 203 QPYSCSHCDKTFFDAQSLNKHKLSHKTSADPISSAKGSKL 242 (247)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~ 242 (247)
.-|.||.|++.|+. |..-...-.....|.|..|++.+
T Consensus 127 ~~Y~Cp~C~kkyt~---Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTS---LEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccCCccccchhh---hHHHHhhcccCceEEEecCCCch
Confidence 34555555555542 33333333334455555555544
No 101
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=80.96 E-value=1 Score=24.69 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=3.7
Q ss_pred eecccccc
Q psy2288 205 YSCSHCDK 212 (247)
Q Consensus 205 ~~C~~C~~ 212 (247)
..|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 44444443
No 102
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=80.90 E-value=1.1 Score=32.24 Aligned_cols=11 Identities=36% Similarity=0.845 Sum_probs=5.9
Q ss_pred CCCCcccCcCc
Q psy2288 173 GVKPFRCEYCD 183 (247)
Q Consensus 173 ~~~~~~C~~C~ 183 (247)
++.|-.||+||
T Consensus 146 ge~P~~CPiCg 156 (166)
T COG1592 146 GEAPEVCPICG 156 (166)
T ss_pred CCCCCcCCCCC
Confidence 34455566665
No 103
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.53 E-value=0.24 Score=37.45 Aligned_cols=20 Identities=25% Similarity=0.589 Sum_probs=12.9
Q ss_pred CCceecccccccccCHHHHH
Q psy2288 34 QKSLACNICSMVFCDEIVLN 53 (247)
Q Consensus 34 ~~~~~C~~C~~~~~~~~~l~ 53 (247)
.+.+.||.|+..|.+...+.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CCceECCCCCCeeeeeEEEc
Confidence 35677888887777664433
No 104
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.49 E-value=0.44 Score=36.03 Aligned_cols=18 Identities=44% Similarity=0.680 Sum_probs=13.1
Q ss_pred CCceeccccccccCChHH
Q psy2288 62 LGKFTCTVCKKVFNNIKS 79 (247)
Q Consensus 62 ~~~~~C~~C~~~f~~~~~ 79 (247)
++.+.||+|+..|.+..-
T Consensus 3 ~k~~~CPvC~~~F~~~~v 20 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKV 20 (214)
T ss_pred CCceECCCCCCeeeeeEE
Confidence 356788888888876643
No 105
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=79.45 E-value=0.94 Score=26.27 Aligned_cols=25 Identities=20% Similarity=0.506 Sum_probs=11.0
Q ss_pred HHHHHHHHhcCCCCCeeccc----ccccc
Q psy2288 190 IIMKEHLNRHKGVQPYSCSH----CDKTF 214 (247)
Q Consensus 190 ~~l~~H~~~h~~~~~~~C~~----C~~~f 214 (247)
..|..|+...=...+..|++ |+..+
T Consensus 24 ~~l~~H~~~~C~~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 24 KELDDHLENECPKRPVPCPYSPYGCKERV 52 (60)
T ss_dssp CCHHHHHHTTSTTSEEE-SS----S--EE
T ss_pred HHHHHHHHccCCCCcEECCCCCCCCCCcc
Confidence 34555555443444555555 55554
No 106
>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=79.24 E-value=2.2 Score=23.00 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=13.3
Q ss_pred CCCeecccccccccCh----HHHHHHHHh
Q psy2288 202 VQPYSCSHCDKTFFDA----QSLNKHKLS 226 (247)
Q Consensus 202 ~~~~~C~~C~~~f~~~----~~l~~H~~~ 226 (247)
....+|.+|++.+... +.|..|++.
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 4456777777766553 567777743
No 107
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=79.20 E-value=1.1 Score=32.10 Aligned_cols=25 Identities=36% Similarity=0.818 Sum_probs=19.3
Q ss_pred CCcccCcCchhcccHHHHHHHHHhcCCCCCeecccccc
Q psy2288 175 KPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDK 212 (247)
Q Consensus 175 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 212 (247)
+.|.|++||+. +.|+.|-+||+||.
T Consensus 133 ~~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 36899999865 34578889999984
No 108
>KOG2186|consensus
Probab=78.44 E-value=2 Score=32.85 Aligned_cols=49 Identities=27% Similarity=0.552 Sum_probs=36.0
Q ss_pred eeccccccccCChHHHHHHHhhccCCCCeeCCCCCcccCChhHHHHHHHHhc
Q psy2288 65 FTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQRGILSSHLAVHA 116 (247)
Q Consensus 65 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 116 (247)
|.|..|+....- ..+..|+..-++ .-|.|--|+..|.. ..+..|..--+
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 789999987654 446668887776 56889999999987 55777765443
No 109
>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=78.32 E-value=1.9 Score=21.57 Aligned_cols=10 Identities=10% Similarity=0.039 Sum_probs=4.2
Q ss_pred CCCCccccCC
Q psy2288 232 DPISSAKGSK 241 (247)
Q Consensus 232 ~~~c~~c~~~ 241 (247)
+.+|..||..
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 3445555443
No 110
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.31 E-value=1.2 Score=38.38 Aligned_cols=9 Identities=22% Similarity=0.907 Sum_probs=5.4
Q ss_pred ccCCCcccc
Q psy2288 150 ACNVCPFKF 158 (247)
Q Consensus 150 ~C~~C~~~~ 158 (247)
.|..||...
T Consensus 215 ~C~~Cg~~~ 223 (505)
T TIGR00595 215 LCRSCGYIL 223 (505)
T ss_pred EhhhCcCcc
Confidence 566666553
No 111
>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=77.43 E-value=0.85 Score=23.56 Aligned_cols=31 Identities=13% Similarity=0.375 Sum_probs=16.0
Q ss_pred eecccccccccChHHHHHHHHhccCCCCCCCccccCCCc
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSHKTSADPISSAKGSKLF 243 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~ 243 (247)
..|+.||..|. +...-...+-.|..||+.|+
T Consensus 2 r~C~~Cg~~Yh--------~~~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYH--------IEFNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEE--------TTTB--SSTTBCTTTTEBEB
T ss_pred cCcCCCCCccc--------cccCCCCCCCccCCCCCeeE
Confidence 35666666663 33333445556666666543
No 112
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=76.13 E-value=7.3 Score=27.50 Aligned_cols=35 Identities=17% Similarity=0.604 Sum_probs=16.9
Q ss_pred ceeccccccccCChHHHHHHHhhccCCCCeeCCCCCccc
Q psy2288 64 KFTCTVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSF 102 (247)
Q Consensus 64 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 102 (247)
.|.||.|+..|.....+.. . . ....|.|+.||...
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~-~--d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQL-L--D-MDGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCCEeeHHHHHHh-c--C-CCCcEECCCCCCEE
Confidence 4666666666653332211 0 1 12336666666543
No 113
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.96 E-value=1.2 Score=25.70 Aligned_cols=38 Identities=24% Similarity=0.579 Sum_probs=16.7
Q ss_pred ccCcCchh-cccHHHHHHHHHhcCCCCCeeccccccccc
Q psy2288 178 RCEYCDKT-FTRQIIMKEHLNRHKGVQPYSCSHCDKTFF 215 (247)
Q Consensus 178 ~C~~C~~~-f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 215 (247)
+|.+|++. +.....+..-.......+.|-|++|.....
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva 42 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVA 42 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhc
Confidence 45555443 223333333333333344466666655443
No 114
>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=75.37 E-value=0.99 Score=34.53 Aligned_cols=39 Identities=21% Similarity=0.480 Sum_probs=19.0
Q ss_pred CCCceeccccccccCChHHHHHHHhh--ccCCCCeeCCCCCc
Q psy2288 61 TLGKFTCTVCKKVFNNIKSLKTHSRI--HTGEKPFRCSVCGK 100 (247)
Q Consensus 61 ~~~~~~C~~C~~~f~~~~~l~~H~~~--~~~~~~~~C~~C~~ 100 (247)
+-..|+|..|.. |.-..+--.|+.. ......|+|..|++
T Consensus 139 GGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNr 179 (314)
T PF06524_consen 139 GGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNR 179 (314)
T ss_pred CCeEEEeecCCC-eeeccchhhhhhhhhhhhccccccccccc
Confidence 444677877765 2233333344321 11223466666654
No 115
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=74.57 E-value=1.5 Score=29.69 Aligned_cols=13 Identities=15% Similarity=0.212 Sum_probs=6.6
Q ss_pred CCeeccccccccc
Q psy2288 203 QPYSCSHCDKTFF 215 (247)
Q Consensus 203 ~~~~C~~C~~~f~ 215 (247)
.|..|++||..|.
T Consensus 25 ~p~vcP~cg~~~~ 37 (129)
T TIGR02300 25 RPAVSPYTGEQFP 37 (129)
T ss_pred CCccCCCcCCccC
Confidence 4455555555543
No 116
>KOG2807|consensus
Probab=74.08 E-value=6.2 Score=31.51 Aligned_cols=88 Identities=20% Similarity=0.430 Sum_probs=55.0
Q ss_pred CCeeCCCCCcccCChhHHHHHHHHhcCCCCeecCcCcccccChhHHHHHHHHhCCCCcc------------ccCCCcccc
Q psy2288 91 KPFRCSVCGKSFSQRGILSSHLAVHAGVKPHICKQCGHAFTQKSQLRLHEMRHGNIRHF------------ACNVCPFKF 158 (247)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~------------~C~~C~~~~ 158 (247)
.-|.|++|+... -..|..|++|+....+...|.+-..-.-.-++| .|-.|+-.
T Consensus 275 ~Gy~CP~Ckakv--------------CsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~- 339 (378)
T KOG2807|consen 275 GGYFCPQCKAKV--------------CSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGE- 339 (378)
T ss_pred CceeCCcccCee--------------ecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccc-
Confidence 348899987653 245678999998887777766543321111221 15555222
Q ss_pred CChHHHHHHHHHhCCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeeccccc
Q psy2288 159 TTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCD 211 (247)
Q Consensus 159 ~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~ 211 (247)
..+.-.|.|+.|...|-..-+...|-..| -|+.|.
T Consensus 340 ------------~~~~~~y~C~~Ck~~FCldCDv~iHesLh------~CpgCe 374 (378)
T KOG2807|consen 340 ------------LLSSGRYRCESCKNVFCLDCDVFIHESLH------NCPGCE 374 (378)
T ss_pred ------------cCCCCcEEchhccceeeccchHHHHhhhh------cCCCcC
Confidence 12344589999999888888877885554 577776
No 117
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=73.77 E-value=3 Score=23.25 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=13.4
Q ss_pred CeecccccccccCh-----HHHHHHHH
Q psy2288 204 PYSCSHCDKTFFDA-----QSLNKHKL 225 (247)
Q Consensus 204 ~~~C~~C~~~f~~~-----~~l~~H~~ 225 (247)
...|..|++.++.. +.|.+|+.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 35666666665443 46777766
No 118
>PF12907 zf-met2: Zinc-binding
Probab=71.06 E-value=2.8 Score=22.20 Aligned_cols=27 Identities=22% Similarity=0.540 Sum_probs=13.7
Q ss_pred eeccccccccc---ChHHHHHHHHhccCCC
Q psy2288 205 YSCSHCDKTFF---DAQSLNKHKLSHKTSA 231 (247)
Q Consensus 205 ~~C~~C~~~f~---~~~~l~~H~~~h~~~~ 231 (247)
++|.+|-..|. +...|..|..+.|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 45666664333 3344666665544443
No 119
>PRK14873 primosome assembly protein PriA; Provisional
Probab=68.47 E-value=2.7 Score=37.61 Aligned_cols=11 Identities=18% Similarity=0.525 Sum_probs=6.4
Q ss_pred CCCeecccccc
Q psy2288 202 VQPYSCSHCDK 212 (247)
Q Consensus 202 ~~~~~C~~C~~ 212 (247)
.+...|.+||.
T Consensus 408 ~~~l~Ch~CG~ 418 (665)
T PRK14873 408 GGTPRCRWCGR 418 (665)
T ss_pred CCeeECCCCcC
Confidence 34566666664
No 120
>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=67.49 E-value=2.5 Score=19.62 Aligned_cols=8 Identities=38% Similarity=1.572 Sum_probs=4.5
Q ss_pred Ceeccccc
Q psy2288 204 PYSCSHCD 211 (247)
Q Consensus 204 ~~~C~~C~ 211 (247)
+|.||.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35555555
No 121
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=67.16 E-value=1.1 Score=27.30 Aligned_cols=19 Identities=26% Similarity=0.579 Sum_probs=11.2
Q ss_pred CCCeecc--cccccccChHHH
Q psy2288 202 VQPYSCS--HCDKTFFDAQSL 220 (247)
Q Consensus 202 ~~~~~C~--~C~~~f~~~~~l 220 (247)
+.-++|. +||..|.....+
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeeecCCCCCCCEEEEEEEE
Confidence 3446776 677777655443
No 122
>KOG2593|consensus
Probab=66.90 E-value=7.7 Score=32.31 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=22.1
Q ss_pred cCCceecccccccccCHHHHHHHHHHhCCCCceecccccc
Q psy2288 33 QQKSLACNICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKK 72 (247)
Q Consensus 33 ~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~ 72 (247)
....|.|+.|.+.|++...++. .-.....|.|..|+-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGG 161 (436)
T ss_pred ccccccCCccccchhhhHHHHh---hcccCceEEEecCCC
Confidence 3455777777777766555542 222334677777754
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=66.09 E-value=7.9 Score=36.94 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=6.7
Q ss_pred Ceecccccccc
Q psy2288 204 PYSCSHCDKTF 214 (247)
Q Consensus 204 ~~~C~~C~~~f 214 (247)
+|.|+.||...
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 46666666654
No 124
>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=65.85 E-value=3.9 Score=28.27 Aligned_cols=23 Identities=30% Similarity=0.602 Sum_probs=12.3
Q ss_pred eecccccccccChHHHHHHHHhccCC
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSHKTS 230 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h~~~ 230 (247)
..|-+||+.|. .|.+|+++|++-
T Consensus 73 i~clecGk~~k---~LkrHL~~~~gl 95 (132)
T PF05443_consen 73 IICLECGKKFK---TLKRHLRTHHGL 95 (132)
T ss_dssp EE-TBT--EES---BHHHHHHHTT-S
T ss_pred eEEccCCcccc---hHHHHHHHccCC
Confidence 67777777665 346777777554
No 125
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.53 E-value=1.5 Score=39.37 Aligned_cols=10 Identities=20% Similarity=0.677 Sum_probs=6.4
Q ss_pred cccCCCcccc
Q psy2288 149 FACNVCPFKF 158 (247)
Q Consensus 149 ~~C~~C~~~~ 158 (247)
..|..||+.+
T Consensus 436 l~C~~Cg~v~ 445 (730)
T COG1198 436 LLCRDCGYIA 445 (730)
T ss_pred eecccCCCcc
Confidence 3477777664
No 126
>PF14353 CpXC: CpXC protein
Probab=64.03 E-value=6.9 Score=26.82 Aligned_cols=10 Identities=30% Similarity=0.723 Sum_probs=5.2
Q ss_pred eccccccccc
Q psy2288 38 ACNICSMVFC 47 (247)
Q Consensus 38 ~C~~C~~~~~ 47 (247)
.||.|+..|.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 4555555443
No 127
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.29 E-value=10 Score=35.29 Aligned_cols=9 Identities=22% Similarity=0.512 Sum_probs=5.0
Q ss_pred cccCCCccc
Q psy2288 149 FACNVCPFK 157 (247)
Q Consensus 149 ~~C~~C~~~ 157 (247)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 456666654
No 128
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.07 E-value=8.5 Score=35.81 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=6.1
Q ss_pred eecCcCccc
Q psy2288 121 HICKQCGHA 129 (247)
Q Consensus 121 ~~C~~C~~~ 129 (247)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 467777766
No 129
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=63.06 E-value=10 Score=20.16 Aligned_cols=25 Identities=20% Similarity=0.428 Sum_probs=17.8
Q ss_pred ceecccccccccC--HHHHHHHHHHhC
Q psy2288 36 SLACNICSMVFCD--EIVLNKHVEEHS 60 (247)
Q Consensus 36 ~~~C~~C~~~~~~--~~~l~~H~~~~~ 60 (247)
...|+.|+..|.. ..+-..|.+-|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 3679999988764 466777776653
No 130
>PF15269 zf-C2H2_7: Zinc-finger
Probab=62.72 E-value=6.1 Score=21.26 Aligned_cols=23 Identities=26% Similarity=0.483 Sum_probs=17.7
Q ss_pred ceeccccccccCChHHHHHHHhh
Q psy2288 64 KFTCTVCKKVFNNIKSLKTHSRI 86 (247)
Q Consensus 64 ~~~C~~C~~~f~~~~~l~~H~~~ 86 (247)
.|+|-.|..+...++.|-.||+.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 37788888888888888888764
No 131
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=60.83 E-value=3.5 Score=18.83 Aligned_cols=6 Identities=33% Similarity=1.376 Sum_probs=2.7
Q ss_pred cccccc
Q psy2288 207 CSHCDK 212 (247)
Q Consensus 207 C~~C~~ 212 (247)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 132
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=60.79 E-value=11 Score=25.99 Aligned_cols=57 Identities=26% Similarity=0.568 Sum_probs=33.2
Q ss_pred hcCCceecccccccccCHHHHHHHHHHhCCCCceec---cccccccCChHHHHHHHhhccCCCCeeCCCCCcccCChh
Q psy2288 32 AQQKSLACNICSMVFCDEIVLNKHVEEHSTLGKFTC---TVCKKVFNNIKSLKTHSRIHTGEKPFRCSVCGKSFSQRG 106 (247)
Q Consensus 32 ~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C---~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 106 (247)
.+.+.|+|.+|..+..+...|. |-.| .+|+.-+ ..|+.|-..+ -.||.|..+|.+..
T Consensus 76 ~d~~lYeCnIC~etS~ee~FLK----------PneCCgY~iCn~Cy---a~LWK~~~~y-----pvCPvCkTSFKss~ 135 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERFLK----------PNECCGYSICNACY---ANLWKFCNLY-----PVCPVCKTSFKSSS 135 (140)
T ss_pred cCCCceeccCcccccchhhcCC----------cccccchHHHHHHH---HHHHHHcccC-----CCCCcccccccccc
Confidence 3457799999998876554332 3333 2233322 4456665433 34888888877654
No 133
>KOG2071|consensus
Probab=60.48 E-value=7.4 Score=33.79 Aligned_cols=42 Identities=24% Similarity=0.545 Sum_probs=0.0
Q ss_pred CCCCcccCcCchhcccHHHHHHHHHhc-----------------------------------------------------
Q psy2288 173 GVKPFRCEYCDKTFTRQIIMKEHLNRH----------------------------------------------------- 199 (247)
Q Consensus 173 ~~~~~~C~~C~~~f~~~~~l~~H~~~h----------------------------------------------------- 199 (247)
...+-+|..||..|........||..|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~dwh~r~n~~~r~s~~~~~sR~Wf~s~s~W~~~K~~e~t~e~~~~~~~~~~~~ 494 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDDWHRRKNTTIRGSSKWQKSRSWFPSKSGWLAAKAGEETDEKEKVEHEELQIK 494 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhhhhhhhhhhcccccccccccceeechhhhccccccccccccccccchhhcch
Q ss_pred --------------CCCCCeecccccccc
Q psy2288 200 --------------KGVQPYSCSHCDKTF 214 (247)
Q Consensus 200 --------------~~~~~~~C~~C~~~f 214 (247)
.++.+..|++|+..|
T Consensus 495 ~~~s~~~k~~~Vp~d~e~~~~C~IC~EkF 523 (579)
T KOG2071|consen 495 KELSLRSKYELVPADSERQASCPICQEKF 523 (579)
T ss_pred hhhhhhccceecccCcccccCCccccccc
No 134
>KOG4167|consensus
Probab=60.28 E-value=2.4 Score=37.50 Aligned_cols=27 Identities=33% Similarity=0.752 Sum_probs=24.1
Q ss_pred CeecccccccccChHHHHHHHHhccCC
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSHKTS 230 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~ 230 (247)
.|.|.+|++.|-...++..||++|..+
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 599999999999999999999999543
No 135
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=60.18 E-value=4.5 Score=25.46 Aligned_cols=11 Identities=27% Similarity=1.059 Sum_probs=5.3
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
+.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 44555554443
No 136
>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=59.19 E-value=8.8 Score=20.91 Aligned_cols=8 Identities=38% Similarity=1.128 Sum_probs=3.6
Q ss_pred eecccccc
Q psy2288 65 FTCTVCKK 72 (247)
Q Consensus 65 ~~C~~C~~ 72 (247)
+.||.|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 34444443
No 137
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=58.19 E-value=4.3 Score=28.61 Aligned_cols=33 Identities=18% Similarity=0.297 Sum_probs=23.5
Q ss_pred CeecccccccccChHHHHHHHHhccCCCCCCCccccCCCcCCC
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSHKTSADPISSAKGSKLFGGI 246 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~ 246 (247)
.|.|..||.... | .+.+..+.|+.|++.-|.+.
T Consensus 112 ~l~C~~Cg~~~~----~------~~~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 112 TLVCENCGHEVE----L------THPERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred eEecccCCCEEE----e------cCCCcCCCCCCCCCCeeeeC
Confidence 488998988542 1 23467888999988888753
No 138
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=54.13 E-value=5.4 Score=21.12 Aligned_cols=21 Identities=38% Similarity=0.719 Sum_probs=13.1
Q ss_pred CCCeecccccccccChHHHHH
Q psy2288 202 VQPYSCSHCDKTFFDAQSLNK 222 (247)
Q Consensus 202 ~~~~~C~~C~~~f~~~~~l~~ 222 (247)
.....|+.|+-.+.....|.+
T Consensus 17 ~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEEECCCCCeEEccHHHHHH
Confidence 344667777777666666643
No 139
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=53.58 E-value=8.5 Score=26.41 Aligned_cols=14 Identities=43% Similarity=1.196 Sum_probs=7.3
Q ss_pred CeecCcCcccccCh
Q psy2288 120 PHICKQCGHAFTQK 133 (247)
Q Consensus 120 ~~~C~~C~~~f~~~ 133 (247)
|++|..||+.|.+.
T Consensus 1 PH~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 1 PHQCTKCGRVFEDG 14 (131)
T ss_pred CcccCcCCCCcCCC
Confidence 34555555555543
No 140
>PRK05580 primosome assembly protein PriA; Validated
Probab=53.40 E-value=7.1 Score=35.25 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=3.7
Q ss_pred ccCCCccc
Q psy2288 150 ACNVCPFK 157 (247)
Q Consensus 150 ~C~~C~~~ 157 (247)
.|..||..
T Consensus 383 ~C~~Cg~~ 390 (679)
T PRK05580 383 LCRDCGWV 390 (679)
T ss_pred EhhhCcCc
Confidence 35555443
No 141
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=52.81 E-value=8.3 Score=24.46 Aligned_cols=12 Identities=50% Similarity=1.259 Sum_probs=5.7
Q ss_pred CeecCcCccccc
Q psy2288 120 PHICKQCGHAFT 131 (247)
Q Consensus 120 ~~~C~~C~~~f~ 131 (247)
|-.|..||..|.
T Consensus 58 Pa~CkkCGfef~ 69 (97)
T COG3357 58 PARCKKCGFEFR 69 (97)
T ss_pred ChhhcccCcccc
Confidence 334555555544
No 142
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.34 E-value=6.4 Score=25.86 Aligned_cols=12 Identities=17% Similarity=0.404 Sum_probs=6.1
Q ss_pred CCeecccccccc
Q psy2288 203 QPYSCSHCDKTF 214 (247)
Q Consensus 203 ~~~~C~~C~~~f 214 (247)
.|..||+||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 445555555554
No 143
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=51.08 E-value=7.3 Score=25.64 Aligned_cols=29 Identities=17% Similarity=0.455 Sum_probs=17.7
Q ss_pred ccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccCh
Q psy2288 178 RCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDA 217 (247)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 217 (247)
.||.|+..|.+.. ...|.||+|+..+...
T Consensus 4 ~CP~C~seytY~d-----------g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHD-----------GTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEec-----------CCeeECcccccccccc
Confidence 4677766666542 2347777777766544
No 144
>KOG3408|consensus
Probab=50.94 E-value=10 Score=25.48 Aligned_cols=28 Identities=21% Similarity=0.409 Sum_probs=23.2
Q ss_pred hcCCceecccccccccCHHHHHHHHHHh
Q psy2288 32 AQQKSLACNICSMVFCDEIVLNKHVEEH 59 (247)
Q Consensus 32 ~~~~~~~C~~C~~~~~~~~~l~~H~~~~ 59 (247)
+|...+-|-+|.+.|.+...|..|.++.
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 4556688999999999999999998763
No 145
>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=50.32 E-value=3.2 Score=22.26 Aligned_cols=29 Identities=14% Similarity=0.402 Sum_probs=15.1
Q ss_pred cccCcCchhcccHHHHHHHHHhcCCCCCeecccccccc
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTF 214 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 214 (247)
|.||.|+.... -.-.....+.|+.||...
T Consensus 1 m~Cp~Cg~~~~---------~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEI---------VFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEE---------EEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCce---------EEcCCCCeEECCCCCCEe
Confidence 46777776532 011223447888887654
No 146
>PF12773 DZR: Double zinc ribbon
Probab=49.43 E-value=10 Score=20.91 Aligned_cols=8 Identities=25% Similarity=0.850 Sum_probs=3.9
Q ss_pred eecccccc
Q psy2288 205 YSCSHCDK 212 (247)
Q Consensus 205 ~~C~~C~~ 212 (247)
..|+.|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 44555554
No 147
>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=48.54 E-value=13 Score=28.11 Aligned_cols=30 Identities=13% Similarity=0.291 Sum_probs=21.0
Q ss_pred CCCccccCCCccccCChHHHHHHHHHhCCC
Q psy2288 145 NIRHFACNVCPFKFTTKSDLQRHQRSHEGV 174 (247)
Q Consensus 145 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~ 174 (247)
.+..|.|+.|++.|........|+...|.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 344588999999998888888888776654
No 148
>KOG4167|consensus
Probab=47.73 E-value=5.5 Score=35.45 Aligned_cols=27 Identities=44% Similarity=0.775 Sum_probs=23.2
Q ss_pred CceeccccccccCChHHHHHHHhhccC
Q psy2288 63 GKFTCTVCKKVFNNIKSLKTHSRIHTG 89 (247)
Q Consensus 63 ~~~~C~~C~~~f~~~~~l~~H~~~~~~ 89 (247)
..|.|..|+++|....++..||++|..
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 358999999999999999999998853
No 149
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.71 E-value=8.8 Score=26.69 Aligned_cols=11 Identities=18% Similarity=0.987 Sum_probs=5.4
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
+.|+.||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 45555554443
No 150
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.74 E-value=5.8 Score=27.35 Aligned_cols=15 Identities=33% Similarity=0.864 Sum_probs=8.6
Q ss_pred CCCcccCcCchhccc
Q psy2288 174 VKPFRCEYCDKTFTR 188 (247)
Q Consensus 174 ~~~~~C~~C~~~f~~ 188 (247)
...|.|+.|++.|..
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 344666666666653
No 151
>KOG1280|consensus
Probab=46.53 E-value=20 Score=28.98 Aligned_cols=37 Identities=22% Similarity=0.524 Sum_probs=24.4
Q ss_pred CceecccccccccCHHHHHHHHHHhCCCCc--eeccccc
Q psy2288 35 KSLACNICSMVFCDEIVLNKHVEEHSTLGK--FTCTVCK 71 (247)
Q Consensus 35 ~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~--~~C~~C~ 71 (247)
..|.|++|+.+-.+...|..|+...|.+-. ..|++|.
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 367788888877777888888776554422 3455554
No 152
>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=46.48 E-value=17 Score=27.50 Aligned_cols=26 Identities=19% Similarity=0.483 Sum_probs=13.3
Q ss_pred ceecccccccccCHHHHHHHHHHhCC
Q psy2288 36 SLACNICSMVFCDEIVLNKHVEEHST 61 (247)
Q Consensus 36 ~~~C~~C~~~~~~~~~l~~H~~~~~~ 61 (247)
.|.|++|++.|........|+...|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 35566666666666666666555443
No 153
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=46.43 E-value=8.9 Score=21.57 Aligned_cols=20 Identities=25% Similarity=0.534 Sum_probs=7.4
Q ss_pred CcccCcCchhcccHHHHHHH
Q psy2288 176 PFRCEYCDKTFTRQIIMKEH 195 (247)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H 195 (247)
.|+|+.|...|=-.-++..|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp EE--TTTT--B-HHHHHTTT
T ss_pred eEECCCCCCccccCcChhhh
Confidence 35555555555544444444
No 154
>PRK10220 hypothetical protein; Provisional
Probab=46.30 E-value=11 Score=24.86 Aligned_cols=29 Identities=28% Similarity=0.677 Sum_probs=17.4
Q ss_pred ccCcCchhcccHHHHHHHHHhcCCCCCeecccccccccCh
Q psy2288 178 RCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFFDA 217 (247)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 217 (247)
.||.|+..|.+.. ...|.|++|+..++..
T Consensus 5 ~CP~C~seytY~d-----------~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYED-----------NGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcC-----------CCeEECCcccCcCCcc
Confidence 4666766665542 2347777777766544
No 155
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=46.04 E-value=11 Score=29.86 Aligned_cols=78 Identities=19% Similarity=0.449 Sum_probs=40.5
Q ss_pred CccccCCCccccCChHHHHHHHHH------------hCCCCCcccCcCchhcccHHHHHHHH-HhcCCCCCeeccccccc
Q psy2288 147 RHFACNVCPFKFTTKSDLQRHQRS------------HEGVKPFRCEYCDKTFTRQIIMKEHL-NRHKGVQPYSCSHCDKT 213 (247)
Q Consensus 147 ~~~~C~~C~~~~~~~~~l~~H~~~------------h~~~~~~~C~~C~~~f~~~~~l~~H~-~~h~~~~~~~C~~C~~~ 213 (247)
-|..||.|.-.+.....|.+-..- -...+.-.|-.|...|.-... |- ..-+....|+|+.|...
T Consensus 321 LPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~---~~~~~~~ss~rY~Ce~CK~~ 397 (421)
T COG5151 321 LPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPV---SPFDESTSSGRYQCELCKST 397 (421)
T ss_pred CCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCC---Ccccccccccceechhhhhh
Confidence 355677776665544444332211 011122346677666653321 10 00122345888888888
Q ss_pred ccChHHHHHHHHhc
Q psy2288 214 FFDAQSLNKHKLSH 227 (247)
Q Consensus 214 f~~~~~l~~H~~~h 227 (247)
|-.--+.-.|-..|
T Consensus 398 FC~dCdvfiHe~Lh 411 (421)
T COG5151 398 FCSDCDVFIHETLH 411 (421)
T ss_pred hhhhhHHHHHHHHh
Confidence 87777777776555
No 156
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=45.14 E-value=11 Score=21.66 Aligned_cols=14 Identities=21% Similarity=0.847 Sum_probs=7.5
Q ss_pred CCCCeecccccccc
Q psy2288 201 GVQPYSCSHCDKTF 214 (247)
Q Consensus 201 ~~~~~~C~~C~~~f 214 (247)
....|-|..|....
T Consensus 28 Pi~tYmC~eC~~RI 41 (56)
T PF09963_consen 28 PIHTYMCDECKERI 41 (56)
T ss_pred CCcceeChhHHHHH
Confidence 34446666665543
No 157
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.09 E-value=11 Score=17.70 Aligned_cols=7 Identities=29% Similarity=0.652 Sum_probs=3.6
Q ss_pred ccCCCcc
Q psy2288 150 ACNVCPF 156 (247)
Q Consensus 150 ~C~~C~~ 156 (247)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555554
No 158
>KOG3408|consensus
Probab=44.90 E-value=15 Score=24.71 Aligned_cols=27 Identities=26% Similarity=0.536 Sum_probs=22.2
Q ss_pred CCCCcccCcCchhcccHHHHHHHHHhc
Q psy2288 173 GVKPFRCEYCDKTFTRQIIMKEHLNRH 199 (247)
Q Consensus 173 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 199 (247)
|.-.|.|-.|.+-|.+...|..|.++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 344578999999999999999998763
No 159
>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=44.08 E-value=11 Score=22.54 Aligned_cols=9 Identities=44% Similarity=1.069 Sum_probs=2.5
Q ss_pred ccCCCcccc
Q psy2288 150 ACNVCPFKF 158 (247)
Q Consensus 150 ~C~~C~~~~ 158 (247)
.|..|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 345555555
No 160
>KOG1701|consensus
Probab=44.03 E-value=6.6 Score=32.61 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=20.7
Q ss_pred ecCcCcccccChhHHHHHHHHhCCCCccccCCCccccCChHH
Q psy2288 122 ICKQCGHAFTQKSQLRLHEMRHGNIRHFACNVCPFKFTTKSD 163 (247)
Q Consensus 122 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~ 163 (247)
.|..|++...-...-..=+...-...-|.|..|++.+.-.+.
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~F 317 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSF 317 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccc
Confidence 466666665544333333332222344666667666554433
No 161
>KOG1280|consensus
Probab=43.60 E-value=24 Score=28.59 Aligned_cols=40 Identities=18% Similarity=0.384 Sum_probs=27.1
Q ss_pred CCCCcccCcCchhcccHHHHHHHHHhcCCCCC--eecccccc
Q psy2288 173 GVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQP--YSCSHCDK 212 (247)
Q Consensus 173 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~--~~C~~C~~ 212 (247)
....|.|+.|+..=.+...|..|....+.+-+ -.|++|+-
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 34468888888877778888888876554432 45566654
No 162
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=42.15 E-value=18 Score=24.94 Aligned_cols=23 Identities=30% Similarity=0.374 Sum_probs=12.1
Q ss_pred eecccccccccChHHHHHHHHhccCC
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSHKTS 230 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h~~~ 230 (247)
..|-++|+.|- +|.+|+.+|++-
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCC
Confidence 45555555552 455555555543
No 163
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=41.98 E-value=13 Score=19.47 Aligned_cols=12 Identities=33% Similarity=1.060 Sum_probs=10.2
Q ss_pred Ceeccccccccc
Q psy2288 204 PYSCSHCDKTFF 215 (247)
Q Consensus 204 ~~~C~~C~~~f~ 215 (247)
||+|..|+..|=
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 789999998884
No 164
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=41.73 E-value=21 Score=19.91 Aligned_cols=38 Identities=24% Similarity=0.400 Sum_probs=18.4
Q ss_pred CCceecccccccccCHHHHHHHHHHhCC-CCceeccccc
Q psy2288 34 QKSLACNICSMVFCDEIVLNKHVEEHST-LGKFTCTVCK 71 (247)
Q Consensus 34 ~~~~~C~~C~~~~~~~~~l~~H~~~~~~-~~~~~C~~C~ 71 (247)
.+.+.|..||..|.--..=+.......- ..|-.|+.|-
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 3566777777765443333333222211 1355566664
No 165
>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=39.43 E-value=9.3 Score=24.36 Aligned_cols=9 Identities=22% Similarity=0.855 Sum_probs=4.1
Q ss_pred cccCCCccc
Q psy2288 149 FACNVCPFK 157 (247)
Q Consensus 149 ~~C~~C~~~ 157 (247)
|.|+.|++.
T Consensus 36 y~Cp~Cgk~ 44 (90)
T PF01780_consen 36 YTCPFCGKT 44 (90)
T ss_dssp BEESSSSSS
T ss_pred CcCCCCCCc
Confidence 444444433
No 166
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=39.43 E-value=35 Score=24.97 Aligned_cols=33 Identities=15% Similarity=0.532 Sum_probs=16.6
Q ss_pred CCCCCcccCcCchhcccHHHHHHHHHhcCCCCCeeccccccc
Q psy2288 172 EGVKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKT 213 (247)
Q Consensus 172 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 213 (247)
..+.-|.|+.|...++...++. ..|.||.||..
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~---------~~F~Cp~Cg~~ 141 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAME---------LGFTCPKCGED 141 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHH---------hCCCCCCCCch
Confidence 3444466666655555444332 12666666653
No 167
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.82 E-value=12 Score=21.36 Aligned_cols=9 Identities=56% Similarity=1.257 Sum_probs=4.4
Q ss_pred ecccccccc
Q psy2288 66 TCTVCKKVF 74 (247)
Q Consensus 66 ~C~~C~~~f 74 (247)
.|+.|++.|
T Consensus 7 ~C~~Cg~~~ 15 (54)
T PF14446_consen 7 KCPVCGKKF 15 (54)
T ss_pred cChhhCCcc
Confidence 345555544
No 168
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=38.29 E-value=14 Score=20.64 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=5.3
Q ss_pred Ceeccccccc
Q psy2288 204 PYSCSHCDKT 213 (247)
Q Consensus 204 ~~~C~~C~~~ 213 (247)
.+.|..||..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 4555555554
No 169
>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=37.96 E-value=19 Score=24.27 Aligned_cols=11 Identities=27% Similarity=0.806 Sum_probs=5.4
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 44555554444
No 170
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=37.51 E-value=21 Score=23.89 Aligned_cols=11 Identities=18% Similarity=0.426 Sum_probs=5.6
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 45555554444
No 171
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=37.35 E-value=19 Score=27.64 Aligned_cols=58 Identities=17% Similarity=0.433 Sum_probs=27.3
Q ss_pred CCeecCcCcccccChhHHHHHHHHhCCCCccccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccH
Q psy2288 119 KPHICKQCGHAFTQKSQLRLHEMRHGNIRHFACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQ 189 (247)
Q Consensus 119 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 189 (247)
..|.|..|...... +.......-.|..|.+.|.-... ..--|-.-|.|+.|+..|...
T Consensus 111 rqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rYDPVP~-----dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 111 RQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRYDPVPC-----DKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeeccccchHHHh--------ccCcccccccccccccccCCCcc-----ccccceeeeecccccccchhh
Confidence 45667776544321 11222233456666666532210 000122336777777777644
No 172
>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=36.88 E-value=5.3 Score=20.61 Aligned_cols=11 Identities=45% Similarity=1.138 Sum_probs=4.7
Q ss_pred CCCCCeecccc
Q psy2288 200 KGVQPYSCSHC 210 (247)
Q Consensus 200 ~~~~~~~C~~C 210 (247)
.|...|.|..|
T Consensus 25 ~G~qryrC~~C 35 (36)
T PF03811_consen 25 SGHQRYRCKDC 35 (36)
T ss_pred CCCEeEecCcC
Confidence 33344444444
No 173
>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=36.46 E-value=1.6e+02 Score=21.14 Aligned_cols=49 Identities=16% Similarity=0.313 Sum_probs=23.1
Q ss_pred ccccCCCccccCChHHHHHHHHHhCCCCCcccCc--CchhcccHHHHHHHHHh
Q psy2288 148 HFACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEY--CDKTFTRQIIMKEHLNR 198 (247)
Q Consensus 148 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~ 198 (247)
...||.|.-......-.. -.+.+...|+-.|.. |... .+...|++|.+.
T Consensus 80 ~L~CPLCRG~V~GWtvve-~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~ 130 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVVE-PARRFLNAKKRSCSQESCSFS-GTYSELRKHARS 130 (162)
T ss_pred cccCccccCceeceEEch-HHHHHhccCCccCcccccccc-cCHHHHHHHHHh
Confidence 356777755544332211 133334444445543 4322 244567777665
No 174
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=36.19 E-value=16 Score=24.52 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=4.6
Q ss_pred eeccccccccc
Q psy2288 205 YSCSHCDKTFF 215 (247)
Q Consensus 205 ~~C~~C~~~f~ 215 (247)
+.|..||+.|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 44444444443
No 175
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=36.01 E-value=23 Score=20.03 Aligned_cols=10 Identities=20% Similarity=0.889 Sum_probs=4.4
Q ss_pred cccCCCcccc
Q psy2288 149 FACNVCPFKF 158 (247)
Q Consensus 149 ~~C~~C~~~~ 158 (247)
+.|+.|+..|
T Consensus 29 W~C~~Cgh~w 38 (55)
T PF14311_consen 29 WKCPKCGHEW 38 (55)
T ss_pred EECCCCCCee
Confidence 4444444443
No 176
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=35.30 E-value=14 Score=19.55 Aligned_cols=12 Identities=17% Similarity=0.708 Sum_probs=8.6
Q ss_pred Cceecccccccc
Q psy2288 35 KSLACNICSMVF 46 (247)
Q Consensus 35 ~~~~C~~C~~~~ 46 (247)
++..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 457788888765
No 177
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=35.17 E-value=17 Score=23.26 Aligned_cols=12 Identities=42% Similarity=0.911 Sum_probs=6.3
Q ss_pred CcccCcCchhcc
Q psy2288 176 PFRCEYCDKTFT 187 (247)
Q Consensus 176 ~~~C~~C~~~f~ 187 (247)
.+.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PTZ00255 54 IWRCKGCKKTVA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 355555555544
No 178
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=35.11 E-value=36 Score=17.18 Aligned_cols=22 Identities=18% Similarity=0.422 Sum_probs=12.8
Q ss_pred eecccccccccChHHHHHHHHhc
Q psy2288 205 YSCSHCDKTFFDAQSLNKHKLSH 227 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h 227 (247)
+.|+.|+..+. .+.+..|+..-
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLekC 26 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLEKC 26 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHHHH
T ss_pred EECCCCcCCcc-hhhhHHHHHHH
Confidence 67777777654 44566666543
No 179
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=35.02 E-value=6.7 Score=23.81 Aligned_cols=9 Identities=22% Similarity=0.693 Sum_probs=3.0
Q ss_pred eeCCCCCcc
Q psy2288 93 FRCSVCGKS 101 (247)
Q Consensus 93 ~~C~~C~~~ 101 (247)
..|..|+..
T Consensus 42 v~Cg~C~~~ 50 (71)
T PF05495_consen 42 VICGKCRTE 50 (71)
T ss_dssp EEETTT--E
T ss_pred eECCCCCCc
Confidence 344444433
No 180
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=34.69 E-value=14 Score=19.81 Aligned_cols=13 Identities=46% Similarity=1.313 Sum_probs=8.2
Q ss_pred CCeeccccccccc
Q psy2288 203 QPYSCSHCDKTFF 215 (247)
Q Consensus 203 ~~~~C~~C~~~f~ 215 (247)
.|++|+.|++.|=
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 4688999998883
No 181
>KOG3214|consensus
Probab=34.49 E-value=11 Score=24.36 Aligned_cols=14 Identities=29% Similarity=0.724 Sum_probs=7.5
Q ss_pred CeecccccccccCh
Q psy2288 204 PYSCSHCDKTFFDA 217 (247)
Q Consensus 204 ~~~C~~C~~~f~~~ 217 (247)
-..|.+|+.+|++.
T Consensus 47 ~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 47 KASCRICEESFQTT 60 (109)
T ss_pred eeeeeehhhhhccc
Confidence 34555555555544
No 182
>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=34.46 E-value=21 Score=23.21 Aligned_cols=16 Identities=38% Similarity=0.941 Sum_probs=11.2
Q ss_pred cCCCCCeeccccccccc
Q psy2288 199 HKGVQPYSCSHCDKTFF 215 (247)
Q Consensus 199 h~~~~~~~C~~C~~~f~ 215 (247)
+.| ++++|++||..|.
T Consensus 75 ~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 75 EKG-KPKRCPECGHVFK 90 (97)
T ss_pred eCC-CceeCCCCCcEEE
Confidence 444 6788888887774
No 183
>PF14369 zf-RING_3: zinc-finger
Probab=34.29 E-value=25 Score=17.95 Aligned_cols=8 Identities=38% Similarity=1.011 Sum_probs=3.5
Q ss_pred cccccccc
Q psy2288 67 CTVCKKVF 74 (247)
Q Consensus 67 C~~C~~~f 74 (247)
||.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 44444333
No 184
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=33.22 E-value=32 Score=29.45 Aligned_cols=26 Identities=31% Similarity=0.534 Sum_probs=18.5
Q ss_pred CCeecccccccccChHHHHHHHHhcc
Q psy2288 203 QPYSCSHCDKTFFDAQSLNKHKLSHK 228 (247)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 228 (247)
+--.|+.|++.|.....+..|+...|
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhh
Confidence 34577888888888888888876533
No 185
>KOG2907|consensus
Probab=33.14 E-value=20 Score=23.88 Aligned_cols=12 Identities=25% Similarity=0.783 Sum_probs=6.3
Q ss_pred CeeCCCCCcccC
Q psy2288 92 PFRCSVCGKSFS 103 (247)
Q Consensus 92 ~~~C~~C~~~f~ 103 (247)
.|.|+.|+..|.
T Consensus 102 FYTC~kC~~k~~ 113 (116)
T KOG2907|consen 102 FYTCPKCKYKFT 113 (116)
T ss_pred EEEcCccceeee
Confidence 355555555543
No 186
>KOG2636|consensus
Probab=32.94 E-value=37 Score=28.60 Aligned_cols=29 Identities=17% Similarity=0.369 Sum_probs=19.1
Q ss_pred HhcCCCCCeeccccc-ccccChHHHHHHHH
Q psy2288 197 NRHKGVQPYSCSHCD-KTFFDAQSLNKHKL 225 (247)
Q Consensus 197 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 225 (247)
+.|.-...|.|.+|| +++.....+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 344445567777777 67777777777753
No 187
>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=32.66 E-value=24 Score=19.90 Aligned_cols=9 Identities=44% Similarity=0.796 Sum_probs=4.2
Q ss_pred cCCCccccC
Q psy2288 151 CNVCPFKFT 159 (247)
Q Consensus 151 C~~C~~~~~ 159 (247)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 444554444
No 188
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=32.63 E-value=35 Score=17.75 Aligned_cols=12 Identities=17% Similarity=0.586 Sum_probs=4.1
Q ss_pred Cceecccccccc
Q psy2288 35 KSLACNICSMVF 46 (247)
Q Consensus 35 ~~~~C~~C~~~~ 46 (247)
+.|-|..|+..+
T Consensus 2 ~ryyCdyC~~~~ 13 (38)
T PF06220_consen 2 PRYYCDYCKKYL 13 (38)
T ss_dssp -S-B-TTT--B-
T ss_pred cCeeccccccee
Confidence 346677777777
No 189
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.47 E-value=25 Score=23.79 Aligned_cols=10 Identities=30% Similarity=1.062 Sum_probs=4.5
Q ss_pred cccCcCchhc
Q psy2288 177 FRCEYCDKTF 186 (247)
Q Consensus 177 ~~C~~C~~~f 186 (247)
..|..|+..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 3455554433
No 190
>PRK04351 hypothetical protein; Provisional
Probab=32.42 E-value=17 Score=25.78 Aligned_cols=33 Identities=21% Similarity=0.690 Sum_probs=17.3
Q ss_pred CCcccCcCchhcccHHHHHHHHHhcCCCCCeeccccccccc
Q psy2288 175 KPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTFF 215 (247)
Q Consensus 175 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 215 (247)
-.|.|..|+..+... +.+ +...|.|..|+..+.
T Consensus 111 y~Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 111 YLYECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKLK 143 (149)
T ss_pred EEEECCCCCCEeeee-------eec-CCCcEEeCCCCcEee
Confidence 346776676544321 111 234577777766543
No 191
>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=32.05 E-value=17 Score=23.29 Aligned_cols=11 Identities=27% Similarity=0.972 Sum_probs=5.8
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
+.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (91)
T TIGR00280 54 WTCRKCGAKFA 64 (91)
T ss_pred EEcCCCCCEEe
Confidence 45555555443
No 192
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=31.83 E-value=43 Score=18.86 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=5.1
Q ss_pred ecccccccccCH
Q psy2288 38 ACNICSMVFCDE 49 (247)
Q Consensus 38 ~C~~C~~~~~~~ 49 (247)
.||.|+..|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 677777766544
No 193
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.47 E-value=25 Score=20.54 Aligned_cols=15 Identities=20% Similarity=0.611 Sum_probs=11.3
Q ss_pred cCCceeccccccccc
Q psy2288 33 QQKSLACNICSMVFC 47 (247)
Q Consensus 33 ~~~~~~C~~C~~~~~ 47 (247)
.+....|++|+..|.
T Consensus 45 ~~gev~CPYC~t~y~ 59 (62)
T COG4391 45 DEGEVVCPYCSTRYR 59 (62)
T ss_pred CCCcEecCccccEEE
Confidence 356678999998874
No 194
>COG2879 Uncharacterized small protein [Function unknown]
Probab=31.29 E-value=63 Score=19.03 Aligned_cols=20 Identities=15% Similarity=0.215 Sum_probs=12.9
Q ss_pred cChHHHHHHHHhccCCCCCC
Q psy2288 215 FDAQSLNKHKLSHKTSADPI 234 (247)
Q Consensus 215 ~~~~~l~~H~~~h~~~~~~~ 234 (247)
++..+...||+.+|..+|++
T Consensus 23 pdYdnYVehmr~~hPd~p~m 42 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKPPM 42 (65)
T ss_pred CcHHHHHHHHHHhCcCCCcc
Confidence 34456667777777776664
No 195
>COG1773 Rubredoxin [Energy production and conversion]
Probab=30.64 E-value=23 Score=20.24 Aligned_cols=14 Identities=21% Similarity=0.574 Sum_probs=10.4
Q ss_pred CeecccccccccCh
Q psy2288 204 PYSCSHCDKTFFDA 217 (247)
Q Consensus 204 ~~~C~~C~~~f~~~ 217 (247)
.|+|..||..|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 47888888887543
No 196
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.61 E-value=17 Score=22.18 Aligned_cols=32 Identities=16% Similarity=0.593 Sum_probs=16.5
Q ss_pred CcccCcCchhcccHHHHHHHHHhcCCCCCeecccccccc
Q psy2288 176 PFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKTF 214 (247)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 214 (247)
.|+|..|+..|. +..++ ++...-.|+.|+..+
T Consensus 12 ~Y~c~~cg~~~d----vvq~~---~ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRFD----VVQAM---TDDPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHHH----HHHhc---ccCccccChhhChHH
Confidence 367777776554 22222 223334677777633
No 197
>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=30.52 E-value=64 Score=19.08 Aligned_cols=6 Identities=50% Similarity=1.531 Sum_probs=2.2
Q ss_pred eCCCCC
Q psy2288 94 RCSVCG 99 (247)
Q Consensus 94 ~C~~C~ 99 (247)
.|+.||
T Consensus 48 ~C~~Cg 53 (69)
T PF07282_consen 48 TCPNCG 53 (69)
T ss_pred EcCCCC
Confidence 333333
No 198
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=30.09 E-value=20 Score=25.35 Aligned_cols=35 Identities=29% Similarity=0.859 Sum_probs=18.4
Q ss_pred CCCcccCcCchhcccHHHHHHHHHhcCCCCCeeccccccc
Q psy2288 174 VKPFRCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDKT 213 (247)
Q Consensus 174 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 213 (247)
..+|.|. |+..+.+. ++|=..-.|+ .|.|..|+..
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred ceeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 4456666 66554433 2333333444 5666666653
No 199
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.88 E-value=45 Score=19.13 Aligned_cols=7 Identities=43% Similarity=1.293 Sum_probs=2.9
Q ss_pred cccCcCc
Q psy2288 177 FRCEYCD 183 (247)
Q Consensus 177 ~~C~~C~ 183 (247)
|.|+.||
T Consensus 15 ~~Cp~cG 21 (55)
T PF13824_consen 15 FECPDCG 21 (55)
T ss_pred CcCCCCC
Confidence 3444443
No 200
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.79 E-value=31 Score=31.45 Aligned_cols=13 Identities=23% Similarity=0.514 Sum_probs=7.2
Q ss_pred CCCCcccCcCchh
Q psy2288 173 GVKPFRCEYCDKT 185 (247)
Q Consensus 173 ~~~~~~C~~C~~~ 185 (247)
...|..|+.||..
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 3445566666544
No 201
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.46 E-value=10 Score=26.73 Aligned_cols=14 Identities=29% Similarity=0.472 Sum_probs=9.5
Q ss_pred cccCcCchhcccHH
Q psy2288 177 FRCEYCDKTFTRQI 190 (247)
Q Consensus 177 ~~C~~C~~~f~~~~ 190 (247)
-+|+.|+..|++..
T Consensus 29 ReC~~C~~RFTTfE 42 (156)
T COG1327 29 RECLECGERFTTFE 42 (156)
T ss_pred hcccccccccchhh
Confidence 46777777777654
No 202
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=29.09 E-value=25 Score=19.40 Aligned_cols=36 Identities=14% Similarity=0.277 Sum_probs=17.6
Q ss_pred eecccccccccChHHHHHH-----HHhccCCCCCCCccccC
Q psy2288 205 YSCSHCDKTFFDAQSLNKH-----KLSHKTSADPISSAKGS 240 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H-----~~~h~~~~~~~c~~c~~ 240 (247)
|+|.+||..+.....-... ..-..-...+.|..|+.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSS
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCC
Confidence 7899999877655431100 01112245667777753
No 203
>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 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=28.45 E-value=16 Score=25.86 Aligned_cols=10 Identities=30% Similarity=1.089 Sum_probs=5.0
Q ss_pred eecccccccc
Q psy2288 205 YSCSHCDKTF 214 (247)
Q Consensus 205 ~~C~~C~~~f 214 (247)
|.|+.|+..+
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 5555555433
No 205
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=28.43 E-value=23 Score=20.01 Aligned_cols=11 Identities=18% Similarity=0.582 Sum_probs=7.5
Q ss_pred eeccccccccc
Q psy2288 205 YSCSHCDKTFF 215 (247)
Q Consensus 205 ~~C~~C~~~f~ 215 (247)
+.||+||..+.
T Consensus 1 i~CPyCge~~~ 11 (52)
T PF14255_consen 1 IQCPYCGEPIE 11 (52)
T ss_pred CCCCCCCCeeE
Confidence 36888887654
No 206
>KOG2272|consensus
Probab=28.32 E-value=41 Score=26.00 Aligned_cols=19 Identities=32% Similarity=0.766 Sum_probs=10.4
Q ss_pred HhCCCCccccCCCccccCC
Q psy2288 142 RHGNIRHFACNVCPFKFTT 160 (247)
Q Consensus 142 ~~~~~~~~~C~~C~~~~~~ 160 (247)
.|.....|.|..|.+-|..
T Consensus 215 KhWHveHFvCa~CekPFlG 233 (332)
T KOG2272|consen 215 KHWHVEHFVCAKCEKPFLG 233 (332)
T ss_pred cccchhheeehhcCCcccc
Confidence 3344455666666666543
No 207
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.26 E-value=12 Score=28.33 Aligned_cols=8 Identities=25% Similarity=0.646 Sum_probs=5.6
Q ss_pred ccCcCchh
Q psy2288 178 RCEYCDKT 185 (247)
Q Consensus 178 ~C~~C~~~ 185 (247)
.||.|..+
T Consensus 64 vCP~C~yA 71 (267)
T COG1655 64 VCPICYYA 71 (267)
T ss_pred EcchhhHH
Confidence 57888764
No 208
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.17 E-value=10 Score=24.58 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=5.7
Q ss_pred ccccCCCcccc
Q psy2288 148 HFACNVCPFKF 158 (247)
Q Consensus 148 ~~~C~~C~~~~ 158 (247)
.|.|+.||..-
T Consensus 22 ~FtCp~Cghe~ 32 (104)
T COG4888 22 TFTCPRCGHEK 32 (104)
T ss_pred eEecCccCCee
Confidence 35555555443
No 209
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.51 E-value=38 Score=28.50 Aligned_cols=29 Identities=24% Similarity=0.626 Sum_probs=16.9
Q ss_pred ccCCCccccCChHHHHHHHHHhCCCCCcccCcCchhcccH
Q psy2288 150 ACNVCPFKFTTKSDLQRHQRSHEGVKPFRCEYCDKTFTRQ 189 (247)
Q Consensus 150 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 189 (247)
.|+.||....+. |..-|+|+.|++.+...
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCcc
Confidence 577777554432 22267777777766644
No 210
>KOG0717|consensus
Probab=27.38 E-value=40 Score=28.67 Aligned_cols=22 Identities=41% Similarity=0.777 Sum_probs=18.0
Q ss_pred eeccccccccCChHHHHHHHhh
Q psy2288 65 FTCTVCKKVFNNIKSLKTHSRI 86 (247)
Q Consensus 65 ~~C~~C~~~f~~~~~l~~H~~~ 86 (247)
+-|++|+++|.+...+..|.+.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999888888888643
No 211
>PLN02294 cytochrome c oxidase subunit Vb
Probab=27.16 E-value=33 Score=24.78 Aligned_cols=14 Identities=21% Similarity=0.667 Sum_probs=10.8
Q ss_pred CCCeeccccccccc
Q psy2288 202 VQPYSCSHCDKTFF 215 (247)
Q Consensus 202 ~~~~~C~~C~~~f~ 215 (247)
.+++.|++||..|.
T Consensus 139 Gkp~RCpeCG~~fk 152 (174)
T PLN02294 139 GKSFECPVCTQYFE 152 (174)
T ss_pred CCceeCCCCCCEEE
Confidence 36788989988774
No 212
>KOG0717|consensus
Probab=27.09 E-value=36 Score=28.92 Aligned_cols=22 Identities=32% Similarity=0.688 Sum_probs=20.1
Q ss_pred cccCcCchhcccHHHHHHHHHh
Q psy2288 177 FRCEYCDKTFTRQIIMKEHLNR 198 (247)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~ 198 (247)
+.|.+|.++|.+..+|.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999865
No 213
>KOG4118|consensus
Probab=26.37 E-value=34 Score=20.22 Aligned_cols=26 Identities=19% Similarity=0.474 Sum_probs=18.1
Q ss_pred eecccccccccCHHHHHHHHHHhCCC
Q psy2288 37 LACNICSMVFCDEIVLNKHVEEHSTL 62 (247)
Q Consensus 37 ~~C~~C~~~~~~~~~l~~H~~~~~~~ 62 (247)
|+|..|-...++...+.+|..+.+..
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk 64 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPK 64 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCC
Confidence 66777777777777777777665543
No 214
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=26.14 E-value=15 Score=17.71 Aligned_cols=9 Identities=33% Similarity=1.025 Sum_probs=4.2
Q ss_pred ecCcCcccc
Q psy2288 122 ICKQCGHAF 130 (247)
Q Consensus 122 ~C~~C~~~f 130 (247)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344444444
No 215
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=25.90 E-value=24 Score=22.57 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=5.6
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
+.|..|++.|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PRK03976 55 WECRKCGAKFA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 45555555443
No 216
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=25.77 E-value=35 Score=22.26 Aligned_cols=13 Identities=38% Similarity=1.004 Sum_probs=7.9
Q ss_pred CeecccccccccC
Q psy2288 204 PYSCSHCDKTFFD 216 (247)
Q Consensus 204 ~~~C~~C~~~f~~ 216 (247)
|++|..||..|.+
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 4566666666655
No 217
>PRK00420 hypothetical protein; Validated
Probab=25.62 E-value=42 Score=22.52 Aligned_cols=9 Identities=22% Similarity=0.372 Sum_probs=4.9
Q ss_pred cccCcCchh
Q psy2288 177 FRCEYCDKT 185 (247)
Q Consensus 177 ~~C~~C~~~ 185 (247)
..|+.||..
T Consensus 41 ~~Cp~Cg~~ 49 (112)
T PRK00420 41 VVCPVHGKV 49 (112)
T ss_pred eECCCCCCe
Confidence 456666554
No 218
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=25.53 E-value=5.1 Score=21.18 Aligned_cols=7 Identities=43% Similarity=1.322 Sum_probs=2.8
Q ss_pred eeccccc
Q psy2288 65 FTCTVCK 71 (247)
Q Consensus 65 ~~C~~C~ 71 (247)
|.|..|+
T Consensus 29 y~C~~C~ 35 (40)
T smart00440 29 YVCTKCG 35 (40)
T ss_pred EEeCCCC
Confidence 3344443
No 219
>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=24.94 E-value=29 Score=19.41 Aligned_cols=36 Identities=17% Similarity=0.254 Sum_probs=19.8
Q ss_pred eecccccccccChHHHHHH-H----HhccCCCCCCCccccC
Q psy2288 205 YSCSHCDKTFFDAQSLNKH-K----LSHKTSADPISSAKGS 240 (247)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H-~----~~h~~~~~~~c~~c~~ 240 (247)
|+|.+||..+.-...-... . .--.-...+.|+.|+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 7899999988744211000 0 0001235678888864
No 220
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=24.92 E-value=68 Score=27.55 Aligned_cols=21 Identities=29% Similarity=0.656 Sum_probs=11.0
Q ss_pred eeccccccccCChHHHHHHHh
Q psy2288 65 FTCTVCKKVFNNIKSLKTHSR 85 (247)
Q Consensus 65 ~~C~~C~~~f~~~~~l~~H~~ 85 (247)
..|+.|.+.|.+...+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 445555555555555555544
No 221
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.92 E-value=82 Score=23.38 Aligned_cols=11 Identities=27% Similarity=0.640 Sum_probs=5.8
Q ss_pred ceecccccccc
Q psy2288 64 KFTCTVCKKVF 74 (247)
Q Consensus 64 ~~~C~~C~~~f 74 (247)
.+.|..|+.++
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 35555555554
No 222
>KOG0978|consensus
Probab=24.88 E-value=27 Score=31.44 Aligned_cols=10 Identities=30% Similarity=1.082 Sum_probs=6.0
Q ss_pred eecccccccc
Q psy2288 65 FTCTVCKKVF 74 (247)
Q Consensus 65 ~~C~~C~~~f 74 (247)
.+|+.|+..+
T Consensus 644 LkCs~Cn~R~ 653 (698)
T KOG0978|consen 644 LKCSVCNTRW 653 (698)
T ss_pred eeCCCccCch
Confidence 5677776444
No 223
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=24.72 E-value=32 Score=23.12 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=4.9
Q ss_pred cccCcCchhc
Q psy2288 177 FRCEYCDKTF 186 (247)
Q Consensus 177 ~~C~~C~~~f 186 (247)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4455555433
No 224
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=24.52 E-value=64 Score=18.28 Aligned_cols=31 Identities=16% Similarity=0.325 Sum_probs=17.2
Q ss_pred ecccccccccCHHHHHHHHHHhCCCCceecccccc
Q psy2288 38 ACNICSMVFCDEIVLNKHVEEHSTLGKFTCTVCKK 72 (247)
Q Consensus 38 ~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~ 72 (247)
.|.-|....+........ .++....|+.|+.
T Consensus 24 ~C~gC~~~l~~~~~~~i~----~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIR----KGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHH----cCCCeEECcCCCc
Confidence 577777766554433331 1244567777765
No 225
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=24.50 E-value=57 Score=26.61 Aligned_cols=30 Identities=13% Similarity=0.396 Sum_probs=21.4
Q ss_pred HhcCCCCCeeccccc-ccccChHHHHHHHHh
Q psy2288 197 NRHKGVQPYSCSHCD-KTFFDAQSLNKHKLS 226 (247)
Q Consensus 197 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~~ 226 (247)
+.|.-.+.|.|.+|| +++.....+.+|..-
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF~E 397 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHFEE 397 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhhhh
Confidence 445556678888888 777777778877644
No 226
>PRK12496 hypothetical protein; Provisional
Probab=24.43 E-value=47 Score=23.98 Aligned_cols=9 Identities=33% Similarity=0.925 Sum_probs=4.1
Q ss_pred ccCCCcccc
Q psy2288 150 ACNVCPFKF 158 (247)
Q Consensus 150 ~C~~C~~~~ 158 (247)
.|.-|++.|
T Consensus 129 ~C~gC~~~~ 137 (164)
T PRK12496 129 VCKGCKKKY 137 (164)
T ss_pred ECCCCCccc
Confidence 344444444
No 227
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=24.29 E-value=15 Score=24.61 Aligned_cols=9 Identities=22% Similarity=0.988 Sum_probs=3.9
Q ss_pred cccCcCchh
Q psy2288 177 FRCEYCDKT 185 (247)
Q Consensus 177 ~~C~~C~~~ 185 (247)
|.|..||..
T Consensus 101 y~C~~Cg~~ 109 (113)
T COG1594 101 YKCTRCGYR 109 (113)
T ss_pred EEecccCCE
Confidence 444444433
No 228
>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=24.02 E-value=32 Score=19.65 Aligned_cols=30 Identities=13% Similarity=0.267 Sum_probs=18.6
Q ss_pred CeecccccccccChHHHHHHHHhccCCCCCCCccccCC
Q psy2288 204 PYSCSHCDKTFFDAQSLNKHKLSHKTSADPISSAKGSK 241 (247)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~ 241 (247)
.|+|+.||..+.=.... ......|..||-.
T Consensus 2 ~~~CP~CG~~iev~~~~--------~GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPE--------LGELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCc--------cCCEEeCCCCCCE
Confidence 37899999977422211 1346678888754
No 229
>PRK11032 hypothetical protein; Provisional
Probab=23.62 E-value=33 Score=24.63 Aligned_cols=34 Identities=15% Similarity=0.291 Sum_probs=23.8
Q ss_pred CCeecccccccccChHHHHHHHHhccCCCCCCCccccCCCcCCC
Q psy2288 203 QPYSCSHCDKTFFDAQSLNKHKLSHKTSADPISSAKGSKLFGGI 246 (247)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~c~~~~~~~~ 246 (247)
..+.|..||... ...+.+..+-|+.||..-|.+.
T Consensus 123 G~LvC~~Cg~~~----------~~~~p~~i~pCp~C~~~~F~R~ 156 (160)
T PRK11032 123 GNLVCEKCHHHL----------AFYTPEVLPLCPKCGHDQFQRR 156 (160)
T ss_pred ceEEecCCCCEE----------EecCCCcCCCCCCCCCCeeeeC
Confidence 358888888743 2345677788888888887653
No 230
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.32 E-value=49 Score=29.82 Aligned_cols=13 Identities=15% Similarity=0.350 Sum_probs=8.3
Q ss_pred eecccccccccCh
Q psy2288 205 YSCSHCDKTFFDA 217 (247)
Q Consensus 205 ~~C~~C~~~f~~~ 217 (247)
--|+.||....+.
T Consensus 42 ~fC~~CG~~~~~~ 54 (645)
T PRK14559 42 AHCPNCGAETGTI 54 (645)
T ss_pred ccccccCCcccch
Confidence 4677777666555
No 231
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=23.13 E-value=1.1e+02 Score=22.91 Aligned_cols=12 Identities=17% Similarity=0.509 Sum_probs=5.7
Q ss_pred CcccCcCchhcc
Q psy2288 176 PFRCEYCDKTFT 187 (247)
Q Consensus 176 ~~~C~~C~~~f~ 187 (247)
...|..|+..+.
T Consensus 95 ~~~C~~C~~~~~ 106 (206)
T cd01410 95 IEVCKSCGPEYV 106 (206)
T ss_pred cccCCCCCCccc
Confidence 344555554443
No 232
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=23.04 E-value=86 Score=24.32 Aligned_cols=10 Identities=10% Similarity=-0.047 Sum_probs=5.4
Q ss_pred CCCCccccCC
Q psy2288 232 DPISSAKGSK 241 (247)
Q Consensus 232 ~~~c~~c~~~ 241 (247)
.+.|..|++.
T Consensus 143 ~p~Cp~Cgg~ 152 (244)
T PRK14138 143 VPRCDDCSGL 152 (244)
T ss_pred CCCCCCCCCe
Confidence 4556666543
No 233
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=23.00 E-value=77 Score=24.45 Aligned_cols=9 Identities=22% Similarity=0.276 Sum_probs=4.2
Q ss_pred CCCccccCC
Q psy2288 233 PISSAKGSK 241 (247)
Q Consensus 233 ~~c~~c~~~ 241 (247)
+.|+.|++.
T Consensus 143 p~C~~Cgg~ 151 (242)
T PRK00481 143 PRCPKCGGI 151 (242)
T ss_pred CCCCCCCCc
Confidence 335555443
No 234
>KOG1842|consensus
Probab=23.00 E-value=48 Score=28.00 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=12.9
Q ss_pred eecccccccccCHHHHHHHHHHhC
Q psy2288 37 LACNICSMVFCDEIVLNKHVEEHS 60 (247)
Q Consensus 37 ~~C~~C~~~~~~~~~l~~H~~~~~ 60 (247)
+.||+|...|.+...|..|....|
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhc
Confidence 445555555555555555555444
No 235
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=22.92 E-value=57 Score=18.77 Aligned_cols=12 Identities=17% Similarity=0.520 Sum_probs=4.4
Q ss_pred Cceecccccccc
Q psy2288 35 KSLACNICSMVF 46 (247)
Q Consensus 35 ~~~~C~~C~~~~ 46 (247)
.|+....|+-+|
T Consensus 23 ~PV~s~~C~H~f 34 (57)
T PF11789_consen 23 DPVKSKKCGHTF 34 (57)
T ss_dssp SEEEESSS--EE
T ss_pred CCcCcCCCCCee
Confidence 344444454444
No 236
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.36 E-value=74 Score=17.44 Aligned_cols=6 Identities=50% Similarity=1.425 Sum_probs=2.2
Q ss_pred eCCCCC
Q psy2288 94 RCSVCG 99 (247)
Q Consensus 94 ~C~~C~ 99 (247)
.|+.|+
T Consensus 22 vC~~Cg 27 (52)
T smart00661 22 VCRKCG 27 (52)
T ss_pred ECCcCC
Confidence 333333
No 237
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=22.22 E-value=28 Score=19.78 Aligned_cols=9 Identities=22% Similarity=0.567 Sum_probs=4.0
Q ss_pred CccccCCCc
Q psy2288 147 RHFACNVCP 155 (247)
Q Consensus 147 ~~~~C~~C~ 155 (247)
-|..|+.|.
T Consensus 27 fPlyCpKCK 35 (55)
T PF14205_consen 27 FPLYCPKCK 35 (55)
T ss_pred ccccCCCCC
Confidence 344444443
No 238
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.16 E-value=44 Score=16.78 Aligned_cols=10 Identities=30% Similarity=0.869 Sum_probs=5.0
Q ss_pred eecccccccc
Q psy2288 205 YSCSHCDKTF 214 (247)
Q Consensus 205 ~~C~~C~~~f 214 (247)
+.|..||.+|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4555555444
No 239
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=21.88 E-value=59 Score=21.71 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=6.4
Q ss_pred CCcccCcCchhc
Q psy2288 175 KPFRCEYCDKTF 186 (247)
Q Consensus 175 ~~~~C~~C~~~f 186 (247)
...+||.|++..
T Consensus 68 v~V~CP~C~K~T 79 (114)
T PF11023_consen 68 VQVECPNCGKQT 79 (114)
T ss_pred eeeECCCCCChH
Confidence 345566666543
No 240
>KOG2636|consensus
Probab=21.03 E-value=70 Score=27.09 Aligned_cols=27 Identities=19% Similarity=0.443 Sum_probs=16.1
Q ss_pred HhCCCCCcccCcCc-hhcccHHHHHHHH
Q psy2288 170 SHEGVKPFRCEYCD-KTFTRQIIMKEHL 196 (247)
Q Consensus 170 ~h~~~~~~~C~~C~-~~f~~~~~l~~H~ 196 (247)
.|.-...|.|.+|| +++.-+..+.+|-
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHh
Confidence 34455556666666 5556666666664
No 241
>KOG1842|consensus
Probab=20.83 E-value=63 Score=27.34 Aligned_cols=22 Identities=27% Similarity=0.623 Sum_probs=10.8
Q ss_pred cccCCCccccCChHHHHHHHHH
Q psy2288 149 FACNVCPFKFTTKSDLQRHQRS 170 (247)
Q Consensus 149 ~~C~~C~~~~~~~~~l~~H~~~ 170 (247)
|.||+|...|.+...|..|.-.
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhh
Confidence 4455555555555555554433
No 242
>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=20.58 E-value=9.1 Score=30.51 Aligned_cols=14 Identities=21% Similarity=0.683 Sum_probs=6.4
Q ss_pred CCCccccCCCcccc
Q psy2288 145 NIRHFACNVCPFKF 158 (247)
Q Consensus 145 ~~~~~~C~~C~~~~ 158 (247)
+.+-..|..|+..+
T Consensus 194 G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 194 GKRYLHCSLCGTEW 207 (290)
T ss_dssp -EEEEEETTT--EE
T ss_pred ccEEEEcCCCCCee
Confidence 34555666666554
No 243
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.56 E-value=18 Score=32.41 Aligned_cols=29 Identities=31% Similarity=0.865 Sum_probs=16.6
Q ss_pred ccCcCchhcccHHHHHHHHHhcCCCCCeecccccc
Q psy2288 178 RCEYCDKTFTRQIIMKEHLNRHKGVQPYSCSHCDK 212 (247)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 212 (247)
-|+.|.+.+.+..+-+-| -.|..|+.||=
T Consensus 153 lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP 181 (750)
T COG0068 153 LCPFCDKEYKDPLNRRFH------AQPIACPKCGP 181 (750)
T ss_pred CCHHHHHHhcCccccccc------cccccCcccCC
Confidence 366666666655544433 34566777764
No 244
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.47 E-value=60 Score=25.82 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=7.1
Q ss_pred eeccccccccc
Q psy2288 205 YSCSHCDKTFF 215 (247)
Q Consensus 205 ~~C~~C~~~f~ 215 (247)
|.|+.|.-.|-
T Consensus 256 yvCs~Clsi~C 266 (279)
T TIGR00627 256 FVCSVCLSVLC 266 (279)
T ss_pred EECCCccCCcC
Confidence 66666666554
No 245
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=20.40 E-value=1.2e+02 Score=23.15 Aligned_cols=11 Identities=18% Similarity=0.637 Sum_probs=5.1
Q ss_pred cccCcCchhcc
Q psy2288 177 FRCEYCDKTFT 187 (247)
Q Consensus 177 ~~C~~C~~~f~ 187 (247)
..|..|+..+.
T Consensus 114 ~~C~~C~~~~~ 124 (222)
T cd01413 114 AYCVNCGSKYD 124 (222)
T ss_pred ceECCCCCCcc
Confidence 44555554443
No 246
>KOG4377|consensus
Probab=20.40 E-value=45 Score=27.84 Aligned_cols=25 Identities=20% Similarity=0.408 Sum_probs=17.8
Q ss_pred eec--cccccccCChHHHHHHHhhccC
Q psy2288 65 FTC--TVCKKVFNNIKSLKTHSRIHTG 89 (247)
Q Consensus 65 ~~C--~~C~~~f~~~~~l~~H~~~~~~ 89 (247)
|.| +.|+..+..+.++..|.+.|-.
T Consensus 272 yhcl~e~C~ykr~~k~DvirH~~~hkk 298 (480)
T KOG4377|consen 272 YHCLNEYCFYKRGQKNDVIRHVEIHKK 298 (480)
T ss_pred hcccCccccccccchhhhHHHHHHHhh
Confidence 555 4588777778888888877643
No 247
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=20.19 E-value=51 Score=21.63 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=19.9
Q ss_pred CCceecccccccccCHHHHHHHHHH
Q psy2288 34 QKSLACNICSMVFCDEIVLNKHVEE 58 (247)
Q Consensus 34 ~~~~~C~~C~~~~~~~~~l~~H~~~ 58 (247)
-..+-|-+|.+.|.+...|..|.+.
T Consensus 53 lGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhcc
Confidence 3447788999999999888888765
Done!