Query psy12030
Match_columns 245
No_of_seqs 223 out of 1850
Neff 10.4
Searched_HMMs 46136
Date Fri Aug 16 16:51:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12030.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12030hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 4.7E-32 1E-36 204.5 5.9 124 120-244 129-254 (279)
2 KOG2462|consensus 100.0 6E-29 1.3E-33 187.7 7.0 136 67-227 128-265 (279)
3 KOG1074|consensus 99.9 1E-27 2.2E-32 203.8 2.4 79 122-201 606-693 (958)
4 KOG3623|consensus 99.9 1.6E-26 3.5E-31 193.7 2.2 100 70-170 211-329 (1007)
5 KOG3608|consensus 99.9 1.2E-25 2.5E-30 174.5 3.2 224 7-230 130-377 (467)
6 KOG3608|consensus 99.9 1.9E-24 4.2E-29 167.8 2.5 170 70-245 178-364 (467)
7 KOG1074|consensus 99.8 7.2E-22 1.6E-26 168.5 3.7 59 177-236 880-938 (958)
8 KOG3576|consensus 99.7 2E-18 4.4E-23 124.8 2.4 110 67-201 115-237 (267)
9 KOG3576|consensus 99.7 7.2E-18 1.6E-22 121.9 2.0 112 121-233 117-240 (267)
10 KOG3623|consensus 99.6 4.2E-17 9.2E-22 137.8 1.5 105 122-227 211-331 (1007)
11 PLN03086 PRLI-interacting fact 99.5 1.5E-13 3.3E-18 116.6 8.1 129 99-244 408-552 (567)
12 PLN03086 PRLI-interacting fact 99.3 5E-12 1.1E-16 107.5 8.9 145 69-230 407-565 (567)
13 PHA00733 hypothetical protein 99.3 6.8E-12 1.5E-16 87.6 4.7 80 148-230 38-124 (128)
14 PHA00733 hypothetical protein 99.2 4.9E-11 1.1E-15 83.3 4.7 78 122-201 41-124 (128)
15 PHA02768 hypothetical protein; 99.1 6.3E-11 1.4E-15 68.4 2.7 42 177-221 6-47 (55)
16 PHA02768 hypothetical protein; 99.0 9.8E-11 2.1E-15 67.6 1.7 37 206-244 6-42 (55)
17 KOG3993|consensus 98.9 2.2E-10 4.7E-15 92.1 0.1 160 69-230 267-483 (500)
18 PF13465 zf-H2C2_2: Zinc-finge 98.9 8.4E-10 1.8E-14 54.5 1.3 24 221-244 2-25 (26)
19 PHA00616 hypothetical protein 98.9 1E-09 2.2E-14 60.2 1.6 34 205-238 1-34 (44)
20 PF13465 zf-H2C2_2: Zinc-finge 98.8 2.7E-09 5.8E-14 52.7 2.0 26 191-217 1-26 (26)
21 KOG3993|consensus 98.8 4.5E-10 9.7E-15 90.4 -1.9 146 98-243 267-468 (500)
22 PHA00732 hypothetical protein 98.6 4.1E-08 8.9E-13 62.3 2.7 44 177-226 2-45 (79)
23 PHA00616 hypothetical protein 98.5 3.2E-08 6.9E-13 54.4 1.1 39 176-215 1-39 (44)
24 PHA00732 hypothetical protein 98.5 9.8E-08 2.1E-12 60.5 3.4 38 205-244 1-38 (79)
25 PF05605 zf-Di19: Drought indu 98.5 3.2E-07 6.9E-12 54.1 4.4 51 177-230 3-54 (54)
26 PF00096 zf-C2H2: Zinc finger, 98.2 1.2E-06 2.5E-11 41.9 1.7 22 206-227 1-22 (23)
27 PF13894 zf-C2H2_4: C2H2-type 98.0 3.4E-06 7.5E-11 40.6 2.0 24 206-229 1-24 (24)
28 PF00096 zf-C2H2: Zinc finger, 98.0 3.6E-06 7.8E-11 40.2 2.0 23 177-199 1-23 (23)
29 PF05605 zf-Di19: Drought indu 98.0 7.4E-06 1.6E-10 48.2 3.4 37 122-159 3-40 (54)
30 PF09237 GAGA: GAGA factor; I 98.0 4E-06 8.6E-11 47.1 1.7 41 193-233 12-52 (54)
31 PF13912 zf-C2H2_6: C2H2-type 97.9 5.2E-06 1.1E-10 41.3 1.7 26 205-230 1-26 (27)
32 PF12756 zf-C2H2_2: C2H2 type 97.8 1.1E-05 2.3E-10 54.1 2.4 71 124-199 2-73 (100)
33 PF13894 zf-C2H2_4: C2H2-type 97.8 1.9E-05 4.1E-10 37.9 2.4 24 177-200 1-24 (24)
34 PF12756 zf-C2H2_2: C2H2 type 97.8 1.7E-05 3.8E-10 53.1 2.5 69 71-144 1-73 (100)
35 PF13912 zf-C2H2_6: C2H2-type 97.6 3.6E-05 7.9E-10 38.2 1.5 26 69-94 1-26 (27)
36 COG5189 SFP1 Putative transcri 97.6 3.1E-05 6.7E-10 60.8 1.6 43 203-245 347-410 (423)
37 KOG2231|consensus 97.4 0.00032 7E-09 61.4 6.0 121 100-228 117-262 (669)
38 PF13909 zf-H2C2_5: C2H2-type 97.4 8.9E-05 1.9E-09 35.6 1.5 23 206-229 1-23 (24)
39 smart00355 ZnF_C2H2 zinc finge 97.4 0.00022 4.7E-09 34.7 2.5 23 206-228 1-23 (26)
40 PRK04860 hypothetical protein; 97.3 0.00014 3E-09 52.8 1.8 35 177-216 120-154 (160)
41 COG5189 SFP1 Putative transcri 97.2 8.9E-05 1.9E-09 58.3 0.5 25 202-226 395-419 (423)
42 PF12874 zf-met: Zinc-finger o 97.1 0.00029 6.3E-09 34.1 1.5 23 206-228 1-23 (25)
43 smart00355 ZnF_C2H2 zinc finge 97.0 0.00052 1.1E-08 33.2 2.0 24 177-200 1-24 (26)
44 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00089 1.9E-08 32.0 2.5 24 177-201 1-24 (24)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.00079 1.7E-08 33.3 1.3 22 206-227 2-23 (27)
46 KOG2231|consensus 96.7 0.0028 6.1E-08 55.7 5.2 115 99-229 100-236 (669)
47 PF09237 GAGA: GAGA factor; I 96.7 0.0018 3.9E-08 36.5 2.5 29 176-205 24-52 (54)
48 PF12874 zf-met: Zinc-finger o 96.7 0.0012 2.7E-08 31.8 1.6 23 177-199 1-23 (25)
49 PRK04860 hypothetical protein; 96.6 0.0018 3.9E-08 47.1 2.8 37 204-244 118-154 (160)
50 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0019 4.1E-08 31.9 1.8 22 70-91 2-23 (27)
51 COG5236 Uncharacterized conser 96.3 0.0059 1.3E-07 48.9 4.0 122 70-201 152-306 (493)
52 PF13913 zf-C2HC_2: zinc-finge 95.5 0.013 2.8E-07 28.3 2.0 20 206-226 3-22 (25)
53 smart00451 ZnF_U1 U1-like zinc 95.5 0.012 2.7E-07 30.8 2.0 23 205-227 3-25 (35)
54 KOG1146|consensus 95.4 0.0057 1.2E-07 57.3 1.0 103 127-229 442-613 (1406)
55 TIGR00622 ssl1 transcription f 95.4 0.046 1E-06 36.9 4.8 21 177-197 82-102 (112)
56 PF13913 zf-C2HC_2: zinc-finge 94.7 0.028 6.1E-07 27.1 1.9 19 178-197 4-22 (25)
57 smart00451 ZnF_U1 U1-like zinc 94.5 0.04 8.6E-07 28.8 2.3 24 175-198 2-25 (35)
58 cd00350 rubredoxin_like Rubred 94.3 0.026 5.7E-07 29.2 1.3 11 177-187 2-12 (33)
59 KOG2482|consensus 94.1 0.065 1.4E-06 43.1 3.7 24 69-92 195-218 (423)
60 COG5236 Uncharacterized conser 93.9 0.06 1.3E-06 43.4 3.1 74 152-230 222-306 (493)
61 COG5048 FOG: Zn-finger [Genera 93.8 0.019 4.1E-07 48.8 0.2 119 121-241 289-454 (467)
62 PF12013 DUF3505: Protein of u 93.7 0.18 4E-06 34.2 4.9 25 206-230 81-109 (109)
63 KOG1146|consensus 93.2 0.0068 1.5E-07 56.8 -3.6 29 203-232 1327-1355(1406)
64 KOG2785|consensus 93.0 0.26 5.7E-06 40.4 5.4 52 177-228 167-243 (390)
65 COG4049 Uncharacterized protei 92.8 0.044 9.5E-07 31.5 0.6 27 203-229 15-41 (65)
66 PF10571 UPF0547: Uncharacteri 92.7 0.1 2.2E-06 25.4 1.8 12 234-245 15-26 (26)
67 COG5048 FOG: Zn-finger [Genera 92.7 0.029 6.2E-07 47.7 -0.3 62 176-238 289-356 (467)
68 TIGR00622 ssl1 transcription f 92.6 0.17 3.7E-06 34.2 3.3 79 148-229 13-105 (112)
69 KOG2893|consensus 92.4 0.037 8E-07 42.2 -0.1 41 100-140 12-53 (341)
70 cd00729 rubredoxin_SM Rubredox 91.0 0.14 2.9E-06 26.7 1.2 10 204-213 17-26 (34)
71 COG2888 Predicted Zn-ribbon RN 91.0 0.19 4.2E-06 29.4 1.9 8 205-212 50-57 (61)
72 COG2888 Predicted Zn-ribbon RN 90.9 0.24 5.1E-06 29.1 2.2 9 99-107 28-36 (61)
73 TIGR02098 MJ0042_CXXC MJ0042 f 90.7 0.16 3.5E-06 27.1 1.4 12 71-82 4-15 (38)
74 COG4049 Uncharacterized protei 90.7 0.079 1.7E-06 30.5 0.2 31 64-94 12-42 (65)
75 KOG2893|consensus 90.6 0.062 1.3E-06 41.0 -0.5 47 179-230 13-59 (341)
76 KOG4173|consensus 90.5 0.096 2.1E-06 39.1 0.5 46 121-170 79-126 (253)
77 PF13717 zinc_ribbon_4: zinc-r 90.3 0.2 4.4E-06 26.5 1.5 8 122-129 26-33 (36)
78 PHA00626 hypothetical protein 90.1 0.21 4.6E-06 28.8 1.6 14 175-188 22-35 (59)
79 PF13719 zinc_ribbon_5: zinc-r 90.1 0.23 4.9E-06 26.5 1.6 9 122-130 26-34 (37)
80 COG1592 Rubrerythrin [Energy p 89.2 0.32 6.9E-06 35.5 2.3 22 177-212 135-156 (166)
81 smart00659 RPOLCX RNA polymera 89.1 0.22 4.7E-06 27.7 1.1 26 177-214 3-28 (44)
82 smart00531 TFIIE Transcription 88.4 0.34 7.4E-06 34.9 2.0 35 97-131 98-133 (147)
83 KOG2482|consensus 88.1 0.68 1.5E-05 37.5 3.6 24 206-229 280-303 (423)
84 PRK14890 putative Zn-ribbon RN 87.9 0.41 8.9E-06 28.2 1.7 8 205-212 48-55 (59)
85 KOG2186|consensus 87.7 0.28 6E-06 37.9 1.2 47 122-172 4-50 (276)
86 smart00834 CxxC_CXXC_SSSS Puta 87.3 0.16 3.4E-06 27.6 -0.2 11 177-187 6-16 (41)
87 COG1997 RPL43A Ribosomal prote 87.2 0.51 1.1E-05 30.1 2.0 33 149-189 34-66 (89)
88 TIGR02605 CxxC_CxxC_SSSS putat 86.9 0.18 3.8E-06 29.1 -0.2 29 177-213 6-34 (52)
89 PRK14890 putative Zn-ribbon RN 86.2 0.6 1.3E-05 27.5 1.8 10 98-107 25-34 (59)
90 PF09986 DUF2225: Uncharacteri 86.2 0.23 5E-06 38.2 0.1 13 177-189 49-61 (214)
91 KOG2186|consensus 85.9 0.48 1E-05 36.7 1.6 45 151-197 4-49 (276)
92 PF09538 FYDLN_acid: Protein o 85.9 0.68 1.5E-05 31.3 2.2 15 149-163 25-39 (108)
93 COG5151 SSL1 RNA polymerase II 85.6 0.73 1.6E-05 36.8 2.5 79 121-199 322-411 (421)
94 KOG4173|consensus 85.3 0.3 6.5E-06 36.5 0.3 75 69-170 79-166 (253)
95 PF02892 zf-BED: BED zinc fing 85.2 0.79 1.7E-05 25.3 2.0 26 203-228 14-43 (45)
96 PF03604 DNA_RNApol_7kD: DNA d 84.4 0.7 1.5E-05 23.7 1.3 10 205-214 17-26 (32)
97 TIGR00373 conserved hypothetic 84.2 1.2 2.7E-05 32.4 3.1 16 177-192 110-125 (158)
98 PRK06266 transcription initiat 84.2 0.6 1.3E-05 34.8 1.5 28 177-214 118-145 (178)
99 COG1592 Rubrerythrin [Energy p 83.6 0.83 1.8E-05 33.4 1.9 23 205-240 134-156 (166)
100 KOG2807|consensus 83.0 2.1 4.6E-05 34.6 4.1 23 177-199 346-368 (378)
101 COG1198 PriA Primosomal protei 82.7 1 2.3E-05 41.0 2.7 24 203-241 460-483 (730)
102 PF09538 FYDLN_acid: Protein o 82.1 1 2.3E-05 30.4 1.9 30 177-218 10-39 (108)
103 PF06524 NOA36: NOA36 protein; 82.0 0.91 2E-05 35.4 1.7 26 148-173 207-232 (314)
104 smart00614 ZnF_BED BED zinc fi 81.6 1.3 2.9E-05 25.2 1.9 21 206-226 19-44 (50)
105 PRK09678 DNA-binding transcrip 81.6 0.39 8.5E-06 29.8 -0.3 41 177-220 2-44 (72)
106 smart00531 TFIIE Transcription 81.5 0.94 2E-05 32.6 1.6 34 177-215 100-133 (147)
107 PRK04023 DNA polymerase II lar 80.0 2.5 5.3E-05 39.7 4.0 9 151-159 627-635 (1121)
108 PF09986 DUF2225: Uncharacteri 78.9 2.6 5.6E-05 32.5 3.4 57 13-82 5-61 (214)
109 COG1996 RPC10 DNA-directed RNA 78.9 0.98 2.1E-05 25.6 0.8 27 177-214 7-33 (49)
110 smart00734 ZnF_Rad18 Rad18-lik 78.6 2.1 4.5E-05 20.7 1.8 20 206-226 2-21 (26)
111 PF09723 Zn-ribbon_8: Zinc rib 78.1 0.54 1.2E-05 25.8 -0.4 12 70-81 6-17 (42)
112 TIGR00373 conserved hypothetic 78.0 1.3 2.9E-05 32.3 1.4 32 96-131 107-138 (158)
113 PF13240 zinc_ribbon_2: zinc-r 77.1 1 2.2E-05 21.1 0.4 6 236-241 16-21 (23)
114 PRK00464 nrdR transcriptional 76.2 0.82 1.8E-05 33.1 -0.0 13 122-134 29-41 (154)
115 PRK06266 transcription initiat 75.8 1.6 3.5E-05 32.5 1.4 31 97-131 116-146 (178)
116 PRK00398 rpoP DNA-directed RNA 75.8 0.91 2E-05 25.4 0.1 10 70-79 4-13 (46)
117 TIGR02300 FYDLN_acid conserved 75.1 2.4 5.2E-05 29.3 1.9 13 149-161 25-37 (129)
118 PF04959 ARS2: Arsenite-resist 74.6 1.2 2.7E-05 34.1 0.5 24 177-200 78-101 (214)
119 PF06524 NOA36: NOA36 protein; 74.2 1.6 3.4E-05 34.1 1.0 26 203-228 207-232 (314)
120 cd00730 rubredoxin Rubredoxin; 73.5 1.6 3.6E-05 24.9 0.7 7 177-183 35-41 (50)
121 PF12013 DUF3505: Protein of u 71.9 3.5 7.6E-05 27.9 2.2 25 177-201 81-109 (109)
122 PF15269 zf-C2H2_7: Zinc-finge 70.4 4.8 0.0001 22.2 2.0 21 206-226 21-41 (54)
123 smart00440 ZnF_C2C2 C2C2 Zinc 70.3 0.34 7.3E-06 26.3 -2.5 11 234-244 29-39 (40)
124 PF13878 zf-C2H2_3: zinc-finge 69.6 5.1 0.00011 21.8 2.1 23 206-228 14-38 (41)
125 TIGR00280 L37a ribosomal prote 69.0 2.7 5.9E-05 27.3 1.1 33 149-189 34-66 (91)
126 PF00301 Rubredoxin: Rubredoxi 68.3 3.4 7.4E-05 23.3 1.3 13 70-82 2-14 (47)
127 COG1773 Rubredoxin [Energy pro 68.2 2 4.4E-05 25.0 0.4 11 151-161 4-14 (55)
128 PF05443 ROS_MUCR: ROS/MUCR tr 68.1 2.9 6.2E-05 29.4 1.1 22 206-230 73-94 (132)
129 PTZ00255 60S ribosomal protein 68.1 3.5 7.5E-05 26.8 1.4 34 148-189 34-67 (90)
130 PF09845 DUF2072: Zn-ribbon co 68.0 3.9 8.5E-05 28.5 1.8 13 122-134 2-14 (131)
131 COG3357 Predicted transcriptio 67.6 4 8.6E-05 26.4 1.6 13 205-217 58-70 (97)
132 PF08274 PhnA_Zn_Ribbon: PhnA 67.2 1.6 3.4E-05 22.0 -0.2 9 204-212 18-26 (30)
133 PF07754 DUF1610: Domain of un 67.2 2.3 5E-05 20.1 0.4 8 205-212 16-23 (24)
134 PF01780 Ribosomal_L37ae: Ribo 67.2 1.7 3.7E-05 28.2 -0.1 32 149-188 34-65 (90)
135 PF12907 zf-met2: Zinc-binding 66.8 3.1 6.8E-05 22.5 0.9 27 206-232 2-31 (40)
136 cd00924 Cyt_c_Oxidase_Vb Cytoc 66.6 2.9 6.2E-05 27.7 0.9 12 204-215 78-89 (97)
137 PF14353 CpXC: CpXC protein 64.3 1.5 3.3E-05 30.6 -0.8 24 149-172 37-60 (128)
138 PF01096 TFIIS_C: Transcriptio 63.3 0.11 2.3E-06 28.1 -5.3 11 234-244 29-39 (39)
139 COG3091 SprT Zn-dependent meta 63.1 2.9 6.2E-05 29.9 0.4 32 176-213 117-148 (156)
140 PRK14714 DNA polymerase II lar 63.0 11 0.00024 36.6 4.2 8 151-158 668-675 (1337)
141 PRK03824 hypA hydrogenase nick 62.9 3 6.5E-05 29.5 0.5 13 177-189 71-83 (135)
142 PRK03976 rpl37ae 50S ribosomal 62.5 4.2 9.1E-05 26.4 1.0 32 149-188 35-66 (90)
143 KOG4167|consensus 62.4 1.6 3.5E-05 39.2 -1.2 27 68-94 791-817 (907)
144 KOG2593|consensus 60.7 6.6 0.00014 33.2 2.1 36 96-131 126-163 (436)
145 COG1571 Predicted DNA-binding 59.7 6.1 0.00013 33.5 1.8 12 205-216 367-378 (421)
146 KOG2785|consensus 59.4 8.6 0.00019 31.9 2.5 70 69-143 166-242 (390)
147 PRK00432 30S ribosomal protein 58.9 9 0.00019 21.9 1.9 11 175-185 36-46 (50)
148 KOG2907|consensus 58.5 4.1 8.9E-05 27.5 0.5 11 206-216 103-113 (116)
149 PRK04023 DNA polymerase II lar 58.5 11 0.00024 35.7 3.3 9 177-185 664-672 (1121)
150 PRK12380 hydrogenase nickel in 58.1 4.9 0.00011 27.5 0.8 11 177-187 71-81 (113)
151 COG3364 Zn-ribbon containing p 58.1 7.6 0.00016 25.7 1.6 12 151-162 3-14 (112)
152 TIGR00595 priA primosomal prot 57.3 6.9 0.00015 34.4 1.8 10 152-161 215-224 (505)
153 PLN02294 cytochrome c oxidase 57.0 5.7 0.00012 29.1 1.0 13 203-215 139-151 (174)
154 COG1594 RPB9 DNA-directed RNA 55.5 8.2 0.00018 26.4 1.6 10 69-78 72-81 (113)
155 COG4888 Uncharacterized Zn rib 55.1 1.8 3.9E-05 28.5 -1.6 35 177-216 23-57 (104)
156 COG3677 Transposase and inacti 55.0 10 0.00022 26.6 2.0 13 205-217 53-65 (129)
157 PF13451 zf-trcl: Probable zin 55.0 6.7 0.00015 22.3 0.9 15 204-218 3-17 (49)
158 PF05290 Baculo_IE-1: Baculovi 53.6 5.4 0.00012 27.9 0.5 24 135-164 112-135 (140)
159 TIGR00100 hypA hydrogenase nic 53.3 5.8 0.00013 27.2 0.6 11 177-187 71-81 (115)
160 PF08271 TF_Zn_Ribbon: TFIIB z 53.2 3.7 8E-05 22.5 -0.3 9 122-130 20-28 (43)
161 PF13824 zf-Mss51: Zinc-finger 53.1 14 0.00031 21.6 2.0 16 203-218 12-27 (55)
162 PRK14873 primosome assembly pr 53.1 9.3 0.0002 34.9 2.0 49 98-185 383-431 (665)
163 PF14446 Prok-RING_1: Prokaryo 53.0 6.4 0.00014 22.9 0.6 8 206-213 22-29 (54)
164 KOG3214|consensus 52.9 2.8 6E-05 27.5 -1.0 12 206-217 48-59 (109)
165 KOG4167|consensus 52.7 2.8 6E-05 37.8 -1.3 24 206-229 793-816 (907)
166 PF12760 Zn_Tnp_IS1595: Transp 52.5 10 0.00022 21.1 1.4 8 151-158 19-26 (46)
167 PF07295 DUF1451: Protein of u 51.8 5.4 0.00012 28.6 0.2 27 205-241 112-138 (146)
168 PF04959 ARS2: Arsenite-resist 50.5 13 0.00029 28.5 2.2 25 148-172 75-99 (214)
169 COG1998 RPS31 Ribosomal protei 49.8 14 0.0003 21.0 1.6 10 176-185 37-46 (51)
170 TIGR00595 priA primosomal prot 49.7 10 0.00022 33.4 1.6 39 98-161 213-251 (505)
171 PRK05978 hypothetical protein; 49.7 6.1 0.00013 28.4 0.3 10 207-216 54-63 (148)
172 PF02176 zf-TRAF: TRAF-type zi 48.9 9.4 0.0002 22.3 1.0 39 177-216 10-53 (60)
173 COG1198 PriA Primosomal protei 48.7 6.2 0.00013 36.2 0.2 19 98-130 435-453 (730)
174 PRK00564 hypA hydrogenase nick 48.3 11 0.00024 25.9 1.3 10 177-186 72-81 (117)
175 COG4530 Uncharacterized protei 47.7 11 0.00025 25.2 1.3 14 148-161 24-37 (129)
176 PF07649 C1_3: C1-like domain; 47.0 8.9 0.00019 19.0 0.6 7 177-183 16-22 (30)
177 cd00065 FYVE FYVE domain; Zinc 46.6 17 0.00036 21.0 1.8 28 178-218 4-31 (57)
178 smart00154 ZnF_AN1 AN1-like Zi 46.3 10 0.00022 20.3 0.8 14 205-218 12-25 (39)
179 PF03811 Zn_Tnp_IS1: InsA N-te 45.6 4.4 9.4E-05 21.4 -0.8 30 206-239 6-35 (36)
180 COG2331 Uncharacterized protei 45.5 13 0.00029 23.1 1.2 30 177-214 13-42 (82)
181 COG4957 Predicted transcriptio 45.3 15 0.00032 25.8 1.5 22 206-230 77-98 (148)
182 COG1675 TFA1 Transcription ini 45.1 34 0.00073 25.5 3.5 11 177-187 114-124 (176)
183 PRK03681 hypA hydrogenase nick 44.7 12 0.00026 25.6 1.1 9 177-185 71-79 (114)
184 PF01363 FYVE: FYVE zinc finge 44.5 13 0.00029 22.5 1.2 11 70-80 10-20 (69)
185 PF08792 A2L_zn_ribbon: A2L zi 44.4 9.5 0.00021 19.6 0.4 11 233-243 21-31 (33)
186 KOG2593|consensus 44.0 19 0.00042 30.5 2.3 33 205-240 128-160 (436)
187 PHA02998 RNA polymerase subuni 44.0 3.3 7.1E-05 30.4 -1.8 11 206-216 172-182 (195)
188 smart00661 RPOL9 RNA polymeras 43.1 10 0.00022 21.4 0.5 13 205-217 20-32 (52)
189 smart00064 FYVE Protein presen 43.0 16 0.00035 22.1 1.4 28 177-217 11-38 (68)
190 PF03107 C1_2: C1 domain; Int 42.9 18 0.00038 18.0 1.3 7 177-183 16-22 (30)
191 KOG1280|consensus 42.9 22 0.00047 29.3 2.4 36 177-213 80-117 (381)
192 PF14311 DUF4379: Domain of un 42.7 20 0.00044 20.7 1.7 15 177-191 29-43 (55)
193 PF07282 OrfB_Zn_ribbon: Putat 42.4 15 0.00033 22.3 1.2 28 178-216 30-57 (69)
194 PF05191 ADK_lid: Adenylate ki 41.5 20 0.00044 18.8 1.4 11 70-80 2-12 (36)
195 KOG3408|consensus 41.2 13 0.00028 25.5 0.8 23 205-227 57-79 (129)
196 COG0068 HypF Hydrogenase matur 40.3 18 0.00038 33.0 1.7 40 16-55 126-165 (750)
197 KOG4377|consensus 39.6 23 0.00049 29.9 2.1 101 122-229 272-427 (480)
198 KOG3352|consensus 39.5 15 0.00033 26.3 1.0 12 204-215 132-143 (153)
199 KOG4124|consensus 39.3 9.4 0.0002 31.3 -0.1 42 203-244 347-409 (442)
200 COG1655 Uncharacterized protei 38.8 8.4 0.00018 29.7 -0.4 9 177-185 63-71 (267)
201 PF03833 PolC_DP2: DNA polymer 37.9 11 0.00023 35.0 0.0 12 203-214 678-689 (900)
202 PRK05580 primosome assembly pr 37.8 20 0.00044 32.9 1.7 20 98-131 381-400 (679)
203 TIGR01206 lysW lysine biosynth 37.0 16 0.00034 21.3 0.6 10 70-79 3-12 (54)
204 PF10013 DUF2256: Uncharacteri 36.6 30 0.00066 18.9 1.6 12 178-189 10-21 (42)
205 PF01215 COX5B: Cytochrome c o 36.6 6.3 0.00014 27.8 -1.3 13 203-215 110-122 (136)
206 PF06220 zf-U1: U1 zinc finger 36.5 33 0.00071 18.2 1.7 21 205-225 3-25 (38)
207 PF01155 HypA: Hydrogenase exp 36.3 11 0.00025 25.6 -0.1 12 177-188 71-82 (113)
208 PF13453 zf-TFIIB: Transcripti 36.2 18 0.0004 19.4 0.8 14 99-112 20-33 (41)
209 KOG0978|consensus 35.7 22 0.00048 32.4 1.6 20 205-224 678-697 (698)
210 KOG0782|consensus 35.5 4.1 8.8E-05 35.7 -2.8 51 84-135 240-290 (1004)
211 PF01927 Mut7-C: Mut7-C RNAse 35.3 41 0.00089 24.1 2.7 17 177-193 125-141 (147)
212 TIGR01384 TFS_arch transcripti 35.0 4.3 9.4E-05 27.1 -2.3 11 234-244 91-101 (104)
213 PF08790 zf-LYAR: LYAR-type C2 34.6 7.8 0.00017 19.1 -0.8 9 178-186 2-10 (28)
214 PF07975 C1_4: TFIIH C1-like d 34.5 23 0.00049 20.4 1.0 22 151-172 22-43 (51)
215 PF04216 FdhE: Protein involve 34.2 4.4 9.5E-05 32.8 -2.8 8 177-184 239-246 (290)
216 PF04780 DUF629: Protein of un 34.1 29 0.00063 30.1 2.0 26 205-230 57-82 (466)
217 KOG3408|consensus 33.9 21 0.00045 24.6 0.8 27 66-92 54-80 (129)
218 PF14445 Prok-RING_2: Prokaryo 33.8 14 0.00029 21.0 -0.0 10 206-215 8-17 (57)
219 COG1779 C4-type Zn-finger prot 33.8 16 0.00035 27.5 0.4 12 177-188 44-55 (201)
220 KOG0717|consensus 33.5 24 0.00052 30.4 1.3 22 206-227 293-314 (508)
221 COG1656 Uncharacterized conser 33.1 53 0.0011 24.1 2.9 16 177-192 131-146 (165)
222 KOG1280|consensus 32.9 38 0.00083 27.9 2.3 37 148-184 77-117 (381)
223 PF01428 zf-AN1: AN1-like Zinc 32.7 13 0.00027 20.4 -0.3 15 204-218 12-26 (43)
224 KOG0782|consensus 32.1 4.7 0.0001 35.3 -3.0 54 53-112 237-290 (1004)
225 KOG2636|consensus 31.7 31 0.00068 29.5 1.7 29 197-226 394-423 (497)
226 KOG1842|consensus 31.6 20 0.00043 30.6 0.6 29 68-96 14-42 (505)
227 PF14205 Cys_rich_KTR: Cystein 31.5 17 0.00037 21.1 0.1 8 233-240 28-35 (55)
228 PF05129 Elf1: Transcription e 31.3 5.1 0.00011 25.5 -2.2 10 67-76 20-29 (81)
229 KOG2272|consensus 31.3 48 0.001 26.1 2.5 19 70-88 100-118 (332)
230 PTZ00448 hypothetical protein; 31.2 36 0.00078 28.4 2.0 24 205-228 314-337 (373)
231 KOG3507|consensus 31.1 17 0.00037 21.4 0.1 31 176-218 20-50 (62)
232 PTZ00043 cytochrome c oxidase 30.1 29 0.00063 26.7 1.2 13 203-215 179-191 (268)
233 PRK00420 hypothetical protein; 29.9 51 0.0011 22.5 2.2 11 176-186 40-50 (112)
234 KOG0402|consensus 29.2 22 0.00048 22.6 0.4 31 150-188 36-66 (92)
235 COG4896 Uncharacterized protei 29.1 26 0.00057 20.8 0.7 7 71-77 4-10 (68)
236 KOG2071|consensus 29.1 39 0.00084 30.1 1.9 27 203-229 416-442 (579)
237 CHL00174 accD acetyl-CoA carbo 29.0 43 0.00093 27.2 2.0 33 177-219 39-71 (296)
238 COG0068 HypF Hydrogenase matur 28.8 13 0.00029 33.7 -0.9 78 69-160 101-183 (750)
239 PF10263 SprT-like: SprT-like 28.7 24 0.00053 25.3 0.6 10 177-186 124-133 (157)
240 COG2879 Uncharacterized small 28.6 72 0.0016 19.2 2.4 18 216-233 23-40 (65)
241 smart00731 SprT SprT homologue 27.4 41 0.00089 24.0 1.6 11 177-187 113-123 (146)
242 PF15135 UPF0515: Uncharacteri 27.1 39 0.00084 26.5 1.4 14 66-79 109-122 (278)
243 KOG3362|consensus 26.9 21 0.00046 25.3 -0.0 21 177-197 130-150 (156)
244 PF10276 zf-CHCC: Zinc-finger 26.2 22 0.00049 19.2 0.0 11 205-215 29-39 (40)
245 COG1326 Uncharacterized archae 26.0 62 0.0013 24.4 2.2 13 203-215 28-40 (201)
246 KOG4118|consensus 25.7 40 0.00087 20.3 1.0 30 206-235 39-68 (74)
247 KOG0227|consensus 25.7 39 0.00086 25.3 1.2 27 170-196 47-73 (222)
248 COG4306 Uncharacterized protei 25.5 42 0.00092 23.2 1.2 44 70-113 40-83 (160)
249 PF04423 Rad50_zn_hook: Rad50 25.4 28 0.00061 20.0 0.3 13 71-83 22-34 (54)
250 KOG0717|consensus 25.3 44 0.00095 28.9 1.5 22 177-198 293-314 (508)
251 KOG1701|consensus 24.9 6.1 0.00013 33.3 -3.4 37 151-187 395-438 (468)
252 PRK12496 hypothetical protein; 24.8 56 0.0012 24.0 1.9 26 177-215 128-153 (164)
253 PF05495 zf-CHY: CHY zinc fing 24.8 22 0.00048 21.9 -0.2 11 98-108 41-51 (71)
254 TIGR00310 ZPR1_znf ZPR1 zinc f 24.8 24 0.00053 26.6 0.0 9 177-185 31-39 (192)
255 PRK14892 putative transcriptio 24.5 21 0.00045 23.8 -0.4 33 177-217 22-54 (99)
256 PRK11032 hypothetical protein; 24.4 32 0.00069 25.2 0.5 13 228-240 137-149 (160)
257 PF06397 Desulfoferrod_N: Desu 24.1 32 0.00069 18.1 0.4 10 205-214 6-15 (36)
258 PF14787 zf-CCHC_5: GAG-polypr 23.9 44 0.00095 17.6 0.8 10 234-243 3-12 (36)
259 COG5216 Uncharacterized conser 23.7 44 0.00094 19.7 0.9 10 70-80 23-32 (67)
260 PF11781 RRN7: RNA polymerase 23.6 62 0.0013 16.9 1.4 9 151-159 9-17 (36)
261 PF11789 zf-Nse: Zinc-finger o 23.4 31 0.00067 20.2 0.3 12 176-187 24-35 (57)
262 PF04780 DUF629: Protein of un 23.3 69 0.0015 27.9 2.4 25 177-201 58-82 (466)
263 KOG1842|consensus 23.0 46 0.001 28.5 1.3 20 151-170 16-35 (505)
264 KOG1994|consensus 22.5 48 0.001 25.6 1.1 23 67-89 237-259 (268)
265 PF09963 DUF2197: Uncharacteri 22.4 26 0.00057 20.5 -0.2 9 71-79 4-12 (56)
266 PF03145 Sina: Seven in absent 22.1 59 0.0013 24.5 1.6 46 182-231 24-73 (198)
267 PRK00762 hypA hydrogenase nick 22.1 43 0.00093 23.3 0.8 15 67-82 68-82 (124)
268 KOG2636|consensus 21.7 61 0.0013 27.8 1.7 22 148-169 399-421 (497)
269 PF12773 DZR: Double zinc ribb 21.5 65 0.0014 17.9 1.4 25 178-214 14-38 (50)
270 KOG2923|consensus 21.5 71 0.0015 19.2 1.5 10 70-80 23-32 (67)
271 PRK04351 hypothetical protein; 21.1 48 0.001 23.9 0.9 32 121-161 112-143 (149)
272 PF01286 XPA_N: XPA protein N- 21.1 35 0.00075 17.7 0.1 14 206-219 4-17 (34)
273 COG4391 Uncharacterized protei 21.1 50 0.0011 19.7 0.8 43 61-108 16-58 (62)
274 PF11672 DUF3268: Protein of u 21.0 38 0.00083 22.7 0.3 7 206-212 32-38 (102)
275 COG0846 SIR2 NAD-dependent pro 20.2 70 0.0015 25.3 1.7 12 177-188 123-134 (250)
276 TIGR03830 CxxCG_CxxCG_HTH puta 20.1 73 0.0016 21.8 1.6 16 177-192 32-47 (127)
No 1
>KOG2462|consensus
Probab=99.97 E-value=4.7e-32 Score=204.48 Aligned_cols=124 Identities=25% Similarity=0.463 Sum_probs=117.6
Q ss_pred CccccCcCCCccCchhHHHhHHhhhcC--CCCCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCChhHHHHHHh
Q psy12030 120 GMFACDVCGKEYKYKRGLYRHKKFECG--QEPKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRYKTGLYRHKR 197 (245)
Q Consensus 120 ~~~~C~~C~~~f~~~~~l~~H~~~h~~--~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~~ 197 (245)
..|+|..||+.+.+..+|.+|+++|.. ..+.+.|++|++.|.+-..|+.|+++|+-+.+|.+||+.|....-|+.|+|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiR 208 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIR 208 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccc
Confidence 469999999999999999999999854 267899999999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCCcccc
Q psy12030 198 EECGQEPKYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGRVWTR 244 (245)
Q Consensus 198 ~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 244 (245)
+|+| ||||.|+.|++.|+++++|+.||++|.+.|+|.|..|+|.|-
T Consensus 209 THTG-EKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 209 THTG-EKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred cccC-CCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHH
Confidence 9999 999999999999999999999999999999999999999983
No 2
>KOG2462|consensus
Probab=99.95 E-value=6e-29 Score=187.70 Aligned_cols=136 Identities=29% Similarity=0.544 Sum_probs=120.9
Q ss_pred CCceecccccccccChhHHhcchhcccCCCCCccCCCCcccccChHHHHHhcCCccccCcCCCccCchhHHHhHHhhhcC
Q psy12030 67 SKGFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEYKYKRGLYRHKKFECG 146 (245)
Q Consensus 67 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 146 (245)
...|.|..||+.+.+.+.|.+|.++|...+. .+.+.|.+||++|.+...|..|+++|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s---------------------~ka~~C~~C~K~YvSmpALkMHirTH-- 184 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDS---------------------KKAFSCKYCGKVYVSMPALKMHIRTH-- 184 (279)
T ss_pred CCceeccccccccccccccchhhcccccccc---------------------cccccCCCCCceeeehHHHhhHhhcc--
Confidence 3458999999999999999999988865322 23478999999999999999999999
Q ss_pred CCCCccCCCCCCcCCChHHHHhhhcCCCCc--eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChHHHHHh
Q psy12030 147 QEPKYQCPHCPHRAKHKANLKTHIAPQLGV--FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKANLKTH 224 (245)
Q Consensus 147 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~--~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H 224 (245)
.-+++|.+|||.|...+.|+-|+++|+|+ |.|..|+++|..+++|+.|+++|.+ .|+|+|..|+|.|+..+.|.+|
T Consensus 185 -~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~-~K~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 185 -TLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD-VKKHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred -CCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcC-CccccCcchhhHHHHHHHHHHh
Confidence 45799999999999999999999999985 9999999999999999999999988 8899999999999999999999
Q ss_pred Hhh
Q psy12030 225 IAI 227 (245)
Q Consensus 225 ~~~ 227 (245)
...
T Consensus 263 ~ES 265 (279)
T KOG2462|consen 263 SES 265 (279)
T ss_pred hhh
Confidence 863
No 3
>KOG1074|consensus
Probab=99.94 E-value=1e-27 Score=203.80 Aligned_cols=79 Identities=27% Similarity=0.516 Sum_probs=73.9
Q ss_pred cccCcCCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcCCCCc------eeCC---CCCCccCChhHH
Q psy12030 122 FACDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAPQLGV------FACN---VCGKGYRYKTGL 192 (245)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~------~~C~---~C~~~f~~~~~l 192 (245)
..|.+|.+++.-...|+.|+|+|+| |+||+|.+||+.|.++.+|+.|+..|... +.|+ +|-+.|.+...|
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtG-ERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTG-ERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccC-cCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 3499999999999999999999999 99999999999999999999999988752 8999 999999999999
Q ss_pred HHHHhHHhC
Q psy12030 193 YRHKREECG 201 (245)
Q Consensus 193 ~~H~~~h~~ 201 (245)
..|+++|.+
T Consensus 685 pQhIriH~~ 693 (958)
T KOG1074|consen 685 PQHIRIHLG 693 (958)
T ss_pred cceEEeecC
Confidence 999999874
No 4
>KOG3623|consensus
Probab=99.92 E-value=1.6e-26 Score=193.75 Aligned_cols=100 Identities=28% Similarity=0.711 Sum_probs=92.0
Q ss_pred eecccccccccChhHHhcchhc-ccCCCCCccCCCCcccccChHHHHHhcC------------------CccccCcCCCc
Q psy12030 70 FECQVCGKRYKYKRGLHRHKQD-ECGQEPKYQCPQCKDSFFSWSAFHKNLS------------------GMFACDVCGKE 130 (245)
Q Consensus 70 ~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~~C~~C~~~f~~~~~l~~h~~------------------~~~~C~~C~~~ 130 (245)
.+|++|.+.+....+|+.|++- |-.++..|.|.+|.++|..+..|.+|+. +.|+|.+||+.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 6899999999999999999875 4445778999999999999999988872 36999999999
Q ss_pred cCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhh
Q psy12030 131 YKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHI 170 (245)
Q Consensus 131 f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~ 170 (245)
|..+..|..|+|+|.| ++||.|+.|+|.|.....+..|+
T Consensus 291 FKfKHHLKEHlRIHSG-EKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSG-EKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred hhhHHHHHhhheeecC-CCCcCCcccccccccCCcccccc
Confidence 9999999999999999 99999999999999999999996
No 5
>KOG3608|consensus
Probab=99.91 E-value=1.2e-25 Score=174.50 Aligned_cols=224 Identities=18% Similarity=0.344 Sum_probs=185.7
Q ss_pred cccccccccccccceeeeeecccCcceeeeecc------CCCCCC---------cccccccccCCCCCccccccCCCcee
Q psy12030 7 STGQQYNKIMPVCLYAMFVEKSTNTKMEFIAIR------NSNVDK---------SLNTNVLNAHGFNIWPLVQQYSKGFE 71 (245)
Q Consensus 7 ~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~------~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 (245)
..++.+.+.=..|+..|.+.....+|......- ....++ .+...+.+...|+.|.+.|+++|...
T Consensus 130 ~~g~~f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvA 209 (467)
T KOG3608|consen 130 ALGQNFRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVA 209 (467)
T ss_pred cchhhhccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEe
Confidence 445666666677888888766666665532221 111111 24444666778889999999999999
Q ss_pred cccccccccChhHHhcchhcccC-CCCCccCCCCcccccChHHHHHhcCC---ccccCcCCCccCchhHHHhHHhhhcCC
Q psy12030 72 CQVCGKRYKYKRGLHRHKQDECG-QEPKYQCPQCKDSFFSWSAFHKNLSG---MFACDVCGKEYKYKRGLYRHKKFECGQ 147 (245)
Q Consensus 72 C~~C~~~f~~~~~l~~H~~~h~~-~~~~~~C~~C~~~f~~~~~l~~h~~~---~~~C~~C~~~f~~~~~l~~H~~~h~~~ 147 (245)
|+.||..|.++..|..|++..+. +..+|.|..|.+.|.....|..|+.+ -|+|+.|+.+....++|..|++..+..
T Consensus 210 Cp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~ 289 (467)
T KOG3608|consen 210 CPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSK 289 (467)
T ss_pred cchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhcc
Confidence 99999999999999999886543 25689999999999999999999854 699999999999999999999988888
Q ss_pred CCCccCCCCCCcCCChHHHHhhhcCCCCc-eeCCC--CCCccCChhHHHHHHhHHhC--CCCCcccCCCcccCCChHHHH
Q psy12030 148 EPKYQCPHCPHRAKHKANLKTHIAPQLGV-FACNV--CGKGYRYKTGLYRHKREECG--QEPKYQCPHCPHKAKHKANLK 222 (245)
Q Consensus 148 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~C~~--C~~~f~~~~~l~~H~~~h~~--~~~~~~C~~C~~~f~~~~~l~ 222 (245)
++||+|+.|.+.|.+.+.|..|+..|..+ |.|+. |...|.+...+.+|++.++. ++.+|.|-.|++.|++..+|.
T Consensus 290 dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~ 369 (467)
T KOG3608|consen 290 DKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLS 369 (467)
T ss_pred CCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHH
Confidence 99999999999999999999999999987 99988 99999999999999998883 356799999999999999999
Q ss_pred HhHhhhCC
Q psy12030 223 THIAIKHS 230 (245)
Q Consensus 223 ~H~~~~~~ 230 (245)
.|++..|+
T Consensus 370 ~HL~kkH~ 377 (467)
T KOG3608|consen 370 AHLMKKHG 377 (467)
T ss_pred HHHHHhhc
Confidence 99988876
No 6
>KOG3608|consensus
Probab=99.89 E-value=1.9e-24 Score=167.78 Aligned_cols=170 Identities=22% Similarity=0.446 Sum_probs=153.7
Q ss_pred eeccc--ccccccChhHHhcchhcccCCCCCccCCCCcccccChHHHHHhcC-------CccccCcCCCccCchhHHHhH
Q psy12030 70 FECQV--CGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHKNLS-------GMFACDVCGKEYKYKRGLYRH 140 (245)
Q Consensus 70 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~h~~-------~~~~C~~C~~~f~~~~~l~~H 140 (245)
+.|.+ |-+.|.++..|.+|++.|.+ ++..-|+.||..|..+..|-.|++ .+|.|..|.+.|.++..|..|
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs~-eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~H 256 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHSN-EKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSH 256 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcCC-CeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHH
Confidence 55654 99999999999999999988 999999999999999999988873 489999999999999999999
Q ss_pred HhhhcCCCCCccCCCCCCcCCChHHHHhhhcCCC---CceeCCCCCCccCChhHHHHHHhHHhCCCCCcccCC--CcccC
Q psy12030 141 KKFECGQEPKYQCPHCPHRAKHKANLKTHIAPQL---GVFACNVCGKGYRYKTGLYRHKREECGQEPKYQCPH--CPHKA 215 (245)
Q Consensus 141 ~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~---~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~--C~~~f 215 (245)
+..| ...|+|+.|.......+.|.+|++..+ +||+|+.|.+.|.+.++|.+|..+| + +..|+|.. |..+|
T Consensus 257 v~rH---vn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H-S-~~~y~C~h~~C~~s~ 331 (467)
T KOG3608|consen 257 VVRH---VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH-S-KTVYQCEHPDCHYSV 331 (467)
T ss_pred HHHh---hhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc-c-ccceecCCCCCcHHH
Confidence 9999 567999999999999999999987533 4699999999999999999999987 4 78899988 99999
Q ss_pred CChHHHHHhHhhhC-CCC--CCCCCCCCccccC
Q psy12030 216 KHKANLKTHIAIKH-SDR--ILPPQEGRVWTRA 245 (245)
Q Consensus 216 ~~~~~l~~H~~~~~-~~~--~~~C~~C~~~f~~ 245 (245)
....+|++|++.+| |.. +|.|-.|.+-|++
T Consensus 332 r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~ 364 (467)
T KOG3608|consen 332 RTYTQMRRHFLEVHEGNNPILYACHCCDRFFTS 364 (467)
T ss_pred HHHHHHHHHHHHhccCCCCCceeeecchhhhcc
Confidence 99999999999888 555 4999999998864
No 7
>KOG1074|consensus
Probab=99.84 E-value=7.2e-22 Score=168.49 Aligned_cols=59 Identities=27% Similarity=0.505 Sum_probs=53.9
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChHHHHHhHhhhCCCCCCCC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKANLKTHIAIKHSDRILPP 236 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C 236 (245)
..|.+||+.|...+.|+.|+++|++ +|||.|.+|++.|..+.+|+.||.+|+...++.-
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg-~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~sr 938 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTG-PKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSR 938 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCC-CCCccchhhhhhhhhhhhhhhhhccccccCCCcc
Confidence 4599999999999999999999999 9999999999999999999999999998776543
No 8
>KOG3576|consensus
Probab=99.72 E-value=2e-18 Score=124.75 Aligned_cols=110 Identities=26% Similarity=0.594 Sum_probs=89.1
Q ss_pred CCceecccccccccChhHHhcchhcccCCCCCccCCCCcccccChHHHHHhcCCccccCcCCCccCchhHHHhHHhhhcC
Q psy12030 67 SKGFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEYKYKRGLYRHKKFECG 146 (245)
Q Consensus 67 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 146 (245)
...|.|.+|++.|.-+..|.+|++-|....+ |.|..||+.|.....|.+|+++|+|
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr------------------------~lct~cgkgfndtfdlkrh~rthtg 170 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKR------------------------HLCTFCGKGFNDTFDLKRHTRTHTG 170 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHH------------------------HHHhhccCcccchhhhhhhhccccC
Confidence 4458899999999888888888888866222 7788888888999999999999999
Q ss_pred CCCCccCCCCCCcCCChHHHHhhhcCCCC-------------ceeCCCCCCccCChhHHHHHHhHHhC
Q psy12030 147 QEPKYQCPHCPHRAKHKANLKTHIAPQLG-------------VFACNVCGKGYRYKTGLYRHKREECG 201 (245)
Q Consensus 147 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-------------~~~C~~C~~~f~~~~~l~~H~~~h~~ 201 (245)
.+||+|..|++.|..+..|..|++.-++ .|.|+.||.+-.....+..|+..|+.
T Consensus 171 -vrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 171 -VRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred -ccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 8899999999999999999998754333 17788888887777788888887766
No 9
>KOG3576|consensus
Probab=99.69 E-value=7.2e-18 Score=121.93 Aligned_cols=112 Identities=25% Similarity=0.538 Sum_probs=102.2
Q ss_pred ccccCcCCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcCCCC--ceeCCCCCCccCChhHHHHHHhH
Q psy12030 121 MFACDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAPQLG--VFACNVCGKGYRYKTGLYRHKRE 198 (245)
Q Consensus 121 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~--~~~C~~C~~~f~~~~~l~~H~~~ 198 (245)
.|.|..|++.|.-...|.+|++-|.. .+.+.|..||+.|.....|++|+++|+| ||+|..|+++|+..-.|..|.+.
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~-vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~k 195 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSD-VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKK 195 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccH-HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHH
Confidence 58999999999999999999999987 8889999999999999999999999998 59999999999999999999988
Q ss_pred HhC----------CCCCcccCCCcccCCChHHHHHhHhhhCCCCC
Q psy12030 199 ECG----------QEPKYQCPHCPHKAKHKANLKTHIAIKHSDRI 233 (245)
Q Consensus 199 h~~----------~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 233 (245)
-|| .++.|.|..||.+-.....+..|++.||..-|
T Consensus 196 vhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 196 VHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 776 26779999999999999999999999987543
No 10
>KOG3623|consensus
Probab=99.64 E-value=4.2e-17 Score=137.78 Aligned_cols=105 Identities=28% Similarity=0.676 Sum_probs=95.0
Q ss_pred cccCcCCCccCchhHHHhHHhhhc-CCCCCccCCCCCCcCCChHHHHhhhcCCCC---------------ceeCCCCCCc
Q psy12030 122 FACDVCGKEYKYKRGLYRHKKFEC-GQEPKYQCPHCPHRAKHKANLKTHIAPQLG---------------VFACNVCGKG 185 (245)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~~h~-~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~---------------~~~C~~C~~~ 185 (245)
.+|++|++.+.....|..|++..+ ..+..|.|..|.++|.++..|.+|+..|.. .|+|.+||++
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 579999999999999999987554 346679999999999999999999977653 1999999999
Q ss_pred cCChhHHHHHHhHHhCCCCCcccCCCcccCCChHHHHHhHhh
Q psy12030 186 YRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKANLKTHIAI 227 (245)
Q Consensus 186 f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 227 (245)
|+.+..|..|+|+|.| ||||.|+.|+|+|+.+.++..||-.
T Consensus 291 FKfKHHLKEHlRIHSG-EKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSG-EKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhHHHHHhhheeecC-CCCcCCcccccccccCCcccccccc
Confidence 9999999999999999 9999999999999999999999864
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.46 E-value=1.5e-13 Score=116.56 Aligned_cols=129 Identities=17% Similarity=0.356 Sum_probs=91.7
Q ss_pred ccCCCCcccccChHHHHHhc----CCccccCc--CCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcC
Q psy12030 99 YQCPQCKDSFFSWSAFHKNL----SGMFACDV--CGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAP 172 (245)
Q Consensus 99 ~~C~~C~~~f~~~~~l~~h~----~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 172 (245)
..|+.|....... .|..|. ...-.|+. |+..|.... + ++.+.|+.|++.|. ...|..|+..
T Consensus 408 V~C~NC~~~i~l~-~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~e-l----------~~H~~C~~Cgk~f~-~s~LekH~~~ 474 (567)
T PLN03086 408 VECRNCKHYIPSR-SIALHEAYCSRHNVVCPHDGCGIVLRVEE-A----------KNHVHCEKCGQAFQ-QGEMEKHMKV 474 (567)
T ss_pred EECCCCCCccchh-HHHHHHhhCCCcceeCCcccccceeeccc-c----------ccCccCCCCCCccc-hHHHHHHHHh
Confidence 4677777665433 333444 23445764 887773222 2 34467888888885 5778888888
Q ss_pred CCCceeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCC----------ChHHHHHhHhhhCCCCCCCCCCCCcc
Q psy12030 173 QLGVFACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAK----------HKANLKTHIAIKHSDRILPPQEGRVW 242 (245)
Q Consensus 173 h~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~----------~~~~l~~H~~~~~~~~~~~C~~C~~~ 242 (245)
++.++.|+ ||+.+ ....|..|+.+|.+ ++++.|+.|++.|. ..+.|..|..+ .|.+++.|..||+.
T Consensus 475 ~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp-~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt~~C~~Cgk~ 550 (567)
T PLN03086 475 FHEPLQCP-CGVVL-EKEQMVQHQASTCP-LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRTAPCDSCGRS 550 (567)
T ss_pred cCCCccCC-CCCCc-chhHHHhhhhccCC-CCceeCCCCCCccccCccccchhhhhhhHHHHHHh-cCCcceEccccCCe
Confidence 77788888 88654 66888888888877 88888888888884 23578888877 48888888888887
Q ss_pred cc
Q psy12030 243 TR 244 (245)
Q Consensus 243 f~ 244 (245)
|+
T Consensus 551 Vr 552 (567)
T PLN03086 551 VM 552 (567)
T ss_pred ee
Confidence 75
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.33 E-value=5e-12 Score=107.48 Aligned_cols=145 Identities=21% Similarity=0.450 Sum_probs=113.4
Q ss_pred ceecccccccccChhHHhcchhcccCCCCCccCCC--CcccccChHHHHHhcCCccccCcCCCccCchhHHHhHHhhhcC
Q psy12030 69 GFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQ--CKDSFFSWSAFHKNLSGMFACDVCGKEYKYKRGLYRHKKFECG 146 (245)
Q Consensus 69 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~--C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 146 (245)
.-.|..|....... .|..|..... .....|+. ||..| .+..+..| +.|..|++.|. ...|..|++.++
T Consensus 407 ~V~C~NC~~~i~l~-~l~lHe~~C~--r~~V~Cp~~~Cg~v~-~r~el~~H----~~C~~Cgk~f~-~s~LekH~~~~H- 476 (567)
T PLN03086 407 TVECRNCKHYIPSR-SIALHEAYCS--RHNVVCPHDGCGIVL-RVEEAKNH----VHCEKCGQAFQ-QGEMEKHMKVFH- 476 (567)
T ss_pred eEECCCCCCccchh-HHHHHHhhCC--CcceeCCccccccee-eccccccC----ccCCCCCCccc-hHHHHHHHHhcC-
Confidence 35799998876654 4558875442 34567885 99988 34444555 68999999996 678999999984
Q ss_pred CCCCccCCCCCCcCCChHHHHhhhcCCCC--ceeCCCCCCccCC----------hhHHHHHHhHHhCCCCCcccCCCccc
Q psy12030 147 QEPKYQCPHCPHRAKHKANLKTHIAPQLG--VFACNVCGKGYRY----------KTGLYRHKREECGQEPKYQCPHCPHK 214 (245)
Q Consensus 147 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~--~~~C~~C~~~f~~----------~~~l~~H~~~h~~~~~~~~C~~C~~~ 214 (245)
.++.|+ |++.+ .+..|..|+.+|-+ ++.|..|++.|.. .+.|..|.... | .+++.|..||+.
T Consensus 477 --kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G-~rt~~C~~Cgk~ 550 (567)
T PLN03086 477 --EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-G-SRTAPCDSCGRS 550 (567)
T ss_pred --CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-C-CcceEccccCCe
Confidence 689999 99755 67999999887764 5999999999852 45899999986 7 999999999988
Q ss_pred CCChHHHHHhHhhhCC
Q psy12030 215 AKHKANLKTHIAIKHS 230 (245)
Q Consensus 215 f~~~~~l~~H~~~~~~ 230 (245)
+..+ .|..|+...|.
T Consensus 551 Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 551 VMLK-EMDIHQIAVHQ 565 (567)
T ss_pred eeeh-hHHHHHHHhhc
Confidence 8766 67888877765
No 13
>PHA00733 hypothetical protein
Probab=99.26 E-value=6.8e-12 Score=87.58 Aligned_cols=80 Identities=16% Similarity=0.314 Sum_probs=57.3
Q ss_pred CCCccCCCCCCcCCChHHHHhh------hcCCC-CceeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChHH
Q psy12030 148 EPKYQCPHCPHRAKHKANLKTH------IAPQL-GVFACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKAN 220 (245)
Q Consensus 148 ~~~~~C~~C~~~f~~~~~l~~H------~~~h~-~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~ 220 (245)
++++.|.+|.+.|.+...|..+ +..+. .+|.|+.||+.|.....|..|++.+ +.+|.|+.|++.|.....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h---~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC---CcCccCCCCCCccCCHHH
Confidence 4566777777776666555554 22222 2588888888888888888888765 346888888888888888
Q ss_pred HHHhHhhhCC
Q psy12030 221 LKTHIAIKHS 230 (245)
Q Consensus 221 l~~H~~~~~~ 230 (245)
|..|+...|+
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 8888887775
No 14
>PHA00733 hypothetical protein
Probab=99.15 E-value=4.9e-11 Score=83.28 Aligned_cols=78 Identities=22% Similarity=0.284 Sum_probs=60.0
Q ss_pred cccCcCCCccCchhHHH------hHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCChhHHHHH
Q psy12030 122 FACDVCGKEYKYKRGLY------RHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRYKTGLYRH 195 (245)
Q Consensus 122 ~~C~~C~~~f~~~~~l~------~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H 195 (245)
+.|.+|...|.....|. .|+. +++ .++|.|+.|++.|.+...|..|++.+..+|.|.+|+++|.....|..|
T Consensus 41 ~~~~~~~~~~~~~~~l~~~~~l~~~~~-~~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H 118 (128)
T PHA00733 41 LIRAVVKTLIYNPQLLDESSYLYKLLT-SKA-VSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDH 118 (128)
T ss_pred HHHHHHhhhccChhhhcchHHHHhhcc-cCC-CCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHH
Confidence 44444554444444444 4432 234 788999999999999999999999877779999999999999999999
Q ss_pred HhHHhC
Q psy12030 196 KREECG 201 (245)
Q Consensus 196 ~~~h~~ 201 (245)
+...|+
T Consensus 119 ~~~~h~ 124 (128)
T PHA00733 119 VCKKHN 124 (128)
T ss_pred HHHhcC
Confidence 988776
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.10 E-value=6.3e-11 Score=68.36 Aligned_cols=42 Identities=17% Similarity=0.504 Sum_probs=26.1
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChHHH
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKANL 221 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l 221 (245)
|+|+.||+.|...++|..|+++|+ ++|+|..|++.|...+.|
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 566666666666666666666664 456666666666655544
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.03 E-value=9.8e-11 Score=67.55 Aligned_cols=37 Identities=19% Similarity=0.367 Sum_probs=27.1
Q ss_pred cccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCCcccc
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGRVWTR 244 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 244 (245)
|.|+.||+.|+.++.|..|+++|+ ++|+|..|++.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~ 42 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISL 42 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceec
Confidence 677777777777777777777776 5777777777663
No 17
>KOG3993|consensus
Probab=98.91 E-value=2.2e-10 Score=92.14 Aligned_cols=160 Identities=19% Similarity=0.324 Sum_probs=91.9
Q ss_pred ceecccccccccChhHHhcchhcccCCCCCccCCCCcccccChHHHHHhcC-----------------------------
Q psy12030 69 GFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHKNLS----------------------------- 119 (245)
Q Consensus 69 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~h~~----------------------------- 119 (245)
.|.|..|-..|.+...|.+|.-...- ...|+|++|++.|..-.+|-.|.+
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV-~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIV-HVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeE-EeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 48899999899999999888754433 445777777777766666644431
Q ss_pred ---------CccccCcCCCccCchhHHHhHHhhhcCCCCC----------------ccCCCCCCcCCChHHHHhhhcCCC
Q psy12030 120 ---------GMFACDVCGKEYKYKRGLYRHKKFECGQEPK----------------YQCPHCPHRAKHKANLKTHIAPQL 174 (245)
Q Consensus 120 ---------~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~----------------~~C~~C~~~f~~~~~l~~H~~~h~ 174 (245)
+.|.|.+|++.|....-|+.|+.+|+..... +.+..+.-.+.....--.+.-.+.
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a 425 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVA 425 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeee
Confidence 1255666666666666666665555431110 112222211111111000101111
Q ss_pred Cc---eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChHHHHHhHhhhCC
Q psy12030 175 GV---FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 175 ~~---~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
+. ..+++||..+..+..--.+.+.-.. +.-|.|.+|.-.|.++..|.+|+..-|.
T Consensus 426 ~sael~~pp~~~~ppsss~~sgg~~rlg~~-~q~f~~ky~~atfyss~~ltrhin~~Hp 483 (500)
T KOG3993|consen 426 GSAELELPPYDGSPPSSSGSSGGYGRLGIA-EQGFTCKYCPATFYSSPGLTRHINKCHP 483 (500)
T ss_pred ccccccCCCCCCCCcccCCCCCccccccch-hhccccccchHhhhcCcchHhHhhhcCh
Confidence 11 3356677666665554444444444 5569999999999999999999877663
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.87 E-value=8.4e-10 Score=54.53 Aligned_cols=24 Identities=8% Similarity=0.007 Sum_probs=13.4
Q ss_pred HHHhHhhhCCCCCCCCCCCCcccc
Q psy12030 221 LKTHIAIKHSDRILPPQEGRVWTR 244 (245)
Q Consensus 221 l~~H~~~~~~~~~~~C~~C~~~f~ 244 (245)
|.+|+++|+|++||.|++|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 455555555555555555555553
No 19
>PHA00616 hypothetical protein
Probab=98.86 E-value=1e-09 Score=60.24 Aligned_cols=34 Identities=24% Similarity=0.390 Sum_probs=27.6
Q ss_pred CcccCCCcccCCChHHHHHhHhhhCCCCCCCCCC
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQE 238 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~ 238 (245)
||+|+.||+.|..++.|.+|++.|||++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5788888888888888888888888888887754
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.81 E-value=2.7e-09 Score=52.71 Aligned_cols=26 Identities=38% Similarity=0.784 Sum_probs=23.8
Q ss_pred HHHHHHhHHhCCCCCcccCCCcccCCC
Q psy12030 191 GLYRHKREECGQEPKYQCPHCPHKAKH 217 (245)
Q Consensus 191 ~l~~H~~~h~~~~~~~~C~~C~~~f~~ 217 (245)
+|.+|+++|++ ++||.|++|++.|.+
T Consensus 1 ~l~~H~~~H~~-~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTG-EKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSS-SSSEEESSSSEEESS
T ss_pred CHHHHhhhcCC-CCCCCCCCCcCeeCc
Confidence 58999999999 999999999999974
No 21
>KOG3993|consensus
Probab=98.79 E-value=4.5e-10 Score=90.37 Aligned_cols=146 Identities=15% Similarity=0.254 Sum_probs=93.6
Q ss_pred CccCCCCcccccChHHHHHhc-----CCccccCcCCCccCchhHHHhHHhhhcCCCCCcc--CCCCCCcCCChHHHHhhh
Q psy12030 98 KYQCPQCKDSFFSWSAFHKNL-----SGMFACDVCGKEYKYKRGLYRHKKFECGQEPKYQ--CPHCPHRAKHKANLKTHI 170 (245)
Q Consensus 98 ~~~C~~C~~~f~~~~~l~~h~-----~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~--C~~C~~~f~~~~~l~~H~ 170 (245)
.|.|.+|...|.+...|-+|. ...|+|++|+++|.-..+|..|.|+|-.....-. -+-=.+....+...+.=.
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 499999999999999998887 3479999999999999999999999954111000 000000000011111101
Q ss_pred c----CCCCceeCCCCCCccCChhHHHHHHhHHhCCC-------------------------------------------
Q psy12030 171 A----PQLGVFACNVCGKGYRYKTGLYRHKREECGQE------------------------------------------- 203 (245)
Q Consensus 171 ~----~h~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~------------------------------------------- 203 (245)
+ .-.+.|.|..|++.|....+|+.|+.+|+..+
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 1 12224888888888888888888877775411
Q ss_pred --CCcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCCccc
Q psy12030 204 --PKYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGRVWT 243 (245)
Q Consensus 204 --~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 243 (245)
--..|++||-.+.++..-..+.+.-+.+..|.|.+|.-.|
T Consensus 427 sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atf 468 (500)
T KOG3993|consen 427 SAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATF 468 (500)
T ss_pred cccccCCCCCCCCcccCCCCCccccccchhhccccccchHhh
Confidence 1244666776666666555565555666677777776554
No 22
>PHA00732 hypothetical protein
Probab=98.57 E-value=4.1e-08 Score=62.27 Aligned_cols=44 Identities=27% Similarity=0.556 Sum_probs=20.2
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChHHHHHhHh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKANLKTHIA 226 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~ 226 (245)
|.|+.||+.|.+.+.|..|++.++. ++.|+.||+.|. .|..|++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhc
Confidence 4455555555555555555543211 134555555554 2444443
No 23
>PHA00616 hypothetical protein
Probab=98.52 E-value=3.2e-08 Score=54.37 Aligned_cols=39 Identities=18% Similarity=0.208 Sum_probs=33.5
Q ss_pred ceeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccC
Q psy12030 176 VFACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKA 215 (245)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f 215 (245)
||.|..||+.|...+.|..|++.||+ ++++.|+.=-..|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCccceeEEEEEE
Confidence 48899999999999999999999999 8999987643333
No 24
>PHA00732 hypothetical protein
Probab=98.52 E-value=9.8e-08 Score=60.53 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=33.4
Q ss_pred CcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCCcccc
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGRVWTR 244 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 244 (245)
||.|+.||+.|.+.+.|..|++.+|. ++.|++||+.|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC
Confidence 68999999999999999999986443 368999999986
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=98.46 E-value=3.2e-07 Score=54.08 Aligned_cols=51 Identities=29% Similarity=0.602 Sum_probs=40.5
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCC-CCCcccCCCcccCCChHHHHHhHhhhCC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQ-EPKYQCPHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
|.|+.|++ ..+...|..|....|.. .+.+.||+|...+. .+|..|+..+|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 78999999 45677899998876653 45799999998654 489999998875
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.16 E-value=1.2e-06 Score=41.93 Aligned_cols=22 Identities=41% Similarity=0.833 Sum_probs=13.8
Q ss_pred cccCCCcccCCChHHHHHhHhh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAI 227 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~ 227 (245)
|.|+.|++.|.+.+.|..|++.
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 4566666666666666666654
No 27
>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=98.04 E-value=3.4e-06 Score=40.58 Aligned_cols=24 Identities=33% Similarity=0.851 Sum_probs=13.9
Q ss_pred cccCCCcccCCChHHHHHhHhhhC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKH 229 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~ 229 (245)
|.|++|++.|.+...|..|++++|
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 456666666666666666666554
No 28
>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=98.03 E-value=3.6e-06 Score=40.16 Aligned_cols=23 Identities=39% Similarity=0.940 Sum_probs=19.2
Q ss_pred eeCCCCCCccCChhHHHHHHhHH
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREE 199 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h 199 (245)
|.|+.|++.|.++..|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 67888888888888888888774
No 29
>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=98.01 E-value=7.4e-06 Score=48.21 Aligned_cols=37 Identities=32% Similarity=0.600 Sum_probs=20.3
Q ss_pred cccCcCCCccCchhHHHhHHhhhcCC-CCCccCCCCCCc
Q psy12030 122 FACDVCGKEYKYKRGLYRHKKFECGQ-EPKYQCPHCPHR 159 (245)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~~~C~~C~~~ 159 (245)
|+|++|++ ..+...|..|....|.. .+.+.|++|...
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 66666766 34455666665544432 234556655543
No 30
>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=97.97 E-value=4e-06 Score=47.07 Aligned_cols=41 Identities=22% Similarity=0.499 Sum_probs=26.8
Q ss_pred HHHHhHHhCCCCCcccCCCcccCCChHHHHHhHhhhCCCCC
Q psy12030 193 YRHKREECGQEPKYQCPHCPHKAKHKANLKTHIAIKHSDRI 233 (245)
Q Consensus 193 ~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 233 (245)
..+.+.+...+.|-.|++|+..+.+..+|++|+.+.|+.+|
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 55666666668889999999999999999999999998876
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=97.95 E-value=5.2e-06 Score=41.33 Aligned_cols=26 Identities=19% Similarity=0.436 Sum_probs=19.6
Q ss_pred CcccCCCcccCCChHHHHHhHhhhCC
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
||.|..|++.|.+...|..|++.|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 57788888888888888888776653
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.84 E-value=1.1e-05 Score=54.14 Aligned_cols=71 Identities=21% Similarity=0.400 Sum_probs=13.3
Q ss_pred cCcCCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcCCCC-ceeCCCCCCccCChhHHHHHHhHH
Q psy12030 124 CDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAPQLG-VFACNVCGKGYRYKTGLYRHKREE 199 (245)
Q Consensus 124 C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-~~~C~~C~~~f~~~~~l~~H~~~h 199 (245)
|..|+..|.+...|..|+...|+-..+ ....+.....+..+.+.... .+.|..|++.|.+...|..|++.+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccc-----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 666777777777777776655551111 11111122233333332222 255666666666666666666543
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.81 E-value=1.9e-05 Score=37.88 Aligned_cols=24 Identities=42% Similarity=0.916 Sum_probs=18.7
Q ss_pred eeCCCCCCccCChhHHHHHHhHHh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREEC 200 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~ 200 (245)
|.|++|++.|.+...|..|+.+||
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 678889999999999999988774
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.77 E-value=1.7e-05 Score=53.05 Aligned_cols=69 Identities=16% Similarity=0.399 Sum_probs=18.6
Q ss_pred ecccccccccChhHHhcchhcccCCCCCccCCCCcccccChHHHHHh----cCCccccCcCCCccCchhHHHhHHhhh
Q psy12030 71 ECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHKN----LSGMFACDVCGKEYKYKRGLYRHKKFE 144 (245)
Q Consensus 71 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~h----~~~~~~C~~C~~~f~~~~~l~~H~~~h 144 (245)
+|..|+..|.+...|..||...|+...+ ....+.....+... +...+.|..|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc-----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 4899999999999999999877763222 11111122222222 223578888888888888888888764
No 35
>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=97.59 E-value=3.6e-05 Score=38.18 Aligned_cols=26 Identities=38% Similarity=0.905 Sum_probs=22.8
Q ss_pred ceecccccccccChhHHhcchhcccC
Q psy12030 69 GFECQVCGKRYKYKRGLHRHKQDECG 94 (245)
Q Consensus 69 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 94 (245)
+|.|..|++.|.+...|..|++.|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 58899999999999999999988754
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.57 E-value=3.1e-05 Score=60.81 Aligned_cols=43 Identities=26% Similarity=0.416 Sum_probs=35.8
Q ss_pred CCCcccCC--CcccCCChHHHHHhHhhhC-------------------CCCCCCCCCCCccccC
Q psy12030 203 EPKYQCPH--CPHKAKHKANLKTHIAIKH-------------------SDRILPPQEGRVWTRA 245 (245)
Q Consensus 203 ~~~~~C~~--C~~~f~~~~~l~~H~~~~~-------------------~~~~~~C~~C~~~f~~ 245 (245)
+|||+|++ |+|++.....|+-|+.--| .+|||+|++|+|++++
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKN 410 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKN 410 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhcc
Confidence 68999987 9999999999999986433 3699999999998864
No 37
>KOG2231|consensus
Probab=97.42 E-value=0.00032 Score=61.40 Aligned_cols=121 Identities=20% Similarity=0.409 Sum_probs=74.0
Q ss_pred cCCCCcccccChHHHHHhcC---CccccCcC---------CCccCchhHHHhHHhhhcCCCC----CccCCCCCCcCCCh
Q psy12030 100 QCPQCKDSFFSWSAFHKNLS---GMFACDVC---------GKEYKYKRGLYRHKKFECGQEP----KYQCPHCPHRAKHK 163 (245)
Q Consensus 100 ~C~~C~~~f~~~~~l~~h~~---~~~~C~~C---------~~~f~~~~~l~~H~~~h~~~~~----~~~C~~C~~~f~~~ 163 (245)
.|..| -.|.+...|+.|+. +.+.|..| .....+...|.+|++.-...++ .-.|..|...|...
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~ 195 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDD 195 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccH
Confidence 34445 44455555555551 23334333 2223455677777664322122 24588999999999
Q ss_pred HHHHhhhcCCCCceeCCCC------CCccCChhHHHHHHhHHhCCCCCcccC--CC-cccCCChHHHHHhHhhh
Q psy12030 164 ANLKTHIAPQLGVFACNVC------GKGYRYKTGLYRHKREECGQEPKYQCP--HC-PHKAKHKANLKTHIAIK 228 (245)
Q Consensus 164 ~~l~~H~~~h~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~~~~~~C~--~C-~~~f~~~~~l~~H~~~~ 228 (245)
..|.+|++.++ |.|..| +.-|....+|..|.+.+| |.|. .| .+.|.....+..|++.|
T Consensus 196 ~el~rH~~~~h--~~chfC~~~~~~neyy~~~~dLe~HfR~~H-----flCE~~~C~~~~f~~~~~~ei~lk~~ 262 (669)
T KOG2231|consen 196 DELYRHLRFDH--EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH-----FLCEEEFCRTKKFYVAFELEIELKAH 262 (669)
T ss_pred HHHHHhhccce--eheeecCcccccchhcccchHHHHHhhhcC-----ccccccccccceeeehhHHHHHHHhh
Confidence 99999988766 444444 566888899999988764 6787 56 34455555666666633
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.41 E-value=8.9e-05 Score=35.62 Aligned_cols=23 Identities=48% Similarity=1.051 Sum_probs=12.9
Q ss_pred cccCCCcccCCChHHHHHhHhhhC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKH 229 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~ 229 (245)
|+|+.|+.... ...|..|++.+|
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 45666666665 666666666655
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.35 E-value=0.00022 Score=34.66 Aligned_cols=23 Identities=39% Similarity=0.830 Sum_probs=13.8
Q ss_pred cccCCCcccCCChHHHHHhHhhh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIK 228 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~ 228 (245)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666666666666666666543
No 40
>PRK04860 hypothetical protein; Provisional
Probab=97.27 E-value=0.00014 Score=52.82 Aligned_cols=35 Identities=29% Similarity=0.690 Sum_probs=18.8
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAK 216 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~ 216 (245)
|.|. |+. ....+.+|.++|.+ +++|.|..|+..|.
T Consensus 120 Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~~C~~~l~ 154 (160)
T PRK04860 120 YRCK-CQE---HQLTVRRHNRVVRG-EAVYRCRRCGETLV 154 (160)
T ss_pred EEcC-CCC---eeCHHHHHHHHhcC-CccEECCCCCceeE
Confidence 5554 554 44445555555555 55555555555544
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.23 E-value=8.9e-05 Score=58.30 Aligned_cols=25 Identities=28% Similarity=0.588 Sum_probs=22.4
Q ss_pred CCCCcccCCCcccCCChHHHHHhHh
Q psy12030 202 QEPKYQCPHCPHKAKHKANLKTHIA 226 (245)
Q Consensus 202 ~~~~~~C~~C~~~f~~~~~l~~H~~ 226 (245)
+.|||+|++|+|++.....|+-|..
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 3789999999999999999999865
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.12 E-value=0.00029 Score=34.11 Aligned_cols=23 Identities=22% Similarity=0.566 Sum_probs=16.1
Q ss_pred cccCCCcccCCChHHHHHhHhhh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIK 228 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~ 228 (245)
|.|.+|++.|.+...|..|++.+
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 56777777777777777777643
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.03 E-value=0.00052 Score=33.23 Aligned_cols=24 Identities=33% Similarity=0.750 Sum_probs=19.8
Q ss_pred eeCCCCCCccCChhHHHHHHhHHh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREEC 200 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~ 200 (245)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 568888999998889998888663
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.98 E-value=0.00089 Score=32.03 Aligned_cols=24 Identities=25% Similarity=0.523 Sum_probs=18.7
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECG 201 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~ 201 (245)
|.|+.|++... ...|..|++.+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999998888 8899999988764
No 45
>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=96.75 E-value=0.00079 Score=33.28 Aligned_cols=22 Identities=23% Similarity=0.537 Sum_probs=17.2
Q ss_pred cccCCCcccCCChHHHHHhHhh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAI 227 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~ 227 (245)
|.|..|++.|.+...|..|+++
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 6788888888888888888764
No 46
>KOG2231|consensus
Probab=96.72 E-value=0.0028 Score=55.74 Aligned_cols=115 Identities=24% Similarity=0.427 Sum_probs=81.6
Q ss_pred ccCCCCcccccChHHHHHhcCCccccCcCCCccCchhHHHhHHhhhcCCCCCccCCCC---------CCcCCChHHHHhh
Q psy12030 99 YQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHC---------PHRAKHKANLKTH 169 (245)
Q Consensus 99 ~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C---------~~~f~~~~~l~~H 169 (245)
+.|.+|+..|.- +.....|..| ..|.+...|..|+...|+ .+.|..| .....++..|..|
T Consensus 100 ~~C~~C~~~~~~-------~~~~~~~~~c-~~~~s~~~Lk~H~~~~H~---~~~c~lC~~~~kif~~e~k~Yt~~el~~h 168 (669)
T KOG2231|consen 100 HSCHICDRRFRA-------LYNKKECLHC-TEFKSVENLKNHMRDQHK---LHLCSLCLQNLKIFINERKLYTRAELNLH 168 (669)
T ss_pred hhcCccccchhh-------hcccCCCccc-cchhHHHHHHHHHHHhhh---hhccccccccceeeeeeeehehHHHHHHH
Confidence 678888877521 0112468888 888899999999966544 2444443 2233446678888
Q ss_pred hcC-------CCCceeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCC------cccCCChHHHHHhHhhhC
Q psy12030 170 IAP-------QLGVFACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHC------PHKAKHKANLKTHIAIKH 229 (245)
Q Consensus 170 ~~~-------h~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C------~~~f~~~~~l~~H~~~~~ 229 (245)
+.. +.|--.|..|...|.....|++|++.+| |.|..| +..|..-..|..|.+..|
T Consensus 169 ~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 169 LMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred HhcCCCccccccCCccchhhhhhhccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 643 2333679999999999999999998765 466666 567888999999999776
No 47
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.69 E-value=0.0018 Score=36.55 Aligned_cols=29 Identities=24% Similarity=0.341 Sum_probs=19.4
Q ss_pred ceeCCCCCCccCChhHHHHHHhHHhCCCCC
Q psy12030 176 VFACNVCGKGYRYKTGLYRHKREECGQEPK 205 (245)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 205 (245)
|-.|++|+..+....+|.+|+.+.|+ .+|
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~-~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHF-KKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTT-TS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhc-ccC
Confidence 47788888888888888888888777 443
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.67 E-value=0.0012 Score=31.82 Aligned_cols=23 Identities=30% Similarity=0.810 Sum_probs=17.7
Q ss_pred eeCCCCCCccCChhHHHHHHhHH
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREE 199 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h 199 (245)
|.|.+|+..|.+...|..|++.+
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 56888888888888888887654
No 49
>PRK04860 hypothetical protein; Provisional
Probab=96.60 E-value=0.0018 Score=47.10 Aligned_cols=37 Identities=14% Similarity=0.317 Sum_probs=33.3
Q ss_pred CCcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCCcccc
Q psy12030 204 PKYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGRVWTR 244 (245)
Q Consensus 204 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 244 (245)
-+|.|. |+. ....+.+|.+++.++++|.|..|+..|.
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 997 7888999999999999999999998874
No 50
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.53 E-value=0.0019 Score=31.89 Aligned_cols=22 Identities=27% Similarity=0.702 Sum_probs=19.4
Q ss_pred eecccccccccChhHHhcchhc
Q psy12030 70 FECQVCGKRYKYKRGLHRHKQD 91 (245)
Q Consensus 70 ~~C~~C~~~f~~~~~l~~H~~~ 91 (245)
|.|..|++.|.+...|..|++.
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 6799999999999999999875
No 51
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.26 E-value=0.0059 Score=48.92 Aligned_cols=122 Identities=24% Similarity=0.483 Sum_probs=69.6
Q ss_pred eeccc--ccccccChhHHhcchhcccCCCCCccCCCCc---ccc------cChHHHHHhcCC---------ccccCcCCC
Q psy12030 70 FECQV--CGKRYKYKRGLHRHKQDECGQEPKYQCPQCK---DSF------FSWSAFHKNLSG---------MFACDVCGK 129 (245)
Q Consensus 70 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~---~~f------~~~~~l~~h~~~---------~~~C~~C~~ 129 (245)
|.|+. |..+......|+.|....|+ .+.|.+|- +.| .++..|+.|..+ .-.|..|..
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~~ 228 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG---FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC---cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 77876 77777778889999887765 45666663 233 234455666522 345777777
Q ss_pred ccCchhHHHhHHhhhcCCCCCccCCCCCCc-------CCChHHHHhhhcCCCCceeCCC--CC----CccCChhHHHHHH
Q psy12030 130 EYKYKRGLYRHKKFECGQEPKYQCPHCPHR-------AKHKANLKTHIAPQLGVFACNV--CG----KGYRYKTGLYRHK 196 (245)
Q Consensus 130 ~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~-------f~~~~~l~~H~~~h~~~~~C~~--C~----~~f~~~~~l~~H~ 196 (245)
-|.+-..|..|+|..|. .|-+|.+. |.+-..|.+|.+.-+ |.|.+ |. .+|.....|+.|+
T Consensus 229 ~FYdDDEL~~HcR~~HE-----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h--y~ct~qtc~~~k~~vf~~~~el~~h~ 301 (493)
T COG5236 229 YFYDDDELRRHCRLRHE-----ACHICDMVGPIRYQYFKSYEDLEAHFRNAH--YCCTFQTCRVGKCYVFPYHTELLEHL 301 (493)
T ss_pred eecChHHHHHHHHhhhh-----hhhhhhccCccchhhhhCHHHHHHHhhcCc--eEEEEEEEecCcEEEeccHHHHHHHH
Confidence 77777777777775443 34444433 333444555533222 33322 21 2456666666666
Q ss_pred hHHhC
Q psy12030 197 REECG 201 (245)
Q Consensus 197 ~~h~~ 201 (245)
...|+
T Consensus 302 ~~~h~ 306 (493)
T COG5236 302 TRFHK 306 (493)
T ss_pred HHHhh
Confidence 55443
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.50 E-value=0.013 Score=28.26 Aligned_cols=20 Identities=30% Similarity=0.597 Sum_probs=12.1
Q ss_pred cccCCCcccCCChHHHHHhHh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIA 226 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~ 226 (245)
..|+.||..| ....|.+|++
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 5556666654
No 53
>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=95.46 E-value=0.012 Score=30.80 Aligned_cols=23 Identities=13% Similarity=0.392 Sum_probs=17.1
Q ss_pred CcccCCCcccCCChHHHHHhHhh
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAI 227 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~ 227 (245)
+|.|.+|++.|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47778888888877777777653
No 54
>KOG1146|consensus
Probab=95.44 E-value=0.0057 Score=57.26 Aligned_cols=103 Identities=18% Similarity=0.358 Sum_probs=70.1
Q ss_pred CCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcCCC---------------------------CceeC
Q psy12030 127 CGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAPQL---------------------------GVFAC 179 (245)
Q Consensus 127 C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~---------------------------~~~~C 179 (245)
++..+..+..+..|+...+...+.+.|+.|+..|.....|..|++.-+ ++|.|
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C 521 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPC 521 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccc
Confidence 344444445555555444444577888888888888888888876511 02778
Q ss_pred CCCCCccCChhHHHHHHhHHhC------------------------------------------CCCCcccCCCcccCCC
Q psy12030 180 NVCGKGYRYKTGLYRHKREECG------------------------------------------QEPKYQCPHCPHKAKH 217 (245)
Q Consensus 180 ~~C~~~f~~~~~l~~H~~~h~~------------------------------------------~~~~~~C~~C~~~f~~ 217 (245)
..|...+....+|..|+..--. .+.++.|.+|++-.+-
T Consensus 522 ~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetni 601 (1406)
T KOG1146|consen 522 RACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNI 601 (1406)
T ss_pred eeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhh
Confidence 8888888888888888764200 0235889999888888
Q ss_pred hHHHHHhHhhhC
Q psy12030 218 KANLKTHIAIKH 229 (245)
Q Consensus 218 ~~~l~~H~~~~~ 229 (245)
.-+|+.|+..-+
T Consensus 602 arnlrihmtss~ 613 (1406)
T KOG1146|consen 602 ARNLRIHMTASP 613 (1406)
T ss_pred hhccccccccCC
Confidence 888888886543
No 55
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.35 E-value=0.046 Score=36.91 Aligned_cols=21 Identities=19% Similarity=0.659 Sum_probs=9.5
Q ss_pred eeCCCCCCccCChhHHHHHHh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKR 197 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~ 197 (245)
|.|+.|...|--.-+...|..
T Consensus 82 y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 82 YVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred eeCCCCCCccccccchhhhhh
Confidence 444444444444444444433
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.73 E-value=0.028 Score=27.07 Aligned_cols=19 Identities=26% Similarity=0.871 Sum_probs=11.4
Q ss_pred eCCCCCCccCChhHHHHHHh
Q psy12030 178 ACNVCGKGYRYKTGLYRHKR 197 (245)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~ 197 (245)
.|+.||+.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 4555666654
No 57
>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=94.51 E-value=0.04 Score=28.80 Aligned_cols=24 Identities=21% Similarity=0.538 Sum_probs=19.1
Q ss_pred CceeCCCCCCccCChhHHHHHHhH
Q psy12030 175 GVFACNVCGKGYRYKTGLYRHKRE 198 (245)
Q Consensus 175 ~~~~C~~C~~~f~~~~~l~~H~~~ 198 (245)
++|.|++|+..|.+...+..|+..
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 357788888888888888888764
No 58
>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=94.34 E-value=0.026 Score=29.24 Aligned_cols=11 Identities=45% Similarity=1.156 Sum_probs=6.6
Q ss_pred eeCCCCCCccC
Q psy12030 177 FACNVCGKGYR 187 (245)
Q Consensus 177 ~~C~~C~~~f~ 187 (245)
|.|.+||..+.
T Consensus 2 ~~C~~CGy~y~ 12 (33)
T cd00350 2 YVCPVCGYIYD 12 (33)
T ss_pred EECCCCCCEEC
Confidence 56666665544
No 59
>KOG2482|consensus
Probab=94.10 E-value=0.065 Score=43.11 Aligned_cols=24 Identities=25% Similarity=0.582 Sum_probs=21.8
Q ss_pred ceecccccccccChhHHhcchhcc
Q psy12030 69 GFECQVCGKRYKYKRGLHRHKQDE 92 (245)
Q Consensus 69 ~~~C~~C~~~f~~~~~l~~H~~~h 92 (245)
.+.|-.|.+.|.++..|+.||+..
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhc
Confidence 489999999999999999999864
No 60
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.86 E-value=0.06 Score=43.37 Aligned_cols=74 Identities=20% Similarity=0.364 Sum_probs=46.5
Q ss_pred cCCCCCCcCCChHHHHhhhcCCCCc-eeCCCCCC----ccCChhHHHHHHhHHhCCCCCcccCC--Cc----ccCCChHH
Q psy12030 152 QCPHCPHRAKHKANLKTHIAPQLGV-FACNVCGK----GYRYKTGLYRHKREECGQEPKYQCPH--CP----HKAKHKAN 220 (245)
Q Consensus 152 ~C~~C~~~f~~~~~l~~H~~~h~~~-~~C~~C~~----~f~~~~~l~~H~~~h~~~~~~~~C~~--C~----~~f~~~~~ 220 (245)
.|..|...|.....|.+|++..+.. |.|+.=+. -|.+...|..|.+.- .|.|.. |- .+|.+...
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~-----hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNA-----HYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcC-----ceEEEEEEEecCcEEEeccHHH
Confidence 4777777777777777776654443 44443222 366667777776532 366643 42 36788888
Q ss_pred HHHhHhhhCC
Q psy12030 221 LKTHIAIKHS 230 (245)
Q Consensus 221 l~~H~~~~~~ 230 (245)
|..|+-..|+
T Consensus 297 l~~h~~~~h~ 306 (493)
T COG5236 297 LLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHhh
Confidence 8888877775
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.76 E-value=0.019 Score=48.76 Aligned_cols=119 Identities=19% Similarity=0.296 Sum_probs=85.9
Q ss_pred ccccCcCCCccCchhHHHhHHh--hhcCCC--CCccCC--CCCCcCCChHHHHhhhcCCCCc--eeCC------------
Q psy12030 121 MFACDVCGKEYKYKRGLYRHKK--FECGQE--PKYQCP--HCPHRAKHKANLKTHIAPQLGV--FACN------------ 180 (245)
Q Consensus 121 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~--~~C~------------ 180 (245)
.+.|..|...|.....|..|.+ .|.+ + +++.|+ .|++.|.....+..|...|.+. +.+.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred CCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 5889999999999999999999 7877 6 899999 7999999999999998777653 2211
Q ss_pred -------------------------CCCCccCChhHHHHHHhHHhCCCC--CcccCCCcccCCChHHHHHhHhhhCCCCC
Q psy12030 181 -------------------------VCGKGYRYKTGLYRHKREECGQEP--KYQCPHCPHKAKHKANLKTHIAIKHSDRI 233 (245)
Q Consensus 181 -------------------------~C~~~f~~~~~l~~H~~~h~~~~~--~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 233 (245)
.|...+.....+..|...+.. .. .+.+..|++.+.....+..|++.+....+
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLS-FRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAP 446 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccc-cCCcCCCCCcchhhccCcccccccccccccCCc
Confidence 133333444444444444333 22 46677899999999999999888887777
Q ss_pred CCCCCCCc
Q psy12030 234 LPPQEGRV 241 (245)
Q Consensus 234 ~~C~~C~~ 241 (245)
+.|..++.
T Consensus 447 ~~~~~~~~ 454 (467)
T COG5048 447 LLCSILKS 454 (467)
T ss_pred eeeccccc
Confidence 76665554
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=93.69 E-value=0.18 Score=34.21 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=23.8
Q ss_pred ccc----CCCcccCCChHHHHHhHhhhCC
Q psy12030 206 YQC----PHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 206 ~~C----~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
|.| +.|++.+.+...+.+|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 999 9999999999999999999986
No 63
>KOG1146|consensus
Probab=93.20 E-value=0.0068 Score=56.79 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=22.0
Q ss_pred CCCcccCCCcccCCChHHHHHhHhhhCCCC
Q psy12030 203 EPKYQCPHCPHKAKHKANLKTHIAIKHSDR 232 (245)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 232 (245)
-.+| |+.|...|.....|..||++.+++.
T Consensus 1327 ~~~~-c~~c~~~~~~~~alqihm~~~~~~~ 1355 (1406)
T KOG1146|consen 1327 CTYH-CLACEVLLSGREALQIHMRSSAHRR 1355 (1406)
T ss_pred cccc-chHHHhhcchhHHHHHHHHHhhhcc
Confidence 3345 8888888888888888888766544
No 64
>KOG2785|consensus
Probab=92.99 E-value=0.26 Score=40.44 Aligned_cols=52 Identities=19% Similarity=0.324 Sum_probs=42.0
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCC----------------------CCCcccCCCc---ccCCChHHHHHhHhhh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQ----------------------EPKYQCPHCP---HKAKHKANLKTHIAIK 228 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~~ 228 (245)
-.|-.|+..+.+...-..|+..+||= ..-+.|-.|+ +.|.+..+.++||...
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 56888999999998899999988871 2347788888 8899999999998754
No 65
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.80 E-value=0.044 Score=31.52 Aligned_cols=27 Identities=22% Similarity=0.536 Sum_probs=13.9
Q ss_pred CCCcccCCCcccCCChHHHHHhHhhhC
Q psy12030 203 EPKYQCPHCPHKAKHKANLKTHIAIKH 229 (245)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 229 (245)
|--+.||.||..|....++.+|....|
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 444555555555555555555554444
No 66
>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=92.73 E-value=0.1 Score=25.36 Aligned_cols=12 Identities=8% Similarity=-0.482 Sum_probs=7.8
Q ss_pred CCCCCCCccccC
Q psy12030 234 LPPQEGRVWTRA 245 (245)
Q Consensus 234 ~~C~~C~~~f~~ 245 (245)
-.|+.||+.|.+
T Consensus 15 ~~Cp~CG~~F~~ 26 (26)
T PF10571_consen 15 KFCPHCGYDFEA 26 (26)
T ss_pred CcCCCCCCCCcC
Confidence 347777777754
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.72 E-value=0.029 Score=47.66 Aligned_cols=62 Identities=24% Similarity=0.419 Sum_probs=56.3
Q ss_pred ceeCCCCCCccCChhHHHHHHh--HHhCCC--CCcccC--CCcccCCChHHHHHhHhhhCCCCCCCCCC
Q psy12030 176 VFACNVCGKGYRYKTGLYRHKR--EECGQE--PKYQCP--HCPHKAKHKANLKTHIAIKHSDRILPPQE 238 (245)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C~~ 238 (245)
++.|..|...|.....|..|.+ .|.+ + +|+.|+ .|++.|.....+..|...|.+..++.+..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred CCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 4789999999999999999999 7877 7 999999 79999999999999999999988877654
No 68
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.59 E-value=0.17 Score=34.20 Aligned_cols=79 Identities=16% Similarity=0.215 Sum_probs=54.1
Q ss_pred CCCccCCCCCCcCCChHHHHhhhcC--CCCc------------eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcc
Q psy12030 148 EPKYQCPHCPHRAKHKANLKTHIAP--QLGV------------FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPH 213 (245)
Q Consensus 148 ~~~~~C~~C~~~f~~~~~l~~H~~~--h~~~------------~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~ 213 (245)
+-|..|++||-...+...|.+-... ...+ ..|-.|+..|........ ..-.. ...|.|+.|..
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~-~~~y~C~~C~~ 89 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKD-SHRYVCAVCKN 89 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--ccccc-ccceeCCCCCC
Confidence 6789999999999999998876321 0111 248889998876532110 00111 44699999999
Q ss_pred cCCChHHHHHhHhhhC
Q psy12030 214 KAKHKANLKTHIAIKH 229 (245)
Q Consensus 214 ~f~~~~~l~~H~~~~~ 229 (245)
.|-..-+.-.|...|.
T Consensus 90 ~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 90 VFCVDCDVFVHESLHC 105 (112)
T ss_pred ccccccchhhhhhccC
Confidence 9998888888876655
No 69
>KOG2893|consensus
Probab=92.35 E-value=0.037 Score=42.16 Aligned_cols=41 Identities=24% Similarity=0.433 Sum_probs=19.0
Q ss_pred cCCCCcccccChHHHHHhc-CCccccCcCCCccCchhHHHhH
Q psy12030 100 QCPQCKDSFFSWSAFHKNL-SGMFACDVCGKEYKYKRGLYRH 140 (245)
Q Consensus 100 ~C~~C~~~f~~~~~l~~h~-~~~~~C~~C~~~f~~~~~l~~H 140 (245)
.|.+|++.|.+..-|..|. .+.|+|.+|.+.+.+...|..|
T Consensus 12 wcwycnrefddekiliqhqkakhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhhccceeeeehhhhccCCCceee
Confidence 3445555555444444444 2344455554444444444444
No 70
>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=91.02 E-value=0.14 Score=26.74 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=5.4
Q ss_pred CCcccCCCcc
Q psy12030 204 PKYQCPHCPH 213 (245)
Q Consensus 204 ~~~~C~~C~~ 213 (245)
.|..|++||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4455666653
No 71
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.01 E-value=0.19 Score=29.45 Aligned_cols=8 Identities=50% Similarity=1.593 Sum_probs=3.8
Q ss_pred CcccCCCc
Q psy12030 205 KYQCPHCP 212 (245)
Q Consensus 205 ~~~C~~C~ 212 (245)
+|.|+.||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 44444444
No 72
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.90 E-value=0.24 Score=29.10 Aligned_cols=9 Identities=33% Similarity=1.361 Sum_probs=4.0
Q ss_pred ccCCCCccc
Q psy12030 99 YQCPQCKDS 107 (245)
Q Consensus 99 ~~C~~C~~~ 107 (245)
|.|+.||+.
T Consensus 28 F~CPnCGe~ 36 (61)
T COG2888 28 FPCPNCGEV 36 (61)
T ss_pred eeCCCCCce
Confidence 444444433
No 73
>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=90.74 E-value=0.16 Score=27.13 Aligned_cols=12 Identities=17% Similarity=0.725 Sum_probs=5.5
Q ss_pred ecccccccccCh
Q psy12030 71 ECQVCGKRYKYK 82 (245)
Q Consensus 71 ~C~~C~~~f~~~ 82 (245)
.|+.|+..|.-.
T Consensus 4 ~CP~C~~~~~v~ 15 (38)
T TIGR02098 4 QCPNCKTSFRVV 15 (38)
T ss_pred ECCCCCCEEEeC
Confidence 444454444433
No 74
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.74 E-value=0.079 Score=30.50 Aligned_cols=31 Identities=19% Similarity=0.493 Sum_probs=25.7
Q ss_pred ccCCCceecccccccccChhHHhcchhcccC
Q psy12030 64 QQYSKGFECQVCGKRYKYKRGLHRHKQDECG 94 (245)
Q Consensus 64 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 94 (245)
..++..+.|+.||..|..+.++.+|....|+
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3456778999999999999999999876654
No 75
>KOG2893|consensus
Probab=90.57 E-value=0.062 Score=40.99 Aligned_cols=47 Identities=21% Similarity=0.487 Sum_probs=32.8
Q ss_pred CCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChHHHHHhHhhhCC
Q psy12030 179 CNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 179 C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
|=+|++.|....-|.+|++ .|.|+|.+|-+..-+...|..|-...|.
T Consensus 13 cwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceeehhhhhh
Confidence 5567788888777777765 3457888888777777777777544443
No 76
>KOG4173|consensus
Probab=90.52 E-value=0.096 Score=39.06 Aligned_cols=46 Identities=26% Similarity=0.478 Sum_probs=26.0
Q ss_pred ccccCc--CCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhh
Q psy12030 121 MFACDV--CGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHI 170 (245)
Q Consensus 121 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~ 170 (245)
.+.|.. |...|.+......|..+-|+ -.|..|.+.|.+...|..|+
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI 126 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHI 126 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHH
Confidence 355554 55566665556666555555 35666666666665555553
No 77
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.30 E-value=0.2 Score=26.45 Aligned_cols=8 Identities=38% Similarity=1.186 Sum_probs=3.1
Q ss_pred cccCcCCC
Q psy12030 122 FACDVCGK 129 (245)
Q Consensus 122 ~~C~~C~~ 129 (245)
.+|+.|+.
T Consensus 26 v~C~~C~~ 33 (36)
T PF13717_consen 26 VRCSKCGH 33 (36)
T ss_pred EECCCCCC
Confidence 33444433
No 78
>PHA00626 hypothetical protein
Probab=90.13 E-value=0.21 Score=28.85 Aligned_cols=14 Identities=21% Similarity=0.489 Sum_probs=7.7
Q ss_pred CceeCCCCCCccCC
Q psy12030 175 GVFACNVCGKGYRY 188 (245)
Q Consensus 175 ~~~~C~~C~~~f~~ 188 (245)
..|+|+.||+.|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 34666666655543
No 79
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.06 E-value=0.23 Score=26.45 Aligned_cols=9 Identities=33% Similarity=0.940 Sum_probs=3.6
Q ss_pred cccCcCCCc
Q psy12030 122 FACDVCGKE 130 (245)
Q Consensus 122 ~~C~~C~~~ 130 (245)
.+|+.|+..
T Consensus 26 vrC~~C~~~ 34 (37)
T PF13719_consen 26 VRCPKCGHV 34 (37)
T ss_pred EECCCCCcE
Confidence 334444433
No 80
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=89.16 E-value=0.32 Score=35.53 Aligned_cols=22 Identities=41% Similarity=0.907 Sum_probs=16.3
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCc
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCP 212 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~ 212 (245)
|.|++||..+ -+ +.|-.||+||
T Consensus 135 ~vC~vCGy~~-------------~g-e~P~~CPiCg 156 (166)
T COG1592 135 WVCPVCGYTH-------------EG-EAPEVCPICG 156 (166)
T ss_pred EEcCCCCCcc-------------cC-CCCCcCCCCC
Confidence 8888887653 25 7788888887
No 81
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.14 E-value=0.22 Score=27.69 Aligned_cols=26 Identities=23% Similarity=0.728 Sum_probs=15.5
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCccc
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHK 214 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~ 214 (245)
|.|..||..|.-. . ..+.+|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~-~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------S-KDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------C-CCceECCCCCce
Confidence 6677777665532 1 345677777654
No 82
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.37 E-value=0.34 Score=34.87 Aligned_cols=35 Identities=31% Similarity=0.854 Sum_probs=19.2
Q ss_pred CCccCCCCcccccChHHHHH-hcCCccccCcCCCcc
Q psy12030 97 PKYQCPQCKDSFFSWSAFHK-NLSGMFACDVCGKEY 131 (245)
Q Consensus 97 ~~~~C~~C~~~f~~~~~l~~-h~~~~~~C~~C~~~f 131 (245)
..|.|+.|+..|.....+.. ...+.|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 45666666666655444432 234446666666544
No 83
>KOG2482|consensus
Probab=88.12 E-value=0.68 Score=37.53 Aligned_cols=24 Identities=25% Similarity=0.412 Sum_probs=21.9
Q ss_pred cccCCCcccCCChHHHHHhHhhhC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKH 229 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~ 229 (245)
..|-.|.....+...|..||++.|
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHH
Confidence 589999999899999999999887
No 84
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.85 E-value=0.41 Score=28.19 Aligned_cols=8 Identities=50% Similarity=1.530 Sum_probs=3.8
Q ss_pred CcccCCCc
Q psy12030 205 KYQCPHCP 212 (245)
Q Consensus 205 ~~~C~~C~ 212 (245)
+|.|+.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 44444444
No 85
>KOG2186|consensus
Probab=87.71 E-value=0.28 Score=37.95 Aligned_cols=47 Identities=23% Similarity=0.497 Sum_probs=33.0
Q ss_pred cccCcCCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcC
Q psy12030 122 FACDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAP 172 (245)
Q Consensus 122 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 172 (245)
|.|..||....- ..+..|+-+-++ ..|.|..|++.|.. ..+..|..-
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn--~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN--AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC--CeeEEeeccccccc-chhhhhhhh
Confidence 788888876544 446678766555 55888888888886 677777543
No 86
>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=87.26 E-value=0.16 Score=27.56 Aligned_cols=11 Identities=27% Similarity=1.123 Sum_probs=6.5
Q ss_pred eeCCCCCCccC
Q psy12030 177 FACNVCGKGYR 187 (245)
Q Consensus 177 ~~C~~C~~~f~ 187 (245)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 55666666554
No 87
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=87.25 E-value=0.51 Score=30.13 Aligned_cols=33 Identities=27% Similarity=0.625 Sum_probs=22.2
Q ss_pred CCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCCh
Q psy12030 149 PKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRYK 189 (245)
Q Consensus 149 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~ 189 (245)
..|.|+.|++. .+.+.-++.|.|..||..|.--
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccCeEEcCCCCCeeccc
Confidence 35778888765 2345566678888888877643
No 88
>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=86.91 E-value=0.18 Score=29.10 Aligned_cols=29 Identities=24% Similarity=0.810 Sum_probs=16.3
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcc
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPH 213 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~ 213 (245)
|.|..||..|.....+. . +.+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~-------~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS-------D-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC-------C-CCCCCCCCCCC
Confidence 67777777766432211 1 33456777775
No 89
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.23 E-value=0.6 Score=27.51 Aligned_cols=10 Identities=40% Similarity=1.285 Sum_probs=4.9
Q ss_pred CccCCCCccc
Q psy12030 98 KYQCPQCKDS 107 (245)
Q Consensus 98 ~~~C~~C~~~ 107 (245)
.|.|+.||+.
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 3455555544
No 90
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.20 E-value=0.23 Score=38.20 Aligned_cols=13 Identities=23% Similarity=0.562 Sum_probs=9.6
Q ss_pred eeCCCCCCccCCh
Q psy12030 177 FACNVCGKGYRYK 189 (245)
Q Consensus 177 ~~C~~C~~~f~~~ 189 (245)
+.|+.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 6788888876644
No 91
>KOG2186|consensus
Probab=85.87 E-value=0.48 Score=36.68 Aligned_cols=45 Identities=22% Similarity=0.605 Sum_probs=24.4
Q ss_pred ccCCCCCCcCCChHHHHhhhcCCCCc-eeCCCCCCccCChhHHHHHHh
Q psy12030 151 YQCPHCPHRAKHKANLKTHIAPQLGV-FACNVCGKGYRYKTGLYRHKR 197 (245)
Q Consensus 151 ~~C~~C~~~f~~~~~l~~H~~~h~~~-~~C~~C~~~f~~~~~l~~H~~ 197 (245)
|.|.+||.+..- ..+.+|+-.-++. |.|-.||.+|.. .++..|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhh
Confidence 556666666553 3444455444443 666666666665 34445544
No 92
>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=85.86 E-value=0.68 Score=31.34 Aligned_cols=15 Identities=20% Similarity=0.521 Sum_probs=7.1
Q ss_pred CCccCCCCCCcCCCh
Q psy12030 149 PKYQCPHCPHRAKHK 163 (245)
Q Consensus 149 ~~~~C~~C~~~f~~~ 163 (245)
.|..|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 344455555544433
No 93
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=85.59 E-value=0.73 Score=36.83 Aligned_cols=79 Identities=14% Similarity=0.313 Sum_probs=39.6
Q ss_pred ccccCcCCCccCchhHHHhHHhhhc----------C-CCCCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCCh
Q psy12030 121 MFACDVCGKEYKYKRGLYRHKKFEC----------G-QEPKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRYK 189 (245)
Q Consensus 121 ~~~C~~C~~~f~~~~~l~~H~~~h~----------~-~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~ 189 (245)
|..|+.|+........|.+-...-- + +-+.-.|-.|.-.|.-...-..-..+-.+.|.|+.|...|-..
T Consensus 322 Pi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~d 401 (421)
T COG5151 322 PISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSD 401 (421)
T ss_pred CccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcccccccccceechhhhhhhhhh
Confidence 4567777666555544443322110 1 0112235556555554322111122233447777777777777
Q ss_pred hHHHHHHhHH
Q psy12030 190 TGLYRHKREE 199 (245)
Q Consensus 190 ~~l~~H~~~h 199 (245)
-+...|...|
T Consensus 402 CdvfiHe~Lh 411 (421)
T COG5151 402 CDVFIHETLH 411 (421)
T ss_pred hHHHHHHHHh
Confidence 7777776655
No 94
>KOG4173|consensus
Probab=85.29 E-value=0.3 Score=36.53 Aligned_cols=75 Identities=24% Similarity=0.448 Sum_probs=51.0
Q ss_pred ceeccc--ccccccChhHHhcchhcccCCCCCccCCCCcccccChHHHHHhcCCccccCcCCCccCchhHHHhHHhhhcC
Q psy12030 69 GFECQV--CGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEYKYKRGLYRHKKFECG 146 (245)
Q Consensus 69 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 146 (245)
.+.|++ |...|........|...-|+ ..|..|.+.|.+...|..|+...|.
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~---------------------------~sCs~C~r~~Pt~hLLd~HI~E~HD 131 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG---------------------------NSCSFCKRAFPTGHLLDAHILEWHD 131 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc---------------------------chhHHHHHhCCchhhhhHHHHHHHH
Confidence 366766 66777777777777666555 4677888888888888888765432
Q ss_pred ---------CCCCccCCC--CCCcCCChHHHHhhh
Q psy12030 147 ---------QEPKYQCPH--CPHRAKHKANLKTHI 170 (245)
Q Consensus 147 ---------~~~~~~C~~--C~~~f~~~~~l~~H~ 170 (245)
+..-|.|-+ |+..|.+...-+.|+
T Consensus 132 s~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 132 SLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred HHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 133467743 777777777777774
No 95
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=85.19 E-value=0.79 Score=25.34 Aligned_cols=26 Identities=35% Similarity=0.543 Sum_probs=15.2
Q ss_pred CCCcccCCCcccCCCh----HHHHHhHhhh
Q psy12030 203 EPKYQCPHCPHKAKHK----ANLKTHIAIK 228 (245)
Q Consensus 203 ~~~~~C~~C~~~f~~~----~~l~~H~~~~ 228 (245)
.....|.+|++.+... +.|..|++..
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 5557788888777663 7788887543
No 96
>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=84.35 E-value=0.7 Score=23.69 Aligned_cols=10 Identities=40% Similarity=1.275 Sum_probs=5.0
Q ss_pred CcccCCCccc
Q psy12030 205 KYQCPHCPHK 214 (245)
Q Consensus 205 ~~~C~~C~~~ 214 (245)
+.+|+.||..
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 4556666544
No 97
>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=84.23 E-value=1.2 Score=32.42 Aligned_cols=16 Identities=13% Similarity=0.480 Sum_probs=8.4
Q ss_pred eeCCCCCCccCChhHH
Q psy12030 177 FACNVCGKGYRYKTGL 192 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l 192 (245)
|.|+.|+..|+....+
T Consensus 110 Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 110 FICPNMCVRFTFNEAM 125 (158)
T ss_pred EECCCCCcEeeHHHHH
Confidence 5555555555544444
No 98
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=84.19 E-value=0.6 Score=34.77 Aligned_cols=28 Identities=21% Similarity=0.746 Sum_probs=16.3
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCccc
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHK 214 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~ 214 (245)
|.|+.|+..|+....+. ..|.|+.||-.
T Consensus 118 Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~ 145 (178)
T PRK06266 118 FFCPNCHIRFTFDEAME----------YGFRCPQCGEM 145 (178)
T ss_pred EECCCCCcEEeHHHHhh----------cCCcCCCCCCC
Confidence 66666666666554431 23666666654
No 99
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=83.57 E-value=0.83 Score=33.41 Aligned_cols=23 Identities=13% Similarity=0.192 Sum_probs=19.9
Q ss_pred CcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCC
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGR 240 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 240 (245)
-|.|++||.. +-|+.|-.||+||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 5999999965 4568999999999
No 100
>KOG2807|consensus
Probab=83.04 E-value=2.1 Score=34.59 Aligned_cols=23 Identities=13% Similarity=0.521 Sum_probs=16.8
Q ss_pred eeCCCCCCccCChhHHHHHHhHH
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREE 199 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h 199 (245)
|.|..|...|-..-+...|...|
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred EEchhccceeeccchHHHHhhhh
Confidence 77777877777777777766555
No 101
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=82.74 E-value=1 Score=41.01 Aligned_cols=24 Identities=13% Similarity=0.115 Sum_probs=15.4
Q ss_pred CCCcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCCc
Q psy12030 203 EPKYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGRV 241 (245)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 241 (245)
.....|.+|| ++...|..|+.||-
T Consensus 460 ~~~L~CH~Cg---------------~~~~~p~~Cp~Cgs 483 (730)
T COG1198 460 TGQLRCHYCG---------------YQEPIPQSCPECGS 483 (730)
T ss_pred CCeeEeCCCC---------------CCCCCCCCCCCCCC
Confidence 3456777777 34456777777773
No 102
>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=82.09 E-value=1 Score=30.42 Aligned_cols=30 Identities=20% Similarity=0.532 Sum_probs=22.0
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCCh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHK 218 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~ 218 (245)
..|+.||..|..- + ..|..||+||..|.-.
T Consensus 10 R~Cp~CG~kFYDL-----------n-k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------N-KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------C-CCCccCCCCCCccCcc
Confidence 5688888887642 2 4678888888887765
No 103
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=82.03 E-value=0.91 Score=35.36 Aligned_cols=26 Identities=15% Similarity=0.424 Sum_probs=15.9
Q ss_pred CCCccCCCCCCcCCChHHHHhhhcCC
Q psy12030 148 EPKYQCPHCPHRAKHKANLKTHIAPQ 173 (245)
Q Consensus 148 ~~~~~C~~C~~~f~~~~~l~~H~~~h 173 (245)
.+++.|+.|+........|..-.++|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 35667777776666666665554444
No 104
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=81.58 E-value=1.3 Score=25.22 Aligned_cols=21 Identities=29% Similarity=0.649 Sum_probs=11.3
Q ss_pred cccCCCcccCCCh-----HHHHHhHh
Q psy12030 206 YQCPHCPHKAKHK-----ANLKTHIA 226 (245)
Q Consensus 206 ~~C~~C~~~f~~~-----~~l~~H~~ 226 (245)
-.|.+|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3455555555433 46666665
No 105
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=81.56 E-value=0.39 Score=29.79 Aligned_cols=41 Identities=22% Similarity=0.428 Sum_probs=25.2
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccC--CCcccCCChHH
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCP--HCPHKAKHKAN 220 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~--~C~~~f~~~~~ 220 (245)
+.|+.||....-...-..... .. +.-+.|. .||.+|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~-~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TK-ERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hh-eeeeecCCCCCCCEEEEEEE
Confidence 468888876644444333322 22 6778887 78888876543
No 106
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.52 E-value=0.94 Score=32.60 Aligned_cols=34 Identities=18% Similarity=0.590 Sum_probs=17.3
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKA 215 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f 215 (245)
|.|+.|+..|.....+.. . . . ...|.||.||...
T Consensus 100 Y~Cp~C~~~y~~~ea~~~-~--d-~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 100 YKCPNCQSKYTFLEANQL-L--D-M-DGTFTCPRCGEEL 133 (147)
T ss_pred EECcCCCCEeeHHHHHHh-c--C-C-CCcEECCCCCCEE
Confidence 677777766664333221 0 0 1 2236777776543
No 107
>PRK04023 DNA polymerase II large subunit; Validated
Probab=80.03 E-value=2.5 Score=39.67 Aligned_cols=9 Identities=33% Similarity=1.091 Sum_probs=5.6
Q ss_pred ccCCCCCCc
Q psy12030 151 YQCPHCPHR 159 (245)
Q Consensus 151 ~~C~~C~~~ 159 (245)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 456666665
No 108
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=78.94 E-value=2.6 Score=32.46 Aligned_cols=57 Identities=16% Similarity=0.239 Sum_probs=33.1
Q ss_pred cccccccceeeeeecccCcceeeeeccCCCCCCcccccccccCCCCCccccccCCCceecccccccccCh
Q psy12030 13 NKIMPVCLYAMFVEKSTNTKMEFIAIRNSNVDKSLNTNVLNAHGFNIWPLVQQYSKGFECQVCGKRYKYK 82 (245)
Q Consensus 13 ~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 82 (245)
...||.|+..|.+................ +...+...+ .---....|+.||.+|...
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D-----~~~~Y~~vn--------P~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSD-----FCPRYKGVN--------PLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCC-----CccccCCCC--------CeeeeEEECCCCCCccccc
Confidence 34789999999998777776665532221 111111100 0011347899999886654
No 109
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=78.85 E-value=0.98 Score=25.61 Aligned_cols=27 Identities=22% Similarity=0.667 Sum_probs=16.9
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCccc
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHK 214 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~ 214 (245)
|.|..||+.|.. + .. .....|++||..
T Consensus 7 Y~C~~Cg~~~~~---~-------~~-~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGREVEL---D-------QE-TRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCCeeeh---h-------hc-cCceeCCCCCcE
Confidence 788888877711 1 11 445778888764
No 110
>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=78.65 E-value=2.1 Score=20.72 Aligned_cols=20 Identities=25% Similarity=0.645 Sum_probs=14.2
Q ss_pred cccCCCcccCCChHHHHHhHh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIA 226 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~ 226 (245)
..||+|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3588888887 5567777764
No 111
>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=78.08 E-value=0.54 Score=25.78 Aligned_cols=12 Identities=25% Similarity=1.140 Sum_probs=7.3
Q ss_pred eecccccccccC
Q psy12030 70 FECQVCGKRYKY 81 (245)
Q Consensus 70 ~~C~~C~~~f~~ 81 (245)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 566666666643
No 112
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=77.96 E-value=1.3 Score=32.25 Aligned_cols=32 Identities=25% Similarity=0.441 Sum_probs=19.3
Q ss_pred CCCccCCCCcccccChHHHHHhcCCccccCcCCCcc
Q psy12030 96 EPKYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEY 131 (245)
Q Consensus 96 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f 131 (245)
...|.|+.|+..|+....+.. .|.|+.||..+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~----~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMEL----NFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHc----CCcCCCCCCEe
Confidence 345667777766665555542 46677776544
No 113
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.09 E-value=1 Score=21.09 Aligned_cols=6 Identities=0% Similarity=-0.296 Sum_probs=3.0
Q ss_pred CCCCCc
Q psy12030 236 PQEGRV 241 (245)
Q Consensus 236 C~~C~~ 241 (245)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
No 114
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=76.20 E-value=0.82 Score=33.08 Aligned_cols=13 Identities=31% Similarity=0.669 Sum_probs=6.1
Q ss_pred cccCcCCCccCch
Q psy12030 122 FACDVCGKEYKYK 134 (245)
Q Consensus 122 ~~C~~C~~~f~~~ 134 (245)
++|+.||..|.+.
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 4444455444443
No 115
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=75.80 E-value=1.6 Score=32.47 Aligned_cols=31 Identities=29% Similarity=0.555 Sum_probs=17.9
Q ss_pred CCccCCCCcccccChHHHHHhcCCccccCcCCCcc
Q psy12030 97 PKYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEY 131 (245)
Q Consensus 97 ~~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f 131 (245)
..|.|+.|+..|+....+. ..|.|+.||..+
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~----~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME----YGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhh----cCCcCCCCCCCC
Confidence 4566766666665554443 246666666544
No 116
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.77 E-value=0.91 Score=25.38 Aligned_cols=10 Identities=30% Similarity=1.188 Sum_probs=4.8
Q ss_pred eecccccccc
Q psy12030 70 FECQVCGKRY 79 (245)
Q Consensus 70 ~~C~~C~~~f 79 (245)
|.|+.||..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 4455555444
No 117
>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=75.07 E-value=2.4 Score=29.33 Aligned_cols=13 Identities=8% Similarity=-0.069 Sum_probs=6.2
Q ss_pred CCccCCCCCCcCC
Q psy12030 149 PKYQCPHCPHRAK 161 (245)
Q Consensus 149 ~~~~C~~C~~~f~ 161 (245)
.|..|+.||..|.
T Consensus 25 ~p~vcP~cg~~~~ 37 (129)
T TIGR02300 25 RPAVSPYTGEQFP 37 (129)
T ss_pred CCccCCCcCCccC
Confidence 3444555554443
No 118
>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=74.59 E-value=1.2 Score=34.05 Aligned_cols=24 Identities=21% Similarity=0.479 Sum_probs=11.9
Q ss_pred eeCCCCCCccCChhHHHHHHhHHh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREEC 200 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~ 200 (245)
|.|..|++.|....-..+|+..-|
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-
T ss_pred ECCCCCCcccCChHHHHHHHhhcC
Confidence 555555555555555555555443
No 119
>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=74.19 E-value=1.6 Score=34.10 Aligned_cols=26 Identities=15% Similarity=0.399 Sum_probs=19.1
Q ss_pred CCCcccCCCcccCCChHHHHHhHhhh
Q psy12030 203 EPKYQCPHCPHKAKHKANLKTHIAIK 228 (245)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 228 (245)
.+++.||.||.-......|.+-.++|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 56788888888877777776665555
No 120
>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=73.49 E-value=1.6 Score=24.92 Aligned_cols=7 Identities=57% Similarity=1.701 Sum_probs=2.9
Q ss_pred eeCCCCC
Q psy12030 177 FACNVCG 183 (245)
Q Consensus 177 ~~C~~C~ 183 (245)
|.|++|+
T Consensus 35 w~CP~C~ 41 (50)
T cd00730 35 WVCPVCG 41 (50)
T ss_pred CCCCCCC
Confidence 3444443
No 121
>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=71.93 E-value=3.5 Score=27.88 Aligned_cols=25 Identities=36% Similarity=0.650 Sum_probs=22.2
Q ss_pred eeC----CCCCCccCChhHHHHHHhHHhC
Q psy12030 177 FAC----NVCGKGYRYKTGLYRHKREECG 201 (245)
Q Consensus 177 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 201 (245)
|.| ..|++.+.+...+..|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8899999999999999988875
No 122
>PF15269 zf-C2H2_7: Zinc-finger
Probab=70.39 E-value=4.8 Score=22.16 Aligned_cols=21 Identities=33% Similarity=0.853 Sum_probs=14.9
Q ss_pred cccCCCcccCCChHHHHHhHh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIA 226 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~ 226 (245)
|+|-.|+.+...++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 667777777777777777765
No 123
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=70.32 E-value=0.34 Score=26.29 Aligned_cols=11 Identities=9% Similarity=-0.272 Sum_probs=5.9
Q ss_pred CCCCCCCcccc
Q psy12030 234 LPPQEGRVWTR 244 (245)
Q Consensus 234 ~~C~~C~~~f~ 244 (245)
|.|..||+.++
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 55555555543
No 124
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=69.60 E-value=5.1 Score=21.78 Aligned_cols=23 Identities=22% Similarity=0.366 Sum_probs=14.3
Q ss_pred cccCCCcccCC--ChHHHHHhHhhh
Q psy12030 206 YQCPHCPHKAK--HKANLKTHIAIK 228 (245)
Q Consensus 206 ~~C~~C~~~f~--~~~~l~~H~~~~ 228 (245)
-.|+.||..|. ...+-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 56777777665 445566666554
No 125
>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=68.95 E-value=2.7 Score=27.29 Aligned_cols=33 Identities=27% Similarity=0.790 Sum_probs=21.5
Q ss_pred CCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCCh
Q psy12030 149 PKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRYK 189 (245)
Q Consensus 149 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~ 189 (245)
..|.|+.|++.-.. +.-.+.|.|..|++.|.--
T Consensus 34 a~y~CpfCgk~~vk--------R~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTVK--------RGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCceE--------EEeeEEEEcCCCCCEEeCC
Confidence 45788888754332 3445668888888876543
No 126
>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=68.33 E-value=3.4 Score=23.26 Aligned_cols=13 Identities=38% Similarity=1.073 Sum_probs=6.6
Q ss_pred eecccccccccCh
Q psy12030 70 FECQVCGKRYKYK 82 (245)
Q Consensus 70 ~~C~~C~~~f~~~ 82 (245)
|.|..||..+...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 4555555555433
No 127
>COG1773 Rubredoxin [Energy production and conversion]
Probab=68.23 E-value=2 Score=24.97 Aligned_cols=11 Identities=18% Similarity=0.591 Sum_probs=4.9
Q ss_pred ccCCCCCCcCC
Q psy12030 151 YQCPHCPHRAK 161 (245)
Q Consensus 151 ~~C~~C~~~f~ 161 (245)
|+|..||..|.
T Consensus 4 ~~C~~CG~vYd 14 (55)
T COG1773 4 WRCSVCGYVYD 14 (55)
T ss_pred eEecCCceEec
Confidence 44444444444
No 128
>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=68.08 E-value=2.9 Score=29.43 Aligned_cols=22 Identities=32% Similarity=0.558 Sum_probs=9.6
Q ss_pred cccCCCcccCCChHHHHHhHhhhCC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
..|-+||+.|... .+|++.|||
T Consensus 73 i~clecGk~~k~L---krHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-
T ss_pred eEEccCCcccchH---HHHHHHccC
Confidence 4555555555443 555555554
No 129
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=68.08 E-value=3.5 Score=26.79 Aligned_cols=34 Identities=29% Similarity=0.674 Sum_probs=21.4
Q ss_pred CCCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCCh
Q psy12030 148 EPKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRYK 189 (245)
Q Consensus 148 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~ 189 (245)
...|.|+.|++.-.. +.-.+.|.|..|++.|.--
T Consensus 34 ~a~y~CpfCgk~~vk--------R~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 34 HAKYFCPFCGKHAVK--------RQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred hCCccCCCCCCCcee--------eeeeEEEEcCCCCCEEeCC
Confidence 345788888754332 3334668888888876643
No 130
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=68.04 E-value=3.9 Score=28.52 Aligned_cols=13 Identities=23% Similarity=0.790 Sum_probs=6.7
Q ss_pred cccCcCCCccCch
Q psy12030 122 FACDVCGKEYKYK 134 (245)
Q Consensus 122 ~~C~~C~~~f~~~ 134 (245)
++|..||+.|.+.
T Consensus 2 H~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 2 HQCTKCGRVFEDG 14 (131)
T ss_pred cccCcCCCCcCCC
Confidence 4555555555443
No 131
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=67.63 E-value=4 Score=26.35 Aligned_cols=13 Identities=15% Similarity=0.565 Sum_probs=7.3
Q ss_pred CcccCCCcccCCC
Q psy12030 205 KYQCPHCPHKAKH 217 (245)
Q Consensus 205 ~~~C~~C~~~f~~ 217 (245)
|-.|..||+.|.+
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4556666655554
No 132
>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=67.24 E-value=1.6 Score=22.03 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=4.4
Q ss_pred CCcccCCCc
Q psy12030 204 PKYQCPHCP 212 (245)
Q Consensus 204 ~~~~C~~C~ 212 (245)
-.|.|+.|+
T Consensus 18 ~~~vCp~C~ 26 (30)
T PF08274_consen 18 ELLVCPECG 26 (30)
T ss_dssp SSEEETTTT
T ss_pred CEEeCCccc
Confidence 345555554
No 133
>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=67.20 E-value=2.3 Score=20.15 Aligned_cols=8 Identities=38% Similarity=1.435 Sum_probs=4.3
Q ss_pred CcccCCCc
Q psy12030 205 KYQCPHCP 212 (245)
Q Consensus 205 ~~~C~~C~ 212 (245)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45555555
No 134
>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=67.16 E-value=1.7 Score=28.17 Aligned_cols=32 Identities=31% Similarity=0.842 Sum_probs=19.6
Q ss_pred CCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCC
Q psy12030 149 PKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRY 188 (245)
Q Consensus 149 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~ 188 (245)
..|.|+.|++.-.. +.-.+.|.|..|++.|.-
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEE--------EEETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeE--------EeeeEEeecCCCCCEEeC
Confidence 34778877765432 344566888888876643
No 135
>PF12907 zf-met2: Zinc-binding
Probab=66.82 E-value=3.1 Score=22.50 Aligned_cols=27 Identities=26% Similarity=0.537 Sum_probs=15.8
Q ss_pred cccCCCcc---cCCChHHHHHhHhhhCCCC
Q psy12030 206 YQCPHCPH---KAKHKANLKTHIAIKHSDR 232 (245)
Q Consensus 206 ~~C~~C~~---~f~~~~~l~~H~~~~~~~~ 232 (245)
+.|.+|-. .......|..|....|...
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 45666663 3344566777766666554
No 136
>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=66.58 E-value=2.9 Score=27.69 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=5.8
Q ss_pred CCcccCCCcccC
Q psy12030 204 PKYQCPHCPHKA 215 (245)
Q Consensus 204 ~~~~C~~C~~~f 215 (245)
+|++|+.||..|
T Consensus 78 ~~~rC~eCG~~f 89 (97)
T cd00924 78 KPKRCPECGHVF 89 (97)
T ss_pred CceeCCCCCcEE
Confidence 345555555443
No 137
>PF14353 CpXC: CpXC protein
Probab=64.32 E-value=1.5 Score=30.59 Aligned_cols=24 Identities=25% Similarity=0.522 Sum_probs=14.3
Q ss_pred CCccCCCCCCcCCChHHHHhhhcC
Q psy12030 149 PKYQCPHCPHRAKHKANLKTHIAP 172 (245)
Q Consensus 149 ~~~~C~~C~~~f~~~~~l~~H~~~ 172 (245)
..+.|+.||..|.-...+.-|-..
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCC
Confidence 346677777777665555555333
No 138
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=63.26 E-value=0.11 Score=28.08 Aligned_cols=11 Identities=9% Similarity=-0.353 Sum_probs=6.0
Q ss_pred CCCCCCCcccc
Q psy12030 234 LPPQEGRVWTR 244 (245)
Q Consensus 234 ~~C~~C~~~f~ 244 (245)
|.|..||+.||
T Consensus 29 y~C~~C~~~wr 39 (39)
T PF01096_consen 29 YVCCNCGHRWR 39 (39)
T ss_dssp EEESSSTEEEE
T ss_pred EEeCCCCCeeC
Confidence 55555555543
No 139
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=63.05 E-value=2.9 Score=29.94 Aligned_cols=32 Identities=31% Similarity=0.727 Sum_probs=15.0
Q ss_pred ceeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcc
Q psy12030 176 VFACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPH 213 (245)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~ 213 (245)
+|.|. |+..|.+. ++|-..-.| + .|.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g-~-~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRG-E-VYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccchh---hhccccccc-c-eEEeccCCc
Confidence 36666 66554432 223223223 3 566666653
No 140
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=63.05 E-value=11 Score=36.57 Aligned_cols=8 Identities=38% Similarity=1.173 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q psy12030 151 YQCPHCPH 158 (245)
Q Consensus 151 ~~C~~C~~ 158 (245)
+.|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 45555554
No 141
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.89 E-value=3 Score=29.53 Aligned_cols=13 Identities=31% Similarity=0.933 Sum_probs=9.0
Q ss_pred eeCCCCCCccCCh
Q psy12030 177 FACNVCGKGYRYK 189 (245)
Q Consensus 177 ~~C~~C~~~f~~~ 189 (245)
+.|..||..|...
T Consensus 71 ~~C~~CG~~~~~~ 83 (135)
T PRK03824 71 LKCRNCGNEWSLK 83 (135)
T ss_pred EECCCCCCEEecc
Confidence 7787787766543
No 142
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=62.50 E-value=4.2 Score=26.41 Aligned_cols=32 Identities=25% Similarity=0.634 Sum_probs=20.6
Q ss_pred CCccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCC
Q psy12030 149 PKYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRY 188 (245)
Q Consensus 149 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~ 188 (245)
..|.|+.|++.-.. +.-.+.|.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vk--------R~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVK--------RVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceE--------EEEEEEEEcCCCCCEEeC
Confidence 44788888654332 344566888888887654
No 143
>KOG4167|consensus
Probab=62.42 E-value=1.6 Score=39.19 Aligned_cols=27 Identities=22% Similarity=0.417 Sum_probs=24.5
Q ss_pred CceecccccccccChhHHhcchhcccC
Q psy12030 68 KGFECQVCGKRYKYKRGLHRHKQDECG 94 (245)
Q Consensus 68 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 94 (245)
..|.|.+|++.|....+++.||++|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 349999999999999999999999864
No 144
>KOG2593|consensus
Probab=60.65 E-value=6.6 Score=33.19 Aligned_cols=36 Identities=36% Similarity=0.842 Sum_probs=27.7
Q ss_pred CCCccCCCCcccccChHHHHH--hcCCccccCcCCCcc
Q psy12030 96 EPKYQCPQCKDSFFSWSAFHK--NLSGMFACDVCGKEY 131 (245)
Q Consensus 96 ~~~~~C~~C~~~f~~~~~l~~--h~~~~~~C~~C~~~f 131 (245)
...|.|+.|.++|.+...++- ...+.|.|..|+...
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 567999999999988777643 446789999997544
No 145
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=59.73 E-value=6.1 Score=33.50 Aligned_cols=12 Identities=25% Similarity=0.955 Sum_probs=5.7
Q ss_pred CcccCCCcccCC
Q psy12030 205 KYQCPHCPHKAK 216 (245)
Q Consensus 205 ~~~C~~C~~~f~ 216 (245)
-|+|+.||..+.
T Consensus 367 g~rC~kCg~~~~ 378 (421)
T COG1571 367 GFRCKKCGTRAR 378 (421)
T ss_pred CcccccccccCC
Confidence 455555554443
No 146
>KOG2785|consensus
Probab=59.38 E-value=8.6 Score=31.95 Aligned_cols=70 Identities=16% Similarity=0.223 Sum_probs=44.2
Q ss_pred ceecccccccccChhHHhcchhcccCCCCCccCCCCcccccChHHH----HHhcCCccccCcCC---CccCchhHHHhHH
Q psy12030 69 GFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAF----HKNLSGMFACDVCG---KEYKYKRGLYRHK 141 (245)
Q Consensus 69 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l----~~h~~~~~~C~~C~---~~f~~~~~l~~H~ 141 (245)
|-.|-.|+..+.+...-..||..+|+---| .=. -..+...| -.-+...+.|-.|+ +.|.+....+.||
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIP----dre-YL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM 240 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIP----DRE-YLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHM 240 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCC----chH-hhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHH
Confidence 467888999998888888999888772111 000 00112222 12223457788887 8888888888888
Q ss_pred hh
Q psy12030 142 KF 143 (245)
Q Consensus 142 ~~ 143 (245)
..
T Consensus 241 ~~ 242 (390)
T KOG2785|consen 241 RD 242 (390)
T ss_pred hh
Confidence 64
No 147
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=58.90 E-value=9 Score=21.88 Aligned_cols=11 Identities=27% Similarity=0.788 Sum_probs=5.6
Q ss_pred CceeCCCCCCc
Q psy12030 175 GVFACNVCGKG 185 (245)
Q Consensus 175 ~~~~C~~C~~~ 185 (245)
+.+.|..||..
T Consensus 36 ~r~~C~~Cgyt 46 (50)
T PRK00432 36 DRWHCGKCGYT 46 (50)
T ss_pred CcEECCCcCCE
Confidence 34555555544
No 148
>KOG2907|consensus
Probab=58.54 E-value=4.1 Score=27.46 Aligned_cols=11 Identities=45% Similarity=1.126 Sum_probs=5.6
Q ss_pred cccCCCcccCC
Q psy12030 206 YQCPHCPHKAK 216 (245)
Q Consensus 206 ~~C~~C~~~f~ 216 (245)
|.|+.|++.|.
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 55555555443
No 149
>PRK04023 DNA polymerase II large subunit; Validated
Probab=58.51 E-value=11 Score=35.65 Aligned_cols=9 Identities=33% Similarity=0.970 Sum_probs=5.1
Q ss_pred eeCCCCCCc
Q psy12030 177 FACNVCGKG 185 (245)
Q Consensus 177 ~~C~~C~~~ 185 (245)
+.|+.||..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 556666643
No 150
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=58.12 E-value=4.9 Score=27.47 Aligned_cols=11 Identities=18% Similarity=0.259 Sum_probs=6.4
Q ss_pred eeCCCCCCccC
Q psy12030 177 FACNVCGKGYR 187 (245)
Q Consensus 177 ~~C~~C~~~f~ 187 (245)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 56666665544
No 151
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=58.10 E-value=7.6 Score=25.68 Aligned_cols=12 Identities=25% Similarity=0.545 Sum_probs=5.8
Q ss_pred ccCCCCCCcCCC
Q psy12030 151 YQCPHCPHRAKH 162 (245)
Q Consensus 151 ~~C~~C~~~f~~ 162 (245)
+.|..||..|..
T Consensus 3 H~CtrCG~vf~~ 14 (112)
T COG3364 3 HQCTRCGEVFDD 14 (112)
T ss_pred ceeccccccccc
Confidence 444445554444
No 152
>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=57.30 E-value=6.9 Score=34.43 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=5.3
Q ss_pred cCCCCCCcCC
Q psy12030 152 QCPHCPHRAK 161 (245)
Q Consensus 152 ~C~~C~~~f~ 161 (245)
.|..||....
T Consensus 215 ~C~~Cg~~~~ 224 (505)
T TIGR00595 215 LCRSCGYILC 224 (505)
T ss_pred EhhhCcCccC
Confidence 4666655443
No 153
>PLN02294 cytochrome c oxidase subunit Vb
Probab=56.96 E-value=5.7 Score=29.07 Aligned_cols=13 Identities=23% Similarity=0.795 Sum_probs=7.6
Q ss_pred CCCcccCCCcccC
Q psy12030 203 EPKYQCPHCPHKA 215 (245)
Q Consensus 203 ~~~~~C~~C~~~f 215 (245)
.+|++|++||..|
T Consensus 139 Gkp~RCpeCG~~f 151 (174)
T PLN02294 139 GKSFECPVCTQYF 151 (174)
T ss_pred CCceeCCCCCCEE
Confidence 4456666666554
No 154
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=55.53 E-value=8.2 Score=26.38 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=6.9
Q ss_pred ceeccccccc
Q psy12030 69 GFECQVCGKR 78 (245)
Q Consensus 69 ~~~C~~C~~~ 78 (245)
...|+.||..
T Consensus 72 ~~~CpkCg~~ 81 (113)
T COG1594 72 KEKCPKCGNK 81 (113)
T ss_pred cccCCCCCCc
Confidence 3678888754
No 155
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=55.07 E-value=1.8 Score=28.50 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=16.1
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAK 216 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~ 216 (245)
|.|+.||..-...-.+..- ...-...|..||..|.
T Consensus 23 FtCp~Cghe~vs~ctvkk~-----~~~g~~~Cg~CGls~e 57 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKT-----VNIGTAVCGNCGLSFE 57 (104)
T ss_pred EecCccCCeeeeEEEEEec-----CceeEEEcccCcceEE
Confidence 6666666554433221110 1122345666666553
No 156
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=55.04 E-value=10 Score=26.60 Aligned_cols=13 Identities=23% Similarity=0.725 Sum_probs=7.8
Q ss_pred CcccCCCcccCCC
Q psy12030 205 KYQCPHCPHKAKH 217 (245)
Q Consensus 205 ~~~C~~C~~~f~~ 217 (245)
.|+|+.|++.|..
T Consensus 53 RyrC~~C~~tf~~ 65 (129)
T COG3677 53 RYKCKSCGSTFTV 65 (129)
T ss_pred ccccCCcCcceee
Confidence 3666666666653
No 157
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=54.97 E-value=6.7 Score=22.28 Aligned_cols=15 Identities=13% Similarity=0.381 Sum_probs=7.3
Q ss_pred CCcccCCCcccCCCh
Q psy12030 204 PKYQCPHCPHKAKHK 218 (245)
Q Consensus 204 ~~~~C~~C~~~f~~~ 218 (245)
+++.|..||..|.-.
T Consensus 3 k~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFT 17 (49)
T ss_pred eeEEcccCCCeEEEe
Confidence 344555555554433
No 158
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=53.63 E-value=5.4 Score=27.85 Aligned_cols=24 Identities=21% Similarity=0.454 Sum_probs=14.9
Q ss_pred hHHHhHHhhhcCCCCCccCCCCCCcCCChH
Q psy12030 135 RGLYRHKKFECGQEPKYQCPHCPHRAKHKA 164 (245)
Q Consensus 135 ~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~ 164 (245)
..|..|-..| -+|++|..+|.+..
T Consensus 112 a~LWK~~~~y------pvCPvCkTSFKss~ 135 (140)
T PF05290_consen 112 ANLWKFCNLY------PVCPVCKTSFKSSS 135 (140)
T ss_pred HHHHHHcccC------CCCCcccccccccc
Confidence 4565554433 36888888877654
No 159
>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=53.30 E-value=5.8 Score=27.20 Aligned_cols=11 Identities=18% Similarity=0.597 Sum_probs=6.6
Q ss_pred eeCCCCCCccC
Q psy12030 177 FACNVCGKGYR 187 (245)
Q Consensus 177 ~~C~~C~~~f~ 187 (245)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 56666665554
No 160
>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=53.18 E-value=3.7 Score=22.50 Aligned_cols=9 Identities=33% Similarity=0.918 Sum_probs=3.6
Q ss_pred cccCcCCCc
Q psy12030 122 FACDVCGKE 130 (245)
Q Consensus 122 ~~C~~C~~~ 130 (245)
+.|..||..
T Consensus 20 ~vC~~CG~V 28 (43)
T PF08271_consen 20 LVCPNCGLV 28 (43)
T ss_dssp EEETTT-BB
T ss_pred EECCCCCCE
Confidence 444444443
No 161
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=53.13 E-value=14 Score=21.55 Aligned_cols=16 Identities=19% Similarity=0.684 Sum_probs=11.2
Q ss_pred CCCcccCCCcccCCCh
Q psy12030 203 EPKYQCPHCPHKAKHK 218 (245)
Q Consensus 203 ~~~~~C~~C~~~f~~~ 218 (245)
...|.|+.||..+--+
T Consensus 12 ~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 12 HVNFECPDCGIPTHCS 27 (55)
T ss_pred ccCCcCCCCCCcCccC
Confidence 5568888888765543
No 162
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.13 E-value=9.3 Score=34.86 Aligned_cols=49 Identities=20% Similarity=0.570 Sum_probs=32.4
Q ss_pred CccCCCCcccccChHHHHHhcCCccccCcCCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCCChHHHHhhhcCCCCce
Q psy12030 98 KYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAKHKANLKTHIAPQLGVF 177 (245)
Q Consensus 98 ~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 177 (245)
...|..||.. ..|+.|+-.+. .|. . .....|..||.... ++
T Consensus 383 ~l~C~~Cg~~--------------~~C~~C~~~L~------~h~----~-~~~l~Ch~CG~~~~--------------p~ 423 (665)
T PRK14873 383 SLACARCRTP--------------ARCRHCTGPLG------LPS----A-GGTPRCRWCGRAAP--------------DW 423 (665)
T ss_pred eeEhhhCcCe--------------eECCCCCCcee------Eec----C-CCeeECCCCcCCCc--------------Cc
Confidence 4578888877 67888886532 232 2 45678888885321 36
Q ss_pred eCCCCCCc
Q psy12030 178 ACNVCGKG 185 (245)
Q Consensus 178 ~C~~C~~~ 185 (245)
.|+.||..
T Consensus 424 ~Cp~Cgs~ 431 (665)
T PRK14873 424 RCPRCGSD 431 (665)
T ss_pred cCCCCcCC
Confidence 78888865
No 163
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.04 E-value=6.4 Score=22.86 Aligned_cols=8 Identities=38% Similarity=1.082 Sum_probs=3.8
Q ss_pred cccCCCcc
Q psy12030 206 YQCPHCPH 213 (245)
Q Consensus 206 ~~C~~C~~ 213 (245)
..|+.|+.
T Consensus 22 VvCp~Cga 29 (54)
T PF14446_consen 22 VVCPECGA 29 (54)
T ss_pred EECCCCCC
Confidence 44555543
No 164
>KOG3214|consensus
Probab=52.90 E-value=2.8 Score=27.52 Aligned_cols=12 Identities=17% Similarity=0.467 Sum_probs=6.3
Q ss_pred cccCCCcccCCC
Q psy12030 206 YQCPHCPHKAKH 217 (245)
Q Consensus 206 ~~C~~C~~~f~~ 217 (245)
..|.+|+..|..
T Consensus 48 ~sC~iC~esFqt 59 (109)
T KOG3214|consen 48 ASCRICEESFQT 59 (109)
T ss_pred eeeeehhhhhcc
Confidence 445555555543
No 165
>KOG4167|consensus
Probab=52.67 E-value=2.8 Score=37.78 Aligned_cols=24 Identities=13% Similarity=0.362 Sum_probs=22.6
Q ss_pred cccCCCcccCCChHHHHHhHhhhC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKH 229 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~ 229 (245)
|.|.+|++.|--..++..||++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 899999999999999999999986
No 166
>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=52.47 E-value=10 Score=21.10 Aligned_cols=8 Identities=50% Similarity=1.597 Sum_probs=4.2
Q ss_pred ccCCCCCC
Q psy12030 151 YQCPHCPH 158 (245)
Q Consensus 151 ~~C~~C~~ 158 (245)
+.|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44555554
No 167
>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=51.82 E-value=5.4 Score=28.64 Aligned_cols=27 Identities=22% Similarity=0.565 Sum_probs=14.4
Q ss_pred CcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCCc
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGRV 241 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 241 (245)
.|.|..||... ...+.+..-+|+.||.
T Consensus 112 ~l~C~~Cg~~~----------~~~~~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 112 TLVCENCGHEV----------ELTHPERLPPCPKCGH 138 (146)
T ss_pred eEecccCCCEE----------EecCCCcCCCCCCCCC
Confidence 36677776431 1223455666777663
No 168
>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=50.55 E-value=13 Score=28.55 Aligned_cols=25 Identities=32% Similarity=0.592 Sum_probs=18.5
Q ss_pred CCCccCCCCCCcCCChHHHHhhhcC
Q psy12030 148 EPKYQCPHCPHRAKHKANLKTHIAP 172 (245)
Q Consensus 148 ~~~~~C~~C~~~f~~~~~l~~H~~~ 172 (245)
+..|.|..|+|.|....-...|+..
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhh
Confidence 4459999999999999888888543
No 169
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=49.77 E-value=14 Score=20.98 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=5.6
Q ss_pred ceeCCCCCCc
Q psy12030 176 VFACNVCGKG 185 (245)
Q Consensus 176 ~~~C~~C~~~ 185 (245)
.|.|..||.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 4566666544
No 170
>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=49.72 E-value=10 Score=33.43 Aligned_cols=39 Identities=26% Similarity=0.555 Sum_probs=23.0
Q ss_pred CccCCCCcccccChHHHHHhcCCccccCcCCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCC
Q psy12030 98 KYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAK 161 (245)
Q Consensus 98 ~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~ 161 (245)
...|..||.. ..|+.|+... ..|. . .....|..||....
T Consensus 213 ~~~C~~Cg~~--------------~~C~~C~~~l------~~h~----~-~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 213 NLLCRSCGYI--------------LCCPNCDVSL------TYHK----K-EGKLRCHYCGYQEP 251 (505)
T ss_pred eeEhhhCcCc--------------cCCCCCCCce------EEec----C-CCeEEcCCCcCcCC
Confidence 3578888877 5788887543 2232 1 44566777765543
No 171
>PRK05978 hypothetical protein; Provisional
Probab=49.69 E-value=6.1 Score=28.38 Aligned_cols=10 Identities=20% Similarity=0.693 Sum_probs=6.0
Q ss_pred ccCCCcccCC
Q psy12030 207 QCPHCPHKAK 216 (245)
Q Consensus 207 ~C~~C~~~f~ 216 (245)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 5666666554
No 172
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=48.95 E-value=9.4 Score=22.35 Aligned_cols=39 Identities=23% Similarity=0.539 Sum_probs=19.9
Q ss_pred eeCCC-CCCccCChhHHHHHHhHHhCCCCCcccCC----CcccCC
Q psy12030 177 FACNV-CGKGYRYKTGLYRHKREECGQEPKYQCPH----CPHKAK 216 (245)
Q Consensus 177 ~~C~~-C~~~f~~~~~l~~H~~~h~~~~~~~~C~~----C~~~f~ 216 (245)
..|+. |+..-..+..|..|+...-. .++..|++ |+..+.
T Consensus 10 v~C~~~cc~~~i~r~~l~~H~~~~C~-~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 10 VPCPNGCCNEMIPRKELDDHLENECP-KRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EE-TT--S-BEEECCCHHHHHHTTST-TSEEE-SS----S--EEE
T ss_pred eeCCCCCcccceeHHHHHHHHHccCC-CCcEECCCCCCCCCCccc
Confidence 55665 33333345567777775545 66677777 776554
No 173
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.67 E-value=6.2 Score=36.23 Aligned_cols=19 Identities=21% Similarity=0.546 Sum_probs=13.7
Q ss_pred CccCCCCcccccChHHHHHhcCCccccCcCCCc
Q psy12030 98 KYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKE 130 (245)
Q Consensus 98 ~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~ 130 (245)
...|..||.. ..|+.|+..
T Consensus 435 ~l~C~~Cg~v--------------~~Cp~Cd~~ 453 (730)
T COG1198 435 LLLCRDCGYI--------------AECPNCDSP 453 (730)
T ss_pred eeecccCCCc--------------ccCCCCCcc
Confidence 4668888877 577777754
No 174
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.29 E-value=11 Score=25.92 Aligned_cols=10 Identities=20% Similarity=0.856 Sum_probs=5.2
Q ss_pred eeCCCCCCcc
Q psy12030 177 FACNVCGKGY 186 (245)
Q Consensus 177 ~~C~~C~~~f 186 (245)
..|..||..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 5555555443
No 175
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.69 E-value=11 Score=25.21 Aligned_cols=14 Identities=7% Similarity=-0.047 Sum_probs=7.7
Q ss_pred CCCccCCCCCCcCC
Q psy12030 148 EPKYQCPHCPHRAK 161 (245)
Q Consensus 148 ~~~~~C~~C~~~f~ 161 (245)
..|..|+.||++|.
T Consensus 24 rdPiVsPytG~s~P 37 (129)
T COG4530 24 RDPIVSPYTGKSYP 37 (129)
T ss_pred CCccccCcccccch
Confidence 44555555665553
No 176
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=47.03 E-value=8.9 Score=19.01 Aligned_cols=7 Identities=29% Similarity=1.265 Sum_probs=2.3
Q ss_pred eeCCCCC
Q psy12030 177 FACNVCG 183 (245)
Q Consensus 177 ~~C~~C~ 183 (245)
|.|..|+
T Consensus 16 Y~C~~Cd 22 (30)
T PF07649_consen 16 YRCSECD 22 (30)
T ss_dssp EE-TTT-
T ss_pred EECccCC
Confidence 4444443
No 177
>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=46.63 E-value=17 Score=20.98 Aligned_cols=28 Identities=25% Similarity=0.594 Sum_probs=17.8
Q ss_pred eCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCCh
Q psy12030 178 ACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHK 218 (245)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~ 218 (245)
.|..|++.|.. . .+.+.|..||..|-..
T Consensus 4 ~C~~C~~~F~~------------~-~rk~~Cr~Cg~~~C~~ 31 (57)
T cd00065 4 SCMGCGKPFTL------------T-RRRHHCRNCGRIFCSK 31 (57)
T ss_pred cCcccCccccC------------C-ccccccCcCcCCcChH
Confidence 46677777763 2 4456777777776543
No 178
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=46.35 E-value=10 Score=20.31 Aligned_cols=14 Identities=21% Similarity=0.615 Sum_probs=11.7
Q ss_pred CcccCCCcccCCCh
Q psy12030 205 KYQCPHCPHKAKHK 218 (245)
Q Consensus 205 ~~~C~~C~~~f~~~ 218 (245)
||.|..|+..|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78999999888765
No 179
>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=45.56 E-value=4.4 Score=21.38 Aligned_cols=30 Identities=13% Similarity=0.316 Sum_probs=14.6
Q ss_pred cccCCCcccCCChHHHHHhHhhhCCCCCCCCCCC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEG 239 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C 239 (245)
..||.|+.. ..+.+|=+...|-..|+|..|
T Consensus 6 v~CP~C~s~----~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQST----EGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCC----CcceeCCCCCCCCEeEecCcC
Confidence 345666532 113334444445555666655
No 180
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.52 E-value=13 Score=23.12 Aligned_cols=30 Identities=20% Similarity=0.747 Sum_probs=18.3
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCccc
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHK 214 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~ 214 (245)
|+|..||..|. +.+|+ .+...-.|+.|+-.
T Consensus 13 Y~c~~cg~~~d----vvq~~----~ddplt~ce~c~a~ 42 (82)
T COG2331 13 YECTECGNRFD----VVQAM----TDDPLTTCEECGAR 42 (82)
T ss_pred EeecccchHHH----HHHhc----ccCccccChhhChH
Confidence 88888886654 44443 22444568888753
No 181
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=45.33 E-value=15 Score=25.81 Aligned_cols=22 Identities=27% Similarity=0.341 Sum_probs=10.9
Q ss_pred cccCCCcccCCChHHHHHhHhhhCC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
..|-++|+.|. +|++|+.+|+|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 34555555543 34555555554
No 182
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=45.15 E-value=34 Score=25.46 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=5.9
Q ss_pred eeCCCCCCccC
Q psy12030 177 FACNVCGKGYR 187 (245)
Q Consensus 177 ~~C~~C~~~f~ 187 (245)
|.|+.|...|+
T Consensus 114 y~C~~~~~r~s 124 (176)
T COG1675 114 YVCPNCHVKYS 124 (176)
T ss_pred eeCCCCCCccc
Confidence 55655554444
No 183
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=44.65 E-value=12 Score=25.57 Aligned_cols=9 Identities=22% Similarity=0.593 Sum_probs=5.3
Q ss_pred eeCCCCCCc
Q psy12030 177 FACNVCGKG 185 (245)
Q Consensus 177 ~~C~~C~~~ 185 (245)
..|..||..
T Consensus 71 ~~C~~Cg~~ 79 (114)
T PRK03681 71 CWCETCQQY 79 (114)
T ss_pred EEcccCCCe
Confidence 566666643
No 184
>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=44.54 E-value=13 Score=22.52 Aligned_cols=11 Identities=36% Similarity=1.238 Sum_probs=3.9
Q ss_pred eeccccccccc
Q psy12030 70 FECQVCGKRYK 80 (245)
Q Consensus 70 ~~C~~C~~~f~ 80 (245)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 35666666663
No 185
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=44.44 E-value=9.5 Score=19.63 Aligned_cols=11 Identities=0% Similarity=-0.713 Sum_probs=5.1
Q ss_pred CCCCCCCCccc
Q psy12030 233 ILPPQEGRVWT 243 (245)
Q Consensus 233 ~~~C~~C~~~f 243 (245)
-+.|..||..|
T Consensus 21 ~~~C~~Cg~~~ 31 (33)
T PF08792_consen 21 YEVCIFCGSSF 31 (33)
T ss_pred eEEcccCCcEe
Confidence 34455555444
No 186
>KOG2593|consensus
Probab=44.03 E-value=19 Score=30.55 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=15.5
Q ss_pred CcccCCCcccCCChHHHHHhHhhhCCCCCCCCCCCC
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIKHSDRILPPQEGR 240 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 240 (245)
.|.|+.|.+.|+....++. .-....-|.|..|+
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQL---LDNETGEFHCENCG 160 (436)
T ss_pred cccCCccccchhhhHHHHh---hcccCceEEEecCC
Confidence 4555555555555444432 11223345555554
No 187
>PHA02998 RNA polymerase subunit; Provisional
Probab=43.96 E-value=3.3 Score=30.43 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=6.8
Q ss_pred cccCCCcccCC
Q psy12030 206 YQCPHCPHKAK 216 (245)
Q Consensus 206 ~~C~~C~~~f~ 216 (245)
|.|..||+.|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 56666666554
No 188
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=43.12 E-value=10 Score=21.44 Aligned_cols=13 Identities=15% Similarity=0.606 Sum_probs=8.5
Q ss_pred CcccCCCcccCCC
Q psy12030 205 KYQCPHCPHKAKH 217 (245)
Q Consensus 205 ~~~C~~C~~~f~~ 217 (245)
.|.|+.||..+..
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 5777777765543
No 189
>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 PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=42.90 E-value=18 Score=17.98 Aligned_cols=7 Identities=29% Similarity=1.156 Sum_probs=3.2
Q ss_pred eeCCCCC
Q psy12030 177 FACNVCG 183 (245)
Q Consensus 177 ~~C~~C~ 183 (245)
|.|..|+
T Consensus 16 Y~C~~c~ 22 (30)
T PF03107_consen 16 YHCSECC 22 (30)
T ss_pred EEeCCCC
Confidence 4444444
No 191
>KOG1280|consensus
Probab=42.86 E-value=22 Score=29.30 Aligned_cols=36 Identities=25% Similarity=0.444 Sum_probs=27.7
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCc--ccCCCcc
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKY--QCPHCPH 213 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~--~C~~C~~ 213 (245)
|.|++|+..=.+...|..|....|. +-++ .|++|+-
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~Hp-da~~~~icp~c~~ 117 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQHP-EASTSVICPLCAA 117 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcCc-ccCcceeeecccc
Confidence 8999999888888889999888777 4443 4677753
No 192
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=42.75 E-value=20 Score=20.68 Aligned_cols=15 Identities=20% Similarity=0.780 Sum_probs=8.8
Q ss_pred eeCCCCCCccCChhH
Q psy12030 177 FACNVCGKGYRYKTG 191 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~ 191 (245)
++|+.||..|.....
T Consensus 29 W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN 43 (55)
T ss_pred EECCCCCCeeEccHh
Confidence 666666666554433
No 193
>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=42.43 E-value=15 Score=22.28 Aligned_cols=28 Identities=21% Similarity=0.666 Sum_probs=16.2
Q ss_pred eCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCC
Q psy12030 178 ACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAK 216 (245)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~ 216 (245)
.|+.||..-.. ....+.|.|+.||....
T Consensus 30 ~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKK-----------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccccccc-----------ccccceEEcCCCCCEEC
Confidence 46667655443 12255677777776643
No 194
>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=41.48 E-value=20 Score=18.82 Aligned_cols=11 Identities=36% Similarity=0.923 Sum_probs=7.2
Q ss_pred eeccccccccc
Q psy12030 70 FECQVCGKRYK 80 (245)
Q Consensus 70 ~~C~~C~~~f~ 80 (245)
+.|+.||.+|.
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 45777777764
No 195
>KOG3408|consensus
Probab=41.16 E-value=13 Score=25.51 Aligned_cols=23 Identities=26% Similarity=0.509 Sum_probs=15.4
Q ss_pred CcccCCCcccCCChHHHHHhHhh
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAI 227 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~ 227 (245)
.|-|-.|.+-|.+...|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 46677777777777777776654
No 196
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=40.32 E-value=18 Score=32.96 Aligned_cols=40 Identities=5% Similarity=-0.057 Sum_probs=21.0
Q ss_pred ccccceeeeeecccCcceeeeeccCCCCCCcccccccccC
Q psy12030 16 MPVCLYAMFVEKSTNTKMEFIAIRNSNVDKSLNTNVLNAH 55 (245)
Q Consensus 16 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 (245)
|..||.+|...+.+.=..+...+.....|..|.+.+.+..
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~ 165 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPL 165 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcc
Confidence 4555555555555555555555555555555554444433
No 197
>KOG4377|consensus
Probab=39.64 E-value=23 Score=29.93 Aligned_cols=101 Identities=17% Similarity=0.405 Sum_probs=63.6
Q ss_pred ccc--CcCCCccCchhHHHhHHhhhcCCC-----------CCccCC--CCCCcCCChHHHHhhhcCCCCc---------e
Q psy12030 122 FAC--DVCGKEYKYKRGLYRHKKFECGQE-----------PKYQCP--HCPHRAKHKANLKTHIAPQLGV---------F 177 (245)
Q Consensus 122 ~~C--~~C~~~f~~~~~l~~H~~~h~~~~-----------~~~~C~--~C~~~f~~~~~l~~H~~~h~~~---------~ 177 (245)
|.| ..|+..+.++..+.+|..+|...+ ..|.|. .|.+ +-++...|..-|+.. |
T Consensus 272 yhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~Gfrrthf 348 (480)
T KOG4377|consen 272 YHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHF 348 (480)
T ss_pred hcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceeccee
Confidence 555 359888888999999988885422 225564 4877 444555665555542 7
Q ss_pred eCCCCC--CccCChhHHHHHHhHHhCC---------------CC------------CcccCC--CcccCCChHHHHHhHh
Q psy12030 178 ACNVCG--KGYRYKTGLYRHKREECGQ---------------EP------------KYQCPH--CPHKAKHKANLKTHIA 226 (245)
Q Consensus 178 ~C~~C~--~~f~~~~~l~~H~~~h~~~---------------~~------------~~~C~~--C~~~f~~~~~l~~H~~ 226 (245)
.|..+| .+|. ...|...|-.+ +- .+-|.. |+..+.+.+.+..|.+
T Consensus 349 hC~r~gCTdtfK----~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkr 424 (480)
T KOG4377|consen 349 HCQRIGCTDTFK----DSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASHKR 424 (480)
T ss_pred EEeccCCccccc----cccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhhhh
Confidence 788877 5555 33444333110 11 134533 8999999999999988
Q ss_pred hhC
Q psy12030 227 IKH 229 (245)
Q Consensus 227 ~~~ 229 (245)
.|-
T Consensus 425 khe 427 (480)
T KOG4377|consen 425 KHE 427 (480)
T ss_pred hhh
Confidence 774
No 198
>KOG3352|consensus
Probab=39.45 E-value=15 Score=26.25 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=6.1
Q ss_pred CCcccCCCcccC
Q psy12030 204 PKYQCPHCPHKA 215 (245)
Q Consensus 204 ~~~~C~~C~~~f 215 (245)
++.+|++||..|
T Consensus 132 e~~rc~eCG~~f 143 (153)
T KOG3352|consen 132 ETQRCPECGHYF 143 (153)
T ss_pred CcccCCcccceE
Confidence 344555555444
No 199
>KOG4124|consensus
Probab=39.35 E-value=9.4 Score=31.34 Aligned_cols=42 Identities=21% Similarity=0.374 Sum_probs=28.9
Q ss_pred CCCcccCC--CcccCCChHHHHHhHhhhC-------------------CCCCCCCCCCCcccc
Q psy12030 203 EPKYQCPH--CPHKAKHKANLKTHIAIKH-------------------SDRILPPQEGRVWTR 244 (245)
Q Consensus 203 ~~~~~C~~--C~~~f~~~~~l~~H~~~~~-------------------~~~~~~C~~C~~~f~ 244 (245)
.++|+|++ |.+.+.....|..|...-| ..|+|+|++|.++.+
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k 409 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYK 409 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhc
Confidence 45677744 7777777667776654333 358899999988764
No 200
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.77 E-value=8.4 Score=29.68 Aligned_cols=9 Identities=22% Similarity=0.733 Sum_probs=6.8
Q ss_pred eeCCCCCCc
Q psy12030 177 FACNVCGKG 185 (245)
Q Consensus 177 ~~C~~C~~~ 185 (245)
+.|+.|+.+
T Consensus 63 vvCP~C~yA 71 (267)
T COG1655 63 VVCPICYYA 71 (267)
T ss_pred EEcchhhHH
Confidence 678888864
No 201
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=37.92 E-value=11 Score=34.99 Aligned_cols=12 Identities=50% Similarity=1.226 Sum_probs=0.0
Q ss_pred CCCcccCCCccc
Q psy12030 203 EPKYQCPHCPHK 214 (245)
Q Consensus 203 ~~~~~C~~C~~~ 214 (245)
+.-|.|+.|+..
T Consensus 678 ~~~~~Cp~C~~~ 689 (900)
T PF03833_consen 678 EPVYVCPDCGIE 689 (900)
T ss_dssp ------------
T ss_pred ccceeccccccc
Confidence 344566666544
No 202
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.82 E-value=20 Score=32.91 Aligned_cols=20 Identities=20% Similarity=0.479 Sum_probs=13.8
Q ss_pred CccCCCCcccccChHHHHHhcCCccccCcCCCcc
Q psy12030 98 KYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEY 131 (245)
Q Consensus 98 ~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f 131 (245)
...|..||.. ..|+.|+..+
T Consensus 381 ~~~C~~Cg~~--------------~~C~~C~~~l 400 (679)
T PRK05580 381 FLLCRDCGWV--------------AECPHCDASL 400 (679)
T ss_pred ceEhhhCcCc--------------cCCCCCCCce
Confidence 4667778776 5777787643
No 203
>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=36.97 E-value=16 Score=21.30 Aligned_cols=10 Identities=50% Similarity=1.212 Sum_probs=4.9
Q ss_pred eecccccccc
Q psy12030 70 FECQVCGKRY 79 (245)
Q Consensus 70 ~~C~~C~~~f 79 (245)
+.|+.||..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 3455555544
No 204
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=36.65 E-value=30 Score=18.89 Aligned_cols=12 Identities=33% Similarity=1.223 Sum_probs=5.7
Q ss_pred eCCCCCCccCCh
Q psy12030 178 ACNVCGKGYRYK 189 (245)
Q Consensus 178 ~C~~C~~~f~~~ 189 (245)
.|.+||+.|...
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 344555555443
No 205
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=36.56 E-value=6.3 Score=27.84 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=8.6
Q ss_pred CCCcccCCCcccC
Q psy12030 203 EPKYQCPHCPHKA 215 (245)
Q Consensus 203 ~~~~~C~~C~~~f 215 (245)
.+|.+|+.||..|
T Consensus 110 g~~~RCpeCG~~f 122 (136)
T PF01215_consen 110 GKPQRCPECGQVF 122 (136)
T ss_dssp TSEEEETTTEEEE
T ss_pred CCccCCCCCCeEE
Confidence 3467777777655
No 206
>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=36.46 E-value=33 Score=18.25 Aligned_cols=21 Identities=24% Similarity=0.458 Sum_probs=8.3
Q ss_pred CcccCCCcccCC-Ch-HHHHHhH
Q psy12030 205 KYQCPHCPHKAK-HK-ANLKTHI 225 (245)
Q Consensus 205 ~~~C~~C~~~f~-~~-~~l~~H~ 225 (245)
.|-|++|...|+ +. +.-+.|.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~ 25 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHE 25 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT
T ss_pred CeecccccceecCCChHHHHHhh
Confidence 477888887773 33 3335554
No 207
>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=36.31 E-value=11 Score=25.63 Aligned_cols=12 Identities=25% Similarity=0.730 Sum_probs=6.8
Q ss_pred eeCCCCCCccCC
Q psy12030 177 FACNVCGKGYRY 188 (245)
Q Consensus 177 ~~C~~C~~~f~~ 188 (245)
..|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 566666666653
No 208
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=36.23 E-value=18 Score=19.42 Aligned_cols=14 Identities=29% Similarity=0.752 Sum_probs=5.7
Q ss_pred ccCCCCcccccChH
Q psy12030 99 YQCPQCKDSFFSWS 112 (245)
Q Consensus 99 ~~C~~C~~~f~~~~ 112 (245)
..|+.|+..+.+..
T Consensus 20 d~C~~C~G~W~d~~ 33 (41)
T PF13453_consen 20 DVCPSCGGIWFDAG 33 (41)
T ss_pred EECCCCCeEEccHH
Confidence 33444444443333
No 209
>KOG0978|consensus
Probab=35.69 E-value=22 Score=32.41 Aligned_cols=20 Identities=20% Similarity=0.511 Sum_probs=12.8
Q ss_pred CcccCCCcccCCChHHHHHh
Q psy12030 205 KYQCPHCPHKAKHKANLKTH 224 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H 224 (245)
.-+||.||..|....-+..|
T Consensus 678 qRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 678 QRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred cCCCCCCCCCCCcccccccC
Confidence 34777787777766555444
No 210
>KOG0782|consensus
Probab=35.50 E-value=4.1 Score=35.71 Aligned_cols=51 Identities=24% Similarity=0.423 Sum_probs=28.4
Q ss_pred HHhcchhcccCCCCCccCCCCcccccChHHHHHhcCCccccCcCCCccCchh
Q psy12030 84 GLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHKNLSGMFACDVCGKEYKYKR 135 (245)
Q Consensus 84 ~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~C~~C~~~f~~~~ 135 (245)
.|.+|--.|.. ...-+|..||+.|..+..++.-......|+.|-..|..+.
T Consensus 240 ~fvrHHWVHrr-RqeGkC~~CgKgFQQKf~FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRR-RQEGKCNTCGKGFQQKFFFHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHh-hhccccchhhhhhhhheeeccccEEEEEehHHHHHhhcch
Confidence 34444444433 3345677777777666665554444566666666665543
No 211
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=35.31 E-value=41 Score=24.08 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=10.6
Q ss_pred eeCCCCCCccCChhHHH
Q psy12030 177 FACNVCGKGYRYKTGLY 193 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~ 193 (245)
|.|+.||+.|-.-+++.
T Consensus 125 ~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 125 WRCPGCGKIYWEGSHWR 141 (147)
T ss_pred EECCCCCCEecccccHH
Confidence 66777777666555443
No 212
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=35.01 E-value=4.3 Score=27.13 Aligned_cols=11 Identities=9% Similarity=-0.239 Sum_probs=6.2
Q ss_pred CCCCCCCcccc
Q psy12030 234 LPPQEGRVWTR 244 (245)
Q Consensus 234 ~~C~~C~~~f~ 244 (245)
|.|..||+.++
T Consensus 91 y~C~~C~~~w~ 101 (104)
T TIGR01384 91 YKCTKCGYVWR 101 (104)
T ss_pred EEeCCCCCeeE
Confidence 55655655544
No 213
>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=34.60 E-value=7.8 Score=19.13 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=4.7
Q ss_pred eCCCCCCcc
Q psy12030 178 ACNVCGKGY 186 (245)
Q Consensus 178 ~C~~C~~~f 186 (245)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455555555
No 214
>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=34.48 E-value=23 Score=20.37 Aligned_cols=22 Identities=23% Similarity=0.563 Sum_probs=7.7
Q ss_pred ccCCCCCCcCCChHHHHhhhcC
Q psy12030 151 YQCPHCPHRAKHKANLKTHIAP 172 (245)
Q Consensus 151 ~~C~~C~~~f~~~~~l~~H~~~ 172 (245)
|.|+.|+..|-..-.+..|...
T Consensus 22 y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp E--TTTT--B-HHHHHTTTTTS
T ss_pred EECCCCCCccccCcChhhhccc
Confidence 4444444444444444444333
No 215
>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=34.20 E-value=4.4 Score=32.81 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.1
Q ss_pred eeCCCCCC
Q psy12030 177 FACNVCGK 184 (245)
Q Consensus 177 ~~C~~C~~ 184 (245)
+.|..|+.
T Consensus 239 e~C~~C~~ 246 (290)
T PF04216_consen 239 EVCESCGS 246 (290)
T ss_dssp EEETTTTE
T ss_pred EECCcccc
Confidence 45555553
No 216
>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=34.12 E-value=29 Score=30.08 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=20.0
Q ss_pred CcccCCCcccCCChHHHHHhHhhhCC
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIKHS 230 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 230 (245)
-+.|+.|.+.|.+...+..|+...|.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhh
Confidence 36688888888888888888876654
No 217
>KOG3408|consensus
Probab=33.88 E-value=21 Score=24.57 Aligned_cols=27 Identities=19% Similarity=0.396 Sum_probs=23.3
Q ss_pred CCCceecccccccccChhHHhcchhcc
Q psy12030 66 YSKGFECQVCGKRYKYKRGLHRHKQDE 92 (245)
Q Consensus 66 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 92 (245)
+-..|.|-.|.+-|.+...|+.|.++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 445699999999999999999998753
No 218
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=33.79 E-value=14 Score=21.02 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=4.3
Q ss_pred cccCCCcccC
Q psy12030 206 YQCPHCPHKA 215 (245)
Q Consensus 206 ~~C~~C~~~f 215 (245)
|.|..|+.+|
T Consensus 8 y~CDLCn~~~ 17 (57)
T PF14445_consen 8 YSCDLCNSSH 17 (57)
T ss_pred HhHHhhcccC
Confidence 4444444433
No 219
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=33.75 E-value=16 Score=27.50 Aligned_cols=12 Identities=25% Similarity=0.429 Sum_probs=7.2
Q ss_pred eeCCCCCCccCC
Q psy12030 177 FACNVCGKGYRY 188 (245)
Q Consensus 177 ~~C~~C~~~f~~ 188 (245)
+.|..||+.+..
T Consensus 44 ~~C~~CgYR~~D 55 (201)
T COG1779 44 GVCERCGYRSTD 55 (201)
T ss_pred EEccccCCcccc
Confidence 556666665554
No 220
>KOG0717|consensus
Probab=33.51 E-value=24 Score=30.36 Aligned_cols=22 Identities=27% Similarity=0.431 Sum_probs=18.5
Q ss_pred cccCCCcccCCChHHHHHhHhh
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAI 227 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~ 227 (245)
+-|.+|+++|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7888888888888888888764
No 221
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.13 E-value=53 Score=24.07 Aligned_cols=16 Identities=31% Similarity=0.679 Sum_probs=9.2
Q ss_pred eeCCCCCCccCChhHH
Q psy12030 177 FACNVCGKGYRYKTGL 192 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l 192 (245)
|.|+.||+.|-.-+++
T Consensus 131 ~~C~~CgkiYW~GsHw 146 (165)
T COG1656 131 YRCPKCGKIYWKGSHW 146 (165)
T ss_pred eECCCCcccccCchHH
Confidence 5566666666554444
No 222
>KOG1280|consensus
Probab=32.93 E-value=38 Score=27.95 Aligned_cols=37 Identities=22% Similarity=0.522 Sum_probs=28.5
Q ss_pred CCCccCCCCCCcCCChHHHHhhhcCCCCc----eeCCCCCC
Q psy12030 148 EPKYQCPHCPHRAKHKANLKTHIAPQLGV----FACNVCGK 184 (245)
Q Consensus 148 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~----~~C~~C~~ 184 (245)
...|.|+.|+.+-.+...|..|+...+.. ..|++|+.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 44699999999999999999997544332 67888764
No 223
>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=32.67 E-value=13 Score=20.37 Aligned_cols=15 Identities=27% Similarity=0.609 Sum_probs=9.0
Q ss_pred CCcccCCCcccCCCh
Q psy12030 204 PKYQCPHCPHKAKHK 218 (245)
Q Consensus 204 ~~~~C~~C~~~f~~~ 218 (245)
.|+.|+.|+..|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 468888888887655
No 224
>KOG0782|consensus
Probab=32.14 E-value=4.7 Score=35.34 Aligned_cols=54 Identities=20% Similarity=0.381 Sum_probs=38.1
Q ss_pred ccCCCCCccccccCCCceecccccccccChhHHhcchhcccCCCCCccCCCCcccccChH
Q psy12030 53 NAHGFNIWPLVQQYSKGFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWS 112 (245)
Q Consensus 53 ~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~ 112 (245)
....+..|..+|.....=+|..||+.|..+..+ |..+.....|.+|...|..+.
T Consensus 237 rE~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F------hsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 237 RESGFVRHHWVHRRRQEGKCNTCGKGFQQKFFF------HSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccccchHHhHhhHhhhccccchhhhhhhhheee------ccccEEEEEehHHHHHhhcch
Confidence 334666677777655556899999999766543 333245688999999997765
No 225
>KOG2636|consensus
Probab=31.68 E-value=31 Score=29.48 Aligned_cols=29 Identities=17% Similarity=0.336 Sum_probs=23.4
Q ss_pred hHHhCCCCCcccCCCc-ccCCChHHHHHhHh
Q psy12030 197 REECGQEPKYQCPHCP-HKAKHKANLKTHIA 226 (245)
Q Consensus 197 ~~h~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 226 (245)
+.|.- ...|.|.+|| +++..+..+.+|..
T Consensus 394 KLHGL-~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGL-DIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCC-CcccceeeccCccccCcHHHHHHhH
Confidence 45544 7789999998 89999999999964
No 226
>KOG1842|consensus
Probab=31.64 E-value=20 Score=30.60 Aligned_cols=29 Identities=28% Similarity=0.421 Sum_probs=25.4
Q ss_pred CceecccccccccChhHHhcchhcccCCC
Q psy12030 68 KGFECQVCGKRYKYKRGLHRHKQDECGQE 96 (245)
Q Consensus 68 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 96 (245)
+.|.|++|...|.+...|..|....|+++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 56999999999999999999998877643
No 227
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=31.47 E-value=17 Score=21.07 Aligned_cols=8 Identities=13% Similarity=-0.126 Sum_probs=4.0
Q ss_pred CCCCCCCC
Q psy12030 233 ILPPQEGR 240 (245)
Q Consensus 233 ~~~C~~C~ 240 (245)
|.-|++|.
T Consensus 28 PlyCpKCK 35 (55)
T PF14205_consen 28 PLYCPKCK 35 (55)
T ss_pred cccCCCCC
Confidence 44455554
No 228
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=31.31 E-value=5.1 Score=25.54 Aligned_cols=10 Identities=40% Similarity=1.109 Sum_probs=3.1
Q ss_pred CCceeccccc
Q psy12030 67 SKGFECQVCG 76 (245)
Q Consensus 67 ~~~~~C~~C~ 76 (245)
++.|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 4557777776
No 229
>KOG2272|consensus
Probab=31.30 E-value=48 Score=26.07 Aligned_cols=19 Identities=21% Similarity=0.553 Sum_probs=13.6
Q ss_pred eecccccccccChhHHhcc
Q psy12030 70 FECQVCGKRYKYKRGLHRH 88 (245)
Q Consensus 70 ~~C~~C~~~f~~~~~l~~H 88 (245)
|.|++|++...+...+...
T Consensus 100 F~Cd~Cn~~Lad~gf~rnq 118 (332)
T KOG2272|consen 100 FRCDLCNKHLADQGFYRNQ 118 (332)
T ss_pred chhHHHHHHHhhhhhHhhc
Confidence 7888888877776665543
No 230
>PTZ00448 hypothetical protein; Provisional
Probab=31.16 E-value=36 Score=28.44 Aligned_cols=24 Identities=17% Similarity=0.351 Sum_probs=19.9
Q ss_pred CcccCCCcccCCChHHHHHhHhhh
Q psy12030 205 KYQCPHCPHKAKHKANLKTHIAIK 228 (245)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~ 228 (245)
.|.|..|+..|.+....+.|+++-
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 588999999998888888888753
No 231
>KOG3507|consensus
Probab=31.15 E-value=17 Score=21.38 Aligned_cols=31 Identities=23% Similarity=0.555 Sum_probs=19.9
Q ss_pred ceeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCCh
Q psy12030 176 VFACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHK 218 (245)
Q Consensus 176 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~ 218 (245)
.|.|..|+..-. |. . .-.++|.+||....++
T Consensus 20 iYiCgdC~~en~----lk-------~-~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 20 IYICGDCGQENT----LK-------R-GDVIRCRECGYRILYK 50 (62)
T ss_pred EEEecccccccc----cc-------C-CCcEehhhcchHHHHH
Confidence 488988885422 11 1 4468899998765544
No 232
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=30.14 E-value=29 Score=26.74 Aligned_cols=13 Identities=23% Similarity=0.526 Sum_probs=6.6
Q ss_pred CCCcccCCCcccC
Q psy12030 203 EPKYQCPHCPHKA 215 (245)
Q Consensus 203 ~~~~~C~~C~~~f 215 (245)
.++.+|+.||..|
T Consensus 179 GkpqRCpECGqVF 191 (268)
T PTZ00043 179 GFLYRCGECDQIF 191 (268)
T ss_pred CCCccCCCCCcEE
Confidence 3455555555443
No 233
>PRK00420 hypothetical protein; Validated
Probab=29.85 E-value=51 Score=22.48 Aligned_cols=11 Identities=45% Similarity=0.767 Sum_probs=5.7
Q ss_pred ceeCCCCCCcc
Q psy12030 176 VFACNVCGKGY 186 (245)
Q Consensus 176 ~~~C~~C~~~f 186 (245)
...|+.||...
T Consensus 40 ~~~Cp~Cg~~~ 50 (112)
T PRK00420 40 EVVCPVHGKVY 50 (112)
T ss_pred ceECCCCCCee
Confidence 35555555543
No 234
>KOG0402|consensus
Probab=29.19 E-value=22 Score=22.57 Aligned_cols=31 Identities=26% Similarity=0.692 Sum_probs=17.7
Q ss_pred CccCCCCCCcCCChHHHHhhhcCCCCceeCCCCCCccCC
Q psy12030 150 KYQCPHCPHRAKHKANLKTHIAPQLGVFACNVCGKGYRY 188 (245)
Q Consensus 150 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~ 188 (245)
.|.|+.||+.-.. +.-.+.|.|..|.+.+.-
T Consensus 36 ky~CsfCGK~~vK--------R~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 36 KYTCSFCGKKTVK--------RKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhcchhhhh--------hhceeEEecCCccceecc
Confidence 3677777765432 223345777777766543
No 235
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.15 E-value=26 Score=20.78 Aligned_cols=7 Identities=29% Similarity=1.341 Sum_probs=3.6
Q ss_pred ecccccc
Q psy12030 71 ECQVCGK 77 (245)
Q Consensus 71 ~C~~C~~ 77 (245)
+|-+|++
T Consensus 4 kCiiCd~ 10 (68)
T COG4896 4 KCIICDR 10 (68)
T ss_pred eEEEecc
Confidence 4555554
No 236
>KOG2071|consensus
Probab=29.12 E-value=39 Score=30.06 Aligned_cols=27 Identities=19% Similarity=0.445 Sum_probs=23.7
Q ss_pred CCCcccCCCcccCCChHHHHHhHhhhC
Q psy12030 203 EPKYQCPHCPHKAKHKANLKTHIAIKH 229 (245)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 229 (245)
..|..|..||.+|........||..|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 667899999999999999999888775
No 237
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=28.98 E-value=43 Score=27.23 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=21.2
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCChH
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKHKA 219 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~ 219 (245)
.+|+.|+.....+. |. +..+.|+.|+.-|.-..
T Consensus 39 ~kc~~C~~~~~~~~-l~---------~~~~vcp~c~~h~rltA 71 (296)
T CHL00174 39 VQCENCYGLNYKKF-LK---------SKMNICEQCGYHLKMSS 71 (296)
T ss_pred eECCCccchhhHHH-HH---------HcCCCCCCCCCCcCCCH
Confidence 67888887654332 21 33578999988776543
No 238
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=28.83 E-value=13 Score=33.70 Aligned_cols=78 Identities=21% Similarity=0.373 Sum_probs=49.5
Q ss_pred ceecccccccccChhHHhcchhcccCCCCCccCCCCcccccChHHHHH-----hcCCccccCcCCCccCchhHHHhHHhh
Q psy12030 69 GFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSAFHK-----NLSGMFACDVCGKEYKYKRGLYRHKKF 143 (245)
Q Consensus 69 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~-----h~~~~~~C~~C~~~f~~~~~l~~H~~~ 143 (245)
.-.|+.|-+-+.+.++-.-+ =+-..|..||-.|+--..|-- -|..--.|+.|.+.+.+..+-+-
T Consensus 101 ~a~C~~Cl~Ei~dp~~rrY~-------YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRf---- 169 (750)
T COG0068 101 AATCEDCLEEIFDPNSRRYL-------YPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRF---- 169 (750)
T ss_pred hhhhHHHHHHhcCCCCccee-------ccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcccccc----
Confidence 35788887766655442221 123458889999987777722 22333458999888887776333
Q ss_pred hcCCCCCccCCCCCCcC
Q psy12030 144 ECGQEPKYQCPHCPHRA 160 (245)
Q Consensus 144 h~~~~~~~~C~~C~~~f 160 (245)
| -.+..|+.||-..
T Consensus 170 H---AQp~aCp~CGP~~ 183 (750)
T COG0068 170 H---AQPIACPKCGPHL 183 (750)
T ss_pred c---cccccCcccCCCe
Confidence 3 3467899998643
No 239
>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=28.73 E-value=24 Score=25.33 Aligned_cols=10 Identities=40% Similarity=1.394 Sum_probs=6.1
Q ss_pred eeCCCCCCcc
Q psy12030 177 FACNVCGKGY 186 (245)
Q Consensus 177 ~~C~~C~~~f 186 (245)
|.|..|+..+
T Consensus 124 ~~C~~C~~~~ 133 (157)
T PF10263_consen 124 YRCPSCGREY 133 (157)
T ss_pred EEcCCCCCEe
Confidence 6666666554
No 240
>COG2879 Uncharacterized small protein [Function unknown]
Probab=28.58 E-value=72 Score=19.15 Aligned_cols=18 Identities=28% Similarity=0.364 Sum_probs=12.1
Q ss_pred CChHHHHHhHhhhCCCCC
Q psy12030 216 KHKANLKTHIAIKHSDRI 233 (245)
Q Consensus 216 ~~~~~l~~H~~~~~~~~~ 233 (245)
.+-.++..||+.+|.++|
T Consensus 23 pdYdnYVehmr~~hPd~p 40 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CcHHHHHHHHHHhCcCCC
Confidence 345566777777777766
No 241
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.36 E-value=41 Score=24.02 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=6.5
Q ss_pred eeCCCCCCccC
Q psy12030 177 FACNVCGKGYR 187 (245)
Q Consensus 177 ~~C~~C~~~f~ 187 (245)
|.|..|+..+.
T Consensus 113 y~C~~C~~~~~ 123 (146)
T smart00731 113 YRCTGCGQRYL 123 (146)
T ss_pred EECCCCCCCCc
Confidence 66666665543
No 242
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=27.08 E-value=39 Score=26.51 Aligned_cols=14 Identities=21% Similarity=0.795 Sum_probs=8.7
Q ss_pred CCCceecccccccc
Q psy12030 66 YSKGFECQVCGKRY 79 (245)
Q Consensus 66 ~~~~~~C~~C~~~f 79 (245)
....|.|..|...+
T Consensus 109 ~drqFaC~~Cd~~W 122 (278)
T PF15135_consen 109 VDRQFACSSCDHMW 122 (278)
T ss_pred cceeeeccccchHH
Confidence 34567777776543
No 243
>KOG3362|consensus
Probab=26.92 E-value=21 Score=25.33 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=14.9
Q ss_pred eeCCCCCCccCChhHHHHHHh
Q psy12030 177 FACNVCGKGYRYKTGLYRHKR 197 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~ 197 (245)
|.|.-||-.+-+..-|..|..
T Consensus 130 ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 130 YSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred hHHHhcCCceeechhhhhccc
Confidence 667778777777777776654
No 244
>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=26.24 E-value=22 Score=19.20 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=7.2
Q ss_pred CcccCCCcccC
Q psy12030 205 KYQCPHCPHKA 215 (245)
Q Consensus 205 ~~~C~~C~~~f 215 (245)
+-.|++||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 46677777655
No 245
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=25.95 E-value=62 Score=24.41 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=6.8
Q ss_pred CCCcccCCCcccC
Q psy12030 203 EPKYQCPHCPHKA 215 (245)
Q Consensus 203 ~~~~~C~~C~~~f 215 (245)
+..+.|..||..+
T Consensus 28 ~~lvrC~eCG~V~ 40 (201)
T COG1326 28 EPLVRCEECGTVH 40 (201)
T ss_pred ceEEEccCCCcEe
Confidence 3445555555554
No 246
>KOG4118|consensus
Probab=25.69 E-value=40 Score=20.32 Aligned_cols=30 Identities=27% Similarity=0.501 Sum_probs=18.2
Q ss_pred cccCCCcccCCChHHHHHhHhhhCCCCCCC
Q psy12030 206 YQCPHCPHKAKHKANLKTHIAIKHSDRILP 235 (245)
Q Consensus 206 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 235 (245)
|+|.+|-..-.....+..|....|...|++
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~~~P 68 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKEPLP 68 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCCCCC
Confidence 566666666666666666666666555543
No 247
>KOG0227|consensus
Probab=25.69 E-value=39 Score=25.29 Aligned_cols=27 Identities=19% Similarity=0.445 Sum_probs=19.0
Q ss_pred hcCCCCceeCCCCCCccCChhHHHHHH
Q psy12030 170 IAPQLGVFACNVCGKGYRYKTGLYRHK 196 (245)
Q Consensus 170 ~~~h~~~~~C~~C~~~f~~~~~l~~H~ 196 (245)
++.|.|.|.|..|.-.-.+..+..+|.
T Consensus 47 mkNh~G~yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 47 MKNHLGKYECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred hhccCcceeehhhhhhhcchhhhhhhh
Confidence 466777788888876666666666664
No 248
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.54 E-value=42 Score=23.19 Aligned_cols=44 Identities=16% Similarity=0.225 Sum_probs=22.7
Q ss_pred eecccccccccChhHHhcchhcccCCCCCccCCCCcccccChHH
Q psy12030 70 FECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSFFSWSA 113 (245)
Q Consensus 70 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~ 113 (245)
-.|+.|+....-.....-=+-.-+.-+.|.-|..||..|.+...
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwter 83 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWTER 83 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcHHH
Confidence 45666665544332222212222223566777778877776544
No 249
>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=25.41 E-value=28 Score=20.00 Aligned_cols=13 Identities=23% Similarity=0.759 Sum_probs=7.1
Q ss_pred ecccccccccChh
Q psy12030 71 ECQVCGKRYKYKR 83 (245)
Q Consensus 71 ~C~~C~~~f~~~~ 83 (245)
.|++|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999999887653
No 250
>KOG0717|consensus
Probab=25.33 E-value=44 Score=28.86 Aligned_cols=22 Identities=27% Similarity=0.668 Sum_probs=18.3
Q ss_pred eeCCCCCCccCChhHHHHHHhH
Q psy12030 177 FACNVCGKGYRYKTGLYRHKRE 198 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~ 198 (245)
+-|.+|+++|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7788899999988888888664
No 251
>KOG1701|consensus
Probab=24.86 E-value=6.1 Score=33.33 Aligned_cols=37 Identities=14% Similarity=0.389 Sum_probs=19.8
Q ss_pred ccCCCCCCcCCChHHHHhhhc-------CCCCceeCCCCCCccC
Q psy12030 151 YQCPHCPHRAKHKANLKTHIA-------PQLGVFACNVCGKGYR 187 (245)
Q Consensus 151 ~~C~~C~~~f~~~~~l~~H~~-------~h~~~~~C~~C~~~f~ 187 (245)
=+|.+|++-..=+..-..-++ -|..=|+|+.||....
T Consensus 395 PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS 438 (468)
T KOG1701|consen 395 PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLS 438 (468)
T ss_pred cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCcccc
Confidence 357777765544333222222 2333388888887655
No 252
>PRK12496 hypothetical protein; Provisional
Probab=24.84 E-value=56 Score=24.00 Aligned_cols=26 Identities=27% Similarity=0.535 Sum_probs=16.9
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKA 215 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f 215 (245)
|.|..|++.|.. . ...-.|+.||...
T Consensus 128 ~~C~gC~~~~~~------------~-~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPE------------D-YPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccC------------C-CCCCcCCCCCChh
Confidence 789889887751 1 1224599998553
No 253
>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=24.80 E-value=22 Score=21.93 Aligned_cols=11 Identities=18% Similarity=0.694 Sum_probs=4.3
Q ss_pred CccCCCCcccc
Q psy12030 98 KYQCPQCKDSF 108 (245)
Q Consensus 98 ~~~C~~C~~~f 108 (245)
...|..|+...
T Consensus 41 ~v~Cg~C~~~~ 51 (71)
T PF05495_consen 41 RVICGKCRTEQ 51 (71)
T ss_dssp EEEETTT--EE
T ss_pred CeECCCCCCcc
Confidence 44455554443
No 254
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=24.80 E-value=24 Score=26.63 Aligned_cols=9 Identities=33% Similarity=0.829 Sum_probs=4.9
Q ss_pred eeCCCCCCc
Q psy12030 177 FACNVCGKG 185 (245)
Q Consensus 177 ~~C~~C~~~ 185 (245)
+.|+.||+.
T Consensus 31 f~C~~CGyr 39 (192)
T TIGR00310 31 TICEHCGYR 39 (192)
T ss_pred EECCCCCCc
Confidence 555555544
No 255
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.47 E-value=21 Score=23.78 Aligned_cols=33 Identities=21% Similarity=0.518 Sum_probs=18.6
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCcccCCC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHKAKH 217 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~ 217 (245)
|.|+.||. ..-...+.+ + .....|+.||..+..
T Consensus 22 f~CP~Cge-~~v~v~~~k------~-~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 22 FECPRCGK-VSISVKIKK------N-IAIITCGNCGLYTEF 54 (99)
T ss_pred eECCCCCC-eEeeeecCC------C-cceEECCCCCCccCE
Confidence 88888883 222111211 2 445678888877654
No 256
>PRK11032 hypothetical protein; Provisional
Probab=24.39 E-value=32 Score=25.16 Aligned_cols=13 Identities=0% Similarity=-0.207 Sum_probs=7.2
Q ss_pred hCCCCCCCCCCCC
Q psy12030 228 KHSDRILPPQEGR 240 (245)
Q Consensus 228 ~~~~~~~~C~~C~ 240 (245)
.+.+..-+|+.||
T Consensus 137 ~~p~~i~pCp~C~ 149 (160)
T PRK11032 137 YTPEVLPLCPKCG 149 (160)
T ss_pred cCCCcCCCCCCCC
Confidence 3445555666665
No 257
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=24.14 E-value=32 Score=18.14 Aligned_cols=10 Identities=40% Similarity=1.065 Sum_probs=4.8
Q ss_pred CcccCCCccc
Q psy12030 205 KYQCPHCPHK 214 (245)
Q Consensus 205 ~~~C~~C~~~ 214 (245)
-|+|..||-.
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4778777754
No 258
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.94 E-value=44 Score=17.56 Aligned_cols=10 Identities=0% Similarity=-0.679 Sum_probs=5.2
Q ss_pred CCCCCCCccc
Q psy12030 234 LPPQEGRVWT 243 (245)
Q Consensus 234 ~~C~~C~~~f 243 (245)
-.|+.|++.|
T Consensus 3 ~~CprC~kg~ 12 (36)
T PF14787_consen 3 GLCPRCGKGF 12 (36)
T ss_dssp -C-TTTSSSC
T ss_pred ccCcccCCCc
Confidence 3566777665
No 259
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=23.70 E-value=44 Score=19.69 Aligned_cols=10 Identities=40% Similarity=1.514 Sum_probs=6.3
Q ss_pred eeccccccccc
Q psy12030 70 FECQVCGKRYK 80 (245)
Q Consensus 70 ~~C~~C~~~f~ 80 (245)
|.|+ ||..|.
T Consensus 23 yPCP-CGDRFe 32 (67)
T COG5216 23 YPCP-CGDRFE 32 (67)
T ss_pred ecCC-CCCEeE
Confidence 5565 777665
No 260
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=23.56 E-value=62 Score=16.95 Aligned_cols=9 Identities=44% Similarity=1.058 Sum_probs=4.6
Q ss_pred ccCCCCCCc
Q psy12030 151 YQCPHCPHR 159 (245)
Q Consensus 151 ~~C~~C~~~ 159 (245)
+.|++|+..
T Consensus 9 ~~C~~C~~~ 17 (36)
T PF11781_consen 9 EPCPVCGSR 17 (36)
T ss_pred CcCCCCCCe
Confidence 345555544
No 261
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=23.43 E-value=31 Score=20.25 Aligned_cols=12 Identities=17% Similarity=0.562 Sum_probs=5.3
Q ss_pred ceeCCCCCCccC
Q psy12030 176 VFACNVCGKGYR 187 (245)
Q Consensus 176 ~~~C~~C~~~f~ 187 (245)
|+....||-+|.
T Consensus 24 PV~s~~C~H~fe 35 (57)
T PF11789_consen 24 PVKSKKCGHTFE 35 (57)
T ss_dssp EEEESSS--EEE
T ss_pred CcCcCCCCCeec
Confidence 455555655554
No 262
>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=23.26 E-value=69 Score=27.90 Aligned_cols=25 Identities=20% Similarity=0.442 Sum_probs=21.9
Q ss_pred eeCCCCCCccCChhHHHHHHhHHhC
Q psy12030 177 FACNVCGKGYRYKTGLYRHKREECG 201 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l~~H~~~h~~ 201 (245)
|.|+.|.+.|.....+..|+..-|.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhh
Confidence 8899999999999999999986554
No 263
>KOG1842|consensus
Probab=22.98 E-value=46 Score=28.50 Aligned_cols=20 Identities=25% Similarity=0.652 Sum_probs=10.3
Q ss_pred ccCCCCCCcCCChHHHHhhh
Q psy12030 151 YQCPHCPHRAKHKANLKTHI 170 (245)
Q Consensus 151 ~~C~~C~~~f~~~~~l~~H~ 170 (245)
|.|++|...|.+-..|..|.
T Consensus 16 flCPiC~~dl~~~~~L~~H~ 35 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHL 35 (505)
T ss_pred ccCchHhhhhhhHHHHHHHH
Confidence 44555555555555555554
No 264
>KOG1994|consensus
Probab=22.46 E-value=48 Score=25.63 Aligned_cols=23 Identities=35% Similarity=0.687 Sum_probs=20.1
Q ss_pred CCceecccccccccChhHHhcch
Q psy12030 67 SKGFECQVCGKRYKYKRGLHRHK 89 (245)
Q Consensus 67 ~~~~~C~~C~~~f~~~~~l~~H~ 89 (245)
..-|-|-+||..|.+...|..|-
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhC
Confidence 44599999999999999998883
No 265
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=22.36 E-value=26 Score=20.53 Aligned_cols=9 Identities=33% Similarity=1.014 Sum_probs=5.3
Q ss_pred ecccccccc
Q psy12030 71 ECQVCGKRY 79 (245)
Q Consensus 71 ~C~~C~~~f 79 (245)
+|-.|++.+
T Consensus 4 kC~lCdk~~ 12 (56)
T PF09963_consen 4 KCILCDKKE 12 (56)
T ss_pred EEEecCCEE
Confidence 566666653
No 266
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=22.10 E-value=59 Score=24.52 Aligned_cols=46 Identities=24% Similarity=0.381 Sum_probs=19.3
Q ss_pred CCCccCChhHHHHHHhHHhCCCCCcccCC----CcccCCChHHHHHhHhhhCCC
Q psy12030 182 CGKGYRYKTGLYRHKREECGQEPKYQCPH----CPHKAKHKANLKTHIAIKHSD 231 (245)
Q Consensus 182 C~~~f~~~~~l~~H~~~h~~~~~~~~C~~----C~~~f~~~~~l~~H~~~~~~~ 231 (245)
|...+. ......|.... . -+||.||. |+..= ....|..|+...|++
T Consensus 24 C~~~~~-~~~~~~HE~~C-~-~~p~~CP~~~~~C~~~G-~~~~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 24 CTETFP-YSEKREHEEEC-P-FRPCSCPFPGSGCDWQG-SYKELLDHLRDKHSW 73 (198)
T ss_dssp ---EE--GGGHHHHHHT--T-TSEEE-SSSSTT---EE-ECCCHHHHHHHHTTT
T ss_pred Cccccc-ccChhhHhccC-C-CcCCcCCCCCCCccccC-CHHHHHHHHHHHCCC
Confidence 555433 33455555544 2 45666665 54332 234566666666655
No 267
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.09 E-value=43 Score=23.27 Aligned_cols=15 Identities=27% Similarity=0.494 Sum_probs=9.0
Q ss_pred CCceecccccccccCh
Q psy12030 67 SKGFECQVCGKRYKYK 82 (245)
Q Consensus 67 ~~~~~C~~C~~~f~~~ 82 (245)
+-.+.| .||..|...
T Consensus 68 p~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 68 PVEIEC-ECGYEGVVD 82 (124)
T ss_pred CeeEEe-eCcCccccc
Confidence 334677 777666543
No 268
>KOG2636|consensus
Probab=21.71 E-value=61 Score=27.84 Aligned_cols=22 Identities=23% Similarity=0.519 Sum_probs=16.0
Q ss_pred CCCccCCCCC-CcCCChHHHHhh
Q psy12030 148 EPKYQCPHCP-HRAKHKANLKTH 169 (245)
Q Consensus 148 ~~~~~C~~C~-~~f~~~~~l~~H 169 (245)
...|.|.+|| +++..+..+.+|
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred CcccceeeccCccccCcHHHHHH
Confidence 4557777777 777777777777
No 269
>PF12773 DZR: Double zinc ribbon
Probab=21.52 E-value=65 Score=17.90 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=15.0
Q ss_pred eCCCCCCccCChhHHHHHHhHHhCCCCCcccCCCccc
Q psy12030 178 ACNVCGKGYRYKTGLYRHKREECGQEPKYQCPHCPHK 214 (245)
Q Consensus 178 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~ 214 (245)
.|+.||.... ........|+.||..
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAE 38 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCC
Confidence 4777776655 111445778888764
No 270
>KOG2923|consensus
Probab=21.47 E-value=71 Score=19.24 Aligned_cols=10 Identities=40% Similarity=1.524 Sum_probs=5.2
Q ss_pred eeccccccccc
Q psy12030 70 FECQVCGKRYK 80 (245)
Q Consensus 70 ~~C~~C~~~f~ 80 (245)
|.|+ ||..|.
T Consensus 23 yPCp-CGDrf~ 32 (67)
T KOG2923|consen 23 YPCP-CGDRFQ 32 (67)
T ss_pred cCCC-CCCeee
Confidence 4443 666654
No 271
>PRK04351 hypothetical protein; Provisional
Probab=21.14 E-value=48 Score=23.91 Aligned_cols=32 Identities=28% Similarity=0.839 Sum_probs=17.3
Q ss_pred ccccCcCCCccCchhHHHhHHhhhcCCCCCccCCCCCCcCC
Q psy12030 121 MFACDVCGKEYKYKRGLYRHKKFECGQEPKYQCPHCPHRAK 161 (245)
Q Consensus 121 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~ 161 (245)
.|.|..||..+... +.+ . ...|.|..|+-.+.
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~-n-~~~yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRI-N-TKRYRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeeee-------eec-C-CCcEEeCCCCcEee
Confidence 36676677554321 112 2 35577777775554
No 272
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=21.09 E-value=35 Score=17.74 Aligned_cols=14 Identities=14% Similarity=0.337 Sum_probs=7.0
Q ss_pred cccCCCcccCCChH
Q psy12030 206 YQCPHCPHKAKHKA 219 (245)
Q Consensus 206 ~~C~~C~~~f~~~~ 219 (245)
-.|..|++.|..+.
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 36888888887764
No 273
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.06 E-value=50 Score=19.72 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=18.9
Q ss_pred cccccCCCceecccccccccChhHHhcchhcccCCCCCccCCCCcccc
Q psy12030 61 PLVQQYSKGFECQVCGKRYKYKRGLHRHKQDECGQEPKYQCPQCKDSF 108 (245)
Q Consensus 61 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f 108 (245)
..+.....++.|+-=+..|.....+.. -+.+....|+.|+..|
T Consensus 16 ~~I~~~~~~l~C~g~~~p~~HPrV~L~-----mg~~gev~CPYC~t~y 58 (62)
T COG4391 16 ETIEIGDLPLMCPGPEPPNDHPRVFLD-----MGDEGEVVCPYCSTRY 58 (62)
T ss_pred eEEEeCCeeEEcCCCCCCCCCCEEEEE-----cCCCCcEecCccccEE
Confidence 334444555666554444333222111 1334455555555554
No 274
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.95 E-value=38 Score=22.66 Aligned_cols=7 Identities=43% Similarity=1.312 Sum_probs=4.0
Q ss_pred cccCCCc
Q psy12030 206 YQCPHCP 212 (245)
Q Consensus 206 ~~C~~C~ 212 (245)
|.|..|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 5555554
No 275
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.21 E-value=70 Score=25.34 Aligned_cols=12 Identities=33% Similarity=0.869 Sum_probs=7.5
Q ss_pred eeCCCCCCccCC
Q psy12030 177 FACNVCGKGYRY 188 (245)
Q Consensus 177 ~~C~~C~~~f~~ 188 (245)
+.|..|+..+..
T Consensus 123 ~~C~~C~~~~~~ 134 (250)
T COG0846 123 VRCSKCGNQYYD 134 (250)
T ss_pred eEeCCCcCccch
Confidence 667777666553
No 276
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.08 E-value=73 Score=21.80 Aligned_cols=16 Identities=19% Similarity=0.459 Sum_probs=8.7
Q ss_pred eeCCCCCCccCChhHH
Q psy12030 177 FACNVCGKGYRYKTGL 192 (245)
Q Consensus 177 ~~C~~C~~~f~~~~~l 192 (245)
+.|+.||..+......
T Consensus 32 ~~C~~CGe~~~~~e~~ 47 (127)
T TIGR03830 32 WYCPACGEELLDPEES 47 (127)
T ss_pred eECCCCCCEEEcHHHH
Confidence 5566666655554433
Done!