Query psy16829
Match_columns 243
No_of_seqs 176 out of 1948
Neff 10.8
Searched_HMMs 46136
Date Fri Aug 16 23:05:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16829.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16829hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 1.4E-30 3E-35 192.0 5.5 133 86-222 130-264 (279)
2 KOG2462|consensus 100.0 1.5E-29 3.2E-34 186.5 8.0 136 55-193 126-265 (279)
3 KOG1074|consensus 99.9 7.9E-26 1.7E-30 188.1 4.1 80 116-195 606-692 (958)
4 KOG3608|consensus 99.9 5.2E-25 1.1E-29 167.0 8.1 181 42-226 190-377 (467)
5 KOG3608|consensus 99.9 1.7E-24 3.6E-29 164.3 7.7 177 60-241 178-365 (467)
6 KOG3623|consensus 99.9 1.5E-24 3.3E-29 178.1 5.0 69 172-242 895-964 (1007)
7 KOG3623|consensus 99.9 1.4E-22 3E-27 166.7 3.3 77 144-222 895-971 (1007)
8 KOG1074|consensus 99.8 4.3E-22 9.3E-27 166.2 0.5 51 59-109 353-404 (958)
9 KOG3576|consensus 99.7 8.4E-19 1.8E-23 123.7 2.6 111 86-197 117-238 (267)
10 KOG3576|consensus 99.7 1.4E-18 3.1E-23 122.6 3.0 116 112-227 114-238 (267)
11 PLN03086 PRLI-interacting fact 99.5 4E-13 8.7E-18 111.6 12.0 146 56-222 404-561 (567)
12 PLN03086 PRLI-interacting fact 99.4 1.6E-12 3.4E-17 108.1 6.9 134 87-241 408-554 (567)
13 PHA00733 hypothetical protein 99.3 2E-12 4.3E-17 88.2 4.9 83 141-227 38-125 (128)
14 PHA02768 hypothetical protein; 99.2 1.5E-11 3.2E-16 69.2 3.0 42 201-243 5-46 (55)
15 PHA00733 hypothetical protein 99.1 5.3E-11 1.2E-15 81.2 4.3 82 113-196 38-124 (128)
16 PHA02768 hypothetical protein; 99.0 1.9E-10 4E-15 64.8 1.8 43 171-217 5-47 (55)
17 KOG3993|consensus 98.9 3.1E-10 6.6E-15 89.3 1.0 163 59-223 267-480 (500)
18 KOG3993|consensus 98.9 3.6E-10 7.9E-15 88.9 -0.1 155 86-241 267-471 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.7 6.9E-09 1.5E-13 50.0 2.2 24 187-212 2-25 (26)
20 PF13465 zf-H2C2_2: Zinc-finge 98.7 4.3E-09 9.4E-14 50.7 0.9 25 216-240 1-26 (26)
21 PHA00616 hypothetical protein 98.7 3.7E-09 8.1E-14 56.6 0.1 33 201-233 1-34 (44)
22 PF05605 zf-Di19: Drought indu 98.6 7.9E-08 1.7E-12 55.4 4.3 53 171-226 2-54 (54)
23 PHA00616 hypothetical protein 98.6 3.3E-08 7.1E-13 53.0 1.7 36 171-208 1-36 (44)
24 PHA00732 hypothetical protein 98.4 1.4E-07 3E-12 58.5 2.7 48 171-225 1-48 (79)
25 PHA00732 hypothetical protein 98.4 1.8E-07 4E-12 57.9 3.0 39 201-241 1-40 (79)
26 PF00096 zf-C2H2: Zinc finger, 98.3 4.5E-07 9.7E-12 42.4 1.6 23 202-224 1-23 (23)
27 PF05605 zf-Di19: Drought indu 98.1 5.3E-06 1.2E-10 47.7 4.3 49 144-195 3-53 (54)
28 PF13894 zf-C2H2_4: C2H2-type 98.0 3.8E-06 8.2E-11 39.5 2.0 24 202-225 1-24 (24)
29 PF13912 zf-C2H2_6: C2H2-type 98.0 3.5E-06 7.5E-11 41.0 1.7 26 201-226 1-26 (27)
30 PF00096 zf-C2H2: Zinc finger, 98.0 7.1E-06 1.5E-10 38.2 2.1 23 172-194 1-23 (23)
31 PF13894 zf-C2H2_4: C2H2-type 97.8 2.2E-05 4.9E-10 36.7 2.4 24 172-195 1-24 (24)
32 PF12756 zf-C2H2_2: C2H2 type 97.7 2.4E-05 5.1E-10 51.3 2.5 22 118-139 2-23 (100)
33 PF12756 zf-C2H2_2: C2H2 type 97.7 3.8E-05 8.3E-10 50.3 3.1 21 202-222 51-71 (100)
34 PF13912 zf-C2H2_6: C2H2-type 97.6 3.4E-05 7.4E-10 37.4 1.5 25 171-195 1-25 (27)
35 smart00355 ZnF_C2H2 zinc finge 97.6 6.7E-05 1.4E-09 35.7 2.5 24 202-225 1-24 (26)
36 PF13909 zf-H2C2_5: C2H2-type 97.4 0.00011 2.3E-09 34.5 1.4 23 202-225 1-23 (24)
37 PF09237 GAGA: GAGA factor; I 97.4 0.00011 2.5E-09 40.3 1.6 26 201-226 24-49 (54)
38 KOG2231|consensus 97.3 0.00091 2E-08 57.5 7.0 99 89-195 118-236 (669)
39 COG5189 SFP1 Putative transcri 97.2 0.0001 2.3E-09 56.7 0.8 55 168-222 346-419 (423)
40 KOG2231|consensus 97.2 0.00086 1.9E-08 57.7 5.7 121 87-232 100-240 (669)
41 COG5189 SFP1 Putative transcri 97.1 0.00014 3E-09 56.0 0.5 25 168-192 395-419 (423)
42 PF12874 zf-met: Zinc-finger o 97.1 0.00031 6.7E-09 33.2 1.3 22 202-223 1-22 (25)
43 PRK04860 hypothetical protein; 97.0 0.00032 7E-09 49.8 1.7 36 201-240 119-155 (160)
44 PF09237 GAGA: GAGA factor; I 97.0 0.00046 1E-08 38.0 1.7 25 85-109 23-47 (54)
45 smart00355 ZnF_C2H2 zinc finge 96.9 0.001 2.2E-08 31.4 2.2 24 172-195 1-24 (26)
46 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00081 1.7E-08 31.4 1.8 23 172-195 1-23 (24)
47 PF12874 zf-met: Zinc-finger o 96.6 0.0012 2.5E-08 31.2 1.2 20 61-80 2-21 (25)
48 PRK04860 hypothetical protein; 96.6 0.0018 3.9E-08 46.1 2.4 39 170-214 118-156 (160)
49 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.00092 2E-08 32.2 0.2 22 202-223 2-23 (27)
50 PF13913 zf-C2HC_2: zinc-finge 96.4 0.0032 6.8E-08 29.7 2.0 21 202-223 3-23 (25)
51 KOG1146|consensus 96.4 0.0024 5.3E-08 58.5 2.7 160 60-224 437-641 (1406)
52 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.0024 5.3E-08 30.7 1.2 22 60-81 2-23 (27)
53 KOG1146|consensus 95.5 0.0019 4E-08 59.2 -1.8 147 89-238 439-628 (1406)
54 COG5048 FOG: Zn-finger [Genera 95.3 0.0029 6.4E-08 52.8 -1.2 147 86-233 289-451 (467)
55 smart00451 ZnF_U1 U1-like zinc 95.3 0.015 3.3E-07 29.7 2.0 22 201-222 3-24 (35)
56 KOG2482|consensus 95.1 0.076 1.7E-06 41.9 6.0 50 173-222 281-355 (423)
57 cd00350 rubredoxin_like Rubred 95.0 0.017 3.7E-07 29.3 1.5 24 172-209 2-25 (33)
58 PF12013 DUF3505: Protein of u 94.8 0.064 1.4E-06 35.7 4.3 26 201-226 80-109 (109)
59 KOG2785|consensus 94.2 0.17 3.7E-06 40.7 6.0 52 171-222 166-241 (390)
60 KOG2482|consensus 94.1 0.18 3.9E-06 39.9 6.0 53 114-166 143-218 (423)
61 COG5236 Uncharacterized conser 94.0 0.07 1.5E-06 42.2 3.6 130 87-226 152-306 (493)
62 PF12013 DUF3505: Protein of u 93.9 0.12 2.6E-06 34.4 4.1 25 172-196 81-109 (109)
63 COG5048 FOG: Zn-finger [Genera 93.4 0.02 4.4E-07 47.8 -0.2 148 58-208 288-453 (467)
64 smart00451 ZnF_U1 U1-like zinc 93.4 0.057 1.2E-06 27.5 1.5 21 60-80 4-24 (35)
65 TIGR00622 ssl1 transcription f 93.3 0.15 3.3E-06 33.7 3.7 54 173-235 57-110 (112)
66 TIGR00622 ssl1 transcription f 92.1 0.33 7.1E-06 32.2 4.1 48 145-194 57-104 (112)
67 cd00729 rubredoxin_SM Rubredox 91.9 0.087 1.9E-06 26.8 1.0 25 171-209 2-26 (34)
68 KOG2893|consensus 91.9 0.044 9.5E-07 40.9 -0.2 43 61-106 12-54 (341)
69 KOG2893|consensus 91.6 0.048 1E-06 40.7 -0.2 42 89-135 13-54 (341)
70 KOG4173|consensus 91.3 0.15 3.2E-06 37.3 2.0 77 59-137 79-168 (253)
71 PF09538 FYDLN_acid: Protein o 90.7 0.2 4.2E-06 33.2 2.0 15 114-128 25-39 (108)
72 COG4049 Uncharacterized protei 89.1 0.16 3.5E-06 28.6 0.5 23 201-223 17-39 (65)
73 COG4049 Uncharacterized protei 88.9 0.21 4.6E-06 28.1 0.9 29 168-196 14-42 (65)
74 KOG2785|consensus 88.5 0.79 1.7E-05 37.0 4.2 28 57-84 164-191 (390)
75 KOG2186|consensus 88.1 0.37 7.9E-06 36.6 2.0 47 59-107 3-49 (276)
76 COG2888 Predicted Zn-ribbon RN 88.0 0.48 1.1E-05 27.2 2.0 13 201-213 27-39 (61)
77 PF09538 FYDLN_acid: Protein o 87.8 0.35 7.5E-06 32.0 1.6 30 60-99 10-39 (108)
78 KOG4173|consensus 87.7 0.53 1.1E-05 34.5 2.6 19 146-164 109-127 (253)
79 COG1592 Rubrerythrin [Energy p 87.5 0.31 6.7E-06 34.9 1.3 23 171-208 134-156 (166)
80 PF10571 UPF0547: Uncharacteri 87.2 0.43 9.3E-06 22.6 1.3 8 204-211 17-24 (26)
81 PF13719 zinc_ribbon_5: zinc-r 86.9 0.49 1.1E-05 24.6 1.5 10 172-181 26-35 (37)
82 COG5236 Uncharacterized conser 86.7 0.83 1.8E-05 36.4 3.3 75 60-139 221-305 (493)
83 PF13717 zinc_ribbon_4: zinc-r 86.6 0.55 1.2E-05 24.2 1.6 11 145-155 4-14 (36)
84 TIGR02098 MJ0042_CXXC MJ0042 f 86.1 0.51 1.1E-05 24.5 1.4 12 145-156 4-15 (38)
85 PF09986 DUF2225: Uncharacteri 85.9 0.14 3.1E-06 38.6 -1.2 45 170-214 4-61 (214)
86 TIGR00373 conserved hypothetic 85.4 0.8 1.7E-05 32.7 2.5 33 139-180 105-137 (158)
87 PF06524 NOA36: NOA36 protein; 85.3 0.34 7.3E-06 36.9 0.6 79 60-151 98-179 (314)
88 TIGR00373 conserved hypothetic 84.7 1.2 2.6E-05 31.9 3.1 32 168-210 106-137 (158)
89 TIGR02300 FYDLN_acid conserved 84.3 0.86 1.9E-05 30.8 2.1 15 114-128 25-39 (129)
90 smart00659 RPOLCX RNA polymera 83.8 0.83 1.8E-05 24.8 1.5 11 172-182 3-13 (44)
91 PHA00626 hypothetical protein 83.7 0.23 4.9E-06 28.1 -0.7 12 201-212 23-34 (59)
92 PF09986 DUF2225: Uncharacteri 83.3 0.36 7.8E-06 36.4 -0.0 42 58-99 4-61 (214)
93 smart00734 ZnF_Rad18 Rad18-lik 82.7 1.3 2.9E-05 20.9 1.8 20 202-222 2-21 (26)
94 smart00834 CxxC_CXXC_SSSS Puta 82.0 0.58 1.3E-05 24.7 0.5 31 58-94 4-34 (41)
95 PRK06266 transcription initiat 81.2 1.2 2.6E-05 32.5 2.1 33 140-181 114-146 (178)
96 PRK06266 transcription initiat 81.1 1.8 3.8E-05 31.7 2.9 34 168-212 114-147 (178)
97 PF09723 Zn-ribbon_8: Zinc rib 80.6 0.97 2.1E-05 24.2 1.1 31 58-94 4-34 (42)
98 TIGR02605 CxxC_CxxC_SSSS putat 80.6 0.69 1.5E-05 26.0 0.5 31 58-94 4-34 (52)
99 TIGR02300 FYDLN_acid conserved 80.2 1.2 2.5E-05 30.2 1.5 33 60-102 10-42 (129)
100 PF02892 zf-BED: BED zinc fing 80.1 1.2 2.6E-05 24.0 1.4 21 201-221 16-40 (45)
101 PRK14890 putative Zn-ribbon RN 79.9 0.97 2.1E-05 26.0 0.9 8 201-208 48-55 (59)
102 smart00614 ZnF_BED BED zinc fi 79.3 1.7 3.6E-05 24.2 1.8 21 202-222 19-44 (50)
103 PF05443 ROS_MUCR: ROS/MUCR tr 78.1 1.6 3.4E-05 30.1 1.7 27 55-84 68-94 (132)
104 smart00531 TFIIE Transcription 77.9 2.6 5.6E-05 29.7 2.8 37 169-211 97-133 (147)
105 PF14353 CpXC: CpXC protein 77.8 1.9 4E-05 29.6 2.1 40 60-101 2-53 (128)
106 COG1592 Rubrerythrin [Energy p 77.7 1.5 3.3E-05 31.4 1.6 24 86-123 134-157 (166)
107 PF08274 PhnA_Zn_Ribbon: PhnA 77.4 0.72 1.6E-05 22.7 -0.0 9 201-209 19-27 (30)
108 smart00531 TFIIE Transcription 77.4 2.4 5.1E-05 29.9 2.5 38 140-181 96-133 (147)
109 PF15269 zf-C2H2_7: Zinc-finge 77.4 1.9 4.1E-05 23.1 1.5 23 201-223 20-42 (54)
110 PRK00464 nrdR transcriptional 77.2 0.43 9.3E-06 33.8 -1.2 12 172-183 29-40 (154)
111 KOG2807|consensus 76.5 4.7 0.0001 32.1 4.0 30 201-235 345-374 (378)
112 PRK04023 DNA polymerase II lar 75.5 3.9 8.4E-05 37.8 3.8 12 229-240 664-675 (1121)
113 PRK00398 rpoP DNA-directed RNA 74.7 1.7 3.8E-05 23.7 1.0 9 60-68 4-12 (46)
114 KOG2186|consensus 74.2 2.8 6.1E-05 32.0 2.3 46 144-192 4-49 (276)
115 PF03604 DNA_RNApol_7kD: DNA d 73.9 1.9 4.1E-05 21.6 0.9 9 201-209 17-25 (32)
116 COG1997 RPL43A Ribosomal prote 73.4 1.9 4.2E-05 27.0 1.1 12 201-212 53-64 (89)
117 PF02176 zf-TRAF: TRAF-type zi 73.1 2.2 4.9E-05 24.6 1.3 40 170-212 8-53 (60)
118 PRK09678 DNA-binding transcrip 72.9 0.74 1.6E-05 27.9 -0.8 39 172-214 2-42 (72)
119 PF05443 ROS_MUCR: ROS/MUCR tr 72.3 2.2 4.8E-05 29.3 1.3 25 201-228 72-96 (132)
120 PRK04023 DNA polymerase II lar 71.5 4.6 9.9E-05 37.4 3.3 10 201-210 663-672 (1121)
121 PF13451 zf-trcl: Probable zin 67.2 5.1 0.00011 22.3 1.8 39 169-208 2-40 (49)
122 PF07975 C1_4: TFIIH C1-like d 66.6 1.7 3.6E-05 24.4 -0.2 30 201-235 21-50 (51)
123 COG1996 RPC10 DNA-directed RNA 66.5 3.5 7.7E-05 22.9 1.1 12 58-69 5-16 (49)
124 COG5151 SSL1 RNA polymerase II 63.4 5.7 0.00012 31.4 2.0 30 201-235 388-417 (421)
125 KOG2593|consensus 62.4 10 0.00022 31.6 3.4 40 139-181 124-163 (436)
126 PRK14714 DNA polymerase II lar 60.3 11 0.00024 36.0 3.5 30 201-240 692-721 (1337)
127 PF07754 DUF1610: Domain of un 59.2 4.2 9.2E-05 18.8 0.5 8 201-208 16-23 (24)
128 COG3357 Predicted transcriptio 58.9 7.1 0.00015 24.7 1.5 30 85-125 57-86 (97)
129 COG4530 Uncharacterized protei 58.4 5.9 0.00013 26.0 1.1 26 61-96 11-36 (129)
130 COG4957 Predicted transcriptio 58.4 20 0.00044 24.6 3.7 25 57-84 74-98 (148)
131 PF12760 Zn_Tnp_IS1595: Transp 57.9 11 0.00024 20.5 2.1 8 201-208 37-44 (46)
132 PF12907 zf-met2: Zinc-binding 56.9 7.4 0.00016 20.6 1.2 8 100-107 18-25 (40)
133 KOG3408|consensus 56.4 6.1 0.00013 26.5 1.0 22 201-222 57-78 (129)
134 KOG2907|consensus 55.5 6.2 0.00013 26.1 0.9 39 60-98 75-114 (116)
135 COG1998 RPS31 Ribosomal protei 54.9 7 0.00015 21.6 0.9 8 202-209 38-45 (51)
136 PF05191 ADK_lid: Adenylate ki 54.7 2.5 5.3E-05 21.8 -0.8 10 173-182 3-12 (36)
137 KOG3408|consensus 53.4 20 0.00043 24.2 3.0 31 51-81 49-79 (129)
138 KOG4167|consensus 53.3 4.6 0.0001 35.8 0.1 27 57-83 790-816 (907)
139 PRK03824 hypA hydrogenase nick 53.2 4.1 9E-05 28.2 -0.2 12 144-155 71-82 (135)
140 PF13878 zf-C2H2_3: zinc-finge 52.7 15 0.00033 19.5 2.0 22 203-224 15-38 (41)
141 COG1198 PriA Primosomal protei 52.7 9.6 0.00021 34.4 1.9 46 60-124 436-484 (730)
142 PF05290 Baculo_IE-1: Baculovi 52.7 13 0.00028 25.5 2.1 58 139-215 76-135 (140)
143 TIGR01206 lysW lysine biosynth 52.0 4.6 9.9E-05 23.0 -0.1 12 172-183 3-14 (54)
144 KOG2807|consensus 50.7 18 0.00039 28.9 2.9 88 58-178 275-374 (378)
145 KOG1280|consensus 50.6 15 0.00032 29.7 2.4 36 143-178 79-116 (381)
146 smart00154 ZnF_AN1 AN1-like Zi 50.4 8.1 0.00018 20.3 0.7 14 201-214 12-25 (39)
147 KOG2593|consensus 49.8 16 0.00034 30.5 2.5 16 170-185 127-142 (436)
148 PF01155 HypA: Hydrogenase exp 49.6 6.8 0.00015 26.2 0.4 12 172-183 71-82 (113)
149 PF06524 NOA36: NOA36 protein; 49.0 19 0.00042 27.8 2.7 85 139-224 138-232 (314)
150 KOG2272|consensus 48.8 13 0.00028 28.5 1.8 14 229-242 281-294 (332)
151 PF07800 DUF1644: Protein of u 48.7 98 0.0021 22.1 6.0 54 58-115 79-137 (162)
152 PF10013 DUF2256: Uncharacteri 48.2 10 0.00022 20.2 0.8 11 230-240 10-20 (42)
153 PRK12380 hydrogenase nickel in 48.0 9.2 0.0002 25.6 0.9 12 172-183 71-82 (113)
154 PF04959 ARS2: Arsenite-resist 46.4 8.5 0.00018 29.0 0.6 22 172-193 78-99 (214)
155 PF04959 ARS2: Arsenite-resist 46.0 9.9 0.00021 28.7 0.9 29 140-168 74-102 (214)
156 PF13453 zf-TFIIB: Transcripti 45.9 9.7 0.00021 20.1 0.6 19 201-219 19-37 (41)
157 KOG4167|consensus 45.2 5.1 0.00011 35.5 -0.8 23 87-109 793-815 (907)
158 PRK00432 30S ribosomal protein 44.4 12 0.00026 20.9 0.8 8 172-179 38-45 (50)
159 PTZ00255 60S ribosomal protein 44.2 9.2 0.0002 24.3 0.4 12 114-125 53-64 (90)
160 PF01780 Ribosomal_L37ae: Ribo 43.7 5.7 0.00012 25.3 -0.6 11 85-95 34-44 (90)
161 PF09963 DUF2197: Uncharacteri 43.1 8.7 0.00019 22.0 0.1 12 60-71 3-14 (56)
162 PF04216 FdhE: Protein involve 42.4 3.2 6.9E-05 33.0 -2.3 35 145-182 174-208 (290)
163 PRK00564 hypA hydrogenase nick 41.3 14 0.00029 25.0 0.9 11 172-182 72-82 (117)
164 COG5151 SSL1 RNA polymerase II 41.2 14 0.00031 29.2 1.1 26 141-166 386-411 (421)
165 PF14311 DUF4379: Domain of un 41.1 20 0.00044 20.2 1.5 12 172-183 29-40 (55)
166 COG4888 Uncharacterized Zn rib 41.1 5.5 0.00012 25.7 -0.9 8 172-179 23-30 (104)
167 PF08790 zf-LYAR: LYAR-type C2 40.5 9.7 0.00021 18.3 0.1 9 61-69 2-10 (28)
168 TIGR00280 L37a ribosomal prote 39.9 9.9 0.00021 24.2 0.1 12 114-125 52-63 (91)
169 PF01096 TFIIS_C: Transcriptio 39.7 3.5 7.6E-05 21.6 -1.7 9 87-95 29-37 (39)
170 COG1773 Rubredoxin [Energy pro 39.7 15 0.00032 21.0 0.7 14 171-184 3-16 (55)
171 PRK10220 hypothetical protein; 39.2 19 0.00041 23.8 1.2 12 115-126 20-31 (111)
172 smart00440 ZnF_C2C2 C2C2 Zinc 38.7 7.5 0.00016 20.5 -0.5 9 87-95 29-37 (40)
173 PF01428 zf-AN1: AN1-like Zinc 38.5 9 0.00019 20.5 -0.3 14 201-214 13-26 (43)
174 TIGR00100 hypA hydrogenase nic 38.1 18 0.00038 24.3 1.1 28 56-94 67-94 (115)
175 TIGR00686 phnA alkylphosphonat 38.1 17 0.00037 23.9 0.9 12 115-126 19-30 (109)
176 PRK03681 hypA hydrogenase nick 37.7 16 0.00035 24.5 0.8 11 172-182 71-81 (114)
177 TIGR00595 priA primosomal prot 37.4 18 0.0004 31.3 1.3 10 114-123 252-261 (505)
178 KOG0717|consensus 36.7 20 0.00043 30.3 1.3 21 202-222 293-313 (508)
179 PF01286 XPA_N: XPA protein N- 36.5 13 0.00027 18.9 0.1 9 231-239 6-14 (34)
180 PRK04351 hypothetical protein; 36.2 16 0.00034 25.9 0.6 10 229-238 133-142 (149)
181 KOG1280|consensus 36.0 36 0.00077 27.6 2.5 37 57-93 77-116 (381)
182 COG1675 TFA1 Transcription ini 35.8 40 0.00086 24.6 2.6 34 139-181 109-142 (176)
183 COG1198 PriA Primosomal protei 35.7 28 0.0006 31.6 2.2 9 229-237 476-484 (730)
184 TIGR01562 FdhE formate dehydro 35.6 24 0.00051 28.3 1.6 15 167-181 206-220 (305)
185 PRK03564 formate dehydrogenase 35.5 18 0.00039 29.0 0.9 15 167-181 208-222 (309)
186 PF07282 OrfB_Zn_ribbon: Putat 35.3 25 0.00054 20.8 1.3 7 172-178 47-53 (69)
187 PRK03976 rpl37ae 50S ribosomal 35.1 12 0.00026 23.8 -0.1 12 114-125 53-64 (90)
188 PF01363 FYVE: FYVE zinc finge 34.4 24 0.00052 20.9 1.2 8 146-153 12-19 (69)
189 PF04780 DUF629: Protein of un 34.0 30 0.00065 29.5 2.0 21 202-222 58-78 (466)
190 COG3091 SprT Zn-dependent meta 34.0 17 0.00036 25.7 0.4 10 171-181 117-126 (156)
191 COG4896 Uncharacterized protei 33.8 29 0.00062 20.2 1.3 8 172-179 32-39 (68)
192 KOG0978|consensus 33.7 13 0.00029 33.1 -0.1 47 59-105 643-697 (698)
193 KOG1842|consensus 33.2 25 0.00055 29.5 1.4 26 171-196 15-40 (505)
194 PF10276 zf-CHCC: Zinc-finger 33.1 20 0.00043 19.0 0.6 12 58-69 28-39 (40)
195 KOG3214|consensus 33.1 11 0.00023 24.4 -0.6 12 202-213 48-59 (109)
196 PF14787 zf-CCHC_5: GAG-polypr 32.4 36 0.00078 17.5 1.4 11 203-213 4-14 (36)
197 COG0068 HypF Hydrogenase matur 32.2 7.8 0.00017 34.5 -1.7 29 173-209 153-181 (750)
198 COG4338 Uncharacterized protei 32.1 13 0.00027 20.4 -0.3 11 230-240 14-24 (54)
199 PRK12496 hypothetical protein; 31.8 28 0.00061 25.1 1.3 11 172-182 128-138 (164)
200 PF11672 DUF3268: Protein of u 31.5 24 0.00051 23.2 0.8 10 59-68 2-11 (102)
201 PF10263 SprT-like: SprT-like 31.3 12 0.00025 26.5 -0.7 10 172-181 124-133 (157)
202 KOG0782|consensus 31.1 5.4 0.00012 34.4 -2.7 25 74-98 240-265 (1004)
203 PRK14873 primosome assembly pr 31.0 35 0.00076 30.8 2.0 47 60-124 384-431 (665)
204 cd00924 Cyt_c_Oxidase_Vb Cytoc 30.9 27 0.00059 22.7 1.0 16 168-183 76-91 (97)
205 PF04423 Rad50_zn_hook: Rad50 30.5 17 0.00037 20.5 0.0 9 203-211 22-30 (54)
206 PF07649 C1_3: C1-like domain; 30.5 21 0.00046 17.2 0.4 10 201-210 15-24 (30)
207 COG4391 Uncharacterized protei 30.4 25 0.00054 20.5 0.7 15 56-70 45-59 (62)
208 COG2331 Uncharacterized protei 30.4 26 0.00056 21.4 0.8 37 54-96 7-43 (82)
209 PF01927 Mut7-C: Mut7-C RNAse 29.9 36 0.00077 23.9 1.6 16 171-186 124-139 (147)
210 KOG4602|consensus 29.8 91 0.002 24.2 3.7 37 58-94 232-276 (318)
211 PF04810 zf-Sec23_Sec24: Sec23 29.7 13 0.00028 19.5 -0.5 12 168-179 21-32 (40)
212 PF04780 DUF629: Protein of un 29.7 44 0.00095 28.5 2.3 23 172-194 58-80 (466)
213 PF00301 Rubredoxin: Rubredoxi 29.4 25 0.00054 19.4 0.5 13 172-184 2-14 (47)
214 KOG2636|consensus 29.3 42 0.00092 28.2 2.0 44 59-107 249-292 (497)
215 PF09332 Mcm10: Mcm10 replicat 28.9 13 0.00029 30.2 -0.8 40 172-212 253-296 (344)
216 KOG1842|consensus 28.8 36 0.00078 28.6 1.6 27 58-84 14-40 (505)
217 cd00730 rubredoxin Rubredoxin; 28.7 24 0.00052 19.7 0.4 13 172-184 2-14 (50)
218 cd00065 FYVE FYVE domain; Zinc 28.0 34 0.00074 19.2 1.0 9 174-182 5-13 (57)
219 PF07295 DUF1451: Protein of u 27.7 24 0.00052 24.9 0.4 32 55-95 108-139 (146)
220 PF13824 zf-Mss51: Zinc-finger 27.6 27 0.00059 19.9 0.5 11 229-239 15-25 (55)
221 PF14369 zf-RING_3: zinc-finge 27.3 47 0.001 16.9 1.3 8 89-96 24-31 (35)
222 PF15135 UPF0515: Uncharacteri 27.3 56 0.0012 25.2 2.2 39 113-156 130-168 (278)
223 PLN02294 cytochrome c oxidase 27.2 33 0.00072 24.7 1.0 17 168-184 138-154 (174)
224 PF14446 Prok-RING_1: Prokaryo 27.2 42 0.00091 19.1 1.2 8 61-68 7-14 (54)
225 COG1655 Uncharacterized protei 27.1 10 0.00022 28.7 -1.6 9 202-210 63-71 (267)
226 smart00132 LIM Zinc-binding do 25.9 22 0.00048 17.8 -0.0 9 87-95 28-36 (39)
227 COG1594 RPB9 DNA-directed RNA 25.3 16 0.00035 24.4 -0.8 10 172-181 101-110 (113)
228 PRK05580 primosome assembly pr 25.2 50 0.0011 29.9 2.0 10 60-69 382-391 (679)
229 TIGR00627 tfb4 transcription f 25.1 52 0.0011 26.1 1.8 11 172-182 256-266 (279)
230 PRK14892 putative transcriptio 24.9 19 0.00042 23.4 -0.4 13 201-213 42-54 (99)
231 KOG3362|consensus 24.9 24 0.00052 24.5 -0.0 22 201-222 129-150 (156)
232 KOG2071|consensus 24.6 36 0.00078 29.7 1.0 24 59-82 418-441 (579)
233 KOG4317|consensus 24.6 18 0.00039 28.8 -0.8 13 172-184 20-32 (383)
234 PF10058 DUF2296: Predicted in 24.5 86 0.0019 17.8 2.2 35 55-94 18-52 (54)
235 COG1571 Predicted DNA-binding 24.3 50 0.0011 27.8 1.7 14 115-128 367-380 (421)
236 PTZ00448 hypothetical protein; 23.9 60 0.0013 26.7 2.0 22 201-222 314-335 (373)
237 PF08209 Sgf11: Sgf11 (transcr 23.2 78 0.0017 15.9 1.6 8 173-180 6-13 (33)
238 PF09845 DUF2072: Zn-ribbon co 23.2 39 0.00085 23.2 0.7 15 86-100 1-15 (131)
239 KOG2071|consensus 23.0 50 0.0011 28.9 1.5 27 201-227 418-444 (579)
240 smart00064 FYVE Protein presen 22.8 48 0.001 19.5 1.0 10 145-154 12-21 (68)
241 PF05495 zf-CHY: CHY zinc fing 22.3 37 0.0008 20.5 0.5 55 60-123 11-69 (71)
242 smart00661 RPOL9 RNA polymeras 22.2 52 0.0011 18.0 1.0 9 87-95 21-29 (52)
243 PF14205 Cys_rich_KTR: Cystein 21.8 28 0.0006 19.8 -0.2 9 201-209 28-36 (55)
244 KOG4377|consensus 21.6 42 0.00091 27.9 0.8 22 206-227 408-429 (480)
245 smart00731 SprT SprT homologue 21.5 29 0.00064 24.3 -0.1 11 201-211 112-122 (146)
246 PF07503 zf-HYPF: HypF finger; 21.0 44 0.00095 17.0 0.5 30 62-96 2-31 (35)
247 PRK14559 putative protein seri 20.9 1.1E+02 0.0025 27.5 3.3 11 145-155 43-53 (645)
248 PF05741 zf-nanos: Nanos RNA b 20.8 36 0.00077 19.5 0.2 8 87-94 34-41 (55)
249 PF02591 DUF164: Putative zinc 20.2 65 0.0014 18.2 1.2 8 115-122 46-53 (56)
No 1
>KOG2462|consensus
Probab=99.96 E-value=1.4e-30 Score=191.95 Aligned_cols=133 Identities=24% Similarity=0.504 Sum_probs=102.2
Q ss_pred cccccccccccCChHHHHHHHHhhc--CCCCcccCCcccccccChHHHHHHHHhhcCCCCcccccccccccChhHHHHHH
Q psy16829 86 SHVCDICLEAFPSSDDRDLHFLSHL--TSDGLYQCNECEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHK 163 (243)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~--~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 163 (243)
.|+|+.|++.+.+.+.|-+|.+.|- ...+.+.|.+|++.+.....|+.|+++|. -+++|.+||+.|+..+.|+.|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 3566666666666666666665551 23456777888888888888888888776 4678888888888888888888
Q ss_pred HHhcCCCCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHh
Q psy16829 164 IKEHNAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 164 ~~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
+.|+|+|||.|+.|++.|.++++|+.|+++|.+.+ +|+|..|+++|...+-|.+|..
T Consensus 208 RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K--~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 208 RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK--KHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred ccccCCCCccCCcccchhcchHHHHHHHHhhcCCc--cccCcchhhHHHHHHHHHHhhh
Confidence 88888888888888888888888888888888887 8888888888888888888864
No 2
>KOG2462|consensus
Probab=99.96 E-value=1.5e-29 Score=186.50 Aligned_cols=136 Identities=24% Similarity=0.424 Sum_probs=128.6
Q ss_pred CCcceeeccccchhccChhhHHhhhhccCC----CcccccccccccCChHHHHHHHHhhcCCCCcccCCcccccccChHH
Q psy16829 55 DKPLLLTCVECNEDFINVNDFVSHLRGHDS----TSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTH 130 (243)
Q Consensus 55 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~----~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~ 130 (243)
.....++|..||+.|.+..+|.+|.++|.. +.+.|+.|++.+.+...|.-|+++| . -++.|.+||+.|...+.
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH-~--l~c~C~iCGKaFSRPWL 202 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTH-T--LPCECGICGKAFSRPWL 202 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhcc-C--CCcccccccccccchHH
Confidence 355679999999999999999999999976 6799999999999999999999988 2 47999999999999999
Q ss_pred HHHHHHhhcCCCCcccccccccccChhHHHHHHHHhcCCCCeeccccccccCChhHHHHHHHH
Q psy16829 131 LKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTNKSTMWSHKKA 193 (243)
Q Consensus 131 l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~~~~l~~H~~~ 193 (243)
|+.|+++|.||+||.|+.|++.|.+.++|+.|+++|.+.|+|.|..|++.|...+.|.+|...
T Consensus 203 LQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 203 LQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999764
No 3
>KOG1074|consensus
Probab=99.92 E-value=7.9e-26 Score=188.15 Aligned_cols=80 Identities=30% Similarity=0.517 Sum_probs=69.8
Q ss_pred ccCCcccccccChHHHHHHHHhhcCCCCcccccccccccChhHHHHHHHHhcCC----CCeecc---ccccccCChhHHH
Q psy16829 116 YQCNECEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNA----FPFQCE---ICHKIFTNKSTMW 188 (243)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~----k~~~C~---~C~~~f~~~~~l~ 188 (243)
.+|.+|.++..-..+|+-|.++|.+++||+|.+||+.|.++..|+.|+..|-.. -++.|+ +|.+.|...-.|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lp 685 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLP 685 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccccc
Confidence 899999999999999999999999999999999999999999999999877533 235677 7777787777777
Q ss_pred HHHHHhC
Q psy16829 189 SHKKAHK 195 (243)
Q Consensus 189 ~H~~~h~ 195 (243)
.|++.|.
T Consensus 686 QhIriH~ 692 (958)
T KOG1074|consen 686 QHIRIHL 692 (958)
T ss_pred ceEEeec
Confidence 7777776
No 4
>KOG3608|consensus
Probab=99.92 E-value=5.2e-25 Score=167.04 Aligned_cols=181 Identities=21% Similarity=0.417 Sum_probs=151.7
Q ss_pred ccccccCCCCCCCCCcceeeccccchhccChhhHHhhhhccCC---CcccccccccccCChHHHHHHHHhhcCCCCcccC
Q psy16829 42 VQYEEDKDYDDGEDKPLLLTCVECNEDFINVNDFVSHLRGHDS---TSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQC 118 (243)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~---~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C 118 (243)
.+.....++.+.+..++.+.|+.||.-|.++..|..|++.-.. .+|.|..|.+.|.+...|..|+..| . ..|+|
T Consensus 190 ~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rH-v--n~ykC 266 (467)
T KOG3608|consen 190 GNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRH-V--NCYKC 266 (467)
T ss_pred ccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHh-h--hcccc
Confidence 3444556677788888999999999999999999999876544 6899999999999999999999887 2 45899
Q ss_pred CcccccccChHHHHHHHHh-hcCCCCcccccccccccChhHHHHHHHHhcCCCCeeccc--cccccCChhHHHHHHHHhC
Q psy16829 119 NECEFVGKRLTHLKTHKKI-HEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEI--CHKIFTNKSTMWSHKKAHK 195 (243)
Q Consensus 119 ~~C~~~f~~~~~l~~H~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~--C~~~f~~~~~l~~H~~~h~ 195 (243)
+.|+++....+.|.+|++. |...++|+|..|...|.+.++|.+|...|. +-.|.|.. |.++|.+...|++|.+.++
T Consensus 267 plCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 267 PLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred cccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 9999999999999999885 777889999999999999999999988665 77789977 9999999999999988876
Q ss_pred -CCCCCCcccccccCccCChHHHHHHHhhcCC
Q psy16829 196 -PEDQIPWECEHCHKVYPNKRSYKRHKQVHLG 226 (243)
Q Consensus 196 -~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 226 (243)
|....+|.|..|++.|++-.+|.+|++.-++
T Consensus 346 Eg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 346 EGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred cCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 5555689999999999999999999865544
No 5
>KOG3608|consensus
Probab=99.91 E-value=1.7e-24 Score=164.28 Aligned_cols=177 Identities=23% Similarity=0.376 Sum_probs=159.0
Q ss_pred eec--cccchhccChhhHHhhhhccCC-CcccccccccccCChHHHHHHHHhhc-CCCCcccCCcccccccChHHHHHHH
Q psy16829 60 LTC--VECNEDFINVNDFVSHLRGHDS-TSHVCDICLEAFPSSDDRDLHFLSHL-TSDGLYQCNECEFVGKRLTHLKTHK 135 (243)
Q Consensus 60 ~~C--~~C~~~~~~~~~l~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~~h~-~~~~~~~C~~C~~~f~~~~~l~~H~ 135 (243)
+.| ..|-+.+.++..|+.|+++|.+ +...|+.|+.-|..+..|-.|++... ....+|.|..|.+.|.+...|..|+
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv 257 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHV 257 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHH
Confidence 455 5799999999999999999998 78899999999999999999998653 2455899999999999999999999
Q ss_pred HhhcCCCCcccccccccccChhHHHHHHHHhc-CCCCeeccccccccCChhHHHHHHHHhCCCCCCCccccc--ccCccC
Q psy16829 136 KIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEH-NAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEH--CHKVYP 212 (243)
Q Consensus 136 ~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~-~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~--C~~~f~ 212 (243)
..|.. .|+|+.|.-.....+.|..|++..| .+|||+|..|.+.+.+.+.|.+|+..|. +. .|.|.. |.++|.
T Consensus 258 ~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~--~y~C~h~~C~~s~r 332 (467)
T KOG3608|consen 258 VRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KT--VYQCEHPDCHYSVR 332 (467)
T ss_pred HHhhh--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-cc--ceecCCCCCcHHHH
Confidence 98864 6899999999999999999998755 7899999999999999999999999988 44 799988 999999
Q ss_pred ChHHHHHHHhh-cCCCC---CCCCCCCCCccCc
Q psy16829 213 NKRSYKRHKQV-HLGVK---HECEGGPIPALAL 241 (243)
Q Consensus 213 ~~~~l~~H~~~-H~~~~---~~c~~c~~~~~~~ 241 (243)
+...|++|.+. |.|.+ |.|.-|++.|+++
T Consensus 333 ~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G 365 (467)
T KOG3608|consen 333 TYTQMRRHFLEVHEGNNPILYACHCCDRFFTSG 365 (467)
T ss_pred HHHHHHHHHHHhccCCCCCceeeecchhhhccc
Confidence 99999999875 44666 9999999999875
No 6
>KOG3623|consensus
Probab=99.90 E-value=1.5e-24 Score=178.08 Aligned_cols=69 Identities=28% Similarity=0.585 Sum_probs=65.1
Q ss_pred eeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHhhcCCCC-CCCCCCCCCccCcC
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQVHLGVK-HECEGGPIPALALF 242 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~-~~c~~c~~~~~~~~ 242 (243)
|.|..|.+.|...++|.+|.-.|+|.+ ||+|.+|.+.|+.+-+|..|+|.|.|++ |.|..|+|.|+..+
T Consensus 895 yaCDqCDK~FqKqSSLaRHKYEHsGqR--PyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSG 964 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLARHKYEHSGQR--PYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSG 964 (1007)
T ss_pred chHHHHHHHHHhhHHHHHhhhhhcCCC--CcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccccc
Confidence 679999999999999999999999999 9999999999999999999999999999 99999999998764
No 7
>KOG3623|consensus
Probab=99.86 E-value=1.4e-22 Score=166.68 Aligned_cols=77 Identities=32% Similarity=0.773 Sum_probs=75.6
Q ss_pred cccccccccccChhHHHHHHHHhcCCCCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHh
Q psy16829 144 VYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
|.|+.|.+.|...+.|.+|.-.|+|.+||+|.+|.+.|..+-.|..|.|.|.|++ ||.|..|+++|....++.+||.
T Consensus 895 yaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEK--PfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEK--PFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCC--cchhhhhhhhcccccchHhhhc
Confidence 8999999999999999999999999999999999999999999999999999999 9999999999999999999985
No 8
>KOG1074|consensus
Probab=99.83 E-value=4.3e-22 Score=166.16 Aligned_cols=51 Identities=25% Similarity=0.549 Sum_probs=45.1
Q ss_pred eeeccccchhccChhhHHhhhhccCC-CcccccccccccCChHHHHHHHHhh
Q psy16829 59 LLTCVECNEDFINVNDFVSHLRGHDS-TSHVCDICLEAFPSSDDRDLHFLSH 109 (243)
Q Consensus 59 ~~~C~~C~~~~~~~~~l~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~~h 109 (243)
+.+|.+|.+.|...+.|+.|++.|++ +||+|.+||..|.++.+|..|...|
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH 404 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRH 404 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeec
Confidence 46799999999999999999999988 8999999999999999998888777
No 9
>KOG3576|consensus
Probab=99.74 E-value=8.4e-19 Score=123.74 Aligned_cols=111 Identities=25% Similarity=0.381 Sum_probs=64.4
Q ss_pred cccccccccccCChHHHHHHHHhhcCCCCcccCCcccccccChHHHHHHHHhhcCCCCcccccccccccChhHHHHHHHH
Q psy16829 86 SHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIK 165 (243)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 165 (243)
.+.|.+|++.|.-...|.+|++.| ...+.|.|..|++.|.+.-+|++|+++|.+.+||+|..|++.|.....|..|.+.
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch-~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~k 195 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCH-SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKK 195 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhc-cHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHH
Confidence 355555555555555555555555 4555555555555555555555555555555555555555555555555555554
Q ss_pred hcC-----------CCCeeccccccccCChhHHHHHHHHhCCC
Q psy16829 166 EHN-----------AFPFQCEICHKIFTNKSTMWSHKKAHKPE 197 (243)
Q Consensus 166 ~~~-----------~k~~~C~~C~~~f~~~~~l~~H~~~h~~~ 197 (243)
.|+ +|.|.|..||+.-.....+..|++.|+..
T Consensus 196 vhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 196 VHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred HcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 442 45566666666666666666666666543
No 10
>KOG3576|consensus
Probab=99.73 E-value=1.4e-18 Score=122.57 Aligned_cols=116 Identities=24% Similarity=0.472 Sum_probs=104.5
Q ss_pred CCCcccCCcccccccChHHHHHHHHhhcCCCCcccccccccccChhHHHHHHHHhcCCCCeeccccccccCChhHHHHHH
Q psy16829 112 SDGLYQCNECEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTNKSTMWSHK 191 (243)
Q Consensus 112 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~~~~l~~H~ 191 (243)
+...|.|.+|++.|.....|.+|++.|...+.+.|..||+.|.+..+|.+|.++|+|-+||+|..|++.|.+..+|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 44569999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCC---------CCCCcccccccCccCChHHHHHHHhhcCCC
Q psy16829 192 KAHKPE---------DQIPWECEHCHKVYPNKRSYKRHKQVHLGV 227 (243)
Q Consensus 192 ~~h~~~---------~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~ 227 (243)
+.-|+. +.+.|.|+.||.+-.....+..|++.|+..
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 987753 234799999999999999999999988753
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.49 E-value=4e-13 Score=111.59 Aligned_cols=146 Identities=15% Similarity=0.314 Sum_probs=112.9
Q ss_pred CcceeeccccchhccChhhHHhhhhccCCCcccccc--cccccCChHHHHHHHHhhcCCCCcccCCcccccccChHHHHH
Q psy16829 56 KPLLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDI--CLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTHLKT 133 (243)
Q Consensus 56 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~ 133 (243)
......|+.|..... ...|..|........-.|+. |+..|.. .. .+..+.|+.|+..|. ...|..
T Consensus 404 ~~~~V~C~NC~~~i~-l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r-~e----------l~~H~~C~~Cgk~f~-~s~Lek 470 (567)
T PLN03086 404 DVDTVECRNCKHYIP-SRSIALHEAYCSRHNVVCPHDGCGIVLRV-EE----------AKNHVHCEKCGQAFQ-QGEMEK 470 (567)
T ss_pred CCCeEECCCCCCccc-hhHHHHHHhhCCCcceeCCcccccceeec-cc----------cccCccCCCCCCccc-hHHHHH
Confidence 344578999988655 44677887655545567885 9988832 22 233468999999985 677999
Q ss_pred HHHhhcCCCCcccccccccccChhHHHHHHHHhcCCCCeeccccccccCC----------hhHHHHHHHHhCCCCCCCcc
Q psy16829 134 HKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTN----------KSTMWSHKKAHKPEDQIPWE 203 (243)
Q Consensus 134 H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~----------~~~l~~H~~~h~~~~~~~~~ 203 (243)
|+..++ .++.|+ |+..+ ....|..|+..+...+++.|+.|++.|.. .+.|..|.... +.+ ++.
T Consensus 471 H~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~r--t~~ 543 (567)
T PLN03086 471 HMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSR--TAP 543 (567)
T ss_pred HHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCc--ceE
Confidence 999875 789999 99755 56899999999999999999999999852 35899998885 777 999
Q ss_pred cccccCccCChHHHHHHHh
Q psy16829 204 CEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 204 C~~C~~~f~~~~~l~~H~~ 222 (243)
|..|++.|..+ .|..|+-
T Consensus 544 C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 544 CDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred ccccCCeeeeh-hHHHHHH
Confidence 99999998766 5788864
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.36 E-value=1.6e-12 Score=108.13 Aligned_cols=134 Identities=23% Similarity=0.437 Sum_probs=104.9
Q ss_pred ccccccccccCChHHHHHHHHhhcCCCCcccCCc--ccccccChHHHHHHHHhhcCCCCcccccccccccChhHHHHHHH
Q psy16829 87 HVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNE--CEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKI 164 (243)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 164 (243)
-.|+.|..... ...|..|.... . ...-.|+. |+..|... .+ +..+.|+.|++.|. ...|..|+.
T Consensus 408 V~C~NC~~~i~-l~~l~lHe~~C-~-r~~V~Cp~~~Cg~v~~r~-el---------~~H~~C~~Cgk~f~-~s~LekH~~ 473 (567)
T PLN03086 408 VECRNCKHYIP-SRSIALHEAYC-S-RHNVVCPHDGCGIVLRVE-EA---------KNHVHCEKCGQAFQ-QGEMEKHMK 473 (567)
T ss_pred EECCCCCCccc-hhHHHHHHhhC-C-CcceeCCcccccceeecc-cc---------ccCccCCCCCCccc-hHHHHHHHH
Confidence 46999987654 56677888655 2 22345774 88887333 23 33368999999996 678999999
Q ss_pred HhcCCCCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccC----------ChHHHHHHHhhcCCCC-CCCCC
Q psy16829 165 KEHNAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYP----------NKRSYKRHKQVHLGVK-HECEG 233 (243)
Q Consensus 165 ~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~----------~~~~l~~H~~~H~~~~-~~c~~ 233 (243)
.+| +++.|+ ||+.+ .+..|..|+..|.+.+ |+.|+.|++.|. ..+.|..|+.+. |.+ +.|..
T Consensus 474 ~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~K--pi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~ 546 (567)
T PLN03086 474 VFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLR--LITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDS 546 (567)
T ss_pred hcC--CCccCC-CCCCc-chhHHHhhhhccCCCC--ceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccc
Confidence 886 889999 99765 6789999999999998 999999999995 246899999986 777 99999
Q ss_pred CCCCccCc
Q psy16829 234 GPIPALAL 241 (243)
Q Consensus 234 c~~~~~~~ 241 (243)
||+.|..+
T Consensus 547 Cgk~Vrlr 554 (567)
T PLN03086 547 CGRSVMLK 554 (567)
T ss_pred cCCeeeeh
Confidence 99987643
No 13
>PHA00733 hypothetical protein
Probab=99.32 E-value=2e-12 Score=88.20 Aligned_cols=83 Identities=16% Similarity=0.232 Sum_probs=63.7
Q ss_pred CCCcccccccccccChhHHHHH--H---HHhcCCCCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChH
Q psy16829 141 VYGVYCDVCGRGFHQNNEVTLH--K---IKEHNAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKR 215 (243)
Q Consensus 141 ~~~~~C~~C~~~f~~~~~l~~H--~---~~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~ 215 (243)
.+++.|.+|.+.|.....|..+ + ...++.+||.|+.|++.|.....|..|++.+ .. +|.|+.|++.|....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~--~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EH--SKVCPVCGKEFRNTD 113 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--Cc--CccCCCCCCccCCHH
Confidence 4456677776666655555444 1 2334688999999999999999999999876 34 799999999999999
Q ss_pred HHHHHHhhcCCC
Q psy16829 216 SYKRHKQVHLGV 227 (243)
Q Consensus 216 ~l~~H~~~H~~~ 227 (243)
.|.+|++..+++
T Consensus 114 sL~~H~~~~h~~ 125 (128)
T PHA00733 114 STLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHHhcCc
Confidence 999999877763
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.19 E-value=1.5e-11 Score=69.22 Aligned_cols=42 Identities=21% Similarity=0.321 Sum_probs=31.0
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCCCCCCCCCCCccCcCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVKHECEGGPIPALALFE 243 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~c~~c~~~~~~~~~ 243 (243)
.|+|+.||+.|...++|..|+++|+ ..|.|..|++.|+++++
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGE 46 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccce
Confidence 5777778888877777888877777 23777777777776653
No 15
>PHA00733 hypothetical protein
Probab=99.14 E-value=5.3e-11 Score=81.22 Aligned_cols=82 Identities=15% Similarity=0.143 Sum_probs=50.2
Q ss_pred CCcccCCcccccccChHHHHHH--HH---hhcCCCCcccccccccccChhHHHHHHHHhcCCCCeeccccccccCChhHH
Q psy16829 113 DGLYQCNECEFVGKRLTHLKTH--KK---IHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTNKSTM 187 (243)
Q Consensus 113 ~~~~~C~~C~~~f~~~~~l~~H--~~---~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~~~~l 187 (243)
.+++.|.+|...|.....|..+ +. .+.+.++|.|+.|++.|.....|..|++.+ ..+|.|+.|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 3445555555555554444443 11 223456677777777777777777776654 3457777777777777777
Q ss_pred HHHHHHhCC
Q psy16829 188 WSHKKAHKP 196 (243)
Q Consensus 188 ~~H~~~h~~ 196 (243)
..|+...|+
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 777776654
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.99 E-value=1.9e-10 Score=64.79 Aligned_cols=43 Identities=21% Similarity=0.641 Sum_probs=34.3
Q ss_pred CeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHH
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSY 217 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l 217 (243)
.|.|+.||+.|...+.|..|+++|+ + ||+|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k--~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--T--NLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--C--cccCCcccceeccccee
Confidence 3678888888888888888888887 4 78888888888876655
No 17
>KOG3993|consensus
Probab=98.91 E-value=3.1e-10 Score=89.32 Aligned_cols=163 Identities=12% Similarity=0.158 Sum_probs=102.6
Q ss_pred eeeccccchhccChhhHHhhhhccCC-CcccccccccccCChHHHHHHHHhhcCCCCcccCCcc-cc-cccChHHHHHHH
Q psy16829 59 LLTCVECNEDFINVNDFVSHLRGHDS-TSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNEC-EF-VGKRLTHLKTHK 135 (243)
Q Consensus 59 ~~~C~~C~~~~~~~~~l~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C-~~-~f~~~~~l~~H~ 135 (243)
-|+|.+|...|.+.-.|..|.=.-.- ..|+|+.|+++|....+|-.|.++|-.....-.=..= .+ ........+.-.
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 49999999999999999999532222 6899999999999999999999999311111100000 00 000000000000
Q ss_pred Hh--hcCCCCcccccccccccChhHHHHHHHHhcCC--------------------------------------------
Q psy16829 136 KI--HEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNA-------------------------------------------- 169 (243)
Q Consensus 136 ~~--~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~-------------------------------------------- 169 (243)
+. ...+..|.|..|++.|....-|+.|+..|+..
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 00 11223566666666666666666666555421
Q ss_pred --CCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHhh
Q psy16829 170 --FPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQV 223 (243)
Q Consensus 170 --k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 223 (243)
-...|+.|+..+..+..--.+.+....+. .|.|.+|.-+|-+.-+|.+|+..
T Consensus 427 sael~~pp~~~~ppsss~~sgg~~rlg~~~q--~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 427 SAELELPPYDGSPPSSSGSSGGYGRLGIAEQ--GFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred cccccCCCCCCCCcccCCCCCccccccchhh--ccccccchHhhhcCcchHhHhhh
Confidence 00247778877777655555555555555 79999999999999999999864
No 18
>KOG3993|consensus
Probab=98.86 E-value=3.6e-10 Score=88.90 Aligned_cols=155 Identities=15% Similarity=0.199 Sum_probs=100.6
Q ss_pred cccccccccccCChHHHHHHHHhhcCCCCcccCCcccccccChHHHHHHHHhhcCCCCcc---cccccccccChhHHHHH
Q psy16829 86 SHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTHLKTHKKIHEKVYGVY---CDVCGRGFHQNNEVTLH 162 (243)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~---C~~C~~~f~~~~~l~~H 162 (243)
.|.|++|...|.+...|-+|.-.. .-..-|+|+.|++.|.-..+|..|.+=|.....-. -+-=.+........+.-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~R-IV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPR-IVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCe-eEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 388999999999999999997433 22235999999999999999999988764221100 00000000111111110
Q ss_pred HHH--hcCCCCeeccccccccCChhHHHHHHHHhCCCCC-----------------------------------------
Q psy16829 163 KIK--EHNAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQ----------------------------------------- 199 (243)
Q Consensus 163 ~~~--~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~----------------------------------------- 199 (243)
.+. ...+.-|.|..|++.|.....|+.|+.+|+....
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 000 0123469999999999999999999888763210
Q ss_pred ---CCcccccccCccCChHHHHHHHhhcCCCC-CCCCCCCCCccCc
Q psy16829 200 ---IPWECEHCHKVYPNKRSYKRHKQVHLGVK-HECEGGPIPALAL 241 (243)
Q Consensus 200 ---~~~~C~~C~~~f~~~~~l~~H~~~H~~~~-~~c~~c~~~~~~~ 241 (243)
..-.|+.|+--+.++..=..+.+.-.-+- |.|..|.-.|.+.
T Consensus 426 ~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss 471 (500)
T KOG3993|consen 426 GSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSS 471 (500)
T ss_pred ccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcC
Confidence 02457778877777766666666544444 8899888888764
No 19
>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=98.74 E-value=6.9e-09 Score=49.98 Aligned_cols=24 Identities=29% Similarity=0.791 Sum_probs=14.6
Q ss_pred HHHHHHHhCCCCCCCcccccccCccC
Q psy16829 187 MWSHKKAHKPEDQIPWECEHCHKVYP 212 (243)
Q Consensus 187 l~~H~~~h~~~~~~~~~C~~C~~~f~ 212 (243)
|.+|++.|++++ ||.|+.|+++|.
T Consensus 2 l~~H~~~H~~~k--~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEK--PYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSS--SEEESSSSEEES
T ss_pred HHHHhhhcCCCC--CCCCCCCcCeeC
Confidence 556666666665 666666666654
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=98.71 E-value=4.3e-09 Score=50.70 Aligned_cols=25 Identities=24% Similarity=0.308 Sum_probs=23.2
Q ss_pred HHHHHHhhcCCCC-CCCCCCCCCccC
Q psy16829 216 SYKRHKQVHLGVK-HECEGGPIPALA 240 (243)
Q Consensus 216 ~l~~H~~~H~~~~-~~c~~c~~~~~~ 240 (243)
+|.+|+++|+|++ |.|+.|+++|..
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 5899999999999 999999999974
No 21
>PHA00616 hypothetical protein
Probab=98.68 E-value=3.7e-09 Score=56.60 Aligned_cols=33 Identities=15% Similarity=0.252 Sum_probs=18.3
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCC-CCCCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVK-HECEG 233 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~-~~c~~ 233 (243)
||+|+.||+.|...++|.+|++.|+|++ +.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4555555555555555555555555555 54443
No 22
>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=98.60 E-value=7.9e-08 Score=55.37 Aligned_cols=53 Identities=19% Similarity=0.332 Sum_probs=39.7
Q ss_pred CeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHhhcCC
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQVHLG 226 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 226 (243)
.|.||+|++. .+...|..|....|....+.+.||+|...+. .+|.+|+..+++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 3789999994 5567889998876655444788999988654 489999887653
No 23
>PHA00616 hypothetical protein
Probab=98.56 E-value=3.3e-08 Score=53.00 Aligned_cols=36 Identities=22% Similarity=0.333 Sum_probs=28.1
Q ss_pred CeeccccccccCChhHHHHHHHHhCCCCCCCccccccc
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCH 208 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~ 208 (243)
||+|+.||+.|...+.|..|++.||+++ |+.|+.=-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~--~~~~~~~y 36 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQN--KLTLEYFY 36 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCC--ccceeEEE
Confidence 5778888888888888888888888887 77776543
No 24
>PHA00732 hypothetical protein
Probab=98.45 E-value=1.4e-07 Score=58.47 Aligned_cols=48 Identities=21% Similarity=0.417 Sum_probs=25.6
Q ss_pred CeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHhhcC
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQVHL 225 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~ 225 (243)
||.|..|++.|.....|..|++.++. ++.|+.|+++|. .|..|.+.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~----~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT----LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC----CCccCCCCCEeC---ChhhhhcccC
Confidence 35566666666666666666553221 334666666665 3555554433
No 25
>PHA00732 hypothetical protein
Probab=98.44 E-value=1.8e-07 Score=57.92 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=35.0
Q ss_pred CcccccccCccCChHHHHHHHhh-cCCCCCCCCCCCCCccCc
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQV-HLGVKHECEGGPIPALAL 241 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~-H~~~~~~c~~c~~~~~~~ 241 (243)
||.|+.|++.|.+.++|..|++. |.+ +.|+.||++|.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~--~~C~~CgKsF~~l 40 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL--TKCPVCNKSYRRL 40 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC--CccCCCCCEeCCh
Confidence 68999999999999999999984 664 6899999999865
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=98.28 E-value=4.5e-07 Score=42.37 Aligned_cols=23 Identities=35% Similarity=0.793 Sum_probs=16.7
Q ss_pred cccccccCccCChHHHHHHHhhc
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQVH 224 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~~H 224 (243)
|.|+.|++.|.+..+|.+|++.|
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 56777777777777777777654
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.12 E-value=5.3e-06 Score=47.70 Aligned_cols=49 Identities=24% Similarity=0.537 Sum_probs=25.1
Q ss_pred cccccccccccChhHHHHHHHHhcC--CCCeeccccccccCChhHHHHHHHHhC
Q psy16829 144 VYCDVCGRGFHQNNEVTLHKIKEHN--AFPFQCEICHKIFTNKSTMWSHKKAHK 195 (243)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~~~~--~k~~~C~~C~~~f~~~~~l~~H~~~h~ 195 (243)
|.|+.|++. .+...|..|....|. .+.+.||+|...+. .+|..|+..+|
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 455666553 334455555554442 23455666655433 25666665544
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.03 E-value=3.8e-06 Score=39.49 Aligned_cols=24 Identities=25% Similarity=0.682 Sum_probs=14.7
Q ss_pred cccccccCccCChHHHHHHHhhcC
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQVHL 225 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~~H~ 225 (243)
|.|++|++.|.+...|..|++.|+
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 457777777777777777766553
No 29
>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=98.01 E-value=3.5e-06 Score=40.97 Aligned_cols=26 Identities=31% Similarity=0.841 Sum_probs=20.3
Q ss_pred CcccccccCccCChHHHHHHHhhcCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLG 226 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~ 226 (243)
||.|..|++.|.+...|..|++.|.+
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 57788888888888888888877753
No 30
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.95 E-value=7.1e-06 Score=38.18 Aligned_cols=23 Identities=39% Similarity=0.872 Sum_probs=16.8
Q ss_pred eeccccccccCChhHHHHHHHHh
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAH 194 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h 194 (243)
|.|+.|++.|.....|..|++.|
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 56777777777777777777663
No 31
>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=97.79 E-value=2.2e-05 Score=36.73 Aligned_cols=24 Identities=46% Similarity=0.904 Sum_probs=16.7
Q ss_pred eeccccccccCChhHHHHHHHHhC
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAHK 195 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h~ 195 (243)
|.|++|++.|.+...|..|+++|+
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 567778888888888888877764
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.72 E-value=2.4e-05 Score=51.34 Aligned_cols=22 Identities=23% Similarity=0.295 Sum_probs=0.0
Q ss_pred CCcccccccChHHHHHHHHhhc
Q psy16829 118 CNECEFVGKRLTHLKTHKKIHE 139 (243)
Q Consensus 118 C~~C~~~f~~~~~l~~H~~~~~ 139 (243)
|..|+..|.+...|..|+...+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H 23 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKH 23 (100)
T ss_dssp ----------------------
T ss_pred cccccccccccccccccccccc
Confidence 4555555555555555554433
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.69 E-value=3.8e-05 Score=50.34 Aligned_cols=21 Identities=19% Similarity=0.730 Sum_probs=10.7
Q ss_pred cccccccCccCChHHHHHHHh
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~ 222 (243)
+.|..|++.|.+...|..|++
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHH
T ss_pred CCCCccCCCCcCHHHHHHHHc
Confidence 455555555555555555554
No 34
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.61 E-value=3.4e-05 Score=37.38 Aligned_cols=25 Identities=40% Similarity=0.909 Sum_probs=19.2
Q ss_pred CeeccccccccCChhHHHHHHHHhC
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHK 195 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~ 195 (243)
||.|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4778888888888888888877665
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.59 E-value=6.7e-05 Score=35.72 Aligned_cols=24 Identities=33% Similarity=0.797 Sum_probs=18.8
Q ss_pred cccccccCccCChHHHHHHHhhcC
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQVHL 225 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~~H~ 225 (243)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 568888888888888888887664
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.37 E-value=0.00011 Score=34.50 Aligned_cols=23 Identities=35% Similarity=0.700 Sum_probs=13.9
Q ss_pred cccccccCccCChHHHHHHHhhcC
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQVHL 225 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~~H~ 225 (243)
|.|+.|++... ...|.+|++.|+
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 56777776666 667777766654
No 37
>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=97.35 E-value=0.00011 Score=40.29 Aligned_cols=26 Identities=27% Similarity=0.516 Sum_probs=13.4
Q ss_pred CcccccccCccCChHHHHHHHhhcCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLG 226 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~ 226 (243)
|-.|++|+..+.+..+|.+|+.++++
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCcchhhccchhhHHHHHHHHhc
Confidence 56666666666666666666655544
No 38
>KOG2231|consensus
Probab=97.28 E-value=0.00091 Score=57.51 Aligned_cols=99 Identities=19% Similarity=0.337 Sum_probs=64.5
Q ss_pred ccccccccCChHHHHHHHHhhcCCCCcccCCcccc---------cccChHHHHHHHHhh-cCCC----Cccccccccccc
Q psy16829 89 CDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEF---------VGKRLTHLKTHKKIH-EKVY----GVYCDVCGRGFH 154 (243)
Q Consensus 89 C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~---------~f~~~~~l~~H~~~~-~~~~----~~~C~~C~~~f~ 154 (243)
|..| -.|.....|+.|+...| +.+.|.+|-. ...+...|..|++.- .++. .-.|..|...|.
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H---~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fl 193 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQH---KLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFL 193 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhh---hhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhc
Confidence 4444 33446778888885432 3455555432 334455677777642 1122 246889999999
Q ss_pred ChhHHHHHHHHhcCCCCeeccccc------cccCChhHHHHHHHHhC
Q psy16829 155 QNNEVTLHKIKEHNAFPFQCEICH------KIFTNKSTMWSHKKAHK 195 (243)
Q Consensus 155 ~~~~l~~H~~~~~~~k~~~C~~C~------~~f~~~~~l~~H~~~h~ 195 (243)
....|..|++..| |.|.+|. .-|..-..|..|.+.+|
T Consensus 194 d~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 194 DDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 9999999988776 5666663 44677788888888875
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.23 E-value=0.0001 Score=56.71 Aligned_cols=55 Identities=27% Similarity=0.659 Sum_probs=43.7
Q ss_pred CCCCeeccc--cccccCChhHHHHHHHHhCC-----------------CCCCCcccccccCccCChHHHHHHHh
Q psy16829 168 NAFPFQCEI--CHKIFTNKSTMWSHKKAHKP-----------------EDQIPWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 168 ~~k~~~C~~--C~~~f~~~~~l~~H~~~h~~-----------------~~~~~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
++|||.|++ |.+.|.+...|.-|+.-.|- -+.+||.|+.|+++++....|+-|++
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 358999987 99999999999988775441 01249999999999999988888865
No 40
>KOG2231|consensus
Probab=97.17 E-value=0.00086 Score=57.66 Aligned_cols=121 Identities=24% Similarity=0.494 Sum_probs=82.1
Q ss_pred ccccccccccCChHHHHHHHHhhcCCCCcccCCcccccccChHHHHHHHHhhcCCCCcccccc---------cccccChh
Q psy16829 87 HVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTHLKTHKKIHEKVYGVYCDVC---------GRGFHQNN 157 (243)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C---------~~~f~~~~ 157 (243)
+.|..|++.|.-. .....|..| ..|.....|+.|+...++. +.|..| .....+..
T Consensus 100 ~~C~~C~~~~~~~-------------~~~~~~~~c-~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~ 163 (669)
T KOG2231|consen 100 HSCHICDRRFRAL-------------YNKKECLHC-TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRA 163 (669)
T ss_pred hhcCccccchhhh-------------cccCCCccc-cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHH
Confidence 6788888876321 112457888 7888999999999764432 234333 22334566
Q ss_pred HHHHHHHHhcC-CCC----eeccccccccCChhHHHHHHHHhCCCCCCCcccccc------cCccCChHHHHHHHhhcCC
Q psy16829 158 EVTLHKIKEHN-AFP----FQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHC------HKVYPNKRSYKRHKQVHLG 226 (243)
Q Consensus 158 ~l~~H~~~~~~-~k~----~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~H~~ 226 (243)
.|..|+..--. +.. -.|..|...|.....|.+|++.+| |.|..| +..|.....|..|-|.+|
T Consensus 164 el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h------~~chfC~~~~~~neyy~~~~dLe~HfR~~H- 236 (669)
T KOG2231|consen 164 ELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH- 236 (669)
T ss_pred HHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce------eheeecCcccccchhcccchHHHHHhhhcC-
Confidence 77777664321 211 369999999999999999998865 445555 566888889999888777
Q ss_pred CCCCCC
Q psy16829 227 VKHECE 232 (243)
Q Consensus 227 ~~~~c~ 232 (243)
|.|+
T Consensus 237 --flCE 240 (669)
T KOG2231|consen 237 --FLCE 240 (669)
T ss_pred --cccc
Confidence 5665
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.12 E-value=0.00014 Score=56.01 Aligned_cols=25 Identities=32% Similarity=0.777 Sum_probs=21.6
Q ss_pred CCCCeeccccccccCChhHHHHHHH
Q psy16829 168 NAFPFQCEICHKIFTNKSTMWSHKK 192 (243)
Q Consensus 168 ~~k~~~C~~C~~~f~~~~~l~~H~~ 192 (243)
..|||+|++|++.|.+...|.-|..
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 4699999999999999988887754
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.07 E-value=0.00031 Score=33.20 Aligned_cols=22 Identities=23% Similarity=0.705 Sum_probs=17.3
Q ss_pred cccccccCccCChHHHHHHHhh
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQV 223 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~~ 223 (243)
|.|.+|+..|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5688888888888888888764
No 43
>PRK04860 hypothetical protein; Provisional
Probab=97.03 E-value=0.00032 Score=49.80 Aligned_cols=36 Identities=22% Similarity=0.556 Sum_probs=22.0
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCC-CCCCCCCCCccC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVK-HECEGGPIPALA 240 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~-~~c~~c~~~~~~ 240 (243)
+|.|. |+. ...++.+|.++|+|++ |.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 56665 664 4555666666666666 666666666543
No 44
>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=97.00 E-value=0.00046 Score=37.96 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=10.8
Q ss_pred CcccccccccccCChHHHHHHHHhh
Q psy16829 85 TSHVCDICLEAFPSSDDRDLHFLSH 109 (243)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~~h 109 (243)
.|.+|+.|+..+....+|++|+...
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~ 47 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIR 47 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHHHH
Confidence 4455555555555555555555443
No 45
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.87 E-value=0.001 Score=31.38 Aligned_cols=24 Identities=33% Similarity=0.805 Sum_probs=16.0
Q ss_pred eeccccccccCChhHHHHHHHHhC
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAHK 195 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h~ 195 (243)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 456777777777777777776543
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.87 E-value=0.00081 Score=31.41 Aligned_cols=23 Identities=30% Similarity=0.583 Sum_probs=16.3
Q ss_pred eeccccccccCChhHHHHHHHHhC
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAHK 195 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h~ 195 (243)
|.|+.|++... ...|..|++.++
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 57888888887 778888887765
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.59 E-value=0.0012 Score=31.16 Aligned_cols=20 Identities=40% Similarity=0.740 Sum_probs=9.9
Q ss_pred eccccchhccChhhHHhhhh
Q psy16829 61 TCVECNEDFINVNDFVSHLR 80 (243)
Q Consensus 61 ~C~~C~~~~~~~~~l~~H~~ 80 (243)
.|.+|++.|.+...|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 44555555555555555544
No 48
>PRK04860 hypothetical protein; Provisional
Probab=96.55 E-value=0.0018 Score=46.08 Aligned_cols=39 Identities=26% Similarity=0.748 Sum_probs=31.2
Q ss_pred CCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCCh
Q psy16829 170 FPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNK 214 (243)
Q Consensus 170 k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~ 214 (243)
-+|.|. |+. ....+++|.++|.+++ +|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~--~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEA--VYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCc--cEECCCCCceeEEe
Confidence 468887 886 6667888888888888 89998898887643
No 49
>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=96.41 E-value=0.00092 Score=32.24 Aligned_cols=22 Identities=23% Similarity=0.700 Sum_probs=17.6
Q ss_pred cccccccCccCChHHHHHHHhh
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQV 223 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~~ 223 (243)
|-|..|++.|.+...|..|++.
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 6788888888888888888753
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.40 E-value=0.0032 Score=29.70 Aligned_cols=21 Identities=19% Similarity=0.640 Sum_probs=15.5
Q ss_pred cccccccCccCChHHHHHHHhh
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQV 223 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~~ 223 (243)
..|+.|+++| ..+.|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4688888888 66778888653
No 51
>KOG1146|consensus
Probab=96.37 E-value=0.0024 Score=58.46 Aligned_cols=160 Identities=10% Similarity=0.113 Sum_probs=100.6
Q ss_pred eeccccchhccChhhHHhhhhccCC--CcccccccccccCChHHHHHHHHhhc------------------------CCC
Q psy16829 60 LTCVECNEDFINVNDFVSHLRGHDS--TSHVCDICLEAFPSSDDRDLHFLSHL------------------------TSD 113 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~~h~~--~~~~C~~C~~~f~~~~~l~~H~~~h~------------------------~~~ 113 (243)
..|.-|+..+.....+..|+..-+. +.++|+.|+..|.....|..|++..| .+.
T Consensus 437 ~e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~ 516 (1406)
T KOG1146|consen 437 VELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPG 516 (1406)
T ss_pred ccccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCC
Confidence 4566666666666666666554333 67888888888888888888887632 234
Q ss_pred CcccCCcccccccChHHHHHHHHhh--cCC----------C----Cc-cccccccccc--ChhHHHHHHHHhcCCCCeec
Q psy16829 114 GLYQCNECEFVGKRLTHLKTHKKIH--EKV----------Y----GV-YCDVCGRGFH--QNNEVTLHKIKEHNAFPFQC 174 (243)
Q Consensus 114 ~~~~C~~C~~~f~~~~~l~~H~~~~--~~~----------~----~~-~C~~C~~~f~--~~~~l~~H~~~~~~~k~~~C 174 (243)
++|.|..|...+....+|.+|+... ..+ . +. .+..+...-. ..+.... .-..-.|.|
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~----pktkP~~~C 592 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSG----PKTKPSWRC 592 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCC----CCCCCCcch
Confidence 5688888888888888888887642 111 0 00 0111100000 0000000 001223789
Q ss_pred cccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHhhc
Q psy16829 175 EICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQVH 224 (243)
Q Consensus 175 ~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H 224 (243)
.+|++...-..+|+.|+........ |..|-.++-.+.....+..+.+.+
T Consensus 593 ~vc~yetniarnlrihmtss~~s~~-p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 593 EVCSYETNIARNLRIHMTASPSSSP-PSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred hhhcchhhhhhccccccccCCCCCC-hHHHhhhcchhhccccccCcCCCC
Confidence 9999999888899999887554442 588888888888887777777766
No 52
>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=96.26 E-value=0.0024 Score=30.73 Aligned_cols=22 Identities=23% Similarity=0.638 Sum_probs=15.6
Q ss_pred eeccccchhccChhhHHhhhhc
Q psy16829 60 LTCVECNEDFINVNDFVSHLRG 81 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~~ 81 (243)
|.|..|++.|.+...|..|+++
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 5677777777777777777654
No 53
>KOG1146|consensus
Probab=95.50 E-value=0.0019 Score=59.16 Aligned_cols=147 Identities=14% Similarity=0.205 Sum_probs=90.7
Q ss_pred ccccccccCChHHHHHHHHhhcCCCCcccCCcccccccChHHHHHHHHhhcCCCCcccccccccccChhHHHHHHHHhcC
Q psy16829 89 CDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHN 168 (243)
Q Consensus 89 C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 168 (243)
|..|+..+.+...+--|+..-+...+.++|+.|+..|.....|-.|+++.+.+..- ..|.. +.....+.+=.....+
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c~~-gq~~~~~arg~~~~~~ 515 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYCKA-GQNHPRLARGEVYRCP 515 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch--hHhHh-ccccccccccccccCC
Confidence 44555566666666555554335567899999999999999999999974332211 22211 1111111111111225
Q ss_pred CCCeeccccccccCChhHHHHHHHH--hCCC----------C-----------------------------CCCcccccc
Q psy16829 169 AFPFQCEICHKIFTNKSTMWSHKKA--HKPE----------D-----------------------------QIPWECEHC 207 (243)
Q Consensus 169 ~k~~~C~~C~~~f~~~~~l~~H~~~--h~~~----------~-----------------------------~~~~~C~~C 207 (243)
.++|.|..|.+.+....+|.+|+.. |..+ . .-++.|.+|
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc 595 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVC 595 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhh
Confidence 6788999999999999999999774 2111 0 005899999
Q ss_pred cCccCChHHHHHHHh-hcCCCC-CCCCCCCCCc
Q psy16829 208 HKVYPNKRSYKRHKQ-VHLGVK-HECEGGPIPA 238 (243)
Q Consensus 208 ~~~f~~~~~l~~H~~-~H~~~~-~~c~~c~~~~ 238 (243)
++.-.-..+|.-|+. .++-.+ -.|-++..++
T Consensus 596 ~yetniarnlrihmtss~~s~~p~~~Lq~~it~ 628 (1406)
T KOG1146|consen 596 SYETNIARNLRIHMTASPSSSPPSLVLQQNITS 628 (1406)
T ss_pred cchhhhhhccccccccCCCCCChHHHhhhcchh
Confidence 999888889999986 333333 4444444444
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.32 E-value=0.0029 Score=52.85 Aligned_cols=147 Identities=17% Similarity=0.198 Sum_probs=86.5
Q ss_pred cccccccccccCChHHHHHHHH--hhcCCC--CcccCC--cccccccChHHHHHHHHhhcCCCCcccccc--cccccChh
Q psy16829 86 SHVCDICLEAFPSSDDRDLHFL--SHLTSD--GLYQCN--ECEFVGKRLTHLKTHKKIHEKVYGVYCDVC--GRGFHQNN 157 (243)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C--~~~f~~~~ 157 (243)
++.|..|...|.....|.+|.. .| .++ +++.|+ .|++.|.....+..|...+.+..++.+..- ...+....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h-~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNH-SGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred CCCCccccCCcccccccccccccccc-ccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 5667777777777777777777 45 666 777777 677777777777777777766665555332 22222111
Q ss_pred HHHHHHH-----HhcCCCCeecc--ccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHhhcCCCC-C
Q psy16829 158 EVTLHKI-----KEHNAFPFQCE--ICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQVHLGVK-H 229 (243)
Q Consensus 158 ~l~~H~~-----~~~~~k~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~-~ 229 (243)
.-..+.. .......+.+. .|...+.....+..|...|-......+.+..|...|.....+..|++.|.... .
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCce
Confidence 1000000 11122233332 25555666666666666666555335667778888888888888877776655 3
Q ss_pred CCCC
Q psy16829 230 ECEG 233 (243)
Q Consensus 230 ~c~~ 233 (243)
.|..
T Consensus 448 ~~~~ 451 (467)
T COG5048 448 LCSI 451 (467)
T ss_pred eecc
Confidence 3333
No 55
>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=95.29 E-value=0.015 Score=29.72 Aligned_cols=22 Identities=18% Similarity=0.522 Sum_probs=19.8
Q ss_pred CcccccccCccCChHHHHHHHh
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
+|.|.+|+..|.+..++..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 6889999999999999999975
No 56
>KOG2482|consensus
Probab=95.09 E-value=0.076 Score=41.87 Aligned_cols=50 Identities=18% Similarity=0.371 Sum_probs=31.7
Q ss_pred eccccccccCChhHHHHHHHHhCCCC-------------------------CCCcccccccCccCChHHHHHHHh
Q psy16829 173 QCEICHKIFTNKSTMWSHKKAHKPED-------------------------QIPWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 173 ~C~~C~~~f~~~~~l~~H~~~h~~~~-------------------------~~~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
.|-.|...+.+...|..|+..-|.-. ...-.|-.|...|-....|..|+.
T Consensus 281 ~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~ 355 (423)
T KOG2482|consen 281 VCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMV 355 (423)
T ss_pred EEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcc
Confidence 56666666666666666666543211 002457778888888888888875
No 57
>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=94.96 E-value=0.017 Score=29.25 Aligned_cols=24 Identities=29% Similarity=1.039 Sum_probs=16.6
Q ss_pred eeccccccccCChhHHHHHHHHhCCCCCCCcccccccC
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHK 209 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~ 209 (243)
|.|.+||+.+.... . ++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~--~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------A--PWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------C--CCcCcCCCC
Confidence 67888887765432 3 778888874
No 58
>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=94.76 E-value=0.064 Score=35.69 Aligned_cols=26 Identities=23% Similarity=0.630 Sum_probs=23.5
Q ss_pred Cccc----ccccCccCChHHHHHHHhhcCC
Q psy16829 201 PWEC----EHCHKVYPNKRSYKRHKQVHLG 226 (243)
Q Consensus 201 ~~~C----~~C~~~f~~~~~l~~H~~~H~~ 226 (243)
.|.| ..|++.+.+...+.+|.+.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4899 9999999999999999998775
No 59
>KOG2785|consensus
Probab=94.17 E-value=0.17 Score=40.69 Aligned_cols=52 Identities=17% Similarity=0.333 Sum_probs=42.9
Q ss_pred CeeccccccccCChhHHHHHHHHhCCCC---------------------CCCccccccc---CccCChHHHHHHHh
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKPED---------------------QIPWECEHCH---KVYPNKRSYKRHKQ 222 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~---------------------~~~~~C~~C~---~~f~~~~~l~~H~~ 222 (243)
|-.|-.|+..+.+...-..|+..+|+-- .+.|.|-.|+ +.|.+....+.||.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 3568889999999888889998888632 1258899999 99999999999986
No 60
>KOG2482|consensus
Probab=94.14 E-value=0.18 Score=39.87 Aligned_cols=53 Identities=21% Similarity=0.261 Sum_probs=35.4
Q ss_pred CcccCCcccccc-cChHHHHHHHHhhcC----------------------CCCcccccccccccChhHHHHHHHHh
Q psy16829 114 GLYQCNECEFVG-KRLTHLKTHKKIHEK----------------------VYGVYCDVCGRGFHQNNEVTLHKIKE 166 (243)
Q Consensus 114 ~~~~C~~C~~~f-~~~~~l~~H~~~~~~----------------------~~~~~C~~C~~~f~~~~~l~~H~~~~ 166 (243)
...+|-.|...+ .+.+....|+-.-++ -..+.|-.|.+.|..+..|+.||+..
T Consensus 143 fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 143 FSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred eeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhc
Confidence 346788887655 455566666532111 12478888888898888888888754
No 61
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.03 E-value=0.07 Score=42.15 Aligned_cols=130 Identities=22% Similarity=0.360 Sum_probs=81.4
Q ss_pred ccccc--cccccCChHHHHHHHHhhcCCCCcccCCcccc---cc------cChHHHHHHHHhhcCCCCc----ccccccc
Q psy16829 87 HVCDI--CLEAFPSSDDRDLHFLSHLTSDGLYQCNECEF---VG------KRLTHLKTHKKIHEKVYGV----YCDVCGR 151 (243)
Q Consensus 87 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~---~f------~~~~~l~~H~~~~~~~~~~----~C~~C~~ 151 (243)
|.||. |..+......|..|....| ..+.|..|.. .| -+...|..|...-..+..| .|..|..
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 FKCPKSKCHRRCGSLKELKKHYKAQH---GFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhc---CcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 66876 7777777788888887543 2355665533 22 2233466665533222222 5888999
Q ss_pred cccChhHHHHHHHHhcCCCCeeccccc----cccCChhHHHHHHHHhCCCCCCCccccc--cc----CccCChHHHHHHH
Q psy16829 152 GFHQNNEVTLHKIKEHNAFPFQCEICH----KIFTNKSTMWSHKKAHKPEDQIPWECEH--CH----KVYPNKRSYKRHK 221 (243)
Q Consensus 152 ~f~~~~~l~~H~~~~~~~k~~~C~~C~----~~f~~~~~l~~H~~~h~~~~~~~~~C~~--C~----~~f~~~~~l~~H~ 221 (243)
.|.+...|..|++..|.. -|.|..-+ .-|.+-.+|..|.+.- -|.|.. |. ..|.....|+.|+
T Consensus 229 ~FYdDDEL~~HcR~~HE~-ChICD~v~p~~~QYFK~Y~~Le~HF~~~------hy~ct~qtc~~~k~~vf~~~~el~~h~ 301 (493)
T COG5236 229 YFYDDDELRRHCRLRHEA-CHICDMVGPIRYQYFKSYEDLEAHFRNA------HYCCTFQTCRVGKCYVFPYHTELLEHL 301 (493)
T ss_pred eecChHHHHHHHHhhhhh-hhhhhccCccchhhhhCHHHHHHHhhcC------ceEEEEEEEecCcEEEeccHHHHHHHH
Confidence 999999999999987733 23443322 2366667777776542 466643 43 4688999999998
Q ss_pred hhcCC
Q psy16829 222 QVHLG 226 (243)
Q Consensus 222 ~~H~~ 226 (243)
..-+|
T Consensus 302 ~~~h~ 306 (493)
T COG5236 302 TRFHK 306 (493)
T ss_pred HHHhh
Confidence 64443
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=93.88 E-value=0.12 Score=34.42 Aligned_cols=25 Identities=28% Similarity=0.517 Sum_probs=23.4
Q ss_pred eec----cccccccCChhHHHHHHHHhCC
Q psy16829 172 FQC----EICHKIFTNKSTMWSHKKAHKP 196 (243)
Q Consensus 172 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 196 (243)
|.| ..|++.+.+...++.|++.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999999875
No 63
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.41 E-value=0.02 Score=47.77 Aligned_cols=148 Identities=22% Similarity=0.323 Sum_probs=101.1
Q ss_pred ceeeccccchhccChhhHHhhhh--ccCCC---ccccc--ccccccCChHHHHHHHHhhcCCCCcccCCc--ccccccCh
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLR--GHDST---SHVCD--ICLEAFPSSDDRDLHFLSHLTSDGLYQCNE--CEFVGKRL 128 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~--~h~~~---~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~--C~~~f~~~ 128 (243)
..+.|..|...|.....|.+|.+ .|.+. ++.|+ .|++.|.+...+.+|...| ....++.+.. +...+...
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 366 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH-TSISPAKEKLLNSSSKFSPL 366 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc-cCCCccccccccCccccccc
Confidence 46899999999999999999999 67654 89999 7999999999999999988 6666666654 33333332
Q ss_pred HHHHHHHH-----hhcCCCCccc--ccccccccChhHHHHHHHHhcCCC--CeeccccccccCChhHHHHHHHHhCCCCC
Q psy16829 129 THLKTHKK-----IHEKVYGVYC--DVCGRGFHQNNEVTLHKIKEHNAF--PFQCEICHKIFTNKSTMWSHKKAHKPEDQ 199 (243)
Q Consensus 129 ~~l~~H~~-----~~~~~~~~~C--~~C~~~f~~~~~l~~H~~~~~~~k--~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 199 (243)
..-..+.. .........+ ..|...+.....+..|...+-... .+.+..|...+.....+..|.+.+....
T Consensus 367 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 445 (467)
T COG5048 367 LNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHA- 445 (467)
T ss_pred cCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCC-
Confidence 22111111 1112222333 224455666666666666655444 3566789999999999999999988776
Q ss_pred CCccccccc
Q psy16829 200 IPWECEHCH 208 (243)
Q Consensus 200 ~~~~C~~C~ 208 (243)
++.|..+.
T Consensus 446 -~~~~~~~~ 453 (467)
T COG5048 446 -PLLCSILK 453 (467)
T ss_pred -ceeecccc
Confidence 55554444
No 64
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.35 E-value=0.057 Score=27.51 Aligned_cols=21 Identities=29% Similarity=0.586 Sum_probs=11.4
Q ss_pred eeccccchhccChhhHHhhhh
Q psy16829 60 LTCVECNEDFINVNDFVSHLR 80 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~ 80 (243)
+.|.+|++.|.+...+..|++
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 455555555555555555543
No 65
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.29 E-value=0.15 Score=33.70 Aligned_cols=54 Identities=20% Similarity=0.342 Sum_probs=33.1
Q ss_pred eccccccccCChhHHHHHHHHhCCCCCCCcccccccCccCChHHHHHHHhhcCCCCCCCCCCC
Q psy16829 173 QCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYKRHKQVHLGVKHECEGGP 235 (243)
Q Consensus 173 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~c~~c~ 235 (243)
.|-.|...|....... ...-.... .|.|+.|...|-..-..-.|..+|. |++|.
T Consensus 57 ~C~~C~~~f~~~~~~~--~~~~~~~~--~y~C~~C~~~FC~dCD~fiHe~Lh~-----CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSP--FDELKDSH--RYVCAVCKNVFCVDCDVFVHESLHC-----CPGCI 110 (112)
T ss_pred cccCcCCCCCCccccc--cccccccc--ceeCCCCCCccccccchhhhhhccC-----CcCCC
Confidence 3777777776542100 00011122 6888888888888777777766655 77776
No 66
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.12 E-value=0.33 Score=32.17 Aligned_cols=48 Identities=17% Similarity=0.517 Sum_probs=24.5
Q ss_pred ccccccccccChhHHHHHHHHhcCCCCeeccccccccCChhHHHHHHHHh
Q psy16829 145 YCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTNKSTMWSHKKAH 194 (243)
Q Consensus 145 ~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h 194 (243)
.|-.|...|........ ........|.|+.|...|-..-++..|...|
T Consensus 57 ~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cccCcCCCCCCcccccc--cccccccceeCCCCCCccccccchhhhhhcc
Confidence 36666666654321000 0012234567777777776666666665444
No 67
>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=91.94 E-value=0.087 Score=26.83 Aligned_cols=25 Identities=24% Similarity=0.676 Sum_probs=16.5
Q ss_pred CeeccccccccCChhHHHHHHHHhCCCCCCCcccccccC
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHK 209 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~ 209 (243)
.|.|..||+.+.... . |..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g~~------------~--p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEE------------A--PEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCc------------C--CCcCcCCCC
Confidence 377888887765321 2 677888874
No 68
>KOG2893|consensus
Probab=91.89 E-value=0.044 Score=40.91 Aligned_cols=43 Identities=23% Similarity=0.508 Sum_probs=21.4
Q ss_pred eccccchhccChhhHHhhhhccCCCcccccccccccCChHHHHHHH
Q psy16829 61 TCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAFPSSDDRDLHF 106 (243)
Q Consensus 61 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~ 106 (243)
.|.+|++.|.....|..|++. +.|+|.+|.+...+--.|..|.
T Consensus 12 wcwycnrefddekiliqhqka---khfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA---KHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeeecccccchhhhhhhhhhh---ccceeeeehhhhccCCCceeeh
Confidence 455555555555555555543 3355555555444444444443
No 69
>KOG2893|consensus
Probab=91.62 E-value=0.048 Score=40.70 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=34.1
Q ss_pred ccccccccCChHHHHHHHHhhcCCCCcccCCcccccccChHHHHHHH
Q psy16829 89 CDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTHLKTHK 135 (243)
Q Consensus 89 C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~ 135 (243)
|.+|++.|.+..-|+.|++.. -|+|.+|.+...+--.|..|-
T Consensus 13 cwycnrefddekiliqhqkak-----hfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK-----HFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeecccccchhhhhhhhhhhc-----cceeeeehhhhccCCCceeeh
Confidence 999999999999999997644 499999988766555666663
No 70
>KOG4173|consensus
Probab=91.29 E-value=0.15 Score=37.31 Aligned_cols=77 Identities=26% Similarity=0.470 Sum_probs=58.9
Q ss_pred eeeccc--cchhccChhhHHhhhhccCCCcccccccccccCChHHHHHHHHhhc---------CCCCcccCCc--ccccc
Q psy16829 59 LLTCVE--CNEDFINVNDFVSHLRGHDSTSHVCDICLEAFPSSDDRDLHFLSHL---------TSDGLYQCNE--CEFVG 125 (243)
Q Consensus 59 ~~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~---------~~~~~~~C~~--C~~~f 125 (243)
.+.|++ |...|........|-.+- ....|..|.+.|++.-.|..|+...| .+...|.|-+ |+..|
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~--h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTL--HGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhc--ccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 377875 677888888788774433 34579999999999999999996543 3466788854 88889
Q ss_pred cChHHHHHHHHh
Q psy16829 126 KRLTHLKTHKKI 137 (243)
Q Consensus 126 ~~~~~l~~H~~~ 137 (243)
.+...-+.|+..
T Consensus 157 kT~r~RkdH~I~ 168 (253)
T KOG4173|consen 157 KTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhHHHH
Confidence 888888888764
No 71
>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=90.68 E-value=0.2 Score=33.19 Aligned_cols=15 Identities=13% Similarity=0.102 Sum_probs=7.7
Q ss_pred CcccCCcccccccCh
Q psy16829 114 GLYQCNECEFVGKRL 128 (243)
Q Consensus 114 ~~~~C~~C~~~f~~~ 128 (243)
.|-.|+.|+..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 455555555555443
No 72
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.10 E-value=0.16 Score=28.57 Aligned_cols=23 Identities=26% Similarity=0.634 Sum_probs=12.8
Q ss_pred CcccccccCccCChHHHHHHHhh
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQV 223 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~ 223 (243)
-+.||.|+..|....++.+|+..
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhH
Confidence 45555555555555555555543
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.89 E-value=0.21 Score=28.09 Aligned_cols=29 Identities=14% Similarity=0.314 Sum_probs=21.6
Q ss_pred CCCCeeccccccccCChhHHHHHHHHhCC
Q psy16829 168 NAFPFQCEICHKIFTNKSTMWSHKKAHKP 196 (243)
Q Consensus 168 ~~k~~~C~~C~~~f~~~~~l~~H~~~h~~ 196 (243)
|+-.+.|+.|+..|....+..+|...-|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 55667888888888888888888765443
No 74
>KOG2785|consensus
Probab=88.55 E-value=0.79 Score=37.02 Aligned_cols=28 Identities=11% Similarity=0.330 Sum_probs=24.1
Q ss_pred cceeeccccchhccChhhHHhhhhccCC
Q psy16829 57 PLLLTCVECNEDFINVNDFVSHLRGHDS 84 (243)
Q Consensus 57 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~ 84 (243)
..|.-|-+|++.+.+...-..||..+|+
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~Hg 191 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHG 191 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccC
Confidence 3347899999999999999999998876
No 75
>KOG2186|consensus
Probab=88.07 E-value=0.37 Score=36.56 Aligned_cols=47 Identities=19% Similarity=0.318 Sum_probs=37.5
Q ss_pred eeeccccchhccChhhHHhhhhccCCCcccccccccccCChHHHHHHHH
Q psy16829 59 LLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAFPSSDDRDLHFL 107 (243)
Q Consensus 59 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 107 (243)
.|.|..||-...-. .+.+|+-.-++.-|.|..|+..|.. .++..|..
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccCCeeEEeeccccccc-chhhhhhh
Confidence 37899999876644 6777988877788999999999987 67777764
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=87.99 E-value=0.48 Score=27.19 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=5.8
Q ss_pred CcccccccCccCC
Q psy16829 201 PWECEHCHKVYPN 213 (243)
Q Consensus 201 ~~~C~~C~~~f~~ 213 (243)
.|.|+.||..-..
T Consensus 27 ~F~CPnCGe~~I~ 39 (61)
T COG2888 27 KFPCPNCGEVEIY 39 (61)
T ss_pred EeeCCCCCceeee
Confidence 3445555444333
No 77
>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=87.79 E-value=0.35 Score=32.02 Aligned_cols=30 Identities=33% Similarity=0.770 Sum_probs=24.4
Q ss_pred eeccccchhccChhhHHhhhhccCCCcccccccccccCCh
Q psy16829 60 LTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAFPSS 99 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~ 99 (243)
..|+.||..|...+ ..|-.||.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLn----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC----------CCCccCCCCCCccCcc
Confidence 58999999998662 2577899999998766
No 78
>KOG4173|consensus
Probab=87.75 E-value=0.53 Score=34.52 Aligned_cols=19 Identities=26% Similarity=0.697 Sum_probs=8.5
Q ss_pred cccccccccChhHHHHHHH
Q psy16829 146 CDVCGRGFHQNNEVTLHKI 164 (243)
Q Consensus 146 C~~C~~~f~~~~~l~~H~~ 164 (243)
|..|.+.|.+.-.|..|+.
T Consensus 109 Cs~C~r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 109 CSFCKRAFPTGHLLDAHIL 127 (253)
T ss_pred hHHHHHhCCchhhhhHHHH
Confidence 4444444444444444433
No 79
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=87.47 E-value=0.31 Score=34.86 Aligned_cols=23 Identities=26% Similarity=0.632 Sum_probs=18.2
Q ss_pred CeeccccccccCChhHHHHHHHHhCCCCCCCccccccc
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCH 208 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~ 208 (243)
.|.|++||+.+. ++. |-.||+|+
T Consensus 134 ~~vC~vCGy~~~-------------ge~--P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHE-------------GEA--PEVCPICG 156 (166)
T ss_pred EEEcCCCCCccc-------------CCC--CCcCCCCC
Confidence 599999997653 334 89999998
No 80
>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=87.16 E-value=0.43 Score=22.61 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=4.5
Q ss_pred cccccCcc
Q psy16829 204 CEHCHKVY 211 (243)
Q Consensus 204 C~~C~~~f 211 (243)
|+.||+.|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 55555555
No 81
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.87 E-value=0.49 Score=24.56 Aligned_cols=10 Identities=30% Similarity=1.042 Sum_probs=4.3
Q ss_pred eecccccccc
Q psy16829 172 FQCEICHKIF 181 (243)
Q Consensus 172 ~~C~~C~~~f 181 (243)
.+|+.|+..|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4444444433
No 82
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.65 E-value=0.83 Score=36.37 Aligned_cols=75 Identities=27% Similarity=0.477 Sum_probs=45.4
Q ss_pred eeccccchhccChhhHHhhhhccCCCcccccccc----cccCChHHHHHHHHhhcCCCCcccCCc--cc----ccccChH
Q psy16829 60 LTCVECNEDFINVNDFVSHLRGHDSTSHVCDICL----EAFPSSDDRDLHFLSHLTSDGLYQCNE--CE----FVGKRLT 129 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~----~~f~~~~~l~~H~~~h~~~~~~~~C~~--C~----~~f~~~~ 129 (243)
-.|.+|...|..-..|.+|++.-+.+-|.|..=+ .-|....+|.+|.+..| |.|.+ |. .+|....
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h-----y~ct~qtc~~~k~~vf~~~~ 295 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAH-----YCCTFQTCRVGKCYVFPYHT 295 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCc-----eEEEEEEEecCcEEEeccHH
Confidence 4688888778888888888776554444443221 34666677777765432 55533 32 2567777
Q ss_pred HHHHHHHhhc
Q psy16829 130 HLKTHKKIHE 139 (243)
Q Consensus 130 ~l~~H~~~~~ 139 (243)
.|+.|+...+
T Consensus 296 el~~h~~~~h 305 (493)
T COG5236 296 ELLEHLTRFH 305 (493)
T ss_pred HHHHHHHHHh
Confidence 7777765433
No 83
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.55 E-value=0.55 Score=24.23 Aligned_cols=11 Identities=18% Similarity=0.579 Sum_probs=4.8
Q ss_pred ccccccccccC
Q psy16829 145 YCDVCGRGFHQ 155 (243)
Q Consensus 145 ~C~~C~~~f~~ 155 (243)
.|+.|+..|.-
T Consensus 4 ~Cp~C~~~y~i 14 (36)
T PF13717_consen 4 TCPNCQAKYEI 14 (36)
T ss_pred ECCCCCCEEeC
Confidence 34444444433
No 84
>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=86.08 E-value=0.51 Score=24.53 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=5.5
Q ss_pred ccccccccccCh
Q psy16829 145 YCDVCGRGFHQN 156 (243)
Q Consensus 145 ~C~~C~~~f~~~ 156 (243)
.|+.|+..|.-.
T Consensus 4 ~CP~C~~~~~v~ 15 (38)
T TIGR02098 4 QCPNCKTSFRVV 15 (38)
T ss_pred ECCCCCCEEEeC
Confidence 445555444333
No 85
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.90 E-value=0.14 Score=38.56 Aligned_cols=45 Identities=20% Similarity=0.415 Sum_probs=24.0
Q ss_pred CCeeccccccccCChhHHHHHHHHh-C---------CCC---CCCcccccccCccCCh
Q psy16829 170 FPFQCEICHKIFTNKSTMWSHKKAH-K---------PED---QIPWECEHCHKVYPNK 214 (243)
Q Consensus 170 k~~~C~~C~~~f~~~~~l~~H~~~h-~---------~~~---~~~~~C~~C~~~f~~~ 214 (243)
+.+.||+|+..|....-.....+.- . +.. -....||.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 4456777777776654444333321 1 111 0135688888887643
No 86
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=85.37 E-value=0.8 Score=32.73 Aligned_cols=33 Identities=18% Similarity=0.349 Sum_probs=19.3
Q ss_pred cCCCCcccccccccccChhHHHHHHHHhcCCCCeeccccccc
Q psy16829 139 EKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKI 180 (243)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~ 180 (243)
.....|.|+.|+..|+...++. ..|.|+.||..
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 3445566777766666555442 24667777655
No 87
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=85.30 E-value=0.34 Score=36.88 Aligned_cols=79 Identities=15% Similarity=0.240 Sum_probs=38.9
Q ss_pred eeccccch-hccChhhHHhhhhccCCCcccccccccccCChHHHHHHHHhhcCCCCcccCCcccccccChHHHHHHHHhh
Q psy16829 60 LTCVECNE-DFINVNDFVSHLRGHDSTSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVGKRLTHLKTHKKIH 138 (243)
Q Consensus 60 ~~C~~C~~-~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 138 (243)
-+|.+|.. ..-.+..|..|.=.-.-..-.|..|.+... . .+.+.|.|.+|.... -...-..|+.+-
T Consensus 98 aiCDfCEawvCHgrkCl~~HaC~Cpl~da~C~EC~R~vw-----------~-hGGrif~CsfC~~fl-CEDDQFEHQAsC 164 (314)
T PF06524_consen 98 AICDFCEAWVCHGRKCLSTHACTCPLQDAVCIECERGVW-----------D-HGGRIFKCSFCDNFL-CEDDQFEHQASC 164 (314)
T ss_pred hhhccchhheeccccccccccccCcCCCcEeeeeecccc-----------c-CCCeEEEeecCCCee-eccchhhhhhhh
Confidence 46777753 233334444443221112335666665431 2 456678888777532 233344555432
Q ss_pred --cCCCCcccccccc
Q psy16829 139 --EKVYGVYCDVCGR 151 (243)
Q Consensus 139 --~~~~~~~C~~C~~ 151 (243)
.....|+|..|++
T Consensus 165 QvLe~E~~KC~SCNr 179 (314)
T PF06524_consen 165 QVLESETFKCQSCNR 179 (314)
T ss_pred hhhhccccccccccc
Confidence 2334567776654
No 88
>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=84.68 E-value=1.2 Score=31.85 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=19.9
Q ss_pred CCCCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCc
Q psy16829 168 NAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKV 210 (243)
Q Consensus 168 ~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~ 210 (243)
+..-|.|+.|+..|+....+. . -|.|+.||..
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~--~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------L--NFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------c--CCcCCCCCCE
Confidence 445567777777776655553 2 4777777754
No 89
>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=84.32 E-value=0.86 Score=30.78 Aligned_cols=15 Identities=0% Similarity=-0.589 Sum_probs=7.7
Q ss_pred CcccCCcccccccCh
Q psy16829 114 GLYQCNECEFVGKRL 128 (243)
Q Consensus 114 ~~~~C~~C~~~f~~~ 128 (243)
.|-.|+.|+..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 455555555554433
No 90
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=83.82 E-value=0.83 Score=24.78 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=6.0
Q ss_pred eeccccccccC
Q psy16829 172 FQCEICHKIFT 182 (243)
Q Consensus 172 ~~C~~C~~~f~ 182 (243)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55555555554
No 91
>PHA00626 hypothetical protein
Probab=83.71 E-value=0.23 Score=28.06 Aligned_cols=12 Identities=17% Similarity=0.384 Sum_probs=7.4
Q ss_pred CcccccccCccC
Q psy16829 201 PWECEHCHKVYP 212 (243)
Q Consensus 201 ~~~C~~C~~~f~ 212 (243)
.|+|+.|++.|+
T Consensus 23 rYkCkdCGY~ft 34 (59)
T PHA00626 23 DYVCCDCGYNDS 34 (59)
T ss_pred ceEcCCCCCeec
Confidence 566666666664
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=83.32 E-value=0.36 Score=36.41 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=27.7
Q ss_pred ceeeccccchhccChhhHHhhhhcc----------CC-C-----cccccccccccCCh
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLRGH----------DS-T-----SHVCDICLEAFPSS 99 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~~h----------~~-~-----~~~C~~C~~~f~~~ 99 (243)
+.+.||+|+..|.+..-+....+.- .+ . ...||.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 4579999999998886655555421 11 1 13688898776544
No 93
>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=82.72 E-value=1.3 Score=20.90 Aligned_cols=20 Identities=15% Similarity=0.375 Sum_probs=14.1
Q ss_pred cccccccCccCChHHHHHHHh
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~ 222 (243)
..||+|++.+ ....+.+|+.
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 94
>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=82.00 E-value=0.58 Score=24.68 Aligned_cols=31 Identities=19% Similarity=0.469 Sum_probs=18.3
Q ss_pred ceeeccccchhccChhhHHhhhhccCCCccccccccc
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLE 94 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~ 94 (243)
..|.|..||..|....... .+....|+.|+.
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~------~~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKIS------DDPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecC------CCCCCCCCCCCC
Confidence 3577888887766443221 134556777775
No 95
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.17 E-value=1.2 Score=32.48 Aligned_cols=33 Identities=18% Similarity=0.599 Sum_probs=18.8
Q ss_pred CCCCcccccccccccChhHHHHHHHHhcCCCCeecccccccc
Q psy16829 140 KVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIF 181 (243)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f 181 (243)
....|.|+.|+..|+....+. ..|.|+.||...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 344566777766665554431 246677776653
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.10 E-value=1.8 Score=31.65 Aligned_cols=34 Identities=29% Similarity=0.577 Sum_probs=21.6
Q ss_pred CCCCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCccC
Q psy16829 168 NAFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYP 212 (243)
Q Consensus 168 ~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f~ 212 (243)
...-|.|+.|+..|+....+. . -|.|+.||....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~--~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------Y--GFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------c--CCcCCCCCCCCe
Confidence 345577877877777665442 2 577888876543
No 97
>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=80.62 E-value=0.97 Score=24.19 Aligned_cols=31 Identities=19% Similarity=0.463 Sum_probs=18.2
Q ss_pred ceeeccccchhccChhhHHhhhhccCCCccccccccc
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLE 94 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~ 94 (243)
..|.|..||..|.....+.. .....|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~------~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISE------DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCC------CCCCcCCCCCC
Confidence 34777778777665532211 24556777775
No 98
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=80.58 E-value=0.69 Score=25.98 Aligned_cols=31 Identities=19% Similarity=0.463 Sum_probs=18.3
Q ss_pred ceeeccccchhccChhhHHhhhhccCCCccccccccc
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLE 94 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~ 94 (243)
..|.|..||..|.....+. ....-.|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMS------DDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEecC------CCCCCCCCCCCC
Confidence 4577888887776542221 124456888775
No 99
>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=80.17 E-value=1.2 Score=30.16 Aligned_cols=33 Identities=21% Similarity=0.382 Sum_probs=25.3
Q ss_pred eeccccchhccChhhHHhhhhccCCCcccccccccccCChHHH
Q psy16829 60 LTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAFPSSDDR 102 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l 102 (243)
..|+.||+.|.... ..|..|+.||..|.....+
T Consensus 10 r~Cp~cg~kFYDLn----------k~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 10 RICPNTGSKFYDLN----------RRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred ccCCCcCccccccC----------CCCccCCCcCCccCcchhh
Confidence 58999999987652 2578899999988766443
No 100
>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=80.10 E-value=1.2 Score=24.03 Aligned_cols=21 Identities=33% Similarity=0.542 Sum_probs=9.7
Q ss_pred CcccccccCccCCh----HHHHHHH
Q psy16829 201 PWECEHCHKVYPNK----RSYKRHK 221 (243)
Q Consensus 201 ~~~C~~C~~~f~~~----~~l~~H~ 221 (243)
...|..|++.+... ++|.+|+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 35566666555542 5666666
No 101
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=79.88 E-value=0.97 Score=26.04 Aligned_cols=8 Identities=38% Similarity=1.385 Sum_probs=4.1
Q ss_pred Cccccccc
Q psy16829 201 PWECEHCH 208 (243)
Q Consensus 201 ~~~C~~C~ 208 (243)
+|.|+.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 45555554
No 102
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=79.31 E-value=1.7 Score=24.23 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=10.3
Q ss_pred cccccccCccCCh-----HHHHHHHh
Q psy16829 202 WECEHCHKVYPNK-----RSYKRHKQ 222 (243)
Q Consensus 202 ~~C~~C~~~f~~~-----~~l~~H~~ 222 (243)
-.|..|++.+... ++|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3455555544332 45555555
No 103
>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=78.06 E-value=1.6 Score=30.06 Aligned_cols=27 Identities=33% Similarity=0.720 Sum_probs=17.2
Q ss_pred CCcceeeccccchhccChhhHHhhhhccCC
Q psy16829 55 DKPLLLTCVECNEDFINVNDFVSHLRGHDS 84 (243)
Q Consensus 55 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~ 84 (243)
..+..+.|-+||+.|... .+|++.|++
T Consensus 68 I~~d~i~clecGk~~k~L---krHL~~~~g 94 (132)
T PF05443_consen 68 ITPDYIICLECGKKFKTL---KRHLRTHHG 94 (132)
T ss_dssp B-SS-EE-TBT--EESBH---HHHHHHTT-
T ss_pred cccCeeEEccCCcccchH---HHHHHHccC
Confidence 345568999999998854 999999976
No 104
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.88 E-value=2.6 Score=29.72 Aligned_cols=37 Identities=14% Similarity=0.358 Sum_probs=18.7
Q ss_pred CCCeeccccccccCChhHHHHHHHHhCCCCCCCcccccccCcc
Q psy16829 169 AFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHKVY 211 (243)
Q Consensus 169 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~~f 211 (243)
...|.|+.|+..|.....+.. ..... .|.|+.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~----~d~~~--~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL----LDMDG--TFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh----cCCCC--cEECCCCCCEE
Confidence 345677777776664322211 01122 47777776543
No 105
>PF14353 CpXC: CpXC protein
Probab=77.75 E-value=1.9 Score=29.56 Aligned_cols=40 Identities=23% Similarity=0.383 Sum_probs=21.4
Q ss_pred eeccccchhccChhh----------HHhhhhccCC--CcccccccccccCChHH
Q psy16829 60 LTCVECNEDFINVND----------FVSHLRGHDS--TSHVCDICLEAFPSSDD 101 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~----------l~~H~~~h~~--~~~~C~~C~~~f~~~~~ 101 (243)
++|+.|+..|..... |+.-+. .+ -.+.||.||..|.-...
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il--~g~l~~~~CP~Cg~~~~~~~p 53 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKIL--DGSLFSFTCPSCGHKFRLEYP 53 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHH--cCCcCEEECCCCCCceecCCC
Confidence 478888876643321 222221 22 45678888777654333
No 106
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=77.70 E-value=1.5 Score=31.40 Aligned_cols=24 Identities=21% Similarity=0.469 Sum_probs=14.6
Q ss_pred cccccccccccCChHHHHHHHHhhcCCCCcccCCcccc
Q psy16829 86 SHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEF 123 (243)
Q Consensus 86 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~ 123 (243)
.|.|+.||..+ .++.|-.|++|+.
T Consensus 134 ~~vC~vCGy~~--------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH--------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc--------------cCCCCCcCCCCCC
Confidence 36677776544 4455666666663
No 107
>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=77.45 E-value=0.72 Score=22.67 Aligned_cols=9 Identities=22% Similarity=0.637 Sum_probs=5.0
Q ss_pred CcccccccC
Q psy16829 201 PWECEHCHK 209 (243)
Q Consensus 201 ~~~C~~C~~ 209 (243)
.|.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 455665553
No 108
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.41 E-value=2.4 Score=29.91 Aligned_cols=38 Identities=16% Similarity=0.248 Sum_probs=23.0
Q ss_pred CCCCcccccccccccChhHHHHHHHHhcCCCCeecccccccc
Q psy16829 140 KVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIF 181 (243)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f 181 (243)
....|.|+.|+..|.....+.. .. ....|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LD-MDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cC-CCCcEECCCCCCEE
Confidence 4456888888888775433222 01 13338888888765
No 109
>PF15269 zf-C2H2_7: Zinc-finger
Probab=77.41 E-value=1.9 Score=23.12 Aligned_cols=23 Identities=17% Similarity=0.362 Sum_probs=19.9
Q ss_pred CcccccccCccCChHHHHHHHhh
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQV 223 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~ 223 (243)
.|+|-.|..+..-+++|-.|++-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 47899999999999999999873
No 110
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=77.22 E-value=0.43 Score=33.83 Aligned_cols=12 Identities=42% Similarity=0.758 Sum_probs=5.3
Q ss_pred eeccccccccCC
Q psy16829 172 FQCEICHKIFTN 183 (243)
Q Consensus 172 ~~C~~C~~~f~~ 183 (243)
++|+.||+.|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 444444444443
No 111
>KOG2807|consensus
Probab=76.48 E-value=4.7 Score=32.07 Aligned_cols=30 Identities=27% Similarity=0.590 Sum_probs=23.2
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCCCCCCCCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVKHECEGGP 235 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~c~~c~ 235 (243)
.|.|..|...|-..-+.-.|...|. |++|.
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh~-----CpgCe 374 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLHN-----CPGCE 374 (378)
T ss_pred cEEchhccceeeccchHHHHhhhhc-----CCCcC
Confidence 6889999999988877777766554 77775
No 112
>PRK04023 DNA polymerase II large subunit; Validated
Probab=75.48 E-value=3.9 Score=37.79 Aligned_cols=12 Identities=25% Similarity=0.302 Sum_probs=7.5
Q ss_pred CCCCCCCCCccC
Q psy16829 229 HECEGGPIPALA 240 (243)
Q Consensus 229 ~~c~~c~~~~~~ 240 (243)
+.|+.||.....
T Consensus 664 y~CPKCG~El~~ 675 (1121)
T PRK04023 664 DECEKCGREPTP 675 (1121)
T ss_pred CcCCCCCCCCCc
Confidence 667777765543
No 113
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=74.70 E-value=1.7 Score=23.68 Aligned_cols=9 Identities=22% Similarity=1.003 Sum_probs=4.1
Q ss_pred eeccccchh
Q psy16829 60 LTCVECNED 68 (243)
Q Consensus 60 ~~C~~C~~~ 68 (243)
|.|+.||..
T Consensus 4 y~C~~CG~~ 12 (46)
T PRK00398 4 YKCARCGRE 12 (46)
T ss_pred EECCCCCCE
Confidence 444444443
No 114
>KOG2186|consensus
Probab=74.23 E-value=2.8 Score=31.99 Aligned_cols=46 Identities=30% Similarity=0.573 Sum_probs=26.6
Q ss_pred cccccccccccChhHHHHHHHHhcCCCCeeccccccccCChhHHHHHHH
Q psy16829 144 VYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTNKSTMWSHKK 192 (243)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~~~~l~~H~~ 192 (243)
|.|..||....- ..+..|+-.-++ ..|.|-.|+..|.. .+...|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 566667665543 345556655555 34666667776665 45555544
No 115
>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=73.91 E-value=1.9 Score=21.57 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=4.5
Q ss_pred CcccccccC
Q psy16829 201 PWECEHCHK 209 (243)
Q Consensus 201 ~~~C~~C~~ 209 (243)
+..|+.||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 455666654
No 116
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.36 E-value=1.9 Score=26.96 Aligned_cols=12 Identities=25% Similarity=1.074 Sum_probs=7.2
Q ss_pred CcccccccCccC
Q psy16829 201 PWECEHCHKVYP 212 (243)
Q Consensus 201 ~~~C~~C~~~f~ 212 (243)
.+.|..|+..|+
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 466666666654
No 117
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=73.10 E-value=2.2 Score=24.57 Aligned_cols=40 Identities=23% Similarity=0.599 Sum_probs=20.2
Q ss_pred CCeeccc--cccccCChhHHHHHHHHhCCCCCCCccccc----ccCccC
Q psy16829 170 FPFQCEI--CHKIFTNKSTMWSHKKAHKPEDQIPWECEH----CHKVYP 212 (243)
Q Consensus 170 k~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~----C~~~f~ 212 (243)
.+..|+. |...+ .+..|..|+...-..+ +..|+. |+..+.
T Consensus 8 ~~v~C~~~cc~~~i-~r~~l~~H~~~~C~~~--~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMI-PRKELDDHLENECPKR--PVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEE-ECCCHHHHHHTTSTTS--EEE-SS----S--EEE
T ss_pred CEeeCCCCCcccce-eHHHHHHHHHccCCCC--cEECCCCCCCCCCccc
Confidence 3455665 33333 3456777777655555 667777 766654
No 118
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=72.91 E-value=0.74 Score=27.94 Aligned_cols=39 Identities=15% Similarity=0.556 Sum_probs=18.2
Q ss_pred eeccccccccCChhHHHHHHHHhCCCCCCCcccc--cccCccCCh
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECE--HCHKVYPNK 214 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~--~C~~~f~~~ 214 (243)
+.|+.||....-..+-..... ..+. -+.|. .||.+|...
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~--Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKER--YHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hhee--eeecCCCCCCCEEEEE
Confidence 356666655433222221111 2222 56666 677666543
No 119
>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=72.34 E-value=2.2 Score=29.34 Aligned_cols=25 Identities=32% Similarity=0.587 Sum_probs=13.6
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVK 228 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~ 228 (243)
-..|-+||+.|.. |.+|++.|+|..
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred eeEEccCCcccch---HHHHHHHccCCC
Confidence 3567788877764 478888777653
No 120
>PRK04023 DNA polymerase II large subunit; Validated
Probab=71.46 E-value=4.6 Score=37.36 Aligned_cols=10 Identities=40% Similarity=0.817 Sum_probs=6.9
Q ss_pred CcccccccCc
Q psy16829 201 PWECEHCHKV 210 (243)
Q Consensus 201 ~~~C~~C~~~ 210 (243)
++.|+.|+..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 5668888754
No 121
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=67.16 E-value=5.1 Score=22.27 Aligned_cols=39 Identities=21% Similarity=0.335 Sum_probs=20.1
Q ss_pred CCCeeccccccccCChhHHHHHHHHhCCCCCCCccccccc
Q psy16829 169 AFPFQCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCH 208 (243)
Q Consensus 169 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~ 208 (243)
++.+.|..||..|.....=+..... -|-.+.|-.|+.|.
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~e-Kgf~n~p~RC~~CR 40 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAE-KGFDNEPKRCPSCR 40 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHh-cCCcCCCccCHHHH
Confidence 4556777777776554433333332 22222266677665
No 122
>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=66.58 E-value=1.7 Score=24.43 Aligned_cols=30 Identities=20% Similarity=0.537 Sum_probs=13.1
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCCCCCCCCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVKHECEGGP 235 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~c~~c~ 235 (243)
.|.|+.|...|-..-.+-.|..+| .|++|.
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH-----~CPGC~ 50 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLH-----NCPGCE 50 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS------SSSTT-
T ss_pred eEECCCCCCccccCcChhhhcccc-----CCcCCC
Confidence 577777777776555554444333 366653
No 123
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=66.47 E-value=3.5 Score=22.86 Aligned_cols=12 Identities=17% Similarity=0.755 Sum_probs=7.6
Q ss_pred ceeeccccchhc
Q psy16829 58 LLLTCVECNEDF 69 (243)
Q Consensus 58 ~~~~C~~C~~~~ 69 (243)
..|.|..||+.|
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 346677776665
No 124
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=63.36 E-value=5.7 Score=31.37 Aligned_cols=30 Identities=23% Similarity=0.613 Sum_probs=24.0
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCCCCCCCCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVKHECEGGP 235 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~c~~c~ 235 (243)
.|.|+.|...|-...+.-.|...|. |.+|.
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh~-----C~gCe 417 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLHF-----CIGCE 417 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHhh-----CCCCc
Confidence 6999999999999888888877665 55554
No 125
>KOG2593|consensus
Probab=62.42 E-value=10 Score=31.56 Aligned_cols=40 Identities=20% Similarity=0.508 Sum_probs=25.6
Q ss_pred cCCCCcccccccccccChhHHHHHHHHhcCCCCeecccccccc
Q psy16829 139 EKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIF 181 (243)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f 181 (243)
.....|.|+.|.+.|.....+. ..-.....|.|..|+-..
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccCceEEEecCCCch
Confidence 4456788998888887654432 223335568888887543
No 126
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=60.29 E-value=11 Score=36.00 Aligned_cols=30 Identities=20% Similarity=0.474 Sum_probs=16.1
Q ss_pred CcccccccCccCChHHHHHHHhhcCCCCCCCCCCCCCccC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGVKHECEGGPIPALA 240 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~c~~c~~~~~~ 240 (243)
+|.|+.|+...... -++ ...|+.||.+...
T Consensus 692 vy~CPsCGaev~~d---------es~-a~~CP~CGtplv~ 721 (1337)
T PRK14714 692 VYVCPDCGAEVPPD---------ESG-RVECPRCDVELTP 721 (1337)
T ss_pred ceeCccCCCccCCC---------ccc-cccCCCCCCcccc
Confidence 56777777643321 011 2467777766543
No 127
>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=59.17 E-value=4.2 Score=18.80 Aligned_cols=8 Identities=38% Similarity=1.373 Sum_probs=5.3
Q ss_pred Cccccccc
Q psy16829 201 PWECEHCH 208 (243)
Q Consensus 201 ~~~C~~C~ 208 (243)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 56666665
No 128
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=58.94 E-value=7.1 Score=24.69 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=18.9
Q ss_pred CcccccccccccCChHHHHHHHHhhcCCCCcccCCcccccc
Q psy16829 85 TSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFVG 125 (243)
Q Consensus 85 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~f 125 (243)
.|-.|..||..|.+. ...+|..|+.|...+
T Consensus 57 ~Pa~CkkCGfef~~~-----------~ik~pSRCP~CKSE~ 86 (97)
T COG3357 57 RPARCKKCGFEFRDD-----------KIKKPSRCPKCKSEW 86 (97)
T ss_pred cChhhcccCcccccc-----------ccCCcccCCcchhhc
Confidence 566788888877541 234467777776543
No 129
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.37 E-value=5.9 Score=25.98 Aligned_cols=26 Identities=12% Similarity=0.190 Sum_probs=14.0
Q ss_pred eccccchhccChhhHHhhhhccCCCccccccccccc
Q psy16829 61 TCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAF 96 (243)
Q Consensus 61 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f 96 (243)
+|+.||+.|... ...|..||.||++|
T Consensus 11 idPetg~KFYDL----------NrdPiVsPytG~s~ 36 (129)
T COG4530 11 IDPETGKKFYDL----------NRDPIVSPYTGKSY 36 (129)
T ss_pred cCccccchhhcc----------CCCccccCcccccc
Confidence 556666555433 12455566666665
No 130
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=58.36 E-value=20 Score=24.61 Aligned_cols=25 Identities=28% Similarity=0.526 Sum_probs=20.6
Q ss_pred cceeeccccchhccChhhHHhhhhccCC
Q psy16829 57 PLLLTCVECNEDFINVNDFVSHLRGHDS 84 (243)
Q Consensus 57 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~ 84 (243)
+.-+.|-.+|+.|+ +|.+|+.+|.+
T Consensus 74 pD~IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 74 PDYIICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred CCeEEEeccCcchH---HHHHHHhcccC
Confidence 33478999999987 68999999876
No 131
>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=57.93 E-value=11 Score=20.47 Aligned_cols=8 Identities=25% Similarity=1.149 Sum_probs=3.8
Q ss_pred Cccccccc
Q psy16829 201 PWECEHCH 208 (243)
Q Consensus 201 ~~~C~~C~ 208 (243)
.|+|..|+
T Consensus 37 ~~~C~~C~ 44 (46)
T PF12760_consen 37 RYRCKACR 44 (46)
T ss_pred eEECCCCC
Confidence 44454444
No 132
>PF12907 zf-met2: Zinc-binding
Probab=56.87 E-value=7.4 Score=20.58 Aligned_cols=8 Identities=13% Similarity=-0.139 Sum_probs=3.5
Q ss_pred HHHHHHHH
Q psy16829 100 DDRDLHFL 107 (243)
Q Consensus 100 ~~l~~H~~ 107 (243)
..|..|..
T Consensus 18 ~~L~eH~e 25 (40)
T PF12907_consen 18 PQLKEHAE 25 (40)
T ss_pred HHHHHHHH
Confidence 33444444
No 133
>KOG3408|consensus
Probab=56.38 E-value=6.1 Score=26.49 Aligned_cols=22 Identities=18% Similarity=0.569 Sum_probs=19.3
Q ss_pred CcccccccCccCChHHHHHHHh
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
-|-|-.|.+.|.+...|+.|.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHh
Confidence 4889999999999999999976
No 134
>KOG2907|consensus
Probab=55.51 E-value=6.2 Score=26.09 Aligned_cols=39 Identities=13% Similarity=0.327 Sum_probs=23.0
Q ss_pred eeccccchhccChhhHHhhhhccCC-CcccccccccccCC
Q psy16829 60 LTCVECNEDFINVNDFVSHLRGHDS-TSHVCDICLEAFPS 98 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~~h~~-~~~~C~~C~~~f~~ 98 (243)
.+|+.||..=-.++.|+.--..... .=|.|+.|+..|..
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 5788888754444444433222222 45888888887753
No 135
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=54.91 E-value=7 Score=21.62 Aligned_cols=8 Identities=38% Similarity=1.394 Sum_probs=3.8
Q ss_pred cccccccC
Q psy16829 202 WECEHCHK 209 (243)
Q Consensus 202 ~~C~~C~~ 209 (243)
+.|..|++
T Consensus 38 ~~CGkCgy 45 (51)
T COG1998 38 WACGKCGY 45 (51)
T ss_pred eEeccccc
Confidence 44544443
No 136
>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=54.73 E-value=2.5 Score=21.80 Aligned_cols=10 Identities=30% Similarity=0.952 Sum_probs=5.6
Q ss_pred eccccccccC
Q psy16829 173 QCEICHKIFT 182 (243)
Q Consensus 173 ~C~~C~~~f~ 182 (243)
.|+.||..|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4556665553
No 137
>KOG3408|consensus
Probab=53.41 E-value=20 Score=24.15 Aligned_cols=31 Identities=23% Similarity=0.476 Sum_probs=24.0
Q ss_pred CCCCCCcceeeccccchhccChhhHHhhhhc
Q psy16829 51 DDGEDKPLLLTCVECNEDFINVNDFVSHLRG 81 (243)
Q Consensus 51 ~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~ 81 (243)
.....+-..|-|..|.+.|.+...|..|.++
T Consensus 49 D~dlPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 49 DPDLPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 3444556668899999999999999998764
No 138
>KOG4167|consensus
Probab=53.32 E-value=4.6 Score=35.79 Aligned_cols=27 Identities=22% Similarity=0.604 Sum_probs=16.8
Q ss_pred cceeeccccchhccChhhHHhhhhccC
Q psy16829 57 PLLLTCVECNEDFINVNDFVSHLRGHD 83 (243)
Q Consensus 57 ~~~~~C~~C~~~~~~~~~l~~H~~~h~ 83 (243)
...|.|..|++.|.....+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 334666666666666666666666664
No 139
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.22 E-value=4.1 Score=28.23 Aligned_cols=12 Identities=25% Similarity=0.780 Sum_probs=6.3
Q ss_pred cccccccccccC
Q psy16829 144 VYCDVCGRGFHQ 155 (243)
Q Consensus 144 ~~C~~C~~~f~~ 155 (243)
+.|..||..|..
T Consensus 71 ~~C~~CG~~~~~ 82 (135)
T PRK03824 71 LKCRNCGNEWSL 82 (135)
T ss_pred EECCCCCCEEec
Confidence 555555555443
No 140
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=52.70 E-value=15 Score=19.46 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=9.5
Q ss_pred ccccccCccC--ChHHHHHHHhhc
Q psy16829 203 ECEHCHKVYP--NKRSYKRHKQVH 224 (243)
Q Consensus 203 ~C~~C~~~f~--~~~~l~~H~~~H 224 (243)
.|+.|+-.|. ....-..|.+.|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 4555554433 234444444443
No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.68 E-value=9.6 Score=34.43 Aligned_cols=46 Identities=22% Similarity=0.285 Sum_probs=28.0
Q ss_pred eeccccchhccChh---hHHhhhhccCCCcccccccccccCChHHHHHHHHhhcCCCCcccCCccccc
Q psy16829 60 LTCVECNEDFINVN---DFVSHLRGHDSTSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFV 124 (243)
Q Consensus 60 ~~C~~C~~~~~~~~---~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~ 124 (243)
..|..||..+.... .|.-|+.. ....|.+||. ....|..|+.|+..
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~~---~~L~CH~Cg~----------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKAT---GQLRCHYCGY----------------QEPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCCCcceEEecCC---CeeEeCCCCC----------------CCCCCCCCCCCCCC
Confidence 56777777665442 23334322 4567888876 34557888888764
No 142
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=52.66 E-value=13 Score=25.55 Aligned_cols=58 Identities=16% Similarity=0.377 Sum_probs=32.7
Q ss_pred cCCCCcccccccccccChhHHHHHHHHhcCCCCeeccccccccCC--hhHHHHHHHHhCCCCCCCcccccccCccCChH
Q psy16829 139 EKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFTN--KSTMWSHKKAHKPEDQIPWECEHCHKVYPNKR 215 (243)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~~--~~~l~~H~~~h~~~~~~~~~C~~C~~~f~~~~ 215 (243)
...+.|+|.+|......+.- -||-.| ||+..-. -..|+.|-..|. .||.|.-+|++.+
T Consensus 76 ~d~~lYeCnIC~etS~ee~F----------LKPneC--CgY~iCn~Cya~LWK~~~~yp-------vCPvCkTSFKss~ 135 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERF----------LKPNEC--CGYSICNACYANLWKFCNLYP-------VCPVCKTSFKSSS 135 (140)
T ss_pred cCCCceeccCcccccchhhc----------CCcccc--cchHHHHHHHHHHHHHcccCC-------CCCcccccccccc
Confidence 44567888888765443321 234344 4433211 245666654332 4899998888764
No 143
>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=51.99 E-value=4.6 Score=23.00 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=7.2
Q ss_pred eeccccccccCC
Q psy16829 172 FQCEICHKIFTN 183 (243)
Q Consensus 172 ~~C~~C~~~f~~ 183 (243)
|.|+.||..+.-
T Consensus 3 ~~CP~CG~~iev 14 (54)
T TIGR01206 3 FECPDCGAEIEL 14 (54)
T ss_pred cCCCCCCCEEec
Confidence 467777765543
No 144
>KOG2807|consensus
Probab=50.72 E-value=18 Score=28.95 Aligned_cols=88 Identities=19% Similarity=0.275 Sum_probs=50.7
Q ss_pred ceeeccccchhccChhhHHhhhhccCCCcccccccccccCChHHHHHHHHhhcCC-----CCc-------ccCCcccccc
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAFPSSDDRDLHFLSHLTS-----DGL-------YQCNECEFVG 125 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-----~~~-------~~C~~C~~~f 125 (243)
..|.|+.|... +-.-|..|+.|+-.......|.+-..-- .. +.| --|-.|+.
T Consensus 275 ~Gy~CP~Ckak-------------vCsLP~eCpiC~ltLVss~hLARSyhhL-~PL~~F~Eip~~~~~~~~~Cf~C~~-- 338 (378)
T KOG2807|consen 275 GGYFCPQCKAK-------------VCSLPIECPICSLTLVSSPHLARSYHHL-FPLKPFVEIPETEYNGSRFCFACQG-- 338 (378)
T ss_pred CceeCCcccCe-------------eecCCccCCccceeEecchHHHHHHHhh-cCCcchhhccccccCCCcceeeecc--
Confidence 34788887642 2235777888888777777765532110 01 111 11444421
Q ss_pred cChHHHHHHHHhhcCCCCcccccccccccChhHHHHHHHHhcCCCCeeccccc
Q psy16829 126 KRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICH 178 (243)
Q Consensus 126 ~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~ 178 (243)
...+...|.|..|...|-..-+...|...| .|+.|.
T Consensus 339 -----------~~~~~~~y~C~~Ck~~FCldCDv~iHesLh------~CpgCe 374 (378)
T KOG2807|consen 339 -----------ELLSSGRYRCESCKNVFCLDCDVFIHESLH------NCPGCE 374 (378)
T ss_pred -----------ccCCCCcEEchhccceeeccchHHHHhhhh------cCCCcC
Confidence 123344688888888888887777777665 366554
No 145
>KOG1280|consensus
Probab=50.57 E-value=15 Score=29.68 Aligned_cols=36 Identities=19% Similarity=0.469 Sum_probs=19.1
Q ss_pred CcccccccccccChhHHHHHHHHhcCCCC--eeccccc
Q psy16829 143 GVYCDVCGRGFHQNNEVTLHKIKEHNAFP--FQCEICH 178 (243)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~~~~~k~--~~C~~C~ 178 (243)
.|.|+.|+..-.+...+..|....|.+-+ ..|++|+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 56666666555555566666555553322 2345444
No 146
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=50.39 E-value=8.1 Score=20.26 Aligned_cols=14 Identities=21% Similarity=0.890 Sum_probs=12.1
Q ss_pred CcccccccCccCCh
Q psy16829 201 PWECEHCHKVYPNK 214 (243)
Q Consensus 201 ~~~C~~C~~~f~~~ 214 (243)
||.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999999754
No 147
>KOG2593|consensus
Probab=49.76 E-value=16 Score=30.52 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=8.5
Q ss_pred CCeeccccccccCChh
Q psy16829 170 FPFQCEICHKIFTNKS 185 (243)
Q Consensus 170 k~~~C~~C~~~f~~~~ 185 (243)
..|.|+.|.+.|....
T Consensus 127 ~~Y~Cp~C~kkyt~Le 142 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLE 142 (436)
T ss_pred ccccCCccccchhhhH
Confidence 3455666665555443
No 148
>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=49.57 E-value=6.8 Score=26.20 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=6.7
Q ss_pred eeccccccccCC
Q psy16829 172 FQCEICHKIFTN 183 (243)
Q Consensus 172 ~~C~~C~~~f~~ 183 (243)
+.|..||..|.-
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 456666666654
No 149
>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=49.01 E-value=19 Score=27.79 Aligned_cols=85 Identities=15% Similarity=0.270 Sum_probs=42.4
Q ss_pred cCCCCcccccccccccChhHHHHHHHHh--cCCCCeeccccccccCCh------hHHHHHHHHh--CCCCCCCccccccc
Q psy16829 139 EKVYGVYCDVCGRGFHQNNEVTLHKIKE--HNAFPFQCEICHKIFTNK------STMWSHKKAH--KPEDQIPWECEHCH 208 (243)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~--~~~k~~~C~~C~~~f~~~------~~l~~H~~~h--~~~~~~~~~C~~C~ 208 (243)
++.+.|+|..|....- ...--.|+..- .....|+|..|++.=... .--..|++.- .-++.+++.||.|+
T Consensus 138 hGGrif~CsfC~~flC-EDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 138 HGGRIFKCSFCDNFLC-EDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred CCCeEEEeecCCCeee-ccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCC
Confidence 5677788888875433 33333444322 234557777776542211 0112344431 11222377788887
Q ss_pred CccCChHHHHHHHhhc
Q psy16829 209 KVYPNKRSYKRHKQVH 224 (243)
Q Consensus 209 ~~f~~~~~l~~H~~~H 224 (243)
.--.....|..=.|.|
T Consensus 217 ~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 217 YETQETKDLSMSTRSH 232 (314)
T ss_pred Ccccccccceeeeecc
Confidence 6665555554444443
No 150
>KOG2272|consensus
Probab=48.85 E-value=13 Score=28.51 Aligned_cols=14 Identities=7% Similarity=-0.059 Sum_probs=10.3
Q ss_pred CCCCCCCCCccCcC
Q psy16829 229 HECEGGPIPALALF 242 (243)
Q Consensus 229 ~~c~~c~~~~~~~~ 242 (243)
|.|..|++..++|.
T Consensus 281 f~Cs~Cdkkl~~K~ 294 (332)
T KOG2272|consen 281 FSCSTCDKKLTQKN 294 (332)
T ss_pred cccccccccccccc
Confidence 67788888777664
No 151
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=48.68 E-value=98 Score=22.14 Aligned_cols=54 Identities=19% Similarity=0.142 Sum_probs=26.4
Q ss_pred ceeecccc-chhccCh--hhHHhhhhccCCCcccccc--cccccCChHHHHHHHHhhcCCCCc
Q psy16829 58 LLLTCVEC-NEDFINV--NDFVSHLRGHDSTSHVCDI--CLEAFPSSDDRDLHFLSHLTSDGL 115 (243)
Q Consensus 58 ~~~~C~~C-~~~~~~~--~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~ 115 (243)
....|++| |..+... ..-+.+|. .++..|.. |..+ .+...|+.|.+..|...+|
T Consensus 79 ~~L~CPLCRG~V~GWtvve~AR~~LN---~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP 137 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVVEPARRFLN---AKKRSCSQESCSFS-GTYSELRKHARSEHPSARP 137 (162)
T ss_pred ccccCccccCceeceEEchHHHHHhc---cCCccCcccccccc-cCHHHHHHHHHhhCCCCCC
Confidence 34688888 4332211 22223332 24444543 4432 3456677777765555544
No 152
>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=48.15 E-value=10 Score=20.25 Aligned_cols=11 Identities=18% Similarity=-0.016 Sum_probs=7.8
Q ss_pred CCCCCCCCccC
Q psy16829 230 ECEGGPIPALA 240 (243)
Q Consensus 230 ~c~~c~~~~~~ 240 (243)
.|..||++|+.
T Consensus 10 ~C~~C~rpf~W 20 (42)
T PF10013_consen 10 ICPVCGRPFTW 20 (42)
T ss_pred cCcccCCcchH
Confidence 57777777764
No 153
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=47.98 E-value=9.2 Score=25.60 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=7.2
Q ss_pred eeccccccccCC
Q psy16829 172 FQCEICHKIFTN 183 (243)
Q Consensus 172 ~~C~~C~~~f~~ 183 (243)
+.|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 566677765543
No 154
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=46.39 E-value=8.5 Score=29.02 Aligned_cols=22 Identities=23% Similarity=0.611 Sum_probs=9.7
Q ss_pred eeccccccccCChhHHHHHHHH
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKA 193 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~ 193 (243)
|.|+.|++.|.-..-+..|+..
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHH
T ss_pred ECCCCCCcccCChHHHHHHHhh
Confidence 4455555555444444444443
No 155
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=46.03 E-value=9.9 Score=28.66 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=22.4
Q ss_pred CCCCcccccccccccChhHHHHHHHHhcC
Q psy16829 140 KVYGVYCDVCGRGFHQNNEVTLHKIKEHN 168 (243)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 168 (243)
.+..|.|+.|++.|....-+.+|+...|.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 44569999999999999999999987764
No 156
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=45.93 E-value=9.7 Score=20.07 Aligned_cols=19 Identities=11% Similarity=0.324 Sum_probs=10.5
Q ss_pred CcccccccCccCChHHHHH
Q psy16829 201 PWECEHCHKVYPNKRSYKR 219 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~ 219 (243)
.+.|+.|+-.|-....|.+
T Consensus 19 id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEECCCCCeEEccHHHHHH
Confidence 3556666666555555543
No 157
>KOG4167|consensus
Probab=45.22 E-value=5.1 Score=35.52 Aligned_cols=23 Identities=26% Similarity=0.525 Sum_probs=21.9
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy16829 87 HVCDICLEAFPSSDDRDLHFLSH 109 (243)
Q Consensus 87 ~~C~~C~~~f~~~~~l~~H~~~h 109 (243)
|.|..|++.|.....+..||++|
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHH
Confidence 78999999999999999999988
No 158
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.38 E-value=12 Score=20.91 Aligned_cols=8 Identities=25% Similarity=0.891 Sum_probs=3.5
Q ss_pred eecccccc
Q psy16829 172 FQCEICHK 179 (243)
Q Consensus 172 ~~C~~C~~ 179 (243)
+.|..||+
T Consensus 38 ~~C~~Cgy 45 (50)
T PRK00432 38 WHCGKCGY 45 (50)
T ss_pred EECCCcCC
Confidence 34444443
No 159
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=44.22 E-value=9.2 Score=24.34 Aligned_cols=12 Identities=25% Similarity=0.905 Sum_probs=6.4
Q ss_pred CcccCCcccccc
Q psy16829 114 GLYQCNECEFVG 125 (243)
Q Consensus 114 ~~~~C~~C~~~f 125 (243)
..+.|..|+..|
T Consensus 53 GIW~C~~C~~~~ 64 (90)
T PTZ00255 53 GIWRCKGCKKTV 64 (90)
T ss_pred EEEEcCCCCCEE
Confidence 345555555544
No 160
>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=43.67 E-value=5.7 Score=25.27 Aligned_cols=11 Identities=18% Similarity=0.582 Sum_probs=5.8
Q ss_pred Ccccccccccc
Q psy16829 85 TSHVCDICLEA 95 (243)
Q Consensus 85 ~~~~C~~C~~~ 95 (243)
..|.|+.|++.
T Consensus 34 ~ky~Cp~Cgk~ 44 (90)
T PF01780_consen 34 AKYTCPFCGKT 44 (90)
T ss_dssp S-BEESSSSSS
T ss_pred CCCcCCCCCCc
Confidence 45666666653
No 161
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=43.09 E-value=8.7 Score=22.00 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=7.3
Q ss_pred eeccccchhccC
Q psy16829 60 LTCVECNEDFIN 71 (243)
Q Consensus 60 ~~C~~C~~~~~~ 71 (243)
++|.+|++.+..
T Consensus 3 vkC~lCdk~~~I 14 (56)
T PF09963_consen 3 VKCILCDKKEEI 14 (56)
T ss_pred eEEEecCCEEEe
Confidence 467777765543
No 162
>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=42.44 E-value=3.2 Score=32.95 Aligned_cols=35 Identities=20% Similarity=0.467 Sum_probs=12.6
Q ss_pred ccccccccccChhHHHHHHHHhcCCCCeeccccccccC
Q psy16829 145 YCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIFT 182 (243)
Q Consensus 145 ~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f~ 182 (243)
.|++||.. ...+.+..-.. .|.+...|..|+..+.
T Consensus 174 ~CPvCGs~-P~~s~l~~~~~--~G~R~L~Cs~C~t~W~ 208 (290)
T PF04216_consen 174 YCPVCGSP-PVLSVLRGGER--EGKRYLHCSLCGTEWR 208 (290)
T ss_dssp S-TTT----EEEEEEE--------EEEEEETTT--EEE
T ss_pred cCCCCCCc-CceEEEecCCC--CccEEEEcCCCCCeee
Confidence 68888754 22222211111 2556667777776654
No 163
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.28 E-value=14 Score=24.97 Aligned_cols=11 Identities=27% Similarity=1.050 Sum_probs=6.0
Q ss_pred eeccccccccC
Q psy16829 172 FQCEICHKIFT 182 (243)
Q Consensus 172 ~~C~~C~~~f~ 182 (243)
+.|..||..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 45666665554
No 164
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=41.17 E-value=14 Score=29.22 Aligned_cols=26 Identities=19% Similarity=0.439 Sum_probs=18.8
Q ss_pred CCCcccccccccccChhHHHHHHHHh
Q psy16829 141 VYGVYCDVCGRGFHQNNEVTLHKIKE 166 (243)
Q Consensus 141 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 166 (243)
...|.|..|...|....+...|...|
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHh
Confidence 34577888887787777777777655
No 165
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=41.14 E-value=20 Score=20.23 Aligned_cols=12 Identities=17% Similarity=0.706 Sum_probs=5.9
Q ss_pred eeccccccccCC
Q psy16829 172 FQCEICHKIFTN 183 (243)
Q Consensus 172 ~~C~~C~~~f~~ 183 (243)
++|+.||..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 455555554443
No 166
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=41.14 E-value=5.5 Score=25.71 Aligned_cols=8 Identities=38% Similarity=1.094 Sum_probs=3.5
Q ss_pred eecccccc
Q psy16829 172 FQCEICHK 179 (243)
Q Consensus 172 ~~C~~C~~ 179 (243)
|.|+.||.
T Consensus 23 FtCp~Cgh 30 (104)
T COG4888 23 FTCPRCGH 30 (104)
T ss_pred EecCccCC
Confidence 44444443
No 167
>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=40.48 E-value=9.7 Score=18.35 Aligned_cols=9 Identities=44% Similarity=1.630 Sum_probs=4.9
Q ss_pred eccccchhc
Q psy16829 61 TCVECNEDF 69 (243)
Q Consensus 61 ~C~~C~~~~ 69 (243)
.|-.|++.|
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 168
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=39.91 E-value=9.9 Score=24.24 Aligned_cols=12 Identities=25% Similarity=0.778 Sum_probs=6.3
Q ss_pred CcccCCcccccc
Q psy16829 114 GLYQCNECEFVG 125 (243)
Q Consensus 114 ~~~~C~~C~~~f 125 (243)
..+.|..|+..|
T Consensus 52 GIW~C~~C~~~~ 63 (91)
T TIGR00280 52 GIWTCRKCGAKF 63 (91)
T ss_pred EEEEcCCCCCEE
Confidence 345555555544
No 169
>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=39.72 E-value=3.5 Score=21.62 Aligned_cols=9 Identities=33% Similarity=0.504 Sum_probs=4.7
Q ss_pred ccccccccc
Q psy16829 87 HVCDICLEA 95 (243)
Q Consensus 87 ~~C~~C~~~ 95 (243)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 455555543
No 170
>COG1773 Rubredoxin [Energy production and conversion]
Probab=39.69 E-value=15 Score=21.00 Aligned_cols=14 Identities=14% Similarity=0.845 Sum_probs=11.4
Q ss_pred CeeccccccccCCh
Q psy16829 171 PFQCEICHKIFTNK 184 (243)
Q Consensus 171 ~~~C~~C~~~f~~~ 184 (243)
.|+|..||+.|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 58899999998754
No 171
>PRK10220 hypothetical protein; Provisional
Probab=39.20 E-value=19 Score=23.76 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=5.8
Q ss_pred cccCCccccccc
Q psy16829 115 LYQCNECEFVGK 126 (243)
Q Consensus 115 ~~~C~~C~~~f~ 126 (243)
.|.|+.|+..+.
T Consensus 20 ~~vCpeC~hEW~ 31 (111)
T PRK10220 20 MYICPECAHEWN 31 (111)
T ss_pred eEECCcccCcCC
Confidence 355555554443
No 172
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=38.67 E-value=7.5 Score=20.50 Aligned_cols=9 Identities=33% Similarity=0.648 Sum_probs=4.5
Q ss_pred ccccccccc
Q psy16829 87 HVCDICLEA 95 (243)
Q Consensus 87 ~~C~~C~~~ 95 (243)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 455555543
No 173
>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=38.48 E-value=9 Score=20.50 Aligned_cols=14 Identities=43% Similarity=1.084 Sum_probs=9.4
Q ss_pred CcccccccCccCCh
Q psy16829 201 PWECEHCHKVYPNK 214 (243)
Q Consensus 201 ~~~C~~C~~~f~~~ 214 (243)
||.|+.|+..|-..
T Consensus 13 ~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 13 PFKCKHCGKSFCLK 26 (43)
T ss_dssp HEE-TTTS-EE-TT
T ss_pred CeECCCCCcccCcc
Confidence 89999999998754
No 174
>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=38.14 E-value=18 Score=24.32 Aligned_cols=28 Identities=21% Similarity=0.490 Sum_probs=18.2
Q ss_pred CcceeeccccchhccChhhHHhhhhccCCCccccccccc
Q psy16829 56 KPLLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLE 94 (243)
Q Consensus 56 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~ 94 (243)
.+....|..|+..|.... ..+.||.|+.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~-----------~~~~CP~Cgs 94 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEI-----------DLYRCPKCHG 94 (115)
T ss_pred eCcEEEcccCCCEEecCC-----------cCccCcCCcC
Confidence 344578888887765432 1356888874
No 175
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=38.12 E-value=17 Score=23.92 Aligned_cols=12 Identities=17% Similarity=0.445 Sum_probs=5.8
Q ss_pred cccCCccccccc
Q psy16829 115 LYQCNECEFVGK 126 (243)
Q Consensus 115 ~~~C~~C~~~f~ 126 (243)
.|.|+.|+..+.
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 345555554443
No 176
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=37.65 E-value=16 Score=24.47 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=6.5
Q ss_pred eeccccccccC
Q psy16829 172 FQCEICHKIFT 182 (243)
Q Consensus 172 ~~C~~C~~~f~ 182 (243)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 45666665553
No 177
>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=37.39 E-value=18 Score=31.27 Aligned_cols=10 Identities=20% Similarity=0.378 Sum_probs=6.1
Q ss_pred CcccCCcccc
Q psy16829 114 GLYQCNECEF 123 (243)
Q Consensus 114 ~~~~C~~C~~ 123 (243)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3566777665
No 178
>KOG0717|consensus
Probab=36.68 E-value=20 Score=30.27 Aligned_cols=21 Identities=24% Similarity=0.635 Sum_probs=19.5
Q ss_pred cccccccCccCChHHHHHHHh
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~ 222 (243)
+-|.+|+++|.+...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999999999974
No 179
>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=36.50 E-value=13 Score=18.93 Aligned_cols=9 Identities=22% Similarity=0.586 Sum_probs=2.7
Q ss_pred CCCCCCCcc
Q psy16829 231 CEGGPIPAL 239 (243)
Q Consensus 231 c~~c~~~~~ 239 (243)
|.+|++.|.
T Consensus 6 C~eC~~~f~ 14 (34)
T PF01286_consen 6 CDECGKPFM 14 (34)
T ss_dssp -TTT--EES
T ss_pred HhHhCCHHH
Confidence 444444443
No 180
>PRK04351 hypothetical protein; Provisional
Probab=36.16 E-value=16 Score=25.86 Aligned_cols=10 Identities=10% Similarity=-0.044 Sum_probs=4.6
Q ss_pred CCCCCCCCCc
Q psy16829 229 HECEGGPIPA 238 (243)
Q Consensus 229 ~~c~~c~~~~ 238 (243)
|.|..|+-.+
T Consensus 133 yrCg~C~g~L 142 (149)
T PRK04351 133 YRCGKCRGKL 142 (149)
T ss_pred EEeCCCCcEe
Confidence 4555544433
No 181
>KOG1280|consensus
Probab=36.03 E-value=36 Score=27.59 Aligned_cols=37 Identities=27% Similarity=0.542 Sum_probs=26.9
Q ss_pred cceeeccccchhccChhhHHhhhhccCC---Ccccccccc
Q psy16829 57 PLLLTCVECNEDFINVNDFVSHLRGHDS---TSHVCDICL 93 (243)
Q Consensus 57 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~---~~~~C~~C~ 93 (243)
+..|.|++|+..=.+...|..|+..-+. ....|++|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3369999999887888889999876544 334567665
No 182
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=35.83 E-value=40 Score=24.62 Aligned_cols=34 Identities=15% Similarity=0.351 Sum_probs=18.8
Q ss_pred cCCCCcccccccccccChhHHHHHHHHhcCCCCeecccccccc
Q psy16829 139 EKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCEICHKIF 181 (243)
Q Consensus 139 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~k~~~C~~C~~~f 181 (243)
.....|.|+.|.-.++...+.. . .|.|+.||...
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~------~---~F~Cp~Cg~~L 142 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAME------L---GFTCPKCGEDL 142 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHH------h---CCCCCCCCchh
Confidence 4455677777765554433211 1 16777777653
No 183
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=35.67 E-value=28 Score=31.64 Aligned_cols=9 Identities=11% Similarity=0.213 Sum_probs=4.9
Q ss_pred CCCCCCCCC
Q psy16829 229 HECEGGPIP 237 (243)
Q Consensus 229 ~~c~~c~~~ 237 (243)
..|+.||-.
T Consensus 476 ~~Cp~Cgs~ 484 (730)
T COG1198 476 QSCPECGSE 484 (730)
T ss_pred CCCCCCCCC
Confidence 555555543
No 184
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=35.59 E-value=24 Score=28.33 Aligned_cols=15 Identities=13% Similarity=0.467 Sum_probs=8.8
Q ss_pred cCCCCeecccccccc
Q psy16829 167 HNAFPFQCEICHKIF 181 (243)
Q Consensus 167 ~~~k~~~C~~C~~~f 181 (243)
.|.+...|..|+-.+
T Consensus 206 ~G~RyL~CslC~teW 220 (305)
T TIGR01562 206 TGLRYLSCSLCATEW 220 (305)
T ss_pred CCceEEEcCCCCCcc
Confidence 345556677776544
No 185
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.50 E-value=18 Score=28.99 Aligned_cols=15 Identities=13% Similarity=0.565 Sum_probs=8.2
Q ss_pred cCCCCeecccccccc
Q psy16829 167 HNAFPFQCEICHKIF 181 (243)
Q Consensus 167 ~~~k~~~C~~C~~~f 181 (243)
.|.+...|..|+-.+
T Consensus 208 ~G~RyL~CslC~teW 222 (309)
T PRK03564 208 QGLRYLHCNLCESEW 222 (309)
T ss_pred CCceEEEcCCCCCcc
Confidence 345555666666444
No 186
>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=35.30 E-value=25 Score=20.83 Aligned_cols=7 Identities=43% Similarity=1.203 Sum_probs=2.7
Q ss_pred eeccccc
Q psy16829 172 FQCEICH 178 (243)
Q Consensus 172 ~~C~~C~ 178 (243)
|.|+.||
T Consensus 47 ~~C~~Cg 53 (69)
T PF07282_consen 47 FTCPNCG 53 (69)
T ss_pred EEcCCCC
Confidence 3333333
No 187
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=35.12 E-value=12 Score=23.80 Aligned_cols=12 Identities=25% Similarity=0.825 Sum_probs=6.3
Q ss_pred CcccCCcccccc
Q psy16829 114 GLYQCNECEFVG 125 (243)
Q Consensus 114 ~~~~C~~C~~~f 125 (243)
..+.|..|+..|
T Consensus 53 GIW~C~~C~~~~ 64 (90)
T PRK03976 53 GIWECRKCGAKF 64 (90)
T ss_pred EEEEcCCCCCEE
Confidence 345555555544
No 188
>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=34.36 E-value=24 Score=20.89 Aligned_cols=8 Identities=50% Similarity=1.593 Sum_probs=1.8
Q ss_pred cccccccc
Q psy16829 146 CDVCGRGF 153 (243)
Q Consensus 146 C~~C~~~f 153 (243)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 44444444
No 189
>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=34.04 E-value=30 Score=29.50 Aligned_cols=21 Identities=29% Similarity=0.782 Sum_probs=10.2
Q ss_pred cccccccCccCChHHHHHHHh
Q psy16829 202 WECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 202 ~~C~~C~~~f~~~~~l~~H~~ 222 (243)
+.|+.|.+.|.....+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 344445555555555555543
No 190
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=34.03 E-value=17 Score=25.66 Aligned_cols=10 Identities=30% Similarity=1.481 Sum_probs=4.7
Q ss_pred Ceecccccccc
Q psy16829 171 PFQCEICHKIF 181 (243)
Q Consensus 171 ~~~C~~C~~~f 181 (243)
+|.|. |+..|
T Consensus 117 ~Y~C~-C~q~~ 126 (156)
T COG3091 117 PYRCQ-CQQHY 126 (156)
T ss_pred eEEee-cCCcc
Confidence 34554 55443
No 191
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.78 E-value=29 Score=20.19 Aligned_cols=8 Identities=25% Similarity=1.036 Sum_probs=3.5
Q ss_pred eecccccc
Q psy16829 172 FQCEICHK 179 (243)
Q Consensus 172 ~~C~~C~~ 179 (243)
|.|+.|..
T Consensus 32 ymC~eC~~ 39 (68)
T COG4896 32 YMCPECEH 39 (68)
T ss_pred EechhhHh
Confidence 44444443
No 192
>KOG0978|consensus
Probab=33.74 E-value=13 Score=33.12 Aligned_cols=47 Identities=26% Similarity=0.518 Sum_probs=25.3
Q ss_pred eeeccccchhccChhhHH-hhh------hc-cCCCcccccccccccCChHHHHHH
Q psy16829 59 LLTCVECNEDFINVNDFV-SHL------RG-HDSTSHVCDICLEAFPSSDDRDLH 105 (243)
Q Consensus 59 ~~~C~~C~~~~~~~~~l~-~H~------~~-h~~~~~~C~~C~~~f~~~~~l~~H 105 (243)
..+|+.|...+....-.. -|. +. ...+.-+||.|+..|.....+..|
T Consensus 643 ~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred ceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 479999985544332111 121 11 111456788888888766554443
No 193
>KOG1842|consensus
Probab=33.21 E-value=25 Score=29.46 Aligned_cols=26 Identities=27% Similarity=0.392 Sum_probs=17.1
Q ss_pred CeeccccccccCChhHHHHHHHHhCC
Q psy16829 171 PFQCEICHKIFTNKSTMWSHKKAHKP 196 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 196 (243)
.|.||+|...|.+...|..|...-|+
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcc
Confidence 36677777777777777777665443
No 194
>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=33.12 E-value=20 Score=18.96 Aligned_cols=12 Identities=17% Similarity=0.520 Sum_probs=9.8
Q ss_pred ceeeccccchhc
Q psy16829 58 LLLTCVECNEDF 69 (243)
Q Consensus 58 ~~~~C~~C~~~~ 69 (243)
....|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 358999999876
No 195
>KOG3214|consensus
Probab=33.11 E-value=11 Score=24.36 Aligned_cols=12 Identities=17% Similarity=0.661 Sum_probs=6.5
Q ss_pred cccccccCccCC
Q psy16829 202 WECEHCHKVYPN 213 (243)
Q Consensus 202 ~~C~~C~~~f~~ 213 (243)
..|.+|+.+|.+
T Consensus 48 ~sC~iC~esFqt 59 (109)
T KOG3214|consen 48 ASCRICEESFQT 59 (109)
T ss_pred eeeeehhhhhcc
Confidence 345555555554
No 196
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=32.42 E-value=36 Score=17.47 Aligned_cols=11 Identities=27% Similarity=0.582 Sum_probs=5.4
Q ss_pred ccccccCccCC
Q psy16829 203 ECEHCHKVYPN 213 (243)
Q Consensus 203 ~C~~C~~~f~~ 213 (243)
.|+.|++.|..
T Consensus 4 ~CprC~kg~Hw 14 (36)
T PF14787_consen 4 LCPRCGKGFHW 14 (36)
T ss_dssp C-TTTSSSCS-
T ss_pred cCcccCCCcch
Confidence 46666666543
No 197
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=32.17 E-value=7.8 Score=34.46 Aligned_cols=29 Identities=24% Similarity=0.644 Sum_probs=15.5
Q ss_pred eccccccccCChhHHHHHHHHhCCCCCCCcccccccC
Q psy16829 173 QCEICHKIFTNKSTMWSHKKAHKPEDQIPWECEHCHK 209 (243)
Q Consensus 173 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~C~~C~~ 209 (243)
.|+.|.+.|.+..+-+-| . . |..|+.||-
T Consensus 153 lC~~C~~EY~dP~nRRfH-----A-Q--p~aCp~CGP 181 (750)
T COG0068 153 LCPFCDKEYKDPLNRRFH-----A-Q--PIACPKCGP 181 (750)
T ss_pred CCHHHHHHhcCccccccc-----c-c--cccCcccCC
Confidence 466666666655443322 1 1 566666664
No 198
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.08 E-value=13 Score=20.42 Aligned_cols=11 Identities=18% Similarity=0.003 Sum_probs=8.0
Q ss_pred CCCCCCCCccC
Q psy16829 230 ECEGGPIPALA 240 (243)
Q Consensus 230 ~c~~c~~~~~~ 240 (243)
.|+.|+++|+.
T Consensus 14 ICpvCqRPFsW 24 (54)
T COG4338 14 ICPVCQRPFSW 24 (54)
T ss_pred hhhhhcCchHH
Confidence 57778888764
No 199
>PRK12496 hypothetical protein; Provisional
Probab=31.82 E-value=28 Score=25.06 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=6.8
Q ss_pred eeccccccccC
Q psy16829 172 FQCEICHKIFT 182 (243)
Q Consensus 172 ~~C~~C~~~f~ 182 (243)
|.|+-|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 45666666664
No 200
>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=31.47 E-value=24 Score=23.17 Aligned_cols=10 Identities=20% Similarity=0.577 Sum_probs=6.5
Q ss_pred eeeccccchh
Q psy16829 59 LLTCVECNED 68 (243)
Q Consensus 59 ~~~C~~C~~~ 68 (243)
+..|+.||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 4577777653
No 201
>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=31.34 E-value=12 Score=26.51 Aligned_cols=10 Identities=20% Similarity=1.032 Sum_probs=4.8
Q ss_pred eecccccccc
Q psy16829 172 FQCEICHKIF 181 (243)
Q Consensus 172 ~~C~~C~~~f 181 (243)
|.|+.|+..+
T Consensus 124 ~~C~~C~~~~ 133 (157)
T PF10263_consen 124 YRCPSCGREY 133 (157)
T ss_pred EEcCCCCCEe
Confidence 4455555444
No 202
>KOG0782|consensus
Probab=31.10 E-value=5.4 Score=34.36 Aligned_cols=25 Identities=28% Similarity=0.547 Sum_probs=11.5
Q ss_pred hHHhhhhccCC-CcccccccccccCC
Q psy16829 74 DFVSHLRGHDS-TSHVCDICLEAFPS 98 (243)
Q Consensus 74 ~l~~H~~~h~~-~~~~C~~C~~~f~~ 98 (243)
.|.+|...|.. ..-+|..|+++|-.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQ 265 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQ 265 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhh
Confidence 34444444433 33455555555533
No 203
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.02 E-value=35 Score=30.75 Aligned_cols=47 Identities=19% Similarity=0.350 Sum_probs=25.1
Q ss_pred eeccccchhccChhhHHhhhhccCC-CcccccccccccCChHHHHHHHHhhcCCCCcccCCccccc
Q psy16829 60 LTCVECNEDFINVNDFVSHLRGHDS-TSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEFV 124 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~l~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~~ 124 (243)
+.|..||..+..... ...+..|.. ....|..||.. . .|+.|+.|+..
T Consensus 384 l~C~~Cg~~~~C~~C-~~~L~~h~~~~~l~Ch~CG~~----------------~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCRTPARCRHC-TGPLGLPSAGGTPRCRWCGRA----------------A-PDWRCPRCGSD 431 (665)
T ss_pred eEhhhCcCeeECCCC-CCceeEecCCCeeECCCCcCC----------------C-cCccCCCCcCC
Confidence 467777765544321 011122222 45678888752 2 36788888764
No 204
>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=30.93 E-value=27 Score=22.66 Aligned_cols=16 Identities=25% Similarity=0.625 Sum_probs=12.3
Q ss_pred CCCCeeccccccccCC
Q psy16829 168 NAFPFQCEICHKIFTN 183 (243)
Q Consensus 168 ~~k~~~C~~C~~~f~~ 183 (243)
..++.+|+.||..|..
T Consensus 76 ~g~~~rC~eCG~~fkL 91 (97)
T cd00924 76 KGKPKRCPECGHVFKL 91 (97)
T ss_pred CCCceeCCCCCcEEEE
Confidence 3478889999988864
No 205
>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=30.52 E-value=17 Score=20.48 Aligned_cols=9 Identities=22% Similarity=0.634 Sum_probs=2.8
Q ss_pred ccccccCcc
Q psy16829 203 ECEHCHKVY 211 (243)
Q Consensus 203 ~C~~C~~~f 211 (243)
.||+|++.|
T Consensus 22 ~CPlC~r~l 30 (54)
T PF04423_consen 22 CCPLCGRPL 30 (54)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCCC
Confidence 455555443
No 206
>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=30.48 E-value=21 Score=17.20 Aligned_cols=10 Identities=20% Similarity=0.617 Sum_probs=3.8
Q ss_pred CcccccccCc
Q psy16829 201 PWECEHCHKV 210 (243)
Q Consensus 201 ~~~C~~C~~~ 210 (243)
.|.|..|+..
T Consensus 15 ~Y~C~~Cdf~ 24 (30)
T PF07649_consen 15 FYRCSECDFD 24 (30)
T ss_dssp EEE-TTT---
T ss_pred eEECccCCCc
Confidence 5666666543
No 207
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.42 E-value=25 Score=20.50 Aligned_cols=15 Identities=13% Similarity=0.363 Sum_probs=11.4
Q ss_pred Ccceeeccccchhcc
Q psy16829 56 KPLLLTCVECNEDFI 70 (243)
Q Consensus 56 ~~~~~~C~~C~~~~~ 70 (243)
.+....|++|+..|.
T Consensus 45 ~~gev~CPYC~t~y~ 59 (62)
T COG4391 45 DEGEVVCPYCSTRYR 59 (62)
T ss_pred CCCcEecCccccEEE
Confidence 344589999998775
No 208
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.37 E-value=26 Score=21.44 Aligned_cols=37 Identities=22% Similarity=0.458 Sum_probs=22.3
Q ss_pred CCCcceeeccccchhccChhhHHhhhhccCCCccccccccccc
Q psy16829 54 EDKPLLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAF 96 (243)
Q Consensus 54 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f 96 (243)
..+...|.|..|+..|. +..++. ......|+.|+..+
T Consensus 7 lMPtY~Y~c~~cg~~~d----vvq~~~--ddplt~ce~c~a~~ 43 (82)
T COG2331 7 LMPTYSYECTECGNRFD----VVQAMT--DDPLTTCEECGARL 43 (82)
T ss_pred cccceEEeecccchHHH----HHHhcc--cCccccChhhChHH
Confidence 34556688888887653 344443 22455788887643
No 209
>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=29.89 E-value=36 Score=23.94 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=9.9
Q ss_pred CeeccccccccCChhH
Q psy16829 171 PFQCEICHKIFTNKST 186 (243)
Q Consensus 171 ~~~C~~C~~~f~~~~~ 186 (243)
-+.|+.||+.|-.-+.
T Consensus 124 f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSH 139 (147)
T ss_pred EEECCCCCCEeccccc
Confidence 4667777777655443
No 210
>KOG4602|consensus
Probab=29.85 E-value=91 Score=24.17 Aligned_cols=37 Identities=30% Similarity=0.474 Sum_probs=23.1
Q ss_pred ceeeccccchhccChhhHHhhhhcc-CC-------Cccccccccc
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLRGH-DS-------TSHVCDICLE 94 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~~h-~~-------~~~~C~~C~~ 94 (243)
.+.-|.+|...-.....+..|...- .+ +.|.|++||.
T Consensus 232 r~l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGA 276 (318)
T KOG4602|consen 232 RPLCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGA 276 (318)
T ss_pred CceeEEeecCCCchhhheecccccCCCCcEechhHhhhcCccccc
Confidence 3467888976655556666665422 12 3577888875
No 211
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=29.70 E-value=13 Score=19.53 Aligned_cols=12 Identities=17% Similarity=0.639 Sum_probs=5.5
Q ss_pred CCCCeecccccc
Q psy16829 168 NAFPFQCEICHK 179 (243)
Q Consensus 168 ~~k~~~C~~C~~ 179 (243)
+.+.|.|++|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 344566666654
No 212
>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=29.66 E-value=44 Score=28.55 Aligned_cols=23 Identities=26% Similarity=0.599 Sum_probs=13.1
Q ss_pred eeccccccccCChhHHHHHHHHh
Q psy16829 172 FQCEICHKIFTNKSTMWSHKKAH 194 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~H~~~h 194 (243)
+.|+.|.+.|.....+..|+...
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~e 80 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQE 80 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHh
Confidence 45555655565555555555543
No 213
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=29.37 E-value=25 Score=19.36 Aligned_cols=13 Identities=23% Similarity=0.984 Sum_probs=10.3
Q ss_pred eeccccccccCCh
Q psy16829 172 FQCEICHKIFTNK 184 (243)
Q Consensus 172 ~~C~~C~~~f~~~ 184 (243)
|+|..|++.|.-.
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 7888999888654
No 214
>KOG2636|consensus
Probab=29.30 E-value=42 Score=28.23 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=29.4
Q ss_pred eeeccccchhccChhhHHhhhhccCCCcccccccccccCChHHHHHHHH
Q psy16829 59 LLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAFPSSDDRDLHFL 107 (243)
Q Consensus 59 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 107 (243)
.+.|..|++.+.....|..|... -.|+.|++.|.+++.-..|+.
T Consensus 249 el~~~g~erlk~al~alglk~gG-----t~~~ra~rlf~Tk~~~l~~L~ 292 (497)
T KOG2636|consen 249 ELYCLGCERLKSALTALGLKCGG-----TLHERAQRLFSTKSKSLSHLD 292 (497)
T ss_pred HHHhhchhHHHHHHHHHHHhcCC-----eecHHHHhhhhhcCcchhhhh
Confidence 36788888887777677766532 236677777877766655554
No 215
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=28.89 E-value=13 Score=30.19 Aligned_cols=40 Identities=20% Similarity=0.352 Sum_probs=15.4
Q ss_pred eeccccccccCChhHHHH---HH-HHhCCCCCCCcccccccCccC
Q psy16829 172 FQCEICHKIFTNKSTMWS---HK-KAHKPEDQIPWECEHCHKVYP 212 (243)
Q Consensus 172 ~~C~~C~~~f~~~~~l~~---H~-~~h~~~~~~~~~C~~C~~~f~ 212 (243)
+.|..|.+.+......-. |. ..|.+.+ +=|+|..|++...
T Consensus 253 v~C~~C~yt~~~~~~~C~~~~H~l~~~~a~K-RFFkC~~C~~Rt~ 296 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDRCKEEGHPLKWHDAVK-RFFKCKDCGNRTI 296 (344)
T ss_dssp EEETTT--EESS--HHHHHTT--EEEEEEE--EEEE-T-TS-EEE
T ss_pred EEcCCCCCcccCcchhHHhcCCceEEeeeee-eeEECCCCCCeee
Confidence 668888777555443321 11 0111111 2477888887654
No 216
>KOG1842|consensus
Probab=28.82 E-value=36 Score=28.63 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=20.8
Q ss_pred ceeeccccchhccChhhHHhhhhccCC
Q psy16829 58 LLLTCVECNEDFINVNDFVSHLRGHDS 84 (243)
Q Consensus 58 ~~~~C~~C~~~~~~~~~l~~H~~~h~~ 84 (243)
..|.||+|...|.+...|..|...-|.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcc
Confidence 347888888888888888888765443
No 217
>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=28.74 E-value=24 Score=19.69 Aligned_cols=13 Identities=31% Similarity=0.986 Sum_probs=10.5
Q ss_pred eeccccccccCCh
Q psy16829 172 FQCEICHKIFTNK 184 (243)
Q Consensus 172 ~~C~~C~~~f~~~ 184 (243)
|+|..||+.|.-.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7899999988753
No 218
>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=28.05 E-value=34 Score=19.22 Aligned_cols=9 Identities=56% Similarity=0.933 Sum_probs=3.7
Q ss_pred ccccccccC
Q psy16829 174 CEICHKIFT 182 (243)
Q Consensus 174 C~~C~~~f~ 182 (243)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 334444443
No 219
>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=27.66 E-value=24 Score=24.86 Aligned_cols=32 Identities=22% Similarity=0.395 Sum_probs=19.6
Q ss_pred CCcceeeccccchhccChhhHHhhhhccCCCcccccccccc
Q psy16829 55 DKPLLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLEA 95 (243)
Q Consensus 55 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~ 95 (243)
.+...+.|..||..... .+.+..-.|+.|+..
T Consensus 108 ~g~G~l~C~~Cg~~~~~---------~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVEL---------THPERLPPCPKCGHT 139 (146)
T ss_pred ecCceEecccCCCEEEe---------cCCCcCCCCCCCCCC
Confidence 34556889999875321 123345578888754
No 220
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.63 E-value=27 Score=19.95 Aligned_cols=11 Identities=36% Similarity=0.646 Sum_probs=7.1
Q ss_pred CCCCCCCCCcc
Q psy16829 229 HECEGGPIPAL 239 (243)
Q Consensus 229 ~~c~~c~~~~~ 239 (243)
|+|+.||.++-
T Consensus 15 ~~Cp~cGipth 25 (55)
T PF13824_consen 15 FECPDCGIPTH 25 (55)
T ss_pred CcCCCCCCcCc
Confidence 66777766653
No 221
>PF14369 zf-RING_3: zinc-finger
Probab=27.29 E-value=47 Score=16.86 Aligned_cols=8 Identities=38% Similarity=1.028 Sum_probs=4.0
Q ss_pred cccccccc
Q psy16829 89 CDICLEAF 96 (243)
Q Consensus 89 C~~C~~~f 96 (243)
||.|+-+|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 55555444
No 222
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=27.26 E-value=56 Score=25.18 Aligned_cols=39 Identities=13% Similarity=0.264 Sum_probs=19.8
Q ss_pred CCcccCCcccccccChHHHHHHHHhhcCCCCcccccccccccCh
Q psy16829 113 DGLYQCNECEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQN 156 (243)
Q Consensus 113 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 156 (243)
.....|.-|.+.|.-... ..--|..-|.|+.|+..|.--
T Consensus 130 KeVSRCr~C~~rYDPVP~-----dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 130 KEVSRCRKCRKRYDPVPC-----DKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred cccccccccccccCCCcc-----ccccceeeeecccccccchhh
Confidence 334567666665533221 001123346777777777643
No 223
>PLN02294 cytochrome c oxidase subunit Vb
Probab=27.23 E-value=33 Score=24.73 Aligned_cols=17 Identities=24% Similarity=0.751 Sum_probs=13.6
Q ss_pred CCCCeeccccccccCCh
Q psy16829 168 NAFPFQCEICHKIFTNK 184 (243)
Q Consensus 168 ~~k~~~C~~C~~~f~~~ 184 (243)
..+|.+|++||..|...
T Consensus 138 kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 138 KGKSFECPVCTQYFELE 154 (174)
T ss_pred CCCceeCCCCCCEEEEE
Confidence 46788999999988653
No 224
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=27.20 E-value=42 Score=19.10 Aligned_cols=8 Identities=25% Similarity=0.895 Sum_probs=3.4
Q ss_pred eccccchh
Q psy16829 61 TCVECNED 68 (243)
Q Consensus 61 ~C~~C~~~ 68 (243)
+|+.||+.
T Consensus 7 ~C~~Cg~~ 14 (54)
T PF14446_consen 7 KCPVCGKK 14 (54)
T ss_pred cChhhCCc
Confidence 34444443
No 225
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.13 E-value=10 Score=28.72 Aligned_cols=9 Identities=22% Similarity=0.431 Sum_probs=6.0
Q ss_pred cccccccCc
Q psy16829 202 WECEHCHKV 210 (243)
Q Consensus 202 ~~C~~C~~~ 210 (243)
..||.|..+
T Consensus 63 vvCP~C~yA 71 (267)
T COG1655 63 VVCPICYYA 71 (267)
T ss_pred EEcchhhHH
Confidence 457777754
No 226
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=25.94 E-value=22 Score=17.76 Aligned_cols=9 Identities=22% Similarity=0.619 Sum_probs=4.0
Q ss_pred ccccccccc
Q psy16829 87 HVCDICLEA 95 (243)
Q Consensus 87 ~~C~~C~~~ 95 (243)
+.|..|++.
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 444444443
No 227
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=25.29 E-value=16 Score=24.43 Aligned_cols=10 Identities=20% Similarity=0.826 Sum_probs=4.6
Q ss_pred eecccccccc
Q psy16829 172 FQCEICHKIF 181 (243)
Q Consensus 172 ~~C~~C~~~f 181 (243)
|.|..||+.|
T Consensus 101 y~C~~Cg~~w 110 (113)
T COG1594 101 YKCTRCGYRW 110 (113)
T ss_pred EEecccCCEe
Confidence 4444444443
No 228
>PRK05580 primosome assembly protein PriA; Validated
Probab=25.22 E-value=50 Score=29.91 Aligned_cols=10 Identities=30% Similarity=0.577 Sum_probs=5.6
Q ss_pred eeccccchhc
Q psy16829 60 LTCVECNEDF 69 (243)
Q Consensus 60 ~~C~~C~~~~ 69 (243)
+.|..||...
T Consensus 382 ~~C~~Cg~~~ 391 (679)
T PRK05580 382 LLCRDCGWVA 391 (679)
T ss_pred eEhhhCcCcc
Confidence 4566666544
No 229
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.06 E-value=52 Score=26.09 Aligned_cols=11 Identities=27% Similarity=1.047 Sum_probs=5.7
Q ss_pred eeccccccccC
Q psy16829 172 FQCEICHKIFT 182 (243)
Q Consensus 172 ~~C~~C~~~f~ 182 (243)
|.|+.|.-.|-
T Consensus 256 yvCs~Clsi~C 266 (279)
T TIGR00627 256 FVCSVCLSVLC 266 (279)
T ss_pred EECCCccCCcC
Confidence 55555555443
No 230
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.90 E-value=19 Score=23.43 Aligned_cols=13 Identities=15% Similarity=0.227 Sum_probs=8.8
Q ss_pred CcccccccCccCC
Q psy16829 201 PWECEHCHKVYPN 213 (243)
Q Consensus 201 ~~~C~~C~~~f~~ 213 (243)
-..|+.|+..+..
T Consensus 42 h~~C~~CG~y~~~ 54 (99)
T PRK14892 42 IITCGNCGLYTEF 54 (99)
T ss_pred eEECCCCCCccCE
Confidence 4568888877653
No 231
>KOG3362|consensus
Probab=24.87 E-value=24 Score=24.54 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=17.0
Q ss_pred CcccccccCccCChHHHHHHHh
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
+|.|.-||-.+-+...|..|..
T Consensus 129 ~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred hhHHHhcCCceeechhhhhccc
Confidence 6788888888888877777743
No 232
>KOG2071|consensus
Probab=24.61 E-value=36 Score=29.73 Aligned_cols=24 Identities=21% Similarity=0.382 Sum_probs=11.4
Q ss_pred eeeccccchhccChhhHHhhhhcc
Q psy16829 59 LLTCVECNEDFINVNDFVSHLRGH 82 (243)
Q Consensus 59 ~~~C~~C~~~~~~~~~l~~H~~~h 82 (243)
+-.|..||..|.+......||..|
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cchhcccccccccchhhhhHhhhh
Confidence 344555555554444444444443
No 233
>KOG4317|consensus
Probab=24.58 E-value=18 Score=28.77 Aligned_cols=13 Identities=15% Similarity=0.782 Sum_probs=7.4
Q ss_pred eeccccccccCCh
Q psy16829 172 FQCEICHKIFTNK 184 (243)
Q Consensus 172 ~~C~~C~~~f~~~ 184 (243)
|.|+.|+..|-+.
T Consensus 20 YtCPRCn~~YCsl 32 (383)
T KOG4317|consen 20 YTCPRCNLLYCSL 32 (383)
T ss_pred ccCCCCCccceee
Confidence 6666666555443
No 234
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=24.46 E-value=86 Score=17.80 Aligned_cols=35 Identities=14% Similarity=0.250 Sum_probs=18.0
Q ss_pred CCcceeeccccchhccChhhHHhhhhccCCCccccccccc
Q psy16829 55 DKPLLLTCVECNEDFINVNDFVSHLRGHDSTSHVCDICLE 94 (243)
Q Consensus 55 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~ 94 (243)
.....+.|..|...-... . ...-....|.|+.|+.
T Consensus 18 ~~r~aLIC~~C~~hNGla----~-~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLA----P-KEEFEEIQYRCPYCGA 52 (54)
T ss_pred cCceeEECcccchhhccc----c-cccCCceEEEcCCCCC
Confidence 344567888886542221 1 1111114577887764
No 235
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.30 E-value=50 Score=27.75 Aligned_cols=14 Identities=14% Similarity=0.584 Sum_probs=7.3
Q ss_pred cccCCcccccccCh
Q psy16829 115 LYQCNECEFVGKRL 128 (243)
Q Consensus 115 ~~~C~~C~~~f~~~ 128 (243)
-|.|+-|+..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 45565555554433
No 236
>PTZ00448 hypothetical protein; Provisional
Probab=23.89 E-value=60 Score=26.69 Aligned_cols=22 Identities=18% Similarity=0.496 Sum_probs=18.8
Q ss_pred CcccccccCccCChHHHHHHHh
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQ 222 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~ 222 (243)
.|.|..|+..|.+....+.|.+
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~K 335 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYR 335 (373)
T ss_pred CccccccccccCCHHHHHHHhh
Confidence 5789999999988888888877
No 237
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=23.18 E-value=78 Score=15.91 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=2.9
Q ss_pred eccccccc
Q psy16829 173 QCEICHKI 180 (243)
Q Consensus 173 ~C~~C~~~ 180 (243)
.|+.|++.
T Consensus 6 ~C~nC~R~ 13 (33)
T PF08209_consen 6 ECPNCGRP 13 (33)
T ss_dssp E-TTTSSE
T ss_pred ECCCCcCC
Confidence 34444443
No 238
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=23.18 E-value=39 Score=23.20 Aligned_cols=15 Identities=27% Similarity=0.662 Sum_probs=11.4
Q ss_pred cccccccccccCChH
Q psy16829 86 SHVCDICLEAFPSSD 100 (243)
Q Consensus 86 ~~~C~~C~~~f~~~~ 100 (243)
|++|..|++.|.+.+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567888888887654
No 239
>KOG2071|consensus
Probab=22.98 E-value=50 Score=28.89 Aligned_cols=27 Identities=19% Similarity=0.502 Sum_probs=21.9
Q ss_pred CcccccccCccCChHHHHHHHhhcCCC
Q psy16829 201 PWECEHCHKVYPNKRSYKRHKQVHLGV 227 (243)
Q Consensus 201 ~~~C~~C~~~f~~~~~l~~H~~~H~~~ 227 (243)
|.+|..||.+|........|+-.|...
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred cchhcccccccccchhhhhHhhhhhhh
Confidence 788999999999988877777766544
No 240
>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 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=22.32 E-value=37 Score=20.48 Aligned_cols=55 Identities=16% Similarity=0.271 Sum_probs=22.0
Q ss_pred eeccccchhccChhh---HHhhhhccCC-CcccccccccccCChHHHHHHHHhhcCCCCcccCCcccc
Q psy16829 60 LTCVECNEDFINVND---FVSHLRGHDS-TSHVCDICLEAFPSSDDRDLHFLSHLTSDGLYQCNECEF 123 (243)
Q Consensus 60 ~~C~~C~~~~~~~~~---l~~H~~~h~~-~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~~C~~ 123 (243)
++++-|++.|.-..- +..|...... ....|..|+........ . .+ ..+.|+.|+.
T Consensus 11 ~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~------~--c~-~~~~C~~C~~ 69 (71)
T PF05495_consen 11 IRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEY------S--CG-ADYFCPICGL 69 (71)
T ss_dssp EEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SB------T--T---SEEETTTTE
T ss_pred EECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhh------h--cC-CCccCcCcCC
Confidence 455556555544421 2222221111 35567777665544322 0 11 3466766654
No 242
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.24 E-value=52 Score=18.04 Aligned_cols=9 Identities=33% Similarity=0.622 Sum_probs=4.3
Q ss_pred ccccccccc
Q psy16829 87 HVCDICLEA 95 (243)
Q Consensus 87 ~~C~~C~~~ 95 (243)
+.|+.|+..
T Consensus 21 ~vC~~Cg~~ 29 (52)
T smart00661 21 FVCRKCGYE 29 (52)
T ss_pred EECCcCCCe
Confidence 445555543
No 243
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=21.77 E-value=28 Score=19.80 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=5.2
Q ss_pred CcccccccC
Q psy16829 201 PWECEHCHK 209 (243)
Q Consensus 201 ~~~C~~C~~ 209 (243)
|.-|+.|.+
T Consensus 28 PlyCpKCK~ 36 (55)
T PF14205_consen 28 PLYCPKCKQ 36 (55)
T ss_pred cccCCCCCc
Confidence 555666654
No 244
>KOG4377|consensus
Probab=21.62 E-value=42 Score=27.90 Aligned_cols=22 Identities=18% Similarity=0.230 Sum_probs=17.3
Q ss_pred cccCccCChHHHHHHHhhcCCC
Q psy16829 206 HCHKVYPNKRSYKRHKQVHLGV 227 (243)
Q Consensus 206 ~C~~~f~~~~~l~~H~~~H~~~ 227 (243)
-|+.++.+.+.+..|.|.|.+.
T Consensus 408 Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 408 GCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred CCceEEEehhhhhhhhhhhhhh
Confidence 3888888888888888877654
No 245
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=21.48 E-value=29 Score=24.29 Aligned_cols=11 Identities=36% Similarity=1.195 Sum_probs=5.3
Q ss_pred CcccccccCcc
Q psy16829 201 PWECEHCHKVY 211 (243)
Q Consensus 201 ~~~C~~C~~~f 211 (243)
.|.|..|+..+
T Consensus 112 ~y~C~~C~~~~ 122 (146)
T smart00731 112 PYRCTGCGQRY 122 (146)
T ss_pred EEECCCCCCCC
Confidence 45555555443
No 246
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=20.96 E-value=44 Score=17.05 Aligned_cols=30 Identities=13% Similarity=0.460 Sum_probs=11.4
Q ss_pred ccccchhccChhhHHhhhhccCCCccccccccccc
Q psy16829 62 CVECNEDFINVNDFVSHLRGHDSTSHVCDICLEAF 96 (243)
Q Consensus 62 C~~C~~~~~~~~~l~~H~~~h~~~~~~C~~C~~~f 96 (243)
|+.|.+.+.+..+- ..+.....|..||-.+
T Consensus 2 C~~C~~Ey~~p~~R-----R~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEYFDPSNR-----RFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHHCSTTST-----TTT-TT--BTTCC-SC
T ss_pred CHHHHHHHcCCCCC-----cccCcCccCCCCCCCE
Confidence 45555555444321 1122344566666443
No 247
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.95 E-value=1.1e+02 Score=27.53 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=5.1
Q ss_pred ccccccccccC
Q psy16829 145 YCDVCGRGFHQ 155 (243)
Q Consensus 145 ~C~~C~~~f~~ 155 (243)
-|+.||.....
T Consensus 43 fC~~CG~~~~~ 53 (645)
T PRK14559 43 HCPNCGAETGT 53 (645)
T ss_pred cccccCCcccc
Confidence 35555544433
No 248
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=20.82 E-value=36 Score=19.48 Aligned_cols=8 Identities=50% Similarity=0.962 Sum_probs=1.6
Q ss_pred cccccccc
Q psy16829 87 HVCDICLE 94 (243)
Q Consensus 87 ~~C~~C~~ 94 (243)
|.|++|+.
T Consensus 34 y~Cp~CgA 41 (55)
T PF05741_consen 34 YVCPICGA 41 (55)
T ss_dssp ---TTT--
T ss_pred CcCCCCcC
Confidence 45555543
No 249
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.23 E-value=65 Score=18.21 Aligned_cols=8 Identities=25% Similarity=0.887 Sum_probs=3.5
Q ss_pred cccCCccc
Q psy16829 115 LYQCNECE 122 (243)
Q Consensus 115 ~~~C~~C~ 122 (243)
...|+.|+
T Consensus 46 i~~Cp~Cg 53 (56)
T PF02591_consen 46 IVFCPNCG 53 (56)
T ss_pred eEECcCCC
Confidence 34444444
Done!