Query psy6674
Match_columns 258
No_of_seqs 245 out of 1725
Neff 6.5
Searched_HMMs 46136
Date Sat Aug 17 00:12:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6674.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6674hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.5 3.4E-14 7.3E-19 127.1 6.6 49 210-258 187-235 (279)
2 KOG2462|consensus 99.4 4.1E-14 9E-19 126.5 2.2 71 188-258 190-263 (279)
3 KOG3623|consensus 99.3 4.9E-13 1.1E-17 131.9 0.6 75 184-258 893-970 (1007)
4 KOG3623|consensus 99.1 3.2E-11 6.9E-16 119.3 1.7 51 208-258 279-329 (1007)
5 PHA02768 hypothetical protein; 99.0 2.2E-10 4.8E-15 79.5 1.8 44 210-255 5-48 (55)
6 KOG3576|consensus 99.0 1.1E-10 2.4E-15 100.8 0.3 73 185-257 117-192 (267)
7 KOG1074|consensus 98.8 9.6E-10 2.1E-14 110.4 1.1 49 209-257 352-400 (958)
8 KOG1074|consensus 98.8 1.3E-09 2.7E-14 109.5 1.5 50 209-258 604-653 (958)
9 PF13465 zf-H2C2_2: Zinc-finge 98.6 1E-08 2.2E-13 60.8 1.2 26 225-250 1-26 (26)
10 PHA00733 hypothetical protein 98.5 5.3E-08 1.1E-12 79.2 3.2 51 206-258 69-119 (128)
11 KOG3576|consensus 98.3 1.1E-06 2.3E-11 76.4 5.4 52 207-258 114-165 (267)
12 PHA00616 hypothetical protein 98.2 3.3E-07 7.2E-12 60.9 0.4 39 210-248 1-39 (44)
13 PHA00732 hypothetical protein 98.1 1.8E-06 3.9E-11 64.6 2.5 42 210-257 1-43 (79)
14 COG5189 SFP1 Putative transcri 97.9 3.6E-06 7.8E-11 77.3 1.8 51 208-258 347-418 (423)
15 KOG3993|consensus 97.8 4.7E-06 1E-10 78.9 0.7 48 211-258 296-376 (500)
16 PF00096 zf-C2H2: Zinc finger, 97.4 4.6E-05 9.9E-10 43.2 0.7 23 211-233 1-23 (23)
17 KOG3608|consensus 97.3 9.8E-05 2.1E-09 68.9 2.2 48 210-257 263-311 (467)
18 PHA00733 hypothetical protein 97.3 6.4E-05 1.4E-09 61.2 0.7 51 208-258 38-93 (128)
19 PLN03086 PRLI-interacting fact 97.2 0.00014 3.1E-09 72.1 2.1 39 209-249 477-515 (567)
20 PLN03086 PRLI-interacting fact 97.2 0.00017 3.7E-09 71.6 1.9 56 200-257 494-559 (567)
21 PF05605 zf-Di19: Drought indu 97.1 0.00026 5.7E-09 48.8 2.0 46 210-258 2-49 (54)
22 PRK04860 hypothetical protein; 97.1 0.00022 4.7E-09 60.3 1.7 40 209-252 118-157 (160)
23 KOG3608|consensus 97.0 0.00022 4.8E-09 66.6 1.2 49 209-257 176-226 (467)
24 PF13894 zf-C2H2_4: C2H2-type 96.8 0.00049 1.1E-08 38.5 1.1 23 211-233 1-23 (24)
25 PF13912 zf-C2H2_6: C2H2-type 96.6 0.00089 1.9E-08 39.2 1.2 26 210-235 1-26 (27)
26 PF09237 GAGA: GAGA factor; I 96.5 0.0022 4.8E-08 43.9 2.5 35 204-238 18-52 (54)
27 PF00096 zf-C2H2: Zinc finger, 96.5 0.00058 1.3E-08 38.5 -0.4 20 239-258 1-20 (23)
28 PF12756 zf-C2H2_2: C2H2 type 96.4 0.00096 2.1E-08 50.1 0.2 47 212-258 1-70 (100)
29 smart00355 ZnF_C2H2 zinc finge 96.3 0.0023 5E-08 36.0 1.6 24 211-234 1-24 (26)
30 PF13465 zf-H2C2_2: Zinc-finge 96.1 0.00087 1.9E-08 39.4 -0.9 22 201-222 5-26 (26)
31 PHA02768 hypothetical protein; 96.0 0.0021 4.5E-08 44.8 0.3 21 238-258 5-25 (55)
32 PF13894 zf-C2H2_4: C2H2-type 95.5 0.0034 7.4E-08 34.9 -0.1 20 239-258 1-20 (24)
33 PHA00616 hypothetical protein 95.5 0.0027 6E-08 42.2 -0.7 21 238-258 1-21 (44)
34 PF13912 zf-C2H2_6: C2H2-type 95.3 0.0042 9.1E-08 36.3 -0.3 21 238-258 1-21 (27)
35 COG5048 FOG: Zn-finger [Genera 95.0 0.013 2.9E-07 53.8 2.0 50 209-258 288-343 (467)
36 PF12874 zf-met: Zinc-finger o 94.5 0.014 3.1E-07 33.3 0.7 23 211-233 1-23 (25)
37 COG5189 SFP1 Putative transcri 94.2 0.051 1.1E-06 50.5 3.9 25 207-231 395-419 (423)
38 smart00355 ZnF_C2H2 zinc finge 94.0 0.019 4.2E-07 32.1 0.5 20 239-258 1-20 (26)
39 PF12171 zf-C2H2_jaz: Zinc-fin 94.0 0.025 5.5E-07 33.2 1.0 22 211-232 2-23 (27)
40 KOG3993|consensus 94.0 0.011 2.4E-07 56.6 -1.0 48 211-258 268-315 (500)
41 PF09237 GAGA: GAGA factor; I 92.5 0.038 8.2E-07 37.9 0.1 26 233-258 19-44 (54)
42 PF12171 zf-C2H2_jaz: Zinc-fin 92.4 0.084 1.8E-06 30.9 1.5 20 239-258 2-21 (27)
43 PF13909 zf-H2C2_5: C2H2-type 91.5 0.071 1.5E-06 30.2 0.5 23 211-234 1-23 (24)
44 cd00350 rubredoxin_like Rubred 90.5 0.17 3.7E-06 31.3 1.5 24 211-246 2-25 (33)
45 PF12874 zf-met: Zinc-finger o 89.9 0.074 1.6E-06 30.2 -0.4 20 239-258 1-20 (25)
46 PHA00732 hypothetical protein 88.4 0.18 4E-06 37.6 0.6 23 210-235 27-49 (79)
47 smart00451 ZnF_U1 U1-like zinc 88.2 0.29 6.2E-06 29.9 1.4 24 209-232 2-25 (35)
48 PF13913 zf-C2HC_2: zinc-finge 87.7 0.32 6.8E-06 28.3 1.2 20 211-231 3-22 (25)
49 PF09538 FYDLN_acid: Protein o 86.4 0.48 1E-05 37.5 2.0 30 211-251 10-39 (108)
50 KOG4124|consensus 86.0 0.28 6E-06 46.2 0.5 52 207-258 346-418 (442)
51 COG1592 Rubrerythrin [Energy p 85.6 0.49 1.1E-05 40.3 1.7 24 210-246 134-157 (166)
52 KOG1146|consensus 85.4 0.31 6.8E-06 52.7 0.6 51 208-258 463-538 (1406)
53 COG5048 FOG: Zn-finger [Genera 85.4 1 2.2E-05 41.3 4.0 65 184-248 291-363 (467)
54 PF12756 zf-C2H2_2: C2H2 type 85.2 0.58 1.3E-05 34.7 1.9 24 210-233 50-73 (100)
55 smart00451 ZnF_U1 U1-like zinc 84.8 0.4 8.6E-06 29.3 0.7 21 238-258 3-23 (35)
56 smart00531 TFIIE Transcription 83.7 0.58 1.2E-05 38.7 1.4 39 207-249 96-134 (147)
57 cd00729 rubredoxin_SM Rubredox 82.9 0.77 1.7E-05 28.7 1.4 25 210-246 2-26 (34)
58 TIGR02300 FYDLN_acid conserved 82.0 1.1 2.5E-05 36.3 2.4 30 211-251 10-39 (129)
59 COG4049 Uncharacterized protei 79.1 0.54 1.2E-05 32.9 -0.3 27 207-233 14-40 (65)
60 TIGR02098 MJ0042_CXXC MJ0042 f 78.8 1.3 2.8E-05 27.8 1.4 34 211-249 3-36 (38)
61 KOG2071|consensus 78.8 1.5 3.3E-05 43.9 2.6 27 207-233 415-441 (579)
62 smart00834 CxxC_CXXC_SSSS Puta 77.5 1.1 2.4E-05 28.3 0.8 32 210-248 5-36 (41)
63 PRK06266 transcription initiat 77.4 1.1 2.4E-05 38.3 1.1 34 208-250 115-148 (178)
64 TIGR00373 conserved hypothetic 77.1 1 2.3E-05 37.7 0.8 34 207-249 106-139 (158)
65 PRK09678 DNA-binding transcrip 76.4 1 2.3E-05 33.0 0.5 15 236-250 25-41 (72)
66 PRK00398 rpoP DNA-directed RNA 76.1 1.1 2.4E-05 29.6 0.5 31 210-250 3-33 (46)
67 PF14353 CpXC: CpXC protein 75.6 0.45 9.8E-06 38.1 -1.7 12 239-250 39-50 (128)
68 TIGR02605 CxxC_CxxC_SSSS putat 74.7 1.4 3E-05 29.6 0.8 29 211-246 6-34 (52)
69 PF05443 ROS_MUCR: ROS/MUCR tr 74.1 1.5 3.1E-05 36.0 0.9 27 209-238 71-97 (132)
70 PF13719 zinc_ribbon_5: zinc-r 74.0 2.4 5.3E-05 26.8 1.7 34 211-249 3-36 (37)
71 KOG4167|consensus 73.3 3.1 6.7E-05 42.9 3.1 27 208-234 790-816 (907)
72 smart00659 RPOLCX RNA polymera 72.5 2.6 5.7E-05 27.9 1.7 26 211-247 3-28 (44)
73 COG3364 Zn-ribbon containing p 72.4 2 4.3E-05 33.7 1.2 31 210-250 2-33 (112)
74 PF13717 zinc_ribbon_4: zinc-r 71.5 3.3 7.2E-05 26.1 1.9 34 211-249 3-36 (36)
75 PF05605 zf-Di19: Drought indu 71.4 2.9 6.3E-05 28.4 1.8 26 207-234 28-53 (54)
76 PF09723 Zn-ribbon_8: Zinc rib 69.6 2.2 4.8E-05 27.7 0.8 29 211-246 6-34 (42)
77 COG1997 RPL43A Ribosomal prote 69.4 2.5 5.4E-05 32.2 1.2 32 209-250 34-65 (89)
78 PF05191 ADK_lid: Adenylate ki 68.2 2.4 5.2E-05 26.9 0.7 33 211-251 2-34 (36)
79 PF02892 zf-BED: BED zinc fing 65.3 3.8 8.2E-05 26.5 1.3 24 208-231 14-41 (45)
80 COG2888 Predicted Zn-ribbon RN 65.0 3.8 8.2E-05 29.0 1.3 33 209-246 26-58 (61)
81 COG4530 Uncharacterized protei 64.7 3.4 7.5E-05 32.8 1.1 27 212-249 11-37 (129)
82 smart00614 ZnF_BED BED zinc fi 62.8 4.8 0.0001 26.9 1.4 25 210-234 18-48 (50)
83 COG1996 RPC10 DNA-directed RNA 62.4 4.1 8.8E-05 27.7 1.0 29 209-247 5-33 (49)
84 PRK03824 hypA hydrogenase nick 60.4 4.4 9.6E-05 33.1 1.1 39 209-247 69-116 (135)
85 COG1198 PriA Primosomal protei 58.6 5.6 0.00012 41.3 1.7 24 224-247 461-484 (730)
86 KOG2593|consensus 58.3 5.6 0.00012 38.6 1.6 39 206-247 124-162 (436)
87 COG4049 Uncharacterized protei 57.7 3.3 7.1E-05 29.1 -0.1 27 231-257 10-36 (65)
88 COG4957 Predicted transcriptio 57.2 4.8 0.0001 33.2 0.8 25 211-238 77-101 (148)
89 PRK12496 hypothetical protein; 56.0 5.8 0.00013 33.5 1.2 31 209-251 126-156 (164)
90 COG1655 Uncharacterized protei 55.2 4.2 9.2E-05 36.4 0.2 38 208-245 17-69 (267)
91 KOG2785|consensus 54.3 6.8 0.00015 37.5 1.4 49 210-258 166-240 (390)
92 PF02176 zf-TRAF: TRAF-type zi 54.3 6.2 0.00013 26.9 0.9 47 209-257 8-60 (60)
93 PF15269 zf-C2H2_7: Zinc-finge 54.0 17 0.00036 24.5 2.8 24 209-232 19-42 (54)
94 PF03604 DNA_RNApol_7kD: DNA d 53.7 11 0.00025 23.2 1.9 26 211-247 1-26 (32)
95 PF01363 FYVE: FYVE zinc finge 52.8 7 0.00015 27.6 1.0 27 211-249 10-36 (69)
96 PRK14890 putative Zn-ribbon RN 52.3 11 0.00023 26.7 1.8 33 209-246 24-56 (59)
97 PF10263 SprT-like: SprT-like 52.0 5.2 0.00011 32.7 0.2 34 209-250 122-155 (157)
98 KOG0978|consensus 50.3 7.6 0.00017 40.0 1.1 23 235-257 675-697 (698)
99 COG3357 Predicted transcriptio 50.2 9.2 0.0002 29.4 1.3 28 209-246 57-84 (97)
100 PF09538 FYDLN_acid: Protein o 48.9 13 0.00029 29.3 2.1 31 186-224 10-40 (108)
101 COG1571 Predicted DNA-binding 48.7 11 0.00024 36.6 1.9 28 212-250 352-379 (421)
102 TIGR01206 lysW lysine biosynth 48.6 7.9 0.00017 26.8 0.7 31 211-249 3-33 (54)
103 cd00730 rubredoxin Rubredoxin; 48.1 11 0.00024 25.6 1.3 35 211-246 2-42 (50)
104 PRK00464 nrdR transcriptional 46.9 12 0.00025 31.5 1.5 16 210-225 28-43 (154)
105 PRK04860 hypothetical protein; 46.7 4.3 9.4E-05 34.2 -1.1 38 186-224 120-157 (160)
106 PRK12380 hydrogenase nickel in 46.3 11 0.00023 29.8 1.2 26 209-246 69-94 (113)
107 PF10571 UPF0547: Uncharacteri 46.2 16 0.00035 21.4 1.6 10 240-249 16-25 (26)
108 KOG4124|consensus 45.8 42 0.00091 32.1 5.1 26 206-231 394-419 (442)
109 cd00065 FYVE FYVE domain; Zinc 45.6 15 0.00034 24.6 1.8 13 210-222 18-30 (57)
110 PHA00626 hypothetical protein 45.6 12 0.00026 26.2 1.2 15 209-223 22-36 (59)
111 PTZ00255 60S ribosomal protein 45.4 11 0.00023 29.0 1.0 32 209-250 35-66 (90)
112 TIGR00100 hypA hydrogenase nic 45.1 11 0.00024 29.8 1.1 27 209-247 69-95 (115)
113 COG4888 Uncharacterized Zn rib 43.8 12 0.00026 29.3 1.0 38 208-249 20-57 (104)
114 PF00301 Rubredoxin: Rubredoxi 43.6 17 0.00037 24.4 1.6 36 211-247 2-43 (47)
115 PF01927 Mut7-C: Mut7-C RNAse 43.4 14 0.00031 30.3 1.6 19 210-228 124-142 (147)
116 PF07282 OrfB_Zn_ribbon: Putat 43.3 16 0.00034 25.8 1.6 12 237-248 45-56 (69)
117 PF10013 DUF2256: Uncharacteri 43.2 14 0.0003 24.3 1.1 16 212-227 10-25 (42)
118 PF12760 Zn_Tnp_IS1595: Transp 43.0 13 0.00029 24.4 1.1 27 211-246 19-45 (46)
119 COG3091 SprT Zn-dependent meta 42.4 13 0.00029 31.2 1.2 37 207-248 114-150 (156)
120 KOG2482|consensus 42.1 14 0.00029 35.1 1.4 23 210-232 195-217 (423)
121 smart00064 FYVE Protein presen 42.0 18 0.00039 25.3 1.7 10 211-220 27-36 (68)
122 TIGR00280 L37a ribosomal prote 41.8 12 0.00025 28.8 0.7 32 209-250 34-65 (91)
123 PRK00564 hypA hydrogenase nick 41.8 14 0.0003 29.4 1.2 28 209-247 70-97 (117)
124 smart00734 ZnF_Rad18 Rad18-lik 40.7 15 0.00031 21.5 0.9 9 240-248 3-11 (26)
125 cd00924 Cyt_c_Oxidase_Vb Cytoc 40.5 11 0.00023 29.3 0.4 21 228-249 70-90 (97)
126 PRK05978 hypothetical protein; 40.3 16 0.00035 30.5 1.4 32 211-251 34-65 (148)
127 PLN02294 cytochrome c oxidase 40.3 11 0.00024 32.2 0.4 13 209-221 140-152 (174)
128 PRK03681 hypA hydrogenase nick 40.0 14 0.0003 29.3 0.9 28 209-247 69-96 (114)
129 PF01927 Mut7-C: Mut7-C RNAse 38.9 22 0.00048 29.2 2.0 20 237-256 123-142 (147)
130 PF14379 Myb_CC_LHEQLE: MYB-CC 37.3 77 0.0017 21.7 4.1 29 34-63 13-42 (51)
131 smart00440 ZnF_C2C2 C2C2 Zinc 36.8 12 0.00027 24.0 0.2 12 238-249 28-39 (40)
132 PF13240 zinc_ribbon_2: zinc-r 36.7 21 0.00045 20.2 1.1 6 241-246 16-21 (23)
133 PF04959 ARS2: Arsenite-resist 35.9 13 0.00028 32.9 0.2 22 236-257 75-96 (214)
134 PF01780 Ribosomal_L37ae: Ribo 35.6 12 0.00025 28.7 -0.1 31 209-249 34-64 (90)
135 PF14446 Prok-RING_1: Prokaryo 35.5 18 0.00039 25.1 0.8 11 212-222 7-17 (54)
136 TIGR02300 FYDLN_acid conserved 35.3 31 0.00067 28.2 2.2 34 186-227 10-43 (129)
137 PRK03976 rpl37ae 50S ribosomal 35.0 16 0.00035 28.0 0.6 32 209-250 35-66 (90)
138 PF12013 DUF3505: Protein of u 34.9 21 0.00046 27.6 1.2 25 211-235 81-109 (109)
139 PF14311 DUF4379: Domain of un 34.0 27 0.00059 23.6 1.5 28 210-244 28-55 (55)
140 PF04959 ARS2: Arsenite-resist 32.9 9.6 0.00021 33.7 -1.1 24 209-232 76-99 (214)
141 PF01155 HypA: Hydrogenase exp 32.6 20 0.00043 28.3 0.7 27 209-247 69-95 (113)
142 PF01096 TFIIS_C: Transcriptio 32.5 7.1 0.00015 25.0 -1.5 10 239-248 29-38 (39)
143 TIGR00244 transcriptional regu 32.4 29 0.00062 29.0 1.7 19 208-226 26-44 (147)
144 COG3677 Transposase and inacti 31.5 33 0.00071 27.8 1.9 16 208-223 51-66 (129)
145 PF11494 Ta0938: Ta0938; Inte 31.5 31 0.00068 26.8 1.6 38 207-250 11-49 (105)
146 PRK05452 anaerobic nitric oxid 31.0 39 0.00084 33.3 2.6 41 206-247 421-467 (479)
147 KOG3408|consensus 30.8 20 0.00043 29.0 0.5 26 207-232 54-79 (129)
148 smart00731 SprT SprT homologue 30.8 27 0.00059 28.5 1.3 34 209-249 111-144 (146)
149 KOG4173|consensus 30.7 8.8 0.00019 33.9 -1.7 48 211-258 107-166 (253)
150 PTZ00303 phosphatidylinositol 30.7 32 0.0007 36.2 2.0 11 212-222 462-472 (1374)
151 PF10083 DUF2321: Uncharacteri 30.5 24 0.00052 29.7 0.9 16 236-251 66-81 (158)
152 COG1327 Predicted transcriptio 30.3 32 0.0007 28.9 1.6 18 208-225 26-43 (156)
153 COG1656 Uncharacterized conser 29.6 42 0.0009 28.6 2.2 22 210-231 130-151 (165)
154 COG1675 TFA1 Transcription ini 29.4 28 0.0006 29.9 1.1 33 207-248 110-142 (176)
155 COG2331 Uncharacterized protei 29.4 11 0.00023 28.1 -1.2 35 209-250 11-45 (82)
156 PF01286 XPA_N: XPA protein N- 29.3 26 0.00057 22.0 0.7 14 212-225 5-18 (34)
157 PF13824 zf-Mss51: Zinc-finger 29.3 40 0.00088 23.5 1.7 10 209-218 13-22 (55)
158 PRK14559 putative protein seri 29.3 47 0.001 34.2 2.9 10 240-249 43-52 (645)
159 PRK04351 hypothetical protein; 29.1 26 0.00056 29.2 0.9 35 209-251 111-145 (149)
160 PF13453 zf-TFIIB: Transcripti 29.0 27 0.00058 22.3 0.8 21 235-255 16-36 (41)
161 COG4306 Uncharacterized protei 28.9 32 0.0007 28.1 1.4 16 236-251 66-81 (160)
162 PRK00762 hypA hydrogenase nick 28.1 29 0.00063 27.8 1.0 32 209-246 69-100 (124)
163 KOG1146|consensus 28.0 22 0.00047 39.2 0.3 46 213-258 439-485 (1406)
164 PF10276 zf-CHCC: Zinc-finger 27.9 21 0.00046 23.1 0.2 10 211-220 30-39 (40)
165 KOG2231|consensus 27.7 26 0.00056 36.1 0.8 45 211-258 100-169 (669)
166 smart00661 RPOL9 RNA polymeras 27.3 39 0.00085 22.2 1.4 12 210-221 20-31 (52)
167 PRK05580 primosome assembly pr 27.3 39 0.00084 34.8 2.0 24 224-247 407-430 (679)
168 PF07975 C1_4: TFIIH C1-like d 27.0 27 0.00058 23.9 0.5 31 208-244 19-49 (51)
169 PRK03564 formate dehydrogenase 26.7 54 0.0012 30.7 2.6 18 23-40 25-42 (309)
170 COG4391 Uncharacterized protei 26.6 50 0.0011 23.5 1.9 41 206-250 20-60 (62)
171 PRK14873 primosome assembly pr 26.4 35 0.00076 35.2 1.5 11 237-247 421-431 (665)
172 PF08274 PhnA_Zn_Ribbon: PhnA 26.2 29 0.00063 21.1 0.5 25 212-247 4-28 (30)
173 PF08271 TF_Zn_Ribbon: TFIIB z 26.2 33 0.00072 22.0 0.8 10 237-246 18-27 (43)
174 COG1439 Predicted nucleic acid 26.1 32 0.0007 29.6 1.0 25 209-247 138-162 (177)
175 PF11672 DUF3268: Protein of u 25.9 45 0.00097 26.1 1.7 9 210-218 2-10 (102)
176 COG0675 Transposase and inacti 25.7 36 0.00078 30.5 1.3 15 209-223 321-335 (364)
177 PHA02998 RNA polymerase subuni 25.4 30 0.00066 29.9 0.7 39 210-250 143-183 (195)
178 PF13878 zf-C2H2_3: zinc-finge 25.3 45 0.00098 21.5 1.4 24 211-234 14-39 (41)
179 KOG4173|consensus 25.3 20 0.00044 31.7 -0.4 46 209-257 78-125 (253)
180 PF05129 Elf1: Transcription e 25.1 16 0.00035 27.2 -0.9 40 208-251 20-59 (81)
181 PRK00432 30S ribosomal protein 25.1 44 0.00095 22.6 1.3 27 212-249 22-48 (50)
182 PF04810 zf-Sec23_Sec24: Sec23 25.0 35 0.00077 21.7 0.8 31 211-247 3-33 (40)
183 PF07295 DUF1451: Protein of u 24.1 38 0.00083 28.1 1.0 33 208-250 110-143 (146)
184 COG5236 Uncharacterized conser 23.9 35 0.00076 32.6 0.8 31 212-246 222-252 (493)
185 COG1779 C4-type Zn-finger prot 23.9 27 0.00059 30.6 0.1 37 211-249 15-54 (201)
186 TIGR00622 ssl1 transcription f 23.7 1.4E+02 0.003 23.8 4.1 32 208-245 79-110 (112)
187 PF09845 DUF2072: Zn-ribbon co 23.6 41 0.00088 27.6 1.1 15 210-224 1-15 (131)
188 TIGR00595 priA primosomal prot 23.5 46 0.001 33.0 1.7 21 226-246 241-261 (505)
189 PF08684 ocr: DNA mimic ocr; 23.0 94 0.002 23.9 2.9 29 17-45 62-90 (101)
190 PF05502 Dynactin_p62: Dynacti 22.9 56 0.0012 32.4 2.1 66 184-249 25-97 (483)
191 TIGR00627 tfb4 transcription f 22.7 59 0.0013 29.9 2.1 26 209-248 254-279 (279)
192 PF03811 Zn_Tnp_IS1: InsA N-te 22.7 45 0.00097 21.0 0.9 29 212-244 7-35 (36)
193 PRK14873 primosome assembly pr 22.6 40 0.00087 34.7 1.1 35 212-247 385-419 (665)
194 PF06220 zf-U1: U1 zinc finger 22.5 53 0.0011 20.9 1.2 23 209-231 2-26 (38)
195 PF11789 zf-Nse: Zinc-finger o 22.5 39 0.00084 23.4 0.6 31 209-243 23-53 (57)
196 smart00154 ZnF_AN1 AN1-like Zi 22.0 45 0.00097 21.3 0.8 15 238-252 12-26 (39)
197 COG3464 Transposase and inacti 21.8 45 0.00098 32.1 1.2 14 236-249 75-88 (402)
198 PF04216 FdhE: Protein involve 21.8 17 0.00037 33.2 -1.7 19 23-41 8-26 (290)
199 KOG1280|consensus 21.8 62 0.0013 30.8 2.0 37 209-245 78-116 (381)
200 KOG4602|consensus 21.6 2.1E+02 0.0045 26.3 5.2 15 209-223 267-281 (318)
201 PRK14714 DNA polymerase II lar 21.4 1.2E+02 0.0027 33.6 4.3 8 239-246 710-717 (1337)
202 PF07754 DUF1610: Domain of un 21.3 45 0.00097 19.3 0.6 8 210-217 16-23 (24)
203 PF11931 DUF3449: Domain of un 21.2 32 0.00069 30.1 0.0 21 209-229 100-121 (196)
204 PF08790 zf-LYAR: LYAR-type C2 20.6 43 0.00094 20.1 0.5 20 211-231 1-20 (28)
205 TIGR01385 TFSII transcription 20.3 43 0.00093 31.1 0.7 38 210-249 258-297 (299)
206 COG0068 HypF Hydrogenase matur 20.0 31 0.00067 35.8 -0.4 44 213-257 126-170 (750)
207 PF01428 zf-AN1: AN1-like Zinc 20.0 34 0.00074 22.1 -0.1 16 237-252 12-27 (43)
No 1
>KOG2462|consensus
Probab=99.49 E-value=3.4e-14 Score=127.08 Aligned_cols=49 Identities=41% Similarity=0.821 Sum_probs=30.6
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
+++|.+|||.|.+.+-|+.|+|+|||||||.|+.|+|+|..+++|+.||
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH
Confidence 5566666666666666666666666666666666666666666666554
No 2
>KOG2462|consensus
Probab=99.43 E-value=4.1e-14 Score=126.51 Aligned_cols=71 Identities=27% Similarity=0.445 Sum_probs=63.8
Q ss_pred cCCCCCCCC---CCCCCccCCCCCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 188 TDSISKPVQ---KSTPVASTARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 188 ~~~~~k~~~---~~~~~~~~~~~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
|..|+|.|. -...|.+.|.|+|||.|..|+|+|..+++|+.||++|.+.|+|.|..|+|.|.+++.|.+|.
T Consensus 190 C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 190 CGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred cccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhh
Confidence 444555554 45889999999999999999999999999999999999999999999999999999999983
No 3
>KOG3623|consensus
Probab=99.29 E-value=4.9e-13 Score=131.86 Aligned_cols=75 Identities=25% Similarity=0.547 Sum_probs=65.2
Q ss_pred cccccCCCCCCCCCCCCC---ccCCCCCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 184 KTIVTDSISKPVQKSTPV---ASTARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 184 ~~~~~~~~~k~~~~~~~~---~~~~~~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
-.+.|+.|.|.|.+.... +-.|.|++||+|.+|.|+|+++.+|..|+|.|.|+|||+|+-|+|+|+..+.+..||
T Consensus 893 gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred ccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 345677777777666544 445789999999999999999999999999999999999999999999999999887
No 4
>KOG3623|consensus
Probab=99.08 E-value=3.2e-11 Score=119.30 Aligned_cols=51 Identities=29% Similarity=0.654 Sum_probs=48.6
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
-+.|+|..|||+|+.+.+|+.|+|+|.|+|||.|+-|+|+|+..+.+..||
T Consensus 279 lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 279 LRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred hccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccc
Confidence 467999999999999999999999999999999999999999999998886
No 5
>PHA02768 hypothetical protein; Provisional
Probab=98.97 E-value=2.2e-10 Score=79.52 Aligned_cols=44 Identities=18% Similarity=0.431 Sum_probs=41.1
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhh
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLR 255 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~ 255 (258)
.|.|+.||+.|....+|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4899999999999999999999998 8999999999999988764
No 6
>KOG3576|consensus
Probab=98.97 E-value=1.1e-10 Score=100.81 Aligned_cols=73 Identities=30% Similarity=0.625 Sum_probs=60.2
Q ss_pred ccccCCCCCCCCCC---CCCccCCCCCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhc
Q psy6674 185 TIVTDSISKPVQKS---TPVASTARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 185 ~~~~~~~~k~~~~~---~~~~~~~~~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
.+.|..|.+.|.-. ..+..-|..-|+|-|..|||.|.....|++|+|+|+|.|||+|..|+|+|.++..|..|
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 34566666665433 34444456678899999999999999999999999999999999999999999988776
No 7
>KOG1074|consensus
Probab=98.82 E-value=9.6e-10 Score=110.37 Aligned_cols=49 Identities=41% Similarity=0.889 Sum_probs=47.0
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
.+++|.+|+|.|...+.|+.|.|.|||+|||+|.+||.+|.++++|+.|
T Consensus 352 ~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH 400 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVH 400 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeee
Confidence 4578999999999999999999999999999999999999999999988
No 8
>KOG1074|consensus
Probab=98.81 E-value=1.3e-09 Score=109.54 Aligned_cols=50 Identities=36% Similarity=0.758 Sum_probs=48.2
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
.|.+|.+|-++...++.|+.|-|+|+|||||+|.+||++|.++++|+.||
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~ 653 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM 653 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc
Confidence 46799999999999999999999999999999999999999999999997
No 9
>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=98.64 E-value=1e-08 Score=60.79 Aligned_cols=26 Identities=54% Similarity=0.997 Sum_probs=24.1
Q ss_pred hhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 225 NLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 225 ~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
+|.+|+++|+|+|||.|+.|+++|.+
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 48899999999999999999999974
No 10
>PHA00733 hypothetical protein
Probab=98.54 E-value=5.3e-08 Score=79.21 Aligned_cols=51 Identities=33% Similarity=0.638 Sum_probs=46.6
Q ss_pred CCCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 206 RPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 206 ~~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
.+.++|.|+.||+.|.....|..|++.| .++|.|..|++.|.+...|.+|+
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHH
Confidence 3578999999999999999999999987 46899999999999999999884
No 11
>KOG3576|consensus
Probab=98.29 E-value=1.1e-06 Score=76.41 Aligned_cols=52 Identities=29% Similarity=0.600 Sum_probs=48.6
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
....|.|.+|+|.|....-|.+|++.|...|.|.|.+|||+|...-.|++|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~ 165 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHT 165 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhh
Confidence 3567999999999999999999999999999999999999999999999985
No 12
>PHA00616 hypothetical protein
Probab=98.21 E-value=3.3e-07 Score=60.85 Aligned_cols=39 Identities=15% Similarity=0.275 Sum_probs=34.7
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcc
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 248 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F 248 (258)
||+|..||+.|..++.|..|++.|+|+++|.|+.--..|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEEEEEE
Confidence 689999999999999999999999999999998644434
No 13
>PHA00732 hypothetical protein
Probab=98.10 E-value=1.8e-06 Score=64.59 Aligned_cols=42 Identities=40% Similarity=0.785 Sum_probs=35.9
Q ss_pred CcccCCCCcccCCchhhhhhhhh-cCCCCcccCCCCCCcccCchhhhhc
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERT-HTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~-HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
||.|..||+.|.....|+.|++. |. ++.|+.||+.|.+ +..|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H 43 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQH 43 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhh
Confidence 58999999999999999999984 65 4689999999984 5555
No 14
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.94 E-value=3.6e-06 Score=77.29 Aligned_cols=51 Identities=29% Similarity=0.802 Sum_probs=44.7
Q ss_pred CCCcccCC--CCcccCCchhhhhhhhh-c------------------CCCCcccCCCCCCcccCchhhhhcC
Q psy6674 208 KKQFICRF--CSRHFTKSYNLLIHERT-H------------------TDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 208 ~kp~~C~~--Cgk~F~~~~~L~~H~r~-H------------------tgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
.|||+|++ |.|.|+....|+.|+.. | ...|||+|++|+|+|+....|+.|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 59999998 99999999999999873 3 1239999999999999999999986
No 15
>KOG3993|consensus
Probab=97.83 E-value=4.7e-06 Score=78.94 Aligned_cols=48 Identities=40% Similarity=0.753 Sum_probs=42.6
Q ss_pred cccCCCCcccCCchhhhhhhhhcC--------CCC-------------------------cccCCCCCCcccCchhhhhc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHT--------DER-------------------------PYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~Ht--------geK-------------------------pf~C~~Cgk~F~~~~~L~~H 257 (258)
|.|+.|+|+|+...+|..|+|+|. |.. .|.|.+|+|.|++...|+.|
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKH 375 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKH 375 (500)
T ss_pred ecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHh
Confidence 999999999999999999999993 222 38899999999999999998
Q ss_pred C
Q psy6674 258 R 258 (258)
Q Consensus 258 ~ 258 (258)
+
T Consensus 376 q 376 (500)
T KOG3993|consen 376 Q 376 (500)
T ss_pred H
Confidence 4
No 16
>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=97.43 E-value=4.6e-05 Score=43.15 Aligned_cols=23 Identities=35% Similarity=0.777 Sum_probs=20.1
Q ss_pred cccCCCCcccCCchhhhhhhhhc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTH 233 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~H 233 (258)
|.|+.|++.|..+..|..|++.|
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 68999999999999999998865
No 17
>KOG3608|consensus
Probab=97.35 E-value=9.8e-05 Score=68.91 Aligned_cols=48 Identities=27% Similarity=0.709 Sum_probs=41.5
Q ss_pred CcccCCCCcccCCchhhhhhhh-hcCCCCcccCCCCCCcccCchhhhhc
Q psy6674 210 QFICRFCSRHFTKSYNLLIHER-THTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r-~HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
.|+|+.|..+...++.|..|+| .|...|||+|+.|++.|.+...|.+|
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 3788888888888888888888 57888999999999999999988887
No 18
>PHA00733 hypothetical protein
Probab=97.33 E-value=6.4e-05 Score=61.16 Aligned_cols=51 Identities=22% Similarity=0.295 Sum_probs=41.8
Q ss_pred CCCcccCCCCcccCCchhhhhh--hh---hcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIH--ER---THTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H--~r---~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
.+++.|.+|.+.|.....|..| ++ .+.+.+||.|+.||+.|.....|..|+
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~ 93 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHI 93 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHH
Confidence 5789999999998887777665 22 334589999999999999999998884
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.23 E-value=0.00014 Score=72.11 Aligned_cols=39 Identities=15% Similarity=0.477 Sum_probs=26.8
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
+++.|+ ||+.| .+..|..|+++|.+.|++.|.+|++.|.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 566777 77544 4566777777777777777777777764
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.17 E-value=0.00017 Score=71.63 Aligned_cols=56 Identities=21% Similarity=0.478 Sum_probs=45.2
Q ss_pred CCccCCCCCCCcccCCCCcccCC----------chhhhhhhhhcCCCCcccCCCCCCcccCchhhhhc
Q psy6674 200 PVASTARPKKQFICRFCSRHFTK----------SYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 200 ~~~~~~~~~kp~~C~~Cgk~F~~----------~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
.|...+-+.+++.|.+|++.|.. ...|..|+.++ |.+++.|..||+.|..++ |..|
T Consensus 494 ~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlrd-m~~H 559 (567)
T PLN03086 494 QHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLKE-MDIH 559 (567)
T ss_pred hhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeehh-HHHH
Confidence 34455678899999999999952 34799999986 999999999999998775 4444
No 21
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.13 E-value=0.00026 Score=48.81 Aligned_cols=46 Identities=26% Similarity=0.659 Sum_probs=34.9
Q ss_pred CcccCCCCcccCCchhhhhhhh-hcCCC-CcccCCCCCCcccCchhhhhcC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHER-THTDE-RPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r-~Htge-Kpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
.|.|++|++.|. ...|..|.. .|.++ +.+.|++|...+.. +|.+|+
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHL 49 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHH
Confidence 489999999655 567999966 46654 67999999987553 677663
No 22
>PRK04860 hypothetical protein; Provisional
Probab=97.12 E-value=0.00022 Score=60.26 Aligned_cols=40 Identities=20% Similarity=0.531 Sum_probs=35.7
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCch
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQD 252 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~ 252 (258)
-+|.|. |++ ....+.+|.++|+|+++|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 579998 998 6778999999999999999999999987654
No 23
>KOG3608|consensus
Probab=97.04 E-value=0.00022 Score=66.58 Aligned_cols=49 Identities=35% Similarity=0.778 Sum_probs=42.2
Q ss_pred CCcccCC--CCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhc
Q psy6674 209 KQFICRF--CSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 209 kp~~C~~--Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
..+.|.| |.+.|..++.|.+|.|+|+++|-..|+.||.-|+++..|..|
T Consensus 176 pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH 226 (467)
T KOG3608|consen 176 PVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDH 226 (467)
T ss_pred ceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHH
Confidence 3467776 889999999999999999999999999999999988887766
No 24
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.85 E-value=0.00049 Score=38.53 Aligned_cols=23 Identities=39% Similarity=0.785 Sum_probs=18.5
Q ss_pred cccCCCCcccCCchhhhhhhhhc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTH 233 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~H 233 (258)
|.|++|++.|.....|..|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999998876
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.63 E-value=0.00089 Score=39.24 Aligned_cols=26 Identities=31% Similarity=0.622 Sum_probs=23.0
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTD 235 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~Htg 235 (258)
+|.|..|++.|.....|..|++.|.+
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 58999999999999999999988753
No 26
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.49 E-value=0.0022 Score=43.89 Aligned_cols=35 Identities=20% Similarity=0.380 Sum_probs=25.2
Q ss_pred CCCCCCCcccCCCCcccCCchhhhhhhhhcCCCCc
Q psy6674 204 TARPKKQFICRFCSRHFTKSYNLLIHERTHTDERP 238 (258)
Q Consensus 204 ~~~~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKp 238 (258)
......|..|++|+..+....+|++|+.++++.||
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34456889999999999999999999998888886
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.45 E-value=0.00058 Score=38.49 Aligned_cols=20 Identities=35% Similarity=0.974 Sum_probs=18.7
Q ss_pred ccCCCCCCcccCchhhhhcC
Q psy6674 239 YSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 239 f~C~~Cgk~F~~~~~L~~H~ 258 (258)
|.|+.|++.|.+...|..|+
T Consensus 1 y~C~~C~~~f~~~~~l~~H~ 20 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHM 20 (23)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHH
Confidence 78999999999999999985
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.38 E-value=0.00096 Score=50.14 Aligned_cols=47 Identities=32% Similarity=0.780 Sum_probs=18.3
Q ss_pred ccCCCCcccCCchhhhhhhhhcCC-----------------------CCcccCCCCCCcccCchhhhhcC
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTD-----------------------ERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~Htg-----------------------eKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
+|..|+..|.....|..|+....+ ...+.|..|++.|.....|..|+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHM 70 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHH
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHH
Confidence 477777777777777777753211 13588999999999999999885
No 29
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.32 E-value=0.0023 Score=36.04 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=21.5
Q ss_pred cccCCCCcccCCchhhhhhhhhcC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHT 234 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~Ht 234 (258)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998775
No 30
>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=96.14 E-value=0.00087 Score=39.44 Aligned_cols=22 Identities=23% Similarity=0.661 Sum_probs=17.9
Q ss_pred CccCCCCCCCcccCCCCcccCC
Q psy6674 201 VASTARPKKQFICRFCSRHFTK 222 (258)
Q Consensus 201 ~~~~~~~~kp~~C~~Cgk~F~~ 222 (258)
+.+.|.+++||.|++|++.|..
T Consensus 5 H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 5 HMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHSSSSSEEESSSSEEESS
T ss_pred HhhhcCCCCCCCCCCCcCeeCc
Confidence 3445778999999999999963
No 31
>PHA02768 hypothetical protein; Provisional
Probab=95.99 E-value=0.0021 Score=44.81 Aligned_cols=21 Identities=19% Similarity=0.698 Sum_probs=19.6
Q ss_pred cccCCCCCCcccCchhhhhcC
Q psy6674 238 PYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 238 pf~C~~Cgk~F~~~~~L~~H~ 258 (258)
-|.|+.||+.|.+.++|.+||
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~ 25 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHL 25 (55)
T ss_pred ccCcchhCCeeccHHHHHHHH
Confidence 489999999999999999996
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.52 E-value=0.0034 Score=34.95 Aligned_cols=20 Identities=40% Similarity=1.052 Sum_probs=16.5
Q ss_pred ccCCCCCCcccCchhhhhcC
Q psy6674 239 YSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 239 f~C~~Cgk~F~~~~~L~~H~ 258 (258)
|.|++|++.|.....|..|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 78999999999999999884
No 33
>PHA00616 hypothetical protein
Probab=95.46 E-value=0.0027 Score=42.20 Aligned_cols=21 Identities=29% Similarity=0.695 Sum_probs=19.5
Q ss_pred cccCCCCCCcccCchhhhhcC
Q psy6674 238 PYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 238 pf~C~~Cgk~F~~~~~L~~H~ 258 (258)
||+|..||+.|.....|.+|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH
Confidence 799999999999999999984
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=95.25 E-value=0.0042 Score=36.30 Aligned_cols=21 Identities=43% Similarity=1.073 Sum_probs=19.4
Q ss_pred cccCCCCCCcccCchhhhhcC
Q psy6674 238 PYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 238 pf~C~~Cgk~F~~~~~L~~H~ 258 (258)
||.|..|++.|.....|..|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK 21 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH
T ss_pred CCCCCccCCccCChhHHHHHh
Confidence 689999999999999999885
No 35
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.98 E-value=0.013 Score=53.85 Aligned_cols=50 Identities=36% Similarity=0.715 Sum_probs=46.3
Q ss_pred CCcccCCCCcccCCchhhhhhhh--hcCCC--CcccCC--CCCCcccCchhhhhcC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHER--THTDE--RPYSCD--VCNKAFRRQDHLRDHR 258 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r--~Htge--Kpf~C~--~Cgk~F~~~~~L~~H~ 258 (258)
.++.|..|...|.....|.+|.+ .|+++ +||.|+ .|++.|.+...+.+|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc
Confidence 47899999999999999999999 89999 999999 7999999999888773
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.54 E-value=0.014 Score=33.32 Aligned_cols=23 Identities=30% Similarity=0.748 Sum_probs=19.9
Q ss_pred cccCCCCcccCCchhhhhhhhhc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTH 233 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~H 233 (258)
|.|..|++.|.....+..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999998754
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=94.24 E-value=0.051 Score=50.50 Aligned_cols=25 Identities=20% Similarity=0.615 Sum_probs=22.6
Q ss_pred CCCCcccCCCCcccCCchhhhhhhh
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHER 231 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r 231 (258)
..|||.|++|+|.|+....|+.|+.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 4589999999999999999999964
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.00 E-value=0.019 Score=32.07 Aligned_cols=20 Identities=35% Similarity=0.934 Sum_probs=18.1
Q ss_pred ccCCCCCCcccCchhhhhcC
Q psy6674 239 YSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 239 f~C~~Cgk~F~~~~~L~~H~ 258 (258)
|.|..|++.|.....|..|+
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCCCcchhCCHHHHHHHH
Confidence 68999999999999998884
No 39
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.98 E-value=0.025 Score=33.19 Aligned_cols=22 Identities=27% Similarity=0.667 Sum_probs=19.0
Q ss_pred cccCCCCcccCCchhhhhhhhh
Q psy6674 211 FICRFCSRHFTKSYNLLIHERT 232 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~ 232 (258)
|.|..|++.|.....+..|++.
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 7899999999999999888874
No 40
>KOG3993|consensus
Probab=93.97 E-value=0.011 Score=56.60 Aligned_cols=48 Identities=27% Similarity=0.706 Sum_probs=42.6
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
|.|..|.-.|.....|..|.....-..-|+|++|+|-|+-..+|..|+
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHR 315 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHR 315 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhh
Confidence 999999999999999999977554456799999999999999998885
No 41
>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=92.51 E-value=0.038 Score=37.92 Aligned_cols=26 Identities=31% Similarity=0.747 Sum_probs=18.4
Q ss_pred cCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 233 HTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 233 HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
+..+.|..|++|+..+++..+|++|+
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHl 44 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHL 44 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHH
T ss_pred hccCCCCCCCcchhhccchhhHHHHH
Confidence 44678999999999999999999995
No 42
>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=92.42 E-value=0.084 Score=30.92 Aligned_cols=20 Identities=35% Similarity=0.963 Sum_probs=18.6
Q ss_pred ccCCCCCCcccCchhhhhcC
Q psy6674 239 YSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 239 f~C~~Cgk~F~~~~~L~~H~ 258 (258)
|-|..|++.|.....|..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 78999999999999999985
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.48 E-value=0.071 Score=30.20 Aligned_cols=23 Identities=30% Similarity=0.543 Sum_probs=17.5
Q ss_pred cccCCCCcccCCchhhhhhhhhcC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHT 234 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~Ht 234 (258)
|.|..|+.... +..|..|++.|.
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 68999998887 888999998764
No 44
>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=90.52 E-value=0.17 Score=31.32 Aligned_cols=24 Identities=25% Similarity=0.890 Sum_probs=19.1
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
|+|..||..+.... .++.|+.||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 78999997765432 7899999985
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=89.91 E-value=0.074 Score=30.24 Aligned_cols=20 Identities=45% Similarity=1.095 Sum_probs=18.1
Q ss_pred ccCCCCCCcccCchhhhhcC
Q psy6674 239 YSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 239 f~C~~Cgk~F~~~~~L~~H~ 258 (258)
|.|.+|++.|.....|..|+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCCcCCHHHHHHHH
Confidence 68999999999999998884
No 46
>PHA00732 hypothetical protein
Probab=88.40 E-value=0.18 Score=37.59 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=18.6
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTD 235 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~Htg 235 (258)
++.|+.||+.|. .+..|.+++.+
T Consensus 27 ~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 27 LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CCccCCCCCEeC---ChhhhhcccCC
Confidence 468999999998 58899876643
No 47
>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=88.21 E-value=0.29 Score=29.93 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=20.1
Q ss_pred CCcccCCCCcccCCchhhhhhhhh
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERT 232 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~ 232 (258)
.+|.|.+|++.|.....+..|+..
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 358899999999988888888763
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=87.67 E-value=0.32 Score=28.28 Aligned_cols=20 Identities=35% Similarity=0.723 Sum_probs=15.4
Q ss_pred cccCCCCcccCCchhhhhhhh
Q psy6674 211 FICRFCSRHFTKSYNLLIHER 231 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r 231 (258)
..|+.||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3688899988 6667888865
No 49
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=86.40 E-value=0.48 Score=37.49 Aligned_cols=30 Identities=27% Similarity=0.695 Sum_probs=20.3
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~ 251 (258)
..|+.||+.|-- | +..|-.|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYD---L--------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD---L--------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc---C--------CCCCccCCCCCCccCcc
Confidence 478888887733 2 24677788888777543
No 50
>KOG4124|consensus
Probab=86.01 E-value=0.28 Score=46.21 Aligned_cols=52 Identities=29% Similarity=0.768 Sum_probs=40.7
Q ss_pred CCCCcccCC--CCcccCCchhhhhhhhh-c--------------CC----CCcccCCCCCCcccCchhhhhcC
Q psy6674 207 PKKQFICRF--CSRHFTKSYNLLIHERT-H--------------TD----ERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 207 ~~kp~~C~~--Cgk~F~~~~~L~~H~r~-H--------------tg----eKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
..++|.|++ |.+.++....|+.|... | +| .|+|+|++|.++++-...|+.|+
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 357899987 99999988888877542 2 22 48999999999998887777663
No 51
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=85.55 E-value=0.49 Score=40.26 Aligned_cols=24 Identities=29% Similarity=0.888 Sum_probs=20.3
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
.|.|++||.. |.|+-|-.|++||.
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 6999999854 56788999999993
No 52
>KOG1146|consensus
Probab=85.44 E-value=0.31 Score=52.68 Aligned_cols=51 Identities=29% Similarity=0.596 Sum_probs=44.6
Q ss_pred CCCcccCCCCcccCCchhhhhhhhh-c------------------------CCCCcccCCCCCCcccCchhhhhcC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERT-H------------------------TDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~-H------------------------tgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
.+.|+|+.|+..|+....|-.|+|. | -+.+||.|..|...|....+|-.|+
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 3779999999999999999999997 2 2248899999999999999998884
No 53
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=85.39 E-value=1 Score=41.27 Aligned_cols=65 Identities=20% Similarity=0.257 Sum_probs=48.7
Q ss_pred cccccCCCCCCCCCCCCCcc--CCCCC--CCcccC--CCCcccCCchhhhhhhhhcCCCCcccCCC--CCCcc
Q psy6674 184 KTIVTDSISKPVQKSTPVAS--TARPK--KQFICR--FCSRHFTKSYNLLIHERTHTDERPYSCDV--CNKAF 248 (258)
Q Consensus 184 ~~~~~~~~~k~~~~~~~~~~--~~~~~--kp~~C~--~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~--Cgk~F 248 (258)
.+..|............+.. .+..+ +++.|+ .|++.|.+...+..|...|++.+++.|.. |.+.+
T Consensus 291 ~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 363 (467)
T COG5048 291 KSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKF 363 (467)
T ss_pred CCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccc
Confidence 34444444444444555555 67777 999999 79999999999999999999999998876 44443
No 54
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=85.22 E-value=0.58 Score=34.70 Aligned_cols=24 Identities=29% Similarity=0.688 Sum_probs=21.5
Q ss_pred CcccCCCCcccCCchhhhhhhhhc
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTH 233 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~H 233 (258)
.+.|.+|++.|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 699999999999999999999965
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=84.78 E-value=0.4 Score=29.27 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=18.3
Q ss_pred cccCCCCCCcccCchhhhhcC
Q psy6674 238 PYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 238 pf~C~~Cgk~F~~~~~L~~H~ 258 (258)
+|.|++|++.|.....+..|+
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred CeEccccCCccCCHHHHHHHH
Confidence 588999999999888888773
No 56
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=83.66 E-value=0.58 Score=38.68 Aligned_cols=39 Identities=13% Similarity=0.420 Sum_probs=26.6
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
...-|.|+.|++.|.....+.. .+. ...|.|+.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEEE
Confidence 3456999999999986544432 111 33499999997653
No 57
>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=82.93 E-value=0.77 Score=28.66 Aligned_cols=25 Identities=24% Similarity=0.748 Sum_probs=18.6
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
.|.|..||..+... +.|..|++||.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 48999999765432 25789999995
No 58
>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=82.04 E-value=1.1 Score=36.35 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=17.6
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~ 251 (258)
..|+.||+.|-- | +..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYD---L--------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD---L--------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc---c--------CCCCccCCCcCCccCcc
Confidence 467777766632 2 23566777777666433
No 59
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=79.10 E-value=0.54 Score=32.93 Aligned_cols=27 Identities=15% Similarity=0.333 Sum_probs=22.1
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhc
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTH 233 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~H 233 (258)
++--+.|+.||+.|.......+|...-
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 556678999999999998888888743
No 60
>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=78.78 E-value=1.3 Score=27.82 Aligned_cols=34 Identities=18% Similarity=0.436 Sum_probs=23.8
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
+.|+.|+..|.-..... ......+.|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEEE
Confidence 57999999887765432 12223588999998875
No 61
>KOG2071|consensus
Probab=78.77 E-value=1.5 Score=43.87 Aligned_cols=27 Identities=22% Similarity=0.336 Sum_probs=22.7
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhc
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTH 233 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~H 233 (258)
...+..|..||.+|........||..|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhh
Confidence 456789999999999998888777777
No 62
>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=77.47 E-value=1.1 Score=28.35 Aligned_cols=32 Identities=16% Similarity=0.491 Sum_probs=21.8
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcc
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 248 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F 248 (258)
.|.|..||+.|...... .. ...-.|+.||...
T Consensus 5 ~y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI------SD-DPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEec------CC-CCCCCCCCCCCcc
Confidence 37899999988654322 11 4556899999743
No 63
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.40 E-value=1.1 Score=38.35 Aligned_cols=34 Identities=21% Similarity=0.506 Sum_probs=26.4
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
..-|.|+.|++.|+....+. --|.|+.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 35689999999998877653 36999999976543
No 64
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=77.12 E-value=1 Score=37.74 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=26.9
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
...-|.|+.|+..|+....+. --|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 345689999999998887775 2699999997654
No 65
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=76.37 E-value=1 Score=33.04 Aligned_cols=15 Identities=33% Similarity=0.676 Sum_probs=7.7
Q ss_pred CCcccCC--CCCCcccC
Q psy6674 236 ERPYSCD--VCNKAFRR 250 (258)
Q Consensus 236 eKpf~C~--~Cgk~F~~ 250 (258)
++-+.|. .||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 3445555 55555543
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.08 E-value=1.1 Score=29.59 Aligned_cols=31 Identities=16% Similarity=0.370 Sum_probs=21.3
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
.|.|..||..|..... ...+.|+.||..+..
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEEECCC----------CCceECCCCCCeEEE
Confidence 5889999987755321 126899999976543
No 67
>PF14353 CpXC: CpXC protein
Probab=75.59 E-value=0.45 Score=38.12 Aligned_cols=12 Identities=33% Similarity=1.054 Sum_probs=7.3
Q ss_pred ccCCCCCCcccC
Q psy6674 239 YSCDVCNKAFRR 250 (258)
Q Consensus 239 f~C~~Cgk~F~~ 250 (258)
|.|+.||+.|.-
T Consensus 39 ~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 39 FTCPSCGHKFRL 50 (128)
T ss_pred EECCCCCCceec
Confidence 566666666543
No 68
>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=74.65 E-value=1.4 Score=29.57 Aligned_cols=29 Identities=17% Similarity=0.553 Sum_probs=19.6
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
|.|..||..|...... +. ..+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 7899999888754222 11 34567999985
No 69
>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=74.06 E-value=1.5 Score=36.02 Aligned_cols=27 Identities=37% Similarity=0.641 Sum_probs=17.5
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERP 238 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKp 238 (258)
....|-+|||.|+. |++|++.|.|.-|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34689999999976 6999999988644
No 70
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=74.02 E-value=2.4 Score=26.80 Aligned_cols=34 Identities=24% Similarity=0.555 Sum_probs=24.2
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
..|+.|+..|.-...- +..+.+..+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 3689999888776532 223456789999998875
No 71
>KOG4167|consensus
Probab=73.35 E-value=3.1 Score=42.86 Aligned_cols=27 Identities=33% Similarity=0.500 Sum_probs=24.0
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHT 234 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~Ht 234 (258)
..-|.|..|+|+|..-..+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 355999999999999999999999984
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=72.45 E-value=2.6 Score=27.88 Aligned_cols=26 Identities=23% Similarity=0.569 Sum_probs=19.4
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
|.|..||..|... ..-+.+|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 7899999887644 2356789999854
No 73
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=72.45 E-value=2 Score=33.72 Aligned_cols=31 Identities=19% Similarity=0.471 Sum_probs=20.6
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCC-CcccC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN-KAFRR 250 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cg-k~F~~ 250 (258)
||.|..||+.|...+... --.|+.|| ..|.+
T Consensus 2 pH~CtrCG~vf~~g~~~i----------l~GCp~CG~nkF~y 33 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEI----------LSGCPKCGCNKFLY 33 (112)
T ss_pred CceecccccccccccHHH----------HccCccccchheEe
Confidence 578999999998854322 12688887 44543
No 74
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=71.46 E-value=3.3 Score=26.08 Aligned_cols=34 Identities=18% Similarity=0.458 Sum_probs=23.9
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
..|+.|+..|.-.... +-.+.+..+|..|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEeC
Confidence 4688898888776543 223445688999998773
No 75
>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=71.42 E-value=2.9 Score=28.42 Aligned_cols=26 Identities=31% Similarity=0.594 Sum_probs=20.2
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhcC
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTHT 234 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~Ht 234 (258)
..+.+.|++|...+. .+|..|+..+.
T Consensus 28 ~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 28 ESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 346799999998755 38999988654
No 76
>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=69.57 E-value=2.2 Score=27.72 Aligned_cols=29 Identities=21% Similarity=0.674 Sum_probs=21.3
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
|.|..||..|...... .. ..+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 7899999988664322 22 46678999997
No 77
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=69.37 E-value=2.5 Score=32.18 Aligned_cols=32 Identities=25% Similarity=0.697 Sum_probs=22.7
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
..|.|+.|++. .+.|+ +..-+.|.-||..|.-
T Consensus 34 ~~~~Cp~C~~~--------~VkR~--a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRI--ATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc--------ceeee--ccCeEEcCCCCCeecc
Confidence 56899999875 22233 3456899999998864
No 78
>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=68.21 E-value=2.4 Score=26.85 Aligned_cols=33 Identities=21% Similarity=0.532 Sum_probs=21.6
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~ 251 (258)
+.|+.||+.|.... .....+-.|+.||-.+.++
T Consensus 2 r~C~~Cg~~Yh~~~--------~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIEF--------NPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETTT--------B--SSTTBCTTTTEBEBEE
T ss_pred cCcCCCCCcccccc--------CCCCCCCccCCCCCeeEeC
Confidence 57899998875432 2245567899998766554
No 79
>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=65.25 E-value=3.8 Score=26.46 Aligned_cols=24 Identities=33% Similarity=0.610 Sum_probs=15.3
Q ss_pred CCCcccCCCCcccCCc----hhhhhhhh
Q psy6674 208 KKQFICRFCSRHFTKS----YNLLIHER 231 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~----~~L~~H~r 231 (258)
.....|.+|++.+... ++|.+|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3557899999988775 67888883
No 80
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=64.95 E-value=3.8 Score=29.03 Aligned_cols=33 Identities=21% Similarity=0.466 Sum_probs=22.2
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
-.|.|+.||..--.+. .+-..-..+|.|+.||-
T Consensus 26 v~F~CPnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 4589999997654432 22223357899999983
No 81
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.73 E-value=3.4 Score=32.85 Aligned_cols=27 Identities=19% Similarity=0.294 Sum_probs=15.8
Q ss_pred ccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
.|+.||+.|-. | ...|..|+.||+.|.
T Consensus 11 idPetg~KFYD---L--------NrdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYD---L--------NRDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhc---c--------CCCccccCcccccch
Confidence 56666666532 1 245666677776664
No 82
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=62.83 E-value=4.8 Score=26.93 Aligned_cols=25 Identities=32% Similarity=0.739 Sum_probs=19.1
Q ss_pred CcccCCCCcccCCc-----hhhhhhhh-hcC
Q psy6674 210 QFICRFCSRHFTKS-----YNLLIHER-THT 234 (258)
Q Consensus 210 p~~C~~Cgk~F~~~-----~~L~~H~r-~Ht 234 (258)
.-.|.+|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 34899999988766 57888887 453
No 83
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=62.44 E-value=4.1 Score=27.75 Aligned_cols=29 Identities=21% Similarity=0.600 Sum_probs=19.8
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..|.|..||+.|.. -.......|+.||.+
T Consensus 5 ~~Y~C~~Cg~~~~~----------~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVEL----------DQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeeh----------hhccCceeCCCCCcE
Confidence 45889999998821 113456789999853
No 84
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.38 E-value=4.4 Score=33.10 Aligned_cols=39 Identities=21% Similarity=0.392 Sum_probs=22.7
Q ss_pred CCcccCCCCcccCCch---hh------hhhhhhcCCCCcccCCCCCCc
Q psy6674 209 KQFICRFCSRHFTKSY---NL------LIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~---~L------~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..|.|..||..|.... .| ..|..--+...-+.|+.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 5689999998886641 11 111111112345789999954
No 85
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=58.61 E-value=5.6 Score=41.33 Aligned_cols=24 Identities=25% Similarity=0.335 Sum_probs=17.3
Q ss_pred hhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 224 YNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 224 ~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..|..|..-|....|+.|+.||..
T Consensus 461 ~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 461 GQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CeeEeCCCCCCCCCCCCCCCCCCC
Confidence 345556555667789999999964
No 86
>KOG2593|consensus
Probab=58.33 E-value=5.6 Score=38.61 Aligned_cols=39 Identities=15% Similarity=0.494 Sum_probs=27.6
Q ss_pred CCCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 206 RPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 206 ~~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
.....|.|+.|.+.|+....+. ..-...--|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccCceEEEecCCCc
Confidence 4557799999999998766554 22223456999999853
No 87
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=57.68 E-value=3.3 Score=29.08 Aligned_cols=27 Identities=30% Similarity=0.580 Sum_probs=23.5
Q ss_pred hhcCCCCcccCCCCCCcccCchhhhhc
Q psy6674 231 RTHTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 231 r~HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
+...|+.-+.|+-||.-|++...+.+|
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RH 36 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRH 36 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHH
Confidence 456789999999999999998888877
No 88
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=57.22 E-value=4.8 Score=33.17 Aligned_cols=25 Identities=32% Similarity=0.426 Sum_probs=21.4
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERP 238 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKp 238 (258)
..|-+|||.|+. |++|+.+|.|.-|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 479999999964 9999999988755
No 89
>PRK12496 hypothetical protein; Provisional
Probab=55.97 E-value=5.8 Score=33.47 Aligned_cols=31 Identities=19% Similarity=0.748 Sum_probs=20.7
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~ 251 (258)
+.|.|.-|++.|.... ..-.|+.||..-.++
T Consensus 126 w~~~C~gC~~~~~~~~------------~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 126 WRKVCKGCKKKYPEDY------------PDDVCEICGSPVKRK 156 (164)
T ss_pred eeEECCCCCccccCCC------------CCCcCCCCCChhhhc
Confidence 5688999999886421 112699999654443
No 90
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.22 E-value=4.2 Score=36.43 Aligned_cols=38 Identities=24% Similarity=0.416 Sum_probs=28.6
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCc---------------ccCCCCC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERP---------------YSCDVCN 245 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKp---------------f~C~~Cg 245 (258)
++.+.|++|+..|..+..+..-.|+-.|.-. ..|+.|+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~ 69 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICY 69 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhh
Confidence 4678999999999988777777776555422 2699998
No 91
>KOG2785|consensus
Probab=54.33 E-value=6.8 Score=37.45 Aligned_cols=49 Identities=22% Similarity=0.393 Sum_probs=38.2
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCC-----------------------CcccCCCCC---CcccCchhhhhcC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDE-----------------------RPYSCDVCN---KAFRRQDHLRDHR 258 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~Htge-----------------------Kpf~C~~Cg---k~F~~~~~L~~H~ 258 (258)
|-.|-+|++.|..-.....||-.|+|- +-|.|-.|. +.|......+.||
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM 240 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHM 240 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHH
Confidence 347888888888888888888877652 446788888 8888888888886
No 92
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=54.27 E-value=6.2 Score=26.86 Aligned_cols=47 Identities=23% Similarity=0.516 Sum_probs=30.0
Q ss_pred CCcccCC--CCcccCCchhhhhhhhhcCCCCcccCCC----CCCcccCchhhhhc
Q psy6674 209 KQFICRF--CSRHFTKSYNLLIHERTHTDERPYSCDV----CNKAFRRQDHLRDH 257 (258)
Q Consensus 209 kp~~C~~--Cgk~F~~~~~L~~H~r~HtgeKpf~C~~----Cgk~F~~~~~L~~H 257 (258)
.+..|+. |...+. +..|..|....-..++..|.+ |+..|.+. .|..|
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~-~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPRE-DLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEHH-HHHHC
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccchh-HHhCC
Confidence 4567887 445454 557999999777788999999 99887764 34444
No 93
>PF15269 zf-C2H2_7: Zinc-finger
Probab=54.03 E-value=17 Score=24.47 Aligned_cols=24 Identities=17% Similarity=0.329 Sum_probs=19.8
Q ss_pred CCcccCCCCcccCCchhhhhhhhh
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERT 232 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~ 232 (258)
-.|+|-.|.-+...+++|-.||+-
T Consensus 19 ~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 19 FKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ccceeecCCcccchHHHHHHHHHH
Confidence 347899999899999999999863
No 94
>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=53.73 E-value=11 Score=23.19 Aligned_cols=26 Identities=23% Similarity=0.655 Sum_probs=16.4
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
|.|..||..+... ..-+.+|..||.+
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCe
Confidence 6788888877622 1245688888854
No 95
>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=52.78 E-value=7 Score=27.56 Aligned_cols=27 Identities=22% Similarity=0.565 Sum_probs=11.0
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
-.|..|++.|.. ..+.+.|..||..|-
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVC 36 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEE
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEEC
Confidence 367778777743 134566777776653
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=52.32 E-value=11 Score=26.73 Aligned_cols=33 Identities=24% Similarity=0.674 Sum_probs=21.5
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
-.|.|+.||+.--.+ -.+-..-..+|.|+.||-
T Consensus 24 ~~F~CPnCG~~~I~R-----C~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYR-----CEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEee-----chhHHhcCCceECCCCCC
Confidence 458999999862222 222223357899999984
No 97
>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=52.03 E-value=5.2 Score=32.67 Aligned_cols=34 Identities=24% Similarity=0.754 Sum_probs=23.4
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
-.|.|..|+..+.. |.++ ..+.|.|..|+..|..
T Consensus 122 ~~~~C~~C~~~~~r------~~~~--~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 122 YVYRCPSCGREYKR------HRRS--KRKRYRCGRCGGPLVQ 155 (157)
T ss_pred eEEEcCCCCCEeee------eccc--chhhEECCCCCCEEEE
Confidence 46899999987633 3333 3344999999977653
No 98
>KOG0978|consensus
Probab=50.29 E-value=7.6 Score=40.01 Aligned_cols=23 Identities=39% Similarity=0.661 Sum_probs=18.0
Q ss_pred CCCcccCCCCCCcccCchhhhhc
Q psy6674 235 DERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 235 geKpf~C~~Cgk~F~~~~~L~~H 257 (258)
+-|--+||.|+.+|.-.+.+.-|
T Consensus 675 etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 675 ETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HHhcCCCCCCCCCCCcccccccC
Confidence 34555899999999988777665
No 99
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=50.19 E-value=9.2 Score=29.42 Aligned_cols=28 Identities=21% Similarity=0.637 Sum_probs=20.3
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
+|-.|..||..|... - -.+|-+|+.|..
T Consensus 57 ~Pa~CkkCGfef~~~-~---------ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRDD-K---------IKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCcccccc-c---------cCCcccCCcchh
Confidence 567899999888762 1 136888999864
No 100
>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=48.86 E-value=13 Score=29.30 Aligned_cols=31 Identities=16% Similarity=0.253 Sum_probs=21.1
Q ss_pred cccCCCCCCCCCCCCCccCCCCCCCcccCCCCcccCCch
Q psy6674 186 IVTDSISKPVQKSTPVASTARPKKQFICRFCSRHFTKSY 224 (258)
Q Consensus 186 ~~~~~~~k~~~~~~~~~~~~~~~kp~~C~~Cgk~F~~~~ 224 (258)
.+|..|++.|--. ++.|-.|++||..|.-..
T Consensus 10 R~Cp~CG~kFYDL--------nk~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 10 RTCPSCGAKFYDL--------NKDPIVCPKCGTEFPPEP 40 (108)
T ss_pred ccCCCCcchhccC--------CCCCccCCCCCCccCccc
Confidence 3566666655332 236789999999998773
No 101
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=48.70 E-value=11 Score=36.60 Aligned_cols=28 Identities=18% Similarity=0.637 Sum_probs=16.5
Q ss_pred ccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
.|+.||...... |..-|+|+-||.++..
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCc
Confidence 577777554332 3336777777766654
No 102
>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=48.59 E-value=7.9 Score=26.82 Aligned_cols=31 Identities=23% Similarity=0.446 Sum_probs=20.7
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
|.|+.||..+.-.... .|+ ...|+.||..|.
T Consensus 3 ~~CP~CG~~iev~~~~-------~Ge-iV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGE-LVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCC-EEeCCCCCCEEE
Confidence 6899999876443222 133 468999997663
No 103
>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=48.07 E-value=11 Score=25.62 Aligned_cols=35 Identities=17% Similarity=0.438 Sum_probs=20.0
Q ss_pred cccCCCCcccCCchhhhhhhhhcCC------CCcccCCCCCC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTD------ERPYSCDVCNK 246 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~Htg------eKpf~C~~Cgk 246 (258)
|+|..||..|.-...-..+ .+-.| ...|.|+.|+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~-~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 2 YECRICGYIYDPAEGDPDE-GIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred cCCCCCCeEECCCCCCccc-CcCCCCCHhHCCCCCCCCCCCC
Confidence 7899999888754221111 11111 23478999984
No 104
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=46.92 E-value=12 Score=31.51 Aligned_cols=16 Identities=25% Similarity=0.463 Sum_probs=10.6
Q ss_pred CcccCCCCcccCCchh
Q psy6674 210 QFICRFCSRHFTKSYN 225 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~ 225 (258)
.++|+-||+.|..--.
T Consensus 28 ~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 28 RRECLACGKRFTTFER 43 (154)
T ss_pred eeeccccCCcceEeEe
Confidence 3777777777765543
No 105
>PRK04860 hypothetical protein; Provisional
Probab=46.67 E-value=4.3 Score=34.24 Aligned_cols=38 Identities=11% Similarity=0.124 Sum_probs=27.4
Q ss_pred cccCCCCCCCCCCCCCccCCCCCCCcccCCCCcccCCch
Q psy6674 186 IVTDSISKPVQKSTPVASTARPKKQFICRFCSRHFTKSY 224 (258)
Q Consensus 186 ~~~~~~~k~~~~~~~~~~~~~~~kp~~C~~Cgk~F~~~~ 224 (258)
+.|. |.........+.+.+.++++|.|..|+..|....
T Consensus 120 Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 120 YRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 4454 5554445566677788899999999999887543
No 106
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.26 E-value=11 Score=29.83 Aligned_cols=26 Identities=23% Similarity=0.400 Sum_probs=18.1
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
..+.|..||..|.... ..|.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC------------cCccCcCCCC
Confidence 4578999997775532 3456999984
No 107
>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=46.24 E-value=16 Score=21.40 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=6.1
Q ss_pred cCCCCCCccc
Q psy6674 240 SCDVCNKAFR 249 (258)
Q Consensus 240 ~C~~Cgk~F~ 249 (258)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5666666653
No 108
>KOG4124|consensus
Probab=45.82 E-value=42 Score=32.05 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=21.8
Q ss_pred CCCCCcccCCCCcccCCchhhhhhhh
Q psy6674 206 RPKKQFICRFCSRHFTKSYNLLIHER 231 (258)
Q Consensus 206 ~~~kp~~C~~Cgk~F~~~~~L~~H~r 231 (258)
...|+|.|++|.+.++....|+.|..
T Consensus 394 ~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 394 VENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred eccCcccChhhhhhhccCCCCCceee
Confidence 35689999999999999888887754
No 109
>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=45.63 E-value=15 Score=24.59 Aligned_cols=13 Identities=38% Similarity=0.854 Sum_probs=6.5
Q ss_pred CcccCCCCcccCC
Q psy6674 210 QFICRFCSRHFTK 222 (258)
Q Consensus 210 p~~C~~Cgk~F~~ 222 (258)
.+.|..||+.|-.
T Consensus 18 k~~Cr~Cg~~~C~ 30 (57)
T cd00065 18 RHHCRNCGRIFCS 30 (57)
T ss_pred ccccCcCcCCcCh
Confidence 3455555555433
No 110
>PHA00626 hypothetical protein
Probab=45.60 E-value=12 Score=26.23 Aligned_cols=15 Identities=20% Similarity=0.587 Sum_probs=9.1
Q ss_pred CCcccCCCCcccCCc
Q psy6674 209 KQFICRFCSRHFTKS 223 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~ 223 (258)
..|.|..||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 456666666666543
No 111
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=45.43 E-value=11 Score=28.98 Aligned_cols=32 Identities=25% Similarity=0.703 Sum_probs=21.6
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
..|.|++||+.--.+ .+...+.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR----------QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceee----------eeeEEEEcCCCCCEEeC
Confidence 568999998642111 13356899999988754
No 112
>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=45.12 E-value=11 Score=29.81 Aligned_cols=27 Identities=22% Similarity=0.572 Sum_probs=18.9
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..+.|..||+.|..... .|.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 45789999987765422 3679999853
No 113
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=43.77 E-value=12 Score=29.31 Aligned_cols=38 Identities=21% Similarity=0.428 Sum_probs=23.8
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
++.|.|+.||+.-.....++.- .+.--..|..||.+|-
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEec----CceeEEEcccCcceEE
Confidence 4679999999765443333211 1223457999998874
No 114
>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=43.61 E-value=17 Score=24.40 Aligned_cols=36 Identities=14% Similarity=0.393 Sum_probs=19.7
Q ss_pred cccCCCCcccCCchhhhhhhhhcCC------CCcccCCCCCCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTD------ERPYSCDVCNKA 247 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~Htg------eKpf~C~~Cgk~ 247 (258)
|+|.+||..|.-...-..+ .+..| ...|.|+.|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~-~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPEN-GIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGG-TB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCccc-CcCCCCCHHHCCCCCcCcCCCCc
Confidence 7899999887665433222 11111 244889999853
No 115
>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=43.44 E-value=14 Score=30.30 Aligned_cols=19 Identities=11% Similarity=0.240 Sum_probs=11.6
Q ss_pred CcccCCCCcccCCchhhhh
Q psy6674 210 QFICRFCSRHFTKSYNLLI 228 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~ 228 (258)
-|.|+.|||.|-..++..+
T Consensus 124 f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred EEECCCCCCEecccccHHH
Confidence 4566666666666655544
No 116
>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=43.28 E-value=16 Score=25.77 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=6.2
Q ss_pred CcccCCCCCCcc
Q psy6674 237 RPYSCDVCNKAF 248 (258)
Q Consensus 237 Kpf~C~~Cgk~F 248 (258)
+-|.|+.||..+
T Consensus 45 r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 45 RVFTCPNCGFEM 56 (69)
T ss_pred ceEEcCCCCCEE
Confidence 445555555443
No 117
>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=43.19 E-value=14 Score=24.32 Aligned_cols=16 Identities=38% Similarity=0.684 Sum_probs=10.9
Q ss_pred ccCCCCcccCCchhhh
Q psy6674 212 ICRFCSRHFTKSYNLL 227 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~ 227 (258)
.|.+||+.|..+.-..
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6777777777765444
No 118
>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=42.99 E-value=13 Score=24.37 Aligned_cols=27 Identities=37% Similarity=0.965 Sum_probs=17.3
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
+.|+.||.. ....+. +...|+|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~-------~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLK-------TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeC-------CCCeEECCCCCC
Confidence 679999864 222222 157789988875
No 119
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=42.44 E-value=13 Score=31.20 Aligned_cols=37 Identities=22% Similarity=0.647 Sum_probs=27.5
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcc
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 248 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F 248 (258)
...+|.|. |+..|-+. .+|-.+-.|+ -|.|..|+...
T Consensus 114 ~~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred cceeEEee-cCCccchh---hhcccccccc-eEEeccCCceE
Confidence 34679999 99887653 4666666677 89999998654
No 120
>KOG2482|consensus
Probab=42.13 E-value=14 Score=35.13 Aligned_cols=23 Identities=26% Similarity=0.612 Sum_probs=21.3
Q ss_pred CcccCCCCcccCCchhhhhhhhh
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERT 232 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~ 232 (258)
.+.|-+|.|.|+.+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 48999999999999999999984
No 121
>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 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=41.82 E-value=12 Score=28.84 Aligned_cols=32 Identities=22% Similarity=0.731 Sum_probs=21.3
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
..|.|++||+.--.+ .+-..+.|..|++.|.-
T Consensus 34 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVKR----------GSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceEE----------EeeEEEEcCCCCCEEeC
Confidence 568999998642111 13356899999988753
No 123
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.81 E-value=14 Score=29.41 Aligned_cols=28 Identities=21% Similarity=0.477 Sum_probs=18.1
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..+.|..||..|..... .-+.|+.||..
T Consensus 70 ~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 97 (117)
T PRK00564 70 VELECKDCSHVFKPNAL-----------DYGVCEKCHSK 97 (117)
T ss_pred CEEEhhhCCCccccCCc-----------cCCcCcCCCCC
Confidence 45789999977765421 11359999853
No 124
>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=40.69 E-value=15 Score=21.47 Aligned_cols=9 Identities=33% Similarity=0.947 Sum_probs=5.0
Q ss_pred cCCCCCCcc
Q psy6674 240 SCDVCNKAF 248 (258)
Q Consensus 240 ~C~~Cgk~F 248 (258)
.|++|++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 455555555
No 125
>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=40.45 E-value=11 Score=29.27 Aligned_cols=21 Identities=24% Similarity=0.605 Sum_probs=14.5
Q ss_pred hhhhhcCCCCcccCCCCCCccc
Q psy6674 228 IHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 228 ~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
..+..|.| +|++|..||.-|.
T Consensus 70 ~W~~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 70 IWMWLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEEEEeCC-CceeCCCCCcEEE
Confidence 34555666 6888888887765
No 126
>PRK05978 hypothetical protein; Provisional
Probab=40.31 E-value=16 Score=30.52 Aligned_cols=32 Identities=19% Similarity=0.264 Sum_probs=21.2
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~ 251 (258)
..|+.||+.--.+..|+.+ -.|+.||..|...
T Consensus 34 grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPV---------DHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccccccccC---------CCccccCCccccC
Confidence 5799998754444445433 3799999877653
No 127
>PLN02294 cytochrome c oxidase subunit Vb
Probab=40.28 E-value=11 Score=32.25 Aligned_cols=13 Identities=38% Similarity=0.963 Sum_probs=6.6
Q ss_pred CCcccCCCCcccC
Q psy6674 209 KQFICRFCSRHFT 221 (258)
Q Consensus 209 kp~~C~~Cgk~F~ 221 (258)
+++.|+.||..|.
T Consensus 140 kp~RCpeCG~~fk 152 (174)
T PLN02294 140 KSFECPVCTQYFE 152 (174)
T ss_pred CceeCCCCCCEEE
Confidence 4455555555553
No 128
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=40.00 E-value=14 Score=29.29 Aligned_cols=28 Identities=21% Similarity=0.454 Sum_probs=18.0
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..+.|..||..|..... ..+.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 96 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ-----------RVRRCPQCHGD 96 (114)
T ss_pred cEEEcccCCCeeecCCc-----------cCCcCcCcCCC
Confidence 45789999976654311 12579999843
No 129
>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=38.92 E-value=22 Score=29.15 Aligned_cols=20 Identities=25% Similarity=0.591 Sum_probs=16.4
Q ss_pred CcccCCCCCCcccCchhhhh
Q psy6674 237 RPYSCDVCNKAFRRQDHLRD 256 (258)
Q Consensus 237 Kpf~C~~Cgk~F~~~~~L~~ 256 (258)
+-+.|+.|||.|-..+++.+
T Consensus 123 ~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred eEEECCCCCCEecccccHHH
Confidence 45799999999988887654
No 130
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=37.30 E-value=77 Score=21.73 Aligned_cols=29 Identities=34% Similarity=0.520 Sum_probs=21.2
Q ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Q psy6674 34 SLQTTLQEEL-LQRSLQNVALTLQTAMVSSL 63 (258)
Q Consensus 34 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 63 (258)
.+|.+|||+| .||.|| +.+.-|.-.+.+|
T Consensus 13 EvQrrLhEQLEvQr~Lq-lrieaqgkyl~~i 42 (51)
T PF14379_consen 13 EVQRRLHEQLEVQRHLQ-LRIEAQGKYLQSI 42 (51)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHhhHHHHHH
Confidence 5789999998 589888 6676666555443
No 131
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=36.84 E-value=12 Score=23.97 Aligned_cols=12 Identities=33% Similarity=0.916 Sum_probs=8.3
Q ss_pred cccCCCCCCccc
Q psy6674 238 PYSCDVCNKAFR 249 (258)
Q Consensus 238 pf~C~~Cgk~F~ 249 (258)
-|.|..|+..|+
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 477877877654
No 132
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=36.67 E-value=21 Score=20.19 Aligned_cols=6 Identities=33% Similarity=1.143 Sum_probs=2.8
Q ss_pred CCCCCC
Q psy6674 241 CDVCNK 246 (258)
Q Consensus 241 C~~Cgk 246 (258)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444543
No 133
>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=35.87 E-value=13 Score=32.91 Aligned_cols=22 Identities=32% Similarity=0.866 Sum_probs=11.7
Q ss_pred CCcccCCCCCCcccCchhhhhc
Q psy6674 236 ERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 236 eKpf~C~~Cgk~F~~~~~L~~H 257 (258)
+-.|.|.+|+|.|+-......|
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KH 96 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKH 96 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHH
Confidence 3446777777766655555544
No 134
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=35.63 E-value=12 Score=28.74 Aligned_cols=31 Identities=32% Similarity=0.820 Sum_probs=20.0
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
..|.|++||+.--. |.-+ --+.|.-|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~--GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVAT--GIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEE--------EEET--TEEEETTTTEEEE
T ss_pred CCCcCCCCCCceeE--------Eeee--EEeecCCCCCEEe
Confidence 45899999975311 2222 3489999998775
No 135
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=35.49 E-value=18 Score=25.12 Aligned_cols=11 Identities=27% Similarity=0.951 Sum_probs=6.2
Q ss_pred ccCCCCcccCC
Q psy6674 212 ICRFCSRHFTK 222 (258)
Q Consensus 212 ~C~~Cgk~F~~ 222 (258)
.|..||+.|..
T Consensus 7 ~C~~Cg~~~~~ 17 (54)
T PF14446_consen 7 KCPVCGKKFKD 17 (54)
T ss_pred cChhhCCcccC
Confidence 56666665543
No 136
>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=35.27 E-value=31 Score=28.16 Aligned_cols=34 Identities=6% Similarity=0.130 Sum_probs=22.7
Q ss_pred cccCCCCCCCCCCCCCccCCCCCCCcccCCCCcccCCchhhh
Q psy6674 186 IVTDSISKPVQKSTPVASTARPKKQFICRFCSRHFTKSYNLL 227 (258)
Q Consensus 186 ~~~~~~~k~~~~~~~~~~~~~~~kp~~C~~Cgk~F~~~~~L~ 227 (258)
..|..|++.|--. ++.|-.|++||..|.....++
T Consensus 10 r~Cp~cg~kFYDL--------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 10 RICPNTGSKFYDL--------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccCCCcCcccccc--------CCCCccCCCcCCccCcchhhc
Confidence 3466666655332 336789999999997775554
No 137
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.96 E-value=16 Score=27.96 Aligned_cols=32 Identities=22% Similarity=0.591 Sum_probs=21.0
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
..|.|++|++.--.+ .+-..+.|.-|++.|.-
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKR----------VGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEE----------EEEEEEEcCCCCCEEeC
Confidence 568999997642211 13356889999987753
No 138
>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=34.88 E-value=21 Score=27.57 Aligned_cols=25 Identities=16% Similarity=0.302 Sum_probs=22.2
Q ss_pred ccc----CCCCcccCCchhhhhhhhhcCC
Q psy6674 211 FIC----RFCSRHFTKSYNLLIHERTHTD 235 (258)
Q Consensus 211 ~~C----~~Cgk~F~~~~~L~~H~r~Htg 235 (258)
|.| ..|+..+.....+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 788 8899999999999999987654
No 139
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=33.99 E-value=27 Score=23.64 Aligned_cols=28 Identities=32% Similarity=0.636 Sum_probs=17.5
Q ss_pred CcccCCCCcccCCchhhhhhhhhcCCCCcccCCCC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVC 244 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~C 244 (258)
-++|..||..|...-.- |+ .+...|+.|
T Consensus 28 ~W~C~~Cgh~w~~~v~~----R~---~~~~~CP~C 55 (55)
T PF14311_consen 28 WWKCPKCGHEWKASVND----RT---RRGKGCPYC 55 (55)
T ss_pred EEECCCCCCeeEccHhh----hc---cCCCCCCCC
Confidence 37899998877665322 22 344577776
No 140
>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=32.91 E-value=9.6 Score=33.73 Aligned_cols=24 Identities=17% Similarity=0.379 Sum_probs=19.6
Q ss_pred CCcccCCCCcccCCchhhhhhhhh
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERT 232 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~ 232 (258)
..|.|..|+|.|.-......|+..
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHhh
Confidence 559999999999999999999875
No 141
>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=32.60 E-value=20 Score=28.26 Aligned_cols=27 Identities=26% Similarity=0.614 Sum_probs=17.2
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..+.|..||+.|.-... .|.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEF------------DFSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHC------------CHH-SSSSSS
T ss_pred CcEECCCCCCEEecCCC------------CCCCcCCcCC
Confidence 44789999998865432 1569999965
No 142
>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=32.53 E-value=7.1 Score=24.96 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=7.0
Q ss_pred ccCCCCCCcc
Q psy6674 239 YSCDVCNKAF 248 (258)
Q Consensus 239 f~C~~Cgk~F 248 (258)
|.|..||+.|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6777777665
No 143
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=32.36 E-value=29 Score=29.01 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=13.6
Q ss_pred CCCcccCCCCcccCCchhh
Q psy6674 208 KKQFICRFCSRHFTKSYNL 226 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L 226 (258)
++.-.|..||+.|+.-...
T Consensus 26 RRRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 26 RRRRECLECHERFTTFERA 44 (147)
T ss_pred eecccCCccCCccceeeec
Confidence 3556899999988876443
No 144
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.54 E-value=33 Score=27.85 Aligned_cols=16 Identities=25% Similarity=0.779 Sum_probs=11.1
Q ss_pred CCCcccCCCCcccCCc
Q psy6674 208 KKQFICRFCSRHFTKS 223 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~ 223 (258)
.-.|.|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4567777777777654
No 145
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=31.50 E-value=31 Score=26.84 Aligned_cols=38 Identities=29% Similarity=0.673 Sum_probs=15.0
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhcCCCCc-ccCCCCCCcccC
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTHTDERP-YSCDVCNKAFRR 250 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKp-f~C~~Cgk~F~~ 250 (258)
+.|--.|..||+.+... +..+- |+|. |.|+.|.+.|..
T Consensus 11 g~ke~~CalCG~tWg~~-----y~Ev~-G~rLfFCCd~ca~EF~n 49 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDY-----YEEVD-GERLFFCCDDCAKEFKN 49 (105)
T ss_dssp -SGGGS-SS---S---S-----S-B-T-T--BSSS--SSSS-TTS
T ss_pred ccccccccccCCcHHHH-----HHhhc-CCEEEEEcHHHHHHHHH
Confidence 34556899999888743 22233 5554 678889988865
No 146
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=30.98 E-value=39 Score=33.30 Aligned_cols=41 Identities=10% Similarity=0.317 Sum_probs=25.0
Q ss_pred CCCCCcccCCCCcccCCchhhhhhhhhcCC------CCcccCCCCCCc
Q psy6674 206 RPKKQFICRFCSRHFTKSYNLLIHERTHTD------ERPYSCDVCNKA 247 (258)
Q Consensus 206 ~~~kp~~C~~Cgk~F~~~~~L~~H~r~Htg------eKpf~C~~Cgk~ 247 (258)
...+.|+|..||..|.-...-..+ .+-.| .-.|.|+.||..
T Consensus 421 ~~~~~~~c~~c~~~yd~~~g~~~~-~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPAKGEPMQ-DVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCCeEEECCCCeEECCCCCCccc-CCCCCCChhhCCCCCcCcCCCCc
Confidence 355779999999888764222111 11212 134799999953
No 147
>KOG3408|consensus
Probab=30.78 E-value=20 Score=29.02 Aligned_cols=26 Identities=35% Similarity=0.510 Sum_probs=22.8
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhh
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERT 232 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~ 232 (258)
|-..|.|-.|.+.|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 33668999999999999999999885
No 148
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.77 E-value=27 Score=28.47 Aligned_cols=34 Identities=18% Similarity=0.511 Sum_probs=23.0
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
-.|.|..|+..+. +|.+ |.....|.|..|+..|.
T Consensus 111 ~~y~C~~C~~~~~------~~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 111 YPYRCTGCGQRYL------RVRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEEECCCCCCCCc------eEcc-ccCcceEEcCCCCCEEE
Confidence 5789999998764 2222 22226699999997664
No 149
>KOG4173|consensus
Probab=30.74 E-value=8.8 Score=33.93 Aligned_cols=48 Identities=29% Similarity=0.537 Sum_probs=36.8
Q ss_pred cccCCCCcccCCchhhhhhhh-hc---------CCCCcccCC--CCCCcccCchhhhhcC
Q psy6674 211 FICRFCSRHFTKSYNLLIHER-TH---------TDERPYSCD--VCNKAFRRQDHLRDHR 258 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r-~H---------tgeKpf~C~--~Cgk~F~~~~~L~~H~ 258 (258)
..|.+|.+.|....-|-.|+. .| .|.--|.|- .|+..|.+....++|+
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 389999999999999988865 34 344458884 5999998877777764
No 150
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=30.73 E-value=32 Score=36.25 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=6.2
Q ss_pred ccCCCCcccCC
Q psy6674 212 ICRFCSRHFTK 222 (258)
Q Consensus 212 ~C~~Cgk~F~~ 222 (258)
.|..|++.|..
T Consensus 462 tC~~C~kkFfS 472 (1374)
T PTZ00303 462 SCPSCGRAFIS 472 (1374)
T ss_pred cccCcCCcccc
Confidence 46666666643
No 151
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.46 E-value=24 Score=29.73 Aligned_cols=16 Identities=31% Similarity=0.719 Sum_probs=9.8
Q ss_pred CCcccCCCCCCcccCc
Q psy6674 236 ERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 236 eKpf~C~~Cgk~F~~~ 251 (258)
+.|.-|..||+.|.|-
T Consensus 66 ~~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWT 81 (158)
T ss_pred CCChhHHhCCCCCchH
Confidence 4566666666666653
No 152
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=30.29 E-value=32 Score=28.90 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=13.2
Q ss_pred CCCcccCCCCcccCCchh
Q psy6674 208 KKQFICRFCSRHFTKSYN 225 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~ 225 (258)
++.-.|..||+.|+.-..
T Consensus 26 RRRReC~~C~~RFTTfE~ 43 (156)
T COG1327 26 RRRRECLECGERFTTFER 43 (156)
T ss_pred hhhhcccccccccchhhe
Confidence 455689999998877543
No 153
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=29.56 E-value=42 Score=28.57 Aligned_cols=22 Identities=14% Similarity=0.247 Sum_probs=13.7
Q ss_pred CcccCCCCcccCCchhhhhhhh
Q psy6674 210 QFICRFCSRHFTKSYNLLIHER 231 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r 231 (258)
-|.|+.||+.|-..+++..-.+
T Consensus 130 f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 130 FYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred eeECCCCcccccCchHHHHHHH
Confidence 3557777777766666654433
No 154
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.42 E-value=28 Score=29.94 Aligned_cols=33 Identities=12% Similarity=0.531 Sum_probs=22.2
Q ss_pred CCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcc
Q psy6674 207 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 248 (258)
Q Consensus 207 ~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F 248 (258)
+..-|.|+.|.-.|+...... .-|.|+.||...
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~---------~~F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAME---------LGFTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHHHH---------hCCCCCCCCchh
Confidence 345589988887776554432 129999999643
No 155
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.42 E-value=11 Score=28.14 Aligned_cols=35 Identities=17% Similarity=0.580 Sum_probs=20.8
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
-.|.|..||..|. +..|++ ..---.|+.|+.+|++
T Consensus 11 Y~Y~c~~cg~~~d----vvq~~~---ddplt~ce~c~a~~kk 45 (82)
T COG2331 11 YSYECTECGNRFD----VVQAMT---DDPLTTCEECGARLKK 45 (82)
T ss_pred eEEeecccchHHH----HHHhcc---cCccccChhhChHHHH
Confidence 3488999997764 333332 2222368888865543
No 156
>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=29.32 E-value=26 Score=21.96 Aligned_cols=14 Identities=36% Similarity=0.776 Sum_probs=7.3
Q ss_pred ccCCCCcccCCchh
Q psy6674 212 ICRFCSRHFTKSYN 225 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~ 225 (258)
.|..|++.|....-
T Consensus 5 ~C~eC~~~f~dSyL 18 (34)
T PF01286_consen 5 KCDECGKPFMDSYL 18 (34)
T ss_dssp E-TTT--EES-SSC
T ss_pred hHhHhCCHHHHHHH
Confidence 68889988877653
No 157
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.31 E-value=40 Score=23.45 Aligned_cols=10 Identities=30% Similarity=0.630 Sum_probs=5.5
Q ss_pred CCcccCCCCc
Q psy6674 209 KQFICRFCSR 218 (258)
Q Consensus 209 kp~~C~~Cgk 218 (258)
..|.|+.||-
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 4456666654
No 158
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.30 E-value=47 Score=34.20 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=6.2
Q ss_pred cCCCCCCccc
Q psy6674 240 SCDVCNKAFR 249 (258)
Q Consensus 240 ~C~~Cgk~F~ 249 (258)
-|+.||....
T Consensus 43 fC~~CG~~~~ 52 (645)
T PRK14559 43 HCPNCGAETG 52 (645)
T ss_pred cccccCCccc
Confidence 5777776543
No 159
>PRK04351 hypothetical protein; Provisional
Probab=29.14 E-value=26 Score=29.16 Aligned_cols=35 Identities=17% Similarity=0.617 Sum_probs=24.6
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~ 251 (258)
-.|.|.-||..+.+. |.| ..+.|.|..|+..+...
T Consensus 111 y~Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 111 YLYECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEEECCCCCCEeeee-------eec-CCCcEEeCCCCcEeeec
Confidence 568998899766432 223 34779999999877554
No 160
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.00 E-value=27 Score=22.28 Aligned_cols=21 Identities=19% Similarity=0.341 Sum_probs=13.3
Q ss_pred CCCcccCCCCCCcccCchhhh
Q psy6674 235 DERPYSCDVCNKAFRRQDHLR 255 (258)
Q Consensus 235 geKpf~C~~Cgk~F~~~~~L~ 255 (258)
+..-+.|+.|+-.|.....|.
T Consensus 16 ~~~id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 16 DVEIDVCPSCGGIWFDAGELE 36 (41)
T ss_pred CEEEEECCCCCeEEccHHHHH
Confidence 345567888887766655543
No 161
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.89 E-value=32 Score=28.10 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=9.0
Q ss_pred CCcccCCCCCCcccCc
Q psy6674 236 ERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 236 eKpf~C~~Cgk~F~~~ 251 (258)
+.|--|.-||++|.|.
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 4455566666666553
No 162
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.08 E-value=29 Score=27.82 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=17.9
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
..+.| .||..|.....-..| . .-.+.|+.||.
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~----~-~~~~~CP~Cgs 100 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDH----Y-AAVIECPVCGN 100 (124)
T ss_pred eeEEe-eCcCcccccccchhc----c-ccCCcCcCCCC
Confidence 45789 899887654211111 0 01257999984
No 163
>KOG1146|consensus
Probab=27.98 E-value=22 Score=39.22 Aligned_cols=46 Identities=15% Similarity=0.155 Sum_probs=37.8
Q ss_pred cCCCCcccCCchhhhhhhh-hcCCCCcccCCCCCCcccCchhhhhcC
Q psy6674 213 CRFCSRHFTKSYNLLIHER-THTDERPYSCDVCNKAFRRQDHLRDHR 258 (258)
Q Consensus 213 C~~Cgk~F~~~~~L~~H~r-~HtgeKpf~C~~Cgk~F~~~~~L~~H~ 258 (258)
|.-|+..|.++..+..|+. .|...|.|.|+.|+..|+....|-.||
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhm 485 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHM 485 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcc
Confidence 4557777777777777776 466779999999999999999998886
No 164
>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=27.87 E-value=21 Score=23.13 Aligned_cols=10 Identities=20% Similarity=1.208 Sum_probs=4.8
Q ss_pred cccCCCCccc
Q psy6674 211 FICRFCSRHF 220 (258)
Q Consensus 211 ~~C~~Cgk~F 220 (258)
-.|++||..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 4455555444
No 165
>KOG2231|consensus
Probab=27.75 E-value=26 Score=36.10 Aligned_cols=45 Identities=27% Similarity=0.516 Sum_probs=0.0
Q ss_pred cccCCCCcccC---------------Cchhhhhhh-hhcCCCCcccCCCCCC---------cccCchhhhhcC
Q psy6674 211 FICRFCSRHFT---------------KSYNLLIHE-RTHTDERPYSCDVCNK---------AFRRQDHLRDHR 258 (258)
Q Consensus 211 ~~C~~Cgk~F~---------------~~~~L~~H~-r~HtgeKpf~C~~Cgk---------~F~~~~~L~~H~ 258 (258)
+.|.+|++.|. ....|+.|+ ..| +-+.|.+|-. ...++..|..|+
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H---~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~ 169 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQH---KLHLCSLCLQNLKIFINERKLYTRAELNLHL 169 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhh---hhhccccccccceeeeeeeehehHHHHHHHH
No 166
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.31 E-value=39 Score=22.15 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=5.9
Q ss_pred CcccCCCCcccC
Q psy6674 210 QFICRFCSRHFT 221 (258)
Q Consensus 210 p~~C~~Cgk~F~ 221 (258)
.|.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 455555554433
No 167
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.27 E-value=39 Score=34.78 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=15.9
Q ss_pred hhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 224 YNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 224 ~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..|..|..-++...|..|+.||..
T Consensus 407 ~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 407 RRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CeEECCCCcCCCCCCCCCCCCcCC
Confidence 345555555566678889999754
No 168
>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=27.00 E-value=27 Score=23.90 Aligned_cols=31 Identities=32% Similarity=0.838 Sum_probs=17.7
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVC 244 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~C 244 (258)
...|.|+.|++.|=..-..-.|...| .|+.|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH------~CPGC 49 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH------NCPGC 49 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-------SSSTT
T ss_pred CCeEECCCCCCccccCcChhhhcccc------CCcCC
Confidence 36799999999998777777775554 56666
No 169
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.67 E-value=54 Score=30.67 Aligned_cols=18 Identities=17% Similarity=0.259 Sum_probs=12.4
Q ss_pred cccCCCchhHHHHHHHHH
Q psy6674 23 LALPDAGNIVKSLQTTLQ 40 (258)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~ 40 (258)
+-+||.+|+...=-.||.
T Consensus 25 ll~p~~~~lf~~RA~Rl~ 42 (309)
T PRK03564 25 LLFANLKNLYNRRAERLR 42 (309)
T ss_pred eecCCcccHHHHHHHHHH
Confidence 568888888765555554
No 170
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.64 E-value=50 Score=23.52 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=22.0
Q ss_pred CCCCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccC
Q psy6674 206 RPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 250 (258)
Q Consensus 206 ~~~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~ 250 (258)
...+++.|.--+..|.+...+..- ..+.-..|+.|++.|+.
T Consensus 20 ~~~~~l~C~g~~~p~~HPrV~L~m----g~~gev~CPYC~t~y~l 60 (62)
T COG4391 20 IGDLPLMCPGPEPPNDHPRVFLDM----GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred eCCeeEEcCCCCCCCCCCEEEEEc----CCCCcEecCccccEEEe
Confidence 345667777655555444322211 12333478888887753
No 171
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.38 E-value=35 Score=35.16 Aligned_cols=11 Identities=18% Similarity=0.691 Sum_probs=8.1
Q ss_pred CcccCCCCCCc
Q psy6674 237 RPYSCDVCNKA 247 (258)
Q Consensus 237 Kpf~C~~Cgk~ 247 (258)
.|+.|+.||..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 57788888854
No 172
>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=26.16 E-value=29 Score=21.09 Aligned_cols=25 Identities=24% Similarity=0.672 Sum_probs=10.8
Q ss_pred ccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
+|+.|+..+.. ...--|.|+.|+..
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-----------ccCCEEeCCccccc
Confidence 57777766544 23445788888753
No 173
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=26.16 E-value=33 Score=22.03 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=5.6
Q ss_pred CcccCCCCCC
Q psy6674 237 RPYSCDVCNK 246 (258)
Q Consensus 237 Kpf~C~~Cgk 246 (258)
.-+.|..||.
T Consensus 18 g~~vC~~CG~ 27 (43)
T PF08271_consen 18 GELVCPNCGL 27 (43)
T ss_dssp TEEEETTT-B
T ss_pred CeEECCCCCC
Confidence 3457777764
No 174
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=26.06 E-value=32 Score=29.57 Aligned_cols=25 Identities=24% Similarity=0.614 Sum_probs=17.9
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
+.+.|.-|++.|.. .--.|+.||..
T Consensus 138 w~~rC~GC~~~f~~--------------~~~~Cp~CG~~ 162 (177)
T COG1439 138 WRLRCHGCKRIFPE--------------PKDFCPICGSP 162 (177)
T ss_pred eeEEEecCceecCC--------------CCCcCCCCCCc
Confidence 56789999998871 11368999865
No 175
>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=25.86 E-value=45 Score=26.12 Aligned_cols=9 Identities=33% Similarity=1.161 Sum_probs=5.8
Q ss_pred CcccCCCCc
Q psy6674 210 QFICRFCSR 218 (258)
Q Consensus 210 p~~C~~Cgk 218 (258)
|-.|++||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 456777774
No 176
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.69 E-value=36 Score=30.48 Aligned_cols=15 Identities=20% Similarity=0.516 Sum_probs=9.1
Q ss_pred CCcccCCCCcccCCc
Q psy6674 209 KQFICRFCSRHFTKS 223 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~ 223 (258)
+.|.|+.||..+.+.
T Consensus 321 r~~~C~~cg~~~~rD 335 (364)
T COG0675 321 RLFKCPRCGFVHDRD 335 (364)
T ss_pred eeEECCCCCCeehhh
Confidence 456677776665544
No 177
>PHA02998 RNA polymerase subunit; Provisional
Probab=25.36 E-value=30 Score=29.88 Aligned_cols=39 Identities=21% Similarity=0.466 Sum_probs=20.6
Q ss_pred CcccCCCCcccCCchhhhhhhhhcC-C-CCcccCCCCCCcccC
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERTHT-D-ERPYSCDVCNKAFRR 250 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~Ht-g-eKpf~C~~Cgk~F~~ 250 (258)
.-.|+.|+.. .........|.-. + -.-|.|..||+.|+-
T Consensus 143 ~v~CPkCg~~--~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 143 NTPCPNCKSK--NTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCC--ceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 3578888743 2222233333211 1 133789999987753
No 178
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=25.34 E-value=45 Score=21.47 Aligned_cols=24 Identities=17% Similarity=0.441 Sum_probs=17.3
Q ss_pred cccCCCCcccCCc--hhhhhhhhhcC
Q psy6674 211 FICRFCSRHFTKS--YNLLIHERTHT 234 (258)
Q Consensus 211 ~~C~~Cgk~F~~~--~~L~~H~r~Ht 234 (258)
-.|..||..|... ..-+.|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4899999988665 44567776663
No 179
>KOG4173|consensus
Probab=25.34 E-value=20 Score=31.69 Aligned_cols=46 Identities=28% Similarity=0.551 Sum_probs=34.7
Q ss_pred CCcccCC--CCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCchhhhhc
Q psy6674 209 KQFICRF--CSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 209 kp~~C~~--Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~~~L~~H 257 (258)
+.|.|.+ |...|..-.....|-.+.+| -.|.+|.+.|.+...|..|
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~H 125 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAH 125 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHH
Confidence 4588987 77888887777766543333 2799999999998887766
No 180
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=25.11 E-value=16 Score=27.24 Aligned_cols=40 Identities=28% Similarity=0.595 Sum_probs=16.2
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcccCc
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 251 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~~~ 251 (258)
.+.|.|++|+..-.-.-.+ ..-.+.--..|..||..|...
T Consensus 20 ~~~F~CPfC~~~~sV~v~i----dkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKI----DKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT--SS-EEEEE----ETTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcCCCCCeEEEEE----EccCCEEEEEecCCCCeEEEc
Confidence 3679999998332111111 111333446899999887654
No 181
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.09 E-value=44 Score=22.60 Aligned_cols=27 Identities=22% Similarity=0.559 Sum_probs=16.4
Q ss_pred ccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCccc
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 249 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F~ 249 (258)
.|+.||..| |..| . ..|.|.-||..+.
T Consensus 22 fCP~Cg~~~-----m~~~----~--~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSGF-----MAEH----L--DRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcch-----hecc----C--CcEECCCcCCEEe
Confidence 688887432 2222 1 4678998986543
No 182
>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=25.00 E-value=35 Score=21.73 Aligned_cols=31 Identities=19% Similarity=0.474 Sum_probs=13.9
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
..|..|+-. |.-+..+..+.+-+.|.+|+..
T Consensus 3 ~rC~~C~ay------lNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAY------LNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--B------S-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCE------ECCcceEcCCCCEEECcCCCCc
Confidence 355555433 3333444556667788888764
No 183
>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=24.06 E-value=38 Score=28.12 Aligned_cols=33 Identities=27% Similarity=0.678 Sum_probs=20.3
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC-cccC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK-AFRR 250 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk-~F~~ 250 (258)
...|.|..||..... .|.+ +--.|+.||. .|.|
T Consensus 110 ~G~l~C~~Cg~~~~~---------~~~~-~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 110 PGTLVCENCGHEVEL---------THPE-RLPPCPKCGHTEFTR 143 (146)
T ss_pred CceEecccCCCEEEe---------cCCC-cCCCCCCCCCCeeee
Confidence 366899999864311 2333 3348999984 4544
No 184
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=23.87 E-value=35 Score=32.57 Aligned_cols=31 Identities=32% Similarity=0.701 Sum_probs=22.8
Q ss_pred ccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCC
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk 246 (258)
.|.+|.+.|-....|..|+|- +.-.|-+|++
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~----~HE~ChICD~ 252 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRL----RHEACHICDM 252 (493)
T ss_pred hhhhccceecChHHHHHHHHh----hhhhhhhhhc
Confidence 699999999999999888873 2235555654
No 185
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=23.86 E-value=27 Score=30.56 Aligned_cols=37 Identities=14% Similarity=0.313 Sum_probs=19.0
Q ss_pred cccCCCCcccCCchhhhhhhhhcCCCC---cccCCCCCCccc
Q psy6674 211 FICRFCSRHFTKSYNLLIHERTHTDER---PYSCDVCNKAFR 249 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r~HtgeK---pf~C~~Cgk~F~ 249 (258)
-.|++||..|... ...+..-|-|+. -+.|..||.+|.
T Consensus 15 ~~CPvCg~~l~~~--~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 15 IDCPVCGGTLKAH--MYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred ecCCcccceeeEE--EeeecCCccceEEEEEEEccccCCccc
Confidence 5789998732221 111111233432 247888887664
No 186
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.68 E-value=1.4e+02 Score=23.83 Aligned_cols=32 Identities=25% Similarity=0.787 Sum_probs=25.4
Q ss_pred CCCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCC
Q psy6674 208 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN 245 (258)
Q Consensus 208 ~kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cg 245 (258)
..+|.|+.|.+.|-..-..-.|...| .|+.|.
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh------~CPGC~ 110 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLH------CCPGCI 110 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhcc------CCcCCC
Confidence 45799999999998888888887666 477775
No 187
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=23.61 E-value=41 Score=27.57 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=11.7
Q ss_pred CcccCCCCcccCCch
Q psy6674 210 QFICRFCSRHFTKSY 224 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~ 224 (258)
||+|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578888888887664
No 188
>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=23.54 E-value=46 Score=32.99 Aligned_cols=21 Identities=24% Similarity=0.423 Sum_probs=12.6
Q ss_pred hhhhhhhcCCCCcccCCCCCC
Q psy6674 226 LLIHERTHTDERPYSCDVCNK 246 (258)
Q Consensus 226 L~~H~r~HtgeKpf~C~~Cgk 246 (258)
|..|..-+....|..|+.||.
T Consensus 241 l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 241 LRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred EEcCCCcCcCCCCCCCCCCCC
Confidence 444444444556778888875
No 189
>PF08684 ocr: DNA mimic ocr; InterPro: IPR014798 The structure of an Ocr protein from bacteriophage T7 has shown that this protein mimics the size and shape of a bent DNA molecule []. Ocr has also been shown to be an inhibitor of the complex type I DNA restriction enzymes []. ; PDB: 1S7Z_A 2Y7C_E.
Probab=23.01 E-value=94 Score=23.92 Aligned_cols=29 Identities=28% Similarity=0.504 Sum_probs=19.8
Q ss_pred cccccccccCCCchhHHHHHHHHHHHHHH
Q psy6674 17 HSTEDVLALPDAGNIVKSLQTTLQEELLQ 45 (258)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 (258)
|-.+|---+||...+.+-||.||.|+|.-
T Consensus 62 ~EfdDsgLipdtkDV~~IlqaRIyE~L~n 90 (101)
T PF08684_consen 62 HEFDDSGLIPDTKDVTRILQARIYEQLYN 90 (101)
T ss_dssp SS-SSGGGS---S-HHHHHHHHHHHHHHH
T ss_pred eeccccCCCCCcHHHHHHHHHHHHHHHHH
Confidence 34567777899999999999999999864
No 190
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=22.92 E-value=56 Score=32.36 Aligned_cols=66 Identities=18% Similarity=0.322 Sum_probs=35.2
Q ss_pred cccccCCCCCCCCCCCCCccCCC-CCCCcccCCCCcccCCchhhhh----hhhhcCCCCcc--cCCCCCCccc
Q psy6674 184 KTIVTDSISKPVQKSTPVASTAR-PKKQFICRFCSRHFTKSYNLLI----HERTHTDERPY--SCDVCNKAFR 249 (258)
Q Consensus 184 ~~~~~~~~~k~~~~~~~~~~~~~-~~kp~~C~~Cgk~F~~~~~L~~----H~r~HtgeKpf--~C~~Cgk~F~ 249 (258)
.+..|..|...+..........+ .+..|.|+.|.........-.. .-..-.+.++| .|.+|-....
T Consensus 25 ~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss~ 97 (483)
T PF05502_consen 25 DSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSSR 97 (483)
T ss_pred ceeECccccccCChhhheeccceeccccccCCCCCCcceeEecccccccccccccCCCCCEEEECCCceeecc
Confidence 34567777666554443333333 3477899999866544422210 00112344665 8999876543
No 191
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.75 E-value=59 Score=29.93 Aligned_cols=26 Identities=27% Similarity=0.715 Sum_probs=19.6
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCcc
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 248 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~F 248 (258)
.-|.|++|.-.|-. .|-.|+.||-.|
T Consensus 254 ~GyvCs~Clsi~C~--------------~p~~C~~Cgt~f 279 (279)
T TIGR00627 254 IGFVCSVCLSVLCQ--------------YTPICKTCKTAF 279 (279)
T ss_pred ceEECCCccCCcCC--------------CCCCCCCCCCCC
Confidence 34999999877754 234899999877
No 192
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=22.67 E-value=45 Score=21.05 Aligned_cols=29 Identities=17% Similarity=0.516 Sum_probs=17.3
Q ss_pred ccCCCCcccCCchhhhhhhhhcCCCCcccCCCC
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVC 244 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~C 244 (258)
.|+.|+..- .+.+|=+...|...|.|..|
T Consensus 7 ~CP~C~s~~----~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 7 HCPRCQSTE----GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCC----cceeCCCCCCCCEeEecCcC
Confidence 577776431 14455555666677777776
No 193
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.64 E-value=40 Score=34.73 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=24.0
Q ss_pred ccCCCCcccCCchhhhhhhhhcCCCCcccCCCCCCc
Q psy6674 212 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 247 (258)
Q Consensus 212 ~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~Cgk~ 247 (258)
.|..||..+.... ....+..|.......|..||..
T Consensus 385 ~C~~Cg~~~~C~~-C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 385 ACARCRTPARCRH-CTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred EhhhCcCeeECCC-CCCceeEecCCCeeECCCCcCC
Confidence 7888988766552 3334445556677899999964
No 194
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=22.52 E-value=53 Score=20.86 Aligned_cols=23 Identities=26% Similarity=0.745 Sum_probs=8.6
Q ss_pred CCcccCCCCcccCCch-hh-hhhhh
Q psy6674 209 KQFICRFCSRHFTKSY-NL-LIHER 231 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~-~L-~~H~r 231 (258)
+.|-|++|...|.... .- +.|.+
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT-
T ss_pred cCeecccccceecCCChHHHHHhhc
Confidence 4589999999884443 22 45543
No 195
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=22.47 E-value=39 Score=23.42 Aligned_cols=31 Identities=19% Similarity=0.267 Sum_probs=17.8
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCcccCCC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDV 243 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKpf~C~~ 243 (258)
.|+....||..|.+..-+. ++ ...+...|+.
T Consensus 23 ~PV~s~~C~H~fek~aI~~-~i---~~~~~~~CPv 53 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEAILQ-YI---QRNGSKRCPV 53 (57)
T ss_dssp SEEEESSS--EEEHHHHHH-HC---TTTS-EE-SC
T ss_pred CCcCcCCCCCeecHHHHHH-HH---HhcCCCCCCC
Confidence 5677778999997765443 33 3456788887
No 196
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=22.01 E-value=45 Score=21.27 Aligned_cols=15 Identities=20% Similarity=0.671 Sum_probs=11.6
Q ss_pred cccCCCCCCcccCch
Q psy6674 238 PYSCDVCNKAFRRQD 252 (258)
Q Consensus 238 pf~C~~Cgk~F~~~~ 252 (258)
||.|..|++.|-...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 888999998886543
No 197
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.83 E-value=45 Score=32.12 Aligned_cols=14 Identities=43% Similarity=0.954 Sum_probs=10.4
Q ss_pred CCcccCCCCCCccc
Q psy6674 236 ERPYSCDVCNKAFR 249 (258)
Q Consensus 236 eKpf~C~~Cgk~F~ 249 (258)
.+.|.|..|++.|.
T Consensus 75 ~rR~~c~~c~~~~~ 88 (402)
T COG3464 75 KRRYKCCRCGKRFA 88 (402)
T ss_pred cceeecccCCCCcc
Confidence 45578888888874
No 198
>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=21.82 E-value=17 Score=33.19 Aligned_cols=19 Identities=21% Similarity=0.417 Sum_probs=9.0
Q ss_pred cccCCCchhHHHHHHHHHH
Q psy6674 23 LALPDAGNIVKSLQTTLQE 41 (258)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~ 41 (258)
+-+||..++.+.-..||.+
T Consensus 8 ~~~~~~~~~~~~ra~rl~~ 26 (290)
T PF04216_consen 8 VILPDPATLFARRAERLRA 26 (290)
T ss_dssp -EE---TTHHHHHHHHHHH
T ss_pred eecCCHhhHHHHHHHHHHH
Confidence 3467777777665555543
No 199
>KOG1280|consensus
Probab=21.79 E-value=62 Score=30.80 Aligned_cols=37 Identities=19% Similarity=0.440 Sum_probs=24.7
Q ss_pred CCcccCCCCcccCCchhhhhhhhhcCCCCc--ccCCCCC
Q psy6674 209 KQFICRFCSRHFTKSYNLLIHERTHTDERP--YSCDVCN 245 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~~~L~~H~r~HtgeKp--f~C~~Cg 245 (258)
..|.|++|++.--....|..|...-+.+-+ ..|++|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 479999999876666778788664333332 3466665
No 200
>KOG4602|consensus
Probab=21.56 E-value=2.1e+02 Score=26.31 Aligned_cols=15 Identities=13% Similarity=0.676 Sum_probs=9.9
Q ss_pred CCcccCCCCcccCCc
Q psy6674 209 KQFICRFCSRHFTKS 223 (258)
Q Consensus 209 kp~~C~~Cgk~F~~~ 223 (258)
+.|.|++||..-.+.
T Consensus 267 R~YVCPiCGATgDnA 281 (318)
T KOG4602|consen 267 RSYVCPICGATGDNA 281 (318)
T ss_pred hhhcCccccccCCcc
Confidence 457888888665443
No 201
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.39 E-value=1.2e+02 Score=33.65 Aligned_cols=8 Identities=25% Similarity=0.829 Sum_probs=5.6
Q ss_pred ccCCCCCC
Q psy6674 239 YSCDVCNK 246 (258)
Q Consensus 239 f~C~~Cgk 246 (258)
..|+.||.
T Consensus 710 ~~CP~CGt 717 (1337)
T PRK14714 710 VECPRCDV 717 (1337)
T ss_pred ccCCCCCC
Confidence 36888874
No 202
>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=21.27 E-value=45 Score=19.28 Aligned_cols=8 Identities=38% Similarity=0.983 Sum_probs=3.9
Q ss_pred CcccCCCC
Q psy6674 210 QFICRFCS 217 (258)
Q Consensus 210 p~~C~~Cg 217 (258)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34555554
No 203
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=21.20 E-value=32 Score=30.09 Aligned_cols=21 Identities=14% Similarity=0.517 Sum_probs=0.0
Q ss_pred CCcccCCCCc-ccCCchhhhhh
Q psy6674 209 KQFICRFCSR-HFTKSYNLLIH 229 (258)
Q Consensus 209 kp~~C~~Cgk-~F~~~~~L~~H 229 (258)
+.|.|.+||. +|.-+..+.+|
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ----------------------
T ss_pred CeeeeEeCCCcceecHHHHHHh
Confidence 5689999985 45555555444
No 204
>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=20.56 E-value=43 Score=20.10 Aligned_cols=20 Identities=30% Similarity=0.574 Sum_probs=10.5
Q ss_pred cccCCCCcccCCchhhhhhhh
Q psy6674 211 FICRFCSRHFTKSYNLLIHER 231 (258)
Q Consensus 211 ~~C~~Cgk~F~~~~~L~~H~r 231 (258)
|.|-.|++.| .....+.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 4577788777 3344555543
No 205
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=20.34 E-value=43 Score=31.13 Aligned_cols=38 Identities=16% Similarity=0.489 Sum_probs=21.4
Q ss_pred CcccCCCCcccCCchhhhhhhhh-cCC-CCcccCCCCCCccc
Q psy6674 210 QFICRFCSRHFTKSYNLLIHERT-HTD-ERPYSCDVCNKAFR 249 (258)
Q Consensus 210 p~~C~~Cgk~F~~~~~L~~H~r~-Htg-eKpf~C~~Cgk~F~ 249 (258)
-|.|+.||..=.. .+..+.|. -.+ -.-|.|..||..|.
T Consensus 258 ~~~C~~C~~~~~~--~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCT--YYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccce--EEEecccCCCCCCeEEEEcCCCCCeee
Confidence 4899999853222 22222332 112 13479999998765
No 206
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.04 E-value=31 Score=35.79 Aligned_cols=44 Identities=27% Similarity=0.520 Sum_probs=0.0
Q ss_pred cCCCCcccCCchhhhhhhhhcCCCCcc-cCCCCCCcccCchhhhhc
Q psy6674 213 CRFCSRHFTKSYNLLIHERTHTDERPY-SCDVCNKAFRRQDHLRDH 257 (258)
Q Consensus 213 C~~Cgk~F~~~~~L~~H~r~HtgeKpf-~C~~Cgk~F~~~~~L~~H 257 (258)
|..||.+|+.-..|-.- |-+|.-+.| .|+.|.+.|....+.+-|
T Consensus 126 CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfH 170 (750)
T COG0068 126 CTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFH 170 (750)
T ss_pred cCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccccc
No 207
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=20.02 E-value=34 Score=22.09 Aligned_cols=16 Identities=31% Similarity=0.860 Sum_probs=9.8
Q ss_pred CcccCCCCCCcccCch
Q psy6674 237 RPYSCDVCNKAFRRQD 252 (258)
Q Consensus 237 Kpf~C~~Cgk~F~~~~ 252 (258)
.||.|..|++.|-...
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5788999998886543
Done!