Query psy6673
Match_columns 286
No_of_seqs 249 out of 1725
Neff 6.4
Searched_HMMs 46136
Date Sat Aug 17 00:10:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6673.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6673hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.5 3.7E-15 8.1E-20 135.6 2.5 75 212-286 160-235 (279)
2 KOG2462|consensus 99.4 1.1E-13 2.3E-18 126.1 2.2 74 213-286 187-263 (279)
3 KOG3623|consensus 99.3 2.6E-13 5.7E-18 136.1 -0.0 79 208-286 889-970 (1007)
4 KOG3623|consensus 99.0 6.3E-11 1.4E-15 119.3 1.8 52 235-286 278-329 (1007)
5 PHA02768 hypothetical protein; 99.0 1.2E-10 2.7E-15 82.3 1.9 44 238-283 5-48 (55)
6 KOG3576|consensus 98.9 3.9E-11 8.6E-16 105.4 -3.2 76 210-285 114-192 (267)
7 KOG1074|consensus 98.9 4.1E-10 9E-15 115.0 1.6 50 237-286 604-653 (958)
8 KOG1074|consensus 98.9 4.2E-10 9.1E-15 114.9 1.2 50 236-285 351-400 (958)
9 PF13465 zf-H2C2_2: Zinc-finge 98.7 6.1E-09 1.3E-13 62.8 1.3 26 253-278 1-26 (26)
10 PHA00733 hypothetical protein 98.5 4.5E-08 9.7E-13 81.1 2.9 51 234-286 69-119 (128)
11 KOG3576|consensus 98.3 3.6E-07 7.7E-12 80.7 2.8 52 235-286 114-165 (267)
12 PHA00616 hypothetical protein 98.2 1.9E-07 4E-12 63.2 -0.6 40 238-277 1-40 (44)
13 PHA00732 hypothetical protein 98.2 1.1E-06 2.4E-11 66.9 2.5 42 238-285 1-43 (79)
14 COG5189 SFP1 Putative transcri 98.1 4.6E-06 1E-10 77.9 5.1 52 235-286 346-418 (423)
15 KOG3993|consensus 98.0 1.3E-06 2.8E-11 84.1 0.4 48 239-286 296-376 (500)
16 PF00096 zf-C2H2: Zinc finger, 97.4 4.6E-05 1E-09 43.9 0.6 23 239-261 1-23 (23)
17 KOG3608|consensus 97.4 7.3E-05 1.6E-09 71.0 2.0 49 237-285 262-311 (467)
18 PLN03086 PRLI-interacting fact 97.3 8.5E-05 1.8E-09 75.1 1.9 63 212-277 452-515 (567)
19 PHA00733 hypothetical protein 97.3 5.9E-05 1.3E-09 62.5 0.4 53 234-286 36-93 (128)
20 PF05605 zf-Di19: Drought indu 97.3 0.00013 2.9E-09 51.2 1.9 46 238-286 2-49 (54)
21 PRK04860 hypothetical protein; 97.2 0.00014 3E-09 62.5 1.7 41 237-281 118-158 (160)
22 PLN03086 PRLI-interacting fact 97.1 0.0003 6.4E-09 71.3 2.4 54 230-285 496-559 (567)
23 KOG3608|consensus 96.9 0.00033 7.2E-09 66.6 1.1 49 237-285 176-226 (467)
24 PF13894 zf-C2H2_4: C2H2-type 96.8 0.00049 1.1E-08 39.2 1.1 23 239-261 1-23 (24)
25 PF09237 GAGA: GAGA factor; I 96.7 0.0011 2.5E-08 46.1 2.5 36 231-266 17-52 (54)
26 PF12756 zf-C2H2_2: C2H2 type 96.6 0.0005 1.1E-08 52.7 -0.0 47 240-286 1-70 (100)
27 PF13912 zf-C2H2_6: C2H2-type 96.6 0.00091 2E-08 39.9 1.1 25 238-262 1-25 (27)
28 PF00096 zf-C2H2: Zinc finger, 96.6 0.00041 8.9E-09 39.9 -0.7 20 267-286 1-20 (23)
29 smart00355 ZnF_C2H2 zinc finge 96.2 0.0027 5.9E-08 36.4 1.5 24 239-262 1-24 (26)
30 PHA02768 hypothetical protein; 96.1 0.0016 3.5E-08 46.2 0.1 21 266-286 5-25 (55)
31 PHA00616 hypothetical protein 95.9 0.0013 2.8E-08 44.6 -1.0 21 266-286 1-21 (44)
32 PF13894 zf-C2H2_4: C2H2-type 95.7 0.0023 5E-08 36.4 -0.4 20 267-286 1-20 (24)
33 PF13465 zf-H2C2_2: Zinc-finge 95.5 0.0025 5.4E-08 38.2 -0.7 20 231-250 7-26 (26)
34 PF13912 zf-C2H2_6: C2H2-type 95.5 0.0029 6.2E-08 37.7 -0.5 21 266-286 1-21 (27)
35 COG5048 FOG: Zn-finger [Genera 95.4 0.0083 1.8E-07 56.3 2.1 50 237-286 288-343 (467)
36 PF12874 zf-met: Zinc-finger o 94.4 0.015 3.3E-07 33.9 0.6 23 239-261 1-23 (25)
37 smart00355 ZnF_C2H2 zinc finge 94.2 0.014 3.1E-07 33.2 0.2 20 267-286 1-20 (26)
38 KOG3993|consensus 94.1 0.0098 2.1E-07 58.0 -1.1 49 238-286 267-315 (500)
39 PF12171 zf-C2H2_jaz: Zinc-fin 94.0 0.026 5.6E-07 33.8 1.0 22 239-260 2-23 (27)
40 PF09237 GAGA: GAGA factor; I 93.0 0.026 5.6E-07 39.5 -0.2 26 261-286 19-44 (54)
41 PF12171 zf-C2H2_jaz: Zinc-fin 92.9 0.06 1.3E-06 32.2 1.3 20 267-286 2-21 (27)
42 PF09538 FYDLN_acid: Protein o 92.2 0.083 1.8E-06 42.6 1.7 30 239-279 10-39 (108)
43 PF13909 zf-H2C2_5: C2H2-type 91.6 0.069 1.5E-06 30.8 0.5 23 239-262 1-23 (24)
44 cd00350 rubredoxin_like Rubred 90.6 0.16 3.4E-06 32.1 1.5 24 239-274 2-25 (33)
45 PF12874 zf-met: Zinc-finger o 90.4 0.057 1.2E-06 31.4 -0.7 20 267-286 1-20 (25)
46 PHA00732 hypothetical protein 90.4 0.11 2.5E-06 39.4 0.8 46 215-263 3-49 (79)
47 TIGR02300 FYDLN_acid conserved 89.7 0.23 4.9E-06 41.1 2.1 30 239-279 10-39 (129)
48 COG5189 SFP1 Putative transcri 88.5 0.27 5.9E-06 46.6 2.0 25 235-259 395-419 (423)
49 PF13913 zf-C2HC_2: zinc-finge 88.2 0.28 6E-06 29.1 1.2 21 239-260 3-23 (25)
50 KOG1146|consensus 88.2 0.17 3.8E-06 55.5 0.6 51 236-286 463-538 (1406)
51 smart00451 ZnF_U1 U1-like zinc 88.2 0.27 5.9E-06 30.6 1.3 23 238-260 3-25 (35)
52 COG1592 Rubrerythrin [Energy p 86.1 0.43 9.3E-06 41.4 1.7 23 238-273 134-156 (166)
53 KOG4124|consensus 85.6 0.74 1.6E-05 44.3 3.1 52 235-286 346-418 (442)
54 PF12756 zf-C2H2_2: C2H2 type 85.5 0.45 9.7E-06 36.0 1.4 24 238-261 50-73 (100)
55 smart00531 TFIIE Transcription 85.1 0.39 8.5E-06 40.5 1.0 39 235-277 96-134 (147)
56 COG5048 FOG: Zn-finger [Genera 85.1 0.62 1.4E-05 43.5 2.4 52 234-285 29-82 (467)
57 smart00451 ZnF_U1 U1-like zinc 84.9 0.34 7.5E-06 30.2 0.4 21 266-286 3-23 (35)
58 KOG2071|consensus 83.6 0.81 1.8E-05 46.6 2.6 27 235-261 415-441 (579)
59 PF14353 CpXC: CpXC protein 82.8 0.21 4.5E-06 40.9 -1.6 17 266-282 38-54 (128)
60 cd00729 rubredoxin_SM Rubredox 82.3 0.84 1.8E-05 29.1 1.4 25 238-274 2-26 (34)
61 TIGR02098 MJ0042_CXXC MJ0042 f 79.4 1.2 2.6E-05 28.5 1.5 34 239-277 3-36 (38)
62 COG4049 Uncharacterized protei 78.6 0.53 1.1E-05 33.6 -0.5 31 233-263 12-42 (65)
63 TIGR00373 conserved hypothetic 77.7 1 2.2E-05 38.6 0.9 35 235-278 106-140 (158)
64 COG3364 Zn-ribbon containing p 77.6 1.2 2.6E-05 35.6 1.2 31 238-278 2-33 (112)
65 PRK09678 DNA-binding transcrip 77.1 1.1 2.3E-05 33.6 0.8 38 239-278 2-41 (72)
66 PRK06266 transcription initiat 76.8 1.2 2.6E-05 38.9 1.1 35 235-278 114-148 (178)
67 COG1997 RPL43A Ribosomal prote 76.5 1.7 3.6E-05 33.8 1.7 34 236-279 33-66 (89)
68 smart00834 CxxC_CXXC_SSSS Puta 76.5 1.2 2.6E-05 28.7 0.8 32 238-276 5-36 (41)
69 COG4530 Uncharacterized protei 76.3 1.4 3.1E-05 35.7 1.3 27 240-277 11-37 (129)
70 PRK00398 rpoP DNA-directed RNA 75.1 1.2 2.7E-05 29.9 0.6 31 238-278 3-33 (46)
71 KOG4167|consensus 73.0 1.7 3.7E-05 45.4 1.3 28 235-262 789-816 (907)
72 COG4049 Uncharacterized protei 72.6 1.1 2.5E-05 31.9 -0.1 27 259-285 10-36 (65)
73 TIGR02605 CxxC_CxxC_SSSS putat 72.2 1.7 3.7E-05 29.7 0.8 30 238-274 5-34 (52)
74 PF13717 zinc_ribbon_4: zinc-r 72.0 2.6 5.6E-05 27.1 1.5 34 239-277 3-36 (36)
75 PF13719 zinc_ribbon_5: zinc-r 71.9 2.7 5.8E-05 27.1 1.6 34 239-277 3-36 (37)
76 PF05605 zf-Di19: Drought indu 71.5 2.7 5.9E-05 29.1 1.7 26 235-262 28-53 (54)
77 smart00659 RPOLCX RNA polymera 67.4 3.7 8.1E-05 27.7 1.6 26 239-275 3-28 (44)
78 PRK14890 putative Zn-ribbon RN 66.8 4.1 8.8E-05 29.4 1.7 33 237-274 24-56 (59)
79 PF09723 Zn-ribbon_8: Zinc rib 66.4 3 6.5E-05 27.6 0.9 30 238-274 5-34 (42)
80 PF05191 ADK_lid: Adenylate ki 65.7 2.7 5.9E-05 27.1 0.6 33 239-279 2-34 (36)
81 smart00614 ZnF_BED BED zinc fi 65.4 3.9 8.4E-05 27.9 1.4 25 238-262 18-48 (50)
82 PTZ00255 60S ribosomal protein 65.0 3.1 6.6E-05 32.5 0.9 34 236-279 34-67 (90)
83 PF02892 zf-BED: BED zinc fing 64.5 3.8 8.2E-05 27.0 1.2 25 235-259 13-41 (45)
84 PF05443 ROS_MUCR: ROS/MUCR tr 64.3 2.8 6E-05 35.0 0.6 27 237-266 71-97 (132)
85 TIGR00280 L37a ribosomal prote 64.0 2.9 6.4E-05 32.7 0.6 34 236-279 33-66 (91)
86 COG2888 Predicted Zn-ribbon RN 63.8 5.1 0.00011 28.9 1.8 34 236-274 25-58 (61)
87 KOG2785|consensus 63.2 3.6 7.8E-05 40.0 1.2 48 239-286 167-240 (390)
88 KOG0978|consensus 62.0 3.7 8.1E-05 43.0 1.2 29 258-286 670-698 (698)
89 PRK12496 hypothetical protein; 61.6 4.3 9.3E-05 35.0 1.3 32 236-279 125-156 (164)
90 COG1571 Predicted DNA-binding 61.0 5.4 0.00012 39.5 2.0 31 238-279 350-380 (421)
91 PF01363 FYVE: FYVE zinc finge 60.3 4.3 9.4E-05 29.2 1.0 28 239-278 10-37 (69)
92 COG1198 PriA Primosomal protei 59.8 4.9 0.00011 42.5 1.6 24 252-275 461-484 (730)
93 PHA00626 hypothetical protein 59.7 5.1 0.00011 28.6 1.2 15 237-251 22-36 (59)
94 COG4957 Predicted transcriptio 58.9 5.1 0.00011 33.6 1.2 25 239-266 77-101 (148)
95 PRK03824 hypA hydrogenase nick 58.9 4.8 0.0001 33.6 1.1 40 236-275 68-116 (135)
96 KOG2593|consensus 58.7 4.8 0.0001 39.8 1.2 38 235-275 125-162 (436)
97 PRK03976 rpl37ae 50S ribosomal 58.6 4.1 8.9E-05 31.8 0.6 34 236-279 34-67 (90)
98 COG1996 RPC10 DNA-directed RNA 56.8 5.7 0.00012 27.6 1.0 29 237-275 5-33 (49)
99 PF01780 Ribosomal_L37ae: Ribo 56.4 3.5 7.6E-05 32.2 -0.1 33 237-279 34-66 (90)
100 PF10263 SprT-like: SprT-like 55.7 4.1 8.9E-05 33.9 0.2 36 235-278 120-155 (157)
101 COG3357 Predicted transcriptio 55.1 6.7 0.00014 30.7 1.2 28 237-274 57-84 (97)
102 PF02176 zf-TRAF: TRAF-type zi 54.5 5.5 0.00012 27.7 0.6 47 237-285 8-60 (60)
103 smart00440 ZnF_C2C2 C2C2 Zinc 54.4 4.6 9.9E-05 26.6 0.2 37 239-277 1-39 (40)
104 COG1655 Uncharacterized protei 54.1 4.6 9.9E-05 36.9 0.2 40 235-274 16-70 (267)
105 cd00065 FYVE FYVE domain; Zinc 53.1 9.9 0.00021 26.1 1.8 11 240-250 4-14 (57)
106 PF09538 FYDLN_acid: Protein o 52.5 14 0.0003 29.8 2.7 35 212-254 8-42 (108)
107 PF12760 Zn_Tnp_IS1595: Transp 52.3 7.7 0.00017 26.0 1.1 27 239-274 19-45 (46)
108 TIGR01206 lysW lysine biosynth 52.1 7.9 0.00017 27.3 1.1 31 239-277 3-33 (54)
109 COG3091 SprT Zn-dependent meta 52.1 7.2 0.00016 33.4 1.1 38 235-277 114-151 (156)
110 PF01096 TFIIS_C: Transcriptio 49.9 2.7 6E-05 27.4 -1.4 11 267-277 29-39 (39)
111 PF10013 DUF2256: Uncharacteri 49.9 8.6 0.00019 25.8 1.0 16 240-255 10-25 (42)
112 COG4888 Uncharacterized Zn rib 49.6 8.4 0.00018 30.7 1.0 39 235-277 19-57 (104)
113 PF04959 ARS2: Arsenite-resist 49.4 3.6 7.9E-05 37.1 -1.2 27 235-261 74-100 (214)
114 smart00064 FYVE Protein presen 49.2 12 0.00025 26.8 1.7 10 240-249 12-21 (68)
115 PRK05978 hypothetical protein; 46.8 11 0.00024 32.1 1.4 32 239-279 34-65 (148)
116 PRK12380 hydrogenase nickel in 46.7 10 0.00022 30.5 1.2 27 236-274 68-94 (113)
117 PTZ00303 phosphatidylinositol 45.9 13 0.00029 39.6 2.1 30 26-55 166-200 (1374)
118 COG1773 Rubredoxin [Energy pro 45.9 13 0.00028 26.4 1.4 37 237-274 2-44 (55)
119 PF03604 DNA_RNApol_7kD: DNA d 45.4 18 0.00039 22.7 1.9 27 239-276 1-27 (32)
120 PF00301 Rubredoxin: Rubredoxi 45.3 11 0.00024 25.8 1.0 37 238-275 1-43 (47)
121 COG3677 Transposase and inacti 45.2 12 0.00025 31.1 1.3 17 235-251 50-66 (129)
122 PF07282 OrfB_Zn_ribbon: Putat 45.0 14 0.0003 26.6 1.5 13 264-276 44-56 (69)
123 PRK00464 nrdR transcriptional 44.6 12 0.00027 32.0 1.4 16 239-254 29-44 (154)
124 TIGR00100 hypA hydrogenase nic 44.4 11 0.00025 30.3 1.1 28 236-275 68-95 (115)
125 PF07295 DUF1451: Protein of u 44.1 14 0.0003 31.4 1.6 36 234-279 108-144 (146)
126 cd00730 rubredoxin Rubredoxin; 42.4 17 0.00036 25.2 1.5 36 238-274 1-42 (50)
127 PF13878 zf-C2H2_3: zinc-finge 41.9 16 0.00036 24.0 1.4 24 239-262 14-39 (41)
128 PHA02998 RNA polymerase subuni 41.7 11 0.00024 33.1 0.6 12 267-278 172-183 (195)
129 PRK00564 hypA hydrogenase nick 41.6 14 0.0003 30.0 1.2 29 236-275 69-97 (117)
130 TIGR02300 FYDLN_acid conserved 41.2 23 0.0005 29.4 2.4 35 213-255 9-43 (129)
131 PF13240 zinc_ribbon_2: zinc-r 40.4 17 0.00037 21.0 1.1 7 269-275 16-22 (23)
132 PRK03681 hypA hydrogenase nick 40.2 13 0.00029 29.9 0.9 30 235-275 67-96 (114)
133 PF04959 ARS2: Arsenite-resist 40.0 9.4 0.0002 34.5 -0.0 23 263-285 74-96 (214)
134 PF14446 Prok-RING_1: Prokaryo 39.4 14 0.00031 26.1 0.8 12 240-251 7-18 (54)
135 PRK04860 hypothetical protein; 38.0 7.5 0.00016 33.5 -1.0 39 213-252 119-157 (160)
136 PRK14873 primosome assembly pr 37.9 17 0.00037 38.1 1.5 21 254-275 411-431 (665)
137 PRK05580 primosome assembly pr 37.6 20 0.00044 37.6 2.0 25 251-275 406-430 (679)
138 smart00734 ZnF_Rad18 Rad18-lik 37.5 21 0.00045 21.2 1.2 19 240-259 3-21 (26)
139 TIGR00595 priA primosomal prot 36.9 19 0.0004 36.4 1.5 22 253-274 240-261 (505)
140 COG3677 Transposase and inacti 36.9 24 0.00053 29.2 2.0 36 239-279 31-66 (129)
141 PF12013 DUF3505: Protein of u 36.4 19 0.00041 28.4 1.2 25 239-263 81-109 (109)
142 KOG2482|consensus 35.4 19 0.00042 34.8 1.3 24 237-260 194-217 (423)
143 PF04810 zf-Sec23_Sec24: Sec23 35.4 16 0.00036 23.8 0.6 32 238-275 2-33 (40)
144 cd00924 Cyt_c_Oxidase_Vb Cytoc 35.3 14 0.00031 29.1 0.4 21 256-277 70-90 (97)
145 PLN02294 cytochrome c oxidase 35.2 14 0.00031 32.1 0.4 13 237-249 140-152 (174)
146 KOG1146|consensus 34.9 16 0.00034 41.0 0.6 52 234-286 1280-1348(1406)
147 PF01927 Mut7-C: Mut7-C RNAse 34.7 24 0.00052 29.5 1.6 20 237-256 123-142 (147)
148 PF13824 zf-Mss51: Zinc-finger 34.5 29 0.00063 24.7 1.7 14 235-248 11-24 (55)
149 smart00731 SprT SprT homologue 34.3 17 0.00037 30.3 0.7 35 236-277 110-144 (146)
150 PF11494 Ta0938: Ta0938; Inte 34.1 25 0.00054 27.9 1.5 39 234-278 10-49 (105)
151 PRK14873 primosome assembly pr 33.9 19 0.00041 37.8 1.0 41 234-275 378-419 (665)
152 COG1779 C4-type Zn-finger prot 33.5 15 0.00032 32.9 0.1 37 239-277 15-54 (201)
153 PRK04351 hypothetical protein; 33.4 21 0.00045 30.3 1.0 37 236-280 110-146 (149)
154 PF14311 DUF4379: Domain of un 33.3 27 0.00059 24.1 1.5 28 238-272 28-55 (55)
155 KOG3408|consensus 33.2 18 0.00039 29.8 0.6 27 234-260 53-79 (129)
156 PRK05452 anaerobic nitric oxid 32.6 35 0.00075 34.3 2.6 43 231-274 418-466 (479)
157 COG1675 TFA1 Transcription ini 32.6 22 0.00049 31.1 1.1 33 235-276 110-142 (176)
158 KOG2907|consensus 32.4 25 0.00053 28.7 1.2 40 237-278 73-114 (116)
159 KOG4173|consensus 32.2 9.2 0.0002 34.4 -1.3 48 239-286 107-166 (253)
160 PF01155 HypA: Hydrogenase exp 32.0 20 0.00043 28.8 0.6 28 236-275 68-95 (113)
161 PF15269 zf-C2H2_7: Zinc-finge 31.9 59 0.0013 22.3 2.8 25 236-260 18-42 (54)
162 PF14379 Myb_CC_LHEQLE: MYB-CC 31.3 1.1E+02 0.0023 21.4 4.1 29 34-63 13-42 (51)
163 PF11672 DUF3268: Protein of u 31.0 31 0.00068 27.5 1.6 11 237-247 1-11 (102)
164 COG0068 HypF Hydrogenase matur 30.9 15 0.00032 38.7 -0.3 58 214-277 124-184 (750)
165 KOG0782|consensus 30.9 19 0.00041 37.1 0.5 30 251-280 238-267 (1004)
166 PF08274 PhnA_Zn_Ribbon: PhnA 30.9 22 0.00047 22.1 0.5 25 240-275 4-28 (30)
167 PF08271 TF_Zn_Ribbon: TFIIB z 30.2 26 0.00056 23.0 0.9 28 239-275 1-28 (43)
168 COG1594 RPB9 DNA-directed RNA 30.0 21 0.00045 28.9 0.4 38 238-277 72-111 (113)
169 PRK04023 DNA polymerase II lar 30.0 46 0.00099 36.7 3.1 10 265-274 662-671 (1121)
170 PRK01343 zinc-binding protein; 29.9 43 0.00094 23.9 2.0 12 238-249 9-20 (57)
171 PF10276 zf-CHCC: Zinc-finger 29.8 18 0.0004 23.9 0.1 11 238-248 29-39 (40)
172 TIGR01385 TFSII transcription 29.7 22 0.00048 33.7 0.6 37 237-277 257-297 (299)
173 PRK00762 hypA hydrogenase nick 29.7 26 0.00056 28.7 1.0 32 236-274 68-100 (124)
174 PF07975 C1_4: TFIIH C1-like d 29.4 26 0.00056 24.5 0.8 32 236-273 19-50 (51)
175 PF08684 ocr: DNA mimic ocr; 28.9 71 0.0015 25.1 3.2 31 17-47 62-92 (101)
176 COG1656 Uncharacterized conser 28.6 43 0.00094 29.0 2.2 23 237-259 129-151 (165)
177 PF13453 zf-TFIIB: Transcripti 28.4 25 0.00054 22.9 0.5 21 263-283 16-36 (41)
178 PRK00432 30S ribosomal protein 28.2 34 0.00073 23.6 1.2 26 240-276 22-47 (50)
179 KOG1842|consensus 28.0 16 0.00035 36.4 -0.6 22 241-274 183-204 (505)
180 PF01286 XPA_N: XPA protein N- 27.3 29 0.00063 22.2 0.7 26 239-274 4-29 (34)
181 TIGR00622 ssl1 transcription f 26.8 1E+02 0.0023 25.0 4.0 33 235-273 78-110 (112)
182 smart00661 RPOL9 RNA polymeras 26.6 40 0.00087 22.6 1.4 10 267-276 21-30 (52)
183 COG0675 Transposase and inacti 26.6 33 0.00072 31.3 1.3 13 264-276 320-332 (364)
184 smart00154 ZnF_AN1 AN1-like Zi 26.6 32 0.00069 22.4 0.8 14 266-279 12-25 (39)
185 PF01927 Mut7-C: Mut7-C RNAse 25.8 49 0.0011 27.6 2.0 21 264-284 122-142 (147)
186 PF08790 zf-LYAR: LYAR-type C2 25.7 28 0.00062 21.3 0.4 20 239-259 1-20 (28)
187 TIGR00595 priA primosomal prot 24.8 36 0.00078 34.4 1.2 38 239-277 214-251 (505)
188 COG1439 Predicted nucleic acid 24.7 35 0.00075 30.0 0.9 27 236-276 137-163 (177)
189 PF10083 DUF2321: Uncharacteri 24.7 36 0.00077 29.3 1.0 15 264-278 66-80 (158)
190 PRK11032 hypothetical protein; 24.5 43 0.00094 28.9 1.5 35 235-279 121-156 (160)
191 PF09845 DUF2072: Zn-ribbon co 24.3 35 0.00077 28.5 0.8 15 238-252 1-15 (131)
192 PRK03564 formate dehydrogenase 24.1 63 0.0014 30.8 2.6 18 23-40 25-42 (309)
193 PF04641 Rtf2: Rtf2 RING-finge 24.1 36 0.00078 31.3 1.0 15 266-280 150-164 (260)
194 COG4391 Uncharacterized protei 23.9 50 0.0011 24.0 1.5 42 232-277 18-59 (62)
195 PF05290 Baculo_IE-1: Baculovi 23.9 63 0.0014 27.2 2.3 14 268-281 123-136 (140)
196 PF10071 DUF2310: Zn-ribbon-co 23.9 42 0.00091 31.2 1.3 30 237-273 219-248 (258)
197 PF04216 FdhE: Protein involve 23.7 15 0.00033 34.1 -1.6 39 23-62 8-46 (290)
198 COG3464 Transposase and inacti 23.7 43 0.00094 32.9 1.5 40 239-279 39-90 (402)
199 PF03811 Zn_Tnp_IS1: InsA N-te 23.7 43 0.00093 21.6 1.0 30 239-272 6-35 (36)
200 PF01428 zf-AN1: AN1-like Zinc 23.5 26 0.00056 23.1 -0.1 16 265-280 12-27 (43)
201 TIGR00627 tfb4 transcription f 23.3 55 0.0012 30.7 2.0 25 238-276 255-279 (279)
202 PRK14892 putative transcriptio 23.3 74 0.0016 25.2 2.5 36 236-278 19-54 (99)
203 PF10571 UPF0547: Uncharacteri 23.2 44 0.00095 19.9 0.9 11 239-249 15-25 (26)
204 PF07754 DUF1610: Domain of un 23.1 38 0.00083 20.0 0.6 8 238-245 16-23 (24)
205 PF04606 Ogr_Delta: Ogr/Delta- 23.0 27 0.00059 23.5 -0.1 38 240-279 1-40 (47)
206 COG5216 Uncharacterized conser 22.8 42 0.00091 24.3 0.9 31 238-274 22-52 (67)
207 PF09332 Mcm10: Mcm10 replicat 22.8 18 0.00039 35.0 -1.3 40 238-277 252-296 (344)
208 KOG1280|consensus 22.2 61 0.0013 31.4 2.1 37 237-273 78-116 (381)
209 PLN03238 probable histone acet 22.1 57 0.0012 30.8 1.8 26 236-261 46-71 (290)
210 COG4306 Uncharacterized protei 22.1 52 0.0011 27.4 1.4 15 264-278 66-80 (160)
211 COG1198 PriA Primosomal protei 22.0 46 0.001 35.4 1.4 36 239-275 436-471 (730)
212 PRK03564 formate dehydrogenase 21.9 56 0.0012 31.1 1.8 14 265-278 251-264 (309)
213 COG2331 Uncharacterized protei 21.7 18 0.00039 27.5 -1.2 34 237-277 11-44 (82)
214 cd01410 SIRT7 SIRT7: Eukaryoti 21.7 90 0.0019 27.6 3.0 43 230-275 87-129 (206)
215 KOG2231|consensus 21.6 41 0.00088 35.4 0.9 29 240-272 117-146 (669)
216 PF15296 Codanin-1_C: Codanin- 21.3 1.6E+02 0.0035 24.2 4.2 54 26-79 58-118 (121)
217 KOG2071|consensus 21.0 44 0.00095 34.5 0.9 23 264-286 416-438 (579)
218 PRK14559 putative protein seri 21.0 81 0.0018 33.1 2.9 10 268-277 43-52 (645)
219 PRK00420 hypothetical protein; 20.7 66 0.0014 26.1 1.7 10 267-276 41-50 (112)
220 PLN02748 tRNA dimethylallyltra 20.5 54 0.0012 33.0 1.4 25 236-260 416-441 (468)
221 KOG2231|consensus 20.4 45 0.00098 35.0 0.9 23 239-261 183-205 (669)
222 PF04423 Rad50_zn_hook: Rad50 20.3 36 0.00077 23.5 0.1 11 268-278 22-32 (54)
223 KOG0402|consensus 20.3 34 0.00073 26.5 -0.0 31 238-278 36-66 (92)
224 KOG4124|consensus 20.3 55 0.0012 31.9 1.4 25 235-259 395-419 (442)
225 KOG3362|consensus 20.1 64 0.0014 27.5 1.6 20 266-285 129-148 (156)
No 1
>KOG2462|consensus
Probab=99.52 E-value=3.7e-15 Score=135.60 Aligned_cols=75 Identities=31% Similarity=0.553 Sum_probs=55.1
Q ss_pred cccccCCCCCCCCCCCCCcccCCCCC-CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 212 KTIVTDSISKPVQKSTPVASTARPKK-QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 212 ~~~~~~~~~k~~~~~~~~~~~~~~~k-~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
+...|..|.|.+......+.+.+.-. +++|.+|||.|.+.+-|+.|+|+|||||||.|..|+|+|..+++|+.||
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH
Confidence 34456666666666555555544433 7888888888888888888888888888888888888888888888775
No 2
>KOG2462|consensus
Probab=99.39 E-value=1.1e-13 Score=126.11 Aligned_cols=74 Identities=26% Similarity=0.446 Sum_probs=67.8
Q ss_pred ccccCCCCCCCCCC---CCCcccCCCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 213 TIVTDSISKPVQKS---TPVASTARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 213 ~~~~~~~~k~~~~~---~~~~~~~~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
...|..|+|.|.+. ..+.+.|.|+|||.|+.|+|.|..+++|+.||++|.+.|+|+|..|+|.|.+++.|.+|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhh
Confidence 45577888888854 778888999999999999999999999999999999999999999999999999999983
No 3
>KOG3623|consensus
Probab=99.31 E-value=2.6e-13 Score=136.08 Aligned_cols=79 Identities=27% Similarity=0.547 Sum_probs=71.1
Q ss_pred CCCccccccCCCCCCCCCCCCCccc---CCCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhh
Q psy6673 208 STPTKTIVTDSISKPVQKSTPVAST---ARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRD 284 (286)
Q Consensus 208 s~~~~~~~~~~~~k~~~~~~~~~~~---~~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~ 284 (286)
.++...+.|+.|.|.|.+.+..+++ |.|++||+|.+|.|.|+++.+|..|+|-|.|||||+|+.|+|+|+..+....
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQ 968 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQ 968 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHh
Confidence 3455567899999999888766655 7899999999999999999999999999999999999999999999999998
Q ss_pred cC
Q psy6673 285 HR 286 (286)
Q Consensus 285 H~ 286 (286)
||
T Consensus 969 HM 970 (1007)
T KOG3623|consen 969 HM 970 (1007)
T ss_pred hh
Confidence 87
No 4
>KOG3623|consensus
Probab=99.04 E-value=6.3e-11 Score=119.27 Aligned_cols=52 Identities=29% Similarity=0.627 Sum_probs=49.4
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
.-+.|+|..|||.|+.+.+|+.|+|+|.|||||.|+-|+|+|+..+....||
T Consensus 278 ~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 278 LLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred hhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccc
Confidence 4577999999999999999999999999999999999999999999998886
No 5
>PHA02768 hypothetical protein; Provisional
Probab=99.01 E-value=1.2e-10 Score=82.27 Aligned_cols=44 Identities=18% Similarity=0.431 Sum_probs=41.2
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhh
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLR 283 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~ 283 (286)
-|.|+.|||.|.+..+|.+|+++|+ +||+|..|+|.|.+.+.|.
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 3899999999999999999999998 8999999999999988775
No 6
>KOG3576|consensus
Probab=98.94 E-value=3.9e-11 Score=105.39 Aligned_cols=76 Identities=29% Similarity=0.606 Sum_probs=63.5
Q ss_pred CccccccCCCCCCCCCCCCC---cccCCCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhc
Q psy6673 210 PTKTIVTDSISKPVQKSTPV---ASTARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 210 ~~~~~~~~~~~k~~~~~~~~---~~~~~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H 285 (286)
....+.|..|.|.+.-.+-. ..-+..-+.|-|..|||.|.....|++|+|+|+|.|||+|..|+|+|.++..|..|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 34567788888887654332 23345668899999999999999999999999999999999999999999888776
No 7
>KOG1074|consensus
Probab=98.90 E-value=4.1e-10 Score=114.98 Aligned_cols=50 Identities=36% Similarity=0.758 Sum_probs=48.5
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
.|-+|-+|-+..+.++.|+.|.|+|+|||||+|.+|||+|.++++|+.||
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~ 653 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM 653 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc
Confidence 46899999999999999999999999999999999999999999999997
No 8
>KOG1074|consensus
Probab=98.89 E-value=4.2e-10 Score=114.94 Aligned_cols=50 Identities=40% Similarity=0.850 Sum_probs=47.9
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H 285 (286)
..+++|.+|+|.|...+.|++|.|.|||+|||+|.+||.+|.++++|+.|
T Consensus 351 ~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH 400 (958)
T KOG1074|consen 351 FFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVH 400 (958)
T ss_pred cccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeee
Confidence 45689999999999999999999999999999999999999999999988
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=98.68 E-value=6.1e-09 Score=62.85 Aligned_cols=26 Identities=54% Similarity=0.997 Sum_probs=24.1
Q ss_pred hhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 253 NLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 253 ~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
+|.+|+++|+|+|||.|+.|+++|.+
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 58899999999999999999999974
No 10
>PHA00733 hypothetical protein
Probab=98.54 E-value=4.5e-08 Score=81.14 Aligned_cols=51 Identities=33% Similarity=0.638 Sum_probs=46.8
Q ss_pred CCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 234 RPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 234 ~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
.+.++|.|+.||+.|.....|..|++.| .++|.|..|++.|.+...|.+|+
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 46899999999999999999985
No 11
>KOG3576|consensus
Probab=98.30 E-value=3.6e-07 Score=80.71 Aligned_cols=52 Identities=29% Similarity=0.600 Sum_probs=49.0
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
....|.|.+|+|.|....-|.+|++.|...|.|.|..|||+|...-+|++|+
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 4567999999999999999999999999999999999999999999999995
No 12
>PHA00616 hypothetical protein
Probab=98.22 E-value=1.9e-07 Score=63.18 Aligned_cols=40 Identities=18% Similarity=0.307 Sum_probs=35.6
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
||+|+.||+.|..+..|.+|++.|+|++||.|+.---.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f~ 40 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFYIYFR 40 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEEEEEEE
Confidence 6899999999999999999999999999999986544444
No 13
>PHA00732 hypothetical protein
Probab=98.16 E-value=1.1e-06 Score=66.93 Aligned_cols=42 Identities=40% Similarity=0.785 Sum_probs=36.1
Q ss_pred CccCCCCCcccCCchhhhhhhhh-cCCCCccccCCCCCcccCchhhhhc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERT-HTDERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~-HtgeKPf~C~~CgK~F~~~~~L~~H 285 (286)
||.|..||+.|.....|+.|++. |. ++.|+.||+.|.+ +..|
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=98.07 E-value=4.6e-06 Score=77.93 Aligned_cols=52 Identities=29% Similarity=0.782 Sum_probs=45.4
Q ss_pred CCCCccCCC--CCcccCCchhhhhhhhh-c------------------CCCCccccCCCCCcccCchhhhhcC
Q psy6673 235 PKKQFICRF--CSRHFTKSYNLLIHERT-H------------------TDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 235 ~~k~~~C~~--Cgk~F~~~~~L~~H~r~-H------------------tgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
..|||+|++ |.|.|+....|+.|+.- | ...|||+|++|+|+|+-...|+.|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 359999998 99999999999999863 4 1149999999999999999999986
No 15
>KOG3993|consensus
Probab=98.01 E-value=1.3e-06 Score=84.12 Aligned_cols=48 Identities=40% Similarity=0.753 Sum_probs=42.9
Q ss_pred ccCCCCCcccCCchhhhhhhhhcC--------CCC-------------------------ccccCCCCCcccCchhhhhc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHT--------DER-------------------------PYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~Ht--------geK-------------------------Pf~C~~CgK~F~~~~~L~~H 285 (286)
|+|+.|+|.|+...+|..|+|+|. |.. -|.|..|+|.|+++..|+.|
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 38899999999999999999
Q ss_pred C
Q psy6673 286 R 286 (286)
Q Consensus 286 ~ 286 (286)
+
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=97.42 E-value=4.6e-05 Score=43.94 Aligned_cols=23 Identities=35% Similarity=0.777 Sum_probs=19.9
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
|.|+.|++.|..+..|+.|++.|
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 67999999999999999998865
No 17
>KOG3608|consensus
Probab=97.40 E-value=7.3e-05 Score=70.99 Aligned_cols=49 Identities=27% Similarity=0.689 Sum_probs=43.3
Q ss_pred CCccCCCCCcccCCchhhhhhhhh-cCCCCccccCCCCCcccCchhhhhc
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERT-HTDERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~-HtgeKPf~C~~CgK~F~~~~~L~~H 285 (286)
..|+|+.|..+....+.|.+|+|. |...|||+|+.|.+.|.+...|.+|
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 458888888888888999999885 8889999999999999999999888
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.34 E-value=8.5e-05 Score=75.10 Aligned_cols=63 Identities=11% Similarity=0.346 Sum_probs=38.6
Q ss_pred cccccCCCCCCCCCCCCCcccCC-CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 212 KTIVTDSISKPVQKSTPVASTAR-PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 212 ~~~~~~~~~k~~~~~~~~~~~~~-~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
.+..|..|++.+... ....|.. -.+++.|+ ||+.| .+..|..|+++|.+.||+.|.+|++.|.
T Consensus 452 ~H~~C~~Cgk~f~~s-~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 452 NHVHCEKCGQAFQQG-EMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred cCccCCCCCCccchH-HHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 445566666655321 1111100 02667787 88655 4577888888888888888888888774
No 19
>PHA00733 hypothetical protein
Probab=97.32 E-value=5.9e-05 Score=62.50 Aligned_cols=53 Identities=21% Similarity=0.273 Sum_probs=42.5
Q ss_pred CCCCCccCCCCCcccCCchhhhhh--h---hhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 234 RPKKQFICRFCSRHFTKSYNLLIH--E---RTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 234 ~~~k~~~C~~Cgk~F~~~~~L~~H--~---r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
...+++.|.+|.+.|.....|..| + ..+.+.+||.|+.||+.|.....|..|+
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~ 93 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHI 93 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHH
Confidence 346789999999998887776655 1 1344589999999999999999999885
No 20
>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=97.30 E-value=0.00013 Score=51.24 Aligned_cols=46 Identities=28% Similarity=0.696 Sum_probs=35.5
Q ss_pred CccCCCCCcccCCchhhhhhhhh-cCCC-CccccCCCCCcccCchhhhhcC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERT-HTDE-RPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~-Htge-KPf~C~~CgK~F~~~~~L~~H~ 286 (286)
.|.||+|++.|. ...|..|... |.++ +.+.|++|...+. .+|.+|+
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHL 49 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHH
Confidence 489999999655 5689999664 6654 5799999998755 3777774
No 21
>PRK04860 hypothetical protein; Provisional
Probab=97.23 E-value=0.00014 Score=62.55 Aligned_cols=41 Identities=20% Similarity=0.521 Sum_probs=36.5
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchh
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDH 281 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~ 281 (286)
.+|.|. |++ ....+++|.++|+|+++|.|..|++.|.....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEecc
Confidence 579998 998 77889999999999999999999999986543
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.06 E-value=0.0003 Score=71.25 Aligned_cols=54 Identities=22% Similarity=0.509 Sum_probs=44.2
Q ss_pred cccCCCCCCccCCCCCcccCC----------chhhhhhhhhcCCCCccccCCCCCcccCchhhhhc
Q psy6673 230 ASTARPKKQFICRFCSRHFTK----------SYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 230 ~~~~~~~k~~~C~~Cgk~F~~----------~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H 285 (286)
...+-+.+++.|.+|++.|.. ...|..|..++ |.+++.|..||+.|+.++ |..|
T Consensus 496 ~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlrd-m~~H 559 (567)
T PLN03086 496 QASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLKE-MDIH 559 (567)
T ss_pred hhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeehh-HHHH
Confidence 334567899999999999952 35799999997 999999999999998774 5555
No 23
>KOG3608|consensus
Probab=96.90 E-value=0.00033 Score=66.60 Aligned_cols=49 Identities=35% Similarity=0.778 Sum_probs=42.7
Q ss_pred CCccCCC--CCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhc
Q psy6673 237 KQFICRF--CSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 237 k~~~C~~--Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H 285 (286)
..+.|.+ |.+.|..++.|++|.|+|+++|...|+.||.-|+++..|..|
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 3467765 999999999999999999999999999999999998888766
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=39.23 Aligned_cols=23 Identities=39% Similarity=0.785 Sum_probs=18.5
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
|.|++|++.|.....|+.|+++|
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
>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=96.74 E-value=0.0011 Score=46.13 Aligned_cols=36 Identities=22% Similarity=0.390 Sum_probs=26.1
Q ss_pred ccCCCCCCccCCCCCcccCCchhhhhhhhhcCCCCc
Q psy6673 231 STARPKKQFICRFCSRHFTKSYNLLIHERTHTDERP 266 (286)
Q Consensus 231 ~~~~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKP 266 (286)
.......|..|++|+..+....+|++|+..+++.||
T Consensus 17 ~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 17 SKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred HhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 344567889999999999999999999998888887
No 26
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.61 E-value=0.0005 Score=52.68 Aligned_cols=47 Identities=32% Similarity=0.780 Sum_probs=18.5
Q ss_pred cCCCCCcccCCchhhhhhhhhcCC-----------------------CCccccCCCCCcccCchhhhhcC
Q psy6673 240 ICRFCSRHFTKSYNLLIHERTHTD-----------------------ERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~~H~r~Htg-----------------------eKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
+|.+|+..|.....|..|+....+ ...|.|..|++.|.....|..||
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 488888888888888888864322 13588999999999999999885
No 27
>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=96.60 E-value=0.00091 Score=39.93 Aligned_cols=25 Identities=32% Similarity=0.640 Sum_probs=22.5
Q ss_pred CccCCCCCcccCCchhhhhhhhhcC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHT 262 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~Ht 262 (286)
+|.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5899999999999999999998874
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.55 E-value=0.00041 Score=39.86 Aligned_cols=20 Identities=35% Similarity=0.974 Sum_probs=18.9
Q ss_pred cccCCCCCcccCchhhhhcC
Q psy6673 267 YSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 267 f~C~~CgK~F~~~~~L~~H~ 286 (286)
|.|+.|++.|.++..|++||
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 78999999999999999995
No 29
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.20 E-value=0.0027 Score=36.40 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=21.4
Q ss_pred ccCCCCCcccCCchhhhhhhhhcC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHT 262 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~Ht 262 (286)
|.|..|++.|.....|..|++.|.
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
>PHA02768 hypothetical protein; Provisional
Probab=96.09 E-value=0.0016 Score=46.20 Aligned_cols=21 Identities=19% Similarity=0.698 Sum_probs=19.7
Q ss_pred ccccCCCCCcccCchhhhhcC
Q psy6673 266 PYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 266 Pf~C~~CgK~F~~~~~L~~H~ 286 (286)
-|.|+.|||.|.+.++|.+||
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~ 25 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHL 25 (55)
T ss_pred ccCcchhCCeeccHHHHHHHH
Confidence 489999999999999999996
No 31
>PHA00616 hypothetical protein
Probab=95.90 E-value=0.0013 Score=44.55 Aligned_cols=21 Identities=29% Similarity=0.695 Sum_probs=19.7
Q ss_pred ccccCCCCCcccCchhhhhcC
Q psy6673 266 PYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 266 Pf~C~~CgK~F~~~~~L~~H~ 286 (286)
||+|..||+.|..+..|.+|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH
Confidence 799999999999999999984
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=95.70 E-value=0.0023 Score=36.36 Aligned_cols=20 Identities=40% Similarity=1.052 Sum_probs=16.7
Q ss_pred cccCCCCCcccCchhhhhcC
Q psy6673 267 YSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 267 f~C~~CgK~F~~~~~L~~H~ 286 (286)
|.|++|++.|.....|+.|+
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 78999999999999999985
No 33
>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=95.51 E-value=0.0025 Score=38.17 Aligned_cols=20 Identities=25% Similarity=0.771 Sum_probs=16.9
Q ss_pred ccCCCCCCccCCCCCcccCC
Q psy6673 231 STARPKKQFICRFCSRHFTK 250 (286)
Q Consensus 231 ~~~~~~k~~~C~~Cgk~F~~ 250 (286)
..+.+++||.|++|++.|..
T Consensus 7 ~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 7 RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHSSSSSEEESSSSEEESS
T ss_pred hhcCCCCCCCCCCCcCeeCc
Confidence 34678999999999999963
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=95.47 E-value=0.0029 Score=37.73 Aligned_cols=21 Identities=43% Similarity=1.073 Sum_probs=19.6
Q ss_pred ccccCCCCCcccCchhhhhcC
Q psy6673 266 PYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 266 Pf~C~~CgK~F~~~~~L~~H~ 286 (286)
||.|..|++.|.....|..||
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 799999999999999999885
No 35
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.42 E-value=0.0083 Score=56.25 Aligned_cols=50 Identities=36% Similarity=0.715 Sum_probs=46.8
Q ss_pred CCccCCCCCcccCCchhhhhhhh--hcCCC--CccccC--CCCCcccCchhhhhcC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHER--THTDE--RPYSCD--VCNKAFRRQDHLRDHR 286 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r--~Htge--KPf~C~--~CgK~F~~~~~L~~H~ 286 (286)
.++.|..|.+.|.....|.+|.+ .|+++ +||.|. .|++.|.+.+.+.+|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc
Confidence 47999999999999999999999 89999 999999 7999999999888873
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.44 E-value=0.015 Score=33.87 Aligned_cols=23 Identities=30% Similarity=0.748 Sum_probs=19.8
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
|.|.+|++.|.....++.|++.+
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 67999999999999999998764
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.21 E-value=0.014 Score=33.25 Aligned_cols=20 Identities=35% Similarity=0.934 Sum_probs=18.3
Q ss_pred cccCCCCCcccCchhhhhcC
Q psy6673 267 YSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 267 f~C~~CgK~F~~~~~L~~H~ 286 (286)
|.|..|++.|.....|..|+
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCCCcchhCCHHHHHHHH
Confidence 68999999999999999885
No 38
>KOG3993|consensus
Probab=94.07 E-value=0.0098 Score=57.95 Aligned_cols=49 Identities=27% Similarity=0.698 Sum_probs=43.5
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
-|.|..|.-.|.....|.+|+....-..-|+|+.|+|.|....+|..||
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHR 315 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHR 315 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhh
Confidence 3999999999999999999987655557799999999999999998885
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=93.97 E-value=0.026 Score=33.79 Aligned_cols=22 Identities=27% Similarity=0.667 Sum_probs=18.0
Q ss_pred ccCCCCCcccCCchhhhhhhhh
Q psy6673 239 FICRFCSRHFTKSYNLLIHERT 260 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~ 260 (286)
|.|..|++.|.....+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788888888888888888764
No 40
>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=93.00 E-value=0.026 Score=39.46 Aligned_cols=26 Identities=31% Similarity=0.747 Sum_probs=18.4
Q ss_pred cCCCCccccCCCCCcccCchhhhhcC
Q psy6673 261 HTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 261 HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
+..+.|..|++|+..+++.-+|++|+
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 34678999999999999999999995
No 41
>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=92.86 E-value=0.06 Score=32.16 Aligned_cols=20 Identities=35% Similarity=0.963 Sum_probs=18.8
Q ss_pred cccCCCCCcccCchhhhhcC
Q psy6673 267 YSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 267 f~C~~CgK~F~~~~~L~~H~ 286 (286)
|.|..|++.|.....|..|+
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 78999999999999999996
No 42
>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=92.16 E-value=0.083 Score=42.61 Aligned_cols=30 Identities=30% Similarity=0.763 Sum_probs=22.2
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
..|+.||+.| +.|. ..|-.|+.||..|.-.
T Consensus 10 R~Cp~CG~kF---YDLn--------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKF---YDLN--------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchh---ccCC--------CCCccCCCCCCccCcc
Confidence 5888888888 5553 4688888888877544
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.59 E-value=0.069 Score=30.83 Aligned_cols=23 Identities=30% Similarity=0.543 Sum_probs=17.6
Q ss_pred ccCCCCCcccCCchhhhhhhhhcC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHT 262 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~Ht 262 (286)
|.|+.|..... ...|..|++.|.
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 889999998764
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=90.64 E-value=0.16 Score=32.07 Aligned_cols=24 Identities=25% Similarity=0.890 Sum_probs=19.1
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
|+|.+||..+.-.. .|+.|+.||.
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=90.42 E-value=0.057 Score=31.35 Aligned_cols=20 Identities=45% Similarity=1.095 Sum_probs=18.2
Q ss_pred cccCCCCCcccCchhhhhcC
Q psy6673 267 YSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 267 f~C~~CgK~F~~~~~L~~H~ 286 (286)
|.|.+|.+.|.....|+.|+
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 68999999999999999884
No 46
>PHA00732 hypothetical protein
Probab=90.41 E-value=0.11 Score=39.45 Aligned_cols=46 Identities=15% Similarity=0.176 Sum_probs=29.7
Q ss_pred ccCCCCCCCCCCCCCcccCC-CCCCccCCCCCcccCCchhhhhhhhhcCC
Q psy6673 215 VTDSISKPVQKSTPVASTAR-PKKQFICRFCSRHFTKSYNLLIHERTHTD 263 (286)
Q Consensus 215 ~~~~~~k~~~~~~~~~~~~~-~~k~~~C~~Cgk~F~~~~~L~~H~r~Htg 263 (286)
.|..|++.+........+.+ ...++.|+.||+.|. .+..|.+++.+
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---ChhhhhcccCC
Confidence 35666666655444333332 133578999999997 58899877643
No 47
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=89.72 E-value=0.23 Score=41.12 Aligned_cols=30 Identities=27% Similarity=0.470 Sum_probs=19.9
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
+.|+.||+.| +.|. ..|..|+.||..|...
T Consensus 10 r~Cp~cg~kF---YDLn--------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKF---YDLN--------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccc---cccC--------CCCccCCCcCCccCcc
Confidence 4777888777 4442 4677788888776443
No 48
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=88.51 E-value=0.27 Score=46.64 Aligned_cols=25 Identities=20% Similarity=0.615 Sum_probs=22.5
Q ss_pred CCCCccCCCCCcccCCchhhhhhhh
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHER 259 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r 259 (286)
..|||+|++|+|.|+....|+.|+.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 4599999999999999999999954
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=88.24 E-value=0.28 Score=29.09 Aligned_cols=21 Identities=33% Similarity=0.680 Sum_probs=16.2
Q ss_pred ccCCCCCcccCCchhhhhhhhh
Q psy6673 239 FICRFCSRHFTKSYNLLIHERT 260 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~ 260 (286)
..|+.||+.| ....|.+|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4789999999 56778888653
No 50
>KOG1146|consensus
Probab=88.20 E-value=0.17 Score=55.54 Aligned_cols=51 Identities=29% Similarity=0.596 Sum_probs=45.1
Q ss_pred CCCccCCCCCcccCCchhhhhhhhh-c------------------------CCCCccccCCCCCcccCchhhhhcC
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERT-H------------------------TDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~-H------------------------tgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
.+.|.|+.|+..|+....|..|||. | -+.+||.|..|...|..+.+|-+||
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 4779999999999999999999997 2 2248899999999999999998885
No 51
>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=88.18 E-value=0.27 Score=30.63 Aligned_cols=23 Identities=26% Similarity=0.652 Sum_probs=19.8
Q ss_pred CccCCCCCcccCCchhhhhhhhh
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERT 260 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~ 260 (286)
+|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999988888888764
No 52
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=86.14 E-value=0.43 Score=41.37 Aligned_cols=23 Identities=35% Similarity=0.973 Sum_probs=19.6
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN 273 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~Cg 273 (286)
.|.|++||. +|.|+-|.+|++||
T Consensus 134 ~~vC~vCGy-------------~~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGY-------------THEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCC-------------cccCCCCCcCCCCC
Confidence 699999984 35678899999999
No 53
>KOG4124|consensus
Probab=85.60 E-value=0.74 Score=44.26 Aligned_cols=52 Identities=29% Similarity=0.784 Sum_probs=41.4
Q ss_pred CCCCccCCC--CCcccCCchhhhhhhhh-c--------------C----CCCccccCCCCCcccCchhhhhcC
Q psy6673 235 PKKQFICRF--CSRHFTKSYNLLIHERT-H--------------T----DERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 235 ~~k~~~C~~--Cgk~F~~~~~L~~H~r~-H--------------t----geKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
..++|.|++ |.|.++....|+.|... | + ..|||+|++|.++++-...|+.|+
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 468899977 99999998888887543 3 2 258999999999998887777663
No 54
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=85.51 E-value=0.45 Score=36.03 Aligned_cols=24 Identities=29% Similarity=0.688 Sum_probs=21.5
Q ss_pred CccCCCCCcccCCchhhhhhhhhc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
.+.|.+|++.|.....|..|++.+
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 699999999999999999999975
No 55
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.11 E-value=0.39 Score=40.47 Aligned_cols=39 Identities=13% Similarity=0.420 Sum_probs=27.0
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
....|.|+.|++.|.....+.. .+. ..-|.|+.||....
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 4456999999999986554432 111 33399999997654
No 56
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=85.05 E-value=0.62 Score=43.54 Aligned_cols=52 Identities=33% Similarity=0.645 Sum_probs=43.0
Q ss_pred CCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCC--CCCcccCchhhhhc
Q psy6673 234 RPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDV--CNKAFRRQDHLRDH 285 (286)
Q Consensus 234 ~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~--CgK~F~~~~~L~~H 285 (286)
.....+.|+.|...|.......+|.+.|++++++.|.. |.+.|.+...+.+|
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (467)
T COG5048 29 NAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRH 82 (467)
T ss_pred cCCchhhcccccccccccchhhhhcccccccCCccccccccccccCCcchhhhh
Confidence 34567899999999999999999999999999999987 55666666555544
No 57
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=84.89 E-value=0.34 Score=30.16 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=18.4
Q ss_pred ccccCCCCCcccCchhhhhcC
Q psy6673 266 PYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 266 Pf~C~~CgK~F~~~~~L~~H~ 286 (286)
+|.|.+|++.|.....+..|+
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred CeEccccCCccCCHHHHHHHH
Confidence 689999999999888888774
No 58
>KOG2071|consensus
Probab=83.56 E-value=0.81 Score=46.63 Aligned_cols=27 Identities=22% Similarity=0.336 Sum_probs=23.2
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
...+..|..||++|........||..|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhh
Confidence 467799999999999998888887777
No 59
>PF14353 CpXC: CpXC protein
Probab=82.82 E-value=0.21 Score=40.89 Aligned_cols=17 Identities=29% Similarity=0.788 Sum_probs=10.1
Q ss_pred ccccCCCCCcccCchhh
Q psy6673 266 PYSCDVCNKAFRRQDHL 282 (286)
Q Consensus 266 Pf~C~~CgK~F~~~~~L 282 (286)
-|.|+.||+.|.-...+
T Consensus 38 ~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPL 54 (128)
T ss_pred EEECCCCCCceecCCCE
Confidence 36677777766544333
No 60
>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=82.26 E-value=0.84 Score=29.05 Aligned_cols=25 Identities=24% Similarity=0.748 Sum_probs=18.6
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
.|.|.+||..+.-. +.|..|+.||.
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 48999999665432 26789999985
No 61
>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=79.43 E-value=1.2 Score=28.52 Aligned_cols=34 Identities=18% Similarity=0.406 Sum_probs=24.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
+.|+.|+..|.-...... .....+.|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEEE
Confidence 579999999877754421 1223588999998875
No 62
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.64 E-value=0.53 Score=33.61 Aligned_cols=31 Identities=13% Similarity=0.279 Sum_probs=25.3
Q ss_pred CCCCCCccCCCCCcccCCchhhhhhhhhcCC
Q psy6673 233 ARPKKQFICRFCSRHFTKSYNLLIHERTHTD 263 (286)
Q Consensus 233 ~~~~k~~~C~~Cgk~F~~~~~L~~H~r~Htg 263 (286)
..++.-+.|+.||+.|.......+|...-+|
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3467778999999999999999999875333
No 63
>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=77.69 E-value=1 Score=38.57 Aligned_cols=35 Identities=20% Similarity=0.375 Sum_probs=27.8
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
...-|.|+.|+..|+....+. --|.|+.||.....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 445699999999998887774 36999999976543
No 64
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=77.60 E-value=1.2 Score=35.58 Aligned_cols=31 Identities=19% Similarity=0.525 Sum_probs=21.6
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCC-CcccC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN-KAFRR 278 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~Cg-K~F~~ 278 (286)
||+|..||..|..-+..-. -.|+.|| ..|.+
T Consensus 2 pH~CtrCG~vf~~g~~~il----------~GCp~CG~nkF~y 33 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEIL----------SGCPKCGCNKFLY 33 (112)
T ss_pred CceecccccccccccHHHH----------ccCccccchheEe
Confidence 6899999999988643321 2688887 45543
No 65
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=77.07 E-value=1.1 Score=33.63 Aligned_cols=38 Identities=26% Similarity=0.545 Sum_probs=18.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccC--CCCCcccC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCD--VCNKAFRR 278 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~--~CgK~F~~ 278 (286)
+.|+.||........-..+.. .-++-++|. .||.+|..
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCCEEEE
Confidence 356666654433322222211 334556666 66666643
No 66
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=76.85 E-value=1.2 Score=38.92 Aligned_cols=35 Identities=20% Similarity=0.483 Sum_probs=27.2
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
...-|.|+.|++.|+....+. --|.|+.||.....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 345699999999998887663 36999999976543
No 67
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.49 E-value=1.7 Score=33.76 Aligned_cols=34 Identities=24% Similarity=0.657 Sum_probs=24.1
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
...|.|+.|++.- +.|. +...|.|..||..|.-.
T Consensus 33 ~~~~~Cp~C~~~~--------VkR~--a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 33 RAKHVCPFCGRTT--------VKRI--ATGIWKCRKCGAKFAGG 66 (89)
T ss_pred hcCCcCCCCCCcc--------eeee--ccCeEEcCCCCCeeccc
Confidence 4569999998652 2222 34579999999998754
No 68
>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=76.45 E-value=1.2 Score=28.74 Aligned_cols=32 Identities=16% Similarity=0.472 Sum_probs=22.3
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 276 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F 276 (286)
-|+|+.||+.|....... . ...-.|+.||...
T Consensus 5 ~y~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS------D-DPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecC------C-CCCCCCCCCCCcc
Confidence 489999999887553331 1 4566899999743
No 69
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.35 E-value=1.4 Score=35.66 Aligned_cols=27 Identities=22% Similarity=0.370 Sum_probs=17.3
Q ss_pred cCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 240 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
.|+.||+.| +.|. ..|..|+.||+.|.
T Consensus 11 idPetg~KF---YDLN--------rdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKF---YDLN--------RDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchh---hccC--------CCccccCcccccch
Confidence 677777666 3332 46777777777773
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.13 E-value=1.2 Score=29.89 Aligned_cols=31 Identities=16% Similarity=0.331 Sum_probs=21.7
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
.|.|+.||..|...... ..+.|+.||..+..
T Consensus 3 ~y~C~~CG~~~~~~~~~----------~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVELDEYG----------TGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEEECCCC----------CceECCCCCCeEEE
Confidence 58999999887654221 16899999976543
No 71
>KOG4167|consensus
Probab=73.03 E-value=1.7 Score=45.43 Aligned_cols=28 Identities=36% Similarity=0.572 Sum_probs=24.6
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHT 262 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~Ht 262 (286)
...-|.|..|+|.|-.-..+..||++|.
T Consensus 789 ~~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 789 PTGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CCceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3566999999999999999999999984
No 72
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=72.59 E-value=1.1 Score=31.94 Aligned_cols=27 Identities=30% Similarity=0.580 Sum_probs=23.6
Q ss_pred hhcCCCCccccCCCCCcccCchhhhhc
Q psy6673 259 RTHTDERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 259 r~HtgeKPf~C~~CgK~F~~~~~L~~H 285 (286)
++..||.-+.|+.||.-|++..+..+|
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RH 36 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRH 36 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHH
Confidence 456789999999999999998888777
No 73
>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=72.22 E-value=1.7 Score=29.73 Aligned_cols=30 Identities=17% Similarity=0.554 Sum_probs=20.5
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
-|.|..||..|...... +. ..+-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 37999999988754222 11 35567999985
No 74
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.05 E-value=2.6 Score=27.12 Aligned_cols=34 Identities=18% Similarity=0.491 Sum_probs=24.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
..|+.|+..|.-..... -...+..+|..|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcEEECCCCCCEeC
Confidence 47889998888776542 12345678999988773
No 75
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=71.86 E-value=2.7 Score=27.13 Aligned_cols=34 Identities=26% Similarity=0.606 Sum_probs=24.4
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
..|+.|+..|.-...-. ..+.+..+|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~l-----~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKL-----PAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHc-----ccCCcEEECCCCCcEee
Confidence 37999999988775421 22356789999998875
No 76
>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=71.51 E-value=2.7 Score=29.13 Aligned_cols=26 Identities=31% Similarity=0.594 Sum_probs=20.3
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHT 262 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~Ht 262 (286)
..+.+.|++|...+. .+|.+|+..+.
T Consensus 28 ~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 28 ESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 456799999998765 48999988654
No 77
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=67.43 E-value=3.7 Score=27.67 Aligned_cols=26 Identities=23% Similarity=0.569 Sum_probs=19.8
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
|.|..||..|... ..-+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 7899999888754 2356889999854
No 78
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.78 E-value=4.1 Score=29.36 Aligned_cols=33 Identities=24% Similarity=0.674 Sum_probs=21.9
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
..|.|+.||+.--.+ ..+-..-..+|.|+.||.
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 459999999863222 222233358999999984
No 79
>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=66.38 E-value=3 Score=27.64 Aligned_cols=30 Identities=20% Similarity=0.670 Sum_probs=22.1
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
-|.|..||..|.....+ .. ..+-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 38999999999765433 22 46778999997
No 80
>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=65.72 E-value=2.7 Score=27.11 Aligned_cols=33 Identities=24% Similarity=0.558 Sum_probs=22.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
+.|+.||+.|..... ....+-.|+.||-.+.++
T Consensus 2 r~C~~Cg~~Yh~~~~--------pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN--------PPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETTTB----------SSTTBCTTTTEBEBEE
T ss_pred cCcCCCCCccccccC--------CCCCCCccCCCCCeeEeC
Confidence 579999998864332 235567899999766544
No 81
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=65.40 E-value=3.9 Score=27.91 Aligned_cols=25 Identities=32% Similarity=0.739 Sum_probs=19.6
Q ss_pred CccCCCCCcccCCc-----hhhhhhhh-hcC
Q psy6673 238 QFICRFCSRHFTKS-----YNLLIHER-THT 262 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~-----~~L~~H~r-~Ht 262 (286)
.-.|.+|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 35899999999776 58888887 553
No 82
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=65.02 E-value=3.1 Score=32.54 Aligned_cols=34 Identities=24% Similarity=0.658 Sum_probs=23.4
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
...|.|++||+.--.+ .+.-.|.|..|++.|.-.
T Consensus 34 ~a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKR----------QAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred hCCccCCCCCCCceee----------eeeEEEEcCCCCCEEeCC
Confidence 4569999998542221 133578999999988643
No 83
>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=64.46 E-value=3.8 Score=26.98 Aligned_cols=25 Identities=32% Similarity=0.576 Sum_probs=15.6
Q ss_pred CCCCccCCCCCcccCCc----hhhhhhhh
Q psy6673 235 PKKQFICRFCSRHFTKS----YNLLIHER 259 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~----~~L~~H~r 259 (286)
......|.+|++.+... ..|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 34557999999998875 67888883
No 84
>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=64.31 E-value=2.8 Score=35.03 Aligned_cols=27 Identities=37% Similarity=0.641 Sum_probs=17.3
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCc
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERP 266 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKP 266 (286)
..-.|-.|||.|+. |++|++.|.|.-|
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 44699999999964 5999999988655
No 85
>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=64.02 E-value=2.9 Score=32.69 Aligned_cols=34 Identities=24% Similarity=0.710 Sum_probs=23.2
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
...|.|++|++.--.+ .+.-.|.|..|++.|.-.
T Consensus 33 ~a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKR----------GSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred hcCccCCCCCCCceEE----------EeeEEEEcCCCCCEEeCC
Confidence 3569999998543221 133568999999988643
No 86
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.80 E-value=5.1 Score=28.93 Aligned_cols=34 Identities=21% Similarity=0.445 Sum_probs=22.9
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
...|.|+.||..--.+.. +...-..+|.|+.||.
T Consensus 25 ~v~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeeehhh-----hHHHcCCceECCCcCc
Confidence 345999999966554432 2222358999999983
No 87
>KOG2785|consensus
Probab=63.17 E-value=3.6 Score=39.98 Aligned_cols=48 Identities=23% Similarity=0.424 Sum_probs=40.2
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCC-----------------------CCccccCCCC---CcccCchhhhhcC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTD-----------------------ERPYSCDVCN---KAFRRQDHLRDHR 286 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~Htg-----------------------eKPf~C~~Cg---K~F~~~~~L~~H~ 286 (286)
-.|-+|++.|..-.....||..|+| .+-|.|-.|. +.|......+.||
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM 240 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHM 240 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHH
Confidence 5889999999998888899988766 2457788888 8999888888887
No 88
>KOG0978|consensus
Probab=62.02 E-value=3.7 Score=42.99 Aligned_cols=29 Identities=34% Similarity=0.509 Sum_probs=21.3
Q ss_pred hhhcCCCCccccCCCCCcccCchhhhhcC
Q psy6673 258 ERTHTDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 258 ~r~HtgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
++...+-|--+|+.|+.+|...+.++.|+
T Consensus 670 vq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 670 VQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred HHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 33344456668999999999988777664
No 89
>PRK12496 hypothetical protein; Provisional
Probab=61.55 E-value=4.3 Score=34.97 Aligned_cols=32 Identities=22% Similarity=0.758 Sum_probs=21.7
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
.+.|.|.-|++.|..... .-.|+.||....++
T Consensus 125 ~w~~~C~gC~~~~~~~~~------------~~~C~~CG~~~~r~ 156 (164)
T PRK12496 125 KWRKVCKGCKKKYPEDYP------------DDVCEICGSPVKRK 156 (164)
T ss_pred eeeEECCCCCccccCCCC------------CCcCCCCCChhhhc
Confidence 456899999999864311 12599999665444
No 90
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=61.00 E-value=5.4 Score=39.47 Aligned_cols=31 Identities=16% Similarity=0.543 Sum_probs=21.4
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
.-.|+.||.+...+ |..-|+|+.||.++...
T Consensus 350 ~p~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 350 NPVCPRCGGRMKSA-----------GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCCCccCCchhhc-----------CCCCcccccccccCCcc
Confidence 34788888665443 44478888888877654
No 91
>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=60.32 E-value=4.3 Score=29.22 Aligned_cols=28 Identities=21% Similarity=0.562 Sum_probs=13.3
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
-.|..|++.|... .+.+.|..||+.|-.
T Consensus 10 ~~C~~C~~~F~~~------------~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 10 SNCMICGKKFSLF------------RRRHHCRNCGRVVCS 37 (69)
T ss_dssp SB-TTT--B-BSS------------S-EEE-TTT--EEEC
T ss_pred CcCcCcCCcCCCc------------eeeEccCCCCCEECC
Confidence 4788899999531 355678888887743
No 92
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=59.81 E-value=4.9 Score=42.53 Aligned_cols=24 Identities=25% Similarity=0.335 Sum_probs=17.8
Q ss_pred hhhhhhhhhcCCCCccccCCCCCc
Q psy6673 252 YNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 252 ~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
..|+.|...|....|+.|+.||..
T Consensus 461 ~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 461 GQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CeeEeCCCCCCCCCCCCCCCCCCC
Confidence 346666666677889999999854
No 93
>PHA00626 hypothetical protein
Probab=59.74 E-value=5.1 Score=28.59 Aligned_cols=15 Identities=20% Similarity=0.587 Sum_probs=8.0
Q ss_pred CCccCCCCCcccCCc
Q psy6673 237 KQFICRFCSRHFTKS 251 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~ 251 (286)
..|.|+.||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 345565565555543
No 94
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=58.91 E-value=5.1 Score=33.65 Aligned_cols=25 Identities=32% Similarity=0.408 Sum_probs=22.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERP 266 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKP 266 (286)
..|-.|||.| .+|+||+.+|.|.-|
T Consensus 77 IicLEDGkkf---KSLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKF---KSLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcch---HHHHHHHhcccCCCH
Confidence 5899999999 579999999988766
No 95
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=58.89 E-value=4.8 Score=33.56 Aligned_cols=40 Identities=20% Similarity=0.392 Sum_probs=23.1
Q ss_pred CCCccCCCCCcccCCch---hh------hhhhhhcCCCCccccCCCCCc
Q psy6673 236 KKQFICRFCSRHFTKSY---NL------LIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~---~L------~~H~r~HtgeKPf~C~~CgK~ 275 (286)
+..+.|..||..|.... .| ..|..--....-+.|+.||..
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 35689999998887641 11 111111111345779999953
No 96
>KOG2593|consensus
Probab=58.74 E-value=4.8 Score=39.77 Aligned_cols=38 Identities=16% Similarity=0.547 Sum_probs=27.0
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
...-|.|+.|.+.|+....++.- --..--|.|..|+-.
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L~---~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQLL---DNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccchhhhHHHHhh---cccCceEEEecCCCc
Confidence 45669999999999887666532 222345999999853
No 97
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=58.59 E-value=4.1 Score=31.82 Aligned_cols=34 Identities=21% Similarity=0.573 Sum_probs=23.0
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
...|.|++|++.--.+ .+.-.|.|..|++.|.-.
T Consensus 34 ~a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 34 RAKHVCPVCGRPKVKR----------VGTGIWECRKCGAKFAGG 67 (90)
T ss_pred hcCccCCCCCCCceEE----------EEEEEEEcCCCCCEEeCC
Confidence 3569999997553222 123568999999988643
No 98
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=56.79 E-value=5.7 Score=27.58 Aligned_cols=29 Identities=21% Similarity=0.602 Sum_probs=20.1
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
..|.|..||+.|... .......|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCceeCCCCCcE
Confidence 358999999999211 12456789999853
No 99
>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=56.41 E-value=3.5 Score=32.21 Aligned_cols=33 Identities=30% Similarity=0.750 Sum_probs=21.4
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
..|.|++||+.--. |.-+ --|.|..|++.|.-.
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~--GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVAT--GIWKCKKCGKKFAGG 66 (90)
T ss_dssp S-BEESSSSSSEEE--------EEET--TEEEETTTTEEEE-B
T ss_pred CCCcCCCCCCceeE--------Eeee--EEeecCCCCCEEeCC
Confidence 56999999975422 2222 348999999988643
No 100
>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=55.71 E-value=4.1 Score=33.94 Aligned_cols=36 Identities=25% Similarity=0.736 Sum_probs=24.6
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
....|.|..|+..+.+ |.+. ..+.|.|..|+..|..
T Consensus 120 ~~~~~~C~~C~~~~~r------~~~~--~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKR------HRRS--KRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeee------eccc--chhhEECCCCCCEEEE
Confidence 3456899999977743 3333 2344899999977653
No 101
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=55.14 E-value=6.7 Score=30.74 Aligned_cols=28 Identities=21% Similarity=0.715 Sum_probs=20.7
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
+|-.|..||..|... -+ .+|-+|+.|.-
T Consensus 57 ~Pa~CkkCGfef~~~-~i---------k~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRDD-KI---------KKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCcccccc-cc---------CCcccCCcchh
Confidence 567999999988762 11 36889999853
No 102
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=54.54 E-value=5.5 Score=27.69 Aligned_cols=47 Identities=23% Similarity=0.516 Sum_probs=29.7
Q ss_pred CCccCCC--CCcccCCchhhhhhhhhcCCCCccccCC----CCCcccCchhhhhc
Q psy6673 237 KQFICRF--CSRHFTKSYNLLIHERTHTDERPYSCDV----CNKAFRRQDHLRDH 285 (286)
Q Consensus 237 k~~~C~~--Cgk~F~~~~~L~~H~r~HtgeKPf~C~~----CgK~F~~~~~L~~H 285 (286)
.+-.|+. |...+. +..|..|....-..++..|.+ |...|.+. .|..|
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 3468888 445455 468999999766778999999 98887664 34444
No 103
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=54.36 E-value=4.6 Score=26.56 Aligned_cols=37 Identities=19% Similarity=0.442 Sum_probs=18.7
Q ss_pred ccCCCCCcccCCchhhhhhhhhc-CC-CCccccCCCCCccc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTH-TD-ERPYSCDVCNKAFR 277 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~H-tg-eKPf~C~~CgK~F~ 277 (286)
+.|+.||..-... +....|.- .+ -.-|.|..|+..|+
T Consensus 1 ~~Cp~C~~~~a~~--~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATF--FQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEE--EEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 4688887332222 22222221 11 12388888887764
No 104
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.08 E-value=4.6 Score=36.91 Aligned_cols=40 Identities=25% Similarity=0.421 Sum_probs=28.0
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCC----------c-----cccCCCCC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDER----------P-----YSCDVCNK 274 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeK----------P-----f~C~~CgK 274 (286)
-++.+.||+|+-.|.....+..-.|+-.|+- | ..|+.|+-
T Consensus 16 ~kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 16 YKKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred hhceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 3567899999999988876665555544432 1 45898973
No 105
>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=53.09 E-value=9.9 Score=26.09 Aligned_cols=11 Identities=36% Similarity=0.718 Sum_probs=5.5
Q ss_pred cCCCCCcccCC
Q psy6673 240 ICRFCSRHFTK 250 (286)
Q Consensus 240 ~C~~Cgk~F~~ 250 (286)
.|..|++.|..
T Consensus 4 ~C~~C~~~F~~ 14 (57)
T cd00065 4 SCMGCGKPFTL 14 (57)
T ss_pred cCcccCccccC
Confidence 35555555543
No 106
>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=52.47 E-value=14 Score=29.78 Aligned_cols=35 Identities=17% Similarity=0.256 Sum_probs=25.0
Q ss_pred cccccCCCCCCCCCCCCCcccCCCCCCccCCCCCcccCCchhh
Q psy6673 212 KTIVTDSISKPVQKSTPVASTARPKKQFICRFCSRHFTKSYNL 254 (286)
Q Consensus 212 ~~~~~~~~~k~~~~~~~~~~~~~~~k~~~C~~Cgk~F~~~~~L 254 (286)
....|..|++.|-.. ++.|-.|++||..|.....+
T Consensus 8 tKR~Cp~CG~kFYDL--------nk~PivCP~CG~~~~~~~~~ 42 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL--------NKDPIVCPKCGTEFPPEPPL 42 (108)
T ss_pred CcccCCCCcchhccC--------CCCCccCCCCCCccCccccc
Confidence 345677888777553 34678999999999887333
No 107
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=52.30 E-value=7.7 Score=26.02 Aligned_cols=27 Identities=37% Similarity=0.957 Sum_probs=18.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
+.|+.||.. ..+.++. ...|+|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~~-------~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT-------RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC-------CCeEECCCCCC
Confidence 679999865 2222221 57799999975
No 108
>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=52.15 E-value=7.9 Score=27.33 Aligned_cols=31 Identities=23% Similarity=0.446 Sum_probs=21.4
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
|.|+.||..+.-.... .|+ ...|+.||..|.
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 6899999877554332 133 468999997664
No 109
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=52.05 E-value=7.2 Score=33.36 Aligned_cols=38 Identities=21% Similarity=0.613 Sum_probs=28.8
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
...+|.|. |+..|.+. ++|-.+-.|+ -|.|..|+-...
T Consensus 114 ~~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL~ 151 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKLV 151 (156)
T ss_pred cceeEEee-cCCccchh---hhcccccccc-eEEeccCCceEE
Confidence 45679998 99887543 6676777777 899999986543
No 110
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=49.93 E-value=2.7 Score=27.43 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=8.5
Q ss_pred cccCCCCCccc
Q psy6673 267 YSCDVCNKAFR 277 (286)
Q Consensus 267 f~C~~CgK~F~ 277 (286)
|.|..||+.|+
T Consensus 29 y~C~~C~~~wr 39 (39)
T PF01096_consen 29 YVCCNCGHRWR 39 (39)
T ss_dssp EEESSSTEEEE
T ss_pred EEeCCCCCeeC
Confidence 88888887763
No 111
>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=49.92 E-value=8.6 Score=25.81 Aligned_cols=16 Identities=38% Similarity=0.684 Sum_probs=11.9
Q ss_pred cCCCCCcccCCchhhh
Q psy6673 240 ICRFCSRHFTKSYNLL 255 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~ 255 (286)
.|.+||+.|+.+.-..
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6888888887776554
No 112
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=49.61 E-value=8.4 Score=30.71 Aligned_cols=39 Identities=21% Similarity=0.381 Sum_probs=25.0
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
=++.|.|+.||..-.....++.-. ..--..|..||-+|-
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~----~~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTV----NIGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecC----ceeEEEcccCcceEE
Confidence 457799999997665544443211 122357999998874
No 113
>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=49.41 E-value=3.6 Score=37.07 Aligned_cols=27 Identities=15% Similarity=0.351 Sum_probs=21.1
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
.+..|.|+.|+|.|.-...++.|+...
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhc
Confidence 345699999999999999999998763
No 114
>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 PRK05978 hypothetical protein; Provisional
Probab=46.84 E-value=11 Score=32.13 Aligned_cols=32 Identities=19% Similarity=0.264 Sum_probs=22.2
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
-+|+.||+.--.+..|+.+ -.|+.||-.|...
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 5899999664445555533 3799999887654
No 116
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.68 E-value=10 Score=30.54 Aligned_cols=27 Identities=22% Similarity=0.378 Sum_probs=19.0
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
+..+.|..||..|.... ..|.|+.||.
T Consensus 68 p~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred CcEEEcccCCCEEecCC------------cCccCcCCCC
Confidence 44579999997775532 3456999984
No 117
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=45.94 E-value=13 Score=39.59 Aligned_cols=30 Identities=37% Similarity=0.592 Sum_probs=22.3
Q ss_pred CCCchhHHHHHHHHHHHHHHHH-----HHHHHHHh
Q psy6673 26 PDAGNIVKSLQTTLQEELLQRS-----LQNVALTL 55 (286)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~ 55 (286)
|..|.+-..|..+|.|+|-..+ +-+||.-|
T Consensus 166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 (1374)
T PTZ00303 166 PAGGPVPRKLEETLRETLSENSDFFFRVSSVAYHL 200 (1374)
T ss_pred CCCCCCchhHHHHHHHHhhccCceEEEeeeeeeec
Confidence 5677788899999999987654 45666655
No 118
>COG1773 Rubredoxin [Energy production and conversion]
Probab=45.92 E-value=13 Score=26.41 Aligned_cols=37 Identities=14% Similarity=0.323 Sum_probs=22.6
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCC------CccccCCCCC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDE------RPYSCDVCNK 274 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~Htge------KPf~C~~CgK 274 (286)
+.|+|.+||..|.-...-..+-. -.|. --+.|+.||-
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp~~gi-~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDPRCGI-APGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred CceEecCCceEeccccCCccCCC-CCCCchhhCCCccCCCCCCC
Confidence 35899999988876654443322 1111 1277999983
No 119
>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=45.39 E-value=18 Score=22.75 Aligned_cols=27 Identities=22% Similarity=0.643 Sum_probs=17.1
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 276 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F 276 (286)
|.|..||..+... ..-+.+|..||.+-
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCeE
Confidence 6788888887622 13456899998543
No 120
>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=45.34 E-value=11 Score=25.80 Aligned_cols=37 Identities=14% Similarity=0.396 Sum_probs=20.2
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCC------CCccccCCCCCc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTD------ERPYSCDVCNKA 275 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~Htg------eKPf~C~~CgK~ 275 (286)
.|+|.+||..|.....-..+ .+-.| -.-|.|+.|+-.
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~-~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPEN-GIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGG-TB-TT--GGGS-TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCccc-CcCCCCCHHHCCCCCcCcCCCCc
Confidence 37899999888766543222 11111 234889999853
No 121
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.19 E-value=12 Score=31.09 Aligned_cols=17 Identities=24% Similarity=0.702 Sum_probs=10.7
Q ss_pred CCCCccCCCCCcccCCc
Q psy6673 235 PKKQFICRFCSRHFTKS 251 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~ 251 (286)
+...|.|+.|++.|...
T Consensus 50 ~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 50 GHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccccCCcCcceeee
Confidence 35556777777766554
No 122
>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=45.04 E-value=14 Score=26.55 Aligned_cols=13 Identities=23% Similarity=0.705 Sum_probs=7.7
Q ss_pred CCccccCCCCCcc
Q psy6673 264 ERPYSCDVCNKAF 276 (286)
Q Consensus 264 eKPf~C~~CgK~F 276 (286)
.+-|.|+.||..+
T Consensus 44 ~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 44 GRVFTCPNCGFEM 56 (69)
T ss_pred cceEEcCCCCCEE
Confidence 3556677676543
No 123
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=44.56 E-value=12 Score=31.96 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=10.6
Q ss_pred ccCCCCCcccCCchhh
Q psy6673 239 FICRFCSRHFTKSYNL 254 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L 254 (286)
++|+-||++|...-.+
T Consensus 29 ~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLACGKRFTTFERV 44 (154)
T ss_pred eeccccCCcceEeEec
Confidence 6777777777665443
No 124
>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=44.40 E-value=11 Score=30.35 Aligned_cols=28 Identities=21% Similarity=0.545 Sum_probs=19.6
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
+....|..||+.|..... -|.|+.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 345799999988766422 3679999853
No 125
>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=44.08 E-value=14 Score=31.35 Aligned_cols=36 Identities=25% Similarity=0.569 Sum_probs=22.3
Q ss_pred CCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCC-CcccCc
Q psy6673 234 RPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN-KAFRRQ 279 (286)
Q Consensus 234 ~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~Cg-K~F~~~ 279 (286)
.+...|.|..||..... .|.+. --.|+.|| ..|.|.
T Consensus 108 ~g~G~l~C~~Cg~~~~~---------~~~~~-l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVEL---------THPER-LPPCPKCGHTEFTRQ 144 (146)
T ss_pred ecCceEecccCCCEEEe---------cCCCc-CCCCCCCCCCeeeeC
Confidence 35567899999854322 23333 34799998 456553
No 126
>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=42.43 E-value=17 Score=25.22 Aligned_cols=36 Identities=17% Similarity=0.440 Sum_probs=20.6
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCC------CCccccCCCCC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTD------ERPYSCDVCNK 274 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~Htg------eKPf~C~~CgK 274 (286)
.|+|..||..|.-...-..+ .+-.| -..|.|+.|+.
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~-~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDE-GIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CcCCCCCCeEECCCCCCccc-CcCCCCCHhHCCCCCCCCCCCC
Confidence 37899999888754322111 11111 12479999984
No 127
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=41.90 E-value=16 Score=24.05 Aligned_cols=24 Identities=17% Similarity=0.441 Sum_probs=18.5
Q ss_pred ccCCCCCcccCCc--hhhhhhhhhcC
Q psy6673 239 FICRFCSRHFTKS--YNLLIHERTHT 262 (286)
Q Consensus 239 ~~C~~Cgk~F~~~--~~L~~H~r~Ht 262 (286)
-.|+.||..|... ..-+.|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4999999988765 45678887774
No 128
>PHA02998 RNA polymerase subunit; Provisional
Probab=41.70 E-value=11 Score=33.12 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=8.4
Q ss_pred cccCCCCCcccC
Q psy6673 267 YSCDVCNKAFRR 278 (286)
Q Consensus 267 f~C~~CgK~F~~ 278 (286)
|.|..||+.|+-
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 677778776653
No 129
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.60 E-value=14 Score=30.02 Aligned_cols=29 Identities=24% Similarity=0.497 Sum_probs=18.9
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
+..+.|..||+.|..... .-+.|+.||..
T Consensus 69 p~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNAL-----------DYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCc-----------cCCcCcCCCCC
Confidence 445799999987765421 11359999853
No 130
>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=41.20 E-value=23 Score=29.43 Aligned_cols=35 Identities=6% Similarity=0.127 Sum_probs=25.2
Q ss_pred ccccCCCCCCCCCCCCCcccCCCCCCccCCCCCcccCCchhhh
Q psy6673 213 TIVTDSISKPVQKSTPVASTARPKKQFICRFCSRHFTKSYNLL 255 (286)
Q Consensus 213 ~~~~~~~~k~~~~~~~~~~~~~~~k~~~C~~Cgk~F~~~~~L~ 255 (286)
...|..|++.|-.. ++.|-.|++||..|.....++
T Consensus 9 Kr~Cp~cg~kFYDL--------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGSKFYDL--------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCcccccc--------CCCCccCCCcCCccCcchhhc
Confidence 45677777766543 346789999999998775555
No 131
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=40.36 E-value=17 Score=21.00 Aligned_cols=7 Identities=29% Similarity=0.994 Sum_probs=3.7
Q ss_pred cCCCCCc
Q psy6673 269 CDVCNKA 275 (286)
Q Consensus 269 C~~CgK~ 275 (286)
|+.||..
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 5555543
No 132
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=40.21 E-value=13 Score=29.95 Aligned_cols=30 Identities=20% Similarity=0.435 Sum_probs=19.2
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
.+..+.|..||..|..... ..+.|+.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQ-----------RVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecCCc-----------cCCcCcCcCCC
Confidence 3455799999977654311 12679999843
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=40.03 E-value=9.4 Score=34.45 Aligned_cols=23 Identities=35% Similarity=0.897 Sum_probs=17.0
Q ss_pred CCCccccCCCCCcccCchhhhhc
Q psy6673 263 DERPYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 263 geKPf~C~~CgK~F~~~~~L~~H 285 (286)
++-.|.|.+|+|.|.-...+++|
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KH 96 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKH 96 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHH
Confidence 45569999999999988777776
No 134
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.44 E-value=14 Score=26.14 Aligned_cols=12 Identities=25% Similarity=0.883 Sum_probs=7.4
Q ss_pred cCCCCCcccCCc
Q psy6673 240 ICRFCSRHFTKS 251 (286)
Q Consensus 240 ~C~~Cgk~F~~~ 251 (286)
.|+.||+.|...
T Consensus 7 ~C~~Cg~~~~~~ 18 (54)
T PF14446_consen 7 KCPVCGKKFKDG 18 (54)
T ss_pred cChhhCCcccCC
Confidence 566677666543
No 135
>PRK04860 hypothetical protein; Provisional
Probab=38.04 E-value=7.5 Score=33.46 Aligned_cols=39 Identities=10% Similarity=0.122 Sum_probs=27.7
Q ss_pred ccccCCCCCCCCCCCCCcccCCCCCCccCCCCCcccCCch
Q psy6673 213 TIVTDSISKPVQKSTPVASTARPKKQFICRFCSRHFTKSY 252 (286)
Q Consensus 213 ~~~~~~~~k~~~~~~~~~~~~~~~k~~~C~~Cgk~F~~~~ 252 (286)
.+.|. |.........+...+.++++|.|..|++.|....
T Consensus 119 ~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 35565 6654444455666778899999999999987643
No 136
>PRK14873 primosome assembly protein PriA; Provisional
Probab=37.87 E-value=17 Score=38.13 Aligned_cols=21 Identities=10% Similarity=0.183 Sum_probs=12.9
Q ss_pred hhhhhhhcCCCCccccCCCCCc
Q psy6673 254 LLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 254 L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
|+.|..-+. ..|+.|+.||..
T Consensus 411 l~Ch~CG~~-~~p~~Cp~Cgs~ 431 (665)
T PRK14873 411 PRCRWCGRA-APDWRCPRCGSD 431 (665)
T ss_pred eECCCCcCC-CcCccCCCCcCC
Confidence 445544443 368888888854
No 137
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.64 E-value=20 Score=37.56 Aligned_cols=25 Identities=20% Similarity=0.377 Sum_probs=17.6
Q ss_pred chhhhhhhhhcCCCCccccCCCCCc
Q psy6673 251 SYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 251 ~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
...|..|...++...|..|+.||..
T Consensus 406 ~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 406 QRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCeEECCCCcCCCCCCCCCCCCcCC
Confidence 3445666666666778999999854
No 138
>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=37.47 E-value=21 Score=21.22 Aligned_cols=19 Identities=21% Similarity=0.331 Sum_probs=13.6
Q ss_pred cCCCCCcccCCchhhhhhhh
Q psy6673 240 ICRFCSRHFTKSYNLLIHER 259 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~~H~r 259 (286)
.||+|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 688998888 4456666654
No 139
>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=36.89 E-value=19 Score=36.44 Aligned_cols=22 Identities=23% Similarity=0.416 Sum_probs=14.3
Q ss_pred hhhhhhhhcCCCCccccCCCCC
Q psy6673 253 NLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 253 ~L~~H~r~HtgeKPf~C~~CgK 274 (286)
.|..|...+....|..|+.||.
T Consensus 240 ~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 240 KLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred eEEcCCCcCcCCCCCCCCCCCC
Confidence 3555555555566788888875
No 140
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.85 E-value=24 Score=29.15 Aligned_cols=36 Identities=17% Similarity=0.453 Sum_probs=22.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~ 279 (286)
-.||.|+.....+.. ..-.|...|.|..|++.|...
T Consensus 31 ~~cP~C~s~~~~k~g-----~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSNVVKIG-----GIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccceeeEC-----CccccccccccCCcCcceeee
Confidence 478888754412211 122235669999999999654
No 141
>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=36.44 E-value=19 Score=28.39 Aligned_cols=25 Identities=16% Similarity=0.302 Sum_probs=22.4
Q ss_pred ccC----CCCCcccCCchhhhhhhhhcCC
Q psy6673 239 FIC----RFCSRHFTKSYNLLIHERTHTD 263 (286)
Q Consensus 239 ~~C----~~Cgk~F~~~~~L~~H~r~Htg 263 (286)
|.| ..|+..+.....++.|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8999999999999999987654
No 142
>KOG2482|consensus
Probab=35.44 E-value=19 Score=34.79 Aligned_cols=24 Identities=25% Similarity=0.603 Sum_probs=22.0
Q ss_pred CCccCCCCCcccCCchhhhhhhhh
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERT 260 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~ 260 (286)
..+.|-+|.|.|+.+..|+.|||.
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHh
Confidence 358999999999999999999985
No 143
>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=35.41 E-value=16 Score=23.79 Aligned_cols=32 Identities=16% Similarity=0.473 Sum_probs=15.0
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
|.+|..|+-.+. -+.....+.+-|.|.+|+..
T Consensus 2 p~rC~~C~aylN------p~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLN------PFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-------TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEEC------CcceEcCCCCEEECcCCCCc
Confidence 346777753332 23334445677888888764
No 144
>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=35.34 E-value=14 Score=29.14 Aligned_cols=21 Identities=24% Similarity=0.605 Sum_probs=14.8
Q ss_pred hhhhhcCCCCccccCCCCCccc
Q psy6673 256 IHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 256 ~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
..++.|.| +|++|..||.-|.
T Consensus 70 ~W~~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 70 IWMWLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEEEEeCC-CceeCCCCCcEEE
Confidence 34556666 7888888887765
No 145
>PLN02294 cytochrome c oxidase subunit Vb
Probab=35.19 E-value=14 Score=32.11 Aligned_cols=13 Identities=38% Similarity=0.963 Sum_probs=6.2
Q ss_pred CCccCCCCCcccC
Q psy6673 237 KQFICRFCSRHFT 249 (286)
Q Consensus 237 k~~~C~~Cgk~F~ 249 (286)
++++|+.||..|.
T Consensus 140 kp~RCpeCG~~fk 152 (174)
T PLN02294 140 KSFECPVCTQYFE 152 (174)
T ss_pred CceeCCCCCCEEE
Confidence 3444555554443
No 146
>KOG1146|consensus
Probab=34.87 E-value=16 Score=41.04 Aligned_cols=52 Identities=23% Similarity=0.460 Sum_probs=41.5
Q ss_pred CCCCCccCCCCCcccCCchhhhhhhhhc-----------------CCCCccccCCCCCcccCchhhhhcC
Q psy6673 234 RPKKQFICRFCSRHFTKSYNLLIHERTH-----------------TDERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 234 ~~~k~~~C~~Cgk~F~~~~~L~~H~r~H-----------------tgeKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
....+|.|.+|...|.....|..|.+.. ...++| |..|-..|+....|..||
T Consensus 1280 ~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm 1348 (1406)
T KOG1146|consen 1280 DVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHM 1348 (1406)
T ss_pred ccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHH
Confidence 3567799999999999988888887542 224567 999999999999999886
No 147
>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=34.72 E-value=24 Score=29.54 Aligned_cols=20 Identities=10% Similarity=0.248 Sum_probs=12.7
Q ss_pred CCccCCCCCcccCCchhhhh
Q psy6673 237 KQFICRFCSRHFTKSYNLLI 256 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~ 256 (286)
.-|.|+.|||.|-..+++++
T Consensus 123 ~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred eEEECCCCCCEecccccHHH
Confidence 35677777777766655554
No 148
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=34.47 E-value=29 Score=24.66 Aligned_cols=14 Identities=21% Similarity=0.394 Sum_probs=7.6
Q ss_pred CCCCccCCCCCccc
Q psy6673 235 PKKQFICRFCSRHF 248 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F 248 (286)
+...|.|+.||..+
T Consensus 11 ~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 11 AHVNFECPDCGIPT 24 (55)
T ss_pred cccCCcCCCCCCcC
Confidence 34456666666443
No 149
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=34.28 E-value=17 Score=30.26 Aligned_cols=35 Identities=20% Similarity=0.526 Sum_probs=23.6
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
...|.|..|+..+. +|.| |.....|.|..|+..|.
T Consensus 110 ~~~y~C~~C~~~~~------~~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 110 KYPYRCTGCGQRYL------RVRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred eEEEECCCCCCCCc------eEcc-ccCcceEEcCCCCCEEE
Confidence 45799998997764 2222 22226699999997764
No 150
>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=34.09 E-value=25 Score=27.90 Aligned_cols=39 Identities=28% Similarity=0.697 Sum_probs=15.7
Q ss_pred CCCCCccCCCCCcccCCchhhhhhhhhcCCCC-ccccCCCCCcccC
Q psy6673 234 RPKKQFICRFCSRHFTKSYNLLIHERTHTDER-PYSCDVCNKAFRR 278 (286)
Q Consensus 234 ~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeK-Pf~C~~CgK~F~~ 278 (286)
.+.|--.|..||+++.-.+. .+ .|+| -|.|..|.+.|..
T Consensus 10 ag~ke~~CalCG~tWg~~y~-----Ev-~G~rLfFCCd~ca~EF~n 49 (105)
T PF11494_consen 10 AGTKEMGCALCGATWGDYYE-----EV-DGERLFFCCDDCAKEFKN 49 (105)
T ss_dssp --SGGGS-SS---S---SS------B--TT--BSSS--SSSS-TTS
T ss_pred cccccccccccCCcHHHHHH-----hh-cCCEEEEEcHHHHHHHHH
Confidence 34556789999999875432 22 3555 4778999998875
No 151
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.86 E-value=19 Score=37.80 Aligned_cols=41 Identities=15% Similarity=0.133 Sum_probs=28.2
Q ss_pred CCCCCc-cCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 234 RPKKQF-ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 234 ~~~k~~-~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
+|..++ .|..||..+... +....+..|.......|..||..
T Consensus 378 rGyap~l~C~~Cg~~~~C~-~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 378 RGYVPSLACARCRTPARCR-HCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred CCCCCeeEhhhCcCeeECC-CCCCceeEecCCCeeECCCCcCC
Confidence 455555 899999888775 33334455656677899999964
No 152
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=33.48 E-value=15 Score=32.85 Aligned_cols=37 Identities=14% Similarity=0.313 Sum_probs=19.3
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCC---ccccCCCCCccc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDER---PYSCDVCNKAFR 277 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeK---Pf~C~~CgK~F~ 277 (286)
-.||+||..|... ...+..-|-|+. -+.|..||.+|+
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 4899998632211 111111233432 256999987664
No 153
>PRK04351 hypothetical protein; Provisional
Probab=33.43 E-value=21 Score=30.34 Aligned_cols=37 Identities=16% Similarity=0.610 Sum_probs=25.6
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccCch
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRRQD 280 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~ 280 (286)
...|.|..||..+.+. |.| ..+.|.|..|+..+....
T Consensus 110 ~y~Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L~~~~ 146 (149)
T PRK04351 110 NYLYECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKLKLIN 146 (149)
T ss_pred eEEEECCCCCCEeeee-------eec-CCCcEEeCCCCcEeeecc
Confidence 3569998899766432 223 347799999998776543
No 154
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=33.33 E-value=27 Score=24.09 Aligned_cols=28 Identities=29% Similarity=0.554 Sum_probs=18.0
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVC 272 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~C 272 (286)
-++|+.||..|...-.-+ + .+...|+.|
T Consensus 28 ~W~C~~Cgh~w~~~v~~R----~---~~~~~CP~C 55 (55)
T PF14311_consen 28 WWKCPKCGHEWKASVNDR----T---RRGKGCPYC 55 (55)
T ss_pred EEECCCCCCeeEccHhhh----c---cCCCCCCCC
Confidence 489999988776653332 2 344567776
No 155
>KOG3408|consensus
Probab=33.22 E-value=18 Score=29.83 Aligned_cols=27 Identities=33% Similarity=0.480 Sum_probs=24.1
Q ss_pred CCCCCccCCCCCcccCCchhhhhhhhh
Q psy6673 234 RPKKQFICRFCSRHFTKSYNLLIHERT 260 (286)
Q Consensus 234 ~~~k~~~C~~Cgk~F~~~~~L~~H~r~ 260 (286)
.|...|.|-.|.+.|.....|+.|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 466779999999999999999999885
No 156
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=32.58 E-value=35 Score=34.28 Aligned_cols=43 Identities=14% Similarity=0.348 Sum_probs=26.3
Q ss_pred ccCCCCCCccCCCCCcccCCchhhhhhhhhcCC------CCccccCCCCC
Q psy6673 231 STARPKKQFICRFCSRHFTKSYNLLIHERTHTD------ERPYSCDVCNK 274 (286)
Q Consensus 231 ~~~~~~k~~~C~~Cgk~F~~~~~L~~H~r~Htg------eKPf~C~~CgK 274 (286)
......+.|+|..||..|.-...-..+ .+-.| -..|.|+.||-
T Consensus 418 ~~~~~~~~~~c~~c~~~yd~~~g~~~~-~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 418 TTADLGPRMQCSVCQWIYDPAKGEPMQ-DVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred cccCCCCeEEECCCCeEECCCCCCccc-CCCCCCChhhCCCCCcCcCCCC
Confidence 334566789999999888765332211 11112 12489999984
No 157
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.57 E-value=22 Score=31.09 Aligned_cols=33 Identities=12% Similarity=0.531 Sum_probs=23.2
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 276 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F 276 (286)
+..-|.|+.|.-.|+....+. .-|.|+.||-..
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 455699999987776654442 229999999643
No 158
>KOG2907|consensus
Probab=32.38 E-value=25 Score=28.65 Aligned_cols=40 Identities=20% Similarity=0.392 Sum_probs=23.9
Q ss_pred CCccCCCCCcccCCchhhhhhhhh-cCCC-CccccCCCCCcccC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERT-HTDE-RPYSCDVCNKAFRR 278 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~-Htge-KPf~C~~CgK~F~~ 278 (286)
-.++|+.||..--....|+ +|. -.|. .-|.|..|+.+|+.
T Consensus 73 I~~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 73 IKHKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hhccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 3478999985433333333 232 2222 34899999988865
No 159
>KOG4173|consensus
Probab=32.23 E-value=9.2 Score=34.42 Aligned_cols=48 Identities=29% Similarity=0.584 Sum_probs=36.2
Q ss_pred ccCCCCCcccCCchhhhhhhh-hc---------CCCCcccc--CCCCCcccCchhhhhcC
Q psy6673 239 FICRFCSRHFTKSYNLLIHER-TH---------TDERPYSC--DVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r-~H---------tgeKPf~C--~~CgK~F~~~~~L~~H~ 286 (286)
-.|.+|.+.|....-|-.|.. .| .|.--|+| +.|+-.|.+.-..++||
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 389999999999988888865 34 34334888 45999998877777774
No 160
>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=31.99 E-value=20 Score=28.82 Aligned_cols=28 Identities=25% Similarity=0.585 Sum_probs=17.5
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
+..+.|..||+.|..... .|.|+.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEF------------DFSCPRCGSP 95 (113)
T ss_dssp --EEEETTTS-EEECHHC------------CHH-SSSSSS
T ss_pred CCcEECCCCCCEEecCCC------------CCCCcCCcCC
Confidence 345799999999866432 2569999865
No 161
>PF15269 zf-C2H2_7: Zinc-finger
Probab=31.87 E-value=59 Score=22.31 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=19.0
Q ss_pred CCCccCCCCCcccCCchhhhhhhhh
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERT 260 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~ 260 (286)
...|+|=+|.-+...+++|-.||+.
T Consensus 18 p~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 18 PFKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred CccceeecCCcccchHHHHHHHHHH
Confidence 3447888888888888888888764
No 162
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=31.35 E-value=1.1e+02 Score=21.45 Aligned_cols=29 Identities=34% Similarity=0.468 Sum_probs=21.7
Q ss_pred HHHHHHHHHHH-HHHHHHHHHHhhHHHHHHH
Q psy6673 34 SLQTTLQEELL-QRSLQNVALTLQTAMVSSL 63 (286)
Q Consensus 34 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 63 (286)
.+|.+|||+|- ||.|| +-+--||-.+.++
T Consensus 13 EvQrrLhEQLEvQr~Lq-lrieaqgkyl~~i 42 (51)
T PF14379_consen 13 EVQRRLHEQLEVQRHLQ-LRIEAQGKYLQSI 42 (51)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHhhHHHHHH
Confidence 57899999984 88888 6677777665443
No 163
>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=30.97 E-value=31 Score=27.51 Aligned_cols=11 Identities=36% Similarity=1.014 Sum_probs=7.1
Q ss_pred CCccCCCCCcc
Q psy6673 237 KQFICRFCSRH 247 (286)
Q Consensus 237 k~~~C~~Cgk~ 247 (286)
||-.|++||..
T Consensus 1 ~p~~CpYCg~~ 11 (102)
T PF11672_consen 1 KPIICPYCGGP 11 (102)
T ss_pred CCcccCCCCCe
Confidence 35578888743
No 164
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.95 E-value=15 Score=38.73 Aligned_cols=58 Identities=16% Similarity=0.390 Sum_probs=35.1
Q ss_pred cccCCCCCCCCCCCCCccc--CCCCCC-ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 214 IVTDSISKPVQKSTPVAST--ARPKKQ-FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 214 ~~~~~~~k~~~~~~~~~~~--~~~~k~-~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
+.|..|+..+.-.+...-. ...-+. --|+.|.+.|....+-+-| -.|..|+.||-...
T Consensus 124 ~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP~~~ 184 (750)
T COG0068 124 INCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFH------AQPIACPKCGPHLF 184 (750)
T ss_pred cccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccc------cccccCcccCCCeE
Confidence 4466776665543322221 112222 3789999888887766555 36889999996443
No 165
>KOG0782|consensus
Probab=30.94 E-value=19 Score=37.14 Aligned_cols=30 Identities=20% Similarity=0.492 Sum_probs=21.7
Q ss_pred chhhhhhhhhcCCCCccccCCCCCcccCch
Q psy6673 251 SYNLLIHERTHTDERPYSCDVCNKAFRRQD 280 (286)
Q Consensus 251 ~~~L~~H~r~HtgeKPf~C~~CgK~F~~~~ 280 (286)
...+.+|-++|.....=+|..|||+|-++-
T Consensus 238 E~~fvrHHWVHrrRqeGkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 238 ESGFVRHHWVHRRRQEGKCNTCGKGFQQKF 267 (1004)
T ss_pred cccchHHhHhhHhhhccccchhhhhhhhhe
Confidence 346777878777666667888888886653
No 166
>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=30.85 E-value=22 Score=22.09 Aligned_cols=25 Identities=24% Similarity=0.672 Sum_probs=11.7
Q ss_pred cCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 240 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
.|+.|+-.+.. ...--|.|+.|+..
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 68888877665 23456888888753
No 167
>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=30.21 E-value=26 Score=23.00 Aligned_cols=28 Identities=14% Similarity=0.361 Sum_probs=15.1
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
|.|+.||.... ......--+.|..||..
T Consensus 1 m~Cp~Cg~~~~---------~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEI---------VFDPERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEE---------EEETTTTEEEETTT-BB
T ss_pred CCCcCCcCCce---------EEcCCCCeEECCCCCCE
Confidence 57888886541 01112344688888753
No 168
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=29.98 E-value=21 Score=28.91 Aligned_cols=38 Identities=24% Similarity=0.500 Sum_probs=20.7
Q ss_pred CccCCCCCcccCCchhhhhhhhh-cCC-CCccccCCCCCccc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERT-HTD-ERPYSCDVCNKAFR 277 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~-Htg-eKPf~C~~CgK~F~ 277 (286)
...|+.||..--....++ .|. -.+ .+=|.|..||..|+
T Consensus 72 ~~~CpkCg~~ea~y~~~Q--tRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQ--TRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cccCCCCCCceeEEEeee--hhccCCCceEEEEecccCCEee
Confidence 467888874333322222 221 111 23389999998775
No 169
>PRK04023 DNA polymerase II large subunit; Validated
Probab=29.97 E-value=46 Score=36.65 Aligned_cols=10 Identities=20% Similarity=0.813 Sum_probs=6.5
Q ss_pred CccccCCCCC
Q psy6673 265 RPYSCDVCNK 274 (286)
Q Consensus 265 KPf~C~~CgK 274 (286)
.++.|+.||.
T Consensus 662 ~~y~CPKCG~ 671 (1121)
T PRK04023 662 EEDECEKCGR 671 (1121)
T ss_pred CCCcCCCCCC
Confidence 3466777774
No 170
>PRK01343 zinc-binding protein; Provisional
Probab=29.93 E-value=43 Score=23.94 Aligned_cols=12 Identities=25% Similarity=0.393 Sum_probs=9.9
Q ss_pred CccCCCCCcccC
Q psy6673 238 QFICRFCSRHFT 249 (286)
Q Consensus 238 ~~~C~~Cgk~F~ 249 (286)
...|++|+|.|.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 458999999885
No 171
>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=29.80 E-value=18 Score=23.92 Aligned_cols=11 Identities=18% Similarity=1.093 Sum_probs=5.9
Q ss_pred CccCCCCCccc
Q psy6673 238 QFICRFCSRHF 248 (286)
Q Consensus 238 ~~~C~~Cgk~F 248 (286)
+-.|++||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 34555555544
No 172
>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=29.67 E-value=22 Score=33.65 Aligned_cols=37 Identities=22% Similarity=0.701 Sum_probs=22.4
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCc----cccCCCCCccc
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERP----YSCDVCNKAFR 277 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKP----f~C~~CgK~F~ 277 (286)
..|.|+.|+..=.....+ +. .....| |.|..||..|+
T Consensus 257 ~~~~C~~C~~~~~~~~q~--Qt--rsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQL--QT--RSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEe--cc--cCCCCCCeEEEEcCCCCCeee
Confidence 358999998443333222 22 223333 79999998765
No 173
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.66 E-value=26 Score=28.69 Aligned_cols=32 Identities=19% Similarity=0.339 Sum_probs=19.0
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCC-ccccCCCCC
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDER-PYSCDVCNK 274 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeK-Pf~C~~CgK 274 (286)
+..+.| .||..|.....-..| .. .|.|+.||.
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~------~~~~~~CP~Cgs 100 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDH------YAAVIECPVCGN 100 (124)
T ss_pred CeeEEe-eCcCcccccccchhc------cccCCcCcCCCC
Confidence 445799 999887654311111 11 357999984
No 174
>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=29.37 E-value=26 Score=24.47 Aligned_cols=32 Identities=31% Similarity=0.822 Sum_probs=18.6
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCC
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN 273 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~Cg 273 (286)
...|+|+.|++.|=..-.+-.|...| .|+.|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH------~CPGC~ 50 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH------NCPGCE 50 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-------SSSTT-
T ss_pred CCeEECCCCCCccccCcChhhhcccc------CCcCCC
Confidence 45699999999998888887775444 677763
No 175
>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=28.90 E-value=71 Score=25.06 Aligned_cols=31 Identities=26% Similarity=0.446 Sum_probs=21.2
Q ss_pred cccccccccCCCchhHHHHHHHHHHHHHHHH
Q psy6673 17 HSTEDVLALPDAGNIVKSLQTTLQEELLQRS 47 (286)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (286)
|-.+|---+||...+.+-||.||.|+|.+--
T Consensus 62 ~EfdDsgLipdtkDV~~IlqaRIyE~L~ndl 92 (101)
T PF08684_consen 62 HEFDDSGLIPDTKDVTRILQARIYEQLYNDL 92 (101)
T ss_dssp SS-SSGGGS---S-HHHHHHHHHHHHHHHHH
T ss_pred eeccccCCCCCcHHHHHHHHHHHHHHHHHHh
Confidence 3456777789999999999999999997643
No 176
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=28.57 E-value=43 Score=29.03 Aligned_cols=23 Identities=13% Similarity=0.254 Sum_probs=15.3
Q ss_pred CCccCCCCCcccCCchhhhhhhh
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHER 259 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r 259 (286)
..|.|+.||+.|-..+++.+-.+
T Consensus 129 ~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred ceeECCCCcccccCchHHHHHHH
Confidence 34668888888877776654433
No 177
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.38 E-value=25 Score=22.89 Aligned_cols=21 Identities=19% Similarity=0.341 Sum_probs=13.9
Q ss_pred CCCccccCCCCCcccCchhhh
Q psy6673 263 DERPYSCDVCNKAFRRQDHLR 283 (286)
Q Consensus 263 geKPf~C~~CgK~F~~~~~L~ 283 (286)
+..-+.|..|+..|-..+.|.
T Consensus 16 ~~~id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 16 DVEIDVCPSCGGIWFDAGELE 36 (41)
T ss_pred CEEEEECCCCCeEEccHHHHH
Confidence 345577888887776655543
No 178
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.22 E-value=34 Score=23.64 Aligned_cols=26 Identities=19% Similarity=0.473 Sum_probs=16.4
Q ss_pred cCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcc
Q psy6673 240 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 276 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F 276 (286)
.||.||.. .|..| ...|.|..||..+
T Consensus 22 fCP~Cg~~-----~m~~~------~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-----FMAEH------LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-----hhecc------CCcEECCCcCCEE
Confidence 78888843 22222 2568899998654
No 179
>KOG1842|consensus
Probab=27.99 E-value=16 Score=36.43 Aligned_cols=22 Identities=27% Similarity=0.819 Sum_probs=0.0
Q ss_pred CCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 241 CRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 241 C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
|+.|++.|.-. .|.+.|.+||+
T Consensus 183 CP~Ca~~F~l~------------rRrHHCRLCG~ 204 (505)
T KOG1842|consen 183 CPECANSFGLT------------RRRHHCRLCGR 204 (505)
T ss_pred cccccchhhhH------------HHhhhhhhcch
No 180
>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=27.27 E-value=29 Score=22.20 Aligned_cols=26 Identities=35% Similarity=0.717 Sum_probs=12.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
-.|..|++.|...+-+ +-|.+.+|.+
T Consensus 4 ~~C~eC~~~f~dSyL~----------~~F~~~VCD~ 29 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLL----------NNFDLPVCDK 29 (34)
T ss_dssp EE-TTT--EES-SSCC----------CCTS-S--TT
T ss_pred chHhHhCCHHHHHHHH----------HhCCcccccc
Confidence 3788899998876544 3366666654
No 181
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.84 E-value=1e+02 Score=25.00 Aligned_cols=33 Identities=24% Similarity=0.756 Sum_probs=26.4
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCC
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN 273 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~Cg 273 (286)
....|+|+.|.+.|-..-..-.|...| .|+.|.
T Consensus 78 ~~~~y~C~~C~~~FC~dCD~fiHe~Lh------~CPGC~ 110 (112)
T TIGR00622 78 DSHRYVCAVCKNVFCVDCDVFVHESLH------CCPGCI 110 (112)
T ss_pred cccceeCCCCCCccccccchhhhhhcc------CCcCCC
Confidence 345799999999999988888886655 588775
No 182
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.65 E-value=40 Score=22.57 Aligned_cols=10 Identities=20% Similarity=0.650 Sum_probs=4.8
Q ss_pred cccCCCCCcc
Q psy6673 267 YSCDVCNKAF 276 (286)
Q Consensus 267 f~C~~CgK~F 276 (286)
|.|+.||..+
T Consensus 21 ~vC~~Cg~~~ 30 (52)
T smart00661 21 FVCRKCGYEE 30 (52)
T ss_pred EECCcCCCeE
Confidence 4455555433
No 183
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.59 E-value=33 Score=31.30 Aligned_cols=13 Identities=23% Similarity=0.621 Sum_probs=9.0
Q ss_pred CCccccCCCCCcc
Q psy6673 264 ERPYSCDVCNKAF 276 (286)
Q Consensus 264 eKPf~C~~CgK~F 276 (286)
.+-|.|+.||..+
T Consensus 320 ~r~~~C~~cg~~~ 332 (364)
T COG0675 320 GRLFKCPRCGFVH 332 (364)
T ss_pred ceeEECCCCCCee
Confidence 4567888888654
No 184
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=26.58 E-value=32 Score=22.42 Aligned_cols=14 Identities=21% Similarity=0.710 Sum_probs=11.6
Q ss_pred ccccCCCCCcccCc
Q psy6673 266 PYSCDVCNKAFRRQ 279 (286)
Q Consensus 266 Pf~C~~CgK~F~~~ 279 (286)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999988654
No 185
>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=25.85 E-value=49 Score=27.65 Aligned_cols=21 Identities=24% Similarity=0.605 Sum_probs=16.0
Q ss_pred CCccccCCCCCcccCchhhhh
Q psy6673 264 ERPYSCDVCNKAFRRQDHLRD 284 (286)
Q Consensus 264 eKPf~C~~CgK~F~~~~~L~~ 284 (286)
.+-|.|+.|||.|=..+++++
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CeEEECCCCCCEecccccHHH
Confidence 346899999999877666654
No 186
>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=25.70 E-value=28 Score=21.31 Aligned_cols=20 Identities=30% Similarity=0.574 Sum_probs=10.1
Q ss_pred ccCCCCCcccCCchhhhhhhh
Q psy6673 239 FICRFCSRHFTKSYNLLIHER 259 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r 259 (286)
|.|-.|++.| .....+.|..
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 4566677777 3345555543
No 187
>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=24.82 E-value=36 Score=34.40 Aligned_cols=38 Identities=21% Similarity=0.400 Sum_probs=27.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
..|..||...... +....+..|.......|..||....
T Consensus 214 ~~C~~Cg~~~~C~-~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 214 LLCRSCGYILCCP-NCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred eEhhhCcCccCCC-CCCCceEEecCCCeEEcCCCcCcCC
Confidence 3888888887765 3344556666677889999997654
No 188
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=24.70 E-value=35 Score=29.97 Aligned_cols=27 Identities=26% Similarity=0.632 Sum_probs=19.3
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 276 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F 276 (286)
.+.+.|.-|++.|.. .--.|+.||-.-
T Consensus 137 ~w~~rC~GC~~~f~~--------------~~~~Cp~CG~~~ 163 (177)
T COG1439 137 KWRLRCHGCKRIFPE--------------PKDFCPICGSPL 163 (177)
T ss_pred eeeEEEecCceecCC--------------CCCcCCCCCCce
Confidence 456899999999971 113699999653
No 189
>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=24.67 E-value=36 Score=29.29 Aligned_cols=15 Identities=33% Similarity=0.767 Sum_probs=9.0
Q ss_pred CCccccCCCCCcccC
Q psy6673 264 ERPYSCDVCNKAFRR 278 (286)
Q Consensus 264 eKPf~C~~CgK~F~~ 278 (286)
+.|.-|..||+.|-|
T Consensus 66 ~~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPW 80 (158)
T ss_pred CCChhHHhCCCCCch
Confidence 356666666666655
No 190
>PRK11032 hypothetical protein; Provisional
Probab=24.54 E-value=43 Score=28.86 Aligned_cols=35 Identities=23% Similarity=0.617 Sum_probs=20.6
Q ss_pred CCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCC-CcccCc
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN-KAFRRQ 279 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~Cg-K~F~~~ 279 (286)
+...+.|..||..... .|.+..| .|+.|| ..|.|.
T Consensus 121 g~G~LvC~~Cg~~~~~---------~~p~~i~-pCp~C~~~~F~R~ 156 (160)
T PRK11032 121 GLGNLVCEKCHHHLAF---------YTPEVLP-LCPKCGHDQFQRR 156 (160)
T ss_pred ecceEEecCCCCEEEe---------cCCCcCC-CCCCCCCCeeeeC
Confidence 4456789999844311 2333333 799998 455554
No 191
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.27 E-value=35 Score=28.47 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=13.0
Q ss_pred CccCCCCCcccCCch
Q psy6673 238 QFICRFCSRHFTKSY 252 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~ 252 (286)
||+|..||+.|....
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 689999999998765
No 192
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.10 E-value=63 Score=30.80 Aligned_cols=18 Identities=17% Similarity=0.259 Sum_probs=12.6
Q ss_pred cccCCCchhHHHHHHHHH
Q psy6673 23 LALPDAGNIVKSLQTTLQ 40 (286)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~ 40 (286)
+-+||.+++...=-.||.
T Consensus 25 ll~p~~~~lf~~RA~Rl~ 42 (309)
T PRK03564 25 LLFANLKNLYNRRAERLR 42 (309)
T ss_pred eecCCcccHHHHHHHHHH
Confidence 668888888766555554
No 193
>PF04641 Rtf2: Rtf2 RING-finger
Probab=24.09 E-value=36 Score=31.27 Aligned_cols=15 Identities=40% Similarity=0.924 Sum_probs=11.8
Q ss_pred ccccCCCCCcccCch
Q psy6673 266 PYSCDVCNKAFRRQD 280 (286)
Q Consensus 266 Pf~C~~CgK~F~~~~ 280 (286)
-..|..||+.|...+
T Consensus 150 ~~~Cp~c~~~f~~~D 164 (260)
T PF04641_consen 150 SKKCPVCGKPFTEED 164 (260)
T ss_pred cccccccCCccccCC
Confidence 356999999998654
No 194
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.95 E-value=50 Score=24.00 Aligned_cols=42 Identities=17% Similarity=0.227 Sum_probs=22.6
Q ss_pred cCCCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 232 TARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 232 ~~~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
...+..++.|+.-+-.|.+...+.-- ..+.--.|+.|++.|+
T Consensus 18 I~~~~~~l~C~g~~~p~~HPrV~L~m----g~~gev~CPYC~t~y~ 59 (62)
T COG4391 18 IEIGDLPLMCPGPEPPNDHPRVFLDM----GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEeCCeeEEcCCCCCCCCCCEEEEEc----CCCCcEecCccccEEE
Confidence 34456677777655555544332211 1223346888887775
No 195
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=23.88 E-value=63 Score=27.16 Aligned_cols=14 Identities=29% Similarity=0.873 Sum_probs=11.4
Q ss_pred ccCCCCCcccCchh
Q psy6673 268 SCDVCNKAFRRQDH 281 (286)
Q Consensus 268 ~C~~CgK~F~~~~~ 281 (286)
.|+.|.-+|+....
T Consensus 123 vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 123 VCPVCKTSFKSSSS 136 (140)
T ss_pred CCCccccccccccc
Confidence 79999999987653
No 196
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=23.86 E-value=42 Score=31.18 Aligned_cols=30 Identities=27% Similarity=0.583 Sum_probs=23.0
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN 273 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~Cg 273 (286)
..-.||.||+-+.-...| | +.-.|+|+.|.
T Consensus 219 ~~r~CP~Cg~~W~L~~pl--h-----~iFdFKCD~CR 248 (258)
T PF10071_consen 219 QARKCPSCGGDWRLKEPL--H-----DIFDFKCDPCR 248 (258)
T ss_pred hCCCCCCCCCccccCCch--h-----hceeccCCcce
Confidence 345899999988777666 2 45679999995
No 197
>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=23.71 E-value=15 Score=34.13 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=18.2
Q ss_pred cccCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Q psy6673 23 LALPDAGNIVKSLQTTLQEELLQRSLQNVALTLQTAMVSS 62 (286)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (286)
+-+||..++.+.-..||.+---..-+. =-|.+...++.+
T Consensus 8 ~~~~~~~~~~~~ra~rl~~La~~~p~~-~~L~~~~~l~~~ 46 (290)
T PF04216_consen 8 VILPDPATLFARRAERLRALAEKHPLA-EYLDFFAELAEA 46 (290)
T ss_dssp -EE---TTHHHHHHHHHHHHHTT-TTH-HHHHHHHHHHHH
T ss_pred eecCCHhhHHHHHHHHHHHHHHhCChH-HHHHHHHHHHHH
Confidence 457888888877766665422222222 224555555555
No 198
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.69 E-value=43 Score=32.88 Aligned_cols=40 Identities=20% Similarity=0.458 Sum_probs=22.7
Q ss_pred ccCCCCCcccCCchhhhhhhhhc------------CCCCccccCCCCCcccCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTH------------TDERPYSCDVCNKAFRRQ 279 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~H------------tgeKPf~C~~CgK~F~~~ 279 (286)
+.|+.||..-...... +++++| ...+.|.|..|++.|.-.
T Consensus 39 ~~CP~Cg~~~~~~~~~-~~~~I~~L~~~~~~~~L~~r~rR~~c~~c~~~~~~~ 90 (402)
T COG3464 39 HRCPECGQRTIRRHGW-RIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRFAEK 90 (402)
T ss_pred CCCCCCCCcceecccc-ceeeeeecccCCeeEEEEeccceeecccCCCCcccc
Confidence 6888888665333222 222222 223558888898888543
No 199
>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=23.66 E-value=43 Score=21.58 Aligned_cols=30 Identities=17% Similarity=0.500 Sum_probs=19.6
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCC
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVC 272 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~C 272 (286)
-.|+.|+..- .+.+|-+...|...|.|..|
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEeEecCcC
Confidence 3677776432 24566666667777888877
No 200
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=23.49 E-value=26 Score=23.11 Aligned_cols=16 Identities=31% Similarity=0.860 Sum_probs=10.1
Q ss_pred CccccCCCCCcccCch
Q psy6673 265 RPYSCDVCNKAFRRQD 280 (286)
Q Consensus 265 KPf~C~~CgK~F~~~~ 280 (286)
.||.|..|++.|-...
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 5889999999886543
No 201
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.33 E-value=55 Score=30.71 Aligned_cols=25 Identities=28% Similarity=0.772 Sum_probs=18.8
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcc
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAF 276 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F 276 (286)
-|.|++|.-.|.. .|-.|..||-.|
T Consensus 255 GyvCs~Clsi~C~--------------~p~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQ--------------YTPICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCC--------------CCCCCCCCCCCC
Confidence 3999999876653 344899999776
No 202
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.26 E-value=74 Score=25.22 Aligned_cols=36 Identities=19% Similarity=0.336 Sum_probs=20.6
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
...|.|+.||. ....-.+.+ +.--..|..||-.|.+
T Consensus 19 pt~f~CP~Cge-~~v~v~~~k------~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGK-VSISVKIKK------NIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCC-eEeeeecCC------CcceEECCCCCCccCE
Confidence 45689999993 222111111 3333579999976654
No 203
>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=23.23 E-value=44 Score=19.94 Aligned_cols=11 Identities=27% Similarity=0.775 Sum_probs=8.7
Q ss_pred ccCCCCCcccC
Q psy6673 239 FICRFCSRHFT 249 (286)
Q Consensus 239 ~~C~~Cgk~F~ 249 (286)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 37889998885
No 204
>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=23.10 E-value=38 Score=19.97 Aligned_cols=8 Identities=38% Similarity=0.983 Sum_probs=3.8
Q ss_pred CccCCCCC
Q psy6673 238 QFICRFCS 245 (286)
Q Consensus 238 ~~~C~~Cg 245 (286)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34555444
No 205
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=22.97 E-value=27 Score=23.54 Aligned_cols=38 Identities=18% Similarity=0.338 Sum_probs=22.1
Q ss_pred cCCCCCcccCCchhhhhhhhhcCCCCccccCC--CCCcccCc
Q psy6673 240 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDV--CNKAFRRQ 279 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~--CgK~F~~~ 279 (286)
.||.||.....+.....+... .+.-|+|.- ||-.|...
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~--~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLT--RELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCcce--EEEEEEECCCcCCCEEEEE
Confidence 488888665555444333222 245577865 88877643
No 206
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=22.84 E-value=42 Score=24.27 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=21.6
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNK 274 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK 274 (286)
.|.|+ ||..|...-. -...|++--+|+-|.-
T Consensus 22 tyPCP-CGDRFeIsLe-----Dl~~GE~VArCPSCSL 52 (67)
T COG5216 22 TYPCP-CGDRFEISLE-----DLRNGEVVARCPSCSL 52 (67)
T ss_pred EecCC-CCCEeEEEHH-----HhhCCceEEEcCCceE
Confidence 46776 9988865421 1246889999999863
No 207
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=22.78 E-value=18 Score=34.97 Aligned_cols=40 Identities=20% Similarity=0.353 Sum_probs=14.4
Q ss_pred CccCCCCCcccCCchh-h--hhhh-hhcCCC-CccccCCCCCccc
Q psy6673 238 QFICRFCSRHFTKSYN-L--LIHE-RTHTDE-RPYSCDVCNKAFR 277 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~-L--~~H~-r~Htge-KPf~C~~CgK~F~ 277 (286)
-+.|..|.+++-.... . ..|. ..|.+. |=|+|..|+++..
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~ 296 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTI 296 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEE
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeee
Confidence 3667777644433322 1 2232 123333 3466777765443
No 208
>KOG1280|consensus
Probab=22.21 E-value=61 Score=31.43 Aligned_cols=37 Identities=19% Similarity=0.485 Sum_probs=24.6
Q ss_pred CCccCCCCCcccCCchhhhhhhhh-cCCCCc-cccCCCC
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERT-HTDERP-YSCDVCN 273 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~-HtgeKP-f~C~~Cg 273 (286)
..|.|++|++.-.....|..|... |-.-.+ ..|++|+
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 479999999776666778888664 533221 3466665
No 209
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=22.08 E-value=57 Score=30.82 Aligned_cols=26 Identities=31% Similarity=0.618 Sum_probs=22.8
Q ss_pred CCCccCCCCCcccCCchhhhhhhhhc
Q psy6673 236 KKQFICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 236 ~k~~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
..-|.|+.|-+.|.....|.+|+...
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C 71 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKC 71 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhC
Confidence 45699999999999999999998743
No 210
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.06 E-value=52 Score=27.44 Aligned_cols=15 Identities=33% Similarity=0.694 Sum_probs=7.9
Q ss_pred CCccccCCCCCcccC
Q psy6673 264 ERPYSCDVCNKAFRR 278 (286)
Q Consensus 264 eKPf~C~~CgK~F~~ 278 (286)
+.|--|.-||++|.|
T Consensus 66 e~psfchncgs~fpw 80 (160)
T COG4306 66 EPPSFCHNCGSRFPW 80 (160)
T ss_pred CCcchhhcCCCCCCc
Confidence 444455555555554
No 211
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.03 E-value=46 Score=35.42 Aligned_cols=36 Identities=17% Similarity=0.281 Sum_probs=24.8
Q ss_pred ccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
..|..||..+.... .-.-+..|....-..|-.||+.
T Consensus 436 l~C~~Cg~v~~Cp~-Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 436 LLCRDCGYIAECPN-CDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred eecccCCCcccCCC-CCcceEEecCCCeeEeCCCCCC
Confidence 47999998887763 2222444555677899999975
No 212
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.91 E-value=56 Score=31.13 Aligned_cols=14 Identities=21% Similarity=0.555 Sum_probs=8.4
Q ss_pred CccccCCCCCcccC
Q psy6673 265 RPYSCDVCNKAFRR 278 (286)
Q Consensus 265 KPf~C~~CgK~F~~ 278 (286)
|-..|..|+.-++.
T Consensus 251 r~e~C~~C~~YlK~ 264 (309)
T PRK03564 251 KAESCGDCGTYLKI 264 (309)
T ss_pred Eeeeccccccccee
Confidence 44667777655444
No 213
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.74 E-value=18 Score=27.47 Aligned_cols=34 Identities=18% Similarity=0.570 Sum_probs=20.9
Q ss_pred CCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCccc
Q psy6673 237 KQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFR 277 (286)
Q Consensus 237 k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~ 277 (286)
..|+|..||..|. +..|++ ..---.|+.|+-+|+
T Consensus 11 Y~Y~c~~cg~~~d----vvq~~~---ddplt~ce~c~a~~k 44 (82)
T COG2331 11 YSYECTECGNRFD----VVQAMT---DDPLTTCEECGARLK 44 (82)
T ss_pred eEEeecccchHHH----HHHhcc---cCccccChhhChHHH
Confidence 4589999998774 333332 222246888886554
No 214
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=21.67 E-value=90 Score=27.61 Aligned_cols=43 Identities=12% Similarity=0.277 Sum_probs=25.7
Q ss_pred cccCCCCCCccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCc
Q psy6673 230 ASTARPKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA 275 (286)
Q Consensus 230 ~~~~~~~k~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~ 275 (286)
...|..-....|..|+..|....... ..+.......|+.||..
T Consensus 87 ielHG~~~~~~C~~C~~~~~~~~~~~---~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 87 SELHGNMFIEVCKSCGPEYVRDDVVE---TRGDKETGRRCHACGGI 129 (206)
T ss_pred EEecCCcCcccCCCCCCccchHHHHH---HhhcCCCCCcCCCCcCc
Confidence 33445556678999998876554332 11222334579999854
No 215
>KOG2231|consensus
Probab=21.57 E-value=41 Score=35.35 Aligned_cols=29 Identities=34% Similarity=0.698 Sum_probs=19.8
Q ss_pred cCCCCCcccCCchhhhhhhh-hcCCCCccccCCC
Q psy6673 240 ICRFCSRHFTKSYNLLIHER-THTDERPYSCDVC 272 (286)
Q Consensus 240 ~C~~Cgk~F~~~~~L~~H~r-~HtgeKPf~C~~C 272 (286)
.|..| ..|.....|+.|++ .| +-+.|.+|
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H---~~~~c~lC 146 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQH---KLHLCSLC 146 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhh---hhhccccc
Confidence 56666 56667788999995 56 44566665
No 216
>PF15296 Codanin-1_C: Codanin-1 C-terminus
Probab=21.25 E-value=1.6e+02 Score=24.16 Aligned_cols=54 Identities=30% Similarity=0.439 Sum_probs=42.5
Q ss_pred CCCchhHHHHHHHHHHHHH-------HHHHHHHHHHhhHHHHHHHHHhhcCCCCChHHhhh
Q psy6673 26 PDAGNIVKSLQTTLQEELL-------QRSLQNVALTLQTAMVSSLQQAALLPPNSPAAAAL 79 (286)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~ 79 (286)
|-....-+.||.+|.|.|+ .|++-=|+=+.=+..|..+++..|+|..-+|.+-+
T Consensus 58 ~~~~~~~~~lQ~qLeeaFfh~Qp~SlRRtVeFV~ERv~sn~VK~i~~~ll~~~~~~a~~~l 118 (121)
T PF15296_consen 58 PSRSSSPKQLQLQLEEAFFHSQPASLRRTVEFVSERVASNCVKHIKQTLLLPAVKAADAQL 118 (121)
T ss_pred ccccccHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 3445667899999999997 57888888888888899999888888776655543
No 217
>KOG2071|consensus
Probab=20.96 E-value=44 Score=34.47 Aligned_cols=23 Identities=22% Similarity=0.598 Sum_probs=18.7
Q ss_pred CCccccCCCCCcccCchhhhhcC
Q psy6673 264 ERPYSCDVCNKAFRRQDHLRDHR 286 (286)
Q Consensus 264 eKPf~C~~CgK~F~~~~~L~~H~ 286 (286)
.+|.+|..||++|.......+||
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~m 438 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHM 438 (579)
T ss_pred CCcchhcccccccccchhhhhHh
Confidence 56799999999998877666664
No 218
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.95 E-value=81 Score=33.10 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=6.5
Q ss_pred ccCCCCCccc
Q psy6673 268 SCDVCNKAFR 277 (286)
Q Consensus 268 ~C~~CgK~F~ 277 (286)
-|+.||....
T Consensus 43 fC~~CG~~~~ 52 (645)
T PRK14559 43 HCPNCGAETG 52 (645)
T ss_pred cccccCCccc
Confidence 5777876543
No 219
>PRK00420 hypothetical protein; Validated
Probab=20.74 E-value=66 Score=26.12 Aligned_cols=10 Identities=30% Similarity=0.654 Sum_probs=6.1
Q ss_pred cccCCCCCcc
Q psy6673 267 YSCDVCNKAF 276 (286)
Q Consensus 267 f~C~~CgK~F 276 (286)
..|+.||...
T Consensus 41 ~~Cp~Cg~~~ 50 (112)
T PRK00420 41 VVCPVHGKVY 50 (112)
T ss_pred eECCCCCCee
Confidence 4677776644
No 220
>PLN02748 tRNA dimethylallyltransferase
Probab=20.47 E-value=54 Score=33.05 Aligned_cols=25 Identities=16% Similarity=0.401 Sum_probs=21.1
Q ss_pred CCCccCCCCCc-ccCCchhhhhhhhh
Q psy6673 236 KKQFICRFCSR-HFTKSYNLLIHERT 260 (286)
Q Consensus 236 ~k~~~C~~Cgk-~F~~~~~L~~H~r~ 260 (286)
.+.|.|++|++ ++.-...+..|++.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcc
Confidence 46789999997 89988889888764
No 221
>KOG2231|consensus
Probab=20.35 E-value=45 Score=35.03 Aligned_cols=23 Identities=30% Similarity=0.652 Sum_probs=15.8
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q psy6673 239 FICRFCSRHFTKSYNLLIHERTH 261 (286)
Q Consensus 239 ~~C~~Cgk~F~~~~~L~~H~r~H 261 (286)
-.|.+|...|-....|.+|++.+
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~ 205 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFD 205 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccc
Confidence 36777777777777777776643
No 222
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=20.34 E-value=36 Score=23.45 Aligned_cols=11 Identities=18% Similarity=0.899 Sum_probs=5.4
Q ss_pred ccCCCCCcccC
Q psy6673 268 SCDVCNKAFRR 278 (286)
Q Consensus 268 ~C~~CgK~F~~ 278 (286)
.|++|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 78888888753
No 223
>KOG0402|consensus
Probab=20.31 E-value=34 Score=26.47 Aligned_cols=31 Identities=23% Similarity=0.659 Sum_probs=19.9
Q ss_pred CccCCCCCcccCCchhhhhhhhhcCCCCccccCCCCCcccC
Q psy6673 238 QFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKAFRR 278 (286)
Q Consensus 238 ~~~C~~Cgk~F~~~~~L~~H~r~HtgeKPf~C~~CgK~F~~ 278 (286)
.|.|++|||.--.+. ..-.|.|..|.|.|.-
T Consensus 36 ky~CsfCGK~~vKR~----------AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRK----------AVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhcchhhhhhh----------ceeEEecCCccceecc
Confidence 589999987532221 1234788888887753
No 224
>KOG4124|consensus
Probab=20.29 E-value=55 Score=31.87 Aligned_cols=25 Identities=24% Similarity=0.604 Sum_probs=21.5
Q ss_pred CCCCccCCCCCcccCCchhhhhhhh
Q psy6673 235 PKKQFICRFCSRHFTKSYNLLIHER 259 (286)
Q Consensus 235 ~~k~~~C~~Cgk~F~~~~~L~~H~r 259 (286)
..|+|+|++|.|.++....|+.|+.
T Consensus 395 ~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 395 ENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred ccCcccChhhhhhhccCCCCCceee
Confidence 4689999999999999988888754
No 225
>KOG3362|consensus
Probab=20.15 E-value=64 Score=27.46 Aligned_cols=20 Identities=30% Similarity=0.662 Sum_probs=13.0
Q ss_pred ccccCCCCCcccCchhhhhc
Q psy6673 266 PYSCDVCNKAFRRQDHLRDH 285 (286)
Q Consensus 266 Pf~C~~CgK~F~~~~~L~~H 285 (286)
+|.|.-||-.+....-+..|
T Consensus 129 ~ysC~~CG~kyCsv~C~~~H 148 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTH 148 (156)
T ss_pred hhHHHhcCCceeechhhhhc
Confidence 46677777776666666555
Done!