Query psy12012
Match_columns 79
No_of_seqs 109 out of 1417
Neff 11.5
Searched_HMMs 46136
Date Fri Aug 16 16:25:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12012.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12012hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 9.3E-21 2E-25 100.7 2.6 70 2-73 193-263 (279)
2 KOG2462|consensus 99.8 3.3E-20 7.1E-25 98.7 2.9 73 2-78 167-240 (279)
3 KOG3623|consensus 99.6 7.3E-16 1.6E-20 91.2 1.1 68 5-74 904-971 (1007)
4 KOG3576|consensus 99.4 8.9E-15 1.9E-19 75.8 -1.1 71 5-77 127-197 (267)
5 KOG3623|consensus 99.3 8.1E-13 1.8E-17 78.7 3.1 61 18-79 888-948 (1007)
6 KOG1074|consensus 99.2 1.1E-12 2.4E-17 78.8 -0.4 70 8-78 618-693 (958)
7 PHA02768 hypothetical protein; 99.2 6.2E-12 1.4E-16 52.9 1.7 43 25-70 6-48 (55)
8 KOG3576|consensus 99.2 1.9E-11 4.2E-16 63.6 3.7 75 2-77 151-236 (267)
9 PHA00733 hypothetical protein 99.2 3.9E-11 8.5E-16 59.0 4.0 56 20-78 69-124 (128)
10 KOG1074|consensus 99.2 4.9E-12 1.1E-16 76.1 0.4 54 24-78 353-406 (958)
11 PF13465 zf-H2C2_2: Zinc-finge 99.0 2.1E-10 4.6E-15 41.7 1.5 26 39-65 1-26 (26)
12 PHA00616 hypothetical protein 98.8 3.5E-09 7.6E-14 42.7 2.0 34 24-58 1-34 (44)
13 PHA00732 hypothetical protein 98.8 3.3E-09 7.1E-14 48.2 2.0 46 24-75 1-46 (79)
14 PHA00616 hypothetical protein 98.7 3.7E-09 8.1E-14 42.6 1.1 27 53-79 1-27 (44)
15 KOG3608|consensus 98.6 6.7E-09 1.4E-13 58.2 -0.2 73 5-78 189-288 (467)
16 KOG3608|consensus 98.6 1.7E-08 3.8E-13 56.6 1.3 52 25-76 264-315 (467)
17 PF05605 zf-Di19: Drought indu 98.6 1.9E-07 4.2E-12 39.5 3.6 52 24-78 2-54 (54)
18 PF13465 zf-H2C2_2: Zinc-finge 98.5 2.5E-09 5.3E-14 38.8 -2.1 24 11-35 2-25 (26)
19 PHA02768 hypothetical protein; 98.5 1E-07 2.2E-12 40.2 1.6 25 53-77 5-29 (55)
20 PHA00733 hypothetical protein 98.4 2.1E-07 4.5E-12 45.9 2.2 55 21-76 37-96 (128)
21 PF00096 zf-C2H2: Zinc finger, 98.4 1.3E-07 2.8E-12 33.1 1.1 22 54-75 1-22 (23)
22 KOG3993|consensus 98.3 1.9E-07 4.2E-12 53.5 0.7 54 24-77 295-380 (500)
23 PF00096 zf-C2H2: Zinc finger, 98.3 4E-07 8.6E-12 31.8 0.9 23 25-47 1-23 (23)
24 PF13894 zf-C2H2_4: C2H2-type 98.3 7.3E-07 1.6E-11 31.2 1.6 24 54-77 1-24 (24)
25 PLN03086 PRLI-interacting fact 98.2 1.1E-06 2.5E-11 52.3 3.0 51 8-64 465-515 (567)
26 PLN03086 PRLI-interacting fact 98.2 1.4E-06 3.1E-11 51.9 3.3 72 2-77 483-564 (567)
27 PF13912 zf-C2H2_6: C2H2-type 98.2 5E-07 1.1E-11 32.8 0.7 25 53-77 1-25 (27)
28 COG5189 SFP1 Putative transcri 98.0 2.2E-06 4.9E-11 47.8 1.0 53 21-73 346-418 (423)
29 PF13912 zf-C2H2_6: C2H2-type 98.0 2.7E-06 6E-11 30.8 0.6 25 24-48 1-25 (27)
30 smart00355 ZnF_C2H2 zinc finge 97.9 1.3E-05 2.9E-10 28.2 2.2 24 54-77 1-24 (26)
31 PF13894 zf-C2H2_4: C2H2-type 97.9 5.8E-06 1.3E-10 28.8 1.0 23 25-47 1-23 (24)
32 PF12756 zf-C2H2_2: C2H2 type 97.9 9.2E-06 2E-10 38.0 1.8 24 53-76 50-73 (100)
33 PF09237 GAGA: GAGA factor; I 97.8 2.2E-05 4.8E-10 32.5 2.3 35 18-53 18-52 (54)
34 KOG3993|consensus 97.6 1.7E-05 3.7E-10 45.8 0.6 53 23-76 266-318 (500)
35 PRK04860 hypothetical protein; 97.5 4.6E-05 9.9E-10 39.1 1.4 38 24-66 119-156 (160)
36 smart00355 ZnF_C2H2 zinc finge 97.5 7.2E-05 1.6E-09 26.2 1.5 24 25-48 1-24 (26)
37 PHA00732 hypothetical protein 97.5 0.00011 2.4E-09 33.5 2.1 26 53-78 1-27 (79)
38 PF13909 zf-H2C2_5: C2H2-type 97.5 8.7E-05 1.9E-09 26.0 1.3 23 54-77 1-23 (24)
39 PF09237 GAGA: GAGA factor; I 97.4 0.00014 3.1E-09 30.2 1.8 28 51-78 22-49 (54)
40 PF12874 zf-met: Zinc-finger o 97.3 9.8E-05 2.1E-09 26.1 0.6 21 55-75 2-22 (25)
41 PF05605 zf-Di19: Drought indu 97.0 0.00044 9.6E-09 29.1 1.5 45 2-48 8-53 (54)
42 PF13913 zf-C2HC_2: zinc-finge 96.9 0.0015 3.2E-08 23.2 2.0 21 54-75 3-23 (25)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.0007 1.5E-08 24.4 0.3 22 25-46 2-23 (27)
44 smart00451 ZnF_U1 U1-like zinc 95.6 0.01 2.2E-07 22.4 1.4 22 53-74 3-24 (35)
45 COG5189 SFP1 Putative transcri 95.4 0.0036 7.9E-08 35.6 -0.1 24 22-45 396-419 (423)
46 KOG2893|consensus 95.2 0.0043 9.3E-08 34.0 -0.4 45 22-72 9-53 (341)
47 PF09538 FYDLN_acid: Protein o 95.0 0.016 3.5E-07 28.0 1.4 33 21-66 7-39 (108)
48 KOG1146|consensus 95.0 0.023 5.1E-07 37.8 2.3 64 12-75 453-540 (1406)
49 cd00350 rubredoxin_like Rubred 94.7 0.017 3.6E-07 21.8 0.7 24 25-61 2-25 (33)
50 COG4049 Uncharacterized protei 94.6 0.03 6.4E-07 23.8 1.5 30 20-49 13-42 (65)
51 COG5048 FOG: Zn-finger [Genera 94.3 0.0069 1.5E-07 34.8 -0.9 55 23-78 288-348 (467)
52 COG1592 Rubrerythrin [Energy p 93.9 0.034 7.3E-07 28.9 1.1 24 24-61 134-157 (166)
53 PF12756 zf-C2H2_2: C2H2 type 93.9 0.032 6.9E-07 25.9 1.0 24 24-47 50-73 (100)
54 PRK04860 hypothetical protein; 93.7 0.012 2.5E-07 30.4 -0.7 29 8-37 128-156 (160)
55 PF09986 DUF2225: Uncharacteri 92.1 0.024 5.3E-07 30.6 -1.0 45 22-66 3-61 (214)
56 cd00729 rubredoxin_SM Rubredox 91.9 0.079 1.7E-06 20.2 0.6 25 24-61 2-26 (34)
57 TIGR02300 FYDLN_acid conserved 91.5 0.13 2.8E-06 25.6 1.3 32 26-69 11-42 (129)
58 KOG2186|consensus 91.2 0.15 3.2E-06 28.4 1.4 45 25-73 4-48 (276)
59 smart00659 RPOLCX RNA polymera 90.8 0.13 2.8E-06 20.8 0.8 26 25-62 3-28 (44)
60 PRK00464 nrdR transcriptional 88.9 0.077 1.7E-06 27.3 -0.7 12 54-65 29-40 (154)
61 PF12013 DUF3505: Protein of u 88.5 0.42 9.2E-06 23.0 1.7 25 54-78 81-109 (109)
62 TIGR00373 conserved hypothetic 88.4 0.23 5E-06 25.6 0.8 35 20-64 105-139 (158)
63 PRK06266 transcription initiat 88.2 0.25 5.5E-06 26.0 0.9 35 21-65 114-148 (178)
64 smart00834 CxxC_CXXC_SSSS Puta 88.1 0.18 3.9E-06 19.6 0.2 30 24-61 5-34 (41)
65 TIGR02098 MJ0042_CXXC MJ0042 f 87.8 0.26 5.5E-06 18.9 0.6 34 25-64 3-36 (38)
66 PF09723 Zn-ribbon_8: Zinc rib 87.6 0.15 3.3E-06 20.3 -0.1 29 25-61 6-34 (42)
67 PF05443 ROS_MUCR: ROS/MUCR tr 87.3 0.32 6.9E-06 24.5 0.9 23 24-49 72-94 (132)
68 TIGR02605 CxxC_CxxC_SSSS putat 87.2 0.17 3.6E-06 20.9 -0.1 29 25-61 6-34 (52)
69 smart00531 TFIIE Transcription 86.6 0.41 8.8E-06 24.4 1.1 38 21-63 96-133 (147)
70 PF04959 ARS2: Arsenite-resist 86.3 0.23 4.9E-06 27.0 0.1 28 51-78 75-102 (214)
71 PF13719 zinc_ribbon_5: zinc-r 86.1 0.39 8.4E-06 18.5 0.7 33 26-64 4-36 (37)
72 PF13717 zinc_ribbon_4: zinc-r 86.0 0.35 7.6E-06 18.6 0.5 32 26-63 4-35 (36)
73 COG2888 Predicted Zn-ribbon RN 85.7 0.48 1E-05 20.5 0.9 31 24-60 27-57 (61)
74 COG1996 RPC10 DNA-directed RNA 85.2 0.44 9.6E-06 19.8 0.6 28 24-62 6-33 (49)
75 PF15269 zf-C2H2_7: Zinc-finge 85.0 0.66 1.4E-05 18.9 1.1 21 54-74 21-41 (54)
76 smart00614 ZnF_BED BED zinc fi 85.0 1.1 2.3E-05 18.4 1.8 7 68-74 38-44 (50)
77 PRK00398 rpoP DNA-directed RNA 84.5 0.25 5.4E-06 20.0 -0.2 30 24-64 3-32 (46)
78 COG1997 RPL43A Ribosomal prote 83.9 0.31 6.7E-06 22.7 -0.1 33 22-65 33-65 (89)
79 COG5048 FOG: Zn-finger [Genera 83.9 0.47 1E-05 27.4 0.6 51 5-57 299-355 (467)
80 COG2331 Uncharacterized protei 82.3 0.61 1.3E-05 21.2 0.5 32 23-62 11-42 (82)
81 KOG2593|consensus 81.0 1.1 2.3E-05 27.1 1.3 40 18-61 122-161 (436)
82 PF10571 UPF0547: Uncharacteri 80.9 1.1 2.5E-05 15.9 0.9 10 55-64 16-25 (26)
83 COG4957 Predicted transcriptio 80.2 1 2.2E-05 22.8 0.9 21 55-78 78-98 (148)
84 smart00734 ZnF_Rad18 Rad18-lik 80.1 2.2 4.7E-05 15.1 1.6 19 55-74 3-21 (26)
85 KOG4167|consensus 79.8 0.97 2.1E-05 29.2 0.9 26 23-48 791-816 (907)
86 TIGR01206 lysW lysine biosynth 79.8 0.51 1.1E-05 20.0 -0.1 30 25-63 3-32 (54)
87 PF03604 DNA_RNApol_7kD: DNA d 79.8 1 2.2E-05 16.9 0.7 10 53-62 17-26 (32)
88 PF12907 zf-met2: Zinc-binding 78.1 1.4 3E-05 17.5 0.8 25 25-49 2-29 (40)
89 PRK14890 putative Zn-ribbon RN 77.5 1.7 3.7E-05 18.8 1.1 32 24-61 25-56 (59)
90 PHA00626 hypothetical protein 77.1 1.3 2.9E-05 18.9 0.7 16 52-67 22-37 (59)
91 PF07754 DUF1610: Domain of un 76.1 1.4 3.1E-05 15.4 0.6 8 53-60 16-23 (24)
92 KOG4167|consensus 75.8 0.37 8E-06 30.9 -1.5 24 53-76 792-815 (907)
93 cd00730 rubredoxin Rubredoxin; 74.6 1.1 2.3E-05 18.7 0.1 13 25-37 2-14 (50)
94 KOG3408|consensus 74.3 1.4 3E-05 21.9 0.5 24 52-75 56-79 (129)
95 PF07503 zf-HYPF: HypF finger; 73.2 2.2 4.8E-05 16.3 0.8 31 27-64 2-32 (35)
96 PRK09678 DNA-binding transcrip 72.5 1.2 2.7E-05 20.0 0.1 14 24-37 27-42 (72)
97 PF00301 Rubredoxin: Rubredoxi 71.4 2.5 5.4E-05 17.3 0.8 37 25-62 2-43 (47)
98 PRK03824 hypA hydrogenase nick 70.2 1.4 3.1E-05 22.2 0.0 15 23-37 69-83 (135)
99 PF11672 DUF3268: Protein of u 67.8 1.9 4.1E-05 20.8 0.1 14 23-36 1-14 (102)
100 PF02892 zf-BED: BED zinc fing 67.6 4.3 9.4E-05 15.9 1.2 11 54-64 17-27 (45)
101 smart00154 ZnF_AN1 AN1-like Zi 67.1 3.4 7.4E-05 16.1 0.8 13 53-65 12-24 (39)
102 KOG1146|consensus 67.0 4.7 0.0001 28.1 1.7 55 22-77 1282-1352(1406)
103 PF02176 zf-TRAF: TRAF-type zi 66.3 1.8 4E-05 18.1 -0.1 40 24-64 9-53 (60)
104 COG5236 Uncharacterized conser 65.9 9.8 0.00021 22.8 2.7 47 26-74 222-272 (493)
105 PTZ00255 60S ribosomal protein 65.8 1.2 2.5E-05 21.0 -0.7 31 23-64 35-65 (90)
106 KOG1842|consensus 64.4 3.5 7.6E-05 25.2 0.8 23 24-46 15-37 (505)
107 PF07975 C1_4: TFIIH C1-like d 64.3 2.1 4.6E-05 17.9 -0.0 26 22-47 19-44 (51)
108 KOG2482|consensus 63.9 4.6 9.9E-05 24.0 1.2 22 53-74 195-216 (423)
109 KOG2785|consensus 63.7 8.9 0.00019 23.0 2.3 51 24-74 166-241 (390)
110 PF13878 zf-C2H2_3: zinc-finge 61.7 10 0.00023 14.9 2.0 23 54-76 14-38 (41)
111 COG1571 Predicted DNA-binding 60.1 7.4 0.00016 23.7 1.6 29 26-66 352-380 (421)
112 TIGR00280 L37a ribosomal prote 59.6 2.1 4.5E-05 20.2 -0.5 31 23-64 34-64 (91)
113 PF04423 Rad50_zn_hook: Rad50 58.9 3.5 7.7E-05 17.1 0.2 11 55-65 22-32 (54)
114 PF09963 DUF2197: Uncharacteri 58.9 3.1 6.8E-05 17.8 -0.0 8 24-31 31-38 (56)
115 KOG2071|consensus 58.8 7.6 0.00016 24.6 1.5 27 51-77 416-442 (579)
116 PF05191 ADK_lid: Adenylate ki 58.6 4.9 0.00011 15.4 0.5 11 53-63 21-31 (36)
117 TIGR00244 transcriptional regu 57.2 2.3 5E-05 21.9 -0.6 12 54-65 29-40 (147)
118 PLN02294 cytochrome c oxidase 57.0 6.2 0.00013 21.0 0.8 25 40-66 130-154 (174)
119 PF07295 DUF1451: Protein of u 56.8 3.2 6.9E-05 21.4 -0.2 32 20-62 108-139 (146)
120 KOG2636|consensus 56.2 9.6 0.00021 23.5 1.6 27 45-72 394-421 (497)
121 COG4306 Uncharacterized protei 56.0 3.4 7.3E-05 20.8 -0.2 16 51-66 66-81 (160)
122 COG4888 Uncharacterized Zn rib 55.6 1.1 2.3E-05 21.6 -1.8 38 21-63 19-56 (104)
123 PF13451 zf-trcl: Probable zin 55.3 4.9 0.00011 16.7 0.3 15 52-66 3-17 (49)
124 PF08274 PhnA_Zn_Ribbon: PhnA 55.0 6.2 0.00013 14.6 0.5 10 52-61 18-27 (30)
125 COG0068 HypF Hydrogenase matur 54.5 11 0.00024 24.7 1.7 49 5-62 133-182 (750)
126 PF13824 zf-Mss51: Zinc-finger 54.4 9.6 0.00021 16.3 1.1 9 52-60 13-21 (55)
127 PRK03976 rpl37ae 50S ribosomal 54.3 2.8 6.1E-05 19.8 -0.5 31 23-64 35-65 (90)
128 COG3091 SprT Zn-dependent meta 54.2 4.6 0.0001 21.0 0.2 34 23-62 116-149 (156)
129 PF01428 zf-AN1: AN1-like Zinc 52.7 3.8 8.3E-05 16.2 -0.2 13 52-64 12-24 (43)
130 COG1327 Predicted transcriptio 51.1 3.5 7.6E-05 21.4 -0.5 10 55-64 30-39 (156)
131 cd00924 Cyt_c_Oxidase_Vb Cytoc 51.0 9 0.00019 18.4 0.8 22 42-65 70-91 (97)
132 COG4530 Uncharacterized protei 50.1 9.3 0.0002 18.8 0.8 33 21-66 7-39 (129)
133 PF08790 zf-LYAR: LYAR-type C2 50.0 3.6 7.9E-05 15.0 -0.4 9 26-34 2-10 (28)
134 PF04780 DUF629: Protein of un 49.8 14 0.00031 22.9 1.7 22 54-75 58-79 (466)
135 COG3357 Predicted transcriptio 49.5 8.6 0.00019 18.2 0.6 15 51-65 56-70 (97)
136 PF12230 PRP21_like_P: Pre-mRN 49.1 5.7 0.00012 21.8 0.0 25 24-49 168-192 (229)
137 KOG0717|consensus 48.0 9.3 0.0002 23.7 0.7 22 25-46 293-314 (508)
138 PF10013 DUF2256: Uncharacteri 47.8 11 0.00024 15.1 0.7 12 55-66 10-21 (42)
139 PF02891 zf-MIZ: MIZ/SP-RING z 47.5 14 0.00031 15.2 1.1 23 34-61 27-49 (50)
140 PRK12380 hydrogenase nickel in 47.5 8.2 0.00018 18.9 0.4 25 24-61 70-94 (113)
141 COG1198 PriA Primosomal protei 47.4 4.9 0.00011 26.2 -0.4 12 51-62 473-484 (730)
142 KOG0978|consensus 47.3 9.6 0.00021 24.8 0.8 19 52-70 677-695 (698)
143 KOG2231|consensus 46.7 27 0.00058 22.9 2.5 46 26-76 184-235 (669)
144 PRK05452 anaerobic nitric oxid 46.7 7.4 0.00016 24.0 0.2 41 21-62 422-467 (479)
145 TIGR00100 hypA hydrogenase nic 45.5 8.1 0.00018 18.9 0.2 25 24-61 70-94 (115)
146 PF02591 DUF164: Putative zinc 45.4 19 0.00041 15.0 1.4 31 26-61 24-54 (56)
147 PF10083 DUF2321: Uncharacteri 44.3 3.8 8.2E-05 21.4 -1.0 16 51-66 66-81 (158)
148 PF10276 zf-CHCC: Zinc-finger 44.0 7.7 0.00017 15.4 0.0 12 23-34 28-39 (40)
149 PF07282 OrfB_Zn_ribbon: Putat 43.5 12 0.00026 16.2 0.6 13 51-63 44-56 (69)
150 COG3677 Transposase and inacti 43.1 16 0.00034 18.4 1.0 16 51-66 51-66 (129)
151 PF14353 CpXC: CpXC protein 43.1 12 0.00027 18.4 0.7 14 52-65 37-50 (128)
152 PF01155 HypA: Hydrogenase exp 42.8 9.2 0.0002 18.7 0.2 12 25-36 71-82 (113)
153 COG1773 Rubredoxin [Energy pro 42.8 10 0.00023 16.2 0.3 11 53-63 3-13 (55)
154 PF09845 DUF2072: Zn-ribbon co 41.7 16 0.00035 18.6 0.9 12 54-65 2-13 (131)
155 KOG4173|consensus 41.6 30 0.00066 19.2 2.0 50 26-75 108-168 (253)
156 PF11931 DUF3449: Domain of un 39.8 9.6 0.00021 20.7 0.0 22 51-72 99-121 (196)
157 PF06397 Desulfoferrod_N: Desu 39.7 12 0.00027 14.4 0.3 10 53-62 6-15 (36)
158 PF05741 zf-nanos: Nanos RNA b 38.4 10 0.00022 16.2 -0.0 8 54-61 34-41 (55)
159 COG1675 TFA1 Transcription ini 38.3 23 0.0005 19.0 1.2 34 20-63 109-142 (176)
160 PF14369 zf-RING_3: zinc-finge 38.3 18 0.0004 13.7 0.7 10 55-64 23-32 (35)
161 PF10263 SprT-like: SprT-like 38.3 8.3 0.00018 19.6 -0.4 31 24-63 123-153 (157)
162 PF03811 Zn_Tnp_IS1: InsA N-te 38.1 5.1 0.00011 15.4 -0.9 18 41-59 18-35 (36)
163 PF11789 zf-Nse: Zinc-finger o 37.6 21 0.00046 15.2 0.9 32 22-58 22-53 (57)
164 TIGR00622 ssl1 transcription f 37.0 31 0.00067 17.1 1.5 49 26-77 57-105 (112)
165 PF14311 DUF4379: Domain of un 36.6 24 0.00051 14.6 1.0 13 25-37 29-41 (55)
166 cd00065 FYVE FYVE domain; Zinc 35.4 30 0.00066 14.1 1.2 9 27-35 5-13 (57)
167 PF01927 Mut7-C: Mut7-C RNAse 35.4 27 0.00058 17.9 1.2 47 24-70 91-141 (147)
168 PF14803 Nudix_N_2: Nudix N-te 35.3 6.2 0.00013 15.0 -0.9 7 54-60 23-29 (34)
169 COG1655 Uncharacterized protei 34.9 6.2 0.00013 22.1 -1.2 24 23-46 18-41 (267)
170 KOG1994|consensus 34.5 17 0.00037 20.4 0.4 20 24-43 239-258 (268)
171 PF02146 SIR2: Sir2 family; I 34.4 20 0.00043 18.8 0.6 40 18-62 99-138 (178)
172 PF14787 zf-CCHC_5: GAG-polypr 34.1 35 0.00075 13.2 1.1 13 55-67 4-16 (36)
173 PTZ00043 cytochrome c oxidase 34.1 26 0.00055 19.8 1.0 15 51-65 179-193 (268)
174 PF08209 Sgf11: Sgf11 (transcr 33.8 36 0.00078 12.8 1.3 20 53-73 4-23 (33)
175 PRK11032 hypothetical protein; 33.0 17 0.00036 19.2 0.2 31 21-62 121-151 (160)
176 PF05180 zf-DNL: DNL zinc fing 32.7 2.4 5.3E-05 18.8 -2.4 34 25-62 5-38 (66)
177 PF08271 TF_Zn_Ribbon: TFIIB z 32.1 29 0.00062 13.6 0.8 8 55-62 2-9 (43)
178 smart00064 FYVE Protein presen 31.9 33 0.0007 14.7 1.0 12 25-36 11-22 (68)
179 KOG4124|consensus 31.5 12 0.00027 22.3 -0.4 23 22-44 396-418 (442)
180 PF01215 COX5B: Cytochrome c o 31.3 12 0.00026 19.2 -0.4 16 22-37 110-125 (136)
181 PTZ00448 hypothetical protein; 30.9 43 0.00093 20.3 1.6 22 53-74 314-335 (373)
182 KOG0562|consensus 30.9 43 0.00093 18.0 1.5 27 51-77 151-177 (184)
183 PRK12860 transcriptional activ 30.4 27 0.00059 19.0 0.8 28 24-60 134-161 (189)
184 KOG3214|consensus 30.4 31 0.00066 16.8 0.8 12 54-65 48-59 (109)
185 PF04810 zf-Sec23_Sec24: Sec23 30.0 22 0.00047 13.8 0.3 13 21-33 21-33 (40)
186 PRK12722 transcriptional activ 29.9 31 0.00066 18.7 0.9 29 24-61 134-162 (187)
187 PRK01343 zinc-binding protein; 29.6 44 0.00096 14.4 1.2 13 52-64 8-20 (57)
188 KOG3352|consensus 29.3 32 0.0007 18.0 0.9 22 43-66 125-146 (153)
189 COG0675 Transposase and inacti 28.5 26 0.00057 19.9 0.5 11 52-62 321-331 (364)
190 PF04606 Ogr_Delta: Ogr/Delta- 28.1 8.9 0.00019 15.5 -1.0 11 54-64 26-38 (47)
191 PF02748 PyrI_C: Aspartate car 28.0 26 0.00056 14.7 0.4 17 21-37 32-48 (52)
192 PRK14873 primosome assembly pr 27.8 46 0.00099 21.8 1.5 11 52-62 421-431 (665)
193 KOG4118|consensus 27.4 59 0.0013 14.5 1.4 26 24-49 38-63 (74)
194 COG5539 Predicted cysteine pro 27.2 30 0.00066 20.2 0.6 22 24-45 275-296 (306)
195 PF14690 zf-ISL3: zinc-finger 27.2 40 0.00086 13.2 0.9 9 53-61 2-10 (47)
196 PF06524 NOA36: NOA36 protein; 27.1 15 0.00031 21.1 -0.6 21 51-71 207-227 (314)
197 COG3364 Zn-ribbon containing p 27.1 31 0.00067 16.9 0.5 14 24-37 2-15 (112)
198 COG0846 SIR2 NAD-dependent pro 26.7 42 0.00091 19.1 1.1 40 17-61 115-154 (250)
199 TIGR03831 YgiT_finger YgiT-typ 26.3 32 0.0007 13.2 0.5 13 52-64 31-43 (46)
200 PF01286 XPA_N: XPA protein N- 26.3 29 0.00062 13.2 0.3 11 55-65 5-15 (34)
201 cd00974 DSRD Desulforedoxin (D 26.2 36 0.00078 12.5 0.6 11 53-63 4-14 (34)
202 COG4338 Uncharacterized protei 26.2 21 0.00045 14.8 -0.1 12 55-66 14-25 (54)
203 PRK05580 primosome assembly pr 26.2 22 0.00047 23.1 -0.0 12 51-62 419-430 (679)
204 PF05766 NinG: Bacteriophage L 26.2 32 0.0007 18.7 0.6 14 23-36 5-18 (189)
205 TIGR00319 desulf_FeS4 desulfof 25.9 36 0.00078 12.5 0.6 11 53-63 7-17 (34)
206 PLN03238 probable histone acet 25.7 59 0.0013 19.1 1.5 24 51-74 46-69 (290)
207 PF10272 Tmpp129: Putative tra 25.6 34 0.00075 20.6 0.7 36 27-65 316-352 (358)
208 PRK09951 hypothetical protein; 25.6 32 0.0007 19.1 0.5 10 1-10 1-10 (222)
209 CHL00174 accD acetyl-CoA carbo 25.5 60 0.0013 19.1 1.6 30 26-65 40-69 (296)
210 PF14447 Prok-RING_4: Prokaryo 25.5 51 0.0011 14.1 1.0 10 56-65 42-51 (55)
211 PF14255 Cys_rich_CPXG: Cystei 25.4 41 0.00089 14.1 0.7 9 55-63 2-10 (52)
212 PRK04351 hypothetical protein; 25.4 21 0.00046 18.5 -0.1 33 24-65 112-144 (149)
213 KOG0782|consensus 25.2 19 0.00041 23.3 -0.4 14 54-67 254-267 (1004)
214 PF15135 UPF0515: Uncharacteri 25.2 28 0.00061 19.9 0.3 13 53-65 155-167 (278)
215 PF08792 A2L_zn_ribbon: A2L zi 25.0 32 0.00069 12.9 0.3 11 54-64 22-32 (33)
216 COG4391 Uncharacterized protei 25.0 45 0.00097 14.7 0.8 43 18-65 18-60 (62)
217 PF06676 DUF1178: Protein of u 24.9 95 0.002 16.3 2.1 9 53-61 32-40 (148)
218 PF04216 FdhE: Protein involve 24.9 23 0.00049 20.3 -0.1 10 53-62 211-220 (290)
219 COG5112 UFD2 U1-like Zn-finger 24.6 95 0.0021 15.3 1.9 27 20-46 51-77 (126)
220 KOG0402|consensus 24.5 23 0.0005 16.6 -0.1 30 24-64 36-65 (92)
221 PF13821 DUF4187: Domain of un 24.4 29 0.00063 14.7 0.2 17 25-41 28-44 (55)
222 TIGR00595 priA primosomal prot 23.8 25 0.00054 22.0 -0.1 10 52-61 252-261 (505)
223 PF11494 Ta0938: Ta0938; Inte 23.4 44 0.00095 16.2 0.7 42 18-66 8-50 (105)
224 PF01096 TFIIS_C: Transcriptio 23.3 17 0.00036 14.1 -0.6 10 25-34 29-38 (39)
225 KOG3456|consensus 23.3 40 0.00087 16.6 0.6 13 24-36 104-116 (120)
226 COG5151 SSL1 RNA polymerase II 23.1 95 0.0021 18.6 2.0 48 26-76 364-411 (421)
227 PF09889 DUF2116: Uncharacteri 22.7 33 0.00071 14.9 0.2 7 27-33 6-12 (59)
228 COG4847 Uncharacterized protei 22.6 21 0.00045 17.1 -0.4 11 23-33 5-15 (103)
229 PF09943 DUF2175: Uncharacteri 22.6 21 0.00045 17.3 -0.5 10 24-33 2-11 (101)
230 PF10122 Mu-like_Com: Mu-like 22.4 26 0.00057 14.7 -0.1 10 53-62 24-33 (51)
231 PLN02748 tRNA dimethylallyltra 22.3 79 0.0017 19.9 1.7 23 52-74 417-440 (468)
232 COG5216 Uncharacterized conser 22.2 43 0.00093 14.6 0.5 11 54-65 23-33 (67)
233 PF01844 HNH: HNH endonuclease 22.2 13 0.00028 14.4 -1.1 11 27-37 1-11 (47)
234 smart00586 ZnF_DBF Zinc finger 22.1 82 0.0018 13.1 1.5 22 22-46 3-24 (49)
235 PF10071 DUF2310: Zn-ribbon-co 21.6 39 0.00085 19.4 0.4 29 24-60 220-248 (258)
236 PTZ00409 Sir2 (Silent Informat 21.4 1.1E+02 0.0024 17.6 2.1 21 18-38 131-151 (271)
237 PF10164 DUF2367: Uncharacteri 21.3 62 0.0013 15.7 1.0 13 51-63 86-98 (98)
238 PF14354 Lar_restr_allev: Rest 21.2 42 0.0009 14.1 0.4 12 23-34 2-13 (61)
239 TIGR03829 YokU_near_AblA uncha 21.0 83 0.0018 14.9 1.3 16 52-67 34-49 (89)
240 PF14375 Cys_rich_CWC: Cystein 21.0 61 0.0013 13.2 0.8 7 57-63 2-8 (50)
241 KOG3362|consensus 20.9 27 0.00058 18.2 -0.3 21 53-73 129-149 (156)
242 COG1579 Zn-ribbon protein, pos 20.7 87 0.0019 17.8 1.6 12 51-62 219-230 (239)
243 PRK12496 hypothetical protein; 20.7 48 0.001 17.4 0.6 12 53-64 127-138 (164)
244 TIGR00515 accD acetyl-CoA carb 20.3 89 0.0019 18.2 1.6 31 25-65 27-57 (285)
245 PF00412 LIM: LIM domain; Int 20.2 14 0.0003 15.1 -1.3 10 54-63 27-36 (58)
246 PRK14138 NAD-dependent deacety 20.2 1.2E+02 0.0027 17.0 2.1 40 17-61 112-151 (244)
No 1
>KOG2462|consensus
Probab=99.81 E-value=9.3e-21 Score=100.75 Aligned_cols=70 Identities=23% Similarity=0.396 Sum_probs=41.2
Q ss_pred Ccc-cccccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHH
Q psy12012 2 FGQ-FRFSESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHM 73 (79)
Q Consensus 2 ~~~-f~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~ 73 (79)
||+ |++.=-|+.| ++.|+|||||.|..|++.|..+++|..||++|.+ .++|+|..|+++|...+.|..|.
T Consensus 193 CGKaFSRPWLLQGH-iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~-~K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 193 CGKAFSRPWLLQGH-IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD-VKKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred ccccccchHHhhcc-cccccCCCCccCCcccchhcchHHHHHHHHhhcC-CccccCcchhhHHHHHHHHHHhh
Confidence 444 5544445555 5566666666666666666666666666666655 55566666666666666665554
No 2
>KOG2462|consensus
Probab=99.80 E-value=3.3e-20 Score=98.69 Aligned_cols=73 Identities=19% Similarity=0.419 Sum_probs=64.5
Q ss_pred Ccc-cccccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhhcC
Q psy12012 2 FGQ-FRFSESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 2 ~~~-f~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
||+ |++.-.|+.| ++.|+ -+..|.+||+.|.++.-|+.|++.|+| ++||.|+.|++.|..++.|..|+++|.+
T Consensus 167 C~K~YvSmpALkMH-irTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTG-EKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 167 CGKVYVSMPALKMH-IRTHT--LPCECGICGKAFSRPWLLQGHIRTHTG-EKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred CCceeeehHHHhhH-hhccC--CCcccccccccccchHHhhcccccccC-CCCccCCcccchhcchHHHHHHHHhhcC
Confidence 444 6666777777 55554 679999999999999999999999999 9999999999999999999999999976
No 3
>KOG3623|consensus
Probab=99.56 E-value=7.3e-16 Score=91.15 Aligned_cols=68 Identities=28% Similarity=0.555 Sum_probs=59.7
Q ss_pred cccccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHH
Q psy12012 5 FRFSESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMA 74 (79)
Q Consensus 5 f~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 74 (79)
|.-.++|..| ...|+|.+||.|.+|.+.|..+..|..|.+.|.| ++||.|..|++.|.++.+...||-
T Consensus 904 FqKqSSLaRH-KYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSG-EKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 904 FQKQSSLARH-KYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSG-EKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred HHhhHHHHHh-hhhhcCCCCcccchhhHhhhhhhhhhhhhhhccC-CCcchhhhhhhhcccccchHhhhc
Confidence 5556778888 7889999999999999999999999999999999 999999999999999988888863
No 4
>KOG3576|consensus
Probab=99.43 E-value=8.9e-15 Score=75.75 Aligned_cols=71 Identities=20% Similarity=0.450 Sum_probs=49.0
Q ss_pred cccccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhhc
Q psy12012 5 FRFSESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 5 f~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
|....-|-.| +.-|...+.+.|..||+.|...-+|.+|++.|+| .+||+|..|++.|.+..+|..|.+--+
T Consensus 127 F~lQRmlnrh-~kch~~vkr~lct~cgkgfndtfdlkrh~rthtg-vrpykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 127 FGLQRMLNRH-LKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTG-VRPYKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred hhHHHHHHHH-hhhccHHHHHHHhhccCcccchhhhhhhhccccC-ccccchhhhhHHHHhhccHHHHHHHHc
Confidence 3333333444 5556666777777777777777777788887777 777888888888887777777765433
No 5
>KOG3623|consensus
Probab=99.34 E-value=8.1e-13 Score=78.68 Aligned_cols=61 Identities=30% Similarity=0.643 Sum_probs=57.1
Q ss_pred CCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhhcCC
Q psy12012 18 EPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKHSD 79 (79)
Q Consensus 18 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e 79 (79)
..+...+|.|..|++.|...+.|.+|.--|+| .+||+|.+|.+.|.++-.|..|+|.|.||
T Consensus 888 ~kte~gmyaCDqCDK~FqKqSSLaRHKYEHsG-qRPyqC~iCkKAFKHKHHLtEHkRLHSGE 948 (1007)
T KOG3623|consen 888 AKTEDGMYACDQCDKAFQKQSSLARHKYEHSG-QRPYQCIICKKAFKHKHHLTEHKRLHSGE 948 (1007)
T ss_pred ccCccccchHHHHHHHHHhhHHHHHhhhhhcC-CCCcccchhhHhhhhhhhhhhhhhhccCC
Confidence 34556789999999999999999999999999 99999999999999999999999999997
No 6
>KOG1074|consensus
Probab=99.23 E-value=1.1e-12 Score=78.75 Aligned_cols=70 Identities=19% Similarity=0.444 Sum_probs=49.3
Q ss_pred ccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhcC---CCCccCC---CCCCcccCcchHHHHHHhhcC
Q psy12012 8 SESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGK---EPRYQCP---QCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~---~~~~~c~---~c~~~f~~~~~l~~h~~~h~~ 78 (79)
.++|+.| .+.|+|++||+|.+||+.|..+.+|+.|+.+|... ..++.|+ +|-+.|.+.-.|+.|+++|++
T Consensus 618 ~saLqmH-yrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 618 PSALQMH-YRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHLG 693 (958)
T ss_pred hhhhhhh-hhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccceEEeecC
Confidence 4566666 67777777777777777777777777777776541 2346677 777777777777777777764
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.21 E-value=6.2e-12 Score=52.85 Aligned_cols=43 Identities=12% Similarity=0.379 Sum_probs=38.3
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHH
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLK 70 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~ 70 (79)
|.|+.||+.|...+.|..|++.|. ++++|..|++.|...+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~---k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN---TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC---CcccCCcccceecccceeE
Confidence 799999999999999999999985 5889999999998776653
No 8
>KOG3576|consensus
Probab=99.21 E-value=1.9e-11 Score=63.60 Aligned_cols=75 Identities=17% Similarity=0.410 Sum_probs=61.4
Q ss_pred Ccc-cccccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhcC----------CCCccCCCCCCcccCcchHH
Q psy12012 2 FGQ-FRFSESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGK----------EPRYQCPQCPHRTKQKSSLK 70 (79)
Q Consensus 2 ~~~-f~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~----------~~~~~c~~c~~~f~~~~~l~ 70 (79)
||+ |-....|+.| .+.|+|.+||.|..|++.|+....|..|.+--+|- .+.|.|..||.+-.......
T Consensus 151 cgkgfndtfdlkrh-~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~ 229 (267)
T KOG3576|consen 151 CGKGFNDTFDLKRH-TRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYY 229 (267)
T ss_pred ccCcccchhhhhhh-hccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHH
Confidence 555 6666788889 89999999999999999999999999998743331 46799999998887777777
Q ss_pred HHHHhhc
Q psy12012 71 THMAVKH 77 (79)
Q Consensus 71 ~h~~~h~ 77 (79)
.|...|+
T Consensus 230 ~h~~~~h 236 (267)
T KOG3576|consen 230 LHLKLHH 236 (267)
T ss_pred HHHHhcC
Confidence 7877665
No 9
>PHA00733 hypothetical protein
Probab=99.19 E-value=3.9e-11 Score=58.99 Aligned_cols=56 Identities=27% Similarity=0.538 Sum_probs=49.4
Q ss_pred CCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhhcC
Q psy12012 20 NHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 20 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
.+.+||.|..|++.|.....|..|++.+ ..++.|..|++.|.....|..|+...++
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3578999999999999999999999875 3479999999999999999999887654
No 10
>KOG1074|consensus
Probab=99.17 E-value=4.9e-12 Score=76.12 Aligned_cols=54 Identities=28% Similarity=0.538 Sum_probs=50.3
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhhcC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
..+|..|.+.|...+.|+.|.+.|+| ++||+|++|+..|..+..|+.|...|+.
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTG-ERPfqCnvCG~~FSTkGNLKvH~~rH~e 406 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTG-ERPFQCNVCGNRFSTKGNLKVHFQRHRE 406 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCC-CCCeeecccccccccccceeeeeeeccc
Confidence 46899999999999999999999999 9999999999999999999999877754
No 11
>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=99.00 E-value=2.1e-10 Score=41.68 Aligned_cols=26 Identities=31% Similarity=0.689 Sum_probs=22.1
Q ss_pred hHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 39 GLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 39 ~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
+|..|++.|.+ ++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~-~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTG-EKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSS-SSSEEESSSSEEESS
T ss_pred CHHHHhhhcCC-CCCCCCCCCcCeeCc
Confidence 47889999988 899999999988863
No 12
>PHA00616 hypothetical protein
Probab=98.82 E-value=3.5e-09 Score=42.65 Aligned_cols=34 Identities=12% Similarity=0.261 Sum_probs=30.1
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQ 58 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~ 58 (79)
||.|..||+.|...+.|..|++.+++ +.++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCccceeE
Confidence 68899999999999999999999999 88887664
No 13
>PHA00732 hypothetical protein
Probab=98.80 E-value=3.3e-09 Score=48.16 Aligned_cols=46 Identities=24% Similarity=0.489 Sum_probs=36.6
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHh
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAV 75 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 75 (79)
||.|..|++.|.....|..|++.++. ++.|+.|++.|.. +..|.++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhcc
Confidence 57899999999999999999985322 3579999999974 5667654
No 14
>PHA00616 hypothetical protein
Probab=98.74 E-value=3.7e-09 Score=42.57 Aligned_cols=27 Identities=26% Similarity=0.527 Sum_probs=25.5
Q ss_pred CccCCCCCCcccCcchHHHHHHhhcCC
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMAVKHSD 79 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~~h~~e 79 (79)
||+|..||+.|.+.+.+..|++.|+|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCC
Confidence 689999999999999999999999985
No 15
>KOG3608|consensus
Probab=98.60 E-value=6.7e-09 Score=58.20 Aligned_cols=73 Identities=22% Similarity=0.458 Sum_probs=46.0
Q ss_pred cccccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhc-C--------------------------CCCccCC
Q psy12012 5 FRFSESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECG-K--------------------------EPRYQCP 57 (79)
Q Consensus 5 f~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~-~--------------------------~~~~~c~ 57 (79)
+.++..|+.| +..|+++|...|+.||..|..+..|..|.+..+. . ..-|+|+
T Consensus 189 ~~~k~~LreH-~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCp 267 (467)
T KOG3608|consen 189 MGNKYRLREH-IRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCP 267 (467)
T ss_pred hccHHHHHHH-HHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhccccc
Confidence 4556667777 6677777777777777766666666666554321 1 1246667
Q ss_pred CCCCcccCcchHHHHHHhhcC
Q psy12012 58 QCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 58 ~c~~~f~~~~~l~~h~~~h~~ 78 (79)
.|..+....+.|.+|++..+.
T Consensus 268 lCdmtc~~~ssL~~H~r~rHs 288 (467)
T KOG3608|consen 268 LCDMTCSSASSLTTHIRYRHS 288 (467)
T ss_pred ccccCCCChHHHHHHHHhhhc
Confidence 777777777777777765543
No 16
>KOG3608|consensus
Probab=98.60 E-value=1.7e-08 Score=56.60 Aligned_cols=52 Identities=29% Similarity=0.662 Sum_probs=25.1
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhh
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVK 76 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h 76 (79)
|+|+.|+-.....+.|..|++..+...+||+|..|...+...+.|+.|..+|
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc
Confidence 3444444444444444444443222245555555555555555555555544
No 17
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.55 E-value=1.9e-07 Score=39.50 Aligned_cols=52 Identities=25% Similarity=0.523 Sum_probs=38.9
Q ss_pred ccccchhhhhhcchhhHHhHhhh-hhcCCCCccCCCCCCcccCcchHHHHHHhhcC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKY-ECGKEPRYQCPQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
.|.|+.|++. .....|..|... |....+.+.|++|...+. ..|..|+..+++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4899999995 445779999776 444245788999987654 488899988764
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.53 E-value=2.5e-09 Score=38.84 Aligned_cols=24 Identities=8% Similarity=0.373 Sum_probs=20.4
Q ss_pred cccccccCCCCCCccccchhhhhhc
Q psy12012 11 FTSWEASEPNHAGLFVCDVCDRRYK 35 (79)
Q Consensus 11 ~~~~~~~~~~~~~~~~c~~c~~~~~ 35 (79)
|..| +..|++++||.|..|++.|.
T Consensus 2 l~~H-~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRH-MRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHH-HHHHSSSSSEEESSSSEEES
T ss_pred HHHH-hhhcCCCCCCCCCCCcCeeC
Confidence 5667 66799999999999999885
No 19
>PHA02768 hypothetical protein; Provisional
Probab=98.46 E-value=1e-07 Score=40.22 Aligned_cols=25 Identities=28% Similarity=0.635 Sum_probs=23.6
Q ss_pred CccCCCCCCcccCcchHHHHHHhhc
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
-|.|+.|++.|...+.|..|+++|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4899999999999999999999997
No 20
>PHA00733 hypothetical protein
Probab=98.41 E-value=2.1e-07 Score=45.95 Aligned_cols=55 Identities=18% Similarity=0.187 Sum_probs=42.8
Q ss_pred CCCccccchhhhhhcchhhHHhHhh-----hhhcCCCCccCCCCCCcccCcchHHHHHHhh
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKK-----YECGKEPRYQCPQCPHRTKQKSSLKTHMAVK 76 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~-----~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h 76 (79)
..+++.|.+|...+..+..|..+.. ...+ .+||.|..|++.|...+.|..|++.+
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKA-VSPYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCC-CCCccCCCCCCcCCCHHHHHHHHhcC
Confidence 4577899999988887776665511 1223 67999999999999999999998854
No 21
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.41 E-value=1.3e-07 Score=33.13 Aligned_cols=22 Identities=45% Similarity=0.846 Sum_probs=13.3
Q ss_pred ccCCCCCCcccCcchHHHHHHh
Q psy12012 54 YQCPQCPHRTKQKSSLKTHMAV 75 (79)
Q Consensus 54 ~~c~~c~~~f~~~~~l~~h~~~ 75 (79)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3466666666666666666654
No 22
>KOG3993|consensus
Probab=98.30 E-value=1.9e-07 Score=53.48 Aligned_cols=54 Identities=17% Similarity=0.544 Sum_probs=46.2
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcC-------C-------------------------CCccCCCCCCcccCcchHHH
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGK-------E-------------------------PRYQCPQCPHRTKQKSSLKT 71 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~-------~-------------------------~~~~c~~c~~~f~~~~~l~~ 71 (79)
-|+|.+|+|-|..+.+|..|.++|... . -.|.|..|++.|.....|..
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 489999999999999999999988421 1 13789999999999999999
Q ss_pred HHHhhc
Q psy12012 72 HMAVKH 77 (79)
Q Consensus 72 h~~~h~ 77 (79)
|+-+|+
T Consensus 375 Hqlthq 380 (500)
T KOG3993|consen 375 HQLTHQ 380 (500)
T ss_pred hHHhhh
Confidence 988775
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.26 E-value=4e-07 Score=31.84 Aligned_cols=23 Identities=26% Similarity=0.722 Sum_probs=20.9
Q ss_pred cccchhhhhhcchhhHHhHhhhh
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYE 47 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~ 47 (79)
|.|..|++.|.....|..|++.|
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 67999999999999999999863
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=98.25 E-value=7.3e-07 Score=31.21 Aligned_cols=24 Identities=42% Similarity=0.897 Sum_probs=15.0
Q ss_pred ccCCCCCCcccCcchHHHHHHhhc
Q psy12012 54 YQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 54 ~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
|.|+.|+..|.....|..|++.++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 456777777777777777776653
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.24 E-value=1.1e-06 Score=52.32 Aligned_cols=51 Identities=16% Similarity=0.262 Sum_probs=32.5
Q ss_pred ccccccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 8 SESFTSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
...+..|.. .++ +++.|. |+..+ ....|..|+..+.+ .+++.|+.|+..|.
T Consensus 465 ~s~LekH~~-~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp-~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 465 QGEMEKHMK-VFH--EPLQCP-CGVVL-EKEQMVQHQASTCP-LRLITCRFCGDMVQ 515 (567)
T ss_pred hHHHHHHHH-hcC--CCccCC-CCCCc-chhHHHhhhhccCC-CCceeCCCCCCccc
Confidence 445556632 232 667777 77544 44677777777777 77777777777664
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.23 E-value=1.4e-06 Score=51.94 Aligned_cols=72 Identities=18% Similarity=0.326 Sum_probs=55.4
Q ss_pred CcccccccccccccccCCCCCCccccchhhhhhcc----------hhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHH
Q psy12012 2 FGQFRFSESFTSWEASEPNHAGLFVCDVCDRRYKY----------KSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKT 71 (79)
Q Consensus 2 ~~~f~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~----------~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~ 71 (79)
||.+.....|..| ...+.+.+++.|..|+..+.. ...|..|.... + .+++.|..|++.+..+ .+..
T Consensus 483 Cg~~~~R~~L~~H-~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G-~rt~~C~~Cgk~Vrlr-dm~~ 558 (567)
T PLN03086 483 CGVVLEKEQMVQH-QASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-G-SRTAPCDSCGRSVMLK-EMDI 558 (567)
T ss_pred CCCCcchhHHHhh-hhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-C-CcceEccccCCeeeeh-hHHH
Confidence 5665556777788 667888999999999998852 34788898875 6 7899999999998876 4567
Q ss_pred HHHhhc
Q psy12012 72 HMAVKH 77 (79)
Q Consensus 72 h~~~h~ 77 (79)
|+..-|
T Consensus 559 H~~~~h 564 (567)
T PLN03086 559 HQIAVH 564 (567)
T ss_pred HHHHhh
Confidence 765433
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=98.21 E-value=5e-07 Score=32.82 Aligned_cols=25 Identities=20% Similarity=0.493 Sum_probs=14.9
Q ss_pred CccCCCCCCcccCcchHHHHHHhhc
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
|+.|..|+..|.....|..|++.|.
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 3556666666666666666665553
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.00 E-value=2.2e-06 Score=47.83 Aligned_cols=53 Identities=32% Similarity=0.641 Sum_probs=43.2
Q ss_pred CCCccccch--hhhhhcchhhHHhHhhhhh------------------cCCCCccCCCCCCcccCcchHHHHH
Q psy12012 21 HAGLFVCDV--CDRRYKYKSGLYQHKKYEC------------------GKEPRYQCPQCPHRTKQKSSLKTHM 73 (79)
Q Consensus 21 ~~~~~~c~~--c~~~~~~~~~l~~h~~~~~------------------~~~~~~~c~~c~~~f~~~~~l~~h~ 73 (79)
++|||.|++ |++.+.....|+-|+.--+ .+.+||.|++|++.+.+.-.|+.|.
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 459999988 9999999999998876311 1148999999999999998887773
No 29
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.96 E-value=2.7e-06 Score=30.79 Aligned_cols=25 Identities=36% Similarity=0.812 Sum_probs=22.7
Q ss_pred ccccchhhhhhcchhhHHhHhhhhh
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYEC 48 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~ 48 (79)
||.|..|++.|.....|..|++.|.
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 5899999999999999999998764
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.93 E-value=1.3e-05 Score=28.21 Aligned_cols=24 Identities=46% Similarity=0.873 Sum_probs=14.9
Q ss_pred ccCCCCCCcccCcchHHHHHHhhc
Q psy12012 54 YQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 54 ~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
+.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 356666666666666666666543
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.89 E-value=5.8e-06 Score=28.77 Aligned_cols=23 Identities=35% Similarity=0.792 Sum_probs=19.1
Q ss_pred cccchhhhhhcchhhHHhHhhhh
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYE 47 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~ 47 (79)
|.|+.|+..|.....|..|+..+
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 57999999999999999999875
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.88 E-value=9.2e-06 Score=38.01 Aligned_cols=24 Identities=29% Similarity=0.789 Sum_probs=20.5
Q ss_pred CccCCCCCCcccCcchHHHHHHhh
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMAVK 76 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~~h 76 (79)
.+.|..|+..|.....|..|++.+
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 588999999999999999999864
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.84 E-value=2.2e-05 Score=32.51 Aligned_cols=35 Identities=11% Similarity=0.208 Sum_probs=20.4
Q ss_pred CCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCC
Q psy12012 18 EPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPR 53 (79)
Q Consensus 18 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~ 53 (79)
....+.|-+|++|+..+.+..+|.+|+.+.++ .+|
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~-~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHF-KKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTT-TS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhc-ccC
Confidence 34456677888888888888888888877666 443
No 34
>KOG3993|consensus
Probab=97.62 E-value=1.7e-05 Score=45.84 Aligned_cols=53 Identities=25% Similarity=0.561 Sum_probs=45.6
Q ss_pred CccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhh
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVK 76 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h 76 (79)
..|.|..|...|...=.|.+|...-+- ...|+|++|++.|+-...|..|.|=|
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV-~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIV-HVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeE-EeeecCCcccccccCchhhhhhhccc
Confidence 358999999999988899999876555 56799999999999999999997754
No 35
>PRK04860 hypothetical protein; Provisional
Probab=97.54 E-value=4.6e-05 Score=39.08 Aligned_cols=38 Identities=24% Similarity=0.572 Sum_probs=32.3
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQK 66 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 66 (79)
+|.|. |+. ....+..|.+++.+ +++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRG-EAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcC-CccEECCCCCceeEEe
Confidence 68997 986 56678999999999 8899999999887654
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.52 E-value=7.2e-05 Score=26.22 Aligned_cols=24 Identities=29% Similarity=0.636 Sum_probs=20.9
Q ss_pred cccchhhhhhcchhhHHhHhhhhh
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYEC 48 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~ 48 (79)
+.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998653
No 37
>PHA00732 hypothetical protein
Probab=97.48 E-value=0.00011 Score=33.48 Aligned_cols=26 Identities=27% Similarity=0.473 Sum_probs=22.6
Q ss_pred CccCCCCCCcccCcchHHHHHHh-hcC
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMAV-KHS 78 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~~-h~~ 78 (79)
||.|..|++.|...+.|..|++. |.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC
Confidence 58899999999999999999984 543
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.46 E-value=8.7e-05 Score=26.00 Aligned_cols=23 Identities=48% Similarity=0.985 Sum_probs=12.8
Q ss_pred ccCCCCCCcccCcchHHHHHHhhc
Q psy12012 54 YQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 54 ~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
|.|+.|+.... ...|..|++.++
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 35666665555 556666666654
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.41 E-value=0.00014 Score=30.17 Aligned_cols=28 Identities=29% Similarity=0.649 Sum_probs=21.1
Q ss_pred CCCccCCCCCCcccCcchHHHHHHhhcC
Q psy12012 51 EPRYQCPQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
+.|-.|++|+..+.+...|.+|+.++|+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 6789999999999999999999988875
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.29 E-value=9.8e-05 Score=26.05 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=12.2
Q ss_pred cCCCCCCcccCcchHHHHHHh
Q psy12012 55 QCPQCPHRTKQKSSLKTHMAV 75 (79)
Q Consensus 55 ~c~~c~~~f~~~~~l~~h~~~ 75 (79)
.|.+|...|.....+..|++.
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCcCCHHHHHHHHCc
Confidence 455666666666666666543
No 41
>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=97.04 E-value=0.00044 Score=29.15 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=32.8
Q ss_pred CcccccccccccccccCCCCC-CccccchhhhhhcchhhHHhHhhhhh
Q psy12012 2 FGQFRFSESFTSWEASEPNHA-GLFVCDVCDRRYKYKSGLYQHKKYEC 48 (79)
Q Consensus 2 ~~~f~~~~~~~~~~~~~~~~~-~~~~c~~c~~~~~~~~~l~~h~~~~~ 48 (79)
||+......|..|....|..+ +.+.|++|...+. .+|..|+...+
T Consensus 8 C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 8 CGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 566555678888877777654 6799999987654 47888887654
No 42
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.86 E-value=0.0015 Score=23.23 Aligned_cols=21 Identities=24% Similarity=0.624 Sum_probs=13.5
Q ss_pred ccCCCCCCcccCcchHHHHHHh
Q psy12012 54 YQCPQCPHRTKQKSSLKTHMAV 75 (79)
Q Consensus 54 ~~c~~c~~~f~~~~~l~~h~~~ 75 (79)
..|+.|++.| ..+.|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4577787777 44566667543
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.59 E-value=0.0007 Score=24.37 Aligned_cols=22 Identities=41% Similarity=0.821 Sum_probs=14.3
Q ss_pred cccchhhhhhcchhhHHhHhhh
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKY 46 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~ 46 (79)
|.|..|++.|.....+..|+..
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 4566677777776666666653
No 44
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.58 E-value=0.01 Score=22.38 Aligned_cols=22 Identities=18% Similarity=0.493 Sum_probs=14.0
Q ss_pred CccCCCCCCcccCcchHHHHHH
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMA 74 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~ 74 (79)
++.|..|...|.....+..|..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4567777777776666666643
No 45
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.45 E-value=0.0036 Score=35.58 Aligned_cols=24 Identities=46% Similarity=0.940 Sum_probs=21.0
Q ss_pred CCccccchhhhhhcchhhHHhHhh
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKK 45 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~ 45 (79)
.|||+|++|++.+.....|+-|+.
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CCceeccccchhhccCccceeccc
Confidence 489999999999999888887765
No 46
>KOG2893|consensus
Probab=95.16 E-value=0.0043 Score=33.97 Aligned_cols=45 Identities=24% Similarity=0.485 Sum_probs=33.6
Q ss_pred CCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHH
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTH 72 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h 72 (79)
.|+ .|=+|++.|.....|.+|++. +-|+|-+|-+.+-.-..|..|
T Consensus 9 ~kp-wcwycnrefddekiliqhqka-----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKP-WCWYCNREFDDEKILIQHQKA-----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCc-eeeecccccchhhhhhhhhhh-----ccceeeeehhhhccCCCceee
Confidence 456 477899999999999999884 568999998665444445444
No 47
>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=95.04 E-value=0.016 Score=28.00 Aligned_cols=33 Identities=18% Similarity=0.490 Sum_probs=23.7
Q ss_pred CCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCc
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQK 66 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 66 (79)
|.|. .|+.||..|-- |. ..|..|+.||..|.-.
T Consensus 7 GtKR-~Cp~CG~kFYD---Ln---------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKR-TCPSCGAKFYD---LN---------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcc-cCCCCcchhcc---CC---------CCCccCCCCCCccCcc
Confidence 4444 79999988743 32 5678899999887665
No 48
>KOG1146|consensus
Probab=94.99 E-value=0.023 Score=37.81 Aligned_cols=64 Identities=19% Similarity=0.324 Sum_probs=49.0
Q ss_pred ccccccCCCCCCccccchhhhhhcchhhHHhHhhhhhc------------------------CCCCccCCCCCCcccCcc
Q psy12012 12 TSWEASEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECG------------------------KEPRYQCPQCPHRTKQKS 67 (79)
Q Consensus 12 ~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~------------------------~~~~~~c~~c~~~f~~~~ 67 (79)
-.+....+.-.+.+.|+.|+-.|.....|..||+.-+. ..++|.|..|...+....
T Consensus 453 ~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng 532 (1406)
T KOG1146|consen 453 EGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNG 532 (1406)
T ss_pred ccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecch
Confidence 33334455556889999999999999999999997110 035788999999999988
Q ss_pred hHHHHHHh
Q psy12012 68 SLKTHMAV 75 (79)
Q Consensus 68 ~l~~h~~~ 75 (79)
.|..|+..
T Consensus 533 ~LsihlqS 540 (1406)
T KOG1146|consen 533 NLSIHLQS 540 (1406)
T ss_pred HHHHHHHH
Confidence 88888764
No 49
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.65 E-value=0.017 Score=21.84 Aligned_cols=24 Identities=38% Similarity=0.942 Sum_probs=15.4
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
|.|.+||..+... ..++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~-------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE-------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC-------------cCCCcCcCCCC
Confidence 5677887554332 24678888875
No 50
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.65 E-value=0.03 Score=23.78 Aligned_cols=30 Identities=13% Similarity=0.409 Sum_probs=25.4
Q ss_pred CCCCccccchhhhhhcchhhHHhHhhhhhc
Q psy12012 20 NHAGLFVCDVCDRRYKYKSGLYQHKKYECG 49 (79)
Q Consensus 20 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 49 (79)
.|+.-+.|+.|+..|....++.+|..-.++
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 467788999999999999999999876554
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.34 E-value=0.0069 Score=34.83 Aligned_cols=55 Identities=24% Similarity=0.464 Sum_probs=40.4
Q ss_pred CccccchhhhhhcchhhHHhHhh--hhhcCC--CCccCC--CCCCcccCcchHHHHHHhhcC
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKK--YECGKE--PRYQCP--QCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~--~~~~~~--~~~~c~--~c~~~f~~~~~l~~h~~~h~~ 78 (79)
.++.|..|...+.....+..|.+ .|.+ + +++.|+ .|+..|.....+..|...|++
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred cCCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcccccC
Confidence 35677778778888888888888 6777 6 778887 688888777777766665543
No 52
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=93.88 E-value=0.034 Score=28.93 Aligned_cols=24 Identities=38% Similarity=0.820 Sum_probs=18.6
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
.|+|.+||..+ .+ +.|-.||+|+.
T Consensus 134 ~~vC~vCGy~~-------------~g-e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EG-EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cC-CCCCcCCCCCC
Confidence 79999997542 35 67889999983
No 53
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.87 E-value=0.032 Score=25.88 Aligned_cols=24 Identities=21% Similarity=0.676 Sum_probs=21.2
Q ss_pred ccccchhhhhhcchhhHHhHhhhh
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYE 47 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~ 47 (79)
.+.|..|++.|.....|..|++.+
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 589999999999999999999975
No 54
>PRK04860 hypothetical protein; Provisional
Probab=93.70 E-value=0.012 Score=30.43 Aligned_cols=29 Identities=10% Similarity=0.295 Sum_probs=23.0
Q ss_pred ccccccccccCCCCCCccccchhhhhhcch
Q psy12012 8 SESFTSWEASEPNHAGLFVCDVCDRRYKYK 37 (79)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~ 37 (79)
..+++.| ...++++++|.|..|+..|...
T Consensus 128 ~~~~rrH-~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 128 QLTVRRH-NRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred eCHHHHH-HHHhcCCccEECCCCCceeEEe
Confidence 4455667 7788899999999999887654
No 55
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.06 E-value=0.024 Score=30.57 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=27.8
Q ss_pred CCccccchhhhhhcchhhHHhHhhhhh---c------CCC-----CccCCCCCCcccCc
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKKYEC---G------KEP-----RYQCPQCPHRTKQK 66 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~~~~---~------~~~-----~~~c~~c~~~f~~~ 66 (79)
.+..+|++|++.|....-.....+.-. . ... ...|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 356789999999988754443333210 0 012 26799999876543
No 56
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.85 E-value=0.079 Score=20.16 Aligned_cols=25 Identities=32% Similarity=0.729 Sum_probs=16.3
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
.|.|.+||..+... ..|..|++|+.
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 47788887554321 34678999875
No 57
>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=91.52 E-value=0.13 Score=25.61 Aligned_cols=32 Identities=13% Similarity=0.218 Sum_probs=21.9
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchH
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSL 69 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l 69 (79)
.|+.||+.|.- |. ..|..|+.||..|.....+
T Consensus 11 ~Cp~cg~kFYD---Ln---------k~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 11 ICPNTGSKFYD---LN---------RRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred cCCCcCccccc---cC---------CCCccCCCcCCccCcchhh
Confidence 78888877643 22 5678899998877655333
No 58
>KOG2186|consensus
Probab=91.20 E-value=0.15 Score=28.37 Aligned_cols=45 Identities=24% Similarity=0.506 Sum_probs=27.3
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHH
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHM 73 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~ 73 (79)
|.|.+||....-+. +..|+..-.+ .-|.|-.|+..|..- +...|.
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn--~~fSCIDC~k~F~~~-sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN--AYFSCIDCGKTFERV-SYKNHT 48 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC--CeeEEeecccccccc-hhhhhh
Confidence 56777776655443 6667766544 347777777777663 334453
No 59
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.83 E-value=0.13 Score=20.83 Aligned_cols=26 Identities=27% Similarity=0.781 Sum_probs=17.9
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
|.|..||..+... . ..+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~-~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------S-KDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------C-CCceECCCCCce
Confidence 7788888776543 1 345788888854
No 60
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.87 E-value=0.077 Score=27.32 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=7.7
Q ss_pred ccCCCCCCcccC
Q psy12012 54 YQCPQCPHRTKQ 65 (79)
Q Consensus 54 ~~c~~c~~~f~~ 65 (79)
++|+.|+.+|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 566667666654
No 61
>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=88.51 E-value=0.42 Score=22.95 Aligned_cols=25 Identities=32% Similarity=0.813 Sum_probs=22.3
Q ss_pred ccC----CCCCCcccCcchHHHHHHhhcC
Q psy12012 54 YQC----PQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 54 ~~c----~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
|.| ..|+........+..|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 788 8899999999999999998876
No 62
>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=88.42 E-value=0.23 Score=25.65 Aligned_cols=35 Identities=17% Similarity=0.566 Sum_probs=25.6
Q ss_pred CCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 20 NHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 20 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
....-|.|+.|+..|+...++. .-|.|+.||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEee
Confidence 3445689999998888776663 2489999986543
No 63
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.22 E-value=0.25 Score=26.04 Aligned_cols=35 Identities=23% Similarity=0.718 Sum_probs=25.3
Q ss_pred CCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
...-|.|+.|+..|+...++. .-|.|+.||.....
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 345689999998888766542 25899999976443
No 64
>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=88.10 E-value=0.18 Score=19.57 Aligned_cols=30 Identities=20% Similarity=0.698 Sum_probs=19.5
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
.|.|..||..|........ .....|+.|+.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~--------~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD--------DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCC--------CCCCCCCCCCC
Confidence 3788999988766433311 23467888886
No 65
>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=87.77 E-value=0.26 Score=18.95 Aligned_cols=34 Identities=15% Similarity=0.435 Sum_probs=21.3
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
..|+.|+..|....+... .. .....|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~-~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----AN-GGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CC-CCEEECCCCCCEEE
Confidence 468888888777654431 11 22467898887664
No 66
>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=87.62 E-value=0.15 Score=20.25 Aligned_cols=29 Identities=17% Similarity=0.742 Sum_probs=19.3
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
|.|..||..|.....+.. ..+..|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~--------~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE--------DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC--------CCCCcCCCCCC
Confidence 788899888766433221 24567888886
No 67
>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=87.29 E-value=0.32 Score=24.50 Aligned_cols=23 Identities=26% Similarity=0.680 Sum_probs=15.0
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECG 49 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 49 (79)
-..|-+||+.|.. |.+|.+.|+|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-
T ss_pred eeEEccCCcccch---HHHHHHHccC
Confidence 4579999999887 7889888855
No 68
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=87.23 E-value=0.17 Score=20.92 Aligned_cols=29 Identities=24% Similarity=0.804 Sum_probs=18.7
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
|.|..|+..|.....+. . ..+..|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~-------~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS-------D-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC-------C-CCCCCCCCCCC
Confidence 78899998887642221 1 23456898885
No 69
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.62 E-value=0.41 Score=24.38 Aligned_cols=38 Identities=16% Similarity=0.568 Sum_probs=25.1
Q ss_pred CCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcc
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRT 63 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 63 (79)
...-|.|+.|+..|.....+..- . . ...|.|+.|+...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~-d---~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLL-D---M-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhc-C---C-CCcEECCCCCCEE
Confidence 44568999999888865444321 1 1 2239999998764
No 70
>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=86.29 E-value=0.23 Score=27.03 Aligned_cols=28 Identities=29% Similarity=0.619 Sum_probs=19.7
Q ss_pred CCCccCCCCCCcccCcchHHHHHHhhcC
Q psy12012 51 EPRYQCPQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
+..|.|..|++.|.-......|+..-|.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 3458899999999999888888775543
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.07 E-value=0.39 Score=18.54 Aligned_cols=33 Identities=24% Similarity=0.737 Sum_probs=20.8
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
.|+.|+..|....+-. . .+ .....|+.|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~l---~--~~-~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKL---P--AG-GRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHc---c--cC-CcEEECCCCCcEee
Confidence 5888888877764321 1 12 34578888887664
No 72
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.05 E-value=0.35 Score=18.59 Aligned_cols=32 Identities=19% Similarity=0.527 Sum_probs=20.2
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcc
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRT 63 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 63 (79)
.|+.|+..|....... . .. ....+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~i---p--~~-g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKI---P--PK-GRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHC---C--CC-CcEEECCCCCCEe
Confidence 5778887777765432 1 11 3457788888765
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.69 E-value=0.48 Score=20.48 Aligned_cols=31 Identities=26% Similarity=0.626 Sum_probs=18.6
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCP 60 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 60 (79)
.|.|+.||........- -... ..+|.|+.||
T Consensus 27 ~F~CPnCGe~~I~Rc~~----CRk~--g~~Y~Cp~CG 57 (61)
T COG2888 27 KFPCPNCGEVEIYRCAK----CRKL--GNPYRCPKCG 57 (61)
T ss_pred EeeCCCCCceeeehhhh----HHHc--CCceECCCcC
Confidence 47888888554433211 1112 3589999997
No 74
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.15 E-value=0.44 Score=19.77 Aligned_cols=28 Identities=25% Similarity=0.604 Sum_probs=18.4
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
.|.|..|++.+.. +. . .....|+.|+..
T Consensus 6 ~Y~C~~Cg~~~~~---~~-------~-~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVEL---DQ-------E-TRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeeh---hh-------c-cCceeCCCCCcE
Confidence 4889999988721 11 1 345788988854
No 75
>PF15269 zf-C2H2_7: Zinc-finger
Probab=85.00 E-value=0.66 Score=18.85 Aligned_cols=21 Identities=48% Similarity=0.901 Sum_probs=13.9
Q ss_pred ccCCCCCCcccCcchHHHHHH
Q psy12012 54 YQCPQCPHRTKQKSSLKTHMA 74 (79)
Q Consensus 54 ~~c~~c~~~f~~~~~l~~h~~ 74 (79)
|+|-+|+.+...++.|..|+.
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 456667666666777777765
No 76
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=84.95 E-value=1.1 Score=18.40 Aligned_cols=7 Identities=29% Similarity=0.743 Sum_probs=3.4
Q ss_pred hHHHHHH
Q psy12012 68 SLKTHMA 74 (79)
Q Consensus 68 ~l~~h~~ 74 (79)
.|..|+.
T Consensus 38 ~L~rHl~ 44 (50)
T smart00614 38 NLRRHLR 44 (50)
T ss_pred HHHHHHH
Confidence 4445544
No 77
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.50 E-value=0.25 Score=19.96 Aligned_cols=30 Identities=23% Similarity=0.546 Sum_probs=18.1
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
.|.|..||..+..... .....|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCeEE
Confidence 4778888776655321 11467888876543
No 78
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=83.93 E-value=0.31 Score=22.70 Aligned_cols=33 Identities=24% Similarity=0.616 Sum_probs=21.0
Q ss_pred CCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
...|.|+.|++. ...+...+ .+.|..|+..|.-
T Consensus 33 ~~~~~Cp~C~~~--------~VkR~a~G---IW~C~kCg~~fAG 65 (89)
T COG1997 33 RAKHVCPFCGRT--------TVKRIATG---IWKCRKCGAKFAG 65 (89)
T ss_pred hcCCcCCCCCCc--------ceeeeccC---eEEcCCCCCeecc
Confidence 346789998755 11233333 5789999887754
No 79
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=83.93 E-value=0.47 Score=27.43 Aligned_cols=51 Identities=16% Similarity=0.252 Sum_probs=39.5
Q ss_pred ccccccccccccc--CCCCC--Cccccc--hhhhhhcchhhHHhHhhhhhcCCCCccCC
Q psy12012 5 FRFSESFTSWEAS--EPNHA--GLFVCD--VCDRRYKYKSGLYQHKKYECGKEPRYQCP 57 (79)
Q Consensus 5 f~~~~~~~~~~~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~~c~ 57 (79)
|.....+..| .. .|.++ +++.|. .|++.|.....+..|...+.. ..+..+.
T Consensus 299 ~s~~~~l~~~-~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 355 (467)
T COG5048 299 FSRSSPLTRH-LRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS-ISPAKEK 355 (467)
T ss_pred cccccccccc-ccccccccccCCceeeeccCCCccccccccccCCcccccC-CCccccc
Confidence 5556666777 44 78888 999999 799999999999999998877 4444443
No 80
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.26 E-value=0.61 Score=21.20 Aligned_cols=32 Identities=25% Similarity=0.626 Sum_probs=20.9
Q ss_pred CccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
-.|.|..|+..|. +.+++.- ...-.|+.|+..
T Consensus 11 Y~Y~c~~cg~~~d----vvq~~~d----dplt~ce~c~a~ 42 (82)
T COG2331 11 YSYECTECGNRFD----VVQAMTD----DPLTTCEECGAR 42 (82)
T ss_pred eEEeecccchHHH----HHHhccc----CccccChhhChH
Confidence 3588999987764 4555542 344568888754
No 81
>KOG2593|consensus
Probab=81.01 E-value=1.1 Score=27.05 Aligned_cols=40 Identities=18% Similarity=0.541 Sum_probs=26.0
Q ss_pred CCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 18 EPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 18 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
..+...-|.|+.|.+.|..-..+. -+... .-.|.|..|+-
T Consensus 122 d~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~-~~~F~C~~C~g 161 (436)
T KOG2593|consen 122 DDTNVAGYVCPNCQKKYTSLEALQ---LLDNE-TGEFHCENCGG 161 (436)
T ss_pred hccccccccCCccccchhhhHHHH---hhccc-CceEEEecCCC
Confidence 345566799999999988755443 22211 23588888864
No 82
>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=80.91 E-value=1.1 Score=15.90 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=7.4
Q ss_pred cCCCCCCccc
Q psy12012 55 QCPQCPHRTK 64 (79)
Q Consensus 55 ~c~~c~~~f~ 64 (79)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5788887774
No 83
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=80.16 E-value=1 Score=22.82 Aligned_cols=21 Identities=24% Similarity=0.380 Sum_probs=12.1
Q ss_pred cCCCCCCcccCcchHHHHHHhhcC
Q psy12012 55 QCPQCPHRTKQKSSLKTHMAVKHS 78 (79)
Q Consensus 55 ~c~~c~~~f~~~~~l~~h~~~h~~ 78 (79)
.|-++|+.|.. |.+|.++|.|
T Consensus 78 icLEDGkkfKS---LKRHL~t~~g 98 (148)
T COG4957 78 ICLEDGKKFKS---LKRHLTTHYG 98 (148)
T ss_pred EEeccCcchHH---HHHHHhcccC
Confidence 35555655543 5667666654
No 84
>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=80.13 E-value=2.2 Score=15.08 Aligned_cols=19 Identities=26% Similarity=0.744 Sum_probs=10.6
Q ss_pred cCCCCCCcccCcchHHHHHH
Q psy12012 55 QCPQCPHRTKQKSSLKTHMA 74 (79)
Q Consensus 55 ~c~~c~~~f~~~~~l~~h~~ 74 (79)
.|++|...+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 477777666 3344455543
No 85
>KOG4167|consensus
Probab=79.85 E-value=0.97 Score=29.17 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=22.6
Q ss_pred CccccchhhhhhcchhhHHhHhhhhh
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKYEC 48 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~~~ 48 (79)
..|.|.+|++.|..-..+..||+.|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 45899999999998888999998875
No 86
>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=79.83 E-value=0.51 Score=19.99 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=18.0
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcc
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRT 63 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 63 (79)
+.|+.|+..+..+.... + + ...|+.|+..+
T Consensus 3 ~~CP~CG~~iev~~~~~-------G-e-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL-------G-E-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc-------C-C-EEeCCCCCCEE
Confidence 57888887665543221 3 2 45788887543
No 87
>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=79.78 E-value=1 Score=16.90 Aligned_cols=10 Identities=50% Similarity=1.374 Sum_probs=6.3
Q ss_pred CccCCCCCCc
Q psy12012 53 RYQCPQCPHR 62 (79)
Q Consensus 53 ~~~c~~c~~~ 62 (79)
+..|+.||..
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 5677878754
No 88
>PF12907 zf-met2: Zinc-binding
Probab=78.09 E-value=1.4 Score=17.51 Aligned_cols=25 Identities=16% Similarity=0.541 Sum_probs=17.0
Q ss_pred cccchhhhhhcch---hhHHhHhhhhhc
Q psy12012 25 FVCDVCDRRYKYK---SGLYQHKKYECG 49 (79)
Q Consensus 25 ~~c~~c~~~~~~~---~~l~~h~~~~~~ 49 (79)
+.|.+|...|... ..|..|....+.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHp 29 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHP 29 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCC
Confidence 4688888666554 458888776444
No 89
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.47 E-value=1.7 Score=18.78 Aligned_cols=32 Identities=25% Similarity=0.721 Sum_probs=17.7
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
.|.|+.||......-.-- + . . ..+|.|+.||.
T Consensus 25 ~F~CPnCG~~~I~RC~~C---R-k-~-~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKC---R-K-Q-SNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeechhH---H-h-c-CCceECCCCCC
Confidence 478888886522221111 1 1 1 35799998873
No 90
>PHA00626 hypothetical protein
Probab=77.10 E-value=1.3 Score=18.90 Aligned_cols=16 Identities=19% Similarity=0.538 Sum_probs=12.5
Q ss_pred CCccCCCCCCcccCcc
Q psy12012 52 PRYQCPQCPHRTKQKS 67 (79)
Q Consensus 52 ~~~~c~~c~~~f~~~~ 67 (79)
..|.|+.|+..|+..+
T Consensus 22 nrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DDYVCCDCGYNDSKDA 37 (59)
T ss_pred cceEcCCCCCeechhh
Confidence 4799999998887643
No 91
>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=76.05 E-value=1.4 Score=15.43 Aligned_cols=8 Identities=38% Similarity=1.402 Sum_probs=4.6
Q ss_pred CccCCCCC
Q psy12012 53 RYQCPQCP 60 (79)
Q Consensus 53 ~~~c~~c~ 60 (79)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45566655
No 92
>KOG4167|consensus
Probab=75.83 E-value=0.37 Score=30.88 Aligned_cols=24 Identities=21% Similarity=0.407 Sum_probs=21.6
Q ss_pred CccCCCCCCcccCcchHHHHHHhh
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMAVK 76 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~~h 76 (79)
-|-|.+|++.|-...++..||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 488999999999998999999887
No 93
>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=74.59 E-value=1.1 Score=18.67 Aligned_cols=13 Identities=23% Similarity=0.761 Sum_probs=9.1
Q ss_pred cccchhhhhhcch
Q psy12012 25 FVCDVCDRRYKYK 37 (79)
Q Consensus 25 ~~c~~c~~~~~~~ 37 (79)
|.|..|+..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6788888766543
No 94
>KOG3408|consensus
Probab=74.32 E-value=1.4 Score=21.95 Aligned_cols=24 Identities=25% Similarity=0.540 Sum_probs=19.9
Q ss_pred CCccCCCCCCcccCcchHHHHHHh
Q psy12012 52 PRYQCPQCPHRTKQKSSLKTHMAV 75 (79)
Q Consensus 52 ~~~~c~~c~~~f~~~~~l~~h~~~ 75 (79)
-.|.|-.|.+.|.....|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 358889999999999999988664
No 95
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=73.23 E-value=2.2 Score=16.35 Aligned_cols=31 Identities=26% Similarity=0.601 Sum_probs=14.7
Q ss_pred cchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 27 CDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 27 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
|..|.+.+..+.+ .+.| -.+..|..||..+.
T Consensus 2 C~~C~~Ey~~p~~----RR~~---~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSN----RRFH---YQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTS----TTTT----TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCC----Cccc---CcCccCCCCCCCEE
Confidence 5666666554432 2222 24577888887654
No 96
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=72.48 E-value=1.2 Score=20.01 Aligned_cols=14 Identities=14% Similarity=0.448 Sum_probs=6.3
Q ss_pred ccccc--hhhhhhcch
Q psy12012 24 LFVCD--VCDRRYKYK 37 (79)
Q Consensus 24 ~~~c~--~c~~~~~~~ 37 (79)
.+.|. .||..|...
T Consensus 27 Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 27 YHQCQNVNCSATFITY 42 (72)
T ss_pred eeecCCCCCCCEEEEE
Confidence 34444 455444443
No 97
>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=71.39 E-value=2.5 Score=17.34 Aligned_cols=37 Identities=24% Similarity=0.559 Sum_probs=15.9
Q ss_pred cccchhhhhhcchhhHHhH-----hhhhhcCCCCccCCCCCCc
Q psy12012 25 FVCDVCDRRYKYKSGLYQH-----KKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h-----~~~~~~~~~~~~c~~c~~~ 62 (79)
|.|..|+..+.....-... ...... ..-+.|+.|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~L-p~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDL-PDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS--TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHC-CCCCcCcCCCCc
Confidence 5677787655544321111 111111 234788888743
No 98
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.23 E-value=1.4 Score=22.20 Aligned_cols=15 Identities=20% Similarity=0.696 Sum_probs=11.7
Q ss_pred Cccccchhhhhhcch
Q psy12012 23 GLFVCDVCDRRYKYK 37 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~ 37 (79)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 458899999877664
No 99
>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=67.85 E-value=1.9 Score=20.81 Aligned_cols=14 Identities=14% Similarity=0.456 Sum_probs=8.8
Q ss_pred Cccccchhhhhhcc
Q psy12012 23 GLFVCDVCDRRYKY 36 (79)
Q Consensus 23 ~~~~c~~c~~~~~~ 36 (79)
||-.|..||.....
T Consensus 1 ~p~~CpYCg~~~~l 14 (102)
T PF11672_consen 1 KPIICPYCGGPAEL 14 (102)
T ss_pred CCcccCCCCCeeEE
Confidence 45678888765443
No 100
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=67.60 E-value=4.3 Score=15.93 Aligned_cols=11 Identities=27% Similarity=0.594 Sum_probs=4.5
Q ss_pred ccCCCCCCccc
Q psy12012 54 YQCPQCPHRTK 64 (79)
Q Consensus 54 ~~c~~c~~~f~ 64 (79)
..|..|+..+.
T Consensus 17 a~C~~C~~~~~ 27 (45)
T PF02892_consen 17 AKCKYCGKVIK 27 (45)
T ss_dssp EEETTTTEE--
T ss_pred EEeCCCCeEEe
Confidence 44555554433
No 101
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=67.07 E-value=3.4 Score=16.12 Aligned_cols=13 Identities=15% Similarity=0.521 Sum_probs=9.9
Q ss_pred CccCCCCCCcccC
Q psy12012 53 RYQCPQCPHRTKQ 65 (79)
Q Consensus 53 ~~~c~~c~~~f~~ 65 (79)
|+.|..|+..|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7888888877754
No 102
>KOG1146|consensus
Probab=66.99 E-value=4.7 Score=28.06 Aligned_cols=55 Identities=18% Similarity=0.372 Sum_probs=40.3
Q ss_pred CCccccchhhhhhcchhhHHhHhhhhhcC----------------CCCccCCCCCCcccCcchHHHHHHhhc
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKKYECGK----------------EPRYQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~----------------~~~~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
..+|.|..|...|.....|..|++.-... ...+ |..|...|.....|+.|+++-+
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSA 1352 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhh
Confidence 34678888888888888888887532110 2235 8889889999999999988654
No 103
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=66.34 E-value=1.8 Score=18.14 Aligned_cols=40 Identities=25% Similarity=0.504 Sum_probs=20.8
Q ss_pred ccccch-hhhhhcchhhHHhHhhhhhcCCCCccCCC----CCCccc
Q psy12012 24 LFVCDV-CDRRYKYKSGLYQHKKYECGKEPRYQCPQ----CPHRTK 64 (79)
Q Consensus 24 ~~~c~~-c~~~~~~~~~l~~h~~~~~~~~~~~~c~~----c~~~f~ 64 (79)
+..|+. |+..-.....|..|...... ..+..|+. |...+.
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~-~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP-KRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST-TSEEE-SS----S--EEE
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC-CCcEECCCCCCCCCCccc
Confidence 445665 33333345568888886555 56677887 765544
No 104
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=65.89 E-value=9.8 Score=22.75 Aligned_cols=47 Identities=19% Similarity=0.316 Sum_probs=31.5
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCC----CcccCcchHHHHHH
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCP----HRTKQKSSLKTHMA 74 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~----~~f~~~~~l~~h~~ 74 (79)
.|..|..-|-....|..|++..+ ++-+.|...+ ..|.....|..|.+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H--E~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH--EACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh--hhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 69999999999999999999643 3334443332 23566666666644
No 105
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=65.83 E-value=1.2 Score=21.01 Aligned_cols=31 Identities=16% Similarity=0.629 Sum_probs=18.6
Q ss_pred CccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
..|.|+.|++.- +. +...| .+.|..|++.|.
T Consensus 35 a~y~CpfCgk~~-----vk---R~a~G---IW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHA-----VK---RQAVG---IWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCc-----ee---eeeeE---EEEcCCCCCEEe
Confidence 467888887532 22 11223 578888887664
No 106
>KOG1842|consensus
Probab=64.40 E-value=3.5 Score=25.21 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=14.1
Q ss_pred ccccchhhhhhcchhhHHhHhhh
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKY 46 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~ 46 (79)
-+.|+.|...|..-..|..|...
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhh
Confidence 45666666666666666666554
No 107
>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=64.27 E-value=2.1 Score=17.91 Aligned_cols=26 Identities=12% Similarity=0.506 Sum_probs=15.2
Q ss_pred CCccccchhhhhhcchhhHHhHhhhh
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKKYE 47 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~~~ 47 (79)
...|.|+.|...|=..-++-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 45799999999999888888775543
No 108
>KOG2482|consensus
Probab=63.88 E-value=4.6 Score=23.95 Aligned_cols=22 Identities=36% Similarity=0.708 Sum_probs=20.2
Q ss_pred CccCCCCCCcccCcchHHHHHH
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMA 74 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~ 74 (79)
.+.|-.|.+.|..+..|..|||
T Consensus 195 r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred hheeeeeccccCCcHHHHHHHH
Confidence 4789999999999999999987
No 109
>KOG2785|consensus
Probab=63.73 E-value=8.9 Score=23.03 Aligned_cols=51 Identities=22% Similarity=0.326 Sum_probs=37.0
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcC----------------------CCCccCCCCC---CcccCcchHHHHHH
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGK----------------------EPRYQCPQCP---HRTKQKSSLKTHMA 74 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~----------------------~~~~~c~~c~---~~f~~~~~l~~h~~ 74 (79)
|-.|-.|++.+..-..-..||-.++|- ..-+.|-.|. +.|......+.||.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 556888988888777777888776542 1235666676 78888888888876
No 110
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=61.70 E-value=10 Score=14.90 Aligned_cols=23 Identities=22% Similarity=0.356 Sum_probs=11.0
Q ss_pred ccCCCCCCcccC--cchHHHHHHhh
Q psy12012 54 YQCPQCPHRTKQ--KSSLKTHMAVK 76 (79)
Q Consensus 54 ~~c~~c~~~f~~--~~~l~~h~~~h 76 (79)
..|+.|+..+.. ..+-..|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 456666654433 33344454433
No 111
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=60.09 E-value=7.4 Score=23.69 Aligned_cols=29 Identities=31% Similarity=0.834 Sum_probs=17.8
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCc
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQK 66 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 66 (79)
.|+.||.+..+ .| ..-|.|+.|+..+...
T Consensus 352 ~Cp~Cg~~m~S-----------~G-~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKS-----------AG-RNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhh-----------cC-CCCcccccccccCCcc
Confidence 78888765332 13 2267888888766543
No 112
>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=59.63 E-value=2.1 Score=20.23 Aligned_cols=31 Identities=19% Similarity=0.652 Sum_probs=18.5
Q ss_pred CccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
..|.|+.|++.- +. +...| .+.|..|++.|.
T Consensus 34 a~y~CpfCgk~~-----vk---R~a~G---IW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKT-----VK---RGSTG---IWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCc-----eE---EEeeE---EEEcCCCCCEEe
Confidence 457888887542 21 22223 577888887664
No 113
>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=58.95 E-value=3.5 Score=17.13 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=5.7
Q ss_pred cCCCCCCcccC
Q psy12012 55 QCPQCPHRTKQ 65 (79)
Q Consensus 55 ~c~~c~~~f~~ 65 (79)
.|+.|++.|..
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 79999988765
No 114
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=58.86 E-value=3.1 Score=17.81 Aligned_cols=8 Identities=38% Similarity=1.319 Sum_probs=3.6
Q ss_pred ccccchhh
Q psy12012 24 LFVCDVCD 31 (79)
Q Consensus 24 ~~~c~~c~ 31 (79)
.|.|..|.
T Consensus 31 tYmC~eC~ 38 (56)
T PF09963_consen 31 TYMCDECK 38 (56)
T ss_pred ceeChhHH
Confidence 34444443
No 115
>KOG2071|consensus
Probab=58.77 E-value=7.6 Score=24.62 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=20.4
Q ss_pred CCCccCCCCCCcccCcchHHHHHHhhc
Q psy12012 51 EPRYQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
..|-.|..||..|........|+-.|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456778888888888877777776664
No 116
>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=58.64 E-value=4.9 Score=15.44 Aligned_cols=11 Identities=18% Similarity=0.425 Sum_probs=5.7
Q ss_pred CccCCCCCCcc
Q psy12012 53 RYQCPQCPHRT 63 (79)
Q Consensus 53 ~~~c~~c~~~f 63 (79)
+-.|..|+..+
T Consensus 21 ~~~Cd~cg~~L 31 (36)
T PF05191_consen 21 EGVCDNCGGEL 31 (36)
T ss_dssp TTBCTTTTEBE
T ss_pred CCccCCCCCee
Confidence 34566665443
No 117
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=57.22 E-value=2.3 Score=21.92 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=6.3
Q ss_pred ccCCCCCCcccC
Q psy12012 54 YQCPQCPHRTKQ 65 (79)
Q Consensus 54 ~~c~~c~~~f~~ 65 (79)
-+|..|++.|+.
T Consensus 29 ReC~~C~~RFTT 40 (147)
T TIGR00244 29 RECLECHERFTT 40 (147)
T ss_pred ccCCccCCccce
Confidence 445555555543
No 118
>PLN02294 cytochrome c oxidase subunit Vb
Probab=56.96 E-value=6.2 Score=20.96 Aligned_cols=25 Identities=20% Similarity=0.353 Sum_probs=16.7
Q ss_pred HHhHhhhhhcCCCCccCCCCCCcccCc
Q psy12012 40 LYQHKKYECGKEPRYQCPQCPHRTKQK 66 (79)
Q Consensus 40 l~~h~~~~~~~~~~~~c~~c~~~f~~~ 66 (79)
...++..+.+ +|..|+.|+..|...
T Consensus 130 ~v~Wf~L~kG--kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 130 DVVWFWLEKG--KSFECPVCTQYFELE 154 (174)
T ss_pred eeEEEEecCC--CceeCCCCCCEEEEE
Confidence 3344455444 688999999887653
No 119
>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=56.78 E-value=3.2 Score=21.37 Aligned_cols=32 Identities=28% Similarity=0.672 Sum_probs=19.6
Q ss_pred CCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 20 NHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 20 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
.|.+.++|..||...... + . .....|+.|+..
T Consensus 108 ~g~G~l~C~~Cg~~~~~~---------~-~-~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVELT---------H-P-ERLPPCPKCGHT 139 (146)
T ss_pred ecCceEecccCCCEEEec---------C-C-CcCCCCCCCCCC
Confidence 345679999998654321 1 1 234469999754
No 120
>KOG2636|consensus
Probab=56.25 E-value=9.6 Score=23.48 Aligned_cols=27 Identities=22% Similarity=0.415 Sum_probs=18.8
Q ss_pred hhhhcCCCCccCCCCC-CcccCcchHHHH
Q psy12012 45 KYECGKEPRYQCPQCP-HRTKQKSSLKTH 72 (79)
Q Consensus 45 ~~~~~~~~~~~c~~c~-~~f~~~~~l~~h 72 (79)
+.|.. ...|.|.+|| +++.-+..+.+|
T Consensus 394 KLHGL-~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGL-DIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCC-CcccceeeccCccccCcHHHHHH
Confidence 44544 6678999998 566666667776
No 121
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.98 E-value=3.4 Score=20.79 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=11.2
Q ss_pred CCCccCCCCCCcccCc
Q psy12012 51 EPRYQCPQCPHRTKQK 66 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~ 66 (79)
+.|.-|..||..|+..
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 4566678888887653
No 122
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=55.64 E-value=1.1 Score=21.57 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=21.0
Q ss_pred CCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcc
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRT 63 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 63 (79)
-++.|.|+.|+..-.....+..-.. .-...|..||.+|
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~-----~g~~~Cg~CGls~ 56 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVN-----IGTAVCGNCGLSF 56 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCc-----eeEEEcccCcceE
Confidence 4567899999865443322221111 1235688887665
No 123
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=55.26 E-value=4.9 Score=16.70 Aligned_cols=15 Identities=13% Similarity=0.315 Sum_probs=9.3
Q ss_pred CCccCCCCCCcccCc
Q psy12012 52 PRYQCPQCPHRTKQK 66 (79)
Q Consensus 52 ~~~~c~~c~~~f~~~ 66 (79)
+.+.|..||..|...
T Consensus 3 k~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFT 17 (49)
T ss_pred eeEEcccCCCeEEEe
Confidence 456677777666544
No 124
>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=54.95 E-value=6.2 Score=14.56 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=5.8
Q ss_pred CCccCCCCCC
Q psy12012 52 PRYQCPQCPH 61 (79)
Q Consensus 52 ~~~~c~~c~~ 61 (79)
..+.|+.|+.
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 3466666653
No 125
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=54.50 E-value=11 Score=24.68 Aligned_cols=49 Identities=24% Similarity=0.567 Sum_probs=27.8
Q ss_pred cccccccccccccCCCCCCcc-ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 5 FRFSESFTSWEASEPNHAGLF-VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 5 f~~~~~~~~~~~~~~~~~~~~-~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
|+...++... +.+|.=..| .|+.|.+.+..+.+= +.| ..|..|+.||..
T Consensus 133 fTIi~alPYD--R~nTsM~~F~lC~~C~~EY~dP~nR----RfH---AQp~aCp~CGP~ 182 (750)
T COG0068 133 FTIIEALPYD--RENTSMADFPLCPFCDKEYKDPLNR----RFH---AQPIACPKCGPH 182 (750)
T ss_pred eeeeccCCCC--cccCccccCcCCHHHHHHhcCcccc----ccc---cccccCcccCCC
Confidence 4444444433 233333333 488888877665432 333 357889999864
No 126
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=54.41 E-value=9.6 Score=16.27 Aligned_cols=9 Identities=33% Similarity=1.302 Sum_probs=4.9
Q ss_pred CCccCCCCC
Q psy12012 52 PRYQCPQCP 60 (79)
Q Consensus 52 ~~~~c~~c~ 60 (79)
..|.|+.||
T Consensus 13 v~~~Cp~cG 21 (55)
T PF13824_consen 13 VNFECPDCG 21 (55)
T ss_pred cCCcCCCCC
Confidence 445555555
No 127
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=54.32 E-value=2.8 Score=19.76 Aligned_cols=31 Identities=26% Similarity=0.651 Sum_probs=17.7
Q ss_pred CccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
..|.|+.|++.- +. +...| .+.|..|++.|.
T Consensus 35 a~y~CpfCgk~~-----vk---R~a~G---IW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPK-----VK---RVGTG---IWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCc-----eE---EEEEE---EEEcCCCCCEEe
Confidence 457888886432 11 22223 577888877654
No 128
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=54.24 E-value=4.6 Score=21.00 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=21.5
Q ss_pred CccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
-+|.|. |+.-+.. ...|...-.| + .|.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~---~RRhn~~~~g-~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLR---IRRHNTVRRG-E-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccch---hhhccccccc-c-eEEeccCCce
Confidence 468888 8877655 2344444444 4 6888888754
No 129
>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=52.66 E-value=3.8 Score=16.23 Aligned_cols=13 Identities=15% Similarity=0.534 Sum_probs=7.0
Q ss_pred CCccCCCCCCccc
Q psy12012 52 PRYQCPQCPHRTK 64 (79)
Q Consensus 52 ~~~~c~~c~~~f~ 64 (79)
.|+.|..|+..|-
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 3677887877664
No 130
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=51.15 E-value=3.5 Score=21.40 Aligned_cols=10 Identities=30% Similarity=0.850 Sum_probs=4.8
Q ss_pred cCCCCCCccc
Q psy12012 55 QCPQCPHRTK 64 (79)
Q Consensus 55 ~c~~c~~~f~ 64 (79)
.|..|+..|+
T Consensus 30 eC~~C~~RFT 39 (156)
T COG1327 30 ECLECGERFT 39 (156)
T ss_pred cccccccccc
Confidence 4555554443
No 131
>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=50.96 E-value=9 Score=18.35 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=14.9
Q ss_pred hHhhhhhcCCCCccCCCCCCcccC
Q psy12012 42 QHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 42 ~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
.++..+.+ +|..|..|+.-|..
T Consensus 70 ~W~~l~~g--~~~rC~eCG~~fkL 91 (97)
T cd00924 70 IWMWLEKG--KPKRCPECGHVFKL 91 (97)
T ss_pred EEEEEeCC--CceeCCCCCcEEEE
Confidence 33444444 68899999988764
No 132
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.10 E-value=9.3 Score=18.81 Aligned_cols=33 Identities=6% Similarity=0.013 Sum_probs=21.9
Q ss_pred CCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCc
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQK 66 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 66 (79)
|.|. .|+.|++.|-- |. ..|..|+.||++|+.+
T Consensus 7 GtKr-idPetg~KFYD---LN---------rdPiVsPytG~s~P~s 39 (129)
T COG4530 7 GTKR-IDPETGKKFYD---LN---------RDPIVSPYTGKSYPRS 39 (129)
T ss_pred cccc-cCccccchhhc---cC---------CCccccCcccccchHH
Confidence 3443 67777776532 21 5688999999998543
No 133
>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=49.98 E-value=3.6 Score=14.98 Aligned_cols=9 Identities=22% Similarity=0.863 Sum_probs=5.0
Q ss_pred ccchhhhhh
Q psy12012 26 VCDVCDRRY 34 (79)
Q Consensus 26 ~c~~c~~~~ 34 (79)
.|.-|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455565555
No 134
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=49.83 E-value=14 Score=22.89 Aligned_cols=22 Identities=27% Similarity=0.690 Sum_probs=17.9
Q ss_pred ccCCCCCCcccCcchHHHHHHh
Q psy12012 54 YQCPQCPHRTKQKSSLKTHMAV 75 (79)
Q Consensus 54 ~~c~~c~~~f~~~~~l~~h~~~ 75 (79)
+.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 6688888889888888888763
No 135
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=49.52 E-value=8.6 Score=18.25 Aligned_cols=15 Identities=13% Similarity=0.437 Sum_probs=12.1
Q ss_pred CCCccCCCCCCcccC
Q psy12012 51 EPRYQCPQCPHRTKQ 65 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~ 65 (79)
..|-.|..||..|..
T Consensus 56 v~Pa~CkkCGfef~~ 70 (97)
T COG3357 56 VRPARCKKCGFEFRD 70 (97)
T ss_pred ecChhhcccCccccc
Confidence 357889999988865
No 136
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=49.07 E-value=5.7 Score=21.80 Aligned_cols=25 Identities=12% Similarity=0.285 Sum_probs=0.0
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECG 49 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 49 (79)
...|+.||..+... .+..||++...
T Consensus 168 ~~~cPitGe~IP~~-e~~eHmRi~Ll 192 (229)
T PF12230_consen 168 MIICPITGEMIPAD-EMDEHMRIELL 192 (229)
T ss_dssp --------------------------
T ss_pred cccccccccccccc-ccccccccccc
Confidence 35677776655443 36677776554
No 137
>KOG0717|consensus
Probab=48.04 E-value=9.3 Score=23.68 Aligned_cols=22 Identities=27% Similarity=0.674 Sum_probs=19.6
Q ss_pred cccchhhhhhcchhhHHhHhhh
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKY 46 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~ 46 (79)
+-|.+|.++|.....+..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6799999999999999888765
No 138
>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=47.83 E-value=11 Score=15.14 Aligned_cols=12 Identities=25% Similarity=0.645 Sum_probs=8.8
Q ss_pred cCCCCCCcccCc
Q psy12012 55 QCPQCPHRTKQK 66 (79)
Q Consensus 55 ~c~~c~~~f~~~ 66 (79)
.|..|++.|.-.
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 588888887654
No 139
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=47.53 E-value=14 Score=15.18 Aligned_cols=23 Identities=26% Similarity=0.795 Sum_probs=9.3
Q ss_pred hcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 34 YKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 34 ~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
|....-|....+ ...+.|++|++
T Consensus 27 FDl~~fl~~~~~-----~~~W~CPiC~~ 49 (50)
T PF02891_consen 27 FDLESFLESNQR-----TPKWKCPICNK 49 (50)
T ss_dssp EEHHHHHHHHHH-----S---B-TTT--
T ss_pred ECHHHHHHHhhc-----cCCeECcCCcC
Confidence 555444443333 23488999864
No 140
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=47.53 E-value=8.2 Score=18.87 Aligned_cols=25 Identities=24% Similarity=0.494 Sum_probs=15.0
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
...|..|+..|.... ..+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ-------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC-------------cCccCcCCCC
Confidence 357888876554421 2345888874
No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.37 E-value=4.9 Score=26.17 Aligned_cols=12 Identities=25% Similarity=0.706 Sum_probs=8.7
Q ss_pred CCCccCCCCCCc
Q psy12012 51 EPRYQCPQCPHR 62 (79)
Q Consensus 51 ~~~~~c~~c~~~ 62 (79)
..|..|+.|+..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 467788888754
No 142
>KOG0978|consensus
Probab=47.32 E-value=9.6 Score=24.82 Aligned_cols=19 Identities=16% Similarity=0.487 Sum_probs=14.4
Q ss_pred CCccCCCCCCcccCcchHH
Q psy12012 52 PRYQCPQCPHRTKQKSSLK 70 (79)
Q Consensus 52 ~~~~c~~c~~~f~~~~~l~ 70 (79)
+.-+||.|+..|.....+.
T Consensus 677 RqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred hcCCCCCCCCCCCcccccc
Confidence 4467999999998766543
No 143
>KOG2231|consensus
Probab=46.67 E-value=27 Score=22.85 Aligned_cols=46 Identities=22% Similarity=0.575 Sum_probs=25.2
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCC------CCcccCcchHHHHHHhh
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQC------PHRTKQKSSLKTHMAVK 76 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c------~~~f~~~~~l~~h~~~h 76 (79)
.|..|...|.....|..|++.++- .|..| ...|.....|..|-+-.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~-----~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHE-----FCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred cchhhhhhhccHHHHHHhhcccee-----heeecCcccccchhcccchHHHHHhhhc
Confidence 466666666666666666664322 23333 23455556666665543
No 144
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=46.66 E-value=7.4 Score=23.96 Aligned_cols=41 Identities=22% Similarity=0.488 Sum_probs=22.8
Q ss_pred CCCccccchhhhhhcchhhHHhHhhhhhcC-----CCCccCCCCCCc
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKKYECGK-----EPRYQCPQCPHR 62 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~-----~~~~~c~~c~~~ 62 (79)
..+.|.|..|+..+.....-... .+..|. ...+.|+.|+..
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~-~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQ-DVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCccc-CCCCCCChhhCCCCCcCcCCCCc
Confidence 34579999999777654221111 111110 124799999854
No 145
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=45.51 E-value=8.1 Score=18.94 Aligned_cols=25 Identities=24% Similarity=0.665 Sum_probs=15.2
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
...|..|+..|.... .-+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEI-------------DLYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCC-------------cCccCcCCcC
Confidence 357888876665431 1355888874
No 146
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=45.38 E-value=19 Score=15.01 Aligned_cols=31 Identities=19% Similarity=0.446 Sum_probs=16.6
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
.|.-|.-..+. ....-. ..+ .....|+.|++
T Consensus 24 ~C~gC~~~l~~--~~~~~i--~~~-~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPP--QELNEI--RKG-DEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCH--HHHHHH--HcC-CCeEECcCCCc
Confidence 67767544333 222222 223 45678999986
No 147
>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=44.27 E-value=3.8 Score=21.37 Aligned_cols=16 Identities=19% Similarity=0.314 Sum_probs=12.1
Q ss_pred CCCccCCCCCCcccCc
Q psy12012 51 EPRYQCPQCPHRTKQK 66 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~ 66 (79)
..|.-|..||+.|+.-
T Consensus 66 ~~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWT 81 (158)
T ss_pred CCChhHHhCCCCCchH
Confidence 4677788898888764
No 148
>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=43.96 E-value=7.7 Score=15.36 Aligned_cols=12 Identities=50% Similarity=1.149 Sum_probs=7.1
Q ss_pred Cccccchhhhhh
Q psy12012 23 GLFVCDVCDRRY 34 (79)
Q Consensus 23 ~~~~c~~c~~~~ 34 (79)
++-.|..|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 355677776554
No 149
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=43.48 E-value=12 Score=16.19 Aligned_cols=13 Identities=23% Similarity=0.789 Sum_probs=9.3
Q ss_pred CCCccCCCCCCcc
Q psy12012 51 EPRYQCPQCPHRT 63 (79)
Q Consensus 51 ~~~~~c~~c~~~f 63 (79)
...+.|+.|+...
T Consensus 44 ~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 44 GRVFTCPNCGFEM 56 (69)
T ss_pred cceEEcCCCCCEE
Confidence 4568888888653
No 150
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.10 E-value=16 Score=18.42 Aligned_cols=16 Identities=25% Similarity=0.675 Sum_probs=12.6
Q ss_pred CCCccCCCCCCcccCc
Q psy12012 51 EPRYQCPQCPHRTKQK 66 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~ 66 (79)
...|.|+.|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4569999999988653
No 151
>PF14353 CpXC: CpXC protein
Probab=43.09 E-value=12 Score=18.43 Aligned_cols=14 Identities=29% Similarity=0.902 Sum_probs=10.8
Q ss_pred CCccCCCCCCcccC
Q psy12012 52 PRYQCPQCPHRTKQ 65 (79)
Q Consensus 52 ~~~~c~~c~~~f~~ 65 (79)
..+.|+.||..|.-
T Consensus 37 ~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 37 FSFTCPSCGHKFRL 50 (128)
T ss_pred CEEECCCCCCceec
Confidence 45889999987644
No 152
>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=42.80 E-value=9.2 Score=18.66 Aligned_cols=12 Identities=17% Similarity=0.551 Sum_probs=8.0
Q ss_pred cccchhhhhhcc
Q psy12012 25 FVCDVCDRRYKY 36 (79)
Q Consensus 25 ~~c~~c~~~~~~ 36 (79)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 568888877755
No 153
>COG1773 Rubredoxin [Energy production and conversion]
Probab=42.76 E-value=10 Score=16.17 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=6.0
Q ss_pred CccCCCCCCcc
Q psy12012 53 RYQCPQCPHRT 63 (79)
Q Consensus 53 ~~~c~~c~~~f 63 (79)
.++|..|+..|
T Consensus 3 ~~~C~~CG~vY 13 (55)
T COG1773 3 RWRCSVCGYVY 13 (55)
T ss_pred ceEecCCceEe
Confidence 35566665443
No 154
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=41.67 E-value=16 Score=18.58 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=6.3
Q ss_pred ccCCCCCCcccC
Q psy12012 54 YQCPQCPHRTKQ 65 (79)
Q Consensus 54 ~~c~~c~~~f~~ 65 (79)
.+|..|++.|..
T Consensus 2 H~Ct~Cg~~f~d 13 (131)
T PF09845_consen 2 HQCTKCGRVFED 13 (131)
T ss_pred cccCcCCCCcCC
Confidence 345555555544
No 155
>KOG4173|consensus
Probab=41.61 E-value=30 Score=19.22 Aligned_cols=50 Identities=26% Similarity=0.410 Sum_probs=24.9
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcC---------CCCccCC--CCCCcccCcchHHHHHHh
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGK---------EPRYQCP--QCPHRTKQKSSLKTHMAV 75 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~---------~~~~~c~--~c~~~f~~~~~l~~h~~~ 75 (79)
.|.+|.+.|....-|..|+.-.+.. ..-|+|- .|+-.|........|+..
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 5666666666655555555422110 1224443 355566665555555543
No 156
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=39.85 E-value=9.6 Score=20.73 Aligned_cols=22 Identities=23% Similarity=0.641 Sum_probs=0.0
Q ss_pred CCCccCCCCCCc-ccCcchHHHH
Q psy12012 51 EPRYQCPQCPHR-TKQKSSLKTH 72 (79)
Q Consensus 51 ~~~~~c~~c~~~-f~~~~~l~~h 72 (79)
.+.|.|.+||.. +.-+..+..|
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp -----------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHh
Confidence 466888888853 3333344444
No 157
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=39.70 E-value=12 Score=14.43 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=4.5
Q ss_pred CccCCCCCCc
Q psy12012 53 RYQCPQCPHR 62 (79)
Q Consensus 53 ~~~c~~c~~~ 62 (79)
-|+|..|+..
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4677777754
No 158
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=38.42 E-value=10 Score=16.18 Aligned_cols=8 Identities=50% Similarity=1.356 Sum_probs=1.6
Q ss_pred ccCCCCCC
Q psy12012 54 YQCPQCPH 61 (79)
Q Consensus 54 ~~c~~c~~ 61 (79)
+.|++|+.
T Consensus 34 y~Cp~CgA 41 (55)
T PF05741_consen 34 YVCPICGA 41 (55)
T ss_dssp ---TTT--
T ss_pred CcCCCCcC
Confidence 44555543
No 159
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=38.34 E-value=23 Score=18.99 Aligned_cols=34 Identities=21% Similarity=0.746 Sum_probs=20.1
Q ss_pred CCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcc
Q psy12012 20 NHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRT 63 (79)
Q Consensus 20 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 63 (79)
+...-|.|+.|...+....++. ..|.|+.||...
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~----------~~F~Cp~Cg~~L 142 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAME----------LGFTCPKCGEDL 142 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHH----------hCCCCCCCCchh
Confidence 4445678877765554433221 238899998643
No 160
>PF14369 zf-RING_3: zinc-finger
Probab=38.33 E-value=18 Score=13.69 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=7.5
Q ss_pred cCCCCCCccc
Q psy12012 55 QCPQCPHRTK 64 (79)
Q Consensus 55 ~c~~c~~~f~ 64 (79)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5888887774
No 161
>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=38.30 E-value=8.3 Score=19.58 Aligned_cols=31 Identities=32% Similarity=0.865 Sum_probs=17.7
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRT 63 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 63 (79)
.|.|..|+..+.. +.+. . ...+.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~-~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--K-RKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeee------eccc--c-hhhEECCCCCCEE
Confidence 4678888766533 2222 1 2347788887544
No 162
>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=38.13 E-value=5.1 Score=15.43 Aligned_cols=18 Identities=33% Similarity=0.824 Sum_probs=8.3
Q ss_pred HhHhhhhhcCCCCccCCCC
Q psy12012 41 YQHKKYECGKEPRYQCPQC 59 (79)
Q Consensus 41 ~~h~~~~~~~~~~~~c~~c 59 (79)
..|-....| ...|.|..|
T Consensus 18 ~k~G~~~~G-~qryrC~~C 35 (36)
T PF03811_consen 18 KKNGKSPSG-HQRYRCKDC 35 (36)
T ss_pred eeCCCCCCC-CEeEecCcC
Confidence 333333334 444666655
No 163
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=37.58 E-value=21 Score=15.15 Aligned_cols=32 Identities=13% Similarity=0.249 Sum_probs=16.3
Q ss_pred CCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCC
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQ 58 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~ 58 (79)
+.|.....|+..|.....+. ..+ . .....|+.
T Consensus 22 ~~PV~s~~C~H~fek~aI~~-~i~---~-~~~~~CPv 53 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAILQ-YIQ---R-NGSKRCPV 53 (57)
T ss_dssp SSEEEESSS--EEEHHHHHH-HCT---T-TS-EE-SC
T ss_pred hCCcCcCCCCCeecHHHHHH-HHH---h-cCCCCCCC
Confidence 45666677888887765443 321 1 34567776
No 164
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.97 E-value=31 Score=17.09 Aligned_cols=49 Identities=14% Similarity=0.215 Sum_probs=28.1
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhhc
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
.|.-|...|........-. -.. ...|.|+.|...|-..-+.-.|...|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~--~~~-~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDE--LKD-SHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccccc--ccc-ccceeCCCCCCccccccchhhhhhccC
Confidence 3666766665432111000 011 335888888888887777777766654
No 165
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=36.64 E-value=24 Score=14.63 Aligned_cols=13 Identities=23% Similarity=0.738 Sum_probs=8.5
Q ss_pred cccchhhhhhcch
Q psy12012 25 FVCDVCDRRYKYK 37 (79)
Q Consensus 25 ~~c~~c~~~~~~~ 37 (79)
+.|..|+..+...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 6777777666553
No 166
>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=35.39 E-value=30 Score=14.13 Aligned_cols=9 Identities=22% Similarity=0.881 Sum_probs=4.0
Q ss_pred cchhhhhhc
Q psy12012 27 CDVCDRRYK 35 (79)
Q Consensus 27 c~~c~~~~~ 35 (79)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 444444443
No 167
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=35.36 E-value=27 Score=17.85 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=25.6
Q ss_pred ccccchhhhhhcchhhHHh--Hh--hhhhcCCCCccCCCCCCcccCcchHH
Q psy12012 24 LFVCDVCDRRYKYKSGLYQ--HK--KYECGKEPRYQCPQCPHRTKQKSSLK 70 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~--h~--~~~~~~~~~~~c~~c~~~f~~~~~l~ 70 (79)
...|..|+..+..-..-.. -. .+......=+.|+.|++.|..-++..
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHH
Confidence 3689999875544221111 00 01101123477999999998876654
No 168
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=35.29 E-value=6.2 Score=14.99 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=3.7
Q ss_pred ccCCCCC
Q psy12012 54 YQCPQCP 60 (79)
Q Consensus 54 ~~c~~c~ 60 (79)
..|+.|+
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 4455554
No 169
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.88 E-value=6.2 Score=22.11 Aligned_cols=24 Identities=17% Similarity=0.364 Sum_probs=13.6
Q ss_pred CccccchhhhhhcchhhHHhHhhh
Q psy12012 23 GLFVCDVCDRRYKYKSGLYQHKKY 46 (79)
Q Consensus 23 ~~~~c~~c~~~~~~~~~l~~h~~~ 46 (79)
+...|++|+..|....-...-.++
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRi 41 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRI 41 (267)
T ss_pred ceeccCcccchhhhhheeccceeE
Confidence 455677777666665544444443
No 170
>KOG1994|consensus
Probab=34.48 E-value=17 Score=20.42 Aligned_cols=20 Identities=35% Similarity=0.838 Sum_probs=17.1
Q ss_pred ccccchhhhhhcchhhHHhH
Q psy12012 24 LFVCDVCDRRYKYKSGLYQH 43 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h 43 (79)
-|-|-+||-.|....+|..|
T Consensus 239 h~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred ceEEEEeccccCCHHHHHHh
Confidence 47899999999999988866
No 171
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=34.42 E-value=20 Score=18.79 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=23.2
Q ss_pred CCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 18 EPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 18 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
.|..-....|..|++.+....... .. .. ..+..|+.|+..
T Consensus 99 lHG~l~~~~C~~C~~~~~~~~~~~-~~--~~--~~~~~C~~C~~~ 138 (178)
T PF02146_consen 99 LHGSLFRLRCSKCGKEYDREDIVD-SI--DE--EEPPRCPKCGGL 138 (178)
T ss_dssp TTEEEEEEEETTTSBEEEGHHHHH-HH--HT--TSSCBCTTTSCB
T ss_pred HHhhhceeeecCCCccccchhhcc-cc--cc--cccccccccCcc
Confidence 444445678999998876543222 11 11 233478989853
No 172
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=34.07 E-value=35 Score=13.23 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=6.6
Q ss_pred cCCCCCCcccCcc
Q psy12012 55 QCPQCPHRTKQKS 67 (79)
Q Consensus 55 ~c~~c~~~f~~~~ 67 (79)
.|+.|++.|...+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 4666776665543
No 173
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=34.06 E-value=26 Score=19.77 Aligned_cols=15 Identities=20% Similarity=0.412 Sum_probs=12.2
Q ss_pred CCCccCCCCCCcccC
Q psy12012 51 EPRYQCPQCPHRTKQ 65 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~ 65 (79)
.++..|+.||..|..
T Consensus 179 GkpqRCpECGqVFKL 193 (268)
T PTZ00043 179 GFLYRCGECDQIFML 193 (268)
T ss_pred CCCccCCCCCcEEEE
Confidence 468899999988765
No 174
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=33.75 E-value=36 Score=12.83 Aligned_cols=20 Identities=20% Similarity=0.634 Sum_probs=9.8
Q ss_pred CccCCCCCCcccCcchHHHHH
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHM 73 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~ 73 (79)
.+.|+.|++.+... -+..|+
T Consensus 4 ~~~C~nC~R~v~a~-RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVAAS-RFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEEGG-GHHHHH
T ss_pred eEECCCCcCCcchh-hhHHHH
Confidence 35677777654432 334443
No 175
>PRK11032 hypothetical protein; Provisional
Probab=32.96 E-value=17 Score=19.18 Aligned_cols=31 Identities=29% Similarity=0.678 Sum_probs=18.3
Q ss_pred CCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 21 HAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
|.+..+|..||..... ... ...-.|+.|+..
T Consensus 121 g~G~LvC~~Cg~~~~~----------~~p-~~i~pCp~C~~~ 151 (160)
T PRK11032 121 GLGNLVCEKCHHHLAF----------YTP-EVLPLCPKCGHD 151 (160)
T ss_pred ecceEEecCCCCEEEe----------cCC-CcCCCCCCCCCC
Confidence 3456889999754321 112 334468999754
No 176
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=32.72 E-value=2.4 Score=18.76 Aligned_cols=34 Identities=32% Similarity=0.721 Sum_probs=16.0
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCc
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHR 62 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 62 (79)
|+|..|+..-.. .+ ..+.-+.| ....+|+.|...
T Consensus 5 FTC~~C~~Rs~~--~~-sk~aY~~G-vViv~C~gC~~~ 38 (66)
T PF05180_consen 5 FTCNKCGTRSAK--MF-SKQAYHKG-VVIVQCPGCKNR 38 (66)
T ss_dssp EEETTTTEEEEE--EE-EHHHHHTS-EEEEE-TTS--E
T ss_pred EEcCCCCCccce--ee-CHHHHhCC-eEEEECCCCcce
Confidence 678888643222 11 22233445 556678888653
No 177
>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=32.08 E-value=29 Score=13.57 Aligned_cols=8 Identities=38% Similarity=1.402 Sum_probs=4.5
Q ss_pred cCCCCCCc
Q psy12012 55 QCPQCPHR 62 (79)
Q Consensus 55 ~c~~c~~~ 62 (79)
.|+.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 46666543
No 178
>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 KOG4124|consensus
Probab=31.52 E-value=12 Score=22.35 Aligned_cols=23 Identities=39% Similarity=0.873 Sum_probs=17.1
Q ss_pred CCccccchhhhhhcchhhHHhHh
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHK 44 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~ 44 (79)
.|+|+|++|.+.+.....|.-|.
T Consensus 396 nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 396 NKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCcccChhhhhhhccCCCCCcee
Confidence 57899999998887766655443
No 180
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=31.33 E-value=12 Score=19.16 Aligned_cols=16 Identities=25% Similarity=0.501 Sum_probs=12.3
Q ss_pred CCccccchhhhhhcch
Q psy12012 22 AGLFVCDVCDRRYKYK 37 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~ 37 (79)
.++.+|..||.-|...
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 3588999999887654
No 181
>PTZ00448 hypothetical protein; Provisional
Probab=30.94 E-value=43 Score=20.30 Aligned_cols=22 Identities=18% Similarity=0.454 Sum_probs=16.0
Q ss_pred CccCCCCCCcccCcchHHHHHH
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHMA 74 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~~ 74 (79)
.+.|..|+-.|........|.+
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~K 335 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYR 335 (373)
T ss_pred CccccccccccCCHHHHHHHhh
Confidence 4779999988876655566654
No 182
>KOG0562|consensus
Probab=30.86 E-value=43 Score=17.96 Aligned_cols=27 Identities=19% Similarity=0.341 Sum_probs=19.8
Q ss_pred CCCccCCCCCCcccCcchHHHHHHhhc
Q psy12012 51 EPRYQCPQCPHRTKQKSSLKTHMAVKH 77 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~~~l~~h~~~h~ 77 (79)
+.+..|..|+..-+..+-|+.|.+.+.
T Consensus 151 k~dLrC~~Cq~~~~~~~kLK~Hl~~~~ 177 (184)
T KOG0562|consen 151 KEDLRCWRCQTFGPHFPKLKAHLREEY 177 (184)
T ss_pred ccceeehhhhhcccccHHHHHHHHHHH
Confidence 346789999855566778899988653
No 183
>PRK12860 transcriptional activator FlhC; Provisional
Probab=30.42 E-value=27 Score=18.96 Aligned_cols=28 Identities=18% Similarity=0.433 Sum_probs=17.2
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCP 60 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 60 (79)
...|..|+..|..... .. ...|.|+.|.
T Consensus 134 l~~C~~Cgg~fv~~~~--------e~-~~~f~CplC~ 161 (189)
T PRK12860 134 LARCCRCGGKFVTHAH--------DL-RHNFVCGLCQ 161 (189)
T ss_pred eccCCCCCCCeecccc--------cc-CCCCcCCCCC
Confidence 4578888877753211 12 3468888885
No 184
>KOG3214|consensus
Probab=30.41 E-value=31 Score=16.77 Aligned_cols=12 Identities=17% Similarity=0.479 Sum_probs=8.1
Q ss_pred ccCCCCCCcccC
Q psy12012 54 YQCPQCPHRTKQ 65 (79)
Q Consensus 54 ~~c~~c~~~f~~ 65 (79)
..|.+|+..|..
T Consensus 48 ~sC~iC~esFqt 59 (109)
T KOG3214|consen 48 ASCRICEESFQT 59 (109)
T ss_pred eeeeehhhhhcc
Confidence 567777777654
No 185
>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=30.03 E-value=22 Score=13.80 Aligned_cols=13 Identities=15% Similarity=0.802 Sum_probs=7.7
Q ss_pred CCCccccchhhhh
Q psy12012 21 HAGLFVCDVCDRR 33 (79)
Q Consensus 21 ~~~~~~c~~c~~~ 33 (79)
+.+.|.|..|+..
T Consensus 21 ~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 21 GGKTWICNFCGTK 33 (40)
T ss_dssp TTTEEEETTT--E
T ss_pred CCCEEECcCCCCc
Confidence 4566888888654
No 186
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.90 E-value=31 Score=18.75 Aligned_cols=29 Identities=17% Similarity=0.466 Sum_probs=17.2
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
...|..|+..|..... .. ...|.|+.|..
T Consensus 134 l~~C~~Cgg~fv~~~~--------e~-~~~f~CplC~~ 162 (187)
T PRK12722 134 LSSCNCCGGHFVTHAH--------DP-VGSFVCGLCQP 162 (187)
T ss_pred eccCCCCCCCeecccc--------cc-CCCCcCCCCCC
Confidence 3468888777653221 12 34688888863
No 187
>PRK01343 zinc-binding protein; Provisional
Probab=29.58 E-value=44 Score=14.41 Aligned_cols=13 Identities=31% Similarity=0.958 Sum_probs=8.8
Q ss_pred CCccCCCCCCccc
Q psy12012 52 PRYQCPQCPHRTK 64 (79)
Q Consensus 52 ~~~~c~~c~~~f~ 64 (79)
+...|++|++.+.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3456888887654
No 188
>KOG3352|consensus
Probab=29.26 E-value=32 Score=18.00 Aligned_cols=22 Identities=32% Similarity=0.507 Sum_probs=14.3
Q ss_pred HhhhhhcCCCCccCCCCCCcccCc
Q psy12012 43 HKKYECGKEPRYQCPQCPHRTKQK 66 (79)
Q Consensus 43 h~~~~~~~~~~~~c~~c~~~f~~~ 66 (79)
++-.+.+ +..+|++|+..|...
T Consensus 125 Wmwl~Kg--e~~rc~eCG~~fkL~ 146 (153)
T KOG3352|consen 125 WMWLEKG--ETQRCPECGHYFKLV 146 (153)
T ss_pred EEEEEcC--CcccCCcccceEEee
Confidence 3444444 567799999887653
No 189
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.49 E-value=26 Score=19.93 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=7.3
Q ss_pred CCccCCCCCCc
Q psy12012 52 PRYQCPQCPHR 62 (79)
Q Consensus 52 ~~~~c~~c~~~ 62 (79)
+.+.|+.||..
T Consensus 321 r~~~C~~cg~~ 331 (364)
T COG0675 321 RLFKCPRCGFV 331 (364)
T ss_pred eeEECCCCCCe
Confidence 45777777754
No 190
>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=28.13 E-value=8.9 Score=15.50 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=5.7
Q ss_pred ccCCC--CCCccc
Q psy12012 54 YQCPQ--CPHRTK 64 (79)
Q Consensus 54 ~~c~~--c~~~f~ 64 (79)
+.|.. ||..|.
T Consensus 26 ~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 26 CQCTNPECGHTFV 38 (47)
T ss_pred EEECCCcCCCEEE
Confidence 44443 666554
No 191
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=28.01 E-value=26 Score=14.67 Aligned_cols=17 Identities=18% Similarity=0.366 Sum_probs=10.3
Q ss_pred CCCccccchhhhhhcch
Q psy12012 21 HAGLFVCDVCDRRYKYK 37 (79)
Q Consensus 21 ~~~~~~c~~c~~~~~~~ 37 (79)
....++|..|++.+...
T Consensus 32 ~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 32 EPIKLRCHYCERIITED 48 (52)
T ss_dssp TTCEEEETTT--EEEHH
T ss_pred CCCEEEeeCCCCEeccc
Confidence 44568888888776554
No 192
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.81 E-value=46 Score=21.82 Aligned_cols=11 Identities=36% Similarity=1.298 Sum_probs=7.3
Q ss_pred CCccCCCCCCc
Q psy12012 52 PRYQCPQCPHR 62 (79)
Q Consensus 52 ~~~~c~~c~~~ 62 (79)
.|..|+.|+..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 46678888754
No 193
>KOG4118|consensus
Probab=27.41 E-value=59 Score=14.50 Aligned_cols=26 Identities=19% Similarity=0.225 Sum_probs=16.4
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECG 49 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 49 (79)
.+.|.+|--....+..+.+|....+.
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCC
Confidence 36788876666666666666665433
No 194
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=27.22 E-value=30 Score=20.20 Aligned_cols=22 Identities=18% Similarity=0.551 Sum_probs=12.6
Q ss_pred ccccchhhhhhcchhhHHhHhh
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKK 45 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~ 45 (79)
..+|+.|+..|.....+..|.-
T Consensus 275 ~ik~n~c~~~~~~e~~~~~Ha~ 296 (306)
T COG5539 275 SIKCNICGTGFVGEKDYYAHAL 296 (306)
T ss_pred eEEeeccccccchhhHHHHHHH
Confidence 3456666666665555555543
No 195
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=27.22 E-value=40 Score=13.17 Aligned_cols=9 Identities=33% Similarity=1.017 Sum_probs=6.4
Q ss_pred CccCCCCCC
Q psy12012 53 RYQCPQCPH 61 (79)
Q Consensus 53 ~~~c~~c~~ 61 (79)
|..|+.|+.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 567888874
No 196
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=27.10 E-value=15 Score=21.14 Aligned_cols=21 Identities=24% Similarity=0.562 Sum_probs=12.2
Q ss_pred CCCccCCCCCCcccCcchHHH
Q psy12012 51 EPRYQCPQCPHRTKQKSSLKT 71 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~~~l~~ 71 (79)
.+++.|+.|+........|..
T Consensus 207 ~k~~PCPKCg~et~eTkdLSm 227 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSM 227 (314)
T ss_pred CCCCCCCCCCCccccccccee
Confidence 356777777765544444443
No 197
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.09 E-value=31 Score=16.85 Aligned_cols=14 Identities=14% Similarity=0.413 Sum_probs=10.0
Q ss_pred ccccchhhhhhcch
Q psy12012 24 LFVCDVCDRRYKYK 37 (79)
Q Consensus 24 ~~~c~~c~~~~~~~ 37 (79)
|+.|..||..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 46788888777663
No 198
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=26.69 E-value=42 Score=19.06 Aligned_cols=40 Identities=18% Similarity=0.280 Sum_probs=22.9
Q ss_pred cCCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 17 SEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 17 ~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
..|..-....|..|+..+......... .. ..+-.|+.|+.
T Consensus 115 ~lHGsl~~~~C~~C~~~~~~~~~~~~~---~~--~~~p~C~~Cg~ 154 (250)
T COG0846 115 ELHGSLKRVRCSKCGNQYYDEDVIKFI---ED--GLIPRCPKCGG 154 (250)
T ss_pred EeccceeeeEeCCCcCccchhhhhhhc---cc--CCCCcCccCCC
Confidence 345455678899998777644311111 11 23456888886
No 199
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=26.35 E-value=32 Score=13.20 Aligned_cols=13 Identities=38% Similarity=0.871 Sum_probs=8.0
Q ss_pred CCccCCCCCCccc
Q psy12012 52 PRYQCPQCPHRTK 64 (79)
Q Consensus 52 ~~~~c~~c~~~f~ 64 (79)
+-+.|+.||..+.
T Consensus 31 p~~~C~~CGE~~~ 43 (46)
T TIGR03831 31 PALVCPQCGEEYL 43 (46)
T ss_pred CccccccCCCEee
Confidence 3356788876543
No 200
>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=26.34 E-value=29 Score=13.24 Aligned_cols=11 Identities=18% Similarity=0.634 Sum_probs=4.0
Q ss_pred cCCCCCCcccC
Q psy12012 55 QCPQCPHRTKQ 65 (79)
Q Consensus 55 ~c~~c~~~f~~ 65 (79)
.|..|++.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 46666665543
No 201
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=26.22 E-value=36 Score=12.53 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=7.2
Q ss_pred CccCCCCCCcc
Q psy12012 53 RYQCPQCPHRT 63 (79)
Q Consensus 53 ~~~c~~c~~~f 63 (79)
-|+|..|+...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 46777777543
No 202
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.18 E-value=21 Score=14.83 Aligned_cols=12 Identities=25% Similarity=0.684 Sum_probs=8.2
Q ss_pred cCCCCCCcccCc
Q psy12012 55 QCPQCPHRTKQK 66 (79)
Q Consensus 55 ~c~~c~~~f~~~ 66 (79)
.|+.|++.|...
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 477787777653
No 203
>PRK05580 primosome assembly protein PriA; Validated
Probab=26.18 E-value=22 Score=23.10 Aligned_cols=12 Identities=25% Similarity=0.667 Sum_probs=7.8
Q ss_pred CCCccCCCCCCc
Q psy12012 51 EPRYQCPQCPHR 62 (79)
Q Consensus 51 ~~~~~c~~c~~~ 62 (79)
..|..|+.|+..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 346678888654
No 204
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=26.18 E-value=32 Score=18.69 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=8.3
Q ss_pred Cccccchhhhhhcc
Q psy12012 23 GLFVCDVCDRRYKY 36 (79)
Q Consensus 23 ~~~~c~~c~~~~~~ 36 (79)
++-.|.+|+..|..
T Consensus 5 k~rKCKvCg~~F~P 18 (189)
T PF05766_consen 5 KRRKCKVCGEWFVP 18 (189)
T ss_pred CCCcCcccCCcccc
Confidence 44566666666654
No 205
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=25.89 E-value=36 Score=12.50 Aligned_cols=11 Identities=27% Similarity=0.772 Sum_probs=7.3
Q ss_pred CccCCCCCCcc
Q psy12012 53 RYQCPQCPHRT 63 (79)
Q Consensus 53 ~~~c~~c~~~f 63 (79)
-|+|..|+..+
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 47788777543
No 206
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=25.70 E-value=59 Score=19.06 Aligned_cols=24 Identities=33% Similarity=0.588 Sum_probs=18.9
Q ss_pred CCCccCCCCCCcccCcchHHHHHH
Q psy12012 51 EPRYQCPQCPHRTKQKSSLKTHMA 74 (79)
Q Consensus 51 ~~~~~c~~c~~~f~~~~~l~~h~~ 74 (79)
...|.|..|-+.|.....+..|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 456888888888888888888865
No 207
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=25.65 E-value=34 Score=20.56 Aligned_cols=36 Identities=17% Similarity=0.528 Sum_probs=19.6
Q ss_pred cchh-hhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 27 CDVC-DRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 27 c~~c-~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
|..| ++.|..+++-........+ ...|+-|...|--
T Consensus 316 C~~Cm~kwFasrQd~~~~~~Wl~~---~~~CPtCRa~FCi 352 (358)
T PF10272_consen 316 CLECMGKWFASRQDQQHPETWLSG---KCPCPTCRAKFCI 352 (358)
T ss_pred HHHHHHHHhhhcCCCCChhhhhcC---CCCCCCCccccee
Confidence 3344 6677776643322222323 3568889887743
No 208
>PRK09951 hypothetical protein; Provisional
Probab=25.59 E-value=32 Score=19.05 Aligned_cols=10 Identities=40% Similarity=0.694 Sum_probs=7.5
Q ss_pred CCcccccccc
Q psy12012 1 MFGQFRFSES 10 (79)
Q Consensus 1 ~~~~f~~~~~ 10 (79)
|||+|.....
T Consensus 1 MCGRf~~~~~ 10 (222)
T PRK09951 1 MCGRFAQSQT 10 (222)
T ss_pred CCCCccccCC
Confidence 8999976554
No 209
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.52 E-value=60 Score=19.06 Aligned_cols=30 Identities=27% Similarity=0.337 Sum_probs=16.7
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
+|+.|+..+..+. |. +..+.|+.|+.-|..
T Consensus 40 kc~~C~~~~~~~~-l~---------~~~~vcp~c~~h~rl 69 (296)
T CHL00174 40 QCENCYGLNYKKF-LK---------SKMNICEQCGYHLKM 69 (296)
T ss_pred ECCCccchhhHHH-HH---------HcCCCCCCCCCCcCC
Confidence 5777765432221 21 234678888876554
No 210
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=25.50 E-value=51 Score=14.12 Aligned_cols=10 Identities=30% Similarity=0.720 Sum_probs=6.3
Q ss_pred CCCCCCcccC
Q psy12012 56 CPQCPHRTKQ 65 (79)
Q Consensus 56 c~~c~~~f~~ 65 (79)
|+.|+..|..
T Consensus 42 CPfC~~~~~~ 51 (55)
T PF14447_consen 42 CPFCGTPFEF 51 (55)
T ss_pred CCCCCCcccC
Confidence 6777766543
No 211
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=25.44 E-value=41 Score=14.13 Aligned_cols=9 Identities=44% Similarity=1.069 Sum_probs=5.4
Q ss_pred cCCCCCCcc
Q psy12012 55 QCPQCPHRT 63 (79)
Q Consensus 55 ~c~~c~~~f 63 (79)
.|+.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 467776544
No 212
>PRK04351 hypothetical protein; Provisional
Probab=25.44 E-value=21 Score=18.47 Aligned_cols=33 Identities=27% Similarity=0.805 Sum_probs=19.0
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
.|.|..|+..+.. +.+. . ...|.|..|+..+..
T Consensus 112 ~Y~C~~Cg~~~~r------~Rr~--n-~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLR------KRRI--N-TKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeee------eeec--C-CCcEEeCCCCcEeee
Confidence 4778778755432 2222 2 346888888765543
No 213
>KOG0782|consensus
Probab=25.23 E-value=19 Score=23.26 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=8.0
Q ss_pred ccCCCCCCcccCcc
Q psy12012 54 YQCPQCPHRTKQKS 67 (79)
Q Consensus 54 ~~c~~c~~~f~~~~ 67 (79)
-+|..|++.|.++.
T Consensus 254 GkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 254 GKCNTCGKGFQQKF 267 (1004)
T ss_pred cccchhhhhhhhhe
Confidence 45666666665543
No 214
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=25.17 E-value=28 Score=19.89 Aligned_cols=13 Identities=31% Similarity=1.119 Sum_probs=8.5
Q ss_pred CccCCCCCCcccC
Q psy12012 53 RYQCPQCPHRTKQ 65 (79)
Q Consensus 53 ~~~c~~c~~~f~~ 65 (79)
.|.|+.|+..|.-
T Consensus 155 ef~C~~C~h~F~G 167 (278)
T PF15135_consen 155 EFHCPKCRHNFRG 167 (278)
T ss_pred eeecccccccchh
Confidence 4677777776653
No 215
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=25.05 E-value=32 Score=12.87 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=6.6
Q ss_pred ccCCCCCCccc
Q psy12012 54 YQCPQCPHRTK 64 (79)
Q Consensus 54 ~~c~~c~~~f~ 64 (79)
+.|..|+..|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 45777766553
No 216
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.98 E-value=45 Score=14.65 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=22.6
Q ss_pred CCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 18 EPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 18 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
.+.+..++.|.--+..+..+.-+. .. +.+....|+.|+..|..
T Consensus 18 I~~~~~~l~C~g~~~p~~HPrV~L---~m--g~~gev~CPYC~t~y~l 60 (62)
T COG4391 18 IEIGDLPLMCPGPEPPNDHPRVFL---DM--GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred EEeCCeeEEcCCCCCCCCCCEEEE---Ec--CCCCcEecCccccEEEe
Confidence 344566777765443333322111 11 32445679999887653
No 217
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=24.93 E-value=95 Score=16.26 Aligned_cols=9 Identities=33% Similarity=0.896 Sum_probs=4.8
Q ss_pred CccCCCCCC
Q psy12012 53 RYQCPQCPH 61 (79)
Q Consensus 53 ~~~c~~c~~ 61 (79)
...|+.||.
T Consensus 32 lv~CP~Cgs 40 (148)
T PF06676_consen 32 LVSCPVCGS 40 (148)
T ss_pred CccCCCCCC
Confidence 445555553
No 218
>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=24.91 E-value=23 Score=20.29 Aligned_cols=10 Identities=40% Similarity=1.125 Sum_probs=3.4
Q ss_pred CccCCCCCCc
Q psy12012 53 RYQCPQCPHR 62 (79)
Q Consensus 53 ~~~c~~c~~~ 62 (79)
...|+.||..
T Consensus 211 R~~Cp~Cg~~ 220 (290)
T PF04216_consen 211 RIKCPYCGNT 220 (290)
T ss_dssp TTS-TTT---
T ss_pred CCCCcCCCCC
Confidence 3456666644
No 219
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=24.56 E-value=95 Score=15.35 Aligned_cols=27 Identities=30% Similarity=0.458 Sum_probs=21.5
Q ss_pred CCCCccccchhhhhhcchhhHHhHhhh
Q psy12012 20 NHAGLFVCDVCDRRYKYKSGLYQHKKY 46 (79)
Q Consensus 20 ~~~~~~~c~~c~~~~~~~~~l~~h~~~ 46 (79)
.|-..+-|-+|.+-|.....|..|.+.
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhcc
Confidence 345567899999999999999888763
No 220
>KOG0402|consensus
Probab=24.51 E-value=23 Score=16.56 Aligned_cols=30 Identities=17% Similarity=0.661 Sum_probs=18.0
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCccc
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 64 (79)
-|.|+.||+.- +. +...| .+.|..|.+.+.
T Consensus 36 ky~CsfCGK~~-----vK---R~AvG---iW~C~~C~kv~a 65 (92)
T KOG0402|consen 36 KYTCSFCGKKT-----VK---RKAVG---IWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhcchhh-----hh---hhcee---EEecCCccceec
Confidence 48999999753 22 11223 467777776553
No 221
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=24.36 E-value=29 Score=14.71 Aligned_cols=17 Identities=24% Similarity=0.444 Sum_probs=13.3
Q ss_pred cccchhhhhhcchhhHH
Q psy12012 25 FVCDVCDRRYKYKSGLY 41 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~ 41 (79)
+=|-.||..|.....|.
T Consensus 28 ~YC~~Cg~~Y~d~~dL~ 44 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLE 44 (55)
T ss_pred ceeeeeCCccCCHHHHH
Confidence 56888988888877775
No 222
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.81 E-value=25 Score=21.98 Aligned_cols=10 Identities=40% Similarity=0.863 Sum_probs=6.6
Q ss_pred CCccCCCCCC
Q psy12012 52 PRYQCPQCPH 61 (79)
Q Consensus 52 ~~~~c~~c~~ 61 (79)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 4566777764
No 223
>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=23.40 E-value=44 Score=16.15 Aligned_cols=42 Identities=17% Similarity=0.426 Sum_probs=15.3
Q ss_pred CCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCC-ccCCCCCCcccCc
Q psy12012 18 EPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPR-YQCPQCPHRTKQK 66 (79)
Q Consensus 18 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~-~~c~~c~~~f~~~ 66 (79)
...+.|...|..|+..+.. + ++.+. + ++. |-|..|.+.|.+-
T Consensus 8 ~~ag~ke~~CalCG~tWg~---~--y~Ev~-G-~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 8 REAGTKEMGCALCGATWGD---Y--YEEVD-G-ERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp S---SGGGS-SS---S------S--S-B-T-T---BSSS--SSSS-TTS-
T ss_pred eecccccccccccCCcHHH---H--HHhhc-C-CEEEEEcHHHHHHHHHH
Confidence 3456677889999987653 2 22332 3 333 5678888777664
No 224
>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=23.35 E-value=17 Score=14.09 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=7.1
Q ss_pred cccchhhhhh
Q psy12012 25 FVCDVCDRRY 34 (79)
Q Consensus 25 ~~c~~c~~~~ 34 (79)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6788887654
No 225
>KOG3456|consensus
Probab=23.33 E-value=40 Score=16.59 Aligned_cols=13 Identities=23% Similarity=0.692 Sum_probs=9.8
Q ss_pred ccccchhhhhhcc
Q psy12012 24 LFVCDVCDRRYKY 36 (79)
Q Consensus 24 ~~~c~~c~~~~~~ 36 (79)
+..|.+||..|..
T Consensus 104 ~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 104 PHICGYCGLRFVQ 116 (120)
T ss_pred Ccccccchhhhhh
Confidence 4788899887754
No 226
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=23.05 E-value=95 Score=18.62 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=28.0
Q ss_pred ccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccCcchHHHHHHhh
Q psy12012 26 VCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVK 76 (79)
Q Consensus 26 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h 76 (79)
-|-.|...|+....-..-... . ...|.|+.|...|-.....-.|...|
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~~--s-s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDEST--S-SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceeccCCCCCCCCCcccccc--c-ccceechhhhhhhhhhhHHHHHHHHh
Confidence 477777767664321111111 1 23588888888887776666666555
No 227
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.72 E-value=33 Score=14.88 Aligned_cols=7 Identities=43% Similarity=1.312 Sum_probs=3.1
Q ss_pred cchhhhh
Q psy12012 27 CDVCDRR 33 (79)
Q Consensus 27 c~~c~~~ 33 (79)
|.+||+.
T Consensus 6 C~~CG~~ 12 (59)
T PF09889_consen 6 CPVCGKP 12 (59)
T ss_pred CCcCCCc
Confidence 4444433
No 228
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.63 E-value=21 Score=17.13 Aligned_cols=11 Identities=27% Similarity=0.622 Sum_probs=8.0
Q ss_pred Cccccchhhhh
Q psy12012 23 GLFVCDVCDRR 33 (79)
Q Consensus 23 ~~~~c~~c~~~ 33 (79)
+.|.|.+|+..
T Consensus 5 kewkC~VCg~~ 15 (103)
T COG4847 5 KEWKCYVCGGT 15 (103)
T ss_pred ceeeEeeeCCE
Confidence 45788888755
No 229
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=22.58 E-value=21 Score=17.32 Aligned_cols=10 Identities=20% Similarity=0.833 Sum_probs=6.6
Q ss_pred ccccchhhhh
Q psy12012 24 LFVCDVCDRR 33 (79)
Q Consensus 24 ~~~c~~c~~~ 33 (79)
-|+|.+||+.
T Consensus 2 kWkC~iCg~~ 11 (101)
T PF09943_consen 2 KWKCYICGKP 11 (101)
T ss_pred ceEEEecCCe
Confidence 3677777654
No 230
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=22.37 E-value=26 Score=14.72 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=6.6
Q ss_pred CccCCCCCCc
Q psy12012 53 RYQCPQCPHR 62 (79)
Q Consensus 53 ~~~c~~c~~~ 62 (79)
..+|+.|+..
T Consensus 24 eIKCpRC~ti 33 (51)
T PF10122_consen 24 EIKCPRCKTI 33 (51)
T ss_pred EEECCCCCcc
Confidence 4678877643
No 231
>PLN02748 tRNA dimethylallyltransferase
Probab=22.27 E-value=79 Score=19.87 Aligned_cols=23 Identities=17% Similarity=0.475 Sum_probs=15.6
Q ss_pred CCccCCCCCC-cccCcchHHHHHH
Q psy12012 52 PRYQCPQCPH-RTKQKSSLKTHMA 74 (79)
Q Consensus 52 ~~~~c~~c~~-~f~~~~~l~~h~~ 74 (79)
+.|.|..|+. .+.-......|+.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhc
Confidence 4577999986 6766655666644
No 232
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=22.23 E-value=43 Score=14.56 Aligned_cols=11 Identities=45% Similarity=1.174 Sum_probs=6.2
Q ss_pred ccCCCCCCcccC
Q psy12012 54 YQCPQCPHRTKQ 65 (79)
Q Consensus 54 ~~c~~c~~~f~~ 65 (79)
|.|+ ||..|.-
T Consensus 23 yPCP-CGDRFeI 33 (67)
T COG5216 23 YPCP-CGDRFEI 33 (67)
T ss_pred ecCC-CCCEeEE
Confidence 4455 7766643
No 233
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=22.19 E-value=13 Score=14.45 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=3.5
Q ss_pred cchhhhhhcch
Q psy12012 27 CDVCDRRYKYK 37 (79)
Q Consensus 27 c~~c~~~~~~~ 37 (79)
|..|+..+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 56676665544
No 234
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=22.10 E-value=82 Score=13.10 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=13.7
Q ss_pred CCccccchhhhhhcchhhHHhHhhh
Q psy12012 22 AGLFVCDVCDRRYKYKSGLYQHKKY 46 (79)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~l~~h~~~ 46 (79)
.||--|+.|...|.. |..|...
T Consensus 3 ~k~GYCE~Cr~kfd~---l~~Hi~s 24 (49)
T smart00586 3 KKPGYCENCREKYDD---LETHLLS 24 (49)
T ss_pred CCCcccccHhHHHhh---HHHHhcc
Confidence 355568888777654 5666553
No 235
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=21.61 E-value=39 Score=19.36 Aligned_cols=29 Identities=21% Similarity=0.524 Sum_probs=18.8
Q ss_pred ccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCC
Q psy12012 24 LFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCP 60 (79)
Q Consensus 24 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 60 (79)
.-.|+.||+.+.....|. + --.|+|..|.
T Consensus 220 ~r~CP~Cg~~W~L~~plh-------~-iFdFKCD~CR 248 (258)
T PF10071_consen 220 ARKCPSCGGDWRLKEPLH-------D-IFDFKCDPCR 248 (258)
T ss_pred CCCCCCCCCccccCCchh-------h-ceeccCCcce
Confidence 346888888777666551 2 3457787774
No 236
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=21.36 E-value=1.1e+02 Score=17.61 Aligned_cols=21 Identities=10% Similarity=0.126 Sum_probs=12.7
Q ss_pred CCCCCCccccchhhhhhcchh
Q psy12012 18 EPNHAGLFVCDVCDRRYKYKS 38 (79)
Q Consensus 18 ~~~~~~~~~c~~c~~~~~~~~ 38 (79)
.|..-....|..|+..+....
T Consensus 131 lHG~l~~~~C~~C~~~~~~~~ 151 (271)
T PTZ00409 131 LHGSVFEARCCTCRKTIQLNK 151 (271)
T ss_pred eccCcCcceeCCCCCCcccCH
Confidence 343344567888987765443
No 237
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=21.32 E-value=62 Score=15.65 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=8.9
Q ss_pred CCCccCCCCCCcc
Q psy12012 51 EPRYQCPQCPHRT 63 (79)
Q Consensus 51 ~~~~~c~~c~~~f 63 (79)
.+..+|..|+..|
T Consensus 86 ~r~~rC~nCG~~f 98 (98)
T PF10164_consen 86 MRERRCSNCGATF 98 (98)
T ss_pred cCccccCCCCccC
Confidence 3456788888665
No 238
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.24 E-value=42 Score=14.05 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=7.6
Q ss_pred Cccccchhhhhh
Q psy12012 23 GLFVCDVCDRRY 34 (79)
Q Consensus 23 ~~~~c~~c~~~~ 34 (79)
+...|+.||...
T Consensus 2 ~LkPCPFCG~~~ 13 (61)
T PF14354_consen 2 ELKPCPFCGSAD 13 (61)
T ss_pred CCcCCCCCCCcc
Confidence 345688887543
No 239
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=21.03 E-value=83 Score=14.95 Aligned_cols=16 Identities=19% Similarity=0.656 Sum_probs=10.2
Q ss_pred CCccCCCCCCcccCcc
Q psy12012 52 PRYQCPQCPHRTKQKS 67 (79)
Q Consensus 52 ~~~~c~~c~~~f~~~~ 67 (79)
+-..|+.||..+....
T Consensus 34 Pa~~C~~CGe~y~~de 49 (89)
T TIGR03829 34 PSISCSHCGMEYQDDT 49 (89)
T ss_pred CcccccCCCcEeecHH
Confidence 3466888887665543
No 240
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=20.96 E-value=61 Score=13.23 Aligned_cols=7 Identities=29% Similarity=0.719 Sum_probs=2.8
Q ss_pred CCCCCcc
Q psy12012 57 PQCPHRT 63 (79)
Q Consensus 57 ~~c~~~f 63 (79)
+.|+..|
T Consensus 2 P~Cg~~f 8 (50)
T PF14375_consen 2 PRCGAPF 8 (50)
T ss_pred CCCCCcC
Confidence 3444433
No 241
>KOG3362|consensus
Probab=20.91 E-value=27 Score=18.17 Aligned_cols=21 Identities=33% Similarity=0.645 Sum_probs=12.3
Q ss_pred CccCCCCCCcccCcchHHHHH
Q psy12012 53 RYQCPQCPHRTKQKSSLKTHM 73 (79)
Q Consensus 53 ~~~c~~c~~~f~~~~~l~~h~ 73 (79)
+|.|..||..+-....+..|.
T Consensus 129 ~ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred hhHHHhcCCceeechhhhhcc
Confidence 455666666666555665554
No 242
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.74 E-value=87 Score=17.81 Aligned_cols=12 Identities=25% Similarity=0.600 Sum_probs=9.0
Q ss_pred CCCccCCCCCCc
Q psy12012 51 EPRYQCPQCPHR 62 (79)
Q Consensus 51 ~~~~~c~~c~~~ 62 (79)
.....|+.||+-
T Consensus 219 d~iv~CP~CgRI 230 (239)
T COG1579 219 DEIVFCPYCGRI 230 (239)
T ss_pred CCCccCCccchH
Confidence 456779999864
No 243
>PRK12496 hypothetical protein; Provisional
Probab=20.68 E-value=48 Score=17.43 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=9.0
Q ss_pred CccCCCCCCccc
Q psy12012 53 RYQCPQCPHRTK 64 (79)
Q Consensus 53 ~~~c~~c~~~f~ 64 (79)
.+.|..|++.|.
T Consensus 127 ~~~C~gC~~~~~ 138 (164)
T PRK12496 127 RKVCKGCKKKYP 138 (164)
T ss_pred eEECCCCCcccc
Confidence 467888888775
No 244
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.29 E-value=89 Score=18.22 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=17.2
Q ss_pred cccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCCcccC
Q psy12012 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQ 65 (79)
Q Consensus 25 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 65 (79)
..|+.|+.....+ .|. ...+.|+.|+.-|..
T Consensus 27 ~~c~~c~~~~~~~-~l~---------~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 27 TKCPKCGQVLYTK-ELE---------RNLEVCPKCDHHMRM 57 (285)
T ss_pred eECCCCcchhhHH-HHH---------hhCCCCCCCCCcCcC
Confidence 3588887543222 121 234678888876554
No 245
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=20.24 E-value=14 Score=15.13 Aligned_cols=10 Identities=20% Similarity=0.943 Sum_probs=4.7
Q ss_pred ccCCCCCCcc
Q psy12012 54 YQCPQCPHRT 63 (79)
Q Consensus 54 ~~c~~c~~~f 63 (79)
|.|..|+..+
T Consensus 27 f~C~~C~~~l 36 (58)
T PF00412_consen 27 FKCSKCGKPL 36 (58)
T ss_dssp SBETTTTCBT
T ss_pred cccCCCCCcc
Confidence 4455554433
No 246
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=20.23 E-value=1.2e+02 Score=17.01 Aligned_cols=40 Identities=20% Similarity=0.444 Sum_probs=22.1
Q ss_pred cCCCCCCccccchhhhhhcchhhHHhHhhhhhcCCCCccCCCCCC
Q psy12012 17 SEPNHAGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPH 61 (79)
Q Consensus 17 ~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 61 (79)
..|..-....|..|++.+.....+. ... . ...-.|+.|+.
T Consensus 112 elHG~~~~~~C~~C~~~~~~~~~~~---~~~-~-~~~p~Cp~Cgg 151 (244)
T PRK14138 112 ELHGNVEEYYCVRCGKRYTVEDVIE---KLE-K-SDVPRCDDCSG 151 (244)
T ss_pred EccCCcCeeEECCCCCcccHHHHHH---HHh-c-CCCCCCCCCCC
Confidence 3444445567988988776543332 111 1 22346888873
Done!