Query psy12166
Match_columns 94
No_of_seqs 121 out of 1251
Neff 10.9
Searched_HMMs 46136
Date Fri Aug 16 20:23:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12166hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.3E-24 2.8E-29 126.6 3.6 87 1-91 162-248 (279)
2 KOG2462|consensus 99.8 1.2E-20 2.6E-25 110.1 3.5 78 1-80 188-265 (279)
3 KOG3623|consensus 99.7 7.1E-18 1.5E-22 109.1 -0.9 66 26-92 891-956 (1007)
4 KOG3623|consensus 99.6 1.9E-16 4E-21 102.7 1.4 77 1-79 895-971 (1007)
5 KOG3576|consensus 99.5 1.8E-15 3.9E-20 85.7 -2.2 64 26-90 114-177 (267)
6 KOG3576|consensus 99.4 1.3E-14 2.8E-19 82.2 0.1 81 1-83 118-198 (267)
7 PHA02768 hypothetical protein; 99.2 6.1E-12 1.3E-16 57.6 1.8 43 29-74 5-47 (55)
8 PHA00733 hypothetical protein 99.2 2.3E-11 5.1E-16 65.5 4.2 56 25-83 69-124 (128)
9 KOG1074|consensus 99.2 1.9E-12 4.1E-17 85.4 -1.4 54 29-83 605-658 (958)
10 KOG3608|consensus 99.1 9.9E-12 2.1E-16 75.7 -0.9 79 2-82 265-345 (467)
11 KOG3608|consensus 99.0 2.3E-10 4.9E-15 69.9 2.5 86 1-90 238-323 (467)
12 KOG1074|consensus 99.0 1.4E-10 3.1E-15 76.9 1.7 81 2-84 607-694 (958)
13 PHA00616 hypothetical protein 98.9 6.7E-10 1.4E-14 48.7 2.3 31 59-89 2-32 (44)
14 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.3E-09 2.9E-14 43.0 2.1 26 44-70 1-26 (26)
15 PLN03086 PRLI-interacting fact 98.9 2.3E-09 5E-14 69.5 3.5 82 2-91 455-546 (567)
16 PHA00616 hypothetical protein 98.8 4.1E-09 8.8E-14 46.2 1.5 34 29-63 1-34 (44)
17 PHA02768 hypothetical protein; 98.7 9.1E-09 2E-13 47.2 2.0 30 58-89 5-34 (55)
18 PF05605 zf-Di19: Drought indu 98.7 6.1E-08 1.3E-12 44.8 4.8 52 29-83 2-54 (54)
19 PHA00732 hypothetical protein 98.7 1.2E-08 2.6E-13 50.6 2.4 47 29-81 1-47 (79)
20 PF13465 zf-H2C2_2: Zinc-finge 98.6 8.2E-09 1.8E-13 40.7 -0.6 24 18-41 3-26 (26)
21 PLN03086 PRLI-interacting fact 98.4 7.6E-07 1.7E-11 58.1 5.0 60 25-90 449-508 (567)
22 PHA00733 hypothetical protein 98.4 2.3E-07 5E-12 50.1 2.1 63 26-90 37-103 (128)
23 KOG3993|consensus 98.3 4.9E-08 1.1E-12 61.0 -1.0 79 3-83 270-381 (500)
24 PF00096 zf-C2H2: Zinc finger, 98.3 6.7E-07 1.4E-11 34.0 2.4 22 59-80 1-22 (23)
25 PF00096 zf-C2H2: Zinc finger, 98.1 1.6E-06 3.5E-11 32.9 1.4 21 30-50 1-21 (23)
26 PF13894 zf-C2H2_4: C2H2-type 98.1 4.1E-06 9E-11 31.8 2.6 23 59-81 1-23 (24)
27 PF09237 GAGA: GAGA factor; I 98.1 8.2E-06 1.8E-10 36.7 3.2 34 53-86 19-52 (54)
28 PF13894 zf-C2H2_4: C2H2-type 98.0 8.6E-06 1.9E-10 30.9 2.1 22 30-51 1-22 (24)
29 PF13912 zf-C2H2_6: C2H2-type 97.9 7.5E-06 1.6E-10 32.2 1.9 20 30-49 2-21 (27)
30 PF12756 zf-C2H2_2: C2H2 type 97.9 9.7E-06 2.1E-10 41.5 2.7 73 2-81 1-73 (100)
31 PF13912 zf-C2H2_6: C2H2-type 97.8 1.6E-05 3.5E-10 31.3 1.8 26 58-83 1-26 (27)
32 COG5189 SFP1 Putative transcri 97.8 6E-06 1.3E-10 50.4 0.4 53 27-79 347-419 (423)
33 PF05605 zf-Di19: Drought indu 97.7 7E-06 1.5E-10 37.8 -0.3 50 1-53 3-53 (54)
34 smart00355 ZnF_C2H2 zinc finge 97.5 0.00013 2.8E-09 27.8 2.5 19 31-49 2-20 (26)
35 KOG3993|consensus 97.4 2.1E-05 4.6E-10 49.7 -0.6 54 29-83 267-320 (500)
36 smart00355 ZnF_C2H2 zinc finge 97.3 0.00028 6.1E-09 26.8 2.3 24 59-82 1-24 (26)
37 PF09237 GAGA: GAGA factor; I 97.3 0.00039 8.6E-09 31.4 2.6 31 24-54 19-49 (54)
38 PF13909 zf-H2C2_5: C2H2-type 97.2 0.0005 1.1E-08 26.1 2.4 21 60-81 2-22 (24)
39 PF12874 zf-met: Zinc-finger o 97.2 0.00039 8.4E-09 26.6 1.8 20 60-79 2-21 (25)
40 PRK04860 hypothetical protein; 97.1 0.00033 7.3E-09 39.3 2.0 38 29-71 119-156 (160)
41 PHA00732 hypothetical protein 97.1 0.00055 1.2E-08 34.0 2.1 26 58-83 1-27 (79)
42 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00073 1.6E-08 25.6 1.7 23 30-53 1-23 (24)
43 PF12874 zf-met: Zinc-finger o 96.9 0.00052 1.1E-08 26.3 1.2 21 30-50 1-21 (25)
44 PF13913 zf-C2HC_2: zinc-finge 96.6 0.0024 5.3E-08 24.6 2.1 18 60-78 4-21 (25)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.0016 3.4E-08 25.5 0.9 20 30-49 2-21 (27)
46 PF12756 zf-C2H2_2: C2H2 type 96.2 0.0056 1.2E-07 31.1 2.5 24 28-51 49-72 (100)
47 PRK04860 hypothetical protein; 95.8 0.0062 1.4E-07 34.3 1.7 30 58-91 119-148 (160)
48 smart00451 ZnF_U1 U1-like zinc 95.4 0.019 4.2E-07 23.5 2.1 22 58-79 3-24 (35)
49 COG5048 FOG: Zn-finger [Genera 95.4 0.0032 7E-08 39.6 -0.6 62 28-90 288-355 (467)
50 KOG1146|consensus 95.1 0.026 5.6E-07 41.0 3.0 57 24-80 460-540 (1406)
51 KOG2186|consensus 94.7 0.023 5E-07 34.1 1.7 45 30-78 4-48 (276)
52 cd00350 rubredoxin_like Rubred 94.2 0.027 5.8E-07 23.1 0.9 10 57-66 16-25 (33)
53 COG4049 Uncharacterized protei 93.9 0.036 7.8E-07 25.5 1.1 33 22-54 10-42 (65)
54 PF12013 DUF3505: Protein of u 93.2 0.39 8.4E-06 25.2 4.5 25 59-83 81-109 (109)
55 PHA00626 hypothetical protein 92.2 0.15 3.3E-06 23.5 1.8 14 28-41 22-35 (59)
56 COG5189 SFP1 Putative transcri 92.0 0.033 7.2E-07 34.7 -0.6 24 26-49 395-418 (423)
57 KOG4173|consensus 91.9 0.045 9.7E-07 32.1 -0.1 53 30-82 107-170 (253)
58 PF09986 DUF2225: Uncharacteri 91.8 0.024 5.3E-07 33.4 -1.2 44 28-71 4-61 (214)
59 PRK00464 nrdR transcriptional 91.0 0.14 3E-06 28.8 1.2 41 1-44 1-43 (154)
60 PF13717 zinc_ribbon_4: zinc-r 90.4 0.29 6.3E-06 20.5 1.7 32 31-68 4-35 (36)
61 PF13719 zinc_ribbon_5: zinc-r 90.4 0.29 6.3E-06 20.6 1.7 11 58-68 25-35 (37)
62 PF05443 ROS_MUCR: ROS/MUCR tr 90.3 0.19 4E-06 27.5 1.4 26 58-86 72-97 (132)
63 COG2888 Predicted Zn-ribbon RN 90.2 0.25 5.3E-06 23.1 1.5 32 28-65 26-57 (61)
64 TIGR02098 MJ0042_CXXC MJ0042 f 89.0 0.36 7.8E-06 20.2 1.5 33 30-68 3-35 (38)
65 PF02892 zf-BED: BED zinc fing 88.1 0.57 1.2E-05 20.2 1.9 25 26-50 13-41 (45)
66 cd00729 rubredoxin_SM Rubredox 87.7 0.3 6.5E-06 20.2 0.8 25 29-66 2-26 (34)
67 PF04959 ARS2: Arsenite-resist 87.6 0.23 5E-06 29.4 0.6 26 58-83 77-102 (214)
68 smart00734 ZnF_Rad18 Rad18-lik 86.9 0.72 1.6E-05 17.8 1.6 18 31-49 3-20 (26)
69 COG1592 Rubrerythrin [Energy p 86.6 0.44 9.5E-06 27.1 1.3 23 29-65 134-156 (166)
70 PRK06266 transcription initiat 86.0 0.44 9.6E-06 27.4 1.1 35 26-70 114-148 (178)
71 TIGR00373 conserved hypothetic 85.8 0.58 1.3E-05 26.4 1.5 35 26-70 106-140 (158)
72 smart00614 ZnF_BED BED zinc fi 85.8 0.89 1.9E-05 20.3 1.9 27 28-54 17-48 (50)
73 PF04959 ARS2: Arsenite-resist 85.4 0.57 1.2E-05 27.8 1.4 31 25-55 73-103 (214)
74 smart00531 TFIIE Transcription 84.9 1 2.3E-05 25.0 2.3 40 26-70 96-135 (147)
75 COG4957 Predicted transcriptio 81.9 0.83 1.8E-05 25.1 1.0 25 59-86 77-101 (148)
76 COG5048 FOG: Zn-finger [Genera 81.6 1.2 2.6E-05 28.1 1.9 57 4-62 293-355 (467)
77 PF09723 Zn-ribbon_8: Zinc rib 81.0 0.55 1.2E-05 20.3 0.2 29 30-66 6-34 (42)
78 smart00659 RPOLCX RNA polymera 80.9 1.3 2.8E-05 19.4 1.3 11 30-40 3-13 (44)
79 PF14353 CpXC: CpXC protein 80.9 2.7 5.8E-05 22.6 2.8 19 28-46 37-55 (128)
80 TIGR02605 CxxC_CxxC_SSSS putat 80.7 0.38 8.3E-06 21.6 -0.4 11 30-40 6-16 (52)
81 PF12013 DUF3505: Protein of u 80.6 1.8 3.8E-05 22.7 2.0 25 29-53 80-108 (109)
82 COG1997 RPL43A Ribosomal prote 79.9 1.2 2.7E-05 22.5 1.2 33 28-71 34-66 (89)
83 PF10571 UPF0547: Uncharacteri 79.2 1.1 2.3E-05 17.4 0.7 11 30-40 15-25 (26)
84 PRK14890 putative Zn-ribbon RN 78.8 1.4 3.1E-05 20.6 1.1 33 28-66 24-56 (59)
85 KOG2785|consensus 77.9 5.9 0.00013 25.7 3.9 55 26-80 163-242 (390)
86 COG1198 PriA Primosomal protei 77.3 3.2 6.9E-05 29.3 2.9 16 22-37 468-483 (730)
87 KOG2893|consensus 76.5 0.35 7.6E-06 29.2 -1.5 16 25-40 30-45 (341)
88 PRK09678 DNA-binding transcrip 76.2 1.5 3.2E-05 21.5 0.9 41 1-44 2-44 (72)
89 PF13451 zf-trcl: Probable zin 75.7 1.9 4.1E-05 19.4 1.1 39 27-65 2-40 (49)
90 KOG4173|consensus 75.1 2.4 5.3E-05 25.1 1.7 51 27-81 77-129 (253)
91 TIGR00244 transcriptional regu 73.3 3 6.4E-05 23.4 1.6 18 28-45 27-44 (147)
92 PF12907 zf-met2: Zinc-binding 72.7 2.7 5.9E-05 18.1 1.1 27 30-56 2-31 (40)
93 PRK00398 rpoP DNA-directed RNA 72.6 1.7 3.6E-05 19.0 0.5 12 29-40 3-14 (46)
94 PF15269 zf-C2H2_7: Zinc-finge 70.8 4.3 9.3E-05 17.9 1.5 22 59-80 21-42 (54)
95 PRK03824 hypA hydrogenase nick 70.6 1.5 3.2E-05 24.1 0.1 16 27-42 68-83 (135)
96 COG1996 RPC10 DNA-directed RNA 69.5 2.9 6.2E-05 18.9 0.9 28 28-66 5-32 (49)
97 PF07754 DUF1610: Domain of un 68.2 2.7 5.8E-05 16.0 0.6 8 29-36 16-23 (24)
98 KOG3408|consensus 68.2 3.7 7.9E-05 22.2 1.3 23 58-80 57-79 (129)
99 KOG1280|consensus 68.2 6.9 0.00015 25.2 2.6 38 28-65 78-116 (381)
100 KOG2593|consensus 67.6 5 0.00011 26.5 2.0 38 25-66 124-161 (436)
101 PF09538 FYDLN_acid: Protein o 66.7 6.1 0.00013 20.9 1.9 30 30-71 10-39 (108)
102 KOG2482|consensus 66.7 9.3 0.0002 24.6 2.9 53 28-80 143-217 (423)
103 COG1198 PriA Primosomal protei 66.3 6.1 0.00013 28.0 2.3 47 2-66 437-483 (730)
104 PF10083 DUF2321: Uncharacteri 66.1 4.9 0.00011 22.7 1.6 18 26-43 65-82 (158)
105 KOG4167|consensus 65.9 1.6 3.4E-05 30.7 -0.4 25 58-82 792-816 (907)
106 KOG2893|consensus 65.8 1.3 2.9E-05 26.8 -0.7 43 28-77 10-53 (341)
107 COG1327 Predicted transcriptio 63.8 6.3 0.00014 22.2 1.7 17 28-44 27-43 (156)
108 COG5236 Uncharacterized conser 62.1 4.3 9.4E-05 26.1 1.0 20 31-50 222-241 (493)
109 COG1773 Rubredoxin [Energy pro 61.9 3.4 7.3E-05 19.1 0.4 36 29-66 3-44 (55)
110 KOG2636|consensus 61.6 6.8 0.00015 26.1 1.8 27 51-77 394-421 (497)
111 KOG2636|consensus 61.2 7 0.00015 26.0 1.8 28 22-49 394-422 (497)
112 smart00834 CxxC_CXXC_SSSS Puta 60.5 3.6 7.8E-05 17.2 0.3 30 29-66 5-34 (41)
113 PF04780 DUF629: Protein of un 60.4 7.9 0.00017 25.9 1.9 28 29-56 57-84 (466)
114 COG3091 SprT Zn-dependent meta 58.0 5.3 0.00012 22.5 0.8 33 28-66 116-148 (156)
115 PTZ00255 60S ribosomal protein 56.4 4.5 9.8E-05 20.7 0.3 32 28-70 35-66 (90)
116 KOG1842|consensus 55.0 8.8 0.00019 25.6 1.5 30 28-57 14-43 (505)
117 smart00154 ZnF_AN1 AN1-like Zi 54.7 7.5 0.00016 16.5 0.8 14 58-71 12-25 (39)
118 KOG1146|consensus 54.5 3.1 6.7E-05 31.2 -0.6 46 35-80 442-487 (1406)
119 KOG4167|consensus 53.7 2.6 5.7E-05 29.7 -1.0 26 28-54 791-816 (907)
120 PF12760 Zn_Tnp_IS1595: Transp 53.3 13 0.00028 16.2 1.5 27 30-66 19-45 (46)
121 PF02176 zf-TRAF: TRAF-type zi 53.1 5.5 0.00012 18.1 0.3 42 28-71 8-55 (60)
122 TIGR00622 ssl1 transcription f 53.0 21 0.00046 19.1 2.5 23 58-80 81-103 (112)
123 TIGR00280 L37a ribosomal prote 52.9 4.8 0.0001 20.7 0.1 13 58-70 53-65 (91)
124 KOG1842|consensus 52.7 9.9 0.00022 25.4 1.5 27 57-83 14-40 (505)
125 cd00924 Cyt_c_Oxidase_Vb Cytoc 52.6 6.9 0.00015 20.3 0.6 20 21-41 72-91 (97)
126 COG3677 Transposase and inacti 51.5 12 0.00026 20.5 1.5 16 27-42 51-66 (129)
127 cd00730 rubredoxin Rubredoxin; 51.4 7 0.00015 17.6 0.5 35 30-66 2-42 (50)
128 COG4306 Uncharacterized protei 51.0 14 0.00031 20.2 1.7 17 26-42 65-81 (160)
129 PF05290 Baculo_IE-1: Baculovi 50.7 9.1 0.0002 21.2 0.9 13 60-72 123-135 (140)
130 PF14255 Cys_rich_CPXG: Cystei 50.3 8.8 0.00019 17.5 0.7 16 1-16 1-16 (52)
131 PF10276 zf-CHCC: Zinc-finger 50.2 7.5 0.00016 16.7 0.5 12 28-39 28-39 (40)
132 PF01096 TFIIS_C: Transcriptio 50.1 3.5 7.6E-05 17.4 -0.6 11 29-39 28-38 (39)
133 PF03604 DNA_RNApol_7kD: DNA d 48.9 14 0.0003 15.0 1.1 11 29-39 17-27 (32)
134 PF04423 Rad50_zn_hook: Rad50 48.2 7.5 0.00016 17.5 0.3 13 60-72 22-34 (54)
135 PF10013 DUF2256: Uncharacteri 47.8 8.8 0.00019 16.7 0.5 15 59-73 9-23 (42)
136 KOG0717|consensus 47.6 14 0.00031 24.8 1.6 22 59-80 293-314 (508)
137 TIGR01206 lysW lysine biosynth 47.0 19 0.00042 16.5 1.6 10 2-11 4-13 (54)
138 PF01428 zf-AN1: AN1-like Zinc 46.8 7.3 0.00016 16.7 0.2 15 57-71 12-26 (43)
139 KOG2071|consensus 46.4 16 0.00034 25.2 1.7 26 27-53 416-441 (579)
140 PF00301 Rubredoxin: Rubredoxi 45.9 7.5 0.00016 17.3 0.1 35 30-66 2-42 (47)
141 KOG1280|consensus 45.7 33 0.0007 22.3 2.9 33 56-88 77-109 (381)
142 PF03811 Zn_Tnp_IS1: InsA N-te 45.2 19 0.0004 15.0 1.3 7 58-64 29-35 (36)
143 PF11789 zf-Nse: Zinc-finger o 44.6 22 0.00047 16.4 1.6 14 28-41 23-36 (57)
144 TIGR00686 phnA alkylphosphonat 44.3 17 0.00038 19.3 1.3 28 3-42 5-32 (109)
145 PF08209 Sgf11: Sgf11 (transcr 44.3 21 0.00045 14.6 1.3 21 58-79 4-24 (33)
146 TIGR02300 FYDLN_acid conserved 44.2 24 0.00051 19.4 1.9 32 30-73 10-41 (129)
147 PF07282 OrfB_Zn_ribbon: Putat 44.1 29 0.00063 16.3 2.1 16 56-71 44-59 (69)
148 PRK03976 rpl37ae 50S ribosomal 43.5 7.5 0.00016 19.9 -0.1 13 58-70 54-66 (90)
149 PF09845 DUF2072: Zn-ribbon co 43.3 12 0.00026 20.6 0.7 15 29-43 1-15 (131)
150 PLN02294 cytochrome c oxidase 43.3 13 0.00029 21.4 0.9 21 21-42 134-154 (174)
151 COG5188 PRP9 Splicing factor 3 42.9 18 0.00039 23.5 1.5 27 23-49 368-395 (470)
152 PF08790 zf-LYAR: LYAR-type C2 42.0 4.1 8.8E-05 16.1 -0.9 9 31-39 2-10 (28)
153 KOG3507|consensus 42.0 14 0.00031 17.3 0.7 9 58-66 37-45 (62)
154 COG1779 C4-type Zn-finger prot 41.8 7.1 0.00015 23.0 -0.3 8 30-37 15-22 (201)
155 PF13878 zf-C2H2_3: zinc-finge 41.2 33 0.00072 14.6 2.4 8 60-67 15-22 (41)
156 PF04780 DUF629: Protein of un 40.1 33 0.00071 23.2 2.4 25 59-83 58-83 (466)
157 smart00440 ZnF_C2C2 C2C2 Zinc 39.8 15 0.00032 15.6 0.6 11 29-39 28-38 (40)
158 PF11931 DUF3449: Domain of un 39.5 9.8 0.00021 22.5 0.0 25 53-77 96-121 (196)
159 TIGR00595 priA primosomal prot 39.1 24 0.00053 23.9 1.7 13 25-37 249-261 (505)
160 COG3357 Predicted transcriptio 38.6 14 0.0003 19.0 0.5 27 28-65 57-83 (97)
161 smart00132 LIM Zinc-binding do 38.5 22 0.00048 14.0 1.1 9 30-38 28-36 (39)
162 PF07975 C1_4: TFIIH C1-like d 38.1 7.7 0.00017 17.6 -0.5 23 27-49 19-41 (51)
163 PF05129 Elf1: Transcription e 37.9 5 0.00011 20.1 -1.2 40 27-71 20-59 (81)
164 PRK10220 hypothetical protein; 36.4 33 0.00071 18.3 1.6 16 28-43 19-34 (111)
165 TIGR00100 hypA hydrogenase nic 36.4 19 0.00042 19.1 0.8 26 28-66 69-94 (115)
166 KOG1994|consensus 36.3 24 0.00052 21.5 1.2 22 56-77 237-258 (268)
167 smart00661 RPOL9 RNA polymeras 36.2 38 0.00083 14.7 1.7 12 29-40 20-31 (52)
168 PF13821 DUF4187: Domain of un 36.1 13 0.00029 17.1 0.2 15 2-16 29-43 (55)
169 COG4530 Uncharacterized protei 35.6 26 0.00055 18.8 1.1 17 56-72 24-40 (129)
170 KOG2932|consensus 35.2 60 0.0013 20.9 2.8 28 56-83 142-172 (389)
171 COG0068 HypF Hydrogenase matur 35.0 32 0.00069 24.6 1.8 28 32-66 154-181 (750)
172 PRK12380 hydrogenase nickel in 34.7 21 0.00045 19.0 0.8 14 28-41 69-82 (113)
173 PF01927 Mut7-C: Mut7-C RNAse 33.8 22 0.00047 19.8 0.8 21 27-47 122-142 (147)
174 COG3364 Zn-ribbon containing p 33.8 27 0.00059 18.4 1.1 14 29-42 2-15 (112)
175 TIGR00310 ZPR1_znf ZPR1 zinc f 33.7 11 0.00025 22.1 -0.3 11 29-39 30-40 (192)
176 PF06524 NOA36: NOA36 protein; 33.5 9.7 0.00021 23.6 -0.7 26 55-80 206-231 (314)
177 smart00731 SprT SprT homologue 32.9 26 0.00056 19.3 1.0 32 29-68 112-143 (146)
178 PF12230 PRP21_like_P: Pre-mRN 32.5 15 0.00032 22.0 0.0 23 59-82 169-191 (229)
179 COG1326 Uncharacterized archae 31.6 59 0.0013 19.3 2.3 13 56-68 28-40 (201)
180 COG1675 TFA1 Transcription ini 31.3 38 0.00083 19.7 1.5 32 26-67 110-141 (176)
181 PF08274 PhnA_Zn_Ribbon: PhnA 31.3 20 0.00043 14.3 0.3 7 59-65 20-26 (30)
182 PF13824 zf-Mss51: Zinc-finger 30.6 34 0.00075 15.8 1.0 16 25-40 10-25 (55)
183 PF10263 SprT-like: SprT-like 30.0 17 0.00037 20.1 -0.0 32 28-68 122-153 (157)
184 PRK14873 primosome assembly pr 29.6 37 0.0008 24.0 1.5 8 29-36 422-429 (665)
185 PF04810 zf-Sec23_Sec24: Sec23 29.5 5.4 0.00012 16.9 -1.6 12 55-66 21-32 (40)
186 PF14311 DUF4379: Domain of un 28.7 45 0.00097 15.0 1.3 13 29-41 28-40 (55)
187 KOG4727|consensus 28.7 34 0.00074 19.9 1.0 23 28-50 74-96 (193)
188 PF05191 ADK_lid: Adenylate ki 28.0 27 0.00059 14.5 0.4 12 59-70 2-13 (36)
189 KOG1008|consensus 27.8 47 0.001 23.7 1.6 13 58-70 766-778 (783)
190 COG1571 Predicted DNA-binding 27.5 52 0.0011 22.0 1.8 12 29-40 367-378 (421)
191 PRK14892 putative transcriptio 27.5 45 0.00097 17.5 1.2 9 28-36 20-28 (99)
192 PLN03238 probable histone acet 27.4 72 0.0016 20.2 2.3 24 56-79 46-69 (290)
193 KOG3214|consensus 26.9 31 0.00067 18.1 0.6 40 27-71 21-60 (109)
194 PF02591 DUF164: Putative zinc 26.7 74 0.0016 14.3 1.8 31 31-66 24-54 (56)
195 PTZ00043 cytochrome c oxidase 26.7 36 0.00078 20.8 0.9 21 21-42 174-194 (268)
196 PRK00762 hypA hydrogenase nick 26.5 23 0.0005 19.2 0.1 14 28-42 69-82 (124)
197 PRK00564 hypA hydrogenase nick 26.2 32 0.0007 18.4 0.6 15 28-42 70-84 (117)
198 PF15135 UPF0515: Uncharacteri 26.0 46 0.00099 20.6 1.3 13 29-41 155-167 (278)
199 COG1594 RPB9 DNA-directed RNA 26.0 33 0.00071 18.3 0.6 39 29-69 72-111 (113)
200 PF06397 Desulfoferrod_N: Desu 25.8 27 0.00058 14.6 0.2 12 28-39 5-16 (36)
201 PLN02748 tRNA dimethylallyltra 25.7 62 0.0013 22.0 1.9 24 57-80 417-441 (468)
202 PF01286 XPA_N: XPA protein N- 25.2 28 0.00061 14.4 0.2 13 59-71 4-16 (34)
203 PF13453 zf-TFIIB: Transcripti 24.9 59 0.0013 13.6 1.2 23 27-49 17-39 (41)
204 PRK08222 hydrogenase 4 subunit 24.6 62 0.0013 18.7 1.6 20 28-47 113-132 (181)
205 PRK03681 hypA hydrogenase nick 24.6 40 0.00088 17.9 0.8 14 28-41 69-82 (114)
206 COG4338 Uncharacterized protei 24.6 20 0.00044 16.1 -0.3 14 59-72 13-26 (54)
207 PF01215 COX5B: Cytochrome c o 24.5 31 0.00066 19.2 0.3 15 56-70 110-124 (136)
208 COG0675 Transposase and inacti 23.8 59 0.0013 20.1 1.5 17 57-73 321-337 (364)
209 PRK12722 transcriptional activ 23.3 85 0.0018 18.5 2.0 29 29-66 134-162 (187)
210 PRK01343 zinc-binding protein; 23.2 64 0.0014 15.1 1.2 10 59-68 10-19 (57)
211 PF08792 A2L_zn_ribbon: A2L zi 23.1 42 0.00092 13.6 0.6 11 58-68 21-31 (33)
212 PRK05978 hypothetical protein; 23.0 30 0.00065 19.5 0.1 31 30-70 34-64 (148)
213 COG4391 Uncharacterized protei 22.9 33 0.00072 16.3 0.3 45 20-69 15-59 (62)
214 PF09963 DUF2197: Uncharacteri 22.7 13 0.00027 17.3 -1.1 9 57-65 30-38 (56)
215 smart00249 PHD PHD zinc finger 22.7 75 0.0016 12.9 1.8 13 27-39 12-24 (47)
216 PF14354 Lar_restr_allev: Rest 22.7 52 0.0011 14.9 0.9 13 28-40 2-14 (61)
217 PF10537 WAC_Acf1_DNA_bd: ATP- 22.4 1.1E+02 0.0025 16.0 2.2 36 29-66 3-38 (102)
218 PTZ00448 hypothetical protein; 21.3 90 0.002 20.6 2.0 23 58-80 314-336 (373)
219 PRK05580 primosome assembly pr 21.2 98 0.0021 22.0 2.3 17 22-38 414-430 (679)
220 KOG4602|consensus 21.1 48 0.001 20.7 0.7 14 57-70 267-280 (318)
221 KOG2807|consensus 21.0 92 0.002 20.3 1.9 19 58-76 290-308 (378)
222 KOG2231|consensus 21.0 1.2E+02 0.0026 21.8 2.6 19 61-79 185-203 (669)
223 PF01780 Ribosomal_L37ae: Ribo 20.8 44 0.00096 17.2 0.5 31 28-69 34-64 (90)
224 PF02891 zf-MIZ: MIZ/SP-RING z 20.7 45 0.00097 14.9 0.4 10 28-37 40-49 (50)
225 PF14369 zf-RING_3: zinc-finge 20.6 44 0.00096 13.7 0.4 10 31-40 23-32 (35)
226 PRK04351 hypothetical protein; 20.4 53 0.0011 18.5 0.8 12 57-68 131-142 (149)
227 PLN00104 MYST -like histone ac 20.2 86 0.0019 21.2 1.8 23 57-79 197-219 (450)
No 1
>KOG2462|consensus
Probab=99.90 E-value=1.3e-24 Score=126.57 Aligned_cols=87 Identities=22% Similarity=0.499 Sum_probs=79.0
Q ss_pred CCCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHH
Q psy12166 1 MDCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
+.|++|++.|..-.. +..|+++|+ -++.|.+||+.|.+.+-|+.|+ +.|++||||.|+.|++.|...++|..|+++
T Consensus 162 ~~C~~C~K~YvSmpA-LkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi-RTHTGEKPF~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMPA-LKMHIRTHT--LPCECGICGKAFSRPWLLQGHI-RTHTGEKPFSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred ccCCCCCceeeehHH-HhhHhhccC--CCcccccccccccchHHhhccc-ccccCCCCccCCcccchhcchHHHHHHHHh
Confidence 578999998887333 367888888 5899999999999999999999 799999999999999999999999999999
Q ss_pred hcCCCCceEee
Q psy12166 81 RHGITGFVVSA 91 (94)
Q Consensus 81 ~~~~k~~~C~~ 91 (94)
|.+.|.|.|..
T Consensus 238 HS~~K~~qC~~ 248 (279)
T KOG2462|consen 238 HSDVKKHQCPR 248 (279)
T ss_pred hcCCccccCcc
Confidence 99999999975
No 2
>KOG2462|consensus
Probab=99.81 E-value=1.2e-20 Score=110.11 Aligned_cols=78 Identities=26% Similarity=0.505 Sum_probs=71.3
Q ss_pred CCCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHH
Q psy12166 1 MDCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
.+|..||+.|..+ =+++.|+++|+|||||.|+.|++.|...++|+.|| ..|.+.|.|+|..|+|+|...+.|.+|...
T Consensus 188 c~C~iCGKaFSRP-WLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm-QTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 188 CECGICGKAFSRP-WLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM-QTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccccccccccch-HHhhcccccccCCCCccCCcccchhcchHHHHHHH-HhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 4699999998863 34578999999999999999999999999999999 799999999999999999999999999764
No 3
>KOG3623|consensus
Probab=99.66 E-value=7.1e-18 Score=109.13 Aligned_cols=66 Identities=27% Similarity=0.504 Sum_probs=48.2
Q ss_pred CCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHhcCCCCceEeee
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHGITGFVVSAR 92 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~C~~~ 92 (94)
.+.+|.|+.|++.|...++|.+|- ..|++.+||+|.+|.+.|+++.+|.-|+|.|.|+|||.|+.+
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHK-YEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKC 956 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHK-YEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKC 956 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhh-hhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhh
Confidence 345777777777777777777775 677777777777777777777777777777777777777654
No 4
>KOG3623|consensus
Probab=99.60 E-value=1.9e-16 Score=102.72 Aligned_cols=77 Identities=22% Similarity=0.494 Sum_probs=70.3
Q ss_pred CCCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHH
Q psy12166 1 MDCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~ 79 (94)
+-|+-|++.|.-..++ .+|.-.|+|++||+|.+|.+.|..+..|..|. +.|.++|||+|..|++.|.+++.+..||-
T Consensus 895 yaCDqCDK~FqKqSSL-aRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHk-RLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSL-ARHKYEHSGQRPYQCIICKKAFKHKHHLTEHK-RLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chHHHHHHHHHhhHHH-HHhhhhhcCCCCcccchhhHhhhhhhhhhhhh-hhccCCCcchhhhhhhhcccccchHhhhc
Confidence 4588899888876665 57788999999999999999999999999998 79999999999999999999999999975
No 5
>KOG3576|consensus
Probab=99.47 E-value=1.8e-15 Score=85.68 Aligned_cols=64 Identities=27% Similarity=0.642 Sum_probs=40.1
Q ss_pred CCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHhcCCCCceEe
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHGITGFVVS 90 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~C~ 90 (94)
+...|.|.+|++.|....-|.+|+ ..|...+.+.|..||+.|.....|..|+++|+|.+||+|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~-kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~ 177 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHL-KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCS 177 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHh-hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchh
Confidence 345566666666666666666666 4566666666666666666666666666666666666664
No 6
>KOG3576|consensus
Probab=99.44 E-value=1.3e-14 Score=82.24 Aligned_cols=81 Identities=23% Similarity=0.485 Sum_probs=72.2
Q ss_pred CCCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHH
Q psy12166 1 MDCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
|.|..|++.|....-+ ..|+..|...+.|-|..||+.|...-+|.+|+ +.|++.+||.|..|+++|.+.-.|..|.+.
T Consensus 118 ftCrvCgK~F~lQRml-nrh~kch~~vkr~lct~cgkgfndtfdlkrh~-rthtgvrpykc~~c~kaftqrcsleshl~k 195 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRML-NRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHT-RTHTGVRPYKCSLCEKAFTQRCSLESHLKK 195 (267)
T ss_pred eeeehhhhhhhHHHHH-HHHhhhccHHHHHHHhhccCcccchhhhhhhh-ccccCccccchhhhhHHHHhhccHHHHHHH
Confidence 5788999888875543 57889999999999999999999999999999 799999999999999999999999999876
Q ss_pred hcC
Q psy12166 81 RHG 83 (94)
Q Consensus 81 ~~~ 83 (94)
-+|
T Consensus 196 vhg 198 (267)
T KOG3576|consen 196 VHG 198 (267)
T ss_pred HcC
Confidence 554
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.22 E-value=6.1e-12 Score=57.62 Aligned_cols=43 Identities=21% Similarity=0.468 Sum_probs=38.4
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHH
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANL 74 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l 74 (94)
-|+|+.||+.|...++|..|+ +.|+ +++.|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~-r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHL-RKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHH-HhcC--CcccCCcccceeccccee
Confidence 489999999999999999999 6788 689999999999977655
No 8
>PHA00733 hypothetical protein
Probab=99.21 E-value=2.3e-11 Score=65.47 Aligned_cols=56 Identities=25% Similarity=0.526 Sum_probs=49.5
Q ss_pred CCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHhcC
Q psy12166 25 DRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 25 ~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
.+++||.|+.|++.|.....|..|+ ..+ +.++.|..|++.|.....|..|+...++
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~-r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHI-RYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHH-hcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3478999999999999999999998 555 3579999999999999999999988765
No 9
>KOG1074|consensus
Probab=99.17 E-value=1.9e-12 Score=85.41 Aligned_cols=54 Identities=28% Similarity=0.645 Sum_probs=28.5
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHhcC
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
|.+|.+|.+...-...|+.|. +.|++++||+|.+||+.|..+.+|+.|+.+|..
T Consensus 605 PNqCiiC~rVlSC~saLqmHy-rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHY-RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred ccceeeeeecccchhhhhhhh-hcccCcCccccccccchhccccchhhccccccc
Confidence 445555555555555555555 455555555555555555555555555555443
No 10
>KOG3608|consensus
Probab=99.08 E-value=9.9e-12 Score=75.69 Aligned_cols=79 Identities=19% Similarity=0.393 Sum_probs=45.5
Q ss_pred CCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCc--cccccCCHHHHHHHHH
Q psy12166 2 DCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNV--CGRTFSSIANLAEHKR 79 (94)
Q Consensus 2 ~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~--C~~~f~~~~~l~~h~~ 79 (94)
.|+-|+.+-....++..+.+..|...+||+|..|++.+.....|.+|. ..|. +..|+|.. |..++.....+..|++
T Consensus 265 kCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~-~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~ 342 (467)
T KOG3608|consen 265 KCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHV-QVHS-KTVYQCEHPDCHYSVRTYTQMRRHFL 342 (467)
T ss_pred cccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHH-Hhcc-ccceecCCCCCcHHHHHHHHHHHHHH
Confidence 455555554444444344444555666666666666666666666665 4555 44566655 6666666666666655
Q ss_pred Hhc
Q psy12166 80 SRH 82 (94)
Q Consensus 80 ~~~ 82 (94)
.++
T Consensus 343 evh 345 (467)
T KOG3608|consen 343 EVH 345 (467)
T ss_pred Hhc
Confidence 543
No 11
>KOG3608|consensus
Probab=99.00 E-value=2.3e-10 Score=69.89 Aligned_cols=86 Identities=19% Similarity=0.297 Sum_probs=71.0
Q ss_pred CCCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHH
Q psy12166 1 MDCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
|.|.-|.+.|..+.- +..|++.|. +.|+|++|+......++|..|++..|...+||.|..|.+.+...+.|++|..+
T Consensus 238 fqC~~C~KrFaTekl-L~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~ 314 (467)
T KOG3608|consen 238 FQCAQCFKRFATEKL-LKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQV 314 (467)
T ss_pred hHHHHHHHHHhHHHH-HHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHh
Confidence 456666666665433 356667776 57999999999999999999998899999999999999999999999999998
Q ss_pred hcCCCCceEe
Q psy12166 81 RHGITGFVVS 90 (94)
Q Consensus 81 ~~~~k~~~C~ 90 (94)
|. +..|.|+
T Consensus 315 HS-~~~y~C~ 323 (467)
T KOG3608|consen 315 HS-KTVYQCE 323 (467)
T ss_pred cc-ccceecC
Confidence 87 6778885
No 12
>KOG1074|consensus
Probab=99.00 E-value=1.4e-10 Score=76.85 Aligned_cols=81 Identities=22% Similarity=0.486 Sum_probs=66.2
Q ss_pred CCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCC----CeecC---ccccccCCHHHH
Q psy12166 2 DCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHP----SVTCN---VCGRTFSSIANL 74 (94)
Q Consensus 2 ~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~----~~~c~---~C~~~f~~~~~l 74 (94)
+|-+|-........ ++.|+++|+|++||+|.+||+.|+.+-+|+.|+ .+|.... .+.|+ +|-+.|...-.|
T Consensus 607 qCiiC~rVlSC~sa-LqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~-~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 607 QCIICLRVLSCPSA-LQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM-SVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ceeeeeecccchhh-hhhhhhcccCcCccccccccchhccccchhhcc-cccccCccccccccCCchhhhcccccccccc
Confidence 35555555555444 368999999999999999999999999999999 8887654 46788 899999999999
Q ss_pred HHHHHHhcCC
Q psy12166 75 AEHKRSRHGI 84 (94)
Q Consensus 75 ~~h~~~~~~~ 84 (94)
..|++.|.+.
T Consensus 685 pQhIriH~~~ 694 (958)
T KOG1074|consen 685 PQHIRIHLGG 694 (958)
T ss_pred cceEEeecCC
Confidence 9999998843
No 13
>PHA00616 hypothetical protein
Probab=98.95 E-value=6.7e-10 Score=48.67 Aligned_cols=31 Identities=26% Similarity=0.430 Sum_probs=15.0
Q ss_pred eecCccccccCCHHHHHHHHHHhcCCCCceE
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRSRHGITGFVV 89 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~C 89 (94)
|+|+.||+.|.....+..|++.|+|++++.|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 4444444444444444444444444444444
No 14
>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=98.90 E-value=1.3e-09 Score=42.99 Aligned_cols=26 Identities=35% Similarity=0.824 Sum_probs=21.5
Q ss_pred HHHhHHHhhcCCCCCeecCccccccCC
Q psy12166 44 HLWGHVKSAHQGHPSVTCNVCGRTFSS 70 (94)
Q Consensus 44 ~l~~H~~~~h~~~~~~~c~~C~~~f~~ 70 (94)
+|.+|+ ..|++++||.|+.|++.|.+
T Consensus 1 ~l~~H~-~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHM-RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHH-HHHSSSSSEEESSSSEEESS
T ss_pred CHHHHh-hhcCCCCCCCCCCCcCeeCc
Confidence 478888 68999999999999988863
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.86 E-value=2.3e-09 Score=69.46 Aligned_cols=82 Identities=20% Similarity=0.399 Sum_probs=62.0
Q ss_pred CCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCC----------H
Q psy12166 2 DCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSS----------I 71 (94)
Q Consensus 2 ~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~----------~ 71 (94)
.|..|+..+.. ..+..|+..+. .++.|+ ||+.+ ....|..|+ ..|...+++.|.+|+..+.. .
T Consensus 455 ~C~~Cgk~f~~--s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~-~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~ 527 (567)
T PLN03086 455 HCEKCGQAFQQ--GEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQ-ASTCPLRLITCRFCGDMVQAGGSAMDVRDRL 527 (567)
T ss_pred cCCCCCCccch--HHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhh-hccCCCCceeCCCCCCccccCccccchhhhh
Confidence 57888777642 33356666664 689999 99755 568899998 78888999999999988852 3
Q ss_pred HHHHHHHHHhcCCCCceEee
Q psy12166 72 ANLAEHKRSRHGITGFVVSA 91 (94)
Q Consensus 72 ~~l~~h~~~~~~~k~~~C~~ 91 (94)
..|..|..+. |.+++.|..
T Consensus 528 s~Lt~HE~~C-G~rt~~C~~ 546 (567)
T PLN03086 528 RGMSEHESIC-GSRTAPCDS 546 (567)
T ss_pred hhHHHHHHhc-CCcceEccc
Confidence 4788898875 888998853
No 16
>PHA00616 hypothetical protein
Probab=98.76 E-value=4.1e-09 Score=46.20 Aligned_cols=34 Identities=18% Similarity=0.299 Sum_probs=31.1
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNV 63 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~ 63 (94)
||+|+.||+.|.....|..|+ ..|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~-r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL-LSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH-HHhcCCCccceeE
Confidence 689999999999999999999 6888889988775
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.71 E-value=9.1e-09 Score=47.21 Aligned_cols=30 Identities=20% Similarity=0.553 Sum_probs=26.5
Q ss_pred CeecCccccccCCHHHHHHHHHHhcCCCCceE
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRSRHGITGFVV 89 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~C 89 (94)
.|.|+.||+.|...++|..|+++|. ++|+|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc 34 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKL 34 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccC
Confidence 5899999999999999999999999 45544
No 18
>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=98.71 E-value=6.1e-08 Score=44.78 Aligned_cols=52 Identities=29% Similarity=0.594 Sum_probs=41.4
Q ss_pred CccccccccccCChHHHHhHHHhhcCCC-CCeecCccccccCCHHHHHHHHHHhcC
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGH-PSVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~-~~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
.|+|+.|++ ......|..|....|..+ +.+.|++|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 589999999 455788999987788765 5799999987544 488899887653
No 19
>PHA00732 hypothetical protein
Probab=98.70 E-value=1.2e-08 Score=50.60 Aligned_cols=47 Identities=28% Similarity=0.544 Sum_probs=37.2
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHh
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSR 81 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~ 81 (94)
||.|..|++.|.....|..|++..|. ++.|+.|++.|.. +..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhccc
Confidence 68899999999999999999832455 3589999999984 56676543
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.55 E-value=8.2e-09 Score=40.70 Aligned_cols=24 Identities=25% Similarity=0.595 Sum_probs=20.9
Q ss_pred CCCcccCCCCCCccccccccccCC
Q psy12166 18 AEPLFRFDRTKPHSCDLCGKTYTL 41 (94)
Q Consensus 18 ~~~~~~h~~~~~~~c~~c~~~f~~ 41 (94)
..|++.|++++||.|+.|++.|.+
T Consensus 3 ~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 3 RRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHhhhcCCCCCCCCCCCcCeeCc
Confidence 357889999999999999999863
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.39 E-value=7.6e-07 Score=58.14 Aligned_cols=60 Identities=15% Similarity=0.453 Sum_probs=50.0
Q ss_pred CCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHhcCCCCceEe
Q psy12166 25 DRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHGITGFVVS 90 (94)
Q Consensus 25 ~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~C~ 90 (94)
..++++.|+.|++.|. ...|..|+ ..+. +++.|+ ||+.+ ....|..|+.+|-+++++.|.
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~-~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~ 508 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHM-KVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCR 508 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHH-HhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCC
Confidence 3456789999999996 57799998 5553 789999 99755 568899999999999999985
No 22
>PHA00733 hypothetical protein
Probab=98.38 E-value=2.3e-07 Score=50.08 Aligned_cols=63 Identities=17% Similarity=0.129 Sum_probs=48.1
Q ss_pred CCCCccccccccccCChHHHHhH--HH--hhcCCCCCeecCccccccCCHHHHHHHHHHhcCCCCceEe
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGH--VK--SAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHGITGFVVS 90 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H--~~--~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~C~ 90 (94)
..+++.|.+|...|.....|..+ +. ..+.+.++|.|..|++.|.....|..|++.+ +.+|.|.
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~ 103 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP 103 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCC
Confidence 35789999999888777666555 10 1233478999999999999999999999875 3567775
No 23
>KOG3993|consensus
Probab=98.35 E-value=4.9e-08 Score=61.03 Aligned_cols=79 Identities=23% Similarity=0.400 Sum_probs=58.4
Q ss_pred CCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCC--------------------------
Q psy12166 3 CGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGH-------------------------- 56 (94)
Q Consensus 3 C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~-------------------------- 56 (94)
|.-|...|+..-.+ .+|.-...-...|+|+.|++.|.-..+|..|. ++|.-.
T Consensus 270 CqLCK~kYeD~F~L-AQHrC~RIV~vEYrCPEC~KVFsCPANLASHR-RWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 270 CQLCKEKYEDAFAL-AQHRCPRIVHVEYRCPECDKVFSCPANLASHR-RWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHhhhhHHHH-hhccCCeeEEeeecCCcccccccCchhhhhhh-cccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 55555555553333 44444434445699999999999999999996 788421
Q ss_pred -------CCeecCccccccCCHHHHHHHHHHhcC
Q psy12166 57 -------PSVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 57 -------~~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
-.|.|..|++.|.+...|..|+-+|+.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 137899999999999999999888763
No 24
>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=98.33 E-value=6.7e-07 Score=34.00 Aligned_cols=22 Identities=45% Similarity=0.943 Sum_probs=11.2
Q ss_pred eecCccccccCCHHHHHHHHHH
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
|.|+.|++.|.....|..|++.
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 3455555555555555555443
No 25
>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=98.12 E-value=1.6e-06 Score=32.91 Aligned_cols=21 Identities=29% Similarity=0.786 Sum_probs=19.6
Q ss_pred ccccccccccCChHHHHhHHH
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVK 50 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~ 50 (94)
|.|+.|++.|.....|..|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 689999999999999999984
No 26
>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=98.12 E-value=4.1e-06 Score=31.79 Aligned_cols=23 Identities=35% Similarity=0.891 Sum_probs=10.8
Q ss_pred eecCccccccCCHHHHHHHHHHh
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRSR 81 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~~ 81 (94)
|.|++|++.|.....|..|+.++
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 34555555555555555555443
No 27
>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=98.07 E-value=8.2e-06 Score=36.71 Aligned_cols=34 Identities=29% Similarity=0.471 Sum_probs=21.1
Q ss_pred cCCCCCeecCccccccCCHHHHHHHHHHhcCCCC
Q psy12166 53 HQGHPSVTCNVCGRTFSSIANLAEHKRSRHGITG 86 (94)
Q Consensus 53 h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~k~ 86 (94)
..++.|-.|++|+..+.++.+|..|+...++.||
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3456677788888888888888888877777765
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.96 E-value=8.6e-06 Score=30.86 Aligned_cols=22 Identities=27% Similarity=0.797 Sum_probs=18.0
Q ss_pred ccccccccccCChHHHHhHHHh
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKS 51 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~ 51 (94)
|.|++|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 6899999999999999999943
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=97.95 E-value=7.5e-06 Score=32.23 Aligned_cols=20 Identities=40% Similarity=0.763 Sum_probs=10.0
Q ss_pred ccccccccccCChHHHHhHH
Q psy12166 30 HSCDLCGKTYTLAKHLWGHV 49 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~ 49 (94)
|+|..|++.|.....|..|+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHK 21 (27)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCccCCccCChhHHHHHh
Confidence 44555555555555555554
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.94 E-value=9.7e-06 Score=41.50 Aligned_cols=73 Identities=21% Similarity=0.261 Sum_probs=21.8
Q ss_pred CCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHh
Q psy12166 2 DCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSR 81 (94)
Q Consensus 2 ~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~ 81 (94)
+|..|+..+.....+..+....|.-..+ ....+.....+..++ .. .....+.|.+|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~-~~-~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYL-RK-KVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc-----ccccccccccccccc-cc-ccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 5888888877755554333334443222 011122233333333 11 1223699999999999999999999974
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.82 E-value=1.6e-05 Score=31.26 Aligned_cols=26 Identities=50% Similarity=0.939 Sum_probs=23.4
Q ss_pred CeecCccccccCCHHHHHHHHHHhcC
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
+|.|..|++.|.....|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 58999999999999999999987753
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.79 E-value=6e-06 Score=50.43 Aligned_cols=53 Identities=26% Similarity=0.608 Sum_probs=42.9
Q ss_pred CCCccccc--cccccCChHHHHhHHHhhc------------------CCCCCeecCccccccCCHHHHHHHHH
Q psy12166 27 TKPHSCDL--CGKTYTLAKHLWGHVKSAH------------------QGHPSVTCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 27 ~~~~~c~~--c~~~f~~~~~l~~H~~~~h------------------~~~~~~~c~~C~~~f~~~~~l~~h~~ 79 (94)
++||.|++ |.+.+.....|.-|++.-| ...|||+|++|++.++..-.|+.|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 49999997 9999999999998874333 11379999999999999888887754
No 33
>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=97.68 E-value=7e-06 Score=37.85 Aligned_cols=50 Identities=18% Similarity=0.355 Sum_probs=33.8
Q ss_pred CCCCCCccccccCCCCCCCCcccCCC-CCCccccccccccCChHHHHhHHHhhc
Q psy12166 1 MDCGWKKTAYEIGLGIPAEPLFRFDR-TKPHSCDLCGKTYTLAKHLWGHVKSAH 53 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~~~~~~~~h~~-~~~~~c~~c~~~f~~~~~l~~H~~~~h 53 (94)
|.|++|+..++ ...+..+-...|.. .+.+.|++|...+. .+|..|+...|
T Consensus 3 f~CP~C~~~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKGFS-ESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCccC-HHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 68999999433 34444444555654 35799999998654 48999985433
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.54 E-value=0.00013 Score=27.82 Aligned_cols=19 Identities=32% Similarity=0.674 Sum_probs=9.5
Q ss_pred cccccccccCChHHHHhHH
Q psy12166 31 SCDLCGKTYTLAKHLWGHV 49 (94)
Q Consensus 31 ~c~~c~~~f~~~~~l~~H~ 49 (94)
.|..|++.|.....|..|+
T Consensus 2 ~C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 2 RCPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCCcchhCCHHHHHHHH
Confidence 4445555555555555554
No 35
>KOG3993|consensus
Probab=97.45 E-value=2.1e-05 Score=49.67 Aligned_cols=54 Identities=33% Similarity=0.494 Sum_probs=45.2
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHhcC
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
-|-|.+|...|...-.|.+|. -.-....-|+|+.|+|.|+-+.+|..|++.|.-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHr-C~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHR-CPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhcc-CCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 478999998888888888884 444445579999999999999999999998853
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.34 E-value=0.00028 Score=26.83 Aligned_cols=24 Identities=38% Similarity=0.750 Sum_probs=21.2
Q ss_pred eecCccccccCCHHHHHHHHHHhc
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRSRH 82 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~~~ 82 (94)
+.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578999999999999999998664
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.29 E-value=0.00039 Score=31.36 Aligned_cols=31 Identities=23% Similarity=0.568 Sum_probs=21.4
Q ss_pred CCCCCCccccccccccCChHHHHhHHHhhcC
Q psy12166 24 FDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQ 54 (94)
Q Consensus 24 h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~ 54 (94)
+..+.|..|++|+..+.+..+|.+|++..|.
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 3457899999999999999999999965554
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.22 E-value=0.0005 Score=26.11 Aligned_cols=21 Identities=29% Similarity=0.542 Sum_probs=9.2
Q ss_pred ecCccccccCCHHHHHHHHHHh
Q psy12166 60 TCNVCGRTFSSIANLAEHKRSR 81 (94)
Q Consensus 60 ~c~~C~~~f~~~~~l~~h~~~~ 81 (94)
.|+.|+.... ...|..|++.+
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHhh
Confidence 4455554444 44555555443
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.17 E-value=0.00039 Score=26.63 Aligned_cols=20 Identities=40% Similarity=0.899 Sum_probs=10.2
Q ss_pred ecCccccccCCHHHHHHHHH
Q psy12166 60 TCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 60 ~c~~C~~~f~~~~~l~~h~~ 79 (94)
.|.+|.+.|.....+..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555544
No 40
>PRK04860 hypothetical protein; Provisional
Probab=97.14 E-value=0.00033 Score=39.29 Aligned_cols=38 Identities=24% Similarity=0.516 Sum_probs=27.6
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCH
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSI 71 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~ 71 (94)
+|.|. |+. ....+.+|. .++.++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~-ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHN-RVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHH-HHhcCCccEECCCCCceeEEe
Confidence 57786 776 455677887 678888888888888766543
No 41
>PHA00732 hypothetical protein
Probab=97.06 E-value=0.00055 Score=34.01 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=22.9
Q ss_pred CeecCccccccCCHHHHHHHHHH-hcC
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRS-RHG 83 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~-~~~ 83 (94)
||.|..|++.|.....|..|++. |.+
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 57899999999999999999985 554
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.96 E-value=0.00073 Score=25.63 Aligned_cols=23 Identities=26% Similarity=0.495 Sum_probs=17.2
Q ss_pred ccccccccccCChHHHHhHHHhhc
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAH 53 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h 53 (94)
|.|+.|++... ...|.+|++..|
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 68999999888 889999985433
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.94 E-value=0.00052 Score=26.26 Aligned_cols=21 Identities=29% Similarity=0.803 Sum_probs=19.2
Q ss_pred ccccccccccCChHHHHhHHH
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVK 50 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~ 50 (94)
|.|.+|+..|.....+..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 679999999999999999983
No 44
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.64 E-value=0.0024 Score=24.61 Aligned_cols=18 Identities=39% Similarity=1.006 Sum_probs=8.7
Q ss_pred ecCccccccCCHHHHHHHH
Q psy12166 60 TCNVCGRTFSSIANLAEHK 78 (94)
Q Consensus 60 ~c~~C~~~f~~~~~l~~h~ 78 (94)
.|+.||+.| .++.|..|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 455555555 333344443
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.41 E-value=0.0016 Score=25.47 Aligned_cols=20 Identities=30% Similarity=0.659 Sum_probs=14.3
Q ss_pred ccccccccccCChHHHHhHH
Q psy12166 30 HSCDLCGKTYTLAKHLWGHV 49 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~ 49 (94)
|.|..|++.|.....+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 56777777777777777665
No 46
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.22 E-value=0.0056 Score=31.10 Aligned_cols=24 Identities=29% Similarity=0.630 Sum_probs=20.6
Q ss_pred CCccccccccccCChHHHHhHHHh
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKS 51 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~ 51 (94)
..+.|..|+..|.....|..|++.
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCCccCCCCcCHHHHHHHHcC
Confidence 369999999999999999999953
No 47
>PRK04860 hypothetical protein; Provisional
Probab=95.83 E-value=0.0062 Score=34.27 Aligned_cols=30 Identities=17% Similarity=0.376 Sum_probs=25.4
Q ss_pred CeecCccccccCCHHHHHHHHHHhcCCCCceEee
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRSRHGITGFVVSA 91 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~C~~ 91 (94)
+|.|. |+. ....+..|.+++.|+++|.|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~ 148 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRR 148 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCC
Confidence 58898 986 6667889999999999999953
No 48
>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=95.38 E-value=0.019 Score=23.52 Aligned_cols=22 Identities=23% Similarity=0.605 Sum_probs=12.9
Q ss_pred CeecCccccccCCHHHHHHHHH
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~ 79 (94)
+|.|.+|.+.|..+..+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 3556666666666655555543
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.35 E-value=0.0032 Score=39.63 Aligned_cols=62 Identities=23% Similarity=0.428 Sum_probs=54.6
Q ss_pred CCccccccccccCChHHHHhHHHh--hcCCC--CCeecC--ccccccCCHHHHHHHHHHhcCCCCceEe
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKS--AHQGH--PSVTCN--VCGRTFSSIANLAEHKRSRHGITGFVVS 90 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~--~h~~~--~~~~c~--~C~~~f~~~~~l~~h~~~~~~~k~~~C~ 90 (94)
.++.|..|...|.....+..|. . .|..+ +++.|+ .|++.|.....+..|...|.+.+++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~-~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHL-RSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccc-cccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 4688899999999999999998 5 79998 999999 7999999999999999999888777664
No 50
>KOG1146|consensus
Probab=95.08 E-value=0.026 Score=40.96 Aligned_cols=57 Identities=28% Similarity=0.444 Sum_probs=46.4
Q ss_pred CCCCCCccccccccccCChHHHHhHHHhhcCC------------------------CCCeecCccccccCCHHHHHHHHH
Q psy12166 24 FDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQG------------------------HPSVTCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 24 h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~------------------------~~~~~c~~C~~~f~~~~~l~~h~~ 79 (94)
+.-.+.+.|+.|+..|.....|..|++..|.. .++|.|..|...+....+|..|+.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 44458899999999999999999999653321 246889999999999999999976
Q ss_pred H
Q psy12166 80 S 80 (94)
Q Consensus 80 ~ 80 (94)
.
T Consensus 540 S 540 (1406)
T KOG1146|consen 540 S 540 (1406)
T ss_pred H
Confidence 5
No 51
>KOG2186|consensus
Probab=94.68 E-value=0.023 Score=34.13 Aligned_cols=45 Identities=24% Similarity=0.631 Sum_probs=23.7
Q ss_pred ccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHH
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHK 78 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~ 78 (94)
|.|..||....- ..+.+|+ ....+ .-|.|..|+..|.. ..+..|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~-srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHM-SRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHH-HhccC-CeeEEeeccccccc-chhhhhh
Confidence 556666655442 3455565 44444 34666666666666 2334443
No 52
>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=94.15 E-value=0.027 Score=23.11 Aligned_cols=10 Identities=40% Similarity=0.986 Sum_probs=5.9
Q ss_pred CCeecCcccc
Q psy12166 57 PSVTCNVCGR 66 (94)
Q Consensus 57 ~~~~c~~C~~ 66 (94)
.++.|++|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4566666653
No 53
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.92 E-value=0.036 Score=25.55 Aligned_cols=33 Identities=27% Similarity=0.386 Sum_probs=24.8
Q ss_pred ccCCCCCCccccccccccCChHHHHhHHHhhcC
Q psy12166 22 FRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQ 54 (94)
Q Consensus 22 ~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~ 54 (94)
....|+.-+.|+-|+..|....++.+|.+..|.
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 345677788888888888888888888755543
No 54
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=93.22 E-value=0.39 Score=25.16 Aligned_cols=25 Identities=32% Similarity=0.594 Sum_probs=21.9
Q ss_pred eec----CccccccCCHHHHHHHHHHhcC
Q psy12166 59 VTC----NVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 59 ~~c----~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
|.| ..|+..+.....+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 679 8899999999999999988765
No 55
>PHA00626 hypothetical protein
Probab=92.22 E-value=0.15 Score=23.54 Aligned_cols=14 Identities=21% Similarity=0.335 Sum_probs=10.5
Q ss_pred CCccccccccccCC
Q psy12166 28 KPHSCDLCGKTYTL 41 (94)
Q Consensus 28 ~~~~c~~c~~~f~~ 41 (94)
..|.|+.||+.|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 56888888877764
No 56
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=91.97 E-value=0.033 Score=34.71 Aligned_cols=24 Identities=33% Similarity=0.630 Sum_probs=21.3
Q ss_pred CCCCccccccccccCChHHHHhHH
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHV 49 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~ 49 (94)
..+||+|++|++++.....|.-|.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 459999999999999998888885
No 57
>KOG4173|consensus
Probab=91.94 E-value=0.045 Score=32.07 Aligned_cols=53 Identities=25% Similarity=0.543 Sum_probs=38.7
Q ss_pred ccccccccccCChHHHHhHHHhhcC---------CCCCeecCc--cccccCCHHHHHHHHHHhc
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQ---------GHPSVTCNV--CGRTFSSIANLAEHKRSRH 82 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~---------~~~~~~c~~--C~~~f~~~~~l~~h~~~~~ 82 (94)
..|..|.+.|....-|..|+.-.|- +..-|+|.+ |+..|.+...-..|+...+
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 4788899999988888888754442 233477765 8888888888888876544
No 58
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.84 E-value=0.024 Score=33.37 Aligned_cols=44 Identities=25% Similarity=0.513 Sum_probs=26.2
Q ss_pred CCccccccccccCChHHHHhHHHhhc---------CCCCC-----eecCccccccCCH
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAH---------QGHPS-----VTCNVCGRTFSSI 71 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h---------~~~~~-----~~c~~C~~~f~~~ 71 (94)
+...|++|+..|....-.....+... .+..| ..|+.||.++...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 56789999988877644433331111 11122 4699999876654
No 59
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.95 E-value=0.14 Score=28.76 Aligned_cols=41 Identities=20% Similarity=0.288 Sum_probs=22.7
Q ss_pred CCCCCCcccccc--CCCCCCCCcccCCCCCCccccccccccCChHH
Q psy12166 1 MDCGWKKTAYEI--GLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKH 44 (94)
Q Consensus 1 ~~C~~~~~~~~~--~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~ 44 (94)
+.|++|+..... ....+.. ..... +.++|+.||+.|.....
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~--~~~~~-~~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED--GNAIR-RRRECLACGKRFTTFER 43 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC--CCcee-eeeeccccCCcceEeEe
Confidence 469999865421 1111111 11222 34899999999976543
No 60
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.41 E-value=0.29 Score=20.47 Aligned_cols=32 Identities=25% Similarity=0.676 Sum_probs=15.3
Q ss_pred cccccccccCChHHHHhHHHhhcCCCCCeecCcccccc
Q psy12166 31 SCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTF 68 (94)
Q Consensus 31 ~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f 68 (94)
.|+.|+..|...+. .........+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~------~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDE------KIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHH------HCCCCCcEEECCCCCCEe
Confidence 45556555554443 122223345666665544
No 61
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.38 E-value=0.29 Score=20.56 Aligned_cols=11 Identities=45% Similarity=1.147 Sum_probs=6.0
Q ss_pred CeecCcccccc
Q psy12166 58 SVTCNVCGRTF 68 (94)
Q Consensus 58 ~~~c~~C~~~f 68 (94)
..+|+.|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 45566555544
No 62
>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=90.33 E-value=0.19 Score=27.53 Aligned_cols=26 Identities=38% Similarity=0.867 Sum_probs=14.9
Q ss_pred CeecCccccccCCHHHHHHHHHHhcCCCC
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRSRHGITG 86 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~~~~~k~ 86 (94)
...|.+||+.|.. |..|+..|+|..|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 4678888888877 4788888877554
No 63
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.20 E-value=0.25 Score=23.15 Aligned_cols=32 Identities=19% Similarity=0.415 Sum_probs=19.9
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCG 65 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~ 65 (94)
..|.|+.||......-. .--....+|.|+.||
T Consensus 26 v~F~CPnCGe~~I~Rc~------~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA------KCRKLGNPYRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehhh------hHHHcCCceECCCcC
Confidence 46888888866554432 122234578888887
No 64
>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=89.04 E-value=0.36 Score=20.16 Aligned_cols=33 Identities=18% Similarity=0.543 Sum_probs=15.7
Q ss_pred ccccccccccCChHHHHhHHHhhcCCCCCeecCcccccc
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTF 68 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f 68 (94)
..|+.|+..|...... .........|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCEE
Confidence 3566666655543321 11111245666666554
No 65
>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=88.11 E-value=0.57 Score=20.23 Aligned_cols=25 Identities=32% Similarity=0.631 Sum_probs=14.2
Q ss_pred CCCCccccccccccCCh----HHHHhHHH
Q psy12166 26 RTKPHSCDLCGKTYTLA----KHLWGHVK 50 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~----~~l~~H~~ 50 (94)
++....|..|++.+... ..|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45667888888777653 66777763
No 66
>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=87.71 E-value=0.3 Score=20.15 Aligned_cols=25 Identities=24% Similarity=0.643 Sum_probs=14.1
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
.|.|..||+.+... ..|..|++|+.
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 36677777553321 13557777764
No 67
>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=87.55 E-value=0.23 Score=29.39 Aligned_cols=26 Identities=23% Similarity=0.540 Sum_probs=15.5
Q ss_pred CeecCccccccCCHHHHHHHHHHhcC
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
.|.|..|+|.|.....+.+|+..-|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 46677777777777777777665443
No 68
>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=86.93 E-value=0.72 Score=17.77 Aligned_cols=18 Identities=17% Similarity=0.457 Sum_probs=11.2
Q ss_pred cccccccccCChHHHHhHH
Q psy12166 31 SCDLCGKTYTLAKHLWGHV 49 (94)
Q Consensus 31 ~c~~c~~~f~~~~~l~~H~ 49 (94)
.|++|++.+ ....+..|+
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 567777666 445566665
No 69
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=86.60 E-value=0.44 Score=27.13 Aligned_cols=23 Identities=39% Similarity=1.054 Sum_probs=16.0
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCccc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCG 65 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~ 65 (94)
.|.|++||+. +.++.|-.||+||
T Consensus 134 ~~vC~vCGy~--------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT--------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc--------------ccCCCCCcCCCCC
Confidence 5888888743 3336677888887
No 70
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.98 E-value=0.44 Score=27.40 Aligned_cols=35 Identities=17% Similarity=0.412 Sum_probs=25.4
Q ss_pred CCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCC
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSS 70 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~ 70 (94)
...-|.|+.|+..|+....+. -.|.|+.||.....
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 345788999999888766531 26999999976544
No 71
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=85.79 E-value=0.58 Score=26.36 Aligned_cols=35 Identities=17% Similarity=0.308 Sum_probs=24.9
Q ss_pred CCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCC
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSS 70 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~ 70 (94)
...-|.|+.|+..|+....+. ..|.|+.||.....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEeee
Confidence 446688988988888766542 26889999865443
No 72
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.75 E-value=0.89 Score=20.30 Aligned_cols=27 Identities=26% Similarity=0.644 Sum_probs=18.6
Q ss_pred CCccccccccccCCh-----HHHHhHHHhhcC
Q psy12166 28 KPHSCDLCGKTYTLA-----KHLWGHVKSAHQ 54 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~-----~~l~~H~~~~h~ 54 (94)
..-.|..|++.+... +.|.+|++..|.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 356788899887655 578888743444
No 73
>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=85.43 E-value=0.57 Score=27.81 Aligned_cols=31 Identities=23% Similarity=0.523 Sum_probs=23.1
Q ss_pred CCCCCccccccccccCChHHHHhHHHhhcCC
Q psy12166 25 DRTKPHSCDLCGKTYTLAKHLWGHVKSAHQG 55 (94)
Q Consensus 25 ~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~ 55 (94)
..+..|.|..|+|.|.-.....+|+...|..
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 3456799999999999999999999766653
No 74
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.92 E-value=1 Score=24.97 Aligned_cols=40 Identities=20% Similarity=0.400 Sum_probs=24.9
Q ss_pred CCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCC
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSS 70 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~ 70 (94)
...-|.|+.|+..|.....+. .... ...|.|+.||.....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~----~~d~-~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQ----LLDM-DGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHH----hcCC-CCcEECCCCCCEEEE
Confidence 345788999998888644322 1112 334899999876543
No 75
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=81.89 E-value=0.83 Score=25.10 Aligned_cols=25 Identities=32% Similarity=0.567 Sum_probs=14.5
Q ss_pred eecCccccccCCHHHHHHHHHHhcCCCC
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRSRHGITG 86 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~~~~~k~ 86 (94)
+.|..+|+.|+. |.+|+.+|.|-.|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 345566665543 5667666666443
No 76
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=81.59 E-value=1.2 Score=28.12 Aligned_cols=57 Identities=21% Similarity=0.306 Sum_probs=40.7
Q ss_pred CCCccccccCCCCCCCCcc--cCCCC--CCcccc--ccccccCChHHHHhHHHhhcCCCCCeecC
Q psy12166 4 GWKKTAYEIGLGIPAEPLF--RFDRT--KPHSCD--LCGKTYTLAKHLWGHVKSAHQGHPSVTCN 62 (94)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~--~h~~~--~~~~c~--~c~~~f~~~~~l~~H~~~~h~~~~~~~c~ 62 (94)
..|...+..... ...+.. .|.++ +++.|+ .|++.|.....+..|. ..|....++.+.
T Consensus 293 ~~~~~~~s~~~~-l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 355 (467)
T COG5048 293 KQCNISFSRSSP-LTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI-LLHTSISPAKEK 355 (467)
T ss_pred ccccCCcccccc-ccccccccccccccCCceeeeccCCCccccccccccCCc-ccccCCCccccc
Confidence 333334443333 345566 78888 999999 7999999999999998 778876655443
No 77
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=80.95 E-value=0.55 Score=20.26 Aligned_cols=29 Identities=24% Similarity=0.752 Sum_probs=15.4
Q ss_pred ccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
|.|..||..|..... ... ..+..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~-------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS-------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEE-------cCC-CCCCcCCCCCC
Confidence 567777766654321 111 34566777664
No 78
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.91 E-value=1.3 Score=19.42 Aligned_cols=11 Identities=27% Similarity=0.727 Sum_probs=5.8
Q ss_pred ccccccccccC
Q psy12166 30 HSCDLCGKTYT 40 (94)
Q Consensus 30 ~~c~~c~~~f~ 40 (94)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55555555443
No 79
>PF14353 CpXC: CpXC protein
Probab=80.85 E-value=2.7 Score=22.64 Aligned_cols=19 Identities=26% Similarity=0.614 Sum_probs=12.8
Q ss_pred CCccccccccccCChHHHH
Q psy12166 28 KPHSCDLCGKTYTLAKHLW 46 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~ 46 (94)
..+.|+.||..|.....+.
T Consensus 37 ~~~~CP~Cg~~~~~~~p~l 55 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLL 55 (128)
T ss_pred CEEECCCCCCceecCCCEE
Confidence 4677888887776655543
No 80
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=80.74 E-value=0.38 Score=21.59 Aligned_cols=11 Identities=27% Similarity=0.951 Sum_probs=6.1
Q ss_pred ccccccccccC
Q psy12166 30 HSCDLCGKTYT 40 (94)
Q Consensus 30 ~~c~~c~~~f~ 40 (94)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45556665554
No 81
>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=80.58 E-value=1.8 Score=22.66 Aligned_cols=25 Identities=24% Similarity=0.413 Sum_probs=21.4
Q ss_pred Cccc----cccccccCChHHHHhHHHhhc
Q psy12166 29 PHSC----DLCGKTYTLAKHLWGHVKSAH 53 (94)
Q Consensus 29 ~~~c----~~c~~~f~~~~~l~~H~~~~h 53 (94)
-|.| ..|++.......+..|.+..|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 4899 999999999999999985444
No 82
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=79.93 E-value=1.2 Score=22.55 Aligned_cols=33 Identities=30% Similarity=0.635 Sum_probs=21.3
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCH
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSI 71 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~ 71 (94)
.+|.|+.|+.. . +. + ...-.+.|..|+..|.--
T Consensus 34 ~~~~Cp~C~~~-~-------Vk-R--~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT-T-------VK-R--IATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc-c-------ee-e--eccCeEEcCCCCCeeccc
Confidence 46889888755 1 11 2 223468899998877653
No 83
>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=79.17 E-value=1.1 Score=17.35 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=7.9
Q ss_pred ccccccccccC
Q psy12166 30 HSCDLCGKTYT 40 (94)
Q Consensus 30 ~~c~~c~~~f~ 40 (94)
-.|+.||+.|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35788888774
No 84
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.83 E-value=1.4 Score=20.64 Aligned_cols=33 Identities=21% Similarity=0.450 Sum_probs=19.0
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
-.|.|+.||......-. .--....+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~------~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE------KCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeech------hHHhcCCceECCCCCC
Confidence 46888888876333221 1122235788888873
No 85
>KOG2785|consensus
Probab=77.87 E-value=5.9 Score=25.72 Aligned_cols=55 Identities=25% Similarity=0.440 Sum_probs=42.0
Q ss_pred CCCCccccccccccCChHHHHhHHHhhcCCCC----------------------CeecCccc---cccCCHHHHHHHHHH
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHP----------------------SVTCNVCG---RTFSSIANLAEHKRS 80 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~----------------------~~~c~~C~---~~f~~~~~l~~h~~~ 80 (94)
...|-.|-.|++.+.....-..||...|.--. .+.|..|. +.|........||..
T Consensus 163 e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 163 ELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred ccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 34567788999999999989999954443322 25688887 889999889999875
No 86
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=77.30 E-value=3.2 Score=29.27 Aligned_cols=16 Identities=31% Similarity=0.829 Sum_probs=8.2
Q ss_pred ccCCCCCCcccccccc
Q psy12166 22 FRFDRTKPHSCDLCGK 37 (94)
Q Consensus 22 ~~h~~~~~~~c~~c~~ 37 (94)
.-+....|..|+.||.
T Consensus 468 Cg~~~~~p~~Cp~Cgs 483 (730)
T COG1198 468 CGYQEPIPQSCPECGS 483 (730)
T ss_pred CCCCCCCCCCCCCCCC
Confidence 3334445566666653
No 87
>KOG2893|consensus
Probab=76.47 E-value=0.35 Score=29.18 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=7.4
Q ss_pred CCCCCccccccccccC
Q psy12166 25 DRTKPHSCDLCGKTYT 40 (94)
Q Consensus 25 ~~~~~~~c~~c~~~f~ 40 (94)
...+.|.|.+|.+.+.
T Consensus 30 qkakhfkchichkkl~ 45 (341)
T KOG2893|consen 30 QKAKHFKCHICHKKLF 45 (341)
T ss_pred hhhccceeeeehhhhc
Confidence 3334455555554433
No 88
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=76.19 E-value=1.5 Score=21.46 Aligned_cols=41 Identities=15% Similarity=0.248 Sum_probs=22.7
Q ss_pred CCCCCCccccccCCCCCCCCcccCCCCCCcccc--ccccccCChHH
Q psy12166 1 MDCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCD--LCGKTYTLAKH 44 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~--~c~~~f~~~~~ 44 (94)
|.|+.|+.......+... ..-..+.-++|. .||..|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~---s~~~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYI---TDTTKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhc---ChhhheeeeecCCCCCCCEEEEEEE
Confidence 467777755543222111 111445677787 78888876544
No 89
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=75.69 E-value=1.9 Score=19.44 Aligned_cols=39 Identities=15% Similarity=0.355 Sum_probs=19.7
Q ss_pred CCCccccccccccCChHHHHhHHHhhcCCCCCeecCccc
Q psy12166 27 TKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCG 65 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~ 65 (94)
.+++.|..||..|.....=+......-....|-.|+.|.
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 356788888887765443222221101112455666663
No 90
>KOG4173|consensus
Probab=75.15 E-value=2.4 Score=25.15 Aligned_cols=51 Identities=20% Similarity=0.437 Sum_probs=36.9
Q ss_pred CCCccccc--cccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHHh
Q psy12166 27 TKPHSCDL--CGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSR 81 (94)
Q Consensus 27 ~~~~~c~~--c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~~ 81 (94)
...+.|++ |...|...+.+..|....|+ -.|.+|.+.|.+...|..|+...
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~ 129 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEW 129 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHH
Confidence 34567776 66787777777777533444 46899999999999888886543
No 91
>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=73.26 E-value=3 Score=23.37 Aligned_cols=18 Identities=17% Similarity=0.427 Sum_probs=13.4
Q ss_pred CCccccccccccCChHHH
Q psy12166 28 KPHSCDLCGKTYTLAKHL 45 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l 45 (94)
+.=.|..|++.|++...+
T Consensus 27 RRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 27 RRRECLECHERFTTFERA 44 (147)
T ss_pred ecccCCccCCccceeeec
Confidence 345899999999876543
No 92
>PF12907 zf-met2: Zinc-binding
Probab=72.71 E-value=2.7 Score=18.07 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=14.5
Q ss_pred cccccccccc---CChHHHHhHHHhhcCCC
Q psy12166 30 HSCDLCGKTY---TLAKHLWGHVKSAHQGH 56 (94)
Q Consensus 30 ~~c~~c~~~f---~~~~~l~~H~~~~h~~~ 56 (94)
+.|.+|...| .....|..|....|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 3566666444 33455666664455543
No 93
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.56 E-value=1.7 Score=19.02 Aligned_cols=12 Identities=25% Similarity=0.719 Sum_probs=6.7
Q ss_pred CccccccccccC
Q psy12166 29 PHSCDLCGKTYT 40 (94)
Q Consensus 29 ~~~c~~c~~~f~ 40 (94)
.|.|+.||..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 356666665544
No 94
>PF15269 zf-C2H2_7: Zinc-finger
Probab=70.76 E-value=4.3 Score=17.91 Aligned_cols=22 Identities=23% Similarity=0.359 Sum_probs=15.1
Q ss_pred eecCccccccCCHHHHHHHHHH
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
|.|-.|..+...++.|..|+.-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5566676677777777777654
No 95
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.62 E-value=1.5 Score=24.09 Aligned_cols=16 Identities=25% Similarity=0.669 Sum_probs=12.5
Q ss_pred CCCccccccccccCCh
Q psy12166 27 TKPHSCDLCGKTYTLA 42 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~ 42 (94)
...+.|..||+.|...
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 3568999999888754
No 96
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=69.55 E-value=2.9 Score=18.86 Aligned_cols=28 Identities=29% Similarity=0.718 Sum_probs=17.4
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
..|.|..||..|.. -.......|+.||.
T Consensus 5 ~~Y~C~~Cg~~~~~-----------~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVEL-----------DQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeeh-----------hhccCceeCCCCCc
Confidence 45888888877621 11234578888874
No 97
>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=68.22 E-value=2.7 Score=15.97 Aligned_cols=8 Identities=50% Similarity=1.406 Sum_probs=3.9
Q ss_pred Cccccccc
Q psy12166 29 PHSCDLCG 36 (94)
Q Consensus 29 ~~~c~~c~ 36 (94)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45555444
No 98
>KOG3408|consensus
Probab=68.17 E-value=3.7 Score=22.23 Aligned_cols=23 Identities=26% Similarity=0.502 Sum_probs=19.5
Q ss_pred CeecCccccccCCHHHHHHHHHH
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
.|.|..|.+.|.....|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 48899999999999999888664
No 99
>KOG1280|consensus
Probab=68.15 E-value=6.9 Score=25.15 Aligned_cols=38 Identities=29% Similarity=0.580 Sum_probs=27.1
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCC-CeecCccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHP-SVTCNVCG 65 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~-~~~c~~C~ 65 (94)
..|+|+.|+..-.....|..|....|.... ...|++|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 578889998877778888888866666543 23466665
No 100
>KOG2593|consensus
Probab=67.64 E-value=5 Score=26.46 Aligned_cols=38 Identities=24% Similarity=0.420 Sum_probs=25.1
Q ss_pred CCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 25 DRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 25 ~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
+....|.|+.|.+.|.....++ ..-...-.|.|..|+-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~----L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ----LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHH----hhcccCceEEEecCCC
Confidence 3446799999999888766543 2222234688888864
No 101
>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=66.68 E-value=6.1 Score=20.94 Aligned_cols=30 Identities=27% Similarity=0.705 Sum_probs=21.1
Q ss_pred ccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCH
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSI 71 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~ 71 (94)
..|+.||.+|-- |. ..|..|++||..|...
T Consensus 10 R~Cp~CG~kFYD---Ln---------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD---LN---------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc---CC---------CCCccCCCCCCccCcc
Confidence 578888887653 21 1377888998877766
No 102
>KOG2482|consensus
Probab=66.66 E-value=9.3 Score=24.65 Aligned_cols=53 Identities=21% Similarity=0.377 Sum_probs=37.9
Q ss_pred CCccccccccccC-ChHHHHhHHHhhcCCC---------------------CCeecCccccccCCHHHHHHHHHH
Q psy12166 28 KPHSCDLCGKTYT-LAKHLWGHVKSAHQGH---------------------PSVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 28 ~~~~c~~c~~~f~-~~~~l~~H~~~~h~~~---------------------~~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
..-+|-.|...+. ..+....|+..+|.-. ..++|..|.+.|..+..|..||+.
T Consensus 143 fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 143 FSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 4556878877553 4455666765555422 146899999999999999999986
No 103
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.32 E-value=6.1 Score=27.98 Aligned_cols=47 Identities=23% Similarity=0.319 Sum_probs=28.9
Q ss_pred CCCCCccccccCCCCCCCCcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 2 DCGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 2 ~C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
.|..|+.....+.. ...+.-|...+...|..||+. ...|..|+.||-
T Consensus 437 ~C~~Cg~v~~Cp~C--d~~lt~H~~~~~L~CH~Cg~~----------------~~~p~~Cp~Cgs 483 (730)
T COG1198 437 LCRDCGYIAECPNC--DSPLTLHKATGQLRCHYCGYQ----------------EPIPQSCPECGS 483 (730)
T ss_pred ecccCCCcccCCCC--CcceEEecCCCeeEeCCCCCC----------------CCCCCCCCCCCC
Confidence 46666666655333 233555666667778777632 345788888874
No 104
>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=66.08 E-value=4.9 Score=22.72 Aligned_cols=18 Identities=33% Similarity=0.787 Sum_probs=13.3
Q ss_pred CCCCccccccccccCChH
Q psy12166 26 RTKPHSCDLCGKTYTLAK 43 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~ 43 (94)
-+.|..|..||+.|..-.
T Consensus 65 ~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred CCCChhHHhCCCCCchHH
Confidence 347888888998887543
No 105
>KOG4167|consensus
Probab=65.86 E-value=1.6 Score=30.67 Aligned_cols=25 Identities=24% Similarity=0.606 Sum_probs=21.9
Q ss_pred CeecCccccccCCHHHHHHHHHHhc
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRSRH 82 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~~~ 82 (94)
-|.|..|++.|.--..+..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3889999999999888999998875
No 106
>KOG2893|consensus
Probab=65.85 E-value=1.3 Score=26.81 Aligned_cols=43 Identities=33% Similarity=0.659 Sum_probs=29.0
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCccccc-cCCHHHHHHH
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRT-FSSIANLAEH 77 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~-f~~~~~l~~h 77 (94)
++| |=.|...|..+.-|.+|++ .+-|.|-+|-+. |+... |..|
T Consensus 10 kpw-cwycnrefddekiliqhqk-----akhfkchichkkl~sgpg-lsih 53 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPG-LSIH 53 (341)
T ss_pred Cce-eeecccccchhhhhhhhhh-----hccceeeeehhhhccCCC-ceee
Confidence 555 3478899998888887774 456889999754 44433 4444
No 107
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=63.76 E-value=6.3 Score=22.24 Aligned_cols=17 Identities=24% Similarity=0.632 Sum_probs=13.0
Q ss_pred CCccccccccccCChHH
Q psy12166 28 KPHSCDLCGKTYTLAKH 44 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~ 44 (94)
+.=.|..|+..|++...
T Consensus 27 RRReC~~C~~RFTTfE~ 43 (156)
T COG1327 27 RRRECLECGERFTTFER 43 (156)
T ss_pred hhhcccccccccchhhe
Confidence 44579999999987654
No 108
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=62.07 E-value=4.3 Score=26.13 Aligned_cols=20 Identities=20% Similarity=0.400 Sum_probs=13.9
Q ss_pred cccccccccCChHHHHhHHH
Q psy12166 31 SCDLCGKTYTLAKHLWGHVK 50 (94)
Q Consensus 31 ~c~~c~~~f~~~~~l~~H~~ 50 (94)
.|..|...|-..+.|..|++
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhhccceecChHHHHHHHH
Confidence 36667777777777777774
No 109
>COG1773 Rubredoxin [Energy production and conversion]
Probab=61.90 E-value=3.4 Score=19.12 Aligned_cols=36 Identities=25% Similarity=0.471 Sum_probs=21.1
Q ss_pred CccccccccccCChHHHHhHHHhhcCCC------CCeecCcccc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGH------PSVTCNVCGR 66 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~------~~~~c~~C~~ 66 (94)
.|+|..||+.|--...-... ....+. ..+.|+.||.
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~--gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRC--GIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccC--CCCCCCchhhCCCccCCCCCCC
Confidence 58999999888654332222 122221 2467899884
No 110
>KOG2636|consensus
Probab=61.59 E-value=6.8 Score=26.06 Aligned_cols=27 Identities=19% Similarity=0.486 Sum_probs=21.9
Q ss_pred hhcCCCCCeecCccc-cccCCHHHHHHH
Q psy12166 51 SAHQGHPSVTCNVCG-RTFSSIANLAEH 77 (94)
Q Consensus 51 ~~h~~~~~~~c~~C~-~~f~~~~~l~~h 77 (94)
..|.-.+.|.|.+|| +++..+..+..|
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHH
Confidence 357777889999999 788888888877
No 111
>KOG2636|consensus
Probab=61.23 E-value=7 Score=26.01 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=23.4
Q ss_pred ccCCCCCCccccccc-cccCChHHHHhHH
Q psy12166 22 FRFDRTKPHSCDLCG-KTYTLAKHLWGHV 49 (94)
Q Consensus 22 ~~h~~~~~~~c~~c~-~~f~~~~~l~~H~ 49 (94)
..|.-...|.|.+|| +++.-...+.+|.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHh
Confidence 456767899999999 7888888888886
No 112
>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=60.45 E-value=3.6 Score=17.15 Aligned_cols=30 Identities=30% Similarity=0.822 Sum_probs=20.0
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
.|.|..||..|...... .. .....|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~-------~~-~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI-------SD-DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEec-------CC-CCCCCCCCCCC
Confidence 37899999888753221 11 44678999986
No 113
>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=60.37 E-value=7.9 Score=25.93 Aligned_cols=28 Identities=21% Similarity=0.424 Sum_probs=23.6
Q ss_pred CccccccccccCChHHHHhHHHhhcCCC
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGH 56 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~ 56 (94)
=+.|+.|.+.|.....+..|+...|.+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 4668999999999999999997777764
No 114
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=58.02 E-value=5.3 Score=22.53 Aligned_cols=33 Identities=27% Similarity=0.683 Sum_probs=16.2
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
-+|.|. |+..+.+. .+|- .+-.++ .|.|..|+.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn-~~~~g~-~YrC~~C~g 148 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHN-TVRRGE-VYRCGKCGG 148 (156)
T ss_pred eeEEee-cCCccchh---hhcc-cccccc-eEEeccCCc
Confidence 356666 66554432 2332 233333 566666653
No 115
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=56.44 E-value=4.5 Score=20.71 Aligned_cols=32 Identities=25% Similarity=0.476 Sum_probs=17.7
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCC
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSS 70 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~ 70 (94)
..|.|+.|++.-. ++.- .-.+.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~v---------kR~a--~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAV---------KRQA--VGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCce---------eeee--eEEEEcCCCCCEEeC
Confidence 3577887764311 1111 235778888776544
No 116
>KOG1842|consensus
Probab=55.00 E-value=8.8 Score=25.60 Aligned_cols=30 Identities=17% Similarity=0.238 Sum_probs=26.2
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCC
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHP 57 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~ 57 (94)
.-|.|++|..-|...+.|..|....|..+.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 569999999999999999999977787654
No 117
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=54.67 E-value=7.5 Score=16.46 Aligned_cols=14 Identities=29% Similarity=0.769 Sum_probs=10.1
Q ss_pred CeecCccccccCCH
Q psy12166 58 SVTCNVCGRTFSSI 71 (94)
Q Consensus 58 ~~~c~~C~~~f~~~ 71 (94)
++.|..|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 77888888776543
No 118
>KOG1146|consensus
Probab=54.54 E-value=3.1 Score=31.20 Aligned_cols=46 Identities=20% Similarity=0.296 Sum_probs=34.5
Q ss_pred cccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHHHHHHHHH
Q psy12166 35 CGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 35 c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
++..+.....+..|+...+...+.+.|++|+..|.....|..|+++
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccc
Confidence 4444555555555554455666889999999999999999999988
No 119
>KOG4167|consensus
Probab=53.71 E-value=2.6 Score=29.66 Aligned_cols=26 Identities=31% Similarity=0.551 Sum_probs=21.6
Q ss_pred CCccccccccccCChHHHHhHHHhhcC
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQ 54 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~ 54 (94)
.-|.|..|++.|-...++..||+ .|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK-~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMK-THR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHH-HHH
Confidence 46899999999998888899984 554
No 120
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=53.34 E-value=13 Score=16.16 Aligned_cols=27 Identities=22% Similarity=0.580 Sum_probs=15.0
Q ss_pred ccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
+.|+.||.. . . ........|.|..|++
T Consensus 19 ~~CP~Cg~~-~-~--------~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-K-H--------YRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-e-e--------EEeCCCCeEECCCCCC
Confidence 668888754 1 1 1112245677877764
No 121
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=53.08 E-value=5.5 Score=18.12 Aligned_cols=42 Identities=21% Similarity=0.443 Sum_probs=21.3
Q ss_pred CCccccc--cccccCChHHHHhHHHhhcCCCCCeecCc----cccccCCH
Q psy12166 28 KPHSCDL--CGKTYTLAKHLWGHVKSAHQGHPSVTCNV----CGRTFSSI 71 (94)
Q Consensus 28 ~~~~c~~--c~~~f~~~~~l~~H~~~~h~~~~~~~c~~----C~~~f~~~ 71 (94)
.+-.|+. |...+. ...|..|+ ...=...+..|++ |+..+...
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~-~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHL-ENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHH-HTTSTTSEEE-SS----S--EEEHH
T ss_pred CEeeCCCCCccccee-HHHHHHHH-HccCCCCcEECCCCCCCCCCccchh
Confidence 3456766 434344 45688897 4233345677887 77655543
No 122
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.03 E-value=21 Score=19.10 Aligned_cols=23 Identities=22% Similarity=0.457 Sum_probs=10.5
Q ss_pred CeecCccccccCCHHHHHHHHHH
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
.|+|+.|...|-..-++-.|...
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred ceeCCCCCCccccccchhhhhhc
Confidence 34455555544444444444333
No 123
>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=52.95 E-value=4.8 Score=20.65 Aligned_cols=13 Identities=38% Similarity=0.879 Sum_probs=8.7
Q ss_pred CeecCccccccCC
Q psy12166 58 SVTCNVCGRTFSS 70 (94)
Q Consensus 58 ~~~c~~C~~~f~~ 70 (94)
.+.|..|++.|.-
T Consensus 53 IW~C~~C~~~~AG 65 (91)
T TIGR00280 53 IWTCRKCGAKFAG 65 (91)
T ss_pred EEEcCCCCCEEeC
Confidence 5778888766543
No 124
>KOG1842|consensus
Probab=52.68 E-value=9.9 Score=25.36 Aligned_cols=27 Identities=19% Similarity=0.426 Sum_probs=23.4
Q ss_pred CCeecCccccccCCHHHHHHHHHHhcC
Q psy12166 57 PSVTCNVCGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 57 ~~~~c~~C~~~f~~~~~l~~h~~~~~~ 83 (94)
..|.|++|...|.....|..|...-|+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcc
Confidence 469999999999999999999877443
No 125
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=52.55 E-value=6.9 Score=20.33 Aligned_cols=20 Identities=30% Similarity=0.781 Sum_probs=14.2
Q ss_pred cccCCCCCCccccccccccCC
Q psy12166 21 LFRFDRTKPHSCDLCGKTYTL 41 (94)
Q Consensus 21 ~~~h~~~~~~~c~~c~~~f~~ 41 (94)
++.+.+ ++++|..||.-|..
T Consensus 72 ~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCC-CceeCCCCCcEEEE
Confidence 445555 68888888887754
No 126
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.51 E-value=12 Score=20.48 Aligned_cols=16 Identities=31% Similarity=0.796 Sum_probs=10.4
Q ss_pred CCCccccccccccCCh
Q psy12166 27 TKPHSCDLCGKTYTLA 42 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~ 42 (94)
...|.|+.|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4567777777776543
No 127
>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=51.42 E-value=7 Score=17.63 Aligned_cols=35 Identities=29% Similarity=0.563 Sum_probs=19.8
Q ss_pred ccccccccccCChHHHHhHHHhhcCC------CCCeecCcccc
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQG------HPSVTCNVCGR 66 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~------~~~~~c~~C~~ 66 (94)
|.|..||+.+.-...-..+ .+-.+ ...|.|+.|+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~--~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 2 YECRICGYIYDPAEGDPDE--GIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred cCCCCCCeEECCCCCCccc--CcCCCCCHhHCCCCCCCCCCCC
Confidence 7899999887643211111 11111 23578999974
No 128
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.96 E-value=14 Score=20.19 Aligned_cols=17 Identities=24% Similarity=0.669 Sum_probs=12.3
Q ss_pred CCCCccccccccccCCh
Q psy12166 26 RTKPHSCDLCGKTYTLA 42 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~ 42 (94)
=+.|.-|.-||..|...
T Consensus 65 ye~psfchncgs~fpwt 81 (160)
T COG4306 65 YEPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCCcchhhcCCCCCCcH
Confidence 35677788888888754
No 129
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=50.65 E-value=9.1 Score=21.17 Aligned_cols=13 Identities=38% Similarity=0.879 Sum_probs=9.8
Q ss_pred ecCccccccCCHH
Q psy12166 60 TCNVCGRTFSSIA 72 (94)
Q Consensus 60 ~c~~C~~~f~~~~ 72 (94)
.||+|.-+|..+.
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 5888888887764
No 130
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=50.32 E-value=8.8 Score=17.49 Aligned_cols=16 Identities=19% Similarity=0.345 Sum_probs=11.2
Q ss_pred CCCCCCccccccCCCC
Q psy12166 1 MDCGWKKTAYEIGLGI 16 (94)
Q Consensus 1 ~~C~~~~~~~~~~~~~ 16 (94)
+.|+||+..+....+.
T Consensus 1 i~CPyCge~~~~~iD~ 16 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDP 16 (52)
T ss_pred CCCCCCCCeeEEEEec
Confidence 4788888877764443
No 131
>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=50.23 E-value=7.5 Score=16.69 Aligned_cols=12 Identities=42% Similarity=1.113 Sum_probs=7.3
Q ss_pred CCcccccccccc
Q psy12166 28 KPHSCDLCGKTY 39 (94)
Q Consensus 28 ~~~~c~~c~~~f 39 (94)
++-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356677776554
No 132
>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=50.11 E-value=3.5 Score=17.44 Aligned_cols=11 Identities=27% Similarity=0.633 Sum_probs=6.0
Q ss_pred Ccccccccccc
Q psy12166 29 PHSCDLCGKTY 39 (94)
Q Consensus 29 ~~~c~~c~~~f 39 (94)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 45566665543
No 133
>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=48.91 E-value=14 Score=15.00 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=5.1
Q ss_pred Ccccccccccc
Q psy12166 29 PHSCDLCGKTY 39 (94)
Q Consensus 29 ~~~c~~c~~~f 39 (94)
+-.|+.||...
T Consensus 17 ~irC~~CG~RI 27 (32)
T PF03604_consen 17 PIRCPECGHRI 27 (32)
T ss_dssp TSSBSSSS-SE
T ss_pred cEECCcCCCeE
Confidence 34555555443
No 134
>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=48.18 E-value=7.5 Score=17.55 Aligned_cols=13 Identities=31% Similarity=0.871 Sum_probs=7.0
Q ss_pred ecCccccccCCHH
Q psy12166 60 TCNVCGRTFSSIA 72 (94)
Q Consensus 60 ~c~~C~~~f~~~~ 72 (94)
.||+|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999998887653
No 135
>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=47.77 E-value=8.8 Score=16.69 Aligned_cols=15 Identities=40% Similarity=0.839 Sum_probs=10.8
Q ss_pred eecCccccccCCHHH
Q psy12166 59 VTCNVCGRTFSSIAN 73 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~ 73 (94)
-.|++|++.|.-..-
T Consensus 9 K~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 9 KICPVCGRPFTWRKK 23 (42)
T ss_pred CcCcccCCcchHHHH
Confidence 468889988876543
No 136
>KOG0717|consensus
Probab=47.56 E-value=14 Score=24.80 Aligned_cols=22 Identities=36% Similarity=0.754 Sum_probs=17.1
Q ss_pred eecCccccccCCHHHHHHHHHH
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
+.|.+|.++|.+.-.+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7788888888888888777543
No 137
>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=47.04 E-value=19 Score=16.52 Aligned_cols=10 Identities=20% Similarity=0.235 Sum_probs=4.5
Q ss_pred CCCCCccccc
Q psy12166 2 DCGWKKTAYE 11 (94)
Q Consensus 2 ~C~~~~~~~~ 11 (94)
+|..|+..+.
T Consensus 4 ~CP~CG~~ie 13 (54)
T TIGR01206 4 ECPDCGAEIE 13 (54)
T ss_pred CCCCCCCEEe
Confidence 4444444443
No 138
>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=46.81 E-value=7.3 Score=16.74 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=8.2
Q ss_pred CCeecCccccccCCH
Q psy12166 57 PSVTCNVCGRTFSSI 71 (94)
Q Consensus 57 ~~~~c~~C~~~f~~~ 71 (94)
.++.|..|+..|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 467888887776543
No 139
>KOG2071|consensus
Probab=46.44 E-value=16 Score=25.25 Aligned_cols=26 Identities=23% Similarity=0.581 Sum_probs=19.8
Q ss_pred CCCccccccccccCChHHHHhHHHhhc
Q psy12166 27 TKPHSCDLCGKTYTLAKHLWGHVKSAH 53 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~~~l~~H~~~~h 53 (94)
..|.+|..||.+|........|| ..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~m-d~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHM-DIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHh-hhh
Confidence 46788999999998877766666 444
No 140
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=45.93 E-value=7.5 Score=17.31 Aligned_cols=35 Identities=29% Similarity=0.551 Sum_probs=17.7
Q ss_pred ccccccccccCChHHHHhHHHhhcCC------CCCeecCcccc
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQG------HPSVTCNVCGR 66 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~------~~~~~c~~C~~ 66 (94)
|.|..|++.+.-...-..+ .+..+ ...|.|+.|+.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~--~i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPEN--GIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EEETTTSBEEETTTBBGGG--TB-TT--GGGS-TT-B-TTTSS
T ss_pred cCCCCCCEEEcCCcCCccc--CcCCCCCHHHCCCCCcCcCCCC
Confidence 7899999877644321111 11111 23588999974
No 141
>KOG1280|consensus
Probab=45.71 E-value=33 Score=22.31 Aligned_cols=33 Identities=24% Similarity=0.271 Sum_probs=26.1
Q ss_pred CCCeecCccccccCCHHHHHHHHHHhcCCCCce
Q psy12166 56 HPSVTCNVCGRTFSSIANLAEHKRSRHGITGFV 88 (94)
Q Consensus 56 ~~~~~c~~C~~~f~~~~~l~~h~~~~~~~k~~~ 88 (94)
...|.|++|+..--....+..|....+.+..+.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~ 109 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTS 109 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcc
Confidence 457999999988777888899988877666543
No 142
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=45.20 E-value=19 Score=15.03 Aligned_cols=7 Identities=29% Similarity=0.923 Sum_probs=2.9
Q ss_pred CeecCcc
Q psy12166 58 SVTCNVC 64 (94)
Q Consensus 58 ~~~c~~C 64 (94)
.|.|..|
T Consensus 29 ryrC~~C 35 (36)
T PF03811_consen 29 RYRCKDC 35 (36)
T ss_pred eEecCcC
Confidence 3444433
No 143
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=44.56 E-value=22 Score=16.42 Aligned_cols=14 Identities=29% Similarity=0.686 Sum_probs=6.4
Q ss_pred CCccccccccccCC
Q psy12166 28 KPHSCDLCGKTYTL 41 (94)
Q Consensus 28 ~~~~c~~c~~~f~~ 41 (94)
.|.....|+..|..
T Consensus 23 ~PV~s~~C~H~fek 36 (57)
T PF11789_consen 23 DPVKSKKCGHTFEK 36 (57)
T ss_dssp SEEEESSS--EEEH
T ss_pred CCcCcCCCCCeecH
Confidence 45555556666553
No 144
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=44.31 E-value=17 Score=19.29 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=18.4
Q ss_pred CCCCccccccCCCCCCCCcccCCCCCCccccccccccCCh
Q psy12166 3 CGWKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGKTYTLA 42 (94)
Q Consensus 3 C~~~~~~~~~~~~~~~~~~~~h~~~~~~~c~~c~~~f~~~ 42 (94)
|+.|...|-|+.. ..|-|+.|+..|...
T Consensus 5 CP~C~seytY~dg------------~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEYTYHDG------------TQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcceEecC------------CeeECcccccccccc
Confidence 6666655555322 358899999888754
No 145
>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=44.25 E-value=21 Score=14.63 Aligned_cols=21 Identities=33% Similarity=0.648 Sum_probs=10.1
Q ss_pred CeecCccccccCCHHHHHHHHH
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~ 79 (94)
.+.|+.|++...... +..|+.
T Consensus 4 ~~~C~nC~R~v~a~R-fA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAASR-FAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEGGG-HHHHHH
T ss_pred eEECCCCcCCcchhh-hHHHHH
Confidence 356666666544433 344543
No 146
>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=44.20 E-value=24 Score=19.40 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=20.4
Q ss_pred ccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCHHH
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIAN 73 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~~~ 73 (94)
..|+.||.+|-- |. ..|..|++||..|.....
T Consensus 10 r~Cp~cg~kFYD---Ln---------k~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 10 RICPNTGSKFYD---LN---------RRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccCCCcCccccc---cC---------CCCccCCCcCCccCcchh
Confidence 577888877653 11 136778888877766533
No 147
>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=44.13 E-value=29 Score=16.27 Aligned_cols=16 Identities=25% Similarity=0.430 Sum_probs=10.6
Q ss_pred CCCeecCccccccCCH
Q psy12166 56 HPSVTCNVCGRTFSSI 71 (94)
Q Consensus 56 ~~~~~c~~C~~~f~~~ 71 (94)
...+.|+.||......
T Consensus 44 ~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 44 GRVFTCPNCGFEMDRD 59 (69)
T ss_pred cceEEcCCCCCEECcH
Confidence 4467888888665543
No 148
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=43.49 E-value=7.5 Score=19.92 Aligned_cols=13 Identities=31% Similarity=0.813 Sum_probs=8.3
Q ss_pred CeecCccccccCC
Q psy12166 58 SVTCNVCGRTFSS 70 (94)
Q Consensus 58 ~~~c~~C~~~f~~ 70 (94)
.+.|..|++.|.-
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PRK03976 54 IWECRKCGAKFAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4677777765543
No 149
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=43.27 E-value=12 Score=20.62 Aligned_cols=15 Identities=33% Similarity=1.012 Sum_probs=11.9
Q ss_pred CccccccccccCChH
Q psy12166 29 PHSCDLCGKTYTLAK 43 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~ 43 (94)
|++|..||..|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 688999999987543
No 150
>PLN02294 cytochrome c oxidase subunit Vb
Probab=43.26 E-value=13 Score=21.43 Aligned_cols=21 Identities=19% Similarity=0.545 Sum_probs=15.5
Q ss_pred cccCCCCCCccccccccccCCh
Q psy12166 21 LFRFDRTKPHSCDLCGKTYTLA 42 (94)
Q Consensus 21 ~~~h~~~~~~~c~~c~~~f~~~ 42 (94)
++.+.+ +|.+|+.||..|..+
T Consensus 134 f~L~kG-kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 134 FWLEKG-KSFECPVCTQYFELE 154 (174)
T ss_pred EEecCC-CceeCCCCCCEEEEE
Confidence 455554 799999999888643
No 151
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=42.94 E-value=18 Score=23.52 Aligned_cols=27 Identities=19% Similarity=0.372 Sum_probs=20.7
Q ss_pred cCCCCCCccccccc-cccCChHHHHhHH
Q psy12166 23 RFDRTKPHSCDLCG-KTYTLAKHLWGHV 49 (94)
Q Consensus 23 ~h~~~~~~~c~~c~-~~f~~~~~l~~H~ 49 (94)
.|.-.+.|+|.+|| +.+--...+.+|.
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhh
Confidence 46667889999999 6777677777775
No 152
>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=42.04 E-value=4.1 Score=16.09 Aligned_cols=9 Identities=44% Similarity=0.966 Sum_probs=5.0
Q ss_pred ccccccccc
Q psy12166 31 SCDLCGKTY 39 (94)
Q Consensus 31 ~c~~c~~~f 39 (94)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455555555
No 153
>KOG3507|consensus
Probab=42.00 E-value=14 Score=17.33 Aligned_cols=9 Identities=33% Similarity=1.040 Sum_probs=6.2
Q ss_pred CeecCcccc
Q psy12166 58 SVTCNVCGR 66 (94)
Q Consensus 58 ~~~c~~C~~ 66 (94)
.++|..||.
T Consensus 37 ~irCReCG~ 45 (62)
T KOG3507|consen 37 VIRCRECGY 45 (62)
T ss_pred cEehhhcch
Confidence 567777774
No 154
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=41.84 E-value=7.1 Score=23.03 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=4.3
Q ss_pred cccccccc
Q psy12166 30 HSCDLCGK 37 (94)
Q Consensus 30 ~~c~~c~~ 37 (94)
-.|+.||.
T Consensus 15 ~~CPvCg~ 22 (201)
T COG1779 15 IDCPVCGG 22 (201)
T ss_pred ecCCcccc
Confidence 34555554
No 155
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=41.22 E-value=33 Score=14.60 Aligned_cols=8 Identities=50% Similarity=1.174 Sum_probs=4.0
Q ss_pred ecCccccc
Q psy12166 60 TCNVCGRT 67 (94)
Q Consensus 60 ~c~~C~~~ 67 (94)
.|+.||..
T Consensus 15 ~C~~CgM~ 22 (41)
T PF13878_consen 15 TCPTCGML 22 (41)
T ss_pred CCCCCCCE
Confidence 45555543
No 156
>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=40.05 E-value=33 Score=23.19 Aligned_cols=25 Identities=20% Similarity=0.436 Sum_probs=21.0
Q ss_pred eecCccccccCCHHHHHHHHHH-hcC
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRS-RHG 83 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~-~~~ 83 (94)
+.|+.|.+.|.....+..|+.. |.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 5689999999999999999875 544
No 157
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=39.84 E-value=15 Score=15.60 Aligned_cols=11 Identities=27% Similarity=0.757 Sum_probs=5.0
Q ss_pred Ccccccccccc
Q psy12166 29 PHSCDLCGKTY 39 (94)
Q Consensus 29 ~~~c~~c~~~f 39 (94)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 34454454433
No 158
>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=39.54 E-value=9.8 Score=22.45 Aligned_cols=25 Identities=20% Similarity=0.583 Sum_probs=0.0
Q ss_pred cCCCCCeecCcccc-ccCCHHHHHHH
Q psy12166 53 HQGHPSVTCNVCGR-TFSSIANLAEH 77 (94)
Q Consensus 53 h~~~~~~~c~~C~~-~f~~~~~l~~h 77 (94)
|.-.+.|.|.+||- ++..+..+..|
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp --------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHh
Confidence 44455677888773 34344444444
No 159
>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=39.11 E-value=24 Score=23.87 Aligned_cols=13 Identities=31% Similarity=0.933 Sum_probs=7.1
Q ss_pred CCCCCcccccccc
Q psy12166 25 DRTKPHSCDLCGK 37 (94)
Q Consensus 25 ~~~~~~~c~~c~~ 37 (94)
....|..|+.|+.
T Consensus 249 ~~~~~~~Cp~C~s 261 (505)
T TIGR00595 249 QEPIPKTCPQCGS 261 (505)
T ss_pred cCCCCCCCCCCCC
Confidence 3344566666654
No 160
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=38.62 E-value=14 Score=19.03 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=19.3
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCG 65 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~ 65 (94)
+|-.|..||+.|... .-.+|..|+.|.
T Consensus 57 ~Pa~CkkCGfef~~~-----------~ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDD-----------KIKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCcccccc-----------ccCCcccCCcch
Confidence 688999999887651 113477888885
No 161
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=38.54 E-value=22 Score=14.00 Aligned_cols=9 Identities=44% Similarity=1.158 Sum_probs=4.5
Q ss_pred ccccccccc
Q psy12166 30 HSCDLCGKT 38 (94)
Q Consensus 30 ~~c~~c~~~ 38 (94)
|.|..|+..
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 455555543
No 162
>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=38.15 E-value=7.7 Score=17.64 Aligned_cols=23 Identities=13% Similarity=0.401 Sum_probs=10.5
Q ss_pred CCCccccccccccCChHHHHhHH
Q psy12166 27 TKPHSCDLCGKTYTLAKHLWGHV 49 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~~~l~~H~ 49 (94)
...|+|+.|+..|-..=++-.|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTT
T ss_pred CCeEECCCCCCccccCcChhhhc
Confidence 35688888877776655544443
No 163
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=37.85 E-value=5 Score=20.05 Aligned_cols=40 Identities=23% Similarity=0.664 Sum_probs=13.6
Q ss_pred CCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCH
Q psy12166 27 TKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSI 71 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~ 71 (94)
.+.|.|+.|+..=+-.-.+ ..-.+.-...|..|+..|...
T Consensus 20 ~~~F~CPfC~~~~sV~v~i-----dkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKI-----DKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT--SS-EEEEE-----ETTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcCCCCCeEEEEE-----EccCCEEEEEecCCCCeEEEc
Confidence 3578899888332111111 001111236788888766543
No 164
>PRK10220 hypothetical protein; Provisional
Probab=36.42 E-value=33 Score=18.33 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=11.3
Q ss_pred CCccccccccccCChH
Q psy12166 28 KPHSCDLCGKTYTLAK 43 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~ 43 (94)
..|-|+.|+..|....
T Consensus 19 ~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 19 GMYICPECAHEWNDAE 34 (111)
T ss_pred CeEECCcccCcCCccc
Confidence 3578888888776543
No 165
>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=36.35 E-value=19 Score=19.13 Aligned_cols=26 Identities=15% Similarity=0.397 Sum_probs=17.1
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
-...|..|+..|..... .+.||.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEID-------------LYRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCCc-------------CccCcCCcC
Confidence 45788888877765321 256888873
No 166
>KOG1994|consensus
Probab=36.25 E-value=24 Score=21.47 Aligned_cols=22 Identities=27% Similarity=0.561 Sum_probs=18.6
Q ss_pred CCCeecCccccccCCHHHHHHH
Q psy12166 56 HPSVTCNVCGRTFSSIANLAEH 77 (94)
Q Consensus 56 ~~~~~c~~C~~~f~~~~~l~~h 77 (94)
.--|.|.+||..|.....|..|
T Consensus 237 ~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred ccceEEEEeccccCCHHHHHHh
Confidence 3458999999999999998776
No 167
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=36.17 E-value=38 Score=14.74 Aligned_cols=12 Identities=25% Similarity=0.567 Sum_probs=7.4
Q ss_pred CccccccccccC
Q psy12166 29 PHSCDLCGKTYT 40 (94)
Q Consensus 29 ~~~c~~c~~~f~ 40 (94)
.+.|+.||+.+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 566777775543
No 168
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=36.08 E-value=13 Score=17.05 Aligned_cols=15 Identities=27% Similarity=0.488 Sum_probs=10.0
Q ss_pred CCCCCccccccCCCC
Q psy12166 2 DCGWKKTAYEIGLGI 16 (94)
Q Consensus 2 ~C~~~~~~~~~~~~~ 16 (94)
-|.||+..|.....+
T Consensus 29 YC~~Cg~~Y~d~~dL 43 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDL 43 (55)
T ss_pred eeeeeCCccCCHHHH
Confidence 477888777765443
No 169
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.57 E-value=26 Score=18.78 Aligned_cols=17 Identities=6% Similarity=0.259 Sum_probs=12.8
Q ss_pred CCCeecCccccccCCHH
Q psy12166 56 HPSVTCNVCGRTFSSIA 72 (94)
Q Consensus 56 ~~~~~c~~C~~~f~~~~ 72 (94)
..|..|++||++|..+.
T Consensus 24 rdPiVsPytG~s~P~s~ 40 (129)
T COG4530 24 RDPIVSPYTGKSYPRSY 40 (129)
T ss_pred CCccccCcccccchHHH
Confidence 35788999999985544
No 170
>KOG2932|consensus
Probab=35.24 E-value=60 Score=20.92 Aligned_cols=28 Identities=36% Similarity=0.599 Sum_probs=21.5
Q ss_pred CCCeecCc---cccccCCHHHHHHHHHHhcC
Q psy12166 56 HPSVTCNV---CGRTFSSIANLAEHKRSRHG 83 (94)
Q Consensus 56 ~~~~~c~~---C~~~f~~~~~l~~h~~~~~~ 83 (94)
.-.|.|.. |.++|....+|+.|+--.++
T Consensus 142 g~iFmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 142 GGIFMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred cceEEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 34688865 88999999999988765444
No 171
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=34.95 E-value=32 Score=24.60 Aligned_cols=28 Identities=29% Similarity=0.795 Sum_probs=15.4
Q ss_pred ccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 32 CDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 32 c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
|+.|.+.+....+ |+.|. .+..|+.||.
T Consensus 154 C~~C~~EY~dP~n-----RRfHA--Qp~aCp~CGP 181 (750)
T COG0068 154 CPFCDKEYKDPLN-----RRFHA--QPIACPKCGP 181 (750)
T ss_pred CHHHHHHhcCccc-----ccccc--ccccCcccCC
Confidence 6666665555443 22333 2567777775
No 172
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=34.69 E-value=21 Score=18.97 Aligned_cols=14 Identities=14% Similarity=0.302 Sum_probs=10.0
Q ss_pred CCccccccccccCC
Q psy12166 28 KPHSCDLCGKTYTL 41 (94)
Q Consensus 28 ~~~~c~~c~~~f~~ 41 (94)
-...|..||..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 69 AQAWCWDCSQVVEI 82 (113)
T ss_pred cEEEcccCCCEEec
Confidence 45778888877664
No 173
>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=33.85 E-value=22 Score=19.75 Aligned_cols=21 Identities=29% Similarity=0.450 Sum_probs=15.8
Q ss_pred CCCccccccccccCChHHHHh
Q psy12166 27 TKPHSCDLCGKTYTLAKHLWG 47 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~~~l~~ 47 (94)
+.-+.|+.||+.|..-++..+
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CeEEECCCCCCEecccccHHH
Confidence 357889999999987665443
No 174
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.79 E-value=27 Score=18.40 Aligned_cols=14 Identities=36% Similarity=1.047 Sum_probs=10.9
Q ss_pred CccccccccccCCh
Q psy12166 29 PHSCDLCGKTYTLA 42 (94)
Q Consensus 29 ~~~c~~c~~~f~~~ 42 (94)
|++|..||..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 67888888888764
No 175
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=33.67 E-value=11 Score=22.07 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=7.9
Q ss_pred Ccccccccccc
Q psy12166 29 PHSCDLCGKTY 39 (94)
Q Consensus 29 ~~~c~~c~~~f 39 (94)
.+.|+.||+..
T Consensus 30 sf~C~~CGyr~ 40 (192)
T TIGR00310 30 STICEHCGYRS 40 (192)
T ss_pred EEECCCCCCcc
Confidence 57788888654
No 176
>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=33.50 E-value=9.7 Score=23.60 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=16.7
Q ss_pred CCCCeecCccccccCCHHHHHHHHHH
Q psy12166 55 GHPSVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 55 ~~~~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
..+++.|+.|+........|..-.++
T Consensus 206 k~k~~PCPKCg~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 206 KGKPIPCPKCGYETQETKDLSMSTRS 231 (314)
T ss_pred cCCCCCCCCCCCcccccccceeeeec
Confidence 34678888888766666555544443
No 177
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=32.88 E-value=26 Score=19.34 Aligned_cols=32 Identities=25% Similarity=0.611 Sum_probs=16.8
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCcccccc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTF 68 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f 68 (94)
.|.|..|+..+.. +. .+.....+.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~------~r--r~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VR--RSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------Ec--cccCcceEEcCCCCCEE
Confidence 5777777765432 11 12222457777776543
No 178
>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=32.48 E-value=15 Score=21.97 Aligned_cols=23 Identities=22% Similarity=0.491 Sum_probs=0.0
Q ss_pred eecCccccccCCHHHHHHHHHHhc
Q psy12166 59 VTCNVCGRTFSSIANLAEHKRSRH 82 (94)
Q Consensus 59 ~~c~~C~~~f~~~~~l~~h~~~~~ 82 (94)
..|++||...... .+..|+++..
T Consensus 169 ~~cPitGe~IP~~-e~~eHmRi~L 191 (229)
T PF12230_consen 169 IICPITGEMIPAD-EMDEHMRIEL 191 (229)
T ss_dssp ------------------------
T ss_pred ccccccccccccc-cccccccccc
Confidence 3455555433332 2344444443
No 179
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=31.58 E-value=59 Score=19.34 Aligned_cols=13 Identities=38% Similarity=0.958 Sum_probs=8.0
Q ss_pred CCCeecCcccccc
Q psy12166 56 HPSVTCNVCGRTF 68 (94)
Q Consensus 56 ~~~~~c~~C~~~f 68 (94)
+....|..||..+
T Consensus 28 ~~lvrC~eCG~V~ 40 (201)
T COG1326 28 EPLVRCEECGTVH 40 (201)
T ss_pred ceEEEccCCCcEe
Confidence 3456777777554
No 180
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.32 E-value=38 Score=19.70 Aligned_cols=32 Identities=22% Similarity=0.562 Sum_probs=20.0
Q ss_pred CCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccc
Q psy12166 26 RTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRT 67 (94)
Q Consensus 26 ~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~ 67 (94)
...-|.|+.|...++.... + .. .|.|+.||..
T Consensus 110 ~~~~y~C~~~~~r~sfdeA----~---~~---~F~Cp~Cg~~ 141 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEA----M---EL---GFTCPKCGED 141 (176)
T ss_pred cCCceeCCCCCCcccHHHH----H---Hh---CCCCCCCCch
Confidence 3456888777766664432 1 11 2889999864
No 181
>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=31.30 E-value=20 Score=14.33 Aligned_cols=7 Identities=43% Similarity=1.360 Sum_probs=3.2
Q ss_pred eecCccc
Q psy12166 59 VTCNVCG 65 (94)
Q Consensus 59 ~~c~~C~ 65 (94)
+.|+.|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 4444443
No 182
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=30.56 E-value=34 Score=15.83 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=11.5
Q ss_pred CCCCCccccccccccC
Q psy12166 25 DRTKPHSCDLCGKTYT 40 (94)
Q Consensus 25 ~~~~~~~c~~c~~~f~ 40 (94)
.+...|.|+.||..+-
T Consensus 10 ~~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTH 25 (55)
T ss_pred ccccCCcCCCCCCcCc
Confidence 3456799999987654
No 183
>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=29.98 E-value=17 Score=20.06 Aligned_cols=32 Identities=22% Similarity=0.606 Sum_probs=18.6
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCcccccc
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTF 68 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f 68 (94)
-.|.|..|+..+.... .+ ....+.|..|+..+
T Consensus 122 ~~~~C~~C~~~~~r~~-------~~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHR-------RS--KRKRYRCGRCGGPL 153 (157)
T ss_pred eEEEcCCCCCEeeeec-------cc--chhhEECCCCCCEE
Confidence 3577888876653322 12 23347888887554
No 184
>PRK14873 primosome assembly protein PriA; Provisional
Probab=29.63 E-value=37 Score=24.04 Aligned_cols=8 Identities=38% Similarity=1.041 Sum_probs=3.6
Q ss_pred Cccccccc
Q psy12166 29 PHSCDLCG 36 (94)
Q Consensus 29 ~~~c~~c~ 36 (94)
|+.|+.||
T Consensus 422 p~~Cp~Cg 429 (665)
T PRK14873 422 DWRCPRCG 429 (665)
T ss_pred CccCCCCc
Confidence 44444444
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=29.54 E-value=5.4 Score=16.91 Aligned_cols=12 Identities=42% Similarity=1.005 Sum_probs=5.7
Q ss_pred CCCCeecCcccc
Q psy12166 55 GHPSVTCNVCGR 66 (94)
Q Consensus 55 ~~~~~~c~~C~~ 66 (94)
+.+.+.|.+|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 344566666654
No 186
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=28.73 E-value=45 Score=14.97 Aligned_cols=13 Identities=23% Similarity=0.631 Sum_probs=7.0
Q ss_pred CccccccccccCC
Q psy12166 29 PHSCDLCGKTYTL 41 (94)
Q Consensus 29 ~~~c~~c~~~f~~ 41 (94)
-+.|+.||..|..
T Consensus 28 ~W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 28 WWKCPKCGHEWKA 40 (55)
T ss_pred EEECCCCCCeeEc
Confidence 3556666555543
No 187
>KOG4727|consensus
Probab=28.71 E-value=34 Score=19.87 Aligned_cols=23 Identities=17% Similarity=0.385 Sum_probs=19.9
Q ss_pred CCccccccccccCChHHHHhHHH
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVK 50 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~ 50 (94)
--|.|.+|.-.|....++..|++
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred CceeeeecceeehhhHHHHHHhc
Confidence 46999999999998888888874
No 188
>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=28.00 E-value=27 Score=14.47 Aligned_cols=12 Identities=33% Similarity=0.877 Sum_probs=8.0
Q ss_pred eecCccccccCC
Q psy12166 59 VTCNVCGRTFSS 70 (94)
Q Consensus 59 ~~c~~C~~~f~~ 70 (94)
..|+.||+.|..
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 457778876654
No 189
>KOG1008|consensus
Probab=27.76 E-value=47 Score=23.67 Aligned_cols=13 Identities=31% Similarity=0.820 Sum_probs=7.5
Q ss_pred CeecCccccccCC
Q psy12166 58 SVTCNVCGRTFSS 70 (94)
Q Consensus 58 ~~~c~~C~~~f~~ 70 (94)
.+.|+.|+..|..
T Consensus 766 ~~~cp~c~s~~pr 778 (783)
T KOG1008|consen 766 KNGCPHCGSSFPR 778 (783)
T ss_pred ccCCCCCCCCCcc
Confidence 3456666665543
No 190
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.45 E-value=52 Score=22.00 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=5.7
Q ss_pred CccccccccccC
Q psy12166 29 PHSCDLCGKTYT 40 (94)
Q Consensus 29 ~~~c~~c~~~f~ 40 (94)
-|+|+.||+.+.
T Consensus 367 g~rC~kCg~~~~ 378 (421)
T COG1571 367 GFRCKKCGTRAR 378 (421)
T ss_pred CcccccccccCC
Confidence 455555554443
No 191
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.45 E-value=45 Score=17.45 Aligned_cols=9 Identities=44% Similarity=1.014 Sum_probs=6.8
Q ss_pred CCccccccc
Q psy12166 28 KPHSCDLCG 36 (94)
Q Consensus 28 ~~~~c~~c~ 36 (94)
..|.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 467888887
No 192
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=27.35 E-value=72 Score=20.22 Aligned_cols=24 Identities=17% Similarity=0.292 Sum_probs=21.1
Q ss_pred CCCeecCccccccCCHHHHHHHHH
Q psy12166 56 HPSVTCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 56 ~~~~~c~~C~~~f~~~~~l~~h~~ 79 (94)
...|.|..|-+-|.....+..|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 457899999999999999999976
No 193
>KOG3214|consensus
Probab=26.86 E-value=31 Score=18.13 Aligned_cols=40 Identities=18% Similarity=0.505 Sum_probs=20.1
Q ss_pred CCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCCH
Q psy12166 27 TKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSI 71 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~~ 71 (94)
+..|.|+.|...-.-.-.|. ..+. .-...|.+|+.+|...
T Consensus 21 dt~FnClfcnHek~v~~~~D----k~~~-iG~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 21 DTQFNCLFCNHEKSVSCTLD----KKHN-IGKASCRICEESFQTT 60 (109)
T ss_pred heeeccCccccccceeeeeh----hhcC-cceeeeeehhhhhccc
Confidence 35677887764322111111 1111 1135688888877764
No 194
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.67 E-value=74 Score=14.33 Aligned_cols=31 Identities=29% Similarity=0.597 Sum_probs=17.1
Q ss_pred cccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 31 SCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 31 ~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
.|.-|+-..+... +. ....+.....|+.||+
T Consensus 24 ~C~gC~~~l~~~~-~~----~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQE-LN----EIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHH-HH----HHHcCCCeEECcCCCc
Confidence 5666665544322 21 2233356788888886
No 195
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=26.67 E-value=36 Score=20.77 Aligned_cols=21 Identities=14% Similarity=0.270 Sum_probs=15.3
Q ss_pred cccCCCCCCccccccccccCCh
Q psy12166 21 LFRFDRTKPHSCDLCGKTYTLA 42 (94)
Q Consensus 21 ~~~h~~~~~~~c~~c~~~f~~~ 42 (94)
+..+. .++.+|..||..|...
T Consensus 174 FwLrE-GkpqRCpECGqVFKLV 194 (268)
T PTZ00043 174 FRCRE-GFLYRCGECDQIFMLV 194 (268)
T ss_pred EEecC-CCCccCCCCCcEEEEE
Confidence 33444 4699999999988753
No 196
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.52 E-value=23 Score=19.15 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=9.8
Q ss_pred CCccccccccccCCh
Q psy12166 28 KPHSCDLCGKTYTLA 42 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~ 42 (94)
-...| .||..|...
T Consensus 69 ~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 69 VEIEC-ECGYEGVVD 82 (124)
T ss_pred eeEEe-eCcCccccc
Confidence 45788 888776643
No 197
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.24 E-value=32 Score=18.38 Aligned_cols=15 Identities=13% Similarity=0.428 Sum_probs=10.5
Q ss_pred CCccccccccccCCh
Q psy12166 28 KPHSCDLCGKTYTLA 42 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~ 42 (94)
-...|..||..|...
T Consensus 70 ~~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 70 VELECKDCSHVFKPN 84 (117)
T ss_pred CEEEhhhCCCccccC
Confidence 457788888776643
No 198
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=26.00 E-value=46 Score=20.65 Aligned_cols=13 Identities=15% Similarity=0.513 Sum_probs=9.0
Q ss_pred CccccccccccCC
Q psy12166 29 PHSCDLCGKTYTL 41 (94)
Q Consensus 29 ~~~c~~c~~~f~~ 41 (94)
.|.|+.|+..|.-
T Consensus 155 ef~C~~C~h~F~G 167 (278)
T PF15135_consen 155 EFHCPKCRHNFRG 167 (278)
T ss_pred eeecccccccchh
Confidence 4777777777653
No 199
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=25.98 E-value=33 Score=18.31 Aligned_cols=39 Identities=23% Similarity=0.507 Sum_probs=19.5
Q ss_pred CccccccccccCChHHHHhHHHhhcCCC-CCeecCccccccC
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGH-PSVTCNVCGRTFS 69 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~-~~~~c~~C~~~f~ 69 (94)
...|+.||..=.....+ +.+.....+ .=|.|..||..+.
T Consensus 72 ~~~CpkCg~~ea~y~~~--QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 72 KEKCPKCGNKEAYYWQL--QTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cccCCCCCCceeEEEee--ehhccCCCceEEEEecccCCEee
Confidence 35688887532222211 222222222 2378999987654
No 200
>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=25.84 E-value=27 Score=14.62 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=6.0
Q ss_pred CCcccccccccc
Q psy12166 28 KPHSCDLCGKTY 39 (94)
Q Consensus 28 ~~~~c~~c~~~f 39 (94)
+-|.|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 457888887653
No 201
>PLN02748 tRNA dimethylallyltransferase
Probab=25.72 E-value=62 Score=21.96 Aligned_cols=24 Identities=21% Similarity=0.607 Sum_probs=17.2
Q ss_pred CCeecCcccc-ccCCHHHHHHHHHH
Q psy12166 57 PSVTCNVCGR-TFSSIANLAEHKRS 80 (94)
Q Consensus 57 ~~~~c~~C~~-~f~~~~~l~~h~~~ 80 (94)
+.|.|.+|++ ++........|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4567888886 78777777777543
No 202
>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=25.21 E-value=28 Score=14.36 Aligned_cols=13 Identities=31% Similarity=0.905 Sum_probs=5.5
Q ss_pred eecCccccccCCH
Q psy12166 59 VTCNVCGRTFSSI 71 (94)
Q Consensus 59 ~~c~~C~~~f~~~ 71 (94)
-.|..|++.|..+
T Consensus 4 ~~C~eC~~~f~dS 16 (34)
T PF01286_consen 4 PKCDECGKPFMDS 16 (34)
T ss_dssp EE-TTT--EES-S
T ss_pred chHhHhCCHHHHH
Confidence 3566777766654
No 203
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.94 E-value=59 Score=13.59 Aligned_cols=23 Identities=22% Similarity=0.309 Sum_probs=17.3
Q ss_pred CCCccccccccccCChHHHHhHH
Q psy12166 27 TKPHSCDLCGKTYTLAKHLWGHV 49 (94)
Q Consensus 27 ~~~~~c~~c~~~f~~~~~l~~H~ 49 (94)
-.-+.|+.|+..|.....|.+-+
T Consensus 17 ~~id~C~~C~G~W~d~~el~~~~ 39 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELEKLL 39 (41)
T ss_pred EEEEECCCCCeEEccHHHHHHHH
Confidence 35678999999998887776543
No 204
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=24.65 E-value=62 Score=18.71 Aligned_cols=20 Identities=15% Similarity=0.376 Sum_probs=15.5
Q ss_pred CCccccccccccCChHHHHh
Q psy12166 28 KPHSCDLCGKTYTLAKHLWG 47 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~ 47 (94)
....|..||+.|.....+..
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVAL 132 (181)
T ss_pred ccCcCcccCCccCcHhHHHH
Confidence 57889999999987655443
No 205
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=24.64 E-value=40 Score=17.92 Aligned_cols=14 Identities=29% Similarity=0.546 Sum_probs=9.5
Q ss_pred CCccccccccccCC
Q psy12166 28 KPHSCDLCGKTYTL 41 (94)
Q Consensus 28 ~~~~c~~c~~~f~~ 41 (94)
-...|..|+..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (114)
T PRK03681 69 AECWCETCQQYVTL 82 (114)
T ss_pred cEEEcccCCCeeec
Confidence 45778888876654
No 206
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.58 E-value=20 Score=16.10 Aligned_cols=14 Identities=43% Similarity=0.716 Sum_probs=10.2
Q ss_pred eecCccccccCCHH
Q psy12166 59 VTCNVCGRTFSSIA 72 (94)
Q Consensus 59 ~~c~~C~~~f~~~~ 72 (94)
-.|++|++.|.-..
T Consensus 13 KICpvCqRPFsWRk 26 (54)
T COG4338 13 KICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhhcCchHHHH
Confidence 46888988887643
No 207
>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=24.49 E-value=31 Score=19.19 Aligned_cols=15 Identities=27% Similarity=0.667 Sum_probs=11.2
Q ss_pred CCCeecCccccccCC
Q psy12166 56 HPSVTCNVCGRTFSS 70 (94)
Q Consensus 56 ~~~~~c~~C~~~f~~ 70 (94)
.++.+|+.||..|.-
T Consensus 110 g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 110 GKPQRCPECGQVFKL 124 (136)
T ss_dssp TSEEEETTTEEEEEE
T ss_pred CCccCCCCCCeEEEE
Confidence 357889999877754
No 208
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.82 E-value=59 Score=20.12 Aligned_cols=17 Identities=24% Similarity=0.413 Sum_probs=10.6
Q ss_pred CCeecCccccccCCHHH
Q psy12166 57 PSVTCNVCGRTFSSIAN 73 (94)
Q Consensus 57 ~~~~c~~C~~~f~~~~~ 73 (94)
..+.|+.||..+...-+
T Consensus 321 r~~~C~~cg~~~~rD~n 337 (364)
T COG0675 321 RLFKCPRCGFVHDRDVN 337 (364)
T ss_pred eeEECCCCCCeehhhHH
Confidence 45778888865555433
No 209
>PRK12722 transcriptional activator FlhC; Provisional
Probab=23.34 E-value=85 Score=18.53 Aligned_cols=29 Identities=28% Similarity=0.673 Sum_probs=16.7
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
...|..||-.|.... +.....|.|+.|..
T Consensus 134 l~~C~~Cgg~fv~~~---------~e~~~~f~CplC~~ 162 (187)
T PRK12722 134 LSSCNCCGGHFVTHA---------HDPVGSFVCGLCQP 162 (187)
T ss_pred eccCCCCCCCeeccc---------cccCCCCcCCCCCC
Confidence 456777777666321 22234677877753
No 210
>PRK01343 zinc-binding protein; Provisional
Probab=23.19 E-value=64 Score=15.07 Aligned_cols=10 Identities=30% Similarity=0.830 Sum_probs=4.5
Q ss_pred eecCcccccc
Q psy12166 59 VTCNVCGRTF 68 (94)
Q Consensus 59 ~~c~~C~~~f 68 (94)
..|++|++.+
T Consensus 10 ~~CP~C~k~~ 19 (57)
T PRK01343 10 RPCPECGKPS 19 (57)
T ss_pred CcCCCCCCcC
Confidence 3455555433
No 211
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.14 E-value=42 Score=13.61 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=6.2
Q ss_pred CeecCcccccc
Q psy12166 58 SVTCNVCGRTF 68 (94)
Q Consensus 58 ~~~c~~C~~~f 68 (94)
-+.|..|+.+|
T Consensus 21 ~~~C~~Cg~~~ 31 (33)
T PF08792_consen 21 YEVCIFCGSSF 31 (33)
T ss_pred eEEcccCCcEe
Confidence 34566666554
No 212
>PRK05978 hypothetical protein; Provisional
Probab=23.02 E-value=30 Score=19.52 Aligned_cols=31 Identities=29% Similarity=0.750 Sum_probs=16.6
Q ss_pred ccccccccccCChHHHHhHHHhhcCCCCCeecCccccccCC
Q psy12166 30 HSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSS 70 (94)
Q Consensus 30 ~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~~ 70 (94)
-+|+.||+.=.....| ...-.|+.||..|..
T Consensus 34 grCP~CG~G~LF~g~L----------kv~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAFL----------KPVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCccccccc----------ccCCCccccCCcccc
Confidence 4678887653322111 113467888866554
No 213
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.90 E-value=33 Score=16.26 Aligned_cols=45 Identities=11% Similarity=0.118 Sum_probs=26.5
Q ss_pred CcccCCCCCCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccC
Q psy12166 20 PLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFS 69 (94)
Q Consensus 20 ~~~~h~~~~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~ 69 (94)
+..++.+..++-|+.-+-.+....-+ + .. ..+....|+.|+..|.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~---L-~m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVF---L-DM-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEE---E-Ec-CCCCcEecCccccEEE
Confidence 45566677888887665554433211 1 11 3344568999998775
No 214
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=22.75 E-value=13 Score=17.32 Aligned_cols=9 Identities=22% Similarity=0.774 Sum_probs=5.4
Q ss_pred CCeecCccc
Q psy12166 57 PSVTCNVCG 65 (94)
Q Consensus 57 ~~~~c~~C~ 65 (94)
..|.|..|.
T Consensus 30 ~tYmC~eC~ 38 (56)
T PF09963_consen 30 HTYMCDECK 38 (56)
T ss_pred cceeChhHH
Confidence 346666664
No 215
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=22.67 E-value=52 Score=14.94 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=8.6
Q ss_pred CCccccccccccC
Q psy12166 28 KPHSCDLCGKTYT 40 (94)
Q Consensus 28 ~~~~c~~c~~~f~ 40 (94)
+..+|+.||....
T Consensus 2 ~LkPCPFCG~~~~ 14 (61)
T PF14354_consen 2 ELKPCPFCGSADV 14 (61)
T ss_pred CCcCCCCCCCcce
Confidence 3467999975543
No 217
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=22.37 E-value=1.1e+02 Score=15.99 Aligned_cols=36 Identities=11% Similarity=0.208 Sum_probs=21.4
Q ss_pred CccccccccccCChHHHHhHHHhhcCCCCCeecCcccc
Q psy12166 29 PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGR 66 (94)
Q Consensus 29 ~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~ 66 (94)
.|.|+.-|..|..-..+...+ . .-..+.|.|.+.|+
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~-~-~y~~~vwtC~~TGk 38 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRM-I-LYNQRVWTCEITGK 38 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHH-H-HHhCCeeEEecCCC
Confidence 466666667777666555544 2 23345677777665
No 218
>PTZ00448 hypothetical protein; Provisional
Probab=21.29 E-value=90 Score=20.57 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=17.8
Q ss_pred CeecCccccccCCHHHHHHHHHH
Q psy12166 58 SVTCNVCGRTFSSIANLAEHKRS 80 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~h~~~ 80 (94)
.|.|..|+..|........|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57799999889877777777664
No 219
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.17 E-value=98 Score=22.03 Aligned_cols=17 Identities=29% Similarity=0.796 Sum_probs=10.2
Q ss_pred ccCCCCCCccccccccc
Q psy12166 22 FRFDRTKPHSCDLCGKT 38 (94)
Q Consensus 22 ~~h~~~~~~~c~~c~~~ 38 (94)
--+....|..|+.||..
T Consensus 414 Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 414 CGYQEPIPKACPECGST 430 (679)
T ss_pred CcCCCCCCCCCCCCcCC
Confidence 33344557778888653
No 220
>KOG4602|consensus
Probab=21.09 E-value=48 Score=20.66 Aligned_cols=14 Identities=36% Similarity=0.717 Sum_probs=9.2
Q ss_pred CCeecCccccccCC
Q psy12166 57 PSVTCNVCGRTFSS 70 (94)
Q Consensus 57 ~~~~c~~C~~~f~~ 70 (94)
+.|.|++||.+-..
T Consensus 267 R~YVCPiCGATgDn 280 (318)
T KOG4602|consen 267 RSYVCPICGATGDN 280 (318)
T ss_pred hhhcCccccccCCc
Confidence 45778888865444
No 221
>KOG2807|consensus
Probab=21.00 E-value=92 Score=20.27 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=12.4
Q ss_pred CeecCccccccCCHHHHHH
Q psy12166 58 SVTCNVCGRTFSSIANLAE 76 (94)
Q Consensus 58 ~~~c~~C~~~f~~~~~l~~ 76 (94)
|..|++|+-+.....+|.+
T Consensus 290 P~eCpiC~ltLVss~hLAR 308 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLAR 308 (378)
T ss_pred CccCCccceeEecchHHHH
Confidence 5667777766666666654
No 222
>KOG2231|consensus
Probab=20.98 E-value=1.2e+02 Score=21.79 Aligned_cols=19 Identities=32% Similarity=0.627 Sum_probs=7.9
Q ss_pred cCccccccCCHHHHHHHHH
Q psy12166 61 CNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 61 c~~C~~~f~~~~~l~~h~~ 79 (94)
|..|...|.....+..|++
T Consensus 185 C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLR 203 (669)
T ss_pred chhhhhhhccHHHHHHhhc
Confidence 3344444444444444433
No 223
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=20.85 E-value=44 Score=17.19 Aligned_cols=31 Identities=35% Similarity=0.830 Sum_probs=20.1
Q ss_pred CCccccccccccCChHHHHhHHHhhcCCCCCeecCccccccC
Q psy12166 28 KPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFS 69 (94)
Q Consensus 28 ~~~~c~~c~~~f~~~~~l~~H~~~~h~~~~~~~c~~C~~~f~ 69 (94)
..|.|+.||+.-. ++.-.+ .+.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~v---------kR~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSV---------KRVATG--IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEE---------EEEETT--EEEETTTTEEEE
T ss_pred CCCcCCCCCCcee---------EEeeeE--EeecCCCCCEEe
Confidence 4699999986532 133333 489999987654
No 224
>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=20.70 E-value=45 Score=14.85 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=3.3
Q ss_pred CCcccccccc
Q psy12166 28 KPHSCDLCGK 37 (94)
Q Consensus 28 ~~~~c~~c~~ 37 (94)
..|.|++|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 3478888864
No 225
>PF14369 zf-RING_3: zinc-finger
Probab=20.64 E-value=44 Score=13.71 Aligned_cols=10 Identities=20% Similarity=0.757 Sum_probs=8.2
Q ss_pred cccccccccC
Q psy12166 31 SCDLCGKTYT 40 (94)
Q Consensus 31 ~c~~c~~~f~ 40 (94)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999988875
No 226
>PRK04351 hypothetical protein; Provisional
Probab=20.44 E-value=53 Score=18.48 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=7.1
Q ss_pred CCeecCcccccc
Q psy12166 57 PSVTCNVCGRTF 68 (94)
Q Consensus 57 ~~~~c~~C~~~f 68 (94)
..|.|..|+..+
T Consensus 131 ~~yrCg~C~g~L 142 (149)
T PRK04351 131 KRYRCGKCRGKL 142 (149)
T ss_pred CcEEeCCCCcEe
Confidence 456676666544
No 227
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.24 E-value=86 Score=21.24 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=20.7
Q ss_pred CCeecCccccccCCHHHHHHHHH
Q psy12166 57 PSVTCNVCGRTFSSIANLAEHKR 79 (94)
Q Consensus 57 ~~~~c~~C~~~f~~~~~l~~h~~ 79 (94)
..|.|..|-+-|.....|..|+.
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHh
Confidence 46889999999999999999976
Done!