Query psy12265
Match_columns 71
No_of_seqs 106 out of 1117
Neff 11.4
Searched_HMMs 46136
Date Fri Aug 16 22:56:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12265.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12265hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.8E-22 3.9E-27 104.2 3.6 66 3-69 199-264 (279)
2 KOG2462|consensus 99.8 6.2E-22 1.3E-26 102.3 3.2 66 3-71 173-238 (279)
3 KOG3623|consensus 99.7 1.4E-18 3E-23 99.3 2.6 70 1-71 904-973 (1007)
4 KOG3576|consensus 99.6 2.7E-16 5.9E-21 79.1 1.2 67 2-69 128-194 (267)
5 KOG3623|consensus 99.6 4.7E-16 1E-20 89.3 1.8 70 1-71 250-332 (1007)
6 PHA00733 hypothetical protein 99.4 2E-13 4.4E-18 65.2 3.3 60 7-70 62-121 (128)
7 PHA02768 hypothetical protein; 99.4 7.2E-14 1.6E-18 57.3 1.0 45 19-66 5-49 (55)
8 KOG1074|consensus 99.4 9.9E-14 2.2E-18 80.7 0.7 69 2-71 616-691 (958)
9 KOG3576|consensus 99.3 9.8E-13 2.1E-17 66.5 2.0 70 1-70 155-234 (267)
10 PF13465 zf-H2C2_2: Zinc-finge 99.2 1E-11 2.2E-16 44.2 2.5 25 6-30 1-25 (26)
11 PF13465 zf-H2C2_2: Zinc-finge 99.2 6.8E-12 1.5E-16 44.7 0.6 26 34-60 1-26 (26)
12 KOG1074|consensus 99.2 1.9E-11 4.2E-16 71.5 2.6 51 20-71 880-930 (958)
13 KOG3608|consensus 99.1 5.2E-11 1.1E-15 64.5 3.2 70 1-70 189-259 (467)
14 KOG3608|consensus 99.1 1.9E-10 4.1E-15 62.4 4.5 63 6-70 252-314 (467)
15 PHA00732 hypothetical protein 99.0 1.7E-10 3.7E-15 51.0 1.6 46 19-70 1-46 (79)
16 PHA00616 hypothetical protein 98.9 7.2E-10 1.6E-14 43.6 1.1 35 19-54 1-35 (44)
17 PHA00733 hypothetical protein 98.7 4.8E-09 1E-13 50.3 1.2 65 6-70 27-95 (128)
18 KOG3993|consensus 98.7 1.5E-08 3.2E-13 56.3 2.3 66 4-70 280-378 (500)
19 COG5189 SFP1 Putative transcri 98.7 1E-08 2.2E-13 55.3 1.3 53 17-69 347-419 (423)
20 PF05605 zf-Di19: Drought indu 98.6 8.6E-08 1.9E-12 39.6 3.3 49 19-70 2-51 (54)
21 PLN03086 PRLI-interacting fact 98.6 1E-07 2.3E-12 54.9 4.3 50 5-59 466-515 (567)
22 PF00096 zf-C2H2: Zinc finger, 98.6 1.6E-08 3.5E-13 34.7 0.3 21 49-69 1-21 (23)
23 PHA00616 hypothetical protein 98.5 9.3E-08 2E-12 37.7 1.4 23 48-70 1-23 (44)
24 PLN03086 PRLI-interacting fact 98.4 5E-07 1.1E-11 52.2 3.8 62 4-68 489-560 (567)
25 PF13912 zf-C2H2_6: C2H2-type 98.4 1.1E-07 2.4E-12 33.8 0.6 21 49-69 2-22 (27)
26 PF00096 zf-C2H2: Zinc finger, 98.3 3.9E-07 8.5E-12 31.1 1.6 21 20-40 1-21 (23)
27 PHA02768 hypothetical protein; 98.3 3.4E-07 7.4E-12 37.7 1.4 34 1-36 15-48 (55)
28 PF12756 zf-C2H2_2: C2H2 type 98.3 2.6E-07 5.7E-12 42.1 1.1 23 48-70 50-72 (100)
29 PF13894 zf-C2H2_4: C2H2-type 98.3 2.8E-07 6.1E-12 31.5 0.8 22 49-70 1-22 (24)
30 PF13912 zf-C2H2_6: C2H2-type 98.1 3.9E-06 8.5E-11 29.7 1.9 24 19-43 1-24 (27)
31 PF13894 zf-C2H2_4: C2H2-type 98.1 5.8E-06 1.3E-10 28.1 2.2 22 20-41 1-22 (24)
32 PRK04860 hypothetical protein; 98.0 3.6E-06 7.8E-11 41.9 1.4 39 19-62 119-157 (160)
33 smart00355 ZnF_C2H2 zinc finge 97.9 3.9E-06 8.5E-11 28.9 0.9 20 50-69 2-21 (26)
34 PF12171 zf-C2H2_jaz: Zinc-fin 97.8 2.6E-06 5.5E-11 30.3 -0.5 22 49-70 2-23 (27)
35 PF12874 zf-met: Zinc-finger o 97.8 4.1E-06 9E-11 29.1 -0.1 19 21-39 2-20 (25)
36 smart00355 ZnF_C2H2 zinc finge 97.6 6.8E-05 1.5E-09 25.6 1.8 24 20-44 1-24 (26)
37 PF09237 GAGA: GAGA factor; I 97.6 2.2E-05 4.7E-10 31.8 0.5 26 45-70 21-46 (54)
38 PF09237 GAGA: GAGA factor; I 97.6 3.7E-05 8.1E-10 31.2 1.1 32 15-47 20-51 (54)
39 KOG3993|consensus 97.6 9.5E-06 2.1E-10 45.6 -0.8 50 20-70 268-317 (500)
40 PHA00732 hypothetical protein 97.6 2.9E-05 6.3E-10 34.4 0.7 22 48-69 1-22 (79)
41 PF13913 zf-C2HC_2: zinc-finge 97.5 3.2E-05 7E-10 27.0 0.6 20 49-69 3-22 (25)
42 PF12874 zf-met: Zinc-finger o 97.3 0.00019 4E-09 24.7 1.6 22 49-70 1-22 (25)
43 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00016 3.5E-09 24.7 0.6 21 49-70 1-21 (24)
44 smart00451 ZnF_U1 U1-like zinc 97.0 0.00022 4.9E-09 26.5 0.5 20 20-39 4-23 (35)
45 PRK04860 hypothetical protein; 96.5 0.0025 5.4E-08 31.9 1.9 29 5-33 129-157 (160)
46 COG4049 Uncharacterized protei 96.3 0.004 8.6E-08 25.8 1.7 26 43-68 12-37 (65)
47 cd00350 rubredoxin_like Rubred 96.0 0.0043 9.3E-08 22.9 1.0 24 20-56 2-25 (33)
48 KOG1146|consensus 95.9 0.004 8.7E-08 39.9 1.0 56 14-69 460-539 (1406)
49 COG5048 FOG: Zn-finger [Genera 95.5 0.0024 5.2E-08 35.5 -0.6 53 18-70 288-345 (467)
50 KOG2893|consensus 95.4 0.0049 1.1E-07 32.9 0.2 42 21-67 12-53 (341)
51 TIGR00373 conserved hypothetic 95.3 0.022 4.8E-07 28.5 2.4 33 15-57 105-137 (158)
52 PF09538 FYDLN_acid: Protein o 95.3 0.0067 1.4E-07 28.6 0.5 32 18-61 8-39 (108)
53 COG1592 Rubrerythrin [Energy p 95.1 0.011 2.5E-07 29.8 1.0 25 18-56 133-157 (166)
54 smart00531 TFIIE Transcription 95.1 0.049 1.1E-06 26.9 3.3 38 16-58 96-133 (147)
55 PF13719 zinc_ribbon_5: zinc-r 94.7 0.022 4.7E-07 21.6 1.1 34 20-59 3-36 (37)
56 PRK06266 transcription initiat 94.7 0.037 8E-07 28.3 2.2 32 16-57 114-145 (178)
57 PF12756 zf-C2H2_2: C2H2 type 94.6 0.041 8.9E-07 24.8 2.1 23 19-41 50-72 (100)
58 TIGR02098 MJ0042_CXXC MJ0042 f 94.4 0.027 5.8E-07 21.3 1.1 34 20-59 3-36 (38)
59 PF13717 zinc_ribbon_4: zinc-r 94.2 0.04 8.7E-07 20.8 1.3 33 20-58 3-35 (36)
60 KOG2186|consensus 94.0 0.036 7.8E-07 29.9 1.3 38 20-60 4-41 (276)
61 PF09986 DUF2225: Uncharacteri 93.5 0.016 3.5E-07 30.4 -0.4 44 17-60 3-60 (214)
62 COG2888 Predicted Zn-ribbon RN 93.2 0.1 2.2E-06 21.9 1.8 32 19-56 27-58 (61)
63 KOG1146|consensus 93.2 0.058 1.3E-06 35.1 1.5 54 16-70 1281-1350(1406)
64 COG5189 SFP1 Putative transcri 93.0 0.028 6.1E-07 31.3 0.1 24 16-39 395-418 (423)
65 cd00729 rubredoxin_SM Rubredox 92.7 0.076 1.6E-06 19.7 1.0 25 19-56 2-26 (34)
66 PRK00398 rpoP DNA-directed RNA 92.7 0.11 2.4E-06 20.5 1.6 31 18-59 2-32 (46)
67 TIGR02300 FYDLN_acid conserved 92.5 0.054 1.2E-06 26.2 0.6 32 18-61 8-39 (129)
68 smart00659 RPOLCX RNA polymera 92.3 0.12 2.7E-06 20.4 1.4 27 19-57 2-28 (44)
69 KOG2593|consensus 92.2 0.16 3.5E-06 29.4 2.3 38 15-56 124-161 (436)
70 PF09723 Zn-ribbon_8: Zinc rib 92.1 0.066 1.4E-06 20.8 0.5 29 20-56 6-34 (42)
71 KOG2893|consensus 91.6 0.062 1.3E-06 28.9 0.3 25 46-71 9-33 (341)
72 KOG3408|consensus 91.6 0.22 4.7E-06 24.0 2.0 24 48-71 57-80 (129)
73 PRK00464 nrdR transcriptional 91.2 0.036 7.7E-07 27.8 -0.8 14 48-61 28-41 (154)
74 KOG2785|consensus 91.2 0.23 5.1E-06 28.4 2.2 24 47-70 67-90 (390)
75 PF07754 DUF1610: Domain of un 91.0 0.072 1.6E-06 18.3 0.1 11 46-56 14-24 (24)
76 PF02892 zf-BED: BED zinc fing 90.9 0.14 3.1E-06 19.9 0.9 20 49-68 17-40 (45)
77 KOG4167|consensus 90.8 0.11 2.3E-06 32.2 0.7 24 48-71 792-815 (907)
78 PF15269 zf-C2H2_7: Zinc-finge 90.7 0.12 2.6E-06 20.5 0.6 21 49-69 21-41 (54)
79 smart00734 ZnF_Rad18 Rad18-lik 90.7 0.15 3.2E-06 17.8 0.8 18 50-68 3-20 (26)
80 PF04959 ARS2: Arsenite-resist 90.5 0.068 1.5E-06 28.2 -0.2 25 46-70 75-99 (214)
81 TIGR02605 CxxC_CxxC_SSSS putat 90.4 0.072 1.6E-06 21.5 -0.1 29 20-56 6-34 (52)
82 COG5048 FOG: Zn-finger [Genera 90.4 0.057 1.2E-06 30.1 -0.6 49 3-52 301-355 (467)
83 PF13451 zf-trcl: Probable zin 90.1 0.62 1.3E-05 18.9 2.4 41 17-57 2-42 (49)
84 COG1996 RPC10 DNA-directed RNA 90.0 0.19 4.1E-06 20.4 0.9 29 18-57 5-33 (49)
85 KOG2482|consensus 89.5 0.14 3.1E-06 29.0 0.5 67 5-71 129-218 (423)
86 PRK14890 putative Zn-ribbon RN 88.2 0.52 1.1E-05 19.9 1.6 32 19-56 25-56 (59)
87 PF05191 ADK_lid: Adenylate ki 87.9 0.14 3.1E-06 19.3 -0.1 32 20-60 2-33 (36)
88 PF02176 zf-TRAF: TRAF-type zi 87.1 1.3 2.9E-05 18.1 2.6 44 16-60 6-54 (60)
89 PF10571 UPF0547: Uncharacteri 86.9 0.14 3.1E-06 17.9 -0.3 10 50-59 16-25 (26)
90 PHA00626 hypothetical protein 86.6 0.26 5.7E-06 20.5 0.3 17 46-62 21-37 (59)
91 PF03604 DNA_RNApol_7kD: DNA d 86.2 0.59 1.3E-05 17.2 1.1 27 20-58 1-27 (32)
92 PF10013 DUF2256: Uncharacteri 85.6 0.33 7.1E-06 19.0 0.3 16 50-65 10-25 (42)
93 smart00614 ZnF_BED BED zinc fi 85.2 1.2 2.5E-05 17.8 1.9 22 19-40 18-44 (50)
94 PRK03824 hypA hydrogenase nick 85.0 0.36 7.7E-06 23.7 0.4 15 18-32 69-83 (135)
95 PF04780 DUF629: Protein of un 84.7 0.91 2E-05 26.9 1.9 29 18-46 56-84 (466)
96 smart00834 CxxC_CXXC_SSSS Puta 84.2 0.24 5.3E-06 18.7 -0.3 11 49-59 6-16 (41)
97 PF04959 ARS2: Arsenite-resist 84.0 0.93 2E-05 24.1 1.6 29 16-44 74-102 (214)
98 PF12907 zf-met2: Zinc-binding 83.9 0.28 6.1E-06 19.0 -0.2 27 20-46 2-31 (40)
99 PF07282 OrfB_Zn_ribbon: Putat 83.8 0.99 2.2E-05 19.2 1.5 24 45-68 43-66 (69)
100 PF09963 DUF2197: Uncharacteri 83.4 1.9 4E-05 18.0 2.1 42 20-62 3-45 (56)
101 COG1675 TFA1 Transcription ini 83.3 1.9 4.2E-05 22.3 2.6 34 14-57 108-141 (176)
102 COG3364 Zn-ribbon containing p 83.0 0.92 2E-05 21.3 1.3 15 18-32 1-15 (112)
103 PLN02748 tRNA dimethylallyltra 83.0 0.57 1.2E-05 27.7 0.7 25 47-71 417-442 (468)
104 PF07975 C1_4: TFIIH C1-like d 82.9 0.55 1.2E-05 19.2 0.5 21 48-68 21-41 (51)
105 COG4530 Uncharacterized protei 82.4 0.72 1.6E-05 22.0 0.8 13 47-59 25-37 (129)
106 COG3091 SprT Zn-dependent meta 82.2 0.61 1.3E-05 23.5 0.6 35 17-57 115-149 (156)
107 COG4338 Uncharacterized protei 81.7 0.56 1.2E-05 18.9 0.3 16 50-65 14-29 (54)
108 COG5236 Uncharacterized conser 81.6 1.7 3.7E-05 25.0 2.2 47 21-69 222-272 (493)
109 KOG2231|consensus 81.3 5 0.00011 25.2 4.1 19 51-69 185-203 (669)
110 smart00154 ZnF_AN1 AN1-like Zi 79.8 0.62 1.3E-05 17.8 0.1 12 48-59 12-23 (39)
111 COG3357 Predicted transcriptio 79.0 1.5 3.2E-05 20.2 1.1 28 18-56 57-84 (97)
112 KOG0717|consensus 78.9 0.75 1.6E-05 27.3 0.3 22 49-70 293-314 (508)
113 TIGR00100 hypA hydrogenase nic 78.6 1.1 2.3E-05 21.4 0.7 24 20-56 71-94 (115)
114 PF04423 Rad50_zn_hook: Rad50 77.0 0.71 1.5E-05 18.8 -0.1 12 50-61 22-33 (54)
115 PF01428 zf-AN1: AN1-like Zinc 76.9 0.6 1.3E-05 18.1 -0.3 13 47-59 12-24 (43)
116 KOG2231|consensus 75.4 2.5 5.5E-05 26.3 1.8 45 20-69 183-233 (669)
117 COG2331 Uncharacterized protei 74.9 2.7 5.9E-05 18.7 1.4 32 20-59 13-44 (82)
118 KOG4173|consensus 74.7 2.5 5.4E-05 22.6 1.4 19 21-39 108-126 (253)
119 PF12013 DUF3505: Protein of u 74.6 3.9 8.4E-05 19.1 2.0 22 20-41 81-106 (109)
120 PRK12380 hydrogenase nickel in 74.1 1.8 3.8E-05 20.6 0.8 24 20-56 71-94 (113)
121 PLN02294 cytochrome c oxidase 74.0 0.98 2.1E-05 23.2 -0.1 16 46-61 139-154 (174)
122 KOG2785|consensus 73.8 4.7 0.0001 23.5 2.5 54 17-70 164-242 (390)
123 KOG1842|consensus 73.4 2.6 5.6E-05 25.1 1.4 23 47-69 14-36 (505)
124 KOG3507|consensus 73.3 3.8 8.3E-05 17.3 1.6 32 18-61 19-50 (62)
125 COG3677 Transposase and inacti 73.3 0.9 1.9E-05 22.2 -0.3 36 20-61 31-66 (129)
126 PF14353 CpXC: CpXC protein 73.2 0.35 7.7E-06 23.2 -1.7 18 47-64 37-54 (128)
127 COG1326 Uncharacterized archae 72.5 5 0.00011 21.2 2.2 36 19-59 6-41 (201)
128 PF08790 zf-LYAR: LYAR-type C2 72.2 1.3 2.8E-05 15.8 0.1 18 20-38 1-18 (28)
129 PF08274 PhnA_Zn_Ribbon: PhnA 72.1 1.8 4E-05 15.6 0.5 10 47-56 18-27 (30)
130 cd00924 Cyt_c_Oxidase_Vb Cytoc 71.9 1.1 2.3E-05 20.9 -0.2 18 42-60 74-91 (97)
131 PRK09678 DNA-binding transcrip 71.5 0.85 1.9E-05 20.0 -0.5 15 46-60 25-41 (72)
132 PF07295 DUF1451: Protein of u 71.3 2.4 5.2E-05 21.2 0.9 28 19-57 112-139 (146)
133 PRK11823 DNA repair protein Ra 70.4 3.1 6.7E-05 24.5 1.3 11 18-28 6-16 (446)
134 COG4306 Uncharacterized protei 70.4 1.4 3E-05 21.6 -0.0 49 12-60 31-80 (160)
135 TIGR00416 sms DNA repair prote 69.6 3.3 7.2E-05 24.5 1.3 10 19-28 7-16 (454)
136 PF10276 zf-CHCC: Zinc-finger 69.2 0.91 2E-05 17.6 -0.6 12 47-58 28-39 (40)
137 KOG1280|consensus 68.6 6.2 0.00013 22.8 2.2 38 18-55 78-116 (381)
138 PRK00564 hypA hydrogenase nick 68.5 2.2 4.8E-05 20.4 0.5 11 20-30 72-82 (117)
139 PRK03681 hypA hydrogenase nick 68.3 2 4.3E-05 20.5 0.2 25 20-56 71-95 (114)
140 COG1571 Predicted DNA-binding 68.3 2.6 5.7E-05 24.8 0.7 29 21-61 352-380 (421)
141 PF05443 ROS_MUCR: ROS/MUCR tr 67.4 2.8 6E-05 20.7 0.7 18 49-69 73-90 (132)
142 PLN03238 probable histone acet 67.2 4.2 9.2E-05 22.8 1.4 24 46-69 46-69 (290)
143 KOG0782|consensus 66.8 2.8 6E-05 26.0 0.7 49 6-61 240-289 (1004)
144 KOG2807|consensus 66.4 8 0.00017 22.3 2.3 22 48-69 345-366 (378)
145 COG0675 Transposase and inacti 65.6 3.7 8.1E-05 22.6 1.0 19 46-64 320-338 (364)
146 KOG2636|consensus 65.2 3.6 7.7E-05 24.5 0.9 26 42-67 395-421 (497)
147 PLN00104 MYST -like histone ac 64.5 5.9 0.00013 23.7 1.7 24 46-69 196-219 (450)
148 PTZ00064 histone acetyltransfe 63.7 6 0.00013 24.1 1.6 24 46-69 278-301 (552)
149 PF09845 DUF2072: Zn-ribbon co 63.5 3.8 8.1E-05 20.2 0.7 15 19-33 1-15 (131)
150 PLN03239 histone acetyltransfe 63.4 6.2 0.00014 22.8 1.6 24 46-69 104-127 (351)
151 PF01155 HypA: Hydrogenase exp 63.1 3 6.5E-05 19.8 0.3 25 20-57 71-95 (113)
152 PF10537 WAC_Acf1_DNA_bd: ATP- 62.8 6.7 0.00014 18.4 1.4 10 18-27 29-38 (102)
153 COG1773 Rubredoxin [Energy pro 62.7 1.9 4E-05 18.0 -0.4 9 49-57 4-12 (55)
154 PF09416 UPF1_Zn_bind: RNA hel 62.3 14 0.00031 18.8 2.6 43 15-57 10-69 (152)
155 PRK05978 hypothetical protein; 62.3 1.7 3.7E-05 21.8 -0.6 32 20-61 34-65 (148)
156 PF08209 Sgf11: Sgf11 (transcr 62.2 1.6 3.5E-05 16.2 -0.5 12 48-59 4-15 (33)
157 KOG1994|consensus 62.0 3.1 6.8E-05 22.5 0.3 24 44-67 235-258 (268)
158 KOG2747|consensus 62.0 6.9 0.00015 23.0 1.6 24 46-69 156-179 (396)
159 KOG0978|consensus 61.9 1.7 3.7E-05 27.1 -0.7 20 49-68 679-698 (698)
160 PF06397 Desulfoferrod_N: Desu 61.8 4.1 8.8E-05 15.4 0.5 11 47-57 5-15 (36)
161 TIGR00622 ssl1 transcription f 61.7 4.5 9.7E-05 19.4 0.8 24 47-70 80-103 (112)
162 PF04810 zf-Sec23_Sec24: Sec23 61.6 1.8 3.9E-05 16.5 -0.5 15 43-57 19-33 (40)
163 KOG3362|consensus 61.4 1.6 3.5E-05 21.8 -0.7 24 48-71 129-152 (156)
164 PF03811 Zn_Tnp_IS1: InsA N-te 61.2 3.1 6.6E-05 15.7 0.1 30 20-54 6-35 (36)
165 PF04606 Ogr_Delta: Ogr/Delta- 61.1 1.5 3.2E-05 17.4 -0.8 16 45-60 22-39 (47)
166 PTZ00448 hypothetical protein; 60.0 4.9 0.00011 23.3 0.8 23 48-70 314-336 (373)
167 KOG2907|consensus 59.8 3.9 8.5E-05 19.6 0.4 41 19-61 74-115 (116)
168 PRK00762 hypA hydrogenase nick 59.5 3.8 8.1E-05 19.9 0.3 30 20-56 71-100 (124)
169 PF02748 PyrI_C: Aspartate car 59.2 4.2 9E-05 16.6 0.4 17 45-61 32-48 (52)
170 COG5112 UFD2 U1-like Zn-finger 58.7 15 0.00032 17.6 2.1 21 49-69 56-76 (126)
171 PF14255 Cys_rich_CPXG: Cystei 58.5 2.1 4.6E-05 17.5 -0.5 10 50-59 2-11 (52)
172 PF12230 PRP21_like_P: Pre-mRN 58.4 3.3 7.1E-05 22.1 0.0 24 46-70 166-189 (229)
173 PTZ00043 cytochrome c oxidase 56.7 3.1 6.6E-05 22.6 -0.3 15 46-60 179-193 (268)
174 cd01121 Sms Sms (bacterial rad 56.3 7.2 0.00016 22.6 1.1 9 19-27 14-22 (372)
175 PF01194 RNA_pol_N: RNA polyme 55.2 4.3 9.2E-05 17.2 0.1 14 48-61 4-17 (60)
176 COG1655 Uncharacterized protei 55.1 4.5 9.8E-05 22.0 0.2 17 46-62 17-33 (267)
177 TIGR01206 lysW lysine biosynth 55.0 2.5 5.4E-05 17.5 -0.6 11 49-59 3-13 (54)
178 TIGR00686 phnA alkylphosphonat 54.9 6.6 0.00014 18.7 0.7 12 48-59 19-30 (109)
179 smart00440 ZnF_C2C2 C2C2 Zinc 54.9 1.2 2.5E-05 17.1 -1.5 10 49-58 29-38 (40)
180 PF13824 zf-Mss51: Zinc-finger 54.8 5.8 0.00013 16.5 0.5 14 44-57 10-23 (55)
181 smart00731 SprT SprT homologue 54.7 6.7 0.00014 19.4 0.7 32 19-58 112-143 (146)
182 COG5151 SSL1 RNA polymerase II 54.7 8.4 0.00018 22.1 1.2 46 22-70 365-410 (421)
183 PF11931 DUF3449: Domain of un 54.5 4.1 8.9E-05 21.5 0.0 14 42-55 95-108 (196)
184 COG5188 PRP9 Splicing factor 3 54.5 8.4 0.00018 22.5 1.2 14 42-55 368-381 (470)
185 PF01844 HNH: HNH endonuclease 54.0 1.6 3.5E-05 16.8 -1.2 7 52-58 2-8 (47)
186 PF13878 zf-C2H2_3: zinc-finge 53.8 15 0.00032 14.1 1.6 22 19-40 13-36 (41)
187 PF08271 TF_Zn_Ribbon: TFIIB z 53.4 5.1 0.00011 15.4 0.2 8 49-56 1-8 (43)
188 PRK10220 hypothetical protein; 52.9 7.9 0.00017 18.5 0.8 12 48-59 20-31 (111)
189 PRK05452 anaerobic nitric oxid 52.9 6.2 0.00013 23.6 0.5 38 16-56 422-466 (479)
190 PF11672 DUF3268: Protein of u 52.8 8.2 0.00018 18.2 0.8 11 18-28 1-11 (102)
191 PF01215 COX5B: Cytochrome c o 52.8 3.2 6.8E-05 20.6 -0.5 17 43-60 108-124 (136)
192 COG5319 Uncharacterized protei 52.4 14 0.0003 18.3 1.6 26 27-57 16-41 (142)
193 PRK11788 tetratricopeptide rep 52.1 28 0.00061 19.6 3.0 7 20-26 355-361 (389)
194 PF05180 zf-DNL: DNL zinc fing 51.4 3.4 7.4E-05 17.9 -0.5 34 19-56 4-37 (66)
195 PRK08222 hydrogenase 4 subunit 51.2 7.3 0.00016 20.1 0.6 19 47-65 113-131 (181)
196 COG1997 RPL43A Ribosomal prote 50.5 4.7 0.0001 18.5 -0.1 33 17-60 33-65 (89)
197 COG5027 SAS2 Histone acetyltra 50.4 13 0.00029 21.6 1.5 24 46-69 156-179 (395)
198 TIGR00627 tfb4 transcription f 50.2 8.5 0.00018 21.5 0.8 7 50-56 271-277 (279)
199 KOG2071|consensus 50.1 7.5 0.00016 24.0 0.6 24 46-69 416-439 (579)
200 COG4640 Predicted membrane pro 50.0 8.8 0.00019 22.7 0.8 18 19-36 15-32 (465)
201 PF13240 zinc_ribbon_2: zinc-r 49.8 3.5 7.5E-05 13.8 -0.5 6 51-56 16-21 (23)
202 PF01927 Mut7-C: Mut7-C RNAse 49.6 4.6 0.0001 20.0 -0.3 39 20-58 92-134 (147)
203 COG4391 Uncharacterized protei 49.4 7 0.00015 16.7 0.3 43 12-59 17-59 (62)
204 PF06170 DUF983: Protein of un 47.8 4.9 0.00011 18.3 -0.3 11 50-60 10-20 (86)
205 PRK12722 transcriptional activ 47.4 14 0.0003 19.5 1.2 28 20-56 135-162 (187)
206 PF10263 SprT-like: SprT-like 47.2 4.4 9.5E-05 20.0 -0.6 31 19-58 123-153 (157)
207 PHA02942 putative transposase; 47.2 9.9 0.00021 22.1 0.7 15 46-60 340-354 (383)
208 PF06676 DUF1178: Protein of u 46.7 21 0.00045 18.1 1.7 9 48-56 32-40 (148)
209 PF02146 SIR2: Sir2 family; I 46.7 24 0.00052 17.9 2.0 33 19-56 105-137 (178)
210 PRK12860 transcriptional activ 46.3 15 0.00032 19.4 1.2 27 20-55 135-161 (189)
211 PRK12387 formate hydrogenlyase 46.2 10 0.00022 19.5 0.6 18 47-64 113-130 (180)
212 COG5432 RAD18 RING-finger-cont 46.0 9.5 0.00021 21.7 0.5 27 24-57 42-68 (391)
213 COG1779 C4-type Zn-finger prot 46.0 3.7 8.1E-05 21.7 -0.9 40 18-60 13-55 (201)
214 PRK04016 DNA-directed RNA poly 45.8 8.3 0.00018 16.5 0.3 13 48-60 4-16 (62)
215 PF10083 DUF2321: Uncharacteri 45.6 2.1 4.6E-05 21.7 -1.7 15 46-60 66-80 (158)
216 PF02891 zf-MIZ: MIZ/SP-RING z 45.5 13 0.00029 14.9 0.8 8 49-56 42-49 (50)
217 PF05129 Elf1: Transcription e 45.5 9.6 0.00021 17.1 0.4 12 45-56 19-30 (81)
218 PF14690 zf-ISL3: zinc-finger 45.4 8.3 0.00018 14.8 0.2 9 48-56 2-10 (47)
219 PF01286 XPA_N: XPA protein N- 45.3 9.8 0.00021 14.2 0.4 12 20-31 4-15 (34)
220 PF11789 zf-Nse: Zinc-finger o 45.0 9.3 0.0002 15.9 0.3 20 46-65 22-41 (57)
221 KOG3352|consensus 44.8 5.5 0.00012 20.2 -0.4 14 47-60 132-145 (153)
222 PF10058 DUF2296: Predicted in 44.6 9.6 0.00021 15.7 0.4 11 46-56 42-52 (54)
223 PF13821 DUF4187: Domain of un 44.5 7.4 0.00016 16.1 0.0 21 46-66 25-45 (55)
224 PF05741 zf-nanos: Nanos RNA b 44.4 9.1 0.0002 15.9 0.3 11 47-57 32-42 (55)
225 PF00301 Rubredoxin: Rubredoxi 44.1 12 0.00027 14.9 0.6 35 20-56 2-42 (47)
226 COG0068 HypF Hydrogenase matur 43.9 5.9 0.00013 25.1 -0.4 14 21-34 125-138 (750)
227 PF13248 zf-ribbon_3: zinc-rib 43.6 5.5 0.00012 13.6 -0.4 6 51-56 19-24 (26)
228 COG1198 PriA Primosomal protei 43.5 17 0.00036 23.3 1.3 12 46-57 473-484 (730)
229 smart00586 ZnF_DBF Zinc finger 43.5 24 0.00052 14.3 1.4 20 17-39 3-22 (49)
230 TIGR00319 desulf_FeS4 desulfof 43.3 11 0.00023 13.7 0.4 10 48-57 7-16 (34)
231 PHA02998 RNA polymerase subuni 42.9 3.8 8.3E-05 21.4 -1.1 37 18-59 142-182 (195)
232 cd00974 DSRD Desulforedoxin (D 42.9 11 0.00023 13.7 0.3 9 48-56 4-12 (34)
233 KOG2857|consensus 42.8 8.3 0.00018 19.4 0.0 21 48-68 17-37 (157)
234 PF11023 DUF2614: Protein of u 42.3 11 0.00023 18.2 0.3 15 44-58 65-79 (114)
235 cd00730 rubredoxin Rubredoxin; 42.2 12 0.00026 15.2 0.4 34 20-56 2-42 (50)
236 COG4888 Uncharacterized Zn rib 42.1 10 0.00022 17.9 0.2 12 46-57 20-31 (104)
237 COG1656 Uncharacterized conser 42.1 9.5 0.00021 19.6 0.2 39 20-58 98-140 (165)
238 PRK01343 zinc-binding protein; 41.8 7.6 0.00016 16.3 -0.2 12 48-59 9-20 (57)
239 COG5152 Uncharacterized conser 41.6 15 0.00032 19.7 0.8 16 46-61 194-209 (259)
240 PRK11032 hypothetical protein; 41.1 9 0.0002 19.6 0.0 28 19-57 124-151 (160)
241 PF14369 zf-RING_3: zinc-finge 40.6 14 0.0003 13.7 0.5 10 21-30 23-32 (35)
242 KOG4124|consensus 40.4 7.2 0.00016 22.7 -0.4 51 17-67 347-417 (442)
243 COG4896 Uncharacterized protei 39.3 37 0.0008 14.6 2.0 9 48-56 31-39 (68)
244 PF06524 NOA36: NOA36 protein; 39.3 21 0.00046 20.0 1.2 16 47-62 208-223 (314)
245 COG1781 PyrI Aspartate carbamo 39.2 7.1 0.00015 19.8 -0.5 15 48-62 135-149 (153)
246 PRK04351 hypothetical protein; 39.1 16 0.00034 18.4 0.7 31 20-59 113-143 (149)
247 KOG3497|consensus 39.1 11 0.00024 16.1 0.1 14 48-61 4-17 (69)
248 COG1644 RPB10 DNA-directed RNA 38.4 12 0.00025 16.1 0.1 13 48-60 4-16 (63)
249 COG3880 Modulator of heat shoc 38.4 14 0.00031 19.2 0.5 32 19-61 74-105 (176)
250 PF01780 Ribosomal_L37ae: Ribo 38.4 6.2 0.00014 18.2 -0.7 31 18-59 34-64 (90)
251 PF03884 DUF329: Domain of unk 38.2 16 0.00034 15.3 0.5 12 49-60 3-14 (57)
252 PF04438 zf-HIT: HIT zinc fing 38.2 11 0.00024 13.5 0.1 11 48-58 13-23 (30)
253 PF13453 zf-TFIIB: Transcripti 37.8 30 0.00064 13.0 1.8 21 18-38 18-38 (41)
254 PF10164 DUF2367: Uncharacteri 36.9 11 0.00024 17.6 -0.0 12 47-58 87-98 (98)
255 PF05864 Chordopox_RPO7: Chord 36.8 14 0.00031 15.5 0.3 11 50-60 6-16 (63)
256 PF14149 YhfH: YhfH-like prote 36.0 21 0.00046 13.6 0.7 11 50-60 15-25 (37)
257 PF07649 C1_3: C1-like domain; 35.6 18 0.0004 12.6 0.5 12 46-57 13-24 (30)
258 PF14311 DUF4379: Domain of un 35.2 13 0.00029 15.0 0.1 13 49-61 29-41 (55)
259 PF02591 DUF164: Putative zinc 34.8 19 0.00042 14.6 0.5 33 20-57 23-55 (56)
260 PF14446 Prok-RING_1: Prokaryo 34.8 5.7 0.00012 16.5 -1.0 9 50-58 7-15 (54)
261 COG5109 Uncharacterized conser 34.6 16 0.00034 21.1 0.3 18 42-59 370-387 (396)
262 PF08792 A2L_zn_ribbon: A2L zi 34.1 23 0.00051 12.9 0.6 11 19-29 21-31 (33)
263 TIGR03826 YvyF flagellar opero 34.1 17 0.00036 18.1 0.3 11 50-60 5-15 (137)
264 KOG2817|consensus 34.0 37 0.00081 20.2 1.7 29 25-57 355-383 (394)
265 TIGR03831 YgiT_finger YgiT-typ 33.8 20 0.00042 13.5 0.5 11 20-30 33-43 (46)
266 TIGR00240 ATCase_reg aspartate 33.5 8.5 0.00018 19.5 -0.7 13 48-60 132-144 (150)
267 PF05876 Terminase_GpA: Phage 33.0 15 0.00032 22.6 0.0 40 20-60 201-241 (557)
268 PF06220 zf-U1: U1 zinc finger 32.8 37 0.00081 12.8 1.1 10 20-29 4-13 (38)
269 TIGR00595 priA primosomal prot 32.6 27 0.00058 21.2 1.0 10 47-56 252-261 (505)
270 PF03119 DNA_ligase_ZBD: NAD-d 32.5 19 0.00041 12.6 0.3 9 50-58 1-9 (28)
271 PRK14873 primosome assembly pr 32.0 36 0.00078 21.6 1.5 10 47-56 421-430 (665)
272 PHA03082 DNA-dependent RNA pol 31.5 21 0.00045 15.1 0.3 11 50-60 6-16 (63)
273 PLN00032 DNA-directed RNA poly 31.5 18 0.00039 16.0 0.2 13 48-60 4-16 (71)
274 PF14787 zf-CCHC_5: GAG-polypr 31.4 9.5 0.00021 14.4 -0.6 10 50-59 4-13 (36)
275 PRK00893 aspartate carbamoyltr 31.3 11 0.00024 19.2 -0.6 17 45-61 131-147 (152)
276 KOG4118|consensus 31.0 30 0.00065 15.0 0.8 26 19-44 38-63 (74)
277 PF09855 DUF2082: Nucleic-acid 30.9 16 0.00035 15.7 -0.0 6 50-55 2-7 (64)
278 PF15135 UPF0515: Uncharacteri 30.6 72 0.0016 17.9 2.3 13 49-61 156-168 (278)
279 COG1579 Zn-ribbon protein, pos 30.6 45 0.00096 18.4 1.6 15 45-59 218-232 (239)
280 smart00132 LIM Zinc-binding do 30.0 12 0.00027 13.2 -0.4 11 48-58 27-37 (39)
281 PF07535 zf-DBF: DBF zinc fing 29.9 23 0.0005 14.3 0.4 12 18-29 4-15 (49)
282 PF14354 Lar_restr_allev: Rest 29.8 22 0.00047 14.6 0.3 6 50-55 5-10 (61)
283 COG4957 Predicted transcriptio 29.3 54 0.0012 16.5 1.6 22 20-45 77-98 (148)
284 PF09332 Mcm10: Mcm10 replicat 29.2 32 0.00069 20.0 0.9 39 19-57 252-294 (344)
285 PRK12496 hypothetical protein; 29.2 20 0.00043 18.3 0.1 13 48-60 127-139 (164)
286 PF01096 TFIIS_C: Transcriptio 29.2 28 0.00061 13.1 0.5 10 20-29 29-38 (39)
287 TIGR01053 LSD1 zinc finger dom 28.9 41 0.00089 12.1 0.9 13 43-55 14-26 (31)
288 KOG4727|consensus 28.7 40 0.00086 17.7 1.1 22 19-40 75-96 (193)
289 PF05280 FlhC: Flagellar trans 28.6 26 0.00056 18.2 0.5 27 20-55 135-161 (175)
290 KOG3214|consensus 27.3 24 0.00051 16.7 0.2 40 18-62 22-61 (109)
291 COG3024 Uncharacterized protei 27.2 19 0.0004 15.6 -0.1 10 49-58 8-17 (65)
292 PRK06260 threonine synthase; V 27.1 42 0.00091 19.6 1.2 9 20-28 4-12 (397)
293 KOG3456|consensus 27.0 29 0.00062 16.7 0.4 13 48-60 104-116 (120)
294 PRK00418 DNA gyrase inhibitor; 26.9 20 0.00043 15.4 -0.1 11 48-58 6-16 (62)
295 PF07503 zf-HYPF: HypF finger; 26.9 18 0.00038 13.5 -0.2 12 48-59 21-32 (35)
296 PF14952 zf-tcix: Putative tre 26.6 24 0.00052 14.0 0.1 7 50-56 13-19 (44)
297 KOG0402|consensus 26.3 18 0.00039 16.5 -0.3 11 48-58 36-46 (92)
298 PRK02935 hypothetical protein; 25.8 29 0.00064 16.6 0.3 14 44-57 66-79 (110)
299 PF01722 BolA: BolA-like prote 25.6 46 0.001 14.7 1.0 24 46-69 27-50 (76)
300 smart00647 IBR In Between Ring 25.6 27 0.00058 14.1 0.2 17 45-61 37-53 (64)
301 KOG4602|consensus 25.5 20 0.00044 20.0 -0.2 10 48-57 268-277 (318)
302 TIGR01385 TFSII transcription 25.4 34 0.00074 19.4 0.6 35 19-58 258-296 (299)
303 PF13462 Thioredoxin_4: Thiore 25.2 39 0.00084 16.4 0.8 18 49-66 22-39 (162)
304 PF02148 zf-UBP: Zn-finger in 25.2 37 0.00079 14.1 0.6 15 17-31 9-23 (63)
305 PF14447 Prok-RING_4: Prokaryo 25.0 21 0.00046 14.9 -0.1 16 45-60 36-51 (55)
306 COG1885 Uncharacterized protei 24.9 19 0.00041 17.2 -0.3 11 49-59 50-60 (115)
307 COG4311 SoxD Sarcosine oxidase 24.6 28 0.00062 16.3 0.2 9 48-56 3-11 (97)
308 TIGR00280 L37a ribosomal prote 24.6 40 0.00088 15.6 0.7 11 20-30 54-64 (91)
309 PF12760 Zn_Tnp_IS1595: Transp 24.6 61 0.0013 12.5 2.6 39 8-56 7-45 (46)
310 cd01410 SIRT7 SIRT7: Eukaryoti 24.5 91 0.002 16.5 2.0 35 18-56 94-128 (206)
311 smart00661 RPOL9 RNA polymeras 24.5 44 0.00096 13.0 0.8 13 19-31 20-32 (52)
312 PF10122 Mu-like_Com: Mu-like 24.4 45 0.00098 13.7 0.7 11 49-59 5-15 (51)
313 TIGR03830 CxxCG_CxxCG_HTH puta 24.2 86 0.0019 14.7 1.8 18 19-36 31-48 (127)
314 PF09082 DUF1922: Domain of un 24.0 16 0.00035 15.9 -0.6 6 50-56 22-27 (68)
315 KOG0562|consensus 23.8 63 0.0014 17.0 1.3 23 47-69 152-174 (184)
316 TIGR00244 transcriptional regu 23.7 37 0.00079 17.3 0.5 16 20-35 29-44 (147)
317 PF10609 ParA: ParA/MinD ATPas 23.4 40 0.00086 15.2 0.5 10 48-57 65-74 (81)
318 COG1545 Predicted nucleic-acid 23.2 20 0.00044 17.8 -0.5 9 50-58 31-39 (140)
319 COG1327 Predicted transcriptio 23.1 37 0.0008 17.4 0.4 15 20-34 29-43 (156)
320 cd04476 RPA1_DBD_C RPA1_DBD_C: 23.0 33 0.00072 17.2 0.3 11 47-57 50-60 (166)
321 COG1631 RPL42A Ribosomal prote 22.9 28 0.00061 16.2 0.0 11 49-59 69-79 (94)
322 PRK14892 putative transcriptio 22.9 36 0.00078 16.0 0.4 10 46-55 19-28 (99)
323 PTZ00255 60S ribosomal protein 22.9 46 0.001 15.4 0.7 11 20-30 55-65 (90)
324 PHA03019 hypothetical protein; 22.8 52 0.0011 14.3 0.8 12 49-60 21-32 (77)
325 KOG3134|consensus 22.6 68 0.0015 17.6 1.3 33 20-57 1-33 (225)
326 PF08273 Prim_Zn_Ribbon: Zinc- 22.4 33 0.00072 13.2 0.2 8 49-56 4-11 (40)
327 PF10367 Vps39_2: Vacuolar sor 22.3 23 0.00049 16.1 -0.4 11 50-60 80-90 (109)
328 PRK05580 primosome assembly pr 21.9 54 0.0012 20.8 1.0 10 47-56 420-429 (679)
329 PF10825 DUF2752: Protein of u 21.9 32 0.0007 13.9 0.1 9 49-57 10-18 (52)
330 TIGR03829 YokU_near_AblA uncha 21.8 69 0.0015 14.8 1.1 17 20-36 36-52 (89)
331 PF04777 Evr1_Alr: Erv1 / Alr 21.3 44 0.00094 15.1 0.5 15 47-61 35-49 (95)
332 COG3478 Predicted nucleic-acid 21.3 40 0.00087 14.6 0.3 6 50-55 6-11 (68)
333 PRK03976 rpl37ae 50S ribosomal 21.3 52 0.0011 15.3 0.7 11 20-30 55-65 (90)
334 PF14803 Nudix_N_2: Nudix N-te 21.3 37 0.00081 12.5 0.2 7 51-57 3-9 (34)
335 TIGR03655 anti_R_Lar restricti 21.3 32 0.0007 13.8 0.0 6 50-55 3-8 (53)
336 PF03367 zf-ZPR1: ZPR1 zinc-fi 21.3 30 0.00066 17.6 -0.1 13 47-59 29-41 (161)
337 PF14599 zinc_ribbon_6: Zinc-r 20.6 29 0.00064 14.7 -0.2 10 20-29 31-40 (61)
338 TIGR00340 zpr1_rel ZPR1-relate 20.6 38 0.00082 17.4 0.2 12 48-59 28-39 (163)
339 PF01363 FYVE: FYVE zinc finge 20.5 35 0.00077 14.3 0.1 10 50-59 11-20 (69)
340 PF12677 DUF3797: Domain of un 20.4 36 0.00077 13.9 0.1 8 49-56 14-21 (49)
341 COG4847 Uncharacterized protei 20.3 49 0.0011 15.5 0.5 12 17-28 4-15 (103)
342 PF04032 Rpr2: RNAse P Rpr2/Rp 20.2 12 0.00026 16.4 -1.5 13 18-30 45-57 (85)
343 KOG2932|consensus 20.1 73 0.0016 18.6 1.2 24 46-69 142-168 (389)
344 PF09943 DUF2175: Uncharacteri 20.0 49 0.0011 15.7 0.5 10 19-28 2-11 (101)
No 1
>KOG2462|consensus
Probab=99.86 E-value=1.8e-22 Score=104.19 Aligned_cols=66 Identities=39% Similarity=0.677 Sum_probs=56.5
Q ss_pred ChHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhh
Q psy12265 3 KFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 3 ~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
-+=.|+-|+|+|+||+||.|..|+++|...++|..||+ +|.+.++|+|..|++.|+..+.|.+|..
T Consensus 199 RPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQ-THS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 199 RPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQ-THSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred chHHhhcccccccCCCCccCCcccchhcchHHHHHHHH-hhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 33456678899999999999999999999999999988 7988889999999999999999988864
No 2
>KOG2462|consensus
Probab=99.85 E-value=6.2e-22 Score=102.25 Aligned_cols=66 Identities=33% Similarity=0.578 Sum_probs=61.9
Q ss_pred ChHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhcC
Q psy12265 3 KFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 3 ~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~ 71 (71)
+...|..|+++|+ -+.+|.+||+.|+.+.-|+.|++ .|+||+||.|+.|++.|+.+++|+-||+++
T Consensus 173 SmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiR-THTGEKPF~C~hC~kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 173 SMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIR-THTGEKPFSCPHCGKAFADRSNLRAHMQTH 238 (279)
T ss_pred ehHHHhhHhhccC--CCcccccccccccchHHhhcccc-cccCCCCccCCcccchhcchHHHHHHHHhh
Confidence 4678899999985 78999999999999999999998 899999999999999999999999999875
No 3
>KOG3623|consensus
Probab=99.73 E-value=1.4e-18 Score=99.34 Aligned_cols=70 Identities=34% Similarity=0.586 Sum_probs=66.2
Q ss_pred CcChHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhcC
Q psy12265 1 MEKFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 1 f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~ 71 (71)
|.+.++|.+|.-.|+|.+||.|.+|.++|..+-.|+.|++ .|.|++||+|..|++.|+....+.+||-.|
T Consensus 904 FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkR-LHSGEKPfQCdKClKRFSHSGSYSQHMNHR 973 (1007)
T KOG3623|consen 904 FQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKR-LHSGEKPFQCDKCLKRFSHSGSYSQHMNHR 973 (1007)
T ss_pred HHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhh-hccCCCcchhhhhhhhcccccchHhhhccc
Confidence 6678999999999999999999999999999999999998 899999999999999999999999998654
No 4
>KOG3576|consensus
Probab=99.59 E-value=2.7e-16 Score=79.14 Aligned_cols=67 Identities=28% Similarity=0.523 Sum_probs=60.7
Q ss_pred cChHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhh
Q psy12265 2 EKFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 2 ~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
.-+.-|.+|++.|...+.+.|..||++|-..-+|++|++ .|+|.+||+|..|++.|.++-.|+.|.+
T Consensus 128 ~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~r-thtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 128 GLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTR-THTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred hHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhc-cccCccccchhhhhHHHHhhccHHHHHH
Confidence 334567889999999999999999999999999999998 8999999999999999999999999864
No 5
>KOG3623|consensus
Probab=99.59 E-value=4.7e-16 Score=89.27 Aligned_cols=70 Identities=30% Similarity=0.507 Sum_probs=61.8
Q ss_pred CcChHHHHHHHhHhhC-------------CCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHh
Q psy12265 1 MEKFTYLKVHNRVHLG-------------LKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSY 67 (71)
Q Consensus 1 f~~~~~l~~h~~~~~~-------------~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h 67 (71)
|-.++.|.+|+.+|.. -+.|+|..|+++|..+-.|+.|.+ +|.|++||.|+.|++.|+....+..|
T Consensus 250 FAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlR-IHSGEKPfeCpnCkKRFSHSGSySSH 328 (1007)
T KOG3623|consen 250 FAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLR-IHSGEKPFECPNCKKRFSHSGSYSSH 328 (1007)
T ss_pred hhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhhe-eecCCCCcCCcccccccccCCccccc
Confidence 4567889999988842 256999999999999999999998 99999999999999999999999999
Q ss_pred hhcC
Q psy12265 68 HQIR 71 (71)
Q Consensus 68 ~~~~ 71 (71)
|..+
T Consensus 329 mSSK 332 (1007)
T KOG3623|consen 329 MSSK 332 (1007)
T ss_pred cccc
Confidence 8653
No 6
>PHA00733 hypothetical protein
Probab=99.42 E-value=2e-13 Score=65.15 Aligned_cols=60 Identities=23% Similarity=0.331 Sum_probs=50.2
Q ss_pred HHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 7 LKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 7 l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|.+++..+ +++||.|..|++.|.....|..|++ .+ +.+|.|..|++.|.....|..|+..
T Consensus 62 l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r-~h--~~~~~C~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 62 LYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIR-YT--EHSKVCPVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred HHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHh-cC--CcCccCCCCCCccCCHHHHHHHHHH
Confidence 44554443 5889999999999999999999987 45 4579999999999999999999864
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.40 E-value=7.2e-14 Score=57.30 Aligned_cols=45 Identities=18% Similarity=0.364 Sum_probs=40.1
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHH
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHS 66 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~ 66 (71)
-|.|+.||+.|+..++|..|++ .|+ ++++|..|++.|...+.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r-~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLR-KHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHH-hcC--CcccCCcccceecccceeEE
Confidence 3799999999999999999998 687 68999999999998877653
No 8
>KOG1074|consensus
Probab=99.37 E-value=9.9e-14 Score=80.65 Aligned_cols=69 Identities=32% Similarity=0.655 Sum_probs=58.9
Q ss_pred cChHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcC----ceeCC---hhhHhhhchHHHHHhhhcC
Q psy12265 2 EKFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVK----AFQCE---YCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 2 ~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~----~~~C~---~c~~~f~~~~~l~~h~~~~ 71 (71)
..+++|+.|.++|+||+||+|.+|+.+|+.+++|+.|+. .|.... .+.|+ +|-+.|.+-..|..|++.+
T Consensus 616 SC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~-vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH 691 (958)
T KOG1074|consen 616 SCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMS-VHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIH 691 (958)
T ss_pred cchhhhhhhhhcccCcCccccccccchhccccchhhccc-ccccCccccccccCCchhhhcccccccccccceEEee
Confidence 456889999999999999999999999999999999987 675543 36788 8999999999999888753
No 9
>KOG3576|consensus
Probab=99.31 E-value=9.8e-13 Score=66.54 Aligned_cols=70 Identities=30% Similarity=0.533 Sum_probs=59.2
Q ss_pred CcChHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCC----------cCceeCChhhHhhhchHHHHHhhhc
Q psy12265 1 MEKFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSD----------VKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 1 f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~----------~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|-....|++|+++|++.+||.|..|+++|++..+|..|....|.. ++.|.|..||.+-.....+..|+++
T Consensus 155 fndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~ 234 (267)
T KOG3576|consen 155 FNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKL 234 (267)
T ss_pred ccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHh
Confidence 445578999999999999999999999999999999998766643 3568999999988888777777654
No 10
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.24 E-value=1e-11 Score=44.20 Aligned_cols=25 Identities=48% Similarity=1.000 Sum_probs=16.2
Q ss_pred HHHHHHhHhhCCCceeccccccccc
Q psy12265 6 YLKVHNRVHLGLKPYGCEVCGRHFR 30 (71)
Q Consensus 6 ~l~~h~~~~~~~~~~~c~~c~~~~~ 30 (71)
+|..|+++|.+++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3566666666666666666666654
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.17 E-value=6.8e-12 Score=44.65 Aligned_cols=26 Identities=38% Similarity=0.956 Sum_probs=23.1
Q ss_pred hHHHhHhhhcCCcCceeCChhhHhhhc
Q psy12265 34 DLKYHKASLHSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 34 ~l~~h~~~~~~~~~~~~C~~c~~~f~~ 60 (71)
+|.+|++ .|++++||.|+.|++.|.+
T Consensus 1 ~l~~H~~-~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMR-THTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHH-HHSSSSSEEESSSSEEESS
T ss_pred CHHHHhh-hcCCCCCCCCCCCcCeeCc
Confidence 4789998 7999999999999998863
No 12
>KOG1074|consensus
Probab=99.17 E-value=1.9e-11 Score=71.52 Aligned_cols=51 Identities=25% Similarity=0.565 Sum_probs=48.3
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhcC
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~ 71 (71)
..|..|++.|...++|..|++ +|++++||.|..|++.|..+..|+.||.++
T Consensus 880 h~C~vCgk~FsSSsALqiH~r-THtg~KPF~C~fC~~aFttrgnLKvHMgtH 930 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMR-THTGPKPFFCHFCEEAFTTRGNLKVHMGTH 930 (958)
T ss_pred hhhccchhcccchHHHHHhhh-cCCCCCCccchhhhhhhhhhhhhhhhhccc
Confidence 789999999999999999998 899999999999999999999999998753
No 13
>KOG3608|consensus
Probab=99.14 E-value=5.2e-11 Score=64.52 Aligned_cols=70 Identities=30% Similarity=0.364 Sum_probs=60.5
Q ss_pred CcChHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhh-cCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 1 MEKFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASL-HSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 1 f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~-~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|+++..|..|.+.|++++...|..|+..|.....|..|.+.. -...++|.|..|-+.|+....|..|+..
T Consensus 189 ~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~r 259 (467)
T KOG3608|consen 189 MGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVR 259 (467)
T ss_pred hccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHH
Confidence 467889999999999999999999999999999999998731 2246789999999999999999888754
No 14
>KOG3608|consensus
Probab=99.10 E-value=1.9e-10 Score=62.41 Aligned_cols=63 Identities=27% Similarity=0.441 Sum_probs=42.0
Q ss_pred HHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 6 YLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 6 ~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.|..|+..|. ..|.|+.|+.+....++|..|++..|..++||+|..|...+.+.++|++|..+
T Consensus 252 lL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~ 314 (467)
T KOG3608|consen 252 LLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQV 314 (467)
T ss_pred HHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHh
Confidence 3444444442 34677777777677777777776667777777777777777777777777654
No 15
>PHA00732 hypothetical protein
Probab=99.01 E-value=1.7e-10 Score=50.99 Aligned_cols=46 Identities=22% Similarity=0.426 Sum_probs=37.2
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
||.|..|++.|....+|..|++..|. ++.|+.|++.|. .|..|+.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 68899999999999999999863354 358999999998 47777654
No 16
>PHA00616 hypothetical protein
Probab=98.88 E-value=7.2e-10 Score=43.62 Aligned_cols=35 Identities=26% Similarity=0.413 Sum_probs=31.5
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYC 54 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c 54 (71)
||.|..||+.|...+++..|++ .+++++++.|+.-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r-~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLL-SVHKQNKLTLEYF 35 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHH-HhcCCCccceeEE
Confidence 6899999999999999999998 7889999988753
No 17
>PHA00733 hypothetical protein
Probab=98.72 E-value=4.8e-09 Score=50.26 Aligned_cols=65 Identities=14% Similarity=0.033 Sum_probs=46.0
Q ss_pred HHHHHHhHhhCCCceecccccccccchhhHHHhH--h--hhcCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 6 YLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHK--A--SLHSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 6 ~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~--~--~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.|..+-......+++.|.+|...+..+..+..+. . ..+.+.+||.|+.|++.|.....|..|++.
T Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 27 ELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred HhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhc
Confidence 3443333333467799999998877766665541 1 123457899999999999999999999873
No 18
>KOG3993|consensus
Probab=98.67 E-value=1.5e-08 Score=56.26 Aligned_cols=66 Identities=24% Similarity=0.407 Sum_probs=49.7
Q ss_pred hHHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcC--------Cc-------------------------Ccee
Q psy12265 4 FTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHS--------DV-------------------------KAFQ 50 (71)
Q Consensus 4 ~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~--------~~-------------------------~~~~ 50 (71)
...|.+|.-...-...|.|.+|++.|.-.++|..|.+ .|. +. --|.
T Consensus 280 ~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRR-WHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~ 358 (500)
T KOG3993|consen 280 AFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRR-WHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFS 358 (500)
T ss_pred HHHHhhccCCeeEEeeecCCcccccccCchhhhhhhc-ccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceee
Confidence 3445555433333456999999999999999999987 341 11 1388
Q ss_pred CChhhHhhhchHHHHHhhhc
Q psy12265 51 CEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 51 C~~c~~~f~~~~~l~~h~~~ 70 (71)
|..|++.|.+...|..|+-+
T Consensus 359 C~~C~KkFrRqAYLrKHqlt 378 (500)
T KOG3993|consen 359 CHTCGKKFRRQAYLRKHQLT 378 (500)
T ss_pred cHHhhhhhHHHHHHHHhHHh
Confidence 99999999999999999643
No 19
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.65 E-value=1e-08 Score=55.27 Aligned_cols=53 Identities=30% Similarity=0.654 Sum_probs=44.8
Q ss_pred CCceeccc--ccccccchhhHHHhHhhhc------------------CCcCceeCChhhHhhhchHHHHHhhh
Q psy12265 17 LKPYGCEV--CGRHFRQWGDLKYHKASLH------------------SDVKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 17 ~~~~~c~~--c~~~~~~~~~l~~h~~~~~------------------~~~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
++||+|+. |.+.|.....|+-|+...| ...+||+|++|++.+.+...|..|+.
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 59999986 9999999999999986333 12378999999999999999998875
No 20
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.61 E-value=8.6e-08 Score=39.55 Aligned_cols=49 Identities=18% Similarity=0.302 Sum_probs=39.1
Q ss_pred ceecccccccccchhhHHHhHhhhcCCc-CceeCChhhHhhhchHHHHHhhhc
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDV-KAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~-~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.|.|+.|++ ..+...|..|....|..+ +.+.|++|...+.. +|..|+..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl~~ 51 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHLNS 51 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHHHH
Confidence 488999999 566788999987677764 57899999987553 78888864
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.59 E-value=1e-07 Score=54.89 Aligned_cols=50 Identities=22% Similarity=0.552 Sum_probs=32.5
Q ss_pred HHHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 5 TYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 5 ~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
..|..|+.++. +++.|. |+..+ ....|..|+. .+.+.+++.|..|+..+.
T Consensus 466 s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~-thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 466 GEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQA-STCPLRLITCRFCGDMVQ 515 (567)
T ss_pred HHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhh-ccCCCCceeCCCCCCccc
Confidence 45666766653 667777 77543 4567777765 566777777777776663
No 22
>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=98.56 E-value=1.6e-08 Score=34.70 Aligned_cols=21 Identities=29% Similarity=0.727 Sum_probs=13.3
Q ss_pred eeCChhhHhhhchHHHHHhhh
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~ 69 (71)
|.|+.|++.|.....|..|++
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 456666666666666666665
No 23
>PHA00616 hypothetical protein
Probab=98.47 E-value=9.3e-08 Score=37.68 Aligned_cols=23 Identities=26% Similarity=0.432 Sum_probs=21.4
Q ss_pred ceeCChhhHhhhchHHHHHhhhc
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
||+|+.||..|.+.++|..|++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~ 23 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS 23 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH
Confidence 68999999999999999999875
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.40 E-value=5e-07 Score=52.22 Aligned_cols=62 Identities=16% Similarity=0.392 Sum_probs=49.6
Q ss_pred hHHHHHHHhHhhCCCceeccccccccc----------chhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhh
Q psy12265 4 FTYLKVHNRVHLGLKPYGCEVCGRHFR----------QWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYH 68 (71)
Q Consensus 4 ~~~l~~h~~~~~~~~~~~c~~c~~~~~----------~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~ 68 (71)
+..|..|+.+|.+++++.|..|+..+. ....|..|.. . .|.+++.|..||+.+..+ ++..|+
T Consensus 489 R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~-~-CG~rt~~C~~Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 489 KEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHES-I-CGSRTAPCDSCGRSVMLK-EMDIHQ 560 (567)
T ss_pred hhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHH-h-cCCcceEccccCCeeeeh-hHHHHH
Confidence 467889999999999999999999884 2357889976 3 589999999999887654 455554
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.37 E-value=1.1e-07 Score=33.76 Aligned_cols=21 Identities=29% Similarity=0.710 Sum_probs=10.6
Q ss_pred eeCChhhHhhhchHHHHHhhh
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~ 69 (71)
|.|..|++.|.....|..|++
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 445555555555555555543
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.33 E-value=3.9e-07 Score=31.12 Aligned_cols=21 Identities=38% Similarity=0.903 Sum_probs=19.8
Q ss_pred eecccccccccchhhHHHhHh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKA 40 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~ 40 (71)
|.|..|++.|..+..|..|++
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 689999999999999999987
No 27
>PHA02768 hypothetical protein; Provisional
Probab=98.31 E-value=3.4e-07 Score=37.73 Aligned_cols=34 Identities=21% Similarity=0.127 Sum_probs=29.3
Q ss_pred CcChHHHHHHHhHhhCCCceecccccccccchhhHH
Q psy12265 1 MEKFTYLKVHNRVHLGLKPYGCEVCGRHFRQWGDLK 36 (71)
Q Consensus 1 f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~ 36 (71)
|....+|..|+++|. +++.|..|++.|...+.|.
T Consensus 15 Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 15 YIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred eccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 667889999999998 7999999999998777654
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.30 E-value=2.6e-07 Score=42.06 Aligned_cols=23 Identities=26% Similarity=0.665 Sum_probs=18.1
Q ss_pred ceeCChhhHhhhchHHHHHhhhc
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.+.|..|++.|.....|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 57888888888888888888864
No 29
>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=98.29 E-value=2.8e-07 Score=31.54 Aligned_cols=22 Identities=36% Similarity=0.727 Sum_probs=13.5
Q ss_pred eeCChhhHhhhchHHHHHhhhc
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|.|+.|++.|.....|..|+..
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 4677777777777777777653
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.07 E-value=3.9e-06 Score=29.66 Aligned_cols=24 Identities=38% Similarity=0.938 Sum_probs=21.7
Q ss_pred ceecccccccccchhhHHHhHhhhc
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLH 43 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~ 43 (71)
||.|..|++.|.+..+|..|++ .|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~-~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR-SH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC-TT
T ss_pred CCCCCccCCccCChhHHHHHhH-Hh
Confidence 6899999999999999999986 44
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.05 E-value=5.8e-06 Score=28.08 Aligned_cols=22 Identities=32% Similarity=0.921 Sum_probs=18.2
Q ss_pred eecccccccccchhhHHHhHhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKAS 41 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~ 41 (71)
|.|+.|+..|.+...|..|+..
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 6899999999999999999873
No 32
>PRK04860 hypothetical protein; Provisional
Probab=97.98 E-value=3.6e-06 Score=41.86 Aligned_cols=39 Identities=23% Similarity=0.621 Sum_probs=32.6
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchH
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKY 62 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~ 62 (71)
+|.|. |+. ....+.+|.+ +++++++|.|..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~r-i~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNR-VVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHH-HhcCCccEECCCCCceeEEec
Confidence 59998 987 5677788987 899999999999998876543
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.95 E-value=3.9e-06 Score=28.94 Aligned_cols=20 Identities=30% Similarity=0.555 Sum_probs=12.0
Q ss_pred eCChhhHhhhchHHHHHhhh
Q psy12265 50 QCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 50 ~C~~c~~~f~~~~~l~~h~~ 69 (71)
.|..|++.|.....|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 45566666666666666654
No 34
>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=97.82 E-value=2.6e-06 Score=30.26 Aligned_cols=22 Identities=27% Similarity=0.538 Sum_probs=13.9
Q ss_pred eeCChhhHhhhchHHHHHhhhc
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|.|..|++.|.+...+..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 4566666666666666666653
No 35
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.80 E-value=4.1e-06 Score=29.05 Aligned_cols=19 Identities=26% Similarity=0.705 Sum_probs=9.2
Q ss_pred ecccccccccchhhHHHhH
Q psy12265 21 GCEVCGRHFRQWGDLKYHK 39 (71)
Q Consensus 21 ~c~~c~~~~~~~~~l~~h~ 39 (71)
.|..|+..|.+...+..|+
T Consensus 2 ~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCcCCHHHHHHHH
Confidence 4444555555444444443
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.60 E-value=6.8e-05 Score=25.63 Aligned_cols=24 Identities=38% Similarity=0.764 Sum_probs=20.7
Q ss_pred eecccccccccchhhHHHhHhhhcC
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHS 44 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~ 44 (71)
|.|..|++.|.....+..|++ .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 579999999999999999987 553
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=97.59 E-value=2.2e-05 Score=31.82 Aligned_cols=26 Identities=15% Similarity=0.321 Sum_probs=16.5
Q ss_pred CcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 45 DVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 45 ~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.+.|-.|++|+..+.+..+|.+|+.+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHH
T ss_pred cCCCCCCCcchhhccchhhHHHHHHH
Confidence 45677888888888888888888754
No 38
>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=97.58 E-value=3.7e-05 Score=31.15 Aligned_cols=32 Identities=28% Similarity=0.487 Sum_probs=21.7
Q ss_pred hCCCceecccccccccchhhHHHhHhhhcCCcC
Q psy12265 15 LGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVK 47 (71)
Q Consensus 15 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 47 (71)
..+.|..|+.|+..+.+..+|.+|+. ...+.+
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle-~~H~~k 51 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLE-IRHFKK 51 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHH-HHTTTS
T ss_pred ccCCCCCCCcchhhccchhhHHHHHH-HHhccc
Confidence 45678999999999999999999997 444444
No 39
>KOG3993|consensus
Probab=97.58 E-value=9.5e-06 Score=45.58 Aligned_cols=50 Identities=20% Similarity=0.380 Sum_probs=41.0
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|.|..|.-.|...-.|.+|.= ....-..|+|+.|++.|+=.++|..|++-
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC-~RIV~vEYrCPEC~KVFsCPANLASHRRW 317 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRC-PRIVHVEYRCPECDKVFSCPANLASHRRW 317 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccC-CeeEEeeecCCcccccccCchhhhhhhcc
Confidence 899999988988888888842 22234569999999999999999999874
No 40
>PHA00732 hypothetical protein
Probab=97.56 E-value=2.9e-05 Score=34.43 Aligned_cols=22 Identities=18% Similarity=0.478 Sum_probs=20.7
Q ss_pred ceeCChhhHhhhchHHHHHhhh
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
||.|..|++.|.....|..|++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhh
Confidence 5889999999999999999986
No 41
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=97.54 E-value=3.2e-05 Score=26.98 Aligned_cols=20 Identities=20% Similarity=0.599 Sum_probs=12.8
Q ss_pred eeCChhhHhhhchHHHHHhhh
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~ 69 (71)
..|+.||+.| ....|..|++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3567777777 5666666654
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.35 E-value=0.00019 Score=24.71 Aligned_cols=22 Identities=23% Similarity=0.569 Sum_probs=20.2
Q ss_pred eeCChhhHhhhchHHHHHhhhc
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|.|..|+..|.....++.|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 6799999999999999999875
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.17 E-value=0.00016 Score=24.69 Aligned_cols=21 Identities=14% Similarity=0.331 Sum_probs=10.9
Q ss_pred eeCChhhHhhhchHHHHHhhhc
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|+|+.|+.... ...|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 45666665555 5566666543
No 44
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=97.03 E-value=0.00022 Score=26.47 Aligned_cols=20 Identities=20% Similarity=0.489 Sum_probs=10.2
Q ss_pred eecccccccccchhhHHHhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHK 39 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~ 39 (71)
|.|..|+..|.....+..|+
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred eEccccCCccCCHHHHHHHH
Confidence 45555555555554444443
No 45
>PRK04860 hypothetical protein; Provisional
Probab=96.46 E-value=0.0025 Score=31.94 Aligned_cols=29 Identities=34% Similarity=0.575 Sum_probs=24.8
Q ss_pred HHHHHHHhHhhCCCceecccccccccchh
Q psy12265 5 TYLKVHNRVHLGLKPYGCEVCGRHFRQWG 33 (71)
Q Consensus 5 ~~l~~h~~~~~~~~~~~c~~c~~~~~~~~ 33 (71)
..+.+|.+++.++++|.|..|++.|....
T Consensus 129 ~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 129 LTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred CHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 46788999999999999999998876543
No 46
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=96.31 E-value=0.004 Score=25.79 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=19.5
Q ss_pred cCCcCceeCChhhHhhhchHHHHHhh
Q psy12265 43 HSDVKAFQCEYCGKDFARKYQAHSYH 68 (71)
Q Consensus 43 ~~~~~~~~C~~c~~~f~~~~~l~~h~ 68 (71)
..|+.-++|+-|+..|....++.+|.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHh
Confidence 34666778888888888887777774
No 47
>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=95.99 E-value=0.0043 Score=22.93 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=16.4
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
|.|..||..+... ..++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~-------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE-------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC-------------cCCCcCcCCCC
Confidence 6788888554321 25788999975
No 48
>KOG1146|consensus
Probab=95.86 E-value=0.004 Score=39.90 Aligned_cols=56 Identities=23% Similarity=0.344 Sum_probs=45.1
Q ss_pred hhCCCceecccccccccchhhHHHhHhhhc------------------------CCcCceeCChhhHhhhchHHHHHhhh
Q psy12265 14 HLGLKPYGCEVCGRHFRQWGDLKYHKASLH------------------------SDVKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 14 ~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~------------------------~~~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
+...+.++|..|+..|...+.|..|++..| .+-++|.|..|...+..+..|.+|+.
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 334478999999999999999999998522 12346889999999999999999975
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.54 E-value=0.0024 Score=35.49 Aligned_cols=53 Identities=30% Similarity=0.468 Sum_probs=42.3
Q ss_pred CceecccccccccchhhHHHhHhh-hcCCc--CceeCC--hhhHhhhchHHHHHhhhc
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKAS-LHSDV--KAFQCE--YCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~-~~~~~--~~~~C~--~c~~~f~~~~~l~~h~~~ 70 (71)
.++.|..|...|.....+..|.+. .|.++ +++.|+ .|++.|.....+..|..+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ 345 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILL 345 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccc
Confidence 367888888888888888888763 58888 888888 699888888887777543
No 50
>KOG2893|consensus
Probab=95.39 E-value=0.0049 Score=32.89 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=30.1
Q ss_pred ecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHh
Q psy12265 21 GCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSY 67 (71)
Q Consensus 21 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h 67 (71)
.|..|..-|....-|++|+. .+.|+|-+|-+..-.--.|.+|
T Consensus 12 wcwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceee
Confidence 57789999999888888876 5678999997654433344433
No 51
>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=95.33 E-value=0.022 Score=28.52 Aligned_cols=33 Identities=18% Similarity=0.284 Sum_probs=25.2
Q ss_pred hCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 15 LGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 15 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
....-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCE
Confidence 3445699999999988776653 25899999864
No 52
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=95.27 E-value=0.0067 Score=28.55 Aligned_cols=32 Identities=25% Similarity=0.697 Sum_probs=21.9
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhch
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARK 61 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 61 (71)
....|..||..|-- .+..|..|++||..|.-.
T Consensus 8 tKR~Cp~CG~kFYD------------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYD------------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhcc------------CCCCCccCCCCCCccCcc
Confidence 34688889877632 223577899999877644
No 53
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=95.13 E-value=0.011 Score=29.82 Aligned_cols=25 Identities=36% Similarity=0.793 Sum_probs=19.4
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
+.|.|..||.. +-++.|..||+||.
T Consensus 133 ~~~vC~vCGy~--------------~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYT--------------HEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCc--------------ccCCCCCcCCCCCC
Confidence 36999999733 44588899999983
No 54
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=95.12 E-value=0.049 Score=26.91 Aligned_cols=38 Identities=21% Similarity=0.519 Sum_probs=25.5
Q ss_pred CCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhh
Q psy12265 16 GLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDF 58 (71)
Q Consensus 16 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f 58 (71)
...-|.|+.|+..|+....+.. ... ...|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~----~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL----LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh----cCC-CCcEECCCCCCEE
Confidence 3456999999999886544322 122 3349999999754
No 55
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.70 E-value=0.022 Score=21.58 Aligned_cols=34 Identities=29% Similarity=0.604 Sum_probs=23.3
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
..|+.|+..|.-..+- ...+....+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~------l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK------LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH------cccCCcEEECCCCCcEee
Confidence 4788999888766542 233345679999987764
No 56
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=94.67 E-value=0.037 Score=28.29 Aligned_cols=32 Identities=22% Similarity=0.455 Sum_probs=24.1
Q ss_pred CCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 16 GLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 16 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
...-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~ 145 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEM 145 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCC
Confidence 345699999999988766532 25899999864
No 57
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.61 E-value=0.041 Score=24.76 Aligned_cols=23 Identities=30% Similarity=0.680 Sum_probs=20.4
Q ss_pred ceecccccccccchhhHHHhHhh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKAS 41 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~ 41 (71)
.+.|..|+..|.+...|..|+..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 59999999999999999999984
No 58
>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=94.40 E-value=0.027 Score=21.25 Aligned_cols=34 Identities=21% Similarity=0.453 Sum_probs=22.2
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
..|+.|+..|.-..+.. ........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~------~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL------GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc------CCCCCEEECCCCCCEEE
Confidence 57899998876654421 22223578999987664
No 59
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.18 E-value=0.04 Score=20.75 Aligned_cols=33 Identities=18% Similarity=0.528 Sum_probs=22.7
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDF 58 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f 58 (71)
..|+.|+..|.-.... ........+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~------ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK------IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH------CCCCCcEEECCCCCCEe
Confidence 5788898888766542 23334467899998766
No 60
>KOG2186|consensus
Probab=93.96 E-value=0.036 Score=29.86 Aligned_cols=38 Identities=32% Similarity=0.749 Sum_probs=17.0
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhc
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~ 60 (71)
|.|..||.... +..+.+|+. ...+ ..|.|.-|+..|..
T Consensus 4 FtCnvCgEsvK-Kp~vekH~s-rCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMS-RCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHH-hccC-CeeEEeeccccccc
Confidence 44555554432 233444543 2333 34555555555544
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.54 E-value=0.016 Score=30.37 Aligned_cols=44 Identities=23% Similarity=0.366 Sum_probs=27.0
Q ss_pred CCceecccccccccchhhHHHhHhh---------hcCCcCc-----eeCChhhHhhhc
Q psy12265 17 LKPYGCEVCGRHFRQWGDLKYHKAS---------LHSDVKA-----FQCEYCGKDFAR 60 (71)
Q Consensus 17 ~~~~~c~~c~~~~~~~~~l~~h~~~---------~~~~~~~-----~~C~~c~~~f~~ 60 (71)
++...|+.|+..|..+.-.....+. ...+..| ..|+.||..+..
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 4678999999998766443332221 1122333 479999976553
No 62
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.24 E-value=0.1 Score=21.95 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=19.0
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
.|.|+.||........- -.....+|.|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~~------CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCAK------CRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhhh------HHHcCCceECCCcCc
Confidence 47888888554433221 122356889988874
No 63
>KOG1146|consensus
Probab=93.16 E-value=0.058 Score=35.13 Aligned_cols=54 Identities=17% Similarity=0.208 Sum_probs=42.0
Q ss_pred CCCceecccccccccchhhHHHhHhh----------------hcCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 16 GLKPYGCEVCGRHFRQWGDLKYHKAS----------------LHSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 16 ~~~~~~c~~c~~~~~~~~~l~~h~~~----------------~~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.+.+|.|..|...|.....+..|.+. .+....+| |..|...|+....|++|++.
T Consensus 1281 ~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1281 VTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred cchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 34678999999999999888888753 11222345 99999999999999999874
No 64
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.04 E-value=0.028 Score=31.33 Aligned_cols=24 Identities=46% Similarity=1.081 Sum_probs=21.1
Q ss_pred CCCceecccccccccchhhHHHhH
Q psy12265 16 GLKPYGCEVCGRHFRQWGDLKYHK 39 (71)
Q Consensus 16 ~~~~~~c~~c~~~~~~~~~l~~h~ 39 (71)
..+||.|+.|++.|.....|+-|.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 459999999999999988888885
No 65
>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=92.72 E-value=0.076 Score=19.73 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=16.5
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
.|.|..||..+.. .+.|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g-------------~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEG-------------EEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeEC-------------CcCCCcCcCCCC
Confidence 4788999855321 124668999975
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=92.69 E-value=0.11 Score=20.48 Aligned_cols=31 Identities=29% Similarity=0.665 Sum_probs=20.2
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
..|.|..|+..+..... ...+.|+.||..+.
T Consensus 2 ~~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEY-----------GTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCC-----------CCceECCCCCCeEE
Confidence 35889999877653211 11678999986543
No 67
>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=92.54 E-value=0.054 Score=26.24 Aligned_cols=32 Identities=19% Similarity=0.362 Sum_probs=21.2
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhch
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARK 61 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 61 (71)
....|..|+..|- -.+..|..|++||..|.-.
T Consensus 8 tKr~Cp~cg~kFY------------DLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFY------------DLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCcccc------------ccCCCCccCCCcCCccCcc
Confidence 3467888887763 2224577889998876544
No 68
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.28 E-value=0.12 Score=20.36 Aligned_cols=27 Identities=30% Similarity=0.624 Sum_probs=18.5
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
.|.|..|+..+... ...+.+|+.||..
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCce
Confidence 47899998766532 2345789999864
No 69
>KOG2593|consensus
Probab=92.20 E-value=0.16 Score=29.43 Aligned_cols=38 Identities=26% Similarity=0.707 Sum_probs=26.7
Q ss_pred hCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 15 LGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 15 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
+...-|.|+.|.+.|+....+.. .....-.|.|..|+-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L----~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQL----LDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHHh----hcccCceEEEecCCC
Confidence 34566999999999987766542 233344699998863
No 70
>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=92.07 E-value=0.066 Score=20.81 Aligned_cols=29 Identities=31% Similarity=0.815 Sum_probs=19.8
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
|.|..|+..|..... ... ..+..|+.||.
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 789999988864332 122 44568999986
No 71
>KOG2893|consensus
Probab=91.63 E-value=0.062 Score=28.92 Aligned_cols=25 Identities=20% Similarity=0.525 Sum_probs=21.7
Q ss_pred cCceeCChhhHhhhchHHHHHhhhcC
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~~~ 71 (71)
.++| |.+|++.|.....|.+|++.+
T Consensus 9 ~kpw-cwycnrefddekiliqhqkak 33 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKAK 33 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhhc
Confidence 4566 899999999999999999864
No 72
>KOG3408|consensus
Probab=91.60 E-value=0.22 Score=24.05 Aligned_cols=24 Identities=17% Similarity=0.397 Sum_probs=20.0
Q ss_pred ceeCChhhHhhhchHHHHHhhhcC
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~~~ 71 (71)
.|.|..|.+.|.....|..|.+.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhcc
Confidence 478999999999999999887753
No 73
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.25 E-value=0.036 Score=27.76 Aligned_cols=14 Identities=36% Similarity=0.702 Sum_probs=10.4
Q ss_pred ceeCChhhHhhhch
Q psy12265 48 AFQCEYCGKDFARK 61 (71)
Q Consensus 48 ~~~C~~c~~~f~~~ 61 (71)
.++|+.||.+|...
T Consensus 28 ~~~c~~c~~~f~~~ 41 (154)
T PRK00464 28 RRECLACGKRFTTF 41 (154)
T ss_pred eeeccccCCcceEe
Confidence 37888888888643
No 74
>KOG2785|consensus
Probab=91.16 E-value=0.23 Score=28.37 Aligned_cols=24 Identities=25% Similarity=0.411 Sum_probs=17.3
Q ss_pred CceeCChhhHhhhchHHHHHhhhc
Q psy12265 47 KAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.++.|..|.+.|...-....|++.
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred cceehHHhhccccChhhHHHHHHH
Confidence 456778888888777777777654
No 75
>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=90.98 E-value=0.072 Score=18.32 Aligned_cols=11 Identities=36% Similarity=0.905 Sum_probs=7.6
Q ss_pred cCceeCChhhH
Q psy12265 46 VKAFQCEYCGK 56 (71)
Q Consensus 46 ~~~~~C~~c~~ 56 (71)
..+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 34688888873
No 76
>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=90.88 E-value=0.14 Score=19.87 Aligned_cols=20 Identities=25% Similarity=0.516 Sum_probs=8.1
Q ss_pred eeCChhhHhhhch----HHHHHhh
Q psy12265 49 FQCEYCGKDFARK----YQAHSYH 68 (71)
Q Consensus 49 ~~C~~c~~~f~~~----~~l~~h~ 68 (71)
..|..|++.+... +.|..|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4455555444332 4455554
No 77
>KOG4167|consensus
Probab=90.79 E-value=0.11 Score=32.21 Aligned_cols=24 Identities=25% Similarity=0.510 Sum_probs=21.0
Q ss_pred ceeCChhhHhhhchHHHHHhhhcC
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~~~ 71 (71)
-|.|..|++.|-....+.-||+++
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 389999999999999999998864
No 78
>PF15269 zf-C2H2_7: Zinc-finger
Probab=90.69 E-value=0.12 Score=20.51 Aligned_cols=21 Identities=14% Similarity=0.295 Sum_probs=15.2
Q ss_pred eeCChhhHhhhchHHHHHhhh
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~ 69 (71)
|+|-.|+.+...++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 467777777777777777775
No 79
>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=90.66 E-value=0.15 Score=17.76 Aligned_cols=18 Identities=22% Similarity=0.375 Sum_probs=9.3
Q ss_pred eCChhhHhhhchHHHHHhh
Q psy12265 50 QCEYCGKDFARKYQAHSYH 68 (71)
Q Consensus 50 ~C~~c~~~f~~~~~l~~h~ 68 (71)
.|++|++.+ ....+..|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 466666555 334444443
No 80
>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=90.55 E-value=0.068 Score=28.18 Aligned_cols=25 Identities=20% Similarity=0.299 Sum_probs=14.7
Q ss_pred cCceeCChhhHhhhchHHHHHhhhc
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
+..|.|+.|++.|.-..-+..|+..
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhh
Confidence 3446777777777766666666643
No 81
>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=90.39 E-value=0.072 Score=21.47 Aligned_cols=29 Identities=28% Similarity=0.732 Sum_probs=19.1
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
|.|..|+..|..... ... ..+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~-------~~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQK-------MSD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEe-------cCC-CCCCCCCCCCC
Confidence 789999988874422 121 34457999985
No 82
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.38 E-value=0.057 Score=30.14 Aligned_cols=49 Identities=33% Similarity=0.593 Sum_probs=39.0
Q ss_pred ChHHHHHHHh--HhhCC--Cceecc--cccccccchhhHHHhHhhhcCCcCceeCC
Q psy12265 3 KFTYLKVHNR--VHLGL--KPYGCE--VCGRHFRQWGDLKYHKASLHSDVKAFQCE 52 (71)
Q Consensus 3 ~~~~l~~h~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~~C~ 52 (71)
....+..|.+ .|.++ +++.|. .|++.|.....+..|.. .|.+..++.+.
T Consensus 301 ~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 355 (467)
T COG5048 301 RSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHIL-LHTSISPAKEK 355 (467)
T ss_pred ccccccccccccccccccCCceeeeccCCCccccccccccCCcc-cccCCCccccc
Confidence 3455667777 78889 999999 79999999999999987 67777666553
No 83
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=90.09 E-value=0.62 Score=18.90 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=23.1
Q ss_pred CCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 17 LKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 17 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
++++.|..||..|.-.+.=+..-....-...|-+|+.|-..
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~~ 42 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQA 42 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHHH
Confidence 46789999998776543322111101112346788888643
No 84
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=89.99 E-value=0.19 Score=20.38 Aligned_cols=29 Identities=31% Similarity=0.943 Sum_probs=19.3
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
..|.|..|+..+.. -......+|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~-----------~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVEL-----------DQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeeh-----------hhccCceeCCCCCcE
Confidence 45899999988721 112345689999854
No 85
>KOG2482|consensus
Probab=89.53 E-value=0.14 Score=28.97 Aligned_cols=67 Identities=16% Similarity=0.317 Sum_probs=41.4
Q ss_pred HHHHHHHhHhhC-CCceeccccccccc-chhhHHHhHhhhcC---Cc------------------CceeCChhhHhhhch
Q psy12265 5 TYLKVHNRVHLG-LKPYGCEVCGRHFR-QWGDLKYHKASLHS---DV------------------KAFQCEYCGKDFARK 61 (71)
Q Consensus 5 ~~l~~h~~~~~~-~~~~~c~~c~~~~~-~~~~l~~h~~~~~~---~~------------------~~~~C~~c~~~f~~~ 61 (71)
..|.++++...+ .....|-.|..-+. ..+.+..|+...|. |. ..+.|.+|.+.|..+
T Consensus 129 eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdk 208 (423)
T KOG2482|consen 129 EALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDK 208 (423)
T ss_pred HHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCc
Confidence 345555554422 23467888875433 33555555532221 11 125899999999999
Q ss_pred HHHHHhhhcC
Q psy12265 62 YQAHSYHQIR 71 (71)
Q Consensus 62 ~~l~~h~~~~ 71 (71)
..|..||+-|
T Consensus 209 ntLkeHMrkK 218 (423)
T KOG2482|consen 209 NTLKEHMRKK 218 (423)
T ss_pred HHHHHHHHhc
Confidence 9999999754
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.18 E-value=0.52 Score=19.87 Aligned_cols=32 Identities=19% Similarity=0.504 Sum_probs=16.9
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
.|.|+.||........- -.....+|.|+.||.
T Consensus 25 ~F~CPnCG~~~I~RC~~------CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEK------CRKQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeechh------HHhcCCceECCCCCC
Confidence 47777777542222111 112245788888874
No 87
>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=87.89 E-value=0.14 Score=19.28 Aligned_cols=32 Identities=22% Similarity=0.585 Sum_probs=17.0
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhc
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~ 60 (71)
..|..|+..|- .. ..+....-.|..||..+.+
T Consensus 2 r~C~~Cg~~Yh--------~~-~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYH--------IE-FNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEE--------TT-TB--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccc--------cc-cCCCCCCCccCCCCCeeEe
Confidence 35777777653 22 2333444567777765443
No 88
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=87.06 E-value=1.3 Score=18.08 Aligned_cols=44 Identities=20% Similarity=0.492 Sum_probs=24.3
Q ss_pred CCCceeccc-ccccccchhhHHHhHhhhcCCcCceeCCh----hhHhhhc
Q psy12265 16 GLKPYGCEV-CGRHFRQWGDLKYHKASLHSDVKAFQCEY----CGKDFAR 60 (71)
Q Consensus 16 ~~~~~~c~~-c~~~~~~~~~l~~h~~~~~~~~~~~~C~~----c~~~f~~ 60 (71)
...+..|+. |...-.....|..|.. ..-...+..|++ |+..+..
T Consensus 6 ~~~~v~C~~~cc~~~i~r~~l~~H~~-~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 6 PFRPVPCPNGCCNEMIPRKELDDHLE-NECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp TTSEEE-TT--S-BEEECCCHHHHHH-TTSTTSEEE-SS----S--EEEH
T ss_pred CCCEeeCCCCCcccceeHHHHHHHHH-ccCCCCcEECCCCCCCCCCccch
Confidence 345667776 3333344678889976 344566788998 8776543
No 89
>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=86.89 E-value=0.14 Score=17.85 Aligned_cols=10 Identities=50% Similarity=1.129 Sum_probs=7.5
Q ss_pred eCChhhHhhh
Q psy12265 50 QCEYCGKDFA 59 (71)
Q Consensus 50 ~C~~c~~~f~ 59 (71)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 6888887774
No 90
>PHA00626 hypothetical protein
Probab=86.59 E-value=0.26 Score=20.51 Aligned_cols=17 Identities=18% Similarity=0.477 Sum_probs=13.3
Q ss_pred cCceeCChhhHhhhchH
Q psy12265 46 VKAFQCEYCGKDFARKY 62 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~ 62 (71)
...|.|+.||..|...+
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 56799999998877543
No 91
>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=86.20 E-value=0.59 Score=17.15 Aligned_cols=27 Identities=26% Similarity=0.698 Sum_probs=15.0
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDF 58 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f 58 (71)
|.|..|+..+.. . ...+.+|+.||...
T Consensus 1 Y~C~~Cg~~~~~-----------~-~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVEL-----------K-PGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-B-----------S-TSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEc-----------C-CCCcEECCcCCCeE
Confidence 567777765431 1 12356888888643
No 92
>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=85.55 E-value=0.33 Score=19.01 Aligned_cols=16 Identities=25% Similarity=0.663 Sum_probs=11.9
Q ss_pred eCChhhHhhhchHHHH
Q psy12265 50 QCEYCGKDFARKYQAH 65 (71)
Q Consensus 50 ~C~~c~~~f~~~~~l~ 65 (71)
.|+.|++.|..+..++
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5888888888766554
No 93
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.23 E-value=1.2 Score=17.82 Aligned_cols=22 Identities=23% Similarity=0.600 Sum_probs=16.1
Q ss_pred ceecccccccccch-----hhHHHhHh
Q psy12265 19 PYGCEVCGRHFRQW-----GDLKYHKA 40 (71)
Q Consensus 19 ~~~c~~c~~~~~~~-----~~l~~h~~ 40 (71)
--.|..|++.++.. +.|.+|+.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 36788899877554 57888875
No 94
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.99 E-value=0.36 Score=23.67 Aligned_cols=15 Identities=20% Similarity=0.523 Sum_probs=11.6
Q ss_pred Cceecccccccccch
Q psy12265 18 KPYGCEVCGRHFRQW 32 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~ 32 (71)
..+.|..|+..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 348999999887654
No 95
>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=84.67 E-value=0.91 Score=26.91 Aligned_cols=29 Identities=17% Similarity=0.298 Sum_probs=24.7
Q ss_pred CceecccccccccchhhHHHhHhhhcCCc
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDV 46 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~ 46 (71)
+-|.|+.|.+.|.....+..|+...|.+.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 34899999999999999999998667654
No 96
>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=84.20 E-value=0.24 Score=18.70 Aligned_cols=11 Identities=45% Similarity=1.349 Sum_probs=7.9
Q ss_pred eeCChhhHhhh
Q psy12265 49 FQCEYCGKDFA 59 (71)
Q Consensus 49 ~~C~~c~~~f~ 59 (71)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 67888877664
No 97
>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=83.97 E-value=0.93 Score=24.10 Aligned_cols=29 Identities=21% Similarity=0.456 Sum_probs=21.6
Q ss_pred CCCceecccccccccchhhHHHhHhhhcC
Q psy12265 16 GLKPYGCEVCGRHFRQWGDLKYHKASLHS 44 (71)
Q Consensus 16 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 44 (71)
.+..|.|..|++.|.-...+..|+..-|.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 34569999999999999999999875453
No 98
>PF12907 zf-met2: Zinc-binding
Probab=83.90 E-value=0.28 Score=19.01 Aligned_cols=27 Identities=30% Similarity=0.491 Sum_probs=15.6
Q ss_pred eecccccccccch---hhHHHhHhhhcCCc
Q psy12265 20 YGCEVCGRHFRQW---GDLKYHKASLHSDV 46 (71)
Q Consensus 20 ~~c~~c~~~~~~~---~~l~~h~~~~~~~~ 46 (71)
+.|.+|...|... ..|..|-..-|+..
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 4677787555433 44777765445443
No 99
>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=83.84 E-value=0.99 Score=19.17 Aligned_cols=24 Identities=25% Similarity=0.529 Sum_probs=15.8
Q ss_pred CcCceeCChhhHhhhchHHHHHhh
Q psy12265 45 DVKAFQCEYCGKDFARKYQAHSYH 68 (71)
Q Consensus 45 ~~~~~~C~~c~~~f~~~~~l~~h~ 68 (71)
....|.|+.||........-...+
T Consensus 43 ~~r~~~C~~Cg~~~~rD~naA~NI 66 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMDRDVNAARNI 66 (69)
T ss_pred ccceEEcCCCCCEECcHHHHHHHH
Confidence 345789999998766554444443
No 100
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=83.39 E-value=1.9 Score=18.05 Aligned_cols=42 Identities=10% Similarity=0.320 Sum_probs=22.9
Q ss_pred eecccccccccchh-hHHHhHhhhcCCcCceeCChhhHhhhchH
Q psy12265 20 YGCEVCGRHFRQWG-DLKYHKASLHSDVKAFQCEYCGKDFARKY 62 (71)
Q Consensus 20 ~~c~~c~~~~~~~~-~l~~h~~~~~~~~~~~~C~~c~~~f~~~~ 62 (71)
..|..|++.+.-.. .+..-.. ..-.-..|-|..|......+.
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrL-rnrPi~tYmC~eC~~RI~~~t 45 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRL-RNRPIHTYMCDECKERIREET 45 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHh-hcCCCcceeChhHHHHHhHHH
Confidence 36778887654332 2222212 233455689999977655443
No 101
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=83.34 E-value=1.9 Score=22.26 Aligned_cols=34 Identities=24% Similarity=0.515 Sum_probs=22.4
Q ss_pred hhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 14 HLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 14 ~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
..+..-|.|+.|...++...+. .. -|.|+.||..
T Consensus 108 ~~~~~~y~C~~~~~r~sfdeA~-------~~---~F~Cp~Cg~~ 141 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDEAM-------EL---GFTCPKCGED 141 (176)
T ss_pred hccCCceeCCCCCCcccHHHHH-------Hh---CCCCCCCCch
Confidence 3455669998887776654432 22 2899999864
No 102
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=83.01 E-value=0.92 Score=21.31 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=12.0
Q ss_pred Cceecccccccccch
Q psy12265 18 KPYGCEVCGRHFRQW 32 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~ 32 (71)
.|+.|.-||..|..-
T Consensus 1 MpH~CtrCG~vf~~g 15 (112)
T COG3364 1 MPHQCTRCGEVFDDG 15 (112)
T ss_pred CCceecccccccccc
Confidence 478899999988764
No 103
>PLN02748 tRNA dimethylallyltransferase
Probab=82.96 E-value=0.57 Score=27.69 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=20.6
Q ss_pred CceeCChhhH-hhhchHHHHHhhhcC
Q psy12265 47 KAFQCEYCGK-DFARKYQAHSYHQIR 71 (71)
Q Consensus 47 ~~~~C~~c~~-~f~~~~~l~~h~~~~ 71 (71)
+.|.|..|+. .+.....++.|++.|
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcch
Confidence 4578999997 799999999998754
No 104
>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=82.91 E-value=0.55 Score=19.19 Aligned_cols=21 Identities=14% Similarity=0.460 Sum_probs=7.2
Q ss_pred ceeCChhhHhhhchHHHHHhh
Q psy12265 48 AFQCEYCGKDFARKYQAHSYH 68 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~ 68 (71)
.|+|+.|...|-..-++-.|.
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTT
T ss_pred eEECCCCCCccccCcChhhhc
Confidence 455555555444444444443
No 105
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.45 E-value=0.72 Score=21.96 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=7.5
Q ss_pred CceeCChhhHhhh
Q psy12265 47 KAFQCEYCGKDFA 59 (71)
Q Consensus 47 ~~~~C~~c~~~f~ 59 (71)
.|..|++||++|+
T Consensus 25 dPiVsPytG~s~P 37 (129)
T COG4530 25 DPIVSPYTGKSYP 37 (129)
T ss_pred CccccCcccccch
Confidence 3555666666654
No 106
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=82.22 E-value=0.61 Score=23.46 Aligned_cols=35 Identities=26% Similarity=0.786 Sum_probs=21.9
Q ss_pred CCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 17 LKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 17 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
.-+|.|. |+..|...- +|-. .-.|+ .|.|..|+-.
T Consensus 115 ~~~Y~C~-C~q~~l~~R---Rhn~-~~~g~-~YrC~~C~gk 149 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIR---RHNT-VRRGE-VYRCGKCGGK 149 (156)
T ss_pred ceeEEee-cCCccchhh---hccc-ccccc-eEEeccCCce
Confidence 3469999 998765432 2221 23345 8999999753
No 107
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.68 E-value=0.56 Score=18.93 Aligned_cols=16 Identities=19% Similarity=0.515 Sum_probs=11.9
Q ss_pred eCChhhHhhhchHHHH
Q psy12265 50 QCEYCGKDFARKYQAH 65 (71)
Q Consensus 50 ~C~~c~~~f~~~~~l~ 65 (71)
.|+.|++.|+.+..++
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 5888888888766554
No 108
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=81.56 E-value=1.7 Score=25.00 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=25.7
Q ss_pred ecccccccccchhhHHHhHhhhcCCcCceeCChh----hHhhhchHHHHHhhh
Q psy12265 21 GCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYC----GKDFARKYQAHSYHQ 69 (71)
Q Consensus 21 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c----~~~f~~~~~l~~h~~ 69 (71)
.|..|...|-....|..|++..| ++-+.|..- ...|..-.+|..|.+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H--E~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH--EACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh--hhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 56777777777777777776222 322333221 234566666666643
No 109
>KOG2231|consensus
Probab=81.35 E-value=5 Score=25.16 Aligned_cols=19 Identities=16% Similarity=0.483 Sum_probs=10.2
Q ss_pred CChhhHhhhchHHHHHhhh
Q psy12265 51 CEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 51 C~~c~~~f~~~~~l~~h~~ 69 (71)
|..|...|-....|..|++
T Consensus 185 C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLR 203 (669)
T ss_pred chhhhhhhccHHHHHHhhc
Confidence 4555555555555555544
No 110
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=79.84 E-value=0.62 Score=17.82 Aligned_cols=12 Identities=42% Similarity=1.140 Sum_probs=9.3
Q ss_pred ceeCChhhHhhh
Q psy12265 48 AFQCEYCGKDFA 59 (71)
Q Consensus 48 ~~~C~~c~~~f~ 59 (71)
||.|..|+..|-
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 788888887764
No 111
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=78.96 E-value=1.5 Score=20.23 Aligned_cols=28 Identities=32% Similarity=0.745 Sum_probs=17.4
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
.|-.|..||..|.. -...+|-+|+.|..
T Consensus 57 ~Pa~CkkCGfef~~-----------~~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD-----------DKIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc-----------cccCCcccCCcchh
Confidence 56788888876643 11234667887754
No 112
>KOG0717|consensus
Probab=78.91 E-value=0.75 Score=27.25 Aligned_cols=22 Identities=23% Similarity=0.455 Sum_probs=17.7
Q ss_pred eeCChhhHhhhchHHHHHhhhc
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
+-|.+|.++|.+.-.|..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 5688888888888888888654
No 113
>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=78.57 E-value=1.1 Score=21.42 Aligned_cols=24 Identities=21% Similarity=0.533 Sum_probs=15.8
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
..|..|+..|.... ..+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~-------------~~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEI-------------DLYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCC-------------cCccCcCCcC
Confidence 78888886665321 1357888874
No 114
>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=77.01 E-value=0.71 Score=18.79 Aligned_cols=12 Identities=25% Similarity=0.888 Sum_probs=6.1
Q ss_pred eCChhhHhhhch
Q psy12265 50 QCEYCGKDFARK 61 (71)
Q Consensus 50 ~C~~c~~~f~~~ 61 (71)
.||.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 799999877644
No 115
>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=76.89 E-value=0.6 Score=18.13 Aligned_cols=13 Identities=46% Similarity=1.191 Sum_probs=7.6
Q ss_pred CceeCChhhHhhh
Q psy12265 47 KAFQCEYCGKDFA 59 (71)
Q Consensus 47 ~~~~C~~c~~~f~ 59 (71)
.|+.|..|+..|-
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 5788888887764
No 116
>KOG2231|consensus
Probab=75.41 E-value=2.5 Score=26.31 Aligned_cols=45 Identities=16% Similarity=0.296 Sum_probs=30.7
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChh------hHhhhchHHHHHhhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYC------GKDFARKYQAHSYHQ 69 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c------~~~f~~~~~l~~h~~ 69 (71)
-.|..|...|.....+.+|++. + -|.|..| +..|....+|+.|-+
T Consensus 183 p~C~~C~~~fld~~el~rH~~~-~----h~~chfC~~~~~~neyy~~~~dLe~HfR 233 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRF-D----HEFCHFCDYKTGQNEYYNDYDDLEEHFR 233 (669)
T ss_pred ccchhhhhhhccHHHHHHhhcc-c----eeheeecCcccccchhcccchHHHHHhh
Confidence 4677788888888888887762 2 2334444 456788888888865
No 117
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.86 E-value=2.7 Score=18.73 Aligned_cols=32 Identities=31% Similarity=0.710 Sum_probs=19.9
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
|.|..|+..|. +.+++. ....-.|+.|+..+.
T Consensus 13 Y~c~~cg~~~d----vvq~~~----ddplt~ce~c~a~~k 44 (82)
T COG2331 13 YECTECGNRFD----VVQAMT----DDPLTTCEECGARLK 44 (82)
T ss_pred EeecccchHHH----HHHhcc----cCccccChhhChHHH
Confidence 89999987754 333332 333346888886544
No 118
>KOG4173|consensus
Probab=74.69 E-value=2.5 Score=22.58 Aligned_cols=19 Identities=32% Similarity=0.516 Sum_probs=8.8
Q ss_pred ecccccccccchhhHHHhH
Q psy12265 21 GCEVCGRHFRQWGDLKYHK 39 (71)
Q Consensus 21 ~c~~c~~~~~~~~~l~~h~ 39 (71)
.|..|.+.|.+.--|..|+
T Consensus 108 sCs~C~r~~Pt~hLLd~HI 126 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHI 126 (253)
T ss_pred hhHHHHHhCCchhhhhHHH
Confidence 4455555554444444443
No 119
>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=74.60 E-value=3.9 Score=19.11 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=15.6
Q ss_pred eec----ccccccccchhhHHHhHhh
Q psy12265 20 YGC----EVCGRHFRQWGDLKYHKAS 41 (71)
Q Consensus 20 ~~c----~~c~~~~~~~~~l~~h~~~ 41 (71)
|.| ..|+....+...+..|.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~ 106 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRK 106 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHH
Confidence 677 7777777777777777653
No 120
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=74.12 E-value=1.8 Score=20.61 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=15.3
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
..|..|+..|... ...+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~-------------~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIH-------------QHDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecC-------------CcCccCcCCCC
Confidence 7888888655422 12346888874
No 121
>PLN02294 cytochrome c oxidase subunit Vb
Probab=73.96 E-value=0.98 Score=23.18 Aligned_cols=16 Identities=31% Similarity=0.723 Sum_probs=12.4
Q ss_pred cCceeCChhhHhhhch
Q psy12265 46 VKAFQCEYCGKDFARK 61 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~ 61 (71)
.+|.+|+.||..|.-+
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 3688999999887643
No 122
>KOG2785|consensus
Probab=73.79 E-value=4.7 Score=23.46 Aligned_cols=54 Identities=19% Similarity=0.354 Sum_probs=39.2
Q ss_pred CCceecccccccccchhhHHHhHhhhcCCc----------------------CceeCChhh---HhhhchHHHHHhhhc
Q psy12265 17 LKPYGCEVCGRHFRQWGDLKYHKASLHSDV----------------------KAFQCEYCG---KDFARKYQAHSYHQI 70 (71)
Q Consensus 17 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~----------------------~~~~C~~c~---~~f~~~~~l~~h~~~ 70 (71)
..|-.|-.|++.+.+-..-..||...|.-- .-+.|..|. +.|..-...+.||..
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 356678889988888777778886444211 125788888 889999899999864
No 123
>KOG1842|consensus
Probab=73.37 E-value=2.6 Score=25.07 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=19.7
Q ss_pred CceeCChhhHhhhchHHHHHhhh
Q psy12265 47 KAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
.-|.|+.|...|.+-..|.-|..
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHh
Confidence 45899999999999999988853
No 124
>KOG3507|consensus
Probab=73.32 E-value=3.8 Score=17.30 Aligned_cols=32 Identities=25% Similarity=0.497 Sum_probs=20.5
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhch
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARK 61 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 61 (71)
..|.|..|+.--. -...-+++|..||.....+
T Consensus 19 miYiCgdC~~en~------------lk~~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 19 MIYICGDCGQENT------------LKRGDVIRCRECGYRILYK 50 (62)
T ss_pred EEEEecccccccc------------ccCCCcEehhhcchHHHHH
Confidence 3489999974311 1123478999999876544
No 125
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.30 E-value=0.9 Score=22.17 Aligned_cols=36 Identities=17% Similarity=0.464 Sum_probs=21.3
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhch
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARK 61 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 61 (71)
-.|+.|+...... .-. .-.+...|.|..|+++|...
T Consensus 31 ~~cP~C~s~~~~k-----~g~-~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSNVVK-----IGG-IRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccceee-----ECC-ccccccccccCCcCcceeee
Confidence 5677776443111 101 12235679999999988754
No 126
>PF14353 CpXC: CpXC protein
Probab=73.21 E-value=0.35 Score=23.22 Aligned_cols=18 Identities=33% Similarity=0.831 Sum_probs=12.9
Q ss_pred CceeCChhhHhhhchHHH
Q psy12265 47 KAFQCEYCGKDFARKYQA 64 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~~l 64 (71)
-.+.|+.||..|.-...+
T Consensus 37 ~~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPL 54 (128)
T ss_pred CEEECCCCCCceecCCCE
Confidence 458999999887654443
No 127
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=72.54 E-value=5 Score=21.19 Aligned_cols=36 Identities=19% Similarity=0.365 Sum_probs=20.5
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
-+.|+.|+ .-.....+. + ....+..++|..||..+.
T Consensus 6 y~~Cp~Cg-~eev~hEVi---k-~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 6 YIECPSCG-SEEVSHEVI---K-ERGREPLVRCEECGTVHP 41 (201)
T ss_pred EEECCCCC-cchhhHHHH---H-hcCCceEEEccCCCcEee
Confidence 46899998 211111111 1 234456789999997663
No 128
>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=72.21 E-value=1.3 Score=15.81 Aligned_cols=18 Identities=28% Similarity=0.741 Sum_probs=10.2
Q ss_pred eecccccccccchhhHHHh
Q psy12265 20 YGCEVCGRHFRQWGDLKYH 38 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h 38 (71)
+.|..|++.|.. .....|
T Consensus 1 ~sCiDC~~~F~~-~~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDFDG-DSYKSH 18 (28)
T ss_dssp EEETTTTEEEEG-GGTTT-
T ss_pred CeeecCCCCcCc-CCcCCC
Confidence 467788888843 333334
No 129
>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=72.13 E-value=1.8 Score=15.63 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=6.2
Q ss_pred CceeCChhhH
Q psy12265 47 KAFQCEYCGK 56 (71)
Q Consensus 47 ~~~~C~~c~~ 56 (71)
..+.|+.|+.
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 3567777763
No 130
>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=71.90 E-value=1.1 Score=20.88 Aligned_cols=18 Identities=33% Similarity=0.645 Sum_probs=13.4
Q ss_pred hcCCcCceeCChhhHhhhc
Q psy12265 42 LHSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 42 ~~~~~~~~~C~~c~~~f~~ 60 (71)
.+.+ ++.+|+.||.-|.-
T Consensus 74 l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 74 LEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EeCC-CceeCCCCCcEEEE
Confidence 3444 68999999988763
No 131
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=71.47 E-value=0.85 Score=20.02 Aligned_cols=15 Identities=27% Similarity=0.678 Sum_probs=8.5
Q ss_pred cCceeCC--hhhHhhhc
Q psy12265 46 VKAFQCE--YCGKDFAR 60 (71)
Q Consensus 46 ~~~~~C~--~c~~~f~~ 60 (71)
+..++|. .||..|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 4445665 66666643
No 132
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=71.29 E-value=2.4 Score=21.22 Aligned_cols=28 Identities=29% Similarity=0.666 Sum_probs=17.5
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
.+.|..|+..... .+++. .-.|+.|+..
T Consensus 112 ~l~C~~Cg~~~~~----------~~~~~-l~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHEVEL----------THPER-LPPCPKCGHT 139 (146)
T ss_pred eEecccCCCEEEe----------cCCCc-CCCCCCCCCC
Confidence 3899999865321 23333 3479999753
No 133
>PRK11823 DNA repair protein RadA; Provisional
Probab=70.41 E-value=3.1 Score=24.52 Aligned_cols=11 Identities=36% Similarity=1.032 Sum_probs=8.1
Q ss_pred Cceeccccccc
Q psy12265 18 KPYGCEVCGRH 28 (71)
Q Consensus 18 ~~~~c~~c~~~ 28 (71)
..|.|..||..
T Consensus 6 ~~y~C~~Cg~~ 16 (446)
T PRK11823 6 TAYVCQECGAE 16 (446)
T ss_pred CeEECCcCCCC
Confidence 35899999854
No 134
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.41 E-value=1.4 Score=21.57 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=24.3
Q ss_pred hHhhCCCc-eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhc
Q psy12265 12 RVHLGLKP-YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 12 ~~~~~~~~-~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~ 60 (71)
-.+.++.. -.|+.|..+..-...+..-....+.-+.|--|-.||+.|+.
T Consensus 31 cskcgeati~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpw 80 (160)
T COG4306 31 CSKCGEATITQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPW 80 (160)
T ss_pred HhhhchHHHhcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCc
Confidence 34444433 56777765443332222211111223456668888888774
No 135
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=69.58 E-value=3.3 Score=24.50 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=7.2
Q ss_pred ceeccccccc
Q psy12265 19 PYGCEVCGRH 28 (71)
Q Consensus 19 ~~~c~~c~~~ 28 (71)
.|.|..||..
T Consensus 7 ~y~C~~Cg~~ 16 (454)
T TIGR00416 7 KFVCQHCGAD 16 (454)
T ss_pred eEECCcCCCC
Confidence 4888888744
No 136
>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=69.20 E-value=0.91 Score=17.58 Aligned_cols=12 Identities=33% Similarity=1.099 Sum_probs=8.8
Q ss_pred CceeCChhhHhh
Q psy12265 47 KAFQCEYCGKDF 58 (71)
Q Consensus 47 ~~~~C~~c~~~f 58 (71)
.+..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356899998765
No 137
>KOG1280|consensus
Probab=68.62 E-value=6.2 Score=22.80 Aligned_cols=38 Identities=21% Similarity=0.450 Sum_probs=26.3
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCc-eeCChhh
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKA-FQCEYCG 55 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~-~~C~~c~ 55 (71)
..|.|+.|+..-.....+.-|....|....+ ..|+.|+
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 4689999998777778888887766664432 3455553
No 138
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=68.48 E-value=2.2 Score=20.40 Aligned_cols=11 Identities=27% Similarity=0.884 Sum_probs=8.2
Q ss_pred eeccccccccc
Q psy12265 20 YGCEVCGRHFR 30 (71)
Q Consensus 20 ~~c~~c~~~~~ 30 (71)
..|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 78888886654
No 139
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=68.29 E-value=2 Score=20.49 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=15.3
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
..|..|+..|.... ...+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~------------~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLT------------QRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCC------------ccCCcCcCcCC
Confidence 78888986554211 11256998984
No 140
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=68.26 E-value=2.6 Score=24.79 Aligned_cols=29 Identities=24% Similarity=0.720 Sum_probs=18.4
Q ss_pred ecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhch
Q psy12265 21 GCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARK 61 (71)
Q Consensus 21 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 61 (71)
.|+.|+.+.. ..|..-|+|+.||..+...
T Consensus 352 ~Cp~Cg~~m~------------S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMK------------SAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchh------------hcCCCCcccccccccCCcc
Confidence 6778875532 2233378888888776543
No 141
>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=67.45 E-value=2.8 Score=20.67 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=9.7
Q ss_pred eeCChhhHhhhchHHHHHhhh
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~ 69 (71)
..|.+||+.|.. |.+|.+
T Consensus 73 i~clecGk~~k~---LkrHL~ 90 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLR 90 (132)
T ss_dssp EE-TBT--EESB---HHHHHH
T ss_pred eEEccCCcccch---HHHHHH
Confidence 578889987764 355554
No 142
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=67.17 E-value=4.2 Score=22.76 Aligned_cols=24 Identities=29% Similarity=0.459 Sum_probs=19.1
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
...|.|..|-+-|.....|.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 456888888888888888888864
No 143
>KOG0782|consensus
Probab=66.84 E-value=2.8 Score=25.96 Aligned_cols=49 Identities=29% Similarity=0.497 Sum_probs=28.7
Q ss_pred HHHHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCc-CceeCChhhHhhhch
Q psy12265 6 YLKVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDV-KAFQCEYCGKDFARK 61 (71)
Q Consensus 6 ~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~-~~~~C~~c~~~f~~~ 61 (71)
.+.+|.=+|-....-.|..|+++|-++-. .|..+ ....|..|...|-.+
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~-------FhsKEivAisCSWCKqayH~K 289 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFF-------FHSKEIVAISCSWCKQAYHLK 289 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhhee-------eccccEEEEEehHHHHHhhcc
Confidence 34455455555556778888888765433 23323 335688887766544
No 144
>KOG2807|consensus
Probab=66.37 E-value=8 Score=22.26 Aligned_cols=22 Identities=18% Similarity=0.460 Sum_probs=13.7
Q ss_pred ceeCChhhHhhhchHHHHHhhh
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
.|+|..|...|-..-+.-.|..
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred cEEchhccceeeccchHHHHhh
Confidence 4677777777766555555543
No 145
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=65.56 E-value=3.7 Score=22.57 Aligned_cols=19 Identities=32% Similarity=0.607 Sum_probs=12.2
Q ss_pred cCceeCChhhHhhhchHHH
Q psy12265 46 VKAFQCEYCGKDFARKYQA 64 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l 64 (71)
...|.|+.||..+......
T Consensus 320 ~r~~~C~~cg~~~~rD~na 338 (364)
T COG0675 320 GRLFKCPRCGFVHDRDVNA 338 (364)
T ss_pred ceeEECCCCCCeehhhHHH
Confidence 3467899998765544333
No 146
>KOG2636|consensus
Probab=65.18 E-value=3.6 Score=24.52 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=16.2
Q ss_pred hcCCcCceeCChhh-HhhhchHHHHHh
Q psy12265 42 LHSDVKAFQCEYCG-KDFARKYQAHSY 67 (71)
Q Consensus 42 ~~~~~~~~~C~~c~-~~f~~~~~l~~h 67 (71)
.|.-...|.|.+|| .++.-+...++|
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHH
Confidence 57667788999998 444444444433
No 147
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=64.45 E-value=5.9 Score=23.66 Aligned_cols=24 Identities=33% Similarity=0.506 Sum_probs=21.0
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
...|.|..|-+-|.....|.+|+.
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHh
Confidence 456899999999999999999975
No 148
>PTZ00064 histone acetyltransferase; Provisional
Probab=63.66 E-value=6 Score=24.06 Aligned_cols=24 Identities=21% Similarity=0.227 Sum_probs=20.7
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
...|.|..|-+-|.....|.+|+.
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~ 301 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLS 301 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHh
Confidence 456899999999999999999975
No 149
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=63.53 E-value=3.8 Score=20.22 Aligned_cols=15 Identities=40% Similarity=0.879 Sum_probs=11.9
Q ss_pred ceecccccccccchh
Q psy12265 19 PYGCEVCGRHFRQWG 33 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~ 33 (71)
|+.|..|+..|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999987543
No 150
>PLN03239 histone acetyltransferase; Provisional
Probab=63.35 E-value=6.2 Score=22.76 Aligned_cols=24 Identities=25% Similarity=0.379 Sum_probs=20.8
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
...|.|..|-+-|.....|.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 457899999999999999999874
No 151
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=63.14 E-value=3 Score=19.80 Aligned_cols=25 Identities=32% Similarity=0.736 Sum_probs=14.5
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
..|..|+..|..... .+.||.||..
T Consensus 71 ~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEF-------------DFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHC-------------CHH-SSSSSS
T ss_pred EECCCCCCEEecCCC-------------CCCCcCCcCC
Confidence 788888877764321 1458888753
No 152
>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=62.78 E-value=6.7 Score=18.44 Aligned_cols=10 Identities=30% Similarity=1.029 Sum_probs=4.4
Q ss_pred Cceecccccc
Q psy12265 18 KPYGCEVCGR 27 (71)
Q Consensus 18 ~~~~c~~c~~ 27 (71)
+.|.|...|+
T Consensus 29 ~vwtC~~TGk 38 (102)
T PF10537_consen 29 RVWTCEITGK 38 (102)
T ss_pred CeeEEecCCC
Confidence 3444444443
No 153
>COG1773 Rubredoxin [Energy production and conversion]
Probab=62.75 E-value=1.9 Score=17.98 Aligned_cols=9 Identities=33% Similarity=1.066 Sum_probs=4.4
Q ss_pred eeCChhhHh
Q psy12265 49 FQCEYCGKD 57 (71)
Q Consensus 49 ~~C~~c~~~ 57 (71)
|+|..||..
T Consensus 4 ~~C~~CG~v 12 (55)
T COG1773 4 WRCSVCGYV 12 (55)
T ss_pred eEecCCceE
Confidence 455555443
No 154
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=62.35 E-value=14 Score=18.76 Aligned_cols=43 Identities=19% Similarity=0.352 Sum_probs=18.7
Q ss_pred hCCCceeccccccccc------chhhHHHhHhhh-------c----CCcCceeCChhhHh
Q psy12265 15 LGLKPYGCEVCGRHFR------QWGDLKYHKASL-------H----SDVKAFQCEYCGKD 57 (71)
Q Consensus 15 ~~~~~~~c~~c~~~~~------~~~~l~~h~~~~-------~----~~~~~~~C~~c~~~ 57 (71)
.......|..|++-|. +.+.+..|+... | .|+...+|..||..
T Consensus 10 ~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 10 DPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp -CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT---
T ss_pred CcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCC
Confidence 3444567777777664 345566665421 1 23445788888753
No 155
>PRK05978 hypothetical protein; Provisional
Probab=62.30 E-value=1.7 Score=21.80 Aligned_cols=32 Identities=31% Similarity=0.573 Sum_probs=17.8
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhch
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARK 61 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 61 (71)
-.|+.|++.-.....++ ..-.|+.||..|...
T Consensus 34 grCP~CG~G~LF~g~Lk----------v~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLK----------PVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccccccc----------cCCCccccCCccccC
Confidence 46788876533222222 122688888776543
No 156
>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=62.15 E-value=1.6 Score=16.16 Aligned_cols=12 Identities=33% Similarity=0.883 Sum_probs=7.7
Q ss_pred ceeCChhhHhhh
Q psy12265 48 AFQCEYCGKDFA 59 (71)
Q Consensus 48 ~~~C~~c~~~f~ 59 (71)
.+.|+.|++.+.
T Consensus 4 ~~~C~nC~R~v~ 15 (33)
T PF08209_consen 4 YVECPNCGRPVA 15 (33)
T ss_dssp EEE-TTTSSEEE
T ss_pred eEECCCCcCCcc
Confidence 478999987543
No 157
>KOG1994|consensus
Probab=61.97 E-value=3.1 Score=22.53 Aligned_cols=24 Identities=13% Similarity=0.390 Sum_probs=19.8
Q ss_pred CCcCceeCChhhHhhhchHHHHHh
Q psy12265 44 SDVKAFQCEYCGKDFARKYQAHSY 67 (71)
Q Consensus 44 ~~~~~~~C~~c~~~f~~~~~l~~h 67 (71)
.....|-|-.||..|...-+|..|
T Consensus 235 LR~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 235 LRSEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred HhccceEEEEeccccCCHHHHHHh
Confidence 345568899999999999998877
No 158
>KOG2747|consensus
Probab=61.96 E-value=6.9 Score=22.97 Aligned_cols=24 Identities=21% Similarity=0.407 Sum_probs=21.2
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
...|.|..|.+.+.....|++|+.
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~ 179 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLK 179 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHH
Confidence 456899999999999999999975
No 159
>KOG0978|consensus
Probab=61.92 E-value=1.7 Score=27.14 Aligned_cols=20 Identities=15% Similarity=0.263 Sum_probs=15.9
Q ss_pred eeCChhhHhhhchHHHHHhh
Q psy12265 49 FQCEYCGKDFARKYQAHSYH 68 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~ 68 (71)
-+||.|+..|..+.-+.+|+
T Consensus 679 RKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred CCCCCCCCCCCcccccccCC
Confidence 48999999999887666653
No 160
>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=61.80 E-value=4.1 Score=15.41 Aligned_cols=11 Identities=36% Similarity=1.014 Sum_probs=5.3
Q ss_pred CceeCChhhHh
Q psy12265 47 KAFQCEYCGKD 57 (71)
Q Consensus 47 ~~~~C~~c~~~ 57 (71)
+-|+|..||-.
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 35788888743
No 161
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.73 E-value=4.5 Score=19.42 Aligned_cols=24 Identities=13% Similarity=0.402 Sum_probs=16.0
Q ss_pred CceeCChhhHhhhchHHHHHhhhc
Q psy12265 47 KAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
..|+|+.|...|-..-+.-.|..+
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred cceeCCCCCCccccccchhhhhhc
Confidence 357788887777766666666544
No 162
>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=61.59 E-value=1.8 Score=16.52 Aligned_cols=15 Identities=27% Similarity=0.875 Sum_probs=8.7
Q ss_pred cCCcCceeCChhhHh
Q psy12265 43 HSDVKAFQCEYCGKD 57 (71)
Q Consensus 43 ~~~~~~~~C~~c~~~ 57 (71)
..+.+.|.|..|+..
T Consensus 19 ~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 19 DDGGKTWICNFCGTK 33 (40)
T ss_dssp ETTTTEEEETTT--E
T ss_pred cCCCCEEECcCCCCc
Confidence 334567888888764
No 163
>KOG3362|consensus
Probab=61.43 E-value=1.6 Score=21.83 Aligned_cols=24 Identities=17% Similarity=0.515 Sum_probs=15.5
Q ss_pred ceeCChhhHhhhchHHHHHhhhcC
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQIR 71 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~~~ 71 (71)
+|.|..||-.+-.-..+..|..+|
T Consensus 129 ~ysC~~CG~kyCsv~C~~~HneTR 152 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNETR 152 (156)
T ss_pred hhHHHhcCCceeechhhhhccccc
Confidence 355666776676777777776553
No 164
>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=61.16 E-value=3.1 Score=15.67 Aligned_cols=30 Identities=20% Similarity=0.494 Sum_probs=16.5
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYC 54 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c 54 (71)
..|+.|+.. ..+.+|=. ...|...|.|..|
T Consensus 6 v~CP~C~s~----~~v~k~G~-~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQST----EGVKKNGK-SPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCC----CcceeCCC-CCCCCEeEecCcC
Confidence 467767643 11333322 3456677888877
No 165
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=61.10 E-value=1.5 Score=17.39 Aligned_cols=16 Identities=31% Similarity=0.638 Sum_probs=10.1
Q ss_pred CcCceeCCh--hhHhhhc
Q psy12265 45 DVKAFQCEY--CGKDFAR 60 (71)
Q Consensus 45 ~~~~~~C~~--c~~~f~~ 60 (71)
.+.-+.|.. ||..|..
T Consensus 22 ~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 22 RELYCQCTNPECGHTFVA 39 (47)
T ss_pred EEEEEEECCCcCCCEEEE
Confidence 345567765 8877653
No 166
>PTZ00448 hypothetical protein; Provisional
Probab=59.97 E-value=4.9 Score=23.32 Aligned_cols=23 Identities=9% Similarity=0.205 Sum_probs=17.6
Q ss_pred ceeCChhhHhhhchHHHHHhhhc
Q psy12265 48 AFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.|.|..|+..|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999888777777777653
No 167
>KOG2907|consensus
Probab=59.80 E-value=3.9 Score=19.64 Aligned_cols=41 Identities=17% Similarity=0.426 Sum_probs=22.2
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCc-eeCChhhHhhhch
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKA-FQCEYCGKDFARK 61 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~-~~C~~c~~~f~~~ 61 (71)
...|+.|+..=..-.. ..++...-|+-. |.|+.|+..|...
T Consensus 74 ~~kCpkCghe~m~Y~T--~QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHT--LQLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred hccCcccCCchhhhhh--hhcccccCCceEEEEcCccceeeecc
Confidence 3788888854222122 122212223333 7899999887643
No 168
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.46 E-value=3.8 Score=19.85 Aligned_cols=30 Identities=27% Similarity=0.473 Sum_probs=16.7
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
..| .|+..|.....-..+ . ...+.||.||.
T Consensus 71 ~~C-~Cg~~~~~~~~~~~~-----~-~~~~~CP~Cgs 100 (124)
T PRK00762 71 IEC-ECGYEGVVDEDEIDH-----Y-AAVIECPVCGN 100 (124)
T ss_pred EEe-eCcCcccccccchhc-----c-ccCCcCcCCCC
Confidence 789 999776543211111 0 11357999983
No 169
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=59.24 E-value=4.2 Score=16.65 Aligned_cols=17 Identities=18% Similarity=0.661 Sum_probs=10.6
Q ss_pred CcCceeCChhhHhhhch
Q psy12265 45 DVKAFQCEYCGKDFARK 61 (71)
Q Consensus 45 ~~~~~~C~~c~~~f~~~ 61 (71)
....++|.+|++.+...
T Consensus 32 ~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 32 EPIKLRCHYCERIITED 48 (52)
T ss_dssp TTCEEEETTT--EEEHH
T ss_pred CCCEEEeeCCCCEeccc
Confidence 44568999998877654
No 170
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=58.70 E-value=15 Score=17.59 Aligned_cols=21 Identities=14% Similarity=0.298 Sum_probs=12.9
Q ss_pred eeCChhhHhhhchHHHHHhhh
Q psy12265 49 FQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~h~~ 69 (71)
+-|..|.+-|...-.|..|.+
T Consensus 56 hYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 56 HYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhc
Confidence 456666666666666666643
No 171
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=58.45 E-value=2.1 Score=17.55 Aligned_cols=10 Identities=50% Similarity=1.368 Sum_probs=6.1
Q ss_pred eCChhhHhhh
Q psy12265 50 QCEYCGKDFA 59 (71)
Q Consensus 50 ~C~~c~~~f~ 59 (71)
.|++||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5777776543
No 172
>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=58.37 E-value=3.3 Score=22.07 Aligned_cols=24 Identities=17% Similarity=0.221 Sum_probs=0.0
Q ss_pred cCceeCChhhHhhhchHHHHHhhhc
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
.....|++||..++- +.+..||++
T Consensus 166 ~~~~~cPitGe~IP~-~e~~eHmRi 189 (229)
T PF12230_consen 166 EKMIICPITGEMIPA-DEMDEHMRI 189 (229)
T ss_dssp -------------------------
T ss_pred ccccccccccccccc-ccccccccc
Confidence 344679999887653 356677664
No 173
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=56.69 E-value=3.1 Score=22.56 Aligned_cols=15 Identities=20% Similarity=0.450 Sum_probs=11.8
Q ss_pred cCceeCChhhHhhhc
Q psy12265 46 VKAFQCEYCGKDFAR 60 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~ 60 (71)
.++.+|+.||..|.-
T Consensus 179 GkpqRCpECGqVFKL 193 (268)
T PTZ00043 179 GFLYRCGECDQIFML 193 (268)
T ss_pred CCCccCCCCCcEEEE
Confidence 457899999987763
No 174
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=56.28 E-value=7.2 Score=22.57 Aligned_cols=9 Identities=33% Similarity=0.748 Sum_probs=4.8
Q ss_pred ceecccccc
Q psy12265 19 PYGCEVCGR 27 (71)
Q Consensus 19 ~~~c~~c~~ 27 (71)
-+.|+.|+.
T Consensus 14 ~g~cp~c~~ 22 (372)
T cd01121 14 LGKCPECGE 22 (372)
T ss_pred cEECcCCCC
Confidence 355666653
No 175
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=55.22 E-value=4.3 Score=17.24 Aligned_cols=14 Identities=36% Similarity=0.738 Sum_probs=7.6
Q ss_pred ceeCChhhHhhhch
Q psy12265 48 AFQCEYCGKDFARK 61 (71)
Q Consensus 48 ~~~C~~c~~~f~~~ 61 (71)
|.+|-.||+..++.
T Consensus 4 PVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 4 PVRCFTCGKVIGNK 17 (60)
T ss_dssp SSS-STTTSBTCGH
T ss_pred ceecCCCCCChhHh
Confidence 45677777655443
No 176
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.09 E-value=4.5 Score=22.04 Aligned_cols=17 Identities=24% Similarity=0.686 Sum_probs=12.4
Q ss_pred cCceeCChhhHhhhchH
Q psy12265 46 VKAFQCEYCGKDFARKY 62 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~ 62 (71)
++.+.||+|+-.|....
T Consensus 17 kk~ieCPvC~tkFkkee 33 (267)
T COG1655 17 KKTIECPVCNTKFKKEE 33 (267)
T ss_pred hceeccCcccchhhhhh
Confidence 55678999988876543
No 177
>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=55.01 E-value=2.5 Score=17.50 Aligned_cols=11 Identities=36% Similarity=1.159 Sum_probs=6.8
Q ss_pred eeCChhhHhhh
Q psy12265 49 FQCEYCGKDFA 59 (71)
Q Consensus 49 ~~C~~c~~~f~ 59 (71)
|.|+.||..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 56777776543
No 178
>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=54.93 E-value=6.6 Score=18.74 Aligned_cols=12 Identities=17% Similarity=0.556 Sum_probs=7.2
Q ss_pred ceeCChhhHhhh
Q psy12265 48 AFQCEYCGKDFA 59 (71)
Q Consensus 48 ~~~C~~c~~~f~ 59 (71)
.|.|+.|+...+
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 466777765543
No 179
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=54.88 E-value=1.2 Score=17.14 Aligned_cols=10 Identities=30% Similarity=1.162 Sum_probs=7.5
Q ss_pred eeCChhhHhh
Q psy12265 49 FQCEYCGKDF 58 (71)
Q Consensus 49 ~~C~~c~~~f 58 (71)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 7888888654
No 180
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=54.83 E-value=5.8 Score=16.53 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=10.1
Q ss_pred CCcCceeCChhhHh
Q psy12265 44 SDVKAFQCEYCGKD 57 (71)
Q Consensus 44 ~~~~~~~C~~c~~~ 57 (71)
.+...|.|+.||-.
T Consensus 10 ~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 10 PAHVNFECPDCGIP 23 (55)
T ss_pred ccccCCcCCCCCCc
Confidence 34567899998854
No 181
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=54.68 E-value=6.7 Score=19.38 Aligned_cols=32 Identities=28% Similarity=0.879 Sum_probs=17.8
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDF 58 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f 58 (71)
.|.|..|+..+. ++.+ +.....|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~------~~rr--~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYL------RVRR--SNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCc------eEcc--ccCcceEEcCCCCCEE
Confidence 577877876543 2222 2222557888887543
No 182
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=54.66 E-value=8.4 Score=22.07 Aligned_cols=46 Identities=20% Similarity=0.417 Sum_probs=26.8
Q ss_pred cccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchHHHHHhhhc
Q psy12265 22 CEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKYQAHSYHQI 70 (71)
Q Consensus 22 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~ 70 (71)
|-.|...|+-...-... .-+....|+|+.|...|-..-+.-.|..+
T Consensus 365 Cf~CQ~~fp~~~~~~~~---~~~ss~rY~Ce~CK~~FC~dCdvfiHe~L 410 (421)
T COG5151 365 CFVCQGPFPKPPVSPFD---ESTSSGRYQCELCKSTFCSDCDVFIHETL 410 (421)
T ss_pred ceeccCCCCCCCCCccc---ccccccceechhhhhhhhhhhHHHHHHHH
Confidence 55566666544321111 12234568999999888877776666543
No 183
>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=54.50 E-value=4.1 Score=21.49 Aligned_cols=14 Identities=43% Similarity=0.963 Sum_probs=0.0
Q ss_pred hcCCcCceeCChhh
Q psy12265 42 LHSDVKAFQCEYCG 55 (71)
Q Consensus 42 ~~~~~~~~~C~~c~ 55 (71)
.|.-...|.|.+||
T Consensus 95 LhGL~~ey~CEICG 108 (196)
T PF11931_consen 95 LHGLGVEYKCEICG 108 (196)
T ss_dssp --------------
T ss_pred HhCCCCeeeeEeCC
Confidence 34445667888886
No 184
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=54.46 E-value=8.4 Score=22.46 Aligned_cols=14 Identities=50% Similarity=1.013 Sum_probs=11.4
Q ss_pred hcCCcCceeCChhh
Q psy12265 42 LHSDVKAFQCEYCG 55 (71)
Q Consensus 42 ~~~~~~~~~C~~c~ 55 (71)
.|.-.+.|+|.+||
T Consensus 368 lhgLd~ef~CEICg 381 (470)
T COG5188 368 LHGLDIEFECEICG 381 (470)
T ss_pred hcCCCcceeeeecc
Confidence 56667789999998
No 185
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=54.04 E-value=1.6 Score=16.76 Aligned_cols=7 Identities=57% Similarity=1.184 Sum_probs=1.6
Q ss_pred ChhhHhh
Q psy12265 52 EYCGKDF 58 (71)
Q Consensus 52 ~~c~~~f 58 (71)
..|+..+
T Consensus 2 ~~C~~~~ 8 (47)
T PF01844_consen 2 QYCGKPG 8 (47)
T ss_dssp TTT--B-
T ss_pred CCCCCcC
Confidence 3444433
No 186
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=53.80 E-value=15 Score=14.13 Aligned_cols=22 Identities=32% Similarity=0.546 Sum_probs=14.3
Q ss_pred ceeccccccccc--chhhHHHhHh
Q psy12265 19 PYGCEVCGRHFR--QWGDLKYHKA 40 (71)
Q Consensus 19 ~~~c~~c~~~~~--~~~~l~~h~~ 40 (71)
.-.|..|+..|. ...+-..|.+
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~ 36 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKK 36 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHH
Confidence 358999997765 3455555654
No 187
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=53.41 E-value=5.1 Score=15.39 Aligned_cols=8 Identities=38% Similarity=1.286 Sum_probs=4.4
Q ss_pred eeCChhhH
Q psy12265 49 FQCEYCGK 56 (71)
Q Consensus 49 ~~C~~c~~ 56 (71)
|.|+.|+.
T Consensus 1 m~Cp~Cg~ 8 (43)
T PF08271_consen 1 MKCPNCGS 8 (43)
T ss_dssp ESBTTTSS
T ss_pred CCCcCCcC
Confidence 34666654
No 188
>PRK10220 hypothetical protein; Provisional
Probab=52.89 E-value=7.9 Score=18.52 Aligned_cols=12 Identities=17% Similarity=0.816 Sum_probs=7.2
Q ss_pred ceeCChhhHhhh
Q psy12265 48 AFQCEYCGKDFA 59 (71)
Q Consensus 48 ~~~C~~c~~~f~ 59 (71)
.|.|+.|+..+.
T Consensus 20 ~~vCpeC~hEW~ 31 (111)
T PRK10220 20 MYICPECAHEWN 31 (111)
T ss_pred eEECCcccCcCC
Confidence 466777765443
No 189
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=52.86 E-value=6.2 Score=23.58 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=22.0
Q ss_pred CCCceecccccccccch-hhHHHhHhhhcCCc------CceeCChhhH
Q psy12265 16 GLKPYGCEVCGRHFRQW-GDLKYHKASLHSDV------KAFQCEYCGK 56 (71)
Q Consensus 16 ~~~~~~c~~c~~~~~~~-~~l~~h~~~~~~~~------~~~~C~~c~~ 56 (71)
....|.|..|+..|... ++-..- ...|. ..|.|+.|+.
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~---~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQD---VAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccC---CCCCCChhhCCCCCcCcCCCC
Confidence 34569999999877643 211111 12221 2379999984
No 190
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=52.77 E-value=8.2 Score=18.21 Aligned_cols=11 Identities=45% Similarity=0.954 Sum_probs=7.4
Q ss_pred Cceeccccccc
Q psy12265 18 KPYGCEVCGRH 28 (71)
Q Consensus 18 ~~~~c~~c~~~ 28 (71)
+|-.|+.|+..
T Consensus 1 ~p~~CpYCg~~ 11 (102)
T PF11672_consen 1 KPIICPYCGGP 11 (102)
T ss_pred CCcccCCCCCe
Confidence 45678888754
No 191
>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=52.76 E-value=3.2 Score=20.61 Aligned_cols=17 Identities=35% Similarity=0.745 Sum_probs=12.5
Q ss_pred cCCcCceeCChhhHhhhc
Q psy12265 43 HSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 43 ~~~~~~~~C~~c~~~f~~ 60 (71)
+.+ ++.+|+.||.-|.-
T Consensus 108 ~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 108 HKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp ETT-SEEEETTTEEEEEE
T ss_pred eCC-CccCCCCCCeEEEE
Confidence 444 57899999987763
No 192
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.42 E-value=14 Score=18.28 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=15.2
Q ss_pred ccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 27 RHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 27 ~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
..|.++.++.+... .....|+.|+.+
T Consensus 16 GWF~ssaDfd~Q~~-----rgLv~CPvCgs~ 41 (142)
T COG5319 16 GWFGSSADFDRQRE-----RGLVTCPVCGST 41 (142)
T ss_pred ccccCchhHHHHHH-----cCceeCCCCCcH
Confidence 35666666665432 234578888754
No 193
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=52.14 E-value=28 Score=19.62 Aligned_cols=7 Identities=57% Similarity=1.644 Sum_probs=5.1
Q ss_pred eeccccc
Q psy12265 20 YGCEVCG 26 (71)
Q Consensus 20 ~~c~~c~ 26 (71)
|.|..||
T Consensus 355 ~~c~~cg 361 (389)
T PRK11788 355 YRCRNCG 361 (389)
T ss_pred EECCCCC
Confidence 7777776
No 194
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=51.38 E-value=3.4 Score=17.87 Aligned_cols=34 Identities=24% Similarity=0.537 Sum_probs=18.5
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
.|.|..|+.... ..+..+. .+.|..-.+|+.|..
T Consensus 4 ~FTC~~C~~Rs~--~~~sk~a--Y~~GvViv~C~gC~~ 37 (66)
T PF05180_consen 4 TFTCNKCGTRSA--KMFSKQA--YHKGVVIVQCPGCKN 37 (66)
T ss_dssp EEEETTTTEEEE--EEEEHHH--HHTSEEEEE-TTS--
T ss_pred EEEcCCCCCccc--eeeCHHH--HhCCeEEEECCCCcc
Confidence 378888875432 2222332 456666778998864
No 195
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=51.16 E-value=7.3 Score=20.12 Aligned_cols=19 Identities=21% Similarity=0.494 Sum_probs=14.0
Q ss_pred CceeCChhhHhhhchHHHH
Q psy12265 47 KAFQCEYCGKDFARKYQAH 65 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~~l~ 65 (71)
....|..||+.|.....++
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4678999999988554443
No 196
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=50.53 E-value=4.7 Score=18.47 Aligned_cols=33 Identities=30% Similarity=0.681 Sum_probs=21.9
Q ss_pred CCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhc
Q psy12265 17 LKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 17 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~ 60 (71)
..+|.|+.|++. . +.+ . ..--|.|..|+..|.-
T Consensus 33 ~~~~~Cp~C~~~-~-------VkR-~--a~GIW~C~kCg~~fAG 65 (89)
T COG1997 33 RAKHVCPFCGRT-T-------VKR-I--ATGIWKCRKCGAKFAG 65 (89)
T ss_pred hcCCcCCCCCCc-c-------eee-e--ccCeEEcCCCCCeecc
Confidence 357999999855 1 112 2 2346899999988763
No 197
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=50.39 E-value=13 Score=21.64 Aligned_cols=24 Identities=17% Similarity=0.386 Sum_probs=20.7
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
...|.|..|-+.|.....+.+|++
T Consensus 156 d~vyICefClkY~~s~~~~~rH~~ 179 (395)
T COG5027 156 DIVYICEFCLKYYGSQTSLVRHRK 179 (395)
T ss_pred ceEEEhhhhHHHhcchhHHHHHHh
Confidence 346899999999999999999975
No 198
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.20 E-value=8.5 Score=21.49 Aligned_cols=7 Identities=29% Similarity=0.923 Sum_probs=3.3
Q ss_pred eCChhhH
Q psy12265 50 QCEYCGK 56 (71)
Q Consensus 50 ~C~~c~~ 56 (71)
.|+.||.
T Consensus 271 ~C~~Cgt 277 (279)
T TIGR00627 271 ICKTCKT 277 (279)
T ss_pred CCCCCCC
Confidence 4555543
No 199
>KOG2071|consensus
Probab=50.15 E-value=7.5 Score=23.98 Aligned_cols=24 Identities=21% Similarity=0.360 Sum_probs=16.5
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
..+-.|..||..|........||-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md 439 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMD 439 (579)
T ss_pred CCcchhcccccccccchhhhhHhh
Confidence 345678888888877766665553
No 200
>COG4640 Predicted membrane protein [Function unknown]
Probab=49.96 E-value=8.8 Score=22.71 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=10.9
Q ss_pred ceecccccccccchhhHH
Q psy12265 19 PYGCEVCGRHFRQWGDLK 36 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~ 36 (71)
...|.+||..|.......
T Consensus 15 ~~qC~qCG~~~t~~~sqa 32 (465)
T COG4640 15 DVQCTQCGHKFTSRQSQA 32 (465)
T ss_pred cccccccCCcCCchhhhh
Confidence 345777777766554433
No 201
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.77 E-value=3.5 Score=13.78 Aligned_cols=6 Identities=50% Similarity=1.542 Sum_probs=3.6
Q ss_pred CChhhH
Q psy12265 51 CEYCGK 56 (71)
Q Consensus 51 C~~c~~ 56 (71)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 666654
No 202
>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=49.59 E-value=4.6 Score=20.02 Aligned_cols=39 Identities=21% Similarity=0.439 Sum_probs=20.1
Q ss_pred eecccccccccchhh--HHHhHh--hhcCCcCceeCChhhHhh
Q psy12265 20 YGCEVCGRHFRQWGD--LKYHKA--SLHSDVKAFQCEYCGKDF 58 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~--l~~h~~--~~~~~~~~~~C~~c~~~f 58 (71)
-.|..|+..+..-+. +..-.. .....+.-+.|+.|++.|
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 588899875543221 110000 011122347899999865
No 203
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.44 E-value=7 Score=16.68 Aligned_cols=43 Identities=16% Similarity=0.308 Sum_probs=23.5
Q ss_pred hHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 12 RVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 12 ~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
.++.+..++.|.--+..+..+--+. . + ..+.-..|++|+..|.
T Consensus 17 ~I~~~~~~l~C~g~~~p~~HPrV~L---~-m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 17 TIEIGDLPLMCPGPEPPNDHPRVFL---D-M-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEeCCeeEEcCCCCCCCCCCEEEE---E-c-CCCCcEecCccccEEE
Confidence 3455667788875544433221111 0 1 2234468999998775
No 204
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=47.80 E-value=4.9 Score=18.25 Aligned_cols=11 Identities=36% Similarity=1.144 Sum_probs=8.1
Q ss_pred eCChhhHhhhc
Q psy12265 50 QCEYCGKDFAR 60 (71)
Q Consensus 50 ~C~~c~~~f~~ 60 (71)
+|+.||..|..
T Consensus 10 ~C~~CG~d~~~ 20 (86)
T PF06170_consen 10 RCPHCGLDYSH 20 (86)
T ss_pred cccccCCcccc
Confidence 68888877654
No 205
>PRK12722 transcriptional activator FlhC; Provisional
Probab=47.38 E-value=14 Score=19.47 Aligned_cols=28 Identities=36% Similarity=0.880 Sum_probs=18.1
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
..|..|+..|.... +.....|.|+.|.-
T Consensus 135 ~~C~~Cgg~fv~~~---------~e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHA---------HDPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeeccc---------cccCCCCcCCCCCC
Confidence 57888888776321 22245688998853
No 206
>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=47.18 E-value=4.4 Score=20.00 Aligned_cols=31 Identities=32% Similarity=0.950 Sum_probs=17.4
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDF 58 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f 58 (71)
.|.|..|+..+.. +.+ . ....|.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r------~~~-~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRR-S--KRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeee------ecc-c--chhhEECCCCCCEE
Confidence 4778888766532 211 1 22347888887543
No 207
>PHA02942 putative transposase; Provisional
Probab=47.16 E-value=9.9 Score=22.13 Aligned_cols=15 Identities=33% Similarity=0.795 Sum_probs=10.8
Q ss_pred cCceeCChhhHhhhc
Q psy12265 46 VKAFQCEYCGKDFAR 60 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~ 60 (71)
...|.|+.||.....
T Consensus 340 ~r~f~C~~CG~~~dr 354 (383)
T PHA02942 340 HRYFHCPSCGYENDR 354 (383)
T ss_pred CCEEECCCCCCEeCc
Confidence 357999999876543
No 208
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=46.70 E-value=21 Score=18.12 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=4.7
Q ss_pred ceeCChhhH
Q psy12265 48 AFQCEYCGK 56 (71)
Q Consensus 48 ~~~C~~c~~ 56 (71)
...|++||.
T Consensus 32 lv~CP~Cgs 40 (148)
T PF06676_consen 32 LVSCPVCGS 40 (148)
T ss_pred CccCCCCCC
Confidence 345666653
No 209
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=46.67 E-value=24 Score=17.94 Aligned_cols=33 Identities=18% Similarity=0.520 Sum_probs=18.4
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
...|..|+..+....... .. .. ..+-.|+.|+.
T Consensus 105 ~~~C~~C~~~~~~~~~~~-~~---~~-~~~~~C~~C~~ 137 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVD-SI---DE-EEPPRCPKCGG 137 (178)
T ss_dssp EEEETTTSBEEEGHHHHH-HH---HT-TSSCBCTTTSC
T ss_pred eeeecCCCccccchhhcc-cc---cc-cccccccccCc
Confidence 468888988776543222 11 11 12237888864
No 210
>PRK12860 transcriptional activator FlhC; Provisional
Probab=46.33 E-value=15 Score=19.41 Aligned_cols=27 Identities=30% Similarity=0.636 Sum_probs=17.6
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCG 55 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~ 55 (71)
..|..|+..|... .+.....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~---------~~e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTH---------AHDLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecc---------ccccCCCCcCCCCC
Confidence 6788888877632 12234468898884
No 211
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=46.19 E-value=10 Score=19.49 Aligned_cols=18 Identities=28% Similarity=0.683 Sum_probs=13.4
Q ss_pred CceeCChhhHhhhchHHH
Q psy12265 47 KAFQCEYCGKDFARKYQA 64 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~~l 64 (71)
.++.|..||+.|.....+
T Consensus 113 ~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred CcccchhhCCccccHHHH
Confidence 467899999988755443
No 212
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=45.98 E-value=9.5 Score=21.66 Aligned_cols=27 Identities=30% Similarity=0.678 Sum_probs=17.6
Q ss_pred cccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 24 VCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 24 ~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
.||.+|.+.. ++ .|.+..|+ |+.|...
T Consensus 42 tCgHtFCslC-----IR-~hL~~qp~-CP~Cr~~ 68 (391)
T COG5432 42 TCGHTFCSLC-----IR-RHLGTQPF-CPVCRED 68 (391)
T ss_pred ccccchhHHH-----HH-HHhcCCCC-Ccccccc
Confidence 4888887643 23 57777776 7877543
No 213
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=45.97 E-value=3.7 Score=21.70 Aligned_cols=40 Identities=23% Similarity=0.309 Sum_probs=21.9
Q ss_pred CceecccccccccchhhHHHhHhhhcCCc---CceeCChhhHhhhc
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDV---KAFQCEYCGKDFAR 60 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~---~~~~C~~c~~~f~~ 60 (71)
....|+.|+..+.....+.. . -|.|+ ..+.|..||..+..
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~--I-PyFG~V~i~t~~C~~CgYR~~D 55 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYD--I-PYFGEVLISTGVCERCGYRSTD 55 (201)
T ss_pred eeecCCcccceeeEEEeeec--C-CccceEEEEEEEccccCCcccc
Confidence 34679999874433222211 1 23343 23578889876653
No 214
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=45.76 E-value=8.3 Score=16.49 Aligned_cols=13 Identities=38% Similarity=0.764 Sum_probs=7.9
Q ss_pred ceeCChhhHhhhc
Q psy12265 48 AFQCEYCGKDFAR 60 (71)
Q Consensus 48 ~~~C~~c~~~f~~ 60 (71)
|.+|-.||+..++
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 4566677765544
No 215
>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=45.59 E-value=2.1 Score=21.69 Aligned_cols=15 Identities=27% Similarity=0.632 Sum_probs=11.1
Q ss_pred cCceeCChhhHhhhc
Q psy12265 46 VKAFQCEYCGKDFAR 60 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~ 60 (71)
+.|.-|..||+.|++
T Consensus 66 ~~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPW 80 (158)
T ss_pred CCChhHHhCCCCCch
Confidence 456678888888774
No 216
>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=45.48 E-value=13 Score=14.89 Aligned_cols=8 Identities=38% Similarity=1.269 Sum_probs=3.1
Q ss_pred eeCChhhH
Q psy12265 49 FQCEYCGK 56 (71)
Q Consensus 49 ~~C~~c~~ 56 (71)
|.|+.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 77777764
No 217
>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=45.45 E-value=9.6 Score=17.09 Aligned_cols=12 Identities=33% Similarity=0.944 Sum_probs=3.8
Q ss_pred CcCceeCChhhH
Q psy12265 45 DVKAFQCEYCGK 56 (71)
Q Consensus 45 ~~~~~~C~~c~~ 56 (71)
-.+.|.|+.|+.
T Consensus 19 l~~~F~CPfC~~ 30 (81)
T PF05129_consen 19 LPKVFDCPFCNH 30 (81)
T ss_dssp -SS----TTT--
T ss_pred CCceEcCCcCCC
Confidence 346789998873
No 218
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=45.36 E-value=8.3 Score=14.83 Aligned_cols=9 Identities=33% Similarity=0.925 Sum_probs=6.3
Q ss_pred ceeCChhhH
Q psy12265 48 AFQCEYCGK 56 (71)
Q Consensus 48 ~~~C~~c~~ 56 (71)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 456888874
No 219
>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=45.32 E-value=9.8 Score=14.18 Aligned_cols=12 Identities=33% Similarity=0.944 Sum_probs=5.7
Q ss_pred eecccccccccc
Q psy12265 20 YGCEVCGRHFRQ 31 (71)
Q Consensus 20 ~~c~~c~~~~~~ 31 (71)
-.|..|++.|..
T Consensus 4 ~~C~eC~~~f~d 15 (34)
T PF01286_consen 4 PKCDECGKPFMD 15 (34)
T ss_dssp EE-TTT--EES-
T ss_pred chHhHhCCHHHH
Confidence 367888887764
No 220
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=45.01 E-value=9.3 Score=15.86 Aligned_cols=20 Identities=15% Similarity=0.421 Sum_probs=11.5
Q ss_pred cCceeCChhhHhhhchHHHH
Q psy12265 46 VKAFQCEYCGKDFARKYQAH 65 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~ 65 (71)
+.|+....|+..|...+-++
T Consensus 22 ~~PV~s~~C~H~fek~aI~~ 41 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAILQ 41 (57)
T ss_dssp SSEEEESSS--EEEHHHHHH
T ss_pred hCCcCcCCCCCeecHHHHHH
Confidence 34666667888887665544
No 221
>KOG3352|consensus
Probab=44.82 E-value=5.5 Score=20.17 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=10.4
Q ss_pred CceeCChhhHhhhc
Q psy12265 47 KAFQCEYCGKDFAR 60 (71)
Q Consensus 47 ~~~~C~~c~~~f~~ 60 (71)
+..+|++||.-|.-
T Consensus 132 e~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 132 ETQRCPECGHYFKL 145 (153)
T ss_pred CcccCCcccceEEe
Confidence 35689999987753
No 222
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=44.62 E-value=9.6 Score=15.70 Aligned_cols=11 Identities=36% Similarity=1.177 Sum_probs=8.4
Q ss_pred cCceeCChhhH
Q psy12265 46 VKAFQCEYCGK 56 (71)
Q Consensus 46 ~~~~~C~~c~~ 56 (71)
...|.|+.|+.
T Consensus 42 ~i~y~C~~Cg~ 52 (54)
T PF10058_consen 42 EIQYRCPYCGA 52 (54)
T ss_pred ceEEEcCCCCC
Confidence 44699999974
No 223
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=44.50 E-value=7.4 Score=16.10 Aligned_cols=21 Identities=14% Similarity=0.430 Sum_probs=12.7
Q ss_pred cCceeCChhhHhhhchHHHHH
Q psy12265 46 VKAFQCEYCGKDFARKYQAHS 66 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~ 66 (71)
..-+-|-.||..|.....|..
T Consensus 25 ~~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 25 EEHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred hhCceeeeeCCccCCHHHHHh
Confidence 344557777777766666543
No 224
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=44.43 E-value=9.1 Score=15.94 Aligned_cols=11 Identities=27% Similarity=1.026 Sum_probs=3.6
Q ss_pred CceeCChhhHh
Q psy12265 47 KAFQCEYCGKD 57 (71)
Q Consensus 47 ~~~~C~~c~~~ 57 (71)
+.|.|+.||.+
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 34789999875
No 225
>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=44.05 E-value=12 Score=14.92 Aligned_cols=35 Identities=23% Similarity=0.552 Sum_probs=17.1
Q ss_pred eecccccccccchhhHHHhHhhhcCC------cCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSD------VKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~------~~~~~C~~c~~ 56 (71)
|.|..|+..|.....-...- ...| ..-|.|+.|+.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~--i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENG--IPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EEETTTSBEEETTTBBGGGT--B-TT--GGGS-TT-B-TTTSS
T ss_pred cCCCCCCEEEcCCcCCcccC--cCCCCCHHHCCCCCcCcCCCC
Confidence 78999997765443211110 1111 12489999974
No 226
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=43.94 E-value=5.9 Score=25.09 Aligned_cols=14 Identities=29% Similarity=0.700 Sum_probs=8.4
Q ss_pred ecccccccccchhh
Q psy12265 21 GCEVCGRHFRQWGD 34 (71)
Q Consensus 21 ~c~~c~~~~~~~~~ 34 (71)
.|+.||-.|+-..+
T Consensus 125 ~CT~CGPRfTIi~a 138 (750)
T COG0068 125 NCTNCGPRFTIIEA 138 (750)
T ss_pred ccCCCCcceeeecc
Confidence 56677776654433
No 227
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.58 E-value=5.5 Score=13.56 Aligned_cols=6 Identities=50% Similarity=1.514 Sum_probs=3.6
Q ss_pred CChhhH
Q psy12265 51 CEYCGK 56 (71)
Q Consensus 51 C~~c~~ 56 (71)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 666664
No 228
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=43.53 E-value=17 Score=23.32 Aligned_cols=12 Identities=25% Similarity=0.645 Sum_probs=8.5
Q ss_pred cCceeCChhhHh
Q psy12265 46 VKAFQCEYCGKD 57 (71)
Q Consensus 46 ~~~~~C~~c~~~ 57 (71)
..|..|+.||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 457788888753
No 229
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=43.46 E-value=24 Score=14.32 Aligned_cols=20 Identities=40% Similarity=0.697 Sum_probs=11.1
Q ss_pred CCceecccccccccchhhHHHhH
Q psy12265 17 LKPYGCEVCGRHFRQWGDLKYHK 39 (71)
Q Consensus 17 ~~~~~c~~c~~~~~~~~~l~~h~ 39 (71)
.+|.-|..|...|. ++..|+
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi 22 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHL 22 (49)
T ss_pred CCCcccccHhHHHh---hHHHHh
Confidence 34566777766553 444454
No 230
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=43.33 E-value=11 Score=13.66 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=6.7
Q ss_pred ceeCChhhHh
Q psy12265 48 AFQCEYCGKD 57 (71)
Q Consensus 48 ~~~C~~c~~~ 57 (71)
-|+|..||-.
T Consensus 7 ~ykC~~Cgni 16 (34)
T TIGR00319 7 VYKCEVCGNI 16 (34)
T ss_pred EEEcCCCCcE
Confidence 5778777643
No 231
>PHA02998 RNA polymerase subunit; Provisional
Probab=42.95 E-value=3.8 Score=21.36 Aligned_cols=37 Identities=16% Similarity=0.278 Sum_probs=20.6
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCc----eeCChhhHhhh
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKA----FQCEYCGKDFA 59 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~----~~C~~c~~~f~ 59 (71)
....|+.|+..=.....++ +...+.| |.|..||..|.
T Consensus 142 t~v~CPkCg~~~A~f~qlQ-----TRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQ-----TRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEe-----eccCCCCceEEEEcCCCCCccC
Confidence 3467888885433322221 2222222 78999997654
No 232
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=42.88 E-value=11 Score=13.67 Aligned_cols=9 Identities=44% Similarity=1.479 Sum_probs=6.1
Q ss_pred ceeCChhhH
Q psy12265 48 AFQCEYCGK 56 (71)
Q Consensus 48 ~~~C~~c~~ 56 (71)
-|+|..||.
T Consensus 4 ~ykC~~CGn 12 (34)
T cd00974 4 VYKCEICGN 12 (34)
T ss_pred EEEcCCCCc
Confidence 467777764
No 233
>KOG2857|consensus
Probab=42.82 E-value=8.3 Score=19.39 Aligned_cols=21 Identities=10% Similarity=0.276 Sum_probs=11.3
Q ss_pred ceeCChhhHhhhchHHHHHhh
Q psy12265 48 AFQCEYCGKDFARKYQAHSYH 68 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~~l~~h~ 68 (71)
.|+|+.|...+-+-..+..|+
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk 37 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHK 37 (157)
T ss_pred hccCCCCCCccccchhhhhcc
Confidence 356666655555555555553
No 234
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=42.25 E-value=11 Score=18.22 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=9.4
Q ss_pred CCcCceeCChhhHhh
Q psy12265 44 SDVKAFQCEYCGKDF 58 (71)
Q Consensus 44 ~~~~~~~C~~c~~~f 58 (71)
+.....+|+.|++..
T Consensus 65 tkav~V~CP~C~K~T 79 (114)
T PF11023_consen 65 TKAVQVECPNCGKQT 79 (114)
T ss_pred ccceeeECCCCCChH
Confidence 344556788887653
No 235
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=42.23 E-value=12 Score=15.19 Aligned_cols=34 Identities=26% Similarity=0.714 Sum_probs=19.0
Q ss_pred eecccccccccch-hhHHHhHhhhcCC------cCceeCChhhH
Q psy12265 20 YGCEVCGRHFRQW-GDLKYHKASLHSD------VKAFQCEYCGK 56 (71)
Q Consensus 20 ~~c~~c~~~~~~~-~~l~~h~~~~~~~------~~~~~C~~c~~ 56 (71)
|.|..|+..|... .+...- .-.| ...|.|+.|+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~---i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEG---IPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred cCCCCCCeEECCCCCCcccC---cCCCCCHhHCCCCCCCCCCCC
Confidence 7899999877643 111110 1111 12479999974
No 236
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=42.13 E-value=10 Score=17.93 Aligned_cols=12 Identities=42% Similarity=1.099 Sum_probs=8.2
Q ss_pred cCceeCChhhHh
Q psy12265 46 VKAFQCEYCGKD 57 (71)
Q Consensus 46 ~~~~~C~~c~~~ 57 (71)
.+.|.|+.|+..
T Consensus 20 ~k~FtCp~Cghe 31 (104)
T COG4888 20 PKTFTCPRCGHE 31 (104)
T ss_pred CceEecCccCCe
Confidence 456888888753
No 237
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=42.07 E-value=9.5 Score=19.64 Aligned_cols=39 Identities=18% Similarity=0.471 Sum_probs=19.5
Q ss_pred eecccccccccch--hhHHHhHh--hhcCCcCceeCChhhHhh
Q psy12265 20 YGCEVCGRHFRQW--GDLKYHKA--SLHSDVKAFQCEYCGKDF 58 (71)
Q Consensus 20 ~~c~~c~~~~~~~--~~l~~h~~--~~~~~~~~~~C~~c~~~f 58 (71)
-.|+.|+...... .....-.. ..-..+.-+.|+.||+.|
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 4788998754322 22111100 001112346799999865
No 238
>PRK01343 zinc-binding protein; Provisional
Probab=41.75 E-value=7.6 Score=16.32 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=8.3
Q ss_pred ceeCChhhHhhh
Q psy12265 48 AFQCEYCGKDFA 59 (71)
Q Consensus 48 ~~~C~~c~~~f~ 59 (71)
...|+.|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 456888887654
No 239
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=41.61 E-value=15 Score=19.72 Aligned_cols=16 Identities=31% Similarity=0.719 Sum_probs=11.4
Q ss_pred cCceeCChhhHhhhch
Q psy12265 46 VKAFQCEYCGKDFARK 61 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~ 61 (71)
..||.|.+|.+.|..+
T Consensus 194 ~IPF~C~iCKkdy~sp 209 (259)
T COG5152 194 KIPFLCGICKKDYESP 209 (259)
T ss_pred CCceeehhchhhccch
Confidence 4688898887766554
No 240
>PRK11032 hypothetical protein; Provisional
Probab=41.13 E-value=9 Score=19.60 Aligned_cols=28 Identities=32% Similarity=0.666 Sum_probs=17.0
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
..+|..|+.... . .+++. .-.|+.|+..
T Consensus 124 ~LvC~~Cg~~~~--------~--~~p~~-i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHHLA--------F--YTPEV-LPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCEEE--------e--cCCCc-CCCCCCCCCC
Confidence 488999985532 1 23333 3379999854
No 241
>PF14369 zf-RING_3: zinc-finger
Probab=40.60 E-value=14 Score=13.73 Aligned_cols=10 Identities=30% Similarity=0.740 Sum_probs=8.2
Q ss_pred eccccccccc
Q psy12265 21 GCEVCGRHFR 30 (71)
Q Consensus 21 ~c~~c~~~~~ 30 (71)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998875
No 242
>KOG4124|consensus
Probab=40.35 E-value=7.2 Score=22.66 Aligned_cols=51 Identities=33% Similarity=0.695 Sum_probs=31.9
Q ss_pred CCceeccc--ccccccchhhHHHhHhhh--------------c----CCcCceeCChhhHhhhchHHHHHh
Q psy12265 17 LKPYGCEV--CGRHFRQWGDLKYHKASL--------------H----SDVKAFQCEYCGKDFARKYQAHSY 67 (71)
Q Consensus 17 ~~~~~c~~--c~~~~~~~~~l~~h~~~~--------------~----~~~~~~~C~~c~~~f~~~~~l~~h 67 (71)
.+++.|.. |.+.+.....+..|.... | ..-++|+|++|-+.......|..|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 36777753 777777666665554311 1 123678999998887766555544
No 243
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.33 E-value=37 Score=14.57 Aligned_cols=9 Identities=22% Similarity=0.899 Sum_probs=4.6
Q ss_pred ceeCChhhH
Q psy12265 48 AFQCEYCGK 56 (71)
Q Consensus 48 ~~~C~~c~~ 56 (71)
.|-|+.|..
T Consensus 31 tymC~eC~~ 39 (68)
T COG4896 31 TYMCPECEH 39 (68)
T ss_pred eEechhhHh
Confidence 455555543
No 244
>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=39.32 E-value=21 Score=20.03 Aligned_cols=16 Identities=25% Similarity=0.582 Sum_probs=8.4
Q ss_pred CceeCChhhHhhhchH
Q psy12265 47 KAFQCEYCGKDFARKY 62 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~ 62 (71)
++++|+.|+.....-.
T Consensus 208 k~~PCPKCg~et~eTk 223 (314)
T PF06524_consen 208 KPIPCPKCGYETQETK 223 (314)
T ss_pred CCCCCCCCCCcccccc
Confidence 4556666665544333
No 245
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=39.23 E-value=7.1 Score=19.79 Aligned_cols=15 Identities=40% Similarity=1.034 Sum_probs=11.6
Q ss_pred ceeCChhhHhhhchH
Q psy12265 48 AFQCEYCGKDFARKY 62 (71)
Q Consensus 48 ~~~C~~c~~~f~~~~ 62 (71)
.++|.+|++.|+...
T Consensus 135 ~lrC~YCe~~~~~~~ 149 (153)
T COG1781 135 ALRCKYCEKTFSEDE 149 (153)
T ss_pred EEEEEecCcEechhh
Confidence 489999998887543
No 246
>PRK04351 hypothetical protein; Provisional
Probab=39.14 E-value=16 Score=18.44 Aligned_cols=31 Identities=23% Similarity=0.821 Sum_probs=17.2
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
|.|..|+..+.. +.+ + ....|.|..|+-.+.
T Consensus 113 Y~C~~Cg~~~~r------~Rr--~-n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 113 YECQSCGQQYLR------KRR--I-NTKRYRCGKCRGKLK 143 (149)
T ss_pred EECCCCCCEeee------eee--c-CCCcEEeCCCCcEee
Confidence 777777755432 111 2 235578888875443
No 247
>KOG3497|consensus
Probab=39.05 E-value=11 Score=16.07 Aligned_cols=14 Identities=36% Similarity=0.745 Sum_probs=7.9
Q ss_pred ceeCChhhHhhhch
Q psy12265 48 AFQCEYCGKDFARK 61 (71)
Q Consensus 48 ~~~C~~c~~~f~~~ 61 (71)
|.+|-.||+....+
T Consensus 4 PiRCFtCGKvig~K 17 (69)
T KOG3497|consen 4 PIRCFTCGKVIGDK 17 (69)
T ss_pred eeEeeecccccccc
Confidence 45666666655443
No 248
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=38.45 E-value=12 Score=16.05 Aligned_cols=13 Identities=31% Similarity=0.720 Sum_probs=7.8
Q ss_pred ceeCChhhHhhhc
Q psy12265 48 AFQCEYCGKDFAR 60 (71)
Q Consensus 48 ~~~C~~c~~~f~~ 60 (71)
|.+|-.||+....
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 5567667765443
No 249
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=38.44 E-value=14 Score=19.16 Aligned_cols=32 Identities=31% Similarity=0.829 Sum_probs=19.2
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhch
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARK 61 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 61 (71)
...|..|+.+|... .+ ...|-|..|.++|...
T Consensus 74 ~l~C~~C~~Tfk~f---------~~--~g~fGCaeCY~tf~~~ 105 (176)
T COG3880 74 LLGCHNCGMTFKEF---------IQ--SGLFGCAECYKTFESQ 105 (176)
T ss_pred HhcCccccccHHHH---------HH--hcccchHHHHHHHHHH
Confidence 46777787666421 11 2246788888877654
No 250
>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=38.41 E-value=6.2 Score=18.18 Aligned_cols=31 Identities=32% Similarity=0.882 Sum_probs=19.5
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhh
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 59 (71)
..|.|+.|++.-.. + ..+| -|.|..|++.|+
T Consensus 34 ~ky~Cp~Cgk~~vk--------R-~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------R-VATG--IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEE--------E-EETT--EEEETTTTEEEE
T ss_pred CCCcCCCCCCceeE--------E-eeeE--EeecCCCCCEEe
Confidence 57999999865211 1 2333 479999987665
No 251
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=38.22 E-value=16 Score=15.34 Aligned_cols=12 Identities=33% Similarity=0.861 Sum_probs=5.5
Q ss_pred eeCChhhHhhhc
Q psy12265 49 FQCEYCGKDFAR 60 (71)
Q Consensus 49 ~~C~~c~~~f~~ 60 (71)
..|+.|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 578888876543
No 252
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=38.20 E-value=11 Score=13.46 Aligned_cols=11 Identities=27% Similarity=1.147 Sum_probs=4.8
Q ss_pred ceeCChhhHhh
Q psy12265 48 AFQCEYCGKDF 58 (71)
Q Consensus 48 ~~~C~~c~~~f 58 (71)
.|.|+.|+..+
T Consensus 13 kY~Cp~C~~~~ 23 (30)
T PF04438_consen 13 KYRCPRCGARY 23 (30)
T ss_dssp SEE-TTT--EE
T ss_pred EEECCCcCCce
Confidence 46777776543
No 253
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=37.79 E-value=30 Score=13.05 Aligned_cols=21 Identities=24% Similarity=0.408 Sum_probs=15.6
Q ss_pred CceecccccccccchhhHHHh
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYH 38 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h 38 (71)
....|..|+..+.....+..-
T Consensus 18 ~id~C~~C~G~W~d~~el~~~ 38 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELEKL 38 (41)
T ss_pred EEEECCCCCeEEccHHHHHHH
Confidence 347899999888877776653
No 254
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=36.92 E-value=11 Score=17.64 Aligned_cols=12 Identities=33% Similarity=0.999 Sum_probs=7.7
Q ss_pred CceeCChhhHhh
Q psy12265 47 KAFQCEYCGKDF 58 (71)
Q Consensus 47 ~~~~C~~c~~~f 58 (71)
+..+|..||..|
T Consensus 87 r~~rC~nCG~~f 98 (98)
T PF10164_consen 87 RERRCSNCGATF 98 (98)
T ss_pred CccccCCCCccC
Confidence 345777787654
No 255
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=36.83 E-value=14 Score=15.54 Aligned_cols=11 Identities=36% Similarity=1.129 Sum_probs=6.5
Q ss_pred eCChhhHhhhc
Q psy12265 50 QCEYCGKDFAR 60 (71)
Q Consensus 50 ~C~~c~~~f~~ 60 (71)
.|..||+..+.
T Consensus 6 vCSTCGrDlSe 16 (63)
T PF05864_consen 6 VCSTCGRDLSE 16 (63)
T ss_pred eecccCCcchH
Confidence 46666665543
No 256
>PF14149 YhfH: YhfH-like protein
Probab=36.03 E-value=21 Score=13.61 Aligned_cols=11 Identities=36% Similarity=1.078 Sum_probs=7.7
Q ss_pred eCChhhHhhhc
Q psy12265 50 QCEYCGKDFAR 60 (71)
Q Consensus 50 ~C~~c~~~f~~ 60 (71)
.|..||+.+..
T Consensus 15 ~C~~CG~~i~E 25 (37)
T PF14149_consen 15 KCTECGKEIEE 25 (37)
T ss_pred ccHHHHHHHHH
Confidence 68888876543
No 257
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=35.57 E-value=18 Score=12.55 Aligned_cols=12 Identities=25% Similarity=0.542 Sum_probs=4.8
Q ss_pred cCceeCChhhHh
Q psy12265 46 VKAFQCEYCGKD 57 (71)
Q Consensus 46 ~~~~~C~~c~~~ 57 (71)
...|.|..|...
T Consensus 13 ~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 13 GWFYRCSECDFD 24 (30)
T ss_dssp --EEE-TTT---
T ss_pred CceEECccCCCc
Confidence 356788888654
No 258
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=35.25 E-value=13 Score=15.02 Aligned_cols=13 Identities=23% Similarity=0.976 Sum_probs=8.7
Q ss_pred eeCChhhHhhhch
Q psy12265 49 FQCEYCGKDFARK 61 (71)
Q Consensus 49 ~~C~~c~~~f~~~ 61 (71)
++|+.||..+...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 6788887665544
No 259
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=34.80 E-value=19 Score=14.61 Aligned_cols=33 Identities=18% Similarity=0.434 Sum_probs=17.8
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
-.|.-|.-..+. +.+ .. ...++....|+.||+.
T Consensus 23 ~~C~gC~~~l~~-~~~-~~---i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 23 GTCSGCHMELPP-QEL-NE---IRKGDEIVFCPNCGRI 55 (56)
T ss_pred CccCCCCEEcCH-HHH-HH---HHcCCCeEECcCCCcc
Confidence 356666544332 222 22 2333667789999863
No 260
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=34.75 E-value=5.7 Score=16.48 Aligned_cols=9 Identities=56% Similarity=1.486 Sum_probs=4.2
Q ss_pred eCChhhHhh
Q psy12265 50 QCEYCGKDF 58 (71)
Q Consensus 50 ~C~~c~~~f 58 (71)
+|..|+..|
T Consensus 7 ~C~~Cg~~~ 15 (54)
T PF14446_consen 7 KCPVCGKKF 15 (54)
T ss_pred cChhhCCcc
Confidence 344444444
No 261
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=34.57 E-value=16 Score=21.08 Aligned_cols=18 Identities=28% Similarity=0.643 Sum_probs=13.1
Q ss_pred hcCCcCceeCChhhHhhh
Q psy12265 42 LHSDVKAFQCEYCGKDFA 59 (71)
Q Consensus 42 ~~~~~~~~~C~~c~~~f~ 59 (71)
...|...|+|++|+..-.
T Consensus 370 S~nG~~~FKCPYCP~~~~ 387 (396)
T COG5109 370 SQNGVLSFKCPYCPEMSK 387 (396)
T ss_pred hhcCcEEeeCCCCCcchh
Confidence 355677999999985433
No 262
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=34.13 E-value=23 Score=12.94 Aligned_cols=11 Identities=36% Similarity=0.742 Sum_probs=7.3
Q ss_pred ceecccccccc
Q psy12265 19 PYGCEVCGRHF 29 (71)
Q Consensus 19 ~~~c~~c~~~~ 29 (71)
-+.|..|+..|
T Consensus 21 ~~~C~~Cg~~~ 31 (33)
T PF08792_consen 21 YEVCIFCGSSF 31 (33)
T ss_pred eEEcccCCcEe
Confidence 46777777655
No 263
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=34.09 E-value=17 Score=18.14 Aligned_cols=11 Identities=36% Similarity=1.096 Sum_probs=8.2
Q ss_pred eCChhhHhhhc
Q psy12265 50 QCEYCGKDFAR 60 (71)
Q Consensus 50 ~C~~c~~~f~~ 60 (71)
.|+.||+.|..
T Consensus 5 nC~~CgklF~~ 15 (137)
T TIGR03826 5 NCPKCGRLFVK 15 (137)
T ss_pred cccccchhhhh
Confidence 57888887765
No 264
>KOG2817|consensus
Probab=34.05 E-value=37 Score=20.15 Aligned_cols=29 Identities=24% Similarity=0.597 Sum_probs=17.5
Q ss_pred ccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 25 CGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 25 c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
||.. .++.++.+ . ...|...|+||+|+..
T Consensus 355 CGHV-ISkdAlnr--L-S~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 355 CGHV-ISKDALNR--L-SKNGSQSFKCPYCPVE 383 (394)
T ss_pred ccce-ecHHHHHH--H-hhCCCeeeeCCCCCcc
Confidence 5443 33455443 2 3556668999999854
No 265
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=33.84 E-value=20 Score=13.50 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=7.9
Q ss_pred eeccccccccc
Q psy12265 20 YGCEVCGRHFR 30 (71)
Q Consensus 20 ~~c~~c~~~~~ 30 (71)
+.|+.|+..+-
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 67888886653
No 266
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=33.49 E-value=8.5 Score=19.49 Aligned_cols=13 Identities=38% Similarity=1.043 Sum_probs=10.7
Q ss_pred ceeCChhhHhhhc
Q psy12265 48 AFQCEYCGKDFAR 60 (71)
Q Consensus 48 ~~~C~~c~~~f~~ 60 (71)
.|+|.+|++.|..
T Consensus 132 ~lrC~YCe~~~~~ 144 (150)
T TIGR00240 132 ALRCYYCEKEIEH 144 (150)
T ss_pred EEEEECCCCEEec
Confidence 5999999988753
No 267
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=33.00 E-value=15 Score=22.58 Aligned_cols=40 Identities=23% Similarity=0.516 Sum_probs=22.3
Q ss_pred eecccccccccch-hhHHHhHhhhcCCcCceeCChhhHhhhc
Q psy12265 20 YGCEVCGRHFRQW-GDLKYHKASLHSDVKAFQCEYCGKDFAR 60 (71)
Q Consensus 20 ~~c~~c~~~~~~~-~~l~~h~~~~~~~~~~~~C~~c~~~f~~ 60 (71)
..|+.|+..+... ..+..... .....-.|.|+.||.....
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~-~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKG-EAPETARYVCPHCGCEIEE 241 (557)
T ss_pred ccCCCCCCCccccccceeecCC-CCccceEEECCCCcCCCCH
Confidence 5889999776543 22221100 0112334899999876554
No 268
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=32.76 E-value=37 Score=12.78 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=2.9
Q ss_pred eecccccccc
Q psy12265 20 YGCEVCGRHF 29 (71)
Q Consensus 20 ~~c~~c~~~~ 29 (71)
|-|..|...+
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 5566665555
No 269
>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=32.58 E-value=27 Score=21.22 Aligned_cols=10 Identities=30% Similarity=0.746 Sum_probs=6.3
Q ss_pred CceeCChhhH
Q psy12265 47 KAFQCEYCGK 56 (71)
Q Consensus 47 ~~~~C~~c~~ 56 (71)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3566777764
No 270
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=32.49 E-value=19 Score=12.59 Aligned_cols=9 Identities=33% Similarity=1.132 Sum_probs=3.5
Q ss_pred eCChhhHhh
Q psy12265 50 QCEYCGKDF 58 (71)
Q Consensus 50 ~C~~c~~~f 58 (71)
.|+.|+...
T Consensus 1 ~CP~C~s~l 9 (28)
T PF03119_consen 1 TCPVCGSKL 9 (28)
T ss_dssp B-TTT--BE
T ss_pred CcCCCCCEe
Confidence 377777543
No 271
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.98 E-value=36 Score=21.63 Aligned_cols=10 Identities=30% Similarity=1.052 Sum_probs=6.9
Q ss_pred CceeCChhhH
Q psy12265 47 KAFQCEYCGK 56 (71)
Q Consensus 47 ~~~~C~~c~~ 56 (71)
.++.|+.||.
T Consensus 421 ~p~~Cp~Cgs 430 (665)
T PRK14873 421 PDWRCPRCGS 430 (665)
T ss_pred cCccCCCCcC
Confidence 4667888764
No 272
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=31.51 E-value=21 Score=15.07 Aligned_cols=11 Identities=36% Similarity=1.129 Sum_probs=6.3
Q ss_pred eCChhhHhhhc
Q psy12265 50 QCEYCGKDFAR 60 (71)
Q Consensus 50 ~C~~c~~~f~~ 60 (71)
.|..||+..+.
T Consensus 6 VCsTCGrDlSe 16 (63)
T PHA03082 6 VCSTCGRDLSE 16 (63)
T ss_pred eecccCcchhH
Confidence 46666665543
No 273
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=31.50 E-value=18 Score=15.96 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=7.3
Q ss_pred ceeCChhhHhhhc
Q psy12265 48 AFQCEYCGKDFAR 60 (71)
Q Consensus 48 ~~~C~~c~~~f~~ 60 (71)
|.+|-.||+...+
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 4566666665443
No 274
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=31.38 E-value=9.5 Score=14.44 Aligned_cols=10 Identities=50% Similarity=1.172 Sum_probs=5.3
Q ss_pred eCChhhHhhh
Q psy12265 50 QCEYCGKDFA 59 (71)
Q Consensus 50 ~C~~c~~~f~ 59 (71)
.|+.|++.|-
T Consensus 4 ~CprC~kg~H 13 (36)
T PF14787_consen 4 LCPRCGKGFH 13 (36)
T ss_dssp C-TTTSSSCS
T ss_pred cCcccCCCcc
Confidence 4666766554
No 275
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=31.34 E-value=11 Score=19.16 Aligned_cols=17 Identities=29% Similarity=0.940 Sum_probs=12.5
Q ss_pred CcCceeCChhhHhhhch
Q psy12265 45 DVKAFQCEYCGKDFARK 61 (71)
Q Consensus 45 ~~~~~~C~~c~~~f~~~ 61 (71)
....|+|.+|++.+...
T Consensus 131 ~~~~~rC~YCe~~~~~~ 147 (152)
T PRK00893 131 EPIKLRCKYCEKEFSED 147 (152)
T ss_pred CCCEEEeeCCCCEechh
Confidence 34468999999887643
No 276
>KOG4118|consensus
Probab=30.98 E-value=30 Score=15.03 Aligned_cols=26 Identities=23% Similarity=0.316 Sum_probs=18.7
Q ss_pred ceecccccccccchhhHHHhHhhhcC
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHS 44 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 44 (71)
.|.|..|......+..+..|....|+
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCC
Confidence 37898888777777777777654443
No 277
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=30.86 E-value=16 Score=15.66 Aligned_cols=6 Identities=50% Similarity=1.580 Sum_probs=2.6
Q ss_pred eCChhh
Q psy12265 50 QCEYCG 55 (71)
Q Consensus 50 ~C~~c~ 55 (71)
.|+.|+
T Consensus 2 ~C~KCg 7 (64)
T PF09855_consen 2 KCPKCG 7 (64)
T ss_pred CCCCCC
Confidence 344443
No 278
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=30.63 E-value=72 Score=17.93 Aligned_cols=13 Identities=31% Similarity=0.833 Sum_probs=10.2
Q ss_pred eeCChhhHhhhch
Q psy12265 49 FQCEYCGKDFARK 61 (71)
Q Consensus 49 ~~C~~c~~~f~~~ 61 (71)
|.|+.|+..|.--
T Consensus 156 f~C~~C~h~F~G~ 168 (278)
T PF15135_consen 156 FHCPKCRHNFRGF 168 (278)
T ss_pred eecccccccchhh
Confidence 7899998888644
No 279
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=30.60 E-value=45 Score=18.41 Aligned_cols=15 Identities=27% Similarity=0.691 Sum_probs=11.1
Q ss_pred CcCceeCChhhHhhh
Q psy12265 45 DVKAFQCEYCGKDFA 59 (71)
Q Consensus 45 ~~~~~~C~~c~~~f~ 59 (71)
+.....||+||+...
T Consensus 218 ~d~iv~CP~CgRILy 232 (239)
T COG1579 218 KDEIVFCPYCGRILY 232 (239)
T ss_pred CCCCccCCccchHHH
Confidence 555678999998644
No 280
>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=30.04 E-value=12 Score=13.21 Aligned_cols=11 Identities=45% Similarity=1.247 Sum_probs=7.0
Q ss_pred ceeCChhhHhh
Q psy12265 48 AFQCEYCGKDF 58 (71)
Q Consensus 48 ~~~C~~c~~~f 58 (71)
-|.|..|+..+
T Consensus 27 Cf~C~~C~~~L 37 (39)
T smart00132 27 CFKCSKCGKPL 37 (39)
T ss_pred CCCCcccCCcC
Confidence 36777776554
No 281
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=29.88 E-value=23 Score=14.34 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=6.1
Q ss_pred Cceecccccccc
Q psy12265 18 KPYGCEVCGRHF 29 (71)
Q Consensus 18 ~~~~c~~c~~~~ 29 (71)
++.-|..|...|
T Consensus 4 k~GYCE~C~~ky 15 (49)
T PF07535_consen 4 KPGYCENCRVKY 15 (49)
T ss_pred CCccCccccchh
Confidence 344555555444
No 282
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=29.79 E-value=22 Score=14.56 Aligned_cols=6 Identities=50% Similarity=1.885 Sum_probs=3.1
Q ss_pred eCChhh
Q psy12265 50 QCEYCG 55 (71)
Q Consensus 50 ~C~~c~ 55 (71)
.|+.||
T Consensus 5 PCPFCG 10 (61)
T PF14354_consen 5 PCPFCG 10 (61)
T ss_pred CCCCCC
Confidence 455554
No 283
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=29.26 E-value=54 Score=16.53 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=15.8
Q ss_pred eecccccccccchhhHHHhHhhhcCC
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSD 45 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~ 45 (71)
..|-++|+.| .+|++|.. .|.+
T Consensus 77 IicLEDGkkf---KSLKRHL~-t~~g 98 (148)
T COG4957 77 IICLEDGKKF---KSLKRHLT-THYG 98 (148)
T ss_pred EEEeccCcch---HHHHHHHh-cccC
Confidence 5788888887 56788876 5544
No 284
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=29.25 E-value=32 Score=20.02 Aligned_cols=39 Identities=26% Similarity=0.508 Sum_probs=14.2
Q ss_pred ceecccccccccchhhH---HHhHhhhcCCc-CceeCChhhHh
Q psy12265 19 PYGCEVCGRHFRQWGDL---KYHKASLHSDV-KAFQCEYCGKD 57 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l---~~h~~~~~~~~-~~~~C~~c~~~ 57 (71)
.+.|.+|.+..-..... ..|....+... +-|+|..|+..
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~R 294 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNR 294 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-E
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCe
Confidence 47888887654333322 12221111222 33678877754
No 285
>PRK12496 hypothetical protein; Provisional
Probab=29.24 E-value=20 Score=18.34 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=9.7
Q ss_pred ceeCChhhHhhhc
Q psy12265 48 AFQCEYCGKDFAR 60 (71)
Q Consensus 48 ~~~C~~c~~~f~~ 60 (71)
.+.|.-|++.|..
T Consensus 127 ~~~C~gC~~~~~~ 139 (164)
T PRK12496 127 RKVCKGCKKKYPE 139 (164)
T ss_pred eEECCCCCccccC
Confidence 3678888888853
No 286
>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=29.19 E-value=28 Score=13.11 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=7.2
Q ss_pred eecccccccc
Q psy12265 20 YGCEVCGRHF 29 (71)
Q Consensus 20 ~~c~~c~~~~ 29 (71)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 7888887654
No 287
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=28.89 E-value=41 Score=12.12 Aligned_cols=13 Identities=15% Similarity=0.608 Sum_probs=9.3
Q ss_pred cCCcCceeCChhh
Q psy12265 43 HSDVKAFQCEYCG 55 (71)
Q Consensus 43 ~~~~~~~~C~~c~ 55 (71)
..|...++|..|.
T Consensus 14 P~gA~~vrCs~C~ 26 (31)
T TIGR01053 14 PRGASSVRCALCQ 26 (31)
T ss_pred CCCCCeEECCCCC
Confidence 3466778888884
No 288
>KOG4727|consensus
Probab=28.72 E-value=40 Score=17.72 Aligned_cols=22 Identities=23% Similarity=0.395 Sum_probs=18.6
Q ss_pred ceecccccccccchhhHHHhHh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKA 40 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~ 40 (71)
-|-|.+|+-.+..+.++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 3899999999988888888864
No 289
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=28.59 E-value=26 Score=18.22 Aligned_cols=27 Identities=33% Similarity=0.882 Sum_probs=9.7
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCG 55 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~ 55 (71)
..|..|+..|.... +.....|.|+.|.
T Consensus 135 ~~C~~C~~~fv~~~---------~~~~~~~~Cp~C~ 161 (175)
T PF05280_consen 135 APCRRCGGHFVTHA---------HDPRHSFVCPFCQ 161 (175)
T ss_dssp EE-TTT--EEEEES---------S--SS----TT--
T ss_pred cCCCCCCCCeECcC---------CCCCcCcCCCCCC
Confidence 67888887776431 1123457888886
No 290
>KOG3214|consensus
Probab=27.25 E-value=24 Score=16.73 Aligned_cols=40 Identities=18% Similarity=0.408 Sum_probs=21.0
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhHhhhchH
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKDFARKY 62 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~ 62 (71)
..|.|..|..--.-.-.+. +. ...| ...|.+|+..|....
T Consensus 22 t~FnClfcnHek~v~~~~D--k~-~~iG--~~sC~iC~esFqt~i 61 (109)
T KOG3214|consen 22 TQFNCLFCNHEKSVSCTLD--KK-HNIG--KASCRICEESFQTTI 61 (109)
T ss_pred eeeccCccccccceeeeeh--hh-cCcc--eeeeeehhhhhccch
Confidence 4478888764322111111 11 1222 347999999987543
No 291
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.24 E-value=19 Score=15.58 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=7.2
Q ss_pred eeCChhhHhh
Q psy12265 49 FQCEYCGKDF 58 (71)
Q Consensus 49 ~~C~~c~~~f 58 (71)
..|+.||+..
T Consensus 8 v~CP~Cgkpv 17 (65)
T COG3024 8 VPCPTCGKPV 17 (65)
T ss_pred ccCCCCCCcc
Confidence 4788888753
No 292
>PRK06260 threonine synthase; Validated
Probab=27.07 E-value=42 Score=19.62 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=4.2
Q ss_pred eeccccccc
Q psy12265 20 YGCEVCGRH 28 (71)
Q Consensus 20 ~~c~~c~~~ 28 (71)
+.|..|+..
T Consensus 4 ~~C~~cg~~ 12 (397)
T PRK06260 4 LKCIECGKE 12 (397)
T ss_pred EEECCCCCC
Confidence 345555544
No 293
>KOG3456|consensus
Probab=26.98 E-value=29 Score=16.68 Aligned_cols=13 Identities=38% Similarity=1.053 Sum_probs=10.0
Q ss_pred ceeCChhhHhhhc
Q psy12265 48 AFQCEYCGKDFAR 60 (71)
Q Consensus 48 ~~~C~~c~~~f~~ 60 (71)
+..|.+||-.|-+
T Consensus 104 ~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 104 PHICGYCGLRFVQ 116 (120)
T ss_pred Ccccccchhhhhh
Confidence 3578999988864
No 294
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=26.91 E-value=20 Score=15.37 Aligned_cols=11 Identities=36% Similarity=0.945 Sum_probs=7.7
Q ss_pred ceeCChhhHhh
Q psy12265 48 AFQCEYCGKDF 58 (71)
Q Consensus 48 ~~~C~~c~~~f 58 (71)
...|+.|++..
T Consensus 6 ~v~CP~C~k~~ 16 (62)
T PRK00418 6 TVNCPTCGKPV 16 (62)
T ss_pred cccCCCCCCcc
Confidence 35788888753
No 295
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=26.85 E-value=18 Score=13.50 Aligned_cols=12 Identities=25% Similarity=0.897 Sum_probs=5.9
Q ss_pred ceeCChhhHhhh
Q psy12265 48 AFQCEYCGKDFA 59 (71)
Q Consensus 48 ~~~C~~c~~~f~ 59 (71)
+..|..||..+.
T Consensus 21 ~isC~~CGPr~~ 32 (35)
T PF07503_consen 21 FISCTNCGPRYS 32 (35)
T ss_dssp T--BTTCC-SCC
T ss_pred CccCCCCCCCEE
Confidence 456888876543
No 296
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=26.64 E-value=24 Score=14.01 Aligned_cols=7 Identities=43% Similarity=1.360 Sum_probs=4.9
Q ss_pred eCChhhH
Q psy12265 50 QCEYCGK 56 (71)
Q Consensus 50 ~C~~c~~ 56 (71)
+|+.||-
T Consensus 13 kCp~CGt 19 (44)
T PF14952_consen 13 KCPKCGT 19 (44)
T ss_pred cCCcCcC
Confidence 6777764
No 297
>KOG0402|consensus
Probab=26.30 E-value=18 Score=16.52 Aligned_cols=11 Identities=36% Similarity=1.244 Sum_probs=8.3
Q ss_pred ceeCChhhHhh
Q psy12265 48 AFQCEYCGKDF 58 (71)
Q Consensus 48 ~~~C~~c~~~f 58 (71)
.|.|+.||+.-
T Consensus 36 ky~CsfCGK~~ 46 (92)
T KOG0402|consen 36 KYTCSFCGKKT 46 (92)
T ss_pred hhhhhhcchhh
Confidence 47899998753
No 298
>PRK02935 hypothetical protein; Provisional
Probab=25.76 E-value=29 Score=16.60 Aligned_cols=14 Identities=21% Similarity=0.494 Sum_probs=8.9
Q ss_pred CCcCceeCChhhHh
Q psy12265 44 SDVKAFQCEYCGKD 57 (71)
Q Consensus 44 ~~~~~~~C~~c~~~ 57 (71)
+......|+.|++.
T Consensus 66 tkavqV~CP~C~K~ 79 (110)
T PRK02935 66 TKAVQVICPSCEKP 79 (110)
T ss_pred ccceeeECCCCCch
Confidence 34455678888764
No 299
>PF01722 BolA: BolA-like protein; InterPro: IPR002634 This family consist of the morpho-protein BolA from Escherichia coli and its various homologs. In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division []. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase []. BolA is also induced by stress during early stages of growth [] and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5 [, ].; PDB: 1XS3_A 1V60_A 3O2E_A 1NY8_A 3TR3_A 2KZ0_A 2DHM_A 2KDN_A 1V9J_A.
Probab=25.62 E-value=46 Score=14.66 Aligned_cols=24 Identities=13% Similarity=0.124 Sum_probs=13.5
Q ss_pred cCceeCChhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
..-|...+....|...+.+++|+.
T Consensus 27 ~sHf~i~IvS~~F~g~s~i~rhr~ 50 (76)
T PF01722_consen 27 GSHFKIIIVSDEFEGKSRIKRHRL 50 (76)
T ss_dssp SSEEEEEEECGGGTTS-HHHHHHH
T ss_pred CceEEEEEEcHHhCCCCHHHHHHH
Confidence 444555555566666666666653
No 300
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=25.58 E-value=27 Score=14.12 Aligned_cols=17 Identities=24% Similarity=0.620 Sum_probs=10.9
Q ss_pred CcCceeCChhhHhhhch
Q psy12265 45 DVKAFQCEYCGKDFARK 61 (71)
Q Consensus 45 ~~~~~~C~~c~~~f~~~ 61 (71)
+.....|+.|+..|-..
T Consensus 37 ~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 37 GCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCCeeECCCCCCeECCC
Confidence 34456787787766544
No 301
>KOG4602|consensus
Probab=25.54 E-value=20 Score=20.01 Aligned_cols=10 Identities=30% Similarity=1.089 Sum_probs=6.7
Q ss_pred ceeCChhhHh
Q psy12265 48 AFQCEYCGKD 57 (71)
Q Consensus 48 ~~~C~~c~~~ 57 (71)
.|.|++||.+
T Consensus 268 ~YVCPiCGAT 277 (318)
T KOG4602|consen 268 SYVCPICGAT 277 (318)
T ss_pred hhcCcccccc
Confidence 3777777754
No 302
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=25.41 E-value=34 Score=19.44 Aligned_cols=35 Identities=23% Similarity=0.532 Sum_probs=19.2
Q ss_pred ceecccccccccchhhHHHhHhhhcCCcC----ceeCChhhHhh
Q psy12265 19 PYGCEVCGRHFRQWGDLKYHKASLHSDVK----AFQCEYCGKDF 58 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~----~~~C~~c~~~f 58 (71)
-+.|..|+..=.....+ . ....+. -|.|..||..+
T Consensus 258 ~~~C~~C~~~~~~~~q~--Q---trsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQL--Q---TRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred cccCCCCCCccceEEEe--c---ccCCCCCCeEEEEcCCCCCee
Confidence 48999998643322221 1 122222 26899998654
No 303
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=25.17 E-value=39 Score=16.40 Aligned_cols=18 Identities=28% Similarity=0.431 Sum_probs=10.9
Q ss_pred eeCChhhHhhhchHHHHH
Q psy12265 49 FQCEYCGKDFARKYQAHS 66 (71)
Q Consensus 49 ~~C~~c~~~f~~~~~l~~ 66 (71)
|.|+.|.+....-..+..
T Consensus 22 ~~Cp~C~~~~~~~~~~~~ 39 (162)
T PF13462_consen 22 FQCPHCAKFHEELEKLLK 39 (162)
T ss_dssp TTSHHHHHHHHHHHHHHH
T ss_pred CCCHhHHHHHHHHhhhhh
Confidence 578888776554444433
No 304
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=25.16 E-value=37 Score=14.14 Aligned_cols=15 Identities=20% Similarity=0.239 Sum_probs=8.4
Q ss_pred CCceecccccccccc
Q psy12265 17 LKPYGCEVCGRHFRQ 31 (71)
Q Consensus 17 ~~~~~c~~c~~~~~~ 31 (71)
...|.|-.|+..+..
T Consensus 9 ~~lw~CL~Cg~~~C~ 23 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCG 23 (63)
T ss_dssp SSEEEETTTS-EEET
T ss_pred CceEEeCCCCccccc
Confidence 445677777665544
No 305
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=25.00 E-value=21 Score=14.88 Aligned_cols=16 Identities=25% Similarity=0.667 Sum_probs=10.4
Q ss_pred CcCceeCChhhHhhhc
Q psy12265 45 DVKAFQCEYCGKDFAR 60 (71)
Q Consensus 45 ~~~~~~C~~c~~~f~~ 60 (71)
+++---|+.|+..|..
T Consensus 36 ~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 36 GERYNGCPFCGTPFEF 51 (55)
T ss_pred hhhccCCCCCCCcccC
Confidence 3444468889887653
No 306
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.94 E-value=19 Score=17.16 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=7.8
Q ss_pred eeCChhhHhhh
Q psy12265 49 FQCEYCGKDFA 59 (71)
Q Consensus 49 ~~C~~c~~~f~ 59 (71)
..|+.||..|.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred ccCCCCCCccc
Confidence 37888887654
No 307
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=24.57 E-value=28 Score=16.27 Aligned_cols=9 Identities=44% Similarity=1.394 Sum_probs=6.4
Q ss_pred ceeCChhhH
Q psy12265 48 AFQCEYCGK 56 (71)
Q Consensus 48 ~~~C~~c~~ 56 (71)
.+.|+.||.
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 357888875
No 308
>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=24.57 E-value=40 Score=15.65 Aligned_cols=11 Identities=36% Similarity=1.141 Sum_probs=6.9
Q ss_pred eeccccccccc
Q psy12265 20 YGCEVCGRHFR 30 (71)
Q Consensus 20 ~~c~~c~~~~~ 30 (71)
|.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (91)
T TIGR00280 54 WTCRKCGAKFA 64 (91)
T ss_pred EEcCCCCCEEe
Confidence 66666666553
No 309
>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=24.55 E-value=61 Score=12.53 Aligned_cols=39 Identities=18% Similarity=0.347 Sum_probs=20.8
Q ss_pred HHHHhHhhCCCceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 8 KVHNRVHLGLKPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 8 ~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
..++...-....+.|+.|+.. . +- .-.....|+|..|++
T Consensus 7 ~~~l~~~RW~~g~~CP~Cg~~-~-------~~--~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 7 REYLEEIRWPDGFVCPHCGST-K-------HY--RLKTRGRYRCKACRK 45 (46)
T ss_pred HHHHHHhcCCCCCCCCCCCCe-e-------eE--EeCCCCeEECCCCCC
Confidence 334443334444779999854 1 00 111245788888864
No 310
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=24.55 E-value=91 Score=16.54 Aligned_cols=35 Identities=17% Similarity=0.361 Sum_probs=17.6
Q ss_pred CceecccccccccchhhHHHhHhhhcCCcCceeCChhhH
Q psy12265 18 KPYGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGK 56 (71)
Q Consensus 18 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~ 56 (71)
....|..|+..+.....+. - .......-.|+.|+.
T Consensus 94 ~~~~C~~C~~~~~~~~~~~-~---~~~~~~~p~C~~Cgg 128 (206)
T cd01410 94 FIEVCKSCGPEYVRDDVVE-T---RGDKETGRRCHACGG 128 (206)
T ss_pred CcccCCCCCCccchHHHHH-H---hhcCCCCCcCCCCcC
Confidence 4467888886654332221 1 111222346888863
No 311
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.47 E-value=44 Score=13.00 Aligned_cols=13 Identities=23% Similarity=0.542 Sum_probs=9.9
Q ss_pred ceecccccccccc
Q psy12265 19 PYGCEVCGRHFRQ 31 (71)
Q Consensus 19 ~~~c~~c~~~~~~ 31 (71)
.+.|..|+..+.-
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 6899999966543
No 312
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=24.35 E-value=45 Score=13.71 Aligned_cols=11 Identities=36% Similarity=0.803 Sum_probs=6.7
Q ss_pred eeCChhhHhhh
Q psy12265 49 FQCEYCGKDFA 59 (71)
Q Consensus 49 ~~C~~c~~~f~ 59 (71)
++|..|++...
T Consensus 5 iRC~~CnklLa 15 (51)
T PF10122_consen 5 IRCGHCNKLLA 15 (51)
T ss_pred eeccchhHHHh
Confidence 56777766543
No 313
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.18 E-value=86 Score=14.75 Aligned_cols=18 Identities=22% Similarity=0.504 Sum_probs=12.9
Q ss_pred ceecccccccccchhhHH
Q psy12265 19 PYGCEVCGRHFRQWGDLK 36 (71)
Q Consensus 19 ~~~c~~c~~~~~~~~~l~ 36 (71)
-+.|+.||..+.......
T Consensus 31 ~~~C~~CGe~~~~~e~~~ 48 (127)
T TIGR03830 31 GWYCPACGEELLDPEESK 48 (127)
T ss_pred eeECCCCCCEEEcHHHHH
Confidence 478999998776655543
No 314
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=24.02 E-value=16 Score=15.95 Aligned_cols=6 Identities=67% Similarity=1.841 Sum_probs=2.7
Q ss_pred eCChhhH
Q psy12265 50 QCEYCGK 56 (71)
Q Consensus 50 ~C~~c~~ 56 (71)
.| .||+
T Consensus 22 kC-~CG~ 27 (68)
T PF09082_consen 22 KC-VCGK 27 (68)
T ss_dssp EE-TTTE
T ss_pred Ee-cCCC
Confidence 44 4443
No 315
>KOG0562|consensus
Probab=23.84 E-value=63 Score=16.96 Aligned_cols=23 Identities=9% Similarity=0.069 Sum_probs=16.7
Q ss_pred CceeCChhhHhhhchHHHHHhhh
Q psy12265 47 KAFQCEYCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~~~l~~h~~ 69 (71)
.+.+|..|+..-..-..|..|.+
T Consensus 152 ~dLrC~~Cq~~~~~~~kLK~Hl~ 174 (184)
T KOG0562|consen 152 EDLRCWRCQTFGPHFPKLKAHLR 174 (184)
T ss_pred cceeehhhhhcccccHHHHHHHH
Confidence 45689999855566777887765
No 316
>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=23.70 E-value=37 Score=17.28 Aligned_cols=16 Identities=19% Similarity=0.488 Sum_probs=12.1
Q ss_pred eecccccccccchhhH
Q psy12265 20 YGCEVCGRHFRQWGDL 35 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l 35 (71)
=.|..|++.|++-..+
T Consensus 29 ReC~~C~~RFTTyErv 44 (147)
T TIGR00244 29 RECLECHERFTTFERA 44 (147)
T ss_pred ccCCccCCccceeeec
Confidence 5789999999865543
No 317
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=23.37 E-value=40 Score=15.24 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=5.2
Q ss_pred ceeCChhhHh
Q psy12265 48 AFQCEYCGKD 57 (71)
Q Consensus 48 ~~~C~~c~~~ 57 (71)
.|.|+.|++.
T Consensus 65 ~~~Cp~Cg~~ 74 (81)
T PF10609_consen 65 YFVCPHCGER 74 (81)
T ss_dssp EEE-TTT--E
T ss_pred ccCCCCCCCe
Confidence 3789988864
No 318
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=23.16 E-value=20 Score=17.77 Aligned_cols=9 Identities=33% Similarity=1.298 Sum_probs=6.4
Q ss_pred eCChhhHhh
Q psy12265 50 QCEYCGKDF 58 (71)
Q Consensus 50 ~C~~c~~~f 58 (71)
+|..||..|
T Consensus 31 kC~~CG~v~ 39 (140)
T COG1545 31 KCKKCGRVY 39 (140)
T ss_pred EcCCCCeEE
Confidence 688887653
No 319
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=23.14 E-value=37 Score=17.40 Aligned_cols=15 Identities=27% Similarity=0.724 Sum_probs=11.6
Q ss_pred eecccccccccchhh
Q psy12265 20 YGCEVCGRHFRQWGD 34 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~ 34 (71)
=.|..|+..|++-..
T Consensus 29 ReC~~C~~RFTTfE~ 43 (156)
T COG1327 29 RECLECGERFTTFER 43 (156)
T ss_pred hcccccccccchhhe
Confidence 579999999986544
No 320
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=23.01 E-value=33 Score=17.22 Aligned_cols=11 Identities=36% Similarity=1.050 Sum_probs=6.5
Q ss_pred CceeCChhhHh
Q psy12265 47 KAFQCEYCGKD 57 (71)
Q Consensus 47 ~~~~C~~c~~~ 57 (71)
..|.|..|+..
T Consensus 50 ~~~~C~~C~~~ 60 (166)
T cd04476 50 GTYRCEKCNKS 60 (166)
T ss_pred CcEECCCCCCc
Confidence 34666666654
No 321
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=22.90 E-value=28 Score=16.18 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=8.5
Q ss_pred eeCChhhHhhh
Q psy12265 49 FQCEYCGKDFA 59 (71)
Q Consensus 49 ~~C~~c~~~f~ 59 (71)
|.|.+|++.-.
T Consensus 69 ~~Ct~Cgkah~ 79 (94)
T COG1631 69 LRCTECGKAHQ 79 (94)
T ss_pred EEehhhccccc
Confidence 79999987643
No 322
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.87 E-value=36 Score=16.01 Aligned_cols=10 Identities=50% Similarity=1.218 Sum_probs=8.0
Q ss_pred cCceeCChhh
Q psy12265 46 VKAFQCEYCG 55 (71)
Q Consensus 46 ~~~~~C~~c~ 55 (71)
...|.|+.|+
T Consensus 19 pt~f~CP~Cg 28 (99)
T PRK14892 19 PKIFECPRCG 28 (99)
T ss_pred CcEeECCCCC
Confidence 3568999998
No 323
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.85 E-value=46 Score=15.43 Aligned_cols=11 Identities=18% Similarity=0.751 Sum_probs=6.8
Q ss_pred eeccccccccc
Q psy12265 20 YGCEVCGRHFR 30 (71)
Q Consensus 20 ~~c~~c~~~~~ 30 (71)
|.|..|+..|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PTZ00255 55 WRCKGCKKTVA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 66666666554
No 324
>PHA03019 hypothetical protein; Provisional
Probab=22.78 E-value=52 Score=14.28 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=8.1
Q ss_pred eeCChhhHhhhc
Q psy12265 49 FQCEYCGKDFAR 60 (71)
Q Consensus 49 ~~C~~c~~~f~~ 60 (71)
..|..|.+.|..
T Consensus 21 ~kcd~c~kn~nd 32 (77)
T PHA03019 21 IKCDECEKNFND 32 (77)
T ss_pred hhHHHHHHHHHH
Confidence 367777777654
No 325
>KOG3134|consensus
Probab=22.61 E-value=68 Score=17.57 Aligned_cols=33 Identities=21% Similarity=0.525 Sum_probs=17.5
Q ss_pred eecccccccccchhhHHHhHhhhcCCcCceeCChhhHh
Q psy12265 20 YGCEVCGRHFRQWGDLKYHKASLHSDVKAFQCEYCGKD 57 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 57 (71)
+.|..||..- .+|-. +-.+..-+.=+|+.|++.
T Consensus 1 ~~CVeCg~~v---ksLy~--~Ys~g~irlt~C~nC~e~ 33 (225)
T KOG3134|consen 1 YRCVECGSEV---KSLYT--QYSPGNIRLTKCPNCQEV 33 (225)
T ss_pred CcccccCchH---HHHHH--hcCCCcEEEeeCCchhhH
Confidence 4678887442 22221 112333455689999765
No 326
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=22.44 E-value=33 Score=13.22 Aligned_cols=8 Identities=38% Similarity=0.912 Sum_probs=3.5
Q ss_pred eeCChhhH
Q psy12265 49 FQCEYCGK 56 (71)
Q Consensus 49 ~~C~~c~~ 56 (71)
-.|+.|+-
T Consensus 4 ~pCP~CGG 11 (40)
T PF08273_consen 4 GPCPICGG 11 (40)
T ss_dssp E--TTTT-
T ss_pred CCCCCCcC
Confidence 36888864
No 327
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=22.34 E-value=23 Score=16.08 Aligned_cols=11 Identities=36% Similarity=1.075 Sum_probs=8.4
Q ss_pred eCChhhHhhhc
Q psy12265 50 QCEYCGKDFAR 60 (71)
Q Consensus 50 ~C~~c~~~f~~ 60 (71)
.|..|++.+..
T Consensus 80 ~C~vC~k~l~~ 90 (109)
T PF10367_consen 80 KCSVCGKPLGN 90 (109)
T ss_pred CccCcCCcCCC
Confidence 59999887654
No 328
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.92 E-value=54 Score=20.84 Aligned_cols=10 Identities=30% Similarity=0.707 Sum_probs=6.9
Q ss_pred CceeCChhhH
Q psy12265 47 KAFQCEYCGK 56 (71)
Q Consensus 47 ~~~~C~~c~~ 56 (71)
.+..|+.|+.
T Consensus 420 ~~~~Cp~Cg~ 429 (679)
T PRK05580 420 IPKACPECGS 429 (679)
T ss_pred CCCCCCCCcC
Confidence 4567888865
No 329
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=21.86 E-value=32 Score=13.91 Aligned_cols=9 Identities=33% Similarity=0.907 Sum_probs=6.5
Q ss_pred eeCChhhHh
Q psy12265 49 FQCEYCGKD 57 (71)
Q Consensus 49 ~~C~~c~~~ 57 (71)
+.|+-||-+
T Consensus 10 ~~CPgCG~t 18 (52)
T PF10825_consen 10 IPCPGCGMT 18 (52)
T ss_pred CCCCCCcHH
Confidence 468889854
No 330
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=21.81 E-value=69 Score=14.83 Aligned_cols=17 Identities=24% Similarity=0.636 Sum_probs=13.1
Q ss_pred eecccccccccchhhHH
Q psy12265 20 YGCEVCGRHFRQWGDLK 36 (71)
Q Consensus 20 ~~c~~c~~~~~~~~~l~ 36 (71)
..|+.||..|....-+.
T Consensus 36 ~~C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTVK 52 (89)
T ss_pred ccccCCCcEeecHHHHH
Confidence 78999999887665544
No 331
>PF04777 Evr1_Alr: Erv1 / Alr family; InterPro: IPR006863 Biogenesis of Fe/S clusters involves a number of essential mitochondrial proteins. Erv1p of Saccharomyces cerevisiae (Baker's yeast) mitochondria is required for the maturation of Fe/S proteins in the cytosol. The ALR (augmenter of liver regeneration) represents a mammalian ortholog of yeast Erv1p. Both Erv1p and full-length ALR are located in the mitochondrial intermembrane and it is thought to operate downstream of the mitochondrial ABC transporter [].; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process; PDB: 3MBG_C 3U2L_A 3U2M_A 3QD9_D 3QCP_A 3O55_A 2HJ3_B 3GWN_A 3T58_D 3T59_B ....
Probab=21.35 E-value=44 Score=15.10 Aligned_cols=15 Identities=33% Similarity=0.842 Sum_probs=10.8
Q ss_pred CceeCChhhHhhhch
Q psy12265 47 KAFQCEYCGKDFARK 61 (71)
Q Consensus 47 ~~~~C~~c~~~f~~~ 61 (71)
.-|.|..|...|...
T Consensus 35 ~~~pC~~C~~hf~~~ 49 (95)
T PF04777_consen 35 HFFPCEECRNHFSKY 49 (95)
T ss_dssp HHSSSHHHHHHHHHH
T ss_pred HHCCcHHHHHHHHHH
Confidence 347899998777644
No 332
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.31 E-value=40 Score=14.63 Aligned_cols=6 Identities=50% Similarity=1.580 Sum_probs=3.0
Q ss_pred eCChhh
Q psy12265 50 QCEYCG 55 (71)
Q Consensus 50 ~C~~c~ 55 (71)
.|+.||
T Consensus 6 kCpKCg 11 (68)
T COG3478 6 KCPKCG 11 (68)
T ss_pred cCCCcC
Confidence 455554
No 333
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.29 E-value=52 Score=15.27 Aligned_cols=11 Identities=36% Similarity=1.150 Sum_probs=6.5
Q ss_pred eeccccccccc
Q psy12265 20 YGCEVCGRHFR 30 (71)
Q Consensus 20 ~~c~~c~~~~~ 30 (71)
|.|..|+..|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PRK03976 55 WECRKCGAKFA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 66666665543
No 334
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.28 E-value=37 Score=12.52 Aligned_cols=7 Identities=43% Similarity=1.217 Sum_probs=2.7
Q ss_pred CChhhHh
Q psy12265 51 CEYCGKD 57 (71)
Q Consensus 51 C~~c~~~ 57 (71)
|+.||..
T Consensus 3 C~~CG~~ 9 (34)
T PF14803_consen 3 CPQCGGP 9 (34)
T ss_dssp -TTT--B
T ss_pred cccccCh
Confidence 6777754
No 335
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=21.28 E-value=32 Score=13.82 Aligned_cols=6 Identities=50% Similarity=1.885 Sum_probs=3.3
Q ss_pred eCChhh
Q psy12265 50 QCEYCG 55 (71)
Q Consensus 50 ~C~~c~ 55 (71)
.|+.||
T Consensus 3 PCPfCG 8 (53)
T TIGR03655 3 PCPFCG 8 (53)
T ss_pred CCCCCC
Confidence 455565
No 336
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=21.25 E-value=30 Score=17.65 Aligned_cols=13 Identities=38% Similarity=0.882 Sum_probs=6.7
Q ss_pred CceeCChhhHhhh
Q psy12265 47 KAFQCEYCGKDFA 59 (71)
Q Consensus 47 ~~~~C~~c~~~f~ 59 (71)
..|.|+.||....
T Consensus 29 ~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 29 MSFECEHCGYKNN 41 (161)
T ss_dssp EEEE-TTT--EEE
T ss_pred EEeECCCCCCEee
Confidence 3479999987543
No 337
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=20.60 E-value=29 Score=14.74 Aligned_cols=10 Identities=20% Similarity=0.451 Sum_probs=5.3
Q ss_pred eecccccccc
Q psy12265 20 YGCEVCGRHF 29 (71)
Q Consensus 20 ~~c~~c~~~~ 29 (71)
..|..|+...
T Consensus 31 IlCNDC~~~s 40 (61)
T PF14599_consen 31 ILCNDCNAKS 40 (61)
T ss_dssp EEESSS--EE
T ss_pred EECCCCCCcc
Confidence 5678887654
No 338
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=20.57 E-value=38 Score=17.45 Aligned_cols=12 Identities=33% Similarity=0.841 Sum_probs=9.0
Q ss_pred ceeCChhhHhhh
Q psy12265 48 AFQCEYCGKDFA 59 (71)
Q Consensus 48 ~~~C~~c~~~f~ 59 (71)
.|.|+.||....
T Consensus 28 sf~C~~CGyr~~ 39 (163)
T TIGR00340 28 TYICEKCGYRST 39 (163)
T ss_pred EEECCCCCCchh
Confidence 478999987644
No 339
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=20.51 E-value=35 Score=14.26 Aligned_cols=10 Identities=50% Similarity=1.311 Sum_probs=4.3
Q ss_pred eCChhhHhhh
Q psy12265 50 QCEYCGKDFA 59 (71)
Q Consensus 50 ~C~~c~~~f~ 59 (71)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 5777888774
No 340
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=20.42 E-value=36 Score=13.86 Aligned_cols=8 Identities=38% Similarity=1.186 Sum_probs=5.5
Q ss_pred eeCChhhH
Q psy12265 49 FQCEYCGK 56 (71)
Q Consensus 49 ~~C~~c~~ 56 (71)
-.|+.||-
T Consensus 14 ~~Cp~CGN 21 (49)
T PF12677_consen 14 CKCPKCGN 21 (49)
T ss_pred ccCcccCC
Confidence 36888874
No 341
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.26 E-value=49 Score=15.55 Aligned_cols=12 Identities=50% Similarity=1.074 Sum_probs=8.8
Q ss_pred CCceeccccccc
Q psy12265 17 LKPYGCEVCGRH 28 (71)
Q Consensus 17 ~~~~~c~~c~~~ 28 (71)
-+.|.|..|+..
T Consensus 4 lkewkC~VCg~~ 15 (103)
T COG4847 4 LKEWKCYVCGGT 15 (103)
T ss_pred cceeeEeeeCCE
Confidence 356889888864
No 342
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=20.20 E-value=12 Score=16.44 Aligned_cols=13 Identities=31% Similarity=0.577 Sum_probs=4.9
Q ss_pred Cceeccccccccc
Q psy12265 18 KPYGCEVCGRHFR 30 (71)
Q Consensus 18 ~~~~c~~c~~~~~ 30 (71)
+...|..|+..+.
T Consensus 45 kr~~Ck~C~~~li 57 (85)
T PF04032_consen 45 KRTICKKCGSLLI 57 (85)
T ss_dssp CCTB-TTT--B--
T ss_pred hcccccCCCCEEe
Confidence 4456777775443
No 343
>KOG2932|consensus
Probab=20.14 E-value=73 Score=18.57 Aligned_cols=24 Identities=13% Similarity=0.276 Sum_probs=19.0
Q ss_pred cCceeCC---hhhHhhhchHHHHHhhh
Q psy12265 46 VKAFQCE---YCGKDFARKYQAHSYHQ 69 (71)
Q Consensus 46 ~~~~~C~---~c~~~f~~~~~l~~h~~ 69 (71)
.-.|-|. -|.++|-...+|+-|+-
T Consensus 142 g~iFmC~~~~GC~RTyLsqrDlqAHIn 168 (389)
T KOG2932|consen 142 GGIFMCAAPHGCLRTYLSQRDLQAHIN 168 (389)
T ss_pred cceEEeecchhHHHHHhhHHHHHHHhh
Confidence 4467775 39999999999998874
No 344
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=20.01 E-value=49 Score=15.71 Aligned_cols=10 Identities=30% Similarity=1.132 Sum_probs=7.4
Q ss_pred ceeccccccc
Q psy12265 19 PYGCEVCGRH 28 (71)
Q Consensus 19 ~~~c~~c~~~ 28 (71)
.|.|..|++.
T Consensus 2 kWkC~iCg~~ 11 (101)
T PF09943_consen 2 KWKCYICGKP 11 (101)
T ss_pred ceEEEecCCe
Confidence 4788888864
Done!