Query psy2647
Match_columns 72
No_of_seqs 123 out of 1187
Neff 12.0
Searched_HMMs 46136
Date Fri Aug 16 21:33:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2647.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2647hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 6.7E-23 1.5E-27 101.6 3.3 64 8-72 184-247 (279)
2 KOG2462|consensus 99.8 5E-19 1.1E-23 88.0 3.2 60 2-61 206-265 (279)
3 KOG3623|consensus 99.6 7.8E-17 1.7E-21 88.9 2.6 63 9-72 892-954 (1007)
4 KOG3623|consensus 99.6 2.5E-16 5.3E-21 87.0 1.9 62 3-64 914-975 (1007)
5 KOG3576|consensus 99.4 1.7E-14 3.8E-19 69.9 0.1 52 9-60 143-194 (267)
6 KOG3576|consensus 99.4 6.6E-14 1.4E-18 67.9 -0.3 63 9-72 115-177 (267)
7 PHA02768 hypothetical protein; 99.3 3.3E-13 7.1E-18 53.2 1.1 44 11-56 5-48 (55)
8 KOG1074|consensus 99.3 1.4E-13 3.1E-18 77.1 0.1 56 11-67 353-408 (958)
9 PHA00733 hypothetical protein 99.2 2.3E-11 5E-16 55.9 4.6 56 7-64 69-124 (128)
10 KOG1074|consensus 99.2 8.1E-12 1.8E-16 70.3 1.6 58 11-69 605-662 (958)
11 PF13465 zf-H2C2_2: Zinc-finge 99.1 3.6E-11 7.8E-16 41.1 1.8 25 26-50 1-25 (26)
12 KOG3608|consensus 99.1 1E-10 2.2E-15 61.1 2.7 62 9-72 235-296 (467)
13 PHA00616 hypothetical protein 99.0 2.2E-10 4.8E-15 43.3 2.0 31 39-70 1-31 (44)
14 PHA02768 hypothetical protein; 98.8 4.6E-09 1E-13 41.5 2.4 25 39-63 5-29 (55)
15 PHA00616 hypothetical protein 98.8 3.5E-09 7.6E-14 40.1 1.8 34 11-44 1-34 (44)
16 KOG3608|consensus 98.7 2.4E-08 5.2E-13 52.5 4.3 51 11-61 263-314 (467)
17 PHA00732 hypothetical protein 98.7 1.4E-08 2.9E-13 43.3 1.9 45 11-61 1-46 (79)
18 PF05605 zf-Di19: Drought indu 98.6 1.4E-07 3.1E-12 37.4 4.2 51 11-64 2-54 (54)
19 PLN03086 PRLI-interacting fact 98.6 8.9E-08 1.9E-12 53.2 4.2 57 9-71 451-507 (567)
20 PHA00733 hypothetical protein 98.5 7.5E-08 1.6E-12 44.5 2.4 54 8-61 37-95 (128)
21 PF00096 zf-C2H2: Zinc finger, 98.5 6.3E-08 1.4E-12 31.9 1.6 22 40-61 1-22 (23)
22 PF13465 zf-H2C2_2: Zinc-finge 98.5 1.3E-08 2.9E-13 34.6 -0.4 21 2-22 5-25 (26)
23 PF13894 zf-C2H2_4: C2H2-type 98.4 2.2E-07 4.7E-12 30.6 2.0 24 40-63 1-24 (24)
24 KOG3993|consensus 98.4 2E-07 4.4E-12 50.0 2.3 54 11-64 295-381 (500)
25 PF13912 zf-C2H2_6: C2H2-type 98.4 1.2E-07 2.7E-12 32.3 0.8 24 39-62 1-24 (27)
26 PLN03086 PRLI-interacting fact 98.4 5.2E-07 1.1E-11 50.3 3.3 58 10-71 477-544 (567)
27 PF00096 zf-C2H2: Zinc finger, 98.3 4.7E-07 1E-11 29.7 1.3 23 12-34 1-23 (23)
28 KOG3993|consensus 98.3 9.8E-08 2.1E-12 51.2 -0.6 52 11-62 267-318 (500)
29 COG5189 SFP1 Putative transcri 98.0 1.6E-06 3.5E-11 45.3 0.7 52 9-60 347-419 (423)
30 smart00355 ZnF_C2H2 zinc finge 97.9 1.9E-05 4E-10 26.1 2.5 22 40-61 1-22 (26)
31 PF13912 zf-C2H2_6: C2H2-type 97.9 4.3E-06 9.4E-11 28.4 0.7 25 11-35 1-25 (27)
32 PF13894 zf-C2H2_4: C2H2-type 97.9 1.5E-05 3.2E-10 26.0 1.7 23 12-34 1-23 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.8 3E-05 6.4E-10 34.0 2.6 49 14-62 2-73 (100)
34 PF09237 GAGA: GAGA factor; I 97.8 4E-05 8.6E-10 29.9 2.4 29 36-64 21-49 (54)
35 PF13909 zf-H2C2_5: C2H2-type 97.8 3E-05 6.6E-10 25.5 1.9 23 40-63 1-23 (24)
36 PHA00732 hypothetical protein 97.7 4E-05 8.6E-10 32.8 2.2 26 39-64 1-26 (79)
37 PF09237 GAGA: GAGA factor; I 97.7 6.7E-05 1.5E-09 29.3 2.5 32 8-39 21-52 (54)
38 PRK04860 hypothetical protein; 97.7 3.2E-05 6.9E-10 37.2 1.9 37 11-51 119-155 (160)
39 PF12874 zf-met: Zinc-finger o 97.4 9.3E-05 2E-09 24.5 0.9 22 40-61 1-22 (25)
40 PF13913 zf-C2HC_2: zinc-finge 96.9 0.0014 3.1E-08 21.9 1.9 20 40-60 3-22 (25)
41 PF12171 zf-C2H2_jaz: Zinc-fin 96.8 0.00034 7.4E-09 23.7 0.3 21 12-32 2-22 (27)
42 KOG2893|consensus 96.6 0.00046 9.9E-09 35.3 -0.2 43 9-56 9-51 (341)
43 PF05605 zf-Di19: Drought indu 96.5 0.0051 1.1E-07 24.3 2.6 32 39-71 2-34 (54)
44 smart00451 ZnF_U1 U1-like zinc 96.1 0.0045 9.7E-08 22.0 1.3 22 39-60 3-24 (35)
45 PRK04860 hypothetical protein; 95.6 0.0081 1.8E-07 29.1 1.3 28 39-71 119-146 (160)
46 cd00350 rubredoxin_like Rubred 95.5 0.0083 1.8E-07 21.3 1.0 24 12-47 2-25 (33)
47 COG5048 FOG: Zn-finger [Genera 95.4 0.0025 5.5E-08 34.3 -0.9 56 11-67 289-350 (467)
48 PF09538 FYDLN_acid: Protein o 95.2 0.013 2.8E-07 26.7 1.2 30 12-52 10-39 (108)
49 COG4049 Uncharacterized protei 95.2 0.016 3.5E-07 23.1 1.3 25 36-60 14-38 (65)
50 KOG1146|consensus 95.1 0.022 4.8E-07 35.7 2.2 55 7-61 461-540 (1406)
51 COG1592 Rubrerythrin [Energy p 93.6 0.046 1E-06 26.8 1.2 23 11-46 134-156 (166)
52 COG2888 Predicted Zn-ribbon RN 93.4 0.039 8.5E-07 22.3 0.7 32 11-47 27-58 (61)
53 KOG2186|consensus 93.0 0.065 1.4E-06 28.0 1.3 47 11-60 3-49 (276)
54 smart00659 RPOLCX RNA polymera 93.0 0.07 1.5E-06 20.3 1.1 29 11-50 2-30 (44)
55 PF13719 zinc_ribbon_5: zinc-r 93.0 0.076 1.6E-06 19.3 1.1 33 13-50 4-36 (37)
56 PF09986 DUF2225: Uncharacteri 92.6 0.021 4.5E-07 28.9 -0.7 42 10-51 4-60 (214)
57 PRK00464 nrdR transcriptional 92.4 0.018 3.8E-07 27.8 -1.1 13 39-51 28-40 (154)
58 cd00729 rubredoxin_SM Rubredox 92.1 0.097 2.1E-06 18.7 0.9 25 11-47 2-26 (34)
59 TIGR02300 FYDLN_acid conserved 92.0 0.11 2.4E-06 24.4 1.2 30 12-52 10-39 (129)
60 TIGR00373 conserved hypothetic 91.9 0.084 1.8E-06 25.6 0.9 33 9-50 107-139 (158)
61 TIGR02605 CxxC_CxxC_SSSS putat 91.3 0.047 1E-06 21.2 -0.3 29 12-47 6-34 (52)
62 PRK06266 transcription initiat 91.1 0.1 2.3E-06 25.8 0.7 32 10-50 116-147 (178)
63 PF13717 zinc_ribbon_4: zinc-r 91.0 0.16 3.4E-06 18.4 1.0 33 12-49 3-35 (36)
64 smart00734 ZnF_Rad18 Rad18-lik 90.9 0.31 6.8E-06 16.3 1.6 20 40-60 2-21 (26)
65 COG5189 SFP1 Putative transcri 90.6 0.062 1.4E-06 29.1 -0.3 24 8-31 395-418 (423)
66 smart00834 CxxC_CXXC_SSSS Puta 90.1 0.068 1.5E-06 19.6 -0.3 29 12-47 6-34 (41)
67 PF02892 zf-BED: BED zinc fing 90.1 0.27 5.9E-06 18.3 1.4 25 37-61 14-42 (45)
68 PRK00398 rpoP DNA-directed RNA 90.1 0.13 2.7E-06 19.6 0.4 31 10-50 2-32 (46)
69 PF03604 DNA_RNApol_7kD: DNA d 90.0 0.19 4E-06 17.8 0.8 28 12-50 1-28 (32)
70 PF05443 ROS_MUCR: ROS/MUCR tr 89.8 0.22 4.8E-06 23.6 1.2 24 39-65 72-95 (132)
71 PF04959 ARS2: Arsenite-resist 89.8 0.13 2.8E-06 26.3 0.4 25 39-63 77-101 (214)
72 PF13451 zf-trcl: Probable zin 89.7 0.23 5E-06 19.4 1.0 38 9-46 2-40 (49)
73 TIGR02098 MJ0042_CXXC MJ0042 f 89.6 0.22 4.8E-06 18.0 0.9 34 12-50 3-36 (38)
74 PF12013 DUF3505: Protein of u 89.2 0.44 9.6E-06 21.5 1.9 25 40-64 81-109 (109)
75 smart00531 TFIIE Transcription 88.7 0.18 3.8E-06 24.2 0.4 38 9-50 97-134 (147)
76 PRK14890 putative Zn-ribbon RN 88.3 0.16 3.5E-06 20.6 0.1 32 11-47 25-56 (59)
77 COG1996 RPC10 DNA-directed RNA 88.0 0.24 5.2E-06 19.4 0.5 30 10-49 5-34 (49)
78 KOG2893|consensus 87.1 0.31 6.7E-06 25.5 0.8 26 37-63 9-34 (341)
79 smart00614 ZnF_BED BED zinc fi 86.0 0.93 2E-05 17.5 1.7 21 40-60 19-44 (50)
80 COG3357 Predicted transcriptio 85.6 0.52 1.1E-05 20.9 1.0 12 11-22 58-69 (97)
81 PF12907 zf-met2: Zinc-binding 85.4 0.22 4.7E-06 18.6 -0.2 20 41-60 3-25 (40)
82 COG5048 FOG: Zn-finger [Genera 83.1 0.94 2E-05 24.7 1.5 53 9-61 31-85 (467)
83 COG1997 RPL43A Ribosomal prote 82.1 0.64 1.4E-05 20.4 0.5 30 11-50 35-64 (89)
84 PHA00626 hypothetical protein 81.1 0.86 1.9E-05 18.4 0.7 16 37-52 21-36 (59)
85 PF10571 UPF0547: Uncharacteri 80.6 0.85 1.8E-05 15.3 0.5 10 41-50 16-25 (26)
86 PF07754 DUF1610: Domain of un 80.4 0.69 1.5E-05 15.3 0.3 9 38-46 15-23 (24)
87 KOG4167|consensus 80.2 0.47 1E-05 28.7 -0.3 24 39-62 792-815 (907)
88 KOG1842|consensus 79.4 1.7 3.8E-05 24.9 1.7 21 12-32 16-36 (505)
89 COG4391 Uncharacterized protei 78.7 0.46 9.9E-06 19.5 -0.4 42 5-50 18-59 (62)
90 PRK09678 DNA-binding transcrip 78.0 0.66 1.4E-05 19.7 -0.1 39 12-52 2-42 (72)
91 KOG1146|consensus 77.9 0.56 1.2E-05 30.2 -0.4 47 17-63 442-489 (1406)
92 PRK03824 hypA hydrogenase nick 77.1 0.84 1.8E-05 21.7 0.1 15 10-24 69-83 (135)
93 COG1571 Predicted DNA-binding 76.5 2 4.3E-05 24.5 1.4 29 13-52 352-380 (421)
94 PF08790 zf-LYAR: LYAR-type C2 76.4 0.38 8.1E-06 16.5 -0.8 8 42-49 3-10 (28)
95 TIGR00622 ssl1 transcription f 75.7 2.9 6.2E-05 19.4 1.6 20 11-30 15-34 (112)
96 PF09723 Zn-ribbon_8: Zinc rib 75.5 0.96 2.1E-05 16.9 0.1 12 40-51 6-17 (42)
97 KOG3408|consensus 75.5 2.6 5.6E-05 19.8 1.4 24 38-61 56-79 (129)
98 PF15269 zf-C2H2_7: Zinc-finge 75.4 2.4 5.2E-05 16.3 1.1 22 40-61 21-42 (54)
99 PF05191 ADK_lid: Adenylate ki 75.2 0.63 1.4E-05 16.9 -0.4 31 13-51 3-33 (36)
100 PF04780 DUF629: Protein of un 75.0 3.2 7E-05 24.0 2.0 26 39-64 57-82 (466)
101 KOG4167|consensus 74.7 0.82 1.8E-05 27.8 -0.3 25 11-35 792-816 (907)
102 COG4530 Uncharacterized protei 73.6 2 4.3E-05 19.8 0.8 27 13-50 11-37 (129)
103 KOG2482|consensus 72.5 2.7 5.9E-05 23.4 1.3 22 40-61 196-217 (423)
104 cd00924 Cyt_c_Oxidase_Vb Cytoc 70.8 2.1 4.6E-05 19.3 0.6 13 10-22 78-90 (97)
105 COG4957 Predicted transcriptio 70.2 2.1 4.6E-05 20.5 0.6 20 41-63 78-97 (148)
106 KOG2785|consensus 70.1 7.4 0.00016 22.1 2.6 51 11-61 166-242 (390)
107 PF09845 DUF2072: Zn-ribbon co 69.2 2.6 5.6E-05 20.1 0.7 14 39-52 1-14 (131)
108 PF08274 PhnA_Zn_Ribbon: PhnA 68.6 1.9 4E-05 15.0 0.2 11 37-47 17-27 (30)
109 COG3091 SprT Zn-dependent meta 68.1 1.9 4.2E-05 21.1 0.2 33 11-48 117-149 (156)
110 TIGR00100 hypA hydrogenase nic 67.7 2.4 5.1E-05 19.6 0.4 24 12-47 71-94 (115)
111 smart00154 ZnF_AN1 AN1-like Zi 66.9 2.7 5.8E-05 15.5 0.4 13 39-51 12-24 (39)
112 COG1326 Uncharacterized archae 66.7 5.6 0.00012 20.4 1.6 34 12-49 7-40 (201)
113 COG3364 Zn-ribbon containing p 66.5 3 6.4E-05 19.0 0.6 13 39-51 2-14 (112)
114 COG0068 HypF Hydrogenase matur 66.2 2.7 5.9E-05 25.7 0.5 28 14-47 154-181 (750)
115 KOG0717|consensus 65.8 3.9 8.4E-05 23.8 1.1 22 40-61 293-314 (508)
116 PLN02294 cytochrome c oxidase 65.4 3.3 7.1E-05 20.7 0.7 14 10-23 140-153 (174)
117 PF08209 Sgf11: Sgf11 (transcr 65.3 5.2 0.00011 14.2 1.0 20 40-60 5-24 (33)
118 KOG0978|consensus 64.9 2.5 5.4E-05 25.7 0.3 18 38-55 677-694 (698)
119 COG1655 Uncharacterized protei 64.8 0.85 1.8E-05 23.8 -1.4 25 9-33 17-41 (267)
120 PRK12380 hydrogenase nickel in 64.7 3.5 7.5E-05 19.0 0.7 24 12-47 71-94 (113)
121 KOG2071|consensus 64.0 6.6 0.00014 23.5 1.7 25 37-61 416-440 (579)
122 PF07975 C1_4: TFIIH C1-like d 62.1 4.2 9.1E-05 16.1 0.6 13 12-24 22-34 (51)
123 COG2331 Uncharacterized protei 62.0 5.8 0.00012 17.1 1.0 32 11-49 12-43 (82)
124 PF14311 DUF4379: Domain of un 61.9 7.9 0.00017 15.2 1.4 11 40-50 29-39 (55)
125 PF01428 zf-AN1: AN1-like Zinc 61.8 1.9 4.1E-05 16.1 -0.4 15 38-52 12-26 (43)
126 PF02176 zf-TRAF: TRAF-type zi 61.8 3.9 8.4E-05 16.1 0.5 39 11-50 9-53 (60)
127 PF02891 zf-MIZ: MIZ/SP-RING z 61.2 3.9 8.4E-05 15.9 0.4 10 38-47 40-49 (50)
128 PF13878 zf-C2H2_3: zinc-finge 60.4 9.7 0.00021 14.1 2.2 22 40-61 14-37 (41)
129 COG1675 TFA1 Transcription ini 59.8 7.2 0.00016 19.6 1.3 33 8-49 110-142 (176)
130 KOG3507|consensus 59.8 4.1 8.9E-05 16.6 0.4 31 11-52 20-50 (62)
131 PF04423 Rad50_zn_hook: Rad50 59.3 3.5 7.6E-05 16.1 0.2 12 41-52 22-33 (54)
132 PF07503 zf-HYPF: HypF finger; 59.3 1.4 2.9E-05 15.9 -0.9 12 39-50 21-32 (35)
133 PTZ00255 60S ribosomal protein 58.7 2.6 5.7E-05 18.7 -0.3 12 39-50 54-65 (90)
134 KOG4173|consensus 58.3 11 0.00023 19.7 1.7 52 13-64 108-171 (253)
135 TIGR00627 tfb4 transcription f 57.7 8 0.00017 20.9 1.3 8 41-48 271-278 (279)
136 smart00440 ZnF_C2C2 C2C2 Zinc 56.9 0.5 1.1E-05 17.5 -2.3 10 40-49 29-38 (40)
137 PF07282 OrfB_Zn_ribbon: Putat 56.9 6.6 0.00014 16.0 0.8 30 12-51 29-58 (69)
138 KOG2907|consensus 56.8 3.6 7.8E-05 19.1 -0.0 11 40-50 103-113 (116)
139 KOG2593|consensus 56.4 13 0.00028 21.6 2.0 35 10-47 127-161 (436)
140 PF14803 Nudix_N_2: Nudix N-te 55.9 1.4 3.1E-05 15.8 -1.1 11 38-48 21-31 (34)
141 COG3677 Transposase and inacti 55.9 6.4 0.00014 18.7 0.7 35 12-51 31-65 (129)
142 PRK00564 hypA hydrogenase nick 55.4 5.1 0.00011 18.6 0.4 13 11-23 71-83 (117)
143 KOG2636|consensus 54.8 12 0.00025 21.9 1.7 27 33-59 395-422 (497)
144 COG1773 Rubredoxin [Energy pro 53.0 5.8 0.00013 16.0 0.3 15 10-24 2-16 (55)
145 KOG0562|consensus 51.4 16 0.00035 18.4 1.7 27 37-63 151-177 (184)
146 cd00730 rubredoxin Rubredoxin; 51.3 6.5 0.00014 15.4 0.3 11 40-50 2-12 (50)
147 PF01155 HypA: Hydrogenase exp 50.6 4.1 8.8E-05 18.7 -0.3 25 12-48 71-95 (113)
148 PF10013 DUF2256: Uncharacteri 50.6 9.6 0.00021 14.4 0.7 14 13-26 10-23 (42)
149 PF10276 zf-CHCC: Zinc-finger 49.9 6.1 0.00013 14.7 0.1 9 40-48 30-38 (40)
150 COG5112 UFD2 U1-like Zn-finger 49.4 9.4 0.0002 17.6 0.7 23 10-32 54-76 (126)
151 PF14353 CpXC: CpXC protein 48.7 7.4 0.00016 18.1 0.3 15 38-52 37-51 (128)
152 PHA02998 RNA polymerase subuni 48.4 1.8 3.9E-05 21.8 -1.7 13 40-52 172-184 (195)
153 PF10263 SprT-like: SprT-like 47.8 6.5 0.00014 18.8 0.1 10 40-49 144-153 (157)
154 cd00065 FYVE FYVE domain; Zinc 46.8 17 0.00037 14.0 1.2 10 13-22 4-13 (57)
155 PRK05452 anaerobic nitric oxid 46.3 5.9 0.00013 23.0 -0.2 39 9-47 423-466 (479)
156 PRK03681 hypA hydrogenase nick 45.9 6.4 0.00014 18.2 -0.1 26 11-47 70-95 (114)
157 PF01286 XPA_N: XPA protein N- 45.8 8.4 0.00018 13.9 0.2 12 41-52 5-16 (34)
158 PRK12860 transcriptional activ 45.1 15 0.00033 18.8 1.1 27 12-46 135-161 (189)
159 PF11672 DUF3268: Protein of u 44.3 8.2 0.00018 17.6 0.1 10 11-20 2-11 (102)
160 PF04810 zf-Sec23_Sec24: Sec23 44.3 11 0.00023 13.9 0.4 11 9-19 22-32 (40)
161 PF01927 Mut7-C: Mut7-C RNAse 44.2 8.9 0.00019 18.4 0.3 13 39-51 124-136 (147)
162 PRK12722 transcriptional activ 44.1 16 0.00035 18.6 1.1 28 12-47 135-162 (187)
163 PF14255 Cys_rich_CPXG: Cystei 44.0 11 0.00023 15.0 0.4 9 41-49 2-10 (52)
164 PRK04351 hypothetical protein; 43.8 9.6 0.00021 18.6 0.3 12 38-49 131-142 (149)
165 PF01194 RNA_pol_N: RNA polyme 43.4 14 0.00031 15.2 0.7 14 39-52 4-17 (60)
166 PF01215 COX5B: Cytochrome c o 43.3 7.7 0.00017 18.7 -0.0 14 10-23 111-124 (136)
167 PTZ00043 cytochrome c oxidase 42.9 13 0.00028 19.7 0.7 16 9-24 179-194 (268)
168 PLN03238 probable histone acet 42.9 27 0.00058 19.3 1.8 25 37-61 46-70 (290)
169 PF01363 FYVE: FYVE zinc finge 42.3 13 0.00028 15.1 0.6 10 13-22 11-20 (69)
170 COG4888 Uncharacterized Zn rib 41.3 1.8 3.8E-05 19.7 -2.1 38 9-50 20-57 (104)
171 smart00064 FYVE Protein presen 41.0 20 0.00044 14.5 1.1 11 12-22 11-21 (68)
172 KOG1994|consensus 40.8 15 0.00032 19.5 0.7 22 10-31 238-259 (268)
173 PF13824 zf-Mss51: Zinc-finger 40.1 18 0.0004 14.6 0.8 13 9-21 12-24 (55)
174 PF05180 zf-DNL: DNL zinc fing 39.3 1.4 2.9E-05 18.4 -2.5 35 11-48 4-38 (66)
175 PRK14873 primosome assembly pr 38.9 25 0.00054 21.7 1.5 11 38-48 421-431 (665)
176 PF11931 DUF3449: Domain of un 38.8 10 0.00022 19.5 0.0 23 37-59 99-122 (196)
177 PF10537 WAC_Acf1_DNA_bd: ATP- 38.6 44 0.00096 15.3 2.0 37 11-48 3-39 (102)
178 TIGR00244 transcriptional regu 38.3 13 0.00029 18.2 0.4 13 39-51 28-40 (147)
179 PLN02748 tRNA dimethylallyltra 38.2 30 0.00066 20.4 1.7 23 38-60 417-440 (468)
180 TIGR00416 sms DNA repair prote 38.2 18 0.0004 21.0 0.9 10 11-20 7-16 (454)
181 PF09963 DUF2197: Uncharacteri 38.1 11 0.00023 15.3 -0.0 38 13-50 4-42 (56)
182 COG1379 PHP family phosphoeste 37.8 15 0.00033 20.7 0.5 12 39-50 265-276 (403)
183 COG0675 Transposase and inacti 37.6 16 0.00035 19.6 0.6 15 37-51 320-334 (364)
184 PF06676 DUF1178: Protein of u 37.4 45 0.00097 16.4 2.0 26 20-49 17-42 (148)
185 PRK11823 DNA repair protein Ra 37.1 21 0.00045 20.7 1.0 11 10-20 6-16 (446)
186 PF10083 DUF2321: Uncharacteri 36.9 19 0.0004 17.9 0.7 21 9-29 66-86 (158)
187 PF06397 Desulfoferrod_N: Desu 36.3 14 0.00031 13.5 0.2 10 39-48 6-15 (36)
188 KOG2231|consensus 36.3 66 0.0014 20.2 2.8 47 13-63 184-236 (669)
189 PF12230 PRP21_like_P: Pre-mRN 36.2 12 0.00026 19.4 0.0 22 39-61 168-189 (229)
190 PF12773 DZR: Double zinc ribb 36.1 21 0.00046 13.4 0.7 11 39-49 29-39 (50)
191 PF08792 A2L_zn_ribbon: A2L zi 36.0 14 0.00029 13.1 0.1 12 39-50 21-32 (33)
192 COG0846 SIR2 NAD-dependent pro 35.6 21 0.00046 19.1 0.8 34 10-47 121-154 (250)
193 PRK08222 hydrogenase 4 subunit 35.3 34 0.00073 17.2 1.5 19 38-56 113-131 (181)
194 smart00731 SprT SprT homologue 35.3 12 0.00026 17.9 -0.0 11 39-49 133-143 (146)
195 PF09855 DUF2082: Nucleic-acid 35.2 18 0.0004 15.0 0.5 8 40-47 1-8 (64)
196 PF14369 zf-RING_3: zinc-finge 35.1 17 0.00037 13.0 0.3 10 13-22 23-32 (35)
197 PF03811 Zn_Tnp_IS1: InsA N-te 35.0 5.8 0.00013 14.4 -0.9 12 34-45 24-35 (36)
198 KOG4727|consensus 35.0 22 0.00047 18.0 0.7 22 11-32 75-96 (193)
199 COG4338 Uncharacterized protei 34.7 13 0.00029 14.5 0.0 11 41-51 14-24 (54)
200 PTZ00448 hypothetical protein; 34.5 41 0.00089 19.3 1.8 23 39-61 314-336 (373)
201 TIGR03831 YgiT_finger YgiT-typ 33.8 16 0.00035 13.3 0.2 11 12-22 33-43 (46)
202 PTZ00409 Sir2 (Silent Informat 33.7 62 0.0013 17.6 2.3 15 10-24 136-150 (271)
203 PLN00104 MYST -like histone ac 33.6 35 0.00077 20.1 1.5 24 38-61 197-220 (450)
204 TIGR00595 priA primosomal prot 33.5 37 0.00081 20.1 1.6 10 38-47 252-261 (505)
205 PF00301 Rubredoxin: Rubredoxi 33.3 13 0.00029 14.3 -0.1 36 12-47 2-42 (47)
206 PRK05978 hypothetical protein; 33.3 16 0.00034 17.9 0.2 11 40-50 53-63 (148)
207 cd01410 SIRT7 SIRT7: Eukaryoti 33.1 73 0.0016 16.4 2.5 36 10-48 94-129 (206)
208 PRK06260 threonine synthase; V 32.8 21 0.00045 20.2 0.6 10 12-21 4-13 (397)
209 TIGR01206 lysW lysine biosynth 32.2 20 0.00044 14.3 0.4 10 40-49 3-12 (54)
210 COG1594 RPB9 DNA-directed RNA 32.0 5.8 0.00013 18.3 -1.4 10 40-49 101-110 (113)
211 PLN03239 histone acetyltransfe 31.6 43 0.00093 19.1 1.6 24 37-60 104-127 (351)
212 PTZ00064 histone acetyltransfe 31.4 45 0.00097 20.1 1.7 25 37-61 278-302 (552)
213 TIGR00515 accD acetyl-CoA carb 31.2 27 0.00059 19.1 0.8 12 39-50 45-56 (285)
214 COG1198 PriA Primosomal protei 31.2 40 0.00087 21.2 1.5 13 36-48 472-484 (730)
215 PF07800 DUF1644: Protein of u 31.1 79 0.0017 15.9 3.7 59 11-71 80-140 (162)
216 cd01413 SIR2_Af2 SIR2_Af2: Arc 30.8 58 0.0013 16.9 1.9 33 10-47 112-144 (222)
217 COG1327 Predicted transcriptio 30.6 22 0.00047 17.6 0.4 14 39-52 28-41 (156)
218 KOG4118|consensus 30.6 41 0.00088 14.2 1.1 26 39-64 38-63 (74)
219 PF14690 zf-ISL3: zinc-finger 30.6 28 0.00061 12.8 0.7 9 39-47 2-10 (47)
220 PF14787 zf-CCHC_5: GAG-polypr 30.5 21 0.00045 13.1 0.2 12 41-52 4-15 (36)
221 KOG0227|consensus 29.8 32 0.0007 17.8 0.9 21 11-31 53-73 (222)
222 PF06524 NOA36: NOA36 protein; 29.8 11 0.00024 20.4 -0.7 25 10-34 208-232 (314)
223 PRK14138 NAD-dependent deacety 29.7 61 0.0013 17.2 1.9 34 10-47 118-151 (244)
224 PF02748 PyrI_C: Aspartate car 29.4 21 0.00047 14.1 0.2 13 9-21 33-45 (52)
225 KOG1280|consensus 29.3 65 0.0014 18.5 2.0 22 11-32 79-100 (381)
226 COG1066 Sms Predicted ATP-depe 28.8 27 0.00058 20.5 0.6 12 10-21 6-17 (456)
227 PF10071 DUF2310: Zn-ribbon-co 28.8 29 0.00064 18.8 0.7 29 11-46 220-248 (258)
228 KOG3497|consensus 28.7 18 0.00039 14.9 -0.0 14 39-52 4-17 (69)
229 PF13248 zf-ribbon_3: zinc-rib 28.6 18 0.00039 11.8 -0.1 7 13-19 4-10 (26)
230 PF02146 SIR2: Sir2 family; I 28.5 18 0.00039 17.8 -0.1 35 11-49 105-139 (178)
231 PRK12387 formate hydrogenlyase 27.7 48 0.001 16.6 1.3 18 38-55 113-130 (180)
232 KOG2857|consensus 27.4 33 0.00072 16.8 0.7 22 11-32 17-38 (157)
233 PF13240 zinc_ribbon_2: zinc-r 27.4 24 0.00051 11.2 0.1 6 42-47 16-21 (23)
234 KOG3352|consensus 27.2 30 0.00065 17.1 0.5 14 10-23 132-145 (153)
235 PF14446 Prok-RING_1: Prokaryo 26.9 24 0.00052 14.2 0.1 11 40-50 6-16 (54)
236 PRK00481 NAD-dependent deacety 26.8 55 0.0012 17.2 1.5 19 6-24 117-135 (242)
237 PF08271 TF_Zn_Ribbon: TFIIB z 26.7 29 0.00062 12.8 0.3 7 41-47 2-8 (43)
238 CHL00174 accD acetyl-CoA carbo 26.6 35 0.00076 18.9 0.8 13 38-50 56-68 (296)
239 PF01780 Ribosomal_L37ae: Ribo 26.4 19 0.00041 16.1 -0.2 30 11-50 35-64 (90)
240 PRK14892 putative transcriptio 26.3 19 0.0004 16.4 -0.2 34 10-50 20-53 (99)
241 PF03966 Trm112p: Trm112p-like 26.3 22 0.00047 14.6 -0.0 12 11-22 53-64 (68)
242 PF12760 Zn_Tnp_IS1595: Transp 26.3 52 0.0011 12.3 2.5 8 40-47 19-26 (46)
243 TIGR02159 PA_CoA_Oxy4 phenylac 26.0 9.4 0.0002 18.5 -1.2 12 39-50 130-141 (146)
244 TIGR00319 desulf_FeS4 desulfof 26.0 27 0.00059 12.1 0.2 10 39-48 7-16 (34)
245 PRK04016 DNA-directed RNA poly 25.9 28 0.00062 14.4 0.3 14 38-51 3-16 (62)
246 PRK12496 hypothetical protein; 25.7 29 0.00063 17.2 0.4 11 40-50 128-138 (164)
247 KOG2747|consensus 25.7 45 0.00097 19.3 1.1 25 37-61 156-180 (396)
248 COG1579 Zn-ribbon protein, pos 25.7 56 0.0012 17.5 1.4 34 12-49 198-231 (239)
249 PF01096 TFIIS_C: Transcriptio 25.6 20 0.00044 13.0 -0.2 10 40-49 29-38 (39)
250 PF13821 DUF4187: Domain of un 25.3 40 0.00087 13.5 0.7 19 11-29 27-45 (55)
251 TIGR00280 L37a ribosomal prote 25.1 26 0.00057 15.7 0.1 31 10-50 34-64 (91)
252 cd00974 DSRD Desulforedoxin (D 24.9 32 0.00069 11.9 0.3 11 39-49 4-14 (34)
253 PF06220 zf-U1: U1 zinc finger 24.6 54 0.0012 11.9 1.3 10 40-49 4-13 (38)
254 PLN00032 DNA-directed RNA poly 24.5 27 0.00058 14.9 0.1 15 38-52 3-17 (71)
255 PF15616 TerY-C: TerY-C metal 24.3 9.4 0.0002 18.3 -1.4 11 37-47 103-113 (131)
256 PF04438 zf-HIT: HIT zinc fing 24.2 37 0.00079 11.6 0.4 12 11-22 13-24 (30)
257 PF02591 DUF164: Putative zinc 24.2 17 0.00038 14.3 -0.5 10 38-47 45-54 (56)
258 COG5236 Uncharacterized conser 23.8 68 0.0015 18.5 1.5 23 41-63 222-244 (493)
259 COG1644 RPB10 DNA-directed RNA 23.4 28 0.00061 14.4 0.1 15 38-52 3-17 (63)
260 PRK01343 zinc-binding protein; 23.4 49 0.0011 13.5 0.7 11 40-50 10-20 (57)
261 PF14169 YdjO: Cold-inducible 23.2 73 0.0016 13.1 1.2 8 40-47 40-47 (59)
262 smart00132 LIM Zinc-binding do 22.9 39 0.00084 11.3 0.4 10 40-49 28-37 (39)
263 cd01412 SIRT5_Af1_CobB SIRT5_A 22.9 97 0.0021 16.0 1.9 14 10-23 108-121 (224)
264 TIGR03830 CxxCG_CxxCG_HTH puta 22.8 81 0.0018 14.4 1.5 20 11-30 31-50 (127)
265 smart00661 RPOL9 RNA polymeras 22.6 59 0.0013 12.2 0.9 12 39-50 20-31 (52)
266 PF13453 zf-TFIIB: Transcripti 22.4 61 0.0013 11.7 1.0 19 39-57 19-37 (41)
267 KOG3362|consensus 22.4 19 0.00042 17.6 -0.6 22 39-60 129-150 (156)
268 COG5319 Uncharacterized protei 22.4 1.1E+02 0.0024 14.9 1.8 27 19-49 16-42 (142)
269 PRK03976 rpl37ae 50S ribosomal 22.3 33 0.00071 15.4 0.1 12 39-50 54-65 (90)
270 COG5152 Uncharacterized conser 22.1 45 0.00097 17.5 0.6 16 37-52 194-209 (259)
271 COG5188 PRP9 Splicing factor 3 22.1 52 0.0011 18.9 0.9 22 39-60 238-259 (470)
272 PF10367 Vps39_2: Vacuolar sor 22.1 45 0.00099 14.6 0.6 12 40-51 79-90 (109)
273 COG1885 Uncharacterized protei 22.1 43 0.00092 15.5 0.5 11 40-50 50-60 (115)
274 PF09943 DUF2175: Uncharacteri 21.9 24 0.00053 16.2 -0.3 8 40-47 3-10 (101)
275 COG3478 Predicted nucleic-acid 21.8 54 0.0012 13.8 0.7 8 40-47 5-12 (68)
276 KOG1088|consensus 21.8 27 0.00058 16.5 -0.2 11 12-22 99-109 (124)
277 PF07295 DUF1451: Protein of u 21.7 29 0.00063 17.0 -0.1 28 10-47 111-138 (146)
278 COG1656 Uncharacterized conser 21.7 40 0.00086 17.0 0.4 18 39-56 130-147 (165)
279 PF04328 DUF466: Protein of un 21.5 85 0.0018 13.0 2.2 13 57-69 30-42 (65)
280 PF06170 DUF983: Protein of un 21.5 45 0.00097 14.7 0.5 11 40-50 9-19 (86)
281 COG2879 Uncharacterized small 21.5 86 0.0019 13.1 2.4 15 53-67 26-40 (65)
282 PF01844 HNH: HNH endonuclease 21.4 39 0.00084 12.2 0.3 9 42-50 1-9 (47)
283 KOG3456|consensus 21.4 40 0.00088 15.7 0.3 13 39-51 104-116 (120)
284 PF03884 DUF329: Domain of unk 21.3 35 0.00075 13.9 0.1 11 40-50 3-13 (57)
285 COG5027 SAS2 Histone acetyltra 21.1 62 0.0013 18.6 1.0 24 38-61 157-180 (395)
286 PRK05654 acetyl-CoA carboxylas 21.0 47 0.001 18.3 0.6 12 39-50 46-57 (292)
287 PF14375 Cys_rich_CWC: Cystein 20.9 45 0.00097 12.9 0.4 7 43-49 2-8 (50)
288 KOG3277|consensus 20.7 25 0.00054 17.5 -0.4 34 11-47 79-112 (165)
289 KOG0402|consensus 20.7 31 0.00067 15.3 -0.1 10 39-48 36-45 (92)
290 PRK06450 threonine synthase; V 20.6 64 0.0014 18.1 1.0 10 12-21 4-13 (338)
291 PF14205 Cys_rich_KTR: Cystein 20.6 23 0.0005 14.3 -0.4 11 37-47 26-36 (55)
292 PRK05580 primosome assembly pr 20.5 30 0.00064 21.3 -0.2 12 37-48 419-430 (679)
293 PF14599 zinc_ribbon_6: Zinc-r 20.4 18 0.00039 14.9 -0.8 6 14-19 33-38 (61)
294 PF10058 DUF2296: Predicted in 20.3 43 0.00093 13.3 0.3 10 38-47 43-52 (54)
295 TIGR03829 YokU_near_AblA uncha 20.3 67 0.0015 14.4 0.9 18 12-29 36-53 (89)
296 COG4847 Uncharacterized protei 20.2 36 0.00078 15.5 0.1 13 8-20 3-15 (103)
No 1
>KOG2462|consensus
Probab=99.87 E-value=6.7e-23 Score=101.56 Aligned_cols=64 Identities=42% Similarity=0.819 Sum_probs=59.7
Q ss_pred CCCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhccCCCCCCCC
Q psy2647 8 GEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMRPVPVT 72 (72)
Q Consensus 8 ~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~~~~ 72 (72)
..-++.|..||+.|...+.|+.|+++|+|++||.|+.|++.|.++++|..|+++ |++.++|.|.
T Consensus 184 H~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQT-HS~~K~~qC~ 247 (279)
T KOG2462|consen 184 HTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQT-HSDVKKHQCP 247 (279)
T ss_pred cCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHh-hcCCccccCc
Confidence 345789999999999999999999999999999999999999999999999999 8888899873
No 2
>KOG2462|consensus
Probab=99.76 E-value=5e-19 Score=88.04 Aligned_cols=60 Identities=40% Similarity=0.747 Sum_probs=56.6
Q ss_pred ccccccCCCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHH
Q psy2647 2 ISNIWHGEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 2 ~~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
+-++|+|+|||.|..|++.|..+.+|..|+.+|.+.++|+|..|++.|...+.|..|...
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 357899999999999999999999999999999999999999999999999999999764
No 3
>KOG3623|consensus
Probab=99.65 E-value=7.8e-17 Score=88.87 Aligned_cols=63 Identities=33% Similarity=0.720 Sum_probs=51.3
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhccCCCCCCCC
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMRPVPVT 72 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~~~~ 72 (72)
+.+|.|+.|++.|.-...|.+|.-.|+|.+||+|.+|.+.|..+..|..|+|+ |+|++||-|+
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRL-HSGEKPfQCd 954 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRL-HSGEKPFQCD 954 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhh-ccCCCcchhh
Confidence 45688888888888888888888888888888888888888888888888888 8888888774
No 4
>KOG3623|consensus
Probab=99.61 E-value=2.5e-16 Score=86.96 Aligned_cols=62 Identities=32% Similarity=0.680 Sum_probs=56.8
Q ss_pred cccccCCCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhcc
Q psy2647 3 SNIWHGEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 3 ~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
..-|+|.+||.|.+|.+.|+.+-+|..|++.|.|++||+|.+|+++|+...+..+|+....+
T Consensus 914 KYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMNHRYS 975 (1007)
T KOG3623|consen 914 KYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMNHRYS 975 (1007)
T ss_pred hhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhccchh
Confidence 34589999999999999999999999999999999999999999999999999999874333
No 5
>KOG3576|consensus
Probab=99.43 E-value=1.7e-14 Score=69.90 Aligned_cols=52 Identities=40% Similarity=0.925 Sum_probs=26.9
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHH
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
.+.+.|..|+++|.....|++|+++|+|-+||+|..|++.|.++-+|..|++
T Consensus 143 vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 143 VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 3444455555555555555555555555555555555555555555555544
No 6
>KOG3576|consensus
Probab=99.36 E-value=6.6e-14 Score=67.92 Aligned_cols=63 Identities=37% Similarity=0.772 Sum_probs=58.2
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhccCCCCCCCC
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMRPVPVT 72 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~~~~ 72 (72)
...+.|..|++.|.....|.+|++.|..-+.+.|..||+.|...-.|++|.++ |++-+||.|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rt-htgvrpykc~ 177 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRT-HTGVRPYKCS 177 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcc-ccCccccchh
Confidence 45688999999999999999999999888889999999999999999999999 9999999985
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.34 E-value=3.3e-13 Score=53.19 Aligned_cols=44 Identities=27% Similarity=0.546 Sum_probs=39.0
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLR 56 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~ 56 (72)
-|.|+.|++.|....+|..|++.|+ ++++|..|++.|...+.|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3789999999999999999999998 6899999999998776653
No 8
>KOG1074|consensus
Probab=99.34 E-value=1.4e-13 Score=77.06 Aligned_cols=56 Identities=43% Similarity=0.851 Sum_probs=51.0
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhccCCC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMR 67 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~~~~ 67 (72)
+++|..|.+.|.+...|+.|.++|+|++||+|.+||..|..+.+|+.|... |.+..
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~r-H~e~~ 408 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQR-HREKY 408 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeee-ccccC
Confidence 467999999999999999999999999999999999999999999999887 44443
No 9
>PHA00733 hypothetical protein
Probab=99.25 E-value=2.3e-11 Score=55.93 Aligned_cols=56 Identities=27% Similarity=0.485 Sum_probs=48.8
Q ss_pred cCCCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhcc
Q psy2647 7 HGEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 7 ~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
.+.++|.|..|++.|.....|..|++.+ ..++.|..|++.|.....|..|+...|.
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3478999999999999999999998865 3579999999999999999999887665
No 10
>KOG1074|consensus
Probab=99.18 E-value=8.1e-12 Score=70.31 Aligned_cols=58 Identities=41% Similarity=0.843 Sum_probs=48.1
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhccCCCCC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMRPV 69 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~ 69 (72)
|..|-.|.+...-...|+.|.++|+|++||+|.+||+.|..+.+|+.|+.+ |...-|+
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~v-Hka~p~~ 662 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSV-HKAKPPA 662 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccc-cccCccc
Confidence 567888888888888888898899999999999999999988888888887 5555444
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=99.14 E-value=3.6e-11 Score=41.09 Aligned_cols=25 Identities=52% Similarity=1.081 Sum_probs=22.5
Q ss_pred HHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 26 NLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 26 ~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
+|..|++.|++++||.|+.|++.|.
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 4788999999999999999999886
No 12
>KOG3608|consensus
Probab=99.08 E-value=1e-10 Score=61.07 Aligned_cols=62 Identities=23% Similarity=0.486 Sum_probs=45.7
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhccCCCCCCCC
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMRPVPVT 72 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~~~~ 72 (72)
.++|.|..|.+.|..+..|..|+..|.. .|+|+.|..+....+.|..|++..|..++|++|+
T Consensus 235 ~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd 296 (467)
T KOG3608|consen 235 TNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCD 296 (467)
T ss_pred CCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCCcccc
Confidence 3456666677777666667666666643 4778888888888888888888888888888875
No 13
>PHA00616 hypothetical protein
Probab=99.03 E-value=2.2e-10 Score=43.30 Aligned_cols=31 Identities=19% Similarity=0.446 Sum_probs=16.6
Q ss_pred CccCCcchhhcCChHHHHHHHHHhccCCCCCC
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQHTEMRPVP 70 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~~ 70 (72)
||+|..||+.|.+.+.+..|++. +.++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcCCCccc
Confidence 35555566666655666666555 33334443
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.82 E-value=4.6e-09 Score=41.52 Aligned_cols=25 Identities=16% Similarity=0.656 Sum_probs=23.1
Q ss_pred CccCCcchhhcCChHHHHHHHHHhc
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
.|+|+.||+.|...+.|..|+++|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4799999999999999999999955
No 15
>PHA00616 hypothetical protein
Probab=98.81 E-value=3.5e-09 Score=40.05 Aligned_cols=34 Identities=18% Similarity=0.353 Sum_probs=31.4
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCc
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDL 44 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~ 44 (72)
||.|..||..|.....+..|++.+++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6889999999999999999999999999988764
No 16
>KOG3608|consensus
Probab=98.75 E-value=2.4e-08 Score=52.54 Aligned_cols=51 Identities=39% Similarity=0.675 Sum_probs=31.9
Q ss_pred cccCcccchhccCcHHHHHhHHH-hcCCCCccCCcchhhcCChHHHHHHHHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRK-HTGFKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~-~~~~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
.|.|+.|+........|..|++. |...+|++|..|.+.+...+.|+.|..+
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~ 314 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQV 314 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHh
Confidence 45666666666666666666654 5555666666666666666666666665
No 17
>PHA00732 hypothetical protein
Probab=98.68 E-value=1.4e-08 Score=43.25 Aligned_cols=45 Identities=31% Similarity=0.659 Sum_probs=37.0
Q ss_pred cccCcccchhccCcHHHHHhHHH-hcCCCCccCCcchhhcCChHHHHHHHHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRK-HTGFKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~-~~~~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
||.|..|++.|.....|..|++. |. ++.|+.|++.|.. +..|.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhcc
Confidence 57899999999999999999984 54 3589999999973 5667654
No 18
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.64 E-value=1.4e-07 Score=37.42 Aligned_cols=51 Identities=31% Similarity=0.605 Sum_probs=38.9
Q ss_pred cccCcccchhccCcHHHHHhHHH-hcC-CCCccCCcchhhcCChHHHHHHHHHhcc
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRK-HTG-FKPFACDLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~-~~~-~~~~~c~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
.|.|+.|++ ..+...|..|... |.. .+.+.|+.|...+. .+|..|+..+|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 478999999 4567889999775 544 35789999998644 488899887653
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.61 E-value=8.9e-08 Score=53.15 Aligned_cols=57 Identities=23% Similarity=0.630 Sum_probs=37.4
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHhccCCCCCCC
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMRPVPV 71 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~~~ 71 (72)
++++.|..|+..|. ...+..|+..++ .++.|+ |+..+ .+..|..|+.+ +..++|+.|
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~t-hCp~Kpi~C 507 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQAS-TCPLRLITC 507 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhc-cCCCCceeC
Confidence 45567777777774 456777776653 567777 77544 45677777766 666677666
No 20
>PHA00733 hypothetical protein
Probab=98.54 E-value=7.5e-08 Score=44.48 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=41.8
Q ss_pred CCCcccCcccchhccCcHHHHHh--HH---HhcCCCCccCCcchhhcCChHHHHHHHHH
Q psy2647 8 GEKPHKCQVCGKAFSQSSNLITH--SR---KHTGFKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 8 ~~~~~~c~~c~~~~~~~~~l~~~--~~---~~~~~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
..+++.|..|...+.....+..+ .. ...+.+||.|..|++.|.....|..|++.
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhc
Confidence 35678899998887776665554 11 22346799999999999999999999986
No 21
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.54 E-value=6.3e-08 Score=31.87 Aligned_cols=22 Identities=36% Similarity=1.026 Sum_probs=16.1
Q ss_pred ccCCcchhhcCChHHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
|+|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4677777777777777777765
No 22
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.51 E-value=1.3e-08 Score=34.62 Aligned_cols=21 Identities=52% Similarity=0.933 Sum_probs=18.5
Q ss_pred ccccccCCCcccCcccchhcc
Q psy2647 2 ISNIWHGEKPHKCQVCGKAFS 22 (72)
Q Consensus 2 ~~~~~~~~~~~~c~~c~~~~~ 22 (72)
++++|++++||.|+.|++.|.
T Consensus 5 H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 5 HMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHSSSSSEEESSSSEEES
T ss_pred HhhhcCCCCCCCCCCCcCeeC
Confidence 456899999999999999885
No 23
>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=98.44 E-value=2.2e-07 Score=30.61 Aligned_cols=24 Identities=46% Similarity=1.115 Sum_probs=16.4
Q ss_pred ccCCcchhhcCChHHHHHHHHHhc
Q psy2647 40 FACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
|.|+.|++.|.....+..|+..+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 467788888888888888877643
No 24
>KOG3993|consensus
Probab=98.41 E-value=2e-07 Score=50.04 Aligned_cols=54 Identities=37% Similarity=0.732 Sum_probs=35.6
Q ss_pred cccCcccchhccCcHHHHHhHHHhcC--------CC-------------------------CccCCcchhhcCChHHHHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTG--------FK-------------------------PFACDLCGRAFQRKVDLRR 57 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~--------~~-------------------------~~~c~~c~~~~~~~~~l~~ 57 (72)
-|.|.+|++.|.-..+|..|.++|-. .. .|.|..|++.|.....|..
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 36777777777777777777765521 11 2567777777777777777
Q ss_pred HHHHhcc
Q psy2647 58 HKETQHT 64 (72)
Q Consensus 58 H~~~~~~ 64 (72)
|+-+|+.
T Consensus 375 Hqlthq~ 381 (500)
T KOG3993|consen 375 HQLTHQR 381 (500)
T ss_pred hHHhhhc
Confidence 7666543
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=98.39 E-value=1.2e-07 Score=32.35 Aligned_cols=24 Identities=46% Similarity=1.032 Sum_probs=17.2
Q ss_pred CccCCcchhhcCChHHHHHHHHHh
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQ 62 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~ 62 (72)
+++|..|++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 466777777777777777777654
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.37 E-value=5.2e-07 Score=50.28 Aligned_cols=58 Identities=21% Similarity=0.588 Sum_probs=46.8
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCC----------hHHHHHHHHHhccCCCCCCC
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQR----------KVDLRRHKETQHTEMRPVPV 71 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~----------~~~l~~H~~~~~~~~~p~~~ 71 (72)
+++.|+ |+..+ ....|..|+..+.+.+++.|..|+..+.. .+.|..|... .+.+++.|
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~--CG~rt~~C 544 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI--CGSRTAPC 544 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh--cCCcceEc
Confidence 678898 99655 56889999988999999999999988842 3578889886 47777776
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.29 E-value=4.7e-07 Score=29.71 Aligned_cols=23 Identities=57% Similarity=1.057 Sum_probs=20.6
Q ss_pred ccCcccchhccCcHHHHHhHHHh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKH 34 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~ 34 (72)
|.|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 57999999999999999998763
No 28
>KOG3993|consensus
Probab=98.29 E-value=9.8e-08 Score=51.18 Aligned_cols=52 Identities=19% Similarity=0.454 Sum_probs=45.5
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHHHh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQ 62 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~~~ 62 (72)
-|.|..|...|.....|.+|.-.......|+|+.|++.|+...+|..|+|.|
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhccc
Confidence 4889999999999999999876555556799999999999999999999984
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.03 E-value=1.6e-06 Score=45.34 Aligned_cols=52 Identities=29% Similarity=0.680 Sum_probs=42.6
Q ss_pred CCcccCcc--cchhccCcHHHHHhHHHhc-------------------CCCCccCCcchhhcCChHHHHHHHH
Q psy2647 9 EKPHKCQV--CGKAFSQSSNLITHSRKHT-------------------GFKPFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 9 ~~~~~c~~--c~~~~~~~~~l~~~~~~~~-------------------~~~~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
++||.|+. |.+.|+....|+-|+.... ..+||+|++|++++.....|+-|+.
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 48999977 9999999988888876421 1389999999999998888887765
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.93 E-value=1.9e-05 Score=26.09 Aligned_cols=22 Identities=36% Similarity=0.881 Sum_probs=15.8
Q ss_pred ccCCcchhhcCChHHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
++|..|++.|.....+..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 3577777777777777777764
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.91 E-value=4.3e-06 Score=28.39 Aligned_cols=25 Identities=48% Similarity=0.909 Sum_probs=22.1
Q ss_pred cccCcccchhccCcHHHHHhHHHhc
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHT 35 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~ 35 (72)
+|.|..|+..|.....+..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5789999999999999999987653
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.85 E-value=1.5e-05 Score=25.95 Aligned_cols=23 Identities=43% Similarity=0.947 Sum_probs=18.8
Q ss_pred ccCcccchhccCcHHHHHhHHHh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKH 34 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~ 34 (72)
|.|+.|+..|.....+..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 57999999999999999998864
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.80 E-value=3e-05 Score=33.97 Aligned_cols=49 Identities=29% Similarity=0.717 Sum_probs=20.8
Q ss_pred CcccchhccCcHHHHHhHHH-hcC----------------------CCCccCCcchhhcCChHHHHHHHHHh
Q psy2647 14 CQVCGKAFSQSSNLITHSRK-HTG----------------------FKPFACDLCGRAFQRKVDLRRHKETQ 62 (72)
Q Consensus 14 c~~c~~~~~~~~~l~~~~~~-~~~----------------------~~~~~c~~c~~~~~~~~~l~~H~~~~ 62 (72)
|..|+..|.....+..|+.. |.- ...+.|..|++.|.....|..|++.+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 55666666666666666542 210 12478999999999999999999864
No 34
>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=97.78 E-value=4e-05 Score=29.89 Aligned_cols=29 Identities=34% Similarity=0.747 Sum_probs=19.5
Q ss_pred CCCCccCCcchhhcCChHHHHHHHHHhcc
Q psy2647 36 GFKPFACDLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 36 ~~~~~~c~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
.+.|-.|+.|+..+.+..+|.+|+.+.|.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 35678899999999999999999987444
No 35
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.77 E-value=3e-05 Score=25.54 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=14.8
Q ss_pred ccCCcchhhcCChHHHHHHHHHhc
Q psy2647 40 FACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
|+|..|+.... ...|..|++.+|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 46777777666 777777777655
No 36
>PHA00732 hypothetical protein
Probab=97.72 E-value=4e-05 Score=32.75 Aligned_cols=26 Identities=31% Similarity=0.645 Sum_probs=22.4
Q ss_pred CccCCcchhhcCChHHHHHHHHHhcc
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
||.|..|++.|.....|..|++.+|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC
Confidence 57899999999999999999984344
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=97.70 E-value=6.7e-05 Score=29.27 Aligned_cols=32 Identities=38% Similarity=0.626 Sum_probs=22.3
Q ss_pred CCCcccCcccchhccCcHHHHHhHHHhcCCCC
Q psy2647 8 GEKPHKCQVCGKAFSQSSNLITHSRKHTGFKP 39 (72)
Q Consensus 8 ~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~ 39 (72)
.+.|..|+.|+....+..+|.+|+....+.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45688999999999999999999987666554
No 38
>PRK04860 hypothetical protein; Provisional
Probab=97.69 E-value=3.2e-05 Score=37.17 Aligned_cols=37 Identities=24% Similarity=0.630 Sum_probs=29.4
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQR 51 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~ 51 (72)
+|.|. |+. ....+..|.+.+.++++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 57887 876 45667888889999889999999887654
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.37 E-value=9.3e-05 Score=24.51 Aligned_cols=22 Identities=36% Similarity=0.939 Sum_probs=14.4
Q ss_pred ccCCcchhhcCChHHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
|.|..|...|.....+..|++.
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 3566677777777777766653
No 40
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.87 E-value=0.0014 Score=21.85 Aligned_cols=20 Identities=35% Similarity=0.923 Sum_probs=12.3
Q ss_pred ccCCcchhhcCChHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~ 60 (72)
..|+.||+.| ....+..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3577777777 3555566654
No 41
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.85 E-value=0.00034 Score=23.67 Aligned_cols=21 Identities=33% Similarity=0.687 Sum_probs=11.1
Q ss_pred ccCcccchhccCcHHHHHhHH
Q psy2647 12 HKCQVCGKAFSQSSNLITHSR 32 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~ 32 (72)
|.|..|++.|.+...+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 345555555555555555543
No 42
>KOG2893|consensus
Probab=96.60 E-value=0.00046 Score=35.29 Aligned_cols=43 Identities=30% Similarity=0.709 Sum_probs=31.3
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHH
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLR 56 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~ 56 (72)
.++| |.+|++.|..+.-|..|++ .+.|+|-+|-+.+.+-..|.
T Consensus 9 ~kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpgls 51 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLS 51 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCce
Confidence 3454 6789999999999988876 45789999986554443333
No 43
>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=96.53 E-value=0.0051 Score=24.28 Aligned_cols=32 Identities=28% Similarity=0.528 Sum_probs=23.5
Q ss_pred CccCCcchhhcCChHHHHHHHHHhccCC-CCCCC
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQHTEM-RPVPV 71 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~~~~-~p~~~ 71 (72)
.|.|+.|++ ......|..|....|..+ +.+.|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~C 34 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVC 34 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccC
Confidence 478999999 456788999988767665 33433
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=96.11 E-value=0.0045 Score=21.96 Aligned_cols=22 Identities=27% Similarity=0.726 Sum_probs=15.9
Q ss_pred CccCCcchhhcCChHHHHHHHH
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
++.|..|+..|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667888888877777777754
No 45
>PRK04860 hypothetical protein; Provisional
Probab=95.58 E-value=0.0081 Score=29.11 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=23.1
Q ss_pred CccCCcchhhcCChHHHHHHHHHhccCCCCCCC
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQHTEMRPVPV 71 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~~~~~p~~~ 71 (72)
+|.|. |+. ....+..|.++ +.++++|.|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri-~~g~~~YrC 146 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRV-VRGEAVYRC 146 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHH-hcCCccEEC
Confidence 68897 876 56677899999 888889887
No 46
>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=95.55 E-value=0.0083 Score=21.30 Aligned_cols=24 Identities=33% Similarity=0.999 Sum_probs=16.6
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
|.|..|+..+.... .++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 67888887654322 5788999874
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.36 E-value=0.0025 Score=34.29 Aligned_cols=56 Identities=46% Similarity=0.842 Sum_probs=46.7
Q ss_pred cccCcccchhccCcHHHHHhHH--HhcCC--CCccCC--cchhhcCChHHHHHHHHHhccCCC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSR--KHTGF--KPFACD--LCGRAFQRKVDLRRHKETQHTEMR 67 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~H~~~~~~~~~ 67 (72)
++.|..|...+.....+..+.+ .|.++ +++.|+ .|++.|.....+..|..+ +....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~-~~~~~ 350 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILL-HTSIS 350 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccc-ccCCC
Confidence 5778888899999999999999 78888 899999 799999998888888777 44443
No 48
>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=95.21 E-value=0.013 Score=26.65 Aligned_cols=30 Identities=30% Similarity=0.811 Sum_probs=22.9
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCCh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRK 52 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~ 52 (72)
..|+.||..|.- .+..|..|++||..|...
T Consensus 10 R~Cp~CG~kFYD-----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD-----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc-----------CCCCCccCCCCCCccCcc
Confidence 479999988754 224688999999888755
No 49
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.16 E-value=0.016 Score=23.13 Aligned_cols=25 Identities=36% Similarity=0.707 Sum_probs=14.7
Q ss_pred CCCCccCCcchhhcCChHHHHHHHH
Q psy2647 36 GFKPFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 36 ~~~~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
|+.-+.|+-|+..|.......+|..
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhh
Confidence 4445566666666666655555554
No 50
>KOG1146|consensus
Probab=95.06 E-value=0.022 Score=35.71 Aligned_cols=55 Identities=24% Similarity=0.386 Sum_probs=44.0
Q ss_pred cCCCcccCcccchhccCcHHHHHhHHHhc-------------------------CCCCccCCcchhhcCChHHHHHHHHH
Q psy2647 7 HGEKPHKCQVCGKAFSQSSNLITHSRKHT-------------------------GFKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 7 ~~~~~~~c~~c~~~~~~~~~l~~~~~~~~-------------------------~~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
+-.+.+.|+.|++.|+....|..|++..+ +.++|.|..|...+....+|..|+..
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 33477899999999999999999998711 12568888999999888888888763
No 51
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=93.59 E-value=0.046 Score=26.75 Aligned_cols=23 Identities=39% Similarity=0.936 Sum_probs=17.4
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcch
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCG 46 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~ 46 (72)
-|.|..||..+ .++.|.+|+.||
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 58899997542 346688999998
No 52
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.36 E-value=0.039 Score=22.33 Aligned_cols=32 Identities=22% Similarity=0.504 Sum_probs=17.7
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
.|.|+.|+...-.+- .+......+|+|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 467777775432221 22222346788888873
No 53
>KOG2186|consensus
Probab=93.00 E-value=0.065 Score=27.97 Aligned_cols=47 Identities=28% Similarity=0.682 Sum_probs=33.3
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCChHHHHHHHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
.|.|..|+.... ...+..|+..-.+ .-|.|..|++.|-. .....|..
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 467999998766 4446677765444 46899999999976 45556654
No 54
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.97 E-value=0.07 Score=20.30 Aligned_cols=29 Identities=21% Similarity=0.422 Sum_probs=20.0
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.|.|..|+..+... ...+..|+.||....
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCceEE
Confidence 37899999876533 234689999986543
No 55
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.97 E-value=0.076 Score=19.33 Aligned_cols=33 Identities=24% Similarity=0.626 Sum_probs=21.8
Q ss_pred cCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 13 KCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 13 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.|+.|+..|.....- ...+....+|+.|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 588888888765542 112344688999987764
No 56
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.61 E-value=0.021 Score=28.95 Aligned_cols=42 Identities=33% Similarity=0.641 Sum_probs=27.6
Q ss_pred CcccCcccchhccCcHHHHHhHHH---h-------cCCCC-----ccCCcchhhcCC
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRK---H-------TGFKP-----FACDLCGRAFQR 51 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~---~-------~~~~~-----~~c~~c~~~~~~ 51 (72)
+...|+.|+..|..........+. . .+..| +.|+.||.++..
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 567899999999877554444432 1 12233 489999987753
No 57
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=92.39 E-value=0.018 Score=27.82 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=9.8
Q ss_pred CccCCcchhhcCC
Q psy2647 39 PFACDLCGRAFQR 51 (72)
Q Consensus 39 ~~~c~~c~~~~~~ 51 (72)
.++|+.||.+|..
T Consensus 28 ~~~c~~c~~~f~~ 40 (154)
T PRK00464 28 RRECLACGKRFTT 40 (154)
T ss_pred eeeccccCCcceE
Confidence 3788888888764
No 58
>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=92.12 E-value=0.097 Score=18.72 Aligned_cols=25 Identities=32% Similarity=0.733 Sum_probs=16.4
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
.|.|..||..+... ..|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 37788888654321 24668888874
No 59
>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=92.03 E-value=0.11 Score=24.37 Aligned_cols=30 Identities=20% Similarity=0.403 Sum_probs=22.5
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCCh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRK 52 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~ 52 (72)
..|+.|+..|.- .+..|..|++||..+...
T Consensus 10 r~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc-----------cCCCCccCCCcCCccCcc
Confidence 579999987753 234688999999887655
No 60
>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=91.89 E-value=0.084 Score=25.58 Aligned_cols=33 Identities=18% Similarity=0.376 Sum_probs=24.2
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
..-|.|+.|+..|+...++. ..|.|+.||....
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 34578999998887766653 2589999997543
No 61
>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=91.33 E-value=0.047 Score=21.22 Aligned_cols=29 Identities=24% Similarity=0.596 Sum_probs=18.7
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
|.|..|+..|.....+. . .....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS------D-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC------C-CCCCCCCCCCC
Confidence 77999998776432211 1 34567999985
No 62
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.06 E-value=0.1 Score=25.79 Aligned_cols=32 Identities=22% Similarity=0.498 Sum_probs=23.7
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.-|.|+.|+..|....++. ..|.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 4588999998887666542 3699999997554
No 63
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.01 E-value=0.16 Score=18.40 Aligned_cols=33 Identities=21% Similarity=0.545 Sum_probs=21.2
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
..|+.|...|....... .......+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcEEECCCCCCEe
Confidence 35888888877655422 1223457899998766
No 64
>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=90.87 E-value=0.31 Score=16.28 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=12.2
Q ss_pred ccCCcchhhcCChHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~ 60 (72)
..|+.|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3577777766 4455566654
No 65
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=90.64 E-value=0.062 Score=29.05 Aligned_cols=24 Identities=33% Similarity=0.758 Sum_probs=20.0
Q ss_pred CCCcccCcccchhccCcHHHHHhH
Q psy2647 8 GEKPHKCQVCGKAFSQSSNLITHS 31 (72)
Q Consensus 8 ~~~~~~c~~c~~~~~~~~~l~~~~ 31 (72)
..|||.|+.|++.|+....|+-|.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 468999999999999887777664
No 66
>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=90.13 E-value=0.068 Score=19.56 Aligned_cols=29 Identities=24% Similarity=0.595 Sum_probs=18.7
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
|.|..|+..|....... . .....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS------D-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecC------C-CCCCCCCCCCC
Confidence 67999998775433221 1 34567999886
No 67
>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=90.10 E-value=0.27 Score=18.35 Aligned_cols=25 Identities=28% Similarity=0.642 Sum_probs=13.9
Q ss_pred CCCccCCcchhhcCC----hHHHHHHHHH
Q psy2647 37 FKPFACDLCGRAFQR----KVDLRRHKET 61 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~----~~~l~~H~~~ 61 (72)
.....|..|++.+.. .+.|..|++.
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 345677778776654 3677777743
No 68
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.07 E-value=0.13 Score=19.59 Aligned_cols=31 Identities=23% Similarity=0.505 Sum_probs=19.7
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
..|.|..|+..+..... .....|+.||..+.
T Consensus 2 ~~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEY----------GTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCC----------CCceECCCCCCeEE
Confidence 35789999876644221 11578999986543
No 69
>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=90.00 E-value=0.19 Score=17.82 Aligned_cols=28 Identities=25% Similarity=0.572 Sum_probs=16.2
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
|.|..|+..+... ...+.+|..||....
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCeEE
Confidence 4677787655421 134678999986543
No 70
>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=89.84 E-value=0.22 Score=23.56 Aligned_cols=24 Identities=38% Similarity=0.722 Sum_probs=14.6
Q ss_pred CccCCcchhhcCChHHHHHHHHHhccC
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQHTE 65 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~~~ 65 (72)
-..|-.||+.|.. |.+|++.||+.
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eeEEccCCcccch---HHHHHHHccCC
Confidence 4689999998875 48899986543
No 71
>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=89.77 E-value=0.13 Score=26.26 Aligned_cols=25 Identities=32% Similarity=0.727 Sum_probs=13.1
Q ss_pred CccCCcchhhcCChHHHHHHHHHhc
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
.|.|..|+|.|.-..-...|+...|
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred EECCCCCCcccCChHHHHHHHhhcC
Confidence 4566666666666655566655444
No 72
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=89.68 E-value=0.23 Score=19.42 Aligned_cols=38 Identities=21% Similarity=0.456 Sum_probs=23.3
Q ss_pred CCcccCcccchhccCcHHHHHhHHHh-cCCCCccCCcch
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKH-TGFKPFACDLCG 46 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~-~~~~~~~c~~c~ 46 (72)
++.+.|..|+..|.....-+..-..- ....|-.|..|-
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 45678999998887766544443331 123466777664
No 73
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.61 E-value=0.22 Score=17.97 Aligned_cols=34 Identities=18% Similarity=0.487 Sum_probs=21.0
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
..|+.|+..|........ .....+.|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEEE
Confidence 468888887765543211 1122578999987664
No 74
>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=89.16 E-value=0.44 Score=21.51 Aligned_cols=25 Identities=28% Similarity=0.658 Sum_probs=21.4
Q ss_pred ccC----CcchhhcCChHHHHHHHHHhcc
Q psy2647 40 FAC----DLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 40 ~~c----~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
|.| ..|+....+...+..|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 688 8899999999999999887664
No 75
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.71 E-value=0.18 Score=24.15 Aligned_cols=38 Identities=18% Similarity=0.388 Sum_probs=23.9
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
..-|.|+.|+..|.....+..- .. ...|.|+.||....
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEEE
Confidence 3458899999888754433210 11 23489999987553
No 76
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.32 E-value=0.16 Score=20.60 Aligned_cols=32 Identities=22% Similarity=0.588 Sum_probs=16.4
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
.|.|+.|+.....+ -.+......+|.|+.||.
T Consensus 25 ~F~CPnCG~~~I~R-----C~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYR-----CEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEee-----chhHHhcCCceECCCCCC
Confidence 46677776542111 111222245788888763
No 77
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=87.97 E-value=0.24 Score=19.36 Aligned_cols=30 Identities=23% Similarity=0.623 Sum_probs=19.7
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
..|.|..|++.+... .....+.|+.||...
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCceeCCCCCcEE
Confidence 458899999877211 123467899998643
No 78
>KOG2893|consensus
Probab=87.09 E-value=0.31 Score=25.49 Aligned_cols=26 Identities=35% Similarity=0.718 Sum_probs=21.1
Q ss_pred CCCccCCcchhhcCChHHHHHHHHHhc
Q psy2647 37 FKPFACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
.++| |.+|++-|.....|++|++..|
T Consensus 9 ~kpw-cwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhhcc
Confidence 3455 7899999999999999987533
No 79
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=86.02 E-value=0.93 Score=17.48 Aligned_cols=21 Identities=38% Similarity=0.882 Sum_probs=14.0
Q ss_pred ccCCcchhhcCCh-----HHHHHHHH
Q psy2647 40 FACDLCGRAFQRK-----VDLRRHKE 60 (72)
Q Consensus 40 ~~c~~c~~~~~~~-----~~l~~H~~ 60 (72)
..|..|++.+... ++|.+|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4677777666443 57778877
No 80
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=85.65 E-value=0.52 Score=20.88 Aligned_cols=12 Identities=42% Similarity=1.176 Sum_probs=6.4
Q ss_pred cccCcccchhcc
Q psy2647 11 PHKCQVCGKAFS 22 (72)
Q Consensus 11 ~~~c~~c~~~~~ 22 (72)
|-.|..||..|.
T Consensus 58 Pa~CkkCGfef~ 69 (97)
T COG3357 58 PARCKKCGFEFR 69 (97)
T ss_pred ChhhcccCcccc
Confidence 445566655543
No 81
>PF12907 zf-met2: Zinc-binding
Probab=85.44 E-value=0.22 Score=18.62 Aligned_cols=20 Identities=30% Similarity=0.845 Sum_probs=8.5
Q ss_pred cCCcchhhcCC---hHHHHHHHH
Q psy2647 41 ACDLCGRAFQR---KVDLRRHKE 60 (72)
Q Consensus 41 ~c~~c~~~~~~---~~~l~~H~~ 60 (72)
.|.+|...|.. ...|..|..
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHH
Confidence 45555433332 233445544
No 82
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=83.12 E-value=0.94 Score=24.67 Aligned_cols=53 Identities=40% Similarity=0.824 Sum_probs=42.4
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCc--chhhcCChHHHHHHHHH
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDL--CGRAFQRKVDLRRHKET 61 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~--c~~~~~~~~~l~~H~~~ 61 (72)
...+.|..|...|........+...+.++++..|.. |...+.....+..+.+.
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (467)
T COG5048 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRT 85 (467)
T ss_pred CchhhcccccccccccchhhhhcccccccCCccccccccccccCCcchhhhhccc
Confidence 345778999999999999999999999999998875 55666666677777665
No 83
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.09 E-value=0.64 Score=20.45 Aligned_cols=30 Identities=30% Similarity=0.717 Sum_probs=19.1
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.|.|+.|++.- ..+.. ...|.|..|+..|.
T Consensus 35 ~~~Cp~C~~~~--------VkR~a--~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRTT--------VKRIA--TGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCcc--------eeeec--cCeEEcCCCCCeec
Confidence 57888887541 11222 33689999988775
No 84
>PHA00626 hypothetical protein
Probab=81.14 E-value=0.86 Score=18.36 Aligned_cols=16 Identities=19% Similarity=0.447 Sum_probs=12.7
Q ss_pred CCCccCCcchhhcCCh
Q psy2647 37 FKPFACDLCGRAFQRK 52 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~ 52 (72)
...|.|..||..|...
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4579999999988643
No 85
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=80.56 E-value=0.85 Score=15.28 Aligned_cols=10 Identities=40% Similarity=1.042 Sum_probs=7.5
Q ss_pred cCCcchhhcC
Q psy2647 41 ACDLCGRAFQ 50 (72)
Q Consensus 41 ~c~~c~~~~~ 50 (72)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 6888887774
No 86
>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=80.45 E-value=0.69 Score=15.28 Aligned_cols=9 Identities=56% Similarity=1.446 Sum_probs=5.7
Q ss_pred CCccCCcch
Q psy2647 38 KPFACDLCG 46 (72)
Q Consensus 38 ~~~~c~~c~ 46 (72)
.+|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 356677665
No 87
>KOG4167|consensus
Probab=80.17 E-value=0.47 Score=28.74 Aligned_cols=24 Identities=29% Similarity=0.623 Sum_probs=21.1
Q ss_pred CccCCcchhhcCChHHHHHHHHHh
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQ 62 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~ 62 (72)
-|.|..|++.|-...++..|+++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 478999999999989999999885
No 88
>KOG1842|consensus
Probab=79.43 E-value=1.7 Score=24.93 Aligned_cols=21 Identities=24% Similarity=0.392 Sum_probs=10.5
Q ss_pred ccCcccchhccCcHHHHHhHH
Q psy2647 12 HKCQVCGKAFSQSSNLITHSR 32 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~ 32 (72)
+.|+.|...|.....|..|..
T Consensus 16 flCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHh
Confidence 445555555555555544443
No 89
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.67 E-value=0.46 Score=19.45 Aligned_cols=42 Identities=14% Similarity=0.279 Sum_probs=22.7
Q ss_pred cccCCCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 5 IWHGEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 5 ~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
++.+..++.|.--+-.+........ . ..+....|+.|+..|.
T Consensus 18 I~~~~~~l~C~g~~~p~~HPrV~L~---m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 18 IEIGDLPLMCPGPEPPNDHPRVFLD---M-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEeCCeeEEcCCCCCCCCCCEEEEE---c-CCCCcEecCccccEEE
Confidence 4556667777655444333221111 1 2234568999988775
No 90
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=78.04 E-value=0.66 Score=19.66 Aligned_cols=39 Identities=18% Similarity=0.371 Sum_probs=20.3
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCC--cchhhcCCh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACD--LCGRAFQRK 52 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~--~c~~~~~~~ 52 (72)
+.|+.|+..-..... +.+.....+.-++|. .||.+|...
T Consensus 2 m~CP~Cg~~a~irtS--r~~s~~~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTS--RYITDTTKERYHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEC--hhcChhhheeeeecCCCCCCCEEEEE
Confidence 467888754322211 111112334556787 788888643
No 91
>KOG1146|consensus
Probab=77.94 E-value=0.56 Score=30.18 Aligned_cols=47 Identities=19% Similarity=0.357 Sum_probs=31.8
Q ss_pred cchhccCcHHHHHhHHH-hcCCCCccCCcchhhcCChHHHHHHHHHhc
Q psy2647 17 CGKAFSQSSNLITHSRK-HTGFKPFACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 17 c~~~~~~~~~l~~~~~~-~~~~~~~~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
++..+.+...+..++.. +...+-+.|++|+..+.....|..|+|..|
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskh 489 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKH 489 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccc
Confidence 33334444444444432 344567899999999999999999998744
No 92
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=77.11 E-value=0.84 Score=21.65 Aligned_cols=15 Identities=33% Similarity=0.736 Sum_probs=11.2
Q ss_pred CcccCcccchhccCc
Q psy2647 10 KPHKCQVCGKAFSQS 24 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~ 24 (72)
..+.|..|+..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 457899999877654
No 93
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=76.50 E-value=2 Score=24.48 Aligned_cols=29 Identities=28% Similarity=0.723 Sum_probs=19.5
Q ss_pred cCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCCh
Q psy2647 13 KCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRK 52 (72)
Q Consensus 13 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~ 52 (72)
.|+.|+....+. |.+-|+|..||..+...
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCcc
Confidence 688888654332 23378999998877654
No 94
>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=76.41 E-value=0.38 Score=16.54 Aligned_cols=8 Identities=38% Similarity=1.041 Sum_probs=3.8
Q ss_pred CCcchhhc
Q psy2647 42 CDLCGRAF 49 (72)
Q Consensus 42 c~~c~~~~ 49 (72)
|..|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 44444444
No 95
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.72 E-value=2.9 Score=19.40 Aligned_cols=20 Identities=30% Similarity=0.735 Sum_probs=12.8
Q ss_pred cccCcccchhccCcHHHHHh
Q psy2647 11 PHKCQVCGKAFSQSSNLITH 30 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~ 30 (72)
|-.|+.|+-...+..+|.+.
T Consensus 15 P~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARS 34 (112)
T ss_pred CCcCCcCCCEEeccchHHHh
Confidence 55677777666666666554
No 96
>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=75.52 E-value=0.96 Score=16.85 Aligned_cols=12 Identities=33% Similarity=1.146 Sum_probs=8.3
Q ss_pred ccCCcchhhcCC
Q psy2647 40 FACDLCGRAFQR 51 (72)
Q Consensus 40 ~~c~~c~~~~~~ 51 (72)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 678888876653
No 97
>KOG3408|consensus
Probab=75.50 E-value=2.6 Score=19.83 Aligned_cols=24 Identities=33% Similarity=0.531 Sum_probs=19.1
Q ss_pred CCccCCcchhhcCChHHHHHHHHH
Q psy2647 38 KPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
-.|-|..|.+-|.....+..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 346788899999999888888653
No 98
>PF15269 zf-C2H2_7: Zinc-finger
Probab=75.40 E-value=2.4 Score=16.26 Aligned_cols=22 Identities=23% Similarity=0.384 Sum_probs=15.2
Q ss_pred ccCCcchhhcCChHHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
|+|-.|+....-.+.|-.|+..
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 4666777776677777777763
No 99
>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=75.19 E-value=0.63 Score=16.87 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=15.8
Q ss_pred cCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCC
Q psy2647 13 KCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQR 51 (72)
Q Consensus 13 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~ 51 (72)
.|..|+..|-.... .....-.|..||..+.+
T Consensus 3 ~C~~Cg~~Yh~~~~--------pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 3 ICPKCGRIYHIEFN--------PPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EETTTTEEEETTTB----------SSTTBCTTTTEBEBE
T ss_pred CcCCCCCccccccC--------CCCCCCccCCCCCeeEe
Confidence 56777766542221 12334567777765443
No 100
>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=74.98 E-value=3.2 Score=24.04 Aligned_cols=26 Identities=23% Similarity=0.501 Sum_probs=19.5
Q ss_pred CccCCcchhhcCChHHHHHHHHHhcc
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
-+.|+.|.+.|.....+..|+...|.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhh
Confidence 35788888888888888888764443
No 101
>KOG4167|consensus
Probab=74.67 E-value=0.82 Score=27.81 Aligned_cols=25 Identities=28% Similarity=0.573 Sum_probs=21.5
Q ss_pred cccCcccchhccCcHHHHHhHHHhc
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHT 35 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~ 35 (72)
-|.|.+|++.|.-...+..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4889999999988888889988774
No 102
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.63 E-value=2 Score=19.84 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=18.8
Q ss_pred cCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 13 KCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 13 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.|+.|++.|.. ....|..|++||++|.
T Consensus 11 idPetg~KFYD-----------LNrdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYD-----------LNRDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhc-----------cCCCccccCcccccch
Confidence 57777766532 2346888999999884
No 103
>KOG2482|consensus
Probab=72.46 E-value=2.7 Score=23.43 Aligned_cols=22 Identities=27% Similarity=0.650 Sum_probs=20.2
Q ss_pred ccCCcchhhcCChHHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
++|-.|-+.|..+..|..|++.
T Consensus 196 ~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred heeeeeccccCCcHHHHHHHHh
Confidence 5899999999999999999984
No 104
>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=70.80 E-value=2.1 Score=19.27 Aligned_cols=13 Identities=46% Similarity=1.265 Sum_probs=7.6
Q ss_pred CcccCcccchhcc
Q psy2647 10 KPHKCQVCGKAFS 22 (72)
Q Consensus 10 ~~~~c~~c~~~~~ 22 (72)
++..|..|+..|.
T Consensus 78 ~~~rC~eCG~~fk 90 (97)
T cd00924 78 KPKRCPECGHVFK 90 (97)
T ss_pred CceeCCCCCcEEE
Confidence 4566666665554
No 105
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=70.24 E-value=2.1 Score=20.50 Aligned_cols=20 Identities=35% Similarity=0.589 Sum_probs=13.0
Q ss_pred cCCcchhhcCChHHHHHHHHHhc
Q psy2647 41 ACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 41 ~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
.|-.+|+.|. +|++|+.+|+
T Consensus 78 icLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEeccCcchH---HHHHHHhccc
Confidence 5666676654 5777887743
No 106
>KOG2785|consensus
Probab=70.15 E-value=7.4 Score=22.07 Aligned_cols=51 Identities=29% Similarity=0.585 Sum_probs=37.5
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCC-----------------------CCccCCcch---hhcCChHHHHHHHHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGF-----------------------KPFACDLCG---RAFQRKVDLRRHKET 61 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~-----------------------~~~~c~~c~---~~~~~~~~l~~H~~~ 61 (72)
|=.|-.|+..++.-.....||..+.+- .-+.|..|+ +.|.+......|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 445788988888888888888765431 235777787 888888888888874
No 107
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=69.21 E-value=2.6 Score=20.09 Aligned_cols=14 Identities=43% Similarity=1.115 Sum_probs=7.8
Q ss_pred CccCCcchhhcCCh
Q psy2647 39 PFACDLCGRAFQRK 52 (72)
Q Consensus 39 ~~~c~~c~~~~~~~ 52 (72)
|++|..||+.|..-
T Consensus 1 PH~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 1 PHQCTKCGRVFEDG 14 (131)
T ss_pred CcccCcCCCCcCCC
Confidence 34566666666543
No 108
>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=68.58 E-value=1.9 Score=15.03 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=6.7
Q ss_pred CCCccCCcchh
Q psy2647 37 FKPFACDLCGR 47 (72)
Q Consensus 37 ~~~~~c~~c~~ 47 (72)
...+.|+.|+.
T Consensus 17 ~~~~vCp~C~~ 27 (30)
T PF08274_consen 17 GELLVCPECGH 27 (30)
T ss_dssp SSSEEETTTTE
T ss_pred CCEEeCCcccc
Confidence 34567777753
No 109
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=68.07 E-value=1.9 Score=21.07 Aligned_cols=33 Identities=27% Similarity=0.759 Sum_probs=16.7
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRA 48 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~ 48 (72)
+|.|. |+..|.. ..+|.....|+ .|.|..|+..
T Consensus 117 ~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccch---hhhcccccccc-eEEeccCCce
Confidence 46666 6655433 22333333344 5777777643
No 110
>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=67.71 E-value=2.4 Score=19.57 Aligned_cols=24 Identities=21% Similarity=0.639 Sum_probs=15.4
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
..|..|+..|..... .+.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~~~------------~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEID------------LYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCCc------------CccCcCCcC
Confidence 568888866654321 357888874
No 111
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=66.89 E-value=2.7 Score=15.46 Aligned_cols=13 Identities=38% Similarity=0.899 Sum_probs=10.3
Q ss_pred CccCCcchhhcCC
Q psy2647 39 PFACDLCGRAFQR 51 (72)
Q Consensus 39 ~~~c~~c~~~~~~ 51 (72)
|+.|..|+..|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7889888887754
No 112
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=66.72 E-value=5.6 Score=20.38 Aligned_cols=34 Identities=18% Similarity=0.412 Sum_probs=20.0
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
+.|+.|+. ......-++....+..+.|..||..+
T Consensus 7 ~~Cp~Cg~----eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 7 IECPSCGS----EEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EECCCCCc----chhhHHHHHhcCCceEEEccCCCcEe
Confidence 56999982 22222333333334467899999766
No 113
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=66.55 E-value=3 Score=19.04 Aligned_cols=13 Identities=38% Similarity=1.096 Sum_probs=9.1
Q ss_pred CccCCcchhhcCC
Q psy2647 39 PFACDLCGRAFQR 51 (72)
Q Consensus 39 ~~~c~~c~~~~~~ 51 (72)
|.+|..||..|..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 5677777777765
No 114
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=66.16 E-value=2.7 Score=25.68 Aligned_cols=28 Identities=36% Similarity=0.829 Sum_probs=17.3
Q ss_pred CcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 14 CQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 14 c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
|+.|.+.|....+-.-| ..|..|+.||.
T Consensus 154 C~~C~~EY~dP~nRRfH------AQp~aCp~CGP 181 (750)
T COG0068 154 CPFCDKEYKDPLNRRFH------AQPIACPKCGP 181 (750)
T ss_pred CHHHHHHhcCccccccc------cccccCcccCC
Confidence 77777766655543222 34678888875
No 115
>KOG0717|consensus
Probab=65.77 E-value=3.9 Score=23.79 Aligned_cols=22 Identities=23% Similarity=0.776 Sum_probs=18.5
Q ss_pred ccCCcchhhcCChHHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
+-|.+|.+.|.+...+..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6799999999999888888653
No 116
>PLN02294 cytochrome c oxidase subunit Vb
Probab=65.42 E-value=3.3 Score=20.70 Aligned_cols=14 Identities=36% Similarity=0.826 Sum_probs=9.5
Q ss_pred CcccCcccchhccC
Q psy2647 10 KPHKCQVCGKAFSQ 23 (72)
Q Consensus 10 ~~~~c~~c~~~~~~ 23 (72)
+++.|+.|+..|..
T Consensus 140 kp~RCpeCG~~fkL 153 (174)
T PLN02294 140 KSFECPVCTQYFEL 153 (174)
T ss_pred CceeCCCCCCEEEE
Confidence 56777777776653
No 117
>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=65.25 E-value=5.2 Score=14.24 Aligned_cols=20 Identities=30% Similarity=0.620 Sum_probs=10.8
Q ss_pred ccCCcchhhcCChHHHHHHHH
Q psy2647 40 FACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~H~~ 60 (72)
+.|+.|++.+. .+.+..|+.
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLe 24 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLE 24 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHH
T ss_pred EECCCCcCCcc-hhhhHHHHH
Confidence 56777776543 444556654
No 118
>KOG0978|consensus
Probab=64.93 E-value=2.5 Score=25.69 Aligned_cols=18 Identities=22% Similarity=0.368 Sum_probs=13.3
Q ss_pred CCccCCcchhhcCChHHH
Q psy2647 38 KPFACDLCGRAFQRKVDL 55 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~~~l 55 (72)
+--.||.|+..|.....+
T Consensus 677 RqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVH 694 (698)
T ss_pred hcCCCCCCCCCCCccccc
Confidence 345899999999866443
No 119
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.83 E-value=0.85 Score=23.83 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=17.6
Q ss_pred CCcccCcccchhccCcHHHHHhHHH
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRK 33 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~ 33 (72)
++...|+.|+..|..........+.
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRi 41 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRI 41 (267)
T ss_pred hceeccCcccchhhhhheeccceeE
Confidence 3567899999988777655555443
No 120
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=64.73 E-value=3.5 Score=18.99 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=15.0
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
..|..|+..|.... ..+.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCC------------cCccCcCCCC
Confidence 56888886654322 2356888874
No 121
>KOG2071|consensus
Probab=64.00 E-value=6.6 Score=23.51 Aligned_cols=25 Identities=24% Similarity=0.542 Sum_probs=19.5
Q ss_pred CCCccCCcchhhcCChHHHHHHHHH
Q psy2647 37 FKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
..+-+|..||.+|........|+..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~ 440 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDI 440 (579)
T ss_pred CCcchhcccccccccchhhhhHhhh
Confidence 4567999999999988776666655
No 122
>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=62.10 E-value=4.2 Score=16.07 Aligned_cols=13 Identities=23% Similarity=0.672 Sum_probs=3.7
Q ss_pred ccCcccchhccCc
Q psy2647 12 HKCQVCGKAFSQS 24 (72)
Q Consensus 12 ~~c~~c~~~~~~~ 24 (72)
|.|+.|...|-..
T Consensus 22 y~C~~C~~~FC~d 34 (51)
T PF07975_consen 22 YRCPKCKNHFCID 34 (51)
T ss_dssp E--TTTT--B-HH
T ss_pred EECCCCCCccccC
Confidence 4455555444433
No 123
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.03 E-value=5.8 Score=17.13 Aligned_cols=32 Identities=22% Similarity=0.616 Sum_probs=19.0
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
.|.|..|+..|. +.+++.. .....|+.|+-.+
T Consensus 12 ~Y~c~~cg~~~d----vvq~~~d---dplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRFD----VVQAMTD---DPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHHH----HHHhccc---CccccChhhChHH
Confidence 378999987654 3444432 2234688887543
No 124
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=61.93 E-value=7.9 Score=15.16 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=5.6
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
++|..|+..+.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 45555554443
No 125
>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=61.85 E-value=1.9 Score=16.09 Aligned_cols=15 Identities=47% Similarity=1.103 Sum_probs=8.7
Q ss_pred CCccCCcchhhcCCh
Q psy2647 38 KPFACDLCGRAFQRK 52 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~ 52 (72)
.++.|..|+..|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 468898888887543
No 126
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=61.79 E-value=3.9 Score=16.07 Aligned_cols=39 Identities=21% Similarity=0.519 Sum_probs=19.5
Q ss_pred cccCcc--cchhccCcHHHHHhHHHhcCCCCccCCc----chhhcC
Q psy2647 11 PHKCQV--CGKAFSQSSNLITHSRKHTGFKPFACDL----CGRAFQ 50 (72)
Q Consensus 11 ~~~c~~--c~~~~~~~~~l~~~~~~~~~~~~~~c~~----c~~~~~ 50 (72)
+-.|+. |...+. +..|..|....=...+..|.. |+..+.
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 345655 433333 456777877444455677877 766554
No 127
>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=61.20 E-value=3.9 Score=15.88 Aligned_cols=10 Identities=20% Similarity=1.006 Sum_probs=3.6
Q ss_pred CCccCCcchh
Q psy2647 38 KPFACDLCGR 47 (72)
Q Consensus 38 ~~~~c~~c~~ 47 (72)
..|.|+.|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 3489999864
No 128
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=60.38 E-value=9.7 Score=14.11 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=13.1
Q ss_pred ccCCcchhhcC--ChHHHHHHHHH
Q psy2647 40 FACDLCGRAFQ--RKVDLRRHKET 61 (72)
Q Consensus 40 ~~c~~c~~~~~--~~~~l~~H~~~ 61 (72)
..|..||..+. ....-..|.+.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~y 37 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKY 37 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHH
Confidence 47777776554 34455566664
No 129
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=59.83 E-value=7.2 Score=19.64 Aligned_cols=33 Identities=21% Similarity=0.496 Sum_probs=20.1
Q ss_pred CCCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 8 GEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 8 ~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
...-|.|+.|.-.++...+.. ..|.|+.||...
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~---------~~F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAME---------LGFTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHHHH---------hCCCCCCCCchh
Confidence 345578877766554433321 138999998644
No 130
>KOG3507|consensus
Probab=59.80 E-value=4.1 Score=16.62 Aligned_cols=31 Identities=26% Similarity=0.403 Sum_probs=19.5
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCCh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRK 52 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~ 52 (72)
.|.|..|+..- .|+ ....++|..||.....+
T Consensus 20 iYiCgdC~~en----~lk-------~~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 20 IYICGDCGQEN----TLK-------RGDVIRCRECGYRILYK 50 (62)
T ss_pred EEEeccccccc----ccc-------CCCcEehhhcchHHHHH
Confidence 47888887532 111 13468999999776544
No 131
>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=59.34 E-value=3.5 Score=16.13 Aligned_cols=12 Identities=42% Similarity=1.190 Sum_probs=6.2
Q ss_pred cCCcchhhcCCh
Q psy2647 41 ACDLCGRAFQRK 52 (72)
Q Consensus 41 ~c~~c~~~~~~~ 52 (72)
.|+.|+..|...
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 899999888643
No 132
>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=59.29 E-value=1.4 Score=15.94 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=6.0
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
+..|..||..+.
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 457788886553
No 133
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=58.72 E-value=2.6 Score=18.73 Aligned_cols=12 Identities=17% Similarity=0.600 Sum_probs=8.9
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
.|.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PTZ00255 54 IWRCKGCKKTVA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 578888887664
No 134
>KOG4173|consensus
Probab=58.33 E-value=11 Score=19.71 Aligned_cols=52 Identities=25% Similarity=0.472 Sum_probs=31.4
Q ss_pred cCcccchhccCcHHHHHhHHHhc----------CCCCccCC--cchhhcCChHHHHHHHHHhcc
Q psy2647 13 KCQVCGKAFSQSSNLITHSRKHT----------GFKPFACD--LCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 13 ~c~~c~~~~~~~~~l~~~~~~~~----------~~~~~~c~--~c~~~~~~~~~l~~H~~~~~~ 64 (72)
.|..|.+.|++...|..|+.... |..-|+|. .|+..|......+.|+-..|.
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 57777777777766666665321 12235664 477777777666666655443
No 135
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.67 E-value=8 Score=20.93 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=4.1
Q ss_pred cCCcchhh
Q psy2647 41 ACDLCGRA 48 (72)
Q Consensus 41 ~c~~c~~~ 48 (72)
.|..|+-.
T Consensus 271 ~C~~Cgt~ 278 (279)
T TIGR00627 271 ICKTCKTA 278 (279)
T ss_pred CCCCCCCC
Confidence 55555543
No 136
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=56.94 E-value=0.5 Score=17.49 Aligned_cols=10 Identities=30% Similarity=1.208 Sum_probs=6.9
Q ss_pred ccCCcchhhc
Q psy2647 40 FACDLCGRAF 49 (72)
Q Consensus 40 ~~c~~c~~~~ 49 (72)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6777777654
No 137
>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=56.93 E-value=6.6 Score=16.02 Aligned_cols=30 Identities=27% Similarity=0.680 Sum_probs=18.1
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCC
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQR 51 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~ 51 (72)
..|+.|+..... ......+.|+.||.....
T Consensus 29 q~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 29 QTCPRCGHRNKK----------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred cCccCccccccc----------ccccceEEcCCCCCEECc
Confidence 457777754332 123456889999876543
No 138
>KOG2907|consensus
Probab=56.81 E-value=3.6 Score=19.11 Aligned_cols=11 Identities=27% Similarity=0.896 Sum_probs=7.5
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
|.|..|++.|.
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 67777776654
No 139
>KOG2593|consensus
Probab=56.37 E-value=13 Score=21.56 Aligned_cols=35 Identities=23% Similarity=0.485 Sum_probs=16.9
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
..|.|+.|.+.|.....+.-- ....-.|.|..|+.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~---~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLL---DNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhh---cccCceEEEecCCC
Confidence 346666666666554433221 11112456666653
No 140
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=55.94 E-value=1.4 Score=15.77 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=6.4
Q ss_pred CCccCCcchhh
Q psy2647 38 KPFACDLCGRA 48 (72)
Q Consensus 38 ~~~~c~~c~~~ 48 (72)
..+.|+.|+..
T Consensus 21 ~R~vC~~Cg~I 31 (34)
T PF14803_consen 21 ERLVCPACGFI 31 (34)
T ss_dssp -EEEETTTTEE
T ss_pred cceECCCCCCE
Confidence 34667777653
No 141
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=55.86 E-value=6.4 Score=18.66 Aligned_cols=35 Identities=20% Similarity=0.524 Sum_probs=20.1
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcCC
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQR 51 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~ 51 (72)
-.|+.|+... .. ..-....+...|.|..|++.|..
T Consensus 31 ~~cP~C~s~~-~~----k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSN-VV----KIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccc-ee----eECCccccccccccCCcCcceee
Confidence 3577777543 11 11111223457999999998864
No 142
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.43 E-value=5.1 Score=18.57 Aligned_cols=13 Identities=23% Similarity=0.728 Sum_probs=8.5
Q ss_pred cccCcccchhccC
Q psy2647 11 PHKCQVCGKAFSQ 23 (72)
Q Consensus 11 ~~~c~~c~~~~~~ 23 (72)
...|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 3568888866543
No 143
>KOG2636|consensus
Probab=54.75 E-value=12 Score=21.92 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=19.3
Q ss_pred HhcCCCCccCCcch-hhcCChHHHHHHH
Q psy2647 33 KHTGFKPFACDLCG-RAFQRKVDLRRHK 59 (72)
Q Consensus 33 ~~~~~~~~~c~~c~-~~~~~~~~l~~H~ 59 (72)
.|.-...|.|.+|| +++.-+..+.+|.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHh
Confidence 45556678888888 6777777777774
No 144
>COG1773 Rubredoxin [Energy production and conversion]
Probab=52.95 E-value=5.8 Score=15.96 Aligned_cols=15 Identities=33% Similarity=0.911 Sum_probs=10.8
Q ss_pred CcccCcccchhccCc
Q psy2647 10 KPHKCQVCGKAFSQS 24 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~ 24 (72)
+.|.|..|+..|.-.
T Consensus 2 ~~~~C~~CG~vYd~e 16 (55)
T COG1773 2 KRWRCSVCGYVYDPE 16 (55)
T ss_pred CceEecCCceEeccc
Confidence 357899998877543
No 145
>KOG0562|consensus
Probab=51.35 E-value=16 Score=18.40 Aligned_cols=27 Identities=15% Similarity=0.139 Sum_probs=20.4
Q ss_pred CCCccCCcchhhcCChHHHHHHHHHhc
Q psy2647 37 FKPFACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
+.+..|..|+..-.....|+.|++.++
T Consensus 151 k~dLrC~~Cq~~~~~~~kLK~Hl~~~~ 177 (184)
T KOG0562|consen 151 KEDLRCWRCQTFGPHFPKLKAHLREEY 177 (184)
T ss_pred ccceeehhhhhcccccHHHHHHHHHHH
Confidence 346789999855567788999998744
No 146
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=51.33 E-value=6.5 Score=15.40 Aligned_cols=11 Identities=27% Similarity=1.228 Sum_probs=7.1
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
|+|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56777776554
No 147
>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=50.64 E-value=4.1 Score=18.72 Aligned_cols=25 Identities=32% Similarity=0.926 Sum_probs=13.5
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRA 48 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~ 48 (72)
..|..|+..|..... .+.|+.|+..
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 567888877654321 2458877753
No 148
>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=50.60 E-value=9.6 Score=14.44 Aligned_cols=14 Identities=36% Similarity=0.956 Sum_probs=10.7
Q ss_pred cCcccchhccCcHH
Q psy2647 13 KCQVCGKAFSQSSN 26 (72)
Q Consensus 13 ~c~~c~~~~~~~~~ 26 (72)
.|..|++.|.....
T Consensus 10 ~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 10 ICPVCGRPFTWRKK 23 (42)
T ss_pred cCcccCCcchHHHH
Confidence 58999998876554
No 149
>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=49.89 E-value=6.1 Score=14.74 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=4.0
Q ss_pred ccCCcchhh
Q psy2647 40 FACDLCGRA 48 (72)
Q Consensus 40 ~~c~~c~~~ 48 (72)
..|+.|+..
T Consensus 30 ~~CpYCg~~ 38 (40)
T PF10276_consen 30 VVCPYCGTR 38 (40)
T ss_dssp EEETTTTEE
T ss_pred EECCCCCCE
Confidence 344444443
No 150
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=49.43 E-value=9.4 Score=17.61 Aligned_cols=23 Identities=26% Similarity=0.627 Sum_probs=18.2
Q ss_pred CcccCcccchhccCcHHHHHhHH
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSR 32 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~ 32 (72)
..+.|-.|.+-|.+...|..|.+
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhc
Confidence 34678889998988888888865
No 151
>PF14353 CpXC: CpXC protein
Probab=48.71 E-value=7.4 Score=18.11 Aligned_cols=15 Identities=33% Similarity=0.871 Sum_probs=11.2
Q ss_pred CCccCCcchhhcCCh
Q psy2647 38 KPFACDLCGRAFQRK 52 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~ 52 (72)
..+.|+.||..|.-.
T Consensus 37 ~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLE 51 (128)
T ss_pred CEEECCCCCCceecC
Confidence 357999999877543
No 152
>PHA02998 RNA polymerase subunit; Provisional
Probab=48.43 E-value=1.8 Score=21.77 Aligned_cols=13 Identities=31% Similarity=0.738 Sum_probs=10.1
Q ss_pred ccCCcchhhcCCh
Q psy2647 40 FACDLCGRAFQRK 52 (72)
Q Consensus 40 ~~c~~c~~~~~~~ 52 (72)
|.|..||..+..+
T Consensus 172 YkC~~CG~~wkpp 184 (195)
T PHA02998 172 HACRDCKKHFKPP 184 (195)
T ss_pred EEcCCCCCccCCc
Confidence 6899999887654
No 153
>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=47.75 E-value=6.5 Score=18.78 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=6.2
Q ss_pred ccCCcchhhc
Q psy2647 40 FACDLCGRAF 49 (72)
Q Consensus 40 ~~c~~c~~~~ 49 (72)
+.|..|+..+
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 6677776544
No 154
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=46.77 E-value=17 Score=14.03 Aligned_cols=10 Identities=50% Similarity=1.245 Sum_probs=5.4
Q ss_pred cCcccchhcc
Q psy2647 13 KCQVCGKAFS 22 (72)
Q Consensus 13 ~c~~c~~~~~ 22 (72)
.|..|++.|.
T Consensus 4 ~C~~C~~~F~ 13 (57)
T cd00065 4 SCMGCGKPFT 13 (57)
T ss_pred cCcccCcccc
Confidence 3555665554
No 155
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=46.35 E-value=5.9 Score=22.97 Aligned_cols=39 Identities=18% Similarity=0.353 Sum_probs=21.3
Q ss_pred CCcccCcccchhccCcHHH-HHhHHHhc----CCCCccCCcchh
Q psy2647 9 EKPHKCQVCGKAFSQSSNL-ITHSRKHT----GFKPFACDLCGR 47 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l-~~~~~~~~----~~~~~~c~~c~~ 47 (72)
...|.|..|+..|.-..-- ..-+...+ -...|.|+.|+.
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCC
Confidence 4568999999887643211 11111110 012479999974
No 156
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.86 E-value=6.4 Score=18.17 Aligned_cols=26 Identities=15% Similarity=0.427 Sum_probs=14.9
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
...|..|+..|..... ..+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs 95 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ-----------RVRRCPQCHG 95 (114)
T ss_pred EEEcccCCCeeecCCc-----------cCCcCcCcCC
Confidence 3568888865532111 1256888874
No 157
>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=45.85 E-value=8.4 Score=13.86 Aligned_cols=12 Identities=42% Similarity=1.107 Sum_probs=5.1
Q ss_pred cCCcchhhcCCh
Q psy2647 41 ACDLCGRAFQRK 52 (72)
Q Consensus 41 ~c~~c~~~~~~~ 52 (72)
.|..|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 567777766543
No 158
>PRK12860 transcriptional activator FlhC; Provisional
Probab=45.07 E-value=15 Score=18.78 Aligned_cols=27 Identities=33% Similarity=0.787 Sum_probs=16.6
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcch
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCG 46 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~ 46 (72)
..|..|+..|.... +.....+.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHA--------HDLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 45778887775322 1223468888885
No 159
>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=44.35 E-value=8.2 Score=17.63 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=6.6
Q ss_pred cccCcccchh
Q psy2647 11 PHKCQVCGKA 20 (72)
Q Consensus 11 ~~~c~~c~~~ 20 (72)
|-.|+.|+..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 4567888753
No 160
>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=44.28 E-value=11 Score=13.85 Aligned_cols=11 Identities=36% Similarity=0.912 Sum_probs=4.6
Q ss_pred CCcccCcccch
Q psy2647 9 EKPHKCQVCGK 19 (72)
Q Consensus 9 ~~~~~c~~c~~ 19 (72)
.+.|.|..|+.
T Consensus 22 ~~~w~C~~C~~ 32 (40)
T PF04810_consen 22 GKTWICNFCGT 32 (40)
T ss_dssp TTEEEETTT--
T ss_pred CCEEECcCCCC
Confidence 34455555543
No 161
>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=44.22 E-value=8.9 Score=18.43 Aligned_cols=13 Identities=23% Similarity=0.728 Sum_probs=10.1
Q ss_pred CccCCcchhhcCC
Q psy2647 39 PFACDLCGRAFQR 51 (72)
Q Consensus 39 ~~~c~~c~~~~~~ 51 (72)
-+.|+.|++.|=.
T Consensus 124 f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 124 FWRCPGCGKIYWE 136 (147)
T ss_pred EEECCCCCCEecc
Confidence 4789999987743
No 162
>PRK12722 transcriptional activator FlhC; Provisional
Probab=44.10 E-value=16 Score=18.64 Aligned_cols=28 Identities=29% Similarity=0.791 Sum_probs=17.2
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
..|..|+..|..... .....+.|+.|..
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 458888877753221 2234688888864
No 163
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=43.95 E-value=11 Score=14.97 Aligned_cols=9 Identities=33% Similarity=1.125 Sum_probs=5.3
Q ss_pred cCCcchhhc
Q psy2647 41 ACDLCGRAF 49 (72)
Q Consensus 41 ~c~~c~~~~ 49 (72)
.|+.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 466676544
No 164
>PRK04351 hypothetical protein; Provisional
Probab=43.76 E-value=9.6 Score=18.59 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=7.0
Q ss_pred CCccCCcchhhc
Q psy2647 38 KPFACDLCGRAF 49 (72)
Q Consensus 38 ~~~~c~~c~~~~ 49 (72)
..|.|..|+..+
T Consensus 131 ~~yrCg~C~g~L 142 (149)
T PRK04351 131 KRYRCGKCRGKL 142 (149)
T ss_pred CcEEeCCCCcEe
Confidence 346676666544
No 165
>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=43.36 E-value=14 Score=15.18 Aligned_cols=14 Identities=36% Similarity=0.885 Sum_probs=9.6
Q ss_pred CccCCcchhhcCCh
Q psy2647 39 PFACDLCGRAFQRK 52 (72)
Q Consensus 39 ~~~c~~c~~~~~~~ 52 (72)
|..|..||+.....
T Consensus 4 PVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 4 PVRCFTCGKVIGNK 17 (60)
T ss_dssp SSS-STTTSBTCGH
T ss_pred ceecCCCCCChhHh
Confidence 77888898876544
No 166
>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=43.32 E-value=7.7 Score=18.70 Aligned_cols=14 Identities=43% Similarity=1.172 Sum_probs=9.6
Q ss_pred CcccCcccchhccC
Q psy2647 10 KPHKCQVCGKAFSQ 23 (72)
Q Consensus 10 ~~~~c~~c~~~~~~ 23 (72)
++..|..|+..|..
T Consensus 111 ~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 111 KPQRCPECGQVFKL 124 (136)
T ss_dssp SEEEETTTEEEEEE
T ss_pred CccCCCCCCeEEEE
Confidence 46778778777654
No 167
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=42.93 E-value=13 Score=19.71 Aligned_cols=16 Identities=19% Similarity=0.376 Sum_probs=12.4
Q ss_pred CCcccCcccchhccCc
Q psy2647 9 EKPHKCQVCGKAFSQS 24 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~ 24 (72)
.++..|..|+..|...
T Consensus 179 GkpqRCpECGqVFKLV 194 (268)
T PTZ00043 179 GFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCccCCCCCcEEEEE
Confidence 4578999999888653
No 168
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=42.86 E-value=27 Score=19.25 Aligned_cols=25 Identities=28% Similarity=0.575 Sum_probs=21.4
Q ss_pred CCCccCCcchhhcCChHHHHHHHHH
Q psy2647 37 FKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
...|.|..|-+-|.....+.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 4568999999999999999999773
No 169
>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=42.35 E-value=13 Score=15.13 Aligned_cols=10 Identities=60% Similarity=1.481 Sum_probs=3.9
Q ss_pred cCcccchhcc
Q psy2647 13 KCQVCGKAFS 22 (72)
Q Consensus 13 ~c~~c~~~~~ 22 (72)
.|..|++.|.
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 5677777774
No 170
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=41.34 E-value=1.8 Score=19.66 Aligned_cols=38 Identities=24% Similarity=0.540 Sum_probs=19.8
Q ss_pred CCcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 9 EKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.+.|.|+.|+..-.+.-.+..- ...-...|..||..|.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEec----CceeEEEcccCcceEE
Confidence 4568899888643332221111 1111346888887664
No 171
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1994|consensus
Probab=40.83 E-value=15 Score=19.50 Aligned_cols=22 Identities=23% Similarity=0.582 Sum_probs=18.3
Q ss_pred CcccCcccchhccCcHHHHHhH
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHS 31 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~ 31 (72)
..|.|-.||-.|.....|..|-
T Consensus 238 eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred cceEEEEeccccCCHHHHHHhC
Confidence 4688999999999999888763
No 173
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=40.06 E-value=18 Score=14.57 Aligned_cols=13 Identities=23% Similarity=0.549 Sum_probs=8.9
Q ss_pred CCcccCcccchhc
Q psy2647 9 EKPHKCQVCGKAF 21 (72)
Q Consensus 9 ~~~~~c~~c~~~~ 21 (72)
...|.|+.||..+
T Consensus 12 ~v~~~Cp~cGipt 24 (55)
T PF13824_consen 12 HVNFECPDCGIPT 24 (55)
T ss_pred ccCCcCCCCCCcC
Confidence 4567888887643
No 174
>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=39.32 E-value=1.4 Score=18.42 Aligned_cols=35 Identities=20% Similarity=0.497 Sum_probs=17.2
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRA 48 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~ 48 (72)
.|.|..|+..-... .....-+.|-...+|+.|...
T Consensus 4 ~FTC~~C~~Rs~~~---~sk~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRSAKM---FSKQAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEETTTTEEEEEE---EEHHHHHTSEEEEE-TTS--E
T ss_pred EEEcCCCCCcccee---eCHHHHhCCeEEEECCCCcce
Confidence 36788887432211 122233455556788888653
No 175
>PRK14873 primosome assembly protein PriA; Provisional
Probab=38.91 E-value=25 Score=21.69 Aligned_cols=11 Identities=27% Similarity=0.845 Sum_probs=7.5
Q ss_pred CCccCCcchhh
Q psy2647 38 KPFACDLCGRA 48 (72)
Q Consensus 38 ~~~~c~~c~~~ 48 (72)
.++.|+.|+..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 46778888753
No 176
>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=38.83 E-value=10 Score=19.49 Aligned_cols=23 Identities=17% Similarity=0.694 Sum_probs=0.0
Q ss_pred CCCccCCcchh-hcCChHHHHHHH
Q psy2647 37 FKPFACDLCGR-AFQRKVDLRRHK 59 (72)
Q Consensus 37 ~~~~~c~~c~~-~~~~~~~l~~H~ 59 (72)
.+.|.|.+||. .+.-+..+..|.
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhc
Confidence 34578888874 444455555553
No 177
>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=38.55 E-value=44 Score=15.26 Aligned_cols=37 Identities=11% Similarity=0.303 Sum_probs=22.9
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRA 48 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~ 48 (72)
.|.|+..+..|.........+.... ++.|.|...|+.
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~y~-~~vwtC~~TGk~ 39 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMILYN-QRVWTCEITGKS 39 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHHHh-CCeeEEecCCCC
Confidence 3566666777777766665554433 356777776653
No 178
>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=38.35 E-value=13 Score=18.17 Aligned_cols=13 Identities=23% Similarity=0.444 Sum_probs=10.6
Q ss_pred CccCCcchhhcCC
Q psy2647 39 PFACDLCGRAFQR 51 (72)
Q Consensus 39 ~~~c~~c~~~~~~ 51 (72)
.-+|..|++.|.+
T Consensus 28 RReC~~C~~RFTT 40 (147)
T TIGR00244 28 RRECLECHERFTT 40 (147)
T ss_pred cccCCccCCccce
Confidence 4589999999975
No 179
>PLN02748 tRNA dimethylallyltransferase
Probab=38.24 E-value=30 Score=20.39 Aligned_cols=23 Identities=22% Similarity=0.746 Sum_probs=17.9
Q ss_pred CCccCCcchh-hcCChHHHHHHHH
Q psy2647 38 KPFACDLCGR-AFQRKVDLRRHKE 60 (72)
Q Consensus 38 ~~~~c~~c~~-~~~~~~~l~~H~~ 60 (72)
+.|.|..|+. .+........|++
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhc
Confidence 4578999997 7887777777764
No 180
>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=38.24 E-value=18 Score=20.99 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=6.4
Q ss_pred cccCcccchh
Q psy2647 11 PHKCQVCGKA 20 (72)
Q Consensus 11 ~~~c~~c~~~ 20 (72)
.|.|..|+..
T Consensus 7 ~y~C~~Cg~~ 16 (454)
T TIGR00416 7 KFVCQHCGAD 16 (454)
T ss_pred eEECCcCCCC
Confidence 4677777653
No 181
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=38.08 E-value=11 Score=15.30 Aligned_cols=38 Identities=21% Similarity=0.532 Sum_probs=18.5
Q ss_pred cCcccchhccCcHHHHHhHH-HhcCCCCccCCcchhhcC
Q psy2647 13 KCQVCGKAFSQSSNLITHSR-KHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 13 ~c~~c~~~~~~~~~l~~~~~-~~~~~~~~~c~~c~~~~~ 50 (72)
.|..|++.+..........+ ..-....|.|..|.....
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~ 42 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIR 42 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHh
Confidence 46667665443322222211 122334588888875544
No 182
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=37.84 E-value=15 Score=20.68 Aligned_cols=12 Identities=25% Similarity=0.833 Sum_probs=8.0
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
.+.|+.||..+.
T Consensus 265 ~wrCpkCGg~ik 276 (403)
T COG1379 265 RWRCPKCGGKIK 276 (403)
T ss_pred cccCcccccchh
Confidence 467888876543
No 183
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.62 E-value=16 Score=19.56 Aligned_cols=15 Identities=33% Similarity=0.687 Sum_probs=10.5
Q ss_pred CCCccCCcchhhcCC
Q psy2647 37 FKPFACDLCGRAFQR 51 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~ 51 (72)
.+.+.|+.||..+..
T Consensus 320 ~r~~~C~~cg~~~~r 334 (364)
T COG0675 320 GRLFKCPRCGFVHDR 334 (364)
T ss_pred ceeEECCCCCCeehh
Confidence 346889999876543
No 184
>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=37.39 E-value=45 Score=16.45 Aligned_cols=26 Identities=19% Similarity=0.347 Sum_probs=14.4
Q ss_pred hccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 20 AFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 20 ~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
+|.+...+..... ...+.|+.||..-
T Consensus 17 WF~ss~~fd~Q~~----~glv~CP~Cgs~~ 42 (148)
T PF06676_consen 17 WFRSSAAFDRQQA----RGLVSCPVCGSTE 42 (148)
T ss_pred ecCCHHHHHHHHH----cCCccCCCCCCCe
Confidence 4555555554433 2356777777543
No 185
>PRK11823 DNA repair protein RadA; Provisional
Probab=37.08 E-value=21 Score=20.69 Aligned_cols=11 Identities=36% Similarity=0.803 Sum_probs=7.1
Q ss_pred CcccCcccchh
Q psy2647 10 KPHKCQVCGKA 20 (72)
Q Consensus 10 ~~~~c~~c~~~ 20 (72)
..|.|..|+..
T Consensus 6 ~~y~C~~Cg~~ 16 (446)
T PRK11823 6 TAYVCQECGAE 16 (446)
T ss_pred CeEECCcCCCC
Confidence 34777777754
No 186
>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=36.86 E-value=19 Score=17.90 Aligned_cols=21 Identities=33% Similarity=0.800 Sum_probs=15.2
Q ss_pred CCcccCcccchhccCcHHHHH
Q psy2647 9 EKPHKCQVCGKAFSQSSNLIT 29 (72)
Q Consensus 9 ~~~~~c~~c~~~~~~~~~l~~ 29 (72)
..|..|..||+.|++......
T Consensus 66 ~~PsYC~~CGkpyPWt~~~L~ 86 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTENALE 86 (158)
T ss_pred CCChhHHhCCCCCchHHHHHH
Confidence 357788999999988755433
No 187
>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=36.33 E-value=14 Score=13.45 Aligned_cols=10 Identities=30% Similarity=1.026 Sum_probs=4.8
Q ss_pred CccCCcchhh
Q psy2647 39 PFACDLCGRA 48 (72)
Q Consensus 39 ~~~c~~c~~~ 48 (72)
-|+|..||..
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4778888754
No 188
>KOG2231|consensus
Probab=36.30 E-value=66 Score=20.16 Aligned_cols=47 Identities=26% Similarity=0.519 Sum_probs=23.2
Q ss_pred cCcccchhccCcHHHHHhHHHhcCCCCccCCcc------hhhcCChHHHHHHHHHhc
Q psy2647 13 KCQVCGKAFSQSSNLITHSRKHTGFKPFACDLC------GRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 13 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c------~~~~~~~~~l~~H~~~~~ 63 (72)
.|..|...|.....+..|++.+ .+.|..| +.-|..-..|..|-+.+|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~----h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFD----HEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccc----eeheeecCcccccchhcccchHHHHHhhhcC
Confidence 4556666666666666665532 1233333 233444455555555444
No 189
>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=36.22 E-value=12 Score=19.41 Aligned_cols=22 Identities=14% Similarity=0.375 Sum_probs=0.0
Q ss_pred CccCCcchhhcCChHHHHHHHHH
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
-..|+.||.... .+.+..|+|+
T Consensus 168 ~~~cPitGe~IP-~~e~~eHmRi 189 (229)
T PF12230_consen 168 MIICPITGEMIP-ADEMDEHMRI 189 (229)
T ss_dssp -----------------------
T ss_pred cccccccccccc-cccccccccc
Confidence 357888887654 4566777776
No 190
>PF12773 DZR: Double zinc ribbon
Probab=36.13 E-value=21 Score=13.42 Aligned_cols=11 Identities=27% Similarity=0.531 Sum_probs=7.3
Q ss_pred CccCCcchhhc
Q psy2647 39 PFACDLCGRAF 49 (72)
Q Consensus 39 ~~~c~~c~~~~ 49 (72)
...|+.|+...
T Consensus 29 ~~~C~~Cg~~~ 39 (50)
T PF12773_consen 29 KKICPNCGAEN 39 (50)
T ss_pred CCCCcCCcCCC
Confidence 45688887653
No 191
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=35.96 E-value=14 Score=13.09 Aligned_cols=12 Identities=33% Similarity=0.794 Sum_probs=7.8
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
-+.|..|+..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 356788876653
No 192
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=35.59 E-value=21 Score=19.09 Aligned_cols=34 Identities=24% Similarity=0.472 Sum_probs=18.8
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
....|..|+..+..... ... ... ..+-.|+.|+.
T Consensus 121 ~~~~C~~C~~~~~~~~~-~~~--~~~-~~~p~C~~Cg~ 154 (250)
T COG0846 121 KRVRCSKCGNQYYDEDV-IKF--IED-GLIPRCPKCGG 154 (250)
T ss_pred eeeEeCCCcCccchhhh-hhh--ccc-CCCCcCccCCC
Confidence 45678889876653331 111 111 13556888886
No 193
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=35.34 E-value=34 Score=17.21 Aligned_cols=19 Identities=21% Similarity=0.483 Sum_probs=14.1
Q ss_pred CCccCCcchhhcCChHHHH
Q psy2647 38 KPFACDLCGRAFQRKVDLR 56 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~~~l~ 56 (72)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4678999999998654443
No 194
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=35.31 E-value=12 Score=17.91 Aligned_cols=11 Identities=27% Similarity=0.963 Sum_probs=6.1
Q ss_pred CccCCcchhhc
Q psy2647 39 PFACDLCGRAF 49 (72)
Q Consensus 39 ~~~c~~c~~~~ 49 (72)
.+.|..|+..+
T Consensus 133 ~y~C~~C~g~l 143 (146)
T smart00731 133 RYRCGKCGGKL 143 (146)
T ss_pred eEEcCCCCCEE
Confidence 46666665443
No 195
>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=35.18 E-value=18 Score=14.99 Aligned_cols=8 Identities=38% Similarity=1.323 Sum_probs=4.2
Q ss_pred ccCCcchh
Q psy2647 40 FACDLCGR 47 (72)
Q Consensus 40 ~~c~~c~~ 47 (72)
|.|+.|+.
T Consensus 1 y~C~KCg~ 8 (64)
T PF09855_consen 1 YKCPKCGN 8 (64)
T ss_pred CCCCCCCC
Confidence 35666653
No 196
>PF14369 zf-RING_3: zinc-finger
Probab=35.14 E-value=17 Score=12.99 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=7.8
Q ss_pred cCcccchhcc
Q psy2647 13 KCQVCGKAFS 22 (72)
Q Consensus 13 ~c~~c~~~~~ 22 (72)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4999988774
No 197
>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=35.00 E-value=5.8 Score=14.38 Aligned_cols=12 Identities=25% Similarity=0.874 Sum_probs=6.5
Q ss_pred hcCCCCccCCcc
Q psy2647 34 HTGFKPFACDLC 45 (72)
Q Consensus 34 ~~~~~~~~c~~c 45 (72)
..|...|.|..|
T Consensus 24 ~~G~qryrC~~C 35 (36)
T PF03811_consen 24 PSGHQRYRCKDC 35 (36)
T ss_pred CCCCEeEecCcC
Confidence 344455666655
No 198
>KOG4727|consensus
Probab=34.97 E-value=22 Score=18.05 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=18.6
Q ss_pred cccCcccchhccCcHHHHHhHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSR 32 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~ 32 (72)
-|.|..|+-.+....++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4889999999998888888875
No 199
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.66 E-value=13 Score=14.53 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=5.7
Q ss_pred cCCcchhhcCC
Q psy2647 41 ACDLCGRAFQR 51 (72)
Q Consensus 41 ~c~~c~~~~~~ 51 (72)
.|+.|+..|..
T Consensus 14 ICpvCqRPFsW 24 (54)
T COG4338 14 ICPVCQRPFSW 24 (54)
T ss_pred hhhhhcCchHH
Confidence 35555555543
No 200
>PTZ00448 hypothetical protein; Provisional
Probab=34.55 E-value=41 Score=19.30 Aligned_cols=23 Identities=13% Similarity=0.401 Sum_probs=17.0
Q ss_pred CccCCcchhhcCChHHHHHHHHH
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
.+.|..|+-.|........|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57799999999776666666553
No 201
>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=33.81 E-value=16 Score=13.26 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=7.3
Q ss_pred ccCcccchhcc
Q psy2647 12 HKCQVCGKAFS 22 (72)
Q Consensus 12 ~~c~~c~~~~~ 22 (72)
+.|+.|+..+-
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 56888876543
No 202
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=33.65 E-value=62 Score=17.58 Aligned_cols=15 Identities=20% Similarity=0.490 Sum_probs=9.3
Q ss_pred CcccCcccchhccCc
Q psy2647 10 KPHKCQVCGKAFSQS 24 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~ 24 (72)
....|..|+..+...
T Consensus 136 ~~~~C~~C~~~~~~~ 150 (271)
T PTZ00409 136 FEARCCTCRKTIQLN 150 (271)
T ss_pred CcceeCCCCCCcccC
Confidence 345688887766543
No 203
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=33.61 E-value=35 Score=20.09 Aligned_cols=24 Identities=33% Similarity=0.743 Sum_probs=20.7
Q ss_pred CCccCCcchhhcCChHHHHHHHHH
Q psy2647 38 KPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
..|.|..|-+-|.....+..|+..
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHhc
Confidence 468999999999999999999863
No 204
>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=33.47 E-value=37 Score=20.10 Aligned_cols=10 Identities=40% Similarity=0.996 Sum_probs=6.6
Q ss_pred CCccCCcchh
Q psy2647 38 KPFACDLCGR 47 (72)
Q Consensus 38 ~~~~c~~c~~ 47 (72)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 4567777764
No 205
>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=33.33 E-value=13 Score=14.32 Aligned_cols=36 Identities=19% Similarity=0.499 Sum_probs=16.0
Q ss_pred ccCcccchhccCcHHHHHh-----HHHhcCCCCccCCcchh
Q psy2647 12 HKCQVCGKAFSQSSNLITH-----SRKHTGFKPFACDLCGR 47 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~-----~~~~~~~~~~~c~~c~~ 47 (72)
|.|..|+..|.-...-... +.-..-..-|.|+.|+.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSS
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCC
Confidence 6788888776544321111 11111123478888864
No 206
>PRK05978 hypothetical protein; Provisional
Probab=33.30 E-value=16 Score=17.94 Aligned_cols=11 Identities=36% Similarity=0.905 Sum_probs=7.4
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
-.|+.||..|.
T Consensus 53 ~~C~~CG~~~~ 63 (148)
T PRK05978 53 DHCAACGEDFT 63 (148)
T ss_pred CCccccCCccc
Confidence 46777876654
No 207
>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=33.11 E-value=73 Score=16.42 Aligned_cols=36 Identities=17% Similarity=0.405 Sum_probs=17.8
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhh
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRA 48 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~ 48 (72)
....|..|+..+....... ..........|+.|+..
T Consensus 94 ~~~~C~~C~~~~~~~~~~~---~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 94 FIEVCKSCGPEYVRDDVVE---TRGDKETGRRCHACGGI 129 (206)
T ss_pred CcccCCCCCCccchHHHHH---HhhcCCCCCcCCCCcCc
Confidence 3456888886654332221 11112223468888643
No 208
>PRK06260 threonine synthase; Validated
Probab=32.79 E-value=21 Score=20.22 Aligned_cols=10 Identities=50% Similarity=1.178 Sum_probs=4.6
Q ss_pred ccCcccchhc
Q psy2647 12 HKCQVCGKAF 21 (72)
Q Consensus 12 ~~c~~c~~~~ 21 (72)
+.|..|+..|
T Consensus 4 ~~C~~cg~~~ 13 (397)
T PRK06260 4 LKCIECGKEY 13 (397)
T ss_pred EEECCCCCCC
Confidence 3455555443
No 209
>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=32.18 E-value=20 Score=14.31 Aligned_cols=10 Identities=40% Similarity=1.075 Sum_probs=5.7
Q ss_pred ccCCcchhhc
Q psy2647 40 FACDLCGRAF 49 (72)
Q Consensus 40 ~~c~~c~~~~ 49 (72)
+.|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4566666544
No 210
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=31.96 E-value=5.8 Score=18.35 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=6.9
Q ss_pred ccCCcchhhc
Q psy2647 40 FACDLCGRAF 49 (72)
Q Consensus 40 ~~c~~c~~~~ 49 (72)
|.|..||..+
T Consensus 101 y~C~~Cg~~w 110 (113)
T COG1594 101 YKCTRCGYRW 110 (113)
T ss_pred EEecccCCEe
Confidence 6777777654
No 211
>PLN03239 histone acetyltransferase; Provisional
Probab=31.58 E-value=43 Score=19.07 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=20.1
Q ss_pred CCCccCCcchhhcCChHHHHHHHH
Q psy2647 37 FKPFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
...|.|..|-+-|.....+.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 346899999998899999988865
No 212
>PTZ00064 histone acetyltransferase; Provisional
Probab=31.44 E-value=45 Score=20.14 Aligned_cols=25 Identities=24% Similarity=0.297 Sum_probs=21.2
Q ss_pred CCCccCCcchhhcCChHHHHHHHHH
Q psy2647 37 FKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
...|.|..|-+-|.....+.+|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 3468999999999999999999773
No 213
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=31.22 E-value=27 Score=19.09 Aligned_cols=12 Identities=17% Similarity=0.476 Sum_probs=8.9
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
.+.|+.|+..|.
T Consensus 45 ~~vc~~c~~h~r 56 (285)
T TIGR00515 45 LEVCPKCDHHMR 56 (285)
T ss_pred CCCCCCCCCcCc
Confidence 468888887665
No 214
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=31.17 E-value=40 Score=21.22 Aligned_cols=13 Identities=31% Similarity=0.649 Sum_probs=8.9
Q ss_pred CCCCccCCcchhh
Q psy2647 36 GFKPFACDLCGRA 48 (72)
Q Consensus 36 ~~~~~~c~~c~~~ 48 (72)
...|..|+.||..
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 3457788888754
No 215
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=31.09 E-value=79 Score=15.93 Aligned_cols=59 Identities=22% Similarity=0.454 Sum_probs=35.0
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCc--chhhcCChHHHHHHHHHhccCCCCCCC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDL--CGRAFQRKVDLRRHKETQHTEMRPVPV 71 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~--c~~~~~~~~~l~~H~~~~~~~~~p~~~ 71 (72)
...|+.|.........+ ..-+.+...++-.|.. |... ..-..|..|.+..|..-+|-.+
T Consensus 80 ~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~~v 140 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPSEV 140 (162)
T ss_pred cccCccccCceeceEEc-hHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCccC
Confidence 35688886543333222 2234445556666653 4321 2456788999988998888765
No 216
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, 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. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=30.80 E-value=58 Score=16.93 Aligned_cols=33 Identities=18% Similarity=0.417 Sum_probs=16.9
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
....|..|+..+..... . .......-.|+.|+.
T Consensus 112 ~~~~C~~C~~~~~~~~~-~----~~~~~~~p~C~~Cgg 144 (222)
T cd01413 112 QTAYCVNCGSKYDLEEV-K----YAKKHEVPRCPKCGG 144 (222)
T ss_pred CcceECCCCCCcchhHH-H----HhccCCCCcCCCCCC
Confidence 34568888876654432 1 111122345777764
No 217
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=30.63 E-value=22 Score=17.63 Aligned_cols=14 Identities=29% Similarity=0.524 Sum_probs=11.1
Q ss_pred CccCCcchhhcCCh
Q psy2647 39 PFACDLCGRAFQRK 52 (72)
Q Consensus 39 ~~~c~~c~~~~~~~ 52 (72)
.-.|..|+..|.+.
T Consensus 28 RReC~~C~~RFTTf 41 (156)
T COG1327 28 RRECLECGERFTTF 41 (156)
T ss_pred hhcccccccccchh
Confidence 45899999999753
No 218
>KOG4118|consensus
Probab=30.59 E-value=41 Score=14.16 Aligned_cols=26 Identities=19% Similarity=0.474 Sum_probs=19.1
Q ss_pred CccCCcchhhcCChHHHHHHHHHhcc
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKETQHT 64 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~~~~~ 64 (72)
.+.|.+|.........+.+|....|.
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCC
Confidence 46888888777777788888765443
No 219
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=30.59 E-value=28 Score=12.79 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=6.2
Q ss_pred CccCCcchh
Q psy2647 39 PFACDLCGR 47 (72)
Q Consensus 39 ~~~c~~c~~ 47 (72)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 456888874
No 220
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=30.51 E-value=21 Score=13.06 Aligned_cols=12 Identities=33% Similarity=0.969 Sum_probs=6.8
Q ss_pred cCCcchhhcCCh
Q psy2647 41 ACDLCGRAFQRK 52 (72)
Q Consensus 41 ~c~~c~~~~~~~ 52 (72)
.|+.|++.|...
T Consensus 4 ~CprC~kg~Hwa 15 (36)
T PF14787_consen 4 LCPRCGKGFHWA 15 (36)
T ss_dssp C-TTTSSSCS-T
T ss_pred cCcccCCCcchh
Confidence 577787776544
No 221
>KOG0227|consensus
Probab=29.83 E-value=32 Score=17.83 Aligned_cols=21 Identities=14% Similarity=0.526 Sum_probs=12.8
Q ss_pred cccCcccchhccCcHHHHHhH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHS 31 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~ 31 (72)
.|.|..|.....+..+...|.
T Consensus 53 ~yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 53 KYECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred ceeehhhhhhhcchhhhhhhh
Confidence 467777776555555555553
No 222
>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=29.81 E-value=11 Score=20.38 Aligned_cols=25 Identities=32% Similarity=0.678 Sum_probs=15.7
Q ss_pred CcccCcccchhccCcHHHHHhHHHh
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKH 34 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~ 34 (72)
++++|+.|+........|....+.|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecc
Confidence 5677888876665555555555544
No 223
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=29.71 E-value=61 Score=17.20 Aligned_cols=34 Identities=24% Similarity=0.428 Sum_probs=17.7
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
....|..|+..+....... .......-.|+.|+.
T Consensus 118 ~~~~C~~C~~~~~~~~~~~----~~~~~~~p~Cp~Cgg 151 (244)
T PRK14138 118 EEYYCVRCGKRYTVEDVIE----KLEKSDVPRCDDCSG 151 (244)
T ss_pred CeeEECCCCCcccHHHHHH----HHhcCCCCCCCCCCC
Confidence 3456888887765433222 111112345888864
No 224
>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=29.43 E-value=21 Score=14.07 Aligned_cols=13 Identities=15% Similarity=0.585 Sum_probs=6.1
Q ss_pred CCcccCcccchhc
Q psy2647 9 EKPHKCQVCGKAF 21 (72)
Q Consensus 9 ~~~~~c~~c~~~~ 21 (72)
...+.|.+|++.+
T Consensus 33 ~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 33 PIKLRCHYCERII 45 (52)
T ss_dssp TCEEEETTT--EE
T ss_pred CCEEEeeCCCCEe
Confidence 3445666666544
No 225
>KOG1280|consensus
Probab=29.29 E-value=65 Score=18.47 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=11.0
Q ss_pred cccCcccchhccCcHHHHHhHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSR 32 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~ 32 (72)
.|.|+.|+..-.....+..|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccCCcccccccchhHHHHHhh
Confidence 3555555554444444444443
No 226
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=28.82 E-value=27 Score=20.49 Aligned_cols=12 Identities=33% Similarity=0.672 Sum_probs=8.0
Q ss_pred CcccCcccchhc
Q psy2647 10 KPHKCQVCGKAF 21 (72)
Q Consensus 10 ~~~~c~~c~~~~ 21 (72)
..|.|..|+...
T Consensus 6 t~f~C~~CG~~s 17 (456)
T COG1066 6 TAFVCQECGYVS 17 (456)
T ss_pred cEEEcccCCCCC
Confidence 347788887543
No 227
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=28.82 E-value=29 Score=18.75 Aligned_cols=29 Identities=31% Similarity=0.715 Sum_probs=18.1
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcch
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCG 46 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~ 46 (72)
.-.|+.|+..+.....+. +--.|+|..|.
T Consensus 220 ~r~CP~Cg~~W~L~~plh-------~iFdFKCD~CR 248 (258)
T PF10071_consen 220 ARKCPSCGGDWRLKEPLH-------DIFDFKCDPCR 248 (258)
T ss_pred CCCCCCCCCccccCCchh-------hceeccCCcce
Confidence 346888887666555441 22357888874
No 228
>KOG3497|consensus
Probab=28.71 E-value=18 Score=14.90 Aligned_cols=14 Identities=36% Similarity=0.892 Sum_probs=9.9
Q ss_pred CccCCcchhhcCCh
Q psy2647 39 PFACDLCGRAFQRK 52 (72)
Q Consensus 39 ~~~c~~c~~~~~~~ 52 (72)
|..|..||+....+
T Consensus 4 PiRCFtCGKvig~K 17 (69)
T KOG3497|consen 4 PIRCFTCGKVIGDK 17 (69)
T ss_pred eeEeeecccccccc
Confidence 66788888776554
No 229
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.55 E-value=18 Score=11.77 Aligned_cols=7 Identities=43% Similarity=1.118 Sum_probs=3.9
Q ss_pred cCcccch
Q psy2647 13 KCQVCGK 19 (72)
Q Consensus 13 ~c~~c~~ 19 (72)
.|+.|+.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4666654
No 230
>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=28.55 E-value=18 Score=17.84 Aligned_cols=35 Identities=23% Similarity=0.598 Sum_probs=19.3
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
...|..|+..+...... ... . ....-.|+.|+...
T Consensus 105 ~~~C~~C~~~~~~~~~~-~~~--~-~~~~~~C~~C~~~l 139 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIV-DSI--D-EEEPPRCPKCGGLL 139 (178)
T ss_dssp EEEETTTSBEEEGHHHH-HHH--H-TTSSCBCTTTSCBE
T ss_pred eeeecCCCccccchhhc-ccc--c-ccccccccccCccC
Confidence 45788898877643322 111 1 12334788887643
No 231
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=27.67 E-value=48 Score=16.56 Aligned_cols=18 Identities=28% Similarity=0.785 Sum_probs=13.6
Q ss_pred CCccCCcchhhcCChHHH
Q psy2647 38 KPFACDLCGRAFQRKVDL 55 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~~~l 55 (72)
.++.|..||+.|.....+
T Consensus 113 ~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred CcccchhhCCccccHHHH
Confidence 467899999999765543
No 232
>KOG2857|consensus
Probab=27.43 E-value=33 Score=16.84 Aligned_cols=22 Identities=18% Similarity=0.419 Sum_probs=18.1
Q ss_pred cccCcccchhccCcHHHHHhHH
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSR 32 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~ 32 (72)
.|.|+.|.-.|.+..-++.|..
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 5899999988888888877765
No 233
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=27.41 E-value=24 Score=11.25 Aligned_cols=6 Identities=50% Similarity=1.425 Sum_probs=3.4
Q ss_pred CCcchh
Q psy2647 42 CDLCGR 47 (72)
Q Consensus 42 c~~c~~ 47 (72)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
No 234
>KOG3352|consensus
Probab=27.17 E-value=30 Score=17.12 Aligned_cols=14 Identities=29% Similarity=0.871 Sum_probs=9.1
Q ss_pred CcccCcccchhccC
Q psy2647 10 KPHKCQVCGKAFSQ 23 (72)
Q Consensus 10 ~~~~c~~c~~~~~~ 23 (72)
+...|.+|+..|+.
T Consensus 132 e~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 132 ETQRCPECGHYFKL 145 (153)
T ss_pred CcccCCcccceEEe
Confidence 34567788876653
No 235
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=26.95 E-value=24 Score=14.19 Aligned_cols=11 Identities=36% Similarity=1.219 Sum_probs=7.6
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
..|..|++.|.
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 36777877774
No 236
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=26.84 E-value=55 Score=17.22 Aligned_cols=19 Identities=16% Similarity=0.506 Sum_probs=11.0
Q ss_pred ccCCCcccCcccchhccCc
Q psy2647 6 WHGEKPHKCQVCGKAFSQS 24 (72)
Q Consensus 6 ~~~~~~~~c~~c~~~~~~~ 24 (72)
|-.-....|..|+..+...
T Consensus 117 HG~~~~~~C~~C~~~~~~~ 135 (242)
T PRK00481 117 HGSLLRARCTKCGQTYDLD 135 (242)
T ss_pred cCCcCceeeCCCCCCcChh
Confidence 3333446688887766543
No 237
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=26.74 E-value=29 Score=12.78 Aligned_cols=7 Identities=43% Similarity=1.203 Sum_probs=3.5
Q ss_pred cCCcchh
Q psy2647 41 ACDLCGR 47 (72)
Q Consensus 41 ~c~~c~~ 47 (72)
.|+.|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555543
No 238
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=26.63 E-value=35 Score=18.87 Aligned_cols=13 Identities=31% Similarity=0.731 Sum_probs=9.2
Q ss_pred CCccCCcchhhcC
Q psy2647 38 KPFACDLCGRAFQ 50 (72)
Q Consensus 38 ~~~~c~~c~~~~~ 50 (72)
+.+.|+.|+..|.
T Consensus 56 ~~~vcp~c~~h~r 68 (296)
T CHL00174 56 KMNICEQCGYHLK 68 (296)
T ss_pred cCCCCCCCCCCcC
Confidence 3468888887665
No 239
>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=26.40 E-value=19 Score=16.14 Aligned_cols=30 Identities=33% Similarity=0.773 Sum_probs=17.1
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.|.|+.|++.-.. +... -.|.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~vk--------R~a~--GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVK--------RVAT--GIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEE--------EEET--TEEEETTTTEEEE
T ss_pred CCcCCCCCCceeE--------Eeee--EEeecCCCCCEEe
Confidence 4778888753211 1112 2488999988774
No 240
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.32 E-value=19 Score=16.41 Aligned_cols=34 Identities=29% Similarity=0.562 Sum_probs=17.9
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
.-+.|+.|+. ....-.+.. +.-...|..||..+.
T Consensus 20 t~f~CP~Cge-~~v~v~~~k------~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 20 KIFECPRCGK-VSISVKIKK------NIAIITCGNCGLYTE 53 (99)
T ss_pred cEeECCCCCC-eEeeeecCC------CcceEECCCCCCccC
Confidence 3467888883 221111111 233467888886654
No 241
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=26.25 E-value=22 Score=14.64 Aligned_cols=12 Identities=25% Similarity=0.866 Sum_probs=6.7
Q ss_pred cccCcccchhcc
Q psy2647 11 PHKCQVCGKAFS 22 (72)
Q Consensus 11 ~~~c~~c~~~~~ 22 (72)
...|+.|++.|.
T Consensus 53 ~L~Cp~c~r~YP 64 (68)
T PF03966_consen 53 ELICPECGREYP 64 (68)
T ss_dssp EEEETTTTEEEE
T ss_pred EEEcCCCCCEEe
Confidence 445666665554
No 242
>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=26.25 E-value=52 Score=12.30 Aligned_cols=8 Identities=50% Similarity=1.410 Sum_probs=5.2
Q ss_pred ccCCcchh
Q psy2647 40 FACDLCGR 47 (72)
Q Consensus 40 ~~c~~c~~ 47 (72)
+.|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 55777764
No 243
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=26.01 E-value=9.4 Score=18.54 Aligned_cols=12 Identities=25% Similarity=0.888 Sum_probs=6.8
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
.|.|..|...|.
T Consensus 130 ~~~c~~c~epf~ 141 (146)
T TIGR02159 130 LYRCRACKEPFE 141 (146)
T ss_pred HhhhhhhCCcHh
Confidence 356666665554
No 244
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=26.00 E-value=27 Score=12.09 Aligned_cols=10 Identities=30% Similarity=1.215 Sum_probs=5.9
Q ss_pred CccCCcchhh
Q psy2647 39 PFACDLCGRA 48 (72)
Q Consensus 39 ~~~c~~c~~~ 48 (72)
-|+|..|+..
T Consensus 7 ~ykC~~Cgni 16 (34)
T TIGR00319 7 VYKCEVCGNI 16 (34)
T ss_pred EEEcCCCCcE
Confidence 4666666643
No 245
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=25.88 E-value=28 Score=14.42 Aligned_cols=14 Identities=29% Similarity=0.781 Sum_probs=10.7
Q ss_pred CCccCCcchhhcCC
Q psy2647 38 KPFACDLCGRAFQR 51 (72)
Q Consensus 38 ~~~~c~~c~~~~~~ 51 (72)
.|..|..||+....
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 37789999987654
No 246
>PRK12496 hypothetical protein; Provisional
Probab=25.75 E-value=29 Score=17.21 Aligned_cols=11 Identities=18% Similarity=0.667 Sum_probs=8.7
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
+.|..|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 67888888874
No 247
>KOG2747|consensus
Probab=25.71 E-value=45 Score=19.34 Aligned_cols=25 Identities=24% Similarity=0.614 Sum_probs=21.0
Q ss_pred CCCccCCcchhhcCChHHHHHHHHH
Q psy2647 37 FKPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
...|.|..|-+-......|.+|+..
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~k 180 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKK 180 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHh
Confidence 3467899999999999999999874
No 248
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=25.67 E-value=56 Score=17.53 Aligned_cols=34 Identities=26% Similarity=0.548 Sum_probs=18.2
Q ss_pred ccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 12 HKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
..|.-|.-..+ .....-++. +.....|+.||...
T Consensus 198 ~~C~GC~m~l~--~~~~~~V~~--~d~iv~CP~CgRIL 231 (239)
T COG1579 198 RVCGGCHMKLP--SQTLSKVRK--KDEIVFCPYCGRIL 231 (239)
T ss_pred CcccCCeeeec--HHHHHHHhc--CCCCccCCccchHH
Confidence 34666654332 222222222 45577899998754
No 249
>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=25.62 E-value=20 Score=13.04 Aligned_cols=10 Identities=30% Similarity=1.072 Sum_probs=6.4
Q ss_pred ccCCcchhhc
Q psy2647 40 FACDLCGRAF 49 (72)
Q Consensus 40 ~~c~~c~~~~ 49 (72)
|.|..|+..+
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 5677776543
No 250
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=25.27 E-value=40 Score=13.46 Aligned_cols=19 Identities=21% Similarity=0.567 Sum_probs=13.9
Q ss_pred cccCcccchhccCcHHHHH
Q psy2647 11 PHKCQVCGKAFSQSSNLIT 29 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~ 29 (72)
-+-|-+|+..|.+...|..
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred CceeeeeCCccCCHHHHHh
Confidence 3568889888888776654
No 251
>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=25.07 E-value=26 Score=15.72 Aligned_cols=31 Identities=29% Similarity=0.635 Sum_probs=18.0
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchhhcC
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQ 50 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 50 (72)
..|.|+.|++.-. .+.. .-.|.|..|++.|.
T Consensus 34 a~y~CpfCgk~~v--------kR~a--~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTV--------KRGS--TGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCce--------EEEe--eEEEEcCCCCCEEe
Confidence 3577888864211 0111 22588999988775
No 252
>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=24.85 E-value=32 Score=11.92 Aligned_cols=11 Identities=27% Similarity=1.138 Sum_probs=7.1
Q ss_pred CccCCcchhhc
Q psy2647 39 PFACDLCGRAF 49 (72)
Q Consensus 39 ~~~c~~c~~~~ 49 (72)
-|+|..|+...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 46777777543
No 253
>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=24.58 E-value=54 Score=11.91 Aligned_cols=10 Identities=30% Similarity=1.065 Sum_probs=2.6
Q ss_pred ccCCcchhhc
Q psy2647 40 FACDLCGRAF 49 (72)
Q Consensus 40 ~~c~~c~~~~ 49 (72)
|=|..|..-|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 3455555544
No 254
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=24.49 E-value=27 Score=14.91 Aligned_cols=15 Identities=33% Similarity=0.780 Sum_probs=10.5
Q ss_pred CCccCCcchhhcCCh
Q psy2647 38 KPFACDLCGRAFQRK 52 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~ 52 (72)
.|..|-.||+.....
T Consensus 3 iPVRCFTCGkvig~~ 17 (71)
T PLN00032 3 IPVRCFTCGKVIGNK 17 (71)
T ss_pred CceeecCCCCCcHHH
Confidence 367888888876543
No 255
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.33 E-value=9.4 Score=18.29 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=6.4
Q ss_pred CCCccCCcchh
Q psy2647 37 FKPFACDLCGR 47 (72)
Q Consensus 37 ~~~~~c~~c~~ 47 (72)
+....|+.|+.
T Consensus 103 ~~~~~CPwCg~ 113 (131)
T PF15616_consen 103 EGEVTCPWCGN 113 (131)
T ss_pred CCCEECCCCCC
Confidence 33456677664
No 256
>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=24.22 E-value=37 Score=11.65 Aligned_cols=12 Identities=25% Similarity=0.874 Sum_probs=4.9
Q ss_pred cccCcccchhcc
Q psy2647 11 PHKCQVCGKAFS 22 (72)
Q Consensus 11 ~~~c~~c~~~~~ 22 (72)
.|.|+.|+..+-
T Consensus 13 kY~Cp~C~~~~C 24 (30)
T PF04438_consen 13 KYRCPRCGARYC 24 (30)
T ss_dssp SEE-TTT--EES
T ss_pred EEECCCcCCcee
Confidence 456666665443
No 257
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=24.22 E-value=17 Score=14.25 Aligned_cols=10 Identities=40% Similarity=0.899 Sum_probs=6.1
Q ss_pred CCccCCcchh
Q psy2647 38 KPFACDLCGR 47 (72)
Q Consensus 38 ~~~~c~~c~~ 47 (72)
....|+.|+.
T Consensus 45 ~i~~Cp~CgR 54 (56)
T PF02591_consen 45 EIVFCPNCGR 54 (56)
T ss_pred CeEECcCCCc
Confidence 4456777764
No 258
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=23.82 E-value=68 Score=18.48 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=19.0
Q ss_pred cCCcchhhcCChHHHHHHHHHhc
Q psy2647 41 ACDLCGRAFQRKVDLRRHKETQH 63 (72)
Q Consensus 41 ~c~~c~~~~~~~~~l~~H~~~~~ 63 (72)
.|..|...|....-|..|.|..|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh
Confidence 68889999998888888888644
No 259
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=23.43 E-value=28 Score=14.43 Aligned_cols=15 Identities=33% Similarity=0.769 Sum_probs=10.7
Q ss_pred CCccCCcchhhcCCh
Q psy2647 38 KPFACDLCGRAFQRK 52 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~ 52 (72)
.|..|-.||+.....
T Consensus 3 iPiRCFsCGkvi~~~ 17 (63)
T COG1644 3 IPVRCFSCGKVIGHK 17 (63)
T ss_pred CceEeecCCCCHHHH
Confidence 377888898876543
No 260
>PRK01343 zinc-binding protein; Provisional
Probab=23.38 E-value=49 Score=13.49 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=6.9
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
..|+.|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 45777776543
No 261
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=23.24 E-value=73 Score=13.11 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=4.5
Q ss_pred ccCCcchh
Q psy2647 40 FACDLCGR 47 (72)
Q Consensus 40 ~~c~~c~~ 47 (72)
-.|+.|+.
T Consensus 40 p~CPlC~s 47 (59)
T PF14169_consen 40 PVCPLCKS 47 (59)
T ss_pred ccCCCcCC
Confidence 35666653
No 262
>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=22.92 E-value=39 Score=11.34 Aligned_cols=10 Identities=40% Similarity=1.318 Sum_probs=5.7
Q ss_pred ccCCcchhhc
Q psy2647 40 FACDLCGRAF 49 (72)
Q Consensus 40 ~~c~~c~~~~ 49 (72)
+.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5666666543
No 263
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; 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. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=22.90 E-value=97 Score=16.04 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=8.6
Q ss_pred CcccCcccchhccC
Q psy2647 10 KPHKCQVCGKAFSQ 23 (72)
Q Consensus 10 ~~~~c~~c~~~~~~ 23 (72)
....|..|+..+..
T Consensus 108 ~~~~C~~C~~~~~~ 121 (224)
T cd01412 108 FRVRCSSCGYVGEN 121 (224)
T ss_pred CccccCCCCCCCCc
Confidence 34567778766544
No 264
>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=22.78 E-value=81 Score=14.39 Aligned_cols=20 Identities=15% Similarity=0.423 Sum_probs=13.7
Q ss_pred cccCcccchhccCcHHHHHh
Q psy2647 11 PHKCQVCGKAFSQSSNLITH 30 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~ 30 (72)
-+.|+.|+..+........-
T Consensus 31 ~~~C~~CGe~~~~~e~~~~~ 50 (127)
T TIGR03830 31 GWYCPACGEELLDPEESKRN 50 (127)
T ss_pred eeECCCCCCEEEcHHHHHHH
Confidence 46799999887766554433
No 265
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.62 E-value=59 Score=12.20 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=7.5
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
.+.|+.|+..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 466777775543
No 266
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=22.45 E-value=61 Score=11.73 Aligned_cols=19 Identities=21% Similarity=0.436 Sum_probs=12.2
Q ss_pred CccCCcchhhcCChHHHHH
Q psy2647 39 PFACDLCGRAFQRKVDLRR 57 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~ 57 (72)
...|+.|+..+.....+.+
T Consensus 19 id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEECCCCCeEEccHHHHHH
Confidence 3567888777766655543
No 267
>KOG3362|consensus
Probab=22.44 E-value=19 Score=17.64 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=12.4
Q ss_pred CccCCcchhhcCChHHHHHHHH
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
+|.|..||..+-+-..+..|..
T Consensus 129 ~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred hhHHHhcCCceeechhhhhccc
Confidence 3556666665555555555543
No 268
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.40 E-value=1.1e+02 Score=14.85 Aligned_cols=27 Identities=19% Similarity=0.361 Sum_probs=16.1
Q ss_pred hhccCcHHHHHhHHHhcCCCCccCCcchhhc
Q psy2647 19 KAFSQSSNLITHSRKHTGFKPFACDLCGRAF 49 (72)
Q Consensus 19 ~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 49 (72)
.+|.+...+.+... .....|+.|+..-
T Consensus 16 GWF~ssaDfd~Q~~----rgLv~CPvCgs~~ 42 (142)
T COG5319 16 GWFGSSADFDRQRE----RGLVTCPVCGSTE 42 (142)
T ss_pred ccccCchhHHHHHH----cCceeCCCCCcHH
Confidence 35666666655433 3457888887543
No 269
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.29 E-value=33 Score=15.41 Aligned_cols=12 Identities=33% Similarity=0.944 Sum_probs=9.2
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
.|.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PRK03976 54 IWECRKCGAKFA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 578888887765
No 270
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=22.15 E-value=45 Score=17.47 Aligned_cols=16 Identities=25% Similarity=0.858 Sum_probs=11.6
Q ss_pred CCCccCCcchhhcCCh
Q psy2647 37 FKPFACDLCGRAFQRK 52 (72)
Q Consensus 37 ~~~~~c~~c~~~~~~~ 52 (72)
..||.|..|.+.|..+
T Consensus 194 ~IPF~C~iCKkdy~sp 209 (259)
T COG5152 194 KIPFLCGICKKDYESP 209 (259)
T ss_pred CCceeehhchhhccch
Confidence 3678898888777543
No 271
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.14 E-value=52 Score=18.93 Aligned_cols=22 Identities=36% Similarity=0.638 Sum_probs=17.8
Q ss_pred CccCCcchhhcCChHHHHHHHH
Q psy2647 39 PFACDLCGRAFQRKVDLRRHKE 60 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~H~~ 60 (72)
.+-|..|++-|...+-+..|+.
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHh
Confidence 3568999999998888888864
No 272
>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=22.09 E-value=45 Score=14.61 Aligned_cols=12 Identities=25% Similarity=0.933 Sum_probs=9.1
Q ss_pred ccCCcchhhcCC
Q psy2647 40 FACDLCGRAFQR 51 (72)
Q Consensus 40 ~~c~~c~~~~~~ 51 (72)
-.|..|++.+..
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 369999987764
No 273
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.06 E-value=43 Score=15.54 Aligned_cols=11 Identities=36% Similarity=1.062 Sum_probs=8.3
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
..|+.||..|.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred ccCCCCCCccc
Confidence 47899987664
No 274
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=21.93 E-value=24 Score=16.16 Aligned_cols=8 Identities=38% Similarity=1.477 Sum_probs=4.6
Q ss_pred ccCCcchh
Q psy2647 40 FACDLCGR 47 (72)
Q Consensus 40 ~~c~~c~~ 47 (72)
|.|..||+
T Consensus 3 WkC~iCg~ 10 (101)
T PF09943_consen 3 WKCYICGK 10 (101)
T ss_pred eEEEecCC
Confidence 55666654
No 275
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.81 E-value=54 Score=13.78 Aligned_cols=8 Identities=50% Similarity=1.402 Sum_probs=4.9
Q ss_pred ccCCcchh
Q psy2647 40 FACDLCGR 47 (72)
Q Consensus 40 ~~c~~c~~ 47 (72)
++|+.||.
T Consensus 5 ~kCpKCgn 12 (68)
T COG3478 5 FKCPKCGN 12 (68)
T ss_pred ccCCCcCC
Confidence 45777764
No 276
>KOG1088|consensus
Probab=21.78 E-value=27 Score=16.53 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=5.0
Q ss_pred ccCcccchhcc
Q psy2647 12 HKCQVCGKAFS 22 (72)
Q Consensus 12 ~~c~~c~~~~~ 22 (72)
..|+.||+.|+
T Consensus 99 l~CpetG~vfp 109 (124)
T KOG1088|consen 99 LVCPETGRVFP 109 (124)
T ss_pred EecCCCCcEee
Confidence 34444444443
No 277
>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=21.73 E-value=29 Score=16.98 Aligned_cols=28 Identities=25% Similarity=0.600 Sum_probs=15.2
Q ss_pred CcccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 10 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
..+.|..|+..... .++ ...-.|+.|+.
T Consensus 111 G~l~C~~Cg~~~~~---------~~~-~~l~~Cp~C~~ 138 (146)
T PF07295_consen 111 GTLVCENCGHEVEL---------THP-ERLPPCPKCGH 138 (146)
T ss_pred ceEecccCCCEEEe---------cCC-CcCCCCCCCCC
Confidence 34778888754221 112 23446888874
No 278
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=21.66 E-value=40 Score=16.99 Aligned_cols=18 Identities=22% Similarity=0.682 Sum_probs=12.2
Q ss_pred CccCCcchhhcCChHHHH
Q psy2647 39 PFACDLCGRAFQRKVDLR 56 (72)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~ 56 (72)
-+.|+.||+.|=.-+...
T Consensus 130 f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 130 FYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred eeECCCCcccccCchHHH
Confidence 467999998875444433
No 279
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=21.51 E-value=85 Score=13.05 Aligned_cols=13 Identities=23% Similarity=0.552 Sum_probs=8.2
Q ss_pred HHHHHhccCCCCC
Q psy2647 57 RHKETQHTEMRPV 69 (72)
Q Consensus 57 ~H~~~~~~~~~p~ 69 (72)
.|.+.+|.++.|.
T Consensus 30 ~H~~~~HP~~p~m 42 (65)
T PF04328_consen 30 EHMRRHHPDEPPM 42 (65)
T ss_pred HHHHHHCcCCCCC
Confidence 4666667776554
No 280
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=21.50 E-value=45 Score=14.72 Aligned_cols=11 Identities=27% Similarity=0.769 Sum_probs=7.3
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
-.|+.||..|.
T Consensus 9 ~~C~~CG~d~~ 19 (86)
T PF06170_consen 9 PRCPHCGLDYS 19 (86)
T ss_pred CcccccCCccc
Confidence 36778876654
No 281
>COG2879 Uncharacterized small protein [Function unknown]
Probab=21.50 E-value=86 Score=13.12 Aligned_cols=15 Identities=13% Similarity=0.242 Sum_probs=7.4
Q ss_pred HHHHHHHHHhccCCC
Q psy2647 53 VDLRRHKETQHTEMR 67 (72)
Q Consensus 53 ~~l~~H~~~~~~~~~ 67 (72)
.+...|++.+|.+.-
T Consensus 26 dnYVehmr~~hPd~p 40 (65)
T COG2879 26 DNYVEHMRKKHPDKP 40 (65)
T ss_pred HHHHHHHHHhCcCCC
Confidence 344555555454443
No 282
>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=21.45 E-value=39 Score=12.23 Aligned_cols=9 Identities=33% Similarity=1.054 Sum_probs=2.2
Q ss_pred CCcchhhcC
Q psy2647 42 CDLCGRAFQ 50 (72)
Q Consensus 42 c~~c~~~~~ 50 (72)
|..|+..+.
T Consensus 1 C~~C~~~~~ 9 (47)
T PF01844_consen 1 CQYCGKPGS 9 (47)
T ss_dssp -TTT--B--
T ss_pred CCCCCCcCc
Confidence 455655543
No 283
>KOG3456|consensus
Probab=21.42 E-value=40 Score=15.68 Aligned_cols=13 Identities=38% Similarity=1.040 Sum_probs=9.6
Q ss_pred CccCCcchhhcCC
Q psy2647 39 PFACDLCGRAFQR 51 (72)
Q Consensus 39 ~~~c~~c~~~~~~ 51 (72)
+..|.+||..|.+
T Consensus 104 ~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 104 PHICGYCGLRFVQ 116 (120)
T ss_pred Ccccccchhhhhh
Confidence 3578889888764
No 284
>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=21.28 E-value=35 Score=13.87 Aligned_cols=11 Identities=27% Similarity=1.096 Sum_probs=4.6
Q ss_pred ccCCcchhhcC
Q psy2647 40 FACDLCGRAFQ 50 (72)
Q Consensus 40 ~~c~~c~~~~~ 50 (72)
..|+.|++.+.
T Consensus 3 v~CP~C~k~~~ 13 (57)
T PF03884_consen 3 VKCPICGKPVE 13 (57)
T ss_dssp EE-TTT--EEE
T ss_pred ccCCCCCCeec
Confidence 45777776544
No 285
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=21.15 E-value=62 Score=18.61 Aligned_cols=24 Identities=21% Similarity=0.650 Sum_probs=20.4
Q ss_pred CCccCCcchhhcCChHHHHHHHHH
Q psy2647 38 KPFACDLCGRAFQRKVDLRRHKET 61 (72)
Q Consensus 38 ~~~~c~~c~~~~~~~~~l~~H~~~ 61 (72)
..|.|..|-+-+.....+.+|+..
T Consensus 157 ~vyICefClkY~~s~~~~~rH~~k 180 (395)
T COG5027 157 IVYICEFCLKYYGSQTSLVRHRKK 180 (395)
T ss_pred eEEEhhhhHHHhcchhHHHHHHhc
Confidence 457899999999999999999874
No 286
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.96 E-value=47 Score=18.30 Aligned_cols=12 Identities=25% Similarity=0.678 Sum_probs=8.9
Q ss_pred CccCCcchhhcC
Q psy2647 39 PFACDLCGRAFQ 50 (72)
Q Consensus 39 ~~~c~~c~~~~~ 50 (72)
.+.|+.|+..|.
T Consensus 46 ~~vc~~c~~h~r 57 (292)
T PRK05654 46 LNVCPKCGHHMR 57 (292)
T ss_pred CCCCCCCCCCee
Confidence 468888887765
No 287
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=20.88 E-value=45 Score=12.85 Aligned_cols=7 Identities=43% Similarity=1.042 Sum_probs=2.7
Q ss_pred Ccchhhc
Q psy2647 43 DLCGRAF 49 (72)
Q Consensus 43 ~~c~~~~ 49 (72)
+.||..|
T Consensus 2 P~Cg~~f 8 (50)
T PF14375_consen 2 PRCGAPF 8 (50)
T ss_pred CCCCCcC
Confidence 3344333
No 288
>KOG3277|consensus
Probab=20.74 E-value=25 Score=17.52 Aligned_cols=34 Identities=18% Similarity=0.491 Sum_probs=18.7
Q ss_pred cccCcccchhccCcHHHHHhHHHhcCCCCccCCcchh
Q psy2647 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47 (72)
Q Consensus 11 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 47 (72)
.|.|..|+..-... + ..+.-+.|....+|+.|..
T Consensus 79 ~yTCkvCntRs~kt--i-sk~AY~~GvVivqC~gC~~ 112 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKT--I-SKQAYEKGVVIVQCPGCKN 112 (165)
T ss_pred EEEeeccCCccccc--c-ChhhhhCceEEEECCCCcc
Confidence 47888887543211 1 1223344555678888853
No 289
>KOG0402|consensus
Probab=20.73 E-value=31 Score=15.28 Aligned_cols=10 Identities=30% Similarity=1.315 Sum_probs=8.0
Q ss_pred CccCCcchhh
Q psy2647 39 PFACDLCGRA 48 (72)
Q Consensus 39 ~~~c~~c~~~ 48 (72)
.|.|+.||+.
T Consensus 36 ky~CsfCGK~ 45 (92)
T KOG0402|consen 36 KYTCSFCGKK 45 (92)
T ss_pred hhhhhhcchh
Confidence 5889999874
No 290
>PRK06450 threonine synthase; Validated
Probab=20.62 E-value=64 Score=18.06 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=6.7
Q ss_pred ccCcccchhc
Q psy2647 12 HKCQVCGKAF 21 (72)
Q Consensus 12 ~~c~~c~~~~ 21 (72)
+.|..|++.|
T Consensus 4 ~~C~~Cg~~~ 13 (338)
T PRK06450 4 EVCMKCGKER 13 (338)
T ss_pred eEECCcCCcC
Confidence 5677777655
No 291
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.56 E-value=23 Score=14.27 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=6.8
Q ss_pred CCCccCCcchh
Q psy2647 37 FKPFACDLCGR 47 (72)
Q Consensus 37 ~~~~~c~~c~~ 47 (72)
.-|.-|+.|.+
T Consensus 26 NfPlyCpKCK~ 36 (55)
T PF14205_consen 26 NFPLYCPKCKQ 36 (55)
T ss_pred cccccCCCCCc
Confidence 34666777754
No 292
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.45 E-value=30 Score=21.33 Aligned_cols=12 Identities=42% Similarity=0.758 Sum_probs=7.6
Q ss_pred CCCccCCcchhh
Q psy2647 37 FKPFACDLCGRA 48 (72)
Q Consensus 37 ~~~~~c~~c~~~ 48 (72)
..+..|+.|+..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 346678888653
No 293
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=20.36 E-value=18 Score=14.86 Aligned_cols=6 Identities=33% Similarity=1.154 Sum_probs=2.3
Q ss_pred Ccccch
Q psy2647 14 CQVCGK 19 (72)
Q Consensus 14 c~~c~~ 19 (72)
|..|+.
T Consensus 33 CNDC~~ 38 (61)
T PF14599_consen 33 CNDCNA 38 (61)
T ss_dssp ESSS--
T ss_pred CCCCCC
Confidence 555554
No 294
>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=20.28 E-value=43 Score=13.32 Aligned_cols=10 Identities=30% Similarity=1.016 Sum_probs=7.5
Q ss_pred CCccCCcchh
Q psy2647 38 KPFACDLCGR 47 (72)
Q Consensus 38 ~~~~c~~c~~ 47 (72)
..|.|..|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 4688998874
No 295
>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=20.27 E-value=67 Score=14.41 Aligned_cols=18 Identities=17% Similarity=0.604 Sum_probs=13.1
Q ss_pred ccCcccchhccCcHHHHH
Q psy2647 12 HKCQVCGKAFSQSSNLIT 29 (72)
Q Consensus 12 ~~c~~c~~~~~~~~~l~~ 29 (72)
..|..||..|.....+..
T Consensus 36 ~~C~~CGe~y~~dev~~e 53 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTVKE 53 (89)
T ss_pred ccccCCCcEeecHHHHHH
Confidence 569999998877665443
No 296
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.18 E-value=36 Score=15.47 Aligned_cols=13 Identities=54% Similarity=1.017 Sum_probs=9.2
Q ss_pred CCCcccCcccchh
Q psy2647 8 GEKPHKCQVCGKA 20 (72)
Q Consensus 8 ~~~~~~c~~c~~~ 20 (72)
+.+.|.|..|+..
T Consensus 3 ~lkewkC~VCg~~ 15 (103)
T COG4847 3 GLKEWKCYVCGGT 15 (103)
T ss_pred ccceeeEeeeCCE
Confidence 4466888888864
Done!