Query psy4268
Match_columns 86
No_of_seqs 110 out of 1285
Neff 11.5
Searched_HMMs 46136
Date Fri Aug 16 21:13:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4268.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4268hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 5.9E-22 1.3E-26 107.8 3.5 70 2-74 177-246 (279)
2 KOG2462|consensus 99.8 3E-21 6.4E-26 105.1 3.1 64 1-65 202-265 (279)
3 KOG3576|consensus 99.6 3.1E-17 6.8E-22 86.7 -0.8 69 1-70 132-200 (267)
4 KOG3623|consensus 99.5 5.1E-15 1.1E-19 89.9 1.0 61 2-63 910-970 (1007)
5 KOG1074|consensus 99.4 1.2E-14 2.6E-19 89.1 -1.2 68 2-70 621-695 (958)
6 KOG3623|consensus 99.3 1.3E-12 2.7E-17 79.9 1.8 65 10-75 890-954 (1007)
7 PHA02768 hypothetical protein; 99.3 4E-12 8.6E-17 54.6 2.1 42 15-59 6-47 (55)
8 PHA00733 hypothetical protein 99.2 2.3E-11 4.9E-16 61.3 4.9 61 4-68 64-124 (128)
9 KOG3576|consensus 99.1 2.5E-11 5.4E-16 64.7 1.0 66 10-76 113-178 (267)
10 KOG1074|consensus 99.1 1.5E-10 3.2E-15 71.8 3.4 59 15-74 880-938 (958)
11 PF13465 zf-H2C2_2: Zinc-finge 99.0 3.5E-11 7.6E-16 44.7 -1.2 23 31-54 3-25 (26)
12 PF13465 zf-H2C2_2: Zinc-finge 99.0 7.4E-10 1.6E-14 41.1 2.3 24 2-25 2-25 (26)
13 KOG3993|consensus 98.8 1.4E-09 3.1E-14 63.3 1.1 70 1-70 282-383 (500)
14 PHA00616 hypothetical protein 98.7 1.2E-08 2.6E-13 41.9 1.7 33 14-47 1-33 (44)
15 PHA00616 hypothetical protein 98.6 2.5E-08 5.3E-13 41.0 1.8 31 44-74 2-32 (44)
16 PHA00732 hypothetical protein 98.6 4.5E-08 9.7E-13 45.5 2.3 43 14-63 1-44 (79)
17 KOG3608|consensus 98.5 1.5E-08 3.3E-13 58.2 -0.3 66 2-68 195-262 (467)
18 KOG3608|consensus 98.5 1.3E-07 2.9E-12 54.5 3.0 64 2-67 279-345 (467)
19 PF00096 zf-C2H2: Zinc finger, 98.4 4.6E-07 1E-11 32.3 2.0 22 44-65 1-22 (23)
20 PHA02768 hypothetical protein; 98.3 1.3E-06 2.8E-11 37.7 2.9 24 44-67 6-29 (55)
21 PF00096 zf-C2H2: Zinc finger, 98.2 1.6E-06 3.4E-11 30.9 2.3 23 15-37 1-23 (23)
22 PF05605 zf-Di19: Drought indu 98.2 5.9E-06 1.3E-10 35.7 4.4 51 14-68 2-54 (54)
23 PHA00733 hypothetical protein 98.2 1.4E-06 3.1E-11 44.0 2.1 55 11-66 37-96 (128)
24 PF13894 zf-C2H2_4: C2H2-type 98.1 3.6E-06 7.8E-11 30.0 2.3 23 44-66 1-23 (24)
25 PLN03086 PRLI-interacting fact 98.1 4.5E-06 9.7E-11 51.2 2.9 38 13-53 477-514 (567)
26 PLN03086 PRLI-interacting fact 98.0 8.4E-06 1.8E-10 50.1 3.8 63 2-67 492-564 (567)
27 KOG3993|consensus 98.0 6E-07 1.3E-11 52.8 -1.2 59 14-73 267-325 (500)
28 PF13912 zf-C2H2_6: C2H2-type 98.0 5.8E-06 1.3E-10 30.5 1.6 22 44-65 2-23 (27)
29 PF13912 zf-C2H2_6: C2H2-type 98.0 4.1E-06 8.9E-11 31.0 1.1 25 14-38 1-25 (27)
30 PF13894 zf-C2H2_4: C2H2-type 97.8 2.7E-05 5.8E-10 27.6 2.4 23 15-37 1-23 (24)
31 PF09237 GAGA: GAGA factor; I 97.8 2.9E-05 6.2E-10 32.8 2.7 32 40-72 22-53 (54)
32 COG5189 SFP1 Putative transcri 97.8 7.8E-06 1.7E-10 46.8 0.6 51 12-63 347-418 (423)
33 smart00355 ZnF_C2H2 zinc finge 97.6 8.5E-05 1.8E-09 26.6 2.5 20 45-64 2-21 (26)
34 PF09237 GAGA: GAGA factor; I 97.6 0.0002 4.3E-09 30.3 3.5 34 9-42 19-52 (54)
35 PRK04860 hypothetical protein; 97.6 8.3E-05 1.8E-09 39.1 2.6 39 13-56 118-156 (160)
36 smart00355 ZnF_C2H2 zinc finge 97.5 0.00016 3.5E-09 25.8 2.3 24 15-38 1-24 (26)
37 PF12756 zf-C2H2_2: C2H2 type 97.5 0.00012 2.5E-09 35.1 2.3 24 44-67 51-74 (100)
38 PF12874 zf-met: Zinc-finger o 97.3 0.00022 4.7E-09 25.7 1.7 21 15-35 1-21 (25)
39 PF13909 zf-H2C2_5: C2H2-type 97.2 0.0005 1.1E-08 24.5 2.1 22 45-67 2-23 (24)
40 PHA00732 hypothetical protein 97.2 0.00062 1.3E-08 31.7 2.7 24 44-67 2-26 (79)
41 PF12874 zf-met: Zinc-finger o 97.1 0.00031 6.7E-09 25.2 1.3 22 44-65 1-22 (25)
42 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00063 1.4E-08 25.0 0.2 21 15-35 2-22 (27)
43 PF13913 zf-C2HC_2: zinc-finge 96.6 0.0034 7.4E-08 22.7 2.2 20 44-64 3-22 (25)
44 KOG2893|consensus 95.8 0.0022 4.8E-08 35.8 -0.2 45 12-62 9-53 (341)
45 smart00451 ZnF_U1 U1-like zinc 95.6 0.016 3.6E-07 22.3 2.1 22 14-35 3-24 (35)
46 KOG1146|consensus 95.0 0.025 5.5E-07 38.6 2.5 57 8-65 459-540 (1406)
47 cd00350 rubredoxin_like Rubred 94.7 0.028 6E-07 21.7 1.5 24 15-51 2-25 (33)
48 PRK04860 hypothetical protein; 94.4 0.0092 2E-07 31.5 -0.4 25 2-26 131-155 (160)
49 KOG2186|consensus 94.3 0.033 7.1E-07 31.5 1.6 49 14-66 3-51 (276)
50 PF12756 zf-C2H2_2: C2H2 type 94.3 0.083 1.8E-06 25.1 2.9 25 14-38 50-74 (100)
51 PF09538 FYDLN_acid: Protein o 94.2 0.039 8.4E-07 27.3 1.6 30 15-56 10-39 (108)
52 COG5048 FOG: Zn-finger [Genera 93.8 0.015 3.2E-07 34.4 -0.3 60 13-73 288-353 (467)
53 COG1592 Rubrerythrin [Energy p 92.2 0.12 2.5E-06 27.6 1.7 23 14-50 134-156 (166)
54 TIGR00373 conserved hypothetic 91.3 0.23 4.9E-06 26.3 2.2 36 9-54 104-139 (158)
55 COG4049 Uncharacterized protei 91.1 0.16 3.5E-06 22.0 1.2 29 8-36 11-39 (65)
56 TIGR02300 FYDLN_acid conserved 90.9 0.21 4.6E-06 25.4 1.7 32 15-58 10-41 (129)
57 PRK06266 transcription initiat 90.4 0.24 5.2E-06 26.8 1.8 34 11-54 114-147 (178)
58 cd00729 rubredoxin_SM Rubredox 89.5 0.32 6.9E-06 18.9 1.3 25 14-51 2-26 (34)
59 PF12013 DUF3505: Protein of u 89.2 0.45 9.8E-06 23.4 2.1 25 44-68 81-109 (109)
60 PF09986 DUF2225: Uncharacteri 88.8 0.062 1.3E-06 29.8 -1.2 45 12-56 3-61 (214)
61 PF04959 ARS2: Arsenite-resist 88.7 0.51 1.1E-05 26.4 2.3 30 11-40 74-103 (214)
62 smart00531 TFIIE Transcription 88.7 0.32 7E-06 25.4 1.4 39 11-54 96-134 (147)
63 PF05443 ROS_MUCR: ROS/MUCR tr 88.3 0.36 7.8E-06 24.9 1.4 24 44-70 73-96 (132)
64 PF13717 zinc_ribbon_4: zinc-r 86.6 0.73 1.6E-05 18.1 1.6 33 15-53 3-35 (36)
65 TIGR02098 MJ0042_CXXC MJ0042 f 86.5 0.6 1.3E-05 18.3 1.4 34 15-54 3-36 (38)
66 KOG1146|consensus 86.0 0.76 1.7E-05 32.2 2.3 59 12-72 1282-1357(1406)
67 PF04959 ARS2: Arsenite-resist 86.0 0.52 1.1E-05 26.3 1.3 26 44-69 78-103 (214)
68 PF13719 zinc_ribbon_5: zinc-r 85.8 0.87 1.9E-05 17.9 1.6 34 15-54 3-36 (37)
69 COG5189 SFP1 Putative transcri 85.1 1.1 2.3E-05 26.8 2.3 24 40-64 347-372 (423)
70 PRK00398 rpoP DNA-directed RNA 84.4 0.69 1.5E-05 19.0 1.1 30 14-54 3-32 (46)
71 smart00659 RPOLCX RNA polymera 84.3 1.1 2.3E-05 18.5 1.6 27 14-52 2-28 (44)
72 COG5048 FOG: Zn-finger [Genera 83.2 0.46 9.9E-06 28.3 0.4 45 2-47 305-355 (467)
73 PF05191 ADK_lid: Adenylate ki 82.8 0.32 7E-06 19.1 -0.2 32 15-55 2-33 (36)
74 TIGR02605 CxxC_CxxC_SSSS putat 82.8 0.37 8.1E-06 20.3 -0.0 30 14-51 5-34 (52)
75 PRK00464 nrdR transcriptional 82.5 0.16 3.5E-06 26.8 -1.4 12 44-55 29-40 (154)
76 KOG4167|consensus 81.8 0.29 6.3E-06 32.0 -0.8 25 44-68 793-817 (907)
77 COG3357 Predicted transcriptio 80.8 0.88 1.9E-05 21.9 0.8 11 14-24 58-68 (97)
78 KOG4167|consensus 80.5 0.41 8.9E-06 31.4 -0.4 28 13-40 791-818 (907)
79 COG1997 RPL43A Ribosomal prote 80.3 0.53 1.1E-05 22.4 -0.0 30 14-54 35-64 (89)
80 KOG3408|consensus 80.0 1.2 2.5E-05 22.7 1.1 22 44-65 58-79 (129)
81 PF10571 UPF0547: Uncharacteri 78.6 1.3 2.8E-05 16.1 0.8 11 44-54 15-25 (26)
82 smart00614 ZnF_BED BED zinc fi 78.0 2.6 5.7E-05 17.6 1.8 20 45-64 20-44 (50)
83 PF02892 zf-BED: BED zinc fing 77.5 3.3 7.2E-05 16.7 2.0 12 13-24 15-26 (45)
84 COG2888 Predicted Zn-ribbon RN 76.4 2.9 6.2E-05 18.5 1.7 7 44-50 51-57 (61)
85 COG4530 Uncharacterized protei 74.7 2.4 5.2E-05 21.2 1.3 29 16-56 11-39 (129)
86 PHA00626 hypothetical protein 74.6 1.7 3.6E-05 19.0 0.7 16 41-57 22-37 (59)
87 cd00924 Cyt_c_Oxidase_Vb Cytoc 74.4 1.5 3.3E-05 21.4 0.6 18 7-25 73-90 (97)
88 smart00734 ZnF_Rad18 Rad18-lik 74.2 3.9 8.4E-05 14.7 1.8 18 45-63 3-20 (26)
89 PF08790 zf-LYAR: LYAR-type C2 73.0 0.66 1.4E-05 17.3 -0.6 11 44-54 1-11 (28)
90 PF07754 DUF1610: Domain of un 72.9 1.9 4.2E-05 15.4 0.6 8 44-51 17-24 (24)
91 PF13878 zf-C2H2_3: zinc-finge 72.9 5.7 0.00012 16.0 2.4 25 14-38 13-39 (41)
92 PF09723 Zn-ribbon_8: Zinc rib 72.3 1.7 3.6E-05 17.6 0.4 14 44-57 6-19 (42)
93 KOG2593|consensus 71.8 2.5 5.4E-05 26.2 1.2 40 9-52 123-162 (436)
94 PF08209 Sgf11: Sgf11 (transcr 71.8 5.5 0.00012 15.4 1.9 23 44-67 5-27 (33)
95 smart00834 CxxC_CXXC_SSSS Puta 71.1 2 4.3E-05 16.9 0.5 13 44-56 6-18 (41)
96 COG1996 RPC10 DNA-directed RNA 69.9 3.6 7.7E-05 17.5 1.2 30 12-52 4-33 (49)
97 COG1773 Rubredoxin [Energy pro 69.0 2.4 5.3E-05 18.4 0.6 15 14-28 3-17 (55)
98 KOG4173|consensus 64.5 3.4 7.4E-05 23.2 0.7 48 15-63 107-166 (253)
99 PF07295 DUF1451: Protein of u 64.3 5.7 0.00012 20.9 1.5 28 13-51 111-138 (146)
100 PF10013 DUF2256: Uncharacteri 64.3 5.7 0.00012 16.3 1.2 17 44-60 9-25 (42)
101 KOG0978|consensus 62.4 4.7 0.0001 26.7 1.1 16 44-59 679-694 (698)
102 PLN02294 cytochrome c oxidase 60.9 4.8 0.0001 21.8 0.9 11 14-24 141-151 (174)
103 PRK03824 hypA hydrogenase nick 60.8 3.5 7.5E-05 21.3 0.3 15 13-27 69-83 (135)
104 smart00154 ZnF_AN1 AN1-like Zi 60.0 5.2 0.00011 15.9 0.7 14 42-56 12-25 (39)
105 PF11494 Ta0938: Ta0938; Inte 59.8 4.8 0.0001 19.7 0.7 42 9-56 9-50 (105)
106 PF09963 DUF2197: Uncharacteri 58.3 5.2 0.00011 17.5 0.6 37 15-52 3-40 (56)
107 COG3091 SprT Zn-dependent meta 57.7 5.5 0.00012 21.2 0.8 34 13-52 116-149 (156)
108 KOG2785|consensus 57.3 23 0.00049 22.0 3.2 51 13-64 165-241 (390)
109 COG3364 Zn-ribbon containing p 56.3 8.1 0.00018 19.1 1.1 16 13-28 1-16 (112)
110 TIGR00100 hypA hydrogenase nic 56.2 6.5 0.00014 19.7 0.9 12 14-25 70-81 (115)
111 cd00730 rubredoxin Rubredoxin; 56.2 5 0.00011 17.0 0.4 13 15-27 2-14 (50)
112 KOG2071|consensus 55.5 10 0.00022 24.7 1.7 28 12-39 416-443 (579)
113 PRK12380 hydrogenase nickel in 55.2 8 0.00017 19.3 1.1 11 14-24 70-80 (113)
114 PF00301 Rubredoxin: Rubredoxi 54.9 6.1 0.00013 16.5 0.6 36 15-51 2-42 (47)
115 KOG2907|consensus 54.0 4.8 0.00011 20.2 0.2 40 14-55 74-114 (116)
116 PF09845 DUF2072: Zn-ribbon co 53.9 7.2 0.00016 20.2 0.8 15 14-28 1-15 (131)
117 PF13451 zf-trcl: Probable zin 53.2 7.6 0.00016 16.5 0.7 14 13-26 3-16 (49)
118 PF12907 zf-met2: Zinc-binding 52.2 3.7 8.1E-05 16.6 -0.3 7 16-22 3-9 (40)
119 PF01286 XPA_N: XPA protein N- 51.9 6.5 0.00014 15.3 0.4 13 45-57 5-17 (34)
120 KOG0717|consensus 51.8 9.9 0.00021 24.1 1.3 21 44-64 293-313 (508)
121 PF07282 OrfB_Zn_ribbon: Putat 51.4 14 0.00031 16.3 1.5 13 44-56 47-59 (69)
122 PF10537 WAC_Acf1_DNA_bd: ATP- 50.5 32 0.00069 17.0 3.2 38 13-52 2-39 (102)
123 PF13824 zf-Mss51: Zinc-finger 50.5 16 0.00034 16.0 1.5 8 44-51 15-22 (55)
124 COG4391 Uncharacterized protei 50.4 4.6 0.0001 18.0 -0.2 45 5-54 15-59 (62)
125 PRK14890 putative Zn-ribbon RN 50.3 21 0.00045 15.8 1.8 9 44-52 26-34 (59)
126 COG2331 Uncharacterized protei 50.1 7.7 0.00017 18.1 0.5 33 14-54 12-44 (82)
127 KOG2482|consensus 50.0 23 0.0005 21.7 2.5 23 44-66 196-218 (423)
128 PF15269 zf-C2H2_7: Zinc-finge 50.0 17 0.00036 15.2 1.4 21 44-64 21-41 (54)
129 COG4957 Predicted transcriptio 49.8 16 0.00035 19.1 1.7 25 15-42 77-101 (148)
130 PRK14138 NAD-dependent deacety 48.3 37 0.00081 19.4 3.1 39 8-51 113-151 (244)
131 PF02176 zf-TRAF: TRAF-type zi 48.1 6.7 0.00014 16.8 0.2 43 13-56 8-55 (60)
132 KOG2231|consensus 47.6 20 0.00043 23.9 2.2 19 17-35 185-203 (669)
133 PF01428 zf-AN1: AN1-like Zinc 47.1 9.4 0.0002 15.4 0.5 14 13-26 12-25 (43)
134 PF01927 Mut7-C: Mut7-C RNAse 47.0 17 0.00038 19.0 1.6 19 44-62 125-143 (147)
135 COG1571 Predicted DNA-binding 46.9 17 0.00037 22.8 1.7 30 16-57 352-381 (421)
136 PRK05452 anaerobic nitric oxid 46.6 5.9 0.00013 25.0 -0.2 17 11-27 422-438 (479)
137 KOG1842|consensus 46.6 14 0.00031 23.4 1.3 23 14-36 15-37 (505)
138 PF04423 Rad50_zn_hook: Rad50 46.3 8 0.00017 16.4 0.2 13 44-56 21-33 (54)
139 PRK00564 hypA hydrogenase nick 45.8 12 0.00025 18.9 0.8 11 14-24 71-81 (117)
140 PF14353 CpXC: CpXC protein 45.7 10 0.00023 19.1 0.7 21 37-57 32-52 (128)
141 PF01215 COX5B: Cytochrome c o 45.6 5.9 0.00013 20.7 -0.2 20 6-26 105-124 (136)
142 TIGR00627 tfb4 transcription f 45.0 23 0.00051 20.9 2.0 10 15-24 256-265 (279)
143 KOG0782|consensus 44.9 7 0.00015 25.6 -0.1 12 44-55 254-265 (1004)
144 PF03604 DNA_RNApol_7kD: DNA d 44.4 11 0.00025 14.3 0.5 11 44-54 1-11 (32)
145 PF04780 DUF629: Protein of un 44.3 24 0.00053 22.5 2.1 25 44-68 58-82 (466)
146 PF15135 UPF0515: Uncharacteri 44.2 12 0.00026 21.7 0.8 12 44-55 156-167 (278)
147 COG3677 Transposase and inacti 44.0 14 0.0003 19.1 0.9 15 40-55 51-65 (129)
148 PRK11032 hypothetical protein; 44.0 19 0.00041 19.4 1.4 28 13-51 123-150 (160)
149 KOG2636|consensus 43.8 23 0.0005 22.5 1.9 28 8-35 395-423 (497)
150 PF08274 PhnA_Zn_Ribbon: PhnA 43.7 9.1 0.0002 14.4 0.2 9 44-52 20-28 (30)
151 PF10071 DUF2310: Zn-ribbon-co 43.6 11 0.00023 22.0 0.5 31 12-50 218-248 (258)
152 PLN03238 probable histone acet 43.5 35 0.00076 20.3 2.5 22 44-65 49-70 (290)
153 KOG4727|consensus 43.5 16 0.00035 20.0 1.1 22 14-35 75-96 (193)
154 PRK04351 hypothetical protein; 43.0 11 0.00023 20.0 0.4 32 14-54 112-143 (149)
155 KOG3362|consensus 41.8 6.8 0.00015 20.7 -0.4 7 15-21 119-125 (156)
156 PF10276 zf-CHCC: Zinc-finger 40.4 17 0.00038 14.6 0.8 11 14-24 29-39 (40)
157 PF11931 DUF3449: Domain of un 40.3 9.4 0.0002 21.2 0.0 20 44-63 102-122 (196)
158 PRK09678 DNA-binding transcrip 40.0 7.5 0.00016 17.9 -0.3 41 15-58 2-44 (72)
159 PF06397 Desulfoferrod_N: Desu 39.9 15 0.00031 14.5 0.5 11 13-23 5-15 (36)
160 COG4338 Uncharacterized protei 39.7 13 0.00028 15.8 0.3 15 45-59 14-28 (54)
161 cd01413 SIR2_Af2 SIR2_Af2: Arc 39.0 53 0.0011 18.5 2.8 38 8-51 107-144 (222)
162 cd00065 FYVE FYVE domain; Zinc 38.8 33 0.00071 14.4 1.6 13 44-56 19-31 (57)
163 smart00440 ZnF_C2C2 C2C2 Zinc 38.6 17 0.00037 14.5 0.6 11 44-54 29-39 (40)
164 COG1326 Uncharacterized archae 37.5 42 0.00092 18.8 2.2 36 13-54 5-41 (201)
165 PF05290 Baculo_IE-1: Baculovi 37.3 39 0.00084 17.8 1.9 19 12-30 78-96 (140)
166 PLN02748 tRNA dimethylallyltra 37.0 32 0.0007 22.0 1.9 24 13-36 417-441 (468)
167 KOG0227|consensus 36.9 24 0.00052 19.7 1.2 27 6-34 47-73 (222)
168 smart00731 SprT SprT homologue 36.7 13 0.00029 19.3 0.2 32 14-53 112-143 (146)
169 PF10263 SprT-like: SprT-like 36.1 11 0.00024 19.6 -0.1 10 44-53 144-153 (157)
170 PRK03681 hypA hydrogenase nick 35.8 27 0.00058 17.5 1.2 11 14-24 70-80 (114)
171 PTZ00448 hypothetical protein; 35.5 35 0.00075 21.1 1.8 22 44-65 315-336 (373)
172 PF01096 TFIIS_C: Transcriptio 35.4 12 0.00027 14.8 -0.0 10 44-53 29-38 (39)
173 COG1675 TFA1 Transcription ini 35.2 48 0.001 18.2 2.1 33 11-53 110-142 (176)
174 cd01407 SIR2-fam SIR2 family o 34.4 86 0.0019 17.5 3.2 40 8-52 103-142 (218)
175 smart00064 FYVE Protein presen 34.1 36 0.00078 14.9 1.4 29 15-56 11-39 (68)
176 COG0675 Transposase and inacti 33.9 27 0.0006 20.4 1.2 14 44-57 323-336 (364)
177 KOG2857|consensus 33.6 22 0.00047 18.8 0.7 23 13-35 16-38 (157)
178 PF06524 NOA36: NOA36 protein; 33.5 46 0.001 19.7 2.0 13 10-22 138-150 (314)
179 COG5188 PRP9 Splicing factor 3 32.7 35 0.00076 21.1 1.5 28 8-35 368-396 (470)
180 TIGR01206 lysW lysine biosynth 32.4 23 0.0005 15.3 0.6 12 44-55 3-14 (54)
181 PRK10220 hypothetical protein; 32.1 31 0.00068 17.4 1.1 13 44-56 21-33 (111)
182 TIGR00244 transcriptional regu 32.0 23 0.00049 18.9 0.6 13 44-56 29-41 (147)
183 PF03811 Zn_Tnp_IS1: InsA N-te 31.9 41 0.00088 13.2 1.2 11 10-20 25-35 (36)
184 TIGR00686 phnA alkylphosphonat 31.9 27 0.00059 17.5 0.8 13 44-56 20-32 (109)
185 PHA02998 RNA polymerase subuni 31.7 4.6 0.0001 22.1 -1.9 13 44-56 172-184 (195)
186 PF14311 DUF4379: Domain of un 30.9 53 0.0011 13.9 1.8 12 44-55 29-40 (55)
187 PTZ00064 histone acetyltransfe 30.9 50 0.0011 21.5 2.0 22 44-65 281-302 (552)
188 COG0846 SIR2 NAD-dependent pro 30.8 43 0.00092 19.5 1.6 38 9-51 117-154 (250)
189 TIGR00622 ssl1 transcription f 29.9 44 0.00096 16.9 1.4 49 16-67 57-105 (112)
190 PLN00104 MYST -like histone ac 29.8 46 0.00099 21.2 1.7 21 44-64 199-219 (450)
191 KOG1280|consensus 29.8 65 0.0014 19.9 2.2 39 12-50 77-116 (381)
192 PF07975 C1_4: TFIIH C1-like d 29.4 8 0.00017 16.6 -1.1 23 12-34 19-41 (51)
193 PRK05978 hypothetical protein; 28.4 24 0.00052 18.8 0.3 10 45-54 54-63 (148)
194 PRK00481 NAD-dependent deacety 28.4 83 0.0018 18.0 2.5 35 8-51 116-150 (242)
195 KOG1984|consensus 27.8 19 0.00041 24.9 -0.1 54 10-71 334-387 (1007)
196 KOG3014|consensus 27.6 74 0.0016 18.7 2.2 25 14-38 37-63 (257)
197 TIGR03831 YgiT_finger YgiT-typ 27.5 30 0.00064 13.6 0.5 11 15-25 33-43 (46)
198 COG5151 SSL1 RNA polymerase II 27.2 26 0.00057 21.2 0.4 24 44-67 389-412 (421)
199 PRK00762 hypA hydrogenase nick 26.7 28 0.0006 17.8 0.4 12 14-26 70-81 (124)
200 cd00974 DSRD Desulforedoxin (D 26.7 33 0.00071 12.9 0.5 10 44-53 5-14 (34)
201 COG5246 PRP11 Splicing factor 26.5 66 0.0014 18.0 1.8 28 6-35 47-74 (222)
202 PF14369 zf-RING_3: zinc-finge 26.4 36 0.00078 13.2 0.6 10 45-54 23-32 (35)
203 COG5027 SAS2 Histone acetyltra 26.2 40 0.00086 20.8 1.0 25 44-68 159-183 (395)
204 COG1327 Predicted transcriptio 26.2 32 0.00069 18.5 0.5 13 44-56 29-41 (156)
205 PRK12722 transcriptional activ 25.9 51 0.0011 18.3 1.3 7 44-50 155-161 (187)
206 PTZ00043 cytochrome c oxidase 25.8 40 0.00086 19.5 0.9 16 12-27 179-194 (268)
207 PRK08222 hydrogenase 4 subunit 25.8 60 0.0013 17.7 1.6 18 44-61 115-132 (181)
208 PF03107 C1_2: C1 domain; Int 25.1 47 0.001 12.1 0.8 8 45-52 2-9 (30)
209 KOG2747|consensus 24.9 48 0.001 20.8 1.2 25 44-68 159-183 (396)
210 PF13240 zinc_ribbon_2: zinc-r 24.6 35 0.00077 11.7 0.4 6 46-51 16-21 (23)
211 KOG1994|consensus 24.6 55 0.0012 19.0 1.3 21 14-34 239-259 (268)
212 PRK00420 hypothetical protein; 24.6 40 0.00087 17.0 0.7 27 15-53 24-50 (112)
213 cd00296 SIR2 SIR2 superfamily 24.4 1.2E+02 0.0026 16.8 2.7 19 8-26 107-125 (222)
214 PRK12860 transcriptional activ 24.4 53 0.0011 18.3 1.2 9 16-24 136-144 (189)
215 PLN03239 histone acetyltransfe 24.4 54 0.0012 20.2 1.3 21 44-64 107-127 (351)
216 KOG2932|consensus 24.3 1.5E+02 0.0032 18.3 3.0 25 44-68 145-172 (389)
217 PF11672 DUF3268: Protein of u 24.3 25 0.00053 17.5 -0.0 10 13-22 1-10 (102)
218 PF14787 zf-CCHC_5: GAG-polypr 24.0 44 0.00096 13.2 0.6 14 45-58 4-17 (36)
219 TIGR00319 desulf_FeS4 desulfof 23.8 45 0.00097 12.5 0.7 12 13-24 6-17 (34)
220 PRK01343 zinc-binding protein; 23.8 52 0.0011 14.5 0.9 11 44-54 10-20 (57)
221 TIGR03830 CxxCG_CxxCG_HTH puta 23.7 96 0.0021 15.4 2.0 22 14-35 31-52 (127)
222 smart00132 LIM Zinc-binding do 23.5 41 0.00089 12.3 0.6 10 44-53 28-37 (39)
223 PF11789 zf-Nse: Zinc-finger o 23.4 61 0.0013 14.1 1.1 11 47-57 28-38 (57)
224 PF05766 NinG: Bacteriophage L 23.3 24 0.00052 19.6 -0.2 14 13-26 5-18 (189)
225 COG4847 Uncharacterized protei 22.4 41 0.0009 16.5 0.5 12 11-22 3-14 (103)
226 PF08271 TF_Zn_Ribbon: TFIIB z 22.4 48 0.001 13.2 0.7 7 45-51 2-8 (43)
227 KOG4118|consensus 22.3 53 0.0011 14.9 0.8 24 44-67 39-62 (74)
228 PF08792 A2L_zn_ribbon: A2L zi 22.2 41 0.00089 12.8 0.4 11 44-54 22-32 (33)
229 PRK12387 formate hydrogenlyase 21.6 74 0.0016 17.3 1.4 19 13-31 113-131 (180)
230 PF13248 zf-ribbon_3: zinc-rib 21.1 36 0.00078 12.0 0.1 6 46-51 19-24 (26)
231 PF13821 DUF4187: Domain of un 21.0 63 0.0014 14.0 0.9 18 15-32 28-45 (55)
232 PRK06260 threonine synthase; V 20.9 80 0.0017 19.5 1.6 10 15-24 4-13 (397)
233 PF06353 DUF1062: Protein of u 20.5 51 0.0011 17.4 0.7 10 15-24 14-23 (142)
234 KOG0801|consensus 20.4 63 0.0014 17.7 1.0 17 4-23 131-147 (205)
235 COG1656 Uncharacterized conser 20.1 1.3E+02 0.0029 16.5 2.1 20 44-63 131-150 (165)
No 1
>KOG2462|consensus
Probab=99.85 E-value=5.9e-22 Score=107.85 Aligned_cols=70 Identities=20% Similarity=0.379 Sum_probs=57.9
Q ss_pred ccccccCCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhccCCCCCC
Q psy4268 2 LGYYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGEDGAL 74 (86)
Q Consensus 2 l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~~ 74 (86)
|++|+++|+ -++.|.+||+.|+..|.|+.|+|+|+|++| |.|..|++.|..+++|..|+++|.+.|+..+
T Consensus 177 LkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP-F~C~hC~kAFADRSNLRAHmQTHS~~K~~qC 246 (279)
T KOG2462|consen 177 LKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKP-FSCPHCGKAFADRSNLRAHMQTHSDVKKHQC 246 (279)
T ss_pred HhhHhhccC--CCcccccccccccchHHhhcccccccCCCC-ccCCcccchhcchHHHHHHHHhhcCCccccC
Confidence 567777776 578888888888888888888888888888 8888888888888888888888888886544
No 2
>KOG2462|consensus
Probab=99.83 E-value=3e-21 Score=105.14 Aligned_cols=64 Identities=25% Similarity=0.485 Sum_probs=61.1
Q ss_pred CccccccCCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHH
Q psy4268 1 MLGYYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 1 ~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
+|+.|+++|+|||||.|..|+++|..+++|..|+++|.+.++ |.|..|+|.|...+.|.+|...
T Consensus 202 LLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 202 LLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred HhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhHHHHHHHHHHhhhh
Confidence 589999999999999999999999999999999999999999 9999999999999999999743
No 3
>KOG3576|consensus
Probab=99.62 E-value=3.1e-17 Score=86.66 Aligned_cols=69 Identities=33% Similarity=0.577 Sum_probs=65.0
Q ss_pred CccccccCCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhccCC
Q psy4268 1 MLGYYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGE 70 (86)
Q Consensus 1 ~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~ 70 (86)
||.+|++-|+..+.+.|..||++|....+|.+|.++|+|..| |+|..|++.|.+..+|..|.+..+|..
T Consensus 132 mlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsleshl~kvhgv~ 200 (267)
T KOG3576|consen 132 MLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLESHLKKVHGVQ 200 (267)
T ss_pred HHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHHHHHHHcCch
Confidence 688999999999999999999999999999999999999999 999999999999999999998777654
No 4
>KOG3623|consensus
Probab=99.49 E-value=5.1e-15 Score=89.91 Aligned_cols=61 Identities=25% Similarity=0.523 Sum_probs=53.7
Q ss_pred ccccccCCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHH
Q psy4268 2 LGYYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHY 63 (86)
Q Consensus 2 l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~ 63 (86)
|.+|.=-|+|.+||.|.+|.++|..+..|..|.|.|.|++| |.|..|+|.|..+-+...||
T Consensus 910 LaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 910 LARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred HHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchHhhh
Confidence 45676678999999999999999999999999999999999 99999999999888888887
No 5
>KOG1074|consensus
Probab=99.42 E-value=1.2e-14 Score=89.09 Aligned_cols=68 Identities=25% Similarity=0.583 Sum_probs=60.5
Q ss_pred ccccccCCCCCCceecccccccccChHHHHHHHHHhhCC----CCCccCC---CCccccCChhHHHHHHHHhccCC
Q psy4268 2 LGYYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGK----LPAFPCT---LCSYATKRKTSLASHYYRKHVGE 70 (86)
Q Consensus 2 l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~----~~~~~c~---~c~~~f~~~~~l~~h~~~~~~~~ 70 (86)
|++|.++|+||+||+|++|+++|..+.+|..|+.+|... .. +.|. +|.+.|...-.|+.|++.|.++.
T Consensus 621 LqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q-~ScP~~~ic~~kftn~V~lpQhIriH~~~~ 695 (958)
T KOG1074|consen 621 LQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQ-FSCPSTFICQKKFTNAVTLPQHIRIHLGGQ 695 (958)
T ss_pred hhhhhhcccCcCccccccccchhccccchhhcccccccCcccccc-ccCCchhhhcccccccccccceEEeecCCC
Confidence 789999999999999999999999999999999888764 34 6788 89999999999999998888543
No 6
>KOG3623|consensus
Probab=99.28 E-value=1.3e-12 Score=79.88 Aligned_cols=65 Identities=29% Similarity=0.547 Sum_probs=60.5
Q ss_pred CCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhccCCCCCCC
Q psy4268 10 SGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGEDGALP 75 (86)
Q Consensus 10 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~~~ 75 (86)
+.+..|.|..|.+.|-..+.|.+|.--|+|.+| |.|.+|.|.|.....|..|.|+|.|+|++.+.
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRP-yqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCd 954 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRP-YQCIICKKAFKHKHHLTEHKRLHSGEKPFQCD 954 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCC-cccchhhHhhhhhhhhhhhhhhccCCCcchhh
Confidence 345689999999999999999999988999999 99999999999999999999999999998763
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.25 E-value=4e-12 Score=54.56 Aligned_cols=42 Identities=21% Similarity=0.428 Sum_probs=37.8
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHH
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSL 59 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l 59 (86)
|.|..||+.|+....|..|++.|. ++ ++|..|++.|.+.+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceeccccee
Confidence 789999999999999999999988 56 9999999999877654
No 8
>PHA00733 hypothetical protein
Probab=99.25 E-value=2.3e-11 Score=61.27 Aligned_cols=61 Identities=25% Similarity=0.500 Sum_probs=50.9
Q ss_pred ccccCCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhcc
Q psy4268 4 YYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 4 ~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
.|+..+ +.++|.|..|++.|.....|..|++.+ ..+ |.|..|++.|.....|..|+...|+
T Consensus 64 ~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 64 KLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred hhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCccCCHHHHHHHHHHhcC
Confidence 344444 588999999999999999999999865 346 8999999999999999999876654
No 9
>KOG3576|consensus
Probab=99.10 E-value=2.5e-11 Score=64.67 Aligned_cols=66 Identities=17% Similarity=0.311 Sum_probs=59.6
Q ss_pred CCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhccCCCCCCCC
Q psy4268 10 SGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGEDGALPP 76 (86)
Q Consensus 10 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~ 76 (86)
++...+.|.+|++.|.....|.+|++.|...+. +-|..||+.|..-..|.+|.++|+|.+++.+..
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr-~lct~cgkgfndtfdlkrh~rthtgvrpykc~~ 178 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKR-HLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSL 178 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHH-HHHhhccCcccchhhhhhhhccccCccccchhh
Confidence 445669999999999999999999999988888 899999999999999999999999999987643
No 10
>KOG1074|consensus
Probab=99.06 E-value=1.5e-10 Score=71.81 Aligned_cols=59 Identities=24% Similarity=0.473 Sum_probs=54.7
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhccCCCCCC
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGEDGAL 74 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~~ 74 (86)
..|.+|++.|.....|+.|+++|++.++ |.|..|++.|....+|+.|+.+|....+...
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KP-F~C~fC~~aFttrgnLKvHMgtH~w~q~~sr 938 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKP-FFCHFCEEAFTTRGNLKVHMGTHMWVQPPSR 938 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCC-ccchhhhhhhhhhhhhhhhhccccccCCCcc
Confidence 7899999999999999999999999999 9999999999999999999998887665444
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=98.97 E-value=3.5e-11 Score=44.66 Aligned_cols=23 Identities=30% Similarity=0.785 Sum_probs=11.6
Q ss_pred HHHHHHhhCCCCCccCCCCccccC
Q psy4268 31 KRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 31 ~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
..|+++|+++++ |.|..|++.|.
T Consensus 3 ~~H~~~H~~~k~-~~C~~C~k~F~ 25 (26)
T PF13465_consen 3 RRHMRTHTGEKP-YKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHSSSSS-EEESSSSEEES
T ss_pred HHHhhhcCCCCC-CCCCCCcCeeC
Confidence 345555555555 55555555443
No 12
>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=98.96 E-value=7.4e-10 Score=41.05 Aligned_cols=24 Identities=33% Similarity=0.717 Sum_probs=22.1
Q ss_pred ccccccCCCCCCceeccccccccc
Q psy4268 2 LGYYFSAPSGEKRYLCDSCDRTYS 25 (86)
Q Consensus 2 l~~h~~~h~~~~~~~c~~c~~~~~ 25 (86)
|.+|++.|+|++||.|..|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 578999999999999999999985
No 13
>KOG3993|consensus
Probab=98.81 E-value=1.4e-09 Score=63.33 Aligned_cols=70 Identities=21% Similarity=0.416 Sum_probs=56.5
Q ss_pred CccccccCCCCCCceecccccccccChHHHHHHHHHhhCCC--------C------------------------CccCCC
Q psy4268 1 MLGYYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKL--------P------------------------AFPCTL 48 (86)
Q Consensus 1 ~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~--------~------------------------~~~c~~ 48 (86)
||..|+........|.|..|++.|+...||..|.++|.... + .|.|..
T Consensus 282 ~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~ 361 (500)
T KOG3993|consen 282 ALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHT 361 (500)
T ss_pred HHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHH
Confidence 45667666666678999999999999999999999875321 1 167999
Q ss_pred CccccCChhHHHHHHHHhccCC
Q psy4268 49 CSYATKRKTSLASHYYRKHVGE 70 (86)
Q Consensus 49 c~~~f~~~~~l~~h~~~~~~~~ 70 (86)
|+++|.+...|.+|+..|+...
T Consensus 362 C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 362 CGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hhhhhHHHHHHHHhHHhhhccc
Confidence 9999999999999987777543
No 14
>PHA00616 hypothetical protein
Probab=98.68 E-value=1.2e-08 Score=41.93 Aligned_cols=33 Identities=12% Similarity=0.290 Sum_probs=19.9
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCC
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCT 47 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~ 47 (86)
||.|..||+.|...+.+..|++.+++.++ +.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-ccee
Confidence 35566666666666666666666666655 5544
No 15
>PHA00616 hypothetical protein
Probab=98.63 E-value=2.5e-08 Score=41.04 Aligned_cols=31 Identities=19% Similarity=0.398 Sum_probs=28.4
Q ss_pred ccCCCCccccCChhHHHHHHHHhccCCCCCC
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKHVGEDGAL 74 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~~ 74 (86)
|.|..||+.|.....+..|++.++++++...
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 8999999999999999999999999987544
No 16
>PHA00732 hypothetical protein
Probab=98.58 E-value=4.5e-08 Score=45.48 Aligned_cols=43 Identities=26% Similarity=0.524 Sum_probs=35.9
Q ss_pred ceecccccccccChHHHHHHHHH-hhCCCCCccCCCCccccCChhHHHHHH
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNY-ECGKLPAFPCTLCSYATKRKTSLASHY 63 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~ 63 (86)
||.|..|++.|.....|..|++. |. + +.|..|++.|.+ +..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~~---l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYRR---LNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeCC---hhhhh
Confidence 57899999999999999999974 43 4 789999999983 56665
No 17
>KOG3608|consensus
Probab=98.52 E-value=1.5e-08 Score=58.19 Aligned_cols=66 Identities=24% Similarity=0.368 Sum_probs=48.1
Q ss_pred ccccccCCCCCCceecccccccccChHHHHHHHHH--hhCCCCCccCCCCccccCChhHHHHHHHHhcc
Q psy4268 2 LGYYFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNY--ECGKLPAFPCTLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 2 l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~--~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
|..|++.|+++|-..|..||.-|.....|-.|.+- .....+ |.|..|.|.|.....|..|+..|..
T Consensus 195 LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~-fqC~~C~KrFaTeklL~~Hv~rHvn 262 (467)
T KOG3608|consen 195 LREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNS-FQCAQCFKRFATEKLLKSHVVRHVN 262 (467)
T ss_pred HHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCc-hHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 66788999999998888888888888888877753 223345 7777777777776666666655543
No 18
>KOG3608|consensus
Probab=98.49 E-value=1.3e-07 Score=54.46 Aligned_cols=64 Identities=27% Similarity=0.577 Sum_probs=47.5
Q ss_pred cccccc-CCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCC--CccccCChhHHHHHHHHhc
Q psy4268 2 LGYYFS-APSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTL--CSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 2 l~~h~~-~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~--c~~~f~~~~~l~~h~~~~~ 67 (86)
|..|++ .|+..||++|..|.+.+...+.|..|..+|. ... |.|.. |..+|.+...+.+|++.++
T Consensus 279 L~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~-y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 279 LTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTV-YQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred HHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccc-eecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 345655 5777888888888888888888888888776 333 77765 7777777777777776666
No 19
>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=98.35 E-value=4.6e-07 Score=32.32 Aligned_cols=22 Identities=27% Similarity=0.685 Sum_probs=12.6
Q ss_pred ccCCCCccccCChhHHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
|.|..|++.|.....|..|++.
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 3455566666666666666544
No 20
>PHA02768 hypothetical protein; Provisional
Probab=98.29 E-value=1.3e-06 Score=37.68 Aligned_cols=24 Identities=17% Similarity=0.602 Sum_probs=23.4
Q ss_pred ccCCCCccccCChhHHHHHHHHhc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
|.|..||+.|.+..+|..|++.|+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC
Confidence 899999999999999999999998
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=98.23 E-value=1.6e-06 Score=30.89 Aligned_cols=23 Identities=43% Similarity=0.950 Sum_probs=21.0
Q ss_pred eecccccccccChHHHHHHHHHh
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYE 37 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~ 37 (86)
|.|..|++.|.....|..|++.|
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 68999999999999999999864
No 22
>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=98.22 E-value=5.9e-06 Score=35.71 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=38.4
Q ss_pred ceecccccccccChHHHHHHHHH-hhCC-CCCccCCCCccccCChhHHHHHHHHhcc
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNY-ECGK-LPAFPCTLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~-~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
.|.|..|++ ......|..|... |... +. +.|+.|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~-v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKN-VVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCC-ccCCCchhhhh--hHHHHHHHHhcC
Confidence 478999999 5667889999775 5544 45 89999987655 378889877653
No 23
>PHA00733 hypothetical protein
Probab=98.17 E-value=1.4e-06 Score=44.02 Aligned_cols=55 Identities=20% Similarity=0.251 Sum_probs=42.3
Q ss_pred CCCceecccccccccChHHHHHHH--H---HhhCCCCCccCCCCccccCChhHHHHHHHHh
Q psy4268 11 GEKRYLCDSCDRTYSNRSSLKRHM--N---YECGKLPAFPCTLCSYATKRKTSLASHYYRK 66 (86)
Q Consensus 11 ~~~~~~c~~c~~~~~~~~~l~~h~--~---~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 66 (86)
..+++.|.+|...|.....+..+. . .+.+..+ |.|..|++.|.....|..|++.+
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP-y~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP-YVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCC-ccCCCCCCcCCCHHHHHHHHhcC
Confidence 467899999988777766666551 1 2234567 99999999999999999998754
No 24
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.12 E-value=3.6e-06 Score=29.97 Aligned_cols=23 Identities=26% Similarity=0.657 Sum_probs=12.4
Q ss_pred ccCCCCccccCChhHHHHHHHHh
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRK 66 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~ 66 (86)
|.|..|++.|.....|..|+..+
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 34566666666666666665544
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.05 E-value=4.5e-06 Score=51.21 Aligned_cols=38 Identities=16% Similarity=0.479 Sum_probs=16.4
Q ss_pred CceecccccccccChHHHHHHHHHhhCCCCCccCCCCcccc
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYAT 53 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 53 (86)
+++.|. |++.+ ....|..|...+.+.++ +.|..|++.|
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCcc
Confidence 344444 44322 33444444444444444 4444444444
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.02 E-value=8.4e-06 Score=50.05 Aligned_cols=63 Identities=17% Similarity=0.335 Sum_probs=49.9
Q ss_pred ccccccCCCCCCceeccccccccc----------ChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhc
Q psy4268 2 LGYYFSAPSGEKRYLCDSCDRTYS----------NRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 2 l~~h~~~h~~~~~~~c~~c~~~~~----------~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
|..|+..|.+.+++.|..|+..+. ....|..|... .|.++ +.|..|++.+.... +..|+-..|
T Consensus 492 L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt-~~C~~Cgk~Vrlrd-m~~H~~~~h 564 (567)
T PLN03086 492 MVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRT-APCDSCGRSVMLKE-MDIHQIAVH 564 (567)
T ss_pred HHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh-cCCcc-eEccccCCeeeehh-HHHHHHHhh
Confidence 456888899999999999998884 23578899887 48888 99999999887764 677765444
No 27
>KOG3993|consensus
Probab=98.01 E-value=6e-07 Score=52.80 Aligned_cols=59 Identities=22% Similarity=0.430 Sum_probs=49.8
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhccCCCCC
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGEDGA 73 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~ 73 (86)
.|.|..|...|.....|.+|.-.-..... |+|..|+|.|.-..+|..|++.|--+....
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vE-YrCPEC~KVFsCPANLASHRRWHKPR~eaa 325 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVE-YRCPECDKVFSCPANLASHRRWHKPRPEAA 325 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEee-ecCCcccccccCchhhhhhhcccCCchhhh
Confidence 48999999999999999999755555556 999999999999999999998887654433
No 28
>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=97.97 E-value=5.8e-06 Score=30.54 Aligned_cols=22 Identities=23% Similarity=0.445 Sum_probs=11.7
Q ss_pred ccCCCCccccCChhHHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
|.|..|++.|.....|..|++.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 4555555555555555555433
No 29
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.95 E-value=4.1e-06 Score=30.96 Aligned_cols=25 Identities=36% Similarity=0.878 Sum_probs=22.3
Q ss_pred ceecccccccccChHHHHHHHHHhh
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYEC 38 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~ 38 (86)
+|.|..|++.|.....|..|++.|.
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 5899999999999999999997653
No 30
>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=97.84 E-value=2.7e-05 Score=27.58 Aligned_cols=23 Identities=26% Similarity=0.819 Sum_probs=19.1
Q ss_pred eecccccccccChHHHHHHHHHh
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYE 37 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~ 37 (86)
|.|..|++.|.....|..|+..+
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 68999999999999999999865
No 31
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.84 E-value=2.9e-05 Score=32.85 Aligned_cols=32 Identities=22% Similarity=0.548 Sum_probs=19.5
Q ss_pred CCCCccCCCCccccCChhHHHHHHHHhccCCCC
Q psy4268 40 KLPAFPCTLCSYATKRKTSLASHYYRKHVGEDG 72 (86)
Q Consensus 40 ~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~ 72 (86)
..| -.|+.|+..+.+..+|.+|+...|+.+++
T Consensus 22 ~~P-atCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 22 EQP-ATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp S---EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred CCC-CCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 345 67888888888888888888777777653
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.77 E-value=7.8e-06 Score=46.85 Aligned_cols=51 Identities=31% Similarity=0.617 Sum_probs=41.8
Q ss_pred CCceeccc--ccccccChHHHHHHHHH-hh------------------CCCCCccCCCCccccCChhHHHHHH
Q psy4268 12 EKRYLCDS--CDRTYSNRSSLKRHMNY-EC------------------GKLPAFPCTLCSYATKRKTSLASHY 63 (86)
Q Consensus 12 ~~~~~c~~--c~~~~~~~~~l~~h~~~-~~------------------~~~~~~~c~~c~~~f~~~~~l~~h~ 63 (86)
+|||+|.+ |.+.|...-.|..|+.- |- -.+| |.|..|+|.+.....|..|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP-YrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP-YRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc-eeccccchhhccCccceecc
Confidence 59999998 99999999999988752 20 0167 99999999999988888885
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.64 E-value=8.5e-05 Score=26.60 Aligned_cols=20 Identities=30% Similarity=0.537 Sum_probs=11.4
Q ss_pred cCCCCccccCChhHHHHHHH
Q psy4268 45 PCTLCSYATKRKTSLASHYY 64 (86)
Q Consensus 45 ~c~~c~~~f~~~~~l~~h~~ 64 (86)
.|..|++.|.....+..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 45555556655555555554
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=97.60 E-value=0.0002 Score=30.34 Aligned_cols=34 Identities=24% Similarity=0.442 Sum_probs=24.3
Q ss_pred CCCCCceecccccccccChHHHHHHHHHhhCCCC
Q psy4268 9 PSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLP 42 (86)
Q Consensus 9 h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 42 (86)
+..+.|..|.+|+..+.+..+|.+|+....+.++
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4467899999999999999999999988777665
No 35
>PRK04860 hypothetical protein; Provisional
Probab=97.56 E-value=8.3e-05 Score=39.06 Aligned_cols=39 Identities=23% Similarity=0.525 Sum_probs=32.5
Q ss_pred CceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCCh
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRK 56 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 56 (86)
-+|.|. |+. ....+..|.+++.+.++ |.|..|++.|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEe
Confidence 369997 886 56778899999999999 9999999887644
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.48 E-value=0.00016 Score=25.80 Aligned_cols=24 Identities=33% Similarity=0.826 Sum_probs=21.0
Q ss_pred eecccccccccChHHHHHHHHHhh
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYEC 38 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~ 38 (86)
+.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998654
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.47 E-value=0.00012 Score=35.08 Aligned_cols=24 Identities=29% Similarity=0.689 Sum_probs=20.5
Q ss_pred ccCCCCccccCChhHHHHHHHHhc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
+.|..|++.|.....|..|++.+.
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCccCCCCcCHHHHHHHHcCcc
Confidence 789999999999999999997653
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.32 E-value=0.00022 Score=25.66 Aligned_cols=21 Identities=33% Similarity=1.053 Sum_probs=11.3
Q ss_pred eecccccccccChHHHHHHHH
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~ 35 (86)
|.|.+|+..|.....+..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345555555555555555554
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.20 E-value=0.0005 Score=24.49 Aligned_cols=22 Identities=45% Similarity=0.886 Sum_probs=9.5
Q ss_pred cCCCCccccCChhHHHHHHHHhc
Q psy4268 45 PCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 45 ~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
.|..|..... ...|..|++.++
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHhhC
Confidence 4555554444 445555554443
No 40
>PHA00732 hypothetical protein
Probab=97.16 E-value=0.00062 Score=31.72 Aligned_cols=24 Identities=29% Similarity=0.647 Sum_probs=21.5
Q ss_pred ccCCCCccccCChhHHHHHHHH-hc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR-KH 67 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~-~~ 67 (86)
|.|..|++.|.+...|..|++. |.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC
Confidence 8899999999999999999874 44
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.13 E-value=0.00031 Score=25.24 Aligned_cols=22 Identities=27% Similarity=0.588 Sum_probs=19.5
Q ss_pred ccCCCCccccCChhHHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
|.|..|++.|.....+..|++.
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 5799999999999999999854
No 42
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.59 E-value=0.00063 Score=25.00 Aligned_cols=21 Identities=43% Similarity=1.092 Sum_probs=12.2
Q ss_pred eecccccccccChHHHHHHHH
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~ 35 (86)
|.|..|++.|.....+..|++
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 456666666666666555544
No 43
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.59 E-value=0.0034 Score=22.71 Aligned_cols=20 Identities=25% Similarity=0.574 Sum_probs=13.1
Q ss_pred ccCCCCccccCChhHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYY 64 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~ 64 (86)
..|..||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4677788888 4445777753
No 44
>KOG2893|consensus
Probab=95.78 E-value=0.0022 Score=35.84 Aligned_cols=45 Identities=24% Similarity=0.522 Sum_probs=33.2
Q ss_pred CCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHH
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASH 62 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h 62 (86)
.|+ .|..|+.-|.....|++|++. +- |+|.+|.+..-+-..|..|
T Consensus 9 ~kp-wcwycnrefddekiliqhqka----kh-fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKP-WCWYCNREFDDEKILIQHQKA----KH-FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCc-eeeecccccchhhhhhhhhhh----cc-ceeeeehhhhccCCCceee
Confidence 344 577899999999999999875 34 9999998765544444444
No 45
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.62 E-value=0.016 Score=22.27 Aligned_cols=22 Identities=23% Similarity=0.754 Sum_probs=14.2
Q ss_pred ceecccccccccChHHHHHHHH
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~ 35 (86)
+|.|.+|+..|.....+..|..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777766666666654
No 46
>KOG1146|consensus
Probab=94.96 E-value=0.025 Score=38.61 Aligned_cols=57 Identities=28% Similarity=0.511 Sum_probs=46.1
Q ss_pred CCCCCCceecccccccccChHHHHHHHHHhh-------------------------CCCCCccCCCCccccCChhHHHHH
Q psy4268 8 APSGEKRYLCDSCDRTYSNRSSLKRHMNYEC-------------------------GKLPAFPCTLCSYATKRKTSLASH 62 (86)
Q Consensus 8 ~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~-------------------------~~~~~~~c~~c~~~f~~~~~l~~h 62 (86)
.++..+.+.|..|+..|.....|..|++..+ +.++ |.|..|...+....+|.+|
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p-~~C~~C~~stttng~Lsih 537 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP-YPCRACNYSTTTNGNLSIH 537 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc-ccceeeeeeeecchHHHHH
Confidence 4566688999999999999999999998711 1135 7899999999998889888
Q ss_pred HHH
Q psy4268 63 YYR 65 (86)
Q Consensus 63 ~~~ 65 (86)
+..
T Consensus 538 lqS 540 (1406)
T KOG1146|consen 538 LQS 540 (1406)
T ss_pred HHH
Confidence 743
No 47
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.72 E-value=0.028 Score=21.66 Aligned_cols=24 Identities=29% Similarity=0.960 Sum_probs=16.6
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
|.|.+||..+.... .+ +.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~-~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------AP-WVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CC-CcCcCCCC
Confidence 68888987653322 45 78998874
No 48
>PRK04860 hypothetical protein; Provisional
Probab=94.35 E-value=0.0092 Score=31.53 Aligned_cols=25 Identities=24% Similarity=0.353 Sum_probs=21.4
Q ss_pred ccccccCCCCCCceecccccccccC
Q psy4268 2 LGYYFSAPSGEKRYLCDSCDRTYSN 26 (86)
Q Consensus 2 l~~h~~~h~~~~~~~c~~c~~~~~~ 26 (86)
+.+|.++|.|+++|.|..|+..|..
T Consensus 131 ~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 131 VRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred HHHHHHHhcCCccEECCCCCceeEE
Confidence 4578889999999999999987754
No 49
>KOG2186|consensus
Probab=94.28 E-value=0.033 Score=31.51 Aligned_cols=49 Identities=20% Similarity=0.423 Sum_probs=35.3
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHh
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRK 66 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 66 (86)
-|.|.+||....- ..+..|+..-++ .- |.|..|+..|.. .....|...-
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~-fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AY-FSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-Ce-eEEeeccccccc-chhhhhhhhc
Confidence 3789999976543 556778866555 44 999999999998 4567776433
No 50
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.27 E-value=0.083 Score=25.06 Aligned_cols=25 Identities=28% Similarity=0.757 Sum_probs=21.7
Q ss_pred ceecccccccccChHHHHHHHHHhh
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYEC 38 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~ 38 (86)
.+.|..|++.|.....|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5899999999999999999998753
No 51
>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=94.18 E-value=0.039 Score=27.33 Aligned_cols=30 Identities=27% Similarity=0.650 Sum_probs=23.2
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCCh
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRK 56 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 56 (86)
..|..||..| .-.++.| ..|+.||..|.-.
T Consensus 10 R~Cp~CG~kF-----------YDLnk~P-ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKF-----------YDLNKDP-IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchh-----------ccCCCCC-ccCCCCCCccCcc
Confidence 5899999888 2344567 8899999888766
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.78 E-value=0.015 Score=34.43 Aligned_cols=60 Identities=25% Similarity=0.474 Sum_probs=49.9
Q ss_pred CceecccccccccChHHHHHHHH--HhhCC--CCCccCC--CCccccCChhHHHHHHHHhccCCCCC
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMN--YECGK--LPAFPCT--LCSYATKRKTSLASHYYRKHVGEDGA 73 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~~c~--~c~~~f~~~~~l~~h~~~~~~~~~~~ 73 (86)
.++.|..|...|.....+..|.+ .|.++ ++ +.|. .|++.|.+...+..|...+.+.....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCcccccCCCccc
Confidence 36788889999999999999998 78888 78 8998 79999999998888887777665443
No 53
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.23 E-value=0.12 Score=27.63 Aligned_cols=23 Identities=30% Similarity=0.843 Sum_probs=17.6
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCc
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCS 50 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 50 (86)
-|.|.+||+. +.|..| ..|+.||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P-~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAP-EVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCC-CcCCCCC
Confidence 6899999864 345566 8899998
No 54
>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=91.29 E-value=0.23 Score=26.29 Aligned_cols=36 Identities=14% Similarity=0.444 Sum_probs=26.1
Q ss_pred CCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 9 PSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 9 h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
.....-|.|..|+..|+....+. .. |.|+.||....
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEee
Confidence 34566799999998887766553 24 99999987544
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.11 E-value=0.16 Score=22.03 Aligned_cols=29 Identities=28% Similarity=0.555 Sum_probs=21.5
Q ss_pred CCCCCCceecccccccccChHHHHHHHHH
Q psy4268 8 APSGEKRYLCDSCDRTYSNRSSLKRHMNY 36 (86)
Q Consensus 8 ~h~~~~~~~c~~c~~~~~~~~~l~~h~~~ 36 (86)
...|+.-+.|..|+..|-...++.+|...
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 34577778888888888877777777653
No 56
>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=90.88 E-value=0.21 Score=25.43 Aligned_cols=32 Identities=6% Similarity=0.176 Sum_probs=23.6
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhH
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTS 58 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~ 58 (86)
..|..||..|. -.++.| ..|+.||..|.....
T Consensus 10 r~Cp~cg~kFY-----------DLnk~p-~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 10 RICPNTGSKFY-----------DLNRRP-AVSPYTGEQFPPEEA 41 (129)
T ss_pred ccCCCcCcccc-----------ccCCCC-ccCCCcCCccCcchh
Confidence 58999998882 344556 899999988766533
No 57
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.44 E-value=0.24 Score=26.75 Aligned_cols=34 Identities=15% Similarity=0.552 Sum_probs=25.1
Q ss_pred CCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 11 GEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 11 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
...-|.|..|+..|+....+. .. |.|+.||....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCe
Confidence 456799999998887765542 24 99999997654
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=89.45 E-value=0.32 Score=18.86 Aligned_cols=25 Identities=20% Similarity=0.652 Sum_probs=16.1
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
.|.|..||+.+... ..| ..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p-~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAP-EKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCC-CcCcCCCC
Confidence 47888998654221 134 68888875
No 59
>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=89.17 E-value=0.45 Score=23.40 Aligned_cols=25 Identities=28% Similarity=0.797 Sum_probs=22.0
Q ss_pred ccC----CCCccccCChhHHHHHHHHhcc
Q psy4268 44 FPC----TLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 44 ~~c----~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
|.| ..|+....+...+.+|++..||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8899999999999999988775
No 60
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.77 E-value=0.062 Score=29.77 Aligned_cols=45 Identities=20% Similarity=0.578 Sum_probs=27.7
Q ss_pred CCceecccccccccChHHHHHHHHH---h-------hCCCCC----ccCCCCccccCCh
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHMNY---E-------CGKLPA----FPCTLCSYATKRK 56 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~~~---~-------~~~~~~----~~c~~c~~~f~~~ 56 (86)
++...|.+|+..|..........+. . .+..|. ..|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3568999999998877554444332 0 111110 3699999876643
No 61
>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=88.73 E-value=0.51 Score=26.35 Aligned_cols=30 Identities=13% Similarity=0.482 Sum_probs=22.4
Q ss_pred CCCceecccccccccChHHHHHHHHHhhCC
Q psy4268 11 GEKRYLCDSCDRTYSNRSSLKRHMNYECGK 40 (86)
Q Consensus 11 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 40 (86)
.+..|.|..|++.|.....+..|+...+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 455699999999999999999999865443
No 62
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.65 E-value=0.32 Score=25.35 Aligned_cols=39 Identities=18% Similarity=0.424 Sum_probs=24.8
Q ss_pred CCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 11 GEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 11 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
+..-|.|..|+..|.....+... . .... |.|+.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~---d-~~~~-f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLL---D-MDGT-FTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhc---C-CCCc-EECCCCCCEEE
Confidence 45578999999888754432211 1 1233 89999987654
No 63
>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=88.33 E-value=0.36 Score=24.86 Aligned_cols=24 Identities=21% Similarity=0.225 Sum_probs=14.8
Q ss_pred ccCCCCccccCChhHHHHHHHHhccCC
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKHVGE 70 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~~~~ 70 (86)
..|..||+.|... .+|...|+|-.
T Consensus 73 i~clecGk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S-
T ss_pred eEEccCCcccchH---HHHHHHccCCC
Confidence 5799999988765 78888886654
No 64
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.60 E-value=0.73 Score=18.07 Aligned_cols=33 Identities=15% Similarity=0.340 Sum_probs=20.2
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCcccc
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYAT 53 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 53 (86)
..|..|+..|...... +-..... ..|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~-v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRK-VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcE-EECCCCCCEe
Confidence 4678888777655432 2122234 6888888766
No 65
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=86.55 E-value=0.6 Score=18.26 Aligned_cols=34 Identities=15% Similarity=0.298 Sum_probs=20.2
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
+.|..|+..|...... ....... ..|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~-----~~~~~~~-v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ-----LGANGGK-VRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHH-----cCCCCCE-EECCCCCCEEE
Confidence 5788888777554432 1111223 68888887663
No 66
>KOG1146|consensus
Probab=86.02 E-value=0.76 Score=32.15 Aligned_cols=59 Identities=20% Similarity=0.431 Sum_probs=45.3
Q ss_pred CCceecccccccccChHHHHHHHHHhh-----------------CCCCCccCCCCccccCChhHHHHHHHHhccCCCC
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHMNYEC-----------------GKLPAFPCTLCSYATKRKTSLASHYYRKHVGEDG 72 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~~~~~-----------------~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~ 72 (86)
..+|.|.+|...|.....+..|.+... .... | |..|...|.....|+.|++.-+++...
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~-~-c~~c~~~~~~~~alqihm~~~~~~~kt 1357 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTY-H-CLACEVLLSGREALQIHMRSSAHRRKT 1357 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCccccc-c-chHHHhhcchhHHHHHHHHHhhhcccC
Confidence 457999999999999999988875211 1123 5 888999999999999999876665543
No 67
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=85.99 E-value=0.52 Score=26.32 Aligned_cols=26 Identities=27% Similarity=0.539 Sum_probs=19.5
Q ss_pred ccCCCCccccCChhHHHHHHHHhccC
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKHVG 69 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~~~ 69 (86)
|.|..|+|.|.-..-..+|+..-|.+
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred ECCCCCCcccCChHHHHHHHhhcCHH
Confidence 78999999999998889998766544
No 68
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.79 E-value=0.87 Score=17.91 Aligned_cols=34 Identities=15% Similarity=0.462 Sum_probs=20.5
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
..|..|+..|..... +...+... ..|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~-----~l~~~~~~-vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD-----KLPAGGRK-VRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHH-----HcccCCcE-EECCCCCcEee
Confidence 467888877755443 12222334 78888887663
No 69
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=85.09 E-value=1.1 Score=26.76 Aligned_cols=24 Identities=25% Similarity=0.607 Sum_probs=20.9
Q ss_pred CCCCccCCC--CccccCChhHHHHHHH
Q psy4268 40 KLPAFPCTL--CSYATKRKTSLASHYY 64 (86)
Q Consensus 40 ~~~~~~c~~--c~~~f~~~~~l~~h~~ 64 (86)
++| |+|+. |.|.+.....|..|+.
T Consensus 347 ~Kp-ykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 347 GKP-YKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred Cce-ecCCCCCchhhhccccchhhhhh
Confidence 478 99976 9999999999999963
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.44 E-value=0.69 Score=19.05 Aligned_cols=30 Identities=23% Similarity=0.540 Sum_probs=19.0
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
.|.|..||..+.... .... +.|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~----------~~~~-~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDE----------YGTG-VRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECC----------CCCc-eECCCCCCeEE
Confidence 588888987664321 1114 78999986543
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.33 E-value=1.1 Score=18.52 Aligned_cols=27 Identities=30% Similarity=0.735 Sum_probs=17.9
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCccc
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYA 52 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 52 (86)
.|.|..||..|... ...+ ..|..||..
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~-irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDV-VRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------CCCc-eECCCCCce
Confidence 37888898776432 2234 789888854
No 72
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=83.18 E-value=0.46 Score=28.25 Aligned_cols=45 Identities=29% Similarity=0.471 Sum_probs=36.8
Q ss_pred cccccc--CCCCC--Cceecc--cccccccChHHHHHHHHHhhCCCCCccCC
Q psy4268 2 LGYYFS--APSGE--KRYLCD--SCDRTYSNRSSLKRHMNYECGKLPAFPCT 47 (86)
Q Consensus 2 l~~h~~--~h~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~~c~ 47 (86)
+..|.. .|.++ +++.|. .|++.|.....+..|...+.+..+ +.+.
T Consensus 305 l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 355 (467)
T COG5048 305 LTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP-AKEK 355 (467)
T ss_pred ccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc-cccc
Confidence 456677 79999 999999 799999999999999888887765 5543
No 73
>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=82.84 E-value=0.32 Score=19.14 Aligned_cols=32 Identities=22% Similarity=0.490 Sum_probs=18.2
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCC
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKR 55 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 55 (86)
..|..||..|.. ........ -.|..||..+.+
T Consensus 2 r~C~~Cg~~Yh~--------~~~pP~~~-~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHI--------EFNPPKVE-GVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEET--------TTB--SST-TBCTTTTEBEBE
T ss_pred cCcCCCCCcccc--------ccCCCCCC-CccCCCCCeeEe
Confidence 467788877643 22233444 578888765543
No 74
>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=82.82 E-value=0.37 Score=20.29 Aligned_cols=30 Identities=17% Similarity=0.467 Sum_probs=18.1
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
.|.|..|+..|.....+ .. ... ..|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~-~~~-~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKM------SD-DPL-ATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEec------CC-CCC-CCCCCCCC
Confidence 37888888877643221 11 223 46888885
No 75
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=82.52 E-value=0.16 Score=26.78 Aligned_cols=12 Identities=17% Similarity=0.340 Sum_probs=6.8
Q ss_pred ccCCCCccccCC
Q psy4268 44 FPCTLCSYATKR 55 (86)
Q Consensus 44 ~~c~~c~~~f~~ 55 (86)
+.|..||+.|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 456666665554
No 76
>KOG4167|consensus
Probab=81.79 E-value=0.29 Score=32.04 Aligned_cols=25 Identities=24% Similarity=0.430 Sum_probs=21.7
Q ss_pred ccCCCCccccCChhHHHHHHHHhcc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
|.|..|++.|....++..|+++|-.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHH
Confidence 7899999999998889999988753
No 77
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=80.82 E-value=0.88 Score=21.87 Aligned_cols=11 Identities=18% Similarity=0.613 Sum_probs=5.1
Q ss_pred ceecccccccc
Q psy4268 14 RYLCDSCDRTY 24 (86)
Q Consensus 14 ~~~c~~c~~~~ 24 (86)
|-.|..||+.|
T Consensus 58 Pa~CkkCGfef 68 (97)
T COG3357 58 PARCKKCGFEF 68 (97)
T ss_pred ChhhcccCccc
Confidence 34444454444
No 78
>KOG4167|consensus
Probab=80.49 E-value=0.41 Score=31.41 Aligned_cols=28 Identities=18% Similarity=0.405 Sum_probs=24.4
Q ss_pred CceecccccccccChHHHHHHHHHhhCC
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGK 40 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 40 (86)
.-|.|..|++.|.....+..||+.|.-.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 3499999999999999999999988653
No 79
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=80.26 E-value=0.53 Score=22.43 Aligned_cols=30 Identities=23% Similarity=0.528 Sum_probs=18.0
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
.|.|..|++. .+.+.-.| - +.|..|+..|.
T Consensus 35 ~~~Cp~C~~~--------~VkR~a~G--I-W~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRT--------TVKRIATG--I-WKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCc--------ceeeeccC--e-EEcCCCCCeec
Confidence 4778888754 11222233 3 78888887775
No 80
>KOG3408|consensus
Probab=79.97 E-value=1.2 Score=22.66 Aligned_cols=22 Identities=23% Similarity=0.466 Sum_probs=19.0
Q ss_pred ccCCCCccccCChhHHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
|-|..|.+.|.....|..|.+.
T Consensus 58 fyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhc
Confidence 7899999999999999988753
No 81
>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=78.60 E-value=1.3 Score=16.07 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=7.8
Q ss_pred ccCCCCccccC
Q psy4268 44 FPCTLCSYATK 54 (86)
Q Consensus 44 ~~c~~c~~~f~ 54 (86)
-.|..||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35788887774
No 82
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=77.98 E-value=2.6 Score=17.60 Aligned_cols=20 Identities=25% Similarity=0.564 Sum_probs=10.2
Q ss_pred cCCCCccccCCh-----hHHHHHHH
Q psy4268 45 PCTLCSYATKRK-----TSLASHYY 64 (86)
Q Consensus 45 ~c~~c~~~f~~~-----~~l~~h~~ 64 (86)
.|..|++.+... ++|.+|+.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455555544332 45555554
No 83
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=77.53 E-value=3.3 Score=16.65 Aligned_cols=12 Identities=25% Similarity=0.703 Sum_probs=4.6
Q ss_pred Cceecccccccc
Q psy4268 13 KRYLCDSCDRTY 24 (86)
Q Consensus 13 ~~~~c~~c~~~~ 24 (86)
....|..|++.+
T Consensus 15 ~~a~C~~C~~~~ 26 (45)
T PF02892_consen 15 KKAKCKYCGKVI 26 (45)
T ss_dssp S-EEETTTTEE-
T ss_pred CeEEeCCCCeEE
Confidence 334455554433
No 84
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=76.41 E-value=2.9 Score=18.51 Aligned_cols=7 Identities=29% Similarity=1.217 Sum_probs=3.7
Q ss_pred ccCCCCc
Q psy4268 44 FPCTLCS 50 (86)
Q Consensus 44 ~~c~~c~ 50 (86)
|.|+.||
T Consensus 51 Y~Cp~CG 57 (61)
T COG2888 51 YRCPKCG 57 (61)
T ss_pred eECCCcC
Confidence 5555554
No 85
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.74 E-value=2.4 Score=21.22 Aligned_cols=29 Identities=10% Similarity=0.265 Sum_probs=18.9
Q ss_pred ecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCCh
Q psy4268 16 LCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRK 56 (86)
Q Consensus 16 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 56 (86)
.|..|++.| ....+.| ..|+.||+.|..+
T Consensus 11 idPetg~KF-----------YDLNrdP-iVsPytG~s~P~s 39 (129)
T COG4530 11 IDPETGKKF-----------YDLNRDP-IVSPYTGKSYPRS 39 (129)
T ss_pred cCccccchh-----------hccCCCc-cccCcccccchHH
Confidence 566677666 2234456 7788899888544
No 86
>PHA00626 hypothetical protein
Probab=74.63 E-value=1.7 Score=18.99 Aligned_cols=16 Identities=19% Similarity=0.603 Sum_probs=12.9
Q ss_pred CCCccCCCCccccCChh
Q psy4268 41 LPAFPCTLCSYATKRKT 57 (86)
Q Consensus 41 ~~~~~c~~c~~~f~~~~ 57 (86)
.. |.|..||..|+..+
T Consensus 22 nr-YkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DD-YVCCDCGYNDSKDA 37 (59)
T ss_pred cc-eEcCCCCCeechhh
Confidence 35 99999999887664
No 87
>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=74.39 E-value=1.5 Score=21.37 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=9.5
Q ss_pred cCCCCCCceeccccccccc
Q psy4268 7 SAPSGEKRYLCDSCDRTYS 25 (86)
Q Consensus 7 ~~h~~~~~~~c~~c~~~~~ 25 (86)
..+.| +++.|..||..|.
T Consensus 73 ~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 73 WLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEeCC-CceeCCCCCcEEE
Confidence 33444 4666666665553
No 88
>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=74.18 E-value=3.9 Score=14.71 Aligned_cols=18 Identities=22% Similarity=0.547 Sum_probs=10.9
Q ss_pred cCCCCccccCChhHHHHHH
Q psy4268 45 PCTLCSYATKRKTSLASHY 63 (86)
Q Consensus 45 ~c~~c~~~f~~~~~l~~h~ 63 (86)
.|+.|++.+ ....+..|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 577777766 334555554
No 89
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=72.98 E-value=0.66 Score=17.25 Aligned_cols=11 Identities=36% Similarity=0.724 Sum_probs=6.6
Q ss_pred ccCCCCccccC
Q psy4268 44 FPCTLCSYATK 54 (86)
Q Consensus 44 ~~c~~c~~~f~ 54 (86)
|.|..|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 35666666663
No 90
>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=72.93 E-value=1.9 Score=15.38 Aligned_cols=8 Identities=50% Similarity=1.672 Sum_probs=5.7
Q ss_pred ccCCCCcc
Q psy4268 44 FPCTLCSY 51 (86)
Q Consensus 44 ~~c~~c~~ 51 (86)
|.|+.||.
T Consensus 17 f~CPnCG~ 24 (24)
T PF07754_consen 17 FPCPNCGF 24 (24)
T ss_pred EeCCCCCC
Confidence 77777763
No 91
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=72.88 E-value=5.7 Score=16.01 Aligned_cols=25 Identities=20% Similarity=0.355 Sum_probs=16.7
Q ss_pred ceecccccc--cccChHHHHHHHHHhh
Q psy4268 14 RYLCDSCDR--TYSNRSSLKRHMNYEC 38 (86)
Q Consensus 14 ~~~c~~c~~--~~~~~~~l~~h~~~~~ 38 (86)
.-.|..||= .....+....|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 368999984 4445567777777654
No 92
>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=72.35 E-value=1.7 Score=17.61 Aligned_cols=14 Identities=14% Similarity=0.415 Sum_probs=11.1
Q ss_pred ccCCCCccccCChh
Q psy4268 44 FPCTLCSYATKRKT 57 (86)
Q Consensus 44 ~~c~~c~~~f~~~~ 57 (86)
|.|..||..|....
T Consensus 6 y~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 6 YRCEECGHEFEVLQ 19 (42)
T ss_pred EEeCCCCCEEEEEE
Confidence 78999998887653
No 93
>KOG2593|consensus
Probab=71.83 E-value=2.5 Score=26.20 Aligned_cols=40 Identities=20% Similarity=0.538 Sum_probs=26.2
Q ss_pred CCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccc
Q psy4268 9 PSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYA 52 (86)
Q Consensus 9 h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 52 (86)
-+...-|.|..|.+.|.....+.. ...-.-. |.|..|+..
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~-F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQL---LDNETGE-FHCENCGGE 162 (436)
T ss_pred ccccccccCCccccchhhhHHHHh---hcccCce-EEEecCCCc
Confidence 344567999999999987665432 2211223 999998753
No 94
>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=71.82 E-value=5.5 Score=15.38 Aligned_cols=23 Identities=17% Similarity=0.352 Sum_probs=14.0
Q ss_pred ccCCCCccccCChhHHHHHHHHhc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
+.|..|++.+.... +..|...-.
T Consensus 5 ~~C~nC~R~v~a~R-fA~HLekCm 27 (33)
T PF08209_consen 5 VECPNCGRPVAASR-FAPHLEKCM 27 (33)
T ss_dssp EE-TTTSSEEEGGG-HHHHHHHHT
T ss_pred EECCCCcCCcchhh-hHHHHHHHH
Confidence 67888888766543 566665443
No 95
>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=71.10 E-value=2 Score=16.88 Aligned_cols=13 Identities=15% Similarity=0.432 Sum_probs=10.4
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 7899999887644
No 96
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=69.92 E-value=3.6 Score=17.48 Aligned_cols=30 Identities=20% Similarity=0.478 Sum_probs=18.4
Q ss_pred CCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccc
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYA 52 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 52 (86)
...|.|..||+.|.. ...... ..|..||..
T Consensus 4 ~~~Y~C~~Cg~~~~~----------~~~~~~-irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVEL----------DQETRG-IRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeeh----------hhccCc-eeCCCCCcE
Confidence 346889999987711 111123 688888853
No 97
>COG1773 Rubredoxin [Energy production and conversion]
Probab=68.95 E-value=2.4 Score=18.43 Aligned_cols=15 Identities=27% Similarity=0.784 Sum_probs=11.3
Q ss_pred ceecccccccccChH
Q psy4268 14 RYLCDSCDRTYSNRS 28 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~ 28 (86)
.|.|++||..|.-..
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 588999998775543
No 98
>KOG4173|consensus
Probab=64.51 E-value=3.4 Score=23.16 Aligned_cols=48 Identities=23% Similarity=0.425 Sum_probs=34.0
Q ss_pred eecccccccccChHHHHHHHHH----------hhCCCCCccCC--CCccccCChhHHHHHH
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNY----------ECGKLPAFPCT--LCSYATKRKTSLASHY 63 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~----------~~~~~~~~~c~--~c~~~f~~~~~l~~h~ 63 (86)
..|+.|.+.|....-|..|+.- ..|..- |.|. .|+-.|.+......|+
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dM-y~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDM-YQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccH-HHHHHHhhhhhhhhhhhhhhHH
Confidence 3788899999888888777652 223223 6774 3888888887777776
No 99
>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=64.35 E-value=5.7 Score=20.94 Aligned_cols=28 Identities=25% Similarity=0.708 Sum_probs=17.6
Q ss_pred CceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
..+.|..||..... .+.+..| .|+.|+.
T Consensus 111 G~l~C~~Cg~~~~~---------~~~~~l~--~Cp~C~~ 138 (146)
T PF07295_consen 111 GTLVCENCGHEVEL---------THPERLP--PCPKCGH 138 (146)
T ss_pred ceEecccCCCEEEe---------cCCCcCC--CCCCCCC
Confidence 35889999864311 2444444 7888874
No 100
>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=64.28 E-value=5.7 Score=16.26 Aligned_cols=17 Identities=18% Similarity=0.370 Sum_probs=11.5
Q ss_pred ccCCCCccccCChhHHH
Q psy4268 44 FPCTLCSYATKRKTSLA 60 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~ 60 (86)
-.|..|++.|.......
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 35888888887665443
No 101
>KOG0978|consensus
Probab=62.35 E-value=4.7 Score=26.71 Aligned_cols=16 Identities=19% Similarity=0.258 Sum_probs=11.6
Q ss_pred ccCCCCccccCChhHH
Q psy4268 44 FPCTLCSYATKRKTSL 59 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l 59 (86)
-+|+.|+.+|.....+
T Consensus 679 RKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVH 694 (698)
T ss_pred CCCCCCCCCCCccccc
Confidence 4788888888766543
No 102
>PLN02294 cytochrome c oxidase subunit Vb
Probab=60.86 E-value=4.8 Score=21.82 Aligned_cols=11 Identities=18% Similarity=0.851 Sum_probs=5.0
Q ss_pred ceecccccccc
Q psy4268 14 RYLCDSCDRTY 24 (86)
Q Consensus 14 ~~~c~~c~~~~ 24 (86)
++.|..||..|
T Consensus 141 p~RCpeCG~~f 151 (174)
T PLN02294 141 SFECPVCTQYF 151 (174)
T ss_pred ceeCCCCCCEE
Confidence 44444444443
No 103
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.83 E-value=3.5 Score=21.33 Aligned_cols=15 Identities=20% Similarity=0.565 Sum_probs=11.3
Q ss_pred CceecccccccccCh
Q psy4268 13 KRYLCDSCDRTYSNR 27 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~ 27 (86)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 458899999877553
No 104
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=60.05 E-value=5.2 Score=15.93 Aligned_cols=14 Identities=21% Similarity=0.446 Sum_probs=11.0
Q ss_pred CCccCCCCccccCCh
Q psy4268 42 PAFPCTLCSYATKRK 56 (86)
Q Consensus 42 ~~~~c~~c~~~f~~~ 56 (86)
+ |.|..|+..|-..
T Consensus 12 ~-f~C~~C~~~FC~~ 25 (39)
T smart00154 12 G-FKCRHCGNLFCGE 25 (39)
T ss_pred C-eECCccCCccccc
Confidence 5 8899998888644
No 105
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=59.76 E-value=4.8 Score=19.66 Aligned_cols=42 Identities=24% Similarity=0.384 Sum_probs=16.9
Q ss_pred CCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCCh
Q psy4268 9 PSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRK 56 (86)
Q Consensus 9 h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 56 (86)
.+|.|.-.|.+|+..+.... +. -.|.+..|-|..|.+.|..-
T Consensus 9 ~ag~ke~~CalCG~tWg~~y-----~E-v~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 9 EAGTKEMGCALCGATWGDYY-----EE-VDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp ---SGGGS-SS---S---SS------B--TT--BSSS--SSSS-TTS-
T ss_pred ecccccccccccCCcHHHHH-----Hh-hcCCEEEEEcHHHHHHHHHH
Confidence 35678889999998876432 22 23554437889999888764
No 106
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=58.27 E-value=5.2 Score=17.49 Aligned_cols=37 Identities=14% Similarity=0.236 Sum_probs=19.1
Q ss_pred eecccccccccChHHHHHHHHH-hhCCCCCccCCCCccc
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNY-ECGKLPAFPCTLCSYA 52 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~ 52 (86)
..|.+|++.+.-......-.+. ...... |.|..|.-.
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~t-YmC~eC~~R 40 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHT-YMCDECKER 40 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcc-eeChhHHHH
Confidence 4688888755443222222222 222334 889988643
No 107
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=57.69 E-value=5.5 Score=21.19 Aligned_cols=34 Identities=26% Similarity=0.657 Sum_probs=20.9
Q ss_pred CceecccccccccChHHHHHHHHHhhCCCCCccCCCCccc
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYA 52 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 52 (86)
-+|.|. |+.-|... .+|...-.|+ . |.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~-YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-V-YRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-e-EEeccCCce
Confidence 468888 88765432 2344444555 4 888888754
No 108
>KOG2785|consensus
Probab=57.30 E-value=23 Score=21.95 Aligned_cols=51 Identities=22% Similarity=0.336 Sum_probs=36.7
Q ss_pred CceecccccccccChHHHHHHHHHhhCCC-----------------------CCccCCCCc---cccCChhHHHHHHH
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGKL-----------------------PAFPCTLCS---YATKRKTSLASHYY 64 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~-----------------------~~~~c~~c~---~~f~~~~~l~~h~~ 64 (86)
.|-.|-.|++.+.....-..||..++|-- . |.|..|. +.|.+....+.||.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~-~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIG-FICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccC-ceEEEeccccCcccccHHHHHHHh
Confidence 34566678888888777777776554421 3 6787887 88888888888884
No 109
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=56.31 E-value=8.1 Score=19.14 Aligned_cols=16 Identities=19% Similarity=0.546 Sum_probs=12.7
Q ss_pred CceecccccccccChH
Q psy4268 13 KRYLCDSCDRTYSNRS 28 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~ 28 (86)
.|+.|..||..|....
T Consensus 1 MpH~CtrCG~vf~~g~ 16 (112)
T COG3364 1 MPHQCTRCGEVFDDGS 16 (112)
T ss_pred CCceeccccccccccc
Confidence 3689999999997753
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=56.24 E-value=6.5 Score=19.71 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=7.6
Q ss_pred ceeccccccccc
Q psy4268 14 RYLCDSCDRTYS 25 (86)
Q Consensus 14 ~~~c~~c~~~~~ 25 (86)
...|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (115)
T TIGR00100 70 ECECEDCSEEVS 81 (115)
T ss_pred EEEcccCCCEEe
Confidence 367777776553
No 111
>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=56.17 E-value=5 Score=17.05 Aligned_cols=13 Identities=31% Similarity=0.779 Sum_probs=10.2
Q ss_pred eecccccccccCh
Q psy4268 15 YLCDSCDRTYSNR 27 (86)
Q Consensus 15 ~~c~~c~~~~~~~ 27 (86)
|.|..|++.|...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7899999877643
No 112
>KOG2071|consensus
Probab=55.54 E-value=10 Score=24.68 Aligned_cols=28 Identities=18% Similarity=0.477 Sum_probs=21.7
Q ss_pred CCceecccccccccChHHHHHHHHHhhC
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHMNYECG 39 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 39 (86)
..+..|..||..|...+....|+..|..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhh
Confidence 5678999999999988877777765543
No 113
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=55.20 E-value=8 Score=19.34 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=7.3
Q ss_pred ceecccccccc
Q psy4268 14 RYLCDSCDRTY 24 (86)
Q Consensus 14 ~~~c~~c~~~~ 24 (86)
...|..|+..|
T Consensus 70 ~~~C~~Cg~~~ 80 (113)
T PRK12380 70 QAWCWDCSQVV 80 (113)
T ss_pred EEEcccCCCEE
Confidence 36777777655
No 114
>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=54.92 E-value=6.1 Score=16.54 Aligned_cols=36 Identities=19% Similarity=0.467 Sum_probs=17.2
Q ss_pred eecccccccccChHHHHHH-----HHHhhCCCCCccCCCCcc
Q psy4268 15 YLCDSCDRTYSNRSSLKRH-----MNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h-----~~~~~~~~~~~~c~~c~~ 51 (86)
|.|.+|++.|.....-..+ .....-... |.|..|+.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~-w~CP~C~a 42 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDD-WVCPVCGA 42 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT--B-TTTSS
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCC-CcCcCCCC
Confidence 7899999877554321111 011111224 78888874
No 115
>KOG2907|consensus
Probab=53.96 E-value=4.8 Score=20.24 Aligned_cols=40 Identities=18% Similarity=0.491 Sum_probs=20.7
Q ss_pred ceecccccccccChHHHHHHHHH-hhCCCCCccCCCCccccCC
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNY-ECGKLPAFPCTLCSYATKR 55 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~ 55 (86)
...|..||-.-.....++ +|+ ..|..--|.|..|++.|..
T Consensus 74 ~~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 467777775332222222 222 3343222778888877754
No 116
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=53.90 E-value=7.2 Score=20.21 Aligned_cols=15 Identities=27% Similarity=0.709 Sum_probs=12.2
Q ss_pred ceecccccccccChH
Q psy4268 14 RYLCDSCDRTYSNRS 28 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~ 28 (86)
|+.|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578999999997654
No 117
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=53.16 E-value=7.6 Score=16.49 Aligned_cols=14 Identities=21% Similarity=0.622 Sum_probs=8.7
Q ss_pred CceecccccccccC
Q psy4268 13 KRYLCDSCDRTYSN 26 (86)
Q Consensus 13 ~~~~c~~c~~~~~~ 26 (86)
+.+.|..||..|..
T Consensus 3 k~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 3 KTLTCKDCGAEFVF 16 (49)
T ss_pred eeEEcccCCCeEEE
Confidence 55677777765543
No 118
>PF12907 zf-met2: Zinc-binding
Probab=52.19 E-value=3.7 Score=16.61 Aligned_cols=7 Identities=29% Similarity=1.222 Sum_probs=3.1
Q ss_pred ecccccc
Q psy4268 16 LCDSCDR 22 (86)
Q Consensus 16 ~c~~c~~ 22 (86)
.|.+|..
T Consensus 3 ~C~iC~q 9 (40)
T PF12907_consen 3 ICKICRQ 9 (40)
T ss_pred CcHHhhH
Confidence 3444443
No 119
>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=51.86 E-value=6.5 Score=15.31 Aligned_cols=13 Identities=15% Similarity=0.322 Sum_probs=6.2
Q ss_pred cCCCCccccCChh
Q psy4268 45 PCTLCSYATKRKT 57 (86)
Q Consensus 45 ~c~~c~~~f~~~~ 57 (86)
.|..|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 6788888776553
No 120
>KOG0717|consensus
Probab=51.82 E-value=9.9 Score=24.10 Aligned_cols=21 Identities=24% Similarity=0.513 Sum_probs=17.2
Q ss_pred ccCCCCccccCChhHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYY 64 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~ 64 (86)
+-|..|.++|.+...+.+|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 468999999999888888763
No 121
>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=51.39 E-value=14 Score=16.32 Aligned_cols=13 Identities=31% Similarity=0.968 Sum_probs=9.9
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
|.|..||..+...
T Consensus 47 ~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 47 FTCPNCGFEMDRD 59 (69)
T ss_pred EEcCCCCCEECcH
Confidence 8899998776554
No 122
>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=50.53 E-value=32 Score=17.02 Aligned_cols=38 Identities=5% Similarity=0.132 Sum_probs=27.5
Q ss_pred CceecccccccccChHHHHHHHHHhhCCCCCccCCCCccc
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYA 52 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 52 (86)
.-|.|...+..|.....+...+..... +. |.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~-~v-wtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQ-RV-WTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhC-Ce-eEEecCCCC
Confidence 346777888889888888777765544 34 889887764
No 123
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=50.46 E-value=16 Score=15.96 Aligned_cols=8 Identities=38% Similarity=1.053 Sum_probs=4.6
Q ss_pred ccCCCCcc
Q psy4268 44 FPCTLCSY 51 (86)
Q Consensus 44 ~~c~~c~~ 51 (86)
|.|+.||.
T Consensus 15 ~~Cp~cGi 22 (55)
T PF13824_consen 15 FECPDCGI 22 (55)
T ss_pred CcCCCCCC
Confidence 56666654
No 124
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.41 E-value=4.6 Score=17.99 Aligned_cols=45 Identities=13% Similarity=0.267 Sum_probs=25.5
Q ss_pred cccCCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 5 YFSAPSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 5 h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
+..++.+..++-|.--+-.|.....+. ..+......|..|+..|.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~L-----~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVFL-----DMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEEE-----EcCCCCcEecCccccEEE
Confidence 445667788888887655443322111 113222267999988775
No 125
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=50.34 E-value=21 Score=15.84 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=4.9
Q ss_pred ccCCCCccc
Q psy4268 44 FPCTLCSYA 52 (86)
Q Consensus 44 ~~c~~c~~~ 52 (86)
|.|+.||..
T Consensus 26 F~CPnCG~~ 34 (59)
T PRK14890 26 FLCPNCGEV 34 (59)
T ss_pred eeCCCCCCe
Confidence 555555544
No 126
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.12 E-value=7.7 Score=18.13 Aligned_cols=33 Identities=24% Similarity=0.604 Sum_probs=19.4
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
.|.|..|+..| .+.+++. ..|+-.|..|+..+.
T Consensus 12 ~Y~c~~cg~~~----dvvq~~~----ddplt~ce~c~a~~k 44 (82)
T COG2331 12 SYECTECGNRF----DVVQAMT----DDPLTTCEECGARLK 44 (82)
T ss_pred EEeecccchHH----HHHHhcc----cCccccChhhChHHH
Confidence 38899998776 3333332 223256888876443
No 127
>KOG2482|consensus
Probab=50.01 E-value=23 Score=21.72 Aligned_cols=23 Identities=26% Similarity=0.569 Sum_probs=18.8
Q ss_pred ccCCCCccccCChhHHHHHHHHh
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRK 66 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~ 66 (86)
+.|..|.+.|.....|..||+..
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhc
Confidence 57888999999999999988653
No 128
>PF15269 zf-C2H2_7: Zinc-finger
Probab=49.99 E-value=17 Score=15.15 Aligned_cols=21 Identities=24% Similarity=0.656 Sum_probs=12.4
Q ss_pred ccCCCCccccCChhHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYY 64 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~ 64 (86)
|+|-.|.......+.|-+|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 445556555556666666664
No 129
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=49.79 E-value=16 Score=19.13 Aligned_cols=25 Identities=32% Similarity=0.626 Sum_probs=18.6
Q ss_pred eecccccccccChHHHHHHHHHhhCCCC
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLP 42 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 42 (86)
..|-.+|+.| .+|.+|..+|.+-.|
T Consensus 77 IicLEDGkkf---KSLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKF---KSLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcch---HHHHHHHhcccCCCH
Confidence 6777788887 458889888777543
No 130
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=48.28 E-value=37 Score=19.45 Aligned_cols=39 Identities=23% Similarity=0.579 Sum_probs=22.0
Q ss_pred CCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 8 APSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 8 ~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
.|..-....|..|++.|.....+. .......| .|+.|+.
T Consensus 113 lHG~~~~~~C~~C~~~~~~~~~~~---~~~~~~~p--~Cp~Cgg 151 (244)
T PRK14138 113 LHGNVEEYYCVRCGKRYTVEDVIE---KLEKSDVP--RCDDCSG 151 (244)
T ss_pred ccCCcCeeEECCCCCcccHHHHHH---HHhcCCCC--CCCCCCC
Confidence 354445678888988776543332 11122334 6888874
No 131
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=48.15 E-value=6.7 Score=16.75 Aligned_cols=43 Identities=30% Similarity=0.684 Sum_probs=21.8
Q ss_pred Cceeccc-ccccccChHHHHHHHHHhhCCCCCccCCC----CccccCCh
Q psy4268 13 KRYLCDS-CDRTYSNRSSLKRHMNYECGKLPAFPCTL----CSYATKRK 56 (86)
Q Consensus 13 ~~~~c~~-c~~~~~~~~~l~~h~~~~~~~~~~~~c~~----c~~~f~~~ 56 (86)
.+..|.. |+..-.....|..|....-.... ..|.. |...+...
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPKRP-VPCPYSPYGCKERVPRE 55 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTTSE-EE-SS----S--EEEHH
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCCCc-EECCCCCCCCCCccchh
Confidence 4566766 33333335677888875555555 67777 76655443
No 132
>KOG2231|consensus
Probab=47.63 E-value=20 Score=23.93 Aligned_cols=19 Identities=26% Similarity=0.747 Sum_probs=7.8
Q ss_pred cccccccccChHHHHHHHH
Q psy4268 17 CDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 17 c~~c~~~~~~~~~l~~h~~ 35 (86)
|..|...|.....+..|++
T Consensus 185 C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLR 203 (669)
T ss_pred chhhhhhhccHHHHHHhhc
Confidence 3334444444444444433
No 133
>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=47.05 E-value=9.4 Score=15.40 Aligned_cols=14 Identities=14% Similarity=0.710 Sum_probs=8.7
Q ss_pred CceecccccccccC
Q psy4268 13 KRYLCDSCDRTYSN 26 (86)
Q Consensus 13 ~~~~c~~c~~~~~~ 26 (86)
-++.|..|+..|..
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 47888888888865
No 134
>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=46.99 E-value=17 Score=18.95 Aligned_cols=19 Identities=11% Similarity=0.200 Sum_probs=14.5
Q ss_pred ccCCCCccccCChhHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASH 62 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h 62 (86)
+.|..|++.|..-+...+-
T Consensus 125 ~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 125 WRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred EECCCCCCEecccccHHHH
Confidence 5799999999877665543
No 135
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=46.86 E-value=17 Score=22.79 Aligned_cols=30 Identities=20% Similarity=0.603 Sum_probs=20.3
Q ss_pred ecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChh
Q psy4268 16 LCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKT 57 (86)
Q Consensus 16 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~ 57 (86)
.|..||... .+ .|..- |.|..||..+....
T Consensus 352 ~Cp~Cg~~m----------~S-~G~~g-~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRM----------KS-AGRNG-FRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCch----------hh-cCCCC-cccccccccCCccc
Confidence 788888653 22 24435 99999998776654
No 136
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=46.64 E-value=5.9 Score=24.96 Aligned_cols=17 Identities=24% Similarity=0.493 Sum_probs=13.3
Q ss_pred CCCceecccccccccCh
Q psy4268 11 GEKRYLCDSCDRTYSNR 27 (86)
Q Consensus 11 ~~~~~~c~~c~~~~~~~ 27 (86)
..+.|.|..|++.|...
T Consensus 422 ~~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCCeEEECCCCeEECCC
Confidence 45679999999877654
No 137
>KOG1842|consensus
Probab=46.57 E-value=14 Score=23.36 Aligned_cols=23 Identities=30% Similarity=0.611 Sum_probs=15.8
Q ss_pred ceecccccccccChHHHHHHHHH
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNY 36 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~ 36 (86)
-+.|.+|...|.....|..|...
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhh
Confidence 46777777777777777766654
No 138
>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=46.31 E-value=8 Score=16.41 Aligned_cols=13 Identities=23% Similarity=0.475 Sum_probs=6.9
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
-.|+.|++.|...
T Consensus 21 ~~CPlC~r~l~~e 33 (54)
T PF04423_consen 21 GCCPLCGRPLDEE 33 (54)
T ss_dssp EE-TTT--EE-HH
T ss_pred CcCCCCCCCCCHH
Confidence 3899999998754
No 139
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.82 E-value=12 Score=18.89 Aligned_cols=11 Identities=18% Similarity=0.842 Sum_probs=7.2
Q ss_pred ceecccccccc
Q psy4268 14 RYLCDSCDRTY 24 (86)
Q Consensus 14 ~~~c~~c~~~~ 24 (86)
...|..|+..|
T Consensus 71 ~~~C~~Cg~~~ 81 (117)
T PRK00564 71 ELECKDCSHVF 81 (117)
T ss_pred EEEhhhCCCcc
Confidence 46777777555
No 140
>PF14353 CpXC: CpXC protein
Probab=45.68 E-value=10 Score=19.14 Aligned_cols=21 Identities=24% Similarity=0.406 Sum_probs=13.6
Q ss_pred hhCCCCCccCCCCccccCChh
Q psy4268 37 ECGKLPAFPCTLCSYATKRKT 57 (86)
Q Consensus 37 ~~~~~~~~~c~~c~~~f~~~~ 57 (86)
-.|.--.+.|+.||..|.-..
T Consensus 32 l~g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 32 LDGSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred HcCCcCEEECCCCCCceecCC
Confidence 345433388999998875443
No 141
>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=45.57 E-value=5.9 Score=20.66 Aligned_cols=20 Identities=25% Similarity=0.547 Sum_probs=10.9
Q ss_pred ccCCCCCCceecccccccccC
Q psy4268 6 FSAPSGEKRYLCDSCDRTYSN 26 (86)
Q Consensus 6 ~~~h~~~~~~~c~~c~~~~~~ 26 (86)
+..+.| ++..|..||..|..
T Consensus 105 ~~l~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 105 FWLHKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp EEEETT-SEEEETTTEEEEEE
T ss_pred EEEeCC-CccCCCCCCeEEEE
Confidence 333444 36677667765543
No 142
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.99 E-value=23 Score=20.87 Aligned_cols=10 Identities=20% Similarity=0.840 Sum_probs=4.5
Q ss_pred eecccccccc
Q psy4268 15 YLCDSCDRTY 24 (86)
Q Consensus 15 ~~c~~c~~~~ 24 (86)
|.|++|...|
T Consensus 256 yvCs~Clsi~ 265 (279)
T TIGR00627 256 FVCSVCLSVL 265 (279)
T ss_pred EECCCccCCc
Confidence 4444444333
No 143
>KOG0782|consensus
Probab=44.88 E-value=7 Score=25.59 Aligned_cols=12 Identities=17% Similarity=0.445 Sum_probs=5.7
Q ss_pred ccCCCCccccCC
Q psy4268 44 FPCTLCSYATKR 55 (86)
Q Consensus 44 ~~c~~c~~~f~~ 55 (86)
-+|..|++.|.+
T Consensus 254 GkC~~CgKgFQQ 265 (1004)
T KOG0782|consen 254 GKCNTCGKGFQQ 265 (1004)
T ss_pred cccchhhhhhhh
Confidence 345555554443
No 144
>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=44.37 E-value=11 Score=14.33 Aligned_cols=11 Identities=18% Similarity=0.637 Sum_probs=5.6
Q ss_pred ccCCCCccccC
Q psy4268 44 FPCTLCSYATK 54 (86)
Q Consensus 44 ~~c~~c~~~f~ 54 (86)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 35666665544
No 145
>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=44.31 E-value=24 Score=22.47 Aligned_cols=25 Identities=28% Similarity=0.406 Sum_probs=19.0
Q ss_pred ccCCCCccccCChhHHHHHHHHhcc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
+.|..|.+.|.....+..|+..-|.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhh
Confidence 4578888888888888888865443
No 146
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=44.17 E-value=12 Score=21.73 Aligned_cols=12 Identities=25% Similarity=0.658 Sum_probs=8.6
Q ss_pred ccCCCCccccCC
Q psy4268 44 FPCTLCSYATKR 55 (86)
Q Consensus 44 ~~c~~c~~~f~~ 55 (86)
|.|..|+..|.-
T Consensus 156 f~C~~C~h~F~G 167 (278)
T PF15135_consen 156 FHCPKCRHNFRG 167 (278)
T ss_pred eecccccccchh
Confidence 777778777763
No 147
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.96 E-value=14 Score=19.07 Aligned_cols=15 Identities=13% Similarity=0.414 Sum_probs=11.9
Q ss_pred CCCCccCCCCccccCC
Q psy4268 40 KLPAFPCTLCSYATKR 55 (86)
Q Consensus 40 ~~~~~~c~~c~~~f~~ 55 (86)
... |.|..|++.|..
T Consensus 51 ~qR-yrC~~C~~tf~~ 65 (129)
T COG3677 51 HQR-YKCKSCGSTFTV 65 (129)
T ss_pred ccc-cccCCcCcceee
Confidence 445 899999998864
No 148
>PRK11032 hypothetical protein; Provisional
Probab=43.95 E-value=19 Score=19.42 Aligned_cols=28 Identities=25% Similarity=0.668 Sum_probs=17.8
Q ss_pred CceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
..+.|..|+.... ..+.+..+ .|+.|+.
T Consensus 123 G~LvC~~Cg~~~~---------~~~p~~i~--pCp~C~~ 150 (160)
T PRK11032 123 GNLVCEKCHHHLA---------FYTPEVLP--LCPKCGH 150 (160)
T ss_pred ceEEecCCCCEEE---------ecCCCcCC--CCCCCCC
Confidence 4588888886431 13455555 7888875
No 149
>KOG2636|consensus
Probab=43.81 E-value=23 Score=22.49 Aligned_cols=28 Identities=29% Similarity=0.649 Sum_probs=18.4
Q ss_pred CCCCCCceeccccc-ccccChHHHHHHHH
Q psy4268 8 APSGEKRYLCDSCD-RTYSNRSSLKRHMN 35 (86)
Q Consensus 8 ~h~~~~~~~c~~c~-~~~~~~~~l~~h~~ 35 (86)
.|.-.+.|.|.+|| +++.-...+.+|-.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 34445667777777 66666666776654
No 150
>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=43.73 E-value=9.1 Score=14.40 Aligned_cols=9 Identities=22% Similarity=0.693 Sum_probs=6.2
Q ss_pred ccCCCCccc
Q psy4268 44 FPCTLCSYA 52 (86)
Q Consensus 44 ~~c~~c~~~ 52 (86)
+.|..|+..
T Consensus 20 ~vCp~C~~e 28 (30)
T PF08274_consen 20 LVCPECGHE 28 (30)
T ss_dssp EEETTTTEE
T ss_pred EeCCccccc
Confidence 777777643
No 151
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=43.60 E-value=11 Score=22.00 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=19.7
Q ss_pred CCceecccccccccChHHHHHHHHHhhCCCCCccCCCCc
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCS 50 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 50 (86)
+..-.|..||..+.....+ |.. -. |+|..|.
T Consensus 218 e~~r~CP~Cg~~W~L~~pl--h~i-----Fd-FKCD~CR 248 (258)
T PF10071_consen 218 EQARKCPSCGGDWRLKEPL--HDI-----FD-FKCDPCR 248 (258)
T ss_pred hhCCCCCCCCCccccCCch--hhc-----ee-ccCCcce
Confidence 4446788888877666554 222 23 8888884
No 152
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=43.51 E-value=35 Score=20.34 Aligned_cols=22 Identities=27% Similarity=0.582 Sum_probs=18.8
Q ss_pred ccCCCCccccCChhHHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
|.|..|.+-|.....+.+|+..
T Consensus 49 yiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 49 YICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred EEcCCCcchhCCHHHHHHHHHh
Confidence 8899999999999999998753
No 153
>KOG4727|consensus
Probab=43.47 E-value=16 Score=19.97 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=19.4
Q ss_pred ceecccccccccChHHHHHHHH
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~ 35 (86)
-|-|.+|.-.+....++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4899999999999999988875
No 154
>PRK04351 hypothetical protein; Provisional
Probab=42.97 E-value=11 Score=20.01 Aligned_cols=32 Identities=25% Similarity=0.516 Sum_probs=16.7
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccC
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATK 54 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 54 (86)
.|.|..|+..+.. + +.+. ... |.|..|+..+.
T Consensus 112 ~Y~C~~Cg~~~~r------~-Rr~n-~~~-yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLR------K-RRIN-TKR-YRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeee------e-eecC-CCc-EEeCCCCcEee
Confidence 4777767754422 1 1122 233 77777775543
No 155
>KOG3362|consensus
Probab=41.82 E-value=6.8 Score=20.67 Aligned_cols=7 Identities=29% Similarity=1.032 Sum_probs=4.3
Q ss_pred eeccccc
Q psy4268 15 YLCDSCD 21 (86)
Q Consensus 15 ~~c~~c~ 21 (86)
..|.+||
T Consensus 119 ~fCaVCG 125 (156)
T KOG3362|consen 119 KFCAVCG 125 (156)
T ss_pred hhhhhcC
Confidence 3566676
No 156
>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=40.41 E-value=17 Score=14.64 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=5.8
Q ss_pred ceecccccccc
Q psy4268 14 RYLCDSCDRTY 24 (86)
Q Consensus 14 ~~~c~~c~~~~ 24 (86)
+..|..|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45555555443
No 157
>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=40.28 E-value=9.4 Score=21.25 Aligned_cols=20 Identities=20% Similarity=0.790 Sum_probs=0.0
Q ss_pred ccCCCCc-cccCChhHHHHHH
Q psy4268 44 FPCTLCS-YATKRKTSLASHY 63 (86)
Q Consensus 44 ~~c~~c~-~~f~~~~~l~~h~ 63 (86)
|.|.+|| ..+.-...+.+|.
T Consensus 102 y~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 102 YKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ---------------------
T ss_pred eeeEeCCCcceecHHHHHHhc
Confidence 6777775 2333333444443
No 158
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=39.99 E-value=7.5 Score=17.93 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=21.2
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCC--CCccccCChhH
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCT--LCSYATKRKTS 58 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~--~c~~~f~~~~~ 58 (86)
..|..|+..-....+-.... ..-+.- +.|. .||..|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y-~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERY-HQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheee-eecCCCCCCCEEEEEEE
Confidence 35777775432222211111 122233 6787 79999887654
No 159
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=39.88 E-value=15 Score=14.53 Aligned_cols=11 Identities=27% Similarity=0.878 Sum_probs=5.7
Q ss_pred Cceeccccccc
Q psy4268 13 KRYLCDSCDRT 23 (86)
Q Consensus 13 ~~~~c~~c~~~ 23 (86)
+-|+|..||..
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 45888888854
No 160
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.70 E-value=13 Score=15.75 Aligned_cols=15 Identities=13% Similarity=0.434 Sum_probs=9.7
Q ss_pred cCCCCccccCChhHH
Q psy4268 45 PCTLCSYATKRKTSL 59 (86)
Q Consensus 45 ~c~~c~~~f~~~~~l 59 (86)
.|+.|++.|......
T Consensus 14 ICpvCqRPFsWRkKW 28 (54)
T COG4338 14 ICPVCQRPFSWRKKW 28 (54)
T ss_pred hhhhhcCchHHHHHH
Confidence 577777777655433
No 161
>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=39.04 E-value=53 Score=18.51 Aligned_cols=38 Identities=16% Similarity=0.337 Sum_probs=20.5
Q ss_pred CCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 8 APSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 8 ~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
.|..-....|..|+..+..... ........| .|..|+.
T Consensus 107 lHG~l~~~~C~~C~~~~~~~~~----~~~~~~~~p--~C~~Cgg 144 (222)
T cd01413 107 LHGTLQTAYCVNCGSKYDLEEV----KYAKKHEVP--RCPKCGG 144 (222)
T ss_pred ccCCcCcceECCCCCCcchhHH----HHhccCCCC--cCCCCCC
Confidence 3444455778888876654332 111122333 6887864
No 162
>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=38.80 E-value=33 Score=14.35 Aligned_cols=13 Identities=23% Similarity=0.370 Sum_probs=7.1
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
+.|..||+.|-..
T Consensus 19 ~~Cr~Cg~~~C~~ 31 (57)
T cd00065 19 HHCRNCGRIFCSK 31 (57)
T ss_pred cccCcCcCCcChH
Confidence 4556666655543
No 163
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=38.55 E-value=17 Score=14.50 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=7.4
Q ss_pred ccCCCCccccC
Q psy4268 44 FPCTLCSYATK 54 (86)
Q Consensus 44 ~~c~~c~~~f~ 54 (86)
|.|..|+..+.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 67777776553
No 164
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=37.55 E-value=42 Score=18.82 Aligned_cols=36 Identities=22% Similarity=0.408 Sum_probs=20.2
Q ss_pred CceecccccccccChHHHHHHHHHhh-CCCCCccCCCCccccC
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMNYEC-GKLPAFPCTLCSYATK 54 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~~~~-~~~~~~~c~~c~~~f~ 54 (86)
.-+.|..|+ + ... .|..... +..++..|..||.-+.
T Consensus 5 iy~~Cp~Cg--~--eev--~hEVik~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 5 IYIECPSCG--S--EEV--SHEVIKERGREPLVRCEECGTVHP 41 (201)
T ss_pred EEEECCCCC--c--chh--hHHHHHhcCCceEEEccCCCcEee
Confidence 357899887 1 111 2222222 3334478999997663
No 165
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=37.27 E-value=39 Score=17.77 Aligned_cols=19 Identities=32% Similarity=0.593 Sum_probs=12.3
Q ss_pred CCceecccccccccChHHH
Q psy4268 12 EKRYLCDSCDRTYSNRSSL 30 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l 30 (86)
.+-|.|.+|.........|
T Consensus 78 ~~lYeCnIC~etS~ee~FL 96 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFL 96 (140)
T ss_pred CCceeccCcccccchhhcC
Confidence 4678888887765544443
No 166
>PLN02748 tRNA dimethylallyltransferase
Probab=36.98 E-value=32 Score=21.96 Aligned_cols=24 Identities=17% Similarity=0.574 Sum_probs=16.3
Q ss_pred Cceecccccc-cccChHHHHHHHHH
Q psy4268 13 KRYLCDSCDR-TYSNRSSLKRHMNY 36 (86)
Q Consensus 13 ~~~~c~~c~~-~~~~~~~l~~h~~~ 36 (86)
+.|.|.+|+. .+.....+..|.+.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5567777876 56666667777654
No 167
>KOG0227|consensus
Probab=36.86 E-value=24 Score=19.72 Aligned_cols=27 Identities=26% Similarity=0.453 Sum_probs=16.8
Q ss_pred ccCCCCCCceecccccccccChHHHHHHH
Q psy4268 6 FSAPSGEKRYLCDSCDRTYSNRSSLKRHM 34 (86)
Q Consensus 6 ~~~h~~~~~~~c~~c~~~~~~~~~l~~h~ 34 (86)
|+.|.| .|.|..|.-......++..|.
T Consensus 47 mkNh~G--~yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 47 MKNHLG--KYECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred hhccCc--ceeehhhhhhhcchhhhhhhh
Confidence 445555 578888876665655555554
No 168
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=36.65 E-value=13 Score=19.28 Aligned_cols=32 Identities=22% Similarity=0.521 Sum_probs=16.2
Q ss_pred ceecccccccccChHHHHHHHHHhhCCCCCccCCCCcccc
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYAT 53 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 53 (86)
.|.|..|+..+. .+.+.. .... +.|..|+..+
T Consensus 112 ~y~C~~C~~~~~------~~rr~~-~~~~-y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYL------RVRRSN-NVSR-YRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCc------eEcccc-Ccce-EEcCCCCCEE
Confidence 577776765542 122211 1123 6777776554
No 169
>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=36.06 E-value=11 Score=19.57 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=6.1
Q ss_pred ccCCCCcccc
Q psy4268 44 FPCTLCSYAT 53 (86)
Q Consensus 44 ~~c~~c~~~f 53 (86)
+.|..|+..+
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 5677776544
No 170
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=35.82 E-value=27 Score=17.53 Aligned_cols=11 Identities=18% Similarity=0.782 Sum_probs=6.7
Q ss_pred ceecccccccc
Q psy4268 14 RYLCDSCDRTY 24 (86)
Q Consensus 14 ~~~c~~c~~~~ 24 (86)
...|..|+..|
T Consensus 70 ~~~C~~Cg~~~ 80 (114)
T PRK03681 70 ECWCETCQQYV 80 (114)
T ss_pred EEEcccCCCee
Confidence 36677777544
No 171
>PTZ00448 hypothetical protein; Provisional
Probab=35.47 E-value=35 Score=21.13 Aligned_cols=22 Identities=18% Similarity=0.504 Sum_probs=16.8
Q ss_pred ccCCCCccccCChhHHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
|.|..|+-.|........|.++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccccccccccCCHHHHHHHhhh
Confidence 7899999999776666666643
No 172
>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=35.44 E-value=12 Score=14.77 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=5.3
Q ss_pred ccCCCCcccc
Q psy4268 44 FPCTLCSYAT 53 (86)
Q Consensus 44 ~~c~~c~~~f 53 (86)
|.|..|+..|
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 4555565543
No 173
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=35.17 E-value=48 Score=18.25 Aligned_cols=33 Identities=30% Similarity=0.717 Sum_probs=19.8
Q ss_pred CCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCcccc
Q psy4268 11 GEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYAT 53 (86)
Q Consensus 11 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 53 (86)
...-|.|..|...++.-.. ...+ |.|+.||...
T Consensus 110 ~~~~y~C~~~~~r~sfdeA------~~~~----F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEA------MELG----FTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHH------HHhC----CCCCCCCchh
Confidence 4456888777665544322 2222 8899998643
No 174
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=34.38 E-value=86 Score=17.54 Aligned_cols=40 Identities=18% Similarity=0.449 Sum_probs=20.4
Q ss_pred CCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccc
Q psy4268 8 APSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYA 52 (86)
Q Consensus 8 ~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 52 (86)
.|..-....|..|++.+..... . ........| .|..|+..
T Consensus 103 lHG~~~~~~C~~C~~~~~~~~~-~--~~~~~~~~p--~C~~Cg~~ 142 (218)
T cd01407 103 LHGSLFRVRCTKCGKEYPRDEL-Q--ADIDREEVP--RCPKCGGL 142 (218)
T ss_pred CcCCcCcceeCCCcCCCcHHHH-h--HhhccCCCC--cCCCCCCc
Confidence 3444455778888876643321 1 111122233 68888653
No 175
>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 COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.92 E-value=27 Score=20.37 Aligned_cols=14 Identities=29% Similarity=0.911 Sum_probs=10.8
Q ss_pred ccCCCCccccCChh
Q psy4268 44 FPCTLCSYATKRKT 57 (86)
Q Consensus 44 ~~c~~c~~~f~~~~ 57 (86)
+.|..||..+....
T Consensus 323 ~~C~~cg~~~~rD~ 336 (364)
T COG0675 323 FKCPRCGFVHDRDV 336 (364)
T ss_pred EECCCCCCeehhhH
Confidence 89999998766543
No 177
>KOG2857|consensus
Probab=33.61 E-value=22 Score=18.84 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=19.7
Q ss_pred CceecccccccccChHHHHHHHH
Q psy4268 13 KRYLCDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~~h~~ 35 (86)
..|+|..|...|.+...+..|..
T Consensus 16 ~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 16 IKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hhccCCCCCCccccchhhhhccC
Confidence 36999999999999999988865
No 178
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=33.50 E-value=46 Score=19.69 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=8.1
Q ss_pred CCCCceecccccc
Q psy4268 10 SGEKRYLCDSCDR 22 (86)
Q Consensus 10 ~~~~~~~c~~c~~ 22 (86)
.|.+-|.|..|..
T Consensus 138 hGGrif~CsfC~~ 150 (314)
T PF06524_consen 138 HGGRIFKCSFCDN 150 (314)
T ss_pred CCCeEEEeecCCC
Confidence 4556677777654
No 179
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=32.68 E-value=35 Score=21.10 Aligned_cols=28 Identities=21% Similarity=0.551 Sum_probs=19.8
Q ss_pred CCCCCCceeccccc-ccccChHHHHHHHH
Q psy4268 8 APSGEKRYLCDSCD-RTYSNRSSLKRHMN 35 (86)
Q Consensus 8 ~h~~~~~~~c~~c~-~~~~~~~~l~~h~~ 35 (86)
.|.-.+.|.|.+|| +.+.-...+.+|-.
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 35556778999998 66666666666653
No 180
>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=32.41 E-value=23 Score=15.33 Aligned_cols=12 Identities=25% Similarity=0.617 Sum_probs=8.3
Q ss_pred ccCCCCccccCC
Q psy4268 44 FPCTLCSYATKR 55 (86)
Q Consensus 44 ~~c~~c~~~f~~ 55 (86)
|.|+.||..+.-
T Consensus 3 ~~CP~CG~~iev 14 (54)
T TIGR01206 3 FECPDCGAEIEL 14 (54)
T ss_pred cCCCCCCCEEec
Confidence 678888876543
No 181
>PRK10220 hypothetical protein; Provisional
Probab=32.14 E-value=31 Score=17.37 Aligned_cols=13 Identities=15% Similarity=0.470 Sum_probs=8.8
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
|.|+.|+..+...
T Consensus 21 ~vCpeC~hEW~~~ 33 (111)
T PRK10220 21 YICPECAHEWNDA 33 (111)
T ss_pred EECCcccCcCCcc
Confidence 7788887666543
No 182
>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=32.05 E-value=23 Score=18.86 Aligned_cols=13 Identities=15% Similarity=0.158 Sum_probs=10.6
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
-.|..|++.|++-
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 4699999999864
No 183
>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=31.91 E-value=41 Score=13.17 Aligned_cols=11 Identities=55% Similarity=1.361 Sum_probs=5.6
Q ss_pred CCCCceecccc
Q psy4268 10 SGEKRYLCDSC 20 (86)
Q Consensus 10 ~~~~~~~c~~c 20 (86)
.|...|.|..|
T Consensus 25 ~G~qryrC~~C 35 (36)
T PF03811_consen 25 SGHQRYRCKDC 35 (36)
T ss_pred CCCEeEecCcC
Confidence 34455555544
No 184
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=31.87 E-value=27 Score=17.53 Aligned_cols=13 Identities=23% Similarity=0.631 Sum_probs=8.3
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
|.|+.|+..+...
T Consensus 20 ~iCpeC~~EW~~~ 32 (109)
T TIGR00686 20 LICPSCLYEWNEN 32 (109)
T ss_pred eECcccccccccc
Confidence 6777777665543
No 185
>PHA02998 RNA polymerase subunit; Provisional
Probab=31.74 E-value=4.6 Score=22.08 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=9.1
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
|.|..||..|.-.
T Consensus 172 YkC~~CG~~wkpp 184 (195)
T PHA02998 172 HACRDCKKHFKPP 184 (195)
T ss_pred EEcCCCCCccCCc
Confidence 6788888776543
No 186
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.93 E-value=53 Score=13.86 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=5.9
Q ss_pred ccCCCCccccCC
Q psy4268 44 FPCTLCSYATKR 55 (86)
Q Consensus 44 ~~c~~c~~~f~~ 55 (86)
++|..|+..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 445555544443
No 187
>PTZ00064 histone acetyltransferase; Provisional
Probab=30.91 E-value=50 Score=21.52 Aligned_cols=22 Identities=23% Similarity=0.256 Sum_probs=18.9
Q ss_pred ccCCCCccccCChhHHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYYR 65 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~ 65 (86)
|.|..|.+-|.....+.+|+..
T Consensus 281 YICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 281 HFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred EEccchhhhhCCHHHHHHHHhc
Confidence 7899999999999999998743
No 188
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=30.82 E-value=43 Score=19.49 Aligned_cols=38 Identities=29% Similarity=0.619 Sum_probs=20.9
Q ss_pred CCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 9 PSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 9 h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
|..=....|..|+..+....... . ...+..| .|..|+.
T Consensus 117 HGsl~~~~C~~C~~~~~~~~~~~-~--~~~~~~p--~C~~Cg~ 154 (250)
T COG0846 117 HGSLKRVRCSKCGNQYYDEDVIK-F--IEDGLIP--RCPKCGG 154 (250)
T ss_pred ccceeeeEeCCCcCccchhhhhh-h--cccCCCC--cCccCCC
Confidence 44445678888887665433111 1 1122334 6888887
No 189
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.93 E-value=44 Score=16.92 Aligned_cols=49 Identities=10% Similarity=0.192 Sum_probs=31.0
Q ss_pred ecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhc
Q psy4268 16 LCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 16 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
.|-.|...|........-. -..... |.|..|...|-.....-.|...|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~--~~~~~~-y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDE--LKDSHR-YVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccccc--cccccc-eeCCCCCCccccccchhhhhhccC
Confidence 4777888886543211111 122334 999999999988877777765554
No 190
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=29.78 E-value=46 Score=21.25 Aligned_cols=21 Identities=33% Similarity=0.597 Sum_probs=18.8
Q ss_pred ccCCCCccccCChhHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYY 64 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~ 64 (86)
|.|..|.+-|.....+..|+.
T Consensus 199 yiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 199 YFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred EEchhhhhhhcCHHHHHHHHh
Confidence 889999999999999999974
No 191
>KOG1280|consensus
Probab=29.77 E-value=65 Score=19.93 Aligned_cols=39 Identities=15% Similarity=0.347 Sum_probs=23.8
Q ss_pred CCceecccccccccChHHHHHHHHH-hhCCCCCccCCCCc
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHMNY-ECGKLPAFPCTLCS 50 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~ 50 (86)
...|.|..|+..-.....|..|... |........|..|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3468888888866667777777654 33222224566664
No 192
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=29.41 E-value=8 Score=16.55 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=11.2
Q ss_pred CCceecccccccccChHHHHHHH
Q psy4268 12 EKRYLCDSCDRTYSNRSSLKRHM 34 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~~~l~~h~ 34 (86)
...|.|..|...|...=++-.|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTT
T ss_pred CCeEECCCCCCccccCcChhhhc
Confidence 35699999988887665544443
No 193
>PRK05978 hypothetical protein; Provisional
Probab=28.41 E-value=24 Score=18.78 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=6.0
Q ss_pred cCCCCccccC
Q psy4268 45 PCTLCSYATK 54 (86)
Q Consensus 45 ~c~~c~~~f~ 54 (86)
.|..||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 5666665554
No 194
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=28.38 E-value=83 Score=17.96 Aligned_cols=35 Identities=26% Similarity=0.449 Sum_probs=19.8
Q ss_pred CCCCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCcc
Q psy4268 8 APSGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSY 51 (86)
Q Consensus 8 ~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 51 (86)
.|..-....|..|++.+.....+ ....+ .|..|+.
T Consensus 116 lHG~~~~~~C~~C~~~~~~~~~~-------~~~~p--~C~~Cgg 150 (242)
T PRK00481 116 LHGSLLRARCTKCGQTYDLDEYL-------KPEPP--RCPKCGG 150 (242)
T ss_pred ccCCcCceeeCCCCCCcChhhhc-------cCCCC--CCCCCCC
Confidence 45555567888888766543321 12233 5888864
No 195
>KOG1984|consensus
Probab=27.78 E-value=19 Score=24.94 Aligned_cols=54 Identities=19% Similarity=0.356 Sum_probs=29.7
Q ss_pred CCCCceecccccccccChHHHHHHHHHhhCCCCCccCCCCccccCChhHHHHHHHHhccCCC
Q psy4268 10 SGEKRYLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGED 71 (86)
Q Consensus 10 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 71 (86)
....|..|..|. +|.... ++.--+.+. |.|..|+..-.-....-.|+ .+.|++.
T Consensus 334 g~sgPvRC~RCk-aYinPF-----mqF~~~gr~-f~Cn~C~~~n~vp~~yf~~L-~~~grr~ 387 (1007)
T KOG1984|consen 334 GESGPVRCNRCK-AYINPF-----MQFIDGGRK-FICNFCGSKNQVPDDYFNHL-GPTGRRV 387 (1007)
T ss_pred CCCCCcchhhhh-hhcCcc-----eEEecCCce-EEecCCCccccCChhhcccC-CCccccc
Confidence 334578888884 332221 223234445 89999987665555555554 4444443
No 196
>KOG3014|consensus
Probab=27.61 E-value=74 Score=18.68 Aligned_cols=25 Identities=16% Similarity=0.335 Sum_probs=18.5
Q ss_pred ceecccccc--cccChHHHHHHHHHhh
Q psy4268 14 RYLCDSCDR--TYSNRSSLKRHMNYEC 38 (86)
Q Consensus 14 ~~~c~~c~~--~~~~~~~l~~h~~~~~ 38 (86)
.-.|..|+- +-...+.-..|.+.|.
T Consensus 37 ~~~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 37 AVKCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred ceehhhcCceecCCCHHHHHHHHHHHH
Confidence 348888984 5555677888988887
No 197
>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=27.54 E-value=30 Score=13.64 Aligned_cols=11 Identities=27% Similarity=0.920 Sum_probs=7.6
Q ss_pred eeccccccccc
Q psy4268 15 YLCDSCDRTYS 25 (86)
Q Consensus 15 ~~c~~c~~~~~ 25 (86)
+.|..||..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 56888887653
No 198
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=27.24 E-value=26 Score=21.21 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=19.2
Q ss_pred ccCCCCccccCChhHHHHHHHHhc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
|.|..|...|......-.|...|-
T Consensus 389 Y~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 389 YQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred eechhhhhhhhhhhHHHHHHHHhh
Confidence 899999999998888777765553
No 199
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.71 E-value=28 Score=17.77 Aligned_cols=12 Identities=17% Similarity=0.310 Sum_probs=8.0
Q ss_pred ceecccccccccC
Q psy4268 14 RYLCDSCDRTYSN 26 (86)
Q Consensus 14 ~~~c~~c~~~~~~ 26 (86)
...| .|+..|..
T Consensus 70 ~~~C-~Cg~~~~~ 81 (124)
T PRK00762 70 EIEC-ECGYEGVV 81 (124)
T ss_pred eEEe-eCcCcccc
Confidence 4678 78866644
No 200
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=26.68 E-value=33 Score=12.92 Aligned_cols=10 Identities=20% Similarity=0.946 Sum_probs=6.8
Q ss_pred ccCCCCcccc
Q psy4268 44 FPCTLCSYAT 53 (86)
Q Consensus 44 ~~c~~c~~~f 53 (86)
|+|..||-..
T Consensus 5 ykC~~CGniv 14 (34)
T cd00974 5 YKCEICGNIV 14 (34)
T ss_pred EEcCCCCcEE
Confidence 7788777543
No 201
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=26.49 E-value=66 Score=17.95 Aligned_cols=28 Identities=21% Similarity=0.444 Sum_probs=18.5
Q ss_pred ccCCCCCCceecccccccccChHHHHHHHH
Q psy4268 6 FSAPSGEKRYLCDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 6 ~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~ 35 (86)
++.|+| .|.|..|.-......++..|..
T Consensus 47 ~knh~G--k~vC~LC~T~H~~e~Sy~~H~~ 74 (222)
T COG5246 47 SKNHTG--KYVCLLCKTKHLTEMSYVKHRE 74 (222)
T ss_pred hhcCCC--cEEeeeeccccccHHHHHHhhc
Confidence 345555 5888888877666666666643
No 202
>PF14369 zf-RING_3: zinc-finger
Probab=26.42 E-value=36 Score=13.16 Aligned_cols=10 Identities=20% Similarity=0.454 Sum_probs=7.6
Q ss_pred cCCCCccccC
Q psy4268 45 PCTLCSYATK 54 (86)
Q Consensus 45 ~c~~c~~~f~ 54 (86)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4888887775
No 203
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=26.16 E-value=40 Score=20.84 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=20.7
Q ss_pred ccCCCCccccCChhHHHHHHHHhcc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
|.|.-|.+-+.....+.+|+..-..
T Consensus 159 yICefClkY~~s~~~~~rH~~kC~~ 183 (395)
T COG5027 159 YICEFCLKYYGSQTSLVRHRKKCSL 183 (395)
T ss_pred EEhhhhHHHhcchhHHHHHHhcCcC
Confidence 8899999999999999999755443
No 204
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=26.15 E-value=32 Score=18.47 Aligned_cols=13 Identities=15% Similarity=0.174 Sum_probs=10.6
Q ss_pred ccCCCCccccCCh
Q psy4268 44 FPCTLCSYATKRK 56 (86)
Q Consensus 44 ~~c~~c~~~f~~~ 56 (86)
-.|..|+..|++-
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 4799999998864
No 205
>PRK12722 transcriptional activator FlhC; Provisional
Probab=25.90 E-value=51 Score=18.34 Aligned_cols=7 Identities=57% Similarity=1.488 Sum_probs=3.7
Q ss_pred ccCCCCc
Q psy4268 44 FPCTLCS 50 (86)
Q Consensus 44 ~~c~~c~ 50 (86)
|.|..|.
T Consensus 155 f~CplC~ 161 (187)
T PRK12722 155 FVCGLCQ 161 (187)
T ss_pred CcCCCCC
Confidence 5555553
No 206
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=25.83 E-value=40 Score=19.47 Aligned_cols=16 Identities=25% Similarity=0.561 Sum_probs=12.4
Q ss_pred CCceecccccccccCh
Q psy4268 12 EKRYLCDSCDRTYSNR 27 (86)
Q Consensus 12 ~~~~~c~~c~~~~~~~ 27 (86)
.++..|..||..|...
T Consensus 179 GkpqRCpECGqVFKLV 194 (268)
T PTZ00043 179 GFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCccCCCCCcEEEEE
Confidence 4588999999887653
No 207
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=25.76 E-value=60 Score=17.73 Aligned_cols=18 Identities=17% Similarity=0.357 Sum_probs=14.1
Q ss_pred ccCCCCccccCChhHHHH
Q psy4268 44 FPCTLCSYATKRKTSLAS 61 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~ 61 (86)
+.|..||+.|.....+..
T Consensus 115 ~~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 115 QRCSRCERPFAPQKTVAL 132 (181)
T ss_pred CcCcccCCccCcHhHHHH
Confidence 789999999987655543
No 208
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=25.12 E-value=47 Score=12.11 Aligned_cols=8 Identities=25% Similarity=0.725 Sum_probs=3.8
Q ss_pred cCCCCccc
Q psy4268 45 PCTLCSYA 52 (86)
Q Consensus 45 ~c~~c~~~ 52 (86)
.|..|++.
T Consensus 2 ~C~~C~~~ 9 (30)
T PF03107_consen 2 WCDVCRRK 9 (30)
T ss_pred CCCCCCCC
Confidence 45555443
No 209
>KOG2747|consensus
Probab=24.90 E-value=48 Score=20.79 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=20.3
Q ss_pred ccCCCCccccCChhHHHHHHHHhcc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~~ 68 (86)
|.|.-|.+-+.....|++|+..-.-
T Consensus 159 YiCEfCLkY~~s~~~l~rH~~kC~~ 183 (396)
T KOG2747|consen 159 YICEFCLKYMKSRTSLQRHLKKCKL 183 (396)
T ss_pred EEehHHHhHhchHHHHHHHHHhcCC
Confidence 7889999999999999999755443
No 210
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=24.63 E-value=35 Score=11.74 Aligned_cols=6 Identities=33% Similarity=1.032 Sum_probs=2.8
Q ss_pred CCCCcc
Q psy4268 46 CTLCSY 51 (86)
Q Consensus 46 c~~c~~ 51 (86)
|..||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 211
>KOG1994|consensus
Probab=24.60 E-value=55 Score=18.95 Aligned_cols=21 Identities=29% Similarity=0.643 Sum_probs=17.1
Q ss_pred ceecccccccccChHHHHHHH
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHM 34 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~ 34 (86)
-|-|-.||-.|.....|..|.
T Consensus 239 h~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ceEEEEeccccCCHHHHHHhC
Confidence 378888999999988887764
No 212
>PRK00420 hypothetical protein; Validated
Probab=24.60 E-value=40 Score=17.05 Aligned_cols=27 Identities=15% Similarity=0.303 Sum_probs=15.2
Q ss_pred eecccccccccChHHHHHHHHHhhCCCCCccCCCCcccc
Q psy4268 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYAT 53 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 53 (86)
-.|+.||..+.. ...| . ..|+.||...
T Consensus 24 ~~CP~Cg~pLf~---------lk~g--~-~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFE---------LKDG--E-VVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCccee---------cCCC--c-eECCCCCCee
Confidence 467778754421 1223 2 5688887644
No 213
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=24.40 E-value=1.2e+02 Score=16.79 Aligned_cols=19 Identities=26% Similarity=0.597 Sum_probs=11.6
Q ss_pred CCCCCCceecccccccccC
Q psy4268 8 APSGEKRYLCDSCDRTYSN 26 (86)
Q Consensus 8 ~h~~~~~~~c~~c~~~~~~ 26 (86)
.|..-....|..|+..+..
T Consensus 107 lHG~~~~~~C~~C~~~~~~ 125 (222)
T cd00296 107 LHGSLDRVRCTSCGKEYPR 125 (222)
T ss_pred ecCCCCccEECCCCCCcch
Confidence 4555555677778765544
No 214
>PRK12860 transcriptional activator FlhC; Provisional
Probab=24.39 E-value=53 Score=18.32 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=4.1
Q ss_pred ecccccccc
Q psy4268 16 LCDSCDRTY 24 (86)
Q Consensus 16 ~c~~c~~~~ 24 (86)
.|..|+..|
T Consensus 136 ~C~~Cgg~f 144 (189)
T PRK12860 136 RCCRCGGKF 144 (189)
T ss_pred cCCCCCCCe
Confidence 444444444
No 215
>PLN03239 histone acetyltransferase; Provisional
Probab=24.39 E-value=54 Score=20.22 Aligned_cols=21 Identities=19% Similarity=0.213 Sum_probs=18.5
Q ss_pred ccCCCCccccCChhHHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHYY 64 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~ 64 (86)
|.|..|.+-|.+...+.+|+.
T Consensus 107 YiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 107 YVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred EEeccchhhhcCHHHHHHHHH
Confidence 899999999999999988863
No 216
>KOG2932|consensus
Probab=24.33 E-value=1.5e+02 Score=18.29 Aligned_cols=25 Identities=24% Similarity=0.482 Sum_probs=20.0
Q ss_pred ccCCC---CccccCChhHHHHHHHHhcc
Q psy4268 44 FPCTL---CSYATKRKTSLASHYYRKHV 68 (86)
Q Consensus 44 ~~c~~---c~~~f~~~~~l~~h~~~~~~ 68 (86)
|.|.. |.++|.....|+.|+.-.|+
T Consensus 145 FmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 145 FMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred EEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 77754 88999999999999855555
No 217
>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=24.31 E-value=25 Score=17.47 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=6.6
Q ss_pred Cceecccccc
Q psy4268 13 KRYLCDSCDR 22 (86)
Q Consensus 13 ~~~~c~~c~~ 22 (86)
||..|..|+.
T Consensus 1 ~p~~CpYCg~ 10 (102)
T PF11672_consen 1 KPIICPYCGG 10 (102)
T ss_pred CCcccCCCCC
Confidence 4567777774
No 218
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=24.03 E-value=44 Score=13.21 Aligned_cols=14 Identities=14% Similarity=0.370 Sum_probs=8.6
Q ss_pred cCCCCccccCChhH
Q psy4268 45 PCTLCSYATKRKTS 58 (86)
Q Consensus 45 ~c~~c~~~f~~~~~ 58 (86)
.|.-|++.|-..+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 57788888876544
No 219
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=23.84 E-value=45 Score=12.50 Aligned_cols=12 Identities=25% Similarity=0.794 Sum_probs=8.3
Q ss_pred Cceecccccccc
Q psy4268 13 KRYLCDSCDRTY 24 (86)
Q Consensus 13 ~~~~c~~c~~~~ 24 (86)
+-|+|..|+...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468888887544
No 220
>PRK01343 zinc-binding protein; Provisional
Probab=23.79 E-value=52 Score=14.49 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=7.9
Q ss_pred ccCCCCccccC
Q psy4268 44 FPCTLCSYATK 54 (86)
Q Consensus 44 ~~c~~c~~~f~ 54 (86)
..|..|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 56888887654
No 221
>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=23.68 E-value=96 Score=15.36 Aligned_cols=22 Identities=18% Similarity=0.483 Sum_probs=16.0
Q ss_pred ceecccccccccChHHHHHHHH
Q psy4268 14 RYLCDSCDRTYSNRSSLKRHMN 35 (86)
Q Consensus 14 ~~~c~~c~~~~~~~~~l~~h~~ 35 (86)
-+.|..||..+..........+
T Consensus 31 ~~~C~~CGe~~~~~e~~~~~~~ 52 (127)
T TIGR03830 31 GWYCPACGEELLDPEESKRNSA 52 (127)
T ss_pred eeECCCCCCEEEcHHHHHHHHH
Confidence 4789999988887776654443
No 222
>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=23.47 E-value=41 Score=12.31 Aligned_cols=10 Identities=30% Similarity=0.869 Sum_probs=6.7
Q ss_pred ccCCCCcccc
Q psy4268 44 FPCTLCSYAT 53 (86)
Q Consensus 44 ~~c~~c~~~f 53 (86)
|.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 6777777654
No 223
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=23.45 E-value=61 Score=14.05 Aligned_cols=11 Identities=9% Similarity=0.359 Sum_probs=3.9
Q ss_pred CCCccccCChh
Q psy4268 47 TLCSYATKRKT 57 (86)
Q Consensus 47 ~~c~~~f~~~~ 57 (86)
..|+..|...+
T Consensus 28 ~~C~H~fek~a 38 (57)
T PF11789_consen 28 KKCGHTFEKEA 38 (57)
T ss_dssp SSS--EEEHHH
T ss_pred CCCCCeecHHH
Confidence 34444444443
No 224
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=23.33 E-value=24 Score=19.59 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=9.8
Q ss_pred CceecccccccccC
Q psy4268 13 KRYLCDSCDRTYSN 26 (86)
Q Consensus 13 ~~~~c~~c~~~~~~ 26 (86)
++-.|.+|+..|..
T Consensus 5 k~rKCKvCg~~F~P 18 (189)
T PF05766_consen 5 KRRKCKVCGEWFVP 18 (189)
T ss_pred CCCcCcccCCcccc
Confidence 45678888877754
No 225
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.38 E-value=41 Score=16.51 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=8.6
Q ss_pred CCCceecccccc
Q psy4268 11 GEKRYLCDSCDR 22 (86)
Q Consensus 11 ~~~~~~c~~c~~ 22 (86)
|-+.|.|.+|+.
T Consensus 3 ~lkewkC~VCg~ 14 (103)
T COG4847 3 GLKEWKCYVCGG 14 (103)
T ss_pred ccceeeEeeeCC
Confidence 345688888875
No 226
>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=22.36 E-value=48 Score=13.19 Aligned_cols=7 Identities=29% Similarity=0.856 Sum_probs=3.7
Q ss_pred cCCCCcc
Q psy4268 45 PCTLCSY 51 (86)
Q Consensus 45 ~c~~c~~ 51 (86)
.|+.|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555554
No 227
>KOG4118|consensus
Probab=22.27 E-value=53 Score=14.93 Aligned_cols=24 Identities=25% Similarity=0.599 Sum_probs=14.4
Q ss_pred ccCCCCccccCChhHHHHHHHHhc
Q psy4268 44 FPCTLCSYATKRKTSLASHYYRKH 67 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~~~~~ 67 (86)
+.|..|.........+..|...-|
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kH 62 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKH 62 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcC
Confidence 567777666666666666654443
No 228
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.24 E-value=41 Score=12.84 Aligned_cols=11 Identities=18% Similarity=0.470 Sum_probs=7.4
Q ss_pred ccCCCCccccC
Q psy4268 44 FPCTLCSYATK 54 (86)
Q Consensus 44 ~~c~~c~~~f~ 54 (86)
+.|..|+..|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 56777876653
No 229
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=21.62 E-value=74 Score=17.25 Aligned_cols=19 Identities=16% Similarity=0.520 Sum_probs=14.2
Q ss_pred CceecccccccccChHHHH
Q psy4268 13 KRYLCDSCDRTYSNRSSLK 31 (86)
Q Consensus 13 ~~~~c~~c~~~~~~~~~l~ 31 (86)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~CG~~f~~~~~i~ 131 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEID 131 (180)
T ss_pred CcccchhhCCccccHHHHH
Confidence 4578999999988765544
No 230
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.06 E-value=36 Score=11.97 Aligned_cols=6 Identities=33% Similarity=1.016 Sum_probs=3.2
Q ss_pred CCCCcc
Q psy4268 46 CTLCSY 51 (86)
Q Consensus 46 c~~c~~ 51 (86)
|..||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 555554
No 231
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=21.02 E-value=63 Score=13.97 Aligned_cols=18 Identities=28% Similarity=0.654 Sum_probs=13.8
Q ss_pred eecccccccccChHHHHH
Q psy4268 15 YLCDSCDRTYSNRSSLKR 32 (86)
Q Consensus 15 ~~c~~c~~~~~~~~~l~~ 32 (86)
+-|-.||..|.....|..
T Consensus 28 ~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLER 45 (55)
T ss_pred ceeeeeCCccCCHHHHHh
Confidence 678889988888777654
No 232
>PRK06260 threonine synthase; Validated
Probab=20.93 E-value=80 Score=19.53 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=6.3
Q ss_pred eecccccccc
Q psy4268 15 YLCDSCDRTY 24 (86)
Q Consensus 15 ~~c~~c~~~~ 24 (86)
+.|..|+..|
T Consensus 4 ~~C~~cg~~~ 13 (397)
T PRK06260 4 LKCIECGKEY 13 (397)
T ss_pred EEECCCCCCC
Confidence 5666676655
No 233
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.49 E-value=51 Score=17.43 Aligned_cols=10 Identities=50% Similarity=1.361 Sum_probs=8.1
Q ss_pred eecccccccc
Q psy4268 15 YLCDSCDRTY 24 (86)
Q Consensus 15 ~~c~~c~~~~ 24 (86)
|.|..|+.++
T Consensus 14 YrC~~C~~Tw 23 (142)
T PF06353_consen 14 YRCEKCDYTW 23 (142)
T ss_pred EEcccCcCcc
Confidence 8899998765
No 234
>KOG0801|consensus
Probab=20.44 E-value=63 Score=17.67 Aligned_cols=17 Identities=24% Similarity=0.507 Sum_probs=9.7
Q ss_pred ccccCCCCCCceeccccccc
Q psy4268 4 YYFSAPSGEKRYLCDSCDRT 23 (86)
Q Consensus 4 ~h~~~h~~~~~~~c~~c~~~ 23 (86)
.|+..|+| ++|.+|.+.
T Consensus 131 ~hi~~~~g---~KCPvC~K~ 147 (205)
T KOG0801|consen 131 VHIMDHSG---MKCPVCHKV 147 (205)
T ss_pred eeeeccCC---ccCCccccc
Confidence 34444554 567777653
No 235
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.05 E-value=1.3e+02 Score=16.47 Aligned_cols=20 Identities=10% Similarity=0.273 Sum_probs=15.0
Q ss_pred ccCCCCccccCChhHHHHHH
Q psy4268 44 FPCTLCSYATKRKTSLASHY 63 (86)
Q Consensus 44 ~~c~~c~~~f~~~~~l~~h~ 63 (86)
+.|..||+.|..-+....-.
T Consensus 131 ~~C~~CgkiYW~GsHw~~m~ 150 (165)
T COG1656 131 YRCPKCGKIYWKGSHWRRMV 150 (165)
T ss_pred eECCCCcccccCchHHHHHH
Confidence 45999999998777665443
Done!