Query psy12029
Match_columns 81
No_of_seqs 113 out of 1321
Neff 11.5
Searched_HMMs 46136
Date Fri Aug 16 16:49:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12029.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12029hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 3.7E-23 8E-28 110.0 2.8 71 2-73 194-264 (279)
2 KOG2462|consensus 99.9 1.1E-22 2.5E-27 108.1 3.1 76 2-80 168-243 (279)
3 KOG3623|consensus 99.6 7.4E-17 1.6E-21 95.4 1.2 71 2-73 901-971 (1007)
4 KOG3576|consensus 99.6 1.6E-16 3.5E-21 82.2 -0.8 74 3-77 125-198 (267)
5 KOG3623|consensus 99.5 2.5E-14 5.4E-19 85.1 2.2 61 19-80 890-950 (1007)
6 KOG1074|consensus 99.4 3.2E-14 7E-19 85.3 -0.5 76 3-78 613-694 (958)
7 PHA02768 hypothetical protein; 99.4 1.9E-13 4.2E-18 57.4 1.7 44 23-69 5-48 (55)
8 KOG3576|consensus 99.4 7.9E-13 1.7E-17 68.8 3.2 76 3-79 153-239 (267)
9 PHA00733 hypothetical protein 99.3 3.1E-12 6.7E-17 63.0 4.5 63 11-77 62-124 (128)
10 KOG1074|consensus 99.3 1.2E-12 2.5E-17 78.9 0.6 57 23-80 353-409 (958)
11 PF13465 zf-H2C2_2: Zinc-finge 99.1 1.5E-10 3.3E-15 42.1 2.7 24 39-63 2-25 (26)
12 PF13465 zf-H2C2_2: Zinc-finge 99.1 2.4E-11 5.1E-16 44.3 0.2 25 10-34 1-25 (26)
13 KOG3993|consensus 99.0 1.3E-10 2.9E-15 66.0 1.1 72 5-77 277-381 (500)
14 PHA00616 hypothetical protein 98.9 7.9E-10 1.7E-14 44.6 1.8 34 23-57 1-34 (44)
15 KOG3608|consensus 98.9 3.1E-10 6.8E-15 63.5 0.7 69 4-73 188-258 (467)
16 KOG3608|consensus 98.9 9.4E-10 2E-14 61.6 2.3 70 4-76 246-316 (467)
17 PHA00616 hypothetical protein 98.7 5.2E-09 1.1E-13 42.2 1.5 28 53-80 2-29 (44)
18 PHA00732 hypothetical protein 98.7 9E-09 2E-13 46.8 2.3 45 23-74 1-46 (79)
19 PHA02768 hypothetical protein; 98.5 1.2E-07 2.6E-12 40.0 2.0 24 53-76 6-29 (55)
20 PLN03086 PRLI-interacting fact 98.5 2.2E-07 4.8E-12 55.4 3.7 63 8-75 465-537 (567)
21 PF00096 zf-C2H2: Zinc finger, 98.4 2.3E-07 4.9E-12 32.5 2.2 22 53-74 1-22 (23)
22 PF05605 zf-Di19: Drought indu 98.4 9.6E-07 2.1E-11 37.4 3.9 51 23-77 2-54 (54)
23 PF00096 zf-C2H2: Zinc finger, 98.4 3.6E-07 7.8E-12 32.0 1.9 23 24-46 1-23 (23)
24 PF13894 zf-C2H2_4: C2H2-type 98.3 9.9E-07 2.2E-11 30.9 2.4 24 53-76 1-24 (24)
25 PF13912 zf-C2H2_6: C2H2-type 98.3 9E-07 2E-11 32.1 1.9 24 53-76 2-25 (27)
26 PF09237 GAGA: GAGA factor; I 98.2 2.5E-06 5.4E-11 35.3 2.8 29 53-81 25-53 (54)
27 PLN03086 PRLI-interacting fact 98.2 3.7E-06 8E-11 50.4 4.0 67 7-76 488-564 (567)
28 PF09237 GAGA: GAGA factor; I 98.1 5.4E-06 1.2E-10 34.3 3.1 34 18-51 19-52 (54)
29 PHA00733 hypothetical protein 98.1 1.5E-06 3.3E-11 43.0 1.5 55 20-75 37-96 (128)
30 PF13912 zf-C2H2_6: C2H2-type 98.1 1.7E-06 3.7E-11 31.4 1.3 25 23-47 1-25 (27)
31 PF13894 zf-C2H2_4: C2H2-type 98.0 6.2E-06 1.3E-10 28.7 2.1 23 24-46 1-23 (24)
32 COG5189 SFP1 Putative transcri 97.9 3.7E-06 7.9E-11 47.1 1.0 52 21-73 347-419 (423)
33 smart00355 ZnF_C2H2 zinc finge 97.8 2.3E-05 5.1E-10 27.6 2.3 22 54-75 2-23 (26)
34 PRK04860 hypothetical protein; 97.8 2.7E-05 6E-10 40.0 2.9 39 22-65 118-156 (160)
35 PF12756 zf-C2H2_2: C2H2 type 97.6 5.7E-05 1.2E-09 35.4 2.4 23 53-75 51-73 (100)
36 smart00355 ZnF_C2H2 zinc finge 97.6 7.2E-05 1.6E-09 26.2 2.1 24 24-47 1-24 (26)
37 PF13909 zf-H2C2_5: C2H2-type 97.4 0.00023 5E-09 24.9 2.2 23 53-76 1-23 (24)
38 PF12874 zf-met: Zinc-finger o 97.4 0.00018 4E-09 25.4 1.8 21 53-73 1-21 (25)
39 PF12874 zf-met: Zinc-finger o 97.4 0.00014 3E-09 25.7 1.5 23 24-46 1-23 (25)
40 KOG3993|consensus 97.4 2.7E-05 5.9E-10 45.2 -0.7 54 22-76 266-319 (500)
41 PHA00732 hypothetical protein 97.2 0.00032 7E-09 32.0 2.1 25 53-77 2-27 (79)
42 PF12171 zf-C2H2_jaz: Zinc-fin 96.9 0.00035 7.6E-09 25.2 0.4 21 53-73 2-22 (27)
43 PF13913 zf-C2HC_2: zinc-finge 96.6 0.0025 5.3E-08 22.7 1.9 20 53-73 3-22 (25)
44 smart00451 ZnF_U1 U1-like zinc 95.9 0.0087 1.9E-07 22.6 1.9 21 53-73 4-24 (35)
45 COG4049 Uncharacterized protei 95.6 0.01 2.2E-07 25.2 1.5 30 17-46 11-40 (65)
46 KOG2893|consensus 95.5 0.003 6.5E-08 34.6 -0.3 40 25-69 12-51 (341)
47 KOG1146|consensus 95.5 0.011 2.4E-07 39.3 2.1 56 18-74 460-540 (1406)
48 PRK04860 hypothetical protein; 95.5 0.0047 1E-07 31.9 0.4 29 8-36 128-156 (160)
49 cd00350 rubredoxin_like Rubred 95.4 0.011 2.5E-07 22.3 1.3 24 24-60 2-25 (33)
50 KOG2186|consensus 95.0 0.027 5.9E-07 31.2 2.3 47 24-74 4-50 (276)
51 COG5048 FOG: Zn-finger [Genera 94.6 0.0063 1.4E-07 35.1 -0.8 55 23-78 289-349 (467)
52 PF12756 zf-C2H2_2: C2H2 type 94.4 0.044 9.5E-07 25.5 2.1 24 23-46 50-73 (100)
53 PF13719 zinc_ribbon_5: zinc-r 93.5 0.1 2.2E-06 20.2 1.9 34 24-63 3-36 (37)
54 COG2888 Predicted Zn-ribbon RN 93.3 0.068 1.5E-06 23.0 1.4 32 22-59 26-57 (61)
55 PF09538 FYDLN_acid: Protein o 93.1 0.075 1.6E-06 25.8 1.5 30 24-65 10-39 (108)
56 TIGR02098 MJ0042_CXXC MJ0042 f 92.6 0.11 2.5E-06 20.0 1.5 34 24-63 3-36 (38)
57 PF09986 DUF2225: Uncharacteri 92.5 0.022 4.7E-07 30.8 -0.8 45 21-65 3-61 (214)
58 COG1997 RPL43A Ribosomal prote 92.1 0.046 9.9E-07 25.4 0.1 32 22-64 34-65 (89)
59 PF13717 zinc_ribbon_4: zinc-r 92.1 0.18 3.9E-06 19.4 1.7 33 24-62 3-35 (36)
60 COG5048 FOG: Zn-finger [Genera 90.9 0.074 1.6E-06 30.8 0.1 52 3-55 297-354 (467)
61 COG5189 SFP1 Putative transcri 90.9 0.057 1.2E-06 31.1 -0.3 23 20-42 395-417 (423)
62 PF05443 ROS_MUCR: ROS/MUCR tr 90.7 0.2 4.3E-06 25.3 1.5 23 53-78 73-95 (132)
63 PF04959 ARS2: Arsenite-resist 90.7 0.24 5.1E-06 27.0 1.9 30 19-48 73-102 (214)
64 COG1592 Rubrerythrin [Energy p 90.7 0.17 3.6E-06 26.5 1.3 24 22-59 133-156 (166)
65 KOG4167|consensus 90.7 0.076 1.7E-06 33.8 0.1 26 22-47 791-816 (907)
66 cd00729 rubredoxin_SM Rubredox 90.6 0.22 4.8E-06 18.9 1.3 25 23-60 2-26 (34)
67 PF04959 ARS2: Arsenite-resist 90.4 0.14 3.1E-06 27.9 0.9 26 53-78 78-103 (214)
68 PF12013 DUF3505: Protein of u 89.9 0.4 8.7E-06 23.1 2.2 25 53-77 81-109 (109)
69 smart00834 CxxC_CXXC_SSSS Puta 88.7 0.12 2.6E-06 20.1 -0.1 30 23-60 5-34 (41)
70 TIGR02605 CxxC_CxxC_SSSS putat 88.6 0.12 2.7E-06 21.4 -0.1 30 23-60 5-34 (52)
71 smart00659 RPOLCX RNA polymera 88.5 0.5 1.1E-05 19.1 1.6 27 23-61 2-28 (44)
72 smart00614 ZnF_BED BED zinc fi 88.3 0.64 1.4E-05 19.1 2.0 8 66-73 37-44 (50)
73 TIGR02300 FYDLN_acid conserved 87.8 0.44 9.5E-06 23.9 1.5 30 24-65 10-39 (129)
74 TIGR00373 conserved hypothetic 87.5 0.44 9.6E-06 24.7 1.5 38 17-64 103-140 (158)
75 smart00734 ZnF_Rad18 Rad18-lik 87.3 0.85 1.8E-05 16.2 1.8 19 54-73 3-21 (26)
76 PRK00398 rpoP DNA-directed RNA 86.7 0.28 6.1E-06 19.8 0.4 30 22-62 2-31 (46)
77 smart00531 TFIIE Transcription 86.5 0.84 1.8E-05 23.3 2.2 40 19-63 95-134 (147)
78 PRK06266 transcription initiat 85.9 0.55 1.2E-05 24.9 1.4 37 18-64 112-148 (178)
79 PF15269 zf-C2H2_7: Zinc-finge 85.3 0.8 1.7E-05 18.6 1.4 22 53-74 21-42 (54)
80 KOG3408|consensus 85.2 0.9 2E-05 22.6 1.8 27 19-45 53-79 (129)
81 PRK09678 DNA-binding transcrip 84.9 0.28 6E-06 22.1 -0.0 37 25-64 3-41 (72)
82 cd00924 Cyt_c_Oxidase_Vb Cytoc 84.4 0.45 9.8E-06 22.7 0.6 10 53-62 80-89 (97)
83 PRK14890 putative Zn-ribbon RN 84.0 1.3 2.8E-05 19.2 1.8 33 22-60 24-56 (59)
84 PF02892 zf-BED: BED zinc fing 83.3 2.1 4.6E-05 16.9 2.3 11 24-34 17-27 (45)
85 COG3091 SprT Zn-dependent meta 81.8 0.48 1E-05 24.5 0.1 36 21-62 115-150 (156)
86 PRK00464 nrdR transcriptional 81.7 0.23 5.1E-06 25.7 -1.0 11 53-63 29-39 (154)
87 COG1996 RPC10 DNA-directed RNA 81.4 1 2.2E-05 18.7 1.0 29 22-61 5-33 (49)
88 PF10013 DUF2256: Uncharacteri 80.7 1.5 3.2E-05 17.6 1.3 14 26-39 11-24 (42)
89 PTZ00255 60S ribosomal protein 80.5 0.49 1.1E-05 22.3 -0.1 31 22-63 35-65 (90)
90 KOG4167|consensus 80.5 0.31 6.6E-06 31.3 -1.0 24 53-76 793-816 (907)
91 KOG2593|consensus 80.5 1.3 2.9E-05 26.7 1.6 43 15-61 120-162 (436)
92 TIGR00280 L37a ribosomal prote 79.6 0.49 1.1E-05 22.3 -0.2 31 22-63 34-64 (91)
93 KOG2785|consensus 79.6 3.4 7.3E-05 24.7 2.9 52 22-73 165-241 (390)
94 PF07754 DUF1610: Domain of un 79.6 0.94 2E-05 15.9 0.5 10 22-31 15-24 (24)
95 COG3364 Zn-ribbon containing p 79.5 1.1 2.4E-05 21.6 0.9 17 22-38 1-17 (112)
96 PLN02294 cytochrome c oxidase 79.3 0.96 2.1E-05 23.9 0.7 22 14-36 133-154 (174)
97 PF14353 CpXC: CpXC protein 78.6 2.7 5.9E-05 20.8 2.2 12 53-64 39-50 (128)
98 PF13878 zf-C2H2_3: zinc-finge 76.8 3.3 7.2E-05 16.4 1.8 24 24-47 14-39 (41)
99 PRK03824 hypA hydrogenase nick 76.5 0.93 2E-05 22.9 0.2 15 22-36 69-83 (135)
100 PHA00626 hypothetical protein 76.1 1.6 3.4E-05 18.7 0.8 16 21-36 21-36 (59)
101 COG4957 Predicted transcriptio 75.0 2.5 5.3E-05 21.6 1.4 22 53-77 77-98 (148)
102 PRK03976 rpl37ae 50S ribosomal 74.9 0.7 1.5E-05 21.8 -0.4 31 22-63 35-65 (90)
103 PF10571 UPF0547: Uncharacteri 74.2 2 4.4E-05 15.3 0.8 11 53-63 15-25 (26)
104 KOG1842|consensus 74.1 1.9 4E-05 26.4 1.0 25 53-77 16-40 (505)
105 PF09723 Zn-ribbon_8: Zinc rib 74.1 1.8 3.9E-05 17.1 0.7 13 53-65 6-18 (42)
106 KOG1146|consensus 73.1 3.1 6.7E-05 28.9 1.9 58 19-78 1280-1354(1406)
107 PF09845 DUF2072: Zn-ribbon co 72.5 1.6 3.5E-05 22.0 0.5 15 23-37 1-15 (131)
108 PF09963 DUF2197: Uncharacteri 71.1 2.2 4.7E-05 18.3 0.7 37 24-61 3-40 (56)
109 PF01215 COX5B: Cytochrome c o 70.5 1.7 3.7E-05 22.1 0.3 22 14-36 104-125 (136)
110 COG1773 Rubredoxin [Energy pro 70.5 1.8 3.9E-05 18.5 0.3 15 23-37 3-17 (55)
111 COG5236 Uncharacterized conser 69.6 9.9 0.00021 22.8 3.2 65 7-73 200-272 (493)
112 COG2331 Uncharacterized protei 69.3 3 6.5E-05 19.1 0.9 30 23-60 12-41 (82)
113 PF08274 PhnA_Zn_Ribbon: PhnA 67.6 3.5 7.6E-05 15.2 0.8 8 53-60 20-27 (30)
114 TIGR00100 hypA hydrogenase nic 67.4 3 6.4E-05 20.5 0.8 26 22-60 69-94 (115)
115 COG4530 Uncharacterized protei 67.2 3.6 7.8E-05 20.2 1.0 14 50-64 25-38 (129)
116 PTZ00043 cytochrome c oxidase 65.8 2.8 6.1E-05 23.3 0.5 18 20-37 178-195 (268)
117 PF13451 zf-trcl: Probable zin 64.8 3.1 6.6E-05 17.3 0.5 17 21-37 2-18 (49)
118 PRK12380 hydrogenase nickel in 64.4 4.1 8.9E-05 20.0 0.9 26 22-60 69-94 (113)
119 COG1571 Predicted DNA-binding 63.9 5.9 0.00013 24.2 1.6 29 25-65 352-380 (421)
120 PF02176 zf-TRAF: TRAF-type zi 63.8 4.6 9.9E-05 16.9 0.9 40 22-63 8-53 (60)
121 PF04423 Rad50_zn_hook: Rad50 63.6 2.8 6.1E-05 17.5 0.3 13 25-37 22-34 (54)
122 smart00154 ZnF_AN1 AN1-like Zi 61.8 4.2 9E-05 15.9 0.6 14 23-36 12-25 (39)
123 PF01927 Mut7-C: Mut7-C RNAse 61.6 8.6 0.00019 19.7 1.8 47 24-71 92-143 (147)
124 KOG4727|consensus 61.6 4.8 0.0001 21.4 0.9 22 23-44 75-96 (193)
125 COG3357 Predicted transcriptio 61.2 3.2 7E-05 19.6 0.2 32 21-63 56-87 (97)
126 COG5112 UFD2 U1-like Zn-finger 60.9 6.5 0.00014 19.2 1.2 25 20-44 52-76 (126)
127 PF08790 zf-LYAR: LYAR-type C2 60.8 1.6 3.4E-05 15.9 -0.6 9 25-33 2-10 (28)
128 COG4391 Uncharacterized protei 60.4 3 6.4E-05 18.2 0.0 45 14-63 15-59 (62)
129 PF07975 C1_4: TFIIH C1-like d 59.0 1.2 2.5E-05 18.7 -1.3 25 21-45 19-43 (51)
130 KOG0717|consensus 59.0 7.1 0.00015 24.2 1.4 21 53-73 293-313 (508)
131 PF01428 zf-AN1: AN1-like Zinc 58.6 4 8.6E-05 16.2 0.3 15 22-36 12-26 (43)
132 PRK00564 hypA hydrogenase nick 56.5 5.7 0.00012 19.6 0.7 14 22-35 70-83 (117)
133 KOG2231|consensus 56.5 15 0.00032 24.0 2.5 47 25-76 184-236 (669)
134 PF06397 Desulfoferrod_N: Desu 55.5 6.1 0.00013 15.3 0.5 12 22-33 5-16 (36)
135 PRK05452 anaerobic nitric oxid 55.0 3.2 7E-05 25.5 -0.4 38 20-60 422-466 (479)
136 PF15135 UPF0515: Uncharacteri 55.0 9.3 0.0002 21.7 1.4 12 53-64 156-167 (278)
137 PF07282 OrfB_Zn_ribbon: Putat 54.4 12 0.00026 16.2 1.5 30 24-64 29-58 (69)
138 KOG2807|consensus 54.4 30 0.00065 20.7 3.3 55 21-76 288-369 (378)
139 KOG0978|consensus 54.3 2.9 6.2E-05 27.1 -0.7 18 53-70 679-696 (698)
140 PF13824 zf-Mss51: Zinc-finger 54.2 11 0.00025 16.1 1.3 13 20-32 11-23 (55)
141 PRK04351 hypothetical protein; 53.4 7.7 0.00017 20.1 0.9 33 23-64 112-144 (149)
142 PF01286 XPA_N: XPA protein N- 53.2 7.1 0.00015 14.9 0.6 12 54-65 5-16 (34)
143 cd00730 rubredoxin Rubredoxin; 53.1 5.1 0.00011 16.7 0.2 13 24-36 2-14 (50)
144 KOG4173|consensus 53.0 12 0.00025 20.8 1.5 50 25-75 108-169 (253)
145 PF10537 WAC_Acf1_DNA_bd: ATP- 52.9 27 0.00058 16.9 3.1 36 23-60 3-38 (102)
146 PF00301 Rubredoxin: Rubredoxi 52.6 5.7 0.00012 16.3 0.3 14 24-37 2-15 (47)
147 PF12760 Zn_Tnp_IS1595: Transp 51.7 3.8 8.1E-05 16.5 -0.3 27 24-60 19-45 (46)
148 KOG2482|consensus 50.9 12 0.00025 22.5 1.4 22 53-74 196-217 (423)
149 TIGR00622 ssl1 transcription f 50.4 13 0.00029 18.4 1.3 49 25-76 57-105 (112)
150 PF04780 DUF629: Protein of un 49.6 19 0.0004 22.5 2.1 23 53-75 58-80 (466)
151 PF13453 zf-TFIIB: Transcripti 49.0 19 0.00041 14.0 1.6 21 21-41 17-37 (41)
152 PF04606 Ogr_Delta: Ogr/Delta- 48.8 3.3 7.2E-05 16.8 -0.7 37 25-64 1-39 (47)
153 PRK00432 30S ribosomal protein 48.5 12 0.00027 15.5 1.0 10 53-62 38-47 (50)
154 COG1326 Uncharacterized archae 48.2 27 0.00059 19.1 2.4 35 23-62 6-40 (201)
155 PF06651 DUF1163: Protein of u 47.9 8.6 0.00019 17.1 0.5 36 2-37 18-53 (70)
156 KOG2636|consensus 47.8 15 0.00032 22.8 1.5 29 16-44 394-423 (497)
157 COG3677 Transposase and inacti 47.7 8.6 0.00019 19.4 0.5 16 21-36 51-66 (129)
158 PF10263 SprT-like: SprT-like 47.7 11 0.00023 19.2 0.9 32 23-63 123-154 (157)
159 PLN03238 probable histone acet 47.3 32 0.0007 20.1 2.7 21 53-73 49-69 (290)
160 TIGR00416 sms DNA repair prote 47.1 14 0.0003 22.8 1.4 10 23-32 7-16 (454)
161 TIGR00686 phnA alkylphosphonat 46.7 13 0.00028 18.3 1.0 11 53-63 20-30 (109)
162 KOG2071|consensus 46.4 16 0.00035 23.3 1.6 27 21-47 416-442 (579)
163 COG4338 Uncharacterized protei 46.2 6.6 0.00014 16.3 -0.0 14 26-39 15-28 (54)
164 PRK11823 DNA repair protein Ra 46.0 15 0.00032 22.6 1.4 10 23-32 7-16 (446)
165 KOG3352|consensus 45.8 8.6 0.00019 20.0 0.3 15 22-36 132-146 (153)
166 COG0846 SIR2 NAD-dependent pro 44.9 21 0.00046 20.3 1.8 38 18-60 117-154 (250)
167 PRK05978 hypothetical protein; 44.7 7.5 0.00016 20.2 0.0 31 24-64 34-64 (148)
168 PF07295 DUF1451: Protein of u 44.5 10 0.00022 19.7 0.5 28 22-60 111-138 (146)
169 PRK03681 hypA hydrogenase nick 43.7 8.5 0.00018 18.9 0.2 13 22-34 69-81 (114)
170 COG1198 PriA Primosomal protei 43.6 6.1 0.00013 25.9 -0.4 11 50-61 474-484 (730)
171 COG1656 Uncharacterized conser 42.9 24 0.00052 18.8 1.7 47 24-71 98-149 (165)
172 PF02591 DUF164: Putative zinc 42.8 29 0.00063 14.5 1.7 32 25-61 24-55 (56)
173 PRK14138 NAD-dependent deacety 42.6 39 0.00085 19.0 2.6 38 18-60 114-151 (244)
174 COG1655 Uncharacterized protei 42.6 3.4 7.3E-05 23.1 -1.4 31 18-48 14-44 (267)
175 COG4306 Uncharacterized protei 42.3 7.2 0.00016 19.7 -0.2 13 53-65 69-81 (160)
176 PF14369 zf-RING_3: zinc-finge 41.1 11 0.00024 14.3 0.3 10 25-34 23-32 (35)
177 COG5152 Uncharacterized conser 40.7 16 0.00035 20.1 0.9 17 49-65 193-209 (259)
178 PRK08222 hydrogenase 4 subunit 40.7 22 0.00049 18.9 1.4 19 22-40 113-131 (181)
179 PHA02998 RNA polymerase subuni 39.7 3.7 8.1E-05 22.0 -1.5 39 23-65 143-184 (195)
180 TIGR00627 tfb4 transcription f 39.6 28 0.0006 20.2 1.8 7 54-60 271-277 (279)
181 smart00731 SprT SprT homologue 39.6 16 0.00035 18.6 0.8 32 23-62 112-143 (146)
182 PF03604 DNA_RNApol_7kD: DNA d 39.4 20 0.00043 13.4 0.8 11 53-63 1-11 (32)
183 PRK00762 hypA hydrogenase nick 39.3 12 0.00026 18.7 0.3 33 21-60 68-100 (124)
184 PF11931 DUF3449: Domain of un 39.2 10 0.00022 20.7 0.0 26 17-42 95-121 (196)
185 PF06524 NOA36: NOA36 protein; 38.6 31 0.00066 20.0 1.8 16 18-33 137-152 (314)
186 KOG2907|consensus 38.6 12 0.00025 18.6 0.2 41 22-64 73-114 (116)
187 cd00065 FYVE FYVE domain; Zinc 38.2 30 0.00065 14.2 1.4 10 24-33 19-28 (57)
188 COG0068 HypF Hydrogenase matur 37.9 16 0.00034 24.1 0.7 35 20-61 147-182 (750)
189 PF03811 Zn_Tnp_IS1: InsA N-te 37.6 28 0.00061 13.4 1.2 11 47-58 25-35 (36)
190 PF14787 zf-CCHC_5: GAG-polypr 37.6 14 0.0003 14.3 0.3 14 25-38 4-17 (36)
191 PRK12722 transcriptional activ 37.5 24 0.00051 19.2 1.2 28 24-60 135-162 (187)
192 PF14690 zf-ISL3: zinc-finger 37.5 15 0.00033 14.5 0.4 9 23-31 2-10 (47)
193 PRK12860 transcriptional activ 37.4 22 0.00048 19.4 1.1 28 23-59 134-161 (189)
194 COG0675 Transposase and inacti 37.1 21 0.00045 20.4 1.1 12 53-64 323-334 (364)
195 KOG0317|consensus 37.0 21 0.00046 20.8 1.0 32 25-63 253-284 (293)
196 cd01121 Sms Sms (bacterial rad 36.8 23 0.00049 21.3 1.2 9 23-31 14-22 (372)
197 KOG1280|consensus 36.4 49 0.0011 20.0 2.4 43 18-60 74-117 (381)
198 PF12230 PRP21_like_P: Pre-mRN 36.1 12 0.00026 20.6 0.0 24 53-77 169-192 (229)
199 PF10071 DUF2310: Zn-ribbon-co 35.9 16 0.00034 20.9 0.4 32 20-59 217-248 (258)
200 PF10276 zf-CHCC: Zinc-finger 35.2 19 0.00041 14.3 0.5 12 22-33 28-39 (40)
201 cd00974 DSRD Desulforedoxin (D 35.1 20 0.00043 13.3 0.6 11 23-33 4-14 (34)
202 PF05191 ADK_lid: Adenylate ki 34.8 20 0.00043 13.7 0.5 11 53-63 2-12 (36)
203 COG1779 C4-type Zn-finger prot 34.7 6.7 0.00014 21.4 -1.0 39 23-64 14-55 (201)
204 PF02891 zf-MIZ: MIZ/SP-RING z 34.4 25 0.00055 14.5 0.8 23 33-60 27-49 (50)
205 smart00064 FYVE Protein presen 34.2 32 0.00069 14.8 1.2 12 24-35 11-22 (68)
206 TIGR00319 desulf_FeS4 desulfof 34.1 21 0.00046 13.2 0.6 12 22-33 6-17 (34)
207 smart00440 ZnF_C2C2 C2C2 Zinc 33.7 29 0.00064 13.5 0.9 10 53-62 29-38 (40)
208 PF12907 zf-met2: Zinc-binding 33.6 8.9 0.00019 15.2 -0.6 8 54-61 3-10 (40)
209 PTZ00448 hypothetical protein; 33.3 37 0.0008 20.6 1.6 22 53-74 315-336 (373)
210 PTZ00064 histone acetyltransfe 33.3 50 0.0011 21.1 2.2 22 53-74 281-302 (552)
211 PF05876 Terminase_GpA: Phage 33.3 11 0.00025 23.8 -0.4 37 24-64 201-241 (557)
212 TIGR01384 TFS_arch transcripti 33.1 28 0.0006 16.5 1.0 12 23-34 16-27 (104)
213 COG4896 Uncharacterized protei 32.9 29 0.00062 15.3 0.9 7 53-59 32-38 (68)
214 TIGR01206 lysW lysine biosynth 32.7 17 0.00037 15.4 0.2 31 23-62 2-32 (54)
215 PLN00104 MYST -like histone ac 32.3 45 0.00098 20.9 1.9 22 53-74 199-220 (450)
216 KOG3214|consensus 32.0 24 0.00051 17.2 0.6 41 20-65 20-60 (109)
217 PF01096 TFIIS_C: Transcriptio 31.8 25 0.00054 13.6 0.6 10 53-62 29-38 (39)
218 cd01413 SIR2_Af2 SIR2_Af2: Arc 31.8 62 0.0013 17.9 2.3 37 18-60 108-144 (222)
219 PF01780 Ribosomal_L37ae: Ribo 30.6 24 0.00053 16.8 0.5 31 22-63 34-64 (90)
220 PLN02925 4-hydroxy-3-methylbut 29.7 70 0.0015 21.4 2.4 29 53-81 635-663 (733)
221 COG2879 Uncharacterized small 29.7 62 0.0014 14.3 2.0 17 64-80 24-40 (65)
222 PF11789 zf-Nse: Zinc-finger o 29.6 44 0.00096 14.2 1.2 17 21-37 22-38 (57)
223 PLN02748 tRNA dimethylallyltra 29.6 51 0.0011 20.7 1.9 21 53-73 419-440 (468)
224 PF03884 DUF329: Domain of unk 29.5 25 0.00054 15.2 0.4 12 24-35 3-14 (57)
225 PF08273 Prim_Zn_Ribbon: Zinc- 28.3 24 0.00053 13.9 0.3 10 22-31 2-11 (40)
226 TIGR03829 YokU_near_AblA uncha 27.4 61 0.0013 15.4 1.5 18 50-67 33-50 (89)
227 PRK06260 threonine synthase; V 27.2 36 0.00078 20.5 1.0 14 23-36 19-32 (397)
228 PF11672 DUF3268: Protein of u 26.4 24 0.00051 17.2 0.1 9 23-31 2-10 (102)
229 KOG0227|consensus 26.4 51 0.0011 18.2 1.3 27 15-43 47-73 (222)
230 KOG0782|consensus 26.3 11 0.00024 24.3 -1.2 27 11-37 241-267 (1004)
231 PRK01343 zinc-binding protein; 26.2 52 0.0011 14.2 1.1 12 23-34 9-20 (57)
232 KOG0562|consensus 26.1 80 0.0017 17.1 1.9 21 24-44 154-174 (184)
233 KOG3014|consensus 26.1 55 0.0012 18.8 1.4 31 17-47 28-63 (257)
234 COG1379 PHP family phosphoeste 26.0 27 0.00058 21.0 0.3 10 53-62 266-275 (403)
235 PRK05580 primosome assembly pr 26.0 15 0.00032 23.9 -0.8 9 53-61 422-430 (679)
236 PF02146 SIR2: Sir2 family; I 25.9 52 0.0011 17.3 1.3 39 18-61 100-138 (178)
237 PF12773 DZR: Double zinc ribb 25.9 43 0.00094 13.4 0.9 9 53-61 30-38 (50)
238 PF05766 NinG: Bacteriophage L 25.8 20 0.00042 19.5 -0.2 13 23-35 6-18 (189)
239 PF14446 Prok-RING_1: Prokaryo 25.2 29 0.00063 14.8 0.3 13 24-36 6-18 (54)
240 COG4888 Uncharacterized Zn rib 25.0 38 0.00083 16.5 0.7 39 20-63 19-57 (104)
241 COG5188 PRP9 Splicing factor 3 25.0 50 0.0011 20.1 1.2 24 22-45 237-260 (470)
242 PLN03239 histone acetyltransfe 24.9 60 0.0013 19.6 1.5 24 50-74 105-128 (351)
243 TIGR01385 TFSII transcription 24.9 9.9 0.00021 22.1 -1.5 39 22-63 257-297 (299)
244 KOG0801|consensus 24.9 32 0.00069 18.4 0.4 19 11-32 129-147 (205)
245 PF04438 zf-HIT: HIT zinc fing 24.7 45 0.00097 12.2 0.7 12 23-34 13-24 (30)
246 PF05180 zf-DNL: DNL zinc fing 24.5 5.2 0.00011 17.8 -2.1 34 23-60 4-37 (66)
247 KOG2747|consensus 24.5 54 0.0012 20.2 1.3 23 53-75 159-181 (396)
248 PF08271 TF_Zn_Ribbon: TFIIB z 24.4 49 0.0011 12.9 0.9 7 54-60 2-8 (43)
249 PF14311 DUF4379: Domain of un 24.1 46 0.001 13.8 0.8 13 53-65 29-41 (55)
250 smart00132 LIM Zinc-binding do 23.6 33 0.00072 12.3 0.3 11 23-33 27-37 (39)
251 PF06170 DUF983: Protein of un 23.4 35 0.00075 16.0 0.4 11 25-35 10-20 (86)
252 PRK12387 formate hydrogenlyase 23.4 45 0.00098 17.7 0.8 18 22-39 113-130 (180)
253 PRK00481 NAD-dependent deacety 23.3 92 0.002 17.4 2.0 35 17-60 116-150 (242)
254 PF05741 zf-nanos: Nanos RNA b 23.0 36 0.00077 14.6 0.3 11 22-32 32-42 (55)
255 KOG2857|consensus 23.0 38 0.00083 17.6 0.5 23 22-44 16-38 (157)
256 PRK14892 putative transcriptio 23.0 36 0.00078 16.5 0.4 36 21-64 19-54 (99)
257 TIGR03831 YgiT_finger YgiT-typ 22.7 45 0.00097 12.8 0.6 9 53-61 33-41 (46)
258 PF04810 zf-Sec23_Sec24: Sec23 22.7 67 0.0014 12.4 1.1 31 23-60 2-32 (40)
259 PF09943 DUF2175: Uncharacteri 22.7 33 0.00071 16.7 0.2 9 53-61 3-11 (101)
260 COG4847 Uncharacterized protei 22.6 31 0.00067 16.6 0.1 11 22-32 5-15 (103)
261 PF11023 DUF2614: Protein of u 22.6 83 0.0018 15.7 1.6 11 22-32 68-78 (114)
262 COG3024 Uncharacterized protei 22.6 36 0.00078 15.1 0.3 13 23-35 7-19 (65)
263 cd01407 SIR2-fam SIR2 family o 22.5 1.2E+02 0.0026 16.6 2.3 39 17-60 103-141 (218)
264 smart00661 RPOL9 RNA polymeras 22.4 42 0.00091 13.4 0.5 14 23-36 20-33 (52)
265 PF03107 C1_2: C1 domain; Int 22.4 55 0.0012 11.7 0.8 7 54-60 2-8 (30)
266 PF02148 zf-UBP: Zn-finger in 22.4 37 0.00079 14.6 0.3 16 21-36 9-24 (63)
267 COG1998 RPS31 Ribosomal protei 22.2 66 0.0014 13.5 1.0 9 53-61 38-46 (51)
268 COG1675 TFA1 Transcription ini 22.1 22 0.00048 19.1 -0.5 34 19-62 109-142 (176)
269 TIGR00244 transcriptional regu 22.1 44 0.00096 17.5 0.6 12 53-64 29-40 (147)
270 PF10164 DUF2367: Uncharacteri 22.0 41 0.0009 16.3 0.5 10 23-32 88-97 (98)
271 PRK11032 hypothetical protein; 21.9 68 0.0015 17.0 1.3 28 22-60 123-150 (160)
272 PF09855 DUF2082: Nucleic-acid 21.6 45 0.00098 14.7 0.5 7 53-59 1-7 (64)
273 PF08792 A2L_zn_ribbon: A2L zi 21.5 53 0.0011 12.3 0.6 10 53-62 22-31 (33)
274 cd04476 RPA1_DBD_C RPA1_DBD_C: 21.3 61 0.0013 16.8 1.1 10 53-62 52-61 (166)
275 KOG0954|consensus 20.7 47 0.001 22.4 0.6 31 2-32 287-321 (893)
276 PF03966 Trm112p: Trm112p-like 20.6 53 0.0012 14.3 0.7 17 18-34 48-64 (68)
277 PF10083 DUF2321: Uncharacteri 20.5 47 0.001 17.6 0.5 19 21-39 66-84 (158)
278 KOG4118|consensus 20.3 61 0.0013 14.5 0.8 22 53-74 39-60 (74)
279 PF05207 zf-CSL: CSL zinc fing 20.0 39 0.00084 14.3 0.1 30 23-59 18-47 (55)
No 1
>KOG2462|consensus
Probab=99.87 E-value=3.7e-23 Score=109.96 Aligned_cols=71 Identities=20% Similarity=0.376 Sum_probs=56.1
Q ss_pred ccccccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHH
Q psy12029 2 ELQLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 2 ~~~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 73 (81)
.+.|+++.-|+.|.++|+|||||.|..|++.|.++++|..||.+|.+.++ |.|..|+|+|...+.|+.|..
T Consensus 194 GKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 194 GKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhHHHHHHHHHHhhh
Confidence 35677777788888888888888888888888888888888888888777 888888888888888877754
No 2
>KOG2462|consensus
Probab=99.86 E-value=1.1e-22 Score=108.13 Aligned_cols=76 Identities=17% Similarity=0.309 Sum_probs=68.9
Q ss_pred ccccccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhcCCCC
Q psy12029 2 ELQLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKHSHYQ 80 (81)
Q Consensus 2 ~~~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 80 (81)
+++|..-..|..|.++|+ -++.|.+||+.|...+-|+.|+|+|+|++| |.|..|+|.|...+||..|+++|.+.|+
T Consensus 168 ~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP-F~C~hC~kAFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 168 GKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKP-FSCPHCGKAFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred CceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCC-ccCCcccchhcchHHHHHHHHhhcCCcc
Confidence 355666667888999887 489999999999999999999999999999 9999999999999999999999998764
No 3
>KOG3623|consensus
Probab=99.63 E-value=7.4e-17 Score=95.44 Aligned_cols=71 Identities=20% Similarity=0.427 Sum_probs=62.4
Q ss_pred ccccccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHH
Q psy12029 2 ELQLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 2 ~~~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 73 (81)
++.|...++|.+|.--|+|.+||.|.+|.+.|..+-.|+-|.|.|.|++| |.|..|+|.|..+..+..|+.
T Consensus 901 DK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 901 DKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred HHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchHhhhc
Confidence 36777788889998889999999999999999999999999999999999 999999999998888887764
No 4
>KOG3576|consensus
Probab=99.57 E-value=1.6e-16 Score=82.21 Aligned_cols=74 Identities=20% Similarity=0.361 Sum_probs=60.8
Q ss_pred cccccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhcC
Q psy12029 3 LQLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 3 ~~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
+.|....-|.+|++.|...+.+.|.-||+.|...-+|.+|.++|+|.+| |+|..|++.|.+...|..|.+.-+|
T Consensus 125 K~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 125 KKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred hhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHHHHHHHcC
Confidence 3455556677888888888888898899988888888889889988888 8998899888888888888775544
No 5
>KOG3623|consensus
Probab=99.46 E-value=2.5e-14 Score=85.07 Aligned_cols=61 Identities=30% Similarity=0.652 Sum_probs=57.8
Q ss_pred cCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhcCCCC
Q psy12029 19 FADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKHSHYQ 80 (81)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 80 (81)
+.+..|.|+.|++.|.-.++|.+|.--|+|.+| |.|.+|.|.|..+..|..|+|.|.||||
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRP-yqC~iCkKAFKHKHHLtEHkRLHSGEKP 950 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRP-YQCIICKKAFKHKHHLTEHKRLHSGEKP 950 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCC-cccchhhHhhhhhhhhhhhhhhccCCCc
Confidence 345679999999999999999999999999999 9999999999999999999999999997
No 6
>KOG1074|consensus
Probab=99.39 E-value=3.2e-14 Score=85.30 Aligned_cols=76 Identities=25% Similarity=0.489 Sum_probs=62.9
Q ss_pred cccccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcCCCC---CeecC---CCCcccCCchHHHHHHHhhc
Q psy12029 3 LQLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEP---QYFCP---LCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 3 ~~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~---~~~c~---~c~~~f~~~~~l~~h~~~~~ 76 (81)
++.+.++.|+.|.++|+|++||+|++||+.|..+.+|..|+..|....+ .+.|+ +|-+.|...-.+..|+++|.
T Consensus 613 rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 613 RVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred ecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccceEEeec
Confidence 3566788899999999999999999999999999999999988765422 16677 78888888888888999888
Q ss_pred CC
Q psy12029 77 SH 78 (81)
Q Consensus 77 ~~ 78 (81)
+.
T Consensus 693 ~~ 694 (958)
T KOG1074|consen 693 GG 694 (958)
T ss_pred CC
Confidence 43
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.38 E-value=1.9e-13 Score=57.43 Aligned_cols=44 Identities=16% Similarity=0.320 Sum_probs=39.4
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHH
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLM 69 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~ 69 (81)
-|.|+.||+.|.....|..|+++|+ ++ ++|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceecccceeE
Confidence 3789999999999999999999998 57 99999999999877664
No 8
>KOG3576|consensus
Probab=99.35 E-value=7.9e-13 Score=68.78 Aligned_cols=76 Identities=20% Similarity=0.389 Sum_probs=64.7
Q ss_pred cccccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcC-----------CCCCeecCCCCcccCCchHHHHH
Q psy12029 3 LQLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECG-----------QEPQYFCPLCPYRAKQKTNLMTH 71 (81)
Q Consensus 3 ~~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~-----------~~~~~~c~~c~~~f~~~~~l~~h 71 (81)
+-|....+|.+|+++|+|.+||.|..|++.|....+|..|.+.-+| .+. |.|..||.+-.....+..|
T Consensus 153 kgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl-~vcedcg~t~~~~e~~~~h 231 (267)
T KOG3576|consen 153 KGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKL-YVCEDCGYTSERPEVYYLH 231 (267)
T ss_pred CcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhhe-eeecccCCCCCChhHHHHH
Confidence 4577788899999999999999999999999999999999875444 345 8999999998888888888
Q ss_pred HHhhcCCC
Q psy12029 72 MSIKHSHY 79 (81)
Q Consensus 72 ~~~~~~~~ 79 (81)
...++..-
T Consensus 232 ~~~~hp~S 239 (267)
T KOG3576|consen 232 LKLHHPFS 239 (267)
T ss_pred HHhcCCCC
Confidence 88877543
No 9
>PHA00733 hypothetical protein
Probab=99.33 E-value=3.1e-12 Score=62.99 Aligned_cols=63 Identities=22% Similarity=0.442 Sum_probs=52.7
Q ss_pred hhcccccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhcC
Q psy12029 11 FQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 11 l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
|..++.++ +.+||.|..|++.|.....|..|++.+ ..+ +.|..|++.|.....|..|+...|+
T Consensus 62 l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 62 LYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCccCCHHHHHHHHHHhcC
Confidence 44444443 578999999999999999999999865 356 9999999999999999999987764
No 10
>KOG1074|consensus
Probab=99.26 E-value=1.2e-12 Score=78.89 Aligned_cols=57 Identities=28% Similarity=0.585 Sum_probs=52.4
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhcCCCC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKHSHYQ 80 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 80 (81)
.+.|..|++.|...+.|..|.|+|+|++| |+|++||..|..+.+|..|...|+-.+|
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERP-fqCnvCG~~FSTkGNLKvH~~rH~e~~p 409 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERP-FQCNVCGNRFSTKGNLKVHFQRHREKYP 409 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCC-eeecccccccccccceeeeeeeccccCC
Confidence 46799999999999999999999999999 9999999999999999999888876553
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.09 E-value=1.5e-10 Score=42.09 Aligned_cols=24 Identities=38% Similarity=0.791 Sum_probs=15.9
Q ss_pred HHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 39 LARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 39 l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
|..|++.|++++| |.|..|++.|.
T Consensus 2 l~~H~~~H~~~k~-~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKP-YKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSS-EEESSSSEEES
T ss_pred HHHHhhhcCCCCC-CCCCCCcCeeC
Confidence 5566666666666 77777766664
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=99.07 E-value=2.4e-11 Score=44.27 Aligned_cols=25 Identities=8% Similarity=0.400 Sum_probs=22.9
Q ss_pred chhcccccccCCCceecCcchhhcc
Q psy12029 10 YFQITESSYFADRLFSCSGCARVYK 34 (81)
Q Consensus 10 ~l~~~~~~~~~~~~~~C~~c~~~~~ 34 (81)
+|..|+++|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4788999999999999999999885
No 13
>KOG3993|consensus
Probab=98.99 E-value=1.3e-10 Score=65.97 Aligned_cols=72 Identities=15% Similarity=0.339 Sum_probs=59.1
Q ss_pred cccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcC--------CC-------------------------C
Q psy12029 5 LLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECG--------QE-------------------------P 51 (81)
Q Consensus 5 f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~--------~~-------------------------~ 51 (81)
|-....|..|...-.....|+|++|+++|....+|..|.|+|.- .. .
T Consensus 277 YeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi 356 (500)
T KOG3993|consen 277 YEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGI 356 (500)
T ss_pred hhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCce
Confidence 44555677787766666779999999999999999999999841 11 2
Q ss_pred CeecCCCCcccCCchHHHHHHHhhcC
Q psy12029 52 QYFCPLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 52 ~~~c~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
|.|..|++.|.....|..|+.+|+.
T Consensus 357 -~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 357 -FSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred -eecHHhhhhhHHHHHHHHhHHhhhc
Confidence 7899999999999999999888774
No 14
>PHA00616 hypothetical protein
Probab=98.92 E-value=7.9e-10 Score=44.55 Aligned_cols=34 Identities=18% Similarity=0.422 Sum_probs=29.0
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPL 57 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~ 57 (81)
||.|..||+.|...+.+..|++.++++++ +.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-cceeE
Confidence 57899999999999999999999999888 77653
No 15
>KOG3608|consensus
Probab=98.91 E-value=3.1e-10 Score=63.46 Aligned_cols=69 Identities=14% Similarity=0.356 Sum_probs=50.9
Q ss_pred ccccccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcC--CCCCeecCCCCcccCCchHHHHHHH
Q psy12029 4 QLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECG--QEPQYFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 4 ~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~--~~~~~~c~~c~~~f~~~~~l~~h~~ 73 (81)
.|..++.|..|.++|+++|...|+.||..|.....|..|.+..+. ..+ |.|..|-+.|.....|..|+.
T Consensus 188 ~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~-fqC~~C~KrFaTeklL~~Hv~ 258 (467)
T KOG3608|consen 188 HMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNS-FQCAQCFKRFATEKLLKSHVV 258 (467)
T ss_pred hhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCc-hHHHHHHHHHhHHHHHHHHHH
Confidence 467788899999999999999999999999999999999886543 334 555555544444444444433
No 16
>KOG3608|consensus
Probab=98.90 E-value=9.4e-10 Score=61.61 Aligned_cols=70 Identities=17% Similarity=0.411 Sum_probs=39.7
Q ss_pred ccccccchhcccccccCCCceecCcchhhccCchHHHHHHHh-hcCCCCCeecCCCCcccCCchHHHHHHHhhc
Q psy12029 4 QLLVPFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTY-ECGQEPQYFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 4 ~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
+|.+.-.|..|+..|.. .|.|+.|+......++|..|++. |...+| |+|..|.+.+...+.|+.|..+|.
T Consensus 246 rFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkp-fKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 246 RFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKP-FKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCC-ccccchhhhhccHHHHHHHHHhcc
Confidence 44444455555555443 35566666666666666666663 444455 666666666666666666655443
No 17
>PHA00616 hypothetical protein
Probab=98.75 E-value=5.2e-09 Score=42.19 Aligned_cols=28 Identities=21% Similarity=0.437 Sum_probs=26.8
Q ss_pred eecCCCCcccCCchHHHHHHHhhcCCCC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHSHYQ 80 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 80 (81)
|.|..||+.|...+++..|++.+||+++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 8999999999999999999999999875
No 18
>PHA00732 hypothetical protein
Probab=98.74 E-value=9e-09 Score=46.80 Aligned_cols=45 Identities=22% Similarity=0.422 Sum_probs=36.2
Q ss_pred ceecCcchhhccCchHHHHHHHh-hcCCCCCeecCCCCcccCCchHHHHHHHh
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTY-ECGQEPQYFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
||.|..|++.|.....|..|++. |. + +.|..|++.|.+ +..|.++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~~---l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYRR---LNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeCC---hhhhhcc
Confidence 57899999999999999999884 43 4 789999999874 5566643
No 19
>PHA02768 hypothetical protein; Provisional
Probab=98.48 E-value=1.2e-07 Score=40.03 Aligned_cols=24 Identities=25% Similarity=0.661 Sum_probs=23.4
Q ss_pred eecCCCCcccCCchHHHHHHHhhc
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
|.|+.||+.|...++|..|+++|+
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 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.47 E-value=2.2e-07 Score=55.35 Aligned_cols=63 Identities=19% Similarity=0.358 Sum_probs=42.0
Q ss_pred ccchhcccccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC----------chHHHHHHHhh
Q psy12029 8 PFYFQITESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ----------KTNLMTHMSIK 75 (81)
Q Consensus 8 ~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~----------~~~l~~h~~~~ 75 (81)
...+..|+..++ +++.|+ |+..+ ....|..|+..|...++ +.|..|+..+.. .+.|..|..+.
T Consensus 465 ~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 465 QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCccccCccccchhhhhhhHHHHHHhc
Confidence 345667777653 677787 87544 45677777777777777 888888777641 24667776653
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=98.45 E-value=2.3e-07 Score=32.51 Aligned_cols=22 Identities=41% Similarity=0.766 Sum_probs=12.4
Q ss_pred eecCCCCcccCCchHHHHHHHh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
|.|..|++.|.....|..|++.
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 3455555555555555555554
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=98.40 E-value=9.6e-07 Score=37.41 Aligned_cols=51 Identities=27% Similarity=0.613 Sum_probs=38.7
Q ss_pred ceecCcchhhccCchHHHHHHHh-hcCC-CCCeecCCCCcccCCchHHHHHHHhhcC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTY-ECGQ-EPQYFCPLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~-~~~~-~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
.|.|+.|++. .....|..|... |..+ +. +.|++|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~-v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKN-VVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCC-ccCCCchhhhh--hHHHHHHHHhcC
Confidence 4889999994 556789899775 4443 45 89999987544 488999988774
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.38 E-value=3.6e-07 Score=31.98 Aligned_cols=23 Identities=26% Similarity=0.700 Sum_probs=21.0
Q ss_pred eecCcchhhccCchHHHHHHHhh
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYE 46 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~ 46 (81)
|.|+.|++.|.....|..|++.|
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 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=98.30 E-value=9.9e-07 Score=30.88 Aligned_cols=24 Identities=33% Similarity=0.786 Sum_probs=13.7
Q ss_pred eecCCCCcccCCchHHHHHHHhhc
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
|.|..|++.|.+...|..|+..++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 456666666666666666666553
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.25 E-value=9e-07 Score=32.15 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=17.3
Q ss_pred eecCCCCcccCCchHHHHHHHhhc
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
|.|..|++.|.....|..|++.|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 677777777777777777776654
No 26
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.21 E-value=2.5e-06 Score=35.33 Aligned_cols=29 Identities=34% Similarity=0.660 Sum_probs=16.2
Q ss_pred eecCCCCcccCCchHHHHHHHhhcCCCCC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHSHYQG 81 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~ 81 (81)
-.|++|+..+.+..+|..|+.+.|+.+||
T Consensus 25 atCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred CCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 56666666666666666666666666654
No 27
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.17 E-value=3.7e-06 Score=50.40 Aligned_cols=67 Identities=18% Similarity=0.275 Sum_probs=53.4
Q ss_pred cccchhcccccccCCCceecCcchhhccC----------chHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhc
Q psy12029 7 VPFYFQITESSYFADRLFSCSGCARVYKN----------KKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 7 ~~~~l~~~~~~~~~~~~~~C~~c~~~~~~----------~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
....|..|+.+|.+.+++.|..|+..+.. ...|..|...+ |.++ +.|..|++.+... .+..|+..-|
T Consensus 488 ~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt-~~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 488 EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRT-APCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcc-eEccccCCeeeeh-hHHHHHHHhh
Confidence 44678889999999999999999998842 24688888874 8888 9999999987766 4677776544
No 28
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.14 E-value=5.4e-06 Score=34.33 Aligned_cols=34 Identities=21% Similarity=0.415 Sum_probs=24.6
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhcCCCC
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYECGQEP 51 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~ 51 (81)
+..+.|..|++|+..+....+|.+|+...++.+|
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 4467889999999999999999999998887765
No 29
>PHA00733 hypothetical protein
Probab=98.11 E-value=1.5e-06 Score=42.98 Aligned_cols=55 Identities=18% Similarity=0.300 Sum_probs=42.2
Q ss_pred CCCceecCcchhhccCchHHHHH--HH---hhcCCCCCeecCCCCcccCCchHHHHHHHhh
Q psy12029 20 ADRLFSCSGCARVYKNKKSLARH--QT---YECGQEPQYFCPLCPYRAKQKTNLMTHMSIK 75 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h--~~---~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 75 (81)
..+++.|.+|...|.....|..+ .+ ...+..+ |.|..|++.|...+.|..|++.+
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 45778899999888876665544 11 2234667 99999999999999999999865
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.11 E-value=1.7e-06 Score=31.38 Aligned_cols=25 Identities=24% Similarity=0.761 Sum_probs=22.6
Q ss_pred ceecCcchhhccCchHHHHHHHhhc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYEC 47 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~ 47 (81)
+|.|..|+..|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5899999999999999999998764
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.03 E-value=6.2e-06 Score=28.73 Aligned_cols=23 Identities=26% Similarity=0.706 Sum_probs=19.2
Q ss_pred eecCcchhhccCchHHHHHHHhh
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYE 46 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~ 46 (81)
|.|+.|+..|.....|..|+..+
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 67999999999999999999875
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.93 E-value=3.7e-06 Score=47.11 Aligned_cols=52 Identities=29% Similarity=0.598 Sum_probs=41.0
Q ss_pred CCceecCc--chhhccCchHHHHHHHh-h------------------cCCCCCeecCCCCcccCCchHHHHHHH
Q psy12029 21 DRLFSCSG--CARVYKNKKSLARHQTY-E------------------CGQEPQYFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 21 ~~~~~C~~--c~~~~~~~~~l~~h~~~-~------------------~~~~~~~~c~~c~~~f~~~~~l~~h~~ 73 (81)
++||.|++ |++.++..--|.-|+.- | ...+| |+|++|+|.+.....|.-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP-YrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP-YRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc-eeccccchhhccCccceeccc
Confidence 59999987 99999998888777652 2 01267 999999999999888877754
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.84 E-value=2.3e-05 Score=27.59 Aligned_cols=22 Identities=36% Similarity=0.561 Sum_probs=12.6
Q ss_pred ecCCCCcccCCchHHHHHHHhh
Q psy12029 54 FCPLCPYRAKQKTNLMTHMSIK 75 (81)
Q Consensus 54 ~c~~c~~~f~~~~~l~~h~~~~ 75 (81)
.|..|++.|.....+..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4555666666666666665543
No 34
>PRK04860 hypothetical protein; Provisional
Probab=97.81 E-value=2.7e-05 Score=39.95 Aligned_cols=39 Identities=23% Similarity=0.481 Sum_probs=32.7
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQK 65 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 65 (81)
-+|.|. |+. ....+..|.+++.++++ |.|..|+..|...
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 368998 986 56678899999999999 9999999887654
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.64 E-value=5.7e-05 Score=35.39 Aligned_cols=23 Identities=30% Similarity=0.675 Sum_probs=20.4
Q ss_pred eecCCCCcccCCchHHHHHHHhh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIK 75 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~ 75 (81)
+.|..|++.|.+...|..|++.+
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCccCCCCcCHHHHHHHHcCc
Confidence 89999999999999999999864
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.62 E-value=7.2e-05 Score=26.25 Aligned_cols=24 Identities=29% Similarity=0.761 Sum_probs=20.9
Q ss_pred eecCcchhhccCchHHHHHHHhhc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYEC 47 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~ 47 (81)
+.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999988653
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.41 E-value=0.00023 Score=24.90 Aligned_cols=23 Identities=43% Similarity=0.954 Sum_probs=11.9
Q ss_pred eecCCCCcccCCchHHHHHHHhhc
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
|.|..|+.... ...|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 45666665554 556666666554
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.39 E-value=0.00018 Score=25.35 Aligned_cols=21 Identities=19% Similarity=0.692 Sum_probs=12.0
Q ss_pred eecCCCCcccCCchHHHHHHH
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~ 73 (81)
|.|.+|++.|.+...+..|++
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 345556666666666655554
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.37 E-value=0.00014 Score=25.66 Aligned_cols=23 Identities=26% Similarity=0.641 Sum_probs=20.3
Q ss_pred eecCcchhhccCchHHHHHHHhh
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYE 46 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~ 46 (81)
|.|.+|+..|.....+..|.+.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999998753
No 40
>KOG3993|consensus
Probab=97.36 E-value=2.7e-05 Score=45.16 Aligned_cols=54 Identities=24% Similarity=0.407 Sum_probs=45.6
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
..|-|..|...|.+.-.|.+|.-......- |+|.+|+|.|.=.+||..|.+=|.
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vE-YrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVE-YRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEee-ecCCcccccccCchhhhhhhcccC
Confidence 347899999999999899988765555555 999999999999999999998765
No 41
>PHA00732 hypothetical protein
Probab=97.23 E-value=0.00032 Score=32.01 Aligned_cols=25 Identities=20% Similarity=0.485 Sum_probs=22.2
Q ss_pred eecCCCCcccCCchHHHHHHHh-hcC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI-KHS 77 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~-~~~ 77 (81)
|.|..|++.|.+.+.|..|++. |.+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC
Confidence 8999999999999999999984 543
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=96.86 E-value=0.00035 Score=25.20 Aligned_cols=21 Identities=24% Similarity=0.637 Sum_probs=13.4
Q ss_pred eecCCCCcccCCchHHHHHHH
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~ 73 (81)
|.|..|++.|.+...+..|++
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 456666666666666666554
No 43
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.63 E-value=0.0025 Score=22.66 Aligned_cols=20 Identities=25% Similarity=0.536 Sum_probs=11.7
Q ss_pred eecCCCCcccCCchHHHHHHH
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~ 73 (81)
..|..||+.| ..+.|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566677776 4445666654
No 44
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.93 E-value=0.0087 Score=22.61 Aligned_cols=21 Identities=19% Similarity=0.697 Sum_probs=15.5
Q ss_pred eecCCCCcccCCchHHHHHHH
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~ 73 (81)
|.|..|+..|.....+..|..
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 677888887777777777654
No 45
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.57 E-value=0.01 Score=25.16 Aligned_cols=30 Identities=20% Similarity=0.528 Sum_probs=24.0
Q ss_pred cccCCCceecCcchhhccCchHHHHHHHhh
Q psy12029 17 SYFADRLFSCSGCARVYKNKKSLARHQTYE 46 (81)
Q Consensus 17 ~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~ 46 (81)
+--|+.-+.|+.||..|....+...|....
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 345677789999999999999888887643
No 46
>KOG2893|consensus
Probab=95.52 E-value=0.003 Score=34.61 Aligned_cols=40 Identities=25% Similarity=0.521 Sum_probs=30.5
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHH
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLM 69 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~ 69 (81)
.|..|...|.....|.+||+ .+- |+|-+|-+.+.+-..|.
T Consensus 12 wcwycnrefddekiliqhqk----akh-fkchichkkl~sgpgls 51 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----AKH-FKCHICHKKLFSGPGLS 51 (341)
T ss_pred eeeecccccchhhhhhhhhh----hcc-ceeeeehhhhccCCCce
Confidence 48889999999999999988 356 99999976554433343
No 47
>KOG1146|consensus
Probab=95.50 E-value=0.011 Score=39.30 Aligned_cols=56 Identities=25% Similarity=0.460 Sum_probs=45.0
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhc-------------------------CCCCCeecCCCCcccCCchHHHHHH
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYEC-------------------------GQEPQYFCPLCPYRAKQKTNLMTHM 72 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~-------------------------~~~~~~~c~~c~~~f~~~~~l~~h~ 72 (81)
++-.+.+.|+.|++.|+....|..|+|..+ +.++ |.|..|...+....+|.+|+
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p-~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP-YPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc-ccceeeeeeeecchHHHHHH
Confidence 555688999999999999999999999711 1235 88889998888888888887
Q ss_pred Hh
Q psy12029 73 SI 74 (81)
Q Consensus 73 ~~ 74 (81)
..
T Consensus 539 qS 540 (1406)
T KOG1146|consen 539 QS 540 (1406)
T ss_pred HH
Confidence 63
No 48
>PRK04860 hypothetical protein; Provisional
Probab=95.50 E-value=0.0047 Score=31.92 Aligned_cols=29 Identities=10% Similarity=0.284 Sum_probs=24.5
Q ss_pred ccchhcccccccCCCceecCcchhhccCc
Q psy12029 8 PFYFQITESSYFADRLFSCSGCARVYKNK 36 (81)
Q Consensus 8 ~~~l~~~~~~~~~~~~~~C~~c~~~~~~~ 36 (81)
..++..|.++++++++|.|..|+..|...
T Consensus 128 ~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 128 QLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred eCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 34568899999999999999999887654
No 49
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.45 E-value=0.011 Score=22.31 Aligned_cols=24 Identities=29% Similarity=1.075 Sum_probs=16.3
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
|.|.+||..+.... .+ +.|+.|+.
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 67888887654432 45 88888874
No 50
>KOG2186|consensus
Probab=95.01 E-value=0.027 Score=31.18 Aligned_cols=47 Identities=19% Similarity=0.378 Sum_probs=33.8
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHh
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
|.|.+||.... ...+.+|+...++ .. |.|--|++.|... .+.+|...
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn-~~-fSCIDC~k~F~~~-sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRN-AY-FSCIDCGKTFERV-SYKNHTKC 50 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccC-Ce-eEEeecccccccc-hhhhhhhh
Confidence 67888987644 3456778877766 44 8898899999884 46667654
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.57 E-value=0.0063 Score=35.13 Aligned_cols=55 Identities=24% Similarity=0.512 Sum_probs=37.6
Q ss_pred ceecCcchhhccCchHHHHHHH--hhcCC--CCCeecC--CCCcccCCchHHHHHHHhhcCC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQT--YECGQ--EPQYFCP--LCPYRAKQKTNLMTHMSIKHSH 78 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~--~~~~~--~~~~~c~--~c~~~f~~~~~l~~h~~~~~~~ 78 (81)
++.|..|...|.....+..|.+ .|.++ ++ +.|. .|++.|.+...+..|..+|.+-
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCcccccCC
Confidence 5667777777777777777777 57776 66 7777 5777777776666666665543
No 52
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.44 E-value=0.044 Score=25.47 Aligned_cols=24 Identities=21% Similarity=0.674 Sum_probs=21.2
Q ss_pred ceecCcchhhccCchHHHHHHHhh
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYE 46 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~ 46 (81)
.+.|..|+..|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 689999999999999999999964
No 53
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.46 E-value=0.1 Score=20.24 Aligned_cols=34 Identities=18% Similarity=0.532 Sum_probs=22.7
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
..|+.|+..|..... +...+... .+|..|+..|.
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 468999888877653 12233345 88999987764
No 54
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.32 E-value=0.068 Score=23.04 Aligned_cols=32 Identities=28% Similarity=0.591 Sum_probs=19.5
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCP 59 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 59 (81)
..|.|+.||..--... ++-.....+ |.|+.||
T Consensus 26 v~F~CPnCGe~~I~Rc-----~~CRk~g~~-Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRC-----AKCRKLGNP-YRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehh-----hhHHHcCCc-eECCCcC
Confidence 3488999986543322 222223456 9999987
No 55
>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=93.11 E-value=0.075 Score=25.80 Aligned_cols=30 Identities=20% Similarity=0.657 Sum_probs=20.8
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQK 65 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 65 (81)
..|+.||..|-. ....| ..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYD-----------Lnk~P-ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD-----------LNKDP-IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc-----------CCCCC-ccCCCCCCccCcc
Confidence 478999877633 22346 8899999877655
No 56
>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=92.59 E-value=0.11 Score=19.99 Aligned_cols=34 Identities=15% Similarity=0.280 Sum_probs=21.8
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
..|+.|+..|....... ...... ..|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~-v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGK-VRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCE-EECCCCCCEEE
Confidence 57999998877765421 111224 78999987664
No 57
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.48 E-value=0.022 Score=30.82 Aligned_cols=45 Identities=29% Similarity=0.696 Sum_probs=27.9
Q ss_pred CCceecCcchhhccCchHHHHHHHh---hc-------CCCCC----eecCCCCcccCCc
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTY---EC-------GQEPQ----YFCPLCPYRAKQK 65 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~---~~-------~~~~~----~~c~~c~~~f~~~ 65 (81)
++...|++|+..|..........+. .. +..|. +.|+.||.++...
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 4568999999999887654433321 11 11120 4799999876543
No 58
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=92.10 E-value=0.046 Score=25.40 Aligned_cols=32 Identities=16% Similarity=0.328 Sum_probs=21.3
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 64 (81)
..|.|+.|++. . ..+. +... |.|..|+..|.=
T Consensus 34 ~~~~Cp~C~~~-~-------VkR~--a~GI-W~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT-T-------VKRI--ATGI-WKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc-c-------eeee--ccCe-EEcCCCCCeecc
Confidence 46889999865 1 1232 2346 999999987753
No 59
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.06 E-value=0.18 Score=19.43 Aligned_cols=33 Identities=15% Similarity=0.318 Sum_probs=21.7
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCccc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRA 62 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 62 (81)
..|+.|+..|...... ....... .+|..|+..|
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 5788898888776542 2222334 7898888766
No 60
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.88 E-value=0.074 Score=30.78 Aligned_cols=52 Identities=15% Similarity=0.265 Sum_probs=43.3
Q ss_pred cccccccchhcccc--cccCC--CceecC--cchhhccCchHHHHHHHhhcCCCCCeec
Q psy12029 3 LQLLVPFYFQITES--SYFAD--RLFSCS--GCARVYKNKKSLARHQTYECGQEPQYFC 55 (81)
Q Consensus 3 ~~f~~~~~l~~~~~--~~~~~--~~~~C~--~c~~~~~~~~~l~~h~~~~~~~~~~~~c 55 (81)
..|+....+..|.. .|.++ +++.|+ .|++.|.....+..|...|.+..+ +.+
T Consensus 297 ~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 354 (467)
T COG5048 297 ISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP-AKE 354 (467)
T ss_pred CCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc-ccc
Confidence 45677778888999 79999 999999 799999999999888888887665 544
No 61
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=90.86 E-value=0.057 Score=31.07 Aligned_cols=23 Identities=35% Similarity=0.748 Sum_probs=18.6
Q ss_pred CCCceecCcchhhccCchHHHHH
Q psy12029 20 ADRLFSCSGCARVYKNKKSLARH 42 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h 42 (81)
..|||+|.+|++.++.-.-|.-|
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred cCCceeccccchhhccCccceec
Confidence 35999999999999887666554
No 62
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=90.75 E-value=0.2 Score=25.26 Aligned_cols=23 Identities=22% Similarity=0.400 Sum_probs=14.7
Q ss_pred eecCCCCcccCCchHHHHHHHhhcCC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHSH 78 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~~ 78 (81)
..|.+||+.|... ..|.+.|+|-
T Consensus 73 i~clecGk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S
T ss_pred eEEccCCcccchH---HHHHHHccCC
Confidence 6899999987764 7788888763
No 63
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=90.73 E-value=0.24 Score=27.04 Aligned_cols=30 Identities=13% Similarity=0.365 Sum_probs=22.1
Q ss_pred cCCCceecCcchhhccCchHHHHHHHhhcC
Q psy12029 19 FADRLFSCSGCARVYKNKKSLARHQTYECG 48 (81)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~ 48 (81)
.++..|.|..|++.|.....+.+|+...+.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 355679999999999999999999886443
No 64
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.70 E-value=0.17 Score=26.52 Aligned_cols=24 Identities=29% Similarity=0.949 Sum_probs=17.5
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCP 59 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 59 (81)
+.|.|.+||.. +.++.| ..|++||
T Consensus 133 ~~~vC~vCGy~-------------~~ge~P-~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEAP-EVCPICG 156 (166)
T ss_pred CEEEcCCCCCc-------------ccCCCC-CcCCCCC
Confidence 36899999744 344445 8999998
No 65
>KOG4167|consensus
Probab=90.67 E-value=0.076 Score=33.76 Aligned_cols=26 Identities=27% Similarity=0.539 Sum_probs=23.3
Q ss_pred CceecCcchhhccCchHHHHHHHhhc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYEC 47 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~ 47 (81)
.-|.|.+|++.|.-..++..||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 45999999999999999999999885
No 66
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.60 E-value=0.22 Score=18.92 Aligned_cols=25 Identities=24% Similarity=0.797 Sum_probs=15.5
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|.|.+||..+... ..| ..|+.|+.
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 46788888654321 134 67888874
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=90.39 E-value=0.14 Score=27.87 Aligned_cols=26 Identities=31% Similarity=0.498 Sum_probs=20.5
Q ss_pred eecCCCCcccCCchHHHHHHHhhcCC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHSH 78 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~~ 78 (81)
|.|.+|+|.|.-...+..|+..-|.|
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 89999999999999999998876655
No 68
>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=89.86 E-value=0.4 Score=23.09 Aligned_cols=25 Identities=32% Similarity=0.745 Sum_probs=22.4
Q ss_pred eec----CCCCcccCCchHHHHHHHhhcC
Q psy12029 53 YFC----PLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 53 ~~c----~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
|.| ..|+....+...+..|.+..||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8899999999999999998875
No 69
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=88.67 E-value=0.12 Score=20.13 Aligned_cols=30 Identities=17% Similarity=0.510 Sum_probs=19.5
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|.|..||..|...... .. ... ..|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~------~~-~~~-~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI------SD-DPL-ATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEec------CC-CCC-CCCCCCCC
Confidence 47899999887654432 11 233 57888886
No 70
>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=88.65 E-value=0.12 Score=21.37 Aligned_cols=30 Identities=17% Similarity=0.506 Sum_probs=19.3
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|.|..|+..|...... .. ... ..|+.||.
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 47899999887654321 11 234 57888885
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.45 E-value=0.5 Score=19.12 Aligned_cols=27 Identities=30% Similarity=0.752 Sum_probs=17.7
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYR 61 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 61 (81)
.|.|..||..+... ...+ ..|+.||..
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 47888888766543 1234 788888754
No 72
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=88.27 E-value=0.64 Score=19.12 Aligned_cols=8 Identities=38% Similarity=0.667 Sum_probs=3.8
Q ss_pred hHHHHHHH
Q psy12029 66 TNLMTHMS 73 (81)
Q Consensus 66 ~~l~~h~~ 73 (81)
++|..|+.
T Consensus 37 s~L~rHl~ 44 (50)
T smart00614 37 SNLRRHLR 44 (50)
T ss_pred HHHHHHHH
Confidence 34555544
No 73
>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=87.81 E-value=0.44 Score=23.87 Aligned_cols=30 Identities=10% Similarity=0.217 Sum_probs=19.6
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQK 65 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 65 (81)
..|+.||+.|-. ....| ..|+.||..|...
T Consensus 10 r~Cp~cg~kFYD-----------Lnk~p-~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LNRRP-AVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc-----------cCCCC-ccCCCcCCccCcc
Confidence 468888877633 22345 7888888776544
No 74
>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=87.50 E-value=0.44 Score=24.69 Aligned_cols=38 Identities=13% Similarity=0.311 Sum_probs=26.5
Q ss_pred cccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC
Q psy12029 17 SYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 17 ~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 64 (81)
......-|.|+.|+..|+....+. .. |.|+.||.....
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAMLDY 140 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEeee
Confidence 344556688999998877765542 24 999999876543
No 75
>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=87.25 E-value=0.85 Score=16.19 Aligned_cols=19 Identities=21% Similarity=0.607 Sum_probs=11.3
Q ss_pred ecCCCCcccCCchHHHHHHH
Q psy12029 54 FCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 54 ~c~~c~~~f~~~~~l~~h~~ 73 (81)
.|++|++.+ ....++.|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 566776665 4445666654
No 76
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=86.65 E-value=0.28 Score=19.82 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=19.4
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCccc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRA 62 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 62 (81)
..|.|+.||..+..... ... +.|+.||..+
T Consensus 2 ~~y~C~~CG~~~~~~~~----------~~~-~~Cp~CG~~~ 31 (46)
T PRK00398 2 AEYKCARCGREVELDEY----------GTG-VRCPYCGYRI 31 (46)
T ss_pred CEEECCCCCCEEEECCC----------CCc-eECCCCCCeE
Confidence 35889999877655331 114 7888888644
No 77
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.48 E-value=0.84 Score=23.32 Aligned_cols=40 Identities=15% Similarity=0.459 Sum_probs=25.9
Q ss_pred cCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 19 FADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
....-|.|+.|+..|.....+.. ... ... |.|+.||....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~-f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---LDM-DGT-FTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---cCC-CCc-EECCCCCCEEE
Confidence 34556999999988876443221 112 334 99999997654
No 78
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.94 E-value=0.55 Score=24.87 Aligned_cols=37 Identities=16% Similarity=0.437 Sum_probs=25.7
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 64 (81)
.....-|.|+.|+..|+....+. .. |.|+.||.....
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~~ 148 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLEE 148 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCee
Confidence 33455689999998877765431 24 999999976543
No 79
>PF15269 zf-C2H2_7: Zinc-finger
Probab=85.33 E-value=0.8 Score=18.62 Aligned_cols=22 Identities=36% Similarity=0.898 Sum_probs=15.9
Q ss_pred eecCCCCcccCCchHHHHHHHh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
|+|.+|.-+....+.|-+|+.-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5677777777777777777764
No 80
>KOG3408|consensus
Probab=85.20 E-value=0.9 Score=22.60 Aligned_cols=27 Identities=30% Similarity=0.492 Sum_probs=22.6
Q ss_pred cCCCceecCcchhhccCchHHHHHHHh
Q psy12029 19 FADRLFSCSGCARVYKNKKSLARHQTY 45 (81)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~ 45 (81)
+|...|.|..|.+-|.....|..|-++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 455678999999999999999888774
No 81
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=84.87 E-value=0.28 Score=22.11 Aligned_cols=37 Identities=16% Similarity=0.193 Sum_probs=18.2
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecC--CCCcccCC
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCP--LCPYRAKQ 64 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~--~c~~~f~~ 64 (81)
.|+.||.......+-.. .....+.. +.|. .||..|..
T Consensus 3 ~CP~Cg~~a~irtSr~~--s~~~~~~Y-~qC~N~eCg~tF~t 41 (72)
T PRK09678 3 HCPLCQHAAHARTSRYI--TDTTKERY-HQCQNVNCSATFIT 41 (72)
T ss_pred cCCCCCCccEEEEChhc--Chhhheee-eecCCCCCCCEEEE
Confidence 57777765433332111 11123344 6676 67776654
No 82
>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=84.44 E-value=0.45 Score=22.71 Aligned_cols=10 Identities=30% Similarity=0.481 Sum_probs=5.3
Q ss_pred eecCCCCccc
Q psy12029 53 YFCPLCPYRA 62 (81)
Q Consensus 53 ~~c~~c~~~f 62 (81)
.+|.+||..|
T Consensus 80 ~rC~eCG~~f 89 (97)
T cd00924 80 KRCPECGHVF 89 (97)
T ss_pred eeCCCCCcEE
Confidence 5555555444
No 83
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.00 E-value=1.3 Score=19.16 Aligned_cols=33 Identities=27% Similarity=0.695 Sum_probs=18.6
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
..|.|+.||..--... .+-.....+ |.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC-----~~CRk~~~~-Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRC-----EKCRKQSNP-YTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeec-----hhHHhcCCc-eECCCCCC
Confidence 4588999886522221 111112356 89988873
No 84
>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=83.28 E-value=2.1 Score=16.89 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=4.3
Q ss_pred eecCcchhhcc
Q psy12029 24 FSCSGCARVYK 34 (81)
Q Consensus 24 ~~C~~c~~~~~ 34 (81)
..|..|++.+.
T Consensus 17 a~C~~C~~~~~ 27 (45)
T PF02892_consen 17 AKCKYCGKVIK 27 (45)
T ss_dssp EEETTTTEE--
T ss_pred EEeCCCCeEEe
Confidence 44555544433
No 85
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=81.79 E-value=0.48 Score=24.48 Aligned_cols=36 Identities=28% Similarity=0.622 Sum_probs=23.0
Q ss_pred CCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCccc
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRA 62 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 62 (81)
.-+|.|. |+..+.... +|-....|+ . |.|..|+...
T Consensus 115 ~~~Y~C~-C~q~~l~~R---Rhn~~~~g~-~-YrC~~C~gkL 150 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIR---RHNTVRRGE-V-YRCGKCGGKL 150 (156)
T ss_pred ceeEEee-cCCccchhh---hcccccccc-e-EEeccCCceE
Confidence 4468899 987754432 333344455 5 9999997543
No 86
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.66 E-value=0.23 Score=25.67 Aligned_cols=11 Identities=27% Similarity=0.383 Sum_probs=5.8
Q ss_pred eecCCCCcccC
Q psy12029 53 YFCPLCPYRAK 63 (81)
Q Consensus 53 ~~c~~c~~~f~ 63 (81)
+.|+.||++|.
T Consensus 29 ~~c~~c~~~f~ 39 (154)
T PRK00464 29 RECLACGKRFT 39 (154)
T ss_pred eeccccCCcce
Confidence 45555555554
No 87
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=81.43 E-value=1 Score=18.72 Aligned_cols=29 Identities=24% Similarity=0.555 Sum_probs=18.4
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYR 61 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 61 (81)
..|.|..|++.+... ..... ..|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~-irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRG-IRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCc-eeCCCCCcE
Confidence 458899999887211 11233 788888753
No 88
>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=80.72 E-value=1.5 Score=17.60 Aligned_cols=14 Identities=29% Similarity=0.724 Sum_probs=9.2
Q ss_pred cCcchhhccCchHH
Q psy12029 26 CSGCARVYKNKKSL 39 (81)
Q Consensus 26 C~~c~~~~~~~~~l 39 (81)
|.+|+..|......
T Consensus 11 C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 11 CPVCGRPFTWRKKW 24 (42)
T ss_pred CcccCCcchHHHHH
Confidence 77777777665543
No 89
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=80.53 E-value=0.49 Score=22.29 Aligned_cols=31 Identities=13% Similarity=0.319 Sum_probs=19.3
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
..|.|+.|++.- + .+. +.-. |.|..|++.|.
T Consensus 35 a~y~CpfCgk~~-----v---kR~--a~GI-W~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHA-----V---KRQ--AVGI-WRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCc-----e---eee--eeEE-EEcCCCCCEEe
Confidence 468899887531 1 112 1235 99999988764
No 90
>KOG4167|consensus
Probab=80.53 E-value=0.31 Score=31.29 Aligned_cols=24 Identities=17% Similarity=0.236 Sum_probs=21.4
Q ss_pred eecCCCCcccCCchHHHHHHHhhc
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
|-|.+|++.|.-...++.|+++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 889999999998888999998874
No 91
>KOG2593|consensus
Probab=80.47 E-value=1.3 Score=26.74 Aligned_cols=43 Identities=16% Similarity=0.354 Sum_probs=27.1
Q ss_pred cccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcc
Q psy12029 15 ESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYR 61 (81)
Q Consensus 15 ~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 61 (81)
++..+...-|.|+.|.+.|..--.+ +-.....-. |.|..|+.-
T Consensus 120 ~~d~t~~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~-F~C~~C~ge 162 (436)
T KOG2593|consen 120 LRDDTNVAGYVCPNCQKKYTSLEAL---QLLDNETGE-FHCENCGGE 162 (436)
T ss_pred hhhccccccccCCccccchhhhHHH---HhhcccCce-EEEecCCCc
Confidence 3445566779999999888765443 222222234 899888753
No 92
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=79.61 E-value=0.49 Score=22.31 Aligned_cols=31 Identities=13% Similarity=0.358 Sum_probs=19.0
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
..|.|+.|++.- + .+.- .-. |.|..|++.|.
T Consensus 34 a~y~CpfCgk~~-----v---kR~a--~GI-W~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKT-----V---KRGS--TGI-WTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCc-----e---EEEe--eEE-EEcCCCCCEEe
Confidence 458888887531 1 1222 235 89999988764
No 93
>KOG2785|consensus
Probab=79.60 E-value=3.4 Score=24.74 Aligned_cols=52 Identities=19% Similarity=0.269 Sum_probs=38.7
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCC----------------------eecCCCC---cccCCchHHHHHHH
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQ----------------------YFCPLCP---YRAKQKTNLMTHMS 73 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~----------------------~~c~~c~---~~f~~~~~l~~h~~ 73 (81)
.|-.|-.|++.+.....-..||..++|--.| +.|..|+ +.|.+......|+.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 4566888999888877777888877663222 5677776 88888888888876
No 94
>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=79.56 E-value=0.94 Score=15.89 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=7.6
Q ss_pred CceecCcchh
Q psy12029 22 RLFSCSGCAR 31 (81)
Q Consensus 22 ~~~~C~~c~~ 31 (81)
..|.|+.||.
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4688998873
No 95
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=79.45 E-value=1.1 Score=21.62 Aligned_cols=17 Identities=18% Similarity=0.606 Sum_probs=13.8
Q ss_pred CceecCcchhhccCchH
Q psy12029 22 RLFSCSGCARVYKNKKS 38 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~ 38 (81)
.|+.|..||..|.....
T Consensus 1 MpH~CtrCG~vf~~g~~ 17 (112)
T COG3364 1 MPHQCTRCGEVFDDGSE 17 (112)
T ss_pred CCceecccccccccccH
Confidence 37889999999988654
No 96
>PLN02294 cytochrome c oxidase subunit Vb
Probab=79.26 E-value=0.96 Score=23.87 Aligned_cols=22 Identities=14% Similarity=0.230 Sum_probs=15.3
Q ss_pred ccccccCCCceecCcchhhccCc
Q psy12029 14 TESSYFADRLFSCSGCARVYKNK 36 (81)
Q Consensus 14 ~~~~~~~~~~~~C~~c~~~~~~~ 36 (81)
++..+-+ ++++|++||..|...
T Consensus 133 Wf~L~kG-kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 133 WFWLEKG-KSFECPVCTQYFELE 154 (174)
T ss_pred EEEecCC-CceeCCCCCCEEEEE
Confidence 3444444 688999999888654
No 97
>PF14353 CpXC: CpXC protein
Probab=78.65 E-value=2.7 Score=20.80 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=8.2
Q ss_pred eecCCCCcccCC
Q psy12029 53 YFCPLCPYRAKQ 64 (81)
Q Consensus 53 ~~c~~c~~~f~~ 64 (81)
+.|+.||..|.-
T Consensus 39 ~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 39 FTCPSCGHKFRL 50 (128)
T ss_pred EECCCCCCceec
Confidence 678888776543
No 98
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=76.81 E-value=3.3 Score=16.37 Aligned_cols=24 Identities=21% Similarity=0.515 Sum_probs=16.5
Q ss_pred eecCcchhhccCc--hHHHHHHHhhc
Q psy12029 24 FSCSGCARVYKNK--KSLARHQTYEC 47 (81)
Q Consensus 24 ~~C~~c~~~~~~~--~~l~~h~~~~~ 47 (81)
-.|+.||-.|... .+...|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 5799999877654 45667766653
No 99
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.46 E-value=0.93 Score=22.92 Aligned_cols=15 Identities=20% Similarity=0.662 Sum_probs=11.8
Q ss_pred CceecCcchhhccCc
Q psy12029 22 RLFSCSGCARVYKNK 36 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~ 36 (81)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 458899999887664
No 100
>PHA00626 hypothetical protein
Probab=76.08 E-value=1.6 Score=18.73 Aligned_cols=16 Identities=13% Similarity=0.389 Sum_probs=12.1
Q ss_pred CCceecCcchhhccCc
Q psy12029 21 DRLFSCSGCARVYKNK 36 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~ 36 (81)
...|.|+.||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4679999999777553
No 101
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=75.05 E-value=2.5 Score=21.56 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=16.3
Q ss_pred eecCCCCcccCCchHHHHHHHhhcC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
..|.++|+.|. .|..|..+|.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 56888888765 46778888775
No 102
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=74.94 E-value=0.7 Score=21.76 Aligned_cols=31 Identities=16% Similarity=0.343 Sum_probs=18.4
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
..|.|+.|++.- + .+.- .-. |.|..|++.|.
T Consensus 35 a~y~CpfCgk~~-----v---kR~a--~GI-W~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPK-----V---KRVG--TGI-WECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCc-----e---EEEE--EEE-EEcCCCCCEEe
Confidence 457888886431 1 1222 225 88998987664
No 103
>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=74.23 E-value=2 Score=15.26 Aligned_cols=11 Identities=45% Similarity=1.162 Sum_probs=7.0
Q ss_pred eecCCCCcccC
Q psy12029 53 YFCPLCPYRAK 63 (81)
Q Consensus 53 ~~c~~c~~~f~ 63 (81)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35677777664
No 104
>KOG1842|consensus
Probab=74.09 E-value=1.9 Score=26.36 Aligned_cols=25 Identities=24% Similarity=0.727 Sum_probs=13.2
Q ss_pred eecCCCCcccCCchHHHHHHHhhcC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
|.|++|...|.+...|+.|....|+
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhcc
Confidence 4555555555555555555554443
No 105
>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=74.08 E-value=1.8 Score=17.15 Aligned_cols=13 Identities=23% Similarity=0.416 Sum_probs=9.5
Q ss_pred eecCCCCcccCCc
Q psy12029 53 YFCPLCPYRAKQK 65 (81)
Q Consensus 53 ~~c~~c~~~f~~~ 65 (81)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 7788888777544
No 106
>KOG1146|consensus
Probab=73.12 E-value=3.1 Score=28.91 Aligned_cols=58 Identities=21% Similarity=0.387 Sum_probs=44.1
Q ss_pred cCCCceecCcchhhccCchHHHHHHHhhc--C---------------CCCCeecCCCCcccCCchHHHHHHHhhcCC
Q psy12029 19 FADRLFSCSGCARVYKNKKSLARHQTYEC--G---------------QEPQYFCPLCPYRAKQKTNLMTHMSIKHSH 78 (81)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~--~---------------~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~ 78 (81)
....+|.|..|...|.....|..|++... + ..+ | |..|...|.....|..|++.-+++
T Consensus 1280 ~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~-~-c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1280 DVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTY-H-CLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred ccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCccccc-c-chHHHhhcchhHHHHHHHHHhhhc
Confidence 34567889999999999998988886431 1 123 5 888999999999999999975543
No 107
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=72.47 E-value=1.6 Score=22.04 Aligned_cols=15 Identities=27% Similarity=0.829 Sum_probs=12.9
Q ss_pred ceecCcchhhccCch
Q psy12029 23 LFSCSGCARVYKNKK 37 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~ 37 (81)
|+.|..||..|....
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998866
No 108
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=71.13 E-value=2.2 Score=18.29 Aligned_cols=37 Identities=16% Similarity=0.374 Sum_probs=19.1
Q ss_pred eecCcchhhccCchHHHHHHHhhc-CCCCCeecCCCCcc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYEC-GQEPQYFCPLCPYR 61 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~-~~~~~~~c~~c~~~ 61 (81)
..|..|++.+........-.+... .... |.|..|...
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 467788876555332112222212 2234 889888643
No 109
>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=70.53 E-value=1.7 Score=22.13 Aligned_cols=22 Identities=23% Similarity=0.249 Sum_probs=14.0
Q ss_pred ccccccCCCceecCcchhhccCc
Q psy12029 14 TESSYFADRLFSCSGCARVYKNK 36 (81)
Q Consensus 14 ~~~~~~~~~~~~C~~c~~~~~~~ 36 (81)
++..+-+ ++.+|+.||..|...
T Consensus 104 W~~l~~g-~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 104 WFWLHKG-KPQRCPECGQVFKLK 125 (136)
T ss_dssp EEEEETT-SEEEETTTEEEEEEE
T ss_pred EEEEeCC-CccCCCCCCeEEEEE
Confidence 3444444 478888888777654
No 110
>COG1773 Rubredoxin [Energy production and conversion]
Probab=70.48 E-value=1.8 Score=18.47 Aligned_cols=15 Identities=40% Similarity=0.822 Sum_probs=11.9
Q ss_pred ceecCcchhhccCch
Q psy12029 23 LFSCSGCARVYKNKK 37 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~ 37 (81)
.+.|.+||..|.-..
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 588999999887653
No 111
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.65 E-value=9.9 Score=22.78 Aligned_cols=65 Identities=14% Similarity=0.185 Sum_probs=36.4
Q ss_pred cccchhcccccccCC---Cce-ecCcchhhccCchHHHHHHHhhcCCCCCeecCCCC----cccCCchHHHHHHH
Q psy12029 7 VPFYFQITESSYFAD---RLF-SCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCP----YRAKQKTNLMTHMS 73 (81)
Q Consensus 7 ~~~~l~~~~~~~~~~---~~~-~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~----~~f~~~~~l~~h~~ 73 (81)
....|..|+.....+ +-+ .|.-|...|-.-..|..|.+..+.. - +.|...+ ..|..-..|-.|.+
T Consensus 200 ~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~HE~-C-hICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 200 RSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHEA-C-HICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred ecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhhhh-h-hhhhccCccchhhhhCHHHHHHHhh
Confidence 344566676654433 222 3777888787777888888864432 2 4554433 23444455555544
No 112
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.25 E-value=3 Score=19.07 Aligned_cols=30 Identities=20% Similarity=0.631 Sum_probs=17.7
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|.|..|+..|. +.+++. +-|.-.|+.|+.
T Consensus 12 ~Y~c~~cg~~~d----vvq~~~----ddplt~ce~c~a 41 (82)
T COG2331 12 SYECTECGNRFD----VVQAMT----DDPLTTCEECGA 41 (82)
T ss_pred EEeecccchHHH----HHHhcc----cCccccChhhCh
Confidence 478999987763 333333 223246777764
No 113
>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=67.61 E-value=3.5 Score=15.24 Aligned_cols=8 Identities=38% Similarity=1.003 Sum_probs=5.4
Q ss_pred eecCCCCc
Q psy12029 53 YFCPLCPY 60 (81)
Q Consensus 53 ~~c~~c~~ 60 (81)
+.|+.|+.
T Consensus 20 ~vCp~C~~ 27 (30)
T PF08274_consen 20 LVCPECGH 27 (30)
T ss_dssp EEETTTTE
T ss_pred EeCCcccc
Confidence 67777764
No 114
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=67.41 E-value=3 Score=20.50 Aligned_cols=26 Identities=23% Similarity=0.525 Sum_probs=17.2
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
-...|..|+..|..... . +.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~------------~-~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEID------------L-YRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCCc------------C-ccCcCCcC
Confidence 34779999876654321 3 67888874
No 115
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.19 E-value=3.6 Score=20.22 Aligned_cols=14 Identities=14% Similarity=0.280 Sum_probs=9.1
Q ss_pred CCCeecCCCCcccCC
Q psy12029 50 EPQYFCPLCPYRAKQ 64 (81)
Q Consensus 50 ~~~~~c~~c~~~f~~ 64 (81)
.| ..|+.||+.|+.
T Consensus 25 dP-iVsPytG~s~P~ 38 (129)
T COG4530 25 DP-IVSPYTGKSYPR 38 (129)
T ss_pred Cc-cccCcccccchH
Confidence 35 677777777743
No 116
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=65.78 E-value=2.8 Score=23.33 Aligned_cols=18 Identities=17% Similarity=0.637 Sum_probs=14.4
Q ss_pred CCCceecCcchhhccCch
Q psy12029 20 ADRLFSCSGCARVYKNKK 37 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~ 37 (81)
..++.+|.+||..|....
T Consensus 178 EGkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCCccCCCCCcEEEEEE
Confidence 456899999999887754
No 117
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=64.80 E-value=3.1 Score=17.34 Aligned_cols=17 Identities=18% Similarity=0.604 Sum_probs=13.2
Q ss_pred CCceecCcchhhccCch
Q psy12029 21 DRLFSCSGCARVYKNKK 37 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~ 37 (81)
++.+.|..||..|....
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 46788999998877654
No 118
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=64.41 E-value=4.1 Score=19.96 Aligned_cols=26 Identities=23% Similarity=0.461 Sum_probs=16.4
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
....|..|+..|.... .. +.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~------------~~-~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ------------HD-AQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC------------cC-ccCcCCCC
Confidence 3477888986654432 23 66888874
No 119
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=63.88 E-value=5.9 Score=24.16 Aligned_cols=29 Identities=28% Similarity=0.701 Sum_probs=19.0
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCc
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQK 65 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 65 (81)
.|+.||....+ .|..- |+|..||..+...
T Consensus 352 ~Cp~Cg~~m~S-----------~G~~g-~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKS-----------AGRNG-FRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhh-----------cCCCC-cccccccccCCcc
Confidence 68888865322 23445 8898898776554
No 120
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=63.76 E-value=4.6 Score=16.92 Aligned_cols=40 Identities=33% Similarity=0.742 Sum_probs=20.9
Q ss_pred CceecCc--chhhccCchHHHHHHHhhcCCCCCeecCC----CCcccC
Q psy12029 22 RLFSCSG--CARVYKNKKSLARHQTYECGQEPQYFCPL----CPYRAK 63 (81)
Q Consensus 22 ~~~~C~~--c~~~~~~~~~l~~h~~~~~~~~~~~~c~~----c~~~f~ 63 (81)
.+..|+. |...+. ...|..|....-...+ ..|.. |+..+.
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRP-VPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSE-EE-SS----S--EEE
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCc-EECCCCCCCCCCccc
Confidence 4567776 433333 4567788775555555 77877 765543
No 121
>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=63.62 E-value=2.8 Score=17.48 Aligned_cols=13 Identities=23% Similarity=0.659 Sum_probs=7.0
Q ss_pred ecCcchhhccCch
Q psy12029 25 SCSGCARVYKNKK 37 (81)
Q Consensus 25 ~C~~c~~~~~~~~ 37 (81)
.|++|+..|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999998887654
No 122
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=61.80 E-value=4.2 Score=15.90 Aligned_cols=14 Identities=21% Similarity=0.729 Sum_probs=11.0
Q ss_pred ceecCcchhhccCc
Q psy12029 23 LFSCSGCARVYKNK 36 (81)
Q Consensus 23 ~~~C~~c~~~~~~~ 36 (81)
|+.|..|+..|...
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78898888887664
No 123
>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=61.63 E-value=8.6 Score=19.67 Aligned_cols=47 Identities=13% Similarity=0.160 Sum_probs=26.7
Q ss_pred eecCcchhhccCchHHHHHHHhh-----cCCCCCeecCCCCcccCCchHHHHH
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYE-----CGQEPQYFCPLCPYRAKQKTNLMTH 71 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~-----~~~~~~~~c~~c~~~f~~~~~l~~h 71 (81)
-+|..|+..+.....-....... ....- |.|+.|++.|..-+++.+-
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f-~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEF-WRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeE-EECCCCCCEecccccHHHH
Confidence 56999987554432211000010 11223 7899999999887776543
No 124
>KOG4727|consensus
Probab=61.63 E-value=4.8 Score=21.45 Aligned_cols=22 Identities=23% Similarity=0.428 Sum_probs=18.8
Q ss_pred ceecCcchhhccCchHHHHHHH
Q psy12029 23 LFSCSGCARVYKNKKSLARHQT 44 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~ 44 (81)
-|-|.+|+-++...-++..|+-
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 3889999999999888888764
No 125
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=61.21 E-value=3.2 Score=19.65 Aligned_cols=32 Identities=25% Similarity=0.516 Sum_probs=21.9
Q ss_pred CCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
-+|..|..||..|.... -.+| ..|+.|.....
T Consensus 56 v~Pa~CkkCGfef~~~~----------ik~p-SRCP~CKSE~I 87 (97)
T COG3357 56 VRPARCKKCGFEFRDDK----------IKKP-SRCPKCKSEWI 87 (97)
T ss_pred ecChhhcccCccccccc----------cCCc-ccCCcchhhcc
Confidence 46889999998886521 1245 88988875443
No 126
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=60.89 E-value=6.5 Score=19.22 Aligned_cols=25 Identities=28% Similarity=0.515 Sum_probs=20.5
Q ss_pred CCCceecCcchhhccCchHHHHHHH
Q psy12029 20 ADRLFSCSGCARVYKNKKSLARHQT 44 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h~~ 44 (81)
|-..+-|.+|.+.|.....|..|.+
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhc
Confidence 4456789999999999988887765
No 127
>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=60.81 E-value=1.6 Score=15.93 Aligned_cols=9 Identities=33% Similarity=1.091 Sum_probs=4.8
Q ss_pred ecCcchhhc
Q psy12029 25 SCSGCARVY 33 (81)
Q Consensus 25 ~C~~c~~~~ 33 (81)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455555555
No 128
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.41 E-value=3 Score=18.22 Aligned_cols=45 Identities=22% Similarity=0.473 Sum_probs=28.5
Q ss_pred ccccccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 14 TESSYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 14 ~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
+..++.+..++.|+.-+..+.....+. ..+...+..|+.|+..|.
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 667788889999987665544332221 113333368999998765
No 129
>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=58.97 E-value=1.2 Score=18.72 Aligned_cols=25 Identities=16% Similarity=0.377 Sum_probs=13.7
Q ss_pred CCceecCcchhhccCchHHHHHHHh
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTY 45 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~ 45 (81)
...|.|+.|...|...-++-.|...
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CCeEECCCCCCccccCcChhhhccc
Confidence 3569999999999887776655443
No 130
>KOG0717|consensus
Probab=58.96 E-value=7.1 Score=24.21 Aligned_cols=21 Identities=24% Similarity=0.572 Sum_probs=17.5
Q ss_pred eecCCCCcccCCchHHHHHHH
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~ 73 (81)
+-|.+|.+.|.+...+.+|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 578899999999888888865
No 131
>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=58.65 E-value=4 Score=16.20 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=9.7
Q ss_pred CceecCcchhhccCc
Q psy12029 22 RLFSCSGCARVYKNK 36 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~ 36 (81)
.|+.|..|+..|...
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 578999999988764
No 132
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.53 E-value=5.7 Score=19.59 Aligned_cols=14 Identities=29% Similarity=0.788 Sum_probs=9.8
Q ss_pred CceecCcchhhccC
Q psy12029 22 RLFSCSGCARVYKN 35 (81)
Q Consensus 22 ~~~~C~~c~~~~~~ 35 (81)
-.+.|..|+..|..
T Consensus 70 ~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 70 VELECKDCSHVFKP 83 (117)
T ss_pred CEEEhhhCCCcccc
Confidence 34779999866644
No 133
>KOG2231|consensus
Probab=56.50 E-value=15 Score=23.99 Aligned_cols=47 Identities=23% Similarity=0.508 Sum_probs=28.3
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecCCC------CcccCCchHHHHHHHhhc
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCPLC------PYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c------~~~f~~~~~l~~h~~~~~ 76 (81)
.|..|...|.....|..|++.++ |.|..| ...|..-..|..|.+..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 47777777777777777777543 333333 234555566777766544
No 134
>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=55.45 E-value=6.1 Score=15.31 Aligned_cols=12 Identities=17% Similarity=0.894 Sum_probs=6.4
Q ss_pred CceecCcchhhc
Q psy12029 22 RLFSCSGCARVY 33 (81)
Q Consensus 22 ~~~~C~~c~~~~ 33 (81)
+-|.|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 358899998754
No 135
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=55.01 E-value=3.2 Score=25.50 Aligned_cols=38 Identities=26% Similarity=0.616 Sum_probs=22.8
Q ss_pred CCCceecCcchhhccCch-HHHHHHHhhcC------CCCCeecCCCCc
Q psy12029 20 ADRLFSCSGCARVYKNKK-SLARHQTYECG------QEPQYFCPLCPY 60 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~-~l~~h~~~~~~------~~~~~~c~~c~~ 60 (81)
....|.|..|+..+.... .-. +....| ... |.|+.|+.
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~--~~~~~gt~~~~lp~~-~~cp~c~~ 466 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPM--QDVAPGTPWSEVPDN-FLCPECSL 466 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcc--cCCCCCCChhhCCCC-CcCcCCCC
Confidence 456799999998887642 111 111111 123 89999974
No 136
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=54.96 E-value=9.3 Score=21.72 Aligned_cols=12 Identities=25% Similarity=0.836 Sum_probs=8.7
Q ss_pred eecCCCCcccCC
Q psy12029 53 YFCPLCPYRAKQ 64 (81)
Q Consensus 53 ~~c~~c~~~f~~ 64 (81)
|.|..|+..|.-
T Consensus 156 f~C~~C~h~F~G 167 (278)
T PF15135_consen 156 FHCPKCRHNFRG 167 (278)
T ss_pred eecccccccchh
Confidence 778888877653
No 137
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=54.37 E-value=12 Score=16.22 Aligned_cols=30 Identities=20% Similarity=0.610 Sum_probs=17.8
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 64 (81)
..|+.||..... ...... |.|..||..+..
T Consensus 29 q~C~~CG~~~~~----------~~~~r~-~~C~~Cg~~~~r 58 (69)
T PF07282_consen 29 QTCPRCGHRNKK----------RRSGRV-FTCPNCGFEMDR 58 (69)
T ss_pred cCccCccccccc----------ccccce-EEcCCCCCEECc
Confidence 357778755333 122334 899999876443
No 138
>KOG2807|consensus
Probab=54.35 E-value=30 Score=20.70 Aligned_cols=55 Identities=18% Similarity=0.274 Sum_probs=32.4
Q ss_pred CCceecCcchhhccCchHHHHHHHhh---------------------------cCCCCCeecCCCCcccCCchHHHHHHH
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTYE---------------------------CGQEPQYFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~---------------------------~~~~~~~~c~~c~~~f~~~~~l~~h~~ 73 (81)
.-|..|+.|+........|.+.-+.. .+... |.|..|...|....+.-.|-.
T Consensus 288 sLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~-y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 288 SLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGR-YRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred cCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCc-EEchhccceeeccchHHHHhh
Confidence 34667888887777776665322110 00112 667777777777766666666
Q ss_pred hhc
Q psy12029 74 IKH 76 (81)
Q Consensus 74 ~~~ 76 (81)
.|.
T Consensus 367 Lh~ 369 (378)
T KOG2807|consen 367 LHN 369 (378)
T ss_pred hhc
Confidence 554
No 139
>KOG0978|consensus
Probab=54.31 E-value=2.9 Score=27.06 Aligned_cols=18 Identities=17% Similarity=0.196 Sum_probs=13.9
Q ss_pred eecCCCCcccCCchHHHH
Q psy12029 53 YFCPLCPYRAKQKTNLMT 70 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~ 70 (81)
-+|+.|+..|.....+..
T Consensus 679 RKCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHRI 696 (698)
T ss_pred CCCCCCCCCCCccccccc
Confidence 589999999987765543
No 140
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=54.18 E-value=11 Score=16.09 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=7.1
Q ss_pred CCCceecCcchhh
Q psy12029 20 ADRLFSCSGCARV 32 (81)
Q Consensus 20 ~~~~~~C~~c~~~ 32 (81)
+...|.|+.||..
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 3445666666643
No 141
>PRK04351 hypothetical protein; Provisional
Probab=53.42 E-value=7.7 Score=20.09 Aligned_cols=33 Identities=27% Similarity=0.591 Sum_probs=20.2
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 64 (81)
.|.|..|+..+... +.+. ... |.|..|+..+..
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~n-~~~-yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRIN-TKR-YRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee-------eecC-CCc-EEeCCCCcEeee
Confidence 47898888655332 2222 244 899999866543
No 142
>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=53.17 E-value=7.1 Score=14.92 Aligned_cols=12 Identities=17% Similarity=0.249 Sum_probs=5.3
Q ss_pred ecCCCCcccCCc
Q psy12029 54 FCPLCPYRAKQK 65 (81)
Q Consensus 54 ~c~~c~~~f~~~ 65 (81)
.|.+|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 577777766543
No 143
>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=53.07 E-value=5.1 Score=16.69 Aligned_cols=13 Identities=23% Similarity=0.830 Sum_probs=10.5
Q ss_pred eecCcchhhccCc
Q psy12029 24 FSCSGCARVYKNK 36 (81)
Q Consensus 24 ~~C~~c~~~~~~~ 36 (81)
|.|.+||..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6899999888754
No 144
>KOG4173|consensus
Probab=52.95 E-value=12 Score=20.76 Aligned_cols=50 Identities=30% Similarity=0.480 Sum_probs=26.6
Q ss_pred ecCcchhhccCchHHHHHHHh-h---------cCCCCCeecCC--CCcccCCchHHHHHHHhh
Q psy12029 25 SCSGCARVYKNKKSLARHQTY-E---------CGQEPQYFCPL--CPYRAKQKTNLMTHMSIK 75 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~-~---------~~~~~~~~c~~--c~~~f~~~~~l~~h~~~~ 75 (81)
.|..|.+.|....-|..|+.. | .|..- |.|.+ |+-.|.....-.+|+-..
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dM-y~ClvEgCt~KFkT~r~RkdH~I~~ 169 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDM-YQCLVEGCTEKFKTSRDRKDHMIRM 169 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccH-HHHHHHhhhhhhhhhhhhhhHHHHh
Confidence 566666666666555555542 2 12222 55633 666666666666665543
No 145
>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=52.91 E-value=27 Score=16.92 Aligned_cols=36 Identities=8% Similarity=0.231 Sum_probs=21.5
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|.|+..+..|.+-......+... ..+. |.|...|+
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~y-~~~v-wtC~~TGk 38 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMILY-NQRV-WTCEITGK 38 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHHH-hCCe-eEEecCCC
Confidence 466777777777766655444332 2344 77777665
No 146
>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=52.57 E-value=5.7 Score=16.31 Aligned_cols=14 Identities=36% Similarity=0.935 Sum_probs=10.5
Q ss_pred eecCcchhhccCch
Q psy12029 24 FSCSGCARVYKNKK 37 (81)
Q Consensus 24 ~~C~~c~~~~~~~~ 37 (81)
|.|.+|+..+....
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 68999998776643
No 147
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=51.73 E-value=3.8 Score=16.50 Aligned_cols=27 Identities=26% Similarity=0.619 Sum_probs=14.7
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
+.|+.||.. ....+ ..... |.|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~-------~~~~~-~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRL-------KTRGR-YRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEe-------CCCCe-EECCCCCC
Confidence 668888754 11111 11344 88887764
No 148
>KOG2482|consensus
Probab=50.89 E-value=12 Score=22.45 Aligned_cols=22 Identities=27% Similarity=0.433 Sum_probs=19.9
Q ss_pred eecCCCCcccCCchHHHHHHHh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
+.|..|-+.|.....|..||+.
T Consensus 196 ~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred heeeeeccccCCcHHHHHHHHh
Confidence 5888999999999999999984
No 149
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.39 E-value=13 Score=18.38 Aligned_cols=49 Identities=16% Similarity=0.320 Sum_probs=30.5
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCchHHHHHHHhhc
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQKTNLMTHMSIKH 76 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 76 (81)
.|-.|...|........ ..-..... |.|..|...|-..-..-.|..+|.
T Consensus 57 ~C~~C~~~f~~~~~~~~--~~~~~~~~-y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPF--DELKDSHR-YVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccc--cccccccc-eeCCCCCCccccccchhhhhhccC
Confidence 37778887765432110 11223334 899999998887777767766664
No 150
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=49.56 E-value=19 Score=22.49 Aligned_cols=23 Identities=22% Similarity=0.670 Sum_probs=17.9
Q ss_pred eecCCCCcccCCchHHHHHHHhh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIK 75 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~ 75 (81)
|.|+.|.+.|.....+..|+..-
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~e 80 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQE 80 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHh
Confidence 57788888888888888887643
No 151
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=48.96 E-value=19 Score=13.98 Aligned_cols=21 Identities=14% Similarity=0.471 Sum_probs=15.8
Q ss_pred CCceecCcchhhccCchHHHH
Q psy12029 21 DRLFSCSGCARVYKNKKSLAR 41 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~ 41 (81)
-....|..|+..+.....|.+
T Consensus 17 ~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEEECCCCCeEEccHHHHHH
Confidence 345779999998888777654
No 152
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=48.77 E-value=3.3 Score=16.80 Aligned_cols=37 Identities=14% Similarity=0.157 Sum_probs=18.3
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecCC--CCcccCC
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCPL--CPYRAKQ 64 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~--c~~~f~~ 64 (81)
.|+.||.......+... .....+.. +.|.. ||..|..
T Consensus 1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y-~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQL--SPLTRELY-CQCTNPECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhh--CcceEEEE-EEECCCcCCCEEEE
Confidence 37777765544443221 11222334 56643 7776653
No 153
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=48.48 E-value=12 Score=15.49 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=7.9
Q ss_pred eecCCCCccc
Q psy12029 53 YFCPLCPYRA 62 (81)
Q Consensus 53 ~~c~~c~~~f 62 (81)
+.|..|+..+
T Consensus 38 ~~C~~Cgyt~ 47 (50)
T PRK00432 38 WHCGKCGYTE 47 (50)
T ss_pred EECCCcCCEE
Confidence 8899898654
No 154
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=48.24 E-value=27 Score=19.15 Aligned_cols=35 Identities=20% Similarity=0.427 Sum_probs=18.2
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCccc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRA 62 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 62 (81)
-+.|+.|+ .-.....+. +. -+..+.+.|..||..+
T Consensus 6 y~~Cp~Cg-~eev~hEVi---k~-~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 6 YIECPSCG-SEEVSHEVI---KE-RGREPLVRCEECGTVH 40 (201)
T ss_pred EEECCCCC-cchhhHHHH---Hh-cCCceEEEccCCCcEe
Confidence 46799997 211111121 11 1332337899998765
No 155
>PF06651 DUF1163: Protein of unknown function (DUF1163); InterPro: IPR009544 This entry represents the C terminus of hypothetical Arabidopsis thaliana proteins of unknown function.
Probab=47.88 E-value=8.6 Score=17.12 Aligned_cols=36 Identities=6% Similarity=0.152 Sum_probs=25.3
Q ss_pred ccccccccchhcccccccCCCceecCcchhhccCch
Q psy12029 2 ELQLLVPFYFQITESSYFADRLFSCSGCARVYKNKK 37 (81)
Q Consensus 2 ~~~f~~~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~ 37 (81)
|-+|.....|......-+|...|.|.+.-..|-..+
T Consensus 18 evrfGsrl~L~DCR~~ttg~M~y~Cde~~LRFEpgs 53 (70)
T PF06651_consen 18 EVRFGSRLFLTDCRKGTTGVMSYACDEVTLRFEPGS 53 (70)
T ss_pred eeeeeeeEeccccccCccceeeEEecceEEEecCCc
Confidence 346777777777777777888888887665554443
No 156
>KOG2636|consensus
Probab=47.77 E-value=15 Score=22.81 Aligned_cols=29 Identities=31% Similarity=0.511 Sum_probs=21.3
Q ss_pred ccccCCCceecCcch-hhccCchHHHHHHH
Q psy12029 16 SSYFADRLFSCSGCA-RVYKNKKSLARHQT 44 (81)
Q Consensus 16 ~~~~~~~~~~C~~c~-~~~~~~~~l~~h~~ 44 (81)
+-|.-.+.|.|.+|| .++.-...+.+|=.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 446667889999999 56666677776654
No 157
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=47.72 E-value=8.6 Score=19.39 Aligned_cols=16 Identities=13% Similarity=0.686 Sum_probs=11.7
Q ss_pred CCceecCcchhhccCc
Q psy12029 21 DRLFSCSGCARVYKNK 36 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~ 36 (81)
...|.|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 5568888888877664
No 158
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=47.69 E-value=11 Score=19.23 Aligned_cols=32 Identities=25% Similarity=0.640 Sum_probs=18.4
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
.|.|..|+..+.... +. .... |.|..|+..+.
T Consensus 123 ~~~C~~C~~~~~r~~------~~--~~~~-~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHR------RS--KRKR-YRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeec------cc--chhh-EECCCCCCEEE
Confidence 477888876653322 22 1223 78888876543
No 159
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=47.33 E-value=32 Score=20.10 Aligned_cols=21 Identities=29% Similarity=0.782 Sum_probs=12.0
Q ss_pred eecCCCCcccCCchHHHHHHH
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMS 73 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~ 73 (81)
|.|..|-+.|.+...+..|+.
T Consensus 49 yiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 49 YICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEcCCCcchhCCHHHHHHHHH
Confidence 555555555555555555554
No 160
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=47.08 E-value=14 Score=22.78 Aligned_cols=10 Identities=30% Similarity=0.756 Sum_probs=6.6
Q ss_pred ceecCcchhh
Q psy12029 23 LFSCSGCARV 32 (81)
Q Consensus 23 ~~~C~~c~~~ 32 (81)
.|.|..||..
T Consensus 7 ~y~C~~Cg~~ 16 (454)
T TIGR00416 7 KFVCQHCGAD 16 (454)
T ss_pred eEECCcCCCC
Confidence 3777777754
No 161
>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=46.70 E-value=13 Score=18.30 Aligned_cols=11 Identities=36% Similarity=0.987 Sum_probs=5.9
Q ss_pred eecCCCCcccC
Q psy12029 53 YFCPLCPYRAK 63 (81)
Q Consensus 53 ~~c~~c~~~f~ 63 (81)
|.|+.|+..+.
T Consensus 20 ~iCpeC~~EW~ 30 (109)
T TIGR00686 20 LICPSCLYEWN 30 (109)
T ss_pred eECcccccccc
Confidence 55665655443
No 162
>KOG2071|consensus
Probab=46.40 E-value=16 Score=23.35 Aligned_cols=27 Identities=15% Similarity=0.390 Sum_probs=20.7
Q ss_pred CCceecCcchhhccCchHHHHHHHhhc
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTYEC 47 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~ 47 (81)
..+-.|..||..|.+......||..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456789999999999877666666553
No 163
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.19 E-value=6.6 Score=16.28 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=10.9
Q ss_pred cCcchhhccCchHH
Q psy12029 26 CSGCARVYKNKKSL 39 (81)
Q Consensus 26 C~~c~~~~~~~~~l 39 (81)
|++|+..|......
T Consensus 15 CpvCqRPFsWRkKW 28 (54)
T COG4338 15 CPVCQRPFSWRKKW 28 (54)
T ss_pred hhhhcCchHHHHHH
Confidence 88999888876644
No 164
>PRK11823 DNA repair protein RadA; Provisional
Probab=45.96 E-value=15 Score=22.58 Aligned_cols=10 Identities=20% Similarity=0.776 Sum_probs=7.0
Q ss_pred ceecCcchhh
Q psy12029 23 LFSCSGCARV 32 (81)
Q Consensus 23 ~~~C~~c~~~ 32 (81)
.|.|..||..
T Consensus 7 ~y~C~~Cg~~ 16 (446)
T PRK11823 7 AYVCQECGAE 16 (446)
T ss_pred eEECCcCCCC
Confidence 4778888754
No 165
>KOG3352|consensus
Probab=45.84 E-value=8.6 Score=20.04 Aligned_cols=15 Identities=20% Similarity=0.501 Sum_probs=11.1
Q ss_pred CceecCcchhhccCc
Q psy12029 22 RLFSCSGCARVYKNK 36 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~ 36 (81)
+.++|.+||..|...
T Consensus 132 e~~rc~eCG~~fkL~ 146 (153)
T KOG3352|consen 132 ETQRCPECGHYFKLV 146 (153)
T ss_pred CcccCCcccceEEee
Confidence 466799999887643
No 166
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=44.90 E-value=21 Score=20.26 Aligned_cols=38 Identities=26% Similarity=0.481 Sum_probs=22.1
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
|..-....|..|+..+...... . ....+..| .|..|+.
T Consensus 117 HGsl~~~~C~~C~~~~~~~~~~-~--~~~~~~~p--~C~~Cg~ 154 (250)
T COG0846 117 HGSLKRVRCSKCGNQYYDEDVI-K--FIEDGLIP--RCPKCGG 154 (250)
T ss_pred ccceeeeEeCCCcCccchhhhh-h--hcccCCCC--cCccCCC
Confidence 4445668899998877644311 1 11222334 7888886
No 167
>PRK05978 hypothetical protein; Provisional
Probab=44.66 E-value=7.5 Score=20.18 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=16.9
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 64 (81)
-+|+.|++.--....|. .. -.|..||..|..
T Consensus 34 grCP~CG~G~LF~g~Lk---------v~-~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAFLK---------PV-DHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccccccc---------cC-CCccccCCcccc
Confidence 46888886533332221 12 367778765543
No 168
>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=44.47 E-value=10 Score=19.65 Aligned_cols=28 Identities=21% Similarity=0.482 Sum_probs=17.2
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
..+.|..||..... .+++..| .|+.|+.
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 35889999865322 2334444 7888875
No 169
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.72 E-value=8.5 Score=18.90 Aligned_cols=13 Identities=15% Similarity=0.355 Sum_probs=8.8
Q ss_pred CceecCcchhhcc
Q psy12029 22 RLFSCSGCARVYK 34 (81)
Q Consensus 22 ~~~~C~~c~~~~~ 34 (81)
-.+.|..|+..|.
T Consensus 69 ~~~~C~~Cg~~~~ 81 (114)
T PRK03681 69 AECWCETCQQYVT 81 (114)
T ss_pred cEEEcccCCCeee
Confidence 3477888886553
No 170
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=43.64 E-value=6.1 Score=25.86 Aligned_cols=11 Identities=36% Similarity=0.760 Sum_probs=7.1
Q ss_pred CCCeecCCCCcc
Q psy12029 50 EPQYFCPLCPYR 61 (81)
Q Consensus 50 ~~~~~c~~c~~~ 61 (81)
.| ..|+.||..
T Consensus 474 ~p-~~Cp~Cgs~ 484 (730)
T COG1198 474 IP-QSCPECGSE 484 (730)
T ss_pred CC-CCCCCCCCC
Confidence 44 777777753
No 171
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=42.90 E-value=24 Score=18.77 Aligned_cols=47 Identities=15% Similarity=0.212 Sum_probs=26.6
Q ss_pred eecCcchhhccCchHHHHHHHh-----hcCCCCCeecCCCCcccCCchHHHHH
Q psy12029 24 FSCSGCARVYKNKKSLARHQTY-----ECGQEPQYFCPLCPYRAKQKTNLMTH 71 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~-----~~~~~~~~~c~~c~~~f~~~~~l~~h 71 (81)
-+|+.|+......+.-..--+. .....- |.|..||+.|.--+++..-
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f-~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEF-YRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccce-eECCCCcccccCchHHHHH
Confidence 4699998765443321100000 011223 6799999999887776543
No 172
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=42.81 E-value=29 Score=14.47 Aligned_cols=32 Identities=31% Similarity=0.643 Sum_probs=18.0
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcc
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYR 61 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 61 (81)
.|..|.-..+.... .....+... ..|+.|++.
T Consensus 24 ~C~gC~~~l~~~~~----~~i~~~~~i-~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPPQEL----NEIRKGDEI-VFCPNCGRI 55 (56)
T ss_pred ccCCCCEEcCHHHH----HHHHcCCCe-EECcCCCcc
Confidence 57777654433221 223344556 789999863
No 173
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=42.59 E-value=39 Score=18.97 Aligned_cols=38 Identities=18% Similarity=0.361 Sum_probs=21.6
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
|..-....|..|+..+....... .......| .|+.|+.
T Consensus 114 HG~~~~~~C~~C~~~~~~~~~~~---~~~~~~~p--~Cp~Cgg 151 (244)
T PRK14138 114 HGNVEEYYCVRCGKRYTVEDVIE---KLEKSDVP--RCDDCSG 151 (244)
T ss_pred cCCcCeeEECCCCCcccHHHHHH---HHhcCCCC--CCCCCCC
Confidence 44445577999998776543322 11122334 6888874
No 174
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.55 E-value=3.4 Score=23.14 Aligned_cols=31 Identities=16% Similarity=0.380 Sum_probs=21.7
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhcC
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYECG 48 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~ 48 (81)
...++.+.|++|+..|.....+..-.|+-.|
T Consensus 14 ~f~kk~ieCPvC~tkFkkeev~tgsiRiiag 44 (267)
T COG1655 14 LFYKKTIECPVCNTKFKKEEVKTGSIRIIAG 44 (267)
T ss_pred HHhhceeccCcccchhhhhheeccceeEecc
Confidence 3356778999999999887666555554443
No 175
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.27 E-value=7.2 Score=19.69 Aligned_cols=13 Identities=31% Similarity=0.506 Sum_probs=9.8
Q ss_pred eecCCCCcccCCc
Q psy12029 53 YFCPLCPYRAKQK 65 (81)
Q Consensus 53 ~~c~~c~~~f~~~ 65 (81)
--|..||+.|++-
T Consensus 69 sfchncgs~fpwt 81 (160)
T COG4306 69 SFCHNCGSRFPWT 81 (160)
T ss_pred chhhcCCCCCCcH
Confidence 6677888888764
No 176
>PF14369 zf-RING_3: zinc-finger
Probab=41.15 E-value=11 Score=14.33 Aligned_cols=10 Identities=20% Similarity=0.727 Sum_probs=8.1
Q ss_pred ecCcchhhcc
Q psy12029 25 SCSGCARVYK 34 (81)
Q Consensus 25 ~C~~c~~~~~ 34 (81)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998774
No 177
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=40.73 E-value=16 Score=20.13 Aligned_cols=17 Identities=12% Similarity=0.530 Sum_probs=11.6
Q ss_pred CCCCeecCCCCcccCCc
Q psy12029 49 QEPQYFCPLCPYRAKQK 65 (81)
Q Consensus 49 ~~~~~~c~~c~~~f~~~ 65 (81)
++.||.|.+|.+.|.++
T Consensus 193 e~IPF~C~iCKkdy~sp 209 (259)
T COG5152 193 EKIPFLCGICKKDYESP 209 (259)
T ss_pred CCCceeehhchhhccch
Confidence 33339998888777654
No 178
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=40.72 E-value=22 Score=18.94 Aligned_cols=19 Identities=37% Similarity=0.756 Sum_probs=12.9
Q ss_pred CceecCcchhhccCchHHH
Q psy12029 22 RLFSCSGCARVYKNKKSLA 40 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~ 40 (81)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4667888888887655443
No 179
>PHA02998 RNA polymerase subunit; Provisional
Probab=39.69 E-value=3.7 Score=21.99 Aligned_cols=39 Identities=18% Similarity=0.306 Sum_probs=21.1
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCC---eecCCCCcccCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQ---YFCPLCPYRAKQK 65 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~---~~c~~c~~~f~~~ 65 (81)
...|+.|+..-..... .+.| ....|+ |.|..||..|.-+
T Consensus 143 ~v~CPkCg~~~A~f~q--lQTR--SADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPMM--IQTR--AADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEEE--Eeec--cCCCCceEEEEcCCCCCccCCc
Confidence 4678888853222222 2223 222232 7899999876543
No 180
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.63 E-value=28 Score=20.16 Aligned_cols=7 Identities=29% Similarity=0.932 Sum_probs=3.3
Q ss_pred ecCCCCc
Q psy12029 54 FCPLCPY 60 (81)
Q Consensus 54 ~c~~c~~ 60 (81)
.|..|+-
T Consensus 271 ~C~~Cgt 277 (279)
T TIGR00627 271 ICKTCKT 277 (279)
T ss_pred CCCCCCC
Confidence 4444543
No 181
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=39.55 E-value=16 Score=18.60 Aligned_cols=32 Identities=22% Similarity=0.581 Sum_probs=17.6
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCccc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRA 62 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 62 (81)
.|.|..|+..+... .+ +..... |.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~~------rr-~~~~~~-y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLRV------RR-SNNVSR-YRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCceE------cc-ccCcce-EEcCCCCCEE
Confidence 57788787654321 11 111134 7888887654
No 182
>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=39.36 E-value=20 Score=13.42 Aligned_cols=11 Identities=27% Similarity=0.766 Sum_probs=5.2
Q ss_pred eecCCCCcccC
Q psy12029 53 YFCPLCPYRAK 63 (81)
Q Consensus 53 ~~c~~c~~~f~ 63 (81)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 44555655443
No 183
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.28 E-value=12 Score=18.68 Aligned_cols=33 Identities=15% Similarity=0.247 Sum_probs=17.9
Q ss_pred CCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.-.+.| .|+..|.....-.. + -... +.|+.||.
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~----~-~~~~-~~CP~Cgs 100 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEID----H-YAAV-IECPVCGN 100 (124)
T ss_pred CeeEEe-eCcCcccccccchh----c-cccC-CcCcCCCC
Confidence 344789 99977665421000 0 0112 57888874
No 184
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=39.20 E-value=10 Score=20.73 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=0.0
Q ss_pred cccCCCceecCcchh-hccCchHHHHH
Q psy12029 17 SYFADRLFSCSGCAR-VYKNKKSLARH 42 (81)
Q Consensus 17 ~~~~~~~~~C~~c~~-~~~~~~~l~~h 42 (81)
-|.-.+.|.|.+||. +|.-...+.+|
T Consensus 95 LhGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 95 LHGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ---------------------------
T ss_pred HhCCCCeeeeEeCCCcceecHHHHHHh
Confidence 355567789999985 33334444444
No 185
>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=38.63 E-value=31 Score=19.98 Aligned_cols=16 Identities=31% Similarity=0.675 Sum_probs=9.8
Q ss_pred ccCCCceecCcchhhc
Q psy12029 18 YFADRLFSCSGCARVY 33 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~ 33 (81)
..|.+.|.|..|...+
T Consensus 137 ~hGGrif~CsfC~~fl 152 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFL 152 (314)
T ss_pred cCCCeEEEeecCCCee
Confidence 4456677777776543
No 186
>KOG2907|consensus
Probab=38.57 E-value=12 Score=18.58 Aligned_cols=41 Identities=22% Similarity=0.439 Sum_probs=21.7
Q ss_pred CceecCcchhhccCchHHHHHHHh-hcCCCCCeecCCCCcccCC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTY-ECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~ 64 (81)
....|+.||..--. .-...+|+ .-|+---|.|..|+..|..
T Consensus 73 I~~kCpkCghe~m~--Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 73 IKHKCPKCGHEEMS--YHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hhccCcccCCchhh--hhhhhcccccCCceEEEEcCccceeeec
Confidence 34678888753211 11122332 3343322789999877653
No 187
>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=38.16 E-value=30 Score=14.18 Aligned_cols=10 Identities=30% Similarity=1.208 Sum_probs=4.0
Q ss_pred eecCcchhhc
Q psy12029 24 FSCSGCARVY 33 (81)
Q Consensus 24 ~~C~~c~~~~ 33 (81)
+.|..||..|
T Consensus 19 ~~Cr~Cg~~~ 28 (57)
T cd00065 19 HHCRNCGRIF 28 (57)
T ss_pred cccCcCcCCc
Confidence 3344444433
No 188
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=37.86 E-value=16 Score=24.10 Aligned_cols=35 Identities=26% Similarity=0.657 Sum_probs=21.5
Q ss_pred CCCcee-cCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcc
Q psy12029 20 ADRLFS-CSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYR 61 (81)
Q Consensus 20 ~~~~~~-C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 61 (81)
.-+.|+ |+.|.+.|.+..+ .|.|. .| ..|+.||..
T Consensus 147 sM~~F~lC~~C~~EY~dP~n----RRfHA--Qp-~aCp~CGP~ 182 (750)
T COG0068 147 SMADFPLCPFCDKEYKDPLN----RRFHA--QP-IACPKCGPH 182 (750)
T ss_pred ccccCcCCHHHHHHhcCccc----ccccc--cc-ccCcccCCC
Confidence 334444 7778777776654 24443 35 688888863
No 189
>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=37.63 E-value=28 Score=13.37 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=5.7
Q ss_pred cCCCCCeecCCC
Q psy12029 47 CGQEPQYFCPLC 58 (81)
Q Consensus 47 ~~~~~~~~c~~c 58 (81)
.|... |.|..|
T Consensus 25 ~G~qr-yrC~~C 35 (36)
T PF03811_consen 25 SGHQR-YRCKDC 35 (36)
T ss_pred CCCEe-EecCcC
Confidence 34344 666655
No 190
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=37.62 E-value=14 Score=14.32 Aligned_cols=14 Identities=14% Similarity=0.529 Sum_probs=7.8
Q ss_pred ecCcchhhccCchH
Q psy12029 25 SCSGCARVYKNKKS 38 (81)
Q Consensus 25 ~C~~c~~~~~~~~~ 38 (81)
.|..|++.|.....
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 57777777666543
No 191
>PRK12722 transcriptional activator FlhC; Provisional
Probab=37.51 E-value=24 Score=19.21 Aligned_cols=28 Identities=21% Similarity=0.516 Sum_probs=17.1
Q ss_pred eecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
..|..|+..|..... ..... |.|..|..
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~-f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGS-FVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCC-CcCCCCCC
Confidence 568888887764321 11234 88888853
No 192
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=37.49 E-value=15 Score=14.46 Aligned_cols=9 Identities=22% Similarity=0.593 Sum_probs=6.0
Q ss_pred ceecCcchh
Q psy12029 23 LFSCSGCAR 31 (81)
Q Consensus 23 ~~~C~~c~~ 31 (81)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 456777773
No 193
>PRK12860 transcriptional activator FlhC; Provisional
Probab=37.43 E-value=22 Score=19.35 Aligned_cols=28 Identities=21% Similarity=0.585 Sum_probs=17.0
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCP 59 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 59 (81)
...|..|+..|..... ..... |.|..|.
T Consensus 134 l~~C~~Cgg~fv~~~~--------e~~~~-f~CplC~ 161 (189)
T PRK12860 134 LARCCRCGGKFVTHAH--------DLRHN-FVCGLCQ 161 (189)
T ss_pred eccCCCCCCCeecccc--------ccCCC-CcCCCCC
Confidence 3568888887754321 12234 8888885
No 194
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.05 E-value=21 Score=20.41 Aligned_cols=12 Identities=25% Similarity=0.913 Sum_probs=8.6
Q ss_pred eecCCCCcccCC
Q psy12029 53 YFCPLCPYRAKQ 64 (81)
Q Consensus 53 ~~c~~c~~~f~~ 64 (81)
|.|+.||..+..
T Consensus 323 ~~C~~cg~~~~r 334 (364)
T COG0675 323 FKCPRCGFVHDR 334 (364)
T ss_pred EECCCCCCeehh
Confidence 888888865443
No 195
>KOG0317|consensus
Probab=37.02 E-value=21 Score=20.77 Aligned_cols=32 Identities=25% Similarity=0.559 Sum_probs=19.5
Q ss_pred ecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 25 SCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
.|..||..|.+..-+ ...+++. +|+.|...|.
T Consensus 253 SaTpCGHiFCWsCI~-----~w~~ek~--eCPlCR~~~~ 284 (293)
T KOG0317|consen 253 SATPCGHIFCWSCIL-----EWCSEKA--ECPLCREKFQ 284 (293)
T ss_pred CcCcCcchHHHHHHH-----HHHcccc--CCCcccccCC
Confidence 355688888776532 3345554 6888875543
No 196
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=36.81 E-value=23 Score=21.31 Aligned_cols=9 Identities=33% Similarity=0.829 Sum_probs=5.1
Q ss_pred ceecCcchh
Q psy12029 23 LFSCSGCAR 31 (81)
Q Consensus 23 ~~~C~~c~~ 31 (81)
-..|+.|+.
T Consensus 14 ~g~cp~c~~ 22 (372)
T cd01121 14 LGKCPECGE 22 (372)
T ss_pred cEECcCCCC
Confidence 345666654
No 197
>KOG1280|consensus
Probab=36.44 E-value=49 Score=20.02 Aligned_cols=43 Identities=19% Similarity=0.460 Sum_probs=26.7
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHh-hcCCCCCeecCCCCc
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTY-ECGQEPQYFCPLCPY 60 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~ 60 (81)
+-...-|.|+.|+..-.....+.-|... |....+...|..|+.
T Consensus 74 ~y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 74 HYDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 3345578999999866666667666654 333333256777753
No 198
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=36.13 E-value=12 Score=20.64 Aligned_cols=24 Identities=21% Similarity=0.369 Sum_probs=0.0
Q ss_pred eecCCCCcccCCchHHHHHHHhhcC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHS 77 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~ 77 (81)
..|++||...+.. .+..|+++.+.
T Consensus 169 ~~cPitGe~IP~~-e~~eHmRi~Ll 192 (229)
T PF12230_consen 169 IICPITGEMIPAD-EMDEHMRIELL 192 (229)
T ss_dssp -------------------------
T ss_pred ccccccccccccc-ccccccccccc
Confidence 6788898876544 57888887653
No 199
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=35.89 E-value=16 Score=20.93 Aligned_cols=32 Identities=22% Similarity=0.568 Sum_probs=21.1
Q ss_pred CCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCC
Q psy12029 20 ADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCP 59 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 59 (81)
.+..-.|+.||+-......+ | +--. |+|..|.
T Consensus 217 ~e~~r~CP~Cg~~W~L~~pl--h-----~iFd-FKCD~CR 248 (258)
T PF10071_consen 217 SEQARKCPSCGGDWRLKEPL--H-----DIFD-FKCDPCR 248 (258)
T ss_pred HhhCCCCCCCCCccccCCch--h-----hcee-ccCCcce
Confidence 34556799999876665544 2 2234 8999885
No 200
>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=35.24 E-value=19 Score=14.27 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=9.0
Q ss_pred CceecCcchhhc
Q psy12029 22 RLFSCSGCARVY 33 (81)
Q Consensus 22 ~~~~C~~c~~~~ 33 (81)
++..|+-|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467888888765
No 201
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=35.07 E-value=20 Score=13.27 Aligned_cols=11 Identities=18% Similarity=0.863 Sum_probs=8.0
Q ss_pred ceecCcchhhc
Q psy12029 23 LFSCSGCARVY 33 (81)
Q Consensus 23 ~~~C~~c~~~~ 33 (81)
-|.|..||...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 47888888654
No 202
>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=34.82 E-value=20 Score=13.74 Aligned_cols=11 Identities=27% Similarity=0.615 Sum_probs=6.0
Q ss_pred eecCCCCcccC
Q psy12029 53 YFCPLCPYRAK 63 (81)
Q Consensus 53 ~~c~~c~~~f~ 63 (81)
+.|..||+.|-
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 34666665543
No 203
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=34.72 E-value=6.7 Score=21.41 Aligned_cols=39 Identities=23% Similarity=0.433 Sum_probs=21.1
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCC---CCeecCCCCcccCC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQE---PQYFCPLCPYRAKQ 64 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~---~~~~c~~c~~~f~~ 64 (81)
...|++|+..+.....+. --.|-|+. . +.|..||..+..
T Consensus 14 ~~~CPvCg~~l~~~~~~~--~IPyFG~V~i~t-~~C~~CgYR~~D 55 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLY--DIPYFGEVLIST-GVCERCGYRSTD 55 (201)
T ss_pred eecCCcccceeeEEEeee--cCCccceEEEEE-EEccccCCcccc
Confidence 356999987554443321 11233432 2 468888866543
No 204
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=34.38 E-value=25 Score=14.46 Aligned_cols=23 Identities=22% Similarity=0.561 Sum_probs=9.0
Q ss_pred ccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 33 YKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 33 ~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
|.....|...+. ... |.|+.|++
T Consensus 27 FDl~~fl~~~~~----~~~-W~CPiC~~ 49 (50)
T PF02891_consen 27 FDLESFLESNQR----TPK-WKCPICNK 49 (50)
T ss_dssp EEHHHHHHHHHH----S----B-TTT--
T ss_pred ECHHHHHHHhhc----cCC-eECcCCcC
Confidence 544444443332 234 89998874
No 205
>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 TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=34.13 E-value=21 Score=13.17 Aligned_cols=12 Identities=17% Similarity=0.866 Sum_probs=8.9
Q ss_pred CceecCcchhhc
Q psy12029 22 RLFSCSGCARVY 33 (81)
Q Consensus 22 ~~~~C~~c~~~~ 33 (81)
+-|.|..|+...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 358899988754
No 207
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=33.71 E-value=29 Score=13.52 Aligned_cols=10 Identities=40% Similarity=0.873 Sum_probs=7.1
Q ss_pred eecCCCCccc
Q psy12029 53 YFCPLCPYRA 62 (81)
Q Consensus 53 ~~c~~c~~~f 62 (81)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6787787654
No 208
>PF12907 zf-met2: Zinc-binding
Probab=33.55 E-value=8.9 Score=15.23 Aligned_cols=8 Identities=25% Similarity=0.974 Sum_probs=3.5
Q ss_pred ecCCCCcc
Q psy12029 54 FCPLCPYR 61 (81)
Q Consensus 54 ~c~~c~~~ 61 (81)
.|.+|..+
T Consensus 3 ~C~iC~qt 10 (40)
T PF12907_consen 3 ICKICRQT 10 (40)
T ss_pred CcHHhhHH
Confidence 44444433
No 209
>PTZ00448 hypothetical protein; Provisional
Probab=33.31 E-value=37 Score=20.61 Aligned_cols=22 Identities=14% Similarity=0.386 Sum_probs=16.3
Q ss_pred eecCCCCcccCCchHHHHHHHh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
|.|..|+-.|........|.++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccccccccccCCHHHHHHHhhh
Confidence 7799998888776666666653
No 210
>PTZ00064 histone acetyltransferase; Provisional
Probab=33.29 E-value=50 Score=21.12 Aligned_cols=22 Identities=27% Similarity=0.430 Sum_probs=17.3
Q ss_pred eecCCCCcccCCchHHHHHHHh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
|.|..|-+.|.....+..|+..
T Consensus 281 YICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 281 HFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred EEccchhhhhCCHHHHHHHHhc
Confidence 7788888888888888888763
No 211
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=33.25 E-value=11 Score=23.78 Aligned_cols=37 Identities=19% Similarity=0.498 Sum_probs=21.6
Q ss_pred eecCcchhhccCchHHHHHHHhhcC----CCCCeecCCCCcccCC
Q psy12029 24 FSCSGCARVYKNKKSLARHQTYECG----QEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~----~~~~~~c~~c~~~f~~ 64 (81)
.+|+.||..+.....- .+...+ .-. |.|..||..+..
T Consensus 201 vpCPhCg~~~~l~~~~---l~w~~~~~~~~a~-y~C~~Cg~~i~e 241 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWEN---LKWDKGEAPETAR-YVCPHCGCEIEE 241 (557)
T ss_pred ccCCCCCCCccccccc---eeecCCCCccceE-EECCCCcCCCCH
Confidence 5699999876654211 222211 223 899999876543
No 212
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=33.07 E-value=28 Score=16.55 Aligned_cols=12 Identities=17% Similarity=0.711 Sum_probs=6.7
Q ss_pred ceecCcchhhcc
Q psy12029 23 LFSCSGCARVYK 34 (81)
Q Consensus 23 ~~~C~~c~~~~~ 34 (81)
.+.|+.|+..+.
T Consensus 16 ~~~C~~C~~~~~ 27 (104)
T TIGR01384 16 VYVCPSCGYEKE 27 (104)
T ss_pred eEECcCCCCccc
Confidence 456666665433
No 213
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.95 E-value=29 Score=15.25 Aligned_cols=7 Identities=57% Similarity=1.744 Sum_probs=3.5
Q ss_pred eecCCCC
Q psy12029 53 YFCPLCP 59 (81)
Q Consensus 53 ~~c~~c~ 59 (81)
|.|++|.
T Consensus 32 ymC~eC~ 38 (68)
T COG4896 32 YMCPECE 38 (68)
T ss_pred EechhhH
Confidence 4555553
No 214
>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=32.67 E-value=17 Score=15.42 Aligned_cols=31 Identities=19% Similarity=0.469 Sum_probs=20.3
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCccc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRA 62 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 62 (81)
.+.|+.||..+...... .|+ . ..|..||..+
T Consensus 2 ~~~CP~CG~~iev~~~~-------~Ge-i-V~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPE-------LGE-L-VICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCc-------cCC-E-EeCCCCCCEE
Confidence 36899999876543321 233 4 7899998655
No 215
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=32.33 E-value=45 Score=20.85 Aligned_cols=22 Identities=41% Similarity=0.766 Sum_probs=17.3
Q ss_pred eecCCCCcccCCchHHHHHHHh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
|.|..|-+.|.....+..|+..
T Consensus 199 yiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 199 YFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred EEchhhhhhhcCHHHHHHHHhc
Confidence 7788888888888888888763
No 216
>KOG3214|consensus
Probab=31.97 E-value=24 Score=17.17 Aligned_cols=41 Identities=17% Similarity=0.254 Sum_probs=20.9
Q ss_pred CCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCCc
Q psy12029 20 ADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQK 65 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 65 (81)
-...|.|..|..--.....+- +.+. ... ..|.+|+..|...
T Consensus 20 ldt~FnClfcnHek~v~~~~D---k~~~-iG~-~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 20 LDTQFNCLFCNHEKSVSCTLD---KKHN-IGK-ASCRICEESFQTT 60 (109)
T ss_pred hheeeccCccccccceeeeeh---hhcC-cce-eeeeehhhhhccc
Confidence 345677887764332222221 1111 123 5788888777643
No 217
>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=31.80 E-value=25 Score=13.61 Aligned_cols=10 Identities=40% Similarity=0.736 Sum_probs=6.0
Q ss_pred eecCCCCccc
Q psy12029 53 YFCPLCPYRA 62 (81)
Q Consensus 53 ~~c~~c~~~f 62 (81)
|.|..|+..|
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 5666666543
No 218
>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=31.79 E-value=62 Score=17.87 Aligned_cols=37 Identities=19% Similarity=0.294 Sum_probs=20.1
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
|..-....|..|+..+..... . .......| .|+.|+.
T Consensus 108 HG~l~~~~C~~C~~~~~~~~~-~---~~~~~~~p--~C~~Cgg 144 (222)
T cd01413 108 HGTLQTAYCVNCGSKYDLEEV-K---YAKKHEVP--RCPKCGG 144 (222)
T ss_pred cCCcCcceECCCCCCcchhHH-H---HhccCCCC--cCCCCCC
Confidence 444455778889877654432 1 11112233 6888864
No 219
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=30.60 E-value=24 Score=16.76 Aligned_cols=31 Identities=13% Similarity=0.380 Sum_probs=19.1
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
..|.|+.|++.--. +.- .-. |.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a--~GI-W~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVA--TGI-WKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEE--------EEE--TTE-EEETTTTEEEE
T ss_pred CCCcCCCCCCceeE--------Eee--eEE-eecCCCCCEEe
Confidence 45889998865211 122 225 99999988764
No 220
>PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Probab=29.71 E-value=70 Score=21.44 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=19.4
Q ss_pred eecCCCCcccCCchHHHHHHHhhcCCCCC
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIKHSHYQG 81 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~ 81 (81)
..|+-||++....-.+...++..++..+|
T Consensus 635 isCPgCGRT~~dlq~~~~~I~~~~~hl~G 663 (733)
T PLN02925 635 VSCPSCGRTLFDLQEVSAEIREKTSHLPG 663 (733)
T ss_pred EECCCCCCccccHHHHHHHHHHHhhcCCC
Confidence 46888998877665666666666655544
No 221
>COG2879 Uncharacterized small protein [Function unknown]
Probab=29.69 E-value=62 Score=14.32 Aligned_cols=17 Identities=29% Similarity=0.389 Sum_probs=11.9
Q ss_pred CchHHHHHHHhhcCCCC
Q psy12029 64 QKTNLMTHMSIKHSHYQ 80 (81)
Q Consensus 64 ~~~~l~~h~~~~~~~~~ 80 (81)
.-+++-.|++.+|.++|
T Consensus 24 dYdnYVehmr~~hPd~p 40 (65)
T COG2879 24 DYDNYVEHMRKKHPDKP 40 (65)
T ss_pred cHHHHHHHHHHhCcCCC
Confidence 44567778888777665
No 222
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=29.63 E-value=44 Score=14.20 Aligned_cols=17 Identities=6% Similarity=0.391 Sum_probs=8.6
Q ss_pred CCceecCcchhhccCch
Q psy12029 21 DRLFSCSGCARVYKNKK 37 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~ 37 (81)
+.|.....|+..|....
T Consensus 22 ~~PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEA 38 (57)
T ss_dssp SSEEEESSS--EEEHHH
T ss_pred hCCcCcCCCCCeecHHH
Confidence 34566666766665544
No 223
>PLN02748 tRNA dimethylallyltransferase
Probab=29.61 E-value=51 Score=20.70 Aligned_cols=21 Identities=19% Similarity=0.430 Sum_probs=16.3
Q ss_pred eecCCCCc-ccCCchHHHHHHH
Q psy12029 53 YFCPLCPY-RAKQKTNLMTHMS 73 (81)
Q Consensus 53 ~~c~~c~~-~f~~~~~l~~h~~ 73 (81)
|.|..|++ .+.-...+..|++
T Consensus 419 ~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 419 YVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred ccccCCCCcccCCHHHHHHHhc
Confidence 78999997 6777777777765
No 224
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=29.45 E-value=25 Score=15.15 Aligned_cols=12 Identities=17% Similarity=0.473 Sum_probs=5.2
Q ss_pred eecCcchhhccC
Q psy12029 24 FSCSGCARVYKN 35 (81)
Q Consensus 24 ~~C~~c~~~~~~ 35 (81)
..|++|++....
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468888776544
No 225
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=28.34 E-value=24 Score=13.93 Aligned_cols=10 Identities=20% Similarity=0.481 Sum_probs=4.9
Q ss_pred CceecCcchh
Q psy12029 22 RLFSCSGCAR 31 (81)
Q Consensus 22 ~~~~C~~c~~ 31 (81)
+..+|+.|+.
T Consensus 2 ~h~pCP~CGG 11 (40)
T PF08273_consen 2 KHGPCPICGG 11 (40)
T ss_dssp EEE--TTTT-
T ss_pred CCCCCCCCcC
Confidence 3457888885
No 226
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=27.44 E-value=61 Score=15.42 Aligned_cols=18 Identities=22% Similarity=0.519 Sum_probs=10.9
Q ss_pred CCCeecCCCCcccCCchH
Q psy12029 50 EPQYFCPLCPYRAKQKTN 67 (81)
Q Consensus 50 ~~~~~c~~c~~~f~~~~~ 67 (81)
.|...|..||-.+.....
T Consensus 33 VPa~~C~~CGe~y~~dev 50 (89)
T TIGR03829 33 TPSISCSHCGMEYQDDTT 50 (89)
T ss_pred CCcccccCCCcEeecHHH
Confidence 344677777776655443
No 227
>PRK06260 threonine synthase; Validated
Probab=27.18 E-value=36 Score=20.53 Aligned_cols=14 Identities=14% Similarity=0.719 Sum_probs=7.4
Q ss_pred ceecCcchhhccCc
Q psy12029 23 LFSCSGCARVYKNK 36 (81)
Q Consensus 23 ~~~C~~c~~~~~~~ 36 (81)
.+.|+.|+..+...
T Consensus 19 ~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 19 IYTCPECGGLLEVI 32 (397)
T ss_pred cccCCCCCCeEEEE
Confidence 35566666544433
No 228
>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=26.43 E-value=24 Score=17.18 Aligned_cols=9 Identities=22% Similarity=0.586 Sum_probs=5.5
Q ss_pred ceecCcchh
Q psy12029 23 LFSCSGCAR 31 (81)
Q Consensus 23 ~~~C~~c~~ 31 (81)
|-.|+-||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 455666665
No 229
>KOG0227|consensus
Probab=26.39 E-value=51 Score=18.18 Aligned_cols=27 Identities=19% Similarity=0.378 Sum_probs=18.3
Q ss_pred cccccCCCceecCcchhhccCchHHHHHH
Q psy12029 15 ESSYFADRLFSCSGCARVYKNKKSLARHQ 43 (81)
Q Consensus 15 ~~~~~~~~~~~C~~c~~~~~~~~~l~~h~ 43 (81)
++.|.| .|.|..|.....+..++..|.
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 455666 488888887777766666554
No 230
>KOG0782|consensus
Probab=26.32 E-value=11 Score=24.30 Aligned_cols=27 Identities=15% Similarity=0.200 Sum_probs=16.1
Q ss_pred hhcccccccCCCceecCcchhhccCch
Q psy12029 11 FQITESSYFADRLFSCSGCARVYKNKK 37 (81)
Q Consensus 11 l~~~~~~~~~~~~~~C~~c~~~~~~~~ 37 (81)
+..|-=.|.....-.|..|++.|.++-
T Consensus 241 fvrHHWVHrrRqeGkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 241 FVRHHWVHRRRQEGKCNTCGKGFQQKF 267 (1004)
T ss_pred chHHhHhhHhhhccccchhhhhhhhhe
Confidence 344444455555567888887775544
No 231
>PRK01343 zinc-binding protein; Provisional
Probab=26.20 E-value=52 Score=14.22 Aligned_cols=12 Identities=17% Similarity=0.504 Sum_probs=8.5
Q ss_pred ceecCcchhhcc
Q psy12029 23 LFSCSGCARVYK 34 (81)
Q Consensus 23 ~~~C~~c~~~~~ 34 (81)
...|++|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 356888888754
No 232
>KOG0562|consensus
Probab=26.11 E-value=80 Score=17.06 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=8.4
Q ss_pred eecCcchhhccCchHHHHHHH
Q psy12029 24 FSCSGCARVYKNKKSLARHQT 44 (81)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~ 44 (81)
.+|..|+.....-..|..|.+
T Consensus 154 LrC~~Cq~~~~~~~kLK~Hl~ 174 (184)
T KOG0562|consen 154 LRCWRCQTFGPHFPKLKAHLR 174 (184)
T ss_pred eeehhhhhcccccHHHHHHHH
Confidence 444444432222334444444
No 233
>KOG3014|consensus
Probab=26.06 E-value=55 Score=18.81 Aligned_cols=31 Identities=19% Similarity=0.386 Sum_probs=22.0
Q ss_pred cccCCCce---ecCcchhhccCc--hHHHHHHHhhc
Q psy12029 17 SYFADRLF---SCSGCARVYKNK--KSLARHQTYEC 47 (81)
Q Consensus 17 ~~~~~~~~---~C~~c~~~~~~~--~~l~~h~~~~~ 47 (81)
...|.+.+ .|..|+..+... .+...|+..|.
T Consensus 28 ld~Gqk~fg~~~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 28 LDAGQKDFGAVKCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred eecCccccCceehhhcCceecCCCHHHHHHHHHHHH
Confidence 34455544 699999877664 46778988887
No 234
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=26.01 E-value=27 Score=20.98 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=5.8
Q ss_pred eecCCCCccc
Q psy12029 53 YFCPLCPYRA 62 (81)
Q Consensus 53 ~~c~~c~~~f 62 (81)
|.|+.||..+
T Consensus 266 wrCpkCGg~i 275 (403)
T COG1379 266 WRCPKCGGKI 275 (403)
T ss_pred ccCcccccch
Confidence 5666666533
No 235
>PRK05580 primosome assembly protein PriA; Validated
Probab=25.98 E-value=15 Score=23.91 Aligned_cols=9 Identities=33% Similarity=0.729 Sum_probs=6.0
Q ss_pred eecCCCCcc
Q psy12029 53 YFCPLCPYR 61 (81)
Q Consensus 53 ~~c~~c~~~ 61 (81)
..|+.|+..
T Consensus 422 ~~Cp~Cg~~ 430 (679)
T PRK05580 422 KACPECGST 430 (679)
T ss_pred CCCCCCcCC
Confidence 677777643
No 236
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=25.94 E-value=52 Score=17.29 Aligned_cols=39 Identities=23% Similarity=0.401 Sum_probs=22.5
Q ss_pred ccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcc
Q psy12029 18 YFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYR 61 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 61 (81)
|..-....|..|+..+....... ..... .. -.|..|+..
T Consensus 100 HG~l~~~~C~~C~~~~~~~~~~~---~~~~~-~~-~~C~~C~~~ 138 (178)
T PF02146_consen 100 HGSLFRLRCSKCGKEYDREDIVD---SIDEE-EP-PRCPKCGGL 138 (178)
T ss_dssp TEEEEEEEETTTSBEEEGHHHHH---HHHTT-SS-CBCTTTSCB
T ss_pred HhhhceeeecCCCccccchhhcc---ccccc-cc-ccccccCcc
Confidence 44445578999998876543221 12222 23 478888763
No 237
>PF12773 DZR: Double zinc ribbon
Probab=25.93 E-value=43 Score=13.35 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=6.1
Q ss_pred eecCCCCcc
Q psy12029 53 YFCPLCPYR 61 (81)
Q Consensus 53 ~~c~~c~~~ 61 (81)
..|..|+..
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 567777764
No 238
>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=25.80 E-value=20 Score=19.53 Aligned_cols=13 Identities=15% Similarity=0.393 Sum_probs=7.4
Q ss_pred ceecCcchhhccC
Q psy12029 23 LFSCSGCARVYKN 35 (81)
Q Consensus 23 ~~~C~~c~~~~~~ 35 (81)
+-.|.+|+..|..
T Consensus 6 ~rKCKvCg~~F~P 18 (189)
T PF05766_consen 6 RRKCKVCGEWFVP 18 (189)
T ss_pred CCcCcccCCcccc
Confidence 3456666666554
No 239
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.17 E-value=29 Score=14.80 Aligned_cols=13 Identities=23% Similarity=0.777 Sum_probs=9.2
Q ss_pred eecCcchhhccCc
Q psy12029 24 FSCSGCARVYKNK 36 (81)
Q Consensus 24 ~~C~~c~~~~~~~ 36 (81)
..|..|+..|...
T Consensus 6 ~~C~~Cg~~~~~~ 18 (54)
T PF14446_consen 6 CKCPVCGKKFKDG 18 (54)
T ss_pred ccChhhCCcccCC
Confidence 4688888877543
No 240
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=25.04 E-value=38 Score=16.50 Aligned_cols=39 Identities=13% Similarity=0.306 Sum_probs=21.2
Q ss_pred CCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccC
Q psy12029 20 ADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAK 63 (81)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 63 (81)
-.+.|.|+.|+..-.....+.. ........|..||..|.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk-----~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKK-----TVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEEe-----cCceeEEEcccCcceEE
Confidence 3567999999975443322211 11111156778876553
No 241
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=24.96 E-value=50 Score=20.12 Aligned_cols=24 Identities=21% Similarity=0.386 Sum_probs=19.8
Q ss_pred CceecCcchhhccCchHHHHHHHh
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTY 45 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~ 45 (81)
..+-|..|++.|.....+..|...
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~g 260 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEG 260 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhh
Confidence 447799999999998888888763
No 242
>PLN03239 histone acetyltransferase; Provisional
Probab=24.94 E-value=60 Score=19.64 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=20.0
Q ss_pred CCCeecCCCCcccCCchHHHHHHHh
Q psy12029 50 EPQYFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 50 ~~~~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
.. |.|..|-+-|.+...+..|+..
T Consensus 105 ~l-YiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 105 VL-YVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred eE-EEeccchhhhcCHHHHHHHHHh
Confidence 45 8999999999999999888753
No 243
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=24.89 E-value=9.9 Score=22.12 Aligned_cols=39 Identities=21% Similarity=0.286 Sum_probs=19.7
Q ss_pred CceecCcchhhccCchHHHHHHHhh-cC-CCCCeecCCCCcccC
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYE-CG-QEPQYFCPLCPYRAK 63 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~-~~-~~~~~~c~~c~~~f~ 63 (81)
..+.|+.|+..=... ++.+.+.- .+ ..- |.|..||..|.
T Consensus 257 ~~~~C~~C~~~~~~~--~q~QtrsaDEpmT~f-~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTY--YQLQTRSADEPMTTF-VTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceE--EEecccCCCCCCeEE-EEcCCCCCeee
Confidence 358899998532211 11222221 11 122 68988987654
No 244
>KOG0801|consensus
Probab=24.88 E-value=32 Score=18.38 Aligned_cols=19 Identities=16% Similarity=0.415 Sum_probs=10.7
Q ss_pred hhcccccccCCCceecCcchhh
Q psy12029 11 FQITESSYFADRLFSCSGCARV 32 (81)
Q Consensus 11 l~~~~~~~~~~~~~~C~~c~~~ 32 (81)
|..|...|.+ +.|++|.+.
T Consensus 129 lP~hi~~~~g---~KCPvC~K~ 147 (205)
T KOG0801|consen 129 LPVHIMDHSG---MKCPVCHKV 147 (205)
T ss_pred cceeeeccCC---ccCCccccc
Confidence 4444444544 567777654
No 245
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=24.71 E-value=45 Score=12.15 Aligned_cols=12 Identities=25% Similarity=0.780 Sum_probs=5.3
Q ss_pred ceecCcchhhcc
Q psy12029 23 LFSCSGCARVYK 34 (81)
Q Consensus 23 ~~~C~~c~~~~~ 34 (81)
.|.|+.|+..+-
T Consensus 13 kY~Cp~C~~~~C 24 (30)
T PF04438_consen 13 KYRCPRCGARYC 24 (30)
T ss_dssp SEE-TTT--EES
T ss_pred EEECCCcCCcee
Confidence 466777765543
No 246
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=24.51 E-value=5.2 Score=17.77 Aligned_cols=34 Identities=26% Similarity=0.565 Sum_probs=17.8
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|.|..|+..-.. .+ ..+..+.|... .+|+-|..
T Consensus 4 ~FTC~~C~~Rs~~--~~-sk~aY~~GvVi-v~C~gC~~ 37 (66)
T PF05180_consen 4 TFTCNKCGTRSAK--MF-SKQAYHKGVVI-VQCPGCKN 37 (66)
T ss_dssp EEEETTTTEEEEE--EE-EHHHHHTSEEE-EE-TTS--
T ss_pred EEEcCCCCCccce--ee-CHHHHhCCeEE-EECCCCcc
Confidence 4778888743221 11 12345667666 78887753
No 247
>KOG2747|consensus
Probab=24.50 E-value=54 Score=20.17 Aligned_cols=23 Identities=30% Similarity=0.619 Sum_probs=16.2
Q ss_pred eecCCCCcccCCchHHHHHHHhh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSIK 75 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~~ 75 (81)
|.|..|-+.+.+...|..|+...
T Consensus 159 YiCEfCLkY~~s~~~l~rH~~kC 181 (396)
T KOG2747|consen 159 YICEFCLKYMKSRTSLQRHLKKC 181 (396)
T ss_pred EEehHHHhHhchHHHHHHHHHhc
Confidence 67777777777777777776643
No 248
>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=24.43 E-value=49 Score=12.92 Aligned_cols=7 Identities=43% Similarity=0.989 Sum_probs=3.5
Q ss_pred ecCCCCc
Q psy12029 54 FCPLCPY 60 (81)
Q Consensus 54 ~c~~c~~ 60 (81)
.|+.|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555553
No 249
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.12 E-value=46 Score=13.76 Aligned_cols=13 Identities=31% Similarity=0.651 Sum_probs=9.1
Q ss_pred eecCCCCcccCCc
Q psy12029 53 YFCPLCPYRAKQK 65 (81)
Q Consensus 53 ~~c~~c~~~f~~~ 65 (81)
++|..|+..|...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 7888887665544
No 250
>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=23.64 E-value=33 Score=12.32 Aligned_cols=11 Identities=36% Similarity=0.942 Sum_probs=7.4
Q ss_pred ceecCcchhhc
Q psy12029 23 LFSCSGCARVY 33 (81)
Q Consensus 23 ~~~C~~c~~~~ 33 (81)
-|.|..|+..+
T Consensus 27 Cf~C~~C~~~L 37 (39)
T smart00132 27 CFKCSKCGKPL 37 (39)
T ss_pred CCCCcccCCcC
Confidence 46777777654
No 251
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=23.41 E-value=35 Score=15.98 Aligned_cols=11 Identities=27% Similarity=0.797 Sum_probs=7.8
Q ss_pred ecCcchhhccC
Q psy12029 25 SCSGCARVYKN 35 (81)
Q Consensus 25 ~C~~c~~~~~~ 35 (81)
.|+.||..|..
T Consensus 10 ~C~~CG~d~~~ 20 (86)
T PF06170_consen 10 RCPHCGLDYSH 20 (86)
T ss_pred cccccCCcccc
Confidence 68888876644
No 252
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=23.41 E-value=45 Score=17.67 Aligned_cols=18 Identities=28% Similarity=0.678 Sum_probs=13.8
Q ss_pred CceecCcchhhccCchHH
Q psy12029 22 RLFSCSGCARVYKNKKSL 39 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l 39 (81)
..+.|..||+.|.....+
T Consensus 113 ~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred CcccchhhCCccccHHHH
Confidence 467899999999766543
No 253
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=23.27 E-value=92 Score=17.42 Aligned_cols=35 Identities=23% Similarity=0.375 Sum_probs=20.2
Q ss_pred cccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 17 SYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 17 ~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|..-....|..|+..+.....+ ....| .|+.|+.
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 35555567799998776543321 11233 4888864
No 254
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=23.05 E-value=36 Score=14.58 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=3.4
Q ss_pred CceecCcchhh
Q psy12029 22 RLFSCSGCARV 32 (81)
Q Consensus 22 ~~~~C~~c~~~ 32 (81)
+.|.|+.||..
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 45778888754
No 255
>KOG2857|consensus
Probab=23.00 E-value=38 Score=17.64 Aligned_cols=23 Identities=17% Similarity=0.462 Sum_probs=19.3
Q ss_pred CceecCcchhhccCchHHHHHHH
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQT 44 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~ 44 (81)
..|.|+.|.-.|.....+..|+.
T Consensus 16 ~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 16 IKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hhccCCCCCCccccchhhhhccC
Confidence 36899999988888888888876
No 256
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.95 E-value=36 Score=16.47 Aligned_cols=36 Identities=17% Similarity=0.420 Sum_probs=19.7
Q ss_pred CCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCcccCC
Q psy12029 21 DRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRAKQ 64 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 64 (81)
...|.|+.|+.. ...-.+ ..+.-- ..|..||..+..
T Consensus 19 pt~f~CP~Cge~-~v~v~~------~k~~~h-~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKV-SISVKI------KKNIAI-ITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCe-Eeeeec------CCCcce-EECCCCCCccCE
Confidence 356889999842 221111 112223 678889865543
No 257
>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=22.69 E-value=45 Score=12.81 Aligned_cols=9 Identities=33% Similarity=0.933 Sum_probs=4.7
Q ss_pred eecCCCCcc
Q psy12029 53 YFCPLCPYR 61 (81)
Q Consensus 53 ~~c~~c~~~ 61 (81)
+.|..||..
T Consensus 33 ~~C~~CGE~ 41 (46)
T TIGR03831 33 LVCPQCGEE 41 (46)
T ss_pred cccccCCCE
Confidence 455555543
No 258
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=22.67 E-value=67 Score=12.42 Aligned_cols=31 Identities=16% Similarity=0.518 Sum_probs=11.8
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
|.+|..|+..+..-. ....+.+. |.|..|+.
T Consensus 2 p~rC~~C~aylNp~~------~~~~~~~~-w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFC------QFDDGGKT-WICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTS------EEETTTTE-EEETTT--
T ss_pred ccccCCCCCEECCcc------eEcCCCCE-EECcCCCC
Confidence 345666654332221 12223345 77777764
No 259
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=22.67 E-value=33 Score=16.71 Aligned_cols=9 Identities=22% Similarity=0.700 Sum_probs=6.7
Q ss_pred eecCCCCcc
Q psy12029 53 YFCPLCPYR 61 (81)
Q Consensus 53 ~~c~~c~~~ 61 (81)
|+|..||+.
T Consensus 3 WkC~iCg~~ 11 (101)
T PF09943_consen 3 WKCYICGKP 11 (101)
T ss_pred eEEEecCCe
Confidence 788888763
No 260
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.62 E-value=31 Score=16.62 Aligned_cols=11 Identities=18% Similarity=0.634 Sum_probs=8.3
Q ss_pred CceecCcchhh
Q psy12029 22 RLFSCSGCARV 32 (81)
Q Consensus 22 ~~~~C~~c~~~ 32 (81)
+.|.|.+|+..
T Consensus 5 kewkC~VCg~~ 15 (103)
T COG4847 5 KEWKCYVCGGT 15 (103)
T ss_pred ceeeEeeeCCE
Confidence 56888888864
No 261
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=22.61 E-value=83 Score=15.72 Aligned_cols=11 Identities=18% Similarity=0.673 Sum_probs=7.8
Q ss_pred CceecCcchhh
Q psy12029 22 RLFSCSGCARV 32 (81)
Q Consensus 22 ~~~~C~~c~~~ 32 (81)
....|+.|++.
T Consensus 68 v~V~CP~C~K~ 78 (114)
T PF11023_consen 68 VQVECPNCGKQ 78 (114)
T ss_pred eeeECCCCCCh
Confidence 45678888865
No 262
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.57 E-value=36 Score=15.10 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=9.0
Q ss_pred ceecCcchhhccC
Q psy12029 23 LFSCSGCARVYKN 35 (81)
Q Consensus 23 ~~~C~~c~~~~~~ 35 (81)
...|++||+.-..
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 3579999976443
No 263
>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=22.47 E-value=1.2e+02 Score=16.63 Aligned_cols=39 Identities=21% Similarity=0.392 Sum_probs=20.4
Q ss_pred cccCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 17 SYFADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 17 ~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
.|..-....|..|+..+.... +. ........| .|+.|+.
T Consensus 103 lHG~~~~~~C~~C~~~~~~~~-~~--~~~~~~~~p--~C~~Cg~ 141 (218)
T cd01407 103 LHGSLFRVRCTKCGKEYPRDE-LQ--ADIDREEVP--RCPKCGG 141 (218)
T ss_pred CcCCcCcceeCCCcCCCcHHH-Hh--HhhccCCCC--cCCCCCC
Confidence 344445577888987765432 11 111122233 6888864
No 264
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.44 E-value=42 Score=13.45 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=10.4
Q ss_pred ceecCcchhhccCc
Q psy12029 23 LFSCSGCARVYKNK 36 (81)
Q Consensus 23 ~~~C~~c~~~~~~~ 36 (81)
.+.|+.||..+...
T Consensus 20 ~~vC~~Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRKCGYEEPIE 33 (52)
T ss_pred EEECCcCCCeEECC
Confidence 68899999765443
No 265
>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=22.43 E-value=55 Score=11.67 Aligned_cols=7 Identities=29% Similarity=1.189 Sum_probs=3.3
Q ss_pred ecCCCCc
Q psy12029 54 FCPLCPY 60 (81)
Q Consensus 54 ~c~~c~~ 60 (81)
.|..|++
T Consensus 2 ~C~~C~~ 8 (30)
T PF03107_consen 2 WCDVCRR 8 (30)
T ss_pred CCCCCCC
Confidence 3455544
No 266
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=22.37 E-value=37 Score=14.56 Aligned_cols=16 Identities=25% Similarity=0.511 Sum_probs=10.9
Q ss_pred CCceecCcchhhccCc
Q psy12029 21 DRLFSCSGCARVYKNK 36 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~ 36 (81)
...+.|-.|+..+...
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 4578888888776664
No 267
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=22.19 E-value=66 Score=13.52 Aligned_cols=9 Identities=33% Similarity=1.003 Sum_probs=6.9
Q ss_pred eecCCCCcc
Q psy12029 53 YFCPLCPYR 61 (81)
Q Consensus 53 ~~c~~c~~~ 61 (81)
|.|..||.+
T Consensus 38 ~~CGkCgyT 46 (51)
T COG1998 38 WACGKCGYT 46 (51)
T ss_pred eEeccccce
Confidence 788888764
No 268
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.07 E-value=22 Score=19.09 Aligned_cols=34 Identities=21% Similarity=0.561 Sum_probs=19.5
Q ss_pred cCCCceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCccc
Q psy12029 19 FADRLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPYRA 62 (81)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 62 (81)
....-|.|+.|.-.++.-.. ... . |.|+.||...
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA------~~~---~-F~Cp~Cg~~L 142 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEA------MEL---G-FTCPKCGEDL 142 (176)
T ss_pred ccCCceeCCCCCCcccHHHH------HHh---C-CCCCCCCchh
Confidence 34455888777655544322 211 2 8888888543
No 269
>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=22.06 E-value=44 Score=17.48 Aligned_cols=12 Identities=25% Similarity=0.304 Sum_probs=9.6
Q ss_pred eecCCCCcccCC
Q psy12029 53 YFCPLCPYRAKQ 64 (81)
Q Consensus 53 ~~c~~c~~~f~~ 64 (81)
-.|..|++.|..
T Consensus 29 ReC~~C~~RFTT 40 (147)
T TIGR00244 29 RECLECHERFTT 40 (147)
T ss_pred ccCCccCCccce
Confidence 478899988865
No 270
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=21.97 E-value=41 Score=16.26 Aligned_cols=10 Identities=30% Similarity=0.644 Sum_probs=4.8
Q ss_pred ceecCcchhh
Q psy12029 23 LFSCSGCARV 32 (81)
Q Consensus 23 ~~~C~~c~~~ 32 (81)
..+|..||..
T Consensus 88 ~~rC~nCG~~ 97 (98)
T PF10164_consen 88 ERRCSNCGAT 97 (98)
T ss_pred ccccCCCCcc
Confidence 3445555543
No 271
>PRK11032 hypothetical protein; Provisional
Probab=21.93 E-value=68 Score=17.04 Aligned_cols=28 Identities=25% Similarity=0.562 Sum_probs=16.6
Q ss_pred CceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCCc
Q psy12029 22 RLFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCPY 60 (81)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 60 (81)
....|..||..... .+++..| .|+.|+.
T Consensus 123 G~LvC~~Cg~~~~~---------~~p~~i~--pCp~C~~ 150 (160)
T PRK11032 123 GNLVCEKCHHHLAF---------YTPEVLP--LCPKCGH 150 (160)
T ss_pred ceEEecCCCCEEEe---------cCCCcCC--CCCCCCC
Confidence 34678888765311 3344444 6888874
No 272
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=21.62 E-value=45 Score=14.71 Aligned_cols=7 Identities=57% Similarity=1.492 Sum_probs=3.6
Q ss_pred eecCCCC
Q psy12029 53 YFCPLCP 59 (81)
Q Consensus 53 ~~c~~c~ 59 (81)
|.|+.|+
T Consensus 1 y~C~KCg 7 (64)
T PF09855_consen 1 YKCPKCG 7 (64)
T ss_pred CCCCCCC
Confidence 3455554
No 273
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.55 E-value=53 Score=12.29 Aligned_cols=10 Identities=20% Similarity=0.461 Sum_probs=6.1
Q ss_pred eecCCCCccc
Q psy12029 53 YFCPLCPYRA 62 (81)
Q Consensus 53 ~~c~~c~~~f 62 (81)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 5666676554
No 274
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=21.32 E-value=61 Score=16.80 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=7.3
Q ss_pred eecCCCCccc
Q psy12029 53 YFCPLCPYRA 62 (81)
Q Consensus 53 ~~c~~c~~~f 62 (81)
|.|..|+..+
T Consensus 52 ~~C~~C~~~~ 61 (166)
T cd04476 52 YRCEKCNKSV 61 (166)
T ss_pred EECCCCCCcC
Confidence 7888887654
No 275
>KOG0954|consensus
Probab=20.71 E-value=47 Score=22.36 Aligned_cols=31 Identities=16% Similarity=0.285 Sum_probs=21.9
Q ss_pred ccccccccchhccccccc----CCCceecCcchhh
Q psy12029 2 ELQLLVPFYFQITESSYF----ADRLFSCSGCARV 32 (81)
Q Consensus 2 ~~~f~~~~~l~~~~~~~~----~~~~~~C~~c~~~ 32 (81)
|..|....+...|+..+. .+.|+.|..|...
T Consensus 287 eMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 287 EMVFCDKCNICVHQACYGILEVPEGPWLCRTCALG 321 (893)
T ss_pred eeEEeccchhHHHHhhhceeecCCCCeeehhcccc
Confidence 467778888888887754 4577888777543
No 276
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=20.59 E-value=53 Score=14.32 Aligned_cols=17 Identities=24% Similarity=0.600 Sum_probs=10.1
Q ss_pred ccCCCceecCcchhhcc
Q psy12029 18 YFADRLFSCSGCARVYK 34 (81)
Q Consensus 18 ~~~~~~~~C~~c~~~~~ 34 (81)
+..+....|+.|+..|.
T Consensus 48 ~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 48 EIVEGELICPECGREYP 64 (68)
T ss_dssp ETTTTEEEETTTTEEEE
T ss_pred cccCCEEEcCCCCCEEe
Confidence 34445566777776664
No 277
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.46 E-value=47 Score=17.58 Aligned_cols=19 Identities=16% Similarity=0.427 Sum_probs=14.4
Q ss_pred CCceecCcchhhccCchHH
Q psy12029 21 DRLFSCSGCARVYKNKKSL 39 (81)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l 39 (81)
+.|.-|..||+.|.+....
T Consensus 66 ~~PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTENA 84 (158)
T ss_pred CCChhHHhCCCCCchHHHH
Confidence 4677788899988886543
No 278
>KOG4118|consensus
Probab=20.31 E-value=61 Score=14.47 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=11.3
Q ss_pred eecCCCCcccCCchHHHHHHHh
Q psy12029 53 YFCPLCPYRAKQKTNLMTHMSI 74 (81)
Q Consensus 53 ~~c~~c~~~f~~~~~l~~h~~~ 74 (81)
+.|.+|.........+..|...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~ 60 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFEN 60 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhh
Confidence 5566665444554445555443
No 279
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=20.01 E-value=39 Score=14.26 Aligned_cols=30 Identities=20% Similarity=0.491 Sum_probs=17.0
Q ss_pred ceecCcchhhccCchHHHHHHHhhcCCCCCeecCCCC
Q psy12029 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPLCP 59 (81)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 59 (81)
.+.| .||..|.....-. ..+... ..|..|.
T Consensus 18 ~y~C-RCG~~f~i~e~~l-----~~~~~i-v~C~sCS 47 (55)
T PF05207_consen 18 SYPC-RCGGEFEISEEDL-----EEGEVI-VQCDSCS 47 (55)
T ss_dssp EEEE-TTSSEEEEEHHHH-----HCT--E-EEETTTT
T ss_pred EEcC-CCCCEEEEcchhc-----cCcCEE-EECCCCc
Confidence 4778 8998877665321 122344 6777664
Done!