Query psy8696
Match_columns 212
No_of_seqs 322 out of 1791
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 16:53:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8696.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8696hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.6 2.8E-16 6.1E-21 133.6 0.1 75 137-211 188-262 (279)
2 KOG2462|consensus 99.5 3.1E-15 6.7E-20 127.3 1.6 77 134-212 159-235 (279)
3 KOG3623|consensus 99.3 1.2E-13 2.5E-18 130.0 -1.8 79 134-212 892-970 (1007)
4 KOG3576|consensus 99.3 1.8E-13 3.9E-18 112.2 -2.1 79 133-211 114-192 (267)
5 KOG3623|consensus 99.1 5.6E-12 1.2E-16 118.8 -0.4 79 134-212 238-329 (1007)
6 PHA02768 hypothetical protein; 98.9 2.5E-10 5.3E-15 75.3 0.5 44 165-210 6-49 (55)
7 KOG1074|consensus 98.8 1.4E-09 3E-14 104.2 1.1 48 164-211 353-400 (958)
8 KOG1074|consensus 98.8 2E-09 4.2E-14 103.2 1.1 50 163-212 604-653 (958)
9 PF13465 zf-H2C2_2: Zinc-finge 98.6 7E-09 1.5E-13 58.5 0.0 26 179-204 1-26 (26)
10 PHA00733 hypothetical protein 98.5 3.6E-08 7.8E-13 76.4 0.5 50 161-212 70-119 (128)
11 KOG3576|consensus 98.2 6.1E-07 1.3E-11 74.1 2.8 52 161-212 114-165 (267)
12 PHA00616 hypothetical protein 98.1 2.8E-07 6.1E-12 58.1 -0.9 39 164-202 1-39 (44)
13 PHA00732 hypothetical protein 97.9 3.3E-06 7.2E-11 60.1 1.2 38 164-204 1-39 (79)
14 KOG3608|consensus 97.9 4.4E-07 9.5E-12 80.3 -4.8 48 164-211 263-311 (467)
15 KOG3993|consensus 97.9 1E-06 2.3E-11 79.4 -3.2 71 142-212 273-376 (500)
16 COG5189 SFP1 Putative transcri 97.8 9.2E-06 2E-10 71.1 1.8 51 162-212 347-418 (423)
17 KOG3608|consensus 97.6 1.8E-06 3.9E-11 76.5 -5.6 74 138-211 181-256 (467)
18 PLN03086 PRLI-interacting fact 97.5 4E-05 8.7E-10 72.5 1.8 60 138-202 455-514 (567)
19 PF13465 zf-H2C2_2: Zinc-finge 97.4 8.7E-06 1.9E-10 45.7 -2.2 25 152-176 2-26 (26)
20 PLN03086 PRLI-interacting fact 97.4 5.1E-05 1.1E-09 71.8 0.4 67 137-206 479-555 (567)
21 PHA00733 hypothetical protein 97.3 5.3E-05 1.2E-09 58.7 -0.1 53 160-212 36-93 (128)
22 PF00096 zf-C2H2: Zinc finger, 97.3 3.7E-05 8.1E-10 41.4 -0.9 23 165-187 1-23 (23)
23 PRK04860 hypothetical protein; 97.1 0.00017 3.6E-09 58.0 0.7 41 163-207 118-158 (160)
24 PHA02768 hypothetical protein; 96.9 0.00018 4E-09 47.5 -0.4 44 136-181 5-48 (55)
25 PF05605 zf-Di19: Drought indu 96.8 0.00029 6.2E-09 46.3 -0.3 45 164-211 2-48 (54)
26 PF00096 zf-C2H2: Zinc finger, 96.6 0.00027 5.9E-09 37.9 -1.0 20 193-212 1-20 (23)
27 PF13912 zf-C2H2_6: C2H2-type 96.6 0.00051 1.1E-08 38.3 0.0 25 164-188 1-25 (27)
28 PF13894 zf-C2H2_4: C2H2-type 96.5 0.00041 8.9E-09 37.0 -0.7 23 165-187 1-23 (24)
29 PF12756 zf-C2H2_2: C2H2 type 96.4 0.00074 1.6E-08 48.6 -0.5 21 192-212 50-70 (100)
30 PF13912 zf-C2H2_6: C2H2-type 95.9 0.0013 2.9E-08 36.6 -0.9 21 192-212 1-21 (27)
31 PF13894 zf-C2H2_4: C2H2-type 95.8 0.0015 3.2E-08 34.7 -0.8 20 193-212 1-20 (24)
32 smart00355 ZnF_C2H2 zinc finge 95.8 0.0022 4.9E-08 34.4 -0.2 24 165-188 1-24 (26)
33 PF09237 GAGA: GAGA factor; I 95.5 0.0044 9.5E-08 40.3 0.4 33 160-192 20-52 (54)
34 PHA00616 hypothetical protein 95.2 0.003 6.5E-08 39.9 -1.2 21 192-212 1-21 (44)
35 COG5048 FOG: Zn-finger [Genera 94.6 0.024 5.2E-07 50.0 2.6 49 163-211 288-342 (467)
36 KOG3993|consensus 94.5 0.0076 1.6E-07 54.9 -0.8 49 164-212 267-315 (500)
37 smart00355 ZnF_C2H2 zinc finge 94.1 0.01 2.2E-07 31.7 -0.5 20 193-212 1-20 (26)
38 PF12874 zf-met: Zinc-finger o 94.1 0.011 2.3E-07 32.2 -0.5 23 165-187 1-23 (25)
39 PF12171 zf-C2H2_jaz: Zinc-fin 93.9 0.028 6E-07 31.3 1.0 20 193-212 2-21 (27)
40 PHA00732 hypothetical protein 93.8 0.032 7E-07 39.6 1.3 47 137-189 2-49 (79)
41 PF12171 zf-C2H2_jaz: Zinc-fin 93.7 0.024 5.2E-07 31.6 0.5 22 165-186 2-23 (27)
42 PF12874 zf-met: Zinc-finger o 92.7 0.025 5.4E-07 30.7 -0.4 19 193-211 1-19 (25)
43 KOG2461|consensus 92.1 0.15 3.2E-06 46.7 3.4 29 41-69 127-155 (396)
44 PF09237 GAGA: GAGA factor; I 92.0 0.042 9.1E-07 35.7 -0.1 25 188-212 20-44 (54)
45 PF13909 zf-H2C2_5: C2H2-type 91.4 0.029 6.2E-07 30.2 -1.2 23 165-188 1-23 (24)
46 PF05605 zf-Di19: Drought indu 91.1 0.042 9.2E-07 35.8 -0.8 50 136-188 2-53 (54)
47 COG5048 FOG: Zn-finger [Genera 88.9 0.55 1.2E-05 41.3 4.2 67 136-202 289-363 (467)
48 KOG1146|consensus 88.7 0.55 1.2E-05 48.5 4.4 53 160-212 461-538 (1406)
49 smart00451 ZnF_U1 U1-like zinc 88.5 0.13 2.9E-06 29.9 -0.0 20 192-211 3-22 (35)
50 cd00350 rubredoxin_like Rubred 88.0 0.29 6.4E-06 28.7 1.2 24 165-200 2-25 (33)
51 COG5189 SFP1 Putative transcri 87.8 0.28 6E-06 43.6 1.5 25 161-185 395-419 (423)
52 PF13913 zf-C2HC_2: zinc-finge 87.3 0.15 3.2E-06 28.1 -0.3 21 165-186 3-23 (25)
53 KOG4124|consensus 84.9 1.5 3.2E-05 39.6 4.5 52 161-212 346-418 (442)
54 smart00451 ZnF_U1 U1-like zinc 83.0 0.36 7.9E-06 28.0 -0.1 23 164-186 3-25 (35)
55 PF09538 FYDLN_acid: Protein o 82.4 0.83 1.8E-05 34.4 1.6 30 165-205 10-39 (108)
56 TIGR02605 CxxC_CxxC_SSSS putat 77.5 1.2 2.7E-05 28.4 1.1 30 164-200 5-34 (52)
57 cd00729 rubredoxin_SM Rubredox 76.9 1.5 3.2E-05 25.9 1.2 25 164-200 2-26 (34)
58 COG1997 RPL43A Ribosomal prote 76.8 1.7 3.6E-05 31.4 1.6 32 163-204 34-65 (89)
59 PRK04860 hypothetical protein; 76.6 0.51 1.1E-05 37.9 -1.1 40 135-178 118-157 (160)
60 PF12756 zf-C2H2_2: C2H2 type 76.4 0.69 1.5E-05 32.8 -0.4 24 164-187 50-73 (100)
61 smart00531 TFIIE Transcription 76.0 1.4 3E-05 34.6 1.2 41 160-204 95-135 (147)
62 PF14353 CpXC: CpXC protein 76.0 0.93 2E-05 34.6 0.2 14 192-205 38-51 (128)
63 smart00834 CxxC_CXXC_SSSS Puta 75.5 1.6 3.4E-05 26.2 1.1 32 164-202 5-36 (41)
64 TIGR02300 FYDLN_acid conserved 75.4 2.2 4.7E-05 33.0 2.1 30 165-205 10-39 (129)
65 TIGR02098 MJ0042_CXXC MJ0042 f 75.2 1.8 3.9E-05 25.8 1.3 34 165-203 3-36 (38)
66 COG4049 Uncharacterized protei 74.9 0.75 1.6E-05 30.5 -0.5 31 157-187 10-40 (65)
67 COG1592 Rubrerythrin [Energy p 74.3 1.8 3.9E-05 35.0 1.5 23 164-199 134-156 (166)
68 PRK09678 DNA-binding transcrip 74.2 1.3 2.8E-05 30.9 0.5 19 162-180 25-45 (72)
69 PF13717 zinc_ribbon_4: zinc-r 72.8 2.5 5.5E-05 25.2 1.5 34 165-203 3-36 (36)
70 PRK00398 rpoP DNA-directed RNA 72.7 2.1 4.6E-05 26.8 1.2 30 164-203 3-32 (46)
71 COG2888 Predicted Zn-ribbon RN 70.2 2.4 5.1E-05 28.5 1.0 32 164-200 27-58 (61)
72 PF13719 zinc_ribbon_5: zinc-r 69.5 3.1 6.8E-05 24.9 1.4 34 165-203 3-36 (37)
73 PF05191 ADK_lid: Adenylate ki 69.5 2.6 5.7E-05 25.3 1.1 33 165-205 2-34 (36)
74 PRK09979 putative rho operon l 67.8 3 6.6E-05 23.7 1.0 26 24-49 2-27 (33)
75 PF09723 Zn-ribbon_8: Zinc rib 67.4 3.3 7.2E-05 25.5 1.3 30 164-200 5-34 (42)
76 COG4049 Uncharacterized protei 66.7 1.2 2.6E-05 29.6 -0.9 27 185-211 10-36 (65)
77 smart00659 RPOLCX RNA polymera 66.5 4.2 9.2E-05 25.5 1.6 26 165-201 3-28 (44)
78 PRK06266 transcription initiat 65.8 3 6.5E-05 34.0 1.1 36 160-204 113-148 (178)
79 TIGR00373 conserved hypothetic 64.4 3 6.4E-05 33.3 0.8 36 160-204 105-140 (158)
80 PHA00626 hypothetical protein 61.9 6.8 0.00015 26.0 1.9 14 163-176 22-35 (59)
81 PF02892 zf-BED: BED zinc fing 60.1 2.9 6.2E-05 25.7 -0.0 24 161-184 13-40 (45)
82 COG1996 RPC10 DNA-directed RNA 59.7 5.4 0.00012 25.7 1.2 29 163-201 5-33 (49)
83 COG1655 Uncharacterized protei 59.3 4.3 9.3E-05 34.6 0.9 39 162-200 17-70 (267)
84 smart00440 ZnF_C2C2 C2C2 Zinc 59.3 6.1 0.00013 24.1 1.3 12 192-203 28-39 (40)
85 PF05443 ROS_MUCR: ROS/MUCR tr 58.0 3.5 7.5E-05 32.1 0.1 28 162-192 70-97 (132)
86 smart00614 ZnF_BED BED zinc fi 56.5 3.7 8.1E-05 26.1 0.0 25 163-187 17-47 (50)
87 PTZ00255 60S ribosomal protein 56.0 6.1 0.00013 28.7 1.1 32 163-204 35-66 (90)
88 COG4530 Uncharacterized protei 55.7 5.7 0.00012 30.0 0.9 28 166-204 11-38 (129)
89 TIGR00280 L37a ribosomal prote 55.5 5.6 0.00012 29.0 0.8 32 163-204 34-65 (91)
90 PRK14890 putative Zn-ribbon RN 54.0 7.6 0.00016 26.0 1.2 32 164-200 25-56 (59)
91 PF01096 TFIIS_C: Transcriptio 53.6 4.9 0.00011 24.4 0.2 10 193-202 29-38 (39)
92 KOG2593|consensus 53.3 3.9 8.5E-05 37.8 -0.4 44 155-201 119-162 (436)
93 COG4888 Uncharacterized Zn rib 52.8 12 0.00026 27.8 2.2 39 161-203 19-57 (104)
94 PF01780 Ribosomal_L37ae: Ribo 52.4 6.3 0.00014 28.7 0.7 31 163-203 34-64 (90)
95 PF03604 DNA_RNApol_7kD: DNA d 52.1 10 0.00023 22.1 1.5 27 165-202 1-27 (32)
96 PRK03824 hypA hydrogenase nick 52.1 8.3 0.00018 29.9 1.4 39 163-201 69-116 (135)
97 PRK03976 rpl37ae 50S ribosomal 51.1 8.5 0.00018 28.0 1.2 32 163-204 35-66 (90)
98 PF10263 SprT-like: SprT-like 51.0 7.2 0.00016 30.3 0.9 34 162-203 121-154 (157)
99 COG1198 PriA Primosomal protei 51.0 13 0.00028 36.9 2.8 22 180-201 463-484 (730)
100 PF01363 FYVE: FYVE zinc finge 50.3 8.8 0.00019 25.7 1.1 27 165-203 10-36 (69)
101 KOG2785|consensus 49.3 4.4 9.6E-05 36.8 -0.6 51 162-212 164-240 (390)
102 PF04959 ARS2: Arsenite-resist 48.4 2.4 5.1E-05 35.7 -2.4 28 162-189 75-102 (214)
103 PRK00464 nrdR transcriptional 46.5 15 0.00032 29.3 2.0 16 165-180 29-44 (154)
104 PF12760 Zn_Tnp_IS1595: Transp 46.0 15 0.00032 22.9 1.6 27 165-200 19-45 (46)
105 PF05129 Elf1: Transcription e 45.7 9.1 0.0002 27.2 0.6 40 162-205 20-59 (81)
106 COG4957 Predicted transcriptio 44.8 11 0.00024 29.5 1.0 25 165-192 77-101 (148)
107 cd00730 rubredoxin Rubredoxin; 44.2 15 0.00032 23.7 1.4 35 165-200 2-42 (50)
108 PF11494 Ta0938: Ta0938; Inte 43.5 17 0.00036 26.8 1.7 39 161-205 11-50 (105)
109 COG1571 Predicted DNA-binding 43.3 14 0.00031 34.1 1.7 31 165-206 351-381 (421)
110 PF08790 zf-LYAR: LYAR-type C2 42.8 12 0.00026 21.3 0.7 20 165-185 1-20 (28)
111 PF00301 Rubredoxin: Rubredoxi 42.3 21 0.00046 22.7 1.9 36 165-201 2-43 (47)
112 KOG1146|consensus 42.2 8.1 0.00018 40.4 -0.1 73 135-212 1259-1348(1406)
113 PRK12496 hypothetical protein; 41.5 14 0.0003 29.7 1.1 31 163-205 126-156 (164)
114 TIGR01206 lysW lysine biosynth 41.4 16 0.00035 23.9 1.3 31 165-203 3-33 (54)
115 PF03811 Zn_Tnp_IS1: InsA N-te 41.0 21 0.00045 21.4 1.6 30 165-198 6-35 (36)
116 PF11672 DUF3268: Protein of u 40.7 22 0.00048 26.4 2.1 12 163-174 1-12 (102)
117 cd00065 FYVE FYVE domain; Zinc 40.1 19 0.00041 22.9 1.5 10 165-174 19-28 (57)
118 COG3091 SprT Zn-dependent meta 39.5 17 0.00038 29.0 1.4 36 162-202 115-150 (156)
119 COG3677 Transposase and inacti 39.5 18 0.00039 27.9 1.5 17 162-178 51-67 (129)
120 smart00731 SprT SprT homologue 39.2 18 0.00038 28.2 1.4 34 163-203 111-144 (146)
121 smart00064 FYVE Protein presen 38.6 19 0.00042 23.9 1.4 9 167-175 13-21 (68)
122 PF07941 K_channel_TID: Potass 38.5 9.5 0.00021 26.0 -0.2 11 49-59 12-22 (75)
123 PF01927 Mut7-C: Mut7-C RNAse 38.4 20 0.00043 28.0 1.6 19 191-209 123-141 (147)
124 PHA02998 RNA polymerase subuni 38.2 21 0.00045 29.3 1.7 37 164-204 143-183 (195)
125 COG3364 Zn-ribbon containing p 38.0 15 0.00032 27.4 0.7 15 164-178 2-16 (112)
126 KOG4167|consensus 37.9 5.5 0.00012 39.2 -1.9 27 162-188 790-816 (907)
127 smart00734 ZnF_Rad18 Rad18-lik 37.1 11 0.00024 20.8 -0.0 9 194-202 3-11 (26)
128 TIGR00100 hypA hydrogenase nic 34.8 19 0.00042 27.1 1.0 27 163-201 69-95 (115)
129 PF02176 zf-TRAF: TRAF-type zi 34.3 14 0.00029 23.9 0.0 43 162-205 7-55 (60)
130 cd00924 Cyt_c_Oxidase_Vb Cytoc 34.2 21 0.00046 26.3 1.0 21 183-204 71-91 (97)
131 PF01286 XPA_N: XPA protein N- 34.1 19 0.0004 21.4 0.6 16 165-180 4-19 (34)
132 PF09332 Mcm10: Mcm10 replicat 33.8 10 0.00022 34.3 -0.9 42 163-204 251-297 (344)
133 PRK12380 hydrogenase nickel in 33.8 21 0.00045 26.8 1.0 26 163-200 69-94 (113)
134 PF07282 OrfB_Zn_ribbon: Putat 33.8 28 0.00061 23.2 1.6 14 190-203 44-57 (69)
135 KOG3214|consensus 33.5 24 0.00052 26.2 1.2 41 161-205 20-60 (109)
136 PRK05978 hypothetical protein; 33.4 26 0.00056 27.8 1.5 32 165-205 34-65 (148)
137 PF10013 DUF2256: Uncharacteri 33.3 20 0.00044 22.3 0.7 16 166-181 10-25 (42)
138 COG3357 Predicted transcriptio 33.2 24 0.00052 25.8 1.1 29 162-200 56-84 (97)
139 PF04959 ARS2: Arsenite-resist 32.3 16 0.00034 30.8 0.1 24 188-211 73-96 (214)
140 PRK04351 hypothetical protein; 32.2 25 0.00054 27.8 1.2 35 163-205 111-145 (149)
141 smart00154 ZnF_AN1 AN1-like Zi 30.8 27 0.00059 21.1 1.0 14 192-205 12-25 (39)
142 PF08274 PhnA_Zn_Ribbon: PhnA 30.8 25 0.00055 20.2 0.8 25 166-201 4-28 (30)
143 PRK03681 hypA hydrogenase nick 29.4 26 0.00056 26.3 0.9 28 163-201 69-96 (114)
144 PF12013 DUF3505: Protein of u 29.2 16 0.00035 26.9 -0.3 25 165-189 81-109 (109)
145 COG1327 Predicted transcriptio 29.0 35 0.00077 27.2 1.6 19 163-181 27-45 (156)
146 COG5236 Uncharacterized conser 28.9 13 0.00027 33.7 -1.0 22 166-187 222-243 (493)
147 PRK00564 hypA hydrogenase nick 28.5 28 0.0006 26.3 0.9 28 163-201 70-97 (117)
148 PF14446 Prok-RING_1: Prokaryo 28.5 39 0.00085 22.2 1.5 15 165-179 6-20 (54)
149 PF04810 zf-Sec23_Sec24: Sec23 28.2 37 0.0008 20.5 1.3 32 165-202 3-34 (40)
150 KOG4173|consensus 28.0 6.1 0.00013 33.2 -3.0 46 166-211 108-165 (253)
151 PF13240 zinc_ribbon_2: zinc-r 27.7 34 0.00074 18.2 0.9 6 195-200 16-21 (23)
152 PF09082 DUF1922: Domain of un 27.4 27 0.00059 24.0 0.6 15 186-201 14-28 (68)
153 PTZ00303 phosphatidylinositol 27.1 41 0.00089 33.9 1.9 12 165-176 461-472 (1374)
154 PF15135 UPF0515: Uncharacteri 26.8 42 0.00091 29.0 1.8 14 191-204 154-167 (278)
155 smart00661 RPOL9 RNA polymeras 26.6 50 0.0011 20.5 1.7 12 164-175 20-31 (52)
156 COG1594 RPB9 DNA-directed RNA 26.2 36 0.00078 25.6 1.2 39 165-203 73-111 (113)
157 smart00132 LIM Zinc-binding do 26.2 53 0.0011 18.5 1.7 11 192-202 27-37 (39)
158 PLN02294 cytochrome c oxidase 25.9 42 0.00091 27.3 1.5 22 183-205 133-154 (174)
159 COG1656 Uncharacterized conser 25.7 38 0.00083 27.4 1.3 17 192-208 130-146 (165)
160 TIGR00244 transcriptional regu 25.0 52 0.0011 26.1 1.9 19 164-182 28-46 (147)
161 PF01155 HypA: Hydrogenase exp 24.9 28 0.00061 26.0 0.4 26 164-201 70-95 (113)
162 KOG0978|consensus 24.5 23 0.00049 35.0 -0.3 21 191-211 677-697 (698)
163 PF01428 zf-AN1: AN1-like Zinc 24.5 29 0.00062 21.3 0.3 15 191-205 12-26 (43)
164 PF08271 TF_Zn_Ribbon: TFIIB z 23.9 47 0.001 20.2 1.2 28 165-201 1-28 (43)
165 KOG0402|consensus 23.8 32 0.00068 24.7 0.4 29 165-203 37-65 (92)
166 KOG4173|consensus 23.8 15 0.00033 30.9 -1.4 46 163-211 78-125 (253)
167 PF10571 UPF0547: Uncharacteri 23.6 43 0.00093 18.5 0.8 10 194-203 16-25 (26)
168 KOG1280|consensus 23.5 46 0.00099 30.1 1.4 39 161-199 76-116 (381)
169 PF07754 DUF1610: Domain of un 23.4 42 0.00092 18.3 0.8 8 192-199 16-23 (24)
170 COG4391 Uncharacterized protei 23.2 58 0.0013 22.0 1.6 42 158-203 18-59 (62)
171 PRK05452 anaerobic nitric oxid 22.9 56 0.0012 30.7 2.0 40 161-201 422-467 (479)
172 KOG4167|consensus 22.8 1.5E+02 0.0033 29.6 4.9 73 133-205 285-361 (907)
173 PF13451 zf-trcl: Probable zin 22.6 40 0.00088 21.7 0.7 15 190-204 2-16 (49)
174 PF10083 DUF2321: Uncharacteri 22.5 49 0.0011 26.5 1.3 17 189-205 65-81 (158)
175 KOG2482|consensus 21.8 28 0.0006 31.5 -0.2 23 164-186 195-217 (423)
176 PF04606 Ogr_Delta: Ogr/Delta- 21.7 35 0.00077 21.3 0.3 37 167-205 2-40 (47)
177 PF08394 Arc_trans_TRASH: Arch 21.6 18 0.00038 21.9 -1.1 35 167-204 1-35 (37)
178 PRK00762 hypA hydrogenase nick 21.6 49 0.0011 25.2 1.1 32 163-200 69-100 (124)
179 PRK00432 30S ribosomal protein 21.4 64 0.0014 20.6 1.5 27 166-203 22-48 (50)
180 PF10276 zf-CHCC: Zinc-finger 21.4 44 0.00096 20.5 0.7 12 191-202 28-39 (40)
181 COG1779 C4-type Zn-finger prot 21.3 54 0.0012 27.3 1.4 37 165-203 15-54 (201)
182 TIGR01385 TFSII transcription 21.2 56 0.0012 28.9 1.6 39 163-203 257-297 (299)
183 TIGR03831 YgiT_finger YgiT-typ 20.8 71 0.0015 19.0 1.6 13 191-203 31-43 (46)
184 PRK14873 primosome assembly pr 20.6 63 0.0014 31.8 1.9 11 191-201 421-431 (665)
185 KOG2071|consensus 20.5 40 0.00087 32.5 0.5 28 161-188 415-442 (579)
186 PF15269 zf-C2H2_7: Zinc-finge 20.4 44 0.00096 21.2 0.5 23 164-186 20-42 (54)
187 TIGR01384 TFS_arch transcripti 20.4 57 0.0012 23.6 1.2 41 164-204 62-102 (104)
188 PRK14892 putative transcriptio 20.4 80 0.0017 23.3 2.0 36 162-204 19-54 (99)
189 COG1773 Rubredoxin [Energy pro 20.1 45 0.00098 22.0 0.5 11 192-202 3-13 (55)
No 1
>KOG2462|consensus
Probab=99.57 E-value=2.8e-16 Score=133.64 Aligned_cols=75 Identities=28% Similarity=0.475 Sum_probs=57.1
Q ss_pred CCCCCCCccccccccccCCCCCCCCCCccccccccccccccccccccccccCCCcceeCCccCccccCcchhccC
Q psy8696 137 FPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 137 ~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~H 211 (212)
+.|..|.+.|.+...|+.|.|+|+++|||.|..|+|.|..+++|+.|+++|.+.|+|+|..|+|+|.+++.|.+|
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHh
Confidence 345555556666667777788888888888888888888888888888888888888888888888888877777
No 2
>KOG2462|consensus
Probab=99.51 E-value=3.1e-15 Score=127.33 Aligned_cols=77 Identities=31% Similarity=0.555 Sum_probs=70.9
Q ss_pred CCCCCCCCCCccccccccccCCCCCCCCCCccccccccccccccccccccccccCCCcceeCCccCccccCcchhccCC
Q psy8696 134 SSLFPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 134 s~~~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
.+.+.|..|...+...-.++.|.|+|+ -+++|.+|||.|.+.+-|+.|+|+|||||||.|..|+|.|..++||+-|+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH
Confidence 567888888888888888899999886 57999999999999999999999999999999999999999999999885
No 3
>KOG3623|consensus
Probab=99.32 E-value=1.2e-13 Score=129.97 Aligned_cols=79 Identities=20% Similarity=0.494 Sum_probs=74.7
Q ss_pred CCCCCCCCCCccccccccccCCCCCCCCCCccccccccccccccccccccccccCCCcceeCCccCccccCcchhccCC
Q psy8696 134 SSLFPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 134 s~~~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
...|.|..|.+.|.....|.+|..-|++++||+|.+|.|.|+.+.+|..|+|.|.|||||+|+.|+|.|.+...+..||
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 4468888999999999999999999999999999999999999999999999999999999999999999999888876
No 4
>KOG3576|consensus
Probab=99.29 E-value=1.8e-13 Score=112.23 Aligned_cols=79 Identities=30% Similarity=0.617 Sum_probs=74.3
Q ss_pred CCCCCCCCCCCccccccccccCCCCCCCCCCccccccccccccccccccccccccCCCcceeCCccCccccCcchhccC
Q psy8696 133 SSSLFPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 133 ~s~~~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~H 211 (212)
...+|.|..|...|.-++.+.+|.+.|...|.|-|..|||.|.....|++|+|+|+|.+||+|..|+|.|+++..|..|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 3567899999999999999999999999999999999999999999999999999999999999999999999888655
No 5
>KOG3623|consensus
Probab=99.14 E-value=5.6e-12 Score=118.80 Aligned_cols=79 Identities=23% Similarity=0.415 Sum_probs=68.0
Q ss_pred CCCCCCCCCCccccccccccCCCCCCC-------------CCCccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 134 SSLFPGTSSTHSHLDRRLLRAPGRASR-------------PKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 134 s~~~~~~~~~~~~~~~~~l~~h~~~h~-------------~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
...|+|..|...|..+..|.+|+..|. ..+.|+|..|+|.|+.+.+|+.|+|||.|||||.|+.|+|
T Consensus 238 e~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkK 317 (1007)
T KOG3623|consen 238 EPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKK 317 (1007)
T ss_pred CCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCccccc
Confidence 345788889888888888777765552 2356999999999999999999999999999999999999
Q ss_pred cccCcchhccCC
Q psy8696 201 AFRRQDHLRDHR 212 (212)
Q Consensus 201 ~F~~~~~L~~Hr 212 (212)
.|.+...+..|+
T Consensus 318 RFSHSGSySSHm 329 (1007)
T KOG3623|consen 318 RFSHSGSYSSHM 329 (1007)
T ss_pred ccccCCcccccc
Confidence 999999888775
No 6
>PHA02768 hypothetical protein; Provisional
Probab=98.91 E-value=2.5e-10 Score=75.35 Aligned_cols=44 Identities=18% Similarity=0.444 Sum_probs=41.3
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccccCcchhcc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRD 210 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~ 210 (212)
|+|+.||+.|....+|.+|+++|+ ++|+|..|+|.|.+.+.|..
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 899999999999999999999998 79999999999999888753
No 7
>KOG1074|consensus
Probab=98.79 E-value=1.4e-09 Score=104.16 Aligned_cols=48 Identities=40% Similarity=0.951 Sum_probs=46.3
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCccccCcchhccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~H 211 (212)
.++|.+|.|.|...+.|++|+|.||||+||+|.+||..|.++.+|+.|
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH 400 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVH 400 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeee
Confidence 478999999999999999999999999999999999999999999987
No 8
>KOG1074|consensus
Probab=98.76 E-value=2e-09 Score=103.19 Aligned_cols=50 Identities=40% Similarity=0.804 Sum_probs=46.9
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccCcchhccCC
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
.+.+|-+|-++...++.|+.|.|+|+|||||+|++||+.|.++.+|+.|+
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~ 653 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM 653 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc
Confidence 45789999999999999999999999999999999999999999999985
No 9
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.61 E-value=7e-09 Score=58.46 Aligned_cols=26 Identities=58% Similarity=1.081 Sum_probs=23.8
Q ss_pred cccccccccCCCcceeCCccCccccC
Q psy8696 179 NLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 179 ~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
+|.+|+++|+|+|||.|++|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999999974
No 10
>PHA00733 hypothetical protein
Probab=98.47 E-value=3.6e-08 Score=76.43 Aligned_cols=50 Identities=34% Similarity=0.674 Sum_probs=45.6
Q ss_pred CCCccccccccccccccccccccccccCCCcceeCCccCccccCcchhccCC
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
..++|.|..|++.|.....|..|++.| +++|.|.+|++.|.+...|.+|+
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHH
Confidence 478899999999999999999999987 46799999999999999998874
No 11
>KOG3576|consensus
Probab=98.25 E-value=6.1e-07 Score=74.09 Aligned_cols=52 Identities=29% Similarity=0.638 Sum_probs=48.6
Q ss_pred CCCccccccccccccccccccccccccCCCcceeCCccCccccCcchhccCC
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
+...|.|.+|+|.|.....|.+|++.|...|.|-|..|||.|...-+|++|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~ 165 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHT 165 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhh
Confidence 4566999999999999999999999999999999999999999999999984
No 12
>PHA00616 hypothetical protein
Probab=98.14 E-value=2.8e-07 Score=58.09 Aligned_cols=39 Identities=15% Similarity=0.260 Sum_probs=34.5
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCccc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAF 202 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F 202 (212)
+|+|..||+.|.++..|.+|++.|+|++++.|+.---.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEEEEEE
Confidence 589999999999999999999999999999998643333
No 13
>PHA00732 hypothetical protein
Probab=97.93 E-value=3.3e-06 Score=60.09 Aligned_cols=38 Identities=34% Similarity=0.727 Sum_probs=33.3
Q ss_pred ccccccccccccccccccccccc-cCCCcceeCCccCccccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERT-HTDERPYSCDICGKAFRR 204 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~-Htgekpf~C~~Cgk~F~~ 204 (212)
+|.|..|++.|.....|++|++. |.+ +.|+.|++.|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~ 39 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR 39 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC
Confidence 48899999999999999999984 653 589999999984
No 14
>KOG3608|consensus
Probab=97.89 E-value=4.4e-07 Score=80.26 Aligned_cols=48 Identities=27% Similarity=0.693 Sum_probs=36.7
Q ss_pred ccccccccccccccccccccccc-cCCCcceeCCccCccccCcchhccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERT-HTDERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~-Htgekpf~C~~Cgk~F~~~~~L~~H 211 (212)
.|+|+.|..+....+.|.+|++. |...|||+|+.|++.|.+..+|.+|
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 35666666666666666667654 6678999999999999999999887
No 15
>KOG3993|consensus
Probab=97.85 E-value=1e-06 Score=79.37 Aligned_cols=71 Identities=31% Similarity=0.505 Sum_probs=53.3
Q ss_pred CCccccccccccCCCCCCCCCCccccccccccccccccccccccccC--------CC-----------------------
Q psy8696 142 STHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERTHT--------DE----------------------- 190 (212)
Q Consensus 142 ~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Ht--------ge----------------------- 190 (212)
|-..+.+.-.|..|.-...-..-|+|..|+|.|....+|..|.|+|. +.
T Consensus 273 CK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~ds 352 (500)
T KOG3993|consen 273 CKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDS 352 (500)
T ss_pred HHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcc
Confidence 33333344445555544444456999999999999999999999994 11
Q ss_pred --cceeCCccCccccCcchhccCC
Q psy8696 191 --RPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 191 --kpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
..|.|.+|+|.|++...|++|+
T Consensus 353 s~gi~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred cCceeecHHhhhhhHHHHHHHHhH
Confidence 2488999999999999999984
No 16
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.79 E-value=9.2e-06 Score=71.10 Aligned_cols=51 Identities=29% Similarity=0.813 Sum_probs=43.8
Q ss_pred CCcccccc--ccccccccccccccccc-c------------------CCCcceeCCccCccccCcchhccCC
Q psy8696 162 KKQFICKF--CNRQFTKSYNLLIHERT-H------------------TDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 162 ~k~~~C~~--C~k~F~~~~~L~~H~r~-H------------------tgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
+|+|+|++ |.|.|+....|+-|+.- | ...|||+|++|+|.++....|+-||
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 59999987 99999999999988642 2 1349999999999999999999886
No 17
>KOG3608|consensus
Probab=97.59 E-value=1.8e-06 Score=76.47 Aligned_cols=74 Identities=24% Similarity=0.401 Sum_probs=63.7
Q ss_pred CCCCCCccccccccccCCCCCCCCCCccccccccccccccccccccccccC--CCcceeCCccCccccCcchhccC
Q psy8696 138 PGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERTHT--DERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 138 ~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Ht--gekpf~C~~Cgk~F~~~~~L~~H 211 (212)
....|....-++..|++|.++|.++|...|+.||..|.++..|..|.+..+ ...+|.|..|.|.|.+...|+.|
T Consensus 181 ~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~H 256 (467)
T KOG3608|consen 181 NWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSH 256 (467)
T ss_pred cchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHH
Confidence 345678888899999999999999999999999999999999999987654 34589999999999888777766
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.51 E-value=4e-05 Score=72.45 Aligned_cols=60 Identities=12% Similarity=0.308 Sum_probs=31.4
Q ss_pred CCCCCCccccccccccCCCCCCCCCCccccccccccccccccccccccccCCCcceeCCccCccc
Q psy8696 138 PGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAF 202 (212)
Q Consensus 138 ~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F 202 (212)
.|..|...+. ...+..|.+.++ +++.|. |++.+ .+..|..|+++|..+|++.|.+|++.|
T Consensus 455 ~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 455 HCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred cCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 4555555443 233444444432 455565 65433 345555666556666666666666555
No 19
>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=97.44 E-value=8.7e-06 Score=45.67 Aligned_cols=25 Identities=28% Similarity=0.721 Sum_probs=21.3
Q ss_pred ccCCCCCCCCCCccccccccccccc
Q psy8696 152 LRAPGRASRPKKQFICKFCNRQFTK 176 (212)
Q Consensus 152 l~~h~~~h~~~k~~~C~~C~k~F~~ 176 (212)
+..|.++|+++++|.|++|++.|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 4457788999999999999999963
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.35 E-value=5.1e-05 Score=71.76 Aligned_cols=67 Identities=18% Similarity=0.409 Sum_probs=48.7
Q ss_pred CCCCCCCccccccccccCCCCCCCCCCccccccccccccc----------cccccccccccCCCcceeCCccCccccCcc
Q psy8696 137 FPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTK----------SYNLLIHERTHTDERPYSCDICGKAFRRQD 206 (212)
Q Consensus 137 ~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~----------~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~ 206 (212)
+.|. |.. ...+..+..|.+.|.+++++.|.+|++.|.. ...|..|+.++ |.+++.|..|++.|..++
T Consensus 479 v~Cp-Cg~-~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlrd 555 (567)
T PLN03086 479 LQCP-CGV-VLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLKE 555 (567)
T ss_pred ccCC-CCC-CcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeehh
Confidence 3565 664 3455677778777888888888888888742 34678887775 888888888888887654
No 21
>PHA00733 hypothetical protein
Probab=97.30 E-value=5.3e-05 Score=58.70 Aligned_cols=53 Identities=21% Similarity=0.278 Sum_probs=41.6
Q ss_pred CCCCcccccccccccccccccccc--c---cccCCCcceeCCccCccccCcchhccCC
Q psy8696 160 RPKKQFICKFCNRQFTKSYNLLIH--E---RTHTDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 160 ~~~k~~~C~~C~k~F~~~~~L~~H--~---r~Htgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
...+++.|.+|.+.|.....|..+ + ..+.+++||.|+.|++.|.....|..|+
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~ 93 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHI 93 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHH
Confidence 346789999999988877666554 1 1234588999999999999999998774
No 22
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.27 E-value=3.7e-05 Score=41.40 Aligned_cols=23 Identities=35% Similarity=0.787 Sum_probs=17.5
Q ss_pred ccccccccccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTH 187 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~H 187 (212)
|+|..|++.|..+..|..|++.|
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 56888888888888888887654
No 23
>PRK04860 hypothetical protein; Provisional
Probab=97.09 E-value=0.00017 Score=58.05 Aligned_cols=41 Identities=24% Similarity=0.576 Sum_probs=36.1
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccCcch
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDH 207 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~ 207 (212)
-+|.|. |++ ....+.+|.++|+++++|.|..|++.|.....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEecc
Confidence 469998 997 77789999999999999999999999986654
No 24
>PHA02768 hypothetical protein; Provisional
Probab=96.91 E-value=0.00018 Score=47.50 Aligned_cols=44 Identities=9% Similarity=0.089 Sum_probs=39.8
Q ss_pred CCCCCCCCccccccccccCCCCCCCCCCcccccccccccccccccc
Q psy8696 136 LFPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLL 181 (212)
Q Consensus 136 ~~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~ 181 (212)
.|.|..|...+.....+..|.++|. ++|+|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3789999999999999999999998 6899999999999888775
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.78 E-value=0.00029 Score=46.30 Aligned_cols=45 Identities=27% Similarity=0.620 Sum_probs=33.6
Q ss_pred ccccccccccccccccccccccc-cCCC-cceeCCccCccccCcchhccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERT-HTDE-RPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~-Htge-kpf~C~~Cgk~F~~~~~L~~H 211 (212)
.|.|++|++. .....|..|... |..+ +.+.|++|...+.. +|.+|
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~H 48 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRH 48 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHH
Confidence 4899999994 556789999655 5544 57999999986553 66655
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.63 E-value=0.00027 Score=37.93 Aligned_cols=20 Identities=45% Similarity=1.092 Sum_probs=18.6
Q ss_pred eeCCccCccccCcchhccCC
Q psy8696 193 YSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 193 f~C~~Cgk~F~~~~~L~~Hr 212 (212)
|+|+.|++.|.++..|++|+
T Consensus 1 y~C~~C~~~f~~~~~l~~H~ 20 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHM 20 (23)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHH
Confidence 78999999999999999884
No 27
>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=96.61 E-value=0.00051 Score=38.31 Aligned_cols=25 Identities=32% Similarity=0.655 Sum_probs=21.6
Q ss_pred ccccccccccccccccccccccccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHT 188 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Ht 188 (212)
+|+|..|++.|.....|..|++.|.
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 4789999999999999999988774
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.53 E-value=0.00041 Score=36.98 Aligned_cols=23 Identities=39% Similarity=0.795 Sum_probs=15.6
Q ss_pred ccccccccccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTH 187 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~H 187 (212)
|.|++|++.|.....|..|+++|
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 56777888888877777777654
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.36 E-value=0.00074 Score=48.56 Aligned_cols=21 Identities=33% Similarity=0.928 Sum_probs=17.6
Q ss_pred ceeCCccCccccCcchhccCC
Q psy8696 192 PYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 192 pf~C~~Cgk~F~~~~~L~~Hr 212 (212)
.+.|.+|++.|.....|..|+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHM 70 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHH
Confidence 589999999999999888874
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=95.85 E-value=0.0013 Score=36.57 Aligned_cols=21 Identities=48% Similarity=1.159 Sum_probs=19.1
Q ss_pred ceeCCccCccccCcchhccCC
Q psy8696 192 PYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 192 pf~C~~Cgk~F~~~~~L~~Hr 212 (212)
+|+|+.|++.|.....|..|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK 21 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH
T ss_pred CCCCCccCCccCChhHHHHHh
Confidence 689999999999999998874
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=95.84 E-value=0.0015 Score=34.73 Aligned_cols=20 Identities=50% Similarity=1.170 Sum_probs=16.3
Q ss_pred eeCCccCccccCcchhccCC
Q psy8696 193 YSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 193 f~C~~Cgk~F~~~~~L~~Hr 212 (212)
|.|++|++.|.+...|+.|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 78999999999999998874
No 32
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.78 E-value=0.0022 Score=34.39 Aligned_cols=24 Identities=33% Similarity=0.566 Sum_probs=19.9
Q ss_pred cccccccccccccccccccccccC
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHT 188 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Ht 188 (212)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578889999999888988887664
No 33
>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=95.51 E-value=0.0044 Score=40.26 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=23.9
Q ss_pred CCCCccccccccccccccccccccccccCCCcc
Q psy8696 160 RPKKQFICKFCNRQFTKSYNLLIHERTHTDERP 192 (212)
Q Consensus 160 ~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekp 192 (212)
..+.+..|++|+..+....+|++|+.++++.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 457789999999999999999999988888776
No 34
>PHA00616 hypothetical protein
Probab=95.17 E-value=0.003 Score=39.87 Aligned_cols=21 Identities=33% Similarity=0.787 Sum_probs=19.2
Q ss_pred ceeCCccCccccCcchhccCC
Q psy8696 192 PYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 192 pf~C~~Cgk~F~~~~~L~~Hr 212 (212)
||+|..||+.|.++.+|++|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH
Confidence 689999999999999999883
No 35
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.61 E-value=0.024 Score=50.01 Aligned_cols=49 Identities=43% Similarity=0.821 Sum_probs=44.2
Q ss_pred Ccccccccccccccccccccccc--ccCCC--cceeCC--ccCccccCcchhccC
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHER--THTDE--RPYSCD--ICGKAFRRQDHLRDH 211 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r--~Htge--kpf~C~--~Cgk~F~~~~~L~~H 211 (212)
.++.|..|...|.....|.+|.+ .|+++ +++.|. .|++.|.+.+.+..|
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~ 342 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRH 342 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCC
Confidence 46889999999999999999999 89999 999999 799999999988776
No 36
>KOG3993|consensus
Probab=94.54 E-value=0.0076 Score=54.94 Aligned_cols=49 Identities=27% Similarity=0.689 Sum_probs=41.5
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCccccCcchhccCC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
.|.|..|...|.....|.+|.-...-..-|+|..|+|.|.-..||..||
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHR 315 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHR 315 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhh
Confidence 4999999999999999999964333334599999999999999998886
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.13 E-value=0.01 Score=31.68 Aligned_cols=20 Identities=40% Similarity=1.024 Sum_probs=17.8
Q ss_pred eeCCccCccccCcchhccCC
Q psy8696 193 YSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 193 f~C~~Cgk~F~~~~~L~~Hr 212 (212)
|.|..|++.|.....|..|+
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCCCcchhCCHHHHHHHH
Confidence 57999999999999998874
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.09 E-value=0.011 Score=32.17 Aligned_cols=23 Identities=35% Similarity=0.807 Sum_probs=17.1
Q ss_pred ccccccccccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTH 187 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~H 187 (212)
|.|.+|++.|.....|..|++.+
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 56788888888888887777643
No 39
>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=93.93 E-value=0.028 Score=31.34 Aligned_cols=20 Identities=35% Similarity=0.913 Sum_probs=12.1
Q ss_pred eeCCccCccccCcchhccCC
Q psy8696 193 YSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 193 f~C~~Cgk~F~~~~~L~~Hr 212 (212)
|.|++|++.|.....|..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 45666666666666665553
No 40
>PHA00732 hypothetical protein
Probab=93.77 E-value=0.032 Score=39.61 Aligned_cols=47 Identities=19% Similarity=0.287 Sum_probs=37.6
Q ss_pred CCCCCCCccccccccccCCCCC-CCCCCccccccccccccccccccccccccCC
Q psy8696 137 FPGTSSTHSHLDRRLLRAPGRA-SRPKKQFICKFCNRQFTKSYNLLIHERTHTD 189 (212)
Q Consensus 137 ~~~~~~~~~~~~~~~l~~h~~~-h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htg 189 (212)
|.|..|...+.....+..|.+. |.+ +.|..|++.|. .+..|.+++.+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---ChhhhhcccCC
Confidence 5688899999999989999874 543 58999999997 58888876543
No 41
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.74 E-value=0.024 Score=31.59 Aligned_cols=22 Identities=27% Similarity=0.712 Sum_probs=20.5
Q ss_pred cccccccccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERT 186 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~ 186 (212)
|.|..|++.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 7899999999999999999875
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.74 E-value=0.025 Score=30.66 Aligned_cols=19 Identities=47% Similarity=1.148 Sum_probs=17.4
Q ss_pred eeCCccCccccCcchhccC
Q psy8696 193 YSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 193 f~C~~Cgk~F~~~~~L~~H 211 (212)
|.|++|++.|.....|+.|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H 19 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQH 19 (25)
T ss_dssp EEETTTTEEESSHHHHHHH
T ss_pred CCCCCCCCCcCCHHHHHHH
Confidence 6899999999999998877
No 43
>KOG2461|consensus
Probab=92.05 E-value=0.15 Score=46.73 Aligned_cols=29 Identities=14% Similarity=0.257 Sum_probs=25.2
Q ss_pred ccceeeccCCcccccchHHHHHHHHHHHH
Q psy8696 41 SAFVPVVPTRSIHMYQGDELMAMMADKRK 69 (212)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (212)
-+.++|.|+.+|+|||..++++.+...-.
T Consensus 127 rt~r~I~p~eELlVWY~~e~~~~L~~~~~ 155 (396)
T KOG2461|consen 127 RTIRDIRPNEELLVWYGSEYAEELAYGHG 155 (396)
T ss_pred EecccCCCCCeEEEEeccchHhHhcccCC
Confidence 46799999999999999999999886544
No 44
>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=92.00 E-value=0.042 Score=35.74 Aligned_cols=25 Identities=40% Similarity=0.874 Sum_probs=17.6
Q ss_pred CCCcceeCCccCccccCcchhccCC
Q psy8696 188 TDERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 188 tgekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
..+.|-.|++|+..+.+..+|++|+
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHl 44 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHL 44 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHH
T ss_pred ccCCCCCCCcchhhccchhhHHHHH
Confidence 4567999999999999999999984
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.43 E-value=0.029 Score=30.25 Aligned_cols=23 Identities=26% Similarity=0.534 Sum_probs=16.5
Q ss_pred cccccccccccccccccccccccC
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHT 188 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Ht 188 (212)
|+|..|+.... +..|.+|++.|.
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 67889988877 778888887753
No 46
>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=91.12 E-value=0.042 Score=35.84 Aligned_cols=50 Identities=20% Similarity=0.363 Sum_probs=34.7
Q ss_pred CCCCCCCCccccccccccCCCC-CCCC-CCccccccccccccccccccccccccC
Q psy8696 136 LFPGTSSTHSHLDRRLLRAPGR-ASRP-KKQFICKFCNRQFTKSYNLLIHERTHT 188 (212)
Q Consensus 136 ~~~~~~~~~~~~~~~~l~~h~~-~h~~-~k~~~C~~C~k~F~~~~~L~~H~r~Ht 188 (212)
.|.|+.|.. ..+...|..|.. .|.. .+.+.|++|...+.. +|.+|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHHHHhc
Confidence 478888988 566666665543 2332 457999999987553 8888987654
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.87 E-value=0.55 Score=41.28 Aligned_cols=67 Identities=21% Similarity=0.285 Sum_probs=56.7
Q ss_pred CCCCCCCCccccccccccCCCC--CCCCC--Cccccc--cccccccccccccccccccCCCcceeCCc--cCccc
Q psy8696 136 LFPGTSSTHSHLDRRLLRAPGR--ASRPK--KQFICK--FCNRQFTKSYNLLIHERTHTDERPYSCDI--CGKAF 202 (212)
Q Consensus 136 ~~~~~~~~~~~~~~~~l~~h~~--~h~~~--k~~~C~--~C~k~F~~~~~L~~H~r~Htgekpf~C~~--Cgk~F 202 (212)
.+.+..|...+.....+..|.+ .|..+ +++.|. .|++.|.+...+.+|..+|++.+++.|.. |.+.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 363 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKF 363 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccc
Confidence 4667777777888888888988 79999 999999 79999999999999999999999888865 44443
No 48
>KOG1146|consensus
Probab=88.74 E-value=0.55 Score=48.55 Aligned_cols=53 Identities=25% Similarity=0.479 Sum_probs=44.9
Q ss_pred CCCCccccccccccccccccccccccccC-------------------------CCcceeCCccCccccCcchhccCC
Q psy8696 160 RPKKQFICKFCNRQFTKSYNLLIHERTHT-------------------------DERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 160 ~~~k~~~C~~C~k~F~~~~~L~~H~r~Ht-------------------------gekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
.-.|.|+|+.|+..|+....|-.|+|..+ +.++|.|..|...+..+.+|.+|+
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 34588999999999999999999999821 237899999999999999888773
No 49
>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=88.52 E-value=0.13 Score=29.91 Aligned_cols=20 Identities=20% Similarity=0.655 Sum_probs=11.7
Q ss_pred ceeCCccCccccCcchhccC
Q psy8696 192 PYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 192 pf~C~~Cgk~F~~~~~L~~H 211 (212)
+|.|++|++.|.....+..|
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H 22 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAH 22 (35)
T ss_pred CeEccccCCccCCHHHHHHH
Confidence 35566666666655555544
No 50
>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=87.96 E-value=0.29 Score=28.67 Aligned_cols=24 Identities=29% Similarity=1.067 Sum_probs=18.2
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
|.|..||..+.-. +.++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC------------cCCCcCcCCCC
Confidence 7899999765432 26889999985
No 51
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=87.79 E-value=0.28 Score=43.58 Aligned_cols=25 Identities=20% Similarity=0.660 Sum_probs=22.2
Q ss_pred CCCcccccccccccccccccccccc
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHER 185 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r 185 (212)
..|||.|++|+|.|++...|+-|+.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 4599999999999999999998853
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=87.31 E-value=0.15 Score=28.13 Aligned_cols=21 Identities=33% Similarity=0.698 Sum_probs=15.5
Q ss_pred cccccccccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERT 186 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~ 186 (212)
..|..||+.| ....|.+|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4688888888 56677777653
No 53
>KOG4124|consensus
Probab=84.93 E-value=1.5 Score=39.56 Aligned_cols=52 Identities=27% Similarity=0.796 Sum_probs=40.1
Q ss_pred CCCcccccc--ccccccccccccccccc---------------cC----CCcceeCCccCccccCcchhccCC
Q psy8696 161 PKKQFICKF--CNRQFTKSYNLLIHERT---------------HT----DERPYSCDICGKAFRRQDHLRDHR 212 (212)
Q Consensus 161 ~~k~~~C~~--C~k~F~~~~~L~~H~r~---------------Ht----gekpf~C~~Cgk~F~~~~~L~~Hr 212 (212)
..++|+|.+ |.+.++....|+.|... |+ ..|+|+|++|.+.++....|+-|+
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 367899976 99999888888777532 22 358999999999998888777664
No 54
>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=82.97 E-value=0.36 Score=27.99 Aligned_cols=23 Identities=35% Similarity=0.706 Sum_probs=20.0
Q ss_pred ccccccccccccccccccccccc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERT 186 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~ 186 (212)
.|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 48899999999998889888764
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=82.37 E-value=0.83 Score=34.36 Aligned_cols=30 Identities=30% Similarity=0.791 Sum_probs=21.8
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
..|..||+.|- .| +..|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFY---DL--------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFY---DL--------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhc---cC--------CCCCccCCCCCCccCcc
Confidence 46889998883 33 23588899999888654
No 56
>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=77.54 E-value=1.2 Score=28.37 Aligned_cols=30 Identities=20% Similarity=0.606 Sum_probs=20.4
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
.|+|..|+..|.....+. . ...-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMS------D-DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecC------C-CCCCCCCCCCC
Confidence 488999999887542221 1 34567999986
No 57
>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=76.95 E-value=1.5 Score=25.91 Aligned_cols=25 Identities=32% Similarity=0.850 Sum_probs=17.9
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
.|.|..||..+... +.|..|++|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 48899999764321 25679999986
No 58
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.83 E-value=1.7 Score=31.44 Aligned_cols=32 Identities=28% Similarity=0.758 Sum_probs=23.1
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
..|.|+.|++. .+.|+- ..-+.|..|+..|.-
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a--~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIA--TGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc--------ceeeec--cCeEEcCCCCCeecc
Confidence 45899999975 233433 346999999999864
No 59
>PRK04860 hypothetical protein; Provisional
Probab=76.62 E-value=0.51 Score=37.93 Aligned_cols=40 Identities=13% Similarity=0.238 Sum_probs=30.4
Q ss_pred CCCCCCCCCccccccccccCCCCCCCCCCccccccccccccccc
Q psy8696 135 SLFPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSY 178 (212)
Q Consensus 135 ~~~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~ 178 (212)
-.|.|. |.. ....++.|.++++++++|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 356676 654 4445677889999999999999999887543
No 60
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=76.36 E-value=0.69 Score=32.76 Aligned_cols=24 Identities=33% Similarity=0.736 Sum_probs=21.2
Q ss_pred cccccccccccccccccccccccc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTH 187 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~H 187 (212)
.+.|.+|++.|.....|..|++.+
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 589999999999999999999864
No 61
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=76.04 E-value=1.4 Score=34.65 Aligned_cols=41 Identities=15% Similarity=0.457 Sum_probs=28.0
Q ss_pred CCCCccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 160 RPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 160 ~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
....-|.|+.|++.|.....+..- .. ...|.|+.||.....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEELEE 135 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEEEE
Confidence 345679999999999865544321 11 334999999987543
No 62
>PF14353 CpXC: CpXC protein
Probab=75.95 E-value=0.93 Score=34.58 Aligned_cols=14 Identities=36% Similarity=1.082 Sum_probs=7.8
Q ss_pred ceeCCccCccccCc
Q psy8696 192 PYSCDICGKAFRRQ 205 (212)
Q Consensus 192 pf~C~~Cgk~F~~~ 205 (212)
-|.|+.||+.|.-.
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 35566666655433
No 63
>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=75.53 E-value=1.6 Score=26.20 Aligned_cols=32 Identities=22% Similarity=0.588 Sum_probs=21.8
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCccc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAF 202 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F 202 (212)
.|+|..||+.|....... ......|+.||...
T Consensus 5 ~y~C~~Cg~~fe~~~~~~-------~~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS-------DDPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecC-------CCCCCCCCCCCCcc
Confidence 488999999886543321 13456799998743
No 64
>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=75.43 E-value=2.2 Score=32.99 Aligned_cols=30 Identities=27% Similarity=0.488 Sum_probs=20.4
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
..|+.||+.|-. | +..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYD---L--------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD---L--------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc---c--------CCCCccCCCcCCccCcc
Confidence 468888887733 2 23577888888877544
No 65
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=75.20 E-value=1.8 Score=25.78 Aligned_cols=34 Identities=21% Similarity=0.476 Sum_probs=22.8
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
+.|+.|+..|.-...... .....+.|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEEE
Confidence 679999988766543321 1223588999998875
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=74.89 E-value=0.75 Score=30.52 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=24.8
Q ss_pred CCCCCCCcccccccccccccccccccccccc
Q psy8696 157 RASRPKKQFICKFCNRQFTKSYNLLIHERTH 187 (212)
Q Consensus 157 ~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~H 187 (212)
+...++.-+.|+.|+..|.......+|...-
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 3456777889999999999998898888653
No 67
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.34 E-value=1.8 Score=35.00 Aligned_cols=23 Identities=39% Similarity=1.044 Sum_probs=19.4
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICG 199 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cg 199 (212)
.|.|.+||.. |.|+-|-+|++||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 6999999854 4567899999998
No 68
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=74.18 E-value=1.3 Score=30.88 Aligned_cols=19 Identities=16% Similarity=0.466 Sum_probs=10.5
Q ss_pred CCccccc--cccccccccccc
Q psy8696 162 KKQFICK--FCNRQFTKSYNL 180 (212)
Q Consensus 162 ~k~~~C~--~C~k~F~~~~~L 180 (212)
+..++|. .||.+|.....+
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeeecCCCCCCCEEEEEEEE
Confidence 4445665 566666555444
No 69
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.79 E-value=2.5 Score=25.21 Aligned_cols=34 Identities=21% Similarity=0.550 Sum_probs=23.6
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
..|+.|+..|.-...... ...+..+|..|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~ip-----~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP-----PKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHCC-----CCCcEEECCCCCCEeC
Confidence 468899988876654321 2344688999998874
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.74 E-value=2.1 Score=26.76 Aligned_cols=30 Identities=20% Similarity=0.468 Sum_probs=20.6
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
.|.|..||..|...... ..+.|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~~----------~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYG----------TGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCC----------CceECCCCCCeEE
Confidence 48899999877553211 1678999987654
No 71
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=70.21 E-value=2.4 Score=28.46 Aligned_cols=32 Identities=25% Similarity=0.535 Sum_probs=19.3
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
.|.|+.||+.--. +-.+-.....+|+|+.||-
T Consensus 27 ~F~CPnCGe~~I~-----Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIY-----RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeee-----hhhhHHHcCCceECCCcCc
Confidence 3788888865322 2222223346899999974
No 72
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=69.54 E-value=3.1 Score=24.91 Aligned_cols=34 Identities=26% Similarity=0.628 Sum_probs=23.4
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
..|+.|+..|.-...- +-.+.+..+|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 4688998888665432 123445789999998875
No 73
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=69.53 E-value=2.6 Score=25.26 Aligned_cols=33 Identities=24% Similarity=0.521 Sum_probs=20.3
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
..|..||+.|... ...-...-.|+.||-.+.++
T Consensus 2 r~C~~Cg~~Yh~~--------~~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIE--------FNPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETT--------TB--SSTTBCTTTTEBEBEE
T ss_pred cCcCCCCCccccc--------cCCCCCCCccCCCCCeeEeC
Confidence 4688898887432 22234456799998765543
No 74
>PRK09979 putative rho operon leader peptide; Provisional
Probab=67.77 E-value=3 Score=23.71 Aligned_cols=26 Identities=42% Similarity=0.409 Sum_probs=22.3
Q ss_pred cccccCCCCCCccccccccceeeccC
Q psy8696 24 RSLQMSNSPYHLLHRESSAFVPVVPT 49 (212)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (212)
++.|++|+.....-|-||||-||.-.
T Consensus 2 rseqisgsslnpscrfssayspvtrq 27 (33)
T PRK09979 2 RSEQISGSSLNPSCRFSSAYSPVTRQ 27 (33)
T ss_pred ccccccCCcCCcccccccccChHhhh
Confidence 56789999999999999999998643
No 75
>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=67.45 E-value=3.3 Score=25.48 Aligned_cols=30 Identities=23% Similarity=0.753 Sum_probs=21.5
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
.|.|..||..|.....+ .. .....|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 48899999988664332 22 45678999987
No 76
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=66.74 E-value=1.2 Score=29.59 Aligned_cols=27 Identities=33% Similarity=0.651 Sum_probs=22.6
Q ss_pred cccCCCcceeCCccCccccCcchhccC
Q psy8696 185 RTHTDERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 185 r~Htgekpf~C~~Cgk~F~~~~~L~~H 211 (212)
++..||.-+.|+-|+..|+...++.+|
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RH 36 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRH 36 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHH
Confidence 445688889999999999988877776
No 77
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=66.50 E-value=4.2 Score=25.46 Aligned_cols=26 Identities=27% Similarity=0.653 Sum_probs=18.8
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
|.|..||..|... ...+.+|..||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 8899999877643 2346789999854
No 78
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.80 E-value=3 Score=34.00 Aligned_cols=36 Identities=22% Similarity=0.551 Sum_probs=27.4
Q ss_pred CCCCccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 160 RPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 160 ~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
....-|.|+.|+..|+....+. .-|.|+.||.....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 3456699999999998877653 36999999976543
No 79
>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=64.41 E-value=3 Score=33.31 Aligned_cols=36 Identities=22% Similarity=0.410 Sum_probs=28.0
Q ss_pred CCCCccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 160 RPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 160 ~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
....-|.|+.|+..|+....+. .-|.|+.||.....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 3456699999999998877774 26999999976543
No 80
>PHA00626 hypothetical protein
Probab=61.92 E-value=6.8 Score=25.99 Aligned_cols=14 Identities=21% Similarity=0.591 Sum_probs=7.4
Q ss_pred Cccccccccccccc
Q psy8696 163 KQFICKFCNRQFTK 176 (212)
Q Consensus 163 k~~~C~~C~k~F~~ 176 (212)
..|+|..||..|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 34556666555543
No 81
>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=60.08 E-value=2.9 Score=25.67 Aligned_cols=24 Identities=38% Similarity=0.577 Sum_probs=14.6
Q ss_pred CCCcccccccccccccc----ccccccc
Q psy8696 161 PKKQFICKFCNRQFTKS----YNLLIHE 184 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~----~~L~~H~ 184 (212)
.++..+|.+|++.+... .+|.+|+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 35567899999988774 5677777
No 82
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=59.65 E-value=5.4 Score=25.72 Aligned_cols=29 Identities=24% Similarity=0.643 Sum_probs=19.8
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
..|.|..||+.|.. + .......|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~---~-------~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVEL---D-------QETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeeh---h-------hccCceeCCCCCcE
Confidence 45899999998821 1 12346789999854
No 83
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.31 E-value=4.3 Score=34.63 Aligned_cols=39 Identities=31% Similarity=0.479 Sum_probs=29.3
Q ss_pred CCccccccccccccccccccccccccCCCc----------c-----eeCCccCc
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDER----------P-----YSCDICGK 200 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htgek----------p-----f~C~~Cgk 200 (212)
++.+.|++|+..|..+..+..-.|+-.|+- | +.|++|.-
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 566899999999999888777777655542 2 35999973
No 84
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=59.28 E-value=6.1 Score=24.09 Aligned_cols=12 Identities=42% Similarity=1.077 Sum_probs=8.8
Q ss_pred ceeCCccCcccc
Q psy8696 192 PYSCDICGKAFR 203 (212)
Q Consensus 192 pf~C~~Cgk~F~ 203 (212)
-|.|..|+..|+
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 478888887664
No 85
>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=57.97 E-value=3.5 Score=32.13 Aligned_cols=28 Identities=36% Similarity=0.623 Sum_probs=17.3
Q ss_pred CCccccccccccccccccccccccccCCCcc
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDERP 192 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htgekp 192 (212)
+....|-+||+.|+. |++|++.|+|..|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 344789999999875 5999999977643
No 86
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=56.47 E-value=3.7 Score=26.06 Aligned_cols=25 Identities=36% Similarity=0.776 Sum_probs=18.9
Q ss_pred Ccccccccccccccc-----cccccccc-cc
Q psy8696 163 KQFICKFCNRQFTKS-----YNLLIHER-TH 187 (212)
Q Consensus 163 k~~~C~~C~k~F~~~-----~~L~~H~r-~H 187 (212)
..-.|.+|++.+... ++|.+|++ .|
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 346799999998766 47888877 44
No 87
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=56.02 E-value=6.1 Score=28.73 Aligned_cols=32 Identities=19% Similarity=0.565 Sum_probs=21.8
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
..|.|++|++.- +.+ .....+.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~-----vkR-----~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHA-----VKR-----QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCc-----eee-----eeeEEEEcCCCCCEEeC
Confidence 459999998642 211 13356899999998863
No 88
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.69 E-value=5.7 Score=30.02 Aligned_cols=28 Identities=25% Similarity=0.432 Sum_probs=19.3
Q ss_pred ccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 166 ICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 166 ~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
.|+.|++.|-. | ...|..|++||++|.+
T Consensus 11 idPetg~KFYD---L--------NrdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKFYD---L--------NRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchhhc---c--------CCCccccCcccccchH
Confidence 57788877733 2 3457888888888843
No 89
>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=55.45 E-value=5.6 Score=28.98 Aligned_cols=32 Identities=28% Similarity=0.855 Sum_probs=21.6
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
..|.|++|++.-.. | .....+.|..|++.|.-
T Consensus 34 a~y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVK--------R--GSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceE--------E--EeeEEEEcCCCCCEEeC
Confidence 45999999864211 1 13346899999998863
No 90
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.02 E-value=7.6 Score=26.00 Aligned_cols=32 Identities=28% Similarity=0.780 Sum_probs=19.1
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
.|.|+.||+..- .|-.+-.....+|+|+.||-
T Consensus 25 ~F~CPnCG~~~I-----~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVII-----YRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeE-----eechhHHhcCCceECCCCCC
Confidence 488888887521 12222222346899999974
No 91
>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=53.61 E-value=4.9 Score=24.38 Aligned_cols=10 Identities=40% Similarity=1.132 Sum_probs=7.5
Q ss_pred eeCCccCccc
Q psy8696 193 YSCDICGKAF 202 (212)
Q Consensus 193 f~C~~Cgk~F 202 (212)
|.|..|++.|
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 7788887765
No 92
>KOG2593|consensus
Probab=53.28 E-value=3.9 Score=37.76 Aligned_cols=44 Identities=18% Similarity=0.523 Sum_probs=30.5
Q ss_pred CCCCCCCCCccccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 155 PGRASRPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 155 h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
-.+..+...-|.|+.|.+.|.....++.- -...--|.|..|+-.
T Consensus 119 ~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~---~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 119 RLRDDTNVAGYVCPNCQKKYTSLEALQLL---DNETGEFHCENCGGE 162 (436)
T ss_pred HhhhccccccccCCccccchhhhHHHHhh---cccCceEEEecCCCc
Confidence 33445667779999999999887666432 122346999999743
No 93
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=52.82 E-value=12 Score=27.79 Aligned_cols=39 Identities=23% Similarity=0.459 Sum_probs=23.5
Q ss_pred CCCccccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
-++.|.|++||..-...-.++.- .+.-...|.+||..|.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEEec----CceeEEEcccCcceEE
Confidence 36779999999654332222211 1222467999998875
No 94
>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=52.38 E-value=6.3 Score=28.66 Aligned_cols=31 Identities=32% Similarity=0.863 Sum_probs=20.9
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
..|.|++|++.- +. |.-+| -|.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~-----vk---R~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTS-----VK---RVATG--IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSE-----EE---EEETT--EEEETTTTEEEE
T ss_pred CCCcCCCCCCce-----eE---EeeeE--EeecCCCCCEEe
Confidence 459999999753 21 22223 589999999885
No 95
>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=52.10 E-value=10 Score=22.08 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=16.3
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAF 202 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F 202 (212)
|.|..|+..+..+ ...+.+|..||..-
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCeE
Confidence 5788888776522 12356888888643
No 96
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.09 E-value=8.3 Score=29.95 Aligned_cols=39 Identities=21% Similarity=0.435 Sum_probs=21.9
Q ss_pred Cccccccccccccccc---cc------cccccccCCCcceeCCccCcc
Q psy8696 163 KQFICKFCNRQFTKSY---NL------LIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~---~L------~~H~r~Htgekpf~C~~Cgk~ 201 (212)
..+.|..||..|.... .| ..|..--+...-+.|+.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4588999998876541 11 111111112345779999854
No 97
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=51.12 E-value=8.5 Score=27.99 Aligned_cols=32 Identities=28% Similarity=0.715 Sum_probs=21.4
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
..|.|++|++.-.. | ...-.+.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVK--------R--VGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceE--------E--EEEEEEEcCCCCCEEeC
Confidence 34999999764221 1 12346899999998863
No 98
>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=51.00 E-value=7.2 Score=30.33 Aligned_cols=34 Identities=29% Similarity=0.793 Sum_probs=23.3
Q ss_pred CCccccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
.-.|.|..|+..+. +|.+. ..+.|.|..|+..|.
T Consensus 121 ~~~~~C~~C~~~~~------r~~~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 121 KYVYRCPSCGREYK------RHRRS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred ceEEEcCCCCCEee------eeccc--chhhEECCCCCCEEE
Confidence 34589999997763 34444 334599999987665
No 99
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=50.96 E-value=13 Score=36.87 Aligned_cols=22 Identities=32% Similarity=0.496 Sum_probs=14.3
Q ss_pred ccccccccCCCcceeCCccCcc
Q psy8696 180 LLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 180 L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
|.-|.--|....|..|+.||..
T Consensus 463 L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 463 LRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eEeCCCCCCCCCCCCCCCCCCC
Confidence 4444444556678899999854
No 100
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=50.34 E-value=8.8 Score=25.69 Aligned_cols=27 Identities=26% Similarity=0.648 Sum_probs=10.8
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
-.|..|++.|.. ..+.+.|..||+.|-
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVC 36 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEE
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEEC
Confidence 457778887742 134456777776654
No 101
>KOG2785|consensus
Probab=49.32 E-value=4.4 Score=36.81 Aligned_cols=51 Identities=20% Similarity=0.352 Sum_probs=40.3
Q ss_pred CCccccccccccccccccccccccccCCC-----------------------cceeCCccC---ccccCcchhccCC
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDE-----------------------RPYSCDICG---KAFRRQDHLRDHR 212 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htge-----------------------kpf~C~~Cg---k~F~~~~~L~~Hr 212 (212)
..|-.|-+|++.+..-.....||..++|- +-|.|-.|. +.|......+.||
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM 240 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHM 240 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHH
Confidence 44567999999999988888999877652 347799998 8888877777775
No 102
>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=48.44 E-value=2.4 Score=35.75 Aligned_cols=28 Identities=14% Similarity=0.342 Sum_probs=20.9
Q ss_pred CCccccccccccccccccccccccccCC
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTD 189 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htg 189 (212)
+..|.|..|+|.|.-...+.+|+...+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 4459999999999999999999876544
No 103
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=46.50 E-value=15 Score=29.34 Aligned_cols=16 Identities=25% Similarity=0.490 Sum_probs=9.7
Q ss_pred cccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNL 180 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L 180 (212)
++|+.||++|.....+
T Consensus 29 ~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLACGKRFTTFERV 44 (154)
T ss_pred eeccccCCcceEeEec
Confidence 6666666666655443
No 104
>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=46.05 E-value=15 Score=22.87 Aligned_cols=27 Identities=37% Similarity=0.945 Sum_probs=17.5
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
+.|+.|+.. ....+. +...|+|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~-------~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLK-------TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeC-------CCCeEECCCCCC
Confidence 779999865 211221 256799999875
No 105
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=45.71 E-value=9.1 Score=27.16 Aligned_cols=40 Identities=28% Similarity=0.658 Sum_probs=15.5
Q ss_pred CCccccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
.+.|.|++|+..= .+..-+....+.-...|.+|+..|...
T Consensus 20 ~~~F~CPfC~~~~----sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFCNHEK----SVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT--SS-----EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcCCCCC----eEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 4668899888321 111111111233356788888877644
No 106
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=44.80 E-value=11 Score=29.53 Aligned_cols=25 Identities=32% Similarity=0.450 Sum_probs=21.0
Q ss_pred cccccccccccccccccccccccCCCcc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERP 192 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekp 192 (212)
..|-.|||.|+ +|++|+.+|.|.-|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 57999999996 68999999987654
No 107
>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=44.21 E-value=15 Score=23.66 Aligned_cols=35 Identities=14% Similarity=0.478 Sum_probs=19.9
Q ss_pred cccccccccccccccccccccccCC------CcceeCCccCc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTD------ERPYSCDICGK 200 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htg------ekpf~C~~Cgk 200 (212)
|+|..||..|.-...-..+ .+-.| ...|.|++|+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~-~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 2 YECRICGYIYDPAEGDPDE-GIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred cCCCCCCeEECCCCCCccc-CcCCCCCHhHCCCCCCCCCCCC
Confidence 7899999887654322111 11111 12478999974
No 108
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=43.53 E-value=17 Score=26.84 Aligned_cols=39 Identities=31% Similarity=0.732 Sum_probs=15.7
Q ss_pred CCCccccccccccccccccccccccccCCCcc-eeCCccCccccCc
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHERTHTDERP-YSCDICGKAFRRQ 205 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekp-f~C~~Cgk~F~~~ 205 (212)
+.|.-.|..|++++...+ ..+ .|+|. |.|++|-+.|.+-
T Consensus 11 g~ke~~CalCG~tWg~~y-----~Ev-~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDYY-----EEV-DGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp -SGGGS-SS---S---SS------B--TT--BSSS--SSSS-TTS-
T ss_pred ccccccccccCCcHHHHH-----Hhh-cCCEEEEEcHHHHHHHHHH
Confidence 345567999999876432 222 35554 7889999998753
No 109
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.30 E-value=14 Score=34.14 Aligned_cols=31 Identities=19% Similarity=0.567 Sum_probs=22.0
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccccCcc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQD 206 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~ 206 (212)
-.|+.||.+...+ |.+-|+|..||..+....
T Consensus 351 p~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 351 PVCPRCGGRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCCccCCchhhc-----------CCCCcccccccccCCccc
Confidence 3699998765443 444799999998877543
No 110
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=42.83 E-value=12 Score=21.26 Aligned_cols=20 Identities=25% Similarity=0.565 Sum_probs=10.7
Q ss_pred ccccccccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHER 185 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r 185 (212)
|.|-.|++.| .....+.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 4577777777 4445555543
No 111
>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=42.30 E-value=21 Score=22.66 Aligned_cols=36 Identities=14% Similarity=0.455 Sum_probs=19.5
Q ss_pred cccccccccccccccccccccccCC------CcceeCCccCcc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTD------ERPYSCDICGKA 201 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htg------ekpf~C~~Cgk~ 201 (212)
|+|..|+..|.-...-..+ .+-.| -.-|.|++|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~-~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPEN-GIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGG-TB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCccc-CcCCCCCHHHCCCCCcCcCCCCc
Confidence 7899999887665443222 11111 234889999753
No 112
>KOG1146|consensus
Probab=42.22 E-value=8.1 Score=40.43 Aligned_cols=73 Identities=15% Similarity=0.196 Sum_probs=49.3
Q ss_pred CCCCCCCCCccccccccccCCCCCCCCCCccccccccccccccccccccccc-----------------cCCCcceeCCc
Q psy8696 135 SLFPGTSSTHSHLDRRLLRAPGRASRPKKQFICKFCNRQFTKSYNLLIHERT-----------------HTDERPYSCDI 197 (212)
Q Consensus 135 ~~~~~~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~r~-----------------Htgekpf~C~~ 197 (212)
..+.|..|.+.+.....+. + -.....|.|..|...|.....|..|.+. +...++| |.+
T Consensus 1259 Ge~~c~~~~~~~~~~~~~~-~---l~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~ 1333 (1406)
T KOG1146|consen 1259 GEGECGAVDELLTPSFGIS-T---LDVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLA 1333 (1406)
T ss_pred CcchhhhccccccCcccee-e---cccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chH
Confidence 3445555554443333332 2 2345669999999999999888888742 2234566 999
Q ss_pred cCccccCcchhccCC
Q psy8696 198 CGKAFRRQDHLRDHR 212 (212)
Q Consensus 198 Cgk~F~~~~~L~~Hr 212 (212)
|...|.....|..|+
T Consensus 1334 c~~~~~~~~alqihm 1348 (1406)
T KOG1146|consen 1334 CEVLLSGREALQIHM 1348 (1406)
T ss_pred HHhhcchhHHHHHHH
Confidence 999999999888875
No 113
>PRK12496 hypothetical protein; Provisional
Probab=41.47 E-value=14 Score=29.70 Aligned_cols=31 Identities=29% Similarity=0.847 Sum_probs=20.7
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
..|.|.-|++.|.... ..-.|++||....++
T Consensus 126 w~~~C~gC~~~~~~~~------------~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 126 WRKVCKGCKKKYPEDY------------PDDVCEICGSPVKRK 156 (164)
T ss_pred eeEECCCCCccccCCC------------CCCcCCCCCChhhhc
Confidence 4588999999885421 112599999765544
No 114
>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=41.39 E-value=16 Score=23.92 Aligned_cols=31 Identities=26% Similarity=0.521 Sum_probs=20.3
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
|+|+.|+..+.-.... .|+ ...|+.||..|.
T Consensus 3 ~~CP~CG~~iev~~~~-------~Ge-iV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGE-LVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCC-EEeCCCCCCEEE
Confidence 6899999876443222 133 568999987653
No 115
>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=40.97 E-value=21 Score=21.35 Aligned_cols=30 Identities=17% Similarity=0.515 Sum_probs=18.7
Q ss_pred cccccccccccccccccccccccCCCcceeCCcc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDIC 198 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~C 198 (212)
..|+.|+.. ..+.+|=+...|...|.|..|
T Consensus 6 v~CP~C~s~----~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQST----EGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCC----CcceeCCCCCCCCEeEecCcC
Confidence 457777643 125566666666667888777
No 116
>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=40.69 E-value=22 Score=26.41 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=8.0
Q ss_pred Cccccccccccc
Q psy8696 163 KQFICKFCNRQF 174 (212)
Q Consensus 163 k~~~C~~C~k~F 174 (212)
|+-.|++||..-
T Consensus 1 ~p~~CpYCg~~~ 12 (102)
T PF11672_consen 1 KPIICPYCGGPA 12 (102)
T ss_pred CCcccCCCCCee
Confidence 456788888643
No 117
>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=40.07 E-value=19 Score=22.92 Aligned_cols=10 Identities=40% Similarity=1.016 Sum_probs=4.9
Q ss_pred cccccccccc
Q psy8696 165 FICKFCNRQF 174 (212)
Q Consensus 165 ~~C~~C~k~F 174 (212)
+.|..||+.|
T Consensus 19 ~~Cr~Cg~~~ 28 (57)
T cd00065 19 HHCRNCGRIF 28 (57)
T ss_pred cccCcCcCCc
Confidence 4455555544
No 118
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=39.51 E-value=17 Score=28.95 Aligned_cols=36 Identities=22% Similarity=0.720 Sum_probs=26.2
Q ss_pred CCccccccccccccccccccccccccCCCcceeCCccCccc
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAF 202 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F 202 (212)
..+|.|. |+..|.+ .++|-.+-.|+ .|.|..|+-..
T Consensus 115 ~~~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 115 TYPYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred ceeEEee-cCCccch---hhhcccccccc-eEEeccCCceE
Confidence 4569999 9987654 35666666677 89999997543
No 119
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.47 E-value=18 Score=27.92 Aligned_cols=17 Identities=29% Similarity=0.712 Sum_probs=12.4
Q ss_pred CCccccccccccccccc
Q psy8696 162 KKQFICKFCNRQFTKSY 178 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~ 178 (212)
...|.|..|++.|....
T Consensus 51 ~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 51 HQRYKCKSCGSTFTVET 67 (129)
T ss_pred ccccccCCcCcceeeec
Confidence 55588888888886654
No 120
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=39.19 E-value=18 Score=28.17 Aligned_cols=34 Identities=21% Similarity=0.579 Sum_probs=21.9
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
-.|.|..|+..+. ++.+ |.....|.|..|+-.|.
T Consensus 111 ~~y~C~~C~~~~~------~~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 111 YPYRCTGCGQRYL------RVRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEEECCCCCCCCc------eEcc-ccCcceEEcCCCCCEEE
Confidence 3589988997763 2222 22226699999987654
No 121
>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 PF07941 K_channel_TID: Potassium channel Kv1.4 tandem inactivation domain; InterPro: IPR012897 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The first Kv1 sequence (also known as Shaker) was found in Drosophila melanogaster (Fruit fly). Several vertebrate potassium channels with similar amino acid sequences were subsequently found and, together with the D. melanogaster Shaker channel, now constitute the Kv1 family. The family consists of at least 6 genes (Kv1.1, Kv1.2, Kv1.3, Kv1.4, Kv1.5 and Kv1.6) which each play distinct physiological roles. A conserved motif found towards the C terminus of these channels is required for efficient processing and surface expression []. Variations in this motif account for the differences in cell surface expression and localisation between family members. These channels are mostly expressed in the brain, but can also be found in non-excitable cells, such as lymphocytes []. This entry features the tandem inactivation domain found at the N terminus of the Kv1.4 potassium channel. It is composed of two subdomains. Inactivation domain 1 (ID1, residues 1-38) consists of a flexible N terminus anchored at a 5-turn helix, and is thought to work by occluding the ion pathway, as is the case with a classical ball domain. Inactivation domain 2 (ID2, residues 40-50) is a 2.5 turn helix with a high proportion of hydrophobic residues that probably serves to attach ID1 to the cytoplasmic face of the channel. In this way, it can promote rapid access of ID1 to the receptor site in the open channel. ID1 and ID2 function together to bring about fast inactivation of the Kv1.4 channel, which is important for the role of the channel in short-term plasticity []. ; GO: 0005249 voltage-gated potassium channel activity, 0030955 potassium ion binding, 0006813 potassium ion transport, 0016021 integral to membrane; PDB: 1KN7_A 1ZTO_A.
Probab=38.49 E-value=9.5 Score=26.04 Aligned_cols=11 Identities=18% Similarity=0.111 Sum_probs=4.9
Q ss_pred CCcccccchHH
Q psy8696 49 TRSIHMYQGDE 59 (212)
Q Consensus 49 ~~~~~~~~~~~ 59 (212)
+++-||=|++-
T Consensus 12 GCnsHlPYGYA 22 (75)
T PF07941_consen 12 GCNSHLPYGYA 22 (75)
T ss_dssp TTTT-S-TTGG
T ss_pred CccccCCchHH
Confidence 45666645553
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=38.40 E-value=20 Score=28.04 Aligned_cols=19 Identities=32% Similarity=0.714 Sum_probs=13.6
Q ss_pred cceeCCccCccccCcchhc
Q psy8696 191 RPYSCDICGKAFRRQDHLR 209 (212)
Q Consensus 191 kpf~C~~Cgk~F~~~~~L~ 209 (212)
+-+.|..|+|.|-..++++
T Consensus 123 ~f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred eEEECCCCCCEecccccHH
Confidence 3577888888887766654
No 124
>PHA02998 RNA polymerase subunit; Provisional
Probab=38.18 E-value=21 Score=29.31 Aligned_cols=37 Identities=22% Similarity=0.475 Sum_probs=22.1
Q ss_pred ccccccccccccccccccccccccCCCc----ceeCCccCccccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDER----PYSCDICGKAFRR 204 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgek----pf~C~~Cgk~F~~ 204 (212)
.-.|+.|+..=.....+ ++..... -|.|..|++.|.-
T Consensus 143 ~v~CPkCg~~~A~f~ql----QTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMI----QTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCCceEEEEE----eeccCCCCceEEEEcCCCCCccCC
Confidence 36799998543332222 2222333 3899999998764
No 125
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=37.97 E-value=15 Score=27.44 Aligned_cols=15 Identities=20% Similarity=0.512 Sum_probs=11.9
Q ss_pred ccccccccccccccc
Q psy8696 164 QFICKFCNRQFTKSY 178 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~ 178 (212)
++.|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 578999999988743
No 126
>KOG4167|consensus
Probab=37.94 E-value=5.5 Score=39.25 Aligned_cols=27 Identities=30% Similarity=0.481 Sum_probs=23.8
Q ss_pred CCccccccccccccccccccccccccC
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHT 188 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Ht 188 (212)
...|.|..|+|.|..-..+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 456999999999999999999999884
No 127
>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=37.12 E-value=11 Score=20.75 Aligned_cols=9 Identities=22% Similarity=0.859 Sum_probs=5.1
Q ss_pred eCCccCccc
Q psy8696 194 SCDICGKAF 202 (212)
Q Consensus 194 ~C~~Cgk~F 202 (212)
.|++|++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 456665555
No 128
>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=34.85 E-value=19 Score=27.07 Aligned_cols=27 Identities=19% Similarity=0.545 Sum_probs=18.7
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
-...|..|++.|..... -+.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 34789999987765321 3679999854
No 129
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=34.27 E-value=14 Score=23.86 Aligned_cols=43 Identities=23% Similarity=0.450 Sum_probs=26.3
Q ss_pred CCcccccc--ccccccccccccccccccCCCcceeCCc----cCccccCc
Q psy8696 162 KKQFICKF--CNRQFTKSYNLLIHERTHTDERPYSCDI----CGKAFRRQ 205 (212)
Q Consensus 162 ~k~~~C~~--C~k~F~~~~~L~~H~r~Htgekpf~C~~----Cgk~F~~~ 205 (212)
..+..|+. |...+. +..|..|+...=..++..|.+ |...+.+.
T Consensus 7 ~~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp TSEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEHH
T ss_pred CCEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccchh
Confidence 34567877 444454 568889988655667889999 98877653
No 130
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=34.23 E-value=21 Score=26.27 Aligned_cols=21 Identities=24% Similarity=0.593 Sum_probs=14.4
Q ss_pred cccccCCCcceeCCccCccccC
Q psy8696 183 HERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 183 H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
.+..+.| ++++|..||..|.-
T Consensus 71 W~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 71 WMWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEEeCC-CceeCCCCCcEEEE
Confidence 3455555 68888888887763
No 131
>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=34.10 E-value=19 Score=21.40 Aligned_cols=16 Identities=38% Similarity=0.719 Sum_probs=8.0
Q ss_pred cccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYNL 180 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L 180 (212)
-.|..|++.|...+-+
T Consensus 4 ~~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLL 19 (34)
T ss_dssp EE-TTT--EES-SSCC
T ss_pred chHhHhCCHHHHHHHH
Confidence 3588899888776543
No 132
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=33.81 E-value=10 Score=34.28 Aligned_cols=42 Identities=24% Similarity=0.374 Sum_probs=19.8
Q ss_pred Cccccccccccccccccc---ccc-ccccCCCc-ceeCCccCccccC
Q psy8696 163 KQFICKFCNRQFTKSYNL---LIH-ERTHTDER-PYSCDICGKAFRR 204 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L---~~H-~r~Htgek-pf~C~~Cgk~F~~ 204 (212)
+.+.|..|.+++...... ..| +..|...| -|+|..|++....
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEE
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeee
Confidence 347899998765544432 234 33444444 4899999876543
No 133
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=33.77 E-value=21 Score=26.83 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=17.8
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
-.+.|..|+..|.... ..|.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC------------cCccCcCCCC
Confidence 3478999997775432 3456999984
No 134
>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=33.76 E-value=28 Score=23.18 Aligned_cols=14 Identities=29% Similarity=0.781 Sum_probs=8.5
Q ss_pred CcceeCCccCcccc
Q psy8696 190 ERPYSCDICGKAFR 203 (212)
Q Consensus 190 ekpf~C~~Cgk~F~ 203 (212)
.+.|.|..||..+.
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 44567777776543
No 135
>KOG3214|consensus
Probab=33.47 E-value=24 Score=26.20 Aligned_cols=41 Identities=29% Similarity=0.566 Sum_probs=22.5
Q ss_pred CCCccccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
-...|.|.+|+.--.-.-. +..........|.+|+.+|...
T Consensus 20 ldt~FnClfcnHek~v~~~----~Dk~~~iG~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 20 LDTQFNCLFCNHEKSVSCT----LDKKHNIGKASCRICEESFQTT 60 (109)
T ss_pred hheeeccCccccccceeee----ehhhcCcceeeeeehhhhhccc
Confidence 3556889888743211111 1111223346799999888754
No 136
>PRK05978 hypothetical protein; Provisional
Probab=33.37 E-value=26 Score=27.84 Aligned_cols=32 Identities=22% Similarity=0.326 Sum_probs=18.8
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
-+|+.|++.=-.+..|+.+ -.|+.||..|...
T Consensus 34 grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPV---------DHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccccccccC---------CCccccCCccccC
Confidence 4688888653333333322 2588888777654
No 137
>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=33.35 E-value=20 Score=22.28 Aligned_cols=16 Identities=38% Similarity=0.709 Sum_probs=10.5
Q ss_pred cccccccccccccccc
Q psy8696 166 ICKFCNRQFTKSYNLL 181 (212)
Q Consensus 166 ~C~~C~k~F~~~~~L~ 181 (212)
.|.+|++.|..+..+.
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 3777777777665444
No 138
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.20 E-value=24 Score=25.77 Aligned_cols=29 Identities=24% Similarity=0.590 Sum_probs=20.4
Q ss_pred CCccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
-+|-.|..||..|..- . -.+|-+|+.|..
T Consensus 56 v~Pa~CkkCGfef~~~-~---------ik~pSRCP~CKS 84 (97)
T COG3357 56 VRPARCKKCGFEFRDD-K---------IKKPSRCPKCKS 84 (97)
T ss_pred ecChhhcccCcccccc-c---------cCCcccCCcchh
Confidence 3567899999988651 1 135788998854
No 139
>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=32.34 E-value=16 Score=30.82 Aligned_cols=24 Identities=38% Similarity=0.958 Sum_probs=16.6
Q ss_pred CCCcceeCCccCccccCcchhccC
Q psy8696 188 TDERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 188 tgekpf~C~~Cgk~F~~~~~L~~H 211 (212)
..+..|.|..|+|.|.-..-.++|
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KH 96 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKH 96 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHH
Confidence 355679999999999877666555
No 140
>PRK04351 hypothetical protein; Provisional
Probab=32.21 E-value=25 Score=27.84 Aligned_cols=35 Identities=20% Similarity=0.625 Sum_probs=23.1
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCccccCc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
-.|.|..|+..+.+ +.+ | ..+.|.|..|+-.+...
T Consensus 111 y~Y~C~~Cg~~~~r------~Rr-~-n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 111 YLYECQSCGQQYLR------KRR-I-NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEEECCCCCCEeee------eee-c-CCCcEEeCCCCcEeeec
Confidence 45899889876533 222 2 34679999998766544
No 141
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=30.83 E-value=27 Score=21.08 Aligned_cols=14 Identities=29% Similarity=0.852 Sum_probs=11.7
Q ss_pred ceeCCccCccccCc
Q psy8696 192 PYSCDICGKAFRRQ 205 (212)
Q Consensus 192 pf~C~~Cgk~F~~~ 205 (212)
||+|..|++.|-.+
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 88999999988654
No 142
>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=30.78 E-value=25 Score=20.18 Aligned_cols=25 Identities=28% Similarity=0.765 Sum_probs=11.4
Q ss_pred ccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 166 ICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 166 ~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
+|+.|+-.+.. .....|.|+.|+..
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-----------ccCCEEeCCccccc
Confidence 47777766654 23446888888754
No 143
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.44 E-value=26 Score=26.32 Aligned_cols=28 Identities=21% Similarity=0.440 Sum_probs=17.8
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
-.+.|..|+..|..... ..+.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 96 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ-----------RVRRCPQCHGD 96 (114)
T ss_pred cEEEcccCCCeeecCCc-----------cCCcCcCcCCC
Confidence 34789999976644211 12579999854
No 144
>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=29.16 E-value=16 Score=26.88 Aligned_cols=25 Identities=16% Similarity=0.309 Sum_probs=21.3
Q ss_pred ccc----ccccccccccccccccccccCC
Q psy8696 165 FIC----KFCNRQFTKSYNLLIHERTHTD 189 (212)
Q Consensus 165 ~~C----~~C~k~F~~~~~L~~H~r~Htg 189 (212)
|.| ..|+..+.....+.+|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 778 8899999999999999887654
No 145
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.05 E-value=35 Score=27.21 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=14.5
Q ss_pred Ccccccccccccccccccc
Q psy8696 163 KQFICKFCNRQFTKSYNLL 181 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~ 181 (212)
+.-.|..|++.|++.....
T Consensus 27 RRReC~~C~~RFTTfE~~E 45 (156)
T COG1327 27 RRRECLECGERFTTFERAE 45 (156)
T ss_pred hhhcccccccccchhheee
Confidence 4457999999998876544
No 146
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.88 E-value=13 Score=33.75 Aligned_cols=22 Identities=32% Similarity=0.576 Sum_probs=15.3
Q ss_pred cccccccccccccccccccccc
Q psy8696 166 ICKFCNRQFTKSYNLLIHERTH 187 (212)
Q Consensus 166 ~C~~C~k~F~~~~~L~~H~r~H 187 (212)
.|.+|.+.|-.-..|.+|.|..
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~ 243 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLR 243 (493)
T ss_pred hhhhccceecChHHHHHHHHhh
Confidence 4777777777777777776653
No 147
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.47 E-value=28 Score=26.30 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=17.8
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
-.+.|..|++.|..... .-+.|+.||..
T Consensus 70 ~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 97 (117)
T PRK00564 70 VELECKDCSHVFKPNAL-----------DYGVCEKCHSK 97 (117)
T ss_pred CEEEhhhCCCccccCCc-----------cCCcCcCCCCC
Confidence 34789999977755321 11359999854
No 148
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=28.45 E-value=39 Score=22.19 Aligned_cols=15 Identities=20% Similarity=0.702 Sum_probs=10.4
Q ss_pred ccccccccccccccc
Q psy8696 165 FICKFCNRQFTKSYN 179 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~ 179 (212)
..|..|++.|.....
T Consensus 6 ~~C~~Cg~~~~~~dD 20 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDD 20 (54)
T ss_pred ccChhhCCcccCCCC
Confidence 468888888865433
No 149
>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=28.17 E-value=37 Score=20.49 Aligned_cols=32 Identities=19% Similarity=0.490 Sum_probs=14.6
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAF 202 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F 202 (212)
..|..|+-- |.-+..+..+.+.|.|.+|+...
T Consensus 3 ~rC~~C~ay------lNp~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 3 VRCRRCRAY------LNPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp -B-TTT--B------S-TTSEEETTTTEEEETTT--EE
T ss_pred cccCCCCCE------ECCcceEcCCCCEEECcCCCCcC
Confidence 456666532 22233444466778888887643
No 150
>KOG4173|consensus
Probab=28.01 E-value=6.1 Score=33.20 Aligned_cols=46 Identities=30% Similarity=0.611 Sum_probs=28.5
Q ss_pred ccccccccccccccccccccc-c---------CCCcceeCC--ccCccccCcchhccC
Q psy8696 166 ICKFCNRQFTKSYNLLIHERT-H---------TDERPYSCD--ICGKAFRRQDHLRDH 211 (212)
Q Consensus 166 ~C~~C~k~F~~~~~L~~H~r~-H---------tgekpf~C~--~Cgk~F~~~~~L~~H 211 (212)
.|.+|.+.|.+..-|-.|+-. | .|.--|+|- .|+..|.+...-++|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH 165 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDH 165 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhH
Confidence 677777777777777777532 2 233347774 377777665554444
No 151
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=27.66 E-value=34 Score=18.21 Aligned_cols=6 Identities=50% Similarity=1.453 Sum_probs=3.1
Q ss_pred CCccCc
Q psy8696 195 CDICGK 200 (212)
Q Consensus 195 C~~Cgk 200 (212)
|..||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
No 152
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=27.44 E-value=27 Score=24.02 Aligned_cols=15 Identities=27% Similarity=0.855 Sum_probs=7.5
Q ss_pred ccCCCcceeCCccCcc
Q psy8696 186 THTDERPYSCDICGKA 201 (212)
Q Consensus 186 ~Htgekpf~C~~Cgk~ 201 (212)
.+.+.|--+| .||+.
T Consensus 14 a~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 14 AKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EETT-SEEEE-TTTEE
T ss_pred ecCCcceeEe-cCCCe
Confidence 3344455566 66654
No 153
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=27.05 E-value=41 Score=33.91 Aligned_cols=12 Identities=33% Similarity=0.686 Sum_probs=7.5
Q ss_pred cccccccccccc
Q psy8696 165 FICKFCNRQFTK 176 (212)
Q Consensus 165 ~~C~~C~k~F~~ 176 (212)
-.|..|++.|..
T Consensus 461 dtC~~C~kkFfS 472 (1374)
T PTZ00303 461 DSCPSCGRAFIS 472 (1374)
T ss_pred CcccCcCCcccc
Confidence 347777777654
No 154
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=26.78 E-value=42 Score=29.02 Aligned_cols=14 Identities=29% Similarity=0.809 Sum_probs=9.7
Q ss_pred cceeCCccCccccC
Q psy8696 191 RPYSCDICGKAFRR 204 (212)
Q Consensus 191 kpf~C~~Cgk~F~~ 204 (212)
--|.|..|++.|+-
T Consensus 154 aef~C~~C~h~F~G 167 (278)
T PF15135_consen 154 AEFHCPKCRHNFRG 167 (278)
T ss_pred eeeecccccccchh
Confidence 35778888777763
No 155
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.58 E-value=50 Score=20.53 Aligned_cols=12 Identities=25% Similarity=0.847 Sum_probs=5.9
Q ss_pred cccccccccccc
Q psy8696 164 QFICKFCNRQFT 175 (212)
Q Consensus 164 ~~~C~~C~k~F~ 175 (212)
.|.|..|+..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 355555554443
No 156
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=26.22 E-value=36 Score=25.62 Aligned_cols=39 Identities=23% Similarity=0.509 Sum_probs=21.6
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
..|+.|+..=.....|+.-.---.-.+-|+|..||..|+
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 678888865433333322111111223489999998875
No 157
>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=26.17 E-value=53 Score=18.45 Aligned_cols=11 Identities=36% Similarity=1.077 Sum_probs=7.2
Q ss_pred ceeCCccCccc
Q psy8696 192 PYSCDICGKAF 202 (212)
Q Consensus 192 pf~C~~Cgk~F 202 (212)
=|.|..|++.+
T Consensus 27 Cf~C~~C~~~L 37 (39)
T smart00132 27 CFKCSKCGKPL 37 (39)
T ss_pred CCCCcccCCcC
Confidence 36677777655
No 158
>PLN02294 cytochrome c oxidase subunit Vb
Probab=25.95 E-value=42 Score=27.31 Aligned_cols=22 Identities=14% Similarity=0.484 Sum_probs=15.8
Q ss_pred cccccCCCcceeCCccCccccCc
Q psy8696 183 HERTHTDERPYSCDICGKAFRRQ 205 (212)
Q Consensus 183 H~r~Htgekpf~C~~Cgk~F~~~ 205 (212)
.+..+.| +|++|..||..|.-+
T Consensus 133 Wf~L~kG-kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 133 WFWLEKG-KSFECPVCTQYFELE 154 (174)
T ss_pred EEEecCC-CceeCCCCCCEEEEE
Confidence 3444544 799999999988643
No 159
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=25.66 E-value=38 Score=27.37 Aligned_cols=17 Identities=35% Similarity=0.862 Sum_probs=11.2
Q ss_pred ceeCCccCccccCcchh
Q psy8696 192 PYSCDICGKAFRRQDHL 208 (212)
Q Consensus 192 pf~C~~Cgk~F~~~~~L 208 (212)
-|.|..||+.|-..+++
T Consensus 130 f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 130 FYRCPKCGKIYWKGSHW 146 (165)
T ss_pred eeECCCCcccccCchHH
Confidence 45677777777665554
No 160
>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=24.99 E-value=52 Score=26.10 Aligned_cols=19 Identities=21% Similarity=0.333 Sum_probs=13.7
Q ss_pred ccccccccccccccccccc
Q psy8696 164 QFICKFCNRQFTKSYNLLI 182 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~ 182 (212)
.=+|..|++.|++...+..
T Consensus 28 RReC~~C~~RFTTyErve~ 46 (147)
T TIGR00244 28 RRECLECHERFTTFERAEL 46 (147)
T ss_pred cccCCccCCccceeeeccc
Confidence 3568889988888766543
No 161
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=24.91 E-value=28 Score=26.00 Aligned_cols=26 Identities=27% Similarity=0.708 Sum_probs=16.6
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
.+.|..|++.|..... .+.|+.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF------------DFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHC------------CHH-SSSSSS
T ss_pred cEECCCCCCEEecCCC------------CCCCcCCcCC
Confidence 4789999988865321 2569999865
No 162
>KOG0978|consensus
Probab=24.52 E-value=23 Score=34.95 Aligned_cols=21 Identities=38% Similarity=0.623 Sum_probs=16.8
Q ss_pred cceeCCccCccccCcchhccC
Q psy8696 191 RPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 191 kpf~C~~Cgk~F~~~~~L~~H 211 (212)
|--+|+.|+..|.-.+-+..|
T Consensus 677 RqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred hcCCCCCCCCCCCcccccccC
Confidence 345799999999988877666
No 163
>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=24.51 E-value=29 Score=21.26 Aligned_cols=15 Identities=40% Similarity=1.041 Sum_probs=9.3
Q ss_pred cceeCCccCccccCc
Q psy8696 191 RPYSCDICGKAFRRQ 205 (212)
Q Consensus 191 kpf~C~~Cgk~F~~~ 205 (212)
-||.|..|++.|-.+
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 478899999888654
No 164
>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=23.86 E-value=47 Score=20.16 Aligned_cols=28 Identities=18% Similarity=0.441 Sum_probs=14.1
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKA 201 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~ 201 (212)
|.|+.|+.... .......-+.|..||..
T Consensus 1 m~Cp~Cg~~~~---------~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEI---------VFDPERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEE---------EEETTTTEEEETTT-BB
T ss_pred CCCcCCcCCce---------EEcCCCCeEECCCCCCE
Confidence 46777775431 11122334678888754
No 165
>KOG0402|consensus
Probab=23.83 E-value=32 Score=24.74 Aligned_cols=29 Identities=24% Similarity=0.682 Sum_probs=19.5
Q ss_pred cccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
|.|.+||+.--.+. -.--|.|.-|.+.|.
T Consensus 37 y~CsfCGK~~vKR~----------AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 37 YTCSFCGKKTVKRK----------AVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhcchhhhhhh----------ceeEEecCCccceec
Confidence 89999997532221 123578999988775
No 166
>KOG4173|consensus
Probab=23.78 E-value=15 Score=30.85 Aligned_cols=46 Identities=28% Similarity=0.550 Sum_probs=35.6
Q ss_pred Ccccccc--ccccccccccccccccccCCCcceeCCccCccccCcchhccC
Q psy8696 163 KQFICKF--CNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRRQDHLRDH 211 (212)
Q Consensus 163 k~~~C~~--C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~~~~L~~H 211 (212)
..|.|++ |-+.|.....+..|..+-++. .|.+|.+.|.+..-|..|
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~H 125 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAH 125 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHH
Confidence 4478987 888998888888886654443 699999999988777655
No 167
>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=23.58 E-value=43 Score=18.47 Aligned_cols=10 Identities=40% Similarity=0.963 Sum_probs=7.2
Q ss_pred eCCccCcccc
Q psy8696 194 SCDICGKAFR 203 (212)
Q Consensus 194 ~C~~Cgk~F~ 203 (212)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5777887774
No 168
>KOG1280|consensus
Probab=23.52 E-value=46 Score=30.15 Aligned_cols=39 Identities=18% Similarity=0.457 Sum_probs=26.7
Q ss_pred CCCcccccccccccccccccccccc-ccCCCcc-eeCCccC
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHER-THTDERP-YSCDICG 199 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r-~Htgekp-f~C~~Cg 199 (212)
....|.|++|++.-.+...|..|.. .|....+ ..|.+|.
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3457999999998888888888854 4543322 4566664
No 169
>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=23.42 E-value=42 Score=18.28 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=4.5
Q ss_pred ceeCCccC
Q psy8696 192 PYSCDICG 199 (212)
Q Consensus 192 pf~C~~Cg 199 (212)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45555555
No 170
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.16 E-value=58 Score=21.97 Aligned_cols=42 Identities=17% Similarity=0.275 Sum_probs=22.0
Q ss_pred CCCCCCccccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 158 ASRPKKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 158 ~h~~~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
.+...+++-|..-+-.|....-+. .+ -.+.-..|++|++.|+
T Consensus 18 I~~~~~~l~C~g~~~p~~HPrV~L---~m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 18 IEIGDLPLMCPGPEPPNDHPRVFL---DM-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEeCCeeEEcCCCCCCCCCCEEEE---Ec-CCCCcEecCccccEEE
Confidence 345566777775444432221111 11 2234467888888775
No 171
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=22.91 E-value=56 Score=30.66 Aligned_cols=40 Identities=10% Similarity=0.326 Sum_probs=24.0
Q ss_pred CCCccccccccccccccccccccccccCC------CcceeCCccCcc
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHERTHTD------ERPYSCDICGKA 201 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r~Htg------ekpf~C~~Cgk~ 201 (212)
..+.|+|..|+..|.-...-... .+-.| -..|.|+.|+..
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~-~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQ-DVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCccc-CCCCCCChhhCCCCCcCcCCCCc
Confidence 45679999999888654322111 11112 124899999853
No 172
>KOG4167|consensus
Probab=22.79 E-value=1.5e+02 Score=29.62 Aligned_cols=73 Identities=14% Similarity=0.060 Sum_probs=41.4
Q ss_pred CCCCCCCCCCCccccccccccCCCCCCCCCCc--cccccccccccccccccccccccCCCcc--eeCCccCccccCc
Q psy8696 133 SSSLFPGTSSTHSHLDRRLLRAPGRASRPKKQ--FICKFCNRQFTKSYNLLIHERTHTDERP--YSCDICGKAFRRQ 205 (212)
Q Consensus 133 ~s~~~~~~~~~~~~~~~~~l~~h~~~h~~~k~--~~C~~C~k~F~~~~~L~~H~r~Htgekp--f~C~~Cgk~F~~~ 205 (212)
....+++..|...+...--...+..++....+ +.|..|++.|.....-..|...+.-..| -.|.+|.+.|...
T Consensus 285 ~~~~~p~k~~St~p~~e~G~~s~~~~psa~wpqhlP~g~~~~~~p~s~g~s~~a~~~Qv~~P~g~~~si~~~~~~ll 361 (907)
T KOG4167|consen 285 TLPHRPLKSPSTIPLNEMGPQSQQLSPSAMWPQHLPDGRAQPGSPESSGQSKGAFGEQVDAPNGLTCSICLKEFKLL 361 (907)
T ss_pred ccccccccccccchhhhcCCccccccchhhccccCcccccCCCCCCcccccccchHhhhcCCCCCccccccCCCCcC
Confidence 34455565555555554444555555555444 7788888766655555555544432222 4578888777543
No 173
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=22.65 E-value=40 Score=21.65 Aligned_cols=15 Identities=27% Similarity=0.771 Sum_probs=11.2
Q ss_pred CcceeCCccCccccC
Q psy8696 190 ERPYSCDICGKAFRR 204 (212)
Q Consensus 190 ekpf~C~~Cgk~F~~ 204 (212)
.+.+.|..||..|..
T Consensus 2 Dk~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVF 16 (49)
T ss_pred CeeEEcccCCCeEEE
Confidence 466788888887764
No 174
>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=22.52 E-value=49 Score=26.51 Aligned_cols=17 Identities=35% Similarity=0.731 Sum_probs=11.9
Q ss_pred CCcceeCCccCccccCc
Q psy8696 189 DERPYSCDICGKAFRRQ 205 (212)
Q Consensus 189 gekpf~C~~Cgk~F~~~ 205 (212)
-+.|.-|..||+.|.|.
T Consensus 65 ~~~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWT 81 (158)
T ss_pred CCCChhHHhCCCCCchH
Confidence 34677788888887764
No 175
>KOG2482|consensus
Probab=21.85 E-value=28 Score=31.52 Aligned_cols=23 Identities=26% Similarity=0.628 Sum_probs=20.9
Q ss_pred ccccccccccccccccccccccc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERT 186 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~ 186 (212)
.+.|-+|.+.|..+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 37899999999999999999875
No 176
>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=21.65 E-value=35 Score=21.31 Aligned_cols=37 Identities=22% Similarity=0.430 Sum_probs=18.6
Q ss_pred cccccccccccccccccccccCCCcceeCCc--cCccccCc
Q psy8696 167 CKFCNRQFTKSYNLLIHERTHTDERPYSCDI--CGKAFRRQ 205 (212)
Q Consensus 167 C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~--Cgk~F~~~ 205 (212)
|+.||.....+.....+.. ..+.-|+|.. ||..|...
T Consensus 2 CP~Cg~~a~ir~S~~~s~~--~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPL--TRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred cCCCCCeeEEEEchhhCcc--eEEEEEEECCCcCCCEEEEE
Confidence 6677755443333322211 1234566754 77777643
No 177
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=21.63 E-value=18 Score=21.92 Aligned_cols=35 Identities=17% Similarity=0.508 Sum_probs=18.9
Q ss_pred cccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 167 CKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 167 C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
|++||+.........+. .....-|-|..|.+.|..
T Consensus 1 Cd~CG~~I~~eP~~~k~---~~~~y~fCC~tC~~~fk~ 35 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKI---GNKVYYFCCPTCLSQFKK 35 (37)
T ss_pred CCccCCcccCCEEEEEE---CCeEEEEECHHHHHHHHh
Confidence 67788766554433221 222223557778777654
No 178
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.61 E-value=49 Score=25.19 Aligned_cols=32 Identities=19% Similarity=0.420 Sum_probs=17.5
Q ss_pred CccccccccccccccccccccccccCCCcceeCCccCc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGK 200 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk 200 (212)
-.+.| .|+..|.....-..|. .-.+.|+.||.
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~-----~~~~~CP~Cgs 100 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHY-----AAVIECPVCGN 100 (124)
T ss_pred eeEEe-eCcCcccccccchhcc-----ccCCcCcCCCC
Confidence 34789 8998776542111110 00257999984
No 179
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.44 E-value=64 Score=20.64 Aligned_cols=27 Identities=22% Similarity=0.496 Sum_probs=16.7
Q ss_pred ccccccccccccccccccccccCCCcceeCCccCcccc
Q psy8696 166 ICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFR 203 (212)
Q Consensus 166 ~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~ 203 (212)
.|+.|+.. .|..| ...+.|..|+..+-
T Consensus 22 fCP~Cg~~-----~m~~~------~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSG-----FMAEH------LDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcc-----hhecc------CCcEECCCcCCEEe
Confidence 58888753 22222 25688999987653
No 180
>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=21.42 E-value=44 Score=20.46 Aligned_cols=12 Identities=33% Similarity=1.035 Sum_probs=7.9
Q ss_pred cceeCCccCccc
Q psy8696 191 RPYSCDICGKAF 202 (212)
Q Consensus 191 kpf~C~~Cgk~F 202 (212)
++..|..|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 456777777665
No 181
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=21.29 E-value=54 Score=27.31 Aligned_cols=37 Identities=16% Similarity=0.383 Sum_probs=19.5
Q ss_pred cccccccccccccccccccccccCCCc---ceeCCccCcccc
Q psy8696 165 FICKFCNRQFTKSYNLLIHERTHTDER---PYSCDICGKAFR 203 (212)
Q Consensus 165 ~~C~~C~k~F~~~~~L~~H~r~Htgek---pf~C~~Cgk~F~ 203 (212)
-.|+.|+..+.. ....+.--|.|+. -+.|+.||..++
T Consensus 15 ~~CPvCg~~l~~--~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 15 IDCPVCGGTLKA--HMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred ecCCcccceeeE--EEeeecCCccceEEEEEEEccccCCccc
Confidence 568888873322 1111222244543 356888887665
No 182
>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=21.21 E-value=56 Score=28.89 Aligned_cols=39 Identities=23% Similarity=0.622 Sum_probs=22.0
Q ss_pred Ccccccccccccccccccccccccc-CC-CcceeCCccCcccc
Q psy8696 163 KQFICKFCNRQFTKSYNLLIHERTH-TD-ERPYSCDICGKAFR 203 (212)
Q Consensus 163 k~~~C~~C~k~F~~~~~L~~H~r~H-tg-ekpf~C~~Cgk~F~ 203 (212)
..|.|..|+..=.....+ ..|.- .+ ..-|.|..|+..|.
T Consensus 257 ~~~~C~~C~~~~~~~~q~--QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQL--QTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEe--cccCCCCCCeEEEEcCCCCCeee
Confidence 348999998543333222 22221 11 12478999998765
No 183
>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=20.80 E-value=71 Score=19.04 Aligned_cols=13 Identities=23% Similarity=0.756 Sum_probs=8.8
Q ss_pred cceeCCccCcccc
Q psy8696 191 RPYSCDICGKAFR 203 (212)
Q Consensus 191 kpf~C~~Cgk~F~ 203 (212)
.-+.|+.||..+-
T Consensus 31 p~~~C~~CGE~~~ 43 (46)
T TIGR03831 31 PALVCPQCGEEYL 43 (46)
T ss_pred CccccccCCCEee
Confidence 3467888887654
No 184
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.60 E-value=63 Score=31.79 Aligned_cols=11 Identities=27% Similarity=0.866 Sum_probs=7.4
Q ss_pred cceeCCccCcc
Q psy8696 191 RPYSCDICGKA 201 (212)
Q Consensus 191 kpf~C~~Cgk~ 201 (212)
.|+.|+.|+..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 46777777653
No 185
>KOG2071|consensus
Probab=20.47 E-value=40 Score=32.50 Aligned_cols=28 Identities=25% Similarity=0.341 Sum_probs=22.2
Q ss_pred CCCccccccccccccccccccccccccC
Q psy8696 161 PKKQFICKFCNRQFTKSYNLLIHERTHT 188 (212)
Q Consensus 161 ~~k~~~C~~C~k~F~~~~~L~~H~r~Ht 188 (212)
...+.+|..||.+|.+......|+.+|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3566899999999999888777776653
No 186
>PF15269 zf-C2H2_7: Zinc-finger
Probab=20.40 E-value=44 Score=21.21 Aligned_cols=23 Identities=17% Similarity=0.375 Sum_probs=17.0
Q ss_pred ccccccccccccccccccccccc
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERT 186 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~ 186 (212)
.|+|-+|..+...+++|..|++.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 36788887777777888888753
No 187
>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=20.38 E-value=57 Score=23.64 Aligned_cols=41 Identities=22% Similarity=0.510 Sum_probs=22.5
Q ss_pred ccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 164 QFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 164 ~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
...|+.||..-.....++.....-.-..-|.|..|+..++.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 36799998654433333221111111235899999987653
No 188
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.36 E-value=80 Score=23.29 Aligned_cols=36 Identities=25% Similarity=0.446 Sum_probs=19.4
Q ss_pred CCccccccccccccccccccccccccCCCcceeCCccCccccC
Q psy8696 162 KKQFICKFCNRQFTKSYNLLIHERTHTDERPYSCDICGKAFRR 204 (212)
Q Consensus 162 ~k~~~C~~C~k~F~~~~~L~~H~r~Htgekpf~C~~Cgk~F~~ 204 (212)
...|.|+.|+. .... ..+ ..+.--..|..||..|.+
T Consensus 19 pt~f~CP~Cge-~~v~--v~~----~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGK-VSIS--VKI----KKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCC-eEee--eec----CCCcceEECCCCCCccCE
Confidence 35688999983 1111 111 113333678888876654
No 189
>COG1773 Rubredoxin [Energy production and conversion]
Probab=20.05 E-value=45 Score=21.98 Aligned_cols=11 Identities=27% Similarity=1.189 Sum_probs=6.6
Q ss_pred ceeCCccCccc
Q psy8696 192 PYSCDICGKAF 202 (212)
Q Consensus 192 pf~C~~Cgk~F 202 (212)
.|+|.+||..|
T Consensus 3 ~~~C~~CG~vY 13 (55)
T COG1773 3 RWRCSVCGYVY 13 (55)
T ss_pred ceEecCCceEe
Confidence 46666666554
Done!