Query psy8937
Match_columns 147
No_of_seqs 122 out of 1214
Neff 11.3
Searched_HMMs 46136
Date Fri Aug 16 23:14:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8937.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8937hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 1.1E-29 2.3E-34 161.3 5.5 106 17-140 159-264 (279)
2 KOG2462|consensus 99.9 1.5E-28 3.2E-33 156.1 5.2 113 16-146 127-242 (279)
3 KOG1074|consensus 99.9 8.4E-23 1.8E-27 146.0 1.9 54 91-144 605-658 (958)
4 KOG3576|consensus 99.8 1.2E-21 2.6E-26 119.8 2.9 115 16-146 114-239 (267)
5 KOG1074|consensus 99.8 8E-21 1.7E-25 136.1 5.0 56 92-147 880-935 (958)
6 KOG3623|consensus 99.8 3.7E-20 8E-25 131.3 3.3 122 17-141 208-331 (1007)
7 KOG3608|consensus 99.7 4.5E-17 9.7E-22 107.4 5.6 132 10-143 198-345 (467)
8 KOG3576|consensus 99.7 1.3E-17 2.9E-22 102.2 1.1 84 46-145 116-199 (267)
9 KOG3608|consensus 99.6 8E-16 1.7E-20 101.6 7.2 111 18-145 262-378 (467)
10 KOG3623|consensus 99.6 3.4E-16 7.3E-21 111.6 2.9 81 16-112 891-971 (1007)
11 PHA00733 hypothetical protein 99.5 1.1E-13 2.4E-18 81.3 4.7 88 45-145 38-125 (128)
12 PLN03086 PRLI-interacting fact 99.4 3.1E-13 6.8E-18 95.9 7.1 106 17-145 451-566 (567)
13 PHA02768 hypothetical protein; 99.2 3.8E-12 8.2E-17 62.6 1.5 43 92-136 6-48 (55)
14 PHA00733 hypothetical protein 99.2 1.6E-11 3.5E-16 72.2 4.1 83 16-116 37-124 (128)
15 PHA02768 hypothetical protein; 99.2 1.1E-11 2.4E-16 61.0 1.6 44 18-63 4-47 (55)
16 KOG3993|consensus 99.2 1E-11 2.3E-16 84.1 1.3 99 17-115 265-380 (500)
17 PLN03086 PRLI-interacting fact 99.0 2.1E-10 4.5E-15 81.9 4.2 107 17-147 405-541 (567)
18 PF13465 zf-H2C2_2: Zinc-finge 99.0 2.3E-10 5E-15 48.4 2.1 26 106-131 1-26 (26)
19 PHA00616 hypothetical protein 99.0 2.1E-10 4.5E-15 53.9 1.9 27 120-146 2-28 (44)
20 PF05605 zf-Di19: Drought indu 98.7 2.9E-08 6.4E-13 49.7 4.3 50 92-144 3-54 (54)
21 PHA00732 hypothetical protein 98.7 9E-09 1.9E-13 55.4 2.0 47 91-142 1-47 (79)
22 PHA00616 hypothetical protein 98.7 1.4E-08 3E-13 47.7 1.9 34 19-52 1-34 (44)
23 PF13465 zf-H2C2_2: Zinc-finge 98.6 1.5E-08 3.2E-13 42.8 1.3 26 34-59 1-26 (26)
24 PF05605 zf-Di19: Drought indu 98.6 1.5E-07 3.2E-12 47.1 4.8 51 18-71 1-53 (54)
25 PF00096 zf-C2H2: Zinc finger, 98.6 3.7E-08 8.1E-13 40.4 1.7 23 120-142 1-23 (23)
26 PHA00732 hypothetical protein 98.6 3.7E-08 7.9E-13 53.0 1.9 46 19-69 1-46 (79)
27 KOG3993|consensus 98.5 1.8E-08 3.9E-13 68.8 0.4 82 47-144 267-381 (500)
28 PF13894 zf-C2H2_4: C2H2-type 98.5 9.8E-08 2.1E-12 39.4 2.0 24 120-143 1-24 (24)
29 PF13912 zf-C2H2_6: C2H2-type 98.4 1.6E-07 3.5E-12 40.0 1.1 26 119-144 1-26 (27)
30 PF12756 zf-C2H2_2: C2H2 type 98.3 2.9E-07 6.3E-12 52.0 2.2 23 119-141 50-72 (100)
31 PF09237 GAGA: GAGA factor; I 98.3 8E-07 1.7E-11 42.7 2.5 32 116-147 21-52 (54)
32 PF00096 zf-C2H2: Zinc finger, 98.3 6.6E-07 1.4E-11 36.6 1.8 22 20-41 1-22 (23)
33 PF13894 zf-C2H2_4: C2H2-type 98.1 2.3E-06 5E-11 35.1 1.9 24 20-43 1-24 (24)
34 PF13909 zf-H2C2_5: C2H2-type 98.1 3.5E-06 7.6E-11 34.7 2.0 24 120-144 1-24 (24)
35 smart00355 ZnF_C2H2 zinc finge 98.0 8.5E-06 1.8E-10 33.9 2.2 24 120-143 1-24 (26)
36 PF13912 zf-C2H2_6: C2H2-type 97.9 3.4E-06 7.3E-11 35.8 0.8 24 19-42 1-24 (27)
37 COG5189 SFP1 Putative transcri 97.9 2.9E-06 6.3E-11 56.4 0.5 52 89-140 347-419 (423)
38 PF12756 zf-C2H2_2: C2H2 type 97.9 7.5E-06 1.6E-10 46.2 2.1 53 21-73 1-76 (100)
39 COG5189 SFP1 Putative transcri 97.9 7.9E-06 1.7E-10 54.4 1.9 68 44-112 346-419 (423)
40 PF12874 zf-met: Zinc-finger o 97.7 1.7E-05 3.7E-10 32.9 1.3 23 120-142 1-23 (25)
41 PF09237 GAGA: GAGA factor; I 97.7 4.6E-05 1E-09 36.7 2.3 31 16-46 21-51 (54)
42 smart00355 ZnF_C2H2 zinc finge 97.4 0.0002 4.3E-09 29.6 2.4 21 20-40 1-21 (26)
43 PF12171 zf-C2H2_jaz: Zinc-fin 97.4 7.7E-05 1.7E-09 31.6 0.8 23 120-142 2-24 (27)
44 PF12874 zf-met: Zinc-finger o 97.3 9.6E-05 2.1E-09 30.6 0.9 21 20-40 1-21 (25)
45 PRK04860 hypothetical protein; 97.2 0.00024 5.2E-09 43.6 1.7 39 90-132 118-156 (160)
46 KOG2785|consensus 97.1 0.0013 2.8E-08 45.2 5.0 51 91-141 166-242 (390)
47 KOG1146|consensus 97.0 0.00051 1.1E-08 54.0 2.2 120 22-141 439-611 (1406)
48 PF12171 zf-C2H2_jaz: Zinc-fin 96.9 0.00019 4.1E-09 30.3 -0.3 21 20-40 2-22 (27)
49 PRK04860 hypothetical protein; 96.9 0.00057 1.2E-08 42.0 1.6 40 18-61 118-157 (160)
50 PF13909 zf-H2C2_5: C2H2-type 96.9 0.0008 1.7E-08 27.4 1.6 23 20-43 1-23 (24)
51 KOG2231|consensus 96.7 0.0019 4.1E-08 47.9 3.3 108 19-144 99-237 (669)
52 PF13913 zf-C2HC_2: zinc-finge 96.5 0.0028 6.1E-08 26.2 2.0 20 120-140 3-22 (25)
53 KOG1146|consensus 96.4 0.00062 1.3E-08 53.5 -0.5 121 16-136 462-635 (1406)
54 smart00451 ZnF_U1 U1-like zinc 96.4 0.0025 5.4E-08 28.5 1.7 23 119-141 3-25 (35)
55 KOG4173|consensus 96.4 0.0047 1E-07 39.1 3.1 79 47-144 79-171 (253)
56 COG4049 Uncharacterized protei 96.3 0.0023 4.9E-08 31.5 1.2 24 120-143 18-41 (65)
57 TIGR00622 ssl1 transcription f 96.3 0.0093 2E-07 34.2 3.7 101 20-142 2-104 (112)
58 PF12013 DUF3505: Protein of u 96.1 0.012 2.6E-07 33.8 3.8 25 120-144 81-109 (109)
59 COG5048 FOG: Zn-finger [Genera 95.9 0.0012 2.6E-08 46.7 -1.3 128 18-145 288-444 (467)
60 smart00451 ZnF_U1 U1-like zinc 95.8 0.0082 1.8E-07 26.8 1.8 22 19-40 3-24 (35)
61 KOG2482|consensus 95.6 0.068 1.5E-06 36.7 6.1 49 93-141 281-356 (423)
62 COG5236 Uncharacterized conser 94.5 0.053 1.1E-06 37.3 3.4 83 18-115 150-244 (493)
63 PF09538 FYDLN_acid: Protein o 94.5 0.025 5.3E-07 32.5 1.5 30 92-132 10-39 (108)
64 cd00350 rubredoxin_like Rubred 94.2 0.024 5.1E-07 25.1 0.8 24 92-127 2-25 (33)
65 PF02892 zf-BED: BED zinc fing 93.8 0.044 9.6E-07 25.9 1.5 27 117-143 14-44 (45)
66 COG4049 Uncharacterized protei 93.7 0.036 7.9E-07 27.3 1.0 30 87-116 13-42 (65)
67 COG5048 FOG: Zn-finger [Genera 93.6 0.011 2.3E-07 41.9 -1.4 56 90-145 288-349 (467)
68 TIGR00373 conserved hypothetic 93.5 0.039 8.5E-07 34.0 1.2 35 15-58 105-139 (158)
69 KOG2807|consensus 93.1 0.26 5.6E-06 33.8 4.5 37 17-67 274-310 (378)
70 KOG2893|consensus 93.1 0.037 7.9E-07 36.0 0.6 47 88-139 8-54 (341)
71 PF05443 ROS_MUCR: ROS/MUCR tr 92.9 0.044 9.5E-07 32.6 0.7 24 119-145 72-95 (132)
72 PF04959 ARS2: Arsenite-resist 92.9 0.044 9.5E-07 35.4 0.8 27 119-145 77-103 (214)
73 COG5236 Uncharacterized conser 92.5 0.09 2E-06 36.2 1.8 80 48-145 152-246 (493)
74 PRK06266 transcription initiat 92.3 0.075 1.6E-06 33.4 1.2 36 15-59 113-148 (178)
75 PF12013 DUF3505: Protein of u 92.2 0.3 6.6E-06 28.0 3.6 54 17-71 9-108 (109)
76 PHA00626 hypothetical protein 92.0 0.046 9.9E-07 27.0 0.0 36 93-133 2-37 (59)
77 smart00734 ZnF_Rad18 Rad18-lik 91.4 0.21 4.5E-06 20.7 1.7 20 120-140 2-21 (26)
78 cd00729 rubredoxin_SM Rubredox 90.9 0.12 2.5E-06 23.0 0.7 25 19-55 2-26 (34)
79 PRK00464 nrdR transcriptional 90.7 0.023 4.9E-07 34.8 -2.2 44 20-63 1-44 (154)
80 COG2888 Predicted Zn-ribbon RN 90.6 0.2 4.4E-06 25.2 1.5 33 90-127 26-58 (61)
81 KOG4173|consensus 90.3 0.23 5E-06 31.7 1.9 52 90-144 78-131 (253)
82 KOG2186|consensus 90.2 0.13 2.7E-06 33.9 0.8 49 48-115 4-52 (276)
83 smart00614 ZnF_BED BED zinc fi 90.2 0.24 5.2E-06 24.1 1.6 22 120-141 19-45 (50)
84 TIGR02605 CxxC_CxxC_SSSS putat 90.2 0.051 1.1E-06 26.6 -0.8 30 19-55 5-34 (52)
85 COG1592 Rubrerythrin [Energy p 90.0 0.2 4.3E-06 31.1 1.4 24 18-54 133-156 (166)
86 PF13717 zinc_ribbon_4: zinc-r 89.8 0.15 3.3E-06 23.0 0.6 32 93-129 4-35 (36)
87 TIGR02098 MJ0042_CXXC MJ0042 f 89.7 0.13 2.8E-06 23.4 0.4 34 92-130 3-36 (38)
88 PF13719 zinc_ribbon_5: zinc-r 89.6 0.17 3.7E-06 22.9 0.8 33 93-130 4-36 (37)
89 TIGR00373 conserved hypothetic 89.6 0.16 3.4E-06 31.4 0.9 35 88-131 106-140 (158)
90 smart00834 CxxC_CXXC_SSSS Puta 89.6 0.054 1.2E-06 25.0 -1.0 31 19-56 5-35 (41)
91 smart00659 RPOLCX RNA polymera 89.5 0.16 3.6E-06 24.0 0.7 29 19-58 2-30 (44)
92 PF09986 DUF2225: Uncharacteri 89.4 0.051 1.1E-06 35.3 -1.5 13 92-104 49-61 (214)
93 PF06524 NOA36: NOA36 protein; 89.0 0.13 2.9E-06 34.0 0.2 84 43-142 138-232 (314)
94 smart00531 TFIIE Transcription 88.9 0.19 4.1E-06 30.6 0.8 40 15-58 95-134 (147)
95 COG4957 Predicted transcriptio 88.8 0.19 4.1E-06 29.8 0.7 23 120-145 77-99 (148)
96 PRK06266 transcription initiat 88.5 0.21 4.7E-06 31.4 0.9 35 88-131 114-148 (178)
97 KOG2482|consensus 88.1 1.5 3.3E-05 30.4 4.7 50 93-142 146-218 (423)
98 KOG2893|consensus 88.0 0.11 2.5E-06 33.8 -0.6 46 50-115 13-58 (341)
99 KOG4727|consensus 87.7 0.36 7.8E-06 29.9 1.4 34 7-40 63-96 (193)
100 KOG2186|consensus 87.6 0.3 6.5E-06 32.2 1.2 47 91-140 3-49 (276)
101 PRK00398 rpoP DNA-directed RNA 87.3 0.073 1.6E-06 25.4 -1.4 31 18-58 2-32 (46)
102 KOG4167|consensus 87.2 0.15 3.2E-06 38.6 -0.4 25 119-143 792-816 (907)
103 PF12907 zf-met2: Zinc-binding 86.9 0.61 1.3E-05 21.6 1.6 26 120-145 2-30 (40)
104 KOG2231|consensus 86.8 2 4.4E-05 32.7 5.1 84 33-140 163-260 (669)
105 TIGR02300 FYDLN_acid conserved 86.3 0.35 7.6E-06 28.5 0.8 30 92-132 10-39 (129)
106 KOG2785|consensus 85.8 0.98 2.1E-05 31.8 2.9 55 18-72 165-245 (390)
107 PRK14890 putative Zn-ribbon RN 85.1 0.57 1.2E-05 23.6 1.1 33 90-127 24-56 (59)
108 COG2879 Uncharacterized small 84.2 1.3 2.8E-05 22.6 2.1 19 129-147 22-40 (65)
109 PF09845 DUF2072: Zn-ribbon co 83.7 0.66 1.4E-05 27.5 1.2 30 91-130 1-31 (131)
110 PF05443 ROS_MUCR: ROS/MUCR tr 82.9 0.99 2.1E-05 27.0 1.7 27 16-45 69-95 (132)
111 KOG2593|consensus 82.7 0.67 1.4E-05 33.1 1.1 43 12-57 121-163 (436)
112 COG1996 RPC10 DNA-directed RNA 82.1 0.53 1.1E-05 22.8 0.3 31 17-57 4-34 (49)
113 COG5151 SSL1 RNA polymerase II 81.7 2.7 5.8E-05 28.9 3.5 91 46-142 321-411 (421)
114 PF07975 C1_4: TFIIH C1-like d 81.3 0.39 8.5E-06 23.5 -0.3 22 46-67 20-41 (51)
115 PF13451 zf-trcl: Probable zin 81.2 1.1 2.4E-05 21.8 1.2 39 17-55 2-41 (49)
116 PF10571 UPF0547: Uncharacteri 81.2 0.76 1.7E-05 19.1 0.6 10 121-130 16-25 (26)
117 KOG3408|consensus 81.1 1.4 2.9E-05 25.8 1.8 26 16-41 54-79 (129)
118 PF07754 DUF1610: Domain of un 80.2 0.71 1.5E-05 18.8 0.3 8 119-126 16-23 (24)
119 PF03604 DNA_RNApol_7kD: DNA d 78.2 1.5 3.2E-05 19.2 1.1 27 20-57 1-27 (32)
120 COG5188 PRP9 Splicing factor 3 77.1 4.1 8.8E-05 28.6 3.4 25 17-41 236-260 (470)
121 COG3364 Zn-ribbon containing p 76.8 1.8 4E-05 24.4 1.4 26 91-126 2-27 (112)
122 COG1997 RPL43A Ribosomal prote 76.0 1.5 3.3E-05 24.0 1.0 33 90-132 34-66 (89)
123 PF13240 zinc_ribbon_2: zinc-r 75.3 1.1 2.3E-05 18.0 0.2 6 122-127 16-21 (23)
124 PF08274 PhnA_Zn_Ribbon: PhnA 74.4 0.91 2E-05 19.6 -0.1 12 43-54 15-26 (30)
125 PF14353 CpXC: CpXC protein 73.8 3.5 7.6E-05 24.3 2.2 41 93-134 3-53 (128)
126 KOG3408|consensus 72.9 2.5 5.4E-05 24.7 1.4 22 91-112 57-78 (129)
127 KOG4167|consensus 72.7 1.9 4.1E-05 33.2 1.0 28 17-44 790-817 (907)
128 COG1675 TFA1 Transcription ini 72.6 2.3 5E-05 26.8 1.3 35 15-58 109-143 (176)
129 PRK04023 DNA polymerase II lar 71.3 4.3 9.3E-05 32.7 2.7 11 18-28 625-635 (1121)
130 KOG1842|consensus 71.2 4.3 9.3E-05 29.4 2.4 29 17-45 13-41 (505)
131 PRK09678 DNA-binding transcrip 71.0 0.87 1.9E-05 24.1 -0.7 39 92-132 2-42 (72)
132 PF15269 zf-C2H2_7: Zinc-finge 70.9 3.2 6.8E-05 19.6 1.2 20 92-111 21-40 (54)
133 KOG1280|consensus 70.8 4 8.6E-05 28.5 2.2 47 80-126 68-116 (381)
134 COG0068 HypF Hydrogenase matur 70.3 0.51 1.1E-05 35.9 -2.2 46 22-67 126-171 (750)
135 PF13878 zf-C2H2_3: zinc-finge 70.3 5.7 0.00012 18.4 2.0 10 93-102 15-24 (41)
136 PF04959 ARS2: Arsenite-resist 68.9 2 4.4E-05 28.0 0.5 30 88-117 74-103 (214)
137 PF02176 zf-TRAF: TRAF-type zi 68.3 0.95 2.1E-05 22.7 -0.9 40 92-132 10-55 (60)
138 TIGR00244 transcriptional regu 68.2 0.54 1.2E-05 28.5 -2.0 43 21-63 2-44 (147)
139 COG1327 Predicted transcriptio 68.2 0.74 1.6E-05 28.0 -1.5 42 21-62 2-43 (156)
140 KOG2593|consensus 67.2 3 6.5E-05 30.0 1.1 39 88-129 125-163 (436)
141 PF01363 FYVE: FYVE zinc finge 67.1 2.5 5.4E-05 21.9 0.5 33 15-59 5-37 (69)
142 PF09723 Zn-ribbon_8: Zinc rib 65.2 2.3 5E-05 19.8 0.2 14 119-132 5-18 (42)
143 KOG2807|consensus 64.8 8 0.00017 26.9 2.6 54 17-71 288-369 (378)
144 COG4530 Uncharacterized protei 63.9 3 6.5E-05 23.9 0.5 29 93-132 11-39 (129)
145 KOG2636|consensus 63.0 6.2 0.00013 28.7 1.9 29 112-140 394-423 (497)
146 PF04780 DUF629: Protein of un 62.8 6.4 0.00014 28.9 2.0 22 92-113 58-79 (466)
147 TIGR00100 hypA hydrogenase nic 62.8 2.7 6E-05 24.4 0.2 28 17-56 68-95 (115)
148 PRK03824 hypA hydrogenase nick 62.3 1.8 3.8E-05 26.0 -0.7 39 90-128 69-116 (135)
149 PRK12380 hydrogenase nickel in 60.4 3.9 8.5E-05 23.7 0.6 28 17-56 68-95 (113)
150 PF04780 DUF629: Protein of un 60.3 7.3 0.00016 28.6 2.0 27 19-45 57-83 (466)
151 PF13824 zf-Mss51: Zinc-finger 59.3 7.3 0.00016 19.4 1.3 13 118-130 13-25 (55)
152 KOG0978|consensus 59.0 5 0.00011 31.0 1.0 47 92-138 644-697 (698)
153 PTZ00255 60S ribosomal protein 58.9 3.8 8.3E-05 22.7 0.3 33 90-132 35-67 (90)
154 smart00064 FYVE Protein presen 58.8 9 0.00019 19.7 1.7 30 18-59 9-38 (68)
155 PF13453 zf-TFIIB: Transcripti 58.3 2.7 5.8E-05 19.4 -0.3 20 46-65 18-37 (41)
156 COG1655 Uncharacterized protei 58.1 1.9 4E-05 28.3 -1.1 41 16-56 16-71 (267)
157 PF07282 OrfB_Zn_ribbon: Putat 57.8 6 0.00013 20.4 1.0 30 93-132 30-59 (69)
158 PF14369 zf-RING_3: zinc-finge 57.6 3.6 7.8E-05 18.4 0.1 10 49-58 23-32 (35)
159 COG5112 UFD2 U1-like Zn-finger 57.2 6.2 0.00013 22.5 1.0 26 15-40 51-76 (126)
160 PF05290 Baculo_IE-1: Baculovi 56.8 15 0.00032 22.1 2.5 14 93-106 123-136 (140)
161 KOG4118|consensus 56.7 6.7 0.00014 20.2 0.9 26 120-145 39-64 (74)
162 PF14311 DUF4379: Domain of un 56.5 7.9 0.00017 19.1 1.2 15 20-34 29-43 (55)
163 TIGR00280 L37a ribosomal prote 56.1 3.6 7.9E-05 22.8 -0.0 33 90-132 34-66 (91)
164 PTZ00448 hypothetical protein; 55.8 9.4 0.0002 27.1 1.8 23 119-141 314-336 (373)
165 smart00661 RPOL9 RNA polymeras 55.5 5.9 0.00013 19.1 0.7 13 119-131 20-32 (52)
166 COG1773 Rubredoxin [Energy pro 55.0 4.8 0.0001 20.1 0.3 12 119-130 3-14 (55)
167 smart00154 ZnF_AN1 AN1-like Zi 54.9 5.2 0.00011 18.3 0.4 14 19-32 12-25 (39)
168 PF04423 Rad50_zn_hook: Rad50 54.6 4.7 0.0001 19.8 0.2 12 121-132 22-33 (54)
169 PF11931 DUF3449: Domain of un 54.6 4.1 8.9E-05 26.2 0.0 27 114-140 96-123 (196)
170 PF06220 zf-U1: U1 zinc finger 54.4 12 0.00026 17.0 1.5 12 119-130 3-14 (38)
171 KOG1280|consensus 54.0 17 0.00038 25.6 2.8 32 116-147 76-107 (381)
172 PRK00564 hypA hydrogenase nick 53.3 5.3 0.00012 23.3 0.3 29 17-56 69-97 (117)
173 PRK00432 30S ribosomal protein 53.0 5.5 0.00012 19.4 0.3 26 93-129 22-47 (50)
174 COG1571 Predicted DNA-binding 51.9 9.3 0.0002 27.7 1.4 30 21-61 352-381 (421)
175 COG2331 Uncharacterized protei 50.8 9.3 0.0002 20.4 0.9 33 18-57 11-43 (82)
176 COG4896 Uncharacterized protei 50.7 9 0.00019 19.5 0.8 41 20-60 3-44 (68)
177 PF09963 DUF2197: Uncharacteri 50.0 7.1 0.00015 19.6 0.4 41 20-61 3-45 (56)
178 PF07295 DUF1451: Protein of u 49.8 5.1 0.00011 24.5 -0.1 31 16-56 109-139 (146)
179 PF10058 DUF2296: Predicted in 49.6 9.4 0.0002 18.9 0.8 35 15-55 18-52 (54)
180 PRK05978 hypothetical protein; 49.6 4.6 9.9E-05 24.7 -0.3 17 48-64 34-50 (148)
181 COG3677 Transposase and inacti 49.5 8.4 0.00018 23.0 0.8 35 93-132 32-66 (129)
182 PF10276 zf-CHCC: Zinc-finger 49.4 6.1 0.00013 18.3 0.1 12 18-29 28-39 (40)
183 PF04328 DUF466: Protein of un 49.4 18 0.00039 18.8 1.9 15 133-147 26-40 (65)
184 cd00924 Cyt_c_Oxidase_Vb Cytoc 49.3 7.8 0.00017 21.9 0.6 15 117-131 77-91 (97)
185 PF10013 DUF2256: Uncharacteri 49.3 7.3 0.00016 18.2 0.4 13 121-133 10-22 (42)
186 PF01428 zf-AN1: AN1-like Zinc 49.3 5.1 0.00011 18.7 -0.1 15 118-132 12-26 (43)
187 PRK03976 rpl37ae 50S ribosomal 48.4 5.4 0.00012 22.2 -0.1 33 90-132 35-67 (90)
188 COG4391 Uncharacterized protei 48.2 3.6 7.7E-05 21.0 -0.8 52 3-58 8-59 (62)
189 COG3357 Predicted transcriptio 48.2 8.2 0.00018 21.4 0.5 14 118-131 57-70 (97)
190 PF15135 UPF0515: Uncharacteri 48.2 13 0.00028 24.9 1.5 22 83-104 147-168 (278)
191 PF07503 zf-HYPF: HypF finger; 48.0 1.9 4.1E-05 19.3 -1.6 10 93-102 23-32 (35)
192 cd00065 FYVE FYVE domain; Zinc 47.1 13 0.00028 18.2 1.1 28 20-59 3-30 (57)
193 PF08790 zf-LYAR: LYAR-type C2 46.9 2.8 6E-05 17.7 -1.1 18 120-138 1-18 (28)
194 KOG0717|consensus 46.6 12 0.00026 27.5 1.3 21 120-140 293-313 (508)
195 PF01155 HypA: Hydrogenase exp 46.2 4.7 0.0001 23.4 -0.6 28 17-56 68-95 (113)
196 PLN02294 cytochrome c oxidase 45.0 7.2 0.00016 24.4 0.0 13 46-58 140-152 (174)
197 KOG2071|consensus 44.7 17 0.00037 27.5 1.8 27 17-43 416-442 (579)
198 PF08792 A2L_zn_ribbon: A2L zi 44.6 9.9 0.00021 16.7 0.4 13 17-29 19-31 (33)
199 PF02591 DUF164: Putative zinc 44.4 14 0.0003 18.3 1.0 32 93-128 24-55 (56)
200 KOG0717|consensus 44.3 14 0.00031 27.1 1.3 24 18-41 291-314 (508)
201 PRK03681 hypA hydrogenase nick 44.2 6.4 0.00014 22.9 -0.3 29 17-56 68-96 (114)
202 COG3091 SprT Zn-dependent meta 43.4 7.9 0.00017 23.8 0.0 36 17-57 115-150 (156)
203 cd00730 rubredoxin Rubredoxin; 43.1 10 0.00023 18.5 0.4 11 120-130 2-12 (50)
204 COG4888 Uncharacterized Zn rib 42.3 2.2 4.8E-05 24.0 -2.2 39 88-130 19-57 (104)
205 KOG2907|consensus 42.2 7.3 0.00016 22.5 -0.2 38 92-131 75-114 (116)
206 PTZ00448 hypothetical protein; 41.4 23 0.0005 25.3 2.0 23 19-41 314-336 (373)
207 PRK12496 hypothetical protein; 40.7 13 0.00029 23.2 0.7 29 92-132 128-156 (164)
208 KOG3507|consensus 39.9 35 0.00077 17.3 2.0 37 16-63 17-53 (62)
209 COG1198 PriA Primosomal protei 37.7 5.9 0.00013 30.9 -1.3 38 19-56 444-484 (730)
210 PF06397 Desulfoferrod_N: Desu 37.5 12 0.00027 16.8 0.2 11 118-128 5-15 (36)
211 COG4306 Uncharacterized protei 37.3 6.4 0.00014 23.2 -1.0 14 46-59 67-80 (160)
212 TIGR00143 hypF [NiFe] hydrogen 37.3 2 4.4E-05 33.3 -3.8 9 93-101 142-150 (711)
213 PF08209 Sgf11: Sgf11 (transcr 37.3 17 0.00037 16.0 0.6 19 48-67 5-23 (33)
214 KOG2071|consensus 37.3 24 0.00051 26.8 1.6 28 116-143 415-442 (579)
215 PF00301 Rubredoxin: Rubredoxi 37.3 11 0.00024 18.1 -0.0 11 120-130 2-12 (47)
216 COG4338 Uncharacterized protei 36.2 13 0.00028 17.9 0.1 12 121-132 14-25 (54)
217 PRK11032 hypothetical protein; 35.6 11 0.00024 23.4 -0.2 31 16-56 121-151 (160)
218 PRK00762 hypA hydrogenase nick 35.6 18 0.00039 21.4 0.7 34 17-56 68-101 (124)
219 TIGR03831 YgiT_finger YgiT-typ 35.5 15 0.00033 16.9 0.3 15 17-31 30-44 (46)
220 TIGR03829 YokU_near_AblA uncha 35.4 24 0.00052 19.6 1.1 20 19-38 35-54 (89)
221 smart00731 SprT SprT homologue 35.4 7.9 0.00017 23.5 -0.9 34 18-58 111-144 (146)
222 PF13821 DUF4187: Domain of un 35.3 22 0.00047 17.7 0.8 20 18-37 26-45 (55)
223 PF10537 WAC_Acf1_DNA_bd: ATP- 35.2 34 0.00073 19.6 1.7 41 18-59 2-42 (102)
224 PF12230 PRP21_like_P: Pre-mRN 35.2 13 0.00027 24.5 0.0 26 117-143 166-191 (229)
225 TIGR00686 phnA alkylphosphonat 35.1 13 0.00028 21.4 0.0 28 94-132 5-32 (109)
226 TIGR01206 lysW lysine biosynth 35.1 17 0.00037 18.1 0.5 11 120-130 3-13 (54)
227 PTZ00409 Sir2 (Silent Informat 34.7 39 0.00084 23.1 2.2 42 14-56 132-173 (271)
228 KOG1842|consensus 34.3 28 0.00061 25.5 1.5 28 90-117 14-41 (505)
229 CHL00174 accD acetyl-CoA carbo 34.2 15 0.00032 25.4 0.2 33 91-132 38-70 (296)
230 PF10071 DUF2310: Zn-ribbon-co 33.5 26 0.00057 23.7 1.3 63 59-128 187-250 (258)
231 cd01413 SIR2_Af2 SIR2_Af2: Arc 32.8 42 0.00091 22.0 2.1 39 13-56 107-145 (222)
232 PHA02893 hypothetical protein; 32.7 34 0.00074 18.7 1.4 47 17-63 32-85 (88)
233 PRK14138 NAD-dependent deacety 32.7 46 0.00099 22.3 2.3 39 14-56 114-152 (244)
234 PLN02748 tRNA dimethylallyltra 32.5 34 0.00074 25.4 1.8 24 118-141 417-441 (468)
235 PF03966 Trm112p: Trm112p-like 32.2 16 0.00035 18.9 0.1 16 15-30 49-64 (68)
236 PRK10220 hypothetical protein; 32.1 18 0.00039 20.9 0.3 28 94-132 6-33 (111)
237 COG0846 SIR2 NAD-dependent pro 31.2 25 0.00054 23.7 0.9 39 14-56 117-155 (250)
238 KOG0320|consensus 30.8 36 0.00077 21.7 1.4 47 12-58 124-178 (187)
239 PLN03238 probable histone acet 30.8 52 0.0011 22.7 2.3 26 16-41 45-70 (290)
240 PF10263 SprT-like: SprT-like 30.6 12 0.00026 22.8 -0.6 33 18-58 122-154 (157)
241 PF02891 zf-MIZ: MIZ/SP-RING z 30.2 34 0.00073 16.5 1.1 10 118-127 40-49 (50)
242 PF11789 zf-Nse: Zinc-finger o 29.8 14 0.00031 18.5 -0.3 32 17-52 22-53 (57)
243 PF01215 COX5B: Cytochrome c o 29.7 15 0.00032 22.2 -0.3 16 117-132 110-125 (136)
244 PTZ00303 phosphatidylinositol 29.6 20 0.00043 28.5 0.2 13 20-32 461-473 (1374)
245 cd01410 SIRT7 SIRT7: Eukaryoti 29.5 68 0.0015 20.8 2.6 40 14-56 90-129 (206)
246 TIGR00515 accD acetyl-CoA carb 29.3 29 0.00063 23.9 1.0 34 90-132 25-58 (285)
247 KOG4602|consensus 29.3 28 0.00061 23.5 0.9 41 90-130 232-279 (318)
248 KOG2857|consensus 29.2 26 0.00057 21.3 0.6 22 47-68 17-38 (157)
249 PRK05654 acetyl-CoA carboxylas 29.1 19 0.00042 24.8 0.1 33 91-132 27-59 (292)
250 PTZ00043 cytochrome c oxidase 29.0 27 0.00058 23.1 0.7 16 116-131 178-193 (268)
251 PRK01343 zinc-binding protein; 28.9 33 0.00072 17.3 0.9 9 121-129 11-19 (57)
252 PRK14714 DNA polymerase II lar 28.9 34 0.00073 28.8 1.3 28 92-130 693-720 (1337)
253 PF08271 TF_Zn_Ribbon: TFIIB z 28.8 24 0.00052 16.3 0.4 8 120-127 1-8 (43)
254 PLN03238 probable histone acet 28.5 47 0.001 23.0 1.8 24 117-140 46-69 (290)
255 PF05191 ADK_lid: Adenylate ki 28.5 18 0.00039 16.2 -0.1 9 21-29 3-11 (36)
256 PF12773 DZR: Double zinc ribb 28.5 35 0.00076 16.1 1.0 30 16-56 9-38 (50)
257 PF14787 zf-CCHC_5: GAG-polypr 28.5 25 0.00054 15.8 0.4 12 121-132 4-15 (36)
258 TIGR01384 TFS_arch transcripti 28.4 23 0.00051 20.0 0.3 26 94-131 3-28 (104)
259 PRK00481 NAD-dependent deacety 28.3 42 0.00091 22.3 1.6 36 13-56 116-151 (242)
260 PF02748 PyrI_C: Aspartate car 28.1 21 0.00045 17.6 0.1 17 16-32 32-48 (52)
261 COG5432 RAD18 RING-finger-cont 27.6 35 0.00077 23.5 1.1 29 96-130 42-70 (391)
262 cd01407 SIR2-fam SIR2 family o 27.5 63 0.0014 21.1 2.3 40 13-56 103-142 (218)
263 PF01286 XPA_N: XPA protein N- 27.4 26 0.00055 15.6 0.3 13 121-133 5-17 (34)
264 PF11672 DUF3268: Protein of u 27.1 15 0.00033 21.0 -0.5 11 18-28 1-11 (102)
265 KOG1088|consensus 26.9 23 0.0005 20.7 0.1 16 16-31 95-110 (124)
266 PF14255 Cys_rich_CPXG: Cystei 26.8 27 0.00058 17.2 0.3 9 49-57 2-10 (52)
267 PRK08222 hydrogenase 4 subunit 26.6 48 0.001 21.0 1.6 19 118-136 113-131 (181)
268 PRK05452 anaerobic nitric oxid 26.5 15 0.00032 27.3 -0.8 42 85-127 419-466 (479)
269 COG1326 Uncharacterized archae 26.0 50 0.0011 21.4 1.5 34 92-129 7-40 (201)
270 PF04438 zf-HIT: HIT zinc fing 25.9 27 0.00059 14.9 0.3 13 119-131 13-25 (30)
271 PRK04351 hypothetical protein; 25.8 24 0.00052 21.7 0.1 33 91-131 112-144 (149)
272 COG1579 Zn-ribbon protein, pos 25.5 52 0.0011 22.1 1.6 35 92-130 198-232 (239)
273 PHA02998 RNA polymerase subuni 24.7 5.7 0.00012 25.0 -2.7 38 92-132 144-184 (195)
274 PF09855 DUF2082: Nucleic-acid 24.5 34 0.00075 17.7 0.5 7 120-126 1-7 (64)
275 KOG1940|consensus 24.3 74 0.0016 21.9 2.1 42 92-134 197-249 (276)
276 cd00974 DSRD Desulforedoxin (D 24.2 32 0.00069 14.9 0.3 12 118-129 3-14 (34)
277 PF03884 DUF329: Domain of unk 24.1 28 0.00061 17.5 0.1 12 120-131 3-14 (57)
278 COG0675 Transposase and inacti 24.1 35 0.00077 23.5 0.7 25 93-132 311-335 (364)
279 PF01780 Ribosomal_L37ae: Ribo 23.9 32 0.00069 19.2 0.3 9 119-127 35-43 (90)
280 KOG4477|consensus 23.7 52 0.0011 21.0 1.2 28 85-126 18-45 (228)
281 KOG0801|consensus 23.4 16 0.00035 22.7 -0.9 21 47-68 138-158 (205)
282 TIGR00627 tfb4 transcription f 23.4 53 0.0011 22.6 1.4 10 120-129 270-279 (279)
283 PF07649 C1_3: C1-like domain; 23.2 31 0.00067 14.4 0.2 11 118-128 14-24 (30)
284 KOG0782|consensus 23.0 23 0.00049 27.0 -0.4 28 106-133 240-267 (1004)
285 TIGR03830 CxxCG_CxxCG_HTH puta 23.0 65 0.0014 18.7 1.6 25 16-40 28-52 (127)
286 PLN03239 histone acetyltransfe 22.9 58 0.0013 23.2 1.5 25 117-141 104-128 (351)
287 PF14447 Prok-RING_4: Prokaryo 22.8 35 0.00076 17.1 0.3 17 16-32 36-52 (55)
288 TIGR00319 desulf_FeS4 desulfof 22.7 35 0.00075 14.8 0.3 12 118-129 6-17 (34)
289 PLN00104 MYST -like histone ac 22.3 57 0.0012 24.2 1.4 25 116-140 195-219 (450)
290 smart00249 PHD PHD zinc finger 22.2 56 0.0012 14.5 1.0 12 90-101 13-24 (47)
291 KOG3352|consensus 22.0 41 0.0009 20.7 0.6 15 117-131 131-145 (153)
292 PF07535 zf-DBF: DBF zinc fing 21.8 67 0.0015 15.6 1.2 19 119-140 5-23 (49)
293 PF03107 C1_2: C1 domain; Int 21.4 56 0.0012 13.7 0.8 9 121-129 2-10 (30)
294 smart00109 C1 Protein kinase C 21.3 67 0.0015 14.6 1.2 26 91-128 11-36 (49)
295 PF14446 Prok-RING_1: Prokaryo 21.3 21 0.00046 17.7 -0.6 32 18-61 4-35 (54)
296 PTZ00064 histone acetyltransfe 21.2 67 0.0015 24.2 1.6 24 117-140 278-301 (552)
297 PRK03564 formate dehydrogenase 21.2 35 0.00075 23.8 0.2 44 10-56 178-221 (309)
298 PF13696 zf-CCHC_2: Zinc knuck 21.0 35 0.00075 15.0 0.1 11 18-28 7-17 (32)
299 PF05741 zf-nanos: Nanos RNA b 20.9 37 0.00081 17.0 0.2 12 17-28 31-42 (55)
300 PRK11823 DNA repair protein Ra 20.9 55 0.0012 24.2 1.1 13 90-102 6-18 (446)
301 smart00440 ZnF_C2C2 C2C2 Zinc 20.9 40 0.00086 15.4 0.3 10 120-129 29-38 (40)
302 PLN00104 MYST -like histone ac 20.9 73 0.0016 23.6 1.7 26 16-41 195-220 (450)
303 smart00586 ZnF_DBF Zinc finger 20.8 66 0.0014 15.7 1.1 20 118-140 4-23 (49)
304 PF12760 Zn_Tnp_IS1595: Transp 20.8 1.1E+02 0.0025 14.2 2.9 20 37-56 8-27 (46)
305 KOG2747|consensus 20.7 52 0.0011 23.8 1.0 25 117-141 156-180 (396)
306 smart00132 LIM Zinc-binding do 20.4 49 0.0011 14.1 0.6 9 120-128 28-36 (39)
307 PTZ00064 histone acetyltransfe 20.4 85 0.0018 23.7 1.9 26 16-41 277-302 (552)
308 COG1379 PHP family phosphoeste 20.2 31 0.00068 24.3 -0.2 28 22-58 249-276 (403)
309 PF14690 zf-ISL3: zinc-finger 20.1 53 0.0011 15.2 0.7 9 119-127 2-10 (47)
310 PF02146 SIR2: Sir2 family; I 20.0 34 0.00073 21.5 -0.1 39 14-56 100-138 (178)
No 1
>KOG2462|consensus
Probab=99.96 E-value=1.1e-29 Score=161.27 Aligned_cols=106 Identities=35% Similarity=0.557 Sum_probs=79.8
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCccccc
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKI 96 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~ 96 (147)
.+.+.|.+||+.|...-+|..|+++|. .++.|.+||+.|...+.|+-|+++|+ |||||.|+.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHT----------------GEKPF~C~h 220 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHT----------------GEKPFSCPH 220 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccccccc----------------CCCCccCCc
Confidence 566777777777777777777776444 56677777777777777777776666 567777888
Q ss_pred ccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHH
Q psy8937 97 CGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 97 c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
|+++|.++++|+.|+++|.+.|.|+|..|+|.|++++.|.+|..
T Consensus 221 C~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 221 CGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred ccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 88888888888888888888888888888888888888887764
No 2
>KOG2462|consensus
Probab=99.95 E-value=1.5e-28 Score=156.11 Aligned_cols=113 Identities=32% Similarity=0.500 Sum_probs=102.9
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCC---CCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCc
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLP---GILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDAR 92 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~---~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (147)
....|+|+.||+.+.+.++|.+|...|..- +.+.|..|++.|.+...|++|+++|. -++
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~------------------l~c 188 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT------------------LPC 188 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC------------------CCc
Confidence 356799999999999999999999866543 67899999999999999999997766 235
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHhhhccC
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVISFHENA 146 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 146 (147)
+|.+||+.|...+-|+-|+++|+|||||.|+.|++.|..+++|+.||++|-+.|
T Consensus 189 ~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 189 ECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred ccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 699999999999999999999999999999999999999999999999998765
No 3
>KOG1074|consensus
Probab=99.86 E-value=8.4e-23 Score=146.04 Aligned_cols=54 Identities=26% Similarity=0.418 Sum_probs=50.7
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHhhhc
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
+..|.+|.+.+.=.++|+.|+++|+||+||+|.+||+.|..+.+|+.||.+|-.
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhccccccc
Confidence 457999999999999999999999999999999999999999999999998743
No 4
>KOG3576|consensus
Probab=99.84 E-value=1.2e-21 Score=119.80 Aligned_cols=115 Identities=23% Similarity=0.480 Sum_probs=103.7
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccc
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCK 95 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ 95 (147)
+...|.|.+|++.|.....|.+|+.-|...+.+.|..||+.|...-+|++|+++|+ +.+||+|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rtht----------------gvrpykc~ 177 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHT----------------GVRPYKCS 177 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcccc----------------Cccccchh
Confidence 46889999999999999999999996666699999999999999999999998888 55778899
Q ss_pred cccccCCChHHHHHHHHHHhC-----------CCcccCCCchhccCChHHHHhHHHhhhccC
Q psy8937 96 ICGKHYSNSSNLKQHIRLIHL-----------PGILFCPLCQKCFKNKLYLRRHVISFHENA 146 (147)
Q Consensus 96 ~c~~~~~~~~~l~~H~~~~~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 146 (147)
.|+++|.+...|..|.+..++ +|.|.|+.||..-.....+..|+..||+.-
T Consensus 178 ~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 178 LCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred hhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 999999999999999987664 467999999999999999999999998753
No 5
>KOG1074|consensus
Probab=99.82 E-value=8e-21 Score=136.10 Aligned_cols=56 Identities=29% Similarity=0.613 Sum_probs=52.8
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHhhhccCC
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVISFHENAT 147 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (147)
..|..|++.|..+++|..|+++|.++|+|.|..|++.|..+..|..||.+|++..|
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 35999999999999999999999999999999999999999999999999988643
No 6
>KOG3623|consensus
Probab=99.79 E-value=3.7e-20 Score=131.27 Aligned_cols=122 Identities=25% Similarity=0.407 Sum_probs=104.7
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCC--CCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCccc
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLP--GILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYC 94 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~--~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C 94 (147)
.....|++|++.+.....|+.|+...|.. ..|.|..|..+|.+...|.+||..|.....- ....+.....+.|+|
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dq---a~sltqsa~lRKFKC 284 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQ---AISLTQSALLRKFKC 284 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcc---cccccchhhhccccc
Confidence 45678999999999999999999987776 5689999999999999999999876543222 123333446788999
Q ss_pred ccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHh
Q psy8937 95 KICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVIS 141 (147)
Q Consensus 95 ~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 141 (147)
..|+++|..+..|+.|+++|.|||||.|+.|+|.|+...++.-||..
T Consensus 285 tECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 285 TECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999999999999998888865
No 7
>KOG3608|consensus
Probab=99.69 E-value=4.5e-17 Score=107.43 Aligned_cols=132 Identities=18% Similarity=0.334 Sum_probs=68.0
Q ss_pred CCCccCccCcccccccccccCChHHHHHHHHHhcCC--CCcCCCCchhhhcChHHHHHHHhhhcCCC--Ccc--------
Q psy8937 10 GSKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLP--GILFCPLCQKCFKNKLYLRRHVGTYTHTP--SYR-------- 77 (147)
Q Consensus 10 ~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~--~~~~C~~C~~~f~~~~~l~~H~~~~~~~~--~~~-------- 77 (147)
+.+.+++++..-|+.||.-|.+...|..|.+--..- ++|.|..|.+.|.++..|..|+..|-..- |..
T Consensus 198 H~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~s 277 (467)
T KOG3608|consen 198 HIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSAS 277 (467)
T ss_pred HHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChH
Confidence 334555666666666666666666666665533322 45666666666666666666664443210 000
Q ss_pred --CCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCC--chhccCChHHHHhHHHhhh
Q psy8937 78 --SVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPL--CQKCFKNKLYLRRHVISFH 143 (147)
Q Consensus 78 --~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~h 143 (147)
....... ....++|+|..|...+...+.|..|..+|. +..|.|.. |...|..+..|++|++.+|
T Consensus 278 sL~~H~r~r-Hs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 278 SLTTHIRYR-HSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred HHHHHHHhh-hccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 0000000 013455555555555555555555555444 44555543 5555555556666665555
No 8
>KOG3576|consensus
Probab=99.67 E-value=1.3e-17 Score=102.23 Aligned_cols=84 Identities=27% Similarity=0.545 Sum_probs=77.7
Q ss_pred CCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCc
Q psy8937 46 GILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLC 125 (147)
Q Consensus 46 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C 125 (147)
..+.|.+|++.|.....|.+|+..|. ..+.+-|..||+.|...-.|.+|.++|+|.+||+|+.|
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~----------------~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c 179 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHS----------------DVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLC 179 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhcc----------------HHHHHHHhhccCcccchhhhhhhhccccCccccchhhh
Confidence 56899999999999999999998776 44667799999999999999999999999999999999
Q ss_pred hhccCChHHHHhHHHhhhcc
Q psy8937 126 QKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 126 ~~~f~~~~~l~~H~~~~h~~ 145 (147)
++.|.++-+|..|++..||-
T Consensus 180 ~kaftqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 180 EKAFTQRCSLESHLKKVHGV 199 (267)
T ss_pred hHHHHhhccHHHHHHHHcCc
Confidence 99999999999999998874
No 9
>KOG3608|consensus
Probab=99.64 E-value=8e-16 Score=101.62 Aligned_cols=111 Identities=23% Similarity=0.420 Sum_probs=94.3
Q ss_pred CcccccccccccCChHHHHHHHHHhcCC-CCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCccccc
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLP-GILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKI 96 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~-~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~ 96 (147)
+-|+|+.|+.+....+.|..|++..|.. +||+|+.|...|.+++.|.+|.+.|. +-.|.|..
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-----------------~~~y~C~h 324 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-----------------KTVYQCEH 324 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-----------------ccceecCC
Confidence 4678888888888888888888887776 88999999999999999999987544 23467877
Q ss_pred --ccccCCChHHHHHHHHHHh---CCCcccCCCchhccCChHHHHhHHHhhhcc
Q psy8937 97 --CGKHYSNSSNLKQHIRLIH---LPGILFCPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 97 --c~~~~~~~~~l~~H~~~~~---~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
|..++.+..++..|++.++ .+-+|.|-.|++.|.+..+|.+|+...|+-
T Consensus 325 ~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 325 PDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred CCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 9999999999999999887 245699999999999999999999998874
No 10
>KOG3623|consensus
Probab=99.60 E-value=3.4e-16 Score=111.57 Aligned_cols=81 Identities=26% Similarity=0.407 Sum_probs=76.2
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccc
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCK 95 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ 95 (147)
+...|.|++|+++|...+.|.+|.-.|.+.+||+|.+|.+.|+-+..|..|++.|. |||||.|.
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHS----------------GEKPfQCd 954 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHS----------------GEKPFQCD 954 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhcc----------------CCCcchhh
Confidence 56789999999999999999999999999999999999999999999999999888 66888899
Q ss_pred cccccCCChHHHHHHHH
Q psy8937 96 ICGKHYSNSSNLKQHIR 112 (147)
Q Consensus 96 ~c~~~~~~~~~l~~H~~ 112 (147)
.|++.|..+..+-.||.
T Consensus 955 KClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 955 KCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred hhhhhcccccchHhhhc
Confidence 99999999999998886
No 11
>PHA00733 hypothetical protein
Probab=99.46 E-value=1.1e-13 Score=81.33 Aligned_cols=88 Identities=26% Similarity=0.361 Sum_probs=69.8
Q ss_pred CCCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCC
Q psy8937 45 PGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPL 124 (147)
Q Consensus 45 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~ 124 (147)
.+++.|.+|+..|.....|..+.-..... .....++|.|..|++.|.....|..|++.+ +.+|.|++
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~-----------~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~ 104 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLL-----------TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPV 104 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhc-----------ccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCC
Confidence 47888999999988877776663211111 011457889999999999999999999875 45799999
Q ss_pred chhccCChHHHHhHHHhhhcc
Q psy8937 125 CQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 125 C~~~f~~~~~l~~H~~~~h~~ 145 (147)
|++.|.....|.+|+..+|+-
T Consensus 105 CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 105 CGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CCCccCCHHHHHHHHHHhcCc
Confidence 999999999999999998873
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.44 E-value=3.1e-13 Score=95.94 Aligned_cols=106 Identities=21% Similarity=0.485 Sum_probs=87.1
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCccccc
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKI 96 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~ 96 (147)
++.+.|+.|++.|. ...|..|+..+| .++.|+ |+..+ ....|..|+..+. .++++.|..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thC----------------p~Kpi~C~f 509 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTC----------------PLRLITCRF 509 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccC----------------CCCceeCCC
Confidence 46679999999996 678999999876 789999 99765 5678999986555 557788999
Q ss_pred ccccCCC----------hHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHhhhcc
Q psy8937 97 CGKHYSN----------SSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 97 c~~~~~~----------~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
|+..+.. .+.|..|.... +.+++.|..||+.|..+ .|..|+...|..
T Consensus 510 C~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 510 CGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred CCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 9998852 35899998884 88999999999988876 788998887764
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.23 E-value=3.8e-12 Score=62.63 Aligned_cols=43 Identities=21% Similarity=0.308 Sum_probs=39.8
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHH
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLR 136 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~ 136 (147)
|.|+.||+.|...+.|..|++.|. ++|+|..|++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 679999999999999999999988 6899999999999887764
No 14
>PHA00733 hypothetical protein
Probab=99.22 E-value=1.6e-11 Score=72.24 Aligned_cols=83 Identities=19% Similarity=0.378 Sum_probs=68.0
Q ss_pred ccCcccccccccccCChHHHHHH--HH---HhcCCCCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcC
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQH--IR---LIHLPGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLD 90 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h--~~---~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~ 90 (147)
.++.+.|.+|...|.....|..+ +. .++...+|.|+.|++.|.....|..|+..+. .
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~------------------~ 98 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTE------------------H 98 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCC------------------c
Confidence 47889999999999888777665 22 1344689999999999999999999986421 2
Q ss_pred CcccccccccCCChHHHHHHHHHHhC
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHL 116 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~ 116 (147)
++.|..|++.|.....|..|+...++
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 46799999999999999999987765
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.17 E-value=1.1e-11 Score=60.98 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=39.7
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHH
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYL 63 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 63 (147)
..|.|+.||+.|...++|..|++.|+ ++++|..|++.|...+.|
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 46899999999999999999999877 689999999999877665
No 16
>KOG3993|consensus
Probab=99.15 E-value=1e-11 Score=84.11 Aligned_cols=99 Identities=22% Similarity=0.348 Sum_probs=73.6
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHHhhhcCCCCcc--------CC---------
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYR--------SV--------- 79 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~--------~~--------- 79 (147)
...|+|..|-..|.+.-.|.+|.-..-....|+|++|++.|....||..|.+.|...+... ..
T Consensus 265 iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 265 IGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 3569999999999999999998753333378999999999999999999998774322111 00
Q ss_pred CCCCCCCCCcCCcccccccccCCChHHHHHHHHHHh
Q psy8937 80 PGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIH 115 (147)
Q Consensus 80 ~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~ 115 (147)
.........+..|.|..|++.|....-|+.|+..|+
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 000111134457899999999999999999987776
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.05 E-value=2.1e-10 Score=81.92 Aligned_cols=107 Identities=16% Similarity=0.353 Sum_probs=79.1
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCC--------------------CCcCCCCchhhhcChHHHHHHHhhhcCCCCc
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLP--------------------GILFCPLCQKCFKNKLYLRRHVGTYTHTPSY 76 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~--------------------~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 76 (147)
...-.|+-|...... ..|..|... ... +.+.|+.|++.|. ...|..|+..++
T Consensus 405 ~~~V~C~NC~~~i~l-~~l~lHe~~-C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H----- 476 (567)
T PLN03086 405 VDTVECRNCKHYIPS-RSIALHEAY-CSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH----- 476 (567)
T ss_pred CCeEECCCCCCccch-hHHHHHHhh-CCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC-----
Confidence 344568888886554 556678763 322 2356889999996 577999987653
Q ss_pred cCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccC----------ChHHHHhHHHhhhccC
Q psy8937 77 RSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK----------NKLYLRRHVISFHENA 146 (147)
Q Consensus 77 ~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~----------~~~~l~~H~~~~h~~~ 146 (147)
+++.|+ |++.+ ....|..|+..|...+++.|+.|++.|. ....|..|..+. |.+
T Consensus 477 -------------kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~r 540 (567)
T PLN03086 477 -------------EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSR 540 (567)
T ss_pred -------------CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCc
Confidence 345699 99755 6799999999999999999999999995 245889998873 554
Q ss_pred C
Q psy8937 147 T 147 (147)
Q Consensus 147 ~ 147 (147)
|
T Consensus 541 t 541 (567)
T PLN03086 541 T 541 (567)
T ss_pred c
Confidence 3
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.01 E-value=2.3e-10 Score=48.43 Aligned_cols=26 Identities=38% Similarity=0.683 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCCcccCCCchhccCC
Q psy8937 106 NLKQHIRLIHLPGILFCPLCQKCFKN 131 (147)
Q Consensus 106 ~l~~H~~~~~~~~~~~C~~C~~~f~~ 131 (147)
+|..|++.|.++++|.|+.|++.|.+
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 19
>PHA00616 hypothetical protein
Probab=99.01 E-value=2.1e-10 Score=53.85 Aligned_cols=27 Identities=26% Similarity=0.518 Sum_probs=13.6
Q ss_pred ccCCCchhccCChHHHHhHHHhhhccC
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISFHENA 146 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h~~~ 146 (147)
|+|+.||+.|..++.|.+|++.|||++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~ 28 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQN 28 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCC
Confidence 445555555555555555555555443
No 20
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.73 E-value=2.9e-08 Score=49.69 Aligned_cols=50 Identities=32% Similarity=0.482 Sum_probs=41.3
Q ss_pred cccccccccCCChHHHHHHHHHHhC--CCcccCCCchhccCChHHHHhHHHhhhc
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHL--PGILFCPLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~--~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
|.|+.|++ ..+...|..|....+. .+.+.|++|...+. .+|.+||.++|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 67999999 5667889999887664 35799999998755 489999999885
No 21
>PHA00732 hypothetical protein
Probab=98.70 E-value=9e-09 Score=55.36 Aligned_cols=47 Identities=36% Similarity=0.615 Sum_probs=38.7
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHhh
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVISF 142 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 142 (147)
+|.|..|++.|.....|..|++.++. ++.|+.|++.|. .|.+|+.++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhccc
Confidence 46799999999999999999985332 368999999998 477887654
No 22
>PHA00616 hypothetical protein
Probab=98.67 E-value=1.4e-08 Score=47.74 Aligned_cols=34 Identities=18% Similarity=0.346 Sum_probs=28.7
Q ss_pred cccccccccccCChHHHHHHHHHhcCCCCcCCCC
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPL 52 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~ 52 (147)
+|+|..||+.|...+.|..|++.+|+.++++|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5788888888888888888888888888887764
No 23
>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=98.63 E-value=1.5e-08 Score=42.84 Aligned_cols=26 Identities=38% Similarity=0.683 Sum_probs=23.2
Q ss_pred HHHHHHHHhcCCCCcCCCCchhhhcC
Q psy8937 34 NLKQHIRLIHLPGILFCPLCQKCFKN 59 (147)
Q Consensus 34 ~l~~h~~~~~~~~~~~C~~C~~~f~~ 59 (147)
+|..|++.|.++++|.|+.|++.|.+
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 58899999999999999999998863
No 24
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.61 E-value=1.5e-07 Score=47.15 Aligned_cols=51 Identities=29% Similarity=0.489 Sum_probs=40.7
Q ss_pred CcccccccccccCChHHHHHHHHHhcCC--CCcCCCCchhhhcChHHHHHHHhhhc
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLP--GILFCPLCQKCFKNKLYLRRHVGTYT 71 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~--~~~~C~~C~~~f~~~~~l~~H~~~~~ 71 (147)
+.|.|++|++ ..+...|..|....|.. +.+.||+|...+. .+|..|+..++
T Consensus 1 ~~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 1 DSFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 3689999999 56678899998887775 6789999998654 48999986543
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.57 E-value=3.7e-08 Score=40.39 Aligned_cols=23 Identities=39% Similarity=0.817 Sum_probs=19.6
Q ss_pred ccCCCchhccCChHHHHhHHHhh
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISF 142 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~ 142 (147)
|.|+.|++.|.....|.+|++.|
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 67888999999999999998873
No 26
>PHA00732 hypothetical protein
Probab=98.56 E-value=3.7e-08 Score=53.01 Aligned_cols=46 Identities=35% Similarity=0.618 Sum_probs=38.1
Q ss_pred cccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHHhh
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVGT 69 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 69 (147)
+|.|+.|++.|.....|+.|++.+|. ++.|+.|++.|. .+..|+.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhcc
Confidence 58899999999999999999985343 358999999998 47778743
No 27
>KOG3993|consensus
Probab=98.54 E-value=1.8e-08 Score=68.81 Aligned_cols=82 Identities=28% Similarity=0.555 Sum_probs=68.1
Q ss_pred CcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhC----------
Q psy8937 47 ILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHL---------- 116 (147)
Q Consensus 47 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~---------- 116 (147)
.|.|..|...|...=.|.+|.-... .--.|+|+.|++.|+=..+|..|++=|.-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RI----------------V~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~ 330 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRI----------------VHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSP 330 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCee----------------EEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCC
Confidence 3789999999999999999974333 22347899999999999999999987651
Q ss_pred -----------------------CCcccCCCchhccCChHHHHhHHHhhhc
Q psy8937 117 -----------------------PGILFCPLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 117 -----------------------~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
+..|.|..|+|.|.+...|+.|+.+|+.
T Consensus 331 P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 331 PPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 1238899999999999999999988874
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=98.49 E-value=9.8e-08 Score=39.42 Aligned_cols=24 Identities=42% Similarity=0.928 Sum_probs=19.4
Q ss_pred ccCCCchhccCChHHHHhHHHhhh
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISFH 143 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h 143 (147)
|.|++|++.|.+...|.+|++++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 678999999999999999998876
No 29
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.37 E-value=1.6e-07 Score=40.03 Aligned_cols=26 Identities=31% Similarity=0.390 Sum_probs=22.7
Q ss_pred cccCCCchhccCChHHHHhHHHhhhc
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
+|.|..|++.|.....|..|++.|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 57899999999999999999988764
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.35 E-value=2.9e-07 Score=52.03 Aligned_cols=23 Identities=35% Similarity=0.762 Sum_probs=13.1
Q ss_pred cccCCCchhccCChHHHHhHHHh
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVIS 141 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~ 141 (147)
.+.|..|++.|.....|..||+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 35566666666666666666654
No 31
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.29 E-value=8e-07 Score=42.72 Aligned_cols=32 Identities=25% Similarity=0.411 Sum_probs=23.1
Q ss_pred CCCcccCCCchhccCChHHHHhHHHhhhccCC
Q psy8937 116 LPGILFCPLCQKCFKNKLYLRRHVISFHENAT 147 (147)
Q Consensus 116 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (147)
.++|..|++|+..+.+..+|.+||.+.|+.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45778899999999999999999999998875
No 32
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.26 E-value=6.6e-07 Score=36.56 Aligned_cols=22 Identities=55% Similarity=1.001 Sum_probs=16.0
Q ss_pred ccccccccccCChHHHHHHHHH
Q psy8937 20 RYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
|+|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5677777777777777777764
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.10 E-value=2.3e-06 Score=35.10 Aligned_cols=24 Identities=46% Similarity=0.905 Sum_probs=15.7
Q ss_pred ccccccccccCChHHHHHHHHHhc
Q psy8937 20 RYCKICGKHYSNSSNLKQHIRLIH 43 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~ 43 (147)
|.|++|++.|.+...|..|+..+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 567777777777777777776553
No 34
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=98.07 E-value=3.5e-06 Score=34.74 Aligned_cols=24 Identities=33% Similarity=0.604 Sum_probs=19.5
Q ss_pred ccCCCchhccCChHHHHhHHHhhhc
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
|+|+.|++... ...|.+|++++|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999999888 8899999999885
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.95 E-value=8.5e-06 Score=33.93 Aligned_cols=24 Identities=38% Similarity=0.690 Sum_probs=20.4
Q ss_pred ccCCCchhccCChHHHHhHHHhhh
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISFH 143 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h 143 (147)
|.|..|++.|.....|..|+++|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578999999999999999998654
No 36
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.94 E-value=3.4e-06 Score=35.84 Aligned_cols=24 Identities=38% Similarity=0.631 Sum_probs=17.2
Q ss_pred cccccccccccCChHHHHHHHHHh
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLI 42 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~ 42 (147)
+|.|..|++.|....+|..|++.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 467777777777777777777644
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.91 E-value=2.9e-06 Score=56.42 Aligned_cols=52 Identities=31% Similarity=0.469 Sum_probs=44.4
Q ss_pred cCCccccc--ccccCCChHHHHHHHHHHh-------------------CCCcccCCCchhccCChHHHHhHHH
Q psy8937 89 LDARYCKI--CGKHYSNSSNLKQHIRLIH-------------------LPGILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 89 ~~~~~C~~--c~~~~~~~~~l~~H~~~~~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
+|||+|+. |++.|.....|+-|+..-+ ..|||.|++|+|.++....|.-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 59999976 9999999999999987533 2389999999999999999888764
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.90 E-value=7.5e-06 Score=46.18 Aligned_cols=53 Identities=28% Similarity=0.609 Sum_probs=22.4
Q ss_pred cccccccccCChHHHHHHHHHhcCC-----------------------CCcCCCCchhhhcChHHHHHHHhhhcCC
Q psy8937 21 YCKICGKHYSNSSNLKQHIRLIHLP-----------------------GILFCPLCQKCFKNKLYLRRHVGTYTHT 73 (147)
Q Consensus 21 ~C~~C~~~f~~~~~l~~h~~~~~~~-----------------------~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 73 (147)
.|..|+..|.....|..|+...|+. ..+.|..|+..|.+...|..|+..+.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H~ 76 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKHHK 76 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTTT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCccCC
Confidence 4889999999999999999876652 1367999999999999999999876544
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.86 E-value=7.9e-06 Score=54.42 Aligned_cols=68 Identities=25% Similarity=0.338 Sum_probs=44.7
Q ss_pred CCCCcCCCC--chhhhcChHHHHHHHhhhcCCCCccCCCCCC----CCCCCcCCcccccccccCCChHHHHHHHH
Q psy8937 44 LPGILFCPL--CQKCFKNKLYLRRHVGTYTHTPSYRSVPGAS----KPLHSLDARYCKICGKHYSNSSNLKQHIR 112 (147)
Q Consensus 44 ~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~----~~~~~~~~~~C~~c~~~~~~~~~l~~H~~ 112 (147)
+++||+|++ |.+.|+..--|+-|+. |.+..+....--+. -+....|||+|..|++.|.....|+-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~l-hGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHML-HGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhh-ccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 347888875 8888888877888874 32222221111111 22335699999999999999999888754
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.73 E-value=1.7e-05 Score=32.94 Aligned_cols=23 Identities=35% Similarity=0.797 Sum_probs=19.3
Q ss_pred ccCCCchhccCChHHHHhHHHhh
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISF 142 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~ 142 (147)
|.|.+|++.|.....|..|++.+
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 56888999999999998888765
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.67 E-value=4.6e-05 Score=36.75 Aligned_cols=31 Identities=32% Similarity=0.628 Sum_probs=14.8
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCCC
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLPG 46 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~ 46 (147)
+..+-.|++|+..+.+..+|++|+...|..+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 3455556666666666666666665555443
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.41 E-value=0.0002 Score=29.56 Aligned_cols=21 Identities=43% Similarity=0.858 Sum_probs=13.5
Q ss_pred ccccccccccCChHHHHHHHH
Q psy8937 20 RYCKICGKHYSNSSNLKQHIR 40 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~ 40 (147)
|.|..|++.|.....|..|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 456666666666666666665
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.36 E-value=7.7e-05 Score=31.56 Aligned_cols=23 Identities=30% Similarity=0.709 Sum_probs=19.3
Q ss_pred ccCCCchhccCChHHHHhHHHhh
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISF 142 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~ 142 (147)
|.|..|++.|.....|..|+++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 67889999999999998888763
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.33 E-value=9.6e-05 Score=30.58 Aligned_cols=21 Identities=48% Similarity=1.088 Sum_probs=14.9
Q ss_pred ccccccccccCChHHHHHHHH
Q psy8937 20 RYCKICGKHYSNSSNLKQHIR 40 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~ 40 (147)
|.|.+|++.|.+...|+.|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 467777777777777777765
No 45
>PRK04860 hypothetical protein; Provisional
Probab=97.15 E-value=0.00024 Score=43.60 Aligned_cols=39 Identities=21% Similarity=0.456 Sum_probs=34.0
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
-+|.|. |+. ....+..|.+++.++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 468897 987 677889999999999999999999988754
No 46
>KOG2785|consensus
Probab=97.13 E-value=0.0013 Score=45.24 Aligned_cols=51 Identities=20% Similarity=0.298 Sum_probs=42.8
Q ss_pred CcccccccccCCChHHHHHHHHHHhCC-----------------------CcccCCCch---hccCChHHHHhHHHh
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLP-----------------------GILFCPLCQ---KCFKNKLYLRRHVIS 141 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 141 (147)
|-.|..|++.+.+...-..|+..+++- .-+.|-.|+ +.|.+....++||.-
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 345999999999999999999988852 226688888 999999999999974
No 47
>KOG1146|consensus
Probab=96.96 E-value=0.00051 Score=53.99 Aligned_cols=120 Identities=16% Similarity=0.184 Sum_probs=79.2
Q ss_pred ccccccccCChHHHHHHHHHhcCC-CCcCCCCchhhhcChHHHHHHHhhhcCCCCcc---------CCCCCCCCCCCcCC
Q psy8937 22 CKICGKHYSNSSNLKQHIRLIHLP-GILFCPLCQKCFKNKLYLRRHVGTYTHTPSYR---------SVPGASKPLHSLDA 91 (147)
Q Consensus 22 C~~C~~~f~~~~~l~~h~~~~~~~-~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~---------~~~~~~~~~~~~~~ 91 (147)
|..|+..+.....+..++..-+.. +-+.|+.|+..|+....|-.||++.+.+.... ............++
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p 518 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP 518 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc
Confidence 444555555555554444433333 66788899888888888888887744332211 11111223335578
Q ss_pred cccccccccCCChHHHHHHHHHHhC-------------------------------------------CCcccCCCchhc
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHL-------------------------------------------PGILFCPLCQKC 128 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~-------------------------------------------~~~~~C~~C~~~ 128 (147)
|.|..|...+.....|..|+..... ...+.|.+|++.
T Consensus 519 ~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~ye 598 (1406)
T KOG1146|consen 519 YPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYE 598 (1406)
T ss_pred ccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcch
Confidence 8999999999999999988865320 023779999999
Q ss_pred cCChHHHHhHHHh
Q psy8937 129 FKNKLYLRRHVIS 141 (147)
Q Consensus 129 f~~~~~l~~H~~~ 141 (147)
.+-..+|+.||..
T Consensus 599 tniarnlrihmts 611 (1406)
T KOG1146|consen 599 TNIARNLRIHMTA 611 (1406)
T ss_pred hhhhhcccccccc
Confidence 9988888888764
No 48
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.90 E-value=0.00019 Score=30.32 Aligned_cols=21 Identities=43% Similarity=0.944 Sum_probs=14.8
Q ss_pred ccccccccccCChHHHHHHHH
Q psy8937 20 RYCKICGKHYSNSSNLKQHIR 40 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~ 40 (147)
|.|..|++.|.+...+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 567777777777777766654
No 49
>PRK04860 hypothetical protein; Provisional
Probab=96.88 E-value=0.00057 Score=41.98 Aligned_cols=40 Identities=20% Similarity=0.409 Sum_probs=34.1
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChH
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKL 61 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~ 61 (147)
-+|.|. |+. ....+.+|.+++.+.++|.|..|+..|....
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 469998 998 5677899999999999999999999886543
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.88 E-value=0.0008 Score=27.44 Aligned_cols=23 Identities=39% Similarity=0.618 Sum_probs=12.4
Q ss_pred ccccccccccCChHHHHHHHHHhc
Q psy8937 20 RYCKICGKHYSNSSNLKQHIRLIH 43 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~ 43 (147)
|.|+.|+.... ...|..|++.+|
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 45666666555 556666666544
No 51
>KOG2231|consensus
Probab=96.69 E-value=0.0019 Score=47.92 Aligned_cols=108 Identities=27% Similarity=0.571 Sum_probs=66.9
Q ss_pred cccccccccccC---------------ChHHHHHHHHHhcCCCCcCCCCc----------hhhhcChHHHHHHHhhhcCC
Q psy8937 19 ARYCKICGKHYS---------------NSSNLKQHIRLIHLPGILFCPLC----------QKCFKNKLYLRRHVGTYTHT 73 (147)
Q Consensus 19 ~~~C~~C~~~f~---------------~~~~l~~h~~~~~~~~~~~C~~C----------~~~f~~~~~l~~H~~~~~~~ 73 (147)
.+.|.+|++.|. ..-.|+.|+..-|.. +.|..| .+.| +...|..|+. .+.
T Consensus 99 ~~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Y-t~~el~~h~~--~gd 173 (669)
T KOG2231|consen 99 HHSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLY-TRAELNLHLM--FGD 173 (669)
T ss_pred hhhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehe-hHHHHHHHHh--cCC
Confidence 356777777773 667788888654543 333332 2333 3345666662 222
Q ss_pred CCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCc------hhccCChHHHHhHHHhhhc
Q psy8937 74 PSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLC------QKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 74 ~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~~h~ 144 (147)
...+ . -..--.|..|...|.....|..|++.++ |.|..| +..|.....|..|.+..|-
T Consensus 174 ~d~~-------s--~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~Hf 237 (669)
T KOG2231|consen 174 PDDE-------S--CRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHF 237 (669)
T ss_pred Cccc-------c--ccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcCc
Confidence 2010 0 1111259999999999999999988655 445555 4667777899999888773
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.51 E-value=0.0028 Score=26.19 Aligned_cols=20 Identities=35% Similarity=0.730 Sum_probs=11.4
Q ss_pred ccCCCchhccCChHHHHhHHH
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~ 140 (147)
..|+.||+.| ....|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566666666 4445556654
No 53
>KOG1146|consensus
Probab=96.44 E-value=0.00062 Score=53.54 Aligned_cols=121 Identities=17% Similarity=0.189 Sum_probs=80.7
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcC-------------------------CCCcCCCCchhhhcChHHHHHHHhhh
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHL-------------------------PGILFCPLCQKCFKNKLYLRRHVGTY 70 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~-------------------------~~~~~C~~C~~~f~~~~~l~~H~~~~ 70 (147)
-.+.++|+.|+..|.....|..|++..|. .++|.|..|..++....+|..|++..
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~ 541 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSD 541 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHH
Confidence 34789999999999999999999998332 24688999999999999999999653
Q ss_pred cCCCCc------------------------cCC---CCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCc-ccC
Q psy8937 71 THTPSY------------------------RSV---PGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGI-LFC 122 (147)
Q Consensus 71 ~~~~~~------------------------~~~---~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~-~~C 122 (147)
.+.... ... .........+-.|.|..|....+-.-+|+.|+..-.-..+ .-|
T Consensus 542 ~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s~~p~~~ 621 (1406)
T KOG1146|consen 542 LHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSSSPPSLV 621 (1406)
T ss_pred hhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCCCChHHH
Confidence 222110 000 0001113344568899998887777788887765433333 445
Q ss_pred CCchhccCChHHHH
Q psy8937 123 PLCQKCFKNKLYLR 136 (147)
Q Consensus 123 ~~C~~~f~~~~~l~ 136 (147)
..|+..+..-..+.
T Consensus 622 Lq~~it~~l~~~~~ 635 (1406)
T KOG1146|consen 622 LQQNITSSLASLLG 635 (1406)
T ss_pred hhhcchhhcccccc
Confidence 55655555544443
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=96.42 E-value=0.0025 Score=28.50 Aligned_cols=23 Identities=22% Similarity=0.675 Sum_probs=17.2
Q ss_pred cccCCCchhccCChHHHHhHHHh
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVIS 141 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~ 141 (147)
+|.|.+|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46788888888877777777764
No 55
>KOG4173|consensus
Probab=96.37 E-value=0.0047 Score=39.06 Aligned_cols=79 Identities=23% Similarity=0.442 Sum_probs=58.7
Q ss_pred CcCCCC--chhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHh---------
Q psy8937 47 ILFCPL--CQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIH--------- 115 (147)
Q Consensus 47 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~--------- 115 (147)
.+-|++ |...|........|.-..++. .|..|.+.|++..-|..|+..-+
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~-------------------sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~ve 139 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN-------------------SCSFCKRAFPTGHLLDAHILEWHDSLFQALVE 139 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc-------------------hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHH
Confidence 355765 667777777777776322221 49999999999999998886544
Q ss_pred -CCCcccC--CCchhccCChHHHHhHHHhhhc
Q psy8937 116 -LPGILFC--PLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 116 -~~~~~~C--~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
|.-.|+| +.|+..|.....-.+||...|.
T Consensus 140 RG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 140 RGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred cCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 3446889 6799999999999999887764
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=96.30 E-value=0.0023 Score=31.48 Aligned_cols=24 Identities=38% Similarity=0.657 Sum_probs=11.5
Q ss_pred ccCCCchhccCChHHHHhHHHhhh
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISFH 143 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h 143 (147)
+.|+.|++.|....++.+|...-|
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHh
Confidence 444455555544444444444433
No 57
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.26 E-value=0.0093 Score=34.22 Aligned_cols=101 Identities=15% Similarity=0.272 Sum_probs=59.0
Q ss_pred ccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHHhhhcC--CCCccCCCCCCCCCCCcCCcccccc
Q psy8937 20 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVGTYTH--TPSYRSVPGASKPLHSLDARYCKIC 97 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~--~~~~~~~~~~~~~~~~~~~~~C~~c 97 (147)
|.|++|+-.. -..|..|+.|+-.......|.+-. |+- .+++...+.+. ......|-.|
T Consensus 2 Y~CPrC~skv--------------C~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~----~~~~~~C~~C 61 (112)
T TIGR00622 2 YFCPQCRAKV--------------CELPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEE----YNGSRFCFGC 61 (112)
T ss_pred ccCCCCCCCc--------------cCCCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccc----cCCCCcccCc
Confidence 6677776542 345788999998888887787654 321 22333222111 1111248888
Q ss_pred cccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHhh
Q psy8937 98 GKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVISF 142 (147)
Q Consensus 98 ~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 142 (147)
...|........ ........|.|+.|...|-..-++-.|-..|
T Consensus 62 ~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 62 QGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred CCCCCCcccccc--cccccccceeCCCCCCccccccchhhhhhcc
Confidence 888876431110 0012234688999999888777766666554
No 58
>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=96.09 E-value=0.012 Score=33.82 Aligned_cols=25 Identities=28% Similarity=0.461 Sum_probs=23.8
Q ss_pred ccC----CCchhccCChHHHHhHHHhhhc
Q psy8937 120 LFC----PLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 120 ~~C----~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
|.| +.|++.+.+...|.+|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 779 9999999999999999999996
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.86 E-value=0.0012 Score=46.67 Aligned_cols=128 Identities=26% Similarity=0.278 Sum_probs=86.3
Q ss_pred CcccccccccccCChHHHHHHHH--HhcCC--CCcCCC--CchhhhcChHHHHHHHhhhcCCCCccCCCCCC--------
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIR--LIHLP--GILFCP--LCQKCFKNKLYLRRHVGTYTHTPSYRSVPGAS-------- 83 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~-------- 83 (147)
..+.|..|...|.....|..|.+ .|.+. +++.|+ .|++.|.....+..|...+....+........
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 57899999999999999999999 68888 899999 79999999999999998776654332110000
Q ss_pred -----------CCCCCcCCccc--ccccccCCChHHHHHHHHHHhCCC--cccCCCchhccCChHHHHhHHHhhhcc
Q psy8937 84 -----------KPLHSLDARYC--KICGKHYSNSSNLKQHIRLIHLPG--ILFCPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 84 -----------~~~~~~~~~~C--~~c~~~~~~~~~l~~H~~~~~~~~--~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
......+.+.+ ..|...+.....+..|...+.... .+.+..|.+.|.....+..|++++...
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNH 444 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccC
Confidence 00001111112 224444455555555555555444 455678888888888888888776544
No 60
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.81 E-value=0.0082 Score=26.75 Aligned_cols=22 Identities=23% Similarity=0.831 Sum_probs=16.0
Q ss_pred cccccccccccCChHHHHHHHH
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIR 40 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~ 40 (147)
.|.|.+|++.|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4677777777777777777765
No 61
>KOG2482|consensus
Probab=95.60 E-value=0.068 Score=36.68 Aligned_cols=49 Identities=24% Similarity=0.484 Sum_probs=39.9
Q ss_pred ccccccccCCChHHHHHHHHHHhC---------------------------CCcccCCCchhccCChHHHHhHHHh
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHL---------------------------PGILFCPLCQKCFKNKLYLRRHVIS 141 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~~ 141 (147)
.|-.|...+.+...|..|+...+. .+...|-+|...|-....|..||..
T Consensus 281 ~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 281 VCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred EEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 699999999999999999987652 1224478899999999999999864
No 62
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.55 E-value=0.053 Score=37.29 Aligned_cols=83 Identities=25% Similarity=0.472 Sum_probs=45.5
Q ss_pred Ccccccc--cccccCChHHHHHHHHHhcCCCCcCCCCch---hhhcChH------HHHHHHhhhcCCCCccCCCCCCCCC
Q psy8937 18 DARYCKI--CGKHYSNSSNLKQHIRLIHLPGILFCPLCQ---KCFKNKL------YLRRHVGTYTHTPSYRSVPGASKPL 86 (147)
Q Consensus 18 ~~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~---~~f~~~~------~l~~H~~~~~~~~~~~~~~~~~~~~ 86 (147)
..|.|+. |..+....-.|..|...-|.. +-|.+|- +.|..+. .|..|... +. . .
T Consensus 150 L~F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~--G~---------~--e 214 (493)
T COG5236 150 LSFKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNG--GL---------E--E 214 (493)
T ss_pred HHhcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccC--Cc---------c--c
Confidence 3566765 666666677788887765543 3344432 3343322 23333210 00 0 0
Q ss_pred CCcCCc-ccccccccCCChHHHHHHHHHHh
Q psy8937 87 HSLDAR-YCKICGKHYSNSSNLKQHIRLIH 115 (147)
Q Consensus 87 ~~~~~~-~C~~c~~~~~~~~~l~~H~~~~~ 115 (147)
.+.+-+ .|..|...|.+...|..|.+..+
T Consensus 215 ~GFKGHP~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 215 EGFKGHPLCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred cCcCCCchhhhccceecChHHHHHHHHhhh
Confidence 011111 48888888888888888887654
No 63
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=94.49 E-value=0.025 Score=32.48 Aligned_cols=30 Identities=27% Similarity=0.728 Sum_probs=24.4
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
..|+.||..|.... ..|..|+.||..|...
T Consensus 10 R~Cp~CG~kFYDLn-----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN-----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC-----------CCCccCCCCCCccCcc
Confidence 36999999998763 3688999999988765
No 64
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.19 E-value=0.024 Score=25.08 Aligned_cols=24 Identities=29% Similarity=0.865 Sum_probs=17.4
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchh
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQK 127 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~ 127 (147)
|.|..||..+.... .++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 56888887765443 5788999985
No 65
>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=93.83 E-value=0.044 Score=25.93 Aligned_cols=27 Identities=30% Similarity=0.440 Sum_probs=14.2
Q ss_pred CCcccCCCchhccCCh----HHHHhHHHhhh
Q psy8937 117 PGILFCPLCQKCFKNK----LYLRRHVISFH 143 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~~----~~l~~H~~~~h 143 (147)
.....|..|++.+... +.|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3456677777776664 57777775443
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.72 E-value=0.036 Score=27.35 Aligned_cols=30 Identities=17% Similarity=0.361 Sum_probs=26.1
Q ss_pred CCcCCcccccccccCCChHHHHHHHHHHhC
Q psy8937 87 HSLDARYCKICGKHYSNSSNLKQHIRLIHL 116 (147)
Q Consensus 87 ~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~ 116 (147)
++|..+.|+.|+..|........|.+..++
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 477788999999999999999999987665
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.57 E-value=0.011 Score=41.89 Aligned_cols=56 Identities=30% Similarity=0.440 Sum_probs=51.2
Q ss_pred CCcccccccccCCChHHHHHHHH--HHhCC--CcccCC--CchhccCChHHHHhHHHhhhcc
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIR--LIHLP--GILFCP--LCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
.++.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.+...+..|..+|.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 46789999999999999999999 89999 999999 8999999999999999888664
No 68
>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=93.51 E-value=0.039 Score=33.99 Aligned_cols=35 Identities=11% Similarity=0.211 Sum_probs=28.7
Q ss_pred CccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 15 HSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
.+..-|.|+.|+..|+...++. ..|.||.||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 3567799999999999988875 2699999998754
No 69
>KOG2807|consensus
Probab=93.10 E-value=0.26 Score=33.76 Aligned_cols=37 Identities=19% Similarity=0.384 Sum_probs=26.6
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHH
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHV 67 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 67 (147)
...|.|++|... ....|..|+.|+-.......|.+-.
T Consensus 274 ~~Gy~CP~Ckak--------------vCsLP~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 274 GGGYFCPQCKAK--------------VCSLPIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred cCceeCCcccCe--------------eecCCccCCccceeEecchHHHHHH
Confidence 456777777653 3345788999998888888787654
No 70
>KOG2893|consensus
Probab=93.05 E-value=0.037 Score=36.04 Aligned_cols=47 Identities=21% Similarity=0.390 Sum_probs=37.2
Q ss_pred CcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHH
Q psy8937 88 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHV 139 (147)
Q Consensus 88 ~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 139 (147)
..|+| |=.|++.|.....|..|++ .|-|+|.+|-|.+-+.-.|..|-
T Consensus 8 ~~kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 8 VDKPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred cCCce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceeeh
Confidence 34555 7789999999999988876 46799999998777776777773
No 71
>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=92.91 E-value=0.044 Score=32.61 Aligned_cols=24 Identities=38% Similarity=0.715 Sum_probs=15.3
Q ss_pred cccCCCchhccCChHHHHhHHHhhhcc
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
-..|-+||+.|.. |.+|++.|||-
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eeEEccCCcccch---HHHHHHHccCC
Confidence 3669999998885 48999999874
No 72
>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=92.89 E-value=0.044 Score=35.42 Aligned_cols=27 Identities=37% Similarity=0.801 Sum_probs=17.7
Q ss_pred cccCCCchhccCChHHHHhHHHhhhcc
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
.|.|+.|+|.|.-......|+...|++
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHH
Confidence 477777777777777777777777765
No 73
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.46 E-value=0.09 Score=36.22 Aligned_cols=80 Identities=26% Similarity=0.350 Sum_probs=53.8
Q ss_pred cCCCC--chhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCccccccc---c------cCCChHHHHHHHHHHhC
Q psy8937 48 LFCPL--CQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICG---K------HYSNSSNLKQHIRLIHL 116 (147)
Q Consensus 48 ~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~---~------~~~~~~~l~~H~~~~~~ 116 (147)
|.||. |...+.....|..|....++. +.|..|- + ..-.+..|+.|...-..
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~------------------~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~ 213 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF------------------VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLE 213 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc------------------EEhHhhhcCcccCccceeeeecccccccccCCcc
Confidence 66864 666666666788888655532 2355443 2 23346677777765444
Q ss_pred CCccc----CCCchhccCChHHHHhHHHhhhcc
Q psy8937 117 PGILF----CPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 117 ~~~~~----C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
+.-|+ |..|.+.|.....|.+|+|..|..
T Consensus 214 e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~HE~ 246 (493)
T COG5236 214 EEGFKGHPLCIFCKIYFYDDDELRRHCRLRHEA 246 (493)
T ss_pred ccCcCCCchhhhccceecChHHHHHHHHhhhhh
Confidence 43343 899999999999999999988763
No 74
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=92.28 E-value=0.075 Score=33.43 Aligned_cols=36 Identities=14% Similarity=0.392 Sum_probs=28.6
Q ss_pred CccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcC
Q psy8937 15 HSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 59 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 59 (147)
.+..-|.|+.|+..|+...++. ..|.|+.||.....
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 3456799999999998887763 36999999987643
No 75
>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=92.22 E-value=0.3 Score=28.01 Aligned_cols=54 Identities=22% Similarity=0.338 Sum_probs=39.8
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCC------------------------------------------CcCC----
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPG------------------------------------------ILFC---- 50 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~------------------------------------------~~~C---- 50 (147)
-+..+|..|+.+... +.+..|++..|... .|.|
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~ 87 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDP 87 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCC
Confidence 456789999987766 77888888544321 1678
Q ss_pred CCchhhhcChHHHHHHHhhhc
Q psy8937 51 PLCQKCFKNKLYLRRHVGTYT 71 (147)
Q Consensus 51 ~~C~~~f~~~~~l~~H~~~~~ 71 (147)
+.|+..+.+...|..|.+..+
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhc
Confidence 889888888888998886544
No 76
>PHA00626 hypothetical protein
Probab=91.96 E-value=0.046 Score=27.04 Aligned_cols=36 Identities=14% Similarity=0.201 Sum_probs=21.4
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChH
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKL 133 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 133 (147)
.|+.|+..-........ .....|+|+.||+.|+...
T Consensus 2 ~CP~CGS~~Ivrcg~cr-----~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR-----GWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeeceec-----ccCcceEcCCCCCeechhh
Confidence 37777764322322111 1246799999999988653
No 77
>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=91.35 E-value=0.21 Score=20.75 Aligned_cols=20 Identities=20% Similarity=0.551 Sum_probs=14.2
Q ss_pred ccCCCchhccCChHHHHhHHH
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~ 140 (147)
..||+|++.+ ....+..|+-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3588888887 5567777764
No 78
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.90 E-value=0.12 Score=23.05 Aligned_cols=25 Identities=24% Similarity=0.628 Sum_probs=16.9
Q ss_pred cccccccccccCChHHHHHHHHHhcCCCCcCCCCchh
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQK 55 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 55 (147)
.|+|..||..+... ..|..|+.|+.
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 47888888765432 14568888874
No 79
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.67 E-value=0.023 Score=34.80 Aligned_cols=44 Identities=16% Similarity=0.202 Sum_probs=23.2
Q ss_pred ccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHH
Q psy8937 20 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYL 63 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 63 (147)
+.|+.||..+.....-..--......+.++|+.||+.|.....+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERV 44 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEec
Confidence 46889987653322211100000112347899999998765443
No 80
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.57 E-value=0.2 Score=25.16 Aligned_cols=33 Identities=21% Similarity=0.305 Sum_probs=21.8
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQK 127 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~ 127 (147)
..|.|+.||........ +--....+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhh-----hHHHcCCceECCCcCc
Confidence 45679999966554433 1223357899999984
No 81
>KOG4173|consensus
Probab=90.26 E-value=0.23 Score=31.71 Aligned_cols=52 Identities=21% Similarity=0.619 Sum_probs=42.3
Q ss_pred CCccccc--ccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHHhhhc
Q psy8937 90 DARYCKI--CGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVISFHE 144 (147)
Q Consensus 90 ~~~~C~~--c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (147)
..+.|+. |-..|.+......|...-++. .|++|.+.|.+...|..|+..-|.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HD 131 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHD 131 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHH
Confidence 4566765 778888888888888776664 699999999999999999987664
No 82
>KOG2186|consensus
Probab=90.22 E-value=0.13 Score=33.92 Aligned_cols=49 Identities=22% Similarity=0.530 Sum_probs=32.6
Q ss_pred cCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHh
Q psy8937 48 LFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIH 115 (147)
Q Consensus 48 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~ 115 (147)
|.|.+||.+..-.. +.+|+...++ ..|.|..|+..|.. ..+..|...-.
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-----------------~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-----------------AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-----------------CeeEEeeccccccc-chhhhhhhhcc
Confidence 67888887776554 6678765553 23568888888877 55666665433
No 83
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=90.17 E-value=0.24 Score=24.09 Aligned_cols=22 Identities=32% Similarity=0.529 Sum_probs=13.2
Q ss_pred ccCCCchhccCCh-----HHHHhHHHh
Q psy8937 120 LFCPLCQKCFKNK-----LYLRRHVIS 141 (147)
Q Consensus 120 ~~C~~C~~~f~~~-----~~l~~H~~~ 141 (147)
..|..|++.++.. +.|.+|+..
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 4466666666544 467777763
No 84
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=90.17 E-value=0.051 Score=26.64 Aligned_cols=30 Identities=20% Similarity=0.558 Sum_probs=20.9
Q ss_pred cccccccccccCChHHHHHHHHHhcCCCCcCCCCchh
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQK 55 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 55 (147)
.|.|..||..|.....+. ......|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~-------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMS-------DDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecC-------CCCCCCCCCCCC
Confidence 478999999887653321 134567999986
No 85
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.01 E-value=0.2 Score=31.11 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=19.2
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCch
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQ 54 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~ 54 (147)
+.|+|++||.. +-+..|-+||+||
T Consensus 133 ~~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred CEEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 47999999875 3456788999998
No 86
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.80 E-value=0.15 Score=23.00 Aligned_cols=32 Identities=19% Similarity=0.374 Sum_probs=23.3
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhcc
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 129 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 129 (147)
.|+.|+..|....... -......+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHC-----CCCCcEEECCCCCCEe
Confidence 5899999988877632 2334568899999876
No 87
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.74 E-value=0.13 Score=23.36 Aligned_cols=34 Identities=15% Similarity=0.303 Sum_probs=23.2
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccC
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 130 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 130 (147)
+.|+.|+..|........ .......|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEEE
Confidence 359999998887765321 2223588999998774
No 88
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.65 E-value=0.17 Score=22.94 Aligned_cols=33 Identities=21% Similarity=0.496 Sum_probs=23.5
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhccC
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 130 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 130 (147)
.|+.|+..|....+- ...+....+|+.|+-.|.
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 589999988887652 123345688999997774
No 89
>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=89.65 E-value=0.16 Score=31.36 Aligned_cols=35 Identities=11% Similarity=0.201 Sum_probs=27.7
Q ss_pred CcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCC
Q psy8937 88 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 131 (147)
Q Consensus 88 ~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 131 (147)
+...|.|+.|+..|+...++. ..|.|+.||.....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 446688999999999988874 26999999976543
No 90
>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=89.60 E-value=0.054 Score=25.02 Aligned_cols=31 Identities=19% Similarity=0.473 Sum_probs=21.4
Q ss_pred cccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
.|.|..||..|.....+ .......|+.||..
T Consensus 5 ~y~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI-------SDDPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEec-------CCCCCCCCCCCCCc
Confidence 47899999988654432 11456679999863
No 91
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.54 E-value=0.16 Score=24.04 Aligned_cols=29 Identities=17% Similarity=0.388 Sum_probs=21.0
Q ss_pred cccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
.|.|..||..|... ...+..|+.||....
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCceEE
Confidence 48899999987643 345678999986544
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=89.40 E-value=0.051 Score=35.26 Aligned_cols=13 Identities=23% Similarity=0.445 Sum_probs=9.3
Q ss_pred cccccccccCCCh
Q psy8937 92 RYCKICGKHYSNS 104 (147)
Q Consensus 92 ~~C~~c~~~~~~~ 104 (147)
+.|+.||.++...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 4599999876543
No 93
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=89.04 E-value=0.13 Score=33.97 Aligned_cols=84 Identities=19% Similarity=0.233 Sum_probs=44.8
Q ss_pred cCCCCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHH-------HHHHHHH-
Q psy8937 43 HLPGILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNL-------KQHIRLI- 114 (147)
Q Consensus 43 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l-------~~H~~~~- 114 (147)
|+++.|+|..|..- .-+..--.|+.+.... +...|+|..|++.-.. +-| ..|++.-
T Consensus 138 hGGrif~CsfC~~f-lCEDDQFEHQAsCQvL--------------e~E~~KC~SCNrlGq~-sCLRCK~cfCddHvrrKg 201 (314)
T PF06524_consen 138 HGGRIFKCSFCDNF-LCEDDQFEHQASCQVL--------------ESETFKCQSCNRLGQY-SCLRCKICFCDDHVRRKG 201 (314)
T ss_pred CCCeEEEeecCCCe-eeccchhhhhhhhhhh--------------hcccccccccccccch-hhhheeeeehhhhhhhcc
Confidence 44566777777643 3333333455433221 2334566666653221 111 2344431
Q ss_pred ---hCCCcccCCCchhccCChHHHHhHHHhh
Q psy8937 115 ---HLPGILFCPLCQKCFKNKLYLRRHVISF 142 (147)
Q Consensus 115 ---~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 142 (147)
...+++.|+.|+.....-..|..-.|+|
T Consensus 202 ~ky~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 202 FKYEKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred cccccCCCCCCCCCCCcccccccceeeeecc
Confidence 2347899999998887777766555544
No 94
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.90 E-value=0.19 Score=30.61 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=27.6
Q ss_pred CccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 15 HSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
.+...|.|+.|+..|.....+..- . ....|.|+.||....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~---d-~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLL---D-MDGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhc---C-CCCcEECCCCCCEEE
Confidence 345689999999999865544321 1 234499999998764
No 95
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=88.79 E-value=0.19 Score=29.76 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=18.1
Q ss_pred ccCCCchhccCChHHHHhHHHhhhcc
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
..|-++|+.|. +|.+|+.+|+|=
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCC
Confidence 55888888887 678888888763
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.52 E-value=0.21 Score=31.43 Aligned_cols=35 Identities=14% Similarity=0.399 Sum_probs=27.3
Q ss_pred CcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCC
Q psy8937 88 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 131 (147)
Q Consensus 88 ~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 131 (147)
....|.|+.|+..|+...++. ..|.|+.||-....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 345688999999999887753 36999999976654
No 97
>KOG2482|consensus
Probab=88.12 E-value=1.5 Score=30.43 Aligned_cols=50 Identities=28% Similarity=0.499 Sum_probs=37.6
Q ss_pred ccccccccC-CChHHHHHHHHHHhCC----------------------CcccCCCchhccCChHHHHhHHHhh
Q psy8937 93 YCKICGKHY-SNSSNLKQHIRLIHLP----------------------GILFCPLCQKCFKNKLYLRRHVISF 142 (147)
Q Consensus 93 ~C~~c~~~~-~~~~~l~~H~~~~~~~----------------------~~~~C~~C~~~f~~~~~l~~H~~~~ 142 (147)
.|-.|+..+ ..++.+..|+-..++- ..+.|-.|.+.|..+..|+.|||..
T Consensus 146 qClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 146 QCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred EEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhc
Confidence 588888544 4677777777544321 2377999999999999999999864
No 98
>KOG2893|consensus
Probab=88.01 E-value=0.11 Score=33.84 Aligned_cols=46 Identities=26% Similarity=0.496 Sum_probs=35.1
Q ss_pred CCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHh
Q psy8937 50 CPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIH 115 (147)
Q Consensus 50 C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~ 115 (147)
|=.|.+.|..+.-|..|+. .|-|+|.+|.+.+-+...|..|--..+
T Consensus 13 cwycnrefddekiliqhqk--------------------akhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK--------------------AKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhh--------------------hccceeeeehhhhccCCCceeehhhhh
Confidence 6678999999999999983 355789999988877766666654433
No 99
>KOG4727|consensus
Probab=87.65 E-value=0.36 Score=29.86 Aligned_cols=34 Identities=29% Similarity=0.483 Sum_probs=27.3
Q ss_pred CCCCCCccCccCcccccccccccCChHHHHHHHH
Q psy8937 7 VPGGSKPLHSLDARYCKICGKHYSNSSNLKQHIR 40 (147)
Q Consensus 7 ~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 40 (147)
|.....+.+....|.|++|+-+|....++..|++
T Consensus 63 vitk~tp~sq~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 63 VITKSTPRSQKGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred EeccCCcccccCceeeeecceeehhhHHHHHHhc
Confidence 3444555566789999999999999999988876
No 100
>KOG2186|consensus
Probab=87.63 E-value=0.3 Score=32.22 Aligned_cols=47 Identities=19% Similarity=0.480 Sum_probs=36.6
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCChHHHHhHHH
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
.|.|..||....- ..+..|+..-++ .-|.|-.|++.|.+ .++..|..
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 3679999988654 456679888777 56999999999998 56677754
No 101
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.29 E-value=0.073 Score=25.42 Aligned_cols=31 Identities=19% Similarity=0.366 Sum_probs=21.1
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
..|.|+.||..|...... ....|+.||..+.
T Consensus 2 ~~y~C~~CG~~~~~~~~~----------~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEYG----------TGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCCC----------CceECCCCCCeEE
Confidence 368899999977553221 1578999987654
No 102
>KOG4167|consensus
Probab=87.19 E-value=0.15 Score=38.64 Aligned_cols=25 Identities=24% Similarity=0.362 Sum_probs=23.2
Q ss_pred cccCCCchhccCChHHHHhHHHhhh
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVISFH 143 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h 143 (147)
.|.|.+|++.|-...++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4889999999999999999999985
No 103
>PF12907 zf-met2: Zinc-binding
Probab=86.88 E-value=0.61 Score=21.61 Aligned_cols=26 Identities=23% Similarity=0.513 Sum_probs=13.5
Q ss_pred ccCCCch---hccCChHHHHhHHHhhhcc
Q psy8937 120 LFCPLCQ---KCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 120 ~~C~~C~---~~f~~~~~l~~H~~~~h~~ 145 (147)
+.|.+|. ........|..|....|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 4566666 2333445566666555544
No 104
>KOG2231|consensus
Probab=86.80 E-value=2 Score=32.73 Aligned_cols=84 Identities=24% Similarity=0.521 Sum_probs=52.4
Q ss_pred HHHHHHHHHhcC-CC----CcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccc------cccC
Q psy8937 33 SNLKQHIRLIHL-PG----ILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKIC------GKHY 101 (147)
Q Consensus 33 ~~l~~h~~~~~~-~~----~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c------~~~~ 101 (147)
..|..|+...-. .. --.|..|...|.....|.+|++..+ |.|..| +.-|
T Consensus 163 ~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h--------------------~~chfC~~~~~~neyy 222 (669)
T KOG2231|consen 163 AELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH--------------------EFCHFCDYKTGQNEYY 222 (669)
T ss_pred HHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce--------------------eheeecCcccccchhc
Confidence 456666653222 11 1468999999999999999996444 346666 3566
Q ss_pred CChHHHHHHHHHHhCCCcccCC--Cch-hccCChHHHHhHHH
Q psy8937 102 SNSSNLKQHIRLIHLPGILFCP--LCQ-KCFKNKLYLRRHVI 140 (147)
Q Consensus 102 ~~~~~l~~H~~~~~~~~~~~C~--~C~-~~f~~~~~l~~H~~ 140 (147)
.....|..|.+.++ |.|. .|. +.|.....+..+++
T Consensus 223 ~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 223 NDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred ccchHHHHHhhhcC----ccccccccccceeeehhHHHHHHH
Confidence 77888999888655 5565 454 33333334444444
No 105
>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=86.34 E-value=0.35 Score=28.46 Aligned_cols=30 Identities=17% Similarity=0.326 Sum_probs=23.8
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
..|+.|+..|.... ..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYDLn-----------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLN-----------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccC-----------CCCccCCCcCCccCcc
Confidence 46999999987653 3688999999988665
No 106
>KOG2785|consensus
Probab=85.82 E-value=0.98 Score=31.76 Aligned_cols=55 Identities=20% Similarity=0.288 Sum_probs=44.7
Q ss_pred CcccccccccccCChHHHHHHHHHhcCC-CC----------------------cCCCCch---hhhcChHHHHHHHhhhc
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLP-GI----------------------LFCPLCQ---KCFKNKLYLRRHVGTYT 71 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~-~~----------------------~~C~~C~---~~f~~~~~l~~H~~~~~ 71 (147)
.|=-|-.|++.+.....-..||..+|+- .| +.|-.|. +.|.+....+.||....
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~ 244 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKG 244 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhcc
Confidence 4567999999999999999999988874 22 5677777 99999999999997554
Q ss_pred C
Q psy8937 72 H 72 (147)
Q Consensus 72 ~ 72 (147)
+
T Consensus 245 H 245 (390)
T KOG2785|consen 245 H 245 (390)
T ss_pred C
Confidence 3
No 107
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.11 E-value=0.57 Score=23.63 Aligned_cols=33 Identities=18% Similarity=0.343 Sum_probs=20.8
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQK 127 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~ 127 (147)
..|.|+.||.....+.. +--....+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~-----~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE-----KCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeech-----hHHhcCCceECCCCCC
Confidence 45679999876333321 1123346899999985
No 108
>COG2879 Uncharacterized small protein [Function unknown]
Probab=84.15 E-value=1.3 Score=22.62 Aligned_cols=19 Identities=11% Similarity=0.037 Sum_probs=14.9
Q ss_pred cCChHHHHhHHHhhhccCC
Q psy8937 129 FKNKLYLRRHVISFHENAT 147 (147)
Q Consensus 129 f~~~~~l~~H~~~~h~~~~ 147 (147)
......+..||+.+|+++|
T Consensus 22 vpdYdnYVehmr~~hPd~p 40 (65)
T COG2879 22 VPDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CCcHHHHHHHHHHhCcCCC
Confidence 3456778899999998876
No 109
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=83.69 E-value=0.66 Score=27.53 Aligned_cols=30 Identities=30% Similarity=0.704 Sum_probs=20.6
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCch-hccC
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQ-KCFK 130 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~-~~f~ 130 (147)
|++|..|++.|...+.- +. -.|+.|| +.|.
T Consensus 1 PH~Ct~Cg~~f~dgs~e---il-------~GCP~CGg~kF~ 31 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKE---IL-------SGCPECGGNKFQ 31 (131)
T ss_pred CcccCcCCCCcCCCcHH---HH-------ccCcccCCcceE
Confidence 46799999999987631 11 2488898 4444
No 110
>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=82.87 E-value=0.99 Score=26.99 Aligned_cols=27 Identities=37% Similarity=0.629 Sum_probs=16.1
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCC
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLP 45 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~ 45 (147)
..+..+|-+||+.|.. |.+|++.||+-
T Consensus 69 ~~d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 69 TPDYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -SS-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred ccCeeEEccCCcccch---HHHHHHHccCC
Confidence 4567789999998876 47888877654
No 111
>KOG2593|consensus
Probab=82.68 E-value=0.67 Score=33.11 Aligned_cols=43 Identities=19% Similarity=0.366 Sum_probs=30.9
Q ss_pred CccCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhh
Q psy8937 12 KPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 57 (147)
Q Consensus 12 ~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f 57 (147)
+..++...|.|+.|.+.|.....++.- -.....|.|..|+...
T Consensus 121 ~d~t~~~~Y~Cp~C~kkyt~Lea~~L~---~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 121 RDDTNVAGYVCPNCQKKYTSLEALQLL---DNETGEFHCENCGGEL 163 (436)
T ss_pred hhccccccccCCccccchhhhHHHHhh---cccCceEEEecCCCch
Confidence 344567889999999999877666532 3334578899888664
No 112
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.07 E-value=0.53 Score=22.85 Aligned_cols=31 Identities=19% Similarity=0.422 Sum_probs=21.1
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 57 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f 57 (147)
...|.|..||+.|.. -.......|+.||...
T Consensus 4 ~~~Y~C~~Cg~~~~~----------~~~~~~irCp~Cg~rI 34 (49)
T COG1996 4 MMEYKCARCGREVEL----------DQETRGIRCPYCGSRI 34 (49)
T ss_pred eEEEEhhhcCCeeeh----------hhccCceeCCCCCcEE
Confidence 457999999998822 1223457899998654
No 113
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=81.69 E-value=2.7 Score=28.93 Aligned_cols=91 Identities=16% Similarity=0.265 Sum_probs=43.1
Q ss_pred CCcCCCCchhhhcChHHHHHHHhhhcCCCCccCCCCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCc
Q psy8937 46 GILFCPLCQKCFKNKLYLRRHVGTYTHTPSYRSVPGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLC 125 (147)
Q Consensus 46 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C 125 (147)
.|..||.|.-.......|.+-..--...+++...+....+. .--|-.|--.|+-...-.. ..-.....|.|+.|
T Consensus 321 LPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~k----s~~Cf~CQ~~fp~~~~~~~--~~~~ss~rY~Ce~C 394 (421)
T COG5151 321 LPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPK----STHCFVCQGPFPKPPVSPF--DESTSSGRYQCELC 394 (421)
T ss_pred CCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCC----CccceeccCCCCCCCCCcc--cccccccceechhh
Confidence 46778888766665555654431112233443333222211 1124445444433211000 00112234778888
Q ss_pred hhccCChHHHHhHHHhh
Q psy8937 126 QKCFKNKLYLRRHVISF 142 (147)
Q Consensus 126 ~~~f~~~~~l~~H~~~~ 142 (147)
...|-..-+.-.|-..|
T Consensus 395 K~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 395 KSTFCSDCDVFIHETLH 411 (421)
T ss_pred hhhhhhhhHHHHHHHHh
Confidence 87777776666665443
No 114
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=81.27 E-value=0.39 Score=23.54 Aligned_cols=22 Identities=23% Similarity=0.338 Sum_probs=8.7
Q ss_pred CCcCCCCchhhhcChHHHHHHH
Q psy8937 46 GILFCPLCQKCFKNKLYLRRHV 67 (147)
Q Consensus 46 ~~~~C~~C~~~f~~~~~l~~H~ 67 (147)
..|.|+.|+..|-..=++-.|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTT
T ss_pred CeEECCCCCCccccCcChhhhc
Confidence 3455555555555555554444
No 115
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=81.24 E-value=1.1 Score=21.77 Aligned_cols=39 Identities=18% Similarity=0.364 Sum_probs=26.8
Q ss_pred cCcccccccccccCChHHHHHHHHHhcC-CCCcCCCCchh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHL-PGILFCPLCQK 55 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~-~~~~~C~~C~~ 55 (147)
++.++|..||..|.....-+.......- ..|-.|+.|-.
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHH
Confidence 4678999999988877766655554222 24677887754
No 116
>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=81.19 E-value=0.76 Score=19.06 Aligned_cols=10 Identities=50% Similarity=1.251 Sum_probs=6.7
Q ss_pred cCCCchhccC
Q psy8937 121 FCPLCQKCFK 130 (147)
Q Consensus 121 ~C~~C~~~f~ 130 (147)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4777777664
No 117
>KOG3408|consensus
Probab=81.08 E-value=1.4 Score=25.79 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=21.8
Q ss_pred ccCcccccccccccCChHHHHHHHHH
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
+...|.|-.|.+.|.+...|..|.+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 55678899999999999999888774
No 118
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=80.15 E-value=0.71 Score=18.77 Aligned_cols=8 Identities=38% Similarity=0.924 Sum_probs=4.9
Q ss_pred cccCCCch
Q psy8937 119 ILFCPLCQ 126 (147)
Q Consensus 119 ~~~C~~C~ 126 (147)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 46666665
No 119
>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=78.19 E-value=1.5 Score=19.23 Aligned_cols=27 Identities=22% Similarity=0.487 Sum_probs=14.7
Q ss_pred ccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhh
Q psy8937 20 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 57 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f 57 (147)
|.|..|+..+.. ....+..|+.||...
T Consensus 1 Y~C~~Cg~~~~~-----------~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVEL-----------KPGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-B-----------STSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEc-----------CCCCcEECCcCCCeE
Confidence 567777776541 123456788777543
No 120
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=77.14 E-value=4.1 Score=28.60 Aligned_cols=25 Identities=28% Similarity=0.661 Sum_probs=21.5
Q ss_pred cCcccccccccccCChHHHHHHHHH
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
-..+.|..|++-|.....+..|...
T Consensus 236 ~~~~YC~~C~r~f~~~~VFe~Hl~g 260 (470)
T COG5188 236 FPKVYCVKCGREFSRSKVFEYHLEG 260 (470)
T ss_pred ccceeeHhhhhHhhhhHHHHHHHhh
Confidence 4678899999999999999988764
No 121
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=76.77 E-value=1.8 Score=24.42 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=18.2
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCch
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQ 126 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~ 126 (147)
++.|..||..|...+.... -.|+.||
T Consensus 2 pH~CtrCG~vf~~g~~~il----------~GCp~CG 27 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEIL----------SGCPKCG 27 (112)
T ss_pred CceecccccccccccHHHH----------ccCcccc
Confidence 4569999999998644321 2488887
No 122
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.02 E-value=1.5 Score=23.99 Aligned_cols=33 Identities=27% Similarity=0.610 Sum_probs=22.6
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
..|.|+.|++. ... + .+...+.|..|+..|.-.
T Consensus 34 ~~~~Cp~C~~~-~Vk-------R--~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT-TVK-------R--IATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc-cee-------e--eccCeEEcCCCCCeeccc
Confidence 34679999876 221 1 334579999999998754
No 123
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=75.29 E-value=1.1 Score=17.96 Aligned_cols=6 Identities=50% Similarity=1.481 Sum_probs=2.8
Q ss_pred CCCchh
Q psy8937 122 CPLCQK 127 (147)
Q Consensus 122 C~~C~~ 127 (147)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444543
No 124
>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=74.36 E-value=0.91 Score=19.57 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=5.7
Q ss_pred cCCCCcCCCCch
Q psy8937 43 HLPGILFCPLCQ 54 (147)
Q Consensus 43 ~~~~~~~C~~C~ 54 (147)
.+...+.|+.|+
T Consensus 15 ~D~~~~vCp~C~ 26 (30)
T PF08274_consen 15 EDGELLVCPECG 26 (30)
T ss_dssp E-SSSEEETTTT
T ss_pred ccCCEEeCCccc
Confidence 334455555554
No 125
>PF14353 CpXC: CpXC protein
Probab=73.77 E-value=3.5 Score=24.35 Aligned_cols=41 Identities=24% Similarity=0.444 Sum_probs=23.5
Q ss_pred ccccccccCCC----------hHHHHHHHHHHhCCCcccCCCchhccCChHH
Q psy8937 93 YCKICGKHYSN----------SSNLKQHIRLIHLPGILFCPLCQKCFKNKLY 134 (147)
Q Consensus 93 ~C~~c~~~~~~----------~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~ 134 (147)
.|+.|+..|.. ...++.-+. ...-..|.|+.||..|.-...
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il-~g~l~~~~CP~Cg~~~~~~~p 53 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKIL-DGSLFSFTCPSCGHKFRLEYP 53 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHH-cCCcCEEECCCCCCceecCCC
Confidence 58888876642 223333222 122235889999988875433
No 126
>KOG3408|consensus
Probab=72.94 E-value=2.5 Score=24.73 Aligned_cols=22 Identities=27% Similarity=0.711 Sum_probs=11.7
Q ss_pred CcccccccccCCChHHHHHHHH
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIR 112 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~ 112 (147)
-|-|..|.+-|.+...|..|.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHh
Confidence 3445555555555555555543
No 127
>KOG4167|consensus
Probab=72.70 E-value=1.9 Score=33.18 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=23.3
Q ss_pred cCcccccccccccCChHHHHHHHHHhcC
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHL 44 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 44 (147)
..-|.|..|++.|..+..+..||..|.-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 4568899999999999999999986653
No 128
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=72.57 E-value=2.3 Score=26.79 Aligned_cols=35 Identities=20% Similarity=0.428 Sum_probs=25.4
Q ss_pred CccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 15 HSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
.+..-|.|+.|...|+...++.. .|.||.||....
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~~---------~F~Cp~Cg~~L~ 143 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAMEL---------GFTCPKCGEDLE 143 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHHh---------CCCCCCCCchhh
Confidence 35667899999998877655431 289999997754
No 129
>PRK04023 DNA polymerase II large subunit; Validated
Probab=71.34 E-value=4.3 Score=32.65 Aligned_cols=11 Identities=45% Similarity=0.996 Sum_probs=6.3
Q ss_pred Ccccccccccc
Q psy8937 18 DARYCKICGKH 28 (147)
Q Consensus 18 ~~~~C~~C~~~ 28 (147)
....|+.||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 44556666664
No 130
>KOG1842|consensus
Probab=71.23 E-value=4.3 Score=29.43 Aligned_cols=29 Identities=31% Similarity=0.565 Sum_probs=26.2
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCC
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLP 45 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~ 45 (147)
.+.|.|++|...|.+...|..|...-|..
T Consensus 13 ~egflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 13 LEGFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred hhcccCchHhhhhhhHHHHHHHHhhhccc
Confidence 47899999999999999999999887765
No 131
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=71.03 E-value=0.87 Score=24.12 Aligned_cols=39 Identities=13% Similarity=0.180 Sum_probs=22.6
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCC--CchhccCCh
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCP--LCQKCFKNK 132 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~--~C~~~f~~~ 132 (147)
+.|+.|+..-.....-...-. ..+.-++|. .||..|...
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCCEEEEE
Confidence 458888865433322222111 345567887 899888754
No 132
>PF15269 zf-C2H2_7: Zinc-finger
Probab=70.94 E-value=3.2 Score=19.62 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=9.9
Q ss_pred cccccccccCCChHHHHHHH
Q psy8937 92 RYCKICGKHYSNSSNLKQHI 111 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~ 111 (147)
|+|-+|.......+.|-.|+
T Consensus 21 ykcfqcpftc~~kshl~nhm 40 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHM 40 (54)
T ss_pred ceeecCCcccchHHHHHHHH
Confidence 34555555555555554443
No 133
>KOG1280|consensus
Probab=70.85 E-value=4 Score=28.54 Aligned_cols=47 Identities=21% Similarity=0.405 Sum_probs=31.3
Q ss_pred CCCCCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCc--ccCCCch
Q psy8937 80 PGASKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGI--LFCPLCQ 126 (147)
Q Consensus 80 ~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~--~~C~~C~ 126 (147)
.++.-...-..-|.|+.|+..-.+...+..|....+.+-. ..|++|+
T Consensus 68 ~Ge~i~~y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 68 GGEPISHYDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cCccccccccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3334444445578899998888888888888877665543 3356665
No 134
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=70.30 E-value=0.51 Score=35.93 Aligned_cols=46 Identities=26% Similarity=0.584 Sum_probs=29.6
Q ss_pred ccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHHHHHH
Q psy8937 22 CKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYLRRHV 67 (147)
Q Consensus 22 C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 67 (147)
|..||..|+-...|-.-+.......--.|+.|.+.|....+-+-|-
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHA 171 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHA 171 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcccccccc
Confidence 8888888877776654443222233345889988888877755443
No 135
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=70.28 E-value=5.7 Score=18.41 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=5.2
Q ss_pred ccccccccCC
Q psy8937 93 YCKICGKHYS 102 (147)
Q Consensus 93 ~C~~c~~~~~ 102 (147)
.|+.||..|.
T Consensus 15 ~C~~CgM~Y~ 24 (41)
T PF13878_consen 15 TCPTCGMLYS 24 (41)
T ss_pred CCCCCCCEEC
Confidence 4555555443
No 136
>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=68.89 E-value=2 Score=27.98 Aligned_cols=30 Identities=27% Similarity=0.509 Sum_probs=23.2
Q ss_pred CcCCcccccccccCCChHHHHHHHHHHhCC
Q psy8937 88 SLDARYCKICGKHYSNSSNLKQHIRLIHLP 117 (147)
Q Consensus 88 ~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~ 117 (147)
.+..|.|..|++.|.-..-+..|+..-|.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 445689999999999999999999887755
No 137
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=68.31 E-value=0.95 Score=22.66 Aligned_cols=40 Identities=18% Similarity=0.378 Sum_probs=24.4
Q ss_pred ccccc--ccccCCChHHHHHHHHHHhCCCcccCCC----chhccCCh
Q psy8937 92 RYCKI--CGKHYSNSSNLKQHIRLIHLPGILFCPL----CQKCFKNK 132 (147)
Q Consensus 92 ~~C~~--c~~~~~~~~~l~~H~~~~~~~~~~~C~~----C~~~f~~~ 132 (147)
..|+. |...+ ....|..|+...-..++..|+. |+..+...
T Consensus 10 v~C~~~cc~~~i-~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 10 VPCPNGCCNEMI-PRKELDDHLENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp EE-TT--S-BEE-ECCCHHHHHHTTSTTSEEE-SS----S--EEEHH
T ss_pred eeCCCCCcccce-eHHHHHHHHHccCCCCcEECCCCCCCCCCccchh
Confidence 35766 44433 3667889988767777888998 98877644
No 138
>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=68.20 E-value=0.54 Score=28.50 Aligned_cols=43 Identities=14% Similarity=0.179 Sum_probs=23.1
Q ss_pred cccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHH
Q psy8937 21 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYL 63 (147)
Q Consensus 21 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 63 (147)
.|+.|+..-...-.-+.-.........-.|..|++.|++...+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERA 44 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeec
Confidence 5788877544332221111111122456799999888776544
No 139
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=68.17 E-value=0.74 Score=28.01 Aligned_cols=42 Identities=14% Similarity=0.201 Sum_probs=22.2
Q ss_pred cccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHH
Q psy8937 21 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLY 62 (147)
Q Consensus 21 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~ 62 (147)
.|+.|+..-+..-+-+.--..........|+.|+..|++-..
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~ 43 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFER 43 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhhe
Confidence 577777754443322111111122245678888888876543
No 140
>KOG2593|consensus
Probab=67.24 E-value=3 Score=29.99 Aligned_cols=39 Identities=23% Similarity=0.473 Sum_probs=25.3
Q ss_pred CcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhcc
Q psy8937 88 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 129 (147)
Q Consensus 88 ~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 129 (147)
...-|.|+.|.+.|.....++. .....-.|.|..|+-..
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccCCccccchhhhHHHHh---hcccCceEEEecCCCch
Confidence 3355788888888877766543 23334468888887443
No 141
>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=67.06 E-value=2.5 Score=21.88 Aligned_cols=33 Identities=27% Similarity=0.516 Sum_probs=14.7
Q ss_pred CccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcC
Q psy8937 15 HSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 59 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 59 (147)
.+...-.|..|++.|... .+.+.|..||..|-.
T Consensus 5 ~d~~~~~C~~C~~~F~~~------------~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 5 PDSEASNCMICGKKFSLF------------RRRHHCRNCGRVVCS 37 (69)
T ss_dssp SGGG-SB-TTT--B-BSS------------S-EEE-TTT--EEEC
T ss_pred CCCCCCcCcCcCCcCCCc------------eeeEccCCCCCEECC
Confidence 345567899999999541 334567777776643
No 142
>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=65.20 E-value=2.3 Score=19.77 Aligned_cols=14 Identities=21% Similarity=0.342 Sum_probs=9.9
Q ss_pred cccCCCchhccCCh
Q psy8937 119 ILFCPLCQKCFKNK 132 (147)
Q Consensus 119 ~~~C~~C~~~f~~~ 132 (147)
.|.|..||..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 5 EYRCEECGHEFEVL 18 (42)
T ss_pred EEEeCCCCCEEEEE
Confidence 37788888777643
No 143
>KOG2807|consensus
Probab=64.75 E-value=8 Score=26.95 Aligned_cols=54 Identities=19% Similarity=0.243 Sum_probs=37.7
Q ss_pred cCcccccccccccCChHHHHHHHHHhcC----------------------------CCCcCCCCchhhhcChHHHHHHHh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHL----------------------------PGILFCPLCQKCFKNKLYLRRHVG 68 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~----------------------------~~~~~C~~C~~~f~~~~~l~~H~~ 68 (147)
.-|..|++|+-.......|.+-.. |-- ...|.|..|...|...-+.-.|..
T Consensus 288 sLP~eCpiC~ltLVss~hLARSyh-hL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 288 SLPIECPICSLTLVSSPHLARSYH-HLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred cCCccCCccceeEecchHHHHHHH-hhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhh
Confidence 357889999998877777765443 110 123778889888888888878875
Q ss_pred hhc
Q psy8937 69 TYT 71 (147)
Q Consensus 69 ~~~ 71 (147)
.|.
T Consensus 367 Lh~ 369 (378)
T KOG2807|consen 367 LHN 369 (378)
T ss_pred hhc
Confidence 544
No 144
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.91 E-value=3 Score=23.94 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=21.1
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
.|+.|++.|.... ..|..|+.||+.|...
T Consensus 11 idPetg~KFYDLN-----------rdPiVsPytG~s~P~s 39 (129)
T COG4530 11 IDPETGKKFYDLN-----------RDPIVSPYTGKSYPRS 39 (129)
T ss_pred cCccccchhhccC-----------CCccccCcccccchHH
Confidence 3788888876543 3678899999988543
No 145
>KOG2636|consensus
Probab=63.04 E-value=6.2 Score=28.66 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=23.1
Q ss_pred HHHhCCCcccCCCch-hccCChHHHHhHHH
Q psy8937 112 RLIHLPGILFCPLCQ-KCFKNKLYLRRHVI 140 (147)
Q Consensus 112 ~~~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 140 (147)
+.|.-...|.|.+|| +.+..+..+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 455666779999999 88888888888864
No 146
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=62.81 E-value=6.4 Score=28.93 Aligned_cols=22 Identities=23% Similarity=0.569 Sum_probs=11.7
Q ss_pred cccccccccCCChHHHHHHHHH
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRL 113 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~ 113 (147)
|.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 4455555555555555555543
No 147
>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=62.80 E-value=2.7 Score=24.44 Aligned_cols=28 Identities=21% Similarity=0.479 Sum_probs=19.8
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
.-...|..|+..|..... .+.||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 456889999987765422 3679999854
No 148
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.35 E-value=1.8 Score=26.04 Aligned_cols=39 Identities=26% Similarity=0.499 Sum_probs=22.2
Q ss_pred CCcccccccccCCChH---HH------HHHHHHHhCCCcccCCCchhc
Q psy8937 90 DARYCKICGKHYSNSS---NL------KQHIRLIHLPGILFCPLCQKC 128 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~---~l------~~H~~~~~~~~~~~C~~C~~~ 128 (147)
..+.|..||..|.... .| ..|...-.....+.||.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4578999998887652 11 111111111344779999953
No 149
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=60.43 E-value=3.9 Score=23.74 Aligned_cols=28 Identities=18% Similarity=0.351 Sum_probs=19.0
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
.-.+.|..|+..|.... ..+.||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQ------------HDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCC------------cCccCcCCCCC
Confidence 35688999997765432 34569999843
No 150
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=60.32 E-value=7.3 Score=28.64 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=23.5
Q ss_pred cccccccccccCChHHHHHHHHHhcCC
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRLIHLP 45 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~~~~~ 45 (147)
-+.|+.|.+.|.....+..|+..-|..
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 367999999999999999999987765
No 151
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=59.29 E-value=7.3 Score=19.45 Aligned_cols=13 Identities=23% Similarity=0.278 Sum_probs=6.7
Q ss_pred CcccCCCchhccC
Q psy8937 118 GILFCPLCQKCFK 130 (147)
Q Consensus 118 ~~~~C~~C~~~f~ 130 (147)
..|.|+.||..+-
T Consensus 13 v~~~Cp~cGipth 25 (55)
T PF13824_consen 13 VNFECPDCGIPTH 25 (55)
T ss_pred cCCcCCCCCCcCc
Confidence 3455666654443
No 152
>KOG0978|consensus
Probab=59.02 E-value=5 Score=30.96 Aligned_cols=47 Identities=17% Similarity=0.366 Sum_probs=27.4
Q ss_pred cccccccccCCChHH-------HHHHHHHHhCCCcccCCCchhccCChHHHHhH
Q psy8937 92 RYCKICGKHYSNSSN-------LKQHIRLIHLPGILFCPLCQKCFKNKLYLRRH 138 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~-------l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H 138 (147)
.+|+.|+..+...-- ...-++.-...+.-+||.|+..|....-+..|
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 358888754433211 11122333345567899999999877655443
No 153
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=58.87 E-value=3.8 Score=22.73 Aligned_cols=33 Identities=30% Similarity=0.660 Sum_probs=21.2
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
..|.|+.|++.-... .+...+.|..|++.|.-.
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR----------QAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCceee----------eeeEEEEcCCCCCEEeCC
Confidence 346799997542211 123468899999888754
No 154
>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 PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=58.28 E-value=2.7 Score=19.37 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=13.3
Q ss_pred CCcCCCCchhhhcChHHHHH
Q psy8937 46 GILFCPLCQKCFKNKLYLRR 65 (147)
Q Consensus 46 ~~~~C~~C~~~f~~~~~l~~ 65 (147)
....|+.|+..+-....|.+
T Consensus 18 ~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEECCCCCeEEccHHHHHH
Confidence 45567777777776666654
No 156
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.07 E-value=1.9 Score=28.33 Aligned_cols=41 Identities=20% Similarity=0.481 Sum_probs=27.7
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCC----------CC-----cCCCCchhh
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLP----------GI-----LFCPLCQKC 56 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~----------~~-----~~C~~C~~~ 56 (147)
..+.+.|++|+..|.....+..-.++..+. .| -.||.|..+
T Consensus 16 ~kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yA 71 (267)
T COG1655 16 YKKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYA 71 (267)
T ss_pred hhceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHH
Confidence 467899999999998876555444443332 11 359999855
No 157
>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=57.75 E-value=6 Score=20.42 Aligned_cols=30 Identities=20% Similarity=0.501 Sum_probs=20.6
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
.|+.||..... ....+.|.|+.||..+..-
T Consensus 30 ~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 30 TCPRCGHRNKK----------RRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CccCccccccc----------ccccceEEcCCCCCEECcH
Confidence 38888876555 1334679999999876554
No 158
>PF14369 zf-RING_3: zinc-finger
Probab=57.57 E-value=3.6 Score=18.37 Aligned_cols=10 Identities=40% Similarity=0.982 Sum_probs=6.9
Q ss_pred CCCCchhhhc
Q psy8937 49 FCPLCQKCFK 58 (147)
Q Consensus 49 ~C~~C~~~f~ 58 (147)
.||.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4777777664
No 159
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=57.24 E-value=6.2 Score=22.51 Aligned_cols=26 Identities=23% Similarity=0.584 Sum_probs=20.1
Q ss_pred CccCcccccccccccCChHHHHHHHH
Q psy8937 15 HSLDARYCKICGKHYSNSSNLKQHIR 40 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~ 40 (147)
.+...+.|-.|.+.|.....|..|.+
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhc
Confidence 35667888888888888888877765
No 160
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=56.83 E-value=15 Score=22.10 Aligned_cols=14 Identities=29% Similarity=0.823 Sum_probs=10.0
Q ss_pred ccccccccCCChHH
Q psy8937 93 YCKICGKHYSNSSN 106 (147)
Q Consensus 93 ~C~~c~~~~~~~~~ 106 (147)
.|+.|.-+|.+++.
T Consensus 123 vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 123 VCPVCKTSFKSSSS 136 (140)
T ss_pred CCCccccccccccc
Confidence 48888888877643
No 161
>KOG4118|consensus
Probab=56.65 E-value=6.7 Score=20.23 Aligned_cols=26 Identities=15% Similarity=0.344 Sum_probs=18.3
Q ss_pred ccCCCchhccCChHHHHhHHHhhhcc
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVISFHEN 145 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (147)
|+|.+|.........+..|..+.|+.
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk 64 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPK 64 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCC
Confidence 66777777777667777777766654
No 162
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=56.48 E-value=7.9 Score=19.07 Aligned_cols=15 Identities=33% Similarity=0.736 Sum_probs=10.5
Q ss_pred ccccccccccCChHH
Q psy8937 20 RYCKICGKHYSNSSN 34 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~ 34 (147)
++|+.||..|...-.
T Consensus 29 W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN 43 (55)
T ss_pred EECCCCCCeeEccHh
Confidence 678888887765443
No 163
>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=56.06 E-value=3.6 Score=22.85 Aligned_cols=33 Identities=27% Similarity=0.545 Sum_probs=21.0
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
..|.|+.|++.-... .+.-.+.|..|++.|.-.
T Consensus 34 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTVKR----------GSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCceEE----------EeeEEEEcCCCCCEEeCC
Confidence 346799997542111 223468899999888754
No 164
>PTZ00448 hypothetical protein; Provisional
Probab=55.82 E-value=9.4 Score=27.10 Aligned_cols=23 Identities=22% Similarity=0.491 Sum_probs=19.0
Q ss_pred cccCCCchhccCChHHHHhHHHh
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVIS 141 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~ 141 (147)
.|.|..|+..|......+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57799999999888888888775
No 165
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=55.47 E-value=5.9 Score=19.05 Aligned_cols=13 Identities=15% Similarity=0.163 Sum_probs=9.1
Q ss_pred cccCCCchhccCC
Q psy8937 119 ILFCPLCQKCFKN 131 (147)
Q Consensus 119 ~~~C~~C~~~f~~ 131 (147)
.+.|+.||..+.-
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 5778888876554
No 166
>COG1773 Rubredoxin [Energy production and conversion]
Probab=54.99 E-value=4.8 Score=20.09 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=7.2
Q ss_pred cccCCCchhccC
Q psy8937 119 ILFCPLCQKCFK 130 (147)
Q Consensus 119 ~~~C~~C~~~f~ 130 (147)
.|+|.+||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 466666666553
No 167
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=54.86 E-value=5.2 Score=18.31 Aligned_cols=14 Identities=21% Similarity=0.714 Sum_probs=11.3
Q ss_pred cccccccccccCCh
Q psy8937 19 ARYCKICGKHYSNS 32 (147)
Q Consensus 19 ~~~C~~C~~~f~~~ 32 (147)
++.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999888653
No 168
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=54.62 E-value=4.7 Score=19.81 Aligned_cols=12 Identities=33% Similarity=1.027 Sum_probs=6.6
Q ss_pred cCCCchhccCCh
Q psy8937 121 FCPLCQKCFKNK 132 (147)
Q Consensus 121 ~C~~C~~~f~~~ 132 (147)
.||+|+..|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 799999998855
No 169
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=54.56 E-value=4.1 Score=26.18 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=0.0
Q ss_pred HhCCCcccCCCch-hccCChHHHHhHHH
Q psy8937 114 IHLPGILFCPLCQ-KCFKNKLYLRRHVI 140 (147)
Q Consensus 114 ~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 140 (147)
|.-.+.|.|.+|| ..|.-+..+.+|..
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ----------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 3344668899998 44555666666643
No 170
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=54.36 E-value=12 Score=17.00 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=4.7
Q ss_pred cccCCCchhccC
Q psy8937 119 ILFCPLCQKCFK 130 (147)
Q Consensus 119 ~~~C~~C~~~f~ 130 (147)
.|-|..|+..|.
T Consensus 3 ryyCdyC~~~~~ 14 (38)
T PF06220_consen 3 RYYCDYCKKYLT 14 (38)
T ss_dssp S-B-TTT--B-S
T ss_pred Ceecccccceec
Confidence 466778887773
No 171
>KOG1280|consensus
Probab=54.04 E-value=17 Score=25.57 Aligned_cols=32 Identities=28% Similarity=0.411 Sum_probs=27.5
Q ss_pred CCCcccCCCchhccCChHHHHhHHHhhhccCC
Q psy8937 116 LPGILFCPLCQKCFKNKLYLRRHVISFHENAT 147 (147)
Q Consensus 116 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (147)
.+..|.|++|+++=.....|..|+...|.+++
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~ 107 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEAS 107 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccC
Confidence 34579999999888888999999999998864
No 172
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.32 E-value=5.3 Score=23.34 Aligned_cols=29 Identities=17% Similarity=0.332 Sum_probs=19.0
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
+-.+.|..||..|..... ....||.||..
T Consensus 69 p~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNAL-----------DYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCc-----------cCCcCcCCCCC
Confidence 456889999987755321 12359999854
No 173
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=53.00 E-value=5.5 Score=19.42 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=16.3
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhcc
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 129 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 129 (147)
.|+.|+..|... | ...+.|..||..+
T Consensus 22 fCP~Cg~~~m~~-----~------~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSGFMAE-----H------LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcchhec-----c------CCcEECCCcCCEE
Confidence 488887532211 1 2468899999764
No 174
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.93 E-value=9.3 Score=27.67 Aligned_cols=30 Identities=20% Similarity=0.441 Sum_probs=21.8
Q ss_pred cccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChH
Q psy8937 21 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKL 61 (147)
Q Consensus 21 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~ 61 (147)
.|+.||.. |. ..+.+-|+|+.||..+....
T Consensus 352 ~Cp~Cg~~----------m~-S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGR----------MK-SAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCc----------hh-hcCCCCcccccccccCCccc
Confidence 69999986 33 34445899999998876554
No 175
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.79 E-value=9.3 Score=20.42 Aligned_cols=33 Identities=18% Similarity=0.436 Sum_probs=20.6
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhh
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 57 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f 57 (147)
-.|.|..|+..|. +..++ .....-.|+.|+-.+
T Consensus 11 Y~Y~c~~cg~~~d----vvq~~---~ddplt~ce~c~a~~ 43 (82)
T COG2331 11 YSYECTECGNRFD----VVQAM---TDDPLTTCEECGARL 43 (82)
T ss_pred eEEeecccchHHH----HHHhc---ccCccccChhhChHH
Confidence 3588999998753 22222 333445699998654
No 176
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.65 E-value=9 Score=19.50 Aligned_cols=41 Identities=20% Similarity=0.330 Sum_probs=24.3
Q ss_pred ccccccccc-cCChHHHHHHHHHhcCCCCcCCCCchhhhcCh
Q psy8937 20 RYCKICGKH-YSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 60 (147)
Q Consensus 20 ~~C~~C~~~-f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 60 (147)
-+|.+|++. +-....+..-........-|.|+.|......+
T Consensus 3 vkCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~k 44 (68)
T COG4896 3 VKCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAIK 44 (68)
T ss_pred ceEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhchh
Confidence 368888885 33334444433323334678999998665443
No 177
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=50.01 E-value=7.1 Score=19.57 Aligned_cols=41 Identities=15% Similarity=0.367 Sum_probs=25.0
Q ss_pred ccccccccccCChHH-H-HHHHHHhcCCCCcCCCCchhhhcChH
Q psy8937 20 RYCKICGKHYSNSSN-L-KQHIRLIHLPGILFCPLCQKCFKNKL 61 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~-l-~~h~~~~~~~~~~~C~~C~~~f~~~~ 61 (147)
-+|-+|++.+.-... + ..-++ ......|-|..|......+.
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLr-nrPi~tYmC~eC~~RI~~~t 45 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLR-NRPIHTYMCDECKERIREET 45 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhh-cCCCcceeChhHHHHHhHHH
Confidence 368899996654433 2 22333 33446789999987665443
No 178
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=49.82 E-value=5.1 Score=24.50 Aligned_cols=31 Identities=23% Similarity=0.501 Sum_probs=20.9
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
+.+.|+|..||..... .+....-.|+.|+..
T Consensus 109 g~G~l~C~~Cg~~~~~----------~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 109 GPGTLVCENCGHEVEL----------THPERLPPCPKCGHT 139 (146)
T ss_pred cCceEecccCCCEEEe----------cCCCcCCCCCCCCCC
Confidence 6678999999985321 223345579999854
No 179
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=49.64 E-value=9.4 Score=18.95 Aligned_cols=35 Identities=20% Similarity=0.268 Sum_probs=20.6
Q ss_pred CccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchh
Q psy8937 15 HSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQK 55 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 55 (147)
....+..|..|........ ..-.....|.|+.|+.
T Consensus 18 ~~r~aLIC~~C~~hNGla~------~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAP------KEEFEEIQYRCPYCGA 52 (54)
T ss_pred cCceeEECcccchhhcccc------cccCCceEEEcCCCCC
Confidence 3456788988877432221 1122335788999873
No 180
>PRK05978 hypothetical protein; Provisional
Probab=49.56 E-value=4.6 Score=24.74 Aligned_cols=17 Identities=24% Similarity=0.487 Sum_probs=9.3
Q ss_pred cCCCCchhhhcChHHHH
Q psy8937 48 LFCPLCQKCFKNKLYLR 64 (147)
Q Consensus 48 ~~C~~C~~~f~~~~~l~ 64 (147)
-+||.||+.=.....|+
T Consensus 34 grCP~CG~G~LF~g~Lk 50 (148)
T PRK05978 34 GRCPACGEGKLFRAFLK 50 (148)
T ss_pred CcCCCCCCCcccccccc
Confidence 46777776544444333
No 181
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.48 E-value=8.4 Score=22.99 Aligned_cols=35 Identities=14% Similarity=0.233 Sum_probs=20.7
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
.|+.|+........ ..-.+.+.|.|..|++.|...
T Consensus 32 ~cP~C~s~~~~k~g-----~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 32 NCPRCKSSNVVKIG-----GIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cCCCCCccceeeEC-----CccccccccccCCcCcceeee
Confidence 37777655411111 111235679999999999754
No 182
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=49.45 E-value=6.1 Score=18.29 Aligned_cols=12 Identities=33% Similarity=0.946 Sum_probs=9.6
Q ss_pred Cccccccccccc
Q psy8937 18 DARYCKICGKHY 29 (147)
Q Consensus 18 ~~~~C~~C~~~f 29 (147)
++-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 457899999876
No 183
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=49.37 E-value=18 Score=18.75 Aligned_cols=15 Identities=13% Similarity=0.146 Sum_probs=10.8
Q ss_pred HHHHhHHHhhhccCC
Q psy8937 133 LYLRRHVISFHENAT 147 (147)
Q Consensus 133 ~~l~~H~~~~h~~~~ 147 (147)
..+..|++.+|+++|
T Consensus 26 e~Yv~H~~~~HP~~p 40 (65)
T PF04328_consen 26 ERYVEHMRRHHPDEP 40 (65)
T ss_pred HHHHHHHHHHCcCCC
Confidence 455678888888764
No 184
>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=49.33 E-value=7.8 Score=21.89 Aligned_cols=15 Identities=33% Similarity=0.534 Sum_probs=12.4
Q ss_pred CCcccCCCchhccCC
Q psy8937 117 PGILFCPLCQKCFKN 131 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~ 131 (147)
.+++.|+.||..|..
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 378999999988864
No 185
>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=49.31 E-value=7.3 Score=18.21 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=9.6
Q ss_pred cCCCchhccCChH
Q psy8937 121 FCPLCQKCFKNKL 133 (147)
Q Consensus 121 ~C~~C~~~f~~~~ 133 (147)
.|.+|+..|+-+.
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 4888888887554
No 186
>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=49.30 E-value=5.1 Score=18.69 Aligned_cols=15 Identities=33% Similarity=0.421 Sum_probs=8.8
Q ss_pred CcccCCCchhccCCh
Q psy8937 118 GILFCPLCQKCFKNK 132 (147)
Q Consensus 118 ~~~~C~~C~~~f~~~ 132 (147)
-++.|+.|+..|-..
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 367888888888654
No 187
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=48.41 E-value=5.4 Score=22.15 Aligned_cols=33 Identities=24% Similarity=0.520 Sum_probs=20.3
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
..|.|+.|++.--.. .+.-.+.|..|++.|.-.
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 35 AKHVCPVCGRPKVKR----------VGTGIWECRKCGAKFAGG 67 (90)
T ss_pred cCccCCCCCCCceEE----------EEEEEEEcCCCCCEEeCC
Confidence 346788886542211 123468898898888754
No 188
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.23 E-value=3.6 Score=20.96 Aligned_cols=52 Identities=12% Similarity=0.185 Sum_probs=26.0
Q ss_pred CccCCCCCCCccCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 3 SYRSVPGGSKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
.+++..+......+..++.|+--+..|.....+. . ......-.|+.|+..|.
T Consensus 8 ~~q~~~~~~~I~~~~~~l~C~g~~~p~~HPrV~L---~-mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 8 HFQNDGGHETIEIGDLPLMCPGPEPPNDHPRVFL---D-MGDEGEVVCPYCSTRYR 59 (62)
T ss_pred cccCCCcceEEEeCCeeEEcCCCCCCCCCCEEEE---E-cCCCCcEecCccccEEE
Confidence 3444444444555667777766555433222110 0 12224456888887765
No 189
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=48.22 E-value=8.2 Score=21.42 Aligned_cols=14 Identities=21% Similarity=0.403 Sum_probs=11.3
Q ss_pred CcccCCCchhccCC
Q psy8937 118 GILFCPLCQKCFKN 131 (147)
Q Consensus 118 ~~~~C~~C~~~f~~ 131 (147)
+|-.|..||+.|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 56779999988876
No 190
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=48.18 E-value=13 Score=24.91 Aligned_cols=22 Identities=9% Similarity=0.351 Sum_probs=14.7
Q ss_pred CCCCCCcCCcccccccccCCCh
Q psy8937 83 SKPLHSLDARYCKICGKHYSNS 104 (147)
Q Consensus 83 ~~~~~~~~~~~C~~c~~~~~~~ 104 (147)
.+...|-..|.|+.|+..|.-.
T Consensus 147 ~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 147 CDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred cccccceeeeecccccccchhh
Confidence 3344466668888888888754
No 191
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=47.97 E-value=1.9 Score=19.31 Aligned_cols=10 Identities=50% Similarity=1.165 Sum_probs=4.9
Q ss_pred ccccccccCC
Q psy8937 93 YCKICGKHYS 102 (147)
Q Consensus 93 ~C~~c~~~~~ 102 (147)
.|..||..+.
T Consensus 23 sC~~CGPr~~ 32 (35)
T PF07503_consen 23 SCTNCGPRYS 32 (35)
T ss_dssp -BTTCC-SCC
T ss_pred cCCCCCCCEE
Confidence 3666765543
No 192
>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=47.05 E-value=13 Score=18.22 Aligned_cols=28 Identities=25% Similarity=0.530 Sum_probs=17.4
Q ss_pred ccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcC
Q psy8937 20 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 59 (147)
Q Consensus 20 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 59 (147)
-.|..|++.|.. ..+.+.|..||+.|-.
T Consensus 3 ~~C~~C~~~F~~------------~~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 3 SSCMGCGKPFTL------------TRRRHHCRNCGRIFCS 30 (57)
T ss_pred CcCcccCccccC------------CccccccCcCcCCcCh
Confidence 357778887764 1234567777777654
No 193
>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=46.94 E-value=2.8 Score=17.74 Aligned_cols=18 Identities=28% Similarity=0.460 Sum_probs=9.4
Q ss_pred ccCCCchhccCChHHHHhH
Q psy8937 120 LFCPLCQKCFKNKLYLRRH 138 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H 138 (147)
|.|-.|++.|. ......|
T Consensus 1 ~sCiDC~~~F~-~~~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDFD-GDSYKSH 18 (28)
T ss_dssp EEETTTTEEEE-GGGTTT-
T ss_pred CeeecCCCCcC-cCCcCCC
Confidence 34667777773 3333444
No 194
>KOG0717|consensus
Probab=46.64 E-value=12 Score=27.48 Aligned_cols=21 Identities=38% Similarity=0.839 Sum_probs=14.1
Q ss_pred ccCCCchhccCChHHHHhHHH
Q psy8937 120 LFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~ 140 (147)
+-|.+|++.|.+-..|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 457777777777766666654
No 195
>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=46.15 E-value=4.7 Score=23.39 Aligned_cols=28 Identities=21% Similarity=0.542 Sum_probs=16.4
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
+-...|..||..|...... +.||.|+..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~------------~~CP~Cgs~ 95 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFD------------FSCPRCGSP 95 (113)
T ss_dssp --EEEETTTS-EEECHHCC------------HH-SSSSSS
T ss_pred CCcEECCCCCCEEecCCCC------------CCCcCCcCC
Confidence 3457899999988664322 348888864
No 196
>PLN02294 cytochrome c oxidase subunit Vb
Probab=45.02 E-value=7.2 Score=24.41 Aligned_cols=13 Identities=31% Similarity=0.943 Sum_probs=6.6
Q ss_pred CCcCCCCchhhhc
Q psy8937 46 GILFCPLCQKCFK 58 (147)
Q Consensus 46 ~~~~C~~C~~~f~ 58 (147)
++..|+.||..|.
T Consensus 140 kp~RCpeCG~~fk 152 (174)
T PLN02294 140 KSFECPVCTQYFE 152 (174)
T ss_pred CceeCCCCCCEEE
Confidence 4445555555543
No 197
>KOG2071|consensus
Probab=44.71 E-value=17 Score=27.52 Aligned_cols=27 Identities=22% Similarity=0.551 Sum_probs=22.6
Q ss_pred cCcccccccccccCChHHHHHHHHHhc
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIH 43 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~ 43 (147)
..+..|..||..|.+......||..|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 467899999999999998888887543
No 198
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=44.61 E-value=9.9 Score=16.71 Aligned_cols=13 Identities=31% Similarity=0.802 Sum_probs=6.5
Q ss_pred cCccccccccccc
Q psy8937 17 LDARYCKICGKHY 29 (147)
Q Consensus 17 ~~~~~C~~C~~~f 29 (147)
+..++|..|+..|
T Consensus 19 ~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 19 DDYEVCIFCGSSF 31 (33)
T ss_pred CCeEEcccCCcEe
Confidence 3445555555544
No 199
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=44.44 E-value=14 Score=18.28 Aligned_cols=32 Identities=22% Similarity=0.426 Sum_probs=21.2
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhc
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 128 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 128 (147)
.|..|+...+....... ..++....|+.||.-
T Consensus 24 ~C~gC~~~l~~~~~~~i----~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEI----RKGDEIVFCPNCGRI 55 (56)
T ss_pred ccCCCCEEcCHHHHHHH----HcCCCeEECcCCCcc
Confidence 58889877665543222 234677889999863
No 200
>KOG0717|consensus
Probab=44.33 E-value=14 Score=27.14 Aligned_cols=24 Identities=29% Similarity=0.732 Sum_probs=20.6
Q ss_pred CcccccccccccCChHHHHHHHHH
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
..+.|.+|++.|.+...|.-|...
T Consensus 291 e~lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 291 EVLYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred CceEEeeccccccchHHHHhhHHH
Confidence 349999999999999999888764
No 201
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=44.24 E-value=6.4 Score=22.88 Aligned_cols=29 Identities=17% Similarity=0.470 Sum_probs=18.3
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
+..+.|..|+..|..... ..+.||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 96 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQ-----------RVRRCPQCHGD 96 (114)
T ss_pred CcEEEcccCCCeeecCCc-----------cCCcCcCcCCC
Confidence 456889999976543211 12569999844
No 202
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=43.41 E-value=7.9 Score=23.78 Aligned_cols=36 Identities=19% Similarity=0.404 Sum_probs=24.0
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 57 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f 57 (147)
.-+|.|. |+..|.... +|-....++ .|.|..|+...
T Consensus 115 ~~~Y~C~-C~q~~l~~R---Rhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIR---RHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred ceeEEee-cCCccchhh---hcccccccc-eEEeccCCceE
Confidence 3478999 999876543 444333333 79999998654
No 203
>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=43.09 E-value=10 Score=18.46 Aligned_cols=11 Identities=18% Similarity=0.679 Sum_probs=7.8
Q ss_pred ccCCCchhccC
Q psy8937 120 LFCPLCQKCFK 130 (147)
Q Consensus 120 ~~C~~C~~~f~ 130 (147)
|+|.+||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 67777776665
No 204
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=42.26 E-value=2.2 Score=24.03 Aligned_cols=39 Identities=23% Similarity=0.402 Sum_probs=24.0
Q ss_pred CcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccC
Q psy8937 88 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 130 (147)
Q Consensus 88 ~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 130 (147)
-++.|.|+.|+..-.++..+..- ...-...|..||..|.
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 45678999999766554432211 1112356899998775
No 205
>KOG2907|consensus
Probab=42.16 E-value=7.3 Score=22.54 Aligned_cols=38 Identities=24% Similarity=0.428 Sum_probs=22.2
Q ss_pred cccccccccCCChHHHHHHHHH-HhCC-CcccCCCchhccCC
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRL-IHLP-GILFCPLCQKCFKN 131 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~-~~~~-~~~~C~~C~~~f~~ 131 (147)
.+|+.||..=.....++. |. .-|. --|.|+.|++.|.-
T Consensus 75 ~kCpkCghe~m~Y~T~Ql--RSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQL--RSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhc--ccccCCceEEEEcCccceeeec
Confidence 469999865444333322 22 1121 23889999988864
No 206
>PTZ00448 hypothetical protein; Provisional
Probab=41.39 E-value=23 Score=25.27 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=19.5
Q ss_pred cccccccccccCChHHHHHHHHH
Q psy8937 19 ARYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
.|.|..|+..|.+....+.|++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999888888888874
No 207
>PRK12496 hypothetical protein; Provisional
Probab=40.70 E-value=13 Score=23.15 Aligned_cols=29 Identities=31% Similarity=0.612 Sum_probs=19.6
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
+.|..|++.|..... .-.|++||....++
T Consensus 128 ~~C~gC~~~~~~~~~------------~~~C~~CG~~~~r~ 156 (164)
T PRK12496 128 KVCKGCKKKYPEDYP------------DDVCEICGSPVKRK 156 (164)
T ss_pred EECCCCCccccCCCC------------CCcCCCCCChhhhc
Confidence 569999998865321 13599999665443
No 208
>KOG3507|consensus
Probab=39.85 E-value=35 Score=17.26 Aligned_cols=37 Identities=16% Similarity=0.281 Sum_probs=25.3
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChHHH
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKLYL 63 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 63 (147)
....|.|..|+.. +.-.....+.|.+||....++...
T Consensus 17 ~~miYiCgdC~~e-----------n~lk~~D~irCReCG~RIlyKkRt 53 (62)
T KOG3507|consen 17 ATMIYICGDCGQE-----------NTLKRGDVIRCRECGYRILYKKRT 53 (62)
T ss_pred ccEEEEecccccc-----------ccccCCCcEehhhcchHHHHHHHH
Confidence 4567999999874 122344678999999876655443
No 209
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.70 E-value=5.9 Score=30.89 Aligned_cols=38 Identities=21% Similarity=0.321 Sum_probs=20.4
Q ss_pred cccccccccccCC---hHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 19 ARYCKICGKHYSN---SSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 19 ~~~C~~C~~~f~~---~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
.+.|+.|+..+.. ...|.-|.-.+....|..|+.||..
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3455555553221 1223334433444578899999977
No 210
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=37.54 E-value=12 Score=16.83 Aligned_cols=11 Identities=18% Similarity=0.492 Sum_probs=5.6
Q ss_pred CcccCCCchhc
Q psy8937 118 GILFCPLCQKC 128 (147)
Q Consensus 118 ~~~~C~~C~~~ 128 (147)
+.|+|..||..
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 35888888854
No 211
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.32 E-value=6.4 Score=23.23 Aligned_cols=14 Identities=29% Similarity=0.460 Sum_probs=10.5
Q ss_pred CCcCCCCchhhhcC
Q psy8937 46 GILFCPLCQKCFKN 59 (147)
Q Consensus 46 ~~~~C~~C~~~f~~ 59 (147)
.|.-|..||+.|+-
T Consensus 67 ~psfchncgs~fpw 80 (160)
T COG4306 67 PPSFCHNCGSRFPW 80 (160)
T ss_pred CcchhhcCCCCCCc
Confidence 45668899988863
No 212
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=37.32 E-value=2 Score=33.25 Aligned_cols=9 Identities=33% Similarity=0.925 Sum_probs=6.5
Q ss_pred ccccccccC
Q psy8937 93 YCKICGKHY 101 (147)
Q Consensus 93 ~C~~c~~~~ 101 (147)
.|+.||...
T Consensus 142 ~C~~Cgp~l 150 (711)
T TIGR00143 142 ACPRCGPQL 150 (711)
T ss_pred cCCCCCcEE
Confidence 488888654
No 213
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=37.31 E-value=17 Score=16.02 Aligned_cols=19 Identities=21% Similarity=0.522 Sum_probs=8.7
Q ss_pred cCCCCchhhhcChHHHHHHH
Q psy8937 48 LFCPLCQKCFKNKLYLRRHV 67 (147)
Q Consensus 48 ~~C~~C~~~f~~~~~l~~H~ 67 (147)
+.|+.|++.+.-.. +..|.
T Consensus 5 ~~C~nC~R~v~a~R-fA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAASR-FAPHL 23 (33)
T ss_dssp EE-TTTSSEEEGGG-HHHHH
T ss_pred EECCCCcCCcchhh-hHHHH
Confidence 45666665554332 44444
No 214
>KOG2071|consensus
Probab=37.30 E-value=24 Score=26.82 Aligned_cols=28 Identities=14% Similarity=0.137 Sum_probs=22.7
Q ss_pred CCCcccCCCchhccCChHHHHhHHHhhh
Q psy8937 116 LPGILFCPLCQKCFKNKLYLRRHVISFH 143 (147)
Q Consensus 116 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h 143 (147)
...+-+|..||+.|........||-+|-
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3456789999999999988888877764
No 215
>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=37.27 E-value=11 Score=18.13 Aligned_cols=11 Identities=27% Similarity=0.978 Sum_probs=6.8
Q ss_pred ccCCCchhccC
Q psy8937 120 LFCPLCQKCFK 130 (147)
Q Consensus 120 ~~C~~C~~~f~ 130 (147)
|+|.+|+..+.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 56777775554
No 216
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.16 E-value=13 Score=17.90 Aligned_cols=12 Identities=42% Similarity=1.162 Sum_probs=7.6
Q ss_pred cCCCchhccCCh
Q psy8937 121 FCPLCQKCFKNK 132 (147)
Q Consensus 121 ~C~~C~~~f~~~ 132 (147)
.|++|+..|+..
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 367777666644
No 217
>PRK11032 hypothetical protein; Provisional
Probab=35.62 E-value=11 Score=23.45 Aligned_cols=31 Identities=23% Similarity=0.535 Sum_probs=21.2
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
+.+.++|..||..- + ..+....-.|+.|+..
T Consensus 121 g~G~LvC~~Cg~~~--------~--~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 121 GLGNLVCEKCHHHL--------A--FYTPEVLPLCPKCGHD 151 (160)
T ss_pred ecceEEecCCCCEE--------E--ecCCCcCCCCCCCCCC
Confidence 56789999999852 1 1344455679999865
No 218
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.58 E-value=18 Score=21.38 Aligned_cols=34 Identities=21% Similarity=0.394 Sum_probs=19.6
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
...+.| .||..|.....-. .+....+.||.||..
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~-----~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEI-----DHYAAVIECPVCGNK 101 (124)
T ss_pred CeeEEe-eCcCcccccccch-----hccccCCcCcCCCCC
Confidence 456889 9998876542100 011113579999843
No 219
>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=35.46 E-value=15 Score=16.87 Aligned_cols=15 Identities=33% Similarity=0.817 Sum_probs=10.8
Q ss_pred cCcccccccccccCC
Q psy8937 17 LDARYCKICGKHYSN 31 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~ 31 (147)
--.++|+.||..+..
T Consensus 30 vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 30 VPALVCPQCGEEYLD 44 (46)
T ss_pred CCccccccCCCEeeC
Confidence 345789999987643
No 220
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=35.44 E-value=24 Score=19.63 Aligned_cols=20 Identities=25% Similarity=0.675 Sum_probs=15.0
Q ss_pred cccccccccccCChHHHHHH
Q psy8937 19 ARYCKICGKHYSNSSNLKQH 38 (147)
Q Consensus 19 ~~~C~~C~~~f~~~~~l~~h 38 (147)
...|+.||..|.....+..-
T Consensus 35 a~~C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 35 SISCSHCGMEYQDDTTVKEI 54 (89)
T ss_pred cccccCCCcEeecHHHHHHH
Confidence 47799999998887765543
No 221
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=35.39 E-value=7.9 Score=23.50 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=21.9
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
-.|.|..|+..+.. +.+ +.....|.|..|+..+.
T Consensus 111 ~~y~C~~C~~~~~~------~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 111 YPYRCTGCGQRYLR------VRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEEECCCCCCCCce------Ecc-ccCcceEEcCCCCCEEE
Confidence 37889889987642 222 22226688999987653
No 222
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=35.28 E-value=22 Score=17.74 Aligned_cols=20 Identities=30% Similarity=0.916 Sum_probs=14.7
Q ss_pred CcccccccccccCChHHHHH
Q psy8937 18 DARYCKICGKHYSNSSNLKQ 37 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~ 37 (147)
.-+.|-.||..|.....|..
T Consensus 26 ~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 26 EHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred hCceeeeeCCccCCHHHHHh
Confidence 44678888888888777753
No 223
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=35.24 E-value=34 Score=19.56 Aligned_cols=41 Identities=10% Similarity=0.211 Sum_probs=32.2
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcC
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 59 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 59 (147)
..|.|+.-|..|.+.......+. --..+.+.|...|++-.+
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~-~y~~~vwtC~~TGk~~LT 42 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMI-LYNQRVWTCEITGKSNLT 42 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHH-HHhCCeeEEecCCCCCCC
Confidence 57889999999999988776665 566678999988876543
No 224
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=35.20 E-value=13 Score=24.54 Aligned_cols=26 Identities=12% Similarity=0.307 Sum_probs=0.0
Q ss_pred CCcccCCCchhccCChHHHHhHHHhhh
Q psy8937 117 PGILFCPLCQKCFKNKLYLRRHVISFH 143 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~~~h 143 (147)
.....|++||....-. .|..|||+..
T Consensus 166 ~~~~~cPitGe~IP~~-e~~eHmRi~L 191 (229)
T PF12230_consen 166 EKMIICPITGEMIPAD-EMDEHMRIEL 191 (229)
T ss_dssp ---------------------------
T ss_pred cccccccccccccccc-cccccccccc
Confidence 3457899999877644 6789998754
No 225
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=35.14 E-value=13 Score=21.40 Aligned_cols=28 Identities=25% Similarity=0.687 Sum_probs=18.1
Q ss_pred cccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 94 CKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 94 C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
|+.|+..|.... ...|.|+.|+......
T Consensus 5 CP~C~seytY~d-----------g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEYTYHD-----------GTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcceEec-----------CCeeECcccccccccc
Confidence 777876665542 2347788888766543
No 226
>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=35.07 E-value=17 Score=18.06 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=7.4
Q ss_pred ccCCCchhccC
Q psy8937 120 LFCPLCQKCFK 130 (147)
Q Consensus 120 ~~C~~C~~~f~ 130 (147)
+.|+.||..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 56777776554
No 227
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=34.65 E-value=39 Score=23.08 Aligned_cols=42 Identities=19% Similarity=0.185 Sum_probs=22.5
Q ss_pred cCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 14 LHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 14 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
|.+-....|..|+..+.....+...........+-.|+ |+..
T Consensus 132 HG~l~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cgg~ 173 (271)
T PTZ00409 132 HGSVFEARCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CGGI 173 (271)
T ss_pred ccCcCcceeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CCCc
Confidence 33456778999998876544333221111112234687 8744
No 228
>KOG1842|consensus
Probab=34.26 E-value=28 Score=25.55 Aligned_cols=28 Identities=29% Similarity=0.538 Sum_probs=23.8
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCC
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLP 117 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~ 117 (147)
..|.|++|...|.+.++|..|.-..+.+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhccc
Confidence 4567999999999999999999876643
No 229
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=34.19 E-value=15 Score=25.42 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.5
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
+.+|+.|+....... | .+.-+.|+.|+..|...
T Consensus 38 w~kc~~C~~~~~~~~-l--------~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 38 WVQCENCYGLNYKKF-L--------KSKMNICEQCGYHLKMS 70 (296)
T ss_pred eeECCCccchhhHHH-H--------HHcCCCCCCCCCCcCCC
Confidence 557999987754433 2 22457899999988754
No 230
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=33.51 E-value=26 Score=23.69 Aligned_cols=63 Identities=24% Similarity=0.335 Sum_probs=35.9
Q ss_pred ChHHHHHHHhhhcCCCCccCCCCC-CCCCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhc
Q psy8937 59 NKLYLRRHVGTYTHTPSYRSVPGA-SKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 128 (147)
Q Consensus 59 ~~~~l~~H~~~~~~~~~~~~~~~~-~~~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 128 (147)
....|.+-+...++.+.+-....- ......+..-.|+.||........| ++--.|+|..|.-.
T Consensus 187 ~G~~l~~~Ie~~T~iPtYYyLyrv~g~~~~~e~~r~CP~Cg~~W~L~~pl-------h~iFdFKCD~CRLV 250 (258)
T PF10071_consen 187 RGRDLCKRIEKLTGIPTYYYLYRVGGESLASEQARKCPSCGGDWRLKEPL-------HDIFDFKCDPCRLV 250 (258)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEEccCcchHHhhCCCCCCCCCccccCCch-------hhceeccCCcceee
Confidence 334444444555666555422211 1222234445699999877766655 34467999999854
No 231
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=32.83 E-value=42 Score=22.02 Aligned_cols=39 Identities=26% Similarity=0.512 Sum_probs=23.1
Q ss_pred ccCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 13 PLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 13 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
.|.+-....|..|+..+..... . .........|+.|+..
T Consensus 107 lHG~l~~~~C~~C~~~~~~~~~-~----~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 107 LHGTLQTAYCVNCGSKYDLEEV-K----YAKKHEVPRCPKCGGI 145 (222)
T ss_pred ccCCcCcceECCCCCCcchhHH-H----HhccCCCCcCCCCCCc
Confidence 3445567889999988765432 1 1112234578888744
No 232
>PHA02893 hypothetical protein; Provisional
Probab=32.72 E-value=34 Score=18.67 Aligned_cols=47 Identities=19% Similarity=0.228 Sum_probs=27.5
Q ss_pred cCccccccccc---ccCChHHHHHHHHHhcC----CCCcCCCCchhhhcChHHH
Q psy8937 17 LDARYCKICGK---HYSNSSNLKQHIRLIHL----PGILFCPLCQKCFKNKLYL 63 (147)
Q Consensus 17 ~~~~~C~~C~~---~f~~~~~l~~h~~~~~~----~~~~~C~~C~~~f~~~~~l 63 (147)
+.--.|..|.- .|.....+....-...+ .....|..||........|
T Consensus 32 d~C~TCSsC~SKLV~~Sdvtk~sl~~~~~~Gk~~~~~tL~CaACGS~L~~L~d~ 85 (88)
T PHA02893 32 DACTTCQICQSKLVMFSGVNKYKLKDYLNIGKAFSNSNIKCIACGSSLCHLRDL 85 (88)
T ss_pred CCCcchhhhhcceeeeeccchhhhHHHHhccccCCCCceeehhhchhhhhhHhh
Confidence 34455777776 35555555433222222 3567899999887655544
No 233
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=32.69 E-value=46 Score=22.28 Aligned_cols=39 Identities=21% Similarity=0.537 Sum_probs=23.7
Q ss_pred cCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 14 LHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 14 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
|.+-....|..|++.|.....+. . ......-.|+.|+..
T Consensus 114 HG~~~~~~C~~C~~~~~~~~~~~-~---~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 114 HGNVEEYYCVRCGKRYTVEDVIE-K---LEKSDVPRCDDCSGL 152 (244)
T ss_pred cCCcCeeEECCCCCcccHHHHHH-H---HhcCCCCCCCCCCCe
Confidence 33456678999999877644332 1 112234569999854
No 234
>PLN02748 tRNA dimethylallyltransferase
Probab=32.53 E-value=34 Score=25.42 Aligned_cols=24 Identities=13% Similarity=0.311 Sum_probs=17.4
Q ss_pred CcccCCCchh-ccCChHHHHhHHHh
Q psy8937 118 GILFCPLCQK-CFKNKLYLRRHVIS 141 (147)
Q Consensus 118 ~~~~C~~C~~-~f~~~~~l~~H~~~ 141 (147)
+.|.|.+|++ .+........|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4577888886 67777777777654
No 235
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=32.15 E-value=16 Score=18.90 Aligned_cols=16 Identities=25% Similarity=0.600 Sum_probs=12.0
Q ss_pred CccCcccccccccccC
Q psy8937 15 HSLDARYCKICGKHYS 30 (147)
Q Consensus 15 ~~~~~~~C~~C~~~f~ 30 (147)
..+...+|+.|++.|.
T Consensus 49 i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 49 IVEGELICPECGREYP 64 (68)
T ss_dssp TTTTEEEETTTTEEEE
T ss_pred ccCCEEEcCCCCCEEe
Confidence 3467788888888775
No 236
>PRK10220 hypothetical protein; Provisional
Probab=32.12 E-value=18 Score=20.87 Aligned_cols=28 Identities=29% Similarity=0.893 Sum_probs=18.4
Q ss_pred cccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 94 CKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 94 C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
|+.|...|..... ..|.|+.|+..+...
T Consensus 6 CP~C~seytY~d~-----------~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCNSEYTYEDN-----------GMYICPECAHEWNDA 33 (111)
T ss_pred CCCCCCcceEcCC-----------CeEECCcccCcCCcc
Confidence 7888766655432 247888888776544
No 237
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=31.17 E-value=25 Score=23.71 Aligned_cols=39 Identities=28% Similarity=0.416 Sum_probs=24.6
Q ss_pred cCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 14 LHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 14 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
|.+-....|..|+..+......... ....+-.|+.|+..
T Consensus 117 HGsl~~~~C~~C~~~~~~~~~~~~~----~~~~~p~C~~Cg~~ 155 (250)
T COG0846 117 HGSLKRVRCSKCGNQYYDEDVIKFI----EDGLIPRCPKCGGP 155 (250)
T ss_pred ccceeeeEeCCCcCccchhhhhhhc----ccCCCCcCccCCCc
Confidence 3456778899999887654421111 11146689999973
No 238
>KOG0320|consensus
Probab=30.78 E-value=36 Score=21.68 Aligned_cols=47 Identities=26% Similarity=0.424 Sum_probs=25.8
Q ss_pred CccCccCcccccccccccCChHHHHH---HHH-----HhcCCCCcCCCCchhhhc
Q psy8937 12 KPLHSLDARYCKICGKHYSNSSNLKQ---HIR-----LIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 12 ~~~~~~~~~~C~~C~~~f~~~~~l~~---h~~-----~~~~~~~~~C~~C~~~f~ 58 (147)
..+..+..|.|++|-..|..+..... |+= .-....-.+||.|++...
T Consensus 124 ~~~~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 124 DPLRKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccccccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 34445567999999887766653210 100 011123467888886543
No 239
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.78 E-value=52 Score=22.72 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=22.5
Q ss_pred ccCcccccccccccCChHHHHHHHHH
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
....|.|..|-+.|.....|.+|+..
T Consensus 45 ~~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 45 CTKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CCeEEEcCCCcchhCCHHHHHHHHHh
Confidence 45679999999999999999999874
No 240
>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=30.63 E-value=12 Score=22.80 Aligned_cols=33 Identities=18% Similarity=0.351 Sum_probs=21.5
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
-.|.|..|+..+.....+ ....|.|..|+..+.
T Consensus 122 ~~~~C~~C~~~~~r~~~~--------~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRS--------KRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCEeeeeccc--------chhhEECCCCCCEEE
Confidence 468899999876443322 223488999986653
No 241
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=30.21 E-value=34 Score=16.55 Aligned_cols=10 Identities=40% Similarity=0.986 Sum_probs=3.8
Q ss_pred CcccCCCchh
Q psy8937 118 GILFCPLCQK 127 (147)
Q Consensus 118 ~~~~C~~C~~ 127 (147)
..+.|++|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 3499999985
No 242
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=29.79 E-value=14 Score=18.47 Aligned_cols=32 Identities=28% Similarity=0.502 Sum_probs=14.9
Q ss_pred cCcccccccccccCChHHHHHHHHHhcCCCCcCCCC
Q psy8937 17 LDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPL 52 (147)
Q Consensus 17 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~ 52 (147)
.+|.+...|+..|.....+. .+ .......||.
T Consensus 22 ~~PV~s~~C~H~fek~aI~~-~i---~~~~~~~CPv 53 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAILQ-YI---QRNGSKRCPV 53 (57)
T ss_dssp SSEEEESSS--EEEHHHHHH-HC---TTTS-EE-SC
T ss_pred hCCcCcCCCCCeecHHHHHH-HH---HhcCCCCCCC
Confidence 35566667777776654433 22 2234566766
No 243
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=29.72 E-value=15 Score=22.24 Aligned_cols=16 Identities=38% Similarity=0.596 Sum_probs=13.0
Q ss_pred CCcccCCCchhccCCh
Q psy8937 117 PGILFCPLCQKCFKNK 132 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~~ 132 (147)
.++..|+.||..|...
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 4689999999988754
No 244
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=29.59 E-value=20 Score=28.52 Aligned_cols=13 Identities=23% Similarity=0.743 Sum_probs=10.9
Q ss_pred ccccccccccCCh
Q psy8937 20 RYCKICGKHYSNS 32 (147)
Q Consensus 20 ~~C~~C~~~f~~~ 32 (147)
-.|..|++.|...
T Consensus 461 dtC~~C~kkFfSl 473 (1374)
T PTZ00303 461 DSCPSCGRAFISL 473 (1374)
T ss_pred CcccCcCCccccc
Confidence 6799999999765
No 245
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.48 E-value=68 Score=20.82 Aligned_cols=40 Identities=18% Similarity=0.266 Sum_probs=23.0
Q ss_pred cCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 14 LHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 14 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
|.+-....|..|+..+.....+.. .........|+.|+..
T Consensus 90 HG~~~~~~C~~C~~~~~~~~~~~~---~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 90 HGNMFIEVCKSCGPEYVRDDVVET---RGDKETGRRCHACGGI 129 (206)
T ss_pred cCCcCcccCCCCCCccchHHHHHH---hhcCCCCCcCCCCcCc
Confidence 344567789999987654433221 1112234569999754
No 246
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=29.34 E-value=29 Score=23.91 Aligned_cols=34 Identities=21% Similarity=0.516 Sum_probs=22.8
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
-+.+|+.|+....... |. ..-+.|+.|+..|...
T Consensus 25 ~~~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKE-LE--------RNLEVCPKCDHHMRMD 58 (285)
T ss_pred CeeECCCCcchhhHHH-HH--------hhCCCCCCCCCcCcCC
Confidence 3567999987755443 21 2347899999988743
No 247
>KOG4602|consensus
Probab=29.30 E-value=28 Score=23.49 Aligned_cols=41 Identities=15% Similarity=0.237 Sum_probs=24.4
Q ss_pred CCcccccccccCCChHHHHHHHHHHhCC-------CcccCCCchhccC
Q psy8937 90 DARYCKICGKHYSNSSNLKQHIRLIHLP-------GILFCPLCQKCFK 130 (147)
Q Consensus 90 ~~~~C~~c~~~~~~~~~l~~H~~~~~~~-------~~~~C~~C~~~f~ 130 (147)
++.-|.+|...-.....+..|....... +.|.|++||.+=.
T Consensus 232 r~l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGATgD 279 (318)
T KOG4602|consen 232 RPLCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGATGD 279 (318)
T ss_pred CceeEEeecCCCchhhheecccccCCCCcEechhHhhhcCccccccCC
Confidence 3445777865555555555555433322 3489999996543
No 248
>KOG2857|consensus
Probab=29.19 E-value=26 Score=21.28 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=19.7
Q ss_pred CcCCCCchhhhcChHHHHHHHh
Q psy8937 47 ILFCPLCQKCFKNKLYLRRHVG 68 (147)
Q Consensus 47 ~~~C~~C~~~f~~~~~l~~H~~ 68 (147)
.|+|+.|.-.|.+..-++.|..
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 6899999999999999999874
No 249
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=29.05 E-value=19 Score=24.82 Aligned_cols=33 Identities=21% Similarity=0.543 Sum_probs=22.0
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
+.+|+.|+..+.... |. ...+.|+.|+..|...
T Consensus 27 ~~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQVLYRKE-LE--------ANLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccchhhHHH-HH--------hcCCCCCCCCCCeeCC
Confidence 567999987654432 21 2346899999988743
No 250
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=28.99 E-value=27 Score=23.14 Aligned_cols=16 Identities=19% Similarity=0.262 Sum_probs=13.2
Q ss_pred CCCcccCCCchhccCC
Q psy8937 116 LPGILFCPLCQKCFKN 131 (147)
Q Consensus 116 ~~~~~~C~~C~~~f~~ 131 (147)
..++.+|++||..|..
T Consensus 178 EGkpqRCpECGqVFKL 193 (268)
T PTZ00043 178 EGFLYRCGECDQIFML 193 (268)
T ss_pred CCCCccCCCCCcEEEE
Confidence 4568999999998874
No 251
>PRK01343 zinc-binding protein; Provisional
Probab=28.91 E-value=33 Score=17.30 Aligned_cols=9 Identities=44% Similarity=0.752 Sum_probs=4.5
Q ss_pred cCCCchhcc
Q psy8937 121 FCPLCQKCF 129 (147)
Q Consensus 121 ~C~~C~~~f 129 (147)
.|++|++.+
T Consensus 11 ~CP~C~k~~ 19 (57)
T PRK01343 11 PCPECGKPS 19 (57)
T ss_pred cCCCCCCcC
Confidence 455555544
No 252
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.89 E-value=34 Score=28.80 Aligned_cols=28 Identities=21% Similarity=0.465 Sum_probs=16.7
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccC
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 130 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 130 (147)
|.|+.|+....... .+ ...|+.|+....
T Consensus 693 y~CPsCGaev~~de---------s~--a~~CP~CGtplv 720 (1337)
T PRK14714 693 YVCPDCGAEVPPDE---------SG--RVECPRCDVELT 720 (1337)
T ss_pred eeCccCCCccCCCc---------cc--cccCCCCCCccc
Confidence 46888887644321 11 346999985444
No 253
>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=28.77 E-value=24 Score=16.30 Aligned_cols=8 Identities=38% Similarity=1.090 Sum_probs=4.8
Q ss_pred ccCCCchh
Q psy8937 120 LFCPLCQK 127 (147)
Q Consensus 120 ~~C~~C~~ 127 (147)
|.|+.|+.
T Consensus 1 m~Cp~Cg~ 8 (43)
T PF08271_consen 1 MKCPNCGS 8 (43)
T ss_dssp ESBTTTSS
T ss_pred CCCcCCcC
Confidence 45666664
No 254
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=28.53 E-value=47 Score=22.95 Aligned_cols=24 Identities=29% Similarity=0.614 Sum_probs=19.3
Q ss_pred CCcccCCCchhccCChHHHHhHHH
Q psy8937 117 PGILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
...|.|+.|-+-|.....|.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 456888888888888888888876
No 255
>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=28.49 E-value=18 Score=16.22 Aligned_cols=9 Identities=44% Similarity=1.276 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy8937 21 YCKICGKHY 29 (147)
Q Consensus 21 ~C~~C~~~f 29 (147)
.|+.||..|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 344444443
No 256
>PF12773 DZR: Double zinc ribbon
Probab=28.48 E-value=35 Score=16.15 Aligned_cols=30 Identities=27% Similarity=0.556 Sum_probs=18.0
Q ss_pred ccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
....-.|+.||.... ........|+.|+..
T Consensus 9 ~~~~~fC~~CG~~l~-----------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP-----------PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChh-----------hccCCCCCCcCCcCC
Confidence 344567888887655 122234568888764
No 257
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.47 E-value=25 Score=15.85 Aligned_cols=12 Identities=42% Similarity=0.949 Sum_probs=6.9
Q ss_pred cCCCchhccCCh
Q psy8937 121 FCPLCQKCFKNK 132 (147)
Q Consensus 121 ~C~~C~~~f~~~ 132 (147)
.|+.|++.|-..
T Consensus 4 ~CprC~kg~Hwa 15 (36)
T PF14787_consen 4 LCPRCGKGFHWA 15 (36)
T ss_dssp C-TTTSSSCS-T
T ss_pred cCcccCCCcchh
Confidence 477788777544
No 258
>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=28.39 E-value=23 Score=19.97 Aligned_cols=26 Identities=27% Similarity=0.713 Sum_probs=15.5
Q ss_pred cccccccCCChHHHHHHHHHHhCCCcccCCCchhccCC
Q psy8937 94 CKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 131 (147)
Q Consensus 94 C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 131 (147)
|+.||..+... +..+.|+.|+..+..
T Consensus 3 C~~Cg~~l~~~------------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 3 CPKCGSLMTPK------------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CcccCcccccC------------CCeEECcCCCCcccc
Confidence 67777665321 124778888766554
No 259
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=28.27 E-value=42 Score=22.33 Aligned_cols=36 Identities=33% Similarity=0.539 Sum_probs=22.3
Q ss_pred ccCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 13 PLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 13 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
.|.+-....|..|+..+.....+. .....|+.|+..
T Consensus 116 lHG~~~~~~C~~C~~~~~~~~~~~--------~~~p~C~~Cgg~ 151 (242)
T PRK00481 116 LHGSLLRARCTKCGQTYDLDEYLK--------PEPPRCPKCGGI 151 (242)
T ss_pred ccCCcCceeeCCCCCCcChhhhcc--------CCCCCCCCCCCc
Confidence 444566788999988876543321 123349989754
No 260
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=28.14 E-value=21 Score=17.59 Aligned_cols=17 Identities=12% Similarity=0.286 Sum_probs=11.2
Q ss_pred ccCcccccccccccCCh
Q psy8937 16 SLDARYCKICGKHYSNS 32 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~ 32 (147)
+...|.|.+|++.+...
T Consensus 32 ~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 32 EPIKLRCHYCERIITED 48 (52)
T ss_dssp TTCEEEETTT--EEEHH
T ss_pred CCCEEEeeCCCCEeccc
Confidence 56779999999987543
No 261
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=27.56 E-value=35 Score=23.55 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=19.0
Q ss_pred cccccCCChHHHHHHHHHHhCCCcccCCCchhccC
Q psy8937 96 ICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 130 (147)
Q Consensus 96 ~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 130 (147)
.||..|-+. -++.|.+++|+ |++|...|.
T Consensus 42 tCgHtFCsl-----CIR~hL~~qp~-CP~Cr~~~~ 70 (391)
T COG5432 42 TCGHTFCSL-----CIRRHLGTQPF-CPVCREDPC 70 (391)
T ss_pred ccccchhHH-----HHHHHhcCCCC-CccccccHH
Confidence 355555543 25677888777 999986554
No 262
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=27.46 E-value=63 Score=21.07 Aligned_cols=40 Identities=30% Similarity=0.511 Sum_probs=23.5
Q ss_pred ccCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 13 PLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 13 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
.|.+-....|..|+..+.... +... ........|+.|+..
T Consensus 103 lHG~~~~~~C~~C~~~~~~~~-~~~~---~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 103 LHGSLFRVRCTKCGKEYPRDE-LQAD---IDREEVPRCPKCGGL 142 (218)
T ss_pred CcCCcCcceeCCCcCCCcHHH-HhHh---hccCCCCcCCCCCCc
Confidence 344556788999998876442 2111 122334579999754
No 263
>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=27.35 E-value=26 Score=15.60 Aligned_cols=13 Identities=31% Similarity=0.595 Sum_probs=6.2
Q ss_pred cCCCchhccCChH
Q psy8937 121 FCPLCQKCFKNKL 133 (147)
Q Consensus 121 ~C~~C~~~f~~~~ 133 (147)
.|..|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 4788888887553
No 264
>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=27.11 E-value=15 Score=20.97 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=8.2
Q ss_pred Ccccccccccc
Q psy8937 18 DARYCKICGKH 28 (147)
Q Consensus 18 ~~~~C~~C~~~ 28 (147)
++-.|+.||..
T Consensus 1 ~p~~CpYCg~~ 11 (102)
T PF11672_consen 1 KPIICPYCGGP 11 (102)
T ss_pred CCcccCCCCCe
Confidence 45678899884
No 265
>KOG1088|consensus
Probab=26.90 E-value=23 Score=20.74 Aligned_cols=16 Identities=13% Similarity=0.208 Sum_probs=10.5
Q ss_pred ccCcccccccccccCC
Q psy8937 16 SLDARYCKICGKHYSN 31 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~ 31 (147)
.++..+|+.||+.|.-
T Consensus 95 ~EG~l~CpetG~vfpI 110 (124)
T KOG1088|consen 95 IEGELVCPETGRVFPI 110 (124)
T ss_pred ccceEecCCCCcEeec
Confidence 3556777777777654
No 266
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=26.85 E-value=27 Score=17.23 Aligned_cols=9 Identities=33% Similarity=0.966 Sum_probs=4.3
Q ss_pred CCCCchhhh
Q psy8937 49 FCPLCQKCF 57 (147)
Q Consensus 49 ~C~~C~~~f 57 (147)
.||.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 355555444
No 267
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=26.63 E-value=48 Score=21.04 Aligned_cols=19 Identities=16% Similarity=0.413 Sum_probs=14.5
Q ss_pred CcccCCCchhccCChHHHH
Q psy8937 118 GILFCPLCQKCFKNKLYLR 136 (147)
Q Consensus 118 ~~~~C~~C~~~f~~~~~l~ 136 (147)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4678999999998765543
No 268
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=26.54 E-value=15 Score=27.28 Aligned_cols=42 Identities=17% Similarity=0.321 Sum_probs=24.3
Q ss_pred CCCCcCCcccccccccCCChHHHHHHHHHHhC------CCcccCCCchh
Q psy8937 85 PLHSLDARYCKICGKHYSNSSNLKQHIRLIHL------PGILFCPLCQK 127 (147)
Q Consensus 85 ~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~------~~~~~C~~C~~ 127 (147)
.....+.|.|..|+..|.-...-.. ..+-.+ .-.+.||+|+.
T Consensus 419 ~~~~~~~~~c~~c~~~yd~~~g~~~-~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 419 TADLGPRMQCSVCQWIYDPAKGEPM-QDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred ccCCCCeEEECCCCeEECCCCCCcc-cCCCCCCChhhCCCCCcCcCCCC
Confidence 3446678999999988865321100 001111 12478999994
No 269
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=26.03 E-value=50 Score=21.36 Aligned_cols=34 Identities=21% Similarity=0.372 Sum_probs=19.4
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhcc
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCF 129 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 129 (147)
+.|+.|+ .-.....+ ++.-..+-.+.|..||..+
T Consensus 7 ~~Cp~Cg-~eev~hEV---ik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 7 IECPSCG-SEEVSHEV---IKERGREPLVRCEECGTVH 40 (201)
T ss_pred EECCCCC-cchhhHHH---HHhcCCceEEEccCCCcEe
Confidence 4699998 22222222 1222334468899999776
No 270
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=25.90 E-value=27 Score=14.89 Aligned_cols=13 Identities=23% Similarity=0.582 Sum_probs=5.7
Q ss_pred cccCCCchhccCC
Q psy8937 119 ILFCPLCQKCFKN 131 (147)
Q Consensus 119 ~~~C~~C~~~f~~ 131 (147)
.|.|+.|+..+-+
T Consensus 13 kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 13 KYRCPRCGARYCS 25 (30)
T ss_dssp SEE-TTT--EESS
T ss_pred EEECCCcCCceeC
Confidence 3667777665443
No 271
>PRK04351 hypothetical protein; Provisional
Probab=25.75 E-value=24 Score=21.67 Aligned_cols=33 Identities=24% Similarity=0.447 Sum_probs=22.2
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCC
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKN 131 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 131 (147)
.|.|..|+..+...- + +....|.|..|+-.+..
T Consensus 112 ~Y~C~~Cg~~~~r~R------r--~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRKR------R--INTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeeee------e--cCCCcEEeCCCCcEeee
Confidence 478988987664331 1 23467999999976653
No 272
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=25.48 E-value=52 Score=22.08 Aligned_cols=35 Identities=26% Similarity=0.603 Sum_probs=22.9
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCcccCCCchhccC
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 130 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 130 (147)
..|..|+...+....- -++. +.-+..||.||.-..
T Consensus 198 ~~C~GC~m~l~~~~~~--~V~~--~d~iv~CP~CgRILy 232 (239)
T COG1579 198 RVCGGCHMKLPSQTLS--KVRK--KDEIVFCPYCGRILY 232 (239)
T ss_pred CcccCCeeeecHHHHH--HHhc--CCCCccCCccchHHH
Confidence 3599998877665432 2232 556788999997543
No 273
>PHA02998 RNA polymerase subunit; Provisional
Probab=24.65 E-value=5.7 Score=25.03 Aligned_cols=38 Identities=21% Similarity=0.333 Sum_probs=22.6
Q ss_pred cccccccccCCChHHHHHHHHHHhCCC---cccCCCchhccCCh
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPG---ILFCPLCQKCFKNK 132 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~---~~~C~~C~~~f~~~ 132 (147)
-.|+.|+..-.....++. +. ..|. -|.|..||..|.-.
T Consensus 144 v~CPkCg~~~A~f~qlQT--RS-ADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQT--RA-ADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEEEEee--cc-CCCCceEEEEcCCCCCccCCc
Confidence 359999865444433322 21 2222 28899999888754
No 274
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=24.47 E-value=34 Score=17.67 Aligned_cols=7 Identities=43% Similarity=1.151 Sum_probs=4.1
Q ss_pred ccCCCch
Q psy8937 120 LFCPLCQ 126 (147)
Q Consensus 120 ~~C~~C~ 126 (147)
|.|+.|+
T Consensus 1 y~C~KCg 7 (64)
T PF09855_consen 1 YKCPKCG 7 (64)
T ss_pred CCCCCCC
Confidence 4566665
No 275
>KOG1940|consensus
Probab=24.34 E-value=74 Score=21.91 Aligned_cols=42 Identities=19% Similarity=0.278 Sum_probs=26.5
Q ss_pred cccccccccCCChHHHHHHHHHHhCCCc-----------ccCCCchhccCChHH
Q psy8937 92 RYCKICGKHYSNSSNLKQHIRLIHLPGI-----------LFCPLCQKCFKNKLY 134 (147)
Q Consensus 92 ~~C~~c~~~~~~~~~l~~H~~~~~~~~~-----------~~C~~C~~~f~~~~~ 134 (147)
|.|+.|.+ ....+.+-.+........+ ..|+.|+..-..+..
T Consensus 197 y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~ 249 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYH 249 (276)
T ss_pred CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCcccee
Confidence 77888888 6666666666665554422 457777765554433
No 276
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=24.18 E-value=32 Score=14.94 Aligned_cols=12 Identities=17% Similarity=0.642 Sum_probs=8.4
Q ss_pred CcccCCCchhcc
Q psy8937 118 GILFCPLCQKCF 129 (147)
Q Consensus 118 ~~~~C~~C~~~f 129 (147)
+.|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 358888888544
No 277
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=24.12 E-value=28 Score=17.55 Aligned_cols=12 Identities=33% Similarity=0.797 Sum_probs=5.7
Q ss_pred ccCCCchhccCC
Q psy8937 120 LFCPLCQKCFKN 131 (147)
Q Consensus 120 ~~C~~C~~~f~~ 131 (147)
..|++|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468888877654
No 278
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.11 E-value=35 Score=23.51 Aligned_cols=25 Identities=24% Similarity=0.624 Sum_probs=17.9
Q ss_pred ccccccccCCChHHHHHHHHHHhCCCcccCCCchhccCCh
Q psy8937 93 YCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNK 132 (147)
Q Consensus 93 ~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 132 (147)
.|+.||. ...+.+.|+.||..+..-
T Consensus 311 ~C~~cg~---------------~~~r~~~C~~cg~~~~rD 335 (364)
T COG0675 311 TCPCCGH---------------LSGRLFKCPRCGFVHDRD 335 (364)
T ss_pred cccccCC---------------ccceeEECCCCCCeehhh
Confidence 3888888 123568999999876554
No 279
>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=23.90 E-value=32 Score=19.20 Aligned_cols=9 Identities=44% Similarity=1.128 Sum_probs=5.1
Q ss_pred cccCCCchh
Q psy8937 119 ILFCPLCQK 127 (147)
Q Consensus 119 ~~~C~~C~~ 127 (147)
.|.|+.|++
T Consensus 35 ky~Cp~Cgk 43 (90)
T PF01780_consen 35 KYTCPFCGK 43 (90)
T ss_dssp -BEESSSSS
T ss_pred CCcCCCCCC
Confidence 466666664
No 280
>KOG4477|consensus
Probab=23.65 E-value=52 Score=21.04 Aligned_cols=28 Identities=25% Similarity=0.665 Sum_probs=17.5
Q ss_pred CCCCcCCcccccccccCCChHHHHHHHHHHhCCCcccCCCch
Q psy8937 85 PLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQ 126 (147)
Q Consensus 85 ~~~~~~~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~ 126 (147)
+...+..|-|..|. |.++.. -|+|-+|+
T Consensus 18 p~~Deg~WdCsvCT--FrNsAe------------AfkC~vCd 45 (228)
T KOG4477|consen 18 PNDDEGKWDCSVCT--FRNSAE------------AFKCFVCD 45 (228)
T ss_pred CccccCceeeeeee--ecchhh------------hhheeeec
Confidence 33456678898884 444332 37788887
No 281
>KOG0801|consensus
Probab=23.40 E-value=16 Score=22.70 Aligned_cols=21 Identities=24% Similarity=0.477 Sum_probs=14.1
Q ss_pred CcCCCCchhhhcChHHHHHHHh
Q psy8937 47 ILFCPLCQKCFKNKLYLRRHVG 68 (147)
Q Consensus 47 ~~~C~~C~~~f~~~~~l~~H~~ 68 (147)
-++|++|.+...... +..|..
T Consensus 138 g~KCPvC~K~V~sDd-~e~Hlv 158 (205)
T KOG0801|consen 138 GMKCPVCHKVVPSDD-AEIHLV 158 (205)
T ss_pred CccCCccccccCCCc-ceEEEE
Confidence 478999988765543 555553
No 282
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.36 E-value=53 Score=22.62 Aligned_cols=10 Identities=30% Similarity=0.962 Sum_probs=6.3
Q ss_pred ccCCCchhcc
Q psy8937 120 LFCPLCQKCF 129 (147)
Q Consensus 120 ~~C~~C~~~f 129 (147)
-.|+.|+-.|
T Consensus 270 ~~C~~Cgt~f 279 (279)
T TIGR00627 270 PICKTCKTAF 279 (279)
T ss_pred CCCCCCCCCC
Confidence 3677777554
No 283
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=23.24 E-value=31 Score=14.42 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=4.3
Q ss_pred CcccCCCchhc
Q psy8937 118 GILFCPLCQKC 128 (147)
Q Consensus 118 ~~~~C~~C~~~ 128 (147)
..|.|..|+..
T Consensus 14 ~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 14 WFYRCSECDFD 24 (30)
T ss_dssp -EEE-TTT---
T ss_pred ceEECccCCCc
Confidence 35777777643
No 284
>KOG0782|consensus
Probab=23.04 E-value=23 Score=27.00 Aligned_cols=28 Identities=21% Similarity=0.305 Sum_probs=15.5
Q ss_pred HHHHHHHHHhCCCcccCCCchhccCChH
Q psy8937 106 NLKQHIRLIHLPGILFCPLCQKCFKNKL 133 (147)
Q Consensus 106 ~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 133 (147)
.+..|-=+|...+.-+|..|+|.|.++.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKF 267 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhhe
Confidence 4444444444444455777777776553
No 285
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=23.00 E-value=65 Score=18.66 Aligned_cols=25 Identities=20% Similarity=0.547 Sum_probs=18.7
Q ss_pred ccCcccccccccccCChHHHHHHHH
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIR 40 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~ 40 (147)
....++|+.||..+..........+
T Consensus 28 ~~~~~~C~~CGe~~~~~e~~~~~~~ 52 (127)
T TIGR03830 28 GVPGWYCPACGEELLDPEESKRNSA 52 (127)
T ss_pred eeeeeECCCCCCEEEcHHHHHHHHH
Confidence 4567899999998888776655444
No 286
>PLN03239 histone acetyltransferase; Provisional
Probab=22.86 E-value=58 Score=23.22 Aligned_cols=25 Identities=20% Similarity=0.228 Sum_probs=21.5
Q ss_pred CCcccCCCchhccCChHHHHhHHHh
Q psy8937 117 PGILFCPLCQKCFKNKLYLRRHVIS 141 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~~ 141 (147)
...|.|+.|-+-|.....|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4579999999999999999999754
No 287
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=22.82 E-value=35 Score=17.06 Aligned_cols=17 Identities=18% Similarity=0.454 Sum_probs=11.9
Q ss_pred ccCcccccccccccCCh
Q psy8937 16 SLDARYCKICGKHYSNS 32 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~ 32 (147)
+++..-|+.|+..|...
T Consensus 36 ~~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 36 GERYNGCPFCGTPFEFD 52 (55)
T ss_pred hhhccCCCCCCCcccCC
Confidence 34556699999887653
No 288
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=22.71 E-value=35 Score=14.79 Aligned_cols=12 Identities=17% Similarity=0.609 Sum_probs=8.4
Q ss_pred CcccCCCchhcc
Q psy8937 118 GILFCPLCQKCF 129 (147)
Q Consensus 118 ~~~~C~~C~~~f 129 (147)
+.|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468888888544
No 289
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=22.32 E-value=57 Score=24.16 Aligned_cols=25 Identities=36% Similarity=0.699 Sum_probs=21.9
Q ss_pred CCCcccCCCchhccCChHHHHhHHH
Q psy8937 116 LPGILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 116 ~~~~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
....|.|+.|-+-|.....|.+|+.
T Consensus 195 ~~~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 195 CSKLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred CCeEEEchhhhhhhcCHHHHHHHHh
Confidence 3457999999999999999999986
No 290
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG3352|consensus
Probab=21.98 E-value=41 Score=20.70 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=11.8
Q ss_pred CCcccCCCchhccCC
Q psy8937 117 PGILFCPLCQKCFKN 131 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~ 131 (147)
.+..+|++||-.|..
T Consensus 131 ge~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 131 GETQRCPECGHYFKL 145 (153)
T ss_pred CCcccCCcccceEEe
Confidence 356789999988874
No 292
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=21.80 E-value=67 Score=15.61 Aligned_cols=19 Identities=21% Similarity=0.516 Sum_probs=11.1
Q ss_pred cccCCCchhccCChHHHHhHHH
Q psy8937 119 ILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
+--|+.|...|. .|..|+.
T Consensus 5 ~GYCE~C~~ky~---~l~~Hi~ 23 (49)
T PF07535_consen 5 PGYCENCRVKYD---DLEEHIQ 23 (49)
T ss_pred CccCccccchhh---hHHHHhC
Confidence 334777776665 4555554
No 293
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=21.36 E-value=56 Score=13.69 Aligned_cols=9 Identities=22% Similarity=1.113 Sum_probs=4.3
Q ss_pred cCCCchhcc
Q psy8937 121 FCPLCQKCF 129 (147)
Q Consensus 121 ~C~~C~~~f 129 (147)
.|.+|++..
T Consensus 2 ~C~~C~~~~ 10 (30)
T PF03107_consen 2 WCDVCRRKI 10 (30)
T ss_pred CCCCCCCCc
Confidence 455555433
No 294
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=21.30 E-value=67 Score=14.65 Aligned_cols=26 Identities=27% Similarity=0.438 Sum_probs=16.2
Q ss_pred CcccccccccCCChHHHHHHHHHHhCCCcccCCCchhc
Q psy8937 91 ARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 128 (147)
Q Consensus 91 ~~~C~~c~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 128 (147)
+-.|..|++.+.... +-++|..|+..
T Consensus 11 ~~~C~~C~~~i~~~~------------~~~~C~~C~~~ 36 (49)
T smart00109 11 PTKCCVCRKSIWGSF------------QGLRCSWCKVK 36 (49)
T ss_pred CCCccccccccCcCC------------CCcCCCCCCch
Confidence 345888887654321 34788888754
No 295
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.30 E-value=21 Score=17.75 Aligned_cols=32 Identities=25% Similarity=0.828 Sum_probs=20.7
Q ss_pred CcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhcChH
Q psy8937 18 DARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFKNKL 61 (147)
Q Consensus 18 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~ 61 (147)
..-.|..|++.|..... .-.|+.|+-.+...=
T Consensus 4 ~~~~C~~Cg~~~~~~dD------------iVvCp~CgapyHR~C 35 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDD------------IVVCPECGAPYHRDC 35 (54)
T ss_pred cCccChhhCCcccCCCC------------EEECCCCCCcccHHH
Confidence 34578899988754332 236888887765443
No 296
>PTZ00064 histone acetyltransferase; Provisional
Probab=21.25 E-value=67 Score=24.22 Aligned_cols=24 Identities=29% Similarity=0.481 Sum_probs=21.5
Q ss_pred CCcccCCCchhccCChHHHHhHHH
Q psy8937 117 PGILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
...|.|+.|-+-|.....|.+|+.
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~ 301 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLS 301 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHh
Confidence 456899999999999999999986
No 297
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.15 E-value=35 Score=23.85 Aligned_cols=44 Identities=23% Similarity=0.434 Sum_probs=22.1
Q ss_pred CCCccCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 10 GSKPLHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 10 ~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
......+...-.|++||..=. .+.+ +.....+.+-..|+.|+-.
T Consensus 178 ~~~~~~~~~~~~CPvCGs~P~-~s~v--~~~~~~G~RyL~CslC~te 221 (309)
T PRK03564 178 KARAEYGEQRQFCPVCGSMPV-SSVV--QIGTTQGLRYLHCNLCESE 221 (309)
T ss_pred ccccccccCCCCCCCCCCcch-hhee--eccCCCCceEEEcCCCCCc
Confidence 333334556778999998521 1111 1222223355567777643
No 298
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.99 E-value=35 Score=14.95 Aligned_cols=11 Identities=27% Similarity=0.812 Sum_probs=7.9
Q ss_pred Ccccccccccc
Q psy8937 18 DARYCKICGKH 28 (147)
Q Consensus 18 ~~~~C~~C~~~ 28 (147)
..|+|..|+..
T Consensus 7 ~~Y~C~~C~~~ 17 (32)
T PF13696_consen 7 PGYVCHRCGQK 17 (32)
T ss_pred CCCEeecCCCC
Confidence 45788888764
No 299
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=20.93 E-value=37 Score=16.97 Aligned_cols=12 Identities=42% Similarity=0.908 Sum_probs=4.3
Q ss_pred cCcccccccccc
Q psy8937 17 LDARYCKICGKH 28 (147)
Q Consensus 17 ~~~~~C~~C~~~ 28 (147)
...|+|++||..
T Consensus 31 Lr~y~Cp~CgAt 42 (55)
T PF05741_consen 31 LRKYVCPICGAT 42 (55)
T ss_dssp GGG---TTT---
T ss_pred HhcCcCCCCcCc
Confidence 456888888874
No 300
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.92 E-value=55 Score=24.15 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=7.7
Q ss_pred CCcccccccccCC
Q psy8937 90 DARYCKICGKHYS 102 (147)
Q Consensus 90 ~~~~C~~c~~~~~ 102 (147)
..|.|..||..+.
T Consensus 6 ~~y~C~~Cg~~~~ 18 (446)
T PRK11823 6 TAYVCQECGAESP 18 (446)
T ss_pred CeEECCcCCCCCc
Confidence 3466777765543
No 301
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=20.89 E-value=40 Score=15.42 Aligned_cols=10 Identities=20% Similarity=0.737 Sum_probs=5.3
Q ss_pred ccCCCchhcc
Q psy8937 120 LFCPLCQKCF 129 (147)
Q Consensus 120 ~~C~~C~~~f 129 (147)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5555555443
No 302
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.88 E-value=73 Score=23.64 Aligned_cols=26 Identities=19% Similarity=0.536 Sum_probs=21.3
Q ss_pred ccCcccccccccccCChHHHHHHHHH
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
....|+|..|-+.|.....|.+|+..
T Consensus 195 ~~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 195 CSKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CCeEEEchhhhhhhcCHHHHHHHHhc
Confidence 34678899999999999999988864
No 303
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=20.81 E-value=66 Score=15.65 Aligned_cols=20 Identities=20% Similarity=0.567 Sum_probs=11.6
Q ss_pred CcccCCCchhccCChHHHHhHHH
Q psy8937 118 GILFCPLCQKCFKNKLYLRRHVI 140 (147)
Q Consensus 118 ~~~~C~~C~~~f~~~~~l~~H~~ 140 (147)
++--|+.|...|. .|..|+.
T Consensus 4 k~GYCE~Cr~kfd---~l~~Hi~ 23 (49)
T smart00586 4 KPGYCENCREKYD---DLETHLL 23 (49)
T ss_pred CCcccccHhHHHh---hHHHHhc
Confidence 4445777777665 4445543
No 304
>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=20.76 E-value=1.1e+02 Score=14.23 Aligned_cols=20 Identities=25% Similarity=0.607 Sum_probs=12.1
Q ss_pred HHHHHhcCCCCcCCCCchhh
Q psy8937 37 QHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 37 ~h~~~~~~~~~~~C~~C~~~ 56 (147)
.++...--...+.||.||..
T Consensus 8 ~~l~~~RW~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 8 EYLEEIRWPDGFVCPHCGST 27 (46)
T ss_pred HHHHHhcCCCCCCCCCCCCe
Confidence 34443444455789999854
No 305
>KOG2747|consensus
Probab=20.74 E-value=52 Score=23.85 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=21.7
Q ss_pred CCcccCCCchhccCChHHHHhHHHh
Q psy8937 117 PGILFCPLCQKCFKNKLYLRRHVIS 141 (147)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~~ 141 (147)
...|.|+.|-+-+.....|.+|+..
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~k 180 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKK 180 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHh
Confidence 4568899999999999999999874
No 306
>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=20.41 E-value=49 Score=14.09 Aligned_cols=9 Identities=33% Similarity=0.707 Sum_probs=3.9
Q ss_pred ccCCCchhc
Q psy8937 120 LFCPLCQKC 128 (147)
Q Consensus 120 ~~C~~C~~~ 128 (147)
|.|..|+..
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 344444443
No 307
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.35 E-value=85 Score=23.72 Aligned_cols=26 Identities=15% Similarity=0.418 Sum_probs=22.5
Q ss_pred ccCcccccccccccCChHHHHHHHHH
Q psy8937 16 SLDARYCKICGKHYSNSSNLKQHIRL 41 (147)
Q Consensus 16 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 41 (147)
....|+|..|-+.|.....|.+|+..
T Consensus 277 ~d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 277 VDTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CCeEEEccchhhhhCCHHHHHHHHhc
Confidence 45679999999999999999999874
No 308
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=20.17 E-value=31 Score=24.30 Aligned_cols=28 Identities=29% Similarity=0.472 Sum_probs=18.2
Q ss_pred ccccccccCChHHHHHHHHHhcCCCCcCCCCchhhhc
Q psy8937 22 CKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKCFK 58 (147)
Q Consensus 22 C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 58 (147)
|..|...|....+.. ....|+.||..++
T Consensus 249 C~rC~t~y~le~A~~---------~~wrCpkCGg~ik 276 (403)
T COG1379 249 CSRCYTRYSLEEAKS---------LRWRCPKCGGKIK 276 (403)
T ss_pred HHHhhhccCcchhhh---------hcccCcccccchh
Confidence 677776666544432 2357999998664
No 309
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.09 E-value=53 Score=15.19 Aligned_cols=9 Identities=33% Similarity=0.730 Sum_probs=6.8
Q ss_pred cccCCCchh
Q psy8937 119 ILFCPLCQK 127 (147)
Q Consensus 119 ~~~C~~C~~ 127 (147)
+..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 567899984
No 310
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=20.03 E-value=34 Score=21.46 Aligned_cols=39 Identities=28% Similarity=0.438 Sum_probs=23.8
Q ss_pred cCccCcccccccccccCChHHHHHHHHHhcCCCCcCCCCchhh
Q psy8937 14 LHSLDARYCKICGKHYSNSSNLKQHIRLIHLPGILFCPLCQKC 56 (147)
Q Consensus 14 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 56 (147)
|.+.....|..|++.+...... .. ........|+.|+..
T Consensus 100 HG~l~~~~C~~C~~~~~~~~~~-~~---~~~~~~~~C~~C~~~ 138 (178)
T PF02146_consen 100 HGSLFRLRCSKCGKEYDREDIV-DS---IDEEEPPRCPKCGGL 138 (178)
T ss_dssp TEEEEEEEETTTSBEEEGHHHH-HH---HHTTSSCBCTTTSCB
T ss_pred HhhhceeeecCCCccccchhhc-cc---ccccccccccccCcc
Confidence 3445668899999987654322 22 223334488988874
Done!