Query psy8966
Match_columns 175
No_of_seqs 119 out of 1119
Neff 10.8
Searched_HMMs 46136
Date Sat Aug 17 00:15:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8966hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.4E-28 5.3E-33 167.2 5.8 123 10-168 129-254 (279)
2 KOG2462|consensus 99.9 9E-23 2E-27 140.0 6.6 107 9-151 159-265 (279)
3 KOG3608|consensus 99.8 4.2E-20 9.1E-25 130.7 6.2 160 7-171 172-366 (467)
4 KOG1074|consensus 99.8 1.1E-19 2.4E-24 140.5 3.3 71 96-170 604-681 (958)
5 KOG3608|consensus 99.8 9.6E-19 2.1E-23 123.9 5.3 123 41-168 177-332 (467)
6 KOG3576|consensus 99.7 2.5E-17 5.4E-22 108.6 2.6 97 39-167 115-222 (267)
7 KOG1074|consensus 99.6 9E-17 2E-21 124.7 2.6 61 99-163 881-941 (958)
8 KOG3623|consensus 99.6 1.4E-15 3E-20 116.8 3.5 97 42-168 211-320 (1007)
9 KOG3576|consensus 99.5 2.5E-15 5.4E-20 99.2 2.1 115 9-157 115-240 (267)
10 KOG3623|consensus 99.5 5.1E-15 1.1E-19 113.7 2.6 119 12-151 211-331 (1007)
11 PHA00733 hypothetical protein 99.0 3.2E-10 6.8E-15 71.9 4.5 101 25-154 24-124 (128)
12 PF13465 zf-H2C2_2: Zinc-finge 99.0 2.3E-10 5E-15 51.8 1.4 25 144-168 1-25 (26)
13 PLN03086 PRLI-interacting fact 99.0 5.6E-10 1.2E-14 86.0 4.1 136 13-170 409-554 (567)
14 PHA02768 hypothetical protein; 98.9 6.7E-10 1.4E-14 58.6 1.5 42 98-145 6-47 (55)
15 PHA02768 hypothetical protein; 98.9 7.7E-10 1.7E-14 58.4 1.7 38 127-168 5-42 (55)
16 PLN03086 PRLI-interacting fact 98.8 2.5E-08 5.5E-13 77.1 7.6 101 42-153 454-564 (567)
17 PHA00616 hypothetical protein 98.8 6.4E-09 1.4E-13 52.3 2.3 35 127-163 1-35 (44)
18 PF13465 zf-H2C2_2: Zinc-finge 98.7 2.9E-09 6.3E-14 48.2 0.7 26 114-141 1-26 (26)
19 PHA00733 hypothetical protein 98.7 2.3E-08 5.1E-13 63.4 4.4 84 7-124 36-124 (128)
20 KOG3993|consensus 98.6 2.5E-08 5.4E-13 73.2 2.8 106 12-123 268-380 (500)
21 PHA00616 hypothetical protein 98.4 1.5E-07 3.2E-12 47.4 1.7 32 97-130 1-32 (44)
22 PHA00732 hypothetical protein 98.1 1E-06 2.2E-11 50.9 1.4 47 97-153 1-48 (79)
23 PHA00732 hypothetical protein 98.1 1.5E-06 3.3E-11 50.2 1.7 38 127-169 1-39 (79)
24 KOG3993|consensus 98.1 1.1E-06 2.4E-11 64.8 1.0 81 42-154 268-381 (500)
25 COG5189 SFP1 Putative transcri 98.0 1.6E-06 3.5E-11 61.7 0.9 54 95-150 347-419 (423)
26 PF05605 zf-Di19: Drought indu 98.0 2.1E-05 4.5E-10 42.2 4.6 51 97-154 2-54 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.0 2.4E-06 5.2E-11 37.3 0.5 22 128-151 1-22 (23)
28 PF00096 zf-C2H2: Zinc finger, 97.6 5.7E-05 1.2E-09 32.8 2.3 22 42-65 1-22 (23)
29 PF13894 zf-C2H2_4: C2H2-type 97.6 2.6E-05 5.6E-10 34.1 1.0 23 128-152 1-23 (24)
30 PF13912 zf-C2H2_6: C2H2-type 97.6 1.8E-05 3.9E-10 35.9 0.1 23 128-152 2-24 (27)
31 smart00355 ZnF_C2H2 zinc finge 97.2 0.00027 5.8E-09 31.3 2.0 24 128-153 1-24 (26)
32 PF05605 zf-Di19: Drought indu 97.2 0.00084 1.8E-08 35.9 4.2 50 11-67 2-53 (54)
33 PF13894 zf-C2H2_4: C2H2-type 97.2 0.00046 1E-08 29.9 2.5 23 42-66 1-23 (24)
34 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00035 7.5E-09 31.5 1.9 24 42-67 2-25 (27)
35 COG5189 SFP1 Putative transcri 97.2 0.00022 4.8E-09 51.2 1.8 72 39-120 347-419 (423)
36 PF09237 GAGA: GAGA factor; I 97.1 0.00031 6.8E-09 36.3 1.6 31 125-157 22-52 (54)
37 PF12756 zf-C2H2_2: C2H2 type 97.0 0.0008 1.7E-08 40.6 3.1 24 97-122 50-73 (100)
38 PRK04860 hypothetical protein; 96.9 0.0005 1.1E-08 45.3 1.5 35 127-167 119-153 (160)
39 PF12756 zf-C2H2_2: C2H2 type 96.5 0.0011 2.4E-08 40.0 1.0 47 104-152 4-73 (100)
40 PF13909 zf-H2C2_5: C2H2-type 96.5 0.0011 2.4E-08 29.0 0.6 19 133-152 4-22 (24)
41 PF12874 zf-met: Zinc-finger o 96.5 0.0007 1.5E-08 29.9 -0.0 22 128-151 1-22 (25)
42 PF09237 GAGA: GAGA factor; I 96.4 0.0059 1.3E-07 31.6 3.0 33 93-127 20-52 (54)
43 PF12874 zf-met: Zinc-finger o 96.2 0.0044 9.6E-08 27.2 1.9 23 42-66 1-23 (25)
44 smart00355 ZnF_C2H2 zinc finge 96.1 0.0071 1.5E-07 26.4 2.5 17 49-65 6-22 (26)
45 PF13909 zf-H2C2_5: C2H2-type 96.0 0.009 1.9E-07 25.9 2.4 23 42-67 1-23 (24)
46 PRK04860 hypothetical protein; 95.9 0.0037 8E-08 41.3 1.2 40 96-143 118-157 (160)
47 COG5048 FOG: Zn-finger [Genera 95.2 0.0041 9E-08 47.4 -0.5 151 11-165 289-454 (467)
48 PF12171 zf-C2H2_jaz: Zinc-fin 95.0 0.0019 4.2E-08 29.1 -1.7 18 133-150 5-22 (27)
49 KOG4173|consensus 94.8 0.015 3.2E-07 39.5 1.4 91 11-122 79-170 (253)
50 PF12171 zf-C2H2_jaz: Zinc-fin 94.3 0.015 3.1E-07 26.1 0.3 22 42-65 2-23 (27)
51 cd00350 rubredoxin_like Rubred 94.1 0.014 3E-07 27.7 -0.0 24 128-165 2-25 (33)
52 KOG1146|consensus 92.9 0.034 7.5E-07 47.6 0.4 140 18-165 441-626 (1406)
53 COG5236 Uncharacterized conser 92.2 0.07 1.5E-06 39.3 1.1 105 41-150 151-272 (493)
54 PF13913 zf-C2HC_2: zinc-finge 92.1 0.079 1.7E-06 23.3 0.9 17 133-150 6-22 (25)
55 smart00451 ZnF_U1 U1-like zinc 91.6 0.21 4.7E-06 23.6 2.2 23 41-65 3-25 (35)
56 smart00451 ZnF_U1 U1-like zinc 91.5 0.096 2.1E-06 24.8 0.9 22 127-150 3-24 (35)
57 COG5236 Uncharacterized conser 90.6 1 2.2E-05 33.5 5.6 74 48-121 225-303 (493)
58 cd00729 rubredoxin_SM Rubredox 90.2 0.095 2.1E-06 25.0 0.2 25 127-165 2-26 (34)
59 COG1592 Rubrerythrin [Energy p 90.2 0.12 2.6E-06 34.3 0.7 24 126-164 133-156 (166)
60 PF09538 FYDLN_acid: Protein o 89.8 0.17 3.6E-06 31.2 1.1 14 154-167 23-36 (108)
61 COG5048 FOG: Zn-finger [Genera 89.1 0.058 1.3E-06 41.1 -1.7 63 97-163 289-357 (467)
62 COG2888 Predicted Zn-ribbon RN 88.6 0.23 5.1E-06 26.7 0.9 32 127-165 27-58 (61)
63 KOG2893|consensus 88.1 0.16 3.5E-06 35.5 0.2 40 103-148 14-53 (341)
64 KOG2893|consensus 87.6 0.19 4.1E-06 35.2 0.3 50 9-67 9-59 (341)
65 PF10571 UPF0547: Uncharacteri 86.7 0.22 4.8E-06 22.1 0.1 9 159-167 16-24 (26)
66 smart00659 RPOLCX RNA polymera 85.6 0.23 4.9E-06 25.2 -0.1 11 156-166 18-28 (44)
67 PRK14890 putative Zn-ribbon RN 84.7 0.28 6E-06 26.4 -0.1 10 156-165 47-56 (59)
68 COG4049 Uncharacterized protei 84.1 0.82 1.8E-05 24.2 1.5 25 8-34 14-38 (65)
69 TIGR02300 FYDLN_acid conserved 83.4 0.54 1.2E-05 29.6 0.8 13 126-140 25-37 (129)
70 TIGR00373 conserved hypothetic 82.9 0.96 2.1E-05 30.0 1.9 30 125-165 107-136 (158)
71 PHA00626 hypothetical protein 82.3 0.18 3.9E-06 26.7 -1.3 13 126-140 22-34 (59)
72 KOG1146|consensus 81.7 0.95 2.1E-05 39.5 1.8 56 92-151 460-540 (1406)
73 smart00834 CxxC_CXXC_SSSS Puta 80.9 0.44 9.6E-06 23.4 -0.2 10 156-165 25-34 (41)
74 COG4049 Uncharacterized protei 80.8 1.5 3.2E-05 23.3 1.7 25 124-150 14-38 (65)
75 PRK06266 transcription initiat 80.1 1.1 2.4E-05 30.3 1.4 29 126-165 116-144 (178)
76 PF07754 DUF1610: Domain of un 80.1 0.69 1.5E-05 20.1 0.3 9 156-164 15-23 (24)
77 PF09723 Zn-ribbon_8: Zinc rib 78.9 0.41 8.8E-06 24.0 -0.7 29 128-165 6-34 (42)
78 smart00531 TFIIE Transcription 78.4 1.1 2.4E-05 29.3 1.0 36 125-166 97-132 (147)
79 COG1996 RPC10 DNA-directed RNA 77.9 0.55 1.2E-05 24.4 -0.4 28 127-166 6-33 (49)
80 PF03604 DNA_RNApol_7kD: DNA d 77.8 0.67 1.5E-05 21.7 -0.1 12 156-167 16-27 (32)
81 KOG4173|consensus 77.0 1.7 3.7E-05 29.9 1.6 80 42-152 80-170 (253)
82 TIGR02605 CxxC_CxxC_SSSS putat 76.5 0.4 8.7E-06 25.1 -1.2 11 128-140 6-16 (52)
83 PF07975 C1_4: TFIIH C1-like d 75.3 0.42 9E-06 25.1 -1.3 32 125-164 19-50 (51)
84 COG4530 Uncharacterized protei 75.1 1.1 2.4E-05 27.4 0.3 12 156-167 25-36 (129)
85 KOG2231|consensus 74.7 8.5 0.00018 31.6 5.1 43 21-65 122-171 (669)
86 PRK00398 rpoP DNA-directed RNA 74.6 0.82 1.8E-05 23.3 -0.3 9 157-165 21-29 (46)
87 TIGR00622 ssl1 transcription f 71.1 7.8 0.00017 24.1 3.3 54 99-164 57-110 (112)
88 PF15269 zf-C2H2_7: Zinc-finge 69.2 4.5 9.7E-05 20.4 1.6 27 96-122 17-43 (54)
89 TIGR02098 MJ0042_CXXC MJ0042 f 68.8 1.2 2.6E-05 21.5 -0.5 8 158-165 26-33 (38)
90 PF08209 Sgf11: Sgf11 (transcr 68.4 1.5 3.2E-05 20.7 -0.2 17 156-172 3-19 (33)
91 KOG4124|consensus 66.1 1 2.2E-05 33.5 -1.4 53 95-149 347-418 (442)
92 smart00614 ZnF_BED BED zinc fi 66.0 3.1 6.8E-05 21.5 0.8 17 104-120 23-44 (50)
93 PF12013 DUF3505: Protein of u 64.4 4 8.6E-05 25.1 1.2 19 104-122 89-107 (109)
94 PF12013 DUF3505: Protein of u 63.8 7.6 0.00016 23.8 2.3 25 42-68 81-109 (109)
95 KOG2482|consensus 62.9 31 0.00066 26.1 5.5 103 42-151 196-356 (423)
96 PF05443 ROS_MUCR: ROS/MUCR tr 61.8 3.7 7.9E-05 26.3 0.7 24 98-126 73-96 (132)
97 PRK09678 DNA-binding transcrip 60.2 1.5 3.2E-05 24.9 -1.2 18 125-142 25-42 (72)
98 KOG4377|consensus 57.4 10 0.00023 29.1 2.4 29 9-37 269-297 (480)
99 KOG3408|consensus 56.5 8.3 0.00018 24.2 1.5 27 93-121 53-79 (129)
100 PF02176 zf-TRAF: TRAF-type zi 55.0 3.8 8.3E-05 21.9 -0.1 17 114-130 25-41 (60)
101 PF02892 zf-BED: BED zinc fing 54.6 7.3 0.00016 19.4 1.0 17 133-149 20-40 (45)
102 smart00734 ZnF_Rad18 Rad18-lik 54.6 8.6 0.00019 16.9 1.1 19 129-150 3-21 (26)
103 COG2331 Uncharacterized protei 54.3 8.7 0.00019 21.9 1.2 6 159-164 35-40 (82)
104 COG4957 Predicted transcriptio 54.0 7.3 0.00016 24.9 1.0 20 104-126 81-100 (148)
105 PF14446 Prok-RING_1: Prokaryo 52.7 5.9 0.00013 21.0 0.4 8 133-140 9-16 (54)
106 PF12907 zf-met2: Zinc-binding 52.3 11 0.00023 18.7 1.2 26 128-155 2-30 (40)
107 KOG2593|consensus 51.8 14 0.00029 28.7 2.3 36 124-164 125-160 (436)
108 PF13719 zinc_ribbon_5: zinc-r 51.2 14 0.0003 17.7 1.6 33 13-54 4-36 (37)
109 KOG4167|consensus 50.9 7.7 0.00017 32.1 1.0 25 128-154 793-817 (907)
110 PF13824 zf-Mss51: Zinc-finger 50.5 8.3 0.00018 20.6 0.8 17 124-142 11-27 (55)
111 PF09986 DUF2225: Uncharacteri 49.3 2.2 4.7E-05 29.9 -2.0 16 96-113 4-19 (214)
112 KOG2231|consensus 48.9 32 0.0007 28.5 4.1 102 51-164 122-245 (669)
113 PF05290 Baculo_IE-1: Baculovi 47.5 20 0.00043 23.0 2.2 62 89-171 72-135 (140)
114 PHA03082 DNA-dependent RNA pol 47.3 2.8 6.1E-05 22.3 -1.3 20 156-175 3-22 (63)
115 PF05864 Chordopox_RPO7: Chord 46.8 2.8 6.2E-05 22.3 -1.3 20 156-175 3-22 (63)
116 PF13717 zinc_ribbon_4: zinc-r 46.3 19 0.00041 17.2 1.6 32 13-53 4-35 (36)
117 PF08274 PhnA_Zn_Ribbon: PhnA 45.9 6.8 0.00015 18.0 -0.0 8 157-164 19-26 (30)
118 KOG2186|consensus 44.8 19 0.00041 25.9 2.0 46 12-64 4-49 (276)
119 PF05191 ADK_lid: Adenylate ki 43.1 6.7 0.00015 18.9 -0.3 12 154-165 18-29 (36)
120 COG1997 RPL43A Ribosomal prote 41.8 11 0.00023 22.2 0.4 13 126-140 52-64 (89)
121 PF07295 DUF1451: Protein of u 40.7 5 0.00011 26.2 -1.2 37 121-169 102-142 (146)
122 KOG4167|consensus 40.6 11 0.00024 31.3 0.4 24 11-36 792-815 (907)
123 TIGR03831 YgiT_finger YgiT-typ 40.5 12 0.00025 18.6 0.4 12 158-169 33-44 (46)
124 KOG3408|consensus 40.5 19 0.00042 22.6 1.4 23 127-151 57-79 (129)
125 COG3357 Predicted transcriptio 40.1 11 0.00024 22.3 0.2 14 156-169 57-70 (97)
126 PF14311 DUF4379: Domain of un 38.5 13 0.00028 19.6 0.4 13 128-142 29-41 (55)
127 KOG2807|consensus 37.7 34 0.00075 25.6 2.5 59 96-164 289-374 (378)
128 COG1675 TFA1 Transcription ini 37.2 30 0.00066 23.4 2.0 29 125-164 111-139 (176)
129 KOG1280|consensus 36.7 24 0.00052 26.6 1.6 21 97-119 79-99 (381)
130 PRK12380 hydrogenase nickel in 36.3 12 0.00026 23.3 0.0 11 128-140 71-81 (113)
131 KOG2907|consensus 35.8 13 0.00028 23.0 0.1 13 42-56 26-38 (116)
132 PTZ00255 60S ribosomal protein 35.0 11 0.00025 22.3 -0.2 17 156-172 53-69 (90)
133 TIGR00100 hypA hydrogenase nic 34.8 13 0.00029 23.1 0.1 11 128-140 71-81 (115)
134 PF01780 Ribosomal_L37ae: Ribo 32.7 6.6 0.00014 23.3 -1.4 16 157-172 53-68 (90)
135 PF13878 zf-C2H2_3: zinc-finge 32.7 51 0.0011 16.2 2.0 23 12-36 14-38 (41)
136 PF10276 zf-CHCC: Zinc-finger 32.2 11 0.00024 18.6 -0.5 11 157-167 29-39 (40)
137 PRK00564 hypA hydrogenase nick 32.0 18 0.00039 22.6 0.3 11 128-140 72-82 (117)
138 KOG2636|consensus 31.5 30 0.00066 27.0 1.5 29 120-150 394-423 (497)
139 KOG2785|consensus 31.3 57 0.0012 25.0 2.8 52 96-151 165-242 (390)
140 PF04959 ARS2: Arsenite-resist 31.3 15 0.00032 25.8 -0.2 25 127-153 77-101 (214)
141 PF06524 NOA36: NOA36 protein; 30.9 11 0.00025 27.0 -0.8 27 124-152 206-232 (314)
142 PF04423 Rad50_zn_hook: Rad50 30.5 17 0.00036 19.1 0.0 11 159-169 22-32 (54)
143 KOG2186|consensus 30.5 33 0.00071 24.7 1.4 46 98-150 4-49 (276)
144 smart00154 ZnF_AN1 AN1-like Zi 30.4 20 0.00042 17.5 0.2 11 157-167 12-22 (39)
145 PF07649 C1_3: C1-like domain; 29.3 22 0.00048 16.0 0.3 11 156-166 14-24 (30)
146 TIGR00280 L37a ribosomal prote 29.0 15 0.00033 21.9 -0.4 17 156-172 52-68 (91)
147 PRK03824 hypA hydrogenase nick 28.7 11 0.00025 24.2 -1.0 7 158-164 108-114 (135)
148 smart00661 RPOL9 RNA polymeras 27.8 23 0.00049 18.1 0.2 12 127-140 20-31 (52)
149 PF01428 zf-AN1: AN1-like Zinc 27.8 16 0.00036 18.1 -0.3 12 156-167 12-23 (43)
150 PF01155 HypA: Hydrogenase exp 27.7 8.4 0.00018 23.9 -1.7 25 128-166 71-95 (113)
151 COG1571 Predicted DNA-binding 26.8 34 0.00074 26.6 1.1 14 127-142 367-380 (421)
152 PF07282 OrfB_Zn_ribbon: Putat 26.6 23 0.0005 19.5 0.1 12 125-138 44-55 (69)
153 PRK14892 putative transcriptio 26.5 13 0.00029 22.5 -0.9 11 128-140 43-53 (99)
154 PRK03681 hypA hydrogenase nick 26.4 22 0.00049 22.1 0.0 7 158-164 88-94 (114)
155 KOG2785|consensus 25.6 1E+02 0.0022 23.8 3.2 74 41-121 166-242 (390)
156 COG5112 UFD2 U1-like Zn-finger 25.3 37 0.00079 20.8 0.8 25 94-120 52-76 (126)
157 COG3677 Transposase and inacti 25.2 33 0.00071 21.9 0.6 14 155-168 51-64 (129)
158 KOG2482|consensus 24.9 37 0.00081 25.6 0.9 51 97-151 144-217 (423)
159 PF14353 CpXC: CpXC protein 24.2 26 0.00057 22.1 0.1 12 156-167 37-48 (128)
160 TIGR01206 lysW lysine biosynth 24.1 29 0.00063 18.4 0.2 9 158-166 3-11 (54)
161 KOG3507|consensus 23.9 27 0.00058 18.9 0.0 15 126-142 36-50 (62)
162 COG4888 Uncharacterized Zn rib 23.9 10 0.00022 22.9 -1.7 16 95-112 20-35 (104)
163 PF13451 zf-trcl: Probable zin 23.6 36 0.00079 17.7 0.5 14 96-111 3-16 (49)
164 PF14690 zf-ISL3: zinc-finger 22.3 40 0.00087 16.8 0.5 11 156-166 1-11 (47)
165 PF14255 Cys_rich_CPXG: Cystei 22.0 36 0.00077 17.9 0.3 9 159-167 2-10 (52)
166 PRK00432 30S ribosomal protein 22.0 35 0.00076 17.7 0.3 12 126-139 36-47 (50)
167 PF12760 Zn_Tnp_IS1595: Transp 21.8 25 0.00055 17.7 -0.3 10 155-164 35-44 (46)
168 PF08273 Prim_Zn_Ribbon: Zinc- 21.7 32 0.00069 17.0 0.1 7 158-164 4-10 (40)
169 CHL00174 accD acetyl-CoA carbo 21.7 21 0.00046 26.4 -0.8 33 97-142 38-70 (296)
170 KOG0717|consensus 21.4 44 0.00096 26.4 0.8 22 128-151 293-314 (508)
171 PF01286 XPA_N: XPA protein N- 21.3 35 0.00076 16.2 0.2 14 159-172 5-18 (34)
172 PRK03976 rpl37ae 50S ribosomal 21.1 23 0.0005 21.1 -0.6 16 156-171 53-68 (90)
173 PRK06393 rpoE DNA-directed RNA 20.6 49 0.0011 18.3 0.7 14 159-172 19-32 (64)
174 COG2879 Uncharacterized small 20.1 1E+02 0.0022 17.0 1.8 14 144-157 27-40 (65)
No 1
>KOG2462|consensus
Probab=99.95 E-value=2.4e-28 Score=167.18 Aligned_cols=123 Identities=38% Similarity=0.737 Sum_probs=108.8
Q ss_pred CCccCCCccchhhccChHHHHHHHhhhcC---CCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccc
Q psy8966 10 RPYKCPVEYCEKAFSTQYSRKAHIRTHTG---EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDF 86 (175)
Q Consensus 10 ~~~~C~~~~C~~~f~~~~~L~~h~~~~~~---~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~ 86 (175)
..|.|. .||+.|...++|.+|..+|.. .+.+.|.. |++.|.+..+|..|+++|.-
T Consensus 129 ~r~~c~--eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~--C~K~YvSmpALkMHirTH~l------------------ 186 (279)
T KOG2462|consen 129 PRYKCP--ECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKY--CGKVYVSMPALKMHIRTHTL------------------ 186 (279)
T ss_pred Cceecc--ccccccccccccchhhcccccccccccccCCC--CCceeeehHHHhhHhhccCC------------------
Confidence 358897 899999999999999999854 45699965 99999999999999999862
Q ss_pred hhhhhccCCcceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhh
Q psy8966 87 VHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILD 166 (175)
Q Consensus 87 ~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~ 166 (175)
+.+|+ .||+.|....-|+.|+++|+|||||.| +.|+++|..+++|+.||++|.+.++|.|+.|+++
T Consensus 187 ----------~c~C~--iCGKaFSRPWLLQGHiRTHTGEKPF~C--~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 187 ----------PCECG--ICGKAFSRPWLLQGHIRTHTGEKPFSC--PHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred ----------Ccccc--cccccccchHHhhcccccccCCCCccC--CcccchhcchHHHHHHHHhhcCCccccCcchhhH
Confidence 56776 899999999999999999999999999 7799999999999999999999999999999988
Q ss_pred hc
Q psy8966 167 CL 168 (175)
Q Consensus 167 ~~ 168 (175)
|.
T Consensus 253 Fs 254 (279)
T KOG2462|consen 253 FA 254 (279)
T ss_pred HH
Confidence 85
No 2
>KOG2462|consensus
Probab=99.88 E-value=9e-23 Score=140.00 Aligned_cols=107 Identities=41% Similarity=0.796 Sum_probs=97.3
Q ss_pred CCCccCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchh
Q psy8966 9 IRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVH 88 (175)
Q Consensus 9 ~~~~~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~ 88 (175)
.+-+.|. .||++|.+...|+.|+++|. .+++|.. ||+.|...=-|+.|+++|+|
T Consensus 159 ~ka~~C~--~C~K~YvSmpALkMHirTH~--l~c~C~i--CGKaFSRPWLLQGHiRTHTG-------------------- 212 (279)
T KOG2462|consen 159 KKAFSCK--YCGKVYVSMPALKMHIRTHT--LPCECGI--CGKAFSRPWLLQGHIRTHTG-------------------- 212 (279)
T ss_pred cccccCC--CCCceeeehHHHhhHhhccC--CCccccc--ccccccchHHhhcccccccC--------------------
Confidence 5568897 99999999999999999997 5799955 99999988888888777665
Q ss_pred hhhccCCcceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHH
Q psy8966 89 LRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRT 151 (175)
Q Consensus 89 ~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~ 151 (175)
||||.|+ .|++.|.+.++|..|+.+|.+.|+|.| ..|+|.|..++.|..|..+
T Consensus 213 ------EKPF~C~--hC~kAFADRSNLRAHmQTHS~~K~~qC--~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 213 ------EKPFSCP--HCGKAFADRSNLRAHMQTHSDVKKHQC--PRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ------CCCccCC--cccchhcchHHHHHHHHhhcCCccccC--cchhhHHHHHHHHHHhhhh
Confidence 8899998 899999999999999999999999999 8899999999999999865
No 3
>KOG3608|consensus
Probab=99.81 E-value=4.2e-20 Score=130.68 Aligned_cols=160 Identities=27% Similarity=0.457 Sum_probs=113.5
Q ss_pred CCCCC-ccCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHH---------------------
Q psy8966 7 SGIRP-YKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVR--------------------- 64 (175)
Q Consensus 7 ~~~~~-~~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~--------------------- 64 (175)
.+++| +.|.|..|-..+.++..|++|+++|++++...|+. ||..|.....|..|++
T Consensus 172 ~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~--Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaT 249 (467)
T KOG3608|consen 172 EDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPH--CGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFAT 249 (467)
T ss_pred CCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecch--HHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhH
Confidence 34444 55666677777777777777777776666666654 6666666666655554
Q ss_pred ---------HhcCCCCCCCCCCccchhcccchhhh-hccCCcceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCccc
Q psy8966 65 ---------THTGKYTPGPGIDSRLIVREDFVHLR-IHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEF 134 (175)
Q Consensus 65 ---------~h~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~ 134 (175)
.|..-..|--+.......+++..|++ .|...+||+|. .|++.+...++|+.|..+|. +..|.|.++.
T Consensus 250 eklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd--~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~ 326 (467)
T KOG3608|consen 250 EKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCD--ECDTRCVRESDLAKHVQVHS-KTVYQCEHPD 326 (467)
T ss_pred HHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCcccc--chhhhhccHHHHHHHHHhcc-ccceecCCCC
Confidence 34333323222223333334445655 46779999995 89999999999999999996 7789996666
Q ss_pred chHHHhchhhHHHHHHHhc-C--CccccCCcchhhhcccc
Q psy8966 135 CSKSFKTSGDLQKHVRTHT-G--KYTAEVPGSILDCLSGR 171 (175)
Q Consensus 135 C~~~f~~~~~l~~H~~~h~-~--~~~~~C~~c~~~~~~~~ 171 (175)
|.+++++...|.+|++.++ | +.+|.|..|.+.|.+|.
T Consensus 327 C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~ 366 (467)
T KOG3608|consen 327 CHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGK 366 (467)
T ss_pred CcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccch
Confidence 9999999999999999655 4 36699999999999885
No 4
>KOG1074|consensus
Probab=99.77 E-value=1.1e-19 Score=140.52 Aligned_cols=71 Identities=31% Similarity=0.675 Sum_probs=64.5
Q ss_pred cceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHHhcCC----ccccCC---cchhhhc
Q psy8966 96 RPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGK----YTAEVP---GSILDCL 168 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~----~~~~C~---~c~~~~~ 168 (175)
.|..|+ .|.+.....+.|+.|+++|+|++||+| .+||.+|.++.+|+.||.+|-.. .++.|| +|...|.
T Consensus 604 dPNqCi--iC~rVlSC~saLqmHyrtHtGERPFkC--KiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 604 DPNQCI--ICLRVLSCPSALQMHYRTHTGERPFKC--KICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred Ccccee--eeeecccchhhhhhhhhcccCcCcccc--ccccchhccccchhhcccccccCccccccccCCchhhhccccc
Confidence 466797 899999999999999999999999999 99999999999999999998765 568999 9988887
Q ss_pred cc
Q psy8966 169 SG 170 (175)
Q Consensus 169 ~~ 170 (175)
++
T Consensus 680 n~ 681 (958)
T KOG1074|consen 680 NA 681 (958)
T ss_pred cc
Confidence 65
No 5
>KOG3608|consensus
Probab=99.75 E-value=9.6e-19 Score=123.87 Aligned_cols=123 Identities=28% Similarity=0.519 Sum_probs=81.3
Q ss_pred CeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchh--cccchhhhhcc--C----------------------
Q psy8966 41 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIV--REDFVHLRIHS--G---------------------- 94 (175)
Q Consensus 41 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~--~~~~~~~~~~~--~---------------------- 94 (175)
.+.|.+..|-..+.++..|..|++.|.+++.-.......++. ....+|.+..+ .
T Consensus 177 v~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~H 256 (467)
T KOG3608|consen 177 VTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSH 256 (467)
T ss_pred eeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHH
Confidence 488988889999999999999999999987632222222211 22233333221 1
Q ss_pred ----CcceeccCCCcccccCCHHHHHHHHh-hhcCCCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCc--chhhh
Q psy8966 95 ----IRPYKCPVEYCEKAFSTQYSRKAHIR-THTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPG--SILDC 167 (175)
Q Consensus 95 ----~~~~~C~~~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--c~~~~ 167 (175)
..-|+|| .|+.+....++|..|++ .|..++||+| +.|++.+.+.++|..|..+|. +..|.|+. |.+++
T Consensus 257 v~rHvn~ykCp--lCdmtc~~~ssL~~H~r~rHs~dkpfKC--d~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~ 331 (467)
T KOG3608|consen 257 VVRHVNCYKCP--LCDMTCSSASSLTTHIRYRHSKDKPFKC--DECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSV 331 (467)
T ss_pred HHHhhhccccc--ccccCCCChHHHHHHHHhhhccCCCccc--cchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHH
Confidence 2345565 66666666677777754 4666778888 778888888888888877776 66677776 76655
Q ss_pred c
Q psy8966 168 L 168 (175)
Q Consensus 168 ~ 168 (175)
.
T Consensus 332 r 332 (467)
T KOG3608|consen 332 R 332 (467)
T ss_pred H
Confidence 4
No 6
>KOG3576|consensus
Probab=99.67 E-value=2.5e-17 Score=108.56 Aligned_cols=97 Identities=28% Similarity=0.673 Sum_probs=82.2
Q ss_pred CCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCCcccccCCHHHHHHH
Q psy8966 39 EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAH 118 (175)
Q Consensus 39 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H 118 (175)
...|.| ++|++.|.-..-|++|++.|.. .+.+.|. .||+.|.+--+|++|
T Consensus 115 ~d~ftC--rvCgK~F~lQRmlnrh~kch~~--------------------------vkr~lct--~cgkgfndtfdlkrh 164 (267)
T KOG3576|consen 115 QDSFTC--RVCGKKFGLQRMLNRHLKCHSD--------------------------VKRHLCT--FCGKGFNDTFDLKRH 164 (267)
T ss_pred CCeeee--ehhhhhhhHHHHHHHHhhhccH--------------------------HHHHHHh--hccCcccchhhhhhh
Confidence 345899 5699999999999999887654 5567887 799999999999999
Q ss_pred HhhhcCCCcccCCcccchHHHhchhhHHHHHHHhcC-----------CccccCCcchhhh
Q psy8966 119 IRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTG-----------KYTAEVPGSILDC 167 (175)
Q Consensus 119 ~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~-----------~~~~~C~~c~~~~ 167 (175)
+++|+|.+||+| +.|+++|.++..|..|.+.-+| ++.|.|+.||++.
T Consensus 165 ~rthtgvrpykc--~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 165 TRTHTGVRPYKC--SLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTS 222 (267)
T ss_pred hccccCccccch--hhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCC
Confidence 999999999999 9999999999999999974333 2669999999764
No 7
>KOG1074|consensus
Probab=99.63 E-value=9e-17 Score=124.69 Aligned_cols=61 Identities=39% Similarity=0.761 Sum_probs=55.0
Q ss_pred eccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcc
Q psy8966 99 KCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGS 163 (175)
Q Consensus 99 ~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c 163 (175)
.|. .|++.|.+.++|..|+++|+++|||.| ..|++.|..+.+|..||..|...+|..=.+|
T Consensus 881 ~C~--vCgk~FsSSsALqiH~rTHtg~KPF~C--~fC~~aFttrgnLKvHMgtH~w~q~~srrG~ 941 (958)
T KOG1074|consen 881 VCN--VCGKQFSSSAALEIHMRTHTGPKPFFC--HFCEEAFTTRGNLKVHMGTHMWVQPPSRRGP 941 (958)
T ss_pred hhc--cchhcccchHHHHHhhhcCCCCCCccc--hhhhhhhhhhhhhhhhhccccccCCCccCCC
Confidence 475 899999999999999999999999999 9999999999999999999988877654443
No 8
>KOG3623|consensus
Probab=99.57 E-value=1.4e-15 Score=116.76 Aligned_cols=97 Identities=24% Similarity=0.547 Sum_probs=82.0
Q ss_pred eeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCCcccccCCHHHHHHHHhh
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRT 121 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~ 121 (175)
..|++ |.+.+....+|+.|++..+.. .+..|.|. .|.++|...+.|.+|+.+
T Consensus 211 ltcpy--cdrgykrltslkeHikyrhek------------------------ne~nfsC~--lCsytFAyRtQLErhm~~ 262 (1007)
T KOG3623|consen 211 LTCPY--CDRGYKRLTSLKEHIKYRHEK------------------------NEPNFSCM--LCSYTFAYRTQLERHMQL 262 (1007)
T ss_pred hcchh--HHHHHHHHHHHHHHHHHHHhh------------------------CCCCCcch--hhhhhhhhHHHHHHHHHh
Confidence 57876 999999999999998875431 14457786 899999999999999998
Q ss_pred hcC-------------CCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhhhc
Q psy8966 122 HTG-------------EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILDCL 168 (175)
Q Consensus 122 h~~-------------~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~~~ 168 (175)
|.- .+.|+| .+|||+|+.+..|..|+|+|.||+||+|+.|++.|.
T Consensus 263 hkpg~dqa~sltqsa~lRKFKC--tECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFS 320 (1007)
T KOG3623|consen 263 HKPGGDQAISLTQSALLRKFKC--TECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFS 320 (1007)
T ss_pred hcCCCcccccccchhhhccccc--cccchhhhhHHHHHhhheeecCCCCcCCcccccccc
Confidence 842 245999 779999999999999999999999999999998874
No 9
>KOG3576|consensus
Probab=99.53 E-value=2.5e-15 Score=99.19 Aligned_cols=115 Identities=35% Similarity=0.671 Sum_probs=100.2
Q ss_pred CCCccCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchh
Q psy8966 9 IRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVH 88 (175)
Q Consensus 9 ~~~~~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~ 88 (175)
...|.|. .||+.|.....|.+|++.|...+.+.|.. ||+.|...-.|.+|+++|+|
T Consensus 115 ~d~ftCr--vCgK~F~lQRmlnrh~kch~~vkr~lct~--cgkgfndtfdlkrh~rthtg-------------------- 170 (267)
T KOG3576|consen 115 QDSFTCR--VCGKKFGLQRMLNRHLKCHSDVKRHLCTF--CGKGFNDTFDLKRHTRTHTG-------------------- 170 (267)
T ss_pred CCeeeee--hhhhhhhHHHHHHHHhhhccHHHHHHHhh--ccCcccchhhhhhhhccccC--------------------
Confidence 3458887 99999999999999999999999999966 99999999999999888766
Q ss_pred hhhccCCcceeccCCCcccccCCHHHHHHHHh-hhc----------CCCcccCCcccchHHHhchhhHHHHHHHhcCCcc
Q psy8966 89 LRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIR-THT----------GEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYT 157 (175)
Q Consensus 89 ~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~-~h~----------~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~ 157 (175)
.+||+|. .|++.|...-+|..|.+ +|. .++.|.| +.||+.-.....+..|++.|++--|
T Consensus 171 ------vrpykc~--~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vc--edcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 171 ------VRPYKCS--LCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVC--EDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred ------ccccchh--hhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeee--cccCCCCCChhHHHHHHHhcCCCCH
Confidence 7899996 89999999999999964 442 3467999 9999999999999999999877544
No 10
>KOG3623|consensus
Probab=99.51 E-value=5.1e-15 Score=113.74 Aligned_cols=119 Identities=33% Similarity=0.700 Sum_probs=97.4
Q ss_pred ccCCCccchhhccChHHHHHHHhhhcC--CCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhh
Q psy8966 12 YKCPVEYCEKAFSTQYSRKAHIRTHTG--EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHL 89 (175)
Q Consensus 12 ~~C~~~~C~~~f~~~~~L~~h~~~~~~--~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~ 89 (175)
..|+ +|+..+.....|++|++..+. +..|.|.. |...|.....|.+||..|..-.... .+.
T Consensus 211 ltcp--ycdrgykrltslkeHikyrhekne~nfsC~l--CsytFAyRtQLErhm~~hkpg~dqa-------------~sl 273 (1007)
T KOG3623|consen 211 LTCP--YCDRGYKRLTSLKEHIKYRHEKNEPNFSCML--CSYTFAYRTQLERHMQLHKPGGDQA-------------ISL 273 (1007)
T ss_pred hcch--hHHHHHHHHHHHHHHHHHHHhhCCCCCcchh--hhhhhhhHHHHHHHHHhhcCCCccc-------------ccc
Confidence 5687 999999999999999986433 34599965 9999999999999999986522110 111
Q ss_pred hhccCCcceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHH
Q psy8966 90 RIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRT 151 (175)
Q Consensus 90 ~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~ 151 (175)
-.....+.|+|+ +|++.|+.+-.|+.|+++|.|+|||.| +.|+|.|..+..+..||.+
T Consensus 274 tqsa~lRKFKCt--ECgKAFKfKHHLKEHlRIHSGEKPfeC--pnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 274 TQSALLRKFKCT--ECGKAFKFKHHLKEHLRIHSGEKPFEC--PNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cchhhhcccccc--ccchhhhhHHHHHhhheeecCCCCcCC--cccccccccCCcccccccc
Confidence 122335689998 999999999999999999999999999 8899999999999999864
No 11
>PHA00733 hypothetical protein
Probab=99.04 E-value=3.2e-10 Score=71.86 Aligned_cols=101 Identities=25% Similarity=0.331 Sum_probs=74.1
Q ss_pred ChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCC
Q psy8966 25 TQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEY 104 (175)
Q Consensus 25 ~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~ 104 (175)
+.+.|.++-..-...+.+.|. +|...|.....|..+.... .++ ...+.+||.|+ .
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~~~l~--------------------~~~-~~~~~kPy~C~--~ 78 (128)
T PHA00733 24 TLEELKRYHSLTPEQKRLIRA--VVKTLIYNPQLLDESSYLY--------------------KLL-TSKAVSPYVCP--L 78 (128)
T ss_pred CHHHhhhhhcCChhhhhHHHH--HHhhhccChhhhcchHHHH--------------------hhc-ccCCCCCccCC--C
Confidence 444554443333345668895 4999998877777662211 112 22347899997 8
Q ss_pred cccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHHhcC
Q psy8966 105 CEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTG 154 (175)
Q Consensus 105 C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~ 154 (175)
|++.|.+..+|..|+..+ +.+|.| ++|++.|.....|..|+...++
T Consensus 79 Cgk~Fss~s~L~~H~r~h--~~~~~C--~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 79 CLMPFSSSVSLKQHIRYT--EHSKVC--PVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCcCCCHHHHHHHHhcC--CcCccC--CCCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999876 467999 8899999999999999987665
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.97 E-value=2.3e-10 Score=51.83 Aligned_cols=25 Identities=32% Similarity=0.444 Sum_probs=17.7
Q ss_pred hHHHHHHHhcCCccccCCcchhhhc
Q psy8966 144 DLQKHVRTHTGKYTAEVPGSILDCL 168 (175)
Q Consensus 144 ~l~~H~~~h~~~~~~~C~~c~~~~~ 168 (175)
+|.+|+++|+|++||.|+.|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3667777777777777777777664
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.97 E-value=5.6e-10 Score=85.99 Aligned_cols=136 Identities=17% Similarity=0.317 Sum_probs=86.3
Q ss_pred cCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhc
Q psy8966 13 KCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIH 92 (175)
Q Consensus 13 ~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (175)
.|+ .|...... .+|..|...- ....-.|+..+|+..|.. ..+..|. .|..+... +....+..|++.+
T Consensus 409 ~C~--NC~~~i~l-~~l~lHe~~C-~r~~V~Cp~~~Cg~v~~r-~el~~H~-------~C~~Cgk~-f~~s~LekH~~~~ 475 (567)
T PLN03086 409 ECR--NCKHYIPS-RSIALHEAYC-SRHNVVCPHDGCGIVLRV-EEAKNHV-------HCEKCGQA-FQQGEMEKHMKVF 475 (567)
T ss_pred ECC--CCCCccch-hHHHHHHhhC-CCcceeCCcccccceeec-cccccCc-------cCCCCCCc-cchHHHHHHHHhc
Confidence 465 67775433 5566776432 112245643246666632 2233332 22222211 1223334566665
Q ss_pred cCCcceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhc----------hhhHHHHHHHhcCCccccCCc
Q psy8966 93 SGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKT----------SGDLQKHVRTHTGKYTAEVPG 162 (175)
Q Consensus 93 ~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~----------~~~l~~H~~~h~~~~~~~C~~ 162 (175)
. .++.|+ |++.+ ....|..|+.+|...+++.| ..|++.+.. .+.|..|..+. |.+++.|..
T Consensus 476 H--kpv~Cp---Cg~~~-~R~~L~~H~~thCp~Kpi~C--~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~ 546 (567)
T PLN03086 476 H--EPLQCP---CGVVL-EKEQMVQHQASTCPLRLITC--RFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDS 546 (567)
T ss_pred C--CCccCC---CCCCc-chhHHHhhhhccCCCCceeC--CCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccc
Confidence 3 688995 98755 66899999999999999999 889998852 35799999885 889999999
Q ss_pred chhhhccc
Q psy8966 163 SILDCLSG 170 (175)
Q Consensus 163 c~~~~~~~ 170 (175)
||..+.-.
T Consensus 547 Cgk~Vrlr 554 (567)
T PLN03086 547 CGRSVMLK 554 (567)
T ss_pred cCCeeeeh
Confidence 99876544
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.89 E-value=6.7e-10 Score=58.65 Aligned_cols=42 Identities=24% Similarity=0.604 Sum_probs=29.2
Q ss_pred eeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhH
Q psy8966 98 YKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDL 145 (175)
Q Consensus 98 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l 145 (175)
|.|+ .||+.|...++|..|+++|+ ++|+| .+|++.|.+.+.|
T Consensus 6 y~C~--~CGK~Fs~~~~L~~H~r~H~--k~~kc--~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECP--ICGEIYIKRKSMITHLRKHN--TNLKL--SNCKRISLRTGEY 47 (55)
T ss_pred cCcc--hhCCeeccHHHHHHHHHhcC--CcccC--Ccccceeccccee
Confidence 5665 67777777777777777775 57777 6677777766554
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.89 E-value=7.7e-10 Score=58.40 Aligned_cols=38 Identities=18% Similarity=0.436 Sum_probs=35.0
Q ss_pred cccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhhhc
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILDCL 168 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~~~ 168 (175)
.|.| ++||+.|....+|..|+++|+ .++.|..|++.|.
T Consensus 5 ~y~C--~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~ 42 (55)
T PHA02768 5 GYEC--PICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISL 42 (55)
T ss_pred ccCc--chhCCeeccHHHHHHHHHhcC--CcccCCcccceec
Confidence 4899 889999999999999999999 6999999998765
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.79 E-value=2.5e-08 Score=77.07 Aligned_cols=101 Identities=17% Similarity=0.358 Sum_probs=68.3
Q ss_pred eeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCCcccccC----------C
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCEKAFS----------T 111 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~~~f~----------~ 111 (175)
+.|.. |+..|. ...|..|+..++....|. +. .......+..|+..+-..+++.|+ .|++.+. .
T Consensus 454 ~~C~~--Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg-~~~~R~~L~~H~~thCp~Kpi~C~--fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 454 VHCEK--CGQAFQ-QGEMEKHMKVFHEPLQCP-CG-VVLEKEQMVQHQASTCPLRLITCR--FCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred ccCCC--CCCccc-hHHHHHHHHhcCCCccCC-CC-CCcchhHHHhhhhccCCCCceeCC--CCCCccccCccccchhhh
Confidence 46644 777664 456677776655333343 22 222222334466667778999997 8999985 2
Q ss_pred HHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHHhc
Q psy8966 112 QYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHT 153 (175)
Q Consensus 112 ~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~ 153 (175)
.++|..|..+. +.+++.| ..||+.+..+ +|..|+..-+
T Consensus 527 ~s~Lt~HE~~C-G~rt~~C--~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 527 LRGMSEHESIC-GSRTAPC--DSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred hhhHHHHHHhc-CCcceEc--cccCCeeeeh-hHHHHHHHhh
Confidence 45899998886 8999999 8999988865 6778886543
No 17
>PHA00616 hypothetical protein
Probab=98.75 E-value=6.4e-09 Score=52.30 Aligned_cols=35 Identities=14% Similarity=0.298 Sum_probs=29.9
Q ss_pred cccCCcccchHHHhchhhHHHHHHHhcCCccccCCcc
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGS 163 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c 163 (175)
||+| +.||+.|..+++|.+|++.|+|+.++.|+.-
T Consensus 1 pYqC--~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQC--LRCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CCcc--chhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 6888 7799999999999999999999988888753
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=98.74 E-value=2.9e-09 Score=48.16 Aligned_cols=26 Identities=58% Similarity=1.248 Sum_probs=22.7
Q ss_pred HHHHHHhhhcCCCcccCCcccchHHHhc
Q psy8966 114 SRKAHIRTHTGEKPYRCAHEFCSKSFKT 141 (175)
Q Consensus 114 ~l~~H~~~h~~~~~~~C~~~~C~~~f~~ 141 (175)
+|..|+++|++++||.| ++|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C--~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKC--PYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEE--SSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCC--CCCcCeeCc
Confidence 57899999999999999 889998863
No 19
>PHA00733 hypothetical protein
Probab=98.71 E-value=2.3e-08 Score=63.38 Aligned_cols=84 Identities=20% Similarity=0.346 Sum_probs=64.8
Q ss_pred CCCCCccCCCccchhhccChHHHHHH--Hh---hhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccch
Q psy8966 7 SGIRPYKCPVEYCEKAFSTQYSRKAH--IR---THTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLI 81 (175)
Q Consensus 7 ~~~~~~~C~~~~C~~~f~~~~~L~~h--~~---~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 81 (175)
..++++.|. .|...|.....|..+ +. .+.+..+|.|.. |++.|.+...|..|++.+
T Consensus 36 ~~~~~~~~~--~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~--Cgk~Fss~s~L~~H~r~h--------------- 96 (128)
T PHA00733 36 PEQKRLIRA--VVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPL--CLMPFSSSVSLKQHIRYT--------------- 96 (128)
T ss_pred hhhhhHHHH--HHhhhccChhhhcchHHHHhhcccCCCCCccCCC--CCCcCCCHHHHHHHHhcC---------------
Confidence 346778997 899888877776665 22 234467899965 999999999999997754
Q ss_pred hcccchhhhhccCCcceeccCCCcccccCCHHHHHHHHhhhcC
Q psy8966 82 VREDFVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTG 124 (175)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~ 124 (175)
..++.|. .|++.|.....|..|+...++
T Consensus 97 -------------~~~~~C~--~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 97 -------------EHSKVCP--VCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred -------------CcCccCC--CCCCccCCHHHHHHHHHHhcC
Confidence 1257886 899999999999999876543
No 20
>KOG3993|consensus
Probab=98.61 E-value=2.5e-08 Score=73.20 Aligned_cols=106 Identities=23% Similarity=0.405 Sum_probs=75.6
Q ss_pred ccCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCC--C-ccchhcccchh
Q psy8966 12 YKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGI--D-SRLIVREDFVH 88 (175)
Q Consensus 12 ~~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~--~-~~~~~~~~~~~ 88 (175)
|.|. .|...|.+...|.+|....+-...|.|++ |++.|+-.++|..|++.|.......... . +..........
T Consensus 268 yiCq--LCK~kYeD~F~LAQHrC~RIV~vEYrCPE--C~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ 343 (500)
T KOG3993|consen 268 YICQ--LCKEKYEDAFALAQHRCPRIVHVEYRCPE--CDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQ 343 (500)
T ss_pred HHHH--HHHHhhhhHHHHhhccCCeeEEeeecCCc--ccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhh
Confidence 8887 99999999999999998777777899987 9999999999999999998754322100 0 00000000000
Q ss_pred ----hhhccCCcceeccCCCcccccCCHHHHHHHHhhhc
Q psy8966 89 ----LRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHT 123 (175)
Q Consensus 89 ----~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~ 123 (175)
.-....+..|.|. .|++.|..+.-|..|+.+|.
T Consensus 344 ea~rsg~dss~gi~~C~--~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 344 EAERSGDDSSSGIFSCH--TCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hccccCCcccCceeecH--HhhhhhHHHHHHHHhHHhhh
Confidence 0011335688896 89999999999999976653
No 21
>PHA00616 hypothetical protein
Probab=98.41 E-value=1.5e-07 Score=47.39 Aligned_cols=32 Identities=16% Similarity=0.318 Sum_probs=30.2
Q ss_pred ceeccCCCcccccCCHHHHHHHHhhhcCCCcccC
Q psy8966 97 PYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRC 130 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C 130 (175)
||.|+ .||+.|..+++|..|++.|++++++.|
T Consensus 1 pYqC~--~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCL--RCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccc--hhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 68897 999999999999999999999999888
No 22
>PHA00732 hypothetical protein
Probab=98.14 E-value=1e-06 Score=50.91 Aligned_cols=47 Identities=34% Similarity=0.719 Sum_probs=37.3
Q ss_pred ceeccCCCcccccCCHHHHHHHHhh-hcCCCcccCCcccchHHHhchhhHHHHHHHhc
Q psy8966 97 PYKCPVEYCEKAFSTQYSRKAHIRT-HTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHT 153 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~ 153 (175)
||.|. .|++.|.+.++|..|++. |. ++.| ++|++.|. .+..|..++.
T Consensus 1 py~C~--~Cgk~F~s~s~Lk~H~r~~H~---~~~C--~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCP--ICGFTTVTLFALKQHARRNHT---LTKC--PVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCC--CCCCccCCHHHHHHHhhcccC---CCcc--CCCCCEeC---ChhhhhcccC
Confidence 57786 899999999999999874 54 4589 88999998 5778886543
No 23
>PHA00732 hypothetical protein
Probab=98.10 E-value=1.5e-06 Score=50.18 Aligned_cols=38 Identities=24% Similarity=0.344 Sum_probs=33.0
Q ss_pred cccCCcccchHHHhchhhHHHHHHH-hcCCccccCCcchhhhcc
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRT-HTGKYTAEVPGSILDCLS 169 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~c~~~~~~ 169 (175)
||.| +.|++.|.....|..|++. |++ +.|+.||+.|.+
T Consensus 1 py~C--~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~ 39 (79)
T PHA00732 1 MFKC--PICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR 39 (79)
T ss_pred CccC--CCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC
Confidence 6889 8899999999999999985 654 589999998874
No 24
>KOG3993|consensus
Probab=98.08 E-value=1.1e-06 Score=64.80 Aligned_cols=81 Identities=31% Similarity=0.638 Sum_probs=65.2
Q ss_pred eeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCCcccccCCHHHHHHHHhh
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRT 121 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~ 121 (175)
|.| ++|...|.+.-.|.+|.-... .-..|+|+ +|++.|+...+|..|.++
T Consensus 268 yiC--qLCK~kYeD~F~LAQHrC~RI--------------------------V~vEYrCP--EC~KVFsCPANLASHRRW 317 (500)
T KOG3993|consen 268 YIC--QLCKEKYEDAFALAQHRCPRI--------------------------VHVEYRCP--ECDKVFSCPANLASHRRW 317 (500)
T ss_pred HHH--HHHHHhhhhHHHHhhccCCee--------------------------EEeeecCC--cccccccCchhhhhhhcc
Confidence 788 569999999988888843211 12358997 999999999999999999
Q ss_pred hc--------CCC-------------------------cccCCcccchHHHhchhhHHHHHHHhcC
Q psy8966 122 HT--------GEK-------------------------PYRCAHEFCSKSFKTSGDLQKHVRTHTG 154 (175)
Q Consensus 122 h~--------~~~-------------------------~~~C~~~~C~~~f~~~~~l~~H~~~h~~ 154 (175)
|. +.+ .|.| .+|+|.|+....|+.|+.+|+.
T Consensus 318 HKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C--~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 318 HKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSC--HTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeec--HHhhhhhHHHHHHHHhHHhhhc
Confidence 83 111 3999 8999999999999999888764
No 25
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.02 E-value=1.6e-06 Score=61.74 Aligned_cols=54 Identities=43% Similarity=0.845 Sum_probs=43.2
Q ss_pred CcceeccCCCcccccCCHHHHHHHHhhhc-------------------CCCcccCCcccchHHHhchhhHHHHHH
Q psy8966 95 IRPYKCPVEYCEKAFSTQYSRKAHIRTHT-------------------GEKPYRCAHEFCSKSFKTSGDLQKHVR 150 (175)
Q Consensus 95 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~-------------------~~~~~~C~~~~C~~~f~~~~~l~~H~~ 150 (175)
++||+|++..|++.+..+.+|+-|+.-.+ .+|||.| ++|+|.|+.--.|.-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrC--evC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRC--EVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceec--cccchhhccCccceeccc
Confidence 48999999999999999999999975321 2478888 888888888877777754
No 26
>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=97.99 E-value=2.1e-05 Score=42.18 Aligned_cols=51 Identities=27% Similarity=0.597 Sum_probs=39.5
Q ss_pred ceeccCCCcccccCCHHHHHHHHhh-hcC-CCcccCCcccchHHHhchhhHHHHHHHhcC
Q psy8966 97 PYKCPVEYCEKAFSTQYSRKAHIRT-HTG-EKPYRCAHEFCSKSFKTSGDLQKHVRTHTG 154 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~~~l~~H~~~-h~~-~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~ 154 (175)
.|.|| .|++ ..+..+|..|... |.. .+.+.| ++|...+. .+|.+|+.++++
T Consensus 2 ~f~CP--~C~~-~~~~~~L~~H~~~~H~~~~~~v~C--PiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCP--YCGK-GFSESSLVEHCEDEHRSESKNVVC--PICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCC--CCCC-ccCHHHHHHHHHhHCcCCCCCccC--CCchhhhh--hHHHHHHHHhcC
Confidence 47897 7999 5667899999755 544 357999 99998655 489999987653
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.96 E-value=2.4e-06 Score=37.31 Aligned_cols=22 Identities=41% Similarity=1.081 Sum_probs=12.9
Q ss_pred ccCCcccchHHHhchhhHHHHHHH
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRT 151 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~ 151 (175)
|+| ++|++.|..+..|..|++.
T Consensus 1 y~C--~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKC--PICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEE--TTTTEEESSHHHHHHHHHH
T ss_pred CCC--CCCCCccCCHHHHHHHHhH
Confidence 455 5566666666666666554
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.64 E-value=5.7e-05 Score=32.79 Aligned_cols=22 Identities=41% Similarity=1.044 Sum_probs=13.0
Q ss_pred eeccccccCcccCChHHHHHHHHH
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRT 65 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~ 65 (175)
|.|+. |++.|.+...|..|++.
T Consensus 1 y~C~~--C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPI--CGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETT--TTEEESSHHHHHHHHHH
T ss_pred CCCCC--CCCccCCHHHHHHHHhH
Confidence 45533 66666666666666654
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.61 E-value=2.6e-05 Score=34.11 Aligned_cols=23 Identities=43% Similarity=1.131 Sum_probs=12.1
Q ss_pred ccCCcccchHHHhchhhHHHHHHHh
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRTH 152 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~h 152 (175)
|.| ++|++.|.+...|..|++.|
T Consensus 1 ~~C--~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQC--PICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE---SSTS-EESSHHHHHHHHHHH
T ss_pred CCC--cCCCCcCCcHHHHHHHHHhh
Confidence 455 55666666666666666554
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.56 E-value=1.8e-05 Score=35.92 Aligned_cols=23 Identities=35% Similarity=0.901 Sum_probs=12.7
Q ss_pred ccCCcccchHHHhchhhHHHHHHHh
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRTH 152 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~h 152 (175)
|.| .+|++.|.+..+|..|++.|
T Consensus 2 ~~C--~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FEC--DECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEE--TTTTEEESSHHHHHHHHCTT
T ss_pred CCC--CccCCccCChhHHHHHhHHh
Confidence 455 55555555555555555544
No 31
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.25 E-value=0.00027 Score=31.26 Aligned_cols=24 Identities=50% Similarity=0.964 Sum_probs=16.6
Q ss_pred ccCCcccchHHHhchhhHHHHHHHhc
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRTHT 153 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~h~ 153 (175)
|.| +.|++.|.....|..|++.|.
T Consensus 1 ~~C--~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRC--PECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCC--CCCcchhCCHHHHHHHHHHhc
Confidence 456 667777777777777777554
No 32
>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=97.24 E-value=0.00084 Score=35.87 Aligned_cols=50 Identities=30% Similarity=0.622 Sum_probs=38.3
Q ss_pred CccCCCccchhhccChHHHHHHHhh-hcCC-CCeeccccccCcccCChHHHHHHHHHhc
Q psy8966 11 PYKCPVEYCEKAFSTQYSRKAHIRT-HTGE-KPYRCAHEFCSKSFKTSGDLQKHVRTHT 67 (175)
Q Consensus 11 ~~~C~~~~C~~~f~~~~~L~~h~~~-~~~~-~~~~C~~~~C~~~f~~~~~l~~H~~~h~ 67 (175)
.|.|+ .|++ ..+...|..|... |..+ +.+.|+. |...+. .+|..|+..++
T Consensus 2 ~f~CP--~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPi--C~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCP--YCGK-GFSESSLVEHCEDEHRSESKNVVCPI--CSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCC--CCCC-ccCHHHHHHHHHhHCcCCCCCccCCC--chhhhh--hHHHHHHHHhc
Confidence 48898 9999 6778999999885 5443 4589966 998654 48999988765
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=97.20 E-value=0.00046 Score=29.91 Aligned_cols=23 Identities=43% Similarity=1.096 Sum_probs=11.6
Q ss_pred eeccccccCcccCChHHHHHHHHHh
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTH 66 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h 66 (175)
|.|+. |+..|.+...|..|+..+
T Consensus 1 ~~C~~--C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPI--CGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SS--TS-EESSHHHHHHHHHHH
T ss_pred CCCcC--CCCcCCcHHHHHHHHHhh
Confidence 34533 666666666666665544
No 34
>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=97.17 E-value=0.00035 Score=31.53 Aligned_cols=24 Identities=33% Similarity=0.875 Sum_probs=14.7
Q ss_pred eeccccccCcccCChHHHHHHHHHhc
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTHT 67 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h~ 67 (175)
|.|.. |+..|.+..+|..|++.|.
T Consensus 2 ~~C~~--C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDE--CGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETT--TTEEESSHHHHHHHHCTTT
T ss_pred CCCCc--cCCccCChhHHHHHhHHhc
Confidence 56633 6666666666666665553
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.16 E-value=0.00022 Score=51.21 Aligned_cols=72 Identities=25% Similarity=0.466 Sum_probs=50.0
Q ss_pred CCCeeccccccCcccCChHHHHHHHHH-hcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCCcccccCCHHHHHH
Q psy8966 39 EKPYRCAHEFCSKSFKTSGDLQKHVRT-HTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKA 117 (175)
Q Consensus 39 ~~~~~C~~~~C~~~f~~~~~l~~H~~~-h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~ 117 (175)
.++|+|+.++|.+.+++.-.|.=|+.- |.......... +..+.-.-...+||+|+ .|++.++...+|+-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~--------p~~~~~F~~~~KPYrCe--vC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPS--------PEKMNIFSAKDKPYRCE--VCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCC--------ccccccccccCCceecc--ccchhhccCcccee
Confidence 488999988999999999999988764 33322211110 01112223446899997 79999999999998
Q ss_pred HHh
Q psy8966 118 HIR 120 (175)
Q Consensus 118 H~~ 120 (175)
|+.
T Consensus 417 Hr~ 419 (423)
T COG5189 417 HRK 419 (423)
T ss_pred ccc
Confidence 864
No 36
>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=97.10 E-value=0.00031 Score=36.26 Aligned_cols=31 Identities=26% Similarity=0.560 Sum_probs=14.6
Q ss_pred CCcccCCcccchHHHhchhhHHHHHHHhcCCcc
Q psy8966 125 EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYT 157 (175)
Q Consensus 125 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~ 157 (175)
++|-.| ++|+..+.+..+|.+|+.+.++.+|
T Consensus 22 ~~PatC--P~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATC--PICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE---TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCC--CcchhhccchhhHHHHHHHHhcccC
Confidence 455566 5566666666666666665555443
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.01 E-value=0.0008 Score=40.61 Aligned_cols=24 Identities=33% Similarity=1.028 Sum_probs=16.5
Q ss_pred ceeccCCCcccccCCHHHHHHHHhhh
Q psy8966 97 PYKCPVEYCEKAFSTQYSRKAHIRTH 122 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~~~l~~H~~~h 122 (175)
.+.|. .|++.|.+..+|..|++.+
T Consensus 50 ~~~C~--~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCP--YCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBS--SSS-EESSHHHHHHHHHHT
T ss_pred CCCCC--ccCCCCcCHHHHHHHHcCc
Confidence 56776 6777777777777777654
No 38
>PRK04860 hypothetical protein; Provisional
Probab=96.89 E-value=0.0005 Score=45.33 Aligned_cols=35 Identities=23% Similarity=0.446 Sum_probs=24.0
Q ss_pred cccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhhh
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILDC 167 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~~ 167 (175)
+|.| . |+. ....+.+|.++|+++.+|.|..|+..+
T Consensus 119 ~Y~C--~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 119 PYRC--K-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEc--C-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 4777 5 765 556667777777777777777776554
No 39
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.52 E-value=0.0011 Score=40.01 Aligned_cols=47 Identities=30% Similarity=0.852 Sum_probs=21.3
Q ss_pred CcccccCCHHHHHHHHhhhcC-----------------------CCcccCCcccchHHHhchhhHHHHHHHh
Q psy8966 104 YCEKAFSTQYSRKAHIRTHTG-----------------------EKPYRCAHEFCSKSFKTSGDLQKHVRTH 152 (175)
Q Consensus 104 ~C~~~f~~~~~l~~H~~~h~~-----------------------~~~~~C~~~~C~~~f~~~~~l~~H~~~h 152 (175)
.|+..|.+...|..|+...++ ...+.| ..|++.|.+...|..||+.+
T Consensus 4 ~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C--~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 4 FCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRC--PYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ---------------------------------------------SSEEB--SSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccCCCCCC--CccCCCCcCHHHHHHHHcCc
Confidence 566666666666666532211 124899 89999999999999999974
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.47 E-value=0.0011 Score=28.95 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=8.6
Q ss_pred ccchHHHhchhhHHHHHHHh
Q psy8966 133 EFCSKSFKTSGDLQKHVRTH 152 (175)
Q Consensus 133 ~~C~~~f~~~~~l~~H~~~h 152 (175)
+.|++... ...|..|++.+
T Consensus 4 ~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 4 PHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCcCC-HHHHHHHHHhh
Confidence 44554444 44555555443
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.46 E-value=0.0007 Score=29.87 Aligned_cols=22 Identities=36% Similarity=1.014 Sum_probs=13.9
Q ss_pred ccCCcccchHHHhchhhHHHHHHH
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRT 151 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~ 151 (175)
|.| ++|++.|.+...|..|++.
T Consensus 1 ~~C--~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYC--DICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEE--TTTTEEESSHHHHHHHHTT
T ss_pred CCC--CCCCCCcCCHHHHHHHHCc
Confidence 456 6666666666666666654
No 42
>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=96.37 E-value=0.0059 Score=31.65 Aligned_cols=33 Identities=21% Similarity=0.500 Sum_probs=23.7
Q ss_pred cCCcceeccCCCcccccCCHHHHHHHHhhhcCCCc
Q psy8966 93 SGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKP 127 (175)
Q Consensus 93 ~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~ 127 (175)
..+.|-.|| .|+..+.+..+|.+|+.+.++.+|
T Consensus 20 ~S~~PatCP--~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCP--ICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-T--TT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCC--cchhhccchhhHHHHHHHHhcccC
Confidence 346788998 899999999999999988888776
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.20 E-value=0.0044 Score=27.20 Aligned_cols=23 Identities=35% Similarity=0.979 Sum_probs=16.3
Q ss_pred eeccccccCcccCChHHHHHHHHHh
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTH 66 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h 66 (175)
|.| +.|+..|.+...|..|++.+
T Consensus 1 ~~C--~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYC--DICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEE--TTTTEEESSHHHHHHHHTTH
T ss_pred CCC--CCCCCCcCCHHHHHHHHCcC
Confidence 467 44888888888888877653
No 44
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.14 E-value=0.0071 Score=26.37 Aligned_cols=17 Identities=47% Similarity=0.931 Sum_probs=8.9
Q ss_pred cCcccCChHHHHHHHHH
Q psy8966 49 CSKSFKTSGDLQKHVRT 65 (175)
Q Consensus 49 C~~~f~~~~~l~~H~~~ 65 (175)
|++.|.+...|..|++.
T Consensus 6 C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 6 CGKVFKSKSALKEHMRT 22 (26)
T ss_pred CcchhCCHHHHHHHHHH
Confidence 55555555555555543
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.04 E-value=0.009 Score=25.94 Aligned_cols=23 Identities=39% Similarity=0.969 Sum_probs=13.8
Q ss_pred eeccccccCcccCChHHHHHHHHHhc
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTHT 67 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h~ 67 (175)
|.|+. |+.... ...|..|++.++
T Consensus 1 y~C~~--C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPH--CSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SS--SS-EES-HHHHHHHHHHHH
T ss_pred CCCCC--CCCcCC-HHHHHHHHHhhC
Confidence 46744 777766 667777776654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=95.91 E-value=0.0037 Score=41.30 Aligned_cols=40 Identities=35% Similarity=0.808 Sum_probs=33.1
Q ss_pred cceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchh
Q psy8966 96 RPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSG 143 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~ 143 (175)
-+|.| .|+. ....+.+|.++|+++++|.| ..|+..|....
T Consensus 118 ~~Y~C---~C~~---~~~~~rrH~ri~~g~~~YrC--~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRC---KCQE---HQLTVRRHNRVVRGEAVYRC--RRCGETLVFKG 157 (160)
T ss_pred EEEEc---CCCC---eeCHHHHHHHHhcCCccEEC--CCCCceeEEec
Confidence 47888 4877 55678899999999999999 88999887543
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.22 E-value=0.0041 Score=47.42 Aligned_cols=151 Identities=23% Similarity=0.344 Sum_probs=104.5
Q ss_pred CccCCCccchhhccChHHHHHHHh--hhcCC--CCeeccccccCcccCChHHHHHHHHHhcCCCCCCC----CCCccchh
Q psy8966 11 PYKCPVEYCEKAFSTQYSRKAHIR--THTGE--KPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGP----GIDSRLIV 82 (175)
Q Consensus 11 ~~~C~~~~C~~~f~~~~~L~~h~~--~~~~~--~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~----~~~~~~~~ 82 (175)
++.|. .|...|.....|..|.. .|.++ .++.|+...|++.|.....+..|...|.+..+... ........
T Consensus 289 ~~~~~--~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 366 (467)
T COG5048 289 PIKSK--QCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPL 366 (467)
T ss_pred CCCCc--cccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccc
Confidence 56776 89999999999999999 79998 89999722599999999999999999887553211 10000000
Q ss_pred cc-----cchhhhhccCCcceeccCCCcccccCCHHHHHHHHhhhcCCC--cccCCcccchHHHhchhhHHHHHHHhcCC
Q psy8966 83 RE-----DFVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEK--PYRCAHEFCSKSFKTSGDLQKHVRTHTGK 155 (175)
Q Consensus 83 ~~-----~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~--~~~C~~~~C~~~f~~~~~l~~H~~~h~~~ 155 (175)
.. ...............+....|...+.....+..|...+.... .+.+ ..|.+.+.....+..|++.+...
T Consensus 367 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~ 444 (467)
T COG5048 367 LNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKN--PPCSKSFNRHYNLIPHKKIHTNH 444 (467)
T ss_pred cCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCC--CcchhhccCcccccccccccccC
Confidence 00 001111112233444554457677777777777777776655 3566 88999999999999999999888
Q ss_pred ccccCCcchh
Q psy8966 156 YTAEVPGSIL 165 (175)
Q Consensus 156 ~~~~C~~c~~ 165 (175)
.+..|..++.
T Consensus 445 ~~~~~~~~~~ 454 (467)
T COG5048 445 APLLCSILKS 454 (467)
T ss_pred Cceeeccccc
Confidence 7777766553
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=95.05 E-value=0.0019 Score=29.09 Aligned_cols=18 Identities=28% Similarity=0.761 Sum_probs=9.7
Q ss_pred ccchHHHhchhhHHHHHH
Q psy8966 133 EFCSKSFKTSGDLQKHVR 150 (175)
Q Consensus 133 ~~C~~~f~~~~~l~~H~~ 150 (175)
..|++.|.+...|..|++
T Consensus 5 ~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 5 DACDKYFSSENQLKQHMK 22 (27)
T ss_dssp TTTTBBBSSHHHHHCCTT
T ss_pred ccCCCCcCCHHHHHHHHc
Confidence 455555555555555544
No 49
>KOG4173|consensus
Probab=94.84 E-value=0.015 Score=39.45 Aligned_cols=91 Identities=29% Similarity=0.572 Sum_probs=67.9
Q ss_pred CccCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhh
Q psy8966 11 PYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLR 90 (175)
Q Consensus 11 ~~~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~ 90 (175)
.+.|++..|-.+|....+...|-.+.++. .|.. |.+.|.+..-|..|+...+... --..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~--C~r~~Pt~hLLd~HI~E~HDs~----------------Fqa~ 137 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSF--CKRAFPTGHLLDAHILEWHDSL----------------FQAL 137 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc---hhHH--HHHhCCchhhhhHHHHHHHHHH----------------HHHH
Confidence 37787778999999988888887765553 7866 9999999999999987655311 0112
Q ss_pred hccCCcceeccCCCcccccCCHHHHHHHH-hhh
Q psy8966 91 IHSGIRPYKCPVEYCEKAFSTQYSRKAHI-RTH 122 (175)
Q Consensus 91 ~~~~~~~~~C~~~~C~~~f~~~~~l~~H~-~~h 122 (175)
...|..-|.|-+.+|+..|.+..+...|+ ..|
T Consensus 138 veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 138 VERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred HHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 23345678898889999999998888885 444
No 50
>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=94.33 E-value=0.015 Score=26.13 Aligned_cols=22 Identities=27% Similarity=0.824 Sum_probs=16.8
Q ss_pred eeccccccCcccCChHHHHHHHHH
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRT 65 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~ 65 (175)
|.|. .|++.|.+...|..|+++
T Consensus 2 ~~C~--~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCD--ACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBT--TTTBBBSSHHHHHCCTTS
T ss_pred CCcc--cCCCCcCCHHHHHHHHcc
Confidence 6784 488888888888887664
No 51
>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=94.10 E-value=0.014 Score=27.69 Aligned_cols=24 Identities=17% Similarity=0.278 Sum_probs=14.3
Q ss_pred ccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchh
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSIL 165 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~ 165 (175)
|+| .+||+.+.... .++.||.||.
T Consensus 2 ~~C--~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVC--PVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EEC--CCCCCEECCCc------------CCCcCcCCCC
Confidence 567 66776544221 6677777764
No 52
>KOG1146|consensus
Probab=92.90 E-value=0.034 Score=47.62 Aligned_cols=140 Identities=18% Similarity=0.300 Sum_probs=85.1
Q ss_pred cchhhccChHHHHHHHh-hhcCCCCeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchh-hhhccCC
Q psy8966 18 YCEKAFSTQYSRKAHIR-THTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVH-LRIHSGI 95 (175)
Q Consensus 18 ~C~~~f~~~~~L~~h~~-~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 95 (175)
-|+..+.....+.-++. .+.-.+.+.|+. |+..|.....|..||++-+.+..- .............. .....+.
T Consensus 441 ~~e~~~~s~r~~~~~t~~L~S~~kt~~cpk--c~~~yk~a~~L~vhmRskhp~~~~--~~c~~gq~~~~~arg~~~~~~~ 516 (1406)
T KOG1146|consen 441 KAEPLLESKRSLEGQTVVLHSFFKTLKCPK--CNWHYKLAQTLGVHMRSKHPESQS--AYCKAGQNHPRLARGEVYRCPG 516 (1406)
T ss_pred chhhhhhhhcccccceeeeecccccccCCc--cchhhhhHHHhhhcccccccccch--hHhHhccccccccccccccCCC
Confidence 34444444444444443 244446689976 999999999999999984432211 00000000000000 0112235
Q ss_pred cceeccCCCcccccCCHHHHHHHHhhh--c-----------------------------------C------CCcccCCc
Q psy8966 96 RPYKCPVEYCEKAFSTQYSRKAHIRTH--T-----------------------------------G------EKPYRCAH 132 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~~~~l~~H~~~h--~-----------------------------------~------~~~~~C~~ 132 (175)
+||.|. .|...+....+|.+|+..- . + ..+|.|
T Consensus 517 ~p~~C~--~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C-- 592 (1406)
T KOG1146|consen 517 KPYPCR--ACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRC-- 592 (1406)
T ss_pred Ccccce--eeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcch--
Confidence 788896 8999999999999997531 0 0 013999
Q ss_pred ccchHHHhchhhHHHHHHH-hcCCccccCCcchh
Q psy8966 133 EFCSKSFKTSGDLQKHVRT-HTGKYTAEVPGSIL 165 (175)
Q Consensus 133 ~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~c~~ 165 (175)
.+|++--.-..+|+.||.. ++...|-.+-.++.
T Consensus 593 ~vc~yetniarnlrihmtss~~s~~p~~~Lq~~i 626 (1406)
T KOG1146|consen 593 EVCSYETNIARNLRIHMTASPSSSPPSLVLQQNI 626 (1406)
T ss_pred hhhcchhhhhhccccccccCCCCCChHHHhhhcc
Confidence 9999999999999999974 44444455554443
No 53
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.16 E-value=0.07 Score=39.29 Aligned_cols=105 Identities=22% Similarity=0.338 Sum_probs=60.6
Q ss_pred CeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCC-c-------cchh-cccchhhhhccCC----cceeccCCCccc
Q psy8966 41 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGID-S-------RLIV-REDFVHLRIHSGI----RPYKCPVEYCEK 107 (175)
Q Consensus 41 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~-~-------~~~~-~~~~~~~~~~~~~----~~~~C~~~~C~~ 107 (175)
.|.|+.+-|.........|+.|.++.++...|..+.. . .++. ..+..|......+ +--.|. .|..
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~--FC~~ 228 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCI--FCKI 228 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhh--hccc
Confidence 3777766677777777888888888777655443221 1 1111 1122233333222 122476 7999
Q ss_pred ccCCHHHHHHHHhhhcCCCcccCCcccch----HHHhchhhHHHHHH
Q psy8966 108 AFSTQYSRKAHIRTHTGEKPYRCAHEFCS----KSFKTSGDLQKHVR 150 (175)
Q Consensus 108 ~f~~~~~l~~H~~~h~~~~~~~C~~~~C~----~~f~~~~~l~~H~~ 150 (175)
.|-+...|..|.+.-+ ++-+.| +.-+ .-|+.-.+|.+|.+
T Consensus 229 ~FYdDDEL~~HcR~~H-E~ChIC--D~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 229 YFYDDDELRRHCRLRH-EACHIC--DMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred eecChHHHHHHHHhhh-hhhhhh--hccCccchhhhhCHHHHHHHhh
Confidence 9999999999976542 344444 2222 24666667777765
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.15 E-value=0.079 Score=23.30 Aligned_cols=17 Identities=29% Similarity=0.757 Sum_probs=8.0
Q ss_pred ccchHHHhchhhHHHHHH
Q psy8966 133 EFCSKSFKTSGDLQKHVR 150 (175)
Q Consensus 133 ~~C~~~f~~~~~l~~H~~ 150 (175)
+.||..| ....|..|++
T Consensus 6 ~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 6 PICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CCCCCEE-CHHHHHHHHH
Confidence 4455555 3344445543
No 55
>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=91.55 E-value=0.21 Score=23.56 Aligned_cols=23 Identities=17% Similarity=0.644 Sum_probs=18.4
Q ss_pred CeeccccccCcccCChHHHHHHHHH
Q psy8966 41 PYRCAHEFCSKSFKTSGDLQKHVRT 65 (175)
Q Consensus 41 ~~~C~~~~C~~~f~~~~~l~~H~~~ 65 (175)
+|.| +.|+..|.+..++..|+..
T Consensus 3 ~~~C--~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYC--KLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEc--cccCCccCCHHHHHHHHCh
Confidence 4788 5599999988888888765
No 56
>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=91.47 E-value=0.096 Score=24.82 Aligned_cols=22 Identities=18% Similarity=0.689 Sum_probs=14.7
Q ss_pred cccCCcccchHHHhchhhHHHHHH
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVR 150 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~ 150 (175)
+|.| +.|+..|.....+..|++
T Consensus 3 ~~~C--~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYC--KLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEc--cccCCccCCHHHHHHHHC
Confidence 4567 667777776666666664
No 57
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.55 E-value=1 Score=33.47 Aligned_cols=74 Identities=19% Similarity=0.281 Sum_probs=36.0
Q ss_pred ccCcccCChHHHHHHHHHhcCC-CCCCCCCCccchhcccchhhhhccCCcceeccCCCccc----ccCCHHHHHHHHhh
Q psy8966 48 FCSKSFKTSGDLQKHVRTHTGK-YTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCEK----AFSTQYSRKAHIRT 121 (175)
Q Consensus 48 ~C~~~f~~~~~l~~H~~~h~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~~----~f~~~~~l~~H~~~ 121 (175)
+|...|.+...|..|++..+.. ..|.........+.........|-..--|.|+.+.|.. .|.....|..|+..
T Consensus 225 FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 225 FCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred hccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 3777777777777777764432 23433333333333333333333333344444433432 35555556666543
No 58
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.23 E-value=0.095 Score=24.98 Aligned_cols=25 Identities=12% Similarity=0.234 Sum_probs=16.8
Q ss_pred cccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchh
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSIL 165 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~ 165 (175)
.|+| .+||+.+... +.|-.||.||.
T Consensus 2 ~~~C--~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVC--PVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEEC--CCCCCEeECC------------cCCCcCcCCCC
Confidence 3778 7788654422 25678888885
No 59
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.22 E-value=0.12 Score=34.33 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=19.2
Q ss_pred CcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcch
Q psy8966 126 KPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSI 164 (175)
Q Consensus 126 ~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~ 164 (175)
+.|+| ++||+... |+.|-.||+||
T Consensus 133 ~~~vC--~vCGy~~~-------------ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVC--PVCGYTHE-------------GEAPEVCPICG 156 (166)
T ss_pred CEEEc--CCCCCccc-------------CCCCCcCCCCC
Confidence 36999 88997443 68999999998
No 60
>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=89.83 E-value=0.17 Score=31.18 Aligned_cols=14 Identities=14% Similarity=0.024 Sum_probs=7.9
Q ss_pred CCccccCCcchhhh
Q psy8966 154 GKYTAEVPGSILDC 167 (175)
Q Consensus 154 ~~~~~~C~~c~~~~ 167 (175)
++.|-.||+||..|
T Consensus 23 nk~PivCP~CG~~~ 36 (108)
T PF09538_consen 23 NKDPIVCPKCGTEF 36 (108)
T ss_pred CCCCccCCCCCCcc
Confidence 44566666666544
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.10 E-value=0.058 Score=41.13 Aligned_cols=63 Identities=33% Similarity=0.628 Sum_probs=51.3
Q ss_pred ceeccCCCcccccCCHHHHHHHHh--hhcCC--CcccCCcc--cchHHHhchhhHHHHHHHhcCCccccCCcc
Q psy8966 97 PYKCPVEYCEKAFSTQYSRKAHIR--THTGE--KPYRCAHE--FCSKSFKTSGDLQKHVRTHTGKYTAEVPGS 163 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~~~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c 163 (175)
++.|. .|...|.....|..|.. .|.++ +++.| + .|++.|.....+.+|...|++..+..+..-
T Consensus 289 ~~~~~--~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~--p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (467)
T COG5048 289 PIKSK--QCNISFSRSSPLTRHLRSVNHSGESLKPFSC--PYSLCGKLFSRNDALKRHILLHTSISPAKEKLL 357 (467)
T ss_pred CCCCc--cccCCccccccccccccccccccccCCceee--eccCCCccccccccccCCcccccCCCccccccc
Confidence 46665 88888888888888988 78888 88999 6 699999999888899888888766666543
No 62
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.56 E-value=0.23 Score=26.67 Aligned_cols=32 Identities=9% Similarity=0.075 Sum_probs=15.8
Q ss_pred cccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchh
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSIL 165 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~ 165 (175)
.|.| +.||..-..+....+ ....+|.|+.||+
T Consensus 27 ~F~C--PnCGe~~I~Rc~~CR-----k~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPC--PNCGEVEIYRCAKCR-----KLGNPYRCPKCGF 58 (61)
T ss_pred EeeC--CCCCceeeehhhhHH-----HcCCceECCCcCc
Confidence 3666 556654443332222 1235667777664
No 63
>KOG2893|consensus
Probab=88.11 E-value=0.16 Score=35.48 Aligned_cols=40 Identities=25% Similarity=0.591 Sum_probs=33.1
Q ss_pred CCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHH
Q psy8966 103 EYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKH 148 (175)
Q Consensus 103 ~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H 148 (175)
+.|++.|.+...|.+|++ .|-|+| -+|.+...+--.|..|
T Consensus 14 wycnrefddekiliqhqk----akhfkc--hichkkl~sgpglsih 53 (341)
T KOG2893|consen 14 WYCNREFDDEKILIQHQK----AKHFKC--HICHKKLFSGPGLSIH 53 (341)
T ss_pred eecccccchhhhhhhhhh----hcccee--eeehhhhccCCCceee
Confidence 489999999999999965 457999 9999988777666655
No 64
>KOG2893|consensus
Probab=87.65 E-value=0.19 Score=35.16 Aligned_cols=50 Identities=24% Similarity=0.612 Sum_probs=38.6
Q ss_pred CCCccCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHH-HHHhc
Q psy8966 9 IRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKH-VRTHT 67 (175)
Q Consensus 9 ~~~~~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H-~~~h~ 67 (175)
.++|-+ .|++.|.+..-|.+|++. +-|+| .+|.+...+...|..| |.+|.
T Consensus 9 ~kpwcw---ycnrefddekiliqhqka----khfkc--hichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 9 DKPWCW---YCNREFDDEKILIQHQKA----KHFKC--HICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred CCceee---ecccccchhhhhhhhhhh----cccee--eeehhhhccCCCceeehhhhhh
Confidence 356655 899999999999999875 34899 5599987777777777 55564
No 65
>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=86.69 E-value=0.22 Score=22.13 Aligned_cols=9 Identities=22% Similarity=0.069 Sum_probs=5.3
Q ss_pred cCCcchhhh
Q psy8966 159 EVPGSILDC 167 (175)
Q Consensus 159 ~C~~c~~~~ 167 (175)
.|+.||+.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 566666655
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=85.60 E-value=0.23 Score=25.22 Aligned_cols=11 Identities=0% Similarity=-0.260 Sum_probs=6.4
Q ss_pred ccccCCcchhh
Q psy8966 156 YTAEVPGSILD 166 (175)
Q Consensus 156 ~~~~C~~c~~~ 166 (175)
.+..|+.||..
T Consensus 18 ~~irC~~CG~r 28 (44)
T smart00659 18 DVVRCRECGYR 28 (44)
T ss_pred CceECCCCCce
Confidence 55666666644
No 67
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.75 E-value=0.28 Score=26.43 Aligned_cols=10 Identities=10% Similarity=0.019 Sum_probs=6.9
Q ss_pred ccccCCcchh
Q psy8966 156 YTAEVPGSIL 165 (175)
Q Consensus 156 ~~~~C~~c~~ 165 (175)
.+|.|+.||+
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 5677777765
No 68
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.09 E-value=0.82 Score=24.22 Aligned_cols=25 Identities=24% Similarity=0.551 Sum_probs=13.1
Q ss_pred CCCCccCCCccchhhccChHHHHHHHh
Q psy8966 8 GIRPYKCPVEYCEKAFSTQYSRKAHIR 34 (175)
Q Consensus 8 ~~~~~~C~~~~C~~~f~~~~~L~~h~~ 34 (175)
|+.-+.|+ -||..|....+..+|++
T Consensus 14 GE~~lrCP--RC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRCP--RCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeCC--chhHHHHHhHHHHHHhh
Confidence 44445554 55555555555555554
No 69
>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=83.42 E-value=0.54 Score=29.60 Aligned_cols=13 Identities=15% Similarity=0.475 Sum_probs=6.1
Q ss_pred CcccCCcccchHHHh
Q psy8966 126 KPYRCAHEFCSKSFK 140 (175)
Q Consensus 126 ~~~~C~~~~C~~~f~ 140 (175)
.|..| ++||..|.
T Consensus 25 ~p~vc--P~cg~~~~ 37 (129)
T TIGR02300 25 RPAVS--PYTGEQFP 37 (129)
T ss_pred CCccC--CCcCCccC
Confidence 34455 44554443
No 70
>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=82.86 E-value=0.96 Score=29.97 Aligned_cols=30 Identities=10% Similarity=0.134 Sum_probs=21.6
Q ss_pred CCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchh
Q psy8966 125 EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSIL 165 (175)
Q Consensus 125 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~ 165 (175)
..-|.| +.|+..|....++. .-|.||.||.
T Consensus 107 ~~~Y~C--p~c~~r~tf~eA~~---------~~F~Cp~Cg~ 136 (158)
T TIGR00373 107 NMFFIC--PNMCVRFTFNEAME---------LNFTCPRCGA 136 (158)
T ss_pred CCeEEC--CCCCcEeeHHHHHH---------cCCcCCCCCC
Confidence 345888 77888887777663 3688888874
No 71
>PHA00626 hypothetical protein
Probab=82.32 E-value=0.18 Score=26.70 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=6.2
Q ss_pred CcccCCcccchHHHh
Q psy8966 126 KPYRCAHEFCSKSFK 140 (175)
Q Consensus 126 ~~~~C~~~~C~~~f~ 140 (175)
..|+| +.||+.|.
T Consensus 22 nrYkC--kdCGY~ft 34 (59)
T PHA00626 22 DDYVC--CDCGYNDS 34 (59)
T ss_pred cceEc--CCCCCeec
Confidence 34555 44555444
No 72
>KOG1146|consensus
Probab=81.68 E-value=0.95 Score=39.47 Aligned_cols=56 Identities=34% Similarity=0.694 Sum_probs=43.0
Q ss_pred ccCCcceeccCCCcccccCCHHHHHHHHhh-hc------------------------CCCcccCCcccchHHHhchhhHH
Q psy8966 92 HSGIRPYKCPVEYCEKAFSTQYSRKAHIRT-HT------------------------GEKPYRCAHEFCSKSFKTSGDLQ 146 (175)
Q Consensus 92 ~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~-h~------------------------~~~~~~C~~~~C~~~f~~~~~l~ 146 (175)
+...+.+.|+ .|+..|.....|..|++. |. +-++|.| ..|...+..+.+|.
T Consensus 460 ~S~~kt~~cp--kc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C--~~C~~stttng~Ls 535 (1406)
T KOG1146|consen 460 HSFFKTLKCP--KCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPC--RACNYSTTTNGNLS 535 (1406)
T ss_pred ecccccccCC--ccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccc--eeeeeeeecchHHH
Confidence 3345677887 899999999899999876 11 1246888 88999999999999
Q ss_pred HHHHH
Q psy8966 147 KHVRT 151 (175)
Q Consensus 147 ~H~~~ 151 (175)
+|+.+
T Consensus 536 ihlqS 540 (1406)
T KOG1146|consen 536 IHLQS 540 (1406)
T ss_pred HHHHH
Confidence 99874
No 73
>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=80.91 E-value=0.44 Score=23.41 Aligned_cols=10 Identities=20% Similarity=-0.134 Sum_probs=5.4
Q ss_pred ccccCCcchh
Q psy8966 156 YTAEVPGSIL 165 (175)
Q Consensus 156 ~~~~C~~c~~ 165 (175)
..-.||.||.
T Consensus 25 ~~~~CP~Cg~ 34 (41)
T smart00834 25 PLATCPECGG 34 (41)
T ss_pred CCCCCCCCCC
Confidence 4445666654
No 74
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=80.76 E-value=1.5 Score=23.31 Aligned_cols=25 Identities=36% Similarity=0.707 Sum_probs=14.0
Q ss_pred CCCcccCCcccchHHHhchhhHHHHHH
Q psy8966 124 GEKPYRCAHEFCSKSFKTSGDLQKHVR 150 (175)
Q Consensus 124 ~~~~~~C~~~~C~~~f~~~~~l~~H~~ 150 (175)
|+.-+.| +.|+..|....+..+|..
T Consensus 14 GE~~lrC--PRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRC--PRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeC--CchhHHHHHhHHHHHHhh
Confidence 3444556 556666666666655553
No 75
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.11 E-value=1.1 Score=30.32 Aligned_cols=29 Identities=17% Similarity=0.301 Sum_probs=19.9
Q ss_pred CcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchh
Q psy8966 126 KPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSIL 165 (175)
Q Consensus 126 ~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~ 165 (175)
.-|.| +.|+..|....++ +.-|.||.||.
T Consensus 116 ~~Y~C--p~C~~rytf~eA~---------~~~F~Cp~Cg~ 144 (178)
T PRK06266 116 MFFFC--PNCHIRFTFDEAM---------EYGFRCPQCGE 144 (178)
T ss_pred CEEEC--CCCCcEEeHHHHh---------hcCCcCCCCCC
Confidence 44888 6688777766655 24688888873
No 76
>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=80.07 E-value=0.69 Score=20.10 Aligned_cols=9 Identities=11% Similarity=-0.005 Sum_probs=4.5
Q ss_pred ccccCCcch
Q psy8966 156 YTAEVPGSI 164 (175)
Q Consensus 156 ~~~~C~~c~ 164 (175)
.+|.||.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 345555554
No 77
>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=78.91 E-value=0.41 Score=23.96 Aligned_cols=29 Identities=24% Similarity=0.486 Sum_probs=14.4
Q ss_pred ccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchh
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSIL 165 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~ 165 (175)
|.| ..||..|.....+ .. ..+..||.||.
T Consensus 6 y~C--~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRC--EECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEe--CCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 556 5566555533221 11 45556666664
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=78.37 E-value=1.1 Score=29.29 Aligned_cols=36 Identities=17% Similarity=0.181 Sum_probs=20.7
Q ss_pred CCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhh
Q psy8966 125 EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILD 166 (175)
Q Consensus 125 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~ 166 (175)
..-|.| +.|+..|.....+.. .. .+.-|.||.||..
T Consensus 97 ~~~Y~C--p~C~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKC--PNCQSKYTFLEANQL---LD-MDGTFTCPRCGEE 132 (147)
T ss_pred CcEEEC--cCCCCEeeHHHHHHh---cC-CCCcEECCCCCCE
Confidence 345888 668877775433321 01 2333888888754
No 79
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=77.89 E-value=0.55 Score=24.36 Aligned_cols=28 Identities=14% Similarity=0.316 Sum_probs=14.9
Q ss_pred cccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhh
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILD 166 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~ 166 (175)
.|+| ..||+.|... .......|+.||..
T Consensus 6 ~Y~C--~~Cg~~~~~~----------~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKC--ARCGREVELD----------QETRGIRCPYCGSR 33 (49)
T ss_pred EEEh--hhcCCeeehh----------hccCceeCCCCCcE
Confidence 4666 6666665211 22345667777654
No 80
>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=77.78 E-value=0.67 Score=21.72 Aligned_cols=12 Identities=8% Similarity=-0.108 Sum_probs=6.7
Q ss_pred ccccCCcchhhh
Q psy8966 156 YTAEVPGSILDC 167 (175)
Q Consensus 156 ~~~~C~~c~~~~ 167 (175)
.+-.|+.||...
T Consensus 16 ~~irC~~CG~RI 27 (32)
T PF03604_consen 16 DPIRCPECGHRI 27 (32)
T ss_dssp STSSBSSSS-SE
T ss_pred CcEECCcCCCeE
Confidence 455666666554
No 81
>KOG4173|consensus
Probab=77.03 E-value=1.7 Score=29.87 Aligned_cols=80 Identities=35% Similarity=0.681 Sum_probs=58.6
Q ss_pred eeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCCcccccCCHHHHHHHH-h
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAHI-R 120 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~-~ 120 (175)
|.|+..+|-..|.+......|..+-++ -.|. .|.+.|.+.--|..|+ .
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~-----------------------------~sCs--~C~r~~Pt~hLLd~HI~E 128 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG-----------------------------NSCS--FCKRAFPTGHLLDAHILE 128 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc-----------------------------chhH--HHHHhCCchhhhhHHHHH
Confidence 677766677777776666666544332 2464 8999999988888886 3
Q ss_pred hh---------cCCCcccCCcccchHHHhchhhHHHHHH-Hh
Q psy8966 121 TH---------TGEKPYRCAHEFCSKSFKTSGDLQKHVR-TH 152 (175)
Q Consensus 121 ~h---------~~~~~~~C~~~~C~~~f~~~~~l~~H~~-~h 152 (175)
+| .|...|.|-.+.|+..|.+..+-..|+- +|
T Consensus 129 ~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 129 WHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred HHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 44 2445699977889999999999999986 45
No 82
>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=76.51 E-value=0.4 Score=25.09 Aligned_cols=11 Identities=45% Similarity=1.274 Sum_probs=5.7
Q ss_pred ccCCcccchHHHh
Q psy8966 128 YRCAHEFCSKSFK 140 (175)
Q Consensus 128 ~~C~~~~C~~~f~ 140 (175)
|.| ..||..|.
T Consensus 6 y~C--~~Cg~~fe 16 (52)
T TIGR02605 6 YRC--TACGHRFE 16 (52)
T ss_pred EEe--CCCCCEeE
Confidence 455 44555444
No 83
>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=75.28 E-value=0.42 Score=25.08 Aligned_cols=32 Identities=31% Similarity=0.592 Sum_probs=17.5
Q ss_pred CCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcch
Q psy8966 125 EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSI 164 (175)
Q Consensus 125 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~ 164 (175)
...|.| +.|+..|=..-++-.|..+| .||+|.
T Consensus 19 ~~~y~C--~~C~~~FC~dCD~fiHE~LH------~CPGC~ 50 (51)
T PF07975_consen 19 SSRYRC--PKCKNHFCIDCDVFIHETLH------NCPGCE 50 (51)
T ss_dssp -EEE----TTTT--B-HHHHHTTTTTS-------SSSTT-
T ss_pred CCeEEC--CCCCCccccCcChhhhcccc------CCcCCC
Confidence 456888 77888888877777776555 677663
No 84
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.07 E-value=1.1 Score=27.36 Aligned_cols=12 Identities=8% Similarity=-0.216 Sum_probs=5.5
Q ss_pred ccccCCcchhhh
Q psy8966 156 YTAEVPGSILDC 167 (175)
Q Consensus 156 ~~~~C~~c~~~~ 167 (175)
.|..||+||.+|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 444444444444
No 85
>KOG2231|consensus
Probab=74.69 E-value=8.5 Score=31.65 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=21.8
Q ss_pred hhccChHHHHHHHhhhcCCCCeeccc-c------ccCcccCChHHHHHHHHH
Q psy8966 21 KAFSTQYSRKAHIRTHTGEKPYRCAH-E------FCSKSFKTSGDLQKHVRT 65 (175)
Q Consensus 21 ~~f~~~~~L~~h~~~~~~~~~~~C~~-~------~C~~~f~~~~~l~~H~~~ 65 (175)
..|....+|+.|+...++. +.|.. . .|.....+...|+.|++.
T Consensus 122 ~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~ 171 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAELNLHLMF 171 (669)
T ss_pred cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHHHHHHHhc
Confidence 4445778888888643332 23321 0 022233445667777664
No 86
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=74.61 E-value=0.82 Score=23.30 Aligned_cols=9 Identities=11% Similarity=-0.049 Sum_probs=5.0
Q ss_pred cccCCcchh
Q psy8966 157 TAEVPGSIL 165 (175)
Q Consensus 157 ~~~C~~c~~ 165 (175)
...||.||.
T Consensus 21 ~~~Cp~CG~ 29 (46)
T PRK00398 21 GVRCPYCGY 29 (46)
T ss_pred ceECCCCCC
Confidence 455666654
No 87
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.12 E-value=7.8 Score=24.05 Aligned_cols=54 Identities=24% Similarity=0.443 Sum_probs=37.8
Q ss_pred eccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcch
Q psy8966 99 KCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSI 164 (175)
Q Consensus 99 ~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~ 164 (175)
.|- .|...|....... ...-.....|.| +.|...|-...++-.|...| .|++|.
T Consensus 57 ~C~--~C~~~f~~~~~~~--~~~~~~~~~y~C--~~C~~~FC~dCD~fiHe~Lh------~CPGC~ 110 (112)
T TIGR00622 57 FCF--GCQGPFPKPPVSP--FDELKDSHRYVC--AVCKNVFCVDCDVFVHESLH------CCPGCI 110 (112)
T ss_pred ccc--CcCCCCCCccccc--ccccccccceeC--CCCCCccccccchhhhhhcc------CCcCCC
Confidence 475 7988887643111 000123446999 88999999999999999888 488875
No 88
>PF15269 zf-C2H2_7: Zinc-finger
Probab=69.17 E-value=4.5 Score=20.42 Aligned_cols=27 Identities=15% Similarity=0.284 Sum_probs=19.4
Q ss_pred cceeccCCCcccccCCHHHHHHHHhhh
Q psy8966 96 RPYKCPVEYCEKAFSTQYSRKAHIRTH 122 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~~~~l~~H~~~h 122 (175)
+||...|-+|......++.|..|++..
T Consensus 17 kp~~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 17 KPFKYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred CCccceeecCCcccchHHHHHHHHHHH
Confidence 444333348999999999999998754
No 89
>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=68.80 E-value=1.2 Score=21.52 Aligned_cols=8 Identities=0% Similarity=-0.350 Sum_probs=3.6
Q ss_pred ccCCcchh
Q psy8966 158 AEVPGSIL 165 (175)
Q Consensus 158 ~~C~~c~~ 165 (175)
..|+.|+.
T Consensus 26 v~C~~C~~ 33 (38)
T TIGR02098 26 VRCGKCGH 33 (38)
T ss_pred EECCCCCC
Confidence 44444443
No 90
>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=68.44 E-value=1.5 Score=20.74 Aligned_cols=17 Identities=24% Similarity=0.225 Sum_probs=10.9
Q ss_pred ccccCCcchhhhccccc
Q psy8966 156 YTAEVPGSILDCLSGRF 172 (175)
Q Consensus 156 ~~~~C~~c~~~~~~~~~ 172 (175)
..+.|+.|+..+..++|
T Consensus 3 ~~~~C~nC~R~v~a~Rf 19 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRF 19 (33)
T ss_dssp -EEE-TTTSSEEEGGGH
T ss_pred CeEECCCCcCCcchhhh
Confidence 34778888887776654
No 91
>KOG4124|consensus
Probab=66.11 E-value=1 Score=33.52 Aligned_cols=53 Identities=45% Similarity=0.840 Sum_probs=39.5
Q ss_pred CcceeccCCCcccccCCHHHHHHHHhhhc-------------------CCCcccCCcccchHHHhchhhHHHHH
Q psy8966 95 IRPYKCPVEYCEKAFSTQYSRKAHIRTHT-------------------GEKPYRCAHEFCSKSFKTSGDLQKHV 149 (175)
Q Consensus 95 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~-------------------~~~~~~C~~~~C~~~f~~~~~l~~H~ 149 (175)
.+++.|+++.|++.+....+|..|....+ ..|+|.| ++|.+.++....|.-|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~--~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRC--EVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccC--hhhhhhhccCCCCCcee
Confidence 58999999999999999888888754321 2367888 88888888766554443
No 92
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=65.98 E-value=3.1 Score=21.52 Aligned_cols=17 Identities=35% Similarity=0.743 Sum_probs=8.2
Q ss_pred CcccccCCH-----HHHHHHHh
Q psy8966 104 YCEKAFSTQ-----YSRKAHIR 120 (175)
Q Consensus 104 ~C~~~f~~~-----~~l~~H~~ 120 (175)
.|++.+... ++|.+|+.
T Consensus 23 ~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 23 YCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred CCCCEeeeCCCCCcHHHHHHHH
Confidence 555555433 34555544
No 93
>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=64.43 E-value=4 Score=25.07 Aligned_cols=19 Identities=16% Similarity=0.275 Sum_probs=11.3
Q ss_pred CcccccCCHHHHHHHHhhh
Q psy8966 104 YCEKAFSTQYSRKAHIRTH 122 (175)
Q Consensus 104 ~C~~~f~~~~~l~~H~~~h 122 (175)
.|++.+.+...+..|.+.+
T Consensus 89 ~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 89 HCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred CCCcEeccHHHHHHHHHHh
Confidence 5666666666666665544
No 94
>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=63.84 E-value=7.6 Score=23.81 Aligned_cols=25 Identities=36% Similarity=0.822 Sum_probs=21.5
Q ss_pred eec----cccccCcccCChHHHHHHHHHhcC
Q psy8966 42 YRC----AHEFCSKSFKTSGDLQKHVRTHTG 68 (175)
Q Consensus 42 ~~C----~~~~C~~~f~~~~~l~~H~~~h~~ 68 (175)
|.| .. |+..+.+...|..|++.+++
T Consensus 81 ~~C~~~~~~--C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPH--CGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCC--CCcEeccHHHHHHHHHHhcC
Confidence 788 65 99999999999999987664
No 95
>KOG2482|consensus
Probab=62.94 E-value=31 Score=26.05 Aligned_cols=103 Identities=22% Similarity=0.409 Sum_probs=63.1
Q ss_pred eeccccccCcccCChHHHHHHHHH--hcCCCCCCCCCCccchh-------------cc--------------cchhhhhc
Q psy8966 42 YRCAHEFCSKSFKTSGDLQKHVRT--HTGKYTPGPGIDSRLIV-------------RE--------------DFVHLRIH 92 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~~~l~~H~~~--h~~~~~~~~~~~~~~~~-------------~~--------------~~~~~~~~ 92 (175)
+.|-. |.+.|..+..|..||+. |....|....++..+.+ .. .+..+..+
T Consensus 196 ~~CLy--CekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed 273 (423)
T KOG2482|consen 196 LRCLY--CEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNED 273 (423)
T ss_pred heeee--eccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcC
Confidence 67866 99999999999999976 33222311111111100 00 01111111
Q ss_pred cCCcc--eeccCCCcccccCCHHHHHHHHhhhcC---------------------------CCcccCCcccchHHHhchh
Q psy8966 93 SGIRP--YKCPVEYCEKAFSTQYSRKAHIRTHTG---------------------------EKPYRCAHEFCSKSFKTSG 143 (175)
Q Consensus 93 ~~~~~--~~C~~~~C~~~f~~~~~l~~H~~~h~~---------------------------~~~~~C~~~~C~~~f~~~~ 143 (175)
+..+ ..|. .|....-+...|..|++.-+. .+.-.| .+|.-.|....
T Consensus 274 -~a~a~~v~CL--fC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c--~~cd~~F~~e~ 348 (423)
T KOG2482|consen 274 -DAEALSVVCL--FCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRC--AECDLSFWKEP 348 (423)
T ss_pred -CCCccceEEE--eeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhcccc--ccccccccCcc
Confidence 1122 4786 899888888999999875321 112567 78889999999
Q ss_pred hHHHHHHH
Q psy8966 144 DLQKHVRT 151 (175)
Q Consensus 144 ~l~~H~~~ 151 (175)
.|..||.-
T Consensus 349 ~l~~hm~e 356 (423)
T KOG2482|consen 349 GLLIHMVE 356 (423)
T ss_pred hhhhhccc
Confidence 99999964
No 96
>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=61.78 E-value=3.7 Score=26.34 Aligned_cols=24 Identities=46% Similarity=0.733 Sum_probs=9.9
Q ss_pred eeccCCCcccccCCHHHHHHHHhhhcCCC
Q psy8966 98 YKCPVEYCEKAFSTQYSRKAHIRTHTGEK 126 (175)
Q Consensus 98 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~ 126 (175)
..|- +||+.|.. |.+|...|+|-.
T Consensus 73 i~cl--ecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 73 IICL--ECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp EE-T--BT--EESB---HHHHHHHTT-S-
T ss_pred eEEc--cCCcccch---HHHHHHHccCCC
Confidence 3453 56666544 356666655543
No 97
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=60.19 E-value=1.5 Score=24.90 Aligned_cols=18 Identities=33% Similarity=0.562 Sum_probs=9.1
Q ss_pred CCcccCCcccchHHHhch
Q psy8966 125 EKPYRCAHEFCSKSFKTS 142 (175)
Q Consensus 125 ~~~~~C~~~~C~~~f~~~ 142 (175)
+.-+.|++.+||..|...
T Consensus 25 ~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 25 ERYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeeecCCCCCCCEEEEE
Confidence 334556333566665543
No 98
>KOG4377|consensus
Probab=57.37 E-value=10 Score=29.09 Aligned_cols=29 Identities=24% Similarity=0.425 Sum_probs=20.8
Q ss_pred CCCccCCCccchhhccChHHHHHHHhhhc
Q psy8966 9 IRPYKCPVEYCEKAFSTQYSRKAHIRTHT 37 (175)
Q Consensus 9 ~~~~~C~~~~C~~~f~~~~~L~~h~~~~~ 37 (175)
...|.|..+.|+..+-.+.++.+|...|.
T Consensus 269 rEhyhcl~e~C~ykr~~k~DvirH~~~hk 297 (480)
T KOG4377|consen 269 REHYHCLNEYCFYKRGQKNDVIRHVEIHK 297 (480)
T ss_pred chhhcccCccccccccchhhhHHHHHHHh
Confidence 44577766678777777888888877664
No 99
>KOG3408|consensus
Probab=56.52 E-value=8.3 Score=24.18 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=22.9
Q ss_pred cCCcceeccCCCcccccCCHHHHHHHHhh
Q psy8966 93 SGIRPYKCPVEYCEKAFSTQYSRKAHIRT 121 (175)
Q Consensus 93 ~~~~~~~C~~~~C~~~f~~~~~l~~H~~~ 121 (175)
.|.+.|.|. .|.+-|.+.+.|..|.++
T Consensus 53 PG~GqfyCi--~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCI--ECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehh--hhhhhhcchHHHHHHHhc
Confidence 356788997 999999999999999754
No 100
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=55.01 E-value=3.8 Score=21.86 Aligned_cols=17 Identities=18% Similarity=0.534 Sum_probs=6.9
Q ss_pred HHHHHHhhhcCCCcccC
Q psy8966 114 SRKAHIRTHTGEKPYRC 130 (175)
Q Consensus 114 ~l~~H~~~h~~~~~~~C 130 (175)
.|..|....-..++..|
T Consensus 25 ~l~~H~~~~C~~~~v~C 41 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPC 41 (60)
T ss_dssp CHHHHHHTTSTTSEEE-
T ss_pred HHHHHHHccCCCCcEEC
Confidence 44455443333334444
No 101
>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=54.62 E-value=7.3 Score=19.39 Aligned_cols=17 Identities=35% Similarity=0.853 Sum_probs=6.2
Q ss_pred ccchHHHhch----hhHHHHH
Q psy8966 133 EFCSKSFKTS----GDLQKHV 149 (175)
Q Consensus 133 ~~C~~~f~~~----~~l~~H~ 149 (175)
..|++.+... +.|.+|+
T Consensus 20 ~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 20 KYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp TTTTEE-----SSTHHHHHHH
T ss_pred CCCCeEEeeCCCcHHHHHHhh
Confidence 4455444432 3444554
No 102
>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=54.55 E-value=8.6 Score=16.90 Aligned_cols=19 Identities=16% Similarity=0.564 Sum_probs=10.9
Q ss_pred cCCcccchHHHhchhhHHHHHH
Q psy8966 129 RCAHEFCSKSFKTSGDLQKHVR 150 (175)
Q Consensus 129 ~C~~~~C~~~f~~~~~l~~H~~ 150 (175)
.| ++|++.+ ....+..|.-
T Consensus 3 ~C--PiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QC--PVCFREV-PENLINSHLD 21 (26)
T ss_pred cC--CCCcCcc-cHHHHHHHHH
Confidence 46 6677766 4445555553
No 103
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.27 E-value=8.7 Score=21.91 Aligned_cols=6 Identities=0% Similarity=-0.319 Sum_probs=2.7
Q ss_pred cCCcch
Q psy8966 159 EVPGSI 164 (175)
Q Consensus 159 ~C~~c~ 164 (175)
.|+.|+
T Consensus 35 ~ce~c~ 40 (82)
T COG2331 35 TCEECG 40 (82)
T ss_pred cChhhC
Confidence 444444
No 104
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=53.96 E-value=7.3 Score=24.93 Aligned_cols=20 Identities=40% Similarity=0.416 Sum_probs=11.1
Q ss_pred CcccccCCHHHHHHHHhhhcCCC
Q psy8966 104 YCEKAFSTQYSRKAHIRTHTGEK 126 (175)
Q Consensus 104 ~C~~~f~~~~~l~~H~~~h~~~~ 126 (175)
++|+.|. +|++|..+|.+--
T Consensus 81 EDGkkfK---SLKRHL~t~~gmT 100 (148)
T COG4957 81 EDGKKFK---SLKRHLTTHYGLT 100 (148)
T ss_pred ccCcchH---HHHHHHhcccCCC
Confidence 5666653 3556666665533
No 105
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=52.71 E-value=5.9 Score=21.05 Aligned_cols=8 Identities=50% Similarity=1.041 Sum_probs=4.4
Q ss_pred ccchHHHh
Q psy8966 133 EFCSKSFK 140 (175)
Q Consensus 133 ~~C~~~f~ 140 (175)
++|++.|.
T Consensus 9 ~~Cg~~~~ 16 (54)
T PF14446_consen 9 PVCGKKFK 16 (54)
T ss_pred hhhCCccc
Confidence 55665554
No 106
>PF12907 zf-met2: Zinc-binding
Probab=52.32 E-value=11 Score=18.72 Aligned_cols=26 Identities=23% Similarity=0.585 Sum_probs=15.9
Q ss_pred ccCCcccchHHHhc---hhhHHHHHHHhcCC
Q psy8966 128 YRCAHEFCSKSFKT---SGDLQKHVRTHTGK 155 (175)
Q Consensus 128 ~~C~~~~C~~~f~~---~~~l~~H~~~h~~~ 155 (175)
++| .+|...|.. ...|..|....+.+
T Consensus 2 i~C--~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IIC--KICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCc--HHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 467 777765554 35577777754443
No 107
>KOG2593|consensus
Probab=51.82 E-value=14 Score=28.70 Aligned_cols=36 Identities=11% Similarity=0.108 Sum_probs=24.5
Q ss_pred CCCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcch
Q psy8966 124 GEKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSI 164 (175)
Q Consensus 124 ~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~ 164 (175)
....|.| +.|.+.|..-. .-.-+-..+.-|.|..|+
T Consensus 125 ~~~~Y~C--p~C~kkyt~Le---a~~L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 125 NVAGYVC--PNCQKKYTSLE---ALQLLDNETGEFHCENCG 160 (436)
T ss_pred ccccccC--CccccchhhhH---HHHhhcccCceEEEecCC
Confidence 3456999 88999888543 333344445778899987
No 108
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=51.18 E-value=14 Score=17.74 Aligned_cols=33 Identities=27% Similarity=0.816 Sum_probs=21.0
Q ss_pred cCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccC
Q psy8966 13 KCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFK 54 (175)
Q Consensus 13 ~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~ 54 (175)
.|+ .|+..|.-..+ +...+.....|+. |+..|.
T Consensus 4 ~CP--~C~~~f~v~~~-----~l~~~~~~vrC~~--C~~~f~ 36 (37)
T PF13719_consen 4 TCP--NCQTRFRVPDD-----KLPAGGRKVRCPK--CGHVFR 36 (37)
T ss_pred ECC--CCCceEEcCHH-----HcccCCcEEECCC--CCcEee
Confidence 466 88888876553 1223334578976 988764
No 109
>KOG4167|consensus
Probab=50.91 E-value=7.7 Score=32.11 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=22.8
Q ss_pred ccCCcccchHHHhchhhHHHHHHHhcC
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRTHTG 154 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~h~~ 154 (175)
|.| -+|++.|---.++..||++|..
T Consensus 793 FpC--reC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 793 FPC--RECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeh--HHHHHHHHHHhhhhHHHHHHHH
Confidence 999 8899999999999999999853
No 110
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=50.54 E-value=8.3 Score=20.58 Aligned_cols=17 Identities=18% Similarity=0.405 Sum_probs=10.2
Q ss_pred CCCcccCCcccchHHHhch
Q psy8966 124 GEKPYRCAHEFCSKSFKTS 142 (175)
Q Consensus 124 ~~~~~~C~~~~C~~~f~~~ 142 (175)
+...|.| +.||..+..+
T Consensus 11 ~~v~~~C--p~cGipthcS 27 (55)
T PF13824_consen 11 AHVNFEC--PDCGIPTHCS 27 (55)
T ss_pred cccCCcC--CCCCCcCccC
Confidence 3455777 6677655544
No 111
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=49.28 E-value=2.2 Score=29.85 Aligned_cols=16 Identities=38% Similarity=0.883 Sum_probs=10.5
Q ss_pred cceeccCCCcccccCCHH
Q psy8966 96 RPYKCPVEYCEKAFSTQY 113 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~~~ 113 (175)
+...|| .|+..|..+.
T Consensus 4 k~~~CP--vC~~~F~~~~ 19 (214)
T PF09986_consen 4 KKITCP--VCGKEFKTKK 19 (214)
T ss_pred CceECC--CCCCeeeeeE
Confidence 446676 6887776653
No 112
>KOG2231|consensus
Probab=48.93 E-value=32 Score=28.50 Aligned_cols=102 Identities=20% Similarity=0.280 Sum_probs=57.7
Q ss_pred cccCChHHHHHHHHHhcCCCCCCC---CCCccchh------cccchhhhhccC-C----cceeccCCCcccccCCHHHHH
Q psy8966 51 KSFKTSGDLQKHVRTHTGKYTPGP---GIDSRLIV------REDFVHLRIHSG-I----RPYKCPVEYCEKAFSTQYSRK 116 (175)
Q Consensus 51 ~~f~~~~~l~~H~~~h~~~~~~~~---~~~~~~~~------~~~~~~~~~~~~-~----~~~~C~~~~C~~~f~~~~~l~ 116 (175)
..|.+.-.|..|+...+....|.. ......+. .....|++...- + +--.|. .|...|.....|.
T Consensus 122 ~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~--~C~~~fld~~el~ 199 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCK--FCHERFLDDDELY 199 (669)
T ss_pred cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccch--hhhhhhccHHHHH
Confidence 444577889999976555433222 11111111 122234442211 1 123576 7999999999999
Q ss_pred HHHhhhcCCCcccCCcccc------hHHHhchhhHHHHHHHhcCCccccCC--cch
Q psy8966 117 AHIRTHTGEKPYRCAHEFC------SKSFKTSGDLQKHVRTHTGKYTAEVP--GSI 164 (175)
Q Consensus 117 ~H~~~h~~~~~~~C~~~~C------~~~f~~~~~l~~H~~~h~~~~~~~C~--~c~ 164 (175)
.|++.++ |-| ..| ...|..-.+|..|.+..+ |.|+ .|.
T Consensus 200 rH~~~~h----~~c--hfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~ 245 (669)
T KOG2231|consen 200 RHLRFDH----EFC--HFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCR 245 (669)
T ss_pred Hhhccce----ehe--eecCcccccchhcccchHHHHHhhhcC----ccccccccc
Confidence 9977653 233 334 456666778888876543 4565 554
No 113
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=47.49 E-value=20 Score=23.04 Aligned_cols=62 Identities=19% Similarity=0.334 Sum_probs=40.2
Q ss_pred hhhccCCcceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhch--hhHHHHHHHhcCCccccCCcchhh
Q psy8966 89 LRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTS--GDLQKHVRTHTGKYTAEVPGSILD 166 (175)
Q Consensus 89 ~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~--~~l~~H~~~h~~~~~~~C~~c~~~ 166 (175)
+..-...+-|+|. .|........ =-||-.| ||++.-.. .+|+.|-.+| -.||+|..+
T Consensus 72 mnvF~d~~lYeCn--IC~etS~ee~----------FLKPneC----CgY~iCn~Cya~LWK~~~~y-----pvCPvCkTS 130 (140)
T PF05290_consen 72 MNVFLDPKLYECN--ICKETSAEER----------FLKPNEC----CGYSICNACYANLWKFCNLY-----PVCPVCKTS 130 (140)
T ss_pred heeecCCCceecc--Ccccccchhh----------cCCcccc----cchHHHHHHHHHHHHHcccC-----CCCCccccc
Confidence 3344455789996 8887765532 2467778 88765543 4565554433 479999999
Q ss_pred hcccc
Q psy8966 167 CLSGR 171 (175)
Q Consensus 167 ~~~~~ 171 (175)
|.|+-
T Consensus 131 FKss~ 135 (140)
T PF05290_consen 131 FKSSS 135 (140)
T ss_pred ccccc
Confidence 98864
No 114
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=47.31 E-value=2.8 Score=22.34 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=14.3
Q ss_pred ccccCCcchhhhcccccccC
Q psy8966 156 YTAEVPGSILDCLSGRFRLF 175 (175)
Q Consensus 156 ~~~~C~~c~~~~~~~~~~~~ 175 (175)
.+..|.-||+....++|||+
T Consensus 3 f~lVCsTCGrDlSeeRy~Ll 22 (63)
T PHA03082 3 FQLVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeeeecccCcchhHHHHHHH
Confidence 35678888887777777764
No 115
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=46.83 E-value=2.8 Score=22.32 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=14.2
Q ss_pred ccccCCcchhhhcccccccC
Q psy8966 156 YTAEVPGSILDCLSGRFRLF 175 (175)
Q Consensus 156 ~~~~C~~c~~~~~~~~~~~~ 175 (175)
.+..|.-||+...-++|||+
T Consensus 3 f~lvCSTCGrDlSeeRy~Ll 22 (63)
T PF05864_consen 3 FQLVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeeeecccCCcchHHHHHHH
Confidence 35677888887777777764
No 116
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=46.31 E-value=19 Score=17.20 Aligned_cols=32 Identities=22% Similarity=0.727 Sum_probs=20.6
Q ss_pred cCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCccc
Q psy8966 13 KCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSF 53 (175)
Q Consensus 13 ~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f 53 (175)
.|+ .|+..|.-..+. .-......+|+. |+..|
T Consensus 4 ~Cp--~C~~~y~i~d~~-----ip~~g~~v~C~~--C~~~f 35 (36)
T PF13717_consen 4 TCP--NCQAKYEIDDEK-----IPPKGRKVRCSK--CGHVF 35 (36)
T ss_pred ECC--CCCCEEeCCHHH-----CCCCCcEEECCC--CCCEe
Confidence 566 888888766542 223334578976 98876
No 117
>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=45.94 E-value=6.8 Score=18.03 Aligned_cols=8 Identities=13% Similarity=-0.081 Sum_probs=3.4
Q ss_pred cccCCcch
Q psy8966 157 TAEVPGSI 164 (175)
Q Consensus 157 ~~~C~~c~ 164 (175)
.+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444443
No 118
>KOG2186|consensus
Probab=44.78 E-value=19 Score=25.86 Aligned_cols=46 Identities=17% Similarity=0.553 Sum_probs=34.2
Q ss_pred ccCCCccchhhccChHHHHHHHhhhcCCCCeeccccccCcccCChHHHHHHHH
Q psy8966 12 YKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVR 64 (175)
Q Consensus 12 ~~C~~~~C~~~f~~~~~L~~h~~~~~~~~~~~C~~~~C~~~f~~~~~l~~H~~ 64 (175)
|.|. .||.+... ..+.+|+.+-.+ ..|.|-. |+..|.. .++..|..
T Consensus 4 FtCn--vCgEsvKK-p~vekH~srCrn-~~fSCID--C~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCN--VCGESVKK-PQVEKHMSRCRN-AYFSCID--CGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehh--hhhhhccc-cchHHHHHhccC-CeeEEee--ccccccc-chhhhhhh
Confidence 5676 89998654 668889887666 5699965 9999998 55666654
No 119
>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=43.08 E-value=6.7 Score=18.85 Aligned_cols=12 Identities=8% Similarity=-0.277 Sum_probs=6.0
Q ss_pred CCccccCCcchh
Q psy8966 154 GKYTAEVPGSIL 165 (175)
Q Consensus 154 ~~~~~~C~~c~~ 165 (175)
+...-.|..||-
T Consensus 18 P~~~~~Cd~cg~ 29 (36)
T PF05191_consen 18 PKVEGVCDNCGG 29 (36)
T ss_dssp -SSTTBCTTTTE
T ss_pred CCCCCccCCCCC
Confidence 344455666654
No 120
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=41.82 E-value=11 Score=22.22 Aligned_cols=13 Identities=23% Similarity=0.767 Sum_probs=7.0
Q ss_pred CcccCCcccchHHHh
Q psy8966 126 KPYRCAHEFCSKSFK 140 (175)
Q Consensus 126 ~~~~C~~~~C~~~f~ 140 (175)
-.|.| ..|+..|.
T Consensus 52 GIW~C--~kCg~~fA 64 (89)
T COG1997 52 GIWKC--RKCGAKFA 64 (89)
T ss_pred CeEEc--CCCCCeec
Confidence 34566 55655554
No 121
>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=40.71 E-value=5 Score=26.25 Aligned_cols=37 Identities=19% Similarity=0.284 Sum_probs=22.3
Q ss_pred hhcCCCc----ccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhhhcc
Q psy8966 121 THTGEKP----YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILDCLS 169 (175)
Q Consensus 121 ~h~~~~~----~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~~~~ 169 (175)
.+.|+.+ |.| ..||.... ..+....-.||.||-.-++
T Consensus 102 Y~sGE~~g~G~l~C--~~Cg~~~~----------~~~~~~l~~Cp~C~~~~F~ 142 (146)
T PF07295_consen 102 YHSGEVVGPGTLVC--ENCGHEVE----------LTHPERLPPCPKCGHTEFT 142 (146)
T ss_pred eecCcEecCceEec--ccCCCEEE----------ecCCCcCCCCCCCCCCeee
Confidence 4455554 888 77885322 2234456788888865443
No 122
>KOG4167|consensus
Probab=40.62 E-value=11 Score=31.30 Aligned_cols=24 Identities=42% Similarity=0.749 Sum_probs=13.2
Q ss_pred CccCCCccchhhccChHHHHHHHhhh
Q psy8966 11 PYKCPVEYCEKAFSTQYSRKAHIRTH 36 (175)
Q Consensus 11 ~~~C~~~~C~~~f~~~~~L~~h~~~~ 36 (175)
.|.|. .||++|....++..|+++|
T Consensus 792 iFpCr--eC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCR--ECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehH--HHHHHHHHHhhhhHHHHHH
Confidence 35554 5555555555555555554
No 123
>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=40.49 E-value=12 Score=18.58 Aligned_cols=12 Identities=17% Similarity=0.086 Sum_probs=6.5
Q ss_pred ccCCcchhhhcc
Q psy8966 158 AEVPGSILDCLS 169 (175)
Q Consensus 158 ~~C~~c~~~~~~ 169 (175)
+.|+.||..+++
T Consensus 33 ~~C~~CGE~~~~ 44 (46)
T TIGR03831 33 LVCPQCGEEYLD 44 (46)
T ss_pred cccccCCCEeeC
Confidence 456666655544
No 124
>KOG3408|consensus
Probab=40.47 E-value=19 Score=22.63 Aligned_cols=23 Identities=26% Similarity=0.622 Sum_probs=21.0
Q ss_pred cccCCcccchHHHhchhhHHHHHHH
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRT 151 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~ 151 (175)
.|.| ..|.+-|.....|..|.++
T Consensus 57 qfyC--i~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYC--IECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeeh--hhhhhhhcchHHHHHHHhc
Confidence 3899 8899999999999999985
No 125
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=40.07 E-value=11 Score=22.35 Aligned_cols=14 Identities=7% Similarity=-0.064 Sum_probs=8.2
Q ss_pred ccccCCcchhhhcc
Q psy8966 156 YTAEVPGSILDCLS 169 (175)
Q Consensus 156 ~~~~C~~c~~~~~~ 169 (175)
.|..|..||+.|.+
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 55566666665554
No 126
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=38.52 E-value=13 Score=19.61 Aligned_cols=13 Identities=31% Similarity=0.943 Sum_probs=6.8
Q ss_pred ccCCcccchHHHhch
Q psy8966 128 YRCAHEFCSKSFKTS 142 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~ 142 (175)
|+| +.||..|..+
T Consensus 29 W~C--~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKC--PKCGHEWKAS 41 (55)
T ss_pred EEC--CCCCCeeEcc
Confidence 556 5565554443
No 127
>KOG2807|consensus
Probab=37.72 E-value=34 Score=25.60 Aligned_cols=59 Identities=25% Similarity=0.490 Sum_probs=41.1
Q ss_pred cceeccCCCcccccCCHHHHHHHHhh----------hcC-----------------CCcccCCcccchHHHhchhhHHHH
Q psy8966 96 RPYKCPVEYCEKAFSTQYSRKAHIRT----------HTG-----------------EKPYRCAHEFCSKSFKTSGDLQKH 148 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~~~~l~~H~~~----------h~~-----------------~~~~~C~~~~C~~~f~~~~~l~~H 148 (175)
-|..|| .|+....+...|.+-.+- ..+ ...|.| ..|...|-...+.-.|
T Consensus 289 LP~eCp--iC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C--~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 289 LPIECP--ICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRC--ESCKNVFCLDCDVFIH 364 (378)
T ss_pred CCccCC--ccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEc--hhccceeeccchHHHH
Confidence 466676 688887777777654321 111 123888 8899999998888888
Q ss_pred HHHhcCCccccCCcch
Q psy8966 149 VRTHTGKYTAEVPGSI 164 (175)
Q Consensus 149 ~~~h~~~~~~~C~~c~ 164 (175)
...| .|++|.
T Consensus 365 esLh------~CpgCe 374 (378)
T KOG2807|consen 365 ESLH------NCPGCE 374 (378)
T ss_pred hhhh------cCCCcC
Confidence 8777 788775
No 128
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=37.17 E-value=30 Score=23.43 Aligned_cols=29 Identities=14% Similarity=0.288 Sum_probs=14.9
Q ss_pred CCcccCCcccchHHHhchhhHHHHHHHhcCCccccCCcch
Q psy8966 125 EKPYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSI 164 (175)
Q Consensus 125 ~~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~ 164 (175)
..-|.| +.|...|....++ .. -|.||.||
T Consensus 111 ~~~y~C--~~~~~r~sfdeA~------~~---~F~Cp~Cg 139 (176)
T COG1675 111 NNYYVC--PNCHVKYSFDEAM------EL---GFTCPKCG 139 (176)
T ss_pred CCceeC--CCCCCcccHHHHH------Hh---CCCCCCCC
Confidence 344666 5566555543332 11 16666666
No 129
>KOG1280|consensus
Probab=36.69 E-value=24 Score=26.60 Aligned_cols=21 Identities=29% Similarity=0.641 Sum_probs=10.9
Q ss_pred ceeccCCCcccccCCHHHHHHHH
Q psy8966 97 PYKCPVEYCEKAFSTQYSRKAHI 119 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~~~l~~H~ 119 (175)
.|.|| .|+.+-.+...|..|+
T Consensus 79 SftCP--yC~~~Gfte~~f~~Hv 99 (381)
T KOG1280|consen 79 SFTCP--YCGIMGFTERQFGTHV 99 (381)
T ss_pred cccCC--cccccccchhHHHHHh
Confidence 44554 4555555555555554
No 130
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.26 E-value=12 Score=23.26 Aligned_cols=11 Identities=27% Similarity=0.438 Sum_probs=6.6
Q ss_pred ccCCcccchHHHh
Q psy8966 128 YRCAHEFCSKSFK 140 (175)
Q Consensus 128 ~~C~~~~C~~~f~ 140 (175)
+.| ..|+..|.
T Consensus 71 ~~C--~~Cg~~~~ 81 (113)
T PRK12380 71 AWC--WDCSQVVE 81 (113)
T ss_pred EEc--ccCCCEEe
Confidence 666 55765554
No 131
>KOG2907|consensus
Probab=35.77 E-value=13 Score=23.04 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=7.5
Q ss_pred eeccccccCcccCCh
Q psy8966 42 YRCAHEFCSKSFKTS 56 (175)
Q Consensus 42 ~~C~~~~C~~~f~~~ 56 (175)
..|.. |...|...
T Consensus 26 ~~C~~--Ck~~~~v~ 38 (116)
T KOG2907|consen 26 VLCIR--CKIEYPVS 38 (116)
T ss_pred eEecc--ccccCCHH
Confidence 45744 77766543
No 132
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=34.99 E-value=11 Score=22.32 Aligned_cols=17 Identities=12% Similarity=0.059 Sum_probs=9.5
Q ss_pred ccccCCcchhhhccccc
Q psy8966 156 YTAEVPGSILDCLSGRF 172 (175)
Q Consensus 156 ~~~~C~~c~~~~~~~~~ 172 (175)
-.+.|..|++.|.-+.+
T Consensus 53 GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 53 GIWRCKGCKKTVAGGAW 69 (90)
T ss_pred EEEEcCCCCCEEeCCcc
Confidence 44666666666555543
No 133
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=34.82 E-value=13 Score=23.12 Aligned_cols=11 Identities=36% Similarity=0.782 Sum_probs=6.8
Q ss_pred ccCCcccchHHHh
Q psy8966 128 YRCAHEFCSKSFK 140 (175)
Q Consensus 128 ~~C~~~~C~~~f~ 140 (175)
..| ..|+..|.
T Consensus 71 ~~C--~~Cg~~~~ 81 (115)
T TIGR00100 71 CEC--EDCSEEVS 81 (115)
T ss_pred EEc--ccCCCEEe
Confidence 667 56775554
No 134
>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=32.73 E-value=6.6 Score=23.32 Aligned_cols=16 Identities=6% Similarity=-0.022 Sum_probs=9.7
Q ss_pred cccCCcchhhhccccc
Q psy8966 157 TAEVPGSILDCLSGRF 172 (175)
Q Consensus 157 ~~~C~~c~~~~~~~~~ 172 (175)
.+.|..|++.|..+.+
T Consensus 53 IW~C~~C~~~~AGGAy 68 (90)
T PF01780_consen 53 IWKCKKCGKKFAGGAY 68 (90)
T ss_dssp EEEETTTTEEEE-BSS
T ss_pred EeecCCCCCEEeCCCc
Confidence 4667777766666554
No 135
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=32.70 E-value=51 Score=16.24 Aligned_cols=23 Identities=30% Similarity=0.624 Sum_probs=16.1
Q ss_pred ccCCCccchhhcc--ChHHHHHHHhhh
Q psy8966 12 YKCPVEYCEKAFS--TQYSRKAHIRTH 36 (175)
Q Consensus 12 ~~C~~~~C~~~f~--~~~~L~~h~~~~ 36 (175)
-.|+ .||..|. ...+-..|.+.|
T Consensus 14 ~~C~--~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCP--TCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCC--CCCCEECCCCHHHHHHHHHHH
Confidence 4686 8999875 556666676655
No 136
>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=32.15 E-value=11 Score=18.64 Aligned_cols=11 Identities=9% Similarity=-0.136 Sum_probs=5.7
Q ss_pred cccCCcchhhh
Q psy8966 157 TAEVPGSILDC 167 (175)
Q Consensus 157 ~~~C~~c~~~~ 167 (175)
+..|++||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45555555443
No 137
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.99 E-value=18 Score=22.64 Aligned_cols=11 Identities=45% Similarity=0.972 Sum_probs=7.2
Q ss_pred ccCCcccchHHHh
Q psy8966 128 YRCAHEFCSKSFK 140 (175)
Q Consensus 128 ~~C~~~~C~~~f~ 140 (175)
+.| ..||..|.
T Consensus 72 ~~C--~~Cg~~~~ 82 (117)
T PRK00564 72 LEC--KDCSHVFK 82 (117)
T ss_pred EEh--hhCCCccc
Confidence 677 66776555
No 138
>KOG2636|consensus
Probab=31.55 E-value=30 Score=27.04 Aligned_cols=29 Identities=24% Similarity=0.605 Sum_probs=23.9
Q ss_pred hhhcCCCcccCCcccch-HHHhchhhHHHHHH
Q psy8966 120 RTHTGEKPYRCAHEFCS-KSFKTSGDLQKHVR 150 (175)
Q Consensus 120 ~~h~~~~~~~C~~~~C~-~~f~~~~~l~~H~~ 150 (175)
+.|.=+..|.| .+|| +++..+.++.+|..
T Consensus 394 KLHGL~~ey~C--EICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNC--EICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccce--eeccCccccCcHHHHHHhH
Confidence 44555677999 9999 89999999999986
No 139
>KOG2785|consensus
Probab=31.30 E-value=57 Score=25.01 Aligned_cols=52 Identities=23% Similarity=0.556 Sum_probs=42.8
Q ss_pred cceeccCCCcccccCCHHHHHHHHhhhcCC-----------------------CcccCCcccch---HHHhchhhHHHHH
Q psy8966 96 RPYKCPVEYCEKAFSTQYSRKAHIRTHTGE-----------------------KPYRCAHEFCS---KSFKTSGDLQKHV 149 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~~~C~---~~f~~~~~l~~H~ 149 (175)
.|-.|. .|+..+.+...-..||..+++- .-|.| ..|. +.|.+-.+.+.||
T Consensus 165 ~Pt~CL--fC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~C--L~CN~~~~~f~sleavr~HM 240 (390)
T KOG2785|consen 165 IPTDCL--FCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFIC--LFCNELGRPFSSLEAVRAHM 240 (390)
T ss_pred CCccee--ecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceE--EEeccccCcccccHHHHHHH
Confidence 456787 8999999999999999877652 12888 8899 8999999999999
Q ss_pred HH
Q psy8966 150 RT 151 (175)
Q Consensus 150 ~~ 151 (175)
..
T Consensus 241 ~~ 242 (390)
T KOG2785|consen 241 RD 242 (390)
T ss_pred hh
Confidence 74
No 140
>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=31.28 E-value=15 Score=25.78 Aligned_cols=25 Identities=32% Similarity=0.688 Sum_probs=12.5
Q ss_pred cccCCcccchHHHhchhhHHHHHHHhc
Q psy8966 127 PYRCAHEFCSKSFKTSGDLQKHVRTHT 153 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~~~l~~H~~~h~ 153 (175)
.|.| ..|+|.|.-..-+..|+...+
T Consensus 77 K~~C--~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 77 KWRC--PLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEE---SSS-EESSHHHHHHHHHHH-
T ss_pred EECC--CCCCcccCChHHHHHHHhhcC
Confidence 3566 556666666655555655433
No 141
>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=30.85 E-value=11 Score=27.04 Aligned_cols=27 Identities=30% Similarity=0.545 Sum_probs=19.8
Q ss_pred CCCcccCCcccchHHHhchhhHHHHHHHh
Q psy8966 124 GEKPYRCAHEFCSKSFKTSGDLQKHVRTH 152 (175)
Q Consensus 124 ~~~~~~C~~~~C~~~f~~~~~l~~H~~~h 152 (175)
..++++| +.|++-.....+|.+-.++|
T Consensus 206 k~k~~PC--PKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 206 KGKPIPC--PKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred cCCCCCC--CCCCCcccccccceeeeecc
Confidence 3478889 88998777777776666655
No 142
>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=30.52 E-value=17 Score=19.07 Aligned_cols=11 Identities=9% Similarity=-0.372 Sum_probs=4.9
Q ss_pred cCCcchhhhcc
Q psy8966 159 EVPGSILDCLS 169 (175)
Q Consensus 159 ~C~~c~~~~~~ 169 (175)
.||+|+..|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 78888766543
No 143
>KOG2186|consensus
Probab=30.49 E-value=33 Score=24.71 Aligned_cols=46 Identities=17% Similarity=0.504 Sum_probs=32.2
Q ss_pred eeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhchhhHHHHHH
Q psy8966 98 YKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVR 150 (175)
Q Consensus 98 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~~~l~~H~~ 150 (175)
|.|. .||....- ..+.+|+..-++ .-|.| ..|++.|.. .+...|.+
T Consensus 4 FtCn--vCgEsvKK-p~vekH~srCrn-~~fSC--IDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCN--VCGESVKK-PQVEKHMSRCRN-AYFSC--IDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehh--hhhhhccc-cchHHHHHhccC-CeeEE--eeccccccc-chhhhhhh
Confidence 5664 78877654 456678777665 66888 778888887 55666765
No 144
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=30.44 E-value=20 Score=17.54 Aligned_cols=11 Identities=0% Similarity=-0.502 Sum_probs=6.9
Q ss_pred cccCCcchhhh
Q psy8966 157 TAEVPGSILDC 167 (175)
Q Consensus 157 ~~~C~~c~~~~ 167 (175)
|+.|..|+..|
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 66677666554
No 145
>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=29.26 E-value=22 Score=15.96 Aligned_cols=11 Identities=9% Similarity=0.084 Sum_probs=3.3
Q ss_pred ccccCCcchhh
Q psy8966 156 YTAEVPGSILD 166 (175)
Q Consensus 156 ~~~~C~~c~~~ 166 (175)
..|.|..|.+.
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 44555555543
No 146
>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=28.99 E-value=15 Score=21.87 Aligned_cols=17 Identities=6% Similarity=-0.113 Sum_probs=9.4
Q ss_pred ccccCCcchhhhccccc
Q psy8966 156 YTAEVPGSILDCLSGRF 172 (175)
Q Consensus 156 ~~~~C~~c~~~~~~~~~ 172 (175)
-.+.|..|++.|.-+.+
T Consensus 52 GIW~C~~C~~~~AGGAy 68 (91)
T TIGR00280 52 GIWTCRKCGAKFAGGAY 68 (91)
T ss_pred EEEEcCCCCCEEeCCcc
Confidence 34566666666555443
No 147
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.71 E-value=11 Score=24.19 Aligned_cols=7 Identities=14% Similarity=0.102 Sum_probs=3.7
Q ss_pred ccCCcch
Q psy8966 158 AEVPGSI 164 (175)
Q Consensus 158 ~~C~~c~ 164 (175)
+.||.||
T Consensus 108 ~~CP~Cg 114 (135)
T PRK03824 108 LKCPKCG 114 (135)
T ss_pred cCCcCCC
Confidence 4455555
No 148
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.79 E-value=23 Score=18.15 Aligned_cols=12 Identities=17% Similarity=0.454 Sum_probs=6.4
Q ss_pred cccCCcccchHHHh
Q psy8966 127 PYRCAHEFCSKSFK 140 (175)
Q Consensus 127 ~~~C~~~~C~~~f~ 140 (175)
-|.| +.||+.+.
T Consensus 20 ~~vC--~~Cg~~~~ 31 (52)
T smart00661 20 RFVC--RKCGYEEP 31 (52)
T ss_pred EEEC--CcCCCeEE
Confidence 4566 55665443
No 149
>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=27.75 E-value=16 Score=18.13 Aligned_cols=12 Identities=0% Similarity=-0.269 Sum_probs=5.9
Q ss_pred ccccCCcchhhh
Q psy8966 156 YTAEVPGSILDC 167 (175)
Q Consensus 156 ~~~~C~~c~~~~ 167 (175)
.|+.|+.|+..|
T Consensus 12 ~~~~C~~C~~~F 23 (43)
T PF01428_consen 12 LPFKCKHCGKSF 23 (43)
T ss_dssp SHEE-TTTS-EE
T ss_pred CCeECCCCCccc
Confidence 456666666544
No 150
>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=27.67 E-value=8.4 Score=23.91 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=14.1
Q ss_pred ccCCcccchHHHhchhhHHHHHHHhcCCccccCCcchhh
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRTHTGKYTAEVPGSILD 166 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~c~~~ 166 (175)
+.| ..||+.|.... ..+.||.||..
T Consensus 71 ~~C--~~Cg~~~~~~~------------~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARC--RDCGHEFEPDE------------FDFSCPRCGSP 95 (113)
T ss_dssp EEE--TTTS-EEECHH------------CCHH-SSSSSS
T ss_pred EEC--CCCCCEEecCC------------CCCCCcCCcCC
Confidence 778 67887776432 22458888743
No 151
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.81 E-value=34 Score=26.63 Aligned_cols=14 Identities=21% Similarity=0.743 Sum_probs=7.6
Q ss_pred cccCCcccchHHHhch
Q psy8966 127 PYRCAHEFCSKSFKTS 142 (175)
Q Consensus 127 ~~~C~~~~C~~~f~~~ 142 (175)
-|+| +.||..+...
T Consensus 367 g~rC--~kCg~~~~~~ 380 (421)
T COG1571 367 GFRC--KKCGTRARET 380 (421)
T ss_pred Cccc--ccccccCCcc
Confidence 5556 5566555543
No 152
>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=26.61 E-value=23 Score=19.47 Aligned_cols=12 Identities=17% Similarity=0.603 Sum_probs=7.0
Q ss_pred CCcccCCcccchHH
Q psy8966 125 EKPYRCAHEFCSKS 138 (175)
Q Consensus 125 ~~~~~C~~~~C~~~ 138 (175)
.+.|.| +.||..
T Consensus 44 ~r~~~C--~~Cg~~ 55 (69)
T PF07282_consen 44 GRVFTC--PNCGFE 55 (69)
T ss_pred cceEEc--CCCCCE
Confidence 455666 556654
No 153
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.47 E-value=13 Score=22.52 Aligned_cols=11 Identities=18% Similarity=0.413 Sum_probs=5.8
Q ss_pred ccCCcccchHHHh
Q psy8966 128 YRCAHEFCSKSFK 140 (175)
Q Consensus 128 ~~C~~~~C~~~f~ 140 (175)
..| ++||..+.
T Consensus 43 ~~C--~~CG~y~~ 53 (99)
T PRK14892 43 ITC--GNCGLYTE 53 (99)
T ss_pred EEC--CCCCCccC
Confidence 456 55665444
No 154
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.36 E-value=22 Score=22.08 Aligned_cols=7 Identities=14% Similarity=0.207 Sum_probs=4.5
Q ss_pred ccCCcch
Q psy8966 158 AEVPGSI 164 (175)
Q Consensus 158 ~~C~~c~ 164 (175)
+.||.||
T Consensus 88 ~~CP~Cg 94 (114)
T PRK03681 88 RRCPQCH 94 (114)
T ss_pred CcCcCcC
Confidence 4577776
No 155
>KOG2785|consensus
Probab=25.65 E-value=1e+02 Score=23.78 Aligned_cols=74 Identities=23% Similarity=0.452 Sum_probs=46.0
Q ss_pred CeeccccccCcccCChHHHHHHHHHhcCCCCCCCCCCccchhcccchhhhhccCCcceeccCCCcc---cccCCHHHHHH
Q psy8966 41 PYRCAHEFCSKSFKTSGDLQKHVRTHTGKYTPGPGIDSRLIVREDFVHLRIHSGIRPYKCPVEYCE---KAFSTQYSRKA 117 (175)
Q Consensus 41 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~C~---~~f~~~~~l~~ 117 (175)
|-.|- +|+..+.+...-..||..+++-+.....+.....---...-.++. .-+.|. .|+ +.|.+......
T Consensus 166 Pt~CL--fC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~---~~~~CL--~CN~~~~~f~sleavr~ 238 (390)
T KOG2785|consen 166 PTDCL--FCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVG---IGFICL--FCNELGRPFSSLEAVRA 238 (390)
T ss_pred Cccee--ecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhc---cCceEE--EeccccCcccccHHHHH
Confidence 34574 499999999999999999888555443222221000001112222 236676 688 88999999999
Q ss_pred HHhh
Q psy8966 118 HIRT 121 (175)
Q Consensus 118 H~~~ 121 (175)
||..
T Consensus 239 HM~~ 242 (390)
T KOG2785|consen 239 HMRD 242 (390)
T ss_pred HHhh
Confidence 9854
No 156
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=25.26 E-value=37 Score=20.81 Aligned_cols=25 Identities=24% Similarity=0.448 Sum_probs=20.7
Q ss_pred CCcceeccCCCcccccCCHHHHHHHHh
Q psy8966 94 GIRPYKCPVEYCEKAFSTQYSRKAHIR 120 (175)
Q Consensus 94 ~~~~~~C~~~~C~~~f~~~~~l~~H~~ 120 (175)
|-+.+.|. +|.+-|.+...|..|.+
T Consensus 52 GlGqhYCi--eCaryf~t~~aL~~Hkk 76 (126)
T COG5112 52 GLGQHYCI--ECARYFITEKALMEHKK 76 (126)
T ss_pred CCceeeee--hhHHHHHHHHHHHHHhc
Confidence 45567786 89999999999999974
No 157
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.20 E-value=33 Score=21.93 Aligned_cols=14 Identities=0% Similarity=-0.261 Sum_probs=7.9
Q ss_pred CccccCCcchhhhc
Q psy8966 155 KYTAEVPGSILDCL 168 (175)
Q Consensus 155 ~~~~~C~~c~~~~~ 168 (175)
.+.|.|+.|++.|.
T Consensus 51 ~qRyrC~~C~~tf~ 64 (129)
T COG3677 51 HQRYKCKSCGSTFT 64 (129)
T ss_pred ccccccCCcCccee
Confidence 45566666665543
No 158
>KOG2482|consensus
Probab=24.87 E-value=37 Score=25.62 Aligned_cols=51 Identities=25% Similarity=0.656 Sum_probs=35.4
Q ss_pred ceeccCCCcccccCCH-HHHHHHH-hhhc---C--C----------------CcccCCcccchHHHhchhhHHHHHHH
Q psy8966 97 PYKCPVEYCEKAFSTQ-YSRKAHI-RTHT---G--E----------------KPYRCAHEFCSKSFKTSGDLQKHVRT 151 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~-~~l~~H~-~~h~---~--~----------------~~~~C~~~~C~~~f~~~~~l~~H~~~ 151 (175)
.-.|. .|+..+... +....|+ ..|. | + ..+.| -.|.+.|+.+..|..||+.
T Consensus 144 slqCl--FCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~C--LyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 144 SLQCL--FCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRC--LYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeEEE--EecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhhee--eeeccccCCcHHHHHHHHh
Confidence 44575 788776554 4455665 3331 1 1 13889 8999999999999999985
No 159
>PF14353 CpXC: CpXC protein
Probab=24.23 E-value=26 Score=22.07 Aligned_cols=12 Identities=8% Similarity=0.157 Sum_probs=6.0
Q ss_pred ccccCCcchhhh
Q psy8966 156 YTAEVPGSILDC 167 (175)
Q Consensus 156 ~~~~C~~c~~~~ 167 (175)
..+.||.||..+
T Consensus 37 ~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 37 FSFTCPSCGHKF 48 (128)
T ss_pred CEEECCCCCCce
Confidence 345555555444
No 160
>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=24.13 E-value=29 Score=18.44 Aligned_cols=9 Identities=22% Similarity=0.228 Sum_probs=5.1
Q ss_pred ccCCcchhh
Q psy8966 158 AEVPGSILD 166 (175)
Q Consensus 158 ~~C~~c~~~ 166 (175)
+.||.||..
T Consensus 3 ~~CP~CG~~ 11 (54)
T TIGR01206 3 FECPDCGAE 11 (54)
T ss_pred cCCCCCCCE
Confidence 456666643
No 161
>KOG3507|consensus
Probab=23.90 E-value=27 Score=18.88 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=9.3
Q ss_pred CcccCCcccchHHHhch
Q psy8966 126 KPYRCAHEFCSKSFKTS 142 (175)
Q Consensus 126 ~~~~C~~~~C~~~f~~~ 142 (175)
-++.| -+||+...++
T Consensus 36 D~irC--ReCG~RIlyK 50 (62)
T KOG3507|consen 36 DVIRC--RECGYRILYK 50 (62)
T ss_pred CcEeh--hhcchHHHHH
Confidence 35677 6677765554
No 162
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=23.86 E-value=10 Score=22.90 Aligned_cols=16 Identities=19% Similarity=0.654 Sum_probs=9.4
Q ss_pred CcceeccCCCcccccCCH
Q psy8966 95 IRPYKCPVEYCEKAFSTQ 112 (175)
Q Consensus 95 ~~~~~C~~~~C~~~f~~~ 112 (175)
.+.|.|| .|+..-...
T Consensus 20 ~k~FtCp--~Cghe~vs~ 35 (104)
T COG4888 20 PKTFTCP--RCGHEKVSS 35 (104)
T ss_pred CceEecC--ccCCeeeeE
Confidence 4566676 676655443
No 163
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=23.64 E-value=36 Score=17.69 Aligned_cols=14 Identities=21% Similarity=0.598 Sum_probs=7.1
Q ss_pred cceeccCCCcccccCC
Q psy8966 96 RPYKCPVEYCEKAFST 111 (175)
Q Consensus 96 ~~~~C~~~~C~~~f~~ 111 (175)
+.+.|. .||..|..
T Consensus 3 k~l~C~--dCg~~Fvf 16 (49)
T PF13451_consen 3 KTLTCK--DCGAEFVF 16 (49)
T ss_pred eeEEcc--cCCCeEEE
Confidence 344554 56655543
No 164
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=22.34 E-value=40 Score=16.76 Aligned_cols=11 Identities=9% Similarity=-0.067 Sum_probs=8.0
Q ss_pred ccccCCcchhh
Q psy8966 156 YTAEVPGSILD 166 (175)
Q Consensus 156 ~~~~C~~c~~~ 166 (175)
+|..|+.||..
T Consensus 1 ~~~~Cp~Cg~~ 11 (47)
T PF14690_consen 1 KPPRCPHCGSP 11 (47)
T ss_pred CCccCCCcCCC
Confidence 36789999844
No 165
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.00 E-value=36 Score=17.94 Aligned_cols=9 Identities=11% Similarity=-0.134 Sum_probs=5.9
Q ss_pred cCCcchhhh
Q psy8966 159 EVPGSILDC 167 (175)
Q Consensus 159 ~C~~c~~~~ 167 (175)
.||+||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 577887543
No 166
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.96 E-value=35 Score=17.74 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=6.8
Q ss_pred CcccCCcccchHHH
Q psy8966 126 KPYRCAHEFCSKSF 139 (175)
Q Consensus 126 ~~~~C~~~~C~~~f 139 (175)
..+.| ..||..+
T Consensus 36 ~r~~C--~~Cgyt~ 47 (50)
T PRK00432 36 DRWHC--GKCGYTE 47 (50)
T ss_pred CcEEC--CCcCCEE
Confidence 45666 5566543
No 167
>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=21.76 E-value=25 Score=17.71 Aligned_cols=10 Identities=0% Similarity=-0.187 Sum_probs=5.1
Q ss_pred CccccCCcch
Q psy8966 155 KYTAEVPGSI 164 (175)
Q Consensus 155 ~~~~~C~~c~ 164 (175)
...|.|..|+
T Consensus 35 ~~~~~C~~C~ 44 (46)
T PF12760_consen 35 RGRYRCKACR 44 (46)
T ss_pred CCeEECCCCC
Confidence 3445555554
No 168
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.72 E-value=32 Score=17.01 Aligned_cols=7 Identities=14% Similarity=-0.059 Sum_probs=3.0
Q ss_pred ccCCcch
Q psy8966 158 AEVPGSI 164 (175)
Q Consensus 158 ~~C~~c~ 164 (175)
-.||.||
T Consensus 4 ~pCP~CG 10 (40)
T PF08273_consen 4 GPCPICG 10 (40)
T ss_dssp E--TTTT
T ss_pred CCCCCCc
Confidence 4566665
No 169
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.72 E-value=21 Score=26.36 Aligned_cols=33 Identities=24% Similarity=0.285 Sum_probs=17.8
Q ss_pred ceeccCCCcccccCCHHHHHHHHhhhcCCCcccCCcccchHHHhch
Q psy8966 97 PYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTS 142 (175)
Q Consensus 97 ~~~C~~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~C~~~f~~~ 142 (175)
..+|+ .|+.....+ .| .++-+.| +.|++-|+-.
T Consensus 38 w~kc~--~C~~~~~~~-~l--------~~~~~vc--p~c~~h~rlt 70 (296)
T CHL00174 38 WVQCE--NCYGLNYKK-FL--------KSKMNIC--EQCGYHLKMS 70 (296)
T ss_pred eeECC--CccchhhHH-HH--------HHcCCCC--CCCCCCcCCC
Confidence 34565 676654332 22 2334677 6687766543
No 170
>KOG0717|consensus
Probab=21.40 E-value=44 Score=26.38 Aligned_cols=22 Identities=36% Similarity=0.751 Sum_probs=19.1
Q ss_pred ccCCcccchHHHhchhhHHHHHHH
Q psy8966 128 YRCAHEFCSKSFKTSGDLQKHVRT 151 (175)
Q Consensus 128 ~~C~~~~C~~~f~~~~~l~~H~~~ 151 (175)
+.| .+|.++|.+...|..|..+
T Consensus 293 lyC--~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYC--VVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEE--eeccccccchHHHHhhHHH
Confidence 779 8899999999999988864
No 171
>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=21.27 E-value=35 Score=16.19 Aligned_cols=14 Identities=0% Similarity=-0.102 Sum_probs=5.6
Q ss_pred cCCcchhhhccccc
Q psy8966 159 EVPGSILDCLSGRF 172 (175)
Q Consensus 159 ~C~~c~~~~~~~~~ 172 (175)
.|..|+..|.-+++
T Consensus 5 ~C~eC~~~f~dSyL 18 (34)
T PF01286_consen 5 KCDECGKPFMDSYL 18 (34)
T ss_dssp E-TTT--EES-SSC
T ss_pred hHhHhCCHHHHHHH
Confidence 56666666555443
No 172
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.11 E-value=23 Score=21.06 Aligned_cols=16 Identities=13% Similarity=-0.149 Sum_probs=8.8
Q ss_pred ccccCCcchhhhcccc
Q psy8966 156 YTAEVPGSILDCLSGR 171 (175)
Q Consensus 156 ~~~~C~~c~~~~~~~~ 171 (175)
-.+.|..|++.|.-+.
T Consensus 53 GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 53 GIWECRKCGAKFAGGA 68 (90)
T ss_pred EEEEcCCCCCEEeCCc
Confidence 3456666665555443
No 173
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=20.63 E-value=49 Score=18.30 Aligned_cols=14 Identities=7% Similarity=-0.033 Sum_probs=9.1
Q ss_pred cCCcchhhhccccc
Q psy8966 159 EVPGSILDCLSGRF 172 (175)
Q Consensus 159 ~C~~c~~~~~~~~~ 172 (175)
.||.||-..+|..+
T Consensus 19 ~Cp~Cgs~~~S~~w 32 (64)
T PRK06393 19 TCPVHGDEKTTTEW 32 (64)
T ss_pred cCCCCCCCcCCcCc
Confidence 78888776655443
No 174
>COG2879 Uncharacterized small protein [Function unknown]
Probab=20.13 E-value=1e+02 Score=16.99 Aligned_cols=14 Identities=14% Similarity=0.275 Sum_probs=9.3
Q ss_pred hHHHHHHHhcCCcc
Q psy8966 144 DLQKHVRTHTGKYT 157 (175)
Q Consensus 144 ~l~~H~~~h~~~~~ 157 (175)
+...||+.+++.+|
T Consensus 27 nYVehmr~~hPd~p 40 (65)
T COG2879 27 NYVEHMRKKHPDKP 40 (65)
T ss_pred HHHHHHHHhCcCCC
Confidence 45678887766655
Done!