Query psy3356
Match_columns 180
No_of_seqs 169 out of 2267
Neff 10.9
Searched_HMMs 46136
Date Fri Aug 16 22:55:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3356.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3356hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 1.1E-30 2.5E-35 178.8 4.4 130 20-179 127-259 (279)
2 KOG2462|consensus 99.9 6.8E-25 1.5E-29 150.5 5.4 127 1-149 135-265 (279)
3 KOG3608|consensus 99.8 3.4E-22 7.4E-27 141.3 0.4 167 1-179 184-368 (467)
4 KOG1074|consensus 99.8 1E-19 2.3E-24 140.9 1.9 76 100-179 606-684 (958)
5 KOG3608|consensus 99.8 9.1E-20 2E-24 129.2 0.7 164 1-180 141-309 (467)
6 KOG1074|consensus 99.7 1.4E-18 3.1E-23 134.7 2.3 87 36-123 603-692 (958)
7 KOG3576|consensus 99.7 7E-18 1.5E-22 111.2 2.3 113 36-153 115-238 (267)
8 KOG3576|consensus 99.7 3.6E-17 7.9E-22 107.9 2.0 106 63-173 114-222 (267)
9 KOG3623|consensus 99.6 1.8E-15 3.8E-20 116.4 4.3 100 67-177 211-323 (1007)
10 KOG3623|consensus 99.6 4.9E-16 1.1E-20 119.4 0.4 116 20-150 207-332 (1007)
11 PLN03086 PRLI-interacting fact 99.3 3.5E-12 7.6E-17 98.1 6.7 126 22-176 406-554 (567)
12 PLN03086 PRLI-interacting fact 99.3 7.6E-12 1.6E-16 96.2 6.8 129 9-149 419-562 (567)
13 PHA00733 hypothetical protein 99.2 6.3E-11 1.4E-15 75.1 5.1 85 63-151 37-123 (128)
14 PHA02768 hypothetical protein; 99.1 5.6E-11 1.2E-15 62.7 2.9 43 127-179 5-47 (55)
15 PHA00733 hypothetical protein 99.0 2.2E-10 4.8E-15 72.7 2.3 75 95-179 36-115 (128)
16 PF13465 zf-H2C2_2: Zinc-finge 98.8 1.8E-09 3.9E-14 48.9 1.3 24 143-174 2-25 (26)
17 PHA02768 hypothetical protein; 98.8 3.3E-09 7.1E-14 56.0 1.7 43 99-143 5-47 (55)
18 KOG3993|consensus 98.7 4.9E-09 1.1E-13 76.9 0.4 56 36-91 265-320 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.7 2.2E-08 4.7E-13 45.3 2.3 25 114-138 1-25 (26)
20 KOG3993|consensus 98.5 5E-08 1.1E-12 71.8 1.6 80 67-151 268-380 (500)
21 PHA00616 hypothetical protein 98.4 1.3E-07 2.8E-12 47.6 1.5 34 127-168 1-34 (44)
22 PHA00732 hypothetical protein 98.3 6.8E-07 1.5E-11 51.7 2.9 45 99-149 1-46 (79)
23 PF05605 zf-Di19: Drought indu 98.3 1.8E-06 3.9E-11 46.4 3.9 50 67-122 3-52 (54)
24 PHA00616 hypothetical protein 98.2 5.3E-07 1.1E-11 45.4 1.4 32 100-131 2-33 (44)
25 PHA00732 hypothetical protein 98.1 1.9E-06 4.1E-11 49.8 2.4 48 66-123 1-48 (79)
26 PF00096 zf-C2H2: Zinc finger, 98.0 4.2E-06 9E-11 36.5 2.0 22 128-149 1-22 (23)
27 PF05605 zf-Di19: Drought indu 98.0 1.3E-05 2.9E-10 43.0 3.9 49 99-150 2-52 (54)
28 PF00096 zf-C2H2: Zinc finger, 97.8 1.2E-05 2.5E-10 35.1 1.6 22 67-88 1-22 (23)
29 PF13894 zf-C2H2_4: C2H2-type 97.8 1.9E-05 4.2E-10 34.6 2.3 23 128-150 1-23 (24)
30 PF12756 zf-C2H2_2: C2H2 type 97.8 2.6E-05 5.6E-10 47.4 2.9 73 68-150 1-73 (100)
31 PF13912 zf-C2H2_6: C2H2-type 97.7 2.3E-05 4.9E-10 35.6 1.7 24 127-150 1-24 (27)
32 KOG2231|consensus 97.7 7.2E-05 1.6E-09 59.3 4.8 120 25-151 101-236 (669)
33 PF13894 zf-C2H2_4: C2H2-type 97.6 4.7E-05 1E-09 33.2 1.9 23 67-89 1-23 (24)
34 COG5189 SFP1 Putative transcri 97.5 6.1E-05 1.3E-09 54.0 1.8 56 125-180 347-415 (423)
35 COG5189 SFP1 Putative transcri 97.4 5.9E-05 1.3E-09 54.1 1.1 72 63-148 346-419 (423)
36 PF13912 zf-C2H2_6: C2H2-type 97.4 0.00019 4.1E-09 32.5 2.3 23 100-122 2-24 (27)
37 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00019 4.2E-09 43.5 2.8 72 41-122 2-73 (100)
38 smart00355 ZnF_C2H2 zinc finge 97.1 0.00039 8.5E-09 30.7 2.0 23 128-150 1-23 (26)
39 PRK04860 hypothetical protein; 97.1 0.00044 9.6E-09 45.7 2.5 42 126-179 118-159 (160)
40 PF12874 zf-met: Zinc-finger o 96.9 0.00049 1.1E-08 30.4 1.3 22 128-149 1-22 (25)
41 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00076 1.6E-08 29.5 1.5 22 128-150 1-22 (24)
42 PF09237 GAGA: GAGA factor; I 96.8 0.0017 3.7E-08 33.6 2.8 20 67-86 25-44 (54)
43 smart00355 ZnF_C2H2 zinc finge 96.7 0.0015 3.3E-08 28.7 2.1 23 67-89 1-23 (26)
44 PF09237 GAGA: GAGA factor; I 96.5 0.0038 8.2E-08 32.4 2.6 33 95-127 20-52 (54)
45 PF13909 zf-H2C2_5: C2H2-type 96.4 0.0026 5.7E-08 27.7 1.7 22 67-89 1-22 (24)
46 PF12874 zf-met: Zinc-finger o 96.3 0.0041 8.9E-08 27.3 1.9 20 101-120 2-21 (25)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.2 0.001 2.3E-08 30.0 -0.3 21 128-148 2-22 (27)
48 KOG2231|consensus 96.1 0.0054 1.2E-07 49.1 3.1 125 4-148 122-260 (669)
49 KOG1146|consensus 96.0 0.0029 6.4E-08 53.8 1.4 100 50-149 448-611 (1406)
50 PRK04860 hypothetical protein; 96.0 0.007 1.5E-07 40.1 2.7 39 98-140 118-156 (160)
51 PF13913 zf-C2HC_2: zinc-finge 95.2 0.02 4.4E-07 25.2 2.0 21 128-149 3-23 (25)
52 PF12171 zf-C2H2_jaz: Zinc-fin 94.7 0.011 2.4E-07 26.5 0.4 21 100-120 2-22 (27)
53 smart00451 ZnF_U1 U1-like zinc 94.6 0.031 6.8E-07 26.6 1.9 23 127-149 3-25 (35)
54 COG5236 Uncharacterized conser 94.1 0.046 9.9E-07 40.3 2.6 133 2-151 159-305 (493)
55 TIGR00622 ssl1 transcription f 94.1 0.063 1.4E-06 33.1 2.8 48 101-150 57-104 (112)
56 PF12013 DUF3505: Protein of u 93.6 0.24 5.2E-06 30.6 4.9 24 128-151 81-108 (109)
57 cd00350 rubredoxin_like Rubred 93.4 0.054 1.2E-06 25.6 1.3 9 126-134 16-24 (33)
58 cd00729 rubredoxin_SM Rubredox 92.7 0.094 2E-06 25.0 1.6 11 127-137 2-12 (34)
59 PF13717 zinc_ribbon_4: zinc-r 92.6 0.14 3E-06 24.7 2.2 33 128-173 3-35 (36)
60 smart00451 ZnF_U1 U1-like zinc 92.5 0.088 1.9E-06 25.0 1.4 22 66-87 3-24 (35)
61 KOG2482|consensus 92.0 0.15 3.3E-06 37.6 2.6 112 38-150 195-357 (423)
62 KOG2893|consensus 91.9 0.046 1E-06 38.1 0.0 44 38-85 10-53 (341)
63 COG1592 Rubrerythrin [Energy p 91.7 0.13 2.8E-06 34.2 1.9 23 127-170 134-156 (166)
64 PF09538 FYDLN_acid: Protein o 91.4 0.2 4.4E-06 30.9 2.4 30 100-140 10-39 (108)
65 PF10571 UPF0547: Uncharacteri 90.9 0.078 1.7E-06 23.6 0.2 23 25-48 2-24 (26)
66 PF13719 zinc_ribbon_5: zinc-r 90.9 0.23 5.1E-06 24.1 1.9 34 128-174 3-36 (37)
67 KOG4173|consensus 90.5 0.034 7.3E-07 37.9 -1.7 76 66-149 79-168 (253)
68 KOG1146|consensus 90.4 0.17 3.7E-06 43.8 1.8 100 67-176 1261-1393(1406)
69 KOG1280|consensus 90.2 0.32 6.9E-06 36.0 2.9 81 23-106 8-116 (381)
70 KOG4173|consensus 90.0 0.32 6.9E-06 33.3 2.6 77 44-123 87-171 (253)
71 PF09538 FYDLN_acid: Protein o 90.0 0.21 4.6E-06 30.8 1.6 14 162-175 25-38 (108)
72 TIGR02098 MJ0042_CXXC MJ0042 f 89.9 0.27 5.8E-06 23.9 1.7 14 128-141 3-16 (38)
73 TIGR00622 ssl1 transcription f 89.8 0.62 1.3E-05 28.8 3.5 91 24-122 2-104 (112)
74 COG4049 Uncharacterized protei 89.8 0.15 3.3E-06 26.9 0.7 26 124-149 14-39 (65)
75 KOG2186|consensus 89.7 0.31 6.7E-06 34.5 2.4 46 67-120 4-49 (276)
76 PHA00626 hypothetical protein 89.4 0.06 1.3E-06 28.5 -0.9 14 126-139 22-35 (59)
77 KOG2893|consensus 89.4 0.099 2.1E-06 36.5 -0.2 42 68-118 12-53 (341)
78 KOG2482|consensus 89.3 0.57 1.2E-05 34.7 3.6 142 38-179 144-350 (423)
79 KOG2186|consensus 88.5 0.41 8.9E-06 33.9 2.3 48 99-149 3-50 (276)
80 COG5236 Uncharacterized conser 88.4 0.41 8.8E-06 35.5 2.3 77 66-149 151-242 (493)
81 COG4049 Uncharacterized protei 88.1 0.34 7.4E-06 25.6 1.3 30 61-90 12-41 (65)
82 PF09723 Zn-ribbon_8: Zinc rib 87.2 0.31 6.8E-06 24.4 0.9 11 24-34 6-16 (42)
83 PF09986 DUF2225: Uncharacteri 86.8 0.15 3.2E-06 35.7 -0.6 12 128-139 49-60 (214)
84 smart00531 TFIIE Transcription 86.5 1.4 3.1E-05 28.8 3.9 14 126-139 98-111 (147)
85 COG2888 Predicted Zn-ribbon RN 86.4 0.44 9.5E-06 25.7 1.2 10 161-170 48-57 (61)
86 COG5048 FOG: Zn-finger [Genera 86.1 0.28 6.1E-06 37.5 0.5 47 43-89 294-346 (467)
87 TIGR02300 FYDLN_acid conserved 85.7 0.75 1.6E-05 29.0 2.1 31 99-140 9-39 (129)
88 PF12013 DUF3505: Protein of u 85.3 2.9 6.3E-05 25.7 4.7 26 99-124 80-109 (109)
89 PRK14890 putative Zn-ribbon RN 84.7 1 2.2E-05 24.3 2.1 11 161-171 46-56 (59)
90 TIGR00373 conserved hypothetic 84.5 1.1 2.4E-05 29.7 2.7 18 126-143 108-125 (158)
91 PF00301 Rubredoxin: Rubredoxi 83.7 0.85 1.8E-05 23.5 1.5 14 24-37 2-15 (47)
92 KOG2071|consensus 83.1 0.99 2.1E-05 36.0 2.3 16 161-176 511-526 (579)
93 PRK00398 rpoP DNA-directed RNA 81.5 0.84 1.8E-05 23.3 1.0 10 67-76 4-13 (46)
94 PRK06266 transcription initiat 80.7 1.6 3.4E-05 29.6 2.3 16 127-142 117-132 (178)
95 PRK00464 nrdR transcriptional 79.7 0.28 6.1E-06 32.3 -1.4 12 100-111 29-40 (154)
96 KOG2785|consensus 79.7 3 6.6E-05 31.5 3.6 51 100-150 167-243 (390)
97 smart00531 TFIIE Transcription 79.2 2.1 4.6E-05 28.0 2.6 38 96-137 96-133 (147)
98 cd00730 rubredoxin Rubredoxin; 78.6 1.5 3.3E-05 22.9 1.4 13 24-36 2-14 (50)
99 smart00734 ZnF_Rad18 Rad18-lik 78.6 2.1 4.6E-05 18.9 1.7 19 129-148 3-21 (26)
100 COG5048 FOG: Zn-finger [Genera 78.1 0.76 1.6E-05 35.2 0.2 53 99-151 289-347 (467)
101 TIGR00373 conserved hypothetic 77.7 3.4 7.3E-05 27.4 3.2 34 95-137 105-138 (158)
102 smart00834 CxxC_CXXC_SSSS Puta 77.6 1.4 3E-05 21.6 1.1 11 24-34 6-16 (41)
103 PF14353 CpXC: CpXC protein 77.6 3.9 8.5E-05 26.0 3.4 19 65-83 37-55 (128)
104 KOG2785|consensus 77.0 4.5 9.7E-05 30.7 3.8 56 66-121 166-242 (390)
105 smart00659 RPOLCX RNA polymera 76.6 2.4 5.2E-05 21.5 1.7 10 100-109 3-12 (44)
106 COG1198 PriA Primosomal protei 76.2 1.2 2.5E-05 37.1 0.8 54 16-75 428-484 (730)
107 PF07800 DUF1644: Protein of u 75.0 12 0.00026 24.8 5.0 53 98-152 79-133 (162)
108 PF06524 NOA36: NOA36 protein; 74.5 2.9 6.2E-05 30.0 2.2 18 161-178 207-224 (314)
109 PF02176 zf-TRAF: TRAF-type zi 73.8 3.6 7.7E-05 22.0 2.1 21 112-132 23-43 (60)
110 COG1997 RPL43A Ribosomal prote 73.7 1.6 3.4E-05 25.6 0.7 31 98-138 34-64 (89)
111 PRK06266 transcription initiat 73.3 4 8.6E-05 27.7 2.7 34 96-138 114-147 (178)
112 PF02892 zf-BED: BED zinc fing 72.2 4.1 8.8E-05 20.4 2.0 23 126-148 15-41 (45)
113 TIGR02605 CxxC_CxxC_SSSS putat 71.9 1.1 2.5E-05 23.3 -0.1 10 100-109 6-15 (52)
114 KOG2593|consensus 71.9 4.5 9.7E-05 31.2 2.9 38 124-172 125-162 (436)
115 PF07754 DUF1610: Domain of un 70.2 2.1 4.5E-05 18.6 0.5 9 162-170 15-23 (24)
116 KOG2807|consensus 69.4 9.5 0.00021 28.4 3.9 26 125-150 343-368 (378)
117 PRK09678 DNA-binding transcrip 69.0 0.8 1.7E-05 26.0 -1.2 20 123-142 23-44 (72)
118 KOG2807|consensus 68.5 9.6 0.00021 28.4 3.8 91 67-173 245-355 (378)
119 PF04959 ARS2: Arsenite-resist 67.5 5.6 0.00012 27.9 2.4 31 95-125 73-103 (214)
120 PF12907 zf-met2: Zinc-binding 66.9 4.9 0.00011 19.9 1.5 22 128-149 2-26 (40)
121 PF07975 C1_4: TFIIH C1-like d 65.8 1.7 3.6E-05 22.9 -0.3 14 21-34 19-32 (51)
122 COG5151 SSL1 RNA polymerase II 65.7 9.4 0.0002 28.2 3.3 83 66-150 322-411 (421)
123 PF08274 PhnA_Zn_Ribbon: PhnA 65.0 2.9 6.3E-05 19.2 0.5 9 127-135 19-27 (30)
124 PF15269 zf-C2H2_7: Zinc-finge 63.7 6.2 0.00013 19.9 1.5 24 99-122 20-43 (54)
125 COG1996 RPC10 DNA-directed RNA 63.1 3.2 6.9E-05 21.6 0.5 12 23-34 6-17 (49)
126 smart00440 ZnF_C2C2 C2C2 Zinc 62.7 1.3 2.8E-05 21.9 -1.0 8 128-135 29-36 (40)
127 smart00154 ZnF_AN1 AN1-like Zi 61.9 4.2 9.1E-05 19.9 0.7 11 163-173 12-22 (39)
128 TIGR01206 lysW lysine biosynth 61.8 5.6 0.00012 21.2 1.3 11 24-34 3-13 (54)
129 COG1198 PriA Primosomal protei 61.7 7.8 0.00017 32.5 2.6 13 160-172 472-484 (730)
130 COG5151 SSL1 RNA polymerase II 61.6 4.3 9.2E-05 29.9 1.0 99 15-122 301-411 (421)
131 PF13878 zf-C2H2_3: zinc-finge 61.0 10 0.00023 18.8 2.1 12 23-34 13-24 (41)
132 PF03604 DNA_RNApol_7kD: DNA d 60.4 4.4 9.5E-05 19.0 0.6 8 100-107 18-25 (32)
133 KOG3408|consensus 58.2 7.4 0.00016 24.4 1.5 27 124-150 54-80 (129)
134 PF04959 ARS2: Arsenite-resist 57.5 8.8 0.00019 26.9 2.0 27 125-151 75-101 (214)
135 COG3677 Transposase and inacti 57.2 5.7 0.00012 25.4 1.0 16 161-176 51-66 (129)
136 PRK03824 hypA hydrogenase nick 55.9 4.9 0.00011 25.9 0.5 11 100-110 71-81 (135)
137 KOG2593|consensus 55.0 16 0.00035 28.4 3.1 37 63-107 125-161 (436)
138 smart00614 ZnF_BED BED zinc fi 54.5 12 0.00026 19.3 1.8 21 128-148 19-44 (50)
139 PF10013 DUF2256: Uncharacteri 53.5 5.1 0.00011 20.0 0.2 12 165-176 10-21 (42)
140 PF00628 PHD: PHD-finger; Int 53.5 1.8 3.9E-05 22.3 -1.5 23 26-48 2-24 (51)
141 PF13453 zf-TFIIB: Transcripti 53.1 10 0.00022 18.6 1.3 16 128-143 20-35 (41)
142 PF08790 zf-LYAR: LYAR-type C2 52.3 2.8 6.1E-05 18.9 -0.7 19 128-147 1-19 (28)
143 KOG2907|consensus 51.9 9.9 0.00021 23.5 1.3 12 25-36 9-20 (116)
144 PF13248 zf-ribbon_3: zinc-rib 51.4 5.3 0.00011 17.5 0.1 8 25-32 4-11 (26)
145 PF01428 zf-AN1: AN1-like Zinc 50.6 3.9 8.5E-05 20.5 -0.5 12 162-173 12-23 (43)
146 PF05443 ROS_MUCR: ROS/MUCR tr 50.5 14 0.0003 23.8 1.9 27 97-126 70-96 (132)
147 KOG4167|consensus 50.0 4.2 9.1E-05 33.6 -0.6 25 127-151 792-816 (907)
148 COG3357 Predicted transcriptio 49.7 9 0.00019 22.7 0.9 13 99-111 58-70 (97)
149 PTZ00255 60S ribosomal protein 49.6 5.4 0.00012 23.7 -0.0 33 16-48 29-64 (90)
150 PF05191 ADK_lid: Adenylate ki 49.5 19 0.00041 17.3 1.9 10 25-34 3-12 (36)
151 PF04423 Rad50_zn_hook: Rad50 48.4 5.6 0.00012 21.0 -0.1 10 165-174 22-31 (54)
152 PF13451 zf-trcl: Probable zin 47.9 15 0.00033 19.1 1.5 14 98-111 3-16 (49)
153 KOG1280|consensus 47.9 23 0.0005 26.7 2.9 27 125-151 77-103 (381)
154 smart00249 PHD PHD zinc finger 46.7 8.6 0.00019 18.8 0.5 21 26-46 2-22 (47)
155 COG4530 Uncharacterized protei 46.1 14 0.0003 22.8 1.3 27 100-137 10-36 (129)
156 COG4391 Uncharacterized protei 45.6 19 0.00041 19.7 1.6 16 19-34 44-59 (62)
157 KOG0717|consensus 45.4 15 0.00032 28.9 1.7 22 128-149 293-314 (508)
158 COG1571 Predicted DNA-binding 45.4 15 0.00032 28.6 1.7 13 163-175 367-379 (421)
159 cd00065 FYVE FYVE domain; Zinc 45.3 18 0.00039 19.0 1.6 10 128-137 19-28 (57)
160 PF10276 zf-CHCC: Zinc-finger 45.3 28 0.0006 17.2 2.1 11 23-33 29-39 (40)
161 TIGR00280 L37a ribosomal prote 45.1 6.1 0.00013 23.5 -0.3 33 16-48 28-63 (91)
162 smart00661 RPOL9 RNA polymeras 45.1 12 0.00025 19.3 0.8 12 66-77 20-31 (52)
163 PF01096 TFIIS_C: Transcriptio 45.0 0.71 1.5E-05 22.7 -3.6 8 128-135 29-36 (39)
164 PF12773 DZR: Double zinc ribb 44.7 8.7 0.00019 19.7 0.3 7 68-74 31-37 (50)
165 KOG2817|consensus 43.9 21 0.00045 27.4 2.2 71 2-75 309-383 (394)
166 PF04780 DUF629: Protein of un 43.3 36 0.00077 27.1 3.5 33 119-151 49-81 (466)
167 PF13240 zinc_ribbon_2: zinc-r 43.3 8.9 0.00019 16.3 0.2 9 26-34 2-10 (23)
168 PF07282 OrfB_Zn_ribbon: Putat 43.0 19 0.00041 19.9 1.5 13 125-137 44-56 (69)
169 PRK14714 DNA polymerase II lar 42.9 16 0.00034 32.6 1.6 37 23-77 667-703 (1337)
170 TIGR00595 priA primosomal prot 42.7 13 0.00029 29.8 1.2 18 17-34 207-224 (505)
171 PF01780 Ribosomal_L37ae: Ribo 40.7 4.4 9.6E-05 24.1 -1.3 31 18-48 30-63 (90)
172 PF05495 zf-CHY: CHY zinc fing 40.5 5.5 0.00012 22.5 -0.9 9 163-171 61-69 (71)
173 PRK12496 hypothetical protein; 40.5 10 0.00023 25.3 0.2 26 23-48 127-153 (164)
174 PRK03976 rpl37ae 50S ribosomal 40.2 8.1 0.00017 23.0 -0.3 33 16-48 29-64 (90)
175 COG0068 HypF Hydrogenase matur 39.9 5.6 0.00012 32.9 -1.2 75 23-108 101-182 (750)
176 PF14446 Prok-RING_1: Prokaryo 39.9 14 0.0003 19.7 0.6 14 164-177 6-19 (54)
177 PF14369 zf-RING_3: zinc-finge 39.8 31 0.00068 16.4 1.8 13 22-34 20-32 (35)
178 PF04810 zf-Sec23_Sec24: Sec23 39.5 8.8 0.00019 18.8 -0.2 8 163-170 24-31 (40)
179 COG1773 Rubredoxin [Energy pro 39.4 12 0.00026 20.0 0.3 12 163-174 3-14 (55)
180 KOG4377|consensus 39.4 13 0.00029 28.6 0.7 104 43-151 278-427 (480)
181 PRK04023 DNA polymerase II lar 39.3 26 0.00057 30.6 2.3 21 24-47 627-647 (1121)
182 KOG1842|consensus 38.7 34 0.00075 26.8 2.7 26 98-123 14-39 (505)
183 COG1594 RPB9 DNA-directed RNA 38.5 9.4 0.0002 23.8 -0.2 9 67-75 23-31 (113)
184 COG3091 SprT Zn-dependent meta 37.9 14 0.0003 24.4 0.5 35 125-172 115-149 (156)
185 PRK14873 primosome assembly pr 37.7 16 0.00035 30.4 1.0 27 15-47 375-401 (665)
186 PF08792 A2L_zn_ribbon: A2L zi 37.4 23 0.00049 16.7 1.1 12 22-33 20-31 (33)
187 PRK05580 primosome assembly pr 36.4 20 0.00043 30.0 1.3 17 18-34 376-392 (679)
188 PF14787 zf-CCHC_5: GAG-polypr 36.1 26 0.00056 16.9 1.1 13 165-177 4-16 (36)
189 COG1327 Predicted transcriptio 36.1 8.9 0.00019 25.2 -0.6 12 101-112 30-41 (156)
190 KOG2636|consensus 36.0 32 0.00069 27.0 2.2 29 120-148 394-423 (497)
191 PF06397 Desulfoferrod_N: Desu 36.0 15 0.00032 17.7 0.3 11 162-172 5-15 (36)
192 COG1675 TFA1 Transcription ini 35.7 52 0.0011 22.4 2.9 8 164-171 133-140 (176)
193 KOG4167|consensus 35.6 13 0.00027 31.0 0.1 26 65-90 791-816 (907)
194 smart00064 FYVE Protein presen 35.5 29 0.00062 19.0 1.5 11 127-137 26-36 (68)
195 PF11023 DUF2614: Protein of u 35.3 13 0.00029 23.0 0.1 28 20-47 66-94 (114)
196 PHA02998 RNA polymerase subuni 34.8 8.7 0.00019 25.9 -0.8 10 164-173 172-181 (195)
197 TIGR00244 transcriptional regu 34.7 8.5 0.00019 25.2 -0.8 14 100-113 29-42 (147)
198 PRK03564 formate dehydrogenase 34.3 24 0.00053 26.3 1.3 14 161-174 250-263 (309)
199 TIGR00686 phnA alkylphosphonat 34.2 27 0.00058 21.6 1.3 29 101-140 4-32 (109)
200 PF09963 DUF2197: Uncharacteri 33.5 13 0.00029 19.9 -0.1 15 65-79 30-44 (56)
201 PF12760 Zn_Tnp_IS1595: Transp 33.4 70 0.0015 16.1 3.0 10 162-171 36-45 (46)
202 PF03884 DUF329: Domain of unk 33.3 18 0.00039 19.5 0.4 12 24-35 3-14 (57)
203 cd00924 Cyt_c_Oxidase_Vb Cytoc 33.3 20 0.00043 21.7 0.6 13 162-174 78-90 (97)
204 PRK14559 putative protein seri 33.2 36 0.00078 28.4 2.2 23 25-48 3-25 (645)
205 PF07295 DUF1451: Protein of u 33.0 37 0.00079 22.3 1.9 11 126-136 111-121 (146)
206 PF14803 Nudix_N_2: Nudix N-te 32.9 16 0.00036 17.3 0.2 9 67-75 23-31 (34)
207 PF01286 XPA_N: XPA protein N- 32.7 22 0.00048 16.9 0.6 12 165-176 5-16 (34)
208 COG1655 Uncharacterized protei 32.3 11 0.00023 26.7 -0.7 9 128-136 63-71 (267)
209 PF15135 UPF0515: Uncharacteri 32.2 30 0.00064 24.9 1.4 60 65-142 111-170 (278)
210 PRK10220 hypothetical protein; 31.3 32 0.0007 21.2 1.3 12 99-110 20-31 (111)
211 PRK12380 hydrogenase nickel in 31.2 24 0.00053 21.9 0.8 12 23-34 70-81 (113)
212 PF01363 FYVE: FYVE zinc finge 31.2 34 0.00074 18.8 1.3 9 101-109 11-19 (69)
213 PRK05452 anaerobic nitric oxid 30.6 33 0.00072 27.4 1.6 17 20-36 422-438 (479)
214 PRK04351 hypothetical protein; 30.5 25 0.00054 23.1 0.8 34 127-176 112-145 (149)
215 smart00731 SprT SprT homologue 30.3 27 0.00058 22.7 0.9 33 127-174 112-144 (146)
216 COG4957 Predicted transcriptio 30.0 27 0.00058 22.5 0.8 14 53-66 88-101 (148)
217 PF04438 zf-HIT: HIT zinc fing 30.0 18 0.00039 16.6 0.1 11 162-172 12-22 (30)
218 COG0068 HypF Hydrogenase matur 29.7 6.5 0.00014 32.5 -2.3 56 101-171 125-181 (750)
219 COG1998 RPS31 Ribosomal protei 29.6 18 0.00039 18.8 0.0 8 128-135 38-45 (51)
220 TIGR00100 hypA hydrogenase nic 29.6 43 0.00093 20.9 1.7 12 23-34 70-81 (115)
221 PF10263 SprT-like: SprT-like 29.3 14 0.00031 24.1 -0.5 32 127-174 123-154 (157)
222 TIGR01562 FdhE formate dehydro 29.1 52 0.0011 24.6 2.3 13 161-173 250-262 (305)
223 COG3024 Uncharacterized protei 28.5 25 0.00054 19.4 0.5 14 21-34 5-18 (65)
224 PRK05978 hypothetical protein; 28.2 20 0.00043 23.6 0.0 10 129-138 54-63 (148)
225 PF14122 YokU: YokU-like prote 28.1 51 0.0011 19.4 1.7 29 9-37 21-49 (87)
226 PRK00420 hypothetical protein; 27.3 31 0.00068 21.5 0.8 11 24-34 24-34 (112)
227 PF08209 Sgf11: Sgf11 (transcr 26.8 83 0.0018 14.8 2.1 21 100-121 5-25 (33)
228 PF03119 DNA_ligase_ZBD: NAD-d 26.6 49 0.0011 14.8 1.2 13 25-37 1-13 (28)
229 PF14447 Prok-RING_4: Prokaryo 25.9 43 0.00094 17.9 1.0 12 165-176 41-52 (55)
230 COG4338 Uncharacterized protei 25.6 26 0.00056 18.1 0.2 17 101-117 14-30 (54)
231 PRK03681 hypA hydrogenase nick 25.5 54 0.0012 20.4 1.6 12 23-34 70-81 (114)
232 PF08271 TF_Zn_Ribbon: TFIIB z 24.9 38 0.00081 16.8 0.7 9 164-172 1-9 (43)
233 PF01155 HypA: Hydrogenase exp 24.8 35 0.00076 21.2 0.7 11 100-110 71-81 (113)
234 COG2331 Uncharacterized protei 24.7 46 0.00099 19.1 1.1 11 99-109 12-22 (82)
235 PF14634 zf-RING_5: zinc-RING 24.7 36 0.00077 16.8 0.6 8 26-33 2-9 (44)
236 PF14255 Cys_rich_CPXG: Cystei 24.7 44 0.00095 17.6 0.9 10 25-34 2-11 (52)
237 KOG0782|consensus 24.4 17 0.00037 29.4 -0.9 50 53-112 240-289 (1004)
238 PRK00432 30S ribosomal protein 24.3 39 0.00085 17.6 0.7 11 66-76 37-47 (50)
239 PF11931 DUF3449: Domain of un 24.1 26 0.00056 24.3 0.0 28 121-148 95-123 (196)
240 PF09845 DUF2072: Zn-ribbon co 23.9 38 0.00083 21.7 0.7 15 127-141 1-15 (131)
241 TIGR00627 tfb4 transcription f 23.9 67 0.0014 23.7 2.1 10 128-137 256-265 (279)
242 PLN02294 cytochrome c oxidase 23.9 39 0.00085 22.8 0.8 15 161-175 139-153 (174)
243 PLN02748 tRNA dimethylallyltra 23.8 58 0.0013 26.0 1.8 25 125-149 416-441 (468)
244 PRK02935 hypothetical protein; 23.7 38 0.00083 20.8 0.7 29 20-48 67-96 (110)
245 TIGR00416 sms DNA repair prote 23.6 46 0.001 26.4 1.3 26 66-110 7-32 (454)
246 PRK00418 DNA gyrase inhibitor; 23.4 41 0.00089 18.5 0.7 13 22-34 5-17 (62)
247 PF11238 DUF3039: Protein of u 23.3 23 0.0005 19.1 -0.3 11 23-33 44-54 (58)
248 KOG0978|consensus 23.1 28 0.00061 29.1 0.1 10 99-108 643-652 (698)
249 PF14311 DUF4379: Domain of un 23.0 63 0.0014 16.9 1.4 7 129-135 30-36 (55)
250 PF04780 DUF629: Protein of un 22.9 62 0.0013 25.8 1.8 26 66-91 57-82 (466)
251 PRK12722 transcriptional activ 22.7 66 0.0014 22.2 1.7 47 108-171 116-162 (187)
252 PRK11823 DNA repair protein Ra 22.7 49 0.0011 26.1 1.3 27 65-110 6-32 (446)
253 KOG0717|consensus 22.6 59 0.0013 25.8 1.6 21 100-120 293-313 (508)
254 PF11672 DUF3268: Protein of u 22.5 46 0.00099 20.4 0.9 8 67-74 3-10 (102)
255 PF04216 FdhE: Protein involve 22.5 9.6 0.00021 28.0 -2.5 13 160-172 235-247 (290)
256 PF06827 zf-FPG_IleRS: Zinc fi 22.3 23 0.0005 15.9 -0.4 10 25-34 3-12 (30)
257 TIGR03831 YgiT_finger YgiT-typ 22.2 75 0.0016 15.5 1.6 15 20-34 29-43 (46)
258 PF04606 Ogr_Delta: Ogr/Delta- 21.6 9.8 0.00021 19.4 -1.9 13 126-138 24-38 (47)
259 TIGR01384 TFS_arch transcripti 21.5 16 0.00034 22.2 -1.3 10 25-34 2-11 (104)
260 COG5112 UFD2 U1-like Zn-finger 21.3 48 0.001 20.3 0.8 24 126-149 54-77 (126)
261 TIGR03829 YokU_near_AblA uncha 21.3 67 0.0014 19.1 1.3 22 16-37 28-49 (89)
262 PRK01343 zinc-binding protein; 21.2 1E+02 0.0022 16.6 1.9 10 164-173 10-19 (57)
263 COG4888 Uncharacterized Zn rib 21.2 45 0.00098 20.3 0.6 12 160-171 19-30 (104)
264 KOG4727|consensus 21.1 58 0.0013 22.0 1.2 22 127-148 75-96 (193)
265 PLN03238 probable histone acet 21.1 91 0.002 23.1 2.2 26 124-149 45-70 (290)
266 PF11789 zf-Nse: Zinc-finger o 20.9 1.4E+02 0.003 16.0 2.4 13 127-139 24-36 (57)
267 CHL00174 accD acetyl-CoA carbo 20.7 50 0.0011 24.5 0.9 34 98-140 37-70 (296)
268 cd01121 Sms Sms (bacterial rad 20.5 62 0.0013 24.9 1.4 8 100-107 15-22 (372)
269 PF02748 PyrI_C: Aspartate car 20.3 21 0.00045 18.8 -0.8 15 160-174 32-46 (52)
270 PF03107 C1_2: C1 domain; Int 20.1 68 0.0015 14.4 1.0 8 165-172 2-9 (30)
271 PTZ00448 hypothetical protein; 20.1 80 0.0017 24.3 1.8 23 127-149 314-336 (373)
272 KOG0402|consensus 20.1 15 0.00033 21.4 -1.4 18 17-34 30-47 (92)
No 1
>KOG2462|consensus
Probab=99.96 E-value=1.1e-30 Score=178.76 Aligned_cols=130 Identities=35% Similarity=0.688 Sum_probs=117.7
Q ss_pred cCCcccccccceeeeecCCeeEeeeecccCCCchhhhHhhhcCC---CCCcccccchhhccChHHHHHHHHhccCCCcCC
Q psy3356 20 KNPLVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTHTG---ERPFECDVCGKRFAQKSTLNTHKRVHISYLHVK 96 (180)
Q Consensus 20 ~~~~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h~~---~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 96 (180)
..+.++|+.||+.+. +...|.+|.++|-. .+.+.|++|++.|.+-..|..|+++|
T Consensus 127 ~~~r~~c~eCgk~ys---------------T~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH------- 184 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYS---------------TSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTH------- 184 (279)
T ss_pred cCCceeccccccccc---------------cccccchhhcccccccccccccCCCCCceeeehHHHhhHhhcc-------
Confidence 445667777777777 99999999998854 56799999999999999999999987
Q ss_pred CcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCCCc
Q psy3356 97 DKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFTTK 176 (180)
Q Consensus 97 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~~~ 176 (180)
..+..|.+||+.|...+.|+.|+++|+|+|||.|+.|++.|.++++|+.|+++ |.+.|+|+|..|+++|+..
T Consensus 185 ~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQT--------HS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 185 TLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQT--------HSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred CCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHh--------hcCCccccCcchhhHHHHH
Confidence 47899999999999999999999999999999999999999999999999998 7889999999999999987
Q ss_pred cCC
Q psy3356 177 QNL 179 (180)
Q Consensus 177 ~~L 179 (180)
+-|
T Consensus 257 SyL 259 (279)
T KOG2462|consen 257 SYL 259 (279)
T ss_pred HHH
Confidence 655
No 2
>KOG2462|consensus
Probab=99.91 E-value=6.8e-25 Score=150.52 Aligned_cols=127 Identities=31% Similarity=0.633 Sum_probs=114.8
Q ss_pred CCCcccccCCceeeeeeccc----CCcccccccceeeeecCCeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhhc
Q psy3356 1 ACSSKWITSPSVTFDINIQK----NPLVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRF 76 (180)
Q Consensus 1 ~C~~~f~~~~~~~~~~~~~~----~~~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 76 (180)
.|+..+.|+.+|..|-..+. ...+.|++||+.+. ....|..|+++|. -+++|.+||+.|
T Consensus 135 eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Yv---------------SmpALkMHirTH~--l~c~C~iCGKaF 197 (279)
T KOG2462|consen 135 ECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYV---------------SMPALKMHIRTHT--LPCECGICGKAF 197 (279)
T ss_pred ccccccccccccchhhcccccccccccccCCCCCceee---------------ehHHHhhHhhccC--CCcccccccccc
Confidence 38899999999999977553 44457777776666 9999999999996 578999999999
Q ss_pred cChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHH
Q psy3356 77 AQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 77 ~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
...=.|+.|+++| +|++||.|+.|++.|.+.++|+.|+++|.+.+.|.|..|++.|...+.|.+|...
T Consensus 198 SRPWLLQGHiRTH-----TGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 198 SRPWLLQGHIRTH-----TGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cchHHhhcccccc-----cCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 9999999999999 9999999999999999999999999999999999999999999999999999875
No 3
>KOG3608|consensus
Probab=99.84 E-value=3.4e-22 Score=141.31 Aligned_cols=167 Identities=22% Similarity=0.410 Sum_probs=139.8
Q ss_pred CCCcccccCCceeeeeecccCC-cccccccceeeeecC---------------CeeEeeeecccCCCchhhhHhhhcCCC
Q psy3356 1 ACSSKWITSPSVTFDINIQKNP-LVFIPACVFRFSVEN---------------EKRFFFFSFLFGPLLVPQIHMRTHTGE 64 (180)
Q Consensus 1 ~C~~~f~~~~~~~~~~~~~~~~-~~~c~~C~~~~~~~~---------------~~~~~~C~~~~~~~~~l~~H~~~h~~~ 64 (180)
+|-..+.+...|..|++.+.+. .+-||.||..|.... ...|..|.|.|++...|..|+..|.
T Consensus 184 ~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv-- 261 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV-- 261 (467)
T ss_pred hhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--
Confidence 4778889999999999988664 458999999998654 4455569999999999999998885
Q ss_pred CCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccc--cccccCChHH
Q psy3356 65 RPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEI--CGKRFSQKSA 142 (180)
Q Consensus 65 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~ 142 (180)
..|+|+.|+.+.....+|..|++.-| ...++++|..|...+.+.++|.+|...|. +..|.|.. |..+|.+..+
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rH----s~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q 336 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRH----SKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQ 336 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhh----ccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHH
Confidence 56899999999999999999988765 56899999999999999999999999887 66799977 9999999999
Q ss_pred HHHHHHHcCCCCCCcCCCCCCcccCCCcccCCCccCC
Q psy3356 143 CNTHKRTHIPYLPRVHPKDRPFHCPACEGMFTTKQNL 179 (180)
Q Consensus 143 l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~~~~~L 179 (180)
+.+|++.++. ..++.+|.|..|++.|++..+|
T Consensus 337 ~~~H~~evhE-----g~np~~Y~CH~Cdr~ft~G~~L 368 (467)
T KOG3608|consen 337 MRRHFLEVHE-----GNNPILYACHCCDRFFTSGKSL 368 (467)
T ss_pred HHHHHHHhcc-----CCCCCceeeecchhhhccchhH
Confidence 9999987531 2345679999999999987665
No 4
>KOG1074|consensus
Probab=99.76 E-value=1e-19 Score=140.92 Aligned_cols=76 Identities=38% Similarity=0.805 Sum_probs=63.8
Q ss_pred eeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccC---CCcccCCCc
Q psy3356 100 YHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCP---ACEGMFTTK 176 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~---~C~~~F~~~ 176 (180)
-+|.+|.++..-...|+.|.++|+|++||+|.+|++.|.++.+|..|+.+|-. .+.-.-.++|+ +|.+.|+..
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka----~p~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKA----KPPARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhccccccc----CccccccccCCchhhhccccccc
Confidence 48999999999999999999999999999999999999999999999987631 12223458999 999999876
Q ss_pred cCC
Q psy3356 177 QNL 179 (180)
Q Consensus 177 ~~L 179 (180)
-.|
T Consensus 682 V~l 684 (958)
T KOG1074|consen 682 VTL 684 (958)
T ss_pred ccc
Confidence 554
No 5
>KOG3608|consensus
Probab=99.76 E-value=9.1e-20 Score=129.16 Aligned_cols=164 Identities=24% Similarity=0.491 Sum_probs=125.9
Q ss_pred CCCcccccCCceeeeeecccCCcccccccceeeeecCCeeEe-----eeecccCCCchhhhHhhhcCCCCCcccccchhh
Q psy3356 1 ACSSKWITSPSVTFDINIQKNPLVFIPACVFRFSVENEKRFF-----FFSFLFGPLLVPQIHMRTHTGERPFECDVCGKR 75 (180)
Q Consensus 1 ~C~~~f~~~~~~~~~~~~~~~~~~~c~~C~~~~~~~~~~~~~-----~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 75 (180)
.|+..|++...+..|+..+.- .|.+ +..+....+.+-. .|.+.+..+..|+.|++.|++++...|+.|+..
T Consensus 141 dCe~~F~s~~ef~dHV~~H~l---~cey-d~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~ 216 (467)
T KOG3608|consen 141 DCEREFVSIVEFQDHVVKHAL---FCEY-DIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGEL 216 (467)
T ss_pred hcCCcccCHHHHHHHHHHhhh---hhhh-hhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHH
Confidence 488888888877777653211 1111 1111111111111 367788899999999999999999999999999
Q ss_pred ccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHHcCCCCC
Q psy3356 76 FAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRTHIPYLP 155 (180)
Q Consensus 76 f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 155 (180)
|++++.|..|.+..-. ....+|.|..|-+.|.++..|..|+..|. ..|+|+.|......+++|..|++.
T Consensus 217 F~~~tkl~DH~rRqt~---l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~------ 285 (467)
T KOG3608|consen 217 FRTKTKLFDHLRRQTE---LNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRY------ 285 (467)
T ss_pred hccccHHHHHHHhhhh---hcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHh------
Confidence 9999999999876521 45668999999999999999999998874 458999999999999999999987
Q ss_pred CcCCCCCCcccCCCcccCCCccCCC
Q psy3356 156 RVHPKDRPFHCPACEGMFTTKQNLE 180 (180)
Q Consensus 156 ~~h~~~~~~~C~~C~~~F~~~~~L~ 180 (180)
-|...+||+|..|+..|.++++|.
T Consensus 286 -rHs~dkpfKCd~Cd~~c~~esdL~ 309 (467)
T KOG3608|consen 286 -RHSKDKPFKCDECDTRCVRESDLA 309 (467)
T ss_pred -hhccCCCccccchhhhhccHHHHH
Confidence 477899999999999998888773
No 6
>KOG1074|consensus
Probab=99.72 E-value=1.4e-18 Score=134.74 Aligned_cols=87 Identities=31% Similarity=0.601 Sum_probs=69.7
Q ss_pred cCCeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHHHHhccCCCcCCCcceecc---ccCcccCCh
Q psy3356 36 ENEKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCT---ECEATFSWK 112 (180)
Q Consensus 36 ~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~---~C~~~~~~~ 112 (180)
...+.|-+|.++..-+..|+.|++.|.+++||+|.+|++.|.++.+|+.|+..|.... .....+.|+ +|-+.|...
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p-~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKP-PARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred CCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCc-cccccccCCchhhhccccccc
Confidence 3477788899998899999999999999999999999999999999999999885422 223456666 677777776
Q ss_pred hhHHHHHhhcC
Q psy3356 113 QNLEVHMRTHT 123 (180)
Q Consensus 113 ~~l~~H~~~h~ 123 (180)
-.+..|++.|.
T Consensus 682 V~lpQhIriH~ 692 (958)
T KOG1074|consen 682 VTLPQHIRIHL 692 (958)
T ss_pred ccccceEEeec
Confidence 66666666654
No 7
>KOG3576|consensus
Probab=99.69 E-value=7e-18 Score=111.22 Aligned_cols=113 Identities=27% Similarity=0.561 Sum_probs=90.7
Q ss_pred cCCeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhH
Q psy3356 36 ENEKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNL 115 (180)
Q Consensus 36 ~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l 115 (180)
.....|.+|+|.|+....|.+|++-|...+.+.|..|+++|...-+|++|+++| +|..||+|..|++.|+..-.|
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rth-----tgvrpykc~~c~kaftqrcsl 189 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTH-----TGVRPYKCSLCEKAFTQRCSL 189 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccc-----cCccccchhhhhHHHHhhccH
Confidence 345667777888878888888888888888888888888888888888888888 888888888888888888888
Q ss_pred HHHHhhcCC-----------CCceeccccccccCChHHHHHHHHHcCCC
Q psy3356 116 EVHMRTHTG-----------ERPYECEICGKRFSQKSACNTHKRTHIPY 153 (180)
Q Consensus 116 ~~H~~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 153 (180)
..|++.-++ .+.|.|..||..-.....+..|++.|+|+
T Consensus 190 eshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 190 ESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred HHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 888865443 35588888888888888888888887654
No 8
>KOG3576|consensus
Probab=99.65 E-value=3.6e-17 Score=107.86 Aligned_cols=106 Identities=32% Similarity=0.627 Sum_probs=90.9
Q ss_pred CCCCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHH
Q psy3356 63 GERPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSA 142 (180)
Q Consensus 63 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 142 (180)
+...|.|.+|++.|.....|.+|++-| ...+.+.|..||+.|.+..+|.+|.++|+|.+||+|..|++.|..+-+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch-----~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcs 188 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCH-----SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCS 188 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhc-----cHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhcc
Confidence 345699999999999999999999998 788889999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCCCC---CCcCCCCCCcccCCCcccC
Q psy3356 143 CNTHKRTHIPYL---PRVHPKDRPFHCPACEGMF 173 (180)
Q Consensus 143 l~~H~~~h~~~~---~~~h~~~~~~~C~~C~~~F 173 (180)
|..|++.-|+-. .-....++.|.|..||.+-
T Consensus 189 leshl~kvhgv~~~yaykerr~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 189 LESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTS 222 (267)
T ss_pred HHHHHHHHcCchHHHHHHHhhhheeeecccCCCC
Confidence 999988644211 0011246789999999763
No 9
>KOG3623|consensus
Probab=99.57 E-value=1.8e-15 Score=116.42 Aligned_cols=100 Identities=29% Similarity=0.716 Sum_probs=85.6
Q ss_pred cccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCC-------------CCceecccc
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTG-------------ERPYECEIC 133 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~-------------~~~~~C~~C 133 (180)
.+|++|.+.+...+.|+.|++.-|. ..+..+.|..|..+|.+...|.+|+..|.. .+-|+|.+|
T Consensus 211 ltcpycdrgykrltslkeHikyrhe---kne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtEC 287 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHE---KNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTEC 287 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHh---hCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccccccc
Confidence 6899999999999999999876543 345568899999999999999999988743 234999999
Q ss_pred ccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCCCcc
Q psy3356 134 GKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFTTKQ 177 (180)
Q Consensus 134 ~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~~~~ 177 (180)
++.|..+-.|..|+|+ |.|||||.|+-|+++|+-..
T Consensus 288 gKAFKfKHHLKEHlRI--------HSGEKPfeCpnCkKRFSHSG 323 (1007)
T KOG3623|consen 288 GKAFKFKHHLKEHLRI--------HSGEKPFECPNCKKRFSHSG 323 (1007)
T ss_pred chhhhhHHHHHhhhee--------ecCCCCcCCcccccccccCC
Confidence 9999999999999995 88999999999999998654
No 10
>KOG3623|consensus
Probab=99.56 E-value=4.9e-16 Score=119.43 Aligned_cols=116 Identities=30% Similarity=0.634 Sum_probs=97.1
Q ss_pred cCCcccccccceeeeecCCeeEeeeecccCCCchhhhHhhhcC--CCCCcccccchhhccChHHHHHHHHhccCC-----
Q psy3356 20 KNPLVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTHT--GERPFECDVCGKRFAQKSTLNTHKRVHISY----- 92 (180)
Q Consensus 20 ~~~~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h~--~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~----- 92 (180)
..+..+|++|+..+. ...+|+.|++.-+ .+..|.|..|..+|...+.|.+|+..|.+-
T Consensus 207 fsqlltcpycdrgyk---------------rltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~ 271 (1007)
T KOG3623|consen 207 FSQLLTCPYCDRGYK---------------RLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAI 271 (1007)
T ss_pred hhhhhcchhHHHHHH---------------HHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccc
Confidence 344557777776666 8899999987543 455699999999999999999999988542
Q ss_pred ---CcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHHc
Q psy3356 93 ---LHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 93 ---~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
.....+.++|..|++.|..+..|..|++.|.|++||.|+.|++.|....++..||...
T Consensus 272 sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSK 332 (1007)
T KOG3623|consen 272 SLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSK 332 (1007)
T ss_pred cccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccccc
Confidence 1123456999999999999999999999999999999999999999999999998753
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.32 E-value=3.5e-12 Score=98.06 Aligned_cols=126 Identities=18% Similarity=0.394 Sum_probs=89.3
Q ss_pred CcccccccceeeeecC-----------CeeEee--eecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHHHHh
Q psy3356 22 PLVFIPACVFRFSVEN-----------EKRFFF--FSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRV 88 (180)
Q Consensus 22 ~~~~c~~C~~~~~~~~-----------~~~~~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 88 (180)
....|+.|.+..+..+ ...|.. |+..|. ...+..| +.|+.|++.|. ...|..|+..
T Consensus 406 ~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~-r~el~~H---------~~C~~Cgk~f~-~s~LekH~~~ 474 (567)
T PLN03086 406 DTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLR-VEEAKNH---------VHCEKCGQAFQ-QGEMEKHMKV 474 (567)
T ss_pred CeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceee-ccccccC---------ccCCCCCCccc-hHHHHHHHHh
Confidence 3447888888777544 222332 666662 2333333 57999988885 5678889887
Q ss_pred ccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccC----------ChHHHHHHHHHcCCCCCCcC
Q psy3356 89 HISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFS----------QKSACNTHKRTHIPYLPRVH 158 (180)
Q Consensus 89 ~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~l~~H~~~h~~~~~~~h 158 (180)
+| .++.|+ |+..+ ....|..|+..|...+++.|+.|+..|. ....|..|...
T Consensus 475 ~H-------kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~--------- 536 (567)
T PLN03086 475 FH-------EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI--------- 536 (567)
T ss_pred cC-------CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh---------
Confidence 62 678888 98654 5688888988888889999999998884 23478888775
Q ss_pred CCCCCcccCCCcccCCCc
Q psy3356 159 PKDRPFHCPACEGMFTTK 176 (180)
Q Consensus 159 ~~~~~~~C~~C~~~F~~~ 176 (180)
.|.+++.|..|++.|..+
T Consensus 537 CG~rt~~C~~Cgk~Vrlr 554 (567)
T PLN03086 537 CGSRTAPCDSCGRSVMLK 554 (567)
T ss_pred cCCcceEccccCCeeeeh
Confidence 378889999999887654
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.29 E-value=7.6e-12 Score=96.24 Aligned_cols=129 Identities=20% Similarity=0.346 Sum_probs=103.3
Q ss_pred CCceeeeeecccCCcccccc--cceeeeecC---CeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHH
Q psy3356 9 SPSVTFDINIQKNPLVFIPA--CVFRFSVEN---EKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLN 83 (180)
Q Consensus 9 ~~~~~~~~~~~~~~~~~c~~--C~~~~~~~~---~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 83 (180)
...+..|..........|+. |+..|.... -+.|..|++.|. ...|..|+.+++ +++.|+ |+..+ ....|.
T Consensus 419 l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~ 493 (567)
T PLN03086 419 SRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMV 493 (567)
T ss_pred hhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHH
Confidence 44566677666666678984 999997443 556778999995 688999999975 789999 99755 668999
Q ss_pred HHHHhccCCCcCCCcceeccccCcccC----------ChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHH
Q psy3356 84 THKRVHISYLHVKDKPYHCTECEATFS----------WKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 84 ~H~~~~~~~~~~~~~~~~C~~C~~~~~----------~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
.|+..+ .+.+++.|+.|+..+. ....|..|.... +.+++.|..|++.+..+ .|..|+-.
T Consensus 494 ~H~~th-----Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 494 QHQAST-----CPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred hhhhcc-----CCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHH
Confidence 999888 7889999999999884 235788998885 88999999999998665 47888765
No 13
>PHA00733 hypothetical protein
Probab=99.16 E-value=6.3e-11 Score=75.14 Aligned_cols=85 Identities=21% Similarity=0.336 Sum_probs=69.4
Q ss_pred CCCCcccccchhhccChHHHHHH--HHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCCh
Q psy3356 63 GERPFECDVCGKRFAQKSTLNTH--KRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQK 140 (180)
Q Consensus 63 ~~~~~~C~~C~~~f~~~~~l~~H--~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 140 (180)
.++++.|.+|+..+.....|..+ +..+. ...+..++.|+.|++.|.....|..|+..+ ..+|.|..|++.|...
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~--~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLL--TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhc--ccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 45779999999999988777776 22221 124578899999999999999999999876 3569999999999999
Q ss_pred HHHHHHHHHcC
Q psy3356 141 SACNTHKRTHI 151 (180)
Q Consensus 141 ~~l~~H~~~h~ 151 (180)
..|..|+...|
T Consensus 113 ~sL~~H~~~~h 123 (128)
T PHA00733 113 DSTLDHVCKKH 123 (128)
T ss_pred HHHHHHHHHhc
Confidence 99999998754
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.12 E-value=5.6e-11 Score=62.72 Aligned_cols=43 Identities=26% Similarity=0.566 Sum_probs=36.3
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCCCccCC
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFTTKQNL 179 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~~~~~L 179 (180)
.|.|+.||+.|.....|..|+++| + ++|+|..|++.|++.++|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H--------~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH--------N--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc--------C--CcccCCcccceeccccee
Confidence 378999999999999999999974 3 688899999999888776
No 15
>PHA00733 hypothetical protein
Probab=98.99 E-value=2.2e-10 Score=72.66 Aligned_cols=75 Identities=21% Similarity=0.350 Sum_probs=60.8
Q ss_pred CCCcceeccccCcccCChhhHHHH--H---hhcCCCCceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCC
Q psy3356 95 VKDKPYHCTECEATFSWKQNLEVH--M---RTHTGERPYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPAC 169 (180)
Q Consensus 95 ~~~~~~~C~~C~~~~~~~~~l~~H--~---~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C 169 (180)
+..+.+.|.+|...+.....|..+ + ..+.+.+||.|+.|++.|.+...|..|++. + +.+|.|+.|
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~--------h--~~~~~C~~C 105 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRY--------T--EHSKVCPVC 105 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhc--------C--CcCccCCCC
Confidence 456788999999888887776665 2 133457899999999999999999999986 2 356999999
Q ss_pred cccCCCccCC
Q psy3356 170 EGMFTTKQNL 179 (180)
Q Consensus 170 ~~~F~~~~~L 179 (180)
++.|...+.|
T Consensus 106 gK~F~~~~sL 115 (128)
T PHA00733 106 GKEFRNTDST 115 (128)
T ss_pred CCccCCHHHH
Confidence 9999987765
No 16
>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=98.81 E-value=1.8e-09 Score=48.87 Aligned_cols=24 Identities=38% Similarity=0.940 Sum_probs=16.2
Q ss_pred HHHHHHHcCCCCCCcCCCCCCcccCCCcccCC
Q psy3356 143 CNTHKRTHIPYLPRVHPKDRPFHCPACEGMFT 174 (180)
Q Consensus 143 l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~ 174 (180)
|..|+++ |++++||.|+.|+++|.
T Consensus 2 l~~H~~~--------H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRT--------HTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHH--------HSSSSSEEESSSSEEES
T ss_pred HHHHhhh--------cCCCCCCCCCCCcCeeC
Confidence 5667665 56677777777777665
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.77 E-value=3.3e-09 Score=56.04 Aligned_cols=43 Identities=16% Similarity=0.420 Sum_probs=29.9
Q ss_pred ceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHH
Q psy3356 99 PYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSAC 143 (180)
Q Consensus 99 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 143 (180)
.|.|+.||+.|.....|..|++.|+ ++++|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 4567777777777777777777776 567777777777655443
No 18
>KOG3993|consensus
Probab=98.66 E-value=4.9e-09 Score=76.91 Aligned_cols=56 Identities=16% Similarity=0.233 Sum_probs=44.6
Q ss_pred cCCeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHHHHhccC
Q psy3356 36 ENEKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRVHIS 91 (180)
Q Consensus 36 ~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 91 (180)
.+++.|..|...|.+...|.+|.-.......|+|++|++.|.-..+|..|++.|.+
T Consensus 265 iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 265 IGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 34556666777777999999996544444569999999999999999999999864
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.65 E-value=2.2e-08 Score=45.26 Aligned_cols=25 Identities=72% Similarity=1.362 Sum_probs=19.5
Q ss_pred hHHHHHhhcCCCCceeccccccccC
Q psy3356 114 NLEVHMRTHTGERPYECEICGKRFS 138 (180)
Q Consensus 114 ~l~~H~~~h~~~~~~~C~~C~~~f~ 138 (180)
+|..|++.|.+++||.|+.|++.|.
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 4677888888888888888888775
No 20
>KOG3993|consensus
Probab=98.49 E-value=5e-08 Score=71.78 Aligned_cols=80 Identities=29% Similarity=0.672 Sum_probs=69.0
Q ss_pred cccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCC----------------------
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTG---------------------- 124 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~---------------------- 124 (180)
|.|..|...|...-.|.+|.-.- .....|+|+.|+++|.-..+|..|.+.|--
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R-----IV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~ 342 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR-----IVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEV 342 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe-----eEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhh
Confidence 89999999999999999997543 345679999999999999999999998731
Q ss_pred -----------CCceeccccccccCChHHHHHHHHHcC
Q psy3356 125 -----------ERPYECEICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 125 -----------~~~~~C~~C~~~f~~~~~l~~H~~~h~ 151 (180)
+..|.|..|++.|....-|..|+-+|+
T Consensus 343 ~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 343 QEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 123999999999999999999988876
No 21
>PHA00616 hypothetical protein
Probab=98.40 E-value=1.3e-07 Score=47.58 Aligned_cols=34 Identities=24% Similarity=0.375 Sum_probs=21.6
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCC
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPA 168 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~ 168 (180)
||+|+.||+.|....+|..|++. |.|++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~--------~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS--------VHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH--------hcCCCccceeE
Confidence 46666677777777777777665 44556666554
No 22
>PHA00732 hypothetical protein
Probab=98.29 E-value=6.8e-07 Score=51.69 Aligned_cols=45 Identities=29% Similarity=0.507 Sum_probs=31.7
Q ss_pred ceeccccCcccCChhhHHHHHhh-cCCCCceeccccccccCChHHHHHHHHH
Q psy3356 99 PYHCTECEATFSWKQNLEVHMRT-HTGERPYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 99 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
++.|..|++.|.....|..|++. |. ++.|+.|++.|. .+..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 35688888888888888888774 43 257888888876 36666654
No 23
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.26 E-value=1.8e-06 Score=46.35 Aligned_cols=50 Identities=28% Similarity=0.499 Sum_probs=26.1
Q ss_pred cccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhc
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTH 122 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h 122 (180)
|.||.|++ ..+...|..|....|. ...+.+.|++|...+. .+|..|+..+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~---~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHR---SESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCc---CCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 56666666 3445566666555443 1233456666655322 2555555443
No 24
>PHA00616 hypothetical protein
Probab=98.23 E-value=5.3e-07 Score=45.41 Aligned_cols=32 Identities=22% Similarity=0.463 Sum_probs=15.7
Q ss_pred eeccccCcccCChhhHHHHHhhcCCCCceecc
Q psy3356 100 YHCTECEATFSWKQNLEVHMRTHTGERPYECE 131 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~ 131 (180)
|+|+.||+.|....++..|+..|++.+++.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 44455555555555555555555544444443
No 25
>PHA00732 hypothetical protein
Probab=98.13 E-value=1.9e-06 Score=49.83 Aligned_cols=48 Identities=23% Similarity=0.520 Sum_probs=37.7
Q ss_pred CcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcC
Q psy3356 66 PFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHT 123 (180)
Q Consensus 66 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~ 123 (180)
||.|.+|++.|.+...|..|++.+| . ++.|+.|++.|. .+..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H----~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH----T---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc----C---CCccCCCCCEeC---ChhhhhcccC
Confidence 5789999999999999999988532 2 247999999987 5777876543
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.03 E-value=4.2e-06 Score=36.52 Aligned_cols=22 Identities=55% Similarity=1.026 Sum_probs=15.9
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy3356 128 YECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
|.|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5677777777777777777764
No 27
>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=1.3e-05 Score=42.98 Aligned_cols=49 Identities=18% Similarity=0.376 Sum_probs=36.8
Q ss_pred ceeccccCcccCChhhHHHHHhhcCC--CCceeccccccccCChHHHHHHHHHc
Q psy3356 99 PYHCTECEATFSWKQNLEVHMRTHTG--ERPYECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 99 ~~~C~~C~~~~~~~~~l~~H~~~h~~--~~~~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
.|.||.|++ ..+...|..|....+. .+.+.|++|...+. .+|..|+..+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 478999999 5667888999865443 35688999998654 4888898874
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=97.83 E-value=1.2e-05 Score=35.06 Aligned_cols=22 Identities=45% Similarity=1.020 Sum_probs=11.6
Q ss_pred cccccchhhccChHHHHHHHHh
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRV 88 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~ 88 (180)
|+|++|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3455555555555555555543
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=97.82 E-value=1.9e-05 Score=34.56 Aligned_cols=23 Identities=52% Similarity=1.041 Sum_probs=15.1
Q ss_pred eeccccccccCChHHHHHHHHHc
Q psy3356 128 YECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
|.|+.|++.|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 56777777777777777777654
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.76 E-value=2.6e-05 Score=47.35 Aligned_cols=73 Identities=21% Similarity=0.430 Sum_probs=19.5
Q ss_pred ccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHH
Q psy3356 68 ECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHK 147 (180)
Q Consensus 68 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 147 (180)
+|..|+..|.+...|..|+...|... .+ ....+.....+..++.... ...+.|..|+..|.+...|..|+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~----~~-----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD----IP-----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHM 70 (100)
T ss_dssp ----------------------------------------------------------SSEEBSSSS-EESSHHHHHHHH
T ss_pred Cccccccccccccccccccccccccc----cc-----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHH
Confidence 37778888887777888876554321 11 0011112223333333221 22588888888888888888888
Q ss_pred HHc
Q psy3356 148 RTH 150 (180)
Q Consensus 148 ~~h 150 (180)
+.+
T Consensus 71 ~~~ 73 (100)
T PF12756_consen 71 RSK 73 (100)
T ss_dssp HHT
T ss_pred cCc
Confidence 864
No 31
>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=97.73 E-value=2.3e-05 Score=35.59 Aligned_cols=24 Identities=58% Similarity=1.122 Sum_probs=18.2
Q ss_pred ceeccccccccCChHHHHHHHHHc
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
||.|..|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 467888888888888888887654
No 32
>KOG2231|consensus
Probab=97.67 E-value=7.2e-05 Score=59.33 Aligned_cols=120 Identities=20% Similarity=0.275 Sum_probs=84.0
Q ss_pred cccccceee-eecCCeeEeeeecccCCCchhhhHhhhcCCCCCcccccch---------hhccChHHHHHHHHhccCCCc
Q psy3356 25 FIPACVFRF-SVENEKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCG---------KRFAQKSTLNTHKRVHISYLH 94 (180)
Q Consensus 25 ~c~~C~~~~-~~~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~---------~~f~~~~~l~~H~~~~~~~~~ 94 (180)
+|.+|+..+ ...+..+|.+| ..|.....|+.|+...++ .+.|..|- ...-+...|..|++.-.+--.
T Consensus 101 ~C~~C~~~~~~~~~~~~~~~c-~~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~ 177 (669)
T KOG2231|consen 101 SCHICDRRFRALYNKKECLHC-TEFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDE 177 (669)
T ss_pred hcCccccchhhhcccCCCccc-cchhHHHHHHHHHHHhhh--hhccccccccceeeeeeeehehHHHHHHHHhcCCCccc
Confidence 899999998 45668889999 888899999999954332 23344332 222344678888775432000
Q ss_pred CCCcceeccccCcccCChhhHHHHHhhcCCCCceecccc------ccccCChHHHHHHHHHcC
Q psy3356 95 VKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEIC------GKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 95 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~h~ 151 (180)
.-.....|..|...|.+...|.+|+..++ |.|..| +..|.....|..|.+.+|
T Consensus 178 s~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 178 SCRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 11224679999999999999999998665 455555 456788899999988765
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=97.61 E-value=4.7e-05 Score=33.25 Aligned_cols=23 Identities=52% Similarity=1.089 Sum_probs=11.6
Q ss_pred cccccchhhccChHHHHHHHHhc
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVH 89 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~ 89 (180)
|.|++|+..|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34555555555555555555543
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.47 E-value=6.1e-05 Score=54.04 Aligned_cols=56 Identities=23% Similarity=0.665 Sum_probs=41.0
Q ss_pred CCceeccc--cccccCChHHHHHHHHHcC--------CCC---CCcCCCCCCcccCCCcccCCCccCCC
Q psy3356 125 ERPYECEI--CGKRFSQKSACNTHKRTHI--------PYL---PRVHPKDRPFHCPACEGMFTTKQNLE 180 (180)
Q Consensus 125 ~~~~~C~~--C~~~f~~~~~l~~H~~~h~--------~~~---~~~h~~~~~~~C~~C~~~F~~~~~L~ 180 (180)
++||+|++ |.+.+.....|..|+..-| |.. ...-...|||.|++|+++|..-..|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLK 415 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLK 415 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccce
Confidence 48899976 9999999999999976332 110 01122459999999999998877764
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.41 E-value=5.9e-05 Score=54.12 Aligned_cols=72 Identities=24% Similarity=0.611 Sum_probs=46.3
Q ss_pred CCCCccccc--chhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCCh
Q psy3356 63 GERPFECDV--CGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQK 140 (180)
Q Consensus 63 ~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 140 (180)
+++||+|++ |.+.+.....|+-|+..-|...-..+.| -+ ..+...-...+||.|++|++.++..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p--~p------------~~~~~F~~~~KPYrCevC~KRYKNl 411 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP--SP------------EKMNIFSAKDKPYRCEVCDKRYKNL 411 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCC--Cc------------cccccccccCCceeccccchhhccC
Confidence 358999998 9999999999999987543211011111 00 0111112346788888888888888
Q ss_pred HHHHHHHH
Q psy3356 141 SACNTHKR 148 (180)
Q Consensus 141 ~~l~~H~~ 148 (180)
..|..|+.
T Consensus 412 NGLKYHr~ 419 (423)
T COG5189 412 NGLKYHRK 419 (423)
T ss_pred ccceeccc
Confidence 88877764
No 36
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.37 E-value=0.00019 Score=32.46 Aligned_cols=23 Identities=43% Similarity=0.817 Sum_probs=11.4
Q ss_pred eeccccCcccCChhhHHHHHhhc
Q psy3356 100 YHCTECEATFSWKQNLEVHMRTH 122 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~~h 122 (180)
+.|..|++.|.+...|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 44555555555555555554443
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.34 E-value=0.00019 Score=43.45 Aligned_cols=72 Identities=22% Similarity=0.318 Sum_probs=21.5
Q ss_pred EeeeecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHh
Q psy3356 41 FFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMR 120 (180)
Q Consensus 41 ~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 120 (180)
|.+|+..|.....|..||...++... +. ...+.....+..++.. .....+.|..|+..|.+...|..|+.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~---~~-~~~l~~~~~~~~~~~~------~~~~~~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDI---PD-QKYLVDPNRLLNYLRK------KVKESFRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp ---------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHH
T ss_pred cccccccccccccccccccccccccc---cc-cccccccccccccccc------ccCCCCCCCccCCCCcCHHHHHHHHc
Confidence 55666666699999999866543221 11 1111223333333332 12336899999999999999999998
Q ss_pred hc
Q psy3356 121 TH 122 (180)
Q Consensus 121 ~h 122 (180)
.+
T Consensus 72 ~~ 73 (100)
T PF12756_consen 72 SK 73 (100)
T ss_dssp HT
T ss_pred Cc
Confidence 65
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.14 E-value=0.00039 Score=30.71 Aligned_cols=23 Identities=57% Similarity=0.983 Sum_probs=19.6
Q ss_pred eeccccccccCChHHHHHHHHHc
Q psy3356 128 YECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 57888999999999999998864
No 39
>PRK04860 hypothetical protein; Provisional
Probab=97.07 E-value=0.00044 Score=45.66 Aligned_cols=42 Identities=21% Similarity=0.575 Sum_probs=34.4
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCCCccCC
Q psy3356 126 RPYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFTTKQNL 179 (180)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~~~~~L 179 (180)
-+|.|. |+. ....+.+|.++ |+++++|.|..|+..|....++
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri--------~~g~~~YrC~~C~~~l~~~~~~ 159 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRV--------VRGEAVYRCRRCGETLVFKGEQ 159 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHH--------hcCCccEECCCCCceeEEeccc
Confidence 369998 987 66678899886 7899999999999998876554
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.94 E-value=0.00049 Score=30.39 Aligned_cols=22 Identities=36% Similarity=0.863 Sum_probs=16.8
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy3356 128 YECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
|.|..|+..|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5677888888888888888764
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.86 E-value=0.00076 Score=29.49 Aligned_cols=22 Identities=36% Similarity=0.667 Sum_probs=13.1
Q ss_pred eeccccccccCChHHHHHHHHHc
Q psy3356 128 YECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
|.|+.|..... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 56677776666 66677776654
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=96.81 E-value=0.0017 Score=33.58 Aligned_cols=20 Identities=30% Similarity=0.645 Sum_probs=6.6
Q ss_pred cccccchhhccChHHHHHHH
Q psy3356 67 FECDVCGKRFAQKSTLNTHK 86 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~ 86 (180)
-+|++|+..+.+..+|..|+
T Consensus 25 atCP~C~a~~~~srnLrRHl 44 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHL 44 (54)
T ss_dssp EE-TTT--EESSHHHHHHHH
T ss_pred CCCCcchhhccchhhHHHHH
Confidence 33333333333333333333
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.73 E-value=0.0015 Score=28.71 Aligned_cols=23 Identities=48% Similarity=0.963 Sum_probs=14.7
Q ss_pred cccccchhhccChHHHHHHHHhc
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVH 89 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~ 89 (180)
|.|+.|++.|.....|..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666643
No 44
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.45 E-value=0.0038 Score=32.35 Aligned_cols=33 Identities=24% Similarity=0.516 Sum_probs=24.2
Q ss_pred CCCcceeccccCcccCChhhHHHHHhhcCCCCc
Q psy3356 95 VKDKPYHCTECEATFSWKQNLEVHMRTHTGERP 127 (180)
Q Consensus 95 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~ 127 (180)
..+.|-.|+.|+..+....+|.+|+...++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 567889999999999999999999988887765
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.40 E-value=0.0026 Score=27.71 Aligned_cols=22 Identities=32% Similarity=0.677 Sum_probs=10.9
Q ss_pred cccccchhhccChHHHHHHHHhc
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVH 89 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~ 89 (180)
|+|+.|+.... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 34555555555 55555555543
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.25 E-value=0.0041 Score=27.32 Aligned_cols=20 Identities=35% Similarity=0.753 Sum_probs=10.1
Q ss_pred eccccCcccCChhhHHHHHh
Q psy3356 101 HCTECEATFSWKQNLEVHMR 120 (180)
Q Consensus 101 ~C~~C~~~~~~~~~l~~H~~ 120 (180)
.|..|+..|.+...+..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555543
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.18 E-value=0.001 Score=30.00 Aligned_cols=21 Identities=29% Similarity=0.741 Sum_probs=16.7
Q ss_pred eeccccccccCChHHHHHHHH
Q psy3356 128 YECEICGKRFSQKSACNTHKR 148 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~ 148 (180)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 578888888888888887765
No 48
>KOG2231|consensus
Probab=96.13 E-value=0.0054 Score=49.13 Aligned_cols=125 Identities=20% Similarity=0.361 Sum_probs=83.3
Q ss_pred cccccCCceeeeeecccCCcccccccceeeeecCCeeEeeeecccCCCchhhhHhhhc-CCCC----CcccccchhhccC
Q psy3356 4 SKWITSPSVTFDINIQKNPLVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTH-TGER----PFECDVCGKRFAQ 78 (180)
Q Consensus 4 ~~f~~~~~~~~~~~~~~~~~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h-~~~~----~~~C~~C~~~f~~ 78 (180)
..|.+...|..|+...+... .|..| ..+...+.++.+.| +...|..|+..- .++. --.|..|...|..
T Consensus 122 ~~~~s~~~Lk~H~~~~H~~~-~c~lC-----~~~~kif~~e~k~Y-t~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld 194 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHKLH-LCSLC-----LQNLKIFINERKLY-TRAELNLHLMFGDPDDESCRGHPLCKFCHERFLD 194 (669)
T ss_pred cchhHHHHHHHHHHHhhhhh-ccccc-----cccceeeeeeeehe-hHHHHHHHHhcCCCccccccCCccchhhhhhhcc
Confidence 56678888888887777766 78887 34444556677777 567777776542 2121 1359999999999
Q ss_pred hHHHHHHHHhccCCCcCCCcceecccc------CcccCChhhHHHHHhhcCCCCceecc--ccc-cccCChHHHHHHHH
Q psy3356 79 KSTLNTHKRVHISYLHVKDKPYHCTEC------EATFSWKQNLEVHMRTHTGERPYECE--ICG-KRFSQKSACNTHKR 148 (180)
Q Consensus 79 ~~~l~~H~~~~~~~~~~~~~~~~C~~C------~~~~~~~~~l~~H~~~h~~~~~~~C~--~C~-~~f~~~~~l~~H~~ 148 (180)
...|..|++..| +.|..| +..|.....|..|.+..+ |.|. .|. +.|.....+..+++
T Consensus 195 ~~el~rH~~~~h---------~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 195 DDELYRHLRFDH---------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred HHHHHHhhccce---------eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccceeeehhHHHHHHH
Confidence 999999988653 456666 355666778888877655 6665 454 33444434555555
No 49
>KOG1146|consensus
Probab=96.03 E-value=0.0029 Score=53.78 Aligned_cols=100 Identities=19% Similarity=0.380 Sum_probs=71.5
Q ss_pred CCchhhhHhh-hcCCCCCcccccchhhccChHHHHHHHHhccCC--------------------CcCCCcceeccccCcc
Q psy3356 50 PLLVPQIHMR-THTGERPFECDVCGKRFAQKSTLNTHKRVHISY--------------------LHVKDKPYHCTECEAT 108 (180)
Q Consensus 50 ~~~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~--------------------~~~~~~~~~C~~C~~~ 108 (180)
....+..|+. .+...+.+.|+.|+..|.....|..|++..|.. +..+.++|.|..|...
T Consensus 448 s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~s 527 (1406)
T KOG1146|consen 448 SKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYS 527 (1406)
T ss_pred hhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeee
Confidence 3333444432 344457799999999999999999999884431 2245667889999999
Q ss_pred cCChhhHHHHHhhcCC-------------------------------------------CCceeccccccccCChHHHHH
Q psy3356 109 FSWKQNLEVHMRTHTG-------------------------------------------ERPYECEICGKRFSQKSACNT 145 (180)
Q Consensus 109 ~~~~~~l~~H~~~h~~-------------------------------------------~~~~~C~~C~~~f~~~~~l~~ 145 (180)
+..+.+|.+|++.... .-.|.|.+|++...-..+|..
T Consensus 528 tttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlri 607 (1406)
T KOG1146|consen 528 TTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRI 607 (1406)
T ss_pred eecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccc
Confidence 9999999999864210 012788888888888888888
Q ss_pred HHHH
Q psy3356 146 HKRT 149 (180)
Q Consensus 146 H~~~ 149 (180)
|+..
T Consensus 608 hmts 611 (1406)
T KOG1146|consen 608 HMTA 611 (1406)
T ss_pred cccc
Confidence 8764
No 50
>PRK04860 hypothetical protein; Provisional
Probab=95.98 E-value=0.007 Score=40.07 Aligned_cols=39 Identities=33% Similarity=0.767 Sum_probs=33.5
Q ss_pred cceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCCh
Q psy3356 98 KPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQK 140 (180)
Q Consensus 98 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 140 (180)
-+|.|. |+. ....+.+|.+.+.++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 369998 987 677889999999999999999999987643
No 51
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.24 E-value=0.02 Score=25.24 Aligned_cols=21 Identities=29% Similarity=0.836 Sum_probs=13.8
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy3356 128 YECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
..|+.|++.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3577777777 55567777653
No 52
>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=94.72 E-value=0.011 Score=26.55 Aligned_cols=21 Identities=33% Similarity=0.817 Sum_probs=12.5
Q ss_pred eeccccCcccCChhhHHHHHh
Q psy3356 100 YHCTECEATFSWKQNLEVHMR 120 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~ 120 (180)
|.|..|++.|.+...+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 346666666666666655554
No 53
>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=94.61 E-value=0.031 Score=26.61 Aligned_cols=23 Identities=17% Similarity=0.626 Sum_probs=18.6
Q ss_pred ceeccccccccCChHHHHHHHHH
Q psy3356 127 PYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
+|.|+.|+..|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47788888888888888888753
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.12 E-value=0.046 Score=40.27 Aligned_cols=133 Identities=17% Similarity=0.230 Sum_probs=82.7
Q ss_pred CCcccccCCceeeeeecccCCcccccccceeeeecCCeeEeeeecccCCCchhhhHhhhcCCCC----Ccccccchhhcc
Q psy3356 2 CSSKWITSPSVTFDINIQKNPLVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTHTGER----PFECDVCGKRFA 77 (180)
Q Consensus 2 C~~~f~~~~~~~~~~~~~~~~~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~----~~~C~~C~~~f~ 77 (180)
|.+....+..+..|....+... .|.+|-..=. -+-|....-++..|+.|...-..+. -=.|..|...|.
T Consensus 159 c~~~C~~~k~lk~H~K~~H~~~-~C~~C~~nKk------~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FY 231 (493)
T COG5236 159 CHRRCGSLKELKKHYKAQHGFV-LCSECIGNKK------DFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFY 231 (493)
T ss_pred hhhhhhhHHHHHHHHHhhcCcE-EhHhhhcCcc------cCccceeeeecccccccccCCccccCcCCCchhhhccceec
Confidence 5555566667777777777766 7777743211 1112223335566777754322221 125999999999
Q ss_pred ChHHHHHHHHhccCCCcCCCcceeccccC----cccCChhhHHHHHhhcCCCCceeccc--cc----cccCChHHHHHHH
Q psy3356 78 QKSTLNTHKRVHISYLHVKDKPYHCTECE----ATFSWKQNLEVHMRTHTGERPYECEI--CG----KRFSQKSACNTHK 147 (180)
Q Consensus 78 ~~~~l~~H~~~~~~~~~~~~~~~~C~~C~----~~~~~~~~l~~H~~~h~~~~~~~C~~--C~----~~f~~~~~l~~H~ 147 (180)
....|..|.+.. .+.-+.|.+-+ ..|.+...|..|.+..+ |.|.+ |. ..|.....|+.|+
T Consensus 232 dDDEL~~HcR~~------HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~~~~el~~h~ 301 (493)
T COG5236 232 DDDELRRHCRLR------HEACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFPYHTELLEHL 301 (493)
T ss_pred ChHHHHHHHHhh------hhhhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEeccHHHHHHHH
Confidence 999999998874 34555555543 33666777777776433 55532 32 4688999999998
Q ss_pred HHcC
Q psy3356 148 RTHI 151 (180)
Q Consensus 148 ~~h~ 151 (180)
...|
T Consensus 302 ~~~h 305 (493)
T COG5236 302 TRFH 305 (493)
T ss_pred HHHh
Confidence 6654
No 55
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.06 E-value=0.063 Score=33.10 Aligned_cols=48 Identities=19% Similarity=0.436 Sum_probs=27.2
Q ss_pred eccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHHc
Q psy3356 101 HCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 101 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
.|..|...|........ ..-.....|.|+.|+..|=..-+...|...|
T Consensus 57 ~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cccCcCCCCCCcccccc--cccccccceeCCCCCCccccccchhhhhhcc
Confidence 37777776654321100 0012234577877877777777777776665
No 56
>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=93.65 E-value=0.24 Score=30.59 Aligned_cols=24 Identities=29% Similarity=0.519 Sum_probs=21.9
Q ss_pred eec----cccccccCChHHHHHHHHHcC
Q psy3356 128 YEC----EICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 128 ~~C----~~C~~~f~~~~~l~~H~~~h~ 151 (180)
|.| ..|++...+...+.+|.+.+|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 899 999999999999999998754
No 57
>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=93.42 E-value=0.054 Score=25.63 Aligned_cols=9 Identities=44% Similarity=1.530 Sum_probs=4.2
Q ss_pred Cceeccccc
Q psy3356 126 RPYECEICG 134 (180)
Q Consensus 126 ~~~~C~~C~ 134 (180)
.++.|+.|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 344455554
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=92.66 E-value=0.094 Score=25.00 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=7.6
Q ss_pred ceecccccccc
Q psy3356 127 PYECEICGKRF 137 (180)
Q Consensus 127 ~~~C~~C~~~f 137 (180)
.|.|..||..+
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 36788888664
No 59
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.64 E-value=0.14 Score=24.74 Aligned_cols=33 Identities=24% Similarity=0.696 Sum_probs=17.8
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccC
Q psy3356 128 YECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMF 173 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F 173 (180)
..|+.|+..|.-.... +-.+....+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-------------ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-------------IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-------------CCCCCcEEECCCCCCEe
Confidence 3566666666555442 12233346677776665
No 60
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.49 E-value=0.088 Score=24.98 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=15.1
Q ss_pred CcccccchhhccChHHHHHHHH
Q psy3356 66 PFECDVCGKRFAQKSTLNTHKR 87 (180)
Q Consensus 66 ~~~C~~C~~~f~~~~~l~~H~~ 87 (180)
+|.|..|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 3567777777777767777754
No 61
>KOG2482|consensus
Probab=91.96 E-value=0.15 Score=37.60 Aligned_cols=112 Identities=15% Similarity=0.213 Sum_probs=66.5
Q ss_pred CeeEeeeecccCCCchhhhHhhh--cCCCCC--------cccccchhhccChHHHHHHH--Hhc--cCC--------CcC
Q psy3356 38 EKRFFFFSFLFGPLLVPQIHMRT--HTGERP--------FECDVCGKRFAQKSTLNTHK--RVH--ISY--------LHV 95 (180)
Q Consensus 38 ~~~~~~C~~~~~~~~~l~~H~~~--h~~~~~--------~~C~~C~~~f~~~~~l~~H~--~~~--~~~--------~~~ 95 (180)
..+|.+|.+.|+.+.-|..||+. |....| |.-++-..+ ...+....+. .+. +.. ...
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~-ks~t~~~~e~dret~~d~~E~D~~wsDw~ed 273 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVG-KSWTIVHSEDDRETNEDINETDDTWSDWNED 273 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcC-CccchhhhhhhhhhhccccccccchhhhhcC
Confidence 78888999999999999999874 322211 211111110 1111111111 110 000 001
Q ss_pred CCcc--eeccccCcccCChhhHHHHHhhcCC---------------------------CCceeccccccccCChHHHHHH
Q psy3356 96 KDKP--YHCTECEATFSWKQNLEVHMRTHTG---------------------------ERPYECEICGKRFSQKSACNTH 146 (180)
Q Consensus 96 ~~~~--~~C~~C~~~~~~~~~l~~H~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H 146 (180)
+..+ ..|..|.....+...+..|++.-+. ...-.|-.|.-.|.....|..|
T Consensus 274 ~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~h 353 (423)
T KOG2482|consen 274 DAEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIH 353 (423)
T ss_pred CCCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhh
Confidence 1222 5899999988889999999875332 0114688899999999999999
Q ss_pred HHHc
Q psy3356 147 KRTH 150 (180)
Q Consensus 147 ~~~h 150 (180)
+..+
T Consensus 354 m~e~ 357 (423)
T KOG2482|consen 354 MVED 357 (423)
T ss_pred cccc
Confidence 8754
No 62
>KOG2893|consensus
Probab=91.93 E-value=0.046 Score=38.11 Aligned_cols=44 Identities=18% Similarity=0.417 Sum_probs=29.0
Q ss_pred CeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHH
Q psy3356 38 EKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTH 85 (180)
Q Consensus 38 ~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H 85 (180)
.-+|++|+..|.....|.+|++.- -|+|.+|-+...+--.|..|
T Consensus 10 kpwcwycnrefddekiliqhqkak----hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred Cceeeecccccchhhhhhhhhhhc----cceeeeehhhhccCCCceee
Confidence 346777777777777777776553 37787777665554445544
No 63
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.74 E-value=0.13 Score=34.23 Aligned_cols=23 Identities=35% Similarity=0.977 Sum_probs=18.1
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCc
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACE 170 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~ 170 (180)
.|+|++||+. +.|+.|-.||+||
T Consensus 134 ~~vC~vCGy~---------------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT---------------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc---------------------ccCCCCCcCCCCC
Confidence 5899999855 4457788899998
No 64
>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=91.37 E-value=0.2 Score=30.87 Aligned_cols=30 Identities=30% Similarity=0.770 Sum_probs=18.2
Q ss_pred eeccccCcccCChhhHHHHHhhcCCCCceeccccccccCCh
Q psy3356 100 YHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQK 140 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 140 (180)
..|+.||..|- -.++.|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFY-----------DLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFY-----------DLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhc-----------cCCCCCccCCCCCCccCcc
Confidence 45677776653 3445666677777666544
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=90.90 E-value=0.078 Score=23.60 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=11.0
Q ss_pred cccccceeeeecCCeeEeeeeccc
Q psy3356 25 FIPACVFRFSVENEKRFFFFSFLF 48 (180)
Q Consensus 25 ~c~~C~~~~~~~~~~~~~~C~~~~ 48 (180)
.||.|+...+ .+...|..||..|
T Consensus 2 ~CP~C~~~V~-~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVP-ESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCch-hhcCcCCCCCCCC
Confidence 4666666554 3333344444443
No 66
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.86 E-value=0.23 Score=24.10 Aligned_cols=34 Identities=26% Similarity=0.647 Sum_probs=17.8
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCC
Q psy3356 128 YECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFT 174 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~ 174 (180)
..|+.|+..|.-..+- +-.+....+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-------------l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-------------LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-------------cccCCcEEECCCCCcEee
Confidence 3566666666555431 112334466666666553
No 67
>KOG4173|consensus
Probab=90.51 E-value=0.034 Score=37.85 Aligned_cols=76 Identities=24% Similarity=0.517 Sum_probs=59.1
Q ss_pred Cccccc--chhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhh-c---------CCCCceecc--
Q psy3356 66 PFECDV--CGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRT-H---------TGERPYECE-- 131 (180)
Q Consensus 66 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~-h---------~~~~~~~C~-- 131 (180)
.+.|++ |.+.|........|..+-| + -.|.+|.+.|.+...|..|+.. | -|...|.|-
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h-----~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvE 150 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLH-----G---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVE 150 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcc-----c---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHH
Confidence 367887 8888888888888876552 2 2599999999999999999853 2 234568894
Q ss_pred ccccccCChHHHHHHHHH
Q psy3356 132 ICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 132 ~C~~~f~~~~~l~~H~~~ 149 (180)
.|+..|.+...-..|+-.
T Consensus 151 gCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 151 GCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhhhhhhHHHH
Confidence 599999999999888877
No 68
>KOG1146|consensus
Probab=90.38 E-value=0.17 Score=43.81 Aligned_cols=100 Identities=17% Similarity=0.226 Sum_probs=53.6
Q ss_pred cccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhh-----------------cCCCCcee
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRT-----------------HTGERPYE 129 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~-----------------h~~~~~~~ 129 (180)
+.|..|++++.....+. ++ .....|.|.+|...|.....|..|.+. +....+|
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l--------~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~- 1330 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TL--------DVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH- 1330 (1406)
T ss_pred chhhhccccccCcccee-ec--------ccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-
Confidence 44555555554444433 22 123344555555555555555555431 1122345
Q ss_pred ccccccccCChHHHHHHHHHcCCCC----------------CCcCCCCCCcccCCCcccCCCc
Q psy3356 130 CEICGKRFSQKSACNTHKRTHIPYL----------------PRVHPKDRPFHCPACEGMFTTK 176 (180)
Q Consensus 130 C~~C~~~f~~~~~l~~H~~~h~~~~----------------~~~h~~~~~~~C~~C~~~F~~~ 176 (180)
|..|...|.....|++|+++-+... ..++..+.-+.|+.|...|...
T Consensus 1331 c~~c~~~~~~~~alqihm~~~~~~~kt~~~~p~~~~~~t~~~tst~~~v~~a~~~~~~~~~es 1393 (1406)
T KOG1146|consen 1331 CLACEVLLSGREALQIHMRSSAHRRKTAPPQPGPPISITNAATSTSAAVAFAGSEARLPHTES 1393 (1406)
T ss_pred chHHHhhcchhHHHHHHHHHhhhcccCCCCCCCCccccccccccccccccccccccccccccc
Confidence 8888888888888888887543111 1234444557777776666544
No 69
>KOG1280|consensus
Probab=90.20 E-value=0.32 Score=35.99 Aligned_cols=81 Identities=17% Similarity=0.163 Sum_probs=53.8
Q ss_pred cccccccceeeeecCCeeEeeeec------ccCCCchhhhHhhhc----------------------CCCCCcccccchh
Q psy3356 23 LVFIPACVFRFSVENEKRFFFFSF------LFGPLLVPQIHMRTH----------------------TGERPFECDVCGK 74 (180)
Q Consensus 23 ~~~c~~C~~~~~~~~~~~~~~C~~------~~~~~~~l~~H~~~h----------------------~~~~~~~C~~C~~ 74 (180)
.+.|..|++.--.-..++|..|.. -|.+......|-..| .....|+|++|+.
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~dfeL~f~Ge~i~~y~~qSftCPyC~~ 87 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVDFELYFGGEPISHYDPQSFTCPYCGI 87 (381)
T ss_pred CceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccceeeEecCccccccccccccCCcccc
Confidence 458999999888888999997644 233333333332111 1233589999999
Q ss_pred hccChHHHHHHHHhccCCCcCCCcceeccccC
Q psy3356 75 RFAQKSTLNTHKRVHISYLHVKDKPYHCTECE 106 (180)
Q Consensus 75 ~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~ 106 (180)
+-.+...|..|+...|..+. ....|++|.
T Consensus 88 ~Gfte~~f~~Hv~s~Hpda~---~~~icp~c~ 116 (381)
T KOG1280|consen 88 MGFTERQFGTHVLSQHPEAS---TSVICPLCA 116 (381)
T ss_pred cccchhHHHHHhhhcCcccC---cceeeeccc
Confidence 98889999999887765432 345677665
No 70
>KOG4173|consensus
Probab=90.02 E-value=0.32 Score=33.29 Aligned_cols=77 Identities=22% Similarity=0.370 Sum_probs=44.2
Q ss_pred eecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHHHHhccCC-----CcCCCcceeccc--cCcccCChhhHH
Q psy3356 44 FSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRVHISY-----LHVKDKPYHCTE--CEATFSWKQNLE 116 (180)
Q Consensus 44 C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~-----~~~~~~~~~C~~--C~~~~~~~~~l~ 116 (180)
|-..|.....+..|..+-++ ..|..|.+.|.+...|..|+..-|.. ...|.-.|.|-+ |+..|.+...-.
T Consensus 87 c~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~Rk 163 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRK 163 (253)
T ss_pred hHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhh
Confidence 44455555555555544332 24777777777777777776543311 113455577754 777777777777
Q ss_pred HHHh-hcC
Q psy3356 117 VHMR-THT 123 (180)
Q Consensus 117 ~H~~-~h~ 123 (180)
.|+. .|.
T Consensus 164 dH~I~~Hk 171 (253)
T KOG4173|consen 164 DHMIRMHK 171 (253)
T ss_pred hHHHHhcc
Confidence 7763 443
No 71
>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=90.00 E-value=0.21 Score=30.76 Aligned_cols=14 Identities=36% Similarity=0.947 Sum_probs=7.8
Q ss_pred CCcccCCCcccCCC
Q psy3356 162 RPFHCPACEGMFTT 175 (180)
Q Consensus 162 ~~~~C~~C~~~F~~ 175 (180)
.|-.|+.||..|.-
T Consensus 25 ~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 25 DPIVCPKCGTEFPP 38 (108)
T ss_pred CCccCCCCCCccCc
Confidence 44556666665543
No 72
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.93 E-value=0.27 Score=23.91 Aligned_cols=14 Identities=21% Similarity=0.562 Sum_probs=7.7
Q ss_pred eeccccccccCChH
Q psy3356 128 YECEICGKRFSQKS 141 (180)
Q Consensus 128 ~~C~~C~~~f~~~~ 141 (180)
+.|+.|+..|.-..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 45666666555443
No 73
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.80 E-value=0.62 Score=28.82 Aligned_cols=91 Identities=16% Similarity=0.171 Sum_probs=52.7
Q ss_pred ccccccceeeeecCCeeEeeeecccCCCchhhhHhhhcC-----CCC-------CcccccchhhccChHHHHHHHHhccC
Q psy3356 24 VFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTHT-----GER-------PFECDVCGKRFAQKSTLNTHKRVHIS 91 (180)
Q Consensus 24 ~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h~-----~~~-------~~~C~~C~~~f~~~~~l~~H~~~~~~ 91 (180)
|.||.|+...- .-...|.+|+.+.-....|.+-...-. .+. .-.|--|...|........- .
T Consensus 2 Y~CPrC~skvC-~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~--- 75 (112)
T TIGR00622 2 YFCPQCRAKVC-ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--E--- 75 (112)
T ss_pred ccCCCCCCCcc-CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccccc--c---
Confidence 57888877765 334667778877766666666421100 011 11377777777653211100 0
Q ss_pred CCcCCCcceeccccCcccCChhhHHHHHhhc
Q psy3356 92 YLHVKDKPYHCTECEATFSWKQNLEVHMRTH 122 (180)
Q Consensus 92 ~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h 122 (180)
......|.|+.|...|-..-++..|...|
T Consensus 76 --~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 76 --LKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred --cccccceeCCCCCCccccccchhhhhhcc
Confidence 02345678888888888777777777665
No 74
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.80 E-value=0.15 Score=26.90 Aligned_cols=26 Identities=27% Similarity=0.545 Sum_probs=14.8
Q ss_pred CCCceeccccccccCChHHHHHHHHH
Q psy3356 124 GERPYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 124 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
|+..+.|+-|+..|....++.+|...
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhH
Confidence 44445566666666666666666543
No 75
>KOG2186|consensus
Probab=89.74 E-value=0.31 Score=34.48 Aligned_cols=46 Identities=24% Similarity=0.626 Sum_probs=29.9
Q ss_pred cccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHh
Q psy3356 67 FECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMR 120 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 120 (180)
|.|..||.+.... .+..|+... .+ .-+.|..|+..|.. ..+..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srC-----rn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRC-----RN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhc-----cC-CeeEEeeccccccc-chhhhhhh
Confidence 6677777776654 355677665 23 56777777777766 55666654
No 76
>PHA00626 hypothetical protein
Probab=89.41 E-value=0.06 Score=28.47 Aligned_cols=14 Identities=36% Similarity=0.598 Sum_probs=8.8
Q ss_pred CceeccccccccCC
Q psy3356 126 RPYECEICGKRFSQ 139 (180)
Q Consensus 126 ~~~~C~~C~~~f~~ 139 (180)
..|.|+.|++.|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 45777777766643
No 77
>KOG2893|consensus
Probab=89.37 E-value=0.099 Score=36.53 Aligned_cols=42 Identities=24% Similarity=0.571 Sum_probs=26.9
Q ss_pred ccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHH
Q psy3356 68 ECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVH 118 (180)
Q Consensus 68 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H 118 (180)
+|.+|.+.|..+.-|.+|++. +.++|.+|.+...+-..|..|
T Consensus 12 wcwycnrefddekiliqhqka---------khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA---------KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhh---------ccceeeeehhhhccCCCceee
Confidence 377777777777777777553 456777776554444444444
No 78
>KOG2482|consensus
Probab=89.32 E-value=0.57 Score=34.72 Aligned_cols=142 Identities=17% Similarity=0.257 Sum_probs=76.7
Q ss_pred CeeEeeeecccC-CCchhhhHhh-hcC---C------------------CCCcccccchhhccChHHHHHHHHhccCC-C
Q psy3356 38 EKRFFFFSFLFG-PLLVPQIHMR-THT---G------------------ERPFECDVCGKRFAQKSTLNTHKRVHISY-L 93 (180)
Q Consensus 38 ~~~~~~C~~~~~-~~~~l~~H~~-~h~---~------------------~~~~~C~~C~~~f~~~~~l~~H~~~~~~~-~ 93 (180)
...|.||+..+. ....+..|+- .|. | -..+.|-.|.+.|+.+..|+.||+..... .
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 578888887664 4444445532 221 0 11478999999999999999999754211 1
Q ss_pred cCCCcce----ec--cccCcccCC-hhhHHHHHhhc-------------CCCCc--eeccccccccCChHHHHHHHHHcC
Q psy3356 94 HVKDKPY----HC--TECEATFSW-KQNLEVHMRTH-------------TGERP--YECEICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 94 ~~~~~~~----~C--~~C~~~~~~-~~~l~~H~~~h-------------~~~~~--~~C~~C~~~f~~~~~l~~H~~~h~ 151 (180)
.+...-| .= ..-++.... ...+.+-.... .+..+ ..|-.|.........|..||++-|
T Consensus 224 nPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 224 NPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 0111111 00 001211111 11111000000 01122 589999999998999999999877
Q ss_pred CCC-------------CC------cCCCCCCcccCCCcccCCCccCC
Q psy3356 152 PYL-------------PR------VHPKDRPFHCPACEGMFTTKQNL 179 (180)
Q Consensus 152 ~~~-------------~~------~h~~~~~~~C~~C~~~F~~~~~L 179 (180)
.+. ++ +....+.-.|-.|...|-.+..|
T Consensus 304 e~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l 350 (423)
T KOG2482|consen 304 EFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGL 350 (423)
T ss_pred HhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchh
Confidence 432 00 11122334578888888877665
No 79
>KOG2186|consensus
Probab=88.48 E-value=0.41 Score=33.87 Aligned_cols=48 Identities=25% Similarity=0.593 Sum_probs=38.6
Q ss_pred ceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHH
Q psy3356 99 PYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 99 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
-+.|..||.... +..+.+|+....+ ..|.|..|+..|.. .++..|..-
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 478999998754 6678889988877 56999999999988 678888764
No 80
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.35 E-value=0.41 Score=35.52 Aligned_cols=77 Identities=22% Similarity=0.375 Sum_probs=40.8
Q ss_pred Cccccc--chhhccChHHHHHHHHhccCCCcCCCcceeccccC---c------ccCChhhHHHHHhhcCCC----Cceec
Q psy3356 66 PFECDV--CGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECE---A------TFSWKQNLEVHMRTHTGE----RPYEC 130 (180)
Q Consensus 66 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~---~------~~~~~~~l~~H~~~h~~~----~~~~C 130 (180)
.|.|+. |.........|..|.+..|. .+.|..|- + ...+...|..|...-..+ ..-.|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~-------~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C 223 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHG-------FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLC 223 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC-------cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchh
Confidence 367876 77777777889999886543 12333331 1 112233444444322211 11246
Q ss_pred cccccccCChHHHHHHHHH
Q psy3356 131 EICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 131 ~~C~~~f~~~~~l~~H~~~ 149 (180)
..|...|.+...|.+|++.
T Consensus 224 ~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 224 IFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhccceecChHHHHHHHHh
Confidence 6666666666666666654
No 81
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.09 E-value=0.34 Score=25.63 Aligned_cols=30 Identities=23% Similarity=0.455 Sum_probs=23.8
Q ss_pred cCCCCCcccccchhhccChHHHHHHHHhcc
Q psy3356 61 HTGERPFECDVCGKRFAQKSTLNTHKRVHI 90 (180)
Q Consensus 61 h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 90 (180)
..++..+.|+-|+..|....+...|+...|
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 345667889999999999888998886554
No 82
>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=87.21 E-value=0.31 Score=24.39 Aligned_cols=11 Identities=18% Similarity=0.298 Sum_probs=8.5
Q ss_pred ccccccceeee
Q psy3356 24 VFIPACVFRFS 34 (180)
Q Consensus 24 ~~c~~C~~~~~ 34 (180)
|.|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 47888888877
No 83
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.80 E-value=0.15 Score=35.66 Aligned_cols=12 Identities=25% Similarity=0.639 Sum_probs=8.8
Q ss_pred eeccccccccCC
Q psy3356 128 YECEICGKRFSQ 139 (180)
Q Consensus 128 ~~C~~C~~~f~~ 139 (180)
..|+.||.++..
T Consensus 49 ~vCP~CgyA~~~ 60 (214)
T PF09986_consen 49 WVCPHCGYAAFE 60 (214)
T ss_pred EECCCCCCcccc
Confidence 578888887653
No 84
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.54 E-value=1.4 Score=28.80 Aligned_cols=14 Identities=21% Similarity=0.733 Sum_probs=7.5
Q ss_pred CceeccccccccCC
Q psy3356 126 RPYECEICGKRFSQ 139 (180)
Q Consensus 126 ~~~~C~~C~~~f~~ 139 (180)
..|.|+.|+..|..
T Consensus 98 ~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 98 AYYKCPNCQSKYTF 111 (147)
T ss_pred cEEECcCCCCEeeH
Confidence 34556666555543
No 85
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.43 E-value=0.44 Score=25.66 Aligned_cols=10 Identities=40% Similarity=1.434 Sum_probs=6.4
Q ss_pred CCCcccCCCc
Q psy3356 161 DRPFHCPACE 170 (180)
Q Consensus 161 ~~~~~C~~C~ 170 (180)
..+|.|+.||
T Consensus 48 g~~Y~Cp~CG 57 (61)
T COG2888 48 GNPYRCPKCG 57 (61)
T ss_pred CCceECCCcC
Confidence 3457777776
No 86
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.07 E-value=0.28 Score=37.52 Aligned_cols=47 Identities=34% Similarity=0.700 Sum_probs=38.1
Q ss_pred eeecccCCCchhhhHhh--hcCCC--CCcccc--cchhhccChHHHHHHHHhc
Q psy3356 43 FFSFLFGPLLVPQIHMR--THTGE--RPFECD--VCGKRFAQKSTLNTHKRVH 89 (180)
Q Consensus 43 ~C~~~~~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~ 89 (180)
.|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...+
T Consensus 294 ~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 294 QCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred cccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc
Confidence 34455558888888988 78888 889999 7999999988888888776
No 87
>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=85.70 E-value=0.75 Score=29.02 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=20.7
Q ss_pred ceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCCh
Q psy3356 99 PYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQK 140 (180)
Q Consensus 99 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 140 (180)
...|+.|+..|- -.++.|..|+.||..|...
T Consensus 9 Kr~Cp~cg~kFY-----------DLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSKFY-----------DLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCcccc-----------ccCCCCccCCCcCCccCcc
Confidence 356777777763 3456777788888776544
No 88
>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=85.26 E-value=2.9 Score=25.73 Aligned_cols=26 Identities=27% Similarity=0.567 Sum_probs=23.0
Q ss_pred ceec----cccCcccCChhhHHHHHhhcCC
Q psy3356 99 PYHC----TECEATFSWKQNLEVHMRTHTG 124 (180)
Q Consensus 99 ~~~C----~~C~~~~~~~~~l~~H~~~h~~ 124 (180)
.|.| ..|+..+.+...+.+|+..+++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999987764
No 89
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.70 E-value=1 Score=24.30 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=7.6
Q ss_pred CCCcccCCCcc
Q psy3356 161 DRPFHCPACEG 171 (180)
Q Consensus 161 ~~~~~C~~C~~ 171 (180)
..+|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 35688888874
No 90
>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=84.49 E-value=1.1 Score=29.74 Aligned_cols=18 Identities=22% Similarity=0.253 Sum_probs=8.5
Q ss_pred CceeccccccccCChHHH
Q psy3356 126 RPYECEICGKRFSQKSAC 143 (180)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l 143 (180)
.-|.|+.|+..|.....+
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CeEECCCCCcEeeHHHHH
Confidence 335555555544444443
No 91
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=83.69 E-value=0.85 Score=23.51 Aligned_cols=14 Identities=21% Similarity=0.534 Sum_probs=9.9
Q ss_pred ccccccceeeeecC
Q psy3356 24 VFIPACVFRFSVEN 37 (180)
Q Consensus 24 ~~c~~C~~~~~~~~ 37 (180)
+.|..|+..+....
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 57888888887433
No 92
>KOG2071|consensus
Probab=83.11 E-value=0.99 Score=36.02 Aligned_cols=16 Identities=31% Similarity=0.816 Sum_probs=13.5
Q ss_pred CCCcccCCCcccCCCc
Q psy3356 161 DRPFHCPACEGMFTTK 176 (180)
Q Consensus 161 ~~~~~C~~C~~~F~~~ 176 (180)
+++..|++|+..|..-
T Consensus 511 e~~~~C~IC~EkFe~v 526 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVV 526 (579)
T ss_pred ccccCCccccccccee
Confidence 7889999999988653
No 93
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.54 E-value=0.84 Score=23.28 Aligned_cols=10 Identities=30% Similarity=1.225 Sum_probs=5.3
Q ss_pred cccccchhhc
Q psy3356 67 FECDVCGKRF 76 (180)
Q Consensus 67 ~~C~~C~~~f 76 (180)
|.|+.|+..+
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 4555555544
No 94
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.67 E-value=1.6 Score=29.63 Aligned_cols=16 Identities=31% Similarity=0.569 Sum_probs=7.6
Q ss_pred ceeccccccccCChHH
Q psy3356 127 PYECEICGKRFSQKSA 142 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~ 142 (180)
.|.|+.|+..|.....
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 3555555554444433
No 95
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.74 E-value=0.28 Score=32.31 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=6.0
Q ss_pred eeccccCcccCC
Q psy3356 100 YHCTECEATFSW 111 (180)
Q Consensus 100 ~~C~~C~~~~~~ 111 (180)
++|+.||+.|.+
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 445555555444
No 96
>KOG2785|consensus
Probab=79.66 E-value=3 Score=31.53 Aligned_cols=51 Identities=24% Similarity=0.382 Sum_probs=43.4
Q ss_pred eeccccCcccCChhhHHHHHhhcCCC-----------------------Cceeccccc---cccCChHHHHHHHHHc
Q psy3356 100 YHCTECEATFSWKQNLEVHMRTHTGE-----------------------RPYECEICG---KRFSQKSACNTHKRTH 150 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~h 150 (180)
-.|..|+..+.+...-..|+..+++- ..+.|..|+ +.|.+....+.||...
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 57889999999999999999887762 238999999 9999999999999753
No 97
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.24 E-value=2.1 Score=27.98 Aligned_cols=38 Identities=16% Similarity=0.705 Sum_probs=20.3
Q ss_pred CCcceeccccCcccCChhhHHHHHhhcCCCCceecccccccc
Q psy3356 96 KDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRF 137 (180)
Q Consensus 96 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 137 (180)
...-|.|+.|+..|.....+.. ... ...|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 4456777777776664332211 011 2337777777654
No 98
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=78.63 E-value=1.5 Score=22.89 Aligned_cols=13 Identities=8% Similarity=0.179 Sum_probs=9.5
Q ss_pred ccccccceeeeec
Q psy3356 24 VFIPACVFRFSVE 36 (180)
Q Consensus 24 ~~c~~C~~~~~~~ 36 (180)
+.|..||+.+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 5788888888743
No 99
>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=78.62 E-value=2.1 Score=18.90 Aligned_cols=19 Identities=21% Similarity=0.593 Sum_probs=13.9
Q ss_pred eccccccccCChHHHHHHHH
Q psy3356 129 ECEICGKRFSQKSACNTHKR 148 (180)
Q Consensus 129 ~C~~C~~~f~~~~~l~~H~~ 148 (180)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 588888877 5567777765
No 100
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=78.06 E-value=0.76 Score=35.17 Aligned_cols=53 Identities=38% Similarity=0.823 Sum_probs=36.8
Q ss_pred ceeccccCcccCChhhHHHHHh--hcCCC--Cceecc--ccccccCChHHHHHHHHHcC
Q psy3356 99 PYHCTECEATFSWKQNLEVHMR--THTGE--RPYECE--ICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 99 ~~~C~~C~~~~~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~ 151 (180)
.+.|..|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...|.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccccc
Confidence 4666667777777777777777 56666 677777 57777777777777766543
No 101
>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=77.70 E-value=3.4 Score=27.44 Aligned_cols=34 Identities=18% Similarity=0.573 Sum_probs=24.3
Q ss_pred CCCcceeccccCcccCChhhHHHHHhhcCCCCceecccccccc
Q psy3356 95 VKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRF 137 (180)
Q Consensus 95 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 137 (180)
....-|.|+.|+..|+....+. ..|.|+.||...
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 3456688988888877666653 248899998764
No 102
>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=77.63 E-value=1.4 Score=21.57 Aligned_cols=11 Identities=18% Similarity=0.271 Sum_probs=8.6
Q ss_pred ccccccceeee
Q psy3356 24 VFIPACVFRFS 34 (180)
Q Consensus 24 ~~c~~C~~~~~ 34 (180)
+.|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 47888888877
No 103
>PF14353 CpXC: CpXC protein
Probab=77.62 E-value=3.9 Score=25.95 Aligned_cols=19 Identities=32% Similarity=0.711 Sum_probs=12.4
Q ss_pred CCcccccchhhccChHHHH
Q psy3356 65 RPFECDVCGKRFAQKSTLN 83 (180)
Q Consensus 65 ~~~~C~~C~~~f~~~~~l~ 83 (180)
..++|+.||..+.-...+.
T Consensus 37 ~~~~CP~Cg~~~~~~~p~l 55 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLL 55 (128)
T ss_pred CEEECCCCCCceecCCCEE
Confidence 3477888888776544433
No 104
>KOG2785|consensus
Probab=76.96 E-value=4.5 Score=30.68 Aligned_cols=56 Identities=21% Similarity=0.383 Sum_probs=42.9
Q ss_pred CcccccchhhccChHHHHHHHHhccCCCcCC------------------CcceeccccC---cccCChhhHHHHHhh
Q psy3356 66 PFECDVCGKRFAQKSTLNTHKRVHISYLHVK------------------DKPYHCTECE---ATFSWKQNLEVHMRT 121 (180)
Q Consensus 66 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~------------------~~~~~C~~C~---~~~~~~~~l~~H~~~ 121 (180)
|-.|-.|+..+.+...-..||..+|++.-+. ...+.|..|+ +.|.+......|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4668888888888888888888887653221 2336788888 999999999999974
No 105
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=76.58 E-value=2.4 Score=21.49 Aligned_cols=10 Identities=40% Similarity=0.883 Sum_probs=4.7
Q ss_pred eeccccCccc
Q psy3356 100 YHCTECEATF 109 (180)
Q Consensus 100 ~~C~~C~~~~ 109 (180)
|.|..||..+
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 4455555443
No 106
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=76.22 E-value=1.2 Score=37.08 Aligned_cols=54 Identities=15% Similarity=0.137 Sum_probs=31.1
Q ss_pred eecccCCcccccccceeeeecCCeeEeeeecccC---CCchhhhHhhhcCCCCCcccccchhh
Q psy3356 16 INIQKNPLVFIPACVFRFSVENEKRFFFFSFLFG---PLLVPQIHMRTHTGERPFECDVCGKR 75 (180)
Q Consensus 16 ~~~~~~~~~~c~~C~~~~~~~~~~~~~~C~~~~~---~~~~l~~H~~~h~~~~~~~C~~C~~~ 75 (180)
.+....+...|..||+.+. |..|+..+. ....|.=|.-.+....|..|+.|+-.
T Consensus 428 nRRGys~~l~C~~Cg~v~~------Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 428 NRRGYAPLLLCRDCGYIAE------CPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCccceeecccCCCccc------CCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3455677779999999988 555554432 11223333333344455666666654
No 107
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=75.05 E-value=12 Score=24.83 Aligned_cols=53 Identities=17% Similarity=0.297 Sum_probs=30.2
Q ss_pred cceeccccCcccCChhhHHHHHhhcCCCCceeccc--cccccCChHHHHHHHHHcCC
Q psy3356 98 KPYHCTECEATFSWKQNLEVHMRTHTGERPYECEI--CGKRFSQKSACNTHKRTHIP 152 (180)
Q Consensus 98 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~ 152 (180)
..+.|+.|.-......-+ ...+.+...|+-.|.. |... .+...|.+|.+..||
T Consensus 79 ~~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP 133 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHP 133 (162)
T ss_pred ccccCccccCceeceEEc-hHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCC
Confidence 457899996332221111 2233344445556643 5543 578899999998654
No 108
>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=74.54 E-value=2.9 Score=29.96 Aligned_cols=18 Identities=22% Similarity=0.652 Sum_probs=10.8
Q ss_pred CCCcccCCCcccCCCccC
Q psy3356 161 DRPFHCPACEGMFTTKQN 178 (180)
Q Consensus 161 ~~~~~C~~C~~~F~~~~~ 178 (180)
.+++.||.|+..-+...+
T Consensus 207 ~k~~PCPKCg~et~eTkd 224 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKD 224 (314)
T ss_pred CCCCCCCCCCCccccccc
Confidence 366778887765444333
No 109
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=73.77 E-value=3.6 Score=22.04 Aligned_cols=21 Identities=24% Similarity=0.621 Sum_probs=9.7
Q ss_pred hhhHHHHHhhcCCCCceeccc
Q psy3356 112 KQNLEVHMRTHTGERPYECEI 132 (180)
Q Consensus 112 ~~~l~~H~~~h~~~~~~~C~~ 132 (180)
...|..|+...-..++..|+.
T Consensus 23 r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 23 RKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CCCHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHHHccCCCCcEECCC
Confidence 445555555433344455555
No 110
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.72 E-value=1.6 Score=25.64 Aligned_cols=31 Identities=23% Similarity=0.537 Sum_probs=16.8
Q ss_pred cceeccccCcccCChhhHHHHHhhcCCCCceeccccccccC
Q psy3356 98 KPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFS 138 (180)
Q Consensus 98 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 138 (180)
..+.|+.|++.- +. -.+...|.|..|+..|.
T Consensus 34 ~~~~Cp~C~~~~--------Vk--R~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTT--------VK--RIATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCcc--------ee--eeccCeEEcCCCCCeec
Confidence 446677776541 11 12334567777776664
No 111
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.30 E-value=4 Score=27.73 Aligned_cols=34 Identities=21% Similarity=0.761 Sum_probs=23.6
Q ss_pred CCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccC
Q psy3356 96 KDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFS 138 (180)
Q Consensus 96 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 138 (180)
...-|.|+.|+..|+....+. ..|.|+.||....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 445688888888877665442 2488999987653
No 112
>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=72.24 E-value=4.1 Score=20.39 Aligned_cols=23 Identities=26% Similarity=0.573 Sum_probs=10.7
Q ss_pred CceeccccccccCC----hHHHHHHHH
Q psy3356 126 RPYECEICGKRFSQ----KSACNTHKR 148 (180)
Q Consensus 126 ~~~~C~~C~~~f~~----~~~l~~H~~ 148 (180)
....|..|++.+.. ...|..|++
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 33556666655544 255666664
No 113
>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=71.93 E-value=1.1 Score=23.35 Aligned_cols=10 Identities=50% Similarity=1.301 Sum_probs=4.2
Q ss_pred eeccccCccc
Q psy3356 100 YHCTECEATF 109 (180)
Q Consensus 100 ~~C~~C~~~~ 109 (180)
|.|..|+..|
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 3444444433
No 114
>KOG2593|consensus
Probab=71.90 E-value=4.5 Score=31.24 Aligned_cols=38 Identities=26% Similarity=0.600 Sum_probs=26.6
Q ss_pred CCCceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCccc
Q psy3356 124 GERPYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGM 172 (180)
Q Consensus 124 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~ 172 (180)
....|.|+.|.+.|.+...++.- -...-.|.|..|+--
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L~-----------~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQLL-----------DNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccchhhhHHHHhh-----------cccCceEEEecCCCc
Confidence 34569999999998887766542 223456899999853
No 115
>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=70.16 E-value=2.1 Score=18.61 Aligned_cols=9 Identities=56% Similarity=1.516 Sum_probs=5.4
Q ss_pred CCcccCCCc
Q psy3356 162 RPFHCPACE 170 (180)
Q Consensus 162 ~~~~C~~C~ 170 (180)
.+|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 346666665
No 116
>KOG2807|consensus
Probab=69.42 E-value=9.5 Score=28.42 Aligned_cols=26 Identities=27% Similarity=0.549 Sum_probs=17.9
Q ss_pred CCceeccccccccCChHHHHHHHHHc
Q psy3356 125 ERPYECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
...|.|..|...|-..-+...|-..|
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CCcEEchhccceeeccchHHHHhhhh
Confidence 34577777777777777777776665
No 117
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=69.03 E-value=0.8 Score=25.97 Aligned_cols=20 Identities=30% Similarity=0.537 Sum_probs=11.5
Q ss_pred CCCCceecc--ccccccCChHH
Q psy3356 123 TGERPYECE--ICGKRFSQKSA 142 (180)
Q Consensus 123 ~~~~~~~C~--~C~~~f~~~~~ 142 (180)
..+..+.|. .||..|.....
T Consensus 23 ~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 23 TKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred hheeeeecCCCCCCCEEEEEEE
Confidence 334556675 67776655443
No 118
>KOG2807|consensus
Probab=68.51 E-value=9.6 Score=28.41 Aligned_cols=91 Identities=21% Similarity=0.425 Sum_probs=50.8
Q ss_pred cccccchhhccChHHHHHH-HHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHHHHH
Q psy3356 67 FECDVCGKRFAQKSTLNTH-KRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNT 145 (180)
Q Consensus 67 ~~C~~C~~~f~~~~~l~~H-~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 145 (180)
..|+.=..+|++......- .-..|.. .....|.|++|....- .-|..|+.|+....+...|.+
T Consensus 245 ~~~sLvkmGFP~~~~e~~ps~C~CH~~--~~~~Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLAR 308 (378)
T KOG2807|consen 245 KECSLVKMGFPSRSPEDTPSFCACHSE--LSGGGYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLAR 308 (378)
T ss_pred cCCceEEecCCCcccccCcchheeccc--cccCceeCCcccCeee--------------cCCccCCccceeEecchHHHH
Confidence 3466666777754322211 1222221 3445688998875422 346789999988888777766
Q ss_pred HHHHcCCCC-------------------CCcCCCCCCcccCCCcccC
Q psy3356 146 HKRTHIPYL-------------------PRVHPKDRPFHCPACEGMF 173 (180)
Q Consensus 146 H~~~h~~~~-------------------~~~h~~~~~~~C~~C~~~F 173 (180)
-.+.--|.. ...-.+...|.|..|-..|
T Consensus 309 SyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~F 355 (378)
T KOG2807|consen 309 SYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVF 355 (378)
T ss_pred HHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhcccee
Confidence 443221221 0111233458899988776
No 119
>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=67.51 E-value=5.6 Score=27.88 Aligned_cols=31 Identities=16% Similarity=0.360 Sum_probs=22.0
Q ss_pred CCCcceeccccCcccCChhhHHHHHhhcCCC
Q psy3356 95 VKDKPYHCTECEATFSWKQNLEVHMRTHTGE 125 (180)
Q Consensus 95 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~ 125 (180)
..+..|.|+.|++.|.....+.+|+..-|.+
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 3556688999999999999999998765543
No 120
>PF12907 zf-met2: Zinc-binding
Probab=66.87 E-value=4.9 Score=19.90 Aligned_cols=22 Identities=23% Similarity=0.628 Sum_probs=13.7
Q ss_pred eecccccccc---CChHHHHHHHHH
Q psy3356 128 YECEICGKRF---SQKSACNTHKRT 149 (180)
Q Consensus 128 ~~C~~C~~~f---~~~~~l~~H~~~ 149 (180)
++|.+|...| .....|..|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 4677777444 345667777665
No 121
>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=65.78 E-value=1.7 Score=22.86 Aligned_cols=14 Identities=21% Similarity=0.365 Sum_probs=5.0
Q ss_pred CCcccccccceeee
Q psy3356 21 NPLVFIPACVFRFS 34 (180)
Q Consensus 21 ~~~~~c~~C~~~~~ 34 (180)
...+.|+.|...|-
T Consensus 19 ~~~y~C~~C~~~FC 32 (51)
T PF07975_consen 19 SSRYRCPKCKNHFC 32 (51)
T ss_dssp -EEE--TTTT--B-
T ss_pred CCeEECCCCCCccc
Confidence 34556777766665
No 122
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=65.70 E-value=9.4 Score=28.23 Aligned_cols=83 Identities=20% Similarity=0.423 Sum_probs=44.8
Q ss_pred CcccccchhhccChHHHHHHHHhccC-----CCcCC--CcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccC
Q psy3356 66 PFECDVCGKRFAQKSTLNTHKRVHIS-----YLHVK--DKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFS 138 (180)
Q Consensus 66 ~~~C~~C~~~f~~~~~l~~H~~~~~~-----~~~~~--~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 138 (180)
|..|+.|.-.......|.+-....-+ +...+ -+.-.|-.|.-.|.....- ..-..+....|.|+.|+..|-
T Consensus 322 Pi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~--~~~~~~ss~rY~Ce~CK~~FC 399 (421)
T COG5151 322 PISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVS--PFDESTSSGRYQCELCKSTFC 399 (421)
T ss_pred CccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCC--cccccccccceechhhhhhhh
Confidence 45677777665544444433221100 00011 1223466676666543221 011223345699999999999
Q ss_pred ChHHHHHHHHHc
Q psy3356 139 QKSACNTHKRTH 150 (180)
Q Consensus 139 ~~~~l~~H~~~h 150 (180)
..-+...|-..|
T Consensus 400 ~dCdvfiHe~Lh 411 (421)
T COG5151 400 SDCDVFIHETLH 411 (421)
T ss_pred hhhHHHHHHHHh
Confidence 888888887764
No 123
>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=65.01 E-value=2.9 Score=19.24 Aligned_cols=9 Identities=33% Similarity=0.844 Sum_probs=4.6
Q ss_pred ceecccccc
Q psy3356 127 PYECEICGK 135 (180)
Q Consensus 127 ~~~C~~C~~ 135 (180)
.+.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 355555543
No 124
>PF15269 zf-C2H2_7: Zinc-finger
Probab=63.66 E-value=6.2 Score=19.93 Aligned_cols=24 Identities=33% Similarity=0.545 Sum_probs=18.5
Q ss_pred ceeccccCcccCChhhHHHHHhhc
Q psy3356 99 PYHCTECEATFSWKQNLEVHMRTH 122 (180)
Q Consensus 99 ~~~C~~C~~~~~~~~~l~~H~~~h 122 (180)
.|.|-+|.++...++.|..|++..
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 477888888888888888887754
No 125
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.13 E-value=3.2 Score=21.56 Aligned_cols=12 Identities=8% Similarity=-0.078 Sum_probs=8.2
Q ss_pred cccccccceeee
Q psy3356 23 LVFIPACVFRFS 34 (180)
Q Consensus 23 ~~~c~~C~~~~~ 34 (180)
.|.|..||..+.
T Consensus 6 ~Y~C~~Cg~~~~ 17 (49)
T COG1996 6 EYKCARCGREVE 17 (49)
T ss_pred EEEhhhcCCeee
Confidence 457777777775
No 126
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=62.66 E-value=1.3 Score=21.92 Aligned_cols=8 Identities=50% Similarity=1.410 Sum_probs=3.2
Q ss_pred eecccccc
Q psy3356 128 YECEICGK 135 (180)
Q Consensus 128 ~~C~~C~~ 135 (180)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (40)
T smart00440 29 YVCTKCGH 36 (40)
T ss_pred EEeCCCCC
Confidence 34444433
No 127
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=61.89 E-value=4.2 Score=19.95 Aligned_cols=11 Identities=36% Similarity=1.111 Sum_probs=8.4
Q ss_pred CcccCCCcccC
Q psy3356 163 PFHCPACEGMF 173 (180)
Q Consensus 163 ~~~C~~C~~~F 173 (180)
||.|..|++.|
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 67788888776
No 128
>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=61.83 E-value=5.6 Score=21.17 Aligned_cols=11 Identities=18% Similarity=0.301 Sum_probs=6.8
Q ss_pred ccccccceeee
Q psy3356 24 VFIPACVFRFS 34 (180)
Q Consensus 24 ~~c~~C~~~~~ 34 (180)
+.||.||..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 35666666655
No 129
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=61.71 E-value=7.8 Score=32.48 Aligned_cols=13 Identities=31% Similarity=0.797 Sum_probs=9.0
Q ss_pred CCCCcccCCCccc
Q psy3356 160 KDRPFHCPACEGM 172 (180)
Q Consensus 160 ~~~~~~C~~C~~~ 172 (180)
...|..|+.||..
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 4556778888764
No 130
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=61.59 E-value=4.3 Score=29.93 Aligned_cols=99 Identities=15% Similarity=0.216 Sum_probs=57.4
Q ss_pred eeecccCCcccccccceeeeecCCeeEeeeecccCCCchhhhHhh----------hcCC--CCCcccccchhhccChHHH
Q psy3356 15 DINIQKNPLVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMR----------THTG--ERPFECDVCGKRFAQKSTL 82 (180)
Q Consensus 15 ~~~~~~~~~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~----------~h~~--~~~~~C~~C~~~f~~~~~l 82 (180)
|....... |.||.|....- .-...|.+|+...-....|.+-+. ...+ .+.-.|-.|+-.|+....-
T Consensus 301 Hs~~~~gG-y~CP~CktkVC-sLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~ 378 (421)
T COG5151 301 HSEVKGGG-YECPVCKTKVC-SLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVS 378 (421)
T ss_pred eeeeccCc-eeCCcccceee-cCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCC
Confidence 34444444 48888866654 445677788765433333333211 1111 1223477788777654210
Q ss_pred HHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhc
Q psy3356 83 NTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTH 122 (180)
Q Consensus 83 ~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h 122 (180)
..- .......|.|+.|...|-..-+.-.|...|
T Consensus 379 ~~~-------~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 379 PFD-------ESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccc-------ccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 000 013456799999999999998988888776
No 131
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=60.97 E-value=10 Score=18.76 Aligned_cols=12 Identities=25% Similarity=0.517 Sum_probs=9.7
Q ss_pred cccccccceeee
Q psy3356 23 LVFIPACVFRFS 34 (180)
Q Consensus 23 ~~~c~~C~~~~~ 34 (180)
..+|+.||..+.
T Consensus 13 ~~~C~~CgM~Y~ 24 (41)
T PF13878_consen 13 ATTCPTCGMLYS 24 (41)
T ss_pred CcCCCCCCCEEC
Confidence 458999998887
No 132
>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=60.40 E-value=4.4 Score=18.96 Aligned_cols=8 Identities=38% Similarity=1.041 Sum_probs=3.5
Q ss_pred eeccccCc
Q psy3356 100 YHCTECEA 107 (180)
Q Consensus 100 ~~C~~C~~ 107 (180)
..|+.||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 44555543
No 133
>KOG3408|consensus
Probab=58.18 E-value=7.4 Score=24.42 Aligned_cols=27 Identities=30% Similarity=0.550 Sum_probs=22.2
Q ss_pred CCCceeccccccccCChHHHHHHHHHc
Q psy3356 124 GERPYECEICGKRFSQKSACNTHKRTH 150 (180)
Q Consensus 124 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 150 (180)
|...|-|..|.+.|.+...|..|.++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 444588999999999999999998753
No 134
>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=57.55 E-value=8.8 Score=26.91 Aligned_cols=27 Identities=26% Similarity=0.538 Sum_probs=21.3
Q ss_pred CCceeccccccccCChHHHHHHHHHcC
Q psy3356 125 ERPYECEICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 151 (180)
+.-|.|+.|++.|....=..+|+...|
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 445999999999999999999998766
No 135
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.21 E-value=5.7 Score=25.42 Aligned_cols=16 Identities=25% Similarity=0.831 Sum_probs=11.2
Q ss_pred CCCcccCCCcccCCCc
Q psy3356 161 DRPFHCPACEGMFTTK 176 (180)
Q Consensus 161 ~~~~~C~~C~~~F~~~ 176 (180)
...|.|+.|++.|+..
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4557788887777654
No 136
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.85 E-value=4.9 Score=25.94 Aligned_cols=11 Identities=27% Similarity=0.875 Sum_probs=5.4
Q ss_pred eeccccCcccC
Q psy3356 100 YHCTECEATFS 110 (180)
Q Consensus 100 ~~C~~C~~~~~ 110 (180)
+.|..||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 45555554443
No 137
>KOG2593|consensus
Probab=55.00 E-value=16 Score=28.36 Aligned_cols=37 Identities=16% Similarity=0.547 Sum_probs=21.9
Q ss_pred CCCCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCc
Q psy3356 63 GERPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEA 107 (180)
Q Consensus 63 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~ 107 (180)
...-|.|+.|++.|.... .-+... .....+.|..|+-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Le---a~~L~~-----~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLE---ALQLLD-----NETGEFHCENCGG 161 (436)
T ss_pred ccccccCCccccchhhhH---HHHhhc-----ccCceEEEecCCC
Confidence 345588888888875533 333322 2345677887763
No 138
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=54.47 E-value=12 Score=19.31 Aligned_cols=21 Identities=38% Similarity=0.792 Sum_probs=13.3
Q ss_pred eeccccccccCCh-----HHHHHHHH
Q psy3356 128 YECEICGKRFSQK-----SACNTHKR 148 (180)
Q Consensus 128 ~~C~~C~~~f~~~-----~~l~~H~~ 148 (180)
-.|..|++.+... +.|.+|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4566666665443 57777776
No 139
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=53.54 E-value=5.1 Score=20.01 Aligned_cols=12 Identities=42% Similarity=0.916 Sum_probs=9.0
Q ss_pred ccCCCcccCCCc
Q psy3356 165 HCPACEGMFTTK 176 (180)
Q Consensus 165 ~C~~C~~~F~~~ 176 (180)
.|.+|++.|+.+
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 488888888754
No 140
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=53.52 E-value=1.8 Score=22.35 Aligned_cols=23 Identities=9% Similarity=-0.039 Sum_probs=9.7
Q ss_pred ccccceeeeecCCeeEeeeeccc
Q psy3356 26 IPACVFRFSVENEKRFFFFSFLF 48 (180)
Q Consensus 26 c~~C~~~~~~~~~~~~~~C~~~~ 48 (180)
|.+|+..........|..|+..|
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEE
T ss_pred CcCCCCcCCCCCeEEcCCCChhh
Confidence 44555533333334444444433
No 141
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=53.10 E-value=10 Score=18.64 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=7.4
Q ss_pred eeccccccccCChHHH
Q psy3356 128 YECEICGKRFSQKSAC 143 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l 143 (180)
+.|+.|+-.+.+...|
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 3455555444444443
No 142
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=52.34 E-value=2.8 Score=18.95 Aligned_cols=19 Identities=26% Similarity=0.726 Sum_probs=10.1
Q ss_pred eeccccccccCChHHHHHHH
Q psy3356 128 YECEICGKRFSQKSACNTHK 147 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~ 147 (180)
|.|..|++.| .......|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 4577777777 444444443
No 143
>KOG2907|consensus
Probab=51.94 E-value=9.9 Score=23.54 Aligned_cols=12 Identities=17% Similarity=0.252 Sum_probs=8.2
Q ss_pred cccccceeeeec
Q psy3356 25 FIPACVFRFSVE 36 (180)
Q Consensus 25 ~c~~C~~~~~~~ 36 (180)
.|++||......
T Consensus 9 FC~~CG~ll~~~ 20 (116)
T KOG2907|consen 9 FCSDCGSLLEEP 20 (116)
T ss_pred hhhhhhhhcccc
Confidence 777887776633
No 144
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.45 E-value=5.3 Score=17.51 Aligned_cols=8 Identities=38% Similarity=0.812 Sum_probs=5.5
Q ss_pred ccccccee
Q psy3356 25 FIPACVFR 32 (180)
Q Consensus 25 ~c~~C~~~ 32 (180)
.|+.||..
T Consensus 4 ~Cp~Cg~~ 11 (26)
T PF13248_consen 4 FCPNCGAE 11 (26)
T ss_pred CCcccCCc
Confidence 67777773
No 145
>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=50.57 E-value=3.9 Score=20.46 Aligned_cols=12 Identities=42% Similarity=1.063 Sum_probs=6.2
Q ss_pred CCcccCCCcccC
Q psy3356 162 RPFHCPACEGMF 173 (180)
Q Consensus 162 ~~~~C~~C~~~F 173 (180)
-|+.|+.|++.|
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 356677776665
No 146
>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=50.54 E-value=14 Score=23.78 Aligned_cols=27 Identities=33% Similarity=0.544 Sum_probs=15.5
Q ss_pred CcceeccccCcccCChhhHHHHHhhcCCCC
Q psy3356 97 DKPYHCTECEATFSWKQNLEVHMRTHTGER 126 (180)
Q Consensus 97 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~ 126 (180)
.....|-.||+.|... .+|+..|+|-.
T Consensus 70 ~d~i~clecGk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EESBH---HHHHHHTT-S-
T ss_pred cCeeEEccCCcccchH---HHHHHHccCCC
Confidence 3347888899888653 88888887643
No 147
>KOG4167|consensus
Probab=49.98 E-value=4.2 Score=33.61 Aligned_cols=25 Identities=36% Similarity=0.679 Sum_probs=22.8
Q ss_pred ceeccccccccCChHHHHHHHHHcC
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~ 151 (180)
.|.|.+|++.|..-.++..||+.|-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999874
No 148
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=49.72 E-value=9 Score=22.71 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=7.6
Q ss_pred ceeccccCcccCC
Q psy3356 99 PYHCTECEATFSW 111 (180)
Q Consensus 99 ~~~C~~C~~~~~~ 111 (180)
|-.|..||+.|.+
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4456666666655
No 149
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=49.63 E-value=5.4 Score=23.70 Aligned_cols=33 Identities=18% Similarity=0.052 Sum_probs=18.5
Q ss_pred eecccCCcccccccceeee---ecCCeeEeeeeccc
Q psy3356 16 INIQKNPLVFIPACVFRFS---VENEKRFFFFSFLF 48 (180)
Q Consensus 16 ~~~~~~~~~~c~~C~~~~~---~~~~~~~~~C~~~~ 48 (180)
|+......+.||.|++.-- ..+.|.|.-|++.|
T Consensus 29 ie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 29 IEISQHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred HHHHHhCCccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 4444555669999975432 11245555555554
No 150
>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=49.46 E-value=19 Score=17.28 Aligned_cols=10 Identities=20% Similarity=0.487 Sum_probs=7.3
Q ss_pred cccccceeee
Q psy3356 25 FIPACVFRFS 34 (180)
Q Consensus 25 ~c~~C~~~~~ 34 (180)
+|+.||..|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 6777777776
No 151
>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=48.38 E-value=5.6 Score=20.97 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=4.0
Q ss_pred ccCCCcccCC
Q psy3356 165 HCPACEGMFT 174 (180)
Q Consensus 165 ~C~~C~~~F~ 174 (180)
.||+|++.|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 5777776654
No 152
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=47.94 E-value=15 Score=19.09 Aligned_cols=14 Identities=36% Similarity=0.949 Sum_probs=7.2
Q ss_pred cceeccccCcccCC
Q psy3356 98 KPYHCTECEATFSW 111 (180)
Q Consensus 98 ~~~~C~~C~~~~~~ 111 (180)
+.+.|..||..|..
T Consensus 3 k~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 3 KTLTCKDCGAEFVF 16 (49)
T ss_pred eeEEcccCCCeEEE
Confidence 34555555555443
No 153
>KOG1280|consensus
Probab=47.93 E-value=23 Score=26.70 Aligned_cols=27 Identities=19% Similarity=0.353 Sum_probs=19.5
Q ss_pred CCceeccccccccCChHHHHHHHHHcC
Q psy3356 125 ERPYECEICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 151 (180)
...|.|++|+..=.+...|..|....|
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcC
Confidence 345788888877667777888877644
No 154
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.12 E-value=14 Score=22.77 Aligned_cols=27 Identities=19% Similarity=0.220 Sum_probs=19.1
Q ss_pred eeccccCcccCChhhHHHHHhhcCCCCceecccccccc
Q psy3356 100 YHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRF 137 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 137 (180)
..|+.|++.|- -....|..|+.||++|
T Consensus 10 ridPetg~KFY-----------DLNrdPiVsPytG~s~ 36 (129)
T COG4530 10 RIDPETGKKFY-----------DLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccCccccchhh-----------ccCCCccccCcccccc
Confidence 45777777663 3456778888888887
No 156
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.60 E-value=19 Score=19.68 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=10.5
Q ss_pred ccCCcccccccceeee
Q psy3356 19 QKNPLVFIPACVFRFS 34 (180)
Q Consensus 19 ~~~~~~~c~~C~~~~~ 34 (180)
..+..+.||+|+..|.
T Consensus 44 g~~gev~CPYC~t~y~ 59 (62)
T COG4391 44 GDEGEVVCPYCSTRYR 59 (62)
T ss_pred CCCCcEecCccccEEE
Confidence 3444457888887775
No 157
>KOG0717|consensus
Probab=45.40 E-value=15 Score=28.89 Aligned_cols=22 Identities=23% Similarity=0.638 Sum_probs=19.9
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy3356 128 YECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 128 ~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
+.|.+|.+.|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999764
No 158
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=45.40 E-value=15 Score=28.61 Aligned_cols=13 Identities=23% Similarity=0.560 Sum_probs=8.1
Q ss_pred CcccCCCcccCCC
Q psy3356 163 PFHCPACEGMFTT 175 (180)
Q Consensus 163 ~~~C~~C~~~F~~ 175 (180)
-|+|+.|+..+..
T Consensus 367 g~rC~kCg~~~~~ 379 (421)
T COG1571 367 GFRCKKCGTRARE 379 (421)
T ss_pred CcccccccccCCc
Confidence 4666666666554
No 159
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=45.32 E-value=18 Score=18.97 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=4.3
Q ss_pred eecccccccc
Q psy3356 128 YECEICGKRF 137 (180)
Q Consensus 128 ~~C~~C~~~f 137 (180)
+.|..||..|
T Consensus 19 ~~Cr~Cg~~~ 28 (57)
T cd00065 19 HHCRNCGRIF 28 (57)
T ss_pred cccCcCcCCc
Confidence 3444444443
No 160
>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=45.27 E-value=28 Score=17.24 Aligned_cols=11 Identities=36% Similarity=0.646 Sum_probs=9.1
Q ss_pred cccccccceee
Q psy3356 23 LVFIPACVFRF 33 (180)
Q Consensus 23 ~~~c~~C~~~~ 33 (180)
...|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45999999887
No 161
>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=45.08 E-value=6.1 Score=23.52 Aligned_cols=33 Identities=18% Similarity=0.078 Sum_probs=19.0
Q ss_pred eecccCCcccccccceeee---ecCCeeEeeeeccc
Q psy3356 16 INIQKNPLVFIPACVFRFS---VENEKRFFFFSFLF 48 (180)
Q Consensus 16 ~~~~~~~~~~c~~C~~~~~---~~~~~~~~~C~~~~ 48 (180)
|+......+.||.|++.-- ....|.|.-|++.|
T Consensus 28 ie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 28 IEIQQKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred HHHHHhcCccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 3444555669999975432 22346666666655
No 162
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=45.07 E-value=12 Score=19.34 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=6.9
Q ss_pred Ccccccchhhcc
Q psy3356 66 PFECDVCGKRFA 77 (180)
Q Consensus 66 ~~~C~~C~~~f~ 77 (180)
.+.|+.|+..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 456666665543
No 163
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=45.04 E-value=0.71 Score=22.70 Aligned_cols=8 Identities=50% Similarity=1.261 Sum_probs=3.5
Q ss_pred eecccccc
Q psy3356 128 YECEICGK 135 (180)
Q Consensus 128 ~~C~~C~~ 135 (180)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (39)
T PF01096_consen 29 YVCCNCGH 36 (39)
T ss_dssp EEESSSTE
T ss_pred EEeCCCCC
Confidence 44444443
No 164
>PF12773 DZR: Double zinc ribbon
Probab=44.67 E-value=8.7 Score=19.69 Aligned_cols=7 Identities=43% Similarity=1.122 Sum_probs=3.2
Q ss_pred ccccchh
Q psy3356 68 ECDVCGK 74 (180)
Q Consensus 68 ~C~~C~~ 74 (180)
.|+.|+.
T Consensus 31 ~C~~Cg~ 37 (50)
T PF12773_consen 31 ICPNCGA 37 (50)
T ss_pred CCcCCcC
Confidence 3444444
No 165
>KOG2817|consensus
Probab=43.90 E-value=21 Score=27.41 Aligned_cols=71 Identities=15% Similarity=0.282 Sum_probs=43.5
Q ss_pred CCcccccCCceeeeeecc----cCCcccccccceeeeecCCeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhh
Q psy3356 2 CSSKWITSPSVTFDINIQ----KNPLVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKR 75 (180)
Q Consensus 2 C~~~f~~~~~~~~~~~~~----~~~~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 75 (180)
|...|++..+|-..++.. ..+.+.||+=.....++|.---..||-+.. +.+|.+-.+ .+...|+||+|...
T Consensus 309 ~~~~W~~~deLPveIeL~~~~~fHSvF~CPVlKeqtsdeNPPm~L~CGHVIS-kdAlnrLS~--ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 309 KHGEWNTKDELPVEIELGKEYHFHSVFICPVLKEQTSDENPPMMLICGHVIS-KDALNRLSK--NGSQSFKCPYCPVE 383 (394)
T ss_pred hccCccccccCccceeccccccccceeecccchhhccCCCCCeeeeccceec-HHHHHHHhh--CCCeeeeCCCCCcc
Confidence 456788888887777754 345678998877777666555556766552 233333222 22335778887764
No 166
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=43.35 E-value=36 Score=27.05 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=25.2
Q ss_pred HhhcCCCCceeccccccccCChHHHHHHHHHcC
Q psy3356 119 MRTHTGERPYECEICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 119 ~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 151 (180)
.+.+...+-+.|+.|.+.|.+...+..|+...|
T Consensus 49 ak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 49 AKENKSWRFWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred HHhcCceeEeeCCcccceeCCHHHHHHHHHHhh
Confidence 344556677888888888888888888887654
No 167
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.29 E-value=8.9 Score=16.32 Aligned_cols=9 Identities=22% Similarity=0.508 Sum_probs=4.7
Q ss_pred ccccceeee
Q psy3356 26 IPACVFRFS 34 (180)
Q Consensus 26 c~~C~~~~~ 34 (180)
|+.||....
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 555555544
No 168
>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=42.98 E-value=19 Score=19.88 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=7.1
Q ss_pred CCceecccccccc
Q psy3356 125 ERPYECEICGKRF 137 (180)
Q Consensus 125 ~~~~~C~~C~~~f 137 (180)
.+.|.|+.||..+
T Consensus 44 ~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 44 GRVFTCPNCGFEM 56 (69)
T ss_pred cceEEcCCCCCEE
Confidence 3446666666553
No 169
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.95 E-value=16 Score=32.62 Aligned_cols=37 Identities=19% Similarity=0.199 Sum_probs=25.3
Q ss_pred cccccccceeeeecCCeeEeeeecccCCCchhhhHhhhcCCCCCcccccchhhcc
Q psy3356 23 LVFIPACVFRFSVENEKRFFFFSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFA 77 (180)
Q Consensus 23 ~~~c~~C~~~~~~~~~~~~~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 77 (180)
...||.||.... ...|..||.... .+|.|+.|+....
T Consensus 667 ~rkCPkCG~~t~---~~fCP~CGs~te---------------~vy~CPsCGaev~ 703 (1337)
T PRK14714 667 RRRCPSCGTETY---ENRCPDCGTHTE---------------PVYVCPDCGAEVP 703 (1337)
T ss_pred EEECCCCCCccc---cccCcccCCcCC---------------CceeCccCCCccC
Confidence 469999998643 247777876642 2467888888643
No 170
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.74 E-value=13 Score=29.76 Aligned_cols=18 Identities=6% Similarity=0.150 Sum_probs=12.0
Q ss_pred ecccCCcccccccceeee
Q psy3356 17 NIQKNPLVFIPACVFRFS 34 (180)
Q Consensus 17 ~~~~~~~~~c~~C~~~~~ 34 (180)
+....+...|..||+...
T Consensus 207 rrGya~~~~C~~Cg~~~~ 224 (505)
T TIGR00595 207 RRGYSKNLLCRSCGYILC 224 (505)
T ss_pred CCcCCCeeEhhhCcCccC
Confidence 344556667888877765
No 171
>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=40.71 E-value=4.4 Score=24.06 Aligned_cols=31 Identities=13% Similarity=-0.023 Sum_probs=16.7
Q ss_pred cccCCcccccccceeee---ecCCeeEeeeeccc
Q psy3356 18 IQKNPLVFIPACVFRFS---VENEKRFFFFSFLF 48 (180)
Q Consensus 18 ~~~~~~~~c~~C~~~~~---~~~~~~~~~C~~~~ 48 (180)
......+.||.||+.-- ..+.|.|.-|++.|
T Consensus 30 ~~q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 30 ISQHAKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp HHHHS-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred HHHhCCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 33444558999987654 12245555555544
No 172
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=40.53 E-value=5.5 Score=22.47 Aligned_cols=9 Identities=33% Similarity=1.069 Sum_probs=4.5
Q ss_pred CcccCCCcc
Q psy3356 163 PFHCPACEG 171 (180)
Q Consensus 163 ~~~C~~C~~ 171 (180)
.|.|+.|+.
T Consensus 61 ~~~C~~C~~ 69 (71)
T PF05495_consen 61 DYFCPICGL 69 (71)
T ss_dssp SEEETTTTE
T ss_pred CccCcCcCC
Confidence 355555543
No 173
>PRK12496 hypothetical protein; Provisional
Probab=40.51 E-value=10 Score=25.34 Aligned_cols=26 Identities=4% Similarity=0.024 Sum_probs=16.7
Q ss_pred cccccccceeeeec-CCeeEeeeeccc
Q psy3356 23 LVFIPACVFRFSVE-NEKRFFFFSFLF 48 (180)
Q Consensus 23 ~~~c~~C~~~~~~~-~~~~~~~C~~~~ 48 (180)
.+.|+.|+..|+.. ....|..||...
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChh
Confidence 35799999998743 334566665443
No 174
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=40.18 E-value=8.1 Score=22.98 Aligned_cols=33 Identities=12% Similarity=-0.084 Sum_probs=19.1
Q ss_pred eecccCCcccccccceeee---ecCCeeEeeeeccc
Q psy3356 16 INIQKNPLVFIPACVFRFS---VENEKRFFFFSFLF 48 (180)
Q Consensus 16 ~~~~~~~~~~c~~C~~~~~---~~~~~~~~~C~~~~ 48 (180)
|+......+.||.|++.-- ....|.|.-|++.|
T Consensus 29 ie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 29 IEEKMRAKHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred HHHHHhcCccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 4444555669999965433 22346666666655
No 175
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=39.95 E-value=5.6 Score=32.88 Aligned_cols=75 Identities=15% Similarity=0.293 Sum_probs=46.9
Q ss_pred cccccccceeeeecCCeeEee-------eecccCCCchhhhHhhhcCCCCCcccccchhhccChHHHHHHHHhccCCCcC
Q psy3356 23 LVFIPACVFRFSVENEKRFFF-------FSFLFGPLLVPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRVHISYLHV 95 (180)
Q Consensus 23 ~~~c~~C~~~~~~~~~~~~~~-------C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 95 (180)
..+|+.|....-+.+..++.+ ||=.|+-...|---...-+-...-.|+.|.+.|....+=+-|
T Consensus 101 ~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfH---------- 170 (750)
T COG0068 101 AATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFH---------- 170 (750)
T ss_pred hhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccc----------
Confidence 348999988887777666553 777776555544432222212223499999988776543222
Q ss_pred CCcceeccccCcc
Q psy3356 96 KDKPYHCTECEAT 108 (180)
Q Consensus 96 ~~~~~~C~~C~~~ 108 (180)
.++..|+.||-.
T Consensus 171 -AQp~aCp~CGP~ 182 (750)
T COG0068 171 -AQPIACPKCGPH 182 (750)
T ss_pred -cccccCcccCCC
Confidence 456789999853
No 176
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.87 E-value=14 Score=19.65 Aligned_cols=14 Identities=29% Similarity=0.812 Sum_probs=9.0
Q ss_pred cccCCCcccCCCcc
Q psy3356 164 FHCPACEGMFTTKQ 177 (180)
Q Consensus 164 ~~C~~C~~~F~~~~ 177 (180)
..|+.|++.|....
T Consensus 6 ~~C~~Cg~~~~~~d 19 (54)
T PF14446_consen 6 CKCPVCGKKFKDGD 19 (54)
T ss_pred ccChhhCCcccCCC
Confidence 35777777776443
No 177
>PF14369 zf-RING_3: zinc-finger
Probab=39.83 E-value=31 Score=16.39 Aligned_cols=13 Identities=31% Similarity=0.327 Sum_probs=9.4
Q ss_pred Ccccccccceeee
Q psy3356 22 PLVFIPACVFRFS 34 (180)
Q Consensus 22 ~~~~c~~C~~~~~ 34 (180)
....||.|+..|-
T Consensus 20 ~~~~CP~C~~gFv 32 (35)
T PF14369_consen 20 SDVACPRCHGGFV 32 (35)
T ss_pred CCcCCcCCCCcEe
Confidence 3336999988875
No 178
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=39.50 E-value=8.8 Score=18.85 Aligned_cols=8 Identities=25% Similarity=0.854 Sum_probs=3.3
Q ss_pred CcccCCCc
Q psy3356 163 PFHCPACE 170 (180)
Q Consensus 163 ~~~C~~C~ 170 (180)
.+.|+.|+
T Consensus 24 ~w~C~~C~ 31 (40)
T PF04810_consen 24 TWICNFCG 31 (40)
T ss_dssp EEEETTT-
T ss_pred EEECcCCC
Confidence 34444444
No 179
>COG1773 Rubredoxin [Energy production and conversion]
Probab=39.44 E-value=12 Score=19.99 Aligned_cols=12 Identities=17% Similarity=0.797 Sum_probs=7.6
Q ss_pred CcccCCCcccCC
Q psy3356 163 PFHCPACEGMFT 174 (180)
Q Consensus 163 ~~~C~~C~~~F~ 174 (180)
.|+|.+||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 466777776554
No 180
>KOG4377|consensus
Probab=39.35 E-value=13 Score=28.61 Aligned_cols=104 Identities=21% Similarity=0.392 Sum_probs=61.8
Q ss_pred eeecccCCCchhhhHhhhcCCCC------------Ccccc--cchhhccChHHHHHHHHhccCCCcC--CCcceeccccC
Q psy3356 43 FFSFLFGPLLVPQIHMRTHTGER------------PFECD--VCGKRFAQKSTLNTHKRVHISYLHV--KDKPYHCTECE 106 (180)
Q Consensus 43 ~C~~~~~~~~~l~~H~~~h~~~~------------~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~--~~~~~~C~~C~ 106 (180)
.|+..+.++..+.+|...|.... .|.|. .|.+ +..++..|-..|-..... ....+.|..++
T Consensus 278 ~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~GfrrthfhC~r~g 354 (480)
T KOG4377|consen 278 YCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHFHCQRIG 354 (480)
T ss_pred cccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceecceeEEeccC
Confidence 37777777899999988775422 24564 4777 334555565544221112 22457888877
Q ss_pred cccCChhhHHHHHhhcCCC----------------------------Cceecc--ccccccCChHHHHHHHHHcC
Q psy3356 107 ATFSWKQNLEVHMRTHTGE----------------------------RPYECE--ICGKRFSQKSACNTHKRTHI 151 (180)
Q Consensus 107 ~~~~~~~~l~~H~~~h~~~----------------------------~~~~C~--~C~~~f~~~~~l~~H~~~h~ 151 (180)
=++..+ ...|...|... ..|.|. .|+..+.+.+++..|.+.|.
T Consensus 355 CTdtfK--~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkrkhe 427 (480)
T KOG4377|consen 355 CTDTFK--DSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASHKRKHE 427 (480)
T ss_pred Cccccc--cccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhhhhhhh
Confidence 222222 33444433221 115563 48999999999999998875
No 181
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.29 E-value=26 Score=30.59 Aligned_cols=21 Identities=19% Similarity=0.080 Sum_probs=14.2
Q ss_pred ccccccceeeeecCCeeEeeeecc
Q psy3356 24 VFIPACVFRFSVENEKRFFFFSFL 47 (180)
Q Consensus 24 ~~c~~C~~~~~~~~~~~~~~C~~~ 47 (180)
..|+.||... ....|..||..
T Consensus 627 RfCpsCG~~t---~~frCP~CG~~ 647 (1121)
T PRK04023 627 RKCPSCGKET---FYRRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCcC---CcccCCCCCCC
Confidence 3888888774 44666667655
No 182
>KOG1842|consensus
Probab=38.66 E-value=34 Score=26.82 Aligned_cols=26 Identities=15% Similarity=0.340 Sum_probs=16.4
Q ss_pred cceeccccCcccCChhhHHHHHhhcC
Q psy3356 98 KPYHCTECEATFSWKQNLEVHMRTHT 123 (180)
Q Consensus 98 ~~~~C~~C~~~~~~~~~l~~H~~~h~ 123 (180)
..+.||.|..-|.....|..|...-+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhc
Confidence 34667777777776677777665433
No 183
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=38.55 E-value=9.4 Score=23.80 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=3.9
Q ss_pred cccccchhh
Q psy3356 67 FECDVCGKR 75 (180)
Q Consensus 67 ~~C~~C~~~ 75 (180)
+.|.-|+..
T Consensus 23 l~C~kCgye 31 (113)
T COG1594 23 LVCRKCGYE 31 (113)
T ss_pred EECCCCCcc
Confidence 444444444
No 184
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=37.91 E-value=14 Score=24.36 Aligned_cols=35 Identities=26% Similarity=0.780 Sum_probs=22.4
Q ss_pred CCceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCccc
Q psy3356 125 ERPYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGM 172 (180)
Q Consensus 125 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~ 172 (180)
.-+|.|. |+..+.+..- |-. +-.|+ .|.|..|+..
T Consensus 115 ~~~Y~C~-C~q~~l~~RR---hn~--------~~~g~-~YrC~~C~gk 149 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIRR---HNT--------VRRGE-VYRCGKCGGK 149 (156)
T ss_pred ceeEEee-cCCccchhhh---ccc--------ccccc-eEEeccCCce
Confidence 4468999 9988655432 211 23456 7999999854
No 185
>PRK14873 primosome assembly protein PriA; Provisional
Probab=37.68 E-value=16 Score=30.38 Aligned_cols=27 Identities=7% Similarity=-0.198 Sum_probs=18.2
Q ss_pred eeecccCCcccccccceeeeecCCeeEeeeecc
Q psy3356 15 DINIQKNPLVFIPACVFRFSVENEKRFFFFSFL 47 (180)
Q Consensus 15 ~~~~~~~~~~~c~~C~~~~~~~~~~~~~~C~~~ 47 (180)
..+....+...|..||+... |..|+..
T Consensus 375 lnRrGyap~l~C~~Cg~~~~------C~~C~~~ 401 (665)
T PRK14873 375 VPRRGYVPSLACARCRTPAR------CRHCTGP 401 (665)
T ss_pred ecCCCCCCeeEhhhCcCeeE------CCCCCCc
Confidence 34455667779999988876 5555543
No 186
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=37.41 E-value=23 Score=16.66 Aligned_cols=12 Identities=17% Similarity=0.105 Sum_probs=6.1
Q ss_pred Ccccccccceee
Q psy3356 22 PLVFIPACVFRF 33 (180)
Q Consensus 22 ~~~~c~~C~~~~ 33 (180)
.++.|+.|+..|
T Consensus 20 ~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 20 DYEVCIFCGSSF 31 (33)
T ss_pred CeEEcccCCcEe
Confidence 334555555554
No 187
>PRK05580 primosome assembly protein PriA; Validated
Probab=36.39 E-value=20 Score=30.01 Aligned_cols=17 Identities=12% Similarity=0.257 Sum_probs=11.2
Q ss_pred cccCCcccccccceeee
Q psy3356 18 IQKNPLVFIPACVFRFS 34 (180)
Q Consensus 18 ~~~~~~~~c~~C~~~~~ 34 (180)
....+...|..||+...
T Consensus 376 rGy~~~~~C~~Cg~~~~ 392 (679)
T PRK05580 376 RGYAPFLLCRDCGWVAE 392 (679)
T ss_pred CCCCCceEhhhCcCccC
Confidence 44556667888877654
No 188
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=36.12 E-value=26 Score=16.86 Aligned_cols=13 Identities=31% Similarity=0.659 Sum_probs=7.5
Q ss_pred ccCCCcccCCCcc
Q psy3356 165 HCPACEGMFTTKQ 177 (180)
Q Consensus 165 ~C~~C~~~F~~~~ 177 (180)
.|+.|+++|-..+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 5777887776544
No 189
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=36.09 E-value=8.9 Score=25.16 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=6.3
Q ss_pred eccccCcccCCh
Q psy3356 101 HCTECEATFSWK 112 (180)
Q Consensus 101 ~C~~C~~~~~~~ 112 (180)
.|+.|+..|++.
T Consensus 30 eC~~C~~RFTTf 41 (156)
T COG1327 30 ECLECGERFTTF 41 (156)
T ss_pred cccccccccchh
Confidence 455555555543
No 190
>KOG2636|consensus
Probab=36.03 E-value=32 Score=26.99 Aligned_cols=29 Identities=31% Similarity=0.657 Sum_probs=23.9
Q ss_pred hhcCCCCceeccccc-cccCChHHHHHHHH
Q psy3356 120 RTHTGERPYECEICG-KRFSQKSACNTHKR 148 (180)
Q Consensus 120 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 148 (180)
+.|.-...|.|.+|| +++..+..+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 356666779999999 88999999999975
No 191
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=36.02 E-value=15 Score=17.73 Aligned_cols=11 Identities=18% Similarity=0.791 Sum_probs=5.5
Q ss_pred CCcccCCCccc
Q psy3356 162 RPFHCPACEGM 172 (180)
Q Consensus 162 ~~~~C~~C~~~ 172 (180)
..|+|.+||.-
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 34888888853
No 192
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=35.68 E-value=52 Score=22.40 Aligned_cols=8 Identities=50% Similarity=1.468 Sum_probs=4.1
Q ss_pred cccCCCcc
Q psy3356 164 FHCPACEG 171 (180)
Q Consensus 164 ~~C~~C~~ 171 (180)
|.||.||.
T Consensus 133 F~Cp~Cg~ 140 (176)
T COG1675 133 FTCPKCGE 140 (176)
T ss_pred CCCCCCCc
Confidence 45555553
No 193
>KOG4167|consensus
Probab=35.63 E-value=13 Score=31.03 Aligned_cols=26 Identities=35% Similarity=0.645 Sum_probs=23.2
Q ss_pred CCcccccchhhccChHHHHHHHHhcc
Q psy3356 65 RPFECDVCGKRFAQKSTLNTHKRVHI 90 (180)
Q Consensus 65 ~~~~C~~C~~~f~~~~~l~~H~~~~~ 90 (180)
..|.|.+|++.|....++..||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35899999999999999999999884
No 194
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=35.28 E-value=13 Score=23.02 Aligned_cols=28 Identities=14% Similarity=0.008 Sum_probs=16.6
Q ss_pred cCCcccccccceeeeecC-CeeEeeeecc
Q psy3356 20 KNPLVFIPACVFRFSVEN-EKRFFFFSFL 47 (180)
Q Consensus 20 ~~~~~~c~~C~~~~~~~~-~~~~~~C~~~ 47 (180)
+...+.||.|++.....+ ...|.+|+..
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~p 94 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEP 94 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCc
Confidence 334568999998876333 3345555443
No 196
>PHA02998 RNA polymerase subunit; Provisional
Probab=34.83 E-value=8.7 Score=25.93 Aligned_cols=10 Identities=30% Similarity=0.889 Sum_probs=5.3
Q ss_pred cccCCCcccC
Q psy3356 164 FHCPACEGMF 173 (180)
Q Consensus 164 ~~C~~C~~~F 173 (180)
|.|..|+..|
T Consensus 172 YkC~~CG~~w 181 (195)
T PHA02998 172 HACRDCKKHF 181 (195)
T ss_pred EEcCCCCCcc
Confidence 5555555544
No 197
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=34.74 E-value=8.5 Score=25.15 Aligned_cols=14 Identities=29% Similarity=0.655 Sum_probs=7.7
Q ss_pred eeccccCcccCChh
Q psy3356 100 YHCTECEATFSWKQ 113 (180)
Q Consensus 100 ~~C~~C~~~~~~~~ 113 (180)
-.|..|++.|++..
T Consensus 29 ReC~~C~~RFTTyE 42 (147)
T TIGR00244 29 RECLECHERFTTFE 42 (147)
T ss_pred ccCCccCCccceee
Confidence 34666666665543
No 198
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.30 E-value=24 Score=26.32 Aligned_cols=14 Identities=14% Similarity=0.408 Sum_probs=9.6
Q ss_pred CCCcccCCCcccCC
Q psy3356 161 DRPFHCPACEGMFT 174 (180)
Q Consensus 161 ~~~~~C~~C~~~F~ 174 (180)
.+...|..|+.-..
T Consensus 250 ~r~e~C~~C~~YlK 263 (309)
T PRK03564 250 VKAESCGDCGTYLK 263 (309)
T ss_pred eEeeecccccccce
Confidence 45678999986443
No 199
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=34.22 E-value=27 Score=21.57 Aligned_cols=29 Identities=14% Similarity=0.623 Sum_probs=17.0
Q ss_pred eccccCcccCChhhHHHHHhhcCCCCceeccccccccCCh
Q psy3356 101 HCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQK 140 (180)
Q Consensus 101 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 140 (180)
.|+.|+..|.+. ....|.|+.|+..+...
T Consensus 4 ~CP~C~seytY~-----------dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYH-----------DGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEe-----------cCCeeECcccccccccc
Confidence 467776665432 22347777777766544
No 200
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=33.53 E-value=13 Score=19.90 Aligned_cols=15 Identities=27% Similarity=0.837 Sum_probs=10.2
Q ss_pred CCcccccchhhccCh
Q psy3356 65 RPFECDVCGKRFAQK 79 (180)
Q Consensus 65 ~~~~C~~C~~~f~~~ 79 (180)
..|-|..|.......
T Consensus 30 ~tYmC~eC~~RI~~~ 44 (56)
T PF09963_consen 30 HTYMCDECKERIREE 44 (56)
T ss_pred cceeChhHHHHHhHH
Confidence 348888888765443
No 201
>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=33.42 E-value=70 Score=16.05 Aligned_cols=10 Identities=30% Similarity=0.929 Sum_probs=5.2
Q ss_pred CCcccCCCcc
Q psy3356 162 RPFHCPACEG 171 (180)
Q Consensus 162 ~~~~C~~C~~ 171 (180)
..|.|..|.+
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 3455655543
No 202
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=33.31 E-value=18 Score=19.48 Aligned_cols=12 Identities=25% Similarity=0.210 Sum_probs=6.7
Q ss_pred ccccccceeeee
Q psy3356 24 VFIPACVFRFSV 35 (180)
Q Consensus 24 ~~c~~C~~~~~~ 35 (180)
+.||.|++.+.-
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 479999998884
No 203
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=33.28 E-value=20 Score=21.73 Aligned_cols=13 Identities=38% Similarity=1.145 Sum_probs=9.3
Q ss_pred CCcccCCCcccCC
Q psy3356 162 RPFHCPACEGMFT 174 (180)
Q Consensus 162 ~~~~C~~C~~~F~ 174 (180)
+++.|+.||.-|.
T Consensus 78 ~~~rC~eCG~~fk 90 (97)
T cd00924 78 KPKRCPECGHVFK 90 (97)
T ss_pred CceeCCCCCcEEE
Confidence 5777777777664
No 204
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=33.19 E-value=36 Score=28.35 Aligned_cols=23 Identities=17% Similarity=0.258 Sum_probs=15.7
Q ss_pred cccccceeeeecCCeeEeeeeccc
Q psy3356 25 FIPACVFRFSVENEKRFFFFSFLF 48 (180)
Q Consensus 25 ~c~~C~~~~~~~~~~~~~~C~~~~ 48 (180)
.||.||...+ .+..-|..||..+
T Consensus 3 ~Cp~Cg~~n~-~~akFC~~CG~~l 25 (645)
T PRK14559 3 ICPQCQFENP-NNNRFCQKCGTSL 25 (645)
T ss_pred cCCCCCCcCC-CCCccccccCCCC
Confidence 7888888765 4444577777665
No 205
>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=33.01 E-value=37 Score=22.32 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=7.3
Q ss_pred Cceeccccccc
Q psy3356 126 RPYECEICGKR 136 (180)
Q Consensus 126 ~~~~C~~C~~~ 136 (180)
..|.|..||..
T Consensus 111 G~l~C~~Cg~~ 121 (146)
T PF07295_consen 111 GTLVCENCGHE 121 (146)
T ss_pred ceEecccCCCE
Confidence 34777777754
No 206
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=32.93 E-value=16 Score=17.29 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=4.9
Q ss_pred cccccchhh
Q psy3356 67 FECDVCGKR 75 (180)
Q Consensus 67 ~~C~~C~~~ 75 (180)
+.|+.|+..
T Consensus 23 ~vC~~Cg~I 31 (34)
T PF14803_consen 23 LVCPACGFI 31 (34)
T ss_dssp EEETTTTEE
T ss_pred eECCCCCCE
Confidence 556666543
No 207
>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=32.68 E-value=22 Score=16.88 Aligned_cols=12 Identities=25% Similarity=0.697 Sum_probs=3.9
Q ss_pred ccCCCcccCCCc
Q psy3356 165 HCPACEGMFTTK 176 (180)
Q Consensus 165 ~C~~C~~~F~~~ 176 (180)
.|..|++.|.++
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 355555555443
No 208
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.29 E-value=11 Score=26.70 Aligned_cols=9 Identities=33% Similarity=0.622 Sum_probs=6.2
Q ss_pred eeccccccc
Q psy3356 128 YECEICGKR 136 (180)
Q Consensus 128 ~~C~~C~~~ 136 (180)
..||.|..+
T Consensus 63 vvCP~C~yA 71 (267)
T COG1655 63 VVCPICYYA 71 (267)
T ss_pred EEcchhhHH
Confidence 568888753
No 209
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=32.20 E-value=30 Score=24.87 Aligned_cols=60 Identities=20% Similarity=0.486 Sum_probs=31.8
Q ss_pred CCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCChHH
Q psy3356 65 RPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSA 142 (180)
Q Consensus 65 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 142 (180)
..|.|..|+..- .+ +.- ..+....|..|.+.|.-... ..-.|-.-|.|+.|+..|.....
T Consensus 111 rqFaC~~Cd~~W------wR--rvp-----~rKeVSRCr~C~~rYDPVP~-----dkmwG~aef~C~~C~h~F~G~~q 170 (278)
T PF15135_consen 111 RQFACSSCDHMW------WR--RVP-----QRKEVSRCRKCRKRYDPVPC-----DKMWGIAEFHCPKCRHNFRGFAQ 170 (278)
T ss_pred eeeeccccchHH------Hh--ccC-----cccccccccccccccCCCcc-----ccccceeeeecccccccchhhhh
Confidence 567888886531 11 111 23445567777766543221 01122334788888888875543
No 210
>PRK10220 hypothetical protein; Provisional
Probab=31.31 E-value=32 Score=21.23 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=6.8
Q ss_pred ceeccccCcccC
Q psy3356 99 PYHCTECEATFS 110 (180)
Q Consensus 99 ~~~C~~C~~~~~ 110 (180)
.+.|+.|+..+.
T Consensus 20 ~~vCpeC~hEW~ 31 (111)
T PRK10220 20 MYICPECAHEWN 31 (111)
T ss_pred eEECCcccCcCC
Confidence 466666665544
No 211
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=31.21 E-value=24 Score=21.93 Aligned_cols=12 Identities=8% Similarity=0.055 Sum_probs=9.3
Q ss_pred cccccccceeee
Q psy3356 23 LVFIPACVFRFS 34 (180)
Q Consensus 23 ~~~c~~C~~~~~ 34 (180)
...|+.||..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (113)
T PRK12380 70 QAWCWDCSQVVE 81 (113)
T ss_pred EEEcccCCCEEe
Confidence 448888888877
No 212
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=31.17 E-value=34 Score=18.80 Aligned_cols=9 Identities=33% Similarity=0.992 Sum_probs=2.3
Q ss_pred eccccCccc
Q psy3356 101 HCTECEATF 109 (180)
Q Consensus 101 ~C~~C~~~~ 109 (180)
.|..|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 344454444
No 213
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=30.56 E-value=33 Score=27.37 Aligned_cols=17 Identities=12% Similarity=0.337 Sum_probs=10.9
Q ss_pred cCCcccccccceeeeec
Q psy3356 20 KNPLVFIPACVFRFSVE 36 (180)
Q Consensus 20 ~~~~~~c~~C~~~~~~~ 36 (180)
....+.|..||+.+...
T Consensus 422 ~~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCCeEEECCCCeEECCC
Confidence 44556777777777733
No 214
>PRK04351 hypothetical protein; Provisional
Probab=30.48 E-value=25 Score=23.14 Aligned_cols=34 Identities=29% Similarity=0.879 Sum_probs=22.4
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCCCc
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFTTK 176 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~~~ 176 (180)
.|.|..|+..+.+. ++. +...|.|..|+..+...
T Consensus 112 ~Y~C~~Cg~~~~r~------Rr~----------n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 112 LYECQSCGQQYLRK------RRI----------NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEECCCCCCEeeee------eec----------CCCcEEeCCCCcEeeec
Confidence 48998898766432 221 34669999998766443
No 215
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.30 E-value=27 Score=22.75 Aligned_cols=33 Identities=30% Similarity=0.842 Sum_probs=20.9
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCC
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFT 174 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~ 174 (180)
.|.|..|+..+. .+.+ +.....|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~------~~rr---------~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYL------RVRR---------SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCc------eEcc---------ccCcceEEcCCCCCEEE
Confidence 588988987764 2222 22225689999987653
No 216
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=30.01 E-value=27 Score=22.50 Aligned_cols=14 Identities=36% Similarity=0.529 Sum_probs=10.7
Q ss_pred hhhhHhhhcCCCCC
Q psy3356 53 VPQIHMRTHTGERP 66 (180)
Q Consensus 53 ~l~~H~~~h~~~~~ 66 (180)
+|.+|+.+|.+-.|
T Consensus 88 SLKRHL~t~~gmTP 101 (148)
T COG4957 88 SLKRHLTTHYGLTP 101 (148)
T ss_pred HHHHHHhcccCCCH
Confidence 68899999876543
No 217
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=30.00 E-value=18 Score=16.56 Aligned_cols=11 Identities=27% Similarity=0.984 Sum_probs=4.9
Q ss_pred CCcccCCCccc
Q psy3356 162 RPFHCPACEGM 172 (180)
Q Consensus 162 ~~~~C~~C~~~ 172 (180)
..|.|+.|+..
T Consensus 12 ~kY~Cp~C~~~ 22 (30)
T PF04438_consen 12 AKYRCPRCGAR 22 (30)
T ss_dssp ESEE-TTT--E
T ss_pred CEEECCCcCCc
Confidence 34677777654
No 218
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=29.70 E-value=6.5 Score=32.54 Aligned_cols=56 Identities=27% Similarity=0.620 Sum_probs=33.0
Q ss_pred eccccCcccCChhhHHHHHhhcCCCCc-eeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcc
Q psy3356 101 HCTECEATFSWKQNLEVHMRTHTGERP-YECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEG 171 (180)
Q Consensus 101 ~C~~C~~~~~~~~~l~~H~~~h~~~~~-~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~ 171 (180)
.|..||-.|+....|--= +..+.-.. -.|+.|.+.+.++.+-+-|. .|..|+.||=
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfHA--------------Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFHA--------------QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCcccccccc--------------ccccCcccCC
Confidence 477788777765433111 11222222 35888888888877655543 3467888884
No 219
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=29.57 E-value=18 Score=18.80 Aligned_cols=8 Identities=38% Similarity=1.194 Sum_probs=4.0
Q ss_pred eecccccc
Q psy3356 128 YECEICGK 135 (180)
Q Consensus 128 ~~C~~C~~ 135 (180)
+-|-.|++
T Consensus 38 ~~CGkCgy 45 (51)
T COG1998 38 WACGKCGY 45 (51)
T ss_pred eEeccccc
Confidence 45555544
No 220
>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=29.56 E-value=43 Score=20.89 Aligned_cols=12 Identities=17% Similarity=0.022 Sum_probs=9.4
Q ss_pred cccccccceeee
Q psy3356 23 LVFIPACVFRFS 34 (180)
Q Consensus 23 ~~~c~~C~~~~~ 34 (180)
...|+.|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (115)
T TIGR00100 70 ECECEDCSEEVS 81 (115)
T ss_pred EEEcccCCCEEe
Confidence 348888988887
No 221
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=29.26 E-value=14 Score=24.12 Aligned_cols=32 Identities=25% Similarity=0.833 Sum_probs=20.2
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcccCC
Q psy3356 127 PYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEGMFT 174 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~~F~ 174 (180)
.|.|..|+..+.....+ +...|.|..|+..|.
T Consensus 123 ~~~C~~C~~~~~r~~~~----------------~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRRS----------------KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeeccc----------------chhhEECCCCCCEEE
Confidence 48888898776333221 233488999986653
No 222
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=29.09 E-value=52 Score=24.60 Aligned_cols=13 Identities=23% Similarity=0.726 Sum_probs=8.9
Q ss_pred CCCcccCCCcccC
Q psy3356 161 DRPFHCPACEGMF 173 (180)
Q Consensus 161 ~~~~~C~~C~~~F 173 (180)
.+-..|..|+.-.
T Consensus 250 ~r~e~C~~C~~Yl 262 (305)
T TIGR01562 250 LKAETCDSCQGYL 262 (305)
T ss_pred eEEeeccccccch
Confidence 4557798888543
No 223
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.51 E-value=25 Score=19.38 Aligned_cols=14 Identities=21% Similarity=0.150 Sum_probs=10.6
Q ss_pred CCcccccccceeee
Q psy3356 21 NPLVFIPACVFRFS 34 (180)
Q Consensus 21 ~~~~~c~~C~~~~~ 34 (180)
...+.||.||+...
T Consensus 5 ~~~v~CP~Cgkpv~ 18 (65)
T COG3024 5 RITVPCPTCGKPVV 18 (65)
T ss_pred cccccCCCCCCccc
Confidence 34568999998877
No 224
>PRK05978 hypothetical protein; Provisional
Probab=28.20 E-value=20 Score=23.60 Aligned_cols=10 Identities=40% Similarity=1.285 Sum_probs=5.3
Q ss_pred eccccccccC
Q psy3356 129 ECEICGKRFS 138 (180)
Q Consensus 129 ~C~~C~~~f~ 138 (180)
.|+.|+..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 4555555543
No 225
>PF14122 YokU: YokU-like protein
Probab=28.13 E-value=51 Score=19.43 Aligned_cols=29 Identities=21% Similarity=0.402 Sum_probs=22.1
Q ss_pred CCceeeeeecccCCcccccccceeeeecC
Q psy3356 9 SPSVTFDINIQKNPLVFIPACVFRFSVEN 37 (180)
Q Consensus 9 ~~~~~~~~~~~~~~~~~c~~C~~~~~~~~ 37 (180)
.+.-..-|.+...|...|..||..+.+.+
T Consensus 21 LpdGtraIeI~~tP~i~C~~CgmvYq~d~ 49 (87)
T PF14122_consen 21 LPDGTRAIEITDTPAIICSNCGMVYQDDE 49 (87)
T ss_pred cCCCceEEEecCCceeeecCCCcEEehhH
Confidence 34445567788889889999999988544
No 226
>PRK00420 hypothetical protein; Validated
Probab=27.27 E-value=31 Score=21.50 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=8.0
Q ss_pred ccccccceeee
Q psy3356 24 VFIPACVFRFS 34 (180)
Q Consensus 24 ~~c~~C~~~~~ 34 (180)
..||.||..+-
T Consensus 24 ~~CP~Cg~pLf 34 (112)
T PRK00420 24 KHCPVCGLPLF 34 (112)
T ss_pred CCCCCCCCcce
Confidence 37888887655
No 227
>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=26.77 E-value=83 Score=14.80 Aligned_cols=21 Identities=14% Similarity=0.521 Sum_probs=10.4
Q ss_pred eeccccCcccCChhhHHHHHhh
Q psy3356 100 YHCTECEATFSWKQNLEVHMRT 121 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~~ 121 (180)
+.|+.|++... ...+..|+..
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLek 25 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLEK 25 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHHH
T ss_pred EECCCCcCCcc-hhhhHHHHHH
Confidence 45666665532 4455555543
No 228
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=26.58 E-value=49 Score=14.79 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=5.4
Q ss_pred cccccceeeeecC
Q psy3356 25 FIPACVFRFSVEN 37 (180)
Q Consensus 25 ~c~~C~~~~~~~~ 37 (180)
.||.|+.......
T Consensus 1 ~CP~C~s~l~~~~ 13 (28)
T PF03119_consen 1 TCPVCGSKLVREE 13 (28)
T ss_dssp B-TTT--BEEE-C
T ss_pred CcCCCCCEeEcCC
Confidence 3777877665333
No 229
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=25.91 E-value=43 Score=17.90 Aligned_cols=12 Identities=33% Similarity=0.772 Sum_probs=8.0
Q ss_pred ccCCCcccCCCc
Q psy3356 165 HCPACEGMFTTK 176 (180)
Q Consensus 165 ~C~~C~~~F~~~ 176 (180)
-|+.|+..|...
T Consensus 41 gCPfC~~~~~~~ 52 (55)
T PF14447_consen 41 GCPFCGTPFEFD 52 (55)
T ss_pred CCCCCCCcccCC
Confidence 477777777553
No 230
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.56 E-value=26 Score=18.06 Aligned_cols=17 Identities=29% Similarity=0.899 Sum_probs=12.2
Q ss_pred eccccCcccCChhhHHH
Q psy3356 101 HCTECEATFSWKQNLEV 117 (180)
Q Consensus 101 ~C~~C~~~~~~~~~l~~ 117 (180)
.|++|++.|.....+.+
T Consensus 14 ICpvCqRPFsWRkKW~~ 30 (54)
T COG4338 14 ICPVCQRPFSWRKKWAR 30 (54)
T ss_pred hhhhhcCchHHHHHHHH
Confidence 68889888877655443
No 231
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.55 E-value=54 Score=20.43 Aligned_cols=12 Identities=8% Similarity=0.196 Sum_probs=9.2
Q ss_pred cccccccceeee
Q psy3356 23 LVFIPACVFRFS 34 (180)
Q Consensus 23 ~~~c~~C~~~~~ 34 (180)
...|..|+..|+
T Consensus 70 ~~~C~~Cg~~~~ 81 (114)
T PRK03681 70 ECWCETCQQYVT 81 (114)
T ss_pred EEEcccCCCeee
Confidence 348888888877
No 232
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=24.88 E-value=38 Score=16.76 Aligned_cols=9 Identities=33% Similarity=1.136 Sum_probs=5.4
Q ss_pred cccCCCccc
Q psy3356 164 FHCPACEGM 172 (180)
Q Consensus 164 ~~C~~C~~~ 172 (180)
|.|+.|+..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 456666654
No 233
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=24.79 E-value=35 Score=21.20 Aligned_cols=11 Identities=27% Similarity=0.890 Sum_probs=4.9
Q ss_pred eeccccCcccC
Q psy3356 100 YHCTECEATFS 110 (180)
Q Consensus 100 ~~C~~C~~~~~ 110 (180)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 34555555543
No 234
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.72 E-value=46 Score=19.10 Aligned_cols=11 Identities=55% Similarity=1.313 Sum_probs=6.6
Q ss_pred ceeccccCccc
Q psy3356 99 PYHCTECEATF 109 (180)
Q Consensus 99 ~~~C~~C~~~~ 109 (180)
.|.|..|+..|
T Consensus 12 ~Y~c~~cg~~~ 22 (82)
T COG2331 12 SYECTECGNRF 22 (82)
T ss_pred EEeecccchHH
Confidence 36677776554
No 235
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=24.70 E-value=36 Score=16.85 Aligned_cols=8 Identities=13% Similarity=0.530 Sum_probs=4.1
Q ss_pred ccccceee
Q psy3356 26 IPACVFRF 33 (180)
Q Consensus 26 c~~C~~~~ 33 (180)
|+.|...+
T Consensus 2 C~~C~~~~ 9 (44)
T PF14634_consen 2 CNICFEKY 9 (44)
T ss_pred CcCcCccc
Confidence 45555555
No 236
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.68 E-value=44 Score=17.62 Aligned_cols=10 Identities=20% Similarity=0.212 Sum_probs=8.2
Q ss_pred cccccceeee
Q psy3356 25 FIPACVFRFS 34 (180)
Q Consensus 25 ~c~~C~~~~~ 34 (180)
.||.||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 6888888877
No 237
>KOG0782|consensus
Probab=24.37 E-value=17 Score=29.44 Aligned_cols=50 Identities=24% Similarity=0.423 Sum_probs=29.1
Q ss_pred hhhhHhhhcCCCCCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccCCh
Q psy3356 53 VPQIHMRTHTGERPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFSWK 112 (180)
Q Consensus 53 ~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~~~ 112 (180)
.|.+|--+|.....-+|..|+++|.++-.+.. .......|.+|...|..+
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~Fhs----------KEivAisCSWCKqayH~K 289 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHS----------KEIVAISCSWCKQAYHLK 289 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheeecc----------ccEEEEEehHHHHHhhcc
Confidence 45566555555555668888888766533221 122346677777666554
No 238
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.31 E-value=39 Score=17.57 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=7.1
Q ss_pred Ccccccchhhc
Q psy3356 66 PFECDVCGKRF 76 (180)
Q Consensus 66 ~~~C~~C~~~f 76 (180)
.+.|..|+.++
T Consensus 37 r~~C~~Cgyt~ 47 (50)
T PRK00432 37 RWHCGKCGYTE 47 (50)
T ss_pred cEECCCcCCEE
Confidence 46677777654
No 239
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=24.09 E-value=26 Score=24.28 Aligned_cols=28 Identities=32% Similarity=0.673 Sum_probs=0.0
Q ss_pred hcCCCCceecccccc-ccCChHHHHHHHH
Q psy3356 121 THTGERPYECEICGK-RFSQKSACNTHKR 148 (180)
Q Consensus 121 ~h~~~~~~~C~~C~~-~f~~~~~l~~H~~ 148 (180)
.|.-.+.|.|.+||. ++.-+..+.+|..
T Consensus 95 LhGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 95 LHGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -----------------------------
T ss_pred HhCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 344456699999985 6678888888864
No 240
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=23.90 E-value=38 Score=21.73 Aligned_cols=15 Identities=40% Similarity=0.986 Sum_probs=9.3
Q ss_pred ceeccccccccCChH
Q psy3356 127 PYECEICGKRFSQKS 141 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~ 141 (180)
|++|..||+.|.+-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 356777777776543
No 241
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.90 E-value=67 Score=23.70 Aligned_cols=10 Identities=20% Similarity=0.840 Sum_probs=6.9
Q ss_pred eecccccccc
Q psy3356 128 YECEICGKRF 137 (180)
Q Consensus 128 ~~C~~C~~~f 137 (180)
|.|++|.-.|
T Consensus 256 yvCs~Clsi~ 265 (279)
T TIGR00627 256 FVCSVCLSVL 265 (279)
T ss_pred EECCCccCCc
Confidence 7777777655
No 242
>PLN02294 cytochrome c oxidase subunit Vb
Probab=23.88 E-value=39 Score=22.77 Aligned_cols=15 Identities=33% Similarity=1.012 Sum_probs=11.7
Q ss_pred CCCcccCCCcccCCC
Q psy3356 161 DRPFHCPACEGMFTT 175 (180)
Q Consensus 161 ~~~~~C~~C~~~F~~ 175 (180)
.+|+.|+.||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 368889999988753
No 243
>PLN02748 tRNA dimethylallyltransferase
Probab=23.77 E-value=58 Score=26.00 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=21.3
Q ss_pred CCceecccccc-ccCChHHHHHHHHH
Q psy3356 125 ERPYECEICGK-RFSQKSACNTHKRT 149 (180)
Q Consensus 125 ~~~~~C~~C~~-~f~~~~~l~~H~~~ 149 (180)
.+.|.|..|+. .+.....+..|++.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcc
Confidence 35689999997 89999999999864
No 244
>PRK02935 hypothetical protein; Provisional
Probab=23.67 E-value=38 Score=20.78 Aligned_cols=29 Identities=14% Similarity=0.116 Sum_probs=18.7
Q ss_pred cCCcccccccceeeeecC-CeeEeeeeccc
Q psy3356 20 KNPLVFIPACVFRFSVEN-EKRFFFFSFLF 48 (180)
Q Consensus 20 ~~~~~~c~~C~~~~~~~~-~~~~~~C~~~~ 48 (180)
+...+.||.|++..+-.+ ...|.+|+.-.
T Consensus 67 kavqV~CP~C~K~TKmLGrvD~CM~C~~PL 96 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRVDACMHCNQPL 96 (110)
T ss_pred cceeeECCCCCchhhhccceeecCcCCCcC
Confidence 445569999988877544 44555665543
No 245
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=23.60 E-value=46 Score=26.38 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=17.6
Q ss_pred CcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccC
Q psy3356 66 PFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFS 110 (180)
Q Consensus 66 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~ 110 (180)
.|.|..|+... .+..++|+.|+.+=+
T Consensus 7 ~y~C~~Cg~~~-------------------~~~~g~Cp~C~~w~t 32 (454)
T TIGR00416 7 KFVCQHCGADS-------------------PKWQGKCPACHAWNT 32 (454)
T ss_pred eEECCcCCCCC-------------------ccccEECcCCCCccc
Confidence 48888888763 345567888876533
No 246
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=23.45 E-value=41 Score=18.49 Aligned_cols=13 Identities=23% Similarity=0.202 Sum_probs=9.6
Q ss_pred Ccccccccceeee
Q psy3356 22 PLVFIPACVFRFS 34 (180)
Q Consensus 22 ~~~~c~~C~~~~~ 34 (180)
..+.||.|++...
T Consensus 5 ~~v~CP~C~k~~~ 17 (62)
T PRK00418 5 ITVNCPTCGKPVE 17 (62)
T ss_pred ccccCCCCCCccc
Confidence 3458999988754
No 247
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=23.27 E-value=23 Score=19.10 Aligned_cols=11 Identities=18% Similarity=0.467 Sum_probs=5.9
Q ss_pred cccccccceee
Q psy3356 23 LVFIPACVFRF 33 (180)
Q Consensus 23 ~~~c~~C~~~~ 33 (180)
..+||.|...+
T Consensus 44 ~PVCP~Ck~iy 54 (58)
T PF11238_consen 44 FPVCPECKEIY 54 (58)
T ss_pred CCCCcCHHHHH
Confidence 44666665444
No 248
>KOG0978|consensus
Probab=23.12 E-value=28 Score=29.07 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=6.5
Q ss_pred ceeccccCcc
Q psy3356 99 PYHCTECEAT 108 (180)
Q Consensus 99 ~~~C~~C~~~ 108 (180)
.+.|+.|+..
T Consensus 643 ~LkCs~Cn~R 652 (698)
T KOG0978|consen 643 LLKCSVCNTR 652 (698)
T ss_pred ceeCCCccCc
Confidence 3678887743
No 249
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=23.00 E-value=63 Score=16.91 Aligned_cols=7 Identities=43% Similarity=1.369 Sum_probs=2.6
Q ss_pred ecccccc
Q psy3356 129 ECEICGK 135 (180)
Q Consensus 129 ~C~~C~~ 135 (180)
+|+.|+.
T Consensus 30 ~C~~Cgh 36 (55)
T PF14311_consen 30 KCPKCGH 36 (55)
T ss_pred ECCCCCC
Confidence 3333333
No 250
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=22.89 E-value=62 Score=25.79 Aligned_cols=26 Identities=19% Similarity=0.425 Sum_probs=22.3
Q ss_pred CcccccchhhccChHHHHHHHHhccC
Q psy3356 66 PFECDVCGKRFAQKSTLNTHKRVHIS 91 (180)
Q Consensus 66 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 91 (180)
.+.|+.|.+.|.....+..|+...|.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhh
Confidence 47799999999999999999976553
No 251
>PRK12722 transcriptional activator FlhC; Provisional
Probab=22.68 E-value=66 Score=22.16 Aligned_cols=47 Identities=19% Similarity=0.422 Sum_probs=26.5
Q ss_pred ccCChhhHHHHHhhcCCCCceeccccccccCChHHHHHHHHHcCCCCCCcCCCCCCcccCCCcc
Q psy3356 108 TFSWKQNLEVHMRTHTGERPYECEICGKRFSQKSACNTHKRTHIPYLPRVHPKDRPFHCPACEG 171 (180)
Q Consensus 108 ~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~h~~~~~~~C~~C~~ 171 (180)
.+.....|.+...... -....|..|+-.|.... +.....|.|+.|.-
T Consensus 116 s~tRAw~LvRf~~s~~-L~l~~C~~Cgg~fv~~~----------------~e~~~~f~CplC~~ 162 (187)
T PRK12722 116 SLTRAWTLVRFVDSGM-LQLSSCNCCGGHFVTHA----------------HDPVGSFVCGLCQP 162 (187)
T ss_pred cHHHHHHHHHHHhcCc-EeeccCCCCCCCeeccc----------------cccCCCCcCCCCCC
Confidence 3444455555544332 22356888888776442 22345688999875
No 252
>PRK11823 DNA repair protein RadA; Provisional
Probab=22.68 E-value=49 Score=26.14 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=17.9
Q ss_pred CCcccccchhhccChHHHHHHHHhccCCCcCCCcceeccccCcccC
Q psy3356 65 RPFECDVCGKRFAQKSTLNTHKRVHISYLHVKDKPYHCTECEATFS 110 (180)
Q Consensus 65 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~C~~C~~~~~ 110 (180)
..|.|..|+... .+...+|+.|+.+-+
T Consensus 6 ~~y~C~~Cg~~~-------------------~~~~g~Cp~C~~w~t 32 (446)
T PRK11823 6 TAYVCQECGAES-------------------PKWLGRCPECGAWNT 32 (446)
T ss_pred CeEECCcCCCCC-------------------cccCeeCcCCCCccc
Confidence 348888888763 345567888875533
No 253
>KOG0717|consensus
Probab=22.59 E-value=59 Score=25.81 Aligned_cols=21 Identities=24% Similarity=0.562 Sum_probs=17.5
Q ss_pred eeccccCcccCChhhHHHHHh
Q psy3356 100 YHCTECEATFSWKQNLEVHMR 120 (180)
Q Consensus 100 ~~C~~C~~~~~~~~~l~~H~~ 120 (180)
+-|.+|++.|.+...+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 778888888888888888865
No 254
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.50 E-value=46 Score=20.39 Aligned_cols=8 Identities=38% Similarity=1.041 Sum_probs=3.8
Q ss_pred cccccchh
Q psy3356 67 FECDVCGK 74 (180)
Q Consensus 67 ~~C~~C~~ 74 (180)
-.|+.|+.
T Consensus 3 ~~CpYCg~ 10 (102)
T PF11672_consen 3 IICPYCGG 10 (102)
T ss_pred cccCCCCC
Confidence 34555544
No 255
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.49 E-value=9.6 Score=28.04 Aligned_cols=13 Identities=23% Similarity=0.432 Sum_probs=8.5
Q ss_pred CCCCcccCCCccc
Q psy3356 160 KDRPFHCPACEGM 172 (180)
Q Consensus 160 ~~~~~~C~~C~~~ 172 (180)
+.+-+.|..|+.-
T Consensus 235 ~~rve~C~~C~~Y 247 (290)
T PF04216_consen 235 AYRVEVCESCGSY 247 (290)
T ss_dssp SEEEEEETTTTEE
T ss_pred cEEEEECCcccch
Confidence 4455778888753
No 256
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=22.32 E-value=23 Score=15.90 Aligned_cols=10 Identities=20% Similarity=0.262 Sum_probs=3.8
Q ss_pred cccccceeee
Q psy3356 25 FIPACVFRFS 34 (180)
Q Consensus 25 ~c~~C~~~~~ 34 (180)
.|+.|+....
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 4566655554
No 257
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=22.20 E-value=75 Score=15.49 Aligned_cols=15 Identities=20% Similarity=0.465 Sum_probs=10.9
Q ss_pred cCCcccccccceeee
Q psy3356 20 KNPLVFIPACVFRFS 34 (180)
Q Consensus 20 ~~~~~~c~~C~~~~~ 34 (180)
..|...|+.||..+-
T Consensus 29 ~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 29 NVPALVCPQCGEEYL 43 (46)
T ss_pred CCCccccccCCCEee
Confidence 446668888887765
No 258
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=21.62 E-value=9.8 Score=19.43 Aligned_cols=13 Identities=31% Similarity=0.743 Sum_probs=6.3
Q ss_pred Cceeccc--cccccC
Q psy3356 126 RPYECEI--CGKRFS 138 (180)
Q Consensus 126 ~~~~C~~--C~~~f~ 138 (180)
..+.|.. ||..|.
T Consensus 24 ~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 24 LYCQCTNPECGHTFV 38 (47)
T ss_pred EEEEECCCcCCCEEE
Confidence 3355543 555553
No 259
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=21.50 E-value=16 Score=22.19 Aligned_cols=10 Identities=30% Similarity=0.647 Sum_probs=5.1
Q ss_pred cccccceeee
Q psy3356 25 FIPACVFRFS 34 (180)
Q Consensus 25 ~c~~C~~~~~ 34 (180)
.|+.||..+.
T Consensus 2 fC~~Cg~~l~ 11 (104)
T TIGR01384 2 FCPKCGSLMT 11 (104)
T ss_pred CCcccCcccc
Confidence 3555555543
No 260
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.31 E-value=48 Score=20.33 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=18.8
Q ss_pred CceeccccccccCChHHHHHHHHH
Q psy3356 126 RPYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 126 ~~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
..+-|..|.+-|.+...|..|.+.
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhcc
Confidence 346788888888888888888764
No 261
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=21.27 E-value=67 Score=19.14 Aligned_cols=22 Identities=18% Similarity=0.489 Sum_probs=16.5
Q ss_pred eecccCCcccccccceeeeecC
Q psy3356 16 INIQKNPLVFIPACVFRFSVEN 37 (180)
Q Consensus 16 ~~~~~~~~~~c~~C~~~~~~~~ 37 (180)
+.....|...|+.||..+-+.+
T Consensus 28 IvIknVPa~~C~~CGe~y~~de 49 (89)
T TIGR03829 28 IEIKETPSISCSHCGMEYQDDT 49 (89)
T ss_pred EEEecCCcccccCCCcEeecHH
Confidence 4456778889999999988443
No 262
>PRK01343 zinc-binding protein; Provisional
Probab=21.23 E-value=1e+02 Score=16.63 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=5.2
Q ss_pred cccCCCcccC
Q psy3356 164 FHCPACEGMF 173 (180)
Q Consensus 164 ~~C~~C~~~F 173 (180)
..|++|++.|
T Consensus 10 ~~CP~C~k~~ 19 (57)
T PRK01343 10 RPCPECGKPS 19 (57)
T ss_pred CcCCCCCCcC
Confidence 3455555544
No 263
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=21.21 E-value=45 Score=20.29 Aligned_cols=12 Identities=33% Similarity=0.957 Sum_probs=7.8
Q ss_pred CCCCcccCCCcc
Q psy3356 160 KDRPFHCPACEG 171 (180)
Q Consensus 160 ~~~~~~C~~C~~ 171 (180)
-++.|.|+.|+.
T Consensus 19 L~k~FtCp~Cgh 30 (104)
T COG4888 19 LPKTFTCPRCGH 30 (104)
T ss_pred CCceEecCccCC
Confidence 355677777775
No 264
>KOG4727|consensus
Probab=21.11 E-value=58 Score=21.98 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=19.3
Q ss_pred ceeccccccccCChHHHHHHHH
Q psy3356 127 PYECEICGKRFSQKSACNTHKR 148 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~ 148 (180)
-|-|.+|.-.|.+..++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4889999999999999998875
No 265
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=21.11 E-value=91 Score=23.11 Aligned_cols=26 Identities=27% Similarity=0.415 Sum_probs=22.9
Q ss_pred CCCceeccccccccCChHHHHHHHHH
Q psy3356 124 GERPYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 124 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
....|.|..|-+-|.+...|.+|+..
T Consensus 45 ~~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 45 CTKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CCeEEEcCCCcchhCCHHHHHHHHHh
Confidence 35679999999999999999999874
No 266
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=20.90 E-value=1.4e+02 Score=15.97 Aligned_cols=13 Identities=31% Similarity=0.874 Sum_probs=4.9
Q ss_pred ceeccccccccCC
Q psy3356 127 PYECEICGKRFSQ 139 (180)
Q Consensus 127 ~~~C~~C~~~f~~ 139 (180)
|.....|+..|..
T Consensus 24 PV~s~~C~H~fek 36 (57)
T PF11789_consen 24 PVKSKKCGHTFEK 36 (57)
T ss_dssp EEEESSS--EEEH
T ss_pred CcCcCCCCCeecH
Confidence 3444445555533
No 267
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=20.69 E-value=50 Score=24.54 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=21.5
Q ss_pred cceeccccCcccCChhhHHHHHhhcCCCCceeccccccccCCh
Q psy3356 98 KPYHCTECEATFSWKQNLEVHMRTHTGERPYECEICGKRFSQK 140 (180)
Q Consensus 98 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 140 (180)
.-.+|+.|+..... +.+ .+..+.|+.|+..|.-.
T Consensus 37 lw~kc~~C~~~~~~-----~~l----~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 37 LWVQCENCYGLNYK-----KFL----KSKMNICEQCGYHLKMS 70 (296)
T ss_pred CeeECCCccchhhH-----HHH----HHcCCCCCCCCCCcCCC
Confidence 45678888876321 222 23347899999888654
No 268
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=20.55 E-value=62 Score=24.94 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=3.8
Q ss_pred eeccccCc
Q psy3356 100 YHCTECEA 107 (180)
Q Consensus 100 ~~C~~C~~ 107 (180)
.+|+.|+.
T Consensus 15 g~cp~c~~ 22 (372)
T cd01121 15 GKCPECGE 22 (372)
T ss_pred EECcCCCC
Confidence 44555543
No 269
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=20.32 E-value=21 Score=18.80 Aligned_cols=15 Identities=27% Similarity=0.631 Sum_probs=7.0
Q ss_pred CCCCcccCCCcccCC
Q psy3356 160 KDRPFHCPACEGMFT 174 (180)
Q Consensus 160 ~~~~~~C~~C~~~F~ 174 (180)
+...|+|.+|++.|.
T Consensus 32 ~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 32 EPIKLRCHYCERIIT 46 (52)
T ss_dssp TTCEEEETTT--EEE
T ss_pred CCCEEEeeCCCCEec
Confidence 344466666665543
No 270
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=20.12 E-value=68 Score=14.41 Aligned_cols=8 Identities=25% Similarity=0.816 Sum_probs=4.3
Q ss_pred ccCCCccc
Q psy3356 165 HCPACEGM 172 (180)
Q Consensus 165 ~C~~C~~~ 172 (180)
.|.+|++.
T Consensus 2 ~C~~C~~~ 9 (30)
T PF03107_consen 2 WCDVCRRK 9 (30)
T ss_pred CCCCCCCC
Confidence 45555554
No 271
>PTZ00448 hypothetical protein; Provisional
Probab=20.11 E-value=80 Score=24.28 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=20.4
Q ss_pred ceeccccccccCChHHHHHHHHH
Q psy3356 127 PYECEICGKRFSQKSACNTHKRT 149 (180)
Q Consensus 127 ~~~C~~C~~~f~~~~~l~~H~~~ 149 (180)
.|.|..|+-.|.+......|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999999999999874
No 272
>KOG0402|consensus
Probab=20.07 E-value=15 Score=21.36 Aligned_cols=18 Identities=17% Similarity=0.124 Sum_probs=12.2
Q ss_pred ecccCCcccccccceeee
Q psy3356 17 NIQKNPLVFIPACVFRFS 34 (180)
Q Consensus 17 ~~~~~~~~~c~~C~~~~~ 34 (180)
.++....+.|+.||+.--
T Consensus 30 ei~Qhaky~CsfCGK~~v 47 (92)
T KOG0402|consen 30 EIQQHAKYTCSFCGKKTV 47 (92)
T ss_pred HHHHhhhhhhhhcchhhh
Confidence 344555668999987754
Done!