Query psy13210
Match_columns 155
No_of_seqs 136 out of 1738
Neff 9.8
Searched_HMMs 46136
Date Fri Aug 16 22:58:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13210hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 4.5E-24 9.8E-29 151.0 4.5 112 26-147 142-264 (279)
2 KOG2462|consensus 99.8 1.4E-21 3.1E-26 138.4 4.4 105 42-155 127-243 (279)
3 KOG1074|consensus 99.8 1.7E-19 3.8E-24 143.2 2.3 58 44-109 352-409 (958)
4 KOG3576|consensus 99.6 5.4E-17 1.2E-21 110.6 1.1 102 42-151 114-237 (267)
5 KOG3623|consensus 99.6 2.8E-16 6.1E-21 123.8 3.0 82 41-147 890-971 (1007)
6 KOG1074|consensus 99.6 1.2E-15 2.6E-20 121.7 3.2 60 43-110 603-662 (958)
7 KOG3623|consensus 99.4 1.6E-13 3.4E-18 108.6 3.4 97 45-147 210-330 (1007)
8 KOG3608|consensus 99.4 1.4E-12 3E-17 95.9 6.7 111 44-155 236-381 (467)
9 KOG3608|consensus 99.4 1.7E-12 3.7E-17 95.4 6.5 105 40-151 202-316 (467)
10 PHA00733 hypothetical protein 99.3 1.2E-11 2.6E-16 80.6 6.2 88 42-151 37-124 (128)
11 KOG3576|consensus 99.3 2.3E-12 5.1E-17 88.2 2.5 72 44-123 144-237 (267)
12 PF13465 zf-H2C2_2: Zinc-finge 99.1 5.3E-11 1.2E-15 56.0 2.6 26 113-138 1-26 (26)
13 PHA02768 hypothetical protein; 99.0 1.2E-10 2.5E-15 63.8 1.9 44 81-143 5-48 (55)
14 PHA02768 hypothetical protein; 98.9 3.5E-10 7.6E-15 62.0 0.9 45 44-98 4-48 (55)
15 KOG3993|consensus 98.8 1E-09 2.2E-14 82.6 1.2 103 43-153 265-383 (500)
16 PLN03086 PRLI-interacting fact 98.8 1.3E-08 2.8E-13 80.6 6.0 91 46-151 454-565 (567)
17 PF13465 zf-H2C2_2: Zinc-finge 98.6 1.2E-08 2.7E-13 47.8 1.0 26 60-93 1-26 (26)
18 PHA00733 hypothetical protein 98.6 5.5E-08 1.2E-12 63.5 4.1 54 42-105 70-123 (128)
19 PHA00732 hypothetical protein 98.6 4.1E-08 8.9E-13 58.5 2.7 44 81-147 1-45 (79)
20 KOG3993|consensus 98.6 1E-08 2.2E-13 77.3 0.0 85 13-105 263-380 (500)
21 PHA00616 hypothetical protein 98.6 3.2E-08 7E-13 51.7 1.6 29 126-155 1-29 (44)
22 PHA00616 hypothetical protein 98.5 5.7E-08 1.2E-12 50.8 1.8 29 81-109 1-29 (44)
23 PLN03086 PRLI-interacting fact 98.3 1E-06 2.2E-11 70.1 5.9 100 44-147 406-535 (567)
24 PF00096 zf-C2H2: Zinc finger, 98.3 6.6E-07 1.4E-11 40.6 2.0 23 82-104 1-23 (23)
25 PF05605 zf-Di19: Drought indu 98.3 2.1E-06 4.5E-11 47.5 4.3 52 81-151 2-54 (54)
26 PF00096 zf-C2H2: Zinc finger, 98.2 1.1E-06 2.3E-11 39.9 2.0 22 127-148 1-22 (23)
27 COG5189 SFP1 Putative transcri 98.2 1.8E-07 4E-12 68.4 -1.1 70 78-147 346-419 (423)
28 PHA00732 hypothetical protein 98.2 9.9E-07 2.1E-11 52.6 1.6 47 45-105 1-48 (79)
29 PF13894 zf-C2H2_4: C2H2-type 98.1 2.4E-06 5.2E-11 38.8 2.2 24 127-150 1-24 (24)
30 PF13912 zf-C2H2_6: C2H2-type 98.0 3.3E-06 7.1E-11 39.8 1.9 25 126-150 1-25 (27)
31 PF12756 zf-C2H2_2: C2H2 type 98.0 4.1E-06 9E-11 51.9 2.5 66 83-149 1-73 (100)
32 PF13894 zf-C2H2_4: C2H2-type 97.9 9.9E-06 2.1E-10 36.7 2.2 23 82-104 1-23 (24)
33 PF05605 zf-Di19: Drought indu 97.9 1.4E-05 3E-10 44.2 3.1 51 45-105 2-53 (54)
34 PF09237 GAGA: GAGA factor; I 97.8 2.5E-05 5.4E-10 41.8 2.9 33 77-109 20-52 (54)
35 PF13912 zf-C2H2_6: C2H2-type 97.7 1.8E-05 4E-10 37.1 1.6 25 81-105 1-25 (27)
36 smart00355 ZnF_C2H2 zinc finge 97.5 9.8E-05 2.1E-09 33.8 2.0 25 127-152 1-25 (26)
37 smart00355 ZnF_C2H2 zinc finge 97.4 0.00014 3.1E-09 33.2 2.3 24 82-105 1-24 (26)
38 PF09237 GAGA: GAGA factor; I 97.3 0.00036 7.9E-09 37.4 2.8 30 123-152 21-50 (54)
39 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00034 7.5E-09 31.7 2.2 24 127-151 1-24 (24)
40 PF12756 zf-C2H2_2: C2H2 type 97.2 0.00032 6.9E-09 43.3 2.4 58 47-104 1-73 (100)
41 PF12874 zf-met: Zinc-finger o 97.1 0.00036 7.8E-09 31.9 1.8 21 127-147 1-21 (25)
42 PF12874 zf-met: Zinc-finger o 97.0 0.00043 9.4E-09 31.7 1.7 23 82-104 1-23 (25)
43 COG5189 SFP1 Putative transcri 97.0 0.00017 3.7E-09 53.2 -0.2 60 43-102 347-419 (423)
44 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00093 2E-08 30.3 2.1 23 82-105 1-23 (24)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.8 0.0006 1.3E-08 31.9 0.9 21 127-147 2-22 (27)
46 PRK04860 hypothetical protein; 96.8 0.00083 1.8E-08 45.5 1.9 27 114-140 131-157 (160)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0013 2.9E-08 30.7 0.9 22 82-103 2-23 (27)
48 KOG1146|consensus 96.4 0.00099 2.2E-08 57.4 0.7 96 45-147 436-539 (1406)
49 PF13913 zf-C2HC_2: zinc-finge 96.2 0.0045 9.7E-08 28.4 2.0 21 82-103 3-23 (25)
50 PF13913 zf-C2HC_2: zinc-finge 96.0 0.0054 1.2E-07 28.1 1.6 20 127-147 3-22 (25)
51 smart00451 ZnF_U1 U1-like zinc 95.7 0.0076 1.6E-07 29.7 1.7 22 126-147 3-24 (35)
52 PRK04860 hypothetical protein; 95.7 0.004 8.6E-08 42.2 0.7 39 45-95 119-157 (160)
53 COG5048 FOG: Zn-finger [Genera 95.3 0.0023 5.1E-08 49.2 -1.8 98 45-151 289-442 (467)
54 COG4049 Uncharacterized protei 94.9 0.015 3.3E-07 31.8 1.3 30 122-151 13-42 (65)
55 smart00451 ZnF_U1 U1-like zinc 94.7 0.028 6E-07 27.6 1.9 23 81-103 3-25 (35)
56 PF09538 FYDLN_acid: Protein o 93.9 0.037 8.1E-07 35.0 1.7 31 81-139 9-39 (108)
57 PF12013 DUF3505: Protein of u 93.2 0.47 1E-05 29.9 5.9 71 80-151 10-109 (109)
58 KOG2893|consensus 92.6 0.025 5.4E-07 40.5 -0.7 45 48-104 13-58 (341)
59 PF13717 zinc_ribbon_4: zinc-r 92.1 0.076 1.6E-06 26.6 0.9 34 46-92 3-36 (36)
60 KOG2893|consensus 92.1 0.048 1E-06 39.1 0.2 51 79-151 9-59 (341)
61 KOG2231|consensus 91.7 0.2 4.4E-06 41.2 3.4 95 8-105 90-206 (669)
62 COG5048 FOG: Zn-finger [Genera 91.6 0.047 1E-06 42.0 -0.3 57 80-154 288-350 (467)
63 KOG1146|consensus 91.6 0.03 6.6E-07 48.8 -1.4 98 42-154 1257-1356(1406)
64 PF02892 zf-BED: BED zinc fing 91.4 0.22 4.7E-06 26.0 2.3 28 123-150 13-44 (45)
65 cd00350 rubredoxin_like Rubred 91.3 0.11 2.3E-06 25.4 0.9 11 125-135 16-26 (33)
66 COG4049 Uncharacterized protei 91.0 0.14 3E-06 28.1 1.3 29 75-103 11-39 (65)
67 TIGR02300 FYDLN_acid conserved 90.1 0.21 4.6E-06 32.3 1.7 34 81-142 9-42 (129)
68 TIGR02098 MJ0042_CXXC MJ0042 f 90.0 0.13 2.9E-06 25.8 0.6 34 46-92 3-36 (38)
69 PF13719 zinc_ribbon_5: zinc-r 90.0 0.15 3.3E-06 25.6 0.8 34 46-92 3-36 (37)
70 COG1592 Rubrerythrin [Energy p 89.8 0.19 4.1E-06 34.3 1.4 26 79-134 132-157 (166)
71 smart00614 ZnF_BED BED zinc fi 89.4 0.35 7.6E-06 25.9 2.1 26 126-151 18-48 (50)
72 KOG4173|consensus 89.4 0.39 8.4E-06 33.8 2.7 90 44-151 78-171 (253)
73 PF05443 ROS_MUCR: ROS/MUCR tr 88.6 0.32 7E-06 31.9 1.8 23 126-151 72-94 (132)
74 PRK00398 rpoP DNA-directed RNA 87.3 0.26 5.5E-06 26.0 0.6 30 45-92 3-32 (46)
75 KOG2482|consensus 86.6 0.53 1.1E-05 35.7 2.1 70 82-151 196-304 (423)
76 COG5236 Uncharacterized conser 85.3 0.57 1.2E-05 35.6 1.8 40 112-151 202-245 (493)
77 PF04959 ARS2: Arsenite-resist 84.7 0.44 9.6E-06 33.9 0.9 30 123-152 74-103 (214)
78 smart00531 TFIIE Transcription 83.7 0.84 1.8E-05 30.5 1.9 23 74-96 92-114 (147)
79 smart00734 ZnF_Rad18 Rad18-lik 83.2 1.1 2.3E-05 20.6 1.6 20 127-147 2-21 (26)
80 PHA00626 hypothetical protein 82.8 0.56 1.2E-05 25.8 0.6 17 79-95 21-37 (59)
81 KOG2186|consensus 82.1 0.86 1.9E-05 33.1 1.5 48 45-103 3-50 (276)
82 PF09723 Zn-ribbon_8: Zinc rib 82.1 0.19 4E-06 26.0 -1.4 30 45-89 5-34 (42)
83 KOG2482|consensus 81.9 3.6 7.8E-05 31.4 4.7 65 81-147 144-216 (423)
84 COG2888 Predicted Zn-ribbon RN 81.7 0.5 1.1E-05 26.3 0.2 34 44-90 26-59 (61)
85 TIGR00373 conserved hypothetic 81.5 1.2 2.6E-05 30.2 2.0 38 74-137 102-139 (158)
86 KOG2071|consensus 81.0 0.87 1.9E-05 37.0 1.4 28 78-105 415-442 (579)
87 TIGR02605 CxxC_CxxC_SSSS putat 79.8 0.67 1.4E-05 24.9 0.3 30 45-89 5-34 (52)
88 COG4530 Uncharacterized protei 79.3 1.1 2.4E-05 28.2 1.1 16 123-138 23-38 (129)
89 KOG2231|consensus 79.2 2.4 5.2E-05 35.2 3.3 15 136-150 222-236 (669)
90 KOG4167|consensus 79.0 0.51 1.1E-05 39.3 -0.5 26 80-105 791-816 (907)
91 KOG2785|consensus 78.9 3.9 8.4E-05 31.6 4.1 65 82-147 167-241 (390)
92 COG5236 Uncharacterized conser 78.1 1.9 4.2E-05 32.8 2.3 65 83-151 222-306 (493)
93 PRK14890 putative Zn-ribbon RN 77.9 1 2.2E-05 25.1 0.6 34 44-90 24-57 (59)
94 COG5188 PRP9 Splicing factor 3 77.6 2 4.3E-05 32.9 2.2 24 43-66 236-259 (470)
95 KOG2593|consensus 77.3 2.5 5.5E-05 33.1 2.8 34 65-98 112-145 (436)
96 PRK06266 transcription initiat 77.3 1.9 4E-05 29.9 1.9 23 75-97 111-133 (178)
97 PF10571 UPF0547: Uncharacteri 74.1 1.7 3.6E-05 20.0 0.7 10 83-92 16-25 (26)
98 KOG2186|consensus 73.5 2.3 5E-05 30.9 1.6 47 81-147 3-49 (276)
99 PF07754 DUF1610: Domain of un 73.1 1.6 3.4E-05 19.7 0.5 11 79-89 14-24 (24)
100 PF12013 DUF3505: Protein of u 71.6 3.7 8.1E-05 25.7 2.2 24 82-105 81-108 (109)
101 PF04959 ARS2: Arsenite-resist 71.0 2.8 6E-05 29.9 1.6 29 77-105 73-102 (214)
102 COG4957 Predicted transcriptio 70.9 2.5 5.3E-05 27.7 1.2 22 127-151 77-98 (148)
103 COG5151 SSL1 RNA polymerase II 70.5 0.96 2.1E-05 33.9 -0.8 49 15-65 360-408 (421)
104 COG1198 PriA Primosomal protei 69.9 0.52 1.1E-05 39.6 -2.6 45 83-135 437-484 (730)
105 COG3364 Zn-ribbon containing p 67.6 2.3 5E-05 26.4 0.5 16 46-61 3-18 (112)
106 PF04810 zf-Sec23_Sec24: Sec23 65.1 2.5 5.4E-05 21.5 0.3 32 46-91 3-34 (40)
107 PF06220 zf-U1: U1 zinc finger 64.5 5.3 0.00011 20.1 1.4 23 125-147 2-26 (38)
108 PF01927 Mut7-C: Mut7-C RNAse 64.5 4 8.6E-05 27.2 1.3 53 45-100 91-143 (147)
109 KOG2785|consensus 64.1 4.6 9.9E-05 31.2 1.6 60 44-103 2-90 (390)
110 PF05191 ADK_lid: Adenylate ki 63.8 3.1 6.8E-05 20.7 0.5 30 47-92 3-32 (36)
111 PF15269 zf-C2H2_7: Zinc-finge 63.6 5 0.00011 21.0 1.2 22 127-148 21-42 (54)
112 KOG4167|consensus 63.4 2 4.4E-05 35.9 -0.3 25 126-151 792-816 (907)
113 smart00834 CxxC_CXXC_SSSS Puta 62.8 3.8 8.2E-05 20.5 0.7 13 127-139 6-18 (41)
114 KOG3408|consensus 62.0 5.4 0.00012 25.7 1.4 25 123-147 54-78 (129)
115 COG1996 RPC10 DNA-directed RNA 61.3 3.9 8.4E-05 21.9 0.6 12 44-55 5-16 (49)
116 PRK09678 DNA-binding transcrip 60.7 2 4.4E-05 25.0 -0.6 41 46-96 2-44 (72)
117 KOG2593|consensus 60.6 5.1 0.00011 31.5 1.4 43 37-90 120-162 (436)
118 smart00154 ZnF_AN1 AN1-like Zi 58.7 5.7 0.00012 20.1 0.9 14 126-139 12-25 (39)
119 smart00440 ZnF_C2C2 C2C2 Zinc 58.1 1.6 3.4E-05 22.3 -1.2 12 81-92 28-39 (40)
120 PF13878 zf-C2H2_3: zinc-finge 57.9 11 0.00024 19.2 1.9 23 82-104 14-38 (41)
121 KOG2907|consensus 57.8 4.3 9.4E-05 25.7 0.5 41 45-93 74-114 (116)
122 COG1997 RPL43A Ribosomal prote 57.7 4.5 9.7E-05 24.5 0.5 34 43-94 33-66 (89)
123 PF09986 DUF2225: Uncharacteri 57.2 4.4 9.6E-05 28.9 0.5 53 79-139 3-61 (214)
124 PF10276 zf-CHCC: Zinc-finger 56.8 5.3 0.00012 20.4 0.6 12 80-91 28-39 (40)
125 PRK03824 hypA hydrogenase nick 56.8 3.3 7.1E-05 27.3 -0.2 15 44-58 69-83 (135)
126 PF08790 zf-LYAR: LYAR-type C2 56.2 3.6 7.7E-05 19.3 -0.1 20 127-147 1-20 (28)
127 COG2331 Uncharacterized protei 54.9 4.1 9E-05 23.9 0.1 34 43-91 10-43 (82)
128 PF04780 DUF629: Protein of un 54.8 9.4 0.0002 30.6 2.0 27 127-153 58-84 (466)
129 PF13451 zf-trcl: Probable zin 54.6 6.2 0.00013 21.2 0.7 18 124-141 2-19 (49)
130 COG0068 HypF Hydrogenase matur 54.5 6.5 0.00014 33.0 1.1 44 32-89 137-181 (750)
131 PF01428 zf-AN1: AN1-like Zinc 54.2 5 0.00011 20.6 0.3 15 125-139 12-26 (43)
132 KOG2636|consensus 51.2 11 0.00025 29.8 1.9 29 75-103 395-424 (497)
133 PF07503 zf-HYPF: HypF finger; 51.0 8.8 0.00019 19.0 0.9 31 48-92 2-32 (35)
134 PF09845 DUF2072: Zn-ribbon co 50.9 6.8 0.00015 25.6 0.6 15 81-95 1-15 (131)
135 COG1773 Rubredoxin [Energy pro 49.5 7.5 0.00016 21.4 0.5 15 81-95 3-17 (55)
136 cd00729 rubredoxin_SM Rubredox 49.4 8.1 0.00018 18.8 0.6 11 81-91 2-12 (34)
137 KOG2636|consensus 49.1 12 0.00027 29.6 1.8 27 119-145 394-421 (497)
138 COG1594 RPB9 DNA-directed RNA 49.0 4 8.7E-05 26.0 -0.7 40 45-92 72-111 (113)
139 PF12907 zf-met2: Zinc-binding 48.7 5.4 0.00012 20.4 -0.1 27 127-153 2-31 (40)
140 PF04423 Rad50_zn_hook: Rad50 48.6 7.6 0.00016 21.0 0.5 12 128-139 22-33 (54)
141 PF10013 DUF2256: Uncharacteri 48.4 10 0.00022 19.6 0.9 17 127-143 9-25 (42)
142 PF04780 DUF629: Protein of un 48.3 14 0.0003 29.6 2.0 26 81-106 57-83 (466)
143 PF01096 TFIIS_C: Transcriptio 48.2 1.2 2.5E-05 22.6 -2.7 10 82-91 29-38 (39)
144 PHA02998 RNA polymerase subuni 47.6 3.6 7.9E-05 28.3 -1.1 39 45-95 143-185 (195)
145 COG4888 Uncharacterized Zn rib 47.6 2.3 5E-05 26.4 -1.8 13 79-91 20-32 (104)
146 PTZ00255 60S ribosomal protein 46.8 4.4 9.6E-05 24.7 -0.7 37 40-94 31-67 (90)
147 KOG1842|consensus 45.1 12 0.00027 29.6 1.3 26 81-106 15-41 (505)
148 KOG4173|consensus 43.8 13 0.00027 26.4 1.1 62 44-105 105-171 (253)
149 KOG0717|consensus 43.8 13 0.00028 29.7 1.2 21 127-147 293-313 (508)
150 TIGR00595 priA primosomal prot 43.4 12 0.00026 30.3 1.0 9 126-134 253-261 (505)
151 COG1656 Uncharacterized conser 43.0 24 0.00051 24.1 2.2 50 45-102 97-151 (165)
152 cd00924 Cyt_c_Oxidase_Vb Cytoc 42.7 13 0.00027 23.1 0.8 17 121-138 75-91 (97)
153 PRK14873 primosome assembly pr 42.5 14 0.0003 31.1 1.3 10 47-56 385-394 (665)
154 PRK05978 hypothetical protein; 41.8 7.6 0.00016 26.1 -0.3 34 44-94 32-65 (148)
155 smart00661 RPOL9 RNA polymeras 41.6 15 0.00033 19.3 1.0 14 81-94 20-33 (52)
156 COG3357 Predicted transcriptio 41.4 13 0.00027 22.7 0.7 15 79-93 56-70 (97)
157 KOG4124|consensus 40.4 1.6 3.4E-05 33.3 -4.0 69 79-147 347-419 (442)
158 KOG2071|consensus 40.0 19 0.00041 29.6 1.6 29 123-152 415-443 (579)
159 PRK00464 nrdR transcriptional 39.8 12 0.00026 25.3 0.4 17 126-142 28-44 (154)
160 PF09332 Mcm10: Mcm10 replicat 39.7 4.7 0.0001 30.9 -1.7 69 21-93 223-297 (344)
161 cd00730 rubredoxin Rubredoxin; 39.4 14 0.00029 19.9 0.5 13 82-94 2-14 (50)
162 PRK05452 anaerobic nitric oxid 39.1 32 0.00069 27.7 2.8 42 40-90 420-467 (479)
163 KOG0717|consensus 39.1 18 0.00039 28.9 1.4 22 127-148 461-482 (508)
164 PLN02294 cytochrome c oxidase 38.4 16 0.00035 25.1 0.9 16 79-94 139-154 (174)
165 PF05741 zf-nanos: Nanos RNA b 37.3 25 0.00054 19.3 1.4 12 80-91 32-43 (55)
166 COG4391 Uncharacterized protei 37.2 22 0.00047 20.0 1.1 16 123-138 45-60 (62)
167 COG3677 Transposase and inacti 36.5 17 0.00037 23.7 0.8 17 123-139 50-66 (129)
168 PF00301 Rubredoxin: Rubredoxi 35.6 15 0.00033 19.4 0.4 14 82-95 2-15 (47)
169 KOG3408|consensus 34.6 27 0.00057 22.6 1.4 26 78-103 54-79 (129)
170 PF02748 PyrI_C: Aspartate car 34.4 18 0.00039 19.6 0.5 17 123-139 32-48 (52)
171 PF01155 HypA: Hydrogenase exp 33.9 15 0.00033 23.2 0.2 14 44-57 69-82 (113)
172 PF02176 zf-TRAF: TRAF-type zi 33.7 16 0.00034 19.9 0.2 42 44-94 8-55 (60)
173 PF01363 FYVE: FYVE zinc finge 33.1 18 0.0004 20.3 0.5 30 45-94 9-38 (69)
174 COG4338 Uncharacterized protei 33.0 16 0.00035 19.4 0.2 16 128-143 14-29 (54)
175 COG1571 Predicted DNA-binding 32.9 20 0.00042 28.4 0.7 15 126-140 367-381 (421)
176 CHL00174 accD acetyl-CoA carbo 32.8 16 0.00034 27.5 0.2 35 44-95 37-71 (296)
177 COG5188 PRP9 Splicing factor 3 32.1 30 0.00066 26.7 1.6 29 75-103 368-397 (470)
178 PF01780 Ribosomal_L37ae: Ribo 31.8 22 0.00048 21.7 0.7 10 126-135 35-44 (90)
179 PF07975 C1_4: TFIIH C1-like d 31.7 15 0.00033 19.8 -0.0 25 125-150 20-44 (51)
180 PF14353 CpXC: CpXC protein 31.6 8.9 0.00019 24.7 -1.2 55 82-145 2-57 (128)
181 PF01286 XPA_N: XPA protein N- 30.7 24 0.00051 17.4 0.5 13 127-139 4-16 (34)
182 PRK12380 hydrogenase nickel in 30.7 17 0.00037 23.1 0.0 14 44-57 69-82 (113)
183 TIGR01206 lysW lysine biosynth 30.3 23 0.0005 19.4 0.5 12 82-93 3-14 (54)
184 COG5112 UFD2 U1-like Zn-finger 30.1 28 0.00062 21.9 0.9 25 123-147 52-76 (126)
185 KOG1088|consensus 29.8 23 0.00051 22.7 0.6 22 74-95 91-112 (124)
186 PRK01343 zinc-binding protein; 29.7 35 0.00075 18.9 1.2 14 125-138 8-21 (57)
187 PF09416 UPF1_Zn_bind: RNA hel 29.0 41 0.00089 22.7 1.6 46 44-89 13-68 (152)
188 PRK12722 transcriptional activ 28.9 30 0.00065 24.2 1.0 30 44-89 133-162 (187)
189 PF08792 A2L_zn_ribbon: A2L zi 28.8 31 0.00067 16.7 0.8 12 126-137 21-32 (33)
190 TIGR01385 TFSII transcription 28.7 16 0.00036 27.5 -0.3 44 41-92 254-297 (299)
191 PF06397 Desulfoferrod_N: Desu 28.6 28 0.00061 17.3 0.6 11 126-136 6-16 (36)
192 PRK04351 hypothetical protein; 28.5 22 0.00047 23.9 0.3 35 44-94 111-145 (149)
193 PF07295 DUF1451: Protein of u 28.3 19 0.00041 24.1 -0.1 36 38-91 105-140 (146)
194 PF09082 DUF1922: Domain of un 27.9 7.4 0.00016 22.4 -1.7 14 80-94 19-32 (68)
195 PRK03681 hypA hydrogenase nick 27.6 19 0.00041 22.9 -0.1 9 82-90 71-79 (114)
196 PRK05654 acetyl-CoA carboxylas 27.6 21 0.00045 26.8 0.1 35 44-95 26-60 (292)
197 TIGR00515 accD acetyl-CoA carb 27.4 22 0.00048 26.6 0.2 35 44-95 25-59 (285)
198 PF14803 Nudix_N_2: Nudix N-te 27.3 15 0.00031 18.0 -0.6 12 80-91 21-32 (34)
199 PF14447 Prok-RING_4: Prokaryo 26.9 30 0.00064 19.0 0.6 12 128-139 41-52 (55)
200 PRK12860 transcriptional activ 26.8 33 0.00071 24.1 0.9 29 44-88 133-161 (189)
201 PF11931 DUF3449: Domain of un 26.7 21 0.00046 25.1 0.0 24 79-102 99-123 (196)
202 PF04438 zf-HIT: HIT zinc fing 26.1 42 0.00091 15.8 1.0 14 126-139 13-26 (30)
203 PF13824 zf-Mss51: Zinc-finger 26.0 43 0.00093 18.4 1.1 18 77-94 10-27 (55)
204 KOG2807|consensus 25.8 95 0.002 23.9 3.2 68 80-147 289-366 (378)
205 KOG1994|consensus 25.6 35 0.00075 24.7 0.9 23 124-146 237-259 (268)
206 PF14787 zf-CCHC_5: GAG-polypr 25.4 29 0.00062 17.3 0.3 17 127-143 3-19 (36)
207 TIGR00280 L37a ribosomal prote 25.4 33 0.00071 21.0 0.6 10 126-135 35-44 (91)
208 PF14369 zf-RING_3: zinc-finge 25.4 33 0.00072 16.8 0.6 10 83-92 23-32 (35)
209 PF14255 Cys_rich_CPXG: Cystei 25.2 31 0.00066 18.7 0.4 12 127-138 1-12 (52)
210 PF03884 DUF329: Domain of unk 25.1 34 0.00073 19.0 0.6 12 127-138 3-14 (57)
211 PRK00762 hypA hydrogenase nick 24.6 23 0.00049 22.9 -0.2 14 44-58 69-82 (124)
212 KOG4118|consensus 24.5 46 0.00099 19.0 1.0 22 82-103 39-60 (74)
213 PLN02748 tRNA dimethylallyltra 24.3 55 0.0012 26.4 1.8 24 80-103 417-441 (468)
214 PF13821 DUF4187: Domain of un 24.3 36 0.00077 18.7 0.6 19 127-145 28-46 (55)
215 PLN03238 probable histone acet 23.8 83 0.0018 23.7 2.6 24 124-147 46-69 (290)
216 smart00731 SprT SprT homologue 23.4 35 0.00076 22.5 0.6 33 45-92 112-144 (146)
217 PF08271 TF_Zn_Ribbon: TFIIB z 23.2 40 0.00086 17.1 0.6 10 126-135 19-28 (43)
218 PF01215 COX5B: Cytochrome c o 23.2 30 0.00065 22.9 0.2 16 79-94 110-125 (136)
219 PTZ00448 hypothetical protein; 23.1 63 0.0014 25.2 1.9 23 81-103 314-336 (373)
220 PF14311 DUF4379: Domain of un 23.1 34 0.00075 18.4 0.4 15 44-58 27-41 (55)
221 smart00659 RPOLCX RNA polymera 23.0 44 0.00095 17.3 0.8 13 127-139 3-15 (44)
222 KOG0782|consensus 22.8 25 0.00054 29.1 -0.3 29 112-140 239-267 (1004)
223 PLN02748 tRNA dimethylallyltra 22.7 55 0.0012 26.4 1.6 23 125-147 417-440 (468)
224 PRK03976 rpl37ae 50S ribosomal 22.6 39 0.00085 20.6 0.6 10 126-135 36-45 (90)
225 COG1579 Zn-ribbon protein, pos 22.4 38 0.00083 24.7 0.6 42 41-94 193-234 (239)
226 TIGR00686 phnA alkylphosphonat 22.4 27 0.00059 22.1 -0.1 16 80-95 18-33 (109)
227 PRK00564 hypA hydrogenase nick 22.2 32 0.0007 22.0 0.2 14 44-57 70-83 (117)
228 PTZ00043 cytochrome c oxidase 22.2 45 0.00097 24.1 0.9 31 78-111 178-208 (268)
229 PF08209 Sgf11: Sgf11 (transcr 22.2 45 0.00097 16.2 0.6 21 126-147 4-24 (33)
230 TIGR01384 TFS_arch transcripti 22.0 15 0.00033 22.7 -1.4 41 45-93 62-102 (104)
231 PF03966 Trm112p: Trm112p-like 21.6 34 0.00073 19.4 0.2 18 75-92 47-64 (68)
232 PLN03239 histone acetyltransfe 21.4 61 0.0013 25.1 1.5 24 124-147 104-127 (351)
233 PF03604 DNA_RNApol_7kD: DNA d 21.2 47 0.001 16.0 0.6 11 126-136 17-27 (32)
234 PF10263 SprT-like: SprT-like 21.0 24 0.00052 23.4 -0.6 33 44-92 122-154 (157)
235 COG1439 Predicted nucleic acid 20.6 24 0.00051 24.4 -0.7 13 44-56 138-150 (177)
236 KOG0402|consensus 20.3 32 0.00068 20.7 -0.1 10 126-135 36-45 (92)
237 PF02891 zf-MIZ: MIZ/SP-RING z 20.0 44 0.00094 17.8 0.4 9 81-89 41-49 (50)
No 1
>KOG2462|consensus
Probab=99.89 E-value=4.5e-24 Score=151.05 Aligned_cols=112 Identities=28% Similarity=0.339 Sum_probs=96.9
Q ss_pred CcchhhhhhcccccccccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhc
Q psy13210 26 GFSKLKRALDVNQSMIDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
.+.++...............+.|..|+++|.+...|..|. ++|. -+++|.+||+.|...+-|+-|+++|+
T Consensus 142 T~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHi--------rTH~--l~c~C~iCGKaFSRPWLLQGHiRTHT 211 (279)
T KOG2462|consen 142 TSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHI--------RTHT--LPCECGICGKAFSRPWLLQGHIRTHT 211 (279)
T ss_pred cccccchhhcccccccccccccCCCCCceeeehHHHhhHh--------hccC--CCcccccccccccchHHhhccccccc
Confidence 3344444444455555567888999999999999999999 9987 67899999999999999999999999
Q ss_pred CCCCcH-----------HHHHHHHHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 106 GEKPYA-----------HIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 106 ~~~~~~-----------~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
||+||. ++|+.|+.+|.+.++|.|..|+|+|...+.|.+|..
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 999997 899999999999999999999999999999999975
No 2
>KOG2462|consensus
Probab=99.84 E-value=1.4e-21 Score=138.42 Aligned_cols=105 Identities=30% Similarity=0.529 Sum_probs=92.5
Q ss_pred ccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCC---CCCcccccccccccccHHHHHHHHhHhcC-------CCCcH
Q psy13210 42 DISADRLERLRTQCATSAELTQHEIRTIESMIRTDP---FRHKFVCYACDYFSYNIGCMRSHIRTHTG-------EKPYA 111 (155)
Q Consensus 42 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~---~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-------~~~~~ 111 (155)
....+.|+.|++.+.+.++|.+|. ++|. ..+.+.|++||+.|.....|.+|+++|+- -+.|.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHk--------Q~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHK--------QTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFS 198 (279)
T ss_pred cCCceeccccccccccccccchhh--------cccccccccccccCCCCCceeeehHHHhhHhhccCCCccccccccccc
Confidence 346788999999999999999999 8885 47789999999999999999999999982 12222
Q ss_pred --HHHHHHHHhccCCCCeecCcCcccccCchHHHHHHhhhhCCCCC
Q psy13210 112 --HIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLRRTHGQESI 155 (155)
Q Consensus 112 --~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~p 155 (155)
=-|.-|+|+|||||||.|+.|+|.|.-.++|+.|++ +|++.|+
T Consensus 199 RPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQ-THS~~K~ 243 (279)
T KOG2462|consen 199 RPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQ-THSDVKK 243 (279)
T ss_pred chHHhhcccccccCCCCccCCcccchhcchHHHHHHHH-hhcCCcc
Confidence 367889999999999999999999999999999999 8998874
No 3
>KOG1074|consensus
Probab=99.76 E-value=1.7e-19 Score=143.24 Aligned_cols=58 Identities=17% Similarity=0.276 Sum_probs=53.5
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCC
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKP 109 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 109 (155)
...+|..|.++|.+.+.|..|. +.|++++||+|.+||..|.++.+|+.|...|..+.|
T Consensus 352 ~khkCr~CakvfgS~SaLqiHl--------RSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~p 409 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHL--------RSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKYP 409 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhh--------hccCCCCCeeecccccccccccceeeeeeeccccCC
Confidence 4567999999999999999999 999999999999999999999999999998876553
No 4
>KOG3576|consensus
Probab=99.63 E-value=5.4e-17 Score=110.64 Aligned_cols=102 Identities=22% Similarity=0.296 Sum_probs=82.8
Q ss_pred ccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCCcH----------
Q psy13210 42 DISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYA---------- 111 (155)
Q Consensus 42 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~---------- 111 (155)
+...+.|..|++.|.....|.+|+ ..|...+.+.|..||+.|.+..+|++|+++|+|.+||+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~--------kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHL--------KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHh--------hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 346788999999999999999999 99999999999999999999999999999999888876
Q ss_pred -HHHHHHHH-hcc----------CCCCeecCcCcccccCchHHHHHHhhhhC
Q psy13210 112 -HIIRNHYR-KHT----------GRKPFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 112 -~~l~~H~~-~h~----------~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
..|..|.+ +|. .++-|.|+.||.+-.....+..|+..+|.
T Consensus 186 rcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 186 RCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred hccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 34555643 343 23457788888887777777788775543
No 5
>KOG3623|consensus
Probab=99.61 E-value=2.8e-16 Score=123.81 Aligned_cols=82 Identities=20% Similarity=0.367 Sum_probs=75.8
Q ss_pred cccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHh
Q psy13210 41 IDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRK 120 (155)
Q Consensus 41 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~ 120 (155)
...+.|-|+.|++.|...+.|.+|. =.|++.+||+|.+|.+.|+.+..|..|++.|.
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHK--------YEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHS--------------- 946 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHK--------YEHSGQRPYQCIICKKAFKHKHHLTEHKRLHS--------------- 946 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhh--------hhhcCCCCcccchhhHhhhhhhhhhhhhhhcc---------------
Confidence 3447899999999999999999998 78999999999999999999999888887777
Q ss_pred ccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 121 HTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 121 h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
||+||.|+.|+|+|+...+..+||.
T Consensus 947 --GEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 947 --GEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred --CCCcchhhhhhhhcccccchHhhhc
Confidence 8888999999999999999999987
No 6
>KOG1074|consensus
Probab=99.57 E-value=1.2e-15 Score=121.73 Aligned_cols=60 Identities=18% Similarity=0.274 Sum_probs=54.0
Q ss_pred cChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCCc
Q psy13210 43 ISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPY 110 (155)
Q Consensus 43 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 110 (155)
..+-.|-+|.++..-.+.|+.|. ++|++++||+|.+||+.|.++.+|+-|+.+|-..-++
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHy--------rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~ 662 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHY--------RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA 662 (958)
T ss_pred CCccceeeeeecccchhhhhhhh--------hcccCcCccccccccchhccccchhhcccccccCccc
Confidence 35667999999999999999999 9999999999999999999999999999998754333
No 7
>KOG3623|consensus
Probab=99.40 E-value=1.6e-13 Score=108.59 Aligned_cols=97 Identities=23% Similarity=0.420 Sum_probs=78.7
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCC-------------CCcH
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGE-------------KPYA 111 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-------------~~~~ 111 (155)
...|..|.+.+.....|..|++. +-...+..|.|..|.++|.+...|.+|+.+|..- +.|+
T Consensus 210 lltcpycdrgykrltslkeHiky------rhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFK 283 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKY------RHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFK 283 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHH------HHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccc
Confidence 44599999999999999999742 2223556789999999999999999999988531 2222
Q ss_pred -----------HHHHHHHHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 112 -----------HIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 112 -----------~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
..|+.|+|+|.||+||.|+-|+|+|+...+...|+.
T Consensus 284 CtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 284 CTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 778999999999999999999999999999988875
No 8
>KOG3608|consensus
Probab=99.37 E-value=1.4e-12 Score=95.91 Aligned_cols=111 Identities=23% Similarity=0.439 Sum_probs=79.4
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhh------------------hhhhc-cCCCCCcccccccccccccHHHHHHHHhHh
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTI------------------ESMIR-TDPFRHKFVCYACDYFSYNIGCMRSHIRTH 104 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~------------------~~~~~-~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 104 (155)
+.|.|..|.+.|.+...|..|+..++ ..|++ .|...+||+|+.|++.|.+.+.|.+|...|
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc
Confidence 45666666666666666666654221 12224 456788999999999999999999999888
Q ss_pred cCCCCcH-------------HHHHHHHHh-ccCC--CCeecCcCcccccCchHHHHHHhhhhCCCCC
Q psy13210 105 TGEKPYA-------------HIIRNHYRK-HTGR--KPFKCVVCKQFFATYSGAYQHLRRTHGQESI 155 (155)
Q Consensus 105 ~~~~~~~-------------~~l~~H~~~-h~~~--~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~p 155 (155)
. +-.|. ..+++|++. |.|. .+|.|..|++.|.+-.+|.+|++..|+-..|
T Consensus 316 S-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 316 S-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred c-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCC
Confidence 7 32232 568888765 5454 4699999999999999999999888875443
No 9
>KOG3608|consensus
Probab=99.36 E-value=1.7e-12 Score=95.39 Aligned_cols=105 Identities=24% Similarity=0.311 Sum_probs=84.0
Q ss_pred ccccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCC--Cc-------
Q psy13210 40 MIDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEK--PY------- 110 (155)
Q Consensus 40 ~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~--~~------- 110 (155)
.+..+..-|+.|+.-|++...|-.|... ++-....+|+|..|.+.|.+...|..|+..|..-- |.
T Consensus 202 Hs~eKvvACp~Cg~~F~~~tkl~DH~rR------qt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~ 275 (467)
T KOG3608|consen 202 HSNEKVVACPHCGELFRTKTKLFDHLRR------QTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSS 275 (467)
T ss_pred cCCCeEEecchHHHHhccccHHHHHHHh------hhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCC
Confidence 3444667799999999999999999732 34445678999999999999999999998886421 11
Q ss_pred HHHHHHHHHh-ccCCCCeecCcCcccccCchHHHHHHhhhhC
Q psy13210 111 AHIIRNHYRK-HTGRKPFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 111 ~~~l~~H~~~-h~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
.+.|.+|++. |+.++||+|+.|++.|.+.+.|.+|.. .|+
T Consensus 276 ~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~-~HS 316 (467)
T KOG3608|consen 276 ASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ-VHS 316 (467)
T ss_pred hHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH-hcc
Confidence 2788889887 888899999999999999999999988 776
No 10
>PHA00733 hypothetical protein
Probab=99.27 E-value=1.2e-11 Score=80.59 Aligned_cols=88 Identities=16% Similarity=0.244 Sum_probs=70.4
Q ss_pred ccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhc
Q psy13210 42 DISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKH 121 (155)
Q Consensus 42 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h 121 (155)
....+.|..|...|.....|..+.+ +..++.+ .+.+||+|+.||+.|.....|..|++.|.
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~--l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~---------------- 97 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSY--LYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYTE---------------- 97 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHH--HHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcCC----------------
Confidence 3467789999999998887777732 2223233 34789999999999999999998887552
Q ss_pred cCCCCeecCcCcccccCchHHHHHHhhhhC
Q psy13210 122 TGRKPFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 122 ~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
.+|.|++|++.|.+...|..|++..|+
T Consensus 98 ---~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 98 ---HSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred ---cCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 258999999999999999999997775
No 11
>KOG3576|consensus
Probab=99.26 E-value=2.3e-12 Score=88.19 Aligned_cols=72 Identities=18% Similarity=0.257 Sum_probs=60.2
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhH-hcCCCCcH-----------
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRT-HTGEKPYA----------- 111 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~----------- 111 (155)
..+-|..||+.|...-+|.+|+ ++|++.+||+|..|++.|....+|..|.+. |.....|.
T Consensus 144 kr~lct~cgkgfndtfdlkrh~--------rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vc 215 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLKRHT--------RTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVC 215 (267)
T ss_pred HHHHHhhccCcccchhhhhhhh--------ccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeee
Confidence 5566999999999999999999 999999999999999999999999999875 54333332
Q ss_pred ----------HHHHHHHHhccC
Q psy13210 112 ----------HIIRNHYRKHTG 123 (155)
Q Consensus 112 ----------~~l~~H~~~h~~ 123 (155)
..+..|++.|..
T Consensus 216 edcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 216 EDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred cccCCCCCChhHHHHHHHhcCC
Confidence 567778877543
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.12 E-value=5.3e-11 Score=56.01 Aligned_cols=26 Identities=46% Similarity=0.980 Sum_probs=23.7
Q ss_pred HHHHHHHhccCCCCeecCcCcccccC
Q psy13210 113 IIRNHYRKHTGRKPFKCVVCKQFFAT 138 (155)
Q Consensus 113 ~l~~H~~~h~~~~~~~C~~C~k~f~~ 138 (155)
+|.+|+++|+|++||.|++|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999999974
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.03 E-value=1.2e-10 Score=63.84 Aligned_cols=44 Identities=20% Similarity=0.345 Sum_probs=38.8
Q ss_pred cccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCcccccCchHHH
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATYSGAY 143 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~ 143 (155)
-|+|+.||+.|...++|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-------------------k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-------------------TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-------------------CcccCCcccceecccceeE
Confidence 3799999999999999999988875 3699999999999888774
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.91 E-value=3.5e-10 Score=61.97 Aligned_cols=45 Identities=11% Similarity=0.050 Sum_probs=40.6
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHH
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMR 98 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 98 (155)
-+|.|+.||+.|....+|..|+ ++|. ++++|..|++.|...+.|.
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~--------r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHL--------RKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cccCcchhCCeeccHHHHHHHH--------HhcC--CcccCCcccceecccceeE
Confidence 4689999999999999999999 9998 6899999999999877654
No 15
>KOG3993|consensus
Probab=98.83 E-value=1e-09 Score=82.55 Aligned_cols=103 Identities=17% Similarity=0.205 Sum_probs=75.8
Q ss_pred cChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcC--------CCCcHHH-
Q psy13210 43 ISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTG--------EKPYAHI- 113 (155)
Q Consensus 43 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~--------~~~~~~~- 113 (155)
.+.|-|..|...|...-.|.+|. -...-...|+|++|+|+|+-..+|..|++=|.. ..|-+..
T Consensus 265 iGdyiCqLCK~kYeD~F~LAQHr--------C~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~ 336 (500)
T KOG3993|consen 265 IGDYICQLCKEKYEDAFALAQHR--------CPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAV 336 (500)
T ss_pred HHHHHHHHHHHhhhhHHHHhhcc--------CCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhh
Confidence 47888999999999999999996 444444569999999999999999999998852 2221111
Q ss_pred ----HHHH-HHh--ccCCCCeecCcCcccccCchHHHHHHhhhhCCC
Q psy13210 114 ----IRNH-YRK--HTGRKPFKCVVCKQFFATYSGAYQHLRRTHGQE 153 (155)
Q Consensus 114 ----l~~H-~~~--h~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~ 153 (155)
+.+- .+. -..+.-|.|.+|+|.|..+.-|+.|+.++|..+
T Consensus 337 ~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 337 ETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 0000 000 022346999999999999999999988666544
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.78 E-value=1.3e-08 Score=80.58 Aligned_cols=91 Identities=14% Similarity=0.156 Sum_probs=71.3
Q ss_pred hhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCCcH--------------
Q psy13210 46 DRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYA-------------- 111 (155)
Q Consensus 46 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~-------------- 111 (155)
+.|+.|+..|. ...|..|+ .++. +++.|+ ||+.+ ....|..|+.+|.+++++.
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~--------~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~ 520 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHM--------KVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSA 520 (567)
T ss_pred ccCCCCCCccc-hHHHHHHH--------HhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccc
Confidence 57999999885 57889998 7663 789999 99765 6689999998888877764
Q ss_pred -------HHHHHHHHhccCCCCeecCcCcccccCchHHHHHHhhhhC
Q psy13210 112 -------HIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 112 -------~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
..|..|..+. |.+++.|..||+.+... .+..|+...|.
T Consensus 521 ~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 521 MDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred cchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 1577888885 88889999999888775 56667765664
No 17
>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=98.62 E-value=1.2e-08 Score=47.83 Aligned_cols=26 Identities=27% Similarity=0.367 Sum_probs=22.9
Q ss_pred HHhhhHHhhhhhhhccCCCCCccccccccccccc
Q psy13210 60 ELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYN 93 (155)
Q Consensus 60 ~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~ 93 (155)
+|..|+ ++|++++||+|++|++.|.+
T Consensus 1 ~l~~H~--------~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHM--------RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHH--------HHHSSSSSEEESSSSEEESS
T ss_pred CHHHHh--------hhcCCCCCCCCCCCcCeeCc
Confidence 467777 99999999999999999964
No 18
>PHA00733 hypothetical protein
Probab=98.61 E-value=5.5e-08 Score=63.47 Aligned_cols=54 Identities=22% Similarity=0.209 Sum_probs=47.5
Q ss_pred ccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhc
Q psy13210 42 DISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 42 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
...+|.|+.|++.|.....|..|+ +.+ ..+|.|+.|++.|.....|..|+....
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~--------r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHI--------RYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHH--------hcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 356899999999999999999999 765 357999999999999999999988744
No 19
>PHA00732 hypothetical protein
Probab=98.58 E-value=4.1e-08 Score=58.53 Aligned_cols=44 Identities=30% Similarity=0.618 Sum_probs=29.6
Q ss_pred cccccccccccccHHHHHHHHhH-hcCCCCcHHHHHHHHHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRT-HTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
||.|+.||+.|.+..+|..|++. |. ++.|+.||+.|. .|..|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--------------------~~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--------------------LTKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--------------------CCccCCCCCEeC---Chhhhhc
Confidence 46777777777777777777663 43 246777777776 3666665
No 20
>KOG3993|consensus
Probab=98.58 E-value=1e-08 Score=77.34 Aligned_cols=85 Identities=16% Similarity=0.113 Sum_probs=60.5
Q ss_pred HHHhhhhhcccCCCcchhhhhhcccccccccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccC----------------
Q psy13210 13 RAFYAYEKDAQDGGFSKLKRALDVNQSMIDISADRLERLRTQCATSAELTQHEIRTIESMIRTD---------------- 76 (155)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~---------------- 76 (155)
..+..+.|..|-..+..-.......-..+..-.|+|..|+++|+-..+|..|. +.|
T Consensus 263 n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHR--------RWHKPR~eaa~a~~~P~k~ 334 (500)
T KOG3993|consen 263 NVIGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHR--------RWHKPRPEAAKAGSPPPKQ 334 (500)
T ss_pred ccHHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhh--------cccCCchhhhhcCCCChhh
Confidence 33445555555443322222233334456667899999999999999999998 555
Q ss_pred -----------------CCCCcccccccccccccHHHHHHHHhHhc
Q psy13210 77 -----------------PFRHKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 77 -----------------~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
..+..|.|.+|++.|++...|..|+.+|.
T Consensus 335 ~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 335 AVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 11235899999999999999999998875
No 21
>PHA00616 hypothetical protein
Probab=98.56 E-value=3.2e-08 Score=51.70 Aligned_cols=29 Identities=17% Similarity=0.445 Sum_probs=24.9
Q ss_pred CeecCcCcccccCchHHHHHHhhhhCCCCC
Q psy13210 126 PFKCVVCKQFFATYSGAYQHLRRTHGQESI 155 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~~L~~H~~~~H~~~~p 155 (155)
||+|+.||+.|.+.+.|.+|++ .|.+++|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r-~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLL-SVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHH-HhcCCCc
Confidence 6999999999999999999999 4555454
No 22
>PHA00616 hypothetical protein
Probab=98.51 E-value=5.7e-08 Score=50.77 Aligned_cols=29 Identities=10% Similarity=0.205 Sum_probs=23.5
Q ss_pred cccccccccccccHHHHHHHHhHhcCCCC
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRTHTGEKP 109 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 109 (155)
||+|+.||+.|..++.|..|++.|+++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 57899999999998888888888875544
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.35 E-value=1e-06 Score=70.08 Aligned_cols=100 Identities=15% Similarity=0.274 Sum_probs=72.1
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhh-----------hccCCCCCcccccccccccccHHHHHHHHhHhcCCCCc--
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESM-----------IRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPY-- 110 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~-----------~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~-- 110 (155)
....|..|..... ...|..|...+...- .+...-++.+.|+.|++.|. ...|..|+.+|+ .++
T Consensus 406 ~~V~C~NC~~~i~-l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~C 481 (567)
T PLN03086 406 DTVECRNCKHYIP-SRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQC 481 (567)
T ss_pred CeEECCCCCCccc-hhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccC
Confidence 4456888876654 457778874333211 11112245678999999996 688999999864 222
Q ss_pred -------HHHHHHHHHhccCCCCeecCcCcccccC----------chHHHHHHh
Q psy13210 111 -------AHIIRNHYRKHTGRKPFKCVVCKQFFAT----------YSGAYQHLR 147 (155)
Q Consensus 111 -------~~~l~~H~~~h~~~~~~~C~~C~k~f~~----------~~~L~~H~~ 147 (155)
...|..|+.+|.+++++.|.+|++.|.. .+.|..|+.
T Consensus 482 pCg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~ 535 (567)
T PLN03086 482 PCGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHES 535 (567)
T ss_pred CCCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHH
Confidence 2789999999999999999999999952 458999988
No 24
>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=98.27 E-value=6.6e-07 Score=40.56 Aligned_cols=23 Identities=22% Similarity=0.504 Sum_probs=20.6
Q ss_pred ccccccccccccHHHHHHHHhHh
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRTH 104 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~h 104 (155)
|+|+.|++.|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 67999999999999999998875
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.26 E-value=2.1e-06 Score=47.53 Aligned_cols=52 Identities=21% Similarity=0.494 Sum_probs=39.5
Q ss_pred cccccccccccccHHHHHHHHhH-hcCCCCcHHHHHHHHHhccCCCCeecCcCcccccCchHHHHHHhhhhC
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRT-HTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
.|.||+|++ ..+...|..|... |.. ..+.+.|++|...+. .+|.+|+...|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~----------------~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRS----------------ESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcC----------------CCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 489999999 4556788888665 442 234699999998755 499999997663
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=98.20 E-value=1.1e-06 Score=39.86 Aligned_cols=22 Identities=36% Similarity=0.859 Sum_probs=20.9
Q ss_pred eecCcCcccccCchHHHHHHhh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRR 148 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~ 148 (155)
|.|+.|++.|.+.+.|.+|++.
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 7899999999999999999984
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.20 E-value=1.8e-07 Score=68.40 Aligned_cols=70 Identities=19% Similarity=0.345 Sum_probs=50.5
Q ss_pred CCCcccccc--cccccccHHHHHHHHhH-hcCCCCcHH-HHHHHHHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 78 FRHKFVCYA--CDYFSYNIGCMRSHIRT-HTGEKPYAH-IIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 78 ~~~~~~C~~--C~~~f~~~~~l~~H~~~-h~~~~~~~~-~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
++|||+|++ |.+.++....|+-|+.- |...+.... .-..+..--...+||.|++|+|++.+-..|+.|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 359999998 99999999999999875 432221110 00011111336789999999999999999999976
No 28
>PHA00732 hypothetical protein
Probab=98.15 E-value=9.9e-07 Score=52.60 Aligned_cols=47 Identities=17% Similarity=0.134 Sum_probs=38.9
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhcc-CCCCCcccccccccccccHHHHHHHHhHhc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRT-DPFRHKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
++.|+.|++.|....+|..|+ +. |. ++.|+.||+.|. .+..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~--------r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHA--------RRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHh--------hcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 378999999999999999999 63 54 358999999998 5778876654
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=98.11 E-value=2.4e-06 Score=38.81 Aligned_cols=24 Identities=38% Similarity=0.782 Sum_probs=20.1
Q ss_pred eecCcCcccccCchHHHHHHhhhh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRRTH 150 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~~H 150 (155)
|.|++|++.|.+...|..|++.+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999999654
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.04 E-value=3.3e-06 Score=39.77 Aligned_cols=25 Identities=32% Similarity=0.667 Sum_probs=22.7
Q ss_pred CeecCcCcccccCchHHHHHHhhhh
Q psy13210 126 PFKCVVCKQFFATYSGAYQHLRRTH 150 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~~L~~H~~~~H 150 (155)
||.|..|++.|.+...|..|++.++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999999444
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.01 E-value=4.1e-06 Score=51.90 Aligned_cols=66 Identities=23% Similarity=0.460 Sum_probs=21.6
Q ss_pred cccccccccccHHHHHHHHhH-hcCCCCcH------HHHHHHHHhccCCCCeecCcCcccccCchHHHHHHhhh
Q psy13210 83 VCYACDYFSYNIGCMRSHIRT-HTGEKPYA------HIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLRRT 149 (155)
Q Consensus 83 ~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~------~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~~ 149 (155)
+|..|+..|.+...|..|+.. |.-..+-. ..+..+.+.- -...+.|.+|++.|.+...|..|++..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccccccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 478888888888888888765 43222211 2222232221 122699999999999999999999943
No 32
>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=97.91 E-value=9.9e-06 Score=36.69 Aligned_cols=23 Identities=35% Similarity=0.592 Sum_probs=18.9
Q ss_pred ccccccccccccHHHHHHHHhHh
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRTH 104 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~h 104 (155)
|+|++|++.|.+...|..|+..|
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 67999999999999999999876
No 33
>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=97.91 E-value=1.4e-05 Score=44.21 Aligned_cols=51 Identities=12% Similarity=0.116 Sum_probs=39.1
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCC-CCcccccccccccccHHHHHHHHhHhc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPF-RHKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~-~~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
.|.|+.|++ ..+...|..|.. ..|.. .+.+.||+|...+. .+|..|+..+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~-------~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCE-------DEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHH-------hHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 588999999 566789999973 55654 45799999998654 48888887753
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.81 E-value=2.5e-05 Score=41.84 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=23.8
Q ss_pred CCCCcccccccccccccHHHHHHHHhHhcCCCC
Q psy13210 77 PFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKP 109 (155)
Q Consensus 77 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 109 (155)
.++.|.+|++|+..+....+|.+|+.++.+.+|
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 567899999999999999999999988776665
No 35
>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=97.74 E-value=1.8e-05 Score=37.14 Aligned_cols=25 Identities=28% Similarity=0.583 Sum_probs=21.4
Q ss_pred cccccccccccccHHHHHHHHhHhc
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
||+|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5789999999999999999988764
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.47 E-value=9.8e-05 Score=33.77 Aligned_cols=25 Identities=32% Similarity=0.745 Sum_probs=22.3
Q ss_pred eecCcCcccccCchHHHHHHhhhhCC
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRRTHGQ 152 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~~H~~ 152 (155)
|.|+.|++.|.+.+.|..|++ .|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhcc
Confidence 679999999999999999999 6653
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.43 E-value=0.00014 Score=33.21 Aligned_cols=24 Identities=25% Similarity=0.552 Sum_probs=20.9
Q ss_pred ccccccccccccHHHHHHHHhHhc
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999988765
No 38
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.25 E-value=0.00036 Score=37.42 Aligned_cols=30 Identities=20% Similarity=0.424 Sum_probs=21.9
Q ss_pred CCCCeecCcCcccccCchHHHHHHhhhhCC
Q psy13210 123 GRKPFKCVVCKQFFATYSGAYQHLRRTHGQ 152 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~ 152 (155)
.+.|-.|++|+..+++..+|++|+...|..
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 567899999999999999999999866653
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.22 E-value=0.00034 Score=31.73 Aligned_cols=24 Identities=33% Similarity=0.587 Sum_probs=19.5
Q ss_pred eecCcCcccccCchHHHHHHhhhhC
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
|.|+.|+.... .+.|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 78999999998 9999999997664
No 40
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.16 E-value=0.00032 Score=43.29 Aligned_cols=58 Identities=16% Similarity=0.192 Sum_probs=21.6
Q ss_pred hhhhhhhhccCcHHHhhhHHhhhhhh----------hc--cC---CCCCcccccccccccccHHHHHHHHhHh
Q psy13210 47 RLERLRTQCATSAELTQHEIRTIESM----------IR--TD---PFRHKFVCYACDYFSYNIGCMRSHIRTH 104 (155)
Q Consensus 47 ~c~~C~~~~~~~~~l~~h~~~~~~~~----------~~--~~---~~~~~~~C~~C~~~f~~~~~l~~H~~~h 104 (155)
.|..|+..|.+...|..|+.....-. .+ .. .-...+.|.+|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 37778888888888888863111100 00 00 0122589999999999999999999974
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.12 E-value=0.00036 Score=31.94 Aligned_cols=21 Identities=38% Similarity=0.797 Sum_probs=20.1
Q ss_pred eecCcCcccccCchHHHHHHh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~ 147 (155)
|.|++|++.|.+...|..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 689999999999999999998
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.04 E-value=0.00043 Score=31.65 Aligned_cols=23 Identities=26% Similarity=0.579 Sum_probs=19.2
Q ss_pred ccccccccccccHHHHHHHHhHh
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRTH 104 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~h 104 (155)
|.|.+|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 56888999999999998888764
No 43
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.96 E-value=0.00017 Score=53.19 Aligned_cols=60 Identities=12% Similarity=0.128 Sum_probs=46.1
Q ss_pred cChhhhhh--hhhhccCcHHHhhhHHhhhhhh-----------hccCCCCCcccccccccccccHHHHHHHHh
Q psy13210 43 ISADRLER--LRTQCATSAELTQHEIRTIESM-----------IRTDPFRHKFVCYACDYFSYNIGCMRSHIR 102 (155)
Q Consensus 43 ~~~~~c~~--C~~~~~~~~~l~~h~~~~~~~~-----------~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 102 (155)
..+|+|++ |++.+.....|+-|+.....+. ...-...|||.|++|++.++....|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 37899976 9999999999999985433222 111134589999999999999999988854
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.90 E-value=0.00093 Score=30.26 Aligned_cols=23 Identities=22% Similarity=0.673 Sum_probs=17.9
Q ss_pred ccccccccccccHHHHHHHHhHhc
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
|+|+.|+.... ...|..|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67999999998 889999988854
No 45
>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=96.78 E-value=0.0006 Score=31.92 Aligned_cols=21 Identities=29% Similarity=0.792 Sum_probs=20.1
Q ss_pred eecCcCcccccCchHHHHHHh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~ 147 (155)
|.|+.|++.|.+...|..|++
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 789999999999999999987
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.77 E-value=0.00083 Score=45.49 Aligned_cols=27 Identities=22% Similarity=0.516 Sum_probs=20.5
Q ss_pred HHHHHHhccCCCCeecCcCcccccCch
Q psy13210 114 IRNHYRKHTGRKPFKCVVCKQFFATYS 140 (155)
Q Consensus 114 l~~H~~~h~~~~~~~C~~C~k~f~~~~ 140 (155)
+.+|.++|+++++|.|..|+..|....
T Consensus 131 ~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 131 VRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred HHHHHHHhcCCccEECCCCCceeEEec
Confidence 445555566888999999999987654
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=96.46 E-value=0.0013 Score=30.70 Aligned_cols=22 Identities=27% Similarity=0.699 Sum_probs=18.1
Q ss_pred ccccccccccccHHHHHHHHhH
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
|-|..|++.|.+...|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5688888888888888888765
No 48
>KOG1146|consensus
Probab=96.44 E-value=0.00099 Score=57.44 Aligned_cols=96 Identities=20% Similarity=0.350 Sum_probs=70.0
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhH-hcC-CCCcHHHHHHHHHh--
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRT-HTG-EKPYAHIIRNHYRK-- 120 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~-h~~-~~~~~~~l~~H~~~-- 120 (155)
...|..|+..+...+.+..|++ ..+...+.++|+.|+..|+....|..|++. |.. ...|......|.+.
T Consensus 436 l~e~~~~e~~~~s~r~~~~~t~-------~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~ar 508 (1406)
T KOG1146|consen 436 LVELTKAEPLLESKRSLEGQTV-------VLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLAR 508 (1406)
T ss_pred cccccchhhhhhhhccccccee-------eeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccc
Confidence 3446677777777777777763 456667889999999999999999999998 433 22233222223222
Q ss_pred ----ccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 121 ----HTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 121 ----h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
-.+.+||.|..|..+++....|.+|+.
T Consensus 509 g~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 509 GEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred cccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 124568999999999999999999986
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.23 E-value=0.0045 Score=28.42 Aligned_cols=21 Identities=19% Similarity=0.278 Sum_probs=16.5
Q ss_pred ccccccccccccHHHHHHHHhH
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
.+|+.||+.| ..+.|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4699999999 77778888653
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.97 E-value=0.0054 Score=28.13 Aligned_cols=20 Identities=20% Similarity=0.472 Sum_probs=17.5
Q ss_pred eecCcCcccccCchHHHHHHh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~ 147 (155)
.+|+.||+.| ..+.|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 5799999999 7788999976
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.74 E-value=0.0076 Score=29.74 Aligned_cols=22 Identities=27% Similarity=0.560 Sum_probs=20.4
Q ss_pred CeecCcCcccccCchHHHHHHh
Q psy13210 126 PFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
+|.|++|++.|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 6899999999999999999976
No 52
>PRK04860 hypothetical protein; Provisional
Probab=95.69 E-value=0.004 Score=42.22 Aligned_cols=39 Identities=15% Similarity=0.182 Sum_probs=32.6
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHH
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIG 95 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~ 95 (155)
.|.|. |+. ....+.+|+ +++.++++|.|..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~--------ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHN--------RVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHH--------HHhcCCccEECCCCCceeEEec
Confidence 58897 887 556888998 9999999999999999886543
No 53
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.27 E-value=0.0023 Score=49.19 Aligned_cols=98 Identities=20% Similarity=0.263 Sum_probs=76.2
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhc--cCCCC--Cccccc--ccccccccHHHHHHHHhHhcCCCCcH-------
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIR--TDPFR--HKFVCY--ACDYFSYNIGCMRSHIRTHTGEKPYA------- 111 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~------- 111 (155)
.+.|..|...|.....+..|. + .|..+ +++.|+ .|++.|.....+..|...|.+..++.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~--------~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 360 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHL--------RSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSS 360 (467)
T ss_pred CCCCccccCCccccccccccc--------cccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCc
Confidence 577999999999999999999 7 79998 999999 79999999999999999998766553
Q ss_pred -----------------------------------------HHHHHHHHhccCCC--CeecCcCcccccCchHHHHHHhh
Q psy13210 112 -----------------------------------------HIIRNHYRKHTGRK--PFKCVVCKQFFATYSGAYQHLRR 148 (155)
Q Consensus 112 -----------------------------------------~~l~~H~~~h~~~~--~~~C~~C~k~f~~~~~L~~H~~~ 148 (155)
..+..|...|...+ .+.+..|.+.|.....+..|++
T Consensus 361 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 439 (467)
T COG5048 361 SKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKK- 439 (467)
T ss_pred cccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCccccccccc-
Confidence 11222333343433 3567778888888888888877
Q ss_pred hhC
Q psy13210 149 THG 151 (155)
Q Consensus 149 ~H~ 151 (155)
.|.
T Consensus 440 ~~~ 442 (467)
T COG5048 440 IHT 442 (467)
T ss_pred ccc
Confidence 443
No 54
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.91 E-value=0.015 Score=31.78 Aligned_cols=30 Identities=23% Similarity=0.595 Sum_probs=26.6
Q ss_pred cCCCCeecCcCcccccCchHHHHHHhhhhC
Q psy13210 122 TGRKPFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 122 ~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
-||--+.|+-||+.|...-+..+|....|+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 467779999999999999999999987775
No 55
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.70 E-value=0.028 Score=27.63 Aligned_cols=23 Identities=17% Similarity=0.397 Sum_probs=20.0
Q ss_pred cccccccccccccHHHHHHHHhH
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
+|.|.+|+..|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57899999999999999988875
No 56
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=93.93 E-value=0.037 Score=34.97 Aligned_cols=31 Identities=26% Similarity=0.595 Sum_probs=24.5
Q ss_pred cccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCcccccCc
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATY 139 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~ 139 (155)
...|+.||+.|+.. +..|..|+.||..|.-.
T Consensus 9 KR~Cp~CG~kFYDL----------------------------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDL----------------------------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccC----------------------------CCCCccCCCCCCccCcc
Confidence 35799999999654 34578999999988766
No 57
>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=93.23 E-value=0.47 Score=29.91 Aligned_cols=71 Identities=23% Similarity=0.424 Sum_probs=45.1
Q ss_pred CcccccccccccccHHHHHHHHhH-hcCCCCcH-HHHHHHHHhcc--------------CCC---------Ceec----C
Q psy13210 80 HKFVCYACDYFSYNIGCMRSHIRT-HTGEKPYA-HIIRNHYRKHT--------------GRK---------PFKC----V 130 (155)
Q Consensus 80 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~-~~l~~H~~~h~--------------~~~---------~~~C----~ 130 (155)
+...|..|+..... +.+..|++. |....... ..+..-.+... +.. -|.| .
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~ 88 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPP 88 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCC
Confidence 45679999887766 888888884 43222221 11111111100 011 1889 9
Q ss_pred cCcccccCchHHHHHHhhhhC
Q psy13210 131 VCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 131 ~C~k~f~~~~~L~~H~~~~H~ 151 (155)
.|++...+...+.+|++..|+
T Consensus 89 ~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 89 HCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCcEeccHHHHHHHHHHhcC
Confidence 999999999999999997774
No 58
>KOG2893|consensus
Probab=92.57 E-value=0.025 Score=40.48 Aligned_cols=45 Identities=18% Similarity=0.297 Sum_probs=36.1
Q ss_pred hhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHH-HhHh
Q psy13210 48 LERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSH-IRTH 104 (155)
Q Consensus 48 c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H-~~~h 104 (155)
|..|++.|....-|.+|+ ++ |-|+|.+|-+...+.-.|..| +.+|
T Consensus 13 cwycnrefddekiliqhq--------ka----khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQ--------KA----KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhh--------hh----ccceeeeehhhhccCCCceeehhhhh
Confidence 889999999999999999 33 459999999887777666655 4444
No 59
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.13 E-value=0.076 Score=26.57 Aligned_cols=34 Identities=15% Similarity=0.263 Sum_probs=24.6
Q ss_pred hhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 46 DRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 46 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
..|+.|+..|.-..+ .+.......+|+.|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~-------------~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDE-------------KIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHH-------------HCCCCCcEEECCCCCCEeC
Confidence 458888888876544 4455566789999998873
No 60
>KOG2893|consensus
Probab=92.06 E-value=0.048 Score=39.08 Aligned_cols=51 Identities=20% Similarity=0.434 Sum_probs=41.6
Q ss_pred CCcccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCcccccCchHHHHHHhhhhC
Q psy13210 79 RHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 79 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
.|+| |=+|++.|.+..-|..|++.-. |+|.+|.|..-+--.|..|--++|.
T Consensus 9 ~kpw-cwycnrefddekiliqhqkakh---------------------fkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKAKH---------------------FKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhhcc---------------------ceeeeehhhhccCCCceeehhhhhh
Confidence 3566 7889999999999998877543 8999999998888888888655664
No 61
>KOG2231|consensus
Probab=91.74 E-value=0.2 Score=41.23 Aligned_cols=95 Identities=16% Similarity=0.044 Sum_probs=49.8
Q ss_pred HHHHhHHHhhhhhcccCCCc------------chhhhhhcccccc-cccChhhhhhhh---------hhccCcHHHhhhH
Q psy13210 8 FHQLCRAFYAYEKDAQDGGF------------SKLKRALDVNQSM-IDISADRLERLR---------TQCATSAELTQHE 65 (155)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~-~~~~~~~c~~C~---------~~~~~~~~l~~h~ 65 (155)
....+.++....|..++..+ ..+.....+..++ ..+..+.|..|- ....+...|..|+
T Consensus 90 ~y~~~~~~~~~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~ 169 (669)
T KOG2231|consen 90 TYTKLEACLHHSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHL 169 (669)
T ss_pred HHHHHHHHHhhhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHH
Confidence 34555566667777776655 1233333444443 444555665541 2223445566665
Q ss_pred HhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhc
Q psy13210 66 IRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
.....+ .+.+.+ . -.|..|...|-....|.+|++.+.
T Consensus 170 ~~gd~d-~~s~rG-h-p~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 170 MFGDPD-DESCRG-H-PLCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred hcCCCc-cccccC-C-ccchhhhhhhccHHHHHHhhccce
Confidence 222110 011111 1 258888888888888888887643
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.61 E-value=0.047 Score=41.95 Aligned_cols=57 Identities=25% Similarity=0.502 Sum_probs=47.4
Q ss_pred CcccccccccccccHHHHHHHHh--HhcCCCCcHHHHHHHHHhccCC--CCeecC--cCcccccCchHHHHHHhhhhCCC
Q psy13210 80 HKFVCYACDYFSYNIGCMRSHIR--THTGEKPYAHIIRNHYRKHTGR--KPFKCV--VCKQFFATYSGAYQHLRRTHGQE 153 (155)
Q Consensus 80 ~~~~C~~C~~~f~~~~~l~~H~~--~h~~~~~~~~~l~~H~~~h~~~--~~~~C~--~C~k~f~~~~~L~~H~~~~H~~~ 153 (155)
.++.|..|...|.....|..|.+ .|. ++ +|+.|+ .|++.|.+...+.+|.. .|.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-----------------~~~~~~~~~p~~~~~~~~~~~~~~~~~~~-~~~~~ 349 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-----------------GESLKPFSCPYSLCGKLFSRNDALKRHIL-LHTSI 349 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-----------------cccCCceeeeccCCCccccccccccCCcc-cccCC
Confidence 46789999999999998888877 455 67 789999 79999999999999998 66654
Q ss_pred C
Q psy13210 154 S 154 (155)
Q Consensus 154 ~ 154 (155)
+
T Consensus 350 ~ 350 (467)
T COG5048 350 S 350 (467)
T ss_pred C
Confidence 3
No 63
>KOG1146|consensus
Probab=91.56 E-value=0.03 Score=48.83 Aligned_cols=98 Identities=10% Similarity=0.135 Sum_probs=66.6
Q ss_pred ccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCCcH--HHHHHHHH
Q psy13210 42 DISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYA--HIIRNHYR 119 (155)
Q Consensus 42 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~--~~l~~H~~ 119 (155)
..+.+.|..|...+...-.+. +. ....+|.|..|.-.|.....|..|.+.-. +.+. .....+..
T Consensus 1257 ~sGe~~c~~~~~~~~~~~~~~-~l-----------~~~~~~~~~~~~~~~~~~~~l~~~~~k~~--~~~~~~~~~~~~~l 1322 (1406)
T KOG1146|consen 1257 ASGEGECGAVDELLTPSFGIS-TL-----------DVTHRYLCRQCKMAFDGEAPLTAHQRKFC--FAGRGSGGSMPPPL 1322 (1406)
T ss_pred CCCcchhhhccccccCcccee-ec-----------ccchhHHHHHHHhhhcchhHHHHHHHHHH--hccCccccCCCCcc
Confidence 346677888888777655544 43 22356889999999999988888873211 0000 22233344
Q ss_pred hccCCCCeecCcCcccccCchHHHHHHhhhhCCCC
Q psy13210 120 KHTGRKPFKCVVCKQFFATYSGAYQHLRRTHGQES 154 (155)
Q Consensus 120 ~h~~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~~~ 154 (155)
.+..-.+| |..|...|+....|..|++..+...|
T Consensus 1323 ~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~~k 1356 (1406)
T KOG1146|consen 1323 RVPDCTYH-CLACEVLLSGREALQIHMRSSAHRRK 1356 (1406)
T ss_pred cCcccccc-chHHHhhcchhHHHHHHHHHhhhccc
Confidence 45555667 99999999999999999998776654
No 64
>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=91.43 E-value=0.22 Score=25.95 Aligned_cols=28 Identities=29% Similarity=0.549 Sum_probs=19.3
Q ss_pred CCCCeecCcCcccccC----chHHHHHHhhhh
Q psy13210 123 GRKPFKCVVCKQFFAT----YSGAYQHLRRTH 150 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~----~~~L~~H~~~~H 150 (155)
++....|.+|++.+.. .+.|.+|++..|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 4556789999998876 489999996455
No 65
>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=91.26 E-value=0.11 Score=25.41 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=8.5
Q ss_pred CCeecCcCccc
Q psy13210 125 KPFKCVVCKQF 135 (155)
Q Consensus 125 ~~~~C~~C~k~ 135 (155)
.++.|++||..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 46899999863
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.05 E-value=0.14 Score=28.09 Aligned_cols=29 Identities=10% Similarity=0.075 Sum_probs=20.3
Q ss_pred cCCCCCcccccccccccccHHHHHHHHhH
Q psy13210 75 TDPFRHKFVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 75 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
+..++.-+.||-||..|....+..+|...
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 34456667777777777777777777664
No 67
>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=90.09 E-value=0.21 Score=32.29 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=25.1
Q ss_pred cccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCcccccCchHH
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATYSGA 142 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L 142 (155)
...|+.||+.|+.. +..|..|+.||..|.-...+
T Consensus 9 Kr~Cp~cg~kFYDL----------------------------nk~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 9 KRICPNTGSKFYDL----------------------------NRRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred cccCCCcCcccccc----------------------------CCCCccCCCcCCccCcchhh
Confidence 35799999998653 34578999999988665333
No 68
>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=90.00 E-value=0.13 Score=25.79 Aligned_cols=34 Identities=15% Similarity=0.148 Sum_probs=22.4
Q ss_pred hhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 46 DRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 46 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
+.|+.|+..|.-..+ ..........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~-------------~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS-------------QLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHH-------------HcCCCCCEEECCCCCCEEE
Confidence 468889888876544 2222223578999998774
No 69
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.95 E-value=0.15 Score=25.60 Aligned_cols=34 Identities=12% Similarity=0.093 Sum_probs=23.9
Q ss_pred hhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 46 DRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 46 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
..|+.|+..|.-..+ +........+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~-------------~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD-------------KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHH-------------HcccCCcEEECCCCCcEee
Confidence 358888888876543 3444556778999998874
No 70
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=89.84 E-value=0.19 Score=34.25 Aligned_cols=26 Identities=31% Similarity=0.793 Sum_probs=20.6
Q ss_pred CCcccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCcc
Q psy13210 79 RHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQ 134 (155)
Q Consensus 79 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k 134 (155)
.+.|.|++||.++ .|+.|-+||+||-
T Consensus 132 ~~~~vC~vCGy~~------------------------------~ge~P~~CPiCga 157 (166)
T COG1592 132 GKVWVCPVCGYTH------------------------------EGEAPEVCPICGA 157 (166)
T ss_pred CCEEEcCCCCCcc------------------------------cCCCCCcCCCCCC
Confidence 3479999999853 2677899999994
No 71
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=89.41 E-value=0.35 Score=25.92 Aligned_cols=26 Identities=35% Similarity=0.556 Sum_probs=20.7
Q ss_pred CeecCcCcccccCc-----hHHHHHHhhhhC
Q psy13210 126 PFKCVVCKQFFATY-----SGAYQHLRRTHG 151 (155)
Q Consensus 126 ~~~C~~C~k~f~~~-----~~L~~H~~~~H~ 151 (155)
.-.|..|++.++.. +.|.+|++..|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 35699999988765 799999985554
No 72
>KOG4173|consensus
Probab=89.40 E-value=0.39 Score=33.78 Aligned_cols=90 Identities=17% Similarity=0.128 Sum_probs=61.1
Q ss_pred Chhhhhh--hhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhc
Q psy13210 44 SADRLER--LRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKH 121 (155)
Q Consensus 44 ~~~~c~~--C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h 121 (155)
..+-|+. |...|...-++..|- .+..+ -.|..|.+.|.+..-|..|+..-. ....-..+-
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY--------~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~H-------Ds~Fqa~ve 139 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHY--------HTLHG---NSCSFCKRAFPTGHLLDAHILEWH-------DSLFQALVE 139 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhh--------hhccc---chhHHHHHhCCchhhhhHHHHHHH-------HHHHHHHHH
Confidence 4566765 777777666666665 32222 259999999999999998877522 111223334
Q ss_pred cCCCCeecC--cCcccccCchHHHHHHhhhhC
Q psy13210 122 TGRKPFKCV--VCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 122 ~~~~~~~C~--~C~k~f~~~~~L~~H~~~~H~ 151 (155)
.|..-|.|- .|+..|.+.-....|+-..|.
T Consensus 140 RG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 140 RGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred cCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 455568895 499999999999888876664
No 73
>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=88.63 E-value=0.32 Score=31.87 Aligned_cols=23 Identities=39% Similarity=0.723 Sum_probs=15.2
Q ss_pred CeecCcCcccccCchHHHHHHhhhhC
Q psy13210 126 PFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
...|-+||+.|.. |.+|++.+|+
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-
T ss_pred eeEEccCCcccch---HHHHHHHccC
Confidence 4789999999988 6999995545
No 74
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.33 E-value=0.26 Score=25.98 Aligned_cols=30 Identities=13% Similarity=0.254 Sum_probs=20.3
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
.|+|..||..+.... ......|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~------------------~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDE------------------YGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECC------------------CCCceECCCCCCeEE
Confidence 478899998775432 112578999997654
No 75
>KOG2482|consensus
Probab=86.64 E-value=0.53 Score=35.68 Aligned_cols=70 Identities=16% Similarity=0.399 Sum_probs=48.8
Q ss_pred ccccccccccccHHHHHHHHhH--hcCCCCcH----------------------HHHHHHHH-hc------------cCC
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRT--HTGEKPYA----------------------HIIRNHYR-KH------------TGR 124 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~--h~~~~~~~----------------------~~l~~H~~-~h------------~~~ 124 (155)
+.|-.|.+.|+++..|..||+. |-...|-. +.+.+-.. .+ .+.
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a 275 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDA 275 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCC
Confidence 7899999999999999999986 54433321 12211000 00 012
Q ss_pred CC--eecCcCcccccCchHHHHHHhhhhC
Q psy13210 125 KP--FKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 125 ~~--~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
.+ ..|-+|.....+...|..|+..+|.
T Consensus 276 ~a~~v~CLfC~~~~en~~~l~eHmk~vHe 304 (423)
T KOG2482|consen 276 EALSVVCLFCTNFYENPVFLFEHMKIVHE 304 (423)
T ss_pred CccceEEEeeccchhhHHHHHHHHHHHHH
Confidence 23 6899999999999999999998874
No 76
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.29 E-value=0.57 Score=35.59 Aligned_cols=40 Identities=25% Similarity=0.486 Sum_probs=23.8
Q ss_pred HHHHHHHHhccCCCCe----ecCcCcccccCchHHHHHHhhhhC
Q psy13210 112 HIIRNHYRKHTGRKPF----KCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 112 ~~l~~H~~~h~~~~~~----~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
..|..|......+.-| .|.+|...|-....|.+|.|..|.
T Consensus 202 ~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~HE 245 (493)
T COG5236 202 STLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHE 245 (493)
T ss_pred ccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhhh
Confidence 4455555543322122 377777777777777777775553
No 77
>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=84.68 E-value=0.44 Score=33.91 Aligned_cols=30 Identities=17% Similarity=0.461 Sum_probs=23.7
Q ss_pred CCCCeecCcCcccccCchHHHHHHhhhhCC
Q psy13210 123 GRKPFKCVVCKQFFATYSGAYQHLRRTHGQ 152 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~ 152 (155)
++..|.|+.|+|.|.-..-..+|+...|.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 455799999999999999999999988864
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=83.66 E-value=0.84 Score=30.48 Aligned_cols=23 Identities=9% Similarity=0.173 Sum_probs=16.5
Q ss_pred ccCCCCCcccccccccccccHHH
Q psy13210 74 RTDPFRHKFVCYACDYFSYNIGC 96 (155)
Q Consensus 74 ~~~~~~~~~~C~~C~~~f~~~~~ 96 (155)
+.-.+...|.|+.|+..|.....
T Consensus 92 ~~e~~~~~Y~Cp~C~~~y~~~ea 114 (147)
T smart00531 92 EDETNNAYYKCPNCQSKYTFLEA 114 (147)
T ss_pred hcccCCcEEECcCCCCEeeHHHH
Confidence 34455677999999998875543
No 79
>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=83.20 E-value=1.1 Score=20.62 Aligned_cols=20 Identities=25% Similarity=0.371 Sum_probs=16.4
Q ss_pred eecCcCcccccCchHHHHHHh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~ 147 (155)
..|++|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4699999998 6678888876
No 80
>PHA00626 hypothetical protein
Probab=82.83 E-value=0.56 Score=25.76 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=13.2
Q ss_pred CCcccccccccccccHH
Q psy13210 79 RHKFVCYACDYFSYNIG 95 (155)
Q Consensus 79 ~~~~~C~~C~~~f~~~~ 95 (155)
...|+|+.||+.|....
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 36799999999886554
No 81
>KOG2186|consensus
Probab=82.11 E-value=0.86 Score=33.09 Aligned_cols=48 Identities=10% Similarity=0.091 Sum_probs=34.4
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHHHhH
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
.|.|..||....- ..+..|+ -..++ .-|.|-.||+.|.. .+...|..-
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~--------srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHM--------SRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhccc-cchHHHH--------HhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 3679999987654 4677787 33333 67899999999988 666666553
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=82.09 E-value=0.19 Score=26.03 Aligned_cols=30 Identities=13% Similarity=0.176 Sum_probs=20.0
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDY 89 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~ 89 (155)
.|+|..||..|..... ... ..+..|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~--------------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS--------------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEE--------------cCC-CCCCcCCCCCC
Confidence 5789999988865422 111 35567999987
No 83
>KOG2482|consensus
Probab=81.90 E-value=3.6 Score=31.37 Aligned_cols=65 Identities=17% Similarity=0.436 Sum_probs=47.0
Q ss_pred cccccccccccccH-HHHHHHHhH-hc------CCCCcHHHHHHHHHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 81 KFVCYACDYFSYNI-GCMRSHIRT-HT------GEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 81 ~~~C~~C~~~f~~~-~~l~~H~~~-h~------~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
..+|-.|+..+.-. +....|+.. |. .+-.|...|..|+..-.. .+.|-+|.|.|+.+..|..|||
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~--r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLE--RLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHh--hheeeeeccccCCcHHHHHHHH
Confidence 45799999866544 556666654 42 133455778887765333 3899999999999999999998
No 84
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=81.73 E-value=0.5 Score=26.30 Aligned_cols=34 Identities=6% Similarity=0.088 Sum_probs=20.7
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccc
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYF 90 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~ 90 (155)
-.|.|+.||...-.... +......+|.|+.||..
T Consensus 26 v~F~CPnCGe~~I~Rc~-------------~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA-------------KCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eEeeCCCCCceeeehhh-------------hHHHcCCceECCCcCcc
Confidence 35778888854433222 22233478999999863
No 85
>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=81.54 E-value=1.2 Score=30.16 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=28.5
Q ss_pred ccCCCCCcccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCccccc
Q psy13210 74 RTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFA 137 (155)
Q Consensus 74 ~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~ 137 (155)
....+..-|.|+.|+..|+....+.. -|.|+.||....
T Consensus 102 ~~e~~~~~Y~Cp~c~~r~tf~eA~~~--------------------------~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 102 EFETNNMFFICPNMCVRFTFNEAMEL--------------------------NFTCPRCGAMLD 139 (158)
T ss_pred hhccCCCeEECCCCCcEeeHHHHHHc--------------------------CCcCCCCCCEee
Confidence 44456677999999999888877641 299999997543
No 86
>KOG2071|consensus
Probab=81.04 E-value=0.87 Score=36.96 Aligned_cols=28 Identities=14% Similarity=0.153 Sum_probs=19.3
Q ss_pred CCCcccccccccccccHHHHHHHHhHhc
Q psy13210 78 FRHKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 78 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
...+.+|..||..|.+......||..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3456677778887777776666666654
No 87
>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=79.83 E-value=0.67 Score=24.92 Aligned_cols=30 Identities=10% Similarity=0.068 Sum_probs=19.6
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDY 89 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~ 89 (155)
.|+|..|+..|..... ... ..+-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~--------------~~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQK--------------MSD-DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEe--------------cCC-CCCCCCCCCCC
Confidence 5789999988865321 111 34457999986
No 88
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.32 E-value=1.1 Score=28.24 Aligned_cols=16 Identities=13% Similarity=0.252 Sum_probs=12.6
Q ss_pred CCCCeecCcCcccccC
Q psy13210 123 GRKPFKCVVCKQFFAT 138 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~ 138 (155)
+..|..|++||++|..
T Consensus 23 NrdPiVsPytG~s~P~ 38 (129)
T COG4530 23 NRDPIVSPYTGKSYPR 38 (129)
T ss_pred CCCccccCcccccchH
Confidence 4457999999999843
No 89
>KOG2231|consensus
Probab=79.18 E-value=2.4 Score=35.25 Aligned_cols=15 Identities=27% Similarity=0.696 Sum_probs=8.1
Q ss_pred ccCchHHHHHHhhhh
Q psy13210 136 FATYSGAYQHLRRTH 150 (155)
Q Consensus 136 f~~~~~L~~H~~~~H 150 (155)
|.....|..|-|..|
T Consensus 222 y~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 222 YNDYDDLEEHFRKGH 236 (669)
T ss_pred cccchHHHHHhhhcC
Confidence 555555666655444
No 90
>KOG4167|consensus
Probab=78.99 E-value=0.51 Score=39.25 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=23.7
Q ss_pred CcccccccccccccHHHHHHHHhHhc
Q psy13210 80 HKFVCYACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 80 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 105 (155)
..|.|.+|++.|....+++.||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 34999999999999999999999985
No 91
>KOG2785|consensus
Probab=78.93 E-value=3.9 Score=31.58 Aligned_cols=65 Identities=22% Similarity=0.429 Sum_probs=46.5
Q ss_pred ccccccccccccHHHHHHHHhHhcC----CCCcH---HHHHHHHHhccCCCCeecCcCc---ccccCchHHHHHHh
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRTHTG----EKPYA---HIIRNHYRKHTGRKPFKCVVCK---QFFATYSGAYQHLR 147 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~h~~----~~~~~---~~l~~H~~~h~~~~~~~C~~C~---k~f~~~~~L~~H~~ 147 (155)
-.|-.|++.+.+...-..||..+.| ++-|. ..|..-+..-.+ .-+.|-+|. +.|.+-.+.+.||+
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~-~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVG-IGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhc-cCceEEEeccccCcccccHHHHHHHh
Confidence 5689999999999999999998765 23332 233333322111 237888888 99999999999987
No 92
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.14 E-value=1.9 Score=32.85 Aligned_cols=65 Identities=25% Similarity=0.546 Sum_probs=43.8
Q ss_pred cccccccccccHHHHHHHHhHhcCC-------CCc--H-----HHHHHHHHhccCCCCeecCc--C--c--ccccCchHH
Q psy13210 83 VCYACDYFSYNIGCMRSHIRTHTGE-------KPY--A-----HIIRNHYRKHTGRKPFKCVV--C--K--QFFATYSGA 142 (155)
Q Consensus 83 ~C~~C~~~f~~~~~l~~H~~~h~~~-------~~~--~-----~~l~~H~~~h~~~~~~~C~~--C--~--k~f~~~~~L 142 (155)
.|..|...|.+...|..|++..... .|. . ..|..|.+ .--|.|.+ | + ..|.....|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~~~k~~vf~~~~el 297 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCRVGKCYVFPYHTEL 297 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEecCcEEEeccHHHH
Confidence 5999999999999999998863311 111 1 45555544 33366644 3 2 258888899
Q ss_pred HHHHhhhhC
Q psy13210 143 YQHLRRTHG 151 (155)
Q Consensus 143 ~~H~~~~H~ 151 (155)
..|+-+.|+
T Consensus 298 ~~h~~~~h~ 306 (493)
T COG5236 298 LEHLTRFHK 306 (493)
T ss_pred HHHHHHHhh
Confidence 999877776
No 93
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.87 E-value=1 Score=25.09 Aligned_cols=34 Identities=9% Similarity=0.112 Sum_probs=20.0
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccc
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYF 90 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~ 90 (155)
..|.|+.||...-..-. +-.....+|.|+.||..
T Consensus 24 ~~F~CPnCG~~~I~RC~-------------~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE-------------KCRKQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeEeech-------------hHHhcCCceECCCCCCc
Confidence 45778888865222111 22223368999999863
No 94
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=77.64 E-value=2 Score=32.87 Aligned_cols=24 Identities=8% Similarity=-0.063 Sum_probs=19.6
Q ss_pred cChhhhhhhhhhccCcHHHhhhHH
Q psy13210 43 ISADRLERLRTQCATSAELTQHEI 66 (155)
Q Consensus 43 ~~~~~c~~C~~~~~~~~~l~~h~~ 66 (155)
...+.|..|++.|....-+..|..
T Consensus 236 ~~~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 236 FPKVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ccceeeHhhhhHhhhhHHHHHHHh
Confidence 356779999999999888888863
No 95
>KOG2593|consensus
Probab=77.34 E-value=2.5 Score=33.09 Aligned_cols=34 Identities=18% Similarity=0.355 Sum_probs=25.7
Q ss_pred HHhhhhhhhccCCCCCcccccccccccccHHHHH
Q psy13210 65 EIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMR 98 (155)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 98 (155)
|++-+++-++-.....-|.|+.|.+.|.....+.
T Consensus 112 m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 112 MRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred HHHHHHHHhhhccccccccCCccccchhhhHHHH
Confidence 4555566666677788899999999998776654
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.25 E-value=1.9 Score=29.88 Aligned_cols=23 Identities=17% Similarity=0.151 Sum_probs=17.0
Q ss_pred cCCCCCcccccccccccccHHHH
Q psy13210 75 TDPFRHKFVCYACDYFSYNIGCM 97 (155)
Q Consensus 75 ~~~~~~~~~C~~C~~~f~~~~~l 97 (155)
.-.+..-|.|+.|+..|.....+
T Consensus 111 ~e~~~~~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 111 EEENNMFFFCPNCHIRFTFDEAM 133 (178)
T ss_pred hccCCCEEECCCCCcEEeHHHHh
Confidence 33455678999999988777664
No 97
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=74.07 E-value=1.7 Score=20.00 Aligned_cols=10 Identities=30% Similarity=0.570 Sum_probs=8.2
Q ss_pred cccccccccc
Q psy13210 83 VCYACDYFSY 92 (155)
Q Consensus 83 ~C~~C~~~f~ 92 (155)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5899998885
No 98
>KOG2186|consensus
Probab=73.48 E-value=2.3 Score=30.94 Aligned_cols=47 Identities=19% Similarity=0.404 Sum_probs=33.5
Q ss_pred cccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
-|.|..||-...-+ .+.+|+..-. + .-|.|..|++.|.. .+...|..
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCr-----------------n-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCR-----------------N-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhcc-----------------C-CeeEEeeccccccc-chhhhhhh
Confidence 37899999876544 3555766544 3 34999999999988 66666754
No 99
>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=73.06 E-value=1.6 Score=19.70 Aligned_cols=11 Identities=27% Similarity=0.812 Sum_probs=8.3
Q ss_pred CCccccccccc
Q psy13210 79 RHKFVCYACDY 89 (155)
Q Consensus 79 ~~~~~C~~C~~ 89 (155)
..+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35788999984
No 100
>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=71.61 E-value=3.7 Score=25.74 Aligned_cols=24 Identities=29% Similarity=0.642 Sum_probs=18.2
Q ss_pred ccc----cccccccccHHHHHHHHhHhc
Q psy13210 82 FVC----YACDYFSYNIGCMRSHIRTHT 105 (155)
Q Consensus 82 ~~C----~~C~~~f~~~~~l~~H~~~h~ 105 (155)
|.| +.|++.+.+...|.+|.+.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 677 778888888888888877643
No 101
>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=70.97 E-value=2.8 Score=29.93 Aligned_cols=29 Identities=24% Similarity=0.351 Sum_probs=21.9
Q ss_pred CCCCcccccccccccccHHHHHHHHhH-hc
Q psy13210 77 PFRHKFVCYACDYFSYNIGCMRSHIRT-HT 105 (155)
Q Consensus 77 ~~~~~~~C~~C~~~f~~~~~l~~H~~~-h~ 105 (155)
..+..|.|++|+|.|.-..-+.+|+.. |.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 355679999999999999999999876 54
No 102
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=70.93 E-value=2.5 Score=27.74 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=18.0
Q ss_pred eecCcCcccccCchHHHHHHhhhhC
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
+.|-++||.|.+ |++|+.++++
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccC
Confidence 679999999986 9999994443
No 103
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=70.48 E-value=0.96 Score=33.91 Aligned_cols=49 Identities=12% Similarity=0.020 Sum_probs=23.2
Q ss_pred HhhhhhcccCCCcchhhhhhcccccccccChhhhhhhhhhccCcHHHhhhH
Q psy13210 15 FYAYEKDAQDGGFSKLKRALDVNQSMIDISADRLERLRTQCATSAELTQHE 65 (155)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~ 65 (155)
++...|-.+++.|+...... .........|.|..|...|-..-+.-.|.
T Consensus 360 ~ks~~Cf~CQ~~fp~~~~~~--~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 360 PKSTHCFVCQGPFPKPPVSP--FDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred CCCccceeccCCCCCCCCCc--ccccccccceechhhhhhhhhhhHHHHHH
Confidence 33444555555553322221 12223334566666666666655555554
No 104
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=69.89 E-value=0.52 Score=39.58 Aligned_cols=45 Identities=24% Similarity=0.428 Sum_probs=27.8
Q ss_pred cccccccccccH---HHHHHHHhHhcCCCCcHHHHHHHHHhccCCCCeecCcCccc
Q psy13210 83 VCYACDYFSYNI---GCMRSHIRTHTGEKPYAHIIRNHYRKHTGRKPFKCVVCKQF 135 (155)
Q Consensus 83 ~C~~C~~~f~~~---~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~~~~~C~~C~k~ 135 (155)
.|..||..+.-+ ..|..|+..+. |..|.--+....|..|+.||-.
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~~~~--------L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKATGQ--------LRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCCCcceEEecCCCe--------eEeCCCCCCCCCCCCCCCCCCC
Confidence 466666666554 34555544432 5555555556778999999854
No 105
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=67.56 E-value=2.3 Score=26.45 Aligned_cols=16 Identities=13% Similarity=0.046 Sum_probs=11.0
Q ss_pred hhhhhhhhhccCcHHH
Q psy13210 46 DRLERLRTQCATSAEL 61 (155)
Q Consensus 46 ~~c~~C~~~~~~~~~l 61 (155)
..|..||..|..-+..
T Consensus 3 H~CtrCG~vf~~g~~~ 18 (112)
T COG3364 3 HQCTRCGEVFDDGSEE 18 (112)
T ss_pred ceecccccccccccHH
Confidence 4688888888775443
No 106
>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=65.13 E-value=2.5 Score=21.50 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=15.4
Q ss_pred hhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccccc
Q psy13210 46 DRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFS 91 (155)
Q Consensus 46 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f 91 (155)
.+|..|+.-..-.. ....+.+.++|.+|+..-
T Consensus 3 ~rC~~C~aylNp~~--------------~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 3 VRCRRCRAYLNPFC--------------QFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp -B-TTT--BS-TTS--------------EEETTTTEEEETTT--EE
T ss_pred cccCCCCCEECCcc--------------eEcCCCCEEECcCCCCcC
Confidence 46777765544332 334455779999998753
No 107
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=64.53 E-value=5.3 Score=20.11 Aligned_cols=23 Identities=30% Similarity=0.514 Sum_probs=9.4
Q ss_pred CCeecCcCcccccCch--HHHHHHh
Q psy13210 125 KPFKCVVCKQFFATYS--GAYQHLR 147 (155)
Q Consensus 125 ~~~~C~~C~k~f~~~~--~L~~H~~ 147 (155)
+.|-|++|+..|...+ ....|.+
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT-
T ss_pred cCeecccccceecCCChHHHHHhhc
Confidence 4588999999994433 4456644
No 108
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=64.47 E-value=4 Score=27.19 Aligned_cols=53 Identities=8% Similarity=0.090 Sum_probs=29.4
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHHHHHHH
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIGCMRSH 100 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 100 (155)
.-+|..|+.....-..-..-. .-........+.-+.|+.||+.|...+.+.+-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~---~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKD---RVPPYVYETYDEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CCccCCCCcEeeechhhcccc---ccCccccccCCeEEECCCCCCEecccccHHHH
Confidence 457999987654332211110 00000111223468899999999988876654
No 109
>KOG2785|consensus
Probab=64.13 E-value=4.6 Score=31.21 Aligned_cols=60 Identities=10% Similarity=0.098 Sum_probs=40.6
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhh-----hhh----------------------hc--cCCCCCcccccccccccccH
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTI-----ESM----------------------IR--TDPFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~-----~~~----------------------~~--~~~~~~~~~C~~C~~~f~~~ 94 (155)
..|.|..|...|.....-..|.+... +.. .. .-..+-++.|.+|.+.|...
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~ 81 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASP 81 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccCh
Confidence 35788999988888766666664111 100 00 01234568899999999999
Q ss_pred HHHHHHHhH
Q psy13210 95 GCMRSHIRT 103 (155)
Q Consensus 95 ~~l~~H~~~ 103 (155)
.....|+.+
T Consensus 82 ~a~~~hl~S 90 (390)
T KOG2785|consen 82 KAHENHLKS 90 (390)
T ss_pred hhHHHHHHH
Confidence 999988865
No 110
>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=63.80 E-value=3.1 Score=20.68 Aligned_cols=30 Identities=13% Similarity=0.058 Sum_probs=17.7
Q ss_pred hhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 47 RLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 47 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
.|..|+.+|.. ...+....-+|+.||..+.
T Consensus 3 ~C~~Cg~~Yh~----------------~~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 3 ICPKCGRIYHI----------------EFNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EETTTTEEEET----------------TTB--SSTTBCTTTTEBEB
T ss_pred CcCCCCCcccc----------------ccCCCCCCCccCCCCCeeE
Confidence 37778877753 2333444567888887554
No 111
>PF15269 zf-C2H2_7: Zinc-finger
Probab=63.60 E-value=5 Score=21.01 Aligned_cols=22 Identities=23% Similarity=0.551 Sum_probs=19.8
Q ss_pred eecCcCcccccCchHHHHHHhh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRR 148 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~ 148 (155)
|.|-.|..+..-++.|-.|++.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 7899999999999999999874
No 112
>KOG4167|consensus
Probab=63.35 E-value=2 Score=35.89 Aligned_cols=25 Identities=28% Similarity=0.598 Sum_probs=22.4
Q ss_pred CeecCcCcccccCchHHHHHHhhhhC
Q psy13210 126 PFKCVVCKQFFATYSGAYQHLRRTHG 151 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~~L~~H~~~~H~ 151 (155)
-|.|.+|+|.|...-++..||+ .|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK-~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMK-THR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHH-HHH
Confidence 4999999999999999999999 554
No 113
>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=62.79 E-value=3.8 Score=20.51 Aligned_cols=13 Identities=23% Similarity=0.792 Sum_probs=10.6
Q ss_pred eecCcCcccccCc
Q psy13210 127 FKCVVCKQFFATY 139 (155)
Q Consensus 127 ~~C~~C~k~f~~~ 139 (155)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 7899999988644
No 114
>KOG3408|consensus
Probab=62.02 E-value=5.4 Score=25.66 Aligned_cols=25 Identities=24% Similarity=0.688 Sum_probs=22.6
Q ss_pred CCCCeecCcCcccccCchHHHHHHh
Q psy13210 123 GRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
|...|-|-.|.+-|.....|..|.+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHh
Confidence 5567999999999999999999977
No 115
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.30 E-value=3.9 Score=21.94 Aligned_cols=12 Identities=8% Similarity=0.022 Sum_probs=9.6
Q ss_pred Chhhhhhhhhhc
Q psy13210 44 SADRLERLRTQC 55 (155)
Q Consensus 44 ~~~~c~~C~~~~ 55 (155)
..|.|..|++.+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 357899999887
No 116
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=60.73 E-value=2 Score=25.02 Aligned_cols=41 Identities=5% Similarity=-0.034 Sum_probs=24.0
Q ss_pred hhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccc--ccccccccHHH
Q psy13210 46 DRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCY--ACDYFSYNIGC 96 (155)
Q Consensus 46 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~--~C~~~f~~~~~ 96 (155)
..|+.|+........-.... ...+.-+.|. .||.+|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~----------~~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD----------TTKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcCh----------hhheeeeecCCCCCCCEEEEEEE
Confidence 46888886653332222211 1344567888 89999876654
No 117
>KOG2593|consensus
Probab=60.59 E-value=5.1 Score=31.48 Aligned_cols=43 Identities=12% Similarity=0.116 Sum_probs=29.5
Q ss_pred cccccccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccc
Q psy13210 37 NQSMIDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYF 90 (155)
Q Consensus 37 ~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~ 90 (155)
.........|.|+.|.+.|...-.+.. .-...-.|.|..|+.-
T Consensus 120 ~~d~t~~~~Y~Cp~C~kkyt~Lea~~L-----------~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 120 LRDDTNVAGYVCPNCQKKYTSLEALQL-----------LDNETGEFHCENCGGE 162 (436)
T ss_pred hhhccccccccCCccccchhhhHHHHh-----------hcccCceEEEecCCCc
Confidence 344566689999999999875544332 3333456999999853
No 118
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=58.67 E-value=5.7 Score=20.08 Aligned_cols=14 Identities=36% Similarity=0.783 Sum_probs=12.7
Q ss_pred CeecCcCcccccCc
Q psy13210 126 PFKCVVCKQFFATY 139 (155)
Q Consensus 126 ~~~C~~C~k~f~~~ 139 (155)
||.|..|++.|...
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 79999999999875
No 119
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=58.15 E-value=1.6 Score=22.27 Aligned_cols=12 Identities=25% Similarity=0.431 Sum_probs=8.9
Q ss_pred cccccccccccc
Q psy13210 81 KFVCYACDYFSY 92 (155)
Q Consensus 81 ~~~C~~C~~~f~ 92 (155)
-|.|..||..+.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 478888887764
No 120
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=57.88 E-value=11 Score=19.24 Aligned_cols=23 Identities=17% Similarity=0.238 Sum_probs=13.8
Q ss_pred ccccccccccccH--HHHHHHHhHh
Q psy13210 82 FVCYACDYFSYNI--GCMRSHIRTH 104 (155)
Q Consensus 82 ~~C~~C~~~f~~~--~~l~~H~~~h 104 (155)
-+|+.||-.|... .+-..|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 4677777666544 4555565555
No 121
>KOG2907|consensus
Probab=57.79 E-value=4.3 Score=25.73 Aligned_cols=41 Identities=10% Similarity=0.154 Sum_probs=24.5
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccccccc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYN 93 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~ 93 (155)
..+|+.||..--.+..++... .-.-.-.-|.|+.|++.|..
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRS--------ADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRS--------ADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hccCcccCCchhhhhhhhccc--------ccCCceEEEEcCccceeeec
Confidence 456999987655554444322 11111234899999998864
No 122
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=57.75 E-value=4.5 Score=24.46 Aligned_cols=34 Identities=6% Similarity=-0.117 Sum_probs=22.1
Q ss_pred cChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccH
Q psy13210 43 ISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 43 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 94 (155)
...+.|+.|++.-. .......|+|..||..|.-.
T Consensus 33 ~~~~~Cp~C~~~~V------------------kR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 33 RAKHVCPFCGRTTV------------------KRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred hcCCcCCCCCCcce------------------eeeccCeEEcCCCCCeeccc
Confidence 35577888886521 11233568999999988654
No 123
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=57.23 E-value=4.4 Score=28.86 Aligned_cols=53 Identities=17% Similarity=0.254 Sum_probs=30.4
Q ss_pred CCcccccccccccccHHHHHHHHhH-hcCCCCcHHHHHHHHHhccCCCC-----eecCcCcccccCc
Q psy13210 79 RHKFVCYACDYFSYNIGCMRSHIRT-HTGEKPYAHIIRNHYRKHTGRKP-----FKCVVCKQFFATY 139 (155)
Q Consensus 79 ~~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~~~l~~H~~~h~~~~~-----~~C~~C~k~f~~~ 139 (155)
++...||+|+..|..+.-.....+. ..... +.. .-.+..| ..|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D-----~~~---~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSD-----FCP---RYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCC-----Ccc---ccCCCCCeeeeEEECCCCCCccccc
Confidence 3567999999999888544433332 11110 111 0113334 4699999987654
No 124
>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=56.84 E-value=5.3 Score=20.41 Aligned_cols=12 Identities=25% Similarity=0.343 Sum_probs=9.7
Q ss_pred Cccccccccccc
Q psy13210 80 HKFVCYACDYFS 91 (155)
Q Consensus 80 ~~~~C~~C~~~f 91 (155)
++-.|++||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467899999877
No 125
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.83 E-value=3.3 Score=27.27 Aligned_cols=15 Identities=0% Similarity=-0.049 Sum_probs=11.9
Q ss_pred ChhhhhhhhhhccCc
Q psy13210 44 SADRLERLRTQCATS 58 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~ 58 (155)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 568899999888664
No 126
>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=56.22 E-value=3.6 Score=19.30 Aligned_cols=20 Identities=25% Similarity=0.529 Sum_probs=12.4
Q ss_pred eecCcCcccccCchHHHHHHh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~ 147 (155)
|.|..|++.| .......|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 6799999999 4444555543
No 127
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.91 E-value=4.1 Score=23.90 Aligned_cols=34 Identities=9% Similarity=0.008 Sum_probs=19.5
Q ss_pred cChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccccc
Q psy13210 43 ISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFS 91 (155)
Q Consensus 43 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f 91 (155)
.-.|+|..|+..| ++.+++ . ..-.-.|+.|+..+
T Consensus 10 tY~Y~c~~cg~~~----dvvq~~--------~---ddplt~ce~c~a~~ 43 (82)
T COG2331 10 TYSYECTECGNRF----DVVQAM--------T---DDPLTTCEECGARL 43 (82)
T ss_pred ceEEeecccchHH----HHHHhc--------c---cCccccChhhChHH
Confidence 3457788888765 444444 1 11223588887644
No 128
>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=54.76 E-value=9.4 Score=30.56 Aligned_cols=27 Identities=19% Similarity=0.497 Sum_probs=24.2
Q ss_pred eecCcCcccccCchHHHHHHhhhhCCC
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRRTHGQE 153 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~~H~~~ 153 (155)
+.|+.|.+.|.....+..|+...|.+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 569999999999999999999888764
No 129
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=54.59 E-value=6.2 Score=21.16 Aligned_cols=18 Identities=28% Similarity=0.538 Sum_probs=14.4
Q ss_pred CCCeecCcCcccccCchH
Q psy13210 124 RKPFKCVVCKQFFATYSG 141 (155)
Q Consensus 124 ~~~~~C~~C~k~f~~~~~ 141 (155)
++.+.|..||..|...+.
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 467899999999877654
No 130
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=54.51 E-value=6.5 Score=33.03 Aligned_cols=44 Identities=9% Similarity=0.099 Sum_probs=26.9
Q ss_pred hhhcccccccccChhh-hhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccc
Q psy13210 32 RALDVNQSMIDISADR-LERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDY 89 (155)
Q Consensus 32 ~~~~~~~~~~~~~~~~-c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~ 89 (155)
+..+-....+....|+ |+.|.+.|....+-+ .|. +|.-|+.||-
T Consensus 137 ~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRR------------fHA--Qp~aCp~CGP 181 (750)
T COG0068 137 EALPYDRENTSMADFPLCPFCDKEYKDPLNRR------------FHA--QPIACPKCGP 181 (750)
T ss_pred ccCCCCcccCccccCcCCHHHHHHhcCccccc------------ccc--ccccCcccCC
Confidence 3334444444454454 888888887766533 333 4567999986
No 131
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=54.20 E-value=5 Score=20.64 Aligned_cols=15 Identities=40% Similarity=0.815 Sum_probs=10.2
Q ss_pred CCeecCcCcccccCc
Q psy13210 125 KPFKCVVCKQFFATY 139 (155)
Q Consensus 125 ~~~~C~~C~k~f~~~ 139 (155)
-|+.|+.|++.|...
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 479999999999875
No 132
>KOG2636|consensus
Probab=51.15 E-value=11 Score=29.81 Aligned_cols=29 Identities=14% Similarity=0.350 Sum_probs=23.1
Q ss_pred cCCCCCcccccccc-cccccHHHHHHHHhH
Q psy13210 75 TDPFRHKFVCYACD-YFSYNIGCMRSHIRT 103 (155)
Q Consensus 75 ~~~~~~~~~C~~C~-~~f~~~~~l~~H~~~ 103 (155)
.|.-...|.|.+|| +++.-...+.+|...
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~E 424 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFNE 424 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhHH
Confidence 33445679999999 888888999999763
No 133
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=51.00 E-value=8.8 Score=18.97 Aligned_cols=31 Identities=10% Similarity=0.055 Sum_probs=14.8
Q ss_pred hhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 48 LERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 48 c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
|+.|.+.+....+- +.|. .+..|..||-.+.
T Consensus 2 C~~C~~Ey~~p~~R------------R~~~--~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSNR------------RFHY--QFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTST------------TTT---TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCCC------------cccC--cCccCCCCCCCEE
Confidence 66677666555432 2222 3456888886653
No 134
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=50.87 E-value=6.8 Score=25.63 Aligned_cols=15 Identities=13% Similarity=0.213 Sum_probs=12.0
Q ss_pred cccccccccccccHH
Q psy13210 81 KFVCYACDYFSYNIG 95 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~ 95 (155)
|++|..||+.|.+.+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578888888888765
No 135
>COG1773 Rubredoxin [Energy production and conversion]
Probab=49.47 E-value=7.5 Score=21.37 Aligned_cols=15 Identities=20% Similarity=0.536 Sum_probs=11.9
Q ss_pred cccccccccccccHH
Q psy13210 81 KFVCYACDYFSYNIG 95 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~ 95 (155)
.|+|..||..|.-..
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 588999999986554
No 136
>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=49.42 E-value=8.1 Score=18.84 Aligned_cols=11 Identities=36% Similarity=1.029 Sum_probs=8.4
Q ss_pred ccccccccccc
Q psy13210 81 KFVCYACDYFS 91 (155)
Q Consensus 81 ~~~C~~C~~~f 91 (155)
.|.|..||..+
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 47888888865
No 137
>KOG2636|consensus
Probab=49.09 E-value=12 Score=29.63 Aligned_cols=27 Identities=15% Similarity=0.376 Sum_probs=22.2
Q ss_pred HhccCCCCeecCcCc-ccccCchHHHHH
Q psy13210 119 RKHTGRKPFKCVVCK-QFFATYSGAYQH 145 (155)
Q Consensus 119 ~~h~~~~~~~C~~C~-k~f~~~~~L~~H 145 (155)
+.|.-...|.|.+|| +++.-.-.+.+|
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHH
Confidence 467777889999999 788887778777
No 138
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=48.95 E-value=4 Score=26.02 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=25.3
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
.+.|+.|+..-.....++.-. .--+.-.-|.|..||..|+
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRs--------aDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRS--------ADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cccCCCCCCceeEEEeeehhc--------cCCCceEEEEecccCCEee
Confidence 367999987665555444432 1122234589999999875
No 139
>PF12907 zf-met2: Zinc-binding
Probab=48.68 E-value=5.4 Score=20.39 Aligned_cols=27 Identities=22% Similarity=0.508 Sum_probs=19.2
Q ss_pred eecCcCcccccCc---hHHHHHHhhhhCCC
Q psy13210 127 FKCVVCKQFFATY---SGAYQHLRRTHGQE 153 (155)
Q Consensus 127 ~~C~~C~k~f~~~---~~L~~H~~~~H~~~ 153 (155)
+.|.+|-.+|... ..|..|-...|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 6799999666544 56888877677654
No 140
>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=48.60 E-value=7.6 Score=20.99 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=6.8
Q ss_pred ecCcCcccccCc
Q psy13210 128 KCVVCKQFFATY 139 (155)
Q Consensus 128 ~C~~C~k~f~~~ 139 (155)
.||+|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999998765
No 141
>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=48.40 E-value=10 Score=19.58 Aligned_cols=17 Identities=24% Similarity=0.223 Sum_probs=13.3
Q ss_pred eecCcCcccccCchHHH
Q psy13210 127 FKCVVCKQFFATYSGAY 143 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~ 143 (155)
=.|.+||+.|++.-...
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 46999999999875543
No 142
>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=48.27 E-value=14 Score=29.61 Aligned_cols=26 Identities=19% Similarity=0.365 Sum_probs=21.3
Q ss_pred cccccccccccccHHHHHHHHhH-hcC
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRT-HTG 106 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~-h~~ 106 (155)
-+.|+.|.+.|.+...+..|+.. |.+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 47789999999999999999874 665
No 143
>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=48.17 E-value=1.2 Score=22.62 Aligned_cols=10 Identities=30% Similarity=0.736 Sum_probs=7.5
Q ss_pred cccccccccc
Q psy13210 82 FVCYACDYFS 91 (155)
Q Consensus 82 ~~C~~C~~~f 91 (155)
|.|..||..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 7788888765
No 144
>PHA02998 RNA polymerase subunit; Provisional
Probab=47.62 E-value=3.6 Score=28.34 Aligned_cols=39 Identities=10% Similarity=0.129 Sum_probs=24.0
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCC----CcccccccccccccHH
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFR----HKFVCYACDYFSYNIG 95 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~----~~~~C~~C~~~f~~~~ 95 (155)
..+|+.|+..-...-.+ ++.+.. .-|.|..||..|..+.
T Consensus 143 ~v~CPkCg~~~A~f~ql------------QTRSADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMI------------QTRAADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred CCCCCCCCCCceEEEEE------------eeccCCCCceEEEEcCCCCCccCCcc
Confidence 46799998544333222 333332 3388999999987653
No 145
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=47.57 E-value=2.3 Score=26.35 Aligned_cols=13 Identities=23% Similarity=0.519 Sum_probs=7.2
Q ss_pred CCccccccccccc
Q psy13210 79 RHKFVCYACDYFS 91 (155)
Q Consensus 79 ~~~~~C~~C~~~f 91 (155)
++.|.|+.||..-
T Consensus 20 ~k~FtCp~Cghe~ 32 (104)
T COG4888 20 PKTFTCPRCGHEK 32 (104)
T ss_pred CceEecCccCCee
Confidence 3456666666543
No 146
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=46.82 E-value=4.4 Score=24.70 Aligned_cols=37 Identities=5% Similarity=-0.069 Sum_probs=22.8
Q ss_pred ccccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccH
Q psy13210 40 MIDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 40 ~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 94 (155)
......+.|+.|++.-.. ......+.|..|++.|.-.
T Consensus 31 ~~q~a~y~CpfCgk~~vk------------------R~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 31 ISQHAKYFCPFCGKHAVK------------------RQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred HHHhCCccCCCCCCCcee------------------eeeeEEEEcCCCCCEEeCC
Confidence 344566788888753211 1122568899999887643
No 147
>KOG1842|consensus
Probab=45.05 E-value=12 Score=29.61 Aligned_cols=26 Identities=23% Similarity=0.458 Sum_probs=16.5
Q ss_pred cccccccccccccHHHHHHHHhH-hcC
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRT-HTG 106 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~-h~~ 106 (155)
.|.||+|..-|.....|..|... |.+
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccc
Confidence 36666666666666666666655 443
No 148
>KOG4173|consensus
Probab=43.82 E-value=13 Score=26.44 Aligned_cols=62 Identities=13% Similarity=0.150 Sum_probs=42.2
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhh--hccCCCCCcccccc--cccccccHHHHHHHHhH-hc
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESM--IRTDPFRHKFVCYA--CDYFSYNIGCMRSHIRT-HT 105 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~--~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~-h~ 105 (155)
-+-.|..|.+.|.+...|..|..--..+- ..+..+..-|.|-+ |+-.|.+...-..|+-. |.
T Consensus 105 h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 105 HGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred ccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 34469999999999999999973000000 01112344588955 99999999999999765 53
No 149
>KOG0717|consensus
Probab=43.75 E-value=13 Score=29.70 Aligned_cols=21 Identities=29% Similarity=0.550 Sum_probs=19.7
Q ss_pred eecCcCcccccCchHHHHHHh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~ 147 (155)
+-|.+|.|+|.+.-.|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 889999999999999999976
No 150
>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=43.45 E-value=12 Score=30.32 Aligned_cols=9 Identities=33% Similarity=0.859 Sum_probs=5.3
Q ss_pred CeecCcCcc
Q psy13210 126 PFKCVVCKQ 134 (155)
Q Consensus 126 ~~~C~~C~k 134 (155)
|..|+.||-
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 456666654
No 151
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=43.03 E-value=24 Score=24.14 Aligned_cols=50 Identities=10% Similarity=0.190 Sum_probs=30.7
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccC-----CCCCcccccccccccccHHHHHHHHh
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTD-----PFRHKFVCYACDYFSYNIGCMRSHIR 102 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~-----~~~~~~~C~~C~~~f~~~~~l~~H~~ 102 (155)
.-+|..|+......+.-..-. .+. ....-+.|+.||+.|...+++..-.+
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~--------~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKE--------KVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred cccCcccCCEeccCcHHHHhh--------ccchhhhhcccceeECCCCcccccCchHHHHHHH
Confidence 457999987665443222111 111 12344679999999998888775544
No 152
>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=42.68 E-value=13 Score=23.11 Aligned_cols=17 Identities=35% Similarity=0.825 Sum_probs=13.3
Q ss_pred ccCCCCeecCcCcccccC
Q psy13210 121 HTGRKPFKCVVCKQFFAT 138 (155)
Q Consensus 121 h~~~~~~~C~~C~k~f~~ 138 (155)
+.| +|+.|++||.-|.-
T Consensus 75 ~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 75 EKG-KPKRCPECGHVFKL 91 (97)
T ss_pred eCC-CceeCCCCCcEEEE
Confidence 345 68999999988764
No 153
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.47 E-value=14 Score=31.10 Aligned_cols=10 Identities=30% Similarity=0.268 Sum_probs=6.2
Q ss_pred hhhhhhhhcc
Q psy13210 47 RLERLRTQCA 56 (155)
Q Consensus 47 ~c~~C~~~~~ 56 (155)
.|..|+..+.
T Consensus 385 ~C~~Cg~~~~ 394 (665)
T PRK14873 385 ACARCRTPAR 394 (665)
T ss_pred EhhhCcCeeE
Confidence 4777766554
No 154
>PRK05978 hypothetical protein; Provisional
Probab=41.77 E-value=7.6 Score=26.05 Aligned_cols=34 Identities=18% Similarity=0.005 Sum_probs=21.4
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccH
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 94 (155)
-.-+|+.|++.--...-|+.+. .|+.||..|...
T Consensus 32 l~grCP~CG~G~LF~g~Lkv~~-----------------~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGEGKLFRAFLKPVD-----------------HCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCCCcccccccccCC-----------------CccccCCccccC
Confidence 3456999986654443333332 699999877543
No 155
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=41.59 E-value=15 Score=19.35 Aligned_cols=14 Identities=36% Similarity=0.702 Sum_probs=10.4
Q ss_pred cccccccccccccH
Q psy13210 81 KFVCYACDYFSYNI 94 (155)
Q Consensus 81 ~~~C~~C~~~f~~~ 94 (155)
.+.|+.||..+.-.
T Consensus 20 ~~vC~~Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRKCGYEEPIE 33 (52)
T ss_pred EEECCcCCCeEECC
Confidence 57899998876554
No 156
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=41.37 E-value=13 Score=22.73 Aligned_cols=15 Identities=13% Similarity=0.292 Sum_probs=12.4
Q ss_pred CCccccccccccccc
Q psy13210 79 RHKFVCYACDYFSYN 93 (155)
Q Consensus 79 ~~~~~C~~C~~~f~~ 93 (155)
-+|-.|..||+.|.+
T Consensus 56 v~Pa~CkkCGfef~~ 70 (97)
T COG3357 56 VRPARCKKCGFEFRD 70 (97)
T ss_pred ecChhhcccCccccc
Confidence 357789999999976
No 157
>KOG4124|consensus
Probab=40.38 E-value=1.6 Score=33.35 Aligned_cols=69 Identities=20% Similarity=0.335 Sum_probs=43.0
Q ss_pred CCcccccc--cccccccHHHHHHHHhH-hcCCCCcH-HHHHHHHHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 79 RHKFVCYA--CDYFSYNIGCMRSHIRT-HTGEKPYA-HIIRNHYRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 79 ~~~~~C~~--C~~~f~~~~~l~~H~~~-h~~~~~~~-~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
.++++|++ |.+.++....|+-|-.. |...-... -.-+-|+.--...|+|.|++|.++++....|..|+-
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 46788877 99988888877766443 32100000 001112222234689999999999998888776654
No 158
>KOG2071|consensus
Probab=39.99 E-value=19 Score=29.63 Aligned_cols=29 Identities=21% Similarity=0.429 Sum_probs=24.1
Q ss_pred CCCCeecCcCcccccCchHHHHHHhhhhCC
Q psy13210 123 GRKPFKCVVCKQFFATYSGAYQHLRRTHGQ 152 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~~~~L~~H~~~~H~~ 152 (155)
...|-.|..||.+|........|+. .|.+
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md-~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMD-IHDD 443 (579)
T ss_pred cCCcchhcccccccccchhhhhHhh-hhhh
Confidence 3557889999999999999999888 6643
No 159
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=39.80 E-value=12 Score=25.32 Aligned_cols=17 Identities=24% Similarity=0.661 Sum_probs=13.8
Q ss_pred CeecCcCcccccCchHH
Q psy13210 126 PFKCVVCKQFFATYSGA 142 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~~L 142 (155)
.+.|+.||++|.....+
T Consensus 28 ~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RRECLACGKRFTTFERV 44 (154)
T ss_pred eeeccccCCcceEeEec
Confidence 48999999999876543
No 160
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=39.68 E-value=4.7 Score=30.94 Aligned_cols=69 Identities=14% Similarity=0.247 Sum_probs=22.4
Q ss_pred cccCCCcchhhhhhcccccccc-----cChhhhhhhhhhccCcHHHhhhHHhhhhhhhccC-CCCCccccccccccccc
Q psy13210 21 DAQDGGFSKLKRALDVNQSMID-----ISADRLERLRTQCATSAELTQHEIRTIESMIRTD-PFRHKFVCYACDYFSYN 93 (155)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~-----~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~-~~~~~~~C~~C~~~f~~ 93 (155)
...+..|..+......++.+.. ...+.|..|...+-..+..-.-.... +..+ ...+-|+|..|++....
T Consensus 223 e~~e~yf~~Le~kEkmeekm~~i~e~k~kav~C~~C~yt~~~~~~~C~~~~H~----l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 223 ERQERYFEKLEKKEKMEEKMESIREVKCKAVTCKQCKYTAFKPSDRCKEEGHP----LKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp ---------------------S-S--EEEEEEETTT--EESS--HHHHHTT------EEEEEEE-EEEE-T-TS-EEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCcEEEEEEEEcCCCCCcccCcchhHHhcCCc----eEEeeeeeeeEECCCCCCeeee
Confidence 3344445444444444443333 36778999988777666554322100 1222 23566899999986543
No 161
>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=39.42 E-value=14 Score=19.90 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=10.7
Q ss_pred ccccccccccccH
Q psy13210 82 FVCYACDYFSYNI 94 (155)
Q Consensus 82 ~~C~~C~~~f~~~ 94 (155)
|+|..||+.+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7899999988754
No 162
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=39.10 E-value=32 Score=27.74 Aligned_cols=42 Identities=10% Similarity=-0.002 Sum_probs=25.6
Q ss_pred ccccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCC------CCcccccccccc
Q psy13210 40 MIDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPF------RHKFVCYACDYF 90 (155)
Q Consensus 40 ~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~------~~~~~C~~C~~~ 90 (155)
......|+|..|+..|.....-... .+.++ +..|.||.||..
T Consensus 420 ~~~~~~~~c~~c~~~yd~~~g~~~~---------~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 420 ADLGPRMQCSVCQWIYDPAKGEPMQ---------DVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred cCCCCeEEECCCCeEECCCCCCccc---------CCCCCCChhhCCCCCcCcCCCCc
Confidence 3445788999999888654321111 22222 335899999964
No 163
>KOG0717|consensus
Probab=39.06 E-value=18 Score=28.92 Aligned_cols=22 Identities=23% Similarity=0.773 Sum_probs=19.6
Q ss_pred eecCcCcccccCchHHHHHHhh
Q psy13210 127 FKCVVCKQFFATYSGAYQHLRR 148 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H~~~ 148 (155)
..|..|+..|.+..-|-.|+..
T Consensus 461 ~~C~tCr~~FdSRnkLF~Hlk~ 482 (508)
T KOG0717|consen 461 ISCTTCRESFDSRNKLFAHLKK 482 (508)
T ss_pred HhhhhhhhhccchhHHHHHhhh
Confidence 6799999999999999999873
No 164
>PLN02294 cytochrome c oxidase subunit Vb
Probab=38.41 E-value=16 Score=25.08 Aligned_cols=16 Identities=19% Similarity=0.355 Sum_probs=13.0
Q ss_pred CCcccccccccccccH
Q psy13210 79 RHKFVCYACDYFSYNI 94 (155)
Q Consensus 79 ~~~~~C~~C~~~f~~~ 94 (155)
.+++.|++||..|.-+
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 4688999999998644
No 165
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=37.29 E-value=25 Score=19.34 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=4.1
Q ss_pred Cccccccccccc
Q psy13210 80 HKFVCYACDYFS 91 (155)
Q Consensus 80 ~~~~C~~C~~~f 91 (155)
+.|+|++||.+=
T Consensus 32 r~y~Cp~CgAtG 43 (55)
T PF05741_consen 32 RKYVCPICGATG 43 (55)
T ss_dssp GG---TTT---G
T ss_pred hcCcCCCCcCcC
Confidence 458899998763
No 166
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.23 E-value=22 Score=20.01 Aligned_cols=16 Identities=13% Similarity=0.366 Sum_probs=12.1
Q ss_pred CCCCeecCcCcccccC
Q psy13210 123 GRKPFKCVVCKQFFAT 138 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~ 138 (155)
.+.-..|++|+..|+.
T Consensus 45 ~~gev~CPYC~t~y~l 60 (62)
T COG4391 45 DEGEVVCPYCSTRYRL 60 (62)
T ss_pred CCCcEecCccccEEEe
Confidence 3445789999998864
No 167
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.51 E-value=17 Score=23.73 Aligned_cols=17 Identities=29% Similarity=0.749 Sum_probs=13.5
Q ss_pred CCCCeecCcCcccccCc
Q psy13210 123 GRKPFKCVVCKQFFATY 139 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~~ 139 (155)
|...|.|..|++.|...
T Consensus 50 ~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 50 GHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccccCCcCcceeee
Confidence 34569999999998754
No 168
>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=35.60 E-value=15 Score=19.42 Aligned_cols=14 Identities=21% Similarity=0.529 Sum_probs=10.9
Q ss_pred ccccccccccccHH
Q psy13210 82 FVCYACDYFSYNIG 95 (155)
Q Consensus 82 ~~C~~C~~~f~~~~ 95 (155)
|+|..||..+....
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 78999998876554
No 169
>KOG3408|consensus
Probab=34.58 E-value=27 Score=22.61 Aligned_cols=26 Identities=19% Similarity=0.534 Sum_probs=19.1
Q ss_pred CCCcccccccccccccHHHHHHHHhH
Q psy13210 78 FRHKFVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 78 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
+...|-|-.|.+-|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44456788888888888888877764
No 170
>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=34.38 E-value=18 Score=19.58 Aligned_cols=17 Identities=12% Similarity=0.444 Sum_probs=11.3
Q ss_pred CCCCeecCcCcccccCc
Q psy13210 123 GRKPFKCVVCKQFFATY 139 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~~ 139 (155)
+...|.|.+|++.+...
T Consensus 32 ~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 32 EPIKLRCHYCERIITED 48 (52)
T ss_dssp TTCEEEETTT--EEEHH
T ss_pred CCCEEEeeCCCCEeccc
Confidence 55569999999987643
No 171
>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=33.90 E-value=15 Score=23.25 Aligned_cols=14 Identities=7% Similarity=0.043 Sum_probs=9.2
Q ss_pred ChhhhhhhhhhccC
Q psy13210 44 SADRLERLRTQCAT 57 (155)
Q Consensus 44 ~~~~c~~C~~~~~~ 57 (155)
...+|..|+..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 69 ARARCRDCGHEFEP 82 (113)
T ss_dssp -EEEETTTS-EEEC
T ss_pred CcEECCCCCCEEec
Confidence 34679999988865
No 172
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=33.73 E-value=16 Score=19.88 Aligned_cols=42 Identities=12% Similarity=0.051 Sum_probs=23.7
Q ss_pred Chhhhhh--hhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccc----cccccccH
Q psy13210 44 SADRLER--LRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYA----CDYFSYNI 94 (155)
Q Consensus 44 ~~~~c~~--C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~----C~~~f~~~ 94 (155)
....|+. |...+. ...|..|. ...-..++..|+. |+..+...
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~--------~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHL--------ENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHH--------HTTSTTSEEE-SS----S--EEEHH
T ss_pred CEeeCCCCCccccee-HHHHHHHH--------HccCCCCcEECCCCCCCCCCccchh
Confidence 3456766 444343 56888887 6555666788999 88776543
No 173
>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=33.09 E-value=18 Score=20.35 Aligned_cols=30 Identities=13% Similarity=0.173 Sum_probs=12.8
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccH
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 94 (155)
.-.|..|++.|... .+.+-|..||..|-..
T Consensus 9 ~~~C~~C~~~F~~~--------------------~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 9 ASNCMICGKKFSLF--------------------RRRHHCRNCGRVVCSS 38 (69)
T ss_dssp -SB-TTT--B-BSS--------------------S-EEE-TTT--EEECC
T ss_pred CCcCcCcCCcCCCc--------------------eeeEccCCCCCEECCc
Confidence 34588899888542 1345688888776544
No 174
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.02 E-value=16 Score=19.42 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=12.4
Q ss_pred ecCcCcccccCchHHH
Q psy13210 128 KCVVCKQFFATYSGAY 143 (155)
Q Consensus 128 ~C~~C~k~f~~~~~L~ 143 (155)
.|++|++.|++.-...
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 5999999998865443
No 175
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.91 E-value=20 Score=28.39 Aligned_cols=15 Identities=20% Similarity=0.366 Sum_probs=12.3
Q ss_pred CeecCcCcccccCch
Q psy13210 126 PFKCVVCKQFFATYS 140 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~ 140 (155)
-|.|+-||+.+....
T Consensus 367 g~rC~kCg~~~~~~~ 381 (421)
T COG1571 367 GFRCKKCGTRARETL 381 (421)
T ss_pred CcccccccccCCccc
Confidence 599999999887653
No 176
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=32.80 E-value=16 Score=27.51 Aligned_cols=35 Identities=14% Similarity=0.052 Sum_probs=23.7
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHH
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIG 95 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~ 95 (155)
-+.+|+.|+.....+ .|.. ..+.|+.||.-|+-..
T Consensus 37 lw~kc~~C~~~~~~~-~l~~----------------~~~vcp~c~~h~rltA 71 (296)
T CHL00174 37 LWVQCENCYGLNYKK-FLKS----------------KMNICEQCGYHLKMSS 71 (296)
T ss_pred CeeECCCccchhhHH-HHHH----------------cCCCCCCCCCCcCCCH
Confidence 477899998765433 2333 2368999999887554
No 177
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=32.09 E-value=30 Score=26.72 Aligned_cols=29 Identities=21% Similarity=0.472 Sum_probs=22.0
Q ss_pred cCCCCCcccccccc-cccccHHHHHHHHhH
Q psy13210 75 TDPFRHKFVCYACD-YFSYNIGCMRSHIRT 103 (155)
Q Consensus 75 ~~~~~~~~~C~~C~-~~f~~~~~l~~H~~~ 103 (155)
.|.-.+.|.|.+|| +++.-...+.+|...
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~E 397 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFEE 397 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhhh
Confidence 34445779999999 777777888888653
No 178
>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=31.80 E-value=22 Score=21.71 Aligned_cols=10 Identities=20% Similarity=0.803 Sum_probs=7.2
Q ss_pred CeecCcCccc
Q psy13210 126 PFKCVVCKQF 135 (155)
Q Consensus 126 ~~~C~~C~k~ 135 (155)
.|.|++||+.
T Consensus 35 ky~Cp~Cgk~ 44 (90)
T PF01780_consen 35 KYTCPFCGKT 44 (90)
T ss_dssp -BEESSSSSS
T ss_pred CCcCCCCCCc
Confidence 4888888874
No 179
>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=31.75 E-value=15 Score=19.82 Aligned_cols=25 Identities=24% Similarity=0.608 Sum_probs=15.4
Q ss_pred CCeecCcCcccccCchHHHHHHhhhh
Q psy13210 125 KPFKCVVCKQFFATYSGAYQHLRRTH 150 (155)
Q Consensus 125 ~~~~C~~C~k~f~~~~~L~~H~~~~H 150 (155)
..|.|+.|+..|...-.+-.|.. .|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~-LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET-LH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT-S-
T ss_pred CeEECCCCCCccccCcChhhhcc-cc
Confidence 46999999999998888887776 44
No 180
>PF14353 CpXC: CpXC protein
Probab=31.62 E-value=8.9 Score=24.73 Aligned_cols=55 Identities=18% Similarity=0.254 Sum_probs=29.3
Q ss_pred ccccccccccccHHHHHHHHhHhcCCCCcHHHHHHHHHhccCC-CCeecCcCcccccCchHHHHH
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRTHTGEKPYAHIIRNHYRKHTGR-KPFKCVVCKQFFATYSGAYQH 145 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~l~~H~~~h~~~-~~~~C~~C~k~f~~~~~L~~H 145 (155)
..||.|+..|...... .+.....| .++.-+. .|+ -.|.|+.||..|.-...+..|
T Consensus 2 itCP~C~~~~~~~v~~----~I~~~~~p---~l~e~il--~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWT----SINADEDP---ELKEKIL--DGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeEEEEEe----EEcCcCCH---HHHHHHH--cCCcCEEECCCCCCceecCCCEEEE
Confidence 3688888877554321 11222222 1121111 222 248999999998776555444
No 181
>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=30.72 E-value=24 Score=17.35 Aligned_cols=13 Identities=31% Similarity=0.478 Sum_probs=6.8
Q ss_pred eecCcCcccccCc
Q psy13210 127 FKCVVCKQFFATY 139 (155)
Q Consensus 127 ~~C~~C~k~f~~~ 139 (155)
-.|.+|++.|.-+
T Consensus 4 ~~C~eC~~~f~dS 16 (34)
T PF01286_consen 4 PKCDECGKPFMDS 16 (34)
T ss_dssp EE-TTT--EES-S
T ss_pred chHhHhCCHHHHH
Confidence 3699999988754
No 182
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.67 E-value=17 Score=23.11 Aligned_cols=14 Identities=0% Similarity=-0.256 Sum_probs=9.8
Q ss_pred ChhhhhhhhhhccC
Q psy13210 44 SADRLERLRTQCAT 57 (155)
Q Consensus 44 ~~~~c~~C~~~~~~ 57 (155)
...+|..|+..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 69 AQAWCWDCSQVVEI 82 (113)
T ss_pred cEEEcccCCCEEec
Confidence 45679999976643
No 183
>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=30.31 E-value=23 Score=19.37 Aligned_cols=12 Identities=25% Similarity=0.312 Sum_probs=9.4
Q ss_pred cccccccccccc
Q psy13210 82 FVCYACDYFSYN 93 (155)
Q Consensus 82 ~~C~~C~~~f~~ 93 (155)
++|+.||..+.-
T Consensus 3 ~~CP~CG~~iev 14 (54)
T TIGR01206 3 FECPDCGAEIEL 14 (54)
T ss_pred cCCCCCCCEEec
Confidence 689999987643
No 184
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=30.08 E-value=28 Score=21.88 Aligned_cols=25 Identities=24% Similarity=0.598 Sum_probs=21.5
Q ss_pred CCCCeecCcCcccccCchHHHHHHh
Q psy13210 123 GRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 123 ~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
|-..+-|-+|.+-|-+.-.|..|.+
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhc
Confidence 4456889999999999999999876
No 185
>KOG1088|consensus
Probab=29.77 E-value=23 Score=22.69 Aligned_cols=22 Identities=14% Similarity=0.081 Sum_probs=17.8
Q ss_pred ccCCCCCcccccccccccccHH
Q psy13210 74 RTDPFRHKFVCYACDYFSYNIG 95 (155)
Q Consensus 74 ~~~~~~~~~~C~~C~~~f~~~~ 95 (155)
.++..+...+|+.||..|.-..
T Consensus 91 e~~v~EG~l~CpetG~vfpI~~ 112 (124)
T KOG1088|consen 91 EIDVIEGELVCPETGRVFPISD 112 (124)
T ss_pred hhhhccceEecCCCCcEeeccc
Confidence 5666777889999999997654
No 186
>PRK01343 zinc-binding protein; Provisional
Probab=29.70 E-value=35 Score=18.93 Aligned_cols=14 Identities=14% Similarity=0.221 Sum_probs=10.8
Q ss_pred CCeecCcCcccccC
Q psy13210 125 KPFKCVVCKQFFAT 138 (155)
Q Consensus 125 ~~~~C~~C~k~f~~ 138 (155)
....|+.|++.+.+
T Consensus 8 p~~~CP~C~k~~~~ 21 (57)
T PRK01343 8 PTRPCPECGKPSTR 21 (57)
T ss_pred CCCcCCCCCCcCcC
Confidence 45779999998754
No 187
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=29.04 E-value=41 Score=22.69 Aligned_cols=46 Identities=13% Similarity=0.302 Sum_probs=20.0
Q ss_pred Chhhhhhhhhhcc------CcHHHhhhHHhhhhhhhccCC----CCCccccccccc
Q psy13210 44 SADRLERLRTQCA------TSAELTQHEIRTIESMIRTDP----FRHKFVCYACDY 89 (155)
Q Consensus 44 ~~~~c~~C~~~~~------~~~~l~~h~~~~~~~~~~~~~----~~~~~~C~~C~~ 89 (155)
...+|..|++.|- ..+.+..|.+..-.+....|. ++...+|..||.
T Consensus 13 ~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~ 68 (152)
T PF09416_consen 13 CVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGS 68 (152)
T ss_dssp CEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT--
T ss_pred cEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCC
Confidence 3456777777762 446666776533333223333 455688988875
No 188
>PRK12722 transcriptional activator FlhC; Provisional
Probab=28.94 E-value=30 Score=24.22 Aligned_cols=30 Identities=20% Similarity=0.187 Sum_probs=20.2
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccc
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDY 89 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~ 89 (155)
....|..|+-.|.... +.....|+|+.|.-
T Consensus 133 ~l~~C~~Cgg~fv~~~----------------~e~~~~f~CplC~~ 162 (187)
T PRK12722 133 QLSSCNCCGGHFVTHA----------------HDPVGSFVCGLCQP 162 (187)
T ss_pred eeccCCCCCCCeeccc----------------cccCCCCcCCCCCC
Confidence 3456999998886432 12235789999976
No 189
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.84 E-value=31 Score=16.71 Aligned_cols=12 Identities=25% Similarity=0.586 Sum_probs=9.0
Q ss_pred CeecCcCccccc
Q psy13210 126 PFKCVVCKQFFA 137 (155)
Q Consensus 126 ~~~C~~C~k~f~ 137 (155)
-+.|..||..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 367888888764
No 190
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=28.73 E-value=16 Score=27.48 Aligned_cols=44 Identities=11% Similarity=0.108 Sum_probs=23.9
Q ss_pred cccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 41 IDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 41 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
.....+.|+.|+..-.....++... .--+.-.-|.|..||..+.
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~Qtrs--------aDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRS--------ADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CCcccccCCCCCCccceEEEecccC--------CCCCCeEEEEcCCCCCeee
Confidence 3446789999985544433322211 1111123478999997654
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=28.60 E-value=28 Score=17.31 Aligned_cols=11 Identities=27% Similarity=0.736 Sum_probs=6.1
Q ss_pred CeecCcCcccc
Q psy13210 126 PFKCVVCKQFF 136 (155)
Q Consensus 126 ~~~C~~C~k~f 136 (155)
-|.|..||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 49999999654
No 192
>PRK04351 hypothetical protein; Provisional
Probab=28.48 E-value=22 Score=23.88 Aligned_cols=35 Identities=14% Similarity=0.072 Sum_probs=22.9
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccH
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 94 (155)
-.|.|..|+..+.+.. +. +...|.|..|+..+...
T Consensus 111 y~Y~C~~Cg~~~~r~R--------------r~--n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 111 YLYECQSCGQQYLRKR--------------RI--NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEEECCCCCCEeeeee--------------ec--CCCcEEeCCCCcEeeec
Confidence 3578988997665421 11 23668999999876543
No 193
>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=28.27 E-value=19 Score=24.11 Aligned_cols=36 Identities=14% Similarity=0.107 Sum_probs=22.9
Q ss_pred ccccccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccccc
Q psy13210 38 QSMIDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFS 91 (155)
Q Consensus 38 ~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f 91 (155)
......+.+.|..||..... .+++ ..-+|+.||..-
T Consensus 105 GE~~g~G~l~C~~Cg~~~~~-----------------~~~~-~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 105 GEVVGPGTLVCENCGHEVEL-----------------THPE-RLPPCPKCGHTE 140 (146)
T ss_pred CcEecCceEecccCCCEEEe-----------------cCCC-cCCCCCCCCCCe
Confidence 34455578889999976432 2232 345799998753
No 194
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=27.85 E-value=7.4 Score=22.39 Aligned_cols=14 Identities=14% Similarity=0.147 Sum_probs=8.4
Q ss_pred CcccccccccccccH
Q psy13210 80 HKFVCYACDYFSYNI 94 (155)
Q Consensus 80 ~~~~C~~C~~~f~~~ 94 (155)
+.-+| .||++..-+
T Consensus 19 kTkkC-~CG~~l~vk 32 (68)
T PF09082_consen 19 KTKKC-VCGKTLKVK 32 (68)
T ss_dssp SEEEE-TTTEEEE--
T ss_pred ceeEe-cCCCeeeee
Confidence 45579 899865433
No 195
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=27.64 E-value=19 Score=22.89 Aligned_cols=9 Identities=22% Similarity=0.807 Sum_probs=4.3
Q ss_pred ccccccccc
Q psy13210 82 FVCYACDYF 90 (155)
Q Consensus 82 ~~C~~C~~~ 90 (155)
..|..||..
T Consensus 71 ~~C~~Cg~~ 79 (114)
T PRK03681 71 CWCETCQQY 79 (114)
T ss_pred EEcccCCCe
Confidence 445555543
No 196
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=27.61 E-value=21 Score=26.83 Aligned_cols=35 Identities=14% Similarity=0.038 Sum_probs=23.2
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHH
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIG 95 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~ 95 (155)
-+.+|+.|+.....+ .|... .+.|+.||.-|+-..
T Consensus 26 ~~~~c~~c~~~~~~~-~l~~~----------------~~vc~~c~~h~rl~a 60 (292)
T PRK05654 26 LWTKCPSCGQVLYRK-ELEAN----------------LNVCPKCGHHMRISA 60 (292)
T ss_pred CeeECCCccchhhHH-HHHhc----------------CCCCCCCCCCeeCCH
Confidence 477899998765432 23222 358999999886543
No 197
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=27.41 E-value=22 Score=26.61 Aligned_cols=35 Identities=20% Similarity=0.140 Sum_probs=23.5
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccHH
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNIG 95 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~ 95 (155)
-+.+|+.|+.....+ +|... -+.|+.||.-|+-..
T Consensus 25 ~~~~c~~c~~~~~~~-~l~~~----------------~~vc~~c~~h~rl~a 59 (285)
T TIGR00515 25 VWTKCPKCGQVLYTK-ELERN----------------LEVCPKCDHHMRMDA 59 (285)
T ss_pred CeeECCCCcchhhHH-HHHhh----------------CCCCCCCCCcCcCCH
Confidence 477899999765433 33332 368999999877543
No 198
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.25 E-value=15 Score=18.04 Aligned_cols=12 Identities=33% Similarity=1.021 Sum_probs=8.3
Q ss_pred Cccccccccccc
Q psy13210 80 HKFVCYACDYFS 91 (155)
Q Consensus 80 ~~~~C~~C~~~f 91 (155)
..+.|+.||...
T Consensus 21 ~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 21 ERLVCPACGFIH 32 (34)
T ss_dssp -EEEETTTTEEE
T ss_pred cceECCCCCCEE
Confidence 347788888764
No 199
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=26.92 E-value=30 Score=19.05 Aligned_cols=12 Identities=25% Similarity=0.481 Sum_probs=9.4
Q ss_pred ecCcCcccccCc
Q psy13210 128 KCVVCKQFFATY 139 (155)
Q Consensus 128 ~C~~C~k~f~~~ 139 (155)
-|++|++.|...
T Consensus 41 gCPfC~~~~~~~ 52 (55)
T PF14447_consen 41 GCPFCGTPFEFD 52 (55)
T ss_pred CCCCCCCcccCC
Confidence 499999988653
No 200
>PRK12860 transcriptional activator FlhC; Provisional
Probab=26.77 E-value=33 Score=24.05 Aligned_cols=29 Identities=34% Similarity=0.550 Sum_probs=19.7
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccc
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACD 88 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~ 88 (155)
....|..|+-.|.... +.....|+|+.|.
T Consensus 133 ~l~~C~~Cgg~fv~~~----------------~e~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGGKFVTHA----------------HDLRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCCCeeccc----------------cccCCCCcCCCCC
Confidence 4457999998886432 2223568999997
No 201
>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=26.73 E-value=21 Score=25.12 Aligned_cols=24 Identities=21% Similarity=0.490 Sum_probs=0.0
Q ss_pred CCcccccccccccc-cHHHHHHHHh
Q psy13210 79 RHKFVCYACDYFSY-NIGCMRSHIR 102 (155)
Q Consensus 79 ~~~~~C~~C~~~f~-~~~~l~~H~~ 102 (155)
.+.|+|.+||.... -...+.+|..
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcC
Confidence 45699999997554 5577888865
No 202
>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=26.09 E-value=42 Score=15.81 Aligned_cols=14 Identities=14% Similarity=0.690 Sum_probs=7.8
Q ss_pred CeecCcCcccccCc
Q psy13210 126 PFKCVVCKQFFATY 139 (155)
Q Consensus 126 ~~~C~~C~k~f~~~ 139 (155)
.|.|+.|+..+-+.
T Consensus 13 kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 13 KYRCPRCGARYCSL 26 (30)
T ss_dssp SEE-TTT--EESSH
T ss_pred EEECCCcCCceeCc
Confidence 58888888776653
No 203
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=26.04 E-value=43 Score=18.42 Aligned_cols=18 Identities=22% Similarity=0.384 Sum_probs=13.1
Q ss_pred CCCCcccccccccccccH
Q psy13210 77 PFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 77 ~~~~~~~C~~C~~~f~~~ 94 (155)
.....|.|+.||..+.-.
T Consensus 10 ~~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTHCS 27 (55)
T ss_pred ccccCCcCCCCCCcCccC
Confidence 345679999999865544
No 204
>KOG2807|consensus
Probab=25.75 E-value=95 Score=23.88 Aligned_cols=68 Identities=13% Similarity=0.219 Sum_probs=41.6
Q ss_pred CcccccccccccccHHHHHHHHhHhcCCCCcH-----H-HHHHH----HHhccCCCCeecCcCcccccCchHHHHHHh
Q psy13210 80 HKFVCYACDYFSYNIGCMRSHIRTHTGEKPYA-----H-IIRNH----YRKHTGRKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 80 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~-----~-~l~~H----~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
-|..|++|+-+.-..-+|.+-..--..-++|. . .-.++ ...-.+...|.|..|.-.|...-+.-.|..
T Consensus 289 LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhh
Confidence 36679999988887777774432222233332 0 00000 111123446999999999999988888877
No 205
>KOG1994|consensus
Probab=25.61 E-value=35 Score=24.69 Aligned_cols=23 Identities=17% Similarity=0.507 Sum_probs=19.8
Q ss_pred CCCeecCcCcccccCchHHHHHH
Q psy13210 124 RKPFKCVVCKQFFATYSGAYQHL 146 (155)
Q Consensus 124 ~~~~~C~~C~k~f~~~~~L~~H~ 146 (155)
..-|-|-+||..|.+...|..|=
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhC
Confidence 34599999999999999999873
No 206
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=25.43 E-value=29 Score=17.27 Aligned_cols=17 Identities=24% Similarity=0.153 Sum_probs=10.4
Q ss_pred eecCcCcccccCchHHH
Q psy13210 127 FKCVVCKQFFATYSGAY 143 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~ 143 (155)
=.|+-|++.|-+.+...
T Consensus 3 ~~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECR 19 (36)
T ss_dssp -C-TTTSSSCS-TTT--
T ss_pred ccCcccCCCcchhhhhh
Confidence 36999999998887654
No 207
>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=25.42 E-value=33 Score=21.01 Aligned_cols=10 Identities=20% Similarity=0.707 Sum_probs=7.4
Q ss_pred CeecCcCccc
Q psy13210 126 PFKCVVCKQF 135 (155)
Q Consensus 126 ~~~C~~C~k~ 135 (155)
.|.|++||+.
T Consensus 35 ~y~CpfCgk~ 44 (91)
T TIGR00280 35 KYVCPFCGKK 44 (91)
T ss_pred CccCCCCCCC
Confidence 4888888753
No 208
>PF14369 zf-RING_3: zinc-finger
Probab=25.36 E-value=33 Score=16.80 Aligned_cols=10 Identities=20% Similarity=0.225 Sum_probs=8.1
Q ss_pred cccccccccc
Q psy13210 83 VCYACDYFSY 92 (155)
Q Consensus 83 ~C~~C~~~f~ 92 (155)
.|+.|+..|-
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998874
No 209
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=25.20 E-value=31 Score=18.73 Aligned_cols=12 Identities=17% Similarity=0.551 Sum_probs=8.6
Q ss_pred eecCcCcccccC
Q psy13210 127 FKCVVCKQFFAT 138 (155)
Q Consensus 127 ~~C~~C~k~f~~ 138 (155)
+.|++||..+..
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 468999876643
No 210
>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=25.11 E-value=34 Score=18.97 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=6.6
Q ss_pred eecCcCcccccC
Q psy13210 127 FKCVVCKQFFAT 138 (155)
Q Consensus 127 ~~C~~C~k~f~~ 138 (155)
..|+.|++.+.+
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 579999998766
No 211
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.57 E-value=23 Score=22.94 Aligned_cols=14 Identities=0% Similarity=-0.225 Sum_probs=9.8
Q ss_pred ChhhhhhhhhhccCc
Q psy13210 44 SADRLERLRTQCATS 58 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~ 58 (155)
...+| .|+..|...
T Consensus 69 ~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 69 VEIEC-ECGYEGVVD 82 (124)
T ss_pred eeEEe-eCcCccccc
Confidence 45679 999776543
No 212
>KOG4118|consensus
Probab=24.50 E-value=46 Score=19.00 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=12.3
Q ss_pred ccccccccccccHHHHHHHHhH
Q psy13210 82 FVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 82 ~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
|+|.+|-....+...+..|...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~ 60 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFEN 60 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhh
Confidence 4566665555555555555544
No 213
>PLN02748 tRNA dimethylallyltransferase
Probab=24.30 E-value=55 Score=26.44 Aligned_cols=24 Identities=21% Similarity=0.368 Sum_probs=20.7
Q ss_pred Cccccccccc-ccccHHHHHHHHhH
Q psy13210 80 HKFVCYACDY-FSYNIGCMRSHIRT 103 (155)
Q Consensus 80 ~~~~C~~C~~-~f~~~~~l~~H~~~ 103 (155)
+.|.|+.|++ ++........|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5678999998 89999999999875
No 214
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=24.28 E-value=36 Score=18.65 Aligned_cols=19 Identities=11% Similarity=0.214 Sum_probs=16.1
Q ss_pred eecCcCcccccCchHHHHH
Q psy13210 127 FKCVVCKQFFATYSGAYQH 145 (155)
Q Consensus 127 ~~C~~C~k~f~~~~~L~~H 145 (155)
+=|-+||..|.+...|.++
T Consensus 28 ~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred ceeeeeCCccCCHHHHHhC
Confidence 6799999999999888654
No 215
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=23.83 E-value=83 Score=23.67 Aligned_cols=24 Identities=21% Similarity=0.520 Sum_probs=21.7
Q ss_pred CCCeecCcCcccccCchHHHHHHh
Q psy13210 124 RKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 124 ~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
..-|.|+.|=+-|.+...|.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 445999999999999999999987
No 216
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=23.39 E-value=35 Score=22.55 Aligned_cols=33 Identities=12% Similarity=0.092 Sum_probs=20.6
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
.|.|..|+..+... +.+.....+.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~~~---------------rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLRV---------------RRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCceE---------------ccccCcceEEcCCCCCEEE
Confidence 67788888765421 2222225688999987653
No 217
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=23.20 E-value=40 Score=17.12 Aligned_cols=10 Identities=20% Similarity=0.541 Sum_probs=6.3
Q ss_pred CeecCcCccc
Q psy13210 126 PFKCVVCKQF 135 (155)
Q Consensus 126 ~~~C~~C~k~ 135 (155)
.+.|..||.-
T Consensus 19 ~~vC~~CG~V 28 (43)
T PF08271_consen 19 ELVCPNCGLV 28 (43)
T ss_dssp EEEETTT-BB
T ss_pred eEECCCCCCE
Confidence 3788888754
No 218
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=23.16 E-value=30 Score=22.90 Aligned_cols=16 Identities=13% Similarity=0.061 Sum_probs=12.7
Q ss_pred CCcccccccccccccH
Q psy13210 79 RHKFVCYACDYFSYNI 94 (155)
Q Consensus 79 ~~~~~C~~C~~~f~~~ 94 (155)
.++..|+.||..|.-.
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 3588999999988643
No 219
>PTZ00448 hypothetical protein; Provisional
Probab=23.09 E-value=63 Score=25.19 Aligned_cols=23 Identities=17% Similarity=0.532 Sum_probs=20.1
Q ss_pred cccccccccccccHHHHHHHHhH
Q psy13210 81 KFVCYACDYFSYNIGCMRSHIRT 103 (155)
Q Consensus 81 ~~~C~~C~~~f~~~~~l~~H~~~ 103 (155)
.|.|..|+..|.+......|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999888888888876
No 220
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=23.06 E-value=34 Score=18.39 Aligned_cols=15 Identities=7% Similarity=-0.133 Sum_probs=10.2
Q ss_pred ChhhhhhhhhhccCc
Q psy13210 44 SADRLERLRTQCATS 58 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~ 58 (155)
-.++|..|+..|...
T Consensus 27 v~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 27 VWWKCPKCGHEWKAS 41 (55)
T ss_pred EEEECCCCCCeeEcc
Confidence 347788887776554
No 221
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=23.00 E-value=44 Score=17.34 Aligned_cols=13 Identities=15% Similarity=0.296 Sum_probs=9.5
Q ss_pred eecCcCcccccCc
Q psy13210 127 FKCVVCKQFFATY 139 (155)
Q Consensus 127 ~~C~~C~k~f~~~ 139 (155)
|.|..||..|...
T Consensus 3 Y~C~~Cg~~~~~~ 15 (44)
T smart00659 3 YICGECGRENEIK 15 (44)
T ss_pred EECCCCCCEeecC
Confidence 7788888777644
No 222
>KOG0782|consensus
Probab=22.83 E-value=25 Score=29.11 Aligned_cols=29 Identities=24% Similarity=0.249 Sum_probs=21.4
Q ss_pred HHHHHHHHhccCCCCeecCcCcccccCch
Q psy13210 112 HIIRNHYRKHTGRKPFKCVVCKQFFATYS 140 (155)
Q Consensus 112 ~~l~~H~~~h~~~~~~~C~~C~k~f~~~~ 140 (155)
+.+.+|..+|.-..-=+|..|||.|.++-
T Consensus 239 ~~fvrHHWVHrrRqeGkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 239 SGFVRHHWVHRRRQEGKCNTCGKGFQQKF 267 (1004)
T ss_pred ccchHHhHhhHhhhccccchhhhhhhhhe
Confidence 46777777776555567999999987763
No 223
>PLN02748 tRNA dimethylallyltransferase
Probab=22.68 E-value=55 Score=26.41 Aligned_cols=23 Identities=17% Similarity=0.336 Sum_probs=19.0
Q ss_pred CCeecCcCcc-cccCchHHHHHHh
Q psy13210 125 KPFKCVVCKQ-FFATYSGAYQHLR 147 (155)
Q Consensus 125 ~~~~C~~C~k-~f~~~~~L~~H~~ 147 (155)
+.|.|+.|++ .+........|++
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhc
Confidence 4688999998 7988888888865
No 224
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.60 E-value=39 Score=20.62 Aligned_cols=10 Identities=30% Similarity=0.627 Sum_probs=7.6
Q ss_pred CeecCcCccc
Q psy13210 126 PFKCVVCKQF 135 (155)
Q Consensus 126 ~~~C~~C~k~ 135 (155)
.|.|++|++.
T Consensus 36 ~y~CpfCgk~ 45 (90)
T PRK03976 36 KHVCPVCGRP 45 (90)
T ss_pred CccCCCCCCC
Confidence 4889998753
No 225
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=22.43 E-value=38 Score=24.67 Aligned_cols=42 Identities=10% Similarity=0.116 Sum_probs=25.6
Q ss_pred cccChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccccH
Q psy13210 41 IDISADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYNI 94 (155)
Q Consensus 41 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 94 (155)
....+..|..|....... ...-+ +. +...-.||.||+...+.
T Consensus 193 vpl~g~~C~GC~m~l~~~--~~~~V--------~~--~d~iv~CP~CgRILy~~ 234 (239)
T COG1579 193 VPLEGRVCGGCHMKLPSQ--TLSKV--------RK--KDEIVFCPYCGRILYYD 234 (239)
T ss_pred EeecCCcccCCeeeecHH--HHHHH--------hc--CCCCccCCccchHHHhh
Confidence 334566799998765442 22222 23 44556799999876544
No 226
>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=22.43 E-value=27 Score=22.06 Aligned_cols=16 Identities=19% Similarity=0.413 Sum_probs=12.0
Q ss_pred CcccccccccccccHH
Q psy13210 80 HKFVCYACDYFSYNIG 95 (155)
Q Consensus 80 ~~~~C~~C~~~f~~~~ 95 (155)
..|.|++|+..+....
T Consensus 18 ~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 18 TQLICPSCLYEWNENE 33 (109)
T ss_pred CeeECccccccccccc
Confidence 4588999998876553
No 227
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.23 E-value=32 Score=21.96 Aligned_cols=14 Identities=0% Similarity=-0.230 Sum_probs=9.8
Q ss_pred ChhhhhhhhhhccC
Q psy13210 44 SADRLERLRTQCAT 57 (155)
Q Consensus 44 ~~~~c~~C~~~~~~ 57 (155)
...+|..|+..|..
T Consensus 70 ~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 70 VELECKDCSHVFKP 83 (117)
T ss_pred CEEEhhhCCCcccc
Confidence 45679999976643
No 228
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=22.22 E-value=45 Score=24.13 Aligned_cols=31 Identities=19% Similarity=0.401 Sum_probs=19.7
Q ss_pred CCCcccccccccccccHHHHHHHHhHhcCCCCcH
Q psy13210 78 FRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYA 111 (155)
Q Consensus 78 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~ 111 (155)
..++..|+.||..|.-..-+. ..-.|..||.
T Consensus 178 EGkpqRCpECGqVFKLVr~~~---s~~dg~dp~~ 208 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVRVLY---SLPDGEDPFP 208 (268)
T ss_pred CCCCccCCCCCcEEEEEEEEe---ecCCCCCCCC
Confidence 456789999999997643221 1344666664
No 229
>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=22.18 E-value=45 Score=16.21 Aligned_cols=21 Identities=29% Similarity=0.379 Sum_probs=13.8
Q ss_pred CeecCcCcccccCchHHHHHHh
Q psy13210 126 PFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 126 ~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
-+.|+.|++.+.. +.+..|+.
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHHH
T ss_pred eEECCCCcCCcch-hhhHHHHH
Confidence 4789999997653 45666654
No 230
>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=22.03 E-value=15 Score=22.70 Aligned_cols=41 Identities=15% Similarity=0.175 Sum_probs=22.7
Q ss_pred hhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCccccccccccccc
Q psy13210 45 ADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSYN 93 (155)
Q Consensus 45 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~ 93 (155)
...|+.|+..-.....++... .--+.-.-|.|..||..+..
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~Rs--------adE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRR--------ADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCC--------CCCCcEEEEEeCCCCCeeEe
Confidence 467999986554333322211 11112234889999987653
No 231
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.63 E-value=34 Score=19.40 Aligned_cols=18 Identities=11% Similarity=0.275 Sum_probs=13.3
Q ss_pred cCCCCCcccccccccccc
Q psy13210 75 TDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 75 ~~~~~~~~~C~~C~~~f~ 92 (155)
.+..+....|+.||+.|.
T Consensus 47 ~~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 47 VEIVEGELICPECGREYP 64 (68)
T ss_dssp EETTTTEEEETTTTEEEE
T ss_pred ccccCCEEEcCCCCCEEe
Confidence 445566788999988875
No 232
>PLN03239 histone acetyltransferase; Provisional
Probab=21.38 E-value=61 Score=25.05 Aligned_cols=24 Identities=21% Similarity=0.253 Sum_probs=21.4
Q ss_pred CCCeecCcCcccccCchHHHHHHh
Q psy13210 124 RKPFKCVVCKQFFATYSGAYQHLR 147 (155)
Q Consensus 124 ~~~~~C~~C~k~f~~~~~L~~H~~ 147 (155)
+.-|.|+.|-+-|.+...|.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 346999999999999999999976
No 233
>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=21.24 E-value=47 Score=15.97 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=7.7
Q ss_pred CeecCcCcccc
Q psy13210 126 PFKCVVCKQFF 136 (155)
Q Consensus 126 ~~~C~~C~k~f 136 (155)
+..|+.||..-
T Consensus 17 ~irC~~CG~RI 27 (32)
T PF03604_consen 17 PIRCPECGHRI 27 (32)
T ss_dssp TSSBSSSS-SE
T ss_pred cEECCcCCCeE
Confidence 57899998754
No 234
>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=21.03 E-value=24 Score=23.36 Aligned_cols=33 Identities=15% Similarity=0.169 Sum_probs=20.4
Q ss_pred ChhhhhhhhhhccCcHHHhhhHHhhhhhhhccCCCCCcccccccccccc
Q psy13210 44 SADRLERLRTQCATSAELTQHEIRTIESMIRTDPFRHKFVCYACDYFSY 92 (155)
Q Consensus 44 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 92 (155)
-.|.|..|+..+.... +. ....+.|..|+..+.
T Consensus 122 ~~~~C~~C~~~~~r~~--------------~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHR--------------RS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCEeeeec--------------cc--chhhEECCCCCCEEE
Confidence 3566888887664322 22 223478999987654
No 235
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=20.57 E-value=24 Score=24.45 Aligned_cols=13 Identities=8% Similarity=-0.169 Sum_probs=9.8
Q ss_pred Chhhhhhhhhhcc
Q psy13210 44 SADRLERLRTQCA 56 (155)
Q Consensus 44 ~~~~c~~C~~~~~ 56 (155)
..++|..|.+.|.
T Consensus 138 w~~rC~GC~~~f~ 150 (177)
T COG1439 138 WRLRCHGCKRIFP 150 (177)
T ss_pred eeEEEecCceecC
Confidence 3566888998886
No 236
>KOG0402|consensus
Probab=20.25 E-value=32 Score=20.67 Aligned_cols=10 Identities=20% Similarity=0.793 Sum_probs=8.4
Q ss_pred CeecCcCccc
Q psy13210 126 PFKCVVCKQF 135 (155)
Q Consensus 126 ~~~C~~C~k~ 135 (155)
.|.|++|||.
T Consensus 36 ky~CsfCGK~ 45 (92)
T KOG0402|consen 36 KYTCSFCGKK 45 (92)
T ss_pred hhhhhhcchh
Confidence 3999999985
No 237
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=20.00 E-value=44 Score=17.78 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=3.7
Q ss_pred ccccccccc
Q psy13210 81 KFVCYACDY 89 (155)
Q Consensus 81 ~~~C~~C~~ 89 (155)
.|+|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 389999975
Done!