Query psy9958
Match_columns 181
No_of_seqs 251 out of 1636
Neff 8.9
Searched_HMMs 46136
Date Sat Aug 17 00:00:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9958hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 2.1E-21 4.6E-26 148.9 1.1 82 2-94 182-263 (279)
2 KOG2462|consensus 99.7 8.6E-18 1.9E-22 129.2 2.2 59 1-68 207-265 (279)
3 KOG3623|consensus 99.5 2.1E-15 4.6E-20 128.5 3.1 91 5-104 890-980 (1007)
4 KOG3623|consensus 99.4 1.1E-13 2.4E-18 118.2 2.4 55 4-67 917-971 (1007)
5 KOG3576|consensus 99.4 2E-13 4.4E-18 100.9 1.4 74 6-88 114-187 (267)
6 KOG3576|consensus 99.3 1.2E-13 2.7E-18 102.0 -2.8 75 1-84 137-222 (267)
7 PHA02768 hypothetical protein; 99.2 9.1E-12 2E-16 73.8 1.9 44 9-63 5-48 (55)
8 KOG1074|consensus 99.2 7.2E-12 1.6E-16 108.6 2.0 64 2-70 626-692 (958)
9 KOG1074|consensus 99.1 1.4E-11 3.1E-16 106.8 1.2 79 8-95 604-693 (958)
10 PHA00733 hypothetical protein 99.1 1.9E-10 4.2E-15 81.0 4.3 53 7-70 71-123 (128)
11 PHA00732 hypothetical protein 98.8 3.2E-09 6.9E-14 68.4 2.2 48 9-70 1-48 (79)
12 KOG3608|consensus 98.8 1.9E-09 4.1E-14 86.0 0.8 72 7-79 235-324 (467)
13 PF13465 zf-H2C2_2: Zinc-finge 98.7 5.2E-09 1.1E-13 53.1 1.7 26 24-58 1-26 (26)
14 PHA00733 hypothetical protein 98.7 1.2E-09 2.6E-14 77.0 -1.5 78 7-92 38-117 (128)
15 PHA02768 hypothetical protein; 98.7 5.6E-09 1.2E-13 61.9 0.6 43 45-89 4-46 (55)
16 PF05605 zf-Di19: Drought indu 98.6 5.2E-08 1.1E-12 58.3 3.9 53 9-71 2-54 (54)
17 KOG3608|consensus 98.6 1.3E-08 2.8E-13 81.4 0.4 77 3-89 286-367 (467)
18 PHA00616 hypothetical protein 98.6 3.5E-08 7.6E-13 55.8 2.0 34 9-51 1-34 (44)
19 PF13465 zf-H2C2_2: Zinc-finge 98.5 1.5E-08 3.2E-13 51.4 -0.4 21 1-21 6-26 (26)
20 PHA00616 hypothetical protein 98.5 2.9E-08 6.2E-13 56.1 0.7 33 46-78 1-33 (44)
21 PLN03086 PRLI-interacting fact 98.5 3.8E-08 8.2E-13 84.3 1.7 67 5-85 449-515 (567)
22 KOG3993|consensus 98.4 8.9E-08 1.9E-12 78.1 1.4 63 10-72 296-382 (500)
23 COG5189 SFP1 Putative transcri 98.3 1.8E-07 4E-12 73.8 1.9 62 6-67 346-419 (423)
24 PLN03086 PRLI-interacting fact 98.3 1.9E-07 4.2E-12 80.0 1.2 68 8-87 477-554 (567)
25 PF00096 zf-C2H2: Zinc finger, 98.2 1E-06 2.2E-11 43.1 1.7 22 10-31 1-22 (23)
26 PF00096 zf-C2H2: Zinc finger, 98.1 8.5E-07 1.8E-11 43.4 0.7 23 47-69 1-23 (23)
27 PF13894 zf-C2H2_4: C2H2-type 98.0 4.1E-06 9E-11 41.0 2.0 23 10-32 1-23 (24)
28 PF12756 zf-C2H2_2: C2H2 type 97.9 5.5E-06 1.2E-10 55.2 2.1 60 11-70 1-74 (100)
29 KOG3993|consensus 97.9 1.6E-06 3.4E-11 71.0 -0.9 76 10-94 268-376 (500)
30 PF13894 zf-C2H2_4: C2H2-type 97.9 5.1E-06 1.1E-10 40.6 1.2 24 47-70 1-24 (24)
31 PF13912 zf-C2H2_6: C2H2-type 97.8 7.3E-06 1.6E-10 41.6 1.0 24 9-32 1-24 (27)
32 PF13912 zf-C2H2_6: C2H2-type 97.7 1.1E-05 2.3E-10 41.0 0.7 26 46-71 1-26 (27)
33 PF09237 GAGA: GAGA factor; I 97.6 2.4E-05 5.2E-10 45.3 1.0 33 42-74 20-52 (54)
34 PHA00732 hypothetical protein 97.6 1.1E-05 2.3E-10 52.0 -0.5 38 46-86 1-39 (79)
35 smart00355 ZnF_C2H2 zinc finge 97.4 0.0001 2.2E-09 36.3 1.8 24 47-70 1-24 (26)
36 smart00355 ZnF_C2H2 zinc finge 97.3 0.00018 3.9E-09 35.4 1.7 23 10-32 1-23 (26)
37 PF09237 GAGA: GAGA factor; I 97.0 0.00076 1.6E-08 39.1 2.8 30 5-34 20-49 (54)
38 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00064 1.4E-08 33.3 1.8 23 10-33 1-23 (24)
39 PF12874 zf-met: Zinc-finger o 96.9 0.00043 9.2E-09 34.2 1.1 22 10-31 1-22 (25)
40 PF13909 zf-H2C2_5: C2H2-type 96.8 0.00039 8.5E-09 34.1 0.5 24 47-71 1-24 (24)
41 PF12874 zf-met: Zinc-finger o 96.8 0.00041 8.8E-09 34.3 0.3 23 47-69 1-23 (25)
42 KOG2893|consensus 96.8 0.00036 7.8E-09 53.5 0.2 51 7-71 9-60 (341)
43 COG5189 SFP1 Putative transcri 96.7 0.00072 1.6E-08 53.9 1.5 55 43-97 346-421 (423)
44 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.00093 2E-08 33.8 0.1 22 47-68 2-23 (27)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.2 0.00089 1.9E-08 33.8 -0.6 22 10-31 2-23 (27)
46 COG5048 FOG: Zn-finger [Genera 95.8 0.0018 3.9E-08 53.5 -0.9 62 8-78 288-355 (467)
47 PF13913 zf-C2HC_2: zinc-finge 95.7 0.008 1.7E-07 29.8 1.7 21 47-68 3-23 (25)
48 PF05605 zf-Di19: Drought indu 95.1 0.0043 9.4E-08 36.8 -0.5 39 46-85 2-42 (54)
49 smart00451 ZnF_U1 U1-like zinc 95.1 0.014 3E-07 31.0 1.5 23 9-31 3-25 (35)
50 PRK04860 hypothetical protein; 95.0 0.0038 8.2E-08 45.6 -1.2 38 45-86 118-155 (160)
51 KOG1146|consensus 94.9 0.018 4E-07 53.8 2.6 66 3-68 459-540 (1406)
52 PF09986 DUF2225: Uncharacteri 94.8 0.0075 1.6E-07 46.3 -0.0 53 7-59 3-61 (214)
53 PF06524 NOA36: NOA36 protein; 94.8 0.015 3.3E-07 45.3 1.5 26 5-31 138-163 (314)
54 PF13913 zf-C2HC_2: zinc-finge 94.7 0.02 4.4E-07 28.3 1.4 21 10-31 3-23 (25)
55 smart00451 ZnF_U1 U1-like zinc 94.7 0.019 4.2E-07 30.5 1.4 24 45-68 2-25 (35)
56 COG4049 Uncharacterized protei 94.3 0.028 6E-07 33.3 1.5 29 5-33 13-41 (65)
57 KOG2186|consensus 94.0 0.034 7.5E-07 43.1 2.0 50 9-70 3-52 (276)
58 PF06524 NOA36: NOA36 protein; 94.0 0.031 6.7E-07 43.6 1.6 29 42-70 205-233 (314)
59 PF12756 zf-C2H2_2: C2H2 type 93.8 0.048 1E-06 35.8 2.1 25 9-33 50-74 (100)
60 cd00350 rubredoxin_like Rubred 92.7 0.074 1.6E-06 28.1 1.4 24 10-54 2-25 (33)
61 PF09538 FYDLN_acid: Protein o 92.2 0.087 1.9E-06 35.9 1.6 30 10-59 10-39 (108)
62 COG4049 Uncharacterized protei 92.2 0.046 9.9E-07 32.4 0.2 30 42-71 13-42 (65)
63 PF15269 zf-C2H2_7: Zinc-finge 92.1 0.17 3.6E-06 28.6 2.4 34 35-68 8-42 (54)
64 PF12013 DUF3505: Protein of u 92.0 0.34 7.5E-06 32.9 4.4 63 8-71 10-109 (109)
65 PRK04860 hypothetical protein; 91.1 0.12 2.6E-06 37.8 1.4 31 21-60 127-157 (160)
66 cd00729 rubredoxin_SM Rubredox 90.4 0.19 4E-06 26.8 1.4 25 9-54 2-26 (34)
67 KOG4124|consensus 89.4 0.099 2.1E-06 42.5 -0.2 61 7-67 347-419 (442)
68 PF04959 ARS2: Arsenite-resist 89.1 0.23 5.1E-06 38.0 1.6 29 45-73 76-104 (214)
69 TIGR02300 FYDLN_acid conserved 89.0 0.26 5.6E-06 34.4 1.6 35 9-63 9-43 (129)
70 KOG2071|consensus 88.9 0.27 5.9E-06 42.7 2.1 27 7-33 416-442 (579)
71 PF02892 zf-BED: BED zinc fing 88.8 0.33 7.2E-06 27.2 1.8 24 7-30 14-41 (45)
72 KOG2785|consensus 88.8 0.24 5.1E-06 40.8 1.5 61 9-69 3-91 (390)
73 TIGR02098 MJ0042_CXXC MJ0042 f 87.6 0.26 5.5E-06 26.7 0.8 34 10-57 3-36 (38)
74 KOG4173|consensus 87.6 0.44 9.6E-06 36.1 2.2 68 8-87 78-159 (253)
75 PRK00464 nrdR transcriptional 87.4 0.079 1.7E-06 38.5 -1.8 19 45-63 27-45 (154)
76 PF05443 ROS_MUCR: ROS/MUCR tr 87.3 0.34 7.4E-06 34.2 1.4 22 10-34 73-94 (132)
77 KOG4173|consensus 86.6 0.094 2E-06 39.6 -1.8 58 11-68 108-168 (253)
78 KOG2785|consensus 86.2 0.49 1.1E-05 39.0 2.0 62 8-69 165-243 (390)
79 PF05443 ROS_MUCR: ROS/MUCR tr 85.9 0.45 9.7E-06 33.7 1.4 27 46-75 72-98 (132)
80 PF13717 zinc_ribbon_4: zinc-r 85.7 0.41 8.9E-06 25.8 0.9 34 10-57 3-36 (36)
81 smart00614 ZnF_BED BED zinc fi 85.6 0.6 1.3E-05 27.0 1.7 22 46-67 18-44 (50)
82 COG2888 Predicted Zn-ribbon RN 85.4 0.59 1.3E-05 28.1 1.5 32 9-54 27-58 (61)
83 smart00531 TFIIE Transcription 85.3 0.59 1.3E-05 33.6 1.8 38 7-57 97-134 (147)
84 PRK14890 putative Zn-ribbon RN 85.3 0.58 1.3E-05 28.1 1.5 31 9-54 25-56 (59)
85 PF04959 ARS2: Arsenite-resist 85.1 0.21 4.5E-06 38.3 -0.6 29 5-33 73-101 (214)
86 KOG2231|consensus 84.8 0.69 1.5E-05 41.1 2.3 21 48-68 184-204 (669)
87 COG1997 RPL43A Ribosomal prote 84.4 0.41 8.9E-06 31.1 0.6 35 8-61 34-68 (89)
88 PF09538 FYDLN_acid: Protein o 84.3 0.51 1.1E-05 32.2 1.1 31 46-87 9-39 (108)
89 PF13719 zinc_ribbon_5: zinc-r 84.1 0.52 1.1E-05 25.5 0.9 34 10-57 3-36 (37)
90 PHA00626 hypothetical protein 84.0 0.29 6.3E-06 29.0 -0.2 16 44-59 21-36 (59)
91 COG5048 FOG: Zn-finger [Genera 83.5 0.69 1.5E-05 38.0 1.8 60 7-75 31-92 (467)
92 PRK00398 rpoP DNA-directed RNA 82.4 0.76 1.6E-05 26.0 1.1 31 8-57 2-32 (46)
93 PRK06266 transcription initiat 79.4 1.1 2.3E-05 33.4 1.4 35 7-59 115-149 (178)
94 PF14353 CpXC: CpXC protein 78.5 0.67 1.4E-05 32.4 0.0 47 11-67 3-59 (128)
95 KOG1146|consensus 78.4 1.1 2.4E-05 42.6 1.4 63 7-71 1282-1353(1406)
96 smart00734 ZnF_Rad18 Rad18-lik 78.1 1.8 4E-05 21.4 1.6 19 48-67 3-21 (26)
97 COG5236 Uncharacterized conser 77.9 1.6 3.5E-05 35.7 2.0 47 11-67 222-272 (493)
98 PRK09678 DNA-binding transcrip 77.8 0.57 1.2E-05 29.5 -0.4 41 10-61 2-44 (72)
99 KOG2231|consensus 77.4 1.3 2.9E-05 39.4 1.5 51 11-74 184-240 (669)
100 PF09723 Zn-ribbon_8: Zinc rib 77.4 0.54 1.2E-05 26.2 -0.6 29 10-54 6-34 (42)
101 TIGR00373 conserved hypothetic 76.9 1.2 2.6E-05 32.4 1.0 20 6-25 106-125 (158)
102 COG4957 Predicted transcriptio 76.7 1.2 2.7E-05 31.3 0.9 22 10-34 77-98 (148)
103 TIGR02605 CxxC_CxxC_SSSS putat 75.9 0.72 1.6E-05 26.7 -0.3 29 10-54 6-34 (52)
104 KOG4167|consensus 74.8 1.1 2.4E-05 40.1 0.4 26 8-33 791-816 (907)
105 KOG3214|consensus 74.7 3.4 7.3E-05 27.6 2.5 17 45-61 46-62 (109)
106 COG4957 Predicted transcriptio 73.4 1.8 3.8E-05 30.6 1.0 25 47-74 77-101 (148)
107 KOG4167|consensus 71.1 0.85 1.8E-05 40.8 -1.2 29 45-73 791-819 (907)
108 COG1996 RPC10 DNA-directed RNA 70.9 2 4.3E-05 24.9 0.7 29 8-55 5-33 (49)
109 COG4530 Uncharacterized protei 69.6 2.3 5E-05 28.9 0.9 32 11-63 11-42 (129)
110 COG1571 Predicted DNA-binding 69.4 2.8 6E-05 35.4 1.5 32 11-62 352-383 (421)
111 KOG2593|consensus 68.2 2 4.4E-05 36.1 0.5 38 5-54 124-161 (436)
112 COG3677 Transposase and inacti 66.9 2.1 4.7E-05 30.1 0.3 19 43-61 50-68 (129)
113 COG3357 Predicted transcriptio 66.6 3.2 7E-05 27.2 1.1 14 45-58 57-70 (97)
114 PF10571 UPF0547: Uncharacteri 66.4 3.3 7.1E-05 20.6 0.8 10 48-57 16-25 (26)
115 KOG1280|consensus 65.8 5.1 0.00011 32.8 2.3 31 4-34 74-104 (381)
116 PTZ00255 60S ribosomal protein 65.1 2 4.2E-05 28.3 -0.1 17 44-60 52-68 (90)
117 PRK03824 hypA hydrogenase nick 63.3 2.3 5.1E-05 30.1 -0.0 16 7-22 68-83 (135)
118 KOG3408|consensus 63.3 3.8 8.3E-05 28.4 1.0 28 42-69 53-80 (129)
119 PF05191 ADK_lid: Adenylate ki 63.3 3.2 6.8E-05 22.3 0.5 33 10-59 2-34 (36)
120 KOG2482|consensus 63.0 7.7 0.00017 31.9 2.8 61 9-69 144-218 (423)
121 PF07754 DUF1610: Domain of un 62.7 5.1 0.00011 19.5 1.1 11 44-54 14-24 (24)
122 KOG2482|consensus 62.7 4.1 8.9E-05 33.4 1.2 62 9-70 195-303 (423)
123 COG2331 Uncharacterized protei 62.6 2.1 4.5E-05 27.1 -0.3 11 10-20 13-23 (82)
124 TIGR00280 L37a ribosomal prote 62.5 2 4.3E-05 28.3 -0.4 18 44-61 51-68 (91)
125 COG5188 PRP9 Splicing factor 3 62.5 6.3 0.00014 32.5 2.3 23 9-31 238-260 (470)
126 PRK12380 hydrogenase nickel in 61.7 4.5 9.8E-05 27.7 1.2 11 10-20 71-81 (113)
127 smart00659 RPOLCX RNA polymera 60.1 4.5 9.8E-05 22.8 0.8 26 10-55 3-28 (44)
128 KOG0696|consensus 59.3 5.1 0.00011 34.2 1.3 60 6-83 70-130 (683)
129 PF02176 zf-TRAF: TRAF-type zi 59.2 4.5 9.8E-05 23.8 0.7 41 8-58 8-54 (60)
130 COG1655 Uncharacterized protei 58.0 1.8 3.8E-05 33.5 -1.5 26 7-32 17-42 (267)
131 COG1779 C4-type Zn-finger prot 57.9 1.7 3.7E-05 32.7 -1.5 42 10-62 15-59 (201)
132 smart00154 ZnF_AN1 AN1-like Zi 57.7 4.6 9.9E-05 22.1 0.5 14 9-22 12-25 (39)
133 TIGR00100 hypA hydrogenase nic 57.1 6.1 0.00013 27.1 1.2 12 47-58 71-82 (115)
134 PRK03976 rpl37ae 50S ribosomal 56.3 2.7 5.9E-05 27.6 -0.6 15 45-59 53-67 (90)
135 PF10276 zf-CHCC: Zinc-finger 55.8 4 8.7E-05 22.5 0.1 11 9-19 29-39 (40)
136 PF12907 zf-met2: Zinc-binding 54.3 6 0.00013 21.9 0.6 24 10-33 2-28 (40)
137 PF10537 WAC_Acf1_DNA_bd: ATP- 53.9 14 0.00031 24.8 2.6 38 7-54 1-38 (102)
138 KOG3408|consensus 53.4 10 0.00022 26.4 1.7 24 8-31 56-79 (129)
139 PRK00564 hypA hydrogenase nick 53.4 7.5 0.00016 26.8 1.2 10 10-19 72-81 (117)
140 COG5236 Uncharacterized conser 53.3 12 0.00026 30.9 2.4 61 10-70 152-244 (493)
141 COG1198 PriA Primosomal protei 52.8 3.9 8.5E-05 37.1 -0.4 12 43-54 472-483 (730)
142 PF07282 OrfB_Zn_ribbon: Putat 52.4 7.1 0.00015 23.8 0.8 16 43-58 43-58 (69)
143 PF01155 HypA: Hydrogenase exp 52.2 7.2 0.00016 26.7 0.9 12 10-21 71-82 (113)
144 PF09986 DUF2225: Uncharacteri 52.1 6.2 0.00013 30.2 0.6 43 44-86 3-60 (214)
145 COG4888 Uncharacterized Zn rib 51.5 2.4 5.2E-05 28.3 -1.5 12 46-57 46-57 (104)
146 PRK01343 zinc-binding protein; 51.2 17 0.00037 21.7 2.3 26 45-82 8-33 (57)
147 KOG1832|consensus 50.9 9.4 0.0002 35.6 1.6 11 52-62 1305-1315(1516)
148 smart00834 CxxC_CXXC_SSSS Puta 50.7 6.1 0.00013 21.3 0.3 15 46-60 5-19 (41)
149 PF01428 zf-AN1: AN1-like Zinc 50.0 5.6 0.00012 22.1 0.1 15 8-22 12-26 (43)
150 KOG2071|consensus 49.4 11 0.00024 33.1 1.8 30 43-72 415-444 (579)
151 KOG0978|consensus 49.0 4.9 0.00011 36.1 -0.4 54 9-65 643-697 (698)
152 PRK14873 primosome assembly pr 48.7 12 0.00027 33.7 2.0 10 45-54 421-430 (665)
153 KOG4124|consensus 48.3 8.7 0.00019 31.6 0.9 62 6-72 175-239 (442)
154 smart00440 ZnF_C2C2 C2C2 Zinc 48.3 1.6 3.5E-05 24.0 -2.3 13 45-57 27-39 (40)
155 PRK03681 hypA hydrogenase nick 48.2 9.9 0.00021 26.1 1.1 10 10-19 71-80 (114)
156 PF01363 FYVE: FYVE zinc finge 47.6 7.6 0.00016 23.7 0.4 11 10-20 10-20 (69)
157 KOG2893|consensus 47.4 7.8 0.00017 30.2 0.5 36 44-84 9-44 (341)
158 TIGR00595 priA primosomal prot 47.1 12 0.00027 32.4 1.8 11 44-54 251-261 (505)
159 PF04780 DUF629: Protein of un 46.9 13 0.00027 32.0 1.7 27 8-34 56-82 (466)
160 PF08790 zf-LYAR: LYAR-type C2 46.5 2.7 5.8E-05 21.3 -1.4 9 48-56 2-10 (28)
161 PF03604 DNA_RNApol_7kD: DNA d 46.1 11 0.00023 19.7 0.8 12 45-56 16-27 (32)
162 TIGR00416 sms DNA repair prote 45.2 11 0.00024 32.3 1.2 12 8-19 6-17 (454)
163 COG1773 Rubredoxin [Energy pro 45.1 8.1 0.00018 22.9 0.2 19 8-26 2-20 (55)
164 PF04423 Rad50_zn_hook: Rad50 45.0 7 0.00015 22.8 -0.1 12 48-59 22-33 (54)
165 PRK11823 DNA repair protein Ra 43.8 14 0.0003 31.6 1.6 25 7-54 5-29 (446)
166 PF14311 DUF4379: Domain of un 43.7 15 0.00033 21.4 1.3 12 47-58 29-40 (55)
167 KOG0717|consensus 43.1 13 0.00028 31.8 1.3 22 10-31 293-314 (508)
168 PF04780 DUF629: Protein of un 43.0 15 0.00032 31.7 1.5 29 43-71 54-83 (466)
169 PF07503 zf-HYPF: HypF finger; 42.4 10 0.00022 20.2 0.4 31 12-57 2-32 (35)
170 cd00065 FYVE FYVE domain; Zinc 42.0 17 0.00037 21.1 1.3 11 11-21 4-14 (57)
171 PF14446 Prok-RING_1: Prokaryo 41.6 13 0.00029 21.9 0.8 11 10-20 6-16 (54)
172 PF09845 DUF2072: Zn-ribbon co 41.0 15 0.00032 25.9 1.0 15 46-60 1-15 (131)
173 PRK00762 hypA hydrogenase nick 40.8 13 0.00028 25.9 0.8 11 10-21 71-81 (124)
174 smart00661 RPOL9 RNA polymeras 40.0 16 0.00034 20.8 1.0 14 45-58 19-32 (52)
175 COG4391 Uncharacterized protei 39.6 10 0.00023 22.9 0.1 12 9-20 48-59 (62)
176 PF13878 zf-C2H2_3: zinc-finge 39.3 24 0.00053 19.4 1.6 23 10-32 14-38 (41)
177 KOG1832|consensus 38.0 18 0.00038 33.9 1.3 10 15-24 1305-1314(1516)
178 KOG0717|consensus 37.8 16 0.00034 31.4 0.9 22 47-68 293-314 (508)
179 KOG2636|consensus 37.6 19 0.00041 30.7 1.4 23 44-66 399-422 (497)
180 PRK14892 putative transcriptio 37.2 7.9 0.00017 25.9 -0.7 13 46-58 42-54 (99)
181 smart00064 FYVE Protein presen 36.4 20 0.00043 21.7 1.0 12 10-21 11-22 (68)
182 PF11931 DUF3449: Domain of un 36.4 12 0.00025 28.4 0.0 24 44-67 99-123 (196)
183 PF06220 zf-U1: U1 zinc finger 35.9 24 0.00053 19.1 1.2 14 45-58 2-15 (38)
184 PF09963 DUF2197: Uncharacteri 35.8 9.7 0.00021 22.7 -0.4 11 11-21 4-14 (56)
185 KOG2186|consensus 35.7 7.4 0.00016 30.5 -1.2 39 46-86 3-41 (276)
186 KOG2636|consensus 35.7 23 0.0005 30.2 1.6 26 3-28 395-421 (497)
187 PF10013 DUF2256: Uncharacteri 35.4 18 0.00038 20.2 0.6 17 47-63 9-25 (42)
188 PLN02294 cytochrome c oxidase 35.2 16 0.00035 26.9 0.6 16 43-58 138-153 (174)
189 cd01121 Sms Sms (bacterial rad 35.2 18 0.00039 30.2 0.9 8 10-17 1-8 (372)
190 PRK05580 primosome assembly pr 35.2 26 0.00056 31.7 1.9 12 44-55 419-430 (679)
191 PF02748 PyrI_C: Aspartate car 34.7 16 0.00034 21.4 0.4 17 6-22 32-48 (52)
192 PF04606 Ogr_Delta: Ogr/Delta- 34.0 5.3 0.00011 22.7 -1.7 37 11-58 1-39 (47)
193 COG1656 Uncharacterized conser 33.7 33 0.00071 25.2 1.9 21 44-64 128-148 (165)
194 cd00924 Cyt_c_Oxidase_Vb Cytoc 32.9 18 0.00039 24.1 0.4 15 44-58 77-91 (97)
195 PF12760 Zn_Tnp_IS1595: Transp 32.7 8.8 0.00019 21.6 -0.9 10 45-54 36-45 (46)
196 COG3364 Zn-ribbon containing p 32.4 28 0.00061 23.4 1.3 16 46-61 2-17 (112)
197 PF11672 DUF3268: Protein of u 32.0 13 0.00027 25.1 -0.4 13 8-20 1-13 (102)
198 COG0068 HypF Hydrogenase matur 31.9 21 0.00045 32.3 0.8 10 45-54 172-181 (750)
199 PF03811 Zn_Tnp_IS1: InsA N-te 31.6 8.4 0.00018 20.7 -1.1 11 42-52 25-35 (36)
200 CHL00174 accD acetyl-CoA carbo 31.5 17 0.00036 29.4 0.1 14 45-58 56-69 (296)
201 PTZ00448 hypothetical protein; 31.5 31 0.00067 28.7 1.7 23 46-68 314-336 (373)
202 PF13451 zf-trcl: Probable zin 31.1 19 0.00042 20.8 0.3 14 8-21 3-16 (49)
203 PLN02748 tRNA dimethylallyltra 31.0 30 0.00066 29.8 1.6 26 44-69 416-442 (468)
204 PTZ00303 phosphatidylinositol 30.7 15 0.00033 33.7 -0.3 13 10-22 461-473 (1374)
205 PF12230 PRP21_like_P: Pre-mRN 30.6 17 0.00036 28.0 0.0 34 44-78 166-199 (229)
206 PRK06260 threonine synthase; V 30.5 28 0.00062 29.1 1.4 11 10-20 4-14 (397)
207 COG5112 UFD2 U1-like Zn-finger 30.3 23 0.00051 24.0 0.7 30 39-68 48-77 (126)
208 PHA02998 RNA polymerase subuni 30.1 8.2 0.00018 28.7 -1.7 42 9-59 143-184 (195)
209 PF06397 Desulfoferrod_N: Desu 29.8 22 0.00047 19.1 0.4 12 8-19 5-16 (36)
210 PF14447 Prok-RING_4: Prokaryo 29.2 30 0.00064 20.5 0.9 17 43-59 36-52 (55)
211 KOG2907|consensus 29.1 20 0.00043 24.6 0.2 14 45-58 101-114 (116)
212 PF11789 zf-Nse: Zinc-finger o 28.9 31 0.00066 20.5 0.9 17 7-23 22-38 (57)
213 COG1592 Rubrerythrin [Energy p 28.7 32 0.0007 25.3 1.2 13 41-53 144-156 (166)
214 TIGR00622 ssl1 transcription f 28.4 49 0.0011 22.7 2.0 49 11-70 57-105 (112)
215 PF14787 zf-CCHC_5: GAG-polypr 28.4 32 0.0007 18.5 0.9 15 48-62 4-18 (36)
216 PRK05978 hypothetical protein; 28.4 16 0.00034 26.4 -0.5 12 48-59 54-65 (148)
217 TIGR00515 accD acetyl-CoA carb 28.3 34 0.00074 27.5 1.4 13 46-58 45-57 (285)
218 PTZ00448 hypothetical protein; 28.2 34 0.00075 28.5 1.4 24 9-32 314-337 (373)
219 COG4306 Uncharacterized protei 28.1 17 0.00037 25.4 -0.3 16 44-59 66-81 (160)
220 PLN03238 probable histone acet 28.1 42 0.00092 27.0 1.9 26 7-32 46-71 (290)
221 PF07975 C1_4: TFIIH C1-like d 28.0 11 0.00024 22.0 -1.0 25 45-69 20-44 (51)
222 KOG0782|consensus 27.7 23 0.00049 31.4 0.3 13 48-60 255-267 (1004)
223 COG3464 Transposase and inacti 27.5 16 0.00035 30.8 -0.6 53 10-63 39-94 (402)
224 COG5151 SSL1 RNA polymerase II 26.7 57 0.0012 26.6 2.3 20 9-28 322-341 (421)
225 PF04641 Rtf2: Rtf2 RING-finge 26.4 5.2 0.00011 31.5 -3.5 17 6-22 110-126 (260)
226 KOG4602|consensus 26.3 20 0.00043 28.3 -0.3 48 8-57 232-279 (318)
227 PRK00420 hypothetical protein; 25.7 39 0.00084 23.2 1.1 16 45-60 39-54 (112)
228 cd00730 rubredoxin Rubredoxin; 25.7 23 0.0005 20.5 0.0 14 9-22 1-14 (50)
229 COG0675 Transposase and inacti 25.4 27 0.00059 27.8 0.4 18 45-62 321-338 (364)
230 PF00301 Rubredoxin: Rubredoxi 25.1 23 0.00051 20.2 -0.0 16 9-24 1-16 (47)
231 PF01780 Ribosomal_L37ae: Ribo 25.1 40 0.00087 22.2 1.1 14 45-58 52-65 (90)
232 PTZ00043 cytochrome c oxidase 25.0 30 0.00066 26.8 0.5 15 7-21 179-193 (268)
233 PTZ00064 histone acetyltransfe 24.9 65 0.0014 28.1 2.5 26 7-32 278-303 (552)
234 KOG4727|consensus 24.6 35 0.00077 25.2 0.8 22 10-31 76-97 (193)
235 COG4896 Uncharacterized protei 24.5 28 0.0006 21.1 0.2 14 44-57 29-42 (68)
236 TIGR01206 lysW lysine biosynth 24.2 33 0.00071 20.2 0.5 30 46-83 2-31 (54)
237 PLN00104 MYST -like histone ac 24.2 51 0.0011 28.3 1.7 40 7-50 196-235 (450)
238 PRK05654 acetyl-CoA carboxylas 24.2 57 0.0012 26.3 2.0 12 46-57 46-57 (292)
239 PLN03239 histone acetyltransfe 24.0 54 0.0012 27.2 1.8 25 7-31 104-128 (351)
240 COG1594 RPB9 DNA-directed RNA 24.0 15 0.00032 25.2 -1.2 14 45-58 99-112 (113)
241 COG4338 Uncharacterized protei 23.4 26 0.00055 20.2 -0.1 17 47-63 13-29 (54)
242 COG5188 PRP9 Splicing factor 3 23.2 47 0.001 27.6 1.3 23 44-66 372-395 (470)
243 PF09332 Mcm10: Mcm10 replicat 22.4 10 0.00022 31.3 -2.6 44 8-58 251-297 (344)
244 PLN03238 probable histone acet 22.0 71 0.0015 25.7 2.1 25 44-68 46-70 (290)
245 KOG0943|consensus 22.0 62 0.0013 31.8 2.0 37 94-130 1731-1767(3015)
246 KOG2593|consensus 22.0 56 0.0012 27.8 1.6 21 43-63 125-145 (436)
247 KOG1280|consensus 21.9 45 0.00098 27.5 1.0 38 44-81 77-116 (381)
248 KOG4118|consensus 21.5 52 0.0011 20.2 1.0 31 45-75 37-67 (74)
249 TIGR00244 transcriptional regu 21.4 41 0.00089 24.2 0.6 19 45-63 27-45 (147)
250 PF08209 Sgf11: Sgf11 (transcr 21.3 45 0.00097 17.5 0.6 23 45-68 3-25 (33)
251 KOG2807|consensus 21.1 1.1E+02 0.0025 25.1 3.1 60 8-69 289-368 (378)
252 PF04810 zf-Sec23_Sec24: Sec23 21.0 46 0.001 18.0 0.6 10 45-54 23-32 (40)
253 TIGR00319 desulf_FeS4 desulfof 20.9 39 0.00085 17.5 0.3 13 8-20 6-18 (34)
254 PF15135 UPF0515: Uncharacteri 20.9 31 0.00067 27.1 -0.1 54 6-59 109-168 (278)
255 cd00974 DSRD Desulforedoxin (D 20.9 41 0.00088 17.4 0.4 13 8-20 3-15 (34)
256 COG1326 Uncharacterized archae 20.6 83 0.0018 23.8 2.1 14 44-57 28-41 (201)
257 PRK06450 threonine synthase; V 20.6 54 0.0012 26.9 1.2 10 10-19 4-13 (338)
258 PF01096 TFIIS_C: Transcriptio 20.6 34 0.00073 18.5 0.0 11 10-20 29-39 (39)
259 PRK12722 transcriptional activ 20.6 42 0.00091 25.2 0.5 9 45-53 153-161 (187)
260 COG1675 TFA1 Transcription ini 20.1 71 0.0015 23.8 1.7 14 7-20 111-124 (176)
261 KOG1842|consensus 20.1 50 0.0011 28.3 0.9 28 45-72 14-42 (505)
262 cd01410 SIRT7 SIRT7: Eukaryoti 20.1 94 0.002 23.5 2.4 18 4-21 90-107 (206)
263 KOG1842|consensus 20.1 61 0.0013 27.8 1.4 27 8-34 14-40 (505)
264 PF05180 zf-DNL: DNL zinc fing 20.0 7.6 0.00017 24.0 -2.9 41 9-61 4-44 (66)
No 1
>KOG2462|consensus
Probab=99.82 E-value=2.1e-21 Score=148.94 Aligned_cols=82 Identities=26% Similarity=0.440 Sum_probs=75.1
Q ss_pred cccCCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHH
Q psy9958 2 LIHIDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVA 81 (181)
Q Consensus 2 ~~Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~ 81 (181)
|+|+ -|++|.+|||.|.+.+.|+.|+|+| +|+|||.|+.|+|+|.-++||+.||++|.+.++|.|..|+
T Consensus 182 rTH~--l~c~C~iCGKaFSRPWLLQGHiRTH---------TGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~ 250 (279)
T KOG2462|consen 182 RTHT--LPCECGICGKAFSRPWLLQGHIRTH---------TGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCG 250 (279)
T ss_pred hccC--CCcccccccccccchHHhhcccccc---------cCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchh
Confidence 5666 7899999999999999999999998 8999999999999999999999999999999999999999
Q ss_pred Hhhhcccceeeec
Q psy9958 82 LKLGRQKKVHIID 94 (181)
Q Consensus 82 ~~~~~~~~~~~~~ 94 (181)
+.|.+..-+..|.
T Consensus 251 KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 251 KSFALKSYLNKHS 263 (279)
T ss_pred hHHHHHHHHHHhh
Confidence 9998886555544
No 2
>KOG2462|consensus
Probab=99.68 E-value=8.6e-18 Score=129.18 Aligned_cols=59 Identities=31% Similarity=0.699 Sum_probs=56.1
Q ss_pred CcccCCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHh
Q psy9958 1 MLIHIDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 1 ~~~Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
+|+|||||||.|..|+|.|..+++|+.||++| ++.|+|+|..|+|+|..++.|.+|...
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTH---------S~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTH---------SDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhh---------cCCccccCcchhhHHHHHHHHHHhhhh
Confidence 68999999999999999999999999999999 788999999999999999999999753
No 3
>KOG3623|consensus
Probab=99.54 E-value=2.1e-15 Score=128.48 Aligned_cols=91 Identities=24% Similarity=0.443 Sum_probs=82.0
Q ss_pred CCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhh
Q psy9958 5 IDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKL 84 (181)
Q Consensus 5 t~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 84 (181)
+...+|.|+.|+|.|...+.|.+|.--| +|.+||+|.+|.|.|+++-.|..|+|+|.|++||.|..|+++|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEH---------sGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRF 960 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEH---------SGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRF 960 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhh---------cCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhc
Confidence 3456899999999999999999998777 8999999999999999999999999999999999999999999
Q ss_pred hcccceeeecCcccccCCCC
Q psy9958 85 GRQKKVHIIDGHKVEVIPDD 104 (181)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~ 104 (181)
...-....|..|....-...
T Consensus 961 SHSGSYSQHMNHRYSYCKpy 980 (1007)
T KOG3623|consen 961 SHSGSYSQHMNHRYSYCKPY 980 (1007)
T ss_pred ccccchHhhhccchhcccch
Confidence 98888777888877665443
No 4
>KOG3623|consensus
Probab=99.39 E-value=1.1e-13 Score=118.20 Aligned_cols=55 Identities=38% Similarity=0.771 Sum_probs=54.0
Q ss_pred cCCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHH
Q psy9958 4 HIDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMT 67 (181)
Q Consensus 4 Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~ 67 (181)
|+|+|||+|.+|.|.|+.+-+|..|+|.| +|+|||.|..|+|+|.+.+.+.+||.
T Consensus 917 HsGqRPyqC~iCkKAFKHKHHLtEHkRLH---------SGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 917 HSGQRPYQCIICKKAFKHKHHLTEHKRLH---------SGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred hcCCCCcccchhhHhhhhhhhhhhhhhhc---------cCCCcchhhhhhhhcccccchHhhhc
Confidence 99999999999999999999999999998 89999999999999999999999996
No 5
>KOG3576|consensus
Probab=99.35 E-value=2e-13 Score=100.92 Aligned_cols=74 Identities=24% Similarity=0.437 Sum_probs=66.7
Q ss_pred CCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhhh
Q psy9958 6 DQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLG 85 (181)
Q Consensus 6 ~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~~ 85 (181)
+...|.|.+|+|.|.-..-|.+|++-| ...++|.|..|||.|.-.-+|++|+|+|+|-+||.|..|.+.|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch---------~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCH---------SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFT 184 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhc---------cHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHH
Confidence 456799999999999999999999987 56789999999999999999999999999999999999999987
Q ss_pred ccc
Q psy9958 86 RQK 88 (181)
Q Consensus 86 ~~~ 88 (181)
.+-
T Consensus 185 qrc 187 (267)
T KOG3576|consen 185 QRC 187 (267)
T ss_pred hhc
Confidence 653
No 6
>KOG3576|consensus
Probab=99.29 E-value=1.2e-13 Score=102.03 Aligned_cols=75 Identities=24% Similarity=0.398 Sum_probs=62.9
Q ss_pred CcccCCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCC---------
Q psy9958 1 MLIHIDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDP--------- 71 (181)
Q Consensus 1 ~~~Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~--------- 71 (181)
|+-|+..|.|.|..|||.|.....|++|+|+| +|.+||+|..|+|+|.++-.|..|.+.-++
T Consensus 137 ~kch~~vkr~lct~cgkgfndtfdlkrh~rth---------tgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yayke 207 (267)
T KOG3576|consen 137 LKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTH---------TGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKE 207 (267)
T ss_pred hhhccHHHHHHHhhccCcccchhhhhhhhccc---------cCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHH
Confidence 45688899999999999999999999999998 789999999999999999999999765433
Q ss_pred --CChhHHHHHHHhh
Q psy9958 72 --DSELIEQQVALKL 84 (181)
Q Consensus 72 --~~~~~~~~~~~~~ 84 (181)
.+.|.|..|+...
T Consensus 208 rr~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 208 RRAKLYVCEDCGYTS 222 (267)
T ss_pred hhhheeeecccCCCC
Confidence 3445677776543
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.18 E-value=9.1e-12 Score=73.76 Aligned_cols=44 Identities=18% Similarity=0.446 Sum_probs=39.8
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHH
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLL 63 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~ 63 (181)
-|.|+.||+.|.+.++|.+|+++| + ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H---------~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH---------N--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc---------C--CcccCCcccceecccceeE
Confidence 389999999999999999999998 3 7999999999999888775
No 8
>KOG1074|consensus
Probab=99.18 E-value=7.2e-12 Score=108.63 Aligned_cols=64 Identities=30% Similarity=0.656 Sum_probs=32.8
Q ss_pred cccCCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCC---cccccCCCchhHHHHHHhcC
Q psy9958 2 LIHIDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCP---ECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 2 ~~Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~---~C~k~F~~~~~l~~H~~~h~ 70 (181)
|+|||||||+|++||+.|.++.+|+.||..|... + .-...|.|+ +|-+.|...-.|..|+++|.
T Consensus 626 rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~----p-~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 626 RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK----P-PARVQFSCPSTFICQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred hcccCcCccccccccchhccccchhhcccccccC----c-cccccccCCchhhhcccccccccccceEEeec
Confidence 4555555555555555555555555555554321 0 111345555 55555555555555555554
No 9
>KOG1074|consensus
Probab=99.12 E-value=1.4e-11 Score=106.85 Aligned_cols=79 Identities=27% Similarity=0.436 Sum_probs=65.6
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCCCChh----HHH---HH
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSEL----IEQ---QV 80 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~----~~~---~~ 80 (181)
-|-.|-+|-+....++.|+.|.|+| +|++||+|.+||+.|.++.||+.||.+|....++ .|. .|
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtH---------tGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic 674 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTH---------TGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFIC 674 (958)
T ss_pred Cccceeeeeecccchhhhhhhhhcc---------cCcCccccccccchhccccchhhcccccccCccccccccCCchhhh
Confidence 3678999999999999999999998 8999999999999999999999999998766543 566 67
Q ss_pred HHhhhcc----cceeeecC
Q psy9958 81 ALKLGRQ----KKVHIIDG 95 (181)
Q Consensus 81 ~~~~~~~----~~~~~~~~ 95 (181)
..+|... .++++|.+
T Consensus 675 ~~kftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 675 QKKFTNAVTLPQHIRIHLG 693 (958)
T ss_pred cccccccccccceEEeecC
Confidence 7766443 45666553
No 10
>PHA00733 hypothetical protein
Probab=99.05 E-value=1.9e-10 Score=81.00 Aligned_cols=53 Identities=32% Similarity=0.689 Sum_probs=27.1
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcC
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
.+||.|+.|++.|.....|..|++.+ ..+|.|..|++.|.....|..|++.++
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h-----------~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYT-----------EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcC-----------CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 45555555555555555555555432 134555555555555555555554433
No 11
>PHA00732 hypothetical protein
Probab=98.78 E-value=3.2e-09 Score=68.41 Aligned_cols=48 Identities=31% Similarity=0.544 Sum_probs=40.6
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcC
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
||.|..|++.|.+...|+.|++.+| .++.|+.|+++|. .|..|.+++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H-----------~~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH-----------TLTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc-----------CCCccCCCCCEeC---ChhhhhcccC
Confidence 7899999999999999999998543 2468999999998 5888986553
No 12
>KOG3608|consensus
Probab=98.76 E-value=1.9e-09 Score=85.99 Aligned_cols=72 Identities=28% Similarity=0.504 Sum_probs=39.5
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCC------------------CCCCCCCCCCcccCCcccccCCCchhHHHHHHh
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNP------------------HYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~------------------~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
..+|.|..|.|+|.+...|+.|++.|-+- +.+..|++.|||+|..|.++|.+.+.|.+|..+
T Consensus 235 ~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~ 314 (467)
T KOG3608|consen 235 TNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQV 314 (467)
T ss_pred CCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHh
Confidence 44555555555555555555555554210 111333556666666666666666666666665
Q ss_pred cCCCChhHHHH
Q psy9958 69 HDPDSELIEQQ 79 (181)
Q Consensus 69 h~~~~~~~~~~ 79 (181)
|. +..|.|..
T Consensus 315 HS-~~~y~C~h 324 (467)
T KOG3608|consen 315 HS-KTVYQCEH 324 (467)
T ss_pred cc-ccceecCC
Confidence 55 44555544
No 13
>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=98.73 E-value=5.2e-09 Score=53.08 Aligned_cols=26 Identities=42% Similarity=0.754 Sum_probs=22.7
Q ss_pred hHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCC
Q psy9958 24 LLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRH 58 (181)
Q Consensus 24 ~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~ 58 (181)
+|.+|+++| ++++||.|+.|+++|.+
T Consensus 1 ~l~~H~~~H---------~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTH---------TGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHH---------SSSSSEEESSSSEEESS
T ss_pred CHHHHhhhc---------CCCCCCCCCCCcCeeCc
Confidence 588999998 78999999999999864
No 14
>PHA00733 hypothetical protein
Probab=98.71 E-value=1.2e-09 Score=76.95 Aligned_cols=78 Identities=14% Similarity=0.164 Sum_probs=62.0
Q ss_pred CCceecccchhhccChhhHHHH--HHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhh
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRH--VNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKL 84 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H--~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 84 (181)
++++.|.+|.+.|.....|..| ++.+. +..+.+||.|..|++.|.+...|..|++.| ..++.|..|+..|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~------~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F 109 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLL------TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEF 109 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhc------ccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCcc
Confidence 6889999999999999888877 32221 114578999999999999999999999976 3468999999888
Q ss_pred hcccceee
Q psy9958 85 GRQKKVHI 92 (181)
Q Consensus 85 ~~~~~~~~ 92 (181)
.....+..
T Consensus 110 ~~~~sL~~ 117 (128)
T PHA00733 110 RNTDSTLD 117 (128)
T ss_pred CCHHHHHH
Confidence 76655433
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.66 E-value=5.6e-09 Score=61.89 Aligned_cols=43 Identities=16% Similarity=0.349 Sum_probs=36.5
Q ss_pred CcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhhhcccc
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLGRQKK 89 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~ 89 (181)
.-|.|+.||+.|.+.++|..|+++|+ +++.|..|++.|.+...
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGE 46 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccce
Confidence 35899999999999999999999999 67888888887765443
No 16
>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=98.62 E-value=5.2e-08 Score=58.31 Aligned_cols=53 Identities=25% Similarity=0.521 Sum_probs=42.6
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCC
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDP 71 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~ 71 (181)
.|.|++|++. .....|..|....|. ...+.+.|++|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~-------~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHR-------SESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCc-------CCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 5899999995 456789999988875 3456899999998765 499999987653
No 17
>KOG3608|consensus
Probab=98.57 E-value=1.3e-08 Score=81.35 Aligned_cols=77 Identities=19% Similarity=0.348 Sum_probs=65.5
Q ss_pred ccCCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCc--ccccCCCchhHHHHHHhcC-CC--ChhHH
Q psy9958 3 IHIDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPE--CKKAFRHKGNLLRHMTLHD-PD--SELIE 77 (181)
Q Consensus 3 ~Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~--C~k~F~~~~~l~~H~~~h~-~~--~~~~~ 77 (181)
.|+..|||+|+.|+++|.+.+.|.+|...| + +..|.|.. |..+|+....+.+|++.++ +. .+|.|
T Consensus 286 rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H---------S-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~C 355 (467)
T KOG3608|consen 286 RHSKDKPFKCDECDTRCVRESDLAKHVQVH---------S-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYAC 355 (467)
T ss_pred hhccCCCccccchhhhhccHHHHHHHHHhc---------c-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceee
Confidence 488999999999999999999999999987 3 67899988 9999999999999988765 44 45778
Q ss_pred HHHHHhhhcccc
Q psy9958 78 QQVALKLGRQKK 89 (181)
Q Consensus 78 ~~~~~~~~~~~~ 89 (181)
-.|..-|.+...
T Consensus 356 H~Cdr~ft~G~~ 367 (467)
T KOG3608|consen 356 HCCDRFFTSGKS 367 (467)
T ss_pred ecchhhhccchh
Confidence 888777765544
No 18
>PHA00616 hypothetical protein
Probab=98.56 E-value=3.5e-08 Score=55.77 Aligned_cols=34 Identities=26% Similarity=0.432 Sum_probs=27.3
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCc
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPE 51 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~ 51 (181)
||+|..||+.|..++.|.+|++.|| +++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h---------g~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH---------KQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc---------CCCccceeE
Confidence 6888888888888888888888884 567877764
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.51 E-value=1.5e-08 Score=51.39 Aligned_cols=21 Identities=33% Similarity=0.849 Sum_probs=19.2
Q ss_pred CcccCCCCceecccchhhccC
Q psy9958 1 MLIHIDQNPYLCDHCDQTFRQ 21 (181)
Q Consensus 1 ~~~Ht~ekp~~C~~C~k~f~~ 21 (181)
|++|+|+|||.|++|++.|.+
T Consensus 6 ~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 6 MRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHSSSSSEEESSSSEEESS
T ss_pred hhhcCCCCCCCCCCCcCeeCc
Confidence 578999999999999999974
No 20
>PHA00616 hypothetical protein
Probab=98.51 E-value=2.9e-08 Score=56.11 Aligned_cols=33 Identities=21% Similarity=0.462 Sum_probs=30.5
Q ss_pred cccCCcccccCCCchhHHHHHHhcCCCChhHHH
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTLHDPDSELIEQ 78 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~ 78 (181)
||+|+.||+.|..++.|.+|++.|++.+++.+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999999888653
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.51 E-value=3.8e-08 Score=84.27 Aligned_cols=67 Identities=19% Similarity=0.484 Sum_probs=55.7
Q ss_pred CCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhh
Q psy9958 5 IDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKL 84 (181)
Q Consensus 5 t~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 84 (181)
.-++.+.|+.|++.|. ...|..|++.+| ++|.|+ ||+.| .+..|..|+++|.+.+++.|..|.+.+
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~~~~H-----------kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHMKVFH-----------EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHHHhcC-----------CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 3467789999999996 678999999874 788999 99755 568999999999999999999888766
Q ss_pred h
Q psy9958 85 G 85 (181)
Q Consensus 85 ~ 85 (181)
.
T Consensus 515 ~ 515 (567)
T PLN03086 515 Q 515 (567)
T ss_pred c
Confidence 3
No 22
>KOG3993|consensus
Probab=98.41 E-value=8.9e-08 Score=78.10 Aligned_cols=63 Identities=27% Similarity=0.522 Sum_probs=43.6
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCC-----CCC-------------------CCCCcccCCcccccCCCchhHHHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYV-----PPS-------------------PKEKTHKCPECKKAFRHKGNLLRH 65 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~-----~~~-------------------~~~~~~~C~~C~k~F~~~~~l~~H 65 (181)
|+|+.|+|.|+...+|..|+|+|.-..-. ++. .....|.|..|+|.|.+...|+.|
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKH 375 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKH 375 (500)
T ss_pred ecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHh
Confidence 78888888888888888888876422110 000 112358888888888888888888
Q ss_pred HHhcCCC
Q psy9958 66 MTLHDPD 72 (181)
Q Consensus 66 ~~~h~~~ 72 (181)
+.+|+..
T Consensus 376 qlthq~~ 382 (500)
T KOG3993|consen 376 QLTHQRA 382 (500)
T ss_pred HHhhhcc
Confidence 7777644
No 23
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.35 E-value=1.8e-07 Score=73.82 Aligned_cols=62 Identities=27% Similarity=0.568 Sum_probs=49.1
Q ss_pred CCCceeccc--chhhccChhhHHHHHHHhcCCCCCCC----------CCCCCcccCCcccccCCCchhHHHHHH
Q psy9958 6 DQNPYLCDH--CDQTFRQKQLLKRHVNLYHNPHYVPP----------SPKEKTHKCPECKKAFRHKGNLLRHMT 67 (181)
Q Consensus 6 ~ekp~~C~~--C~k~f~~~~~L~~H~~~hh~~~~~~~----------~~~~~~~~C~~C~k~F~~~~~l~~H~~ 67 (181)
++|||+|++ |.|.|+....|+.|+..-|......+ ..+.|||.|.+|+|+|+.-..|+.|++
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 469999998 99999999999999875452211100 133599999999999999999999865
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.30 E-value=1.9e-07 Score=79.98 Aligned_cols=68 Identities=12% Similarity=0.210 Sum_probs=57.1
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCC----------chhHHHHHHhcCCCChhHH
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRH----------KGNLLRHMTLHDPDSELIE 77 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~----------~~~l~~H~~~h~~~~~~~~ 77 (181)
+|+.|+ |++.| .+..|..|+++| ...+++.|..|++.|.. .+.|..|...+ +.+++.|
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~th---------Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQAST---------CPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhcc---------CCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEc
Confidence 899999 99766 568999999887 57899999999999952 35899999885 9999999
Q ss_pred HHHHHhhhcc
Q psy9958 78 QQVALKLGRQ 87 (181)
Q Consensus 78 ~~~~~~~~~~ 87 (181)
..|++.+..+
T Consensus 545 ~~Cgk~Vrlr 554 (567)
T PLN03086 545 DSCGRSVMLK 554 (567)
T ss_pred cccCCeeeeh
Confidence 9998766544
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.17 E-value=1e-06 Score=43.10 Aligned_cols=22 Identities=41% Similarity=0.816 Sum_probs=13.7
Q ss_pred eecccchhhccChhhHHHHHHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
|+|+.|++.|.++..|..|++.
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 4566666666666666666654
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=98.11 E-value=8.5e-07 Score=43.39 Aligned_cols=23 Identities=57% Similarity=0.964 Sum_probs=21.5
Q ss_pred ccCCcccccCCCchhHHHHHHhc
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTLH 69 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~h 69 (181)
|.|+.|++.|.++..|..|++.|
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 68999999999999999999875
No 27
>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=98.00 E-value=4.1e-06 Score=40.98 Aligned_cols=23 Identities=30% Similarity=0.751 Sum_probs=12.9
Q ss_pred eecccchhhccChhhHHHHHHHh
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLY 32 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~h 32 (181)
|.|++|++.|.+...|..|++.+
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 45666666666666666666554
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.92 E-value=5.5e-06 Score=55.21 Aligned_cols=60 Identities=27% Similarity=0.512 Sum_probs=22.2
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCC-----------CCC---CCCCcccCCcccccCCCchhHHHHHHhcC
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYV-----------PPS---PKEKTHKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~-----------~~~---~~~~~~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
.|.+|+..|.....|..|+...|+.... ... .-...|.|..|++.|.....|..||+.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 4999999999999999999887754211 000 11236899999999999999999999754
No 29
>KOG3993|consensus
Probab=97.91 E-value=1.6e-06 Score=71.02 Aligned_cols=76 Identities=25% Similarity=0.460 Sum_probs=61.7
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcCCC-----------------
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPD----------------- 72 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~----------------- 72 (181)
|.|..|.-.|.....|..|.-.- ..-.-|+|+.|+|.|+...||..|.|+|...
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R---------IV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ 338 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR---------IVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVET 338 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe---------eEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhh
Confidence 89999999999999999995322 1235799999999999999999999998521
Q ss_pred ----------------ChhHHHHHHHhhhcccceeeec
Q psy9958 73 ----------------SELIEQQVALKLGRQKKVHIID 94 (181)
Q Consensus 73 ----------------~~~~~~~~~~~~~~~~~~~~~~ 94 (181)
..|.|..|+++|.++.-++.|.
T Consensus 339 rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 339 RAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred hhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhH
Confidence 1256999999999987766664
No 30
>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=97.90 E-value=5.1e-06 Score=40.63 Aligned_cols=24 Identities=46% Similarity=0.930 Sum_probs=20.3
Q ss_pred ccCCcccccCCCchhHHHHHHhcC
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
|.|++|++.|.+...|..|+++|+
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 689999999999999999998874
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.82 E-value=7.3e-06 Score=41.61 Aligned_cols=24 Identities=33% Similarity=0.742 Sum_probs=17.2
Q ss_pred ceecccchhhccChhhHHHHHHHh
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLY 32 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~h 32 (181)
||.|..|++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 567777777777777777777665
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.73 E-value=1.1e-05 Score=40.99 Aligned_cols=26 Identities=31% Similarity=0.540 Sum_probs=23.9
Q ss_pred cccCCcccccCCCchhHHHHHHhcCC
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTLHDP 71 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~h~~ 71 (181)
||.|..|++.|.....|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999998764
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.60 E-value=2.4e-05 Score=45.31 Aligned_cols=33 Identities=27% Similarity=0.566 Sum_probs=23.0
Q ss_pred CCCCcccCCcccccCCCchhHHHHHHhcCCCCh
Q psy9958 42 PKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSE 74 (181)
Q Consensus 42 ~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~ 74 (181)
..+.|..|++|+..+.+..+|++|+.++|+.++
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 346788999999999999999999988887765
No 34
>PHA00732 hypothetical protein
Probab=97.60 E-value=1.1e-05 Score=52.03 Aligned_cols=38 Identities=21% Similarity=0.158 Sum_probs=32.5
Q ss_pred cccCCcccccCCCchhHHHHHHh-cCCCChhHHHHHHHhhhc
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTL-HDPDSELIEQQVALKLGR 86 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~-h~~~~~~~~~~~~~~~~~ 86 (181)
||.|..|++.|.+..+|..|++. |.+ +.|..|+..|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~ 39 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR 39 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC
Confidence 68999999999999999999985 654 478899888863
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.41 E-value=0.0001 Score=36.33 Aligned_cols=24 Identities=46% Similarity=0.934 Sum_probs=17.2
Q ss_pred ccCCcccccCCCchhHHHHHHhcC
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 467777777777777777777553
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.27 E-value=0.00018 Score=35.43 Aligned_cols=23 Identities=35% Similarity=0.782 Sum_probs=21.4
Q ss_pred eecccchhhccChhhHHHHHHHh
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLY 32 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~h 32 (181)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 68999999999999999999865
No 37
>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=97.02 E-value=0.00076 Score=39.14 Aligned_cols=30 Identities=30% Similarity=0.624 Sum_probs=22.0
Q ss_pred CCCCceecccchhhccChhhHHHHHHHhcC
Q psy9958 5 IDQNPYLCDHCDQTFRQKQLLKRHVNLYHN 34 (181)
Q Consensus 5 t~ekp~~C~~C~k~f~~~~~L~~H~~~hh~ 34 (181)
..+.|..|++|+..+.+..+|++|+..+|.
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 456899999999999999999999988764
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.93 E-value=0.00064 Score=33.29 Aligned_cols=23 Identities=43% Similarity=0.788 Sum_probs=13.1
Q ss_pred eecccchhhccChhhHHHHHHHhc
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYH 33 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh 33 (181)
|+|+.|+.... +..|.+|++.+|
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 56666666665 666666666654
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.93 E-value=0.00043 Score=34.22 Aligned_cols=22 Identities=27% Similarity=0.860 Sum_probs=13.7
Q ss_pred eecccchhhccChhhHHHHHHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
|.|.+|++.|.+...|+.|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566666666666666666554
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.83 E-value=0.00039 Score=34.08 Aligned_cols=24 Identities=46% Similarity=0.880 Sum_probs=19.2
Q ss_pred ccCCcccccCCCchhHHHHHHhcCC
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTLHDP 71 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~h~~ 71 (181)
|+|+.|+.... ...|..|++.|++
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 68999999998 9999999998653
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.77 E-value=0.00041 Score=34.30 Aligned_cols=23 Identities=26% Similarity=0.609 Sum_probs=20.9
Q ss_pred ccCCcccccCCCchhHHHHHHhc
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTLH 69 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~h 69 (181)
|.|.+|++.|.....|..|++.+
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 67999999999999999998754
No 42
>KOG2893|consensus
Probab=96.77 E-value=0.00036 Score=53.48 Aligned_cols=51 Identities=29% Similarity=0.634 Sum_probs=42.2
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHH-HHhcCC
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRH-MTLHDP 71 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H-~~~h~~ 71 (181)
.||| |.+|++-|.....|..|++ .|.|+|.+|-|.+.+--.|..| |++|..
T Consensus 9 ~kpw-cwycnrefddekiliqhqk-------------akhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK-------------AKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh-------------hccceeeeehhhhccCCCceeehhhhhhh
Confidence 3566 9999999999999999965 4789999999988888888888 666643
No 43
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.71 E-value=0.00072 Score=53.91 Aligned_cols=55 Identities=22% Similarity=0.370 Sum_probs=44.3
Q ss_pred CCCcccCCc--ccccCCCchhHHHHHHh-c------------------CCCChhHHHHHHHhhhcccceeeecCcc
Q psy9958 43 KEKTHKCPE--CKKAFRHKGNLLRHMTL-H------------------DPDSELIEQQVALKLGRQKKVHIIDGHK 97 (181)
Q Consensus 43 ~~~~~~C~~--C~k~F~~~~~l~~H~~~-h------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (181)
++|||+|++ |.|.|+....|+.|+.. | ...+||.|..|.++.+....++.|.++.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~Hs 421 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHS 421 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccccc
Confidence 359999998 99999999999999863 2 1348899999999987777776666553
No 44
>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=96.38 E-value=0.00093 Score=33.76 Aligned_cols=22 Identities=32% Similarity=0.640 Sum_probs=14.6
Q ss_pred ccCCcccccCCCchhHHHHHHh
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
|.|..|++.|.....|..|++.
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 4566777777777777666653
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=96.18 E-value=0.00089 Score=33.83 Aligned_cols=22 Identities=36% Similarity=0.887 Sum_probs=20.4
Q ss_pred eecccchhhccChhhHHHHHHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
|.|..|++.|.+...|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 7899999999999999999875
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.78 E-value=0.0018 Score=53.47 Aligned_cols=62 Identities=32% Similarity=0.547 Sum_probs=55.7
Q ss_pred CceecccchhhccChhhHHHHHH--HhcCCCCCCCCCCC--CcccCC--cccccCCCchhHHHHHHhcCCCChhHHH
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVN--LYHNPHYVPPSPKE--KTHKCP--ECKKAFRHKGNLLRHMTLHDPDSELIEQ 78 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~--~hh~~~~~~~~~~~--~~~~C~--~C~k~F~~~~~l~~H~~~h~~~~~~~~~ 78 (181)
.++.|..|...|.....|.+|.+ .| .++ +++.|+ .|++.|.+...+..|..+|.......+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h---------~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNH---------SGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCcccccccccccccccc---------ccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 57999999999999999999999 55 677 999999 7999999999999999999988776544
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.71 E-value=0.008 Score=29.79 Aligned_cols=21 Identities=29% Similarity=0.719 Sum_probs=13.4
Q ss_pred ccCCcccccCCCchhHHHHHHh
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
..|+.||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3577777777 45666677553
No 48
>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=95.11 E-value=0.0043 Score=36.80 Aligned_cols=39 Identities=18% Similarity=0.431 Sum_probs=28.9
Q ss_pred cccCCcccccCCCchhHHHHHHh-cCCC-ChhHHHHHHHhhh
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTL-HDPD-SELIEQQVALKLG 85 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~-h~~~-~~~~~~~~~~~~~ 85 (181)
.|.|+.|++. .....|..|... |..+ +.+.|+.|...+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh
Confidence 5899999994 556889999765 5443 4578888886543
No 49
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.09 E-value=0.014 Score=31.04 Aligned_cols=23 Identities=22% Similarity=0.577 Sum_probs=15.6
Q ss_pred ceecccchhhccChhhHHHHHHH
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
+|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777777677776654
No 50
>PRK04860 hypothetical protein; Provisional
Probab=94.99 E-value=0.0038 Score=45.64 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=30.3
Q ss_pred CcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhhhc
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLGR 86 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~ 86 (181)
-+|.|. |++ ....+.+|.++|.+.++|.|..|...+..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 468887 887 67778899999999999988888766543
No 51
>KOG1146|consensus
Probab=94.92 E-value=0.018 Score=53.83 Aligned_cols=66 Identities=21% Similarity=0.319 Sum_probs=51.7
Q ss_pred ccCCCCceecccchhhccChhhHHHHHHHhcCCC------CCCCC----------CCCCcccCCcccccCCCchhHHHHH
Q psy9958 3 IHIDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPH------YVPPS----------PKEKTHKCPECKKAFRHKGNLLRHM 66 (181)
Q Consensus 3 ~Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~------~~~~~----------~~~~~~~C~~C~k~F~~~~~l~~H~ 66 (181)
+|+-.|-|+|+.|+..|+....|-.|||..|-.. +..++ .+.++|.|..|..+|..+.+|..|+
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 3556688999999999999999999999854210 00000 2357899999999999999999998
Q ss_pred Hh
Q psy9958 67 TL 68 (181)
Q Consensus 67 ~~ 68 (181)
..
T Consensus 539 qS 540 (1406)
T KOG1146|consen 539 QS 540 (1406)
T ss_pred HH
Confidence 64
No 52
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=94.84 E-value=0.0075 Score=46.25 Aligned_cols=53 Identities=17% Similarity=0.464 Sum_probs=34.1
Q ss_pred CCceecccchhhccChhhHHHHHHHhc-CCCCCCCCCCCCc-----ccCCcccccCCCc
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYH-NPHYVPPSPKEKT-----HKCPECKKAFRHK 59 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh-~~~~~~~~~~~~~-----~~C~~C~k~F~~~ 59 (181)
+|...|++|++.|..+..+....+.-. ...+.+.-.+..| +.|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 467899999999999877766665421 1111111123333 4899999987755
No 53
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=94.78 E-value=0.015 Score=45.27 Aligned_cols=26 Identities=19% Similarity=0.316 Sum_probs=14.1
Q ss_pred CCCCceecccchhhccChhhHHHHHHH
Q psy9958 5 IDQNPYLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 5 t~ekp~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
.|.|.|+|.+|.. |...-.--.|+..
T Consensus 138 hGGrif~CsfC~~-flCEDDQFEHQAs 163 (314)
T PF06524_consen 138 HGGRIFKCSFCDN-FLCEDDQFEHQAS 163 (314)
T ss_pred CCCeEEEeecCCC-eeeccchhhhhhh
Confidence 4567788888763 3333333444443
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.73 E-value=0.02 Score=28.31 Aligned_cols=21 Identities=24% Similarity=0.632 Sum_probs=17.5
Q ss_pred eecccchhhccChhhHHHHHHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
..|+.||+.| ....|.+|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 56779999764
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=94.72 E-value=0.019 Score=30.45 Aligned_cols=24 Identities=17% Similarity=0.315 Sum_probs=21.0
Q ss_pred CcccCCcccccCCCchhHHHHHHh
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
.+|.|.+|++.|.....+..|++.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 368899999999999999999764
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.31 E-value=0.028 Score=33.26 Aligned_cols=29 Identities=31% Similarity=0.527 Sum_probs=16.9
Q ss_pred CCCCceecccchhhccChhhHHHHHHHhc
Q psy9958 5 IDQNPYLCDHCDQTFRQKQLLKRHVNLYH 33 (181)
Q Consensus 5 t~ekp~~C~~C~k~f~~~~~L~~H~~~hh 33 (181)
.|+..+.|+.|+..|.......+|....|
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 34555666666666666666666655444
No 57
>KOG2186|consensus
Probab=94.03 E-value=0.034 Score=43.12 Aligned_cols=50 Identities=16% Similarity=0.472 Sum_probs=40.4
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcC
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
.|.|.+||...+.. .|-+|+...+ ...|.|.-|++.|-+ ..+..|.+--+
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCr----------n~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCR----------NAYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhcc----------CCeeEEeeccccccc-chhhhhhhhcc
Confidence 48999999998865 5788988874 378999999999998 66788875433
No 58
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=93.95 E-value=0.031 Score=43.60 Aligned_cols=29 Identities=24% Similarity=0.409 Sum_probs=23.2
Q ss_pred CCCCcccCCcccccCCCchhHHHHHHhcC
Q psy9958 42 PKEKTHKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 42 ~~~~~~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
.+.+++.|+.||.-......|..-.|+|.
T Consensus 205 ~k~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 205 EKGKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred ccCCCCCCCCCCCcccccccceeeeecch
Confidence 34689999999998888888887777663
No 59
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.76 E-value=0.048 Score=35.84 Aligned_cols=25 Identities=32% Similarity=0.804 Sum_probs=22.1
Q ss_pred ceecccchhhccChhhHHHHHHHhc
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYH 33 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh 33 (181)
.|.|.+|++.|.+...|..|++.++
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6999999999999999999999763
No 60
>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=92.75 E-value=0.074 Score=28.12 Aligned_cols=24 Identities=29% Similarity=0.843 Sum_probs=17.5
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
|+|.+||..+... ..++.|+.||.
T Consensus 2 ~~C~~CGy~y~~~---------------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE---------------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC---------------------cCCCcCcCCCC
Confidence 7888898655432 26789999985
No 61
>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=92.21 E-value=0.087 Score=35.93 Aligned_cols=30 Identities=23% Similarity=0.653 Sum_probs=23.1
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCc
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHK 59 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~ 59 (181)
..|+.||++|.-. +..|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL--------------------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL--------------------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC--------------------CCCCccCCCCCCccCcc
Confidence 4799999988752 23677899999988865
No 62
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.18 E-value=0.046 Score=32.36 Aligned_cols=30 Identities=27% Similarity=0.643 Sum_probs=25.9
Q ss_pred CCCCcccCCcccccCCCchhHHHHHHhcCC
Q psy9958 42 PKEKTHKCPECKKAFRHKGNLLRHMTLHDP 71 (181)
Q Consensus 42 ~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~ 71 (181)
.|+.-+.|+.|++.|.....+.+|....|+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 578889999999999999999999765444
No 63
>PF15269 zf-C2H2_7: Zinc-finger
Probab=92.13 E-value=0.17 Score=28.62 Aligned_cols=34 Identities=35% Similarity=0.729 Sum_probs=26.1
Q ss_pred CCCCCCCCC-CCcccCCcccccCCCchhHHHHHHh
Q psy9958 35 PHYVPPSPK-EKTHKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 35 ~~~~~~~~~-~~~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
++|++.+.| .-.|+|-.|..+...++.|-.||+-
T Consensus 8 phyiprp~gkp~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 8 PHYIPRPPGKPFKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred CCcCCCCCCCCccceeecCCcccchHHHHHHHHHH
Confidence 356654444 3468899999999999999999974
No 64
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=92.01 E-value=0.34 Score=32.86 Aligned_cols=63 Identities=17% Similarity=0.374 Sum_probs=44.3
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCC------------------------CCCCCCC---------CCcccC----C
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPH------------------------YVPPSPK---------EKTHKC----P 50 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~------------------------~~~~~~~---------~~~~~C----~ 50 (181)
+-..|..|.....- +.+..|++..|... ...+... -.-|.| .
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 55779999988776 77899988544221 0011111 123789 9
Q ss_pred cccccCCCchhHHHHHHhcCC
Q psy9958 51 ECKKAFRHKGNLLRHMTLHDP 71 (181)
Q Consensus 51 ~C~k~F~~~~~l~~H~~~h~~ 71 (181)
.|+..+.+...+..|++.+|+
T Consensus 89 ~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 89 HCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCcEeccHHHHHHHHHHhcC
Confidence 999999999999999988764
No 65
>PRK04860 hypothetical protein; Provisional
Probab=91.06 E-value=0.12 Score=37.81 Aligned_cols=31 Identities=23% Similarity=0.521 Sum_probs=25.7
Q ss_pred ChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCch
Q psy9958 21 QKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKG 60 (181)
Q Consensus 21 ~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~ 60 (181)
....+++|.++| ++.++|.|..|++.|....
T Consensus 127 ~~~~~rrH~ri~---------~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 127 HQLTVRRHNRVV---------RGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred eeCHHHHHHHHh---------cCCccEECCCCCceeEEec
Confidence 346789999998 6889999999999987654
No 66
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.41 E-value=0.19 Score=26.79 Aligned_cols=25 Identities=28% Similarity=0.747 Sum_probs=17.7
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
.|+|.+||..+... ..|..|+.||.
T Consensus 2 ~~~C~~CG~i~~g~---------------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE---------------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC---------------------cCCCcCcCCCC
Confidence 58899998655421 25678999986
No 67
>KOG4124|consensus
Probab=89.43 E-value=0.099 Score=42.52 Aligned_cols=61 Identities=28% Similarity=0.537 Sum_probs=44.7
Q ss_pred CCceeccc--chhhccChhhHHHHHHHhcCCCCC------CCCCC----CCcccCCcccccCCCchhHHHHHH
Q psy9958 7 QNPYLCDH--CDQTFRQKQLLKRHVNLYHNPHYV------PPSPK----EKTHKCPECKKAFRHKGNLLRHMT 67 (181)
Q Consensus 7 ekp~~C~~--C~k~f~~~~~L~~H~~~hh~~~~~------~~~~~----~~~~~C~~C~k~F~~~~~l~~H~~ 67 (181)
.+||+|.+ |.+.++....|+.|...-|...+- .+|++ .|+|.|++|.++++.-..|..|..
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 57899987 999999999999887655543221 33433 588999999988887777666543
No 68
>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=89.05 E-value=0.23 Score=38.00 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=16.3
Q ss_pred CcccCCcccccCCCchhHHHHHHhcCCCC
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTLHDPDS 73 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~h~~~~ 73 (181)
..|.|++|+|.|.-.....+|+...|.++
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 45666666666666666666666555543
No 69
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.98 E-value=0.26 Score=34.38 Aligned_cols=35 Identities=14% Similarity=0.280 Sum_probs=25.7
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHH
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLL 63 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~ 63 (181)
...|+.||++|.-. +..|..|+.||..|.-...++
T Consensus 9 Kr~Cp~cg~kFYDL--------------------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGSKFYDL--------------------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCcccccc--------------------CCCCccCCCcCCccCcchhhc
Confidence 35799999998742 236889999999987664443
No 70
>KOG2071|consensus
Probab=88.92 E-value=0.27 Score=42.70 Aligned_cols=27 Identities=19% Similarity=0.569 Sum_probs=23.5
Q ss_pred CCceecccchhhccChhhHHHHHHHhc
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYH 33 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh 33 (181)
.+|-.|..||.+|........||..|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 567899999999999999888888764
No 71
>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=88.83 E-value=0.33 Score=27.22 Aligned_cols=24 Identities=25% Similarity=0.557 Sum_probs=11.3
Q ss_pred CCceecccchhhccCh----hhHHHHHH
Q psy9958 7 QNPYLCDHCDQTFRQK----QLLKRHVN 30 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~----~~L~~H~~ 30 (181)
.....|.+|++.++.. ++|.+|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3445666666666553 55666653
No 72
>KOG2785|consensus
Probab=88.80 E-value=0.24 Score=40.81 Aligned_cols=61 Identities=18% Similarity=0.380 Sum_probs=45.6
Q ss_pred ceecccchhhccChhhHHHHHHHh-cCCCCC--------------------------CC-CCCCCcccCCcccccCCCch
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLY-HNPHYV--------------------------PP-SPKEKTHKCPECKKAFRHKG 60 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~h-h~~~~~--------------------------~~-~~~~~~~~C~~C~k~F~~~~ 60 (181)
-|.|.-|...|......+.|+++- |.++.. .+ ..+..++.|..|.|.|....
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 489999999999998888898752 211100 11 23456889999999999999
Q ss_pred hHHHHHHhc
Q psy9958 61 NLLRHMTLH 69 (181)
Q Consensus 61 ~l~~H~~~h 69 (181)
....|++..
T Consensus 83 a~~~hl~Sk 91 (390)
T KOG2785|consen 83 AHENHLKSK 91 (390)
T ss_pred hHHHHHHHh
Confidence 999998653
No 73
>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=87.64 E-value=0.26 Score=26.71 Aligned_cols=34 Identities=18% Similarity=0.489 Sum_probs=24.1
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCC
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFR 57 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~ 57 (181)
+.|+.|+..|.-...... .......|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~--------------~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG--------------ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC--------------CCCCEEECCCCCCEEE
Confidence 679999999887654321 1223678999998875
No 74
>KOG4173|consensus
Probab=87.62 E-value=0.44 Score=36.06 Aligned_cols=68 Identities=21% Similarity=0.331 Sum_probs=47.9
Q ss_pred Cceeccc--chhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcC----------CCChh
Q psy9958 8 NPYLCDH--CDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHD----------PDSEL 75 (181)
Q Consensus 8 kp~~C~~--C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~----------~~~~~ 75 (181)
+.|.|++ |-..|........|..+-|+ -.|..|.+.|.+..-|..|+.-.| |.-.|
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~------------~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy 145 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG------------NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMY 145 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc------------chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHH
Confidence 4578887 88888888877777655432 269999999999999999875432 44456
Q ss_pred HH--HHHHHhhhcc
Q psy9958 76 IE--QQVALKLGRQ 87 (181)
Q Consensus 76 ~~--~~~~~~~~~~ 87 (181)
.| ..|..+|...
T Consensus 146 ~ClvEgCt~KFkT~ 159 (253)
T KOG4173|consen 146 QCLVEGCTEKFKTS 159 (253)
T ss_pred HHHHHhhhhhhhhh
Confidence 65 3566666443
No 75
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.38 E-value=0.079 Score=38.49 Aligned_cols=19 Identities=21% Similarity=0.496 Sum_probs=14.7
Q ss_pred CcccCCcccccCCCchhHH
Q psy9958 45 KTHKCPECKKAFRHKGNLL 63 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~ 63 (181)
+.+.|+.||++|.+--.+.
T Consensus 27 ~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 27 RRRECLACGKRFTTFERVE 45 (154)
T ss_pred eeeeccccCCcceEeEecc
Confidence 3489999999998765543
No 76
>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=87.30 E-value=0.34 Score=34.23 Aligned_cols=22 Identities=36% Similarity=0.845 Sum_probs=13.4
Q ss_pred eecccchhhccChhhHHHHHHHhcC
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHN 34 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~ 34 (181)
-.|-.|||.|+. |++|++.||+
T Consensus 73 i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-
T ss_pred eEEccCCcccch---HHHHHHHccC
Confidence 468888888874 5888888764
No 77
>KOG4173|consensus
Probab=86.59 E-value=0.094 Score=39.59 Aligned_cols=58 Identities=21% Similarity=0.484 Sum_probs=45.1
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCC-CCCCCCCcccCCc--ccccCCCchhHHHHHHh
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYV-PPSPKEKTHKCPE--CKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~-~~~~~~~~~~C~~--C~k~F~~~~~l~~H~~~ 68 (181)
.|.+|.+.|.+...|..|+.-.|..-+- .+..|.--|.|-+ |+-.|.+....+.|+-.
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 7999999999999999999876642111 2224566799966 99999999999999644
No 78
>KOG2785|consensus
Probab=86.24 E-value=0.49 Score=39.01 Aligned_cols=62 Identities=19% Similarity=0.283 Sum_probs=47.9
Q ss_pred CceecccchhhccChhhHHHHHHHhcCC-----CCCCCCCC---------CCcccCCccc---ccCCCchhHHHHHHhc
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNP-----HYVPPSPK---------EKTHKCPECK---KAFRHKGNLLRHMTLH 69 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~-----~~~~~~~~---------~~~~~C~~C~---k~F~~~~~l~~H~~~h 69 (181)
-|--|-+|++.|+....-..||..+|+. .|+.-..| ..-|.|-.|+ +.|.+-...+.||.-.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 4567999999999999999999999864 22211111 3457899999 9999999999999753
No 79
>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=85.87 E-value=0.45 Score=33.65 Aligned_cols=27 Identities=33% Similarity=0.520 Sum_probs=17.7
Q ss_pred cccCCcccccCCCchhHHHHHHhcCCCChh
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTLHDPDSEL 75 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~ 75 (181)
...|-.|||.|.. |++|++.|+|-.+-
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp~ 98 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTPE 98 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-HH
T ss_pred eeEEccCCcccch---HHHHHHHccCCCHH
Confidence 4579999999986 69999999887653
No 80
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.75 E-value=0.41 Score=25.79 Aligned_cols=34 Identities=21% Similarity=0.598 Sum_probs=24.6
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCC
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFR 57 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~ 57 (181)
..|+.|+..|.-...... .+....+|+.|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~ip--------------~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP--------------PKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHCC--------------CCCcEEECCCCCCEeC
Confidence 479999998887654321 3456789999998874
No 81
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.62 E-value=0.6 Score=26.97 Aligned_cols=22 Identities=36% Similarity=0.688 Sum_probs=13.6
Q ss_pred cccCCcccccCCCc-----hhHHHHHH
Q psy9958 46 THKCPECKKAFRHK-----GNLLRHMT 67 (181)
Q Consensus 46 ~~~C~~C~k~F~~~-----~~l~~H~~ 67 (181)
.-.|..|++.+... ++|.+|++
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 34567777666554 46777766
No 82
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.41 E-value=0.59 Score=28.10 Aligned_cols=32 Identities=16% Similarity=0.395 Sum_probs=20.6
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
.|.|+.||+.-..+-.-- |. -..+|.|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~~C---Rk-----------~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCAKC---RK-----------LGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhhhH---HH-----------cCCceECCCcCc
Confidence 488999996655433211 11 147899999985
No 83
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.28 E-value=0.59 Score=33.59 Aligned_cols=38 Identities=21% Similarity=0.537 Sum_probs=22.2
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCC
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFR 57 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~ 57 (181)
..-|.|+.|++.|.....+.. .. . ...|.|+.||....
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d---------~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LD---------M-DGTFTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cC---------C-CCcEECCCCCCEEE
Confidence 445888888888775433221 01 1 23488888887543
No 84
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.27 E-value=0.58 Score=28.13 Aligned_cols=31 Identities=19% Similarity=0.627 Sum_probs=18.2
Q ss_pred ceecccchhh-ccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 9 PYLCDHCDQT-FRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 9 p~~C~~C~k~-f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
.|.|+.||+. ..+-..-+ . -..+|.|+.||+
T Consensus 25 ~F~CPnCG~~~I~RC~~CR----k-----------~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKCR----K-----------QSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeechhHH----h-----------cCCceECCCCCC
Confidence 4788888876 33222111 1 136888888875
No 85
>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=85.09 E-value=0.21 Score=38.29 Aligned_cols=29 Identities=21% Similarity=0.619 Sum_probs=23.3
Q ss_pred CCCCceecccchhhccChhhHHHHHHHhc
Q psy9958 5 IDQNPYLCDHCDQTFRQKQLLKRHVNLYH 33 (181)
Q Consensus 5 t~ekp~~C~~C~k~f~~~~~L~~H~~~hh 33 (181)
.++..|.|..|+|.|+-...+++|+...|
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 35667999999999999999999999876
No 86
>KOG2231|consensus
Probab=84.76 E-value=0.69 Score=41.12 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=11.7
Q ss_pred cCCcccccCCCchhHHHHHHh
Q psy9958 48 KCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 48 ~C~~C~k~F~~~~~l~~H~~~ 68 (181)
.|..|...|.....|.+|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 455555555555555555553
No 87
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=84.44 E-value=0.41 Score=31.10 Aligned_cols=35 Identities=20% Similarity=0.466 Sum_probs=24.6
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchh
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGN 61 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~ 61 (181)
.+|.|+.|++. .+.|. +..-|.|..||..|.-...
T Consensus 34 ~~~~Cp~C~~~--------~VkR~-----------a~GIW~C~kCg~~fAGgay 68 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRI-----------ATGIWKCRKCGAKFAGGAY 68 (89)
T ss_pred cCCcCCCCCCc--------ceeee-----------ccCeEEcCCCCCeeccccc
Confidence 46889999854 22232 3567899999999986554
No 88
>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=84.25 E-value=0.51 Score=32.17 Aligned_cols=31 Identities=16% Similarity=0.481 Sum_probs=21.4
Q ss_pred cccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhhhcc
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLGRQ 87 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~ 87 (181)
...|+.||++|-- | +..|..|+.|+..+...
T Consensus 9 KR~Cp~CG~kFYD---L--------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYD---L--------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhcc---C--------CCCCccCCCCCCccCcc
Confidence 4579999999864 2 22566788888776554
No 89
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.13 E-value=0.52 Score=25.53 Aligned_cols=34 Identities=26% Similarity=0.673 Sum_probs=24.4
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCC
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFR 57 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~ 57 (181)
..|+.|+..|.-...... .+.+..+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~l~--------------~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLP--------------AGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcc--------------cCCcEEECCCCCcEee
Confidence 469999999986653211 2456889999998875
No 90
>PHA00626 hypothetical protein
Probab=84.01 E-value=0.29 Score=29.00 Aligned_cols=16 Identities=13% Similarity=0.258 Sum_probs=12.9
Q ss_pred CCcccCCcccccCCCc
Q psy9958 44 EKTHKCPECKKAFRHK 59 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~ 59 (181)
...|.|+.||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 3689999999988753
No 91
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=83.55 E-value=0.69 Score=37.99 Aligned_cols=60 Identities=28% Similarity=0.572 Sum_probs=51.2
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCc--ccccCCCchhHHHHHHhcCCCChh
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPE--CKKAFRHKGNLLRHMTLHDPDSEL 75 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~--C~k~F~~~~~l~~H~~~h~~~~~~ 75 (181)
.+++.|..|...|....++.+|.+.+ .+++++.|.. |.+.|.....+.+|.+.++.....
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (467)
T COG5048 31 PRPDSCPNCTDSFSRLEHLTRHIRSH---------TGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSD 92 (467)
T ss_pred Cchhhcccccccccccchhhhhcccc---------cccCCccccccccccccCCcchhhhhcccccccccc
Confidence 46788999999999999999999998 7899999977 668899999999998887665443
No 92
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.36 E-value=0.76 Score=26.04 Aligned_cols=31 Identities=19% Similarity=0.544 Sum_probs=21.4
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCC
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFR 57 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~ 57 (181)
..|+|+.||..|.... ....+.|+.||..+.
T Consensus 2 ~~y~C~~CG~~~~~~~-------------------~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDE-------------------YGTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECC-------------------CCCceECCCCCCeEE
Confidence 3689999998776422 112678999997554
No 93
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=79.41 E-value=1.1 Score=33.42 Aligned_cols=35 Identities=17% Similarity=0.616 Sum_probs=23.5
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCc
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHK 59 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~ 59 (181)
..-|.|+.|+..|+....+. .-|.|+.||......
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~------------------~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME------------------YGFRCPQCGEMLEEY 149 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh------------------cCCcCCCCCCCCeec
Confidence 34588888888887655431 357888888765543
No 94
>PF14353 CpXC: CpXC protein
Probab=78.46 E-value=0.67 Score=32.36 Aligned_cols=47 Identities=30% Similarity=0.521 Sum_probs=30.4
Q ss_pred ecccchhhccChh----------hHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHH
Q psy9958 11 LCDHCDQTFRQKQ----------LLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMT 67 (181)
Q Consensus 11 ~C~~C~k~f~~~~----------~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~ 67 (181)
.|+.|+..|.... .|+.-+.. ..-..|.|+.||+.|.-...+..|-.
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~----------g~l~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILD----------GSLFSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHc----------CCcCEEECCCCCCceecCCCEEEEcC
Confidence 6999998886432 22322221 12357899999999987777766643
No 95
>KOG1146|consensus
Probab=78.38 E-value=1.1 Score=42.58 Aligned_cols=63 Identities=22% Similarity=0.388 Sum_probs=46.1
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCC---------CCCCCCCcccCCcccccCCCchhHHHHHHhcCC
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYV---------PPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDP 71 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~---------~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~ 71 (181)
..+|.|..|.-.|.....|..|.+..-- ... ..+.-..+| |..|...|.....|..||+.-++
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~~~-~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKFCF-AGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHHHh-ccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhh
Confidence 4679999999999999999999854210 000 111223556 99999999999999999987433
No 96
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=78.06 E-value=1.8 Score=21.42 Aligned_cols=19 Identities=21% Similarity=0.625 Sum_probs=13.2
Q ss_pred cCCcccccCCCchhHHHHHH
Q psy9958 48 KCPECKKAFRHKGNLLRHMT 67 (181)
Q Consensus 48 ~C~~C~k~F~~~~~l~~H~~ 67 (181)
.|++|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 588888877 4466667754
No 97
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.91 E-value=1.6 Score=35.73 Aligned_cols=47 Identities=30% Similarity=0.555 Sum_probs=31.9
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCccc----ccCCCchhHHHHHH
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECK----KAFRHKGNLLRHMT 67 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~----k~F~~~~~l~~H~~ 67 (181)
.|.+|.+.|..-..|.+|+|..|. +=|.|..-+ .-|..-..|..|.+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE----------~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE----------ACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh----------hhhhhhccCccchhhhhCHHHHHHHhh
Confidence 599999999999999999998764 323332222 14555566666654
No 98
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=77.78 E-value=0.57 Score=29.47 Aligned_cols=41 Identities=20% Similarity=0.465 Sum_probs=26.2
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCC--cccccCCCchh
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCP--ECKKAFRHKGN 61 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~--~C~k~F~~~~~ 61 (181)
+.|+.||........-..+.. ..++.+.|. .||.+|...-.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~-----------~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT-----------TKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcChh-----------hheeeeecCCCCCCCEEEEEEE
Confidence 579999876644333222211 346788998 89999886544
No 99
>KOG2231|consensus
Probab=77.36 E-value=1.3 Score=39.38 Aligned_cols=51 Identities=25% Similarity=0.499 Sum_probs=39.3
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcc------cccCCCchhHHHHHHhcCCCCh
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPEC------KKAFRHKGNLLRHMTLHDPDSE 74 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C------~k~F~~~~~l~~H~~~h~~~~~ 74 (181)
.|.+|...|-....|.+|++.+| |.|.+| +--|..-..|..|-|.+|--..
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h-------------~~chfC~~~~~~neyy~~~~dLe~HfR~~HflCE 240 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH-------------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHFLCE 240 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce-------------eheeecCcccccchhcccchHHHHHhhhcCcccc
Confidence 59999999999999999998764 456666 3467777888888887665444
No 100
>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=77.36 E-value=0.54 Score=26.20 Aligned_cols=29 Identities=31% Similarity=0.865 Sum_probs=21.3
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
|+|..||..|.....+. ...+..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~----------------~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSIS----------------EDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcC----------------CCCCCcCCCCCC
Confidence 88999999998654322 135678999987
No 101
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=76.92 E-value=1.2 Score=32.42 Aligned_cols=20 Identities=10% Similarity=0.323 Sum_probs=12.5
Q ss_pred CCCceecccchhhccChhhH
Q psy9958 6 DQNPYLCDHCDQTFRQKQLL 25 (181)
Q Consensus 6 ~ekp~~C~~C~k~f~~~~~L 25 (181)
+..-|.|+.|+..|+....+
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CCCeEECCCCCcEeeHHHHH
Confidence 34457777777777665554
No 102
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=76.68 E-value=1.2 Score=31.33 Aligned_cols=22 Identities=27% Similarity=0.470 Sum_probs=17.8
Q ss_pred eecccchhhccChhhHHHHHHHhcC
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHN 34 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~ 34 (181)
..|-.|||.|+ .|++|..+|++
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 46888999998 58999988864
No 103
>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=75.86 E-value=0.72 Score=26.74 Aligned_cols=29 Identities=31% Similarity=0.791 Sum_probs=19.5
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
|+|..||..|.....+. ...+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~----------------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS----------------DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC----------------CCCCCCCCCCCC
Confidence 88999999888532211 124557999986
No 104
>KOG4167|consensus
Probab=74.83 E-value=1.1 Score=40.07 Aligned_cols=26 Identities=15% Similarity=0.404 Sum_probs=20.4
Q ss_pred CceecccchhhccChhhHHHHHHHhc
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYH 33 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh 33 (181)
..|.|..|+|.|-.-..+..||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35888888888888777888888873
No 105
>KOG3214|consensus
Probab=74.67 E-value=3.4 Score=27.59 Aligned_cols=17 Identities=18% Similarity=0.501 Sum_probs=12.2
Q ss_pred CcccCCcccccCCCchh
Q psy9958 45 KTHKCPECKKAFRHKGN 61 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~ 61 (181)
....|.+|+.+|...-+
T Consensus 46 G~~sC~iC~esFqt~it 62 (109)
T KOG3214|consen 46 GKASCRICEESFQTTIT 62 (109)
T ss_pred ceeeeeehhhhhccchH
Confidence 34578889888887544
No 106
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=73.41 E-value=1.8 Score=30.57 Aligned_cols=25 Identities=36% Similarity=0.424 Sum_probs=21.2
Q ss_pred ccCCcccccCCCchhHHHHHHhcCCCCh
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTLHDPDSE 74 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~h~~~~~ 74 (181)
..|-.|||.|.+ |++|+.+|.+-.+
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 468899999985 9999999987655
No 107
>KOG4167|consensus
Probab=71.06 E-value=0.85 Score=40.77 Aligned_cols=29 Identities=28% Similarity=0.432 Sum_probs=25.4
Q ss_pred CcccCCcccccCCCchhHHHHHHhcCCCC
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTLHDPDS 73 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~h~~~~ 73 (181)
.-|.|..|+|.|.-...+..||++|.-..
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 45899999999999999999999996543
No 108
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=70.91 E-value=2 Score=24.86 Aligned_cols=29 Identities=21% Similarity=0.598 Sum_probs=19.4
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCccccc
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKA 55 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~ 55 (181)
.-|+|-.||+.|.. + .......|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~---~----------------~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVEL---D----------------QETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeeh---h----------------hccCceeCCCCCcE
Confidence 45889999988821 0 12356789999853
No 109
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.56 E-value=2.3 Score=28.90 Aligned_cols=32 Identities=9% Similarity=0.139 Sum_probs=22.9
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHH
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLL 63 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~ 63 (181)
.|+.|++.|... ...|..|+.||++|.. +.|.
T Consensus 11 idPetg~KFYDL--------------------NrdPiVsPytG~s~P~-s~fe 42 (129)
T COG4530 11 IDPETGKKFYDL--------------------NRDPIVSPYTGKSYPR-SYFE 42 (129)
T ss_pred cCccccchhhcc--------------------CCCccccCcccccchH-HHHH
Confidence 588888888642 2368899999999943 4444
No 110
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=69.45 E-value=2.8 Score=35.38 Aligned_cols=32 Identities=16% Similarity=0.469 Sum_probs=23.2
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhH
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNL 62 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l 62 (181)
+|+.||.+.+++ |..-|+|+.||+++....-.
T Consensus 352 ~Cp~Cg~~m~S~--------------------G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMKSA--------------------GRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchhhc--------------------CCCCcccccccccCCccccc
Confidence 699999765532 33489999999988876443
No 111
>KOG2593|consensus
Probab=68.20 E-value=2 Score=36.10 Aligned_cols=38 Identities=18% Similarity=0.549 Sum_probs=26.6
Q ss_pred CCCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 5 IDQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 5 t~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
+...-|.|+.|.+.|.....|+. .- ...-.|.|..|+-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L---~~---------~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQL---LD---------NETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHHh---hc---------ccCceEEEecCCC
Confidence 44566999999999987666553 21 2246789999974
No 112
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=66.90 E-value=2.1 Score=30.08 Aligned_cols=19 Identities=21% Similarity=0.511 Sum_probs=15.0
Q ss_pred CCCcccCCcccccCCCchh
Q psy9958 43 KEKTHKCPECKKAFRHKGN 61 (181)
Q Consensus 43 ~~~~~~C~~C~k~F~~~~~ 61 (181)
+...|.|..|++.|.....
T Consensus 50 ~~qRyrC~~C~~tf~~~~~ 68 (129)
T COG3677 50 GHQRYKCKSCGSTFTVETG 68 (129)
T ss_pred cccccccCCcCcceeeecc
Confidence 3578999999999886543
No 113
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=66.55 E-value=3.2 Score=27.20 Aligned_cols=14 Identities=29% Similarity=0.857 Sum_probs=7.5
Q ss_pred CcccCCcccccCCC
Q psy9958 45 KTHKCPECKKAFRH 58 (181)
Q Consensus 45 ~~~~C~~C~k~F~~ 58 (181)
+|-.|..||+.|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 34455555555554
No 114
>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=66.35 E-value=3.3 Score=20.57 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=8.4
Q ss_pred cCCcccccCC
Q psy9958 48 KCPECKKAFR 57 (181)
Q Consensus 48 ~C~~C~k~F~ 57 (181)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5899999885
No 115
>KOG1280|consensus
Probab=65.84 E-value=5.1 Score=32.83 Aligned_cols=31 Identities=23% Similarity=0.361 Sum_probs=25.0
Q ss_pred cCCCCceecccchhhccChhhHHHHHHHhcC
Q psy9958 4 HIDQNPYLCDHCDQTFRQKQLLKRHVNLYHN 34 (181)
Q Consensus 4 Ht~ekp~~C~~C~k~f~~~~~L~~H~~~hh~ 34 (181)
|-....|.|++|++.--+...|..|....|-
T Consensus 74 ~y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 74 HYDPQSFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred ccccccccCCcccccccchhHHHHHhhhcCc
Confidence 3345579999999988888889999887764
No 116
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=65.07 E-value=2 Score=28.27 Aligned_cols=17 Identities=24% Similarity=0.479 Sum_probs=12.3
Q ss_pred CCcccCCcccccCCCch
Q psy9958 44 EKTHKCPECKKAFRHKG 60 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~ 60 (181)
...|.|..|++.|.--.
T Consensus 52 ~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 52 VGIWRCKGCKKTVAGGA 68 (90)
T ss_pred eEEEEcCCCCCEEeCCc
Confidence 35688888888877543
No 117
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.35 E-value=2.3 Score=30.10 Aligned_cols=16 Identities=19% Similarity=0.565 Sum_probs=12.7
Q ss_pred CCceecccchhhccCh
Q psy9958 7 QNPYLCDHCDQTFRQK 22 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~ 22 (181)
...|.|..||+.|...
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 3568999999888764
No 118
>KOG3408|consensus
Probab=63.26 E-value=3.8 Score=28.37 Aligned_cols=28 Identities=25% Similarity=0.458 Sum_probs=24.0
Q ss_pred CCCCcccCCcccccCCCchhHHHHHHhc
Q psy9958 42 PKEKTHKCPECKKAFRHKGNLLRHMTLH 69 (181)
Q Consensus 42 ~~~~~~~C~~C~k~F~~~~~l~~H~~~h 69 (181)
+|..-|-|..|.+-|.....|..|.++.
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 4556689999999999999999998764
No 119
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=63.26 E-value=3.2 Score=22.34 Aligned_cols=33 Identities=15% Similarity=0.531 Sum_probs=20.5
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCc
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHK 59 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~ 59 (181)
+.|+.||+.|..... +-...-.|..||-.+.++
T Consensus 2 r~C~~Cg~~Yh~~~~-----------------pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN-----------------PPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETTTB-------------------SSTTBCTTTTEBEBEE
T ss_pred cCcCCCCCccccccC-----------------CCCCCCccCCCCCeeEeC
Confidence 578889988874321 223455788888765443
No 120
>KOG2482|consensus
Probab=62.98 E-value=7.7 Score=31.86 Aligned_cols=61 Identities=25% Similarity=0.397 Sum_probs=41.3
Q ss_pred ceecccchhhccC-hhhHHHHHHHhcCCCCCCCC-------------CCCCcccCCcccccCCCchhHHHHHHhc
Q psy9958 9 PYLCDHCDQTFRQ-KQLLKRHVNLYHNPHYVPPS-------------PKEKTHKCPECKKAFRHKGNLLRHMTLH 69 (181)
Q Consensus 9 p~~C~~C~k~f~~-~~~L~~H~~~hh~~~~~~~~-------------~~~~~~~C~~C~k~F~~~~~l~~H~~~h 69 (181)
.-+|-.|...+.. ++....|+-..|.-..-.|. ..-..+.|-.|.|.|+.+..|+.|||..
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhc
Confidence 3568889886654 56677776655543211111 1113578999999999999999999863
No 121
>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=62.75 E-value=5.1 Score=19.51 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=8.1
Q ss_pred CCcccCCcccc
Q psy9958 44 EKTHKCPECKK 54 (181)
Q Consensus 44 ~~~~~C~~C~k 54 (181)
..+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 46788888874
No 122
>KOG2482|consensus
Probab=62.69 E-value=4.1 Score=33.38 Aligned_cols=62 Identities=23% Similarity=0.443 Sum_probs=44.8
Q ss_pred ceecccchhhccChhhHHHHHHHhcCC---------------CCC-------CC-----------------------CCC
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNP---------------HYV-------PP-----------------------SPK 43 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~---------------~~~-------~~-----------------------~~~ 43 (181)
.+.|-+|.|.|+.+..|+.|||..... +|. .+ ..+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 578999999999999999999974321 011 00 011
Q ss_pred CCc--ccCCcccccCCCchhHHHHHHhcC
Q psy9958 44 EKT--HKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 44 ~~~--~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
..+ ..|-.|....-....|..||++-|
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 112 489999999999999999998643
No 123
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.64 E-value=2.1 Score=27.12 Aligned_cols=11 Identities=36% Similarity=1.081 Sum_probs=7.5
Q ss_pred eecccchhhcc
Q psy9958 10 YLCDHCDQTFR 20 (181)
Q Consensus 10 ~~C~~C~k~f~ 20 (181)
|+|..|+..|.
T Consensus 13 Y~c~~cg~~~d 23 (82)
T COG2331 13 YECTECGNRFD 23 (82)
T ss_pred EeecccchHHH
Confidence 67777776664
No 124
>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=62.54 E-value=2 Score=28.27 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=12.8
Q ss_pred CCcccCCcccccCCCchh
Q psy9958 44 EKTHKCPECKKAFRHKGN 61 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~~ 61 (181)
...|.|..|++.|.--..
T Consensus 51 ~GIW~C~~C~~~~AGGAy 68 (91)
T TIGR00280 51 TGIWTCRKCGAKFAGGAY 68 (91)
T ss_pred eEEEEcCCCCCEEeCCcc
Confidence 356888888888776443
No 125
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=62.51 E-value=6.3 Score=32.47 Aligned_cols=23 Identities=17% Similarity=0.550 Sum_probs=18.9
Q ss_pred ceecccchhhccChhhHHHHHHH
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
-+-|..|++.|++...+..|...
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~g 260 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLEG 260 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHhh
Confidence 36699999999998888888654
No 126
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=61.71 E-value=4.5 Score=27.71 Aligned_cols=11 Identities=27% Similarity=0.577 Sum_probs=6.2
Q ss_pred eecccchhhcc
Q psy9958 10 YLCDHCDQTFR 20 (181)
Q Consensus 10 ~~C~~C~k~f~ 20 (181)
+.|..|++.|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 55666665444
No 127
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=60.06 E-value=4.5 Score=22.79 Aligned_cols=26 Identities=27% Similarity=0.751 Sum_probs=18.5
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCccccc
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKA 55 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~ 55 (181)
|.|..||..|... ...+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~--------------------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK--------------------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC--------------------CCCceECCCCCce
Confidence 7899999877743 1246789999864
No 128
>KOG0696|consensus
Probab=59.35 E-value=5.1 Score=34.17 Aligned_cols=60 Identities=17% Similarity=0.266 Sum_probs=44.8
Q ss_pred CCCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHH-HHhcCCCChhHHHHHHHh
Q psy9958 6 DQNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRH-MTLHDPDSELIEQQVALK 83 (181)
Q Consensus 6 ~ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H-~~~h~~~~~~~~~~~~~~ 83 (181)
|+.=|+|++|. +..|.|-| .-..|.|+--+|.+.+-....+| .++|+=..|.-|..|+.-
T Consensus 70 gKQGfQCqvC~--------fvvHkrCh----------efVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGsL 130 (683)
T KOG0696|consen 70 GKQGFQCQVCC--------FVVHKRCH----------EFVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGSL 130 (683)
T ss_pred ccCceeeeEEe--------ehhhhhhc----------ceEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHHH
Confidence 34557888884 66787876 34688999989999888888888 466777777777777753
No 129
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=59.22 E-value=4.5 Score=23.85 Aligned_cols=41 Identities=22% Similarity=0.553 Sum_probs=23.7
Q ss_pred Cceeccc--chhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCc----ccccCCC
Q psy9958 8 NPYLCDH--CDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPE----CKKAFRH 58 (181)
Q Consensus 8 kp~~C~~--C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~----C~k~F~~ 58 (181)
.+-.|+. |...+.+ ..|..|+... =..++..|+. |...|..
T Consensus 8 ~~v~C~~~cc~~~i~r-~~l~~H~~~~---------C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPR-KELDDHLENE---------CPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp SEEE-TT--S-BEEEC-CCHHHHHHTT---------STTSEEE-SS----S--EEEH
T ss_pred CEeeCCCCCcccceeH-HHHHHHHHcc---------CCCCcEECCCCCCCCCCccch
Confidence 4567887 5555664 4689998743 2356778888 8877654
No 130
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.00 E-value=1.8 Score=33.50 Aligned_cols=26 Identities=12% Similarity=0.510 Sum_probs=20.6
Q ss_pred CCceecccchhhccChhhHHHHHHHh
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLY 32 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~h 32 (181)
++.+.|++|+-.|.....+..-+|+-
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRii 42 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRII 42 (267)
T ss_pred hceeccCcccchhhhhheeccceeEe
Confidence 45688999999999887777666654
No 131
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=57.90 E-value=1.7 Score=32.73 Aligned_cols=42 Identities=31% Similarity=0.459 Sum_probs=24.9
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCCCCCCCC---CcccCCcccccCCCchhH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKE---KTHKCPECKKAFRHKGNL 62 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~---~~~~C~~C~k~F~~~~~l 62 (181)
-.|++||. .|..|++.+.- |+-|+ ..+.|..||++++-...|
T Consensus 15 ~~CPvCg~------~l~~~~~~~~I-----PyFG~V~i~t~~C~~CgYR~~DV~~~ 59 (201)
T COG1779 15 IDCPVCGG------TLKAHMYLYDI-----PYFGEVLISTGVCERCGYRSTDVKTL 59 (201)
T ss_pred ecCCcccc------eeeEEEeeecC-----CccceEEEEEEEccccCCcccceeec
Confidence 46999996 35555554321 11232 245799999887755443
No 132
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=57.71 E-value=4.6 Score=22.09 Aligned_cols=14 Identities=29% Similarity=0.823 Sum_probs=11.3
Q ss_pred ceecccchhhccCh
Q psy9958 9 PYLCDHCDQTFRQK 22 (181)
Q Consensus 9 p~~C~~C~k~f~~~ 22 (181)
||.|..|++.|=.+
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 88899999888743
No 133
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=57.07 E-value=6.1 Score=27.12 Aligned_cols=12 Identities=17% Similarity=0.700 Sum_probs=6.0
Q ss_pred ccCCcccccCCC
Q psy9958 47 HKCPECKKAFRH 58 (181)
Q Consensus 47 ~~C~~C~k~F~~ 58 (181)
+.|..|++.|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 445555555443
No 134
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.32 E-value=2.7 Score=27.60 Aligned_cols=15 Identities=20% Similarity=0.534 Sum_probs=10.8
Q ss_pred CcccCCcccccCCCc
Q psy9958 45 KTHKCPECKKAFRHK 59 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~ 59 (181)
..|.|..|++.|.--
T Consensus 53 GIW~C~~C~~~~AGG 67 (90)
T PRK03976 53 GIWECRKCGAKFAGG 67 (90)
T ss_pred EEEEcCCCCCEEeCC
Confidence 567788888877654
No 135
>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=55.84 E-value=4 Score=22.54 Aligned_cols=11 Identities=27% Similarity=1.011 Sum_probs=5.6
Q ss_pred ceecccchhhc
Q psy9958 9 PYLCDHCDQTF 19 (181)
Q Consensus 9 p~~C~~C~k~f 19 (181)
+-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 44555555544
No 136
>PF12907 zf-met2: Zinc-binding
Probab=54.31 E-value=6 Score=21.86 Aligned_cols=24 Identities=42% Similarity=0.696 Sum_probs=12.3
Q ss_pred eecccchhhccCh---hhHHHHHHHhc
Q psy9958 10 YLCDHCDQTFRQK---QLLKRHVNLYH 33 (181)
Q Consensus 10 ~~C~~C~k~f~~~---~~L~~H~~~hh 33 (181)
+.|.+|-..|..- ..|..|....|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKH 28 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKH 28 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccC
Confidence 4566666544433 34666655443
No 137
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=53.91 E-value=14 Score=24.81 Aligned_cols=38 Identities=16% Similarity=0.355 Sum_probs=32.5
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
+..|.|+.-|..|.........+... ..+.|.|...|+
T Consensus 1 eeVf~i~~T~EiF~dYe~Y~~R~~~y----------~~~vwtC~~TGk 38 (102)
T PF10537_consen 1 EEVFYIPFTGEIFRDYEEYLKRMILY----------NQRVWTCEITGK 38 (102)
T ss_pred CceEEeCCCCcccCCHHHHHHHHHHH----------hCCeeEEecCCC
Confidence 35689999999999999988888776 468999999887
No 138
>KOG3408|consensus
Probab=53.42 E-value=10 Score=26.36 Aligned_cols=24 Identities=25% Similarity=0.587 Sum_probs=21.6
Q ss_pred CceecccchhhccChhhHHHHHHH
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
-.|-|-.|.+-|.....|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 458899999999999999999875
No 139
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.42 E-value=7.5 Score=26.80 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=4.9
Q ss_pred eecccchhhc
Q psy9958 10 YLCDHCDQTF 19 (181)
Q Consensus 10 ~~C~~C~k~f 19 (181)
+.|..||+.|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 4455555444
No 140
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=53.28 E-value=12 Score=30.89 Aligned_cols=61 Identities=25% Similarity=0.368 Sum_probs=40.9
Q ss_pred eeccc--chhhccChhhHHHHHHHhcCCCCC----------------------CCC-------CCCC-cccCCcccccCC
Q psy9958 10 YLCDH--CDQTFRQKQLLKRHVNLYHNPHYV----------------------PPS-------PKEK-THKCPECKKAFR 57 (181)
Q Consensus 10 ~~C~~--C~k~f~~~~~L~~H~~~hh~~~~~----------------------~~~-------~~~~-~~~C~~C~k~F~ 57 (181)
|.|+. |...+.....|+.|.+..|+.-+. +.| .|-| .-.|..|.+.|-
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FY 231 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFY 231 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccceec
Confidence 66775 777766677788888776643100 111 1111 226999999999
Q ss_pred CchhHHHHHHhcC
Q psy9958 58 HKGNLLRHMTLHD 70 (181)
Q Consensus 58 ~~~~l~~H~~~h~ 70 (181)
.-..|.+|+|..|
T Consensus 232 dDDEL~~HcR~~H 244 (493)
T COG5236 232 DDDELRRHCRLRH 244 (493)
T ss_pred ChHHHHHHHHhhh
Confidence 9999999998754
No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.76 E-value=3.9 Score=37.10 Aligned_cols=12 Identities=33% Similarity=0.922 Sum_probs=7.3
Q ss_pred CCCcccCCcccc
Q psy9958 43 KEKTHKCPECKK 54 (181)
Q Consensus 43 ~~~~~~C~~C~k 54 (181)
...|..|+.||.
T Consensus 472 ~~~p~~Cp~Cgs 483 (730)
T COG1198 472 EPIPQSCPECGS 483 (730)
T ss_pred CCCCCCCCCCCC
Confidence 345666666664
No 142
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=52.38 E-value=7.1 Score=23.85 Aligned_cols=16 Identities=19% Similarity=0.646 Sum_probs=11.9
Q ss_pred CCCcccCCcccccCCC
Q psy9958 43 KEKTHKCPECKKAFRH 58 (181)
Q Consensus 43 ~~~~~~C~~C~k~F~~ 58 (181)
..+.|.|+.||..+.+
T Consensus 43 ~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMDR 58 (69)
T ss_pred ccceEEcCCCCCEECc
Confidence 3578889999887654
No 143
>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=52.18 E-value=7.2 Score=26.67 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=7.7
Q ss_pred eecccchhhccC
Q psy9958 10 YLCDHCDQTFRQ 21 (181)
Q Consensus 10 ~~C~~C~k~f~~ 21 (181)
+.|..||+.|.-
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 567777777764
No 144
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=52.13 E-value=6.2 Score=30.22 Aligned_cols=43 Identities=19% Similarity=0.281 Sum_probs=29.0
Q ss_pred CCcccCCcccccCCCchhHHHHHHhcC----------CCChh-----HHHHHHHhhhc
Q psy9958 44 EKTHKCPECKKAFRHKGNLLRHMTLHD----------PDSEL-----IEQQVALKLGR 86 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~~l~~H~~~h~----------~~~~~-----~~~~~~~~~~~ 86 (181)
.+.+.||+|++.|.++.-+....+.-. +-.|+ .|+.|+..+..
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 467899999999999877776655421 22222 48888876543
No 145
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.53 E-value=2.4 Score=28.35 Aligned_cols=12 Identities=33% Similarity=0.767 Sum_probs=6.8
Q ss_pred cccCCcccccCC
Q psy9958 46 THKCPECKKAFR 57 (181)
Q Consensus 46 ~~~C~~C~k~F~ 57 (181)
...|..||.+|.
T Consensus 46 ~~~Cg~CGls~e 57 (104)
T COG4888 46 TAVCGNCGLSFE 57 (104)
T ss_pred EEEcccCcceEE
Confidence 345666666554
No 146
>PRK01343 zinc-binding protein; Provisional
Probab=51.24 E-value=17 Score=21.72 Aligned_cols=26 Identities=23% Similarity=0.419 Sum_probs=17.9
Q ss_pred CcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHH
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVAL 82 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~ 82 (181)
....|+.|+|.|.. ...+|....|..
T Consensus 8 p~~~CP~C~k~~~~------------~~rPFCS~RC~~ 33 (57)
T PRK01343 8 PTRPCPECGKPSTR------------EAYPFCSERCRD 33 (57)
T ss_pred CCCcCCCCCCcCcC------------CCCcccCHHHhh
Confidence 45679999998752 345776666653
No 147
>KOG1832|consensus
Probab=50.90 E-value=9.4 Score=35.57 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=4.8
Q ss_pred ccccCCCchhH
Q psy9958 52 CKKAFRHKGNL 62 (181)
Q Consensus 52 C~k~F~~~~~l 62 (181)
|.-+|.+.++.
T Consensus 1305 c~VtFNstG~V 1315 (1516)
T KOG1832|consen 1305 CAVTFNSTGDV 1315 (1516)
T ss_pred eEEEeccCccc
Confidence 44444444443
No 148
>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=50.69 E-value=6.1 Score=21.29 Aligned_cols=15 Identities=20% Similarity=0.623 Sum_probs=11.5
Q ss_pred cccCCcccccCCCch
Q psy9958 46 THKCPECKKAFRHKG 60 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~ 60 (181)
.|+|..||+.|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 578999999887543
No 149
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=50.03 E-value=5.6 Score=22.12 Aligned_cols=15 Identities=40% Similarity=1.034 Sum_probs=9.2
Q ss_pred CceecccchhhccCh
Q psy9958 8 NPYLCDHCDQTFRQK 22 (181)
Q Consensus 8 kp~~C~~C~k~f~~~ 22 (181)
-||.|..|++.|=.+
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 578899999888643
No 150
>KOG2071|consensus
Probab=49.36 E-value=11 Score=33.07 Aligned_cols=30 Identities=27% Similarity=0.570 Sum_probs=26.1
Q ss_pred CCCcccCCcccccCCCchhHHHHHHhcCCC
Q psy9958 43 KEKTHKCPECKKAFRHKGNLLRHMTLHDPD 72 (181)
Q Consensus 43 ~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~ 72 (181)
...|.+|..||.+|........||-.|..+
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhhh
Confidence 356789999999999999999999888654
No 151
>KOG0978|consensus
Probab=49.00 E-value=4.9 Score=36.13 Aligned_cols=54 Identities=22% Similarity=0.423 Sum_probs=29.9
Q ss_pred ceecccchhhccChhhH-HHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHH
Q psy9958 9 PYLCDHCDQTFRQKQLL-KRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRH 65 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L-~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H 65 (181)
..+|+.|..+|+...-. -.|..-... +.+-...+--+||.|+..|....-+..|
T Consensus 643 ~LkCs~Cn~R~Kd~vI~kC~H~FC~~C---vq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAVITKCGHVFCEEC---VQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred ceeCCCccCchhhHHHHhcchHHHHHH---HHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 35799998777765322 233221100 0000122444799999999877665544
No 152
>PRK14873 primosome assembly protein PriA; Provisional
Probab=48.70 E-value=12 Score=33.69 Aligned_cols=10 Identities=30% Similarity=1.042 Sum_probs=5.5
Q ss_pred CcccCCcccc
Q psy9958 45 KTHKCPECKK 54 (181)
Q Consensus 45 ~~~~C~~C~k 54 (181)
.|+.|+.||.
T Consensus 421 ~p~~Cp~Cgs 430 (665)
T PRK14873 421 PDWRCPRCGS 430 (665)
T ss_pred cCccCCCCcC
Confidence 3555666654
No 153
>KOG4124|consensus
Probab=48.26 E-value=8.7 Score=31.65 Aligned_cols=62 Identities=8% Similarity=0.020 Sum_probs=41.0
Q ss_pred CCCceeccc--chhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHH-HHhcCCC
Q psy9958 6 DQNPYLCDH--CDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRH-MTLHDPD 72 (181)
Q Consensus 6 ~ekp~~C~~--C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H-~~~h~~~ 72 (181)
.|++|.|.+ |.++++.-.....|-..-+- ..-+..+||+|+ |++.+.++..|+.| +..|.+.
T Consensus 175 EE~~~S~~vp~~~~~~~~~Ns~~~~S~~~~~----T~~t~~~p~k~~-~~~~~~T~~~l~~HS~N~~~~~ 239 (442)
T KOG4124|consen 175 EEYRVSVVVPAAAAAAAAANSSDMSSDEASS----TAETTGTPKKMP-ESLVMDTSSPLSDHSMNIDVGE 239 (442)
T ss_pred ccccccccCchhhhhhhcccccccccccccc----ccccccCCccCc-ccccccccchhhhccccCCCCc
Confidence 368888887 77776655444444322211 111456899997 99999999999998 4555554
No 154
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=48.25 E-value=1.6 Score=24.05 Aligned_cols=13 Identities=23% Similarity=0.608 Sum_probs=10.3
Q ss_pred CcccCCcccccCC
Q psy9958 45 KTHKCPECKKAFR 57 (181)
Q Consensus 45 ~~~~C~~C~k~F~ 57 (181)
.-|.|..|+..|+
T Consensus 27 ~fy~C~~C~~~w~ 39 (40)
T smart00440 27 VFYVCTKCGHRWR 39 (40)
T ss_pred EEEEeCCCCCEeC
Confidence 4689999998775
No 155
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=48.19 E-value=9.9 Score=26.06 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=5.8
Q ss_pred eecccchhhc
Q psy9958 10 YLCDHCDQTF 19 (181)
Q Consensus 10 ~~C~~C~k~f 19 (181)
+.|..|++.|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5666666533
No 156
>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=47.64 E-value=7.6 Score=23.68 Aligned_cols=11 Identities=27% Similarity=0.649 Sum_probs=5.0
Q ss_pred eecccchhhcc
Q psy9958 10 YLCDHCDQTFR 20 (181)
Q Consensus 10 ~~C~~C~k~f~ 20 (181)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 45888888885
No 157
>KOG2893|consensus
Probab=47.43 E-value=7.8 Score=30.21 Aligned_cols=36 Identities=22% Similarity=0.391 Sum_probs=26.8
Q ss_pred CCcccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhh
Q psy9958 44 EKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKL 84 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 84 (181)
.|+| |=.|++-|.-..-|.+|++..| |.|-.|-+++
T Consensus 9 ~kpw-cwycnrefddekiliqhqkakh----fkchichkkl 44 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKAKH----FKCHICHKKL 44 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhhcc----ceeeeehhhh
Confidence 4565 7789999999999999987543 5566665554
No 158
>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=47.12 E-value=12 Score=32.44 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=6.7
Q ss_pred CCcccCCcccc
Q psy9958 44 EKTHKCPECKK 54 (181)
Q Consensus 44 ~~~~~C~~C~k 54 (181)
..|+.|+.|+.
T Consensus 251 ~~~~~Cp~C~s 261 (505)
T TIGR00595 251 PIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCCC
Confidence 34666777764
No 159
>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=46.90 E-value=13 Score=32.04 Aligned_cols=27 Identities=19% Similarity=0.504 Sum_probs=23.9
Q ss_pred CceecccchhhccChhhHHHHHHHhcC
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHN 34 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~ 34 (181)
+-+.|+.|.+.|.....+..|+..-|-
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhh
Confidence 357899999999999999999997774
No 160
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=46.50 E-value=2.7 Score=21.33 Aligned_cols=9 Identities=44% Similarity=1.228 Sum_probs=4.4
Q ss_pred cCCcccccC
Q psy9958 48 KCPECKKAF 56 (181)
Q Consensus 48 ~C~~C~k~F 56 (181)
.|.-|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344455555
No 161
>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=46.13 E-value=11 Score=19.72 Aligned_cols=12 Identities=33% Similarity=0.977 Sum_probs=7.9
Q ss_pred CcccCCcccccC
Q psy9958 45 KTHKCPECKKAF 56 (181)
Q Consensus 45 ~~~~C~~C~k~F 56 (181)
-+..|+.||.+-
T Consensus 16 ~~irC~~CG~RI 27 (32)
T PF03604_consen 16 DPIRCPECGHRI 27 (32)
T ss_dssp STSSBSSSS-SE
T ss_pred CcEECCcCCCeE
Confidence 456899998653
No 162
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=45.19 E-value=11 Score=32.28 Aligned_cols=12 Identities=25% Similarity=0.949 Sum_probs=9.0
Q ss_pred Cceecccchhhc
Q psy9958 8 NPYLCDHCDQTF 19 (181)
Q Consensus 8 kp~~C~~C~k~f 19 (181)
..|.|..||..+
T Consensus 6 ~~y~C~~Cg~~~ 17 (454)
T TIGR00416 6 SKFVCQHCGADS 17 (454)
T ss_pred CeEECCcCCCCC
Confidence 359999999543
No 163
>COG1773 Rubredoxin [Energy production and conversion]
Probab=45.06 E-value=8.1 Score=22.91 Aligned_cols=19 Identities=11% Similarity=0.352 Sum_probs=14.3
Q ss_pred CceecccchhhccChhhHH
Q psy9958 8 NPYLCDHCDQTFRQKQLLK 26 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~ 26 (181)
+.|+|.+||..|.-...--
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp 20 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDP 20 (55)
T ss_pred CceEecCCceEeccccCCc
Confidence 4689999999988754433
No 164
>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=44.97 E-value=7 Score=22.81 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=6.5
Q ss_pred cCCcccccCCCc
Q psy9958 48 KCPECKKAFRHK 59 (181)
Q Consensus 48 ~C~~C~k~F~~~ 59 (181)
.||+|++.|...
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 899999998753
No 165
>PRK11823 DNA repair protein RadA; Provisional
Probab=43.84 E-value=14 Score=31.61 Aligned_cols=25 Identities=28% Similarity=0.836 Sum_probs=17.8
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccc
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKK 54 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k 54 (181)
...|.|..||..+. .+-++|+.|+.
T Consensus 5 ~~~y~C~~Cg~~~~-----------------------~~~g~Cp~C~~ 29 (446)
T PRK11823 5 KTAYVCQECGAESP-----------------------KWLGRCPECGA 29 (446)
T ss_pred CCeEECCcCCCCCc-----------------------ccCeeCcCCCC
Confidence 45699999995433 35667888875
No 166
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=43.65 E-value=15 Score=21.36 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=5.8
Q ss_pred ccCCcccccCCC
Q psy9958 47 HKCPECKKAFRH 58 (181)
Q Consensus 47 ~~C~~C~k~F~~ 58 (181)
|+|+.||..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 455555444443
No 167
>KOG0717|consensus
Probab=43.11 E-value=13 Score=31.80 Aligned_cols=22 Identities=32% Similarity=0.721 Sum_probs=18.9
Q ss_pred eecccchhhccChhhHHHHHHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
+-|.+|+|+|++...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6699999999999899988765
No 168
>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=42.96 E-value=15 Score=31.66 Aligned_cols=29 Identities=31% Similarity=0.583 Sum_probs=23.7
Q ss_pred CCCcccCCcccccCCCchhHHHHHHh-cCC
Q psy9958 43 KEKTHKCPECKKAFRHKGNLLRHMTL-HDP 71 (181)
Q Consensus 43 ~~~~~~C~~C~k~F~~~~~l~~H~~~-h~~ 71 (181)
.-+-|.|+.|.+.|.....+..|+.. |.+
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 34567999999999999999999864 533
No 169
>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=42.36 E-value=10 Score=20.23 Aligned_cols=31 Identities=16% Similarity=0.475 Sum_probs=16.9
Q ss_pred cccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCC
Q psy9958 12 CDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFR 57 (181)
Q Consensus 12 C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~ 57 (181)
|+.|-+-+....+ +|.| ..+..|..||-.|.
T Consensus 2 C~~C~~Ey~~p~~----RR~~-----------~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSN----RRFH-----------YQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTS----TTTT------------TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCC----Cccc-----------CcCccCCCCCCCEE
Confidence 6777777766554 2222 35668999998765
No 170
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=42.01 E-value=17 Score=21.05 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=7.7
Q ss_pred ecccchhhccC
Q psy9958 11 LCDHCDQTFRQ 21 (181)
Q Consensus 11 ~C~~C~k~f~~ 21 (181)
.|..|++.|..
T Consensus 4 ~C~~C~~~F~~ 14 (57)
T cd00065 4 SCMGCGKPFTL 14 (57)
T ss_pred cCcccCccccC
Confidence 47777777774
No 171
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.56 E-value=13 Score=21.92 Aligned_cols=11 Identities=27% Similarity=0.881 Sum_probs=7.2
Q ss_pred eecccchhhcc
Q psy9958 10 YLCDHCDQTFR 20 (181)
Q Consensus 10 ~~C~~C~k~f~ 20 (181)
.+|..|++.|+
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 35777777665
No 172
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=40.96 E-value=15 Score=25.93 Aligned_cols=15 Identities=27% Similarity=0.904 Sum_probs=12.7
Q ss_pred cccCCcccccCCCch
Q psy9958 46 THKCPECKKAFRHKG 60 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~ 60 (181)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998655
No 173
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.85 E-value=13 Score=25.87 Aligned_cols=11 Identities=18% Similarity=0.289 Sum_probs=6.5
Q ss_pred eecccchhhccC
Q psy9958 10 YLCDHCDQTFRQ 21 (181)
Q Consensus 10 ~~C~~C~k~f~~ 21 (181)
+.| .|++.|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 556 66665554
No 174
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=39.99 E-value=16 Score=20.78 Aligned_cols=14 Identities=14% Similarity=0.330 Sum_probs=10.2
Q ss_pred CcccCCcccccCCC
Q psy9958 45 KTHKCPECKKAFRH 58 (181)
Q Consensus 45 ~~~~C~~C~k~F~~ 58 (181)
..|.|+.||..+.-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 37889999876544
No 175
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.63 E-value=10 Score=22.92 Aligned_cols=12 Identities=25% Similarity=0.844 Sum_probs=8.8
Q ss_pred ceecccchhhcc
Q psy9958 9 PYLCDHCDQTFR 20 (181)
Q Consensus 9 p~~C~~C~k~f~ 20 (181)
--.|++|+..|+
T Consensus 48 ev~CPYC~t~y~ 59 (62)
T COG4391 48 EVVCPYCSTRYR 59 (62)
T ss_pred cEecCccccEEE
Confidence 346888888776
No 176
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=39.34 E-value=24 Score=19.37 Aligned_cols=23 Identities=17% Similarity=0.277 Sum_probs=16.5
Q ss_pred eecccchhhccCh--hhHHHHHHHh
Q psy9958 10 YLCDHCDQTFRQK--QLLKRHVNLY 32 (181)
Q Consensus 10 ~~C~~C~k~f~~~--~~L~~H~~~h 32 (181)
-+|+.||-.|... ..-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 5799999887763 5567776665
No 177
>KOG1832|consensus
Probab=37.96 E-value=18 Score=33.92 Aligned_cols=10 Identities=30% Similarity=0.494 Sum_probs=4.2
Q ss_pred chhhccChhh
Q psy9958 15 CDQTFRQKQL 24 (181)
Q Consensus 15 C~k~f~~~~~ 24 (181)
|.-+|+....
T Consensus 1305 c~VtFNstG~ 1314 (1516)
T KOG1832|consen 1305 CAVTFNSTGD 1314 (1516)
T ss_pred eEEEeccCcc
Confidence 3334444433
No 178
>KOG0717|consensus
Probab=37.77 E-value=16 Score=31.37 Aligned_cols=22 Identities=27% Similarity=0.536 Sum_probs=19.8
Q ss_pred ccCCcccccCCCchhHHHHHHh
Q psy9958 47 HKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
+-|.+|+|+|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6799999999999999999654
No 179
>KOG2636|consensus
Probab=37.56 E-value=19 Score=30.69 Aligned_cols=23 Identities=17% Similarity=0.491 Sum_probs=17.8
Q ss_pred CCcccCCccc-ccCCCchhHHHHH
Q psy9958 44 EKTHKCPECK-KAFRHKGNLLRHM 66 (181)
Q Consensus 44 ~~~~~C~~C~-k~F~~~~~l~~H~ 66 (181)
..-|.|.+|| +++..+..+.+|.
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred CcccceeeccCccccCcHHHHHHh
Confidence 4678888888 7888888888885
No 180
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=37.15 E-value=7.9 Score=25.93 Aligned_cols=13 Identities=15% Similarity=0.317 Sum_probs=9.5
Q ss_pred cccCCcccccCCC
Q psy9958 46 THKCPECKKAFRH 58 (181)
Q Consensus 46 ~~~C~~C~k~F~~ 58 (181)
...|+.||..|.+
T Consensus 42 h~~C~~CG~y~~~ 54 (99)
T PRK14892 42 IITCGNCGLYTEF 54 (99)
T ss_pred eEECCCCCCccCE
Confidence 3479999887665
No 181
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=36.36 E-value=12 Score=28.37 Aligned_cols=24 Identities=17% Similarity=0.513 Sum_probs=0.0
Q ss_pred CCcccCCccc-ccCCCchhHHHHHH
Q psy9958 44 EKTHKCPECK-KAFRHKGNLLRHMT 67 (181)
Q Consensus 44 ~~~~~C~~C~-k~F~~~~~l~~H~~ 67 (181)
.+.|.|.+|| .+|..+..+.+|..
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcC
Confidence 4789999999 57888899999964
No 183
>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=35.94 E-value=24 Score=19.05 Aligned_cols=14 Identities=36% Similarity=0.631 Sum_probs=4.8
Q ss_pred CcccCCcccccCCC
Q psy9958 45 KTHKCPECKKAFRH 58 (181)
Q Consensus 45 ~~~~C~~C~k~F~~ 58 (181)
++|-|..|...|..
T Consensus 2 ~ryyCdyC~~~~~~ 15 (38)
T PF06220_consen 2 PRYYCDYCKKYLTH 15 (38)
T ss_dssp -S-B-TTT--B-S-
T ss_pred cCeecccccceecC
Confidence 45677888777743
No 184
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=35.80 E-value=9.7 Score=22.68 Aligned_cols=11 Identities=27% Similarity=0.489 Sum_probs=6.2
Q ss_pred ecccchhhccC
Q psy9958 11 LCDHCDQTFRQ 21 (181)
Q Consensus 11 ~C~~C~k~f~~ 21 (181)
+|-.|++.+.-
T Consensus 4 kC~lCdk~~~I 14 (56)
T PF09963_consen 4 KCILCDKKEEI 14 (56)
T ss_pred EEEecCCEEEe
Confidence 46666665544
No 185
>KOG2186|consensus
Probab=35.71 E-value=7.4 Score=30.54 Aligned_cols=39 Identities=13% Similarity=0.254 Sum_probs=31.0
Q ss_pred cccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHhhhc
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLGR 86 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~ 86 (181)
-|.|..||-...- ..+.+|+...++ .-|.|-.|+..|.+
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc
Confidence 4789999987664 567889988777 67888888887766
No 186
>KOG2636|consensus
Probab=35.68 E-value=23 Score=30.19 Aligned_cols=26 Identities=23% Similarity=0.611 Sum_probs=19.5
Q ss_pred ccCCCCceecccch-hhccChhhHHHH
Q psy9958 3 IHIDQNPYLCDHCD-QTFRQKQLLKRH 28 (181)
Q Consensus 3 ~Ht~ekp~~C~~C~-k~f~~~~~L~~H 28 (181)
.|-=..-|.|.+|| +++.....+.+|
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHH
Confidence 45556679999999 777777777766
No 187
>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=35.42 E-value=18 Score=20.19 Aligned_cols=17 Identities=24% Similarity=0.698 Sum_probs=12.7
Q ss_pred ccCCcccccCCCchhHH
Q psy9958 47 HKCPECKKAFRHKGNLL 63 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~ 63 (181)
-.|..|++.|.-.....
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 36999999998765443
No 188
>PLN02294 cytochrome c oxidase subunit Vb
Probab=35.25 E-value=16 Score=26.92 Aligned_cols=16 Identities=38% Similarity=0.870 Sum_probs=12.8
Q ss_pred CCCcccCCcccccCCC
Q psy9958 43 KEKTHKCPECKKAFRH 58 (181)
Q Consensus 43 ~~~~~~C~~C~k~F~~ 58 (181)
..+|+.|+.||..|.-
T Consensus 138 kGkp~RCpeCG~~fkL 153 (174)
T PLN02294 138 KGKSFECPVCTQYFEL 153 (174)
T ss_pred CCCceeCCCCCCEEEE
Confidence 3578999999988863
No 189
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=35.17 E-value=18 Score=30.18 Aligned_cols=8 Identities=38% Similarity=1.327 Sum_probs=4.6
Q ss_pred eecccchh
Q psy9958 10 YLCDHCDQ 17 (181)
Q Consensus 10 ~~C~~C~k 17 (181)
|.|..||.
T Consensus 1 ~~c~~cg~ 8 (372)
T cd01121 1 YVCSECGY 8 (372)
T ss_pred CCCCCCCC
Confidence 55666663
No 190
>PRK05580 primosome assembly protein PriA; Validated
Probab=35.17 E-value=26 Score=31.71 Aligned_cols=12 Identities=33% Similarity=0.874 Sum_probs=7.9
Q ss_pred CCcccCCccccc
Q psy9958 44 EKTHKCPECKKA 55 (181)
Q Consensus 44 ~~~~~C~~C~k~ 55 (181)
..|+.|+.||..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 456777777654
No 191
>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=34.74 E-value=16 Score=21.37 Aligned_cols=17 Identities=12% Similarity=0.485 Sum_probs=9.4
Q ss_pred CCCceecccchhhccCh
Q psy9958 6 DQNPYLCDHCDQTFRQK 22 (181)
Q Consensus 6 ~ekp~~C~~C~k~f~~~ 22 (181)
+...|+|.+|++.|...
T Consensus 32 ~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 32 EPIKLRCHYCERIITED 48 (52)
T ss_dssp TTCEEEETTT--EEEHH
T ss_pred CCCEEEeeCCCCEeccc
Confidence 44557777777766543
No 192
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=33.96 E-value=5.3 Score=22.71 Aligned_cols=37 Identities=22% Similarity=0.457 Sum_probs=23.3
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCc--ccccCCC
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPE--CKKAFRH 58 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~--C~k~F~~ 58 (181)
.|+.||...........+.. ..+.-|.|.- ||.+|..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~-----------~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPL-----------TRELYCQCTNPECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhhCcc-----------eEEEEEEECCCcCCCEEEE
Confidence 48888876665544443322 3456778866 8888764
No 193
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.71 E-value=33 Score=25.21 Aligned_cols=21 Identities=29% Similarity=0.676 Sum_probs=15.5
Q ss_pred CCcccCCcccccCCCchhHHH
Q psy9958 44 EKTHKCPECKKAFRHKGNLLR 64 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~~l~~ 64 (181)
..-|.|+.||+.|=--+.+..
T Consensus 128 ~~f~~C~~CgkiYW~GsHw~~ 148 (165)
T COG1656 128 EEFYRCPKCGKIYWKGSHWRR 148 (165)
T ss_pred cceeECCCCcccccCchHHHH
Confidence 356779999998877666544
No 194
>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=32.90 E-value=18 Score=24.14 Aligned_cols=15 Identities=40% Similarity=1.052 Sum_probs=12.4
Q ss_pred CCcccCCcccccCCC
Q psy9958 44 EKTHKCPECKKAFRH 58 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~ 58 (181)
.+++.|..||..|.-
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 479999999988863
No 195
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=32.71 E-value=8.8 Score=21.59 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=5.9
Q ss_pred CcccCCcccc
Q psy9958 45 KTHKCPECKK 54 (181)
Q Consensus 45 ~~~~C~~C~k 54 (181)
..|.|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 5566666654
No 196
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=32.44 E-value=28 Score=23.42 Aligned_cols=16 Identities=25% Similarity=0.804 Sum_probs=11.9
Q ss_pred cccCCcccccCCCchh
Q psy9958 46 THKCPECKKAFRHKGN 61 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~ 61 (181)
|+.|..||..|..-+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6778888888887543
No 197
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.01 E-value=13 Score=25.11 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=9.8
Q ss_pred Cceecccchhhcc
Q psy9958 8 NPYLCDHCDQTFR 20 (181)
Q Consensus 8 kp~~C~~C~k~f~ 20 (181)
||-.|++||..-.
T Consensus 1 ~p~~CpYCg~~~~ 13 (102)
T PF11672_consen 1 KPIICPYCGGPAE 13 (102)
T ss_pred CCcccCCCCCeeE
Confidence 5778999997443
No 198
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=31.92 E-value=21 Score=32.34 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=7.7
Q ss_pred CcccCCcccc
Q psy9958 45 KTHKCPECKK 54 (181)
Q Consensus 45 ~~~~C~~C~k 54 (181)
.|..|+.||-
T Consensus 172 Qp~aCp~CGP 181 (750)
T COG0068 172 QPIACPKCGP 181 (750)
T ss_pred ccccCcccCC
Confidence 5778888885
No 199
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=31.63 E-value=8.4 Score=20.70 Aligned_cols=11 Identities=18% Similarity=0.806 Sum_probs=7.6
Q ss_pred CCCCcccCCcc
Q psy9958 42 PKEKTHKCPEC 52 (181)
Q Consensus 42 ~~~~~~~C~~C 52 (181)
.|...|.|..|
T Consensus 25 ~G~qryrC~~C 35 (36)
T PF03811_consen 25 SGHQRYRCKDC 35 (36)
T ss_pred CCCEeEecCcC
Confidence 45667777776
No 200
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=31.55 E-value=17 Score=29.44 Aligned_cols=14 Identities=21% Similarity=0.603 Sum_probs=9.4
Q ss_pred CcccCCcccccCCC
Q psy9958 45 KTHKCPECKKAFRH 58 (181)
Q Consensus 45 ~~~~C~~C~k~F~~ 58 (181)
..+.|+.|+.-|+-
T Consensus 56 ~~~vcp~c~~h~rl 69 (296)
T CHL00174 56 KMNICEQCGYHLKM 69 (296)
T ss_pred cCCCCCCCCCCcCC
Confidence 34678888876653
No 201
>PTZ00448 hypothetical protein; Provisional
Probab=31.51 E-value=31 Score=28.74 Aligned_cols=23 Identities=13% Similarity=0.342 Sum_probs=20.4
Q ss_pred cccCCcccccCCCchhHHHHHHh
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
.|.|..|+-.|......+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999988888899875
No 202
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=31.11 E-value=19 Score=20.80 Aligned_cols=14 Identities=21% Similarity=0.612 Sum_probs=7.1
Q ss_pred CceecccchhhccC
Q psy9958 8 NPYLCDHCDQTFRQ 21 (181)
Q Consensus 8 kp~~C~~C~k~f~~ 21 (181)
+.+.|..||..|.-
T Consensus 3 k~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 3 KTLTCKDCGAEFVF 16 (49)
T ss_pred eeEEcccCCCeEEE
Confidence 34555555555543
No 203
>PLN02748 tRNA dimethylallyltransferase
Probab=30.99 E-value=30 Score=29.84 Aligned_cols=26 Identities=15% Similarity=0.225 Sum_probs=22.1
Q ss_pred CCcccCCcccc-cCCCchhHHHHHHhc
Q psy9958 44 EKTHKCPECKK-AFRHKGNLLRHMTLH 69 (181)
Q Consensus 44 ~~~~~C~~C~k-~F~~~~~l~~H~~~h 69 (181)
.+.|.|..|++ .|.....+..|++..
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcch
Confidence 36788999997 899999999998653
No 204
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=30.71 E-value=15 Score=33.74 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=9.8
Q ss_pred eecccchhhccCh
Q psy9958 10 YLCDHCDQTFRQK 22 (181)
Q Consensus 10 ~~C~~C~k~f~~~ 22 (181)
-.|..|++.|...
T Consensus 461 dtC~~C~kkFfSl 473 (1374)
T PTZ00303 461 DSCPSCGRAFISL 473 (1374)
T ss_pred CcccCcCCccccc
Confidence 4588999988653
No 205
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=30.62 E-value=17 Score=28.03 Aligned_cols=34 Identities=26% Similarity=0.326 Sum_probs=0.0
Q ss_pred CCcccCCcccccCCCchhHHHHHHhcCCCChhHHH
Q psy9958 44 EKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQ 78 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~ 78 (181)
.+...|++||.... .+.|..|||+..-+..|...
T Consensus 166 ~~~~~cPitGe~IP-~~e~~eHmRi~LlDP~wkEq 199 (229)
T PF12230_consen 166 EKMIICPITGEMIP-ADEMDEHMRIELLDPRWKEQ 199 (229)
T ss_dssp -----------------------------------
T ss_pred cccccccccccccc-cccccccccccccccccccc
Confidence 45579999999766 47889999999888777543
No 206
>PRK06260 threonine synthase; Validated
Probab=30.49 E-value=28 Score=29.12 Aligned_cols=11 Identities=18% Similarity=0.721 Sum_probs=7.1
Q ss_pred eecccchhhcc
Q psy9958 10 YLCDHCDQTFR 20 (181)
Q Consensus 10 ~~C~~C~k~f~ 20 (181)
++|..||+.|.
T Consensus 4 ~~C~~cg~~~~ 14 (397)
T PRK06260 4 LKCIECGKEYD 14 (397)
T ss_pred EEECCCCCCCC
Confidence 56777776554
No 207
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=30.34 E-value=23 Score=23.95 Aligned_cols=30 Identities=30% Similarity=0.525 Sum_probs=24.1
Q ss_pred CCCCCCCcccCCcccccCCCchhHHHHHHh
Q psy9958 39 PPSPKEKTHKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 39 ~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
+.-+|-.-|-|..|.+-|.+...|..|.+.
T Consensus 48 p~lPGlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 48 PELPGLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCCCCCceeeeehhHHHHHHHHHHHHHhcc
Confidence 334556667899999999999999999764
No 208
>PHA02998 RNA polymerase subunit; Provisional
Probab=30.13 E-value=8.2 Score=28.68 Aligned_cols=42 Identities=21% Similarity=0.447 Sum_probs=22.6
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCc
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHK 59 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~ 59 (181)
.-+|+.|+..=.... ...+|..=. +.-.-|.|..||+.|.-+
T Consensus 143 ~v~CPkCg~~~A~f~--qlQTRSADE-------PmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPM--MIQTRAADE-------PPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEE--EEeeccCCC-------CceEEEEcCCCCCccCCc
Confidence 456888874333222 222333211 223457899999887654
No 209
>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=29.78 E-value=22 Score=19.14 Aligned_cols=12 Identities=33% Similarity=0.966 Sum_probs=6.7
Q ss_pred Cceecccchhhc
Q psy9958 8 NPYLCDHCDQTF 19 (181)
Q Consensus 8 kp~~C~~C~k~f 19 (181)
+.|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 468899998655
No 210
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=29.22 E-value=30 Score=20.53 Aligned_cols=17 Identities=29% Similarity=0.729 Sum_probs=12.4
Q ss_pred CCCcccCCcccccCCCc
Q psy9958 43 KEKTHKCPECKKAFRHK 59 (181)
Q Consensus 43 ~~~~~~C~~C~k~F~~~ 59 (181)
+++---|+.|++.|...
T Consensus 36 ~~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 36 GERYNGCPFCGTPFEFD 52 (55)
T ss_pred hhhccCCCCCCCcccCC
Confidence 34445799999998764
No 211
>KOG2907|consensus
Probab=29.15 E-value=20 Score=24.58 Aligned_cols=14 Identities=36% Similarity=0.802 Sum_probs=10.5
Q ss_pred CcccCCcccccCCC
Q psy9958 45 KTHKCPECKKAFRH 58 (181)
Q Consensus 45 ~~~~C~~C~k~F~~ 58 (181)
.-|.|+.|++.|..
T Consensus 101 VFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 101 VFYTCPKCKYKFTE 114 (116)
T ss_pred EEEEcCccceeeec
Confidence 35788888888764
No 212
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=28.93 E-value=31 Score=20.49 Aligned_cols=17 Identities=24% Similarity=0.681 Sum_probs=9.2
Q ss_pred CCceecccchhhccChh
Q psy9958 7 QNPYLCDHCDQTFRQKQ 23 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~ 23 (181)
+.|.+...|+-.|.+..
T Consensus 22 ~~PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEA 38 (57)
T ss_dssp SSEEEESSS--EEEHHH
T ss_pred hCCcCcCCCCCeecHHH
Confidence 35666666777777544
No 213
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.74 E-value=32 Score=25.30 Aligned_cols=13 Identities=31% Similarity=0.692 Sum_probs=9.2
Q ss_pred CCCCCcccCCccc
Q psy9958 41 SPKEKTHKCPECK 53 (181)
Q Consensus 41 ~~~~~~~~C~~C~ 53 (181)
+.++.|.+||+||
T Consensus 144 ~~ge~P~~CPiCg 156 (166)
T COG1592 144 HEGEAPEVCPICG 156 (166)
T ss_pred ccCCCCCcCCCCC
Confidence 3557777888887
No 214
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.44 E-value=49 Score=22.68 Aligned_cols=49 Identities=20% Similarity=0.409 Sum_probs=35.8
Q ss_pred ecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchhHHHHHHhcC
Q psy9958 11 LCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHD 70 (181)
Q Consensus 11 ~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~h~ 70 (181)
.|--|.+.|........-. . ....+|.|+.|...|--.-+.-.|..+|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~--~---------~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDE--L---------KDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccccc--c---------ccccceeCCCCCCccccccchhhhhhccC
Confidence 4888999998654221110 0 23568999999999999999999988875
No 215
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.41 E-value=32 Score=18.46 Aligned_cols=15 Identities=33% Similarity=0.837 Sum_probs=9.3
Q ss_pred cCCcccccCCCchhH
Q psy9958 48 KCPECKKAFRHKGNL 62 (181)
Q Consensus 48 ~C~~C~k~F~~~~~l 62 (181)
.|+.|+|.|-..+..
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 588888888776664
No 216
>PRK05978 hypothetical protein; Provisional
Probab=28.36 E-value=16 Score=26.43 Aligned_cols=12 Identities=33% Similarity=1.030 Sum_probs=8.5
Q ss_pred cCCcccccCCCc
Q psy9958 48 KCPECKKAFRHK 59 (181)
Q Consensus 48 ~C~~C~k~F~~~ 59 (181)
.|+.||..|...
T Consensus 54 ~C~~CG~~~~~~ 65 (148)
T PRK05978 54 HCAACGEDFTHH 65 (148)
T ss_pred CccccCCccccC
Confidence 588898766544
No 217
>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=28.30 E-value=34 Score=27.48 Aligned_cols=13 Identities=31% Similarity=0.884 Sum_probs=9.2
Q ss_pred cccCCcccccCCC
Q psy9958 46 THKCPECKKAFRH 58 (181)
Q Consensus 46 ~~~C~~C~k~F~~ 58 (181)
.+.|+.|+.-|.-
T Consensus 45 ~~vc~~c~~h~rl 57 (285)
T TIGR00515 45 LEVCPKCDHHMRM 57 (285)
T ss_pred CCCCCCCCCcCcC
Confidence 3578888886663
No 218
>PTZ00448 hypothetical protein; Provisional
Probab=28.15 E-value=34 Score=28.46 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=21.1
Q ss_pred ceecccchhhccChhhHHHHHHHh
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLY 32 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~h 32 (181)
.|.|..|+-.|......+.|+++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 588999999999888889998864
No 219
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.12 E-value=17 Score=25.44 Aligned_cols=16 Identities=25% Similarity=0.547 Sum_probs=12.1
Q ss_pred CCcccCCcccccCCCc
Q psy9958 44 EKTHKCPECKKAFRHK 59 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~ 59 (181)
+.|--|.-||++|...
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 4566788899988754
No 220
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=28.11 E-value=42 Score=26.98 Aligned_cols=26 Identities=31% Similarity=0.643 Sum_probs=22.8
Q ss_pred CCceecccchhhccChhhHHHHHHHh
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLY 32 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~h 32 (181)
..-|.|..|-+-|..+..|.+|+...
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C 71 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKC 71 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhC
Confidence 45699999999999999999998743
No 221
>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=27.97 E-value=11 Score=21.97 Aligned_cols=25 Identities=36% Similarity=0.755 Sum_probs=10.2
Q ss_pred CcccCCcccccCCCchhHHHHHHhc
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTLH 69 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~h 69 (181)
..|.|+.|...|----+.-.|..+|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 4566666666665554444444443
No 222
>KOG0782|consensus
Probab=27.66 E-value=23 Score=31.39 Aligned_cols=13 Identities=46% Similarity=0.910 Sum_probs=7.2
Q ss_pred cCCcccccCCCch
Q psy9958 48 KCPECKKAFRHKG 60 (181)
Q Consensus 48 ~C~~C~k~F~~~~ 60 (181)
+|..|||.|.++-
T Consensus 255 kC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 255 KCNTCGKGFQQKF 267 (1004)
T ss_pred ccchhhhhhhhhe
Confidence 4666666555443
No 223
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.55 E-value=16 Score=30.79 Aligned_cols=53 Identities=21% Similarity=0.358 Sum_probs=29.6
Q ss_pred eecccchhhccChhhHHHHHHHhcCCCCC---CCCCCCCcccCCcccccCCCchhHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYV---PPSPKEKTHKCPECKKAFRHKGNLL 63 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~hh~~~~~---~~~~~~~~~~C~~C~k~F~~~~~l~ 63 (181)
+.|+.||......... .++++++-+... ..+...+.|.|..|++.|.....+.
T Consensus 39 ~~CP~Cg~~~~~~~~~-~~~~I~~L~~~~~~~~L~~r~rR~~c~~c~~~~~~~~~~v 94 (402)
T COG3464 39 HRCPECGQRTIRRHGW-RIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRFAEKVDFV 94 (402)
T ss_pred CCCCCCCCcceecccc-ceeeeeecccCCeeEEEEeccceeecccCCCCcccchhhh
Confidence 7899999877333322 222333211000 1113357789999999996554443
No 224
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=26.70 E-value=57 Score=26.64 Aligned_cols=20 Identities=25% Similarity=0.469 Sum_probs=13.0
Q ss_pred ceecccchhhccChhhHHHH
Q psy9958 9 PYLCDHCDQTFRQKQLLKRH 28 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H 28 (181)
|..|+.|.-......+|.+-
T Consensus 322 Pi~CP~Csl~LilsthLarS 341 (421)
T COG5151 322 PISCPICSLQLILSTHLARS 341 (421)
T ss_pred CccCcchhHHHHHHHHHHHH
Confidence 56677787766666666543
No 225
>PF04641 Rtf2: Rtf2 RING-finger
Probab=26.39 E-value=5.2 Score=31.54 Aligned_cols=17 Identities=18% Similarity=0.567 Sum_probs=12.7
Q ss_pred CCCceecccchhhccCh
Q psy9958 6 DQNPYLCDHCDQTFRQK 22 (181)
Q Consensus 6 ~ekp~~C~~C~k~f~~~ 22 (181)
..-+|.|++.++.|...
T Consensus 110 ~~~~~~CPvt~~~~~~~ 126 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGK 126 (260)
T ss_pred CCceeECCCCCcccCCc
Confidence 35679999988888543
No 226
>KOG4602|consensus
Probab=26.34 E-value=20 Score=28.31 Aligned_cols=48 Identities=19% Similarity=0.234 Sum_probs=24.6
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCC
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFR 57 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~ 57 (181)
++..|-+|...-.....+..|.... ..-+-..+.-+.|.|++||.+=.
T Consensus 232 r~l~CvFC~nN~E~~A~y~tH~lkd--~dgRVLCPkLR~YVCPiCGATgD 279 (318)
T KOG4602|consen 232 RPLCCVFCFNNAEEFARYHTHPLKD--KDGRVLCPKLRSYVCPICGATGD 279 (318)
T ss_pred CceeEEeecCCCchhhheecccccC--CCCcEechhHhhhcCccccccCC
Confidence 4566777754433334444443221 00111123347799999998644
No 227
>PRK00420 hypothetical protein; Validated
Probab=25.73 E-value=39 Score=23.18 Aligned_cols=16 Identities=25% Similarity=0.366 Sum_probs=10.5
Q ss_pred CcccCCcccccCCCch
Q psy9958 45 KTHKCPECKKAFRHKG 60 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~ 60 (181)
....|+.||....-..
T Consensus 39 g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 39 GEVVCPVHGKVYIVKS 54 (112)
T ss_pred CceECCCCCCeeeecc
Confidence 3557888988655443
No 228
>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=25.72 E-value=23 Score=20.51 Aligned_cols=14 Identities=21% Similarity=0.641 Sum_probs=11.4
Q ss_pred ceecccchhhccCh
Q psy9958 9 PYLCDHCDQTFRQK 22 (181)
Q Consensus 9 p~~C~~C~k~f~~~ 22 (181)
.|+|..||+.|.-.
T Consensus 1 ~y~C~~CgyiYd~~ 14 (50)
T cd00730 1 KYECRICGYIYDPA 14 (50)
T ss_pred CcCCCCCCeEECCC
Confidence 37899999988864
No 229
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.38 E-value=27 Score=27.82 Aligned_cols=18 Identities=28% Similarity=0.578 Sum_probs=12.6
Q ss_pred CcccCCcccccCCCchhH
Q psy9958 45 KTHKCPECKKAFRHKGNL 62 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l 62 (181)
+.|.|+.||..+.+--+-
T Consensus 321 r~~~C~~cg~~~~rD~na 338 (364)
T COG0675 321 RLFKCPRCGFVHDRDVNA 338 (364)
T ss_pred eeEECCCCCCeehhhHHH
Confidence 678898898876654443
No 230
>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=25.15 E-value=23 Score=20.19 Aligned_cols=16 Identities=19% Similarity=0.567 Sum_probs=12.1
Q ss_pred ceecccchhhccChhh
Q psy9958 9 PYLCDHCDQTFRQKQL 24 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~ 24 (181)
.|+|.+|+..|.....
T Consensus 1 ky~C~~CgyvYd~~~G 16 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKG 16 (47)
T ss_dssp EEEETTTSBEEETTTB
T ss_pred CcCCCCCCEEEcCCcC
Confidence 4789999988876543
No 231
>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=25.12 E-value=40 Score=22.15 Aligned_cols=14 Identities=36% Similarity=0.738 Sum_probs=8.3
Q ss_pred CcccCCcccccCCC
Q psy9958 45 KTHKCPECKKAFRH 58 (181)
Q Consensus 45 ~~~~C~~C~k~F~~ 58 (181)
--|.|..|++.|..
T Consensus 52 GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 52 GIWKCKKCGKKFAG 65 (90)
T ss_dssp TEEEETTTTEEEE-
T ss_pred EEeecCCCCCEEeC
Confidence 34677777766654
No 232
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=25.03 E-value=30 Score=26.80 Aligned_cols=15 Identities=40% Similarity=0.738 Sum_probs=12.2
Q ss_pred CCceecccchhhccC
Q psy9958 7 QNPYLCDHCDQTFRQ 21 (181)
Q Consensus 7 ekp~~C~~C~k~f~~ 21 (181)
.++.+|..||..|+-
T Consensus 179 GkpqRCpECGqVFKL 193 (268)
T PTZ00043 179 GFLYRCGECDQIFML 193 (268)
T ss_pred CCCccCCCCCcEEEE
Confidence 458889999988884
No 233
>PTZ00064 histone acetyltransferase; Provisional
Probab=24.90 E-value=65 Score=28.13 Aligned_cols=26 Identities=23% Similarity=0.401 Sum_probs=20.6
Q ss_pred CCceecccchhhccChhhHHHHHHHh
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLY 32 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~h 32 (181)
...|.|.+|-+-|.....|.+|+...
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~C 303 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSRC 303 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhcC
Confidence 34688888888888888888887643
No 234
>KOG4727|consensus
Probab=24.58 E-value=35 Score=25.22 Aligned_cols=22 Identities=32% Similarity=0.649 Sum_probs=19.7
Q ss_pred eecccchhhccChhhHHHHHHH
Q psy9958 10 YLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 10 ~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
|-|.+|+-.|+...++..|+..
T Consensus 76 yyCdVCdcvvKDSinflDHiNg 97 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHING 97 (193)
T ss_pred eeeeecceeehhhHHHHHHhcc
Confidence 8899999999999999999763
No 235
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.53 E-value=28 Score=21.11 Aligned_cols=14 Identities=36% Similarity=0.804 Sum_probs=8.0
Q ss_pred CCcccCCcccccCC
Q psy9958 44 EKTHKCPECKKAFR 57 (181)
Q Consensus 44 ~~~~~C~~C~k~F~ 57 (181)
-+.|.|+.|.-+..
T Consensus 29 IrtymC~eC~~Rva 42 (68)
T COG4896 29 IRTYMCPECEHRVA 42 (68)
T ss_pred ceeEechhhHhhhc
Confidence 35566776654444
No 236
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=24.18 E-value=33 Score=20.24 Aligned_cols=30 Identities=13% Similarity=0.313 Sum_probs=17.8
Q ss_pred cccCCcccccCCCchhHHHHHHhcCCCChhHHHHHHHh
Q psy9958 46 THKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALK 83 (181)
Q Consensus 46 ~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~~~~~~~~ 83 (181)
.|.|+.||..+.-.... .+ ....|..|+..
T Consensus 2 ~~~CP~CG~~iev~~~~-------~G-eiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPE-------LG-ELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCc-------cC-CEEeCCCCCCE
Confidence 36899999977654332 12 23356666654
No 237
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=24.16 E-value=51 Score=28.32 Aligned_cols=40 Identities=23% Similarity=0.561 Sum_probs=28.6
Q ss_pred CCceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCC
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCP 50 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~ 50 (181)
...|.|..|-+-|.....|.+|+..... +.++|..-|.+.
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~C~~----~~PPG~eIYr~~ 235 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKKCDL----KHPPGDEIYRHP 235 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhcCCC----CCCCcCeEEEcC
Confidence 4569999999999999999999874321 112455556543
No 238
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=24.15 E-value=57 Score=26.33 Aligned_cols=12 Identities=33% Similarity=0.971 Sum_probs=8.4
Q ss_pred cccCCcccccCC
Q psy9958 46 THKCPECKKAFR 57 (181)
Q Consensus 46 ~~~C~~C~k~F~ 57 (181)
.+.|+.|+.-|.
T Consensus 46 ~~vc~~c~~h~r 57 (292)
T PRK05654 46 LNVCPKCGHHMR 57 (292)
T ss_pred CCCCCCCCCCee
Confidence 357888887665
No 239
>PLN03239 histone acetyltransferase; Provisional
Probab=24.00 E-value=54 Score=27.16 Aligned_cols=25 Identities=24% Similarity=0.316 Sum_probs=21.8
Q ss_pred CCceecccchhhccChhhHHHHHHH
Q psy9958 7 QNPYLCDHCDQTFRQKQLLKRHVNL 31 (181)
Q Consensus 7 ekp~~C~~C~k~f~~~~~L~~H~~~ 31 (181)
..-|.|..|-+-|.+...|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4579999999999999999999753
No 240
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=23.97 E-value=15 Score=25.25 Aligned_cols=14 Identities=29% Similarity=0.712 Sum_probs=11.0
Q ss_pred CcccCCcccccCCC
Q psy9958 45 KTHKCPECKKAFRH 58 (181)
Q Consensus 45 ~~~~C~~C~k~F~~ 58 (181)
.-|.|..||..|+.
T Consensus 99 ~Fy~C~~Cg~~wre 112 (113)
T COG1594 99 RFYKCTRCGYRWRE 112 (113)
T ss_pred EEEEecccCCEeec
Confidence 45899999988763
No 241
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.38 E-value=26 Score=20.17 Aligned_cols=17 Identities=24% Similarity=0.749 Sum_probs=12.6
Q ss_pred ccCCcccccCCCchhHH
Q psy9958 47 HKCPECKKAFRHKGNLL 63 (181)
Q Consensus 47 ~~C~~C~k~F~~~~~l~ 63 (181)
-.|+.|++.|.-...+.
T Consensus 13 KICpvCqRPFsWRkKW~ 29 (54)
T COG4338 13 KICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhhcCchHHHHHHH
Confidence 36999999998654443
No 242
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=23.19 E-value=47 Score=27.59 Aligned_cols=23 Identities=17% Similarity=0.488 Sum_probs=16.0
Q ss_pred CCcccCCccc-ccCCCchhHHHHH
Q psy9958 44 EKTHKCPECK-KAFRHKGNLLRHM 66 (181)
Q Consensus 44 ~~~~~C~~C~-k~F~~~~~l~~H~ 66 (181)
.+-|.|.+|| +.+..+..+.+|.
T Consensus 372 d~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 372 DIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred CcceeeeecccccccchHHHHhhh
Confidence 4667777777 6666667777664
No 243
>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=22.36 E-value=10 Score=31.30 Aligned_cols=44 Identities=18% Similarity=0.338 Sum_probs=19.5
Q ss_pred CceecccchhhccChhhHH---HHHHHhcCCCCCCCCCCCCcccCCcccccCCC
Q psy9958 8 NPYLCDHCDQTFRQKQLLK---RHVNLYHNPHYVPPSPKEKTHKCPECKKAFRH 58 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~---~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~ 58 (181)
+-+.|..|.+.+-.....- .|....+. .-.+-|+|..|++++..
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~-------a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHD-------AVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEE-------EE-EEEE-T-TS-EEEE
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEee-------eeeeeEECCCCCCeeee
Confidence 3478999988666654443 22221111 22356799999987554
No 244
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=21.99 E-value=71 Score=25.74 Aligned_cols=25 Identities=40% Similarity=0.615 Sum_probs=22.6
Q ss_pred CCcccCCcccccCCCchhHHHHHHh
Q psy9958 44 EKTHKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
...|.|..|-+-|.+...|.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 5689999999999999999999863
No 245
>KOG0943|consensus
Probab=21.98 E-value=62 Score=31.79 Aligned_cols=37 Identities=14% Similarity=0.418 Sum_probs=0.0
Q ss_pred cCcccccCCCCCCccCcccccccccCCCCCCCCceEE
Q psy9958 94 DGHKVEVIPDDEEEEEGEETEEEEEGGGEDDGHQYVV 130 (181)
Q Consensus 94 ~~~~~~~~~~~~~~e~~e~~~~e~~~~~~~~~~~~~~ 130 (181)
.+.......+.+++++++++.+++++++++|+.++..
T Consensus 1731 ~GEed~~Dddnddddddd~EaEdddDddDdDdeD~d~ 1767 (3015)
T KOG0943|consen 1731 AGEEDHHDDDNDDDDDDDAEAEDDDDDDDDDDEDMDL 1767 (3015)
T ss_pred cCcccccccccccccccchhhcccccccccccccccc
No 246
>KOG2593|consensus
Probab=21.97 E-value=56 Score=27.80 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=16.7
Q ss_pred CCCcccCCcccccCCCchhHH
Q psy9958 43 KEKTHKCPECKKAFRHKGNLL 63 (181)
Q Consensus 43 ~~~~~~C~~C~k~F~~~~~l~ 63 (181)
...-|.|+.|.+.|..-..++
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred ccccccCCccccchhhhHHHH
Confidence 356799999999998766654
No 247
>KOG1280|consensus
Probab=21.90 E-value=45 Score=27.53 Aligned_cols=38 Identities=18% Similarity=0.298 Sum_probs=27.9
Q ss_pred CCcccCCcccccCCCchhHHHHHHhcCCCChh--HHHHHH
Q psy9958 44 EKTHKCPECKKAFRHKGNLLRHMTLHDPDSEL--IEQQVA 81 (181)
Q Consensus 44 ~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~--~~~~~~ 81 (181)
..-|.|+.|++.=.+...|..|...-|.+..+ .|..|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 45799999999888889999998766655543 344443
No 248
>KOG4118|consensus
Probab=21.51 E-value=52 Score=20.24 Aligned_cols=31 Identities=23% Similarity=0.467 Sum_probs=23.1
Q ss_pred CcccCCcccccCCCchhHHHHHHhcCCCChh
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTLHDPDSEL 75 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~ 75 (181)
..|+|.+|--...-...+..|....++..++
T Consensus 37 L~~kCtVC~~~mpdpktfkqhfe~kHpk~~~ 67 (74)
T KOG4118|consen 37 LHHKCTVCMVQMPDPKTFKQHFENKHPKEPL 67 (74)
T ss_pred HHhhhHhhHhhCCCCchHHHHHhhcCCCCCC
Confidence 3578999988777788888887776665554
No 249
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=21.45 E-value=41 Score=24.23 Aligned_cols=19 Identities=21% Similarity=0.501 Sum_probs=14.7
Q ss_pred CcccCCcccccCCCchhHH
Q psy9958 45 KTHKCPECKKAFRHKGNLL 63 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~ 63 (181)
+.-.|..|+++|++--...
T Consensus 27 RRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 27 RRRECLECHERFTTFERAE 45 (147)
T ss_pred ecccCCccCCccceeeecc
Confidence 4568999999999865543
No 250
>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=21.32 E-value=45 Score=17.52 Aligned_cols=23 Identities=17% Similarity=0.522 Sum_probs=13.7
Q ss_pred CcccCCcccccCCCchhHHHHHHh
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTL 68 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~ 68 (181)
..|.|+.|++.+.. +-+..|+..
T Consensus 3 ~~~~C~nC~R~v~a-~RfA~HLek 25 (33)
T PF08209_consen 3 PYVECPNCGRPVAA-SRFAPHLEK 25 (33)
T ss_dssp -EEE-TTTSSEEEG-GGHHHHHHH
T ss_pred CeEECCCCcCCcch-hhhHHHHHH
Confidence 35678888886553 556677543
No 251
>KOG2807|consensus
Probab=21.15 E-value=1.1e+02 Score=25.13 Aligned_cols=60 Identities=25% Similarity=0.408 Sum_probs=37.5
Q ss_pred CceecccchhhccChhhHHHHHHHhcCCC---CC-------------CCC----CCCCcccCCcccccCCCchhHHHHHH
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPH---YV-------------PPS----PKEKTHKCPECKKAFRHKGNLLRHMT 67 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~~~---~~-------------~~~----~~~~~~~C~~C~k~F~~~~~l~~H~~ 67 (181)
-|-.|+.|+-......+|.+-. ||... |. ... .....|.|..|-..|----+.-.|-.
T Consensus 289 LP~eCpiC~ltLVss~hLARSy--hhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSY--HHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCccCCccceeEecchHHHHHH--HhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhh
Confidence 4677999999988888887653 33211 00 000 22345777777777777777666766
Q ss_pred hc
Q psy9958 68 LH 69 (181)
Q Consensus 68 ~h 69 (181)
.|
T Consensus 367 Lh 368 (378)
T KOG2807|consen 367 LH 368 (378)
T ss_pred hh
Confidence 55
No 252
>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=21.02 E-value=46 Score=18.04 Aligned_cols=10 Identities=40% Similarity=0.667 Sum_probs=4.2
Q ss_pred CcccCCcccc
Q psy9958 45 KTHKCPECKK 54 (181)
Q Consensus 45 ~~~~C~~C~k 54 (181)
+.|.|.+|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 4455555554
No 253
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=20.91 E-value=39 Score=17.46 Aligned_cols=13 Identities=23% Similarity=0.744 Sum_probs=9.3
Q ss_pred Cceecccchhhcc
Q psy9958 8 NPYLCDHCDQTFR 20 (181)
Q Consensus 8 kp~~C~~C~k~f~ 20 (181)
+.|+|..||..+.
T Consensus 6 ~~ykC~~Cgniv~ 18 (34)
T TIGR00319 6 QVYKCEVCGNIVE 18 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4688888886653
No 254
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=20.88 E-value=31 Score=27.13 Aligned_cols=54 Identities=20% Similarity=0.530 Sum_probs=26.8
Q ss_pred CCCceecccchhhccChhhHHHHHHHhc--CCCCCCCCC----CCCcccCCcccccCCCc
Q psy9958 6 DQNPYLCDHCDQTFRQKQLLKRHVNLYH--NPHYVPPSP----KEKTHKCPECKKAFRHK 59 (181)
Q Consensus 6 ~ekp~~C~~C~k~f~~~~~L~~H~~~hh--~~~~~~~~~----~~~~~~C~~C~k~F~~~ 59 (181)
..+.|.|..|...+=++-.-++-....+ ...|-+.+. |---|.|+.|+..|+.-
T Consensus 109 ~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 109 VDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred cceeeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccchhh
Confidence 3477999999765443322221111111 011222221 12347899998888754
No 255
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=20.86 E-value=41 Score=17.44 Aligned_cols=13 Identities=23% Similarity=0.744 Sum_probs=8.3
Q ss_pred Cceecccchhhcc
Q psy9958 8 NPYLCDHCDQTFR 20 (181)
Q Consensus 8 kp~~C~~C~k~f~ 20 (181)
+.|+|..||..+.
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 3577777776553
No 256
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.62 E-value=83 Score=23.81 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=9.3
Q ss_pred CCcccCCcccccCC
Q psy9958 44 EKTHKCPECKKAFR 57 (181)
Q Consensus 44 ~~~~~C~~C~k~F~ 57 (181)
...+.|..||..+.
T Consensus 28 ~~lvrC~eCG~V~~ 41 (201)
T COG1326 28 EPLVRCEECGTVHP 41 (201)
T ss_pred ceEEEccCCCcEee
Confidence 35677888877653
No 257
>PRK06450 threonine synthase; Validated
Probab=20.62 E-value=54 Score=26.90 Aligned_cols=10 Identities=20% Similarity=0.600 Sum_probs=7.8
Q ss_pred eecccchhhc
Q psy9958 10 YLCDHCDQTF 19 (181)
Q Consensus 10 ~~C~~C~k~f 19 (181)
++|..||+.|
T Consensus 4 ~~C~~Cg~~~ 13 (338)
T PRK06450 4 EVCMKCGKER 13 (338)
T ss_pred eEECCcCCcC
Confidence 6788888776
No 258
>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=20.62 E-value=34 Score=18.51 Aligned_cols=11 Identities=36% Similarity=1.210 Sum_probs=8.4
Q ss_pred eecccchhhcc
Q psy9958 10 YLCDHCDQTFR 20 (181)
Q Consensus 10 ~~C~~C~k~f~ 20 (181)
|.|..|++.|+
T Consensus 29 y~C~~C~~~wr 39 (39)
T PF01096_consen 29 YVCCNCGHRWR 39 (39)
T ss_dssp EEESSSTEEEE
T ss_pred EEeCCCCCeeC
Confidence 78888887763
No 259
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.60 E-value=42 Score=25.22 Aligned_cols=9 Identities=22% Similarity=0.693 Sum_probs=4.4
Q ss_pred CcccCCccc
Q psy9958 45 KTHKCPECK 53 (181)
Q Consensus 45 ~~~~C~~C~ 53 (181)
..|.|+.|.
T Consensus 153 ~~f~CplC~ 161 (187)
T PRK12722 153 GSFVCGLCQ 161 (187)
T ss_pred CCCcCCCCC
Confidence 345555554
No 260
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.12 E-value=71 Score=23.76 Aligned_cols=14 Identities=29% Similarity=0.914 Sum_probs=8.4
Q ss_pred CCceecccchhhcc
Q psy9958 7 QNPYLCDHCDQTFR 20 (181)
Q Consensus 7 ekp~~C~~C~k~f~ 20 (181)
..-|.|+.|.-.|+
T Consensus 111 ~~~y~C~~~~~r~s 124 (176)
T COG1675 111 NNYYVCPNCHVKYS 124 (176)
T ss_pred CCceeCCCCCCccc
Confidence 44577766665554
No 261
>KOG1842|consensus
Probab=20.12 E-value=50 Score=28.27 Aligned_cols=28 Identities=21% Similarity=0.437 Sum_probs=20.3
Q ss_pred CcccCCcccccCCCchhHHHHHHh-cCCC
Q psy9958 45 KTHKCPECKKAFRHKGNLLRHMTL-HDPD 72 (181)
Q Consensus 45 ~~~~C~~C~k~F~~~~~l~~H~~~-h~~~ 72 (181)
.-|.||+|.+-|..-..|..|.-. |..+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 457888888888888888888654 4433
No 262
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=20.09 E-value=94 Score=23.52 Aligned_cols=18 Identities=17% Similarity=0.442 Sum_probs=10.1
Q ss_pred cCCCCceecccchhhccC
Q psy9958 4 HIDQNPYLCDHCDQTFRQ 21 (181)
Q Consensus 4 Ht~ekp~~C~~C~k~f~~ 21 (181)
|-.-....|..|+..|..
T Consensus 90 HG~~~~~~C~~C~~~~~~ 107 (206)
T cd01410 90 HGNMFIEVCKSCGPEYVR 107 (206)
T ss_pred cCCcCcccCCCCCCccch
Confidence 444445567777765543
No 263
>KOG1842|consensus
Probab=20.05 E-value=61 Score=27.80 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=24.0
Q ss_pred CceecccchhhccChhhHHHHHHHhcC
Q psy9958 8 NPYLCDHCDQTFRQKQLLKRHVNLYHN 34 (181)
Q Consensus 8 kp~~C~~C~k~f~~~~~L~~H~~~hh~ 34 (181)
.-|.|++|.+-|.+...|..|.-.-|.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcc
Confidence 458999999999999999999887764
No 264
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=20.02 E-value=7.6 Score=23.97 Aligned_cols=41 Identities=17% Similarity=0.490 Sum_probs=20.8
Q ss_pred ceecccchhhccChhhHHHHHHHhcCCCCCCCCCCCCcccCCcccccCCCchh
Q psy9958 9 PYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGN 61 (181)
Q Consensus 9 p~~C~~C~k~f~~~~~L~~H~~~hh~~~~~~~~~~~~~~~C~~C~k~F~~~~~ 61 (181)
-|.|..|+.+-.. .+.++. .+ .|..-.+|+-|.....-..+
T Consensus 4 ~FTC~~C~~Rs~~--~~sk~a-Y~---------~GvViv~C~gC~~~HlIaDn 44 (66)
T PF05180_consen 4 TFTCNKCGTRSAK--MFSKQA-YH---------KGVVIVQCPGCKNRHLIADN 44 (66)
T ss_dssp EEEETTTTEEEEE--EEEHHH-HH---------TSEEEEE-TTS--EEES--S
T ss_pred EEEcCCCCCccce--eeCHHH-Hh---------CCeEEEECCCCcceeeehhh
Confidence 3889999854332 333332 22 36677789999765443333
Done!