Query psy12010
Match_columns 99
No_of_seqs 115 out of 1128
Neff 10.3
Searched_HMMs 46136
Date Fri Aug 16 16:23:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12010.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12010hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 2.7E-21 5.9E-26 119.4 3.1 80 16-96 186-265 (279)
2 KOG2462|consensus 99.8 7E-19 1.5E-23 108.8 3.6 82 15-99 159-240 (279)
3 KOG3623|consensus 99.6 4.4E-16 9.6E-21 106.8 -0.1 83 12-95 889-971 (1007)
4 KOG3576|consensus 99.4 2.1E-14 4.5E-19 86.1 -2.2 80 19-99 119-198 (267)
5 KOG3623|consensus 99.3 2.7E-13 5.9E-18 93.4 -1.2 80 15-95 238-330 (1007)
6 PHA02768 hypothetical protein; 99.2 3.4E-12 7.4E-17 61.7 1.8 43 46-91 6-48 (55)
7 PHA00733 hypothetical protein 99.2 2E-11 4.3E-16 69.5 3.9 56 41-99 69-124 (128)
8 KOG1074|consensus 99.2 2.7E-12 5.8E-17 89.5 0.3 88 12-99 600-693 (958)
9 KOG3576|consensus 99.1 2.7E-11 5.9E-16 72.8 2.2 80 19-98 147-236 (267)
10 KOG1074|consensus 99.0 3.6E-11 7.8E-16 84.0 -0.3 52 46-98 354-405 (958)
11 PF13465 zf-H2C2_2: Zinc-finge 98.8 2.7E-09 5.9E-14 44.4 1.7 26 60-86 1-26 (26)
12 PHA00732 hypothetical protein 98.7 9.9E-09 2.1E-13 53.7 2.5 46 45-97 1-47 (79)
13 PHA00616 hypothetical protein 98.6 1.4E-08 3E-13 47.0 1.3 34 45-79 1-34 (44)
14 PF05605 zf-Di19: Drought indu 98.5 2E-07 4.4E-12 45.4 4.0 52 45-99 2-54 (54)
15 KOG3608|consensus 98.5 1.6E-08 3.5E-13 65.5 -0.7 77 19-95 179-258 (467)
16 PHA00616 hypothetical protein 98.5 7.8E-08 1.7E-12 44.5 1.3 26 74-99 1-26 (44)
17 KOG3608|consensus 98.4 3.2E-08 6.9E-13 64.1 -0.4 56 40-97 287-344 (467)
18 KOG3993|consensus 98.4 1.4E-08 2.9E-13 67.0 -2.3 86 13-98 263-380 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.3 5.8E-08 1.3E-12 40.3 -0.6 24 34-57 3-26 (26)
20 PF00096 zf-C2H2: Zinc finger, 98.3 3.6E-07 7.8E-12 36.7 1.8 22 75-96 1-22 (23)
21 PHA02768 hypothetical protein; 98.3 3.6E-07 7.9E-12 44.3 1.9 24 75-98 6-29 (55)
22 PF00096 zf-C2H2: Zinc finger, 98.3 5.9E-07 1.3E-11 36.0 1.7 23 46-68 1-23 (23)
23 PF13894 zf-C2H2_4: C2H2-type 98.2 1.6E-06 3.4E-11 34.8 2.2 24 75-98 1-24 (24)
24 PF13912 zf-C2H2_6: C2H2-type 98.2 1.1E-06 2.5E-11 36.6 1.6 24 75-98 2-25 (27)
25 PLN03086 PRLI-interacting fact 98.0 7.5E-06 1.6E-10 56.6 4.1 38 44-84 477-514 (567)
26 PHA00733 hypothetical protein 98.0 3.1E-06 6.7E-11 48.3 1.8 56 41-97 36-96 (128)
27 PLN03086 PRLI-interacting fact 98.0 5.3E-06 1.2E-10 57.3 2.8 75 19-98 480-564 (567)
28 COG5189 SFP1 Putative transcri 98.0 2.1E-06 4.5E-11 55.2 0.6 54 42-95 346-419 (423)
29 PF13894 zf-C2H2_4: C2H2-type 97.9 1.1E-05 2.3E-10 32.3 2.0 23 46-68 1-23 (24)
30 PF13912 zf-C2H2_6: C2H2-type 97.9 7.3E-06 1.6E-10 34.0 1.5 26 45-70 1-26 (27)
31 PF09237 GAGA: GAGA factor; I 97.8 4.5E-05 9.8E-10 36.2 3.1 34 40-73 19-52 (54)
32 PF12756 zf-C2H2_2: C2H2 type 97.8 2.3E-05 4.9E-10 42.2 2.4 23 75-97 51-73 (100)
33 smart00355 ZnF_C2H2 zinc finge 97.7 4.9E-05 1.1E-09 30.7 2.4 23 75-97 1-23 (26)
34 PF09237 GAGA: GAGA factor; I 97.5 7.7E-05 1.7E-09 35.5 1.8 37 63-99 13-49 (54)
35 smart00355 ZnF_C2H2 zinc finge 97.5 8.4E-05 1.8E-09 29.9 1.8 24 46-69 1-24 (26)
36 PF13909 zf-H2C2_5: C2H2-type 97.4 0.00011 2.4E-09 29.6 1.8 24 75-99 1-24 (24)
37 PRK04860 hypothetical protein; 97.4 0.00012 2.6E-09 43.3 2.5 39 44-87 118-156 (160)
38 KOG3993|consensus 97.4 2.2E-05 4.8E-10 52.3 -0.7 53 45-98 267-319 (500)
39 PF12874 zf-met: Zinc-finger o 97.1 0.00032 7E-09 28.3 1.5 20 47-66 2-21 (25)
40 PF12874 zf-met: Zinc-finger o 97.1 0.00032 7E-09 28.3 1.4 23 75-97 1-23 (25)
41 PF05605 zf-Di19: Drought indu 97.0 0.00025 5.4E-09 34.4 0.8 51 17-69 2-53 (54)
42 PF13909 zf-H2C2_5: C2H2-type 96.6 0.0023 5E-08 25.5 2.0 23 46-69 1-23 (24)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0015 3.3E-08 26.9 1.2 22 46-67 2-23 (27)
44 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.001 2.2E-08 27.5 0.6 22 75-96 2-23 (27)
45 PF13913 zf-C2HC_2: zinc-finge 96.0 0.0096 2.1E-07 24.2 2.2 21 75-96 3-23 (25)
46 smart00451 ZnF_U1 U1-like zinc 95.4 0.014 3.1E-07 25.2 1.8 21 75-95 4-24 (35)
47 PHA00732 hypothetical protein 95.0 0.0098 2.1E-07 31.1 0.6 47 18-70 2-49 (79)
48 COG5048 FOG: Zn-finger [Genera 94.8 0.0069 1.5E-07 40.1 -0.4 54 44-98 288-347 (467)
49 KOG2893|consensus 94.5 0.0093 2E-07 37.5 -0.2 42 47-93 12-53 (341)
50 COG5189 SFP1 Putative transcri 93.8 0.018 3.8E-07 37.7 -0.0 25 42-66 395-419 (423)
51 PF12756 zf-C2H2_2: C2H2 type 93.5 0.069 1.5E-06 28.4 2.0 25 45-69 50-74 (100)
52 KOG1146|consensus 93.4 0.066 1.4E-06 41.0 2.4 55 41-96 461-540 (1406)
53 cd00350 rubredoxin_like Rubred 93.0 0.086 1.9E-06 22.8 1.6 24 46-82 2-25 (33)
54 PF05443 ROS_MUCR: ROS/MUCR tr 92.5 0.082 1.8E-06 30.4 1.5 22 75-99 73-94 (132)
55 cd00729 rubredoxin_SM Rubredox 92.1 0.13 2.9E-06 22.4 1.6 25 45-82 2-26 (34)
56 KOG2186|consensus 91.8 0.12 2.5E-06 32.9 1.7 44 46-93 4-47 (276)
57 COG1592 Rubrerythrin [Energy p 91.7 0.17 3.6E-06 30.3 2.1 25 44-82 133-157 (166)
58 TIGR02098 MJ0042_CXXC MJ0042 f 91.3 0.18 3.9E-06 22.3 1.6 34 46-85 3-36 (38)
59 PF13719 zinc_ribbon_5: zinc-r 90.9 0.22 4.7E-06 22.1 1.7 34 46-85 3-36 (37)
60 PF09538 FYDLN_acid: Protein o 90.8 0.2 4.3E-06 27.9 1.7 30 46-87 10-39 (108)
61 PF09986 DUF2225: Uncharacteri 90.6 0.076 1.6E-06 33.0 -0.0 45 43-87 3-61 (214)
62 PRK00464 nrdR transcriptional 90.5 0.067 1.5E-06 31.6 -0.3 12 46-57 29-40 (154)
63 PRK04860 hypothetical protein; 88.7 0.1 2.2E-06 31.0 -0.4 30 29-58 127-156 (160)
64 smart00531 TFIIE Transcription 88.5 0.66 1.4E-05 27.1 2.9 39 42-85 96-134 (147)
65 COG4049 Uncharacterized protei 88.3 0.28 6.1E-06 23.9 1.0 30 41-70 13-42 (65)
66 smart00659 RPOLCX RNA polymera 88.2 0.49 1.1E-05 21.9 1.8 26 46-83 3-28 (44)
67 PF13717 zinc_ribbon_4: zinc-r 88.0 0.53 1.1E-05 20.7 1.7 33 46-84 3-35 (36)
68 PF12013 DUF3505: Protein of u 87.8 0.56 1.2E-05 25.8 2.2 25 75-99 81-109 (109)
69 COG1997 RPL43A Ribosomal prote 87.7 0.25 5.5E-06 26.3 0.7 32 44-86 34-65 (89)
70 COG4957 Predicted transcriptio 87.7 0.27 5.9E-06 28.3 0.9 22 75-99 77-98 (148)
71 smart00834 CxxC_CXXC_SSSS Puta 87.6 0.28 6.1E-06 21.8 0.8 31 45-83 5-35 (41)
72 PF02892 zf-BED: BED zinc fing 87.1 0.74 1.6E-05 20.9 2.1 21 75-95 17-41 (45)
73 TIGR02605 CxxC_CxxC_SSSS putat 87.0 0.29 6.2E-06 23.2 0.6 29 46-82 6-34 (52)
74 TIGR00373 conserved hypothetic 86.3 0.77 1.7E-05 27.2 2.3 35 41-85 105-139 (158)
75 COG4049 Uncharacterized protei 86.2 0.4 8.6E-06 23.4 0.9 29 69-98 13-41 (65)
76 COG2888 Predicted Zn-ribbon RN 86.2 0.75 1.6E-05 22.7 1.8 33 44-82 26-58 (61)
77 PF09723 Zn-ribbon_8: Zinc rib 85.7 0.33 7E-06 22.1 0.4 29 46-82 6-34 (42)
78 COG5048 FOG: Zn-finger [Genera 85.6 0.69 1.5E-05 30.6 2.1 60 18-78 290-355 (467)
79 smart00614 ZnF_BED BED zinc fi 85.0 0.84 1.8E-05 21.5 1.7 21 75-95 19-44 (50)
80 TIGR02300 FYDLN_acid conserved 85.0 0.68 1.5E-05 26.5 1.5 30 46-87 10-39 (129)
81 PRK06266 transcription initiat 84.6 1 2.2E-05 27.3 2.3 34 42-85 114-147 (178)
82 PRK09678 DNA-binding transcrip 83.7 0.44 9.5E-06 24.5 0.4 12 75-86 28-41 (72)
83 PF04959 ARS2: Arsenite-resist 83.3 0.7 1.5E-05 28.8 1.3 24 75-98 78-101 (214)
84 PF03604 DNA_RNApol_7kD: DNA d 82.6 0.89 1.9E-05 19.5 1.1 26 46-83 1-26 (32)
85 PRK00398 rpoP DNA-directed RNA 82.4 0.7 1.5E-05 21.3 0.8 29 45-84 3-31 (46)
86 COG1996 RPC10 DNA-directed RNA 82.1 1 2.2E-05 21.4 1.3 29 44-83 5-33 (49)
87 COG4306 Uncharacterized protei 80.5 0.7 1.5E-05 26.4 0.5 42 46-87 40-81 (160)
88 smart00734 ZnF_Rad18 Rad18-lik 79.4 1.8 4E-05 17.5 1.5 19 47-66 3-21 (26)
89 PRK14890 putative Zn-ribbon RN 78.1 2 4.3E-05 21.2 1.6 33 44-82 24-56 (59)
90 PF08790 zf-LYAR: LYAR-type C2 77.1 1 2.2E-05 18.8 0.3 11 46-56 1-11 (28)
91 KOG4167|consensus 75.7 0.52 1.1E-05 34.5 -1.1 24 74-97 792-815 (907)
92 PF05191 ADK_lid: Adenylate ki 75.1 2 4.2E-05 18.9 1.0 33 46-87 2-34 (36)
93 PF07754 DUF1610: Domain of un 73.4 1.8 3.9E-05 17.3 0.6 10 44-53 15-24 (24)
94 PF12013 DUF3505: Protein of u 73.2 3.2 6.9E-05 22.8 1.8 25 46-70 81-109 (109)
95 KOG4173|consensus 73.0 1.4 3E-05 27.5 0.3 50 47-97 108-169 (253)
96 KOG4167|consensus 72.6 0.93 2E-05 33.2 -0.5 27 44-70 791-817 (907)
97 PF13878 zf-C2H2_3: zinc-finge 72.3 3.9 8.5E-05 18.5 1.7 24 46-69 14-39 (41)
98 PHA00626 hypothetical protein 71.9 2.2 4.9E-05 20.8 0.9 16 72-88 22-37 (59)
99 KOG2593|consensus 71.9 2.9 6.4E-05 28.8 1.7 40 41-84 124-163 (436)
100 KOG2482|consensus 71.5 2.3 5E-05 28.5 1.1 23 45-67 195-217 (423)
101 COG2331 Uncharacterized protei 71.1 1 2.2E-05 23.4 -0.4 32 45-84 12-43 (82)
102 PF07975 C1_4: TFIIH C1-like d 69.5 1.9 4.2E-05 20.6 0.4 27 43-69 19-45 (51)
103 PF01780 Ribosomal_L37ae: Ribo 69.2 1.1 2.4E-05 24.1 -0.6 31 44-85 34-64 (90)
104 TIGR00280 L37a ribosomal prote 68.6 1.7 3.6E-05 23.4 0.1 31 44-85 34-64 (91)
105 KOG2231|consensus 68.5 4.3 9.4E-05 29.7 2.0 20 48-67 185-204 (669)
106 KOG2785|consensus 68.4 5.7 0.00012 27.0 2.5 53 44-96 165-242 (390)
107 TIGR00622 ssl1 transcription f 68.2 15 0.00033 20.6 3.8 23 75-97 82-104 (112)
108 PF10571 UPF0547: Uncharacteri 68.1 3.2 7E-05 16.8 0.9 11 75-85 15-25 (26)
109 KOG1146|consensus 66.9 6.5 0.00014 31.0 2.7 50 48-98 439-489 (1406)
110 PTZ00255 60S ribosomal protein 65.6 2.7 5.9E-05 22.6 0.5 32 44-86 35-66 (90)
111 KOG3408|consensus 65.5 3.7 8E-05 23.3 1.0 22 75-96 58-79 (129)
112 COG1327 Predicted transcriptio 64.6 2.2 4.7E-05 25.2 0.0 12 47-58 30-41 (156)
113 PF03811 Zn_Tnp_IS1: InsA N-te 64.2 2 4.2E-05 19.0 -0.2 30 46-80 6-35 (36)
114 PRK03976 rpl37ae 50S ribosomal 62.1 2.4 5.1E-05 22.8 -0.1 31 44-85 35-65 (90)
115 KOG2071|consensus 62.0 5.6 0.00012 28.6 1.6 28 42-69 415-442 (579)
116 PF08274 PhnA_Zn_Ribbon: PhnA 62.0 3.7 7.9E-05 17.3 0.5 9 75-83 20-28 (30)
117 COG5236 Uncharacterized conser 61.2 11 0.00024 25.6 2.7 48 47-96 222-273 (493)
118 PF02176 zf-TRAF: TRAF-type zi 60.9 3.8 8.3E-05 19.6 0.5 41 44-86 8-54 (60)
119 smart00154 ZnF_AN1 AN1-like Zi 60.7 4.8 0.0001 18.0 0.8 12 75-86 13-24 (39)
120 PRK03824 hypA hydrogenase nick 60.6 4.9 0.00011 23.2 1.0 15 44-58 69-83 (135)
121 PF15269 zf-C2H2_7: Zinc-finge 60.4 7.3 0.00016 18.1 1.3 20 75-94 21-40 (54)
122 TIGR00244 transcriptional regu 60.1 2.7 5.8E-05 24.7 -0.2 12 47-58 30-41 (147)
123 PF09963 DUF2197: Uncharacteri 56.5 4.4 9.6E-05 19.8 0.3 37 47-83 4-40 (56)
124 PF12760 Zn_Tnp_IS1595: Transp 55.7 4.4 9.6E-05 18.6 0.2 27 46-82 19-45 (46)
125 KOG1280|consensus 54.2 13 0.00028 25.1 2.2 40 42-81 76-116 (381)
126 PF01927 Mut7-C: Mut7-C RNAse 54.0 9.4 0.0002 22.2 1.4 22 42-63 121-142 (147)
127 PF01428 zf-AN1: AN1-like Zinc 53.6 5 0.00011 18.2 0.2 12 74-85 13-24 (43)
128 COG4530 Uncharacterized protei 53.6 6.9 0.00015 21.9 0.8 12 74-85 26-37 (129)
129 COG4640 Predicted membrane pro 53.5 10 0.00022 26.1 1.7 14 46-59 16-29 (465)
130 KOG2636|consensus 53.4 9.3 0.0002 26.7 1.5 31 36-66 392-423 (497)
131 KOG2071|consensus 53.3 9.8 0.00021 27.4 1.6 24 74-97 418-441 (579)
132 COG4888 Uncharacterized Zn rib 51.9 2.9 6.4E-05 22.9 -0.8 39 42-85 19-57 (104)
133 PF10013 DUF2256: Uncharacteri 51.0 12 0.00025 17.2 1.2 15 76-90 10-24 (42)
134 PF13451 zf-trcl: Probable zin 50.5 7.9 0.00017 18.4 0.6 17 43-59 2-18 (49)
135 PF14446 Prok-RING_1: Prokaryo 50.3 13 0.00028 18.1 1.3 10 47-56 7-16 (54)
136 PF07503 zf-HYPF: HypF finger; 50.0 3.4 7.3E-05 18.1 -0.7 11 75-85 22-32 (35)
137 KOG2482|consensus 49.7 9.9 0.00022 25.7 1.2 53 43-96 142-217 (423)
138 TIGR00100 hypA hydrogenase nic 47.5 11 0.00025 21.0 1.1 27 44-83 69-95 (115)
139 PF08209 Sgf11: Sgf11 (transcr 47.0 22 0.00047 15.3 1.7 10 75-84 5-14 (33)
140 PF10263 SprT-like: SprT-like 46.2 8 0.00017 22.4 0.3 32 45-85 123-154 (157)
141 PF01363 FYVE: FYVE zinc finge 45.8 12 0.00025 18.6 0.9 10 47-56 11-20 (69)
142 PLN02294 cytochrome c oxidase 45.4 12 0.00026 22.7 0.9 17 42-58 138-154 (174)
143 PRK12380 hydrogenase nickel in 45.1 15 0.00032 20.5 1.2 26 44-82 69-94 (113)
144 PF10276 zf-CHCC: Zinc-finger 45.1 12 0.00025 16.9 0.7 12 44-55 28-39 (40)
145 KOG0717|consensus 44.9 13 0.00027 26.2 1.1 22 75-96 293-314 (508)
146 PF09845 DUF2072: Zn-ribbon co 44.8 10 0.00023 21.9 0.6 15 45-59 1-15 (131)
147 PF10537 WAC_Acf1_DNA_bd: ATP- 44.0 36 0.00078 18.7 2.6 38 44-83 2-39 (102)
148 COG1773 Rubredoxin [Energy pro 43.7 11 0.00024 18.4 0.5 10 75-84 4-13 (55)
149 PRK12496 hypothetical protein; 43.2 24 0.00052 21.1 2.0 28 46-86 128-155 (164)
150 PRK04351 hypothetical protein; 43.1 12 0.00026 22.0 0.7 33 45-86 112-144 (149)
151 COG3677 Transposase and inacti 43.0 15 0.00032 21.1 1.1 15 71-86 51-65 (129)
152 PF14353 CpXC: CpXC protein 42.8 5.7 0.00012 22.4 -0.6 23 44-66 37-59 (128)
153 PF11931 DUF3449: Domain of un 42.7 8.2 0.00018 23.9 0.0 28 39-66 95-123 (196)
154 COG0068 HypF Hydrogenase matur 42.6 16 0.00035 27.1 1.4 63 14-84 120-183 (750)
155 PF13824 zf-Mss51: Zinc-finger 42.6 24 0.00051 17.2 1.6 10 44-53 13-22 (55)
156 COG1571 Predicted DNA-binding 42.5 18 0.0004 25.1 1.6 29 47-87 352-380 (421)
157 PF01096 TFIIS_C: Transcriptio 42.5 7.7 0.00017 17.2 -0.1 10 75-84 29-38 (39)
158 TIGR00686 phnA alkylphosphonat 41.4 15 0.00033 20.5 0.9 11 46-56 20-30 (109)
159 cd00065 FYVE FYVE domain; Zinc 40.7 26 0.00056 16.4 1.6 10 47-56 20-29 (57)
160 PF07295 DUF1451: Protein of u 40.6 12 0.00026 22.0 0.5 33 40-83 107-139 (146)
161 PF01155 HypA: Hydrogenase exp 40.3 16 0.00036 20.3 1.0 26 45-83 70-95 (113)
162 cd00924 Cyt_c_Oxidase_Vb Cytoc 40.0 16 0.00035 19.9 0.9 14 44-57 78-91 (97)
163 smart00440 ZnF_C2C2 C2C2 Zinc 40.0 18 0.00038 16.2 0.9 10 75-84 29-38 (40)
164 PF14311 DUF4379: Domain of un 39.7 32 0.00069 16.3 1.8 14 46-59 29-42 (55)
165 COG1656 Uncharacterized conser 39.7 21 0.00046 21.5 1.4 21 44-64 129-149 (165)
166 COG1198 PriA Primosomal protei 39.7 12 0.00025 27.9 0.4 11 73-83 474-484 (730)
167 smart00064 FYVE Protein presen 38.8 25 0.00054 17.3 1.4 10 47-56 28-37 (68)
168 PF04216 FdhE: Protein involve 37.6 10 0.00022 24.7 -0.2 35 18-55 173-207 (290)
169 smart00731 SprT SprT homologue 37.4 15 0.00033 21.2 0.6 33 45-85 112-144 (146)
170 COG3091 SprT Zn-dependent meta 37.4 18 0.00039 21.5 0.9 37 42-84 114-150 (156)
171 cd00730 rubredoxin Rubredoxin; 37.2 18 0.00039 17.1 0.7 11 75-85 2-12 (50)
172 PF04423 Rad50_zn_hook: Rad50 37.2 14 0.0003 17.5 0.3 13 47-59 22-34 (54)
173 PF06397 Desulfoferrod_N: Desu 36.9 16 0.00034 16.1 0.5 12 44-55 5-16 (36)
174 PRK14138 NAD-dependent deacety 36.8 50 0.0011 21.0 2.9 40 39-83 113-152 (244)
175 TIGR00143 hypF [NiFe] hydrogen 36.7 22 0.00048 26.4 1.4 63 15-85 88-151 (711)
176 PRK14892 putative transcriptio 36.4 18 0.0004 19.8 0.7 9 44-52 20-28 (99)
177 PRK00432 30S ribosomal protein 36.3 24 0.00053 16.6 1.1 12 72-84 36-47 (50)
178 KOG2807|consensus 36.3 55 0.0012 22.2 3.0 23 75-97 346-368 (378)
179 PRK05452 anaerobic nitric oxid 36.1 22 0.00048 25.0 1.3 41 42-83 422-467 (479)
180 PF04780 DUF629: Protein of un 36.0 33 0.00072 24.3 2.1 22 75-96 58-79 (466)
181 COG4338 Uncharacterized protei 36.0 15 0.00033 17.4 0.3 14 76-89 14-27 (54)
182 PRK10220 hypothetical protein; 35.5 24 0.00053 19.7 1.1 11 46-56 21-31 (111)
183 PF01286 XPA_N: XPA protein N- 35.4 17 0.00037 15.8 0.4 11 76-86 5-15 (34)
184 PF11023 DUF2614: Protein of u 35.4 36 0.00078 19.2 1.8 34 44-90 68-101 (114)
185 PHA02998 RNA polymerase subuni 35.3 27 0.00059 21.4 1.4 11 75-85 172-182 (195)
186 KOG1842|consensus 35.1 23 0.00049 24.9 1.1 27 44-70 14-40 (505)
187 PRK00564 hypA hydrogenase nick 35.0 22 0.00048 19.9 1.0 14 44-57 70-83 (117)
188 PF11672 DUF3268: Protein of u 34.7 21 0.00047 19.7 0.9 9 45-53 2-10 (102)
189 COG3357 Predicted transcriptio 34.7 19 0.00042 19.4 0.6 13 74-86 58-70 (97)
190 KOG4602|consensus 34.6 32 0.0007 22.4 1.7 13 45-57 268-280 (318)
191 PF12907 zf-met2: Zinc-binding 34.3 23 0.00051 16.0 0.8 25 46-70 2-29 (40)
192 COG1326 Uncharacterized archae 34.3 41 0.00089 20.9 2.1 35 45-85 6-41 (201)
193 KOG3507|consensus 34.0 18 0.0004 17.8 0.5 28 45-84 20-47 (62)
194 COG3364 Zn-ribbon containing p 33.9 24 0.00052 19.5 1.0 15 45-59 2-16 (112)
195 PF10071 DUF2310: Zn-ribbon-co 33.5 21 0.00045 23.1 0.8 28 46-81 221-248 (258)
196 COG4391 Uncharacterized protei 32.8 26 0.00057 17.4 0.9 16 42-57 45-60 (62)
197 PLN02748 tRNA dimethylallyltra 32.8 30 0.00064 24.5 1.5 26 42-67 415-441 (468)
198 PRK03681 hypA hydrogenase nick 32.4 27 0.00059 19.5 1.1 28 44-83 69-96 (114)
199 COG1594 RPB9 DNA-directed RNA 31.7 25 0.00053 19.7 0.8 12 75-86 101-112 (113)
200 COG1779 C4-type Zn-finger prot 31.1 8.5 0.00018 23.8 -1.2 36 45-86 14-55 (201)
201 PLN03238 probable histone acet 30.5 46 0.001 22.0 1.9 22 74-95 48-69 (290)
202 PF06524 NOA36: NOA36 protein; 30.4 41 0.00088 22.0 1.7 11 42-52 139-149 (314)
203 PF00301 Rubredoxin: Rubredoxi 30.4 23 0.00049 16.6 0.4 37 46-83 2-43 (47)
204 cd01413 SIR2_Af2 SIR2_Af2: Arc 29.2 75 0.0016 19.8 2.7 39 39-83 107-145 (222)
205 PF04606 Ogr_Delta: Ogr/Delta- 28.8 14 0.0003 17.1 -0.5 13 75-87 26-40 (47)
206 KOG3014|consensus 27.8 66 0.0014 20.9 2.3 32 38-69 27-63 (257)
207 TIGR00319 desulf_FeS4 desulfof 27.4 32 0.0007 14.5 0.6 13 43-55 5-17 (34)
208 smart00132 LIM Zinc-binding do 27.3 53 0.0012 13.5 1.4 8 75-82 28-35 (39)
209 cd00974 DSRD Desulforedoxin (D 27.1 33 0.0007 14.5 0.6 12 44-55 3-14 (34)
210 TIGR01206 lysW lysine biosynth 27.1 28 0.0006 16.8 0.4 30 46-84 3-32 (54)
211 COG5188 PRP9 Splicing factor 3 27.0 43 0.00094 22.9 1.4 33 34-66 363-396 (470)
212 COG4896 Uncharacterized protei 26.9 51 0.0011 16.5 1.3 8 46-53 32-39 (68)
213 PF01215 COX5B: Cytochrome c o 26.8 28 0.0006 20.3 0.5 16 43-58 110-125 (136)
214 PF02591 DUF164: Putative zinc 26.3 20 0.00042 17.1 -0.2 31 47-82 24-54 (56)
215 PRK00762 hypA hydrogenase nick 26.3 36 0.00078 19.3 0.9 32 44-82 69-100 (124)
216 PTZ00448 hypothetical protein; 26.1 57 0.0012 22.4 1.8 22 75-96 315-336 (373)
217 PF14369 zf-RING_3: zinc-finge 25.5 55 0.0012 14.1 1.2 9 76-84 23-31 (35)
218 PF14803 Nudix_N_2: Nudix N-te 25.4 17 0.00038 15.7 -0.4 8 75-82 23-30 (34)
219 TIGR03831 YgiT_finger YgiT-typ 25.4 30 0.00065 15.3 0.4 13 44-56 31-43 (46)
220 COG1655 Uncharacterized protei 25.3 17 0.00037 23.2 -0.6 29 42-70 16-44 (267)
221 PF10083 DUF2321: Uncharacteri 25.2 57 0.0012 19.5 1.5 14 44-57 67-80 (158)
222 cd01410 SIRT7 SIRT7: Eukaryoti 24.8 1.3E+02 0.0029 18.5 3.2 41 39-83 89-129 (206)
223 PRK11823 DNA repair protein Ra 24.7 52 0.0011 23.0 1.5 10 45-54 7-16 (446)
224 KOG0978|consensus 24.7 29 0.00063 25.8 0.3 17 47-63 680-696 (698)
225 PF02748 PyrI_C: Aspartate car 24.6 38 0.00083 16.1 0.7 17 41-57 31-47 (52)
226 COG1675 TFA1 Transcription ini 24.5 68 0.0015 19.6 1.8 33 42-84 110-142 (176)
227 PF09788 Tmemb_55A: Transmembr 24.4 68 0.0015 20.8 1.9 28 4-31 52-79 (256)
228 cd01407 SIR2-fam SIR2 family o 24.1 1.1E+02 0.0025 18.9 2.9 40 39-83 103-142 (218)
229 TIGR01562 FdhE formate dehydro 24.1 1.1E+02 0.0024 20.4 2.9 9 19-27 186-194 (305)
230 COG0675 Transposase and inacti 23.9 45 0.00097 21.6 1.1 15 44-58 321-335 (364)
231 TIGR00416 sms DNA repair prote 23.2 54 0.0012 23.0 1.4 9 46-54 8-16 (454)
232 PF08792 A2L_zn_ribbon: A2L zi 22.9 43 0.00092 14.3 0.6 12 45-56 21-32 (33)
233 TIGR00515 accD acetyl-CoA carb 22.7 79 0.0017 20.8 2.0 12 75-86 46-57 (285)
234 CHL00174 accD acetyl-CoA carbo 22.5 82 0.0018 20.9 2.1 32 46-87 39-70 (296)
235 PF11494 Ta0938: Ta0938; Inte 22.3 49 0.0011 18.1 0.8 41 40-86 9-49 (105)
236 PF05876 Terminase_GpA: Phage 22.2 34 0.00073 24.7 0.3 40 46-86 201-241 (557)
237 PF11789 zf-Nse: Zinc-finger o 21.8 95 0.0021 15.0 1.8 32 43-79 22-53 (57)
238 PTZ00043 cytochrome c oxidase 21.7 47 0.001 21.3 0.8 17 42-58 178-194 (268)
239 PRK06260 threonine synthase; V 21.7 80 0.0017 21.6 2.0 10 46-55 4-13 (397)
240 PF03966 Trm112p: Trm112p-like 21.7 41 0.0009 16.7 0.5 18 40-57 48-65 (68)
241 PRK05978 hypothetical protein; 21.5 57 0.0012 19.3 1.1 31 46-86 34-64 (148)
242 PLN00104 MYST -like histone ac 21.2 59 0.0013 23.0 1.3 23 74-96 198-220 (450)
243 PF08271 TF_Zn_Ribbon: TFIIB z 21.1 48 0.001 14.8 0.6 30 46-85 1-30 (43)
244 KOG0402|consensus 20.8 30 0.00065 18.4 -0.1 30 45-85 36-65 (92)
245 KOG0801|consensus 20.7 33 0.00072 20.7 0.0 12 75-86 139-150 (205)
246 PTZ00064 histone acetyltransfe 20.5 70 0.0015 23.1 1.5 23 74-96 280-302 (552)
247 PRK03564 formate dehydrogenase 20.5 1.6E+02 0.0034 19.8 3.1 34 17-53 187-220 (309)
248 PRK00420 hypothetical protein; 20.1 70 0.0015 18.0 1.2 9 75-83 41-49 (112)
No 1
>KOG2462|consensus
Probab=99.83 E-value=2.7e-21 Score=119.36 Aligned_cols=80 Identities=18% Similarity=0.271 Sum_probs=73.5
Q ss_pred CCCCCCCCccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHHHH
Q psy12010 16 PEYSFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTHMA 95 (99)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H~~ 95 (99)
....|..|+..|....+++.|.+.|+|+|||.|+.|++.|.++++|..||+.|.+.++ |+|..|+|+|...+.|.+|..
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhHHHHHHHHHHhhh
Confidence 4567888889999999999999999999999999999999999999999999999887 999999999999999999975
Q ss_pred h
Q psy12010 96 I 96 (99)
Q Consensus 96 ~ 96 (99)
.
T Consensus 265 S 265 (279)
T KOG2462|consen 265 S 265 (279)
T ss_pred h
Confidence 3
No 2
>KOG2462|consensus
Probab=99.75 E-value=7e-19 Score=108.78 Aligned_cols=82 Identities=21% Similarity=0.468 Sum_probs=71.3
Q ss_pred CCCCCCCCCccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHHH
Q psy12010 15 FPEYSFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTHM 94 (99)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H~ 94 (99)
.....|..|+.....-..+..|.+.|+ -+++|.+|||.|.+.|-|+.|+|.|+|++| |.|..|+++|.++++|..|+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP-F~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKP-FSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCC-ccCCcccchhcchHHHHHHH
Confidence 345567777777677677777777775 679999999999999999999999999887 99999999999999999999
Q ss_pred HhhcC
Q psy12010 95 AIKHS 99 (99)
Q Consensus 95 ~~~~~ 99 (99)
++|.+
T Consensus 236 QTHS~ 240 (279)
T KOG2462|consen 236 QTHSD 240 (279)
T ss_pred HhhcC
Confidence 99864
No 3
>KOG3623|consensus
Probab=99.56 E-value=4.4e-16 Score=106.76 Aligned_cols=83 Identities=23% Similarity=0.424 Sum_probs=75.7
Q ss_pred CCCCCCCCCCCCccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHH
Q psy12010 12 PDLFPEYSFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLK 91 (99)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~ 91 (99)
-.....|.|+-|+..|.....+..|+=.|+|.+||+|.+|.|.|..+.+|..|+|+|.|+++ |+|..|+|+|+....+-
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYS 967 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYS 967 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchH
Confidence 34456678999999999988899999999999999999999999999999999999999887 99999999999999998
Q ss_pred HHHH
Q psy12010 92 THMA 95 (99)
Q Consensus 92 ~H~~ 95 (99)
.|+.
T Consensus 968 QHMN 971 (1007)
T KOG3623|consen 968 QHMN 971 (1007)
T ss_pred hhhc
Confidence 8873
No 4
>KOG3576|consensus
Probab=99.37 E-value=2.1e-14 Score=86.08 Aligned_cols=80 Identities=23% Similarity=0.468 Sum_probs=70.4
Q ss_pred CCCCCccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHHHHhhc
Q psy12010 19 SFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
.|..|..-|.-..++..|..-|...|.+-|..||+.|...-+|++|++.|+|.+| |+|..|+++|.++..|..|.+..|
T Consensus 119 tCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 119 TCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred eeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHHHHHHHc
Confidence 6666777788888888888888888999999999999999999999999999776 999999999999999999988665
Q ss_pred C
Q psy12010 99 S 99 (99)
Q Consensus 99 ~ 99 (99)
|
T Consensus 198 g 198 (267)
T KOG3576|consen 198 G 198 (267)
T ss_pred C
Confidence 4
No 5
>KOG3623|consensus
Probab=99.28 E-value=2.7e-13 Score=93.38 Aligned_cols=80 Identities=26% Similarity=0.512 Sum_probs=62.4
Q ss_pred CCCCCCCCCccccCCcccccCccccc-------------cCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCC
Q psy12010 15 FPEYSFNWPEVHLNESDFINWPTVRQ-------------YNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCP 81 (99)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~ 81 (99)
-+..+|..|...|.-...+..|...| ...+-|+|.+|||.|..+.+|+.|+|+|.|+++ |.|..|+
T Consensus 238 e~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKP-feCpnCk 316 (1007)
T KOG3623|consen 238 EPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKP-FECPNCK 316 (1007)
T ss_pred CCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCC-cCCcccc
Confidence 34556777766665544444444433 235679999999999999999999999999887 9999999
Q ss_pred ccccChhHHHHHHH
Q psy12010 82 YRASQKATLKTHMA 95 (99)
Q Consensus 82 ~~f~~~~~l~~H~~ 95 (99)
|+|+....+-.|+.
T Consensus 317 KRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 317 KRFSHSGSYSSHMS 330 (1007)
T ss_pred cccccCCccccccc
Confidence 99999888877764
No 6
>PHA02768 hypothetical protein; Provisional
Probab=99.25 E-value=3.4e-12 Score=61.74 Aligned_cols=43 Identities=16% Similarity=0.413 Sum_probs=39.3
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHH
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLK 91 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~ 91 (99)
|+|+.||+.|....+|..|++.|+ ++ ++|..|++.|...+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceecccceeE
Confidence 799999999999999999999998 45 99999999999887764
No 7
>PHA00733 hypothetical protein
Probab=99.20 E-value=2e-11 Score=69.46 Aligned_cols=56 Identities=20% Similarity=0.360 Sum_probs=50.1
Q ss_pred cCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHHHHhhcC
Q psy12010 41 YNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 41 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
.+.++|.|+.|++.|.....|..|++.+. .+ |.|.+|++.|.....|.+|+...|+
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~--~~-~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYTE--HS-KVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcCC--cC-ccCCCCCCccCCHHHHHHHHHHhcC
Confidence 45889999999999999999999999762 44 9999999999999999999987764
No 8
>KOG1074|consensus
Probab=99.20 E-value=2.7e-12 Score=89.47 Aligned_cols=88 Identities=17% Similarity=0.275 Sum_probs=73.1
Q ss_pred CCCCCCCCCCCCccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCC---CCcccCC---CCCcccc
Q psy12010 12 PDLFPEYSFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQ---EPKYQCP---QCPYRAS 85 (99)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~---~~~~~c~---~C~~~f~ 85 (99)
....+...|..|-+.++-...++.|-+.|+|++||+|.+||+.|..+.+|+.|+.+|... +..+.|+ .|.+.|.
T Consensus 600 ~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 600 NKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred cccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccc
Confidence 444555677778888888888999999999999999999999999999999999988652 1237788 8989999
Q ss_pred ChhHHHHHHHhhcC
Q psy12010 86 QKATLKTHMAIKHS 99 (99)
Q Consensus 86 ~~~~l~~H~~~~~~ 99 (99)
..-.|..|+++|.+
T Consensus 680 n~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 680 NAVTLPQHIRIHLG 693 (958)
T ss_pred ccccccceEEeecC
Confidence 98899999998863
No 9
>KOG3576|consensus
Probab=99.13 E-value=2.7e-11 Score=72.84 Aligned_cols=80 Identities=18% Similarity=0.383 Sum_probs=68.2
Q ss_pred CCCCCccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCC----------CCcccCCCCCccccChh
Q psy12010 19 SFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQ----------EPKYQCPQCPYRASQKA 88 (99)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~----------~~~~~c~~C~~~f~~~~ 88 (99)
-|.+|+.-|+..-.++.|.+.|+|.+||+|..|++.|.+...|..|.+-.+|. .+.|.|++||..-....
T Consensus 147 lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e 226 (267)
T KOG3576|consen 147 LCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPE 226 (267)
T ss_pred HHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChh
Confidence 46678888888888999999999999999999999999999999998854442 22499999999988888
Q ss_pred HHHHHHHhhc
Q psy12010 89 TLKTHMAIKH 98 (99)
Q Consensus 89 ~l~~H~~~~~ 98 (99)
.+..|+..||
T Consensus 227 ~~~~h~~~~h 236 (267)
T KOG3576|consen 227 VYYLHLKLHH 236 (267)
T ss_pred HHHHHHHhcC
Confidence 8888888776
No 10
>KOG1074|consensus
Probab=99.03 E-value=3.6e-11 Score=84.01 Aligned_cols=52 Identities=33% Similarity=0.632 Sum_probs=48.9
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHHHHhhc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
.+|.+|.+.|...+.|+.|.|.|+|++| |+|.+||.+|.++.+|+.|...|+
T Consensus 354 hkCr~CakvfgS~SaLqiHlRSHTGERP-fqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 354 HKCRFCAKVFGSDSALQIHLRSHTGERP-FQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred chhhhhHhhcCchhhhhhhhhccCCCCC-eeecccccccccccceeeeeeecc
Confidence 6899999999999999999999999887 999999999999999999987765
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.81 E-value=2.7e-09 Score=44.42 Aligned_cols=26 Identities=42% Similarity=0.898 Sum_probs=21.6
Q ss_pred HHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 60 GLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 60 ~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
+|..|++.|+++++ |.|+.|++.|..
T Consensus 1 ~l~~H~~~H~~~k~-~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP-YKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS-EEESSSSEEESS
T ss_pred CHHHHhhhcCCCCC-CCCCCCcCeeCc
Confidence 47889999999777 999999988863
No 12
>PHA00732 hypothetical protein
Probab=98.72 E-value=9.9e-09 Score=53.72 Aligned_cols=46 Identities=28% Similarity=0.595 Sum_probs=38.4
Q ss_pred ceeCCcccccccchhHHHhhhhh-hhCCCCcccCCCCCccccChhHHHHHHHhh
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRD-ECGQEPKYQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
||.|..|++.|.....|..|++. |. + +.|+.|++.|. .|..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeC---Chhhhhccc
Confidence 58899999999999999999984 54 3 78999999998 477777543
No 13
>PHA00616 hypothetical protein
Probab=98.63 E-value=1.4e-08 Score=47.00 Aligned_cols=34 Identities=21% Similarity=0.313 Sum_probs=30.5
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCC
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQ 79 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~ 79 (99)
||+|..||+.|..+..|..|++.|+|.++ +.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-cceeE
Confidence 68999999999999999999999999877 88764
No 14
>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=98.53 E-value=2e-07 Score=45.39 Aligned_cols=52 Identities=29% Similarity=0.545 Sum_probs=40.5
Q ss_pred ceeCCcccccccchhHHHhhhhh-hhCCCCcccCCCCCccccChhHHHHHHHhhcC
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRD-ECGQEPKYQCPQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
.|.|++|++ .-....|..|... |......+.|+.|...+. .+|..|+.++|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 489999999 4556789999774 555444499999988655 489999999885
No 15
>KOG3608|consensus
Probab=98.49 E-value=1.6e-08 Score=65.47 Aligned_cols=77 Identities=25% Similarity=0.430 Sum_probs=56.6
Q ss_pred CCCC--CccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCC-CCcccCCCCCccccChhHHHHHHH
Q psy12010 19 SFNW--PEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQ-EPKYQCPQCPYRASQKATLKTHMA 95 (99)
Q Consensus 19 ~~~~--~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~-~~~~~c~~C~~~f~~~~~l~~H~~ 95 (99)
.|+| |...+.+...++.|.+.|+++|...|+.||..|..+..|..|.+..+.. ..+|+|..|.|.|.+...|..|+.
T Consensus 179 ~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~ 258 (467)
T KOG3608|consen 179 MCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVV 258 (467)
T ss_pred eccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHH
Confidence 4444 5666777778999999999999999999999999999999998855431 223666666666655555555544
No 16
>PHA00616 hypothetical protein
Probab=98.46 E-value=7.8e-08 Score=44.52 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=24.7
Q ss_pred cccCCCCCccccChhHHHHHHHhhcC
Q psy12010 74 KYQCPQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 74 ~~~c~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
||+|..||+.|...+.|..|++.|||
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg 26 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK 26 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC
Confidence 59999999999999999999999986
No 17
>KOG3608|consensus
Probab=98.43 E-value=3.2e-08 Score=64.13 Aligned_cols=56 Identities=21% Similarity=0.497 Sum_probs=28.3
Q ss_pred ccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCC--CCccccChhHHHHHHHhh
Q psy12010 40 QYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQ--CPYRASQKATLKTHMAIK 97 (99)
Q Consensus 40 ~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~--C~~~f~~~~~l~~H~~~~ 97 (99)
|...|||+|+.|.+.|...+.|..|...|. +.. |.|+. |..+|.+...|.+|.+-+
T Consensus 287 Hs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~-y~C~h~~C~~s~r~~~q~~~H~~ev 344 (467)
T KOG3608|consen 287 HSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTV-YQCEHPDCHYSVRTYTQMRRHFLEV 344 (467)
T ss_pred hccCCCccccchhhhhccHHHHHHHHHhcc-ccc-eecCCCCCcHHHHHHHHHHHHHHHh
Confidence 444555555555555555555555555444 122 55543 555555555555555433
No 18
>KOG3993|consensus
Probab=98.42 E-value=1.4e-08 Score=66.96 Aligned_cols=86 Identities=14% Similarity=0.270 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCccccCCcccccCccccccCCCceeCCcccccccchhHHHhhhhhhhCC--------C------------
Q psy12010 13 DLFPEYSFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQ--------E------------ 72 (99)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~--------~------------ 72 (99)
..+..+.|..|+.-+.+.-.+..|.=...---.|.|++|+|.|.+..+|..|.|.|... .
T Consensus 263 n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~ 342 (500)
T KOG3993|consen 263 NVIGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEV 342 (500)
T ss_pred ccHHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhh
Confidence 34555666667666555444444432222224599999999999999999999988521 1
Q ss_pred ------------CcccCCCCCccccChhHHHHHHHhhc
Q psy12010 73 ------------PKYQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 73 ------------~~~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
..|.|..|+|.|.....|..|+.+|+
T Consensus 343 ~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 343 QEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 13889999999999999999988876
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=98.34 E-value=5.8e-08 Score=40.34 Aligned_cols=24 Identities=17% Similarity=0.426 Sum_probs=20.4
Q ss_pred cCccccccCCCceeCCcccccccc
Q psy12010 34 NWPTVRQYNSGMFPCDVCGKKYKY 57 (99)
Q Consensus 34 ~~~~~~~~~~k~~~C~~c~~~f~~ 57 (99)
..|.+.|++++||+|+.|++.|..
T Consensus 3 ~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 3 RRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHhhhcCCCCCCCCCCCcCeeCc
Confidence 346778999999999999999863
No 20
>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=98.34 E-value=3.6e-07 Score=36.68 Aligned_cols=22 Identities=45% Similarity=0.807 Sum_probs=12.7
Q ss_pred ccCCCCCccccChhHHHHHHHh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
|.|..|++.|.....|..|++.
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 3455566666666666666554
No 21
>PHA02768 hypothetical protein; Provisional
Probab=98.33 E-value=3.6e-07 Score=44.29 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=23.3
Q ss_pred ccCCCCCccccChhHHHHHHHhhc
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
|+|+.||+.|...++|..|+++|+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC
Confidence 899999999999999999999987
No 22
>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=98.28 E-value=5.9e-07 Score=36.04 Aligned_cols=23 Identities=39% Similarity=0.892 Sum_probs=21.4
Q ss_pred eeCCcccccccchhHHHhhhhhh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDE 68 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h 68 (99)
|+|+.|++.|.....|..|++.|
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 68999999999999999999874
No 23
>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=98.19 E-value=1.6e-06 Score=34.83 Aligned_cols=24 Identities=38% Similarity=0.790 Sum_probs=14.4
Q ss_pred ccCCCCCccccChhHHHHHHHhhc
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
|.|..|++.|.+...|..|++.+|
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 456666666666666666666654
No 24
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.17 E-value=1.1e-06 Score=36.56 Aligned_cols=24 Identities=21% Similarity=0.483 Sum_probs=15.7
Q ss_pred ccCCCCCccccChhHHHHHHHhhc
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
|+|..|++.|.+...|..|++.|+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 666666666666666666666554
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.02 E-value=7.5e-06 Score=56.61 Aligned_cols=38 Identities=21% Similarity=0.432 Sum_probs=16.9
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
+++.|+ ||+.+ ....|..|++.|.+.++ +.|..|++.|
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCcc
Confidence 444444 44332 23444444444444333 4454454444
No 26
>PHA00733 hypothetical protein
Probab=98.02 E-value=3.1e-06 Score=48.27 Aligned_cols=56 Identities=20% Similarity=0.215 Sum_probs=42.8
Q ss_pred cCCCceeCCcccccccchhHHHhhhh-----hhhCCCCcccCCCCCccccChhHHHHHHHhh
Q psy12010 41 YNSGMFPCDVCGKKYKYKWGLSRHKR-----DECGQEPKYQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 41 ~~~k~~~C~~c~~~f~~~~~l~~h~~-----~h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
...+++.|.+|.+.|.....|..+.. .+.+..+ |.|..|++.|.....|..|++++
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP-y~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP-YVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCC-ccCCCCCCcCCCHHHHHHHHhcC
Confidence 35688999999998888766655511 1223344 99999999999999999999854
No 27
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.99 E-value=5.3e-06 Score=57.33 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=54.3
Q ss_pred CCCCCccccCCcccccCccccccCCCceeCCcccccccc----------hhHHHhhhhhhhCCCCcccCCCCCccccChh
Q psy12010 19 SFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKYKY----------KWGLSRHKRDECGQEPKYQCPQCPYRASQKA 88 (99)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~----------~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~ 88 (99)
.|. |+..+. ...+..|...|...+++.|.+|+..+.. ...|..|.... |.++ +.|..||+.+..+.
T Consensus 480 ~Cp-Cg~~~~-R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt-~~C~~Cgk~Vrlrd 555 (567)
T PLN03086 480 QCP-CGVVLE-KEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRT-APCDSCGRSVMLKE 555 (567)
T ss_pred cCC-CCCCcc-hhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcc-eEccccCCeeeehh
Confidence 444 544443 3455556677888999999999998852 34788998886 6676 99999999988876
Q ss_pred HHHHHHHhhc
Q psy12010 89 TLKTHMAIKH 98 (99)
Q Consensus 89 ~l~~H~~~~~ 98 (99)
|..|+..-|
T Consensus 556 -m~~H~~~~h 564 (567)
T PLN03086 556 -MDIHQIAVH 564 (567)
T ss_pred -HHHHHHHhh
Confidence 777766544
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.97 E-value=2.1e-06 Score=55.23 Aligned_cols=54 Identities=31% Similarity=0.573 Sum_probs=42.6
Q ss_pred CCCceeCCc--ccccccchhHHHhhhhh-h------h-----------CCCCcccCCCCCccccChhHHHHHHH
Q psy12010 42 NSGMFPCDV--CGKKYKYKWGLSRHKRD-E------C-----------GQEPKYQCPQCPYRASQKATLKTHMA 95 (99)
Q Consensus 42 ~~k~~~C~~--c~~~f~~~~~l~~h~~~-h------~-----------~~~~~~~c~~C~~~f~~~~~l~~H~~ 95 (99)
++|||+|++ |.|.|..+..|+.|+.- | . .+.+||.|++|+|+++..-.|+-|..
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 359999977 88999999999988752 2 0 12245999999999999988987754
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.90 E-value=1.1e-05 Score=32.27 Aligned_cols=23 Identities=39% Similarity=0.899 Sum_probs=19.5
Q ss_pred eeCCcccccccchhHHHhhhhhh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDE 68 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h 68 (99)
|.|+.|++.|.....|..|+..+
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 68999999999999999999876
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.90 E-value=7.3e-06 Score=34.04 Aligned_cols=26 Identities=42% Similarity=0.885 Sum_probs=23.4
Q ss_pred ceeCCcccccccchhHHHhhhhhhhC
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECG 70 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~ 70 (99)
+|+|..|++.|.....|..|++.|..
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 58999999999999999999987743
No 31
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.77 E-value=4.5e-05 Score=36.24 Aligned_cols=34 Identities=21% Similarity=0.357 Sum_probs=21.1
Q ss_pred ccCCCceeCCcccccccchhHHHhhhhhhhCCCC
Q psy12010 40 QYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEP 73 (99)
Q Consensus 40 ~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~ 73 (99)
+..++|-.|++|+..+.+..+|.+|+.+.++.++
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3456778888888888888888888887766543
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.76 E-value=2.3e-05 Score=42.24 Aligned_cols=23 Identities=30% Similarity=0.722 Sum_probs=19.6
Q ss_pred ccCCCCCccccChhHHHHHHHhh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
+.|..|++.|.+...|..|++.+
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCccCCCCcCHHHHHHHHcCc
Confidence 88999999999999999998864
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.70 E-value=4.9e-05 Score=30.68 Aligned_cols=23 Identities=39% Similarity=0.806 Sum_probs=13.2
Q ss_pred ccCCCCCccccChhHHHHHHHhh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
|+|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34555666666666666665543
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.51 E-value=7.7e-05 Score=35.47 Aligned_cols=37 Identities=24% Similarity=0.512 Sum_probs=23.9
Q ss_pred hhhhhhhCCCCcccCCCCCccccChhHHHHHHHhhcC
Q psy12010 63 RHKRDECGQEPKYQCPQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 63 ~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
.+.+.+.....|-.|++|+..+.+..+|.+|+.+.|+
T Consensus 13 ~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 13 KKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp ---CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred hHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 3334444445569999999999999999999998875
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.50 E-value=8.4e-05 Score=29.93 Aligned_cols=24 Identities=38% Similarity=0.743 Sum_probs=21.6
Q ss_pred eeCCcccccccchhHHHhhhhhhh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDEC 69 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~ 69 (99)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998764
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.45 E-value=0.00011 Score=29.57 Aligned_cols=24 Identities=46% Similarity=1.064 Sum_probs=15.0
Q ss_pred ccCCCCCccccChhHHHHHHHhhcC
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
|+|..|+.... ...|.+|++.+|+
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 56777776666 6677777777654
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.43 E-value=0.00012 Score=43.29 Aligned_cols=39 Identities=26% Similarity=0.530 Sum_probs=33.1
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccCh
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQK 87 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~ 87 (99)
-+|.|. |+. ....+..|.++|.+.++ |.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEe
Confidence 369998 987 66778999999999887 9999999987654
No 38
>KOG3993|consensus
Probab=97.43 E-value=2.2e-05 Score=52.26 Aligned_cols=53 Identities=26% Similarity=0.569 Sum_probs=46.7
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHHHHhhc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
.|-|..|-..|...-.|.+|...-.-..- |+|.+|+|.|+-.++|..|.|.|.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vE-YrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVE-YRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEee-ecCCcccccccCchhhhhhhcccC
Confidence 38999999999999999999886554455 999999999999999999999874
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.13 E-value=0.00032 Score=28.33 Aligned_cols=20 Identities=35% Similarity=0.777 Sum_probs=10.3
Q ss_pred eCCcccccccchhHHHhhhh
Q psy12010 47 PCDVCGKKYKYKWGLSRHKR 66 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~ 66 (99)
.|..|++.|.....|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555544
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.12 E-value=0.00032 Score=28.34 Aligned_cols=23 Identities=26% Similarity=0.571 Sum_probs=20.8
Q ss_pred ccCCCCCccccChhHHHHHHHhh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
|.|..|++.|.+...|..|++.+
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 57999999999999999998864
No 41
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.04 E-value=0.00025 Score=34.39 Aligned_cols=51 Identities=14% Similarity=0.271 Sum_probs=38.4
Q ss_pred CCCCCCCccccCCcccccCccccccCC-CceeCCcccccccchhHHHhhhhhhh
Q psy12010 17 EYSFNWPEVHLNESDFINWPTVRQYNS-GMFPCDVCGKKYKYKWGLSRHKRDEC 69 (99)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-k~~~C~~c~~~f~~~~~l~~h~~~h~ 69 (99)
++.|++|...+....+..+-...|..+ +.+.|++|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 567888877777777777767777654 6799999998655 38888988754
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.60 E-value=0.0023 Score=25.53 Aligned_cols=23 Identities=26% Similarity=0.521 Sum_probs=18.0
Q ss_pred eeCCcccccccchhHHHhhhhhhh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDEC 69 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~ 69 (99)
|.|+.|+.... ...|..|++.+.
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 68999998887 889999998865
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.54 E-value=0.0015 Score=26.95 Aligned_cols=22 Identities=32% Similarity=0.700 Sum_probs=14.6
Q ss_pred eeCCcccccccchhHHHhhhhh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRD 67 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~ 67 (99)
|-|..|++.|.....|..|++.
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 4567777777777776666653
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=96.49 E-value=0.001 Score=27.45 Aligned_cols=22 Identities=32% Similarity=0.564 Sum_probs=20.1
Q ss_pred ccCCCCCccccChhHHHHHHHh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
|-|..|++.|.+...|..|+++
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 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.97 E-value=0.0096 Score=24.16 Aligned_cols=21 Identities=29% Similarity=0.586 Sum_probs=12.5
Q ss_pred ccCCCCCccccChhHHHHHHHh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
.+|..||+.| ..+.|..|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4566677776 34446666553
No 46
>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=95.43 E-value=0.014 Score=25.24 Aligned_cols=21 Identities=14% Similarity=0.572 Sum_probs=13.9
Q ss_pred ccCCCCCccccChhHHHHHHH
Q psy12010 75 YQCPQCPYRASQKATLKTHMA 95 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~ 95 (99)
|-|.+|++.|.....+..|++
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 667777777776666666654
No 47
>PHA00732 hypothetical protein
Probab=94.96 E-value=0.0098 Score=31.13 Aligned_cols=47 Identities=15% Similarity=0.222 Sum_probs=33.9
Q ss_pred CCCCCCccccCCcccccCccc-cccCCCceeCCcccccccchhHHHhhhhhhhC
Q psy12010 18 YSFNWPEVHLNESDFINWPTV-RQYNSGMFPCDVCGKKYKYKWGLSRHKRDECG 70 (99)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~ 70 (99)
+.|..|+..+.....+..|.. .|. ++.|+.|++.|. .+..|.+....
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCC
Confidence 457778778888777777776 354 358999999998 46677765443
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.75 E-value=0.0069 Score=40.06 Aligned_cols=54 Identities=26% Similarity=0.544 Sum_probs=44.6
Q ss_pred CceeCCcccccccchhHHHhhhh--hhhCC--CCcccCC--CCCccccChhHHHHHHHhhc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKR--DECGQ--EPKYQCP--QCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~--~h~~~--~~~~~c~--~C~~~f~~~~~l~~H~~~~~ 98 (99)
.++.|..|...|.....|..|.+ .|.+. ++ +.|. .|++.|.+...+..|..+|+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCccccc
Confidence 46788888899999888889988 78887 55 8888 79999988888888877665
No 49
>KOG2893|consensus
Probab=94.47 E-value=0.0093 Score=37.50 Aligned_cols=42 Identities=19% Similarity=0.442 Sum_probs=32.0
Q ss_pred eCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHH
Q psy12010 47 PCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTH 93 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H 93 (99)
.|.+|++.|....-|..|++. +. |+|..|.|.+.+...|..|
T Consensus 12 wcwycnrefddekiliqhqka----kh-fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KH-FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhh----cc-ceeeeehhhhccCCCceee
Confidence 488999999988888888774 44 8898898877666555544
No 50
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.77 E-value=0.018 Score=37.73 Aligned_cols=25 Identities=36% Similarity=0.817 Sum_probs=22.3
Q ss_pred CCCceeCCcccccccchhHHHhhhh
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKR 66 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~ 66 (99)
..|||.|++|+|.|.....|+.|+.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 4699999999999999999988865
No 51
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.46 E-value=0.069 Score=28.38 Aligned_cols=25 Identities=28% Similarity=0.650 Sum_probs=21.8
Q ss_pred ceeCCcccccccchhHHHhhhhhhh
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDEC 69 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~ 69 (99)
.+.|..|++.|.....|..|++.+.
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 6899999999999999999999753
No 52
>KOG1146|consensus
Probab=93.40 E-value=0.066 Score=40.97 Aligned_cols=55 Identities=24% Similarity=0.469 Sum_probs=45.7
Q ss_pred cCCCceeCCcccccccchhHHHhhhhhhh-------------------------CCCCcccCCCCCccccChhHHHHHHH
Q psy12010 41 YNSGMFPCDVCGKKYKYKWGLSRHKRDEC-------------------------GQEPKYQCPQCPYRASQKATLKTHMA 95 (99)
Q Consensus 41 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~-------------------------~~~~~~~c~~C~~~f~~~~~l~~H~~ 95 (99)
.-.+.+.|+.|+..|+....|..|||..+ +.+ +|.|..|...+..+.+|-+|++
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~-p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGK-PYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCC-cccceeeeeeeecchHHHHHHH
Confidence 34588999999999999999999999721 123 4999999999999999999986
Q ss_pred h
Q psy12010 96 I 96 (99)
Q Consensus 96 ~ 96 (99)
.
T Consensus 540 S 540 (1406)
T KOG1146|consen 540 S 540 (1406)
T ss_pred H
Confidence 4
No 53
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=93.03 E-value=0.086 Score=22.76 Aligned_cols=24 Identities=38% Similarity=0.945 Sum_probs=16.5
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
|.|.+||..+... ..++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~-------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE-------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC-------------cCCCcCcCCCC
Confidence 6788898665332 23489999975
No 54
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=92.53 E-value=0.082 Score=30.40 Aligned_cols=22 Identities=27% Similarity=0.579 Sum_probs=12.7
Q ss_pred ccCCCCCccccChhHHHHHHHhhcC
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
..|-+||+.|.. |.+|++.|||
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 667777777765 4777777765
No 55
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.14 E-value=0.13 Score=22.37 Aligned_cols=25 Identities=36% Similarity=0.877 Sum_probs=17.4
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
.|.|..||..+. +..+|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~-------------g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHE-------------GEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeE-------------CCcCCCcCcCCCC
Confidence 478999996542 3334589999975
No 56
>KOG2186|consensus
Probab=91.81 E-value=0.12 Score=32.87 Aligned_cols=44 Identities=25% Similarity=0.578 Sum_probs=23.2
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHHHHH
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATLKTH 93 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l~~H 93 (99)
|.|..||....-. .+..|+....+ .- |.|-.|++.|.. .....|
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~-fSCIDC~k~F~~-~sYknH 47 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AY-FSCIDCGKTFER-VSYKNH 47 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-Ce-eEEeeccccccc-chhhhh
Confidence 5566666554433 33446555555 33 666666666655 334444
No 57
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.65 E-value=0.17 Score=30.27 Aligned_cols=25 Identities=36% Similarity=0.808 Sum_probs=19.5
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
+.|.|.+||.. +.| .+|-+|+.||.
T Consensus 133 ~~~vC~vCGy~-------------~~g-e~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYT-------------HEG-EAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCc-------------ccC-CCCCcCCCCCC
Confidence 37999999854 456 66699999984
No 58
>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=91.34 E-value=0.18 Score=22.25 Aligned_cols=34 Identities=12% Similarity=0.259 Sum_probs=22.5
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
++|+.|+..|.-..... ...... +.|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~-v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGK-VRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCE-EECCCCCCEEE
Confidence 57999998887765422 112234 88999988764
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.94 E-value=0.22 Score=22.08 Aligned_cols=34 Identities=18% Similarity=0.467 Sum_probs=22.5
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
..|+.|+..|.-...- +-.+... .+|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~-vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRK-VRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcE-EECCCCCcEee
Confidence 3688898888765431 2233345 89999988774
No 60
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=90.80 E-value=0.2 Score=27.86 Aligned_cols=30 Identities=23% Similarity=0.577 Sum_probs=21.0
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccCh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQK 87 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~ 87 (99)
..|+.||+.|... + +.|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL-----------n-k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------N-KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------C-CCCccCCCCCCccCcc
Confidence 3799999887542 2 3348899998887554
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.56 E-value=0.076 Score=32.97 Aligned_cols=45 Identities=36% Similarity=0.705 Sum_probs=28.1
Q ss_pred CCceeCCcccccccchhHHHhhhhh---hh-------CCCC----cccCCCCCccccCh
Q psy12010 43 SGMFPCDVCGKKYKYKWGLSRHKRD---EC-------GQEP----KYQCPQCPYRASQK 87 (99)
Q Consensus 43 ~k~~~C~~c~~~f~~~~~l~~h~~~---h~-------~~~~----~~~c~~C~~~f~~~ 87 (99)
+|..+|++|++.|....-.....++ .. +..| ...|+.||.++...
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 4668999999999887544333332 11 1111 26799999887543
No 62
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.52 E-value=0.067 Score=31.57 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=6.0
Q ss_pred eeCCcccccccc
Q psy12010 46 FPCDVCGKKYKY 57 (99)
Q Consensus 46 ~~C~~c~~~f~~ 57 (99)
++|+.||.+|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 455555555443
No 63
>PRK04860 hypothetical protein; Provisional
Probab=88.66 E-value=0.1 Score=30.99 Aligned_cols=30 Identities=13% Similarity=0.339 Sum_probs=24.2
Q ss_pred CcccccCccccccCCCceeCCcccccccch
Q psy12010 29 ESDFINWPTVRQYNSGMFPCDVCGKKYKYK 58 (99)
Q Consensus 29 ~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~ 58 (99)
.....+.|.+++.++++|.|..|+..|...
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 444567788889999999999999887654
No 64
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.50 E-value=0.66 Score=27.06 Aligned_cols=39 Identities=21% Similarity=0.550 Sum_probs=26.4
Q ss_pred CCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
+..-|.|+.|+..|.....+.. ... ... |.|+.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~-f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGT-FTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCc-EECCCCCCEEE
Confidence 4567999999999886543321 011 244 99999998753
No 65
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.28 E-value=0.28 Score=23.86 Aligned_cols=30 Identities=20% Similarity=0.469 Sum_probs=24.0
Q ss_pred cCCCceeCCcccccccchhHHHhhhhhhhC
Q psy12010 41 YNSGMFPCDVCGKKYKYKWGLSRHKRDECG 70 (99)
Q Consensus 41 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~ 70 (99)
.|+.-+.|+-|+..|....+..+|..--++
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 477788999999999999888888764333
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.23 E-value=0.49 Score=21.88 Aligned_cols=26 Identities=31% Similarity=0.953 Sum_probs=18.1
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
|.|..||..|... ...+ ..|++||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~-irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDV-VRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCc-eECCCCCce
Confidence 7888898876543 2244 889999865
No 67
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=87.97 E-value=0.53 Score=20.73 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=21.5
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
..|+.|+..|.-..... -..... .+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~-v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRK-VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcE-EECCCCCCEe
Confidence 46888888887665421 122244 8888888776
No 68
>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=87.83 E-value=0.56 Score=25.84 Aligned_cols=25 Identities=36% Similarity=0.883 Sum_probs=22.9
Q ss_pred ccC----CCCCccccChhHHHHHHHhhcC
Q psy12010 75 YQC----PQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 75 ~~c----~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
|.| ..|+....+...+.+|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8999999999999999999886
No 69
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=87.71 E-value=0.25 Score=26.25 Aligned_cols=32 Identities=22% Similarity=0.557 Sum_probs=21.7
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
..|.|+.|++. .+.++-+ . .+.|..|+..|.-
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~--G-IW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIAT--G-IWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc--------ceeeecc--C-eEEcCCCCCeecc
Confidence 46899999865 2233333 3 3899999988854
No 70
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=87.70 E-value=0.27 Score=28.32 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=12.7
Q ss_pred ccCCCCCccccChhHHHHHHHhhcC
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIKHS 99 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~~~ 99 (99)
..|-++|+.|.+ |++|+.+|+|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccC
Confidence 445566666653 6666666554
No 71
>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=87.59 E-value=0.28 Score=21.84 Aligned_cols=31 Identities=19% Similarity=0.578 Sum_probs=19.9
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
.|.|..||..|...... .. ... ..|+.||..
T Consensus 5 ~y~C~~Cg~~fe~~~~~------~~-~~~-~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI------SD-DPL-ATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEec------CC-CCC-CCCCCCCCc
Confidence 37899999887654322 11 233 688889863
No 72
>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=87.08 E-value=0.74 Score=20.94 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=10.4
Q ss_pred ccCCCCCccccC----hhHHHHHHH
Q psy12010 75 YQCPQCPYRASQ----KATLKTHMA 95 (99)
Q Consensus 75 ~~c~~C~~~f~~----~~~l~~H~~ 95 (99)
..|..|++.+.. .+.|.+|++
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 556666655443 355666663
No 73
>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=86.96 E-value=0.29 Score=23.17 Aligned_cols=29 Identities=24% Similarity=0.700 Sum_probs=17.9
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
|.|..||..|.....+. . ... ..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~-~~~-~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS------D-DPL-ATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC------C-CCC-CCCCCCCC
Confidence 78888888776542211 1 233 67888875
No 74
>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=86.33 E-value=0.77 Score=27.20 Aligned_cols=35 Identities=17% Similarity=0.473 Sum_probs=26.5
Q ss_pred cCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 41 YNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 41 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
.++.-|.|+.|+..|.....+. .- |.|+.||..+.
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEee
Confidence 3456799999998887766653 23 99999998753
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=86.24 E-value=0.4 Score=23.36 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=23.2
Q ss_pred hCCCCcccCCCCCccccChhHHHHHHHhhc
Q psy12010 69 CGQEPKYQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 69 ~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
.|+.- +.|+-|++.|...-...+|..--|
T Consensus 13 DGE~~-lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEF-LRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCcee-eeCCchhHHHHHhHHHHHHhhHHh
Confidence 35555 899999999999999999976544
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.23 E-value=0.75 Score=22.68 Aligned_cols=33 Identities=33% Similarity=0.872 Sum_probs=19.4
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
-.|.|+.||+.--.... +--....+ |.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~-----~CRk~g~~-Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA-----KCRKLGNP-YRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhh-----hHHHcCCc-eECCCcCc
Confidence 35899999954333221 11112255 99999984
No 77
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=85.67 E-value=0.33 Score=22.13 Aligned_cols=29 Identities=24% Similarity=0.872 Sum_probs=19.5
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
|.|..||..|.....+ .. ... ..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~-~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI------SE-DDP-VPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc------CC-CCC-CcCCCCCC
Confidence 7899999887664332 12 233 78888986
No 78
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=85.56 E-value=0.69 Score=30.61 Aligned_cols=60 Identities=17% Similarity=0.217 Sum_probs=46.3
Q ss_pred CCCCCCccccCCcccccCccc--cccCC--CceeCC--cccccccchhHHHhhhhhhhCCCCcccCC
Q psy12010 18 YSFNWPEVHLNESDFINWPTV--RQYNS--GMFPCD--VCGKKYKYKWGLSRHKRDECGQEPKYQCP 78 (99)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~--~~~~~--k~~~C~--~c~~~f~~~~~l~~h~~~h~~~~~~~~c~ 78 (99)
..+..+...+.....+..+.. .|.++ +++.|+ .|++.|.....+..|...|.+... +.+.
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 355 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP-AKEK 355 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc-cccc
Confidence 344445555666666777777 78888 999999 799999999999999999988654 5553
No 79
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.03 E-value=0.84 Score=21.46 Aligned_cols=21 Identities=24% Similarity=0.602 Sum_probs=13.0
Q ss_pred ccCCCCCccccCh-----hHHHHHHH
Q psy12010 75 YQCPQCPYRASQK-----ATLKTHMA 95 (99)
Q Consensus 75 ~~c~~C~~~f~~~-----~~l~~H~~ 95 (99)
..|..|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 5566666655433 56777776
No 80
>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=84.95 E-value=0.68 Score=26.45 Aligned_cols=30 Identities=13% Similarity=0.088 Sum_probs=20.1
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccCh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQK 87 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~ 87 (99)
..|+.||+.|... + +.|..|+.||..|.-.
T Consensus 10 r~Cp~cg~kFYDL-----------n-k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------N-RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------C-CCCccCCCcCCccCcc
Confidence 4788888877542 2 3348888888876544
No 81
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=84.61 E-value=1 Score=27.29 Aligned_cols=34 Identities=24% Similarity=0.627 Sum_probs=25.4
Q ss_pred CCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
+..-|.|+.|+..|.....+. .- |.|+.||..+.
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCe
Confidence 456799999998887765442 24 99999998753
No 82
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=83.66 E-value=0.44 Score=24.52 Aligned_cols=12 Identities=25% Similarity=0.498 Sum_probs=6.1
Q ss_pred ccCC--CCCccccC
Q psy12010 75 YQCP--QCPYRASQ 86 (99)
Q Consensus 75 ~~c~--~C~~~f~~ 86 (99)
++|. +||.+|..
T Consensus 28 ~qC~N~eCg~tF~t 41 (72)
T PRK09678 28 HQCQNVNCSATFIT 41 (72)
T ss_pred eecCCCCCCCEEEE
Confidence 4554 55555543
No 83
>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=83.32 E-value=0.7 Score=28.83 Aligned_cols=24 Identities=25% Similarity=0.555 Sum_probs=16.0
Q ss_pred ccCCCCCccccChhHHHHHHHhhc
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
|.|.+|+|.|.-..-+..|+...|
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-
T ss_pred ECCCCCCcccCChHHHHHHHhhcC
Confidence 778888888887777777776544
No 84
>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=82.59 E-value=0.89 Score=19.53 Aligned_cols=26 Identities=35% Similarity=0.975 Sum_probs=14.7
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
|.|..||..+... ...+ ..|..||..
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~-irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDP-IRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS-----------TSST-SSBSSSS-S
T ss_pred CCCCcCCCeeEcC-----------CCCc-EECCcCCCe
Confidence 5677777665421 1244 788888864
No 85
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.42 E-value=0.7 Score=21.34 Aligned_cols=29 Identities=28% Similarity=0.721 Sum_probs=18.9
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
.|.|+.||..|..... ... +.|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~-~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTG-VRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC----------CCc-eECCCCCCeE
Confidence 5788888876654321 113 7888888654
No 86
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.11 E-value=1 Score=21.35 Aligned_cols=29 Identities=24% Similarity=0.659 Sum_probs=19.3
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
..|.|..||+.|... ..... ..|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~-irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRG-IRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCc-eeCCCCCcE
Confidence 458999999887211 12133 889999864
No 87
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.52 E-value=0.7 Score=26.39 Aligned_cols=42 Identities=17% Similarity=0.276 Sum_probs=21.4
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccCh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQK 87 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~ 87 (99)
..|+.|....+-......=..+-...++|.-|..||+.|.+.
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwt 81 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWT 81 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcH
Confidence 456666554433322221111222235567788888888764
No 88
>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=79.43 E-value=1.8 Score=17.51 Aligned_cols=19 Identities=21% Similarity=0.357 Sum_probs=11.3
Q ss_pred eCCcccccccchhHHHhhhh
Q psy12010 47 PCDVCGKKYKYKWGLSRHKR 66 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~ 66 (99)
.|++|++.+ ....+..|.+
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777766 3345555554
No 89
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.12 E-value=2 Score=21.18 Aligned_cols=33 Identities=30% Similarity=0.811 Sum_probs=18.5
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
-.|.|+.||+..-.... +--....+ |.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~-----~CRk~~~~-Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE-----KCRKQSNP-YTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeech-----hHHhcCCc-eECCCCCC
Confidence 35889999975222111 01112255 99999974
No 90
>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=77.11 E-value=1 Score=18.78 Aligned_cols=11 Identities=36% Similarity=1.011 Sum_probs=7.2
Q ss_pred eeCCccccccc
Q psy12010 46 FPCDVCGKKYK 56 (99)
Q Consensus 46 ~~C~~c~~~f~ 56 (99)
|.|..|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 45677777773
No 91
>KOG4167|consensus
Probab=75.70 E-value=0.52 Score=34.45 Aligned_cols=24 Identities=17% Similarity=0.354 Sum_probs=19.8
Q ss_pred cccCCCCCccccChhHHHHHHHhh
Q psy12010 74 KYQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 74 ~~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
.|.|.+|++.|..--.+..|+++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 488999999998777788888776
No 92
>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=75.09 E-value=2 Score=18.93 Aligned_cols=33 Identities=21% Similarity=0.377 Sum_probs=19.1
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccCh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQK 87 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~ 87 (99)
..|+.||+.|... ....... -.|..||..+.++
T Consensus 2 r~C~~Cg~~Yh~~--------~~pP~~~-~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIE--------FNPPKVE-GVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETT--------TB--SST-TBCTTTTEBEBEE
T ss_pred cCcCCCCCccccc--------cCCCCCC-CccCCCCCeeEeC
Confidence 3688888876432 2223233 6788888765543
No 93
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=73.40 E-value=1.8 Score=17.31 Aligned_cols=10 Identities=50% Similarity=1.075 Sum_probs=7.6
Q ss_pred CceeCCcccc
Q psy12010 44 GMFPCDVCGK 53 (99)
Q Consensus 44 k~~~C~~c~~ 53 (99)
-.|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4688988874
No 94
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=73.25 E-value=3.2 Score=22.79 Aligned_cols=25 Identities=32% Similarity=0.618 Sum_probs=22.0
Q ss_pred eeC----CcccccccchhHHHhhhhhhhC
Q psy12010 46 FPC----DVCGKKYKYKWGLSRHKRDECG 70 (99)
Q Consensus 46 ~~C----~~c~~~f~~~~~l~~h~~~h~~ 70 (99)
|.| ..|+....+...+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 9999999999999999987654
No 95
>KOG4173|consensus
Probab=72.98 E-value=1.4 Score=27.46 Aligned_cols=50 Identities=26% Similarity=0.461 Sum_probs=37.1
Q ss_pred eCCcccccccchhHHHhhhhhh----------hCCCCcccC--CCCCccccChhHHHHHHHhh
Q psy12010 47 PCDVCGKKYKYKWGLSRHKRDE----------CGQEPKYQC--PQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~~h----------~~~~~~~~c--~~C~~~f~~~~~l~~H~~~~ 97 (99)
.|.+|.+.|....-|..|+.-. .|..- |+| +.|+-.|.+...-+.|+..-
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dM-y~ClvEgCt~KFkT~r~RkdH~I~~ 169 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDM-YQCLVEGCTEKFKTSRDRKDHMIRM 169 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccH-HHHHHHhhhhhhhhhhhhhhHHHHh
Confidence 7899999999888887776532 24444 888 45888898888888887543
No 96
>KOG4167|consensus
Probab=72.59 E-value=0.93 Score=33.24 Aligned_cols=27 Identities=30% Similarity=0.614 Sum_probs=24.0
Q ss_pred CceeCCcccccccchhHHHhhhhhhhC
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECG 70 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~ 70 (99)
.-|.|.+|++.|....++..||+.|..
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 459999999999999999999998864
No 97
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=72.34 E-value=3.9 Score=18.46 Aligned_cols=24 Identities=25% Similarity=0.338 Sum_probs=17.3
Q ss_pred eeCCcccccccch--hHHHhhhhhhh
Q psy12010 46 FPCDVCGKKYKYK--WGLSRHKRDEC 69 (99)
Q Consensus 46 ~~C~~c~~~f~~~--~~l~~h~~~h~ 69 (99)
-+|..||..|... .+-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4899999888764 46667766653
No 98
>PHA00626 hypothetical protein
Probab=71.94 E-value=2.2 Score=20.78 Aligned_cols=16 Identities=38% Similarity=0.872 Sum_probs=12.2
Q ss_pred CCcccCCCCCccccChh
Q psy12010 72 EPKYQCPQCPYRASQKA 88 (99)
Q Consensus 72 ~~~~~c~~C~~~f~~~~ 88 (99)
.. |+|..||..|+..+
T Consensus 22 nr-YkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DD-YVCCDCGYNDSKDA 37 (59)
T ss_pred cc-eEcCCCCCeechhh
Confidence 44 99999998886543
No 99
>KOG2593|consensus
Probab=71.91 E-value=2.9 Score=28.78 Aligned_cols=40 Identities=23% Similarity=0.390 Sum_probs=26.5
Q ss_pred cCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 41 YNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 41 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
+...-|.|+.|.+.|.....+.. +-..... |.|..|+-..
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~-F~C~~C~gel 163 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQL---LDNETGE-FHCENCGGEL 163 (436)
T ss_pred cccccccCCccccchhhhHHHHh---hcccCce-EEEecCCCch
Confidence 45677999999999887654432 1112234 9999997554
No 100
>KOG2482|consensus
Probab=71.52 E-value=2.3 Score=28.54 Aligned_cols=23 Identities=30% Similarity=0.514 Sum_probs=21.2
Q ss_pred ceeCCcccccccchhHHHhhhhh
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRD 67 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~ 67 (99)
.+.|-.|.+.|+.+..|+.||+-
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 37899999999999999999995
No 101
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.13 E-value=1 Score=23.39 Aligned_cols=32 Identities=22% Similarity=0.709 Sum_probs=19.0
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
.|+|..|+..|.- .+++. ..+.-.|+.|+..+
T Consensus 12 ~Y~c~~cg~~~dv----vq~~~----ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRFDV----VQAMT----DDPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHHHH----HHhcc----cCccccChhhChHH
Confidence 3889999876533 33322 23336788887654
No 102
>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=69.52 E-value=1.9 Score=20.60 Aligned_cols=27 Identities=15% Similarity=0.315 Sum_probs=16.8
Q ss_pred CCceeCCcccccccchhHHHhhhhhhh
Q psy12010 43 SGMFPCDVCGKKYKYKWGLSRHKRDEC 69 (99)
Q Consensus 43 ~k~~~C~~c~~~f~~~~~l~~h~~~h~ 69 (99)
...|.|+.|...|=..-++-.|..+|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 467999999999998888888877764
No 103
>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=69.22 E-value=1.1 Score=24.09 Aligned_cols=31 Identities=23% Similarity=0.609 Sum_probs=19.0
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
..|.|++|++.-.. +.-. . .+.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~--G-IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVAT--G-IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEE--------EEET--T-EEEETTTTEEEE
T ss_pred CCCcCCCCCCceeE--------Eeee--E-EeecCCCCCEEe
Confidence 45899999864211 1112 2 389999988773
No 104
>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=68.56 E-value=1.7 Score=23.43 Aligned_cols=31 Identities=26% Similarity=0.636 Sum_probs=19.1
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
..|.|++|++.-.. +.-. . .+.|..|++.|.
T Consensus 34 a~y~CpfCgk~~vk--------R~a~--G-IW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVK--------RGST--G-IWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceE--------EEee--E-EEEcCCCCCEEe
Confidence 45899999853111 1111 2 389999988874
No 105
>KOG2231|consensus
Probab=68.46 E-value=4.3 Score=29.66 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=9.6
Q ss_pred CCcccccccchhHHHhhhhh
Q psy12010 48 CDVCGKKYKYKWGLSRHKRD 67 (99)
Q Consensus 48 C~~c~~~f~~~~~l~~h~~~ 67 (99)
|..|...|-....|..|++.
T Consensus 185 C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred chhhhhhhccHHHHHHhhcc
Confidence 44454444444444444443
No 106
>KOG2785|consensus
Probab=68.43 E-value=5.7 Score=27.01 Aligned_cols=53 Identities=25% Similarity=0.212 Sum_probs=41.0
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCC----------------------cccCCCCC---ccccChhHHHHHHHh
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEP----------------------KYQCPQCP---YRASQKATLKTHMAI 96 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~----------------------~~~c~~C~---~~f~~~~~l~~H~~~ 96 (99)
-|-.|-.|++.+...-.-..||..++|.-- =+.|-.|. +.|.+..+...||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 346799999999998877889998876311 16676776 899999999999863
No 107
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.22 E-value=15 Score=20.62 Aligned_cols=23 Identities=17% Similarity=0.413 Sum_probs=11.9
Q ss_pred ccCCCCCccccChhHHHHHHHhh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
|+|..|...|-....+-.|..+|
T Consensus 82 y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 82 YVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred eeCCCCCCccccccchhhhhhcc
Confidence 55555555555554444444433
No 108
>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=68.06 E-value=3.2 Score=16.84 Aligned_cols=11 Identities=36% Similarity=0.936 Sum_probs=7.5
Q ss_pred ccCCCCCcccc
Q psy12010 75 YQCPQCPYRAS 85 (99)
Q Consensus 75 ~~c~~C~~~f~ 85 (99)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36777887764
No 109
>KOG1146|consensus
Probab=66.86 E-value=6.5 Score=31.04 Aligned_cols=50 Identities=22% Similarity=0.297 Sum_probs=35.6
Q ss_pred CCcccccccchhHHHhhhhh-hhCCCCcccCCCCCccccChhHHHHHHHhhc
Q psy12010 48 CDVCGKKYKYKWGLSRHKRD-ECGQEPKYQCPQCPYRASQKATLKTHMAIKH 98 (99)
Q Consensus 48 C~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~C~~~f~~~~~l~~H~~~~~ 98 (99)
|..|+..+.+...+..|+.. +.-.+. +.|..|+..|.....|..|+|..|
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt-~~cpkc~~~yk~a~~L~vhmRskh 489 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKT-LKCPKCNWHYKLAQTLGVHMRSKH 489 (1406)
T ss_pred ccchhhhhhhhcccccceeeeeccccc-ccCCccchhhhhHHHhhhcccccc
Confidence 44455555555555555553 444455 999999999999999999999743
No 110
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=65.56 E-value=2.7 Score=22.58 Aligned_cols=32 Identities=22% Similarity=0.614 Sum_probs=19.7
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
..|.|++|++.- +. +. +.. .+.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~-----vk---R~--a~G-IW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHA-----VK---RQ--AVG-IWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCc-----ee---ee--eeE-EEEcCCCCCEEeC
Confidence 468999998531 11 11 112 3899999888743
No 111
>KOG3408|consensus
Probab=65.47 E-value=3.7 Score=23.34 Aligned_cols=22 Identities=27% Similarity=0.532 Sum_probs=14.4
Q ss_pred ccCCCCCccccChhHHHHHHHh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
|-|-+|.+-|.....|..|.++
T Consensus 58 fyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhc
Confidence 6666666666666666666553
No 112
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=64.61 E-value=2.2 Score=25.21 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=6.7
Q ss_pred eCCcccccccch
Q psy12010 47 PCDVCGKKYKYK 58 (99)
Q Consensus 47 ~C~~c~~~f~~~ 58 (99)
.|..|+..|..-
T Consensus 30 eC~~C~~RFTTf 41 (156)
T COG1327 30 ECLECGERFTTF 41 (156)
T ss_pred cccccccccchh
Confidence 466666555543
No 113
>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=64.22 E-value=2 Score=18.97 Aligned_cols=30 Identities=23% Similarity=0.790 Sum_probs=16.1
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCC
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQC 80 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C 80 (99)
..|+.|+..- .+..|-....|... |.|..|
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qr-yrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQR-YRCKDC 35 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEe-EecCcC
Confidence 3566666321 13344444455555 887776
No 114
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=62.14 E-value=2.4 Score=22.81 Aligned_cols=31 Identities=23% Similarity=0.543 Sum_probs=18.7
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
..|.|++|++.-.. +.-. . .+.|..|++.|.
T Consensus 35 a~y~CpfCgk~~vk--------R~a~--G-IW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKVK--------RVGT--G-IWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCceE--------EEEE--E-EEEcCCCCCEEe
Confidence 45889999753111 1111 2 388988988774
No 115
>KOG2071|consensus
Probab=62.03 E-value=5.6 Score=28.56 Aligned_cols=28 Identities=18% Similarity=0.286 Sum_probs=22.8
Q ss_pred CCCceeCCcccccccchhHHHhhhhhhh
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRDEC 69 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~ 69 (99)
...+-+|..||..|.+......||..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4567899999999999887777777764
No 116
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=61.99 E-value=3.7 Score=17.35 Aligned_cols=9 Identities=33% Similarity=1.014 Sum_probs=6.1
Q ss_pred ccCCCCCcc
Q psy12010 75 YQCPQCPYR 83 (99)
Q Consensus 75 ~~c~~C~~~ 83 (99)
+.|+.|+..
T Consensus 20 ~vCp~C~~e 28 (30)
T PF08274_consen 20 LVCPECGHE 28 (30)
T ss_dssp EEETTTTEE
T ss_pred EeCCccccc
Confidence 777777654
No 117
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=61.23 E-value=11 Score=25.60 Aligned_cols=48 Identities=19% Similarity=0.144 Sum_probs=30.8
Q ss_pred eCCcccccccchhHHHhhhhhhhCCCCcccCCCCC----ccccChhHHHHHHHh
Q psy12010 47 PCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCP----YRASQKATLKTHMAI 96 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~----~~f~~~~~l~~H~~~ 96 (99)
.|.+|...|-....|..|++..+... +.|..-+ ..|.....|.+|.+.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~C--hICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEAC--HICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhh--hhhhccCccchhhhhCHHHHHHHhhc
Confidence 58888888888888888888654422 3443222 236666677777653
No 118
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=60.90 E-value=3.8 Score=19.65 Aligned_cols=41 Identities=29% Similarity=0.703 Sum_probs=21.1
Q ss_pred CceeCCc--ccccccchhHHHhhhhhhhCCCCcccCCC----CCccccC
Q psy12010 44 GMFPCDV--CGKKYKYKWGLSRHKRDECGQEPKYQCPQ----CPYRASQ 86 (99)
Q Consensus 44 k~~~C~~--c~~~f~~~~~l~~h~~~h~~~~~~~~c~~----C~~~f~~ 86 (99)
.+..|+. |...+. +..|..|....=...+ ..|.. |...+..
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRP-VPCPYSPYGCKERVPR 54 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSE-EE-SS----S--EEEH
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCc-EECCCCCCCCCCccch
Confidence 3567777 444344 4467788774334344 78888 7766544
No 119
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=60.69 E-value=4.8 Score=17.96 Aligned_cols=12 Identities=17% Similarity=0.598 Sum_probs=9.1
Q ss_pred ccCCCCCccccC
Q psy12010 75 YQCPQCPYRASQ 86 (99)
Q Consensus 75 ~~c~~C~~~f~~ 86 (99)
|+|..|++.|-.
T Consensus 13 f~C~~C~~~FC~ 24 (39)
T smart00154 13 FKCRHCGNLFCG 24 (39)
T ss_pred eECCccCCcccc
Confidence 888888877743
No 120
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.57 E-value=4.9 Score=23.18 Aligned_cols=15 Identities=27% Similarity=0.888 Sum_probs=11.7
Q ss_pred CceeCCcccccccch
Q psy12010 44 GMFPCDVCGKKYKYK 58 (99)
Q Consensus 44 k~~~C~~c~~~f~~~ 58 (99)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 458999999887654
No 121
>PF15269 zf-C2H2_7: Zinc-finger
Probab=60.41 E-value=7.3 Score=18.11 Aligned_cols=20 Identities=45% Similarity=1.037 Sum_probs=8.8
Q ss_pred ccCCCCCccccChhHHHHHH
Q psy12010 75 YQCPQCPYRASQKATLKTHM 94 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~ 94 (99)
|+|-.|.....-++.|-+|+
T Consensus 21 ykcfqcpftc~~kshl~nhm 40 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHM 40 (54)
T ss_pred ceeecCCcccchHHHHHHHH
Confidence 33444444444444444444
No 122
>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=60.14 E-value=2.7 Score=24.72 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=7.2
Q ss_pred eCCcccccccch
Q psy12010 47 PCDVCGKKYKYK 58 (99)
Q Consensus 47 ~C~~c~~~f~~~ 58 (99)
+|..|++.|...
T Consensus 30 eC~~C~~RFTTy 41 (147)
T TIGR00244 30 ECLECHERFTTF 41 (147)
T ss_pred cCCccCCcccee
Confidence 566666666554
No 123
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=56.45 E-value=4.4 Score=19.79 Aligned_cols=37 Identities=27% Similarity=0.447 Sum_probs=19.8
Q ss_pred eCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 47 PCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
+|..|++.+.-......-.++-......|-|.+|...
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 5777887665543222223333333334888888543
No 124
>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=55.70 E-value=4.4 Score=18.62 Aligned_cols=27 Identities=30% Similarity=0.805 Sum_probs=14.6
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
+.|+.||.. ....+. .... |+|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~-------~~~~-~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLK-------TRGR-YRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeC-------CCCe-EECCCCCC
Confidence 568888853 111111 1244 88888864
No 125
>KOG1280|consensus
Probab=54.18 E-value=13 Score=25.13 Aligned_cols=40 Identities=20% Similarity=0.408 Sum_probs=27.7
Q ss_pred CCCceeCCcccccccchhHHHhhhhh-hhCCCCcccCCCCC
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRD-ECGQEPKYQCPQCP 81 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~C~ 81 (99)
-.+.|.|++|++.--....|..|... |........|..|+
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 44579999999888888888888764 43323335566664
No 126
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=53.98 E-value=9.4 Score=22.22 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=17.2
Q ss_pred CCCceeCCcccccccchhHHHh
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSR 63 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~ 63 (99)
.++-+.|+.||+.|+.-+++..
T Consensus 121 ~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 121 YDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CCeEEECCCCCCEecccccHHH
Confidence 3456889999999998876654
No 127
>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=53.63 E-value=5 Score=18.19 Aligned_cols=12 Identities=17% Similarity=0.653 Sum_probs=6.6
Q ss_pred cccCCCCCcccc
Q psy12010 74 KYQCPQCPYRAS 85 (99)
Q Consensus 74 ~~~c~~C~~~f~ 85 (99)
|+.|..|++.|=
T Consensus 13 ~~~C~~C~~~FC 24 (43)
T PF01428_consen 13 PFKCKHCGKSFC 24 (43)
T ss_dssp HEE-TTTS-EE-
T ss_pred CeECCCCCcccC
Confidence 378888877764
No 128
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.63 E-value=6.9 Score=21.91 Aligned_cols=12 Identities=8% Similarity=-0.081 Sum_probs=8.3
Q ss_pred cccCCCCCcccc
Q psy12010 74 KYQCPQCPYRAS 85 (99)
Q Consensus 74 ~~~c~~C~~~f~ 85 (99)
|..|+.||++|.
T Consensus 26 PiVsPytG~s~P 37 (129)
T COG4530 26 PIVSPYTGKSYP 37 (129)
T ss_pred ccccCcccccch
Confidence 377777777774
No 129
>COG4640 Predicted membrane protein [Function unknown]
Probab=53.49 E-value=10 Score=26.10 Aligned_cols=14 Identities=29% Similarity=0.835 Sum_probs=7.2
Q ss_pred eeCCcccccccchh
Q psy12010 46 FPCDVCGKKYKYKW 59 (99)
Q Consensus 46 ~~C~~c~~~f~~~~ 59 (99)
++|..||..|....
T Consensus 16 ~qC~qCG~~~t~~~ 29 (465)
T COG4640 16 VQCTQCGHKFTSRQ 29 (465)
T ss_pred ccccccCCcCCchh
Confidence 34555555555443
No 130
>KOG2636|consensus
Probab=53.38 E-value=9.3 Score=26.68 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=23.4
Q ss_pred ccccccCCCceeCCccc-ccccchhHHHhhhh
Q psy12010 36 PTVRQYNSGMFPCDVCG-KKYKYKWGLSRHKR 66 (99)
Q Consensus 36 ~~~~~~~~k~~~C~~c~-~~f~~~~~l~~h~~ 66 (99)
.-.-|.-++.|.|.+|| +++.-...+.+|-.
T Consensus 392 LyKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 392 LYKLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred HHhhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 33446667889999999 77777777887765
No 131
>KOG2071|consensus
Probab=53.30 E-value=9.8 Score=27.41 Aligned_cols=24 Identities=29% Similarity=0.530 Sum_probs=20.4
Q ss_pred cccCCCCCccccChhHHHHHHHhh
Q psy12010 74 KYQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 74 ~~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
|-+|..||.+|........|+.+|
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cchhcccccccccchhhhhHhhhh
Confidence 489999999999988887777765
No 132
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.86 E-value=2.9 Score=22.91 Aligned_cols=39 Identities=15% Similarity=0.348 Sum_probs=21.6
Q ss_pred CCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
-.+-|.|+.||..-.....+.. -..... ..|..||.+|.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk----~~~~g~-~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKK----TVNIGT-AVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEEe----cCceeE-EEcccCcceEE
Confidence 4567889988865444333221 111122 67778877763
No 133
>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=50.98 E-value=12 Score=17.16 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=8.6
Q ss_pred cCCCCCccccChhHH
Q psy12010 76 QCPQCPYRASQKATL 90 (99)
Q Consensus 76 ~c~~C~~~f~~~~~l 90 (99)
.|..|+..|..+-.+
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 466666666655433
No 134
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=50.51 E-value=7.9 Score=18.35 Aligned_cols=17 Identities=18% Similarity=0.665 Sum_probs=13.0
Q ss_pred CCceeCCcccccccchh
Q psy12010 43 SGMFPCDVCGKKYKYKW 59 (99)
Q Consensus 43 ~k~~~C~~c~~~f~~~~ 59 (99)
.+.+.|..||..|..-.
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 46788999998877654
No 135
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=50.29 E-value=13 Score=18.05 Aligned_cols=10 Identities=70% Similarity=1.544 Sum_probs=6.0
Q ss_pred eCCccccccc
Q psy12010 47 PCDVCGKKYK 56 (99)
Q Consensus 47 ~C~~c~~~f~ 56 (99)
.|+.||+.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 4666666553
No 136
>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=50.01 E-value=3.4 Score=18.10 Aligned_cols=11 Identities=36% Similarity=0.706 Sum_probs=5.3
Q ss_pred ccCCCCCcccc
Q psy12010 75 YQCPQCPYRAS 85 (99)
Q Consensus 75 ~~c~~C~~~f~ 85 (99)
..|..||..++
T Consensus 22 isC~~CGPr~~ 32 (35)
T PF07503_consen 22 ISCTNCGPRYS 32 (35)
T ss_dssp --BTTCC-SCC
T ss_pred ccCCCCCCCEE
Confidence 56777776654
No 137
>KOG2482|consensus
Probab=49.69 E-value=9.9 Score=25.69 Aligned_cols=53 Identities=25% Similarity=0.290 Sum_probs=37.3
Q ss_pred CCceeCCcccccccch-hHHHhhhhhhhC----------------------CCCcccCCCCCccccChhHHHHHHHh
Q psy12010 43 SGMFPCDVCGKKYKYK-WGLSRHKRDECG----------------------QEPKYQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 43 ~k~~~C~~c~~~f~~~-~~l~~h~~~h~~----------------------~~~~~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
....+|.+|...+.-. +....|+-..++ -. .+.|-.|.+.|..+..|..||+-
T Consensus 142 ~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~-r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 142 IFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLE-RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHh-hheeeeeccccCCcHHHHHHHHh
Confidence 3557899998766553 455555542221 02 38899999999999999999984
No 138
>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=47.46 E-value=11 Score=21.00 Aligned_cols=27 Identities=22% Similarity=0.568 Sum_probs=17.7
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
-...|..|+..|..... . +.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~------------~-~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEID------------L-YRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCCc------------C-ccCcCCcCC
Confidence 34789999977654321 2 678888753
No 139
>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=46.96 E-value=22 Score=15.34 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=4.3
Q ss_pred ccCCCCCccc
Q psy12010 75 YQCPQCPYRA 84 (99)
Q Consensus 75 ~~c~~C~~~f 84 (99)
+.|..|++..
T Consensus 5 ~~C~nC~R~v 14 (33)
T PF08209_consen 5 VECPNCGRPV 14 (33)
T ss_dssp EE-TTTSSEE
T ss_pred EECCCCcCCc
Confidence 4455555443
No 140
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=46.16 E-value=8 Score=22.41 Aligned_cols=32 Identities=31% Similarity=0.884 Sum_probs=20.8
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
.|.|..|+..+.. +.++ .... |.|..|+..|.
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~~~~-~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--KRKR-YRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeee------eccc--chhh-EECCCCCCEEE
Confidence 5889999877633 3333 2244 88999987654
No 141
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=45.77 E-value=12 Score=18.56 Aligned_cols=10 Identities=50% Similarity=1.344 Sum_probs=3.5
Q ss_pred eCCccccccc
Q psy12010 47 PCDVCGKKYK 56 (99)
Q Consensus 47 ~C~~c~~~f~ 56 (99)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 4666666663
No 142
>PLN02294 cytochrome c oxidase subunit Vb
Probab=45.44 E-value=12 Score=22.67 Aligned_cols=17 Identities=24% Similarity=0.720 Sum_probs=13.0
Q ss_pred CCCceeCCcccccccch
Q psy12010 42 NSGMFPCDVCGKKYKYK 58 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~ 58 (99)
..+++.|++||..|.-+
T Consensus 138 kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 138 KGKSFECPVCTQYFELE 154 (174)
T ss_pred CCCceeCCCCCCEEEEE
Confidence 34788999999887654
No 143
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.10 E-value=15 Score=20.53 Aligned_cols=26 Identities=23% Similarity=0.405 Sum_probs=16.9
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
-.+.|..|+..|.... .. +.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~------------~~-~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ------------HD-AQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC------------cC-ccCcCCCC
Confidence 3478999987664421 22 66888874
No 144
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=45.06 E-value=12 Score=16.94 Aligned_cols=12 Identities=42% Similarity=1.135 Sum_probs=9.6
Q ss_pred CceeCCcccccc
Q psy12010 44 GMFPCDVCGKKY 55 (99)
Q Consensus 44 k~~~C~~c~~~f 55 (99)
++-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467899999876
No 145
>KOG0717|consensus
Probab=44.89 E-value=13 Score=26.22 Aligned_cols=22 Identities=23% Similarity=0.353 Sum_probs=17.2
Q ss_pred ccCCCCCccccChhHHHHHHHh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
+-|.+|.+.|.+--.|.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 5688888888888888888654
No 146
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=44.76 E-value=10 Score=21.86 Aligned_cols=15 Identities=20% Similarity=0.563 Sum_probs=12.7
Q ss_pred ceeCCcccccccchh
Q psy12010 45 MFPCDVCGKKYKYKW 59 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~ 59 (99)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578999999998765
No 147
>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=43.98 E-value=36 Score=18.72 Aligned_cols=38 Identities=8% Similarity=0.014 Sum_probs=27.1
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
..|.|+.-|..|.+.......+..... .. |.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~-~v-wtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQ-RV-WTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhC-Ce-eEEecCCCC
Confidence 457788888888888776666665543 44 888888775
No 148
>COG1773 Rubredoxin [Energy production and conversion]
Probab=43.65 E-value=11 Score=18.35 Aligned_cols=10 Identities=30% Similarity=0.982 Sum_probs=5.9
Q ss_pred ccCCCCCccc
Q psy12010 75 YQCPQCPYRA 84 (99)
Q Consensus 75 ~~c~~C~~~f 84 (99)
|+|..||..|
T Consensus 4 ~~C~~CG~vY 13 (55)
T COG1773 4 WRCSVCGYVY 13 (55)
T ss_pred eEecCCceEe
Confidence 5666666554
No 149
>PRK12496 hypothetical protein; Provisional
Probab=43.23 E-value=24 Score=21.09 Aligned_cols=28 Identities=25% Similarity=0.500 Sum_probs=17.7
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
|.|.-|++.|.... .. -.|+.||.....
T Consensus 128 ~~C~gC~~~~~~~~------------~~-~~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKKYPEDY------------PD-DVCEICGSPVKR 155 (164)
T ss_pred EECCCCCccccCCC------------CC-CcCCCCCChhhh
Confidence 67888988774321 11 468889865433
No 150
>PRK04351 hypothetical protein; Provisional
Probab=43.12 E-value=12 Score=22.03 Aligned_cols=33 Identities=27% Similarity=0.752 Sum_probs=21.9
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
.|.|..|+..+... +.+. ... |.|..|+..+..
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~n-~~~-yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRIN-TKR-YRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee-------eecC-CCc-EEeCCCCcEeee
Confidence 48899999766432 2222 255 999999876644
No 151
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.95 E-value=15 Score=21.10 Aligned_cols=15 Identities=20% Similarity=0.620 Sum_probs=11.7
Q ss_pred CCCcccCCCCCccccC
Q psy12010 71 QEPKYQCPQCPYRASQ 86 (99)
Q Consensus 71 ~~~~~~c~~C~~~f~~ 86 (99)
... |.|..|++.|..
T Consensus 51 ~qR-yrC~~C~~tf~~ 65 (129)
T COG3677 51 HQR-YKCKSCGSTFTV 65 (129)
T ss_pred ccc-cccCCcCcceee
Confidence 345 999999998854
No 152
>PF14353 CpXC: CpXC protein
Probab=42.83 E-value=5.7 Score=22.41 Aligned_cols=23 Identities=30% Similarity=0.716 Sum_probs=17.1
Q ss_pred CceeCCcccccccchhHHHhhhh
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKR 66 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~ 66 (99)
-.+.|+.||..|.-...+..|..
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcC
Confidence 35899999999887766655544
No 153
>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=42.68 E-value=8.2 Score=23.88 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=0.0
Q ss_pred cccCCCceeCCcccc-cccchhHHHhhhh
Q psy12010 39 RQYNSGMFPCDVCGK-KYKYKWGLSRHKR 66 (99)
Q Consensus 39 ~~~~~k~~~C~~c~~-~f~~~~~l~~h~~ 66 (99)
-|.-.+.|.|.+||. .|.-...+..|-.
T Consensus 95 LhGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 95 LHGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -----------------------------
T ss_pred HhCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 344456799999984 4444555555543
No 154
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=42.61 E-value=16 Score=27.15 Aligned_cols=63 Identities=21% Similarity=0.433 Sum_probs=39.4
Q ss_pred CCCCCCCCCCccccCCcccccCccccccCCCcee-CCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 14 LFPEYSFNWPEVHLNESDFINWPTVRQYNSGMFP-CDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~-C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
.+|--+|..|+..|.-...+-... ..+.-+.|. |+.|.+.|.+..+-. .|. ++ .-|+.||...
T Consensus 120 ~YPF~~CT~CGPRfTIi~alPYDR-~nTsM~~F~lC~~C~~EY~dP~nRR----fHA--Qp-~aCp~CGP~~ 183 (750)
T COG0068 120 LYPFINCTNCGPRFTIIEALPYDR-ENTSMADFPLCPFCDKEYKDPLNRR----FHA--QP-IACPKCGPHL 183 (750)
T ss_pred eccccccCCCCcceeeeccCCCCc-ccCccccCcCCHHHHHHhcCccccc----ccc--cc-ccCcccCCCe
Confidence 345557777877766654443333 334444555 999999888876533 332 34 8899998753
No 155
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=42.58 E-value=24 Score=17.19 Aligned_cols=10 Identities=40% Similarity=0.830 Sum_probs=5.2
Q ss_pred CceeCCcccc
Q psy12010 44 GMFPCDVCGK 53 (99)
Q Consensus 44 k~~~C~~c~~ 53 (99)
..|+|+.||-
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 3455555553
No 156
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=42.51 E-value=18 Score=25.08 Aligned_cols=29 Identities=31% Similarity=0.820 Sum_probs=17.7
Q ss_pred eCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccCh
Q psy12010 47 PCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQK 87 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~ 87 (99)
.|+.||.+..+ .|..- |.|+.||..+...
T Consensus 352 ~Cp~Cg~~m~S-----------~G~~g-~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKS-----------AGRNG-FRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhh-----------cCCCC-cccccccccCCcc
Confidence 57778755332 23334 8888888776553
No 157
>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=42.49 E-value=7.7 Score=17.24 Aligned_cols=10 Identities=40% Similarity=0.806 Sum_probs=4.8
Q ss_pred ccCCCCCccc
Q psy12010 75 YQCPQCPYRA 84 (99)
Q Consensus 75 ~~c~~C~~~f 84 (99)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 4455555443
No 158
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=41.44 E-value=15 Score=20.47 Aligned_cols=11 Identities=18% Similarity=0.616 Sum_probs=5.1
Q ss_pred eeCCccccccc
Q psy12010 46 FPCDVCGKKYK 56 (99)
Q Consensus 46 ~~C~~c~~~f~ 56 (99)
|.|++|+..|.
T Consensus 20 ~iCpeC~~EW~ 30 (109)
T TIGR00686 20 LICPSCLYEWN 30 (109)
T ss_pred eECcccccccc
Confidence 44555544443
No 159
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=40.67 E-value=26 Score=16.43 Aligned_cols=10 Identities=30% Similarity=0.962 Sum_probs=4.3
Q ss_pred eCCccccccc
Q psy12010 47 PCDVCGKKYK 56 (99)
Q Consensus 47 ~C~~c~~~f~ 56 (99)
.|..||+.|-
T Consensus 20 ~Cr~Cg~~~C 29 (57)
T cd00065 20 HCRNCGRIFC 29 (57)
T ss_pred ccCcCcCCcC
Confidence 3444444433
No 160
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=40.64 E-value=12 Score=22.02 Aligned_cols=33 Identities=21% Similarity=0.570 Sum_probs=20.4
Q ss_pred ccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 40 QYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 40 ~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
-.|...|.|..||....- .+++.- -.|+.|+..
T Consensus 107 ~~g~G~l~C~~Cg~~~~~---------~~~~~l--~~Cp~C~~~ 139 (146)
T PF07295_consen 107 VVGPGTLVCENCGHEVEL---------THPERL--PPCPKCGHT 139 (146)
T ss_pred EecCceEecccCCCEEEe---------cCCCcC--CCCCCCCCC
Confidence 345566999999964221 133323 588999865
No 161
>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=40.30 E-value=16 Score=20.27 Aligned_cols=26 Identities=23% Similarity=0.655 Sum_probs=15.7
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
...|..||..|.-.. .. +.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~-~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDE------------FD-FSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHH------------CC-HH-SSSSSS
T ss_pred cEECCCCCCEEecCC------------CC-CCCcCCcCC
Confidence 377999998875532 12 568888754
No 162
>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=40.04 E-value=16 Score=19.92 Aligned_cols=14 Identities=29% Similarity=0.631 Sum_probs=11.6
Q ss_pred CceeCCcccccccc
Q psy12010 44 GMFPCDVCGKKYKY 57 (99)
Q Consensus 44 k~~~C~~c~~~f~~ 57 (99)
+++.|.+||..|.-
T Consensus 78 ~~~rC~eCG~~fkL 91 (97)
T cd00924 78 KPKRCPECGHVFKL 91 (97)
T ss_pred CceeCCCCCcEEEE
Confidence 78999999987754
No 163
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=39.99 E-value=18 Score=16.16 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=5.9
Q ss_pred ccCCCCCccc
Q psy12010 75 YQCPQCPYRA 84 (99)
Q Consensus 75 ~~c~~C~~~f 84 (99)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5666666554
No 164
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=39.73 E-value=32 Score=16.28 Aligned_cols=14 Identities=29% Similarity=0.824 Sum_probs=9.7
Q ss_pred eeCCcccccccchh
Q psy12010 46 FPCDVCGKKYKYKW 59 (99)
Q Consensus 46 ~~C~~c~~~f~~~~ 59 (99)
+.|..||..|...-
T Consensus 29 W~C~~Cgh~w~~~v 42 (55)
T PF14311_consen 29 WKCPKCGHEWKASV 42 (55)
T ss_pred EECCCCCCeeEccH
Confidence 67888877766543
No 165
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.72 E-value=21 Score=21.48 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=16.6
Q ss_pred CceeCCcccccccchhHHHhh
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRH 64 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h 64 (99)
.-+.|+.||+.|+--+++..=
T Consensus 129 ~f~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred ceeECCCCcccccCchHHHHH
Confidence 457799999999998876543
No 166
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.68 E-value=12 Score=27.92 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=7.9
Q ss_pred CcccCCCCCcc
Q psy12010 73 PKYQCPQCPYR 83 (99)
Q Consensus 73 ~~~~c~~C~~~ 83 (99)
.|..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 34888888755
No 167
>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 PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=37.57 E-value=10 Score=24.69 Aligned_cols=35 Identities=11% Similarity=0.058 Sum_probs=13.3
Q ss_pred CCCCCCccccCCcccccCccccccCCCceeCCcccccc
Q psy12010 18 YSFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGKKY 55 (99)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f 55 (99)
..|..|+.....+....... .|.+-..|..|+..+
T Consensus 173 g~CPvCGs~P~~s~l~~~~~---~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGER---EGKRYLHCSLCGTEW 207 (290)
T ss_dssp SS-TTT---EEEEEEE---------EEEEEETTT--EE
T ss_pred CcCCCCCCcCceEEEecCCC---CccEEEEcCCCCCee
Confidence 57777766644443332221 255666677776544
No 169
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=37.45 E-value=15 Score=21.23 Aligned_cols=33 Identities=24% Similarity=0.682 Sum_probs=20.7
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
.|.|..|+..+.. +.+.. .... |.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~~------~rr~~-~~~~-y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLR------VRRSN-NVSR-YRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCce------Ecccc-Ccce-EEcCCCCCEEE
Confidence 6889889876542 22221 1144 89988987653
No 170
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=37.45 E-value=18 Score=21.51 Aligned_cols=37 Identities=24% Similarity=0.609 Sum_probs=24.6
Q ss_pred CCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
..-+|.|. |+..|-.. .+|-.+-.|+ . |.|..|+...
T Consensus 114 ~~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~-YrC~~C~gkL 150 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRI---RRHNTVRRGE-V-YRCGKCGGKL 150 (156)
T ss_pred cceeEEee-cCCccchh---hhcccccccc-e-EEeccCCceE
Confidence 34579999 99876554 3444444454 5 9999997654
No 171
>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=37.22 E-value=18 Score=17.14 Aligned_cols=11 Identities=36% Similarity=0.963 Sum_probs=7.7
Q ss_pred ccCCCCCcccc
Q psy12010 75 YQCPQCPYRAS 85 (99)
Q Consensus 75 ~~c~~C~~~f~ 85 (99)
|+|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 67777776654
No 172
>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=37.17 E-value=14 Score=17.53 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=7.0
Q ss_pred eCCcccccccchh
Q psy12010 47 PCDVCGKKYKYKW 59 (99)
Q Consensus 47 ~C~~c~~~f~~~~ 59 (99)
.|+.|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 7999999887653
No 173
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=36.92 E-value=16 Score=16.12 Aligned_cols=12 Identities=25% Similarity=0.921 Sum_probs=6.8
Q ss_pred CceeCCcccccc
Q psy12010 44 GMFPCDVCGKKY 55 (99)
Q Consensus 44 k~~~C~~c~~~f 55 (99)
+-|+|..||...
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 468999999654
No 174
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=36.82 E-value=50 Score=20.99 Aligned_cols=40 Identities=23% Similarity=0.390 Sum_probs=23.1
Q ss_pred cccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 39 RQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 39 ~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
.|..-....|..|++.|.....+. ..... .. -.|+.|+..
T Consensus 113 lHG~~~~~~C~~C~~~~~~~~~~~---~~~~~-~~-p~Cp~Cgg~ 152 (244)
T PRK14138 113 LHGNVEEYYCVRCGKRYTVEDVIE---KLEKS-DV-PRCDDCSGL 152 (244)
T ss_pred ccCCcCeeEECCCCCcccHHHHHH---HHhcC-CC-CCCCCCCCe
Confidence 354556678999998877643332 11112 22 368888743
No 175
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=36.72 E-value=22 Score=26.44 Aligned_cols=63 Identities=22% Similarity=0.454 Sum_probs=33.6
Q ss_pred CCCCCCCCCccccCCcccccCccccccCCCcee-CCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 15 FPEYSFNWPEVHLNESDFINWPTVRQYNSGMFP-CDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~-C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
+|--+|..|+..+.-...+.... .++.-+.|. |+.|-+.|.+..+- +-|. .+ ..|..||....
T Consensus 88 YpF~nCt~CGPr~~i~~~lpydr-~~t~m~~f~~C~~C~~ey~~p~~r----r~h~--~~-~~C~~Cgp~l~ 151 (711)
T TIGR00143 88 YPFISCTHCGPRFTIIEALPYDR-ENTSMADFPLCPDCAKEYKDPLDR----RFHA--QP-IACPRCGPQLN 151 (711)
T ss_pred CCcccccCCCCCeEEeecCCCCC-CCcCCCCCcCCHHHHHHhcCCccc----cCCC--CC-ccCCCCCcEEE
Confidence 34446666766655433322222 233334444 88888777655332 2221 33 78999997653
No 176
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.36 E-value=18 Score=19.80 Aligned_cols=9 Identities=44% Similarity=1.287 Sum_probs=5.5
Q ss_pred CceeCCccc
Q psy12010 44 GMFPCDVCG 52 (99)
Q Consensus 44 k~~~C~~c~ 52 (99)
..|.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 346666666
No 177
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=36.35 E-value=24 Score=16.64 Aligned_cols=12 Identities=25% Similarity=0.999 Sum_probs=8.8
Q ss_pred CCcccCCCCCccc
Q psy12010 72 EPKYQCPQCPYRA 84 (99)
Q Consensus 72 ~~~~~c~~C~~~f 84 (99)
.. +.|..||..+
T Consensus 36 ~r-~~C~~Cgyt~ 47 (50)
T PRK00432 36 DR-WHCGKCGYTE 47 (50)
T ss_pred Cc-EECCCcCCEE
Confidence 44 8898888764
No 178
>KOG2807|consensus
Probab=36.33 E-value=55 Score=22.18 Aligned_cols=23 Identities=17% Similarity=0.459 Sum_probs=16.8
Q ss_pred ccCCCCCccccChhHHHHHHHhh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAIK 97 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~~ 97 (99)
|.|..|...|-.....-.|...|
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred EEchhccceeeccchHHHHhhhh
Confidence 77888888887777776676554
No 179
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=36.06 E-value=22 Score=25.01 Aligned_cols=41 Identities=17% Similarity=0.345 Sum_probs=23.4
Q ss_pred CCCceeCCcccccccchh-HHHhhhhh----hhCCCCcccCCCCCcc
Q psy12010 42 NSGMFPCDVCGKKYKYKW-GLSRHKRD----ECGQEPKYQCPQCPYR 83 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~-~l~~h~~~----h~~~~~~~~c~~C~~~ 83 (99)
..+.|.|..||..|.-.. .-..-... -.-... |.|+.|+..
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~-~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDN-FLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCC-CcCcCCCCc
Confidence 456799999998887642 11111110 001133 899999854
No 180
>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=35.98 E-value=33 Score=24.26 Aligned_cols=22 Identities=27% Similarity=0.659 Sum_probs=14.4
Q ss_pred ccCCCCCccccChhHHHHHHHh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
+.|..|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 4566667777777777777653
No 181
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.96 E-value=15 Score=17.35 Aligned_cols=14 Identities=29% Similarity=0.570 Sum_probs=8.0
Q ss_pred cCCCCCccccChhH
Q psy12010 76 QCPQCPYRASQKAT 89 (99)
Q Consensus 76 ~c~~C~~~f~~~~~ 89 (99)
.|++|+..|.++-.
T Consensus 14 ICpvCqRPFsWRkK 27 (54)
T COG4338 14 ICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhcCchHHHHH
Confidence 45666666655443
No 182
>PRK10220 hypothetical protein; Provisional
Probab=35.49 E-value=24 Score=19.72 Aligned_cols=11 Identities=18% Similarity=0.912 Sum_probs=5.2
Q ss_pred eeCCccccccc
Q psy12010 46 FPCDVCGKKYK 56 (99)
Q Consensus 46 ~~C~~c~~~f~ 56 (99)
|.|++|+..|.
T Consensus 21 ~vCpeC~hEW~ 31 (111)
T PRK10220 21 YICPECAHEWN 31 (111)
T ss_pred EECCcccCcCC
Confidence 44555554443
No 183
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=35.40 E-value=17 Score=15.81 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=4.4
Q ss_pred cCCCCCccccC
Q psy12010 76 QCPQCPYRASQ 86 (99)
Q Consensus 76 ~c~~C~~~f~~ 86 (99)
.|.+|++.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 56667766644
No 184
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=35.38 E-value=36 Score=19.17 Aligned_cols=34 Identities=26% Similarity=0.484 Sum_probs=19.8
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccChhHH
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQKATL 90 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~~~l 90 (99)
...+|+.|++... ..| +. ..|..|+....-..+|
T Consensus 68 v~V~CP~C~K~TK-----------mLG-r~-D~CM~C~~pLTLd~~l 101 (114)
T PF11023_consen 68 VQVECPNCGKQTK-----------MLG-RV-DACMHCKEPLTLDPSL 101 (114)
T ss_pred eeeECCCCCChHh-----------hhc-hh-hccCcCCCcCccCchh
Confidence 4567999986432 123 33 5777777665544444
No 185
>PHA02998 RNA polymerase subunit; Provisional
Probab=35.34 E-value=27 Score=21.39 Aligned_cols=11 Identities=18% Similarity=0.495 Sum_probs=8.3
Q ss_pred ccCCCCCcccc
Q psy12010 75 YQCPQCPYRAS 85 (99)
Q Consensus 75 ~~c~~C~~~f~ 85 (99)
|.|..||+.|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 78888887764
No 186
>KOG1842|consensus
Probab=35.07 E-value=23 Score=24.92 Aligned_cols=27 Identities=22% Similarity=0.191 Sum_probs=23.3
Q ss_pred CceeCCcccccccchhHHHhhhhhhhC
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECG 70 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~ 70 (99)
+-|.|++|.+-|.....|..|....++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcc
Confidence 458999999999999999999886544
No 187
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.97 E-value=22 Score=19.93 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=9.9
Q ss_pred CceeCCcccccccc
Q psy12010 44 GMFPCDVCGKKYKY 57 (99)
Q Consensus 44 k~~~C~~c~~~f~~ 57 (99)
-.+.|..||..|..
T Consensus 70 ~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 70 VELECKDCSHVFKP 83 (117)
T ss_pred CEEEhhhCCCcccc
Confidence 34789999876644
No 188
>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=34.74 E-value=21 Score=19.66 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=4.4
Q ss_pred ceeCCcccc
Q psy12010 45 MFPCDVCGK 53 (99)
Q Consensus 45 ~~~C~~c~~ 53 (99)
|-.|+.||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 344555553
No 189
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.72 E-value=19 Score=19.45 Aligned_cols=13 Identities=15% Similarity=0.639 Sum_probs=11.1
Q ss_pred cccCCCCCccccC
Q psy12010 74 KYQCPQCPYRASQ 86 (99)
Q Consensus 74 ~~~c~~C~~~f~~ 86 (99)
|-.|..||..|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4889999999876
No 190
>KOG4602|consensus
Probab=34.58 E-value=32 Score=22.38 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=7.6
Q ss_pred ceeCCcccccccc
Q psy12010 45 MFPCDVCGKKYKY 57 (99)
Q Consensus 45 ~~~C~~c~~~f~~ 57 (99)
.|.|++||.+-.+
T Consensus 268 ~YVCPiCGATgDn 280 (318)
T KOG4602|consen 268 SYVCPICGATGDN 280 (318)
T ss_pred hhcCccccccCCc
Confidence 3667777655443
No 191
>PF12907 zf-met2: Zinc-binding
Probab=34.34 E-value=23 Score=15.97 Aligned_cols=25 Identities=16% Similarity=0.452 Sum_probs=14.4
Q ss_pred eeCCcccccccc---hhHHHhhhhhhhC
Q psy12010 46 FPCDVCGKKYKY---KWGLSRHKRDECG 70 (99)
Q Consensus 46 ~~C~~c~~~f~~---~~~l~~h~~~h~~ 70 (99)
+.|.+|...|-. ...|..|...-+.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHp 29 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHP 29 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCC
Confidence 467777754444 3457777664333
No 192
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=34.33 E-value=41 Score=20.91 Aligned_cols=35 Identities=26% Similarity=0.576 Sum_probs=19.1
Q ss_pred ceeCCcccccccchhHHHhhhhhhh-CCCCcccCCCCCcccc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDEC-GQEPKYQCPQCPYRAS 85 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~-~~~~~~~c~~C~~~f~ 85 (99)
-+.|+.|+ . -.. .|.-+-. |..+.+.|.+||..+.
T Consensus 6 y~~Cp~Cg-~-eev----~hEVik~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 6 YIECPSCG-S-EEV----SHEVIKERGREPLVRCEECGTVHP 41 (201)
T ss_pred EEECCCCC-c-chh----hHHHHHhcCCceEEEccCCCcEee
Confidence 36788888 1 111 1222222 3334588999987763
No 193
>KOG3507|consensus
Probab=34.04 E-value=18 Score=17.82 Aligned_cols=28 Identities=29% Similarity=0.824 Sum_probs=17.2
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
-|.|-.|+..- . +..+ +. +.|.+||.+-
T Consensus 20 iYiCgdC~~en----~------lk~~-D~-irCReCG~RI 47 (62)
T KOG3507|consen 20 IYICGDCGQEN----T------LKRG-DV-IRCRECGYRI 47 (62)
T ss_pred EEEeccccccc----c------ccCC-Cc-EehhhcchHH
Confidence 37888887421 1 1122 44 8999998763
No 194
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.92 E-value=24 Score=19.52 Aligned_cols=15 Identities=20% Similarity=0.507 Sum_probs=11.5
Q ss_pred ceeCCcccccccchh
Q psy12010 45 MFPCDVCGKKYKYKW 59 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~ 59 (99)
|+.|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 567888888887754
No 195
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=33.50 E-value=21 Score=23.14 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=18.5
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCC
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCP 81 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~ 81 (99)
=.|+.||..+.-...| |.- =. |+|+.|.
T Consensus 221 r~CP~Cg~~W~L~~pl------h~i-Fd-FKCD~CR 248 (258)
T PF10071_consen 221 RKCPSCGGDWRLKEPL------HDI-FD-FKCDPCR 248 (258)
T ss_pred CCCCCCCCccccCCch------hhc-ee-ccCCcce
Confidence 4799999877666554 211 22 8888884
No 196
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.85 E-value=26 Score=17.43 Aligned_cols=16 Identities=25% Similarity=0.837 Sum_probs=11.5
Q ss_pred CCCceeCCcccccccc
Q psy12010 42 NSGMFPCDVCGKKYKY 57 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~ 57 (99)
.+..-.|+.|++.|+-
T Consensus 45 ~~gev~CPYC~t~y~l 60 (62)
T COG4391 45 DEGEVVCPYCSTRYRL 60 (62)
T ss_pred CCCcEecCccccEEEe
Confidence 3455689999988753
No 197
>PLN02748 tRNA dimethylallyltransferase
Probab=32.77 E-value=30 Score=24.46 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=20.0
Q ss_pred CCCceeCCcccc-cccchhHHHhhhhh
Q psy12010 42 NSGMFPCDVCGK-KYKYKWGLSRHKRD 67 (99)
Q Consensus 42 ~~k~~~C~~c~~-~f~~~~~l~~h~~~ 67 (99)
..+.|.|+.|++ .+.....+..|.+.
T Consensus 415 ~~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 415 LWTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccccCCCCcccCCHHHHHHHhcc
Confidence 357789999997 78777777777664
No 198
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.36 E-value=27 Score=19.47 Aligned_cols=28 Identities=21% Similarity=0.423 Sum_probs=16.6
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
-.+.|..|+..|..... .. +.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~-----------~~-~~CP~Cgs~ 96 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ-----------RV-RRCPQCHGD 96 (114)
T ss_pred cEEEcccCCCeeecCCc-----------cC-CcCcCcCCC
Confidence 34789999875533210 11 568888743
No 199
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=31.69 E-value=25 Score=19.70 Aligned_cols=12 Identities=42% Similarity=1.184 Sum_probs=9.9
Q ss_pred ccCCCCCccccC
Q psy12010 75 YQCPQCPYRASQ 86 (99)
Q Consensus 75 ~~c~~C~~~f~~ 86 (99)
|.|..||..|..
T Consensus 101 y~C~~Cg~~wre 112 (113)
T COG1594 101 YKCTRCGYRWRE 112 (113)
T ss_pred EEecccCCEeec
Confidence 899999988753
No 200
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=31.12 E-value=8.5 Score=23.85 Aligned_cols=36 Identities=28% Similarity=0.598 Sum_probs=20.8
Q ss_pred ceeCCcccccccchhHHHhhhhh----hhCCC--CcccCCCCCccccC
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRD----ECGQE--PKYQCPQCPYRASQ 86 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~----h~~~~--~~~~c~~C~~~f~~ 86 (99)
...|++||..+ ..|+.. |.|.. ..+.|..||+++..
T Consensus 14 ~~~CPvCg~~l------~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~D 55 (201)
T COG1779 14 RIDCPVCGGTL------KAHMYLYDIPYFGEVLISTGVCERCGYRSTD 55 (201)
T ss_pred eecCCccccee------eEEEeeecCCccceEEEEEEEccccCCcccc
Confidence 35799998643 334332 33321 12678888887654
No 201
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.54 E-value=46 Score=22.01 Aligned_cols=22 Identities=32% Similarity=0.549 Sum_probs=17.4
Q ss_pred cccCCCCCccccChhHHHHHHH
Q psy12010 74 KYQCPQCPYRASQKATLKTHMA 95 (99)
Q Consensus 74 ~~~c~~C~~~f~~~~~l~~H~~ 95 (99)
.|.|+.|-+-|.+...|.+|+.
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHH
Confidence 3888888888888888888865
No 202
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=30.45 E-value=41 Score=22.04 Aligned_cols=11 Identities=27% Similarity=0.981 Sum_probs=5.6
Q ss_pred CCCceeCCccc
Q psy12010 42 NSGMFPCDVCG 52 (99)
Q Consensus 42 ~~k~~~C~~c~ 52 (99)
|.+.|+|.+|.
T Consensus 139 GGrif~CsfC~ 149 (314)
T PF06524_consen 139 GGRIFKCSFCD 149 (314)
T ss_pred CCeEEEeecCC
Confidence 44455555554
No 203
>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=30.43 E-value=23 Score=16.56 Aligned_cols=37 Identities=27% Similarity=0.545 Sum_probs=18.6
Q ss_pred eeCCcccccccchhHHHhh-----hhhhhCCCCcccCCCCCcc
Q psy12010 46 FPCDVCGKKYKYKWGLSRH-----KRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h-----~~~h~~~~~~~~c~~C~~~ 83 (99)
|.|..|+..|.-...-..+ .....-... |.|++|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~-w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDD-WVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT--B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCC-CcCcCCCCc
Confidence 7899999887665321100 001111244 899999754
No 204
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=29.24 E-value=75 Score=19.83 Aligned_cols=39 Identities=26% Similarity=0.330 Sum_probs=21.8
Q ss_pred cccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 39 RQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 39 ~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
.|..-....|..|++.+..... ...... .. -.|+.|+..
T Consensus 107 lHG~l~~~~C~~C~~~~~~~~~----~~~~~~-~~-p~C~~Cgg~ 145 (222)
T cd01413 107 LHGTLQTAYCVNCGSKYDLEEV----KYAKKH-EV-PRCPKCGGI 145 (222)
T ss_pred ccCCcCcceECCCCCCcchhHH----HHhccC-CC-CcCCCCCCc
Confidence 3444556789999987765432 111112 22 468888643
No 205
>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=28.80 E-value=14 Score=17.09 Aligned_cols=13 Identities=23% Similarity=0.496 Sum_probs=8.2
Q ss_pred ccCCC--CCccccCh
Q psy12010 75 YQCPQ--CPYRASQK 87 (99)
Q Consensus 75 ~~c~~--C~~~f~~~ 87 (99)
++|.. ||..|...
T Consensus 26 ~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 26 CQCTNPECGHTFVAN 40 (47)
T ss_pred EEECCCcCCCEEEEE
Confidence 66654 88777543
No 206
>KOG3014|consensus
Probab=27.83 E-value=66 Score=20.86 Aligned_cols=32 Identities=22% Similarity=0.316 Sum_probs=22.3
Q ss_pred ccccCCCce---eCCcccccccch--hHHHhhhhhhh
Q psy12010 38 VRQYNSGMF---PCDVCGKKYKYK--WGLSRHKRDEC 69 (99)
Q Consensus 38 ~~~~~~k~~---~C~~c~~~f~~~--~~l~~h~~~h~ 69 (99)
....|.+.| +|..||..|... .+-..|.+.|+
T Consensus 27 ~ld~Gqk~fg~~~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 27 HLDAGQKDFGAVKCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred EeecCccccCceehhhcCceecCCCHHHHHHHHHHHH
Confidence 334455554 799999887765 46678888876
No 207
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=27.41 E-value=32 Score=14.49 Aligned_cols=13 Identities=31% Similarity=0.994 Sum_probs=9.9
Q ss_pred CCceeCCcccccc
Q psy12010 43 SGMFPCDVCGKKY 55 (99)
Q Consensus 43 ~k~~~C~~c~~~f 55 (99)
.+-|+|..||...
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3578999998765
No 208
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=27.26 E-value=53 Score=13.47 Aligned_cols=8 Identities=25% Similarity=1.157 Sum_probs=3.3
Q ss_pred ccCCCCCc
Q psy12010 75 YQCPQCPY 82 (99)
Q Consensus 75 ~~c~~C~~ 82 (99)
|.|..|+.
T Consensus 28 f~C~~C~~ 35 (39)
T smart00132 28 FKCSKCGK 35 (39)
T ss_pred CCCcccCC
Confidence 34444443
No 209
>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=27.14 E-value=33 Score=14.50 Aligned_cols=12 Identities=25% Similarity=1.063 Sum_probs=9.1
Q ss_pred CceeCCcccccc
Q psy12010 44 GMFPCDVCGKKY 55 (99)
Q Consensus 44 k~~~C~~c~~~f 55 (99)
+-|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468899998665
No 210
>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=27.12 E-value=28 Score=16.81 Aligned_cols=30 Identities=30% Similarity=0.625 Sum_probs=20.2
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
++|+.||..+.-... ..| .. ..|..||..+
T Consensus 3 ~~CP~CG~~iev~~~-------~~G-ei-V~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENP-------ELG-EL-VICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCC-------ccC-CE-EeCCCCCCEE
Confidence 689999987644322 123 44 8999999765
No 211
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=26.99 E-value=43 Score=22.93 Aligned_cols=33 Identities=24% Similarity=0.431 Sum_probs=21.5
Q ss_pred cCccccccCCCceeCCccc-ccccchhHHHhhhh
Q psy12010 34 NWPTVRQYNSGMFPCDVCG-KKYKYKWGLSRHKR 66 (99)
Q Consensus 34 ~~~~~~~~~~k~~~C~~c~-~~f~~~~~l~~h~~ 66 (99)
.|.-.-|.-.+.|.|.+|| +.+--...+.+|..
T Consensus 363 ~WL~klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 363 RWLCKLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hHHHHhcCCCcceeeeecccccccchHHHHhhhh
Confidence 3444456667889999999 55555556665543
No 212
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.87 E-value=51 Score=16.46 Aligned_cols=8 Identities=25% Similarity=0.953 Sum_probs=4.2
Q ss_pred eeCCcccc
Q psy12010 46 FPCDVCGK 53 (99)
Q Consensus 46 ~~C~~c~~ 53 (99)
|-|++|..
T Consensus 32 ymC~eC~~ 39 (68)
T COG4896 32 YMCPECEH 39 (68)
T ss_pred EechhhHh
Confidence 55555543
No 213
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=26.85 E-value=28 Score=20.31 Aligned_cols=16 Identities=31% Similarity=0.661 Sum_probs=12.9
Q ss_pred CCceeCCcccccccch
Q psy12010 43 SGMFPCDVCGKKYKYK 58 (99)
Q Consensus 43 ~k~~~C~~c~~~f~~~ 58 (99)
.++..|+.||..|.-.
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 4689999999888654
No 214
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.31 E-value=20 Score=17.12 Aligned_cols=31 Identities=23% Similarity=0.383 Sum_probs=15.5
Q ss_pred eCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 47 PCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
.|.-|+...+...- .++..+.+- ..|+.||.
T Consensus 24 ~C~gC~~~l~~~~~----~~i~~~~~i-~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQEL----NEIRKGDEI-VFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHH----HHHHcCCCe-EECcCCCc
Confidence 56666655444322 122333343 67777764
No 215
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.25 E-value=36 Score=19.30 Aligned_cols=32 Identities=19% Similarity=0.337 Sum_probs=17.1
Q ss_pred CceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCc
Q psy12010 44 GMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPY 82 (99)
Q Consensus 44 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~ 82 (99)
-.+.| .||..|.....-.. +. .+.+.|+.||.
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~----~~--~~~~~CP~Cgs 100 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEID----HY--AAVIECPVCGN 100 (124)
T ss_pred eeEEe-eCcCcccccccchh----cc--ccCCcCcCCCC
Confidence 34789 99977654321000 00 11157888974
No 216
>PTZ00448 hypothetical protein; Provisional
Probab=26.12 E-value=57 Score=22.40 Aligned_cols=22 Identities=18% Similarity=0.451 Sum_probs=16.7
Q ss_pred ccCCCCCccccChhHHHHHHHh
Q psy12010 75 YQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 75 ~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
|.|..|+-.|.+......|.++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccccccccccCCHHHHHHHhhh
Confidence 7799998888776666667654
No 217
>PF14369 zf-RING_3: zinc-finger
Probab=25.48 E-value=55 Score=14.12 Aligned_cols=9 Identities=33% Similarity=0.870 Sum_probs=5.8
Q ss_pred cCCCCCccc
Q psy12010 76 QCPQCPYRA 84 (99)
Q Consensus 76 ~c~~C~~~f 84 (99)
.|+.|+..|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 477776665
No 218
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=25.43 E-value=17 Score=15.70 Aligned_cols=8 Identities=38% Similarity=1.348 Sum_probs=5.1
Q ss_pred ccCCCCCc
Q psy12010 75 YQCPQCPY 82 (99)
Q Consensus 75 ~~c~~C~~ 82 (99)
+.|..||.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 66666664
No 219
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=25.39 E-value=30 Score=15.28 Aligned_cols=13 Identities=31% Similarity=0.856 Sum_probs=9.4
Q ss_pred CceeCCccccccc
Q psy12010 44 GMFPCDVCGKKYK 56 (99)
Q Consensus 44 k~~~C~~c~~~f~ 56 (99)
..+.|+.||..+-
T Consensus 31 p~~~C~~CGE~~~ 43 (46)
T TIGR03831 31 PALVCPQCGEEYL 43 (46)
T ss_pred CccccccCCCEee
Confidence 4467999997654
No 220
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.33 E-value=17 Score=23.22 Aligned_cols=29 Identities=24% Similarity=0.325 Sum_probs=20.8
Q ss_pred CCCceeCCcccccccchhHHHhhhhhhhC
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRDECG 70 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~~ 70 (99)
.++.+.|++|+..|.....+....++-.|
T Consensus 16 ~kk~ieCPvC~tkFkkeev~tgsiRiiag 44 (267)
T COG1655 16 YKKTIECPVCNTKFKKEEVKTGSIRIIAG 44 (267)
T ss_pred hhceeccCcccchhhhhheeccceeEecc
Confidence 35668999999999887666555555444
No 221
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.23 E-value=57 Score=19.54 Aligned_cols=14 Identities=36% Similarity=0.807 Sum_probs=6.7
Q ss_pred CceeCCcccccccc
Q psy12010 44 GMFPCDVCGKKYKY 57 (99)
Q Consensus 44 k~~~C~~c~~~f~~ 57 (99)
.|.=|..||+.|++
T Consensus 67 ~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 67 APSYCHNCGKPYPW 80 (158)
T ss_pred CChhHHhCCCCCch
Confidence 34445555555544
No 222
>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=24.83 E-value=1.3e+02 Score=18.55 Aligned_cols=41 Identities=17% Similarity=0.203 Sum_probs=22.5
Q ss_pred cccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 39 RQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 39 ~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
.|..-....|..|+..+.....+. ........ -.|..|+..
T Consensus 89 lHG~~~~~~C~~C~~~~~~~~~~~---~~~~~~~~-p~C~~Cgg~ 129 (206)
T cd01410 89 LHGNMFIEVCKSCGPEYVRDDVVE---TRGDKETG-RRCHACGGI 129 (206)
T ss_pred ecCCcCcccCCCCCCccchHHHHH---HhhcCCCC-CcCCCCcCc
Confidence 344455677999997765543221 11112122 468888754
No 223
>PRK11823 DNA repair protein RadA; Provisional
Probab=24.72 E-value=52 Score=22.99 Aligned_cols=10 Identities=30% Similarity=1.066 Sum_probs=6.8
Q ss_pred ceeCCccccc
Q psy12010 45 MFPCDVCGKK 54 (99)
Q Consensus 45 ~~~C~~c~~~ 54 (99)
.|.|..||..
T Consensus 7 ~y~C~~Cg~~ 16 (446)
T PRK11823 7 AYVCQECGAE 16 (446)
T ss_pred eEECCcCCCC
Confidence 4777777754
No 224
>KOG0978|consensus
Probab=24.66 E-value=29 Score=25.81 Aligned_cols=17 Identities=12% Similarity=0.182 Sum_probs=11.8
Q ss_pred eCCcccccccchhHHHh
Q psy12010 47 PCDVCGKKYKYKWGLSR 63 (99)
Q Consensus 47 ~C~~c~~~f~~~~~l~~ 63 (99)
+||.|+..|....-+..
T Consensus 680 KCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVHRI 696 (698)
T ss_pred CCCCCCCCCCccccccc
Confidence 68888888877654433
No 225
>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=24.64 E-value=38 Score=16.15 Aligned_cols=17 Identities=12% Similarity=0.260 Sum_probs=11.0
Q ss_pred cCCCceeCCcccccccc
Q psy12010 41 YNSGMFPCDVCGKKYKY 57 (99)
Q Consensus 41 ~~~k~~~C~~c~~~f~~ 57 (99)
.+...|.|.+|++.+..
T Consensus 31 ~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITE 47 (52)
T ss_dssp TTTCEEEETTT--EEEH
T ss_pred CCCCEEEeeCCCCEecc
Confidence 45567899999987754
No 226
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.46 E-value=68 Score=19.59 Aligned_cols=33 Identities=27% Similarity=0.730 Sum_probs=20.4
Q ss_pred CCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccc
Q psy12010 42 NSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRA 84 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f 84 (99)
.+.-|.|+.|...|+.... ...+ |.|+.||...
T Consensus 110 ~~~~y~C~~~~~r~sfdeA------~~~~----F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEA------MELG----FTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHH------HHhC----CCCCCCCchh
Confidence 3455888777766554332 2223 8899998654
No 227
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=24.39 E-value=68 Score=20.84 Aligned_cols=28 Identities=7% Similarity=-0.032 Sum_probs=11.9
Q ss_pred ccccccCCCCCCCCCCCCCCccccCCcc
Q psy12010 4 WERFVSLAPDLFPEYSFNWPEVHLNESD 31 (99)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 (99)
++...+......+.-.|..|...++-+.
T Consensus 52 y~~~~s~~~~~~p~v~CrVCq~~I~i~g 79 (256)
T PF09788_consen 52 YSPLGSPESGGAPVVTCRVCQSLIDIEG 79 (256)
T ss_pred CCcccCCCCCCCceEEeecCCceecccC
Confidence 3333333444444444544444444433
No 228
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=24.12 E-value=1.1e+02 Score=18.90 Aligned_cols=40 Identities=23% Similarity=0.297 Sum_probs=22.0
Q ss_pred cccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcc
Q psy12010 39 RQYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYR 83 (99)
Q Consensus 39 ~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~ 83 (99)
.|..-....|..|++.+..... . ...... .. -.|+.|+..
T Consensus 103 lHG~~~~~~C~~C~~~~~~~~~-~--~~~~~~-~~-p~C~~Cg~~ 142 (218)
T cd01407 103 LHGSLFRVRCTKCGKEYPRDEL-Q--ADIDRE-EV-PRCPKCGGL 142 (218)
T ss_pred CcCCcCcceeCCCcCCCcHHHH-h--HhhccC-CC-CcCCCCCCc
Confidence 3445556789999987765421 1 111112 22 478888754
No 229
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=24.08 E-value=1.1e+02 Score=20.39 Aligned_cols=9 Identities=0% Similarity=-0.577 Sum_probs=5.4
Q ss_pred CCCCCcccc
Q psy12010 19 SFNWPEVHL 27 (99)
Q Consensus 19 ~~~~~~~~~ 27 (99)
.|..|+...
T Consensus 186 ~CPvCGs~P 194 (305)
T TIGR01562 186 LCPACGSPP 194 (305)
T ss_pred cCCCCCChh
Confidence 666665554
No 230
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.87 E-value=45 Score=21.58 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=8.4
Q ss_pred CceeCCcccccccch
Q psy12010 44 GMFPCDVCGKKYKYK 58 (99)
Q Consensus 44 k~~~C~~c~~~f~~~ 58 (99)
+.+.|+.||..+...
T Consensus 321 r~~~C~~cg~~~~rD 335 (364)
T COG0675 321 RLFKCPRCGFVHDRD 335 (364)
T ss_pred eeEECCCCCCeehhh
Confidence 446666666554443
No 231
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=23.17 E-value=54 Score=23.00 Aligned_cols=9 Identities=44% Similarity=1.250 Sum_probs=5.2
Q ss_pred eeCCccccc
Q psy12010 46 FPCDVCGKK 54 (99)
Q Consensus 46 ~~C~~c~~~ 54 (99)
|.|..||..
T Consensus 8 y~C~~Cg~~ 16 (454)
T TIGR00416 8 FVCQHCGAD 16 (454)
T ss_pred EECCcCCCC
Confidence 666666643
No 232
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.90 E-value=43 Score=14.31 Aligned_cols=12 Identities=25% Similarity=0.686 Sum_probs=8.4
Q ss_pred ceeCCccccccc
Q psy12010 45 MFPCDVCGKKYK 56 (99)
Q Consensus 45 ~~~C~~c~~~f~ 56 (99)
-+.|..|+..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 357888887663
No 233
>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=22.73 E-value=79 Score=20.83 Aligned_cols=12 Identities=25% Similarity=0.658 Sum_probs=7.7
Q ss_pred ccCCCCCccccC
Q psy12010 75 YQCPQCPYRASQ 86 (99)
Q Consensus 75 ~~c~~C~~~f~~ 86 (99)
+.|+.|+.-|.-
T Consensus 46 ~vc~~c~~h~rl 57 (285)
T TIGR00515 46 EVCPKCDHHMRM 57 (285)
T ss_pred CCCCCCCCcCcC
Confidence 567777766543
No 234
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=22.53 E-value=82 Score=20.95 Aligned_cols=32 Identities=22% Similarity=0.397 Sum_probs=17.4
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccCh
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQK 87 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~~ 87 (99)
.+|+.|+.....+. + ...- +.|+.|+.-|.-.
T Consensus 39 ~kc~~C~~~~~~~~-------l--~~~~-~vcp~c~~h~rlt 70 (296)
T CHL00174 39 VQCENCYGLNYKKF-------L--KSKM-NICEQCGYHLKMS 70 (296)
T ss_pred eECCCccchhhHHH-------H--HHcC-CCCCCCCCCcCCC
Confidence 46787876543221 1 1123 6788887766543
No 235
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=22.30 E-value=49 Score=18.14 Aligned_cols=41 Identities=15% Similarity=0.431 Sum_probs=14.9
Q ss_pred ccCCCceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 40 QYNSGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 40 ~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
..|.|.-.|..||..+.... +.+ .|.+.=|-|..|.+.|..
T Consensus 9 ~ag~ke~~CalCG~tWg~~y-----~Ev-~G~rLfFCCd~ca~EF~n 49 (105)
T PF11494_consen 9 EAGTKEMGCALCGATWGDYY-----EEV-DGERLFFCCDDCAKEFKN 49 (105)
T ss_dssp ---SGGGS-SS---S---SS------B--TT--BSSS--SSSS-TTS
T ss_pred ecccccccccccCCcHHHHH-----Hhh-cCCEEEEEcHHHHHHHHH
Confidence 34667778999998876432 222 244442556778777754
No 236
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=22.16 E-value=34 Score=24.65 Aligned_cols=40 Identities=28% Similarity=0.749 Sum_probs=21.0
Q ss_pred eeCCcccccccchh-HHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 46 FPCDVCGKKYKYKW-GLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 46 ~~C~~c~~~f~~~~-~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
..|+.||..+.-.. .|............ |.|..||.....
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~-y~C~~Cg~~i~e 241 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETAR-YVCPHCGCEIEE 241 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceE-EECCCCcCCCCH
Confidence 46888887766542 22221000111233 888888876543
No 237
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=21.75 E-value=95 Score=14.98 Aligned_cols=32 Identities=16% Similarity=0.278 Sum_probs=15.1
Q ss_pred CCceeCCcccccccchhHHHhhhhhhhCCCCcccCCC
Q psy12010 43 SGMFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQ 79 (99)
Q Consensus 43 ~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~ 79 (99)
+.|+....|+..|....-+..- ..... .+|+.
T Consensus 22 ~~PV~s~~C~H~fek~aI~~~i----~~~~~-~~CPv 53 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAILQYI----QRNGS-KRCPV 53 (57)
T ss_dssp SSEEEESSS--EEEHHHHHHHC----TTTS--EE-SC
T ss_pred hCCcCcCCCCCeecHHHHHHHH----HhcCC-CCCCC
Confidence 4566667777777665543322 12233 67765
No 238
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=21.74 E-value=47 Score=21.27 Aligned_cols=17 Identities=12% Similarity=0.507 Sum_probs=13.7
Q ss_pred CCCceeCCcccccccch
Q psy12010 42 NSGMFPCDVCGKKYKYK 58 (99)
Q Consensus 42 ~~k~~~C~~c~~~f~~~ 58 (99)
..++..|.+||..|.-.
T Consensus 178 EGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCCccCCCCCcEEEEE
Confidence 45689999999888664
No 239
>PRK06260 threonine synthase; Validated
Probab=21.67 E-value=80 Score=21.58 Aligned_cols=10 Identities=50% Similarity=1.248 Sum_probs=4.3
Q ss_pred eeCCcccccc
Q psy12010 46 FPCDVCGKKY 55 (99)
Q Consensus 46 ~~C~~c~~~f 55 (99)
++|..||+.|
T Consensus 4 ~~C~~cg~~~ 13 (397)
T PRK06260 4 LKCIECGKEY 13 (397)
T ss_pred EEECCCCCCC
Confidence 3444444433
No 240
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.66 E-value=41 Score=16.70 Aligned_cols=18 Identities=28% Similarity=0.748 Sum_probs=13.7
Q ss_pred ccCCCceeCCcccccccc
Q psy12010 40 QYNSGMFPCDVCGKKYKY 57 (99)
Q Consensus 40 ~~~~k~~~C~~c~~~f~~ 57 (99)
+..+....|+.|++.|.-
T Consensus 48 ~i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 48 EIVEGELICPECGREYPI 65 (68)
T ss_dssp ETTTTEEEETTTTEEEEE
T ss_pred cccCCEEEcCCCCCEEeC
Confidence 445677899999988864
No 241
>PRK05978 hypothetical protein; Provisional
Probab=21.49 E-value=57 Score=19.30 Aligned_cols=31 Identities=19% Similarity=0.398 Sum_probs=16.9
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCccccC
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRASQ 86 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~~ 86 (99)
-+|+.||+.=--+..|+ .. -.|..||-.|..
T Consensus 34 grCP~CG~G~LF~g~Lk---------v~-~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAFLK---------PV-DHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccccccc---------cC-CCccccCCcccc
Confidence 57999985321111111 22 578888876643
No 242
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=21.21 E-value=59 Score=22.96 Aligned_cols=23 Identities=30% Similarity=0.473 Sum_probs=20.4
Q ss_pred cccCCCCCccccChhHHHHHHHh
Q psy12010 74 KYQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 74 ~~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
.|.|+.|-+-|.+...|.+|+..
T Consensus 198 lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 198 LYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred EEEchhhhhhhcCHHHHHHHHhc
Confidence 49999999999999999999763
No 243
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.06 E-value=48 Score=14.78 Aligned_cols=30 Identities=23% Similarity=0.492 Sum_probs=16.2
Q ss_pred eeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 46 FPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 46 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
|.|+.|+.... . ....... +.|..||....
T Consensus 1 m~Cp~Cg~~~~-~--------~D~~~g~-~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKEI-V--------FDPERGE-LVCPNCGLVLE 30 (43)
T ss_dssp ESBTTTSSSEE-E--------EETTTTE-EEETTT-BBEE
T ss_pred CCCcCCcCCce-E--------EcCCCCe-EECCCCCCEee
Confidence 57888886431 0 0111133 78999986643
No 244
>KOG0402|consensus
Probab=20.82 E-value=30 Score=18.41 Aligned_cols=30 Identities=27% Similarity=0.688 Sum_probs=18.5
Q ss_pred ceeCCcccccccchhHHHhhhhhhhCCCCcccCCCCCcccc
Q psy12010 45 MFPCDVCGKKYKYKWGLSRHKRDECGQEPKYQCPQCPYRAS 85 (99)
Q Consensus 45 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~C~~~f~ 85 (99)
.|.|++||+.- +.+ .....+.|..|.+.+.
T Consensus 36 ky~CsfCGK~~-----vKR------~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 36 KYTCSFCGKKT-----VKR------KAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhcchhh-----hhh------hceeEEecCCccceec
Confidence 48999999642 111 1122388888887763
No 245
>KOG0801|consensus
Probab=20.66 E-value=33 Score=20.72 Aligned_cols=12 Identities=25% Similarity=0.719 Sum_probs=8.4
Q ss_pred ccCCCCCccccC
Q psy12010 75 YQCPQCPYRASQ 86 (99)
Q Consensus 75 ~~c~~C~~~f~~ 86 (99)
++|++|.|....
T Consensus 139 ~KCPvC~K~V~s 150 (205)
T KOG0801|consen 139 MKCPVCHKVVPS 150 (205)
T ss_pred ccCCccccccCC
Confidence 788888776543
No 246
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.53 E-value=70 Score=23.06 Aligned_cols=23 Identities=17% Similarity=0.158 Sum_probs=20.3
Q ss_pred cccCCCCCccccChhHHHHHHHh
Q psy12010 74 KYQCPQCPYRASQKATLKTHMAI 96 (99)
Q Consensus 74 ~~~c~~C~~~f~~~~~l~~H~~~ 96 (99)
.|.|+.|-+-|.+...|.+|+..
T Consensus 280 LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 280 LHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred EEEccchhhhhCCHHHHHHHHhc
Confidence 48999999999999999999763
No 247
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.47 E-value=1.6e+02 Score=19.78 Aligned_cols=34 Identities=9% Similarity=-0.001 Sum_probs=15.7
Q ss_pred CCCCCCCccccCCcccccCccccccCCCceeCCcccc
Q psy12010 17 EYSFNWPEVHLNESDFINWPTVRQYNSGMFPCDVCGK 53 (99)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~ 53 (99)
...|..|+.....+.. . .....|.+-..|..|+.
T Consensus 187 ~~~CPvCGs~P~~s~v-~--~~~~~G~RyL~CslC~t 220 (309)
T PRK03564 187 RQFCPVCGSMPVSSVV-Q--IGTTQGLRYLHCNLCES 220 (309)
T ss_pred CCCCCCCCCcchhhee-e--ccCCCCceEEEcCCCCC
Confidence 4567777655443321 1 11123445555555553
No 248
>PRK00420 hypothetical protein; Validated
Probab=20.08 E-value=70 Score=18.00 Aligned_cols=9 Identities=22% Similarity=0.298 Sum_probs=5.2
Q ss_pred ccCCCCCcc
Q psy12010 75 YQCPQCPYR 83 (99)
Q Consensus 75 ~~c~~C~~~ 83 (99)
..|+.||..
T Consensus 41 ~~Cp~Cg~~ 49 (112)
T PRK00420 41 VVCPVHGKV 49 (112)
T ss_pred eECCCCCCe
Confidence 556666654
Done!