Query psy6273
Match_columns 82
No_of_seqs 116 out of 1910
Neff 11.8
Searched_HMMs 46136
Date Fri Aug 16 22:11:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6273.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6273hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.8E-28 6E-33 126.8 2.4 77 3-82 187-263 (279)
2 KOG2462|consensus 99.9 1E-26 2.3E-31 121.0 2.2 76 2-82 160-235 (279)
3 KOG3623|consensus 99.8 1.3E-20 2.7E-25 108.9 1.6 77 3-82 894-970 (1007)
4 KOG3576|consensus 99.7 7.4E-19 1.6E-23 89.1 -1.3 76 3-81 117-192 (267)
5 KOG3623|consensus 99.6 1.2E-16 2.6E-21 92.9 3.1 77 3-82 240-329 (1007)
6 KOG1074|consensus 99.6 1.1E-16 2.4E-21 93.9 0.6 52 4-56 606-657 (958)
7 PHA00733 hypothetical protein 99.5 7.8E-15 1.7E-19 70.8 0.9 77 2-82 39-119 (128)
8 KOG3576|consensus 99.4 3.5E-14 7.6E-19 72.4 1.3 74 2-76 144-226 (267)
9 PHA02768 hypothetical protein; 99.4 1.6E-13 3.6E-18 56.6 2.1 44 32-79 5-48 (55)
10 PF13465 zf-H2C2_2: Zinc-finge 99.3 2.8E-12 6E-17 45.9 2.7 26 47-74 1-26 (26)
11 KOG1074|consensus 99.3 1.4E-12 3E-17 77.2 1.8 50 31-82 604-653 (958)
12 KOG3608|consensus 99.3 5.3E-12 1.1E-16 69.1 3.6 79 1-81 290-371 (467)
13 KOG3608|consensus 99.3 4.9E-12 1.1E-16 69.2 2.9 76 2-81 236-311 (467)
14 PHA02768 hypothetical protein; 99.2 8.5E-12 1.8E-16 51.5 1.7 43 4-49 6-48 (55)
15 PLN03086 PRLI-interacting fact 99.1 7E-11 1.5E-15 68.4 4.1 64 2-73 452-515 (567)
16 PHA00733 hypothetical protein 99.1 1.7E-10 3.7E-15 55.9 4.7 54 1-57 71-124 (128)
17 KOG3993|consensus 99.0 2.5E-11 5.4E-16 67.6 -1.8 78 4-82 268-376 (500)
18 PLN03086 PRLI-interacting fact 99.0 8.7E-10 1.9E-14 64.1 3.7 68 2-75 477-554 (567)
19 PHA00732 hypothetical protein 98.9 1.3E-09 2.8E-14 48.7 1.8 48 3-56 1-48 (79)
20 PF13465 zf-H2C2_2: Zinc-finge 98.9 8.9E-10 1.9E-14 39.3 1.0 25 18-43 1-25 (26)
21 PHA00616 hypothetical protein 98.9 1.5E-09 3.2E-14 43.0 1.7 34 32-67 1-34 (44)
22 PHA00616 hypothetical protein 98.8 4.3E-09 9.3E-14 41.7 1.8 34 3-37 1-34 (44)
23 COG5189 SFP1 Putative transcri 98.8 2E-09 4.4E-14 58.5 0.8 69 2-82 348-418 (423)
24 PF05605 zf-Di19: Drought indu 98.7 9.6E-08 2.1E-12 39.8 5.1 51 3-56 2-53 (54)
25 PHA00732 hypothetical protein 98.7 1.3E-08 2.7E-13 45.5 2.3 39 32-74 1-39 (79)
26 PF05605 zf-Di19: Drought indu 98.4 1.9E-07 4.1E-12 38.9 1.8 48 32-82 2-49 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.4 1.7E-07 3.7E-12 32.2 1.4 21 4-24 1-21 (23)
28 PF00096 zf-C2H2: Zinc finger, 98.3 3.4E-07 7.4E-12 31.4 1.5 23 33-55 1-23 (23)
29 PF12756 zf-C2H2_2: C2H2 type 98.2 1.6E-07 3.4E-12 43.4 -0.4 23 5-27 1-23 (100)
30 KOG3993|consensus 98.2 8.1E-07 1.8E-11 50.3 2.2 54 3-56 295-380 (500)
31 PF13912 zf-C2H2_6: C2H2-type 98.2 1.5E-06 3.3E-11 30.9 2.1 24 3-27 1-24 (27)
32 PF13894 zf-C2H2_4: C2H2-type 98.1 3.3E-06 7.1E-11 29.0 1.6 20 5-24 2-21 (24)
33 PF13912 zf-C2H2_6: C2H2-type 98.0 1.8E-06 3.9E-11 30.8 0.6 25 32-56 1-25 (27)
34 PF13894 zf-C2H2_4: C2H2-type 97.9 1.5E-05 3.2E-10 27.2 2.3 24 33-56 1-24 (24)
35 PF09237 GAGA: GAGA factor; I 97.9 1.9E-05 4.1E-10 32.2 2.5 32 27-58 19-50 (54)
36 PRK04860 hypothetical protein; 97.9 1.1E-05 2.5E-10 40.6 2.3 40 32-77 119-158 (160)
37 smart00355 ZnF_C2H2 zinc finge 97.7 5.4E-05 1.2E-09 26.1 2.1 20 5-24 2-21 (26)
38 PF09237 GAGA: GAGA factor; I 97.6 7.2E-05 1.6E-09 30.5 2.0 30 1-31 22-51 (54)
39 smart00355 ZnF_C2H2 zinc finge 97.6 0.00012 2.6E-09 25.2 2.4 24 33-56 1-24 (26)
40 PF12171 zf-C2H2_jaz: Zinc-fin 97.4 7.2E-05 1.6E-09 26.6 0.8 20 63-82 2-21 (27)
41 PF12874 zf-met: Zinc-finger o 97.4 6.6E-05 1.4E-09 26.1 0.7 19 5-23 2-20 (25)
42 PF12874 zf-met: Zinc-finger o 97.4 0.00011 2.5E-09 25.4 1.3 23 33-55 1-23 (25)
43 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00024 5.3E-09 24.4 1.4 20 34-54 2-21 (24)
44 PRK04860 hypothetical protein; 97.2 0.00018 3.9E-09 36.4 1.3 38 3-45 119-156 (160)
45 PF13913 zf-C2HC_2: zinc-finge 96.4 0.0028 6E-08 22.1 1.4 18 34-52 4-21 (25)
46 KOG2893|consensus 96.3 0.0022 4.8E-08 34.5 1.1 30 35-70 13-42 (341)
47 smart00451 ZnF_U1 U1-like zinc 96.0 0.0071 1.5E-07 22.5 1.8 22 3-24 3-24 (35)
48 COG5189 SFP1 Putative transcri 95.8 0.0015 3.2E-08 36.5 -0.7 24 1-24 396-419 (423)
49 KOG1146|consensus 95.8 0.0093 2E-07 39.1 2.5 53 2-54 464-540 (1406)
50 PF13719 zinc_ribbon_5: zinc-r 95.8 0.01 2.2E-07 22.7 1.8 34 33-73 3-36 (37)
51 COG2888 Predicted Zn-ribbon RN 95.4 0.015 3.2E-07 24.6 1.6 32 32-70 27-58 (61)
52 KOG2186|consensus 95.1 0.015 3.1E-07 31.7 1.5 47 3-53 3-49 (276)
53 PF13717 zinc_ribbon_4: zinc-r 95.1 0.023 5.1E-07 21.6 1.6 33 33-72 3-35 (36)
54 TIGR02098 MJ0042_CXXC MJ0042 f 95.1 0.023 5E-07 21.6 1.6 33 33-72 3-35 (38)
55 PF12756 zf-C2H2_2: C2H2 type 94.9 0.037 8.1E-07 25.3 2.5 21 4-24 51-71 (100)
56 KOG1146|consensus 94.8 0.004 8.6E-08 40.6 -1.2 57 26-82 459-538 (1406)
57 PF09538 FYDLN_acid: Protein o 94.8 0.018 3.8E-07 27.5 1.1 15 61-75 25-39 (108)
58 cd00350 rubredoxin_like Rubred 94.7 0.012 2.7E-07 21.8 0.4 8 62-69 17-24 (33)
59 COG1592 Rubrerythrin [Energy p 94.6 0.016 3.5E-07 29.7 0.8 23 32-69 134-156 (166)
60 COG0068 HypF Hydrogenase matur 94.6 0.0067 1.5E-07 37.4 -0.6 57 5-70 125-181 (750)
61 PF09986 DUF2225: Uncharacteri 94.4 0.0042 9E-08 33.0 -1.6 22 1-22 3-24 (214)
62 COG5048 FOG: Zn-finger [Genera 94.3 0.0053 1.1E-07 34.9 -1.4 62 3-66 289-355 (467)
63 KOG4173|consensus 94.3 0.012 2.7E-07 31.1 0.0 72 4-81 80-165 (253)
64 COG4049 Uncharacterized protei 94.2 0.027 5.9E-07 23.5 1.0 22 3-24 17-38 (65)
65 cd00729 rubredoxin_SM Rubredox 94.1 0.022 4.7E-07 21.4 0.5 9 61-69 17-25 (34)
66 TIGR00373 conserved hypothetic 93.3 0.11 2.3E-06 26.5 2.3 34 28-72 105-138 (158)
67 KOG2186|consensus 92.9 0.061 1.3E-06 29.4 1.2 44 33-81 4-47 (276)
68 KOG2482|consensus 92.8 0.17 3.7E-06 29.1 2.8 80 3-82 195-354 (423)
69 PF08790 zf-LYAR: LYAR-type C2 92.8 0.06 1.3E-06 19.3 0.7 11 63-73 1-11 (28)
70 PRK14890 putative Zn-ribbon RN 92.7 0.097 2.1E-06 22.2 1.4 33 31-70 24-56 (59)
71 PRK00398 rpoP DNA-directed RNA 92.3 0.037 8.1E-07 22.1 -0.1 9 62-70 21-29 (46)
72 smart00531 TFIIE Transcription 92.3 0.48 1E-05 23.8 3.8 38 29-72 96-133 (147)
73 PRK06266 transcription initiat 92.3 0.15 3.2E-06 26.5 2.1 33 29-72 114-146 (178)
74 TIGR02300 FYDLN_acid conserved 91.8 0.11 2.4E-06 25.5 1.2 12 61-72 25-36 (129)
75 PF07754 DUF1610: Domain of un 91.4 0.12 2.5E-06 17.9 0.8 10 61-70 15-24 (24)
76 COG5048 FOG: Zn-finger [Genera 91.3 0.071 1.5E-06 30.5 0.3 51 32-82 289-343 (467)
77 PHA00626 hypothetical protein 91.1 0.12 2.6E-06 21.6 0.8 15 61-75 22-36 (59)
78 PF04959 ARS2: Arsenite-resist 90.8 0.25 5.4E-06 26.6 2.0 26 3-28 77-102 (214)
79 smart00659 RPOLCX RNA polymera 90.7 0.19 4.1E-06 20.0 1.2 10 61-70 18-27 (44)
80 KOG2893|consensus 90.5 0.068 1.5E-06 29.1 -0.2 32 6-42 13-44 (341)
81 PF13451 zf-trcl: Probable zin 90.4 0.28 6.1E-06 20.0 1.5 13 2-14 3-15 (49)
82 PF02176 zf-TRAF: TRAF-type zi 90.0 0.099 2.1E-06 21.8 0.1 41 31-74 8-54 (60)
83 PRK00464 nrdR transcriptional 89.7 0.035 7.7E-07 28.1 -1.6 13 33-45 29-41 (154)
84 KOG2482|consensus 89.0 0.57 1.2E-05 27.1 2.5 66 17-82 129-215 (423)
85 PF10571 UPF0547: Uncharacteri 88.6 0.21 4.6E-06 17.5 0.5 11 63-73 15-25 (26)
86 KOG2593|consensus 87.5 1.2 2.5E-05 26.6 3.2 39 28-71 124-162 (436)
87 PRK09678 DNA-binding transcrip 87.5 0.14 3E-06 22.7 -0.3 15 61-75 26-42 (72)
88 TIGR00622 ssl1 transcription f 87.2 0.72 1.6E-05 22.3 2.0 67 3-75 15-94 (112)
89 smart00834 CxxC_CXXC_SSSS Puta 86.9 0.34 7.5E-06 18.5 0.7 15 61-75 4-18 (41)
90 COG1997 RPL43A Ribosomal prote 86.7 0.35 7.6E-06 22.2 0.8 33 32-76 35-67 (89)
91 PF04423 Rad50_zn_hook: Rad50 86.5 1.1 2.4E-05 18.4 2.2 11 64-74 22-32 (54)
92 smart00154 ZnF_AN1 AN1-like Zi 86.4 0.39 8.5E-06 18.5 0.8 14 62-75 12-25 (39)
93 PF03604 DNA_RNApol_7kD: DNA d 85.5 0.19 4.2E-06 18.6 -0.3 7 63-69 18-24 (32)
94 KOG4173|consensus 85.4 0.27 5.8E-06 26.3 0.1 46 32-82 79-126 (253)
95 PF12013 DUF3505: Protein of u 85.4 0.76 1.7E-05 21.8 1.6 26 32-57 80-109 (109)
96 PF04959 ARS2: Arsenite-resist 85.4 0.34 7.4E-06 26.1 0.4 29 30-58 75-103 (214)
97 PF09723 Zn-ribbon_8: Zinc rib 85.2 0.46 9.9E-06 18.6 0.7 15 62-76 5-19 (42)
98 PF01428 zf-AN1: AN1-like Zinc 84.9 0.39 8.5E-06 18.8 0.4 15 61-75 12-26 (43)
99 smart00734 ZnF_Rad18 Rad18-lik 83.6 1.5 3.2E-05 15.3 1.8 18 5-23 3-20 (26)
100 COG1996 RPC10 DNA-directed RNA 83.3 0.43 9.2E-06 19.5 0.2 10 33-42 7-16 (49)
101 TIGR00143 hypF [NiFe] hydrogen 82.1 0.19 4.2E-06 31.6 -1.4 55 6-69 93-147 (711)
102 PF10013 DUF2256: Uncharacteri 82.1 0.46 1E-05 18.7 0.1 14 63-76 9-22 (42)
103 KOG2231|consensus 81.9 1.1 2.4E-05 28.2 1.6 21 6-27 118-138 (669)
104 PF01927 Mut7-C: Mut7-C RNAse 81.8 0.7 1.5E-05 23.2 0.7 19 61-79 123-141 (147)
105 TIGR02605 CxxC_CxxC_SSSS putat 81.6 0.77 1.7E-05 18.6 0.7 14 62-75 5-18 (52)
106 KOG3408|consensus 81.5 1.5 3.2E-05 21.5 1.7 27 28-54 53-79 (129)
107 smart00614 ZnF_BED BED zinc fi 80.9 2.1 4.6E-05 17.2 1.9 8 46-53 37-44 (50)
108 PF15269 zf-C2H2_7: Zinc-finge 80.8 1.3 2.7E-05 17.7 1.1 23 33-55 21-43 (54)
109 PF02892 zf-BED: BED zinc fing 80.8 2.5 5.4E-05 16.4 2.0 19 34-52 18-40 (45)
110 KOG1280|consensus 80.7 2.5 5.5E-05 24.6 2.6 39 31-69 78-116 (381)
111 KOG2785|consensus 80.0 4.5 9.7E-05 23.9 3.4 25 3-28 166-190 (390)
112 KOG4124|consensus 79.4 0.18 3.9E-06 29.0 -2.0 68 2-81 348-417 (442)
113 KOG2785|consensus 79.0 3.9 8.5E-05 24.1 3.0 23 2-24 2-24 (390)
114 PF08274 PhnA_Zn_Ribbon: PhnA 78.6 1.3 2.9E-05 16.1 0.8 10 61-70 18-27 (30)
115 PRK03824 hypA hydrogenase nick 78.5 0.73 1.6E-05 22.9 0.2 13 32-44 70-82 (135)
116 PTZ00255 60S ribosomal protein 78.5 0.72 1.6E-05 21.4 0.1 33 31-75 35-67 (90)
117 PF01363 FYVE: FYVE zinc finge 77.5 1.5 3.4E-05 18.8 1.0 26 34-73 11-36 (69)
118 PF14353 CpXC: CpXC protein 77.2 1.4 3E-05 21.5 0.9 17 61-77 37-53 (128)
119 PF10276 zf-CHCC: Zinc-finger 76.8 1.4 3E-05 17.2 0.7 12 61-72 28-39 (40)
120 KOG2907|consensus 76.3 1.4 3.1E-05 21.3 0.8 40 33-75 75-115 (116)
121 COG4530 Uncharacterized protei 75.7 1.1 2.5E-05 21.5 0.4 12 61-72 25-36 (129)
122 TIGR00280 L37a ribosomal prote 75.3 0.77 1.7E-05 21.3 -0.2 32 32-75 35-66 (91)
123 PF12907 zf-met2: Zinc-binding 75.2 2.8 6.1E-05 16.4 1.3 11 17-27 18-28 (40)
124 COG1773 Rubredoxin [Energy pro 75.0 1.6 3.6E-05 18.3 0.7 16 1-16 1-16 (55)
125 cd00924 Cyt_c_Oxidase_Vb Cytoc 73.7 1.9 4E-05 20.4 0.8 13 61-73 78-90 (97)
126 KOG4167|consensus 73.4 1.3 2.9E-05 28.3 0.3 25 32-56 792-816 (907)
127 PF04780 DUF629: Protein of un 72.5 3.7 8.1E-05 25.0 2.0 27 4-30 58-84 (466)
128 PF01286 XPA_N: XPA protein N- 72.1 2.3 4.9E-05 16.0 0.7 15 63-77 4-18 (34)
129 PF15135 UPF0515: Uncharacteri 72.1 3.8 8.2E-05 22.8 1.8 14 62-75 155-168 (278)
130 PF07282 OrfB_Zn_ribbon: Putat 72.0 3.1 6.7E-05 17.9 1.3 29 33-73 29-57 (69)
131 KOG4167|consensus 72.0 0.71 1.5E-05 29.4 -1.0 24 4-28 793-816 (907)
132 COG1655 Uncharacterized protei 71.8 0.98 2.1E-05 24.7 -0.4 18 2-19 18-35 (267)
133 PLN02294 cytochrome c oxidase 70.9 2.2 4.8E-05 22.3 0.7 14 61-74 140-153 (174)
134 PRK14873 primosome assembly pr 70.8 2.6 5.7E-05 26.7 1.2 10 61-70 421-430 (665)
135 COG1326 Uncharacterized archae 69.7 7.2 0.00016 20.9 2.4 12 61-72 29-40 (201)
136 PF11672 DUF3268: Protein of u 69.7 1.7 3.6E-05 20.7 0.2 10 2-11 1-10 (102)
137 PRK12380 hydrogenase nickel in 69.4 1.7 3.8E-05 20.9 0.2 25 32-70 70-94 (113)
138 COG5236 Uncharacterized conser 69.4 6.3 0.00014 23.2 2.3 47 5-53 222-272 (493)
139 KOG1842|consensus 69.2 0.75 1.6E-05 27.5 -1.2 18 32-49 15-32 (505)
140 PF01155 HypA: Hydrogenase exp 68.8 1.4 3.1E-05 21.2 -0.2 25 33-71 71-95 (113)
141 COG1675 TFA1 Transcription ini 68.6 7.5 0.00016 20.5 2.4 33 28-71 109-141 (176)
142 PF05443 ROS_MUCR: ROS/MUCR tr 67.2 3.8 8.1E-05 20.5 1.1 25 31-58 71-95 (132)
143 PF02891 zf-MIZ: MIZ/SP-RING z 67.0 4.4 9.6E-05 16.5 1.1 10 61-70 40-49 (50)
144 COG3677 Transposase and inacti 66.9 2.9 6.3E-05 20.7 0.7 15 61-75 52-66 (129)
145 PF08792 A2L_zn_ribbon: A2L zi 65.7 3.6 7.7E-05 15.3 0.7 12 62-73 21-32 (33)
146 PF05191 ADK_lid: Adenylate ki 65.2 3.3 7E-05 15.7 0.5 12 63-74 2-13 (36)
147 PF01215 COX5B: Cytochrome c o 65.1 3.5 7.7E-05 20.7 0.8 13 61-73 111-123 (136)
148 COG1656 Uncharacterized conser 65.1 3.1 6.7E-05 21.6 0.6 19 61-79 129-147 (165)
149 PF09845 DUF2072: Zn-ribbon co 65.1 3.8 8.3E-05 20.4 0.9 15 3-17 1-15 (131)
150 cd00065 FYVE FYVE domain; Zinc 65.0 3.5 7.7E-05 16.8 0.7 9 6-14 5-13 (57)
151 PF11023 DUF2614: Protein of u 65.0 2.9 6.2E-05 20.3 0.4 13 30-42 67-79 (114)
152 TIGR00686 phnA alkylphosphonat 64.3 3 6.5E-05 20.1 0.4 9 33-41 20-28 (109)
153 TIGR00100 hypA hydrogenase nic 64.0 2.7 5.8E-05 20.3 0.3 25 33-71 71-95 (115)
154 KOG0782|consensus 63.7 1.6 3.4E-05 27.3 -0.6 52 17-76 239-290 (1004)
155 PF12760 Zn_Tnp_IS1595: Transp 63.7 6.9 0.00015 15.5 1.4 10 61-70 36-45 (46)
156 KOG0978|consensus 63.3 3.8 8.1E-05 26.2 0.8 22 61-82 677-698 (698)
157 COG4338 Uncharacterized protei 63.1 1.4 3E-05 17.9 -0.7 13 64-76 14-26 (54)
158 PRK03681 hypA hydrogenase nick 63.1 2.3 5E-05 20.5 -0.1 27 32-71 70-96 (114)
159 KOG2636|consensus 62.7 6.4 0.00014 23.9 1.6 28 26-53 395-423 (497)
160 PRK00432 30S ribosomal protein 62.3 4.2 9.1E-05 16.6 0.7 12 61-72 36-47 (50)
161 COG4391 Uncharacterized protei 62.1 3.7 8E-05 17.6 0.5 43 26-74 18-60 (62)
162 smart00064 FYVE Protein presen 61.9 4.1 8.9E-05 17.4 0.6 8 35-42 13-20 (68)
163 PF10537 WAC_Acf1_DNA_bd: ATP- 60.3 9.7 0.00021 18.1 1.7 39 1-41 1-39 (102)
164 COG4957 Predicted transcriptio 60.2 6.9 0.00015 19.7 1.3 23 33-58 77-99 (148)
165 TIGR01206 lysW lysine biosynth 59.7 4.2 9E-05 17.0 0.4 11 63-73 3-13 (54)
166 PRK00564 hypA hydrogenase nick 59.4 3.5 7.6E-05 20.0 0.2 13 32-44 71-83 (117)
167 PF08209 Sgf11: Sgf11 (transcr 59.3 5.2 0.00011 14.9 0.6 13 61-73 3-15 (33)
168 PF07503 zf-HYPF: HypF finger; 58.8 1.1 2.3E-05 16.9 -1.3 9 62-70 21-29 (35)
169 COG1571 Predicted DNA-binding 58.2 4.3 9.2E-05 24.4 0.4 11 32-42 367-377 (421)
170 PF14255 Cys_rich_CPXG: Cystei 58.1 4.2 9.2E-05 16.8 0.3 10 64-73 2-11 (52)
171 PRK10220 hypothetical protein; 57.6 5.5 0.00012 19.3 0.7 9 33-41 21-29 (111)
172 PF00301 Rubredoxin: Rubredoxi 57.3 5.8 0.00013 16.0 0.6 12 63-74 2-13 (47)
173 COG3091 SprT Zn-dependent meta 57.3 4.8 0.0001 20.7 0.5 35 30-71 115-149 (156)
174 PF01844 HNH: HNH endonuclease 56.9 5 0.00011 15.5 0.4 11 65-75 1-11 (47)
175 TIGR03831 YgiT_finger YgiT-typ 56.1 4.9 0.00011 15.5 0.3 13 61-73 31-43 (46)
176 COG1198 PriA Primosomal protei 55.9 1.3 2.9E-05 28.3 -1.9 11 61-71 474-484 (730)
177 cd00730 rubredoxin Rubredoxin; 55.8 5.2 0.00011 16.4 0.4 11 63-73 2-12 (50)
178 PRK05978 hypothetical protein; 55.6 4.1 8.9E-05 20.8 0.1 30 34-74 35-64 (148)
179 PF13878 zf-C2H2_3: zinc-finge 55.5 14 0.0003 14.3 1.7 24 33-56 14-39 (41)
180 PF14690 zf-ISL3: zinc-finger 54.8 5.9 0.00013 15.5 0.5 10 62-71 2-11 (47)
181 KOG0717|consensus 54.4 7.6 0.00016 23.8 1.0 22 33-54 293-314 (508)
182 PF06397 Desulfoferrod_N: Desu 54.1 7.2 0.00016 14.9 0.6 12 61-72 5-16 (36)
183 PF14787 zf-CCHC_5: GAG-polypr 54.0 6.8 0.00015 14.9 0.6 14 64-77 4-17 (36)
184 COG3357 Predicted transcriptio 52.7 7 0.00015 18.3 0.6 12 3-14 58-69 (97)
185 PF08271 TF_Zn_Ribbon: TFIIB z 52.5 6.9 0.00015 15.2 0.5 8 63-70 1-8 (43)
186 PTZ00043 cytochrome c oxidase 51.5 6.8 0.00015 21.6 0.5 14 61-74 180-193 (268)
187 PF09963 DUF2197: Uncharacteri 51.0 6.1 0.00013 16.7 0.2 7 33-39 32-38 (56)
188 PF09889 DUF2116: Uncharacteri 50.8 13 0.00028 15.9 1.2 9 6-14 6-14 (59)
189 PF01096 TFIIS_C: Transcriptio 50.1 8.3 0.00018 14.7 0.5 11 62-72 28-38 (39)
190 smart00440 ZnF_C2C2 C2C2 Zinc 49.8 11 0.00024 14.5 0.9 11 62-72 28-38 (40)
191 PLN03238 probable histone acet 49.6 4.4 9.6E-05 23.0 -0.3 22 61-82 47-68 (290)
192 KOG1088|consensus 49.3 13 0.00028 18.3 1.2 17 61-77 97-113 (124)
193 KOG3507|consensus 49.1 11 0.00025 16.1 0.9 10 62-71 37-46 (62)
194 PF01780 Ribosomal_L37ae: Ribo 48.5 8.3 0.00018 18.0 0.5 32 32-75 35-66 (90)
195 COG4896 Uncharacterized protei 48.2 15 0.00033 15.8 1.2 11 31-41 30-40 (68)
196 PLN02748 tRNA dimethylallyltra 48.1 19 0.0004 22.2 1.9 22 3-24 418-440 (468)
197 PF14447 Prok-RING_4: Prokaryo 47.3 11 0.00024 15.9 0.7 15 61-75 38-52 (55)
198 PRK02935 hypothetical protein; 47.2 16 0.00035 17.6 1.3 36 29-78 67-102 (110)
199 PF03966 Trm112p: Trm112p-like 46.7 9.3 0.0002 16.5 0.5 13 61-73 52-64 (68)
200 COG5112 UFD2 U1-like Zn-finger 46.2 16 0.00036 17.6 1.3 26 29-54 52-77 (126)
201 PF11931 DUF3449: Domain of un 45.8 6.8 0.00015 21.0 0.0 21 61-81 100-121 (196)
202 PF13240 zinc_ribbon_2: zinc-r 45.7 13 0.00028 12.4 0.7 6 65-70 16-21 (23)
203 TIGR00244 transcriptional regu 45.1 9.4 0.0002 19.5 0.4 15 61-75 27-41 (147)
204 COG0675 Transposase and inacti 44.4 15 0.00033 20.7 1.2 12 61-72 321-332 (364)
205 PF13824 zf-Mss51: Zinc-finger 44.4 12 0.00026 15.7 0.6 12 61-72 13-24 (55)
206 cd00974 DSRD Desulforedoxin (D 44.2 14 0.00029 13.5 0.7 12 61-72 3-14 (34)
207 PRK00420 hypothetical protein; 44.1 10 0.00023 18.4 0.5 11 62-72 40-50 (112)
208 PRK04023 DNA polymerase II lar 44.0 20 0.00043 24.5 1.7 11 61-71 662-672 (1121)
209 PF04606 Ogr_Delta: Ogr/Delta- 44.0 4.2 9.2E-05 16.2 -0.7 17 61-77 24-42 (47)
210 PF13453 zf-TFIIB: Transcripti 43.9 23 0.0005 13.5 1.6 17 5-21 21-37 (41)
211 smart00661 RPOL9 RNA polymeras 43.2 16 0.00035 14.5 0.9 13 62-74 20-32 (52)
212 COG4847 Uncharacterized protei 43.0 8.9 0.00019 18.1 0.1 15 1-15 4-18 (103)
213 PF14375 Cys_rich_CWC: Cystein 43.0 12 0.00025 15.2 0.5 9 65-73 1-9 (50)
214 PRK01343 zinc-binding protein; 42.9 14 0.00031 15.7 0.7 10 63-72 10-19 (57)
215 PLN03239 histone acetyltransfe 42.8 5.8 0.00013 23.2 -0.5 22 61-82 105-126 (351)
216 smart00132 LIM Zinc-binding do 42.8 10 0.00022 13.6 0.3 10 63-72 28-37 (39)
217 TIGR00319 desulf_FeS4 desulfof 42.7 15 0.00032 13.4 0.7 12 61-72 6-17 (34)
218 KOG2071|consensus 42.6 18 0.00038 22.9 1.3 26 2-28 417-442 (579)
219 PF03811 Zn_Tnp_IS1: InsA N-te 42.6 2.8 6.1E-05 15.9 -1.3 8 61-68 28-35 (36)
220 PLN00104 MYST -like histone ac 42.4 5.8 0.00013 24.1 -0.6 22 61-82 197-218 (450)
221 COG1327 Predicted transcriptio 41.5 12 0.00025 19.4 0.4 14 61-74 27-40 (156)
222 COG2331 Uncharacterized protei 41.3 11 0.00024 17.0 0.3 13 61-73 11-23 (82)
223 PF14369 zf-RING_3: zinc-finge 41.1 13 0.00028 13.9 0.4 8 65-72 24-31 (35)
224 KOG3352|consensus 40.9 14 0.00031 19.0 0.7 13 61-73 132-144 (153)
225 PRK08222 hydrogenase 4 subunit 40.5 27 0.00058 18.4 1.7 19 3-21 114-132 (181)
226 KOG0402|consensus 40.4 13 0.00027 17.1 0.4 32 32-75 36-67 (92)
227 COG4888 Uncharacterized Zn rib 40.3 17 0.00036 17.4 0.8 10 31-40 21-30 (104)
228 TIGR03829 YokU_near_AblA uncha 40.1 28 0.00062 16.2 1.5 19 4-22 36-54 (89)
229 PRK12722 transcriptional activ 39.9 14 0.00031 19.7 0.6 27 33-69 135-161 (187)
230 TIGR01562 FdhE formate dehydro 39.8 24 0.00053 20.4 1.5 10 61-70 251-260 (305)
231 COG3880 Modulator of heat shoc 39.6 6 0.00013 20.7 -0.7 29 33-73 75-103 (176)
232 PRK03976 rpl37ae 50S ribosomal 39.5 16 0.00035 17.1 0.7 32 32-75 36-67 (90)
233 COG3364 Zn-ribbon containing p 39.5 16 0.00034 17.6 0.6 14 3-16 2-15 (112)
234 PF10263 SprT-like: SprT-like 38.8 9.3 0.0002 19.2 -0.2 13 61-73 142-154 (157)
235 PRK12860 transcriptional activ 38.6 15 0.00032 19.7 0.5 27 33-69 135-161 (189)
236 KOG2231|consensus 38.5 47 0.001 21.7 2.6 19 6-24 185-203 (669)
237 PF02748 PyrI_C: Aspartate car 38.4 15 0.00032 15.2 0.5 14 61-74 34-47 (52)
238 PF07975 C1_4: TFIIH C1-like d 37.9 11 0.00024 15.6 0.0 22 3-24 21-42 (51)
239 PF06524 NOA36: NOA36 protein; 37.9 6.3 0.00014 22.2 -0.8 11 61-71 208-218 (314)
240 smart00647 IBR In Between Ring 37.6 33 0.00072 14.0 1.5 30 35-74 21-52 (64)
241 PF03884 DUF329: Domain of unk 37.6 17 0.00037 15.4 0.6 12 63-74 3-14 (57)
242 PF12773 DZR: Double zinc ribb 37.3 22 0.00048 14.0 0.9 12 61-72 28-39 (50)
243 PTZ00064 histone acetyltransfe 37.2 7.9 0.00017 24.0 -0.6 22 61-82 279-300 (552)
244 PF14311 DUF4379: Domain of un 36.9 21 0.00046 14.6 0.8 15 61-75 27-41 (55)
245 PRK06260 threonine synthase; V 36.3 16 0.00034 21.7 0.5 26 4-42 4-29 (397)
246 PF02591 DUF164: Putative zinc 36.2 38 0.00083 13.9 2.3 32 34-71 24-55 (56)
247 PF05129 Elf1: Transcription e 36.2 16 0.00034 16.6 0.4 9 61-69 21-29 (81)
248 PF06689 zf-C4_ClpX: ClpX C4-t 35.8 23 0.00049 13.7 0.8 12 64-75 3-14 (41)
249 PTZ00448 hypothetical protein; 35.5 30 0.00064 20.7 1.4 23 32-54 314-336 (373)
250 TIGR03830 CxxCG_CxxCG_HTH puta 34.9 50 0.0011 15.8 2.0 19 4-22 32-50 (127)
251 KOG4727|consensus 34.8 27 0.00058 18.5 1.1 21 4-24 76-96 (193)
252 COG1579 Zn-ribbon protein, pos 34.4 42 0.00091 18.8 1.9 34 33-72 198-231 (239)
253 PF14803 Nudix_N_2: Nudix N-te 34.4 32 0.00068 12.8 1.0 11 61-71 21-31 (34)
254 TIGR00515 accD acetyl-CoA carb 33.9 24 0.00051 20.2 0.9 10 34-43 47-56 (285)
255 PF10058 DUF2296: Predicted in 33.5 24 0.00052 14.7 0.7 10 61-70 43-52 (54)
256 PRK12496 hypothetical protein; 33.5 24 0.00052 18.3 0.8 12 63-74 128-139 (164)
257 COG5188 PRP9 Splicing factor 3 33.4 7.9 0.00017 22.9 -1.0 21 61-81 237-257 (470)
258 PHA02942 putative transposase; 33.2 22 0.00048 21.2 0.8 12 61-72 341-352 (383)
259 COG5432 RAD18 RING-finger-cont 33.0 27 0.00058 20.3 1.0 26 9-41 43-68 (391)
260 COG2879 Uncharacterized small 32.3 53 0.0012 14.3 1.8 16 43-58 23-38 (65)
261 PF05741 zf-nanos: Nanos RNA b 32.2 18 0.0004 15.2 0.3 11 61-71 32-42 (55)
262 CHL00174 accD acetyl-CoA carbo 32.2 27 0.00059 20.2 1.0 10 34-43 59-68 (296)
263 PRK12387 formate hydrogenlyase 31.5 41 0.00089 17.6 1.5 18 3-20 114-131 (180)
264 PF13248 zf-ribbon_3: zinc-rib 31.4 26 0.00056 11.9 0.6 7 34-40 4-10 (26)
265 PRK14714 DNA polymerase II lar 31.4 26 0.00057 24.6 0.9 7 64-70 711-717 (1337)
266 PF13821 DUF4187: Domain of un 31.2 15 0.00032 15.4 -0.1 16 62-77 27-42 (55)
267 PF04810 zf-Sec23_Sec24: Sec23 31.2 35 0.00077 13.0 1.0 12 61-72 23-34 (40)
268 PF10083 DUF2321: Uncharacteri 30.9 15 0.00032 19.1 -0.1 15 61-75 67-81 (158)
269 PF06170 DUF983: Protein of un 30.9 24 0.00052 16.3 0.5 11 63-73 9-19 (86)
270 KOG3183|consensus 30.8 22 0.00048 19.9 0.5 14 61-74 22-35 (250)
271 PF14446 Prok-RING_1: Prokaryo 30.5 23 0.0005 14.9 0.4 11 63-73 6-16 (54)
272 PF11789 zf-Nse: Zinc-finger o 29.8 28 0.0006 14.6 0.6 7 8-14 29-35 (57)
273 PF03107 C1_2: C1 domain; Int 29.7 37 0.00079 12.0 0.9 6 33-38 16-21 (30)
274 COG1631 RPL42A Ribosomal prote 29.3 24 0.00051 16.6 0.4 13 62-74 68-80 (94)
275 KOG0227|consensus 29.1 21 0.00046 19.3 0.2 20 33-52 54-73 (222)
276 KOG2857|consensus 28.7 29 0.00063 17.8 0.6 18 62-79 17-34 (157)
277 PF05876 Terminase_GpA: Phage 28.7 14 0.00031 23.1 -0.5 38 32-73 200-240 (557)
278 PRK05654 acetyl-CoA carboxylas 28.3 33 0.00072 19.7 0.9 10 34-43 48-57 (292)
279 PF05290 Baculo_IE-1: Baculovi 28.2 30 0.00065 17.5 0.6 16 62-77 121-136 (140)
280 PF14952 zf-tcix: Putative tre 27.9 27 0.00059 14.0 0.4 10 63-72 12-21 (44)
281 cd07153 Fur_like Ferric uptake 27.6 30 0.00065 16.3 0.6 13 62-74 73-85 (116)
282 PF10609 ParA: ParA/MinD ATPas 27.6 32 0.00069 15.7 0.6 11 61-71 64-74 (81)
283 PRK04351 hypothetical protein; 27.6 28 0.00061 17.8 0.5 13 61-73 131-143 (149)
284 COG1379 PHP family phosphoeste 27.6 26 0.00055 20.8 0.4 11 62-72 265-275 (403)
285 PF04438 zf-HIT: HIT zinc fing 27.5 45 0.00097 12.0 0.9 11 4-14 14-24 (30)
286 PF00412 LIM: LIM domain; Int 27.5 31 0.00067 13.8 0.6 14 62-75 26-39 (58)
287 COG5152 Uncharacterized conser 26.7 28 0.0006 19.0 0.4 15 61-75 195-209 (259)
288 KOG1994|consensus 26.5 32 0.0007 19.2 0.6 21 31-51 238-258 (268)
289 COG1545 Predicted nucleic-acid 26.5 31 0.00068 17.4 0.6 12 62-73 29-40 (140)
290 COG4640 Predicted membrane pro 26.4 55 0.0012 20.0 1.5 19 32-50 15-33 (465)
291 TIGR00627 tfb4 transcription f 26.3 37 0.00081 19.4 0.9 14 61-74 254-267 (279)
292 COG1885 Uncharacterized protei 26.3 31 0.00066 16.7 0.5 11 63-73 50-60 (115)
293 PF07649 C1_3: C1-like domain; 26.3 42 0.00091 11.7 0.8 11 61-71 14-24 (30)
294 PF06220 zf-U1: U1 zinc finger 26.2 54 0.0012 12.5 1.9 12 2-13 2-13 (38)
295 COG1594 RPB9 DNA-directed RNA 26.0 34 0.00075 16.6 0.6 12 62-73 100-111 (113)
296 PF01475 FUR: Ferric uptake re 25.8 33 0.00071 16.4 0.5 13 61-73 79-91 (120)
297 PF10367 Vps39_2: Vacuolar sor 24.6 36 0.00079 15.7 0.6 12 63-74 79-90 (109)
298 PF00935 Ribosomal_L44: Riboso 24.6 37 0.0008 15.4 0.5 13 61-73 52-64 (77)
299 COG4306 Uncharacterized protei 24.3 21 0.00046 17.8 -0.3 14 61-74 67-80 (160)
300 PF02146 SIR2: Sir2 family; I 24.0 1.2E+02 0.0025 15.8 2.4 10 34-43 107-116 (178)
301 KOG3277|consensus 23.8 26 0.00055 18.3 -0.0 9 4-12 80-88 (165)
302 PF14149 YhfH: YhfH-like prote 23.7 18 0.0004 13.9 -0.4 12 62-73 13-24 (37)
303 PF10164 DUF2367: Uncharacteri 23.6 40 0.00086 16.1 0.6 12 61-72 87-98 (98)
304 PF10071 DUF2310: Zn-ribbon-co 23.2 30 0.00064 19.6 0.1 29 32-69 220-248 (258)
305 smart00709 Zpr1 Duplicated dom 23.1 48 0.001 17.3 0.8 12 62-73 29-40 (160)
306 KOG2747|consensus 23.0 57 0.0012 19.8 1.2 26 31-56 157-182 (396)
307 TIGR00340 zpr1_rel ZPR1-relate 22.9 46 0.001 17.4 0.8 12 62-73 28-39 (163)
308 PF01194 RNA_pol_N: RNA polyme 22.6 85 0.0018 13.5 1.4 15 2-16 3-17 (60)
309 smart00507 HNHc HNH nucleases. 22.6 40 0.00087 12.7 0.5 10 63-72 11-20 (52)
310 PF03367 zf-ZPR1: ZPR1 zinc-fi 22.5 42 0.0009 17.4 0.6 12 62-73 30-41 (161)
311 PF01485 IBR: IBR domain; Int 22.4 39 0.00085 13.8 0.4 13 63-75 41-53 (64)
312 PF12230 PRP21_like_P: Pre-mRN 22.4 29 0.00063 18.9 0.0 27 31-58 167-193 (229)
313 PF06353 DUF1062: Protein of u 22.4 39 0.00084 17.3 0.4 11 4-14 14-24 (142)
314 PF09943 DUF2175: Uncharacteri 22.3 33 0.00072 16.5 0.2 13 3-15 2-14 (101)
315 PF02148 zf-UBP: Zn-finger in 21.9 67 0.0015 13.5 1.1 15 61-75 10-24 (63)
316 PF13408 Zn_ribbon_recom: Reco 21.8 46 0.001 13.3 0.6 12 63-74 6-17 (58)
317 PF05766 NinG: Bacteriophage L 21.7 52 0.0011 17.8 0.8 14 2-15 5-18 (189)
318 PHA02998 RNA polymerase subuni 21.7 54 0.0012 17.6 0.9 38 32-73 143-182 (195)
319 KOG3456|consensus 21.6 42 0.0009 16.3 0.4 14 61-74 103-116 (120)
320 COG5246 PRP11 Splicing factor 21.5 33 0.00071 18.4 0.1 21 33-53 54-74 (222)
321 PF12591 DUF3762: Protein of u 21.4 43 0.00093 14.8 0.4 10 66-75 70-79 (80)
322 PRK05580 primosome assembly pr 21.4 21 0.00046 23.0 -0.7 11 30-40 419-429 (679)
323 PF06467 zf-FCS: MYM-type Zinc 21.0 51 0.0011 12.4 0.6 16 61-76 5-20 (43)
324 PRK00019 rpmE 50S ribosomal pr 20.9 46 0.00099 14.9 0.5 15 62-77 13-27 (72)
325 PRK11639 zinc uptake transcrip 20.6 51 0.0011 17.1 0.7 13 62-74 100-112 (169)
326 PF07295 DUF1451: Protein of u 20.3 34 0.00074 17.5 0.0 10 32-41 112-121 (146)
327 TIGR00310 ZPR1_znf ZPR1 zinc f 20.2 59 0.0013 17.5 0.8 12 62-73 30-41 (192)
328 TIGR00240 ATCase_reg aspartate 20.1 44 0.00095 17.3 0.4 14 62-75 132-145 (150)
329 KOG2807|consensus 20.1 96 0.0021 18.5 1.7 20 32-51 290-309 (378)
No 1
>KOG2462|consensus
Probab=99.94 E-value=2.8e-28 Score=126.83 Aligned_cols=77 Identities=29% Similarity=0.520 Sum_probs=70.3
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcccccccC
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
|++|.+||+.|.....|+.|++ +|+||+||.|+.|++.|.++++|+.||++|.+. ++|.|..|+++|+..+.|.+|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiR-THTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~--K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIR-THTGEKPFSCPHCGKAFADRSNLRAHMQTHSDV--KKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred CcccccccccccchHHhhcccc-cccCCCCccCCcccchhcchHHHHHHHHhhcCC--ccccCcchhhHHHHHHHHHHhh
Confidence 6789999999999999999998 999999999999999999999999999999988 8999999999999999888874
No 2
>KOG2462|consensus
Probab=99.93 E-value=1e-26 Score=121.02 Aligned_cols=76 Identities=30% Similarity=0.551 Sum_probs=71.9
Q ss_pred CCcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccccccc
Q psy6273 2 TRYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIH 81 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 81 (82)
+.+.|++|++.|.+...|..|++ +|. .+++|.+||+.|..++-|+-|+++|+|| |||.|+.|+++|+.+++|+.|
T Consensus 160 ka~~C~~C~K~YvSmpALkMHir-TH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGE--KPF~C~hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIR-THT--LPCECGICGKAFSRPWLLQGHIRTHTGE--KPFSCPHCGKAFADRSNLRAH 234 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhh-ccC--CCcccccccccccchHHhhcccccccCC--CCccCCcccchhcchHHHHHH
Confidence 55789999999999999999998 886 5789999999999999999999999999 999999999999999999998
Q ss_pred C
Q psy6273 82 H 82 (82)
Q Consensus 82 ~ 82 (82)
|
T Consensus 235 m 235 (279)
T KOG2462|consen 235 M 235 (279)
T ss_pred H
Confidence 6
No 3
>KOG3623|consensus
Probab=99.80 E-value=1.3e-20 Score=108.92 Aligned_cols=77 Identities=29% Similarity=0.579 Sum_probs=74.1
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcccccccC
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.|.|..|+++|--.+.|.+|.- -|+|.+||+|.+|.++|..+-.|..|++.|.|| +||.|..|++.|+...+..+||
T Consensus 894 myaCDqCDK~FqKqSSLaRHKY-EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGE--KPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKY-EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGE--KPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhh-hhcCCCCcccchhhHhhhhhhhhhhhhhhccCC--CcchhhhhhhhcccccchHhhh
Confidence 5889999999999999999987 999999999999999999999999999999999 9999999999999999988886
No 4
>KOG3576|consensus
Probab=99.70 E-value=7.4e-19 Score=89.05 Aligned_cols=76 Identities=22% Similarity=0.538 Sum_probs=70.4
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccccccc
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIH 81 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 81 (82)
.|.|.+|++.|....-|.+|++ -|...+.+-|..|++.|.+.-.|.+|+++|+|- +||+|..|+++|.+.-+|..|
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~k-ch~~vkr~lct~cgkgfndtfdlkrh~rthtgv--rpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLK-CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGV--RPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhh-hccHHHHHHHhhccCcccchhhhhhhhccccCc--cccchhhhhHHHHhhccHHHH
Confidence 4789999999999999999998 899889999999999999999999999999999 999999999999998887765
No 5
>KOG3623|consensus
Probab=99.64 E-value=1.2e-16 Score=92.91 Aligned_cols=77 Identities=29% Similarity=0.615 Sum_probs=69.7
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCC-------------CCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTE-------------TKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~-------------~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
.|.|..|..+|.....|.+|+. .|.. .+-|.|..|+++|..+-.|..|++.|.|| +||.|+.|+
T Consensus 240 nfsC~lCsytFAyRtQLErhm~-~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGE--KPfeCpnCk 316 (1007)
T KOG3623|consen 240 NFSCMLCSYTFAYRTQLERHMQ-LHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGE--KPFECPNCK 316 (1007)
T ss_pred CCcchhhhhhhhhHHHHHHHHH-hhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCC--CCcCCcccc
Confidence 4789999999999999999987 6642 24589999999999999999999999999 999999999
Q ss_pred ccccCcccccccC
Q psy6273 70 EVFRSHQGYKIHH 82 (82)
Q Consensus 70 ~~f~~~~~l~~H~ 82 (82)
+.|+...++..||
T Consensus 317 KRFSHSGSySSHm 329 (1007)
T KOG3623|consen 317 KRFSHSGSYSSHM 329 (1007)
T ss_pred cccccCCcccccc
Confidence 9999999888876
No 6
>KOG1074|consensus
Probab=99.61 E-value=1.1e-16 Score=93.85 Aligned_cols=52 Identities=27% Similarity=0.420 Sum_probs=26.7
Q ss_pred cccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhc
Q psy6273 4 YKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
..|-.|-+...-...|+.|++ +|+|++||+|.+|+++|..+.+|..|+..|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyr-tHtGERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYR-THTGERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred cceeeeeecccchhhhhhhhh-cccCcCccccccccchhccccchhhcccccc
Confidence 344445555555555555554 5555555555555555555555555554443
No 7
>PHA00733 hypothetical protein
Probab=99.48 E-value=7.8e-15 Score=70.79 Aligned_cols=77 Identities=25% Similarity=0.420 Sum_probs=62.0
Q ss_pred CCcccCcCCccccCHHHHHhH--HH--hhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccc
Q psy6273 2 TRYKCHACDVETKTRQALDNH--IL--CVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQG 77 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h--~~--~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~ 77 (82)
|++.|.+|.+.+.....|..+ .. ..+.+..+|.|+.|++.|.....|..|++.+ + .+|.|..|++.|.....
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~--~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--E--HSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--C--cCccCCCCCCccCCHHH
Confidence 567788888888877766655 11 1234578999999999999999999999876 3 67999999999999999
Q ss_pred ccccC
Q psy6273 78 YKIHH 82 (82)
Q Consensus 78 l~~H~ 82 (82)
|..|+
T Consensus 115 L~~H~ 119 (128)
T PHA00733 115 TLDHV 119 (128)
T ss_pred HHHHH
Confidence 98774
No 8
>KOG3576|consensus
Probab=99.44 E-value=3.5e-14 Score=72.36 Aligned_cols=74 Identities=24% Similarity=0.484 Sum_probs=62.4
Q ss_pred CCcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCC---------CCCeeecCcccccc
Q psy6273 2 TRYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDE---------FVNLFSCPLCGEVF 72 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~---------~~~~~~C~~C~~~f 72 (82)
|.+-|..||+.|.+-.+|++|.+ +|+|.+||.|..|++.|...-+|..|++.-+|. ..+-|.|..||..-
T Consensus 144 kr~lct~cgkgfndtfdlkrh~r-thtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLKRHTR-THTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTS 222 (267)
T ss_pred HHHHHhhccCcccchhhhhhhhc-cccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCC
Confidence 34678999999999999999999 999999999999999999999999998765431 12789999999765
Q ss_pred cCcc
Q psy6273 73 RSHQ 76 (82)
Q Consensus 73 ~~~~ 76 (82)
....
T Consensus 223 ~~~e 226 (267)
T KOG3576|consen 223 ERPE 226 (267)
T ss_pred CChh
Confidence 4443
No 9
>PHA02768 hypothetical protein; Provisional
Probab=99.40 E-value=1.6e-13 Score=56.58 Aligned_cols=44 Identities=16% Similarity=0.394 Sum_probs=36.7
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYK 79 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 79 (82)
.|.|+.|++.|...++|..|++.|+ ++++|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~----k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN----TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC----CcccCCcccceecccceeE
Confidence 4788899999999999999999888 5788888999888777663
No 10
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.31 E-value=2.8e-12 Score=45.90 Aligned_cols=26 Identities=35% Similarity=0.811 Sum_probs=23.0
Q ss_pred HHHHHHHHhcCCCCCeeecCcccccccC
Q psy6273 47 ALLQHKRKMHDEFVNLFSCPLCGEVFRS 74 (82)
Q Consensus 47 ~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 74 (82)
+|..|++.|+++ +||.|+.|++.|..
T Consensus 1 ~l~~H~~~H~~~--k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGE--KPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSS--SSEEESSSSEEESS
T ss_pred CHHHHhhhcCCC--CCCCCCCCcCeeCc
Confidence 578999999999 99999999999863
No 11
>KOG1074|consensus
Probab=99.28 E-value=1.4e-12 Score=77.22 Aligned_cols=50 Identities=30% Similarity=0.572 Sum_probs=47.6
Q ss_pred CccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcccccccC
Q psy6273 31 KSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.+-+|..|.+...-+++|+.|.++|+|| +||+|+.||++|..+.+|+.||
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGE--RPFkCKiCgRAFtTkGNLkaH~ 653 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGE--RPFKCKICGRAFTTKGNLKAHM 653 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCc--Cccccccccchhccccchhhcc
Confidence 4678999999999999999999999999 9999999999999999999996
No 12
>KOG3608|consensus
Probab=99.27 E-value=5.3e-12 Score=69.08 Aligned_cols=79 Identities=24% Similarity=0.570 Sum_probs=50.4
Q ss_pred CCCcccCcCCccccCHHHHHhHHHhhCCCCCcccccc--chhhhcCcHHHHHHHHHhc-CCCCCeeecCcccccccCccc
Q psy6273 1 MTRYKCHACDVETKTRQALDNHILCVHTETKSFACDQ--CVSYFKTNSALLQHKRKMH-DEFVNLFSCPLCGEVFRSHQG 77 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~--c~~~~~~~~~l~~h~~~~~-~~~~~~~~C~~C~~~f~~~~~ 77 (82)
+|||+|..|+..+.....|..|.. .|+ +..|.|.. |...+.+...+.+|++-+. |....+|.|-.|.+.|....+
T Consensus 290 dkpfKCd~Cd~~c~~esdL~kH~~-~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~ 367 (467)
T KOG3608|consen 290 DKPFKCDECDTRCVRESDLAKHVQ-VHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKS 367 (467)
T ss_pred CCCccccchhhhhccHHHHHHHHH-hcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchh
Confidence 356666666666666666666665 555 44566633 6666666666666666543 444456777777777777777
Q ss_pred cccc
Q psy6273 78 YKIH 81 (82)
Q Consensus 78 l~~H 81 (82)
|.+|
T Consensus 368 L~~H 371 (467)
T KOG3608|consen 368 LSAH 371 (467)
T ss_pred HHHH
Confidence 7665
No 13
>KOG3608|consensus
Probab=99.26 E-value=4.9e-12 Score=69.21 Aligned_cols=76 Identities=22% Similarity=0.459 Sum_probs=51.9
Q ss_pred CCcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccccccc
Q psy6273 2 TRYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIH 81 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 81 (82)
.+|.|..|-+.|.++..|..|+. .|. ..|.|+.|+-+...+++|..|+++.+.+ .+||+|..|...|...+.|.+|
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv~-rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHVV-RHV--NCYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHHH-Hhh--hcccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHHH
Confidence 35677777777777777777766 453 3467777777777777777777764433 2777777777777777777665
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.20 E-value=8.5e-12 Score=51.53 Aligned_cols=43 Identities=16% Similarity=0.386 Sum_probs=38.2
Q ss_pred cccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHH
Q psy6273 4 YKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALL 49 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~ 49 (82)
|+|+.||+.|...++|..|++ +|. +++.|..|++.|...+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r-~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLR-KHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHH-hcC--CcccCCcccceecccceeE
Confidence 789999999999999999999 887 6889999999988776553
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.14 E-value=7e-11 Score=68.44 Aligned_cols=64 Identities=19% Similarity=0.589 Sum_probs=51.7
Q ss_pred CCcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccccc
Q psy6273 2 TRYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFR 73 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 73 (82)
+.+.|+.|++.|. ...|..|+. .+. .++.|+ |+..+ ....|..|+..+.++ +++.|..|+..|.
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~-~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~--Kpi~C~fC~~~v~ 515 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMK-VFH--EPLQCP-CGVVL-EKEQMVQHQASTCPL--RLITCRFCGDMVQ 515 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHH-hcC--CCccCC-CCCCc-chhHHHhhhhccCCC--CceeCCCCCCccc
Confidence 4567899999885 677899987 663 678898 98654 568888999888888 8999999998884
No 16
>PHA00733 hypothetical protein
Probab=99.13 E-value=1.7e-10 Score=55.85 Aligned_cols=54 Identities=26% Similarity=0.488 Sum_probs=47.7
Q ss_pred CCCcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcC
Q psy6273 1 MTRYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHD 57 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 57 (82)
.+||.|+.|++.|.....|..|+. .+ ..++.|..|++.|.....|..|+...++
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r-~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIR-YT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHh-cC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 368999999999999999999987 65 3578999999999999999999887654
No 17
>KOG3993|consensus
Probab=98.98 E-value=2.5e-11 Score=67.62 Aligned_cols=78 Identities=26% Similarity=0.520 Sum_probs=64.7
Q ss_pred cccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCC------------------------
Q psy6273 4 YKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEF------------------------ 59 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~------------------------ 59 (82)
|.|..|...|.+...|.+|.. ...-...|.|+.|++.|.-+.+|..|.+.|....
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC-~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRC-PRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccC-CeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 678889999999999999976 6666667999999999999999999998874210
Q ss_pred -------CCeeecCcccccccCcccccccC
Q psy6273 60 -------VNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 60 -------~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
..-|.|..|++.|.....|++|+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhH
Confidence 12489999999999999999984
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.96 E-value=8.7e-10 Score=64.06 Aligned_cols=68 Identities=15% Similarity=0.356 Sum_probs=56.5
Q ss_pred CCcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcC----------cHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 2 TRYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKT----------NSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~----------~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
+|+.|+ |+..+ ....|..|+. ++...+++.|+.|+..+.. .+.|..|+... |. +++.|..||+.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~-thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~--rt~~C~~Cgk~ 550 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQA-STCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GS--RTAPCDSCGRS 550 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhh-ccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CC--cceEccccCCe
Confidence 578899 99755 6789999987 8999999999999998842 34788998885 67 89999999988
Q ss_pred ccCc
Q psy6273 72 FRSH 75 (82)
Q Consensus 72 f~~~ 75 (82)
+..+
T Consensus 551 Vrlr 554 (567)
T PLN03086 551 VMLK 554 (567)
T ss_pred eeeh
Confidence 8654
No 19
>PHA00732 hypothetical protein
Probab=98.87 E-value=1.3e-09 Score=48.67 Aligned_cols=48 Identities=31% Similarity=0.430 Sum_probs=36.4
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhc
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
||.|..|++.|.....|..|++..|. ++.|+.|++.|. .+..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 68899999999999999999862244 357999999886 4666664443
No 20
>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=98.87 E-value=8.9e-10 Score=39.31 Aligned_cols=25 Identities=32% Similarity=0.647 Sum_probs=22.8
Q ss_pred HHHhHHHhhCCCCCccccccchhhhc
Q psy6273 18 ALDNHILCVHTETKSFACDQCVSYFK 43 (82)
Q Consensus 18 ~l~~h~~~~~~~~~~~~c~~c~~~~~ 43 (82)
+|..|++ +|+++++|.|+.|++.|.
T Consensus 1 ~l~~H~~-~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMR-THTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHH-HHSSSSSEEESSSSEEES
T ss_pred CHHHHhh-hcCCCCCCCCCCCcCeeC
Confidence 5789998 999999999999999885
No 21
>PHA00616 hypothetical protein
Probab=98.86 E-value=1.5e-09 Score=42.96 Aligned_cols=34 Identities=18% Similarity=0.513 Sum_probs=20.6
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPL 67 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~ 67 (82)
+++|+.||+.|...+.+..|++.++++ +++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~--~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQ--NKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCC--CccceeE
Confidence 355666666666666666666666666 5665543
No 22
>PHA00616 hypothetical protein
Probab=98.79 E-value=4.3e-09 Score=41.65 Aligned_cols=34 Identities=15% Similarity=0.389 Sum_probs=31.4
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCCCcccccc
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTETKSFACDQ 37 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~ 37 (82)
||.|+.||+.|.....|..|++ .+++++++.++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r-~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLL-SVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHH-HhcCCCccceeE
Confidence 7899999999999999999998 899999988764
No 23
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.77 E-value=2e-09 Score=58.53 Aligned_cols=69 Identities=22% Similarity=0.467 Sum_probs=42.0
Q ss_pred CCcccCc--CCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccccc
Q psy6273 2 TRYKCHA--CDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYK 79 (82)
Q Consensus 2 k~~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 79 (82)
|||+|++ |++.+.....|+-|++..|...+..+-+. -..+.-+-..+ +||.|+.|++.+.....|+
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~----------p~~~~~F~~~~--KPYrCevC~KRYKNlNGLK 415 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPS----------PEKMNIFSAKD--KPYRCEVCDKRYKNLNGLK 415 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCC----------ccccccccccC--CceeccccchhhccCccce
Confidence 6777765 77777777777777653332222211110 01111122233 8999999999999999998
Q ss_pred ccC
Q psy6273 80 IHH 82 (82)
Q Consensus 80 ~H~ 82 (82)
-|+
T Consensus 416 YHr 418 (423)
T COG5189 416 YHR 418 (423)
T ss_pred ecc
Confidence 774
No 24
>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=98.73 E-value=9.6e-08 Score=39.78 Aligned_cols=51 Identities=24% Similarity=0.451 Sum_probs=38.9
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCC-CccccccchhhhcCcHHHHHHHHHhc
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTET-KSFACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~-~~~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
.|.|+.|++ ..+...|..|....|..+ +.+.|+.|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 578999999 566788999977566654 4688999987543 48888888765
No 25
>PHA00732 hypothetical protein
Probab=98.71 E-value=1.3e-08 Score=45.49 Aligned_cols=39 Identities=38% Similarity=0.673 Sum_probs=32.7
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccC
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRS 74 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 74 (82)
+|.|..|++.|....+|..|++.++. ++.|+.|++.|..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~----~~~C~~CgKsF~~ 39 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT----LTKCPVCNKSYRR 39 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC----CCccCCCCCEeCC
Confidence 57899999999999999999985332 3579999999984
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.41 E-value=1.9e-07 Score=38.90 Aligned_cols=48 Identities=25% Similarity=0.448 Sum_probs=35.0
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcccccccC
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.|.|+.|++ ..+...|..|....+....+.+.|+.|...+.. +|..|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHL 49 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHH
Confidence 478999999 566788999987654432368999999876553 555553
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.41 E-value=1.7e-07 Score=32.24 Aligned_cols=21 Identities=29% Similarity=0.695 Sum_probs=11.1
Q ss_pred cccCcCCccccCHHHHHhHHH
Q psy6273 4 YKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~ 24 (82)
|.|+.|++.|.+...|..|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 345555555555555555544
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.34 E-value=3.4e-07 Score=31.45 Aligned_cols=23 Identities=30% Similarity=0.658 Sum_probs=21.0
Q ss_pred cccccchhhhcCcHHHHHHHHHh
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKM 55 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~ 55 (82)
|.|+.|++.|.....|..|++.|
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 57999999999999999999864
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.24 E-value=1.6e-07 Score=43.45 Aligned_cols=23 Identities=26% Similarity=0.434 Sum_probs=0.0
Q ss_pred ccCcCCccccCHHHHHhHHHhhC
Q psy6273 5 KCHACDVETKTRQALDNHILCVH 27 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~h~~~~~ 27 (82)
+|..|+..|.+...|..|+...|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H 23 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKH 23 (100)
T ss_dssp -----------------------
T ss_pred Ccccccccccccccccccccccc
Confidence 48889999999999999986444
No 30
>KOG3993|consensus
Probab=98.24 E-value=8.1e-07 Score=50.30 Aligned_cols=54 Identities=22% Similarity=0.472 Sum_probs=44.6
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCC--------------------------------CCCccccccchhhhcCcHHHHH
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHT--------------------------------ETKSFACDQCVSYFKTNSALLQ 50 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~--------------------------------~~~~~~c~~c~~~~~~~~~l~~ 50 (82)
-|+|++|++.|.-..||..|.++... .+.-|.|..|++.|.....|..
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 38899999999999999999875111 1124899999999999999999
Q ss_pred HHHHhc
Q psy6273 51 HKRKMH 56 (82)
Q Consensus 51 h~~~~~ 56 (82)
|+.+|.
T Consensus 375 Hqlthq 380 (500)
T KOG3993|consen 375 HQLTHQ 380 (500)
T ss_pred hHHhhh
Confidence 988776
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.21 E-value=1.5e-06 Score=30.95 Aligned_cols=24 Identities=25% Similarity=0.531 Sum_probs=17.6
Q ss_pred CcccCcCCccccCHHHHHhHHHhhC
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVH 27 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~ 27 (82)
||.|..|++.|.+...|..|++ .|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~-~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR-SH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC-TT
T ss_pred CCCCCccCCccCChhHHHHHhH-Hh
Confidence 5677777777777777777775 44
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.06 E-value=3.3e-06 Score=28.95 Aligned_cols=20 Identities=20% Similarity=0.614 Sum_probs=9.7
Q ss_pred ccCcCCccccCHHHHHhHHH
Q psy6273 5 KCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~h~~ 24 (82)
.|+.|+..|.+...|..|+.
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHH
Confidence 45555555555555555544
No 33
>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=98.02 E-value=1.8e-06 Score=30.75 Aligned_cols=25 Identities=44% Similarity=0.757 Sum_probs=19.5
Q ss_pred ccccccchhhhcCcHHHHHHHHHhc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
++.|..|+..|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4678888888888888888887664
No 34
>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=97.93 E-value=1.5e-05 Score=27.21 Aligned_cols=24 Identities=42% Similarity=0.762 Sum_probs=19.6
Q ss_pred cccccchhhhcCcHHHHHHHHHhc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
|.|+.|+..|.....|..|+..++
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 579999999999999999998763
No 35
>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=97.89 E-value=1.9e-05 Score=32.16 Aligned_cols=32 Identities=16% Similarity=0.291 Sum_probs=23.1
Q ss_pred CCCCCccccccchhhhcCcHHHHHHHHHhcCC
Q psy6273 27 HTETKSFACDQCVSYFKTNSALLQHKRKMHDE 58 (82)
Q Consensus 27 ~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 58 (82)
...+.|..|+.|+..+....+|.+|+...++.
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 44577889999999999999999999888776
No 36
>PRK04860 hypothetical protein; Provisional
Probab=97.89 E-value=1.1e-05 Score=40.63 Aligned_cols=40 Identities=23% Similarity=0.628 Sum_probs=33.7
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQG 77 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~ 77 (82)
+|.|. |+. ....+..|.+++.++ ++|.|..|+..|.....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~--~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGE--AVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCC--ccEECCCCCceeEEecc
Confidence 58897 876 667889999999999 99999999998875543
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.69 E-value=5.4e-05 Score=26.11 Aligned_cols=20 Identities=30% Similarity=0.677 Sum_probs=9.6
Q ss_pred ccCcCCccccCHHHHHhHHH
Q psy6273 5 KCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~h~~ 24 (82)
.|..|++.|.....|..|+.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 34445555555544444443
No 38
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.59 E-value=7.2e-05 Score=30.49 Aligned_cols=30 Identities=17% Similarity=0.338 Sum_probs=20.2
Q ss_pred CCCcccCcCCccccCHHHHHhHHHhhCCCCC
Q psy6273 1 MTRYKCHACDVETKTRQALDNHILCVHTETK 31 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 31 (82)
+.|-.|++|+..+....+|.+|+. ...+.+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle-~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLE-IRHFKK 51 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHH-HHTTTS
T ss_pred CCCCCCCcchhhccchhhHHHHHH-HHhccc
Confidence 357789999999999999999997 444443
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.57 E-value=0.00012 Score=25.16 Aligned_cols=24 Identities=38% Similarity=0.725 Sum_probs=21.1
Q ss_pred cccccchhhhcCcHHHHHHHHHhc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
+.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468999999999999999998654
No 40
>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=97.39 E-value=7.2e-05 Score=26.58 Aligned_cols=20 Identities=35% Similarity=0.692 Sum_probs=14.4
Q ss_pred eecCcccccccCcccccccC
Q psy6273 63 FSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 63 ~~C~~C~~~f~~~~~l~~H~ 82 (82)
|.|..|++.|.....+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 56777777777777777664
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.39 E-value=6.6e-05 Score=26.06 Aligned_cols=19 Identities=21% Similarity=0.632 Sum_probs=10.2
Q ss_pred ccCcCCccccCHHHHHhHH
Q psy6273 5 KCHACDVETKTRQALDNHI 23 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~h~ 23 (82)
.|..|+..|.+...+..|.
T Consensus 2 ~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCcCCHHHHHHHH
Confidence 4555555555555555554
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.39 E-value=0.00011 Score=25.44 Aligned_cols=23 Identities=39% Similarity=0.723 Sum_probs=20.3
Q ss_pred cccccchhhhcCcHHHHHHHHHh
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKM 55 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~ 55 (82)
|.|..|+..|.+...+..|++.+
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 56999999999999999998764
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.25 E-value=0.00024 Score=24.38 Aligned_cols=20 Identities=25% Similarity=0.527 Sum_probs=8.5
Q ss_pred ccccchhhhcCcHHHHHHHHH
Q psy6273 34 ACDQCVSYFKTNSALLQHKRK 54 (82)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~~~ 54 (82)
.|+.|+.... ...|..|++.
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHh
Confidence 3444544444 4445555444
No 44
>PRK04860 hypothetical protein; Provisional
Probab=97.22 E-value=0.00018 Score=36.41 Aligned_cols=38 Identities=18% Similarity=0.498 Sum_probs=31.3
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCc
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTN 45 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~ 45 (82)
+|.|. |+. ....+.+|.+ ++.++++|.|..|+..+...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~r-i~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNR-VVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHH-HhcCCccEECCCCCceeEEe
Confidence 57897 887 5566789998 99999999999999877544
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.43 E-value=0.0028 Score=22.11 Aligned_cols=18 Identities=28% Similarity=0.584 Sum_probs=7.7
Q ss_pred ccccchhhhcCcHHHHHHH
Q psy6273 34 ACDQCVSYFKTNSALLQHK 52 (82)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~ 52 (82)
+|+.|++.| ..+.|..|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 344444444 333444443
No 46
>KOG2893|consensus
Probab=96.25 E-value=0.0022 Score=34.54 Aligned_cols=30 Identities=30% Similarity=0.765 Sum_probs=15.1
Q ss_pred cccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccc
Q psy6273 35 CDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGE 70 (82)
Q Consensus 35 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 70 (82)
|..|++.|.....|.+|++ . +.|+|-.|-+
T Consensus 13 cwycnrefddekiliqhqk----a--khfkchichk 42 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----A--KHFKCHICHK 42 (341)
T ss_pred eeecccccchhhhhhhhhh----h--ccceeeeehh
Confidence 4455555555555555443 1 3455555544
No 47
>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=96.03 E-value=0.0071 Score=22.46 Aligned_cols=22 Identities=18% Similarity=0.581 Sum_probs=14.7
Q ss_pred CcccCcCCccccCHHHHHhHHH
Q psy6273 3 RYKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~ 24 (82)
+|.|..|+..|.+...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777776666666654
No 48
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.83 E-value=0.0015 Score=36.55 Aligned_cols=24 Identities=29% Similarity=0.542 Sum_probs=17.2
Q ss_pred CCCcccCcCCccccCHHHHHhHHH
Q psy6273 1 MTRYKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~~~~l~~h~~ 24 (82)
+|||.|++|++.+.....|+-|+.
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CCceeccccchhhccCccceeccc
Confidence 367777777777777777776653
No 49
>KOG1146|consensus
Probab=95.83 E-value=0.0093 Score=39.06 Aligned_cols=53 Identities=28% Similarity=0.464 Sum_probs=43.1
Q ss_pred CCcccCcCCccccCHHHHHhHHHhhCC------------------------CCCccccccchhhhcCcHHHHHHHHH
Q psy6273 2 TRYKCHACDVETKTRQALDNHILCVHT------------------------ETKSFACDQCVSYFKTNSALLQHKRK 54 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~~~~~------------------------~~~~~~c~~c~~~~~~~~~l~~h~~~ 54 (82)
|-+.|+.|+..|.....|..|++..|. +.+++.|..|...+..+.+|..|+..
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 457899999999999999999983232 23578899999999999999888764
No 50
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.83 E-value=0.01 Score=22.68 Aligned_cols=34 Identities=29% Similarity=0.710 Sum_probs=20.1
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFR 73 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 73 (82)
..|+.|...|.....- ...+. ....|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~--~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGG--RKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCC--cEEECCCCCcEee
Confidence 3577777777666541 22233 5677777776664
No 51
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.40 E-value=0.015 Score=24.58 Aligned_cols=32 Identities=28% Similarity=0.550 Sum_probs=20.7
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGE 70 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 70 (82)
.|.|++|++.....-. +-..-. .+|.|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~-----~CRk~g--~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCA-----KCRKLG--NPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhh-----hHHHcC--CceECCCcCc
Confidence 4889999965444332 222223 6899999985
No 52
>KOG2186|consensus
Probab=95.14 E-value=0.015 Score=31.68 Aligned_cols=47 Identities=19% Similarity=0.518 Sum_probs=28.0
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHH
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKR 53 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 53 (82)
-|.|..||....- ..+.+|+. .-++ .-|+|.+|++.|.. ..+..|..
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~s-rCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMS-RCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhccc-cchHHHHH-hccC-CeeEEeeccccccc-chhhhhhh
Confidence 3567777766553 33566764 4343 45777778777776 33445543
No 53
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.07 E-value=0.023 Score=21.56 Aligned_cols=33 Identities=21% Similarity=0.599 Sum_probs=17.5
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVF 72 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 72 (82)
..|+.|...|.-.+.. .-... ....|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g--~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKG--RKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCC--cEEECCCCCCEe
Confidence 3566666666555542 11222 456677676655
No 54
>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=95.06 E-value=0.023 Score=21.62 Aligned_cols=33 Identities=21% Similarity=0.563 Sum_probs=15.7
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVF 72 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 72 (82)
..|+.|+..|...... ..... ....|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~-----~~~~~--~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ-----LGANG--GKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHH-----cCCCC--CEEECCCCCCEE
Confidence 3566666555544432 11111 245666666554
No 55
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.94 E-value=0.037 Score=25.30 Aligned_cols=21 Identities=29% Similarity=0.806 Sum_probs=10.0
Q ss_pred cccCcCCccccCHHHHHhHHH
Q psy6273 4 YKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~ 24 (82)
+.|..|++.|.+...|..|+.
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHH
T ss_pred CCCCccCCCCcCHHHHHHHHc
Confidence 445555555555555555544
No 56
>KOG1146|consensus
Probab=94.83 E-value=0.004 Score=40.61 Aligned_cols=57 Identities=25% Similarity=0.419 Sum_probs=45.0
Q ss_pred hCCCCCccccccchhhhcCcHHHHHHHHHhcCCC-----------------------CCeeecCcccccccCcccccccC
Q psy6273 26 VHTETKSFACDQCVSYFKTNSALLQHKRKMHDEF-----------------------VNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 26 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~-----------------------~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.+...+.+.|+.|+-.+.....|..||+..+.+. .++|.|..|..++....+|.+|+
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 4445578999999999999999999998822110 26899999999999988887774
No 57
>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=94.76 E-value=0.018 Score=27.47 Aligned_cols=15 Identities=33% Similarity=0.886 Sum_probs=9.4
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
.|..|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 566777777666543
No 58
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.69 E-value=0.012 Score=21.84 Aligned_cols=8 Identities=50% Similarity=1.634 Sum_probs=4.4
Q ss_pred eeecCccc
Q psy6273 62 LFSCPLCG 69 (82)
Q Consensus 62 ~~~C~~C~ 69 (82)
++.|+.||
T Consensus 17 ~~~CP~Cg 24 (33)
T cd00350 17 PWVCPVCG 24 (33)
T ss_pred CCcCcCCC
Confidence 55555554
No 59
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=94.62 E-value=0.016 Score=29.66 Aligned_cols=23 Identities=30% Similarity=0.749 Sum_probs=18.5
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
-|.|++||.. +.|+ .|..||.||
T Consensus 134 ~~vC~vCGy~-------------~~ge--~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGE--APEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCC--CCCcCCCCC
Confidence 5999999875 3445 899999998
No 60
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=94.57 E-value=0.0067 Score=37.36 Aligned_cols=57 Identities=21% Similarity=0.368 Sum_probs=39.8
Q ss_pred ccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccc
Q psy6273 5 KCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGE 70 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 70 (82)
.|..||-+|+....|---+.++...+-+ .|+.|.+.+.++.+- ++|. .|..|+.||=
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~-lC~~C~~EY~dP~nR----RfHA----Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFP-LCPFCDKEYKDPLNR----RFHA----QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCc-CCHHHHHHhcCcccc----cccc----ccccCcccCC
Confidence 3899999999877765443323333333 689999988887763 4555 5889999984
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=94.41 E-value=0.0042 Score=33.00 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=16.1
Q ss_pred CCCcccCcCCccccCHHHHHhH
Q psy6273 1 MTRYKCHACDVETKTRQALDNH 22 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~~~~l~~h 22 (82)
+|...|++|++.|.++......
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~ 24 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGK 24 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCC
Confidence 4677899999999887544433
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.33 E-value=0.0053 Score=34.95 Aligned_cols=62 Identities=23% Similarity=0.363 Sum_probs=42.9
Q ss_pred CcccCcCCccccCHHHHHhHHHh-hCCCC--Cccccc--cchhhhcCcHHHHHHHHHhcCCCCCeeecC
Q psy6273 3 RYKCHACDVETKTRQALDNHILC-VHTET--KSFACD--QCVSYFKTNSALLQHKRKMHDEFVNLFSCP 66 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~ 66 (82)
++.|..|...+.....+..|... .|.++ .++.|+ .|++.|.....+..|...+.+. .++.+.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 355 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI--SPAKEK 355 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC--Cccccc
Confidence 45667777777777777777652 46667 777777 6777777777777777777766 555543
No 63
>KOG4173|consensus
Probab=94.29 E-value=0.012 Score=31.07 Aligned_cols=72 Identities=22% Similarity=0.471 Sum_probs=45.1
Q ss_pred cccCc--CCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhc----------CCCCCeeec--Cccc
Q psy6273 4 YKCHA--CDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMH----------DEFVNLFSC--PLCG 69 (82)
Q Consensus 4 ~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~----------~~~~~~~~C--~~C~ 69 (82)
+.|++ |-+.+.....+..|.. +..+ -.|..|.+.|.+..-|..|+.-.+ |. .-|.| ..|+
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~-~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~--dMy~ClvEgCt 153 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYH-TLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQ--DMYQCLVEGCT 153 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhh-hccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCc--cHHHHHHHhhh
Confidence 44555 5667777777777765 4333 368888888887777766654322 22 45777 3487
Q ss_pred ccccCccccccc
Q psy6273 70 EVFRSHQGYKIH 81 (82)
Q Consensus 70 ~~f~~~~~l~~H 81 (82)
..|.....-+.|
T Consensus 154 ~KFkT~r~RkdH 165 (253)
T KOG4173|consen 154 EKFKTSRDRKDH 165 (253)
T ss_pred hhhhhhhhhhhH
Confidence 777766554444
No 64
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.22 E-value=0.027 Score=23.49 Aligned_cols=22 Identities=18% Similarity=0.446 Sum_probs=16.2
Q ss_pred CcccCcCCccccCHHHHHhHHH
Q psy6273 3 RYKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~ 24 (82)
-+.|+-|+..|.....+.+|..
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhh
Confidence 3567778888877777777765
No 65
>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=94.05 E-value=0.022 Score=21.37 Aligned_cols=9 Identities=44% Similarity=1.243 Sum_probs=5.0
Q ss_pred CeeecCccc
Q psy6273 61 NLFSCPLCG 69 (82)
Q Consensus 61 ~~~~C~~C~ 69 (82)
.|..|+.||
T Consensus 17 ~p~~CP~Cg 25 (34)
T cd00729 17 APEKCPICG 25 (34)
T ss_pred CCCcCcCCC
Confidence 345666665
No 66
>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=93.27 E-value=0.11 Score=26.51 Aligned_cols=34 Identities=32% Similarity=0.648 Sum_probs=24.1
Q ss_pred CCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccc
Q psy6273 28 TETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVF 72 (82)
Q Consensus 28 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 72 (82)
....-|.|+.|+..|....++. .-|.|+.||...
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~-----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME-----------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH-----------cCCcCCCCCCEe
Confidence 3456788988887776666653 358999998653
No 67
>KOG2186|consensus
Probab=92.94 E-value=0.061 Score=29.42 Aligned_cols=44 Identities=32% Similarity=0.696 Sum_probs=32.5
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIH 81 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 81 (82)
|.|..|+....-+ .+.+|+....+. .|.|-.|+..|.. .+.+.|
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn~---~fSCIDC~k~F~~-~sYknH 47 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRNA---YFSCIDCGKTFER-VSYKNH 47 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccCC---eeEEeeccccccc-chhhhh
Confidence 6889999876554 456788777764 7999999999987 344444
No 68
>KOG2482|consensus
Probab=92.84 E-value=0.17 Score=29.06 Aligned_cols=80 Identities=21% Similarity=0.493 Sum_probs=53.8
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCCCC----------------------------------------------------
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHTET---------------------------------------------------- 30 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~---------------------------------------------------- 30 (82)
.+.|-.|.+.|..+..|..||+......
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 3578889999999999999987411100
Q ss_pred -C--ccccccchhhhcCcHHHHHHHHHhcC--------C-C----------------CCeeecCcccccccCcccccccC
Q psy6273 31 -K--SFACDQCVSYFKTNSALLQHKRKMHD--------E-F----------------VNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 31 -~--~~~c~~c~~~~~~~~~l~~h~~~~~~--------~-~----------------~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
. ...|-.|.........|..||..-+. + + ...-.|..|.-.|.....|..||
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 0 13677787777777888888864321 0 0 02245667778888888887775
No 69
>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=92.76 E-value=0.06 Score=19.32 Aligned_cols=11 Identities=45% Similarity=0.939 Sum_probs=7.8
Q ss_pred eecCccccccc
Q psy6273 63 FSCPLCGEVFR 73 (82)
Q Consensus 63 ~~C~~C~~~f~ 73 (82)
|.|..|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 46777877774
No 70
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=92.68 E-value=0.097 Score=22.18 Aligned_cols=33 Identities=24% Similarity=0.602 Sum_probs=20.1
Q ss_pred CccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccc
Q psy6273 31 KSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGE 70 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 70 (82)
..|.|+.|+......-. +-.... .+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~-----~CRk~~--~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE-----KCRKQS--NPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeech-----hHHhcC--CceECCCCCC
Confidence 35889999876333221 222223 6899999985
No 71
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=92.31 E-value=0.037 Score=22.07 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=4.3
Q ss_pred eeecCcccc
Q psy6273 62 LFSCPLCGE 70 (82)
Q Consensus 62 ~~~C~~C~~ 70 (82)
...|+.||.
T Consensus 21 ~~~Cp~CG~ 29 (46)
T PRK00398 21 GVRCPYCGY 29 (46)
T ss_pred ceECCCCCC
Confidence 345555543
No 72
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=92.30 E-value=0.48 Score=23.82 Aligned_cols=38 Identities=26% Similarity=0.619 Sum_probs=24.5
Q ss_pred CCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccc
Q psy6273 29 ETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVF 72 (82)
Q Consensus 29 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 72 (82)
....|.|+.|+..|.....+. ....+ ..|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~----~~d~~--~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQ----LLDMD--GTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHH----hcCCC--CcEECCCCCCEE
Confidence 455789999998876544332 11113 459999998754
No 73
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=92.27 E-value=0.15 Score=26.54 Aligned_cols=33 Identities=33% Similarity=0.735 Sum_probs=20.9
Q ss_pred CCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccc
Q psy6273 29 ETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVF 72 (82)
Q Consensus 29 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 72 (82)
...-|.|+.|+..|....++. .-|.|+.||...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~-----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME-----------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh-----------cCCcCCCCCCCC
Confidence 345677888877665555442 358888887543
No 74
>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=91.77 E-value=0.11 Score=25.50 Aligned_cols=12 Identities=33% Similarity=0.490 Sum_probs=6.4
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
.|..|+.||..|
T Consensus 25 ~p~vcP~cg~~~ 36 (129)
T TIGR02300 25 RPAVSPYTGEQF 36 (129)
T ss_pred CCccCCCcCCcc
Confidence 455555555544
No 75
>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=91.42 E-value=0.12 Score=17.88 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=6.7
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4677777763
No 76
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.26 E-value=0.071 Score=30.47 Aligned_cols=51 Identities=35% Similarity=0.658 Sum_probs=42.3
Q ss_pred ccccccchhhhcCcHHHHHHHH--HhcCCCCCeeecC--cccccccCcccccccC
Q psy6273 32 SFACDQCVSYFKTNSALLQHKR--KMHDEFVNLFSCP--LCGEVFRSHQGYKIHH 82 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~--~~~~~~~~~~~C~--~C~~~f~~~~~l~~H~ 82 (82)
.+.|..|...|.....+..|.+ .|.++..+|+.|+ .|++.|.....+..|.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc
Confidence 5788889999999999999999 6776522599999 7999999998887763
No 77
>PHA00626 hypothetical protein
Probab=91.11 E-value=0.12 Score=21.63 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=11.1
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
..|.|+.||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 568888888777654
No 78
>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=90.82 E-value=0.25 Score=26.56 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=20.2
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCC
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHT 28 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 28 (82)
.|.|..|++.|.-...+..|+...|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 47899999999999999999986554
No 79
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.72 E-value=0.19 Score=19.99 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=5.5
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
.+..|+.||.
T Consensus 18 ~~irC~~CG~ 27 (44)
T smart00659 18 DVVRCRECGY 27 (44)
T ss_pred CceECCCCCc
Confidence 3556666653
No 80
>KOG2893|consensus
Probab=90.45 E-value=0.068 Score=29.10 Aligned_cols=32 Identities=28% Similarity=0.581 Sum_probs=26.2
Q ss_pred cCcCCccccCHHHHHhHHHhhCCCCCccccccchhhh
Q psy6273 6 CHACDVETKTRQALDNHILCVHTETKSFACDQCVSYF 42 (82)
Q Consensus 6 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~ 42 (82)
|=.|++.|..+..|.+|++. +.|.|-+|.+..
T Consensus 13 cwycnrefddekiliqhqka-----khfkchichkkl 44 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA-----KHFKCHICHKKL 44 (341)
T ss_pred eeecccccchhhhhhhhhhh-----ccceeeeehhhh
Confidence 67799999999999999883 348899998643
No 81
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=90.37 E-value=0.28 Score=20.05 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=7.2
Q ss_pred CCcccCcCCcccc
Q psy6273 2 TRYKCHACDVETK 14 (82)
Q Consensus 2 k~~~c~~c~~~~~ 14 (82)
+.+.|..||..|.
T Consensus 3 k~l~C~dCg~~Fv 15 (49)
T PF13451_consen 3 KTLTCKDCGAEFV 15 (49)
T ss_pred eeEEcccCCCeEE
Confidence 4555666665544
No 82
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=90.04 E-value=0.099 Score=21.83 Aligned_cols=41 Identities=20% Similarity=0.444 Sum_probs=22.9
Q ss_pred Ccccccc--chhhhcCcHHHHHHHHHhcCCCCCeeecCc----ccccccC
Q psy6273 31 KSFACDQ--CVSYFKTNSALLQHKRKMHDEFVNLFSCPL----CGEVFRS 74 (82)
Q Consensus 31 ~~~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~----C~~~f~~ 74 (82)
.+..|+. |... .....|..|....-.. ++..|+. |+..+..
T Consensus 8 ~~v~C~~~cc~~~-i~r~~l~~H~~~~C~~--~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 8 RPVPCPNGCCNEM-IPRKELDDHLENECPK--RPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp SEEE-TT--S-BE-EECCCHHHHHHTTSTT--SEEE-SS----S--EEEH
T ss_pred CEeeCCCCCcccc-eeHHHHHHHHHccCCC--CcEECCCCCCCCCCccch
Confidence 3456766 4333 3355678888866666 7888888 7766543
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.72 E-value=0.035 Score=28.14 Aligned_cols=13 Identities=31% Similarity=0.439 Sum_probs=7.0
Q ss_pred cccccchhhhcCc
Q psy6273 33 FACDQCVSYFKTN 45 (82)
Q Consensus 33 ~~c~~c~~~~~~~ 45 (82)
++|+.|+..|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 4555666555443
No 84
>KOG2482|consensus
Probab=88.97 E-value=0.57 Score=27.07 Aligned_cols=66 Identities=24% Similarity=0.350 Sum_probs=40.7
Q ss_pred HHHHhHHHhhCCCCCccccccchhhhcCc-HHHHHHHHHhcC----CC----------------CCeeecCcccccccCc
Q psy6273 17 QALDNHILCVHTETKSFACDQCVSYFKTN-SALLQHKRKMHD----EF----------------VNLFSCPLCGEVFRSH 75 (82)
Q Consensus 17 ~~l~~h~~~~~~~~~~~~c~~c~~~~~~~-~~l~~h~~~~~~----~~----------------~~~~~C~~C~~~f~~~ 75 (82)
..|.++++-........+|-.|+..+... +.+..|+-.-++ .. ...+.|-.|.+.|..+
T Consensus 129 eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdk 208 (423)
T KOG2482|consen 129 EALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDK 208 (423)
T ss_pred HHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCc
Confidence 44555554222223456788888766555 445556543221 10 1347899999999999
Q ss_pred ccccccC
Q psy6273 76 QGYKIHH 82 (82)
Q Consensus 76 ~~l~~H~ 82 (82)
..|+.||
T Consensus 209 ntLkeHM 215 (423)
T KOG2482|consen 209 NTLKEHM 215 (423)
T ss_pred HHHHHHH
Confidence 9998886
No 85
>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=88.63 E-value=0.21 Score=17.52 Aligned_cols=11 Identities=45% Similarity=0.939 Sum_probs=6.1
Q ss_pred eecCccccccc
Q psy6273 63 FSCPLCGEVFR 73 (82)
Q Consensus 63 ~~C~~C~~~f~ 73 (82)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35566665553
No 86
>KOG2593|consensus
Probab=87.52 E-value=1.2 Score=26.57 Aligned_cols=39 Identities=23% Similarity=0.523 Sum_probs=26.1
Q ss_pred CCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 28 TETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 28 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
.....|.|+.|.+.|.....++ -.-... -.|.|..|+..
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~--~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNET--GEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccC--ceEEEecCCCc
Confidence 3456799999999887766653 222223 46999998743
No 87
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=87.51 E-value=0.14 Score=22.70 Aligned_cols=15 Identities=20% Similarity=0.545 Sum_probs=7.9
Q ss_pred CeeecC--cccccccCc
Q psy6273 61 NLFSCP--LCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~--~C~~~f~~~ 75 (82)
..+.|. +||..|...
T Consensus 26 ~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 26 RYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeecCCCCCCCEEEEE
Confidence 455554 566555443
No 88
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.19 E-value=0.72 Score=22.29 Aligned_cols=67 Identities=18% Similarity=0.369 Sum_probs=38.9
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCC------CCCc-------cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHT------ETKS-------FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~------~~~~-------~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
|..|+.|+-.......|.+..- |. .+.+ -.|..|...|........ ...... ..|.|+.|.
T Consensus 15 P~~CpiCgLtLVss~HLARSyH--HLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~--~~y~C~~C~ 88 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSYH--HLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDS--HRYVCAVCK 88 (112)
T ss_pred CCcCCcCCCEEeccchHHHhhh--ccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccc--cceeCCCCC
Confidence 6778899988877777776532 21 0111 137777777765431110 001122 579999999
Q ss_pred ccccCc
Q psy6273 70 EVFRSH 75 (82)
Q Consensus 70 ~~f~~~ 75 (82)
..|--.
T Consensus 89 ~~FC~d 94 (112)
T TIGR00622 89 NVFCVD 94 (112)
T ss_pred Cccccc
Confidence 888644
No 89
>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=86.94 E-value=0.34 Score=18.46 Aligned_cols=15 Identities=27% Similarity=0.682 Sum_probs=11.0
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
-.|.|..||..|...
T Consensus 4 Y~y~C~~Cg~~fe~~ 18 (41)
T smart00834 4 YEYRCEDCGHTFEVL 18 (41)
T ss_pred EEEEcCCCCCEEEEE
Confidence 358899999877533
No 90
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=86.74 E-value=0.35 Score=22.21 Aligned_cols=33 Identities=18% Similarity=0.438 Sum_probs=21.3
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQ 76 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~ 76 (82)
.+.|+.|++.... ..+. .-|.|..||..|+-.+
T Consensus 35 ~~~Cp~C~~~~Vk----------R~a~--GIW~C~kCg~~fAGga 67 (89)
T COG1997 35 KHVCPFCGRTTVK----------RIAT--GIWKCRKCGAKFAGGA 67 (89)
T ss_pred CCcCCCCCCccee----------eecc--CeEEcCCCCCeecccc
Confidence 4788888865211 1122 5699999998886543
No 91
>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=86.47 E-value=1.1 Score=18.44 Aligned_cols=11 Identities=45% Similarity=1.265 Sum_probs=5.4
Q ss_pred ecCcccccccC
Q psy6273 64 SCPLCGEVFRS 74 (82)
Q Consensus 64 ~C~~C~~~f~~ 74 (82)
.|+.|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 88888887753
No 92
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=86.42 E-value=0.39 Score=18.52 Aligned_cols=14 Identities=36% Similarity=0.899 Sum_probs=11.6
Q ss_pred eeecCcccccccCc
Q psy6273 62 LFSCPLCGEVFRSH 75 (82)
Q Consensus 62 ~~~C~~C~~~f~~~ 75 (82)
||.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999888654
No 93
>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=85.51 E-value=0.19 Score=18.58 Aligned_cols=7 Identities=57% Similarity=1.673 Sum_probs=3.1
Q ss_pred eecCccc
Q psy6273 63 FSCPLCG 69 (82)
Q Consensus 63 ~~C~~C~ 69 (82)
..|+.||
T Consensus 18 irC~~CG 24 (32)
T PF03604_consen 18 IRCPECG 24 (32)
T ss_dssp SSBSSSS
T ss_pred EECCcCC
Confidence 3444444
No 94
>KOG4173|consensus
Probab=85.44 E-value=0.27 Score=26.32 Aligned_cols=46 Identities=26% Similarity=0.606 Sum_probs=32.7
Q ss_pred cccccc--chhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcccccccC
Q psy6273 32 SFACDQ--CVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 32 ~~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.+.|++ |...|...+.+..|-.+.++. .|..|.+.|.+...|..|+
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~-----sCs~C~r~~Pt~hLLd~HI 126 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN-----SCSFCKRAFPTGHLLDAHI 126 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc-----hhHHHHHhCCchhhhhHHH
Confidence 456755 556677667677766655555 7999999999887776664
No 95
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=85.42 E-value=0.76 Score=21.79 Aligned_cols=26 Identities=23% Similarity=0.547 Sum_probs=20.8
Q ss_pred cccc----ccchhhhcCcHHHHHHHHHhcC
Q psy6273 32 SFAC----DQCVSYFKTNSALLQHKRKMHD 57 (82)
Q Consensus 32 ~~~c----~~c~~~~~~~~~l~~h~~~~~~ 57 (82)
.|.| ..|++...+...+..|.+..+|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4788 8888888888888888887653
No 96
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=85.39 E-value=0.34 Score=26.06 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=22.1
Q ss_pred CCccccccchhhhcCcHHHHHHHHHhcCC
Q psy6273 30 TKSFACDQCVSYFKTNSALLQHKRKMHDE 58 (82)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 58 (82)
+.-|.|..|++.|.....+..|+...+.+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 44589999999999999999999876654
No 97
>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=85.20 E-value=0.46 Score=18.58 Aligned_cols=15 Identities=33% Similarity=0.758 Sum_probs=11.0
Q ss_pred eeecCcccccccCcc
Q psy6273 62 LFSCPLCGEVFRSHQ 76 (82)
Q Consensus 62 ~~~C~~C~~~f~~~~ 76 (82)
.|.|..||..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEeCCCCCEEEEEE
Confidence 588999998776443
No 98
>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=84.94 E-value=0.39 Score=18.84 Aligned_cols=15 Identities=33% Similarity=0.720 Sum_probs=9.4
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
-|+.|..|+..|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 489999999888643
No 99
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=83.63 E-value=1.5 Score=15.28 Aligned_cols=18 Identities=22% Similarity=0.654 Sum_probs=9.3
Q ss_pred ccCcCCccccCHHHHHhHH
Q psy6273 5 KCHACDVETKTRQALDNHI 23 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~h~ 23 (82)
.|+.|++.+ ....+..|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 466666665 334444443
No 100
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=83.28 E-value=0.43 Score=19.52 Aligned_cols=10 Identities=20% Similarity=0.760 Sum_probs=5.7
Q ss_pred cccccchhhh
Q psy6273 33 FACDQCVSYF 42 (82)
Q Consensus 33 ~~c~~c~~~~ 42 (82)
|.|..|++.+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555665555
No 101
>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=82.12 E-value=0.19 Score=31.57 Aligned_cols=55 Identities=22% Similarity=0.399 Sum_probs=34.4
Q ss_pred cCcCCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 6 CHACDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 6 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
|..||-.|.....|-.-..++-. ..--.|+.|.+.+.++.+- ++|. .+-.|+.||
T Consensus 93 Ct~CGPr~~i~~~lpydr~~t~m-~~f~~C~~C~~ey~~p~~r----r~h~----~~~~C~~Cg 147 (711)
T TIGR00143 93 CTHCGPRFTIIEALPYDRENTSM-ADFPLCPDCAKEYKDPLDR----RFHA----QPIACPRCG 147 (711)
T ss_pred ccCCCCCeEEeecCCCCCCCcCC-CCCcCCHHHHHHhcCCccc----cCCC----CCccCCCCC
Confidence 88899888876654432211212 2223788898887776542 3444 578899998
No 102
>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=82.12 E-value=0.46 Score=18.72 Aligned_cols=14 Identities=36% Similarity=0.906 Sum_probs=9.6
Q ss_pred eecCcccccccCcc
Q psy6273 63 FSCPLCGEVFRSHQ 76 (82)
Q Consensus 63 ~~C~~C~~~f~~~~ 76 (82)
=.|+.|++.|++.-
T Consensus 9 K~C~~C~rpf~WRK 22 (42)
T PF10013_consen 9 KICPVCGRPFTWRK 22 (42)
T ss_pred CcCcccCCcchHHH
Confidence 36778888887653
No 103
>KOG2231|consensus
Probab=81.88 E-value=1.1 Score=28.24 Aligned_cols=21 Identities=38% Similarity=0.662 Sum_probs=12.7
Q ss_pred cCcCCccccCHHHHHhHHHhhC
Q psy6273 6 CHACDVETKTRQALDNHILCVH 27 (82)
Q Consensus 6 c~~c~~~~~~~~~l~~h~~~~~ 27 (82)
|..| ..|.+...|..|+...|
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H 138 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQH 138 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhh
Confidence 3444 44457788888875334
No 104
>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=81.78 E-value=0.7 Score=23.23 Aligned_cols=19 Identities=21% Similarity=0.899 Sum_probs=15.6
Q ss_pred CeeecCcccccccCccccc
Q psy6273 61 NLFSCPLCGEVFRSHQGYK 79 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~ 79 (82)
.-+.|+.||+.|+..+.+.
T Consensus 123 ~f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred eEEECCCCCCEecccccHH
Confidence 4689999999999876654
No 105
>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=81.56 E-value=0.77 Score=18.59 Aligned_cols=14 Identities=29% Similarity=0.797 Sum_probs=10.2
Q ss_pred eeecCcccccccCc
Q psy6273 62 LFSCPLCGEVFRSH 75 (82)
Q Consensus 62 ~~~C~~C~~~f~~~ 75 (82)
-|.|..||..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 47888888877543
No 106
>KOG3408|consensus
Probab=81.49 E-value=1.5 Score=21.55 Aligned_cols=27 Identities=30% Similarity=0.559 Sum_probs=22.5
Q ss_pred CCCCccccccchhhhcCcHHHHHHHHH
Q psy6273 28 TETKSFACDQCVSYFKTNSALLQHKRK 54 (82)
Q Consensus 28 ~~~~~~~c~~c~~~~~~~~~l~~h~~~ 54 (82)
+|...|-|..|.+.|.+...|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 345568899999999999999988765
No 107
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=80.86 E-value=2.1 Score=17.25 Aligned_cols=8 Identities=50% Similarity=0.576 Sum_probs=4.0
Q ss_pred HHHHHHHH
Q psy6273 46 SALLQHKR 53 (82)
Q Consensus 46 ~~l~~h~~ 53 (82)
++|.+|+.
T Consensus 37 s~L~rHl~ 44 (50)
T smart00614 37 SNLRRHLR 44 (50)
T ss_pred HHHHHHHH
Confidence 44555554
No 108
>PF15269 zf-C2H2_7: Zinc-finger
Probab=80.83 E-value=1.3 Score=17.75 Aligned_cols=23 Identities=26% Similarity=0.465 Sum_probs=17.9
Q ss_pred cccccchhhhcCcHHHHHHHHHh
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKM 55 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~ 55 (82)
|.|-+|.......+.|-.||...
T Consensus 21 ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred ceeecCCcccchHHHHHHHHHHH
Confidence 57778877777888888888754
No 109
>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=80.81 E-value=2.5 Score=16.40 Aligned_cols=19 Identities=32% Similarity=0.511 Sum_probs=8.1
Q ss_pred ccccchhhhcC----cHHHHHHH
Q psy6273 34 ACDQCVSYFKT----NSALLQHK 52 (82)
Q Consensus 34 ~c~~c~~~~~~----~~~l~~h~ 52 (82)
.|..|+..+.. .++|..|+
T Consensus 18 ~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 18 KCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EETTTTEE-----SSTHHHHHHH
T ss_pred EeCCCCeEEeeCCCcHHHHHHhh
Confidence 45555544333 24555555
No 110
>KOG1280|consensus
Probab=80.72 E-value=2.5 Score=24.61 Aligned_cols=39 Identities=31% Similarity=0.490 Sum_probs=26.8
Q ss_pred CccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 31 KSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
..|.|+.|+..-.....+..|....+.+...-..|+.|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 468888888877777888888877665533344556554
No 111
>KOG2785|consensus
Probab=79.97 E-value=4.5 Score=23.92 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=19.0
Q ss_pred CcccCcCCccccCHHHHHhHHHhhCC
Q psy6273 3 RYKCHACDVETKTRQALDNHILCVHT 28 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 28 (82)
|-.|-.|++.+.+...-..|+. .+.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~-~~H 190 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMF-KEH 190 (390)
T ss_pred CcceeecCCCcccHHHHHHHHh-hcc
Confidence 4457889999998888888886 444
No 112
>KOG4124|consensus
Probab=79.37 E-value=0.18 Score=29.05 Aligned_cols=68 Identities=26% Similarity=0.563 Sum_probs=35.8
Q ss_pred CCcccCc--CCccccCHHHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCccccc
Q psy6273 2 TRYKCHA--CDVETKTRQALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGYK 79 (82)
Q Consensus 2 k~~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 79 (82)
+|+.|++ |++.+.....|..|.. +....+. . ...+ .-..|+...... |++.|+.|.+++.....|+
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~--~~h~s~i-----~--~~s~-~~~ph~~~~~~n--k~~r~~i~~~~~k~~~~l~ 415 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKL--HGHCSPI-----T--TPTP-APIPHQGFVVEN--KPYRCEVCSKRYKNLNGLK 415 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccc--cCcCCCC-----C--CCCC-CCCCcceeeecc--CcccChhhhhhhccCCCCC
Confidence 6777754 7777777666666643 1111111 0 0001 112233323333 7888888888777666665
Q ss_pred cc
Q psy6273 80 IH 81 (82)
Q Consensus 80 ~H 81 (82)
-|
T Consensus 416 ~~ 417 (442)
T KOG4124|consen 416 YH 417 (442)
T ss_pred ce
Confidence 44
No 113
>KOG2785|consensus
Probab=79.00 E-value=3.9 Score=24.13 Aligned_cols=23 Identities=26% Similarity=0.585 Sum_probs=17.5
Q ss_pred CCcccCcCCccccCHHHHHhHHH
Q psy6273 2 TRYKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~ 24 (82)
.-|.|..|...|.+...-..|.+
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyK 24 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYK 24 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhh
Confidence 34789999999988876666654
No 114
>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=78.61 E-value=1.3 Score=16.09 Aligned_cols=10 Identities=50% Similarity=1.354 Sum_probs=6.6
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
..+.|+.|+.
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 4677777764
No 115
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=78.47 E-value=0.73 Score=22.92 Aligned_cols=13 Identities=15% Similarity=0.547 Sum_probs=7.5
Q ss_pred ccccccchhhhcC
Q psy6273 32 SFACDQCVSYFKT 44 (82)
Q Consensus 32 ~~~c~~c~~~~~~ 44 (82)
.+.|..|+..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3566666655544
No 116
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=78.46 E-value=0.72 Score=21.38 Aligned_cols=33 Identities=12% Similarity=0.349 Sum_probs=20.8
Q ss_pred CccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCc
Q psy6273 31 KSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSH 75 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~ 75 (82)
..|.|+.|++.-.... +. -.|.|..|++.|+-.
T Consensus 35 a~y~CpfCgk~~vkR~----------a~--GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQ----------AV--GIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCceeee----------ee--EEEEcCCCCCEEeCC
Confidence 3578888875422111 11 568999999888643
No 117
>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=77.50 E-value=1.5 Score=18.78 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=9.7
Q ss_pred ccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccccc
Q psy6273 34 ACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFR 73 (82)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 73 (82)
.|..|++.|... . +.+-|..||..|-
T Consensus 11 ~C~~C~~~F~~~------------~--rrhhCr~CG~~vC 36 (69)
T PF01363_consen 11 NCMICGKKFSLF------------R--RRHHCRNCGRVVC 36 (69)
T ss_dssp B-TTT--B-BSS------------S---EEE-TTT--EEE
T ss_pred cCcCcCCcCCCc------------e--eeEccCCCCCEEC
Confidence 566677766331 1 5566666666553
No 118
>PF14353 CpXC: CpXC protein
Probab=77.19 E-value=1.4 Score=21.51 Aligned_cols=17 Identities=41% Similarity=0.858 Sum_probs=11.7
Q ss_pred CeeecCcccccccCccc
Q psy6273 61 NLFSCPLCGEVFRSHQG 77 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~ 77 (82)
-.+.|+.||..|.-...
T Consensus 37 ~~~~CP~Cg~~~~~~~p 53 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYP 53 (128)
T ss_pred CEEECCCCCCceecCCC
Confidence 46888888877754443
No 119
>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=76.78 E-value=1.4 Score=17.21 Aligned_cols=12 Identities=33% Similarity=1.038 Sum_probs=8.8
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
.+..|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467888888766
No 120
>KOG2907|consensus
Probab=76.26 E-value=1.4 Score=21.26 Aligned_cols=40 Identities=20% Similarity=0.453 Sum_probs=22.5
Q ss_pred cccccchhhhcCcHHHHHHHHH-hcCCCCCeeecCcccccccCc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRK-MHDEFVNLFSCPLCGEVFRSH 75 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~~C~~C~~~f~~~ 75 (82)
..|+.|+..-..-..++ +|+ ..|. ..-|.|+.|+..|...
T Consensus 75 ~kCpkCghe~m~Y~T~Q--lRSADEGQ-TVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQ--LRSADEGQ-TVFYTCPKCKYKFTEN 115 (116)
T ss_pred ccCcccCCchhhhhhhh--cccccCCc-eEEEEcCccceeeecc
Confidence 47888875433222221 122 2232 1468999999888754
No 121
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.68 E-value=1.1 Score=21.53 Aligned_cols=12 Identities=17% Similarity=0.528 Sum_probs=6.3
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
.|..|+.||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 455555555554
No 122
>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=75.31 E-value=0.77 Score=21.33 Aligned_cols=32 Identities=19% Similarity=0.561 Sum_probs=20.1
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSH 75 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~ 75 (82)
.|.|+.|++.-... .+- -.|.|..|++.|+-.
T Consensus 35 ~y~CpfCgk~~vkR----------~a~--GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 35 KYVCPFCGKKTVKR----------GST--GIWTCRKCGAKFAGG 66 (91)
T ss_pred CccCCCCCCCceEE----------Eee--EEEEcCCCCCEEeCC
Confidence 47888887542111 111 468999998887643
No 123
>PF12907 zf-met2: Zinc-binding
Probab=75.20 E-value=2.8 Score=16.37 Aligned_cols=11 Identities=27% Similarity=0.302 Sum_probs=4.5
Q ss_pred HHHHhHHHhhC
Q psy6273 17 QALDNHILCVH 27 (82)
Q Consensus 17 ~~l~~h~~~~~ 27 (82)
..|..|..+.|
T Consensus 18 ~~L~eH~enKH 28 (40)
T PF12907_consen 18 PQLKEHAENKH 28 (40)
T ss_pred HHHHHHHHccC
Confidence 33444443333
No 124
>COG1773 Rubredoxin [Energy production and conversion]
Probab=74.99 E-value=1.6 Score=18.29 Aligned_cols=16 Identities=25% Similarity=0.729 Sum_probs=10.9
Q ss_pred CCCcccCcCCccccCH
Q psy6273 1 MTRYKCHACDVETKTR 16 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~~ 16 (82)
++.|+|..||..|.-.
T Consensus 1 m~~~~C~~CG~vYd~e 16 (55)
T COG1773 1 MKRWRCSVCGYVYDPE 16 (55)
T ss_pred CCceEecCCceEeccc
Confidence 3567788888776654
No 125
>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=73.66 E-value=1.9 Score=20.35 Aligned_cols=13 Identities=46% Similarity=1.099 Sum_probs=11.4
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
+|..|.+||..|.
T Consensus 78 ~~~rC~eCG~~fk 90 (97)
T cd00924 78 KPKRCPECGHVFK 90 (97)
T ss_pred CceeCCCCCcEEE
Confidence 6999999998885
No 126
>KOG4167|consensus
Probab=73.40 E-value=1.3 Score=28.30 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=22.1
Q ss_pred ccccccchhhhcCcHHHHHHHHHhc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
-|.|..|++.|....++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999899999998875
No 127
>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=72.47 E-value=3.7 Score=24.95 Aligned_cols=27 Identities=15% Similarity=0.313 Sum_probs=22.0
Q ss_pred cccCcCCccccCHHHHHhHHHhhCCCC
Q psy6273 4 YKCHACDVETKTRQALDNHILCVHTET 30 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~~~~~~~ 30 (82)
+.|+.|.+.|.....+..|+...|.+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 678999999999999999987666553
No 128
>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=72.10 E-value=2.3 Score=16.00 Aligned_cols=15 Identities=27% Similarity=0.474 Sum_probs=7.1
Q ss_pred eecCcccccccCccc
Q psy6273 63 FSCPLCGEVFRSHQG 77 (82)
Q Consensus 63 ~~C~~C~~~f~~~~~ 77 (82)
-.|.+|++.|..+.-
T Consensus 4 ~~C~eC~~~f~dSyL 18 (34)
T PF01286_consen 4 PKCDECGKPFMDSYL 18 (34)
T ss_dssp EE-TTT--EES-SSC
T ss_pred chHhHhCCHHHHHHH
Confidence 467788887765543
No 129
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=72.09 E-value=3.8 Score=22.83 Aligned_cols=14 Identities=43% Similarity=0.992 Sum_probs=9.6
Q ss_pred eeecCcccccccCc
Q psy6273 62 LFSCPLCGEVFRSH 75 (82)
Q Consensus 62 ~~~C~~C~~~f~~~ 75 (82)
-|.|+.|+..|...
T Consensus 155 ef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 155 EFHCPKCRHNFRGF 168 (278)
T ss_pred eeecccccccchhh
Confidence 37788887777543
No 130
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=72.05 E-value=3.1 Score=17.85 Aligned_cols=29 Identities=28% Similarity=0.639 Sum_probs=17.9
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFR 73 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 73 (82)
..|+.|+..... .... +.|.|+.||..+.
T Consensus 29 q~C~~CG~~~~~----------~~~~--r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRNKK----------RRSG--RVFTCPNCGFEMD 57 (69)
T ss_pred cCccCccccccc----------cccc--ceEEcCCCCCEEC
Confidence 457777654433 1223 6899999987654
No 131
>KOG4167|consensus
Probab=72.00 E-value=0.71 Score=29.38 Aligned_cols=24 Identities=17% Similarity=0.436 Sum_probs=21.3
Q ss_pred cccCcCCccccCHHHHHhHHHhhCC
Q psy6273 4 YKCHACDVETKTRQALDNHILCVHT 28 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~~~~~ 28 (82)
|.|.+|++.|.-...+..|++ +|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK-~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMK-THR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHH-HHH
Confidence 789999999998888999988 775
No 132
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.83 E-value=0.98 Score=24.72 Aligned_cols=18 Identities=17% Similarity=0.501 Sum_probs=10.2
Q ss_pred CCcccCcCCccccCHHHH
Q psy6273 2 TRYKCHACDVETKTRQAL 19 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l 19 (82)
+.+.|++|+..|......
T Consensus 18 k~ieCPvC~tkFkkeev~ 35 (267)
T COG1655 18 KTIECPVCNTKFKKEEVK 35 (267)
T ss_pred ceeccCcccchhhhhhee
Confidence 345677776666554433
No 133
>PLN02294 cytochrome c oxidase subunit Vb
Probab=70.93 E-value=2.2 Score=22.25 Aligned_cols=14 Identities=36% Similarity=1.025 Sum_probs=11.7
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
+|..|++||..|.-
T Consensus 140 kp~RCpeCG~~fkL 153 (174)
T PLN02294 140 KSFECPVCTQYFEL 153 (174)
T ss_pred CceeCCCCCCEEEE
Confidence 68999999988853
No 134
>PRK14873 primosome assembly protein PriA; Provisional
Probab=70.84 E-value=2.6 Score=26.70 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=6.4
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
.|+.|+.||.
T Consensus 421 ~p~~Cp~Cgs 430 (665)
T PRK14873 421 PDWRCPRCGS 430 (665)
T ss_pred cCccCCCCcC
Confidence 4667777764
No 135
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=69.75 E-value=7.2 Score=20.93 Aligned_cols=12 Identities=42% Similarity=0.902 Sum_probs=7.2
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
....|..||..+
T Consensus 29 ~lvrC~eCG~V~ 40 (201)
T COG1326 29 PLVRCEECGTVH 40 (201)
T ss_pred eEEEccCCCcEe
Confidence 456666666555
No 136
>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=69.70 E-value=1.7 Score=20.72 Aligned_cols=10 Identities=20% Similarity=0.431 Sum_probs=5.9
Q ss_pred CCcccCcCCc
Q psy6273 2 TRYKCHACDV 11 (82)
Q Consensus 2 k~~~c~~c~~ 11 (82)
||..|+.|+.
T Consensus 1 ~p~~CpYCg~ 10 (102)
T PF11672_consen 1 KPIICPYCGG 10 (102)
T ss_pred CCcccCCCCC
Confidence 4556666664
No 137
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=69.37 E-value=1.7 Score=20.92 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=15.5
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGE 70 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 70 (82)
...|..|+..|.... ..+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~--------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ--------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC--------------cCccCcCCCC
Confidence 357888876554322 3456888874
No 138
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.37 E-value=6.3 Score=23.20 Aligned_cols=47 Identities=26% Similarity=0.400 Sum_probs=28.0
Q ss_pred ccCcCCccccCHHHHHhHHHhhCCCCCccccccch----hhhcCcHHHHHHHH
Q psy6273 5 KCHACDVETKTRQALDNHILCVHTETKSFACDQCV----SYFKTNSALLQHKR 53 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~----~~~~~~~~l~~h~~ 53 (82)
.|..|...|-+...|..|.+. ..++.+.|..-+ ..|.+-..|..|-+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~--~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRL--RHEACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hhhhccceecChHHHHHHHHh--hhhhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 477788888888888888762 234445554332 13555555655544
No 139
>KOG1842|consensus
Probab=69.17 E-value=0.75 Score=27.52 Aligned_cols=18 Identities=33% Similarity=0.519 Sum_probs=10.4
Q ss_pred ccccccchhhhcCcHHHH
Q psy6273 32 SFACDQCVSYFKTNSALL 49 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~ 49 (82)
.|.|+.|..-|...+.|.
T Consensus 15 gflCPiC~~dl~~~~~L~ 32 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALN 32 (505)
T ss_pred cccCchHhhhhhhHHHHH
Confidence 356666666665555554
No 140
>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=68.84 E-value=1.4 Score=21.16 Aligned_cols=25 Identities=36% Similarity=0.809 Sum_probs=14.4
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
..|..|+..|.... ..+.|+.||..
T Consensus 71 ~~C~~Cg~~~~~~~--------------~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDE--------------FDFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHH--------------CCHH-SSSSSS
T ss_pred EECCCCCCEEecCC--------------CCCCCcCCcCC
Confidence 57788887765433 23568888754
No 141
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=68.63 E-value=7.5 Score=20.50 Aligned_cols=33 Identities=33% Similarity=0.740 Sum_probs=18.6
Q ss_pred CCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 28 TETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 28 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
....-|.|+.|...+..-.+.. ..|.|+.||..
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~-----------~~F~Cp~Cg~~ 141 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAME-----------LGFTCPKCGED 141 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHH-----------hCCCCCCCCch
Confidence 3445677877665443333221 34788888754
No 142
>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=67.16 E-value=3.8 Score=20.51 Aligned_cols=25 Identities=36% Similarity=0.547 Sum_probs=14.7
Q ss_pred CccccccchhhhcCcHHHHHHHHHhcCC
Q psy6273 31 KSFACDQCVSYFKTNSALLQHKRKMHDE 58 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 58 (82)
....|-.||+.|.. |.+|++.|+|.
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred CeeEEccCCcccch---HHHHHHHccCC
Confidence 34678889888755 47888888664
No 143
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=67.00 E-value=4.4 Score=16.46 Aligned_cols=10 Identities=30% Similarity=1.188 Sum_probs=3.1
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
..|.|+.|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 3477777764
No 144
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=66.85 E-value=2.9 Score=20.74 Aligned_cols=15 Identities=27% Similarity=0.822 Sum_probs=12.5
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
..|.|+.|++.|...
T Consensus 52 qRyrC~~C~~tf~~~ 66 (129)
T COG3677 52 QRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccCCcCcceeee
Confidence 689999999988654
No 145
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=65.71 E-value=3.6 Score=15.26 Aligned_cols=12 Identities=33% Similarity=0.816 Sum_probs=7.5
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
-+.|..|+.+|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 466777776653
No 146
>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=65.21 E-value=3.3 Score=15.68 Aligned_cols=12 Identities=33% Similarity=1.041 Sum_probs=8.0
Q ss_pred eecCcccccccC
Q psy6273 63 FSCPLCGEVFRS 74 (82)
Q Consensus 63 ~~C~~C~~~f~~ 74 (82)
+.|+.||+.|.-
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 467778777643
No 147
>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=65.14 E-value=3.5 Score=20.72 Aligned_cols=13 Identities=46% Similarity=1.150 Sum_probs=11.4
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
+|..|+.||..|.
T Consensus 111 ~~~RCpeCG~~fk 123 (136)
T PF01215_consen 111 KPQRCPECGQVFK 123 (136)
T ss_dssp SEEEETTTEEEEE
T ss_pred CccCCCCCCeEEE
Confidence 6899999998885
No 148
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=65.11 E-value=3.1 Score=21.60 Aligned_cols=19 Identities=21% Similarity=0.964 Sum_probs=14.8
Q ss_pred CeeecCcccccccCccccc
Q psy6273 61 NLFSCPLCGEVFRSHQGYK 79 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~ 79 (82)
.-+.|+.||+.|+..+.+.
T Consensus 129 ~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred ceeECCCCcccccCchHHH
Confidence 4578999999998776553
No 149
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=65.09 E-value=3.8 Score=20.45 Aligned_cols=15 Identities=13% Similarity=0.337 Sum_probs=11.9
Q ss_pred CcccCcCCccccCHH
Q psy6273 3 RYKCHACDVETKTRQ 17 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~ 17 (82)
|++|..||+.|.+.+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678888998888654
No 150
>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=65.01 E-value=3.5 Score=16.81 Aligned_cols=9 Identities=22% Similarity=0.667 Sum_probs=4.0
Q ss_pred cCcCCcccc
Q psy6273 6 CHACDVETK 14 (82)
Q Consensus 6 c~~c~~~~~ 14 (82)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 444444443
No 151
>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=64.97 E-value=2.9 Score=20.28 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=8.5
Q ss_pred CCccccccchhhh
Q psy6273 30 TKSFACDQCVSYF 42 (82)
Q Consensus 30 ~~~~~c~~c~~~~ 42 (82)
.....|+.|++..
T Consensus 67 av~V~CP~C~K~T 79 (114)
T PF11023_consen 67 AVQVECPNCGKQT 79 (114)
T ss_pred ceeeECCCCCChH
Confidence 3456788887654
No 152
>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=64.28 E-value=3 Score=20.08 Aligned_cols=9 Identities=22% Similarity=0.774 Sum_probs=4.2
Q ss_pred cccccchhh
Q psy6273 33 FACDQCVSY 41 (82)
Q Consensus 33 ~~c~~c~~~ 41 (82)
+.|+.|+..
T Consensus 20 ~iCpeC~~E 28 (109)
T TIGR00686 20 LICPSCLYE 28 (109)
T ss_pred eECcccccc
Confidence 445555443
No 153
>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=63.96 E-value=2.7 Score=20.33 Aligned_cols=25 Identities=24% Similarity=0.829 Sum_probs=15.8
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
..|..|+..|.... ..+.|+.||..
T Consensus 71 ~~C~~Cg~~~~~~~--------------~~~~CP~Cgs~ 95 (115)
T TIGR00100 71 CECEDCSEEVSPEI--------------DLYRCPKCHGI 95 (115)
T ss_pred EEcccCCCEEecCC--------------cCccCcCCcCC
Confidence 57888876654432 24678888753
No 154
>KOG0782|consensus
Probab=63.71 E-value=1.6 Score=27.31 Aligned_cols=52 Identities=19% Similarity=0.367 Sum_probs=34.5
Q ss_pred HHHHhHHHhhCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcc
Q psy6273 17 QALDNHILCVHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQ 76 (82)
Q Consensus 17 ~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~ 76 (82)
..+.+|-= +|.....-.|..|++.|..+-. +|..|. ....|.+|..+|..+-
T Consensus 239 ~~fvrHHW-VHrrRqeGkC~~CgKgFQQKf~------FhsKEi-vAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHW-VHRRRQEGKCNTCGKGFQQKFF------FHSKEI-VAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhH-hhHhhhccccchhhhhhhhhee------eccccE-EEEEehHHHHHhhcch
Confidence 35556553 6666666789999998865543 454442 4688999988876543
No 155
>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=63.69 E-value=6.9 Score=15.45 Aligned_cols=10 Identities=20% Similarity=0.816 Sum_probs=7.3
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
..|.|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 6788887764
No 156
>KOG0978|consensus
Probab=63.27 E-value=3.8 Score=26.23 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=17.7
Q ss_pred CeeecCcccccccCcccccccC
Q psy6273 61 NLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
+.-+||.|+.+|...--++.|+
T Consensus 677 RqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred hcCCCCCCCCCCCcccccccCC
Confidence 6679999999999877666654
No 157
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.09 E-value=1.4 Score=17.91 Aligned_cols=13 Identities=31% Similarity=0.866 Sum_probs=8.6
Q ss_pred ecCcccccccCcc
Q psy6273 64 SCPLCGEVFRSHQ 76 (82)
Q Consensus 64 ~C~~C~~~f~~~~ 76 (82)
.|+.|++.|++..
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 5777777776543
No 158
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=63.06 E-value=2.3 Score=20.54 Aligned_cols=27 Identities=22% Similarity=0.591 Sum_probs=15.6
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
...|..|+..|..... ..+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~-------------~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ-------------RVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCc-------------cCCcCcCcCCC
Confidence 3578888765433211 12668888843
No 159
>KOG2636|consensus
Probab=62.70 E-value=6.4 Score=23.92 Aligned_cols=28 Identities=21% Similarity=0.439 Sum_probs=22.3
Q ss_pred hCCCCCccccccch-hhhcCcHHHHHHHH
Q psy6273 26 VHTETKSFACDQCV-SYFKTNSALLQHKR 53 (82)
Q Consensus 26 ~~~~~~~~~c~~c~-~~~~~~~~l~~h~~ 53 (82)
.|.-...|.|.+|| +.+..+..+++|-.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 45556789999999 78888888888853
No 160
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=62.32 E-value=4.2 Score=16.62 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=8.3
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 357888887654
No 161
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.07 E-value=3.7 Score=17.65 Aligned_cols=43 Identities=19% Similarity=0.355 Sum_probs=26.0
Q ss_pred hCCCCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccC
Q psy6273 26 VHTETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRS 74 (82)
Q Consensus 26 ~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 74 (82)
++.+..++.|+.-+..+..+..+.. . ..+ .--.|+.|+..|..
T Consensus 18 I~~~~~~l~C~g~~~p~~HPrV~L~---m-g~~--gev~CPYC~t~y~l 60 (62)
T COG4391 18 IEIGDLPLMCPGPEPPNDHPRVFLD---M-GDE--GEVVCPYCSTRYRL 60 (62)
T ss_pred EEeCCeeEEcCCCCCCCCCCEEEEE---c-CCC--CcEecCccccEEEe
Confidence 5667778888765555444433221 1 222 45789999988763
No 162
>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 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=60.29 E-value=9.7 Score=18.15 Aligned_cols=39 Identities=3% Similarity=0.053 Sum_probs=28.4
Q ss_pred CCCcccCcCCccccCHHHHHhHHHhhCCCCCccccccchhh
Q psy6273 1 MTRYKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSY 41 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 41 (82)
++.|.|+.-+..|.+...+...+. . -..+-|.|...|+.
T Consensus 1 eeVf~i~~T~EiF~dYe~Y~~R~~-~-y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 1 EEVFYIPFTGEIFRDYEEYLKRMI-L-YNQRVWTCEITGKS 39 (102)
T ss_pred CceEEeCCCCcccCCHHHHHHHHH-H-HhCCeeEEecCCCC
Confidence 356788888999999988887765 3 33466888877663
No 164
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=60.20 E-value=6.9 Score=19.74 Aligned_cols=23 Identities=17% Similarity=0.148 Sum_probs=16.8
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCC
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDE 58 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~ 58 (82)
..|-.+|+.| .+|.+|+.+|.+.
T Consensus 77 IicLEDGkkf---KSLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKF---KSLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcch---HHHHHHHhcccCC
Confidence 4666677766 5688898888775
No 165
>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=59.71 E-value=4.2 Score=17.00 Aligned_cols=11 Identities=45% Similarity=1.207 Sum_probs=7.4
Q ss_pred eecCccccccc
Q psy6273 63 FSCPLCGEVFR 73 (82)
Q Consensus 63 ~~C~~C~~~f~ 73 (82)
|.|+.||..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 56777776554
No 166
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.36 E-value=3.5 Score=20.03 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=8.2
Q ss_pred ccccccchhhhcC
Q psy6273 32 SFACDQCVSYFKT 44 (82)
Q Consensus 32 ~~~c~~c~~~~~~ 44 (82)
...|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 3577888765543
No 167
>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=59.34 E-value=5.2 Score=14.89 Aligned_cols=13 Identities=31% Similarity=0.812 Sum_probs=8.3
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
..+.|+.|++.+.
T Consensus 3 ~~~~C~nC~R~v~ 15 (33)
T PF08209_consen 3 PYVECPNCGRPVA 15 (33)
T ss_dssp -EEE-TTTSSEEE
T ss_pred CeEECCCCcCCcc
Confidence 4678999987654
No 168
>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=58.80 E-value=1.1 Score=16.93 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=3.5
Q ss_pred eeecCcccc
Q psy6273 62 LFSCPLCGE 70 (82)
Q Consensus 62 ~~~C~~C~~ 70 (82)
+..|..||=
T Consensus 21 ~isC~~CGP 29 (35)
T PF07503_consen 21 FISCTNCGP 29 (35)
T ss_dssp T--BTTCC-
T ss_pred CccCCCCCC
Confidence 455666653
No 169
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=58.25 E-value=4.3 Score=24.38 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=5.3
Q ss_pred ccccccchhhh
Q psy6273 32 SFACDQCVSYF 42 (82)
Q Consensus 32 ~~~c~~c~~~~ 42 (82)
.|.|..|++.+
T Consensus 367 g~rC~kCg~~~ 377 (421)
T COG1571 367 GFRCKKCGTRA 377 (421)
T ss_pred CcccccccccC
Confidence 45555555443
No 170
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=58.11 E-value=4.2 Score=16.84 Aligned_cols=10 Identities=50% Similarity=1.351 Sum_probs=6.5
Q ss_pred ecCccccccc
Q psy6273 64 SCPLCGEVFR 73 (82)
Q Consensus 64 ~C~~C~~~f~ 73 (82)
.|+.||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5777776553
No 171
>PRK10220 hypothetical protein; Provisional
Probab=57.62 E-value=5.5 Score=19.26 Aligned_cols=9 Identities=22% Similarity=0.944 Sum_probs=4.6
Q ss_pred cccccchhh
Q psy6273 33 FACDQCVSY 41 (82)
Q Consensus 33 ~~c~~c~~~ 41 (82)
+.|+.|+..
T Consensus 21 ~vCpeC~hE 29 (111)
T PRK10220 21 YICPECAHE 29 (111)
T ss_pred EECCcccCc
Confidence 555555543
No 172
>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=57.34 E-value=5.8 Score=16.03 Aligned_cols=12 Identities=42% Similarity=1.392 Sum_probs=7.9
Q ss_pred eecCcccccccC
Q psy6273 63 FSCPLCGEVFRS 74 (82)
Q Consensus 63 ~~C~~C~~~f~~ 74 (82)
|.|..|+..+..
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 677777766543
No 173
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=57.25 E-value=4.8 Score=20.70 Aligned_cols=35 Identities=20% Similarity=0.590 Sum_probs=21.0
Q ss_pred CCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 30 TKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 30 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
.-+|.|. |+..+.... +|-....| ..|.|..|+..
T Consensus 115 ~~~Y~C~-C~q~~l~~R---Rhn~~~~g---~~YrC~~C~gk 149 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIR---RHNTVRRG---EVYRCGKCGGK 149 (156)
T ss_pred ceeEEee-cCCccchhh---hccccccc---ceEEeccCCce
Confidence 4568888 887754432 23223333 36999999753
No 174
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=56.88 E-value=5 Score=15.50 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=3.0
Q ss_pred cCcccccccCc
Q psy6273 65 CPLCGEVFRSH 75 (82)
Q Consensus 65 C~~C~~~f~~~ 75 (82)
|..|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 45565555443
No 175
>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=56.09 E-value=4.9 Score=15.46 Aligned_cols=13 Identities=38% Similarity=1.002 Sum_probs=8.7
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
..+.|+.||..+-
T Consensus 31 p~~~C~~CGE~~~ 43 (46)
T TIGR03831 31 PALVCPQCGEEYL 43 (46)
T ss_pred CccccccCCCEee
Confidence 4567888886554
No 176
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.94 E-value=1.3 Score=28.27 Aligned_cols=11 Identities=45% Similarity=0.824 Sum_probs=8.5
Q ss_pred CeeecCccccc
Q psy6273 61 NLFSCPLCGEV 71 (82)
Q Consensus 61 ~~~~C~~C~~~ 71 (82)
.|..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 68888888754
No 177
>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=55.85 E-value=5.2 Score=16.39 Aligned_cols=11 Identities=27% Similarity=1.271 Sum_probs=7.4
Q ss_pred eecCccccccc
Q psy6273 63 FSCPLCGEVFR 73 (82)
Q Consensus 63 ~~C~~C~~~f~ 73 (82)
|.|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56777776655
No 178
>PRK05978 hypothetical protein; Provisional
Probab=55.64 E-value=4.1 Score=20.79 Aligned_cols=30 Identities=27% Similarity=0.445 Sum_probs=17.3
Q ss_pred ccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccC
Q psy6273 34 ACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRS 74 (82)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 74 (82)
.|+.|++.-.....|. -.-.|+.||..|..
T Consensus 35 rCP~CG~G~LF~g~Lk-----------v~~~C~~CG~~~~~ 64 (148)
T PRK05978 35 RCPACGEGKLFRAFLK-----------PVDHCAACGEDFTH 64 (148)
T ss_pred cCCCCCCCcccccccc-----------cCCCccccCCcccc
Confidence 6788876533332221 34578888876653
No 179
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=55.53 E-value=14 Score=14.34 Aligned_cols=24 Identities=17% Similarity=0.317 Sum_probs=13.7
Q ss_pred cccccchhhhcC--cHHHHHHHHHhc
Q psy6273 33 FACDQCVSYFKT--NSALLQHKRKMH 56 (82)
Q Consensus 33 ~~c~~c~~~~~~--~~~l~~h~~~~~ 56 (82)
..|+.|+-.+.. +..-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 477888755443 344555665553
No 180
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=54.80 E-value=5.9 Score=15.45 Aligned_cols=10 Identities=40% Similarity=0.913 Sum_probs=7.2
Q ss_pred eeecCccccc
Q psy6273 62 LFSCPLCGEV 71 (82)
Q Consensus 62 ~~~C~~C~~~ 71 (82)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 5678888843
No 181
>KOG0717|consensus
Probab=54.39 E-value=7.6 Score=23.77 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=18.7
Q ss_pred cccccchhhhcCcHHHHHHHHH
Q psy6273 33 FACDQCVSYFKTNSALLQHKRK 54 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~ 54 (82)
+-|..|++.|.+...+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6799999999999998888654
No 182
>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=54.13 E-value=7.2 Score=14.86 Aligned_cols=12 Identities=25% Similarity=1.093 Sum_probs=6.9
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
+-|+|..||...
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 579999998653
No 183
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=54.02 E-value=6.8 Score=14.93 Aligned_cols=14 Identities=36% Similarity=0.802 Sum_probs=7.3
Q ss_pred ecCcccccccCccc
Q psy6273 64 SCPLCGEVFRSHQG 77 (82)
Q Consensus 64 ~C~~C~~~f~~~~~ 77 (82)
.|+-|++.|-+.+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 46667776655544
No 184
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=52.66 E-value=7 Score=18.29 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=5.3
Q ss_pred CcccCcCCcccc
Q psy6273 3 RYKCHACDVETK 14 (82)
Q Consensus 3 ~~~c~~c~~~~~ 14 (82)
|-.|..||..|.
T Consensus 58 Pa~CkkCGfef~ 69 (97)
T COG3357 58 PARCKKCGFEFR 69 (97)
T ss_pred ChhhcccCcccc
Confidence 334444444443
No 185
>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=52.46 E-value=6.9 Score=15.17 Aligned_cols=8 Identities=50% Similarity=1.502 Sum_probs=4.4
Q ss_pred eecCcccc
Q psy6273 63 FSCPLCGE 70 (82)
Q Consensus 63 ~~C~~C~~ 70 (82)
|.|+.|+.
T Consensus 1 m~Cp~Cg~ 8 (43)
T PF08271_consen 1 MKCPNCGS 8 (43)
T ss_dssp ESBTTTSS
T ss_pred CCCcCCcC
Confidence 35666654
No 186
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=51.48 E-value=6.8 Score=21.59 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=11.8
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
++..|++||..|.-
T Consensus 180 kpqRCpECGqVFKL 193 (268)
T PTZ00043 180 FLYRCGECDQIFML 193 (268)
T ss_pred CCccCCCCCcEEEE
Confidence 68999999988854
No 187
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=50.96 E-value=6.1 Score=16.69 Aligned_cols=7 Identities=43% Similarity=1.526 Sum_probs=3.4
Q ss_pred cccccch
Q psy6273 33 FACDQCV 39 (82)
Q Consensus 33 ~~c~~c~ 39 (82)
|.|..|.
T Consensus 32 YmC~eC~ 38 (56)
T PF09963_consen 32 YMCDECK 38 (56)
T ss_pred eeChhHH
Confidence 4555544
No 188
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=50.82 E-value=13 Score=15.88 Aligned_cols=9 Identities=22% Similarity=0.693 Sum_probs=6.0
Q ss_pred cCcCCcccc
Q psy6273 6 CHACDVETK 14 (82)
Q Consensus 6 c~~c~~~~~ 14 (82)
|..||+...
T Consensus 6 C~~CG~~Ip 14 (59)
T PF09889_consen 6 CPVCGKPIP 14 (59)
T ss_pred CCcCCCcCC
Confidence 777776644
No 189
>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=50.13 E-value=8.3 Score=14.74 Aligned_cols=11 Identities=27% Similarity=0.957 Sum_probs=6.4
Q ss_pred eeecCcccccc
Q psy6273 62 LFSCPLCGEVF 72 (82)
Q Consensus 62 ~~~C~~C~~~f 72 (82)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 36666666544
No 190
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=49.82 E-value=11 Score=14.52 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=6.7
Q ss_pred eeecCcccccc
Q psy6273 62 LFSCPLCGEVF 72 (82)
Q Consensus 62 ~~~C~~C~~~f 72 (82)
-|.|..|+..+
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 46676676544
No 191
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=49.64 E-value=4.4 Score=23.04 Aligned_cols=22 Identities=23% Similarity=0.528 Sum_probs=17.6
Q ss_pred CeeecCcccccccCcccccccC
Q psy6273 61 NLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.-|.|..|-+-|.....+.+|+
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~ 68 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHL 68 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHH
Confidence 6788888888888888877763
No 192
>KOG1088|consensus
Probab=49.33 E-value=13 Score=18.30 Aligned_cols=17 Identities=35% Similarity=0.714 Sum_probs=13.4
Q ss_pred CeeecCcccccccCccc
Q psy6273 61 NLFSCPLCGEVFRSHQG 77 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~ 77 (82)
-...|+.||+.|.-+..
T Consensus 97 G~l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 97 GELVCPETGRVFPISDG 113 (124)
T ss_pred ceEecCCCCcEeecccC
Confidence 67999999999875443
No 193
>KOG3507|consensus
Probab=49.06 E-value=11 Score=16.06 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=6.0
Q ss_pred eeecCccccc
Q psy6273 62 LFSCPLCGEV 71 (82)
Q Consensus 62 ~~~C~~C~~~ 71 (82)
++.|.+||..
T Consensus 37 ~irCReCG~R 46 (62)
T KOG3507|consen 37 VIRCRECGYR 46 (62)
T ss_pred cEehhhcchH
Confidence 5666666643
No 194
>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=48.54 E-value=8.3 Score=18.00 Aligned_cols=32 Identities=19% Similarity=0.559 Sum_probs=20.2
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSH 75 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~ 75 (82)
.|.|+.|++.-.... +. --|.|..|++.|+--
T Consensus 35 ky~Cp~Cgk~~vkR~----------a~--GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRV----------AT--GIWKCKKCGKKFAGG 66 (90)
T ss_dssp -BEESSSSSSEEEEE----------ET--TEEEETTTTEEEE-B
T ss_pred CCcCCCCCCceeEEe----------ee--EEeecCCCCCEEeCC
Confidence 478888887532221 11 469999999888644
No 195
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.21 E-value=15 Score=15.81 Aligned_cols=11 Identities=18% Similarity=0.869 Sum_probs=6.2
Q ss_pred Cccccccchhh
Q psy6273 31 KSFACDQCVSY 41 (82)
Q Consensus 31 ~~~~c~~c~~~ 41 (82)
..|.|+.|...
T Consensus 30 rtymC~eC~~R 40 (68)
T COG4896 30 RTYMCPECEHR 40 (68)
T ss_pred eeEechhhHhh
Confidence 34666666543
No 196
>PLN02748 tRNA dimethylallyltransferase
Probab=48.11 E-value=19 Score=22.20 Aligned_cols=22 Identities=23% Similarity=0.536 Sum_probs=13.7
Q ss_pred CcccCcCCc-cccCHHHHHhHHH
Q psy6273 3 RYKCHACDV-ETKTRQALDNHIL 24 (82)
Q Consensus 3 ~~~c~~c~~-~~~~~~~l~~h~~ 24 (82)
.|.|..|+. .+.....+..|.+
T Consensus 418 ~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 418 QYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred cccccCCCCcccCCHHHHHHHhc
Confidence 455677775 5666666666654
No 197
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=47.35 E-value=11 Score=15.88 Aligned_cols=15 Identities=33% Similarity=0.886 Sum_probs=9.3
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
+--.|+.|++.|...
T Consensus 38 rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 38 RYNGCPFCGTPFEFD 52 (55)
T ss_pred hccCCCCCCCcccCC
Confidence 344677787776543
No 198
>PRK02935 hypothetical protein; Provisional
Probab=47.24 E-value=16 Score=17.62 Aligned_cols=36 Identities=17% Similarity=0.375 Sum_probs=22.0
Q ss_pred CCCccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCcccc
Q psy6273 29 ETKSFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSHQGY 78 (82)
Q Consensus 29 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l 78 (82)
...+..|+.|++..+ ..| +...|..|+....-..++
T Consensus 67 kavqV~CP~C~K~TK-----------mLG---rvD~CM~C~~PLTLd~~l 102 (110)
T PRK02935 67 KAVQVICPSCEKPTK-----------MLG---RVDACMHCNQPLTLDRSL 102 (110)
T ss_pred cceeeECCCCCchhh-----------hcc---ceeecCcCCCcCCcCccc
Confidence 345568888877532 122 567888888765544443
No 199
>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=46.72 E-value=9.3 Score=16.49 Aligned_cols=13 Identities=31% Similarity=0.894 Sum_probs=10.8
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
....|+.|++.|.
T Consensus 52 g~L~Cp~c~r~YP 64 (68)
T PF03966_consen 52 GELICPECGREYP 64 (68)
T ss_dssp TEEEETTTTEEEE
T ss_pred CEEEcCCCCCEEe
Confidence 6789999998875
No 200
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=46.21 E-value=16 Score=17.62 Aligned_cols=26 Identities=35% Similarity=0.685 Sum_probs=20.5
Q ss_pred CCCccccccchhhhcCcHHHHHHHHH
Q psy6273 29 ETKSFACDQCVSYFKTNSALLQHKRK 54 (82)
Q Consensus 29 ~~~~~~c~~c~~~~~~~~~l~~h~~~ 54 (82)
|-..+-|..|.+.|.+...|..|.+.
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhcc
Confidence 34457799999999999999888653
No 201
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=45.81 E-value=6.8 Score=21.03 Aligned_cols=21 Identities=19% Similarity=0.854 Sum_probs=0.0
Q ss_pred CeeecCccc-ccccCccccccc
Q psy6273 61 NLFSCPLCG-EVFRSHQGYKIH 81 (82)
Q Consensus 61 ~~~~C~~C~-~~f~~~~~l~~H 81 (82)
+.|.|..|| .++.-+..+.+|
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ----------------------
T ss_pred CeeeeEeCCCcceecHHHHHHh
Confidence 568888886 344444444333
No 202
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=45.71 E-value=13 Score=12.41 Aligned_cols=6 Identities=67% Similarity=1.890 Sum_probs=3.1
Q ss_pred cCcccc
Q psy6273 65 CPLCGE 70 (82)
Q Consensus 65 C~~C~~ 70 (82)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555553
No 203
>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=45.10 E-value=9.4 Score=19.54 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=11.3
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
+.-.|..|++.|++.
T Consensus 27 RRReC~~C~~RFTTy 41 (147)
T TIGR00244 27 RRRECLECHERFTTF 41 (147)
T ss_pred ecccCCccCCcccee
Confidence 457888898888754
No 204
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.42 E-value=15 Score=20.67 Aligned_cols=12 Identities=58% Similarity=1.270 Sum_probs=8.8
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
+.|.|+.||..+
T Consensus 321 r~~~C~~cg~~~ 332 (364)
T COG0675 321 RLFKCPRCGFVH 332 (364)
T ss_pred eeEECCCCCCee
Confidence 578888888654
No 205
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=44.35 E-value=12 Score=15.74 Aligned_cols=12 Identities=42% Similarity=0.791 Sum_probs=8.8
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
..|.|+.||-.+
T Consensus 13 v~~~Cp~cGipt 24 (55)
T PF13824_consen 13 VNFECPDCGIPT 24 (55)
T ss_pred cCCcCCCCCCcC
Confidence 578898888543
No 206
>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=44.24 E-value=14 Score=13.52 Aligned_cols=12 Identities=25% Similarity=1.218 Sum_probs=9.1
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
+-|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468999998654
No 207
>PRK00420 hypothetical protein; Validated
Probab=44.10 E-value=10 Score=18.44 Aligned_cols=11 Identities=36% Similarity=0.975 Sum_probs=6.7
Q ss_pred eeecCcccccc
Q psy6273 62 LFSCPLCGEVF 72 (82)
Q Consensus 62 ~~~C~~C~~~f 72 (82)
...|+.||...
T Consensus 40 ~~~Cp~Cg~~~ 50 (112)
T PRK00420 40 EVVCPVHGKVY 50 (112)
T ss_pred ceECCCCCCee
Confidence 45677776643
No 208
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.04 E-value=20 Score=24.50 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=6.3
Q ss_pred CeeecCccccc
Q psy6273 61 NLFSCPLCGEV 71 (82)
Q Consensus 61 ~~~~C~~C~~~ 71 (82)
.++.|+.||..
T Consensus 662 ~~y~CPKCG~E 672 (1121)
T PRK04023 662 EEDECEKCGRE 672 (1121)
T ss_pred CCCcCCCCCCC
Confidence 34566666643
No 209
>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=43.96 E-value=4.2 Score=16.23 Aligned_cols=17 Identities=24% Similarity=0.557 Sum_probs=9.4
Q ss_pred CeeecCc--ccccccCccc
Q psy6273 61 NLFSCPL--CGEVFRSHQG 77 (82)
Q Consensus 61 ~~~~C~~--C~~~f~~~~~ 77 (82)
.-+.|.. ||-.|....+
T Consensus 24 ~Y~qC~N~~Cg~tfv~~~~ 42 (47)
T PF04606_consen 24 LYCQCTNPECGHTFVANLE 42 (47)
T ss_pred EEEEECCCcCCCEEEEEEE
Confidence 4556643 7766654433
No 210
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=43.89 E-value=23 Score=13.51 Aligned_cols=17 Identities=18% Similarity=0.286 Sum_probs=11.4
Q ss_pred ccCcCCccccCHHHHHh
Q psy6273 5 KCHACDVETKTRQALDN 21 (82)
Q Consensus 5 ~c~~c~~~~~~~~~l~~ 21 (82)
.|+.|+-.|.....|..
T Consensus 21 ~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 21 VCPSCGGIWFDAGELEK 37 (41)
T ss_pred ECCCCCeEEccHHHHHH
Confidence 46777777777666654
No 211
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=43.19 E-value=16 Score=14.49 Aligned_cols=13 Identities=31% Similarity=0.493 Sum_probs=8.4
Q ss_pred eeecCcccccccC
Q psy6273 62 LFSCPLCGEVFRS 74 (82)
Q Consensus 62 ~~~C~~C~~~f~~ 74 (82)
.+.|+.||..+.-
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 5777777765543
No 212
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.04 E-value=8.9 Score=18.09 Aligned_cols=15 Identities=20% Similarity=0.565 Sum_probs=10.6
Q ss_pred CCCcccCcCCccccC
Q psy6273 1 MTRYKCHACDVETKT 15 (82)
Q Consensus 1 ~k~~~c~~c~~~~~~ 15 (82)
++.|+|.+|+.....
T Consensus 4 lkewkC~VCg~~iie 18 (103)
T COG4847 4 LKEWKCYVCGGTIIE 18 (103)
T ss_pred cceeeEeeeCCEeee
Confidence 356889999876443
No 213
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=42.99 E-value=12 Score=15.18 Aligned_cols=9 Identities=56% Similarity=1.501 Sum_probs=5.6
Q ss_pred cCccccccc
Q psy6273 65 CPLCGEVFR 73 (82)
Q Consensus 65 C~~C~~~f~ 73 (82)
|+.||..|.
T Consensus 1 CP~Cg~~f~ 9 (50)
T PF14375_consen 1 CPRCGAPFE 9 (50)
T ss_pred CCCCCCcCC
Confidence 566666664
No 214
>PRK01343 zinc-binding protein; Provisional
Probab=42.88 E-value=14 Score=15.67 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=4.7
Q ss_pred eecCcccccc
Q psy6273 63 FSCPLCGEVF 72 (82)
Q Consensus 63 ~~C~~C~~~f 72 (82)
..|+.|++.+
T Consensus 10 ~~CP~C~k~~ 19 (57)
T PRK01343 10 RPCPECGKPS 19 (57)
T ss_pred CcCCCCCCcC
Confidence 3455555443
No 215
>PLN03239 histone acetyltransferase; Provisional
Probab=42.83 E-value=5.8 Score=23.24 Aligned_cols=22 Identities=14% Similarity=0.242 Sum_probs=18.2
Q ss_pred CeeecCcccccccCcccccccC
Q psy6273 61 NLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.-|.|..|.+-|.....|.+|+
T Consensus 105 ~lYiCE~Clky~~~~~~l~~H~ 126 (351)
T PLN03239 105 VLYVCEFSFGFFARKSELLRFQ 126 (351)
T ss_pred eEEEeccchhhhcCHHHHHHHH
Confidence 6899999999888888877663
No 216
>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=42.77 E-value=10 Score=13.62 Aligned_cols=10 Identities=40% Similarity=1.212 Sum_probs=5.3
Q ss_pred eecCcccccc
Q psy6273 63 FSCPLCGEVF 72 (82)
Q Consensus 63 ~~C~~C~~~f 72 (82)
|.|..|++.+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5555555443
No 217
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=42.75 E-value=15 Score=13.37 Aligned_cols=12 Identities=25% Similarity=1.185 Sum_probs=9.3
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
+-|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 579999998654
No 218
>KOG2071|consensus
Probab=42.63 E-value=18 Score=22.92 Aligned_cols=26 Identities=15% Similarity=0.516 Sum_probs=19.9
Q ss_pred CCcccCcCCccccCHHHHHhHHHhhCC
Q psy6273 2 TRYKCHACDVETKTRQALDNHILCVHT 28 (82)
Q Consensus 2 k~~~c~~c~~~~~~~~~l~~h~~~~~~ 28 (82)
.|..|..||.+|........|+. .|.
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md-~H~ 442 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMD-IHD 442 (579)
T ss_pred CcchhcccccccccchhhhhHhh-hhh
Confidence 46789999999998877776665 443
No 219
>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=42.60 E-value=2.8 Score=15.90 Aligned_cols=8 Identities=25% Similarity=0.908 Sum_probs=3.7
Q ss_pred CeeecCcc
Q psy6273 61 NLFSCPLC 68 (82)
Q Consensus 61 ~~~~C~~C 68 (82)
..|.|..|
T Consensus 28 qryrC~~C 35 (36)
T PF03811_consen 28 QRYRCKDC 35 (36)
T ss_pred EeEecCcC
Confidence 34555444
No 220
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=42.37 E-value=5.8 Score=24.08 Aligned_cols=22 Identities=18% Similarity=0.572 Sum_probs=18.8
Q ss_pred CeeecCcccccccCcccccccC
Q psy6273 61 NLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.-|.|..|.+-|.....|.+|+
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~ 218 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHM 218 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHH
Confidence 5799999999999988888874
No 221
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=41.51 E-value=12 Score=19.37 Aligned_cols=14 Identities=36% Similarity=0.702 Sum_probs=10.2
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
+.-.|..|+..|.+
T Consensus 27 RRReC~~C~~RFTT 40 (156)
T COG1327 27 RRRECLECGERFTT 40 (156)
T ss_pred hhhcccccccccch
Confidence 45678888888764
No 222
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.31 E-value=11 Score=17.03 Aligned_cols=13 Identities=31% Similarity=0.879 Sum_probs=9.2
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
-.|.|..|+..|.
T Consensus 11 Y~Y~c~~cg~~~d 23 (82)
T COG2331 11 YSYECTECGNRFD 23 (82)
T ss_pred eEEeecccchHHH
Confidence 3578888887664
No 223
>PF14369 zf-RING_3: zinc-finger
Probab=41.14 E-value=13 Score=13.92 Aligned_cols=8 Identities=50% Similarity=1.244 Sum_probs=4.1
Q ss_pred cCcccccc
Q psy6273 65 CPLCGEVF 72 (82)
Q Consensus 65 C~~C~~~f 72 (82)
|+.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 55555444
No 224
>KOG3352|consensus
Probab=40.85 E-value=14 Score=18.99 Aligned_cols=13 Identities=38% Similarity=1.030 Sum_probs=10.5
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
+...|.+||..|.
T Consensus 132 e~~rc~eCG~~fk 144 (153)
T KOG3352|consen 132 ETQRCPECGHYFK 144 (153)
T ss_pred CcccCCcccceEE
Confidence 4778999998775
No 225
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=40.49 E-value=27 Score=18.39 Aligned_cols=19 Identities=11% Similarity=0.366 Sum_probs=12.6
Q ss_pred CcccCcCCccccCHHHHHh
Q psy6273 3 RYKCHACDVETKTRQALDN 21 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~ 21 (82)
...|..||+.|.....+..
T Consensus 114 ~~~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 114 LQRCSRCERPFAPQKTVAL 132 (181)
T ss_pred cCcCcccCCccCcHhHHHH
Confidence 4567788888876655543
No 226
>KOG0402|consensus
Probab=40.42 E-value=13 Score=17.14 Aligned_cols=32 Identities=19% Similarity=0.487 Sum_probs=19.7
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSH 75 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~ 75 (82)
.|.|+.|++....... - --|.|..|.+.+.--
T Consensus 36 ky~CsfCGK~~vKR~A----------v--GiW~C~~C~kv~agg 67 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRKA----------V--GIWKCGSCKKVVAGG 67 (92)
T ss_pred hhhhhhcchhhhhhhc----------e--eEEecCCccceeccc
Confidence 3788888875322211 1 468888888877543
No 227
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=40.30 E-value=17 Score=17.41 Aligned_cols=10 Identities=40% Similarity=1.085 Sum_probs=5.2
Q ss_pred Cccccccchh
Q psy6273 31 KSFACDQCVS 40 (82)
Q Consensus 31 ~~~~c~~c~~ 40 (82)
+-|.|+.|+.
T Consensus 21 k~FtCp~Cgh 30 (104)
T COG4888 21 KTFTCPRCGH 30 (104)
T ss_pred ceEecCccCC
Confidence 3455555553
No 228
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=40.11 E-value=28 Score=16.25 Aligned_cols=19 Identities=16% Similarity=0.485 Sum_probs=13.8
Q ss_pred cccCcCCccccCHHHHHhH
Q psy6273 4 YKCHACDVETKTRQALDNH 22 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h 22 (82)
..|+.||..|.+.+.+..-
T Consensus 36 ~~C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTVKEI 54 (89)
T ss_pred ccccCCCcEeecHHHHHHH
Confidence 4588899888887766543
No 229
>PRK12722 transcriptional activator FlhC; Provisional
Probab=39.93 E-value=14 Score=19.74 Aligned_cols=27 Identities=33% Similarity=0.695 Sum_probs=15.9
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
..|..|+..|....+ +....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~~----------e~~~~f~CplC~ 161 (187)
T PRK12722 135 SSCNCCGGHFVTHAH----------DPVGSFVCGLCQ 161 (187)
T ss_pred ccCCCCCCCeecccc----------ccCCCCcCCCCC
Confidence 467777776653221 212578888885
No 230
>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=39.75 E-value=24 Score=20.42 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=6.5
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
+...|..|+.
T Consensus 251 r~e~C~~C~~ 260 (305)
T TIGR01562 251 KAETCDSCQG 260 (305)
T ss_pred EEeecccccc
Confidence 5667777753
No 231
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=39.58 E-value=6 Score=20.71 Aligned_cols=29 Identities=31% Similarity=0.700 Sum_probs=16.8
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFR 73 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 73 (82)
..|+.|+.+|...- +. ..|-|..|.+.|.
T Consensus 75 l~C~~C~~Tfk~f~--------~~----g~fGCaeCY~tf~ 103 (176)
T COG3880 75 LGCHNCGMTFKEFI--------QS----GLFGCAECYKTFE 103 (176)
T ss_pred hcCccccccHHHHH--------Hh----cccchHHHHHHHH
Confidence 46777776663321 11 3577777777664
No 232
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=39.49 E-value=16 Score=17.07 Aligned_cols=32 Identities=19% Similarity=0.470 Sum_probs=20.9
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccCc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRSH 75 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~ 75 (82)
.|.|+.|++.-... .+- -.|.|..|++.|+-.
T Consensus 36 ~y~CpfCgk~~vkR----------~a~--GIW~C~~C~~~~AGG 67 (90)
T PRK03976 36 KHVCPVCGRPKVKR----------VGT--GIWECRKCGAKFAGG 67 (90)
T ss_pred CccCCCCCCCceEE----------EEE--EEEEcCCCCCEEeCC
Confidence 57899997542211 111 579999999988653
No 233
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=39.46 E-value=16 Score=17.58 Aligned_cols=14 Identities=14% Similarity=0.337 Sum_probs=11.4
Q ss_pred CcccCcCCccccCH
Q psy6273 3 RYKCHACDVETKTR 16 (82)
Q Consensus 3 ~~~c~~c~~~~~~~ 16 (82)
|+.|.-||..|.+-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 67888899888875
No 234
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=38.79 E-value=9.3 Score=19.18 Aligned_cols=13 Identities=23% Similarity=0.685 Sum_probs=7.8
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
..|.|..|+..+.
T Consensus 142 ~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 142 KRYRCGRCGGPLV 154 (157)
T ss_pred hhEECCCCCCEEE
Confidence 3467777765543
No 235
>PRK12860 transcriptional activator FlhC; Provisional
Probab=38.64 E-value=15 Score=19.73 Aligned_cols=27 Identities=30% Similarity=0.588 Sum_probs=15.4
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
..|..|+..|.... +... ..|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~--------~e~~--~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHA--------HDLR--HNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeeccc--------cccC--CCCcCCCCC
Confidence 46777776665322 1112 578888875
No 236
>KOG2231|consensus
Probab=38.50 E-value=47 Score=21.68 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=11.6
Q ss_pred cCcCCccccCHHHHHhHHH
Q psy6273 6 CHACDVETKTRQALDNHIL 24 (82)
Q Consensus 6 c~~c~~~~~~~~~l~~h~~ 24 (82)
|..|...|.....|..|++
T Consensus 185 C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLR 203 (669)
T ss_pred chhhhhhhccHHHHHHhhc
Confidence 5566666666666666654
No 237
>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=38.42 E-value=15 Score=15.18 Aligned_cols=14 Identities=14% Similarity=0.536 Sum_probs=9.0
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
..+.|.+|++.+..
T Consensus 34 ~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 34 IKLRCHYCERIITE 47 (52)
T ss_dssp CEEEETTT--EEEH
T ss_pred CEEEeeCCCCEecc
Confidence 57888888887654
No 238
>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=37.92 E-value=11 Score=15.57 Aligned_cols=22 Identities=23% Similarity=0.354 Sum_probs=11.5
Q ss_pred CcccCcCCccccCHHHHHhHHH
Q psy6273 3 RYKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~~h~~ 24 (82)
.|.|+.|.+.|-..=++-.|..
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTT
T ss_pred eEECCCCCCccccCcChhhhcc
Confidence 3778888888887766655543
No 239
>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=37.86 E-value=6.3 Score=22.21 Aligned_cols=11 Identities=36% Similarity=0.921 Sum_probs=6.5
Q ss_pred CeeecCccccc
Q psy6273 61 NLFSCPLCGEV 71 (82)
Q Consensus 61 ~~~~C~~C~~~ 71 (82)
+++.|+.||..
T Consensus 208 k~~PCPKCg~e 218 (314)
T PF06524_consen 208 KPIPCPKCGYE 218 (314)
T ss_pred CCCCCCCCCCc
Confidence 56666666543
No 240
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=37.64 E-value=33 Score=14.03 Aligned_cols=30 Identities=27% Similarity=0.574 Sum_probs=18.6
Q ss_pred cc--cchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccccC
Q psy6273 35 CD--QCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVFRS 74 (82)
Q Consensus 35 c~--~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 74 (82)
|+ .|+....... ..+. ....|+.|+..|-.
T Consensus 21 CP~~~C~~~~~~~~--------~~~~--~~v~C~~C~~~fC~ 52 (64)
T smart00647 21 CPAPDCSAAIIVTE--------EEGC--NRVTCPKCGFSFCF 52 (64)
T ss_pred CCCCCCcceEEecC--------CCCC--CeeECCCCCCeECC
Confidence 55 7766554432 2233 67889888887754
No 241
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=37.58 E-value=17 Score=15.40 Aligned_cols=12 Identities=33% Similarity=1.021 Sum_probs=5.5
Q ss_pred eecCcccccccC
Q psy6273 63 FSCPLCGEVFRS 74 (82)
Q Consensus 63 ~~C~~C~~~f~~ 74 (82)
..|+.|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468888876654
No 242
>PF12773 DZR: Double zinc ribbon
Probab=37.28 E-value=22 Score=14.02 Aligned_cols=12 Identities=33% Similarity=0.636 Sum_probs=7.5
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
....|+.|+...
T Consensus 28 ~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 28 SKKICPNCGAEN 39 (50)
T ss_pred CCCCCcCCcCCC
Confidence 356777777653
No 243
>PTZ00064 histone acetyltransferase; Provisional
Probab=37.16 E-value=7.9 Score=24.00 Aligned_cols=22 Identities=23% Similarity=0.374 Sum_probs=18.6
Q ss_pred CeeecCcccccccCcccccccC
Q psy6273 61 NLFSCPLCGEVFRSHQGYKIHH 82 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~~H~ 82 (82)
.-|.|..|.+-|.....|.+|+
T Consensus 279 ~LYICEfCLkY~~s~~~l~rH~ 300 (552)
T PTZ00064 279 TLHFCEYCLDFFCFEDELIRHL 300 (552)
T ss_pred eEEEccchhhhhCCHHHHHHHH
Confidence 5699999999999888888774
No 244
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=36.90 E-value=21 Score=14.57 Aligned_cols=15 Identities=27% Similarity=0.924 Sum_probs=10.2
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
.-+.|+.||..|...
T Consensus 27 v~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 27 VWWKCPKCGHEWKAS 41 (55)
T ss_pred EEEECCCCCCeeEcc
Confidence 358888887766543
No 245
>PRK06260 threonine synthase; Validated
Probab=36.31 E-value=16 Score=21.71 Aligned_cols=26 Identities=23% Similarity=0.669 Sum_probs=14.7
Q ss_pred cccCcCCccccCHHHHHhHHHhhCCCCCccccccchhhh
Q psy6273 4 YKCHACDVETKTRQALDNHILCVHTETKSFACDQCVSYF 42 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~~ 42 (82)
+.|..|++.+.. ....+.|+.|+..+
T Consensus 4 ~~C~~cg~~~~~-------------~~~~~~Cp~cg~~l 29 (397)
T PRK06260 4 LKCIECGKEYDP-------------DEIIYTCPECGGLL 29 (397)
T ss_pred EEECCCCCCCCC-------------CCccccCCCCCCeE
Confidence 567777765431 12246787776543
No 246
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=36.21 E-value=38 Score=13.88 Aligned_cols=32 Identities=22% Similarity=0.614 Sum_probs=18.1
Q ss_pred ccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccccc
Q psy6273 34 ACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEV 71 (82)
Q Consensus 34 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 71 (82)
.|..|.-.. +..... ....++ ....|+.||+.
T Consensus 24 ~C~gC~~~l--~~~~~~--~i~~~~--~i~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMEL--PPQELN--EIRKGD--EIVFCPNCGRI 55 (56)
T ss_pred ccCCCCEEc--CHHHHH--HHHcCC--CeEECcCCCcc
Confidence 677775433 222222 233445 68899999874
No 247
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=36.15 E-value=16 Score=16.60 Aligned_cols=9 Identities=44% Similarity=1.593 Sum_probs=3.3
Q ss_pred CeeecCccc
Q psy6273 61 NLFSCPLCG 69 (82)
Q Consensus 61 ~~~~C~~C~ 69 (82)
+.|.|+.|+
T Consensus 21 ~~F~CPfC~ 29 (81)
T PF05129_consen 21 KVFDCPFCN 29 (81)
T ss_dssp S----TTT-
T ss_pred ceEcCCcCC
Confidence 678999887
No 248
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=35.80 E-value=23 Score=13.71 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=5.0
Q ss_pred ecCcccccccCc
Q psy6273 64 SCPLCGEVFRSH 75 (82)
Q Consensus 64 ~C~~C~~~f~~~ 75 (82)
.|..||+.-...
T Consensus 3 ~CSFCgr~~~~v 14 (41)
T PF06689_consen 3 RCSFCGRPESEV 14 (41)
T ss_dssp B-TTT--BTTTS
T ss_pred CccCCCCCHHHH
Confidence 467777655443
No 249
>PTZ00448 hypothetical protein; Provisional
Probab=35.52 E-value=30 Score=20.72 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=18.8
Q ss_pred ccccccchhhhcCcHHHHHHHHH
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRK 54 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~ 54 (82)
.+.|..|+-.|.+......|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999887777777765
No 250
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=34.88 E-value=50 Score=15.84 Aligned_cols=19 Identities=21% Similarity=0.447 Sum_probs=14.3
Q ss_pred cccCcCCccccCHHHHHhH
Q psy6273 4 YKCHACDVETKTRQALDNH 22 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h 22 (82)
+.|+.||..+.+.......
T Consensus 32 ~~C~~CGe~~~~~e~~~~~ 50 (127)
T TIGR03830 32 WYCPACGEELLDPEESKRN 50 (127)
T ss_pred eECCCCCCEEEcHHHHHHH
Confidence 5699999988877665544
No 251
>KOG4727|consensus
Probab=34.80 E-value=27 Score=18.54 Aligned_cols=21 Identities=33% Similarity=0.635 Sum_probs=18.1
Q ss_pred cccCcCCccccCHHHHHhHHH
Q psy6273 4 YKCHACDVETKTRQALDNHIL 24 (82)
Q Consensus 4 ~~c~~c~~~~~~~~~l~~h~~ 24 (82)
|-|.+|+-++...-++..|+.
T Consensus 76 yyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred eeeeecceeehhhHHHHHHhc
Confidence 569999999999988888875
No 252
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=34.40 E-value=42 Score=18.80 Aligned_cols=34 Identities=29% Similarity=0.718 Sum_probs=18.4
Q ss_pred cccccchhhhcCcHHHHHHHHHhcCCCCCeeecCcccccc
Q psy6273 33 FACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCGEVF 72 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 72 (82)
..|..|.-.. +.....-++. ++ ....|+.||+..
T Consensus 198 ~~C~GC~m~l--~~~~~~~V~~--~d--~iv~CP~CgRIL 231 (239)
T COG1579 198 RVCGGCHMKL--PSQTLSKVRK--KD--EIVFCPYCGRIL 231 (239)
T ss_pred CcccCCeeee--cHHHHHHHhc--CC--CCccCCccchHH
Confidence 3566664332 3333333333 44 678899999753
No 253
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=34.39 E-value=32 Score=12.83 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=6.6
Q ss_pred CeeecCccccc
Q psy6273 61 NLFSCPLCGEV 71 (82)
Q Consensus 61 ~~~~C~~C~~~ 71 (82)
..+.|+.||..
T Consensus 21 ~R~vC~~Cg~I 31 (34)
T PF14803_consen 21 ERLVCPACGFI 31 (34)
T ss_dssp -EEEETTTTEE
T ss_pred cceECCCCCCE
Confidence 46777777653
No 254
>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=33.89 E-value=24 Score=20.21 Aligned_cols=10 Identities=20% Similarity=0.763 Sum_probs=4.7
Q ss_pred ccccchhhhc
Q psy6273 34 ACDQCVSYFK 43 (82)
Q Consensus 34 ~c~~c~~~~~ 43 (82)
.|+.|+..|.
T Consensus 47 vc~~c~~h~r 56 (285)
T TIGR00515 47 VCPKCDHHMR 56 (285)
T ss_pred CCCCCCCcCc
Confidence 4555554443
No 255
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=33.51 E-value=24 Score=14.68 Aligned_cols=10 Identities=40% Similarity=1.255 Sum_probs=8.1
Q ss_pred CeeecCcccc
Q psy6273 61 NLFSCPLCGE 70 (82)
Q Consensus 61 ~~~~C~~C~~ 70 (82)
-.|.|+.|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 4799999974
No 256
>PRK12496 hypothetical protein; Provisional
Probab=33.48 E-value=24 Score=18.34 Aligned_cols=12 Identities=17% Similarity=0.459 Sum_probs=9.9
Q ss_pred eecCcccccccC
Q psy6273 63 FSCPLCGEVFRS 74 (82)
Q Consensus 63 ~~C~~C~~~f~~ 74 (82)
+.|..|++.|..
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 779999998854
No 257
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=33.40 E-value=7.9 Score=22.88 Aligned_cols=21 Identities=24% Similarity=0.566 Sum_probs=16.5
Q ss_pred CeeecCcccccccCccccccc
Q psy6273 61 NLFSCPLCGEVFRSHQGYKIH 81 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~~l~~H 81 (82)
+.+-|+.|++.|...+.+..|
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~H 257 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYH 257 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHH
Confidence 567899999999887766555
No 258
>PHA02942 putative transposase; Provisional
Probab=33.17 E-value=22 Score=21.16 Aligned_cols=12 Identities=42% Similarity=0.958 Sum_probs=9.6
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
+.|.|+.||...
T Consensus 341 r~f~C~~CG~~~ 352 (383)
T PHA02942 341 RYFHCPSCGYEN 352 (383)
T ss_pred CEEECCCCCCEe
Confidence 679999998654
No 259
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=32.99 E-value=27 Score=20.27 Aligned_cols=26 Identities=27% Similarity=0.434 Sum_probs=16.4
Q ss_pred CCccccCHHHHHhHHHhhCCCCCccccccchhh
Q psy6273 9 CDVETKTRQALDNHILCVHTETKSFACDQCVSY 41 (82)
Q Consensus 9 c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 41 (82)
||.+|.+. -++ .|.+++|+ |+.|...
T Consensus 43 CgHtFCsl-----CIR-~hL~~qp~-CP~Cr~~ 68 (391)
T COG5432 43 CGHTFCSL-----CIR-RHLGTQPF-CPVCRED 68 (391)
T ss_pred cccchhHH-----HHH-HHhcCCCC-Ccccccc
Confidence 77776653 234 56777775 8888753
No 260
>COG2879 Uncharacterized small protein [Function unknown]
Probab=32.29 E-value=53 Score=14.32 Aligned_cols=16 Identities=25% Similarity=0.434 Sum_probs=11.9
Q ss_pred cCcHHHHHHHHHhcCC
Q psy6273 43 KTNSALLQHKRKMHDE 58 (82)
Q Consensus 43 ~~~~~l~~h~~~~~~~ 58 (82)
.+-+++..||+.++.+
T Consensus 23 pdYdnYVehmr~~hPd 38 (65)
T COG2879 23 PDYDNYVEHMRKKHPD 38 (65)
T ss_pred CcHHHHHHHHHHhCcC
Confidence 3457788899987766
No 261
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=32.21 E-value=18 Score=15.21 Aligned_cols=11 Identities=36% Similarity=1.280 Sum_probs=3.8
Q ss_pred CeeecCccccc
Q psy6273 61 NLFSCPLCGEV 71 (82)
Q Consensus 61 ~~~~C~~C~~~ 71 (82)
+.|.|+.||-.
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 56888888753
No 262
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=32.17 E-value=27 Score=20.18 Aligned_cols=10 Identities=40% Similarity=0.846 Sum_probs=4.7
Q ss_pred ccccchhhhc
Q psy6273 34 ACDQCVSYFK 43 (82)
Q Consensus 34 ~c~~c~~~~~ 43 (82)
.|+.|+..|.
T Consensus 59 vcp~c~~h~r 68 (296)
T CHL00174 59 ICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCcC
Confidence 4555554443
No 263
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=31.49 E-value=41 Score=17.60 Aligned_cols=18 Identities=17% Similarity=0.506 Sum_probs=10.5
Q ss_pred CcccCcCCccccCHHHHH
Q psy6273 3 RYKCHACDVETKTRQALD 20 (82)
Q Consensus 3 ~~~c~~c~~~~~~~~~l~ 20 (82)
++.|..||+.|.....+.
T Consensus 114 ~~~C~~CG~~f~~~~~i~ 131 (180)
T PRK12387 114 LCNCRVCGRPFAVQKEID 131 (180)
T ss_pred cccchhhCCccccHHHHH
Confidence 345667777666554433
No 264
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=31.43 E-value=26 Score=11.90 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=3.2
Q ss_pred ccccchh
Q psy6273 34 ACDQCVS 40 (82)
Q Consensus 34 ~c~~c~~ 40 (82)
.|+.|+.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3444544
No 265
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.40 E-value=26 Score=24.58 Aligned_cols=7 Identities=43% Similarity=1.274 Sum_probs=3.9
Q ss_pred ecCcccc
Q psy6273 64 SCPLCGE 70 (82)
Q Consensus 64 ~C~~C~~ 70 (82)
.|+.|+.
T Consensus 711 ~CP~CGt 717 (1337)
T PRK14714 711 ECPRCDV 717 (1337)
T ss_pred cCCCCCC
Confidence 4666653
No 266
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=31.24 E-value=15 Score=15.38 Aligned_cols=16 Identities=19% Similarity=0.499 Sum_probs=7.5
Q ss_pred eeecCcccccccCccc
Q psy6273 62 LFSCPLCGEVFRSHQG 77 (82)
Q Consensus 62 ~~~C~~C~~~f~~~~~ 77 (82)
-+-|-+||..|.....
T Consensus 27 ~~YC~~Cg~~Y~d~~d 42 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEED 42 (55)
T ss_pred CceeeeeCCccCCHHH
Confidence 3445555555544433
No 267
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=31.15 E-value=35 Score=13.00 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=7.5
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
+.|.|..|+...
T Consensus 23 ~~w~C~~C~~~N 34 (40)
T PF04810_consen 23 KTWICNFCGTKN 34 (40)
T ss_dssp TEEEETTT--EE
T ss_pred CEEECcCCCCcC
Confidence 678888887643
No 268
>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=30.94 E-value=15 Score=19.06 Aligned_cols=15 Identities=20% Similarity=0.405 Sum_probs=12.7
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
.|.-|..||+.|.|-
T Consensus 67 ~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 67 APSYCHNCGKPYPWT 81 (158)
T ss_pred CChhHHhCCCCCchH
Confidence 688899999999764
No 269
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=30.92 E-value=24 Score=16.26 Aligned_cols=11 Identities=36% Similarity=0.923 Sum_probs=6.6
Q ss_pred eecCccccccc
Q psy6273 63 FSCPLCGEVFR 73 (82)
Q Consensus 63 ~~C~~C~~~f~ 73 (82)
-.|+.||..|.
T Consensus 9 ~~C~~CG~d~~ 19 (86)
T PF06170_consen 9 PRCPHCGLDYS 19 (86)
T ss_pred CcccccCCccc
Confidence 35667766554
No 270
>KOG3183|consensus
Probab=30.76 E-value=22 Score=19.87 Aligned_cols=14 Identities=29% Similarity=0.598 Sum_probs=11.2
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
-||.|..|+..|..
T Consensus 22 LPf~Cd~C~~~FC~ 35 (250)
T KOG3183|consen 22 LPFKCDGCSGIFCL 35 (250)
T ss_pred cceeeCCccchhhh
Confidence 58999999888753
No 271
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.54 E-value=23 Score=14.86 Aligned_cols=11 Identities=45% Similarity=1.437 Sum_probs=6.4
Q ss_pred eecCccccccc
Q psy6273 63 FSCPLCGEVFR 73 (82)
Q Consensus 63 ~~C~~C~~~f~ 73 (82)
-.|..||+.|.
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 35666666664
No 272
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=29.80 E-value=28 Score=14.60 Aligned_cols=7 Identities=14% Similarity=0.387 Sum_probs=2.1
Q ss_pred cCCcccc
Q psy6273 8 ACDVETK 14 (82)
Q Consensus 8 ~c~~~~~ 14 (82)
.|+..|.
T Consensus 29 ~C~H~fe 35 (57)
T PF11789_consen 29 KCGHTFE 35 (57)
T ss_dssp SS--EEE
T ss_pred CCCCeec
Confidence 3444444
No 273
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.75 E-value=37 Score=11.96 Aligned_cols=6 Identities=33% Similarity=1.636 Sum_probs=2.5
Q ss_pred cccccc
Q psy6273 33 FACDQC 38 (82)
Q Consensus 33 ~~c~~c 38 (82)
|.|..|
T Consensus 16 Y~C~~c 21 (30)
T PF03107_consen 16 YHCSEC 21 (30)
T ss_pred EEeCCC
Confidence 444443
No 274
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=29.26 E-value=24 Score=16.62 Aligned_cols=13 Identities=23% Similarity=0.743 Sum_probs=10.0
Q ss_pred eeecCcccccccC
Q psy6273 62 LFSCPLCGEVFRS 74 (82)
Q Consensus 62 ~~~C~~C~~~f~~ 74 (82)
.|.|.+|+++-..
T Consensus 68 r~~Ct~Cgkah~~ 80 (94)
T COG1631 68 RLRCTECGKAHQR 80 (94)
T ss_pred EEEehhhcccccc
Confidence 4899999986544
No 275
>KOG0227|consensus
Probab=29.05 E-value=21 Score=19.27 Aligned_cols=20 Identities=20% Similarity=0.730 Sum_probs=12.4
Q ss_pred cccccchhhhcCcHHHHHHH
Q psy6273 33 FACDQCVSYFKTNSALLQHK 52 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~ 52 (82)
|.|..|...-.+..++..|.
T Consensus 54 yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 54 YECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred eeehhhhhhhcchhhhhhhh
Confidence 66777766666666655554
No 276
>KOG2857|consensus
Probab=28.75 E-value=29 Score=17.79 Aligned_cols=18 Identities=28% Similarity=0.696 Sum_probs=8.4
Q ss_pred eeecCcccccccCccccc
Q psy6273 62 LFSCPLCGEVFRSHQGYK 79 (82)
Q Consensus 62 ~~~C~~C~~~f~~~~~l~ 79 (82)
-|+|+.|..-+.+..=++
T Consensus 17 KYKCpkC~vPYCSl~CfK 34 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFK 34 (157)
T ss_pred hccCCCCCCccccchhhh
Confidence 355655554444433333
No 277
>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=28.68 E-value=14 Score=23.07 Aligned_cols=38 Identities=18% Similarity=0.322 Sum_probs=20.9
Q ss_pred ccccccchhhhcCc-HHHHHHHHHhcC--CCCCeeecCccccccc
Q psy6273 32 SFACDQCVSYFKTN-SALLQHKRKMHD--EFVNLFSCPLCGEVFR 73 (82)
Q Consensus 32 ~~~c~~c~~~~~~~-~~l~~h~~~~~~--~~~~~~~C~~C~~~f~ 73 (82)
-.+|+.|+..+... ..|. ...+ ...-.|.|+.||....
T Consensus 200 ~vpCPhCg~~~~l~~~~l~----w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLK----WDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCcccccccee----ecCCCCccceEEECCCCcCCCC
Confidence 45788888765544 2221 1111 1114688888886654
No 278
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=28.29 E-value=33 Score=19.74 Aligned_cols=10 Identities=20% Similarity=0.750 Sum_probs=5.2
Q ss_pred ccccchhhhc
Q psy6273 34 ACDQCVSYFK 43 (82)
Q Consensus 34 ~c~~c~~~~~ 43 (82)
.|+.|+..|.
T Consensus 48 vc~~c~~h~r 57 (292)
T PRK05654 48 VCPKCGHHMR 57 (292)
T ss_pred CCCCCCCCee
Confidence 4555555543
No 279
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=28.20 E-value=30 Score=17.55 Aligned_cols=16 Identities=31% Similarity=0.785 Sum_probs=12.1
Q ss_pred eeecCcccccccCccc
Q psy6273 62 LFSCPLCGEVFRSHQG 77 (82)
Q Consensus 62 ~~~C~~C~~~f~~~~~ 77 (82)
--+|+.|.-+|.+.+.
T Consensus 121 ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 121 YPVCPVCKTSFKSSSS 136 (140)
T ss_pred CCCCCccccccccccc
Confidence 3478999999987654
No 280
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=27.88 E-value=27 Score=13.97 Aligned_cols=10 Identities=40% Similarity=0.923 Sum_probs=6.4
Q ss_pred eecCcccccc
Q psy6273 63 FSCPLCGEVF 72 (82)
Q Consensus 63 ~~C~~C~~~f 72 (82)
-+|+.||-.-
T Consensus 12 rkCp~CGt~N 21 (44)
T PF14952_consen 12 RKCPKCGTYN 21 (44)
T ss_pred ccCCcCcCcc
Confidence 4788887443
No 281
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=27.63 E-value=30 Score=16.31 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=10.4
Q ss_pred eeecCcccccccC
Q psy6273 62 LFSCPLCGEVFRS 74 (82)
Q Consensus 62 ~~~C~~C~~~f~~ 74 (82)
.+.|..||+.+.-
T Consensus 73 H~~C~~Cg~i~~~ 85 (116)
T cd07153 73 HLICTKCGKVIDF 85 (116)
T ss_pred ceEeCCCCCEEEe
Confidence 5899999987753
No 282
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=27.61 E-value=32 Score=15.73 Aligned_cols=11 Identities=55% Similarity=1.325 Sum_probs=5.5
Q ss_pred CeeecCccccc
Q psy6273 61 NLFSCPLCGEV 71 (82)
Q Consensus 61 ~~~~C~~C~~~ 71 (82)
.-|.|+.|++.
T Consensus 64 s~~~Cp~Cg~~ 74 (81)
T PF10609_consen 64 SYFVCPHCGER 74 (81)
T ss_dssp -EEE-TTT--E
T ss_pred CccCCCCCCCe
Confidence 45899998864
No 283
>PRK04351 hypothetical protein; Provisional
Probab=27.57 E-value=28 Score=17.84 Aligned_cols=13 Identities=15% Similarity=0.616 Sum_probs=8.1
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
..|.|..|+..+.
T Consensus 131 ~~yrCg~C~g~L~ 143 (149)
T PRK04351 131 KRYRCGKCRGKLK 143 (149)
T ss_pred CcEEeCCCCcEee
Confidence 4577777765443
No 284
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=27.55 E-value=26 Score=20.77 Aligned_cols=11 Identities=36% Similarity=1.053 Sum_probs=7.3
Q ss_pred eeecCcccccc
Q psy6273 62 LFSCPLCGEVF 72 (82)
Q Consensus 62 ~~~C~~C~~~f 72 (82)
.+.|+.||..+
T Consensus 265 ~wrCpkCGg~i 275 (403)
T COG1379 265 RWRCPKCGGKI 275 (403)
T ss_pred cccCcccccch
Confidence 47777777654
No 285
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=27.55 E-value=45 Score=11.95 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=3.8
Q ss_pred cccCcCCcccc
Q psy6273 4 YKCHACDVETK 14 (82)
Q Consensus 4 ~~c~~c~~~~~ 14 (82)
|.|+.|+..+-
T Consensus 14 Y~Cp~C~~~~C 24 (30)
T PF04438_consen 14 YRCPRCGARYC 24 (30)
T ss_dssp EE-TTT--EES
T ss_pred EECCCcCCcee
Confidence 44555554443
No 286
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=27.53 E-value=31 Score=13.83 Aligned_cols=14 Identities=29% Similarity=0.816 Sum_probs=8.5
Q ss_pred eeecCcccccccCc
Q psy6273 62 LFSCPLCGEVFRSH 75 (82)
Q Consensus 62 ~~~C~~C~~~f~~~ 75 (82)
-|.|..|++.+...
T Consensus 26 Cf~C~~C~~~l~~~ 39 (58)
T PF00412_consen 26 CFKCSKCGKPLNDG 39 (58)
T ss_dssp TSBETTTTCBTTTS
T ss_pred ccccCCCCCccCCC
Confidence 46777776655443
No 287
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=26.65 E-value=28 Score=18.98 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=11.4
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
-||.|..|.+.|...
T Consensus 195 IPF~C~iCKkdy~sp 209 (259)
T COG5152 195 IPFLCGICKKDYESP 209 (259)
T ss_pred Cceeehhchhhccch
Confidence 589999888776543
No 288
>KOG1994|consensus
Probab=26.55 E-value=32 Score=19.16 Aligned_cols=21 Identities=24% Similarity=0.531 Sum_probs=17.6
Q ss_pred CccccccchhhhcCcHHHHHH
Q psy6273 31 KSFACDQCVSYFKTNSALLQH 51 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h 51 (82)
..|-|-.||..|.+...|..|
T Consensus 238 eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred cceEEEEeccccCCHHHHHHh
Confidence 457899999999999988764
No 289
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.48 E-value=31 Score=17.39 Aligned_cols=12 Identities=33% Similarity=0.725 Sum_probs=8.6
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
--+|..||+.|-
T Consensus 29 g~kC~~CG~v~~ 40 (140)
T COG1545 29 GTKCKKCGRVYF 40 (140)
T ss_pred EEEcCCCCeEEc
Confidence 457888887653
No 290
>COG4640 Predicted membrane protein [Function unknown]
Probab=26.40 E-value=55 Score=20.01 Aligned_cols=19 Identities=21% Similarity=0.503 Sum_probs=11.5
Q ss_pred ccccccchhhhcCcHHHHH
Q psy6273 32 SFACDQCVSYFKTNSALLQ 50 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~ 50 (82)
...|..||..|........
T Consensus 15 ~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 15 DVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred cccccccCCcCCchhhhhh
Confidence 3447777777666655433
No 291
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.33 E-value=37 Score=19.42 Aligned_cols=14 Identities=29% Similarity=0.553 Sum_probs=9.0
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
..|.|+.|...|..
T Consensus 254 ~GyvCs~Clsi~C~ 267 (279)
T TIGR00627 254 IGFVCSVCLSVLCQ 267 (279)
T ss_pred ceEECCCccCCcCC
Confidence 34777777666654
No 292
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.32 E-value=31 Score=16.68 Aligned_cols=11 Identities=64% Similarity=1.340 Sum_probs=7.6
Q ss_pred eecCccccccc
Q psy6273 63 FSCPLCGEVFR 73 (82)
Q Consensus 63 ~~C~~C~~~f~ 73 (82)
..|+.||.-|.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred ccCCCCCCccc
Confidence 57888876553
No 293
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=26.25 E-value=42 Score=11.70 Aligned_cols=11 Identities=18% Similarity=0.522 Sum_probs=4.1
Q ss_pred CeeecCccccc
Q psy6273 61 NLFSCPLCGEV 71 (82)
Q Consensus 61 ~~~~C~~C~~~ 71 (82)
..|.|..|...
T Consensus 14 ~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 14 WFYRCSECDFD 24 (30)
T ss_dssp -EEE-TTT---
T ss_pred ceEECccCCCc
Confidence 46677766543
No 294
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=26.18 E-value=54 Score=12.45 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=3.4
Q ss_pred CCcccCcCCccc
Q psy6273 2 TRYKCHACDVET 13 (82)
Q Consensus 2 k~~~c~~c~~~~ 13 (82)
+.|-|..|+.-+
T Consensus 2 ~ryyCdyC~~~~ 13 (38)
T PF06220_consen 2 PRYYCDYCKKYL 13 (38)
T ss_dssp -S-B-TTT--B-
T ss_pred cCeeccccccee
Confidence 445566666555
No 295
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=25.99 E-value=34 Score=16.62 Aligned_cols=12 Identities=33% Similarity=1.063 Sum_probs=9.6
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
-|.|..||..+.
T Consensus 100 Fy~C~~Cg~~wr 111 (113)
T COG1594 100 FYKCTRCGYRWR 111 (113)
T ss_pred EEEecccCCEee
Confidence 489999997765
No 296
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=25.76 E-value=33 Score=16.41 Aligned_cols=13 Identities=38% Similarity=0.971 Sum_probs=9.1
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
-.+.|..||+.+.
T Consensus 79 ~h~iC~~Cg~v~~ 91 (120)
T PF01475_consen 79 HHFICTQCGKVID 91 (120)
T ss_dssp EEEEETTTS-EEE
T ss_pred eEEEECCCCCEEE
Confidence 3588999998764
No 297
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=24.63 E-value=36 Score=15.67 Aligned_cols=12 Identities=25% Similarity=0.861 Sum_probs=9.3
Q ss_pred eecCcccccccC
Q psy6273 63 FSCPLCGEVFRS 74 (82)
Q Consensus 63 ~~C~~C~~~f~~ 74 (82)
-.|..|++.+..
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 469999987765
No 298
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=24.59 E-value=37 Score=15.41 Aligned_cols=13 Identities=23% Similarity=0.600 Sum_probs=8.8
Q ss_pred CeeecCccccccc
Q psy6273 61 NLFSCPLCGEVFR 73 (82)
Q Consensus 61 ~~~~C~~C~~~f~ 73 (82)
-.+.|..|++...
T Consensus 52 Lrl~C~~C~~~~~ 64 (77)
T PF00935_consen 52 LRLECTECGKAHM 64 (77)
T ss_dssp EEEEETTTS-EEE
T ss_pred EEEEeCCCCcccc
Confidence 3589999987643
No 299
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.33 E-value=21 Score=17.83 Aligned_cols=14 Identities=29% Similarity=0.422 Sum_probs=8.0
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
.|--|-.||+.|.+
T Consensus 67 ~psfchncgs~fpw 80 (160)
T COG4306 67 PPSFCHNCGSRFPW 80 (160)
T ss_pred CcchhhcCCCCCCc
Confidence 45556666666554
No 300
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=23.96 E-value=1.2e+02 Score=15.78 Aligned_cols=10 Identities=20% Similarity=0.803 Sum_probs=4.8
Q ss_pred ccccchhhhc
Q psy6273 34 ACDQCVSYFK 43 (82)
Q Consensus 34 ~c~~c~~~~~ 43 (82)
.|..|++.+.
T Consensus 107 ~C~~C~~~~~ 116 (178)
T PF02146_consen 107 RCSKCGKEYD 116 (178)
T ss_dssp EETTTSBEEE
T ss_pred eecCCCcccc
Confidence 4555555443
No 301
>KOG3277|consensus
Probab=23.78 E-value=26 Score=18.26 Aligned_cols=9 Identities=33% Similarity=1.265 Sum_probs=4.7
Q ss_pred cccCcCCcc
Q psy6273 4 YKCHACDVE 12 (82)
Q Consensus 4 ~~c~~c~~~ 12 (82)
|.|..|+..
T Consensus 80 yTCkvCntR 88 (165)
T KOG3277|consen 80 YTCKVCNTR 88 (165)
T ss_pred EEeeccCCc
Confidence 455555543
No 302
>PF14149 YhfH: YhfH-like protein
Probab=23.67 E-value=18 Score=13.87 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=7.3
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
+=.|+.||+...
T Consensus 13 ~K~C~~CG~~i~ 24 (37)
T PF14149_consen 13 PKKCTECGKEIE 24 (37)
T ss_pred CcccHHHHHHHH
Confidence 346777876543
No 303
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=23.57 E-value=40 Score=16.08 Aligned_cols=12 Identities=33% Similarity=0.780 Sum_probs=8.6
Q ss_pred CeeecCcccccc
Q psy6273 61 NLFSCPLCGEVF 72 (82)
Q Consensus 61 ~~~~C~~C~~~f 72 (82)
+..+|..||-.|
T Consensus 87 r~~rC~nCG~~f 98 (98)
T PF10164_consen 87 RERRCSNCGATF 98 (98)
T ss_pred CccccCCCCccC
Confidence 567888887665
No 304
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=23.23 E-value=30 Score=19.61 Aligned_cols=29 Identities=24% Similarity=0.510 Sum_probs=17.2
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCCCCCeeecCccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDEFVNLFSCPLCG 69 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 69 (82)
.-.|+.|+........| | +- =.|+|..|.
T Consensus 220 ~r~CP~Cg~~W~L~~pl------h-~i--FdFKCD~CR 248 (258)
T PF10071_consen 220 ARKCPSCGGDWRLKEPL------H-DI--FDFKCDPCR 248 (258)
T ss_pred CCCCCCCCCccccCCch------h-hc--eeccCCcce
Confidence 34678887766555544 1 11 357777774
No 305
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=23.06 E-value=48 Score=17.26 Aligned_cols=12 Identities=33% Similarity=0.689 Sum_probs=8.7
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
.|.|+.||....
T Consensus 29 sf~C~~CGyk~~ 40 (160)
T smart00709 29 SFECEHCGYRNN 40 (160)
T ss_pred EEECCCCCCccc
Confidence 578888886554
No 306
>KOG2747|consensus
Probab=23.00 E-value=57 Score=19.83 Aligned_cols=26 Identities=31% Similarity=0.779 Sum_probs=21.9
Q ss_pred CccccccchhhhcCcHHHHHHHHHhc
Q psy6273 31 KSFACDQCVSYFKTNSALLQHKRKMH 56 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~~~~~ 56 (82)
.-|.|..|-+.+.+...|++|+....
T Consensus 157 ~lYiCEfCLkY~~s~~~l~rH~~kC~ 182 (396)
T KOG2747|consen 157 KLYICEFCLKYMKSRTSLQRHLKKCK 182 (396)
T ss_pred eEEEehHHHhHhchHHHHHHHHHhcC
Confidence 35789999999999999999997643
No 307
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=22.92 E-value=46 Score=17.40 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=8.5
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
.|.|+.||....
T Consensus 28 sf~C~~CGyr~~ 39 (163)
T TIGR00340 28 TYICEKCGYRST 39 (163)
T ss_pred EEECCCCCCchh
Confidence 578888886554
No 308
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=22.59 E-value=85 Score=13.54 Aligned_cols=15 Identities=13% Similarity=0.481 Sum_probs=9.5
Q ss_pred CCcccCcCCccccCH
Q psy6273 2 TRYKCHACDVETKTR 16 (82)
Q Consensus 2 k~~~c~~c~~~~~~~ 16 (82)
-|..|-.||+....+
T Consensus 3 iPVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNK 17 (60)
T ss_dssp -SSS-STTTSBTCGH
T ss_pred CceecCCCCCChhHh
Confidence 366788888877655
No 309
>smart00507 HNHc HNH nucleases.
Probab=22.58 E-value=40 Score=12.71 Aligned_cols=10 Identities=30% Similarity=0.693 Sum_probs=4.6
Q ss_pred eecCcccccc
Q psy6273 63 FSCPLCGEVF 72 (82)
Q Consensus 63 ~~C~~C~~~f 72 (82)
+.|..|+..+
T Consensus 11 ~~C~~C~~~~ 20 (52)
T smart00507 11 GVCAYCGKPA 20 (52)
T ss_pred CCCcCCcCCC
Confidence 3455555433
No 310
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=22.55 E-value=42 Score=17.44 Aligned_cols=12 Identities=33% Similarity=0.697 Sum_probs=6.0
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
.|.|+.||..+.
T Consensus 30 sf~C~~CGyk~~ 41 (161)
T PF03367_consen 30 SFECEHCGYKNN 41 (161)
T ss_dssp EEE-TTT--EEE
T ss_pred EeECCCCCCEee
Confidence 578888886543
No 311
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=22.41 E-value=39 Score=13.77 Aligned_cols=13 Identities=38% Similarity=0.956 Sum_probs=9.5
Q ss_pred eecCcccccccCc
Q psy6273 63 FSCPLCGEVFRSH 75 (82)
Q Consensus 63 ~~C~~C~~~f~~~ 75 (82)
..|+.|+..|-..
T Consensus 41 ~~C~~C~~~fC~~ 53 (64)
T PF01485_consen 41 VTCPSCGTEFCFK 53 (64)
T ss_dssp CCTTSCCSEECSS
T ss_pred eECCCCCCcCccc
Confidence 7888888777543
No 312
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=22.38 E-value=29 Score=18.92 Aligned_cols=27 Identities=15% Similarity=0.139 Sum_probs=0.0
Q ss_pred CccccccchhhhcCcHHHHHHHHHhcCC
Q psy6273 31 KSFACDQCVSYFKTNSALLQHKRKMHDE 58 (82)
Q Consensus 31 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 58 (82)
.-..|+.||..... +-+..||+....+
T Consensus 167 ~~~~cPitGe~IP~-~e~~eHmRi~LlD 193 (229)
T PF12230_consen 167 KMIICPITGEMIPA-DEMDEHMRIELLD 193 (229)
T ss_dssp ----------------------------
T ss_pred cccccccccccccc-ccccccccccccc
Confidence 44678888876543 4567888877655
No 313
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.37 E-value=39 Score=17.26 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=7.9
Q ss_pred cccCcCCcccc
Q psy6273 4 YKCHACDVETK 14 (82)
Q Consensus 4 ~~c~~c~~~~~ 14 (82)
|.|..|+.++.
T Consensus 14 YrC~~C~~TwN 24 (142)
T PF06353_consen 14 YRCEKCDYTWN 24 (142)
T ss_pred EEcccCcCccc
Confidence 67888887654
No 314
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=22.25 E-value=33 Score=16.46 Aligned_cols=13 Identities=23% Similarity=0.644 Sum_probs=8.6
Q ss_pred CcccCcCCccccC
Q psy6273 3 RYKCHACDVETKT 15 (82)
Q Consensus 3 ~~~c~~c~~~~~~ 15 (82)
.|+|..||+.+..
T Consensus 2 kWkC~iCg~~I~~ 14 (101)
T PF09943_consen 2 KWKCYICGKPIYE 14 (101)
T ss_pred ceEEEecCCeeee
Confidence 4678888875443
No 315
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=21.85 E-value=67 Score=13.51 Aligned_cols=15 Identities=40% Similarity=0.658 Sum_probs=11.0
Q ss_pred CeeecCcccccccCc
Q psy6273 61 NLFSCPLCGEVFRSH 75 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~ 75 (82)
..|.|..|+..+-..
T Consensus 10 ~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 10 NLWLCLTCGYVGCGR 24 (63)
T ss_dssp SEEEETTTS-EEETT
T ss_pred ceEEeCCCCcccccC
Confidence 689999998877654
No 316
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=21.77 E-value=46 Score=13.31 Aligned_cols=12 Identities=25% Similarity=0.767 Sum_probs=8.1
Q ss_pred eecCcccccccC
Q psy6273 63 FSCPLCGEVFRS 74 (82)
Q Consensus 63 ~~C~~C~~~f~~ 74 (82)
..|..||..+..
T Consensus 6 l~C~~CG~~m~~ 17 (58)
T PF13408_consen 6 LRCGHCGSKMTR 17 (58)
T ss_pred EEcccCCcEeEE
Confidence 568888876543
No 317
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=21.70 E-value=52 Score=17.75 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=9.6
Q ss_pred CCcccCcCCccccC
Q psy6273 2 TRYKCHACDVETKT 15 (82)
Q Consensus 2 k~~~c~~c~~~~~~ 15 (82)
++-+|.+|+..|..
T Consensus 5 k~rKCKvCg~~F~P 18 (189)
T PF05766_consen 5 KRRKCKVCGEWFVP 18 (189)
T ss_pred CCCcCcccCCcccc
Confidence 34568888877764
No 318
>PHA02998 RNA polymerase subunit; Provisional
Probab=21.70 E-value=54 Score=17.62 Aligned_cols=38 Identities=18% Similarity=0.367 Sum_probs=20.4
Q ss_pred ccccccchhhhcCcHHHHHHHHHhcCC-C-CCeeecCccccccc
Q psy6273 32 SFACDQCVSYFKTNSALLQHKRKMHDE-F-VNLFSCPLCGEVFR 73 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h~~~~~~~-~-~~~~~C~~C~~~f~ 73 (82)
...|+.|+..-.....+ ++..++ . ..-|.|..||..|.
T Consensus 143 ~v~CPkCg~~~A~f~ql----QTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMI----QTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred CCCCCCCCCCceEEEEE----eeccCCCCceEEEEcCCCCCccC
Confidence 35788887532222211 233332 0 13489999998764
No 319
>KOG3456|consensus
Probab=21.64 E-value=42 Score=16.33 Aligned_cols=14 Identities=29% Similarity=0.586 Sum_probs=10.9
Q ss_pred CeeecCcccccccC
Q psy6273 61 NLFSCPLCGEVFRS 74 (82)
Q Consensus 61 ~~~~C~~C~~~f~~ 74 (82)
.+..|.+||-.|.+
T Consensus 103 ~~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 103 GPHICGYCGLRFVQ 116 (120)
T ss_pred CCcccccchhhhhh
Confidence 45788899988875
No 320
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=21.51 E-value=33 Score=18.44 Aligned_cols=21 Identities=19% Similarity=0.534 Sum_probs=13.5
Q ss_pred cccccchhhhcCcHHHHHHHH
Q psy6273 33 FACDQCVSYFKTNSALLQHKR 53 (82)
Q Consensus 33 ~~c~~c~~~~~~~~~l~~h~~ 53 (82)
+.|..|...-.+..++..|..
T Consensus 54 ~vC~LC~T~H~~e~Sy~~H~~ 74 (222)
T COG5246 54 YVCLLCKTKHLTEMSYVKHRE 74 (222)
T ss_pred EEeeeeccccccHHHHHHhhc
Confidence 677777766666666665553
No 321
>PF12591 DUF3762: Protein of unknown function (DUF3762); InterPro: IPR022239 This domain family is found in viruses, and is approximately 80 amino acids in length. The family is found in association with PF05533 from PFAM.
Probab=21.43 E-value=43 Score=14.82 Aligned_cols=10 Identities=50% Similarity=0.860 Sum_probs=6.8
Q ss_pred CcccccccCc
Q psy6273 66 PLCGEVFRSH 75 (82)
Q Consensus 66 ~~C~~~f~~~ 75 (82)
..||+.|.+.
T Consensus 70 rkcgrvfps~ 79 (80)
T PF12591_consen 70 RKCGRVFPSG 79 (80)
T ss_pred ccccccCCCC
Confidence 3578888764
No 322
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.40 E-value=21 Score=22.96 Aligned_cols=11 Identities=36% Similarity=0.619 Sum_probs=5.7
Q ss_pred CCccccccchh
Q psy6273 30 TKSFACDQCVS 40 (82)
Q Consensus 30 ~~~~~c~~c~~ 40 (82)
..+..|+.|+.
T Consensus 419 ~~~~~Cp~Cg~ 429 (679)
T PRK05580 419 PIPKACPECGS 429 (679)
T ss_pred CCCCCCCCCcC
Confidence 33455666644
No 323
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=21.02 E-value=51 Score=12.37 Aligned_cols=16 Identities=13% Similarity=0.534 Sum_probs=8.3
Q ss_pred CeeecCcccccccCcc
Q psy6273 61 NLFSCPLCGEVFRSHQ 76 (82)
Q Consensus 61 ~~~~C~~C~~~f~~~~ 76 (82)
..-.|..|++.+....
T Consensus 5 ~~~~C~~C~~~~~~~~ 20 (43)
T PF06467_consen 5 KMKTCSYCKKYIPNKP 20 (43)
T ss_dssp SCEE-TTT--EEECCC
T ss_pred cCCcCcccCCcccCCC
Confidence 3467888887776544
No 324
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=20.92 E-value=46 Score=14.85 Aligned_cols=15 Identities=33% Similarity=0.959 Sum_probs=9.3
Q ss_pred eeecCcccccccCccc
Q psy6273 62 LFSCPLCGEVFRSHQG 77 (82)
Q Consensus 62 ~~~C~~C~~~f~~~~~ 77 (82)
.+.|. ||..|...+.
T Consensus 13 ~~~c~-~g~~f~~~ST 27 (72)
T PRK00019 13 TVTCS-CGNVFETRST 27 (72)
T ss_pred EEEEC-CCCEEEEeec
Confidence 45666 7777765554
No 325
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=20.58 E-value=51 Score=17.12 Aligned_cols=13 Identities=38% Similarity=0.907 Sum_probs=10.4
Q ss_pred eeecCcccccccC
Q psy6273 62 LFSCPLCGEVFRS 74 (82)
Q Consensus 62 ~~~C~~C~~~f~~ 74 (82)
.+.|..||+.+.-
T Consensus 100 H~iC~~CGki~~i 112 (169)
T PRK11639 100 MFICDRCGAVKEE 112 (169)
T ss_pred eEEeCCCCCEEEe
Confidence 4899999998753
No 326
>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=20.27 E-value=34 Score=17.52 Aligned_cols=10 Identities=20% Similarity=0.793 Sum_probs=6.6
Q ss_pred ccccccchhh
Q psy6273 32 SFACDQCVSY 41 (82)
Q Consensus 32 ~~~c~~c~~~ 41 (82)
.+.|..|+..
T Consensus 112 ~l~C~~Cg~~ 121 (146)
T PF07295_consen 112 TLVCENCGHE 121 (146)
T ss_pred eEecccCCCE
Confidence 4677777754
No 327
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=20.17 E-value=59 Score=17.53 Aligned_cols=12 Identities=25% Similarity=0.387 Sum_probs=8.6
Q ss_pred eeecCccccccc
Q psy6273 62 LFSCPLCGEVFR 73 (82)
Q Consensus 62 ~~~C~~C~~~f~ 73 (82)
.|.|+.||....
T Consensus 30 sf~C~~CGyr~~ 41 (192)
T TIGR00310 30 STICEHCGYRSN 41 (192)
T ss_pred EEECCCCCCccc
Confidence 578888886544
No 328
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=20.12 E-value=44 Score=17.31 Aligned_cols=14 Identities=14% Similarity=0.510 Sum_probs=11.3
Q ss_pred eeecCcccccccCc
Q psy6273 62 LFSCPLCGEVFRSH 75 (82)
Q Consensus 62 ~~~C~~C~~~f~~~ 75 (82)
.+.|.+|++.|...
T Consensus 132 ~lrC~YCe~~~~~~ 145 (150)
T TIGR00240 132 ALRCYYCEKEIEHN 145 (150)
T ss_pred EEEEECCCCEEecc
Confidence 59999999988643
No 329
>KOG2807|consensus
Probab=20.06 E-value=96 Score=18.53 Aligned_cols=20 Identities=15% Similarity=0.388 Sum_probs=11.1
Q ss_pred ccccccchhhhcCcHHHHHH
Q psy6273 32 SFACDQCVSYFKTNSALLQH 51 (82)
Q Consensus 32 ~~~c~~c~~~~~~~~~l~~h 51 (82)
|.+|+.|+-......+|.+.
T Consensus 290 P~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARS 309 (378)
T ss_pred CccCCccceeEecchHHHHH
Confidence 45666666555555555543
Done!