Query psy12014
Match_columns 78
No_of_seqs 108 out of 1309
Neff 11.6
Searched_HMMs 46136
Date Fri Aug 16 16:28:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12014.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12014hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 5.5E-22 1.2E-26 103.6 4.2 70 7-77 177-246 (279)
2 KOG2462|consensus 99.8 1.7E-20 3.7E-25 98.1 2.9 63 5-68 203-265 (279)
3 KOG3623|consensus 99.7 6.3E-18 1.4E-22 98.0 2.1 64 13-77 890-953 (1007)
4 KOG3576|consensus 99.6 1.9E-16 4.1E-21 80.5 1.1 67 10-77 110-176 (267)
5 KOG3623|consensus 99.6 1.4E-15 3.1E-20 88.5 2.2 62 5-67 910-971 (1007)
6 KOG1074|consensus 99.4 3.6E-14 7.8E-19 83.6 -0.3 68 3-71 619-693 (958)
7 PHA02768 hypothetical protein; 99.3 8.4E-13 1.8E-17 54.6 1.9 44 17-63 5-48 (55)
8 KOG3576|consensus 99.3 3.9E-13 8.5E-18 68.7 0.2 65 6-71 134-198 (267)
9 KOG1074|consensus 99.2 3.9E-12 8.5E-17 75.3 0.8 57 17-74 353-409 (958)
10 PHA00733 hypothetical protein 99.2 9.7E-11 2.1E-15 56.7 4.9 57 12-71 68-124 (128)
11 PHA00616 hypothetical protein 99.1 3.1E-11 6.7E-16 47.8 1.6 32 46-77 1-32 (44)
12 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.7E-10 3.7E-15 41.3 1.8 24 33-57 2-25 (26)
13 PHA02768 hypothetical protein; 98.9 2E-09 4.2E-14 44.7 2.1 29 47-77 6-34 (55)
14 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.2E-09 2.6E-14 39.1 1.1 24 5-28 2-25 (26)
15 PHA00732 hypothetical protein 98.8 4.2E-09 9.2E-14 47.0 2.9 46 17-69 1-47 (79)
16 KOG3608|consensus 98.8 8.2E-09 1.8E-13 57.0 3.7 31 47-77 264-295 (467)
17 KOG3608|consensus 98.8 1E-08 2.2E-13 56.6 3.8 60 16-77 262-322 (467)
18 PHA00616 hypothetical protein 98.7 1.4E-08 3E-13 40.3 1.8 34 17-51 1-34 (44)
19 PHA00733 hypothetical protein 98.6 2.7E-08 5.9E-13 48.3 2.0 61 14-77 37-102 (128)
20 KOG3993|consensus 98.6 3.6E-08 7.9E-13 55.5 2.0 57 15-71 293-381 (500)
21 PF05605 zf-Di19: Drought indu 98.5 4.5E-07 9.7E-12 37.8 4.4 52 17-71 2-54 (54)
22 PLN03086 PRLI-interacting fact 98.5 2.1E-07 4.5E-12 54.5 4.0 58 16-77 477-544 (567)
23 PLN03086 PRLI-interacting fact 98.5 3E-07 6.4E-12 53.9 4.2 59 13-77 449-507 (567)
24 PF00096 zf-C2H2: Zinc finger, 98.4 3E-07 6.6E-12 31.6 1.8 21 48-68 2-22 (23)
25 PF00096 zf-C2H2: Zinc finger, 98.4 2.9E-07 6.3E-12 31.7 1.7 23 18-40 1-23 (23)
26 PF13912 zf-C2H2_6: C2H2-type 98.2 7.5E-07 1.6E-11 31.8 1.5 23 47-69 2-24 (27)
27 PF09237 GAGA: GAGA factor; I 98.2 2.7E-06 5.9E-11 34.6 2.6 32 44-75 22-53 (54)
28 PF13894 zf-C2H2_4: C2H2-type 98.2 2.3E-06 5E-11 29.4 2.0 23 47-69 1-23 (24)
29 PF13912 zf-C2H2_6: C2H2-type 98.1 3.2E-06 6.9E-11 30.1 2.1 25 17-41 1-25 (27)
30 COG5189 SFP1 Putative transcri 98.0 2.5E-06 5.5E-11 46.9 0.9 53 15-67 347-419 (423)
31 PF13894 zf-C2H2_4: C2H2-type 97.9 1.2E-05 2.5E-10 27.5 1.9 23 18-40 1-23 (24)
32 smart00355 ZnF_C2H2 zinc finge 97.8 3E-05 6.4E-10 26.9 2.2 22 48-69 2-23 (26)
33 smart00355 ZnF_C2H2 zinc finge 97.7 5E-05 1.1E-09 26.2 2.0 24 18-41 1-24 (26)
34 PF09237 GAGA: GAGA factor; I 97.6 0.00011 2.4E-09 30.0 2.5 35 11-46 18-52 (54)
35 PF12756 zf-C2H2_2: C2H2 type 97.6 9.1E-05 2E-09 34.1 2.6 24 46-69 50-73 (100)
36 PHA00732 hypothetical protein 97.5 0.00012 2.6E-09 32.9 2.3 27 46-72 1-28 (79)
37 PRK04860 hypothetical protein; 97.4 9.6E-05 2.1E-09 37.3 1.8 37 17-58 119-155 (160)
38 PF13909 zf-H2C2_5: C2H2-type 97.4 0.0002 4.4E-09 24.6 2.0 23 47-70 1-23 (24)
39 PF12874 zf-met: Zinc-finger o 97.4 0.00016 3.5E-09 25.1 1.7 20 19-38 2-21 (25)
40 PF12874 zf-met: Zinc-finger o 97.3 0.00019 4.2E-09 24.9 1.6 23 47-69 1-23 (25)
41 KOG3993|consensus 97.3 4.7E-05 1E-09 43.5 -0.2 53 17-70 267-319 (500)
42 PRK04860 hypothetical protein; 96.8 0.00076 1.6E-08 34.2 1.6 28 46-77 119-146 (160)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.0011 2.4E-08 23.5 1.0 21 47-67 2-22 (27)
44 PF13913 zf-C2HC_2: zinc-finge 96.4 0.0042 9.1E-08 21.7 1.9 19 48-67 4-22 (25)
45 KOG2893|consensus 96.3 0.0012 2.5E-08 35.5 0.4 44 16-65 10-53 (341)
46 smart00451 ZnF_U1 U1-like zinc 96.1 0.0077 1.7E-07 22.4 2.0 22 17-38 3-24 (35)
47 COG5048 FOG: Zn-finger [Genera 96.1 0.0011 2.3E-08 37.5 -0.7 61 16-77 288-354 (467)
48 PF12756 zf-C2H2_2: C2H2 type 95.0 0.034 7.4E-07 25.4 2.4 27 16-42 49-75 (100)
49 cd00350 rubredoxin_like Rubred 94.8 0.019 4.2E-07 21.3 1.1 24 18-54 2-25 (33)
50 KOG2186|consensus 94.2 0.04 8.7E-07 30.0 1.8 49 18-70 4-52 (276)
51 cd00729 rubredoxin_SM Rubredox 93.6 0.081 1.8E-06 19.8 1.7 25 17-54 2-26 (34)
52 COG4049 Uncharacterized protei 93.2 0.074 1.6E-06 22.3 1.4 30 10-39 10-39 (65)
53 COG1592 Rubrerythrin [Energy p 92.6 0.11 2.3E-06 26.7 1.8 24 17-54 134-157 (166)
54 PF05443 ROS_MUCR: ROS/MUCR tr 92.0 0.11 2.3E-06 25.8 1.3 25 47-74 73-97 (132)
55 KOG1146|consensus 91.7 0.23 5.1E-06 33.1 2.7 57 12-68 460-540 (1406)
56 PF09986 DUF2225: Uncharacteri 90.1 0.038 8.1E-07 29.4 -1.4 45 15-59 3-61 (214)
57 PF04959 ARS2: Arsenite-resist 89.6 0.3 6.5E-06 26.2 1.7 26 14-39 74-99 (214)
58 smart00659 RPOLCX RNA polymera 88.8 0.35 7.5E-06 19.3 1.3 27 17-55 2-28 (44)
59 PF13719 zinc_ribbon_5: zinc-r 88.6 0.48 1E-05 18.0 1.6 34 18-57 3-36 (37)
60 PF13717 zinc_ribbon_4: zinc-r 88.5 0.44 9.5E-06 18.0 1.4 33 18-56 3-35 (36)
61 COG3357 Predicted transcriptio 88.1 0.22 4.7E-06 23.0 0.5 13 16-28 57-69 (97)
62 PF09538 FYDLN_acid: Protein o 87.6 0.52 1.1E-05 22.6 1.6 30 18-59 10-39 (108)
63 TIGR00373 conserved hypothetic 87.6 0.71 1.5E-05 23.6 2.2 36 12-57 104-139 (158)
64 COG5189 SFP1 Putative transcri 87.1 0.13 2.9E-06 29.2 -0.6 25 12-36 393-417 (423)
65 KOG4167|consensus 86.8 0.13 2.8E-06 32.3 -0.7 24 47-70 793-816 (907)
66 PRK06266 transcription initiat 86.4 0.86 1.9E-05 23.8 2.2 35 13-57 113-147 (178)
67 PF04959 ARS2: Arsenite-resist 86.2 0.42 9E-06 25.7 1.0 27 47-73 78-104 (214)
68 KOG3408|consensus 85.9 0.91 2E-05 22.2 2.0 28 13-40 53-80 (129)
69 PF12013 DUF3505: Protein of u 85.7 0.89 1.9E-05 21.5 1.9 25 47-71 81-109 (109)
70 COG4957 Predicted transcriptio 85.7 0.5 1.1E-05 23.6 1.0 25 47-74 77-101 (148)
71 smart00734 ZnF_Rad18 Rad18-lik 85.2 1.2 2.5E-05 15.6 1.7 19 48-67 3-21 (26)
72 PF13451 zf-trcl: Probable zin 84.9 0.57 1.2E-05 19.2 0.9 39 15-53 2-40 (49)
73 COG2888 Predicted Zn-ribbon RN 84.6 1.2 2.7E-05 19.0 1.8 33 16-54 26-58 (61)
74 TIGR02098 MJ0042_CXXC MJ0042 f 84.2 0.96 2.1E-05 17.0 1.4 34 18-57 3-36 (38)
75 KOG4167|consensus 83.9 0.26 5.6E-06 31.1 -0.4 25 18-42 793-817 (907)
76 PF03604 DNA_RNApol_7kD: DNA d 83.7 0.57 1.2E-05 17.3 0.6 26 18-55 1-26 (32)
77 PRK00398 rpoP DNA-directed RNA 83.4 1.2 2.6E-05 17.6 1.6 30 17-57 3-32 (46)
78 smart00531 TFIIE Transcription 83.3 1.6 3.4E-05 22.0 2.3 40 13-57 95-134 (147)
79 COG1997 RPL43A Ribosomal prote 82.4 0.58 1.3E-05 21.5 0.5 33 16-59 34-66 (89)
80 smart00614 ZnF_BED BED zinc fi 81.6 1.6 3.5E-05 17.6 1.7 20 48-67 20-44 (50)
81 KOG2593|consensus 81.4 0.65 1.4E-05 27.5 0.5 41 10-54 121-161 (436)
82 PF13878 zf-C2H2_3: zinc-finge 80.2 2 4.2E-05 16.8 1.6 24 18-41 14-39 (41)
83 PF10571 UPF0547: Uncharacteri 79.8 1.1 2.3E-05 15.7 0.7 11 47-57 15-25 (26)
84 COG4391 Uncharacterized protei 79.1 1.1 2.4E-05 19.2 0.8 46 8-58 15-60 (62)
85 COG5048 FOG: Zn-finger [Genera 78.8 1.8 4E-05 24.7 1.8 56 15-71 31-88 (467)
86 PF10013 DUF2256: Uncharacteri 77.5 1.1 2.4E-05 17.7 0.5 12 48-59 10-21 (42)
87 PHA00626 hypothetical protein 75.7 2 4.4E-05 18.1 1.1 17 15-31 21-37 (59)
88 PF07975 C1_4: TFIIH C1-like d 74.5 0.77 1.7E-05 19.0 -0.3 26 15-40 19-44 (51)
89 PF12907 zf-met2: Zinc-binding 73.7 0.7 1.5E-05 18.1 -0.5 9 19-27 3-11 (40)
90 PF02892 zf-BED: BED zinc fing 73.6 4.8 0.0001 15.6 1.9 20 47-66 17-40 (45)
91 COG1996 RPC10 DNA-directed RNA 73.4 2.3 4.9E-05 17.4 0.9 29 15-54 4-32 (49)
92 TIGR02300 FYDLN_acid conserved 73.0 3.3 7.2E-05 20.5 1.6 30 18-59 10-39 (129)
93 PF05191 ADK_lid: Adenylate ki 72.7 2.2 4.8E-05 16.2 0.8 31 18-57 2-32 (36)
94 COG2331 Uncharacterized protei 72.7 2.4 5.2E-05 19.1 1.0 31 18-56 13-43 (82)
95 PF07754 DUF1610: Domain of un 71.9 1.9 4.1E-05 14.9 0.5 8 46-53 16-23 (24)
96 PRK14890 putative Zn-ribbon RN 71.8 3.1 6.8E-05 17.7 1.2 33 16-54 24-56 (59)
97 KOG1146|consensus 71.6 2.8 6.1E-05 28.6 1.5 56 15-71 1282-1353(1406)
98 PRK03824 hypA hydrogenase nick 71.5 1.6 3.6E-05 21.7 0.4 15 16-30 69-83 (135)
99 PLN02294 cytochrome c oxidase 71.0 2.5 5.4E-05 22.0 1.0 15 15-29 139-153 (174)
100 KOG4173|consensus 69.0 4 8.6E-05 22.1 1.4 49 19-68 108-168 (253)
101 cd00924 Cyt_c_Oxidase_Vb Cytoc 68.8 3.1 6.7E-05 19.6 0.9 14 16-29 78-91 (97)
102 KOG2785|consensus 66.7 11 0.00024 22.4 2.9 52 17-68 166-242 (390)
103 PF09723 Zn-ribbon_8: Zinc rib 66.0 2.9 6.2E-05 16.3 0.5 30 17-54 5-34 (42)
104 smart00834 CxxC_CXXC_SSSS Puta 65.7 3.1 6.7E-05 15.7 0.5 30 17-54 5-34 (41)
105 PF15269 zf-C2H2_7: Zinc-finge 65.4 5.6 0.00012 16.0 1.2 23 47-69 21-43 (54)
106 PF09845 DUF2072: Zn-ribbon co 64.8 3.7 8E-05 20.5 0.8 14 46-59 1-14 (131)
107 PF02891 zf-MIZ: MIZ/SP-RING z 64.3 5.5 0.00012 16.2 1.2 30 19-54 20-49 (50)
108 PF07295 DUF1451: Protein of u 63.4 3.7 8.1E-05 20.8 0.7 28 17-55 112-139 (146)
109 COG5112 UFD2 U1-like Zn-finger 63.4 6.7 0.00014 18.9 1.5 26 14-39 52-77 (126)
110 PF08790 zf-LYAR: LYAR-type C2 62.5 1.9 4.1E-05 15.5 -0.3 8 20-27 3-10 (28)
111 PF01155 HypA: Hydrogenase exp 62.3 5.6 0.00012 19.1 1.2 25 18-55 71-95 (113)
112 smart00154 ZnF_AN1 AN1-like Zi 61.4 4.6 9.9E-05 15.5 0.7 14 46-59 12-25 (39)
113 TIGR00622 ssl1 transcription f 61.4 6.8 0.00015 19.0 1.3 49 19-70 57-105 (112)
114 PF04423 Rad50_zn_hook: Rad50 61.0 3.5 7.6E-05 16.9 0.3 12 48-59 22-33 (54)
115 KOG2636|consensus 60.6 7.3 0.00016 23.7 1.6 29 10-38 394-423 (497)
116 KOG2071|consensus 60.1 7.6 0.00017 24.3 1.6 27 44-70 416-442 (579)
117 TIGR02605 CxxC_CxxC_SSSS putat 59.1 4.5 9.8E-05 16.3 0.5 30 17-54 5-34 (52)
118 PF01428 zf-AN1: AN1-like Zinc 58.6 3.3 7.1E-05 16.2 0.0 15 45-59 12-26 (43)
119 KOG0717|consensus 56.0 7.2 0.00016 23.8 1.1 22 47-68 293-314 (508)
120 COG3364 Zn-ribbon containing p 55.0 6.3 0.00014 18.8 0.6 15 16-30 1-15 (112)
121 PTZ00043 cytochrome c oxidase 53.8 7 0.00015 21.5 0.8 18 14-31 178-195 (268)
122 COG1773 Rubredoxin [Energy pro 53.1 6.9 0.00015 16.5 0.5 14 17-30 3-16 (55)
123 PF01215 COX5B: Cytochrome c o 52.1 6 0.00013 19.9 0.3 15 15-29 110-124 (136)
124 PRK05452 anaerobic nitric oxid 51.3 12 0.00026 22.8 1.5 40 14-54 422-466 (479)
125 COG3091 SprT Zn-dependent meta 51.0 8.3 0.00018 19.9 0.7 34 15-54 115-148 (156)
126 COG3677 Transposase and inacti 50.9 7.7 0.00017 19.2 0.6 17 14-30 50-66 (129)
127 KOG2231|consensus 50.9 23 0.00049 22.9 2.6 47 19-70 184-236 (669)
128 TIGR00100 hypA hydrogenase nic 48.3 7.5 0.00016 18.8 0.3 25 17-54 70-94 (115)
129 PRK14873 primosome assembly pr 48.1 18 0.00039 23.2 1.9 10 45-54 421-430 (665)
130 KOG1280|consensus 48.0 25 0.00054 20.8 2.3 39 15-53 77-116 (381)
131 PF04780 DUF629: Protein of un 47.5 22 0.00047 21.9 2.1 25 18-42 58-83 (466)
132 PRK00464 nrdR transcriptional 47.1 8.5 0.00018 19.8 0.4 14 47-60 29-42 (154)
133 PRK12380 hydrogenase nickel in 46.6 10 0.00022 18.3 0.6 25 17-54 70-94 (113)
134 PF01927 Mut7-C: Mut7-C RNAse 46.5 18 0.00038 18.3 1.5 46 18-63 92-141 (147)
135 COG1571 Predicted DNA-binding 45.7 12 0.00025 22.6 0.9 29 19-59 352-380 (421)
136 PF06397 Desulfoferrod_N: Desu 44.7 12 0.00026 14.3 0.6 12 16-27 5-16 (36)
137 COG1198 PriA Primosomal protei 44.2 6.6 0.00014 25.3 -0.2 12 44-55 473-484 (730)
138 KOG2482|consensus 44.0 15 0.00034 21.6 1.2 23 17-39 195-217 (423)
139 PRK03681 hypA hydrogenase nick 43.2 12 0.00027 18.0 0.7 12 17-28 70-81 (114)
140 cd00730 rubredoxin Rubredoxin; 42.7 13 0.00028 15.2 0.6 11 47-57 2-12 (50)
141 PRK04351 hypothetical protein; 42.5 18 0.00039 18.5 1.2 31 18-57 113-143 (149)
142 PRK00564 hypA hydrogenase nick 41.4 14 0.0003 17.9 0.7 13 17-29 71-83 (117)
143 PF10537 WAC_Acf1_DNA_bd: ATP- 41.3 43 0.00094 16.0 2.6 37 16-54 2-38 (102)
144 PF02176 zf-TRAF: TRAF-type zi 41.3 10 0.00022 15.6 0.2 40 16-57 8-53 (60)
145 PF11931 DUF3449: Domain of un 41.1 8.9 0.00019 20.6 0.0 25 12-36 96-121 (196)
146 PF07282 OrfB_Zn_ribbon: Putat 40.7 27 0.00059 14.8 1.5 16 44-59 44-59 (69)
147 PF14353 CpXC: CpXC protein 40.4 8.7 0.00019 18.7 -0.1 18 45-62 37-54 (128)
148 COG5236 Uncharacterized conser 40.1 35 0.00075 20.4 2.1 21 19-39 222-242 (493)
149 PF08274 PhnA_Zn_Ribbon: PhnA 39.6 14 0.0003 13.4 0.4 8 47-54 20-27 (30)
150 PF02146 SIR2: Sir2 family; I 39.6 43 0.00093 17.3 2.3 39 12-55 100-138 (178)
151 COG1655 Uncharacterized protei 39.5 5.1 0.00011 22.1 -1.0 25 15-39 17-41 (267)
152 TIGR00627 tfb4 transcription f 39.4 30 0.00066 19.7 1.8 7 47-53 256-262 (279)
153 PF02591 DUF164: Putative zinc 38.9 33 0.00072 14.1 1.6 8 47-54 47-54 (56)
154 COG4338 Uncharacterized protei 38.6 8.8 0.00019 15.7 -0.2 12 48-59 14-25 (54)
155 PF09963 DUF2197: Uncharacteri 38.3 6.8 0.00015 16.6 -0.6 34 19-54 4-39 (56)
156 PF06220 zf-U1: U1 zinc finger 38.2 30 0.00065 13.2 1.7 10 18-27 4-13 (38)
157 TIGR00595 priA primosomal prot 38.1 35 0.00075 21.1 2.1 10 45-54 252-261 (505)
158 PF06524 NOA36: NOA36 protein; 36.1 9.5 0.00021 21.5 -0.4 26 44-69 207-232 (314)
159 PTZ00448 hypothetical protein; 35.9 34 0.00074 20.4 1.7 23 17-39 314-336 (373)
160 COG5188 PRP9 Splicing factor 3 35.9 33 0.00071 20.5 1.6 26 11-36 368-394 (470)
161 smart00731 SprT SprT homologue 35.5 18 0.00038 18.2 0.5 11 17-27 112-122 (146)
162 PF10263 SprT-like: SprT-like 34.2 11 0.00025 18.8 -0.2 30 18-56 124-153 (157)
163 PF01286 XPA_N: XPA protein N- 34.2 20 0.00043 13.5 0.5 11 19-29 5-15 (34)
164 KOG0978|consensus 33.9 11 0.00023 24.3 -0.5 15 19-33 680-694 (698)
165 TIGR00416 sms DNA repair prote 33.8 30 0.00065 21.1 1.4 11 17-27 7-17 (454)
166 PF00301 Rubredoxin: Rubredoxi 33.7 18 0.00038 14.6 0.3 13 18-30 2-14 (47)
167 TIGR00319 desulf_FeS4 desulfof 33.1 23 0.00049 12.9 0.6 12 16-27 6-17 (34)
168 PF03811 Zn_Tnp_IS1: InsA N-te 33.0 26 0.00056 13.2 0.7 12 12-23 24-35 (36)
169 cd00974 DSRD Desulforedoxin (D 32.7 23 0.0005 12.9 0.6 11 17-27 4-14 (34)
170 PF02748 PyrI_C: Aspartate car 32.5 23 0.00049 14.6 0.5 15 14-28 32-46 (52)
171 PRK11823 DNA repair protein Ra 32.2 36 0.00079 20.7 1.5 11 17-27 7-17 (446)
172 PF12230 PRP21_like_P: Pre-mRN 32.1 15 0.00033 19.9 0.0 26 16-42 167-192 (229)
173 KOG1842|consensus 31.8 30 0.00064 21.3 1.1 24 16-39 14-37 (505)
174 COG5151 SSL1 RNA polymerase II 31.5 48 0.001 19.5 1.8 25 46-70 388-412 (421)
175 KOG1994|consensus 31.0 32 0.00069 19.2 1.0 23 15-37 237-259 (268)
176 PF10276 zf-CHCC: Zinc-finger 30.7 15 0.00033 14.3 -0.1 9 47-55 30-38 (40)
177 PF10083 DUF2321: Uncharacteri 30.5 22 0.00048 18.4 0.4 18 15-32 66-83 (158)
178 COG5539 Predicted cysteine pro 30.5 48 0.001 19.2 1.7 27 12-38 270-296 (306)
179 PLN02748 tRNA dimethylallyltra 29.7 52 0.0011 20.4 1.8 24 16-39 417-441 (468)
180 PRK05978 hypothetical protein; 29.1 34 0.00074 17.6 0.9 11 47-57 53-63 (148)
181 COG1326 Uncharacterized archae 28.9 78 0.0017 17.2 2.2 12 45-56 29-40 (201)
182 TIGR01206 lysW lysine biosynth 28.8 30 0.00066 14.4 0.6 12 47-58 3-14 (54)
183 PF04810 zf-Sec23_Sec24: Sec23 28.8 35 0.00075 13.0 0.8 14 13-26 20-33 (40)
184 KOG3507|consensus 28.5 26 0.00056 15.0 0.4 27 18-56 21-47 (62)
185 KOG0801|consensus 28.1 15 0.00033 19.2 -0.4 11 47-57 139-149 (205)
186 COG1579 Zn-ribbon protein, pos 27.9 58 0.0013 18.2 1.7 34 18-56 198-231 (239)
187 COG1675 TFA1 Transcription ini 27.8 70 0.0015 17.0 1.9 35 12-56 108-142 (176)
188 PF14690 zf-ISL3: zinc-finger 27.5 36 0.00078 13.1 0.7 9 46-54 2-10 (47)
189 PRK08222 hydrogenase 4 subunit 27.5 47 0.001 17.5 1.3 19 16-34 113-131 (181)
190 PRK14138 NAD-dependent deacety 27.3 1.1E+02 0.0023 17.0 2.7 39 11-54 113-151 (244)
191 KOG0227|consensus 27.0 39 0.00084 18.3 0.9 19 47-65 54-72 (222)
192 COG1379 PHP family phosphoeste 26.9 25 0.00053 20.8 0.2 11 47-57 266-276 (403)
193 PF06676 DUF1178: Protein of u 26.6 1E+02 0.0023 15.9 2.6 24 26-54 17-40 (148)
194 PLN03238 probable histone acet 26.6 1.2E+02 0.0026 17.6 2.8 23 16-38 47-69 (290)
195 COG0675 Transposase and inacti 26.2 43 0.00093 18.8 1.1 15 45-59 321-335 (364)
196 PF13821 DUF4187: Domain of un 25.4 41 0.00088 14.1 0.7 20 16-35 26-45 (55)
197 KOG2807|consensus 24.9 82 0.0018 18.7 2.0 22 45-66 289-310 (378)
198 cd01121 Sms Sms (bacterial rad 24.7 49 0.0011 19.7 1.2 8 18-25 15-22 (372)
199 KOG3352|consensus 24.6 45 0.00098 17.3 0.9 14 45-58 132-145 (153)
200 TIGR03831 YgiT_finger YgiT-typ 24.6 39 0.00086 12.8 0.6 11 47-57 33-43 (46)
201 PRK12387 formate hydrogenlyase 24.4 52 0.0011 17.2 1.1 18 16-33 113-130 (180)
202 KOG4727|consensus 24.4 54 0.0012 17.5 1.1 22 17-38 75-96 (193)
203 PRK05580 primosome assembly pr 24.4 18 0.00039 23.2 -0.6 12 44-55 419-430 (679)
204 PLN02925 4-hydroxy-3-methylbut 23.6 1E+02 0.0022 20.5 2.3 26 47-72 635-660 (733)
205 PRK01343 zinc-binding protein; 23.5 56 0.0012 13.9 0.9 11 47-57 10-20 (57)
206 PF09943 DUF2175: Uncharacteri 23.4 30 0.00065 16.6 0.2 11 17-27 2-12 (101)
207 KOG3014|consensus 23.4 65 0.0014 18.3 1.4 31 12-42 29-64 (257)
208 TIGR00244 transcriptional regu 23.0 40 0.00087 17.3 0.6 13 47-59 29-41 (147)
209 COG0846 SIR2 NAD-dependent pro 22.9 74 0.0016 17.9 1.6 39 11-54 116-154 (250)
210 PF14447 Prok-RING_4: Prokaryo 22.5 50 0.0011 14.0 0.7 12 48-59 41-52 (55)
211 PF01194 RNA_pol_N: RNA polyme 22.2 63 0.0014 13.9 1.0 14 46-59 4-17 (60)
212 PF08792 A2L_zn_ribbon: A2L zi 22.2 43 0.00092 12.4 0.4 10 47-56 22-31 (33)
213 PF01363 FYVE: FYVE zinc finge 22.1 43 0.00092 14.2 0.5 15 15-29 23-37 (69)
214 KOG4124|consensus 21.9 14 0.0003 21.9 -1.3 21 44-64 396-416 (442)
215 PF08271 TF_Zn_Ribbon: TFIIB z 21.8 49 0.0011 12.7 0.6 7 48-54 2-8 (43)
216 PF01096 TFIIS_C: Transcriptio 21.8 37 0.0008 12.9 0.2 9 47-55 29-37 (39)
217 smart00440 ZnF_C2C2 C2C2 Zinc 21.7 46 0.00099 12.8 0.5 10 47-56 29-38 (40)
218 PF03107 C1_2: C1 domain; Int 21.7 44 0.00095 11.8 0.4 7 47-53 16-22 (30)
219 PF01780 Ribosomal_L37ae: Ribo 21.6 37 0.00079 15.9 0.2 30 17-57 35-64 (90)
220 PRK06260 threonine synthase; V 21.4 73 0.0016 19.0 1.5 10 18-27 4-13 (397)
221 PF11789 zf-Nse: Zinc-finger o 21.3 44 0.00094 14.0 0.4 19 44-62 22-40 (57)
222 PF08252 Leader_CPA1: arg-2/CP 21.1 59 0.0013 11.0 1.3 11 26-36 7-17 (24)
223 PF12773 DZR: Double zinc ribb 20.8 64 0.0014 12.6 0.9 11 46-56 29-39 (50)
224 PF09855 DUF2082: Nucleic-acid 20.7 52 0.0011 14.3 0.6 7 47-53 1-7 (64)
225 PLN03239 histone acetyltransfe 20.6 1.1E+02 0.0024 18.3 2.0 24 15-38 104-127 (351)
226 COG1656 Uncharacterized conser 20.6 1.1E+02 0.0025 16.1 1.9 19 47-65 131-149 (165)
227 PF14787 zf-CCHC_5: GAG-polypr 20.6 58 0.0013 12.4 0.7 13 48-60 4-16 (36)
228 KOG1818|consensus 20.6 27 0.00057 22.4 -0.4 37 16-52 180-217 (634)
229 TIGR00280 L37a ribosomal prote 20.5 47 0.001 15.6 0.5 12 17-28 53-64 (91)
230 PRK12722 transcriptional activ 20.5 85 0.0018 16.9 1.4 28 18-54 135-162 (187)
231 PRK12860 transcriptional activ 20.5 85 0.0018 17.0 1.4 27 18-53 135-161 (189)
232 PF14311 DUF4379: Domain of un 20.3 60 0.0013 13.2 0.7 13 47-59 29-41 (55)
233 CHL00174 accD acetyl-CoA carbo 20.3 85 0.0018 18.3 1.5 31 19-59 40-70 (296)
No 1
>KOG2462|consensus
Probab=99.86 E-value=5.5e-22 Score=103.63 Aligned_cols=70 Identities=19% Similarity=0.340 Sum_probs=59.6
Q ss_pred hhhhhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 7 LIDSLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 7 ~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
+.+.+-+..-++.|.+||+.|...=.|+.|++.|+| +|||.|..|+++|...++|..|++||.+.|.|+|
T Consensus 177 LkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTG-EKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC 246 (279)
T KOG2462|consen 177 LKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTG-EKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQC 246 (279)
T ss_pred HhhHhhccCCCcccccccccccchHHhhcccccccC-CCCccCCcccchhcchHHHHHHHHhhcCCccccC
Confidence 333444444788999999999988889999999999 8899999999999999999999999999999887
No 2
>KOG2462|consensus
Probab=99.81 E-value=1.7e-20 Score=98.13 Aligned_cols=63 Identities=22% Similarity=0.371 Sum_probs=58.7
Q ss_pred hhhhhhhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhh
Q psy12014 5 PKLIDSLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAI 68 (78)
Q Consensus 5 ~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 68 (78)
++.+.|+|||||||.|..|+++|..+++|..|+.+|.+ .++|+|..|+++|...+.|+.|...
T Consensus 203 LQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~-~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 203 LQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD-VKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcccccccCCCCccCCcccchhcchHHHHHHHHhhcC-CccccCcchhhHHHHHHHHHHhhhh
Confidence 45667999999999999999999999999999999999 8889999999999999999999653
No 3
>KOG3623|consensus
Probab=99.70 E-value=6.3e-18 Score=97.99 Aligned_cols=64 Identities=31% Similarity=0.658 Sum_probs=59.6
Q ss_pred cCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 13 KGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 13 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
+.+..|.|+.|+++|...+.|.+|...|+| ++||+|.+|.++|...-.|..|.|+|+|||||.|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsG-qRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQC 953 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSG-QRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQC 953 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcC-CCCcccchhhHhhhhhhhhhhhhhhccCCCcchh
Confidence 446789999999999999999999999999 8899999999999999999999999999999987
No 4
>KOG3576|consensus
Probab=99.60 E-value=1.9e-16 Score=80.53 Aligned_cols=67 Identities=16% Similarity=0.309 Sum_probs=60.1
Q ss_pred hhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 10 SLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 10 ~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
....+...|.|.+|++.|.....|.+|+..|.. .+.+-|..||+.|...-.|..|.++|+|.+||||
T Consensus 110 gsssd~d~ftCrvCgK~F~lQRmlnrh~kch~~-vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc 176 (267)
T KOG3576|consen 110 GSSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSD-VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKC 176 (267)
T ss_pred cCCCCCCeeeeehhhhhhhHHHHHHHHhhhccH-HHHHHHhhccCcccchhhhhhhhccccCccccch
Confidence 334556779999999999999999999999998 7778999999999999999999999999999998
No 5
>KOG3623|consensus
Probab=99.56 E-value=1.4e-15 Score=88.55 Aligned_cols=62 Identities=23% Similarity=0.434 Sum_probs=56.5
Q ss_pred hhhhhhhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHh
Q psy12014 5 PKLIDSLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMA 67 (78)
Q Consensus 5 ~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~ 67 (78)
+.+|.=-|+|.+||.|.+|.++|..+..|..|++.|.| +|||+|..|++.|+.+.++..|+.
T Consensus 910 LaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSG-EKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 910 LARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSG-EKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred HHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccC-CCcchhhhhhhhcccccchHhhhc
Confidence 34455569999999999999999999999999999999 999999999999999999988875
No 6
>KOG1074|consensus
Probab=99.39 E-value=3.6e-14 Score=83.56 Aligned_cols=68 Identities=22% Similarity=0.532 Sum_probs=55.2
Q ss_pred CchhhhhhhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCC----cccC---CCcccccChhHHHHHHhhhhc
Q psy12014 3 TTPKLIDSLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPK----YRCP---LCSYRAKQKIHLTTHMAIRHH 71 (78)
Q Consensus 3 ~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~----~~c~---~c~~~f~~~~~l~~h~~~~~g 71 (78)
+.++.|.++|+||+||+|++|+++|..+.+|+.|+.+|.. ..| +.|+ +|-+.|...-.|..|+++|.|
T Consensus 619 saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka-~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 619 SALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKA-KPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHLG 693 (958)
T ss_pred hhhhhhhhcccCcCccccccccchhccccchhhccccccc-CccccccccCCchhhhcccccccccccceEEeecC
Confidence 3567788889999999999999999999999999888876 433 5677 787888888888888888874
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.33 E-value=8.4e-13 Score=54.61 Aligned_cols=44 Identities=16% Similarity=0.329 Sum_probs=38.9
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHH
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLT 63 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~ 63 (78)
-|.|+.||+.|...+.|..|++.|+ ++++|..|++.|...+.|.
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 3789999999999999999999998 3689999999999777654
No 8
>KOG3576|consensus
Probab=99.30 E-value=3.9e-13 Score=68.67 Aligned_cols=65 Identities=22% Similarity=0.373 Sum_probs=56.2
Q ss_pred hhhhhhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhhc
Q psy12014 6 KLIDSLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHH 71 (78)
Q Consensus 6 ~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g 71 (78)
..+..-|...+.+.|.-||+.|-..-+|.+|++.|++ .+||+|..|+++|.+..+|..|.+.-+|
T Consensus 134 nrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtg-vrpykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 134 NRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTG-VRPYKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred HHHhhhccHHHHHHHhhccCcccchhhhhhhhccccC-ccccchhhhhHHHHhhccHHHHHHHHcC
Confidence 3445557777889999999999999999999999999 9999999999999999999999876554
No 9
>KOG1074|consensus
Probab=99.19 E-value=3.9e-12 Score=75.30 Aligned_cols=57 Identities=23% Similarity=0.482 Sum_probs=52.7
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhhcCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHHKKL 74 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~ 74 (78)
+++|..|.+.|.+.+.|+.|.+.|++ ++||+|.+||..|....+|..|.+.|....|
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTG-ERPfqCnvCG~~FSTkGNLKvH~~rH~e~~p 409 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTG-ERPFQCNVCGNRFSTKGNLKVHFQRHREKYP 409 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCC-CCCeeecccccccccccceeeeeeeccccCC
Confidence 36899999999999999999999999 8899999999999999999999999876554
No 10
>PHA00733 hypothetical protein
Probab=99.18 E-value=9.7e-11 Score=56.71 Aligned_cols=57 Identities=21% Similarity=0.426 Sum_probs=49.4
Q ss_pred ccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhhc
Q psy12014 12 YKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHH 71 (78)
Q Consensus 12 ~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g 71 (78)
+.+++||.|..|++.|.....|..|++.+.. ++.|..|++.|.....|..|+...++
T Consensus 68 ~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~---~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 68 SKAVSPYVCPLCLMPFSSSVSLKQHIRYTEH---SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCCCCccCCCCCCcCCCHHHHHHHHhcCCc---CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3458899999999999999999999987632 58999999999999999999887664
No 11
>PHA00616 hypothetical protein
Probab=99.13 E-value=3.1e-11 Score=47.83 Aligned_cols=32 Identities=19% Similarity=0.355 Sum_probs=21.9
Q ss_pred CcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 46 KYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 46 ~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
|++|..||+.|...+.+..|++.|+|+++++|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 46677777777777777777777777766654
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.04 E-value=1.7e-10 Score=41.30 Aligned_cols=24 Identities=33% Similarity=0.769 Sum_probs=16.2
Q ss_pred HHHHhhcccCCCCCcccCCCccccc
Q psy12014 33 LTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 33 l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
|..|++.|++ ++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~-~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTG-EKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSS-SSSEEESSSSEEES
T ss_pred HHHHhhhcCC-CCCCCCCCCcCeeC
Confidence 5667777777 66677777776664
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.86 E-value=2e-09 Score=44.66 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=25.7
Q ss_pred cccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
|+|+.||+.|...++|..|+++|+ ++++|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc 34 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKL 34 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccC
Confidence 899999999999999999999999 44444
No 14
>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=98.85 E-value=1.2e-09 Score=39.07 Aligned_cols=24 Identities=13% Similarity=0.347 Sum_probs=21.6
Q ss_pred hhhhhhhccCCCceecCCchhhcC
Q psy12014 5 PKLIDSLYKGGGLFSCSDCSRVYK 28 (78)
Q Consensus 5 ~~~~~~~~~~~~~~~c~~c~~~f~ 28 (78)
+..+++.|+|++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 467888999999999999999986
No 15
>PHA00732 hypothetical protein
Probab=98.84 E-value=4.2e-09 Score=47.05 Aligned_cols=46 Identities=22% Similarity=0.488 Sum_probs=38.0
Q ss_pred ceecCCchhhcCCHHHHHHHhhc-ccCCCCCcccCCCcccccChhHHHHHHhhh
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTY-ECGQQPKYRCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
||.|..|++.|.....|..|++. |.+ +.|..|++.|. .+..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC---Chhhhhccc
Confidence 57899999999999999999984 654 58999999997 466776554
No 16
>KOG3608|consensus
Probab=98.80 E-value=8.2e-09 Score=56.97 Aligned_cols=31 Identities=35% Similarity=0.636 Sum_probs=16.1
Q ss_pred cccCCCcccccChhHHHHHHhh-hhcCccccC
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAI-RHHKKLGKI 77 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~-~~g~k~~~~ 77 (78)
|.|+.|+.+....++|..|+++ |+..||+||
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKC 295 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKC 295 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccc
Confidence 4555555555555555555553 344555554
No 17
>KOG3608|consensus
Probab=98.78 E-value=1e-08 Score=56.60 Aligned_cols=60 Identities=22% Similarity=0.500 Sum_probs=43.4
Q ss_pred CceecCCchhhcCCHHHHHHHhhc-ccCCCCCcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTY-ECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
..|.|..|+.+...++.|..|++. |.. .+||+|..|++.+...+.|..|..+|+ +-.|.|
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C 322 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQC 322 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHHHHHhcc-ccceec
Confidence 356777777777777777777776 444 777888888888888888888888776 444444
No 18
>PHA00616 hypothetical protein
Probab=98.69 E-value=1.4e-08 Score=40.31 Aligned_cols=34 Identities=21% Similarity=0.457 Sum_probs=30.7
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCC
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPL 51 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~ 51 (78)
||.|..||+.|.....+..|++.|++ ++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCccceeE
Confidence 68999999999999999999999999 77787764
No 19
>PHA00733 hypothetical protein
Probab=98.61 E-value=2.7e-08 Score=48.26 Aligned_cols=61 Identities=13% Similarity=0.168 Sum_probs=46.3
Q ss_pred CCCceecCCchhhcCCHHHHHHHh----h-cccCCCCCcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 14 GGGLFSCSDCSRVYKKKASLTRHQ----T-YECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 14 ~~~~~~c~~c~~~f~~~~~l~~h~----~-~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
..+++.|.+|...|.....|..+. . .+.+ .+||.|..|++.|.....|..|++.+ +.+++|
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C 102 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKA-VSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVC 102 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCC-CCCccCCCCCCcCCCHHHHHHHHhcC--CcCccC
Confidence 457788999998888777766551 1 2233 66899999999999999999999876 345655
No 20
>KOG3993|consensus
Probab=98.57 E-value=3.6e-08 Score=55.45 Aligned_cols=57 Identities=19% Similarity=0.530 Sum_probs=47.6
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcccCC-------CC-------------------------CcccCCCcccccChhHH
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYECGQ-------QP-------------------------KYRCPLCSYRAKQKIHL 62 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~-------~~-------------------------~~~c~~c~~~f~~~~~l 62 (78)
...|+|.+|++.|....+|..|.++|-.. .+ -|.|..|++.|.....|
T Consensus 293 ~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYL 372 (500)
T KOG3993|consen 293 HVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYL 372 (500)
T ss_pred EeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHH
Confidence 34799999999999999999999998321 11 26799999999999999
Q ss_pred HHHHhhhhc
Q psy12014 63 TTHMAIRHH 71 (78)
Q Consensus 63 ~~h~~~~~g 71 (78)
..|+-+|..
T Consensus 373 rKHqlthq~ 381 (500)
T KOG3993|consen 373 RKHQLTHQR 381 (500)
T ss_pred HHhHHhhhc
Confidence 999888863
No 21
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.53 E-value=4.5e-07 Score=37.78 Aligned_cols=52 Identities=27% Similarity=0.598 Sum_probs=39.0
Q ss_pred ceecCCchhhcCCHHHHHHHhhc-ccCCCCCcccCCCcccccChhHHHHHHhhhhc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTY-ECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHH 71 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g 71 (78)
.|.|+.|++.|+ ...|..|... |..+.+.+.|++|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 588999999554 5678888654 776556789999987544 488889887764
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.50 E-value=2.1e-07 Score=54.47 Aligned_cols=58 Identities=19% Similarity=0.406 Sum_probs=31.2
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccC----------hhHHHHHHhhhhcCccccC
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQ----------KIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~----------~~~l~~h~~~~~g~k~~~~ 77 (78)
+++.|. |+..+ ....|..|+..|.+ .+|+.|..|+..+.. ...|..|.... |.+++.|
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp-~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCP-LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCC-CCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEc
Confidence 455565 65433 34555566655665 555666666655531 23455565553 5555554
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.48 E-value=3e-07 Score=53.87 Aligned_cols=59 Identities=17% Similarity=0.414 Sum_probs=49.1
Q ss_pred cCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 13 KGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 13 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
..++.+.|..|++.|. ...|..|+..+. .|+.|+ |+..+ ....|..|+.+|.++++++|
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~~~~H---kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C 507 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHMKVFH---EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITC 507 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHHHhcC---CCccCC-CCCCc-chhHHHhhhhccCCCCceeC
Confidence 3456789999999996 567899999864 468999 99755 56899999999999999988
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.39 E-value=3e-07 Score=31.65 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=10.1
Q ss_pred ccCCCcccccChhHHHHHHhh
Q psy12014 48 RCPLCSYRAKQKIHLTTHMAI 68 (78)
Q Consensus 48 ~c~~c~~~f~~~~~l~~h~~~ 68 (78)
.|..|++.|.....|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhH
Confidence 344455555555555544443
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.38 E-value=2.9e-07 Score=31.70 Aligned_cols=23 Identities=26% Similarity=0.719 Sum_probs=20.8
Q ss_pred eecCCchhhcCCHHHHHHHhhcc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYE 40 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h 40 (78)
|.|..|++.|.....|..|++.|
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 68999999999999999998764
No 26
>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=98.25 E-value=7.5e-07 Score=31.84 Aligned_cols=23 Identities=17% Similarity=0.333 Sum_probs=13.1
Q ss_pred cccCCCcccccChhHHHHHHhhh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
++|..|++.|.....|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 45555555555555555555554
No 27
>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=98.18 E-value=2.7e-06 Score=34.65 Aligned_cols=32 Identities=38% Similarity=0.722 Sum_probs=21.9
Q ss_pred CCCcccCCCcccccChhHHHHHHhhhhcCccc
Q psy12014 44 QPKYRCPLCSYRAKQKIHLTTHMAIRHHKKLG 75 (78)
Q Consensus 44 ~~~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~ 75 (78)
..|-.|++|+..+.+..+|..|+.+.++.||.
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 66788999999999999999999888888774
No 28
>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=98.15 E-value=2.3e-06 Score=29.39 Aligned_cols=23 Identities=30% Similarity=0.782 Sum_probs=11.9
Q ss_pred cccCCCcccccChhHHHHHHhhh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
|.|..|++.|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34555666666666666555544
No 29
>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=98.12 E-value=3.2e-06 Score=30.14 Aligned_cols=25 Identities=24% Similarity=0.814 Sum_probs=22.7
Q ss_pred ceecCCchhhcCCHHHHHHHhhccc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYEC 41 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~ 41 (78)
+|.|..|++.|.....|..|++.|.
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 5899999999999999999998764
No 30
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.98 E-value=2.5e-06 Score=46.91 Aligned_cols=53 Identities=28% Similarity=0.577 Sum_probs=41.7
Q ss_pred CCceecCC--chhhcCCHHHHHHHhhc-c-----------------cCCCCCcccCCCcccccChhHHHHHHh
Q psy12014 15 GGLFSCSD--CSRVYKKKASLTRHQTY-E-----------------CGQQPKYRCPLCSYRAKQKIHLTTHMA 67 (78)
Q Consensus 15 ~~~~~c~~--c~~~f~~~~~l~~h~~~-h-----------------~~~~~~~~c~~c~~~f~~~~~l~~h~~ 67 (78)
++||+|.+ |++.+...-.|+-|+.- | ..+.|||+|.+|++.+.....|.-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 59999987 99999988888777653 2 112489999999999998888876654
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.91 E-value=1.2e-05 Score=27.54 Aligned_cols=23 Identities=26% Similarity=0.723 Sum_probs=18.9
Q ss_pred eecCCchhhcCCHHHHHHHhhcc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYE 40 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h 40 (78)
|.|+.|+..|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999998764
No 32
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.80 E-value=3e-05 Score=26.85 Aligned_cols=22 Identities=41% Similarity=0.670 Sum_probs=11.8
Q ss_pred ccCCCcccccChhHHHHHHhhh
Q psy12014 48 RCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 48 ~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
.|..|++.|.....+..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4555555555555555555543
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.68 E-value=5e-05 Score=26.24 Aligned_cols=24 Identities=29% Similarity=0.818 Sum_probs=21.0
Q ss_pred eecCCchhhcCCHHHHHHHhhccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYEC 41 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~ 41 (78)
+.|..|++.|.....|..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998654
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.59 E-value=0.00011 Score=30.04 Aligned_cols=35 Identities=17% Similarity=0.249 Sum_probs=23.5
Q ss_pred hccCCCceecCCchhhcCCHHHHHHHhhcccCCCCC
Q psy12014 11 LYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPK 46 (78)
Q Consensus 11 ~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~ 46 (78)
....+.|..|.+|+..+....+|.+|+....+ .+|
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~-~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHF-KKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTT-TS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhc-ccC
Confidence 34568899999999999999999999977555 443
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.57 E-value=9.1e-05 Score=34.07 Aligned_cols=24 Identities=29% Similarity=0.742 Sum_probs=19.4
Q ss_pred CcccCCCcccccChhHHHHHHhhh
Q psy12014 46 KYRCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 46 ~~~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
.+.|..|++.|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 378899999999899999998865
No 36
>PHA00732 hypothetical protein
Probab=97.50 E-value=0.00012 Score=32.86 Aligned_cols=27 Identities=19% Similarity=0.581 Sum_probs=23.4
Q ss_pred CcccCCCcccccChhHHHHHHhh-hhcC
Q psy12014 46 KYRCPLCSYRAKQKIHLTTHMAI-RHHK 72 (78)
Q Consensus 46 ~~~c~~c~~~f~~~~~l~~h~~~-~~g~ 72 (78)
||.|..|++.|.....|..|++. |.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~ 28 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLT 28 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCC
Confidence 58899999999999999999984 6653
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.44 E-value=9.6e-05 Score=37.34 Aligned_cols=37 Identities=24% Similarity=0.609 Sum_probs=24.2
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccC
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQ 58 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~ 58 (78)
+|.|. |+. ....+.+|.+++++ .++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRG-EAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcC-CccEECCCCCceeEE
Confidence 46776 765 33445677777777 666777777766653
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.41 E-value=0.0002 Score=24.64 Aligned_cols=23 Identities=43% Similarity=0.996 Sum_probs=13.4
Q ss_pred cccCCCcccccChhHHHHHHhhhh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~~ 70 (78)
|+|..|+.... ...|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 45666766655 666777766654
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.39 E-value=0.00016 Score=25.08 Aligned_cols=20 Identities=25% Similarity=0.639 Sum_probs=10.2
Q ss_pred ecCCchhhcCCHHHHHHHhh
Q psy12014 19 SCSDCSRVYKKKASLTRHQT 38 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~ 38 (78)
.|.+|+..|.....+..|.+
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555543
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.32 E-value=0.00019 Score=24.86 Aligned_cols=23 Identities=17% Similarity=0.524 Sum_probs=20.5
Q ss_pred cccCCCcccccChhHHHHHHhhh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
|.|..|...|.....+..|++.+
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 57999999999999999998765
No 41
>KOG3993|consensus
Probab=97.32 E-value=4.7e-05 Score=43.50 Aligned_cols=53 Identities=23% Similarity=0.459 Sum_probs=43.2
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhh
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 70 (78)
.|.|..|...|...-.|..|.-.-.. ...|+|+.|++.|+=..+|..|.|=|-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV-~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIV-HVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeE-EeeecCCcccccccCchhhhhhhcccC
Confidence 48899999999888888888643333 334999999999999999999998873
No 42
>PRK04860 hypothetical protein; Provisional
Probab=96.84 E-value=0.00076 Score=34.17 Aligned_cols=28 Identities=18% Similarity=0.502 Sum_probs=24.4
Q ss_pred CcccCCCcccccChhHHHHHHhhhhcCccccC
Q psy12014 46 KYRCPLCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 46 ~~~c~~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
+|.|. |+. ...++..|.++++|+++|.|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC 146 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRC 146 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEEC
Confidence 58897 886 67778999999999999988
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.66 E-value=0.0011 Score=23.46 Aligned_cols=21 Identities=24% Similarity=0.518 Sum_probs=11.5
Q ss_pred cccCCCcccccChhHHHHHHh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMA 67 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~ 67 (78)
|-|..|++.|.....+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 345555555555555555544
No 44
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.44 E-value=0.0042 Score=21.69 Aligned_cols=19 Identities=26% Similarity=0.632 Sum_probs=9.9
Q ss_pred ccCCCcccccChhHHHHHHh
Q psy12014 48 RCPLCSYRAKQKIHLTTHMA 67 (78)
Q Consensus 48 ~c~~c~~~f~~~~~l~~h~~ 67 (78)
.|+.|++.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455666666 3444555543
No 45
>KOG2893|consensus
Probab=96.34 E-value=0.0012 Score=35.53 Aligned_cols=44 Identities=23% Similarity=0.507 Sum_probs=33.7
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHH
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTH 65 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h 65 (78)
++ .|..|++.|.....|..|+. .+.|+|.+|-+....-..|..|
T Consensus 10 kp-wcwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 10 KP-WCWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred Cc-eeeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceee
Confidence 44 48899999999999999988 5568999997655555555555
No 46
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.09 E-value=0.0077 Score=22.37 Aligned_cols=22 Identities=23% Similarity=0.495 Sum_probs=15.1
Q ss_pred ceecCCchhhcCCHHHHHHHhh
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQT 38 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~ 38 (78)
+|.|+.|+..|.....+..|..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777776666666654
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.07 E-value=0.0011 Score=37.52 Aligned_cols=61 Identities=21% Similarity=0.425 Sum_probs=52.0
Q ss_pred CceecCCchhhcCCHHHHHHHhh--cccCCC--CCcccC--CCcccccChhHHHHHHhhhhcCccccC
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQT--YECGQQ--PKYRCP--LCSYRAKQKIHLTTHMAIRHHKKLGKI 77 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~--~h~~~~--~~~~c~--~c~~~f~~~~~l~~h~~~~~g~k~~~~ 77 (78)
.++.|..|...|.....+..|.+ .|.+ . +|+.|+ .|++.|.....+..|..+|++..+.++
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred cCCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 36788889999999999999999 7988 6 889999 799999999999999999988776554
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.95 E-value=0.034 Score=25.38 Aligned_cols=27 Identities=19% Similarity=0.563 Sum_probs=22.7
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccC
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECG 42 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~ 42 (78)
..+.|..|++.|.+...|..|++.+..
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 369999999999999999999997544
No 49
>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=94.81 E-value=0.019 Score=21.33 Aligned_cols=24 Identities=25% Similarity=0.955 Sum_probs=16.5
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
|.|..||..+... ..++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~-------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE-------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC-------------cCCCcCcCCCC
Confidence 6788888665432 24688999974
No 50
>KOG2186|consensus
Probab=94.18 E-value=0.04 Score=30.05 Aligned_cols=49 Identities=18% Similarity=0.407 Sum_probs=36.1
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhh
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 70 (78)
|.|..||....-+ .+..|+..-++ .. |.|.-|+.+|.. .+...|....+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~-fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AY-FSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-Ce-eEEeeccccccc-chhhhhhhhcc
Confidence 6799999887644 45668887666 54 899999999987 45566766544
No 51
>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=93.59 E-value=0.081 Score=19.82 Aligned_cols=25 Identities=24% Similarity=0.891 Sum_probs=16.6
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|.|..||..+. +...|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~-------------g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHE-------------GEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeE-------------CCcCCCcCcCCCC
Confidence 478888886543 2134678999875
No 52
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.24 E-value=0.074 Score=22.28 Aligned_cols=30 Identities=20% Similarity=0.543 Sum_probs=23.8
Q ss_pred hhccCCCceecCCchhhcCCHHHHHHHhhc
Q psy12014 10 SLYKGGGLFSCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 10 ~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 39 (78)
+...||.-+.|+.|+..|.....+.+|...
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 345677788999999999988888888754
No 53
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.61 E-value=0.11 Score=26.75 Aligned_cols=24 Identities=25% Similarity=0.775 Sum_probs=18.3
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
-|.|.+||.. +.+ ..|..|+.|+-
T Consensus 134 ~~vC~vCGy~-------------~~g-e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEG-EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccC-CCCCcCCCCCC
Confidence 6999999854 345 66789999983
No 54
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=91.96 E-value=0.11 Score=25.77 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=15.7
Q ss_pred cccCCCcccccChhHHHHHHhhhhcCcc
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIRHHKKL 74 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~~g~k~ 74 (78)
..|.+||+.|... ..|++.|+|..|
T Consensus 73 i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eEEccCCcccchH---HHHHHHccCCCH
Confidence 5799999987754 789999987654
No 55
>KOG1146|consensus
Probab=91.66 E-value=0.23 Score=33.14 Aligned_cols=57 Identities=21% Similarity=0.387 Sum_probs=45.3
Q ss_pred ccCCCceecCCchhhcCCHHHHHHHhhcccCC------------------------CCCcccCCCcccccChhHHHHHHh
Q psy12014 12 YKGGGLFSCSDCSRVYKKKASLTRHQTYECGQ------------------------QPKYRCPLCSYRAKQKIHLTTHMA 67 (78)
Q Consensus 12 ~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~------------------------~~~~~c~~c~~~f~~~~~l~~h~~ 67 (78)
++-.+.+.|..|+..|.....|..|++....+ .+|+.|..|...+....+|..|++
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 44458899999999999999999999871110 246889999999988888888877
Q ss_pred h
Q psy12014 68 I 68 (78)
Q Consensus 68 ~ 68 (78)
.
T Consensus 540 S 540 (1406)
T KOG1146|consen 540 S 540 (1406)
T ss_pred H
Confidence 5
No 56
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.09 E-value=0.038 Score=29.43 Aligned_cols=45 Identities=20% Similarity=0.440 Sum_probs=28.3
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcc---cCC------CCC-----cccCCCcccccCh
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYE---CGQ------QPK-----YRCPLCSYRAKQK 59 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h---~~~------~~~-----~~c~~c~~~f~~~ 59 (78)
++...|+.|+..|..........+.- ... ..| +.|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 46678999999998775544443321 110 222 5799999876533
No 57
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=89.62 E-value=0.3 Score=26.21 Aligned_cols=26 Identities=15% Similarity=0.432 Sum_probs=20.9
Q ss_pred CCCceecCCchhhcCCHHHHHHHhhc
Q psy12014 14 GGGLFSCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 14 ~~~~~~c~~c~~~f~~~~~l~~h~~~ 39 (78)
.+..|.|..|++.|.-..++..|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 45569999999999999999999876
No 58
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.79 E-value=0.35 Score=19.27 Aligned_cols=27 Identities=33% Similarity=0.883 Sum_probs=18.6
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYR 55 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~ 55 (78)
.|.|..||..|... . ..+.+|+.||..
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~-~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------S-KDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------C-CCceECCCCCce
Confidence 47899999877532 1 335789999853
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.63 E-value=0.48 Score=18.00 Aligned_cols=34 Identities=24% Similarity=0.621 Sum_probs=20.8
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
-.|+.|+..|...... ....+ . ..+|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~----l~~~~-~-~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK----LPAGG-R-KVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH----cccCC-c-EEECCCCCcEee
Confidence 3688888888755421 11222 3 378998887764
No 60
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.49 E-value=0.44 Score=18.05 Aligned_cols=33 Identities=24% Similarity=0.549 Sum_probs=20.6
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRA 56 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f 56 (78)
..|+.|+..|...+.. ....+ . ..+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~----ip~~g-~-~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK----IPPKG-R-KVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH----CCCCC-c-EEECCCCCCEe
Confidence 4688888888765532 22222 3 37888888766
No 61
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=88.08 E-value=0.22 Score=23.04 Aligned_cols=13 Identities=15% Similarity=0.536 Sum_probs=8.2
Q ss_pred CceecCCchhhcC
Q psy12014 16 GLFSCSDCSRVYK 28 (78)
Q Consensus 16 ~~~~c~~c~~~f~ 28 (78)
+|-.|..||..|.
T Consensus 57 ~Pa~CkkCGfef~ 69 (97)
T COG3357 57 RPARCKKCGFEFR 69 (97)
T ss_pred cChhhcccCcccc
Confidence 4556777776664
No 62
>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=87.61 E-value=0.52 Score=22.59 Aligned_cols=30 Identities=20% Similarity=0.569 Sum_probs=21.1
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccCh
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQK 59 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~ 59 (78)
..|..||..|= .| . +.|..|+.||..|...
T Consensus 10 R~Cp~CG~kFY---DL--------n-k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFY---DL--------N-KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhc---cC--------C-CCCccCCCCCCccCcc
Confidence 47888887652 12 2 5678899999887755
No 63
>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=87.59 E-value=0.71 Score=23.56 Aligned_cols=36 Identities=14% Similarity=0.427 Sum_probs=26.6
Q ss_pred ccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 12 YKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 12 ~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
.+...-|.|+.|+..|+...++. . -|.|+.||....
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~-~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------L-NFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------c-CCcCCCCCCEee
Confidence 44566789999999888766653 1 399999997654
No 64
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=87.06 E-value=0.13 Score=29.18 Aligned_cols=25 Identities=24% Similarity=0.505 Sum_probs=18.9
Q ss_pred ccCCCceecCCchhhcCCHHHHHHH
Q psy12014 12 YKGGGLFSCSDCSRVYKKKASLTRH 36 (78)
Q Consensus 12 ~~~~~~~~c~~c~~~f~~~~~l~~h 36 (78)
-...|||+|..|++.+..--.|+-|
T Consensus 393 ~~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 393 SAKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred cccCCceeccccchhhccCccceec
Confidence 4567999999999998865555444
No 65
>KOG4167|consensus
Probab=86.79 E-value=0.13 Score=32.28 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=22.1
Q ss_pred cccCCCcccccChhHHHHHHhhhh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~~ 70 (78)
|.|..|++.|..-.+++.|+++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 789999999999999999999985
No 66
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=86.42 E-value=0.86 Score=23.77 Aligned_cols=35 Identities=20% Similarity=0.596 Sum_probs=25.2
Q ss_pred cCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 13 KGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 13 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
....-|.|+.|+..|+....+. .-|.|+.||....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEMLE 147 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCCe
Confidence 3456689999999888665442 1399999997554
No 67
>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=86.20 E-value=0.42 Score=25.69 Aligned_cols=27 Identities=33% Similarity=0.656 Sum_probs=21.0
Q ss_pred cccCCCcccccChhHHHHHHhhhhcCc
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIRHHKK 73 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~~g~k 73 (78)
|.|..|+|.|.-......|+..-|.|+
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred ECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 899999999999999999988766553
No 68
>KOG3408|consensus
Probab=85.92 E-value=0.91 Score=22.23 Aligned_cols=28 Identities=32% Similarity=0.736 Sum_probs=22.2
Q ss_pred cCCCceecCCchhhcCCHHHHHHHhhcc
Q psy12014 13 KGGGLFSCSDCSRVYKKKASLTRHQTYE 40 (78)
Q Consensus 13 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h 40 (78)
.|...|.|..|.+-|.....|..|.+.-
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 3455688999999999998888887653
No 69
>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=85.71 E-value=0.89 Score=21.53 Aligned_cols=25 Identities=36% Similarity=0.817 Sum_probs=21.9
Q ss_pred ccc----CCCcccccChhHHHHHHhhhhc
Q psy12014 47 YRC----PLCSYRAKQKIHLTTHMAIRHH 71 (78)
Q Consensus 47 ~~c----~~c~~~f~~~~~l~~h~~~~~g 71 (78)
|.| ..|+........+..|.+..+|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8899999999999999988765
No 70
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=85.71 E-value=0.5 Score=23.56 Aligned_cols=25 Identities=16% Similarity=0.098 Sum_probs=18.6
Q ss_pred cccCCCcccccChhHHHHHHhhhhcCcc
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIRHHKKL 74 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~~g~k~ 74 (78)
..|.++|+.|. +|.+|+.+|.|..|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 35777887665 67889999887654
No 71
>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=85.24 E-value=1.2 Score=15.57 Aligned_cols=19 Identities=21% Similarity=0.691 Sum_probs=11.0
Q ss_pred ccCCCcccccChhHHHHHHh
Q psy12014 48 RCPLCSYRAKQKIHLTTHMA 67 (78)
Q Consensus 48 ~c~~c~~~f~~~~~l~~h~~ 67 (78)
.|+.|++.+ ....++.|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777666 3345555543
No 72
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=84.88 E-value=0.57 Score=19.17 Aligned_cols=39 Identities=21% Similarity=0.439 Sum_probs=20.6
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCS 53 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~ 53 (78)
.+.+.|..||..|.-...-+..-..-.-...|-+|..|.
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 457889999997774432222211111112356777764
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.56 E-value=1.2 Score=18.96 Aligned_cols=33 Identities=27% Similarity=0.638 Sum_probs=18.9
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
-.|.|..||........- - +. . -.+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~~--C-Rk--~-g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAK--C-RK--L-GNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhh--H-HH--c-CCceECCCcCc
Confidence 348888888654433211 1 11 1 34689988873
No 74
>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=84.22 E-value=0.96 Score=17.02 Aligned_cols=34 Identities=24% Similarity=0.447 Sum_probs=20.5
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
..|+.|+..|...... ....+ . ...|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~----~~~~~-~-~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ----LGANG-G-KVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHH----cCCCC-C-EEECCCCCCEEE
Confidence 4688888877654432 11112 2 368999987764
No 75
>KOG4167|consensus
Probab=83.90 E-value=0.26 Score=31.10 Aligned_cols=25 Identities=28% Similarity=0.563 Sum_probs=22.8
Q ss_pred eecCCchhhcCCHHHHHHHhhcccC
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECG 42 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~ 42 (78)
|.|.+|++.|.....+..||..|.-
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHH
Confidence 8999999999988889999998866
No 76
>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=83.69 E-value=0.57 Score=17.34 Aligned_cols=26 Identities=27% Similarity=0.735 Sum_probs=14.3
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYR 55 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~ 55 (78)
|.|..|+..+.. . . ..+.+|..||..
T Consensus 1 Y~C~~Cg~~~~~----------~-~-~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVEL----------K-P-GDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-B----------S-T-SSTSSBSSSS-S
T ss_pred CCCCcCCCeeEc----------C-C-CCcEECCcCCCe
Confidence 457777765531 1 1 234788888853
No 77
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.41 E-value=1.2 Score=17.63 Aligned_cols=30 Identities=30% Similarity=0.734 Sum_probs=18.8
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
.|.|..||..+.... . .....|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~----------~-~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDE----------Y-GTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECC----------C-CCceECCCCCCeEE
Confidence 578888887664311 1 11478999986443
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=83.30 E-value=1.6 Score=21.95 Aligned_cols=40 Identities=15% Similarity=0.512 Sum_probs=26.1
Q ss_pred cCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 13 KGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 13 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
.+..-|.|+.|+..|.....+.. .... . .|.|+.|+....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~d~~-~-~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---LDMD-G-TFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---cCCC-C-cEECCCCCCEEE
Confidence 44567899999999885544321 1111 2 299999997553
No 79
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.39 E-value=0.58 Score=21.53 Aligned_cols=33 Identities=18% Similarity=0.472 Sum_probs=21.7
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccCh
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQK 59 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~ 59 (78)
..|.|+.|++. .+.+.-++ -|.|..|+..|.-.
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~G---IW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATG---IWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccC---eEEcCCCCCeeccc
Confidence 46788888865 22344444 48899998877543
No 80
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=81.63 E-value=1.6 Score=17.58 Aligned_cols=20 Identities=20% Similarity=0.630 Sum_probs=10.7
Q ss_pred ccCCCcccccCh-----hHHHHHHh
Q psy12014 48 RCPLCSYRAKQK-----IHLTTHMA 67 (78)
Q Consensus 48 ~c~~c~~~f~~~-----~~l~~h~~ 67 (78)
.|..|++.+... ++|..|+.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455565544433 45666655
No 81
>KOG2593|consensus
Probab=81.35 E-value=0.65 Score=27.50 Aligned_cols=41 Identities=15% Similarity=0.393 Sum_probs=27.1
Q ss_pred hhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 10 SLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 10 ~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
+-.+....|.|+.|.+.|..-..++ ..... .-.|.|..|+.
T Consensus 121 ~d~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~-~~~F~C~~C~g 161 (436)
T KOG2593|consen 121 RDDTNVAGYVCPNCQKKYTSLEALQ---LLDNE-TGEFHCENCGG 161 (436)
T ss_pred hhccccccccCCccccchhhhHHHH---hhccc-CceEEEecCCC
Confidence 4455667899999999998766553 32221 22488888864
No 82
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=80.21 E-value=2 Score=16.76 Aligned_cols=24 Identities=21% Similarity=0.539 Sum_probs=15.9
Q ss_pred eecCCchhhcC--CHHHHHHHhhccc
Q psy12014 18 FSCSDCSRVYK--KKASLTRHQTYEC 41 (78)
Q Consensus 18 ~~c~~c~~~f~--~~~~l~~h~~~h~ 41 (78)
-.|..||..+. ....-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 47888888776 3455666666553
No 83
>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=79.79 E-value=1.1 Score=15.73 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=8.1
Q ss_pred cccCCCccccc
Q psy12014 47 YRCPLCSYRAK 57 (78)
Q Consensus 47 ~~c~~c~~~f~ 57 (78)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36888888774
No 84
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.05 E-value=1.1 Score=19.20 Aligned_cols=46 Identities=17% Similarity=0.353 Sum_probs=30.0
Q ss_pred hhhhccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccC
Q psy12014 8 IDSLYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQ 58 (78)
Q Consensus 8 ~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~ 58 (78)
+..++.+..++.|..-+..+.....+ ..-+......|+.|+..|..
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~-----L~mg~~gev~CPYC~t~y~l 60 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVF-----LDMGDEGEVVCPYCSTRYRL 60 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEE-----EEcCCCCcEecCccccEEEe
Confidence 56677888999998877666544321 11132444689999987764
No 85
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=78.77 E-value=1.8 Score=24.72 Aligned_cols=56 Identities=23% Similarity=0.526 Sum_probs=43.2
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCC--CcccccChhHHHHHHhhhhc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPL--CSYRAKQKIHLTTHMAIRHH 71 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~--c~~~f~~~~~l~~h~~~~~g 71 (78)
...+.|..|...|........|.+.+.+ .++..|.. |...+.....+..+...++.
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (467)
T COG5048 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTG-EKPSQCSYSGCDKSFSRPLELSRHLRTHHN 88 (467)
T ss_pred Cchhhcccccccccccchhhhhcccccc-cCCccccccccccccCCcchhhhhcccccc
Confidence 4567889999999988889999999999 77788876 45666666667777666653
No 86
>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=77.52 E-value=1.1 Score=17.71 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=9.4
Q ss_pred ccCCCcccccCh
Q psy12014 48 RCPLCSYRAKQK 59 (78)
Q Consensus 48 ~c~~c~~~f~~~ 59 (78)
.|..|++.|...
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 688888888754
No 87
>PHA00626 hypothetical protein
Probab=75.67 E-value=2 Score=18.10 Aligned_cols=17 Identities=29% Similarity=0.554 Sum_probs=13.0
Q ss_pred CCceecCCchhhcCCHH
Q psy12014 15 GGLFSCSDCSRVYKKKA 31 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~ 31 (78)
...|.|..|+..|+...
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 46799999998887543
No 88
>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=74.53 E-value=0.77 Score=18.96 Aligned_cols=26 Identities=15% Similarity=0.453 Sum_probs=13.7
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYE 40 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h 40 (78)
...|.|+.|...|...-++-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 35699999999998776665665544
No 89
>PF12907 zf-met2: Zinc-binding
Probab=73.73 E-value=0.7 Score=18.08 Aligned_cols=9 Identities=22% Similarity=0.885 Sum_probs=4.3
Q ss_pred ecCCchhhc
Q psy12014 19 SCSDCSRVY 27 (78)
Q Consensus 19 ~c~~c~~~f 27 (78)
.|.+|...|
T Consensus 3 ~C~iC~qtF 11 (40)
T PF12907_consen 3 ICKICRQTF 11 (40)
T ss_pred CcHHhhHHH
Confidence 455555433
No 90
>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=73.60 E-value=4.8 Score=15.56 Aligned_cols=20 Identities=25% Similarity=0.536 Sum_probs=8.5
Q ss_pred cccCCCcccccCh----hHHHHHH
Q psy12014 47 YRCPLCSYRAKQK----IHLTTHM 66 (78)
Q Consensus 47 ~~c~~c~~~f~~~----~~l~~h~ 66 (78)
..|..|++.+... +.|..|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4566665544432 4455554
No 91
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=73.42 E-value=2.3 Score=17.44 Aligned_cols=29 Identities=24% Similarity=0.589 Sum_probs=18.6
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
...|.|..|++.+... . . ....+|+.||.
T Consensus 4 ~~~Y~C~~Cg~~~~~~-------~---~-~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELD-------Q---E-TRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehh-------h---c-cCceeCCCCCc
Confidence 3468899999887211 1 1 33478998874
No 92
>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=72.97 E-value=3.3 Score=20.55 Aligned_cols=30 Identities=10% Similarity=0.172 Sum_probs=20.5
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccCh
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQK 59 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~ 59 (78)
..|..||..|= .| . +.|..|+.||..+...
T Consensus 10 r~Cp~cg~kFY---DL--------n-k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFY---DL--------N-RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccc---cc--------C-CCCccCCCcCCccCcc
Confidence 47888887652 11 2 5678899999877554
No 93
>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=72.73 E-value=2.2 Score=16.16 Aligned_cols=31 Identities=19% Similarity=0.462 Sum_probs=15.8
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
+.|..||..|- ...... ..+-.|..||..+.
T Consensus 2 r~C~~Cg~~Yh--------~~~~pP-~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYH--------IEFNPP-KVEGVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEE--------TTTB---SSTTBCTTTTEBEB
T ss_pred cCcCCCCCccc--------cccCCC-CCCCccCCCCCeeE
Confidence 35667776653 222223 33457777775443
No 94
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.70 E-value=2.4 Score=19.08 Aligned_cols=31 Identities=23% Similarity=0.716 Sum_probs=18.3
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRA 56 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f 56 (78)
|.|..|+..|. +-.++. . ..--.|..|+..+
T Consensus 13 Y~c~~cg~~~d----vvq~~~---d-dplt~ce~c~a~~ 43 (82)
T COG2331 13 YECTECGNRFD----VVQAMT---D-DPLTTCEECGARL 43 (82)
T ss_pred EeecccchHHH----HHHhcc---c-CccccChhhChHH
Confidence 78999998774 222333 1 2223688887543
No 95
>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=71.91 E-value=1.9 Score=14.88 Aligned_cols=8 Identities=38% Similarity=1.315 Sum_probs=4.8
Q ss_pred CcccCCCc
Q psy12014 46 KYRCPLCS 53 (78)
Q Consensus 46 ~~~c~~c~ 53 (78)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 46666665
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.81 E-value=3.1 Score=17.74 Aligned_cols=33 Identities=24% Similarity=0.708 Sum_probs=17.5
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
-.|.|..||.....+-. .-.. . -.+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~--~CRk---~-~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE--KCRK---Q-SNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeech--hHHh---c-CCceECCCCCC
Confidence 45788888875222211 0111 1 34688888873
No 97
>KOG1146|consensus
Probab=71.63 E-value=2.8 Score=28.62 Aligned_cols=56 Identities=25% Similarity=0.398 Sum_probs=41.9
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcccCC----------------CCCcccCCCcccccChhHHHHHHhhhhc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYECGQ----------------QPKYRCPLCSYRAKQKIHLTTHMAIRHH 71 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~----------------~~~~~c~~c~~~f~~~~~l~~h~~~~~g 71 (78)
..+|.|..|...|.....|..|++...-. ..++ |..|...|+....|..|++.-.+
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhh
Confidence 56788999999999998888887522100 1235 88899999999999999886544
No 98
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.46 E-value=1.6 Score=21.67 Aligned_cols=15 Identities=20% Similarity=0.744 Sum_probs=11.8
Q ss_pred CceecCCchhhcCCH
Q psy12014 16 GLFSCSDCSRVYKKK 30 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~ 30 (78)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 458999999888654
No 99
>PLN02294 cytochrome c oxidase subunit Vb
Probab=71.04 E-value=2.5 Score=22.04 Aligned_cols=15 Identities=27% Similarity=0.826 Sum_probs=11.0
Q ss_pred CCceecCCchhhcCC
Q psy12014 15 GGLFSCSDCSRVYKK 29 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~ 29 (78)
+++++|..||..|..
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 467788888887753
No 100
>KOG4173|consensus
Probab=69.04 E-value=4 Score=22.12 Aligned_cols=49 Identities=31% Similarity=0.508 Sum_probs=25.6
Q ss_pred ecCCchhhcCCHHHHHHHhhc-c---------cCCCCCcccCC--CcccccChhHHHHHHhh
Q psy12014 19 SCSDCSRVYKKKASLTRHQTY-E---------CGQQPKYRCPL--CSYRAKQKIHLTTHMAI 68 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~~-h---------~~~~~~~~c~~--c~~~f~~~~~l~~h~~~ 68 (78)
.|..|.+.|+....|..|+.. | .| ..-|+|.+ |+.-|........|+..
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG-~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG-QDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC-ccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 566666666666555555432 1 22 22355544 55566555555555544
No 101
>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=68.78 E-value=3.1 Score=19.62 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=10.3
Q ss_pred CceecCCchhhcCC
Q psy12014 16 GLFSCSDCSRVYKK 29 (78)
Q Consensus 16 ~~~~c~~c~~~f~~ 29 (78)
++++|..||..|..
T Consensus 78 ~~~rC~eCG~~fkL 91 (97)
T cd00924 78 KPKRCPECGHVFKL 91 (97)
T ss_pred CceeCCCCCcEEEE
Confidence 67788888877753
No 102
>KOG2785|consensus
Probab=66.71 E-value=11 Score=22.38 Aligned_cols=52 Identities=19% Similarity=0.236 Sum_probs=37.7
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCC----------------------CcccCCCc---ccccChhHHHHHHhh
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQP----------------------KYRCPLCS---YRAKQKIHLTTHMAI 68 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~----------------------~~~c~~c~---~~f~~~~~l~~h~~~ 68 (78)
|=.|..|+..+..-..-..||..+.+..- -+.|..|. +.|........|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 44588898888877666678887655322 25777787 888888888888764
No 103
>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=65.97 E-value=2.9 Score=16.29 Aligned_cols=30 Identities=17% Similarity=0.571 Sum_probs=19.4
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|.|..||..|.... .... ..+..|+.|+.
T Consensus 5 ey~C~~Cg~~fe~~~------~~~~--~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ------SISE--DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEE------EcCC--CCCCcCCCCCC
Confidence 378999998886422 2222 23468999986
No 104
>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=65.70 E-value=3.1 Score=15.70 Aligned_cols=30 Identities=20% Similarity=0.548 Sum_probs=18.8
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|.|..|+..|..... ...+ . ...|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~------~~~~-~-~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQK------ISDD-P-LATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEe------cCCC-C-CCCCCCCCC
Confidence 3789999998763321 1112 2 367999986
No 105
>PF15269 zf-C2H2_7: Zinc-finger
Probab=65.37 E-value=5.6 Score=15.97 Aligned_cols=23 Identities=35% Similarity=0.798 Sum_probs=15.9
Q ss_pred cccCCCcccccChhHHHHHHhhh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
|+|-.|..+....+.|-.|+...
T Consensus 21 ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred ceeecCCcccchHHHHHHHHHHH
Confidence 56777776667777777777643
No 106
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=64.76 E-value=3.7 Score=20.49 Aligned_cols=14 Identities=14% Similarity=0.358 Sum_probs=9.4
Q ss_pred CcccCCCcccccCh
Q psy12014 46 KYRCPLCSYRAKQK 59 (78)
Q Consensus 46 ~~~c~~c~~~f~~~ 59 (78)
|.+|..||+.|...
T Consensus 1 PH~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 1 PHQCTKCGRVFEDG 14 (131)
T ss_pred CcccCcCCCCcCCC
Confidence 46677777777644
No 107
>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=64.33 E-value=5.5 Score=16.18 Aligned_cols=30 Identities=27% Similarity=0.812 Sum_probs=13.0
Q ss_pred ecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 19 SCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|..- ..|+....|...+. ...|.|+.|++
T Consensus 20 ~C~H~-~CFDl~~fl~~~~~-----~~~W~CPiC~~ 49 (50)
T PF02891_consen 20 NCKHL-QCFDLESFLESNQR-----TPKWKCPICNK 49 (50)
T ss_dssp T--SS---EEHHHHHHHHHH-----S---B-TTT--
T ss_pred cCccc-ceECHHHHHHHhhc-----cCCeECcCCcC
Confidence 34443 35777777765554 33389999875
No 108
>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=63.43 E-value=3.7 Score=20.83 Aligned_cols=28 Identities=18% Similarity=0.469 Sum_probs=16.8
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYR 55 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~ 55 (78)
.+.|..||.... ..+++ .- -.|+.|+..
T Consensus 112 ~l~C~~Cg~~~~---------~~~~~-~l-~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHEVE---------LTHPE-RL-PPCPKCGHT 139 (146)
T ss_pred eEecccCCCEEE---------ecCCC-cC-CCCCCCCCC
Confidence 488998886532 12333 33 478888753
No 109
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=63.41 E-value=6.7 Score=18.89 Aligned_cols=26 Identities=27% Similarity=0.593 Sum_probs=21.4
Q ss_pred CCCceecCCchhhcCCHHHHHHHhhc
Q psy12014 14 GGGLFSCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 14 ~~~~~~c~~c~~~f~~~~~l~~h~~~ 39 (78)
|...+.|..|.+-|.....|..|.+.
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhcc
Confidence 44568899999999999989888764
No 110
>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=62.50 E-value=1.9 Score=15.50 Aligned_cols=8 Identities=50% Similarity=1.373 Sum_probs=3.7
Q ss_pred cCCchhhc
Q psy12014 20 CSDCSRVY 27 (78)
Q Consensus 20 c~~c~~~f 27 (78)
|..|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 44444444
No 111
>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=62.28 E-value=5.6 Score=19.13 Aligned_cols=25 Identities=24% Similarity=0.772 Sum_probs=14.4
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYR 55 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~ 55 (78)
..|..|+..|.... .. +.|+.|+..
T Consensus 71 ~~C~~Cg~~~~~~~------------~~-~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDE------------FD-FSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHH------------CC-HH-SSSSSS
T ss_pred EECCCCCCEEecCC------------CC-CCCcCCcCC
Confidence 67888888776533 11 567777653
No 112
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=61.45 E-value=4.6 Score=15.54 Aligned_cols=14 Identities=14% Similarity=0.449 Sum_probs=10.4
Q ss_pred CcccCCCcccccCh
Q psy12014 46 KYRCPLCSYRAKQK 59 (78)
Q Consensus 46 ~~~c~~c~~~f~~~ 59 (78)
|+.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 68888888877544
No 113
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.38 E-value=6.8 Score=19.04 Aligned_cols=49 Identities=14% Similarity=0.288 Sum_probs=30.9
Q ss_pred ecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccChhHHHHHHhhhh
Q psy12014 19 SCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 70 (78)
.|--|...|........-. -.. ...|+|..|...|-.+...-.|..+|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~--~~~-~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDE--LKD-SHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccccc--ccc-ccceeCCCCCCccccccchhhhhhccC
Confidence 3777777776432111110 122 335899999999988888878877764
No 114
>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=61.01 E-value=3.5 Score=16.89 Aligned_cols=12 Identities=33% Similarity=0.897 Sum_probs=6.4
Q ss_pred ccCCCcccccCh
Q psy12014 48 RCPLCSYRAKQK 59 (78)
Q Consensus 48 ~c~~c~~~f~~~ 59 (78)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999988644
No 115
>KOG2636|consensus
Probab=60.57 E-value=7.3 Score=23.66 Aligned_cols=29 Identities=28% Similarity=0.466 Sum_probs=18.0
Q ss_pred hhccCCCceecCCch-hhcCCHHHHHHHhh
Q psy12014 10 SLYKGGGLFSCSDCS-RVYKKKASLTRHQT 38 (78)
Q Consensus 10 ~~~~~~~~~~c~~c~-~~f~~~~~l~~h~~ 38 (78)
..|.-+..|.|.+|| .++--+..+.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 345556777888887 45555555666543
No 116
>KOG2071|consensus
Probab=60.05 E-value=7.6 Score=24.30 Aligned_cols=27 Identities=22% Similarity=0.464 Sum_probs=17.4
Q ss_pred CCCcccCCCcccccChhHHHHHHhhhh
Q psy12014 44 QPKYRCPLCSYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 44 ~~~~~c~~c~~~f~~~~~l~~h~~~~~ 70 (78)
..|-+|..||..|........|+..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 345667777777776666666666554
No 117
>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=59.14 E-value=4.5 Score=16.27 Aligned_cols=30 Identities=20% Similarity=0.586 Sum_probs=19.0
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|.|..|+..|.... .... ..+..|+.|+.
T Consensus 5 ey~C~~Cg~~fe~~~------~~~~--~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ------KMSD--DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEE------ecCC--CCCCCCCCCCC
Confidence 378999999886421 1111 23367999985
No 118
>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=58.64 E-value=3.3 Score=16.19 Aligned_cols=15 Identities=20% Similarity=0.445 Sum_probs=8.6
Q ss_pred CCcccCCCcccccCh
Q psy12014 45 PKYRCPLCSYRAKQK 59 (78)
Q Consensus 45 ~~~~c~~c~~~f~~~ 59 (78)
.|+.|..|+..|-..
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 467888888877543
No 119
>KOG0717|consensus
Probab=55.98 E-value=7.2 Score=23.81 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=18.4
Q ss_pred cccCCCcccccChhHHHHHHhh
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAI 68 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~ 68 (78)
+-|.+|.++|.....+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6799999999998888888654
No 120
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=55.02 E-value=6.3 Score=18.83 Aligned_cols=15 Identities=20% Similarity=0.616 Sum_probs=11.9
Q ss_pred CceecCCchhhcCCH
Q psy12014 16 GLFSCSDCSRVYKKK 30 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~ 30 (78)
.|+.|..||..|..-
T Consensus 1 MpH~CtrCG~vf~~g 15 (112)
T COG3364 1 MPHQCTRCGEVFDDG 15 (112)
T ss_pred CCceecccccccccc
Confidence 378899999998863
No 121
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=53.80 E-value=7 Score=21.53 Aligned_cols=18 Identities=22% Similarity=0.741 Sum_probs=14.2
Q ss_pred CCCceecCCchhhcCCHH
Q psy12014 14 GGGLFSCSDCSRVYKKKA 31 (78)
Q Consensus 14 ~~~~~~c~~c~~~f~~~~ 31 (78)
.+++.+|..||..|....
T Consensus 178 EGkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCCccCCCCCcEEEEEE
Confidence 456889999999997543
No 122
>COG1773 Rubredoxin [Energy production and conversion]
Probab=53.08 E-value=6.9 Score=16.48 Aligned_cols=14 Identities=36% Similarity=0.819 Sum_probs=11.2
Q ss_pred ceecCCchhhcCCH
Q psy12014 17 LFSCSDCSRVYKKK 30 (78)
Q Consensus 17 ~~~c~~c~~~f~~~ 30 (78)
.|+|..||..|...
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 58899999888754
No 123
>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=52.08 E-value=6 Score=19.92 Aligned_cols=15 Identities=33% Similarity=0.844 Sum_probs=10.9
Q ss_pred CCceecCCchhhcCC
Q psy12014 15 GGLFSCSDCSRVYKK 29 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~ 29 (78)
+++.+|..||..|..
T Consensus 110 g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 110 GKPQRCPECGQVFKL 124 (136)
T ss_dssp TSEEEETTTEEEEEE
T ss_pred CCccCCCCCCeEEEE
Confidence 357788888887764
No 124
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=51.30 E-value=12 Score=22.80 Aligned_cols=40 Identities=28% Similarity=0.542 Sum_probs=23.1
Q ss_pred CCCceecCCchhhcCCHHHHHHHhhcccCC-----CCCcccCCCcc
Q psy12014 14 GGGLFSCSDCSRVYKKKASLTRHQTYECGQ-----QPKYRCPLCSY 54 (78)
Q Consensus 14 ~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~-----~~~~~c~~c~~ 54 (78)
..+.|.|..|+..+....--.. +.+..+. ...|.|+.|+.
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~-~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPM-QDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcc-cCCCCCCChhhCCCCCcCcCCCC
Confidence 4567999999998875421111 1111110 12389999974
No 125
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=50.99 E-value=8.3 Score=19.85 Aligned_cols=34 Identities=32% Similarity=0.705 Sum_probs=19.1
Q ss_pred CCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.-+|.|. |+..+.... +|-..-.| + .|.|..|+.
T Consensus 115 ~~~Y~C~-C~q~~l~~R---Rhn~~~~g-~-~YrC~~C~g 148 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIR---RHNTVRRG-E-VYRCGKCGG 148 (156)
T ss_pred ceeEEee-cCCccchhh---hccccccc-c-eEEeccCCc
Confidence 3457777 777665432 33333344 3 477777754
No 126
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.90 E-value=7.7 Score=19.25 Aligned_cols=17 Identities=18% Similarity=0.700 Sum_probs=12.9
Q ss_pred CCCceecCCchhhcCCH
Q psy12014 14 GGGLFSCSDCSRVYKKK 30 (78)
Q Consensus 14 ~~~~~~c~~c~~~f~~~ 30 (78)
|...|.|..|++.|...
T Consensus 50 ~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 50 GHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccccCCcCcceeee
Confidence 35678999999888743
No 127
>KOG2231|consensus
Probab=50.85 E-value=23 Score=22.88 Aligned_cols=47 Identities=21% Similarity=0.414 Sum_probs=29.6
Q ss_pred ecCCchhhcCCHHHHHHHhhcccCCCCCcccCCC------cccccChhHHHHHHhhhh
Q psy12014 19 SCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLC------SYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c------~~~f~~~~~l~~h~~~~~ 70 (78)
.|..|...|.....|..|++.+. +.|..| ...|.....|..|.+..+
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 57778888887777888877432 344444 234555666777766554
No 128
>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=48.34 E-value=7.5 Score=18.80 Aligned_cols=25 Identities=36% Similarity=0.773 Sum_probs=15.4
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
...|..|+..|.... ..+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEI-------------DLYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCC-------------cCccCcCCcC
Confidence 367888887665321 1256888874
No 129
>PRK14873 primosome assembly protein PriA; Provisional
Probab=48.14 E-value=18 Score=23.22 Aligned_cols=10 Identities=50% Similarity=1.457 Sum_probs=6.6
Q ss_pred CCcccCCCcc
Q psy12014 45 PKYRCPLCSY 54 (78)
Q Consensus 45 ~~~~c~~c~~ 54 (78)
.|+.|+.|+.
T Consensus 421 ~p~~Cp~Cgs 430 (665)
T PRK14873 421 PDWRCPRCGS 430 (665)
T ss_pred cCccCCCCcC
Confidence 3567777764
No 130
>KOG1280|consensus
Probab=47.97 E-value=25 Score=20.82 Aligned_cols=39 Identities=21% Similarity=0.415 Sum_probs=25.3
Q ss_pred CCceecCCchhhcCCHHHHHHHhhc-ccCCCCCcccCCCc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTY-ECGQQPKYRCPLCS 53 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~-h~~~~~~~~c~~c~ 53 (78)
...|.|..|+..--....+..|... |........|++|.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3568999999866666667777544 55423234577765
No 131
>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=47.50 E-value=22 Score=21.89 Aligned_cols=25 Identities=20% Similarity=0.449 Sum_probs=16.0
Q ss_pred eecCCchhhcCCHHHHHHHhhc-ccC
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTY-ECG 42 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~-h~~ 42 (78)
|.|..|.+.|.....+..|+.. |.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 4566777777777666666653 444
No 132
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=47.07 E-value=8.5 Score=19.78 Aligned_cols=14 Identities=21% Similarity=0.308 Sum_probs=11.5
Q ss_pred cccCCCcccccChh
Q psy12014 47 YRCPLCSYRAKQKI 60 (78)
Q Consensus 47 ~~c~~c~~~f~~~~ 60 (78)
++|+.||.+|...-
T Consensus 29 ~~c~~c~~~f~~~e 42 (154)
T PRK00464 29 RECLACGKRFTTFE 42 (154)
T ss_pred eeccccCCcceEeE
Confidence 78999999987553
No 133
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.59 E-value=10 Score=18.32 Aligned_cols=25 Identities=32% Similarity=0.612 Sum_probs=15.3
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
...|..|+..|.... ..+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ-------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC-------------cCccCcCCCC
Confidence 367888886664321 1256888874
No 134
>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=46.51 E-value=18 Score=18.25 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=24.7
Q ss_pred eecCCchhhcCCHHHHHHHhhcccC----CCCCcccCCCcccccChhHHH
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECG----QQPKYRCPLCSYRAKQKIHLT 63 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~----~~~~~~c~~c~~~f~~~~~l~ 63 (78)
-.|..|+..+...+.-......... ...=+.|+.|++.|..-++..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHH
Confidence 4799998866433211111111111 012268999999988765554
No 135
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=45.66 E-value=12 Score=22.63 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=17.0
Q ss_pred ecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccCh
Q psy12014 19 SCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQK 59 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~ 59 (78)
.|+.||....+. | .+-|+|..|+..+...
T Consensus 352 ~Cp~Cg~~m~S~-----------G-~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSA-----------G-RNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhc-----------C-CCCcccccccccCCcc
Confidence 677777653321 2 2247888887766544
No 136
>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=44.67 E-value=12 Score=14.25 Aligned_cols=12 Identities=17% Similarity=0.908 Sum_probs=6.2
Q ss_pred CceecCCchhhc
Q psy12014 16 GLFSCSDCSRVY 27 (78)
Q Consensus 16 ~~~~c~~c~~~f 27 (78)
+-|+|..||...
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 347888888754
No 137
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.15 E-value=6.6 Score=25.32 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=8.2
Q ss_pred CCCcccCCCccc
Q psy12014 44 QPKYRCPLCSYR 55 (78)
Q Consensus 44 ~~~~~c~~c~~~ 55 (78)
..|..|+.||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 456778888753
No 138
>KOG2482|consensus
Probab=44.02 E-value=15 Score=21.64 Aligned_cols=23 Identities=22% Similarity=0.632 Sum_probs=20.7
Q ss_pred ceecCCchhhcCCHHHHHHHhhc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~ 39 (78)
.+.|..|.+.|..+.-|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999985
No 139
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.21 E-value=12 Score=18.05 Aligned_cols=12 Identities=17% Similarity=0.442 Sum_probs=8.3
Q ss_pred ceecCCchhhcC
Q psy12014 17 LFSCSDCSRVYK 28 (78)
Q Consensus 17 ~~~c~~c~~~f~ 28 (78)
...|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (114)
T PRK03681 70 ECWCETCQQYVT 81 (114)
T ss_pred EEEcccCCCeee
Confidence 367888886554
No 140
>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=42.71 E-value=13 Score=15.22 Aligned_cols=11 Identities=36% Similarity=1.126 Sum_probs=7.8
Q ss_pred cccCCCccccc
Q psy12014 47 YRCPLCSYRAK 57 (78)
Q Consensus 47 ~~c~~c~~~f~ 57 (78)
|+|..|+..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 67788876655
No 141
>PRK04351 hypothetical protein; Provisional
Probab=42.53 E-value=18 Score=18.49 Aligned_cols=31 Identities=26% Similarity=0.685 Sum_probs=16.6
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
|.|..|+..+.. + +.+.. .+ |.|..|+..+.
T Consensus 113 Y~C~~Cg~~~~r------~-Rr~n~-~~-yrCg~C~g~L~ 143 (149)
T PRK04351 113 YECQSCGQQYLR------K-RRINT-KR-YRCGKCRGKLK 143 (149)
T ss_pred EECCCCCCEeee------e-eecCC-Cc-EEeCCCCcEee
Confidence 667777755432 1 22332 33 77777765443
No 142
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.44 E-value=14 Score=17.94 Aligned_cols=13 Identities=46% Similarity=1.053 Sum_probs=9.1
Q ss_pred ceecCCchhhcCC
Q psy12014 17 LFSCSDCSRVYKK 29 (78)
Q Consensus 17 ~~~c~~c~~~f~~ 29 (78)
...|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 4678888876653
No 143
>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=41.32 E-value=43 Score=15.97 Aligned_cols=37 Identities=5% Similarity=0.190 Sum_probs=22.6
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.-|.|..-+..|..-..+...+..... . -|.|...|+
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~-~-vwtC~~TGk 38 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQ-R-VWTCEITGK 38 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhC-C-eeEEecCCC
Confidence 346677777777766655555444443 3 377777665
No 144
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=41.29 E-value=10 Score=15.58 Aligned_cols=40 Identities=25% Similarity=0.644 Sum_probs=21.2
Q ss_pred CceecCC--chhhcCCHHHHHHHhhcccCCCCCcccCC----Cccccc
Q psy12014 16 GLFSCSD--CSRVYKKKASLTRHQTYECGQQPKYRCPL----CSYRAK 57 (78)
Q Consensus 16 ~~~~c~~--c~~~f~~~~~l~~h~~~h~~~~~~~~c~~----c~~~f~ 57 (78)
.+-.|.. |...+. +..|..|....-. ..+..|.. |...+.
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~-~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECP-KRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTST-TSEEE-SS----S--EEE
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCC-CCcEECCCCCCCCCCccc
Confidence 3456766 444444 3457788876555 55677887 766554
No 145
>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=41.10 E-value=8.9 Score=20.57 Aligned_cols=25 Identities=24% Similarity=0.547 Sum_probs=0.0
Q ss_pred ccCCCceecCCchh-hcCCHHHHHHH
Q psy12014 12 YKGGGLFSCSDCSR-VYKKKASLTRH 36 (78)
Q Consensus 12 ~~~~~~~~c~~c~~-~f~~~~~l~~h 36 (78)
|.-...|.|.+||. .+.-+..+.+|
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp --------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHh
Confidence 33455677777775 33333444444
No 146
>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=40.73 E-value=27 Score=14.83 Aligned_cols=16 Identities=19% Similarity=0.762 Sum_probs=11.0
Q ss_pred CCCcccCCCcccccCh
Q psy12014 44 QPKYRCPLCSYRAKQK 59 (78)
Q Consensus 44 ~~~~~c~~c~~~f~~~ 59 (78)
...+.|+.||.....+
T Consensus 44 ~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 44 GRVFTCPNCGFEMDRD 59 (69)
T ss_pred cceEEcCCCCCEECcH
Confidence 3458899998765544
No 147
>PF14353 CpXC: CpXC protein
Probab=40.41 E-value=8.7 Score=18.71 Aligned_cols=18 Identities=22% Similarity=0.608 Sum_probs=12.8
Q ss_pred CCcccCCCcccccChhHH
Q psy12014 45 PKYRCPLCSYRAKQKIHL 62 (78)
Q Consensus 45 ~~~~c~~c~~~f~~~~~l 62 (78)
..+.|+.||..|.....+
T Consensus 37 ~~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPL 54 (128)
T ss_pred CEEECCCCCCceecCCCE
Confidence 347899999877655443
No 148
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=40.10 E-value=35 Score=20.37 Aligned_cols=21 Identities=24% Similarity=0.430 Sum_probs=16.8
Q ss_pred ecCCchhhcCCHHHHHHHhhc
Q psy12014 19 SCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~~ 39 (78)
.|.-|...|=..+.|.+|++.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhhhccceecChHHHHHHHHh
Confidence 477788888888888888875
No 149
>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=39.57 E-value=14 Score=13.42 Aligned_cols=8 Identities=38% Similarity=0.999 Sum_probs=5.1
Q ss_pred cccCCCcc
Q psy12014 47 YRCPLCSY 54 (78)
Q Consensus 47 ~~c~~c~~ 54 (78)
+.|+.|+.
T Consensus 20 ~vCp~C~~ 27 (30)
T PF08274_consen 20 LVCPECGH 27 (30)
T ss_dssp EEETTTTE
T ss_pred EeCCcccc
Confidence 66776653
No 150
>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=39.56 E-value=43 Score=17.32 Aligned_cols=39 Identities=21% Similarity=0.392 Sum_probs=22.3
Q ss_pred ccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccc
Q psy12014 12 YKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYR 55 (78)
Q Consensus 12 ~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~ 55 (78)
|..-....|..|++.+........ .. . ..+..|+.|+..
T Consensus 100 HG~l~~~~C~~C~~~~~~~~~~~~-~~--~--~~~~~C~~C~~~ 138 (178)
T PF02146_consen 100 HGSLFRLRCSKCGKEYDREDIVDS-ID--E--EEPPRCPKCGGL 138 (178)
T ss_dssp TEEEEEEEETTTSBEEEGHHHHHH-HH--T--TSSCBCTTTSCB
T ss_pred HhhhceeeecCCCccccchhhccc-cc--c--cccccccccCcc
Confidence 333345689999998876543321 11 1 222478888763
No 151
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.46 E-value=5.1 Score=22.12 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=12.0
Q ss_pred CCceecCCchhhcCCHHHHHHHhhc
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~~ 39 (78)
++...|+.|+..|.....+....++
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRi 41 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRI 41 (267)
T ss_pred hceeccCcccchhhhhheeccceeE
Confidence 3445566666555544433333333
No 152
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.41 E-value=30 Score=19.71 Aligned_cols=7 Identities=29% Similarity=1.246 Sum_probs=3.2
Q ss_pred cccCCCc
Q psy12014 47 YRCPLCS 53 (78)
Q Consensus 47 ~~c~~c~ 53 (78)
|.|+.|.
T Consensus 256 yvCs~Cl 262 (279)
T TIGR00627 256 FVCSVCL 262 (279)
T ss_pred EECCCcc
Confidence 4444443
No 153
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=38.88 E-value=33 Score=14.06 Aligned_cols=8 Identities=38% Similarity=0.912 Sum_probs=4.9
Q ss_pred cccCCCcc
Q psy12014 47 YRCPLCSY 54 (78)
Q Consensus 47 ~~c~~c~~ 54 (78)
..|+.|++
T Consensus 47 ~~Cp~CgR 54 (56)
T PF02591_consen 47 VFCPNCGR 54 (56)
T ss_pred EECcCCCc
Confidence 55666664
No 154
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.65 E-value=8.8 Score=15.68 Aligned_cols=12 Identities=25% Similarity=0.703 Sum_probs=9.8
Q ss_pred ccCCCcccccCh
Q psy12014 48 RCPLCSYRAKQK 59 (78)
Q Consensus 48 ~c~~c~~~f~~~ 59 (78)
+|++|++.|...
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 799999988755
No 155
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=38.27 E-value=6.8 Score=16.57 Aligned_cols=34 Identities=15% Similarity=0.325 Sum_probs=16.6
Q ss_pred ecCCchhhcCCHHH--HHHHhhcccCCCCCcccCCCcc
Q psy12014 19 SCSDCSRVYKKKAS--LTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 19 ~c~~c~~~f~~~~~--l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|..|++.+..... ...-.+.. + ...|.|..|..
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnr-P-i~tYmC~eC~~ 39 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNR-P-IHTYMCDECKE 39 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcC-C-CcceeChhHHH
Confidence 56677776553322 22222221 2 33477887753
No 156
>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=38.16 E-value=30 Score=13.18 Aligned_cols=10 Identities=20% Similarity=0.853 Sum_probs=3.0
Q ss_pred eecCCchhhc
Q psy12014 18 FSCSDCSRVY 27 (78)
Q Consensus 18 ~~c~~c~~~f 27 (78)
|-|+.|...+
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 5566666555
No 157
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.13 E-value=35 Score=21.12 Aligned_cols=10 Identities=30% Similarity=0.733 Sum_probs=6.6
Q ss_pred CCcccCCCcc
Q psy12014 45 PKYRCPLCSY 54 (78)
Q Consensus 45 ~~~~c~~c~~ 54 (78)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 4567777764
No 158
>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=36.09 E-value=9.5 Score=21.54 Aligned_cols=26 Identities=19% Similarity=0.485 Sum_probs=18.5
Q ss_pred CCCcccCCCcccccChhHHHHHHhhh
Q psy12014 44 QPKYRCPLCSYRAKQKIHLTTHMAIR 69 (78)
Q Consensus 44 ~~~~~c~~c~~~f~~~~~l~~h~~~~ 69 (78)
.+++.|+.|+.-......|....++|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 45788999987766666666666555
No 159
>PTZ00448 hypothetical protein; Provisional
Probab=35.91 E-value=34 Score=20.43 Aligned_cols=23 Identities=13% Similarity=0.426 Sum_probs=19.0
Q ss_pred ceecCCchhhcCCHHHHHHHhhc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~ 39 (78)
.+.|..|+-.|........|.+.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57799999999877777778775
No 160
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=35.87 E-value=33 Score=20.50 Aligned_cols=26 Identities=31% Similarity=0.478 Sum_probs=15.0
Q ss_pred hccCCCceecCCch-hhcCCHHHHHHH
Q psy12014 11 LYKGGGLFSCSDCS-RVYKKKASLTRH 36 (78)
Q Consensus 11 ~~~~~~~~~c~~c~-~~f~~~~~l~~h 36 (78)
.|.-.+.|.|.+|| +++--...+.+|
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrH 394 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRH 394 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhh
Confidence 45556777888887 344444444444
No 161
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=35.47 E-value=18 Score=18.16 Aligned_cols=11 Identities=27% Similarity=1.056 Sum_probs=6.4
Q ss_pred ceecCCchhhc
Q psy12014 17 LFSCSDCSRVY 27 (78)
Q Consensus 17 ~~~c~~c~~~f 27 (78)
.|.|..|+..+
T Consensus 112 ~y~C~~C~~~~ 122 (146)
T smart00731 112 PYRCTGCGQRY 122 (146)
T ss_pred EEECCCCCCCC
Confidence 45666666544
No 162
>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=34.21 E-value=11 Score=18.80 Aligned_cols=30 Identities=33% Similarity=0.865 Sum_probs=15.6
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRA 56 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f 56 (78)
|.|..|+..+.. +.+. . ...+.|..|+..+
T Consensus 124 ~~C~~C~~~~~r------~~~~-~--~~~~~C~~C~~~l 153 (157)
T PF10263_consen 124 YRCPSCGREYKR------HRRS-K--RKRYRCGRCGGPL 153 (157)
T ss_pred EEcCCCCCEeee------eccc-c--hhhEECCCCCCEE
Confidence 567777765432 2222 1 2226777776544
No 163
>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=34.19 E-value=20 Score=13.47 Aligned_cols=11 Identities=18% Similarity=0.963 Sum_probs=5.3
Q ss_pred ecCCchhhcCC
Q psy12014 19 SCSDCSRVYKK 29 (78)
Q Consensus 19 ~c~~c~~~f~~ 29 (78)
.|..|++.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 68888887763
No 164
>KOG0978|consensus
Probab=33.87 E-value=11 Score=24.34 Aligned_cols=15 Identities=13% Similarity=0.570 Sum_probs=8.7
Q ss_pred ecCCchhhcCCHHHH
Q psy12014 19 SCSDCSRVYKKKASL 33 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l 33 (78)
.|+.|+.+|...++.
T Consensus 680 KCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVH 694 (698)
T ss_pred CCCCCCCCCCccccc
Confidence 466666666655443
No 165
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=33.79 E-value=30 Score=21.07 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=7.7
Q ss_pred ceecCCchhhc
Q psy12014 17 LFSCSDCSRVY 27 (78)
Q Consensus 17 ~~~c~~c~~~f 27 (78)
.|.|..||...
T Consensus 7 ~y~C~~Cg~~~ 17 (454)
T TIGR00416 7 KFVCQHCGADS 17 (454)
T ss_pred eEECCcCCCCC
Confidence 47888887654
No 166
>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=33.74 E-value=18 Score=14.64 Aligned_cols=13 Identities=31% Similarity=0.940 Sum_probs=9.7
Q ss_pred eecCCchhhcCCH
Q psy12014 18 FSCSDCSRVYKKK 30 (78)
Q Consensus 18 ~~c~~c~~~f~~~ 30 (78)
|.|..|+..+...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 6788888877644
No 167
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=33.14 E-value=23 Score=12.87 Aligned_cols=12 Identities=17% Similarity=0.805 Sum_probs=8.7
Q ss_pred CceecCCchhhc
Q psy12014 16 GLFSCSDCSRVY 27 (78)
Q Consensus 16 ~~~~c~~c~~~f 27 (78)
+-|+|..|+...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 357888888754
No 168
>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=33.00 E-value=26 Score=13.25 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=7.6
Q ss_pred ccCCCceecCCc
Q psy12014 12 YKGGGLFSCSDC 23 (78)
Q Consensus 12 ~~~~~~~~c~~c 23 (78)
..|...|.|..|
T Consensus 24 ~~G~qryrC~~C 35 (36)
T PF03811_consen 24 PSGHQRYRCKDC 35 (36)
T ss_pred CCCCEeEecCcC
Confidence 345566777766
No 169
>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=32.67 E-value=23 Score=12.88 Aligned_cols=11 Identities=18% Similarity=0.881 Sum_probs=7.7
Q ss_pred ceecCCchhhc
Q psy12014 17 LFSCSDCSRVY 27 (78)
Q Consensus 17 ~~~c~~c~~~f 27 (78)
-|+|..|+...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 47788887654
No 170
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=32.48 E-value=23 Score=14.64 Aligned_cols=15 Identities=20% Similarity=0.450 Sum_probs=8.0
Q ss_pred CCCceecCCchhhcC
Q psy12014 14 GGGLFSCSDCSRVYK 28 (78)
Q Consensus 14 ~~~~~~c~~c~~~f~ 28 (78)
+...++|..|++.+.
T Consensus 32 ~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 32 EPIKLRCHYCERIIT 46 (52)
T ss_dssp TTCEEEETTT--EEE
T ss_pred CCCEEEeeCCCCEec
Confidence 445567777776654
No 171
>PRK11823 DNA repair protein RadA; Provisional
Probab=32.17 E-value=36 Score=20.66 Aligned_cols=11 Identities=18% Similarity=0.751 Sum_probs=8.0
Q ss_pred ceecCCchhhc
Q psy12014 17 LFSCSDCSRVY 27 (78)
Q Consensus 17 ~~~c~~c~~~f 27 (78)
.|.|..||...
T Consensus 7 ~y~C~~Cg~~~ 17 (446)
T PRK11823 7 AYVCQECGAES 17 (446)
T ss_pred eEECCcCCCCC
Confidence 58888887654
No 172
>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=32.12 E-value=15 Score=19.91 Aligned_cols=26 Identities=12% Similarity=0.183 Sum_probs=0.0
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccC
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECG 42 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~ 42 (78)
.-..|.+||...+ ...+..|+++...
T Consensus 167 ~~~~cPitGe~IP-~~e~~eHmRi~Ll 192 (229)
T PF12230_consen 167 KMIICPITGEMIP-ADEMDEHMRIELL 192 (229)
T ss_dssp ---------------------------
T ss_pred ccccccccccccc-ccccccccccccc
Confidence 3456888877655 3446777777665
No 173
>KOG1842|consensus
Probab=31.83 E-value=30 Score=21.30 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=16.0
Q ss_pred CceecCCchhhcCCHHHHHHHhhc
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTY 39 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~ 39 (78)
+-|.|++|..-|..-..|..|.-.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhh
Confidence 346777777777777777666543
No 174
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=31.54 E-value=48 Score=19.51 Aligned_cols=25 Identities=20% Similarity=0.511 Sum_probs=20.3
Q ss_pred CcccCCCcccccChhHHHHHHhhhh
Q psy12014 46 KYRCPLCSYRAKQKIHLTTHMAIRH 70 (78)
Q Consensus 46 ~~~c~~c~~~f~~~~~l~~h~~~~~ 70 (78)
.|+|..|...|-.....-.|...|.
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHhh
Confidence 4889889888888888878877764
No 175
>KOG1994|consensus
Probab=30.98 E-value=32 Score=19.17 Aligned_cols=23 Identities=26% Similarity=0.468 Sum_probs=18.6
Q ss_pred CCceecCCchhhcCCHHHHHHHh
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQ 37 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~ 37 (78)
..-|.|-.||-.|.....|..|-
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhC
Confidence 34688999999999998887664
No 176
>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=30.73 E-value=15 Score=14.32 Aligned_cols=9 Identities=44% Similarity=1.136 Sum_probs=3.9
Q ss_pred cccCCCccc
Q psy12014 47 YRCPLCSYR 55 (78)
Q Consensus 47 ~~c~~c~~~ 55 (78)
..|+.|+..
T Consensus 30 ~~CpYCg~~ 38 (40)
T PF10276_consen 30 VVCPYCGTR 38 (40)
T ss_dssp EEETTTTEE
T ss_pred EECCCCCCE
Confidence 344444443
No 177
>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=30.52 E-value=22 Score=18.45 Aligned_cols=18 Identities=17% Similarity=0.440 Sum_probs=14.7
Q ss_pred CCceecCCchhhcCCHHH
Q psy12014 15 GGLFSCSDCSRVYKKKAS 32 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~ 32 (78)
+.|.-|..||+.|++...
T Consensus 66 ~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCChhHHhCCCCCchHHH
Confidence 478889999999997654
No 178
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=30.45 E-value=48 Score=19.21 Aligned_cols=27 Identities=11% Similarity=0.244 Sum_probs=19.1
Q ss_pred ccCCCceecCCchhhcCCHHHHHHHhh
Q psy12014 12 YKGGGLFSCSDCSRVYKKKASLTRHQT 38 (78)
Q Consensus 12 ~~~~~~~~c~~c~~~f~~~~~l~~h~~ 38 (78)
.++....+|.+|+..|.....+..|..
T Consensus 270 nT~~~~ik~n~c~~~~~~e~~~~~Ha~ 296 (306)
T COG5539 270 NTASPSIKCNICGTGFVGEKDYYAHAL 296 (306)
T ss_pred ecCCceEEeeccccccchhhHHHHHHH
Confidence 345556789999998887766666643
No 179
>PLN02748 tRNA dimethylallyltransferase
Probab=29.67 E-value=52 Score=20.37 Aligned_cols=24 Identities=17% Similarity=0.462 Sum_probs=18.5
Q ss_pred CceecCCchh-hcCCHHHHHHHhhc
Q psy12014 16 GLFSCSDCSR-VYKKKASLTRHQTY 39 (78)
Q Consensus 16 ~~~~c~~c~~-~f~~~~~l~~h~~~ 39 (78)
+.|.|+.|+. .+........|...
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5578999997 78777777777764
No 180
>PRK05978 hypothetical protein; Provisional
Probab=29.13 E-value=34 Score=17.58 Aligned_cols=11 Identities=18% Similarity=0.458 Sum_probs=7.0
Q ss_pred cccCCCccccc
Q psy12014 47 YRCPLCSYRAK 57 (78)
Q Consensus 47 ~~c~~c~~~f~ 57 (78)
-.|..|+..|.
T Consensus 53 ~~C~~CG~~~~ 63 (148)
T PRK05978 53 DHCAACGEDFT 63 (148)
T ss_pred CCccccCCccc
Confidence 46777776554
No 181
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=28.94 E-value=78 Score=17.23 Aligned_cols=12 Identities=33% Similarity=0.681 Sum_probs=8.9
Q ss_pred CCcccCCCcccc
Q psy12014 45 PKYRCPLCSYRA 56 (78)
Q Consensus 45 ~~~~c~~c~~~f 56 (78)
...+|..||..+
T Consensus 29 ~lvrC~eCG~V~ 40 (201)
T COG1326 29 PLVRCEECGTVH 40 (201)
T ss_pred eEEEccCCCcEe
Confidence 347899998765
No 182
>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=28.83 E-value=30 Score=14.45 Aligned_cols=12 Identities=25% Similarity=0.819 Sum_probs=7.8
Q ss_pred cccCCCcccccC
Q psy12014 47 YRCPLCSYRAKQ 58 (78)
Q Consensus 47 ~~c~~c~~~f~~ 58 (78)
+.|+.|+..+..
T Consensus 3 ~~CP~CG~~iev 14 (54)
T TIGR01206 3 FECPDCGAEIEL 14 (54)
T ss_pred cCCCCCCCEEec
Confidence 567777765543
No 183
>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=28.78 E-value=35 Score=13.03 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=7.8
Q ss_pred cCCCceecCCchhh
Q psy12014 13 KGGGLFSCSDCSRV 26 (78)
Q Consensus 13 ~~~~~~~c~~c~~~ 26 (78)
.+.+.|.|..|+..
T Consensus 20 ~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 20 DGGKTWICNFCGTK 33 (40)
T ss_dssp TTTTEEEETTT--E
T ss_pred CCCCEEECcCCCCc
Confidence 34567777777653
No 184
>KOG3507|consensus
Probab=28.55 E-value=26 Score=15.03 Aligned_cols=27 Identities=30% Similarity=0.754 Sum_probs=16.0
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRA 56 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f 56 (78)
|.|..|+..-. ... .-+++|..||...
T Consensus 21 YiCgdC~~en~----------lk~--~D~irCReCG~RI 47 (62)
T KOG3507|consen 21 YICGDCGQENT----------LKR--GDVIRCRECGYRI 47 (62)
T ss_pred EEecccccccc----------ccC--CCcEehhhcchHH
Confidence 77888875321 111 2348899998643
No 185
>KOG0801|consensus
Probab=28.14 E-value=15 Score=19.20 Aligned_cols=11 Identities=27% Similarity=0.911 Sum_probs=7.4
Q ss_pred cccCCCccccc
Q psy12014 47 YRCPLCSYRAK 57 (78)
Q Consensus 47 ~~c~~c~~~f~ 57 (78)
++|++|.+...
T Consensus 139 ~KCPvC~K~V~ 149 (205)
T KOG0801|consen 139 MKCPVCHKVVP 149 (205)
T ss_pred ccCCccccccC
Confidence 67888876543
No 186
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=27.85 E-value=58 Score=18.24 Aligned_cols=34 Identities=18% Similarity=0.358 Sum_probs=19.0
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRA 56 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f 56 (78)
..|.-|....+... + .-++. . .....|+.||+-.
T Consensus 198 ~~C~GC~m~l~~~~-~-~~V~~--~-d~iv~CP~CgRIL 231 (239)
T COG1579 198 RVCGGCHMKLPSQT-L-SKVRK--K-DEIVFCPYCGRIL 231 (239)
T ss_pred CcccCCeeeecHHH-H-HHHhc--C-CCCccCCccchHH
Confidence 45777766554332 2 22232 3 4457899998743
No 187
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.77 E-value=70 Score=17.03 Aligned_cols=35 Identities=23% Similarity=0.643 Sum_probs=21.4
Q ss_pred ccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccc
Q psy12014 12 YKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRA 56 (78)
Q Consensus 12 ~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f 56 (78)
-++..-|.|+.|...++.... ...+ |.|+.||...
T Consensus 108 ~~~~~~y~C~~~~~r~sfdeA------~~~~----F~Cp~Cg~~L 142 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDEA------MELG----FTCPKCGEDL 142 (176)
T ss_pred hccCCceeCCCCCCcccHHHH------HHhC----CCCCCCCchh
Confidence 455566889777766553322 2222 8999998644
No 188
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=27.53 E-value=36 Score=13.10 Aligned_cols=9 Identities=44% Similarity=1.043 Sum_probs=6.5
Q ss_pred CcccCCCcc
Q psy12014 46 KYRCPLCSY 54 (78)
Q Consensus 46 ~~~c~~c~~ 54 (78)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 467888874
No 189
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=27.48 E-value=47 Score=17.48 Aligned_cols=19 Identities=26% Similarity=0.648 Sum_probs=14.7
Q ss_pred CceecCCchhhcCCHHHHH
Q psy12014 16 GLFSCSDCSRVYKKKASLT 34 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~ 34 (78)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 5678999999998665544
No 190
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=27.27 E-value=1.1e+02 Score=17.05 Aligned_cols=39 Identities=23% Similarity=0.430 Sum_probs=22.0
Q ss_pred hccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 11 LYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 11 ~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|..-....|..|+..+.....+.. .... . .-.|+.|+.
T Consensus 113 lHG~~~~~~C~~C~~~~~~~~~~~~---~~~~-~-~p~Cp~Cgg 151 (244)
T PRK14138 113 LHGNVEEYYCVRCGKRYTVEDVIEK---LEKS-D-VPRCDDCSG 151 (244)
T ss_pred ccCCcCeeEECCCCCcccHHHHHHH---HhcC-C-CCCCCCCCC
Confidence 3444455779889988776544331 1111 2 236888864
No 191
>KOG0227|consensus
Probab=26.96 E-value=39 Score=18.32 Aligned_cols=19 Identities=26% Similarity=0.543 Sum_probs=8.7
Q ss_pred cccCCCcccccChhHHHHH
Q psy12014 47 YRCPLCSYRAKQKIHLTTH 65 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h 65 (78)
|.|..|.-......+...|
T Consensus 54 yeCkLClT~H~ne~Syl~H 72 (222)
T KOG0227|consen 54 YECKLCLTLHNNEGSYLAH 72 (222)
T ss_pred eeehhhhhhhcchhhhhhh
Confidence 4555554444444443333
No 192
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=26.86 E-value=25 Score=20.79 Aligned_cols=11 Identities=45% Similarity=1.174 Sum_probs=7.0
Q ss_pred cccCCCccccc
Q psy12014 47 YRCPLCSYRAK 57 (78)
Q Consensus 47 ~~c~~c~~~f~ 57 (78)
|+|+.||..+.
T Consensus 266 wrCpkCGg~ik 276 (403)
T COG1379 266 WRCPKCGGKIK 276 (403)
T ss_pred ccCcccccchh
Confidence 67777776443
No 193
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=26.58 E-value=1e+02 Score=15.90 Aligned_cols=24 Identities=25% Similarity=0.660 Sum_probs=12.6
Q ss_pred hcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 26 VYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 26 ~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|.+...+..... .....|++||.
T Consensus 17 WF~ss~~fd~Q~~-----~glv~CP~Cgs 40 (148)
T PF06676_consen 17 WFRSSAAFDRQQA-----RGLVSCPVCGS 40 (148)
T ss_pred ecCCHHHHHHHHH-----cCCccCCCCCC
Confidence 4555555544333 23356777764
No 194
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=26.57 E-value=1.2e+02 Score=17.64 Aligned_cols=23 Identities=39% Similarity=0.713 Sum_probs=15.8
Q ss_pred CceecCCchhhcCCHHHHHHHhh
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQT 38 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~ 38 (78)
.-|.|+.|-+-|.....+.+|+.
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHH
Confidence 44667777777777777777765
No 195
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.22 E-value=43 Score=18.84 Aligned_cols=15 Identities=20% Similarity=0.853 Sum_probs=10.5
Q ss_pred CCcccCCCcccccCh
Q psy12014 45 PKYRCPLCSYRAKQK 59 (78)
Q Consensus 45 ~~~~c~~c~~~f~~~ 59 (78)
..+.|+.||..+..+
T Consensus 321 r~~~C~~cg~~~~rD 335 (364)
T COG0675 321 RLFKCPRCGFVHDRD 335 (364)
T ss_pred eeEECCCCCCeehhh
Confidence 348899998765544
No 196
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=25.36 E-value=41 Score=14.06 Aligned_cols=20 Identities=25% Similarity=0.416 Sum_probs=15.2
Q ss_pred CceecCCchhhcCCHHHHHH
Q psy12014 16 GLFSCSDCSRVYKKKASLTR 35 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~ 35 (78)
+-+-|-+|+..|.....|..
T Consensus 26 ~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 26 EHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred hCceeeeeCCccCCHHHHHh
Confidence 34568999999998877753
No 197
>KOG2807|consensus
Probab=24.86 E-value=82 Score=18.75 Aligned_cols=22 Identities=27% Similarity=0.561 Sum_probs=15.4
Q ss_pred CCcccCCCcccccChhHHHHHH
Q psy12014 45 PKYRCPLCSYRAKQKIHLTTHM 66 (78)
Q Consensus 45 ~~~~c~~c~~~f~~~~~l~~h~ 66 (78)
.|.+|+.|+-+.-...+|....
T Consensus 289 LP~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred CCccCCccceeEecchHHHHHH
Confidence 4678888887777776765443
No 198
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=24.66 E-value=49 Score=19.67 Aligned_cols=8 Identities=25% Similarity=0.908 Sum_probs=4.3
Q ss_pred eecCCchh
Q psy12014 18 FSCSDCSR 25 (78)
Q Consensus 18 ~~c~~c~~ 25 (78)
++|+.|+.
T Consensus 15 g~cp~c~~ 22 (372)
T cd01121 15 GKCPECGE 22 (372)
T ss_pred EECcCCCC
Confidence 45555554
No 199
>KOG3352|consensus
Probab=24.63 E-value=45 Score=17.27 Aligned_cols=14 Identities=36% Similarity=0.622 Sum_probs=10.4
Q ss_pred CCcccCCCcccccC
Q psy12014 45 PKYRCPLCSYRAKQ 58 (78)
Q Consensus 45 ~~~~c~~c~~~f~~ 58 (78)
+..+|.+||.-|..
T Consensus 132 e~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 132 ETQRCPECGHYFKL 145 (153)
T ss_pred CcccCCcccceEEe
Confidence 34689999987764
No 200
>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=24.56 E-value=39 Score=12.76 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=7.0
Q ss_pred cccCCCccccc
Q psy12014 47 YRCPLCSYRAK 57 (78)
Q Consensus 47 ~~c~~c~~~f~ 57 (78)
+.|..||..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 56777776543
No 201
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=24.42 E-value=52 Score=17.18 Aligned_cols=18 Identities=22% Similarity=0.647 Sum_probs=14.0
Q ss_pred CceecCCchhhcCCHHHH
Q psy12014 16 GLFSCSDCSRVYKKKASL 33 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l 33 (78)
....|..||+.|.....+
T Consensus 113 ~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred CcccchhhCCccccHHHH
Confidence 467899999999866543
No 202
>KOG4727|consensus
Probab=24.39 E-value=54 Score=17.47 Aligned_cols=22 Identities=23% Similarity=0.439 Sum_probs=17.2
Q ss_pred ceecCCchhhcCCHHHHHHHhh
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQT 38 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~ 38 (78)
-|-|.+|+-++...-++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4899999999887766666654
No 203
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.38 E-value=18 Score=23.18 Aligned_cols=12 Identities=25% Similarity=0.556 Sum_probs=7.9
Q ss_pred CCCcccCCCccc
Q psy12014 44 QPKYRCPLCSYR 55 (78)
Q Consensus 44 ~~~~~c~~c~~~ 55 (78)
..|..|+.|+..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 346778888653
No 204
>PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Probab=23.57 E-value=1e+02 Score=20.46 Aligned_cols=26 Identities=12% Similarity=0.318 Sum_probs=19.2
Q ss_pred cccCCCcccccChhHHHHHHhhhhcC
Q psy12014 47 YRCPLCSYRAKQKIHLTTHMAIRHHK 72 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h~~~~~g~ 72 (78)
..|+.||++......+...++..++.
T Consensus 635 isCPgCGRT~~dlq~~~~~I~~~~~h 660 (733)
T PLN02925 635 VSCPSCGRTLFDLQEVSAEIREKTSH 660 (733)
T ss_pred EECCCCCCccccHHHHHHHHHHHhhc
Confidence 46999999877777777777666543
No 205
>PRK01343 zinc-binding protein; Provisional
Probab=23.53 E-value=56 Score=13.92 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=8.1
Q ss_pred cccCCCccccc
Q psy12014 47 YRCPLCSYRAK 57 (78)
Q Consensus 47 ~~c~~c~~~f~ 57 (78)
..|+.|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 56888887654
No 206
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=23.43 E-value=30 Score=16.58 Aligned_cols=11 Identities=18% Similarity=0.591 Sum_probs=7.2
Q ss_pred ceecCCchhhc
Q psy12014 17 LFSCSDCSRVY 27 (78)
Q Consensus 17 ~~~c~~c~~~f 27 (78)
.|.|..||+..
T Consensus 2 kWkC~iCg~~I 12 (101)
T PF09943_consen 2 KWKCYICGKPI 12 (101)
T ss_pred ceEEEecCCee
Confidence 46777777644
No 207
>KOG3014|consensus
Probab=23.41 E-value=65 Score=18.25 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=21.6
Q ss_pred ccCCCce---ecCCchhhcC--CHHHHHHHhhcccC
Q psy12014 12 YKGGGLF---SCSDCSRVYK--KKASLTRHQTYECG 42 (78)
Q Consensus 12 ~~~~~~~---~c~~c~~~f~--~~~~l~~h~~~h~~ 42 (78)
..|.+.+ .|..|+..++ ++.+-..|+..|..
T Consensus 29 d~Gqk~fg~~~C~~Cgm~Yt~~s~EDe~~H~~fH~~ 64 (257)
T KOG3014|consen 29 DAGQKDFGAVKCKECGMKYTVTSPEDEALHEKFHNR 64 (257)
T ss_pred ecCccccCceehhhcCceecCCCHHHHHHHHHHHHh
Confidence 3455555 6999999776 45566678888764
No 208
>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=23.04 E-value=40 Score=17.35 Aligned_cols=13 Identities=23% Similarity=0.329 Sum_probs=10.4
Q ss_pred cccCCCcccccCh
Q psy12014 47 YRCPLCSYRAKQK 59 (78)
Q Consensus 47 ~~c~~c~~~f~~~ 59 (78)
-+|..|++.|...
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 5799999988754
No 209
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=22.94 E-value=74 Score=17.92 Aligned_cols=39 Identities=26% Similarity=0.393 Sum_probs=21.7
Q ss_pred hccCCCceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 11 LYKGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 11 ~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
.|..=..+.|..|+..+....... .... ..+-.|+.|+.
T Consensus 116 lHGsl~~~~C~~C~~~~~~~~~~~---~~~~--~~~p~C~~Cg~ 154 (250)
T COG0846 116 LHGSLKRVRCSKCGNQYYDEDVIK---FIED--GLIPRCPKCGG 154 (250)
T ss_pred eccceeeeEeCCCcCccchhhhhh---hccc--CCCCcCccCCC
Confidence 344446678999987776433111 1111 12347888876
No 210
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=22.48 E-value=50 Score=13.96 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=8.1
Q ss_pred ccCCCcccccCh
Q psy12014 48 RCPLCSYRAKQK 59 (78)
Q Consensus 48 ~c~~c~~~f~~~ 59 (78)
-|+.|++.|...
T Consensus 41 gCPfC~~~~~~~ 52 (55)
T PF14447_consen 41 GCPFCGTPFEFD 52 (55)
T ss_pred CCCCCCCcccCC
Confidence 478888776543
No 211
>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=22.25 E-value=63 Score=13.93 Aligned_cols=14 Identities=29% Similarity=0.458 Sum_probs=9.2
Q ss_pred CcccCCCcccccCh
Q psy12014 46 KYRCPLCSYRAKQK 59 (78)
Q Consensus 46 ~~~c~~c~~~f~~~ 59 (78)
|.+|..||+.....
T Consensus 4 PVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 4 PVRCFTCGKVIGNK 17 (60)
T ss_dssp SSS-STTTSBTCGH
T ss_pred ceecCCCCCChhHh
Confidence 67888898866533
No 212
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.24 E-value=43 Score=12.35 Aligned_cols=10 Identities=20% Similarity=0.457 Sum_probs=7.0
Q ss_pred cccCCCcccc
Q psy12014 47 YRCPLCSYRA 56 (78)
Q Consensus 47 ~~c~~c~~~f 56 (78)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 5677787665
No 213
>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=22.08 E-value=43 Score=14.19 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=7.6
Q ss_pred CCceecCCchhhcCC
Q psy12014 15 GGLFSCSDCSRVYKK 29 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~ 29 (78)
.+.+.|..||..|..
T Consensus 23 ~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 23 RRRHHCRNCGRVVCS 37 (69)
T ss_dssp S-EEE-TTT--EEEC
T ss_pred eeeEccCCCCCEECC
Confidence 566778888877664
No 214
>KOG4124|consensus
Probab=21.94 E-value=14 Score=21.86 Aligned_cols=21 Identities=38% Similarity=0.615 Sum_probs=15.1
Q ss_pred CCCcccCCCcccccChhHHHH
Q psy12014 44 QPKYRCPLCSYRAKQKIHLTT 64 (78)
Q Consensus 44 ~~~~~c~~c~~~f~~~~~l~~ 64 (78)
.|+++|.+|.+.......|..
T Consensus 396 nk~~r~~i~~~~~k~~~~l~~ 416 (442)
T KOG4124|consen 396 NKPYRCEVCSKRYKNLNGLKY 416 (442)
T ss_pred cCcccChhhhhhhccCCCCCc
Confidence 577899999887776655543
No 215
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.84 E-value=49 Score=12.70 Aligned_cols=7 Identities=43% Similarity=1.369 Sum_probs=3.8
Q ss_pred ccCCCcc
Q psy12014 48 RCPLCSY 54 (78)
Q Consensus 48 ~c~~c~~ 54 (78)
.|+.|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555554
No 216
>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=21.78 E-value=37 Score=12.91 Aligned_cols=9 Identities=44% Similarity=0.947 Sum_probs=4.7
Q ss_pred cccCCCccc
Q psy12014 47 YRCPLCSYR 55 (78)
Q Consensus 47 ~~c~~c~~~ 55 (78)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 455555543
No 217
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.74 E-value=46 Score=12.75 Aligned_cols=10 Identities=40% Similarity=0.869 Sum_probs=6.5
Q ss_pred cccCCCcccc
Q psy12014 47 YRCPLCSYRA 56 (78)
Q Consensus 47 ~~c~~c~~~f 56 (78)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5677777554
No 218
>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=21.69 E-value=44 Score=11.76 Aligned_cols=7 Identities=43% Similarity=1.383 Sum_probs=3.6
Q ss_pred cccCCCc
Q psy12014 47 YRCPLCS 53 (78)
Q Consensus 47 ~~c~~c~ 53 (78)
|.|..|.
T Consensus 16 Y~C~~c~ 22 (30)
T PF03107_consen 16 YHCSECC 22 (30)
T ss_pred EEeCCCC
Confidence 5555544
No 219
>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=21.63 E-value=37 Score=15.93 Aligned_cols=30 Identities=17% Similarity=0.584 Sum_probs=18.4
Q ss_pred ceecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCccccc
Q psy12014 17 LFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAK 57 (78)
Q Consensus 17 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~ 57 (78)
.|.|+.|++.-. .+.-.+ -|.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~v--------kR~a~G---IW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSV--------KRVATG---IWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEE--------EEEETT---EEEETTTTEEEE
T ss_pred CCcCCCCCCcee--------EEeeeE---EeecCCCCCEEe
Confidence 678888876421 133333 388999987664
No 220
>PRK06260 threonine synthase; Validated
Probab=21.43 E-value=73 Score=18.99 Aligned_cols=10 Identities=30% Similarity=1.165 Sum_probs=4.4
Q ss_pred eecCCchhhc
Q psy12014 18 FSCSDCSRVY 27 (78)
Q Consensus 18 ~~c~~c~~~f 27 (78)
+.|..|+..+
T Consensus 4 ~~C~~cg~~~ 13 (397)
T PRK06260 4 LKCIECGKEY 13 (397)
T ss_pred EEECCCCCCC
Confidence 3444444443
No 221
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=21.33 E-value=44 Score=14.00 Aligned_cols=19 Identities=11% Similarity=0.204 Sum_probs=11.9
Q ss_pred CCCcccCCCcccccChhHH
Q psy12014 44 QPKYRCPLCSYRAKQKIHL 62 (78)
Q Consensus 44 ~~~~~c~~c~~~f~~~~~l 62 (78)
+.|+....|+..|....-+
T Consensus 22 ~~PV~s~~C~H~fek~aI~ 40 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAIL 40 (57)
T ss_dssp SSEEEESSS--EEEHHHHH
T ss_pred hCCcCcCCCCCeecHHHHH
Confidence 4567777899888866544
No 222
>PF08252 Leader_CPA1: arg-2/CPA1 leader peptide ; InterPro: IPR013203 In this family there are leaders peptides involved in the regulation of the glutaminase subunit (small subunit) of arginine-specific carbamoyl phosphate synthetase. In Neurospora crassa it is a small upstream ORF of 24 codons above the arg-2 locus []. In yeast it is the leader peptide of the CPA1 gene. The 5' region of CPA1 mRNA contains a 25 codon upstream open reading frame. The leader peptide, the product of the upstream open reading frame, plays an essential, negative role in the specific repression of CPA1 by arginine [].; PDB: 2XL1_A.
Probab=21.07 E-value=59 Score=11.02 Aligned_cols=11 Identities=18% Similarity=0.546 Sum_probs=3.2
Q ss_pred hcCCHHHHHHH
Q psy12014 26 VYKKKASLTRH 36 (78)
Q Consensus 26 ~f~~~~~l~~h 36 (78)
.|.....+..|
T Consensus 7 ~~t~qDYiSDh 17 (24)
T PF08252_consen 7 VFTSQDYISDH 17 (24)
T ss_dssp ----HHHHHHH
T ss_pred hhhHHHHHHHH
Confidence 44444444444
No 223
>PF12773 DZR: Double zinc ribbon
Probab=20.81 E-value=64 Score=12.63 Aligned_cols=11 Identities=36% Similarity=0.745 Sum_probs=7.3
Q ss_pred CcccCCCcccc
Q psy12014 46 KYRCPLCSYRA 56 (78)
Q Consensus 46 ~~~c~~c~~~f 56 (78)
...|+.|+...
T Consensus 29 ~~~C~~Cg~~~ 39 (50)
T PF12773_consen 29 KKICPNCGAEN 39 (50)
T ss_pred CCCCcCCcCCC
Confidence 36788887653
No 224
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=20.65 E-value=52 Score=14.29 Aligned_cols=7 Identities=57% Similarity=1.872 Sum_probs=3.7
Q ss_pred cccCCCc
Q psy12014 47 YRCPLCS 53 (78)
Q Consensus 47 ~~c~~c~ 53 (78)
|.|+.|+
T Consensus 1 y~C~KCg 7 (64)
T PF09855_consen 1 YKCPKCG 7 (64)
T ss_pred CCCCCCC
Confidence 3455554
No 225
>PLN03239 histone acetyltransferase; Provisional
Probab=20.62 E-value=1.1e+02 Score=18.30 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=20.5
Q ss_pred CCceecCCchhhcCCHHHHHHHhh
Q psy12014 15 GGLFSCSDCSRVYKKKASLTRHQT 38 (78)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~l~~h~~ 38 (78)
..-|.|..|-+-|.....|.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 456899999999999999988875
No 226
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.60 E-value=1.1e+02 Score=16.13 Aligned_cols=19 Identities=32% Similarity=0.587 Sum_probs=14.1
Q ss_pred cccCCCcccccChhHHHHH
Q psy12014 47 YRCPLCSYRAKQKIHLTTH 65 (78)
Q Consensus 47 ~~c~~c~~~f~~~~~l~~h 65 (78)
+.|+.|++.|..-++...-
T Consensus 131 ~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 131 YRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred eECCCCcccccCchHHHHH
Confidence 6799999998776665433
No 227
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.58 E-value=58 Score=12.44 Aligned_cols=13 Identities=23% Similarity=0.434 Sum_probs=6.1
Q ss_pred ccCCCcccccChh
Q psy12014 48 RCPLCSYRAKQKI 60 (78)
Q Consensus 48 ~c~~c~~~f~~~~ 60 (78)
.|+.|++.|-..+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 4566666655443
No 228
>KOG1818|consensus
Probab=20.58 E-value=27 Score=22.43 Aligned_cols=37 Identities=19% Similarity=0.414 Sum_probs=19.1
Q ss_pred CceecCCchhhcCCHHHHHHHhhcccCCCCCc-ccCCC
Q psy12014 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKY-RCPLC 52 (78)
Q Consensus 16 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~-~c~~c 52 (78)
+.+.|.-||..|........--..+.|-.+|. .|..|
T Consensus 180 rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C 217 (634)
T KOG1818|consen 180 RKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSC 217 (634)
T ss_pred ccccccccchhhccCccccccCcccccccccceehhhh
Confidence 55677778887776544333333334422333 25555
No 229
>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=20.51 E-value=47 Score=15.62 Aligned_cols=12 Identities=17% Similarity=0.944 Sum_probs=8.6
Q ss_pred ceecCCchhhcC
Q psy12014 17 LFSCSDCSRVYK 28 (78)
Q Consensus 17 ~~~c~~c~~~f~ 28 (78)
-|.|..|++.|.
T Consensus 53 IW~C~~C~~~~A 64 (91)
T TIGR00280 53 IWTCRKCGAKFA 64 (91)
T ss_pred EEEcCCCCCEEe
Confidence 377888877665
No 230
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.50 E-value=85 Score=16.93 Aligned_cols=28 Identities=25% Similarity=0.503 Sum_probs=16.0
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSY 54 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~ 54 (78)
..|..|+..|.... +.. ...+.|+.|..
T Consensus 135 ~~C~~Cgg~fv~~~--------~e~-~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHA--------HDP-VGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeeccc--------ccc-CCCCcCCCCCC
Confidence 45777877765221 222 33578888853
No 231
>PRK12860 transcriptional activator FlhC; Provisional
Probab=20.49 E-value=85 Score=16.96 Aligned_cols=27 Identities=19% Similarity=0.527 Sum_probs=15.4
Q ss_pred eecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCc
Q psy12014 18 FSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCS 53 (78)
Q Consensus 18 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~ 53 (78)
..|..|+..|... .+.. ...+.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~--------~~e~-~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTH--------AHDL-RHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecc--------cccc-CCCCcCCCCC
Confidence 4577777776522 1222 3347888874
No 232
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=20.27 E-value=60 Score=13.20 Aligned_cols=13 Identities=31% Similarity=0.856 Sum_probs=9.6
Q ss_pred cccCCCcccccCh
Q psy12014 47 YRCPLCSYRAKQK 59 (78)
Q Consensus 47 ~~c~~c~~~f~~~ 59 (78)
++|..|+..+...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 7888888766554
No 233
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=20.27 E-value=85 Score=18.25 Aligned_cols=31 Identities=29% Similarity=0.585 Sum_probs=17.0
Q ss_pred ecCCchhhcCCHHHHHHHhhcccCCCCCcccCCCcccccCh
Q psy12014 19 SCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQK 59 (78)
Q Consensus 19 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~c~~c~~~f~~~ 59 (78)
+|+.|+...-.+. |. ..-+.|+.|+.-|...
T Consensus 40 kc~~C~~~~~~~~-l~---------~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 40 QCENCYGLNYKKF-LK---------SKMNICEQCGYHLKMS 70 (296)
T ss_pred ECCCccchhhHHH-HH---------HcCCCCCCCCCCcCCC
Confidence 5888876543221 11 2236788888766533
Done!